Query 045160
Match_columns 166
No_of_seqs 216 out of 1212
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 10:26:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045160.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045160hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0773 Transcription factor M 99.8 1.5E-19 3.2E-24 154.9 4.2 149 9-157 143-311 (342)
2 PF05920 Homeobox_KN: Homeobox 99.7 2.6E-18 5.6E-23 105.0 4.3 40 103-142 1-40 (40)
3 PF00046 Homeobox: Homeobox do 99.7 9.6E-17 2.1E-21 103.8 5.4 57 86-145 1-57 (57)
4 cd00086 homeodomain Homeodomai 99.7 2.3E-16 5E-21 101.9 7.1 58 86-146 1-58 (59)
5 smart00389 HOX Homeodomain. DN 99.7 3.8E-16 8.1E-21 100.3 6.9 55 87-144 2-56 (56)
6 KOG0774 Transcription factor P 99.6 6.1E-16 1.3E-20 127.7 3.7 85 64-148 155-251 (334)
7 KOG0775 Transcription factor S 99.5 5.6E-14 1.2E-18 116.6 4.6 48 94-144 185-232 (304)
8 KOG0850 Transcription factor D 99.5 5.3E-14 1.2E-18 114.3 4.2 62 84-148 121-182 (245)
9 KOG0843 Transcription factor E 99.4 7.4E-14 1.6E-18 109.9 4.4 61 84-147 101-161 (197)
10 TIGR01565 homeo_ZF_HD homeobox 99.4 6.2E-13 1.4E-17 87.3 5.3 53 85-140 1-57 (58)
11 KOG0485 Transcription factor N 99.4 3.3E-13 7.2E-18 109.1 4.9 60 84-146 103-162 (268)
12 KOG3802 Transcription factor O 99.4 3.1E-13 6.7E-18 117.2 3.9 65 81-148 290-354 (398)
13 KOG0487 Transcription factor A 99.3 4.7E-13 1E-17 113.5 3.2 63 83-148 233-295 (308)
14 KOG0842 Transcription factor t 99.3 4.7E-13 1E-17 113.5 3.3 62 83-147 151-212 (307)
15 KOG0489 Transcription factor z 99.3 9.4E-13 2E-17 109.8 4.1 62 83-147 157-218 (261)
16 KOG0493 Transcription factor E 99.3 5.2E-12 1.1E-16 104.6 5.8 62 85-149 246-307 (342)
17 KOG0488 Transcription factor B 99.3 4.2E-12 9.2E-17 108.3 5.1 65 82-149 169-233 (309)
18 KOG0484 Transcription factor P 99.3 3.6E-12 7.8E-17 92.5 3.4 73 72-147 4-76 (125)
19 COG5576 Homeodomain-containing 99.2 2E-11 4.2E-16 95.0 4.5 61 84-147 50-110 (156)
20 KOG2251 Homeobox transcription 99.2 1.7E-11 3.8E-16 99.2 4.2 61 83-146 35-95 (228)
21 KOG0483 Transcription factor H 99.2 2E-11 4.3E-16 98.2 4.4 57 85-144 50-106 (198)
22 KOG0492 Transcription factor M 99.2 2.5E-11 5.4E-16 97.7 4.5 65 79-146 138-202 (246)
23 KOG0494 Transcription factor C 99.1 5.1E-11 1.1E-15 98.7 4.5 56 88-146 144-199 (332)
24 KOG0491 Transcription factor B 99.1 2.9E-11 6.2E-16 94.2 1.9 65 82-149 97-161 (194)
25 KOG0486 Transcription factor P 99.0 1.6E-10 3.4E-15 97.8 3.3 65 84-151 111-175 (351)
26 KOG0848 Transcription factor C 98.9 2.5E-10 5.3E-15 94.9 1.6 58 87-147 201-258 (317)
27 KOG4577 Transcription factor L 98.9 1.2E-09 2.5E-14 91.9 3.3 68 78-148 160-227 (383)
28 KOG0844 Transcription factor E 98.8 3.4E-09 7.3E-14 89.7 3.2 61 89-152 185-245 (408)
29 KOG2252 CCAAT displacement pro 98.7 2.2E-08 4.8E-13 90.1 5.7 57 84-143 419-475 (558)
30 KOG1168 Transcription factor A 98.6 8.7E-09 1.9E-13 86.7 1.2 63 81-146 305-367 (385)
31 KOG0490 Transcription factor, 98.6 1.8E-08 4E-13 80.9 2.2 62 83-147 58-119 (235)
32 KOG0849 Transcription factor P 98.6 9E-08 2E-12 83.2 5.4 63 82-147 173-235 (354)
33 KOG0847 Transcription factor, 98.5 4.2E-08 9.1E-13 79.9 2.8 61 83-146 165-225 (288)
34 PF03791 KNOX2: KNOX2 domain ; 98.5 3.9E-08 8.5E-13 63.1 0.3 24 4-27 29-52 (52)
35 PF11569 Homez: Homeodomain le 97.7 3.2E-05 7E-10 50.3 3.3 43 97-142 10-52 (56)
36 KOG0773 Transcription factor M 97.6 3.4E-05 7.4E-10 66.3 2.2 62 85-147 95-156 (342)
37 KOG0490 Transcription factor, 97.4 0.00011 2.4E-09 58.9 2.9 60 84-146 152-211 (235)
38 KOG1146 Homeobox protein [Gene 96.8 0.0015 3.2E-08 64.6 4.4 70 84-156 902-971 (1406)
39 PF03789 ELK: ELK domain ; In 96.5 0.00075 1.6E-08 35.9 0.3 22 63-84 1-22 (22)
40 PF04218 CENP-B_N: CENP-B N-te 95.0 0.065 1.4E-06 34.1 4.6 48 86-141 1-48 (53)
41 KOG3623 Homeobox transcription 94.0 0.1 2.2E-06 49.6 5.2 46 97-145 568-613 (1007)
42 PF01527 HTH_Tnp_1: Transposas 90.0 0.5 1.1E-05 31.2 3.7 47 87-140 2-48 (76)
43 PF08281 Sigma70_r4_2: Sigma-7 89.4 0.74 1.6E-05 28.5 3.9 44 91-142 10-53 (54)
44 cd06171 Sigma70_r4 Sigma70, re 89.0 0.77 1.7E-05 27.1 3.7 46 91-144 10-55 (55)
45 PF04545 Sigma70_r4: Sigma-70, 89.0 0.49 1.1E-05 29.1 2.8 46 91-144 4-49 (50)
46 cd00569 HTH_Hin_like Helix-tur 82.5 4.7 0.0001 21.1 4.6 39 90-136 4-42 (42)
47 PRK06759 RNA polymerase factor 82.5 1.8 3.8E-05 32.1 3.5 48 90-145 105-152 (154)
48 PRK00118 putative DNA-binding 81.5 0.92 2E-05 33.0 1.6 54 91-152 17-70 (104)
49 PRK09642 RNA polymerase sigma 79.0 1.8 3.9E-05 32.3 2.6 51 90-148 105-155 (160)
50 PRK12512 RNA polymerase sigma 77.2 2.5 5.3E-05 32.4 2.9 52 90-149 130-181 (184)
51 TIGR02937 sigma70-ECF RNA poly 77.0 2.9 6.4E-05 29.8 3.1 47 91-145 110-156 (158)
52 PRK03975 tfx putative transcri 76.2 3.2 6.9E-05 31.8 3.2 53 89-150 4-56 (141)
53 TIGR02989 Sig-70_gvs1 RNA poly 75.3 3.8 8.2E-05 30.4 3.4 48 90-145 110-157 (159)
54 PRK11924 RNA polymerase sigma 74.4 3.1 6.8E-05 31.1 2.8 50 90-147 124-173 (179)
55 PRK09646 RNA polymerase sigma 74.4 3.1 6.8E-05 32.3 2.8 50 90-147 141-190 (194)
56 TIGR02985 Sig70_bacteroi1 RNA 73.8 4.1 8.8E-05 29.8 3.2 47 91-145 113-159 (161)
57 PRK09644 RNA polymerase sigma 73.7 4.1 8.8E-05 30.7 3.2 51 90-148 107-157 (165)
58 PRK09652 RNA polymerase sigma 73.6 3.4 7.5E-05 31.0 2.8 50 90-147 127-176 (182)
59 PRK12514 RNA polymerase sigma 73.3 3.5 7.6E-05 31.4 2.8 49 90-146 128-176 (179)
60 PF13518 HTH_28: Helix-turn-he 73.1 4.3 9.3E-05 24.5 2.7 25 118-142 15-39 (52)
61 PRK06811 RNA polymerase factor 72.9 4.4 9.5E-05 31.4 3.3 50 90-147 130-179 (189)
62 TIGR02939 RpoE_Sigma70 RNA pol 72.4 2.9 6.3E-05 31.9 2.2 50 90-147 137-186 (190)
63 PF10668 Phage_terminase: Phag 72.3 3.3 7.2E-05 27.2 2.1 21 117-137 24-44 (60)
64 TIGR02999 Sig-70_X6 RNA polyme 71.9 4.4 9.6E-05 30.8 3.1 48 91-146 134-181 (183)
65 PRK12526 RNA polymerase sigma 71.2 4.3 9.4E-05 32.0 3.0 50 90-147 152-201 (206)
66 PF13443 HTH_26: Cro/C1-type H 71.0 3.5 7.7E-05 26.1 2.0 24 117-140 12-35 (63)
67 PRK05602 RNA polymerase sigma 70.7 3 6.5E-05 32.0 1.9 51 91-149 128-178 (186)
68 PRK12541 RNA polymerase sigma 69.5 5.7 0.00012 29.6 3.2 49 90-146 111-159 (161)
69 smart00421 HTH_LUXR helix_turn 68.9 15 0.00033 21.7 4.6 47 91-146 3-49 (58)
70 TIGR02948 SigW_bacill RNA poly 68.8 4.1 8.9E-05 31.0 2.3 50 90-147 135-184 (187)
71 PRK09648 RNA polymerase sigma 68.7 5.4 0.00012 30.7 3.0 50 90-147 138-187 (189)
72 PRK06930 positive control sigm 68.4 3.4 7.3E-05 32.3 1.8 56 90-153 113-168 (170)
73 PRK12537 RNA polymerase sigma 68.3 5.6 0.00012 30.5 3.0 49 90-146 132-180 (182)
74 PRK09047 RNA polymerase factor 68.2 6.6 0.00014 29.1 3.3 50 90-147 105-154 (161)
75 PF04967 HTH_10: HTH DNA bindi 68.0 16 0.00035 23.3 4.6 46 92-138 1-46 (53)
76 TIGR02959 SigZ RNA polymerase 68.0 3.8 8.2E-05 31.2 2.0 53 90-150 99-151 (170)
77 PRK12515 RNA polymerase sigma 67.8 5.8 0.00013 30.6 3.0 50 90-147 130-179 (189)
78 PRK12530 RNA polymerase sigma 67.7 5.6 0.00012 30.9 2.9 50 90-147 133-182 (189)
79 TIGR02983 SigE-fam_strep RNA p 67.1 6.3 0.00014 29.4 3.0 50 90-147 109-158 (162)
80 PF13936 HTH_38: Helix-turn-he 66.6 6.6 0.00014 23.7 2.5 40 90-137 3-42 (44)
81 PRK12519 RNA polymerase sigma 66.6 4.4 9.5E-05 31.3 2.1 49 90-146 140-188 (194)
82 PRK12547 RNA polymerase sigma 66.0 6.3 0.00014 29.7 2.8 50 90-147 111-160 (164)
83 PRK09639 RNA polymerase sigma 65.4 6.7 0.00014 29.3 2.9 49 90-147 111-159 (166)
84 PRK12546 RNA polymerase sigma 65.3 5.9 0.00013 30.9 2.6 50 91-148 113-162 (188)
85 PRK12536 RNA polymerase sigma 65.3 6.6 0.00014 30.1 2.9 51 90-148 128-178 (181)
86 TIGR02954 Sig70_famx3 RNA poly 65.2 7.2 0.00016 29.3 3.0 48 91-146 119-166 (169)
87 PRK07122 RNA polymerase sigma 64.9 19 0.00041 29.9 5.7 49 90-146 214-262 (264)
88 PRK09649 RNA polymerase sigma 64.6 7.6 0.00017 30.0 3.1 50 90-147 129-178 (185)
89 PRK12524 RNA polymerase sigma 64.2 6.9 0.00015 30.4 2.8 49 91-147 136-184 (196)
90 PRK09413 IS2 repressor TnpA; R 64.1 15 0.00032 26.8 4.4 48 87-141 8-55 (121)
91 PRK13919 putative RNA polymera 63.5 7.8 0.00017 29.6 3.0 50 90-147 134-183 (186)
92 PRK12532 RNA polymerase sigma 62.9 7.9 0.00017 29.9 2.9 50 91-148 136-185 (195)
93 PRK12520 RNA polymerase sigma 61.5 9.4 0.0002 29.4 3.1 50 90-147 130-179 (191)
94 PRK06986 fliA flagellar biosyn 61.2 7.3 0.00016 31.4 2.5 49 91-147 184-232 (236)
95 PRK07037 extracytoplasmic-func 61.1 9.1 0.0002 28.5 2.9 50 90-147 108-157 (163)
96 PF13384 HTH_23: Homeodomain-l 60.9 7.8 0.00017 23.3 2.1 25 117-141 19-43 (50)
97 PRK09637 RNA polymerase sigma 60.9 8.5 0.00018 29.7 2.7 52 90-149 105-156 (181)
98 PRK12523 RNA polymerase sigma 60.7 11 0.00023 28.6 3.3 50 90-147 118-167 (172)
99 PRK12516 RNA polymerase sigma 60.6 8.9 0.00019 29.8 2.8 51 91-149 116-166 (187)
100 TIGR02980 SigBFG RNA polymeras 60.4 9.6 0.00021 30.3 3.1 48 90-145 177-224 (227)
101 PRK12542 RNA polymerase sigma 60.3 9.3 0.0002 29.3 2.9 50 90-147 121-170 (185)
102 PRK12543 RNA polymerase sigma 60.2 11 0.00023 28.8 3.2 51 90-148 116-166 (179)
103 PRK12531 RNA polymerase sigma 59.5 9.9 0.00022 29.5 3.0 50 90-147 140-189 (194)
104 PRK09641 RNA polymerase sigma 59.3 9.7 0.00021 28.9 2.8 49 91-147 136-184 (187)
105 PRK12535 RNA polymerase sigma 59.3 12 0.00026 29.3 3.4 51 90-148 132-182 (196)
106 PF01381 HTH_3: Helix-turn-hel 59.1 7.3 0.00016 23.8 1.7 21 118-138 12-32 (55)
107 PRK12538 RNA polymerase sigma 58.9 7.8 0.00017 31.5 2.3 50 91-148 171-220 (233)
108 PRK15369 two component system 58.0 27 0.00058 25.7 5.0 48 90-146 148-195 (211)
109 PF00196 GerE: Bacterial regul 57.6 17 0.00037 22.7 3.3 47 91-146 3-49 (58)
110 PRK09645 RNA polymerase sigma 57.5 11 0.00025 28.3 2.9 50 91-148 118-167 (173)
111 PRK08583 RNA polymerase sigma 57.4 11 0.00023 30.8 2.9 49 91-147 205-253 (257)
112 PRK10072 putative transcriptio 56.9 7.9 0.00017 27.6 1.8 23 118-140 49-71 (96)
113 PRK12529 RNA polymerase sigma 56.9 15 0.00032 28.2 3.4 49 90-146 126-174 (178)
114 TIGR02479 FliA_WhiG RNA polyme 56.8 11 0.00025 29.9 2.9 49 90-146 174-222 (224)
115 PRK07670 RNA polymerase sigma 56.8 11 0.00025 30.6 3.0 48 91-146 201-248 (251)
116 PRK04217 hypothetical protein; 56.1 16 0.00034 26.8 3.3 53 87-147 38-90 (110)
117 TIGR02943 Sig70_famx1 RNA poly 56.0 13 0.00028 28.8 3.0 50 90-147 130-179 (188)
118 PRK12513 RNA polymerase sigma 55.9 4.7 0.0001 31.1 0.6 50 90-147 138-187 (194)
119 TIGR02947 SigH_actino RNA poly 55.8 5.4 0.00012 30.9 0.9 51 90-148 130-180 (193)
120 cd00131 PAX Paired Box domain 55.8 57 0.0012 24.1 6.4 48 89-139 73-127 (128)
121 PRK12545 RNA polymerase sigma 55.6 12 0.00026 29.3 2.9 50 90-147 138-187 (201)
122 PRK12539 RNA polymerase sigma 55.2 14 0.0003 28.4 3.1 50 90-147 130-179 (184)
123 PRK12511 RNA polymerase sigma 55.0 12 0.00027 28.9 2.8 49 91-147 111-159 (182)
124 TIGR02941 Sigma_B RNA polymera 54.9 12 0.00025 30.5 2.7 49 90-146 204-252 (255)
125 PRK12522 RNA polymerase sigma 54.8 13 0.00029 28.0 2.9 50 90-147 118-167 (173)
126 PF13411 MerR_1: MerR HTH fami 54.8 10 0.00022 24.3 1.9 19 119-137 4-22 (69)
127 PRK11511 DNA-binding transcrip 54.6 45 0.00098 24.3 5.7 42 94-139 8-49 (127)
128 cd06170 LuxR_C_like C-terminal 54.3 33 0.00071 20.3 4.2 45 93-146 2-46 (57)
129 PRK08301 sporulation sigma fac 54.2 11 0.00023 30.2 2.4 54 90-147 177-230 (234)
130 PRK11923 algU RNA polymerase s 54.2 13 0.00028 28.6 2.8 49 91-147 138-186 (193)
131 cd01392 HTH_LacI Helix-turn-he 54.2 7.6 0.00017 23.4 1.2 21 120-140 2-22 (52)
132 PF06056 Terminase_5: Putative 54.1 12 0.00025 24.2 2.1 21 119-139 17-37 (58)
133 PRK12533 RNA polymerase sigma 54.0 12 0.00027 30.0 2.7 52 90-149 133-184 (216)
134 PRK12544 RNA polymerase sigma 54.0 14 0.00031 29.3 3.0 50 90-147 147-196 (206)
135 PRK12528 RNA polymerase sigma 53.7 18 0.0004 26.8 3.5 46 90-143 112-157 (161)
136 PRK09647 RNA polymerase sigma 52.7 14 0.00031 29.1 2.9 50 90-147 137-186 (203)
137 TIGR02952 Sig70_famx2 RNA poly 52.6 17 0.00037 27.0 3.2 48 90-145 121-168 (170)
138 TIGR03070 couple_hipB transcri 52.2 10 0.00022 22.9 1.6 23 118-140 18-40 (58)
139 PRK06288 RNA polymerase sigma 51.8 14 0.00031 30.4 2.8 50 90-147 211-260 (268)
140 PF13730 HTH_36: Helix-turn-he 51.6 53 0.0011 19.9 5.2 48 91-141 2-51 (55)
141 PRK08295 RNA polymerase factor 51.6 16 0.00035 28.3 2.9 48 90-146 154-201 (208)
142 PRK09415 RNA polymerase factor 51.5 11 0.00023 28.9 1.9 50 90-147 126-175 (179)
143 cd04761 HTH_MerR-SF Helix-Turn 50.9 15 0.00032 21.7 2.1 20 119-138 4-23 (49)
144 PRK12518 RNA polymerase sigma 50.9 6.1 0.00013 29.8 0.4 51 90-148 119-169 (175)
145 TIGR03001 Sig-70_gmx1 RNA poly 50.4 16 0.00035 29.9 2.9 51 90-148 160-210 (244)
146 PF13551 HTH_29: Winged helix- 50.3 52 0.0011 22.5 5.2 51 87-137 53-109 (112)
147 PF02796 HTH_7: Helix-turn-hel 50.1 29 0.00064 20.7 3.4 39 90-136 4-42 (45)
148 PRK12534 RNA polymerase sigma 49.9 17 0.00037 27.8 2.8 49 90-146 136-184 (187)
149 PRK12540 RNA polymerase sigma 49.9 17 0.00036 28.1 2.8 51 90-148 110-160 (182)
150 TIGR02859 spore_sigH RNA polym 49.4 22 0.00048 27.2 3.4 29 118-146 168-196 (198)
151 PF05821 NDUF_B8: NADH-ubiquin 49.1 16 0.00036 29.0 2.6 26 107-132 31-57 (179)
152 PRK07408 RNA polymerase sigma 48.8 18 0.00038 29.8 2.9 50 90-147 202-251 (256)
153 TIGR02393 RpoD_Cterm RNA polym 48.6 22 0.00047 28.7 3.4 53 91-147 176-228 (238)
154 TIGR02885 spore_sigF RNA polym 48.6 21 0.00045 28.5 3.2 48 90-145 182-229 (231)
155 cd00093 HTH_XRE Helix-turn-hel 48.6 15 0.00032 21.0 1.8 22 118-139 15-36 (58)
156 PRK09651 RNA polymerase sigma 48.0 14 0.0003 28.0 2.1 47 90-144 118-164 (172)
157 PRK12527 RNA polymerase sigma 47.8 21 0.00045 26.5 2.9 49 91-147 105-153 (159)
158 PRK05911 RNA polymerase sigma 47.0 1.3E+02 0.0029 24.5 7.9 50 90-147 204-253 (257)
159 TIGR00721 tfx DNA-binding prot 46.9 27 0.00059 26.6 3.4 51 89-148 4-54 (137)
160 TIGR02960 SigX5 RNA polymerase 46.4 22 0.00047 29.7 3.1 51 90-148 141-191 (324)
161 PF00376 MerR: MerR family reg 45.6 18 0.0004 21.2 1.9 19 119-137 3-21 (38)
162 PRK12525 RNA polymerase sigma 45.4 28 0.0006 26.2 3.4 47 90-144 117-163 (168)
163 PHA01976 helix-turn-helix prot 45.4 17 0.00037 23.1 1.9 22 118-139 18-39 (67)
164 PRK05657 RNA polymerase sigma 45.1 26 0.00056 30.1 3.5 54 90-147 261-314 (325)
165 COG2963 Transposase and inacti 44.9 87 0.0019 22.2 5.8 48 89-143 5-53 (116)
166 PF12323 HTH_OrfB_IS605: Helix 44.8 13 0.00029 22.3 1.2 34 111-145 9-42 (46)
167 KOG4040 NADH:ubiquinone oxidor 44.3 13 0.00029 29.3 1.4 36 96-131 25-61 (186)
168 PRK09636 RNA polymerase sigma 44.1 28 0.0006 29.0 3.4 50 90-147 114-163 (293)
169 PF07638 Sigma70_ECF: ECF sigm 44.0 35 0.00076 26.4 3.8 47 92-146 136-182 (185)
170 PRK11922 RNA polymerase sigma 43.9 11 0.00024 30.2 1.0 50 90-147 148-197 (231)
171 PRK08241 RNA polymerase factor 43.8 25 0.00054 29.7 3.2 49 90-146 152-200 (339)
172 TIGR02607 antidote_HigA addict 43.7 18 0.00038 23.7 1.8 23 118-140 21-43 (78)
173 PRK09643 RNA polymerase sigma 43.0 17 0.00037 28.2 1.9 51 91-149 134-184 (192)
174 PRK05803 sporulation sigma fac 42.8 22 0.00047 28.6 2.5 54 90-147 174-227 (233)
175 cd01104 HTH_MlrA-CarA Helix-Tu 42.3 24 0.00051 22.4 2.2 19 119-137 4-22 (68)
176 cd04764 HTH_MlrA-like_sg1 Heli 42.3 23 0.00049 22.7 2.1 20 119-138 4-23 (67)
177 KOG3755 SATB1 matrix attachmen 42.2 24 0.00052 33.4 2.9 57 85-143 647-706 (769)
178 PRK05572 sporulation sigma fac 42.1 22 0.00048 28.9 2.5 50 90-147 201-250 (252)
179 cd04762 HTH_MerR-trunc Helix-T 42.1 28 0.0006 19.9 2.3 23 118-140 3-25 (49)
180 TIGR02950 SigM_subfam RNA poly 41.8 19 0.00042 26.3 1.9 47 92-146 106-152 (154)
181 TIGR03826 YvyF flagellar opero 41.8 39 0.00083 25.8 3.6 43 99-145 34-76 (137)
182 smart00530 HTH_XRE Helix-turn- 41.6 21 0.00046 20.1 1.8 22 118-139 13-34 (56)
183 TIGR02957 SigX4 RNA polymerase 41.5 32 0.0007 28.5 3.4 50 90-147 107-156 (281)
184 TIGR02394 rpoS_proteo RNA poly 40.9 28 0.0006 29.0 2.9 55 90-148 221-275 (285)
185 PRK06704 RNA polymerase factor 40.9 25 0.00054 28.7 2.6 51 90-148 115-165 (228)
186 TIGR02984 Sig-70_plancto1 RNA 40.9 31 0.00067 26.0 3.0 48 91-146 140-187 (189)
187 PF14229 DUF4332: Domain of un 40.4 30 0.00065 25.5 2.7 28 112-139 26-53 (122)
188 PRK08215 sporulation sigma fac 40.4 28 0.00061 28.4 2.9 49 90-146 208-256 (258)
189 TIGR02846 spore_sigmaK RNA pol 39.8 29 0.00062 27.8 2.8 53 90-146 173-225 (227)
190 COG3413 Predicted DNA binding 39.8 57 0.0012 26.0 4.5 49 90-139 154-202 (215)
191 PRK12517 RNA polymerase sigma 39.6 34 0.00074 26.4 3.1 50 90-147 127-176 (188)
192 TIGR02392 rpoH_proteo alternat 39.5 35 0.00076 28.2 3.3 51 90-146 217-267 (270)
193 PRK09638 RNA polymerase sigma 38.9 13 0.00029 27.9 0.7 49 90-146 125-173 (176)
194 TIGR02835 spore_sigmaE RNA pol 38.0 29 0.00063 27.9 2.5 54 90-147 177-230 (234)
195 PF13551 HTH_29: Winged helix- 37.7 37 0.0008 23.3 2.8 26 117-142 14-39 (112)
196 PF12844 HTH_19: Helix-turn-he 37.1 26 0.00056 22.0 1.7 24 117-140 14-37 (64)
197 PF01726 LexA_DNA_bind: LexA D 36.7 74 0.0016 20.8 3.9 42 91-137 3-48 (65)
198 PRK09640 RNA polymerase sigma 36.7 12 0.00026 28.8 0.1 49 91-147 134-182 (188)
199 smart00422 HTH_MERR helix_turn 35.9 32 0.0007 21.8 2.1 19 119-137 4-22 (70)
200 PHA02510 X gene X product; Rev 35.7 1.2E+02 0.0025 22.6 5.2 62 60-134 5-77 (116)
201 cd04763 HTH_MlrA-like Helix-Tu 35.0 34 0.00073 22.0 2.1 19 119-137 4-22 (68)
202 PF03672 UPF0154: Uncharacteri 35.0 1.3E+02 0.0028 20.0 4.8 35 96-133 18-54 (64)
203 PRK13870 transcriptional regul 33.6 69 0.0015 26.0 4.1 50 88-146 170-219 (234)
204 PF09607 BrkDBD: Brinker DNA-b 33.5 1.2E+02 0.0025 19.9 4.3 46 89-138 3-48 (58)
205 TIGR03020 EpsA transcriptional 33.4 60 0.0013 26.9 3.8 50 89-147 188-237 (247)
206 PF08671 SinI: Anti-repressor 32.9 53 0.0011 18.5 2.3 20 118-137 8-27 (30)
207 TIGR03541 reg_near_HchA LuxR f 32.7 73 0.0016 25.7 4.1 50 89-147 169-218 (232)
208 TIGR03879 near_KaiC_dom probab 32.5 40 0.00087 22.9 2.1 42 90-138 14-55 (73)
209 PF06971 Put_DNA-bind_N: Putat 32.1 38 0.00083 21.3 1.9 16 119-134 32-47 (50)
210 PF07037 DUF1323: Putative tra 31.8 36 0.00078 25.5 1.9 27 118-147 3-29 (122)
211 TIGR01764 excise DNA binding d 31.6 51 0.0011 18.9 2.3 21 118-138 4-24 (49)
212 PRK07598 RNA polymerase sigma 31.2 59 0.0013 29.2 3.5 54 90-147 349-402 (415)
213 PRK09706 transcriptional repre 30.9 35 0.00076 25.1 1.8 23 118-140 21-43 (135)
214 PRK09480 slmA division inhibit 30.8 61 0.0013 24.4 3.2 30 110-140 26-55 (194)
215 TIGR02997 Sig70-cyanoRpoD RNA 30.7 61 0.0013 27.2 3.4 50 91-144 249-298 (298)
216 PRK13890 conjugal transfer pro 30.4 35 0.00077 25.0 1.7 23 118-140 21-43 (120)
217 PRK07500 rpoH2 RNA polymerase 30.3 53 0.0012 27.5 3.0 53 90-148 226-278 (289)
218 PRK10651 transcriptional regul 30.2 79 0.0017 23.4 3.7 47 91-146 155-201 (216)
219 PF14549 P22_Cro: DNA-binding 28.7 54 0.0012 21.3 2.2 18 118-135 12-29 (60)
220 PF13542 HTH_Tnp_ISL3: Helix-t 28.5 55 0.0012 19.6 2.1 21 117-137 29-49 (52)
221 PRK05988 formate dehydrogenase 28.1 1.5E+02 0.0032 22.9 4.9 37 95-134 24-60 (156)
222 PF04539 Sigma70_r3: Sigma-70 28.0 1.6E+02 0.0035 19.0 4.6 26 111-139 19-44 (78)
223 PF13560 HTH_31: Helix-turn-he 27.3 47 0.001 21.0 1.7 25 117-141 16-40 (64)
224 PF05269 Phage_CII: Bacterioph 27.2 65 0.0014 22.9 2.5 28 115-142 23-50 (91)
225 PRK09726 antitoxin HipB; Provi 27.1 46 0.001 22.7 1.8 22 118-139 28-49 (88)
226 PF04297 UPF0122: Putative hel 26.4 83 0.0018 22.7 3.0 45 91-143 17-61 (101)
227 PF00325 Crp: Bacterial regula 26.3 1.1E+02 0.0023 17.4 2.9 25 117-141 4-28 (32)
228 PF13412 HTH_24: Winged helix- 26.1 1.3E+02 0.0027 17.7 3.5 36 94-136 3-38 (48)
229 PRK10188 DNA-binding transcrip 26.1 1.1E+02 0.0023 25.0 4.0 51 88-147 176-226 (240)
230 PRK04053 rps13p 30S ribosomal 26.0 87 0.0019 24.2 3.3 30 84-113 48-77 (149)
231 COG2938 Uncharacterized conser 25.1 1.2E+02 0.0025 21.7 3.5 42 98-141 31-72 (94)
232 cd01105 HTH_GlnR-like Helix-Tu 24.9 57 0.0012 22.3 1.9 17 119-135 5-21 (88)
233 PF04936 DUF658: Protein of un 24.7 60 0.0013 25.8 2.1 31 116-146 15-45 (186)
234 PRK09635 sigI RNA polymerase s 24.5 84 0.0018 26.4 3.2 50 90-147 117-166 (290)
235 PF01710 HTH_Tnp_IS630: Transp 24.4 1.2E+02 0.0026 21.9 3.6 38 92-137 3-40 (119)
236 PF11304 DUF3106: Protein of u 24.4 1.5E+02 0.0032 21.3 4.1 31 90-123 75-105 (107)
237 TIGR03629 arch_S13P archaeal r 24.4 97 0.0021 23.7 3.2 30 84-114 44-73 (144)
238 PRK09483 response regulator; P 24.3 1.6E+02 0.0035 22.0 4.5 47 90-145 147-193 (217)
239 TIGR01958 nuoE_fam NADH-quinon 24.1 1.9E+02 0.0041 21.8 4.8 44 96-142 18-64 (148)
240 PRK10403 transcriptional regul 24.1 1.1E+02 0.0024 22.5 3.6 49 90-147 152-200 (215)
241 PF04703 FaeA: FaeA-like prote 23.8 75 0.0016 20.8 2.2 24 118-141 18-41 (62)
242 COG1595 RpoE DNA-directed RNA 23.8 71 0.0015 24.3 2.4 51 90-148 126-176 (182)
243 PRK07539 NADH dehydrogenase su 23.6 2E+02 0.0043 21.8 4.9 36 96-134 24-59 (154)
244 TIGR02850 spore_sigG RNA polym 23.5 87 0.0019 25.5 3.0 48 90-145 205-252 (254)
245 PRK12427 flagellar biosynthesi 23.5 1E+02 0.0022 24.9 3.4 47 90-144 182-228 (231)
246 PF07042 TrfA: TrfA protein; 23.4 1.3E+02 0.0027 25.7 4.0 52 87-141 206-257 (282)
247 smart00354 HTH_LACI helix_turn 23.4 62 0.0014 21.0 1.8 23 118-140 3-25 (70)
248 PF03444 HrcA_DNA-bdg: Winged 23.3 2.1E+02 0.0045 19.8 4.4 44 92-137 2-45 (78)
249 PRK10219 DNA-binding transcrip 23.1 1.7E+02 0.0037 20.2 4.2 37 96-136 6-42 (107)
250 PRK06596 RNA polymerase factor 23.0 94 0.002 26.0 3.2 52 90-147 229-280 (284)
251 PHA03308 transcriptional regul 23.0 80 0.0017 31.0 3.0 16 84-99 1293-1308(1463)
252 smart00351 PAX Paired Box doma 22.9 3.1E+02 0.0066 20.0 5.8 46 88-136 72-124 (125)
253 TIGR02054 MerD mercuric resist 22.7 75 0.0016 23.4 2.3 21 118-138 6-26 (120)
254 PRK09191 two-component respons 22.6 1.6E+02 0.0034 23.2 4.3 50 90-147 87-136 (261)
255 PF06299 DUF1045: Protein of u 22.5 1.6E+02 0.0035 23.0 4.2 42 62-103 57-98 (160)
256 cd04788 HTH_NolA-AlbR Helix-Tu 22.5 68 0.0015 22.3 1.9 19 119-137 4-22 (96)
257 cd04780 HTH_MerR-like_sg5 Heli 22.5 67 0.0015 22.4 1.9 19 119-137 4-22 (95)
258 cd01106 HTH_TipAL-Mta Helix-Tu 22.3 75 0.0016 22.2 2.2 20 119-138 4-23 (103)
259 PF01343 Peptidase_S49: Peptid 22.3 1.4E+02 0.0029 22.5 3.7 45 88-138 76-120 (154)
260 cd04766 HTH_HspR Helix-Turn-He 22.2 69 0.0015 21.9 1.9 20 118-137 4-23 (91)
261 PF12728 HTH_17: Helix-turn-he 22.2 85 0.0018 18.7 2.1 21 119-139 5-25 (51)
262 PHA02955 hypothetical protein; 22.1 1.6E+02 0.0036 24.1 4.3 45 96-142 62-106 (213)
263 KOG1146 Homeobox protein [Gene 21.9 81 0.0018 32.5 2.9 61 84-147 704-764 (1406)
264 PRK07571 bidirectional hydroge 21.6 2.3E+02 0.0049 22.2 4.9 36 96-134 38-73 (169)
265 cd01107 HTH_BmrR Helix-Turn-He 20.4 78 0.0017 22.4 1.9 21 118-138 3-23 (108)
266 PF07022 Phage_CI_repr: Bacter 20.3 42 0.00091 21.7 0.4 20 118-137 15-35 (66)
267 cd01111 HTH_MerD Helix-Turn-He 20.0 80 0.0017 22.6 1.9 20 119-138 4-23 (107)
No 1
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.77 E-value=1.5e-19 Score=154.95 Aligned_cols=149 Identities=27% Similarity=0.356 Sum_probs=102.3
Q ss_pred HHHHHHHHHHhhCcCCCCCCCCCCCCC--CCC-------------CCCcccccccccchh--hhhh---hhhhHHHHHHH
Q 045160 9 AAWLSFFFEFIINPSEGCTGLKFSNTK--DGA-------------ASSDEEYSGAETEAQ--DAEA---RDEDRHLKDKL 68 (166)
Q Consensus 9 ~ea~~f~~~ie~qL~sl~~~~~~~~~~--~~~-------------~ss~e~~s~~~~~~~--~~~~---~~~~~elk~~l 68 (166)
.+++.+.++|+..+...+...+..... ... ..+++....++.+.. ...+ ......++..+
T Consensus 143 ~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 222 (342)
T KOG0773|consen 143 TWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSEELLGESEQDDSEDESGPSGSEPPLRLAKQSL 222 (342)
T ss_pred HHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhcccccccccccccccccccccccccccCcccccCCcccccccc
Confidence 789999999999999988754422110 000 011111111111100 0011 12223333444
Q ss_pred HhhhcCCccchhhhhccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 69 LRKFGSHIGSLKLEFSKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 69 ~~~~~~~~~~~~~~~~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
...+..++........++|+++.||+.++.+|+.|+.+|+.+|||+..+|..||++|||+..||+|||+|+|+|+|+++.
T Consensus 223 ~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 223 RQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred cccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence 44444455555555678888999999999999999999999999999999999999999999999999999999999997
Q ss_pred Ccchhhccc
Q 045160 149 NMHFAVMDN 157 (166)
Q Consensus 149 ~~~~~~~d~ 157 (166)
......++.
T Consensus 303 ~~~~~~~~~ 311 (342)
T KOG0773|consen 303 EEMYLLEDK 311 (342)
T ss_pred HHHHHHhhc
Confidence 666555543
No 2
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=99.73 E-value=2.6e-18 Score=104.97 Aligned_cols=40 Identities=53% Similarity=1.019 Sum_probs=36.2
Q ss_pred HHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhh
Q 045160 103 WWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKR 142 (166)
Q Consensus 103 ~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R 142 (166)
||.+|+.||||+.++|..||..|||+.+||.+||+|+|+|
T Consensus 1 Wl~~h~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 1 WLLEHLHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHTTTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 8999999999999999999999999999999999999997
No 3
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.67 E-value=9.6e-17 Score=103.83 Aligned_cols=57 Identities=33% Similarity=0.744 Sum_probs=54.2
Q ss_pred CCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCC
Q 045160 86 KKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWK 145 (166)
Q Consensus 86 kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk 145 (166)
||+|+.|+.++..+|+.+|.. +|||+..++..||..+||+..||.+||+|+|.+.|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE---NPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH---SSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH---hccccccccccccccccccccccccCHHHhHHHhCc
Confidence 578899999999999999999 999999999999999999999999999999998653
No 4
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.67 E-value=2.3e-16 Score=101.90 Aligned_cols=58 Identities=26% Similarity=0.571 Sum_probs=54.3
Q ss_pred CCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 86 KKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 86 kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
++++..|+.++..+|+.||.. +|||+..++..||..|||+..||.+||+|+|.+.++.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEK---NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 356789999999999999999 8999999999999999999999999999999997764
No 5
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.65 E-value=3.8e-16 Score=100.26 Aligned_cols=55 Identities=27% Similarity=0.556 Sum_probs=51.8
Q ss_pred CCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcC
Q 045160 87 KKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHW 144 (166)
Q Consensus 87 r~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~k 144 (166)
+.|+.|+.+++.+|+.+|.. ++||+..++..||..+||+..||.+||+|+|++.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQK---NPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 56778999999999999999 89999999999999999999999999999999854
No 6
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=99.59 E-value=6.1e-16 Score=127.69 Aligned_cols=85 Identities=27% Similarity=0.461 Sum_probs=70.9
Q ss_pred HHHHHHhhhcCCccchhhhh------------ccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhh
Q 045160 64 LKDKLLRKFGSHIGSLKLEF------------SKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQ 131 (166)
Q Consensus 64 lk~~l~~~~~~~~~~~~~~~------------~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~q 131 (166)
+.+.+.++|+...-.++++. -.+|||++|++.++.+|..||..|+.||||+++.|++||+++|++..|
T Consensus 155 m~~~i~~kF~~iq~~lkqstce~vmiLr~r~ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQ 234 (334)
T KOG0774|consen 155 MVQIISKKFSHIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQ 234 (334)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehh
Confidence 44455556655444444331 357889999999999999999999999999999999999999999999
Q ss_pred hhhhhhhHHhhcCCCCC
Q 045160 132 INNWFINQRKRHWKPSE 148 (166)
Q Consensus 132 V~~WF~N~R~R~kk~~~ 148 (166)
|+|||-|+|-|.+|.+.
T Consensus 235 vsnwfgnkrIrykK~~~ 251 (334)
T KOG0774|consen 235 VSNWFGNKRIRYKKNMG 251 (334)
T ss_pred hccccccceeehhhhhh
Confidence 99999999999988763
No 7
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.45 E-value=5.6e-14 Score=116.63 Aligned_cols=48 Identities=44% Similarity=0.833 Sum_probs=45.3
Q ss_pred hHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcC
Q 045160 94 KESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHW 144 (166)
Q Consensus 94 ~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~k 144 (166)
...+.+|++||.. +|||++.+|.+||+.|||+..||.|||.|+|+|.+
T Consensus 185 ekSR~~LrewY~~---~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 185 EKSRSLLREWYLQ---NPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred HhhHHHHHHHHhc---CCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 3468999999998 99999999999999999999999999999999977
No 8
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.45 E-value=5.3e-14 Score=114.28 Aligned_cols=62 Identities=26% Similarity=0.358 Sum_probs=58.4
Q ss_pred ccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 84 SKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 84 ~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
+-||.||+++.-|...|+..|++ +.|..-.||.+||..+||+.+||++||||+|.|.||.+.
T Consensus 121 K~RKPRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 121 KVRKPRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cccCCcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 45677999999999999999999 999999999999999999999999999999999998764
No 9
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.44 E-value=7.4e-14 Score=109.85 Aligned_cols=61 Identities=26% Similarity=0.404 Sum_probs=58.0
Q ss_pred ccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 84 SKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 84 ~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
+.||.||.|+.+|...|+..|.. +.|..-.||+.||+.++|+..||++||||+|.|+|+.-
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~ 161 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQ 161 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHH
Confidence 56788999999999999999999 99999999999999999999999999999999998763
No 10
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.39 E-value=6.2e-13 Score=87.31 Aligned_cols=53 Identities=19% Similarity=0.454 Sum_probs=50.6
Q ss_pred cCCCCCCCChHHHHHHHHHHHHhcCCCC----CCHHHHHHHHHHhCCChhhhhhhhhhHH
Q 045160 85 KKKKKGKLPKESRQTLLDWWNAHYKWPY----PTEADKLQLAESTGLDQKQINNWFINQR 140 (166)
Q Consensus 85 ~kr~r~~~~~~~~~~L~~~f~~h~~~pY----Ps~~ek~~LA~~tgLs~~qV~~WF~N~R 140 (166)
++|.|+.|+.+|+..|+..|.. ++| |+..++..||..+||+..+|++||+|-+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~---~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEK---LGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHH---cCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 4789999999999999999999 999 9999999999999999999999999964
No 11
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.39 E-value=3.3e-13 Score=109.10 Aligned_cols=60 Identities=25% Similarity=0.373 Sum_probs=56.8
Q ss_pred ccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 84 SKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 84 ~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
+|||.|+.|+..|+..|+..|.. ..|.+.++|..||.++.|++.||++||||+|.|.|+.
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~---krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq 162 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFEL---KRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQ 162 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHH---HhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHH
Confidence 57889999999999999999999 8999999999999999999999999999999996655
No 12
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.37 E-value=3.1e-13 Score=117.17 Aligned_cols=65 Identities=25% Similarity=0.411 Sum_probs=61.2
Q ss_pred hhhccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 81 LEFSKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 81 ~~~~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
...+||||||.+...++.+|+..|.+ ||.|+.+|.-.||++++|.+..|++||||||+|.|+...
T Consensus 290 a~~RkRKKRTSie~~vr~aLE~~F~~---npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 290 AQSRKRKKRTSIEVNVRGALEKHFLK---NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccccccceeHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 44478899999999999999999999 999999999999999999999999999999999998865
No 13
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.34 E-value=4.7e-13 Score=113.52 Aligned_cols=63 Identities=24% Similarity=0.333 Sum_probs=58.5
Q ss_pred hccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 83 FSKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 83 ~~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
.+-||||-.+++.|+..|+.-|.- |-|.|++-|.+|++.++||.+||++||||||.|.||-..
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlf---N~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLF---NMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHH---HHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 356788899999999999999999 899999999999999999999999999999999988753
No 14
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.34 E-value=4.7e-13 Score=113.47 Aligned_cols=62 Identities=21% Similarity=0.323 Sum_probs=57.5
Q ss_pred hccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 83 FSKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 83 ~~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
.+|||+|.-|++.|+-.|+..|.+ .-|.+..||+.||..++||.+||++||||+|-|.|+.-
T Consensus 151 ~~kRKrRVLFSqAQV~ELERRFrq---QRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~ 212 (307)
T KOG0842|consen 151 RKKRKRRVLFSQAQVYELERRFRQ---QRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQ 212 (307)
T ss_pred ccccccccccchhHHHHHHHHHHh---hhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhh
Confidence 356777888999999999999999 89999999999999999999999999999999988764
No 15
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.33 E-value=9.4e-13 Score=109.82 Aligned_cols=62 Identities=21% Similarity=0.346 Sum_probs=58.0
Q ss_pred hccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 83 FSKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 83 ~~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
...||.|+.|+..|+..|+.-|.- |.|.+..-|.+||..+.|+++||+|||||||+|.||..
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhf---N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~ 218 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHF---NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKEN 218 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhcc---ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhh
Confidence 357899999999999999999999 99999999999999999999999999999999977653
No 16
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.28 E-value=5.2e-12 Score=104.62 Aligned_cols=62 Identities=29% Similarity=0.442 Sum_probs=58.3
Q ss_pred cCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCCC
Q 045160 85 KKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSEN 149 (166)
Q Consensus 85 ~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~~ 149 (166)
.||.|+-|+.+|.+.|+.-|.+ |-|.++.-|..||..+||.+.||++||||+|.|+||....
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~e---nRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgs 307 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQE---NRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGS 307 (342)
T ss_pred hcCccccccHHHHHHHHHHHhh---hhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCC
Confidence 3577999999999999999999 9999999999999999999999999999999999998643
No 17
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.27 E-value=4.2e-12 Score=108.27 Aligned_cols=65 Identities=23% Similarity=0.428 Sum_probs=58.5
Q ss_pred hhccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCCC
Q 045160 82 EFSKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSEN 149 (166)
Q Consensus 82 ~~~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~~ 149 (166)
..+++|.|+.|+..|+..|+.-|+. -.|.+..+|..||..+||+-.||.+||||||.|-|+..+.
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~~---QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFEK---QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHHH---hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 3566778999999999999999999 8999999999999999999999999999999996655443
No 18
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.26 E-value=3.6e-12 Score=92.48 Aligned_cols=73 Identities=16% Similarity=0.303 Sum_probs=63.1
Q ss_pred hcCCccchhhhhccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 72 FGSHIGSLKLEFSKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 72 ~~~~~~~~~~~~~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
|++.-.++....+.+|-|+.|+..|...|+..|.+ ..||+.-.|++||.+..|+...|++||||+|.+.+|..
T Consensus 4 ~~~~~~~l~ekrKQRRIRTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 4 YGDDPLGLTEKRKQRRIRTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred cCCCCCChhHHHHhhhhhhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 33334445555566788999999999999999999 89999999999999999999999999999999988763
No 19
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.19 E-value=2e-11 Score=94.95 Aligned_cols=61 Identities=23% Similarity=0.409 Sum_probs=57.1
Q ss_pred ccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 84 SKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 84 ~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..+++|++.+..+..+|+..|.. +|||+..+|..|+..+|++++-|++||||+|.+.|+..
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i---~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~ 110 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEI---NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKR 110 (156)
T ss_pred cCcccceechHHHHHHHHHHhcc---CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhc
Confidence 45678888999999999999999 99999999999999999999999999999999988775
No 20
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.18 E-value=1.7e-11 Score=99.17 Aligned_cols=61 Identities=16% Similarity=0.349 Sum_probs=56.9
Q ss_pred hccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 83 FSKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 83 ~~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
.+.+|.||.|+..|..+|+..|.+ ..||+...+++||.+++|...+|+|||.|+|+|.++.
T Consensus 35 RkqRRERTtFtr~QlevLe~LF~k---TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~q 95 (228)
T KOG2251|consen 35 RKQRRERTTFTRKQLEVLEALFAK---TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQ 95 (228)
T ss_pred hhcccccceecHHHHHHHHHHHHh---hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHh
Confidence 356788999999999999999999 9999999999999999999999999999999996654
No 21
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.18 E-value=2e-11 Score=98.16 Aligned_cols=57 Identities=30% Similarity=0.375 Sum_probs=52.6
Q ss_pred cCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcC
Q 045160 85 KKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHW 144 (166)
Q Consensus 85 ~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~k 144 (166)
.+.++.+|+.+|...|+.-|.. +-|..+..|..||+.+||.+.||.+||||||+|-|
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~---~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK 106 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFES---EKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWK 106 (198)
T ss_pred cccccccccHHHHHHhHHhhcc---ccccChHHHHHHHHhhCCChhHHHHHHhhcccccc
Confidence 3566778999999999999999 78999999999999999999999999999999944
No 22
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.17 E-value=2.5e-11 Score=97.67 Aligned_cols=65 Identities=18% Similarity=0.314 Sum_probs=58.9
Q ss_pred hhhhhccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 79 LKLEFSKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 79 ~~~~~~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
+++..-.+|.|+.|+..|...|++-|.+ ..|.+.+|+.+++..+.|+.+||++||||||.|.|+.
T Consensus 138 LrKhk~nRkPRtPFTtqQLlaLErkfre---kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRl 202 (246)
T KOG0492|consen 138 LRKHKPNRKPRTPFTTQQLLALERKFRE---KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRL 202 (246)
T ss_pred hcccCCCCCCCCCCCHHHHHHHHHHHhH---hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHH
Confidence 3444456788999999999999999999 8999999999999999999999999999999998765
No 23
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.12 E-value=5.1e-11 Score=98.67 Aligned_cols=56 Identities=23% Similarity=0.334 Sum_probs=52.3
Q ss_pred CCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 88 KKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 88 ~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
-|++|+..|...|+..|.+ .-||+..-|+.||.+|+|.+.+|++||||||.|-+|.
T Consensus 144 ~RTiFT~~Qle~LEkaFke---aHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~ 199 (332)
T KOG0494|consen 144 FRTIFTSYQLEELEKAFKE---AHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKT 199 (332)
T ss_pred ccchhhHHHHHHHHHHHhh---ccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhh
Confidence 3899999999999999999 8999999999999999999999999999999994443
No 24
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.10 E-value=2.9e-11 Score=94.21 Aligned_cols=65 Identities=22% Similarity=0.419 Sum_probs=59.7
Q ss_pred hhccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCCC
Q 045160 82 EFSKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSEN 149 (166)
Q Consensus 82 ~~~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~~ 149 (166)
.-+++|.|+.|+..+...|+..|+. -.|.+-.++.+||..++|+.+||+.||||+|.|+||-.++
T Consensus 97 ~~~r~K~Rtvfs~~ql~~l~~rFe~---QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~ 161 (194)
T KOG0491|consen 97 HCRRRKARTVFSDPQLSGLEKRFER---QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRN 161 (194)
T ss_pred HHHhhhhcccccCccccccHHHHhh---hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhc
Confidence 3467788999999999999999998 7999999999999999999999999999999999987544
No 25
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.02 E-value=1.6e-10 Score=97.85 Aligned_cols=65 Identities=20% Similarity=0.384 Sum_probs=59.3
Q ss_pred ccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCCCcc
Q 045160 84 SKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSENMH 151 (166)
Q Consensus 84 ~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~~~~ 151 (166)
+++|.|+.|+..|.+.|+.||.+ |-||+.+.|++||..|+|+...|++||.|+|.+-+|...++.
T Consensus 111 KqrrQrthFtSqqlqele~tF~r---NrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQR---NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhh---ccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 45678999999999999999999 999999999999999999999999999999999666655655
No 26
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.94 E-value=2.5e-10 Score=94.94 Aligned_cols=58 Identities=28% Similarity=0.393 Sum_probs=53.1
Q ss_pred CCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 87 KKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 87 r~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
|=|..++..||-.|+.-|.. ++|.|..-|.+||..+||+++||++||||||.|.+|--
T Consensus 201 KYRvVYTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~n 258 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDN 258 (317)
T ss_pred ceeEEecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHH
Confidence 33677999999999999999 99999999999999999999999999999999977653
No 27
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.87 E-value=1.2e-09 Score=91.88 Aligned_cols=68 Identities=26% Similarity=0.442 Sum_probs=60.5
Q ss_pred chhhhhccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 78 SLKLEFSKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 78 ~~~~~~~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
.+..+...||.|+.++..|...|+..|.. .|.|..-.|+.|+..|||+.+.|++||||+|+|.|+--.
T Consensus 160 ~l~gd~~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T KOG4577|consen 160 ELEGDASNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T ss_pred ccccccccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhh
Confidence 34455677999999999999999999998 899999999999999999999999999999988665433
No 28
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=98.79 E-value=3.4e-09 Score=89.74 Aligned_cols=61 Identities=20% Similarity=0.328 Sum_probs=55.8
Q ss_pred CCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCCCcch
Q 045160 89 KGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSENMHF 152 (166)
Q Consensus 89 r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~~~~~ 152 (166)
|+-|+++|+..|+.-|++ -.|-+...|.+||..++|.+..|++||||+|.|.|+....|.+
T Consensus 185 RTAFTReQIaRLEKEFyr---ENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaW 245 (408)
T KOG0844|consen 185 RTAFTREQIARLEKEFYR---ENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAW 245 (408)
T ss_pred HhhhhHHHHHHHHHHHHH---hccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccC
Confidence 689999999999999998 7999999999999999999999999999999998887655544
No 29
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.69 E-value=2.2e-08 Score=90.10 Aligned_cols=57 Identities=19% Similarity=0.330 Sum_probs=54.3
Q ss_pred ccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhc
Q 045160 84 SKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRH 143 (166)
Q Consensus 84 ~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~ 143 (166)
..||.|..|+..|++.|...|.+ ++||+.++.+.|+.++||...-|.|||-|+|+|.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke---~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKE---NKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 35778999999999999999999 9999999999999999999999999999999995
No 30
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.63 E-value=8.7e-09 Score=86.74 Aligned_cols=63 Identities=22% Similarity=0.417 Sum_probs=57.3
Q ss_pred hhhccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 81 LEFSKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 81 ~~~~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
....|||||+.+-..-++-|+++|.. -|-|+-+-...||+++.|-...|++||||+|+|.|+-
T Consensus 305 ~~~ekKRKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 305 PGGEKKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 367 (385)
T ss_pred CccccccccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence 34467889999988889999999999 8999999999999999999999999999999998773
No 31
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.60 E-value=1.8e-08 Score=80.87 Aligned_cols=62 Identities=24% Similarity=0.252 Sum_probs=57.4
Q ss_pred hccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 83 FSKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 83 ~~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
+++++.|+.|+..+...|+..|.. .+||+...++.||..+++++..|++||+|+|++.++..
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~---~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEK---VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcC---CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 356888999999999999999999 79999999999999999999999999999999977653
No 32
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.56 E-value=9e-08 Score=83.19 Aligned_cols=63 Identities=21% Similarity=0.463 Sum_probs=57.2
Q ss_pred hhccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 82 EFSKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 82 ~~~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
+.+.++.|+.|+..+...|+.+|.. ++||.-..++.||.++||+...|++||+|+|.|.++-.
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~r---t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQR---TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccccccchHHHHHHHhcC---CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 3455667899999999999999999 89999999999999999999999999999999866664
No 33
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=98.54 E-value=4.2e-08 Score=79.88 Aligned_cols=61 Identities=23% Similarity=0.352 Sum_probs=55.0
Q ss_pred hccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 83 FSKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 83 ~~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
.+++-.|..|+..+...|+.-|.+ ..||--.++.+||...|++..||.+||||+|.|-+|.
T Consensus 165 G~rk~srPTf~g~qi~~le~~feq---tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKk 225 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQ---TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKK 225 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhh---hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhh
Confidence 455566777999999999999999 8999999999999999999999999999999995554
No 34
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=98.45 E-value=3.9e-08 Score=63.07 Aligned_cols=24 Identities=25% Similarity=0.164 Sum_probs=22.8
Q ss_pred ccccHHHHHHHHHHHhhCcCCCCC
Q 045160 4 LYLPFAAWLSFFFEFIINPSEGCT 27 (166)
Q Consensus 4 L~~p~~ea~~f~~~ie~qL~sl~~ 27 (166)
|+|||+||+.||++||+||++||.
T Consensus 29 L~~p~~EA~~f~~~ie~qL~~Lt~ 52 (52)
T PF03791_consen 29 LQRPFQEAMEFCREIEQQLSSLTG 52 (52)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhC
Confidence 789999999999999999999984
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.74 E-value=3.2e-05 Score=50.30 Aligned_cols=43 Identities=21% Similarity=0.403 Sum_probs=31.6
Q ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhh
Q 045160 97 RQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKR 142 (166)
Q Consensus 97 ~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R 142 (166)
.+.|+++|.. +.++.+.+...|+.++||+..||+.||.-++.+
T Consensus 10 ~~pL~~Yy~~---h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLK---HKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHH---T----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHH---cCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 4569999999 699999999999999999999999999987654
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.58 E-value=3.4e-05 Score=66.26 Aligned_cols=62 Identities=37% Similarity=0.621 Sum_probs=56.6
Q ss_pred cCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 85 KKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 85 ~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..+++++.+.+. ..|..|..+|..+|||++.++..|+..++++..||++||.|.|+|.++..
T Consensus 95 ~~~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~ 156 (342)
T KOG0773|consen 95 KGARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKEL 156 (342)
T ss_pred cccccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhcc
Confidence 445677888888 89999999999999999999999999999999999999999999987764
No 37
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.41 E-value=0.00011 Score=58.92 Aligned_cols=60 Identities=30% Similarity=0.505 Sum_probs=54.6
Q ss_pred ccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 84 SKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 84 ~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
..++.++.+...+...+...|.. .+||....+..|+..+|++...|.+||+|+|.+.++.
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~ 211 (235)
T KOG0490|consen 152 KPRRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKH 211 (235)
T ss_pred ccCCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhh
Confidence 45566788999999999999998 9999999999999999999999999999999998764
No 38
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.78 E-value=0.0015 Score=64.62 Aligned_cols=70 Identities=21% Similarity=0.252 Sum_probs=62.3
Q ss_pred ccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCCCcchhhcc
Q 045160 84 SKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSENMHFAVMD 156 (166)
Q Consensus 84 ~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~~~~~~~~d 156 (166)
.+++.|+.++..+..+++..|.. --||..++-+.|.+..+|....|.+||+|.|.+-+|..++.....++
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~---q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~~~~ss~ 971 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEA---QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNGTAASST 971 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhh---ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcccccccc
Confidence 46778899999999999999999 89999999999999999999999999999999999998865333333
No 39
>PF03789 ELK: ELK domain ; InterPro: IPR005539 This domain is required for the nuclear localisation of these proteins []. All of these proteins are members of the Tale/Knox homeodomain family, a subfamily, containing homeobox IPR001356 from INTERPRO.; GO: 0003677 DNA binding, 0005634 nucleus
Probab=96.52 E-value=0.00075 Score=35.88 Aligned_cols=22 Identities=55% Similarity=0.812 Sum_probs=19.8
Q ss_pred HHHHHHHhhhcCCccchhhhhc
Q 045160 63 HLKDKLLRKFGSHIGSLKLEFS 84 (166)
Q Consensus 63 elk~~l~~~~~~~~~~~~~~~~ 84 (166)
|||.+|+++|+++|+++++++.
T Consensus 1 ELK~~LlrkY~g~i~~Lr~Ef~ 22 (22)
T PF03789_consen 1 ELKHQLLRKYSGYISSLRQEFS 22 (22)
T ss_pred CHHHHHHHHHhHhHHHHHHHhC
Confidence 5899999999999999998863
No 40
>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=94.97 E-value=0.065 Score=34.15 Aligned_cols=48 Identities=19% Similarity=0.315 Sum_probs=34.4
Q ss_pred CCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHh
Q 045160 86 KKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRK 141 (166)
Q Consensus 86 kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~ 141 (166)
+|+|..|+-+....+-..+.. .+ -...||+.+|++..+|..|..|+..
T Consensus 1 krkR~~LTl~eK~~iI~~~e~---g~-----s~~~ia~~fgv~~sTv~~I~K~k~~ 48 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEE---GE-----SKRDIAREFGVSRSTVSTILKNKDK 48 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHC---TT------HHHHHHHHT--CCHHHHHHHCHHH
T ss_pred CCCCccCCHHHHHHHHHHHHc---CC-----CHHHHHHHhCCCHHHHHHHHHhHHH
Confidence 477889998887766666666 33 5789999999999999999999643
No 41
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=93.96 E-value=0.1 Score=49.59 Aligned_cols=46 Identities=17% Similarity=0.385 Sum_probs=42.5
Q ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCC
Q 045160 97 RQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWK 145 (166)
Q Consensus 97 ~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk 145 (166)
..+|+++|.. |+.|+.++-..+|.+.||+...|+.||.+.+.....
T Consensus 568 ~sllkayyal---n~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~s 613 (1007)
T KOG3623|consen 568 TSLLKAYYAL---NGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMS 613 (1007)
T ss_pred HHHHHHHHHh---cCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhh
Confidence 7789999999 999999999999999999999999999999987543
No 42
>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=90.02 E-value=0.5 Score=31.20 Aligned_cols=47 Identities=15% Similarity=0.276 Sum_probs=31.8
Q ss_pred CCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHH
Q 045160 87 KKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQR 140 (166)
Q Consensus 87 r~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R 140 (166)
++++.||.+.+..+-.-... .......+|+..|+++.+|.+|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~-------~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE-------SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHH-------HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH-------CCCceEeeecccccccccccHHHHHHh
Confidence 45678999987755444422 257788999999999999999998887
No 43
>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=89.44 E-value=0.74 Score=28.52 Aligned_cols=44 Identities=20% Similarity=0.377 Sum_probs=32.5
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhh
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKR 142 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R 142 (166)
.+|+..+.++...+.. .-.-.++|+.+|++...|.+|....|++
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 5788888888766555 2345689999999999999999998876
No 44
>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=89.00 E-value=0.77 Score=27.14 Aligned_cols=46 Identities=20% Similarity=0.310 Sum_probs=35.2
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHW 144 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~k 144 (166)
.++...+.++...+.. . ..-..+|..+|++...|..|....+.+.+
T Consensus 10 ~l~~~~~~~~~~~~~~----~----~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGE----G----LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 4677788888777654 2 23457899999999999999988887653
No 45
>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=88.95 E-value=0.49 Score=29.08 Aligned_cols=46 Identities=15% Similarity=0.222 Sum_probs=36.4
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHW 144 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~k 144 (166)
.||+..+.+|...|.+ + ..-.++|+.+|++...|+.+......+++
T Consensus 4 ~L~~~er~vi~~~y~~----~----~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE----G----LTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTS----T-----SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC----C----CCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 5788899999888755 2 33568999999999999999988887765
No 46
>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=82.53 E-value=4.7 Score=21.07 Aligned_cols=39 Identities=15% Similarity=0.194 Sum_probs=27.3
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhh
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWF 136 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF 136 (166)
..++.+.+..+...+.. .+ ....+|+.+|++...|.+|.
T Consensus 4 ~~~~~~~~~~i~~~~~~----~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAA----GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHhC
Confidence 34666666666555543 33 35578899999999999984
No 47
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=82.47 E-value=1.8 Score=32.05 Aligned_cols=48 Identities=8% Similarity=0.077 Sum_probs=38.7
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWK 145 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk 145 (166)
..||+.++.++...|.+. + .-.++|+.+|++...|.+|....|+++++
T Consensus 105 ~~L~~~~r~ii~l~~~~~----~----s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 105 SVLDEKEKYIIFERFFVG----K----TMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred HhCCHHHHHHHHHHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 478888999887666552 2 25689999999999999999999998765
No 48
>PRK00118 putative DNA-binding protein; Validated
Probab=81.53 E-value=0.92 Score=33.02 Aligned_cols=54 Identities=13% Similarity=0.135 Sum_probs=42.5
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCCCcch
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSENMHF 152 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~~~~~ 152 (166)
.+++.++.++..++.. . ..-.++|+.+|+++..|.+|....|.+.++-.+.+.+
T Consensus 17 ~L~ekqRevl~L~y~e----g----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~ 70 (104)
T PRK00118 17 LLTEKQRNYMELYYLD----D----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHL 70 (104)
T ss_pred cCCHHHHHHHHHHHHc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence 5688888888777666 2 2334699999999999999999999998876655544
No 49
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=78.98 E-value=1.8 Score=32.32 Aligned_cols=51 Identities=18% Similarity=0.186 Sum_probs=40.5
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
..||+.++.++...+.+ .++ -.++|+.+|++...|.+.+...|+++++...
T Consensus 105 ~~Lp~~~r~v~~l~~~~----g~s----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (160)
T PRK09642 105 RELPENYRDVVLAHYLE----EKS----YQEIALQEKIEVKTVEMKLYRARKWIKKHWK 155 (160)
T ss_pred HhCCHHHHHHHHHHHHh----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 35899999988776665 222 2489999999999999999999999877653
No 50
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=77.22 E-value=2.5 Score=32.41 Aligned_cols=52 Identities=10% Similarity=-0.008 Sum_probs=42.1
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSEN 149 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~~ 149 (166)
..||+..+.++...+.+. ..-.++|+.+|++...|.+++...|+++++..++
T Consensus 130 ~~L~~~~r~v~~l~~~~g--------~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~~ 181 (184)
T PRK12512 130 ETLPPRQRDVVQSISVEG--------ASIKETAAKLSMSEGAVRVALHRGLAALAAKFRS 181 (184)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 367888999888766552 2345899999999999999999999998877654
No 51
>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=77.02 E-value=2.9 Score=29.75 Aligned_cols=47 Identities=21% Similarity=0.318 Sum_probs=36.4
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWK 145 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk 145 (166)
.|++.++.++...+.. .+ ....+|+.+|+++..|.++....+.+.++
T Consensus 110 ~L~~~~~~ii~~~~~~----g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE----GL----SYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 5677788887554443 33 33489999999999999999999988765
No 52
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=76.16 E-value=3.2 Score=31.81 Aligned_cols=53 Identities=13% Similarity=0.125 Sum_probs=41.5
Q ss_pred CCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCCCc
Q 045160 89 KGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSENM 150 (166)
Q Consensus 89 r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~~~ 150 (166)
...|++.++.+|.. +.+ .+ ...++|+.+|++...|.+|-.+.+.+.++-.+..
T Consensus 4 ~~~Lt~rqreVL~l-r~~----Gl----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl 56 (141)
T PRK03975 4 ESFLTERQIEVLRL-RER----GL----TQQEIADILGTSRANVSSIEKRARENIEKARETL 56 (141)
T ss_pred ccCCCHHHHHHHHH-HHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999976 333 32 3458999999999999999999999887765443
No 53
>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=75.26 E-value=3.8 Score=30.35 Aligned_cols=48 Identities=23% Similarity=0.217 Sum_probs=38.6
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWK 145 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk 145 (166)
..||+.++.++...+.. .+ .-.++|+.+|++...|.++..-.|+++++
T Consensus 110 ~~L~~~~r~v~~l~~~~----g~----~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQR----GV----SLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHhc----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 57889999998876555 22 23579999999999999999988888765
No 54
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=74.39 E-value=3.1 Score=31.10 Aligned_cols=50 Identities=16% Similarity=0.177 Sum_probs=39.1
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+..+.++...+.. .+ .-.++|+.+|++...|.+|..-.|.++++..
T Consensus 124 ~~L~~~~r~i~~l~~~~----~~----~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 124 DALPVKQREVFLLRYVE----GL----SYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred HhCCHHHHHHhhHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34788888888766554 22 2368999999999999999999999987654
No 55
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=74.37 E-value=3.1 Score=32.35 Aligned_cols=50 Identities=10% Similarity=0.028 Sum_probs=40.1
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.+|...+..+ -.-.++|+.+|++...|.++....|+++++..
T Consensus 141 ~~L~~~~r~vl~l~~~~~--------~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 141 DALTDTQRESVTLAYYGG--------LTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 358899999987766552 23357999999999999999999999987654
No 56
>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=73.78 E-value=4.1 Score=29.83 Aligned_cols=47 Identities=21% Similarity=0.232 Sum_probs=37.2
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWK 145 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk 145 (166)
.|+...+.++...+.. .++ ..++|+.+|++...|.++....|++.++
T Consensus 113 ~L~~~~r~il~l~~~~----~~~----~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRFE----GKS----YKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 6788888888765544 333 3469999999999999999999988775
No 57
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=73.69 E-value=4.1 Score=30.66 Aligned_cols=51 Identities=18% Similarity=0.054 Sum_probs=41.2
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
..||+.++.++...+.++ . .-.++|..+|++...|.+|..-.|+++++-..
T Consensus 107 ~~L~~~~r~v~~l~~~~g--~------s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE--L------TYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred HhCCHHHHHHHHhHHHhc--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 567888999988766652 2 23589999999999999999999999887643
No 58
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=73.57 E-value=3.4 Score=30.96 Aligned_cols=50 Identities=16% Similarity=0.100 Sum_probs=39.2
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..|++.++.++...+.. .++ -..+|+.+|++...|.+|....++++++..
T Consensus 127 ~~L~~~~r~vl~l~~~~----~~s----~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 127 ESLPEELRTAITLREIE----GLS----YEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 36888899888766554 222 247999999999999999999999887654
No 59
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=73.25 E-value=3.5 Score=31.39 Aligned_cols=49 Identities=12% Similarity=0.158 Sum_probs=39.5
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
..||+..+.++...+.+ .++ -.++|+.+|++...|.++....|+++++-
T Consensus 128 ~~L~~~~r~i~~l~~~~----g~s----~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 128 EELEKDRAAAVRRAYLE----GLS----YKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 45788888888777765 332 45899999999999999999999988764
No 60
>PF13518 HTH_28: Helix-turn-helix domain
Probab=73.06 E-value=4.3 Score=24.48 Aligned_cols=25 Identities=16% Similarity=0.421 Sum_probs=21.5
Q ss_pred HHHHHHHhCCChhhhhhhhhhHHhh
Q 045160 118 KLQLAESTGLDQKQINNWFINQRKR 142 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~N~R~R 142 (166)
...+|+.+|++..+|..|....+.-
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~~ 39 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYREG 39 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHhc
Confidence 4569999999999999999887763
No 61
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=72.86 E-value=4.4 Score=31.36 Aligned_cols=50 Identities=22% Similarity=0.271 Sum_probs=40.4
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++...|.+ .+ ...++|+.+|++...|.+...-.|+++++.-
T Consensus 130 ~~L~~~~r~i~~l~~~~----g~----s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 130 NDLEKLDREIFIRRYLL----GE----KIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred HhCCHHHHHHHHHHHHc----cC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 47899999998876655 22 2358999999999999999999999988764
No 62
>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=72.37 E-value=2.9 Score=31.95 Aligned_cols=50 Identities=10% Similarity=-0.014 Sum_probs=38.8
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++...+.. . ..-.++|+.+|++...|.++....|+++++-.
T Consensus 137 ~~L~~~~r~v~~l~~~~----~----~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 137 EALPEDLRTAITLRELE----G----LSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred HcCCHHHhhhhhhhhhc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 35677888888665544 2 23458999999999999999999999987754
No 63
>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=72.26 E-value=3.3 Score=27.23 Aligned_cols=21 Identities=24% Similarity=0.472 Sum_probs=17.8
Q ss_pred HHHHHHHHhCCChhhhhhhhh
Q 045160 117 DKLQLAESTGLDQKQINNWFI 137 (166)
Q Consensus 117 ek~~LA~~tgLs~~qV~~WF~ 137 (166)
.-..||+++|++..+|+.|=.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh
Confidence 456899999999999999943
No 64
>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=71.93 E-value=4.4 Score=30.82 Aligned_cols=48 Identities=10% Similarity=0.039 Sum_probs=38.8
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
.||+.++.++...+.+ .+ .-.++|+.+|++...|.+.....|.++++.
T Consensus 134 ~Lp~~~r~v~~l~~~~----g~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 134 QVDPRQAEVVELRFFA----GL----TVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred cCCHHHHHHHHHHHHc----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4888899988777665 22 235799999999999999999999987653
No 65
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=71.22 E-value=4.3 Score=32.00 Aligned_cols=50 Identities=12% Similarity=0.082 Sum_probs=39.7
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.+|...+.. . -.-.++|+.+|++...|.++....++++++-.
T Consensus 152 ~~L~~~~r~vl~l~~~~----g----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 152 EKLPEAQQTVVKGVYFQ----E----LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred HhCCHHHHHHHHHHHHc----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 36888899988766555 2 23458999999999999999999999887654
No 66
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=71.03 E-value=3.5 Score=26.05 Aligned_cols=24 Identities=17% Similarity=0.329 Sum_probs=18.3
Q ss_pred HHHHHHHHhCCChhhhhhhhhhHH
Q 045160 117 DKLQLAESTGLDQKQINNWFINQR 140 (166)
Q Consensus 117 ek~~LA~~tgLs~~qV~~WF~N~R 140 (166)
....||+.+|++..+|..|+.+..
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-
T ss_pred CHHHHHHHHCcCHHHHHHHHhccc
Confidence 466899999999999999999773
No 67
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=70.73 E-value=3 Score=32.04 Aligned_cols=51 Identities=10% Similarity=0.221 Sum_probs=39.7
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSEN 149 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~~ 149 (166)
.||+..+.++...|.+ .+ .-.++|+.+|++...|.++....|+++++...+
T Consensus 128 ~L~~~~r~i~~l~~~~----g~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 178 (186)
T PRK05602 128 ALPERQREAIVLQYYQ----GL----SNIEAAAVMDISVDALESLLARGRRALRAQLAD 178 (186)
T ss_pred hCCHHHHHHhhHHHhc----CC----CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 4688888888665555 22 235799999999999999999999998876543
No 68
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=69.52 E-value=5.7 Score=29.64 Aligned_cols=49 Identities=27% Similarity=0.221 Sum_probs=39.5
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
..||+.++.++.-.+.+ .++ -.++|..+|++...|..+....|+++++.
T Consensus 111 ~~L~~~~r~v~~l~~~~----~~s----~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 111 SSLPLERRNVLLLRDYY----GFS----YKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HHCCHHHHHHhhhHHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 47899999988876655 222 34799999999999999999999998754
No 69
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=68.94 E-value=15 Score=21.72 Aligned_cols=47 Identities=17% Similarity=0.209 Sum_probs=34.8
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
.++.....++.. +.. .+ ...++|+.+|++...|..|....+.+..-.
T Consensus 3 ~l~~~e~~i~~~-~~~----g~----s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 3 SLTPREREVLRL-LAE----GL----TNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCCHHHHHHHHH-HHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 467777777754 333 22 346899999999999999999888776543
No 70
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=68.82 E-value=4.1 Score=31.00 Aligned_cols=50 Identities=14% Similarity=0.120 Sum_probs=39.1
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+..+.++...+.. .+ .-.++|+.+|++...|.+++...|+++++..
T Consensus 135 ~~L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 135 QALPPKYRMVIVLKYME----DL----SLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred HhCCHHHhHHhhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 36888899988765544 22 2357999999999999999999999887644
No 71
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=68.73 E-value=5.4 Score=30.69 Aligned_cols=50 Identities=16% Similarity=0.072 Sum_probs=40.0
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++...+.. . ..-.++|+.+|++...|.++....|+++++..
T Consensus 138 ~~L~~~~r~i~~l~~~~----g----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 187 (189)
T PRK09648 138 DTLPEKQREILILRVVV----G----LSAEETAEAVGSTPGAVRVAQHRALARLRAEI 187 (189)
T ss_pred HhCCHHHHHHHHHHHHc----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 47888899988876665 2 22468999999999999999999999887643
No 72
>PRK06930 positive control sigma-like factor; Validated
Probab=68.37 E-value=3.4 Score=32.34 Aligned_cols=56 Identities=9% Similarity=0.130 Sum_probs=42.6
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCCCcchh
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSENMHFA 153 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~~~~~~ 153 (166)
..||+..+.++...+.+ .+ .-.++|+.+|++...|.++....+++.++......|+
T Consensus 113 ~~L~~rer~V~~L~~~e----g~----s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~l~~ 168 (170)
T PRK06930 113 SVLTEREKEVYLMHRGY----GL----SYSEIADYLNIKKSTVQSMIERAEKKIARQINESLFC 168 (170)
T ss_pred HhCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 36888888888765554 22 2357999999999999999999999988766544444
No 73
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=68.31 E-value=5.6 Score=30.52 Aligned_cols=49 Identities=14% Similarity=0.224 Sum_probs=38.2
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
..||+.++.++...+.+ .+ .-.++|+.+|++...|.++....|+++++-
T Consensus 132 ~~L~~~~r~i~~l~~~~----~~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 132 EQLEPARRNCILHAYVD----GC----SHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred HhCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 46788888877666554 22 235799999999999999999999887653
No 74
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=68.21 E-value=6.6 Score=29.08 Aligned_cols=50 Identities=16% Similarity=0.161 Sum_probs=40.3
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++.-.+.+ .++ -.++|+.+|++...|.+...-.|+++++..
T Consensus 105 ~~Lp~~~r~v~~l~~~~----g~s----~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 105 QKLPARQREAFLLRYWE----DMD----VAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred HhCCHHHHHHHHHHHHh----cCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 57899999988776665 232 358999999999999999999999887654
No 75
>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=67.97 E-value=16 Score=23.27 Aligned_cols=46 Identities=20% Similarity=0.308 Sum_probs=35.7
Q ss_pred CChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhh
Q 045160 92 LPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFIN 138 (166)
Q Consensus 92 ~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N 138 (166)
|+..|+.+|...+..-|. -+|-...-..||+.+|++..-|..=+.+
T Consensus 1 LT~~Q~e~L~~A~~~GYf-d~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYF-DVPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred CCHHHHHHHHHHHHcCCC-CCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 577889999888776433 3477888999999999999888764433
No 76
>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=67.96 E-value=3.8 Score=31.23 Aligned_cols=53 Identities=21% Similarity=0.162 Sum_probs=41.9
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCCCc
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSENM 150 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~~~ 150 (166)
..||+.++.+|...+.+ .| .-.++|+.+|++...|.++..-.|+++++-....
T Consensus 99 ~~L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 151 (170)
T TIGR02959 99 KELPDEYREAIRLTELE----GL----SQQEIAEKLGLSLSGAKSRVQRGRKKLKELLETC 151 (170)
T ss_pred HhCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 46888899988876665 33 2357999999999999999999999988765443
No 77
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=67.83 E-value=5.8 Score=30.56 Aligned_cols=50 Identities=14% Similarity=0.164 Sum_probs=39.9
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.+|...+.+ . -.-.++|+.+|++...|.+-+...|+++++..
T Consensus 130 ~~L~~~~r~vl~l~~~~----~----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 130 AKLSPAHREIIDLVYYH----E----KSVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred HhCCHHHHHHHHHHHHc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 46889999999766555 2 23457999999999999999999999887653
No 78
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=67.71 E-value=5.6 Score=30.87 Aligned_cols=50 Identities=8% Similarity=0.093 Sum_probs=40.3
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++.-.+.. .+ .-.++|..+|+++..|.++..-.|+++++-.
T Consensus 133 ~~Lp~~~R~v~~L~~~~----g~----s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 133 NHLPAQQARVFMMREYL----EL----SSEQICQECDISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred HhCCHHHHHHHhHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46888899988776655 22 2458999999999999999999999988654
No 79
>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=67.10 E-value=6.3 Score=29.35 Aligned_cols=50 Identities=16% Similarity=0.235 Sum_probs=39.6
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++...+.. .++ -.++|..+|++...|.++....|+++++..
T Consensus 109 ~~L~~~~r~i~~l~~~~----g~s----~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 109 RRLPARQRAVVVLRYYE----DLS----EAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred HhCCHHHHHHhhhHHHh----cCC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 36788888888776655 332 347899999999999999999999987654
No 80
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=66.63 E-value=6.6 Score=23.67 Aligned_cols=40 Identities=13% Similarity=0.160 Sum_probs=21.4
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhh
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFI 137 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~ 137 (166)
..|+.+.+..+..++.+ -.-..+||+.+|.++.-|.++..
T Consensus 3 ~~Lt~~eR~~I~~l~~~--------G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQ--------GMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS-----------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHc--------CCCHHHHHHHHCcCcHHHHHHHh
Confidence 46788888888888665 23345799999999999998864
No 81
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=66.60 E-value=4.4 Score=31.27 Aligned_cols=49 Identities=14% Similarity=0.134 Sum_probs=38.2
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
..||+..+.++...+.. . ..-.++|+.+|++...|.+|+...|+++++.
T Consensus 140 ~~L~~~~~~v~~l~~~~----g----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 140 AQLPESQRQVLELAYYE----G----LSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred HhCCHHHhhhhhhhhhc----C----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 36788888888665544 2 2345799999999999999999999987764
No 82
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=65.96 E-value=6.3 Score=29.68 Aligned_cols=50 Identities=14% Similarity=0.102 Sum_probs=39.6
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++.-.+.+. + .-.++|+.+|++...|.++..-.|++.++-.
T Consensus 111 ~~L~~~~r~v~~l~~~~g----~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 111 NLLSADQREAIILIGASG----F----SYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred HhCCHHHHHHHHHHHHcC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 467888999887766552 2 2458999999999999999999999877543
No 83
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=65.40 E-value=6.7 Score=29.26 Aligned_cols=49 Identities=20% Similarity=0.359 Sum_probs=38.9
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||..++.+|...+ . .+ .-.++|..+|++...|.++....|+++++-.
T Consensus 111 ~~L~~~~r~il~l~~-~----g~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 111 AKMTERDRTVLLLRF-S----GY----SYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred HcCCHHHHHHHHHHH-c----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 357888888887666 5 22 3458999999999999999999999887654
No 84
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=65.30 E-value=5.9 Score=30.93 Aligned_cols=50 Identities=20% Similarity=0.207 Sum_probs=40.4
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
.||+.++.++.-.+.+ .++ -.++|..+|++...|.+++.-.|+++++...
T Consensus 113 ~Lp~~~r~v~~L~~~~----g~s----~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 113 QLPDEQREALILVGAS----GFS----YEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred hCCHHHhHHhhhHHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 6889999988776555 332 3478999999999999999999999887653
No 85
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=65.27 E-value=6.6 Score=30.08 Aligned_cols=51 Identities=16% Similarity=0.096 Sum_probs=38.9
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
..||+.++.++...+.+ .+ .-.++|+.+|++...|.+.....|+++++...
T Consensus 128 ~~L~~~~r~v~~l~~~~----g~----s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l~ 178 (181)
T PRK12536 128 EQLPDRQRLPIVHVKLE----GL----SVAETAQLTGLSESAVKVGIHRGLKALAAKIR 178 (181)
T ss_pred HHCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 35677788877655554 22 23579999999999999999999999887543
No 86
>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=65.16 E-value=7.2 Score=29.34 Aligned_cols=48 Identities=10% Similarity=0.128 Sum_probs=38.2
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
.||..++.++...+... ..-.++|+.+|++...|.++..-.|+++++.
T Consensus 119 ~L~~~~r~i~~l~~~~g--------~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD--------LTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred hCCHHHhHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57888888887666652 2235799999999999999999999887764
No 87
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=64.94 E-value=19 Score=29.85 Aligned_cols=49 Identities=20% Similarity=0.325 Sum_probs=39.6
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
..|+...+.+|...|.. .+ .-.++|..+|++...|..+....+.++++.
T Consensus 214 ~~L~~rer~vl~l~y~~----~~----t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 262 (264)
T PRK07122 214 AALPERERTVLVLRFFE----SM----TQTQIAERVGISQMHVSRLLAKTLARLRDQ 262 (264)
T ss_pred HcCCHHHHHHHHHHhcC----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 36888899999887755 33 247899999999999999999998887654
No 88
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=64.57 E-value=7.6 Score=29.99 Aligned_cols=50 Identities=16% Similarity=0.080 Sum_probs=40.1
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++.-.+.+ .+ .-.++|+.+|++...|.++..-.|+++++-.
T Consensus 129 ~~Lp~~~r~v~~L~~~~----g~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~~ 178 (185)
T PRK09649 129 ADLTTDQREALLLTQLL----GL----SYADAAAVCGCPVGTIRSRVARARDALLADA 178 (185)
T ss_pred HhCCHHHhHHhhhHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 46888899888766655 22 2358999999999999999999999988743
No 89
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=64.23 E-value=6.9 Score=30.41 Aligned_cols=49 Identities=12% Similarity=0.126 Sum_probs=39.6
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
.||+.++.++.-.+.+ .|+ -.++|+.+|++...|.+++.-.|+++++-.
T Consensus 136 ~L~~~~r~i~~L~~~~----g~s----~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 136 ALPERQRQAVVLRHIE----GLS----NPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 6888899888765554 333 357999999999999999999999988754
No 90
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=64.06 E-value=15 Score=26.83 Aligned_cols=48 Identities=10% Similarity=0.119 Sum_probs=33.4
Q ss_pred CCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHh
Q 045160 87 KKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRK 141 (166)
Q Consensus 87 r~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~ 141 (166)
+++++|+.+.+...-..... +.+ ....+|+.+|++..+|.+|..-.+.
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~---~g~----sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFE---PGM----TVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHc---CCC----CHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 44567888876544333344 343 3457899999999999999877664
No 91
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=63.53 E-value=7.8 Score=29.58 Aligned_cols=50 Identities=16% Similarity=0.113 Sum_probs=39.4
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+..+.+|...+.+ .+ .-.++|+.+|++...|.++....|.++++..
T Consensus 134 ~~L~~~~r~vl~l~~~~----~~----s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 134 KALSPEERRVIEVLYYQ----GY----THREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred HhCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 35889999998766555 22 2357999999999999999999999877643
No 92
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=62.94 E-value=7.9 Score=29.95 Aligned_cols=50 Identities=8% Similarity=0.106 Sum_probs=40.0
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
.||+.++.++.-.+.+ .+ .-.++|+.+|++...|.+.....|+++++-.+
T Consensus 136 ~L~~~~r~i~~L~~~~----g~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 136 NLPENTARVFTLKEIL----GF----SSDEIQQMCGISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred hCCHHHHHHhhhHHHh----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 6888899888765555 22 23589999999999999999999999887653
No 93
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=61.47 E-value=9.4 Score=29.41 Aligned_cols=50 Identities=8% Similarity=0.044 Sum_probs=39.6
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++...+.+ .++ -.++|..+|++...|.+.....|+++++-.
T Consensus 130 ~~Lp~~~r~v~~l~~~~----g~s----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 130 DRLPPRTGRVFMMREWL----ELE----TEEICQELQITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46888899888776655 222 357999999999999999999999987653
No 94
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=61.24 E-value=7.3 Score=31.35 Aligned_cols=49 Identities=12% Similarity=0.224 Sum_probs=39.7
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
.||+.++.++...|.. .+ .-.++|+.+|++...|.++....++++++..
T Consensus 184 ~L~~~~r~vl~l~~~~----g~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 184 SLPEREQLVLSLYYQE----EL----NLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred hCCHHHHHHHHhHhcc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5788899988776655 22 3468999999999999999999999987643
No 95
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=61.08 E-value=9.1 Score=28.47 Aligned_cols=50 Identities=14% Similarity=0.110 Sum_probs=38.8
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+..+.++...|.. .++ ..++|+.+|++...|.....-.|++.++-.
T Consensus 108 ~~L~~~~r~v~~l~~~~----~~s----~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 108 SELPARTRYAFEMYRLH----GET----QKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46888899988766555 222 457999999999999999888888877643
No 96
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=60.94 E-value=7.8 Score=23.33 Aligned_cols=25 Identities=16% Similarity=0.440 Sum_probs=17.2
Q ss_pred HHHHHHHHhCCChhhhhhhhhhHHh
Q 045160 117 DKLQLAESTGLDQKQINNWFINQRK 141 (166)
Q Consensus 117 ek~~LA~~tgLs~~qV~~WF~N~R~ 141 (166)
....+|+.+|++...|.+|....+.
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr~~~ 43 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKRYRE 43 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT----
T ss_pred CHHHHHHHHCcCHHHHHHHHHHccc
Confidence 4568999999999999999876553
No 97
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=60.87 E-value=8.5 Score=29.72 Aligned_cols=52 Identities=17% Similarity=0.095 Sum_probs=40.7
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSEN 149 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~~ 149 (166)
..||+.++.++...+.+ .+| -.++|..+|++...|.+.+...|+++++-..+
T Consensus 105 ~~L~~~~r~i~~l~~~~----g~~----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 105 DALPEKYAEALRLTELE----GLS----QKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred HhCCHHHHHHHHHHHhc----CCC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 36788899988766555 332 35799999999999999999999998876543
No 98
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=60.65 E-value=11 Score=28.57 Aligned_cols=50 Identities=16% Similarity=0.267 Sum_probs=38.8
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++.-.+.+. .+ -.++|+.+|++...|.++....+++.+...
T Consensus 118 ~~Lp~~~r~v~~L~~~~g--~s------~~EIA~~lgis~~tV~~~l~ra~~~~~~~l 167 (172)
T PRK12523 118 GKLSSKARAAFLYNRLDG--MG------HAEIAERLGVSVSRVRQYLAQGLRQCYIAL 167 (172)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 467888888887665552 22 347999999999999999999999876543
No 99
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=60.65 E-value=8.9 Score=29.82 Aligned_cols=51 Identities=18% Similarity=0.184 Sum_probs=40.6
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSEN 149 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~~ 149 (166)
.||..++.++.-.+.+ .++ -.++|+.+|++...|.+.....|+++++....
T Consensus 116 ~Lp~~~r~i~~L~~~~----g~s----~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~ 166 (187)
T PRK12516 116 QLPDDQREAIILVGAS----GFA----YEEAAEICGCAVGTIKSRVNRARQRLQEILQI 166 (187)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 5788889888776555 332 24799999999999999999999998876643
No 100
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=60.43 E-value=9.6 Score=30.31 Aligned_cols=48 Identities=21% Similarity=0.324 Sum_probs=39.0
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWK 145 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk 145 (166)
..||+.++.++...+.. . ..-.++|+.+|++...|..|....++++++
T Consensus 177 ~~L~~~~r~vl~l~y~~----~----~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 177 AALPERERRILLLRFFE----D----KTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred HcCCHHHHHHHHHHHhc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 46899999998877654 2 235689999999999999999998888764
No 101
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=60.34 E-value=9.3 Score=29.28 Aligned_cols=50 Identities=16% Similarity=0.135 Sum_probs=39.5
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++...+.. .+ .-.++|+.+|++...|.+.....|+++++-.
T Consensus 121 ~~L~~~~r~i~~l~~~~----g~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 121 KELNESNRQVFKYKVFY----NL----TYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred HhCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46888899988775554 22 2357999999999999999999999887754
No 102
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=60.21 E-value=11 Score=28.83 Aligned_cols=51 Identities=14% Similarity=0.154 Sum_probs=40.3
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
..||+.++.++...+.++ -.-.++|+.+|++...|.+.....|+++++-..
T Consensus 116 ~~Lp~~~r~i~~l~~~e~--------~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 166 (179)
T PRK12543 116 HKLPYKLRQVIILRYLHD--------YSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ 166 (179)
T ss_pred HhCCHHHHHHHHHHHHcc--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 368888998887765552 123579999999999999999999999887553
No 103
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=59.53 E-value=9.9 Score=29.46 Aligned_cols=50 Identities=18% Similarity=0.231 Sum_probs=39.2
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++...+.+. .+ -.++|+.+|++...|.+-....|+++++-.
T Consensus 140 ~~Lp~~~r~v~~l~~~eg--~s------~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEE--LP------HQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 568888999887655552 22 347999999999999999999998877643
No 104
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=59.33 E-value=9.7 Score=28.90 Aligned_cols=49 Identities=14% Similarity=0.149 Sum_probs=37.3
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
.||...+.+|...+.. . ..-.++|+.+|++...|.+.....|++.++-.
T Consensus 136 ~L~~~~r~il~l~~~~----~----~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T PRK09641 136 QLPEKYRTVIVLKYIE----D----LSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHHHHhhhHHhh----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5778788888554433 2 22357999999999999999999999887643
No 105
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=59.32 E-value=12 Score=29.30 Aligned_cols=51 Identities=16% Similarity=0.083 Sum_probs=41.0
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
..||+.++.++...+.++ ..-.++|+.+|++...|.++....|+++++-..
T Consensus 132 ~~Lp~~~r~v~~l~~~~g--------~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 132 DALPPERREALILTQVLG--------YTYEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred HcCCHHHHHHhhhHHHhC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 358888898887666652 224589999999999999999999999887754
No 106
>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=59.12 E-value=7.3 Score=23.77 Aligned_cols=21 Identities=24% Similarity=0.295 Sum_probs=18.5
Q ss_pred HHHHHHHhCCChhhhhhhhhh
Q 045160 118 KLQLAESTGLDQKQINNWFIN 138 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~N 138 (166)
...||+.+|+++..|..|..+
T Consensus 12 ~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHHHHhCCCcchhHHHhcC
Confidence 368999999999999999998
No 107
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=58.87 E-value=7.8 Score=31.47 Aligned_cols=50 Identities=12% Similarity=0.195 Sum_probs=38.7
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
.||..++.++...+.+ .+ .-.++|+.+|++...|.+.....|+++++...
T Consensus 171 ~Lp~~~R~v~~L~~~e----g~----s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 171 RLPEQQRIAVILSYHE----NM----SNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred hCCHHHHHHhhhHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 5677788877655554 22 23579999999999999999999999887653
No 108
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=58.03 E-value=27 Score=25.65 Aligned_cols=48 Identities=19% Similarity=0.156 Sum_probs=38.1
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
..|++..+.+|.- +.+ .|. ..++|+.++++.+.|.++..|.++|..-.
T Consensus 148 ~~lt~~e~~vl~l-~~~----g~~----~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~ 195 (211)
T PRK15369 148 PLLTPRERQILKL-ITE----GYT----NRDIAEQLSISIKTVETHRLNMMRKLDVH 195 (211)
T ss_pred cCCCHHHHHHHHH-HHC----CCC----HHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 3488888888876 444 332 46899999999999999999999997644
No 109
>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=57.64 E-value=17 Score=22.69 Aligned_cols=47 Identities=15% Similarity=0.096 Sum_probs=34.3
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
.|++....+|..+. . .+ ...++|...|++++.|..+..+-++|..-.
T Consensus 3 ~LT~~E~~vl~~l~-~----G~----~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~ 49 (58)
T PF00196_consen 3 SLTERELEVLRLLA-Q----GM----SNKEIAEELGISEKTVKSHRRRIMKKLGVK 49 (58)
T ss_dssp SS-HHHHHHHHHHH-T----TS-----HHHHHHHHTSHHHHHHHHHHHHHHHHT-S
T ss_pred ccCHHHHHHHHHHH-h----cC----CcchhHHhcCcchhhHHHHHHHHHHHhCCC
Confidence 46777777775443 3 22 345899999999999999999999997654
No 110
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=57.54 E-value=11 Score=28.31 Aligned_cols=50 Identities=14% Similarity=0.211 Sum_probs=40.2
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
.||+.++.+|...+.+ .++ -.++|+.+|++...|.+...-.|+++++..+
T Consensus 118 ~L~~~~r~vl~L~~~~----g~s----~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 167 (173)
T PRK09645 118 QLSPEHRAVLVRSYYR----GWS----TAQIAADLGIPEGTVKSRLHYALRALRLALQ 167 (173)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 5888999988776665 332 3579999999999999999999998887653
No 111
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=57.44 E-value=11 Score=30.79 Aligned_cols=49 Identities=10% Similarity=0.121 Sum_probs=39.7
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
.||+.++.+|...|.. .+ .-.++|+.+|++...|..|....++++++..
T Consensus 205 ~L~~~~r~vl~l~~~~----g~----s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l 253 (257)
T PRK08583 205 VLSDREKSIIQCTFIE----NL----SQKETGERLGISQMHVSRLQRQAIKKLREAA 253 (257)
T ss_pred hCCHHHHHHHHHHHhC----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 5888899998877665 22 2368999999999999999999999887543
No 112
>PRK10072 putative transcriptional regulator; Provisional
Probab=56.87 E-value=7.9 Score=27.63 Aligned_cols=23 Identities=13% Similarity=0.239 Sum_probs=20.6
Q ss_pred HHHHHHHhCCChhhhhhhhhhHH
Q 045160 118 KLQLAESTGLDQKQINNWFINQR 140 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~N~R 140 (166)
...||+.+|++...|.+|...+|
T Consensus 49 Q~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 49 IDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 66899999999999999998764
No 113
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=56.86 E-value=15 Score=28.16 Aligned_cols=49 Identities=8% Similarity=0.051 Sum_probs=38.7
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
..||+.++.++.-.+.+. | .-.++|+.+|++...|.+.....+.+....
T Consensus 126 ~~Lp~~~R~v~~L~~~~g----~----s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 126 DTLRPRVKQAFLMATLDG----M----KQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred HhCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 468999999887766652 2 235799999999999999999888886544
No 114
>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=56.78 E-value=11 Score=29.93 Aligned_cols=49 Identities=12% Similarity=0.196 Sum_probs=39.7
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
..||...+.+|...|.+ .+ .-.++|+.+|++...|..+....+++.++.
T Consensus 174 ~~L~~~~r~il~l~y~~----~~----s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 174 ESLSEREQLVLSLYYYE----EL----NLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred HhCCHHHHHHHHHHHhC----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 36899999999887765 22 346899999999999999999998887653
No 115
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=56.77 E-value=11 Score=30.61 Aligned_cols=48 Identities=8% Similarity=0.112 Sum_probs=38.8
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
.||+..+.++...|.+ .+ .-.++|..+|++...|.+++...|+++++-
T Consensus 201 ~L~~~~r~vl~l~~~~----~~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 201 QLSEKEQLVISLFYKE----EL----TLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5788899988876655 22 246899999999999999999999987653
No 116
>PRK04217 hypothetical protein; Provisional
Probab=56.06 E-value=16 Score=26.81 Aligned_cols=53 Identities=11% Similarity=-0.031 Sum_probs=41.8
Q ss_pred CCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 87 KKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 87 r~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..-..++.+++.++..++.+ .+ ...++|+.+|++...|.+.+...+++++.-.
T Consensus 38 ~p~~~Lt~eereai~l~~~e----Gl----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 38 KPPIFMTYEEFEALRLVDYE----GL----TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred CCcccCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 33567888898888777655 22 4567999999999999999999998887654
No 117
>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=56.02 E-value=13 Score=28.83 Aligned_cols=50 Identities=6% Similarity=0.015 Sum_probs=40.1
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++...|.++ ..-.++|+.+|++..-|.+...-.|+++++-.
T Consensus 130 ~~L~~~~r~v~~l~~~~g--------~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l 179 (188)
T TIGR02943 130 YHLPEQTARVFMMREVLG--------FESDEICQELEISTSNCHVLLYRARLSLRACL 179 (188)
T ss_pred HhCCHHHHHHHHHHHHhC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 368888888887766652 23458999999999999999999999987654
No 118
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=55.89 E-value=4.7 Score=31.14 Aligned_cols=50 Identities=18% Similarity=0.232 Sum_probs=38.2
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+..+.++...+.+ .+ .-.++|+.+|++...|.++....|+++++..
T Consensus 138 ~~L~~~~r~i~~l~~~~----g~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 138 ETLPDEQREVFLLREHG----DL----ELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred HhCCHhHhhheeeehcc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35777777777655444 22 2357899999999999999999999988754
No 119
>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=55.81 E-value=5.4 Score=30.85 Aligned_cols=51 Identities=22% Similarity=0.128 Sum_probs=39.1
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
..||+.++.++...+.+ .+ .-.++|+.+|++...|.++..-.|+++++-..
T Consensus 130 ~~Lp~~~r~i~~L~~~~----g~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 130 QGLPEEFRQAVYLADVE----GF----AYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred HhCCHHHhhheeehhhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35777788777555444 22 23589999999999999999999999887654
No 120
>cd00131 PAX Paired Box domain
Probab=55.77 E-value=57 Score=24.12 Aligned_cols=48 Identities=13% Similarity=-0.007 Sum_probs=33.6
Q ss_pred CCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCC-------ChhhhhhhhhhH
Q 045160 89 KGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGL-------DQKQINNWFINQ 139 (166)
Q Consensus 89 r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgL-------s~~qV~~WF~N~ 139 (166)
+...+......+..+..+ +|.-|..+...+-...|+ +...|+.||.++
T Consensus 73 pr~~~~~~~~~i~~~v~~---~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 73 PRVATPEVVKKIEIYKQE---NPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred CCcCCHHHHHHHHHHHHH---CCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 334555666666677777 888888777665334566 899999998764
No 121
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=55.63 E-value=12 Score=29.27 Aligned_cols=50 Identities=10% Similarity=0.070 Sum_probs=40.2
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++.-.+.+ .++ -.++|+.+|++...|.+.....|+++++-.
T Consensus 138 ~~Lp~~~r~v~~L~~~e----g~s----~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 138 DHLPEQIGRVFMMREFL----DFE----IDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 46888899988776655 222 357999999999999999999999988754
No 122
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=55.20 E-value=14 Score=28.35 Aligned_cols=50 Identities=12% Similarity=0.055 Sum_probs=39.6
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++...+..+ -.-.++|+.+|++...|.++....|+++++-.
T Consensus 130 ~~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 130 ARLPEKMRLAIQAVKLEG--------LSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred HhCCHHHHHHHHHHHHcC--------CcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 468889999887655552 23357999999999999999999999887654
No 123
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=55.02 E-value=12 Score=28.92 Aligned_cols=49 Identities=16% Similarity=0.039 Sum_probs=39.8
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
.||+.++.++.-.+.+ .++ -.++|+.+|++...|.++..-.|+++++-.
T Consensus 111 ~Lp~~~R~v~~L~~~e----g~s----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 111 DLPEEQRAALHLVAIE----GLS----YQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 6899999998876665 332 357999999999999999999999887654
No 124
>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=54.93 E-value=12 Score=30.54 Aligned_cols=49 Identities=8% Similarity=0.108 Sum_probs=39.7
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
..||+.++.++...|.+. + .-.++|+.+|++...|+.+....++++++.
T Consensus 204 ~~L~~~~r~ii~l~~~~g----~----s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 204 PILSEREKSIIHCTFEEN----L----SQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred HcCCHHHHHHHHHHHcCC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 468899999988777652 2 236899999999999999999999887753
No 125
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=54.84 E-value=13 Score=28.01 Aligned_cols=50 Identities=8% Similarity=0.135 Sum_probs=37.9
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++...+.+. .+ -.++|+.+|++...|.+.....|+++++..
T Consensus 118 ~~L~~~~r~i~~l~~~~~--~s------~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 167 (173)
T PRK12522 118 QLLNEKYKTVLVLYYYEQ--YS------YKEMSEILNIPIGTVKYRLNYAKKQMREHL 167 (173)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 467777887776555442 22 357999999999999999999999887643
No 126
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=54.75 E-value=10 Score=24.31 Aligned_cols=19 Identities=11% Similarity=0.176 Sum_probs=16.8
Q ss_pred HHHHHHhCCChhhhhhhhh
Q 045160 119 LQLAESTGLDQKQINNWFI 137 (166)
Q Consensus 119 ~~LA~~tgLs~~qV~~WF~ 137 (166)
.++|+.+|++...|+.|=.
T Consensus 4 ~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 5799999999999999943
No 127
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=54.59 E-value=45 Score=24.30 Aligned_cols=42 Identities=17% Similarity=0.398 Sum_probs=31.0
Q ss_pred hHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhH
Q 045160 94 KESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQ 139 (166)
Q Consensus 94 ~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~ 139 (166)
......+..|...|+..+ ++ ...||+.+|+++.++..+|...
T Consensus 8 ~~~i~~~~~~I~~~~~~~-~s---l~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 8 AITIHSILDWIEDNLESP-LS---LEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHHHhcCCC-CC---HHHHHHHHCcCHHHHHHHHHHH
Confidence 344556778888876554 34 4678999999999999888754
No 128
>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=54.35 E-value=33 Score=20.33 Aligned_cols=45 Identities=13% Similarity=0.152 Sum_probs=31.5
Q ss_pred ChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 93 PKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 93 ~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
+..+..++..+ .. .+ ....+|+.+|++...|..|....+++..-+
T Consensus 2 ~~~e~~i~~~~-~~----~~----s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 2 TPREREVLRLL-AE----GK----TNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 45566666443 22 22 446889999999999999998777776554
No 129
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=54.23 E-value=11 Score=30.22 Aligned_cols=54 Identities=19% Similarity=0.093 Sum_probs=39.5
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++...|.-+.... -.-.++|+.+|++...|.++....|+++++..
T Consensus 177 ~~Lp~~~R~v~~L~y~l~~~eg----~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l 230 (234)
T PRK08301 177 KKLSDREKQIMELRFGLNGGEE----KTQKEVADMLGISQSYISRLEKRIIKRLKKEI 230 (234)
T ss_pred HhCCHHHHHHHHHHhccCCCCC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4688889998876652100012 23458999999999999999999999987653
No 130
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=54.18 E-value=13 Score=28.56 Aligned_cols=49 Identities=14% Similarity=0.047 Sum_probs=37.4
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
.||...+.++...+.+ .|+ -.++|+.+|++...|.+.....|+++++-.
T Consensus 138 ~L~~~~r~v~~l~~~~----g~s----~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 138 QLPEDLRTALTLREFD----GLS----YEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred hCCHHHhHHHhhHHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4777787777654433 443 357999999999999999999999887653
No 131
>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=54.17 E-value=7.6 Score=23.43 Aligned_cols=21 Identities=10% Similarity=0.273 Sum_probs=19.1
Q ss_pred HHHHHhCCChhhhhhhhhhHH
Q 045160 120 QLAESTGLDQKQINNWFINQR 140 (166)
Q Consensus 120 ~LA~~tgLs~~qV~~WF~N~R 140 (166)
.||+.+|++...|..|+.+.+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999998873
No 132
>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=54.07 E-value=12 Score=24.23 Aligned_cols=21 Identities=19% Similarity=0.397 Sum_probs=17.8
Q ss_pred HHHHHHhCCChhhhhhhhhhH
Q 045160 119 LQLAESTGLDQKQINNWFINQ 139 (166)
Q Consensus 119 ~~LA~~tgLs~~qV~~WF~N~ 139 (166)
.++|+.+|++...|.+|-.--
T Consensus 17 ~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 17 KEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred HHHHHHHCCChHHHHHHHHhh
Confidence 479999999999999996533
No 133
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=54.03 E-value=12 Score=29.99 Aligned_cols=52 Identities=17% Similarity=0.118 Sum_probs=42.2
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSEN 149 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~~ 149 (166)
..||..++.++...+.++ |+ -.++|+.+|++...|.++....|+++++..+.
T Consensus 133 ~~Lp~~~R~v~~L~y~eg----~s----~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~ 184 (216)
T PRK12533 133 AKLPVEYREVLVLRELED----MS----YREIAAIADVPVGTVMSRLARARRRLAALLGG 184 (216)
T ss_pred HcCCHHHHhHhhhHHhcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcc
Confidence 378888999998777663 32 24789999999999999999999998887644
No 134
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=54.02 E-value=14 Score=29.25 Aligned_cols=50 Identities=12% Similarity=0.100 Sum_probs=40.3
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++.-.+.++ ++ -.++|+.+|++...|.+...-.|+++++..
T Consensus 147 ~~L~~~~r~v~~L~~~~g----~s----~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 147 DGLPAKYARVFMMREFIE----LE----TNEICHAVDLSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred HhCCHHHHHHHHHHHHcC----CC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 478888988887766652 22 358999999999999999999999988764
No 135
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=53.74 E-value=18 Score=26.84 Aligned_cols=46 Identities=13% Similarity=0.130 Sum_probs=35.9
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhc
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRH 143 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~ 143 (166)
..||+.++.++...+.+ .++ -.++|+.+|++...|.++....+++.
T Consensus 112 ~~L~~~~r~v~~L~~~~----g~s----~~EIA~~l~is~~tV~~~l~ra~~~~ 157 (161)
T PRK12528 112 DGLPPLVKRAFLLAQVD----GLG----YGEIATELGISLATVKRYLNKAAMRC 157 (161)
T ss_pred HHCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 46788899888766655 222 24799999999999999998888764
No 136
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=52.75 E-value=14 Score=29.12 Aligned_cols=50 Identities=14% Similarity=0.120 Sum_probs=38.8
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++...+.+ .++ -.++|+.+|++...|.++..-.|+++++..
T Consensus 137 ~~L~~~~r~v~~L~~~~----g~s----~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 137 DSLPPEFRAAVVLCDIE----GLS----YEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46788888877655554 222 247999999999999999999999988754
No 137
>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=52.60 E-value=17 Score=27.00 Aligned_cols=48 Identities=10% Similarity=0.108 Sum_probs=37.9
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWK 145 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk 145 (166)
..||+.++.+|...+.. .++ -.++|+.+|++...|.+...-.|+++++
T Consensus 121 ~~L~~~~r~vl~l~~~~----g~s----~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 121 KILTPKQQHVIALRFGQ----NLP----IAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred HhCCHHHHHHHHHHHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 47888899998876555 232 3579999999999999999888887765
No 138
>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=52.23 E-value=10 Score=22.91 Aligned_cols=23 Identities=17% Similarity=0.205 Sum_probs=19.9
Q ss_pred HHHHHHHhCCChhhhhhhhhhHH
Q 045160 118 KLQLAESTGLDQKQINNWFINQR 140 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~N~R 140 (166)
...||+.+|+++..|..|..+++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 46899999999999999987653
No 139
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=51.77 E-value=14 Score=30.36 Aligned_cols=50 Identities=10% Similarity=0.211 Sum_probs=40.4
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+..+.+|...|.+ . ..-.++|..+|++...|.......++++++..
T Consensus 211 ~~L~~~~r~vl~l~~~~----~----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 260 (268)
T PRK06288 211 KTLPEREKKVLILYYYE----D----LTLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260 (268)
T ss_pred HhCCHHHHHHHHHHHHc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 46888899988877765 2 23568999999999999999999998877654
No 140
>PF13730 HTH_36: Helix-turn-helix domain
Probab=51.65 E-value=53 Score=19.93 Aligned_cols=48 Identities=13% Similarity=0.185 Sum_probs=31.0
Q ss_pred CCChHHHHHHHHHHHH--hcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHh
Q 045160 91 KLPKESRQTLLDWWNA--HYKWPYPTEADKLQLAESTGLDQKQINNWFINQRK 141 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~--h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~ 141 (166)
.|++.++.++-..... .....||+ ...||+.+|++...|..+...-..
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS---~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPS---QETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcC---HHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4566666555332222 12237776 568999999999999988765443
No 141
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=51.64 E-value=16 Score=28.31 Aligned_cols=48 Identities=17% Similarity=0.091 Sum_probs=36.7
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
..||+..+.++.. +.+ .| .-.++|..+|++...|.+-+...|+++++-
T Consensus 154 ~~L~~~~r~vl~l-~~e----~~----s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 154 ELLSELEKEVLEL-YLD----GK----SYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred HhCCHHHHHHHHH-HHc----cC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3567888888876 444 22 235799999999999999999988887764
No 142
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=51.51 E-value=11 Score=28.87 Aligned_cols=50 Identities=16% Similarity=0.254 Sum_probs=39.1
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++...+..+ + .-.++|+.+|++...|.++..-.|+++++-.
T Consensus 126 ~~L~~~~r~v~~l~~~~g----~----s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 126 MSLPIKYREVIYLFYYEE----L----SIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred HhCCHHHhhHhHhHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 368898999887665552 2 2357999999999999999999999877643
No 143
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=50.92 E-value=15 Score=21.71 Aligned_cols=20 Identities=20% Similarity=0.182 Sum_probs=17.2
Q ss_pred HHHHHHhCCChhhhhhhhhh
Q 045160 119 LQLAESTGLDQKQINNWFIN 138 (166)
Q Consensus 119 ~~LA~~tgLs~~qV~~WF~N 138 (166)
.++|+.+|++...|..|...
T Consensus 4 ~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 4 GELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 57899999999999999543
No 144
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=50.87 E-value=6.1 Score=29.80 Aligned_cols=51 Identities=18% Similarity=0.164 Sum_probs=39.6
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
..||...+.+|...+.+ .++ -.++|+.+|++...|.+.+...|++.++-..
T Consensus 119 ~~L~~~~r~vl~l~~~~----g~s----~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 119 QTLSLEHRAVLVLHDLE----DLP----QKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred HhCCHHHeeeeeehHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35778888888765544 332 4589999999999999999999999887543
No 145
>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=50.38 E-value=16 Score=29.95 Aligned_cols=51 Identities=12% Similarity=0.234 Sum_probs=40.9
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
..||..++.++.-.+.++ + .-.++|..+|++...|.++....|+++++...
T Consensus 160 ~~Lp~~~R~v~~L~~~eg----~----S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~ 210 (244)
T TIGR03001 160 AALSERERHLLRLHFVDG----L----SMDRIGAMYQVHRSTVSRWVAQARERLLERTR 210 (244)
T ss_pred HhCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 468888888887766652 2 23589999999999999999999999887653
No 146
>PF13551 HTH_29: Winged helix-turn helix
Probab=50.27 E-value=52 Score=22.55 Aligned_cols=51 Identities=16% Similarity=0.165 Sum_probs=31.0
Q ss_pred CCCCCCChHHHHHHHHHHHHhcCCC--CCCHHHHHH-H-HHHh--CCChhhhhhhhh
Q 045160 87 KKKGKLPKESRQTLLDWWNAHYKWP--YPTEADKLQ-L-AEST--GLDQKQINNWFI 137 (166)
Q Consensus 87 r~r~~~~~~~~~~L~~~f~~h~~~p--YPs~~ek~~-L-A~~t--gLs~~qV~~WF~ 137 (166)
+.+..++.++...|.+++.++.... ..+...... | .+.+ .++...|..|+.
T Consensus 53 ~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 53 RPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 3333399999999999999942211 233343333 4 3333 467777888764
No 147
>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=50.06 E-value=29 Score=20.74 Aligned_cols=39 Identities=15% Similarity=0.329 Sum_probs=25.5
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhh
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWF 136 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF 136 (166)
..+++++...+...+.. . .....+|+.+|++...|..++
T Consensus 4 ~~~~~~~~~~i~~l~~~----G----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAE----G----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSSHCCHHHHHHHHHT----T------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHC----C----CCHHHHHHHHCcCHHHHHHHH
Confidence 34666555555555555 2 346789999999999998765
No 148
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=49.89 E-value=17 Score=27.76 Aligned_cols=49 Identities=10% Similarity=0.057 Sum_probs=38.4
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
..||+..+.++...|.+ .+ .-.++|..+|++...|.+-....|+++++-
T Consensus 136 ~~L~~~~r~i~~l~~~~----g~----s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 136 AELEPPRSELIRTAFFE----GI----TYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred HhCCHHHHHHHHHHHHc----CC----CHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 46788888888777655 22 235799999999999999999998887653
No 149
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=49.87 E-value=17 Score=28.12 Aligned_cols=51 Identities=18% Similarity=0.137 Sum_probs=40.7
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
..||+.++.++...+.+ .+ .-.++|+.+|++...|.....-.|+++++...
T Consensus 110 ~~Lp~~~R~v~~L~~~~----g~----s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 110 DKLPQDQREALILVGAS----GF----SYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred HhCCHHHHHHhhHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35788899988776655 22 23589999999999999999999999887754
No 150
>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=49.44 E-value=22 Score=27.21 Aligned_cols=29 Identities=17% Similarity=0.085 Sum_probs=25.6
Q ss_pred HHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 118 KLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
-.++|+.+|++...|.+.+.-.|+++++.
T Consensus 168 ~~eIA~~l~~s~~tV~~~l~r~r~~L~~~ 196 (198)
T TIGR02859 168 YQEIACDLNRHVKSIDNALQRVKRKLEKY 196 (198)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 45899999999999999999999988764
No 151
>PF05821 NDUF_B8: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8); InterPro: IPR008699 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family consists of several eukaryotic NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI) proteins. NADH:ubiquinone oxidoreductase (complex I) is an extremely complicated multiprotein complex located in the inner mitochondrial membrane. Its main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. Human complex I appears to consist of 41 subunits [].; GO: 0003954 NADH dehydrogenase activity, 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=49.05 E-value=16 Score=29.01 Aligned_cols=26 Identities=27% Similarity=0.432 Sum_probs=21.4
Q ss_pred hcCCCCC-CHHHHHHHHHHhCCChhhh
Q 045160 107 HYKWPYP-TEADKLQLAESTGLDQKQI 132 (166)
Q Consensus 107 h~~~pYP-s~~ek~~LA~~tgLs~~qV 132 (166)
+.-.||| |++||...|++.||.+..-
T Consensus 31 ~~PgpyP~t~eer~aaAkKY~l~pedY 57 (179)
T PF05821_consen 31 WKPGPYPKTPEERAAAAKKYGLRPEDY 57 (179)
T ss_pred CCCCCCCCCHHHHHHHHHHcCCCHHHc
Confidence 3446999 8999999999999987653
No 152
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=48.80 E-value=18 Score=29.75 Aligned_cols=50 Identities=14% Similarity=0.090 Sum_probs=40.4
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..|+...+.+|...|.. . ..-.++|..+|++...|..+..-.+.++++..
T Consensus 202 ~~L~~~~r~vl~l~y~~----~----~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 202 AQLEERTREVLEFVFLH----D----LTQKEAAERLGISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred HcCCHHHHHHHHHHHHC----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 46788888888877765 2 23468999999999999999999999887654
No 153
>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=48.62 E-value=22 Score=28.71 Aligned_cols=53 Identities=11% Similarity=0.120 Sum_probs=41.1
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
.|++..+.+|...|.- .-+ ....-.++|..+|++...|+.......++++...
T Consensus 176 ~L~~~er~vl~l~ygl---~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~ 228 (238)
T TIGR02393 176 TLTERERKVLRMRYGL---LDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRHPS 228 (238)
T ss_pred hCCHHHHHHHHHHhCC---CCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhH
Confidence 6888899999877632 111 1234668999999999999999999999988764
No 154
>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=48.58 E-value=21 Score=28.49 Aligned_cols=48 Identities=19% Similarity=0.210 Sum_probs=38.5
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWK 145 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk 145 (166)
..|+...+.++...|.. . ..-.++|+.+|+++..|..+-.....|++.
T Consensus 182 ~~L~~~e~~i~~~~~~~----~----~t~~eIA~~lgis~~~V~~~~~~al~~Lr~ 229 (231)
T TIGR02885 182 SKLDERERQIIMLRYFK----D----KTQTEVANMLGISQVQVSRLEKKVLKKMKE 229 (231)
T ss_pred HcCCHHHHHHHHHHHHc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 47888899888776654 2 246789999999999999998888887664
No 155
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=48.56 E-value=15 Score=20.96 Aligned_cols=22 Identities=23% Similarity=0.279 Sum_probs=19.2
Q ss_pred HHHHHHHhCCChhhhhhhhhhH
Q 045160 118 KLQLAESTGLDQKQINNWFINQ 139 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~N~ 139 (166)
...+|+.+|++...|..|..+.
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCC
Confidence 3589999999999999998875
No 156
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=48.03 E-value=14 Score=28.03 Aligned_cols=47 Identities=11% Similarity=0.135 Sum_probs=35.5
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHW 144 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~k 144 (166)
..||+.++.++...+.++ ..-.++|+.+|++...|.++....+.+..
T Consensus 118 ~~L~~~~r~i~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 118 DGLNGKTREAFLLSQLDG--------LTYSEIAHKLGVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred HhCCHHHhHHhhhhhccC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 467888888876655542 22458999999999999999988777654
No 157
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=47.78 E-value=21 Score=26.51 Aligned_cols=49 Identities=20% Similarity=0.256 Sum_probs=39.0
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
.||+..+.++...+..+ .+ -.++|..+|++..-|.+.....|+++++..
T Consensus 105 ~L~~~~r~v~~l~~~~~--~s------~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 105 ELPPACRDSFLLRKLEG--LS------HQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999887776652 22 357999999999999999998888877654
No 158
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=46.96 E-value=1.3e+02 Score=24.54 Aligned_cols=50 Identities=6% Similarity=0.086 Sum_probs=39.7
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..|++..+.+|...|.+ . ..-.++|..+|++...|..+..-.+.++++..
T Consensus 204 ~~L~~~er~vi~l~y~e----~----~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 253 (257)
T PRK05911 204 LALEEKERKVMALYYYE----E----LVLKEIGKILGVSESRVSQIHSKALLKLRATL 253 (257)
T ss_pred HcCCHHHHHHHHHHHhc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 36888888888877655 2 23468999999999999999998888877643
No 159
>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=46.87 E-value=27 Score=26.56 Aligned_cols=51 Identities=10% Similarity=-0.010 Sum_probs=40.5
Q ss_pred CCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 89 KGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 89 r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
.+.|+..++.+|... .+ .+ ...++|+.+|++...|..+-...+.+.++...
T Consensus 4 ~~~Lte~qr~VL~Lr-~~----Gl----Tq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~ 54 (137)
T TIGR00721 4 KTFLTERQIKVLELR-EK----GL----SQKEIAKELKTTRANVSAIEKRAMENIEKARN 54 (137)
T ss_pred cCCCCHHHHHHHHHH-Hc----CC----CHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhh
Confidence 467899999998763 33 33 45689999999999999999999999886433
No 160
>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=46.40 E-value=22 Score=29.74 Aligned_cols=51 Identities=22% Similarity=0.175 Sum_probs=40.6
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
..||+.++.++.-.+... .+ -.++|+.+|++...|.+...-.|+++++...
T Consensus 141 ~~Lp~~~R~v~~L~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 141 QYLPPRQRAVLLLRDVLG--WR------AAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred HhCCHHHhhHhhhHHHhC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 478888988887665542 22 2479999999999999999999999888664
No 161
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=45.58 E-value=18 Score=21.18 Aligned_cols=19 Identities=11% Similarity=0.181 Sum_probs=15.4
Q ss_pred HHHHHHhCCChhhhhhhhh
Q 045160 119 LQLAESTGLDQKQINNWFI 137 (166)
Q Consensus 119 ~~LA~~tgLs~~qV~~WF~ 137 (166)
.++|+.+|++...|+.|=.
T Consensus 3 ~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHH
Confidence 4789999999999999843
No 162
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=45.44 E-value=28 Score=26.20 Aligned_cols=47 Identities=15% Similarity=0.242 Sum_probs=36.4
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHW 144 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~k 144 (166)
..||+..+.++.-.+.+ .++ -.++|+.+|++...|.++..+.++..+
T Consensus 117 ~~L~~~~r~v~~L~~~e----g~s----~~EIA~~l~is~~tV~~~l~ra~~~~~ 163 (168)
T PRK12525 117 DGLSGKARAAFLMSQLE----GLT----YVEIGERLGVSLSRIHQYMVEAFKCCY 163 (168)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 57888888888776555 222 347999999999999999988887654
No 163
>PHA01976 helix-turn-helix protein
Probab=45.37 E-value=17 Score=23.10 Aligned_cols=22 Identities=14% Similarity=0.306 Sum_probs=19.1
Q ss_pred HHHHHHHhCCChhhhhhhhhhH
Q 045160 118 KLQLAESTGLDQKQINNWFINQ 139 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~N~ 139 (166)
...||+.+|++...|.+|-...
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~ 39 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADK 39 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCC
Confidence 4679999999999999998654
No 164
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=45.05 E-value=26 Score=30.06 Aligned_cols=54 Identities=15% Similarity=0.115 Sum_probs=42.3
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||..++.+|...|.-++... -.-.+||..+|++...|+.+....++++++..
T Consensus 261 ~~L~~~~R~vl~lrygL~~~e~----~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 261 FELNDKQREVLARRFGLLGYEA----ATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred HcCCHHHHHHHHHHhccCCCCC----cCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4788999999987663322223 34568999999999999999999999998765
No 165
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=44.93 E-value=87 Score=22.18 Aligned_cols=48 Identities=17% Similarity=0.208 Sum_probs=37.8
Q ss_pred CCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCC-ChhhhhhhhhhHHhhc
Q 045160 89 KGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGL-DQKQINNWFINQRKRH 143 (166)
Q Consensus 89 r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgL-s~~qV~~WF~N~R~R~ 143 (166)
+++|+.+-+..+-....+ ..+ ....+|+..|+ +..++..|-+..+...
T Consensus 5 ~r~~s~EfK~~iv~~~~~---~g~----sv~~vAr~~gv~~~~~l~~W~~~~~~~~ 53 (116)
T COG2963 5 RKKYSPEFKLEAVALYLR---GGD----TVSEVAREFGIVSATQLYKWRIQLQKGG 53 (116)
T ss_pred cccCCHHHHHHHHHHHHh---cCc----cHHHHHHHhCCCChHHHHHHHHHHHHcc
Confidence 788999987666555555 233 67799999996 9999999999888864
No 166
>PF12323 HTH_OrfB_IS605: Helix-turn-helix domain; InterPro: IPR021027 This entry represents an N-terminal helix-turn-helix domain found in a variety of putative transposases [, , ]. It is usually associated with PF01385 from PFAM and PF07282 from PFAM.
Probab=44.77 E-value=13 Score=22.31 Aligned_cols=34 Identities=29% Similarity=0.530 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCC
Q 045160 111 PYPTEADKLQLAESTGLDQKQINNWFINQRKRHWK 145 (166)
Q Consensus 111 pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk 145 (166)
=||+.++...|.+..|... .|=||.-..|...++
T Consensus 9 l~Pt~~Q~~~L~~~~~~~R-~vyN~~L~~~~~~y~ 42 (46)
T PF12323_consen 9 LYPTKEQEEKLERWFGACR-FVYNWALAERKEAYK 42 (46)
T ss_pred EecCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
Confidence 4789999999988887654 677777777766443
No 167
>KOG4040 consensus NADH:ubiquinone oxidoreductase, NDUFB8/ASHI subunit [Energy production and conversion]
Probab=44.27 E-value=13 Score=29.29 Aligned_cols=36 Identities=31% Similarity=0.599 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHhcCCCCC-CHHHHHHHHHHhCCChhh
Q 045160 96 SRQTLLDWWNAHYKWPYP-TEADKLQLAESTGLDQKQ 131 (166)
Q Consensus 96 ~~~~L~~~f~~h~~~pYP-s~~ek~~LA~~tgLs~~q 131 (166)
.....-.|...|.-.||| +++||..-|++.||-+..
T Consensus 25 g~rt~~gw~kD~kPgpyP~teeER~AAAkKY~lrpEd 61 (186)
T KOG4040|consen 25 GPRTFDGWYKDHKPGPYPTTEEERRAAAKKYGLRPED 61 (186)
T ss_pred ccccccccccccCCCCCCCCHHHHHHHHHHhCCCHhh
Confidence 334556788889889999 788999999999987754
No 168
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=44.09 E-value=28 Score=28.95 Aligned_cols=50 Identities=16% Similarity=0.050 Sum_probs=39.4
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++.-.+... .+ -.++|+.+|++...|++.....|+++++..
T Consensus 114 ~~L~~~~R~v~~L~~~~g--~s------~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~ 163 (293)
T PRK09636 114 ERLSPLERAAFLLHDVFG--VP------FDEIASTLGRSPAACRQLASRARKHVRAAR 163 (293)
T ss_pred HhCCHHHHHHHHHHHHhC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 358888988876655442 22 347999999999999999999999988764
No 169
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=43.99 E-value=35 Score=26.45 Aligned_cols=47 Identities=13% Similarity=0.174 Sum_probs=34.7
Q ss_pred CChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 92 LPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 92 ~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
+++.+..++.-.|.. .| ...++|+.+|+++..|...+...|.+..+.
T Consensus 136 l~~~~~~~v~l~~~~----Gl----s~~EIA~~lgiS~~tV~r~l~~aR~~l~~~ 182 (185)
T PF07638_consen 136 LDPRQRRVVELRFFE----GL----SVEEIAERLGISERTVRRRLRRARAWLRRE 182 (185)
T ss_pred cCHHHHHHHHHHHHC----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 555666666555554 44 345789999999999999999999776544
No 170
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=43.95 E-value=11 Score=30.24 Aligned_cols=50 Identities=14% Similarity=0.150 Sum_probs=38.6
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||..++.++...+.. . ..-.++|+.+|++...|.+.....|.++++-.
T Consensus 148 ~~L~~~~r~i~~l~~~~----g----~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 148 DALPDAFRAVFVLRVVE----E----LSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred HhCCHHHhhhheeehhc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 35788888887654433 2 33458999999999999999999999988765
No 171
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=43.80 E-value=25 Score=29.70 Aligned_cols=49 Identities=16% Similarity=0.113 Sum_probs=39.5
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
..||..++.++.-.+.+ .+ .-.++|+.+|++...|++.....|+++++.
T Consensus 152 ~~Lp~~~R~v~~L~~~~----g~----s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 200 (339)
T PRK08241 152 QHLPPRQRAVLILRDVL----GW----SAAEVAELLDTSVAAVNSALQRARATLAER 200 (339)
T ss_pred HhCCHHHhhhhhhHHhh----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHHhhc
Confidence 46788888888766655 22 234799999999999999999999999884
No 172
>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=43.72 E-value=18 Score=23.66 Aligned_cols=23 Identities=17% Similarity=0.284 Sum_probs=19.9
Q ss_pred HHHHHHHhCCChhhhhhhhhhHH
Q 045160 118 KLQLAESTGLDQKQINNWFINQR 140 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~N~R 140 (166)
...||+.+|++...|..|..+.+
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 45899999999999999997653
No 173
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=42.97 E-value=17 Score=28.17 Aligned_cols=51 Identities=18% Similarity=0.121 Sum_probs=38.6
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSEN 149 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~~ 149 (166)
.||+.++.+|...+.+ . ..-.++|..+|++...|.+=....|+++++....
T Consensus 134 ~Lp~~~r~i~~l~~~~----g----~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l~~ 184 (192)
T PRK09643 134 RLPVEQRAALVAVDMQ----G----YSVADAARMLGVAEGTVKSRCARGRARLAELLGY 184 (192)
T ss_pred hCCHHHHHHHHHHHHc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 4788888888765554 1 2234799999999999999888888887776543
No 174
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=42.83 E-value=22 Score=28.58 Aligned_cols=54 Identities=11% Similarity=0.143 Sum_probs=38.5
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+..+.++...|.-+ -+ ....-.++|..+|++...|.++-...++++++..
T Consensus 174 ~~Lp~~~R~i~~l~y~~~---~~-e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l 227 (233)
T PRK05803 174 DILDEREKEVIEMRYGLG---NG-KEKTQREIAKALGISRSYVSRIEKRALKKLFKEL 227 (233)
T ss_pred HhCCHHHHHHHHHHhCCC---CC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 478888999887755210 01 1123458999999999999999888888776654
No 175
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=42.34 E-value=24 Score=22.42 Aligned_cols=19 Identities=21% Similarity=0.358 Sum_probs=17.3
Q ss_pred HHHHHHhCCChhhhhhhhh
Q 045160 119 LQLAESTGLDQKQINNWFI 137 (166)
Q Consensus 119 ~~LA~~tgLs~~qV~~WF~ 137 (166)
.++|+.+|++...|..|-.
T Consensus 4 ~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 4 GAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999975
No 176
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=42.27 E-value=23 Score=22.69 Aligned_cols=20 Identities=10% Similarity=0.230 Sum_probs=17.6
Q ss_pred HHHHHHhCCChhhhhhhhhh
Q 045160 119 LQLAESTGLDQKQINNWFIN 138 (166)
Q Consensus 119 ~~LA~~tgLs~~qV~~WF~N 138 (166)
.++|+.+|++...|+.|-..
T Consensus 4 ~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 4 KEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHCcCHHHHHHHHHh
Confidence 57899999999999999654
No 177
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=42.17 E-value=24 Score=33.40 Aligned_cols=57 Identities=26% Similarity=0.325 Sum_probs=49.9
Q ss_pred cCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHH---HHHHHHHhCCChhhhhhhhhhHHhhc
Q 045160 85 KKKKKGKLPKESRQTLLDWWNAHYKWPYPTEAD---KLQLAESTGLDQKQINNWFINQRKRH 143 (166)
Q Consensus 85 ~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~e---k~~LA~~tgLs~~qV~~WF~N~R~R~ 143 (166)
++++++....+...+|..+...- .-||+... ...|...+.+..+-|...|+|.|.-.
T Consensus 647 ~p~~~~~isge~~~~~qs~i~~~--gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev 706 (769)
T KOG3755|consen 647 KPRKRTKISGEALGILQSFITDV--GLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEV 706 (769)
T ss_pred CccccceecccchHHHHHHHHHh--ccCchhhcccccchhhhhhcccHHHHHHhhhcceeec
Confidence 67888999999999998887654 78999888 88999999999999999999998653
No 178
>PRK05572 sporulation sigma factor SigF; Validated
Probab=42.14 E-value=22 Score=28.90 Aligned_cols=50 Identities=14% Similarity=0.101 Sum_probs=40.0
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||...+.++...|.. . ....++|+.+|++...|..+-.....++++..
T Consensus 201 ~~L~~~~~~v~~l~~~~----~----~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l 250 (252)
T PRK05572 201 RELDERERLIVYLRYFK----D----KTQSEVAKRLGISQVQVSRLEKKILKQMKEKL 250 (252)
T ss_pred HcCCHHHHHHHHHHHhC----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 46899999998877654 1 34468999999999999999998888877543
No 179
>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=42.13 E-value=28 Score=19.94 Aligned_cols=23 Identities=17% Similarity=0.408 Sum_probs=19.4
Q ss_pred HHHHHHHhCCChhhhhhhhhhHH
Q 045160 118 KLQLAESTGLDQKQINNWFINQR 140 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~N~R 140 (166)
..++|+.+|++...|..|..+-.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCC
Confidence 35789999999999999987644
No 180
>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=41.76 E-value=19 Score=26.26 Aligned_cols=47 Identities=23% Similarity=0.194 Sum_probs=35.0
Q ss_pred CChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 92 LPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 92 ~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
||+..+.++...+.. ...-.++|+.+|++...|.++..-.|+++++-
T Consensus 106 L~~~~r~i~~l~~~~--------g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 106 LPENYRTVLILREFK--------EFSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred CCHhheeeeeehhhc--------cCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 677777766544333 22345899999999999999999999887653
No 181
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=41.76 E-value=39 Score=25.77 Aligned_cols=43 Identities=16% Similarity=0.207 Sum_probs=30.2
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCC
Q 045160 99 TLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWK 145 (166)
Q Consensus 99 ~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk 145 (166)
....++.. ||-+. +...++|+.||++.++|..|..--|=-.+.
T Consensus 34 kV~~yLr~---~p~~~-ati~eV~e~tgVs~~~I~~~IreGRL~~~~ 76 (137)
T TIGR03826 34 KVYKFLRK---HENRQ-ATVSEIVEETGVSEKLILKFIREGRLQLKH 76 (137)
T ss_pred HHHHHHHH---CCCCC-CCHHHHHHHHCcCHHHHHHHHHcCCeeccC
Confidence 34455555 55432 456689999999999999998766655444
No 182
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=41.56 E-value=21 Score=20.05 Aligned_cols=22 Identities=18% Similarity=0.261 Sum_probs=18.7
Q ss_pred HHHHHHHhCCChhhhhhhhhhH
Q 045160 118 KLQLAESTGLDQKQINNWFINQ 139 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~N~ 139 (166)
...+|+.+|++...|..|-.+.
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 4589999999999999997654
No 183
>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=41.49 E-value=32 Score=28.51 Aligned_cols=50 Identities=14% Similarity=0.110 Sum_probs=38.9
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++.-.+.. .|+ -.++|+.+|++...|+..+...|++++...
T Consensus 107 ~~L~~~~R~v~~L~~~~----g~s----~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~ 156 (281)
T TIGR02957 107 ERLSPLERAVFVLREVF----DYP----YEEIASIVGKSEANCRQLVSRARRHLDARR 156 (281)
T ss_pred hhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 46788898887655444 222 357999999999999999999999988653
No 184
>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=40.92 E-value=28 Score=29.00 Aligned_cols=55 Identities=18% Similarity=0.218 Sum_probs=41.9
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
..||+..+.+|...|.-++... -.-.++|..+|++...|+.+....++++++-..
T Consensus 221 ~~Lp~~~R~Vl~l~ygL~~~e~----~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~ 275 (285)
T TIGR02394 221 AELNERQREVLARRFGLLGYEP----ATLEEVAAEVGLTRERVRQIQVEALKKLRRILE 275 (285)
T ss_pred HcCCHHHHHHHHHHhCCCCCCC----ccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5789999999987762111112 345689999999999999999999999887653
No 185
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=40.90 E-value=25 Score=28.74 Aligned_cols=51 Identities=18% Similarity=0.133 Sum_probs=39.1
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
..||..++.++.-.+.+ .| .-.++|+.+|++...|.++..-.|+++++..+
T Consensus 115 ~~Lp~~~R~v~lL~~~e----g~----S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~ 165 (228)
T PRK06704 115 SSLNVQQSAILLLKDVF----QY----SIADIAKVCSVSEGAVKASLFRSRNRLKTVSE 165 (228)
T ss_pred HhCCHHHhhHhhhHHhh----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 36777788777665544 22 23579999999999999999999999887653
No 186
>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=40.87 E-value=31 Score=26.04 Aligned_cols=48 Identities=17% Similarity=0.190 Sum_probs=37.0
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
.||+..+.++...+.. .+ .-.++|..+|++...|.+=....|+++++-
T Consensus 140 ~L~~~~r~vi~l~~~~----g~----s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~ 187 (189)
T TIGR02984 140 KLPEDYREVILLRHLE----GL----SFAEVAERMDRSEGAVSMLWVRGLARLRQI 187 (189)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5888888888764443 22 345799999999999999888888887654
No 187
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=40.36 E-value=30 Score=25.46 Aligned_cols=28 Identities=18% Similarity=0.366 Sum_probs=24.1
Q ss_pred CCCHHHHHHHHHHhCCChhhhhhhhhhH
Q 045160 112 YPTEADKLQLAESTGLDQKQINNWFINQ 139 (166)
Q Consensus 112 YPs~~ek~~LA~~tgLs~~qV~~WF~N~ 139 (166)
-+++..|..||..+|++...|..|-.-.
T Consensus 26 ~~~~~~r~~La~~~~i~~~~l~~w~~~A 53 (122)
T PF14229_consen 26 GDTPLGRKALAKKLGISERNLLKWVNQA 53 (122)
T ss_pred CCCHHHHHHHHHhcCCCHHHHHHHHhHH
Confidence 4788999999999999999999995433
No 188
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=40.36 E-value=28 Score=28.40 Aligned_cols=49 Identities=20% Similarity=0.159 Sum_probs=38.9
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
..|+...+.++...|.+ ++ ...++|+.+|++...|...-.+...++++.
T Consensus 208 ~~L~~~er~vi~~~~~~----~~----t~~eIA~~lgis~~~V~~~~~~al~kLr~~ 256 (258)
T PRK08215 208 KKLNDREKLILNLRFFQ----GK----TQMEVAEEIGISQAQVSRLEKAALKHMRKY 256 (258)
T ss_pred HcCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 35888888888877754 22 356899999999999999988888887654
No 189
>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=39.83 E-value=29 Score=27.78 Aligned_cols=53 Identities=9% Similarity=0.080 Sum_probs=38.0
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
..||+.++.++...|.. .-+ ..-.-.++|+.+|+++..|..+....++++++.
T Consensus 173 ~~L~~~~r~il~l~y~~---~~~-e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~ 225 (227)
T TIGR02846 173 SVLDGREREVIEMRYGL---GDG-RRKTQREIAKILGISRSYVSRIEKRALMKLYKE 225 (227)
T ss_pred HhCCHHHHHHHHHHHcC---CCC-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 47888899988877641 000 012345899999999999999888888877653
No 190
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=39.78 E-value=57 Score=25.98 Aligned_cols=49 Identities=16% Similarity=0.279 Sum_probs=39.0
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhH
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQ 139 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~ 139 (166)
..||..|+.+|+..|..-|. -||-...-..||+.+|+++.-+..=..++
T Consensus 154 ~~LTdrQ~~vL~~A~~~GYF-d~PR~~~l~dLA~~lGISkst~~ehLRrA 202 (215)
T COG3413 154 NDLTDRQLEVLRLAYKMGYF-DYPRRVSLKDLAKELGISKSTLSEHLRRA 202 (215)
T ss_pred ccCCHHHHHHHHHHHHcCCC-CCCccCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 37999999999998887543 35888999999999999998776544333
No 191
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=39.62 E-value=34 Score=26.44 Aligned_cols=50 Identities=20% Similarity=0.209 Sum_probs=39.5
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||..++.++...+..+ ++ -.++|..+|++..-|.++..-.|+++++..
T Consensus 127 ~~Lp~~~r~v~~l~~~~g----~s----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 127 AKLDPEYREPLLLQVIGG----FS----GEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred HhCCHHHHHHHHHHHHhC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 378888888887766662 22 347999999999999999999888877654
No 192
>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=39.50 E-value=35 Score=28.18 Aligned_cols=51 Identities=22% Similarity=0.243 Sum_probs=39.8
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
..||...+.+|...|.. +. ...-.++|+.+|+|...|+....+...|+++.
T Consensus 217 ~~L~~rer~vl~l~y~~-----~~-~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~ 267 (270)
T TIGR02392 217 GSLDARSRRIIEARWLD-----DD-KLTLQELAAEYGVSAERIRQIEKNAMKKLKAA 267 (270)
T ss_pred HcCCHHHHHHHHHHhcC-----CC-CcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46888899999877642 11 22346999999999999999999999888764
No 193
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=38.87 E-value=13 Score=27.91 Aligned_cols=49 Identities=14% Similarity=0.050 Sum_probs=36.2
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
..||+..+.++...+.. . ..-.++|+.+|++...|.++....|.++++.
T Consensus 125 ~~L~~~~r~v~~l~~~~----g----~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 125 SKLDPEFRAPVILKHYY----G----YTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred HcCCHHHhheeeehhhc----C----CCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 35777777766543222 2 2345899999999999999999999988764
No 194
>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=37.95 E-value=29 Score=27.90 Aligned_cols=54 Identities=20% Similarity=0.129 Sum_probs=38.9
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+..+.++...+.. .-+ ..-.-.++|+.+|++...|.++..-.+++.++-.
T Consensus 177 ~~Lp~~~R~ii~L~~~l---~~~-eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l 230 (234)
T TIGR02835 177 AKLNDREKKIMELRFGL---VGG-TEKTQKEVADMLGISQSYISRLEKRILKRLKKEI 230 (234)
T ss_pred HhCCHHHHHHHHHHHcc---CCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 46888888888766531 000 0123457999999999999999999999887654
No 195
>PF13551 HTH_29: Winged helix-turn helix
Probab=37.74 E-value=37 Score=23.33 Aligned_cols=26 Identities=15% Similarity=0.465 Sum_probs=22.7
Q ss_pred HHHHHHHHhCCChhhhhhhhhhHHhh
Q 045160 117 DKLQLAESTGLDQKQINNWFINQRKR 142 (166)
Q Consensus 117 ek~~LA~~tgLs~~qV~~WF~N~R~R 142 (166)
....+|+.+|++...|.+|....+..
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~ 39 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREG 39 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHcc
Confidence 46789999999999999999987754
No 196
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=37.15 E-value=26 Score=21.99 Aligned_cols=24 Identities=25% Similarity=0.340 Sum_probs=19.6
Q ss_pred HHHHHHHHhCCChhhhhhhhhhHH
Q 045160 117 DKLQLAESTGLDQKQINNWFINQR 140 (166)
Q Consensus 117 ek~~LA~~tgLs~~qV~~WF~N~R 140 (166)
....+|+.+|++..+|..|-.+++
T Consensus 14 t~~~~a~~~~i~~~~i~~~e~g~~ 37 (64)
T PF12844_consen 14 TQKDLAEKLGISRSTISKIENGKR 37 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCc
Confidence 356899999999999999999855
No 197
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=36.72 E-value=74 Score=20.80 Aligned_cols=42 Identities=19% Similarity=0.400 Sum_probs=25.8
Q ss_pred CCChHHHHHH---HHHHHHhcCCCCCCHHHHHHHHHHhCCC-hhhhhhhhh
Q 045160 91 KLPKESRQTL---LDWWNAHYKWPYPTEADKLQLAESTGLD-QKQINNWFI 137 (166)
Q Consensus 91 ~~~~~~~~~L---~~~f~~h~~~pYPs~~ek~~LA~~tgLs-~~qV~~WF~ 137 (166)
.|++.|..+| ..++.+ +.||. ...+||+.+|+. ..-|..-..
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~---~G~~P--t~rEIa~~~g~~S~~tv~~~L~ 48 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEE---NGYPP--TVREIAEALGLKSTSTVQRHLK 48 (65)
T ss_dssp ---HHHHHHHHHHHHHHHH---HSS-----HHHHHHHHTSSSHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHH---cCCCC--CHHHHHHHhCCCChHHHHHHHH
Confidence 4666676666 566666 68874 556899999996 777765443
No 198
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=36.71 E-value=12 Score=28.77 Aligned_cols=49 Identities=8% Similarity=0.054 Sum_probs=35.7
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
.+|+.++.++.-.+.+ .+ .-.++|..+|++...|.++....|.++++..
T Consensus 134 ~L~~~~r~v~~l~~~~----g~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 134 HVNPIDREILVLRFVA----EL----EFQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred hcChhheeeeeeHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5566666666544333 22 2368999999999999999999999877643
No 199
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=35.87 E-value=32 Score=21.81 Aligned_cols=19 Identities=11% Similarity=0.191 Sum_probs=16.8
Q ss_pred HHHHHHhCCChhhhhhhhh
Q 045160 119 LQLAESTGLDQKQINNWFI 137 (166)
Q Consensus 119 ~~LA~~tgLs~~qV~~WF~ 137 (166)
.++|+.+|+++..|..|-.
T Consensus 4 ~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 4 GEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999953
No 200
>PHA02510 X gene X product; Reviewed
Probab=35.71 E-value=1.2e+02 Score=22.60 Aligned_cols=62 Identities=21% Similarity=0.355 Sum_probs=41.7
Q ss_pred hhHHHHHHHHhhhcCCccchhhhhccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHH-----------HhCCC
Q 045160 60 EDRHLKDKLLRKFGSHIGSLKLEFSKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAE-----------STGLD 128 (166)
Q Consensus 60 ~~~elk~~l~~~~~~~~~~~~~~~~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~-----------~tgLs 128 (166)
.|.++.+.|..+|.++ -++++++..-...|..|+..+-...| .+.|..+.+ ..|++
T Consensus 5 ~d~~v~~~l~~~~~t~-----------t~~G~~s~aka~~~f~~y~~l~~~g~--~~vk~~l~k~tFyrhr~~L~~iGId 71 (116)
T PHA02510 5 DDSQVIDAIINKFFSI-----------TKSGNLSSAKAMRYFGFYRRLVNEGY--DNVADTMSRATFWRHRKVLKEFGID 71 (116)
T ss_pred cHHHHHHHHHhhheee-----------CCCCCcCHHHHHHHHHHHHhhhhhhH--HHHHHHccHHHHHHHHHHHHHcCCC
Confidence 4567788888888654 34578888888899999887644444 333333332 34888
Q ss_pred hhhhhh
Q 045160 129 QKQINN 134 (166)
Q Consensus 129 ~~qV~~ 134 (166)
..+++|
T Consensus 72 ia~l~n 77 (116)
T PHA02510 72 KAQLMN 77 (116)
T ss_pred hhhccc
Confidence 888776
No 201
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=35.05 E-value=34 Score=21.97 Aligned_cols=19 Identities=21% Similarity=0.328 Sum_probs=17.1
Q ss_pred HHHHHHhCCChhhhhhhhh
Q 045160 119 LQLAESTGLDQKQINNWFI 137 (166)
Q Consensus 119 ~~LA~~tgLs~~qV~~WF~ 137 (166)
.++|+.+|++...|..|..
T Consensus 4 ~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 4 GEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999965
No 202
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=35.00 E-value=1.3e+02 Score=20.01 Aligned_cols=35 Identities=20% Similarity=0.143 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCC--Chhhhh
Q 045160 96 SRQTLLDWWNAHYKWPYPTEADKLQLAESTGL--DQKQIN 133 (166)
Q Consensus 96 ~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgL--s~~qV~ 133 (166)
++..++..+.+ ||=-+++....+..+.|- |++||+
T Consensus 18 ar~~~~k~l~~---NPpine~mir~M~~QMG~kpSekqi~ 54 (64)
T PF03672_consen 18 ARKYMEKQLKE---NPPINEKMIRAMMMQMGRKPSEKQIK 54 (64)
T ss_pred HHHHHHHHHHH---CCCCCHHHHHHHHHHhCCCccHHHHH
Confidence 45677788888 887799999999999885 444454
No 203
>PRK13870 transcriptional regulator TraR; Provisional
Probab=33.55 E-value=69 Score=26.04 Aligned_cols=50 Identities=14% Similarity=0.134 Sum_probs=40.1
Q ss_pred CCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 88 KKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 88 ~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
....|++..+.+| .|..+ .+ .-.++|..+|++..-|+.=..|.|+|+--.
T Consensus 170 ~~~~LT~RE~E~L-~W~A~----GK----T~~EIa~ILgISe~TV~~Hl~na~~KLga~ 219 (234)
T PRK13870 170 DAAWLDPKEATYL-RWIAV----GK----TMEEIADVEGVKYNSVRVKLREAMKRFDVR 219 (234)
T ss_pred ccCCCCHHHHHHH-HHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence 3457999999999 57666 32 334788899999999999999999997655
No 204
>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=33.54 E-value=1.2e+02 Score=19.87 Aligned_cols=46 Identities=9% Similarity=0.259 Sum_probs=24.4
Q ss_pred CCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhh
Q 045160 89 KGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFIN 138 (166)
Q Consensus 89 r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N 138 (166)
|..|+..-.-..-.++..|-.+ ...-..-|++.|++..+|+-|-+-
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc----~~~~RAaarkf~V~r~~Vr~W~kq 48 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNC----KGNQRAAARKFNVSRRQVRKWRKQ 48 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTT----TT-HHHHHHHTTS-HHHHHHHHTT
T ss_pred ccccChHHHHHHHHHHHHccch----hhhHHHHHHHhCccHHHHHHHHHH
Confidence 3455655444444555553222 223356799999999999999753
No 205
>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=33.42 E-value=60 Score=26.90 Aligned_cols=50 Identities=14% Similarity=0.192 Sum_probs=39.5
Q ss_pred CCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 89 KGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 89 r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
...||+..+.+|. |..+ .|. -.++|+.+|++...|++...|.++|..-..
T Consensus 188 ~~~LT~RE~evl~-l~a~----G~s----~~eIA~~L~IS~~TVk~hl~~i~~KL~v~n 237 (247)
T TIGR03020 188 AGLITAREAEILA-WVRD----GKT----NEEIAAILGISSLTVKNHLQHIFKKLDVRN 237 (247)
T ss_pred ccCCCHHHHHHHH-HHHC----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHhCCCC
Confidence 4579999999997 5444 333 347899999999999999999999976553
No 206
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=32.92 E-value=53 Score=18.54 Aligned_cols=20 Identities=20% Similarity=0.473 Sum_probs=14.4
Q ss_pred HHHHHHHhCCChhhhhhhhh
Q 045160 118 KLQLAESTGLDQKQINNWFI 137 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~ 137 (166)
-..-|+..||+..+|+..+.
T Consensus 8 Li~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 8 LIKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 34568899999999998764
No 207
>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=32.74 E-value=73 Score=25.67 Aligned_cols=50 Identities=18% Similarity=0.373 Sum_probs=39.5
Q ss_pred CCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 89 KGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 89 r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
...||+..+.+|. |... . ..-.++|..+|++...|+.+..|.++|.....
T Consensus 169 ~~~Lt~re~evl~-~~a~----G----~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~ 218 (232)
T TIGR03541 169 AGVLSEREREVLA-WTAL----G----RRQADIAAILGISERTVENHLRSARRKLGVAT 218 (232)
T ss_pred hccCCHHHHHHHH-HHHC----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCC
Confidence 4579999999885 4443 2 33457889999999999999999999987654
No 208
>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=32.49 E-value=40 Score=22.93 Aligned_cols=42 Identities=10% Similarity=-0.006 Sum_probs=28.6
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhh
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFIN 138 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N 138 (166)
..+|...+.++.-.... ..+ ...+||+.+|++...|++|+.+
T Consensus 14 ~~l~~~~r~af~L~R~~---eGl----S~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 14 TWVDSLAEAAAALAREE---AGK----TASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred hcCCHHHHHHHHHHHHH---cCC----CHHHHHHHHCcCHHHHHHHHhc
Confidence 45666666665443222 233 3468999999999999999874
No 209
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=32.14 E-value=38 Score=21.27 Aligned_cols=16 Identities=31% Similarity=0.534 Sum_probs=13.0
Q ss_pred HHHHHHhCCChhhhhh
Q 045160 119 LQLAESTGLDQKQINN 134 (166)
Q Consensus 119 ~~LA~~tgLs~~qV~~ 134 (166)
.+||+.+|++..||+-
T Consensus 32 ~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 32 QELAEALGITPAQVRK 47 (50)
T ss_dssp HHHHHHHTS-HHHHHH
T ss_pred HHHHHHHCCCHHHhcc
Confidence 4799999999999974
No 210
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=31.80 E-value=36 Score=25.51 Aligned_cols=27 Identities=44% Similarity=0.812 Sum_probs=21.4
Q ss_pred HHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 118 KLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
.++||..||++..-|+.|. |+..|+..
T Consensus 3 ~eELA~~tG~srQTINrWv---RkegW~T~ 29 (122)
T PF07037_consen 3 PEELAELTGYSRQTINRWV---RKEGWKTE 29 (122)
T ss_pred HHHHHHHhCccHHHHHHHH---HhcCceec
Confidence 3689999999999999996 45555543
No 211
>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=31.61 E-value=51 Score=18.90 Aligned_cols=21 Identities=14% Similarity=0.172 Sum_probs=17.7
Q ss_pred HHHHHHHhCCChhhhhhhhhh
Q 045160 118 KLQLAESTGLDQKQINNWFIN 138 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~N 138 (166)
..++|+.+|++...|..|..+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHc
Confidence 357899999999999999754
No 212
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=31.22 E-value=59 Score=29.22 Aligned_cols=54 Identities=9% Similarity=0.179 Sum_probs=42.0
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..|++.++.+|...|.-+-..++ .-.++|+.+|++...|+.+....+++++.|.
T Consensus 349 ~~L~~reR~VI~LRygl~d~~~~----Tl~EIA~~LGvS~erVRqie~rAl~KLR~~~ 402 (415)
T PRK07598 349 ADLTSRERDVIRMRFGLADGHTY----SLAEIGRALDLSRERVRQIESKALQKLRQPK 402 (415)
T ss_pred HhCCHHHHHHHHHHHhcCCCCCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHhchh
Confidence 35888899999877752100233 3568999999999999999999999999875
No 213
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=30.92 E-value=35 Score=25.09 Aligned_cols=23 Identities=17% Similarity=0.382 Sum_probs=20.4
Q ss_pred HHHHHHHhCCChhhhhhhhhhHH
Q 045160 118 KLQLAESTGLDQKQINNWFINQR 140 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~N~R 140 (166)
...||+.+|++...|..|..+.+
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~ 43 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDET 43 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46899999999999999998864
No 214
>PRK09480 slmA division inhibitor protein; Provisional
Probab=30.82 E-value=61 Score=24.37 Aligned_cols=30 Identities=17% Similarity=0.244 Sum_probs=26.9
Q ss_pred CCCCCHHHHHHHHHHhCCChhhhhhhhhhHH
Q 045160 110 WPYPTEADKLQLAESTGLDQKQINNWFINQR 140 (166)
Q Consensus 110 ~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R 140 (166)
+++ .......||+..|+++-.+-.+|.|+-
T Consensus 26 ~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~ 55 (194)
T PRK09480 26 PPG-ERITTAKLAARVGVSEAALYRHFPSKA 55 (194)
T ss_pred cCC-CccCHHHHHHHhCCCHhHHHHHCCCHH
Confidence 567 888999999999999999999999976
No 215
>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=30.70 E-value=61 Score=27.17 Aligned_cols=50 Identities=12% Similarity=0.114 Sum_probs=37.9
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHW 144 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~k 144 (166)
.||+..+.+|...|.-+-..+ ..-.++|+.+|+|...|+..-...+++++
T Consensus 249 ~L~~rer~Vi~lr~gl~~~~~----~Tl~EIa~~lgiS~erVrq~~~rAl~kLr 298 (298)
T TIGR02997 249 ELTPRERQVLRLRFGLDGGEP----LTLAEIGRRLNLSRERVRQIEAKALRKLR 298 (298)
T ss_pred cCCHHHHHHHHHHhccCCCCC----cCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 589989999988774210023 34678999999999999999888887754
No 216
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=30.37 E-value=35 Score=24.99 Aligned_cols=23 Identities=17% Similarity=0.306 Sum_probs=20.5
Q ss_pred HHHHHHHhCCChhhhhhhhhhHH
Q 045160 118 KLQLAESTGLDQKQINNWFINQR 140 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~N~R 140 (166)
+.+||+.+|++...|..|.++++
T Consensus 21 q~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 21 KKELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHcCCC
Confidence 56799999999999999998875
No 217
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=30.33 E-value=53 Score=27.55 Aligned_cols=53 Identities=9% Similarity=0.040 Sum_probs=41.1
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
..||..++.+|...|.. ..+ ..-.++|+.+|++...|+.+....+++++....
T Consensus 226 ~~L~~rer~vl~lr~~~--~~~----~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~ 278 (289)
T PRK07500 226 QTLNERELRIIRERRLR--EDG----ATLEALGEELGISKERVRQIEARALEKLRRALL 278 (289)
T ss_pred hcCCHHHHHHHHHHhcC--CCC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46888899998876531 012 245789999999999999999999999886543
No 218
>PRK10651 transcriptional regulator NarL; Provisional
Probab=30.21 E-value=79 Score=23.42 Aligned_cols=47 Identities=13% Similarity=0.101 Sum_probs=36.5
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
.|++....+|..+ .+ .++ -..+|+.++++...|.+...|-|+|..-.
T Consensus 155 ~Lt~rE~~vl~~l-~~----g~~----~~~ia~~l~is~~tV~~~~~~l~~Kl~~~ 201 (216)
T PRK10651 155 QLTPRERDILKLI-AQ----GLP----NKMIARRLDITESTVKVHVKHMLKKMKLK 201 (216)
T ss_pred cCCHHHHHHHHHH-Hc----CCC----HHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 4899899888654 33 233 34678899999999999999999997543
No 219
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=28.68 E-value=54 Score=21.30 Aligned_cols=18 Identities=22% Similarity=0.689 Sum_probs=15.5
Q ss_pred HHHHHHHhCCChhhhhhh
Q 045160 118 KLQLAESTGLDQKQINNW 135 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~W 135 (166)
...||+.+|+++.-|..|
T Consensus 12 ~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 12 QSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHh
Confidence 357999999999999999
No 220
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=28.46 E-value=55 Score=19.59 Aligned_cols=21 Identities=14% Similarity=0.175 Sum_probs=18.0
Q ss_pred HHHHHHHHhCCChhhhhhhhh
Q 045160 117 DKLQLAESTGLDQKQINNWFI 137 (166)
Q Consensus 117 ek~~LA~~tgLs~~qV~~WF~ 137 (166)
....+|+.+|++...|..+|.
T Consensus 29 s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 29 SFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 356799999999999999885
No 221
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=28.12 E-value=1.5e+02 Score=22.86 Aligned_cols=37 Identities=16% Similarity=0.191 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhh
Q 045160 95 ESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINN 134 (166)
Q Consensus 95 ~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~ 134 (166)
....+|...=.+ ..|-+.+....+|+.+|+++.+|..
T Consensus 24 ~li~~L~~vQ~~---~G~Ip~e~~~~iA~~l~v~~~~V~~ 60 (156)
T PRK05988 24 ALLPILHAIQDE---FGYVPEDAVPVIAEALNLSRAEVHG 60 (156)
T ss_pred HHHHHHHHHHHH---cCCCCHHHHHHHHHHhCCCHHHHHH
Confidence 345566544334 6899999999999999999999764
No 222
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=28.01 E-value=1.6e+02 Score=18.99 Aligned_cols=26 Identities=19% Similarity=0.431 Sum_probs=18.2
Q ss_pred CCCCHHHHHHHHHHhCCChhhhhhhhhhH
Q 045160 111 PYPTEADKLQLAESTGLDQKQINNWFINQ 139 (166)
Q Consensus 111 pYPs~~ek~~LA~~tgLs~~qV~~WF~N~ 139 (166)
-.|+.+ +||+.+|++...|...+.-.
T Consensus 19 r~Pt~e---EiA~~lgis~~~v~~~l~~~ 44 (78)
T PF04539_consen 19 REPTDE---EIAEELGISVEEVRELLQAS 44 (78)
T ss_dssp S--BHH---HHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCHH---HHHHHHcccHHHHHHHHHhC
Confidence 446654 68999999999999877643
No 223
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=27.33 E-value=47 Score=20.97 Aligned_cols=25 Identities=24% Similarity=0.335 Sum_probs=20.5
Q ss_pred HHHHHHHHhCCChhhhhhhhhhHHh
Q 045160 117 DKLQLAESTGLDQKQINNWFINQRK 141 (166)
Q Consensus 117 ek~~LA~~tgLs~~qV~~WF~N~R~ 141 (166)
....+|..+|++...|+.|-..++.
T Consensus 16 s~~~lA~~~g~s~s~v~~iE~G~~~ 40 (64)
T PF13560_consen 16 SQAQLADRLGVSQSTVSRIERGRRP 40 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCCC
Confidence 4568999999999999999988775
No 224
>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=27.17 E-value=65 Score=22.87 Aligned_cols=28 Identities=21% Similarity=0.464 Sum_probs=22.2
Q ss_pred HHHHHHHHHHhCCChhhhhhhhhhHHhh
Q 045160 115 EADKLQLAESTGLDQKQINNWFINQRKR 142 (166)
Q Consensus 115 ~~ek~~LA~~tgLs~~qV~~WF~N~R~R 142 (166)
.-....+|+..|++..+|+.|..+.+.+
T Consensus 23 ~~gq~~vA~~~Gv~eStISR~k~~~~~~ 50 (91)
T PF05269_consen 23 SVGQKKVAEAMGVDESTISRWKNDFIEK 50 (91)
T ss_dssp HHHHHHHHHHHTSSTTTHHHHHHHHHHH
T ss_pred HHhhHHHHHHhCCCHHHHHHHHhhHHHH
Confidence 3455689999999999999997665443
No 225
>PRK09726 antitoxin HipB; Provisional
Probab=27.11 E-value=46 Score=22.68 Aligned_cols=22 Identities=32% Similarity=0.450 Sum_probs=19.5
Q ss_pred HHHHHHHhCCChhhhhhhhhhH
Q 045160 118 KLQLAESTGLDQKQINNWFINQ 139 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~N~ 139 (166)
...||+.+|++...|..|..+.
T Consensus 28 q~elA~~~gvs~~tis~~e~g~ 49 (88)
T PRK09726 28 QSELAKKIGIKQATISNFENNP 49 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHCCC
Confidence 5689999999999999998864
No 226
>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=26.41 E-value=83 Score=22.72 Aligned_cols=45 Identities=16% Similarity=0.302 Sum_probs=32.1
Q ss_pred CCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhc
Q 045160 91 KLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRH 143 (166)
Q Consensus 91 ~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~ 143 (166)
-||..|+.+|.-++.. .---.++|+.+|.|.--|..|..-.+.+.
T Consensus 17 LLT~kQ~~~l~lyy~e--------DlSlsEIAe~~~iSRqaV~d~ikr~~~~L 61 (101)
T PF04297_consen 17 LLTEKQREILELYYEE--------DLSLSEIAEELGISRQAVYDSIKRAEKKL 61 (101)
T ss_dssp GS-HHHHHHHHHHCTS-----------HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred HCCHHHHHHHHHHHcc--------CCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4778888888766554 34556899999999999999998777654
No 227
>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=26.29 E-value=1.1e+02 Score=17.44 Aligned_cols=25 Identities=12% Similarity=0.331 Sum_probs=18.3
Q ss_pred HHHHHHHHhCCChhhhhhhhhhHHh
Q 045160 117 DKLQLAESTGLDQKQINNWFINQRK 141 (166)
Q Consensus 117 ek~~LA~~tgLs~~qV~~WF~N~R~ 141 (166)
.+.+||..+|++..-|+.=|..-++
T Consensus 4 tr~diA~~lG~t~ETVSR~l~~l~~ 28 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRILKKLER 28 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 4678999999999999876655443
No 228
>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=26.13 E-value=1.3e+02 Score=17.72 Aligned_cols=36 Identities=22% Similarity=0.474 Sum_probs=22.8
Q ss_pred hHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhh
Q 045160 94 KESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWF 136 (166)
Q Consensus 94 ~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF 136 (166)
...+.+| ..+.+ +|.. ...+||+.+|++...|+.-+
T Consensus 3 ~~~~~Il-~~l~~---~~~~---t~~ela~~~~is~~tv~~~l 38 (48)
T PF13412_consen 3 ETQRKIL-NYLRE---NPRI---TQKELAEKLGISRSTVNRYL 38 (48)
T ss_dssp HHHHHHH-HHHHH---CTTS----HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHH-HHHHH---cCCC---CHHHHHHHhCCCHHHHHHHH
Confidence 3445566 44455 5654 45679999999999887644
No 229
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=26.12 E-value=1.1e+02 Score=24.96 Aligned_cols=51 Identities=16% Similarity=0.257 Sum_probs=40.4
Q ss_pred CCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 88 KKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 88 ~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
....|++..+.+| .|..+ .+. -.++|..+|++...|+.=..|.++|..-..
T Consensus 176 ~~~~LT~rE~evl-~~~a~----G~t----~~eIa~~l~is~~TV~~h~~~~~~KL~~~n 226 (240)
T PRK10188 176 PEMNFSKREKEIL-KWTAE----GKT----SAEIAMILSISENTVNFHQKNMQKKFNAPN 226 (240)
T ss_pred CCCCCCHHHHHHH-HHHHc----CCC----HHHHHHHhCCCHHHHHHHHHHHHHHhCCCC
Confidence 3457999999998 46655 432 347899999999999999999999977553
No 230
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=25.99 E-value=87 Score=24.15 Aligned_cols=30 Identities=17% Similarity=0.134 Sum_probs=24.2
Q ss_pred ccCCCCCCCChHHHHHHHHHHHHhcCCCCC
Q 045160 84 SKKKKKGKLPKESRQTLLDWWNAHYKWPYP 113 (166)
Q Consensus 84 ~~kr~r~~~~~~~~~~L~~~f~~h~~~pYP 113 (166)
....+-+.|+.++...|..+....+..++|
T Consensus 48 ~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP 77 (149)
T PRK04053 48 DPNAKLGYLSDEEIEKIEEALEDPAEEGIP 77 (149)
T ss_pred CCCCccCcCCHHHHHHHHHHHHhhccccCc
Confidence 345667889999999999999886666677
No 231
>COG2938 Uncharacterized conserved protein [Function unknown]
Probab=25.06 E-value=1.2e+02 Score=21.73 Aligned_cols=42 Identities=7% Similarity=0.191 Sum_probs=34.8
Q ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHh
Q 045160 98 QTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRK 141 (166)
Q Consensus 98 ~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~ 141 (166)
-+|..++..| .+--+.+++..+-.-+..+-.++-+||.|+..
T Consensus 31 lil~~Fae~~--~~~lsd~el~~f~~LLe~~D~dL~~Wi~g~~~ 72 (94)
T COG2938 31 LILGPFAEKE--FDSLSDEELDEFERLLECEDNDLFNWIMGHGE 72 (94)
T ss_pred HHHHHHHHHH--HhhCCHHHHHHHHHHHcCCcHHHHHHHhCCCC
Confidence 3666677766 55568999999999999999999999999765
No 232
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=24.86 E-value=57 Score=22.35 Aligned_cols=17 Identities=24% Similarity=0.624 Sum_probs=15.9
Q ss_pred HHHHHHhCCChhhhhhh
Q 045160 119 LQLAESTGLDQKQINNW 135 (166)
Q Consensus 119 ~~LA~~tgLs~~qV~~W 135 (166)
.++|+.+|++..+|..|
T Consensus 5 ~evA~~~gvs~~tLR~y 21 (88)
T cd01105 5 GEVSKLTGVSPRQLRYW 21 (88)
T ss_pred HHHHHHHCcCHHHHHHH
Confidence 47899999999999999
No 233
>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 This entry is represented by Bacteriophage r1t, Orf18. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.
Probab=24.72 E-value=60 Score=25.77 Aligned_cols=31 Identities=13% Similarity=0.252 Sum_probs=26.0
Q ss_pred HHHHHHHHHhCCChhhhhhhhhhHHhhcCCC
Q 045160 116 ADKLQLAESTGLDQKQINNWFINQRKRHWKP 146 (166)
Q Consensus 116 ~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~ 146 (166)
..+.+||.-.+++..+|..|..|=+.-.++.
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~ 45 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAK 45 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCccccc
Confidence 4578899999999999999999987665544
No 234
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=24.54 E-value=84 Score=26.38 Aligned_cols=50 Identities=14% Similarity=0.089 Sum_probs=37.9
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++.-.+... .+ -.++|+.+|++...|+....-.|++++...
T Consensus 117 ~~L~p~~R~vf~L~~~~g--~s------~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~ 166 (290)
T PRK09635 117 ERLGPAERVVFVLHEIFG--LP------YQQIATTIGSQASTCRQLAHRARRKINESR 166 (290)
T ss_pred HhCCHHHHHHhhHHHHhC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 467888888775544441 23 247899999999999999999999988753
No 235
>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=24.44 E-value=1.2e+02 Score=21.91 Aligned_cols=38 Identities=16% Similarity=0.338 Sum_probs=27.1
Q ss_pred CChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhh
Q 045160 92 LPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFI 137 (166)
Q Consensus 92 ~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~ 137 (166)
++-+-+....+.+.. ..-...+|+..+++..-|.+||.
T Consensus 3 YS~DlR~rVl~~~~~--------g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 3 YSLDLRQRVLAYIEK--------GKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred CCHHHHHHHHHHHHc--------cchHHHHHHHhCcHHHHHHHHHH
Confidence 445555555566555 12456788999999999999998
No 236
>PF11304 DUF3106: Protein of unknown function (DUF3106); InterPro: IPR021455 Some members in this family of proteins are annotated as transmembrane proteins however this cannot be confirmed. Currently no function is known.
Probab=24.43 E-value=1.5e+02 Score=21.31 Aligned_cols=31 Identities=32% Similarity=0.546 Sum_probs=20.2
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAE 123 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~ 123 (166)
..||++.+..|..-|.. ..--++++|..|++
T Consensus 75 ~~Lpp~qR~~lr~~w~~---yq~l~~eeR~~l~~ 105 (107)
T PF11304_consen 75 KQLPPEQRQALRARWEA---YQQLPPEERQALRE 105 (107)
T ss_pred HcCCHHHHHHHHHHHHH---HHcCCHHHHHHHHh
Confidence 46777777777666655 34456777777764
No 237
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=24.35 E-value=97 Score=23.72 Aligned_cols=30 Identities=23% Similarity=0.347 Sum_probs=21.6
Q ss_pred ccCCCCCCCChHHHHHHHHHHHHhcCCCCCC
Q 045160 84 SKKKKKGKLPKESRQTLLDWWNAHYKWPYPT 114 (166)
Q Consensus 84 ~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs 114 (166)
....+-+.|+.++...|..++.. ...++|.
T Consensus 44 ~~~~~~~~Lt~~qi~~l~~~i~~-~~~~iP~ 73 (144)
T TIGR03629 44 DPNAKLGYLDDEEIEKLEEAVEN-YEYGIPS 73 (144)
T ss_pred CCCCCcccCCHHHHHHHHHHHHh-ccccCCH
Confidence 34566788999999999998876 3334443
No 238
>PRK09483 response regulator; Provisional
Probab=24.34 E-value=1.6e+02 Score=22.03 Aligned_cols=47 Identities=15% Similarity=0.152 Sum_probs=36.6
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWK 145 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk 145 (166)
..|++....+|.. +.+ .+.+. ++|+.++++...|++--.|-++|.--
T Consensus 147 ~~Lt~rE~~vl~~-~~~----G~~~~----~Ia~~l~is~~TV~~~~~~i~~Kl~v 193 (217)
T PRK09483 147 ASLSERELQIMLM-ITK----GQKVN----EISEQLNLSPKTVNSYRYRMFSKLNI 193 (217)
T ss_pred cccCHHHHHHHHH-HHC----CCCHH----HHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 4589989999853 343 45443 89999999999999998888888643
No 239
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=24.13 E-value=1.9e+02 Score=21.77 Aligned_cols=44 Identities=11% Similarity=0.061 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhh---hhhhHHhh
Q 045160 96 SRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINN---WFINQRKR 142 (166)
Q Consensus 96 ~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~---WF~N~R~R 142 (166)
...+|... +++ ..|-+++....+|+.+|++..+|.. ++..-+.+
T Consensus 18 li~~L~~v-Q~~--~G~i~~~~~~~iA~~l~~~~~~v~~v~tFY~~f~~~ 64 (148)
T TIGR01958 18 IMPALMIA-QEQ--KGWVTPEAIAAVAEMLGIPPVWVYEVATFYSMFDTE 64 (148)
T ss_pred HHHHHHHH-HHH--hCCCCHHHHHHHHHHhCcCHHHHHHHHhHHhhcCcC
Confidence 44455443 443 6799999999999999999998654 55544443
No 240
>PRK10403 transcriptional regulator NarP; Provisional
Probab=24.11 E-value=1.1e+02 Score=22.51 Aligned_cols=49 Identities=12% Similarity=0.064 Sum_probs=37.2
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..|+.....+|. ++.. .|+ ..++|+.++++...|.+...|-|+|..-..
T Consensus 152 ~~Lt~~e~~vl~-~~~~----g~s----~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~ 200 (215)
T PRK10403 152 SVLTERELDVLH-ELAQ----GLS----NKQIASVLNISEQTVKVHIRNLLRKLNVRS 200 (215)
T ss_pred ccCCHHHHHHHH-HHHC----CCC----HHHHHHHcCCCHHHHHHHHHHHHHHcCCCC
Confidence 358888888875 4444 232 357899999999999999999999975543
No 241
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=23.79 E-value=75 Score=20.80 Aligned_cols=24 Identities=21% Similarity=0.299 Sum_probs=18.7
Q ss_pred HHHHHHHhCCChhhhhhhhhhHHh
Q 045160 118 KLQLAESTGLDQKQINNWFINQRK 141 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~N~R~ 141 (166)
..++|..+|++..||+.|...--.
T Consensus 18 T~eiA~~~gls~~~aR~yL~~Le~ 41 (62)
T PF04703_consen 18 TREIADALGLSIYQARYYLEKLEK 41 (62)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHH
Confidence 348999999999999999876443
No 242
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=23.78 E-value=71 Score=24.31 Aligned_cols=51 Identities=20% Similarity=0.293 Sum_probs=38.7
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPSE 148 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~~ 148 (166)
..||+.++.++.-.+.+ .|+ -.++|+.+|++...|..+..-.|.+.++..+
T Consensus 126 ~~Lp~~~R~~~~l~~~~----gls----~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 126 ARLPPRQREAFLLRYLE----GLS----YEEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred HhCCHHHhHHhhhHhhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 46788888877555444 332 2478999999999999999999999877653
No 243
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=23.56 E-value=2e+02 Score=21.82 Aligned_cols=36 Identities=8% Similarity=0.029 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhh
Q 045160 96 SRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINN 134 (166)
Q Consensus 96 ~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~ 134 (166)
...+|...=.. ..|-+++....+|+.+|++..+|..
T Consensus 24 ll~~L~~vQ~~---~g~ip~~~~~~iA~~l~v~~~~v~~ 59 (154)
T PRK07539 24 VIPALKIVQEQ---RGWVPDEAIEAVADYLGMPAIDVEE 59 (154)
T ss_pred HHHHHHHHHHH---hCCCCHHHHHHHHHHhCcCHHHHHH
Confidence 44555444334 7899999999999999999999764
No 244
>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=23.48 E-value=87 Score=25.46 Aligned_cols=48 Identities=19% Similarity=0.197 Sum_probs=36.7
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWK 145 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk 145 (166)
..|+...+.++...|.. ++ .-.++|+.+|++...|...-.....++++
T Consensus 205 ~~L~~rer~vi~~~~~~----~~----t~~eIA~~lgis~~~V~~~~~ral~kLr~ 252 (254)
T TIGR02850 205 KRLNEREKMILNMRFFE----GK----TQMEVAEEIGISQAQVSRLEKAALKHMRK 252 (254)
T ss_pred HcCCHHHHHHHHHHHcC----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 46888888888877654 32 35689999999999999877777666554
No 245
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=23.47 E-value=1e+02 Score=24.88 Aligned_cols=47 Identities=11% Similarity=0.074 Sum_probs=36.9
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHW 144 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~k 144 (166)
..|+...+.++...|.+ . ..-.++|+.+|++..+|+.--...+.+++
T Consensus 182 ~~L~~~er~vi~l~~~~----~----~t~~EIA~~lgis~~~V~q~~~~~~~kLr 228 (231)
T PRK12427 182 SQLDEREQLILHLYYQH----E----MSLKEIALVLDLTEARICQLNKKIAQKIK 228 (231)
T ss_pred HcCCHHHHHHHHHHHHc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 46888888888887765 2 22578999999999999988777777765
No 246
>PF07042 TrfA: TrfA protein; InterPro: IPR010751 This family consists of several bacterial TrfA proteins. The trfA operon of broad-host-range IncP plasmids is essential to activate the origin of vegetative replication in diverse species. The trfA operon encodes two ORFs. The first ORF is highly conserved and encodes a putative single-stranded DNA binding protein (Ssb). The second, trfA, contains two translational starts as in the IncP alpha plasmids, generating related polypeptides of 406 (TrfA1) and 282 (TrfA2) amino acids. TrfA2 is very similar to the IncP alpha product, whereas the N-terminal region of TrfA1 shows very little similarity to the equivalent region of IncP alpha TrfA1. This region has been implicated in the ability of IncP alpha plasmids to replicate efficiently in Pseudomonas aeruginosa [].
Probab=23.41 E-value=1.3e+02 Score=25.74 Aligned_cols=52 Identities=21% Similarity=0.424 Sum_probs=37.7
Q ss_pred CCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHh
Q 045160 87 KKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRK 141 (166)
Q Consensus 87 r~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~ 141 (166)
.+|..|++....-|..+|..|. .|||-.-++ |-..+|-...++..|=++-++
T Consensus 206 e~R~~L~~~lA~wLh~yyaSH~-~P~P~kvet--l~~lcGS~~~~l~~FR~~Lk~ 257 (282)
T PF07042_consen 206 EQRRKLSPRLAKWLHGYYASHK-KPYPIKVET--LRELCGSESSRLRKFRQQLKK 257 (282)
T ss_pred HHHhhcCcHHHHHHHHHHhcCC-CCCCccHHH--HHHHcCCCccCHHHHHHHHHH
Confidence 4455666665667899999984 699987775 445688888888888766554
No 247
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=23.36 E-value=62 Score=21.04 Aligned_cols=23 Identities=9% Similarity=0.159 Sum_probs=19.5
Q ss_pred HHHHHHHhCCChhhhhhhhhhHH
Q 045160 118 KLQLAESTGLDQKQINNWFINQR 140 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~N~R 140 (166)
...||+.+|++...|+..+.+.+
T Consensus 3 ~~~iA~~~gvS~~TVSr~ln~~~ 25 (70)
T smart00354 3 IKDVARLAGVSKATVSRVLNGNG 25 (70)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCC
Confidence 35799999999999999987753
No 248
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=23.26 E-value=2.1e+02 Score=19.77 Aligned_cols=44 Identities=20% Similarity=0.173 Sum_probs=31.6
Q ss_pred CChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhh
Q 045160 92 LPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFI 137 (166)
Q Consensus 92 ~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~ 137 (166)
|+..|+.+|..-...+....-|-.. ..||+..+++.--|+|=.+
T Consensus 2 Lt~rq~~IL~alV~~Y~~~~~PVgS--k~ia~~l~~s~aTIRN~M~ 45 (78)
T PF03444_consen 2 LTERQREILKALVELYIETGEPVGS--KTIAEELGRSPATIRNEMA 45 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCcCH--HHHHHHHCCChHHHHHHHH
Confidence 5677888888877776556666443 3678889999988887443
No 249
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=23.12 E-value=1.7e+02 Score=20.16 Aligned_cols=37 Identities=24% Similarity=0.394 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhh
Q 045160 96 SRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWF 136 (166)
Q Consensus 96 ~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF 136 (166)
....+..|...|+..| ++ ...||+.+|++..++..=|
T Consensus 6 ~~~~~~~~i~~~~~~~-~~---~~~lA~~~~~S~~~l~r~f 42 (107)
T PRK10219 6 IIQTLIAWIDEHIDQP-LN---IDVVAKKSGYSKWYLQRMF 42 (107)
T ss_pred HHHHHHHHHHHhcCCC-CC---HHHHHHHHCCCHHHHHHHH
Confidence 4555677888865554 33 4567777888777765444
No 250
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=22.98 E-value=94 Score=25.95 Aligned_cols=52 Identities=17% Similarity=0.177 Sum_probs=40.0
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..|+...+.+|...|.. . ....-.++|+.+|+|..+|+.+-.....|++...
T Consensus 229 ~~L~~rEr~VL~lry~~---~---~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l 280 (284)
T PRK06596 229 EGLDERSRDIIEARWLD---D---DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAI 280 (284)
T ss_pred hcCCHHHHHHHHHHhcC---C---CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35888899999887743 1 2234569999999999999999888888876543
No 251
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=22.96 E-value=80 Score=30.96 Aligned_cols=16 Identities=25% Similarity=0.501 Sum_probs=12.9
Q ss_pred ccCCCCCCCChHHHHH
Q 045160 84 SKKKKKGKLPKESRQT 99 (166)
Q Consensus 84 ~~kr~r~~~~~~~~~~ 99 (166)
.|||.|..||.+++.+
T Consensus 1293 ~KKRGRK~LPpe~Ka~ 1308 (1463)
T PHA03308 1293 GKRRGRQRLPIRDRVY 1308 (1463)
T ss_pred ccccCCCCCChHHhhh
Confidence 5677888899998876
No 252
>smart00351 PAX Paired Box domain.
Probab=22.85 E-value=3.1e+02 Score=19.96 Aligned_cols=46 Identities=15% Similarity=0.063 Sum_probs=30.0
Q ss_pred CCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCC-------Chhhhhhhh
Q 045160 88 KKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGL-------DQKQINNWF 136 (166)
Q Consensus 88 ~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgL-------s~~qV~~WF 136 (166)
+....+......+.....+ +|.-+..+....-...|+ +...|..||
T Consensus 72 rp~~~~~~~~~~I~~~~~~---~p~~t~~el~~~L~~~gv~~~~~~Ps~sti~~~l 124 (125)
T smart00351 72 KPKVATPKVVKKIADYKQE---NPGIFAWEIRDRLLSEGVCDKDNVPSVSSINRIL 124 (125)
T ss_pred CCCccCHHHHHHHHHHHHH---CCCCCHHHHHHHHHHcCCCcCCCCCChhhHHHhh
Confidence 3344555666666666777 788888777543335666 667788776
No 253
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=22.65 E-value=75 Score=23.40 Aligned_cols=21 Identities=19% Similarity=0.472 Sum_probs=18.1
Q ss_pred HHHHHHHhCCChhhhhhhhhh
Q 045160 118 KLQLAESTGLDQKQINNWFIN 138 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~N 138 (166)
..++|+.||++...|+.|-..
T Consensus 6 I~elA~~~gvs~~tlR~Ye~~ 26 (120)
T TIGR02054 6 ISRLAEDAGVSVHVVRDYLLR 26 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 568999999999999999543
No 254
>PRK09191 two-component response regulator; Provisional
Probab=22.60 E-value=1.6e+02 Score=23.15 Aligned_cols=50 Identities=18% Similarity=0.118 Sum_probs=38.2
Q ss_pred CCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 90 GKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 90 ~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
..||+.++.++...+.+. + .-.++|+.+|++..-|..-....|++.++..
T Consensus 87 ~~L~~~~r~v~~l~~~~~----~----s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~ 136 (261)
T PRK09191 87 AGLTPLPRQAFLLTALEG----F----SVEEAAEILGVDPAEAEALLDDARAEIARQV 136 (261)
T ss_pred HhCCHHHhHHHHHHHHhc----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHhccC
Confidence 467888888887665552 2 2457899999999999999988888877654
No 255
>PF06299 DUF1045: Protein of unknown function (DUF1045); InterPro: IPR009389 This family consists of several hypothetical proteins from Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown.
Probab=22.55 E-value=1.6e+02 Score=22.96 Aligned_cols=42 Identities=19% Similarity=0.322 Sum_probs=27.7
Q ss_pred HHHHHHHHhhhcCCccchhhhhccCCCCCCCChHHHHHHHHH
Q 045160 62 RHLKDKLLRKFGSHIGSLKLEFSKKKKKGKLPKESRQTLLDW 103 (166)
Q Consensus 62 ~elk~~l~~~~~~~~~~~~~~~~~kr~r~~~~~~~~~~L~~~ 103 (166)
..|-..+++.+...=-.+...-..+|....++..|...|..|
T Consensus 57 ~~LAa~cV~~~d~fRAPls~aelaRR~~~~Ls~~Q~~~L~rW 98 (160)
T PF06299_consen 57 QALAAACVRAFDPFRAPLSEAELARRRPAGLSPRQRANLERW 98 (160)
T ss_pred HHHHHHHHHhhhhccCCCChHHHhhcCcccCCHHHHHHHHHh
Confidence 345556666665543433333345677889999999999887
No 256
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=22.47 E-value=68 Score=22.30 Aligned_cols=19 Identities=26% Similarity=0.375 Sum_probs=17.1
Q ss_pred HHHHHHhCCChhhhhhhhh
Q 045160 119 LQLAESTGLDQKQINNWFI 137 (166)
Q Consensus 119 ~~LA~~tgLs~~qV~~WF~ 137 (166)
.++|+.+|++...|+.|-.
T Consensus 4 ~eva~~~gvs~~tlR~ye~ 22 (96)
T cd04788 4 GELARRTGLSVRTLHHYDH 22 (96)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4789999999999999974
No 257
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.45 E-value=67 Score=22.44 Aligned_cols=19 Identities=16% Similarity=0.375 Sum_probs=16.9
Q ss_pred HHHHHHhCCChhhhhhhhh
Q 045160 119 LQLAESTGLDQKQINNWFI 137 (166)
Q Consensus 119 ~~LA~~tgLs~~qV~~WF~ 137 (166)
.++|+.+|++...|..|-.
T Consensus 4 ~eva~~~gvs~~tlR~Ye~ 22 (95)
T cd04780 4 SELSKRSGVSVATIKYYLR 22 (95)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 5799999999999999864
No 258
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=22.34 E-value=75 Score=22.21 Aligned_cols=20 Identities=15% Similarity=0.167 Sum_probs=17.6
Q ss_pred HHHHHHhCCChhhhhhhhhh
Q 045160 119 LQLAESTGLDQKQINNWFIN 138 (166)
Q Consensus 119 ~~LA~~tgLs~~qV~~WF~N 138 (166)
.++|+.+|++...|+.|..+
T Consensus 4 ~eva~~~gvs~~tlR~ye~~ 23 (103)
T cd01106 4 GEVAKLTGVSVRTLHYYDEI 23 (103)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 57899999999999999764
No 259
>PF01343 Peptidase_S49: Peptidase family S49 peptidase classification.; InterPro: IPR002142 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain. The domain defines sequences in viruses, archaea, bacteria and plants. These sequences are variously annotated in the different taxonomic groups, examples are: Viruses: capsid protein Archaea: proteinase IV homolog Bacteria: proteinase IV, sohB, SppA, pfaP, putative protease Plants: SppA, protease IV This group also contains proteins classified as non-peptidase homologues that either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases. Related proteins, non-peptidase homologs and unclassified S49 members are also to be found in IPR002810 from INTERPRO.; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3RST_B 3BEZ_D 3BF0_A.
Probab=22.25 E-value=1.4e+02 Score=22.46 Aligned_cols=45 Identities=16% Similarity=0.226 Sum_probs=34.9
Q ss_pred CCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhh
Q 045160 88 KKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFIN 138 (166)
Q Consensus 88 ~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N 138 (166)
.+..++++.+..++.++.. - -..-...+|+..|++..+|..|+..
T Consensus 76 ~~~~~s~~~r~~~~~~l~~----~--~~~f~~~Va~~R~~~~~~v~~~~~~ 120 (154)
T PF01343_consen 76 PRDPMSEEERENLQELLDE----L--YDQFVNDVAEGRGLSPDDVEEIADG 120 (154)
T ss_dssp TTSS--HHHHHHHHHHHHH----H--HHHHHHHHHHHHTS-HHHHHCHHCC
T ss_pred cCCCCCHHHHHHHHHHHHH----H--HHHHHHHHHHccCCCHHHHHHHHhh
Confidence 4678999999999988877 2 2567788999999999999999866
No 260
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=22.19 E-value=69 Score=21.90 Aligned_cols=20 Identities=15% Similarity=0.127 Sum_probs=17.4
Q ss_pred HHHHHHHhCCChhhhhhhhh
Q 045160 118 KLQLAESTGLDQKQINNWFI 137 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~ 137 (166)
...+|+.+|+++..|..|-.
T Consensus 4 i~e~A~~~gvs~~tLr~ye~ 23 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYER 23 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999964
No 261
>PF12728 HTH_17: Helix-turn-helix domain
Probab=22.18 E-value=85 Score=18.74 Aligned_cols=21 Identities=19% Similarity=0.430 Sum_probs=17.5
Q ss_pred HHHHHHhCCChhhhhhhhhhH
Q 045160 119 LQLAESTGLDQKQINNWFINQ 139 (166)
Q Consensus 119 ~~LA~~tgLs~~qV~~WF~N~ 139 (166)
.++|+.+|++...|..|....
T Consensus 5 ~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 5 KEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred HHHHHHHCcCHHHHHHHHHcC
Confidence 468888999999999998543
No 262
>PHA02955 hypothetical protein; Provisional
Probab=22.11 E-value=1.6e+02 Score=24.11 Aligned_cols=45 Identities=11% Similarity=0.054 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhh
Q 045160 96 SRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKR 142 (166)
Q Consensus 96 ~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R 142 (166)
+...|...|.+-+ --.++++|..+|+.+|.+...|..||.+.=.|
T Consensus 62 sf~lli~a~~Et~--~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~~q 106 (213)
T PHA02955 62 NFQLLIEALIETI--ENFPEKEQKEIAADIGINIDDYKAGKKTDLQL 106 (213)
T ss_pred HHHHHHHHHHHHH--HhCCHHHHHHHHHHhCCChhhccCcccchhhh
Confidence 3444444444421 12568999999999999998899999998777
No 263
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=21.89 E-value=81 Score=32.53 Aligned_cols=61 Identities=16% Similarity=0.037 Sum_probs=52.3
Q ss_pred ccCCCCCCCChHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcCCCC
Q 045160 84 SKKKKKGKLPKESRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINNWFINQRKRHWKPS 147 (166)
Q Consensus 84 ~~kr~r~~~~~~~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~WF~N~R~R~kk~~ 147 (166)
.-+.-+...-.++..+|-.|+-. +--|+......|....+.+..++.+||.|-|-|.+|.+
T Consensus 704 ~~~~~~~~~~~~aa~~l~~a~~~---~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 704 RDKLLRLTILPEAAMILGRAYMQ---DNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred ccccCcccccHHHHhhhhhcccC---CCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 34445555666889999999888 78899999999999999999999999999999988876
No 264
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=21.58 E-value=2.3e+02 Score=22.21 Aligned_cols=36 Identities=14% Similarity=0.046 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhh
Q 045160 96 SRQTLLDWWNAHYKWPYPTEADKLQLAESTGLDQKQINN 134 (166)
Q Consensus 96 ~~~~L~~~f~~h~~~pYPs~~ek~~LA~~tgLs~~qV~~ 134 (166)
...+|...=.. ..|-+++....+|+.+|++..+|..
T Consensus 38 li~~L~~iQ~~---~GyIp~e~~~~iA~~l~v~~a~V~g 73 (169)
T PRK07571 38 LIEVLHKAQEL---FGYLERDLLLYVARQLKLPLSRVYG 73 (169)
T ss_pred HHHHHHHHHHH---cCCCCHHHHHHHHHHhCcCHHHHHH
Confidence 45555544344 6899999999999999999998764
No 265
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=20.37 E-value=78 Score=22.44 Aligned_cols=21 Identities=14% Similarity=0.044 Sum_probs=18.0
Q ss_pred HHHHHHHhCCChhhhhhhhhh
Q 045160 118 KLQLAESTGLDQKQINNWFIN 138 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~~WF~N 138 (166)
..++|+.+|++...|+.|-..
T Consensus 3 i~eva~~~gis~~tlR~ye~~ 23 (108)
T cd01107 3 IGEFAKLSNLSIKALRYYDKI 23 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 357999999999999999754
No 266
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=20.31 E-value=42 Score=21.74 Aligned_cols=20 Identities=30% Similarity=0.607 Sum_probs=14.9
Q ss_pred HHHHHHHhCCChhhhh-hhhh
Q 045160 118 KLQLAESTGLDQKQIN-NWFI 137 (166)
Q Consensus 118 k~~LA~~tgLs~~qV~-~WF~ 137 (166)
...||+.+|++...|+ +|..
T Consensus 15 ~~~lA~~lgis~st~s~~~~~ 35 (66)
T PF07022_consen 15 DKELAERLGISKSTLSNNWKK 35 (66)
T ss_dssp CHHHHCCTT--HHHHH-HHHH
T ss_pred HHHHHHHhCcCHHHhhHHHHh
Confidence 4589999999999999 7763
No 267
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=20.01 E-value=80 Score=22.55 Aligned_cols=20 Identities=20% Similarity=0.438 Sum_probs=17.4
Q ss_pred HHHHHHhCCChhhhhhhhhh
Q 045160 119 LQLAESTGLDQKQINNWFIN 138 (166)
Q Consensus 119 ~~LA~~tgLs~~qV~~WF~N 138 (166)
-++|+.+|++...|+.|-..
T Consensus 4 ge~A~~~gvs~~tlR~ye~~ 23 (107)
T cd01111 4 SQLALDAGVSVHIVRDYLLR 23 (107)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 57999999999999999653
Done!