Query psy526
Match_columns 274
No_of_seqs 304 out of 1515
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 21:50:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy526.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/526hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3802|consensus 100.0 3.2E-30 6.9E-35 241.3 1.7 108 12-119 234-353 (398)
2 KOG0842|consensus 99.8 6.5E-21 1.4E-25 175.4 10.0 96 57-152 150-245 (307)
3 KOG0484|consensus 99.8 4.7E-20 1E-24 143.7 7.4 69 56-124 13-81 (125)
4 KOG0486|consensus 99.8 3.3E-19 7.2E-24 162.5 11.9 66 58-123 110-175 (351)
5 KOG2251|consensus 99.8 3.6E-19 7.8E-24 155.6 7.9 68 55-122 32-99 (228)
6 KOG1168|consensus 99.8 3E-20 6.6E-25 167.6 0.7 103 18-120 254-369 (385)
7 KOG0489|consensus 99.8 2.2E-19 4.7E-24 163.7 4.9 66 57-122 156-221 (261)
8 KOG0488|consensus 99.8 1E-18 2.2E-23 162.6 7.0 69 56-124 168-236 (309)
9 KOG0843|consensus 99.7 7.8E-18 1.7E-22 143.0 5.8 64 59-122 101-164 (197)
10 KOG0494|consensus 99.7 9.4E-18 2E-22 149.5 6.4 64 59-122 140-203 (332)
11 KOG0487|consensus 99.7 5.1E-18 1.1E-22 156.4 4.7 65 58-122 233-297 (308)
12 KOG0850|consensus 99.7 2.1E-16 4.5E-21 139.0 13.3 67 55-121 117-183 (245)
13 PF00046 Homeobox: Homeobox do 99.7 3.1E-17 6.6E-22 115.5 6.2 57 61-117 1-57 (57)
14 KOG0485|consensus 99.7 6E-17 1.3E-21 141.2 8.6 68 57-124 101-168 (268)
15 TIGR01565 homeo_ZF_HD homeobox 99.6 1.4E-16 3E-21 113.2 4.8 54 60-113 1-58 (58)
16 KOG0492|consensus 99.6 1.7E-16 3.6E-21 137.6 6.3 65 60-124 144-208 (246)
17 KOG0848|consensus 99.6 4.9E-16 1.1E-20 139.1 4.5 63 60-122 199-261 (317)
18 KOG4577|consensus 99.6 1.5E-14 3.2E-19 130.9 12.8 65 58-122 165-229 (383)
19 cd00086 homeodomain Homeodomai 99.6 5.7E-15 1.2E-19 103.8 6.1 57 61-117 1-57 (59)
20 smart00389 HOX Homeodomain. DN 99.6 4.2E-15 9E-20 103.8 5.2 56 61-116 1-56 (56)
21 KOG0491|consensus 99.6 1.8E-15 4E-20 126.9 3.4 64 59-122 99-162 (194)
22 KOG0493|consensus 99.6 4.9E-15 1.1E-19 132.4 6.1 58 61-118 247-304 (342)
23 KOG0844|consensus 99.5 2.9E-15 6.3E-20 136.3 2.8 63 59-121 180-242 (408)
24 COG5576 Homeodomain-containing 99.5 7.2E-14 1.6E-18 118.2 5.7 64 58-121 49-112 (156)
25 KOG0483|consensus 99.4 5.3E-14 1.2E-18 123.0 4.3 61 62-122 52-112 (198)
26 KOG0847|consensus 99.3 6.8E-13 1.5E-17 116.2 3.8 64 58-121 165-228 (288)
27 KOG0490|consensus 99.3 1E-12 2.2E-17 116.2 3.5 64 57-120 57-120 (235)
28 KOG0849|consensus 99.2 5.1E-11 1.1E-15 113.2 10.8 67 55-121 171-237 (354)
29 KOG0775|consensus 99.1 4.7E-10 1E-14 101.3 8.8 51 67-117 183-233 (304)
30 KOG0774|consensus 98.8 1.6E-08 3.4E-13 91.0 8.7 63 60-122 188-253 (334)
31 KOG2252|consensus 98.5 1.9E-07 4.1E-12 91.7 5.3 58 58-115 418-475 (558)
32 PF05920 Homeobox_KN: Homeobox 98.5 1.2E-07 2.5E-12 62.6 2.6 34 81-114 7-40 (40)
33 KOG0490|consensus 98.4 2.7E-07 5.8E-12 81.5 4.4 66 55-120 148-213 (235)
34 KOG1146|consensus 98.1 3.8E-06 8.2E-11 89.4 5.8 63 58-120 901-963 (1406)
35 PF11569 Homez: Homeodomain le 97.0 0.00067 1.5E-08 47.8 2.8 43 72-114 10-52 (56)
36 KOG0773|consensus 96.5 0.0019 4.1E-08 61.0 3.3 60 59-118 238-300 (342)
37 PF00157 Pou: Pou domain - N-t 96.5 0.00019 4E-09 53.6 -2.9 27 11-37 34-60 (75)
38 KOG3623|consensus 96.4 0.0034 7.4E-08 64.1 4.3 48 72-119 568-615 (1007)
39 PF04218 CENP-B_N: CENP-B N-te 95.3 0.038 8.3E-07 38.3 4.6 46 61-111 1-46 (53)
40 PF04545 Sigma70_r4: Sigma-70, 87.6 1.3 2.9E-05 29.6 4.5 46 66-116 4-49 (50)
41 smart00352 POU Found in Pit-Oc 86.8 0.074 1.6E-06 39.7 -2.3 25 14-38 37-61 (75)
42 cd06171 Sigma70_r4 Sigma70, re 80.2 2.1 4.5E-05 27.6 2.9 44 66-114 10-53 (55)
43 PRK03975 tfx putative transcri 77.0 7.2 0.00016 32.6 5.8 53 64-122 4-56 (141)
44 PF01527 HTH_Tnp_1: Transposas 73.2 3.1 6.7E-05 29.9 2.4 44 62-109 2-45 (76)
45 KOG1146|consensus 71.3 6 0.00013 43.8 4.9 63 57-119 702-764 (1406)
46 PF08281 Sigma70_r4_2: Sigma-7 70.9 10 0.00022 25.4 4.5 43 67-114 11-53 (54)
47 PF00196 GerE: Bacterial regul 69.3 7.8 0.00017 26.6 3.7 45 66-116 3-47 (58)
48 PRK04217 hypothetical protein; 68.1 12 0.00026 29.9 4.9 49 66-119 42-90 (110)
49 cd00569 HTH_Hin_like Helix-tur 68.0 12 0.00026 21.3 3.9 37 67-108 6-42 (42)
50 PRK09646 RNA polymerase sigma 67.1 10 0.00022 32.4 4.7 48 66-118 142-189 (194)
51 PF04967 HTH_10: HTH DNA bindi 63.1 17 0.00036 25.3 4.2 41 67-107 1-43 (53)
52 PRK11924 RNA polymerase sigma 62.9 19 0.00041 29.5 5.4 33 88-120 142-174 (179)
53 KOG3755|consensus 61.1 2.9 6.3E-05 42.6 0.2 53 67-119 699-758 (769)
54 PRK06759 RNA polymerase factor 59.8 20 0.00043 29.0 4.9 47 66-117 106-152 (154)
55 TIGR02937 sigma70-ECF RNA poly 59.6 17 0.00038 28.3 4.5 47 66-117 110-156 (158)
56 PF10668 Phage_terminase: Phag 59.2 5.4 0.00012 28.6 1.2 20 89-108 24-43 (60)
57 PRK09652 RNA polymerase sigma 58.6 26 0.00056 28.8 5.5 49 66-119 128-176 (182)
58 PF00424 REV: REV protein (ant 58.3 20 0.00044 27.8 4.3 38 72-123 14-51 (91)
59 PRK12526 RNA polymerase sigma 57.2 21 0.00046 30.8 4.9 48 67-119 154-201 (206)
60 PRK12519 RNA polymerase sigma 56.9 22 0.00047 30.1 4.9 34 86-119 156-189 (194)
61 smart00421 HTH_LUXR helix_turn 56.7 22 0.00048 23.1 4.0 43 66-114 3-45 (58)
62 PRK00118 putative DNA-binding 55.9 34 0.00073 27.1 5.4 48 67-119 18-65 (104)
63 PRK12514 RNA polymerase sigma 55.7 17 0.00036 30.4 3.9 47 67-118 130-176 (179)
64 PRK09644 RNA polymerase sigma 54.2 32 0.00068 28.3 5.4 33 88-120 125-157 (165)
65 PRK09648 RNA polymerase sigma 54.2 22 0.00049 29.9 4.5 48 66-118 139-186 (189)
66 PRK12515 RNA polymerase sigma 53.8 33 0.00072 28.9 5.5 50 66-120 131-180 (189)
67 PRK09642 RNA polymerase sigma 53.4 32 0.0007 28.0 5.3 31 89-119 124-154 (160)
68 PF13936 HTH_38: Helix-turn-he 52.9 14 0.00031 24.2 2.4 40 65-109 3-42 (44)
69 TIGR02939 RpoE_Sigma70 RNA pol 52.6 21 0.00046 29.8 4.1 35 85-119 152-186 (190)
70 PRK12512 RNA polymerase sigma 52.4 29 0.00063 29.0 4.9 47 67-118 132-178 (184)
71 TIGR02948 SigW_bacill RNA poly 52.3 20 0.00043 29.9 3.9 48 66-118 136-183 (187)
72 TIGR02985 Sig70_bacteroi1 RNA 52.2 20 0.00044 28.7 3.8 46 67-117 114-159 (161)
73 TIGR00721 tfx DNA-binding prot 52.1 46 0.001 27.6 5.9 48 64-117 4-51 (137)
74 PRK09639 RNA polymerase sigma 51.2 37 0.00081 27.7 5.3 48 67-120 113-160 (166)
75 TIGR03879 near_KaiC_dom probab 50.7 6.7 0.00015 29.2 0.6 36 77-112 22-57 (73)
76 KOG3623|consensus 50.5 10 0.00022 39.8 2.0 60 59-118 625-684 (1007)
77 PF13551 HTH_29: Winged helix- 50.1 39 0.00084 25.6 4.9 49 61-109 52-109 (112)
78 TIGR02999 Sig-70_X6 RNA polyme 49.9 34 0.00073 28.5 4.9 47 67-118 135-181 (183)
79 PRK06930 positive control sigm 49.6 41 0.00088 28.7 5.4 50 66-120 114-163 (170)
80 PRK10403 transcriptional regul 49.0 21 0.00046 29.3 3.5 46 65-116 152-197 (215)
81 PRK05602 RNA polymerase sigma 48.9 36 0.00079 28.5 5.0 32 88-119 145-176 (186)
82 TIGR02959 SigZ RNA polymerase 48.6 45 0.00097 27.7 5.4 49 66-119 100-148 (170)
83 PRK12530 RNA polymerase sigma 48.6 44 0.00095 28.3 5.5 49 67-120 135-183 (189)
84 TIGR02989 Sig-70_gvs1 RNA poly 48.5 32 0.00069 27.8 4.4 46 66-116 111-156 (159)
85 cd06170 LuxR_C_like C-terminal 48.4 36 0.00077 22.2 4.0 37 68-110 2-38 (57)
86 TIGR02947 SigH_actino RNA poly 48.1 29 0.00062 29.4 4.3 37 85-121 145-181 (193)
87 PRK12543 RNA polymerase sigma 48.1 52 0.0011 27.5 5.8 35 88-122 134-168 (179)
88 PRK12541 RNA polymerase sigma 48.0 30 0.00066 28.2 4.3 47 67-118 113-159 (161)
89 COG3413 Predicted DNA binding 47.5 34 0.00073 30.0 4.7 47 66-114 155-203 (215)
90 cd04761 HTH_MerR-SF Helix-Turn 46.9 13 0.00028 24.1 1.5 21 90-110 3-23 (49)
91 TIGR02943 Sig70_famx1 RNA poly 46.4 59 0.0013 27.6 5.9 51 67-122 132-182 (188)
92 PF09607 BrkDBD: Brinker DNA-b 45.9 39 0.00085 24.0 3.8 44 64-109 3-47 (58)
93 TIGR02983 SigE-fam_strep RNA p 45.7 33 0.00071 27.9 4.1 47 67-118 111-157 (162)
94 PRK12537 RNA polymerase sigma 45.5 46 0.00099 27.9 5.1 31 88-118 150-180 (182)
95 PRK15369 two component system 45.2 38 0.00083 27.4 4.5 45 66-116 149-193 (211)
96 PRK09047 RNA polymerase factor 45.1 57 0.0012 26.4 5.5 48 66-118 106-153 (161)
97 PF13443 HTH_26: Cro/C1-type H 44.9 21 0.00046 24.5 2.5 30 89-118 12-41 (63)
98 PRK06986 fliA flagellar biosyn 44.9 40 0.00086 29.8 4.8 47 67-118 185-231 (236)
99 PF06056 Terminase_5: Putative 44.6 14 0.00031 26.0 1.5 28 88-117 14-41 (58)
100 TIGR02479 FliA_WhiG RNA polyme 44.5 42 0.0009 29.3 4.8 47 66-117 175-221 (224)
101 TIGR02954 Sig70_famx3 RNA poly 43.4 42 0.00091 27.6 4.5 47 67-118 120-166 (169)
102 PRK12532 RNA polymerase sigma 43.2 57 0.0012 27.6 5.4 49 67-120 137-185 (195)
103 PRK12518 RNA polymerase sigma 43.2 25 0.00055 29.0 3.1 35 85-119 134-168 (175)
104 PRK11923 algU RNA polymerase s 43.2 28 0.00061 29.3 3.4 36 86-121 153-188 (193)
105 PRK10360 DNA-binding transcrip 42.7 32 0.00069 28.2 3.6 45 66-116 137-181 (196)
106 TIGR02952 Sig70_famx2 RNA poly 42.6 44 0.00095 27.3 4.4 46 67-117 123-168 (170)
107 PRK08295 RNA polymerase factor 42.3 60 0.0013 27.6 5.4 33 87-119 170-202 (208)
108 PRK10072 putative transcriptio 41.9 15 0.00032 28.7 1.3 40 67-113 33-72 (96)
109 PRK09637 RNA polymerase sigma 41.9 61 0.0013 27.3 5.3 33 87-119 122-154 (181)
110 PRK09413 IS2 repressor TnpA; R 41.9 42 0.00091 26.8 4.1 43 64-110 10-52 (121)
111 KOG0773|consensus 41.8 48 0.001 31.1 5.1 38 80-117 117-154 (342)
112 PRK12520 RNA polymerase sigma 41.8 88 0.0019 26.3 6.3 51 67-122 132-182 (191)
113 PRK12546 RNA polymerase sigma 41.8 46 0.001 28.4 4.6 33 88-120 130-162 (188)
114 PRK09480 slmA division inhibit 41.3 29 0.00062 28.9 3.2 42 71-113 15-56 (194)
115 PRK12524 RNA polymerase sigma 41.1 54 0.0012 27.9 4.9 48 67-119 137-184 (196)
116 PRK12547 RNA polymerase sigma 41.0 57 0.0012 26.8 4.9 47 67-118 113-159 (164)
117 PRK12536 RNA polymerase sigma 41.0 56 0.0012 27.3 4.9 32 87-118 145-176 (181)
118 PRK06288 RNA polymerase sigma 40.8 76 0.0017 28.6 6.1 51 66-121 212-262 (268)
119 PRK12538 RNA polymerase sigma 40.7 53 0.0012 29.2 5.0 33 88-120 188-220 (233)
120 PRK07037 extracytoplasmic-func 40.5 61 0.0013 26.3 5.0 47 67-118 110-156 (163)
121 PRK05657 RNA polymerase sigma 40.1 47 0.001 31.2 4.7 53 66-119 262-314 (325)
122 PRK06811 RNA polymerase factor 40.0 44 0.00095 28.3 4.1 47 67-118 132-178 (189)
123 PRK08583 RNA polymerase sigma 39.9 54 0.0012 29.3 4.9 48 66-118 205-252 (257)
124 TIGR02941 Sigma_B RNA polymera 39.7 51 0.0011 29.4 4.7 48 66-118 205-252 (255)
125 PRK09643 RNA polymerase sigma 39.1 85 0.0018 26.6 5.8 49 67-120 135-183 (192)
126 PRK13919 putative RNA polymera 38.9 65 0.0014 26.9 5.0 47 67-118 136-182 (186)
127 PRK12516 RNA polymerase sigma 38.9 73 0.0016 27.1 5.3 49 67-120 117-165 (187)
128 COG4367 Uncharacterized protei 38.8 37 0.0008 26.3 3.0 38 67-104 3-40 (97)
129 PRK09645 RNA polymerase sigma 38.5 68 0.0015 26.4 5.0 47 67-118 119-165 (173)
130 PRK09935 transcriptional regul 38.4 39 0.00084 27.8 3.5 45 65-115 148-192 (210)
131 PF13384 HTH_23: Homeodomain-l 38.4 20 0.00043 23.5 1.4 23 88-110 18-40 (50)
132 PF13518 HTH_28: Helix-turn-he 38.2 27 0.00059 22.8 2.1 24 89-112 14-37 (52)
133 PRK09640 RNA polymerase sigma 38.2 36 0.00079 28.7 3.3 35 86-120 149-183 (188)
134 TIGR03001 Sig-70_gmx1 RNA poly 38.1 80 0.0017 28.4 5.7 36 89-124 179-214 (244)
135 PRK12539 RNA polymerase sigma 37.8 64 0.0014 27.0 4.8 48 66-118 131-178 (184)
136 cd04762 HTH_MerR-trunc Helix-T 37.5 23 0.0005 22.3 1.6 23 90-112 3-25 (49)
137 PRK12529 RNA polymerase sigma 37.5 68 0.0015 26.8 4.9 47 66-117 127-173 (178)
138 PF13411 MerR_1: MerR HTH fami 37.4 21 0.00046 25.0 1.5 19 90-108 3-21 (69)
139 TIGR02859 spore_sigH RNA polym 37.2 66 0.0014 27.0 4.8 34 84-117 162-195 (198)
140 PRK12533 RNA polymerase sigma 36.9 73 0.0016 28.0 5.2 47 67-118 135-181 (216)
141 PRK09647 RNA polymerase sigma 36.8 85 0.0018 27.1 5.5 33 88-120 155-187 (203)
142 PRK12513 RNA polymerase sigma 36.8 37 0.0008 28.7 3.2 35 85-119 153-187 (194)
143 PRK08301 sporulation sigma fac 36.8 67 0.0015 28.2 4.9 52 66-118 178-229 (234)
144 PF08280 HTH_Mga: M protein tr 36.7 36 0.00079 23.6 2.6 37 70-110 6-42 (59)
145 PRK12531 RNA polymerase sigma 36.5 80 0.0017 26.7 5.3 47 67-118 142-188 (194)
146 PRK12545 RNA polymerase sigma 36.4 89 0.0019 26.8 5.5 31 89-119 157-187 (201)
147 PRK12511 RNA polymerase sigma 36.2 82 0.0018 26.6 5.3 50 66-120 111-160 (182)
148 PRK10651 transcriptional regul 36.0 58 0.0013 26.7 4.2 45 66-116 155-199 (216)
149 PRK12523 RNA polymerase sigma 35.9 77 0.0017 26.2 5.0 47 67-118 120-166 (172)
150 PRK07670 RNA polymerase sigma 35.7 52 0.0011 29.4 4.1 47 67-118 202-248 (251)
151 TIGR02980 SigBFG RNA polymeras 35.4 57 0.0012 28.4 4.2 47 66-117 178-224 (227)
152 PF00376 MerR: MerR family reg 35.0 24 0.00052 22.6 1.3 18 90-107 2-19 (38)
153 PRK09641 RNA polymerase sigma 34.6 57 0.0012 27.1 4.0 33 86-118 151-183 (187)
154 PRK07122 RNA polymerase sigma 34.1 56 0.0012 29.7 4.1 47 66-117 215-261 (264)
155 PF13565 HTH_32: Homeodomain-l 34.0 1.7E+02 0.0036 20.7 5.9 32 68-99 32-64 (77)
156 TIGR02393 RpoD_Cterm RNA polym 33.6 83 0.0018 27.8 5.0 52 66-118 176-227 (238)
157 KOG0260|consensus 33.5 4E+02 0.0087 30.1 10.6 9 12-20 1240-1248(1605)
158 PRK09651 RNA polymerase sigma 33.4 81 0.0018 26.1 4.7 33 86-118 134-166 (172)
159 TIGR02950 SigM_subfam RNA poly 33.4 38 0.00083 27.2 2.6 34 84-117 118-151 (154)
160 PRK12535 RNA polymerase sigma 33.2 81 0.0017 27.0 4.8 48 67-119 134-181 (196)
161 PRK06424 transcription factor; 33.2 34 0.00074 28.6 2.3 25 90-114 100-124 (144)
162 TIGR02392 rpoH_proteo alternat 33.1 66 0.0014 29.1 4.4 50 66-118 218-267 (270)
163 PRK09649 RNA polymerase sigma 32.9 76 0.0016 26.8 4.5 29 89-117 148-176 (185)
164 PRK07408 RNA polymerase sigma 32.9 62 0.0013 29.1 4.1 48 66-118 203-250 (256)
165 cd01392 HTH_LacI Helix-turn-he 32.9 40 0.00088 22.0 2.2 21 92-112 2-22 (52)
166 PRK12544 RNA polymerase sigma 32.7 1.1E+02 0.0024 26.4 5.6 49 67-120 149-197 (206)
167 PF01381 HTH_3: Helix-turn-hel 31.9 26 0.00057 23.2 1.2 23 90-112 12-34 (55)
168 PRK12542 RNA polymerase sigma 31.4 94 0.002 26.0 4.8 47 67-118 123-169 (185)
169 PRK12540 RNA polymerase sigma 31.0 1.1E+02 0.0024 25.8 5.2 49 67-120 112-160 (182)
170 PRK12534 RNA polymerase sigma 31.0 75 0.0016 26.5 4.1 46 67-117 138-183 (187)
171 PRK08215 sporulation sigma fac 30.7 79 0.0017 28.3 4.4 47 66-117 209-255 (258)
172 cd04763 HTH_MlrA-like Helix-Tu 30.6 33 0.00071 24.2 1.6 20 90-109 3-22 (68)
173 TIGR02885 spore_sigF RNA polym 30.5 80 0.0017 27.6 4.4 46 66-116 183-228 (231)
174 PRK12522 RNA polymerase sigma 29.8 58 0.0013 26.9 3.2 32 88-119 136-167 (173)
175 PRK09390 fixJ response regulat 29.8 72 0.0016 25.6 3.7 46 67-118 142-187 (202)
176 PRK07500 rpoH2 RNA polymerase 29.2 97 0.0021 28.5 4.8 51 66-119 227-277 (289)
177 PRK09638 RNA polymerase sigma 29.2 51 0.0011 27.2 2.8 34 85-118 140-173 (176)
178 smart00027 EH Eps15 homology d 29.1 1E+02 0.0023 23.1 4.3 44 66-109 3-51 (96)
179 PRK12517 RNA polymerase sigma 28.5 1.6E+02 0.0035 24.8 5.8 35 88-122 145-179 (188)
180 PRK05803 sporulation sigma fac 28.4 1.2E+02 0.0026 26.6 5.2 52 66-118 175-226 (233)
181 PRK12528 RNA polymerase sigma 28.3 1.1E+02 0.0024 24.8 4.6 44 67-115 114-157 (161)
182 PRK11511 DNA-binding transcrip 28.1 76 0.0017 25.3 3.5 27 85-111 23-49 (127)
183 TIGR02835 spore_sigmaE RNA pol 28.1 1.1E+02 0.0025 26.8 4.9 53 66-119 178-230 (234)
184 TIGR03070 couple_hipB transcri 28.1 34 0.00074 22.5 1.2 23 90-112 18-40 (58)
185 cd04764 HTH_MlrA-like_sg1 Heli 28.1 40 0.00087 23.6 1.7 21 90-110 3-23 (67)
186 PRK05911 RNA polymerase sigma 27.4 98 0.0021 27.9 4.5 48 66-118 205-252 (257)
187 cd01104 HTH_MlrA-CarA Helix-Tu 27.3 42 0.0009 23.3 1.6 20 90-109 3-22 (68)
188 PRK10100 DNA-binding transcrip 27.2 98 0.0021 27.2 4.3 45 66-116 155-199 (216)
189 PLN03162 golden-2 like transcr 27.0 5.9E+02 0.013 25.0 9.6 62 59-120 232-295 (526)
190 TIGR03020 EpsA transcriptional 26.8 92 0.002 28.3 4.1 48 64-117 188-235 (247)
191 PRK12527 RNA polymerase sigma 26.7 1.5E+02 0.0033 23.9 5.2 31 88-118 122-152 (159)
192 PRK09958 DNA-binding transcrip 26.5 95 0.0021 25.4 4.0 45 65-115 142-186 (204)
193 PRK12525 RNA polymerase sigma 26.5 1.4E+02 0.003 24.6 4.9 46 67-117 119-164 (168)
194 PF02796 HTH_7: Helix-turn-hel 26.4 82 0.0018 20.5 2.8 37 67-108 6-42 (45)
195 PF07037 DUF1323: Putative tra 26.4 28 0.0006 28.4 0.6 27 90-118 3-29 (122)
196 TIGR03541 reg_near_HchA LuxR f 26.4 59 0.0013 28.8 2.8 49 64-118 169-217 (232)
197 TIGR02846 spore_sigmaK RNA pol 25.8 1.3E+02 0.0028 26.4 4.9 51 66-117 174-224 (227)
198 TIGR02957 SigX4 RNA polymerase 25.8 1.2E+02 0.0025 27.7 4.7 30 89-118 126-155 (281)
199 COG2963 Transposase and inacti 25.8 1.7E+02 0.0036 22.7 5.0 41 64-108 5-46 (116)
200 PRK09415 RNA polymerase factor 25.7 1.2E+02 0.0026 25.2 4.5 47 67-118 128-174 (179)
201 PRK05572 sporulation sigma fac 25.6 1.1E+02 0.0024 27.3 4.4 48 65-117 201-248 (252)
202 TIGR01764 excise DNA binding d 25.4 45 0.00098 21.0 1.4 23 90-112 4-26 (49)
203 PF07638 Sigma70_ECF: ECF sigm 25.2 62 0.0013 27.5 2.6 30 88-117 152-181 (185)
204 cd00131 PAX Paired Box domain 24.8 3.1E+02 0.0067 22.1 6.5 45 66-110 75-126 (128)
205 TIGR02984 Sig-70_plancto1 RNA 24.8 1.2E+02 0.0025 25.1 4.2 47 66-117 140-186 (189)
206 cd00093 HTH_XRE Helix-turn-hel 24.5 45 0.00098 20.7 1.3 23 90-112 15-37 (58)
207 PF13730 HTH_36: Helix-turn-he 24.3 78 0.0017 21.0 2.5 44 67-111 3-49 (55)
208 PRK09636 RNA polymerase sigma 24.2 1.3E+02 0.0028 27.4 4.7 30 89-118 133-162 (293)
209 KOG3755|consensus 24.2 45 0.00098 34.4 1.7 60 58-117 645-708 (769)
210 PRK11922 RNA polymerase sigma 24.0 78 0.0017 27.8 3.1 37 84-120 162-198 (231)
211 PF04936 DUF658: Protein of un 23.7 33 0.0007 29.6 0.5 31 88-118 15-45 (186)
212 PRK06596 RNA polymerase factor 23.5 1.2E+02 0.0027 27.7 4.4 50 66-118 230-279 (284)
213 PF12824 MRP-L20: Mitochondria 23.5 2.9E+02 0.0063 23.6 6.3 48 63-112 82-129 (164)
214 TIGR02607 antidote_HigA addict 22.9 48 0.001 23.6 1.3 23 90-112 21-43 (78)
215 PRK09975 DNA-binding transcrip 22.8 59 0.0013 27.6 2.0 43 70-113 15-57 (213)
216 PRK07405 RNA polymerase sigma 22.8 1.9E+02 0.0041 27.1 5.5 52 66-118 256-307 (317)
217 smart00595 MADF subfamily of S 22.7 1.2E+02 0.0025 22.2 3.4 33 90-122 30-62 (89)
218 TIGR02960 SigX5 RNA polymerase 22.2 1.4E+02 0.003 27.3 4.5 30 89-118 160-189 (324)
219 PF08279 HTH_11: HTH domain; 21.9 86 0.0019 20.8 2.3 36 71-109 2-37 (55)
220 PF13412 HTH_24: Winged helix- 21.9 1.5E+02 0.0032 19.1 3.4 37 68-108 2-38 (48)
221 TIGR02394 rpoS_proteo RNA poly 21.4 1.7E+02 0.0038 26.6 5.0 53 66-119 222-274 (285)
222 PHA02955 hypothetical protein; 21.0 1.1E+02 0.0024 27.4 3.4 43 70-112 61-104 (213)
223 COG1595 RpoE DNA-directed RNA 20.8 96 0.0021 25.9 2.9 32 88-119 144-175 (182)
224 COG1905 NuoE NADH:ubiquinone o 20.5 1.4E+02 0.003 25.6 3.7 36 69-104 25-60 (160)
225 PRK05949 RNA polymerase sigma 20.4 2.3E+02 0.0051 26.6 5.7 52 66-118 266-317 (327)
226 PHA01976 helix-turn-helix prot 20.4 59 0.0013 22.5 1.3 23 90-112 18-40 (67)
No 1
>KOG3802|consensus
Probab=99.96 E-value=3.2e-30 Score=241.35 Aligned_cols=108 Identities=23% Similarity=0.314 Sum_probs=89.9
Q ss_pred HHHhCCCCCcccccCcccCCCCcCCCCCCCccCCCC------------CCCCCCCCCCCCCCCCCCcCCHHHHHHHHHHH
Q psy526 12 KKINNNNITNNTMSYYGKKDIRDARDLPKPAALSNL------------PGLAQSQPPTGRKKRSRAAFSHAQVYELEKRF 79 (274)
Q Consensus 12 ~~~~g~~~sqttis~fe~~~ls~~~~~~~~~~~~~~------------~~~~~~~~~~~k~rR~RT~ft~~Ql~~Le~~F 79 (274)
-++|||+||||||||||+|+|++++|+.-...+..| ....+......|||||||+|+...+..||++|
T Consensus 234 G~lyGn~FSQTTIcRFEALqLSFKNMCKLKPLL~KWLeEAes~~~~~~~~~~e~i~a~~RkRKKRTSie~~vr~aLE~~F 313 (398)
T KOG3802|consen 234 GALYGNVFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAESRESTGSPNSIEKIGAQSRKRKKRTSIEVNVRGALEKHF 313 (398)
T ss_pred HhhhCcccchhhhhHhHhhccCHHHHhhhHHHHHHHHHHHhcccccCCCCCHHHhhccccccccccceeHHHHHHHHHHH
Confidence 479999999999999999999999994322222111 11122233445889999999999999999999
Q ss_pred hhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 80 NAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 80 ~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
.+|++|+.+|+.+||++|+|.++||||||||||+|.||..
T Consensus 314 ~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 314 LKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred HhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 9999999999999999999999999999999999999953
No 2
>KOG0842|consensus
Probab=99.84 E-value=6.5e-21 Score=175.41 Aligned_cols=96 Identities=53% Similarity=0.809 Sum_probs=85.4
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHHHhcCCCCCCCCCCC
Q psy526 57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQLLEGSLNTPSAGNGK 136 (274)
Q Consensus 57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~~~~~~~~~~~~~~~ 136 (274)
.++|||.|..|++.|.-+||+.|.+++|.+..||++||..|+|+++||+|||||||.|+||+++............+..+
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~~~~~~~~r 229 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALLLASSPPPR 229 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcccCCCCCccc
Confidence 56778889999999999999999999999999999999999999999999999999999999887766655555555557
Q ss_pred ccceeccccCCCCCCC
Q psy526 137 KVAVKILVRESHPYGS 152 (274)
Q Consensus 137 ~~~~~~l~~~~~p~~~ 152 (274)
.+.++.+.++..+|..
T Consensus 230 ~v~vpvlvrd~kp~~~ 245 (307)
T KOG0842|consen 230 RVAVPVLVRDGKPCSG 245 (307)
T ss_pred ccCCceeccCCCcccC
Confidence 8999999999999854
No 3
>KOG0484|consensus
Probab=99.81 E-value=4.7e-20 Score=143.66 Aligned_cols=69 Identities=33% Similarity=0.595 Sum_probs=64.6
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHHHh
Q psy526 56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQLLE 124 (274)
Q Consensus 56 ~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~~~ 124 (274)
.++|+||-||.||..||.+||+.|...+||++-.|++||.+|.|++.+|||||||||+|.||+.+....
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIA 81 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 457889999999999999999999999999999999999999999999999999999999998766543
No 4
>KOG0486|consensus
Probab=99.80 E-value=3.3e-19 Score=162.49 Aligned_cols=66 Identities=32% Similarity=0.600 Sum_probs=62.7
Q ss_pred CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHHH
Q psy526 58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQLL 123 (274)
Q Consensus 58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~~ 123 (274)
.|+||.||.|+.+||.+||..|.+|+||++..|+|||..++|++.+|+|||+|||+||||+++.+.
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 378899999999999999999999999999999999999999999999999999999999877665
No 5
>KOG2251|consensus
Probab=99.78 E-value=3.6e-19 Score=155.58 Aligned_cols=68 Identities=34% Similarity=0.562 Sum_probs=64.7
Q ss_pred CCCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526 55 PPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL 122 (274)
Q Consensus 55 ~~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~ 122 (274)
...+|+||.||+|+..|+++||+.|.+.+||+...|++||.+|+|.+.+|+|||+|||+|+|++++++
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 45678999999999999999999999999999999999999999999999999999999999988775
No 6
>KOG1168|consensus
Probab=99.78 E-value=3e-20 Score=167.58 Aligned_cols=103 Identities=26% Similarity=0.394 Sum_probs=86.0
Q ss_pred CCCcccccCcccCCCCcCCCCCCCccCCCCCCCCC-------------CCCCCCCCCCCCCcCCHHHHHHHHHHHhhCCC
Q psy526 18 NITNNTMSYYGKKDIRDARDLPKPAALSNLPGLAQ-------------SQPPTGRKKRSRAAFSHAQVYELEKRFNAQKY 84 (274)
Q Consensus 18 ~~sqttis~fe~~~ls~~~~~~~~~~~~~~~~~~~-------------~~~~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~ 84 (274)
.+||+||||||.+.|+.++|+.-...+..|...++ +--..+.||||||++-.-+.+.||++|...+.
T Consensus 254 sLSQSTICRFESLTLSHNNMiALKPILqaWLEeAE~a~keK~~~pd~~~l~~~~ekKRKRTSIAAPEKRsLEayFavQPR 333 (385)
T KOG1168|consen 254 SLSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAAMKEKDTKPDINELLPGGEKKRKRTSIAAPEKRSLEAYFAVQPR 333 (385)
T ss_pred cccccceeeeeeeccccCcchhhhHHHHHHHHHHHHHHHhhccCCchhhccCccccccccccccCcccccHHHHhccCCC
Confidence 46999999999999999999655444444322111 12234578899999999999999999999999
Q ss_pred CCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 85 LSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 85 Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
|+.+.+..||++|.|.+.||+|||||+|+|.||...
T Consensus 334 PS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 334 PSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred CchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence 999999999999999999999999999999999643
No 7
>KOG0489|consensus
Probab=99.77 E-value=2.2e-19 Score=163.75 Aligned_cols=66 Identities=48% Similarity=0.779 Sum_probs=61.9
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526 57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL 122 (274)
Q Consensus 57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~ 122 (274)
.++.||.||.||..|+.+||+.|+.|+|.++..|.|||..|.|+++||+|||||||+||||..+..
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~ 221 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAK 221 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccc
Confidence 356789999999999999999999999999999999999999999999999999999999976554
No 8
>KOG0488|consensus
Probab=99.75 E-value=1e-18 Score=162.59 Aligned_cols=69 Identities=52% Similarity=0.763 Sum_probs=63.5
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHHHh
Q psy526 56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQLLE 124 (274)
Q Consensus 56 ~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~~~ 124 (274)
..+|+||.||.||..||..||+.|++..|.+..+|.+||..|||+..||++||||||+||||......+
T Consensus 168 ~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~ 236 (309)
T KOG0488|consen 168 TPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGE 236 (309)
T ss_pred CCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhc
Confidence 336778889999999999999999999999999999999999999999999999999999998766433
No 9
>KOG0843|consensus
Probab=99.71 E-value=7.8e-18 Score=143.03 Aligned_cols=64 Identities=52% Similarity=0.796 Sum_probs=61.3
Q ss_pred CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526 59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL 122 (274)
Q Consensus 59 k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~ 122 (274)
|.||.||.|+.+||..||..|+.++|-.-.+|++||..|+|++.||+|||||||.|.||.+...
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 7899999999999999999999999999999999999999999999999999999999987654
No 10
>KOG0494|consensus
Probab=99.71 E-value=9.4e-18 Score=149.55 Aligned_cols=64 Identities=31% Similarity=0.541 Sum_probs=59.2
Q ss_pred CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526 59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL 122 (274)
Q Consensus 59 k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~ 122 (274)
|+|+.||.||..|++.||+.|....||+...|+.||.++.|.+++|+|||||||+||||.++..
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence 4444599999999999999999999999999999999999999999999999999999987654
No 11
>KOG0487|consensus
Probab=99.71 E-value=5.1e-18 Score=156.41 Aligned_cols=65 Identities=40% Similarity=0.682 Sum_probs=61.4
Q ss_pred CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526 58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL 122 (274)
Q Consensus 58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~ 122 (274)
++.||||..+|+.|+.+||+.|..|.|.+++.|.||++.|+|++|||+|||||||.|.||..++.
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 56788899999999999999999999999999999999999999999999999999999987644
No 12
>KOG0850|consensus
Probab=99.70 E-value=2.1e-16 Score=139.02 Aligned_cols=67 Identities=46% Similarity=0.704 Sum_probs=62.1
Q ss_pred CCCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHH
Q psy526 55 PPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQ 121 (274)
Q Consensus 55 ~~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~ 121 (274)
+..+|.||.||.++.-||..|.+.|++++|.-..||.+||..|||+.+||+|||||||.|.||..++
T Consensus 117 gk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~ 183 (245)
T KOG0850|consen 117 GKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQ 183 (245)
T ss_pred CCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhc
Confidence 4445667789999999999999999999999999999999999999999999999999999998763
No 13
>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=99.70 E-value=3.1e-17 Score=115.54 Aligned_cols=57 Identities=51% Similarity=0.733 Sum_probs=55.4
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 61 rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
||+|+.|+.+|+.+|+.+|..++||+..++++||..|||+..+|++||+|||+++||
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 678999999999999999999999999999999999999999999999999999986
No 14
>KOG0485|consensus
Probab=99.69 E-value=6e-17 Score=141.25 Aligned_cols=68 Identities=59% Similarity=0.845 Sum_probs=63.2
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHHHh
Q psy526 57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQLLE 124 (274)
Q Consensus 57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~~~ 124 (274)
..||||.||+|+..|+..||..|+..+|.+..+|.-||.+|.|++.||+|||||||.||||+.....+
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~e 168 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLE 168 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhh
Confidence 35888999999999999999999999999999999999999999999999999999999998655544
No 15
>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=99.65 E-value=1.4e-16 Score=113.21 Aligned_cols=54 Identities=20% Similarity=0.360 Sum_probs=51.6
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhCCC----CCHHHHHHHHHHhCCCcccchhhhhhhhh
Q psy526 60 KKRSRAAFSHAQVYELEKRFNAQKY----LSGPERADVAKSLKLTETQVKIWFQNRRY 113 (274)
Q Consensus 60 ~rR~RT~ft~~Ql~~Le~~F~~~~~----Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~ 113 (274)
+||.||.||.+|++.||.+|++++| |+..+|++||..|||++++|+|||||.++
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k~ 58 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNKK 58 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCCC
Confidence 4789999999999999999999999 99999999999999999999999999763
No 16
>KOG0492|consensus
Probab=99.65 E-value=1.7e-16 Score=137.61 Aligned_cols=65 Identities=52% Similarity=0.794 Sum_probs=60.7
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHHHh
Q psy526 60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQLLE 124 (274)
Q Consensus 60 ~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~~~ 124 (274)
.|+.||.||.+||..||+.|.+.+|.++.+|.+++..|.|+++||+|||||||+|.||.+....+
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~E 208 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELE 208 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHH
Confidence 36679999999999999999999999999999999999999999999999999999998766554
No 17
>KOG0848|consensus
Probab=99.60 E-value=4.9e-16 Score=139.14 Aligned_cols=63 Identities=38% Similarity=0.681 Sum_probs=58.5
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526 60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL 122 (274)
Q Consensus 60 ~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~ 122 (274)
|-|-|.++|..|+.+||+.|..++|.++..+.|||..|+|++|||+|||||||+|+||..++.
T Consensus 199 kDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 199 KDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 345588999999999999999999999999999999999999999999999999999976655
No 18
>KOG4577|consensus
Probab=99.59 E-value=1.5e-14 Score=130.90 Aligned_cols=65 Identities=28% Similarity=0.431 Sum_probs=60.7
Q ss_pred CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526 58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL 122 (274)
Q Consensus 58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~ 122 (274)
...||+||+||..||+.|+.+|...++|-+..||+|+.++||..+||||||||||+|+||.++..
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence 34689999999999999999999999999999999999999999999999999999999976544
No 19
>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=99.56 E-value=5.7e-15 Score=103.84 Aligned_cols=57 Identities=56% Similarity=0.815 Sum_probs=54.3
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 61 rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
++.|+.|+..|+.+|+++|..++||+..+++.||.++||++.+|++||+|||.+.++
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 356889999999999999999999999999999999999999999999999999876
No 20
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.56 E-value=4.2e-15 Score=103.83 Aligned_cols=56 Identities=50% Similarity=0.764 Sum_probs=52.7
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHH
Q psy526 61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116 (274)
Q Consensus 61 rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~K 116 (274)
++.|+.|+.+|+.+|+..|..++||+..++.+||..+||+..+|++||+|||.+.|
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 46688899999999999999999999999999999999999999999999998753
No 21
>KOG0491|consensus
Probab=99.55 E-value=1.8e-15 Score=126.94 Aligned_cols=64 Identities=53% Similarity=0.866 Sum_probs=60.5
Q ss_pred CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526 59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL 122 (274)
Q Consensus 59 k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~ 122 (274)
++||-||+|+..|+..||+.|+..+|.+-.+|.|||..|+|++.||+.||||||+|.||+++..
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~ 162 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNN 162 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence 5677899999999999999999999999999999999999999999999999999999987664
No 22
>KOG0493|consensus
Probab=99.55 E-value=4.9e-15 Score=132.39 Aligned_cols=58 Identities=43% Similarity=0.781 Sum_probs=56.2
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 61 rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
||.||.||.+||..|+..|..|+|.+.+.|.+||.+|+|.+.||+|||||+|+|.||.
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 5789999999999999999999999999999999999999999999999999999984
No 23
>KOG0844|consensus
Probab=99.53 E-value=2.9e-15 Score=136.32 Aligned_cols=63 Identities=46% Similarity=0.825 Sum_probs=59.5
Q ss_pred CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHH
Q psy526 59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQ 121 (274)
Q Consensus 59 k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~ 121 (274)
.-||-||.||.+|+..||+.|-+..|-++..|.|||..|||.+..|+|||||||+|+||++..
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 457889999999999999999999999999999999999999999999999999999997654
No 24
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.46 E-value=7.2e-14 Score=118.21 Aligned_cols=64 Identities=31% Similarity=0.490 Sum_probs=58.2
Q ss_pred CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHH
Q psy526 58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQ 121 (274)
Q Consensus 58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~ 121 (274)
...+++|+..+..|+.+|++.|..++||+...|.+|+..|+|+++-||+||||||++.|+....
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 4456667777999999999999999999999999999999999999999999999999987644
No 25
>KOG0483|consensus
Probab=99.45 E-value=5.3e-14 Score=123.02 Aligned_cols=61 Identities=39% Similarity=0.552 Sum_probs=55.8
Q ss_pred CCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526 62 RSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL 122 (274)
Q Consensus 62 R~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~ 122 (274)
+++..|+.+|...||+.|+.+.|....++..||.+|||.++||.|||||||+|||.++...
T Consensus 52 ~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~ 112 (198)
T KOG0483|consen 52 GKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEK 112 (198)
T ss_pred cccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhh
Confidence 3344589999999999999999999999999999999999999999999999999887554
No 26
>KOG0847|consensus
Probab=99.33 E-value=6.8e-13 Score=116.18 Aligned_cols=64 Identities=48% Similarity=0.917 Sum_probs=60.2
Q ss_pred CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHH
Q psy526 58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQ 121 (274)
Q Consensus 58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~ 121 (274)
+++|..|-+|+-.|+..||+.|++.+|+--.+|.+||..+|+++.+|+|||||||.||||+-..
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa 228 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA 228 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence 6777789999999999999999999999999999999999999999999999999999997543
No 27
>KOG0490|consensus
Probab=99.31 E-value=1e-12 Score=116.16 Aligned_cols=64 Identities=31% Similarity=0.415 Sum_probs=61.2
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
..++||.||.|+..|+++||+.|.+.+||+...|+.||..++|++..|+|||||||+||++...
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 5678999999999999999999999999999999999999999999999999999999999764
No 28
>KOG0849|consensus
Probab=99.23 E-value=5.1e-11 Score=113.16 Aligned_cols=67 Identities=34% Similarity=0.514 Sum_probs=62.1
Q ss_pred CCCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHH
Q psy526 55 PPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQ 121 (274)
Q Consensus 55 ~~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~ 121 (274)
..+++.||.||+|+..|+..||+.|++++||+...|++||.+++|++..|+|||+|||+|++|...+
T Consensus 171 ~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 171 ALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred cccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 3456778889999999999999999999999999999999999999999999999999999997643
No 29
>KOG0775|consensus
Probab=99.07 E-value=4.7e-10 Score=101.31 Aligned_cols=51 Identities=31% Similarity=0.478 Sum_probs=47.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
|...-+..|..+|.+++||+..++.+||+.+||+..||-.||+|||+|+|-
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 555568899999999999999999999999999999999999999999983
No 30
>KOG0774|consensus
Probab=98.82 E-value=1.6e-08 Score=90.97 Aligned_cols=63 Identities=29% Similarity=0.447 Sum_probs=57.1
Q ss_pred CCCCCCcCCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526 60 KKRSRAAFSHAQVYELEKRFN---AQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL 122 (274)
Q Consensus 60 ~rR~RT~ft~~Ql~~Le~~F~---~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~ 122 (274)
.||+|..|++...++|..+|. .++||+.+.+++||.++|++..||..||.|+|-+.||.--..
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~ 253 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKN 253 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhh
Confidence 367889999999999999995 589999999999999999999999999999999999865443
No 31
>KOG2252|consensus
Probab=98.46 E-value=1.9e-07 Score=91.66 Aligned_cols=58 Identities=24% Similarity=0.327 Sum_probs=54.5
Q ss_pred CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHH
Q psy526 58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115 (274)
Q Consensus 58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~ 115 (274)
-+.||.|.+||..|++.|.+.|+.+++|+.++.+.|+.+|||....|..||-|.|.|.
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 4567889999999999999999999999999999999999999999999999988664
No 32
>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=98.45 E-value=1.2e-07 Score=62.60 Aligned_cols=34 Identities=32% Similarity=0.557 Sum_probs=29.1
Q ss_pred hCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhH
Q psy526 81 AQKYLSGPERADVAKSLKLTETQVKIWFQNRRYK 114 (274)
Q Consensus 81 ~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k 114 (274)
.+|||+.+++++||.++||+..||..||-|.|.|
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 4799999999999999999999999999999864
No 33
>KOG0490|consensus
Probab=98.40 E-value=2.7e-07 Score=81.55 Aligned_cols=66 Identities=30% Similarity=0.562 Sum_probs=61.1
Q ss_pred CCCCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 55 PPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 55 ~~~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
....+.++.|+.|...|+..|+..|...++|+...++.|+..+|+..++|+|||+|+|++.++...
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 148 PSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 344677889999999999999999999999999999999999999999999999999999998654
No 34
>KOG1146|consensus
Probab=98.10 E-value=3.8e-06 Score=89.43 Aligned_cols=63 Identities=24% Similarity=0.370 Sum_probs=59.3
Q ss_pred CCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
-.+|+.||.++..||+.|...|....||..++.|.|-..++|.+++|+|||||.|+|.|+...
T Consensus 901 ~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 901 MGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 356788999999999999999999999999999999999999999999999999999998765
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.97 E-value=0.00067 Score=47.80 Aligned_cols=43 Identities=21% Similarity=0.403 Sum_probs=31.8
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhH
Q psy526 72 VYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYK 114 (274)
Q Consensus 72 l~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k 114 (274)
+..|+++|...+++...+...|..+.+|+..+|+.||-.|+.+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 4569999999999999999999999999999999999876543
No 36
>KOG0773|consensus
Probab=96.53 E-value=0.0019 Score=61.00 Aligned_cols=60 Identities=27% Similarity=0.331 Sum_probs=50.8
Q ss_pred CCCCCCCcCCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 59 RKKRSRAAFSHAQVYELEKRFNA---QKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 59 k~rR~RT~ft~~Ql~~Le~~F~~---~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
.++|++..|......+|+.+..+ .+||+..++..||.++||+..||..||-|.|-|..+-
T Consensus 238 ~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p 300 (342)
T KOG0773|consen 238 SKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKP 300 (342)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCc
Confidence 35556678999999999987543 5799999999999999999999999999999886653
No 37
>PF00157 Pou: Pou domain - N-terminal to homeobox domain; InterPro: IPR000327 POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain. The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [] and the development of an organism []. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [, ], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1). The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327 from INTERPRO), while the C-terminal subunit is a homeobox domain (IPR007103 from INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions []. The subdomains are connected by a flexible linker [, , ]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ]. This entry represents the POU-specific subunit of the POU domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3D1N_O 1AU7_A 3L1P_A 2XSD_C 1O4X_A 1HF0_B 1GT0_C 1POU_A 1CQT_B 1E3O_C ....
Probab=96.51 E-value=0.00019 Score=53.63 Aligned_cols=27 Identities=4% Similarity=0.123 Sum_probs=24.0
Q ss_pred HHHHhCCCCCcccccCcccCCCCcCCC
Q psy526 11 YKKINNNNITNNTMSYYGKKDIRDARD 37 (274)
Q Consensus 11 ~~~~~g~~~sqttis~fe~~~ls~~~~ 37 (274)
-..+||++|||++|||||+++|+.+++
T Consensus 34 l~~~~G~~~SQttI~RFE~L~LS~kn~ 60 (75)
T PF00157_consen 34 LGRLYGKEFSQTTICRFEALQLSFKNM 60 (75)
T ss_dssp HHHHHSSGGSHHHHHHHHTTTSCHHHH
T ss_pred HHHhcCccccchhhhhhHhcccCHHHH
Confidence 356899999999999999999997765
No 38
>KOG3623|consensus
Probab=96.39 E-value=0.0034 Score=64.09 Aligned_cols=48 Identities=19% Similarity=0.274 Sum_probs=45.2
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 72 VYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 72 l~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
+..|+.+|..|..|+..+...||.++||..++|++||.+++++..+..
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 788999999999999999999999999999999999999999887754
No 39
>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=95.28 E-value=0.038 Score=38.34 Aligned_cols=46 Identities=22% Similarity=0.452 Sum_probs=35.5
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhh
Q psy526 61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNR 111 (274)
Q Consensus 61 rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNr 111 (274)
||+|..+|-++...+-..++... ...+||.++|+...+|..|..|+
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 57899999999888888887666 57789999999999999999885
No 40
>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=87.60 E-value=1.3 Score=29.62 Aligned_cols=46 Identities=13% Similarity=0.214 Sum_probs=34.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~K 116 (274)
.++..+..+|...|- ......+||..+|++...|+.+...-..|.|
T Consensus 4 ~L~~~er~vi~~~y~-----~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYF-----EGLTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHT-----ST-SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhc-----CCCCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 467889999999982 2334778999999999999998766665554
No 41
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=86.81 E-value=0.074 Score=39.75 Aligned_cols=25 Identities=4% Similarity=0.086 Sum_probs=22.6
Q ss_pred HhCCCCCcccccCcccCCCCcCCCC
Q psy526 14 INNNNITNNTMSYYGKKDIRDARDL 38 (274)
Q Consensus 14 ~~g~~~sqttis~fe~~~ls~~~~~ 38 (274)
+||..++|++|||||..+|+.++++
T Consensus 37 ~~g~i~SQstISR~Es~~ls~~n~~ 61 (75)
T smart00352 37 LYGPDFSQTTICRFEALQLSFKNMC 61 (75)
T ss_pred cccCcCCHHHHHHHHhcCccHHHHH
Confidence 6889999999999999999988764
No 42
>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=80.17 E-value=2.1 Score=27.64 Aligned_cols=44 Identities=14% Similarity=0.177 Sum_probs=33.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYK 114 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k 114 (274)
.++..+..++...|... ....+||..+|++...|..|....+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 46777888888776422 346778999999999999998665443
No 43
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=77.00 E-value=7.2 Score=32.61 Aligned_cols=53 Identities=15% Similarity=0.149 Sum_probs=41.5
Q ss_pred CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526 64 RAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL 122 (274)
Q Consensus 64 RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~ 122 (274)
...++..|+.+|...+ .. ....+||..||++...|..|.++.+.|.|+.....
T Consensus 4 ~~~Lt~rqreVL~lr~--~G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl 56 (141)
T PRK03975 4 ESFLTERQIEVLRLRE--RG----LTQQEIADILGTSRANVSSIEKRARENIEKARETL 56 (141)
T ss_pred ccCCCHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3568999999998743 22 34668999999999999999998888888765443
No 44
>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=73.15 E-value=3.1 Score=29.92 Aligned_cols=44 Identities=16% Similarity=0.339 Sum_probs=28.7
Q ss_pred CCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhh
Q psy526 62 RSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQ 109 (274)
Q Consensus 62 R~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFq 109 (274)
++|..|+.++...+-..+... .....+||.++|++..+|..|-+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~----g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES----GESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH----HCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC----CCceEeeecccccccccccHHHH
Confidence 457789998877776665322 35678899999999999999953
No 45
>KOG1146|consensus
Probab=71.30 E-value=6 Score=43.77 Aligned_cols=63 Identities=17% Similarity=0.217 Sum_probs=57.8
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 57 ~~k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
.-+-++.|+.+-.+++..|-.+|..+.-|+...+..|......+.+++.+||+|-|.|.++..
T Consensus 702 ~~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 702 SPRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred CcccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 346678889999999999999999999999999999999999999999999999999988765
No 46
>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=70.85 E-value=10 Score=25.39 Aligned_cols=43 Identities=26% Similarity=0.296 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYK 114 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k 114 (274)
++..+..++.-.|- ......+||..+|++...|+.|.+.-|.+
T Consensus 11 L~~~~r~i~~l~~~-----~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 11 LPERQREIFLLRYF-----QGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp S-HHHHHHHHHHHT-----S---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH-----HCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 55666677766553 34567889999999999999999765543
No 47
>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=69.30 E-value=7.8 Score=26.62 Aligned_cols=45 Identities=16% Similarity=0.133 Sum_probs=34.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~K 116 (274)
.||..++.+|.-...- ....+||..+++++..|..+..+-+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG------MSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTT------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhc------CCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 5788888888777543 34678999999999999999888776654
No 48
>PRK04217 hypothetical protein; Provisional
Probab=68.07 E-value=12 Score=29.93 Aligned_cols=49 Identities=10% Similarity=0.010 Sum_probs=38.4
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
.++.+|+.++...|...- ...+||+.+|++...|+..+..-|.+.|...
T Consensus 42 ~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 478888888877764332 5778999999999999999987777776643
No 49
>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=67.97 E-value=12 Score=21.30 Aligned_cols=37 Identities=16% Similarity=0.289 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhh
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWF 108 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWF 108 (274)
++..+...+...|.. .+ ...++|..++++...|..|.
T Consensus 6 ~~~~~~~~i~~~~~~-~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAA-GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHc-CC----CHHHHHHHHCCCHHHHHHhC
Confidence 566666666666653 22 56678999999998888874
No 50
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=67.15 E-value=10 Score=32.40 Aligned_cols=48 Identities=17% Similarity=0.196 Sum_probs=35.1
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
.++..+..+|...|. ......+||+.||++...|++|...-|++.|+.
T Consensus 142 ~L~~~~r~vl~l~~~-----~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 142 ALTDTQRESVTLAYY-----GGLTYREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred hCCHHHHHHHHHHHH-----cCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 355666666655442 224577899999999999999998777777765
No 51
>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=63.09 E-value=17 Score=25.30 Aligned_cols=41 Identities=12% Similarity=0.110 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHHhhCC--CCCHHHHHHHHHHhCCCcccchhh
Q psy526 67 FSHAQVYELEKRFNAQK--YLSGPERADVAKSLKLTETQVKIW 107 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~--~Ps~~~r~~LA~~l~L~~~~V~vW 107 (274)
+|..|+++|...|+..= +|-.....+||..||+++..|.--
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~ 43 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEH 43 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHH
Confidence 57899999999997644 366777889999999998765543
No 52
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=62.94 E-value=19 Score=29.52 Aligned_cols=33 Identities=15% Similarity=0.071 Sum_probs=27.2
Q ss_pred HHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 88 PERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 88 ~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
....+||..+|++...|+.|..--|.|.|+.-.
T Consensus 142 ~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 142 LSYREIAEILGVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 446789999999999999999887877776543
No 53
>KOG3755|consensus
Probab=61.08 E-value=2.9 Score=42.60 Aligned_cols=53 Identities=21% Similarity=0.219 Sum_probs=39.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCC-------CcccchhhhhhhhhHHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKL-------TETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L-------~~~~V~vWFqNrR~k~Kr~~ 119 (274)
|-....++-+.+|.++..+..-...+--+.+.| ..+-|+.||+|||.++||.+
T Consensus 699 f~~~~~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 699 FQNQRYEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred hhcceeecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
Confidence 334444555778888998888887777666654 34569999999999999864
No 54
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=59.80 E-value=20 Score=28.97 Aligned_cols=47 Identities=19% Similarity=0.290 Sum_probs=33.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
.++..+..++...|-. .....+||..+|++...|+.|...-|.|.|+
T Consensus 106 ~L~~~~r~ii~l~~~~-----~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFV-----GKTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 3455566666554432 2347889999999999999998776666554
No 55
>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=59.64 E-value=17 Score=28.26 Aligned_cols=47 Identities=19% Similarity=0.223 Sum_probs=32.8
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
.++..+..++...|-. .....+||..+|+++..|+.|...-+.|.|+
T Consensus 110 ~L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 3455666665544322 2356689999999999999998776666554
No 56
>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=59.22 E-value=5.4 Score=28.56 Aligned_cols=20 Identities=25% Similarity=0.601 Sum_probs=17.5
Q ss_pred HHHHHHHHhCCCcccchhhh
Q psy526 89 ERADVAKSLKLTETQVKIWF 108 (274)
Q Consensus 89 ~r~~LA~~l~L~~~~V~vWF 108 (274)
.-.+||.+||+++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 45679999999999999993
No 57
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=58.57 E-value=26 Score=28.76 Aligned_cols=49 Identities=12% Similarity=0.062 Sum_probs=35.5
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
.++..++.+|...|- ......+||..+|++...|+.|...-|.|.|+.-
T Consensus 128 ~L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREI-----EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 466666777766543 2234668999999999999999987777766643
No 58
>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=58.25 E-value=20 Score=27.78 Aligned_cols=38 Identities=24% Similarity=0.268 Sum_probs=21.6
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHHH
Q psy526 72 VYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQLL 123 (274)
Q Consensus 72 l~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~~ 123 (274)
+...+-.|+.|+||...--.. | =+|||.+|++.+.+..
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~QI~ 51 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQRQIR 51 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHHHHH
Confidence 344556688899997542111 1 1689999998876653
No 59
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=57.25 E-value=21 Score=30.83 Aligned_cols=48 Identities=17% Similarity=0.143 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
++..+..+|...| .......+||..+|++...|+++...-|.+.|+..
T Consensus 154 L~~~~r~vl~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 154 LPEAQQTVVKGVY-----FQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3444444444332 23345678999999999999999887777776653
No 60
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=56.89 E-value=22 Score=30.11 Aligned_cols=34 Identities=21% Similarity=0.223 Sum_probs=27.7
Q ss_pred CHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 86 SGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 86 s~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
......+||..+|++...|++|+..-|.+.|+.-
T Consensus 156 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 156 EGLSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 3445778999999999999999988777777653
No 61
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=56.66 E-value=22 Score=23.07 Aligned_cols=43 Identities=19% Similarity=0.170 Sum_probs=30.6
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYK 114 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k 114 (274)
.++..+..++...+. . ....+||..+|++...|..|.+.-+.|
T Consensus 3 ~l~~~e~~i~~~~~~--g----~s~~eia~~l~is~~tv~~~~~~~~~k 45 (58)
T smart00421 3 SLTPREREVLRLLAE--G----LTNKEIAERLGISEKTVKTHLSNIMRK 45 (58)
T ss_pred CCCHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 367777777765432 2 256789999999999999997654433
No 62
>PRK00118 putative DNA-binding protein; Validated
Probab=55.86 E-value=34 Score=27.12 Aligned_cols=48 Identities=8% Similarity=0.056 Sum_probs=36.0
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
++..|..++...|.. .....+||..+|++...|..|....|.+.|+..
T Consensus 18 L~ekqRevl~L~y~e-----g~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~ 65 (104)
T PRK00118 18 LTEKQRNYMELYYLD-----DYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYE 65 (104)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 456677777666543 234667999999999999999988777777653
No 63
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=55.67 E-value=17 Score=30.38 Aligned_cols=47 Identities=11% Similarity=0.323 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
+...+..++...| ......++||..+|++...|+++...-|.+.|++
T Consensus 130 L~~~~r~i~~l~~-----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 130 LEKDRAAAVRRAY-----LEGLSYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 3444444444444 2223478899999999999999988777776654
No 64
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=54.24 E-value=32 Score=28.29 Aligned_cols=33 Identities=18% Similarity=0.057 Sum_probs=27.3
Q ss_pred HHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 88 PERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 88 ~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
...++||..+|++...|++|.+.-|.+.|+.-.
T Consensus 125 ~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 125 LTYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999999887777776543
No 65
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=54.21 E-value=22 Score=29.92 Aligned_cols=48 Identities=15% Similarity=0.106 Sum_probs=34.4
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
.+...|..++...|-. ....++||..+|++...|+++...-|.+.|+.
T Consensus 139 ~L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 139 TLPEKQREILILRVVV-----GLSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4556666666655433 24578899999999999999987666666653
No 66
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=53.77 E-value=33 Score=28.91 Aligned_cols=50 Identities=16% Similarity=0.105 Sum_probs=36.1
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
.++..+..+|.-.|- ......+||..+|++...|++....-|.+.|+...
T Consensus 131 ~L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 131 KLSPAHREIIDLVYY-----HEKSVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred hCCHHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 455666666655443 22346789999999999999999888877777543
No 67
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=53.43 E-value=32 Score=27.96 Aligned_cols=31 Identities=16% Similarity=0.128 Sum_probs=25.8
Q ss_pred HHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 89 ERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 89 ~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
...+||..+|++...|++++..-|.+.|+..
T Consensus 124 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 124 SYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3568999999999999999987777777653
No 68
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=52.92 E-value=14 Score=24.21 Aligned_cols=40 Identities=13% Similarity=0.145 Sum_probs=20.9
Q ss_pred CcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhh
Q psy526 65 AAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQ 109 (274)
Q Consensus 65 T~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFq 109 (274)
..||.+|+..++..+... .-..+||..||.+...|..|.+
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 457888888888886533 3456699999999999988864
No 69
>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=52.56 E-value=21 Score=29.80 Aligned_cols=35 Identities=17% Similarity=0.164 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 85 LSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 85 Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
.......+||..+|++...|+++...-|.+.|++-
T Consensus 152 ~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 152 LEGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 34455788999999999999999977777766653
No 70
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=52.41 E-value=29 Score=29.02 Aligned_cols=47 Identities=15% Similarity=0.123 Sum_probs=33.9
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
++..+..+|...|- ......+||..+|++...|+.++..-|.+.|++
T Consensus 132 L~~~~r~v~~l~~~-----~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12512 132 LPPRQRDVVQSISV-----EGASIKETAAKLSMSEGAVRVALHRGLAALAAK 178 (184)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 45555555555432 234567899999999999999998888777764
No 71
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=52.32 E-value=20 Score=29.93 Aligned_cols=48 Identities=13% Similarity=0.193 Sum_probs=34.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
.++..+..++...| ......++||..+|++...|+++++.-|.+.|+.
T Consensus 136 ~L~~~~r~v~~l~~-----~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLKY-----MEDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhHH-----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34555555555433 2334577899999999999999998777776664
No 72
>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=52.16 E-value=20 Score=28.71 Aligned_cols=46 Identities=9% Similarity=0.066 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
++..+..+|...|- ......+||..+|+++..|+.+...-|.|.|+
T Consensus 114 L~~~~r~il~l~~~-----~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 114 LPEQCRKIFILSRF-----EGKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 44555555555432 22356779999999999999988766666554
No 73
>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=52.12 E-value=46 Score=27.64 Aligned_cols=48 Identities=21% Similarity=0.220 Sum_probs=38.6
Q ss_pred CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 64 RAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 64 RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
.+.++..|+.+|+-.+ .. ....+||..+|++...|..|-..-|.|.|+
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 4678999999998742 22 257789999999999999998887777775
No 74
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=51.16 E-value=37 Score=27.67 Aligned_cols=48 Identities=19% Similarity=0.225 Sum_probs=35.3
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
++..+..+|.-.| . .....+||..+|++...|+.+...-|.+.|+.-.
T Consensus 113 L~~~~r~il~l~~--~----g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 113 MTERDRTVLLLRF--S----GYSYKEIAEALGIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred CCHHHHHHHHHHH--c----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5555666665555 2 2356789999999999999999887877777544
No 75
>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=50.74 E-value=6.7 Score=29.17 Aligned_cols=36 Identities=17% Similarity=0.212 Sum_probs=26.7
Q ss_pred HHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhh
Q psy526 77 KRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRR 112 (274)
Q Consensus 77 ~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR 112 (274)
..|....|-..-...+||..+|++...|+.|+.+..
T Consensus 22 ~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 22 AAAALAREEAGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 344444444555678899999999999999987543
No 76
>KOG3623|consensus
Probab=50.51 E-value=10 Score=39.79 Aligned_cols=60 Identities=18% Similarity=0.251 Sum_probs=49.7
Q ss_pred CCCCCCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 59 k~rR~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
++-|.|+.+..++-..|..+++.+--++..+-..++.+|...+.+|.|||++|+...+..
T Consensus 625 ~p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~ 684 (1007)
T KOG3623|consen 625 RPVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPM 684 (1007)
T ss_pred CCccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCC
Confidence 444567888888888899999888888888878888888999999999999999877764
No 77
>PF13551 HTH_29: Winged helix-turn helix
Probab=50.06 E-value=39 Score=25.56 Aligned_cols=49 Identities=14% Similarity=0.203 Sum_probs=31.7
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCC-----CCHHHHHH-H-HHHh--CCCcccchhhhh
Q psy526 61 KRSRAAFSHAQVYELEKRFNAQKY-----LSGPERAD-V-AKSL--KLTETQVKIWFQ 109 (274)
Q Consensus 61 rR~RT~ft~~Ql~~Le~~F~~~~~-----Ps~~~r~~-L-A~~l--~L~~~~V~vWFq 109 (274)
.|.+..++.++...|.+.+..++. .+.....+ | .... .++...|+.|++
T Consensus 52 g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 52 GRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 344444999999999999998763 33344333 3 2222 467778887764
No 78
>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=49.92 E-value=34 Score=28.49 Aligned_cols=47 Identities=19% Similarity=0.146 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
+...+..++.-.|- ......+||..+|++...|++....-|.+.|+.
T Consensus 135 Lp~~~r~v~~l~~~-----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 135 VDPRQAEVVELRFF-----AGLTVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 45555555554432 223467899999999999999998777776653
No 79
>PRK06930 positive control sigma-like factor; Validated
Probab=49.58 E-value=41 Score=28.73 Aligned_cols=50 Identities=12% Similarity=0.119 Sum_probs=36.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
.++..++.++.-.|.. .....+||..+|++...|+++...-|.|.++...
T Consensus 114 ~L~~rer~V~~L~~~e-----g~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 114 VLTEREKEVYLMHRGY-----GLSYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4666677766664422 2346789999999999999999888888776543
No 80
>PRK10403 transcriptional regulator NarP; Provisional
Probab=48.97 E-value=21 Score=29.35 Aligned_cols=46 Identities=17% Similarity=0.243 Sum_probs=36.5
Q ss_pred CcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHH
Q psy526 65 AAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116 (274)
Q Consensus 65 T~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~K 116 (274)
..++..+.++|+..... ..+.+||+.++++++.|+++.+|=|.|..
T Consensus 152 ~~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 152 SVLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred ccCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 35899999988865432 44678999999999999999998887754
No 81
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=48.89 E-value=36 Score=28.52 Aligned_cols=32 Identities=6% Similarity=0.122 Sum_probs=26.2
Q ss_pred HHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 88 PERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 88 ~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
....+||..+|++...|+.+...-|.+.|+..
T Consensus 145 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 145 LSNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 34678999999999999999977777777654
No 82
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=48.61 E-value=45 Score=27.72 Aligned_cols=49 Identities=18% Similarity=0.127 Sum_probs=34.8
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
.++..+..+|.-.|. ......+||..+|++...|+++...-|.+.|+..
T Consensus 100 ~L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 100 ELPDEYREAIRLTEL-----EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred hCCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 355556666655443 2345678999999999999999877777766654
No 83
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=48.56 E-value=44 Score=28.33 Aligned_cols=49 Identities=6% Similarity=0.070 Sum_probs=35.0
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
++..+..++.-.|-. .....+||..+|++...|+++...-|.+.|++..
T Consensus 135 Lp~~~R~v~~L~~~~-----g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 183 (189)
T PRK12530 135 LPAQQARVFMMREYL-----ELSSEQICQECDISTSNLHVLLYRARLQLQACLS 183 (189)
T ss_pred CCHHHHHHHhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 455566666555432 2346789999999999999999877777776543
No 84
>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=48.47 E-value=32 Score=27.81 Aligned_cols=46 Identities=20% Similarity=0.165 Sum_probs=31.5
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~K 116 (274)
.++..+..++...| .......+||..+|++...|+++...-|.+.|
T Consensus 111 ~L~~~~r~v~~l~~-----~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 111 KLPERQRELLQLRY-----QRGVSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred HCCHHHHHHHHHHH-----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 35555656665543 23345778999999999999988765555544
No 85
>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=48.36 E-value=36 Score=22.18 Aligned_cols=37 Identities=19% Similarity=0.207 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhh
Q psy526 68 SHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQN 110 (274)
Q Consensus 68 t~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqN 110 (274)
+..+...+...+ .. ....+||..++++...|+.|...
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~~ 38 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLRN 38 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 455666665543 22 35678999999999999999863
No 86
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=48.13 E-value=29 Score=29.40 Aligned_cols=37 Identities=11% Similarity=0.171 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHH
Q psy526 85 LSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQ 121 (274)
Q Consensus 85 Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~ 121 (274)
-......+||..+|++...|+++...-|.+.|+.-..
T Consensus 145 ~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 181 (193)
T TIGR02947 145 VEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD 181 (193)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3444577899999999999999998888888776543
No 87
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=48.10 E-value=52 Score=27.49 Aligned_cols=35 Identities=17% Similarity=0.152 Sum_probs=29.5
Q ss_pred HHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526 88 PERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL 122 (274)
Q Consensus 88 ~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~ 122 (274)
....+||..+|++...|++....-|++.|+.-...
T Consensus 134 ~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~ 168 (179)
T PRK12543 134 YSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIE 168 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999999999999988865444
No 88
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=48.03 E-value=30 Score=28.23 Aligned_cols=47 Identities=23% Similarity=0.143 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
++..|..+|.-.|- ......+||..+|++...|+++...-|.+.|+.
T Consensus 113 L~~~~r~v~~l~~~-----~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 113 LPLERRNVLLLRDY-----YGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred CCHHHHHHhhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 55555555555432 223467899999999999999987777766653
No 89
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=47.47 E-value=34 Score=30.00 Aligned_cols=47 Identities=19% Similarity=0.216 Sum_probs=36.2
Q ss_pred cCCHHHHHHHHHHHhhCC--CCCHHHHHHHHHHhCCCcccchhhhhhhhhH
Q psy526 66 AFSHAQVYELEKRFNAQK--YLSGPERADVAKSLKLTETQVKIWFQNRRYK 114 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~--~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k 114 (274)
.+|..|+++|..+|...= ||=.-...+||+++|+++..+ |..=||+.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~--~ehLRrAe 203 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTL--SEHLRRAE 203 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH--HHHHHHHH
Confidence 699999999999997533 577777889999999998644 44444444
No 90
>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=46.95 E-value=13 Score=24.09 Aligned_cols=21 Identities=10% Similarity=0.172 Sum_probs=18.0
Q ss_pred HHHHHHHhCCCcccchhhhhh
Q psy526 90 RADVAKSLKLTETQVKIWFQN 110 (274)
Q Consensus 90 r~~LA~~l~L~~~~V~vWFqN 110 (274)
..++|+.+|++...|+.|.++
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 467899999999999999644
No 91
>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=46.43 E-value=59 Score=27.58 Aligned_cols=51 Identities=10% Similarity=0.112 Sum_probs=35.9
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL 122 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~ 122 (274)
+...+..++...|- ......+||..+|++...|+++...-|.+.|+.....
T Consensus 132 L~~~~r~v~~l~~~-----~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~ 182 (188)
T TIGR02943 132 LPEQTARVFMMREV-----LGFESDEICQELEISTSNCHVLLYRARLSLRACLSIN 182 (188)
T ss_pred CCHHHHHHHHHHHH-----hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555555555432 2345778999999999999999887777777765443
No 92
>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=45.90 E-value=39 Score=24.04 Aligned_cols=44 Identities=18% Similarity=0.360 Sum_probs=21.9
Q ss_pred CCcCCHHH-HHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhh
Q psy526 64 RAAFSHAQ-VYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQ 109 (274)
Q Consensus 64 RT~ft~~Q-l~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFq 109 (274)
|..|+... |.+++.+.. ...=-...| ..|.+.|+.+++|+-|.+
T Consensus 3 rrsy~~~FKL~Vv~~a~~-~~nc~~~~R-Aaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEK-DNNCKGNQR-AAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH--TTTTT-HH-HHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHH-ccchhhhHH-HHHHHhCccHHHHHHHHH
Confidence 44566654 445544443 322222223 359999999999999953
No 93
>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=45.65 E-value=33 Score=27.94 Aligned_cols=47 Identities=17% Similarity=0.152 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
++..+..+|...|- ......+||..+|++...|+++...-|.+.|+.
T Consensus 111 L~~~~r~i~~l~~~-----~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 111 LPARQRAVVVLRYY-----EDLSEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred CCHHHHHHhhhHHH-----hcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 34455555554442 233467899999999999999988777776664
No 94
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=45.49 E-value=46 Score=27.89 Aligned_cols=31 Identities=19% Similarity=0.264 Sum_probs=25.0
Q ss_pred HHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 88 PERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 88 ~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
....+||+.+|++...|++|...-|.+.|+.
T Consensus 150 ~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 150 CSHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred CCHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 3467899999999999999987777666553
No 95
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=45.19 E-value=38 Score=27.43 Aligned_cols=45 Identities=18% Similarity=0.178 Sum_probs=34.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~K 116 (274)
.++..+.++|+- +..+ + ...+||+.++++++.|+.|.+|-|.|..
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 488888888876 4333 2 3678999999999999999988776643
No 96
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=45.10 E-value=57 Score=26.36 Aligned_cols=48 Identities=15% Similarity=0.106 Sum_probs=32.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
.++..+..++.-.|-. .....+||..||++...|++....-|.+.|+.
T Consensus 106 ~Lp~~~r~v~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 106 KLPARQREAFLLRYWE-----DMDVAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred hCCHHHHHHHHHHHHh-----cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3555566666554422 22367899999999999999987766666654
No 97
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=44.95 E-value=21 Score=24.48 Aligned_cols=30 Identities=7% Similarity=0.185 Sum_probs=18.6
Q ss_pred HHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 89 ERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 89 ~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
...+||+.+|++..+|.-|+.++..+..-.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~ 41 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLD 41 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HH
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHH
Confidence 466789999999999999998875454443
No 98
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=44.91 E-value=40 Score=29.76 Aligned_cols=47 Identities=9% Similarity=0.154 Sum_probs=34.9
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
+...+..++...|. ......+||..+|++...|+.+...-|.+.|+.
T Consensus 185 L~~~~r~vl~l~~~-----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 185 LPEREQLVLSLYYQ-----EELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CCHHHHHHHHhHhc-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45555666655553 233568899999999999999998888887764
No 99
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=44.62 E-value=14 Score=25.99 Aligned_cols=28 Identities=25% Similarity=0.381 Sum_probs=21.2
Q ss_pred HHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 88 PERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 88 ~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
-...+||..||++...|..|- .|.+|..
T Consensus 14 ~~~~eIA~~Lg~~~~TV~~W~--~r~~W~~ 41 (58)
T PF06056_consen 14 WSIKEIAEELGVPRSTVYSWK--DRYKWDE 41 (58)
T ss_pred CCHHHHHHHHCCChHHHHHHH--HhhCccc
Confidence 346789999999999999995 3444443
No 100
>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=44.52 E-value=42 Score=29.33 Aligned_cols=47 Identities=17% Similarity=0.195 Sum_probs=35.5
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
.++..+..+|...|... ....+||..+|++...|+.+.+.-+.+.|+
T Consensus 175 ~L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred hCCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 46777777777776322 246889999999999999998777766665
No 101
>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=43.37 E-value=42 Score=27.61 Aligned_cols=47 Identities=15% Similarity=0.215 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
+...+.+++...|-. .....+||..+|++...|+++..--|.+.|+.
T Consensus 120 L~~~~r~i~~l~~~~-----g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 120 LNDKYQTAIILRYYH-----DLTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred CCHHHhHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 445555555544422 24567899999999999999987767666653
No 102
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=43.24 E-value=57 Score=27.58 Aligned_cols=49 Identities=4% Similarity=0.024 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
+...+..++.-.|- ......+||..+|++...|+++...-|.+.|+...
T Consensus 137 L~~~~r~i~~L~~~-----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 137 LPENTARVFTLKEI-----LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred CCHHHHHHhhhHHH-----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 34445555543332 22346789999999999999999888888777653
No 103
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=43.21 E-value=25 Score=29.02 Aligned_cols=35 Identities=17% Similarity=0.184 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 85 LSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 85 Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
-.....++||..+|++...|++.+..-|.+.|+.-
T Consensus 134 ~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 134 LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34445788999999999999999988888877754
No 104
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=43.17 E-value=28 Score=29.34 Aligned_cols=36 Identities=14% Similarity=0.128 Sum_probs=29.3
Q ss_pred CHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHH
Q psy526 86 SGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQ 121 (274)
Q Consensus 86 s~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~ 121 (274)
......+||..+|++...|++....-|.+.|+.-+.
T Consensus 153 ~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~ 188 (193)
T PRK11923 153 DGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQP 188 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 334467899999999999999998888888876554
No 105
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=42.71 E-value=32 Score=28.17 Aligned_cols=45 Identities=18% Similarity=0.108 Sum_probs=35.4
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~K 116 (274)
.+|..+.++|+-.... ..+++||..++++++.|++..++-|.|..
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 5888888888766542 26788999999999999999888776643
No 106
>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=42.63 E-value=44 Score=27.26 Aligned_cols=46 Identities=30% Similarity=0.190 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
++..+..+|.-.| -......+||..+|++...|++...--|.+.|+
T Consensus 123 L~~~~r~vl~l~~-----~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 123 LTPKQQHVIALRF-----GQNLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred CCHHHHHHHHHHH-----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4444444444433 223456789999999999999887655555554
No 107
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=42.35 E-value=60 Score=27.58 Aligned_cols=33 Identities=15% Similarity=0.181 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 87 GPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 87 ~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
.....+||..+|++...|++.+..-|.+.|+.-
T Consensus 170 ~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 170 GKSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 355678999999999999988877777766643
No 108
>PRK10072 putative transcriptional regulator; Provisional
Probab=41.90 E-value=15 Score=28.70 Aligned_cols=40 Identities=25% Similarity=0.255 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhh
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRY 113 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~ 113 (274)
.+...+..|...-. -...+||..+|++...|..|.+.+|.
T Consensus 33 ~~~~eik~LR~~~g-------lTQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 33 TSFTEFEQLRKGTG-------LKIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred CChHHHHHHHHHcC-------CCHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 35666666654422 22678999999999999999988775
No 109
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=41.88 E-value=61 Score=27.35 Aligned_cols=33 Identities=27% Similarity=0.291 Sum_probs=26.0
Q ss_pred HHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 87 GPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 87 ~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
.....+||..+|++...|+.++..-|.+.|+.-
T Consensus 122 g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 122 GLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 345678999999999999999877776666543
No 110
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=41.87 E-value=42 Score=26.76 Aligned_cols=43 Identities=12% Similarity=0.132 Sum_probs=28.1
Q ss_pred CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhh
Q psy526 64 RAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQN 110 (274)
Q Consensus 64 RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqN 110 (274)
|..|+.++....-.....+. ....+||.++|++..+|..|.+-
T Consensus 10 rr~ys~EfK~~aV~~~~~~g----~sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPG----MTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCC----CCHHHHHHHHCcCHHHHHHHHHH
Confidence 34477776544333333333 24567899999999999999543
No 111
>KOG0773|consensus
Probab=41.81 E-value=48 Score=31.13 Aligned_cols=38 Identities=39% Similarity=0.473 Sum_probs=34.3
Q ss_pred hhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 80 NAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 80 ~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
..++||+..+...|+...+|+..+|..||-|.|.+.+.
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~ 154 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKK 154 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHh
Confidence 45889999999999999999999999999999887665
No 112
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=41.77 E-value=88 Score=26.30 Aligned_cols=51 Identities=12% Similarity=0.046 Sum_probs=36.2
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL 122 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~ 122 (274)
++..+..++.-.|-. .....+||..+|++...|++....-|.+.|+.....
T Consensus 132 Lp~~~r~v~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 182 (191)
T PRK12520 132 LPPRTGRVFMMREWL-----ELETEEICQELQITATNAWVLLYRARMRLRECLDLH 182 (191)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 555555555554322 233678999999999999999988888877765443
No 113
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=41.77 E-value=46 Score=28.38 Aligned_cols=33 Identities=12% Similarity=-0.035 Sum_probs=27.4
Q ss_pred HHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 88 PERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 88 ~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
....+||..+|++...|++++..-|.+.|+.-.
T Consensus 130 ~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 130 FSYEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 446789999999999999999888877776543
No 114
>PRK09480 slmA division inhibitor protein; Provisional
Probab=41.30 E-value=29 Score=28.92 Aligned_cols=42 Identities=12% Similarity=0.133 Sum_probs=33.2
Q ss_pred HHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhh
Q psy526 71 QVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRY 113 (274)
Q Consensus 71 Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~ 113 (274)
-++.....|...+. ......+||++.|+++..+--+|.|+-.
T Consensus 15 Il~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 15 ILQALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 34444455666656 8888999999999999999999999763
No 115
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=41.05 E-value=54 Score=27.88 Aligned_cols=48 Identities=10% Similarity=0.082 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
++..+..++.-.|- .....++||+.+|++...|++++.--|.+.|+..
T Consensus 137 L~~~~r~i~~L~~~-----~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 137 LPERQRQAVVLRHI-----EGLSNPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 44444444444332 2234678999999999999999987777777654
No 116
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=40.98 E-value=57 Score=26.81 Aligned_cols=47 Identities=17% Similarity=0.006 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
++..+..++.-.|- ......+||..+|++...|+++...-|.+.|+.
T Consensus 113 L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 113 LSADQREAIILIGA-----SGFSYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 44555555554432 234477899999999999999987777666654
No 117
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=40.96 E-value=56 Score=27.35 Aligned_cols=32 Identities=25% Similarity=0.218 Sum_probs=26.3
Q ss_pred HHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 87 GPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 87 ~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
.....+||..+|++...|++....-|.+.|+.
T Consensus 145 g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 145 GLSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34567899999999999999998777776663
No 118
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=40.84 E-value=76 Score=28.64 Aligned_cols=51 Identities=12% Similarity=0.135 Sum_probs=38.1
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQ 121 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~ 121 (274)
.+...+..+|...|.. .....+||..+|++...|+.+...-+.+.|++-..
T Consensus 212 ~L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 262 (268)
T PRK06288 212 TLPEREKKVLILYYYE-----DLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAE 262 (268)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 4666677777766633 23467899999999999999988888887776543
No 119
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=40.67 E-value=53 Score=29.18 Aligned_cols=33 Identities=12% Similarity=0.150 Sum_probs=27.3
Q ss_pred HHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 88 PERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 88 ~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
....+||..+|++...|+++...-|.+.|+...
T Consensus 188 ~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 188 MSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 346789999999999999999888888776543
No 120
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=40.49 E-value=61 Score=26.34 Aligned_cols=47 Identities=17% Similarity=0.266 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
++..+..+|.-.|- ......+||+.+|++...|+.+..--|.+.|+.
T Consensus 110 L~~~~r~v~~l~~~-----~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 110 LPARTRYAFEMYRL-----HGETQKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34444445544332 223467899999999999999876666666554
No 121
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=40.07 E-value=47 Score=31.25 Aligned_cols=53 Identities=19% Similarity=0.181 Sum_probs=40.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
.++..|+.+|...|... |-.....++||..+|++...|+.+...-+.|.|+.-
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 57788888888776322 233456788999999999999999988888877654
No 122
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=40.04 E-value=44 Score=28.26 Aligned_cols=47 Identities=19% Similarity=0.282 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
++..+..++.-.|- ......+||+.+|++...|++..+.-|.+.|+.
T Consensus 132 L~~~~r~i~~l~~~-----~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 132 LEKLDREIFIRRYL-----LGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred CCHHHHHHHHHHHH-----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 45555555554432 223467899999999999988876666665554
No 123
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=39.94 E-value=54 Score=29.31 Aligned_cols=48 Identities=10% Similarity=0.126 Sum_probs=35.4
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
.++..+..+|...|-. .....+||..+|++...|+.|...-+.|.|+.
T Consensus 205 ~L~~~~r~vl~l~~~~-----g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFIE-----NLSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHhC-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4666777777766532 23468899999999999999987777666653
No 124
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=39.70 E-value=51 Score=29.44 Aligned_cols=48 Identities=13% Similarity=0.143 Sum_probs=35.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
.++..+..+|...|... ....+||..+|++...|+.+...-+.|.|+.
T Consensus 205 ~L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred cCCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 46677777777776432 2457899999999999999987777776653
No 125
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=39.12 E-value=85 Score=26.63 Aligned_cols=49 Identities=22% Similarity=0.069 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
+...+..+|+..|- ......+||..+|++...|++=...-|.+.|+.-.
T Consensus 135 Lp~~~r~i~~l~~~-----~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l~ 183 (192)
T PRK09643 135 LPVEQRAALVAVDM-----QGYSVADAARMLGVAEGTVKSRCARGRARLAELLG 183 (192)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 44445555544332 23346789999999999987766555555555443
No 126
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=38.91 E-value=65 Score=26.86 Aligned_cols=47 Identities=17% Similarity=0.136 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
++..+..+|.-.| -......+||..+|++...|+++...-|.+.|+.
T Consensus 136 L~~~~r~vl~l~~-----~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 136 LSPEERRVIEVLY-----YQGYTHREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4555555555433 2234467899999999999999887666665553
No 127
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=38.90 E-value=73 Score=27.06 Aligned_cols=49 Identities=12% Similarity=-0.020 Sum_probs=33.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
+...+..++.-.|- ......+||..||++...|+++...-|.+.|+...
T Consensus 117 Lp~~~r~i~~L~~~-----~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 117 LPDDQREAIILVGA-----SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 44445555544332 22345689999999999999999888877776543
No 128
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.84 E-value=37 Score=26.29 Aligned_cols=38 Identities=18% Similarity=0.231 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccc
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQV 104 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V 104 (274)
+.++|+..-...|+.+--.+.--.++||.+||.++.-|
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~l 40 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKL 40 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHH
Confidence 56667666666666666666678889999999887544
No 129
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=38.49 E-value=68 Score=26.40 Aligned_cols=47 Identities=19% Similarity=0.169 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
+...+..+|.-.|-. ....++||..||++...|+.+...-|.+.|+.
T Consensus 119 L~~~~r~vl~L~~~~-----g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 165 (173)
T PRK09645 119 LSPEHRAVLVRSYYR-----GWSTAQIAADLGIPEGTVKSRLHYALRALRLA 165 (173)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 455566666554422 23467899999999999999987666666654
No 130
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=38.44 E-value=39 Score=27.79 Aligned_cols=45 Identities=20% Similarity=0.143 Sum_probs=35.5
Q ss_pred CcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHH
Q psy526 65 AAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115 (274)
Q Consensus 65 T~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~ 115 (274)
..++..+..+|....+. ..+++||.+++++.+.|+++.++-|.|.
T Consensus 148 ~~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl 192 (210)
T PRK09935 148 TVLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGKL 192 (210)
T ss_pred ccCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 35788888888754432 5578899999999999999998877764
No 131
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=38.39 E-value=20 Score=23.53 Aligned_cols=23 Identities=22% Similarity=0.398 Sum_probs=17.3
Q ss_pred HHHHHHHHHhCCCcccchhhhhh
Q psy526 88 PERADVAKSLKLTETQVKIWFQN 110 (274)
Q Consensus 88 ~~r~~LA~~l~L~~~~V~vWFqN 110 (274)
....+||..+|++...|..|.+.
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 45678999999999999999754
No 132
>PF13518 HTH_28: Helix-turn-helix domain
Probab=38.24 E-value=27 Score=22.82 Aligned_cols=24 Identities=17% Similarity=0.481 Sum_probs=19.8
Q ss_pred HHHHHHHHhCCCcccchhhhhhhh
Q psy526 89 ERADVAKSLKLTETQVKIWFQNRR 112 (274)
Q Consensus 89 ~r~~LA~~l~L~~~~V~vWFqNrR 112 (274)
...++|.++|++..+|..|.+.-+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 456699999999999999976543
No 133
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=38.19 E-value=36 Score=28.68 Aligned_cols=35 Identities=14% Similarity=0.178 Sum_probs=28.3
Q ss_pred CHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 86 SGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 86 s~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
.....++||..+|++...|++|...-|.+.|+...
T Consensus 149 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 183 (188)
T PRK09640 149 AELEFQEIADIMHMGLSATKMRYKRALDKLREKFA 183 (188)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 33456889999999999999999888877777543
No 134
>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=38.10 E-value=80 Score=28.35 Aligned_cols=36 Identities=11% Similarity=0.237 Sum_probs=30.3
Q ss_pred HHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHHHh
Q psy526 89 ERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQLLE 124 (274)
Q Consensus 89 ~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~~~ 124 (274)
...+||..+|++...|+++...-|.+.|++-..+..
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~~ 214 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLERTRRRLA 214 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999999999888887655543
No 135
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=37.82 E-value=64 Score=27.05 Aligned_cols=48 Identities=13% Similarity=0.063 Sum_probs=33.6
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
.++..+..++.-.|- ......+||..+|++...|+.+...-|.+.|+.
T Consensus 131 ~L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 131 RLPEKMRLAIQAVKL-----EGLSVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred hCCHHHHHHHHHHHH-----cCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 355555555554332 334567899999999999999987777666654
No 136
>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=37.49 E-value=23 Score=22.34 Aligned_cols=23 Identities=13% Similarity=0.456 Sum_probs=19.5
Q ss_pred HHHHHHHhCCCcccchhhhhhhh
Q psy526 90 RADVAKSLKLTETQVKIWFQNRR 112 (274)
Q Consensus 90 r~~LA~~l~L~~~~V~vWFqNrR 112 (274)
..++|..+|++...|..|.++.+
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCC
Confidence 46889999999999999986644
No 137
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=37.47 E-value=68 Score=26.81 Aligned_cols=47 Identities=13% Similarity=0.125 Sum_probs=33.6
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
.+...|+.++.-.|-. ....++||..||++...|++....-+.+++.
T Consensus 127 ~Lp~~~R~v~~L~~~~-----g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 127 TLRPRVKQAFLMATLD-----GMKQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3556666666654432 2346789999999999999999877776654
No 138
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=37.41 E-value=21 Score=24.96 Aligned_cols=19 Identities=21% Similarity=0.317 Sum_probs=17.0
Q ss_pred HHHHHHHhCCCcccchhhh
Q psy526 90 RADVAKSLKLTETQVKIWF 108 (274)
Q Consensus 90 r~~LA~~l~L~~~~V~vWF 108 (274)
+.++|+.+|++.++|+.|=
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 4689999999999999994
No 139
>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=37.19 E-value=66 Score=27.00 Aligned_cols=34 Identities=21% Similarity=0.296 Sum_probs=26.0
Q ss_pred CCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 84 YLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 84 ~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
|-......+||..+|++...|++++.--|.+.|+
T Consensus 162 ~~~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 162 YLDGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3345567889999999999999888666666554
No 140
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=36.90 E-value=73 Score=28.00 Aligned_cols=47 Identities=11% Similarity=-0.060 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
+...+..+|...|- .....++||..+|++...|+++...-|.+.|+.
T Consensus 135 Lp~~~R~v~~L~y~-----eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~ 181 (216)
T PRK12533 135 LPVEYREVLVLREL-----EDMSYREIAAIADVPVGTVMSRLARARRRLAAL 181 (216)
T ss_pred CCHHHHhHhhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34444455544332 223467899999999999999987767666664
No 141
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=36.85 E-value=85 Score=27.14 Aligned_cols=33 Identities=12% Similarity=0.129 Sum_probs=26.4
Q ss_pred HHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 88 PERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 88 ~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
....+||..||++...|+++...-|.+.|+...
T Consensus 155 ~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~ 187 (203)
T PRK09647 155 LSYEEIAATLGVKLGTVRSRIHRGRQQLRAALA 187 (203)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 346789999999999999999877777766543
No 142
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=36.83 E-value=37 Score=28.69 Aligned_cols=35 Identities=17% Similarity=0.098 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 85 LSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 85 Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
-......+||..+|++...|+++...-|.+.|+..
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 153 HGDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 44456788999999999999999888777777653
No 143
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=36.80 E-value=67 Score=28.16 Aligned_cols=52 Identities=15% Similarity=0.146 Sum_probs=35.3
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
.++..++.++.-.|... +-......+||..+|++...|+.+...-|.+.|+.
T Consensus 178 ~Lp~~~R~v~~L~y~l~-~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 178 KLSDREKQIMELRFGLN-GGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred hCCHHHHHHHHHHhccC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35566666666655210 12234477899999999999999987777776664
No 144
>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=36.67 E-value=36 Score=23.60 Aligned_cols=37 Identities=24% Similarity=0.326 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhh
Q psy526 70 AQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQN 110 (274)
Q Consensus 70 ~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqN 110 (274)
.|+..|+-.+. +...+.. +||..+|++++.|+.-..+
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i~~ 42 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDINE 42 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHHHH
Confidence 57888888888 6555544 8999999999988766543
No 145
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=36.51 E-value=80 Score=26.72 Aligned_cols=47 Identities=17% Similarity=0.112 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
+...+..++.-.|- .....++||..+|++...|++....-|.+.|+.
T Consensus 142 Lp~~~r~v~~l~~~-----eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 142 LPKAQRDVLQAVYL-----EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 44555555554332 223467899999999999998887766666654
No 146
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=36.40 E-value=89 Score=26.76 Aligned_cols=31 Identities=19% Similarity=0.288 Sum_probs=26.1
Q ss_pred HHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 89 ERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 89 ~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
...+||..+|++...|++....-|.+.|+.-
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999887777777654
No 147
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=36.25 E-value=82 Score=26.63 Aligned_cols=50 Identities=12% Similarity=0.001 Sum_probs=34.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
.++..+..++.-.|-. .....+||..+|++...|+++..--|.+.|+...
T Consensus 111 ~Lp~~~R~v~~L~~~e-----g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 111 DLPEEQRAALHLVAIE-----GLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3555566666554332 2346789999999999999998777777666543
No 148
>PRK10651 transcriptional regulator NarL; Provisional
Probab=35.96 E-value=58 Score=26.72 Aligned_cols=45 Identities=20% Similarity=0.179 Sum_probs=35.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~K 116 (274)
.++..+.++|+-...- ....+||.+++++++.|++..+|-|.|..
T Consensus 155 ~Lt~rE~~vl~~l~~g------~~~~~ia~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 155 QLTPRERDILKLIAQG------LPNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 4899999999765421 23567899999999999999998887754
No 149
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=35.93 E-value=77 Score=26.17 Aligned_cols=47 Identities=13% Similarity=0.113 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
+...+..++.-.|- ......+||+.+|++...|+++...-+.+.+..
T Consensus 120 Lp~~~r~v~~L~~~-----~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 120 LSSKARAAFLYNRL-----DGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 44555555554432 223467899999999999999997777666553
No 150
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=35.72 E-value=52 Score=29.38 Aligned_cols=47 Identities=11% Similarity=0.214 Sum_probs=34.3
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
+...+..++...|. ......+||..+|++...|++++..-|.+.|+.
T Consensus 202 L~~~~r~vl~l~~~-----~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 202 LSEKEQLVISLFYK-----EELTLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 45566666665542 333467899999999999999998777776653
No 151
>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=35.39 E-value=57 Score=28.43 Aligned_cols=47 Identities=17% Similarity=0.232 Sum_probs=35.4
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
.++..+..+|...|.. .....+||..+|++...|+.|...-+.|.|+
T Consensus 178 ~L~~~~r~vl~l~y~~-----~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFFE-----DKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5777777777776642 2357789999999999999998766666554
No 152
>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=34.98 E-value=24 Score=22.57 Aligned_cols=18 Identities=22% Similarity=0.392 Sum_probs=15.3
Q ss_pred HHHHHHHhCCCcccchhh
Q psy526 90 RADVAKSLKLTETQVKIW 107 (274)
Q Consensus 90 r~~LA~~l~L~~~~V~vW 107 (274)
+.++|+.+|++.+.|+.|
T Consensus 2 i~e~A~~~gvs~~tlR~y 19 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYY 19 (38)
T ss_dssp HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHH
Confidence 457899999999999999
No 153
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=34.60 E-value=57 Score=27.06 Aligned_cols=33 Identities=15% Similarity=0.210 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 86 SGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 86 s~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
.....++||..+|++...|+++...-|.|.|+.
T Consensus 151 ~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 151 EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 345567899999999999999887777776654
No 154
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=34.13 E-value=56 Score=29.66 Aligned_cols=47 Identities=13% Similarity=0.186 Sum_probs=35.4
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
.++..+..+|...|.. .....+||..+|++...|+.|...-+.|.|+
T Consensus 215 ~L~~rer~vl~l~y~~-----~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 215 ALPERERTVLVLRFFE-----SMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred cCCHHHHHHHHHHhcC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4666777777777632 3346889999999999999998777766665
No 155
>PF13565 HTH_32: Homeodomain-like domain
Probab=33.96 E-value=1.7e+02 Score=20.68 Aligned_cols=32 Identities=9% Similarity=0.080 Sum_probs=24.2
Q ss_pred CHHHHHHHHHHHhhCCCCCHHHHHH-HHHHhCC
Q psy526 68 SHAQVYELEKRFNAQKYLSGPERAD-VAKSLKL 99 (274)
Q Consensus 68 t~~Ql~~Le~~F~~~~~Ps~~~r~~-LA~~l~L 99 (274)
+.++.+.|.+.+..++.-+..++.+ |+.+.|+
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~ 64 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGI 64 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCC
Confidence 7888799999999888777666665 5666664
No 156
>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=33.61 E-value=83 Score=27.80 Aligned_cols=52 Identities=12% Similarity=0.126 Sum_probs=39.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
.++..+..+|...|....+ ......+||..+|++...|+.+...-+.|.|..
T Consensus 176 ~L~~~er~vl~l~ygl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~ 227 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRHP 227 (238)
T ss_pred hCCHHHHHHHHHHhCCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhh
Confidence 4677788888877743222 223578899999999999999988887777764
No 157
>KOG0260|consensus
Probab=33.51 E-value=4e+02 Score=30.14 Aligned_cols=9 Identities=33% Similarity=0.309 Sum_probs=3.7
Q ss_pred HHHhCCCCC
Q psy526 12 KKINNNNIT 20 (274)
Q Consensus 12 ~~~~g~~~s 20 (274)
..+..|++.
T Consensus 1240 ~~Ie~~ml~ 1248 (1605)
T KOG0260|consen 1240 KCIEANMLG 1248 (1605)
T ss_pred HHHHHhhhh
Confidence 334444443
No 158
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=33.43 E-value=81 Score=26.15 Aligned_cols=33 Identities=15% Similarity=0.176 Sum_probs=25.6
Q ss_pred CHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 86 SGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 86 s~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
......+||..+|++...|+++...-+.+++..
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~ 166 (172)
T PRK09651 134 DGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLF 166 (172)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 334578899999999999999987666665543
No 159
>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=33.37 E-value=38 Score=27.16 Aligned_cols=34 Identities=21% Similarity=0.182 Sum_probs=26.7
Q ss_pred CCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 84 YLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 84 ~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
|......++||..+|++...|+++..--|.|.|+
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3445567899999999999999998766666554
No 160
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=33.23 E-value=81 Score=27.04 Aligned_cols=48 Identities=10% Similarity=-0.019 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
++..+..++.-.|- .-....+||..+|++...|+++...-|.+.|+..
T Consensus 134 Lp~~~r~v~~l~~~-----~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l 181 (196)
T PRK12535 134 LPPERREALILTQV-----LGYTYEEAAKIADVRVGTIRSRVARARADLIAAT 181 (196)
T ss_pred CCHHHHHHhhhHHH-----hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 44444444444432 2234678999999999999999877777766654
No 161
>PRK06424 transcription factor; Provisional
Probab=33.23 E-value=34 Score=28.61 Aligned_cols=25 Identities=12% Similarity=0.045 Sum_probs=21.8
Q ss_pred HHHHHHHhCCCcccchhhhhhhhhH
Q psy526 90 RADVAKSLKLTETQVKIWFQNRRYK 114 (274)
Q Consensus 90 r~~LA~~l~L~~~~V~vWFqNrR~k 114 (274)
.++||..+|++...|.-|..+++.-
T Consensus 100 Q~eLA~~iGvs~stIskiE~G~~~P 124 (144)
T PRK06424 100 QADLAAKIFERKNVIASIERGDLLP 124 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCCC
Confidence 5689999999999999999887754
No 162
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=33.05 E-value=66 Score=29.15 Aligned_cols=50 Identities=12% Similarity=0.084 Sum_probs=38.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
.++..+..+|..+|-. + ......+||..+|++...|+-+..+-..|.|+.
T Consensus 218 ~L~~rer~vl~l~y~~--~-~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~ 267 (270)
T TIGR02392 218 SLDARSRRIIEARWLD--D-DKLTLQELAAEYGVSAERIRQIEKNAMKKLKAA 267 (270)
T ss_pred cCCHHHHHHHHHHhcC--C-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4777788888888742 1 123467899999999999999988877777763
No 163
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=32.94 E-value=76 Score=26.76 Aligned_cols=29 Identities=14% Similarity=-0.008 Sum_probs=23.5
Q ss_pred HHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 89 ERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 89 ~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
..++||..+|++...|+++...-|.+.|+
T Consensus 148 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 46789999999999999998666665554
No 164
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=32.93 E-value=62 Score=29.13 Aligned_cols=48 Identities=15% Similarity=0.088 Sum_probs=35.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
.+...+..+|...|.. .....+||..+|++...|+.+..--+.|.|+.
T Consensus 203 ~L~~~~r~vl~l~y~~-----~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 203 QLEERTREVLEFVFLH-----DLTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred cCCHHHHHHHHHHHHC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3566666677666642 34578899999999999999987777666654
No 165
>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=32.90 E-value=40 Score=22.04 Aligned_cols=21 Identities=14% Similarity=0.273 Sum_probs=18.7
Q ss_pred HHHHHhCCCcccchhhhhhhh
Q psy526 92 DVAKSLKLTETQVKIWFQNRR 112 (274)
Q Consensus 92 ~LA~~l~L~~~~V~vWFqNrR 112 (274)
+||+.+|++...|..|+.+++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999883
No 166
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=32.73 E-value=1.1e+02 Score=26.45 Aligned_cols=49 Identities=8% Similarity=0.101 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
++..|..++.-.|-. .....+||..+|++...|+++...-|.+.|+...
T Consensus 149 L~~~~r~v~~L~~~~-----g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~ 197 (206)
T PRK12544 149 LPAKYARVFMMREFI-----ELETNEICHAVDLSVSNLNVLLYRARLRLRECLE 197 (206)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 445555555554422 2235789999999999999999888888777644
No 167
>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=31.85 E-value=26 Score=23.22 Aligned_cols=23 Identities=13% Similarity=0.320 Sum_probs=19.6
Q ss_pred HHHHHHHhCCCcccchhhhhhhh
Q psy526 90 RADVAKSLKLTETQVKIWFQNRR 112 (274)
Q Consensus 90 r~~LA~~l~L~~~~V~vWFqNrR 112 (274)
..+||..+|+++..|.-|..++|
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 47899999999999999999865
No 168
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=31.40 E-value=94 Score=25.98 Aligned_cols=47 Identities=11% Similarity=0.198 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
++..+..++.-.|- ......+||..+|++...|++....-|.+.|+.
T Consensus 123 L~~~~r~i~~l~~~-----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 169 (185)
T PRK12542 123 LNESNRQVFKYKVF-----YNLTYQEISSVMGITEANVRKQFERARKRVQNM 169 (185)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45555555554332 223467899999999999999887777666654
No 169
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=31.02 E-value=1.1e+02 Score=25.80 Aligned_cols=49 Identities=18% Similarity=-0.012 Sum_probs=33.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
+...+..++...| -.....++||..||++...|++....-|.+.|+...
T Consensus 112 Lp~~~R~v~~L~~-----~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 112 LPQDQREALILVG-----ASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred CCHHHHHHhhHHH-----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4455555554443 233446789999999999999998777777666543
No 170
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=31.01 E-value=75 Score=26.55 Aligned_cols=46 Identities=17% Similarity=0.232 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
+...+..++...| -.....++||..+|++...|++....-|.+.|+
T Consensus 138 L~~~~r~i~~l~~-----~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 138 LEPPRSELIRTAF-----FEGITYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 4444444444443 233456789999999999998887666655554
No 171
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=30.74 E-value=79 Score=28.33 Aligned_cols=47 Identities=15% Similarity=0.208 Sum_probs=35.5
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
.++..+..+|+..|... ....+||..+|++...|+.+-.+-+.|.|+
T Consensus 209 ~L~~~er~vi~~~~~~~-----~t~~eIA~~lgis~~~V~~~~~~al~kLr~ 255 (258)
T PRK08215 209 KLNDREKLILNLRFFQG-----KTQMEVAEEIGISQAQVSRLEKAALKHMRK 255 (258)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 57888888888887432 346789999999999998887665555544
No 172
>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=30.63 E-value=33 Score=24.16 Aligned_cols=20 Identities=15% Similarity=0.270 Sum_probs=17.7
Q ss_pred HHHHHHHhCCCcccchhhhh
Q psy526 90 RADVAKSLKLTETQVKIWFQ 109 (274)
Q Consensus 90 r~~LA~~l~L~~~~V~vWFq 109 (274)
..++|+.+|++...|+.|.+
T Consensus 3 i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46899999999999999964
No 173
>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=30.53 E-value=80 Score=27.60 Aligned_cols=46 Identities=17% Similarity=0.158 Sum_probs=32.4
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~K 116 (274)
.++..+..++...|.. .....+||..+|++...|+.+-..-..|.|
T Consensus 183 ~L~~~e~~i~~~~~~~-----~~t~~eIA~~lgis~~~V~~~~~~al~~Lr 228 (231)
T TIGR02885 183 KLDERERQIIMLRYFK-----DKTQTEVANMLGISQVQVSRLEKKVLKKMK 228 (231)
T ss_pred cCCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 5677777777776642 245788999999999999888554444433
No 174
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=29.78 E-value=58 Score=26.92 Aligned_cols=32 Identities=9% Similarity=0.129 Sum_probs=26.0
Q ss_pred HHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 88 PERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 88 ~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
..-++||+.+|++...|+++...-|.+.|+..
T Consensus 136 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 167 (173)
T PRK12522 136 YSYKEMSEILNIPIGTVKYRLNYAKKQMREHL 167 (173)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 34678999999999999999887777776653
No 175
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=29.76 E-value=72 Score=25.61 Aligned_cols=46 Identities=13% Similarity=0.176 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
++..+..+|+..+... .-.+||..+++++..|+++-++-|.|.+..
T Consensus 142 l~~~e~~vl~~~~~~~------~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~ 187 (202)
T PRK09390 142 LSERERQVMDGLVAGL------SNKVIARDLDISPRTVEVYRANVMTKMQAG 187 (202)
T ss_pred hhhhHHHHHHHHHccC------chHHHHHHcCCCHHHHHHHHHHHHHHHccc
Confidence 4555555555433211 245689999999999999988877776543
No 176
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=29.23 E-value=97 Score=28.54 Aligned_cols=51 Identities=12% Similarity=0.128 Sum_probs=39.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
.++..+..+|...|- +-......+||..+|++...|+.+-..-+.|.|+..
T Consensus 227 ~L~~rer~vl~lr~~---~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l 277 (289)
T PRK07500 227 TLNERELRIIRERRL---REDGATLEALGEELGISKERVRQIEARALEKLRRAL 277 (289)
T ss_pred cCCHHHHHHHHHHhc---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 578888888888773 123345789999999999999999877777776543
No 177
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=29.18 E-value=51 Score=27.17 Aligned_cols=34 Identities=21% Similarity=0.265 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 85 LSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 85 Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
......++||..+|++...|+++...-|.+.|+.
T Consensus 140 ~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 140 YYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred hcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 3445678899999999999999987777776664
No 178
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=29.06 E-value=1e+02 Score=23.05 Aligned_cols=44 Identities=16% Similarity=0.207 Sum_probs=34.2
Q ss_pred cCCHHHHHHHHHHHhh-----CCCCCHHHHHHHHHHhCCCcccchhhhh
Q psy526 66 AFSHAQVYELEKRFNA-----QKYLSGPERADVAKSLKLTETQVKIWFQ 109 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~-----~~~Ps~~~r~~LA~~l~L~~~~V~vWFq 109 (274)
.++.+|+..|...|.. +.+.+..+..++-..+++++..|.-+|.
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 3678899999999874 3478888888877778888877777764
No 179
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=28.54 E-value=1.6e+02 Score=24.85 Aligned_cols=35 Identities=17% Similarity=0.136 Sum_probs=28.5
Q ss_pred HHHHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526 88 PERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL 122 (274)
Q Consensus 88 ~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~ 122 (274)
....+||..||++...|+++..--|.+.++...+.
T Consensus 145 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 179 (188)
T PRK12517 145 FSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKP 179 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 34678999999999999999988787777765544
No 180
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=28.41 E-value=1.2e+02 Score=26.59 Aligned_cols=52 Identities=13% Similarity=0.133 Sum_probs=33.4
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
.++..+..++...|-... -.....++||..+|++...|+.|-..-+.+.|+.
T Consensus 175 ~Lp~~~R~i~~l~y~~~~-~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGN-GKEKTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred hCCHHHHHHHHHHhCCCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 355666666666552110 2234577899999999999988865555555554
No 181
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=28.34 E-value=1.1e+02 Score=24.80 Aligned_cols=44 Identities=11% Similarity=0.120 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~ 115 (274)
++..|..++.-.|- ......+||..+|++...|+++...-+.+.
T Consensus 114 L~~~~r~v~~L~~~-----~g~s~~EIA~~l~is~~tV~~~l~ra~~~~ 157 (161)
T PRK12528 114 LPPLVKRAFLLAQV-----DGLGYGEIATELGISLATVKRYLNKAAMRC 157 (161)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 44555555554432 223467899999999999999986555443
No 182
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=28.15 E-value=76 Score=25.34 Aligned_cols=27 Identities=11% Similarity=0.080 Sum_probs=22.8
Q ss_pred CCHHHHHHHHHHhCCCcccchhhhhhh
Q psy526 85 LSGPERADVAKSLKLTETQVKIWFQNR 111 (274)
Q Consensus 85 Ps~~~r~~LA~~l~L~~~~V~vWFqNr 111 (274)
-.....++||..+|++++.++.+|+..
T Consensus 23 ~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 23 ESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 344667899999999999999999865
No 183
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=28.12 E-value=1.1e+02 Score=26.85 Aligned_cols=53 Identities=13% Similarity=0.134 Sum_probs=35.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
.++..+..++.-.|-... -......+||+.+|++...|+++...-|.+.|+..
T Consensus 178 ~Lp~~~R~ii~L~~~l~~-~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l 230 (234)
T TIGR02835 178 KLNDREKKIMELRFGLVG-GTEKTQKEVADMLGISQSYISRLEKRILKRLKKEI 230 (234)
T ss_pred hCCHHHHHHHHHHHccCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 455666666665542100 12235678999999999999999877777766643
No 184
>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=28.08 E-value=34 Score=22.50 Aligned_cols=23 Identities=13% Similarity=0.037 Sum_probs=20.4
Q ss_pred HHHHHHHhCCCcccchhhhhhhh
Q psy526 90 RADVAKSLKLTETQVKIWFQNRR 112 (274)
Q Consensus 90 r~~LA~~l~L~~~~V~vWFqNrR 112 (274)
..+||..+|++...|.-|..+++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 57899999999999999987765
No 185
>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=28.06 E-value=40 Score=23.56 Aligned_cols=21 Identities=5% Similarity=0.208 Sum_probs=18.0
Q ss_pred HHHHHHHhCCCcccchhhhhh
Q psy526 90 RADVAKSLKLTETQVKIWFQN 110 (274)
Q Consensus 90 r~~LA~~l~L~~~~V~vWFqN 110 (274)
..++|+.+|++.+.|+.|-++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 467999999999999999653
No 186
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=27.42 E-value=98 Score=27.88 Aligned_cols=48 Identities=13% Similarity=0.127 Sum_probs=35.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
.+...+..+|...|. ......+||..+|++...|+.+...-+.|.|+.
T Consensus 205 ~L~~~er~vi~l~y~-----e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 205 ALEEKERKVMALYYY-----EELVLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred cCCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 356666666666663 234567899999999999999987767666664
No 187
>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=27.34 E-value=42 Score=23.32 Aligned_cols=20 Identities=15% Similarity=0.336 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCcccchhhhh
Q psy526 90 RADVAKSLKLTETQVKIWFQ 109 (274)
Q Consensus 90 r~~LA~~l~L~~~~V~vWFq 109 (274)
..++|+.+|++...|+.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46799999999999999964
No 188
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=27.18 E-value=98 Score=27.19 Aligned_cols=45 Identities=24% Similarity=0.208 Sum_probs=36.2
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~K 116 (274)
.+|..++++|+-... . ....+||+.|+++++.|+.+..+-..|..
T Consensus 155 ~Lt~rE~~Vl~l~~~--G----~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 155 LLTHREKEILNKLRI--G----ASNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCHHHHHHHHHHHc--C----CCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 489999999987765 2 23567999999999999999988776654
No 189
>PLN03162 golden-2 like transcription factor; Provisional
Probab=26.99 E-value=5.9e+02 Score=25.00 Aligned_cols=62 Identities=10% Similarity=0.041 Sum_probs=41.1
Q ss_pred CCCCCCCcCCHHHHHH-HHHHHhhC-CCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 59 RKKRSRAAFSHAQVYE-LEKRFNAQ-KYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 59 k~rR~RT~ft~~Ql~~-Le~~F~~~-~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
.+||.|-.+|.+--+. +++....- ..=+...+.+|-..-||+...|+--.|--|...|+...
T Consensus 232 g~KKpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l~~ 295 (526)
T PLN03162 232 GKKKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHLAA 295 (526)
T ss_pred CCCCCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcccccc
Confidence 4567788888865433 33333333 23445566667777789999999999888887665443
No 190
>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=26.75 E-value=92 Score=28.28 Aligned_cols=48 Identities=15% Similarity=0.034 Sum_probs=37.8
Q ss_pred CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 64 RAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 64 RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
...+|..+.++|.-.. .. ....+||..|++++..|+.+.+|-+.|.+-
T Consensus 188 ~~~LT~RE~evl~l~a--~G----~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 188 AGLITAREAEILAWVR--DG----KTNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred ccCCCHHHHHHHHHHH--CC----CCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 4468999999998653 22 345679999999999999999988777654
No 191
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=26.68 E-value=1.5e+02 Score=23.88 Aligned_cols=31 Identities=13% Similarity=0.188 Sum_probs=24.6
Q ss_pred HHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 88 PERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 88 ~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
....+||..+|++...|++....-|.+.|+.
T Consensus 122 ~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 122 LSHQQIAEHLGISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999887666666654
No 192
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=26.52 E-value=95 Score=25.45 Aligned_cols=45 Identities=11% Similarity=0.223 Sum_probs=36.5
Q ss_pred CcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHH
Q psy526 65 AAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115 (274)
Q Consensus 65 T~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~ 115 (274)
..+|..+.++|+-.+.-. .+++||..++++++.|++.-++-|.|.
T Consensus 142 ~~lt~~E~~vl~~l~~g~------~~~~I~~~l~~s~~tv~~~~~~l~~Kl 186 (204)
T PRK09958 142 DSLSKQEISVMRYILDGK------DNNDIAEKMFISNKTVSTYKSRLMEKL 186 (204)
T ss_pred ccCCHHHHHHHHHHHcCC------CHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 358999999998887543 378899999999999999888777664
No 193
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=26.47 E-value=1.4e+02 Score=24.57 Aligned_cols=46 Identities=7% Similarity=0.028 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
++..+..++.-.|- ....-++||..||++...|+.+..+-+.+++.
T Consensus 119 L~~~~r~v~~L~~~-----eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 119 LSGKARAAFLMSQL-----EGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 55555555555432 22346789999999999999988666655543
No 194
>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=26.40 E-value=82 Score=20.51 Aligned_cols=37 Identities=19% Similarity=0.351 Sum_probs=24.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhh
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWF 108 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWF 108 (274)
++.++.+.+...+... ....+||..+|++...|.-|+
T Consensus 6 ~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 6 LSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 5665666666666543 347789999999999887765
No 195
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=26.39 E-value=28 Score=28.41 Aligned_cols=27 Identities=15% Similarity=0.307 Sum_probs=21.9
Q ss_pred HHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 90 RADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 90 r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
-+|||..+|++...|.-|. |..+||..
T Consensus 3 ~eELA~~tG~srQTINrWv--RkegW~T~ 29 (122)
T PF07037_consen 3 PEELAELTGYSRQTINRWV--RKEGWKTE 29 (122)
T ss_pred HHHHHHHhCccHHHHHHHH--HhcCceec
Confidence 4789999999999999997 45556653
No 196
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=26.38 E-value=59 Score=28.80 Aligned_cols=49 Identities=22% Similarity=0.204 Sum_probs=37.0
Q ss_pred CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 64 RAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 64 RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
...++..++++|.-.. ....-.+||..||++++.|+.+..|-+.|.+..
T Consensus 169 ~~~Lt~re~evl~~~a------~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~ 217 (232)
T TIGR03541 169 AGVLSEREREVLAWTA------LGRRQADIAAILGISERTVENHLRSARRKLGVA 217 (232)
T ss_pred hccCCHHHHHHHHHHH------CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence 3457888888887643 124456789999999999999999988776643
No 197
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=25.84 E-value=1.3e+02 Score=26.35 Aligned_cols=51 Identities=14% Similarity=0.116 Sum_probs=33.1
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
.++..+..++...|-... -.....++||+.+|++...|..+...-|.+.|+
T Consensus 174 ~L~~~~r~il~l~y~~~~-~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 174 VLDGREREVIEMRYGLGD-GRRKTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred hCCHHHHHHHHHHHcCCC-CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 466667777776652110 022346789999999999998876555555544
No 198
>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=25.80 E-value=1.2e+02 Score=27.69 Aligned_cols=30 Identities=10% Similarity=0.159 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 89 ERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 89 ~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
...+||..+|+++..|+.++..-|.+.|+.
T Consensus 126 s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 126 PYEEIASIVGKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 357899999999999999998777776653
No 199
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.79 E-value=1.7e+02 Score=22.71 Aligned_cols=41 Identities=20% Similarity=0.243 Sum_probs=32.1
Q ss_pred CCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCC-Ccccchhhh
Q psy526 64 RAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKL-TETQVKIWF 108 (274)
Q Consensus 64 RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L-~~~~V~vWF 108 (274)
|..|+.+....+=+.+....+ -..+||.++|+ ...++..|-
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 677999888777666665554 57789999996 998888884
No 200
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=25.65 E-value=1.2e+02 Score=25.23 Aligned_cols=47 Identities=11% Similarity=0.048 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
++..|..++...|- .....++||..+|++...|+.+..--|.+.|+.
T Consensus 128 L~~~~r~v~~l~~~-----~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~ 174 (179)
T PRK09415 128 LPIKYREVIYLFYY-----EELSIKEIAEVTGVNENTVKTRLKKAKELLKKG 174 (179)
T ss_pred CCHHHhhHhHhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45555555544332 223467899999999999999987777666653
No 201
>PRK05572 sporulation sigma factor SigF; Validated
Probab=25.63 E-value=1.1e+02 Score=27.29 Aligned_cols=48 Identities=17% Similarity=0.167 Sum_probs=35.3
Q ss_pred CcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 65 AAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 65 T~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
..++..+..++...|.. .....+||..+|++...|+.|-..-..|.|+
T Consensus 201 ~~L~~~~~~v~~l~~~~-----~~s~~eIA~~lgis~~~V~~~~~ral~kLr~ 248 (252)
T PRK05572 201 RELDERERLIVYLRYFK-----DKTQSEVAKRLGISQVQVSRLEKKILKQMKE 248 (252)
T ss_pred HcCCHHHHHHHHHHHhC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35777777888777642 2456889999999999998886665555554
No 202
>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=25.43 E-value=45 Score=21.05 Aligned_cols=23 Identities=13% Similarity=0.156 Sum_probs=18.8
Q ss_pred HHHHHHHhCCCcccchhhhhhhh
Q psy526 90 RADVAKSLKLTETQVKIWFQNRR 112 (274)
Q Consensus 90 r~~LA~~l~L~~~~V~vWFqNrR 112 (274)
..++|+.||++...|.-|.++.+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 46789999999999999975543
No 203
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=25.19 E-value=62 Score=27.52 Aligned_cols=30 Identities=20% Similarity=0.292 Sum_probs=24.5
Q ss_pred HHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 88 PERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 88 ~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
-..++||..+|++++.|+..++.-|.+.++
T Consensus 152 ls~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 152 LSVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 356789999999999999988887765554
No 204
>cd00131 PAX Paired Box domain
Probab=24.85 E-value=3.1e+02 Score=22.11 Aligned_cols=45 Identities=11% Similarity=-0.019 Sum_probs=29.2
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCC-------Ccccchhhhhh
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKL-------TETQVKIWFQN 110 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L-------~~~~V~vWFqN 110 (274)
..+..+...++.....++..+..+..++...-|+ +...|--||++
T Consensus 75 ~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~ 126 (128)
T cd00131 75 VATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN 126 (128)
T ss_pred cCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence 3456666667777778888777776654223355 66777777665
No 205
>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=24.80 E-value=1.2e+02 Score=25.13 Aligned_cols=47 Identities=17% Similarity=0.190 Sum_probs=32.2
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
.++..+..++...| .......+||..+|++...|++=...-|.+.|+
T Consensus 140 ~L~~~~r~vi~l~~-----~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 140 KLPEDYREVILLRH-----LEGLSFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred cCCHHHHHHHHHHH-----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35556666665543 234456789999999999998877666666554
No 206
>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=24.53 E-value=45 Score=20.69 Aligned_cols=23 Identities=13% Similarity=0.312 Sum_probs=19.7
Q ss_pred HHHHHHHhCCCcccchhhhhhhh
Q psy526 90 RADVAKSLKLTETQVKIWFQNRR 112 (274)
Q Consensus 90 r~~LA~~l~L~~~~V~vWFqNrR 112 (274)
..++|..+|++...|..|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45789999999999999988764
No 207
>PF13730 HTH_36: Helix-turn-helix domain
Probab=24.29 E-value=78 Score=21.04 Aligned_cols=44 Identities=14% Similarity=0.028 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCcccchhhhhhh
Q psy526 67 FSHAQVYELEKRFNA---QKYLSGPERADVAKSLKLTETQVKIWFQNR 111 (274)
Q Consensus 67 ft~~Ql~~Le~~F~~---~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNr 111 (274)
++..++.++-..+.. +.. ...-...||..+|++++.|+-+...-
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~-~~pS~~~la~~~g~s~~Tv~~~i~~L 49 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGG-CFPSQETLAKDLGVSRRTVQRAIKEL 49 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCC-CCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 445555544444322 222 22347789999999999998887543
No 208
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=24.20 E-value=1.3e+02 Score=27.41 Aligned_cols=30 Identities=10% Similarity=0.119 Sum_probs=24.6
Q ss_pred HHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 89 ERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 89 ~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
..++||+.+|+++..|+...+.-|.+.|+.
T Consensus 133 s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~ 162 (293)
T PRK09636 133 PFDEIASTLGRSPAACRQLASRARKHVRAA 162 (293)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 457899999999999999998777666653
No 209
>KOG3755|consensus
Probab=24.20 E-value=45 Score=34.35 Aligned_cols=60 Identities=23% Similarity=0.313 Sum_probs=50.7
Q ss_pred CCCCCCCCcCCHHHHHHHHHHHhhCC-CCCHHH---HHHHHHHhCCCcccchhhhhhhhhHHHH
Q psy526 58 GRKKRSRAAFSHAQVYELEKRFNAQK-YLSGPE---RADVAKSLKLTETQVKIWFQNRRYKTKR 117 (274)
Q Consensus 58 ~k~rR~RT~ft~~Ql~~Le~~F~~~~-~Ps~~~---r~~LA~~l~L~~~~V~vWFqNrR~k~Kr 117 (274)
..++|+||.+..+-+..|..+-..-. ||+... +.-|...+++.++.+--.|+|.|.-.|+
T Consensus 645 ~~~p~~~~~isge~~~~~qs~i~~~gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~~ 708 (769)
T KOG3755|consen 645 WHKPRKRTKISGEALGILQSFITDVGLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVKH 708 (769)
T ss_pred ccCccccceecccchHHHHHHHHHhccCchhhcccccchhhhhhcccHHHHHHhhhcceeecch
Confidence 34678899999999999988765443 898888 8899999999999999999999877553
No 210
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=23.99 E-value=78 Score=27.79 Aligned_cols=37 Identities=19% Similarity=0.195 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHHH
Q psy526 84 YLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120 (274)
Q Consensus 84 ~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~ 120 (274)
|.......+||+.+|++...|++....-|.|.|+...
T Consensus 162 ~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~ 198 (231)
T PRK11922 162 VVEELSVEETAQALGLPEETVKTRLHRARRLLRESLA 198 (231)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4455667899999999999999999888888777654
No 211
>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=23.67 E-value=33 Score=29.57 Aligned_cols=31 Identities=19% Similarity=0.440 Sum_probs=26.8
Q ss_pred HHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 88 PERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 88 ~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
..+.+|+.-++++..+|-+|.+|-+...++.
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~ 45 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAK 45 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCccccc
Confidence 4578899999999999999999998876653
No 212
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=23.54 E-value=1.2e+02 Score=27.72 Aligned_cols=50 Identities=14% Similarity=0.125 Sum_probs=35.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
.++..+..+|...|... ......+||..+|++..+|+-+-..-..|.|+.
T Consensus 230 ~L~~rEr~VL~lry~~~---~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~ 279 (284)
T PRK06596 230 GLDERSRDIIEARWLDD---DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAA 279 (284)
T ss_pred cCCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46777778888877432 234467999999999999998866555555543
No 213
>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=23.45 E-value=2.9e+02 Score=23.58 Aligned_cols=48 Identities=10% Similarity=0.099 Sum_probs=36.9
Q ss_pred CCCcCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhh
Q psy526 63 SRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRR 112 (274)
Q Consensus 63 ~RT~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR 112 (274)
+...++.+++.++.+.-..+ |..-.+..||++.|++..-|.+=..--.
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~~~~ 129 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAPAPK 129 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcCCCH
Confidence 45689999999998886554 5777899999999998877666544333
No 214
>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=22.86 E-value=48 Score=23.62 Aligned_cols=23 Identities=22% Similarity=0.315 Sum_probs=20.3
Q ss_pred HHHHHHHhCCCcccchhhhhhhh
Q psy526 90 RADVAKSLKLTETQVKIWFQNRR 112 (274)
Q Consensus 90 r~~LA~~l~L~~~~V~vWFqNrR 112 (274)
..+||..+|++...|..|..+++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46899999999999999998765
No 215
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=22.81 E-value=59 Score=27.61 Aligned_cols=43 Identities=14% Similarity=0.176 Sum_probs=32.7
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhh
Q psy526 70 AQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRY 113 (274)
Q Consensus 70 ~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~ 113 (274)
.-++...+.|.+..|-... ..+||+..|+++..+-.+|.++-.
T Consensus 15 ~Il~aa~~lf~~~G~~~~t-i~~Ia~~agvsk~t~Y~~F~sKe~ 57 (213)
T PRK09975 15 ELIETAIAQFALRGVSNTT-LNDIADAANVTRGAIYWHFENKTQ 57 (213)
T ss_pred HHHHHHHHHHHHcCcccCC-HHHHHHHcCCCHHHHHHHcCCHHH
Confidence 3445555667777765544 667899999999999999999865
No 216
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=22.76 E-value=1.9e+02 Score=27.09 Aligned_cols=52 Identities=13% Similarity=0.173 Sum_probs=39.1
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
.++..+..+|.-.|..... .....++||..+|++...|+..-..-+.|.|+.
T Consensus 256 ~L~~rer~Vi~lr~gl~~~-~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~ 307 (317)
T PRK07405 256 DLTPQQKEVIALRFGLEDG-QPLTLAKIGERLNISRERVRQIEREALSKLRKR 307 (317)
T ss_pred cCCHHHHHHHHHHhhcCCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4677777788877753322 224578899999999999999988877777764
No 217
>smart00595 MADF subfamily of SANT domain.
Probab=22.69 E-value=1.2e+02 Score=22.24 Aligned_cols=33 Identities=24% Similarity=0.359 Sum_probs=27.7
Q ss_pred HHHHHHHhCCCcccchhhhhhhhhHHHHHHHHH
Q psy526 90 RADVAKSLKLTETQVKIWFQNRRYKTKRKQLQL 122 (274)
Q Consensus 90 r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~~~~ 122 (274)
-.+||.++|.+...|+.-+.|-|.+-++..+..
T Consensus 30 W~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~ 62 (89)
T smart00595 30 WEEIAEELGLSVEECKKRWKNLRDRYRRELKRL 62 (89)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 346899999999999999999999988875554
No 218
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=22.22 E-value=1.4e+02 Score=27.34 Aligned_cols=30 Identities=20% Similarity=0.157 Sum_probs=24.3
Q ss_pred HHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 89 ERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 89 ~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
...+||..||++...|+.....-|.+.|+.
T Consensus 160 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 189 (324)
T TIGR02960 160 RAAETAELLGTSTASVNSALQRARATLDEV 189 (324)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 357899999999999999887766666654
No 219
>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=21.89 E-value=86 Score=20.82 Aligned_cols=36 Identities=11% Similarity=0.121 Sum_probs=22.3
Q ss_pred HHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhh
Q psy526 71 QVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQ 109 (274)
Q Consensus 71 Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFq 109 (274)
|...|+..+....+ -...+||..++++.+.|+.-..
T Consensus 2 ~~~il~~L~~~~~~---it~~eLa~~l~vS~rTi~~~i~ 37 (55)
T PF08279_consen 2 QKQILKLLLESKEP---ITAKELAEELGVSRRTIRRDIK 37 (55)
T ss_dssp HHHHHHHHHHTTTS---BEHHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHcCCC---cCHHHHHHHhCCCHHHHHHHHH
Confidence 34455544444443 4567899999999988865543
No 220
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=21.86 E-value=1.5e+02 Score=19.11 Aligned_cols=37 Identities=14% Similarity=0.161 Sum_probs=23.6
Q ss_pred CHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhh
Q psy526 68 SHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWF 108 (274)
Q Consensus 68 t~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWF 108 (274)
+..+..+|+..+. ++. -.+.+||..+|++...|.--+
T Consensus 2 ~~~~~~Il~~l~~-~~~---~t~~ela~~~~is~~tv~~~l 38 (48)
T PF13412_consen 2 DETQRKILNYLRE-NPR---ITQKELAEKLGISRSTVNRYL 38 (48)
T ss_dssp -HHHHHHHHHHHH-CTT---S-HHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHHHHH-cCC---CCHHHHHHHhCCCHHHHHHHH
Confidence 4556777766665 333 456689999999988776544
No 221
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=21.45 E-value=1.7e+02 Score=26.57 Aligned_cols=53 Identities=21% Similarity=0.157 Sum_probs=37.5
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
.++..++.+|.-.|... |-......+||..||++...|+.+...-|.|.|+.-
T Consensus 222 ~Lp~~~R~Vl~l~ygL~-~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l 274 (285)
T TIGR02394 222 ELNERQREVLARRFGLL-GYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL 274 (285)
T ss_pred cCCHHHHHHHHHHhCCC-CCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46677777777666211 122244678999999999999999887777776654
No 222
>PHA02955 hypothetical protein; Provisional
Probab=20.99 E-value=1.1e+02 Score=27.37 Aligned_cols=43 Identities=9% Similarity=0.060 Sum_probs=33.2
Q ss_pred HHHHHHHHHHhhC-CCCCHHHHHHHHHHhCCCcccchhhhhhhh
Q psy526 70 AQVYELEKRFNAQ-KYLSGPERADVAKSLKLTETQVKIWFQNRR 112 (274)
Q Consensus 70 ~Ql~~Le~~F~~~-~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR 112 (274)
.++..|-+.|... .-...++|.++|.+||+....|..||.+.-
T Consensus 61 ~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~ 104 (213)
T PHA02955 61 KNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDL 104 (213)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchh
Confidence 4666666666554 467788899999999999988899998753
No 223
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=20.84 E-value=96 Score=25.95 Aligned_cols=32 Identities=19% Similarity=0.226 Sum_probs=26.7
Q ss_pred HHHHHHHHHhCCCcccchhhhhhhhhHHHHHH
Q psy526 88 PERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119 (274)
Q Consensus 88 ~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~~ 119 (274)
..-.+||..+|++...|+.|..--|.+.++..
T Consensus 144 ls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l 175 (182)
T COG1595 144 LSYEEIAEILGISVGTVKSRLHRARKKLREQL 175 (182)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34568999999999999999988888777654
No 224
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=20.46 E-value=1.4e+02 Score=25.60 Aligned_cols=36 Identities=17% Similarity=0.159 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccc
Q psy526 69 HAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQV 104 (274)
Q Consensus 69 ~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V 104 (274)
..-+..|...+.+..|.....++.+|..||++...|
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 466788999999999999999999999999987554
No 225
>PRK05949 RNA polymerase sigma factor; Validated
Probab=20.42 E-value=2.3e+02 Score=26.64 Aligned_cols=52 Identities=19% Similarity=0.194 Sum_probs=38.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccchhhhhhhhhHHHHH
Q psy526 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118 (274)
Q Consensus 66 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~l~L~~~~V~vWFqNrR~k~Kr~ 118 (274)
.++..+..+|...|..... .....++||..+|++...|+.....-+.|.|+.
T Consensus 266 ~L~~rer~Vi~lr~gl~~~-e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~ 317 (327)
T PRK05949 266 ELTPQQREVLTLRFGLEDG-KELSLAKVGERLNLSRERVRQLEHQALAHLRRR 317 (327)
T ss_pred hCCHHHHHHHHHHhccCCC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4677777888877753321 224578899999999999999988877777763
No 226
>PHA01976 helix-turn-helix protein
Probab=20.37 E-value=59 Score=22.47 Aligned_cols=23 Identities=4% Similarity=0.200 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCcccchhhhhhhh
Q psy526 90 RADVAKSLKLTETQVKIWFQNRR 112 (274)
Q Consensus 90 r~~LA~~l~L~~~~V~vWFqNrR 112 (274)
..+||..+|++...|.-|...++
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 56799999999999999987654
Done!