Query psy9529
Match_columns 149
No_of_seqs 209 out of 1455
Neff 7.3
Searched_HMMs 46136
Date Fri Aug 16 21:56:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9529.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9529hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0484|consensus 99.8 1.3E-21 2.7E-26 134.9 3.4 69 6-74 10-78 (125)
2 KOG0489|consensus 99.8 3.3E-20 7.2E-25 148.4 6.7 70 9-78 155-224 (261)
3 KOG0850|consensus 99.8 1.3E-19 2.8E-24 140.3 7.5 72 7-78 116-187 (245)
4 KOG0488|consensus 99.8 1.5E-19 3.3E-24 147.4 7.1 68 7-74 166-233 (309)
5 KOG2251|consensus 99.8 5.9E-19 1.3E-23 136.0 7.7 67 8-74 32-98 (228)
6 KOG0494|consensus 99.8 3.6E-19 7.9E-24 140.1 5.6 62 13-74 141-202 (332)
7 KOG0843|consensus 99.8 5.3E-19 1.1E-23 132.5 5.8 64 12-75 101-164 (197)
8 KOG0842|consensus 99.7 1.9E-18 4E-23 140.0 6.2 69 10-78 150-218 (307)
9 PF00046 Homeobox: Homeobox do 99.7 3E-18 6.5E-23 106.8 5.4 57 14-70 1-57 (57)
10 KOG0487|consensus 99.7 5.5E-18 1.2E-22 137.3 5.2 67 10-76 232-298 (308)
11 KOG0485|consensus 99.7 1.3E-17 2.8E-22 128.5 4.8 63 10-72 101-163 (268)
12 TIGR01565 homeo_ZF_HD homeobox 99.7 6.1E-17 1.3E-21 101.6 4.7 53 13-65 1-57 (58)
13 KOG0848|consensus 99.7 3.4E-17 7.3E-22 129.4 3.7 62 14-75 200-261 (317)
14 KOG0492|consensus 99.6 1.4E-16 3E-21 122.0 5.1 64 11-74 142-205 (246)
15 KOG3802|consensus 99.6 2.3E-16 5E-21 130.6 5.5 64 10-73 291-354 (398)
16 KOG0486|consensus 99.6 2E-16 4.4E-21 127.3 4.1 65 11-75 110-174 (351)
17 KOG0493|consensus 99.6 5.9E-16 1.3E-20 122.1 6.2 62 14-75 247-308 (342)
18 smart00389 HOX Homeodomain. DN 99.6 9.7E-16 2.1E-20 94.7 5.0 56 14-69 1-56 (56)
19 COG5576 Homeodomain-containing 99.6 1.7E-15 3.7E-20 112.7 6.8 65 10-74 48-112 (156)
20 cd00086 homeodomain Homeodomai 99.6 1.7E-15 3.8E-20 94.2 5.6 56 15-70 2-57 (59)
21 KOG0491|consensus 99.5 3E-15 6.6E-20 111.0 3.3 67 10-76 97-163 (194)
22 KOG0483|consensus 99.5 8E-15 1.7E-19 112.7 4.4 61 14-74 51-111 (198)
23 KOG0847|consensus 99.5 1.2E-14 2.6E-19 112.3 5.1 68 7-74 161-228 (288)
24 KOG0844|consensus 99.5 4.9E-15 1.1E-19 119.2 2.5 66 11-76 179-244 (408)
25 KOG4577|consensus 99.5 3.7E-14 8E-19 113.4 5.3 64 11-74 165-228 (383)
26 KOG0490|consensus 99.4 8.1E-14 1.7E-18 108.2 5.1 64 10-73 57-120 (235)
27 KOG0849|consensus 99.3 2.5E-12 5.3E-17 107.0 6.8 66 7-72 170-235 (354)
28 KOG1168|consensus 99.2 3.3E-12 7.2E-17 102.4 2.1 65 10-74 306-370 (385)
29 KOG0775|consensus 99.0 1.2E-09 2.6E-14 87.0 6.5 56 15-70 169-233 (304)
30 KOG0774|consensus 98.7 2.5E-08 5.4E-13 79.3 5.9 58 14-71 189-249 (334)
31 KOG2252|consensus 98.7 6.4E-08 1.4E-12 83.5 7.4 64 5-68 412-475 (558)
32 KOG0490|consensus 98.5 2.9E-07 6.3E-12 71.3 6.4 65 9-73 149-213 (235)
33 PF05920 Homeobox_KN: Homeobox 98.5 6.6E-08 1.4E-12 56.3 2.0 34 34-67 7-40 (40)
34 KOG1146|consensus 97.9 1.5E-05 3.2E-10 74.9 5.7 64 12-75 902-965 (1406)
35 PF11569 Homez: Homeodomain le 96.8 0.00092 2E-08 41.5 2.2 42 25-66 10-51 (56)
36 KOG3623|consensus 96.4 0.0061 1.3E-07 55.1 5.1 50 25-74 568-617 (1007)
37 KOG0773|consensus 96.2 0.0058 1.3E-07 50.5 3.9 58 13-70 239-299 (342)
38 PF04218 CENP-B_N: CENP-B N-te 95.4 0.044 9.5E-07 33.4 4.6 46 14-64 1-46 (53)
39 PF04545 Sigma70_r4: Sigma-70, 82.4 2.4 5.2E-05 24.8 3.4 44 19-67 4-47 (50)
40 KOG1146|consensus 81.6 2.1 4.5E-05 41.6 4.2 67 6-72 698-764 (1406)
41 PF01527 HTH_Tnp_1: Transposas 81.1 2.3 4.9E-05 26.9 3.2 43 15-62 2-45 (76)
42 PF04967 HTH_10: HTH DNA bindi 80.1 2.2 4.8E-05 26.0 2.7 39 20-58 1-41 (53)
43 cd06171 Sigma70_r4 Sigma70, re 79.2 3 6.4E-05 23.5 3.1 43 19-66 10-52 (55)
44 PF08281 Sigma70_r4_2: Sigma-7 76.5 5.1 0.00011 23.6 3.6 41 20-65 11-51 (54)
45 cd00569 HTH_Hin_like Helix-tur 71.5 10 0.00022 18.9 3.7 38 19-61 5-42 (42)
46 PF10668 Phage_terminase: Phag 70.7 2.2 4.7E-05 26.8 0.9 20 42-61 24-43 (60)
47 PRK03975 tfx putative transcri 69.7 9.9 0.00021 27.9 4.3 49 18-72 5-53 (141)
48 PF09607 BrkDBD: Brinker DNA-b 67.8 10 0.00022 23.6 3.5 45 17-62 3-47 (58)
49 PRK09413 IS2 repressor TnpA; R 64.2 18 0.0004 25.3 4.7 42 17-62 10-51 (121)
50 PF00196 GerE: Bacterial regul 62.0 14 0.0003 22.1 3.4 45 19-69 3-47 (58)
51 PRK09646 RNA polymerase sigma 61.8 16 0.00035 27.2 4.4 30 42-71 160-189 (194)
52 PRK06759 RNA polymerase factor 61.1 14 0.0003 26.1 3.8 45 20-69 107-151 (154)
53 PRK09652 RNA polymerase sigma 60.4 15 0.00033 26.4 3.9 46 20-70 129-174 (182)
54 TIGR03879 near_KaiC_dom probab 59.5 2.9 6.3E-05 27.3 -0.1 35 29-63 21-55 (73)
55 PF13936 HTH_38: Helix-turn-he 58.6 9.1 0.0002 22.0 2.0 40 18-62 3-42 (44)
56 PRK00118 putative DNA-binding 58.2 21 0.00046 24.8 4.0 47 20-71 18-64 (104)
57 PRK12526 RNA polymerase sigma 57.7 21 0.00046 26.9 4.5 31 42-72 171-201 (206)
58 COG3413 Predicted DNA binding 57.6 16 0.00034 28.1 3.7 49 19-69 155-205 (215)
59 TIGR02959 SigZ RNA polymerase 56.8 32 0.00069 25.0 5.1 50 20-74 101-150 (170)
60 TIGR02937 sigma70-ECF RNA poly 56.8 19 0.00042 24.5 3.8 46 20-70 111-156 (158)
61 PRK12512 RNA polymerase sigma 56.5 21 0.00046 26.1 4.2 30 42-71 149-178 (184)
62 PRK11924 RNA polymerase sigma 55.5 21 0.00045 25.6 3.9 30 42-71 143-172 (179)
63 PF02796 HTH_7: Helix-turn-hel 54.7 20 0.00043 20.6 3.0 38 19-61 5-42 (45)
64 PRK09642 RNA polymerase sigma 54.1 25 0.00055 25.0 4.2 29 43-71 125-153 (160)
65 PRK12514 RNA polymerase sigma 54.0 28 0.00061 25.3 4.5 29 42-70 147-175 (179)
66 PRK12515 RNA polymerase sigma 53.5 29 0.00062 25.6 4.5 33 42-74 149-181 (189)
67 PRK10072 putative transcriptio 53.1 19 0.00042 24.5 3.2 40 20-66 33-72 (96)
68 TIGR02989 Sig-70_gvs1 RNA poly 52.8 25 0.00054 24.9 3.9 28 42-69 129-156 (159)
69 PRK09644 RNA polymerase sigma 52.5 28 0.0006 25.0 4.2 31 42-72 126-156 (165)
70 TIGR02985 Sig70_bacteroi1 RNA 52.4 27 0.00059 24.4 4.0 28 42-69 131-158 (161)
71 PRK12519 RNA polymerase sigma 52.2 21 0.00045 26.4 3.5 30 41-70 158-187 (194)
72 PRK05602 RNA polymerase sigma 51.3 32 0.00069 25.3 4.4 32 42-73 146-177 (186)
73 TIGR02999 Sig-70_X6 RNA polyme 51.2 29 0.00062 25.3 4.1 29 42-70 152-180 (183)
74 TIGR02948 SigW_bacill RNA poly 50.9 24 0.00053 25.7 3.7 30 41-70 153-182 (187)
75 PRK09648 RNA polymerase sigma 50.6 29 0.00063 25.5 4.1 29 42-70 157-185 (189)
76 cd04761 HTH_MerR-SF Helix-Turn 49.9 10 0.00023 21.4 1.3 21 43-63 3-23 (49)
77 PRK04217 hypothetical protein; 48.9 37 0.0008 23.8 4.1 49 18-71 41-89 (110)
78 TIGR02939 RpoE_Sigma70 RNA pol 48.3 24 0.00052 25.8 3.3 30 42-71 156-185 (190)
79 PRK09639 RNA polymerase sigma 46.9 34 0.00074 24.4 3.9 30 42-71 129-158 (166)
80 PRK06930 positive control sigm 46.4 36 0.00079 25.4 4.0 48 19-71 114-161 (170)
81 smart00421 HTH_LUXR helix_turn 46.1 53 0.0011 18.4 4.0 40 19-64 3-42 (58)
82 PF06056 Terminase_5: Putative 46.1 13 0.00028 23.0 1.3 26 42-69 15-40 (58)
83 PRK12541 RNA polymerase sigma 46.0 32 0.00069 24.6 3.6 29 42-70 130-158 (161)
84 PF13518 HTH_28: Helix-turn-he 45.8 15 0.00033 21.0 1.5 24 42-65 14-37 (52)
85 PRK09047 RNA polymerase factor 45.1 42 0.00091 23.7 4.1 29 43-71 125-153 (161)
86 PRK12537 RNA polymerase sigma 45.0 46 0.001 24.4 4.4 28 42-69 151-178 (182)
87 COG4367 Uncharacterized protei 45.0 27 0.00058 23.8 2.7 40 19-58 2-41 (97)
88 PRK12536 RNA polymerase sigma 44.6 41 0.0009 24.6 4.1 30 42-71 147-176 (181)
89 PRK12530 RNA polymerase sigma 44.5 40 0.00087 25.0 4.1 29 42-70 152-180 (189)
90 PRK09637 RNA polymerase sigma 43.5 42 0.0009 24.8 4.0 33 42-74 124-156 (181)
91 PF08280 HTH_Mga: M protein tr 43.3 24 0.00053 21.4 2.2 36 23-62 6-41 (59)
92 PRK12543 RNA polymerase sigma 42.9 46 0.00099 24.3 4.1 30 42-71 135-164 (179)
93 PRK12520 RNA polymerase sigma 42.4 61 0.0013 23.9 4.8 31 42-72 149-179 (191)
94 TIGR02983 SigE-fam_strep RNA p 42.4 45 0.00097 23.7 3.9 29 42-70 128-156 (162)
95 PRK12546 RNA polymerase sigma 42.1 41 0.00089 25.1 3.8 30 42-71 131-160 (188)
96 PF13443 HTH_26: Cro/C1-type H 41.9 15 0.00033 22.1 1.1 24 42-65 12-35 (63)
97 COG2963 Transposase and inacti 41.7 55 0.0012 22.3 4.1 41 17-61 5-46 (116)
98 PF13384 HTH_23: Homeodomain-l 41.7 16 0.00034 21.0 1.1 23 41-63 18-40 (50)
99 PF13551 HTH_29: Winged helix- 41.1 66 0.0014 21.2 4.4 48 15-62 53-109 (112)
100 PF13411 MerR_1: MerR HTH fami 41.1 17 0.00037 22.2 1.3 19 43-61 3-21 (69)
101 PRK12529 RNA polymerase sigma 40.4 54 0.0012 24.0 4.1 29 42-70 145-173 (178)
102 PRK07037 extracytoplasmic-func 40.1 57 0.0012 23.2 4.2 29 42-70 127-155 (163)
103 PRK12533 RNA polymerase sigma 39.9 92 0.002 23.9 5.5 31 42-72 152-182 (216)
104 TIGR02952 Sig70_famx2 RNA poly 39.8 53 0.0012 23.3 4.0 28 42-69 140-167 (170)
105 PRK12547 RNA polymerase sigma 39.8 55 0.0012 23.5 4.1 29 42-70 130-158 (164)
106 PRK12524 RNA polymerase sigma 39.1 52 0.0011 24.4 3.9 29 43-71 155-183 (196)
107 TIGR02954 Sig70_famx3 RNA poly 39.1 59 0.0013 23.3 4.2 29 42-70 137-165 (169)
108 PRK13919 putative RNA polymera 38.9 62 0.0013 23.6 4.3 29 42-70 153-181 (186)
109 PRK06986 fliA flagellar biosyn 38.6 49 0.0011 25.5 3.8 30 42-71 202-231 (236)
110 PRK12539 RNA polymerase sigma 38.5 61 0.0013 23.8 4.2 29 42-70 149-177 (184)
111 PRK12538 RNA polymerase sigma 38.0 45 0.00097 25.9 3.5 30 42-71 189-218 (233)
112 PRK09480 slmA division inhibit 37.4 36 0.00078 24.7 2.8 36 29-65 20-55 (194)
113 PRK12532 RNA polymerase sigma 37.3 59 0.0013 24.0 4.0 30 42-71 154-183 (195)
114 PRK09645 RNA polymerase sigma 37.1 70 0.0015 23.0 4.3 29 42-70 136-164 (173)
115 cd04762 HTH_MerR-trunc Helix-T 37.1 22 0.00048 19.5 1.3 22 43-64 3-24 (49)
116 PRK06811 RNA polymerase factor 36.8 64 0.0014 23.8 4.1 30 42-71 149-178 (189)
117 COG5484 Uncharacterized conser 36.0 39 0.00084 27.4 2.8 25 42-68 21-45 (279)
118 PF00376 MerR: MerR family reg 35.3 22 0.00048 19.8 1.0 18 44-61 3-20 (38)
119 PRK09649 RNA polymerase sigma 35.3 61 0.0013 23.9 3.8 29 42-70 148-176 (185)
120 cd01392 HTH_LacI Helix-turn-he 34.9 17 0.00036 20.9 0.5 20 45-64 2-21 (52)
121 PRK12523 RNA polymerase sigma 34.8 73 0.0016 23.0 4.1 29 42-70 137-165 (172)
122 PRK12516 RNA polymerase sigma 34.8 72 0.0016 23.7 4.1 30 43-72 135-164 (187)
123 PRK12535 RNA polymerase sigma 34.6 91 0.002 23.3 4.7 30 42-71 151-180 (196)
124 PRK09647 RNA polymerase sigma 34.5 74 0.0016 24.1 4.2 29 43-71 157-185 (203)
125 cd04763 HTH_MlrA-like Helix-Tu 34.2 25 0.00054 21.7 1.3 20 43-62 3-22 (68)
126 TIGR02479 FliA_WhiG RNA polyme 33.8 71 0.0015 24.3 4.0 46 20-70 176-221 (224)
127 PRK08583 RNA polymerase sigma 33.7 71 0.0015 24.9 4.1 46 20-70 206-251 (257)
128 PF01381 HTH_3: Helix-turn-hel 33.7 25 0.00053 20.4 1.1 23 43-65 12-34 (55)
129 PRK12511 RNA polymerase sigma 33.7 75 0.0016 23.5 4.0 32 42-73 129-160 (182)
130 PRK09641 RNA polymerase sigma 33.6 71 0.0015 23.1 3.9 29 42-70 154-182 (187)
131 PRK12531 RNA polymerase sigma 33.3 83 0.0018 23.3 4.2 29 42-70 159-187 (194)
132 TIGR02980 SigBFG RNA polymeras 33.3 74 0.0016 24.2 4.1 45 20-69 179-223 (227)
133 PRK12545 RNA polymerase sigma 33.2 79 0.0017 23.6 4.2 31 42-72 157-187 (201)
134 PRK12542 RNA polymerase sigma 32.7 79 0.0017 23.1 4.0 29 42-70 140-168 (185)
135 PRK12522 RNA polymerase sigma 32.7 83 0.0018 22.7 4.1 29 42-70 137-165 (173)
136 TIGR02943 Sig70_famx1 RNA poly 32.3 85 0.0018 23.2 4.1 30 42-71 149-178 (188)
137 PRK12528 RNA polymerase sigma 32.0 81 0.0018 22.4 3.9 25 42-66 131-155 (161)
138 TIGR00721 tfx DNA-binding prot 32.0 90 0.0019 22.7 4.0 48 17-70 4-51 (137)
139 cd04764 HTH_MlrA-like_sg1 Heli 31.9 29 0.00063 21.2 1.3 20 43-62 3-22 (67)
140 PRK12513 RNA polymerase sigma 31.5 33 0.00072 25.3 1.8 32 40-71 155-186 (194)
141 TIGR02941 Sigma_B RNA polymera 31.4 75 0.0016 24.8 3.9 46 20-70 206-251 (255)
142 PRK12518 RNA polymerase sigma 31.2 40 0.00086 24.3 2.1 33 40-72 136-168 (175)
143 PRK09651 RNA polymerase sigma 31.1 66 0.0014 23.3 3.3 28 42-69 137-164 (172)
144 TIGR03001 Sig-70_gmx1 RNA poly 30.0 89 0.0019 24.5 4.1 30 42-71 179-208 (244)
145 PRK11923 algU RNA polymerase s 29.8 83 0.0018 23.1 3.7 30 42-71 156-185 (193)
146 PF12824 MRP-L20: Mitochondria 29.7 1.6E+02 0.0035 22.0 5.2 44 16-61 82-125 (164)
147 PRK12525 RNA polymerase sigma 29.7 94 0.002 22.3 3.9 28 42-69 136-163 (168)
148 PRK08301 sporulation sigma fac 29.6 83 0.0018 24.1 3.8 29 42-70 200-228 (234)
149 TIGR02947 SigH_actino RNA poly 29.6 46 0.00099 24.6 2.3 32 41-72 148-179 (193)
150 PRK10403 transcriptional regul 29.4 58 0.0013 23.3 2.8 45 18-68 152-196 (215)
151 TIGR03070 couple_hipB transcri 29.2 36 0.00078 19.5 1.3 23 43-65 18-40 (58)
152 PRK09643 RNA polymerase sigma 28.8 1.6E+02 0.0035 21.7 5.1 30 42-71 152-181 (192)
153 PRK07670 RNA polymerase sigma 28.5 91 0.002 24.3 3.9 29 42-70 219-247 (251)
154 cd01104 HTH_MlrA-CarA Helix-Tu 28.2 36 0.00078 20.6 1.3 20 43-62 3-22 (68)
155 PRK08295 RNA polymerase factor 27.8 1E+02 0.0022 22.8 3.9 31 41-71 171-201 (208)
156 PF00424 REV: REV protein (ant 27.7 1.1E+02 0.0025 20.7 3.7 33 26-73 15-48 (91)
157 PF13565 HTH_32: Homeodomain-l 27.3 1.6E+02 0.0034 18.2 6.0 33 21-53 32-65 (77)
158 COG2944 Predicted transcriptio 27.3 87 0.0019 21.8 3.1 39 20-65 44-82 (104)
159 cd06170 LuxR_C_like C-terminal 27.3 1.2E+02 0.0027 16.9 3.8 36 21-62 2-37 (57)
160 PRK07408 RNA polymerase sigma 27.2 1E+02 0.0023 24.2 4.0 30 41-70 220-249 (256)
161 PRK12544 RNA polymerase sigma 27.1 1.2E+02 0.0025 23.0 4.1 29 43-71 167-195 (206)
162 PRK09415 RNA polymerase factor 27.1 91 0.002 22.7 3.5 29 42-70 145-173 (179)
163 PRK12534 RNA polymerase sigma 26.6 1.4E+02 0.003 21.7 4.4 28 42-69 155-182 (187)
164 COG1905 NuoE NADH:ubiquinone o 26.5 1E+02 0.0022 23.1 3.5 36 22-57 25-60 (160)
165 PRK12540 RNA polymerase sigma 26.1 1.2E+02 0.0026 22.3 4.0 32 42-73 129-160 (182)
166 PF13730 HTH_36: Helix-turn-he 26.0 51 0.0011 19.1 1.6 42 20-62 3-47 (55)
167 TIGR02957 SigX4 RNA polymerase 26.0 1E+02 0.0023 24.5 3.9 28 43-70 127-154 (281)
168 cd00093 HTH_XRE Helix-turn-hel 25.7 45 0.00097 18.1 1.3 22 43-64 15-36 (58)
169 KOG0773|consensus 25.7 75 0.0016 26.1 3.1 39 33-71 117-155 (342)
170 PF08279 HTH_11: HTH domain; 25.5 73 0.0016 18.5 2.2 34 25-61 3-36 (55)
171 PRK10360 DNA-binding transcrip 25.5 77 0.0017 22.6 2.8 44 19-68 137-180 (196)
172 PF07638 Sigma70_ECF: ECF sigm 25.4 1.2E+02 0.0027 22.4 4.0 28 42-69 153-180 (185)
173 PF01710 HTH_Tnp_IS630: Transp 25.3 1.1E+02 0.0024 21.2 3.5 38 20-62 3-40 (119)
174 PRK15369 two component system 25.2 1.1E+02 0.0024 21.5 3.6 44 19-68 149-192 (211)
175 TIGR02950 SigM_subfam RNA poly 25.2 54 0.0012 23.0 1.9 33 38-70 119-151 (154)
176 PRK06288 RNA polymerase sigma 25.1 1.2E+02 0.0027 23.8 4.1 47 20-71 213-259 (268)
177 smart00027 EH Eps15 homology d 24.9 1.5E+02 0.0032 19.4 3.9 44 19-62 3-51 (96)
178 PRK05657 RNA polymerase sigma 24.2 1.1E+02 0.0024 25.2 3.7 53 19-72 262-314 (325)
179 PF04936 DUF658: Protein of un 24.1 35 0.00075 25.9 0.7 30 42-71 16-45 (186)
180 PRK07122 RNA polymerase sigma 24.0 1.2E+02 0.0025 24.1 3.8 46 20-70 216-261 (264)
181 TIGR02885 spore_sigF RNA polym 23.5 1.4E+02 0.003 22.8 4.0 38 20-62 184-221 (231)
182 PRK11511 DNA-binding transcrip 23.2 63 0.0014 22.6 1.9 25 39-63 24-48 (127)
183 smart00422 HTH_MERR helix_turn 23.1 49 0.0011 20.0 1.2 19 43-61 3-21 (70)
184 TIGR03629 arch_S13P archaeal r 22.9 88 0.0019 22.9 2.6 15 20-34 52-66 (144)
185 PRK12527 RNA polymerase sigma 22.8 1.7E+02 0.0036 20.6 4.2 29 42-70 123-151 (159)
186 TIGR02607 antidote_HigA addict 22.7 53 0.0011 20.4 1.3 23 43-65 21-43 (78)
187 PRK09636 RNA polymerase sigma 22.6 1.3E+02 0.0029 23.9 3.9 28 43-70 134-161 (293)
188 PHA02955 hypothetical protein; 22.6 1.1E+02 0.0024 24.0 3.3 43 22-64 60-103 (213)
189 TIGR02984 Sig-70_plancto1 RNA 22.4 1.6E+02 0.0034 21.2 4.0 29 42-70 158-186 (189)
190 PRK08215 sporulation sigma fac 22.2 1.5E+02 0.0032 23.2 4.0 45 19-68 209-253 (258)
191 PRK11922 RNA polymerase sigma 22.2 90 0.0019 24.0 2.7 36 38-73 163-198 (231)
192 smart00685 DM14 Repeats in fly 21.5 1.9E+02 0.0042 17.9 3.6 24 111-135 32-55 (59)
193 TIGR01764 excise DNA binding d 21.5 61 0.0013 17.8 1.3 22 43-64 4-25 (49)
194 KOG3755|consensus 21.4 70 0.0015 29.2 2.1 58 13-70 647-708 (769)
195 PRK05988 formate dehydrogenase 21.3 1.5E+02 0.0032 21.9 3.6 36 23-58 24-59 (156)
196 KOG3623|consensus 21.3 76 0.0017 29.7 2.4 58 13-70 626-683 (1007)
197 TIGR02393 RpoD_Cterm RNA polym 21.3 1.4E+02 0.0029 23.1 3.6 50 20-70 177-226 (238)
198 TIGR02859 spore_sigH RNA polym 21.2 70 0.0015 23.4 1.9 31 40-70 165-195 (198)
199 PRK09640 RNA polymerase sigma 21.0 74 0.0016 23.4 2.0 30 42-71 152-181 (188)
200 PHA01976 helix-turn-helix prot 20.7 63 0.0014 19.5 1.3 22 43-64 18-39 (67)
201 PRK05572 sporulation sigma fac 20.5 1.7E+02 0.0036 22.8 4.0 46 19-69 202-247 (252)
202 PRK06424 transcription factor; 20.5 77 0.0017 23.2 1.9 24 43-66 100-123 (144)
203 TIGR02548 casB_cse2 CRISPR sys 20.4 1.9E+02 0.004 20.9 4.0 31 110-140 109-139 (159)
204 TIGR03020 EpsA transcriptional 20.4 1.6E+02 0.0035 23.4 3.9 47 17-69 188-234 (247)
No 1
>KOG0484|consensus
Probab=99.84 E-value=1.3e-21 Score=134.89 Aligned_cols=69 Identities=57% Similarity=0.928 Sum_probs=63.7
Q ss_pred CCCcCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhh
Q psy9529 6 SDDLASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHT 74 (149)
Q Consensus 6 ~~~~~~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~ 74 (149)
+..-.+|.||.||.||..||..||..|...+||++.+|++||.+++|++..|+|||||||+|+||+++.
T Consensus 10 ~l~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~ 78 (125)
T KOG0484|consen 10 GLTEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERA 78 (125)
T ss_pred ChhHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence 334467889999999999999999999999999999999999999999999999999999999998644
No 2
>KOG0489|consensus
Probab=99.81 E-value=3.3e-20 Score=148.37 Aligned_cols=70 Identities=39% Similarity=0.674 Sum_probs=64.5
Q ss_pred cCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhhcCCC
Q psy9529 9 LASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHTKKGP 78 (149)
Q Consensus 9 ~~~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~~~~~ 78 (149)
..++.||.||.||..|+.+||+.|+.|.|.+...|.+||..|.|+++||+|||||||+||||..+.....
T Consensus 155 ~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 155 TGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred ccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 3456899999999999999999999999999999999999999999999999999999999987665544
No 3
>KOG0850|consensus
Probab=99.80 E-value=1.3e-19 Score=140.31 Aligned_cols=72 Identities=38% Similarity=0.652 Sum_probs=66.0
Q ss_pred CCcCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhhcCCC
Q psy9529 7 DDLASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHTKKGP 78 (149)
Q Consensus 7 ~~~~~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~~~~~ 78 (149)
.+.++|.|+.||.|+.-||..|++.|++++|.-..+|.+||..|||+..||+|||||||.|.||..+.+.++
T Consensus 116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~ 187 (245)
T KOG0850|consen 116 NGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSGP 187 (245)
T ss_pred CCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCCc
Confidence 345778889999999999999999999999999999999999999999999999999999999988755444
No 4
>KOG0488|consensus
Probab=99.79 E-value=1.5e-19 Score=147.43 Aligned_cols=68 Identities=43% Similarity=0.689 Sum_probs=63.6
Q ss_pred CCcCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhh
Q psy9529 7 DDLASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHT 74 (149)
Q Consensus 7 ~~~~~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~ 74 (149)
...++|+|+.||.||..|+..||+.|++..|.+..+|.+||..|||+..||++||||||+||||....
T Consensus 166 ~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 166 RSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred cCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 34568888999999999999999999999999999999999999999999999999999999998644
No 5
>KOG2251|consensus
Probab=99.78 E-value=5.9e-19 Score=135.97 Aligned_cols=67 Identities=57% Similarity=0.893 Sum_probs=64.0
Q ss_pred CcCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhh
Q psy9529 8 DLASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHT 74 (149)
Q Consensus 8 ~~~~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~ 74 (149)
..++|.||.||.||-.|+++||..|.+.+||++.+|++||.+|+|.+.+|+|||.|||+|+|++...
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 5678999999999999999999999999999999999999999999999999999999999988765
No 6
>KOG0494|consensus
Probab=99.77 E-value=3.6e-19 Score=140.06 Aligned_cols=62 Identities=63% Similarity=1.039 Sum_probs=57.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhh
Q psy9529 13 RRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHT 74 (149)
Q Consensus 13 ~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~ 74 (149)
+|+.||.||..|+..||+.|...+||+...|+.||..+.|.+.+|+|||||||+||||.++.
T Consensus 141 RRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 141 RRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred cccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence 34449999999999999999999999999999999999999999999999999999998654
No 7
>KOG0843|consensus
Probab=99.77 E-value=5.3e-19 Score=132.53 Aligned_cols=64 Identities=41% Similarity=0.601 Sum_probs=61.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhhc
Q psy9529 12 KRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHTK 75 (149)
Q Consensus 12 k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~~ 75 (149)
+.+|.||.||.+|+..||.+|+.++|....+|+.||..|+|++.||+|||||||.|.||.....
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 7889999999999999999999999999999999999999999999999999999999987664
No 8
>KOG0842|consensus
Probab=99.74 E-value=1.9e-18 Score=139.96 Aligned_cols=69 Identities=38% Similarity=0.538 Sum_probs=64.0
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhhcCCC
Q psy9529 10 ASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHTKKGP 78 (149)
Q Consensus 10 ~~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~~~~~ 78 (149)
..++||.|..|+..|+.+||+-|.+..|.+..+|+.||..|.|++.||+|||||||-|+||....+...
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~ 218 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALE 218 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhh
Confidence 567788899999999999999999999999999999999999999999999999999999987766543
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=99.74 E-value=3e-18 Score=106.77 Aligned_cols=57 Identities=47% Similarity=0.654 Sum_probs=55.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 14 rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
|+.|+.||.+|+.+|+.+|..++||+..+++.||..+||+..+|++||+|+|+++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 578999999999999999999999999999999999999999999999999999885
No 10
>KOG0487|consensus
Probab=99.72 E-value=5.5e-18 Score=137.29 Aligned_cols=67 Identities=36% Similarity=0.543 Sum_probs=62.0
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhhcC
Q psy9529 10 ASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHTKK 76 (149)
Q Consensus 10 ~~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~~~ 76 (149)
.+..|++|..+|+.|+.+||+.|..|.|++.+.|.+|+..|+|+++||+|||||||+|+||..+...
T Consensus 232 ~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 232 ARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred ccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence 3667888999999999999999999999999999999999999999999999999999999876433
No 11
>KOG0485|consensus
Probab=99.70 E-value=1.3e-17 Score=128.46 Aligned_cols=63 Identities=37% Similarity=0.670 Sum_probs=60.0
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhh
Q psy9529 10 ASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKE 72 (149)
Q Consensus 10 ~~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~ 72 (149)
..++|+.||+|+..|+..||..|+...|.+..+|..||.+|.|++.||+|||||||.||||+.
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 446788999999999999999999999999999999999999999999999999999999974
No 12
>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=99.67 E-value=6.1e-17 Score=101.64 Aligned_cols=53 Identities=17% Similarity=0.273 Sum_probs=51.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhCCC----CCHHHHHHHHHhcCCCccchhhhhhhhh
Q psy9529 13 RRRSRTNFNSWQLEELERAFLASHY----PDVFMREALALRLDLKESRVAVWFQNRR 65 (149)
Q Consensus 13 ~rr~Rt~ft~~ql~~Le~~F~~~~~----p~~~~r~~LA~~lgl~~~~V~vWFqNRR 65 (149)
++|.||.||.+|+..|+.+|..++| |+..++.+||..+||++.+|+|||||.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 3789999999999999999999999 9999999999999999999999999975
No 13
>KOG0848|consensus
Probab=99.67 E-value=3.4e-17 Score=129.41 Aligned_cols=62 Identities=40% Similarity=0.595 Sum_probs=57.5
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhhc
Q psy9529 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHTK 75 (149)
Q Consensus 14 rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~~ 75 (149)
-+-|.++|+.|.-+||+.|..++|+++..+.+||..|||+++||+|||||||+|+||..+.+
T Consensus 200 DKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 200 DKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred cceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 35588999999999999999999999999999999999999999999999999999876544
No 14
>KOG0492|consensus
Probab=99.65 E-value=1.4e-16 Score=121.97 Aligned_cols=64 Identities=38% Similarity=0.631 Sum_probs=59.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhh
Q psy9529 11 SKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHT 74 (149)
Q Consensus 11 ~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~ 74 (149)
+..|++||.||..||..||+-|...+|.++.+|.+++..|.|++.||+|||||||+|.||.+..
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQea 205 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEA 205 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHH
Confidence 4457889999999999999999999999999999999999999999999999999999987543
No 15
>KOG3802|consensus
Probab=99.64 E-value=2.3e-16 Score=130.61 Aligned_cols=64 Identities=31% Similarity=0.433 Sum_probs=61.0
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhh
Q psy9529 10 ASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEH 73 (149)
Q Consensus 10 ~~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~ 73 (149)
.+++|++||.|+...+..||.+|..|+.|+..++..||.+|+|...+|+|||||||+|.||...
T Consensus 291 ~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 291 QSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 3478899999999999999999999999999999999999999999999999999999999776
No 16
>KOG0486|consensus
Probab=99.63 E-value=2e-16 Score=127.32 Aligned_cols=65 Identities=55% Similarity=0.937 Sum_probs=61.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhhc
Q psy9529 11 SKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHTK 75 (149)
Q Consensus 11 ~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~~ 75 (149)
.|+||.||.||..|+..||..|.+|.||+..+|++||..++|++..|+|||.|||+||||++...
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~ 174 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQ 174 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhH
Confidence 37889999999999999999999999999999999999999999999999999999999987553
No 17
>KOG0493|consensus
Probab=99.62 E-value=5.9e-16 Score=122.15 Aligned_cols=62 Identities=40% Similarity=0.647 Sum_probs=58.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhhc
Q psy9529 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHTK 75 (149)
Q Consensus 14 rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~~ 75 (149)
||+||.||.+||..|+..|..|.|.+...|..||.+|||.+.||+|||||+|+|.||-....
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgsk 308 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSK 308 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCC
Confidence 68899999999999999999999999999999999999999999999999999999865443
No 18
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.61 E-value=9.7e-16 Score=94.70 Aligned_cols=56 Identities=57% Similarity=0.913 Sum_probs=52.3
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHH
Q psy9529 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWR 69 (149)
Q Consensus 14 rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~r 69 (149)
++.|+.|+..|+.+|+..|..++||+..++..||..+||+..+|++||+|+|.+.+
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 35678899999999999999999999999999999999999999999999998753
No 19
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.60 E-value=1.7e-15 Score=112.67 Aligned_cols=65 Identities=37% Similarity=0.537 Sum_probs=59.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhh
Q psy9529 10 ASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHT 74 (149)
Q Consensus 10 ~~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~ 74 (149)
.+..+++|++.|.+|+.+|+..|..++||+..+|..|+..|+|+++.|+|||||+|++.|+....
T Consensus 48 s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 48 SSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 45567778889999999999999999999999999999999999999999999999999987654
No 20
>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=99.60 E-value=1.7e-15 Score=94.21 Aligned_cols=56 Identities=52% Similarity=0.782 Sum_probs=53.4
Q ss_pred CCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 15 RSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 15 r~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
+.|+.|+..++.+|+..|..++||+..++..||..+||+..+|++||+|+|.+.++
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 56788999999999999999999999999999999999999999999999999875
No 21
>KOG0491|consensus
Probab=99.54 E-value=3e-15 Score=110.97 Aligned_cols=67 Identities=39% Similarity=0.611 Sum_probs=61.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhhcC
Q psy9529 10 ASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHTKK 76 (149)
Q Consensus 10 ~~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~~~ 76 (149)
..++++-||+|+..|+..|++.|+...|.+..+|.+||..|+|++.||+.||||||+|-||..+...
T Consensus 97 ~~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 97 HCRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred HHHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 3456778999999999999999999999999999999999999999999999999999998876544
No 22
>KOG0483|consensus
Probab=99.52 E-value=8e-15 Score=112.72 Aligned_cols=61 Identities=34% Similarity=0.575 Sum_probs=55.3
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhh
Q psy9529 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHT 74 (149)
Q Consensus 14 rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~ 74 (149)
.+++.+|+.+|+..||..|+.+.+..+..+..||..|||.++||.||||||||+||.++..
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE 111 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLE 111 (198)
T ss_pred ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence 3444569999999999999999999999999999999999999999999999999987543
No 23
>KOG0847|consensus
Probab=99.52 E-value=1.2e-14 Score=112.33 Aligned_cols=68 Identities=44% Similarity=0.729 Sum_probs=62.8
Q ss_pred CCcCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhh
Q psy9529 7 DDLASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHT 74 (149)
Q Consensus 7 ~~~~~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~ 74 (149)
....++++..|..|+..|+..|+..|+..+|+-..++.+||..+||++.+|+|||||||.||||+...
T Consensus 161 ~~kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa 228 (288)
T KOG0847|consen 161 PNLNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA 228 (288)
T ss_pred cCcCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence 34567888899999999999999999999999999999999999999999999999999999998543
No 24
>KOG0844|consensus
Probab=99.51 E-value=4.9e-15 Score=119.20 Aligned_cols=66 Identities=36% Similarity=0.537 Sum_probs=60.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhhcC
Q psy9529 11 SKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHTKK 76 (149)
Q Consensus 11 ~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~~~ 76 (149)
..-||-||.||.+|+..||+.|-+..|-+...|.+||..|+|++..|+|||||||+|+||+...-.
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlama 244 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMA 244 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhcc
Confidence 445889999999999999999999999999999999999999999999999999999999765543
No 25
>KOG4577|consensus
Probab=99.48 E-value=3.7e-14 Score=113.41 Aligned_cols=64 Identities=38% Similarity=0.546 Sum_probs=59.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhh
Q psy9529 11 SKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHT 74 (149)
Q Consensus 11 ~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~ 74 (149)
...+|+||.||..||+-|+.+|...+.|....|++|+..+||..++|||||||||+|+||..+.
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence 3468999999999999999999999999999999999999999999999999999999986543
No 26
>KOG0490|consensus
Probab=99.45 E-value=8.1e-14 Score=108.21 Aligned_cols=64 Identities=53% Similarity=0.669 Sum_probs=60.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhh
Q psy9529 10 ASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEH 73 (149)
Q Consensus 10 ~~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~ 73 (149)
..++++.||.|+.+|+++|+..|..++||+...++.||..+++++..|+|||||+|++|++.+.
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 4577899999999999999999999999999999999999999999999999999999998774
No 27
>KOG0849|consensus
Probab=99.33 E-value=2.5e-12 Score=107.03 Aligned_cols=66 Identities=52% Similarity=0.822 Sum_probs=62.1
Q ss_pred CCcCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhh
Q psy9529 7 DDLASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKE 72 (149)
Q Consensus 7 ~~~~~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~ 72 (149)
....++.+|.||+|+..|++.|+..|..++||++..|+.||..+++++..|+|||+|+|++++|..
T Consensus 170 ~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 170 YALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 345677788999999999999999999999999999999999999999999999999999999987
No 28
>KOG1168|consensus
Probab=99.23 E-value=3.3e-12 Score=102.38 Aligned_cols=65 Identities=31% Similarity=0.455 Sum_probs=60.1
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhh
Q psy9529 10 ASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHT 74 (149)
Q Consensus 10 ~~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~ 74 (149)
++.+||+||.+.......||.+|...+.|+.+.+..||++|+|...+|+|||||.|+|.||....
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~S 370 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRS 370 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhh
Confidence 45578899999999999999999999999999999999999999999999999999999986543
No 29
>KOG0775|consensus
Probab=98.98 E-value=1.2e-09 Score=87.04 Aligned_cols=56 Identities=29% Similarity=0.414 Sum_probs=49.5
Q ss_pred CCCCCCCHHH---------HHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 15 RSRTNFNSWQ---------LEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 15 r~Rt~ft~~q---------l~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
-+||.+..++ ...|..+|..|+||++.++.+||+.+||+..||-+||+|||+++|-
T Consensus 169 lPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 169 LPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred CCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 4566655544 5699999999999999999999999999999999999999999993
No 30
>KOG0774|consensus
Probab=98.72 E-value=2.5e-08 Score=79.27 Aligned_cols=58 Identities=34% Similarity=0.614 Sum_probs=54.3
Q ss_pred CCCCCCCCHHHHHHHHHHHh---hCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 14 RRSRTNFNSWQLEELERAFL---ASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 14 rr~Rt~ft~~ql~~Le~~F~---~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
+|+|..|+..-.++|..+|. .|+||+.+.+++||++++++..||-.||.|.|-+++|.
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 67788999999999999996 58999999999999999999999999999999998874
No 31
>KOG2252|consensus
Probab=98.67 E-value=6.4e-08 Score=83.48 Aligned_cols=64 Identities=27% Similarity=0.373 Sum_probs=57.9
Q ss_pred CCCCcCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhH
Q psy9529 5 LSDDLASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKW 68 (149)
Q Consensus 5 ~~~~~~~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~ 68 (149)
..++.....+++|.+||+.|+..|..+|..+++|+.++.+.|+.+|+|....|.+||-|-|.+.
T Consensus 412 p~~d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 412 PTDDKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred CCccccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 3345556678889999999999999999999999999999999999999999999999988774
No 32
>KOG0490|consensus
Probab=98.50 E-value=2.9e-07 Score=71.31 Aligned_cols=65 Identities=49% Similarity=0.631 Sum_probs=60.5
Q ss_pred cCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhh
Q psy9529 9 LASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEH 73 (149)
Q Consensus 9 ~~~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~ 73 (149)
...+.++.|+.|+..|+..+...|..+++|+...+..|+..+|++...|++||+|+|++.++...
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 34677889999999999999999999999999999999999999999999999999999998655
No 33
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.49 E-value=6.6e-08 Score=56.29 Aligned_cols=34 Identities=29% Similarity=0.546 Sum_probs=28.8
Q ss_pred hCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhh
Q psy9529 34 ASHYPDVFMREALALRLDLKESRVAVWFQNRRAK 67 (149)
Q Consensus 34 ~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak 67 (149)
.++||+..++..||..+||+..||..||-|.|.+
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4789999999999999999999999999998864
No 34
>KOG1146|consensus
Probab=97.93 E-value=1.5e-05 Score=74.86 Aligned_cols=64 Identities=31% Similarity=0.415 Sum_probs=59.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhhc
Q psy9529 12 KRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHTK 75 (149)
Q Consensus 12 k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~~ 75 (149)
-+++.||.++..|+..|..+|....||...+.+.|...+++..++|+|||||-|+|.++.....
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence 3578899999999999999999999999999999999999999999999999999999876543
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.81 E-value=0.00092 Score=41.51 Aligned_cols=42 Identities=19% Similarity=0.272 Sum_probs=30.9
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhh
Q psy9529 25 LEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRA 66 (149)
Q Consensus 25 l~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRa 66 (149)
+..|+.+|...+++.......|..+.+|+..+|+.||-.+..
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 456999999999999999999999999999999999975543
No 36
>KOG3623|consensus
Probab=96.36 E-value=0.0061 Score=55.08 Aligned_cols=50 Identities=18% Similarity=0.234 Sum_probs=46.1
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhh
Q psy9529 25 LEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHT 74 (149)
Q Consensus 25 l~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~ 74 (149)
+..|..+|..|..|+..+...+|.++|++...|++||+++++.....++.
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rs 617 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERS 617 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccC
Confidence 78899999999999999999999999999999999999999998876543
No 37
>KOG0773|consensus
Probab=96.17 E-value=0.0058 Score=50.50 Aligned_cols=58 Identities=22% Similarity=0.327 Sum_probs=48.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHhh---CCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 13 RRRSRTNFNSWQLEELERAFLA---SHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 13 ~rr~Rt~ft~~ql~~Le~~F~~---~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
..|++..+......+|+.+... .+||+...+..||.++||+..||.+||-|.|-+.-+
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK 299 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCC
Confidence 4455668999999999877432 479999999999999999999999999999877554
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=95.40 E-value=0.044 Score=33.42 Aligned_cols=46 Identities=15% Similarity=0.261 Sum_probs=35.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhh
Q psy9529 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNR 64 (149)
Q Consensus 14 rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNR 64 (149)
+|+|..+|-++...+-..++... ....||..+|++..+|..|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 46788999999988888888876 57789999999999999999885
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=82.41 E-value=2.4 Score=24.81 Aligned_cols=44 Identities=18% Similarity=0.243 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhh
Q psy9529 19 NFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAK 67 (149)
Q Consensus 19 ~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak 67 (149)
.+++.+..++...|..+ ..-.++|..+|++...|+.+...-..+
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKK 47 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHH
Confidence 46888999999999333 347789999999999999887544443
No 40
>KOG1146|consensus
Probab=81.55 E-value=2.1 Score=41.60 Aligned_cols=67 Identities=18% Similarity=0.320 Sum_probs=58.6
Q ss_pred CCCcCCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhh
Q psy9529 6 SDDLASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKE 72 (149)
Q Consensus 6 ~~~~~~k~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~ 72 (149)
+.+..-..++.++.+-.++..+|-.+|-.+.-|+...+..|......+.+++.+||+|-+.+.++..
T Consensus 698 ~~~~~~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 698 GESLSPRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred CCCCCcccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 3344455677888898999999999999999999999999999999999999999999999887754
No 41
>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=81.08 E-value=2.3 Score=26.85 Aligned_cols=43 Identities=14% Similarity=0.165 Sum_probs=28.4
Q ss_pred CCCCCCCHHHHHHHHHHH-hhCCCCCHHHHHHHHHhcCCCccchhhhhh
Q psy9529 15 RSRTNFNSWQLEELERAF-LASHYPDVFMREALALRLDLKESRVAVWFQ 62 (149)
Q Consensus 15 r~Rt~ft~~ql~~Le~~F-~~~~~p~~~~r~~LA~~lgl~~~~V~vWFq 62 (149)
+.|..||+++...+-..+ ... .....+|..+|+++..|..|-.
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 456789998887776665 333 4678899999999999999953
No 42
>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=80.12 E-value=2.2 Score=26.02 Aligned_cols=39 Identities=28% Similarity=0.343 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHhhCCC--CCHHHHHHHHHhcCCCccchh
Q psy9529 20 FNSWQLEELERAFLASHY--PDVFMREALALRLDLKESRVA 58 (149)
Q Consensus 20 ft~~ql~~Le~~F~~~~~--p~~~~r~~LA~~lgl~~~~V~ 58 (149)
+|+.|..+|..+|...-| |-.....+||..+|++...+.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHH
Confidence 578999999999987754 656677899999999987544
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=79.20 E-value=3 Score=23.53 Aligned_cols=43 Identities=16% Similarity=0.108 Sum_probs=31.5
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhh
Q psy9529 19 NFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRA 66 (149)
Q Consensus 19 ~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRa 66 (149)
.+++.+..++...|... .....+|..+|++...|..|...-+.
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 35677777777776433 24667899999999999999865443
No 44
>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=76.51 E-value=5.1 Score=23.57 Aligned_cols=41 Identities=20% Similarity=0.190 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhh
Q psy9529 20 FNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRR 65 (149)
Q Consensus 20 ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRR 65 (149)
+++.+..++...|-.+ ..-.++|..+|++...|+.|...-+
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4566666666665554 3678899999999999999987433
No 45
>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=71.51 E-value=10 Score=18.89 Aligned_cols=38 Identities=24% Similarity=0.283 Sum_probs=26.5
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhh
Q psy9529 19 NFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWF 61 (149)
Q Consensus 19 ~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWF 61 (149)
.++..+...+...|... + ....+|..+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 36677776666666533 2 45678899999988887773
No 46
>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=70.74 E-value=2.2 Score=26.83 Aligned_cols=20 Identities=25% Similarity=0.429 Sum_probs=17.4
Q ss_pred HHHHHHHhcCCCccchhhhh
Q psy9529 42 MREALALRLDLKESRVAVWF 61 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWF 61 (149)
.-..||..||+++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 45678999999999999994
No 47
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=69.65 E-value=9.9 Score=27.86 Aligned_cols=49 Identities=16% Similarity=0.129 Sum_probs=39.0
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhh
Q psy9529 18 TNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKE 72 (149)
Q Consensus 18 t~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~ 72 (149)
+.+++.|..+|...+ .. ....++|..+|++...|..|-.+-+.+.++..
T Consensus 5 ~~Lt~rqreVL~lr~-~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 5 SFLTERQIEVLRLRE-RG-----LTQQEIADILGTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred cCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 568999999998843 22 24678999999999999999998777777654
No 48
>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=67.84 E-value=10 Score=23.64 Aligned_cols=45 Identities=11% Similarity=0.093 Sum_probs=23.2
Q ss_pred CCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhh
Q psy9529 17 RTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQ 62 (149)
Q Consensus 17 Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFq 62 (149)
|..|+....-..-.+|..+..--...|. -|.++|+++.+|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 4567776544444444433322222344 49999999999999975
No 49
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=64.17 E-value=18 Score=25.26 Aligned_cols=42 Identities=10% Similarity=0.121 Sum_probs=29.5
Q ss_pred CCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhh
Q psy9529 17 RTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQ 62 (149)
Q Consensus 17 Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFq 62 (149)
|..|+.++....-.....+.+ ....+|..+|++...|..|..
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHH
Confidence 455888876655444444433 356789999999999999953
No 50
>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=62.02 E-value=14 Score=22.13 Aligned_cols=45 Identities=18% Similarity=0.119 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHH
Q psy9529 19 NFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWR 69 (149)
Q Consensus 19 ~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~r 69 (149)
.||+.++.+|.....-. ...++|..+|+++..|..+..+=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 57888888887776655 4778999999999999999877665543
No 51
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=61.79 E-value=16 Score=27.19 Aligned_cols=30 Identities=17% Similarity=0.152 Sum_probs=24.4
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
.-.++|..+|++...|+++...-|.+.++.
T Consensus 160 s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 160 TYREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred CHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 457889999999999999997666666654
No 52
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=61.12 E-value=14 Score=26.11 Aligned_cols=45 Identities=13% Similarity=0.132 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHH
Q psy9529 20 FNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWR 69 (149)
Q Consensus 20 ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~r 69 (149)
+++.+..++...|-.+ ....++|..+|++...|+.|...-+.+.|
T Consensus 107 L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 107 LDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 3444444544443332 24678999999999999999875555444
No 53
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=60.38 E-value=15 Score=26.38 Aligned_cols=46 Identities=11% Similarity=-0.003 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 20 FNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 20 ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
+++.+..++...|-.+ ....++|..+|++...|..|...-+.+.++
T Consensus 129 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 129 LPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4445555554443222 235678999999999999998865555554
No 54
>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=59.47 E-value=2.9 Score=27.28 Aligned_cols=35 Identities=17% Similarity=0.035 Sum_probs=25.7
Q ss_pred HHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhh
Q psy9529 29 ERAFLASHYPDVFMREALALRLDLKESRVAVWFQN 63 (149)
Q Consensus 29 e~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqN 63 (149)
+..|....|-......+||..+|+++..|+.|+.+
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 34454444444446788999999999999999864
No 55
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=58.64 E-value=9.1 Score=22.00 Aligned_cols=40 Identities=15% Similarity=0.153 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhh
Q psy9529 18 TNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQ 62 (149)
Q Consensus 18 t~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFq 62 (149)
..+|.++...++..+... ....+||..+|.+...|..|..
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 458888888888887644 3566799999999998887753
No 56
>PRK00118 putative DNA-binding protein; Validated
Probab=58.16 E-value=21 Score=24.76 Aligned_cols=47 Identities=11% Similarity=0.037 Sum_probs=34.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 20 FNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 20 ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
+++.|..++...|.... ...+||..+|++...|..|...-|.+.+..
T Consensus 18 L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 56667777766655542 467799999999999999998666666553
No 57
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=57.73 E-value=21 Score=26.93 Aligned_cols=31 Identities=23% Similarity=0.197 Sum_probs=24.6
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHhh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKKE 72 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~ 72 (149)
...++|..+|++...|+++...-+.+.++.-
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4578899999999999999876666666543
No 58
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=57.61 E-value=16 Score=28.13 Aligned_cols=49 Identities=29% Similarity=0.337 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHHhhCC--CCCHHHHHHHHHhcCCCccchhhhhhhhhhhHH
Q psy9529 19 NFNSWQLEELERAFLASH--YPDVFMREALALRLDLKESRVAVWFQNRRAKWR 69 (149)
Q Consensus 19 ~ft~~ql~~Le~~F~~~~--~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~r 69 (149)
-+|+.|+.+|..+|...= ||-......||+.+|++... +|..=||+..|
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst--~~ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST--LSEHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH--HHHHHHHHHHH
Confidence 599999999999999774 46666778999999999864 45555555543
No 59
>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=56.82 E-value=32 Score=25.04 Aligned_cols=50 Identities=20% Similarity=0.152 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhhh
Q psy9529 20 FNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHT 74 (149)
Q Consensus 20 ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~ 74 (149)
+++.+..++...|-.+ ....++|..+|++...|+++...-|.+.+..-..
T Consensus 101 L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 150 (170)
T TIGR02959 101 LPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET 150 (170)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444443332 2457889999999999999987767766665443
No 60
>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=56.81 E-value=19 Score=24.50 Aligned_cols=46 Identities=20% Similarity=0.195 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 20 FNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 20 ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
+++.+..++...|-. .....++|..+|+++..|..|...-+.+.++
T Consensus 111 L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 455555555444322 2245689999999999999998766555543
No 61
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=56.52 E-value=21 Score=26.09 Aligned_cols=30 Identities=23% Similarity=0.193 Sum_probs=24.8
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
.-.+||..+|++...|++++..-+.+.+..
T Consensus 149 s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12512 149 SIKETAAKLSMSEGAVRVALHRGLAALAAK 178 (184)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999998777776654
No 62
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=55.51 E-value=21 Score=25.55 Aligned_cols=30 Identities=17% Similarity=0.105 Sum_probs=24.1
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
.-.++|..+|++...|..|..--+.+.|+.
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999998666666543
No 63
>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=54.66 E-value=20 Score=20.56 Aligned_cols=38 Identities=16% Similarity=0.282 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhh
Q psy9529 19 NFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWF 61 (149)
Q Consensus 19 ~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWF 61 (149)
.++.++...+...+... + ...+||..+|++...|.-++
T Consensus 5 ~~~~~~~~~i~~l~~~G-~----si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-M----SIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC-C----CHHHHHHHHCcCHHHHHHHH
Confidence 47777777777777666 2 47789999999998887765
No 64
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=54.13 E-value=25 Score=25.00 Aligned_cols=29 Identities=17% Similarity=0.201 Sum_probs=23.5
Q ss_pred HHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 43 REALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
-.++|..+|++...|++....-|.+.|+.
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 125 YQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999988666666554
No 65
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=54.04 E-value=28 Score=25.34 Aligned_cols=29 Identities=24% Similarity=0.369 Sum_probs=23.4
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
...++|..+|++...|+++...-|.+.|+
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 35789999999999999998766666554
No 66
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=53.54 E-value=29 Score=25.61 Aligned_cols=33 Identities=18% Similarity=0.094 Sum_probs=26.0
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHhhhh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKKEHT 74 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~ 74 (149)
.-.++|..+|++...|++-...-|.+.++.-..
T Consensus 149 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 181 (189)
T PRK12515 149 SVEEVGEIVGIPESTVKTRMFYARKKLAELLKA 181 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999988777777765443
No 67
>PRK10072 putative transcriptional regulator; Provisional
Probab=53.14 E-value=19 Score=24.52 Aligned_cols=40 Identities=18% Similarity=0.162 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhh
Q psy9529 20 FNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRA 66 (149)
Q Consensus 20 ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRa 66 (149)
.+...+..|......+ ..+||..+|++...|..|...+|.
T Consensus 33 ~~~~eik~LR~~~glT-------Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 33 TSFTEFEQLRKGTGLK-------IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred CChHHHHHHHHHcCCC-------HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 3555555554433322 678999999999999999976653
No 68
>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=52.85 E-value=25 Score=24.88 Aligned_cols=28 Identities=25% Similarity=0.144 Sum_probs=21.4
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWR 69 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~r 69 (149)
...++|..+|++...|.++...-|.+.+
T Consensus 129 ~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 129 SLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4678899999999999988764444433
No 69
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=52.51 E-value=28 Score=25.04 Aligned_cols=31 Identities=23% Similarity=0.123 Sum_probs=25.0
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHhh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKKE 72 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~ 72 (149)
...++|..+|++...|++|...-|.+.++.-
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4578899999999999999987666666543
No 70
>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=52.37 E-value=27 Score=24.42 Aligned_cols=28 Identities=14% Similarity=0.137 Sum_probs=21.9
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWR 69 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~r 69 (149)
...++|..+|+++..|+.+...-+.+.+
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4567899999999999998875555544
No 71
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=52.21 E-value=21 Score=26.43 Aligned_cols=30 Identities=20% Similarity=0.215 Sum_probs=24.1
Q ss_pred HHHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 41 FMREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 41 ~~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
....++|..+|++...|++|+..-|.+.++
T Consensus 158 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 158 LSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 345788999999999999999766666554
No 72
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=51.32 E-value=32 Score=25.25 Aligned_cols=32 Identities=13% Similarity=0.096 Sum_probs=25.5
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHhhh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKKEH 73 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~ 73 (149)
.-.++|..+|++...|+.+...-|.+.++.-.
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35788999999999999998777777666543
No 73
>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=51.24 E-value=29 Score=25.27 Aligned_cols=29 Identities=21% Similarity=0.063 Sum_probs=23.0
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
.-.++|..+|+++..|++....-|.+.++
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 34778999999999999998766665554
No 74
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=50.91 E-value=24 Score=25.67 Aligned_cols=30 Identities=23% Similarity=0.258 Sum_probs=24.0
Q ss_pred HHHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 41 FMREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 41 ~~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
..-.++|..+|++...|+++++.-|.+.+.
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 153 LSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345788999999999999999766666554
No 75
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=50.64 E-value=29 Score=25.55 Aligned_cols=29 Identities=21% Similarity=0.070 Sum_probs=22.7
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
...++|..+|++...|+.+...-+.+.|+
T Consensus 157 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 157 SAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46789999999999999998655555443
No 76
>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=49.87 E-value=10 Score=21.45 Aligned_cols=21 Identities=14% Similarity=0.004 Sum_probs=17.7
Q ss_pred HHHHHHhcCCCccchhhhhhh
Q psy9529 43 REALALRLDLKESRVAVWFQN 63 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWFqN 63 (149)
..++|+.+|++...|+.|.++
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999643
No 77
>PRK04217 hypothetical protein; Provisional
Probab=48.89 E-value=37 Score=23.77 Aligned_cols=49 Identities=14% Similarity=0.060 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 18 TNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 18 t~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
..++.++..++...|...- ...+||..+|++...|...+..-+.+.+..
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~ 89 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQM 89 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3578888888877765443 567899999999999999987766666554
No 78
>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=48.33 E-value=24 Score=25.80 Aligned_cols=30 Identities=17% Similarity=0.060 Sum_probs=23.6
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
.-.++|..+|++...|+++...-|.+.|+.
T Consensus 156 s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 156 SYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999987656555543
No 79
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=46.85 E-value=34 Score=24.39 Aligned_cols=30 Identities=30% Similarity=0.360 Sum_probs=23.7
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
.-.+||..+|++...|+.+...-+.+.|+.
T Consensus 129 s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 129 SYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999987666665543
No 80
>PRK06930 positive control sigma-like factor; Validated
Probab=46.45 E-value=36 Score=25.42 Aligned_cols=48 Identities=15% Similarity=0.030 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 19 NFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 19 ~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
.+++.+..++...|...- .-.++|..+|++...|+.+...-+.+.++.
T Consensus 114 ~L~~rer~V~~L~~~eg~-----s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~ 161 (170)
T PRK06930 114 VLTEREKEVYLMHRGYGL-----SYSEIADYLNIKKSTVQSMIERAEKKIARQ 161 (170)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 355666666665443332 457889999999999999998777766654
No 81
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=46.14 E-value=53 Score=18.45 Aligned_cols=40 Identities=20% Similarity=0.202 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhh
Q psy9529 19 NFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNR 64 (149)
Q Consensus 19 ~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNR 64 (149)
.+++.+..++...+. . + ...++|..+|++...|..|...-
T Consensus 3 ~l~~~e~~i~~~~~~-g-~----s~~eia~~l~is~~tv~~~~~~~ 42 (58)
T smart00421 3 SLTPREREVLRLLAE-G-L----TNKEIAERLGISEKTVKTHLSNI 42 (58)
T ss_pred CCCHHHHHHHHHHHc-C-C----CHHHHHHHHCCCHHHHHHHHHHH
Confidence 367777777755432 2 2 45788999999999999987643
No 82
>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=46.06 E-value=13 Score=22.96 Aligned_cols=26 Identities=31% Similarity=0.507 Sum_probs=20.2
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWR 69 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~r 69 (149)
...+||..||++...|..|-+ |-+|.
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~--r~~W~ 40 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD--RYKWD 40 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH--hhCcc
Confidence 356899999999999999964 44443
No 83
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=45.99 E-value=32 Score=24.57 Aligned_cols=29 Identities=14% Similarity=0.137 Sum_probs=22.5
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
...++|..+|++...|+++...-|.+.++
T Consensus 130 s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 130 SYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35778999999999999998755555543
No 84
>PF13518 HTH_28: Helix-turn-helix domain
Probab=45.82 E-value=15 Score=21.05 Aligned_cols=24 Identities=21% Similarity=0.375 Sum_probs=19.5
Q ss_pred HHHHHHHhcCCCccchhhhhhhhh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRR 65 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRR 65 (149)
...++|..+|++..+|..|.+.-+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 355689999999999999986433
No 85
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=45.08 E-value=42 Score=23.71 Aligned_cols=29 Identities=14% Similarity=0.048 Sum_probs=22.8
Q ss_pred HHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 43 REALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
-.++|..+|++...|++....-+.+.|..
T Consensus 125 ~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 125 VAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57789999999999999887655555543
No 86
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=45.02 E-value=46 Score=24.35 Aligned_cols=28 Identities=21% Similarity=0.336 Sum_probs=22.1
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWR 69 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~r 69 (149)
...++|..+|++...|++|...-+.+.|
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHH
Confidence 4577899999999999999875555444
No 87
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.00 E-value=27 Score=23.75 Aligned_cols=40 Identities=18% Similarity=0.172 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchh
Q psy9529 19 NFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVA 58 (149)
Q Consensus 19 ~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~ 58 (149)
.++++|...-...|+.|--.+.-..+++|..|++++..|.
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHH
Confidence 4677887777766666665556678889999998875543
No 88
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=44.63 E-value=41 Score=24.60 Aligned_cols=30 Identities=23% Similarity=0.051 Sum_probs=24.4
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
...++|..+|++...|++....-|.+.++.
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999998777666653
No 89
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=44.49 E-value=40 Score=24.99 Aligned_cols=29 Identities=17% Similarity=0.249 Sum_probs=23.2
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
...++|..+|+++..|+++...-|.+.|+
T Consensus 152 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 152 SSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35788999999999999998755555554
No 90
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=43.47 E-value=42 Score=24.79 Aligned_cols=33 Identities=21% Similarity=0.182 Sum_probs=26.0
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHhhhh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKKEHT 74 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~~ 74 (149)
...++|..+|++...|+..+..-|.+.++.-..
T Consensus 124 ~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 124 SQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 357889999999999999998777776665444
No 91
>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=43.30 E-value=24 Score=21.41 Aligned_cols=36 Identities=22% Similarity=0.237 Sum_probs=26.5
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhh
Q psy9529 23 WQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQ 62 (149)
Q Consensus 23 ~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFq 62 (149)
.|+..|+-.+. +...+.. +||..+|++++.|+.-..
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHHH
Confidence 47788888888 5555444 899999999998876543
No 92
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=42.93 E-value=46 Score=24.32 Aligned_cols=30 Identities=23% Similarity=0.232 Sum_probs=24.9
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
...++|..+|++...|++....-+.+.|+.
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 164 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQK 164 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457789999999999999988777777654
No 93
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=42.42 E-value=61 Score=23.87 Aligned_cols=31 Identities=16% Similarity=0.202 Sum_probs=24.8
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHhh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKKE 72 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~ 72 (149)
.-.+||..+|++...|++....-|.+.++.-
T Consensus 149 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 149 ETEEICQELQITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3578899999999999999876666666543
No 94
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=42.39 E-value=45 Score=23.69 Aligned_cols=29 Identities=17% Similarity=0.178 Sum_probs=23.6
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
.-.++|..+|++...|+++-..-|.+.++
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 35778999999999999998766666655
No 95
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=42.11 E-value=41 Score=25.10 Aligned_cols=30 Identities=17% Similarity=0.019 Sum_probs=24.7
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
...++|..+|++...|++++..-|.+.|+.
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~ 160 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAEL 160 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 357889999999999999998777666654
No 96
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=41.87 E-value=15 Score=22.07 Aligned_cols=24 Identities=13% Similarity=0.235 Sum_probs=18.1
Q ss_pred HHHHHHHhcCCCccchhhhhhhhh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRR 65 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRR 65 (149)
....||..+|++...|..|+.++.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-
T ss_pred CHHHHHHHHCcCHHHHHHHHhccc
Confidence 467899999999999999998763
No 97
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=41.71 E-value=55 Score=22.30 Aligned_cols=41 Identities=12% Similarity=0.169 Sum_probs=32.0
Q ss_pred CCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCC-Cccchhhhh
Q psy9529 17 RTNFNSWQLEELERAFLASHYPDVFMREALALRLDL-KESRVAVWF 61 (149)
Q Consensus 17 Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl-~~~~V~vWF 61 (149)
|..|+.+....+-..+....+ ....+|..+|+ ...++..|-
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~ 46 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWR 46 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHH
Confidence 678999988777666665554 57789999996 998888884
No 98
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=41.70 E-value=16 Score=21.02 Aligned_cols=23 Identities=26% Similarity=0.473 Sum_probs=17.2
Q ss_pred HHHHHHHHhcCCCccchhhhhhh
Q psy9529 41 FMREALALRLDLKESRVAVWFQN 63 (149)
Q Consensus 41 ~~r~~LA~~lgl~~~~V~vWFqN 63 (149)
....++|..+|++...|..|.+.
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 35678899999999999999753
No 99
>PF13551 HTH_29: Winged helix-turn helix
Probab=41.14 E-value=66 Score=21.17 Aligned_cols=48 Identities=15% Similarity=0.077 Sum_probs=30.1
Q ss_pred CCCCCCCHHHHHHHHHHHhhCCC-----CCHHHHHH-H-HHhc--CCCccchhhhhh
Q psy9529 15 RSRTNFNSWQLEELERAFLASHY-----PDVFMREA-L-ALRL--DLKESRVAVWFQ 62 (149)
Q Consensus 15 r~Rt~ft~~ql~~Le~~F~~~~~-----p~~~~r~~-L-A~~l--gl~~~~V~vWFq 62 (149)
+++..+++++...|...+..++. .+...... | .... .++...|..|+.
T Consensus 53 ~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 53 RPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 33334899999999999998762 33333333 3 3333 456677777764
No 100
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=41.11 E-value=17 Score=22.21 Aligned_cols=19 Identities=16% Similarity=0.116 Sum_probs=16.7
Q ss_pred HHHHHHhcCCCccchhhhh
Q psy9529 43 REALALRLDLKESRVAVWF 61 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWF 61 (149)
..++|..+|++...|+.|=
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 3578999999999999994
No 101
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=40.38 E-value=54 Score=24.00 Aligned_cols=29 Identities=14% Similarity=0.180 Sum_probs=23.0
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
.-.++|..+|+++..|++....-+.+.+.
T Consensus 145 s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 145 KQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45788999999999999998766655543
No 102
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=40.09 E-value=57 Score=23.16 Aligned_cols=29 Identities=17% Similarity=0.251 Sum_probs=22.4
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
...++|..+|++...|+.....-+.+.++
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35788999999999999987655555554
No 103
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=39.89 E-value=92 Score=23.92 Aligned_cols=31 Identities=13% Similarity=0.041 Sum_probs=25.0
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHhh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKKE 72 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~ 72 (149)
.-.+||..+|+++..|+++...-|.+.++.-
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3578899999999999999887676666653
No 104
>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=39.85 E-value=53 Score=23.35 Aligned_cols=28 Identities=18% Similarity=-0.006 Sum_probs=20.5
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWR 69 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~r 69 (149)
.-.++|..+|++...|+....--|.+.|
T Consensus 140 s~~eIA~~l~is~~tv~~~l~ra~~~Lr 167 (170)
T TIGR02952 140 PIAEVARILGKTEGAVKILQFRAIKKLA 167 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4577899999999999888754444433
No 105
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=39.84 E-value=55 Score=23.48 Aligned_cols=29 Identities=10% Similarity=0.024 Sum_probs=22.8
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
.-.++|..+|+++..|+++...-|.+.+.
T Consensus 130 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 130 SYEDAAAICGCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45788999999999999998755555443
No 106
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=39.14 E-value=52 Score=24.45 Aligned_cols=29 Identities=7% Similarity=0.021 Sum_probs=23.7
Q ss_pred HHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 43 REALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
-.+||..+|++...|++++.--|.+.++.
T Consensus 155 ~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 155 NPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 57789999999999999998666666554
No 107
>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=39.11 E-value=59 Score=23.33 Aligned_cols=29 Identities=17% Similarity=0.237 Sum_probs=22.3
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
...++|..+|++...|+++..--|.+.++
T Consensus 137 s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45778999999999999987655555444
No 108
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=38.85 E-value=62 Score=23.57 Aligned_cols=29 Identities=10% Similarity=0.074 Sum_probs=21.9
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
.-.++|..+|++...|+++...-|.+.+.
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 34678999999999999987655555443
No 109
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=38.60 E-value=49 Score=25.50 Aligned_cols=30 Identities=20% Similarity=0.235 Sum_probs=24.9
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
.-.++|..+|++...|+.+...-+.+.|+.
T Consensus 202 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 202 NLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999998777766653
No 110
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=38.55 E-value=61 Score=23.76 Aligned_cols=29 Identities=21% Similarity=0.075 Sum_probs=23.4
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
...++|..+|++...|+.+...-+.+.++
T Consensus 149 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 149 SVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 46788999999999999998766666554
No 111
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=38.05 E-value=45 Score=25.95 Aligned_cols=30 Identities=17% Similarity=0.183 Sum_probs=24.5
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
.-.+||..+|++...|++....-|.+.|+.
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~ 218 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRDL 218 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 357889999999999999998767666654
No 112
>PRK09480 slmA division inhibitor protein; Provisional
Probab=37.43 E-value=36 Score=24.74 Aligned_cols=36 Identities=14% Similarity=0.199 Sum_probs=29.6
Q ss_pred HHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhh
Q psy9529 29 ERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRR 65 (149)
Q Consensus 29 e~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRR 65 (149)
...|...+. .......||...|++...+-.+|.|+-
T Consensus 20 ~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~ 55 (194)
T PRK09480 20 AQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKA 55 (194)
T ss_pred HHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHH
Confidence 334555556 778899999999999999999999976
No 113
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=37.30 E-value=59 Score=24.02 Aligned_cols=30 Identities=10% Similarity=0.120 Sum_probs=24.3
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
.-.++|..+|++...|++....-|.+.|+.
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 183 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQC 183 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 357889999999999999987666666654
No 114
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=37.09 E-value=70 Score=22.99 Aligned_cols=29 Identities=17% Similarity=0.144 Sum_probs=22.4
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
...++|..+|+++..|+.....-|.+.|+
T Consensus 136 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 136 STAQIAADLGIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35788999999999999987655555554
No 115
>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=37.07 E-value=22 Score=19.54 Aligned_cols=22 Identities=18% Similarity=0.299 Sum_probs=18.5
Q ss_pred HHHHHHhcCCCccchhhhhhhh
Q psy9529 43 REALALRLDLKESRVAVWFQNR 64 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWFqNR 64 (149)
..++|..+|++...|..|..+.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g 24 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 4578999999999999998653
No 116
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=36.84 E-value=64 Score=23.78 Aligned_cols=30 Identities=27% Similarity=0.319 Sum_probs=23.5
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
...++|..+|++...|++..+.-|.+.++.
T Consensus 149 s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 149 KIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 357889999999999999887666665554
No 117
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=36.04 E-value=39 Score=27.42 Aligned_cols=25 Identities=24% Similarity=0.579 Sum_probs=21.2
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKW 68 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~ 68 (149)
.-..||+++|+++.+|+.|= +|..|
T Consensus 21 k~~dIAeklGvspntiksWK--rr~gW 45 (279)
T COG5484 21 KLKDIAEKLGVSPNTIKSWK--RRDGW 45 (279)
T ss_pred cHHHHHHHhCCChHHHHHHH--HhcCC
Confidence 45679999999999999995 57777
No 118
>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=35.33 E-value=22 Score=19.84 Aligned_cols=18 Identities=11% Similarity=0.086 Sum_probs=14.8
Q ss_pred HHHHHhcCCCccchhhhh
Q psy9529 44 EALALRLDLKESRVAVWF 61 (149)
Q Consensus 44 ~~LA~~lgl~~~~V~vWF 61 (149)
.++|+.+|++...|+.|=
T Consensus 3 ~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHH
Confidence 468999999999999994
No 119
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=35.31 E-value=61 Score=23.91 Aligned_cols=29 Identities=7% Similarity=-0.118 Sum_probs=22.4
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
.-.+||..+|+++..|+++...-|.+.++
T Consensus 148 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35788999999999999998655555444
No 120
>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=34.90 E-value=17 Score=20.92 Aligned_cols=20 Identities=10% Similarity=0.129 Sum_probs=18.2
Q ss_pred HHHHhcCCCccchhhhhhhh
Q psy9529 45 ALALRLDLKESRVAVWFQNR 64 (149)
Q Consensus 45 ~LA~~lgl~~~~V~vWFqNR 64 (149)
+||..+|++...|..|+.+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 58999999999999999876
No 121
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=34.83 E-value=73 Score=23.01 Aligned_cols=29 Identities=21% Similarity=0.185 Sum_probs=23.0
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
.-.++|..+|++...|+++...-+.+.+.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35678999999999999998766655544
No 122
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=34.79 E-value=72 Score=23.66 Aligned_cols=30 Identities=10% Similarity=-0.023 Sum_probs=24.5
Q ss_pred HHHHHHhcCCCccchhhhhhhhhhhHHHhh
Q psy9529 43 REALALRLDLKESRVAVWFQNRRAKWRKKE 72 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWFqNRRak~rk~~ 72 (149)
-.++|..+|++...|+++...-|.+.++.-
T Consensus 135 ~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 135 YEEAAEICGCAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999887776666543
No 123
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=34.60 E-value=91 Score=23.33 Aligned_cols=30 Identities=17% Similarity=0.085 Sum_probs=23.8
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
.-.++|..+|++...|+++...-|.+.|+.
T Consensus 151 s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~ 180 (196)
T PRK12535 151 TYEEAAKIADVRVGTIRSRVARARADLIAA 180 (196)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 357789999999999999987666666554
No 124
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=34.51 E-value=74 Score=24.05 Aligned_cols=29 Identities=24% Similarity=0.266 Sum_probs=23.5
Q ss_pred HHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 43 REALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
..++|..+|++...|+++...-|.+.++.
T Consensus 157 ~~EIA~~Lgis~~tV~~~l~RArk~Lr~~ 185 (203)
T PRK09647 157 YEEIAATLGVKLGTVRSRIHRGRQQLRAA 185 (203)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 56789999999999999987666666554
No 125
>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=34.17 E-value=25 Score=21.67 Aligned_cols=20 Identities=20% Similarity=0.302 Sum_probs=17.4
Q ss_pred HHHHHHhcCCCccchhhhhh
Q psy9529 43 REALALRLDLKESRVAVWFQ 62 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWFq 62 (149)
..++|+.+|++...|+.|.+
T Consensus 3 i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999964
No 126
>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=33.78 E-value=71 Score=24.32 Aligned_cols=46 Identities=20% Similarity=0.173 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 20 FNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 20 ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
+++.+..++...|-.. ....++|..+|++...|+.+...-+.+.|+
T Consensus 176 L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 176 LSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3444455555544222 245789999999999999988655555443
No 127
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=33.75 E-value=71 Score=24.93 Aligned_cols=46 Identities=13% Similarity=0.228 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 20 FNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 20 ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
+++.+..+|...|-.. ..-.++|..+|++...|+.|...-+.+.|.
T Consensus 206 L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tV~~~~~ra~~kLr~ 251 (257)
T PRK08583 206 LSDREKSIIQCTFIEN-----LSQKETGERLGISQMHVSRLQRQAIKKLRE 251 (257)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4445555555544322 245789999999999999998755555543
No 128
>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=33.70 E-value=25 Score=20.41 Aligned_cols=23 Identities=22% Similarity=0.341 Sum_probs=19.0
Q ss_pred HHHHHHhcCCCccchhhhhhhhh
Q psy9529 43 REALALRLDLKESRVAVWFQNRR 65 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWFqNRR 65 (149)
..+||..+|++...|.-|..+.+
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 47899999999999999998744
No 129
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=33.70 E-value=75 Score=23.50 Aligned_cols=32 Identities=19% Similarity=0.101 Sum_probs=24.5
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHhhh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKKEH 73 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~ 73 (149)
.-.++|..+|++...|+++..--|.+.++...
T Consensus 129 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 129 SYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35788999999999999998765666555433
No 130
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=33.60 E-value=71 Score=23.14 Aligned_cols=29 Identities=24% Similarity=0.244 Sum_probs=23.0
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
.-.++|..+|++...|.+....-|.+.++
T Consensus 154 s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 154 SLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45778999999999999987766666554
No 131
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=33.34 E-value=83 Score=23.28 Aligned_cols=29 Identities=17% Similarity=0.138 Sum_probs=22.6
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
.-.++|..+|++...|++-...-|.+.++
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr~ 187 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLRH 187 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 35778999999999999888665555554
No 132
>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=33.34 E-value=74 Score=24.19 Aligned_cols=45 Identities=18% Similarity=0.203 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHH
Q psy9529 20 FNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWR 69 (149)
Q Consensus 20 ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~r 69 (149)
+++.+..++...|... ....++|..+|++...|..|...-+.+.+
T Consensus 179 L~~~~r~vl~l~y~~~-----~s~~eIA~~lgis~~~v~~~~~ra~~~Lr 223 (227)
T TIGR02980 179 LPERERRILLLRFFED-----KTQSEIAERLGISQMHVSRLLRRALKKLR 223 (227)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4555555555544322 24678999999999999999765444443
No 133
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=33.19 E-value=79 Score=23.65 Aligned_cols=31 Identities=16% Similarity=0.220 Sum_probs=24.4
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHhh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKKE 72 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~ 72 (149)
.-.++|..+|++...|++....-|.+.|+.-
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3577899999999999999876666666543
No 134
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=32.73 E-value=79 Score=23.12 Aligned_cols=29 Identities=14% Similarity=0.271 Sum_probs=23.0
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
.-.++|..+|++...|++....-|.+.++
T Consensus 140 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 168 (185)
T PRK12542 140 TYQEISSVMGITEANVRKQFERARKRVQN 168 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35778999999999999988766665554
No 135
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=32.69 E-value=83 Score=22.66 Aligned_cols=29 Identities=10% Similarity=0.144 Sum_probs=22.7
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
.-.++|..+|++...|++....-|.+.++
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 165 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMRE 165 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 34678999999999999998765555554
No 136
>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=32.32 E-value=85 Score=23.21 Aligned_cols=30 Identities=17% Similarity=0.234 Sum_probs=23.6
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
...+||..+|++...|++....-|.+.++.
T Consensus 149 s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 149 ESDEICQELEISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 467889999999999999887666655543
No 137
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=31.97 E-value=81 Score=22.37 Aligned_cols=25 Identities=12% Similarity=0.135 Sum_probs=19.5
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRA 66 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRa 66 (149)
.-.++|..+|++...|+++...-+.
T Consensus 131 s~~EIA~~l~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 131 GYGEIATELGISLATVKRYLNKAAM 155 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3567899999999999998764433
No 138
>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=31.96 E-value=90 Score=22.70 Aligned_cols=48 Identities=17% Similarity=0.154 Sum_probs=36.7
Q ss_pred CCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 17 RTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 17 Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
.+.++..|..+|...+ .. ....++|..+|++...|..|-..-+.+.++
T Consensus 4 ~~~Lte~qr~VL~Lr~-~G-----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE-KG-----LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 3568899999998842 22 257789999999999999998766666654
No 139
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=31.93 E-value=29 Score=21.22 Aligned_cols=20 Identities=5% Similarity=0.090 Sum_probs=17.3
Q ss_pred HHHHHHhcCCCccchhhhhh
Q psy9529 43 REALALRLDLKESRVAVWFQ 62 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWFq 62 (149)
..++|+.+|++...|+.|-+
T Consensus 3 i~evA~~~gvs~~tlR~~~~ 22 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEK 22 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999965
No 140
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=31.55 E-value=33 Score=25.34 Aligned_cols=32 Identities=19% Similarity=0.087 Sum_probs=25.5
Q ss_pred HHHHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 40 VFMREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 40 ~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
...-.++|..+|++...|+++...-|.+.|+.
T Consensus 155 g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 155 DLELEEIAELTGVPEETVKSRLRYALQKLREL 186 (194)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34567899999999999999987777666654
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=31.36 E-value=75 Score=24.75 Aligned_cols=46 Identities=11% Similarity=0.172 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 20 FNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 20 ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
+++.+..++...|... ..-.++|..+|++...|+.+...-+.+.|.
T Consensus 206 L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 206 LSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred CCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3455555555554322 245789999999999999998765555543
No 142
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=31.22 E-value=40 Score=24.31 Aligned_cols=33 Identities=18% Similarity=0.109 Sum_probs=26.2
Q ss_pred HHHHHHHHHhcCCCccchhhhhhhhhhhHHHhh
Q psy9529 40 VFMREALALRLDLKESRVAVWFQNRRAKWRKKE 72 (149)
Q Consensus 40 ~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~ 72 (149)
...-.++|..+|++...|++.+..-|.+.++.-
T Consensus 136 g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 136 DLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 334678999999999999999987777766543
No 143
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=31.14 E-value=66 Score=23.32 Aligned_cols=28 Identities=14% Similarity=0.152 Sum_probs=21.9
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWR 69 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~r 69 (149)
...+||..+|++...|+++...-+.+++
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 137 TYSEIAHKLGVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4678999999999999999865444444
No 144
>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=30.04 E-value=89 Score=24.53 Aligned_cols=30 Identities=13% Similarity=0.337 Sum_probs=24.8
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
...++|..+|++...|+++...-|.+.++.
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~ 208 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLER 208 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 357889999999999999998777766654
No 145
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=29.77 E-value=83 Score=23.08 Aligned_cols=30 Identities=17% Similarity=0.051 Sum_probs=23.7
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
.-.++|..+|++...|++....-|.+.|+.
T Consensus 156 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 185 (193)
T PRK11923 156 SYEDIASVMQCPVGTVRSRIFRAREAIDKA 185 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 357889999999999999987666665553
No 146
>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=29.67 E-value=1.6e+02 Score=22.02 Aligned_cols=44 Identities=16% Similarity=0.265 Sum_probs=36.0
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhh
Q psy9529 16 SRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWF 61 (149)
Q Consensus 16 ~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWF 61 (149)
+...+|++++..+...-..+ |..-.+..||+++||+..-|.+-.
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~ 125 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVA 125 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhc
Confidence 34689999999999887776 667789999999999987766654
No 147
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=29.65 E-value=94 Score=22.35 Aligned_cols=28 Identities=14% Similarity=0.087 Sum_probs=21.4
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWR 69 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~r 69 (149)
.-.++|..+|++...|+.+..+-+...+
T Consensus 136 s~~EIA~~l~is~~tV~~~l~ra~~~~~ 163 (168)
T PRK12525 136 TYVEIGERLGVSLSRIHQYMVEAFKCCY 163 (168)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3578899999999999988765554443
No 148
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=29.61 E-value=83 Score=24.07 Aligned_cols=29 Identities=14% Similarity=0.138 Sum_probs=23.2
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
.-.++|..+|++...|+.+...-+.+.|+
T Consensus 200 s~~EIA~~lgis~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 200 TQKEVADMLGISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46788999999999999997766665554
No 149
>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=29.56 E-value=46 Score=24.60 Aligned_cols=32 Identities=19% Similarity=0.195 Sum_probs=25.9
Q ss_pred HHHHHHHHhcCCCccchhhhhhhhhhhHHHhh
Q psy9529 41 FMREALALRLDLKESRVAVWFQNRRAKWRKKE 72 (149)
Q Consensus 41 ~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~ 72 (149)
..-.+||..+|++...|+++...-|.+.++.-
T Consensus 148 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 148 FAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34578999999999999999987777766543
No 150
>PRK10403 transcriptional regulator NarP; Provisional
Probab=29.39 E-value=58 Score=23.28 Aligned_cols=45 Identities=20% Similarity=0.240 Sum_probs=34.2
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhH
Q psy9529 18 TNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKW 68 (149)
Q Consensus 18 t~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~ 68 (149)
..+|..+..+|...... ....+||..++++++.|++..+|=+.|.
T Consensus 152 ~~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl 196 (215)
T PRK10403 152 SVLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKL 196 (215)
T ss_pred ccCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 35888888888765433 2467889999999999999988766553
No 151
>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=29.18 E-value=36 Score=19.53 Aligned_cols=23 Identities=9% Similarity=-0.130 Sum_probs=19.5
Q ss_pred HHHHHHhcCCCccchhhhhhhhh
Q psy9529 43 REALALRLDLKESRVAVWFQNRR 65 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWFqNRR 65 (149)
..+||..+|++...|.-|..+++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 57899999999999999986553
No 152
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=28.79 E-value=1.6e+02 Score=21.74 Aligned_cols=30 Identities=20% Similarity=0.105 Sum_probs=20.6
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
.-.+||..+|++...|++=...-|.+.++.
T Consensus 152 s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~ 181 (192)
T PRK09643 152 SVADAARMLGVAEGTVKSRCARGRARLAEL 181 (192)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 356789999999998877554444444443
No 153
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=28.47 E-value=91 Score=24.30 Aligned_cols=29 Identities=21% Similarity=0.220 Sum_probs=22.8
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
.-.++|..+|++...|+.++..-+.+.|.
T Consensus 219 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 219 TLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45788999999999999998765555543
No 154
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=28.21 E-value=36 Score=20.65 Aligned_cols=20 Identities=15% Similarity=0.212 Sum_probs=17.3
Q ss_pred HHHHHHhcCCCccchhhhhh
Q psy9529 43 REALALRLDLKESRVAVWFQ 62 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWFq 62 (149)
..++|+.+|++...++.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999974
No 155
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=27.76 E-value=1e+02 Score=22.82 Aligned_cols=31 Identities=16% Similarity=0.074 Sum_probs=24.4
Q ss_pred HHHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 41 FMREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 41 ~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
..-.++|..+|++...|++.+..-|.+.++.
T Consensus 171 ~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 171 KSYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3457789999999999999887766666653
No 156
>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=27.69 E-value=1.1e+02 Score=20.71 Aligned_cols=33 Identities=27% Similarity=0.586 Sum_probs=17.9
Q ss_pred HHHHHHHhhCCCCCHH-HHHHHHHhcCCCccchhhhhhhhhhhHHHhhh
Q psy9529 26 EELERAFLASHYPDVF-MREALALRLDLKESRVAVWFQNRRAKWRKKEH 73 (149)
Q Consensus 26 ~~Le~~F~~~~~p~~~-~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~ 73 (149)
.+.+-.|+.|+||... ++.. =.|||.+|++...
T Consensus 15 RiIk~LyqsnPyP~~~GTr~a---------------RRnRRRRWR~rq~ 48 (91)
T PF00424_consen 15 RIIKILYQSNPYPSPEGTRQA---------------RRNRRRRWRARQR 48 (91)
T ss_dssp HHHHHHHHTS-S--S-S-HHH---------------HHHHHHHHHHHHH
T ss_pred HHHHHHHccccCCCCCCcccc---------------ccchhhhHHHHHH
Confidence 3455568889999744 2211 1488999987653
No 157
>PF13565 HTH_32: Homeodomain-like domain
Probab=27.34 E-value=1.6e+02 Score=18.15 Aligned_cols=33 Identities=9% Similarity=-0.136 Sum_probs=24.1
Q ss_pred CHHHHHHHHHHHhhCCCCCHHHHH-HHHHhcCCC
Q psy9529 21 NSWQLEELERAFLASHYPDVFMRE-ALALRLDLK 53 (149)
Q Consensus 21 t~~ql~~Le~~F~~~~~p~~~~r~-~LA~~lgl~ 53 (149)
+.++...+...+..++..+..... .|...+|+.
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~ 65 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGIS 65 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCC
Confidence 678878899999888766666555 467776653
No 158
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=27.30 E-value=87 Score=21.79 Aligned_cols=39 Identities=21% Similarity=0.316 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhh
Q psy9529 20 FNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRR 65 (149)
Q Consensus 20 ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRR 65 (149)
+++..+..+...+... ....|.-||++...|+.|=|+|+
T Consensus 44 ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~ 82 (104)
T COG2944 44 LSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRK 82 (104)
T ss_pred CCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCc
Confidence 6777777777766655 45678999999999999988764
No 159
>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=27.27 E-value=1.2e+02 Score=16.92 Aligned_cols=36 Identities=17% Similarity=0.100 Sum_probs=25.0
Q ss_pred CHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhh
Q psy9529 21 NSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQ 62 (149)
Q Consensus 21 t~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFq 62 (149)
+..+..++...+ .. ....++|..++++...|..|..
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHH
Confidence 445556665433 22 2467789999999999999975
No 160
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=27.17 E-value=1e+02 Score=24.16 Aligned_cols=30 Identities=17% Similarity=0.213 Sum_probs=23.6
Q ss_pred HHHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 41 FMREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 41 ~~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
....++|..+|++...|+.+..--+.+.|.
T Consensus 220 ~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~ 249 (256)
T PRK07408 220 LTQKEAAERLGISPVTVSRRVKKGLDQLKK 249 (256)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 356789999999999999998755555554
No 161
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=27.08 E-value=1.2e+02 Score=23.04 Aligned_cols=29 Identities=21% Similarity=0.295 Sum_probs=23.6
Q ss_pred HHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 43 REALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
..++|..+|++...|++....-|.+.|+.
T Consensus 167 ~~EIAe~lgis~~tV~~~l~RAr~~Lr~~ 195 (206)
T PRK12544 167 TNEICHAVDLSVSNLNVLLYRARLRLREC 195 (206)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 57889999999999999987666666654
No 162
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=27.07 E-value=91 Score=22.72 Aligned_cols=29 Identities=14% Similarity=0.168 Sum_probs=22.2
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
...++|..+|++...|+.+..--|.+.+.
T Consensus 145 s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 145 SIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35788999999999999988755555443
No 163
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=26.57 E-value=1.4e+02 Score=21.70 Aligned_cols=28 Identities=32% Similarity=0.400 Sum_probs=20.6
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWR 69 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~r 69 (149)
.-.++|..+|++...|++....-|.+.|
T Consensus 155 s~~eIA~~lgis~~~v~~~l~Rar~~Lr 182 (187)
T PRK12534 155 TYEELAARTDTPIGTVKSWIRRGLAKLK 182 (187)
T ss_pred CHHHHHHHhCCChhHHHHHHHHHHHHHH
Confidence 4577899999999998887654444443
No 164
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=26.46 E-value=1e+02 Score=23.14 Aligned_cols=36 Identities=22% Similarity=0.025 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccch
Q psy9529 22 SWQLEELERAFLASHYPDVFMREALALRLDLKESRV 57 (149)
Q Consensus 22 ~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V 57 (149)
..-+..|...+....|.+......+|..||++...|
T Consensus 25 sAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v 60 (160)
T COG1905 25 SALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARV 60 (160)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHh
Confidence 456788888899888999999999999999987543
No 165
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=26.10 E-value=1.2e+02 Score=22.32 Aligned_cols=32 Identities=13% Similarity=-0.061 Sum_probs=24.5
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHhhh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKKEH 73 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~ 73 (149)
.-.++|..+|++...|++....-|.+.++.-.
T Consensus 129 s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 129 SYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45788999999999999998766666555433
No 166
>PF13730 HTH_36: Helix-turn-helix domain
Probab=26.03 E-value=51 Score=19.14 Aligned_cols=42 Identities=12% Similarity=-0.129 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHHhh---CCCCCHHHHHHHHHhcCCCccchhhhhh
Q psy9529 20 FNSWQLEELERAFLA---SHYPDVFMREALALRLDLKESRVAVWFQ 62 (149)
Q Consensus 20 ft~~ql~~Le~~F~~---~~~p~~~~r~~LA~~lgl~~~~V~vWFq 62 (149)
+++....++-..+.. +.. ..+....||..+|++.+.|+.+..
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~-~~pS~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGG-CFPSQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCC-CCcCHHHHHHHHCcCHHHHHHHHH
Confidence 455555555444332 222 333577899999999999888764
No 167
>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=26.00 E-value=1e+02 Score=24.47 Aligned_cols=28 Identities=14% Similarity=0.096 Sum_probs=22.4
Q ss_pred HHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 43 REALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
-.++|..+|+++..|+..+..-|.+.+.
T Consensus 127 ~~EIA~~lg~s~~tVr~~l~RAr~~Lr~ 154 (281)
T TIGR02957 127 YEEIASIVGKSEANCRQLVSRARRHLDA 154 (281)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4678999999999999999766665553
No 168
>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=25.74 E-value=45 Score=18.06 Aligned_cols=22 Identities=23% Similarity=0.306 Sum_probs=18.5
Q ss_pred HHHHHHhcCCCccchhhhhhhh
Q psy9529 43 REALALRLDLKESRVAVWFQNR 64 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWFqNR 64 (149)
...+|..+|++...|..|..+.
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCC
Confidence 4578999999999999998765
No 169
>KOG0773|consensus
Probab=25.67 E-value=75 Score=26.08 Aligned_cols=39 Identities=28% Similarity=0.519 Sum_probs=33.8
Q ss_pred hhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 33 LASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 33 ~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
..++||+......++....++..+|.+||-|-|.+.+..
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~ 155 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKE 155 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhc
Confidence 458899999999999999999999999999988776653
No 170
>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=25.52 E-value=73 Score=18.46 Aligned_cols=34 Identities=12% Similarity=0.039 Sum_probs=21.4
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhh
Q psy9529 25 LEELERAFLASHYPDVFMREALALRLDLKESRVAVWF 61 (149)
Q Consensus 25 l~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWF 61 (149)
..+|...+....+ -...+||..++++.+.|..-.
T Consensus 3 ~~il~~L~~~~~~---it~~eLa~~l~vS~rTi~~~i 36 (55)
T PF08279_consen 3 KQILKLLLESKEP---ITAKELAEELGVSRRTIRRDI 36 (55)
T ss_dssp HHHHHHHHHTTTS---BEHHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHcCCC---cCHHHHHHHhCCCHHHHHHHH
Confidence 3455554455443 346789999999998776544
No 171
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=25.51 E-value=77 Score=22.55 Aligned_cols=44 Identities=18% Similarity=0.111 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhH
Q psy9529 19 NFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKW 68 (149)
Q Consensus 19 ~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~ 68 (149)
.+|+.+..+|...+.. + ...+||..++++.+.|++..++=+.|.
T Consensus 137 ~Lt~~E~~il~~l~~g--~----~~~~Ia~~l~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 137 PLTKRERQVAEKLAQG--M----AVKEIAAELGLSPKTVHVHRANLMEKL 180 (196)
T ss_pred CCCHHHHHHHHHHHCC--C----CHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 5788888888776643 2 577889999999999999887766553
No 172
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=25.40 E-value=1.2e+02 Score=22.41 Aligned_cols=28 Identities=32% Similarity=0.329 Sum_probs=22.1
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWR 69 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~r 69 (149)
..+++|..+|+++..|+..+..=|.+.+
T Consensus 153 s~~EIA~~lgiS~~tV~r~l~~aR~~l~ 180 (185)
T PF07638_consen 153 SVEEIAERLGISERTVRRRLRRARAWLR 180 (185)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4578899999999999988876665444
No 173
>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=25.27 E-value=1.1e+02 Score=21.17 Aligned_cols=38 Identities=11% Similarity=0.129 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhh
Q psy9529 20 FNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQ 62 (149)
Q Consensus 20 ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFq 62 (149)
++-+.....-.++.... ...++|..++++...|..||+
T Consensus 3 YS~DlR~rVl~~~~~g~-----s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 3 YSLDLRQRVLAYIEKGK-----SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred CCHHHHHHHHHHHHccc-----hHHHHHHHhCcHHHHHHHHHH
Confidence 34444444555666543 456789999999999999997
No 174
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=25.24 E-value=1.1e+02 Score=21.46 Aligned_cols=44 Identities=16% Similarity=0.124 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhH
Q psy9529 19 NFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKW 68 (149)
Q Consensus 19 ~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~ 68 (149)
.+|+.+..+|.. +..+ + ...++|..+++++..|+.+.+|=+.|.
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl 192 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKL 192 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 488888888876 4333 2 257889999999999999988755543
No 175
>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=25.16 E-value=54 Score=22.96 Aligned_cols=33 Identities=21% Similarity=0.199 Sum_probs=24.5
Q ss_pred CCHHHHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 38 PDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 38 p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
.......++|..+|+++..|+++..--|.+.++
T Consensus 119 ~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 119 FKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344456789999999999999988755555443
No 176
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=25.12 E-value=1.2e+02 Score=23.83 Aligned_cols=47 Identities=15% Similarity=0.175 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 20 FNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 20 ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
+++.+..++...|... ....++|..+|++...|+.....-+.+.|+.
T Consensus 213 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 213 LPEREKKVLILYYYED-----LTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3444444444444322 2467889999999999998887666665554
No 177
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=24.88 E-value=1.5e+02 Score=19.38 Aligned_cols=44 Identities=11% Similarity=0.103 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHhh-----CCCCCHHHHHHHHHhcCCCccchhhhhh
Q psy9529 19 NFNSWQLEELERAFLA-----SHYPDVFMREALALRLDLKESRVAVWFQ 62 (149)
Q Consensus 19 ~ft~~ql~~Le~~F~~-----~~~p~~~~r~~LA~~lgl~~~~V~vWFq 62 (149)
-++.+++..+...|.. +.+.+..+...+-..+|++...|.-+|.
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 3678899999999864 2367777777766678888877777774
No 178
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=24.23 E-value=1.1e+02 Score=25.22 Aligned_cols=53 Identities=23% Similarity=0.114 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhh
Q psy9529 19 NFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKE 72 (149)
Q Consensus 19 ~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~ 72 (149)
.+++.+..+|...|... |.......+||..+|++...|+.+...-+.+.|+.-
T Consensus 262 ~L~~~~R~vl~lrygL~-~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLL-GYEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 35566666666665332 223345688999999999999999887777766543
No 179
>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 This entry is represented by Bacteriophage r1t, Orf18. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.
Probab=24.15 E-value=35 Score=25.88 Aligned_cols=30 Identities=30% Similarity=0.488 Sum_probs=26.3
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
+..+|+..++++..+|-+|..|-+...+..
T Consensus 16 t~~e~~~~~~VS~~sv~~WiKNG~~~~~a~ 45 (186)
T PF04936_consen 16 TIDELADYFDVSRTSVSVWIKNGKDPKRAK 45 (186)
T ss_pred cHHHHHHHHccCHHHHHHHHHcCCCccccc
Confidence 578899999999999999999998876654
No 180
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=23.98 E-value=1.2e+02 Score=24.10 Aligned_cols=46 Identities=15% Similarity=0.227 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 20 FNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 20 ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
+++.+..+|...|.. .....++|..+|++...|+.+...-+.+.|.
T Consensus 216 L~~rer~vl~l~y~~-----~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 216 LPERERTVLVLRFFE-----SMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred CCHHHHHHHHHHhcC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 344444455554432 2346789999999999999988655555443
No 181
>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=23.50 E-value=1.4e+02 Score=22.78 Aligned_cols=38 Identities=8% Similarity=0.108 Sum_probs=25.9
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhh
Q psy9529 20 FNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQ 62 (149)
Q Consensus 20 ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFq 62 (149)
+++.+..++...|..+ ....++|..+|++...|..+-.
T Consensus 184 L~~~e~~i~~~~~~~~-----~t~~eIA~~lgis~~~V~~~~~ 221 (231)
T TIGR02885 184 LDERERQIIMLRYFKD-----KTQTEVANMLGISQVQVSRLEK 221 (231)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHH
Confidence 4555555555554322 3578899999999998887754
No 182
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=23.21 E-value=63 Score=22.57 Aligned_cols=25 Identities=12% Similarity=0.130 Sum_probs=21.0
Q ss_pred CHHHHHHHHHhcCCCccchhhhhhh
Q psy9529 39 DVFMREALALRLDLKESRVAVWFQN 63 (149)
Q Consensus 39 ~~~~r~~LA~~lgl~~~~V~vWFqN 63 (149)
.......||..+|+++..+..+|+.
T Consensus 24 ~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 24 SPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3456788999999999999999964
No 183
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=23.11 E-value=49 Score=20.05 Aligned_cols=19 Identities=5% Similarity=-0.076 Sum_probs=16.5
Q ss_pred HHHHHHhcCCCccchhhhh
Q psy9529 43 REALALRLDLKESRVAVWF 61 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWF 61 (149)
..++|+.+|++...|+.|-
T Consensus 3 ~~eva~~~gvs~~tlr~~~ 21 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYE 21 (70)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 3568999999999999995
No 184
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=22.88 E-value=88 Score=22.93 Aligned_cols=15 Identities=27% Similarity=0.381 Sum_probs=8.7
Q ss_pred CCHHHHHHHHHHHhh
Q psy9529 20 FNSWQLEELERAFLA 34 (149)
Q Consensus 20 ft~~ql~~Le~~F~~ 34 (149)
+|.+|+..|..+...
T Consensus 52 Lt~~qi~~l~~~i~~ 66 (144)
T TIGR03629 52 LDDEEIEKLEEAVEN 66 (144)
T ss_pred CCHHHHHHHHHHHHh
Confidence 566666666555543
No 185
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=22.83 E-value=1.7e+02 Score=20.63 Aligned_cols=29 Identities=21% Similarity=0.177 Sum_probs=21.8
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
...++|..+|++...|++....-+.+.+.
T Consensus 123 s~~eIA~~lgis~~tv~~~l~ra~~~Lr~ 151 (159)
T PRK12527 123 SHQQIAEHLGISRSLVEKHIVNAMKHCRV 151 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 35778999999999999887655555444
No 186
>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=22.71 E-value=53 Score=20.42 Aligned_cols=23 Identities=30% Similarity=0.323 Sum_probs=19.4
Q ss_pred HHHHHHhcCCCccchhhhhhhhh
Q psy9529 43 REALALRLDLKESRVAVWFQNRR 65 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWFqNRR 65 (149)
...||..+|++...|..|+.+++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 56899999999999999986543
No 187
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=22.62 E-value=1.3e+02 Score=23.93 Aligned_cols=28 Identities=14% Similarity=0.071 Sum_probs=22.2
Q ss_pred HHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 43 REALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
-.++|..+|+++..|+...+.-|.+.+.
T Consensus 134 ~~EIA~~lg~s~~tVk~~l~RAr~~Lr~ 161 (293)
T PRK09636 134 FDEIASTLGRSPAACRQLASRARKHVRA 161 (293)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4678999999999999998755555554
No 188
>PHA02955 hypothetical protein; Provisional
Probab=22.56 E-value=1.1e+02 Score=23.98 Aligned_cols=43 Identities=7% Similarity=-0.002 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHhhC-CCCCHHHHHHHHHhcCCCccchhhhhhhh
Q psy9529 22 SWQLEELERAFLAS-HYPDVFMREALALRLDLKESRVAVWFQNR 64 (149)
Q Consensus 22 ~~ql~~Le~~F~~~-~~p~~~~r~~LA~~lgl~~~~V~vWFqNR 64 (149)
..++..|-+.|... .-.+..++..++..+|+....|..||.+.
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~ 103 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTD 103 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccch
Confidence 35666777777654 45677889999999999988788999764
No 189
>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=22.37 E-value=1.6e+02 Score=21.25 Aligned_cols=29 Identities=24% Similarity=0.295 Sum_probs=21.1
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
.-.++|..+|++...|++=...-|.+.|+
T Consensus 158 s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 158 SFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45778999999999888866555555443
No 190
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=22.23 E-value=1.5e+02 Score=23.23 Aligned_cols=45 Identities=11% Similarity=0.105 Sum_probs=30.7
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhH
Q psy9529 19 NFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKW 68 (149)
Q Consensus 19 ~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~ 68 (149)
.+++.+..++...|..+ ....++|..+|++...|...-.+-..+.
T Consensus 209 ~L~~~er~vi~~~~~~~-----~t~~eIA~~lgis~~~V~~~~~~al~kL 253 (258)
T PRK08215 209 KLNDREKLILNLRFFQG-----KTQMEVAEEIGISQAQVSRLEKAALKHM 253 (258)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 46666667777766332 2467899999999999887765444443
No 191
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=22.17 E-value=90 Score=23.96 Aligned_cols=36 Identities=22% Similarity=0.180 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHhcCCCccchhhhhhhhhhhHHHhhh
Q psy9529 38 PDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEH 73 (149)
Q Consensus 38 p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk~~~ 73 (149)
.......++|..+|++...|++....-|.+.|+.-.
T Consensus 163 ~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~ 198 (231)
T PRK11922 163 VEELSVEETAQALGLPEETVKTRLHRARRLLRESLA 198 (231)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 334456789999999999999988777777776544
No 192
>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
Probab=21.54 E-value=1.9e+02 Score=17.91 Aligned_cols=24 Identities=33% Similarity=0.494 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHhhCCCccchHHH
Q psy9529 111 KLMKSLERQQRKLAAKGVTVDLETL 135 (149)
Q Consensus 111 ~~~~a~e~~~~~l~~~~~~~~~~~l 135 (149)
++.+.|+ ........|.+||++.|
T Consensus 32 R~~K~~~-~~I~~~~aG~pVd~~~l 55 (59)
T smart00685 32 RIAKQFD-DAIKAARAGRPVDLSEL 55 (59)
T ss_pred HHHhhHH-HHHHHHHCCCCCChhcC
Confidence 5666666 45566788999999865
No 193
>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=21.52 E-value=61 Score=17.76 Aligned_cols=22 Identities=18% Similarity=0.098 Sum_probs=17.8
Q ss_pred HHHHHHhcCCCccchhhhhhhh
Q psy9529 43 REALALRLDLKESRVAVWFQNR 64 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWFqNR 64 (149)
..++|..+|++...|..|..+.
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcC
Confidence 4577899999999999997543
No 194
>KOG3755|consensus
Probab=21.45 E-value=70 Score=29.18 Aligned_cols=58 Identities=28% Similarity=0.395 Sum_probs=48.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhCC-CCCHHH---HHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 13 RRRSRTNFNSWQLEELERAFLASH-YPDVFM---REALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 13 ~rr~Rt~ft~~ql~~Le~~F~~~~-~p~~~~---r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
..+.|+.+..+-+.+|..+..... ||+... ..-|...++++.+.+-..|+|.|...+.
T Consensus 647 ~p~~~~~isge~~~~~qs~i~~~gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~~ 708 (769)
T KOG3755|consen 647 KPRKRTKISGEALGILQSFITDVGLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVKH 708 (769)
T ss_pred CccccceecccchHHHHHHHHHhccCchhhcccccchhhhhhcccHHHHHHhhhcceeecch
Confidence 467789999999999988876544 888887 7889999999999999999999876553
No 195
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=21.34 E-value=1.5e+02 Score=21.89 Aligned_cols=36 Identities=19% Similarity=0.004 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchh
Q psy9529 23 WQLEELERAFLASHYPDVFMREALALRLDLKESRVA 58 (149)
Q Consensus 23 ~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~ 58 (149)
.-+.+|...=....|.+......+|..+|++...|.
T Consensus 24 ~li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~ 59 (156)
T PRK05988 24 ALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVH 59 (156)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHH
Confidence 345556555556679999999999999999986543
No 196
>KOG3623|consensus
Probab=21.33 E-value=76 Score=29.72 Aligned_cols=58 Identities=19% Similarity=0.198 Sum_probs=38.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 13 RRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 13 ~rr~Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
.-+-++.+..++-..|..++..+-.++-.+-..++..+...+.+|.|||++|+...+.
T Consensus 626 p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp 683 (1007)
T KOG3623|consen 626 PVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSP 683 (1007)
T ss_pred CccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCC
Confidence 3445566666666777777766555554444444555777788899999998876554
No 197
>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=21.26 E-value=1.4e+02 Score=23.09 Aligned_cols=50 Identities=10% Similarity=0.050 Sum_probs=34.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 20 FNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 20 ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
+++.+..+|...|....+ ......++|..+|++...|+.+...-..|.|.
T Consensus 177 L~~~er~vl~l~ygl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~ 226 (238)
T TIGR02393 177 LTERERKVLRMRYGLLDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRH 226 (238)
T ss_pred CCHHHHHHHHHHhCCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 455666667666643222 22357789999999999999998766666554
No 198
>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=21.24 E-value=70 Score=23.44 Aligned_cols=31 Identities=16% Similarity=0.068 Sum_probs=23.2
Q ss_pred HHHHHHHHHhcCCCccchhhhhhhhhhhHHH
Q psy9529 40 VFMREALALRLDLKESRVAVWFQNRRAKWRK 70 (149)
Q Consensus 40 ~~~r~~LA~~lgl~~~~V~vWFqNRRak~rk 70 (149)
.....++|..+|++...|.+++.--|.+.++
T Consensus 165 ~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 165 GKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3345788999999999999988755555443
No 199
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=21.04 E-value=74 Score=23.38 Aligned_cols=30 Identities=17% Similarity=0.158 Sum_probs=24.2
Q ss_pred HHHHHHHhcCCCccchhhhhhhhhhhHHHh
Q psy9529 42 MREALALRLDLKESRVAVWFQNRRAKWRKK 71 (149)
Q Consensus 42 ~r~~LA~~lgl~~~~V~vWFqNRRak~rk~ 71 (149)
...++|..+|++...|+++...-+.+.|..
T Consensus 152 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 152 EFQEIADIMHMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999987666665553
No 200
>PHA01976 helix-turn-helix protein
Probab=20.72 E-value=63 Score=19.49 Aligned_cols=22 Identities=14% Similarity=0.194 Sum_probs=18.6
Q ss_pred HHHHHHhcCCCccchhhhhhhh
Q psy9529 43 REALALRLDLKESRVAVWFQNR 64 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWFqNR 64 (149)
..+||..+|++...|..|....
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~ 39 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADK 39 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCC
Confidence 5679999999999999997554
No 201
>PRK05572 sporulation sigma factor SigF; Validated
Probab=20.52 E-value=1.7e+02 Score=22.79 Aligned_cols=46 Identities=9% Similarity=0.099 Sum_probs=30.7
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHH
Q psy9529 19 NFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWR 69 (149)
Q Consensus 19 ~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~r 69 (149)
.+++.+..++...|..+ ....++|..+|++...|..+-..-..+.+
T Consensus 202 ~L~~~~~~v~~l~~~~~-----~s~~eIA~~lgis~~~V~~~~~ral~kLr 247 (252)
T PRK05572 202 ELDERERLIVYLRYFKD-----KTQSEVAKRLGISQVQVSRLEKKILKQMK 247 (252)
T ss_pred cCCHHHHHHHHHHHhCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 35566666666665332 35678999999999999887654444433
No 202
>PRK06424 transcription factor; Provisional
Probab=20.46 E-value=77 Score=23.19 Aligned_cols=24 Identities=13% Similarity=0.063 Sum_probs=20.2
Q ss_pred HHHHHHhcCCCccchhhhhhhhhh
Q psy9529 43 REALALRLDLKESRVAVWFQNRRA 66 (149)
Q Consensus 43 r~~LA~~lgl~~~~V~vWFqNRRa 66 (149)
..+||..+|++...|.-|..+.+.
T Consensus 100 Q~eLA~~iGvs~stIskiE~G~~~ 123 (144)
T PRK06424 100 QADLAAKIFERKNVIASIERGDLL 123 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 568999999999999999876553
No 203
>TIGR02548 casB_cse2 CRISPR system CASCADE complex protein CasB/Cse2. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family is found in Ecoli subtype CRISPR/Cas regions of many bacteria, most of which are mesophiles, and not in Archaea. It was designated Cse2 originally, and renamed CasB based on its characterization in the CASCADE complex.
Probab=20.43 E-value=1.9e+02 Score=20.92 Aligned_cols=31 Identities=26% Similarity=0.410 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHhhCCCccchHHHHHHHH
Q psy9529 110 KKLMKSLERQQRKLAAKGVTVDLETLKREWE 140 (149)
Q Consensus 110 ~~~~~a~e~~~~~l~~~~~~~~~~~l~~~~~ 140 (149)
..+...+-+--..|.+.+++||+..|..+..
T Consensus 109 ~~l~~~Lrrlv~ll~~~~~~vd~~~La~dL~ 139 (159)
T TIGR02548 109 DELLRRLRRLVSLLKSLAISVDYAQLARDLL 139 (159)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Confidence 3688888889999999999999999988754
No 204
>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=20.35 E-value=1.6e+02 Score=23.39 Aligned_cols=47 Identities=17% Similarity=0.017 Sum_probs=36.4
Q ss_pred CCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhcCCCccchhhhhhhhhhhHH
Q psy9529 17 RTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWR 69 (149)
Q Consensus 17 Rt~ft~~ql~~Le~~F~~~~~p~~~~r~~LA~~lgl~~~~V~vWFqNRRak~r 69 (149)
...+|+.+.++|.-...- ..-.++|..||+++..|+.+..|=+.|..
T Consensus 188 ~~~LT~RE~evl~l~a~G------~s~~eIA~~L~IS~~TVk~hl~~i~~KL~ 234 (247)
T TIGR03020 188 AGLITAREAEILAWVRDG------KTNEEIAAILGISSLTVKNHLQHIFKKLD 234 (247)
T ss_pred ccCCCHHHHHHHHHHHCC------CCHHHHHHHHCcCHHHHHHHHHHHHHHhC
Confidence 446899999999865422 24677899999999999999987766644
Done!