Query psy10105
Match_columns 197
No_of_seqs 219 out of 1085
Neff 5.8
Searched_HMMs 46136
Date Fri Aug 16 18:00:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10105.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10105hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0775|consensus 100.0 2.3E-33 4.9E-38 242.1 4.3 115 10-127 106-235 (304)
2 PF05920 Homeobox_KN: Homeobox 99.7 2.1E-18 4.4E-23 110.4 4.7 40 83-122 1-40 (40)
3 KOG0774|consensus 99.6 1.3E-16 2.7E-21 138.0 2.8 65 64-128 187-251 (334)
4 cd00086 homeodomain Homeodomai 99.6 3E-15 6.5E-20 100.4 7.2 56 67-125 2-57 (59)
5 PF00046 Homeobox: Homeobox do 99.6 2.6E-15 5.6E-20 101.1 6.4 57 66-125 1-57 (57)
6 smart00389 HOX Homeodomain. DN 99.6 5.3E-15 1.1E-19 98.7 6.9 55 67-124 2-56 (56)
7 KOG0773|consensus 99.5 1.1E-14 2.3E-19 130.1 3.7 63 65-127 239-301 (342)
8 KOG0489|consensus 99.3 3.7E-12 8E-17 110.9 7.6 66 62-130 156-221 (261)
9 KOG0487|consensus 99.3 4.4E-12 9.4E-17 112.6 6.5 61 64-127 234-294 (308)
10 KOG0843|consensus 99.3 1.9E-11 4E-16 101.0 8.5 61 64-127 101-161 (197)
11 KOG0850|consensus 99.2 3E-11 6.5E-16 103.0 6.4 69 57-128 114-182 (245)
12 KOG0488|consensus 99.1 4.6E-11 1E-15 106.5 5.7 62 63-127 170-231 (309)
13 KOG0842|consensus 99.1 6E-11 1.3E-15 105.4 3.0 61 64-127 152-212 (307)
14 TIGR01565 homeo_ZF_HD homeobox 99.0 3.1E-10 6.8E-15 78.1 4.6 52 66-120 2-57 (58)
15 KOG3802|consensus 99.0 1.8E-10 3.9E-15 104.8 2.6 68 58-128 287-354 (398)
16 KOG0483|consensus 99.0 4.9E-10 1.1E-14 94.3 5.0 60 64-126 49-108 (198)
17 KOG0485|consensus 99.0 3.5E-10 7.7E-15 96.1 4.0 61 64-127 103-163 (268)
18 COG5576 Homeodomain-containing 99.0 1.7E-09 3.7E-14 87.9 7.1 61 64-127 50-110 (156)
19 KOG0848|consensus 98.9 6E-10 1.3E-14 97.1 2.4 58 69-129 203-260 (317)
20 KOG0491|consensus 98.9 6.8E-10 1.5E-14 90.8 2.5 64 65-131 100-163 (194)
21 KOG0493|consensus 98.9 2.3E-09 4.9E-14 93.4 5.0 58 67-127 248-305 (342)
22 KOG0484|consensus 98.8 2.2E-09 4.7E-14 82.0 3.7 70 55-127 5-76 (125)
23 KOG2251|consensus 98.8 2.7E-09 5.8E-14 90.7 4.3 62 64-128 36-97 (228)
24 KOG0492|consensus 98.8 7.2E-09 1.6E-13 87.6 4.4 59 65-126 144-202 (246)
25 KOG0494|consensus 98.7 3E-08 6.6E-13 86.3 5.5 57 69-128 145-201 (332)
26 KOG0486|consensus 98.5 4.5E-08 9.8E-13 87.0 2.6 55 69-126 116-170 (351)
27 KOG0847|consensus 98.5 2.1E-07 4.6E-12 79.5 5.0 57 68-127 170-226 (288)
28 KOG4577|consensus 98.4 4.9E-07 1.1E-11 79.9 7.2 62 64-128 166-227 (383)
29 KOG0844|consensus 98.4 5.7E-08 1.2E-12 86.3 1.0 67 65-134 181-248 (408)
30 KOG2252|consensus 98.3 8.3E-07 1.8E-11 83.9 6.1 56 66-124 421-476 (558)
31 KOG0773|consensus 98.3 5.1E-07 1.1E-11 80.7 4.5 73 64-137 94-166 (342)
32 KOG0849|consensus 98.2 2.3E-06 4.9E-11 77.8 5.4 59 66-127 177-235 (354)
33 KOG1168|consensus 98.1 8.7E-07 1.9E-11 78.4 1.0 98 25-125 266-366 (385)
34 KOG0490|consensus 98.1 2.2E-06 4.7E-11 71.5 2.7 61 64-127 59-119 (235)
35 PF11569 Homez: Homeodomain le 97.4 0.00013 2.9E-09 49.8 2.7 43 77-122 10-52 (56)
36 KOG0490|consensus 96.5 0.0034 7.4E-08 52.2 4.2 60 65-127 153-212 (235)
37 KOG1146|consensus 94.4 0.037 8E-07 57.6 3.6 60 65-127 903-962 (1406)
38 PF04218 CENP-B_N: CENP-B N-te 93.1 0.29 6.2E-06 32.6 5.0 47 66-120 1-47 (53)
39 KOG3623|consensus 90.5 0.47 1E-05 47.3 5.3 46 77-125 568-613 (1007)
40 cd00569 HTH_Hin_like Helix-tur 85.2 3.4 7.4E-05 22.6 4.9 41 68-116 2-42 (42)
41 PF04545 Sigma70_r4: Sigma-70, 84.2 1.9 4.1E-05 27.6 3.8 47 71-125 4-50 (50)
42 cd06171 Sigma70_r4 Sigma70, re 82.7 3 6.5E-05 25.5 4.2 46 71-124 10-55 (55)
43 PF01527 HTH_Tnp_1: Transposas 80.8 1.6 3.4E-05 30.0 2.6 46 67-120 2-48 (76)
44 PF08281 Sigma70_r4_2: Sigma-7 79.5 7.4 0.00016 25.0 5.3 44 72-123 11-54 (54)
45 PRK06759 RNA polymerase factor 76.3 4.9 0.00011 30.8 4.4 47 71-125 106-152 (154)
46 PRK11924 RNA polymerase sigma 73.6 4.5 9.8E-05 31.4 3.6 51 72-130 126-176 (179)
47 PRK09646 RNA polymerase sigma 73.3 6.3 0.00014 31.9 4.5 49 71-127 142-190 (194)
48 PRK09642 RNA polymerase sigma 71.6 7.5 0.00016 30.1 4.4 48 72-127 107-154 (160)
49 PF13518 HTH_28: Helix-turn-he 71.3 5.6 0.00012 25.1 3.0 25 98-122 15-39 (52)
50 TIGR02985 Sig70_bacteroi1 RNA 70.4 9.6 0.00021 28.9 4.7 48 71-126 113-160 (161)
51 TIGR02939 RpoE_Sigma70 RNA pol 69.2 6 0.00013 31.4 3.4 48 72-127 139-186 (190)
52 PF13443 HTH_26: Cro/C1-type H 69.2 4.1 8.9E-05 26.9 2.1 24 97-120 12-35 (63)
53 PRK00118 putative DNA-binding 68.1 11 0.00024 28.7 4.5 48 71-126 17-64 (104)
54 PRK09652 RNA polymerase sigma 67.7 9.9 0.00021 29.6 4.4 49 71-127 128-176 (182)
55 PRK04217 hypothetical protein; 67.1 26 0.00057 26.9 6.4 49 71-127 42-90 (110)
56 PRK09644 RNA polymerase sigma 66.9 11 0.00024 29.4 4.5 49 71-127 108-156 (165)
57 PRK12526 RNA polymerase sigma 66.5 11 0.00023 31.1 4.5 48 72-127 154-201 (206)
58 PRK03975 tfx putative transcri 66.4 13 0.00028 29.8 4.8 48 70-126 5-52 (141)
59 PRK12520 RNA polymerase sigma 66.2 7.6 0.00017 31.2 3.5 53 71-131 131-183 (191)
60 TIGR02937 sigma70-ECF RNA poly 66.1 15 0.00032 27.0 4.9 48 71-126 110-157 (158)
61 PF00196 GerE: Bacterial regul 65.9 14 0.0003 24.3 4.2 48 71-127 3-50 (58)
62 PRK12516 RNA polymerase sigma 65.8 11 0.00023 30.7 4.3 51 71-129 116-166 (187)
63 smart00421 HTH_LUXR helix_turn 65.5 17 0.00037 22.5 4.4 47 71-126 3-49 (58)
64 TIGR02989 Sig-70_gvs1 RNA poly 64.9 12 0.00027 28.7 4.4 47 71-125 111-157 (159)
65 PRK12514 RNA polymerase sigma 64.9 12 0.00026 29.6 4.4 48 71-126 129-176 (179)
66 PRK09413 IS2 repressor TnpA; R 64.5 19 0.00042 27.4 5.3 47 68-121 9-55 (121)
67 PRK09047 RNA polymerase factor 64.5 13 0.00028 28.6 4.4 50 71-128 106-155 (161)
68 PRK13919 putative RNA polymera 64.3 13 0.00029 29.4 4.6 49 71-127 135-183 (186)
69 PF10668 Phage_terminase: Phag 64.2 6.3 0.00014 27.2 2.3 19 97-115 24-42 (60)
70 TIGR02983 SigE-fam_strep RNA p 63.7 14 0.0003 28.6 4.5 48 72-127 111-158 (162)
71 TIGR02999 Sig-70_X6 RNA polyme 63.3 13 0.00029 29.3 4.4 47 72-126 135-181 (183)
72 PRK12541 RNA polymerase sigma 63.1 13 0.00027 28.9 4.1 47 71-125 112-158 (161)
73 PRK08583 RNA polymerase sigma 62.8 16 0.00035 31.0 5.1 49 71-127 205-253 (257)
74 PRK12547 RNA polymerase sigma 62.8 14 0.00031 28.9 4.4 49 71-127 112-160 (164)
75 PRK12512 RNA polymerase sigma 62.7 15 0.00032 29.3 4.5 49 71-127 131-179 (184)
76 TIGR02948 SigW_bacill RNA poly 62.3 17 0.00036 28.7 4.8 49 71-127 136-184 (187)
77 PRK12536 RNA polymerase sigma 61.9 16 0.00034 29.1 4.6 48 72-127 130-177 (181)
78 PRK06811 RNA polymerase factor 61.5 16 0.00034 29.5 4.5 49 71-127 131-179 (189)
79 PF13384 HTH_23: Homeodomain-l 61.0 8.3 0.00018 24.3 2.3 25 96-120 18-42 (50)
80 PRK12530 RNA polymerase sigma 59.5 12 0.00027 30.1 3.6 49 71-127 134-182 (189)
81 PRK12532 RNA polymerase sigma 59.4 12 0.00027 30.1 3.6 51 71-129 136-186 (195)
82 TIGR02954 Sig70_famx3 RNA poly 59.3 18 0.00038 28.3 4.4 49 71-127 119-167 (169)
83 PRK05602 RNA polymerase sigma 59.2 16 0.00034 29.2 4.1 48 72-127 129-176 (186)
84 PRK09648 RNA polymerase sigma 59.1 18 0.00039 28.9 4.5 48 71-126 139-186 (189)
85 PRK12519 RNA polymerase sigma 58.3 14 0.0003 29.7 3.7 48 72-127 142-189 (194)
86 PRK12523 RNA polymerase sigma 57.3 20 0.00044 28.2 4.4 49 71-127 119-167 (172)
87 PRK12544 RNA polymerase sigma 56.0 17 0.00037 30.1 3.9 53 71-131 148-200 (206)
88 PRK12537 RNA polymerase sigma 55.8 21 0.00046 28.4 4.4 47 72-126 134-180 (182)
89 PRK12540 RNA polymerase sigma 55.6 33 0.0007 27.6 5.5 50 71-128 111-160 (182)
90 PRK11511 DNA-binding transcrip 55.5 28 0.00061 26.6 4.8 44 72-119 6-49 (127)
91 PRK12531 RNA polymerase sigma 55.4 22 0.00048 28.7 4.5 49 71-127 141-189 (194)
92 TIGR02941 Sigma_B RNA polymera 55.4 22 0.00048 30.2 4.6 49 71-127 205-253 (255)
93 PRK09649 RNA polymerase sigma 55.4 21 0.00047 28.6 4.4 49 71-127 130-178 (185)
94 PRK06986 fliA flagellar biosyn 53.6 20 0.00044 30.0 4.1 48 72-127 185-232 (236)
95 PRK09645 RNA polymerase sigma 53.3 26 0.00056 27.4 4.5 49 72-128 119-167 (173)
96 PRK12546 RNA polymerase sigma 53.3 22 0.00047 28.9 4.1 49 71-127 113-161 (188)
97 PRK09639 RNA polymerase sigma 53.2 19 0.00042 27.8 3.7 48 72-128 113-160 (166)
98 TIGR02943 Sig70_famx1 RNA poly 52.9 20 0.00043 29.0 3.8 51 71-129 131-181 (188)
99 cd01392 HTH_LacI Helix-turn-he 52.8 9.5 0.00021 24.1 1.5 20 100-119 2-21 (52)
100 cd06170 LuxR_C_like C-terminal 52.6 36 0.00078 21.1 4.3 29 97-125 17-45 (57)
101 PRK12533 RNA polymerase sigma 52.1 23 0.0005 29.7 4.2 49 71-127 134-182 (216)
102 PF01381 HTH_3: Helix-turn-hel 52.0 9.2 0.0002 24.4 1.4 21 98-118 12-32 (55)
103 PF04967 HTH_10: HTH DNA bindi 51.9 56 0.0012 21.8 5.2 49 72-121 1-49 (53)
104 TIGR02959 SigZ RNA polymerase 51.9 28 0.00061 27.5 4.5 49 71-127 100-148 (170)
105 cd00131 PAX Paired Box domain 51.6 58 0.0013 25.2 6.1 48 69-119 73-127 (128)
106 PRK12524 RNA polymerase sigma 51.1 28 0.00061 28.1 4.4 49 71-127 136-184 (196)
107 PRK12543 RNA polymerase sigma 51.0 30 0.00065 27.4 4.6 49 71-127 117-165 (179)
108 PRK15369 two component system 50.8 52 0.0011 25.0 5.8 46 71-125 149-194 (211)
109 PRK12515 RNA polymerase sigma 49.7 32 0.00069 27.5 4.5 49 71-127 131-179 (189)
110 PRK12535 RNA polymerase sigma 49.2 30 0.00065 28.3 4.3 49 71-127 133-181 (196)
111 TIGR02980 SigBFG RNA polymeras 48.7 31 0.00066 28.6 4.4 48 71-126 178-225 (227)
112 PRK12542 RNA polymerase sigma 48.6 33 0.00071 27.3 4.4 49 71-127 122-170 (185)
113 PRK12528 RNA polymerase sigma 48.6 36 0.00077 26.3 4.5 47 71-125 113-159 (161)
114 PRK12545 RNA polymerase sigma 48.4 32 0.0007 28.0 4.4 49 71-127 139-187 (201)
115 TIGR02479 FliA_WhiG RNA polyme 48.3 38 0.00082 28.0 4.9 48 71-126 175-222 (224)
116 PRK07037 extracytoplasmic-func 48.3 36 0.00077 26.3 4.5 49 71-127 109-157 (163)
117 PRK07670 RNA polymerase sigma 47.9 30 0.00066 29.3 4.3 48 72-127 202-249 (251)
118 TIGR03070 couple_hipB transcri 47.6 12 0.00026 23.6 1.4 22 98-119 18-39 (58)
119 PRK12534 RNA polymerase sigma 47.3 34 0.00074 27.2 4.3 47 72-126 138-184 (187)
120 PRK09415 RNA polymerase factor 47.1 30 0.00065 27.5 3.9 49 71-127 127-175 (179)
121 PF13936 HTH_38: Helix-turn-he 46.9 38 0.00083 21.3 3.7 40 70-117 3-42 (44)
122 TIGR03001 Sig-70_gmx1 RNA poly 46.6 35 0.00075 29.2 4.5 49 71-127 161-209 (244)
123 TIGR02950 SigM_subfam RNA poly 46.2 26 0.00057 26.6 3.4 31 96-126 122-152 (154)
124 PRK12539 RNA polymerase sigma 45.8 36 0.00079 27.1 4.3 49 71-127 131-179 (184)
125 PRK12511 RNA polymerase sigma 45.8 37 0.00081 27.4 4.4 49 71-127 111-159 (182)
126 PRK12538 RNA polymerase sigma 45.7 30 0.00065 29.3 4.0 48 72-127 172-219 (233)
127 PRK12529 RNA polymerase sigma 45.4 47 0.001 26.4 4.8 49 71-127 127-175 (178)
128 PRK08295 RNA polymerase factor 45.4 54 0.0012 26.4 5.3 48 71-127 155-202 (208)
129 PRK09647 RNA polymerase sigma 45.2 40 0.00087 27.8 4.5 50 71-128 138-187 (203)
130 cd00093 HTH_XRE Helix-turn-hel 44.7 23 0.0005 20.9 2.4 22 98-119 15-36 (58)
131 PF02796 HTH_7: Helix-turn-hel 44.4 44 0.00096 21.0 3.7 41 68-116 2-42 (45)
132 TIGR02952 Sig70_famx2 RNA poly 44.3 44 0.00096 25.7 4.5 47 71-125 122-168 (170)
133 PRK10072 putative transcriptio 44.3 15 0.00032 27.5 1.6 40 71-120 32-71 (96)
134 PRK12527 RNA polymerase sigma 44.2 46 0.001 25.6 4.6 48 72-127 106-153 (159)
135 PRK12522 RNA polymerase sigma 43.9 42 0.00092 26.3 4.3 49 71-127 119-167 (173)
136 PRK12518 RNA polymerase sigma 43.7 29 0.00062 27.2 3.3 30 98-127 139-168 (175)
137 PRK12513 RNA polymerase sigma 43.4 29 0.00063 27.8 3.4 48 72-127 140-187 (194)
138 PRK06288 RNA polymerase sigma 43.2 41 0.00089 28.8 4.5 49 71-127 212-260 (268)
139 PF13411 MerR_1: MerR HTH fami 43.0 23 0.0005 23.6 2.3 17 99-115 4-20 (69)
140 PRK09637 RNA polymerase sigma 42.9 44 0.00095 26.8 4.3 49 71-127 106-154 (181)
141 TIGR02859 spore_sigH RNA polym 42.3 31 0.00067 27.5 3.4 30 97-126 167-196 (198)
142 PRK06930 positive control sigm 41.9 48 0.001 27.0 4.4 49 71-127 114-162 (170)
143 PRK09641 RNA polymerase sigma 41.3 31 0.00068 27.1 3.2 48 72-127 137-184 (187)
144 PF06056 Terminase_5: Putative 40.9 26 0.00056 23.7 2.3 18 98-115 16-33 (58)
145 PRK06704 RNA polymerase factor 40.9 48 0.001 28.3 4.5 50 71-128 116-165 (228)
146 PRK07408 RNA polymerase sigma 40.8 46 0.001 28.5 4.4 49 71-127 203-251 (256)
147 PHA01976 helix-turn-helix prot 40.0 20 0.00044 23.8 1.6 22 98-119 18-39 (67)
148 smart00530 HTH_XRE Helix-turn- 39.6 22 0.00047 20.9 1.6 22 98-119 13-34 (56)
149 PRK12517 RNA polymerase sigma 39.3 59 0.0013 26.2 4.6 49 71-127 128-176 (188)
150 TIGR02960 SigX5 RNA polymerase 39.2 53 0.0012 28.5 4.6 50 71-128 142-191 (324)
151 TIGR02947 SigH_actino RNA poly 38.7 37 0.00081 27.2 3.3 48 72-127 132-179 (193)
152 cd04761 HTH_MerR-SF Helix-Turn 38.2 33 0.00071 21.1 2.3 18 99-116 4-21 (49)
153 TIGR02607 antidote_HigA addict 37.8 22 0.00049 24.2 1.6 23 98-120 21-43 (78)
154 PF13551 HTH_29: Winged helix- 37.5 1.5E+02 0.0032 21.1 6.1 46 72-117 58-109 (112)
155 TIGR02885 spore_sigF RNA polym 37.3 67 0.0014 26.7 4.7 48 71-126 183-230 (231)
156 PRK09651 RNA polymerase sigma 37.2 47 0.001 26.2 3.6 47 71-125 119-165 (172)
157 TIGR02846 spore_sigmaK RNA pol 37.0 51 0.0011 27.5 4.0 52 71-126 174-225 (227)
158 PRK08301 sporulation sigma fac 36.7 41 0.00089 28.0 3.4 53 71-127 178-230 (234)
159 PRK07122 RNA polymerase sigma 36.7 63 0.0014 27.9 4.6 48 71-126 215-262 (264)
160 PRK11923 algU RNA polymerase s 35.6 39 0.00084 27.0 2.9 48 72-127 139-186 (193)
161 PRK12525 RNA polymerase sigma 35.4 74 0.0016 24.9 4.5 48 71-126 118-165 (168)
162 PRK08215 sporulation sigma fac 35.0 65 0.0014 27.4 4.4 49 71-127 209-257 (258)
163 COG3413 Predicted DNA binding 34.9 92 0.002 25.9 5.2 52 71-123 155-206 (215)
164 PRK09638 RNA polymerase sigma 33.8 51 0.0011 25.8 3.3 48 72-127 127-174 (176)
165 cd04762 HTH_MerR-trunc Helix-T 33.5 46 0.00099 19.8 2.4 20 99-118 4-23 (49)
166 TIGR00721 tfx DNA-binding prot 33.5 97 0.0021 24.7 4.8 47 70-125 5-51 (137)
167 PF13551 HTH_29: Winged helix- 32.7 54 0.0012 23.5 3.1 27 97-123 14-40 (112)
168 PF05269 Phage_CII: Bacterioph 32.5 49 0.0011 24.7 2.8 26 97-122 25-50 (91)
169 PRK05572 sporulation sigma fac 32.3 74 0.0016 26.9 4.3 49 71-127 202-250 (252)
170 PF12844 HTH_19: Helix-turn-he 32.2 29 0.00062 22.8 1.4 23 98-120 15-37 (64)
171 cd01104 HTH_MlrA-CarA Helix-Tu 32.1 42 0.00091 22.2 2.2 19 99-117 4-22 (68)
172 PRK08241 RNA polymerase factor 32.0 64 0.0014 28.4 4.0 48 71-126 153-200 (339)
173 TIGR02835 spore_sigmaE RNA pol 31.8 52 0.0011 27.6 3.2 53 71-127 178-230 (234)
174 PF07638 Sigma70_ECF: ECF sigm 31.8 56 0.0012 26.4 3.3 31 97-127 153-183 (185)
175 PF14549 P22_Cro: DNA-binding 31.3 48 0.001 22.7 2.4 18 98-115 12-29 (60)
176 TIGR02393 RpoD_Cterm RNA polym 31.0 1.2E+02 0.0027 25.3 5.4 53 71-127 176-228 (238)
177 TIGR03826 YvyF flagellar opero 30.8 64 0.0014 25.7 3.4 44 78-125 33-76 (137)
178 PRK09636 RNA polymerase sigma 30.3 88 0.0019 27.1 4.5 48 72-127 116-163 (293)
179 PRK09640 RNA polymerase sigma 30.2 64 0.0014 25.8 3.4 30 98-127 153-182 (188)
180 PRK10651 transcriptional regul 30.2 90 0.0019 24.0 4.2 47 71-126 155-201 (216)
181 TIGR02392 rpoH_proteo alternat 29.7 1.2E+02 0.0025 26.2 5.1 51 71-127 218-268 (270)
182 PF00376 MerR: MerR family reg 29.0 52 0.0011 20.2 2.1 17 99-115 3-19 (38)
183 PF04703 FaeA: FaeA-like prote 28.8 58 0.0012 22.5 2.5 24 97-120 17-40 (62)
184 PF03672 UPF0154: Uncharacteri 28.6 1.6E+02 0.0034 20.7 4.6 35 76-113 18-54 (64)
185 PRK09643 RNA polymerase sigma 28.6 1E+02 0.0023 24.7 4.4 48 72-127 135-182 (192)
186 PF00325 Crp: Bacterial regula 28.5 1E+02 0.0022 18.5 3.2 26 97-122 4-29 (32)
187 TIGR03020 EpsA transcriptional 28.3 89 0.0019 27.1 4.1 50 69-127 188-237 (247)
188 cd04764 HTH_MlrA-like_sg1 Heli 28.1 55 0.0012 21.8 2.3 19 99-117 4-22 (67)
189 PRK05911 RNA polymerase sigma 27.5 1.1E+02 0.0023 26.3 4.5 49 71-127 205-253 (257)
190 TIGR02957 SigX4 RNA polymerase 27.5 1E+02 0.0023 26.6 4.5 49 71-127 108-156 (281)
191 PRK09480 slmA division inhibit 27.3 1.2E+02 0.0025 23.8 4.4 43 77-120 13-55 (194)
192 COG2963 Transposase and inacti 27.3 2E+02 0.0043 21.2 5.5 49 69-124 5-54 (116)
193 PRK05657 RNA polymerase sigma 27.1 1.3E+02 0.0027 27.0 5.0 53 71-127 262-314 (325)
194 PF13730 HTH_36: Helix-turn-he 27.1 1.7E+02 0.0037 18.5 5.3 47 71-120 2-50 (55)
195 PF14229 DUF4332: Domain of un 27.0 70 0.0015 24.6 3.0 29 92-120 26-54 (122)
196 PRK09706 transcriptional repre 26.1 43 0.00092 25.8 1.6 23 98-120 21-43 (135)
197 TIGR02394 rpoS_proteo RNA poly 25.9 1.4E+02 0.003 25.9 4.9 53 71-127 222-274 (285)
198 smart00422 HTH_MERR helix_turn 25.7 64 0.0014 21.3 2.3 18 99-116 4-21 (70)
199 TIGR03879 near_KaiC_dom probab 25.7 66 0.0014 23.0 2.4 22 97-118 34-55 (73)
200 PF09607 BrkDBD: Brinker DNA-b 25.2 2E+02 0.0044 19.7 4.6 45 69-117 3-47 (58)
201 PRK05803 sporulation sigma fac 25.0 85 0.0019 26.2 3.4 53 71-127 175-227 (233)
202 TIGR01764 excise DNA binding d 24.9 78 0.0017 18.9 2.4 20 98-117 4-23 (49)
203 smart00354 HTH_LACI helix_turn 24.7 48 0.001 22.7 1.5 21 99-119 4-24 (70)
204 PRK15008 HTH-type transcriptio 24.4 1.2E+02 0.0026 24.6 4.1 61 60-121 4-64 (212)
205 cd04763 HTH_MlrA-like Helix-Tu 24.3 78 0.0017 21.2 2.5 19 99-117 4-22 (68)
206 PRK11922 RNA polymerase sigma 24.1 75 0.0016 26.5 2.9 49 72-128 150-198 (231)
207 KOG1146|consensus 24.1 1.6E+02 0.0035 31.9 5.7 54 71-127 711-764 (1406)
208 PF04936 DUF658: Protein of un 23.7 52 0.0011 27.4 1.7 32 96-127 15-46 (186)
209 TIGR02984 Sig-70_plancto1 RNA 23.5 2.1E+02 0.0047 22.2 5.3 48 71-126 140-187 (189)
210 PF13542 HTH_Tnp_ISL3: Helix-t 23.5 84 0.0018 19.7 2.4 20 98-117 30-49 (52)
211 PRK13890 conjugal transfer pro 23.3 52 0.0011 25.3 1.6 23 98-120 21-43 (120)
212 PF06971 Put_DNA-bind_N: Putat 23.1 71 0.0015 21.1 2.0 16 99-114 32-47 (50)
213 PRK09726 antitoxin HipB; Provi 23.0 52 0.0011 23.5 1.4 22 98-119 28-49 (88)
214 PRK07500 rpoH2 RNA polymerase 23.0 1.6E+02 0.0035 25.8 4.8 51 71-127 227-277 (289)
215 PRK10219 DNA-binding transcrip 22.7 1.8E+02 0.0039 21.0 4.4 39 75-117 5-43 (107)
216 PF04297 UPF0122: Putative hel 22.5 2E+02 0.0044 21.8 4.6 45 72-124 18-62 (101)
217 smart00351 PAX Paired Box doma 22.2 3.1E+02 0.0067 20.9 5.8 46 68-116 72-124 (125)
218 KOG4040|consensus 22.2 77 0.0017 26.4 2.4 35 77-111 26-61 (186)
219 PF01726 LexA_DNA_bind: LexA D 22.1 1.8E+02 0.0038 20.0 3.9 42 71-117 3-48 (65)
220 PF08671 SinI: Anti-repressor 21.9 1.2E+02 0.0026 18.0 2.6 20 98-117 8-27 (30)
221 PF13560 HTH_31: Helix-turn-he 21.7 62 0.0013 21.4 1.5 25 97-121 16-40 (64)
222 PRK06596 RNA polymerase factor 21.6 1.8E+02 0.0038 25.4 4.8 51 71-127 230-280 (284)
223 PRK10403 transcriptional regul 21.2 2E+02 0.0043 22.0 4.6 47 71-126 153-199 (215)
224 TIGR03541 reg_near_HchA LuxR f 20.9 1E+02 0.0023 25.9 3.1 48 71-127 171-218 (232)
225 PRK12427 flagellar biosynthesi 20.4 2.7E+02 0.0058 23.4 5.6 46 71-124 183-228 (231)
226 KOG4067|consensus 20.4 74 0.0016 27.0 2.0 49 72-127 132-187 (195)
227 PRK09744 DNA-binding transcrip 20.4 1E+02 0.0022 22.3 2.5 20 96-115 11-30 (75)
228 PHA00542 putative Cro-like pro 20.2 77 0.0017 22.5 1.8 24 97-120 33-56 (82)
No 1
>KOG0775|consensus
Probab=99.97 E-value=2.3e-33 Score=242.11 Aligned_cols=115 Identities=26% Similarity=0.302 Sum_probs=110.6
Q ss_pred CCccccccccCCCeeecccCCCCcchhhhhhhcCcccccccccccccccCCCCCccCCCCCC---------------CCH
Q psy10105 10 TLRPELQLFTQVPIQVNISSTKVPALQSRRQLCGIDKQVIQVSNLTAVRYGAGYDLAARRKN---------------ATR 74 (197)
Q Consensus 10 ~lr~~~q~~~~~~~~~~~s~~~~p~~~~~~q~~~~~~~~~~~~~l~~~~~g~~~~~r~rR~~---------------f~~ 74 (197)
.+++||.+.+.++|.|+++|.|.+++|.++|.+|+++||.|+++++|+++|+|+|||.|||. |++
T Consensus 106 A~vafH~gnf~eLY~iLE~h~Fs~~~h~~LQ~lWl~AhY~EAek~RGR~LgaV~KYRvRrKfPlPrTIWDGEet~yCFKe 185 (304)
T KOG0775|consen 106 AVVAFHSGNFRELYHILENHKFSPHNHPKLQALWLKAHYKEAEKLRGRPLGAVDKYRVRRKFPLPRTIWDGEETVYCFKE 185 (304)
T ss_pred HHHHHhcccHHHHHHHHHhccCChhhhHHHHHHHHHHHHHHHHHhcCCcCCccccceeeccCCCCCccccCceeeeehhH
Confidence 36799999999999999999999999999999999999999999999999999999999994 999
Q ss_pred HHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 75 ESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 75 ~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.++.+|++|| .+||||++++|++||++|||+.+||+|||+|||+|+|...
T Consensus 186 kSR~~LrewY---~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~ 235 (304)
T KOG0775|consen 186 KSRSLLREWY---LQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAA 235 (304)
T ss_pred hhHHHHHHHH---hcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhcc
Confidence 9999999999 8999999999999999999999999999999999999543
No 2
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=99.74 E-value=2.1e-18 Score=110.37 Aligned_cols=40 Identities=58% Similarity=0.927 Sum_probs=36.4
Q ss_pred HHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHh
Q psy10105 83 WLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRR 122 (197)
Q Consensus 83 wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R 122 (197)
||.+|..||||+.+||..||++|||+.+||+|||+|+|+|
T Consensus 1 Wl~~h~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 1 WLLEHLHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHTTTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 8999999999999999999999999999999999999998
No 3
>KOG0774|consensus
Probab=99.62 E-value=1.3e-16 Score=138.00 Aligned_cols=65 Identities=37% Similarity=0.614 Sum_probs=61.7
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhccc
Q psy10105 64 DLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128 (197)
Q Consensus 64 ~~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~ 128 (197)
+.|++|+||++.++.||..||+.|..|||||.++|.+||+++|++.+||+|||.|.|-|.|+.+-
T Consensus 187 darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~ 251 (334)
T KOG0774|consen 187 DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMG 251 (334)
T ss_pred HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhh
Confidence 35788999999999999999999999999999999999999999999999999999999998763
No 4
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.60 E-value=3e-15 Score=100.41 Aligned_cols=56 Identities=38% Similarity=0.570 Sum_probs=52.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhh
Q psy10105 67 ARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125 (197)
Q Consensus 67 ~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~ 125 (197)
+++..|++++..+|++|| ..||||+.+++..||.+|||+..||.+||+|+|.+.++
T Consensus 2 ~~r~~~~~~~~~~Le~~f---~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 2 RKRTRFTPEQLEELEKEF---EKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCCcCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 567789999999999999 77999999999999999999999999999999999774
No 5
>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=99.59 E-value=2.6e-15 Score=101.07 Aligned_cols=57 Identities=39% Similarity=0.621 Sum_probs=53.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhh
Q psy10105 66 AARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125 (197)
Q Consensus 66 r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~ 125 (197)
|++|+.|+.+++.+|+.+| ..++||+.+++..||..+||+..||.+||+|+|.+.|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f---~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYF---QENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHH---HHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHH---HHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 4678899999999999999 67999999999999999999999999999999999874
No 6
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.58 E-value=5.3e-15 Score=98.68 Aligned_cols=55 Identities=35% Similarity=0.550 Sum_probs=51.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhh
Q psy10105 67 ARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 124 (197)
Q Consensus 67 ~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k 124 (197)
+.|..|+.+++.+|++|| ..|+||+.+++..||..+||+..||.+||+|+|.|.+
T Consensus 2 k~r~~~~~~~~~~L~~~f---~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEF---QKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 456679999999999999 8899999999999999999999999999999999854
No 7
>KOG0773|consensus
Probab=99.50 E-value=1.1e-14 Score=130.10 Aligned_cols=63 Identities=43% Similarity=0.655 Sum_probs=59.1
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 65 LAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 65 ~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
..++++.|++.++.+|+.|+++|..+|||+..+|..||++|||+..||+|||+|+|+|.++.+
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~ 301 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPM 301 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCch
Confidence 455566899999999999999999999999999999999999999999999999999998776
No 8
>KOG0489|consensus
Probab=99.32 E-value=3.7e-12 Score=110.87 Aligned_cols=66 Identities=33% Similarity=0.421 Sum_probs=60.9
Q ss_pred CCccCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcccCc
Q psy10105 62 GYDLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMT 130 (197)
Q Consensus 62 ~~~~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~~~ 130 (197)
..+.|+.|+.|+..|+..|++-| ..|.|.+...|++||..++||+.||.+||+|||++.||..+..
T Consensus 156 ~~~~kR~RtayT~~QllELEkEF---hfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~ 221 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEF---HFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAK 221 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhh---ccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccc
Confidence 34578889999999999999999 9999999999999999999999999999999999999887553
No 9
>KOG0487|consensus
Probab=99.29 E-value=4.4e-12 Score=112.61 Aligned_cols=61 Identities=31% Similarity=0.335 Sum_probs=57.3
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 64 DLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 64 ~~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.-||||.-++|.|+..|++-| ..|-|.+.+-|.+|++.++||..||.+||||||+|+||-.
T Consensus 234 ~~RKKRcPYTK~QtlELEkEF---lfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~ 294 (308)
T KOG0487|consen 234 RGRKKRCPYTKHQTLELEKEF---LFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVN 294 (308)
T ss_pred ccccccCCchHHHHHHHHHHH---HHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhh
Confidence 357778889999999999999 9999999999999999999999999999999999999876
No 10
>KOG0843|consensus
Probab=99.27 E-value=1.9e-11 Score=101.03 Aligned_cols=61 Identities=28% Similarity=0.330 Sum_probs=57.3
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 64 DLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 64 ~~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
+-++.|+.|+.++...|+..| ..|.|-...||..||+.++|+++||..||+|||.|.|+..
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F---~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~ 161 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAF---EGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQ 161 (197)
T ss_pred CCCccccccCHHHHHHHHHHH---hcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHH
Confidence 567788899999999999999 9999999999999999999999999999999999988764
No 11
>KOG0850|consensus
Probab=99.19 E-value=3e-11 Score=103.04 Aligned_cols=69 Identities=28% Similarity=0.351 Sum_probs=63.6
Q ss_pred ccCCCCCccCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhccc
Q psy10105 57 VRYGAGYDLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128 (197)
Q Consensus 57 ~~~g~~~~~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~ 128 (197)
+.-|.+.|.||-|+.++--+...|++-| .+..|.-.-||.+||..+|||.+||.+||+|||-+.||.++
T Consensus 114 ~~Ngk~KK~RKPRTIYSS~QLqaL~rRF---QkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 114 RPNGKGKKVRKPRTIYSSLQLQALNRRF---QQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred ccCCCcccccCCcccccHHHHHHHHHHH---hhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 4456666778888999999999999999 99999999999999999999999999999999999999886
No 12
>KOG0488|consensus
Probab=99.15 E-value=4.6e-11 Score=106.47 Aligned_cols=62 Identities=26% Similarity=0.372 Sum_probs=57.2
Q ss_pred CccCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 63 YDLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 63 ~~~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+.|+.|+.|+..++..|++-| .+..|.+..+|.+||+.+|||-.||.+||+|||+|.|+..
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF---~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~ 231 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRF---EKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQT 231 (309)
T ss_pred cccccchhhhhHHHHHHHHHHH---HHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHH
Confidence 3556677789999999999999 9999999999999999999999999999999999988775
No 13
>KOG0842|consensus
Probab=99.07 E-value=6e-11 Score=105.36 Aligned_cols=61 Identities=26% Similarity=0.379 Sum_probs=54.7
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 64 DLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 64 ~~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
++||+|--|++.|+-.|++-| ....|.|.-||+.||+.++||.+||.+||||+|-|-|+..
T Consensus 152 ~kRKrRVLFSqAQV~ELERRF---rqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~ 212 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRF---RQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQ 212 (307)
T ss_pred cccccccccchhHHHHHHHHH---HhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhh
Confidence 345555569999999999999 8899999999999999999999999999999999887653
No 14
>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=99.03 E-value=3.1e-10 Score=78.07 Aligned_cols=52 Identities=17% Similarity=0.260 Sum_probs=49.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhhCCCC----CCHHHHHHHHHHhCCChHHHhhhhhHHH
Q psy10105 66 AARRKNATRESTATLKAWLNEHKKNPY----PTKGEKIMLAIITKMTLTQVSTWFANAR 120 (197)
Q Consensus 66 r~rR~~f~~~~~~~L~~wf~~h~~nPY----Ps~~ek~~LA~~tgLs~~QV~nWF~N~R 120 (197)
++.|+.|+.+|...|+..| ..++| |+..++.+||..+||+..+|.+||+|.+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~f---e~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFA---EKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHH---HHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 6788899999999999999 99999 9999999999999999999999999964
No 15
>KOG3802|consensus
Probab=98.99 E-value=1.8e-10 Score=104.78 Aligned_cols=68 Identities=25% Similarity=0.361 Sum_probs=61.8
Q ss_pred cCCCCCccCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhccc
Q psy10105 58 RYGAGYDLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128 (197)
Q Consensus 58 ~~g~~~~~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~ 128 (197)
.+++..++||||+.+...++..|+..| .+||-|+.+|.-.||..++|.+.-|.+||||||++.|+...
T Consensus 287 ~i~a~~RkRKKRTSie~~vr~aLE~~F---~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 287 KIGAQSRKRKKRTSIEVNVRGALEKHF---LKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred HhhccccccccccceeHHHHHHHHHHH---HhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 345555778899999999999999999 99999999999999999999999999999999999997654
No 16
>KOG0483|consensus
Probab=98.99 E-value=4.9e-10 Score=94.28 Aligned_cols=60 Identities=23% Similarity=0.278 Sum_probs=54.4
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 64 DLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 64 ~~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
+...++++|+.+++..|+.-| ..+-|-.+++|..||+++||.+.||.+||+|||.|.|..
T Consensus 49 ~~~~kk~Rlt~eQ~~~LE~~F---~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~k 108 (198)
T KOG0483|consen 49 KGKGKKRRLTSEQVKFLEKSF---ESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTK 108 (198)
T ss_pred ccccccccccHHHHHHhHHhh---ccccccChHHHHHHHHhhCCChhHHHHHHhhccccccch
Confidence 355677789999999999999 888899999999999999999999999999999997743
No 17
>KOG0485|consensus
Probab=98.98 E-value=3.5e-10 Score=96.07 Aligned_cols=61 Identities=26% Similarity=0.364 Sum_probs=55.7
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 64 DLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 64 ~~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
..||.|+.|++.|+..|+.-| ....|.+.+||..||+.+.||++||..||||+|.+.|+..
T Consensus 103 RKKktRTvFSraQV~qLEs~F---e~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTF---ELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred ccccchhhhhHHHHHHHHHHH---HHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 345667789999999999999 7889999999999999999999999999999999988764
No 18
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.96 E-value=1.7e-09 Score=87.92 Aligned_cols=61 Identities=30% Similarity=0.520 Sum_probs=56.9
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 64 DLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 64 ~~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
..+++|++.+..++.+|+..| ..+|||+..+|..|+..++|+++-|..||+|+|.+.|+..
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F---~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~ 110 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREF---EINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKR 110 (156)
T ss_pred cCcccceechHHHHHHHHHHh---ccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhc
Confidence 346677789999999999999 9999999999999999999999999999999999999775
No 19
>KOG0848|consensus
Probab=98.90 E-value=6e-10 Score=97.08 Aligned_cols=58 Identities=29% Similarity=0.343 Sum_probs=54.3
Q ss_pred CCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcccC
Q psy10105 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 129 (197)
Q Consensus 69 R~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~~ 129 (197)
|-.++..++-.|++-| ..++|.+.+.|.+||..+|||+.||..||+|||.++||.+|+
T Consensus 203 RvVYTDhQRLELEKEf---h~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKK 260 (317)
T KOG0848|consen 203 RVVYTDHQRLELEKEF---HTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKK 260 (317)
T ss_pred eEEecchhhhhhhhhh---ccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHH
Confidence 4469999999999999 999999999999999999999999999999999999988765
No 20
>KOG0491|consensus
Probab=98.89 E-value=6.8e-10 Score=90.81 Aligned_cols=64 Identities=25% Similarity=0.326 Sum_probs=58.1
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcccCcc
Q psy10105 65 LAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTW 131 (197)
Q Consensus 65 ~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~~~~ 131 (197)
.+|.|..|+..+...|++-| ....|.+-.|+.+||..++|+++||.+||+|+|++.|+..+..|
T Consensus 100 r~K~Rtvfs~~ql~~l~~rF---e~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRF---ERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred hhhhcccccCccccccHHHH---hhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 56678889999999999999 88899999999999999999999999999999999998765544
No 21
>KOG0493|consensus
Probab=98.87 E-value=2.3e-09 Score=93.37 Aligned_cols=58 Identities=31% Similarity=0.420 Sum_probs=53.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 67 ARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 67 ~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
+-|+-|+.++.+.|+.-| ..|-|.++..|.+||+++||.+.||..||+|+|.++||..
T Consensus 248 RPRTAFtaeQL~RLK~EF---~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 248 RPRTAFTAEQLQRLKAEF---QENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred CccccccHHHHHHHHHHH---hhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 345569999999999999 8889999999999999999999999999999999999874
No 22
>KOG0484|consensus
Probab=98.85 E-value=2.2e-09 Score=81.98 Aligned_cols=70 Identities=20% Similarity=0.295 Sum_probs=59.2
Q ss_pred ccccCCCCCcc--CCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 55 TAVRYGAGYDL--AARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 55 ~~~~~g~~~~~--r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+.++|-..+. |+-|+.|+-.+.+.|+..| ....||..=.+.+||....||+..|+.||+|+|.+.++..
T Consensus 5 ~~~~~~l~ekrKQRRIRTTFTS~QLkELErvF---~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 5 GDDPLGLTEKRKQRRIRTTFTSAQLKELERVF---AETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred CCCCCChhHHHHhhhhhhhhhHHHHHHHHHHH---HhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 34455555444 3445679999999999999 8889999999999999999999999999999999988763
No 23
>KOG2251|consensus
Probab=98.84 E-value=2.7e-09 Score=90.68 Aligned_cols=62 Identities=24% Similarity=0.414 Sum_probs=57.5
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhccc
Q psy10105 64 DLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128 (197)
Q Consensus 64 ~~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~ 128 (197)
+.|+-|+.|+..+..+|+..| .+..||+...+++||.+++|.+.+|.+||+|+|.+.++.-+
T Consensus 36 kqRRERTtFtr~QlevLe~LF---~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~ 97 (228)
T KOG2251|consen 36 KQRRERTTFTRKQLEVLEALF---AKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQ 97 (228)
T ss_pred hcccccceecHHHHHHHHHHH---HhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhh
Confidence 567778899999999999999 99999999999999999999999999999999999887643
No 24
>KOG0492|consensus
Probab=98.76 E-value=7.2e-09 Score=87.61 Aligned_cols=59 Identities=24% Similarity=0.331 Sum_probs=54.1
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 65 LAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 65 ~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
.|+-|+-|+..|...|++-| ....|.+.+|+.+++..+.||.+||..||+|||.|.|+.
T Consensus 144 nRkPRtPFTtqQLlaLErkf---rekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRl 202 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKF---REKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRL 202 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHH---hHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHH
Confidence 45667779999999999999 778999999999999999999999999999999998865
No 25
>KOG0494|consensus
Probab=98.67 E-value=3e-08 Score=86.32 Aligned_cols=57 Identities=28% Similarity=0.397 Sum_probs=52.6
Q ss_pred CCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhccc
Q psy10105 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128 (197)
Q Consensus 69 R~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~ 128 (197)
|++|+..+...|++-| ..-.||..-.|+.||..|+|.+..|.+||+|||.+.++..+
T Consensus 145 RTiFT~~Qle~LEkaF---keaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek 201 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAF---KEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEK 201 (332)
T ss_pred cchhhHHHHHHHHHHH---hhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhh
Confidence 4579999999999999 78899999999999999999999999999999999887643
No 26
>KOG0486|consensus
Probab=98.52 E-value=4.5e-08 Score=87.03 Aligned_cols=55 Identities=29% Similarity=0.521 Sum_probs=51.4
Q ss_pred CCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 69 R~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
|..|+-.+.+.|+.|| ..|-||+.+.+++||--|+||+..|.+||+|+|.+.++.
T Consensus 116 rthFtSqqlqele~tF---~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkr 170 (351)
T KOG0486|consen 116 RTHFTSQQLQELEATF---QRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 170 (351)
T ss_pred hhhhHHHHHHHHHHHH---hhccCCccchhhHHHhhccccchhhhhhcccchhhhhhh
Confidence 4569999999999999 889999999999999999999999999999999997765
No 27
>KOG0847|consensus
Probab=98.46 E-value=2.1e-07 Score=79.49 Aligned_cols=57 Identities=26% Similarity=0.400 Sum_probs=52.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 68 rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.|..|+-.+...|+.-| ....|+-..++.+||...|++++||.+||+|||.+.++.-
T Consensus 170 srPTf~g~qi~~le~~f---eqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 170 SRPTFTGHQIYQLERKF---EQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred cCCCccchhhhhhhhhh---hhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 44569999999999999 8889999999999999999999999999999999988763
No 28
>KOG4577|consensus
Probab=98.45 E-value=4.9e-07 Score=79.89 Aligned_cols=62 Identities=26% Similarity=0.360 Sum_probs=56.2
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhccc
Q psy10105 64 DLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128 (197)
Q Consensus 64 ~~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~ 128 (197)
..++-|+..+.++...|+.-| ...|-|..--|++|+.+|||...-|+.||+|||.+.|+-.|
T Consensus 166 ~nKRPRTTItAKqLETLK~AY---n~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAY---NTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHh---cCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhh
Confidence 467778899999999999999 88899999999999999999999999999999998776543
No 29
>KOG0844|consensus
Probab=98.44 E-value=5.7e-08 Score=86.31 Aligned_cols=67 Identities=25% Similarity=0.416 Sum_probs=57.3
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc-ccCccCCC
Q psy10105 65 LAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE-NKMTWEPK 134 (197)
Q Consensus 65 ~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~-~~~~~~~~ 134 (197)
-|+-|+-|+++|+..|++-| .+.-|-+.-.|.+||.+++|.++-|..||||||+++|+. ..+.|--.
T Consensus 181 mRRYRTAFTReQIaRLEKEF---yrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaWPhp 248 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEF---YRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAWPHP 248 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHH---HHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccCCCC
Confidence 45667789999999999888 566789999999999999999999999999999999876 35556443
No 30
>KOG2252|consensus
Probab=98.33 E-value=8.3e-07 Score=83.86 Aligned_cols=56 Identities=29% Similarity=0.329 Sum_probs=52.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhh
Q psy10105 66 AARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 124 (197)
Q Consensus 66 r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k 124 (197)
+|-|-.|+..+++.|...| ..+++|+.++-+.|+.++||..+-|.|||-|+|+|.+
T Consensus 421 KKPRlVfTd~QkrTL~aiF---ke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 421 KKPRLVFTDIQKRTLQAIF---KENKRPSREMQETISQQLNLELSTVINFFMNARRRSL 476 (558)
T ss_pred CCceeeecHHHHHHHHHHH---hcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence 4557789999999999999 8999999999999999999999999999999999963
No 31
>KOG0773|consensus
Probab=98.32 E-value=5.1e-07 Score=80.74 Aligned_cols=73 Identities=77% Similarity=1.108 Sum_probs=67.3
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcccCccCCCCCC
Q psy10105 64 DLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEPKNKT 137 (197)
Q Consensus 64 ~~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~~~~~~~~~~ 137 (197)
..+.++++.+.++ .+|+.|+.+|..++||+.-++..++-.++++..||++||+|+|+|.++.+++.|......
T Consensus 94 ~~~~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~ 166 (342)
T KOG0773|consen 94 DKGARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLA 166 (342)
T ss_pred ccccccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCcccc
Confidence 3567888999999 999999999999999999999999999999999999999999999999999988885443
No 32
>KOG0849|consensus
Probab=98.18 E-value=2.3e-06 Score=77.80 Aligned_cols=59 Identities=22% Similarity=0.435 Sum_probs=53.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 66 AARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 66 r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
++.|..|+..+...|+++| ..++||....+..||++++|+...|..||.|+|.|.++..
T Consensus 177 rr~rtsft~~Q~~~le~~f---~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 177 RRNRTSFSPSQLEALEECF---QRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccchHHHHHHHh---cCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 3345579999999999999 8999999999999999999999999999999999888765
No 33
>KOG1168|consensus
Probab=98.10 E-value=8.7e-07 Score=78.41 Aligned_cols=98 Identities=18% Similarity=0.251 Sum_probs=71.8
Q ss_pred ecccCCCCcchhhhhhhcCcccccccccccccc---cCCCCCccCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHH
Q psy10105 25 VNISSTKVPALQSRRQLCGIDKQVIQVSNLTAV---RYGAGYDLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIML 101 (197)
Q Consensus 25 ~~~s~~~~p~~~~~~q~~~~~~~~~~~~~l~~~---~~g~~~~~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~L 101 (197)
..+||+.--++.+.+|..-.++.-.-.++.... .+-.+...+++|+..-.--++.|+++| ...|-|+.+....|
T Consensus 266 LTLSHNNMiALKPILqaWLEeAE~a~keK~~~pd~~~l~~~~ekKRKRTSIAAPEKRsLEayF---avQPRPS~EkIAaI 342 (385)
T KOG1168|consen 266 LTLSHNNMIALKPILQAWLEEAEAAMKEKDTKPDINELLPGGEKKRKRTSIAAPEKRSLEAYF---AVQPRPSGEKIAAI 342 (385)
T ss_pred eccccCcchhhhHHHHHHHHHHHHHHHhhccCCchhhccCccccccccccccCcccccHHHHh---ccCCCCchhHHHHH
Confidence 456777778888888853333333222332222 222333456666666666788999999 99999999999999
Q ss_pred HHHhCCChHHHhhhhhHHHHhhhh
Q psy10105 102 AIITKMTLTQVSTWFANARRRLKK 125 (197)
Q Consensus 102 A~~tgLs~~QV~nWF~N~R~R~k~ 125 (197)
|.++.|..--|..||||.|++.|+
T Consensus 343 AekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 343 AEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred HHhhhhhhceEEEEeeccHHHHHH
Confidence 999999999999999999999886
No 34
>KOG0490|consensus
Probab=98.07 E-value=2.2e-06 Score=71.49 Aligned_cols=61 Identities=23% Similarity=0.254 Sum_probs=55.2
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 64 DLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 64 ~~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
+.++.|..|+..+.+.|+.-| ..++||....+..||..+++++..|.+||+|+|.+.++..
T Consensus 59 ~~rr~rt~~~~~ql~~ler~f---~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 59 SKRCARCKFTISQLDELERAF---EKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred cccccCCCCCcCHHHHHHHhh---cCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 445667789999999999999 7789999999999999999999999999999999988654
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.40 E-value=0.00013 Score=49.84 Aligned_cols=43 Identities=21% Similarity=0.310 Sum_probs=31.1
Q ss_pred HHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHh
Q psy10105 77 TATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRR 122 (197)
Q Consensus 77 ~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R 122 (197)
.+.|+++| ..+.+....+-..|+.+++||..||.+||.-++.+
T Consensus 10 ~~pL~~Yy---~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYY---LKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHH---HHT----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHH---HHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 45599999 77789999999999999999999999999877554
No 36
>KOG0490|consensus
Probab=96.48 E-value=0.0034 Score=52.21 Aligned_cols=60 Identities=23% Similarity=0.398 Sum_probs=54.1
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 65 LAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 65 ~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+..|..+...+...|...| ..++||....+..|+..+|++..-|.+||+|+|.+.++..
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~---~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 153 PRRPRTTFTENQLEVLETVF---RATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred cCCCccccccchhHhhhhcc---cCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 44556678899999999999 9999999999999999999999999999999999988654
No 37
>KOG1146|consensus
Probab=94.36 E-value=0.037 Score=57.64 Aligned_cols=60 Identities=25% Similarity=0.288 Sum_probs=54.7
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 65 LAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 65 ~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+..|..++..++++|+..| ...-||..++-+.|....+|...-|..||+|+|.+.++..
T Consensus 903 r~a~~~~~~d~qlk~i~~~~---~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~ 962 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACY---EAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAK 962 (1406)
T ss_pred hhhhccchhHHHHHHHHHHH---hhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhh
Confidence 45567778899999999999 8889999999999999999999999999999999988764
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=93.09 E-value=0.29 Score=32.63 Aligned_cols=47 Identities=23% Similarity=0.182 Sum_probs=31.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHH
Q psy10105 66 AARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANAR 120 (197)
Q Consensus 66 r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R 120 (197)
+++|+.++-+..-.+=..+ ..++ -...||+..|++.++|++|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~---e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRL---EEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHH---HCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHH---HcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 4567778877754443444 4444 588999999999999999999954
No 39
>KOG3623|consensus
Probab=90.45 E-value=0.47 Score=47.33 Aligned_cols=46 Identities=24% Similarity=0.374 Sum_probs=42.9
Q ss_pred HHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhh
Q psy10105 77 TATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125 (197)
Q Consensus 77 ~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~ 125 (197)
+.+|+.+| ..|+.|+.+|-..||.+.||...-|..||.+.+.....
T Consensus 568 ~sllkayy---aln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~s 613 (1007)
T KOG3623|consen 568 TSLLKAYY---ALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMS 613 (1007)
T ss_pred HHHHHHHH---HhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhh
Confidence 88999999 99999999999999999999999999999999977553
No 40
>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=85.22 E-value=3.4 Score=22.57 Aligned_cols=41 Identities=12% Similarity=0.073 Sum_probs=29.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhh
Q psy10105 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWF 116 (197)
Q Consensus 68 rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF 116 (197)
|++.++.+....+...+. +.+ ....+|+.+|++...|.+|.
T Consensus 2 r~~~~~~~~~~~i~~~~~----~~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 2 RPPKLTPEQIEEARRLLA----AGE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCCcCCHHHHHHHHHHHH----cCC----CHHHHHHHHCCCHHHHHHhC
Confidence 445577777666666652 232 45688999999999999984
No 41
>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=84.20 E-value=1.9 Score=27.62 Aligned_cols=47 Identities=13% Similarity=0.066 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhh
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~ 125 (197)
.+++..+.+|...|++ . ..-.++|..+|+|...|..+...+..++|+
T Consensus 4 ~L~~~er~vi~~~y~~----~----~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE----G----LTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTS----T-----SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC----C----CCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 4788889999888721 1 235789999999999999999999988763
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=82.68 E-value=3 Score=25.47 Aligned_cols=46 Identities=13% Similarity=0.110 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhh
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 124 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k 124 (197)
.++...+.++...|.+. ..-..+|..+|++...|..|....+.+.|
T Consensus 10 ~l~~~~~~~~~~~~~~~--------~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGEG--------LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 36777888887776321 23567899999999999999988887753
No 43
>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=80.76 E-value=1.6 Score=29.99 Aligned_cols=46 Identities=13% Similarity=0.218 Sum_probs=30.3
Q ss_pred CCCCCCCHHHHH-HHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHH
Q psy10105 67 ARRKNATRESTA-TLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANAR 120 (197)
Q Consensus 67 ~rR~~f~~~~~~-~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R 120 (197)
++|+.|+.+.+. ++...+. .......+|++.||+..+|.+|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~--------~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE--------SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHH--------HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH--------CCCceEeeecccccccccccHHHHHHh
Confidence 466788888755 4555542 236788999999999999999977766
No 44
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=79.52 E-value=7.4 Score=24.99 Aligned_cols=44 Identities=14% Similarity=0.082 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhh
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRL 123 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~ 123 (197)
+++..+.++...|. ..-.-.++|+.+|+|...|.+|...+|+++
T Consensus 11 L~~~~r~i~~l~~~--------~g~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 11 LPERQREIFLLRYF--------QGMSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp S-HHHHHHHHHHHT--------S---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH--------HCcCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 67777787776652 223457899999999999999999998763
No 45
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=76.31 E-value=4.9 Score=30.83 Aligned_cols=47 Identities=15% Similarity=0.069 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhh
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~ 125 (197)
.+++..+.++...|.+. -.-.+||..+|++...|.+|...+|.++++
T Consensus 106 ~L~~~~r~ii~l~~~~~--------~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG--------KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 47888888876655322 225789999999999999999999998874
No 46
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=73.64 E-value=4.5 Score=31.43 Aligned_cols=51 Identities=14% Similarity=0.033 Sum_probs=39.0
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcccCc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMT 130 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~~~ 130 (197)
+++..+.++...|.+ . ..-.+||+.+|++...|.+|..-+|.++++.....
T Consensus 126 L~~~~r~i~~l~~~~----~----~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~~ 176 (179)
T PRK11924 126 LPVKQREVFLLRYVE----G----LSYREIAEILGVPVGTVKSRLRRARQLLRECLEAQ 176 (179)
T ss_pred CCHHHHHHhhHHHHc----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 777777777655421 1 23478999999999999999999999998775443
No 47
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=73.27 E-value=6.3 Score=31.91 Aligned_cols=49 Identities=14% Similarity=-0.025 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.|++..+.+|...|.+. -.-.+||+.+|++...|.++...+|+++++..
T Consensus 142 ~L~~~~r~vl~l~~~~~--------~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG--------LTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 38888888887655322 22468999999999999999999999998765
No 48
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=71.59 E-value=7.5 Score=30.12 Aligned_cols=48 Identities=19% Similarity=0.159 Sum_probs=38.0
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
+++..+.++.-.+.+. -+ -.+||+.+|++...|.+.+.-+|.++++..
T Consensus 107 Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 107 LPENYRDVVLAHYLEE--KS------YQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CCHHHHHHHHHHHHhC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 7888888876655322 22 258999999999999999999999998765
No 49
>PF13518 HTH_28: Helix-turn-helix domain
Probab=71.34 E-value=5.6 Score=25.08 Aligned_cols=25 Identities=16% Similarity=0.166 Sum_probs=21.5
Q ss_pred HHHHHHHhCCChHHHhhhhhHHHHh
Q psy10105 98 KIMLAIITKMTLTQVSTWFANARRR 122 (197)
Q Consensus 98 k~~LA~~tgLs~~QV~nWF~N~R~R 122 (197)
..++|+..|++..+|..|....+..
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~~ 39 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYREG 39 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHhc
Confidence 4569999999999999998877763
No 50
>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=70.40 E-value=9.6 Score=28.94 Aligned_cols=48 Identities=13% Similarity=0.043 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
.++...+.+|.-.|. ..+ .-.+||+.+|++...|.++...+|+++++.
T Consensus 113 ~L~~~~r~il~l~~~----~~~----~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~ 160 (161)
T TIGR02985 113 KLPEQCRKIFILSRF----EGK----SYKEIAEELGISVKTVEYHISKALKELRKE 160 (161)
T ss_pred HCCHHHHHHHHHHHH----cCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 367777777776542 222 235699999999999999999999998754
No 51
>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=69.24 E-value=6 Score=31.42 Aligned_cols=48 Identities=13% Similarity=-0.006 Sum_probs=37.2
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
+++..+.++.-.|.++ -.-.+||..+|++...|.++...+|+++++..
T Consensus 139 L~~~~r~v~~l~~~~~--------~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 139 LPEDLRTAITLRELEG--------LSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred CCHHHhhhhhhhhhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 6777777776554211 23468999999999999999999999998765
No 52
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=69.22 E-value=4.1 Score=26.93 Aligned_cols=24 Identities=17% Similarity=0.081 Sum_probs=18.4
Q ss_pred HHHHHHHHhCCChHHHhhhhhHHH
Q psy10105 97 EKIMLAIITKMTLTQVSTWFANAR 120 (197)
Q Consensus 97 ek~~LA~~tgLs~~QV~nWF~N~R 120 (197)
....||+.+|++..+|+.|+.+..
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-
T ss_pred CHHHHHHHHCcCHHHHHHHHhccc
Confidence 457899999999999999999774
No 53
>PRK00118 putative DNA-binding protein; Validated
Probab=68.07 E-value=11 Score=28.65 Aligned_cols=48 Identities=8% Similarity=-0.034 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
.+++.++.++..+|.+. ..-.+||+.+|+|..-|.+|...+|.+.+..
T Consensus 17 ~L~ekqRevl~L~y~eg--------~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD--------YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred cCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 37888999998777422 2346799999999999999999999998865
No 54
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=67.70 E-value=9.9 Score=29.56 Aligned_cols=49 Identities=14% Similarity=0.051 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.+|...|. ...+ -.+||+.+|++...|.+|...+++++++..
T Consensus 128 ~L~~~~r~vl~l~~~--~~~s------~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREI--EGLS------YEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHH--cCCC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 378888888866542 2222 358999999999999999999999988754
No 55
>PRK04217 hypothetical protein; Provisional
Probab=67.06 E-value=26 Score=26.91 Aligned_cols=49 Identities=14% Similarity=-0.021 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.++.+.+.++..++.+.. .-.+||+.+|++...|.+.+..++..++...
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 488888888877764322 4567999999999999999999999998765
No 56
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=66.87 E-value=11 Score=29.42 Aligned_cols=49 Identities=12% Similarity=0.019 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++.-.+.++. .-.+||..+|++...|.+|..-+|+++++..
T Consensus 108 ~L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 108 TLPVIEAQAILLCDVHEL--------TYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred hCCHHHHHHHHhHHHhcC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888876654332 2468999999999999999999999998764
No 57
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=66.54 E-value=11 Score=31.07 Aligned_cols=48 Identities=17% Similarity=0.097 Sum_probs=37.8
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
+++..+.+|...|++.. .-.+||..+|++...|.+++..+++++++..
T Consensus 154 L~~~~r~vl~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 154 LPEAQQTVVKGVYFQEL--------SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 77788888775553222 2468999999999999999999999988765
No 58
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=66.40 E-value=13 Score=29.83 Aligned_cols=48 Identities=19% Similarity=0.109 Sum_probs=38.4
Q ss_pred CCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 70 KNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 70 ~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
..+++.++.+|+..+ ..+ .-.+||..+|+|...|++|..+++.++++.
T Consensus 5 ~~Lt~rqreVL~lr~-----~Gl----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~ 52 (141)
T PRK03975 5 SFLTERQIEVLRLRE-----RGL----TQQEIADILGTSRANVSSIEKRARENIEKA 52 (141)
T ss_pred cCCCHHHHHHHHHHH-----cCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 458999999997732 122 246899999999999999999999988765
No 59
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=66.21 E-value=7.6 Score=31.21 Aligned_cols=53 Identities=13% Similarity=0.078 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcccCcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTW 131 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~~~~ 131 (197)
.+++.++.++.-.|.+ ..+ -.+||..+|++..-|.+....+|+++++.....|
T Consensus 131 ~Lp~~~r~v~~l~~~~--g~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 131 RLPPRTGRVFMMREWL--ELE------TEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred hCCHHHHHHHHHHHHc--CCC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3888888888766532 222 3689999999999999999999999998876555
No 60
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=66.05 E-value=15 Score=26.99 Aligned_cols=48 Identities=15% Similarity=0.143 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
.+++..+.++...|. ..+ .-.+||+.+|+++..|.++....+.+.++.
T Consensus 110 ~L~~~~~~ii~~~~~----~g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~ 157 (158)
T TIGR02937 110 KLPEREREVLVLRYL----EGL----SYKEIAEILGISVGTVKRRLKRARKKLREL 157 (158)
T ss_pred hCCHHHHHHHhhHHh----cCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 367777777755432 233 346899999999999999999999988753
No 61
>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=65.92 E-value=14 Score=24.27 Aligned_cols=48 Identities=13% Similarity=0.053 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.|++....+|+-+. . . ..-.++|...|+++.-|..+..+.++|..-.+
T Consensus 3 ~LT~~E~~vl~~l~---~--G----~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~ 50 (58)
T PF00196_consen 3 SLTERELEVLRLLA---Q--G----MSNKEIAEELGISEKTVKSHRRRIMKKLGVKN 50 (58)
T ss_dssp SS-HHHHHHHHHHH---T--T----S-HHHHHHHHTSHHHHHHHHHHHHHHHHT-SS
T ss_pred ccCHHHHHHHHHHH---h--c----CCcchhHHhcCcchhhHHHHHHHHHHHhCCCC
Confidence 47888888887776 2 2 34578999999999999999999999977443
No 62
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=65.76 E-value=11 Score=30.65 Aligned_cols=51 Identities=12% Similarity=0.048 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcccC
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 129 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~~ 129 (197)
.+++..+.++.-.+. ...+ -.+||+.+|++...|.+....+|+++++....
T Consensus 116 ~Lp~~~r~i~~L~~~--~g~s------~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~ 166 (187)
T PRK12516 116 QLPDDQREAIILVGA--SGFA------YEEAAEICGCAVGTIKSRVNRARQRLQEILQI 166 (187)
T ss_pred hCCHHHHHHHHHHHH--cCCC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 378888887766553 2222 25899999999999999999999999987643
No 63
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=65.52 E-value=17 Score=22.49 Aligned_cols=47 Identities=17% Similarity=0.107 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
.++.....++..++ . . ....++|+.+|++...|..|....+.+....
T Consensus 3 ~l~~~e~~i~~~~~---~--g----~s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 3 SLTPREREVLRLLA---E--G----LTNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCCHHHHHHHHHHH---c--C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 36777777775543 1 1 2457899999999999999999887776533
No 64
>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=64.92 E-value=12 Score=28.67 Aligned_cols=47 Identities=17% Similarity=0.115 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhh
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~ 125 (197)
.+++..+.++...|. ... .-.+||..+|+|...|.++..-+|++++.
T Consensus 111 ~L~~~~r~v~~l~~~--~g~------~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 111 KLPERQRELLQLRYQ--RGV------SLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HCCHHHHHHHHHHHh--cCC------CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 488888888877543 222 24689999999999999999999988774
No 65
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=64.90 E-value=12 Score=29.57 Aligned_cols=48 Identities=17% Similarity=0.218 Sum_probs=37.9
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
.+++..+.++...|.+ .-+ -.+||+.+|++...|.+++..+|.++|+.
T Consensus 129 ~L~~~~r~i~~l~~~~--g~s------~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 129 ELEKDRAAAVRRAYLE--GLS------YKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred hCCHHHHHHHHHHHHc--CCC------HHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 3788888877766632 122 46899999999999999999999998865
No 66
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=64.49 E-value=19 Score=27.43 Aligned_cols=47 Identities=11% Similarity=0.121 Sum_probs=31.4
Q ss_pred CCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHH
Q psy10105 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARR 121 (197)
Q Consensus 68 rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~ 121 (197)
+|++|+.+.....-... ..+.+ ....+|+..|++..+|.+|..-.+.
T Consensus 9 ~rr~ys~EfK~~aV~~~---~~~g~----sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQS---FEPGM----TVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCCHHHHHHHHHHH---HcCCC----CHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 45668877755333333 33332 3567899999999999999665543
No 67
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=64.48 E-value=13 Score=28.63 Aligned_cols=50 Identities=14% Similarity=-0.011 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhccc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~ 128 (197)
.+++..+.++.-.|.+. -+ -.+||..+|++...|.+...-+|+++++...
T Consensus 106 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 155 (161)
T PRK09047 106 KLPARQREAFLLRYWED--MD------VAETAAAMGCSEGSVKTHCSRATHALAKALE 155 (161)
T ss_pred hCCHHHHHHHHHHHHhc--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 48888888887655322 22 3689999999999999999999999987753
No 68
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=64.29 E-value=13 Score=29.44 Aligned_cols=49 Identities=16% Similarity=0.091 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.+|.-.|.+. . .-.+||..+|++...|.++...+|.+++...
T Consensus 135 ~L~~~~r~vl~l~~~~~--~------s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 135 ALSPEERRVIEVLYYQG--Y------THREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 37888888887654322 2 2368999999999999999999999988765
No 69
>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=64.23 E-value=6.3 Score=27.24 Aligned_cols=19 Identities=11% Similarity=0.195 Sum_probs=17.3
Q ss_pred HHHHHHHHhCCChHHHhhh
Q psy10105 97 EKIMLAIITKMTLTQVSTW 115 (197)
Q Consensus 97 ek~~LA~~tgLs~~QV~nW 115 (197)
.-..||.++|++..+|..|
T Consensus 24 ~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 4578999999999999999
No 70
>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=63.70 E-value=14 Score=28.58 Aligned_cols=48 Identities=15% Similarity=0.088 Sum_probs=37.8
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
+++..+.++...|.+. -.-.++|..+|++...|.++...+|+++++..
T Consensus 111 L~~~~r~i~~l~~~~g--------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 111 LPARQRAVVVLRYYED--------LSEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred CCHHHHHHhhhHHHhc--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 7788888886655322 12368999999999999999999999988754
No 71
>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=63.32 E-value=13 Score=29.35 Aligned_cols=47 Identities=13% Similarity=0.053 Sum_probs=37.6
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
+++.++.++.-.|.+. -. -.+||..+|++...|.+....+|.++++.
T Consensus 135 Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG--LT------VEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCHHHHHHHHHHHHcC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 7888888887766422 22 36899999999999999999999998864
No 72
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=63.08 E-value=13 Score=28.95 Aligned_cols=47 Identities=17% Similarity=0.062 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhh
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~ 125 (197)
.++..++.++.-.|.+. -+ -.+||..+|++...|.++...+|.++++
T Consensus 112 ~L~~~~r~v~~l~~~~~--~s------~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 112 SLPLERRNVLLLRDYYG--FS------YKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HCCHHHHHHhhhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 48888888887655322 22 3689999999999999999999999874
No 73
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=62.85 E-value=16 Score=30.99 Aligned_cols=49 Identities=10% Similarity=0.068 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.+|.-.|++.. .-.+||..+|++...|.+|...++.+++...
T Consensus 205 ~L~~~~r~vl~l~~~~g~--------s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l 253 (257)
T PRK08583 205 VLSDREKSIIQCTFIENL--------SQKETGERLGISQMHVSRLQRQAIKKLREAA 253 (257)
T ss_pred hCCHHHHHHHHHHHhCCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 378888888877663221 2378999999999999999999999998765
No 74
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=62.77 E-value=14 Score=28.92 Aligned_cols=49 Identities=12% Similarity=0.014 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++.-.+.+.. .-.+||..+|++...|.++..-+|++++...
T Consensus 112 ~L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 112 LLSADQREAIILIGASGF--------SYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 378888888877653222 2468999999999999999999999998664
No 75
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=62.71 E-value=15 Score=29.25 Aligned_cols=49 Identities=10% Similarity=-0.053 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++...|.+. -.-.+||..+|++...|.+++..+|.+++...
T Consensus 131 ~L~~~~r~v~~l~~~~g--------~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG--------ASIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 47888888887765322 23468999999999999999999999998765
No 76
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=62.34 E-value=17 Score=28.71 Aligned_cols=49 Identities=12% Similarity=0.058 Sum_probs=37.9
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++...|. .. -.-.++|..+|++...|.+++..+|++++...
T Consensus 136 ~L~~~~r~v~~l~~~--~g------~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 136 ALPPKYRMVIVLKYM--ED------LSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHhHHhhhHHh--cC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 378888888766442 22 22468999999999999999999999988764
No 77
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=61.90 E-value=16 Score=29.15 Aligned_cols=48 Identities=10% Similarity=-0.051 Sum_probs=36.7
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
+++..+.++.-.+.+. -.-.+||+.+|++...|.+.+..+|+++++..
T Consensus 130 L~~~~r~v~~l~~~~g--------~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 130 LPDRQRLPIVHVKLEG--------LSVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred CCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 6777777665544222 22468999999999999999999999998765
No 78
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=61.53 E-value=16 Score=29.46 Aligned_cols=49 Identities=10% Similarity=0.107 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++.-.|. ...+ -.+||+.+|+|...|.+...-+|+++++..
T Consensus 131 ~L~~~~r~i~~l~~~--~g~s------~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 131 DLEKLDREIFIRRYL--LGEK------IEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred hCCHHHHHHHHHHHH--ccCC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 488889888876553 2222 368999999999999999999999988653
No 79
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=60.97 E-value=8.3 Score=24.32 Aligned_cols=25 Identities=16% Similarity=0.126 Sum_probs=17.5
Q ss_pred HHHHHHHHHhCCChHHHhhhhhHHH
Q psy10105 96 GEKIMLAIITKMTLTQVSTWFANAR 120 (197)
Q Consensus 96 ~ek~~LA~~tgLs~~QV~nWF~N~R 120 (197)
....++|+.+|++...|.+|....+
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT---
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 3467899999999999999976554
No 80
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=59.53 E-value=12 Score=30.15 Aligned_cols=49 Identities=6% Similarity=-0.019 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++.-.|++. - .-.+||..+|+++..|.++..-+|+++++..
T Consensus 134 ~Lp~~~R~v~~L~~~~g--~------s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 134 HLPAQQARVFMMREYLE--L------SSEQICQECDISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred hCCHHHHHHHhHHHHcC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 37888888777665322 1 2468999999999999999999999998765
No 81
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=59.39 E-value=12 Score=30.08 Aligned_cols=51 Identities=10% Similarity=0.035 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcccC
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 129 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~~ 129 (197)
.+++..+.++.-.|.+. . .-.+||..+|++...|.+....+|+++++....
T Consensus 136 ~L~~~~r~i~~L~~~~g--~------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 186 (195)
T PRK12532 136 NLPENTARVFTLKEILG--F------SSDEIQQMCGISTSNYHTIMHRARESLRQCLQI 186 (195)
T ss_pred hCCHHHHHHhhhHHHhC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 37777777776544322 1 236899999999999999999999999987643
No 82
>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=59.32 E-value=18 Score=28.34 Aligned_cols=49 Identities=14% Similarity=0.095 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.++...+.++..-|.+. . .-.++|..+|+|...|.++..-+|.++++..
T Consensus 119 ~L~~~~r~i~~l~~~~g--~------s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l 167 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD--L------TIKEIAEVMNKPEGTVKTYLHRALKKLKKRL 167 (169)
T ss_pred hCCHHHhHHHHHHHHcC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 37788888886665322 1 2368999999999999999999999988654
No 83
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=59.17 E-value=16 Score=29.18 Aligned_cols=48 Identities=13% Similarity=0.191 Sum_probs=37.1
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
+++..+.++...|+ ..- .-.+||+.+|++...|.++...+|+++++..
T Consensus 129 L~~~~r~i~~l~~~--~g~------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 129 LPERQREAIVLQYY--QGL------SNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred CCHHHHHHhhHHHh--cCC------CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 67777777755442 222 2368999999999999999999999999875
No 84
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=59.09 E-value=18 Score=28.91 Aligned_cols=48 Identities=17% Similarity=-0.058 Sum_probs=38.4
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
.+++..+.++...|.+. -.-.+||..+|++...|.++...+|.++++.
T Consensus 139 ~L~~~~r~i~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 139 TLPEKQREILILRVVVG--------LSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 48888888887765321 2357899999999999999999999998865
No 85
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=58.29 E-value=14 Score=29.66 Aligned_cols=48 Identities=13% Similarity=-0.002 Sum_probs=36.3
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
++++.+.++.-.|.+ . -.-.+||..+|++...|.+|+..+|.++++..
T Consensus 142 L~~~~~~v~~l~~~~--g------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 142 LPESQRQVLELAYYE--G------LSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred CCHHHhhhhhhhhhc--C------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 677777777554421 1 22468999999999999999999999988654
No 86
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=57.35 E-value=20 Score=28.22 Aligned_cols=49 Identities=10% Similarity=0.017 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++.++.++.-.+. ...+ -.+||+.+|++..-|.++...++++.+...
T Consensus 119 ~Lp~~~r~v~~L~~~--~g~s------~~EIA~~lgis~~tV~~~l~ra~~~~~~~l 167 (172)
T PRK12523 119 KLSSKARAAFLYNRL--DGMG------HAEIAERLGVSVSRVRQYLAQGLRQCYIAL 167 (172)
T ss_pred hCCHHHHHHHHHHHH--cCCC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 378888888776553 2223 368999999999999999999999987654
No 87
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=56.00 E-value=17 Score=30.08 Aligned_cols=53 Identities=9% Similarity=0.102 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcccCcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTW 131 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~~~~ 131 (197)
.+++..+.++.-.|++. -+ -.+||..+|++...|.+...-+|+++++..+..|
T Consensus 148 ~L~~~~r~v~~L~~~~g--~s------~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~ 200 (206)
T PRK12544 148 GLPAKYARVFMMREFIE--LE------TNEICHAVDLSVSNLNVLLYRARLRLRECLENKW 200 (206)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 47888888776655422 22 3689999999999999999999999998765444
No 88
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=55.80 E-value=21 Score=28.43 Aligned_cols=47 Identities=11% Similarity=0.090 Sum_probs=35.5
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
+++..+.++..-|. ..-+ -.+||+.+|+|...|.++...+|++++..
T Consensus 134 L~~~~r~i~~l~~~--~~~s------~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 134 LEPARRNCILHAYV--DGCS------HAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred CCHHHHHHHHHHHH--cCCC------HHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 67777776655443 2222 46899999999999999999999998754
No 89
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=55.55 E-value=33 Score=27.65 Aligned_cols=50 Identities=12% Similarity=-0.013 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhccc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~ 128 (197)
.+++..+.++.-.+.+.. .-.+||..+|++...|.....-+|+++++...
T Consensus 111 ~Lp~~~R~v~~L~~~~g~--------s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 111 KLPQDQREALILVGASGF--------SYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred hCCHHHHHHhhHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 378888888766553222 23689999999999999999999999997763
No 90
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=55.53 E-value=28 Score=26.61 Aligned_cols=44 Identities=7% Similarity=0.191 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHH
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANA 119 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~ 119 (197)
-....+..+.+|+.+|...+ ++ -.+||+.+|+++.++..+|+..
T Consensus 6 ~~~~~i~~~~~~I~~~~~~~-~s---l~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 6 TDAITIHSILDWIEDNLESP-LS---LEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred ccHHHHHHHHHHHHHhcCCC-CC---HHHHHHHHCcCHHHHHHHHHHH
Confidence 34455667778887777665 34 4678899999999999998765
No 91
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=55.43 E-value=22 Score=28.66 Aligned_cols=49 Identities=16% Similarity=0.186 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++.-.|. ..-+ -.+||..+|++...|.+-+..+|+++++..
T Consensus 141 ~Lp~~~r~v~~l~~~--eg~s------~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 141 RLPKAQRDVLQAVYL--EELP------HQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred hCCHHHHHHHHHHHH--cCCC------HHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 478888888876553 2223 368999999999999999999999988764
No 92
>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=55.42 E-value=22 Score=30.15 Aligned_cols=49 Identities=12% Similarity=0.072 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++...|.+.. .-.+||..+|++...|..+...++.++|+.+
T Consensus 205 ~L~~~~r~ii~l~~~~g~--------s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 205 ILSEREKSIIHCTFEENL--------SQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred cCCHHHHHHHHHHHcCCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 478888888877763222 2368999999999999999999999988653
No 93
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=55.38 E-value=21 Score=28.63 Aligned_cols=49 Identities=14% Similarity=0.034 Sum_probs=37.7
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++.++.++.-.+.+.. .-.+||..+|++...|.+...-+|+++++..
T Consensus 130 ~Lp~~~r~v~~L~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~~ 178 (185)
T PRK09649 130 DLTTDQREALLLTQLLGL--------SYADAAAVCGCPVGTIRSRVARARDALLADA 178 (185)
T ss_pred hCCHHHhHHhhhHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 377888887766553222 2368999999999999999999999998743
No 94
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=53.58 E-value=20 Score=29.99 Aligned_cols=48 Identities=15% Similarity=0.167 Sum_probs=37.8
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
+++..+.++...|.+. -.-.+||..+|++..-|.++...+++++++..
T Consensus 185 L~~~~r~vl~l~~~~g--------~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 185 LPEREQLVLSLYYQEE--------LNLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred CCHHHHHHHHhHhccC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 6777777776655321 23578999999999999999999999998754
No 95
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=53.35 E-value=26 Score=27.42 Aligned_cols=49 Identities=16% Similarity=0.027 Sum_probs=38.7
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhccc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~ 128 (197)
+++..+.+|.--|.+. .+ -.+||+.+|++..-|.+...-+|.++++..+
T Consensus 119 L~~~~r~vl~L~~~~g--~s------~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 167 (173)
T PRK09645 119 LSPEHRAVLVRSYYRG--WS------TAQIAADLGIPEGTVKSRLHYALRALRLALQ 167 (173)
T ss_pred CCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 7888888887655322 22 3689999999999999999999999987653
No 96
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=53.27 E-value=22 Score=28.94 Aligned_cols=49 Identities=16% Similarity=0.003 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++.-.|. ..-+ -.++|..+|+|...|.+++.-+|+++++..
T Consensus 113 ~Lp~~~r~v~~L~~~--~g~s------~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 113 QLPDEQREALILVGA--SGFS------YEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred hCCHHHhHHhhhHHh--cCCC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 378888888877653 2222 368999999999999999999999998765
No 97
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=53.18 E-value=19 Score=27.82 Aligned_cols=48 Identities=19% Similarity=0.202 Sum_probs=37.7
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhccc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~ 128 (197)
++...+.+|.-.| + .+ .-.+||..+|++...|.++...+|.++|+...
T Consensus 113 L~~~~r~il~l~~-~----g~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 113 MTERDRTVLLLRF-S----GY----SYKEIAEALGIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred CCHHHHHHHHHHH-c----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 7777777776554 2 22 34689999999999999999999999987653
No 98
>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=52.91 E-value=20 Score=28.98 Aligned_cols=51 Identities=8% Similarity=-0.025 Sum_probs=40.0
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcccC
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 129 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~~ 129 (197)
.++...+.++.-.|++. ..-.+||..+|++..-|.+...-+|+++++....
T Consensus 131 ~L~~~~r~v~~l~~~~g--------~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~ 181 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG--------FESDEICQELEISTSNCHVLLYRARLSLRACLSI 181 (188)
T ss_pred hCCHHHHHHHHHHHHhC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 37788888877665432 2247899999999999999999999999877643
No 99
>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=52.80 E-value=9.5 Score=24.08 Aligned_cols=20 Identities=15% Similarity=0.144 Sum_probs=18.6
Q ss_pred HHHHHhCCChHHHhhhhhHH
Q psy10105 100 MLAIITKMTLTQVSTWFANA 119 (197)
Q Consensus 100 ~LA~~tgLs~~QV~nWF~N~ 119 (197)
+||+.+|++...|+.|+.+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 68999999999999999887
No 100
>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=52.58 E-value=36 Score=21.08 Aligned_cols=29 Identities=24% Similarity=0.202 Sum_probs=23.8
Q ss_pred HHHHHHHHhCCChHHHhhhhhHHHHhhhh
Q psy10105 97 EKIMLAIITKMTLTQVSTWFANARRRLKK 125 (197)
Q Consensus 97 ek~~LA~~tgLs~~QV~nWF~N~R~R~k~ 125 (197)
.-.++|+.+|++...|..|....+.+...
T Consensus 17 s~~eia~~l~~s~~tv~~~~~~~~~~l~~ 45 (57)
T cd06170 17 TNKEIADILGISEKTVKTHLRNIMRKLGV 45 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 45789999999999999998877666543
No 101
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=52.11 E-value=23 Score=29.69 Aligned_cols=49 Identities=24% Similarity=0.145 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++.-.|+++ -+ -.+||..+|++..-|.++...+|+++++..
T Consensus 134 ~Lp~~~R~v~~L~y~eg--~s------~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 134 KLPVEYREVLVLRELED--MS------YREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCHHHHhHhhhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888888888776432 22 368999999999999999999999998765
No 102
>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=52.02 E-value=9.2 Score=24.40 Aligned_cols=21 Identities=14% Similarity=-0.007 Sum_probs=18.3
Q ss_pred HHHHHHHhCCChHHHhhhhhH
Q psy10105 98 KIMLAIITKMTLTQVSTWFAN 118 (197)
Q Consensus 98 k~~LA~~tgLs~~QV~nWF~N 118 (197)
..+||+.+|++...|+.|..+
T Consensus 12 ~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHHHHhCCCcchhHHHhcC
Confidence 378999999999999999888
No 103
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=51.90 E-value=56 Score=21.84 Aligned_cols=49 Identities=24% Similarity=0.104 Sum_probs=36.9
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHH
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARR 121 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~ 121 (197)
+++.++.+|+.-+ +.-..-+|-...-.+||+.+|++..-|+.=+.++-+
T Consensus 1 LT~~Q~e~L~~A~-~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 1 LTDRQREILKAAY-ELGYFDVPRRITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred CCHHHHHHHHHHH-HcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 5778888998776 233445688889999999999999998875544433
No 104
>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=51.87 E-value=28 Score=27.47 Aligned_cols=49 Identities=14% Similarity=0.097 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.+|.-.|.+. - .-.+||..+|++...|.++..-+|++++...
T Consensus 100 ~L~~~~r~v~~l~~~~g--~------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG--L------SQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888888887665322 1 2468999999999999999999999988765
No 105
>cd00131 PAX Paired Box domain
Probab=51.55 E-value=58 Score=25.23 Aligned_cols=48 Identities=15% Similarity=0.127 Sum_probs=34.1
Q ss_pred CCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCC-------ChHHHhhhhhHH
Q psy10105 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKM-------TLTQVSTWFANA 119 (197)
Q Consensus 69 R~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgL-------s~~QV~nWF~N~ 119 (197)
++..+......+..+. ..||.-+..|-.++-...|+ +.+.|+.||.++
T Consensus 73 pr~~~~~~~~~i~~~v---~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 73 PRVATPEVVKKIEIYK---QENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred CCcCCHHHHHHHHHHH---HHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 3345566666666666 78898888777666345577 999999998764
No 106
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=51.07 E-value=28 Score=28.12 Aligned_cols=49 Identities=10% Similarity=0.035 Sum_probs=37.9
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++.++.++.-.|. ..-+ -.+||+.+|++...|.+++.-+|+++++..
T Consensus 136 ~L~~~~r~i~~L~~~--~g~s------~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 136 ALPERQRQAVVLRHI--EGLS------NPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred hCCHHHHHHHHHHHH--cCCC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 478888877766542 2222 368999999999999999999999998764
No 107
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=51.02 E-value=30 Score=27.43 Aligned_cols=49 Identities=8% Similarity=0.118 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++.-.|.++. .-.+||..+|++..-|.+....+|.++++..
T Consensus 117 ~Lp~~~r~i~~l~~~e~~--------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 117 KLPYKLRQVIILRYLHDY--------SQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred hCCHHHHHHHHHHHHccC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 378888887776553322 2368999999999999999999999998764
No 108
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=50.84 E-value=52 Score=25.01 Aligned_cols=46 Identities=24% Similarity=0.176 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhh
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~ 125 (197)
.+++...++|+-+- ++ | ...++|+.++++...|.++..+.+++..-
T Consensus 149 ~lt~~e~~vl~l~~-~g----~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~ 194 (211)
T PRK15369 149 LLTPRERQILKLIT-EG----Y----TNRDIAEQLSISIKTVETHRLNMMRKLDV 194 (211)
T ss_pred CCCHHHHHHHHHHH-CC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 48888899998753 22 2 24789999999999999999999999763
No 109
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=49.73 E-value=32 Score=27.52 Aligned_cols=49 Identities=12% Similarity=0.079 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.+|.-.+. ..- .-.+||..+|+|...|.+-+..+|+++++..
T Consensus 131 ~L~~~~r~vl~l~~~--~~~------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 131 KLSPAHREIIDLVYY--HEK------SVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred hCCHHHHHHHHHHHH--cCC------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 488888888866553 222 2468999999999999999999999998765
No 110
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=49.23 E-value=30 Score=28.26 Aligned_cols=49 Identities=16% Similarity=0.015 Sum_probs=38.6
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++.--|++.. .-.+||..+|++...|.++...+|+++++..
T Consensus 133 ~Lp~~~r~v~~l~~~~g~--------s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l 181 (196)
T PRK12535 133 ALPPERREALILTQVLGY--------TYEEAAKIADVRVGTIRSRVARARADLIAAT 181 (196)
T ss_pred cCCHHHHHHhhhHHHhCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 378888887765554332 2468999999999999999999999998765
No 111
>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=48.66 E-value=31 Score=28.57 Aligned_cols=48 Identities=15% Similarity=0.126 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
.+++..+.++...|.+ . -.-.+||+.+|++...|..|...++.++++.
T Consensus 178 ~L~~~~r~vl~l~y~~----~----~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~ 225 (227)
T TIGR02980 178 ALPERERRILLLRFFE----D----KTQSEIAERLGISQMHVSRLLRRALKKLREQ 225 (227)
T ss_pred cCCHHHHHHHHHHHhc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4888888888777631 1 2357899999999999999999999998754
No 112
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=48.63 E-value=33 Score=27.33 Aligned_cols=49 Identities=14% Similarity=0.125 Sum_probs=37.9
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++.-.+. ..-. -.+||..+|++...|.+....+|.++++..
T Consensus 122 ~L~~~~r~i~~l~~~--~g~s------~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 122 ELNESNRQVFKYKVF--YNLT------YQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred hCCHHHHHHHHHHHH--cCCC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 378888888876443 2222 368999999999999999999999988754
No 113
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=48.60 E-value=36 Score=26.34 Aligned_cols=47 Identities=11% Similarity=-0.082 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhh
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~ 125 (197)
.+++.++.++.-.|. ..-+ -.+||..+|++...|.++...++++...
T Consensus 113 ~L~~~~r~v~~L~~~--~g~s------~~EIA~~l~is~~tV~~~l~ra~~~~~~ 159 (161)
T PRK12528 113 GLPPLVKRAFLLAQV--DGLG------YGEIATELGISLATVKRYLNKAAMRCYF 159 (161)
T ss_pred HCCHHHHHHHHHHHH--cCCC------HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 378888888766553 2222 3689999999999999999999888653
No 114
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=48.42 E-value=32 Score=28.04 Aligned_cols=49 Identities=12% Similarity=-0.033 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++.-.+++. -+ -.+||..+|++..-|.+....+|+++++..
T Consensus 139 ~Lp~~~r~v~~L~~~eg--~s------~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 139 HLPEQIGRVFMMREFLD--FE------IDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 37788888776655322 22 368999999999999999999999998765
No 115
>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=48.31 E-value=38 Score=28.05 Aligned_cols=48 Identities=15% Similarity=0.185 Sum_probs=38.4
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
.++...+.+|...|.+. ..-.+||+.+|++...|..+...+++++++.
T Consensus 175 ~L~~~~r~il~l~y~~~--------~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE--------LNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred hCCHHHHHHHHHHHhCC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 37888888888776322 1347899999999999999999999998754
No 116
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=48.27 E-value=36 Score=26.29 Aligned_cols=49 Identities=10% Similarity=-0.014 Sum_probs=37.3
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++.-.|.+ .- .-.++|+.+|++...|.....-+|+++++..
T Consensus 109 ~L~~~~r~v~~l~~~~--~~------s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 109 ELPARTRYAFEMYRLH--GE------TQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred hCCHHHHHHHHHHHHc--CC------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3778888887655422 11 2468999999999999999999999888654
No 117
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=47.86 E-value=30 Score=29.32 Aligned_cols=48 Identities=13% Similarity=0.151 Sum_probs=38.0
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
+++..+.++.-.|.+. -.-.+||..+|+|...|.+++..+|+++|...
T Consensus 202 L~~~~r~vl~l~~~~~--------~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 249 (251)
T PRK07670 202 LSEKEQLVISLFYKEE--------LTLTEIGQVLNLSTSRISQIHSKALFKLKKLL 249 (251)
T ss_pred CCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 7888888887666321 22478999999999999999999999988643
No 118
>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=47.59 E-value=12 Score=23.59 Aligned_cols=22 Identities=14% Similarity=0.009 Sum_probs=19.2
Q ss_pred HHHHHHHhCCChHHHhhhhhHH
Q psy10105 98 KIMLAIITKMTLTQVSTWFANA 119 (197)
Q Consensus 98 k~~LA~~tgLs~~QV~nWF~N~ 119 (197)
-.+||..+|++...|+.|..++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~ 39 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGK 39 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 4689999999999999998665
No 119
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=47.34 E-value=34 Score=27.15 Aligned_cols=47 Identities=17% Similarity=0.151 Sum_probs=36.4
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
+++..+.++...|.+. -.-.+||..+|++...|.+-...+|++++..
T Consensus 138 L~~~~r~i~~l~~~~g--------~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 138 LEPPRSELIRTAFFEG--------ITYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred CCHHHHHHHHHHHHcC--------CCHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 7777777776665322 2236899999999999999999999998864
No 120
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=47.10 E-value=30 Score=27.52 Aligned_cols=49 Identities=16% Similarity=0.106 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++.++.++.-.|. ...+ -.++|..+|++...|.++..-+|.+++...
T Consensus 127 ~L~~~~r~v~~l~~~--~g~s------~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 127 SLPIKYREVIYLFYY--EELS------IKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred hCCHHHhhHhHhHHh--cCCC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 488888888766543 2223 368999999999999999999999988654
No 121
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=46.93 E-value=38 Score=21.28 Aligned_cols=40 Identities=20% Similarity=0.096 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhh
Q psy10105 70 KNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFA 117 (197)
Q Consensus 70 ~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~ 117 (197)
+.|+.+.+..+..++ ... .-..+||+.+|.+.+-|.++..
T Consensus 3 ~~Lt~~eR~~I~~l~---~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALL---EQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHH---CS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHH---HcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 457888888888887 322 3456799999999999999864
No 122
>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=46.57 E-value=35 Score=29.24 Aligned_cols=49 Identities=18% Similarity=0.272 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++.-.+.+... -.+||..+|++..-|.++...+|+++++..
T Consensus 161 ~Lp~~~R~v~~L~~~eg~S--------~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 161 ALSERERHLLRLHFVDGLS--------MDRIGAMYQVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred hCCHHHHHHHHHHHHcCCC--------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3777777777666542222 368999999999999999999999988764
No 123
>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=46.17 E-value=26 Score=26.65 Aligned_cols=31 Identities=26% Similarity=0.251 Sum_probs=26.9
Q ss_pred HHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 96 GEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 96 ~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
-.-.+||..+|++...|.++..-+|.++++.
T Consensus 122 ~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 122 FSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred CcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3457899999999999999999999998753
No 124
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=45.83 E-value=36 Score=27.10 Aligned_cols=49 Identities=12% Similarity=-0.053 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++.-.|.+. -.-.+||+.+|++...|.++...+|+++++..
T Consensus 131 ~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEG--------LSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC--------CcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 48888888887655322 23468999999999999999999999988654
No 125
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=45.78 E-value=37 Score=27.35 Aligned_cols=49 Identities=16% Similarity=0.108 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++.++.++.-.|.+ .-+ -.+||..+|++..-|.++..-+|.++++..
T Consensus 111 ~Lp~~~R~v~~L~~~e--g~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 111 DLPEEQRAALHLVAIE--GLS------YQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred hCCHHHHHHHHHHHHc--CCC------HHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 4888888888776632 222 368999999999999999999999988765
No 126
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=45.71 E-value=30 Score=29.27 Aligned_cols=48 Identities=10% Similarity=0.122 Sum_probs=36.5
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
++..++.++.-.|+ ..-+ -.+||..+|++...|.+....+|+++|+..
T Consensus 172 Lp~~~R~v~~L~~~--eg~s------~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 172 LPEQQRIAVILSYH--ENMS------NGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred CCHHHHHHhhhHHh--cCCC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 67777776654442 2222 368999999999999999999999998765
No 127
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=45.42 E-value=47 Score=26.42 Aligned_cols=49 Identities=8% Similarity=-0.054 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.++++++.++.-.+.+. .. -.+||..+|++..-|.+....++.+....+
T Consensus 127 ~Lp~~~R~v~~L~~~~g--~s------~~EIA~~lgis~~tVk~~l~rAl~~~~~~~ 175 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG--MK------QKDIAQALDIALPTVKKYIHQAYVTCLSLM 175 (178)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 48888888887765322 22 368999999999999999999998877553
No 128
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=45.37 E-value=54 Score=26.36 Aligned_cols=48 Identities=10% Similarity=0.043 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.+|.. +.+ . -.-.+||..+|++...|.+-+..+|+++++..
T Consensus 155 ~L~~~~r~vl~l-~~e--~------~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 155 LLSELEKEVLEL-YLD--G------KSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred hCCHHHHHHHHH-HHc--c------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 477777787766 432 2 22368999999999999999999998888653
No 129
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=45.18 E-value=40 Score=27.77 Aligned_cols=50 Identities=14% Similarity=0.036 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhccc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~ 128 (197)
.++...+.++.-.|. ...+ -.+||+.+|++..-|.++..-+|+++++..+
T Consensus 138 ~L~~~~r~v~~L~~~--~g~s------~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~ 187 (203)
T PRK09647 138 SLPPEFRAAVVLCDI--EGLS------YEEIAATLGVKLGTVRSRIHRGRQQLRAALA 187 (203)
T ss_pred hCCHHHHHHHHHHHH--cCCC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 377777776544432 2233 3689999999999999999999999997753
No 130
>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=44.73 E-value=23 Score=20.95 Aligned_cols=22 Identities=14% Similarity=-0.035 Sum_probs=19.1
Q ss_pred HHHHHHHhCCChHHHhhhhhHH
Q psy10105 98 KIMLAIITKMTLTQVSTWFANA 119 (197)
Q Consensus 98 k~~LA~~tgLs~~QV~nWF~N~ 119 (197)
...+|+.+|++...|+.|..+.
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCC
Confidence 3589999999999999997765
No 131
>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=44.37 E-value=44 Score=20.97 Aligned_cols=41 Identities=12% Similarity=0.117 Sum_probs=26.6
Q ss_pred CCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhh
Q psy10105 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWF 116 (197)
Q Consensus 68 rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF 116 (197)
|++.++++..+.+...+ .. . ....+||+.+|++...|-.++
T Consensus 2 Rp~~~~~~~~~~i~~l~---~~-G----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 2 RPPKLSKEQIEEIKELY---AE-G----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSSSSHCCHHHHHHHH---HT-T------HHHHHHHTTS-HHHHHHHH
T ss_pred cCCCCCHHHHHHHHHHH---HC-C----CCHHHHHHHHCcCHHHHHHHH
Confidence 44556776555555554 22 2 347889999999999998775
No 132
>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=44.35 E-value=44 Score=25.75 Aligned_cols=47 Identities=15% Similarity=0.020 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhh
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~ 125 (197)
.+++..+.+|.-.|. .. -.-.+||+.+|++...|.+...-+|+++|+
T Consensus 122 ~L~~~~r~vl~l~~~--~g------~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 122 ILTPKQQHVIALRFG--QN------LPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred hCCHHHHHHHHHHHh--cC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 377788888776543 12 223689999999999999999888888775
No 133
>PRK10072 putative transcriptional regulator; Provisional
Probab=44.27 E-value=15 Score=27.54 Aligned_cols=40 Identities=10% Similarity=0.061 Sum_probs=28.1
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHH
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANAR 120 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R 120 (197)
..+..-.+.|+.+. .- ...+||+.+|++...|++|...+|
T Consensus 32 ~~~~~eik~LR~~~---gl-------TQ~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 32 TTSFTEFEQLRKGT---GL-------KIDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred cCChHHHHHHHHHc---CC-------CHHHHHHHhCCCHHHHHHHHcCCC
Confidence 33444455666654 11 257899999999999999987665
No 134
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=44.23 E-value=46 Score=25.63 Aligned_cols=48 Identities=10% Similarity=-0.008 Sum_probs=38.7
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
+++..+.++.-.+.+.. + -.+||..+|++..-|.+....+|.++++..
T Consensus 106 L~~~~r~v~~l~~~~~~--s------~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 106 LPPACRDSFLLRKLEGL--S------HQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred CCHHHHHHHHHHHHcCC--C------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 88888888877664222 2 368999999999999999999999988765
No 135
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=43.87 E-value=42 Score=26.31 Aligned_cols=49 Identities=8% Similarity=0.129 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.++...+.++.-.|. ..-+ -.++|..+|++...|.+....+|+++++..
T Consensus 119 ~L~~~~r~i~~l~~~--~~~s------~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 167 (173)
T PRK12522 119 LLNEKYKTVLVLYYY--EQYS------YKEMSEILNIPIGTVKYRLNYAKKQMREHL 167 (173)
T ss_pred hCCHHHHHHHHHHHH--cCCC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 367777776655442 2222 368999999999999999999999998764
No 136
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=43.74 E-value=29 Score=27.17 Aligned_cols=30 Identities=27% Similarity=0.276 Sum_probs=27.3
Q ss_pred HHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 98 KIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 98 k~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
-.+||+.+|++...|.+.+..+|+++++..
T Consensus 139 ~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 139 QKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999999999999998765
No 137
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=43.37 E-value=29 Score=27.80 Aligned_cols=48 Identities=15% Similarity=0.028 Sum_probs=35.4
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
+++..+.++.-.|. . . -.-.+||..+|++...|.++...+|++++...
T Consensus 140 L~~~~r~i~~l~~~--~--g----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 140 LPDEQREVFLLREH--G--D----LELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred CCHhHhhheeeehc--c--C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 56666666654331 1 1 22468999999999999999999999998765
No 138
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=43.18 E-value=41 Score=28.84 Aligned_cols=49 Identities=12% Similarity=0.091 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.+|...|.+. ..-.+||..+|++...|......++++++...
T Consensus 212 ~L~~~~r~vl~l~~~~~--------~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 260 (268)
T PRK06288 212 TLPEREKKVLILYYYED--------LTLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260 (268)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 38888888887776322 23578999999999999999999999988764
No 139
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=43.02 E-value=23 Score=23.61 Aligned_cols=17 Identities=6% Similarity=0.090 Sum_probs=16.0
Q ss_pred HHHHHHhCCChHHHhhh
Q psy10105 99 IMLAIITKMTLTQVSTW 115 (197)
Q Consensus 99 ~~LA~~tgLs~~QV~nW 115 (197)
.++|+.+|++...|..|
T Consensus 4 ~eva~~~gvs~~tlr~y 20 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYY 20 (69)
T ss_dssp HHHHHHTTTTHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHH
Confidence 57999999999999999
No 140
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=42.86 E-value=44 Score=26.81 Aligned_cols=49 Identities=12% Similarity=0.043 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++.-.+. ..- .-.+||..+|++...|.+.+..+|+++++..
T Consensus 106 ~L~~~~r~i~~l~~~--~g~------~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 106 ALPEKYAEALRLTEL--EGL------SQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred hCCHHHHHHHHHHHh--cCC------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 378888887765542 222 2468999999999999999999999988765
No 141
>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=42.29 E-value=31 Score=27.48 Aligned_cols=30 Identities=13% Similarity=0.142 Sum_probs=26.2
Q ss_pred HHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 97 EKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 97 ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
.-.+||..+|++...|.+.+.-+|+++++.
T Consensus 167 s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~ 196 (198)
T TIGR02859 167 SYQEIACDLNRHVKSIDNALQRVKRKLEKY 196 (198)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 346899999999999999999999988754
No 142
>PRK06930 positive control sigma-like factor; Validated
Probab=41.89 E-value=48 Score=27.03 Aligned_cols=49 Identities=8% Similarity=0.022 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++.-.|. .... -.++|..+|++...|.++...++.+++...
T Consensus 114 ~L~~rer~V~~L~~~--eg~s------~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l 162 (170)
T PRK06930 114 VLTEREKEVYLMHRG--YGLS------YSEIADYLNIKKSTVQSMIERAEKKIARQI 162 (170)
T ss_pred hCCHHHHHHHHHHHH--cCCC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 378888887776442 2222 368999999999999999999999988764
No 143
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=41.34 E-value=31 Score=27.14 Aligned_cols=48 Identities=13% Similarity=0.075 Sum_probs=36.0
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
++...+.+|.--+. .. ..-.++|..+|+|...|.+....+|+++++..
T Consensus 137 L~~~~r~il~l~~~--~~------~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T PRK09641 137 LPEKYRTVIVLKYI--ED------LSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred CCHHHHHHhhhHHh--hC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 66667776644331 22 23478999999999999999999999988764
No 144
>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=40.92 E-value=26 Score=23.74 Aligned_cols=18 Identities=17% Similarity=0.176 Sum_probs=16.4
Q ss_pred HHHHHHHhCCChHHHhhh
Q psy10105 98 KIMLAIITKMTLTQVSTW 115 (197)
Q Consensus 98 k~~LA~~tgLs~~QV~nW 115 (197)
-.+||+.+|++...|.+|
T Consensus 16 ~~eIA~~Lg~~~~TV~~W 33 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSW 33 (58)
T ss_pred HHHHHHHHCCChHHHHHH
Confidence 367999999999999999
No 145
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=40.89 E-value=48 Score=28.28 Aligned_cols=50 Identities=18% Similarity=0.122 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhccc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~ 128 (197)
.++..++.++.-.+.+ . | .-.+||+.+|++..-|.++..-+|++++....
T Consensus 116 ~Lp~~~R~v~lL~~~e--g--~----S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~ 165 (228)
T PRK06704 116 SLNVQQSAILLLKDVF--Q--Y----SIADIAKVCSVSEGAVKASLFRSRNRLKTVSE 165 (228)
T ss_pred hCCHHHhhHhhhHHhh--C--C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3677777766554422 1 1 23689999999999999999999999997754
No 146
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=40.76 E-value=46 Score=28.47 Aligned_cols=49 Identities=14% Similarity=-0.008 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.++...+.+|...|.+ .-.-.+||..+|++...|..+..-++.+++...
T Consensus 203 ~L~~~~r~vl~l~y~~--------~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 203 QLEERTREVLEFVFLH--------DLTQKEAAERLGISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred cCCHHHHHHHHHHHHC--------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3777788887776632 123578999999999999999999999998765
No 147
>PHA01976 helix-turn-helix protein
Probab=39.96 E-value=20 Score=23.80 Aligned_cols=22 Identities=9% Similarity=-0.008 Sum_probs=18.8
Q ss_pred HHHHHHHhCCChHHHhhhhhHH
Q psy10105 98 KIMLAIITKMTLTQVSTWFANA 119 (197)
Q Consensus 98 k~~LA~~tgLs~~QV~nWF~N~ 119 (197)
..+||+.+|++...|++|....
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~ 39 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADK 39 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCC
Confidence 4679999999999999997554
No 148
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=39.61 E-value=22 Score=20.91 Aligned_cols=22 Identities=14% Similarity=-0.055 Sum_probs=18.5
Q ss_pred HHHHHHHhCCChHHHhhhhhHH
Q psy10105 98 KIMLAIITKMTLTQVSTWFANA 119 (197)
Q Consensus 98 k~~LA~~tgLs~~QV~nWF~N~ 119 (197)
...||+.+|++...|+.|..+.
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 4589999999999999996544
No 149
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=39.32 E-value=59 Score=26.22 Aligned_cols=49 Identities=20% Similarity=0.076 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++.-.|.++. .-.++|..+|++..-|.++..-+|++++...
T Consensus 128 ~Lp~~~r~v~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 128 KLDPEYREPLLLQVIGGF--------SGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred hCCHHHHHHHHHHHHhCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888776654332 2368999999999999999999999988765
No 150
>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=39.16 E-value=53 Score=28.54 Aligned_cols=50 Identities=14% Similarity=-0.032 Sum_probs=38.6
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhccc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~ 128 (197)
.+++.++.++.-.+. ..-+ -.+||+.+|++...|.+.+.-+|+++++..+
T Consensus 142 ~Lp~~~R~v~~L~~~--~g~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 142 YLPPRQRAVLLLRDV--LGWR------AAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred hCCHHHhhHhhhHHH--hCCC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 377788777765543 2223 3689999999999999999999999988754
No 151
>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=38.65 E-value=37 Score=27.18 Aligned_cols=48 Identities=17% Similarity=0.052 Sum_probs=35.7
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
+++..+.++.-.+.+. -.-.+||+.+|++...|.++..-+|+++++..
T Consensus 132 Lp~~~r~i~~L~~~~g--------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 132 LPEEFRQAVYLADVEG--------FAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred CCHHHhhheeehhhcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 6666666654433211 22468999999999999999999999998765
No 152
>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=38.16 E-value=33 Score=21.09 Aligned_cols=18 Identities=17% Similarity=0.080 Sum_probs=16.2
Q ss_pred HHHHHHhCCChHHHhhhh
Q psy10105 99 IMLAIITKMTLTQVSTWF 116 (197)
Q Consensus 99 ~~LA~~tgLs~~QV~nWF 116 (197)
.++|+.+|++...|..|.
T Consensus 4 ~e~a~~~gv~~~tlr~~~ 21 (49)
T cd04761 4 GELAKLTGVSPSTLRYYE 21 (49)
T ss_pred HHHHHHHCcCHHHHHHHH
Confidence 578999999999999994
No 153
>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=37.80 E-value=22 Score=24.21 Aligned_cols=23 Identities=17% Similarity=0.069 Sum_probs=19.7
Q ss_pred HHHHHHHhCCChHHHhhhhhHHH
Q psy10105 98 KIMLAIITKMTLTQVSTWFANAR 120 (197)
Q Consensus 98 k~~LA~~tgLs~~QV~nWF~N~R 120 (197)
...||+.+|++...|+.|..+.+
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46899999999999999987653
No 154
>PF13551 HTH_29: Winged helix-turn helix
Probab=37.52 E-value=1.5e+02 Score=21.11 Aligned_cols=46 Identities=17% Similarity=0.062 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHHHHHhhCCC--CCCHHHHHH-H-HHHh--CCChHHHhhhhh
Q psy10105 72 ATRESTATLKAWLNEHKKNP--YPTKGEKIM-L-AIIT--KMTLTQVSTWFA 117 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nP--YPs~~ek~~-L-A~~t--gLs~~QV~nWF~ 117 (197)
++++....|.+++.++.... ..+..+-.. | .+.+ .++...|..|+.
T Consensus 58 l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 58 LSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 89999999999995443222 234444443 4 3333 477788888864
No 155
>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=37.34 E-value=67 Score=26.66 Aligned_cols=48 Identities=13% Similarity=0.113 Sum_probs=37.7
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
.+++..+.++...|. . ...-.+||..+|+|...|..+-..+..|++..
T Consensus 183 ~L~~~e~~i~~~~~~---~-----~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~ 230 (231)
T TIGR02885 183 KLDERERQIIMLRYF---K-----DKTQTEVANMLGISQVQVSRLEKKVLKKMKEK 230 (231)
T ss_pred cCCHHHHHHHHHHHH---c-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence 478888888876652 1 13467899999999999999999998888753
No 156
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=37.19 E-value=47 Score=26.17 Aligned_cols=47 Identities=9% Similarity=-0.008 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhh
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~ 125 (197)
.+++..+.++.-.+.+. - .-.+||+.+|++...|.++...++.+.+.
T Consensus 119 ~L~~~~r~i~~l~~~~g--~------s~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 119 GLNGKTREAFLLSQLDG--L------TYSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred hCCHHHhHHhhhhhccC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 37777777766544322 2 24689999999999999999888887664
No 157
>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=37.03 E-value=51 Score=27.46 Aligned_cols=52 Identities=15% Similarity=0.024 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
.+++..+.++.-.|+......+ .-.+||+.+|++...|..+...+++++++.
T Consensus 174 ~L~~~~r~il~l~y~~~~~e~~----S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~ 225 (227)
T TIGR02846 174 VLDGREREVIEMRYGLGDGRRK----TQREIAKILGISRSYVSRIEKRALMKLYKE 225 (227)
T ss_pred hCCHHHHHHHHHHHcCCCCCCc----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4888888888877621001221 346899999999999999988889888764
No 158
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=36.66 E-value=41 Score=27.98 Aligned_cols=53 Identities=13% Similarity=0.100 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++.-.|.-+.... -.-.+||..+|++...|.++...+|+++|+..
T Consensus 178 ~Lp~~~R~v~~L~y~l~~~eg----~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l 230 (234)
T PRK08301 178 KLSDREKQIMELRFGLNGGEE----KTQKEVADMLGISQSYISRLEKRIIKRLKKEI 230 (234)
T ss_pred hCCHHHHHHHHHHhccCCCCC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 377888887765541000111 23478999999999999999999999998764
No 159
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=36.65 E-value=63 Score=27.89 Aligned_cols=48 Identities=17% Similarity=0.155 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
.++...+.+|...|.+ . ..-.+||..+|++...|..+...++.+++..
T Consensus 215 ~L~~rer~vl~l~y~~----~----~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 262 (264)
T PRK07122 215 ALPERERTVLVLRFFE----S----MTQTQIAERVGISQMHVSRLLAKTLARLRDQ 262 (264)
T ss_pred cCCHHHHHHHHHHhcC----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4777788888776632 2 2347899999999999999999999998764
No 160
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=35.64 E-value=39 Score=26.98 Aligned_cols=48 Identities=13% Similarity=0.066 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
++...+.++.-.+. ..| .-.++|..+|++...|.+...-+|++++...
T Consensus 139 L~~~~r~v~~l~~~----~g~----s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 139 LPEDLRTALTLREF----DGL----SYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred CCHHHhHHHhhHHh----cCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 56666655544331 122 2368999999999999999999999998765
No 161
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=35.40 E-value=74 Score=24.86 Aligned_cols=48 Identities=8% Similarity=0.049 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
.+++..+.++.-.|.+. -+ -.++|..+|++..-|.++..+++...+..
T Consensus 118 ~L~~~~r~v~~L~~~eg--~s------~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 165 (168)
T PRK12525 118 GLSGKARAAFLMSQLEG--LT------YVEIGERLGVSLSRIHQYMVEAFKCCYQG 165 (168)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 47888888776655322 22 36899999999999999998888877643
No 162
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=34.97 E-value=65 Score=27.40 Aligned_cols=49 Identities=14% Similarity=0.071 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++...|++ . ..-.+||+.+|+|...|...-.++..++++.+
T Consensus 209 ~L~~~er~vi~~~~~~----~----~t~~eIA~~lgis~~~V~~~~~~al~kLr~~l 257 (258)
T PRK08215 209 KLNDREKLILNLRFFQ----G----KTQMEVAEEIGISQAQVSRLEKAALKHMRKYI 257 (258)
T ss_pred cCCHHHHHHHHHHHhc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 4888888888777632 1 23578999999999999999999999988653
No 163
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=34.90 E-value=92 Score=25.86 Aligned_cols=52 Identities=19% Similarity=0.169 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhh
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRL 123 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~ 123 (197)
.||+.++++|+.-|. .-.--||-...-.+||+++|++..-+..=..++-+++
T Consensus 155 ~LTdrQ~~vL~~A~~-~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl 206 (215)
T COG3413 155 DLTDRQLEVLRLAYK-MGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKL 206 (215)
T ss_pred cCCHHHHHHHHHHHH-cCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 599999999988872 3345678999999999999999998877555554443
No 164
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=33.78 E-value=51 Score=25.76 Aligned_cols=48 Identities=15% Similarity=-0.008 Sum_probs=34.3
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
+++..+.++.--+. .. -.-.+||..+|++..-|.++...+|.++++..
T Consensus 127 L~~~~r~v~~l~~~--~g------~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~l 174 (176)
T PRK09638 127 LDPEFRAPVILKHY--YG------YTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEW 174 (176)
T ss_pred CCHHHhheeeehhh--cC------CCHHHHHHHHCCChhHHHHHHHHHHHHHHHHh
Confidence 56666665543221 11 23478999999999999999999999988643
No 165
>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=33.49 E-value=46 Score=19.85 Aligned_cols=20 Identities=10% Similarity=0.223 Sum_probs=17.8
Q ss_pred HHHHHHhCCChHHHhhhhhH
Q psy10105 99 IMLAIITKMTLTQVSTWFAN 118 (197)
Q Consensus 99 ~~LA~~tgLs~~QV~nWF~N 118 (197)
.++|+.+|++...|..|..+
T Consensus 4 ~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 4 KEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHc
Confidence 57899999999999999765
No 166
>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=33.46 E-value=97 Score=24.68 Aligned_cols=47 Identities=19% Similarity=0.052 Sum_probs=37.7
Q ss_pred CCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhh
Q psy10105 70 KNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125 (197)
Q Consensus 70 ~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~ 125 (197)
..+++.++.+|.-.. ..+ .-.+||+.+|+|...|.++-..++.+++.
T Consensus 5 ~~Lte~qr~VL~Lr~-----~Gl----Tq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 5 TFLTERQIKVLELRE-----KGL----SQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred CCCCHHHHHHHHHHH-----cCC----CHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 358888999987632 222 45789999999999999999999999885
No 167
>PF13551 HTH_29: Winged helix-turn helix
Probab=32.73 E-value=54 Score=23.46 Aligned_cols=27 Identities=15% Similarity=0.119 Sum_probs=23.3
Q ss_pred HHHHHHHHhCCChHHHhhhhhHHHHhh
Q psy10105 97 EKIMLAIITKMTLTQVSTWFANARRRL 123 (197)
Q Consensus 97 ek~~LA~~tgLs~~QV~nWF~N~R~R~ 123 (197)
...++|+.+|++...|.+|....+..-
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 467899999999999999998877554
No 168
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=32.48 E-value=49 Score=24.69 Aligned_cols=26 Identities=12% Similarity=0.166 Sum_probs=21.2
Q ss_pred HHHHHHHHhCCChHHHhhhhhHHHHh
Q psy10105 97 EKIMLAIITKMTLTQVSTWFANARRR 122 (197)
Q Consensus 97 ek~~LA~~tgLs~~QV~nWF~N~R~R 122 (197)
.-..+|+..|++.+||+.|..+.+.+
T Consensus 25 gq~~vA~~~Gv~eStISR~k~~~~~~ 50 (91)
T PF05269_consen 25 GQKKVAEAMGVDESTISRWKNDFIEK 50 (91)
T ss_dssp HHHHHHHHHTSSTTTHHHHHHHHHHH
T ss_pred hhHHHHHHhCCCHHHHHHHHhhHHHH
Confidence 44678999999999999997765544
No 169
>PRK05572 sporulation sigma factor SigF; Validated
Probab=32.34 E-value=74 Score=26.93 Aligned_cols=49 Identities=10% Similarity=0.009 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++...|.+ ...-.+||..+|+|...|..+-..+..+++...
T Consensus 202 ~L~~~~~~v~~l~~~~--------~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l 250 (252)
T PRK05572 202 ELDERERLIVYLRYFK--------DKTQSEVAKRLGISQVQVSRLEKKILKQMKEKL 250 (252)
T ss_pred cCCHHHHHHHHHHHhC--------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 4888888888776631 134578999999999999999999999988654
No 170
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=32.17 E-value=29 Score=22.81 Aligned_cols=23 Identities=17% Similarity=0.046 Sum_probs=19.1
Q ss_pred HHHHHHHhCCChHHHhhhhhHHH
Q psy10105 98 KIMLAIITKMTLTQVSTWFANAR 120 (197)
Q Consensus 98 k~~LA~~tgLs~~QV~nWF~N~R 120 (197)
...+|+.+|++..+|+.|-.+.+
T Consensus 15 ~~~~a~~~~i~~~~i~~~e~g~~ 37 (64)
T PF12844_consen 15 QKDLAEKLGISRSTISKIENGKR 37 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHHCcCHHHHHHHHCCCc
Confidence 56799999999999999988754
No 171
>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=32.14 E-value=42 Score=22.20 Aligned_cols=19 Identities=16% Similarity=0.239 Sum_probs=17.1
Q ss_pred HHHHHHhCCChHHHhhhhh
Q psy10105 99 IMLAIITKMTLTQVSTWFA 117 (197)
Q Consensus 99 ~~LA~~tgLs~~QV~nWF~ 117 (197)
.++|+.+|++...|..|-.
T Consensus 4 ~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 4 GAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999964
No 172
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=32.03 E-value=64 Score=28.36 Aligned_cols=48 Identities=15% Similarity=0.050 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
.++...+.++.-.|.+.. + -.+||..+|++..-|.+....+|+++++.
T Consensus 153 ~Lp~~~R~v~~L~~~~g~--s------~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 200 (339)
T PRK08241 153 HLPPRQRAVLILRDVLGW--S------AAEVAELLDTSVAAVNSALQRARATLAER 200 (339)
T ss_pred hCCHHHhhhhhhHHhhCC--C------HHHHHHHhCCCHHHHHHHHHHHHHHHhhc
Confidence 377777777765543222 2 36899999999999999999999999874
No 173
>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=31.85 E-value=52 Score=27.56 Aligned_cols=53 Identities=13% Similarity=0.072 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++.-.|+...... -.-.+||+.+|++...|.++..-+|+++|+..
T Consensus 178 ~Lp~~~R~ii~L~~~l~~~eg----~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l 230 (234)
T TIGR02835 178 KLNDREKKIMELRFGLVGGTE----KTQKEVADMLGISQSYISRLEKRILKRLKKEI 230 (234)
T ss_pred hCCHHHHHHHHHHHccCCCCC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 378888887765541000011 23467999999999999999999999998764
No 174
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=31.82 E-value=56 Score=26.43 Aligned_cols=31 Identities=19% Similarity=0.115 Sum_probs=26.3
Q ss_pred HHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 97 EKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 97 ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.-.+||+.+|+|+..|...+..+|.+.+.+.
T Consensus 153 s~~EIA~~lgiS~~tV~r~l~~aR~~l~~~l 183 (185)
T PF07638_consen 153 SVEEIAERLGISERTVRRRLRRARAWLRREL 183 (185)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3467899999999999999999998877654
No 175
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=31.35 E-value=48 Score=22.67 Aligned_cols=18 Identities=28% Similarity=0.368 Sum_probs=15.7
Q ss_pred HHHHHHHhCCChHHHhhh
Q psy10105 98 KIMLAIITKMTLTQVSTW 115 (197)
Q Consensus 98 k~~LA~~tgLs~~QV~nW 115 (197)
...||+.+|++..-|+.|
T Consensus 12 ~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 12 QSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHh
Confidence 458999999999999999
No 176
>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=30.99 E-value=1.2e+02 Score=25.34 Aligned_cols=53 Identities=11% Similarity=0.005 Sum_probs=40.0
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.+|...| .-.-+ ....-.+||..+|+|...|+.....+.+++|...
T Consensus 176 ~L~~~er~vl~l~y---gl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~ 228 (238)
T TIGR02393 176 TLTERERKVLRMRY---GLLDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRHPS 228 (238)
T ss_pred hCCHHHHHHHHHHh---CCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhH
Confidence 47888888887766 21111 2234678999999999999999999999998653
No 177
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=30.75 E-value=64 Score=25.75 Aligned_cols=44 Identities=14% Similarity=0.170 Sum_probs=30.7
Q ss_pred HHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhh
Q psy10105 78 ATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125 (197)
Q Consensus 78 ~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~ 125 (197)
...++++ ..||-+. +.-.+++.+||++..+|..|..--|=-...
T Consensus 33 ~kV~~yL---r~~p~~~-ati~eV~e~tgVs~~~I~~~IreGRL~~~~ 76 (137)
T TIGR03826 33 EKVYKFL---RKHENRQ-ATVSEIVEETGVSEKLILKFIREGRLQLKH 76 (137)
T ss_pred HHHHHHH---HHCCCCC-CCHHHHHHHHCcCHHHHHHHHHcCCeeccC
Confidence 4556676 4555322 456789999999999999997665544443
No 178
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=30.32 E-value=88 Score=27.07 Aligned_cols=48 Identities=10% Similarity=-0.035 Sum_probs=36.5
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
+++.++.++.-.+. ...+ -.+||+.+|+|..-|.+.+..+|++++...
T Consensus 116 L~~~~R~v~~L~~~--~g~s------~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~ 163 (293)
T PRK09636 116 LSPLERAAFLLHDV--FGVP------FDEIASTLGRSPAACRQLASRARKHVRAAR 163 (293)
T ss_pred CCHHHHHHHHHHHH--hCCC------HHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 77777776644432 2223 368999999999999999999999998764
No 179
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=30.21 E-value=64 Score=25.76 Aligned_cols=30 Identities=20% Similarity=0.204 Sum_probs=26.8
Q ss_pred HHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 98 KIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 98 k~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
-.+||..+|++...|.++...+|.+++...
T Consensus 153 ~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 153 FQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 378999999999999999999999988754
No 180
>PRK10651 transcriptional regulator NarL; Provisional
Probab=30.17 E-value=90 Score=24.05 Aligned_cols=47 Identities=17% Similarity=0.162 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
.|++...++|+-+. .+ + .-.++|+.++++...|.+...+.|+|..-.
T Consensus 155 ~Lt~rE~~vl~~l~----~g-~----~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~ 201 (216)
T PRK10651 155 QLTPRERDILKLIA----QG-L----PNKMIARRLDITESTVKVHVKHMLKKMKLK 201 (216)
T ss_pred cCCHHHHHHHHHHH----cC-C----CHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 38888999997654 11 2 246788999999999999999999997643
No 181
>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=29.75 E-value=1.2e+02 Score=26.18 Aligned_cols=51 Identities=16% Similarity=0.064 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.+|...|.+ ..+ ..-.+||..+|+|...|+.....+..++|...
T Consensus 218 ~L~~rer~vl~l~y~~--~~~----~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l 268 (270)
T TIGR02392 218 SLDARSRRIIEARWLD--DDK----LTLQELAAEYGVSAERIRQIEKNAMKKLKAAL 268 (270)
T ss_pred cCCHHHHHHHHHHhcC--CCC----cCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 4888888888877621 112 23469999999999999999999999988653
No 182
>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=28.98 E-value=52 Score=20.24 Aligned_cols=17 Identities=6% Similarity=0.010 Sum_probs=14.6
Q ss_pred HHHHHHhCCChHHHhhh
Q psy10105 99 IMLAIITKMTLTQVSTW 115 (197)
Q Consensus 99 ~~LA~~tgLs~~QV~nW 115 (197)
.++|+.+|++...|..|
T Consensus 3 ~e~A~~~gvs~~tlR~y 19 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYY 19 (38)
T ss_dssp HHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHCCCHHHHHHH
Confidence 47899999999999999
No 183
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=28.76 E-value=58 Score=22.45 Aligned_cols=24 Identities=8% Similarity=0.101 Sum_probs=18.6
Q ss_pred HHHHHHHHhCCChHHHhhhhhHHH
Q psy10105 97 EKIMLAIITKMTLTQVSTWFANAR 120 (197)
Q Consensus 97 ek~~LA~~tgLs~~QV~nWF~N~R 120 (197)
...++|..+||+..||..|...--
T Consensus 17 ~T~eiA~~~gls~~~aR~yL~~Le 40 (62)
T PF04703_consen 17 KTREIADALGLSIYQARYYLEKLE 40 (62)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHH
Confidence 345899999999999999976543
No 184
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=28.62 E-value=1.6e+02 Score=20.66 Aligned_cols=35 Identities=14% Similarity=0.094 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCC--hHHHh
Q psy10105 76 STATLKAWLNEHKKNPYPTKGEKIMLAIITKMT--LTQVS 113 (197)
Q Consensus 76 ~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs--~~QV~ 113 (197)
++..+++.+ .+||=.+++.-+.+..+-|-. ++||.
T Consensus 18 ar~~~~k~l---~~NPpine~mir~M~~QMG~kpSekqi~ 54 (64)
T PF03672_consen 18 ARKYMEKQL---KENPPINEKMIRAMMMQMGRKPSEKQIK 54 (64)
T ss_pred HHHHHHHHH---HHCCCCCHHHHHHHHHHhCCCccHHHHH
Confidence 456777777 789988999999999999954 44554
No 185
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=28.56 E-value=1e+02 Score=24.73 Aligned_cols=48 Identities=21% Similarity=0.013 Sum_probs=36.1
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
+++..+.+|.-.|.+ . -.-.+||..+|++...|.+=.-.+|+++++..
T Consensus 135 Lp~~~r~i~~l~~~~--g------~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l 182 (192)
T PRK09643 135 LPVEQRAALVAVDMQ--G------YSVADAARMLGVAEGTVKSRCARGRARLAELL 182 (192)
T ss_pred CCHHHHHHHHHHHHc--C------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 777777777654421 1 12367999999999999998888888888765
No 186
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=28.49 E-value=1e+02 Score=18.55 Aligned_cols=26 Identities=19% Similarity=0.135 Sum_probs=19.6
Q ss_pred HHHHHHHHhCCChHHHhhhhhHHHHh
Q psy10105 97 EKIMLAIITKMTLTQVSTWFANARRR 122 (197)
Q Consensus 97 ek~~LA~~tgLs~~QV~nWF~N~R~R 122 (197)
.+.+||..+|++..-|+.=|..-+++
T Consensus 4 tr~diA~~lG~t~ETVSR~l~~l~~~ 29 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRILKKLERQ 29 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CHHHHHHHhCCcHHHHHHHHHHHHHc
Confidence 46789999999999999877665543
No 187
>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=28.34 E-value=89 Score=27.10 Aligned_cols=50 Identities=16% Similarity=0.226 Sum_probs=39.1
Q ss_pred CCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 69 R~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
...+++..+++|. |+. .. ..-.+||+.+|+|+.-|.+...|.++|..-.+
T Consensus 188 ~~~LT~RE~evl~-l~a----~G----~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~n 237 (247)
T TIGR03020 188 AGLITAREAEILA-WVR----DG----KTNEEIAAILGISSLTVKNHLQHIFKKLDVRN 237 (247)
T ss_pred ccCCCHHHHHHHH-HHH----CC----CCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCC
Confidence 3469999999997 552 22 23467899999999999999999999977543
No 188
>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=28.11 E-value=55 Score=21.80 Aligned_cols=19 Identities=5% Similarity=-0.050 Sum_probs=16.8
Q ss_pred HHHHHHhCCChHHHhhhhh
Q psy10105 99 IMLAIITKMTLTQVSTWFA 117 (197)
Q Consensus 99 ~~LA~~tgLs~~QV~nWF~ 117 (197)
.++|+.+|++...|..|-.
T Consensus 4 ~evA~~~gvs~~tlR~~~~ 22 (67)
T cd04764 4 KEVSEIIGVKPHTLRYYEK 22 (67)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999954
No 189
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=27.49 E-value=1.1e+02 Score=26.29 Aligned_cols=49 Identities=12% Similarity=0.080 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.+|...|.+ ...-.+||..+|+|...|..+..-++.++++..
T Consensus 205 ~L~~~er~vi~l~y~e--------~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 253 (257)
T PRK05911 205 ALEEKERKVMALYYYE--------ELVLKEIGKILGVSESRVSQIHSKALLKLRATL 253 (257)
T ss_pred cCCHHHHHHHHHHHhc--------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4777777777776631 123578999999999999999999999988654
No 190
>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=27.48 E-value=1e+02 Score=26.57 Aligned_cols=49 Identities=16% Similarity=0.078 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++.++.++.-.+. ...+ -.+||+.+|+|...|.+.+..+|++++...
T Consensus 108 ~L~~~~R~v~~L~~~--~g~s------~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~ 156 (281)
T TIGR02957 108 RLSPLERAVFVLREV--FDYP------YEEIASIVGKSEANCRQLVSRARRHLDARR 156 (281)
T ss_pred hCCHHHHHHHHHHHH--cCCC------HHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 367777776644332 2222 368999999999999999999999998653
No 191
>PRK09480 slmA division inhibitor protein; Provisional
Probab=27.34 E-value=1.2e+02 Score=23.76 Aligned_cols=43 Identities=14% Similarity=0.085 Sum_probs=32.5
Q ss_pred HHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHH
Q psy10105 77 TATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANAR 120 (197)
Q Consensus 77 ~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R 120 (197)
.++|+.-..--..+++ ....-..||++.|++..-+-.+|.|+-
T Consensus 13 ~~Il~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~ 55 (194)
T PRK09480 13 EQILQALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKA 55 (194)
T ss_pred HHHHHHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHH
Confidence 3445443322245667 888999999999999999999999977
No 192
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=27.27 E-value=2e+02 Score=21.19 Aligned_cols=49 Identities=16% Similarity=0.055 Sum_probs=36.2
Q ss_pred CCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCC-ChHHHhhhhhHHHHhhh
Q psy10105 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKM-TLTQVSTWFANARRRLK 124 (197)
Q Consensus 69 R~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgL-s~~QV~nWF~N~R~R~k 124 (197)
|++|+.+-+..+-+-+ ....+ -...+|++.|+ ...++..|-+..+....
T Consensus 5 ~r~~s~EfK~~iv~~~---~~~g~----sv~~vAr~~gv~~~~~l~~W~~~~~~~~~ 54 (116)
T COG2963 5 RKKYSPEFKLEAVALY---LRGGD----TVSEVAREFGIVSATQLYKWRIQLQKGGG 54 (116)
T ss_pred cccCCHHHHHHHHHHH---HhcCc----cHHHHHHHhCCCChHHHHHHHHHHHHccc
Confidence 7788988876554444 33332 57889999996 99999999887777643
No 193
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=27.14 E-value=1.3e+02 Score=27.01 Aligned_cols=53 Identities=15% Similarity=0.019 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.+|...|.-+.. ..-.-.+||..+|++...|..+...+++++|+..
T Consensus 262 ~L~~~~R~vl~lrygL~~~----e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGY----EAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccCCC----CCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4777788777655411112 2234578999999999999999999999999775
No 194
>PF13730 HTH_36: Helix-turn-helix domain
Probab=27.07 E-value=1.7e+02 Score=18.45 Aligned_cols=47 Identities=11% Similarity=0.059 Sum_probs=29.8
Q ss_pred CCCHHHHHHHHHHHH--HhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHH
Q psy10105 71 NATRESTATLKAWLN--EHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANAR 120 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~--~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R 120 (197)
+++..+..++-.-.. .....-||| ...||+.+|++...|..+...-.
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS---~~~la~~~g~s~~Tv~~~i~~L~ 50 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPS---QETLAKDLGVSRRTVQRAIKELE 50 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcC---HHHHHHHHCcCHHHHHHHHHHHH
Confidence 355555555422221 112237886 66799999999999999876543
No 195
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=27.00 E-value=70 Score=24.58 Aligned_cols=29 Identities=17% Similarity=0.117 Sum_probs=24.2
Q ss_pred CCCHHHHHHHHHHhCCChHHHhhhhhHHH
Q psy10105 92 YPTKGEKIMLAIITKMTLTQVSTWFANAR 120 (197)
Q Consensus 92 YPs~~ek~~LA~~tgLs~~QV~nWF~N~R 120 (197)
-+++..|..||..+|++...|..|-.-+.
T Consensus 26 ~~~~~~r~~La~~~~i~~~~l~~w~~~Ad 54 (122)
T PF14229_consen 26 GDTPLGRKALAKKLGISERNLLKWVNQAD 54 (122)
T ss_pred CCCHHHHHHHHHhcCCCHHHHHHHHhHHH
Confidence 35788999999999999999999954443
No 196
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=26.09 E-value=43 Score=25.78 Aligned_cols=23 Identities=22% Similarity=0.332 Sum_probs=20.3
Q ss_pred HHHHHHHhCCChHHHhhhhhHHH
Q psy10105 98 KIMLAIITKMTLTQVSTWFANAR 120 (197)
Q Consensus 98 k~~LA~~tgLs~~QV~nWF~N~R 120 (197)
...||..+|++...|++|..+.+
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~ 43 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDET 43 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 36899999999999999988864
No 197
>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=25.93 E-value=1.4e+02 Score=25.89 Aligned_cols=53 Identities=11% Similarity=0.021 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.+|.-.|.-+.. ..-.-.+||..+|++...|..+...++.++|+..
T Consensus 222 ~Lp~~~R~Vl~l~ygL~~~----e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l 274 (285)
T TIGR02394 222 ELNERQREVLARRFGLLGY----EPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL 274 (285)
T ss_pred cCCHHHHHHHHHHhCCCCC----CCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3788888888765410001 1133578999999999999999999999998765
No 198
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=25.67 E-value=64 Score=21.30 Aligned_cols=18 Identities=6% Similarity=0.049 Sum_probs=16.3
Q ss_pred HHHHHHhCCChHHHhhhh
Q psy10105 99 IMLAIITKMTLTQVSTWF 116 (197)
Q Consensus 99 ~~LA~~tgLs~~QV~nWF 116 (197)
.++|+.+|++...|..|-
T Consensus 4 ~eva~~~gvs~~tlr~~~ 21 (70)
T smart00422 4 GEVAKLAGVSVRTLRYYE 21 (70)
T ss_pred HHHHHHHCcCHHHHHHHH
Confidence 578999999999999994
No 199
>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=25.65 E-value=66 Score=23.01 Aligned_cols=22 Identities=14% Similarity=-0.058 Sum_probs=18.9
Q ss_pred HHHHHHHHhCCChHHHhhhhhH
Q psy10105 97 EKIMLAIITKMTLTQVSTWFAN 118 (197)
Q Consensus 97 ek~~LA~~tgLs~~QV~nWF~N 118 (197)
.-.+||+.+|+|...|.+|+.+
T Consensus 34 S~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 34 TASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred CHHHHHHHHCcCHHHHHHHHhc
Confidence 3578999999999999999764
No 200
>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=25.24 E-value=2e+02 Score=19.72 Aligned_cols=45 Identities=18% Similarity=0.231 Sum_probs=23.0
Q ss_pred CCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhh
Q psy10105 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFA 117 (197)
Q Consensus 69 R~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~ 117 (197)
|+.|+-.-.-..-+++.++-... ..-+.-|++.|++..+|.-|.+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~----~~~RAaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCK----GNQRAAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTT----T-HHHHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccchh----hhHHHHHHHhCccHHHHHHHHH
Confidence 45566555433334443332211 2346689999999999999954
No 201
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=24.98 E-value=85 Score=26.18 Aligned_cols=53 Identities=13% Similarity=0.022 Sum_probs=37.7
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.++.-.|+-+.. ....-.+||..+|+|...|.++-..+++++++..
T Consensus 175 ~Lp~~~R~i~~l~y~~~~~----e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l 227 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGNG----KEKTQREIAKALGISRSYVSRIEKRALKKLFKEL 227 (233)
T ss_pred hCCHHHHHHHHHHhCCCCC----CCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4888888888765410001 1123568999999999999999888888887653
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=24.91 E-value=78 Score=18.93 Aligned_cols=20 Identities=10% Similarity=-0.150 Sum_probs=17.0
Q ss_pred HHHHHHHhCCChHHHhhhhh
Q psy10105 98 KIMLAIITKMTLTQVSTWFA 117 (197)
Q Consensus 98 k~~LA~~tgLs~~QV~nWF~ 117 (197)
..++|+.+|++...|.+|..
T Consensus 4 ~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 35788899999999999964
No 203
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=24.70 E-value=48 Score=22.66 Aligned_cols=21 Identities=14% Similarity=0.085 Sum_probs=18.7
Q ss_pred HHHHHHhCCChHHHhhhhhHH
Q psy10105 99 IMLAIITKMTLTQVSTWFANA 119 (197)
Q Consensus 99 ~~LA~~tgLs~~QV~nWF~N~ 119 (197)
.+||+.+|++...|+..+.+.
T Consensus 4 ~~iA~~~gvS~~TVSr~ln~~ 24 (70)
T smart00354 4 KDVARLAGVSKATVSRVLNGN 24 (70)
T ss_pred HHHHHHHCCCHHHHHHHHCCC
Confidence 579999999999999998764
No 204
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=24.38 E-value=1.2e+02 Score=24.61 Aligned_cols=61 Identities=16% Similarity=0.189 Sum_probs=39.4
Q ss_pred CCCCccCCCCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHH
Q psy10105 60 GAGYDLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARR 121 (197)
Q Consensus 60 g~~~~~r~rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~ 121 (197)
|++.+.+.+.+.-...-.++|+.-+..-..+.|-. ..-..||+..|++..-|-.-|.|+..
T Consensus 4 ~~~~~~~~~~~~~~~~r~~IL~AA~~lf~e~Gy~~-~s~~dIA~~aGvs~gtiY~hF~sKe~ 64 (212)
T PRK15008 4 GAVKTTGKRSRAVSAKKKAILSAALDTFSQFGFHG-TRLEQIAELAGVSKTNLLYYFPSKEA 64 (212)
T ss_pred ccCCCCCCcchhhHHHHHHHHHHHHHHHHHhCccc-CCHHHHHHHhCcCHHHHHHHCCCHHH
Confidence 34433333333233334556655554447777743 55678999999999999999998875
No 205
>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=24.33 E-value=78 Score=21.17 Aligned_cols=19 Identities=16% Similarity=0.267 Sum_probs=16.8
Q ss_pred HHHHHHhCCChHHHhhhhh
Q psy10105 99 IMLAIITKMTLTQVSTWFA 117 (197)
Q Consensus 99 ~~LA~~tgLs~~QV~nWF~ 117 (197)
.++|+.+|++...|..|..
T Consensus 4 ~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 4 GEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999954
No 206
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=24.12 E-value=75 Score=26.48 Aligned_cols=49 Identities=16% Similarity=0.015 Sum_probs=37.4
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhccc
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~~ 128 (197)
+++..+.++...|. ..-.-.+||..+|++...|.+...-+|.++|+...
T Consensus 150 L~~~~r~i~~l~~~--------~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~ 198 (231)
T PRK11922 150 LPDAFRAVFVLRVV--------EELSVEETAQALGLPEETVKTRLHRARRLLRESLA 198 (231)
T ss_pred CCHHHhhhheeehh--------cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 66667666654432 22345789999999999999999999999998764
No 207
>KOG1146|consensus
Probab=24.07 E-value=1.6e+02 Score=31.86 Aligned_cols=54 Identities=20% Similarity=0.153 Sum_probs=48.0
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
..-.++..+|-.|| ..+--|+.....-|.-....+..++.+||.|-|-|.+++.
T Consensus 711 ~~~~~aa~~l~~a~---~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 711 TILPEAAMILGRAY---MQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred cccHHHHhhhhhcc---cCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 34458888999999 7778899999999999999999999999999999999886
No 208
>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 This entry is represented by Bacteriophage r1t, Orf18. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.
Probab=23.73 E-value=52 Score=27.43 Aligned_cols=32 Identities=25% Similarity=0.305 Sum_probs=27.2
Q ss_pred HHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 96 GEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 96 ~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
..+.+||.-.++|..+|..|.+|=+--.++.+
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~ 46 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAKP 46 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccccc
Confidence 45778999999999999999999887766654
No 209
>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=23.48 E-value=2.1e+02 Score=22.23 Aligned_cols=48 Identities=10% Similarity=-0.042 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
.+++..+.++...|. .. ..-.+||..+|+|...|.+=...+|+++++.
T Consensus 140 ~L~~~~r~vi~l~~~----~g----~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~ 187 (189)
T TIGR02984 140 KLPEDYREVILLRHL----EG----LSFAEVAERMDRSEGAVSMLWVRGLARLRQI 187 (189)
T ss_pred cCCHHHHHHHHHHHh----cC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 378888887766442 12 2347899999999999999999999888754
No 210
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=23.47 E-value=84 Score=19.69 Aligned_cols=20 Identities=15% Similarity=0.004 Sum_probs=17.9
Q ss_pred HHHHHHHhCCChHHHhhhhh
Q psy10105 98 KIMLAIITKMTLTQVSTWFA 117 (197)
Q Consensus 98 k~~LA~~tgLs~~QV~nWF~ 117 (197)
...+|+.+|++...|.++|.
T Consensus 30 ~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 30 FKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 56899999999999999885
No 211
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=23.33 E-value=52 Score=25.26 Aligned_cols=23 Identities=13% Similarity=0.081 Sum_probs=20.3
Q ss_pred HHHHHHHhCCChHHHhhhhhHHH
Q psy10105 98 KIMLAIITKMTLTQVSTWFANAR 120 (197)
Q Consensus 98 k~~LA~~tgLs~~QV~nWF~N~R 120 (197)
..+||+.+|++...|+.|..+.+
T Consensus 21 q~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 21 KKELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHcCCC
Confidence 56799999999999999998775
No 212
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=23.13 E-value=71 Score=21.10 Aligned_cols=16 Identities=31% Similarity=0.125 Sum_probs=12.9
Q ss_pred HHHHHHhCCChHHHhh
Q psy10105 99 IMLAIITKMTLTQVST 114 (197)
Q Consensus 99 ~~LA~~tgLs~~QV~n 114 (197)
.+||+.+|++..||.-
T Consensus 32 ~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 32 QELAEALGITPAQVRK 47 (50)
T ss_dssp HHHHHHHTS-HHHHHH
T ss_pred HHHHHHHCCCHHHhcc
Confidence 5799999999999963
No 213
>PRK09726 antitoxin HipB; Provisional
Probab=23.03 E-value=52 Score=23.51 Aligned_cols=22 Identities=18% Similarity=0.140 Sum_probs=19.5
Q ss_pred HHHHHHHhCCChHHHhhhhhHH
Q psy10105 98 KIMLAIITKMTLTQVSTWFANA 119 (197)
Q Consensus 98 k~~LA~~tgLs~~QV~nWF~N~ 119 (197)
..+||+.+|++...|+.|..+.
T Consensus 28 q~elA~~~gvs~~tis~~e~g~ 49 (88)
T PRK09726 28 QSELAKKIGIKQATISNFENNP 49 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHCCC
Confidence 5689999999999999998764
No 214
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=22.98 E-value=1.6e+02 Score=25.75 Aligned_cols=51 Identities=10% Similarity=0.044 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+++..+.+|...|. ...+ ..-.+||+.+|+|...|..+...+++++|...
T Consensus 227 ~L~~rer~vl~lr~~--~~~~----~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l 277 (289)
T PRK07500 227 TLNERELRIIRERRL--REDG----ATLEALGEELGISKERVRQIEARALEKLRRAL 277 (289)
T ss_pred cCCHHHHHHHHHHhc--CCCC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888877662 1122 34688999999999999999999999998765
No 215
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=22.68 E-value=1.8e+02 Score=20.96 Aligned_cols=39 Identities=23% Similarity=0.313 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhh
Q psy10105 75 ESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFA 117 (197)
Q Consensus 75 ~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~ 117 (197)
+....+..|+.+|...+ ++ -.+||+.+|++..++..=|+
T Consensus 5 ~~~~~~~~~i~~~~~~~-~~---~~~lA~~~~~S~~~l~r~f~ 43 (107)
T PRK10219 5 KIIQTLIAWIDEHIDQP-LN---IDVVAKKSGYSKWYLQRMFR 43 (107)
T ss_pred HHHHHHHHHHHHhcCCC-CC---HHHHHHHHCCCHHHHHHHHH
Confidence 34566778887776665 33 46788888888887665543
No 216
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=22.45 E-value=2e+02 Score=21.77 Aligned_cols=45 Identities=13% Similarity=0.109 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhh
Q psy10105 72 ATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 124 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k 124 (197)
+|+.++.+|.-+|. . .---.+||...|+|..-|..|..-++.++.
T Consensus 18 LT~kQ~~~l~lyy~---e-----DlSlsEIAe~~~iSRqaV~d~ikr~~~~L~ 62 (101)
T PF04297_consen 18 LTEKQREILELYYE---E-----DLSLSEIAEELGISRQAVYDSIKRAEKKLE 62 (101)
T ss_dssp S-HHHHHHHHHHCT---S--------HHHHHHHCTS-HHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHc---c-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 78999999987762 1 123567999999999999999888887654
No 217
>smart00351 PAX Paired Box domain.
Probab=22.17 E-value=3.1e+02 Score=20.90 Aligned_cols=46 Identities=13% Similarity=0.109 Sum_probs=31.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCC-------ChHHHhhhh
Q psy10105 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKM-------TLTQVSTWF 116 (197)
Q Consensus 68 rR~~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgL-------s~~QV~nWF 116 (197)
+++..+......+.... ..||.-+..|-...-...|+ +.+.|..||
T Consensus 72 rp~~~~~~~~~~I~~~~---~~~p~~t~~el~~~L~~~gv~~~~~~Ps~sti~~~l 124 (125)
T smart00351 72 KPKVATPKVVKKIADYK---QENPGIFAWEIRDRLLSEGVCDKDNVPSVSSINRIL 124 (125)
T ss_pred CCCccCHHHHHHHHHHH---HHCCCCCHHHHHHHHHHcCCCcCCCCCChhhHHHhh
Confidence 34445656666666666 78898888777544446666 778888886
No 218
>KOG4040|consensus
Probab=22.17 E-value=77 Score=26.35 Aligned_cols=35 Identities=29% Similarity=0.533 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhhCCCCCC-HHHHHHHHHHhCCChHH
Q psy10105 77 TATLKAWLNEHKKNPYPT-KGEKIMLAIITKMTLTQ 111 (197)
Q Consensus 77 ~~~L~~wf~~h~~nPYPs-~~ek~~LA~~tgLs~~Q 111 (197)
....-.|+..|.-.|||+ ++||..-|++.||-+..
T Consensus 26 ~rt~~gw~kD~kPgpyP~teeER~AAAkKY~lrpEd 61 (186)
T KOG4040|consen 26 PRTFDGWYKDHKPGPYPTTEEERRAAAKKYGLRPED 61 (186)
T ss_pred cccccccccccCCCCCCCCHHHHHHHHHHhCCCHhh
Confidence 344567998999999995 67888888999887654
No 219
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=22.11 E-value=1.8e+02 Score=19.96 Aligned_cols=42 Identities=17% Similarity=0.298 Sum_probs=25.2
Q ss_pred CCCHHHHHHH---HHHHHHhhCCCCCCHHHHHHHHHHhCCC-hHHHhhhhh
Q psy10105 71 NATRESTATL---KAWLNEHKKNPYPTKGEKIMLAIITKMT-LTQVSTWFA 117 (197)
Q Consensus 71 ~f~~~~~~~L---~~wf~~h~~nPYPs~~ek~~LA~~tgLs-~~QV~nWF~ 117 (197)
.+++.+.++| .+++ ..+.||. .-.+||+.+|++ ..-|..-..
T Consensus 3 ~LT~rQ~~vL~~I~~~~---~~~G~~P--t~rEIa~~~g~~S~~tv~~~L~ 48 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYI---EENGYPP--TVREIAEALGLKSTSTVQRHLK 48 (65)
T ss_dssp ---HHHHHHHHHHHHHH---HHHSS-----HHHHHHHHTSSSHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHH---HHcCCCC--CHHHHHHHhCCCChHHHHHHHH
Confidence 3677777776 4455 4566664 567899999997 777765443
No 220
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=21.90 E-value=1.2e+02 Score=18.01 Aligned_cols=20 Identities=10% Similarity=0.134 Sum_probs=14.4
Q ss_pred HHHHHHHhCCChHHHhhhhh
Q psy10105 98 KIMLAIITKMTLTQVSTWFA 117 (197)
Q Consensus 98 k~~LA~~tgLs~~QV~nWF~ 117 (197)
-..-|+..|||..+|...+.
T Consensus 8 Li~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 8 LIKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 45668899999999998764
No 221
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=21.73 E-value=62 Score=21.38 Aligned_cols=25 Identities=20% Similarity=0.048 Sum_probs=20.1
Q ss_pred HHHHHHHHhCCChHHHhhhhhHHHH
Q psy10105 97 EKIMLAIITKMTLTQVSTWFANARR 121 (197)
Q Consensus 97 ek~~LA~~tgLs~~QV~nWF~N~R~ 121 (197)
...++|+.+|++...|+.|-.+++.
T Consensus 16 s~~~lA~~~g~s~s~v~~iE~G~~~ 40 (64)
T PF13560_consen 16 SQAQLADRLGVSQSTVSRIERGRRP 40 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCCC
Confidence 4578999999999999999887774
No 222
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=21.65 E-value=1.8e+02 Score=25.38 Aligned_cols=51 Identities=20% Similarity=0.111 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.++...+.+|+..|. .. ....-.+||+.+|+|...|+.+-..+..++|...
T Consensus 230 ~L~~rEr~VL~lry~---~~---~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l 280 (284)
T PRK06596 230 GLDERSRDIIEARWL---DD---DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAI 280 (284)
T ss_pred cCCHHHHHHHHHHhc---CC---CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 477788888887762 21 1233569999999999999999999999888654
No 223
>PRK10403 transcriptional regulator NarP; Provisional
Probab=21.17 E-value=2e+02 Score=21.99 Aligned_cols=47 Identities=15% Similarity=0.162 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~ 126 (197)
.++.....+|+-+. .+ + ...+||+.++++..-|.+...|.|+|..-.
T Consensus 153 ~Lt~~e~~vl~~~~----~g-~----s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~ 199 (215)
T PRK10403 153 VLTERELDVLHELA----QG-L----SNKQIASVLNISEQTVKVHIRNLLRKLNVR 199 (215)
T ss_pred cCCHHHHHHHHHHH----CC-C----CHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 47888888886443 22 2 246889999999999999999999997643
No 224
>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=20.86 E-value=1e+02 Score=25.86 Aligned_cols=48 Identities=19% Similarity=0.270 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.|+...+++|. |.. ....-.+||..+|++...|..+..|.++|++..+
T Consensus 171 ~Lt~re~evl~-~~a--------~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~ 218 (232)
T TIGR03541 171 VLSEREREVLA-WTA--------LGRRQADIAAILGISERTVENHLRSARRKLGVAT 218 (232)
T ss_pred cCCHHHHHHHH-HHH--------CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCC
Confidence 46666666663 331 1123457889999999999999999999987553
No 225
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=20.45 E-value=2.7e+02 Score=23.39 Aligned_cols=46 Identities=9% Similarity=0.159 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhh
Q psy10105 71 NATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 124 (197)
Q Consensus 71 ~f~~~~~~~L~~wf~~h~~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k 124 (197)
.++...+.+|...|.+. ..-.++|..+|++..+|+.--..++.+++
T Consensus 183 ~L~~~er~vi~l~~~~~--------~t~~EIA~~lgis~~~V~q~~~~~~~kLr 228 (231)
T PRK12427 183 QLDEREQLILHLYYQHE--------MSLKEIALVLDLTEARICQLNKKIAQKIK 228 (231)
T ss_pred cCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 47777777777776321 23578999999999999998888888776
No 226
>KOG4067|consensus
Probab=20.43 E-value=74 Score=26.96 Aligned_cols=49 Identities=16% Similarity=0.272 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHHHHhh-------CCCCCCHHHHHHHHHHhCCChHHHhhhhhHHHHhhhhcc
Q psy10105 72 ATRESTATLKAWLNEHK-------KNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127 (197)
Q Consensus 72 f~~~~~~~L~~wf~~h~-------~nPYPs~~ek~~LA~~tgLs~~QV~nWF~N~R~R~k~~~ 127 (197)
.+.-+.++|.++|.--. +.|| + +-.++.+..+++.+||.|.++|+.+..
T Consensus 132 ~~~~aqki~~nf~Nf~qsfa~~~~q~~~-n------~~s~~~VP~~v~~~W~~kFq~rl~~np 187 (195)
T KOG4067|consen 132 NKSFAQKILTNFFNFMQSFAVSIAQIPP-N------LPSETFVPIRVFDDWYDKFQNRLANNP 187 (195)
T ss_pred hHHHHHHHHHHHHHHHHHHhhhhhccCC-C------CcccccccHHHHHHHHHHHHHHHhcCC
Confidence 45667788887763111 1222 1 345677999999999999999987654
No 227
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=20.37 E-value=1e+02 Score=22.31 Aligned_cols=20 Identities=35% Similarity=0.597 Sum_probs=17.9
Q ss_pred HHHHHHHHHhCCChHHHhhh
Q psy10105 96 GEKIMLAIITKMTLTQVSTW 115 (197)
Q Consensus 96 ~ek~~LA~~tgLs~~QV~nW 115 (197)
.-+..+|+.+|+|..-|+.|
T Consensus 11 Gs~~kvA~aLGIs~~AVsQW 30 (75)
T PRK09744 11 GSKTKLANAAGVRLASVAAW 30 (75)
T ss_pred CcHHHHHHHHCCCHHHHHHH
Confidence 34678999999999999999
No 228
>PHA00542 putative Cro-like protein
Probab=20.15 E-value=77 Score=22.52 Aligned_cols=24 Identities=8% Similarity=0.155 Sum_probs=20.2
Q ss_pred HHHHHHHHhCCChHHHhhhhhHHH
Q psy10105 97 EKIMLAIITKMTLTQVSTWFANAR 120 (197)
Q Consensus 97 ek~~LA~~tgLs~~QV~nWF~N~R 120 (197)
...+||+.+|++...|+.|..+..
T Consensus 33 Tq~elA~~lgIs~~tIsr~e~g~~ 56 (82)
T PHA00542 33 SQEQIADATDVSQPTICRIYSGRH 56 (82)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCCC
Confidence 345699999999999999987764
Done!