Query psy10851
Match_columns 159
No_of_seqs 156 out of 1581
Neff 8.2
Searched_HMMs 46136
Date Fri Aug 16 20:05:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10851.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10851hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0484|consensus 99.9 3.3E-23 7.1E-28 138.6 8.9 70 4-75 15-84 (125)
2 KOG2251|consensus 99.9 9.6E-22 2.1E-26 147.8 9.7 66 3-70 34-99 (228)
3 KOG0850|consensus 99.9 1.5E-21 3.3E-26 147.4 10.1 66 2-69 118-183 (245)
4 KOG0843|consensus 99.8 2.1E-21 4.5E-26 141.8 6.3 65 4-70 100-164 (197)
5 KOG0842|consensus 99.8 2.5E-21 5.4E-26 153.5 7.3 71 3-75 150-220 (307)
6 KOG0485|consensus 99.8 8.9E-21 1.9E-25 142.2 9.3 68 3-72 101-168 (268)
7 KOG0488|consensus 99.8 3.2E-21 6.9E-26 154.6 7.1 68 4-73 170-237 (309)
8 KOG0489|consensus 99.8 1.3E-21 2.8E-26 154.0 4.7 67 5-73 158-224 (261)
9 PF00046 Homeobox: Homeobox do 99.8 6.2E-20 1.3E-24 112.6 6.9 57 7-65 1-57 (57)
10 KOG0487|consensus 99.8 3.7E-20 8.1E-25 146.9 4.8 68 4-73 233-300 (308)
11 KOG0848|consensus 99.8 3.6E-19 7.8E-24 137.2 6.8 62 8-71 201-262 (317)
12 KOG0492|consensus 99.8 4.5E-19 9.8E-24 132.2 6.8 66 7-74 145-210 (246)
13 KOG0494|consensus 99.8 3.6E-19 7.8E-24 136.7 5.5 65 7-73 142-206 (332)
14 KOG0491|consensus 99.7 4.2E-18 9.1E-23 122.8 4.6 65 5-71 99-163 (194)
15 KOG0493|consensus 99.7 5.4E-18 1.2E-22 130.4 5.0 58 7-66 247-304 (342)
16 smart00389 HOX Homeodomain. DN 99.7 1.7E-17 3.7E-22 101.1 5.8 56 7-64 1-56 (56)
17 cd00086 homeodomain Homeodomai 99.7 3.1E-17 6.8E-22 100.8 6.8 58 7-66 1-58 (59)
18 TIGR01565 homeo_ZF_HD homeobox 99.7 8.4E-18 1.8E-22 102.9 3.9 52 7-60 2-57 (58)
19 KOG4577|consensus 99.7 9.8E-17 2.1E-21 125.0 9.3 62 6-69 167-228 (383)
20 COG5576 Homeodomain-containing 99.7 6.3E-17 1.4E-21 118.0 6.4 66 2-69 47-112 (156)
21 KOG0486|consensus 99.7 2.6E-17 5.6E-22 129.4 3.7 65 5-71 111-175 (351)
22 KOG3802|consensus 99.7 4E-17 8.7E-22 132.3 2.7 63 4-68 292-354 (398)
23 KOG0844|consensus 99.6 3.5E-17 7.5E-22 128.4 1.7 64 3-68 178-241 (408)
24 KOG0483|consensus 99.6 1.2E-16 2.7E-21 120.2 4.5 60 6-67 50-109 (198)
25 KOG0847|consensus 99.6 3.7E-15 8E-20 112.3 6.1 67 5-73 166-232 (288)
26 KOG0775|consensus 99.5 4.8E-14 1E-18 109.3 9.5 59 6-66 167-234 (304)
27 KOG0490|consensus 99.5 3.5E-14 7.5E-19 109.4 5.1 64 3-68 57-120 (235)
28 KOG0849|consensus 99.4 3.5E-13 7.6E-18 110.4 8.3 65 3-69 173-237 (354)
29 KOG0774|consensus 99.4 1.6E-12 3.4E-17 100.4 7.5 63 6-69 188-252 (334)
30 KOG1168|consensus 99.3 4.5E-13 9.8E-18 104.8 2.2 65 2-68 305-369 (385)
31 PF05920 Homeobox_KN: Homeobox 99.1 1.1E-10 2.5E-15 66.2 3.4 33 29-62 8-40 (40)
32 KOG2252|consensus 99.1 4.5E-10 9.7E-15 94.7 7.6 56 6-63 420-475 (558)
33 KOG0490|consensus 98.6 4.2E-08 9.2E-13 75.4 4.2 63 4-68 151-213 (235)
34 KOG1146|consensus 98.4 5.9E-07 1.3E-11 82.4 5.5 63 4-68 901-963 (1406)
35 KOG0773|consensus 97.8 1.5E-05 3.3E-10 65.1 2.5 62 6-68 239-302 (342)
36 PF11569 Homez: Homeodomain le 97.6 4.6E-05 9.9E-10 46.0 2.7 41 18-60 10-50 (56)
37 KOG3623|consensus 97.0 0.0012 2.6E-08 58.3 5.2 49 18-68 568-616 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 96.8 0.005 1.1E-07 36.8 5.4 47 7-60 1-47 (53)
39 PF04545 Sigma70_r4: Sigma-70, 92.8 0.43 9.4E-06 27.6 5.0 47 12-65 4-50 (50)
40 PF01527 HTH_Tnp_1: Transposas 91.9 0.21 4.6E-06 31.3 3.1 43 8-57 2-45 (76)
41 PF06524 NOA36: NOA36 protein; 91.8 0.065 1.4E-06 42.2 0.6 6 53-58 189-194 (314)
42 PF08281 Sigma70_r4_2: Sigma-7 91.5 0.69 1.5E-05 27.0 4.9 44 12-62 10-53 (54)
43 cd06171 Sigma70_r4 Sigma70, re 91.4 0.46 1E-05 26.8 4.0 44 12-62 10-53 (55)
44 KOG1832|consensus 91.1 0.072 1.6E-06 48.7 0.3 10 123-132 1391-1400(1516)
45 KOG1146|consensus 90.8 0.3 6.4E-06 46.3 3.9 63 3-67 702-764 (1406)
46 PRK03975 tfx putative transcri 90.3 1.3 2.7E-05 32.0 6.1 52 10-69 4-55 (141)
47 PRK09646 RNA polymerase sigma 88.2 1.5 3.2E-05 32.6 5.5 31 37-67 160-190 (194)
48 PRK00118 putative DNA-binding 88.1 2.6 5.6E-05 28.8 6.1 50 12-68 17-66 (104)
49 PRK09652 RNA polymerase sigma 87.6 2 4.4E-05 30.9 5.8 49 12-67 128-176 (182)
50 PF04967 HTH_10: HTH DNA bindi 87.2 1.1 2.3E-05 26.8 3.3 41 13-55 1-43 (53)
51 PRK06759 RNA polymerase factor 86.9 1.8 3.9E-05 30.6 5.1 46 13-65 107-152 (154)
52 PRK12526 RNA polymerase sigma 86.7 2 4.4E-05 32.3 5.5 32 36-67 170-201 (206)
53 PRK09644 RNA polymerase sigma 86.3 3 6.5E-05 30.0 6.1 33 37-69 126-158 (165)
54 KOG1832|consensus 85.5 0.26 5.6E-06 45.3 0.1 21 119-139 1391-1411(1516)
55 PRK09642 RNA polymerase sigma 85.5 3.1 6.7E-05 29.6 5.8 31 37-67 124-154 (160)
56 PF00196 GerE: Bacterial regul 85.3 2.8 6E-05 24.9 4.6 46 12-65 3-48 (58)
57 PRK11924 RNA polymerase sigma 85.3 3.3 7.3E-05 29.6 5.9 32 37-68 143-174 (179)
58 PRK04217 hypothetical protein; 85.1 3.5 7.7E-05 28.4 5.5 51 11-68 41-91 (110)
59 PRK06930 positive control sigm 85.0 3.7 8E-05 30.4 6.0 50 12-68 114-163 (170)
60 PRK09639 RNA polymerase sigma 84.7 3.9 8.5E-05 29.2 6.0 48 13-68 113-160 (166)
61 PF00424 REV: REV protein (ant 84.2 2.7 5.8E-05 28.0 4.4 39 18-72 14-52 (91)
62 TIGR02937 sigma70-ECF RNA poly 84.1 3 6.6E-05 28.6 5.1 47 12-65 110-156 (158)
63 PRK12519 RNA polymerase sigma 84.0 2.4 5.2E-05 31.3 4.8 36 32-67 154-189 (194)
64 PRK12512 RNA polymerase sigma 83.8 3.4 7.3E-05 30.2 5.5 32 37-68 149-180 (184)
65 TIGR02985 Sig70_bacteroi1 RNA 83.7 3.6 7.8E-05 28.9 5.4 29 37-65 131-159 (161)
66 TIGR00927 2A1904 K+-dependent 83.6 0.45 9.7E-06 44.0 0.7 12 50-61 606-617 (1096)
67 PRK12530 RNA polymerase sigma 83.6 4.7 0.0001 29.8 6.2 33 36-68 151-183 (189)
68 PRK12514 RNA polymerase sigma 83.4 3.9 8.4E-05 29.7 5.6 30 37-66 147-176 (179)
69 TIGR02999 Sig-70_X6 RNA polyme 83.1 4 8.7E-05 29.7 5.6 30 37-66 152-181 (183)
70 TIGR02989 Sig-70_gvs1 RNA poly 83.0 3.6 7.7E-05 29.1 5.2 30 36-65 128-157 (159)
71 TIGR02939 RpoE_Sigma70 RNA pol 83.0 3.1 6.7E-05 30.4 5.0 35 33-67 152-186 (190)
72 PRK05602 RNA polymerase sigma 83.0 4 8.7E-05 29.9 5.6 32 37-68 146-177 (186)
73 PF13936 HTH_38: Helix-turn-he 82.9 1.8 3.9E-05 24.5 2.9 41 10-57 2-42 (44)
74 KOG3755|consensus 82.8 0.53 1.2E-05 41.3 0.8 45 22-68 708-759 (769)
75 PRK12515 RNA polymerase sigma 82.7 5 0.00011 29.5 6.0 32 37-68 149-180 (189)
76 PRK12543 RNA polymerase sigma 82.6 6 0.00013 28.8 6.4 34 37-70 135-168 (179)
77 TIGR02948 SigW_bacill RNA poly 82.5 3.4 7.3E-05 30.1 5.0 33 35-67 152-184 (187)
78 PRK12532 RNA polymerase sigma 82.3 6 0.00013 29.2 6.3 34 37-70 154-187 (195)
79 PRK09047 RNA polymerase factor 82.1 5.8 0.00013 28.1 6.0 31 37-67 124-154 (161)
80 PRK05657 RNA polymerase sigma 81.3 3.5 7.6E-05 33.6 5.0 54 12-68 262-315 (325)
81 cd00569 HTH_Hin_like Helix-tur 81.0 5 0.00011 19.9 4.2 39 11-56 4-42 (42)
82 TIGR02959 SigZ RNA polymerase 81.0 6.6 0.00014 28.4 6.0 50 12-68 100-149 (170)
83 PRK09413 IS2 repressor TnpA; R 80.8 4 8.7E-05 28.2 4.6 43 8-57 8-51 (121)
84 PRK09648 RNA polymerase sigma 80.6 5.3 0.00012 29.3 5.5 31 36-66 156-186 (189)
85 PRK12537 RNA polymerase sigma 80.2 5.7 0.00012 29.0 5.5 30 37-66 151-180 (182)
86 TIGR02947 SigH_actino RNA poly 80.2 4.3 9.3E-05 30.0 4.9 38 32-69 144-181 (193)
87 PRK12541 RNA polymerase sigma 80.1 4.5 9.8E-05 28.8 4.9 30 37-66 130-159 (161)
88 smart00421 HTH_LUXR helix_turn 79.8 7.4 0.00016 22.0 5.0 43 12-62 3-45 (58)
89 PRK07037 extracytoplasmic-func 79.5 6.3 0.00014 28.0 5.5 30 37-66 127-156 (163)
90 PRK09637 RNA polymerase sigma 79.5 6.5 0.00014 28.9 5.6 33 37-69 124-156 (181)
91 PRK12536 RNA polymerase sigma 79.4 6.3 0.00014 28.8 5.5 31 36-66 146-176 (181)
92 TIGR02943 Sig70_famx1 RNA poly 79.4 9.4 0.0002 28.2 6.5 35 36-70 148-182 (188)
93 PF02796 HTH_7: Helix-turn-hel 79.1 4.9 0.00011 22.7 3.8 39 11-56 4-42 (45)
94 PRK12538 RNA polymerase sigma 79.0 6.1 0.00013 30.5 5.6 32 37-68 189-220 (233)
95 PF10668 Phage_terminase: Phag 79.0 1.7 3.6E-05 26.7 1.9 19 37-55 24-42 (60)
96 PRK12529 RNA polymerase sigma 78.8 6.7 0.00014 28.6 5.5 30 37-66 145-174 (178)
97 KOG0773|consensus 78.7 2.7 5.8E-05 34.3 3.6 41 26-68 117-157 (342)
98 PRK12546 RNA polymerase sigma 78.5 5.9 0.00013 29.4 5.2 32 37-68 131-162 (188)
99 PRK10072 putative transcriptio 78.5 3.2 7E-05 27.8 3.3 41 12-61 32-72 (96)
100 TIGR03001 Sig-70_gmx1 RNA poly 78.3 9.3 0.0002 29.8 6.4 39 36-74 178-216 (244)
101 PRK12547 RNA polymerase sigma 78.2 7.1 0.00015 28.0 5.4 31 36-66 129-159 (164)
102 PRK06811 RNA polymerase factor 78.1 5.9 0.00013 29.2 5.1 31 37-67 149-179 (189)
103 PRK12523 RNA polymerase sigma 78.0 7.7 0.00017 28.0 5.6 30 37-66 137-166 (172)
104 PRK09647 RNA polymerase sigma 77.9 8.5 0.00018 28.9 6.0 33 37-69 156-188 (203)
105 PRK06986 fliA flagellar biosyn 77.9 5.9 0.00013 30.4 5.2 32 36-67 201-232 (236)
106 TIGR02954 Sig70_famx3 RNA poly 77.8 7.1 0.00015 28.0 5.3 31 36-66 136-166 (169)
107 PRK12516 RNA polymerase sigma 77.6 9.4 0.0002 28.2 6.0 33 37-69 134-166 (187)
108 PRK12524 RNA polymerase sigma 77.6 7.3 0.00016 28.9 5.5 32 37-68 154-185 (196)
109 TIGR02983 SigE-fam_strep RNA p 77.5 7.1 0.00015 27.7 5.2 30 37-66 128-157 (162)
110 PRK13919 putative RNA polymera 77.1 8.1 0.00018 28.2 5.5 30 37-66 153-182 (186)
111 PRK12545 RNA polymerase sigma 77.1 9.9 0.00021 28.4 6.1 33 36-68 156-188 (201)
112 PRK12535 RNA polymerase sigma 76.9 7.9 0.00017 28.9 5.5 33 37-69 151-183 (196)
113 PRK12520 RNA polymerase sigma 76.7 11 0.00024 27.6 6.3 35 37-71 149-183 (191)
114 TIGR02952 Sig70_famx2 RNA poly 76.7 8.2 0.00018 27.5 5.4 29 37-65 140-168 (170)
115 COG3413 Predicted DNA binding 76.7 5.7 0.00012 30.2 4.7 52 12-65 155-206 (215)
116 PRK09651 RNA polymerase sigma 76.3 5.9 0.00013 28.7 4.6 34 33-66 133-166 (172)
117 PRK12533 RNA polymerase sigma 75.6 13 0.00027 28.4 6.4 31 37-67 152-182 (216)
118 PRK12531 RNA polymerase sigma 75.3 10 0.00023 28.0 5.8 31 37-67 159-189 (194)
119 PRK09649 RNA polymerase sigma 75.3 7.8 0.00017 28.5 5.0 29 37-65 148-176 (185)
120 PRK08583 RNA polymerase sigma 74.4 9.2 0.0002 29.7 5.5 48 12-66 205-252 (257)
121 PRK12539 RNA polymerase sigma 74.3 10 0.00023 27.7 5.5 32 36-67 148-179 (184)
122 PF13443 HTH_26: Cro/C1-type H 74.3 2.6 5.7E-05 25.2 1.9 30 37-66 12-41 (63)
123 TIGR02980 SigBFG RNA polymeras 74.3 9.7 0.00021 28.9 5.5 47 12-65 178-224 (227)
124 cd04761 HTH_MerR-SF Helix-Turn 74.2 3.3 7.1E-05 23.3 2.2 20 38-57 3-22 (49)
125 PRK12522 RNA polymerase sigma 73.7 13 0.00028 26.8 5.8 33 36-68 136-168 (173)
126 PRK12542 RNA polymerase sigma 73.6 10 0.00023 27.6 5.4 31 37-67 140-170 (185)
127 PRK09643 RNA polymerase sigma 73.5 14 0.00031 27.3 6.1 33 36-68 151-183 (192)
128 TIGR00721 tfx DNA-binding prot 73.4 16 0.00034 26.2 5.9 48 10-65 4-51 (137)
129 TIGR02479 FliA_WhiG RNA polyme 73.2 10 0.00023 28.7 5.4 48 12-66 175-222 (224)
130 PRK12513 RNA polymerase sigma 73.1 5.4 0.00012 29.4 3.7 37 32-68 152-188 (194)
131 PRK12525 RNA polymerase sigma 73.0 12 0.00026 26.9 5.5 30 37-66 136-165 (168)
132 TIGR03879 near_KaiC_dom probab 72.9 1.9 4.1E-05 27.5 1.0 29 32-60 29-57 (73)
133 PRK09645 RNA polymerase sigma 72.9 12 0.00027 26.8 5.5 30 37-66 136-165 (173)
134 PRK09641 RNA polymerase sigma 72.7 11 0.00025 27.3 5.3 32 36-67 153-184 (187)
135 PRK12544 RNA polymerase sigma 72.5 16 0.00035 27.5 6.3 32 37-68 166-197 (206)
136 PRK12528 RNA polymerase sigma 72.4 11 0.00025 26.7 5.2 28 37-64 131-158 (161)
137 TIGR02394 rpoS_proteo RNA poly 72.2 12 0.00027 29.6 5.8 54 12-68 222-275 (285)
138 PRK08295 RNA polymerase factor 72.0 13 0.00029 27.4 5.7 31 37-67 172-202 (208)
139 COG2963 Transposase and inacti 71.9 12 0.00027 25.3 5.0 41 10-56 5-46 (116)
140 PF13384 HTH_23: Homeodomain-l 71.9 3.8 8.2E-05 23.3 2.1 22 37-58 19-40 (50)
141 TIGR02941 Sigma_B RNA polymera 71.3 11 0.00025 29.2 5.3 48 12-66 205-252 (255)
142 PRK08301 sporulation sigma fac 71.3 11 0.00025 28.7 5.2 32 36-67 199-230 (234)
143 PRK12518 RNA polymerase sigma 70.9 4.2 9.2E-05 29.3 2.7 37 32-68 133-169 (175)
144 PRK07670 RNA polymerase sigma 70.9 12 0.00027 28.9 5.4 47 13-66 202-248 (251)
145 PF06056 Terminase_5: Putative 70.8 1.5 3.2E-05 26.6 0.2 27 37-65 15-41 (58)
146 PRK11923 algU RNA polymerase s 70.6 15 0.00033 26.9 5.6 35 34-68 153-187 (193)
147 PF13518 HTH_28: Helix-turn-he 70.6 5.9 0.00013 22.5 2.8 24 37-60 14-37 (52)
148 PRK12511 RNA polymerase sigma 70.3 14 0.0003 27.2 5.4 32 37-68 129-160 (182)
149 PF12824 MRP-L20: Mitochondria 70.1 33 0.00072 25.3 7.2 47 10-60 83-129 (164)
150 PRK09480 slmA division inhibit 69.7 7.4 0.00016 28.3 3.8 41 18-61 16-56 (194)
151 PRK12517 RNA polymerase sigma 69.1 26 0.00056 25.8 6.7 35 37-71 146-180 (188)
152 PRK06288 RNA polymerase sigma 68.7 19 0.00041 28.2 6.1 50 12-68 212-261 (268)
153 PRK09415 RNA polymerase factor 68.3 13 0.00028 27.0 4.8 30 37-66 145-174 (179)
154 PF09607 BrkDBD: Brinker DNA-b 68.3 16 0.00035 22.2 4.3 44 10-57 3-47 (58)
155 PRK12540 RNA polymerase sigma 68.2 19 0.00041 26.4 5.7 33 36-68 128-160 (182)
156 TIGR02859 spore_sigH RNA polym 67.8 18 0.00039 26.5 5.6 30 36-65 166-195 (198)
157 TIGR02957 SigX4 RNA polymerase 67.8 14 0.0003 29.3 5.2 30 37-66 126-155 (281)
158 PRK07408 RNA polymerase sigma 66.2 18 0.00039 28.3 5.5 47 13-66 204-250 (256)
159 PRK07122 RNA polymerase sigma 66.2 16 0.00035 28.8 5.2 48 12-66 215-262 (264)
160 PRK11922 RNA polymerase sigma 65.8 11 0.00024 28.8 4.1 38 32-69 162-199 (231)
161 PRK12527 RNA polymerase sigma 65.5 26 0.00056 24.8 5.8 31 37-67 123-153 (159)
162 PRK12534 RNA polymerase sigma 65.0 22 0.00048 25.9 5.5 31 36-66 154-184 (187)
163 PRK09636 RNA polymerase sigma 65.0 17 0.00037 28.8 5.3 30 37-66 133-162 (293)
164 TIGR02393 RpoD_Cterm RNA polym 64.6 21 0.00046 27.4 5.6 53 12-67 176-228 (238)
165 PRK10403 transcriptional regul 64.5 17 0.00038 26.0 4.9 46 12-65 153-198 (215)
166 PF13411 MerR_1: MerR HTH fami 64.5 6.3 0.00014 23.9 2.1 19 38-56 3-21 (69)
167 PF00376 MerR: MerR family reg 64.3 6.7 0.00015 21.5 2.0 19 38-56 2-20 (38)
168 COG2944 Predicted transcriptio 64.2 9.4 0.0002 26.0 3.0 41 12-61 43-83 (104)
169 TIGR02960 SigX5 RNA polymerase 64.1 17 0.00037 29.1 5.1 31 37-67 160-190 (324)
170 PRK15369 two component system 64.1 18 0.0004 25.6 4.9 45 12-64 149-193 (211)
171 TIGR02950 SigM_subfam RNA poly 63.8 7.5 0.00016 27.2 2.7 34 32-65 118-151 (154)
172 PF07638 Sigma70_ECF: ECF sigm 63.6 23 0.00049 26.1 5.4 30 37-66 153-182 (185)
173 cd04762 HTH_MerR-trunc Helix-T 61.9 8.6 0.00019 21.0 2.3 21 38-58 3-23 (49)
174 PRK05803 sporulation sigma fac 61.7 29 0.00062 26.5 5.8 33 36-68 196-228 (233)
175 cd06170 LuxR_C_like C-terminal 61.2 27 0.0006 19.6 5.2 39 14-60 2-40 (57)
176 PRK06704 RNA polymerase factor 61.0 26 0.00056 27.1 5.4 32 37-68 134-165 (228)
177 PRK05572 sporulation sigma fac 60.9 25 0.00055 27.2 5.4 48 12-66 202-249 (252)
178 TIGR02885 spore_sigF RNA polym 60.5 26 0.00057 26.6 5.4 47 12-65 183-229 (231)
179 PRK10100 DNA-binding transcrip 60.5 27 0.00058 26.6 5.4 47 11-65 154-200 (216)
180 PRK05911 RNA polymerase sigma 60.5 32 0.00069 26.9 5.9 49 12-67 205-253 (257)
181 PRK09640 RNA polymerase sigma 60.4 15 0.00033 26.9 4.0 33 36-68 151-183 (188)
182 cd01392 HTH_LacI Helix-turn-he 59.7 5.5 0.00012 22.7 1.1 21 40-60 2-22 (52)
183 PRK10651 transcriptional regul 59.4 24 0.00053 25.3 4.9 46 12-65 155-200 (216)
184 PRK08215 sporulation sigma fac 59.4 28 0.0006 27.1 5.4 47 12-65 209-255 (258)
185 PF13412 HTH_24: Winged helix- 59.4 23 0.00049 19.8 3.8 37 14-56 2-38 (48)
186 TIGR03020 EpsA transcriptional 59.2 23 0.0005 27.8 4.9 50 10-67 188-237 (247)
187 PRK09638 RNA polymerase sigma 59.2 9.1 0.0002 27.6 2.5 35 32-66 139-173 (176)
188 TIGR02984 Sig-70_plancto1 RNA 59.0 31 0.00067 24.9 5.4 31 36-66 157-187 (189)
189 PF03344 Daxx: Daxx Family; I 59.0 3.1 6.8E-05 37.6 0.0 13 32-44 295-307 (713)
190 PRK10360 DNA-binding transcrip 58.8 29 0.00062 24.8 5.2 45 12-64 137-181 (196)
191 KOG3755|consensus 58.5 7 0.00015 34.6 2.0 60 5-65 646-708 (769)
192 cd04763 HTH_MlrA-like Helix-Tu 58.2 9.9 0.00022 23.1 2.2 20 38-57 3-22 (68)
193 TIGR03541 reg_near_HchA LuxR f 58.2 25 0.00053 27.0 4.9 50 10-67 169-218 (232)
194 cd04764 HTH_MlrA-like_sg1 Heli 57.8 11 0.00023 22.9 2.3 20 38-57 3-22 (67)
195 TIGR02835 spore_sigmaE RNA pol 57.2 36 0.00078 26.0 5.7 32 36-67 199-230 (234)
196 PF13551 HTH_29: Winged helix- 57.1 38 0.00083 22.1 5.2 49 7-57 52-109 (112)
197 PF01381 HTH_3: Helix-turn-hel 55.4 7.8 0.00017 22.3 1.3 23 38-60 12-34 (55)
198 PRK11511 DNA-binding transcrip 55.2 20 0.00044 24.8 3.6 28 32-59 22-49 (127)
199 cd01104 HTH_MlrA-CarA Helix-Tu 55.1 12 0.00026 22.5 2.2 20 38-57 3-22 (68)
200 PF11705 RNA_pol_3_Rpc31: DNA- 54.9 4.5 9.8E-05 31.3 0.3 12 23-36 63-74 (233)
201 TIGR02846 spore_sigmaK RNA pol 54.4 42 0.00091 25.5 5.6 31 36-66 195-225 (227)
202 PHA00542 putative Cro-like pro 54.3 31 0.00067 22.1 4.2 23 37-59 33-55 (82)
203 PRK08241 RNA polymerase factor 54.1 25 0.00054 28.4 4.5 30 36-65 170-199 (339)
204 PRK11552 putative DNA-binding 54.0 23 0.0005 26.9 4.1 56 6-65 6-62 (225)
205 PF08280 HTH_Mga: M protein tr 53.9 27 0.00058 20.8 3.6 36 16-57 6-41 (59)
206 PRK13870 transcriptional regul 52.3 39 0.00086 26.1 5.2 46 11-64 172-217 (234)
207 COG4367 Uncharacterized protei 52.0 27 0.00058 23.2 3.5 40 12-53 2-41 (97)
208 PF04936 DUF658: Protein of un 51.8 6.7 0.00014 29.0 0.7 34 36-69 15-48 (186)
209 COG1595 RpoE DNA-directed RNA 51.6 21 0.00046 26.0 3.5 34 35-68 143-176 (182)
210 PRK10188 DNA-binding transcrip 51.2 53 0.0012 25.4 5.8 49 9-65 176-224 (240)
211 TIGR02392 rpoH_proteo alternat 50.7 43 0.00093 26.3 5.3 50 12-66 218-267 (270)
212 smart00595 MADF subfamily of S 50.0 42 0.0009 21.3 4.3 35 39-73 31-65 (89)
213 PF11705 RNA_pol_3_Rpc31: DNA- 49.8 5.5 0.00012 30.9 0.0 9 55-63 57-65 (233)
214 TIGR03070 couple_hipB transcri 49.6 12 0.00025 21.4 1.5 23 38-60 18-40 (58)
215 cd00093 HTH_XRE Helix-turn-hel 49.6 12 0.00027 20.3 1.6 23 38-60 15-37 (58)
216 PRK09935 transcriptional regul 49.4 45 0.00098 23.8 5.0 45 12-64 149-193 (210)
217 smart00027 EH Eps15 homology d 49.0 59 0.0013 21.1 5.0 46 12-57 3-51 (96)
218 PF13730 HTH_36: Helix-turn-he 48.9 50 0.0011 18.8 4.5 44 12-58 2-48 (55)
219 PF01710 HTH_Tnp_IS630: Transp 48.9 39 0.00084 23.2 4.2 21 37-57 20-40 (119)
220 PF04297 UPF0122: Putative hel 48.6 46 0.00099 22.6 4.4 45 12-63 17-61 (101)
221 PRK09635 sigI RNA polymerase s 48.3 43 0.00093 26.8 4.9 30 37-66 136-165 (290)
222 PF07037 DUF1323: Putative tra 46.7 11 0.00023 26.4 1.0 26 38-65 3-28 (122)
223 PF13542 HTH_Tnp_ISL3: Helix-t 46.5 51 0.0011 18.6 3.9 21 37-57 29-49 (52)
224 PF01726 LexA_DNA_bind: LexA D 45.0 50 0.0011 20.2 3.9 40 12-55 3-46 (65)
225 PRK07500 rpoH2 RNA polymerase 44.8 62 0.0013 25.8 5.4 51 12-67 227-277 (289)
226 TIGR01764 excise DNA binding d 44.4 25 0.00054 19.2 2.3 22 38-59 4-25 (49)
227 smart00422 HTH_MERR helix_turn 43.9 21 0.00045 21.5 2.0 19 38-56 3-21 (70)
228 cd01106 HTH_TipAL-Mta Helix-Tu 43.3 23 0.00049 23.6 2.3 20 38-57 3-22 (103)
229 cd00131 PAX Paired Box domain 43.2 1.1E+02 0.0024 21.3 6.4 46 12-59 75-127 (128)
230 PHA01976 helix-turn-helix prot 43.1 18 0.00039 21.7 1.6 23 38-60 18-40 (67)
231 TIGR02607 antidote_HigA addict 42.9 18 0.00038 22.4 1.6 23 38-60 21-43 (78)
232 PF09862 DUF2089: Protein of u 42.9 55 0.0012 22.7 4.1 38 12-56 33-70 (113)
233 PRK15411 rcsA colanic acid cap 42.4 68 0.0015 24.0 5.1 45 12-64 137-181 (207)
234 PRK09390 fixJ response regulat 42.4 49 0.0011 23.2 4.1 31 38-68 159-189 (202)
235 KOG3623|consensus 41.6 10 0.00022 34.6 0.4 56 10-67 630-685 (1007)
236 PF12728 HTH_17: Helix-turn-he 41.1 29 0.00062 19.6 2.2 22 38-59 4-25 (51)
237 PRK07598 RNA polymerase sigma 40.1 83 0.0018 26.8 5.6 53 12-67 350-402 (415)
238 PRK09958 DNA-binding transcrip 39.7 81 0.0018 22.5 5.0 45 11-63 142-186 (204)
239 cd04774 HTH_YfmP Helix-Turn-He 38.3 30 0.00065 22.9 2.2 19 38-56 3-21 (96)
240 PRK05949 RNA polymerase sigma 38.0 88 0.0019 25.5 5.4 52 12-66 266-317 (327)
241 PRK07405 RNA polymerase sigma 37.3 1E+02 0.0022 25.0 5.6 52 12-66 256-307 (317)
242 TIGR03830 CxxCG_CxxCG_HTH puta 37.3 55 0.0012 22.2 3.6 42 10-60 62-103 (127)
243 cd04779 HTH_MerR-like_sg4 Heli 37.0 30 0.00066 24.5 2.2 20 38-57 3-22 (134)
244 cd04766 HTH_HspR Helix-Turn-He 36.8 33 0.00071 22.2 2.2 19 38-56 4-22 (91)
245 PRK09483 response regulator; P 36.8 96 0.0021 22.4 5.0 45 11-63 147-191 (217)
246 PRK10840 transcriptional regul 36.7 93 0.002 22.9 5.0 45 11-63 149-193 (216)
247 PF13551 HTH_29: Winged helix- 36.6 35 0.00075 22.3 2.4 24 37-60 14-37 (112)
248 cd04768 HTH_BmrR-like Helix-Tu 36.5 34 0.00073 22.5 2.3 20 38-57 3-22 (96)
249 PF05269 Phage_CII: Bacterioph 36.3 52 0.0011 21.8 3.1 29 37-65 25-53 (91)
250 TIGR02850 spore_sigG RNA polym 36.2 96 0.0021 24.0 5.2 47 12-65 206-252 (254)
251 cd01105 HTH_GlnR-like Helix-Tu 36.2 31 0.00067 22.3 2.0 18 38-55 4-21 (88)
252 PRK04019 rplP0 acidic ribosoma 36.1 13 0.00029 30.4 0.2 9 13-21 164-172 (330)
253 PRK10430 DNA-binding transcrip 36.1 67 0.0014 24.3 4.2 45 12-59 158-202 (239)
254 PF14549 P22_Cro: DNA-binding 36.0 33 0.00072 20.8 2.0 18 38-55 12-29 (60)
255 KOG1824|consensus 36.0 17 0.00036 34.2 0.9 12 124-135 306-317 (1233)
256 PF04539 Sigma70_r3: Sigma-70 36.0 48 0.001 20.5 2.8 20 37-56 22-41 (78)
257 PF12844 HTH_19: Helix-turn-he 35.9 52 0.0011 19.4 2.9 23 38-60 15-37 (64)
258 PF04147 Nop14: Nop14-like fam 35.7 16 0.00035 33.8 0.8 7 60-66 281-287 (840)
259 PRK05988 formate dehydrogenase 35.3 81 0.0018 22.9 4.3 36 16-53 24-59 (156)
260 PF11516 DUF3220: Protein of u 35.0 18 0.00039 23.4 0.7 14 50-63 31-44 (106)
261 PF07022 Phage_CI_repr: Bacter 34.9 24 0.00052 21.5 1.3 20 38-57 15-35 (66)
262 PF01047 MarR: MarR family; I 34.6 64 0.0014 18.6 3.1 38 13-56 1-38 (59)
263 smart00530 HTH_XRE Helix-turn- 34.2 29 0.00062 18.5 1.5 23 38-60 13-35 (56)
264 cd04780 HTH_MerR-like_sg5 Heli 34.2 35 0.00075 22.5 2.0 19 38-56 3-21 (95)
265 PF08452 DNAP_B_exo_N: DNA pol 33.7 12 0.00027 17.9 -0.2 8 53-60 6-13 (22)
266 PRK12766 50S ribosomal protein 33.6 14 0.0003 28.9 -0.0 11 39-49 36-46 (232)
267 cd04773 HTH_TioE_rpt2 Second H 33.6 39 0.00085 22.7 2.3 19 38-56 3-21 (108)
268 PRK09706 transcriptional repre 33.3 29 0.00062 24.2 1.6 24 38-61 21-44 (135)
269 PRK13890 conjugal transfer pro 33.2 27 0.00058 24.2 1.4 25 37-61 20-44 (120)
270 PRK07539 NADH dehydrogenase su 32.5 93 0.002 22.4 4.2 35 17-53 24-58 (154)
271 PF14229 DUF4332: Domain of un 32.2 49 0.0011 22.9 2.6 25 32-56 26-50 (122)
272 PRK14996 TetR family transcrip 32.1 79 0.0017 22.9 3.9 42 18-62 14-55 (192)
273 PRK11475 DNA-binding transcrip 31.8 1.4E+02 0.003 22.5 5.3 44 11-62 133-176 (207)
274 TIGR02054 MerD mercuric resist 31.4 41 0.00088 23.4 2.1 20 37-56 5-24 (120)
275 TIGR01557 myb_SHAQKYF myb-like 31.3 1.2E+02 0.0026 18.1 4.4 52 8-61 1-55 (57)
276 PF13700 DUF4158: Domain of un 31.3 1.8E+02 0.0039 20.9 5.6 56 9-65 38-99 (166)
277 PF13560 HTH_31: Helix-turn-he 31.3 31 0.00068 20.5 1.3 25 37-61 16-40 (64)
278 cd04782 HTH_BltR Helix-Turn-He 31.1 46 0.001 21.9 2.2 20 38-57 3-22 (97)
279 PF08279 HTH_11: HTH domain; 31.1 53 0.0012 18.7 2.3 36 17-57 2-37 (55)
280 TIGR01958 nuoE_fam NADH-quinon 31.0 1E+02 0.0022 22.0 4.2 36 16-53 17-52 (148)
281 PF13565 HTH_32: Homeodomain-l 30.9 1.3E+02 0.0028 18.3 5.5 33 14-48 32-65 (77)
282 TIGR02997 Sig70-cyanoRpoD RNA 30.5 74 0.0016 25.4 3.7 48 12-62 249-296 (298)
283 PF01257 2Fe-2S_thioredx: Thio 30.5 85 0.0018 22.3 3.7 34 18-53 16-49 (145)
284 PF07750 GcrA: GcrA cell cycle 30.5 82 0.0018 23.1 3.7 35 12-53 2-37 (162)
285 cd04775 HTH_Cfa-like Helix-Tur 30.5 43 0.00094 22.2 2.0 19 38-56 4-22 (102)
286 PF04712 Radial_spoke: Radial 30.4 26 0.00057 30.4 1.2 19 113-131 333-352 (491)
287 PF05044 HPD: Homeo-prospero d 30.2 32 0.00068 24.9 1.3 53 12-66 2-57 (158)
288 PF03457 HA: Helicase associat 30.1 74 0.0016 19.2 2.9 43 17-67 11-53 (68)
289 cd04767 HTH_HspR-like_MBC Heli 30.0 48 0.001 23.1 2.2 20 38-57 4-23 (120)
290 TIGR03685 L21P_arch 50S riboso 29.9 20 0.00042 24.5 0.2 20 32-51 16-35 (105)
291 PRK07571 bidirectional hydroge 29.9 1.1E+02 0.0024 22.6 4.3 34 18-53 39-72 (169)
292 COG1905 NuoE NADH:ubiquinone o 29.8 1.1E+02 0.0023 22.6 4.1 36 15-52 25-60 (160)
293 cd04788 HTH_NolA-AlbR Helix-Tu 29.7 50 0.0011 21.6 2.2 20 38-57 3-22 (96)
294 PRK12427 flagellar biosynthesi 29.6 1.5E+02 0.0033 22.6 5.3 46 12-64 183-228 (231)
295 PF07219 HemY_N: HemY protein 29.3 86 0.0019 21.0 3.4 21 48-68 43-63 (108)
296 PF00440 TetR_N: Bacterial reg 29.3 51 0.0011 18.4 1.9 26 36-61 17-42 (47)
297 PRK09975 DNA-binding transcrip 29.2 55 0.0012 24.1 2.6 42 18-62 17-58 (213)
298 cd01279 HTH_HspR-like Helix-Tu 29.1 51 0.0011 21.7 2.2 19 38-56 4-22 (98)
299 PRK09726 antitoxin HipB; Provi 29.0 37 0.0008 21.9 1.5 43 12-60 7-50 (88)
300 cd01111 HTH_MerD Helix-Turn-He 29.0 52 0.0011 22.2 2.3 19 38-56 3-21 (107)
301 PF06971 Put_DNA-bind_N: Putat 28.9 43 0.00093 19.6 1.6 17 38-54 31-47 (50)
302 COG5484 Uncharacterized conser 28.8 41 0.0009 26.7 1.9 31 32-64 16-46 (279)
303 smart00354 HTH_LACI helix_turn 28.2 40 0.00087 20.7 1.5 23 38-60 3-25 (70)
304 cd04789 HTH_Cfa Helix-Turn-Hel 28.1 51 0.0011 21.9 2.0 19 38-56 4-22 (102)
305 PTZ00096 40S ribosomal protein 27.9 48 0.001 23.9 2.0 6 46-51 48-53 (143)
306 PF02724 CDC45: CDC45-like pro 27.8 19 0.00042 32.1 -0.1 10 19-28 17-26 (622)
307 PRK00215 LexA repressor; Valid 27.4 81 0.0018 23.5 3.3 41 13-57 2-46 (205)
308 PF07471 Phage_Nu1: Phage DNA 27.4 46 0.001 24.5 1.9 19 38-56 5-23 (164)
309 KOG0044|consensus 27.0 73 0.0016 24.1 2.9 30 32-61 8-37 (193)
310 cd01107 HTH_BmrR Helix-Turn-He 26.7 55 0.0012 21.9 2.1 19 38-56 3-21 (108)
311 cd04765 HTH_MlrA-like_sg2 Heli 26.7 61 0.0013 21.5 2.2 20 38-57 3-22 (99)
312 PF13404 HTH_AsnC-type: AsnC-t 26.7 51 0.0011 18.3 1.6 16 38-53 20-35 (42)
313 PF01294 Ribosomal_L13e: Ribos 26.5 66 0.0014 24.1 2.5 20 50-69 14-34 (179)
314 PF15360 Apelin: APJ endogenou 26.5 25 0.00055 20.7 0.3 12 4-15 38-49 (55)
315 PF12200 DUF3597: Domain of un 26.2 1.2E+02 0.0026 21.4 3.6 27 32-58 82-113 (127)
316 cd01109 HTH_YyaN Helix-Turn-He 26.2 57 0.0012 22.0 2.1 19 38-56 3-21 (113)
317 PRK06596 RNA polymerase factor 26.0 2.1E+02 0.0045 22.7 5.6 50 12-66 230-279 (284)
318 PHA01083 hypothetical protein 25.9 1.3E+02 0.0028 21.9 3.9 18 32-49 43-60 (149)
319 PHA02955 hypothetical protein; 25.8 85 0.0018 24.2 3.1 45 16-61 61-105 (213)
320 PRK15479 transcriptional regul 25.8 1.6E+02 0.0035 21.1 4.6 49 11-63 147-200 (221)
321 PRK13756 tetracycline represso 25.4 1.5E+02 0.0032 22.3 4.4 50 12-64 3-53 (205)
322 cd00592 HTH_MerR-like Helix-Tu 25.2 68 0.0015 20.9 2.3 19 38-56 3-21 (100)
323 PF12802 MarR_2: MarR family; 25.1 81 0.0018 18.2 2.4 37 13-53 3-39 (62)
324 KOG0699|consensus 24.9 32 0.0007 29.0 0.7 7 19-25 89-95 (542)
325 cd08315 Death_TRAILR_DR4_DR5 D 24.9 1.1E+02 0.0023 20.3 3.2 36 18-54 3-38 (96)
326 PRK09191 two-component respons 24.9 1.8E+02 0.004 21.8 4.9 46 13-65 89-134 (261)
327 COG3769 Predicted hydrolase (H 24.8 58 0.0013 25.6 2.0 34 16-52 108-141 (274)
328 COG0789 SoxR Predicted transcr 24.7 63 0.0014 21.8 2.1 18 38-55 3-20 (124)
329 PRK00135 scpB segregation and 24.6 1.4E+02 0.0031 22.4 4.2 36 8-49 83-118 (188)
330 KOG0943|consensus 24.4 29 0.00064 33.9 0.4 11 15-25 1560-1570(3015)
331 cd02413 40S_S3_KH K homology R 24.3 29 0.00063 22.3 0.3 21 37-57 55-75 (81)
332 COG1309 AcrR Transcriptional r 24.3 1.2E+02 0.0026 20.6 3.6 37 21-60 21-57 (201)
333 PF05703 Auxin_canalis: Auxin 24.1 1.6E+02 0.0034 23.2 4.3 23 48-70 99-121 (242)
334 cd01282 HTH_MerR-like_sg3 Heli 24.0 66 0.0014 21.7 2.1 19 38-56 3-21 (112)
335 TIGR01950 SoxR redox-sensitive 23.8 70 0.0015 22.8 2.2 20 38-57 4-23 (142)
336 KOG3241|consensus 23.8 1.6E+02 0.0035 22.2 4.1 19 57-75 126-144 (227)
337 PRK13182 racA polar chromosome 23.7 69 0.0015 23.8 2.2 20 38-57 3-22 (175)
338 PF08595 RXT2_N: RXT2-like, N- 23.5 37 0.00081 24.6 0.8 8 58-65 3-10 (149)
339 PF08671 SinI: Anti-repressor 23.5 62 0.0013 16.8 1.4 18 40-57 10-27 (30)
340 PF09779 Ima1_N: Ima1 N-termin 23.5 12 0.00026 26.5 -1.8 15 52-66 1-15 (131)
341 PF08765 Mor: Mor transcriptio 23.4 90 0.002 21.0 2.6 24 37-60 74-97 (108)
342 TIGR02043 ZntR Zn(II)-responsi 23.2 75 0.0016 22.2 2.3 20 38-57 4-23 (131)
343 KOG2066|consensus 23.1 99 0.0021 28.6 3.4 45 22-68 513-557 (846)
344 PF10078 DUF2316: Uncharacteri 23.0 65 0.0014 21.3 1.7 37 13-55 3-43 (89)
345 PF04889 Cwf_Cwc_15: Cwf15/Cwc 23.0 35 0.00076 26.8 0.6 9 44-52 38-46 (244)
346 PRK09210 RNA polymerase sigma 22.9 2.1E+02 0.0045 23.7 5.2 52 12-66 305-356 (367)
347 PRK09514 zntR zinc-responsive 22.9 75 0.0016 22.5 2.2 20 38-57 4-23 (140)
348 TIGR02051 MerR Hg(II)-responsi 22.8 69 0.0015 22.1 2.0 18 38-55 2-19 (124)
349 cd04776 HTH_GnyR Helix-Turn-He 22.7 71 0.0015 21.9 2.0 18 38-55 3-20 (118)
350 PF08553 VID27: VID27 cytoplas 22.7 29 0.00063 32.0 0.1 13 6-18 159-171 (794)
351 PF00165 HTH_AraC: Bacterial r 22.5 88 0.0019 16.8 2.0 26 32-57 5-30 (42)
352 cd01110 HTH_SoxR Helix-Turn-He 22.4 77 0.0017 22.4 2.2 19 38-56 4-22 (139)
353 PF03444 HrcA_DNA-bdg: Winged 22.2 1.4E+02 0.003 19.3 3.1 38 13-54 2-42 (78)
354 PF11388 DotA: Phagosome traff 21.9 1.1E+02 0.0024 20.5 2.6 20 48-67 28-47 (105)
355 cd04772 HTH_TioE_rpt1 First He 21.9 78 0.0017 20.9 2.0 19 38-56 3-21 (99)
356 PF06163 DUF977: Bacterial pro 21.8 1.4E+02 0.0031 21.1 3.4 42 11-57 3-48 (127)
357 PF12114 Period_C: Period prot 21.8 1.1E+02 0.0023 23.3 2.9 35 13-57 121-155 (195)
358 PF02042 RWP-RK: RWP-RK domain 21.8 1.5E+02 0.0032 17.5 2.9 27 18-53 7-33 (52)
359 TIGR03613 RutR pyrimidine util 21.8 1E+02 0.0022 22.4 2.9 45 18-65 14-58 (202)
360 cd04781 HTH_MerR-like_sg6 Heli 21.8 76 0.0017 21.7 2.0 19 38-56 3-21 (120)
361 PF01372 Melittin: Melittin; 21.7 67 0.0015 16.0 1.2 12 50-61 14-25 (26)
362 TIGR02044 CueR Cu(I)-responsiv 21.7 75 0.0016 21.9 2.0 19 38-56 3-21 (127)
363 PF13613 HTH_Tnp_4: Helix-turn 21.3 1.8E+02 0.0038 16.7 4.0 21 38-58 22-42 (53)
364 PF14410 GH-E: HNH/ENDO VII su 21.3 1.2E+02 0.0025 19.0 2.6 27 31-57 23-51 (70)
365 PF12833 HTH_18: Helix-turn-he 21.3 67 0.0014 19.8 1.5 9 43-51 18-26 (81)
366 PRK10227 DNA-binding transcrip 21.2 79 0.0017 22.3 2.0 18 38-55 3-20 (135)
367 cd01108 HTH_CueR Helix-Turn-He 21.2 79 0.0017 21.8 2.0 19 38-56 3-21 (127)
368 PRK13719 conjugal transfer tra 21.0 3.1E+02 0.0066 21.3 5.3 44 11-62 142-185 (217)
369 TIGR02047 CadR-PbrR Cd(II)/Pb( 20.9 88 0.0019 21.6 2.2 20 38-57 3-22 (127)
370 PTZ00044 ubiquitin; Provisiona 20.8 33 0.00071 21.1 -0.0 25 36-60 25-49 (76)
371 KOG0943|consensus 20.7 39 0.00085 33.1 0.5 9 18-26 1613-1621(3015)
372 cd04770 HTH_HMRTR Helix-Turn-H 20.7 83 0.0018 21.4 2.0 19 38-56 3-21 (123)
373 cd01798 parkin_N amino-termina 20.7 45 0.00098 20.2 0.6 25 36-60 23-47 (70)
374 PF15325 MRI: Modulator of ret 20.6 2.8E+02 0.0061 18.7 4.5 9 124-132 77-85 (106)
375 PRK10336 DNA-binding transcrip 20.4 2.3E+02 0.005 20.2 4.5 49 11-63 148-201 (219)
376 COG0735 Fur Fe2+/Zn2+ uptake r 20.3 2.6E+02 0.0056 19.8 4.6 39 6-46 12-50 (145)
377 PRK13749 transcriptional regul 20.3 88 0.0019 21.8 2.1 19 37-55 5-23 (121)
378 PF13873 Myb_DNA-bind_5: Myb/S 20.2 2.2E+02 0.0048 17.4 5.2 56 10-66 2-75 (78)
379 PRK13558 bacterio-opsin activa 20.2 1.8E+02 0.0038 25.7 4.5 42 11-54 606-649 (665)
No 1
>KOG0484|consensus
Probab=99.89 E-value=3.3e-23 Score=138.60 Aligned_cols=70 Identities=29% Similarity=0.307 Sum_probs=64.0
Q ss_pred cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHhhcC
Q psy10851 4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQEG 75 (159)
Q Consensus 4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~~~~ 75 (159)
++-||-||+||..||..|+..|... |||++-.|++||.++.|++..|||||||||+|.||+.+.......
T Consensus 15 rKQRRIRTTFTS~QLkELErvF~ET--HYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~~~ 84 (125)
T KOG0484|consen 15 RKQRRIRTTFTSAQLKELERVFAET--HYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAKMA 84 (125)
T ss_pred HHhhhhhhhhhHHHHHHHHHHHHhh--cCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHHhh
Confidence 3457789999999999999999999 899999999999999999999999999999999999877665554
No 2
>KOG2251|consensus
Probab=99.87 E-value=9.6e-22 Score=147.83 Aligned_cols=66 Identities=27% Similarity=0.276 Sum_probs=62.7
Q ss_pred CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHH
Q psy10851 3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKA 70 (159)
Q Consensus 3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~ 70 (159)
.++.||.||+|+..|+.+|+.+|.+. + ||+..+|++||.+|+|.+.+|+|||+|||+|||+++...
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~kT-q-YPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAKT-Q-YPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHhh-c-CccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 46788999999999999999999999 7 999999999999999999999999999999999988765
No 3
>KOG0850|consensus
Probab=99.86 E-value=1.5e-21 Score=147.40 Aligned_cols=66 Identities=27% Similarity=0.359 Sum_probs=62.6
Q ss_pred CCcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851 2 PQYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69 (159)
Q Consensus 2 ~~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~ 69 (159)
+.++.|++||.|+.-||..|++.|.++ + |.-..+|.+||..|||+.+||||||||||.|.||..+.
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkT-Q-YLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~ 183 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQT-Q-YLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQ 183 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhc-c-hhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhc
Confidence 356889999999999999999999999 8 99999999999999999999999999999999998874
No 4
>KOG0843|consensus
Probab=99.84 E-value=2.1e-21 Score=141.81 Aligned_cols=65 Identities=29% Similarity=0.382 Sum_probs=61.2
Q ss_pred cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHH
Q psy10851 4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKA 70 (159)
Q Consensus 4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~ 70 (159)
++-||.||.||..||..|+.+|..+ +|-...+|+.||+.|+|++.||+|||||||.|.||.+...
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~~--~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEGN--QYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhcC--CeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 3789999999999999999999999 5999999999999999999999999999999999986654
No 5
>KOG0842|consensus
Probab=99.84 E-value=2.5e-21 Score=153.49 Aligned_cols=71 Identities=23% Similarity=0.245 Sum_probs=64.1
Q ss_pred CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHhhcC
Q psy10851 3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQEG 75 (159)
Q Consensus 3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~~~~ 75 (159)
.+++||+|..||+.|+-.||+-|+++ + |.+..+|+.||..|+|+.+||||||||||.|+||+.+.......
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQ-R-YLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~ 220 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQ-R-YLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEAL 220 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhh-h-ccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcc
Confidence 34678889999999999999999999 7 99999999999999999999999999999999998776554443
No 6
>KOG0485|consensus
Probab=99.84 E-value=8.9e-21 Score=142.19 Aligned_cols=68 Identities=22% Similarity=0.264 Sum_probs=62.6
Q ss_pred CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHh
Q psy10851 3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQ 72 (159)
Q Consensus 3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~ 72 (159)
+.+.||.||+|+..|+-.|+..|... + |.+..+|..||+.|.|+++||||||||||.||||+......
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~k-r-YLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~e 168 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELK-R-YLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLE 168 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHH-h-hhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhh
Confidence 45789999999999999999999999 7 99999999999999999999999999999999998654433
No 7
>KOG0488|consensus
Probab=99.84 E-value=3.2e-21 Score=154.60 Aligned_cols=68 Identities=24% Similarity=0.235 Sum_probs=63.3
Q ss_pred cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHhh
Q psy10851 4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQ 73 (159)
Q Consensus 4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~~ 73 (159)
++.||.||.||..||..||+.|.+. + |.+..+|..||..|||+..||++||||||+||||+.......
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~Q-K-YLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~~ 237 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQ-K-YLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGEL 237 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHh-h-cccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhcc
Confidence 6788899999999999999999999 8 999999999999999999999999999999999997764433
No 8
>KOG0489|consensus
Probab=99.84 E-value=1.3e-21 Score=154.02 Aligned_cols=67 Identities=25% Similarity=0.286 Sum_probs=61.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHhh
Q psy10851 5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQ 73 (159)
Q Consensus 5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~~ 73 (159)
..||.||.||..|+..||+.|..| + |.++..|.+||..|+|+++||||||||||+||||..+.....
T Consensus 158 ~~kR~RtayT~~QllELEkEFhfN-~-YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEFHFN-K-YLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCCcccchhhhhhhhhhhccc-c-ccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 479999999999999999999999 6 999999999999999999999999999999999976644433
No 9
>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=99.81 E-value=6.2e-20 Score=112.58 Aligned_cols=57 Identities=37% Similarity=0.464 Sum_probs=55.4
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
||+|+.||..|+.+|+.+|..+ + ||+..++..||..|||+..+|++||+|||++.||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~-~-~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQEN-P-YPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHS-S-SCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHh-c-cccccccccccccccccccccccCHHHhHHHhCc
Confidence 6899999999999999999999 7 9999999999999999999999999999999986
No 10
>KOG0487|consensus
Probab=99.80 E-value=3.7e-20 Score=146.85 Aligned_cols=68 Identities=25% Similarity=0.313 Sum_probs=62.6
Q ss_pred cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHhh
Q psy10851 4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQ 73 (159)
Q Consensus 4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~~ 73 (159)
+..||||.-+|+.|+..||+.|..| . |++...|.+|++.|+|+++||||||||||+|.||..+....+
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN-~-YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r~~ 300 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFN-M-YITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENRLK 300 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHH-H-HHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhhcc
Confidence 5678999999999999999999999 5 999999999999999999999999999999999988654443
No 11
>KOG0848|consensus
Probab=99.78 E-value=3.6e-19 Score=137.16 Aligned_cols=62 Identities=31% Similarity=0.530 Sum_probs=58.1
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHH
Q psy10851 8 NFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAK 71 (159)
Q Consensus 8 r~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~ 71 (159)
|-|.++|..|+..||+.|..+ + |.++..+.+||..|||+++||||||||||+|.||..++..
T Consensus 201 KYRvVYTDhQRLELEKEfh~S-r-yITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTS-R-YITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred ceeEEecchhhhhhhhhhccc-c-ceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 458899999999999999999 7 9999999999999999999999999999999999977764
No 12
>KOG0492|consensus
Probab=99.78 E-value=4.5e-19 Score=132.19 Aligned_cols=66 Identities=23% Similarity=0.311 Sum_probs=60.6
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHhhc
Q psy10851 7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQE 74 (159)
Q Consensus 7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~~~ 74 (159)
|++||-||.+||..|++.|+.. + |.++.+|.+++..|.|+++||||||||||+|.||.+......-
T Consensus 145 RkPRtPFTtqQLlaLErkfrek-q-YLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~Ek~ 210 (246)
T KOG0492|consen 145 RKPRTPFTTQQLLALERKFREK-Q-YLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELEKL 210 (246)
T ss_pred CCCCCCCCHHHHHHHHHHHhHh-h-hhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHHHh
Confidence 5689999999999999999999 7 9999999999999999999999999999999999876554443
No 13
>KOG0494|consensus
Probab=99.77 E-value=3.6e-19 Score=136.68 Aligned_cols=65 Identities=32% Similarity=0.442 Sum_probs=59.6
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHhh
Q psy10851 7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQ 73 (159)
Q Consensus 7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~~ 73 (159)
|+-||.||..|+..|+..|+.. |||+..-|+.||.++.|.+.+|+|||||||+||||..+.....
T Consensus 142 Rh~RTiFT~~Qle~LEkaFkea--HYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~s 206 (332)
T KOG0494|consen 142 RHFRTIFTSYQLEELEKAFKEA--HYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGS 206 (332)
T ss_pred ccccchhhHHHHHHHHHHHhhc--cCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcc
Confidence 3349999999999999999999 8999999999999999999999999999999999987765443
No 14
>KOG0491|consensus
Probab=99.72 E-value=4.2e-18 Score=122.84 Aligned_cols=65 Identities=31% Similarity=0.321 Sum_probs=60.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHH
Q psy10851 5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAK 71 (159)
Q Consensus 5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~ 71 (159)
++++.||+|+..|+..|++.|... + |.+..+|.+||-+|+|+++||+.||||||+|.||.+++..
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~Q-r-YLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQ-R-YLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred HhhhhcccccCccccccHHHHhhh-h-hcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 356789999999999999999999 7 9999999999999999999999999999999999877654
No 15
>KOG0493|consensus
Probab=99.72 E-value=5.4e-18 Score=130.39 Aligned_cols=58 Identities=34% Similarity=0.483 Sum_probs=56.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
||+||.||.+||..|+..|..+ + |.+...|..||..|+|++.||+|||||+|+|.||.
T Consensus 247 KRPRTAFtaeQL~RLK~EF~en-R-YlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQEN-R-YLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred cCccccccHHHHHHHHHHHhhh-h-hHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 6899999999999999999999 7 99999999999999999999999999999999985
No 16
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.71 E-value=1.7e-17 Score=101.09 Aligned_cols=56 Identities=39% Similarity=0.509 Sum_probs=52.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851 7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK 64 (159)
Q Consensus 7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~r 64 (159)
++.|++|+..|+.+|+..|..+ + ||+..++..||..+||+..+|++||+|||++.|
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~-~-~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKN-P-YPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhC-C-CCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 5788999999999999999999 6 999999999999999999999999999998864
No 17
>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=99.71 E-value=3.1e-17 Score=100.78 Aligned_cols=58 Identities=36% Similarity=0.544 Sum_probs=54.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
++.|+.|+..|+.+|+.+|..+ + ||+..++..||..+||+..+|++||+|||++.++.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~-~-~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKN-P-YPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhC-C-CCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 4688999999999999999999 7 99999999999999999999999999999998863
No 18
>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=99.71 E-value=8.4e-18 Score=102.86 Aligned_cols=52 Identities=17% Similarity=0.297 Sum_probs=50.3
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCC----CCHHHHHHHHHHhCCCchhhhhhhhhHH
Q psy10851 7 QNFQTIRLLNLKVKLKTSFNSCCPGH----KTTQVREALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 7 kr~Rt~~s~~Q~~~Le~~F~~~~~~y----p~~~~r~~La~~l~l~~~~V~vWFqNRR 60 (159)
||.||.||.+|+..|+.+|..+ + | |+..+|.+||..|||+.++|+|||||.+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~-~-y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKL-G-WKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHc-C-CCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 8999999999999999999999 5 9 9999999999999999999999999965
No 19
>KOG4577|consensus
Probab=99.69 E-value=9.8e-17 Score=125.03 Aligned_cols=62 Identities=40% Similarity=0.644 Sum_probs=59.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851 6 FQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69 (159)
Q Consensus 6 ~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~ 69 (159)
-||+||+||..||..|+..|+.. + .|.+..|++|+..+||.-++|||||||||||.||.++.
T Consensus 167 nKRPRTTItAKqLETLK~AYn~S-p-KPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T KOG4577|consen 167 NKRPRTTITAKQLETLKQAYNTS-P-KPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T ss_pred cCCCcceeeHHHHHHHHHHhcCC-C-chhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence 58999999999999999999999 8 99999999999999999999999999999999997653
No 20
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.68 E-value=6.3e-17 Score=117.96 Aligned_cols=66 Identities=24% Similarity=0.239 Sum_probs=61.4
Q ss_pred CCcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851 2 PQYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69 (159)
Q Consensus 2 ~~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~ 69 (159)
..+..+++|++.|..|+.+|+..|..+ + ||+...|..|+..|||+++-|+|||||||++.|+....
T Consensus 47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~-p-~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 47 GSSPPKSKRRRTTDEQLMVLEREFEIN-P-YPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CCCcCcccceechHHHHHHHHHHhccC-C-CCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 346789999999999999999999999 7 99999999999999999999999999999999987554
No 21
>KOG0486|consensus
Probab=99.67 E-value=2.6e-17 Score=129.44 Aligned_cols=65 Identities=28% Similarity=0.320 Sum_probs=61.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHH
Q psy10851 5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAK 71 (159)
Q Consensus 5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~ 71 (159)
+-||.||.||.+|+..|+.+|.++ + ||+...|++||..++|++..|+|||+|||+||||+.+...
T Consensus 111 KqrrQrthFtSqqlqele~tF~rN-r-ypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRN-R-YPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhc-c-CCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 457889999999999999999999 7 9999999999999999999999999999999999988766
No 22
>KOG3802|consensus
Probab=99.65 E-value=4e-17 Score=132.28 Aligned_cols=63 Identities=30% Similarity=0.372 Sum_probs=59.4
Q ss_pred cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
.++||+||.|+...+.+|+.+|.+| + .|+..++..||..|+|.+.+|+|||||||+|.||...
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~n-p-KPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLKN-P-KPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHhC-C-CCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 3678899999999999999999999 8 9999999999999999999999999999999998644
No 23
>KOG0844|consensus
Probab=99.65 E-value=3.5e-17 Score=128.40 Aligned_cols=64 Identities=23% Similarity=0.300 Sum_probs=59.5
Q ss_pred CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
+.+-||-||.||.+|+..|++.|.+. +|-++..|.+||..|||.+..|||||||||+|+||+..
T Consensus 178 ~dqmRRYRTAFTReQIaRLEKEFyrE--NYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 178 DDQMRRYRTAFTREQIARLEKEFYRE--NYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred cHHHHHHHhhhhHHHHHHHHHHHHHh--ccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 34578999999999999999999998 69999999999999999999999999999999999754
No 24
>KOG0483|consensus
Probab=99.64 E-value=1.2e-16 Score=120.25 Aligned_cols=60 Identities=33% Similarity=0.369 Sum_probs=55.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 6 FQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 6 ~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
.+++..+|+.+|+..|+..|... +|..+..+..||+.|||.++||.|||||||||||..+
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~--~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq 109 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESE--KKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ 109 (198)
T ss_pred cccccccccHHHHHHhHHhhccc--cccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence 45667789999999999999999 6999999999999999999999999999999999864
No 25
>KOG0847|consensus
Probab=99.57 E-value=3.7e-15 Score=112.29 Aligned_cols=67 Identities=21% Similarity=0.251 Sum_probs=60.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHhh
Q psy10851 5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQ 73 (159)
Q Consensus 5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~~ 73 (159)
++|..|.+|+..|+..|+..|.+. + |+-...|.+||..+||++.||+|||||||.||||+.......
T Consensus 166 ~rk~srPTf~g~qi~~le~~feqt-k-ylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmas 232 (288)
T KOG0847|consen 166 QRKQSRPTFTGHQIYQLERKFEQT-K-YLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMAS 232 (288)
T ss_pred cccccCCCccchhhhhhhhhhhhh-h-cccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhh
Confidence 455678899999999999999999 7 999999999999999999999999999999999986544433
No 26
>KOG0775|consensus
Probab=99.54 E-value=4.8e-14 Score=109.31 Aligned_cols=59 Identities=25% Similarity=0.380 Sum_probs=51.8
Q ss_pred CCCCCCCCCHHH---------HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 6 FQNFQTIRLLNL---------KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 6 ~kr~Rt~~s~~Q---------~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
|--+||.+..++ ..+|+.+|.++ + ||++.++.+||+++||+..||-+||+|||+|+|..
T Consensus 167 fPlPrTIWDGEet~yCFKekSR~~LrewY~~~-~-YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~ 234 (304)
T KOG0775|consen 167 FPLPRTIWDGEETVYCFKEKSRSLLREWYLQN-P-YPSPREKRELAEATGLTITQVSNWFKNRRQRDRAA 234 (304)
T ss_pred CCCCCccccCceeeeehhHhhHHHHHHHHhcC-C-CCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhc
Confidence 334677766555 68999999999 8 99999999999999999999999999999999944
No 27
>KOG0490|consensus
Probab=99.48 E-value=3.5e-14 Score=109.41 Aligned_cols=64 Identities=28% Similarity=0.255 Sum_probs=60.4
Q ss_pred CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
....||.|++|+..|+..|+..|..+ |||+...|+.||..++|++..|+|||||||+|||++..
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~--h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKV--HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCC--CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 34678899999999999999999999 79999999999999999999999999999999999875
No 28
>KOG0849|consensus
Probab=99.44 E-value=3.5e-13 Score=110.35 Aligned_cols=65 Identities=37% Similarity=0.408 Sum_probs=61.0
Q ss_pred CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851 3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69 (159)
Q Consensus 3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~ 69 (159)
.++.+|.||+|+..|+..|++.|..+ + ||+...|+.||..++|++..|+|||+|||+|+||....
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt-~-yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRT-P-YPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred cccccccccccccchHHHHHHHhcCC-C-CCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 36788899999999999999999999 6 99999999999999999999999999999999998743
No 29
>KOG0774|consensus
Probab=99.37 E-value=1.6e-12 Score=100.41 Aligned_cols=63 Identities=27% Similarity=0.315 Sum_probs=57.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhc--CCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851 6 FQNFQTIRLLNLKVKLKTSFNSC--CPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69 (159)
Q Consensus 6 ~kr~Rt~~s~~Q~~~Le~~F~~~--~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~ 69 (159)
.||+|..|++.-..+|..+|... || ||+...+++||+++|++..||.+||.|+|-+.||....
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nP-YPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k 252 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNP-YPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGK 252 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCC-CCcHHHHHHHHHHcCceehhhccccccceeehhhhhhh
Confidence 47889999999999999999654 69 99999999999999999999999999999999997543
No 30
>KOG1168|consensus
Probab=99.33 E-value=4.5e-13 Score=104.76 Aligned_cols=65 Identities=31% Similarity=0.362 Sum_probs=60.0
Q ss_pred CCcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 2 PQYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 2 ~~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
|---.||+||.+-.-..+.|+.+|..+ | .|+.+.+..||.+|.|...+|+|||||.|+|-||...
T Consensus 305 ~~~ekKRKRTSIAAPEKRsLEayFavQ-P-RPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 305 PGGEKKRKRTSIAAPEKRSLEAYFAVQ-P-RPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred CccccccccccccCcccccHHHHhccC-C-CCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence 344578999999999999999999999 8 9999999999999999999999999999999998654
No 31
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=99.08 E-value=1.1e-10 Score=66.25 Aligned_cols=33 Identities=39% Similarity=0.672 Sum_probs=28.5
Q ss_pred CCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHH
Q psy10851 29 CPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAK 62 (159)
Q Consensus 29 ~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k 62 (159)
|| ||+..++..||..+||+..||.+||-|.|.|
T Consensus 8 nP-YPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 8 NP-YPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp SG-S--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CC-CCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 49 9999999999999999999999999999975
No 32
>KOG2252|consensus
Probab=99.06 E-value=4.5e-10 Score=94.68 Aligned_cols=56 Identities=16% Similarity=0.224 Sum_probs=53.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHH
Q psy10851 6 FQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKM 63 (159)
Q Consensus 6 ~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~ 63 (159)
-||+|.+||..|+..|..+|+.+ + ||+..+.+.|+.+|||..+.|.+||.|.|.|.
T Consensus 420 ~KKPRlVfTd~QkrTL~aiFke~-~-RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 420 TKKPRLVFTDIQKRTLQAIFKEN-K-RPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred CCCceeeecHHHHHHHHHHHhcC-C-CCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 57899999999999999999999 8 99999999999999999999999999999876
No 33
>KOG0490|consensus
Probab=98.61 E-value=4.2e-08 Score=75.43 Aligned_cols=63 Identities=43% Similarity=0.547 Sum_probs=58.9
Q ss_pred cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
.+.++.|+.++..|+..|...|..+ . ||+...+..|+..+|++...|++||+|+|++.++...
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~-~-~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRAT-P-KPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cccCCCccccccchhHhhhhcccCC-C-CCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 4577889999999999999999999 5 9999999999999999999999999999999998755
No 34
>KOG1146|consensus
Probab=98.35 E-value=5.9e-07 Score=82.45 Aligned_cols=63 Identities=33% Similarity=0.374 Sum_probs=59.3
Q ss_pred cCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 4 YWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 4 ~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
+.||+.|+.++..||.+|..+|... . ||.....+-|...++|..++|++||||.|+|.||...
T Consensus 901 ~~r~a~~~~~~d~qlk~i~~~~~~q-~-~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 901 MGRRAYRTQESDLQLKIIKACYEAQ-R-TPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhhccchhHHHHHHHHHHHhhc-c-CChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 4578899999999999999999999 5 9999999999999999999999999999999999876
No 35
>KOG0773|consensus
Probab=97.76 E-value=1.5e-05 Score=65.14 Aligned_cols=62 Identities=26% Similarity=0.171 Sum_probs=51.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhc--CCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 6 FQNFQTIRLLNLKVKLKTSFNSC--CPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 6 ~kr~Rt~~s~~Q~~~Le~~F~~~--~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
.+|++..+......+|+.++..+ .| ||+...+..||..+||+..||.+||-|.|-|..+-..
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~P-YPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHP-YPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCC-CCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence 34556689999999999885442 27 9999999999999999999999999999988776544
No 36
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.64 E-value=4.6e-05 Score=46.03 Aligned_cols=41 Identities=15% Similarity=0.256 Sum_probs=31.1
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHH
Q psy10851 18 KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 18 ~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR 60 (159)
+..|+.+|... + ++.......|..+.+|+..||+.||--|+
T Consensus 10 ~~pL~~Yy~~h-~-~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKH-K-QLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT------TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHHc-C-CccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 46799999999 5 99999999999999999999999996553
No 37
>KOG3623|consensus
Probab=97.00 E-value=0.0012 Score=58.30 Aligned_cols=49 Identities=22% Similarity=0.423 Sum_probs=45.3
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 18 KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 18 ~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
+..|+.+|..| . .|+..+...||...||....|++||++++++-+...+
T Consensus 568 ~sllkayyaln-~-~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~r 616 (1007)
T KOG3623|consen 568 TSLLKAYYALN-G-LPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVER 616 (1007)
T ss_pred HHHHHHHHHhc-C-CCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhcc
Confidence 78999999999 5 9999999999999999999999999999998877554
No 38
>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=96.82 E-value=0.005 Score=36.84 Aligned_cols=47 Identities=15% Similarity=0.237 Sum_probs=35.4
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHH
Q psy10851 7 QNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 7 kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR 60 (159)
||+|..+|-.+...+-..+... . ....||..+|++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g-~------s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEG-E------SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCT-T-------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcC-C------CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 6899999999977777777655 2 578899999999999999999864
No 39
>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=92.83 E-value=0.43 Score=27.57 Aligned_cols=47 Identities=15% Similarity=0.145 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
.+++.+..+|...|-.. ..-.++|..+|++...|+.+...-..|.|+
T Consensus 4 ~L~~~er~vi~~~y~~~-------~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-------LTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTST--------SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-------CCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 46788899999888544 246789999999999999998776666653
No 40
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=91.87 E-value=0.21 Score=31.29 Aligned_cols=43 Identities=14% Similarity=0.227 Sum_probs=28.5
Q ss_pred CCCCCCCHHHHHHHHHHH-hhcCCCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy10851 8 NFQTIRLLNLKVKLKTSF-NSCCPGHKTTQVREALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 8 r~Rt~~s~~Q~~~Le~~F-~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFq 57 (159)
++|.+||.++...+-..+ ... .....||..+||+...|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-------~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-------ESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-------CHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-------CceEeeecccccccccccHHHH
Confidence 577899999976665555 333 3788999999999999999953
No 41
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=91.76 E-value=0.065 Score=42.22 Aligned_cols=6 Identities=17% Similarity=0.578 Sum_probs=2.4
Q ss_pred hhhhhh
Q psy10851 53 QVWFQN 58 (159)
Q Consensus 53 ~vWFqN 58 (159)
++-|+.
T Consensus 189 K~cfCd 194 (314)
T PF06524_consen 189 KICFCD 194 (314)
T ss_pred eeeehh
Confidence 344443
No 42
>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=91.51 E-value=0.69 Score=27.00 Aligned_cols=44 Identities=14% Similarity=0.049 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAK 62 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k 62 (159)
.+++.+..++...|-.. ....++|..+|++...|++|.+.-|.+
T Consensus 10 ~L~~~~r~i~~l~~~~g-------~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG-------MSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHHHTS----------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC-------cCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 34556666666554433 467889999999999999999766654
No 43
>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=91.44 E-value=0.46 Score=26.80 Aligned_cols=44 Identities=16% Similarity=0.058 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAK 62 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k 62 (159)
.++..+..++...|... + ....+|..+|++...|..|....+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~---~----~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEG---L----SYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcC---C----CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 46777888887776433 2 46678999999999999998766554
No 44
>KOG1832|consensus
Probab=91.08 E-value=0.072 Score=48.72 Aligned_cols=10 Identities=30% Similarity=0.202 Sum_probs=4.6
Q ss_pred ccccccCCCC
Q psy10851 123 LKIGYELGFF 132 (159)
Q Consensus 123 ~~~~~~~~~~ 132 (159)
....|+.|--
T Consensus 1391 ~~r~yEIGR~ 1400 (1516)
T KOG1832|consen 1391 SARMYEIGRR 1400 (1516)
T ss_pred hhhhhhhccc
Confidence 3444555543
No 45
>KOG1146|consensus
Probab=90.79 E-value=0.3 Score=46.32 Aligned_cols=63 Identities=19% Similarity=0.213 Sum_probs=57.9
Q ss_pred CcCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 3 QYWFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 3 ~~~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
.+.-|+.|+.+-..++.+|-.+|-.+ +-|+...+..|......+.+++.+||+|-|.|.++..
T Consensus 702 ~~~~~~~~~~~~~~aa~~l~~a~~~~--~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 702 SPRDKLLRLTILPEAAMILGRAYMQD--NSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred CcccccCcccccHHHHhhhhhcccCC--CCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 45667888999999999999999999 6899999999999999999999999999999999865
No 46
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=90.31 E-value=1.3 Score=31.98 Aligned_cols=52 Identities=13% Similarity=0.076 Sum_probs=41.5
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851 10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69 (159)
Q Consensus 10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~ 69 (159)
...+++.|+.+|... ... + ...+||..+|++...|+.|-++.+.|.|+....
T Consensus 4 ~~~Lt~rqreVL~lr-~~G---l----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 4 ESFLTERQIEVLRLR-ERG---L----TQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred ccCCCHHHHHHHHHH-HcC---C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 457899999999874 333 1 356899999999999999999988888886543
No 47
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=88.17 E-value=1.5 Score=32.58 Aligned_cols=31 Identities=6% Similarity=0.179 Sum_probs=26.9
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
...+||..+|++...|+++...-|.+.|+..
T Consensus 160 s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 160 TYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred CHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 5778999999999999999988888887754
No 48
>PRK00118 putative DNA-binding protein; Validated
Probab=88.12 E-value=2.6 Score=28.77 Aligned_cols=50 Identities=6% Similarity=0.002 Sum_probs=38.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
.++..|..++...|... . ...+||..+|++...|..|....|.+.|+...
T Consensus 17 ~L~ekqRevl~L~y~eg-~------S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~ 66 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD-Y------SLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEE 66 (104)
T ss_pred cCCHHHHHHHHHHHHcC-C------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45677777776665554 2 46779999999999999999988888887643
No 49
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=87.62 E-value=2 Score=30.89 Aligned_cols=49 Identities=12% Similarity=0.045 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
.+++.+..+|...|-.. .....||..+|++...|+.|...-+.+.|+..
T Consensus 128 ~L~~~~r~vl~l~~~~~-------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREIEG-------LSYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHHcC-------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45566666666554333 24668899999999999999987777777654
No 50
>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=87.19 E-value=1.1 Score=26.77 Aligned_cols=41 Identities=20% Similarity=0.106 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHHhhcCCC--CCCHHHHHHHHHHhCCCchhhhhh
Q psy10851 13 RLLNLKVKLKTSFNSCCPG--HKTTQVREALAKDTGLSVRVVQVW 55 (159)
Q Consensus 13 ~s~~Q~~~Le~~F~~~~~~--yp~~~~r~~La~~l~l~~~~V~vW 55 (159)
+|..|+.+|...|... . +|.......||..+|++...|..-
T Consensus 1 LT~~Q~e~L~~A~~~G--Yfd~PR~~tl~elA~~lgis~st~~~~ 43 (53)
T PF04967_consen 1 LTDRQREILKAAYELG--YFDVPRRITLEELAEELGISKSTVSEH 43 (53)
T ss_pred CCHHHHHHHHHHHHcC--CCCCCCcCCHHHHHHHhCCCHHHHHHH
Confidence 5789999999998765 1 366678889999999998766543
No 51
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=86.92 E-value=1.8 Score=30.58 Aligned_cols=46 Identities=15% Similarity=0.089 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 13 RLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 13 ~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
+++.+..++...|-.. ....+||..+|++...|++|...-|.+.|+
T Consensus 107 L~~~~r~ii~l~~~~~-------~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 107 LDEKEKYIIFERFFVG-------KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred CCHHHHHHHHHHHhcC-------CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 4455555554444333 347889999999999999999877777665
No 52
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=86.69 E-value=2 Score=32.25 Aligned_cols=32 Identities=22% Similarity=0.216 Sum_probs=27.2
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
....+||..+|++...|+++...-|.+.|+..
T Consensus 170 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 170 LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35778999999999999999988888877754
No 53
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=86.33 E-value=3 Score=29.95 Aligned_cols=33 Identities=15% Similarity=0.206 Sum_probs=27.7
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~ 69 (159)
...+||..+|++...|++|.+--|.+.|+....
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~ 158 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 467899999999999999998888888776443
No 54
>KOG1832|consensus
Probab=85.55 E-value=0.26 Score=45.31 Aligned_cols=21 Identities=29% Similarity=0.246 Sum_probs=8.6
Q ss_pred CCccccccccCCCCCcchhhh
Q psy10851 119 SSSVLKIGYELGFFIQEEEEE 139 (159)
Q Consensus 119 ~s~~~~~~~~~~~~~~ee~ee 139 (159)
+.-..-+|-.-.-.++.++||
T Consensus 1391 ~~r~yEIGR~r~~~dd~Deee 1411 (1516)
T KOG1832|consen 1391 SARMYEIGRRRPTDDDSDEEE 1411 (1516)
T ss_pred hhhhhhhcccCCCccccCccc
Confidence 344444444444344433333
No 55
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=85.53 E-value=3.1 Score=29.61 Aligned_cols=31 Identities=19% Similarity=0.208 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
...+||..+|++...|++.+..-|.+.|+..
T Consensus 124 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 124 SYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999988888877754
No 56
>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=85.30 E-value=2.8 Score=24.88 Aligned_cols=46 Identities=13% Similarity=0.050 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
.||..++.+|.-+..-. ...++|..+|++.+.|..+..+=+.|..-
T Consensus 3 ~LT~~E~~vl~~l~~G~--------~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM--------SNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp SS-HHHHHHHHHHHTTS---------HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred ccCHHHHHHHHHHHhcC--------CcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 57888999887765433 47789999999999999998887777543
No 57
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=85.28 E-value=3.3 Score=29.64 Aligned_cols=32 Identities=16% Similarity=0.239 Sum_probs=27.0
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
...+||..+|++...|+.|..--|.|.|+.-.
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999888888776543
No 58
>PRK04217 hypothetical protein; Provisional
Probab=85.11 E-value=3.5 Score=28.37 Aligned_cols=51 Identities=16% Similarity=0.041 Sum_probs=39.8
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 11 TIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 11 t~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
..++..++.++...|... + ...+||+.+|++...|...+...+.+.|....
T Consensus 41 ~~Lt~eereai~l~~~eG---l----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L~ 91 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEG---L----TQEEAGKRMGVSRGTVWRALTSARKKVAQMLV 91 (110)
T ss_pred ccCCHHHHHHHHHHHHcC---C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 367888888887766544 2 57789999999999999999888887776543
No 59
>PRK06930 positive control sigma-like factor; Validated
Probab=84.98 E-value=3.7 Score=30.37 Aligned_cols=50 Identities=10% Similarity=-0.034 Sum_probs=37.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
.+++.+..++...|... ....+||..+|++...|+++...-+.|.++...
T Consensus 114 ~L~~rer~V~~L~~~eg-------~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-------LSYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred hCCHHHHHHHHHHHHcC-------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45666666666654433 246789999999999999999988888887644
No 60
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=84.71 E-value=3.9 Score=29.16 Aligned_cols=48 Identities=19% Similarity=0.165 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 13 RLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 13 ~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
++..+..+|...| .. ....+||..+|++...|+++...-|.+.|+...
T Consensus 113 L~~~~r~il~l~~-~g-------~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 113 MTERDRTVLLLRF-SG-------YSYKEIAEALGIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred CCHHHHHHHHHHH-cC-------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4444555555444 22 356789999999999999999888888877644
No 61
>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=84.20 E-value=2.7 Score=27.97 Aligned_cols=39 Identities=21% Similarity=0.315 Sum_probs=21.6
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHh
Q psy10851 18 KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQ 72 (159)
Q Consensus 18 ~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~ 72 (159)
+.+.+-+|..| | ||...--.. |. .|||.+||+.+.+...
T Consensus 14 vRiIk~Lyqsn-P-yP~~~GTr~-aR-------------RnRRRRWR~rq~QI~~ 52 (91)
T PF00424_consen 14 VRIIKILYQSN-P-YPSPEGTRQ-AR-------------RNRRRRWRARQRQIRA 52 (91)
T ss_dssp HHHHHHHHHTS---S--S-S-HH-HH-------------HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHccc-c-CCCCCCccc-cc-------------cchhhhHHHHHHHHHH
Confidence 34555668777 9 997441111 11 7999999998765443
No 62
>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=84.08 E-value=3 Score=28.56 Aligned_cols=47 Identities=17% Similarity=0.140 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
.+++.+..++...|-.. .....||..+|++...|..|.+.-+.|.|+
T Consensus 110 ~L~~~~~~ii~~~~~~g-------~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLEG-------LSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhcC-------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45566666665443322 246689999999999999999877777665
No 63
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=84.02 E-value=2.4 Score=31.28 Aligned_cols=36 Identities=14% Similarity=0.196 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 32 HKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 32 yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
|.......+||..+|++...|++|+..-|.+.|+..
T Consensus 154 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 154 YYEGLSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred hhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 334446788999999999999999988888877753
No 64
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=83.81 E-value=3.4 Score=30.19 Aligned_cols=32 Identities=19% Similarity=0.099 Sum_probs=27.5
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
...+||..+|++...|++++..-|.+.|+...
T Consensus 149 s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 149 SIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 56789999999999999999988888887543
No 65
>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=83.69 E-value=3.6 Score=28.87 Aligned_cols=29 Identities=21% Similarity=0.417 Sum_probs=24.1
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
...+||..+|++...|+++...-|.|.|+
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 46778999999999999998777777665
No 66
>TIGR00927 2A1904 K+-dependent Na+/Ca+ exchanger.
Probab=83.62 E-value=0.45 Score=44.05 Aligned_cols=12 Identities=17% Similarity=0.725 Sum_probs=6.4
Q ss_pred hhhhhhhhhHHH
Q psy10851 50 RVVQVWFQNQRA 61 (159)
Q Consensus 50 ~~V~vWFqNRR~ 61 (159)
++|+.|+..+..
T Consensus 606 ~~i~~~~~~~~~ 617 (1096)
T TIGR00927 606 KQIELWVKEQLS 617 (1096)
T ss_pred HHHHHHHHHhhh
Confidence 556666654433
No 67
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=83.60 E-value=4.7 Score=29.78 Aligned_cols=33 Identities=12% Similarity=0.228 Sum_probs=27.6
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
....+||..+|++...|+++...-|.+.|+...
T Consensus 151 ~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 183 (189)
T PRK12530 151 LSSEQICQECDISTSNLHVLLYRARLQLQACLS 183 (189)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 357889999999999999999888877777543
No 68
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=83.43 E-value=3.9 Score=29.71 Aligned_cols=30 Identities=13% Similarity=0.407 Sum_probs=26.2
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
...+||..+|++...|+++.+.-|.+.|+.
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 477899999999999999998888887765
No 69
>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=83.15 E-value=4 Score=29.67 Aligned_cols=30 Identities=30% Similarity=0.278 Sum_probs=26.0
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
...+||..+|++...|++....-|.+.|+.
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999998888877764
No 70
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=83.03 E-value=3.6 Score=29.12 Aligned_cols=30 Identities=23% Similarity=0.283 Sum_probs=24.1
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
....+||..+|++...|+++...-|.+.|.
T Consensus 128 ~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 128 VSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 357789999999999999998766666554
No 71
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=83.02 E-value=3.1 Score=30.37 Aligned_cols=35 Identities=14% Similarity=0.018 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 33 KTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 33 p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
.......+||..+|++...|+++...-|.+.|+..
T Consensus 152 ~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 152 LEGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 33345788999999999999999987777777654
No 72
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=83.01 E-value=4 Score=29.89 Aligned_cols=32 Identities=13% Similarity=0.104 Sum_probs=26.9
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
...+||..+|++...|+++...-|.+.|+...
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999888888777544
No 73
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=82.95 E-value=1.8 Score=24.48 Aligned_cols=41 Identities=12% Similarity=0.008 Sum_probs=21.5
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy10851 10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFq 57 (159)
.+.+|..+...+..++... . -...||..+|.+...|..|.+
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G-~------s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQG-M------SIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ----------HHHHHHCS----------HHHHHHHTT--HHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcC-C------CHHHHHHHHCcCcHHHHHHHh
Confidence 3568888888888887655 2 466799999999999988864
No 74
>KOG3755|consensus
Probab=82.84 E-value=0.53 Score=41.31 Aligned_cols=45 Identities=13% Similarity=0.158 Sum_probs=30.8
Q ss_pred HHHHhhcCCCCCCHHHHHHHHHHhC-------CCchhhhhhhhhHHHHHHHHHH
Q psy10851 22 KTSFNSCCPGHKTTQVREALAKDTG-------LSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 22 e~~F~~~~~~yp~~~~r~~La~~l~-------l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
+.+|.++ . .++.....+.-..+. ...+.|+.||+|||.++++.+.
T Consensus 708 ~~w~~k~-~-s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~ 759 (769)
T KOG3755|consen 708 HHWKLKT-R-SGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKM 759 (769)
T ss_pred hhheecc-c-CchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhc
Confidence 4456666 3 677666655544443 3456799999999999998644
No 75
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=82.66 E-value=5 Score=29.48 Aligned_cols=32 Identities=16% Similarity=0.249 Sum_probs=27.4
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
...+||..+|++...|++-+..-|.+.|+...
T Consensus 149 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 149 SVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46788999999999999999888888887644
No 76
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=82.62 E-value=6 Score=28.81 Aligned_cols=34 Identities=12% Similarity=0.202 Sum_probs=29.4
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKA 70 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~ 70 (159)
...+||..+|++...|++....-|++.|+.-...
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~ 168 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIE 168 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 5778999999999999999999999998875543
No 77
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=82.51 E-value=3.4 Score=30.11 Aligned_cols=33 Identities=15% Similarity=0.180 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 35 TQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 35 ~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
.....+||..+|++...|+++++.-|.+.|+..
T Consensus 152 g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 152 DLSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 345778999999999999999988888777643
No 78
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=82.26 E-value=6 Score=29.22 Aligned_cols=34 Identities=9% Similarity=0.204 Sum_probs=28.7
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKA 70 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~ 70 (159)
...+||..+|++...|++....-|.+.|+.....
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~ 187 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQCLQIK 187 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 4678999999999999999988888888875433
No 79
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=82.08 E-value=5.8 Score=28.07 Aligned_cols=31 Identities=16% Similarity=0.042 Sum_probs=25.6
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
...+||..+|++...|++....-|.+.|+..
T Consensus 124 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 124 DVAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999887777777654
No 80
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=81.26 E-value=3.5 Score=33.62 Aligned_cols=54 Identities=15% Similarity=0.110 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
.++..|..+|...|-.. |-......+||..+|++...|+.+...-+.|.|+...
T Consensus 262 ~L~~~~R~vl~lrygL~---~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~ 315 (325)
T PRK05657 262 ELNDKQREVLARRFGLL---GYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQ 315 (325)
T ss_pred cCCHHHHHHHHHHhccC---CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 56777777777766433 3444567899999999999999999888888887643
No 81
>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=80.99 E-value=5 Score=19.94 Aligned_cols=39 Identities=8% Similarity=0.045 Sum_probs=27.7
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhh
Q psy10851 11 TIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 11 t~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWF 56 (159)
..++..+...+...|... + ....+|..+|++...|..|.
T Consensus 4 ~~~~~~~~~~i~~~~~~~---~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAAG---E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHcC---C----CHHHHHHHHCCCHHHHHHhC
Confidence 346677766666666533 3 45678899999999888874
No 82
>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=80.98 E-value=6.6 Score=28.42 Aligned_cols=50 Identities=16% Similarity=0.147 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
.+++.+..+|...|-.. ....+||..+|++...|+++.+--|.+.|+...
T Consensus 100 ~L~~~~r~v~~l~~~~g-------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG-------LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHHcC-------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 34555555555544333 246789999999999999999877777777544
No 83
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=80.78 E-value=4 Score=28.24 Aligned_cols=43 Identities=16% Similarity=0.291 Sum_probs=30.3
Q ss_pred CCCCCCCHHHHH-HHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy10851 8 NFQTIRLLNLKV-KLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 8 r~Rt~~s~~Q~~-~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFq 57 (159)
++|.+||.+... ++...+... .....||..+|++..+|..|.+
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g-------~sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPG-------MTVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCC-------CCHHHHHHHHCcCHHHHHHHHH
Confidence 456778888854 444444322 2467789999999999999953
No 84
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=80.62 E-value=5.3 Score=29.30 Aligned_cols=31 Identities=19% Similarity=0.157 Sum_probs=25.7
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
....+||..+|++...|+++...-|.+.|+.
T Consensus 156 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 156 LSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3578899999999999999997777777664
No 85
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=80.19 E-value=5.7 Score=29.03 Aligned_cols=30 Identities=13% Similarity=0.402 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
...+||..+|++...|++|...-|.+.|+.
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 467899999999999999998777777654
No 86
>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=80.18 E-value=4.3 Score=29.96 Aligned_cols=38 Identities=13% Similarity=0.143 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851 32 HKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69 (159)
Q Consensus 32 yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~ 69 (159)
|.......+||..+|++...|+++...-|.+.|+....
T Consensus 144 ~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 181 (193)
T TIGR02947 144 DVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD 181 (193)
T ss_pred hhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 34444678899999999999999999888888887554
No 87
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=80.12 E-value=4.5 Score=28.82 Aligned_cols=30 Identities=30% Similarity=0.390 Sum_probs=25.0
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
...+||..+|++...|+++...-|.+.|+.
T Consensus 130 s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 130 SYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 467889999999999999988777776653
No 88
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=79.80 E-value=7.4 Score=21.99 Aligned_cols=43 Identities=16% Similarity=0.159 Sum_probs=30.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAK 62 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k 62 (159)
.++..+..++.. +... + ....||..+|++...|..|.+.-+.|
T Consensus 3 ~l~~~e~~i~~~-~~~g---~----s~~eia~~l~is~~tv~~~~~~~~~k 45 (58)
T smart00421 3 SLTPREREVLRL-LAEG---L----TNKEIAERLGISEKTVKTHLSNIMRK 45 (58)
T ss_pred CCCHHHHHHHHH-HHcC---C----CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 467788887755 3222 2 45788999999999999998754443
No 89
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=79.55 E-value=6.3 Score=28.01 Aligned_cols=30 Identities=17% Similarity=0.359 Sum_probs=25.3
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
...+||..+|++...|+....-.|.+.|+.
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 477899999999999999987777777764
No 90
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=79.47 E-value=6.5 Score=28.90 Aligned_cols=33 Identities=24% Similarity=0.357 Sum_probs=27.3
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~ 69 (159)
...+||..+|++...|+..+..-|.+.|+....
T Consensus 124 ~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 124 SQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999998888777775444
No 91
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=79.41 E-value=6.3 Score=28.78 Aligned_cols=31 Identities=23% Similarity=0.110 Sum_probs=26.7
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
....+||..+|++...|++....-|.+.|+.
T Consensus 146 ~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 146 LSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3577899999999999999998888888774
No 92
>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=79.36 E-value=9.4 Score=28.17 Aligned_cols=35 Identities=9% Similarity=0.133 Sum_probs=28.6
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKA 70 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~ 70 (159)
....+||..+|++...|++....-|.+.|+.....
T Consensus 148 ~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~ 182 (188)
T TIGR02943 148 FESDEICQELEISTSNCHVLLYRARLSLRACLSIN 182 (188)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 35788999999999999999988888887765543
No 93
>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=79.10 E-value=4.9 Score=22.69 Aligned_cols=39 Identities=15% Similarity=0.103 Sum_probs=28.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhh
Q psy10851 11 TIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 11 t~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWF 56 (159)
..++.++...+..++... .....||..+|++...|.-++
T Consensus 4 ~~~~~~~~~~i~~l~~~G-------~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEG-------MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT---------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHCC-------CCHHHHHHHHCcCHHHHHHHH
Confidence 356777777777777655 358889999999999988775
No 94
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=79.01 E-value=6.1 Score=30.49 Aligned_cols=32 Identities=16% Similarity=0.301 Sum_probs=27.7
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
...+||..+|++...|++..+.-|.+.|+...
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 56789999999999999999888888887654
No 95
>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=78.98 E-value=1.7 Score=26.68 Aligned_cols=19 Identities=21% Similarity=0.496 Sum_probs=17.0
Q ss_pred HHHHHHHHhCCCchhhhhh
Q psy10851 37 VREALAKDTGLSVRVVQVW 55 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vW 55 (159)
.-..||..||++..+|+.|
T Consensus 24 ~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 4567899999999999999
No 96
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=78.77 E-value=6.7 Score=28.63 Aligned_cols=30 Identities=7% Similarity=0.213 Sum_probs=25.8
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
...+||..+|++...|++.....+.+++..
T Consensus 145 s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 145 KQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 467899999999999999998888887653
No 97
>KOG0773|consensus
Probab=78.70 E-value=2.7 Score=34.32 Aligned_cols=41 Identities=29% Similarity=0.396 Sum_probs=35.8
Q ss_pred hhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 26 NSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 26 ~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
..+ + ||+......|+..++|+..+|.+||-|.|.+.++...
T Consensus 117 ~~~-~-~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~ 157 (342)
T KOG0773|consen 117 RLN-P-YPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELK 157 (342)
T ss_pred hhc-c-CchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccC
Confidence 335 6 9999999999999999999999999999998887543
No 98
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=78.55 E-value=5.9 Score=29.41 Aligned_cols=32 Identities=22% Similarity=0.298 Sum_probs=27.4
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
...+||..+|++...|++++.--|.+.|+...
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 46789999999999999999888888877654
No 99
>PRK10072 putative transcriptional regulator; Provisional
Probab=78.46 E-value=3.2 Score=27.83 Aligned_cols=41 Identities=17% Similarity=0.209 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRA 61 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~ 61 (159)
+.+...+..|..... . ...+||..+|++...|..|.+.+|.
T Consensus 32 ~~~~~eik~LR~~~g------l---TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTG------L---KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcC------C---CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 335555666644321 2 2678899999999999999987764
No 100
>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=78.31 E-value=9.3 Score=29.76 Aligned_cols=39 Identities=10% Similarity=0.206 Sum_probs=32.3
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHhhc
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQE 74 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~~~ 74 (159)
....+||..+|++...|+++...-|.+.|+...+....-
T Consensus 178 ~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~~~~ 216 (244)
T TIGR03001 178 LSMDRIGAMYQVHRSTVSRWVAQARERLLERTRRRLAER 216 (244)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 357889999999999999999999998888766555444
No 101
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=78.16 E-value=7.1 Score=28.00 Aligned_cols=31 Identities=16% Similarity=0.226 Sum_probs=25.9
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
....+||..+|++...|+++...-|.+.|..
T Consensus 129 ~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 129 FSYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3577899999999999999998777777654
No 102
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=78.06 E-value=5.9 Score=29.17 Aligned_cols=31 Identities=26% Similarity=0.351 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
...+||..+|++...|++..+--|.+.|++.
T Consensus 149 s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 149 KIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 4678999999999999998877777777654
No 103
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=77.97 E-value=7.7 Score=28.02 Aligned_cols=30 Identities=17% Similarity=0.176 Sum_probs=26.0
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
...+||..+|++...|+++...-+.+++..
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999998888887764
No 104
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=77.93 E-value=8.5 Score=28.94 Aligned_cols=33 Identities=15% Similarity=0.255 Sum_probs=27.1
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~ 69 (159)
...+||..+|++...|+++...-|.+.|+....
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~ 188 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQLRAALAA 188 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 467889999999999999998777777775443
No 105
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=77.92 E-value=5.9 Score=30.38 Aligned_cols=32 Identities=9% Similarity=0.026 Sum_probs=27.7
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
....+||..+|++...|+.+...-+.+.|+..
T Consensus 201 ~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 201 LNLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35788999999999999999998888888753
No 106
>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=77.76 E-value=7.1 Score=28.00 Aligned_cols=31 Identities=16% Similarity=0.170 Sum_probs=25.5
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
....+||..+|++...|+++..--|.+.|+.
T Consensus 136 ~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 136 LTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3577899999999999999987777777664
No 107
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=77.65 E-value=9.4 Score=28.21 Aligned_cols=33 Identities=18% Similarity=0.264 Sum_probs=27.7
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~ 69 (159)
...+||..+|++...|+++...-|.+.|+....
T Consensus 134 s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~ 166 (187)
T PRK12516 134 AYEEAAEICGCAVGTIKSRVNRARQRLQEILQI 166 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 467899999999999999998888888876543
No 108
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=77.64 E-value=7.3 Score=28.87 Aligned_cols=32 Identities=9% Similarity=0.133 Sum_probs=26.9
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
...+||..+|++...|++++.--|.+.|+...
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 185 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKRALAALLA 185 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999887877777543
No 109
>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=77.46 E-value=7.1 Score=27.72 Aligned_cols=30 Identities=20% Similarity=0.379 Sum_probs=25.8
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
...+||..+|++...|+++-..-|.+.|+.
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 467889999999999999998888877764
No 110
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=77.14 E-value=8.1 Score=28.15 Aligned_cols=30 Identities=13% Similarity=0.258 Sum_probs=24.5
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
...+||..+|++...|+++.+.-|.+.|+.
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467889999999999999987777666654
No 111
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=77.12 E-value=9.9 Score=28.37 Aligned_cols=33 Identities=9% Similarity=0.175 Sum_probs=27.7
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
....+||..+|++...|++....-|.+.|+...
T Consensus 156 ~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 156 FEIDDICTELTLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 357789999999999999999888888877654
No 112
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=76.87 E-value=7.9 Score=28.88 Aligned_cols=33 Identities=18% Similarity=0.161 Sum_probs=27.5
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~ 69 (159)
...+||..+|++...|+++...-|.+.|+....
T Consensus 151 s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~ 183 (196)
T PRK12535 151 TYEEAAKIADVRVGTIRSRVARARADLIAATAT 183 (196)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 567899999999999999998888887775443
No 113
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=76.75 E-value=11 Score=27.63 Aligned_cols=35 Identities=9% Similarity=0.128 Sum_probs=29.1
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAK 71 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~ 71 (159)
...+||..+|++...|++....-|.+.|+......
T Consensus 149 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 149 ETEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999888888887655443
No 114
>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=76.73 E-value=8.2 Score=27.49 Aligned_cols=29 Identities=14% Similarity=0.100 Sum_probs=23.1
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
...+||..+|++...|++...--|.+.|+
T Consensus 140 s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 140 PIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46789999999999999887666656554
No 115
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=76.70 E-value=5.7 Score=30.21 Aligned_cols=52 Identities=17% Similarity=0.017 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
-+|..|+.+|...|...==.||.......||+.+|++... +|..=||+..|-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst--~~ehLRrAe~Kl 206 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST--LSEHLRRAERKL 206 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH--HHHHHHHHHHHH
Confidence 5999999999999987500146677788899999999865 444445555443
No 116
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=76.29 E-value=5.9 Score=28.69 Aligned_cols=34 Identities=15% Similarity=0.154 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 33 KTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 33 p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
.......+||..+|++...|+++...-+.+++..
T Consensus 133 ~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~ 166 (172)
T PRK09651 133 LDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLF 166 (172)
T ss_pred ccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3334578899999999999999997777777654
No 117
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=75.59 E-value=13 Score=28.42 Aligned_cols=31 Identities=13% Similarity=0.170 Sum_probs=26.1
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
...+||..+|++...|+++...-|.+.|+..
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5678999999999999999987777777753
No 118
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=75.30 E-value=10 Score=27.97 Aligned_cols=31 Identities=10% Similarity=0.128 Sum_probs=25.8
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
...+||..+|++...|++-...-|.+.|+..
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 5678999999999999999887777777643
No 119
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=75.28 E-value=7.8 Score=28.51 Aligned_cols=29 Identities=14% Similarity=0.100 Sum_probs=24.4
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
...+||..+|++...|+++...-|.+.|+
T Consensus 148 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 46789999999999999998777766665
No 120
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=74.39 E-value=9.2 Score=29.71 Aligned_cols=48 Identities=13% Similarity=0.087 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
.+++.+..+|...|-.. ....+||..+|++...|+.|...-+.|.|+.
T Consensus 205 ~L~~~~r~vl~l~~~~g-------~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN-------LSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHhCC-------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35556666666554333 2468899999999999999988777777754
No 121
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=74.31 E-value=10 Score=27.66 Aligned_cols=32 Identities=16% Similarity=0.137 Sum_probs=26.4
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
....+||..+|++...|+.+...-|.+.|+..
T Consensus 148 ~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 148 LSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 35778999999999999999977777777643
No 122
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=74.28 E-value=2.6 Score=25.18 Aligned_cols=30 Identities=17% Similarity=0.219 Sum_probs=19.5
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
....||..+|++...|..|+.++..+..-.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~ 41 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLD 41 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HH
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHH
Confidence 567899999999999999999885554443
No 123
>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=74.27 E-value=9.7 Score=28.88 Aligned_cols=47 Identities=15% Similarity=0.112 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
.++..+..+|...|-.. ....+||..+|++...|+.|...-+.|.|+
T Consensus 178 ~L~~~~r~vl~l~y~~~-------~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFFED-------KTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHhcC-------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45666666666655333 257789999999999999998777777665
No 124
>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=74.20 E-value=3.3 Score=23.26 Aligned_cols=20 Identities=30% Similarity=0.292 Sum_probs=17.4
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFq 57 (159)
..++|..+|++...|+.|.+
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYER 22 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999963
No 125
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=73.69 E-value=13 Score=26.79 Aligned_cols=33 Identities=6% Similarity=0.147 Sum_probs=27.2
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
..-.+||..+|++...|++....-|.+.|+...
T Consensus 136 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 168 (173)
T PRK12522 136 YSYKEMSEILNIPIGTVKYRLNYAKKQMREHLE 168 (173)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999999888888777543
No 126
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=73.60 E-value=10 Score=27.65 Aligned_cols=31 Identities=13% Similarity=0.296 Sum_probs=26.0
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
...+||..+|++...|++....-|.+.|+..
T Consensus 140 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 140 TYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5678999999999999999887777777653
No 127
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=73.47 E-value=14 Score=27.27 Aligned_cols=33 Identities=15% Similarity=0.158 Sum_probs=24.7
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
....+||..+|++...|++=...-|.+.|+...
T Consensus 151 ~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l~ 183 (192)
T PRK09643 151 YSVADAARMLGVAEGTVKSRCARGRARLAELLG 183 (192)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 356788999999999998776666666666544
No 128
>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=73.40 E-value=16 Score=26.21 Aligned_cols=48 Identities=13% Similarity=0.031 Sum_probs=39.2
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
.+.++..|+.+|... ... + ...+||..+|++...|+.|-+.-+.|.|+
T Consensus 4 ~~~Lte~qr~VL~Lr-~~G---l----Tq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELR-EKG---L----SQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHH-HcC---C----CHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 467899999999874 333 2 46789999999999999999888888876
No 129
>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=73.21 E-value=10 Score=28.73 Aligned_cols=48 Identities=10% Similarity=0.003 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
.++..+..+|...|-.. ....+||..+|++...|+.+.+.-+.+.|+.
T Consensus 175 ~L~~~~r~il~l~y~~~-------~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE-------LNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred hCCHHHHHHHHHHHhCC-------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 34566666666655333 2468899999999999999987777776653
No 130
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=73.09 E-value=5.4 Score=29.38 Aligned_cols=37 Identities=16% Similarity=0.203 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 32 HKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 32 yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
|.......+||..+|++...|+++...-|.+.|+...
T Consensus 152 ~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 188 (194)
T PRK12513 152 EHGDLELEEIAELTGVPEETVKSRLRYALQKLRELLA 188 (194)
T ss_pred hccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3444567889999999999999999888888887543
No 131
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=73.00 E-value=12 Score=26.88 Aligned_cols=30 Identities=7% Similarity=0.055 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
...+||..+|++...|+.+..+.+.+++..
T Consensus 136 s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 165 (168)
T PRK12525 136 TYVEIGERLGVSLSRIHQYMVEAFKCCYQG 165 (168)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 467899999999999999998777777653
No 132
>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=72.91 E-value=1.9 Score=27.49 Aligned_cols=29 Identities=10% Similarity=0.264 Sum_probs=23.3
Q ss_pred CCCHHHHHHHHHHhCCCchhhhhhhhhHH
Q psy10851 32 HKTTQVREALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 32 yp~~~~r~~La~~l~l~~~~V~vWFqNRR 60 (159)
|-..-...+||..+|++...|++|+.+..
T Consensus 29 ~~eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 29 EEAGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 44445688999999999999999987533
No 133
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=72.90 E-value=12 Score=26.82 Aligned_cols=30 Identities=13% Similarity=0.191 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
...+||..+|++...|+.....-|.+.|+.
T Consensus 136 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 165 (173)
T PRK09645 136 STAQIAADLGIPEGTVKSRLHYALRALRLA 165 (173)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999987777776664
No 134
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=72.66 E-value=11 Score=27.25 Aligned_cols=32 Identities=16% Similarity=0.185 Sum_probs=26.6
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
....+||..+|++...|++....-|.|.|+..
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T PRK09641 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999888888877643
No 135
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=72.48 E-value=16 Score=27.46 Aligned_cols=32 Identities=16% Similarity=0.271 Sum_probs=27.5
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
...+||..+|++...|++..+.-|.+.|+...
T Consensus 166 s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~ 197 (206)
T PRK12544 166 ETNEICHAVDLSVSNLNVLLYRARLRLRECLE 197 (206)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999888888888654
No 136
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=72.36 E-value=11 Score=26.67 Aligned_cols=28 Identities=14% Similarity=0.267 Sum_probs=23.1
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMK 64 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~r 64 (159)
...+||..+|++...|+++...-+.+++
T Consensus 131 s~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 131 GYGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4678899999999999999877666654
No 137
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=72.21 E-value=12 Score=29.63 Aligned_cols=54 Identities=17% Similarity=0.105 Sum_probs=38.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
.++..+..+|...|... |-......+||..+|++...|+.+...-+.|.|+...
T Consensus 222 ~Lp~~~R~Vl~l~ygL~---~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~ 275 (285)
T TIGR02394 222 ELNERQREVLARRFGLL---GYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILE 275 (285)
T ss_pred cCCHHHHHHHHHHhCCC---CCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45556666666555222 2333467889999999999999999888888877543
No 138
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=71.98 E-value=13 Score=27.44 Aligned_cols=31 Identities=16% Similarity=0.235 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
...+||..+|++...|++.+...|.+.|+.-
T Consensus 172 s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 172 SYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4677899999999999998887777777753
No 139
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=71.92 E-value=12 Score=25.30 Aligned_cols=41 Identities=12% Similarity=0.178 Sum_probs=31.9
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCC-Cchhhhhhh
Q psy10851 10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGL-SVRVVQVWF 56 (159)
Q Consensus 10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l-~~~~V~vWF 56 (159)
|.+||.+....+=..+... . + ....||+.+|+ +..++..|-
T Consensus 5 ~r~~s~EfK~~iv~~~~~~-g-~----sv~~vAr~~gv~~~~~l~~W~ 46 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRG-G-D----TVSEVAREFGIVSATQLYKWR 46 (116)
T ss_pred cccCCHHHHHHHHHHHHhc-C-c----cHHHHHHHhCCCChHHHHHHH
Confidence 7889999876666666555 3 4 68889999996 988888774
No 140
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=71.92 E-value=3.8 Score=23.31 Aligned_cols=22 Identities=27% Similarity=0.439 Sum_probs=17.3
Q ss_pred HHHHHHHHhCCCchhhhhhhhh
Q psy10851 37 VREALAKDTGLSVRVVQVWFQN 58 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqN 58 (159)
....+|..+|++...|..|.+.
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT-
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 4678999999999999999754
No 141
>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=71.30 E-value=11 Score=29.17 Aligned_cols=48 Identities=17% Similarity=0.135 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
.+++.+..+|...|-.. ....+||..+|++...|+.+...-+.|.|+.
T Consensus 205 ~L~~~~r~ii~l~~~~g-------~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN-------LSQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred cCCHHHHHHHHHHHcCC-------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 45566666666655433 2457899999999999999998888777764
No 142
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=71.25 E-value=11 Score=28.70 Aligned_cols=32 Identities=16% Similarity=0.153 Sum_probs=27.0
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
....+||..+|++...|+++...-|.+.|+..
T Consensus 199 ~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l 230 (234)
T PRK08301 199 KTQKEVADMLGISQSYISRLEKRIIKRLKKEI 230 (234)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45778999999999999999888888877753
No 143
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=70.92 E-value=4.2 Score=29.31 Aligned_cols=37 Identities=14% Similarity=0.183 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 32 HKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 32 yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
|.......+||..+|++...|++.+..-|.+.|+...
T Consensus 133 ~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 133 DLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3344467889999999999999999888888887643
No 144
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=70.90 E-value=12 Score=28.94 Aligned_cols=47 Identities=11% Similarity=0.051 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 13 RLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 13 ~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
+++.+..++...|-.. ....+||..+|++...|++++..-|.+.|+.
T Consensus 202 L~~~~r~vl~l~~~~~-------~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 202 LSEKEQLVISLFYKEE-------LTLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred CCHHHHHHHHHHHhcC-------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3444555555444322 3468899999999999999998877777764
No 145
>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=70.81 E-value=1.5 Score=26.60 Aligned_cols=27 Identities=22% Similarity=0.385 Sum_probs=21.2
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
...+||..||++.+.|..|- .|.+|..
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~--~r~~W~~ 41 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWK--DRYKWDE 41 (58)
T ss_pred CHHHHHHHHCCChHHHHHHH--HhhCccc
Confidence 46789999999999999995 3444443
No 146
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=70.58 E-value=15 Score=26.91 Aligned_cols=35 Identities=17% Similarity=0.100 Sum_probs=28.6
Q ss_pred CHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 34 TTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 34 ~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
......+||..+|++...|++..+.-|.+.|+...
T Consensus 153 ~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 153 DGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 33456789999999999999999888888887654
No 147
>PF13518 HTH_28: Helix-turn-helix domain
Probab=70.55 E-value=5.9 Score=22.47 Aligned_cols=24 Identities=25% Similarity=0.486 Sum_probs=19.8
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR 60 (159)
....+|..+|++..+|..|.+.-+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 356689999999999999986544
No 148
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=70.30 E-value=14 Score=27.21 Aligned_cols=32 Identities=13% Similarity=0.216 Sum_probs=26.3
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
...+||..+|++...|+++..--|.+.|+...
T Consensus 129 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 129 SYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999998777777776544
No 149
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=70.11 E-value=33 Score=25.26 Aligned_cols=47 Identities=13% Similarity=-0.051 Sum_probs=37.8
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHH
Q psy10851 10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR 60 (159)
...+|.+++..+..+-..+ |..-.+..||+++|++..-|.+=..--.
T Consensus 83 ~y~Lt~e~i~Eir~LR~~D----P~~wTr~~LAkkF~~S~~fV~~v~~~~~ 129 (164)
T PF12824_consen 83 KYHLTPEDIQEIRRLRAED----PEKWTRKKLAKKFNCSPLFVSMVAPAPK 129 (164)
T ss_pred cccCCHHHHHHHHHHHHcC----chHhhHHHHHHHhCCCHHHHHHhcCCCH
Confidence 4689999999999987766 6777899999999999887776554333
No 150
>PRK09480 slmA division inhibitor protein; Provisional
Probab=69.75 E-value=7.4 Score=28.28 Aligned_cols=41 Identities=20% Similarity=0.187 Sum_probs=32.8
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHH
Q psy10851 18 KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRA 61 (159)
Q Consensus 18 ~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~ 61 (159)
+......|... + . .......||...|++...+-.+|.|+-.
T Consensus 16 l~aa~~l~~~~-~-G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 16 LQALAQMLESP-P-G-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHHhc-C-C-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 34444556555 4 6 8889999999999999999999999874
No 151
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=69.11 E-value=26 Score=25.79 Aligned_cols=35 Identities=20% Similarity=0.211 Sum_probs=28.8
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAK 71 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~ 71 (159)
...+||..+|++...|+++..--|.+.|+......
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 180 (188)
T PRK12517 146 SGEEIAEILDLNKNTVMTRLFRARNQLKEALEKPD 180 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999888888877765444
No 152
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=68.74 E-value=19 Score=28.23 Aligned_cols=50 Identities=8% Similarity=-0.031 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
.+++.+..+|...|-.. ....+||..+|++...|+.....-+.+.|+...
T Consensus 212 ~L~~~~r~vl~l~~~~~-------~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~ 261 (268)
T PRK06288 212 TLPEREKKVLILYYYED-------LTLKEIGKVLGVTESRISQLHTKAVLQLRAKLA 261 (268)
T ss_pred hCCHHHHHHHHHHHHcC-------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 34555555665555333 246889999999999999998888888877643
No 153
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=68.27 E-value=13 Score=27.03 Aligned_cols=30 Identities=20% Similarity=0.271 Sum_probs=25.0
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
...+||..+|++...|+.+..--|.+.|+.
T Consensus 145 s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~ 174 (179)
T PRK09415 145 SIKEIAEVTGVNENTVKTRLKKAKELLKKG 174 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999987777776654
No 154
>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=68.27 E-value=16 Score=22.21 Aligned_cols=44 Identities=16% Similarity=0.135 Sum_probs=22.4
Q ss_pred CCCCCHHH-HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy10851 10 QTIRLLNL-KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 10 Rt~~s~~Q-~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFq 57 (159)
|..|+..- |.+++.++..+ .--...| ..|.++|++.++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~---nc~~~~R-Aaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDN---NCKGNQR-AAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-T---TTTT-HH-HHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHcc---chhhhHH-HHHHHhCccHHHHHHHHH
Confidence 44566555 45555444333 1112233 359999999999999964
No 155
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=68.17 E-value=19 Score=26.43 Aligned_cols=33 Identities=18% Similarity=0.172 Sum_probs=26.6
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
....+||..+|++...|++...--|.+.|+...
T Consensus 128 ~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 128 FSYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999998777777776544
No 156
>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=67.81 E-value=18 Score=26.48 Aligned_cols=30 Identities=20% Similarity=0.263 Sum_probs=24.5
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
....+||..+|++...|++++.--|.+.|+
T Consensus 166 ~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 166 KSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 356789999999999999988777766665
No 157
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=67.80 E-value=14 Score=29.25 Aligned_cols=30 Identities=17% Similarity=0.096 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
...+||..+|++...|+..++.-|.+.|..
T Consensus 126 s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 126 PYEEIASIVGKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 457789999999999999998888887764
No 158
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=66.20 E-value=18 Score=28.26 Aligned_cols=47 Identities=17% Similarity=0.109 Sum_probs=33.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 13 RLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 13 ~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
++..+..+|...|-.. ....+||..+|++...|+.+..--+.|.|+.
T Consensus 204 L~~~~r~vl~l~y~~~-------~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 204 LEERTREVLEFVFLHD-------LTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred CCHHHHHHHHHHHHCC-------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4455555555555333 3568899999999999999987777777764
No 159
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=66.19 E-value=16 Score=28.76 Aligned_cols=48 Identities=15% Similarity=0.131 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
.++..+..+|...|-.. ....+||..+|++...|+.+...-+.|.|+.
T Consensus 215 ~L~~rer~vl~l~y~~~-------~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 262 (264)
T PRK07122 215 ALPERERTVLVLRFFES-------MTQTQIAERVGISQMHVSRLLAKTLARLRDQ 262 (264)
T ss_pred cCCHHHHHHHHHHhcCC-------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 45566666666655333 3468899999999999999998777777763
No 160
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=65.82 E-value=11 Score=28.83 Aligned_cols=38 Identities=16% Similarity=0.174 Sum_probs=31.0
Q ss_pred CCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851 32 HKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69 (159)
Q Consensus 32 yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~ 69 (159)
|.......+||..+|++...|++....-|.|.|+....
T Consensus 162 ~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~ 199 (231)
T PRK11922 162 VVEELSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199 (231)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 44555788999999999999999998888888876543
No 161
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=65.51 E-value=26 Score=24.75 Aligned_cols=31 Identities=16% Similarity=0.203 Sum_probs=25.6
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
...+||..+|++...|++.....|.+.|+..
T Consensus 123 s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 123 SHQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999887777777653
No 162
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=65.03 E-value=22 Score=25.86 Aligned_cols=31 Identities=29% Similarity=0.401 Sum_probs=24.4
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
....+||..+|++...|++-...-|.+.|+.
T Consensus 154 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 154 ITYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred CCHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 3567889999999999988877666666653
No 163
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=65.02 E-value=17 Score=28.82 Aligned_cols=30 Identities=13% Similarity=0.128 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
...+||..+|++...|+...+.-|.+.|+.
T Consensus 133 s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~ 162 (293)
T PRK09636 133 PFDEIASTLGRSPAACRQLASRARKHVRAA 162 (293)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 457889999999999999998888877764
No 164
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=64.56 E-value=21 Score=27.38 Aligned_cols=53 Identities=8% Similarity=0.048 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
.++..+..+|...|... ++ ......+||..+|++...|+.+.+.-+.|.|...
T Consensus 176 ~L~~~er~vl~l~ygl~--~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~ 228 (238)
T TIGR02393 176 TLTERERKVLRMRYGLL--DG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRHPS 228 (238)
T ss_pred hCCHHHHHHHHHHhCCC--CC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhH
Confidence 45677777777777322 11 2235788999999999999999998888888764
No 165
>PRK10403 transcriptional regulator NarP; Provisional
Probab=64.52 E-value=17 Score=26.02 Aligned_cols=46 Identities=15% Similarity=0.042 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
.+|..+..+|..+.. . + .+.+||..++++.+.|++..+|=|.|...
T Consensus 153 ~Lt~~e~~vl~~~~~-g---~----s~~~ia~~l~~s~~tv~~~~~~i~~kl~~ 198 (215)
T PRK10403 153 VLTERELDVLHELAQ-G---L----SNKQIASVLNISEQTVKVHIRNLLRKLNV 198 (215)
T ss_pred cCCHHHHHHHHHHHC-C---C----CHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 578888888875542 1 2 35788999999999999999888877543
No 166
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=64.48 E-value=6.3 Score=23.91 Aligned_cols=19 Identities=21% Similarity=0.211 Sum_probs=16.9
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
..++|+.+|++...|+.|=
T Consensus 3 i~eva~~~gvs~~tlr~y~ 21 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYE 21 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4678999999999999993
No 167
>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=64.33 E-value=6.7 Score=21.49 Aligned_cols=19 Identities=26% Similarity=0.261 Sum_probs=15.5
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
+.++|+.+|++.+.|+.|=
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 4678999999999999993
No 168
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=64.18 E-value=9.4 Score=26.04 Aligned_cols=41 Identities=17% Similarity=0.250 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRA 61 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~ 61 (159)
.++...+..+...+... ...+|..+|++...|+.|=|+|+.
T Consensus 43 ~ls~~eIk~iRe~~~lS---------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 43 TLSPTEIKAIREKLGLS---------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCCHHHHHHHHHHhCCC---------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 37777788887776555 356799999999999999988874
No 169
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=64.13 E-value=17 Score=29.06 Aligned_cols=31 Identities=23% Similarity=0.200 Sum_probs=25.8
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
...+||..+|++...|++...--|.+.|+..
T Consensus 160 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 190 (324)
T TIGR02960 160 RAAETAELLGTSTASVNSALQRARATLDEVG 190 (324)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence 4678999999999999999887777777653
No 170
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=64.06 E-value=18 Score=25.61 Aligned_cols=45 Identities=16% Similarity=0.159 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK 64 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~r 64 (159)
.+|..+..+|.- +..+ |. ...+|..++++.+.|+++.+|-+.|..
T Consensus 149 ~lt~~e~~vl~l-~~~g---~~----~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 149 LLTPRERQILKL-ITEG---YT----NRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCCHHHHHHHHH-HHCC---CC----HHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 488888888876 4333 43 578899999999999999988777654
No 171
>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=63.76 E-value=7.5 Score=27.25 Aligned_cols=34 Identities=21% Similarity=0.145 Sum_probs=27.5
Q ss_pred CCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 32 HKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 32 yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
|.......+||..+|++...|+++..--|.|.|+
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4455578889999999999999998777776665
No 172
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=63.64 E-value=23 Score=26.13 Aligned_cols=30 Identities=27% Similarity=0.377 Sum_probs=25.6
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
...+||..+|++++.|+..++.-|++.++.
T Consensus 153 s~~EIA~~lgiS~~tV~r~l~~aR~~l~~~ 182 (185)
T PF07638_consen 153 SVEEIAERLGISERTVRRRLRRARAWLRRE 182 (185)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 678899999999999999998888766654
No 173
>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=61.88 E-value=8.6 Score=21.02 Aligned_cols=21 Identities=19% Similarity=0.393 Sum_probs=18.1
Q ss_pred HHHHHHHhCCCchhhhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWFQN 58 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFqN 58 (159)
..++|..+|++.+.|..|.++
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 467899999999999999764
No 174
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=61.67 E-value=29 Score=26.53 Aligned_cols=33 Identities=21% Similarity=0.135 Sum_probs=25.8
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
...++||..+|++...|+++-...+.+.|+...
T Consensus 196 ~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~ 228 (233)
T PRK05803 196 KTQREIAKALGISRSYVSRIEKRALKKLFKELY 228 (233)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 357789999999999999887666666666543
No 175
>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=61.21 E-value=27 Score=19.57 Aligned_cols=39 Identities=15% Similarity=0.107 Sum_probs=26.4
Q ss_pred CHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHH
Q psy10851 14 LLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 14 s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR 60 (159)
+..+..++..++ . . + ...++|..++++...|..|...-+
T Consensus 2 ~~~e~~i~~~~~--~-~-~----s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 2 TPREREVLRLLA--E-G-K----TNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred CHHHHHHHHHHH--c-C-C----CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 455666664432 3 2 2 457789999999999999986333
No 176
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=60.96 E-value=26 Score=27.11 Aligned_cols=32 Identities=19% Similarity=0.225 Sum_probs=26.3
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
...+||..+|++...|+++...-|.+.|+...
T Consensus 134 S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~ 165 (228)
T PRK06704 134 SIADIAKVCSVSEGAVKASLFRSRNRLKTVSE 165 (228)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999998877777776543
No 177
>PRK05572 sporulation sigma factor SigF; Validated
Probab=60.86 E-value=25 Score=27.20 Aligned_cols=48 Identities=15% Similarity=0.029 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
.++..+..+|...|... ....+||..+|++...|..+-..-..|.|+.
T Consensus 202 ~L~~~~~~v~~l~~~~~-------~s~~eIA~~lgis~~~V~~~~~ral~kLr~~ 249 (252)
T PRK05572 202 ELDERERLIVYLRYFKD-------KTQSEVAKRLGISQVQVSRLEKKILKQMKEK 249 (252)
T ss_pred cCCHHHHHHHHHHHhCC-------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 46666777776665433 3568899999999999999877666666653
No 178
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=60.51 E-value=26 Score=26.58 Aligned_cols=47 Identities=15% Similarity=0.014 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
.++..+..++...|... ....+||..+|++...|..+-..-..|.|+
T Consensus 183 ~L~~~e~~i~~~~~~~~-------~t~~eIA~~lgis~~~V~~~~~~al~~Lr~ 229 (231)
T TIGR02885 183 KLDERERQIIMLRYFKD-------KTQTEVANMLGISQVQVSRLEKKVLKKMKE 229 (231)
T ss_pred cCCHHHHHHHHHHHHcC-------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45666666666655433 257889999999999998886555555443
No 179
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=60.48 E-value=27 Score=26.64 Aligned_cols=47 Identities=15% Similarity=0.012 Sum_probs=37.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 11 TIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 11 t~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
..+|+.++.+|.-... . ....+||..++++.+.|+.+..|-..|..-
T Consensus 154 ~~Lt~rE~~Vl~l~~~-G-------~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 154 ALLTHREKEILNKLRI-G-------ASNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred CCCCHHHHHHHHHHHc-C-------CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 3589999999987754 2 235788999999999999999887776554
No 180
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=60.45 E-value=32 Score=26.87 Aligned_cols=49 Identities=12% Similarity=0.011 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
.+++.+..+|...|-.. ....+||..+|++...|+.+..--+.|.|+..
T Consensus 205 ~L~~~er~vi~l~y~e~-------~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 253 (257)
T PRK05911 205 ALEEKERKVMALYYYEE-------LVLKEIGKILGVSESRVSQIHSKALLKLRATL 253 (257)
T ss_pred cCCHHHHHHHHHHHhcC-------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 34555555665555333 25688999999999999999877777777653
No 181
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=60.42 E-value=15 Score=26.86 Aligned_cols=33 Identities=6% Similarity=0.104 Sum_probs=27.5
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
....+||..+|++...|+++...-|.+.|+...
T Consensus 151 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 183 (188)
T PRK09640 151 LEFQEIADIMHMGLSATKMRYKRALDKLREKFA 183 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999999888888777543
No 182
>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=59.67 E-value=5.5 Score=22.71 Aligned_cols=21 Identities=24% Similarity=0.382 Sum_probs=19.1
Q ss_pred HHHHHhCCCchhhhhhhhhHH
Q psy10851 40 ALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 40 ~La~~l~l~~~~V~vWFqNRR 60 (159)
.||..+|++...|..|+.|+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999883
No 183
>PRK10651 transcriptional regulator NarL; Provisional
Probab=59.44 E-value=24 Score=25.30 Aligned_cols=46 Identities=17% Similarity=0.068 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
.+|+.+..+|.-+.. . + ....||+.++++.+.|++..+|-|.|..-
T Consensus 155 ~Lt~rE~~vl~~l~~-g---~----~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 155 QLTPRERDILKLIAQ-G---L----PNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred cCCHHHHHHHHHHHc-C---C----CHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 389999999976542 2 2 25667899999999999999988877643
No 184
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=59.40 E-value=28 Score=27.08 Aligned_cols=47 Identities=19% Similarity=0.124 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
.++..+..+|...|... ....+||..+|++...|...-.+-..|.|+
T Consensus 209 ~L~~~er~vi~~~~~~~-------~t~~eIA~~lgis~~~V~~~~~~al~kLr~ 255 (258)
T PRK08215 209 KLNDREKLILNLRFFQG-------KTQMEVAEEIGISQAQVSRLEKAALKHMRK 255 (258)
T ss_pred cCCHHHHHHHHHHHhcC-------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 56677777777776433 246789999999999999887776666665
No 185
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=59.38 E-value=23 Score=19.84 Aligned_cols=37 Identities=19% Similarity=0.192 Sum_probs=24.3
Q ss_pred CHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhh
Q psy10851 14 LLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 14 s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWF 56 (159)
+..+..+|...+. + + . ..+.+||..+|++...|..-+
T Consensus 2 ~~~~~~Il~~l~~-~-~-~---~t~~ela~~~~is~~tv~~~l 38 (48)
T PF13412_consen 2 DETQRKILNYLRE-N-P-R---ITQKELAEKLGISRSTVNRYL 38 (48)
T ss_dssp -HHHHHHHHHHHH-C-T-T---S-HHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHHHHH-c-C-C---CCHHHHHHHhCCCHHHHHHHH
Confidence 4567778866665 3 3 3 457788999999998876554
No 186
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=59.24 E-value=23 Score=27.81 Aligned_cols=50 Identities=16% Similarity=0.017 Sum_probs=38.9
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
...+|+.+..+|.-.. .. + ...+||..+|++...|+.+.+|-+.|..-..
T Consensus 188 ~~~LT~RE~evl~l~a-~G---~----s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~n 237 (247)
T TIGR03020 188 AGLITAREAEILAWVR-DG---K----TNEEIAAILGISSLTVKNHLQHIFKKLDVRN 237 (247)
T ss_pred ccCCCHHHHHHHHHHH-CC---C----CHHHHHHHHCcCHHHHHHHHHHHHHHhCCCC
Confidence 4478999999998643 22 2 4567899999999999999998887766443
No 187
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=59.16 E-value=9.1 Score=27.56 Aligned_cols=35 Identities=17% Similarity=0.138 Sum_probs=28.1
Q ss_pred CCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 32 HKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 32 yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
|.......+||..+|++...|+++...-|.+.|+.
T Consensus 139 ~~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 139 HYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred hhcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 34445678899999999999999998777777764
No 188
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=59.04 E-value=31 Score=24.92 Aligned_cols=31 Identities=16% Similarity=0.172 Sum_probs=24.7
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
....+||..+|++...|++=...-|.+.|+.
T Consensus 157 ~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~ 187 (189)
T TIGR02984 157 LSFAEVAERMDRSEGAVSMLWVRGLARLRQI 187 (189)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3567889999999999998877777776653
No 189
>PF03344 Daxx: Daxx Family; InterPro: IPR005012 Daxx is a ubiquitously expressed protein that functions, in part, as a transcriptional co-repressor through its interaction with a growing number of nuclear, DNA-associated proteins. Human Daxx contains four structural domains commonly found in transcriptional regulatory proteins: two predicted paired amphipathic helices, an acid-rich domain and a Ser/Pro/Thr (SPT)-rich domain. The post-translational modification status of the SPT-domain of hDaxx regulates its association with transcription factors such as Pax3 and ETS-1, effectively bringing hDaxx to sites of active transcription. Through its presence at the site of active transcription, hDaxx could then be able to associate with acetylated histones present in the nucleosomes and Dek that is associated with chromatin. Through its association with the SPT-domain of hDaxx, histone deacetylases may also be brought to the site of active transcription. As a consequence, nucleosomes in the vicinity of the site of active transcription will have the histone tails deacetylated, allowing the deactylated tail to bind to DNA, thereby leading to an inactive chromatin structure and transcriptional repression []. The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis as a component of nuclear promyelocytic leukemia protein (PML) oncogenic domains (PODS). Daxx associates with PODs through a direct interaction with PML, a critical component of PODs. The interaction is a dynamic, cell cycle regulated event and is dependent on the post-translational modification of PML by the small ubiquitin-related modifier SUMO-1. ; PDB: 2KZS_A 2KZU_A.
Probab=58.97 E-value=3.1 Score=37.62 Aligned_cols=13 Identities=0% Similarity=-0.227 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHHH
Q psy10851 32 HKTTQVREALAKD 44 (159)
Q Consensus 32 yp~~~~r~~La~~ 44 (159)
||+-..+-++...
T Consensus 295 fPD~~Dvl~~v~~ 307 (713)
T PF03344_consen 295 FPDYHDVLQCVEK 307 (713)
T ss_dssp -------------
T ss_pred ccccccccccccc
Confidence 6665555554433
No 190
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=58.83 E-value=29 Score=24.76 Aligned_cols=45 Identities=20% Similarity=0.142 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK 64 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~r 64 (159)
.+|+.+..+|.-+.. +| .+..||..++++.+.|++..++=|.|..
T Consensus 137 ~Lt~~E~~il~~l~~----g~----~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRERQVAEKLAQ----GM----AVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHHHHHHHHHC----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 577888888876542 23 4778899999999999999888776643
No 191
>KOG3755|consensus
Probab=58.46 E-value=7 Score=34.65 Aligned_cols=60 Identities=17% Similarity=0.084 Sum_probs=50.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHH---HHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 5 WFQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQV---REALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 5 ~~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~---r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
+.+|+|+.++.+-+.+|..+-... .-||+... ..-|+..+++..+.+...|+|.|.-.++
T Consensus 646 ~~p~~~~~isge~~~~~qs~i~~~-gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~~ 708 (769)
T KOG3755|consen 646 HKPRKRTKISGEALGILQSFITDV-GLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVKH 708 (769)
T ss_pred cCccccceecccchHHHHHHHHHh-ccCchhhcccccchhhhhhcccHHHHHHhhhcceeecch
Confidence 356789999999999999886554 34898888 8899999999999999999999987663
No 192
>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=58.23 E-value=9.9 Score=23.14 Aligned_cols=20 Identities=25% Similarity=0.406 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFq 57 (159)
..++|+.+|++...|+.|.+
T Consensus 3 i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999964
No 193
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=58.19 E-value=25 Score=27.03 Aligned_cols=50 Identities=16% Similarity=0.096 Sum_probs=39.0
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
...+|+.++.+|.-.. .. ..-.+||..+|++.+.|+.+..|-+.|.+-..
T Consensus 169 ~~~Lt~re~evl~~~a-~G-------~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~ 218 (232)
T TIGR03541 169 AGVLSEREREVLAWTA-LG-------RRQADIAAILGISERTVENHLRSARRKLGVAT 218 (232)
T ss_pred hccCCHHHHHHHHHHH-CC-------CCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCC
Confidence 4578999999997742 22 24677899999999999999999888876543
No 194
>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=57.80 E-value=11 Score=22.90 Aligned_cols=20 Identities=5% Similarity=0.164 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFq 57 (159)
..++|+.+|++.+.|+.|-+
T Consensus 3 i~evA~~~gvs~~tlR~~~~ 22 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEK 22 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999964
No 195
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=57.22 E-value=36 Score=26.01 Aligned_cols=32 Identities=16% Similarity=0.155 Sum_probs=26.6
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
....+||..+|++...|+++.+.-|.+.|+..
T Consensus 199 ~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l 230 (234)
T TIGR02835 199 KTQKEVADMLGISQSYISRLEKRILKRLKKEI 230 (234)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 35678999999999999999887787777753
No 196
>PF13551 HTH_29: Winged helix-turn helix
Probab=57.05 E-value=38 Score=22.13 Aligned_cols=49 Identities=10% Similarity=0.040 Sum_probs=30.7
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCC-----CCHHHHHH-H-HHHh--CCCchhhhhhhh
Q psy10851 7 QNFQTIRLLNLKVKLKTSFNSCCPGH-----KTTQVREA-L-AKDT--GLSVRVVQVWFQ 57 (159)
Q Consensus 7 kr~Rt~~s~~Q~~~Le~~F~~~~~~y-----p~~~~r~~-L-a~~l--~l~~~~V~vWFq 57 (159)
.+++..++.++...|..++... + . .+...... | .... .++...|..|++
T Consensus 52 g~~~~~l~~~~~~~l~~~~~~~-p-~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 52 GRPRKRLSEEQRAQLIELLREN-P-PEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCCHHHHHHHHHHHHHC-C-CCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 3444459999999999999877 4 2 22233332 3 2222 467778888774
No 197
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=55.36 E-value=7.8 Score=22.28 Aligned_cols=23 Identities=22% Similarity=0.317 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCchhhhhhhhhHH
Q psy10851 38 REALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFqNRR 60 (159)
...||..+|++...|..|..+++
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 47899999999999999998854
No 198
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=55.20 E-value=20 Score=24.80 Aligned_cols=28 Identities=18% Similarity=0.247 Sum_probs=22.7
Q ss_pred CCCHHHHHHHHHHhCCCchhhhhhhhhH
Q psy10851 32 HKTTQVREALAKDTGLSVRVVQVWFQNQ 59 (159)
Q Consensus 32 yp~~~~r~~La~~l~l~~~~V~vWFqNR 59 (159)
+-.......||..+||+.+.+..+|+..
T Consensus 22 ~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 22 LESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred cCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4444677889999999999999999654
No 199
>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=55.09 E-value=12 Score=22.50 Aligned_cols=20 Identities=30% Similarity=0.473 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFq 57 (159)
..++|+.+|++...|+.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999963
No 200
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=54.90 E-value=4.5 Score=31.34 Aligned_cols=12 Identities=17% Similarity=0.227 Sum_probs=5.4
Q ss_pred HHHhhcCCCCCCHH
Q psy10851 23 TSFNSCCPGHKTTQ 36 (159)
Q Consensus 23 ~~F~~~~~~yp~~~ 36 (159)
..|+.. | |....
T Consensus 63 ~~~~~s-P-yy~~~ 74 (233)
T PF11705_consen 63 ERMRDS-P-YYTES 74 (233)
T ss_pred HHHHhC-C-Ccccc
Confidence 334444 5 54433
No 201
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=54.39 E-value=42 Score=25.51 Aligned_cols=31 Identities=23% Similarity=0.153 Sum_probs=24.3
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
...++||..+|++...|+.+...-+.+.|+.
T Consensus 195 ~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~ 225 (227)
T TIGR02846 195 KTQREIAKILGISRSYVSRIEKRALMKLYKE 225 (227)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3477899999999999988876666666653
No 202
>PHA00542 putative Cro-like protein
Probab=54.35 E-value=31 Score=22.07 Aligned_cols=23 Identities=17% Similarity=0.257 Sum_probs=19.9
Q ss_pred HHHHHHHHhCCCchhhhhhhhhH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQ 59 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNR 59 (159)
....||..+|++...|..|..++
T Consensus 33 Tq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 33 SQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCC
Confidence 45678999999999999998766
No 203
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=54.11 E-value=25 Score=28.36 Aligned_cols=30 Identities=23% Similarity=0.166 Sum_probs=25.0
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
....+||..+|++...|++....-|.+.|+
T Consensus 170 ~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 170 WSAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 356789999999999999998777777666
No 204
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=53.96 E-value=23 Score=26.93 Aligned_cols=56 Identities=7% Similarity=0.083 Sum_probs=40.6
Q ss_pred CCCCCCCCCHHH-HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 6 FQNFQTIRLLNL-KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 6 ~kr~Rt~~s~~Q-~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
.+|+|..-+.++ +.+-...|... . |- .....||+..|++...|-.+|.|+..=...
T Consensus 6 ~~~~~~~~~r~~Il~aA~~lF~~~-G-y~--~s~~~IA~~AGvsk~tiy~~F~sKe~L~~a 62 (225)
T PRK11552 6 AMTTRGEQAKQQLIAAALAQFGEY-G-LH--ATTRDIAAQAGQNIAAITYYFGSKEDLYLA 62 (225)
T ss_pred CCCCchHHHHHHHHHHHHHHHHHh-C-cc--CCHHHHHHHhCCCHHHHHHHcCCHHHHHHH
Confidence 344444333333 45556679998 4 87 578899999999999999999999875443
No 205
>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=53.86 E-value=27 Score=20.80 Aligned_cols=36 Identities=19% Similarity=0.101 Sum_probs=27.1
Q ss_pred HHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy10851 16 NLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 16 ~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFq 57 (159)
.|+..|+-.+. + . ..+.. .||..+|++.+.|+.-..
T Consensus 6 rq~~Ll~~L~~-~-~-~~~~~---ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 6 RQLKLLELLLK-N-K-WITLK---ELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHH-H-T-SBBHH---HHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHc-C-C-CCcHH---HHHHHHCCCHHHHHHHHH
Confidence 57788888888 6 3 66644 899999999999887653
No 206
>PRK13870 transcriptional regulator TraR; Provisional
Probab=52.33 E-value=39 Score=26.06 Aligned_cols=46 Identities=13% Similarity=0.084 Sum_probs=33.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851 11 TIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK 64 (159)
Q Consensus 11 t~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~r 64 (159)
..+|+.++..|.=. .. . ..-.+||.+||++++.|+.-.+|-|.|.-
T Consensus 172 ~~LT~RE~E~L~W~--A~-G-----KT~~EIa~ILgISe~TV~~Hl~na~~KLg 217 (234)
T PRK13870 172 AWLDPKEATYLRWI--AV-G-----KTMEEIADVEGVKYNSVRVKLREAMKRFD 217 (234)
T ss_pred CCCCHHHHHHHHHH--Hc-C-----CCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 45677777666421 12 1 24567899999999999999999988754
No 207
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.03 E-value=27 Score=23.16 Aligned_cols=40 Identities=10% Similarity=-0.030 Sum_probs=29.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhh
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQ 53 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~ 53 (159)
.++++|+..-+..|..+ - -.+....+.||..||.++-.|.
T Consensus 2 SLn~eq~~~Tk~elqan-~-el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 2 SLNPEQKQRTKQELQAN-F-ELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCCHHHHHHHHHHHHHh-h-hhccccHHHHHHHhCCCHHHHH
Confidence 46778877777777766 3 5666778889999998876544
No 208
>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=51.80 E-value=6.7 Score=28.96 Aligned_cols=34 Identities=21% Similarity=0.292 Sum_probs=29.2
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRK 69 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~ 69 (159)
..+.+||..++++..+|-+|.+|-+...++....
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~y 48 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAKPKY 48 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccccchh
Confidence 4688999999999999999999999887776443
No 209
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=51.65 E-value=21 Score=25.98 Aligned_cols=34 Identities=24% Similarity=0.297 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 35 TQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 35 ~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
...-.+||..+|++...|+.+..-.|.++|+...
T Consensus 143 gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 143 GLSYEEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 3456788999999999999999888888887644
No 210
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=51.19 E-value=53 Score=25.40 Aligned_cols=49 Identities=16% Similarity=-0.003 Sum_probs=36.8
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 9 FQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 9 ~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
....+|+.++.+|.-.- .. + .-.+||..++++.+.|+.-.+|-+.|..-
T Consensus 176 ~~~~LT~rE~evl~~~a-~G---~----t~~eIa~~l~is~~TV~~h~~~~~~KL~~ 224 (240)
T PRK10188 176 PEMNFSKREKEILKWTA-EG---K----TSAEIAMILSISENTVNFHQKNMQKKFNA 224 (240)
T ss_pred CCCCCCHHHHHHHHHHH-cC---C----CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 34578888888887553 22 2 35678999999999999999888877543
No 211
>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=50.68 E-value=43 Score=26.28 Aligned_cols=50 Identities=14% Similarity=0.084 Sum_probs=37.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
.++..+..+|...|-.. ....-.+||..+|++...|+....+-..|.|+.
T Consensus 218 ~L~~rer~vl~l~y~~~-----~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~ 267 (270)
T TIGR02392 218 SLDARSRRIIEARWLDD-----DKLTLQELAAEYGVSAERIRQIEKNAMKKLKAA 267 (270)
T ss_pred cCCHHHHHHHHHHhcCC-----CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46667777777766221 123467899999999999999998888888864
No 212
>smart00595 MADF subfamily of SANT domain.
Probab=50.01 E-value=42 Score=21.30 Aligned_cols=35 Identities=23% Similarity=0.430 Sum_probs=28.9
Q ss_pred HHHHHHhCCCchhhhhhhhhHHHHHHHHHHHHHhh
Q psy10851 39 EALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQQ 73 (159)
Q Consensus 39 ~~La~~l~l~~~~V~vWFqNRR~k~rk~~~~~~~~ 73 (159)
..||..+|.+...|+.-+.|-|.+.++........
T Consensus 31 ~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~~~~ 65 (89)
T smart00595 31 EEIAEELGLSVEECKKRWKNLRDRYRRELKRLQNG 65 (89)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45799999999999999999999999876654443
No 213
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=49.81 E-value=5.5 Score=30.87 Aligned_cols=9 Identities=22% Similarity=0.316 Sum_probs=3.5
Q ss_pred hhhhHHHHH
Q psy10851 55 WFQNQRAKM 63 (159)
Q Consensus 55 WFqNRR~k~ 63 (159)
|++.=|..+
T Consensus 57 ~~~~lr~~~ 65 (233)
T PF11705_consen 57 LKRELRERM 65 (233)
T ss_pred HHHHHHHHH
Confidence 333333333
No 214
>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=49.61 E-value=12 Score=21.43 Aligned_cols=23 Identities=17% Similarity=0.248 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCchhhhhhhhhHH
Q psy10851 38 REALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFqNRR 60 (159)
...||..+|++...|..|..+++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 57789999999999999987664
No 215
>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=49.59 E-value=12 Score=20.32 Aligned_cols=23 Identities=26% Similarity=0.338 Sum_probs=19.5
Q ss_pred HHHHHHHhCCCchhhhhhhhhHH
Q psy10851 38 REALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFqNRR 60 (159)
...+|..+|++...|..|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45789999999999999988763
No 216
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=49.40 E-value=45 Score=23.82 Aligned_cols=45 Identities=16% Similarity=0.025 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK 64 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~r 64 (159)
.+|.....+|.-+.. . ..+.+||..++++.+.|+++.++-|.|..
T Consensus 149 ~lt~re~~vl~~l~~-g-------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 149 VLSNREVTILRYLVS-G-------LSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred cCCHHHHHHHHHHHc-C-------CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 467777777754322 1 24788999999999999999988777643
No 217
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=48.97 E-value=59 Score=21.06 Aligned_cols=46 Identities=17% Similarity=0.143 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHHhhcC---CCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy10851 12 IRLLNLKVKLKTSFNSCC---PGHKTTQVREALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~---~~yp~~~~r~~La~~l~l~~~~V~vWFq 57 (159)
-+|..|+..|...|.... .++.+..+...+...+|++...|..+|.
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 468899999999987631 1277888888877778998888888874
No 218
>PF13730 HTH_36: Helix-turn-helix domain
Probab=48.92 E-value=50 Score=18.85 Aligned_cols=44 Identities=25% Similarity=0.101 Sum_probs=28.8
Q ss_pred CCCHHHHHHHHHHHhhcC--C-CCCCHHHHHHHHHHhCCCchhhhhhhhh
Q psy10851 12 IRLLNLKVKLKTSFNSCC--P-GHKTTQVREALAKDTGLSVRVVQVWFQN 58 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~--~-~yp~~~~r~~La~~l~l~~~~V~vWFqN 58 (159)
.+++..+.++-.++...| . -|| -...||..+|++.+.|+.+...
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~p---S~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFP---SQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCc---CHHHHHHHHCcCHHHHHHHHHH
Confidence 456666666555543321 1 145 4778899999999999988753
No 219
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=48.87 E-value=39 Score=23.17 Aligned_cols=21 Identities=29% Similarity=0.401 Sum_probs=18.8
Q ss_pred HHHHHHHHhCCCchhhhhhhh
Q psy10851 37 VREALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFq 57 (159)
.+..+|..++++...|..||+
T Consensus 20 s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 20 SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred hHHHHHHHhCcHHHHHHHHHH
Confidence 466789999999999999998
No 220
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=48.65 E-value=46 Score=22.55 Aligned_cols=45 Identities=13% Similarity=0.135 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKM 63 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~ 63 (159)
-+|..|..+|+-+|..+ .-..+||..+|++..-|.-|.+.-+.+.
T Consensus 17 LLT~kQ~~~l~lyy~eD-------lSlsEIAe~~~iSRqaV~d~ikr~~~~L 61 (101)
T PF04297_consen 17 LLTEKQREILELYYEED-------LSLSEIAEELGISRQAVYDSIKRAEKKL 61 (101)
T ss_dssp GS-HHHHHHHHHHCTS----------HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred HCCHHHHHHHHHHHccC-------CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 47889999998765444 4578899999999999999986555443
No 221
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=48.31 E-value=43 Score=26.76 Aligned_cols=30 Identities=13% Similarity=0.174 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
...+||..+|++...|+...+.-|.+.|+.
T Consensus 136 s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~ 165 (290)
T PRK09635 136 PYQQIATTIGSQASTCRQLAHRARRKINES 165 (290)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 467789999999999999998777777763
No 222
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=46.73 E-value=11 Score=26.44 Aligned_cols=26 Identities=31% Similarity=0.496 Sum_probs=21.0
Q ss_pred HHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 38 REALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
-++||..+|++...|.-|. |...|+.
T Consensus 3 ~eELA~~tG~srQTINrWv--RkegW~T 28 (122)
T PF07037_consen 3 PEELAELTGYSRQTINRWV--RKEGWKT 28 (122)
T ss_pred HHHHHHHhCccHHHHHHHH--HhcCcee
Confidence 3689999999999999997 4555554
No 223
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=46.50 E-value=51 Score=18.56 Aligned_cols=21 Identities=24% Similarity=0.347 Sum_probs=18.5
Q ss_pred HHHHHHHHhCCCchhhhhhhh
Q psy10851 37 VREALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFq 57 (159)
....+|..+|++...|+.+|.
T Consensus 29 s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 29 SFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 467889999999999999984
No 224
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=45.03 E-value=50 Score=20.23 Aligned_cols=40 Identities=18% Similarity=0.046 Sum_probs=23.8
Q ss_pred CCCHHHHHHHH---HHHhhcCCCCCCHHHHHHHHHHhCCC-chhhhhh
Q psy10851 12 IRLLNLKVKLK---TSFNSCCPGHKTTQVREALAKDTGLS-VRVVQVW 55 (159)
Q Consensus 12 ~~s~~Q~~~Le---~~F~~~~~~yp~~~~r~~La~~l~l~-~~~V~vW 55 (159)
.+|..|..+|. .+...+ . || ....+||..+|+. ...|+.-
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~-G-~~--Pt~rEIa~~~g~~S~~tv~~~ 46 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEEN-G-YP--PTVREIAEALGLKSTSTVQRH 46 (65)
T ss_dssp ---HHHHHHHHHHHHHHHHH-S-S-----HHHHHHHHTSSSHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHc-C-CC--CCHHHHHHHhCCCChHHHHHH
Confidence 36777766665 445666 4 77 3678899999997 6666543
No 225
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=44.84 E-value=62 Score=25.79 Aligned_cols=51 Identities=14% Similarity=0.040 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
.++..+..+|...|- |-......+||..+|++...|+.+-..-+.|.|...
T Consensus 227 ~L~~rer~vl~lr~~-----~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l 277 (289)
T PRK07500 227 TLNERELRIIRERRL-----REDGATLEALGEELGISKERVRQIEARALEKLRRAL 277 (289)
T ss_pred cCCHHHHHHHHHHhc-----CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 466677777776652 112235788999999999999999888888877654
No 226
>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=44.41 E-value=25 Score=19.18 Aligned_cols=22 Identities=23% Similarity=0.148 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCchhhhhhhhhH
Q psy10851 38 REALAKDTGLSVRVVQVWFQNQ 59 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFqNR 59 (159)
..++|..+|++...|..|.++.
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcC
Confidence 4678999999999999997543
No 227
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=43.95 E-value=21 Score=21.49 Aligned_cols=19 Identities=32% Similarity=0.385 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
..++|+.+|++...|+.|-
T Consensus 3 ~~eva~~~gvs~~tlr~~~ 21 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYE 21 (70)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4678999999999999994
No 228
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=43.29 E-value=23 Score=23.57 Aligned_cols=20 Identities=35% Similarity=0.418 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFq 57 (159)
..++|+.+|++.+.|+.|..
T Consensus 3 i~eva~~~gvs~~tlR~ye~ 22 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDE 22 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999974
No 229
>cd00131 PAX Paired Box domain
Probab=43.24 E-value=1.1e+02 Score=21.26 Aligned_cols=46 Identities=13% Similarity=0.088 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCC-------CchhhhhhhhhH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGL-------SVRVVQVWFQNQ 59 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l-------~~~~V~vWFqNR 59 (159)
..+..+...|..+...+ | ..+..+...+...-|+ +...|.-||+++
T Consensus 75 ~~~~~~~~~i~~~v~~~-p-~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 75 VATPEVVKKIEIYKQEN-P-GMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred cCCHHHHHHHHHHHHHC-C-CCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 45666767676666666 6 6666666554224455 777888787653
No 230
>PHA01976 helix-turn-helix protein
Probab=43.14 E-value=18 Score=21.68 Aligned_cols=23 Identities=13% Similarity=0.309 Sum_probs=19.8
Q ss_pred HHHHHHHhCCCchhhhhhhhhHH
Q psy10851 38 REALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFqNRR 60 (159)
...||..+|++...|..|...++
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 56799999999999999986654
No 231
>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=42.89 E-value=18 Score=22.38 Aligned_cols=23 Identities=30% Similarity=0.326 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCchhhhhhhhhHH
Q psy10851 38 REALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFqNRR 60 (159)
...||..+|++...|..|+.+++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46799999999999999997765
No 232
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=42.87 E-value=55 Score=22.66 Aligned_cols=38 Identities=13% Similarity=0.009 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhh
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWF 56 (159)
.++.+|+..++.+.... . -.+++++.+|++...|+.=+
T Consensus 33 ~L~~E~~~Fi~~Fi~~r-G------nlKe~e~~lgiSYPTvR~rL 70 (113)
T PF09862_consen 33 RLSPEQLEFIKLFIKNR-G------NLKEMEKELGISYPTVRNRL 70 (113)
T ss_pred cCCHHHHHHHHHHHHhc-C------CHHHHHHHHCCCcHHHHHHH
Confidence 57889999888776555 3 46677788888877765443
No 233
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=42.39 E-value=68 Score=24.04 Aligned_cols=45 Identities=11% Similarity=0.066 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK 64 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~r 64 (159)
.+|+.++.+|.-+- + . +. -++||.+++++++.|+.-..|=..|..
T Consensus 137 ~LT~RE~eVL~lla--~-G-~s----nkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 137 SLSRTESSMLRMWM--A-G-QG----TIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred cCCHHHHHHHHHHH--c-C-CC----HHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 49999999997653 2 2 33 477999999999999988766555544
No 234
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=42.36 E-value=49 Score=23.19 Aligned_cols=31 Identities=29% Similarity=0.360 Sum_probs=24.3
Q ss_pred HHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 38 REALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
-..+|..+|++...|+++-++-|.|.+....
T Consensus 159 ~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~~ 189 (202)
T PRK09390 159 NKVIARDLDISPRTVEVYRANVMTKMQAGSL 189 (202)
T ss_pred hHHHHHHcCCCHHHHHHHHHHHHHHHccccH
Confidence 4557889999999999998888877655433
No 235
>KOG3623|consensus
Probab=41.63 E-value=10 Score=34.57 Aligned_cols=56 Identities=13% Similarity=0.122 Sum_probs=41.0
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
|+-+..++-..|...|..+ .-++..+-..++-.+.....+|.+||++|+..-++..
T Consensus 630 ~sp~k~~dq~ql~~a~elq--~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~p 685 (1007)
T KOG3623|consen 630 RSPIKEEDQQQLKQAYELQ--ASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMP 685 (1007)
T ss_pred cCCCCccchhhhHhhhhcc--cCccCcccchhhhhccCCCcchhhcccCCCCCCCCCc
Confidence 4555566667777888777 3566555556666678888999999999998877653
No 236
>PF12728 HTH_17: Helix-turn-helix domain
Probab=41.06 E-value=29 Score=19.64 Aligned_cols=22 Identities=23% Similarity=0.332 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCchhhhhhhhhH
Q psy10851 38 REALAKDTGLSVRVVQVWFQNQ 59 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFqNR 59 (159)
..++|..||++...|..|.++.
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 4578999999999999997543
No 237
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=40.09 E-value=83 Score=26.79 Aligned_cols=53 Identities=11% Similarity=0.029 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
.+++.+..+|.-.|-.. - . ......+||..+|++...|+.+....+.|.|...
T Consensus 350 ~L~~reR~VI~LRygl~-d-~-~~~Tl~EIA~~LGvS~erVRqie~rAl~KLR~~~ 402 (415)
T PRK07598 350 DLTSRERDVIRMRFGLA-D-G-HTYSLAEIGRALDLSRERVRQIESKALQKLRQPK 402 (415)
T ss_pred hCCHHHHHHHHHHHhcC-C-C-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchh
Confidence 46677777777777522 0 1 1124688999999999999999877777777543
No 238
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=39.68 E-value=81 Score=22.48 Aligned_cols=45 Identities=9% Similarity=0.033 Sum_probs=35.4
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHH
Q psy10851 11 TIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKM 63 (159)
Q Consensus 11 t~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~ 63 (159)
..+|..+..+|.-++.- + .+.+||..++++.+.|++.-.+=|.|.
T Consensus 142 ~~lt~~E~~vl~~l~~g----~----~~~~I~~~l~~s~~tv~~~~~~l~~Kl 186 (204)
T PRK09958 142 DSLSKQEISVMRYILDG----K----DNNDIAEKMFISNKTVSTYKSRLMEKL 186 (204)
T ss_pred ccCCHHHHHHHHHHHcC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 35899999888877632 3 367899999999999999887777664
No 239
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=38.35 E-value=30 Score=22.88 Aligned_cols=19 Identities=26% Similarity=0.422 Sum_probs=17.1
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
+..+|..+|++.+.|+.|.
T Consensus 3 I~e~a~~~gvs~~tLR~ye 21 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYE 21 (96)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5678999999999999995
No 240
>PRK05949 RNA polymerase sigma factor; Validated
Probab=38.03 E-value=88 Score=25.51 Aligned_cols=52 Identities=12% Similarity=-0.002 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
.+++.+..+|...|... . + ......+||..+|++...|+......+.|.|+.
T Consensus 266 ~L~~rer~Vi~lr~gl~-~-~-e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~ 317 (327)
T PRK05949 266 ELTPQQREVLTLRFGLE-D-G-KELSLAKVGERLNLSRERVRQLEHQALAHLRRR 317 (327)
T ss_pred hCCHHHHHHHHHHhccC-C-C-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 35666777777766432 0 1 224678899999999999999988888888774
No 241
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=37.34 E-value=1e+02 Score=25.00 Aligned_cols=52 Identities=12% Similarity=0.002 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
.++..+..+|...|... ++ ......+||..+|++...|+..-...+.|.|+.
T Consensus 256 ~L~~rer~Vi~lr~gl~--~~-~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~ 307 (317)
T PRK07405 256 DLTPQQKEVIALRFGLE--DG-QPLTLAKIGERLNISRERVRQIEREALSKLRKR 307 (317)
T ss_pred cCCHHHHHHHHHHhhcC--CC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 35566667777666433 11 224678899999999999999998888888874
No 242
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=37.32 E-value=55 Score=22.18 Aligned_cols=42 Identities=7% Similarity=0.029 Sum_probs=27.5
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHH
Q psy10851 10 QTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 10 Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR 60 (159)
...++..++..+...+..+ ...||..+|++...|..|-..+.
T Consensus 62 ~~~~~~~~i~~~r~~~glt---------q~~lA~~lg~~~~tis~~e~g~~ 103 (127)
T TIGR03830 62 DGLLTPPEIRRIRKKLGLS---------QREAAELLGGGVNAFSRYERGEV 103 (127)
T ss_pred cCCcCHHHHHHHHHHcCCC---------HHHHHHHhCCCHHHHHHHHCCCC
Confidence 3455555555554443222 35789999999999999976654
No 243
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=36.99 E-value=30 Score=24.48 Aligned_cols=20 Identities=25% Similarity=0.323 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFq 57 (159)
+.++|+.+|++.+.|+.|++
T Consensus 3 I~e~a~~~gvs~~TLR~Ye~ 22 (134)
T cd04779 3 IGQLAHLAGVSKRTIDYYTN 22 (134)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 56789999999999999984
No 244
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=36.80 E-value=33 Score=22.22 Aligned_cols=19 Identities=11% Similarity=0.212 Sum_probs=17.2
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
...+|..+|++.+.|+.|-
T Consensus 4 i~e~A~~~gvs~~tLr~ye 22 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYE 22 (91)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5678999999999999995
No 245
>PRK09483 response regulator; Provisional
Probab=36.80 E-value=96 Score=22.35 Aligned_cols=45 Identities=11% Similarity=0.013 Sum_probs=32.7
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHH
Q psy10851 11 TIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKM 63 (159)
Q Consensus 11 t~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~ 63 (159)
..+|+.++.+|.-+ ... +. -.+||..++++.+.|+.--+|=+.|.
T Consensus 147 ~~Lt~rE~~vl~~~-~~G---~~----~~~Ia~~l~is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 147 ASLSERELQIMLMI-TKG---QK----VNEISEQLNLSPKTVNSYRYRMFSKL 191 (217)
T ss_pred cccCHHHHHHHHHH-HCC---CC----HHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 45899999998643 222 33 33899999999999998776666553
No 246
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=36.72 E-value=93 Score=22.90 Aligned_cols=45 Identities=11% Similarity=0.022 Sum_probs=33.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHH
Q psy10851 11 TIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKM 63 (159)
Q Consensus 11 t~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~ 63 (159)
..+|+.++.+|.-+..- + .-.+||..++++.+.|+.-.+|=-.|.
T Consensus 149 ~~Lt~rE~evl~~~~~G----~----s~~eIA~~l~iS~~TV~~h~~~i~~Kl 193 (216)
T PRK10840 149 KRLSPKESEVLRLFAEG----F----LVTEIAKKLNRSIKTISSQKKSAMMKL 193 (216)
T ss_pred ccCCHHHHHHHHHHHCC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 35899999999876532 2 357799999999999998765544443
No 247
>PF13551 HTH_29: Winged helix-turn helix
Probab=36.59 E-value=35 Score=22.34 Aligned_cols=24 Identities=29% Similarity=0.541 Sum_probs=20.4
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR 60 (159)
....+|..+|++.+.|..|.+.-+
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~ 37 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYR 37 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHH
Confidence 577899999999999999986544
No 248
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=36.51 E-value=34 Score=22.51 Aligned_cols=20 Identities=25% Similarity=0.355 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFq 57 (159)
+.++|+.+|++...++.|.+
T Consensus 3 i~eva~~~gvs~~tLRyye~ 22 (96)
T cd04768 3 IGEFAKLAGVSIRTLRHYDD 22 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 56799999999999999974
No 249
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=36.29 E-value=52 Score=21.84 Aligned_cols=29 Identities=17% Similarity=0.302 Sum_probs=22.8
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
--..+|...|+++.+|.-|..+-+.++-.
T Consensus 25 gq~~vA~~~Gv~eStISR~k~~~~~~~a~ 53 (91)
T PF05269_consen 25 GQKKVAEAMGVDESTISRWKNDFIEKMAM 53 (91)
T ss_dssp HHHHHHHHHTSSTTTHHHHHHHHHHHHHH
T ss_pred hhHHHHHHhCCCHHHHHHHHhhHHHHHHH
Confidence 34568999999999999997776655544
No 250
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=36.23 E-value=96 Score=23.99 Aligned_cols=47 Identities=19% Similarity=0.134 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
.++..+..++...|... ....+||..+|++...|...-..-..|.|+
T Consensus 206 ~L~~rer~vi~~~~~~~-------~t~~eIA~~lgis~~~V~~~~~ral~kLr~ 252 (254)
T TIGR02850 206 RLNEREKMILNMRFFEG-------KTQMEVAEEIGISQAQVSRLEKAALKHMRK 252 (254)
T ss_pred cCCHHHHHHHHHHHcCC-------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 55666667777666333 247789999999999887775544444443
No 251
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=36.19 E-value=31 Score=22.31 Aligned_cols=18 Identities=33% Similarity=0.553 Sum_probs=16.5
Q ss_pred HHHHHHHhCCCchhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVW 55 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vW 55 (159)
..++|+.+|++.+.++.|
T Consensus 4 i~evA~~~gvs~~tLR~y 21 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYW 21 (88)
T ss_pred HHHHHHHHCcCHHHHHHH
Confidence 567899999999999999
No 252
>PRK04019 rplP0 acidic ribosomal protein P0; Validated
Probab=36.06 E-value=13 Score=30.40 Aligned_cols=9 Identities=22% Similarity=-0.079 Sum_probs=3.6
Q ss_pred CCHHHHHHH
Q psy10851 13 RLLNLKVKL 21 (159)
Q Consensus 13 ~s~~Q~~~L 21 (159)
+++.|...|
T Consensus 164 v~~~~a~lL 172 (330)
T PRK04019 164 ISPELANVL 172 (330)
T ss_pred cCHHHHHHH
Confidence 444443333
No 253
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=36.06 E-value=67 Score=24.25 Aligned_cols=45 Identities=9% Similarity=-0.066 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQ 59 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNR 59 (159)
.+|..++..|..+...+ +-....-.+||..++++...|+..+.+-
T Consensus 158 ~Lt~re~~~l~~~i~~~---~~~g~s~~eIA~~l~iS~~Tv~~~~~~~ 202 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH---QDYEFSTDELANAVNISRVSCRKYLIWL 202 (239)
T ss_pred CCCHHHHHHHHHHHHhC---CCCCcCHHHHHHHhCchHHHHHHHHHHH
Confidence 46777766665554322 3334466789999999999999988654
No 254
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=36.00 E-value=33 Score=20.82 Aligned_cols=18 Identities=39% Similarity=0.667 Sum_probs=15.4
Q ss_pred HHHHHHHhCCCchhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVW 55 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vW 55 (159)
...||+.||++..-|..|
T Consensus 12 ~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 12 QSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHh
Confidence 357999999999999999
No 255
>KOG1824|consensus
Probab=35.97 E-value=17 Score=34.22 Aligned_cols=12 Identities=17% Similarity=0.362 Sum_probs=5.4
Q ss_pred cccccCCCCCcc
Q psy10851 124 KIGYELGFFIQE 135 (159)
Q Consensus 124 ~~~~~~~~~~~e 135 (159)
++.|...+..+.
T Consensus 306 yisYDPNy~yd~ 317 (1233)
T KOG1824|consen 306 YISYDPNYNYDT 317 (1233)
T ss_pred HhccCCCCCCCC
Confidence 444544444433
No 256
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=35.97 E-value=48 Score=20.45 Aligned_cols=20 Identities=30% Similarity=0.483 Sum_probs=15.7
Q ss_pred HHHHHHHHhCCCchhhhhhh
Q psy10851 37 VREALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWF 56 (159)
...+||..+||+...|+..+
T Consensus 22 t~eEiA~~lgis~~~v~~~l 41 (78)
T PF04539_consen 22 TDEEIAEELGISVEEVRELL 41 (78)
T ss_dssp BHHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHcccHHHHHHHH
Confidence 46678999999999888765
No 257
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=35.88 E-value=52 Score=19.35 Aligned_cols=23 Identities=22% Similarity=0.317 Sum_probs=15.2
Q ss_pred HHHHHHHhCCCchhhhhhhhhHH
Q psy10851 38 REALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFqNRR 60 (159)
...+|..+|++...|..|-.+++
T Consensus 15 ~~~~a~~~~i~~~~i~~~e~g~~ 37 (64)
T PF12844_consen 15 QKDLAEKLGISRSTISKIENGKR 37 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHHCcCHHHHHHHHCCCc
Confidence 45567777777777777776655
No 258
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=35.72 E-value=16 Score=33.81 Aligned_cols=7 Identities=14% Similarity=0.733 Sum_probs=2.7
Q ss_pred HHHHHHH
Q psy10851 60 RAKMKKI 66 (159)
Q Consensus 60 R~k~rk~ 66 (159)
+.|.++.
T Consensus 281 ~erLekl 287 (840)
T PF04147_consen 281 KERLEKL 287 (840)
T ss_pred HHHHHHH
Confidence 3343443
No 259
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=35.26 E-value=81 Score=22.91 Aligned_cols=36 Identities=19% Similarity=0.122 Sum_probs=28.8
Q ss_pred HHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhh
Q psy10851 16 NLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQ 53 (159)
Q Consensus 16 ~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~ 53 (159)
.-+..|...=... +|.+......||..+|++..+|.
T Consensus 24 ~li~~L~~vQ~~~--G~Ip~e~~~~iA~~l~v~~~~V~ 59 (156)
T PRK05988 24 ALLPILHAIQDEF--GYVPEDAVPVIAEALNLSRAEVH 59 (156)
T ss_pred HHHHHHHHHHHHc--CCCCHHHHHHHHHHhCCCHHHHH
Confidence 3466666666667 49999999999999999988754
No 260
>PF11516 DUF3220: Protein of unknown function (DUF3120); InterPro: IPR021597 This family of proteins with unknown function appears to be restricted to Bordetella. ; PDB: 2JPF_A.
Probab=34.95 E-value=18 Score=23.41 Aligned_cols=14 Identities=36% Similarity=0.520 Sum_probs=10.3
Q ss_pred hhhhhhhhhHHHHH
Q psy10851 50 RVVQVWFQNQRAKM 63 (159)
Q Consensus 50 ~~V~vWFqNRR~k~ 63 (159)
..|+||.||--.-.
T Consensus 31 gdvkvwmqnledlh 44 (106)
T PF11516_consen 31 GDVKVWMQNLEDLH 44 (106)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHh
Confidence 36999999965433
No 261
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=34.89 E-value=24 Score=21.50 Aligned_cols=20 Identities=25% Similarity=0.481 Sum_probs=14.6
Q ss_pred HHHHHHHhCCCchhhh-hhhh
Q psy10851 38 REALAKDTGLSVRVVQ-VWFQ 57 (159)
Q Consensus 38 r~~La~~l~l~~~~V~-vWFq 57 (159)
...||..+|++...|. .|..
T Consensus 15 ~~~lA~~lgis~st~s~~~~~ 35 (66)
T PF07022_consen 15 DKELAERLGISKSTLSNNWKK 35 (66)
T ss_dssp CHHHHCCTT--HHHHH-HHHH
T ss_pred HHHHHHHhCcCHHHhhHHHHh
Confidence 4578999999999888 8874
No 262
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=34.63 E-value=64 Score=18.56 Aligned_cols=38 Identities=16% Similarity=0.090 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhh
Q psy10851 13 RLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 13 ~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWF 56 (159)
+|..|..+|...+... + .....||..++++...|..+-
T Consensus 1 lt~~q~~iL~~l~~~~-~-----~~~~~la~~~~~~~~~~t~~i 38 (59)
T PF01047_consen 1 LTPSQFRILRILYENG-G-----ITQSELAEKLGISRSTVTRII 38 (59)
T ss_dssp STHHHHHHHHHHHHHS-S-----EEHHHHHHHHTS-HHHHHHHH
T ss_pred CCHHHHHHHHHHHHcC-C-----CCHHHHHHHHCCChhHHHHHH
Confidence 4678888898888655 2 334589999999988777664
No 263
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=34.22 E-value=29 Score=18.53 Aligned_cols=23 Identities=26% Similarity=0.319 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCchhhhhhhhhHH
Q psy10851 38 REALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFqNRR 60 (159)
...||..+|++...|..|-.+++
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~~ 35 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGKR 35 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 55789999999999999976654
No 264
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=34.16 E-value=35 Score=22.53 Aligned_cols=19 Identities=26% Similarity=0.544 Sum_probs=16.8
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
+.+||+.+|++.+.|+.|=
T Consensus 3 I~eva~~~gvs~~tlR~Ye 21 (95)
T cd04780 3 MSELSKRSGVSVATIKYYL 21 (95)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5679999999999999994
No 265
>PF08452 DNAP_B_exo_N: DNA polymerase family B exonuclease domain, N-terminal; InterPro: IPR013660 This domain is found in viral DNA polymerases to the N terminus of DNA polymerase family B exonuclease domains (IPR006133 from INTERPRO). ; GO: 0003887 DNA-directed DNA polymerase activity
Probab=33.65 E-value=12 Score=17.88 Aligned_cols=8 Identities=25% Similarity=0.841 Sum_probs=6.3
Q ss_pred hhhhhhHH
Q psy10851 53 QVWFQNQR 60 (159)
Q Consensus 53 ~vWFqNRR 60 (159)
-+||-||.
T Consensus 6 iNWFE~~g 13 (22)
T PF08452_consen 6 INWFESRG 13 (22)
T ss_pred eehhhhCC
Confidence 47998875
No 266
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=33.62 E-value=14 Score=28.90 Aligned_cols=11 Identities=27% Similarity=0.380 Sum_probs=4.8
Q ss_pred HHHHHHhCCCc
Q psy10851 39 EALAKDTGLSV 49 (159)
Q Consensus 39 ~~La~~l~l~~ 49 (159)
..|+...||+.
T Consensus 36 eEL~~V~GIg~ 46 (232)
T PRK12766 36 SELAEVDGIGN 46 (232)
T ss_pred HHHHHccCCCH
Confidence 34444444443
No 267
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=33.60 E-value=39 Score=22.74 Aligned_cols=19 Identities=21% Similarity=0.298 Sum_probs=17.1
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
+.++|+.+|++.+.|+.|.
T Consensus 3 i~eva~~~gvs~~tlR~ye 21 (108)
T cd04773 3 IGELAHLLGVPPSTLRHWE 21 (108)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5678999999999999995
No 268
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=33.28 E-value=29 Score=24.23 Aligned_cols=24 Identities=21% Similarity=0.383 Sum_probs=20.9
Q ss_pred HHHHHHHhCCCchhhhhhhhhHHH
Q psy10851 38 REALAKDTGLSVRVVQVWFQNQRA 61 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFqNRR~ 61 (159)
...||..+|++...|..|..+++.
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~~ 44 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDETE 44 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 468899999999999999988753
No 269
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=33.23 E-value=27 Score=24.16 Aligned_cols=25 Identities=12% Similarity=0.298 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRA 61 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~ 61 (159)
.+.+||..+|++...|..|.++++.
T Consensus 20 sq~eLA~~~Gis~~~is~iE~g~~~ 44 (120)
T PRK13890 20 TKKELSERSGVSISFLSDLTTGKAN 44 (120)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCCCC
Confidence 3677999999999999999998863
No 270
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=32.47 E-value=93 Score=22.38 Aligned_cols=35 Identities=23% Similarity=0.186 Sum_probs=27.3
Q ss_pred HHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhh
Q psy10851 17 LKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQ 53 (159)
Q Consensus 17 Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~ 53 (159)
-+.+|...=... +|.+......||..+||+..+|.
T Consensus 24 ll~~L~~vQ~~~--g~ip~~~~~~iA~~l~v~~~~v~ 58 (154)
T PRK07539 24 VIPALKIVQEQR--GWVPDEAIEAVADYLGMPAIDVE 58 (154)
T ss_pred HHHHHHHHHHHh--CCCCHHHHHHHHHHhCcCHHHHH
Confidence 355565555556 49999999999999999988754
No 271
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=32.23 E-value=49 Score=22.92 Aligned_cols=25 Identities=40% Similarity=0.520 Sum_probs=22.0
Q ss_pred CCCHHHHHHHHHHhCCCchhhhhhh
Q psy10851 32 HKTTQVREALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 32 yp~~~~r~~La~~l~l~~~~V~vWF 56 (159)
-++..-|..||..+|++.+.|..|-
T Consensus 26 ~~~~~~r~~La~~~~i~~~~l~~w~ 50 (122)
T PF14229_consen 26 GDTPLGRKALAKKLGISERNLLKWV 50 (122)
T ss_pred CCCHHHHHHHHHhcCCCHHHHHHHH
Confidence 4677788899999999999999993
No 272
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=32.10 E-value=79 Score=22.91 Aligned_cols=42 Identities=7% Similarity=-0.037 Sum_probs=33.0
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHH
Q psy10851 18 KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAK 62 (159)
Q Consensus 18 ~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k 62 (159)
+..-...|... . |.. .....||+..|++...|-.+|.|+..=
T Consensus 14 l~aA~~lf~e~-G-~~~-tSi~~Ia~~aGvsk~~lY~~F~sK~~L 55 (192)
T PRK14996 14 LQAAMRVALAE-G-FAA-MTVRRIASEAQVAAGQVHHHFSSAGEL 55 (192)
T ss_pred HHHHHHHHHhc-C-hhh-ccHHHHHHHhCCCcHHHHHHcCCHHHH
Confidence 44555568888 4 743 567889999999999999999998773
No 273
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=31.75 E-value=1.4e+02 Score=22.51 Aligned_cols=44 Identities=9% Similarity=0.003 Sum_probs=32.6
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHH
Q psy10851 11 TIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAK 62 (159)
Q Consensus 11 t~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k 62 (159)
..+|+.++.+|.-+-.- + .-++||..++++.+.|++--.|=-.|
T Consensus 133 ~~LT~RE~eVL~ll~~G----~----snkeIA~~L~iS~~TV~~h~~~I~~K 176 (207)
T PRK11475 133 RMLSPTEREILRFMSRG----Y----SMPQIAEQLERNIKTIRAHKFNVMSK 176 (207)
T ss_pred CCCCHHHHHHHHHHHCC----C----CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 35899999999876532 2 35679999999999998775554443
No 274
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=31.40 E-value=41 Score=23.38 Aligned_cols=20 Identities=40% Similarity=0.604 Sum_probs=18.0
Q ss_pred HHHHHHHHhCCCchhhhhhh
Q psy10851 37 VREALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWF 56 (159)
.+.+||..+||+.+.|+.|-
T Consensus 5 tI~elA~~~gvs~~tlR~Ye 24 (120)
T TIGR02054 5 TISRLAEDAGVSVHVVRDYL 24 (120)
T ss_pred cHHHHHHHHCcCHHHHHHHH
Confidence 47789999999999999995
No 275
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=31.33 E-value=1.2e+02 Score=18.09 Aligned_cols=52 Identities=12% Similarity=0.081 Sum_probs=29.9
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHH---HhCCCchhhhhhhhhHHH
Q psy10851 8 NFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAK---DTGLSVRVVQVWFQNQRA 61 (159)
Q Consensus 8 r~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~---~l~l~~~~V~vWFqNRR~ 61 (159)
++|...|.+.-...-..+... . .++...-..|+. ..+|+..||+.=.|--|.
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~-G-~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKL-G-GPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHh-C-CCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 357777877755544555555 2 544433334444 356788888876665554
No 276
>PF13700 DUF4158: Domain of unknown function (DUF4158)
Probab=31.28 E-value=1.8e+02 Score=20.90 Aligned_cols=56 Identities=14% Similarity=-0.004 Sum_probs=36.0
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCCC------HHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 9 FQTIRLLNLKVKLKTSFNSCCPGHKT------TQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 9 ~Rt~~s~~Q~~~Le~~F~~~~~~yp~------~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
.|+..+.--..++-.+|+.... +|+ ......||.++|+....+.......+++.+.
T Consensus 38 ~r~~~~rlgfalqL~~fr~~g~-f~~~~~~~p~~~i~~va~ql~~~~~~~~~y~~r~~T~~~h 99 (166)
T PF13700_consen 38 RRGPANRLGFALQLGYFRALGR-FPDDPEDIPKADIEYVAKQLGLPPSDLSSYAQRSRTRYRH 99 (166)
T ss_pred ccCCccchhHHHHHHHHhcccc-cccccccCCHHHHHHHHHHhCCchHHHHhhhhhhhHHHHH
Confidence 3444444445666666666522 344 5678889999999998888887744444443
No 277
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=31.26 E-value=31 Score=20.55 Aligned_cols=25 Identities=24% Similarity=0.252 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQRA 61 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR~ 61 (159)
....||..+|++...|..|..+++.
T Consensus 16 s~~~lA~~~g~s~s~v~~iE~G~~~ 40 (64)
T PF13560_consen 16 SQAQLADRLGVSQSTVSRIERGRRP 40 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCCC
Confidence 5678999999999999999988874
No 278
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=31.13 E-value=46 Score=21.89 Aligned_cols=20 Identities=20% Similarity=0.199 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFq 57 (159)
+.++|+.+|++...++.|.+
T Consensus 3 i~eva~~~gvs~~tlR~ye~ 22 (97)
T cd04782 3 TGEFAKLCGISKQTLFHYDK 22 (97)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 56789999999999999963
No 279
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=31.08 E-value=53 Score=18.72 Aligned_cols=36 Identities=25% Similarity=0.219 Sum_probs=23.1
Q ss_pred HHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy10851 17 LKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 17 Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFq 57 (159)
|..+|.-++... . + .....||..+|++.+.|+.-..
T Consensus 2 ~~~il~~L~~~~-~-~---it~~eLa~~l~vS~rTi~~~i~ 37 (55)
T PF08279_consen 2 QKQILKLLLESK-E-P---ITAKELAEELGVSRRTIRRDIK 37 (55)
T ss_dssp HHHHHHHHHHTT-T-S---BEHHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHcC-C-C---cCHHHHHHHhCCCHHHHHHHHH
Confidence 345555555544 2 3 4567899999999988876543
No 280
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=31.03 E-value=1e+02 Score=21.96 Aligned_cols=36 Identities=19% Similarity=0.117 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhh
Q psy10851 16 NLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQ 53 (159)
Q Consensus 16 ~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~ 53 (159)
.-+.+|...=... +|.+......+|..+||+...|.
T Consensus 17 ~li~~L~~vQ~~~--G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 17 AIMPALMIAQEQK--GWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHHh--CCCCHHHHHHHHHHhCcCHHHHH
Confidence 3455665555556 49999999999999999987654
No 281
>PF13565 HTH_32: Homeodomain-like domain
Probab=30.90 E-value=1.3e+02 Score=18.29 Aligned_cols=33 Identities=15% Similarity=0.187 Sum_probs=23.1
Q ss_pred CHHHHHHHHHHHhhcCCCCCCHHHHHH-HHHHhCCC
Q psy10851 14 LLNLKVKLKTSFNSCCPGHKTTQVREA-LAKDTGLS 48 (159)
Q Consensus 14 s~~Q~~~Le~~F~~~~~~yp~~~~r~~-La~~l~l~ 48 (159)
+.++...|..++..+ + .-+...... |+..+|+.
T Consensus 32 ~~e~~~~i~~~~~~~-p-~wt~~~i~~~L~~~~g~~ 65 (77)
T PF13565_consen 32 DPEQRERIIALIEEH-P-RWTPREIAEYLEEEFGIS 65 (77)
T ss_pred cHHHHHHHHHHHHhC-C-CCCHHHHHHHHHHHhCCC
Confidence 677778888888887 6 666666555 56666643
No 282
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=30.53 E-value=74 Score=25.37 Aligned_cols=48 Identities=13% Similarity=-0.033 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAK 62 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k 62 (159)
.+++.+..+|...|-.. . + ......+||..+|++...|+..-...+.|
T Consensus 249 ~L~~rer~Vi~lr~gl~-~-~-~~~Tl~EIa~~lgiS~erVrq~~~rAl~k 296 (298)
T TIGR02997 249 ELTPRERQVLRLRFGLD-G-G-EPLTLAEIGRRLNLSRERVRQIEAKALRK 296 (298)
T ss_pred cCCHHHHHHHHHHhccC-C-C-CCcCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 35666677777766422 1 1 22467889999999999999887554444
No 283
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=30.52 E-value=85 Score=22.32 Aligned_cols=34 Identities=18% Similarity=0.130 Sum_probs=24.5
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhh
Q psy10851 18 KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQ 53 (159)
Q Consensus 18 ~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~ 53 (159)
+.+|...=... +|.+......+|..+||+..+|.
T Consensus 16 l~~L~~~Q~~~--g~i~~~~~~~iA~~l~i~~~~v~ 49 (145)
T PF01257_consen 16 LPILHEVQEEY--GYIPEEALEEIAEALGIPPAEVY 49 (145)
T ss_dssp HHHHHHHHHHH--SS--HHHHHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHc--CCCCHHHHHHHHHHHCCCHHHHH
Confidence 55666665566 49999999999999999988754
No 284
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=30.50 E-value=82 Score=23.06 Aligned_cols=35 Identities=14% Similarity=0.092 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhC-CCchhhh
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTG-LSVRVVQ 53 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~-l~~~~V~ 53 (159)
.+|.+.+..|.++|... - ...+||..|| ++..-|.
T Consensus 2 ~Wtde~~~~L~~lw~~G-~------SasqIA~~lg~vsRnAVi 37 (162)
T PF07750_consen 2 SWTDERVERLRKLWAEG-L------SASQIARQLGGVSRNAVI 37 (162)
T ss_pred CCCHHHHHHHHHHHHcC-C------CHHHHHHHhCCcchhhhh
Confidence 47899999999999766 2 4677899999 7776554
No 285
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=30.45 E-value=43 Score=22.24 Aligned_cols=19 Identities=11% Similarity=0.163 Sum_probs=17.1
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
+.++|+.+|++.+.++.|-
T Consensus 4 i~eva~~~gvs~~tLR~ye 22 (102)
T cd04775 4 IGQMSRKFGVSRSTLLYYE 22 (102)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5689999999999999995
No 286
>PF04712 Radial_spoke: Radial spokehead-like protein
Probab=30.37 E-value=26 Score=30.37 Aligned_cols=19 Identities=11% Similarity=0.118 Sum_probs=10.0
Q ss_pred CCCC-CCCCccccccccCCC
Q psy10851 113 VGDK-KKSSSVLKIGYELGF 131 (159)
Q Consensus 113 ~~~~-~~~s~~~~~~~~~~~ 131 (159)
+..| |+...-+++|--.-+
T Consensus 333 l~~WvH~~~~Il~qGR~~~~ 352 (491)
T PF04712_consen 333 LSNWVHHRPYILPQGRCTWY 352 (491)
T ss_pred cccccccccccccCceEeCC
Confidence 3455 444555566655544
No 287
>PF05044 HPD: Homeo-prospero domain; InterPro: IPR007738 The homeobox gene Prox1 is expressed in a subpopulation of endothelial cells that, after budding from veins, gives rise to the mammalian lymphatic system []. Prox1 has been found to be an early specific marker for the developing liver and pancreas in the mammalian foregut endoderm []. This family contains an atypical homeobox domain.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2LMD_A 1XPX_A 1MIJ_A.
Probab=30.24 E-value=32 Score=24.95 Aligned_cols=53 Identities=15% Similarity=0.014 Sum_probs=30.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhC---CCchhhhhhhhhHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTG---LSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~---l~~~~V~vWFqNRR~k~rk~ 66 (159)
.+|+.-|..-+-.|--. + ||+....+.---... ....|+-.||.|=|-=.-.+
T Consensus 2 ~Ltp~HLkKaKlMFfyt-R-YPss~~LK~yFpDv~Fnr~~TsQLiKWFSNFREFyYiQ 57 (158)
T PF05044_consen 2 GLTPMHLKKAKLMFFYT-R-YPSSNMLKSYFPDVKFNRCNTSQLIKWFSNFREFYYIQ 57 (158)
T ss_dssp SS-HHHHHHHHHHCTT--S-S-HHHHHHHCTTTS---HHHHHHHHHHHHHHHHHHHHH
T ss_pred CCChHHHhhhhheeeee-c-CCchHHHHHhCchhhhhhhhHHHHHHHhccchhHHHHH
Confidence 45677777777777778 6 888765443211111 23468889999999744433
No 288
>PF03457 HA: Helicase associated domain; InterPro: IPR005114 This short domain is found in multiple copies in bacterial helicase proteins. The domain is predicted to contain 3 alpha helices. The function of this domain may be to bind nucleic acid.; PDB: 2KTA_A.
Probab=30.15 E-value=74 Score=19.17 Aligned_cols=43 Identities=21% Similarity=0.135 Sum_probs=23.9
Q ss_pred HHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHH
Q psy10851 17 LKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 17 Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~ 67 (159)
-+..|..++... . +......-. .....+-.|..|.|.+.|+..
T Consensus 11 ~~~~l~~y~~~~-G-~~~vp~~~~------~~~~~Lg~Wl~~qR~~~r~g~ 53 (68)
T PF03457_consen 11 RYEALKAYKEEH-G-HLNVPRDYV------TDGFPLGQWLNNQRRKYRKGK 53 (68)
T ss_dssp HHHHHHHHHHHH-S---S-SS-----------SSHHHHHHHHHHHHHHHT-
T ss_pred HHHHHHHHHHHH-C-CCCCCcccC------cCCCcHHHHHHHHHHHHHcCC
Confidence 356677766666 2 332221110 014567899999999999854
No 289
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=30.02 E-value=48 Score=23.13 Aligned_cols=20 Identities=10% Similarity=0.282 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFq 57 (159)
...+|..+|++.+.++.|.+
T Consensus 4 I~eVA~~~GVs~~TLR~wE~ 23 (120)
T cd04767 4 IGVVAELLNIHPETLRIWER 23 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 56789999999999999964
No 290
>TIGR03685 L21P_arch 50S ribosomal protein L12P. This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.
Probab=29.91 E-value=20 Score=24.47 Aligned_cols=20 Identities=15% Similarity=0.194 Sum_probs=15.2
Q ss_pred CCCHHHHHHHHHHhCCCchh
Q psy10851 32 HKTTQVREALAKDTGLSVRV 51 (159)
Q Consensus 32 yp~~~~r~~La~~l~l~~~~ 51 (159)
-|+...+..|....|+....
T Consensus 16 ~iT~e~I~~IL~AAGv~ve~ 35 (105)
T TIGR03685 16 EINEENLKAVLEAAGVEVDE 35 (105)
T ss_pred CCCHHHHHHHHHHhCCcccH
Confidence 58888888888888866543
No 291
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=29.87 E-value=1.1e+02 Score=22.60 Aligned_cols=34 Identities=12% Similarity=-0.038 Sum_probs=26.2
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhh
Q psy10851 18 KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQ 53 (159)
Q Consensus 18 ~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~ 53 (159)
+.+|...=... . |.+......+|..+||+...|.
T Consensus 39 i~~L~~iQ~~~-G-yIp~e~~~~iA~~l~v~~a~V~ 72 (169)
T PRK07571 39 IEVLHKAQELF-G-YLERDLLLYVARQLKLPLSRVY 72 (169)
T ss_pred HHHHHHHHHHc-C-CCCHHHHHHHHHHhCcCHHHHH
Confidence 45555555556 4 9999999999999999987654
No 292
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=29.77 E-value=1.1e+02 Score=22.58 Aligned_cols=36 Identities=17% Similarity=0.068 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhh
Q psy10851 15 LNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVV 52 (159)
Q Consensus 15 ~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V 52 (159)
..-+..|...+.+. . |........+|..|||+...|
T Consensus 25 sAlip~L~~aQ~~~-G-~l~~~ai~~iA~~L~i~~~~v 60 (160)
T COG1905 25 SALIPLLHIAQEQF-G-WLPPEAIEEIADMLGIPRARV 60 (160)
T ss_pred hHHHHHHHHHHHHh-C-CCCHHHHHHHHHHhCCCHHHh
Confidence 45578888899999 5 999999999999999998754
No 293
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=29.72 E-value=50 Score=21.65 Aligned_cols=20 Identities=40% Similarity=0.514 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFq 57 (159)
+.++|+.+|++.+.++.|-+
T Consensus 3 i~eva~~~gvs~~tlR~ye~ 22 (96)
T cd04788 3 IGELARRTGLSVRTLHHYDH 22 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999963
No 294
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=29.62 E-value=1.5e+02 Score=22.60 Aligned_cols=46 Identities=11% Similarity=-0.060 Sum_probs=30.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK 64 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~r 64 (159)
.++..+..+|...|... . ...+||..+|++..+|..--+.-+.|.|
T Consensus 183 ~L~~~er~vi~l~~~~~-~------t~~EIA~~lgis~~~V~q~~~~~~~kLr 228 (231)
T PRK12427 183 QLDEREQLILHLYYQHE-M------SLKEIALVLDLTEARICQLNKKIAQKIK 228 (231)
T ss_pred cCCHHHHHHHHHHHHcC-C------CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 45566666776666444 2 3678999999999877766555444444
No 295
>PF07219 HemY_N: HemY protein N-terminus; InterPro: IPR010817 This entry represents the N terminus (approximately 150 residues) of bacterial HemY porphyrin biosynthesis proteins. These are membrane protein involved in a late step of protoheme IX synthesis [].
Probab=29.32 E-value=86 Score=21.01 Aligned_cols=21 Identities=14% Similarity=0.205 Sum_probs=15.7
Q ss_pred CchhhhhhhhhHHHHHHHHHH
Q psy10851 48 SVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 48 ~~~~V~vWFqNRR~k~rk~~~ 68 (159)
.+..+..||++||.+.-....
T Consensus 43 ~p~~~~~~~~~rr~~ka~~al 63 (108)
T PF07219_consen 43 LPSRVRRWRRRRRRRKAQRAL 63 (108)
T ss_pred ChHHHHHHHHHHHHHHHHHHH
Confidence 467889999999887665543
No 296
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=29.31 E-value=51 Score=18.35 Aligned_cols=26 Identities=15% Similarity=0.250 Sum_probs=21.8
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQRA 61 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR~ 61 (159)
.....||+.+|++...+-..|.|+-.
T Consensus 17 ~s~~~Ia~~~gvs~~~~y~~f~~k~~ 42 (47)
T PF00440_consen 17 VSIRDIARRAGVSKGSFYRYFPSKDD 42 (47)
T ss_dssp SSHHHHHHHHTSCHHHHHHHCSSHHH
T ss_pred CCHHHHHHHHccchhhHHHHcCCHHH
Confidence 44678899999999999999988743
No 297
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=29.23 E-value=55 Score=24.11 Aligned_cols=42 Identities=10% Similarity=0.063 Sum_probs=33.1
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHH
Q psy10851 18 KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAK 62 (159)
Q Consensus 18 ~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k 62 (159)
+......|... . |-. .....||...|++...+-.+|.|+-.=
T Consensus 17 l~aa~~lf~~~-G-~~~-~ti~~Ia~~agvsk~t~Y~~F~sKe~L 58 (213)
T PRK09975 17 IETAIAQFALR-G-VSN-TTLNDIADAANVTRGAIYWHFENKTQL 58 (213)
T ss_pred HHHHHHHHHHc-C-ccc-CCHHHHHHHcCCCHHHHHHHcCCHHHH
Confidence 45556668777 4 655 457789999999999999999998873
No 298
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=29.09 E-value=51 Score=21.75 Aligned_cols=19 Identities=16% Similarity=0.181 Sum_probs=17.0
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
...+|+.+|++.+.++.|.
T Consensus 4 i~eva~~~gVs~~tLR~ye 22 (98)
T cd01279 4 ISVAAELLGIHPQTLRVYD 22 (98)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5678999999999999995
No 299
>PRK09726 antitoxin HipB; Provisional
Probab=29.02 E-value=37 Score=21.86 Aligned_cols=43 Identities=16% Similarity=0.098 Sum_probs=28.4
Q ss_pred CCCHHHHH-HHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHH
Q psy10851 12 IRLLNLKV-KLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 12 ~~s~~Q~~-~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR 60 (159)
.++..++. .|+.+-... .. ....||..+|++...|..|..+++
T Consensus 7 ~~~~~~l~~~lk~~R~~~---gl---tq~elA~~~gvs~~tis~~e~g~~ 50 (88)
T PRK09726 7 IYSPTQLANAMKLVRQQN---GW---TQSELAKKIGIKQATISNFENNPD 50 (88)
T ss_pred ccCHHHHHHHHHHHHHHc---CC---CHHHHHHHHCcCHHHHHHHHCCCC
Confidence 44555553 333333333 33 367889999999999999987654
No 300
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=29.00 E-value=52 Score=22.18 Aligned_cols=19 Identities=37% Similarity=0.579 Sum_probs=17.3
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
+.++|+.+|++.+.|+.|-
T Consensus 3 Ige~A~~~gvs~~tlR~ye 21 (107)
T cd01111 3 ISQLALDAGVSVHIVRDYL 21 (107)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5679999999999999996
No 301
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=28.90 E-value=43 Score=19.58 Aligned_cols=17 Identities=24% Similarity=0.348 Sum_probs=13.4
Q ss_pred HHHHHHHhCCCchhhhh
Q psy10851 38 REALAKDTGLSVRVVQV 54 (159)
Q Consensus 38 r~~La~~l~l~~~~V~v 54 (159)
-.+||..+|++..||+-
T Consensus 31 S~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 31 SQELAEALGITPAQVRK 47 (50)
T ss_dssp HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHCCCHHHhcc
Confidence 45789999999999874
No 302
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=28.83 E-value=41 Score=26.72 Aligned_cols=31 Identities=16% Similarity=0.258 Sum_probs=24.2
Q ss_pred CCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851 32 HKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK 64 (159)
Q Consensus 32 yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~r 64 (159)
|...-.-..||.++|+++.+|+-|- ||..|.
T Consensus 16 yl~gmk~~dIAeklGvspntiksWK--rr~gWs 46 (279)
T COG5484 16 YLKGMKLKDIAEKLGVSPNTIKSWK--RRDGWS 46 (279)
T ss_pred HHhhccHHHHHHHhCCChHHHHHHH--HhcCCC
Confidence 3333346789999999999999995 677774
No 303
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=28.25 E-value=40 Score=20.66 Aligned_cols=23 Identities=17% Similarity=0.177 Sum_probs=20.1
Q ss_pred HHHHHHHhCCCchhhhhhhhhHH
Q psy10851 38 REALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFqNRR 60 (159)
...||+.+|++...|..+|.+++
T Consensus 3 ~~~iA~~~gvS~~TVSr~ln~~~ 25 (70)
T smart00354 3 IKDVARLAGVSKATVSRVLNGNG 25 (70)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCC
Confidence 45799999999999999998765
No 304
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=28.09 E-value=51 Score=21.93 Aligned_cols=19 Identities=21% Similarity=0.268 Sum_probs=17.0
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
+.++|+.+|++.+.++.|-
T Consensus 4 i~eva~~~gvs~~tlR~ye 22 (102)
T cd04789 4 ISELAEKAGISRSTLLYYE 22 (102)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5678999999999999995
No 305
>PTZ00096 40S ribosomal protein S15; Provisional
Probab=27.92 E-value=48 Score=23.93 Aligned_cols=6 Identities=17% Similarity=0.457 Sum_probs=2.8
Q ss_pred CCCchh
Q psy10851 46 GLSVRV 51 (159)
Q Consensus 46 ~l~~~~ 51 (159)
||+..+
T Consensus 48 Gl~~~~ 53 (143)
T PTZ00096 48 GIKRKH 53 (143)
T ss_pred CCCHHH
Confidence 444444
No 306
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=27.84 E-value=19 Score=32.12 Aligned_cols=10 Identities=20% Similarity=0.052 Sum_probs=5.1
Q ss_pred HHHHHHHhhc
Q psy10851 19 VKLKTSFNSC 28 (159)
Q Consensus 19 ~~Le~~F~~~ 28 (159)
.+|..+|+.+
T Consensus 17 kiL~~Llk~d 26 (622)
T PF02724_consen 17 KILTSLLKSD 26 (622)
T ss_pred HHHHHHHHhc
Confidence 4455555554
No 307
>PRK00215 LexA repressor; Validated
Probab=27.40 E-value=81 Score=23.47 Aligned_cols=41 Identities=17% Similarity=0.081 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHh---hcCCCCCCHHHHHHHHHHhCC-Cchhhhhhhh
Q psy10851 13 RLLNLKVKLKTSFN---SCCPGHKTTQVREALAKDTGL-SVRVVQVWFQ 57 (159)
Q Consensus 13 ~s~~Q~~~Le~~F~---~~~~~yp~~~~r~~La~~l~l-~~~~V~vWFq 57 (159)
+|..|..+|..... .. . +| ....+||..+|+ +...|..+.+
T Consensus 2 lt~~q~~il~~i~~~~~~~-~-~~--~s~~ela~~~~~~~~~tv~~~l~ 46 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEET-G-YP--PSRREIADALGLRSPSAVHEHLK 46 (205)
T ss_pred CCHHHHHHHHHHHHHHHHh-C-CC--CCHHHHHHHhCCCChHHHHHHHH
Confidence 57888888877653 33 2 32 246789999999 8888887764
No 308
>PF07471 Phage_Nu1: Phage DNA packaging protein Nu1; InterPro: IPR010906 This entry is represented by the Bacteriophage lambda, Nu1, terminase small subunit. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA [].; PDB: 1J9I_A.
Probab=27.37 E-value=46 Score=24.49 Aligned_cols=19 Identities=32% Similarity=0.576 Sum_probs=14.8
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
+..||..+|++.+.|..|-
T Consensus 5 k~~lA~i~gvS~~ti~~W~ 23 (164)
T PF07471_consen 5 KKELAEIFGVSERTIDKWQ 23 (164)
T ss_dssp HHHHHHHTT--HHHHHHHT
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 6789999999999999885
No 309
>KOG0044|consensus
Probab=26.97 E-value=73 Score=24.13 Aligned_cols=30 Identities=20% Similarity=0.412 Sum_probs=25.3
Q ss_pred CCCHHHHHHHHHHhCCCchhhhhhhhhHHH
Q psy10851 32 HKTTQVREALAKDTGLSVRVVQVWFQNQRA 61 (159)
Q Consensus 32 yp~~~~r~~La~~l~l~~~~V~vWFqNRR~ 61 (159)
.........|.+.+..+.+.|+.|+.|=..
T Consensus 8 ~~~~~~~e~l~~~t~f~~~ei~~~Yr~Fk~ 37 (193)
T KOG0044|consen 8 KLQPESLEQLVQQTKFSKKEIQQWYRGFKN 37 (193)
T ss_pred cCCcHHHHHHHHhcCCCHHHHHHHHHHhcc
Confidence 556677888999999999999999977665
No 310
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=26.74 E-value=55 Score=21.94 Aligned_cols=19 Identities=21% Similarity=0.286 Sum_probs=17.1
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
+..+|+.+|++.+.++.|-
T Consensus 3 i~eva~~~gis~~tlR~ye 21 (108)
T cd01107 3 IGEFAKLSNLSIKALRYYD 21 (108)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5678999999999999996
No 311
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=26.67 E-value=61 Score=21.50 Aligned_cols=20 Identities=25% Similarity=0.381 Sum_probs=17.2
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFq 57 (159)
..++|+.+|++...++.|-+
T Consensus 3 i~EvA~~~gVs~~tLR~ye~ 22 (99)
T cd04765 3 IGEVAEILGLPPHVLRYWET 22 (99)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999954
No 312
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=26.66 E-value=51 Score=18.31 Aligned_cols=16 Identities=38% Similarity=0.476 Sum_probs=12.5
Q ss_pred HHHHHHHhCCCchhhh
Q psy10851 38 REALAKDTGLSVRVVQ 53 (159)
Q Consensus 38 r~~La~~l~l~~~~V~ 53 (159)
-..||..+||+...|.
T Consensus 20 ~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 20 YAELAEELGLSESTVR 35 (42)
T ss_dssp HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHCcCHHHHH
Confidence 5678999999998774
No 313
>PF01294 Ribosomal_L13e: Ribosomal protein L13e; InterPro: IPR001380 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The ribosomal protein L13e is widely found in vertebrates [], Drosophila melanogaster, plants, yeast, amongst others.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A18_U 4A1B_U 4A1D_U 4A19_U.
Probab=26.54 E-value=66 Score=24.11 Aligned_cols=20 Identities=40% Similarity=0.762 Sum_probs=7.5
Q ss_pred hhhhhhh-hhHHHHHHHHHHH
Q psy10851 50 RVVQVWF-QNQRAKMKKIQRK 69 (159)
Q Consensus 50 ~~V~vWF-qNRR~k~rk~~~~ 69 (159)
+.|++|| |.-|.+.|+..+.
T Consensus 14 ~rVktwFnQp~rK~rRr~~R~ 34 (179)
T PF01294_consen 14 RRVKTWFNQPARKKRRRQARQ 34 (179)
T ss_dssp GS----THHHHHHHHHHHHHH
T ss_pred hhhhhhcCcHHHHHHHHHHHH
Confidence 4699999 4444444444333
No 314
>PF15360 Apelin: APJ endogenous ligand
Probab=26.49 E-value=25 Score=20.71 Aligned_cols=12 Identities=8% Similarity=-0.166 Sum_probs=9.2
Q ss_pred cCCCCCCCCCCH
Q psy10851 4 YWFQNFQTIRLL 15 (159)
Q Consensus 4 ~~~kr~Rt~~s~ 15 (159)
++|||.|.++|.
T Consensus 38 rkfRRqRPRLSH 49 (55)
T PF15360_consen 38 RKFRRQRPRLSH 49 (55)
T ss_pred hhhhccCccccc
Confidence 467888888875
No 315
>PF12200 DUF3597: Domain of unknown function (DUF3597); InterPro: IPR022016 This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 126 and 281 amino acids in length. The function of this domain is unknown. The structure of this domain has been found to contain five helices with a long flexible loop between helices one and two. ; PDB: 2GQB_A.
Probab=26.23 E-value=1.2e+02 Score=21.44 Aligned_cols=27 Identities=22% Similarity=0.548 Sum_probs=18.4
Q ss_pred CCCHHHHHHHHHHhCCCc-----hhhhhhhhh
Q psy10851 32 HKTTQVREALAKDTGLSV-----RVVQVWFQN 58 (159)
Q Consensus 32 yp~~~~r~~La~~l~l~~-----~~V~vWFqN 58 (159)
-.+...|++||..||++. .+..||...
T Consensus 82 DSSl~aRkeLA~eL~~~~~~~dsA~~NiwLhk 113 (127)
T PF12200_consen 82 DSSLAARKELAKELGYTGDYNDSASMNIWLHK 113 (127)
T ss_dssp --SHHHHHHHHHHHT---SS-HHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHhCCCCCCCccHHHHHHHHH
Confidence 367889999999999876 367889853
No 316
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=26.18 E-value=57 Score=21.98 Aligned_cols=19 Identities=26% Similarity=0.391 Sum_probs=16.9
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
+.++|+.+|++.+.|+.|-
T Consensus 3 i~e~a~~~gvs~~tlr~ye 21 (113)
T cd01109 3 IKEVAEKTGLSADTLRYYE 21 (113)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5678999999999999994
No 317
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=26.00 E-value=2.1e+02 Score=22.66 Aligned_cols=50 Identities=16% Similarity=0.063 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
.++..+..+|...|-.. ......+||..+|++...|+.+-..-..|.|+.
T Consensus 230 ~L~~rEr~VL~lry~~~-----~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~ 279 (284)
T PRK06596 230 GLDERSRDIIEARWLDD-----DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAA 279 (284)
T ss_pred cCCHHHHHHHHHHhcCC-----CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45666777777766321 123467899999999999998876666666553
No 318
>PHA01083 hypothetical protein
Probab=25.90 E-value=1.3e+02 Score=21.86 Aligned_cols=18 Identities=17% Similarity=0.154 Sum_probs=8.9
Q ss_pred CCCHHHHHHHHHHhCCCc
Q psy10851 32 HKTTQVREALAKDTGLSV 49 (159)
Q Consensus 32 yp~~~~r~~La~~l~l~~ 49 (159)
|++..+...||..+|+.+
T Consensus 43 ~i~de~A~~LAe~aGiDp 60 (149)
T PHA01083 43 YISDEEAIFLAESAGIDP 60 (149)
T ss_pred CCCHHHHHHHHHHhCCCH
Confidence 444444445555555444
No 319
>PHA02955 hypothetical protein; Provisional
Probab=25.80 E-value=85 Score=24.22 Aligned_cols=45 Identities=9% Similarity=0.019 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHH
Q psy10851 16 NLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRA 61 (159)
Q Consensus 16 ~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~ 61 (159)
.|+..|-+.|... =.-....+|..+|..+|+....|..||.+.=.
T Consensus 61 ~sf~lli~a~~Et-~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~~ 105 (213)
T PHA02955 61 KNFQLLIEALIET-IENFPEKEQKEIAADIGINIDDYKAGKKTDLQ 105 (213)
T ss_pred HHHHHHHHHHHHH-HHhCCHHHHHHHHHHhCCChhhccCcccchhh
Confidence 3444444444433 01356688999999999999888999987543
No 320
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=25.79 E-value=1.6e+02 Score=21.05 Aligned_cols=49 Identities=12% Similarity=0.102 Sum_probs=36.4
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhC-----CCchhhhhhhhhHHHHH
Q psy10851 11 TIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTG-----LSVRVVQVWFQNQRAKM 63 (159)
Q Consensus 11 t~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~-----l~~~~V~vWFqNRR~k~ 63 (159)
..+|+.+..+|.-++... .....+.+|+..+. ++.+.|.+..++=|.|.
T Consensus 147 ~~Lt~~E~~il~~l~~~~----~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl 200 (221)
T PRK15479 147 LALTPREQALLTVLMYRR----TRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKL 200 (221)
T ss_pred EecCHHHHHHHHHHHhCC----CCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhc
Confidence 458999999998876533 33345777887775 88999999987777664
No 321
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=25.45 E-value=1.5e+02 Score=22.31 Aligned_cols=50 Identities=14% Similarity=0.017 Sum_probs=34.9
Q ss_pred CCCHHH-HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHH
Q psy10851 12 IRLLNL-KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMK 64 (159)
Q Consensus 12 ~~s~~Q-~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~r 64 (159)
+++.++ +..-...|... . | .......||..+|++..-+-..|.||..=..
T Consensus 3 ~Lsre~Il~aA~~l~~e~-G-~-~~lsmr~lA~~lgv~~~slY~hf~~K~~Ll~ 53 (205)
T PRK13756 3 RLDKEKVIDSALELLNEV-G-I-EGLTTRKLAQKLGVEQPTLYWHVKNKRALLD 53 (205)
T ss_pred ccCHHHHHHHHHHHHHHc-C-c-ccCCHHHHHHHhCCCchHHHHHcCCHHHHHH
Confidence 344444 34445556666 3 4 4455778899999999999999999887543
No 322
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.18 E-value=68 Score=20.86 Aligned_cols=19 Identities=32% Similarity=0.352 Sum_probs=16.6
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
..++|..+|++...|+.|-
T Consensus 3 ~~eva~~~gi~~~tlr~~~ 21 (100)
T cd00592 3 IGEVAKLLGVSVRTLRYYE 21 (100)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4678999999999999994
No 323
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=25.13 E-value=81 Score=18.21 Aligned_cols=37 Identities=16% Similarity=0.006 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhh
Q psy10851 13 RLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQ 53 (159)
Q Consensus 13 ~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~ 53 (159)
+|..|..+|...+... + . ......||..++++...|.
T Consensus 3 lt~~q~~vL~~l~~~~-~-~--~~t~~~la~~l~~~~~~vs 39 (62)
T PF12802_consen 3 LTPSQFRVLMALARHP-G-E--ELTQSELAERLGISKSTVS 39 (62)
T ss_dssp STHHHHHHHHHHHHST-T-S--GEEHHHHHHHHTS-HHHHH
T ss_pred cCHHHHHHHHHHHHCC-C-C--CcCHHHHHHHHCcCHHHHH
Confidence 6788888998777544 2 2 2367789999999987664
No 324
>KOG0699|consensus
Probab=24.93 E-value=32 Score=28.96 Aligned_cols=7 Identities=29% Similarity=0.543 Sum_probs=3.4
Q ss_pred HHHHHHH
Q psy10851 19 VKLKTSF 25 (159)
Q Consensus 19 ~~Le~~F 25 (159)
..|+..|
T Consensus 89 ~aL~~AF 95 (542)
T KOG0699|consen 89 EALQKAF 95 (542)
T ss_pred HHHHHHH
Confidence 3455554
No 325
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=24.89 E-value=1.1e+02 Score=20.30 Aligned_cols=36 Identities=22% Similarity=0.302 Sum_probs=22.7
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhh
Q psy10851 18 KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQV 54 (159)
Q Consensus 18 ~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~v 54 (159)
...|..+|..-.. ......=..||+.+||+...|..
T Consensus 3 ~~~l~~~f~~i~~-~V~~~~Wk~laR~LGLse~~I~~ 38 (96)
T cd08315 3 QETLRRSFDHFIK-EVPFDSWNRLMRQLGLSENEIDV 38 (96)
T ss_pred HhHHHHHHHHHHH-HCCHHHHHHHHHHcCCCHHHHHH
Confidence 3556666654312 23344556699999999987653
No 326
>PRK09191 two-component response regulator; Provisional
Probab=24.87 E-value=1.8e+02 Score=21.81 Aligned_cols=46 Identities=11% Similarity=0.016 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 13 RLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 13 ~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
++..|..++...|-.. ....++|..+|++...|+.-...-|.+.|+
T Consensus 89 L~~~~r~v~~l~~~~~-------~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~ 134 (261)
T PRK09191 89 LTPLPRQAFLLTALEG-------FSVEEAAEILGVDPAEAEALLDDARAEIAR 134 (261)
T ss_pred CCHHHhHHHHHHHHhc-------CCHHHHHHHHCCCHHHHHHHHHHHHHHHhc
Confidence 3445555555433222 247789999999999999988765555553
No 327
>COG3769 Predicted hydrolase (HAD superfamily) [General function prediction only]
Probab=24.76 E-value=58 Score=25.61 Aligned_cols=34 Identities=24% Similarity=0.130 Sum_probs=27.6
Q ss_pred HHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhh
Q psy10851 16 NLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVV 52 (159)
Q Consensus 16 ~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V 52 (159)
+.+..|+..|... |.+.....+++..+||+..++
T Consensus 108 e~l~kLee~~g~~---~~~~~d~~ei~e~TGlpre~a 141 (274)
T COG3769 108 EKLDKLEEHFGFT---TFDDVDDEEIAEWTGLPREQA 141 (274)
T ss_pred HHHHHHHHHhCee---EeccCCHHHHHHHhCCChHHh
Confidence 4567888889888 667788999999999998763
No 328
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=24.70 E-value=63 Score=21.78 Aligned_cols=18 Identities=39% Similarity=0.536 Sum_probs=16.1
Q ss_pred HHHHHHHhCCCchhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVW 55 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vW 55 (159)
+.++|+.+|++.+.++-|
T Consensus 3 I~eva~~~gvs~~tLRyY 20 (124)
T COG0789 3 IGEVAKLTGVSVRTLRFY 20 (124)
T ss_pred HHHHHHHhCCCHHHHHHH
Confidence 567899999999999999
No 329
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=24.63 E-value=1.4e+02 Score=22.36 Aligned_cols=36 Identities=11% Similarity=-0.020 Sum_probs=29.4
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCc
Q psy10851 8 NFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSV 49 (159)
Q Consensus 8 r~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~ 49 (159)
+++.++|...+.+|.-.+... | ..|..|+...|++.
T Consensus 83 ~~~~~LS~aaLEtLaiIay~q-P-----iTr~eI~~irGv~~ 118 (188)
T PRK00135 83 PIKQSLSQAALEVLAIIAYKQ-P-----ITRIEIDEIRGVNS 118 (188)
T ss_pred cccCCCCHHHHHHHHHHHHcC-C-----cCHHHHHHHHCCCH
Confidence 355689999999999887666 5 67888999999875
No 330
>KOG0943|consensus
Probab=24.43 E-value=29 Score=33.90 Aligned_cols=11 Identities=27% Similarity=0.120 Sum_probs=4.1
Q ss_pred HHHHHHHHHHH
Q psy10851 15 LNLKVKLKTSF 25 (159)
Q Consensus 15 ~~Q~~~Le~~F 25 (159)
..-+.....+|
T Consensus 1560 ~amI~k~~qff 1570 (3015)
T KOG0943|consen 1560 PAMIGKCKQFF 1570 (3015)
T ss_pred HHHHHHHHHHH
Confidence 33333333333
No 331
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=24.33 E-value=29 Score=22.34 Aligned_cols=21 Identities=10% Similarity=0.196 Sum_probs=17.1
Q ss_pred HHHHHHHHhCCCchhhhhhhh
Q psy10851 37 VREALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFq 57 (159)
-+..|...++|...++.+||.
T Consensus 55 L~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 55 LTSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHHHHhCCCCCeEEEEEE
Confidence 455678888999999999984
No 332
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=24.29 E-value=1.2e+02 Score=20.55 Aligned_cols=37 Identities=19% Similarity=0.196 Sum_probs=27.6
Q ss_pred HHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHH
Q psy10851 21 LKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 21 Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR 60 (159)
--..|... . |... ....||+.+|++...+-.+|.|+-
T Consensus 21 a~~l~~~~-G-~~~~-t~~~Ia~~agvs~~~~Y~~f~~K~ 57 (201)
T COG1309 21 ALRLFAEK-G-YAAT-TVDEIAKAAGVSKGTLYRHFPSKE 57 (201)
T ss_pred HHHHHHHc-C-cCCC-CHHHHHHHhCCCcchhHHHcCCHH
Confidence 33345556 4 6653 466789999999999999999986
No 333
>PF05703 Auxin_canalis: Auxin canalisation; InterPro: IPR008546 This domain consists of several plant proteins of unknown function.
Probab=24.08 E-value=1.6e+02 Score=23.24 Aligned_cols=23 Identities=17% Similarity=0.447 Sum_probs=16.6
Q ss_pred CchhhhhhhhhHHHHHHHHHHHH
Q psy10851 48 SVRVVQVWFQNQRAKMKKIQRKA 70 (159)
Q Consensus 48 ~~~~V~vWFqNRR~k~rk~~~~~ 70 (159)
....|..||+.++.|.|-..+..
T Consensus 99 ~~~~i~~w~~~~~~kkkee~R~~ 121 (242)
T PF05703_consen 99 GGKTIGRWLKDRKEKKKEEARAH 121 (242)
T ss_pred ccchHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999655544433
No 334
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=24.04 E-value=66 Score=21.73 Aligned_cols=19 Identities=37% Similarity=0.441 Sum_probs=17.1
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
+.++|+.+|++.+.|+.|-
T Consensus 3 i~eva~~~gvs~~tlR~Ye 21 (112)
T cd01282 3 IGELAARTGVSVRSLRYYE 21 (112)
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 5678999999999999996
No 335
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=23.78 E-value=70 Score=22.78 Aligned_cols=20 Identities=25% Similarity=0.406 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFq 57 (159)
+.++|+.+|++.+.++.|.+
T Consensus 4 IgevA~~~Gvs~~tLRyYE~ 23 (142)
T TIGR01950 4 VGELAKRSGVAVSALHFYES 23 (142)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 57899999999999999963
No 336
>KOG3241|consensus
Probab=23.77 E-value=1.6e+02 Score=22.23 Aligned_cols=19 Identities=11% Similarity=0.258 Sum_probs=11.2
Q ss_pred hhHHHHHHHHHHHHHhhcC
Q psy10851 57 QNQRAKMKKIQRKAKQQEG 75 (159)
Q Consensus 57 qNRR~k~rk~~~~~~~~~~ 75 (159)
.|-+-+.||...+.+...+
T Consensus 126 ~n~ser~RRt~lR~m~k~~ 144 (227)
T KOG3241|consen 126 KNASERDRRTLLRAMNKDN 144 (227)
T ss_pred hhhhHHHHHHHHHHHhccc
Confidence 4666666666555554444
No 337
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=23.66 E-value=69 Score=23.83 Aligned_cols=20 Identities=35% Similarity=0.584 Sum_probs=17.7
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFq 57 (159)
...+|..+|++...|+.|..
T Consensus 3 i~evA~~lGVS~~TLRrw~k 22 (175)
T PRK13182 3 TPFVAKKLGVSPKTVQRWVK 22 (175)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999974
No 338
>PF08595 RXT2_N: RXT2-like, N-terminal; InterPro: IPR013904 The entry represents the N-terminal region of RXT2-like proteins. In Saccharomyces cerevisiae (Baker's yeast), RXT2 has been demonstrated to be involved in conjugation with cellular fusion (mating) and invasive growth []. A high throughput localisation study has localised RXT2 to the nucleus [].
Probab=23.49 E-value=37 Score=24.63 Aligned_cols=8 Identities=38% Similarity=0.613 Sum_probs=3.2
Q ss_pred hHHHHHHH
Q psy10851 58 NQRAKMKK 65 (159)
Q Consensus 58 NRR~k~rk 65 (159)
||-.|.++
T Consensus 3 NRGnKL~~ 10 (149)
T PF08595_consen 3 NRGNKLKQ 10 (149)
T ss_pred Ccchhcch
Confidence 34444333
No 339
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=23.46 E-value=62 Score=16.84 Aligned_cols=18 Identities=28% Similarity=0.486 Sum_probs=12.9
Q ss_pred HHHHHhCCCchhhhhhhh
Q psy10851 40 ALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 40 ~La~~l~l~~~~V~vWFq 57 (159)
.-|...||+..+|+..+.
T Consensus 10 ~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 10 KEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHTT--HHHHHHHHH
T ss_pred HHHHHcCCCHHHHHHHHH
Confidence 348889999999998874
No 340
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=23.46 E-value=12 Score=26.47 Aligned_cols=15 Identities=33% Similarity=0.572 Sum_probs=11.5
Q ss_pred hhhhhhhHHHHHHHH
Q psy10851 52 VQVWFQNQRAKMKKI 66 (159)
Q Consensus 52 V~vWFqNRR~k~rk~ 66 (159)
|..||+|++++....
T Consensus 1 v~C~fC~~~s~~~~~ 15 (131)
T PF09779_consen 1 VNCWFCGQNSKVPYD 15 (131)
T ss_pred CeeccCCCCCCCCCC
Confidence 578999999876543
No 341
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=23.41 E-value=90 Score=20.95 Aligned_cols=24 Identities=29% Similarity=0.302 Sum_probs=15.7
Q ss_pred HHHHHHHHhCCCchhhhhhhhhHH
Q psy10851 37 VREALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vWFqNRR 60 (159)
....||.+.||+.++|..=..-.|
T Consensus 74 n~~eLA~kyglS~r~I~~Ii~~~~ 97 (108)
T PF08765_consen 74 NVRELARKYGLSERQIYRIIKRVR 97 (108)
T ss_dssp -HHHHHHHHT--HHHHHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 467999999999988765554333
No 342
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=23.21 E-value=75 Score=22.16 Aligned_cols=20 Identities=20% Similarity=0.262 Sum_probs=17.7
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFq 57 (159)
+.++|+.+|++.+.++.|.+
T Consensus 4 I~e~a~~~gvs~~tlR~Ye~ 23 (131)
T TIGR02043 4 IGELAKLCGVTSDTLRFYEK 23 (131)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 56899999999999999974
No 343
>KOG2066|consensus
Probab=23.13 E-value=99 Score=28.59 Aligned_cols=45 Identities=4% Similarity=-0.167 Sum_probs=35.9
Q ss_pred HHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHHHH
Q psy10851 22 KTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKIQR 68 (159)
Q Consensus 22 e~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~~~ 68 (159)
+.+|..+ + |++...+-..++.+.+-.-..|.||.|++++......
T Consensus 513 ~LYl~d~-~-Y~~Al~~ylklk~~~vf~lI~k~nL~d~i~~~Iv~Lm 557 (846)
T KOG2066|consen 513 HLYLYDN-K-YEKALPIYLKLQDKDVFDLIKKHNLFDQIKDQIVLLM 557 (846)
T ss_pred HHHHHcc-C-hHHHHHHHHhccChHHHHHHHHHhhHHHHHHHHHHHH
Confidence 3445566 7 9999988888888887778889999999998777644
No 344
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=23.04 E-value=65 Score=21.32 Aligned_cols=37 Identities=19% Similarity=0.144 Sum_probs=24.1
Q ss_pred CCHHHH----HHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhh
Q psy10851 13 RLLNLK----VKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVW 55 (159)
Q Consensus 13 ~s~~Q~----~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vW 55 (159)
++.+|. ..|...|... . .....+|..||++...|..=
T Consensus 3 Ln~~Q~~~T~~ELq~nf~~~-~-----ls~~~ia~dL~~s~~~le~v 43 (89)
T PF10078_consen 3 LNPEQRRATRQELQANFELS-G-----LSLEQIAADLGTSPEHLEQV 43 (89)
T ss_pred CCHHHHHHHHHHHHHHHHHc-C-----CCHHHHHHHhCCCHHHHHHH
Confidence 455664 4566677777 3 34567788888887766543
No 345
>PF04889 Cwf_Cwc_15: Cwf15/Cwc15 cell cycle control protein; InterPro: IPR006973 This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing [].; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005681 spliceosomal complex
Probab=23.01 E-value=35 Score=26.81 Aligned_cols=9 Identities=33% Similarity=0.191 Sum_probs=3.8
Q ss_pred HhCCCchhh
Q psy10851 44 DTGLSVRVV 52 (159)
Q Consensus 44 ~l~l~~~~V 52 (159)
.+-|..++.
T Consensus 38 HTkLK~Rq~ 46 (244)
T PF04889_consen 38 HTKLKYRQD 46 (244)
T ss_pred CCeeeeecC
Confidence 344444443
No 346
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=22.93 E-value=2.1e+02 Score=23.69 Aligned_cols=52 Identities=13% Similarity=0.045 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHHH
Q psy10851 12 IRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 12 ~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk~ 66 (159)
.++..+..+|...|... + .....-.+||..+||+...|+..-...-.|.|..
T Consensus 305 ~L~~rEr~Vl~lrygl~--~-~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~ 356 (367)
T PRK09210 305 TLTDREENVLRLRFGLD--D-GRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 356 (367)
T ss_pred hCCHHHHHHHHHHhccC--C-CCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhCh
Confidence 56777778888777532 0 1224578899999999999998855444455543
No 347
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=22.87 E-value=75 Score=22.48 Aligned_cols=20 Identities=15% Similarity=0.144 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFq 57 (159)
+.++|+.+|++.+.|+.|..
T Consensus 4 I~e~a~~~gvs~~tlR~Ye~ 23 (140)
T PRK09514 4 IGELAKLAEVTPDTLRFYEK 23 (140)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 57899999999999999963
No 348
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=22.79 E-value=69 Score=22.08 Aligned_cols=18 Identities=28% Similarity=0.508 Sum_probs=16.1
Q ss_pred HHHHHHHhCCCchhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVW 55 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vW 55 (159)
+.++|+.+|++.+.|+.|
T Consensus 2 I~e~a~~~gvs~~tlR~Y 19 (124)
T TIGR02051 2 IGELAKAAGVNVETIRYY 19 (124)
T ss_pred HHHHHHHHCcCHHHHHHH
Confidence 467899999999999888
No 349
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=22.73 E-value=71 Score=21.87 Aligned_cols=18 Identities=17% Similarity=0.394 Sum_probs=16.4
Q ss_pred HHHHHHHhCCCchhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVW 55 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vW 55 (159)
+.++|+.+|++.+.++.|
T Consensus 3 Igeva~~~gvs~~tlRyY 20 (118)
T cd04776 3 ISELAREFDVTPRTLRFY 20 (118)
T ss_pred HHHHHHHHCcCHHHHHHH
Confidence 567899999999999999
No 350
>PF08553 VID27: VID27 cytoplasmic protein; InterPro: IPR013863 This entry represents fungal and plant proteins and contains many hypothetical proteins. Vid27p is a cytoplasmic protein of unknown function, possibly regulates import of fructose-1,6-bisphosphatase into Vacuolar Import and Degradation (Vid) vesicles and is not essential for proteasome-dependent degradation of fructose-1,6-bisphosphatase (FBPase) [, ].
Probab=22.71 E-value=29 Score=31.98 Aligned_cols=13 Identities=0% Similarity=-0.072 Sum_probs=5.8
Q ss_pred CCCCCCCCCHHHH
Q psy10851 6 FQNFQTIRLLNLK 18 (159)
Q Consensus 6 ~kr~Rt~~s~~Q~ 18 (159)
+||..+..|..+|
T Consensus 159 Yrks~~~at~~dL 171 (794)
T PF08553_consen 159 YRKSSSTATEDDL 171 (794)
T ss_pred hcCCcccCCHHHH
Confidence 4444444444333
No 351
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=22.54 E-value=88 Score=16.82 Aligned_cols=26 Identities=19% Similarity=0.270 Sum_probs=14.5
Q ss_pred CCCHHHHHHHHHHhCCCchhhhhhhh
Q psy10851 32 HKTTQVREALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 32 yp~~~~r~~La~~l~l~~~~V~vWFq 57 (159)
|-..-....||..+|++......=|+
T Consensus 5 ~~~~~~l~~iA~~~g~S~~~f~r~Fk 30 (42)
T PF00165_consen 5 LQQKLTLEDIAEQAGFSPSYFSRLFK 30 (42)
T ss_dssp T-SS--HHHHHHHHTS-HHHHHHHHH
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 44445677788888887765555543
No 352
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=22.44 E-value=77 Score=22.41 Aligned_cols=19 Identities=21% Similarity=0.385 Sum_probs=17.0
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
+.++|+.+|++...|+.|-
T Consensus 4 I~EvA~~~Gvs~~tLRyYE 22 (139)
T cd01110 4 VGEVAKRSGVAVSALHFYE 22 (139)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5688999999999999996
No 353
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=22.21 E-value=1.4e+02 Score=19.25 Aligned_cols=38 Identities=13% Similarity=0.107 Sum_probs=24.5
Q ss_pred CCHHHHHHHHHH---HhhcCCCCCCHHHHHHHHHHhCCCchhhhh
Q psy10851 13 RLLNLKVKLKTS---FNSCCPGHKTTQVREALAKDTGLSVRVVQV 54 (159)
Q Consensus 13 ~s~~Q~~~Le~~---F~~~~~~yp~~~~r~~La~~l~l~~~~V~v 54 (159)
+|..|..+|... |... . -|-. -+.||..++++...|++
T Consensus 2 Lt~rq~~IL~alV~~Y~~~-~-~PVg--Sk~ia~~l~~s~aTIRN 42 (78)
T PF03444_consen 2 LTERQREILKALVELYIET-G-EPVG--SKTIAEELGRSPATIRN 42 (78)
T ss_pred CCHHHHHHHHHHHHHHHhc-C-CCcC--HHHHHHHHCCChHHHHH
Confidence 566777666665 6666 2 5543 35578889988766654
No 354
>PF11388 DotA: Phagosome trafficking protein DotA; InterPro: IPR021528 DotA is essential for intracellular growth in Legionella []. DotA is thought to play an important role in regulating initial phagosome trafficking decisions either upon or immediately after macrophage uptake [].
Probab=21.92 E-value=1.1e+02 Score=20.50 Aligned_cols=20 Identities=35% Similarity=0.687 Sum_probs=13.3
Q ss_pred CchhhhhhhhhHHHHHHHHH
Q psy10851 48 SVRVVQVWFQNQRAKMKKIQ 67 (159)
Q Consensus 48 ~~~~V~vWFqNRR~k~rk~~ 67 (159)
+..-+=+||||.-.|.-..+
T Consensus 28 ~~a~LC~WF~~~s~~l~qiq 47 (105)
T PF11388_consen 28 DYALLCTWFQNKSDKLVQIQ 47 (105)
T ss_pred chHHHHHHHccCCchhhhhh
Confidence 34455689999887765443
No 355
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=21.88 E-value=78 Score=20.90 Aligned_cols=19 Identities=32% Similarity=0.373 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
..++|+.+|++...|+.|-
T Consensus 3 i~e~A~~~gvs~~tlR~Ye 21 (99)
T cd04772 3 TVDLARAIGLSPQTVRNYE 21 (99)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5678999999999999994
No 356
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=21.85 E-value=1.4e+02 Score=21.06 Aligned_cols=42 Identities=17% Similarity=0.191 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHHHH---H-hhcCCCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy10851 11 TIRLLNLKVKLKTS---F-NSCCPGHKTTQVREALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 11 t~~s~~Q~~~Le~~---F-~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFq 57 (159)
..||++|...|... | .++ . . .+...|+..+|++...|+..|.
T Consensus 3 ~~~T~eer~eLk~rIvElVRe~-G-R---iTi~ql~~~TGasR~Tvk~~lr 48 (127)
T PF06163_consen 3 RVFTPEEREELKARIVELVREH-G-R---ITIKQLVAKTGASRNTVKRYLR 48 (127)
T ss_pred CcCCHHHHHHHHHHHHHHHHHc-C-C---ccHHHHHHHHCCCHHHHHHHHH
Confidence 36888887776654 2 222 2 3 4566778888988888887774
No 357
>PF12114 Period_C: Period protein 2/3C-terminal region; InterPro: IPR022728 This domain is found in eukaryotes and is typically between 164 to 200 amino acids in length. Sequences represented by this entry are found C-terminal to PF08447 from PFAM.
Probab=21.81 E-value=1.1e+02 Score=23.35 Aligned_cols=35 Identities=31% Similarity=0.412 Sum_probs=25.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy10851 13 RLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 13 ~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFq 57 (159)
.-++-+..|+.+=+.. | ..+..+|.+|+ +|..|.|
T Consensus 121 VLkeD~ekLk~mq~~Q-P-~fs~~Qk~EL~--------qvh~wiq 155 (195)
T PF12114_consen 121 VLKEDREKLKSMQKQQ-P-RFSNEQKEELA--------QVHPWIQ 155 (195)
T ss_pred HHHHHHHHHHHHHhhC-C-cchHHHHHHHH--------HhhHHHH
Confidence 3455577787777777 8 88888999987 4668874
No 358
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=21.80 E-value=1.5e+02 Score=17.52 Aligned_cols=27 Identities=26% Similarity=0.290 Sum_probs=19.0
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhh
Q psy10851 18 KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQ 53 (159)
Q Consensus 18 ~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~ 53 (159)
+..|..+|... ....|..||++.+.++
T Consensus 7 ~~~L~~~fhlp---------~~eAA~~Lgv~~T~LK 33 (52)
T PF02042_consen 7 LEDLSQYFHLP---------IKEAAKELGVSVTTLK 33 (52)
T ss_pred HHHHHHHhCCC---------HHHHHHHhCCCHHHHH
Confidence 56777788433 4566888999987765
No 359
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=21.79 E-value=1e+02 Score=22.38 Aligned_cols=45 Identities=16% Similarity=0.141 Sum_probs=33.1
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHHHHH
Q psy10851 18 KVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAKMKK 65 (159)
Q Consensus 18 ~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k~rk 65 (159)
+.+-...|... . |=. .....||+..|++..-|-..|.|+-.=...
T Consensus 14 l~aA~~lf~e~-G-~~~-~s~~~IA~~agvs~~~lY~hF~sKe~L~~a 58 (202)
T TIGR03613 14 LSAALDTFSRF-G-FHG-TSLEQIAELAGVSKTNLLYYFPSKDALYLA 58 (202)
T ss_pred HHHHHHHHHHh-C-ccc-CCHHHHHHHhCCCHHHHHHHcCCHHHHHHH
Confidence 44445567777 3 443 557789999999999999999998764433
No 360
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=21.77 E-value=76 Score=21.65 Aligned_cols=19 Identities=16% Similarity=0.356 Sum_probs=16.9
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
+.++|+.+|++.+.|+.|-
T Consensus 3 IgevA~~~gvs~~tlRyYe 21 (120)
T cd04781 3 IAEVARQSGLPASTLRYYE 21 (120)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5678999999999999995
No 361
>PF01372 Melittin: Melittin; InterPro: IPR002116 Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an Arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Api m 3. Melittin is the principal protein component of the venom of the honeybee, Apis mellifera. It inhibits protein kinase C, Ca2+/calmodulin-dependent protein kinase II, myosin light chain kinase and Na+/K+-ATPase (synaptosomal membrane) and is a cell membrane lytic factor. Melittin is a small peptide with no disulphide bridge; the N-terminal part of the molecule is predominantly hydrophobic and the C-terminal part is hydrophilic and strongly basic. The molecular mechanisms underlying the various effects of melittin on membranes have not been completely defined and much of the evidence indicates that different molecular mechanisms may underlie different actions of the peptide []. Extensive work with melittin has shown that the venom has multiple effects, probably, as a result of its interaction with negatively changed phospholipids. It inhibits well known transport pumps such as the Na+-K+-ATPase and the H+-K+-ATPase. Melittin increases the permeability of cell membranes to ions, particularly Na+ and indirectly Ca2+, because of the Na+-Ca2+-exchange. This effect results in marked morphological and functional changes, particularly in excitable tissues such as cardiac myocytes. In some other tissues, e.g., cornea, not only Na+ but Cl- permeability is also increased by melittin. Similar effects to melittin on H+-K+-ATPase have been found with the synthetic amphipathic polypeptide Trp-3 []. The study of melittin in model membranes has been useful for the development of methodology for determination of membrane protein structures. A molecular dynamics simulation of melittin in a hydrated dipalmitoylphosphatidylcholine (DPPC) bilayer was carried out. The effect of melittin on the surrounding membrane was localised to its immediate vicinity, and its asymmetry with respect to the two layers may be a result of the fact that it is not fully transmembranal. Melittin's hydrophilic C terminus anchors it at the extracellular interface, leaving the N terminus "loose" in the lower layer of the membrane [].; GO: 0004860 protein kinase inhibitor activity, 0005576 extracellular region; PDB: 3QRX_B 2MLT_A 1BH1_A.
Probab=21.67 E-value=67 Score=15.97 Aligned_cols=12 Identities=25% Similarity=0.681 Sum_probs=9.1
Q ss_pred hhhhhhhhhHHH
Q psy10851 50 RVVQVWFQNQRA 61 (159)
Q Consensus 50 ~~V~vWFqNRR~ 61 (159)
..+-.|.+|+|+
T Consensus 14 P~lISWIK~kr~ 25 (26)
T PF01372_consen 14 PTLISWIKNKRQ 25 (26)
T ss_dssp HHHHHHHHHHHH
T ss_pred hHHHHHHHHHhc
Confidence 356789999885
No 362
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=21.67 E-value=75 Score=21.92 Aligned_cols=19 Identities=32% Similarity=0.392 Sum_probs=16.9
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
+.++|+.+|++.+.++.|-
T Consensus 3 I~e~a~~~gvs~~tlRyYe 21 (127)
T TIGR02044 3 IGQVAKLTGLSSKMIRYYE 21 (127)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5678999999999999995
No 363
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=21.35 E-value=1.8e+02 Score=16.67 Aligned_cols=21 Identities=29% Similarity=0.300 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhhhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWFQN 58 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFqN 58 (159)
-..||...|++...|..||+.
T Consensus 22 ~~~La~~FgIs~stvsri~~~ 42 (53)
T PF13613_consen 22 FQDLAYRFGISQSTVSRIFHE 42 (53)
T ss_pred HhHHhhheeecHHHHHHHHHH
Confidence 456899999999999999853
No 364
>PF14410 GH-E: HNH/ENDO VII superfamily nuclease with conserved GHE residues
Probab=21.33 E-value=1.2e+02 Score=18.98 Aligned_cols=27 Identities=11% Similarity=0.347 Sum_probs=19.5
Q ss_pred CCCCHHHHHHH--HHHhCCCchhhhhhhh
Q psy10851 31 GHKTTQVREAL--AKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 31 ~yp~~~~r~~L--a~~l~l~~~~V~vWFq 57 (159)
|.|....+... |...+++..+|.-|+.
T Consensus 23 H~~~~e~~~~~~~~~~~~~t~ke~~d~~n 51 (70)
T PF14410_consen 23 HKPGVEYWRLVGRAEEGGITRKEFLDWYN 51 (70)
T ss_pred CchHHHHHHHHHHHHhcCCCHHHHHHHHh
Confidence 56655555554 4448999999999985
No 365
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=21.25 E-value=67 Score=19.78 Aligned_cols=9 Identities=44% Similarity=0.789 Sum_probs=3.5
Q ss_pred HHhCCCchh
Q psy10851 43 KDTGLSVRV 51 (159)
Q Consensus 43 ~~l~l~~~~ 51 (159)
..+|++..+
T Consensus 18 ~~~g~s~~~ 26 (81)
T PF12833_consen 18 KETGMSFKQ 26 (81)
T ss_dssp HHHSS-HHH
T ss_pred HHHCcCHHH
Confidence 335555443
No 366
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=21.20 E-value=79 Score=22.28 Aligned_cols=18 Identities=28% Similarity=0.488 Sum_probs=16.2
Q ss_pred HHHHHHHhCCCchhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVW 55 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vW 55 (159)
+.++|+.+|++.+.|+.|
T Consensus 3 Ige~a~~~gvs~~tlRyY 20 (135)
T PRK10227 3 ISDVAKITGLTSKAIRFY 20 (135)
T ss_pred HHHHHHHHCcCHHHHHHH
Confidence 567899999999999999
No 367
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=21.16 E-value=79 Score=21.83 Aligned_cols=19 Identities=32% Similarity=0.363 Sum_probs=16.9
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
+.++|+.+|++.+.++.|-
T Consensus 3 I~e~a~~~gvs~~tlRyYe 21 (127)
T cd01108 3 IGEAAKLTGLSAKMIRYYE 21 (127)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5678999999999999995
No 368
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=21.01 E-value=3.1e+02 Score=21.27 Aligned_cols=44 Identities=7% Similarity=-0.210 Sum_probs=32.4
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCchhhhhhhhhHHHH
Q psy10851 11 TIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTGLSVRVVQVWFQNQRAK 62 (159)
Q Consensus 11 t~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~l~~~~V~vWFqNRR~k 62 (159)
..+|+.++.+|.-+- ....-.+||..++++.+.|+.-..+-..|
T Consensus 142 ~~LS~RE~eVL~Lia--------~G~SnkEIA~~L~IS~~TVk~hvs~I~~K 185 (217)
T PRK13719 142 NKVTKYQNDVFILYS--------FGFSHEYIAQLLNITVGSSKNKISEILKF 185 (217)
T ss_pred CCCCHHHHHHHHHHH--------CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 468899999997542 22346789999999999998876554444
No 369
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=20.94 E-value=88 Score=21.65 Aligned_cols=20 Identities=30% Similarity=0.476 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWFQ 57 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWFq 57 (159)
+.++|+.+|++.+.|+.|-+
T Consensus 3 I~e~a~~~gvs~~tlR~Ye~ 22 (127)
T TIGR02047 3 IGELAQKTGVSVETIRFYEK 22 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 56799999999999999963
No 370
>PTZ00044 ubiquitin; Provisional
Probab=20.82 E-value=33 Score=21.12 Aligned_cols=25 Identities=24% Similarity=0.566 Sum_probs=20.2
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR 60 (159)
.-+..|+..+|++..+.+.||.++.
T Consensus 25 ~lK~~i~~~~gi~~~~q~L~~~g~~ 49 (76)
T PTZ00044 25 QVKMALQEKEGIDVKQIRLIYSGKQ 49 (76)
T ss_pred HHHHHHHHHHCCCHHHeEEEECCEE
Confidence 3466689999999999999997655
No 371
>KOG0943|consensus
Probab=20.74 E-value=39 Score=33.14 Aligned_cols=9 Identities=22% Similarity=0.205 Sum_probs=4.8
Q ss_pred HHHHHHHHh
Q psy10851 18 KVKLKTSFN 26 (159)
Q Consensus 18 ~~~Le~~F~ 26 (159)
...|+++|.
T Consensus 1613 Md~lEe~Fs 1621 (3015)
T KOG0943|consen 1613 MDGLEELFS 1621 (3015)
T ss_pred hHhHHHHhc
Confidence 445555554
No 372
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.72 E-value=83 Score=21.42 Aligned_cols=19 Identities=26% Similarity=0.333 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy10851 38 REALAKDTGLSVRVVQVWF 56 (159)
Q Consensus 38 r~~La~~l~l~~~~V~vWF 56 (159)
+.++|+.+|++.+.|+.|-
T Consensus 3 I~eva~~~gvs~~tLRyYe 21 (123)
T cd04770 3 IGELAKAAGVSPDTIRYYE 21 (123)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5678999999999999885
No 373
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=20.67 E-value=45 Score=20.22 Aligned_cols=25 Identities=28% Similarity=0.497 Sum_probs=20.4
Q ss_pred HHHHHHHHHhCCCchhhhhhhhhHH
Q psy10851 36 QVREALAKDTGLSVRVVQVWFQNQR 60 (159)
Q Consensus 36 ~~r~~La~~l~l~~~~V~vWFqNRR 60 (159)
.-+..|+...|+...+.+.||.++.
T Consensus 23 ~lK~~i~~~~gi~~~~q~Li~~G~~ 47 (70)
T cd01798 23 QLKEVVAKRQGVPPDQLRVIFAGKE 47 (70)
T ss_pred HHHHHHHHHHCCCHHHeEEEECCeE
Confidence 3566789999999999999997665
No 374
>PF15325 MRI: Modulator of retrovirus infection
Probab=20.63 E-value=2.8e+02 Score=18.73 Aligned_cols=9 Identities=11% Similarity=-0.105 Sum_probs=3.5
Q ss_pred cccccCCCC
Q psy10851 124 KIGYELGFF 132 (159)
Q Consensus 124 ~~~~~~~~~ 132 (159)
+.+...+.+
T Consensus 77 p~~s~s~cs 85 (106)
T PF15325_consen 77 PGGSDSACS 85 (106)
T ss_pred CCCCCcccC
Confidence 333334443
No 375
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=20.39 E-value=2.3e+02 Score=20.22 Aligned_cols=49 Identities=12% Similarity=0.070 Sum_probs=36.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhC-----CCchhhhhhhhhHHHHH
Q psy10851 11 TIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTG-----LSVRVVQVWFQNQRAKM 63 (159)
Q Consensus 11 t~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~-----l~~~~V~vWFqNRR~k~ 63 (159)
..+|+.+..+|.-+.... .....+..||..+. ++.+.|++...+=|.|.
T Consensus 148 ~~Lt~~E~~il~~l~~~~----~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl 201 (219)
T PRK10336 148 LTLKPKEFALLELLMRNA----GRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKL 201 (219)
T ss_pred EecCHHHHHHHHHHHhCC----CccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhc
Confidence 458999999998666432 22335678899886 89999999887777664
No 376
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=20.35 E-value=2.6e+02 Score=19.82 Aligned_cols=39 Identities=8% Similarity=-0.030 Sum_probs=31.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhC
Q psy10851 6 FQNFQTIRLLNLKVKLKTSFNSCCPGHKTTQVREALAKDTG 46 (159)
Q Consensus 6 ~kr~Rt~~s~~Q~~~Le~~F~~~~~~yp~~~~r~~La~~l~ 46 (159)
+|..--++|++++.+|+-++... . +|+..+.-..+..-+
T Consensus 12 lk~~glr~T~qR~~vl~~L~~~~-~-~~sAeei~~~l~~~~ 50 (145)
T COG0735 12 LKEAGLRLTPQRLAVLELLLEAD-G-HLSAEELYEELREEG 50 (145)
T ss_pred HHHcCCCcCHHHHHHHHHHHhcC-C-CCCHHHHHHHHHHhC
Confidence 45566789999999999999988 4 899998888776644
No 377
>PRK13749 transcriptional regulator MerD; Provisional
Probab=20.33 E-value=88 Score=21.78 Aligned_cols=19 Identities=37% Similarity=0.545 Sum_probs=17.0
Q ss_pred HHHHHHHHhCCCchhhhhh
Q psy10851 37 VREALAKDTGLSVRVVQVW 55 (159)
Q Consensus 37 ~r~~La~~l~l~~~~V~vW 55 (159)
.+.+||+.+|++.+.|+.|
T Consensus 5 tIgelA~~~gvS~~tiR~Y 23 (121)
T PRK13749 5 TVSRLALDAGVSVHIVRDY 23 (121)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 4678999999999999988
No 378
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=20.23 E-value=2.2e+02 Score=17.39 Aligned_cols=56 Identities=16% Similarity=0.078 Sum_probs=33.1
Q ss_pred CCCCCHHHHHHHHHHHhhc-----CCCCCCHH---HH----HHHHHHhC------CCchhhhhhhhhHHHHHHHH
Q psy10851 10 QTIRLLNLKVKLKTSFNSC-----CPGHKTTQ---VR----EALAKDTG------LSVRVVQVWFQNQRAKMKKI 66 (159)
Q Consensus 10 Rt~~s~~Q~~~Le~~F~~~-----~~~yp~~~---~r----~~La~~l~------l~~~~V~vWFqNRR~k~rk~ 66 (159)
...||..|+..|-.++... +. +.+.. .+ ..||..++ -+..+++..+.|-+.+.|+.
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k-~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk~ 75 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENK-FSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKKK 75 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcc-cccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 3579999999998886553 11 22211 12 23455552 34456776677777777664
No 379
>PRK13558 bacterio-opsin activator; Provisional
Probab=20.21 E-value=1.8e+02 Score=25.69 Aligned_cols=42 Identities=17% Similarity=0.050 Sum_probs=34.4
Q ss_pred CCCCHHHHHHHHHHHhhcCCCC--CCHHHHHHHHHHhCCCchhhhh
Q psy10851 11 TIRLLNLKVKLKTSFNSCCPGH--KTTQVREALAKDTGLSVRVVQV 54 (159)
Q Consensus 11 t~~s~~Q~~~Le~~F~~~~~~y--p~~~~r~~La~~l~l~~~~V~v 54 (159)
..+|..|..+|+..|... .| |....-..||..+|++...+.-
T Consensus 606 ~~lt~~q~e~l~~a~~~g--yf~~pr~~~~~e~a~~l~is~~t~~~ 649 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSG--YFEWPRRVEGEELAESMGISRSTFHQ 649 (665)
T ss_pred hhCCHHHHHHHHHHHHcC--CCCCCccCCHHHHHHHhCCCHHHHHH
Confidence 479999999999999876 22 7777888999999999876543
Done!