Query psy4078
Match_columns 269
No_of_seqs 349 out of 1515
Neff 7.2
Searched_HMMs 46136
Date Sat Aug 17 00:46:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4078.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4078hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0484|consensus 99.8 1.1E-20 2.4E-25 143.3 5.3 75 79-153 14-88 (125)
2 KOG0488|consensus 99.7 1.8E-18 3.8E-23 158.3 3.6 67 79-145 169-235 (309)
3 KOG0489|consensus 99.7 1.6E-18 3.4E-23 155.7 3.0 64 80-143 157-220 (261)
4 KOG2251|consensus 99.7 1.8E-18 3.9E-23 147.9 3.1 68 77-144 32-99 (228)
5 KOG0850|consensus 99.7 9.1E-18 2E-22 144.3 4.3 75 68-142 108-182 (245)
6 KOG0843|consensus 99.7 1.5E-17 3.3E-22 138.0 4.1 63 81-143 101-163 (197)
7 KOG0494|consensus 99.7 1.4E-17 3E-22 145.2 3.6 63 81-143 140-202 (332)
8 KOG0848|consensus 99.7 3E-17 6.6E-22 143.6 4.5 68 78-145 195-262 (317)
9 KOG0842|consensus 99.7 2.4E-17 5.1E-22 149.1 3.3 65 79-143 150-214 (307)
10 KOG0492|consensus 99.7 7.9E-17 1.7E-21 136.4 5.3 66 82-147 144-209 (246)
11 KOG0487|consensus 99.7 2.3E-17 5E-22 149.2 1.6 66 80-145 233-298 (308)
12 PF00046 Homeobox: Homeobox do 99.6 8.4E-17 1.8E-21 111.5 2.9 57 83-139 1-57 (57)
13 KOG0485|consensus 99.6 5.9E-16 1.3E-20 131.9 6.1 67 78-144 100-166 (268)
14 KOG0486|consensus 99.6 1.5E-15 3.2E-20 135.8 8.5 77 81-159 111-187 (351)
15 KOG0493|consensus 99.6 4.6E-16 9.9E-21 135.8 3.3 61 81-141 245-305 (342)
16 KOG4577|consensus 99.6 3.4E-14 7.3E-19 125.8 11.4 66 78-143 163-228 (383)
17 TIGR01565 homeo_ZF_HD homeobox 99.5 2.5E-15 5.4E-20 104.3 2.6 52 83-134 2-57 (58)
18 KOG0844|consensus 99.5 1.8E-15 4E-20 134.6 0.9 68 78-145 177-244 (408)
19 COG5576 Homeodomain-containing 99.5 2.6E-14 5.7E-19 118.6 6.9 69 75-143 44-112 (156)
20 smart00389 HOX Homeodomain. DN 99.5 8.6E-15 1.9E-19 100.7 2.8 55 84-138 2-56 (56)
21 cd00086 homeodomain Homeodomai 99.5 1.3E-14 2.7E-19 100.7 3.4 57 84-140 2-58 (59)
22 KOG0490|consensus 99.5 2.4E-14 5.1E-19 125.5 6.0 117 26-142 58-213 (235)
23 KOG0491|consensus 99.5 1.3E-14 2.9E-19 118.9 2.4 61 82-142 100-160 (194)
24 KOG0483|consensus 99.5 2.2E-14 4.8E-19 123.0 3.8 60 84-143 52-111 (198)
25 KOG3802|consensus 99.4 2.4E-14 5.3E-19 132.3 1.6 61 81-141 293-353 (398)
26 KOG0847|consensus 99.3 4.7E-13 1E-17 114.4 2.3 66 78-143 163-228 (288)
27 KOG0490|consensus 99.3 1.1E-12 2.5E-17 114.8 2.5 64 79-142 57-120 (235)
28 KOG0849|consensus 99.1 2.3E-11 5.1E-16 113.7 3.8 67 77-143 171-237 (354)
29 KOG1168|consensus 99.0 1.2E-10 2.5E-15 103.6 2.8 63 80-142 307-369 (385)
30 KOG0775|consensus 98.8 1.7E-09 3.8E-14 95.6 3.3 52 88-139 182-233 (304)
31 KOG2251|consensus 98.8 2.7E-09 5.8E-14 91.9 3.2 64 23-86 32-95 (228)
32 KOG0774|consensus 98.7 2.3E-08 4.9E-13 88.0 6.9 62 82-143 188-252 (334)
33 KOG0484|consensus 98.6 3.1E-09 6.8E-14 81.1 -1.2 55 26-80 15-69 (125)
34 TIGR01565 homeo_ZF_HD homeobox 98.6 4E-08 8.7E-13 68.2 4.1 51 29-79 2-56 (58)
35 KOG0494|consensus 98.5 6.8E-08 1.5E-12 85.0 3.8 57 29-85 142-198 (332)
36 PF05920 Homeobox_KN: Homeobox 98.5 1E-07 2.2E-12 61.4 2.3 34 103-136 7-40 (40)
37 KOG0486|consensus 98.4 1.2E-07 2.7E-12 85.4 3.4 62 27-88 111-172 (351)
38 KOG2252|consensus 98.4 3.4E-07 7.3E-12 88.2 4.4 59 79-137 417-475 (558)
39 KOG0843|consensus 98.4 2.1E-07 4.6E-12 77.9 2.5 55 27-81 101-155 (197)
40 PF00046 Homeobox: Homeobox do 98.3 1.4E-07 3.1E-12 64.9 1.1 50 29-78 1-50 (57)
41 smart00389 HOX Homeodomain. DN 98.3 3.5E-07 7.5E-12 62.5 1.8 50 30-79 2-51 (56)
42 KOG0488|consensus 98.2 8E-07 1.7E-11 81.8 2.9 58 26-83 170-227 (309)
43 KOG0493|consensus 98.2 1E-06 2.2E-11 77.8 2.8 67 19-85 237-303 (342)
44 cd00086 homeodomain Homeodomai 98.1 7.3E-07 1.6E-11 61.3 0.5 50 30-79 2-51 (59)
45 COG5576 Homeodomain-containing 98.1 1.5E-06 3.2E-11 72.4 2.4 100 24-136 47-146 (156)
46 KOG0842|consensus 98.0 1E-05 2.2E-10 73.9 5.0 61 23-83 148-208 (307)
47 KOG0485|consensus 97.9 6.1E-06 1.3E-10 71.1 2.7 60 23-82 99-158 (268)
48 KOG0844|consensus 97.8 1.5E-05 3.3E-10 71.8 2.8 59 23-81 176-234 (408)
49 KOG0849|consensus 97.7 3.8E-05 8.3E-10 72.1 4.4 61 23-83 171-231 (354)
50 KOG0489|consensus 97.7 6.6E-06 1.4E-10 74.1 -0.7 60 26-85 157-216 (261)
51 KOG1146|consensus 97.6 3.5E-05 7.5E-10 80.9 3.6 61 82-142 903-963 (1406)
52 KOG0492|consensus 97.6 3.7E-05 8.1E-10 65.9 3.0 56 26-81 142-197 (246)
53 KOG0850|consensus 97.6 3.3E-05 7.2E-10 67.2 2.4 61 20-80 114-174 (245)
54 KOG4577|consensus 97.4 8.5E-05 1.9E-09 66.6 2.6 58 24-81 163-220 (383)
55 KOG0487|consensus 97.3 7.3E-05 1.6E-09 68.3 1.2 58 26-83 233-290 (308)
56 KOG3802|consensus 97.2 0.00034 7.3E-09 65.6 4.0 57 27-83 293-349 (398)
57 KOG0848|consensus 97.1 0.00019 4.1E-09 63.9 1.6 57 25-81 196-252 (317)
58 KOG2252|consensus 97.0 0.00044 9.6E-09 67.1 2.5 59 23-81 415-473 (558)
59 PF11569 Homez: Homeodomain le 96.9 0.00046 9.9E-09 47.4 1.6 41 94-134 10-50 (56)
60 KOG0483|consensus 96.3 0.0031 6.6E-08 54.5 2.8 52 30-81 52-103 (198)
61 KOG0491|consensus 96.0 0.00062 1.4E-08 56.5 -2.6 54 27-80 99-152 (194)
62 KOG1168|consensus 95.9 0.0035 7.6E-08 56.5 1.3 56 27-82 308-363 (385)
63 KOG0773|consensus 95.8 0.0035 7.5E-08 58.5 1.2 61 82-142 239-302 (342)
64 KOG0847|consensus 95.5 0.0047 1E-07 53.6 0.7 65 24-88 163-227 (288)
65 KOG3623|consensus 95.5 0.0072 1.6E-07 60.6 2.0 103 40-142 568-686 (1007)
66 KOG3623|consensus 95.3 0.013 2.8E-07 58.9 2.9 49 94-142 568-616 (1007)
67 KOG0774|consensus 94.9 0.024 5.2E-07 50.6 3.3 52 28-79 188-242 (334)
68 KOG0775|consensus 93.9 0.047 1E-06 49.1 2.9 50 31-80 170-228 (304)
69 PF04218 CENP-B_N: CENP-B N-te 93.8 0.047 1E-06 37.1 2.2 46 83-133 1-46 (53)
70 PF05920 Homeobox_KN: Homeobox 90.2 0.13 2.9E-06 32.8 0.9 29 48-76 6-34 (40)
71 KOG3755|consensus 88.0 0.45 9.8E-06 47.2 3.2 100 28-141 647-758 (769)
72 PF04545 Sigma70_r4: Sigma-70, 82.9 1.4 3E-05 28.9 2.8 46 88-138 4-49 (50)
73 KOG1146|consensus 79.3 0.92 2E-05 48.9 1.3 51 28-78 903-953 (1406)
74 PF04967 HTH_10: HTH DNA bindi 75.5 2.5 5.4E-05 28.7 2.2 40 89-128 1-42 (53)
75 KOG1924|consensus 74.9 29 0.00063 36.1 10.3 15 58-72 421-435 (1102)
76 cd06171 Sigma70_r4 Sigma70, re 72.7 2.4 5.2E-05 26.9 1.6 44 88-136 10-53 (55)
77 PF03529 TF_Otx: Otx1 transcri 71.7 4.5 9.8E-05 30.3 2.9 43 217-259 44-86 (88)
78 PF10668 Phage_terminase: Phag 65.0 4.5 9.7E-05 28.2 1.6 20 111-130 24-43 (60)
79 PRK03975 tfx putative transcri 62.6 11 0.00024 30.8 3.9 51 87-143 5-55 (141)
80 PF01527 HTH_Tnp_1: Transposas 62.3 3 6.5E-05 29.5 0.4 43 85-131 3-45 (76)
81 PF08281 Sigma70_r4_2: Sigma-7 61.0 8.2 0.00018 25.4 2.4 42 89-135 11-52 (54)
82 COG3413 Predicted DNA binding 57.9 9.2 0.0002 33.1 2.8 41 88-128 155-197 (215)
83 cd00569 HTH_Hin_like Helix-tur 53.9 13 0.00028 20.9 2.2 37 89-130 6-42 (42)
84 cd04761 HTH_MerR-SF Helix-Turn 53.3 10 0.00022 24.1 1.8 21 112-132 3-23 (49)
85 PRK04217 hypothetical protein; 53.3 15 0.00033 28.7 3.0 48 87-139 41-88 (110)
86 PF04218 CENP-B_N: CENP-B N-te 53.0 18 0.00039 24.2 3.0 40 29-73 1-40 (53)
87 PF04967 HTH_10: HTH DNA bindi 51.8 22 0.00047 24.1 3.2 38 35-72 1-40 (53)
88 PRK09646 RNA polymerase sigma 50.9 15 0.00032 30.9 2.8 47 89-140 143-189 (194)
89 PF13443 HTH_26: Cro/C1-type H 50.3 17 0.00038 24.5 2.7 31 111-141 12-42 (63)
90 KOG0773|consensus 49.6 13 0.00029 34.4 2.6 55 27-81 238-295 (342)
91 PF00196 GerE: Bacterial regul 48.6 13 0.00028 25.0 1.8 45 88-138 3-47 (58)
92 PRK10072 putative transcriptio 48.0 13 0.00029 28.3 1.9 41 89-136 33-73 (96)
93 PF13551 HTH_29: Winged helix- 47.4 17 0.00036 27.3 2.4 75 57-131 14-109 (112)
94 TIGR03879 near_KaiC_dom probab 47.2 5.7 0.00012 28.8 -0.2 38 100-137 23-60 (73)
95 cd00131 PAX Paired Box domain 47.1 63 0.0014 25.7 5.8 95 34-133 17-127 (128)
96 PRK06759 RNA polymerase factor 47.0 18 0.00039 28.8 2.7 30 110-139 123-152 (154)
97 PRK12526 RNA polymerase sigma 46.3 21 0.00045 30.5 3.1 32 109-140 169-200 (206)
98 TIGR02937 sigma70-ECF RNA poly 46.0 18 0.0004 27.9 2.6 46 89-139 111-156 (158)
99 PF13518 HTH_28: Helix-turn-he 45.6 16 0.00035 23.5 1.8 22 111-132 14-35 (52)
100 PRK12514 RNA polymerase sigma 45.6 17 0.00036 30.0 2.3 30 110-139 146-175 (179)
101 PRK12519 RNA polymerase sigma 45.5 23 0.00049 29.6 3.2 33 108-140 156-188 (194)
102 PRK00118 putative DNA-binding 45.0 33 0.0007 26.6 3.7 50 89-143 18-67 (104)
103 PRK09652 RNA polymerase sigma 44.9 23 0.00051 28.7 3.1 47 89-140 129-175 (182)
104 PF06056 Terminase_5: Putative 44.6 17 0.00037 25.0 1.9 25 112-138 16-40 (58)
105 PRK11924 RNA polymerase sigma 44.1 20 0.00043 29.1 2.5 31 110-140 142-172 (179)
106 TIGR02939 RpoE_Sigma70 RNA pol 44.1 24 0.00053 29.1 3.1 33 108-140 153-185 (190)
107 PF13384 HTH_23: Homeodomain-l 44.0 18 0.00038 23.3 1.8 23 110-132 18-40 (50)
108 COG4367 Uncharacterized protei 43.4 15 0.00033 27.6 1.5 39 89-127 3-41 (97)
109 PF13936 HTH_38: Helix-turn-he 43.4 20 0.00042 23.0 1.9 40 87-131 3-42 (44)
110 cd01392 HTH_LacI Helix-turn-he 43.2 34 0.00075 21.9 3.2 21 114-134 2-22 (52)
111 PF00424 REV: REV protein (ant 41.6 33 0.00073 25.9 3.1 38 95-146 15-52 (91)
112 cd04762 HTH_MerR-trunc Helix-T 41.4 21 0.00045 22.1 1.8 23 112-134 3-25 (49)
113 smart00421 HTH_LUXR helix_turn 41.2 33 0.00072 21.8 2.9 39 89-133 4-42 (58)
114 PRK12546 RNA polymerase sigma 40.8 26 0.00056 29.5 2.8 32 110-141 130-161 (188)
115 PRK12512 RNA polymerase sigma 40.7 29 0.00063 28.6 3.1 31 110-140 148-178 (184)
116 PF13411 MerR_1: MerR HTH fami 39.5 23 0.00049 24.3 1.9 20 112-131 3-22 (69)
117 PRK09648 RNA polymerase sigma 39.4 31 0.00068 28.6 3.1 30 110-139 156-185 (189)
118 PRK05602 RNA polymerase sigma 38.8 32 0.0007 28.5 3.1 30 111-140 146-175 (186)
119 PF00376 MerR: MerR family reg 38.5 24 0.00053 21.9 1.7 19 112-130 2-20 (38)
120 TIGR02948 SigW_bacill RNA poly 38.4 37 0.0008 27.9 3.4 31 109-139 152-182 (187)
121 PRK09413 IS2 repressor TnpA; R 37.7 33 0.00071 26.9 2.8 42 86-132 10-52 (121)
122 TIGR02999 Sig-70_X6 RNA polyme 37.2 36 0.00078 27.9 3.1 29 111-139 152-180 (183)
123 TIGR02989 Sig-70_gvs1 RNA poly 37.2 33 0.00072 27.3 2.8 46 88-138 111-156 (159)
124 PRK09639 RNA polymerase sigma 37.1 56 0.0012 26.2 4.2 46 89-140 113-158 (166)
125 PRK06986 fliA flagellar biosyn 36.4 32 0.00069 30.0 2.8 32 109-140 200-231 (236)
126 PF01381 HTH_3: Helix-turn-hel 36.4 27 0.00059 22.7 1.8 25 112-136 12-36 (55)
127 PRK12513 RNA polymerase sigma 36.2 27 0.00059 29.1 2.2 34 107-140 153-186 (194)
128 cd04763 HTH_MlrA-like Helix-Tu 35.6 27 0.00058 24.1 1.8 20 112-131 3-22 (68)
129 PF11569 Homez: Homeodomain le 35.6 12 0.00025 25.8 -0.1 38 40-77 10-47 (56)
130 PRK12518 RNA polymerase sigma 35.1 32 0.00069 28.0 2.5 34 107-140 134-167 (175)
131 PRK09642 RNA polymerase sigma 34.9 33 0.00071 27.6 2.5 29 112-140 125-153 (160)
132 cd06170 LuxR_C_like C-terminal 34.6 33 0.00072 21.9 2.0 21 111-131 17-37 (57)
133 PRK09480 slmA division inhibit 34.0 30 0.00065 28.5 2.1 37 98-135 20-56 (194)
134 TIGR02959 SigZ RNA polymerase 34.0 40 0.00087 27.6 2.9 47 89-140 101-147 (170)
135 PRK12515 RNA polymerase sigma 33.8 43 0.00092 27.8 3.0 30 111-140 149-178 (189)
136 TIGR02985 Sig70_bacteroi1 RNA 33.6 36 0.00077 26.9 2.4 29 111-139 131-159 (161)
137 PRK06930 positive control sigm 33.2 45 0.00097 28.0 3.0 48 88-140 114-161 (170)
138 PRK12541 RNA polymerase sigma 33.0 41 0.00089 27.0 2.8 46 89-139 113-158 (161)
139 TIGR03070 couple_hipB transcri 32.4 36 0.00077 22.0 1.9 24 112-135 18-41 (58)
140 PRK12530 RNA polymerase sigma 32.2 60 0.0013 27.1 3.7 30 111-140 152-181 (189)
141 PRK12538 RNA polymerase sigma 31.8 64 0.0014 28.2 3.9 32 110-141 188-219 (233)
142 PF13700 DUF4158: Domain of un 31.8 1.2E+02 0.0025 25.0 5.3 90 35-138 2-98 (166)
143 TIGR02950 SigM_subfam RNA poly 31.5 38 0.00082 26.8 2.3 33 107-139 119-151 (154)
144 PRK09644 RNA polymerase sigma 31.3 48 0.001 26.8 2.9 31 111-141 126-156 (165)
145 PF02796 HTH_7: Helix-turn-hel 31.1 43 0.00093 21.4 2.0 38 89-131 6-43 (45)
146 cd04764 HTH_MlrA-like_sg1 Heli 31.0 35 0.00076 23.4 1.7 21 112-132 3-23 (67)
147 TIGR01764 excise DNA binding d 30.9 39 0.00084 21.0 1.8 23 112-134 4-26 (49)
148 TIGR00721 tfx DNA-binding prot 30.9 62 0.0013 26.4 3.4 47 87-139 5-51 (137)
149 PRK12537 RNA polymerase sigma 30.9 52 0.0011 27.2 3.1 30 110-139 150-179 (182)
150 PRK09637 RNA polymerase sigma 30.8 54 0.0012 27.3 3.2 30 110-139 123-152 (181)
151 PRK06811 RNA polymerase factor 30.6 42 0.0009 28.0 2.5 32 110-141 148-179 (189)
152 PF09607 BrkDBD: Brinker DNA-b 30.2 52 0.0011 22.8 2.4 43 87-131 4-47 (58)
153 PF08280 HTH_Mga: M protein tr 30.1 29 0.00062 23.6 1.1 35 92-130 6-40 (59)
154 PRK12524 RNA polymerase sigma 30.1 54 0.0012 27.5 3.1 30 111-140 154-183 (196)
155 PRK08301 sporulation sigma fac 29.6 58 0.0013 28.2 3.3 32 109-140 198-229 (234)
156 TIGR02952 Sig70_famx2 RNA poly 29.4 52 0.0011 26.5 2.8 29 110-138 139-167 (170)
157 TIGR02954 Sig70_famx3 RNA poly 29.4 58 0.0013 26.4 3.1 30 110-139 136-165 (169)
158 TIGR02479 FliA_WhiG RNA polyme 29.3 48 0.001 28.5 2.7 45 90-139 177-221 (224)
159 cd01104 HTH_MlrA-CarA Helix-Tu 29.0 40 0.00086 23.0 1.7 20 112-131 3-22 (68)
160 COG2944 Predicted transcriptio 28.9 46 0.00099 25.8 2.2 41 89-136 44-84 (104)
161 PRK07037 extracytoplasmic-func 28.8 62 0.0013 25.9 3.1 29 111-139 127-155 (163)
162 PRK05657 RNA polymerase sigma 28.7 59 0.0013 30.1 3.3 52 88-140 262-313 (325)
163 smart00351 PAX Paired Box doma 28.6 2E+02 0.0042 22.6 5.9 90 35-130 18-124 (125)
164 PRK12529 RNA polymerase sigma 28.2 60 0.0013 26.8 3.0 29 111-139 145-173 (178)
165 PRK08583 RNA polymerase sigma 27.3 52 0.0011 29.0 2.6 46 89-139 206-251 (257)
166 TIGR02947 SigH_actino RNA poly 27.3 51 0.0011 27.4 2.5 34 107-140 145-178 (193)
167 PRK09651 RNA polymerase sigma 27.0 85 0.0018 25.6 3.7 32 109-140 135-166 (172)
168 PF12728 HTH_17: Helix-turn-he 27.0 48 0.001 21.4 1.8 23 112-134 4-26 (51)
169 cd00093 HTH_XRE Helix-turn-hel 26.9 51 0.0011 20.1 1.9 23 112-134 15-37 (58)
170 COG3413 Predicted DNA binding 26.6 71 0.0015 27.5 3.3 39 34-72 155-195 (215)
171 PRK09645 RNA polymerase sigma 26.6 69 0.0015 26.0 3.1 29 111-139 136-164 (173)
172 TIGR02983 SigE-fam_strep RNA p 26.5 55 0.0012 26.2 2.4 31 110-140 127-157 (162)
173 PRK10403 transcriptional regul 26.5 50 0.0011 26.8 2.2 48 88-141 153-200 (215)
174 PRK12533 RNA polymerase sigma 26.0 70 0.0015 27.7 3.1 31 110-140 151-181 (216)
175 PRK12536 RNA polymerase sigma 25.9 56 0.0012 26.9 2.4 30 110-139 146-175 (181)
176 PRK12539 RNA polymerase sigma 25.8 74 0.0016 26.3 3.1 31 109-139 147-177 (184)
177 PF13730 HTH_36: Helix-turn-he 25.7 63 0.0014 21.1 2.2 21 111-131 27-47 (55)
178 TIGR02941 Sigma_B RNA polymera 25.6 72 0.0016 28.0 3.2 46 89-139 206-251 (255)
179 TIGR02607 antidote_HigA addict 25.6 53 0.0011 23.0 1.9 24 112-135 21-44 (78)
180 PRK09649 RNA polymerase sigma 25.5 68 0.0015 26.6 2.9 29 111-139 148-176 (185)
181 TIGR02859 spore_sigH RNA polym 25.3 56 0.0012 27.1 2.3 32 108-139 164-195 (198)
182 PHA01976 helix-turn-helix prot 25.1 56 0.0012 22.2 1.9 23 112-134 18-40 (67)
183 PRK09640 RNA polymerase sigma 24.7 72 0.0016 26.5 2.9 31 110-140 151-181 (188)
184 PF04936 DUF658: Protein of un 24.7 37 0.00081 28.5 1.0 35 109-143 14-48 (186)
185 PRK13919 putative RNA polymera 24.6 61 0.0013 26.7 2.4 30 110-139 152-181 (186)
186 smart00595 MADF subfamily of S 24.5 1E+02 0.0022 22.2 3.4 34 111-144 29-62 (89)
187 PRK11923 algU RNA polymerase s 24.5 62 0.0013 26.9 2.4 34 108-141 153-186 (193)
188 PRK07122 RNA polymerase sigma 24.1 68 0.0015 28.7 2.8 31 109-139 231-261 (264)
189 PRK09047 RNA polymerase factor 24.1 65 0.0014 25.6 2.4 46 89-139 107-152 (161)
190 smart00027 EH Eps15 homology d 24.0 87 0.0019 23.1 3.0 44 88-131 3-51 (96)
191 PRK09638 RNA polymerase sigma 23.9 66 0.0014 26.1 2.5 32 108-139 141-172 (176)
192 PRK07670 RNA polymerase sigma 23.6 68 0.0015 28.2 2.6 31 109-139 217-247 (251)
193 PF10078 DUF2316: Uncharacteri 23.6 47 0.001 25.0 1.3 36 34-73 2-41 (89)
194 TIGR02980 SigBFG RNA polymeras 23.6 66 0.0014 27.6 2.5 46 89-139 179-224 (227)
195 PRK09641 RNA polymerase sigma 23.6 66 0.0014 26.3 2.4 32 109-140 152-183 (187)
196 PRK12517 RNA polymerase sigma 23.4 1E+02 0.0022 25.8 3.5 32 111-142 146-177 (188)
197 PRK12547 RNA polymerase sigma 23.4 69 0.0015 25.9 2.5 30 110-139 129-158 (164)
198 PRK07408 RNA polymerase sigma 23.2 67 0.0014 28.5 2.5 32 109-140 219-250 (256)
199 TIGR02943 Sig70_famx1 RNA poly 23.0 87 0.0019 26.1 3.1 31 110-140 148-178 (188)
200 PRK12522 RNA polymerase sigma 22.9 71 0.0015 26.0 2.5 30 111-140 137-166 (173)
201 PRK12543 RNA polymerase sigma 22.9 1E+02 0.0022 25.3 3.4 32 111-142 135-166 (179)
202 smart00530 HTH_XRE Helix-turn- 22.6 1.2E+02 0.0026 18.1 3.1 24 112-135 13-36 (56)
203 PRK08295 RNA polymerase factor 22.5 70 0.0015 26.8 2.4 30 110-139 171-200 (208)
204 TIGR02392 rpoH_proteo alternat 22.4 88 0.0019 27.9 3.2 48 89-139 219-266 (270)
205 COG4367 Uncharacterized protei 22.0 59 0.0013 24.5 1.6 39 34-72 2-40 (97)
206 PRK06288 RNA polymerase sigma 21.8 94 0.002 27.6 3.2 31 110-140 229-259 (268)
207 PF07638 Sigma70_ECF: ECF sigm 21.8 74 0.0016 26.6 2.4 31 109-139 151-181 (185)
208 PRK09647 RNA polymerase sigma 21.8 74 0.0016 27.1 2.4 30 111-140 156-185 (203)
209 PRK12532 RNA polymerase sigma 21.8 76 0.0016 26.5 2.5 31 111-141 154-184 (195)
210 PRK10360 DNA-binding transcrip 21.6 72 0.0016 25.7 2.3 45 88-138 137-181 (196)
211 smart00422 HTH_MERR helix_turn 21.6 67 0.0015 21.9 1.8 19 112-130 3-21 (70)
212 PRK12511 RNA polymerase sigma 21.3 94 0.002 25.9 2.9 29 111-139 129-157 (182)
213 PRK12523 RNA polymerase sigma 21.2 80 0.0017 25.7 2.4 29 111-139 137-165 (172)
214 TIGR03001 Sig-70_gmx1 RNA poly 20.8 1.2E+02 0.0025 26.8 3.6 32 111-142 179-210 (244)
215 PRK12540 RNA polymerase sigma 20.6 90 0.0019 25.9 2.7 31 110-140 128-158 (182)
216 PRK11552 putative DNA-binding 20.6 67 0.0014 27.7 1.9 41 96-138 21-61 (225)
217 PRK12516 RNA polymerase sigma 20.1 86 0.0019 26.2 2.4 30 111-140 134-163 (187)
218 PRK09935 transcriptional regul 20.0 79 0.0017 25.6 2.2 45 88-138 149-193 (210)
No 1
>KOG0484|consensus
Probab=99.82 E-value=1.1e-20 Score=143.27 Aligned_cols=75 Identities=27% Similarity=0.479 Sum_probs=66.8
Q ss_pred CCCCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHHHHHHhhHhhh
Q psy4078 79 DGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALAMKQQLQQEKD 153 (269)
Q Consensus 79 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~~~~~~q~~~~ 153 (269)
++|.||.||+||..||..||+.|.+.+||++-.|++||.++.|++.+|||||||||+|.||+++...-.+....+
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~~~~~~~ 88 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAKMAAKSS 88 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHHhhhhcc
Confidence 456789999999999999999999999999999999999999999999999999999999999865544444433
No 2
>KOG0488|consensus
Probab=99.72 E-value=1.8e-18 Score=158.32 Aligned_cols=67 Identities=22% Similarity=0.345 Sum_probs=63.0
Q ss_pred CCCCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHHHH
Q psy4078 79 DGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALAMK 145 (269)
Q Consensus 79 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~~~ 145 (269)
.+|+|+.||.||..||..||+.|++.+|.+..+|.+||+.|||+..||++||||||+||||+.....
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~ 235 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGG 235 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhh
Confidence 4677889999999999999999999999999999999999999999999999999999999987633
No 3
>KOG0489|consensus
Probab=99.72 E-value=1.6e-18 Score=155.68 Aligned_cols=64 Identities=34% Similarity=0.469 Sum_probs=60.8
Q ss_pred CCCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHH
Q psy4078 80 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALA 143 (269)
Q Consensus 80 ~k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~ 143 (269)
.+.||.||.||..|+.+||+.|..|+|.++..|.+||..|.|+|+||+|||||||+||||.++.
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~ 220 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKA 220 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcc
Confidence 4578999999999999999999999999999999999999999999999999999999998754
No 4
>KOG2251|consensus
Probab=99.72 E-value=1.8e-18 Score=147.95 Aligned_cols=68 Identities=32% Similarity=0.563 Sum_probs=63.6
Q ss_pred CCCCCCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHHH
Q psy4078 77 GGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALAM 144 (269)
Q Consensus 77 ~~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~~ 144 (269)
...+|.||+||+|+..|+.+||..|.+..||+...||+||.+|+|.+.+|+|||+|||+|+|+++...
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 44567889999999999999999999999999999999999999999999999999999999987653
No 5
>KOG0850|consensus
Probab=99.70 E-value=9.1e-18 Score=144.28 Aligned_cols=75 Identities=24% Similarity=0.325 Sum_probs=67.4
Q ss_pred ccccccccCCCCCCCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHH
Q psy4078 68 FLGRVRKVSGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRAL 142 (269)
Q Consensus 68 s~~~i~~~~~~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~ 142 (269)
.|..++.-.++.+|.|+.||.|+.-||..|.+.|++++|+-..+|.+||..|||+..||+|||||||.|.||...
T Consensus 108 ~E~~e~~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 108 PEPSERRPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cCcceeccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 344445556677788899999999999999999999999999999999999999999999999999999999864
No 6
>KOG0843|consensus
Probab=99.69 E-value=1.5e-17 Score=137.99 Aligned_cols=63 Identities=32% Similarity=0.548 Sum_probs=60.5
Q ss_pred CCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHH
Q psy4078 81 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALA 143 (269)
Q Consensus 81 k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~ 143 (269)
+.||.||.|+.+||..||.+|+.++|-...+|++||+.|+|++.||+|||||||.|.||++.+
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 778999999999999999999999999999999999999999999999999999999998754
No 7
>KOG0494|consensus
Probab=99.68 E-value=1.4e-17 Score=145.17 Aligned_cols=63 Identities=33% Similarity=0.537 Sum_probs=58.7
Q ss_pred CCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHH
Q psy4078 81 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALA 143 (269)
Q Consensus 81 k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~ 143 (269)
|+|+.||.||..|+..||+.|.+.+||+...|+.||.++.|.|.+|+|||||||+||||.+..
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence 334459999999999999999999999999999999999999999999999999999999865
No 8
>KOG0848|consensus
Probab=99.67 E-value=3e-17 Score=143.63 Aligned_cols=68 Identities=24% Similarity=0.392 Sum_probs=62.3
Q ss_pred CCCCCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHHHH
Q psy4078 78 GDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALAMK 145 (269)
Q Consensus 78 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~~~ 145 (269)
+.+.+-+.|.++|..|+.+||+.|..++|+++..+.+||..|||+|+||+|||||||||+||..++..
T Consensus 195 KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 195 KTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred eeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 44455678999999999999999999999999999999999999999999999999999999987653
No 9
>KOG0842|consensus
Probab=99.67 E-value=2.4e-17 Score=149.08 Aligned_cols=65 Identities=25% Similarity=0.459 Sum_probs=61.0
Q ss_pred CCCCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHH
Q psy4078 79 DGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALA 143 (269)
Q Consensus 79 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~ 143 (269)
..++||.|..|+..|+.+||+.|..++|.+..|||.||..|+|++.||||||||||-|+||+++.
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~d 214 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKD 214 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhh
Confidence 45667788999999999999999999999999999999999999999999999999999998764
No 10
>KOG0492|consensus
Probab=99.66 E-value=7.9e-17 Score=136.42 Aligned_cols=66 Identities=21% Similarity=0.360 Sum_probs=61.5
Q ss_pred CccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHHHHHH
Q psy4078 82 PTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALAMKQQ 147 (269)
Q Consensus 82 ~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~~~~~ 147 (269)
.|+.||.||..||..||+.|.+.+|.++.+|.+++..|.|++.||+|||||||+|.||.++++.+.
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~Ek 209 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELEK 209 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHHH
Confidence 467899999999999999999999999999999999999999999999999999999998765544
No 11
>KOG0487|consensus
Probab=99.65 E-value=2.3e-17 Score=149.21 Aligned_cols=66 Identities=24% Similarity=0.331 Sum_probs=61.3
Q ss_pred CCCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHHHH
Q psy4078 80 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALAMK 145 (269)
Q Consensus 80 ~k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~~~ 145 (269)
+..||+|.-+|+.|+.+||+.|-.|.|++.+.|.+|++.|+|+++||+|||||||.|+||..++.+
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence 456778899999999999999999999999999999999999999999999999999999986533
No 12
>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=99.64 E-value=8.4e-17 Score=111.47 Aligned_cols=57 Identities=37% Similarity=0.644 Sum_probs=55.0
Q ss_pred ccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 83 TRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 83 rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
||.|+.|+.+|+.+|+.+|..++||+..+++.||..|||+..+|++||+|||+++||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 467899999999999999999999999999999999999999999999999999986
No 13
>KOG0485|consensus
Probab=99.61 E-value=5.9e-16 Score=131.93 Aligned_cols=67 Identities=25% Similarity=0.445 Sum_probs=62.2
Q ss_pred CCCCCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHHH
Q psy4078 78 GDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALAM 144 (269)
Q Consensus 78 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~~ 144 (269)
.+.++||.||+|+..|+..||..|+..+|.+..+|..||+.|.|+|.||+|||||||.||||+....
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad 166 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAAD 166 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhh
Confidence 4456778999999999999999999999999999999999999999999999999999999987653
No 14
>KOG0486|consensus
Probab=99.61 E-value=1.5e-15 Score=135.83 Aligned_cols=77 Identities=32% Similarity=0.512 Sum_probs=66.5
Q ss_pred CCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHHHHHHhhHhhhcCCCCC
Q psy4078 81 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALAMKQQLQQEKDGRKMGY 159 (269)
Q Consensus 81 k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~~~~~~q~~~~g~~~~~ 159 (269)
|+||.||.|+..|+..||..|++|.||+...||+||.-++|++.+|+|||+|||+||||+++-.. .+..+.++...+
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~--ae~~k~~f~~~~ 187 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ--AELAKGGFGPQF 187 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH--HHhhhcCCcccc
Confidence 67889999999999999999999999999999999999999999999999999999999987533 334444444333
No 15
>KOG0493|consensus
Probab=99.59 E-value=4.6e-16 Score=135.82 Aligned_cols=61 Identities=31% Similarity=0.503 Sum_probs=57.7
Q ss_pred CCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHH
Q psy4078 81 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRA 141 (269)
Q Consensus 81 k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~ 141 (269)
.-||.||.||.+||..|+..|++|+|.+...|.+||.+|+|+|.||+|||||+|+|.||..
T Consensus 245 eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 245 EEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred hhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 3468999999999999999999999999999999999999999999999999999999763
No 16
>KOG4577|consensus
Probab=99.55 E-value=3.4e-14 Score=125.78 Aligned_cols=66 Identities=44% Similarity=0.747 Sum_probs=61.4
Q ss_pred CCCCCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHH
Q psy4078 78 GDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALA 143 (269)
Q Consensus 78 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~ 143 (269)
.+...||.||++|..||+.|+.+|+..+.|-...||+|+.++||.-++|||||||||||+||-++.
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence 345567999999999999999999999999999999999999999999999999999999988754
No 17
>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=99.54 E-value=2.5e-15 Score=104.26 Aligned_cols=52 Identities=19% Similarity=0.318 Sum_probs=50.4
Q ss_pred ccceeecchhhhhhhhhhcccCCC----CChHHHHHHHHHhCCCchhhhhhhcchh
Q psy4078 83 TRVRTVLNEKQLHTLRTCYNANPR----PDALMKEQLVEMTNLSPRVIRVWFQNKR 134 (269)
Q Consensus 83 rr~Rt~~t~~Ql~~Le~~F~~~~~----p~~~~r~~La~~lgL~~~~V~vWFqNRR 134 (269)
||.||.||.+|+..|+.+|+.++| |+..++++||..|||++++|+|||||.+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 688999999999999999999999 9999999999999999999999999965
No 18
>KOG0844|consensus
Probab=99.52 E-value=1.8e-15 Score=134.62 Aligned_cols=68 Identities=32% Similarity=0.495 Sum_probs=63.3
Q ss_pred CCCCCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHHHH
Q psy4078 78 GDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALAMK 145 (269)
Q Consensus 78 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~~~ 145 (269)
.+...||.||.||.+|+..||+.|-+..|-+...|.+||..|+|+|..|+|||||||+|+||+...+.
T Consensus 177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlama 244 (408)
T KOG0844|consen 177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMA 244 (408)
T ss_pred ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhcc
Confidence 34567899999999999999999999999999999999999999999999999999999999987753
No 19
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.51 E-value=2.6e-14 Score=118.57 Aligned_cols=69 Identities=30% Similarity=0.608 Sum_probs=62.5
Q ss_pred cCCCCCCCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHH
Q psy4078 75 VSGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALA 143 (269)
Q Consensus 75 ~~~~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~ 143 (269)
........++.|++.+.+|+.+|++.|+.++||+..+|.+|+..|+|+++.|+|||||||++.|+....
T Consensus 44 ~~~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 44 KQDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred cccCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 445555677888999999999999999999999999999999999999999999999999999988654
No 20
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.50 E-value=8.6e-15 Score=100.69 Aligned_cols=55 Identities=40% Similarity=0.627 Sum_probs=52.0
Q ss_pred cceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHH
Q psy4078 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDK 138 (269)
Q Consensus 84 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~k 138 (269)
+.|+.|+.+|+.+|+.+|..++||+..+++.||..+||+..+|++||+|||++.|
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 4677899999999999999999999999999999999999999999999998864
No 21
>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=99.50 E-value=1.3e-14 Score=100.67 Aligned_cols=57 Identities=35% Similarity=0.619 Sum_probs=53.9
Q ss_pred cceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 84 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
+.|..|+.+|+.+|+.+|..++||+..+++.||.++||+..+|++||+|||++.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 467889999999999999999999999999999999999999999999999998864
No 22
>KOG0490|consensus
Probab=99.50 E-value=2.4e-14 Score=125.52 Aligned_cols=117 Identities=36% Similarity=0.411 Sum_probs=105.2
Q ss_pred CCCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCC--------------------------
Q psy4078 26 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGD-------------------------- 79 (269)
Q Consensus 26 ~~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~-------------------------- 79 (269)
.+.+|.|+.|+..|++.|+..|..++||++..+++++..+++.+.+|+.|+...
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~~~~~~~~~~~ 137 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGENLPDLSGTAPP 137 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhccccccccCCCCCCCCCc
Confidence 467899999999999999999999999999999999999999999996654221
Q ss_pred -------------CCCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHH
Q psy4078 80 -------------GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRAL 142 (269)
Q Consensus 80 -------------~k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~ 142 (269)
.+.++.|+.+...|+..|+..|..+++|+...++.|+..+|+++..|++||+|+|++.++...
T Consensus 138 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 138 SASRDKLDKGPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cccccccccCCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 233456789999999999999999999999999999999999999999999999999998753
No 23
>KOG0491|consensus
Probab=99.48 E-value=1.3e-14 Score=118.88 Aligned_cols=61 Identities=28% Similarity=0.471 Sum_probs=57.9
Q ss_pred CccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHH
Q psy4078 82 PTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRAL 142 (269)
Q Consensus 82 ~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~ 142 (269)
+++.||+|+..|+..|++.|+..+|.+..+|.+||..|+|++.||+.||||||+|.||..+
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r 160 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQR 160 (194)
T ss_pred hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHh
Confidence 4567999999999999999999999999999999999999999999999999999999865
No 24
>KOG0483|consensus
Probab=99.47 E-value=2.2e-14 Score=123.01 Aligned_cols=60 Identities=27% Similarity=0.499 Sum_probs=56.1
Q ss_pred cceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHH
Q psy4078 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALA 143 (269)
Q Consensus 84 r~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~ 143 (269)
+++.+|+.+|+..||+.|+.+.+.....+..||.+|||.++||.|||||||||||.++.+
T Consensus 52 ~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE 111 (198)
T KOG0483|consen 52 GKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLE 111 (198)
T ss_pred cccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence 445579999999999999999999999999999999999999999999999999988865
No 25
>KOG3802|consensus
Probab=99.44 E-value=2.4e-14 Score=132.25 Aligned_cols=61 Identities=28% Similarity=0.498 Sum_probs=58.4
Q ss_pred CCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHH
Q psy4078 81 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRA 141 (269)
Q Consensus 81 k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~ 141 (269)
++||+||.|....+.+||++|.+|+.|+..++-.||++|+|...+|+|||+|||.|.||..
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 6778999999999999999999999999999999999999999999999999999999864
No 26
>KOG0847|consensus
Probab=99.33 E-value=4.7e-13 Score=114.44 Aligned_cols=66 Identities=24% Similarity=0.403 Sum_probs=60.9
Q ss_pred CCCCCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHH
Q psy4078 78 GDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALA 143 (269)
Q Consensus 78 ~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~ 143 (269)
.+++++..|.+|+-.|+..||+.|+..+|+-..+|.+||..+|+++.+|+|||||||.||||+...
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa 228 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA 228 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence 455666778899999999999999999999999999999999999999999999999999998754
No 27
>KOG0490|consensus
Probab=99.28 E-value=1.1e-12 Score=114.84 Aligned_cols=64 Identities=25% Similarity=0.313 Sum_probs=60.8
Q ss_pred CCCCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHH
Q psy4078 79 DGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRAL 142 (269)
Q Consensus 79 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~ 142 (269)
..++++.|+.|+..|+.+|+++|++++||+...++.||..+++++..|+|||||||+||++++.
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 4567889999999999999999999999999999999999999999999999999999999874
No 28
>KOG0849|consensus
Probab=99.14 E-value=2.3e-11 Score=113.66 Aligned_cols=67 Identities=31% Similarity=0.537 Sum_probs=61.9
Q ss_pred CCCCCCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHH
Q psy4078 77 GGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALA 143 (269)
Q Consensus 77 ~~~~k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~ 143 (269)
..+++.+|.||+|+..|+..|++.|+.++||++..|++||.+++|++.+|+|||+|||+|++|....
T Consensus 171 ~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 171 ALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred cccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 3455667889999999999999999999999999999999999999999999999999999999753
No 29
>KOG1168|consensus
Probab=99.02 E-value=1.2e-10 Score=103.58 Aligned_cols=63 Identities=30% Similarity=0.536 Sum_probs=58.6
Q ss_pred CCCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHH
Q psy4078 80 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRAL 142 (269)
Q Consensus 80 ~k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~ 142 (269)
..+||+||.+.....+.||.+|...+.|+.+.+..||++|+|...+|+|||+|.|.|.||...
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence 356789999999999999999999999999999999999999999999999999999988643
No 30
>KOG0775|consensus
Probab=98.84 E-value=1.7e-09 Score=95.57 Aligned_cols=52 Identities=35% Similarity=0.580 Sum_probs=47.9
Q ss_pred ecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 88 VLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 88 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
+|.+.-..+|.++|..++||+..++.+||+.+||+..||-+||+|||.|+|-
T Consensus 182 CFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 182 CFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred ehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 3556667899999999999999999999999999999999999999999993
No 31
>KOG2251|consensus
Probab=98.81 E-value=2.7e-09 Score=91.90 Aligned_cols=64 Identities=30% Similarity=0.354 Sum_probs=58.9
Q ss_pred CCCCCCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCCCccce
Q psy4078 23 GGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGKPTRVR 86 (269)
Q Consensus 23 ~~~~~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k~rr~R 86 (269)
...++.||.||.||..|+++|+..|++..|||+.+||+||.+++|.+.+|+.|+.+++.++|.+
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~q 95 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQ 95 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHh
Confidence 5567899999999999999999999999999999999999999999999999998877766553
No 32
>KOG0774|consensus
Probab=98.74 E-value=2.3e-08 Score=87.97 Aligned_cols=62 Identities=27% Similarity=0.439 Sum_probs=56.8
Q ss_pred Cccceeecchhhhhhhhhhcc---cCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHH
Q psy4078 82 PTRVRTVLNEKQLHTLRTCYN---ANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALA 143 (269)
Q Consensus 82 ~rr~Rt~~t~~Ql~~Le~~F~---~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~ 143 (269)
.+|+|..|++.-..+|..+|. .|+||+...+++||.++|++..||-.||.|+|-+.||..-.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k 252 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGK 252 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhh
Confidence 357788999999999999995 68999999999999999999999999999999999988654
No 33
>KOG0484|consensus
Probab=98.64 E-value=3.1e-09 Score=81.12 Aligned_cols=55 Identities=24% Similarity=0.318 Sum_probs=51.6
Q ss_pred CCCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCC
Q psy4078 26 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDG 80 (269)
Q Consensus 26 ~~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~ 80 (269)
++.||.||.||..||+.|+..|...+||++-+||+|+..++|.+.+|+.|+.+++
T Consensus 15 rKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRR 69 (125)
T KOG0484|consen 15 RKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRR 69 (125)
T ss_pred HHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhH
Confidence 5789999999999999999999999999999999999999999999999987643
No 34
>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=98.62 E-value=4e-08 Score=68.22 Aligned_cols=51 Identities=12% Similarity=0.016 Sum_probs=47.9
Q ss_pred CcccccCCHHHHHHHHHhhCCCCC----CChhhHHHHHHhhhcccccccccCCCC
Q psy4078 29 TRVRTVLNEKQLHTLRTCYNANPR----PDALMKEQLVEMTNLFLGRVRKVSGGD 79 (269)
Q Consensus 29 ~r~Rt~~t~~Ql~~L~~~F~~n~~----P~~~~re~La~~~gls~~~i~~~~~~~ 79 (269)
+|.||.||.+|++.|+..|..+.| |+..++++|+..+|+++.+|+.|..+.
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~ 56 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNN 56 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccC
Confidence 689999999999999999999999 999999999999999999998877653
No 35
>KOG0494|consensus
Probab=98.52 E-value=6.8e-08 Score=84.96 Aligned_cols=57 Identities=23% Similarity=0.283 Sum_probs=51.8
Q ss_pred CcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCCCccc
Q psy4078 29 TRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGKPTRV 85 (269)
Q Consensus 29 ~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k~rr~ 85 (269)
|+.||+||..|++.|++.|+.-.|||+..||.|+..+.|.|++|+.|+.+++.+.|+
T Consensus 142 Rh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk 198 (332)
T KOG0494|consen 142 RHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRK 198 (332)
T ss_pred ccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhh
Confidence 344999999999999999999999999999999999999999999999887666554
No 36
>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=98.46 E-value=1e-07 Score=61.36 Aligned_cols=34 Identities=41% Similarity=0.622 Sum_probs=29.0
Q ss_pred cCCCCChHHHHHHHHHhCCCchhhhhhhcchhhh
Q psy4078 103 ANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCK 136 (269)
Q Consensus 103 ~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak 136 (269)
.++||+..+++.||.++||+..||..||-|.|.|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4799999999999999999999999999999865
No 37
>KOG0486|consensus
Probab=98.44 E-value=1.2e-07 Score=85.44 Aligned_cols=62 Identities=31% Similarity=0.332 Sum_probs=57.9
Q ss_pred CCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCCCccceee
Q psy4078 27 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGKPTRVRTV 88 (269)
Q Consensus 27 ~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k~rr~Rt~ 88 (269)
|.||.||-||..||+.||..|.+|.||+..+||+|+.-+++.|.+|+.|...++.+.|+|.+
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrEr 172 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRER 172 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhh
Confidence 78899999999999999999999999999999999999999999999999988887777653
No 38
>KOG2252|consensus
Probab=98.36 E-value=3.4e-07 Score=88.20 Aligned_cols=59 Identities=25% Similarity=0.372 Sum_probs=54.9
Q ss_pred CCCCccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhH
Q psy4078 79 DGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKD 137 (269)
Q Consensus 79 ~~k~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~ 137 (269)
.-..||.|.+||..|++.|..+|+.+++|+.++.+.|+.+|||....|.+||-|-|.|.
T Consensus 417 ~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 417 MLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 34567889999999999999999999999999999999999999999999999988775
No 39
>KOG0843|consensus
Probab=98.35 E-value=2.1e-07 Score=77.92 Aligned_cols=55 Identities=22% Similarity=0.279 Sum_probs=52.2
Q ss_pred CCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCC
Q psy4078 27 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGK 81 (269)
Q Consensus 27 ~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k 81 (269)
+.||.||+|+.+||..|+.+|+.|.|-...+|++||..++|++.+|+.|+.+++.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRt 155 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRT 155 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhH
Confidence 7899999999999999999999999999999999999999999999999987543
No 40
>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=98.35 E-value=1.4e-07 Score=64.87 Aligned_cols=50 Identities=26% Similarity=0.357 Sum_probs=46.3
Q ss_pred CcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCC
Q psy4078 29 TRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGG 78 (269)
Q Consensus 29 ~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~ 78 (269)
||.|+.||.+|+.+|+.+|..++||+..+++.|+..+|++..+|..|+..
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~n 50 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQN 50 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHH
Confidence 57889999999999999999999999999999999999999999777643
No 41
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=98.28 E-value=3.5e-07 Score=62.46 Aligned_cols=50 Identities=26% Similarity=0.304 Sum_probs=46.1
Q ss_pred cccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCC
Q psy4078 30 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGD 79 (269)
Q Consensus 30 r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~ 79 (269)
+.|+.|+.+|+.+|++.|..++||+..++++|+..+|++..+|..+....
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nr 51 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNR 51 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHH
Confidence 56788999999999999999999999999999999999999998877654
No 42
>KOG0488|consensus
Probab=98.20 E-value=8e-07 Score=81.77 Aligned_cols=58 Identities=16% Similarity=0.124 Sum_probs=53.8
Q ss_pred CCCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCCCc
Q psy4078 26 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGKPT 83 (269)
Q Consensus 26 ~~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k~r 83 (269)
+|.|+.||+||+.||..||..|.+..|.+..+|.+||..+||++.+|..|+.+++.|.
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKW 227 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKW 227 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHH
Confidence 5788999999999999999999999999999999999999999999999998865444
No 43
>KOG0493|consensus
Probab=98.17 E-value=1e-06 Score=77.78 Aligned_cols=67 Identities=15% Similarity=0.173 Sum_probs=57.2
Q ss_pred CCCCCCCCCCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCCCccc
Q psy4078 19 GKVSGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGKPTRV 85 (269)
Q Consensus 19 ~~~~~~~~~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k~rr~ 85 (269)
++-.+..+..||+||.||.+||+.|+..|..|.|.....|.+|+.++||.|.+|+.|+.+++.+-++
T Consensus 237 kkkk~~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKK 303 (342)
T KOG0493|consen 237 KKKKSSSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKK 303 (342)
T ss_pred cccCCccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhh
Confidence 3444445567899999999999999999999999999999999999999999999999876554333
No 44
>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=98.11 E-value=7.3e-07 Score=61.30 Aligned_cols=50 Identities=26% Similarity=0.304 Sum_probs=46.0
Q ss_pred cccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCC
Q psy4078 30 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGD 79 (269)
Q Consensus 30 r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~ 79 (269)
+.|+.|+.+|+.+|++.|..++||+..++++|+..+|++..+|..++...
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nr 51 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNR 51 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHH
Confidence 46788999999999999999999999999999999999999998877653
No 45
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.10 E-value=1.5e-06 Score=72.37 Aligned_cols=100 Identities=18% Similarity=0.236 Sum_probs=78.0
Q ss_pred CCCCCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCCCccceeecchhhhhhhhhhccc
Q psy4078 24 GDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGKPTRVRTVLNEKQLHTLRTCYNA 103 (269)
Q Consensus 24 ~~~~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k~rr~Rt~~t~~Ql~~Le~~F~~ 103 (269)
.++..++.|++.|.+|+.+|+..|..++||+..+|..|+..+++++.-|+.|+.+++.+ ..+...+..
T Consensus 47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~------------~k~~~~~~~ 114 (156)
T COG5576 47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAK------------EKKKRSGKV 114 (156)
T ss_pred CCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHH------------HHHhcccch
Confidence 34467788889999999999999999999999999999999999999999988764332 233444444
Q ss_pred CCCCChHHHHHHHHHhCCCchhhhhhhcchhhh
Q psy4078 104 NPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCK 136 (269)
Q Consensus 104 ~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak 136 (269)
..++.. +-..++....+.-..+-+||.+...+
T Consensus 115 ~~~~~~-e~~~~~~~~~~~~~~~~~~~~~~~s~ 146 (156)
T COG5576 115 EQRPGE-EEADLAKIGSLSTGQISIIETLEFSR 146 (156)
T ss_pred hccccc-ccccccccccccccchhhHHhhhccc
Confidence 555555 44556777778888888998776655
No 46
>KOG0842|consensus
Probab=97.96 E-value=1e-05 Score=73.87 Aligned_cols=61 Identities=18% Similarity=0.157 Sum_probs=55.4
Q ss_pred CCCCCCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCCCc
Q psy4078 23 GGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGKPT 83 (269)
Q Consensus 23 ~~~~~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k~r 83 (269)
+...+.||.|..|+..|+-+||+.|..+.|.+.-+||.||..+.|++-+|+.|+.+++-|.
T Consensus 148 t~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~ 208 (307)
T KOG0842|consen 148 TGKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKT 208 (307)
T ss_pred cccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhh
Confidence 3345778899999999999999999999999999999999999999999999999877654
No 47
>KOG0485|consensus
Probab=97.92 E-value=6.1e-06 Score=71.11 Aligned_cols=60 Identities=17% Similarity=0.192 Sum_probs=54.3
Q ss_pred CCCCCCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCCC
Q psy4078 23 GGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGKP 82 (269)
Q Consensus 23 ~~~~~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k~ 82 (269)
.++.++||.||||+..|+..||..|+...|.+..+|.-|++.+.|.|-+|+.|+.+++.+
T Consensus 99 ~g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnK 158 (268)
T KOG0485|consen 99 LGDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNK 158 (268)
T ss_pred ccccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHH
Confidence 355678889999999999999999999999999999999999999999999998875443
No 48
>KOG0844|consensus
Probab=97.76 E-value=1.5e-05 Score=71.82 Aligned_cols=59 Identities=15% Similarity=0.114 Sum_probs=54.2
Q ss_pred CCCCCCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCC
Q psy4078 23 GGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGK 81 (269)
Q Consensus 23 ~~~~~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k 81 (269)
+++..-||-||.||.+|+..|++.|.+..|-+.-.|.+|+..++|.|..|+.|+.+++-
T Consensus 176 sa~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRM 234 (408)
T KOG0844|consen 176 SADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRM 234 (408)
T ss_pred CccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchh
Confidence 45567799999999999999999999999999999999999999999999999987654
No 49
>KOG0849|consensus
Probab=97.69 E-value=3.8e-05 Score=72.07 Aligned_cols=61 Identities=26% Similarity=0.294 Sum_probs=54.0
Q ss_pred CCCCCCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCCCc
Q psy4078 23 GGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGKPT 83 (269)
Q Consensus 23 ~~~~~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k~r 83 (269)
...++.+|.||+|+.+|++.|+.+|..++||++..||+|+..+++.+.+|..|....+.+.
T Consensus 171 ~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~ 231 (354)
T KOG0849|consen 171 ALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKW 231 (354)
T ss_pred cccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhh
Confidence 3445677889999999999999999999999999999999999999999998887765543
No 50
>KOG0489|consensus
Probab=97.69 E-value=6.6e-06 Score=74.12 Aligned_cols=60 Identities=18% Similarity=0.137 Sum_probs=54.4
Q ss_pred CCCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCCCccc
Q psy4078 26 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGKPTRV 85 (269)
Q Consensus 26 ~~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k~rr~ 85 (269)
++.||.||.||..|+-.||+.|..|.|..+..|.+|+..+.|+|.+|+.|+.+++-+.++
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk 216 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKK 216 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHH
Confidence 467999999999999999999999999999999999999999999999999876555443
No 51
>KOG1146|consensus
Probab=97.64 E-value=3.5e-05 Score=80.89 Aligned_cols=61 Identities=41% Similarity=0.595 Sum_probs=57.6
Q ss_pred CccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHH
Q psy4078 82 PTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRAL 142 (269)
Q Consensus 82 ~rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~ 142 (269)
.++.|+.++..||.+|..+|+...||...+.|.|...+++..++|+|||||-|+|.||...
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 4678999999999999999999999999999999999999999999999999999998765
No 52
>KOG0492|consensus
Probab=97.63 E-value=3.7e-05 Score=65.92 Aligned_cols=56 Identities=13% Similarity=0.074 Sum_probs=51.8
Q ss_pred CCCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCC
Q psy4078 26 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGK 81 (269)
Q Consensus 26 ~~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k 81 (269)
+.+|++||-||.+||-.|++.|....|.++.+|-+++.-+.|.+-+|+.|+.+++.
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRA 197 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRA 197 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhH
Confidence 36788999999999999999999999999999999999999999999999987544
No 53
>KOG0850|consensus
Probab=97.61 E-value=3.3e-05 Score=67.24 Aligned_cols=61 Identities=16% Similarity=0.153 Sum_probs=54.5
Q ss_pred CCCCCCCCCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCC
Q psy4078 20 KVSGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDG 80 (269)
Q Consensus 20 ~~~~~~~~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~ 80 (269)
++..+-+|-|++||.|+..||..|.+.|.+..|.-.-+|-+|+..+||+..+|+.|+.+++
T Consensus 114 ~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrR 174 (245)
T KOG0850|consen 114 RPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRR 174 (245)
T ss_pred ccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhH
Confidence 3445556778999999999999999999999999999999999999999999999988643
No 54
>KOG4577|consensus
Probab=97.42 E-value=8.5e-05 Score=66.62 Aligned_cols=58 Identities=34% Similarity=0.473 Sum_probs=52.8
Q ss_pred CCCCCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCC
Q psy4078 24 GDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGK 81 (269)
Q Consensus 24 ~~~~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k 81 (269)
++..+||+||++|.-||++|+.+|+..+-|-.-.||+|+.++||.-+.|+.|+.+++.
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRA 220 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRA 220 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhH
Confidence 3557899999999999999999999999999999999999999999999999876543
No 55
>KOG0487|consensus
Probab=97.33 E-value=7.3e-05 Score=68.33 Aligned_cols=58 Identities=14% Similarity=0.001 Sum_probs=53.2
Q ss_pred CCCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCCCc
Q psy4078 26 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGKPT 83 (269)
Q Consensus 26 ~~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k~r 83 (269)
+..|++|.-+|..|+..||+.|..|-|...+.|-+|++.++|+++||+.|+.+++-+.
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~ 290 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKE 290 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHH
Confidence 4678899999999999999999999999999999999999999999999998765443
No 56
>KOG3802|consensus
Probab=97.20 E-value=0.00034 Score=65.59 Aligned_cols=57 Identities=18% Similarity=0.171 Sum_probs=53.3
Q ss_pred CCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCCCc
Q psy4078 27 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGKPT 83 (269)
Q Consensus 27 ~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k~r 83 (269)
++||+||.|+...+.+|++.|.+|+-|+..+-..||+.+++..+.||.|+.+++.+-
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQke 349 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKE 349 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeecccccc
Confidence 678899999999999999999999999999999999999999999999999876643
No 57
>KOG0848|consensus
Probab=97.14 E-value=0.00019 Score=63.87 Aligned_cols=57 Identities=14% Similarity=0.077 Sum_probs=50.9
Q ss_pred CCCCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCC
Q psy4078 25 DGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGK 81 (269)
Q Consensus 25 ~~~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k 81 (269)
-+.+-+-|.|+|+.|.=+||+.|..+.|..+..+.+|+..+||+|++|+.|+.+++.
T Consensus 196 tRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRA 252 (317)
T KOG0848|consen 196 TRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRA 252 (317)
T ss_pred eecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhH
Confidence 334456899999999999999999999999999999999999999999998887544
No 58
>KOG2252|consensus
Probab=96.96 E-value=0.00044 Score=67.11 Aligned_cols=59 Identities=24% Similarity=0.269 Sum_probs=52.0
Q ss_pred CCCCCCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCC
Q psy4078 23 GGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGK 81 (269)
Q Consensus 23 ~~~~~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k 81 (269)
...-..||+|.|||+.|+.+|...|..+++|+.++.+.|+..++|...-|.+++-+.++
T Consensus 415 d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRR 473 (558)
T KOG2252|consen 415 DKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARR 473 (558)
T ss_pred cccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhh
Confidence 34456788999999999999999999999999999999999999999999887765433
No 59
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.91 E-value=0.00046 Score=47.38 Aligned_cols=41 Identities=17% Similarity=0.378 Sum_probs=31.0
Q ss_pred hhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchh
Q psy4078 94 LHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKR 134 (269)
Q Consensus 94 l~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRR 134 (269)
+..|+++|...+++...+...|+.+.+|+..+|+.||-.|+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 45699999999999999999999999999999999996554
No 60
>KOG0483|consensus
Probab=96.28 E-value=0.0031 Score=54.52 Aligned_cols=52 Identities=13% Similarity=0.123 Sum_probs=47.1
Q ss_pred cccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCC
Q psy4078 30 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGK 81 (269)
Q Consensus 30 r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k 81 (269)
+++.+|+.+|+..|+..|..+.+-.-..+..||+.+||.+.+|..|+.+++.
T Consensus 52 ~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRA 103 (198)
T KOG0483|consen 52 GKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRA 103 (198)
T ss_pred cccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccc
Confidence 4445699999999999999999999999999999999999999999987544
No 61
>KOG0491|consensus
Probab=96.01 E-value=0.00062 Score=56.53 Aligned_cols=54 Identities=17% Similarity=0.207 Sum_probs=48.3
Q ss_pred CCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCC
Q psy4078 27 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDG 80 (269)
Q Consensus 27 ~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~ 80 (269)
+.++-||||++.|+..|++.|+...|.+..++.+|+..++|++.+|+.|+.+++
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrR 152 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRR 152 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence 345678999999999999999999999999999999999999999987776543
No 62
>KOG1168|consensus
Probab=95.88 E-value=0.0035 Score=56.52 Aligned_cols=56 Identities=20% Similarity=0.247 Sum_probs=51.6
Q ss_pred CCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCCC
Q psy4078 27 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGKP 82 (269)
Q Consensus 27 ~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k~ 82 (269)
..||+||.+-.-++..|+++|..++.|+.+.--.++++++|..+.||.|+.+.+.+
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQK 363 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQK 363 (385)
T ss_pred ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHH
Confidence 46789999999999999999999999999999999999999999999999886554
No 63
>KOG0773|consensus
Probab=95.83 E-value=0.0035 Score=58.49 Aligned_cols=61 Identities=26% Similarity=0.292 Sum_probs=50.0
Q ss_pred Cccceeecchhhhhhhhhhcc---cCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHH
Q psy4078 82 PTRVRTVLNEKQLHTLRTCYN---ANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRAL 142 (269)
Q Consensus 82 ~rr~Rt~~t~~Ql~~Le~~F~---~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~ 142 (269)
.+|.+..|......+|+.+.. ..+||+..++..||.++||+..||.+||-|.|.|..+-..
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence 345556788888888887633 3589999999999999999999999999999988766544
No 64
>KOG0847|consensus
Probab=95.51 E-value=0.0047 Score=53.65 Aligned_cols=65 Identities=14% Similarity=0.130 Sum_probs=58.0
Q ss_pred CCCCCCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCCCccceee
Q psy4078 24 GDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGKPTRVRTV 88 (269)
Q Consensus 24 ~~~~~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k~rr~Rt~ 88 (269)
.+++.+-.|-+|+-.|+..|+..|+...|+-..+|-+++...|+++.+|..|+.+++.+.|++..
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 45566667788999999999999999999999999999999999999999999988887777653
No 65
>KOG3623|consensus
Probab=95.50 E-value=0.0072 Score=60.64 Aligned_cols=103 Identities=17% Similarity=0.289 Sum_probs=80.4
Q ss_pred HHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccC----------------CCCCCCccceeecchhhhhhhhhhccc
Q psy4078 40 LHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVS----------------GGDGKPTRVRTVLNEKQLHTLRTCYNA 103 (269)
Q Consensus 40 l~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~----------------~~~~k~rr~Rt~~t~~Ql~~Le~~F~~ 103 (269)
+..|+++|..|..|...+...++..+|++...|..|+ .....+.+.|+....++-..|..+|+.
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps~psg~~p~kv~sp~k~~dq~ql~~a~el 647 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPSQPSGERPVKVRSPIKEEDQQQLKQAYEL 647 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCccCCCCCCCccccCCCCccchhhhHhhhhc
Confidence 7789999999999999999999999999988885543 122333456677777777788888887
Q ss_pred CCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHH
Q psy4078 104 NPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRAL 142 (269)
Q Consensus 104 ~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~ 142 (269)
+-.+...+-..++.++-..+.+|.+||++|+..-+....
T Consensus 648 q~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl 686 (1007)
T KOG3623|consen 648 QASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPL 686 (1007)
T ss_pred ccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCcc
Confidence 766666555555666778889999999999998876643
No 66
>KOG3623|consensus
Probab=95.28 E-value=0.013 Score=58.90 Aligned_cols=49 Identities=16% Similarity=0.356 Sum_probs=45.3
Q ss_pred hhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHH
Q psy4078 94 LHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRAL 142 (269)
Q Consensus 94 l~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~ 142 (269)
+.+|..+|..|..|+..+...+|.+.||+.+.|+.||++++++....++
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~r 616 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVER 616 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhcc
Confidence 5678889999999999999999999999999999999999999887764
No 67
>KOG0774|consensus
Probab=94.90 E-value=0.024 Score=50.55 Aligned_cols=52 Identities=23% Similarity=0.366 Sum_probs=46.8
Q ss_pred CCcccccCCHHHHHHHHHhh---CCCCCCChhhHHHHHHhhhcccccccccCCCC
Q psy4078 28 PTRVRTVLNEKQLHTLRTCY---NANPRPDALMKEQLVEMTNLFLGRVRKVSGGD 79 (269)
Q Consensus 28 ~~r~Rt~~t~~Ql~~L~~~F---~~n~~P~~~~re~La~~~gls~~~i~~~~~~~ 79 (269)
.+|+|.-|+..--++|..+| ..|+||+.+.+++||+..++...+|..|.+++
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnk 242 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNK 242 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccc
Confidence 46788889999999999998 47999999999999999999999998887753
No 68
>KOG0775|consensus
Probab=93.89 E-value=0.047 Score=49.07 Aligned_cols=50 Identities=28% Similarity=0.349 Sum_probs=41.8
Q ss_pred ccccCCHHHH---------HHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCC
Q psy4078 31 VRTVLNEKQL---------HTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDG 80 (269)
Q Consensus 31 ~Rt~~t~~Ql---------~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~ 80 (269)
+||++-.||. ..|+++|..|+||+-.++.+|++.+||..-+|-.|+.+++
T Consensus 170 PrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRR 228 (304)
T KOG0775|consen 170 PRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRR 228 (304)
T ss_pred CCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhh
Confidence 4666665554 4599999999999999999999999999999988876543
No 69
>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=93.82 E-value=0.047 Score=37.06 Aligned_cols=46 Identities=15% Similarity=0.173 Sum_probs=34.3
Q ss_pred ccceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcch
Q psy4078 83 TRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNK 133 (269)
Q Consensus 83 rr~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNR 133 (269)
+|+|..+|-++...+-..++... ....||.++|++..+|..|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 46788899888877777777666 47789999999999999999884
No 70
>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=90.17 E-value=0.13 Score=32.81 Aligned_cols=29 Identities=28% Similarity=0.256 Sum_probs=22.2
Q ss_pred CCCCCCChhhHHHHHHhhhcccccccccC
Q psy4078 48 NANPRPDALMKEQLVEMTNLFLGRVRKVS 76 (269)
Q Consensus 48 ~~n~~P~~~~re~La~~~gls~~~i~~~~ 76 (269)
..||||+.+++++|+..+|++..+|..+.
T Consensus 6 ~~nPYPs~~ek~~L~~~tgls~~Qi~~WF 34 (40)
T PF05920_consen 6 LHNPYPSKEEKEELAKQTGLSRKQISNWF 34 (40)
T ss_dssp TTSGS--HHHHHHHHHHHTS-HHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 46899999999999999999998886543
No 71
>KOG3755|consensus
Probab=88.03 E-value=0.45 Score=47.22 Aligned_cols=100 Identities=17% Similarity=0.203 Sum_probs=58.5
Q ss_pred CCcccccCCHHHHHHHHHh-hCCCCCCChhh---HHHHHHhhhcccccccccCCCCCCCccceeecchhhhhh-hhhhcc
Q psy4078 28 PTRVRTVLNEKQLHTLRTC-YNANPRPDALM---KEQLVEMTNLFLGRVRKVSGGDGKPTRVRTVLNEKQLHT-LRTCYN 102 (269)
Q Consensus 28 ~~r~Rt~~t~~Ql~~L~~~-F~~n~~P~~~~---re~La~~~gls~~~i~~~~~~~~k~rr~Rt~~t~~Ql~~-Le~~F~ 102 (269)
..|.|+.+..+.+.+|... -...-||+.+. -.-|...+++ .|+.+..|-.+|.-. -+.+|.
T Consensus 647 ~p~~~~~isge~~~~~qs~i~~~gl~pd~~a~~~~~~LSa~~~~--------------pk~~~~k~f~~~~~ev~~~w~~ 712 (769)
T KOG3755|consen 647 KPRKRTKISGEALGILQSFITDVGLYPDKEAPYFIKTLSAQLDL--------------PKKTIIKFFQNQRYEVKHHWKL 712 (769)
T ss_pred CccccceecccchHHHHHHHHHhccCchhhcccccchhhhhhcc--------------cHHHHHHhhhcceeecchhhee
Confidence 4567777777777777644 33445665433 2223333322 223333333333333 355677
Q ss_pred cCCCCChHHHHHHHHHhCC-------CchhhhhhhcchhhhHHHHH
Q psy4078 103 ANPRPDALMKEQLVEMTNL-------SPRVIRVWFQNKRCKDKKRA 141 (269)
Q Consensus 103 ~~~~p~~~~r~~La~~lgL-------~~~~V~vWFqNRRak~kk~~ 141 (269)
++..+......+.-+++.| ..+.|+.||+|||+++++-+
T Consensus 713 k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 713 KTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred cccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
Confidence 7777776655555444443 45679999999999999764
No 72
>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=82.94 E-value=1.4 Score=28.92 Aligned_cols=46 Identities=20% Similarity=0.250 Sum_probs=32.9
Q ss_pred ecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHH
Q psy4078 88 VLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDK 138 (269)
Q Consensus 88 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~k 138 (269)
.+++.+..+|...|. ......++|..+|++...|+.+...-..|.|
T Consensus 4 ~L~~~er~vi~~~y~-----~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYF-----EGLTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHT-----ST-SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhc-----CCCCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 367778888888882 2334688999999999999988765544444
No 73
>KOG1146|consensus
Probab=79.34 E-value=0.92 Score=48.88 Aligned_cols=51 Identities=24% Similarity=0.226 Sum_probs=46.6
Q ss_pred CCcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCC
Q psy4078 28 PTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGG 78 (269)
Q Consensus 28 ~~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~ 78 (269)
.++.||.+++.||++|+++|....||-..+-|.+.+.+++..+.|..|...
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qn 953 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQN 953 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhh
Confidence 467889999999999999999999999999999999999999999777644
No 74
>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=75.52 E-value=2.5 Score=28.72 Aligned_cols=40 Identities=23% Similarity=0.359 Sum_probs=32.3
Q ss_pred cchhhhhhhhhhcccCC--CCChHHHHHHHHHhCCCchhhhh
Q psy4078 89 LNEKQLHTLRTCYNANP--RPDALMKEQLVEMTNLSPRVIRV 128 (269)
Q Consensus 89 ~t~~Ql~~Le~~F~~~~--~p~~~~r~~La~~lgL~~~~V~v 128 (269)
+|..|..+|..+|+..= +|-.....+||+++|++...|..
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 57889999999988654 36667789999999999887654
No 75
>KOG1924|consensus
Probab=74.91 E-value=29 Score=36.14 Aligned_cols=15 Identities=7% Similarity=0.275 Sum_probs=7.4
Q ss_pred HHHHHHhhhcccccc
Q psy4078 58 KEQLVEMTNLFLGRV 72 (269)
Q Consensus 58 re~La~~~gls~~~i 72 (269)
|-+.-+.+..+..+|
T Consensus 421 rpqYykLIEecISqI 435 (1102)
T KOG1924|consen 421 RPQYYKLIEECISQI 435 (1102)
T ss_pred hHHHHHHHHHHHHHH
Confidence 444445555555554
No 76
>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=72.71 E-value=2.4 Score=26.95 Aligned_cols=44 Identities=18% Similarity=0.263 Sum_probs=31.1
Q ss_pred ecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhh
Q psy4078 88 VLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCK 136 (269)
Q Consensus 88 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak 136 (269)
.++..+..++...|.. .....++|..+|++...|..|...-+.+
T Consensus 10 ~l~~~~~~~~~~~~~~-----~~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGE-----GLSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 3566666777666532 2346788999999999999998654443
No 77
>PF03529 TF_Otx: Otx1 transcription factor; InterPro: IPR013851 Otx proteins constitute a class of vertebrate homeodomain-containing transcription factors that have been shown to be essential for anterior head formation, including brain morphogenesis. They are orthologous to the product of the Drosophila head gap gene, orthodenticle (Otd), and appear to play similar roles in both, since the developmental abnormalities caused by disruption of these transcription factors in one, can be recovered by substitution of the factor(s) from the other. Such studies have provided strong evidence that there exists a conserved genetic programme for insect and mammalian brain development, which presumably arose in a more primitive common ancestor [, ]. Two vertebrate orthodenticle-related transcription factors have been indentified, Otx1 and Otx2, which have sizes of 355 and 289 residues respectively. They contain a bicoid-like homeodomain, which features a conserved lysine residue at position 9 of the DNA recognition helix, which is thought to confer high-affinity binding to TAATCC/T elements on DNA []. Otd-like transcription factors have also been found in zebrafish and certain lamprey species. This entry represents a conserved region found in the C-terminal region of these proteins.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0007275 multicellular organismal development, 0005634 nucleus
Probab=71.70 E-value=4.5 Score=30.28 Aligned_cols=43 Identities=26% Similarity=0.243 Sum_probs=36.7
Q ss_pred hhhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCc
Q psy4078 217 HLVSQMHGYELGHGPPPPHDMGPTPGDMAHPDSTDSYVTYLES 259 (269)
Q Consensus 217 ~~~~~~~g~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~~~~~ 259 (269)
.--+++.|+||+...++++.....++....|.+..+|-.|+..
T Consensus 44 ~ssSYFgg~DC~sYLsPMh~~l~~~~~~Lspm~~~~m~~H~~~ 86 (88)
T PF03529_consen 44 GSSSYFGGMDCGSYLSPMHSQLHPPGSALSPMSAPSMSGHLHQ 86 (88)
T ss_pred CcccccccccccccccccccccCCCccccCcccCCccCCcCCC
Confidence 3456788999999999998888888889999999999998754
No 78
>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=65.04 E-value=4.5 Score=28.24 Aligned_cols=20 Identities=25% Similarity=0.401 Sum_probs=17.7
Q ss_pred HHHHHHHHhCCCchhhhhhh
Q psy4078 111 MKEQLVEMTNLSPRVIRVWF 130 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWF 130 (269)
...+||++||+++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 45689999999999999995
No 79
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=62.58 E-value=11 Score=30.80 Aligned_cols=51 Identities=18% Similarity=0.204 Sum_probs=39.2
Q ss_pred eecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHH
Q psy4078 87 TVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALA 143 (269)
Q Consensus 87 t~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~ 143 (269)
..+++.|..+|...+ ......++|..+|++...|..|.++.+.+.|+....
T Consensus 5 ~~Lt~rqreVL~lr~------~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRLRE------RGLTQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHHHH------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 467888888887732 123467999999999999999999877777766543
No 80
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=62.30 E-value=3 Score=29.50 Aligned_cols=43 Identities=12% Similarity=0.105 Sum_probs=27.4
Q ss_pred ceeecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhc
Q psy4078 85 VRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQ 131 (269)
Q Consensus 85 ~Rt~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFq 131 (269)
.|..|+.++...+-..+. -......++|.++||+...|..|-+
T Consensus 3 ~r~~ys~e~K~~~v~~~~----~~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYL----ESGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp SS----HHHHHHHHHHHH----HHHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHH----HCCCceEeeecccccccccccHHHH
Confidence 456788887766555441 1235678899999999999999974
No 81
>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=60.97 E-value=8.2 Score=25.40 Aligned_cols=42 Identities=17% Similarity=0.264 Sum_probs=26.1
Q ss_pred cchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhh
Q psy4078 89 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRC 135 (269)
Q Consensus 89 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRa 135 (269)
+++.+..++.-.|- ......++|+.+|+++..|+.|.+.-|.
T Consensus 11 L~~~~r~i~~l~~~-----~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 11 LPERQREIFLLRYF-----QGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S-HHHHHHHHHHHT-----S---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH-----HCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 34455555554433 2345689999999999999999975443
No 82
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=57.93 E-value=9.2 Score=33.12 Aligned_cols=41 Identities=22% Similarity=0.344 Sum_probs=34.3
Q ss_pred ecchhhhhhhhhhcccC--CCCChHHHHHHHHHhCCCchhhhh
Q psy4078 88 VLNEKQLHTLRTCYNAN--PRPDALMKEQLVEMTNLSPRVIRV 128 (269)
Q Consensus 88 ~~t~~Ql~~Le~~F~~~--~~p~~~~r~~La~~lgL~~~~V~v 128 (269)
.+|+.|+.+|..+|... -+|-.....+||+++|++...+.-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~e 197 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSE 197 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHH
Confidence 69999999999999865 357777789999999999877543
No 83
>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=53.93 E-value=13 Score=20.87 Aligned_cols=37 Identities=14% Similarity=0.191 Sum_probs=25.0
Q ss_pred cchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhh
Q psy4078 89 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWF 130 (269)
Q Consensus 89 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWF 130 (269)
++.++...+...|.. .+ ...++|..+|++...|..|.
T Consensus 6 ~~~~~~~~i~~~~~~-~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAA-GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHc-CC----CHHHHHHHHCCCHHHHHHhC
Confidence 455555555555542 22 46788999999999988884
No 84
>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=53.33 E-value=10 Score=24.10 Aligned_cols=21 Identities=24% Similarity=0.422 Sum_probs=18.1
Q ss_pred HHHHHHHhCCCchhhhhhhcc
Q psy4078 112 KEQLVEMTNLSPRVIRVWFQN 132 (269)
Q Consensus 112 r~~La~~lgL~~~~V~vWFqN 132 (269)
..++|+.+|++...|+.|.++
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 467899999999999999644
No 85
>PRK04217 hypothetical protein; Provisional
Probab=53.31 E-value=15 Score=28.73 Aligned_cols=48 Identities=13% Similarity=0.086 Sum_probs=34.7
Q ss_pred eecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 87 TVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 87 t~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
..++.+|..++...|...- ...+||+.+|++...|+..+..-+.+.+.
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3467778777766653322 56789999999999999988765555544
No 86
>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=53.01 E-value=18 Score=24.21 Aligned_cols=40 Identities=13% Similarity=0.080 Sum_probs=29.7
Q ss_pred CcccccCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhccccccc
Q psy4078 29 TRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVR 73 (269)
Q Consensus 29 ~r~Rt~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~ 73 (269)
+|.|..+|-+++-.+-..++... ...+++..+|++...|.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~ 40 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVS 40 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHH
Confidence 47889999999998888888766 58999999999988774
No 87
>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=51.76 E-value=22 Score=24.09 Aligned_cols=38 Identities=24% Similarity=0.335 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHhhCCCCC--CChhhHHHHHHhhhcccccc
Q psy4078 35 LNEKQLHTLRTCYNANPR--PDALMKEQLVEMTNLFLGRV 72 (269)
Q Consensus 35 ~t~~Ql~~L~~~F~~n~~--P~~~~re~La~~~gls~~~i 72 (269)
+|+.|.++|+..|...=| |-...-++|++.+|++..-+
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHH
Confidence 588999999988766544 66788999999999986543
No 88
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=50.87 E-value=15 Score=30.94 Aligned_cols=47 Identities=11% Similarity=0.180 Sum_probs=30.9
Q ss_pred cchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 89 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 89 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
++..+..+|.-.| .......++|+.+|++...|+++...-|.+.|+.
T Consensus 143 L~~~~r~vl~l~~-----~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 143 LTDTQRESVTLAY-----YGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 4444555554433 2223467899999999999999987655555543
No 89
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=50.33 E-value=17 Score=24.49 Aligned_cols=31 Identities=13% Similarity=0.170 Sum_probs=19.6
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKKRA 141 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk~~ 141 (269)
...+||+.+|++...|..|+.++..+..-..
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~ 42 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDT 42 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHH
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHH
Confidence 4678999999999999999998755555443
No 90
>KOG0773|consensus
Probab=49.61 E-value=13 Score=34.42 Aligned_cols=55 Identities=20% Similarity=0.081 Sum_probs=45.9
Q ss_pred CCCcccccCCHHHHHHHHHhhC---CCCCCChhhHHHHHHhhhcccccccccCCCCCC
Q psy4078 27 KPTRVRTVLNEKQLHTLRTCYN---ANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGK 81 (269)
Q Consensus 27 ~~~r~Rt~~t~~Ql~~L~~~F~---~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k 81 (269)
..+|++..|-.....+|+.+.. ..+||+..++..|++.+|++..+|..|+-..++
T Consensus 238 ~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~ 295 (342)
T KOG0773|consen 238 SKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARV 295 (342)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhccc
Confidence 3567777999999999997733 368999999999999999999999888876544
No 91
>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=48.61 E-value=13 Score=24.96 Aligned_cols=45 Identities=18% Similarity=0.230 Sum_probs=32.2
Q ss_pred ecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHH
Q psy4078 88 VLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDK 138 (269)
Q Consensus 88 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~k 138 (269)
.||..++.+|.-... .....++|..+++++..|+.+..+=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~------G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ------GMSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHT------TS-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHh------cCCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 467777777765543 233678999999999999998877666654
No 92
>PRK10072 putative transcriptional regulator; Provisional
Probab=48.03 E-value=13 Score=28.26 Aligned_cols=41 Identities=12% Similarity=0.227 Sum_probs=29.8
Q ss_pred cchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhh
Q psy4078 89 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCK 136 (269)
Q Consensus 89 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak 136 (269)
.+...+..|..... ....+||..+|++...|..|.+.+|.-
T Consensus 33 ~~~~eik~LR~~~g-------lTQ~elA~~lGvS~~TVs~WE~G~r~P 73 (96)
T PRK10072 33 TSFTEFEQLRKGTG-------LKIDDFARVLGVSVAMVKEWESRRVKP 73 (96)
T ss_pred CChHHHHHHHHHcC-------CCHHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 35555666644322 226789999999999999999988754
No 93
>PF13551 HTH_29: Winged helix-turn helix
Probab=47.39 E-value=17 Score=27.30 Aligned_cols=75 Identities=20% Similarity=0.115 Sum_probs=46.0
Q ss_pred hHHHHHHhhhccccccccc-------C---CCC--CCCccceeecchhhhhhhhhhcccCCC-----CChHHHHH-H-HH
Q psy4078 57 MKEQLVEMTNLFLGRVRKV-------S---GGD--GKPTRVRTVLNEKQLHTLRTCYNANPR-----PDALMKEQ-L-VE 117 (269)
Q Consensus 57 ~re~La~~~gls~~~i~~~-------~---~~~--~k~rr~Rt~~t~~Ql~~Le~~F~~~~~-----p~~~~r~~-L-a~ 117 (269)
...++++.+|++...|..+ + -.. ....+.+..++.++...|.+.+..++. .+.....+ | .+
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~ 93 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEE 93 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHh
Confidence 4778888888888877331 1 011 112334444899999999999887763 33333333 3 22
Q ss_pred Hh--CCCchhhhhhhc
Q psy4078 118 MT--NLSPRVIRVWFQ 131 (269)
Q Consensus 118 ~l--gL~~~~V~vWFq 131 (269)
.. .++...|..|++
T Consensus 94 ~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 94 EFGIDVSPSTIRRILK 109 (112)
T ss_pred ccCccCCHHHHHHHHH
Confidence 22 467788888874
No 94
>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=47.24 E-value=5.7 Score=28.83 Aligned_cols=38 Identities=5% Similarity=0.046 Sum_probs=27.2
Q ss_pred hcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhH
Q psy4078 100 CYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKD 137 (269)
Q Consensus 100 ~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~ 137 (269)
.|.-..|-......+||+.+|+++..|+.|+.+.....
T Consensus 23 af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~ 60 (73)
T TIGR03879 23 AAALAREEAGKTASEIAEELGRTEQTVRNHLKGETKAG 60 (73)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccc
Confidence 34433444445678999999999999999997644443
No 95
>cd00131 PAX Paired Box domain
Probab=47.08 E-value=63 Score=25.71 Aligned_cols=95 Identities=13% Similarity=0.056 Sum_probs=55.3
Q ss_pred cCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhccccccccc-------CCCCCCCc--cceeecchhhhhhhhhhcccC
Q psy4078 34 VLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKV-------SGGDGKPT--RVRTVLNEKQLHTLRTCYNAN 104 (269)
Q Consensus 34 ~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~-------~~~~~k~r--r~Rt~~t~~Ql~~Le~~F~~~ 104 (269)
.++.+....+-..|... ....++++.++++..-|..+ +.-..+++ +.+...+..+...++.....+
T Consensus 17 ~lS~d~R~rIv~~~~~G-----~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~ 91 (128)
T cd00131 17 PLPDSIRQRIVELAQSG-----IRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQEN 91 (128)
T ss_pred cCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHC
Confidence 36666666555566432 35778899999988877331 21111111 112234556666666666777
Q ss_pred CCCChHHHHHHHHHhCC-------Cchhhhhhhcch
Q psy4078 105 PRPDALMKEQLVEMTNL-------SPRVIRVWFQNK 133 (269)
Q Consensus 105 ~~p~~~~r~~La~~lgL-------~~~~V~vWFqNR 133 (269)
+..+..+..++...-|+ +...|--||+++
T Consensus 92 p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 92 PGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred CCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 77776665443223355 778888887653
No 96
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=47.05 E-value=18 Score=28.82 Aligned_cols=30 Identities=10% Similarity=0.058 Sum_probs=23.8
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
...+++|..+|++...|+.|...-|.+.|+
T Consensus 123 ~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 123 KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 346899999999999999998765555543
No 97
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=46.29 E-value=21 Score=30.45 Aligned_cols=32 Identities=22% Similarity=0.214 Sum_probs=24.7
Q ss_pred hHHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 109 ALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 109 ~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
....+++|+.+|+++..|+++...-|.+.++.
T Consensus 169 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 169 ELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34468899999999999999887666555544
No 98
>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=46.04 E-value=18 Score=27.86 Aligned_cols=46 Identities=20% Similarity=0.292 Sum_probs=30.7
Q ss_pred cchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 89 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 89 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
++..+..+|...|- ......++|..+|+++..|+.|...-+.|.|+
T Consensus 111 L~~~~~~ii~~~~~-----~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYL-----EGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 44555555544332 22346789999999999999998766555543
No 99
>PF13518 HTH_28: Helix-turn-helix domain
Probab=45.62 E-value=16 Score=23.48 Aligned_cols=22 Identities=9% Similarity=0.285 Sum_probs=19.0
Q ss_pred HHHHHHHHhCCCchhhhhhhcc
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQN 132 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqN 132 (269)
...++|.++|++..+|..|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 3567999999999999999864
No 100
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=45.60 E-value=17 Score=29.97 Aligned_cols=30 Identities=20% Similarity=0.403 Sum_probs=24.3
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
...+++|..+|+++..|++++..-|.+.|+
T Consensus 146 ~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 146 LSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 346899999999999999998766666554
No 101
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=45.52 E-value=23 Score=29.60 Aligned_cols=33 Identities=6% Similarity=0.112 Sum_probs=26.0
Q ss_pred ChHHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 108 DALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 108 ~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
......++|..+|++...|+.|+..-|.+.|+.
T Consensus 156 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 156 EGLSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 344568999999999999999997666666553
No 102
>PRK00118 putative DNA-binding protein; Validated
Probab=45.01 E-value=33 Score=26.60 Aligned_cols=50 Identities=16% Similarity=0.074 Sum_probs=34.8
Q ss_pred cchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHH
Q psy4078 89 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALA 143 (269)
Q Consensus 89 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~ 143 (269)
++..|..++...|.. .....+||+.+|+++..|..|...-|.+.|+....
T Consensus 18 L~ekqRevl~L~y~e-----g~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~ 67 (104)
T PRK00118 18 LTEKQRNYMELYYLD-----DYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEK 67 (104)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 445555666554433 23457899999999999999998777776665543
No 103
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=44.90 E-value=23 Score=28.69 Aligned_cols=47 Identities=15% Similarity=0.122 Sum_probs=31.9
Q ss_pred cchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 89 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 89 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
++..+..+|...|- ......++|..+|+++..|+.|...-+.+.|+.
T Consensus 129 L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 129 LPEELRTAITLREI-----EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 55555556654432 223457899999999999999998555555543
No 104
>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=44.57 E-value=17 Score=24.97 Aligned_cols=25 Identities=16% Similarity=0.272 Sum_probs=20.4
Q ss_pred HHHHHHHhCCCchhhhhhhcchhhhHH
Q psy4078 112 KEQLVEMTNLSPRVIRVWFQNKRCKDK 138 (269)
Q Consensus 112 r~~La~~lgL~~~~V~vWFqNRRak~k 138 (269)
..+||+.||++...|..|-+ |.+|.
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~--r~~W~ 40 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD--RYKWD 40 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH--hhCcc
Confidence 57899999999999999975 44444
No 105
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=44.11 E-value=20 Score=29.05 Aligned_cols=31 Identities=10% Similarity=0.159 Sum_probs=24.8
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
...+++|+.+|++...|+.|...-|.+.|+.
T Consensus 142 ~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 142 LSYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3457999999999999999998666666543
No 106
>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=44.07 E-value=24 Score=29.10 Aligned_cols=33 Identities=15% Similarity=0.153 Sum_probs=25.1
Q ss_pred ChHHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 108 DALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 108 ~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
......++|+.+|+++..|+++...-|.+.|+.
T Consensus 153 ~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 153 EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 344568999999999999999986555555543
No 107
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=43.98 E-value=18 Score=23.31 Aligned_cols=23 Identities=9% Similarity=0.271 Sum_probs=17.4
Q ss_pred HHHHHHHHHhCCCchhhhhhhcc
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQN 132 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqN 132 (269)
....++|+.+|++...|..|.+.
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 34678999999999999999854
No 108
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.40 E-value=15 Score=27.60 Aligned_cols=39 Identities=21% Similarity=0.170 Sum_probs=28.9
Q ss_pred cchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhh
Q psy4078 89 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIR 127 (269)
Q Consensus 89 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~ 127 (269)
++++|...-.+.|+.|--.+....+++|.+||+++..|+
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHH
Confidence 456677666666666666666778999999999986554
No 109
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=43.38 E-value=20 Score=22.98 Aligned_cols=40 Identities=5% Similarity=0.080 Sum_probs=20.9
Q ss_pred eecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhc
Q psy4078 87 TVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQ 131 (269)
Q Consensus 87 t~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFq 131 (269)
..||.++...++..++.. ....+||..+|.+...|..|.+
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 457888888888776643 3456799999999999988764
No 110
>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=43.22 E-value=34 Score=21.95 Aligned_cols=21 Identities=10% Similarity=0.158 Sum_probs=19.2
Q ss_pred HHHHHhCCCchhhhhhhcchh
Q psy4078 114 QLVEMTNLSPRVIRVWFQNKR 134 (269)
Q Consensus 114 ~La~~lgL~~~~V~vWFqNRR 134 (269)
+||+.+|++...|..|+.++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999985
No 111
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=41.57 E-value=33 Score=25.94 Aligned_cols=38 Identities=21% Similarity=0.371 Sum_probs=20.9
Q ss_pred hhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHHHHH
Q psy4078 95 HTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALAMKQ 146 (269)
Q Consensus 95 ~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~~~~ 146 (269)
.+..-.|+.|+||...--.. | =.|||.+||+++.+...
T Consensus 15 RiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~QI~~ 52 (91)
T PF00424_consen 15 RIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQRQIRA 52 (91)
T ss_dssp HHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHHHHHH
Confidence 34455588899997431111 0 14899999999876543
No 112
>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=41.36 E-value=21 Score=22.14 Aligned_cols=23 Identities=22% Similarity=0.618 Sum_probs=19.6
Q ss_pred HHHHHHHhCCCchhhhhhhcchh
Q psy4078 112 KEQLVEMTNLSPRVIRVWFQNKR 134 (269)
Q Consensus 112 r~~La~~lgL~~~~V~vWFqNRR 134 (269)
..++|+.+|++...|..|.++.+
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCC
Confidence 46889999999999999986644
No 113
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=41.18 E-value=33 Score=21.82 Aligned_cols=39 Identities=18% Similarity=0.315 Sum_probs=27.5
Q ss_pred cchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcch
Q psy4078 89 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNK 133 (269)
Q Consensus 89 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNR 133 (269)
++..+..++...+. . ....++|..+|++...|..|.+.-
T Consensus 4 l~~~e~~i~~~~~~--g----~s~~eia~~l~is~~tv~~~~~~~ 42 (58)
T smart00421 4 LTPREREVLRLLAE--G----LTNKEIAERLGISEKTVKTHLSNI 42 (58)
T ss_pred CCHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56666666655332 1 246789999999999999887643
No 114
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=40.76 E-value=26 Score=29.54 Aligned_cols=32 Identities=13% Similarity=0.142 Sum_probs=25.8
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRA 141 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~ 141 (269)
...+++|..+|++...|++++..-|.+.|+.-
T Consensus 130 ~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 130 FSYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34678999999999999999987776666543
No 115
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=40.67 E-value=29 Score=28.65 Aligned_cols=31 Identities=10% Similarity=0.052 Sum_probs=25.3
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
...++||..+|++...|+.++..-|.+.|+.
T Consensus 148 ~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12512 148 ASIKETAAKLSMSEGAVRVALHRGLAALAAK 178 (184)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999998777666654
No 116
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=39.47 E-value=23 Score=24.33 Aligned_cols=20 Identities=15% Similarity=0.423 Sum_probs=17.4
Q ss_pred HHHHHHHhCCCchhhhhhhc
Q psy4078 112 KEQLVEMTNLSPRVIRVWFQ 131 (269)
Q Consensus 112 r~~La~~lgL~~~~V~vWFq 131 (269)
..++|+.+|++...|+.|=+
T Consensus 3 i~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46889999999999999953
No 117
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=39.42 E-value=31 Score=28.63 Aligned_cols=30 Identities=20% Similarity=0.236 Sum_probs=23.5
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
...+++|..+|++...|+.+...-|.+.|+
T Consensus 156 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 156 LSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 446899999999999999988655555544
No 118
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=38.82 E-value=32 Score=28.46 Aligned_cols=30 Identities=7% Similarity=0.090 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
..+++|..+|++...|+.+...-|.+.|+.
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 175 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQ 175 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999987666555554
No 119
>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=38.48 E-value=24 Score=21.94 Aligned_cols=19 Identities=21% Similarity=0.469 Sum_probs=15.4
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy4078 112 KEQLVEMTNLSPRVIRVWF 130 (269)
Q Consensus 112 r~~La~~lgL~~~~V~vWF 130 (269)
+-++|+.+|++.+.|+.|=
T Consensus 2 i~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 3578999999999999984
No 120
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=38.37 E-value=37 Score=27.89 Aligned_cols=31 Identities=16% Similarity=0.242 Sum_probs=24.7
Q ss_pred hHHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 109 ALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 109 ~~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
....+++|+.+|++...|+++++.-|.+.|+
T Consensus 152 g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 152 DLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3456899999999999999999766655554
No 121
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=37.68 E-value=33 Score=26.90 Aligned_cols=42 Identities=5% Similarity=0.180 Sum_probs=27.7
Q ss_pred eeecchhhhh-hhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcc
Q psy4078 86 RTVLNEKQLH-TLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQN 132 (269)
Q Consensus 86 Rt~~t~~Ql~-~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqN 132 (269)
|..|+.+... ++..++. +. ....++|.++|++...|..|.+-
T Consensus 10 rr~ys~EfK~~aV~~~~~-~g----~sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFE-PG----MTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCHHHHHHHHHHHHc-CC----CCHHHHHHHHCcCHHHHHHHHHH
Confidence 3446666544 3333333 22 23568899999999999999653
No 122
>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=37.25 E-value=36 Score=27.94 Aligned_cols=29 Identities=17% Similarity=0.163 Sum_probs=23.5
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
..+++|+.+|+++..|++....-|.+.|+
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45789999999999999998766665554
No 123
>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=37.24 E-value=33 Score=27.34 Aligned_cols=46 Identities=17% Similarity=0.156 Sum_probs=30.5
Q ss_pred ecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHH
Q psy4078 88 VLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDK 138 (269)
Q Consensus 88 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~k 138 (269)
.++..+..++...| ......+++|+.+|++...|+++...-|.+.|
T Consensus 111 ~L~~~~r~v~~l~~-----~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 111 KLPERQRELLQLRY-----QRGVSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred HCCHHHHHHHHHHH-----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 35555555555533 22334689999999999999988765444443
No 124
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=37.09 E-value=56 Score=26.22 Aligned_cols=46 Identities=11% Similarity=0.152 Sum_probs=32.1
Q ss_pred cchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 89 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 89 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
++..+..+|.-.| . .....+||..+|++...|+.+...-|.+.|+.
T Consensus 113 L~~~~r~il~l~~--~----g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 113 MTERDRTVLLLRF--S----GYSYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred CCHHHHHHHHHHH--c----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4555555555555 2 23467899999999999999997666665554
No 125
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=36.40 E-value=32 Score=29.96 Aligned_cols=32 Identities=9% Similarity=0.050 Sum_probs=26.2
Q ss_pred hHHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 109 ALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 109 ~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
.....++|..+|++...|+.+...-+.+.|+.
T Consensus 200 g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 200 ELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34568999999999999999998777776654
No 126
>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=36.39 E-value=27 Score=22.72 Aligned_cols=25 Identities=24% Similarity=0.220 Sum_probs=20.8
Q ss_pred HHHHHHHhCCCchhhhhhhcchhhh
Q psy4078 112 KEQLVEMTNLSPRVIRVWFQNKRCK 136 (269)
Q Consensus 112 r~~La~~lgL~~~~V~vWFqNRRak 136 (269)
..+||+.+|++...|.-|..+++.=
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~~~ 36 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKRNP 36 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSSTS
T ss_pred HHHHHHHhCCCcchhHHHhcCCCCC
Confidence 4789999999999999999986643
No 127
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=36.23 E-value=27 Score=29.14 Aligned_cols=34 Identities=15% Similarity=0.192 Sum_probs=26.2
Q ss_pred CChHHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 107 PDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 107 p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
......+++|+.+|++...|+.+...-|.+.|+.
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 153 HGDLELEEIAELTGVPEETVKSRLRYALQKLREL 186 (194)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3444578999999999999998887666666554
No 128
>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=35.63 E-value=27 Score=24.15 Aligned_cols=20 Identities=25% Similarity=0.625 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCchhhhhhhc
Q psy4078 112 KEQLVEMTNLSPRVIRVWFQ 131 (269)
Q Consensus 112 r~~La~~lgL~~~~V~vWFq 131 (269)
..++|+.+|++...|+.|.+
T Consensus 3 i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46889999999999999975
No 129
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=35.58 E-value=12 Score=25.81 Aligned_cols=38 Identities=13% Similarity=0.185 Sum_probs=27.5
Q ss_pred HHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCC
Q psy4078 40 LHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSG 77 (269)
Q Consensus 40 l~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~ 77 (269)
++-|+++|....+....+-+.|.+..+|+..+|+.|+.
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa 47 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFA 47 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHH
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHH
Confidence 34599999999999999999999999999999987764
No 130
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=35.12 E-value=32 Score=28.03 Aligned_cols=34 Identities=15% Similarity=0.213 Sum_probs=26.7
Q ss_pred CChHHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 107 PDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 107 p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
......+++|..+|++...|++.+..-|.+.|+.
T Consensus 134 ~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~ 167 (175)
T PRK12518 134 LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKF 167 (175)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3344578999999999999999997666666654
No 131
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=34.94 E-value=33 Score=27.56 Aligned_cols=29 Identities=10% Similarity=0.099 Sum_probs=23.7
Q ss_pred HHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 112 KEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 112 r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
.+++|+.+|+++..|++++..-|.+.|+.
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 125 YQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57899999999999999987666665554
No 132
>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=34.58 E-value=33 Score=21.94 Aligned_cols=21 Identities=5% Similarity=0.414 Sum_probs=18.6
Q ss_pred HHHHHHHHhCCCchhhhhhhc
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQ 131 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFq 131 (269)
...++|+.++++...|+.|..
T Consensus 17 s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 17 TNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 567899999999999999885
No 133
>PRK09480 slmA division inhibitor protein; Provisional
Probab=34.00 E-value=30 Score=28.48 Aligned_cols=37 Identities=14% Similarity=0.220 Sum_probs=30.3
Q ss_pred hhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhh
Q psy4078 98 RTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRC 135 (269)
Q Consensus 98 e~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRa 135 (269)
...|..++. ......+||++.|++...+..+|.|+-.
T Consensus 20 ~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 20 AQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 344555556 7888999999999999999999999663
No 134
>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=33.98 E-value=40 Score=27.60 Aligned_cols=47 Identities=21% Similarity=0.172 Sum_probs=31.1
Q ss_pred cchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 89 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 89 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
++..+..+|.-.|- .....+++|..+|+++..|+++...-|.+.++.
T Consensus 101 L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 147 (170)
T TIGR02959 101 LPDEYREAIRLTEL-----EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKEL 147 (170)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 44555555554332 223467899999999999999887555555543
No 135
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=33.84 E-value=43 Score=27.85 Aligned_cols=30 Identities=13% Similarity=0.122 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
...++|+.+|++...|++.+..-|.+.|+.
T Consensus 149 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 149 SVEEVGEIVGIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999887666666654
No 136
>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=33.58 E-value=36 Score=26.89 Aligned_cols=29 Identities=10% Similarity=0.119 Sum_probs=23.0
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
...++|..+|+++..|+.+...-|.|.|+
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 46789999999999999988765555553
No 137
>PRK06930 positive control sigma-like factor; Validated
Probab=33.22 E-value=45 Score=27.98 Aligned_cols=48 Identities=13% Similarity=0.178 Sum_probs=34.0
Q ss_pred ecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 88 VLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 88 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
.++..+..+|.-.|.. .....++|..+|++...|+.+...-+.|.++.
T Consensus 114 ~L~~rer~V~~L~~~e-----g~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~ 161 (170)
T PRK06930 114 VLTEREKEVYLMHRGY-----GLSYSEIADYLNIKKSTVQSMIERAEKKIARQ 161 (170)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3566666666654322 22357899999999999999998777766654
No 138
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=33.05 E-value=41 Score=27.04 Aligned_cols=46 Identities=20% Similarity=0.163 Sum_probs=30.3
Q ss_pred cchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 89 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 89 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
++..|..+|.-.| ......+++|..+|++...|+++...-|.+.|+
T Consensus 113 L~~~~r~v~~l~~-----~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 113 LPLERRNVLLLRD-----YYGFSYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CCHHHHHHhhhHH-----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4445555554433 222346789999999999999988765555554
No 139
>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=32.38 E-value=36 Score=22.00 Aligned_cols=24 Identities=21% Similarity=0.278 Sum_probs=21.3
Q ss_pred HHHHHHHhCCCchhhhhhhcchhh
Q psy4078 112 KEQLVEMTNLSPRVIRVWFQNKRC 135 (269)
Q Consensus 112 r~~La~~lgL~~~~V~vWFqNRRa 135 (269)
.++||..+|++...|.-|..+++.
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~~ 41 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKPT 41 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 578999999999999999988753
No 140
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=32.15 E-value=60 Score=27.11 Aligned_cols=30 Identities=17% Similarity=0.200 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
..+++|..+|+++..|+++...-|.+.|+.
T Consensus 152 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 152 SSEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999987655555543
No 141
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=31.85 E-value=64 Score=28.25 Aligned_cols=32 Identities=6% Similarity=0.156 Sum_probs=25.6
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRA 141 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~ 141 (269)
...+++|+.+|+++..|+++...-|.+.|+.-
T Consensus 188 ~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 188 MSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 34578999999999999999987776666543
No 142
>PF13700 DUF4158: Domain of unknown function (DUF4158)
Probab=31.82 E-value=1.2e+02 Score=25.00 Aligned_cols=90 Identities=18% Similarity=0.194 Sum_probs=49.2
Q ss_pred CCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccccccCCCCCCCccceeecchhhhhhhhhhccc-------CCCC
Q psy4078 35 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGKPTRVRTVLNEKQLHTLRTCYNA-------NPRP 107 (269)
Q Consensus 35 ~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~~~~~~k~rr~Rt~~t~~Ql~~Le~~F~~-------~~~p 107 (269)
+|++|.+.| ...|. .+.+++..-..+++..+.--.. . |...+.--+.++-.+|.. ..-.
T Consensus 2 Ls~~e~~~l------~~~P~-l~~~el~~~ftLs~~d~~~i~~----~---r~~~~rlgfalqL~~fr~~g~f~~~~~~~ 67 (166)
T PF13700_consen 2 LSEEEREAL------YSLPR-LSEEELIRYFTLSPEDLELINS----R---RGPANRLGFALQLGYFRALGRFPDDPEDI 67 (166)
T ss_pred cCHHHHHHh------cCCCC-CCHHHHHHHhCCCHHHHHHHhc----c---cCCccchhHHHHHHHHhcccccccccccC
Confidence 455555444 23444 5677777777777665422111 1 111111222333333332 2234
Q ss_pred ChHHHHHHHHHhCCCchhhhhhhcchhhhHH
Q psy4078 108 DALMKEQLVEMTNLSPRVIRVWFQNKRCKDK 138 (269)
Q Consensus 108 ~~~~r~~La~~lgL~~~~V~vWFqNRRak~k 138 (269)
.......||+++|+....+.......+.+.+
T Consensus 68 p~~~i~~va~ql~~~~~~~~~y~~r~~T~~~ 98 (166)
T PF13700_consen 68 PKADIEYVAKQLGLPPSDLSSYAQRSRTRYR 98 (166)
T ss_pred CHHHHHHHHHHhCCchHHHHhhhhhhhHHHH
Confidence 4677889999999999888777764444444
No 143
>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=31.46 E-value=38 Score=26.82 Aligned_cols=33 Identities=21% Similarity=0.179 Sum_probs=25.2
Q ss_pred CChHHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 107 PDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 107 p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
......+++|+.+|+++..|+++...-|.|.|+
T Consensus 119 ~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 119 FKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344557899999999999999988755555543
No 144
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=31.34 E-value=48 Score=26.78 Aligned_cols=31 Identities=13% Similarity=0.057 Sum_probs=25.0
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKKRA 141 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk~~ 141 (269)
..+++|..+|+++..|++|.+.-|.+.|+.-
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999986666665543
No 145
>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=31.11 E-value=43 Score=21.37 Aligned_cols=38 Identities=11% Similarity=0.319 Sum_probs=25.5
Q ss_pred cchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhc
Q psy4078 89 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQ 131 (269)
Q Consensus 89 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFq 131 (269)
++.++...+.+.+... ....+||+.+|++...|.-|+.
T Consensus 6 ~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 6 LSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHHC
T ss_pred CCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHHh
Confidence 5565666665555544 2367899999999999987763
No 146
>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=31.02 E-value=35 Score=23.41 Aligned_cols=21 Identities=14% Similarity=0.423 Sum_probs=18.1
Q ss_pred HHHHHHHhCCCchhhhhhhcc
Q psy4078 112 KEQLVEMTNLSPRVIRVWFQN 132 (269)
Q Consensus 112 r~~La~~lgL~~~~V~vWFqN 132 (269)
..++|+.+|++...|+.|-++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 467899999999999999754
No 147
>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=30.94 E-value=39 Score=20.99 Aligned_cols=23 Identities=13% Similarity=0.134 Sum_probs=18.9
Q ss_pred HHHHHHHhCCCchhhhhhhcchh
Q psy4078 112 KEQLVEMTNLSPRVIRVWFQNKR 134 (269)
Q Consensus 112 r~~La~~lgL~~~~V~vWFqNRR 134 (269)
..++|+.+|++...|..|.++.+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 56889999999999999986543
No 148
>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=30.89 E-value=62 Score=26.35 Aligned_cols=47 Identities=15% Similarity=0.140 Sum_probs=36.3
Q ss_pred eecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 87 TVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 87 t~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
+.++..|..+|.-.+ . ....+++|+.+|++...|..|-..-+.+.++
T Consensus 5 ~~Lte~qr~VL~Lr~--~----GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 5 TFLTERQIKVLELRE--K----GLSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred CCCCHHHHHHHHHHH--c----CCCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 567888888887742 1 2256899999999999999998877777665
No 149
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=30.87 E-value=52 Score=27.16 Aligned_cols=30 Identities=3% Similarity=0.167 Sum_probs=23.3
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
...+++|+.+|++...|++|...-|.+.|+
T Consensus 150 ~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 150 CSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 346789999999999999988755555443
No 150
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=30.76 E-value=54 Score=27.25 Aligned_cols=30 Identities=27% Similarity=0.237 Sum_probs=23.7
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
...+++|..+|++...|+..+..-|.+.|+
T Consensus 123 ~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (181)
T PRK09637 123 LSQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152 (181)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 346889999999999999998755555554
No 151
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=30.63 E-value=42 Score=27.99 Aligned_cols=32 Identities=19% Similarity=0.130 Sum_probs=24.4
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRA 141 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~ 141 (269)
...+++|+.+|++...|++..+.-|.+.|++.
T Consensus 148 ~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 148 EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 34678999999999999988776555555543
No 152
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=30.19 E-value=52 Score=22.80 Aligned_cols=43 Identities=16% Similarity=0.188 Sum_probs=21.7
Q ss_pred eecchh-hhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhc
Q psy4078 87 TVLNEK-QLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQ 131 (269)
Q Consensus 87 t~~t~~-Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFq 131 (269)
..|+.. -|.+++.++..+. +......-|.++|+++++|+-|-+
T Consensus 4 rsy~~~FKL~Vv~~a~~~~n--c~~~~RAaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 4 RSYTAEFKLKVVEYAEKDNN--CKGNQRAAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp ----HHHHHHHHHHHHH-TT--TTT-HHHHHHHTTS-HHHHHHHHT
T ss_pred cccChHHHHHHHHHHHHccc--hhhhHHHHHHHhCccHHHHHHHHH
Confidence 344433 3455555443322 111223458999999999999975
No 153
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=30.15 E-value=29 Score=23.60 Aligned_cols=35 Identities=26% Similarity=0.257 Sum_probs=25.2
Q ss_pred hhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhh
Q psy4078 92 KQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWF 130 (269)
Q Consensus 92 ~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWF 130 (269)
.|+..|+-.|. +...+ ..+||..+|++++.|+.-.
T Consensus 6 rq~~Ll~~L~~-~~~~~---~~ela~~l~~S~rti~~~i 40 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWIT---LKELAKKLNISERTIKNDI 40 (59)
T ss_dssp HHHHHHHHHHH-HTSBB---HHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCc---HHHHHHHHCCCHHHHHHHH
Confidence 46677777777 65554 4499999999999887644
No 154
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=30.10 E-value=54 Score=27.48 Aligned_cols=30 Identities=3% Similarity=0.031 Sum_probs=24.3
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
..++||+.+|++...|++++..-|.+.|+.
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999997666665554
No 155
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=29.61 E-value=58 Score=28.17 Aligned_cols=32 Identities=16% Similarity=0.111 Sum_probs=25.1
Q ss_pred hHHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 109 ALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 109 ~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
....+++|..+|++...|+.+...-|.+.|+.
T Consensus 198 g~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 198 EKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34468899999999999999887666666554
No 156
>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=29.43 E-value=52 Score=26.47 Aligned_cols=29 Identities=7% Similarity=-0.002 Sum_probs=21.8
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDK 138 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~k 138 (269)
....++|+.+|+++..|+....--|.+.|
T Consensus 139 ~s~~eIA~~l~is~~tv~~~l~ra~~~Lr 167 (170)
T TIGR02952 139 LPIAEVARILGKTEGAVKILQFRAIKKLA 167 (170)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 34678999999999999987754444444
No 157
>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=29.43 E-value=58 Score=26.39 Aligned_cols=30 Identities=20% Similarity=0.289 Sum_probs=23.3
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
....++|+.+|++...|+++...-|.+.|+
T Consensus 136 ~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 136 LTIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 346789999999999999988655555554
No 158
>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=29.26 E-value=48 Score=28.55 Aligned_cols=45 Identities=16% Similarity=0.154 Sum_probs=29.2
Q ss_pred chhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 90 NEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 90 t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
+..+..+|...| ......+++|..+|++...|+.+...-+.+.|+
T Consensus 177 ~~~~r~il~l~y-----~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 177 SEREQLVLSLYY-----YEELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred CHHHHHHHHHHH-----hCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 444444444444 223346899999999999999988655555443
No 159
>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=28.97 E-value=40 Score=23.00 Aligned_cols=20 Identities=25% Similarity=0.594 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCchhhhhhhc
Q psy4078 112 KEQLVEMTNLSPRVIRVWFQ 131 (269)
Q Consensus 112 r~~La~~lgL~~~~V~vWFq 131 (269)
..++|+.+|++...|+.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999985
No 160
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=28.94 E-value=46 Score=25.85 Aligned_cols=41 Identities=15% Similarity=0.321 Sum_probs=32.7
Q ss_pred cchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhh
Q psy4078 89 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCK 136 (269)
Q Consensus 89 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak 136 (269)
++..++..+.+.+.-. ...+|..||++...|+.|=|+|+.-
T Consensus 44 ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~kP 84 (104)
T COG2944 44 LSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKKP 84 (104)
T ss_pred CCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcCC
Confidence 6777777777766533 4678999999999999999998754
No 161
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=28.79 E-value=62 Score=25.94 Aligned_cols=29 Identities=10% Similarity=0.283 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
...++|+.+|++...|+.+...-|.+.|+
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 36789999999999999976554444443
No 162
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=28.70 E-value=59 Score=30.11 Aligned_cols=52 Identities=17% Similarity=0.112 Sum_probs=35.4
Q ss_pred ecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 88 VLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 88 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
.++..+..+|...|-- .+......++||..+|++...|+.+...-+.|.|+.
T Consensus 262 ~L~~~~R~vl~lrygL-~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~ 313 (325)
T PRK05657 262 ELNDKQREVLARRFGL-LGYEAATLEDVAREIGLTRERVRQIQVEALRRLREI 313 (325)
T ss_pred cCCHHHHHHHHHHhcc-CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3555566666655422 123345578999999999999999988766666654
No 163
>smart00351 PAX Paired Box domain.
Probab=28.61 E-value=2e+02 Score=22.64 Aligned_cols=90 Identities=13% Similarity=0.074 Sum_probs=52.6
Q ss_pred CCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhccccccccc-------CCCCCCC--ccceeecchhhhhhhhhhcccCC
Q psy4078 35 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKV-------SGGDGKP--TRVRTVLNEKQLHTLRTCYNANP 105 (269)
Q Consensus 35 ~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i~~~-------~~~~~k~--rr~Rt~~t~~Ql~~Le~~F~~~~ 105 (269)
++.++...+-..|... ....++++.+|++...|..+ +.-..++ .+.+...+..+...|+.....++
T Consensus 18 ~s~~~R~riv~~~~~G-----~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p 92 (125)
T smart00351 18 LPDEERQRIVELAQNG-----VRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENP 92 (125)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCC
Confidence 6777777666666532 24678999999998877332 2212221 11223345555666666667788
Q ss_pred CCChHHHH-HHHHHhCC-------Cchhhhhhh
Q psy4078 106 RPDALMKE-QLVEMTNL-------SPRVIRVWF 130 (269)
Q Consensus 106 ~p~~~~r~-~La~~lgL-------~~~~V~vWF 130 (269)
..+..+.. .|+ ..|+ ....|-.||
T Consensus 93 ~~t~~el~~~L~-~~gv~~~~~~Ps~sti~~~l 124 (125)
T smart00351 93 GIFAWEIRDRLL-SEGVCDKDNVPSVSSINRIL 124 (125)
T ss_pred CCCHHHHHHHHH-HcCCCcCCCCCChhhHHHhh
Confidence 77776664 444 4444 445666665
No 164
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=28.19 E-value=60 Score=26.77 Aligned_cols=29 Identities=0% Similarity=0.134 Sum_probs=23.7
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
..+++|..+|+++..|+.....-+.+++.
T Consensus 145 s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 145 KQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46789999999999999998866666544
No 165
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=27.33 E-value=52 Score=28.98 Aligned_cols=46 Identities=11% Similarity=0.139 Sum_probs=30.8
Q ss_pred cchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 89 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 89 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
++..+..+|.-.|- ......++|+.+|++...|+.|...-+.|.|+
T Consensus 206 L~~~~r~vl~l~~~-----~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~ 251 (257)
T PRK08583 206 LSDREKSIIQCTFI-----ENLSQKETGERLGISQMHVSRLQRQAIKKLRE 251 (257)
T ss_pred CCHHHHHHHHHHHh-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44455555555442 22346899999999999999988665555543
No 166
>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=27.31 E-value=51 Score=27.44 Aligned_cols=34 Identities=9% Similarity=0.157 Sum_probs=26.5
Q ss_pred CChHHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 107 PDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 107 p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
.......++|..+|++...|+++...-|.+.|+.
T Consensus 145 ~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 178 (193)
T TIGR02947 145 VEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQ 178 (193)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3344568999999999999999998666666654
No 167
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=27.02 E-value=85 Score=25.65 Aligned_cols=32 Identities=6% Similarity=0.013 Sum_probs=24.5
Q ss_pred hHHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 109 ALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 109 ~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
....+++|+.+|++...|+++...-+.+++..
T Consensus 135 g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~ 166 (172)
T PRK09651 135 GLTYSEIAHKLGVSVSSVKKYVAKATEHCLLF 166 (172)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 33468999999999999999986555555543
No 168
>PF12728 HTH_17: Helix-turn-helix domain
Probab=26.99 E-value=48 Score=21.35 Aligned_cols=23 Identities=13% Similarity=0.404 Sum_probs=19.2
Q ss_pred HHHHHHHhCCCchhhhhhhcchh
Q psy4078 112 KEQLVEMTNLSPRVIRVWFQNKR 134 (269)
Q Consensus 112 r~~La~~lgL~~~~V~vWFqNRR 134 (269)
.+++|+.||++...|..|.++..
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g~ 26 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQGK 26 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCC
Confidence 46889999999999999986543
No 169
>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=26.95 E-value=51 Score=20.11 Aligned_cols=23 Identities=30% Similarity=0.294 Sum_probs=20.2
Q ss_pred HHHHHHHhCCCchhhhhhhcchh
Q psy4078 112 KEQLVEMTNLSPRVIRVWFQNKR 134 (269)
Q Consensus 112 r~~La~~lgL~~~~V~vWFqNRR 134 (269)
..++|..+|+++..|..|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45889999999999999998875
No 170
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=26.65 E-value=71 Score=27.53 Aligned_cols=39 Identities=21% Similarity=0.319 Sum_probs=32.3
Q ss_pred cCCHHHHHHHHHhhCCC--CCCChhhHHHHHHhhhcccccc
Q psy4078 34 VLNEKQLHTLRTCYNAN--PRPDALMKEQLVEMTNLFLGRV 72 (269)
Q Consensus 34 ~~t~~Ql~~L~~~F~~n--~~P~~~~re~La~~~gls~~~i 72 (269)
-+|+-|+++|+.+|... .+|-...-.+||+.+|++..-+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~ 195 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTL 195 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 69999999999887655 4677788999999999985543
No 171
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=26.61 E-value=69 Score=25.97 Aligned_cols=29 Identities=3% Similarity=-0.015 Sum_probs=22.4
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
..+++|+.+|+++..|+.....-|.+.|+
T Consensus 136 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 136 STAQIAADLGIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 36789999999999999987655544444
No 172
>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=26.51 E-value=55 Score=26.22 Aligned_cols=31 Identities=13% Similarity=0.181 Sum_probs=24.5
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
...+++|..+|++...|+.+...-|.+.|+.
T Consensus 127 ~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 127 LSEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3457899999999999999887666666553
No 173
>PRK10403 transcriptional regulator NarP; Provisional
Probab=26.47 E-value=50 Score=26.80 Aligned_cols=48 Identities=27% Similarity=0.384 Sum_probs=36.2
Q ss_pred ecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHH
Q psy4078 88 VLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRA 141 (269)
Q Consensus 88 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~ 141 (269)
.+|..+..+|+..... ..+++||+.++++++.|++..+|=|.|.....
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~ 200 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLNVRS 200 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCC
Confidence 4788888887755432 34678999999999999999988777755443
No 174
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=26.02 E-value=70 Score=27.67 Aligned_cols=31 Identities=3% Similarity=0.085 Sum_probs=24.3
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
...+++|+.+|+++..|+++...-|.+.|+.
T Consensus 151 ~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~ 181 (216)
T PRK12533 151 MSYREIAAIADVPVGTVMSRLARARRRLAAL 181 (216)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999887655555554
No 175
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=25.85 E-value=56 Score=26.94 Aligned_cols=30 Identities=17% Similarity=0.122 Sum_probs=24.3
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
...+++|+.+|+++..|++....-|.+.|+
T Consensus 146 ~s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 146 LSVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 346789999999999999999766666555
No 176
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=25.77 E-value=74 Score=26.29 Aligned_cols=31 Identities=10% Similarity=0.031 Sum_probs=24.0
Q ss_pred hHHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 109 ALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 109 ~~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
....+++|+.+|++...|+.+...-|.+.|+
T Consensus 147 g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 147 GLSVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3456789999999999999988655555554
No 177
>PF13730 HTH_36: Helix-turn-helix domain
Probab=25.72 E-value=63 Score=21.07 Aligned_cols=21 Identities=19% Similarity=0.230 Sum_probs=18.2
Q ss_pred HHHHHHHHhCCCchhhhhhhc
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQ 131 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFq 131 (269)
-.+.||+.+|++.+.|+-+..
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 578999999999999988774
No 178
>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=25.62 E-value=72 Score=28.05 Aligned_cols=46 Identities=15% Similarity=0.171 Sum_probs=31.2
Q ss_pred cchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 89 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 89 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
++..+..+|.-.|.. .....++|..+|++...|+.+...-+.+.|+
T Consensus 206 L~~~~r~ii~l~~~~-----g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 206 LSEREKSIIHCTFEE-----NLSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred CCHHHHHHHHHHHcC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 445555555555432 2345799999999999999988766655554
No 179
>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=25.59 E-value=53 Score=23.00 Aligned_cols=24 Identities=13% Similarity=0.142 Sum_probs=21.0
Q ss_pred HHHHHHHhCCCchhhhhhhcchhh
Q psy4078 112 KEQLVEMTNLSPRVIRVWFQNKRC 135 (269)
Q Consensus 112 r~~La~~lgL~~~~V~vWFqNRRa 135 (269)
..+||+.+|++...|..|+.+++.
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~~ 44 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRRG 44 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 568999999999999999987653
No 180
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=25.52 E-value=68 Score=26.65 Aligned_cols=29 Identities=10% Similarity=-0.061 Sum_probs=22.4
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
..++||+.+|+++..|+++...-|.+.|+
T Consensus 148 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45789999999999999988654444443
No 181
>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=25.35 E-value=56 Score=27.11 Aligned_cols=32 Identities=19% Similarity=0.057 Sum_probs=24.0
Q ss_pred ChHHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 108 DALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 108 ~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
......++|+.+|++...|++++..-|.+.|+
T Consensus 164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 164 DGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34457899999999999999887655554443
No 182
>PHA01976 helix-turn-helix protein
Probab=25.10 E-value=56 Score=22.17 Aligned_cols=23 Identities=17% Similarity=0.212 Sum_probs=20.5
Q ss_pred HHHHHHHhCCCchhhhhhhcchh
Q psy4078 112 KEQLVEMTNLSPRVIRVWFQNKR 134 (269)
Q Consensus 112 r~~La~~lgL~~~~V~vWFqNRR 134 (269)
..+||+.+|++...|..|...++
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 57899999999999999997765
No 183
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=24.70 E-value=72 Score=26.45 Aligned_cols=31 Identities=6% Similarity=0.223 Sum_probs=25.0
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
...+++|..+|++...|++|...-|.+.|+.
T Consensus 151 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 151 LEFQEIADIMHMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3468999999999999999987666665554
No 184
>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=24.67 E-value=37 Score=28.52 Aligned_cols=35 Identities=14% Similarity=0.311 Sum_probs=29.7
Q ss_pred hHHHHHHHHHhCCCchhhhhhhcchhhhHHHHHHH
Q psy4078 109 ALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALA 143 (269)
Q Consensus 109 ~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~ 143 (269)
.-.+++|+..++++..+|-+|..|-+...++....
T Consensus 14 tgt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~y 48 (186)
T PF04936_consen 14 TGTIDELADYFDVSRTSVSVWIKNGKDPKRAKPKY 48 (186)
T ss_pred cccHHHHHHHHccCHHHHHHHHHcCCCcccccchh
Confidence 34678999999999999999999999888766543
No 185
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=24.65 E-value=61 Score=26.65 Aligned_cols=30 Identities=7% Similarity=0.110 Sum_probs=22.8
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
...+++|+.+|++...|+++...-|.+.|+
T Consensus 152 ~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 152 YTHREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 345789999999999999988655555443
No 186
>smart00595 MADF subfamily of SANT domain.
Probab=24.53 E-value=1e+02 Score=22.19 Aligned_cols=34 Identities=18% Similarity=0.186 Sum_probs=28.8
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHHHHHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALAM 144 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~~~ 144 (269)
.-.+||.++|.+...|+.-+.|-|.+.++..+..
T Consensus 29 aW~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~ 62 (89)
T smart00595 29 AWEEIAEELGLSVEECKKRWKNLRDRYRRELKRL 62 (89)
T ss_pred HHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3457899999999999999999999999876543
No 187
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=24.48 E-value=62 Score=26.87 Aligned_cols=34 Identities=18% Similarity=0.139 Sum_probs=26.2
Q ss_pred ChHHHHHHHHHhCCCchhhhhhhcchhhhHHHHH
Q psy4078 108 DALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRA 141 (269)
Q Consensus 108 ~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~~ 141 (269)
.....+++|+.+|+++..|++....-|.+.|+.-
T Consensus 153 ~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 153 DGLSYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3344688999999999999998876666666543
No 188
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=24.14 E-value=68 Score=28.67 Aligned_cols=31 Identities=10% Similarity=0.183 Sum_probs=24.4
Q ss_pred hHHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 109 ALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 109 ~~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
.....++|..+|++...|+.+...-+.|.|+
T Consensus 231 ~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 231 SMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3456899999999999999988766665554
No 189
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=24.11 E-value=65 Score=25.64 Aligned_cols=46 Identities=11% Similarity=0.055 Sum_probs=29.3
Q ss_pred cchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 89 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 89 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
++..+..++.-.|- ......++|..+|++...|++....-|.+.|+
T Consensus 107 Lp~~~r~v~~l~~~-----~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 107 LPARQREAFLLRYW-----EDMDVAETAAAMGCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred CCHHHHHHHHHHHH-----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44455555544332 12235789999999999999987655544443
No 190
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=24.04 E-value=87 Score=23.08 Aligned_cols=44 Identities=2% Similarity=0.131 Sum_probs=31.2
Q ss_pred ecchhhhhhhhhhccc-----CCCCChHHHHHHHHHhCCCchhhhhhhc
Q psy4078 88 VLNEKQLHTLRTCYNA-----NPRPDALMKEQLVEMTNLSPRVIRVWFQ 131 (269)
Q Consensus 88 ~~t~~Ql~~Le~~F~~-----~~~p~~~~r~~La~~lgL~~~~V~vWFq 131 (269)
.++.+|+..|...|.. +.+.+..+..++...+|+++..|..+|.
T Consensus 3 ~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 3 AISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3577788888888753 3466777777766667888877777774
No 191
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=23.94 E-value=66 Score=26.15 Aligned_cols=32 Identities=13% Similarity=0.166 Sum_probs=24.8
Q ss_pred ChHHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 108 DALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 108 ~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
.....++||+.+|++...|+.+...-|.+.|+
T Consensus 141 ~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 141 YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHH
Confidence 34557899999999999999988655555554
No 192
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=23.64 E-value=68 Score=28.20 Aligned_cols=31 Identities=26% Similarity=0.173 Sum_probs=24.0
Q ss_pred hHHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 109 ALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 109 ~~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
.....++|..+|++...|+.++..-|.+.|+
T Consensus 217 ~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 217 ELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3346889999999999999988765555543
No 193
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=23.62 E-value=47 Score=25.04 Aligned_cols=36 Identities=17% Similarity=0.121 Sum_probs=25.8
Q ss_pred cCCHHHHHH----HHHhhCCCCCCChhhHHHHHHhhhccccccc
Q psy4078 34 VLNEKQLHT----LRTCYNANPRPDALMKEQLVEMTNLFLGRVR 73 (269)
Q Consensus 34 ~~t~~Ql~~----L~~~F~~n~~P~~~~re~La~~~gls~~~i~ 73 (269)
.+|.+|..+ |++.|....+ ..++++..+++++..|.
T Consensus 2 SLn~~Q~~~T~~ELq~nf~~~~l----s~~~ia~dL~~s~~~le 41 (89)
T PF10078_consen 2 SLNPEQRRATRQELQANFELSGL----SLEQIAADLGTSPEHLE 41 (89)
T ss_pred CCCHHHHHHHHHHHHHHHHHcCC----CHHHHHHHhCCCHHHHH
Confidence 467777775 6666666554 47899999998887763
No 194
>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=23.61 E-value=66 Score=27.63 Aligned_cols=46 Identities=13% Similarity=0.140 Sum_probs=30.1
Q ss_pred cchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 89 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 89 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
++..+..+|...|- ......++|+.+|++...|+.|...-+.+.|+
T Consensus 179 L~~~~r~vl~l~y~-----~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 179 LPERERRILLLRFF-----EDKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 44444444444432 23456889999999999999998655555443
No 195
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=23.57 E-value=66 Score=26.34 Aligned_cols=32 Identities=16% Similarity=0.250 Sum_probs=24.8
Q ss_pred hHHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 109 ALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 109 ~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
....+++|..+|++...|+++...-|.+.|+.
T Consensus 152 ~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 152 DLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34468899999999999999887666666543
No 196
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=23.44 E-value=1e+02 Score=25.78 Aligned_cols=32 Identities=16% Similarity=0.175 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHHHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKKRAL 142 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~ 142 (269)
..+++|..+|+++..|+++..--|.+.++.-.
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (188)
T PRK12517 146 SGEEIAEILDLNKNTVMTRLFRARNQLKEALE 177 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45789999999999999988766666555543
No 197
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=23.38 E-value=69 Score=25.93 Aligned_cols=30 Identities=10% Similarity=0.110 Sum_probs=23.3
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
...+++|+.+|+++..|+++...-|.+.|+
T Consensus 129 ~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 129 FSYEDAAAICGCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 346789999999999999988755555443
No 198
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=23.18 E-value=67 Score=28.49 Aligned_cols=32 Identities=19% Similarity=0.157 Sum_probs=24.6
Q ss_pred hHHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 109 ALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 109 ~~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
.....++|..+|++...|+.+...-+.|.|+.
T Consensus 219 ~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 219 DLTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 44568899999999999999887555555543
No 199
>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=22.96 E-value=87 Score=26.12 Aligned_cols=31 Identities=10% Similarity=0.122 Sum_probs=24.0
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
...++||+.+|++...|+++...-|.+.|+.
T Consensus 148 ~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 148 FESDEICQELEISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3468999999999999999887555555544
No 200
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=22.95 E-value=71 Score=26.01 Aligned_cols=30 Identities=7% Similarity=0.183 Sum_probs=23.6
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
.-+++|+.+|++...|+++...-|.+.|+.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999887655555543
No 201
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=22.90 E-value=1e+02 Score=25.30 Aligned_cols=32 Identities=6% Similarity=0.169 Sum_probs=26.4
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHHHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKKRAL 142 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~ 142 (269)
...++|+.+|++...|++....-|.+.|+.-.
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 166 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ 166 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999877777776543
No 202
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=22.61 E-value=1.2e+02 Score=18.10 Aligned_cols=24 Identities=25% Similarity=0.227 Sum_probs=19.8
Q ss_pred HHHHHHHhCCCchhhhhhhcchhh
Q psy4078 112 KEQLVEMTNLSPRVIRVWFQNKRC 135 (269)
Q Consensus 112 r~~La~~lgL~~~~V~vWFqNRRa 135 (269)
..+||+.+|++...|..|-.+++.
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~~~ 36 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGKRK 36 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 458899999999999999877654
No 203
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=22.52 E-value=70 Score=26.78 Aligned_cols=30 Identities=20% Similarity=0.087 Sum_probs=23.2
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
..-.++|..+|++...|++.+..-|.+.|+
T Consensus 171 ~s~~EIA~~lgis~~tV~~~l~rar~~Lr~ 200 (208)
T PRK08295 171 KSYQEIAEELNRHVKSIDNALQRVKRKLEK 200 (208)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 446789999999999999877655555554
No 204
>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=22.43 E-value=88 Score=27.92 Aligned_cols=48 Identities=21% Similarity=0.174 Sum_probs=32.0
Q ss_pred cchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 89 LNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 89 ~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
++..+..+|...|-. -......++|..+|++...|+.+..+-..|.|+
T Consensus 219 L~~rer~vl~l~y~~---~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~ 266 (270)
T TIGR02392 219 LDARSRRIIEARWLD---DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKA 266 (270)
T ss_pred CCHHHHHHHHHHhcC---CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 444455555555522 113456799999999999999888766666664
No 205
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.00 E-value=59 Score=24.51 Aligned_cols=39 Identities=21% Similarity=0.124 Sum_probs=31.7
Q ss_pred cCCHHHHHHHHHhhCCCCCCChhhHHHHHHhhhcccccc
Q psy4078 34 VLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRV 72 (269)
Q Consensus 34 ~~t~~Ql~~L~~~F~~n~~P~~~~re~La~~~gls~~~i 72 (269)
.++.+|+++-++.|..|--......+++|..++.++..+
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~l 40 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKL 40 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHH
Confidence 478899998777777777777778899999998887665
No 206
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=21.81 E-value=94 Score=27.62 Aligned_cols=31 Identities=6% Similarity=0.079 Sum_probs=24.4
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
....++|..+|++...|+.....-+.+.|+.
T Consensus 229 ~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 229 LTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3468899999999999998887666665554
No 207
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=21.79 E-value=74 Score=26.61 Aligned_cols=31 Identities=23% Similarity=0.330 Sum_probs=24.3
Q ss_pred hHHHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 109 ALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 109 ~~~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
....+++|+.+|++++.|+..++.-|++.++
T Consensus 151 Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 151 GLSVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3456889999999999999888777755444
No 208
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=21.77 E-value=74 Score=27.07 Aligned_cols=30 Identities=10% Similarity=0.112 Sum_probs=23.5
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
...++|+.+|+++..|+++...-|.+.|+.
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~ 185 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQLRAA 185 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999997655555543
No 209
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=21.76 E-value=76 Score=26.45 Aligned_cols=31 Identities=10% Similarity=0.135 Sum_probs=24.8
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKKRA 141 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk~~ 141 (269)
..+++|+.+|++...|+.+...-|.+.|+.-
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4578999999999999999876666666543
No 210
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=21.58 E-value=72 Score=25.73 Aligned_cols=45 Identities=16% Similarity=0.164 Sum_probs=33.6
Q ss_pred ecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHH
Q psy4078 88 VLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDK 138 (269)
Q Consensus 88 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~k 138 (269)
.+|..+..+|+-..+- ..+++||..++++++.|++..++=|.|..
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 4777777777655432 25789999999999999998887666644
No 211
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=21.55 E-value=67 Score=21.85 Aligned_cols=19 Identities=16% Similarity=0.338 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy4078 112 KEQLVEMTNLSPRVIRVWF 130 (269)
Q Consensus 112 r~~La~~lgL~~~~V~vWF 130 (269)
..++|+.+|++...|+.|-
T Consensus 3 ~~eva~~~gvs~~tlr~~~ 21 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYE 21 (70)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4578999999999999995
No 212
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=21.33 E-value=94 Score=25.86 Aligned_cols=29 Identities=3% Similarity=0.010 Sum_probs=22.7
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
..+++|+.+|++...|+++...-|.+.|+
T Consensus 129 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 157 (182)
T PRK12511 129 SYQEAAAVLGIPIGTLMSRIGRARAALRA 157 (182)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 46789999999999999988655555444
No 213
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=21.18 E-value=80 Score=25.72 Aligned_cols=29 Identities=10% Similarity=0.051 Sum_probs=23.3
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk 139 (269)
...++|+.+|++...|+++...-+.+.+.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45789999999999999998766655543
No 214
>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=20.76 E-value=1.2e+02 Score=26.84 Aligned_cols=32 Identities=13% Similarity=0.235 Sum_probs=26.3
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHHHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKKRAL 142 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk~~~ 142 (269)
..+++|..+|++...|+++...-|.+.|+.-.
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~ 210 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLERTR 210 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999877777666543
No 215
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=20.59 E-value=90 Score=25.95 Aligned_cols=31 Identities=13% Similarity=0.082 Sum_probs=23.2
Q ss_pred HHHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 110 LMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 110 ~~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
...+++|+.+|+++..|+.....-|.+.|+.
T Consensus 128 ~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~ 158 (182)
T PRK12540 128 FSYEDAAAICGCAVGTIKSRVNRARSKLSAL 158 (182)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999886544444443
No 216
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=20.56 E-value=67 Score=27.75 Aligned_cols=41 Identities=7% Similarity=0.006 Sum_probs=33.2
Q ss_pred hhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHH
Q psy4078 96 TLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDK 138 (269)
Q Consensus 96 ~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~k 138 (269)
.-...|.+..|- ....+||+..|++...|..+|.||..=..
T Consensus 21 aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L~~ 61 (225)
T PRK11552 21 AALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDLYL 61 (225)
T ss_pred HHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHHHH
Confidence 334558888877 56889999999999999999999876543
No 217
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=20.13 E-value=86 Score=26.21 Aligned_cols=30 Identities=13% Similarity=0.117 Sum_probs=23.6
Q ss_pred HHHHHHHHhCCCchhhhhhhcchhhhHHHH
Q psy4078 111 MKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140 (269)
Q Consensus 111 ~r~~La~~lgL~~~~V~vWFqNRRak~kk~ 140 (269)
...++|+.+|+++..|+++...-|.+.|+.
T Consensus 134 s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~ 163 (187)
T PRK12516 134 AYEEAAEICGCAVGTIKSRVNRARQRLQEI 163 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999887666555543
No 218
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=20.02 E-value=79 Score=25.63 Aligned_cols=45 Identities=20% Similarity=0.223 Sum_probs=33.3
Q ss_pred ecchhhhhhhhhhcccCCCCChHHHHHHHHHhCCCchhhhhhhcchhhhHH
Q psy4078 88 VLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDK 138 (269)
Q Consensus 88 ~~t~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgL~~~~V~vWFqNRRak~k 138 (269)
.++..+..+|....+- ..+++||.+++++.+.|+++..+=|.|..
T Consensus 149 ~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 149 VLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 4666677777543332 45789999999999999999987776644
Done!