Query psy4868
Match_columns 169
No_of_seqs 215 out of 1775
Neff 7.9
Searched_HMMs 46136
Date Fri Aug 16 19:43:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4868.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4868hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0484|consensus 99.9 1.7E-21 3.8E-26 133.5 9.4 70 54-123 13-82 (125)
2 KOG0485|consensus 99.8 1.3E-19 2.9E-24 139.1 10.6 68 55-122 101-168 (268)
3 KOG0489|consensus 99.8 2.7E-20 5.9E-25 150.0 6.7 68 56-123 157-224 (261)
4 KOG0850|consensus 99.8 1.9E-19 4.1E-24 139.4 9.9 65 54-118 118-182 (245)
5 KOG0488|consensus 99.8 2.2E-19 4.9E-24 147.3 9.5 67 55-121 169-235 (309)
6 KOG0842|consensus 99.8 1.1E-19 2.3E-24 147.6 6.8 71 55-125 150-220 (307)
7 KOG0487|consensus 99.8 4.9E-20 1.1E-24 149.6 4.8 69 53-121 230-298 (308)
8 KOG2251|consensus 99.8 2.6E-18 5.7E-23 132.4 9.5 67 54-120 33-99 (228)
9 KOG0843|consensus 99.8 7E-19 1.5E-23 131.7 5.8 65 56-120 100-164 (197)
10 PF00046 Homeobox: Homeobox do 99.7 5.1E-18 1.1E-22 106.3 6.8 57 59-115 1-57 (57)
11 KOG0492|consensus 99.7 6.2E-18 1.3E-22 129.1 5.7 74 53-126 139-212 (246)
12 KOG0494|consensus 99.7 1E-17 2.2E-22 131.8 6.2 65 57-121 140-204 (332)
13 KOG0848|consensus 99.7 1.1E-17 2.4E-22 132.0 6.2 65 57-121 198-262 (317)
14 KOG0491|consensus 99.7 2.7E-17 5.9E-22 121.5 4.9 68 53-120 95-162 (194)
15 KOG0493|consensus 99.7 6.8E-17 1.5E-21 127.3 6.2 59 58-116 246-304 (342)
16 TIGR01565 homeo_ZF_HD homeobox 99.6 4.2E-16 9E-21 97.6 4.3 53 58-110 1-57 (58)
17 cd00086 homeodomain Homeodomai 99.6 1.4E-15 3.1E-20 95.3 6.6 56 60-115 2-57 (59)
18 smart00389 HOX Homeodomain. DN 99.6 1.1E-15 2.3E-20 95.1 5.7 54 60-113 2-55 (56)
19 KOG0844|consensus 99.6 5.6E-16 1.2E-20 124.5 5.1 63 57-119 180-242 (408)
20 KOG0486|consensus 99.6 1.6E-15 3.4E-20 122.3 4.9 67 55-121 109-175 (351)
21 KOG3802|consensus 99.6 1.4E-15 3.1E-20 126.2 3.9 64 55-118 291-354 (398)
22 KOG0483|consensus 99.6 1.9E-15 4.2E-20 116.5 4.1 60 59-118 51-110 (198)
23 COG5576 Homeodomain-containing 99.6 5.5E-15 1.2E-19 110.3 5.4 65 56-120 49-113 (156)
24 KOG0847|consensus 99.5 2.6E-14 5.6E-19 110.3 3.8 67 56-122 165-231 (288)
25 KOG4577|consensus 99.4 7.2E-14 1.6E-18 111.7 4.7 63 58-120 167-229 (383)
26 KOG0490|consensus 99.3 6.6E-13 1.4E-17 104.5 2.5 64 55-118 57-120 (235)
27 KOG0775|consensus 99.2 6.9E-11 1.5E-15 94.1 8.6 48 67-114 185-232 (304)
28 KOG0849|consensus 99.2 1.8E-11 4E-16 102.6 4.6 66 53-118 171-236 (354)
29 KOG1168|consensus 99.1 1.2E-11 2.6E-16 99.1 1.5 62 57-118 308-369 (385)
30 KOG0774|consensus 99.0 1.1E-09 2.4E-14 86.8 6.6 63 58-120 188-253 (334)
31 PF05920 Homeobox_KN: Homeobox 98.7 1.7E-08 3.6E-13 58.7 3.3 34 79-112 7-40 (40)
32 KOG2252|consensus 98.5 1.4E-07 3E-12 81.7 5.5 57 57-113 419-475 (558)
33 KOG0490|consensus 98.2 1E-06 2.3E-11 69.1 3.8 64 55-118 150-213 (235)
34 KOG1146|consensus 97.8 1.9E-05 4.1E-10 74.5 4.2 62 57-118 902-963 (1406)
35 PF11569 Homez: Homeodomain le 97.5 7.8E-05 1.7E-09 46.1 2.8 41 70-110 10-50 (56)
36 KOG0773|consensus 96.9 0.00063 1.4E-08 56.9 2.5 64 58-121 239-305 (342)
37 KOG3623|consensus 96.6 0.0065 1.4E-07 55.1 6.6 49 70-118 568-616 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 95.8 0.027 5.9E-07 34.4 4.7 47 59-110 1-47 (53)
39 PF04545 Sigma70_r4: Sigma-70, 90.3 0.97 2.1E-05 26.6 4.8 46 64-114 4-49 (50)
40 PF04967 HTH_10: HTH DNA bindi 87.6 1.2 2.6E-05 27.2 3.8 41 65-105 1-43 (53)
41 PF08281 Sigma70_r4_2: Sigma-7 84.3 2.9 6.3E-05 24.8 4.4 42 65-111 11-52 (54)
42 PF01527 HTH_Tnp_1: Transposas 83.4 1 2.3E-05 28.7 2.3 44 60-107 2-45 (76)
43 PRK03975 tfx putative transcri 81.5 6.9 0.00015 28.8 6.2 53 62-120 4-56 (141)
44 cd06171 Sigma70_r4 Sigma70, re 81.4 2.3 4.9E-05 24.3 3.1 43 65-112 11-53 (55)
45 COG3413 Predicted DNA binding 79.7 3.5 7.7E-05 32.1 4.5 49 64-114 155-205 (215)
46 PF10668 Phage_terminase: Phag 79.4 1.6 3.4E-05 27.4 1.9 20 87-106 24-43 (60)
47 PF09607 BrkDBD: Brinker DNA-b 79.2 5.8 0.00013 24.7 4.4 45 62-107 3-47 (58)
48 TIGR03879 near_KaiC_dom probab 74.8 1.7 3.8E-05 28.3 1.2 35 74-108 21-55 (73)
49 cd00569 HTH_Hin_like Helix-tur 74.0 9.7 0.00021 19.2 4.4 37 65-106 6-42 (42)
50 PRK09413 IS2 repressor TnpA; R 73.3 11 0.00024 26.5 5.3 42 62-107 10-51 (121)
51 PF00196 GerE: Bacterial regul 73.2 9 0.0002 23.1 4.2 45 64-114 3-47 (58)
52 PRK09646 RNA polymerase sigma 72.2 8.6 0.00019 29.0 4.7 48 64-116 142-189 (194)
53 PRK12526 RNA polymerase sigma 71.4 9.8 0.00021 29.1 5.0 49 64-117 153-201 (206)
54 PRK06759 RNA polymerase factor 70.3 8.8 0.00019 27.5 4.3 47 64-115 106-152 (154)
55 KOG1146|consensus 69.8 5.1 0.00011 39.3 3.5 60 58-117 705-764 (1406)
56 PRK09652 RNA polymerase sigma 69.8 10 0.00022 27.7 4.6 48 64-116 128-175 (182)
57 PRK04217 hypothetical protein; 68.7 17 0.00038 25.5 5.3 48 64-116 42-89 (110)
58 PRK10072 putative transcriptio 68.3 8.3 0.00018 26.4 3.5 41 64-111 32-72 (96)
59 KOG3755|consensus 68.3 4.9 0.00011 36.4 2.8 45 74-118 708-759 (769)
60 PRK00118 putative DNA-binding 67.7 19 0.00042 25.0 5.3 48 65-117 18-65 (104)
61 PF13936 HTH_38: Helix-turn-he 67.7 6.7 0.00015 22.6 2.6 40 63-107 3-42 (44)
62 PRK11924 RNA polymerase sigma 66.5 17 0.00037 26.4 5.2 47 65-116 126-172 (179)
63 cd04761 HTH_MerR-SF Helix-Turn 66.3 5.7 0.00012 22.7 2.1 21 88-108 3-23 (49)
64 TIGR02937 sigma70-ECF RNA poly 65.3 14 0.0003 25.7 4.4 47 64-115 110-156 (158)
65 PRK12514 RNA polymerase sigma 65.2 16 0.00034 27.0 4.8 46 65-115 130-175 (179)
66 PRK12512 RNA polymerase sigma 65.1 15 0.00032 27.3 4.7 49 64-117 131-179 (184)
67 PRK12519 RNA polymerase sigma 65.0 11 0.00024 28.3 4.0 47 65-116 142-188 (194)
68 PRK09642 RNA polymerase sigma 65.0 16 0.00035 26.4 4.8 48 64-116 106-153 (160)
69 PRK09639 RNA polymerase sigma 65.0 25 0.00054 25.4 5.8 48 64-117 112-159 (166)
70 PRK09644 RNA polymerase sigma 65.0 19 0.00042 26.2 5.2 49 63-116 107-155 (165)
71 TIGR02985 Sig70_bacteroi1 RNA 64.3 16 0.00034 26.0 4.6 47 64-115 113-159 (161)
72 PF13518 HTH_28: Helix-turn-he 63.3 8.8 0.00019 22.2 2.6 23 87-109 14-36 (52)
73 TIGR02989 Sig-70_gvs1 RNA poly 63.2 15 0.00033 26.3 4.4 47 63-114 110-156 (159)
74 TIGR02959 SigZ RNA polymerase 62.9 21 0.00045 26.3 5.1 49 64-117 100-148 (170)
75 PRK09648 RNA polymerase sigma 62.7 17 0.00038 27.1 4.7 48 63-115 138-185 (189)
76 PRK12541 RNA polymerase sigma 62.4 14 0.0003 26.8 4.0 47 64-115 112-158 (161)
77 PRK06930 positive control sigm 61.4 24 0.00052 26.6 5.2 50 64-118 114-163 (170)
78 TIGR02999 Sig-70_X6 RNA polyme 61.3 19 0.00042 26.5 4.7 46 65-115 135-180 (183)
79 TIGR02948 SigW_bacill RNA poly 61.0 18 0.00039 26.7 4.5 48 64-116 136-183 (187)
80 PRK12530 RNA polymerase sigma 60.8 25 0.00055 26.4 5.3 49 64-117 134-182 (189)
81 TIGR02939 RpoE_Sigma70 RNA pol 60.8 16 0.00034 27.1 4.1 47 65-116 139-185 (190)
82 PF08280 HTH_Mga: M protein tr 60.5 20 0.00044 21.8 3.9 36 68-107 6-41 (59)
83 PRK12515 RNA polymerase sigma 60.5 26 0.00056 26.2 5.3 49 64-117 131-179 (189)
84 PRK05602 RNA polymerase sigma 60.4 18 0.00039 26.9 4.4 47 65-116 129-175 (186)
85 PRK09637 RNA polymerase sigma 60.2 20 0.00043 26.8 4.6 49 64-117 106-154 (181)
86 PRK09047 RNA polymerase factor 59.9 23 0.0005 25.4 4.8 47 64-115 106-152 (161)
87 PF13384 HTH_23: Homeodomain-l 59.3 8.9 0.00019 22.2 2.1 23 86-108 18-40 (50)
88 TIGR02983 SigE-fam_strep RNA p 58.7 22 0.00047 25.7 4.5 47 65-116 111-157 (162)
89 PRK12537 RNA polymerase sigma 58.7 23 0.00049 26.3 4.7 47 64-115 133-179 (182)
90 smart00421 HTH_LUXR helix_turn 58.4 33 0.00071 19.5 4.9 42 64-111 3-44 (58)
91 PRK12546 RNA polymerase sigma 58.0 20 0.00044 27.1 4.4 50 64-118 113-162 (188)
92 PF06056 Terminase_5: Putative 57.7 3.7 7.9E-05 25.4 0.2 21 87-107 15-35 (58)
93 PRK12532 RNA polymerase sigma 56.9 35 0.00077 25.5 5.6 50 64-118 136-185 (195)
94 PF13411 MerR_1: MerR HTH fami 56.7 10 0.00022 23.4 2.2 20 88-107 3-22 (69)
95 PF00376 MerR: MerR family reg 56.6 11 0.00023 21.2 2.0 19 88-106 2-20 (38)
96 PRK12543 RNA polymerase sigma 55.9 41 0.0009 24.8 5.7 52 64-120 117-168 (179)
97 PF13443 HTH_26: Cro/C1-type H 55.9 10 0.00022 23.0 2.0 26 87-112 12-37 (63)
98 PRK12524 RNA polymerase sigma 55.6 26 0.00057 26.4 4.7 48 64-116 136-183 (196)
99 TIGR02954 Sig70_famx3 RNA poly 55.1 28 0.0006 25.4 4.6 47 64-115 119-165 (169)
100 PRK12536 RNA polymerase sigma 54.6 30 0.00064 25.7 4.7 47 65-116 130-176 (181)
101 PRK12547 RNA polymerase sigma 54.3 30 0.00066 25.2 4.7 48 64-116 112-159 (164)
102 PRK07037 extracytoplasmic-func 54.0 32 0.0007 24.8 4.8 47 64-115 109-155 (163)
103 PRK12538 RNA polymerase sigma 52.9 28 0.0006 27.4 4.5 49 65-118 172-220 (233)
104 cd04762 HTH_MerR-trunc Helix-T 52.7 14 0.0003 20.6 2.1 23 88-110 3-25 (49)
105 COG4367 Uncharacterized protei 52.5 27 0.00059 23.7 3.6 39 65-103 3-41 (97)
106 PRK12545 RNA polymerase sigma 52.4 43 0.00094 25.4 5.4 50 64-118 139-188 (201)
107 PRK06986 fliA flagellar biosyn 52.3 28 0.0006 27.2 4.4 48 64-116 184-231 (236)
108 TIGR02952 Sig70_famx2 RNA poly 52.0 33 0.00072 24.8 4.6 47 64-115 122-168 (170)
109 PRK12529 RNA polymerase sigma 51.9 35 0.00075 25.3 4.7 47 64-115 127-173 (178)
110 cd04763 HTH_MlrA-like Helix-Tu 51.9 13 0.00029 23.1 2.1 20 88-107 3-22 (68)
111 COG2944 Predicted transcriptio 51.7 26 0.00056 24.4 3.6 40 65-111 44-83 (104)
112 PF02796 HTH_7: Helix-turn-hel 51.7 27 0.00059 20.0 3.3 37 65-106 6-42 (45)
113 PRK13919 putative RNA polymera 51.6 36 0.00078 25.2 4.8 48 63-115 134-181 (186)
114 smart00595 MADF subfamily of S 51.4 39 0.00084 21.9 4.4 34 89-122 31-64 (89)
115 PRK12516 RNA polymerase sigma 51.3 39 0.00085 25.4 5.0 49 65-118 117-165 (187)
116 TIGR03001 Sig-70_gmx1 RNA poly 50.7 45 0.00097 26.5 5.4 52 64-120 161-212 (244)
117 cd04764 HTH_MlrA-like_sg1 Heli 50.6 15 0.00032 22.7 2.2 20 88-107 3-22 (67)
118 PRK06811 RNA polymerase factor 50.4 34 0.00074 25.6 4.5 47 64-115 131-177 (189)
119 PRK12533 RNA polymerase sigma 50.1 34 0.00073 26.6 4.5 48 64-116 134-181 (216)
120 PRK09645 RNA polymerase sigma 50.1 39 0.00085 24.6 4.7 46 65-115 119-164 (173)
121 PRK12520 RNA polymerase sigma 50.0 60 0.0013 24.2 5.8 51 64-119 131-181 (191)
122 PRK12540 RNA polymerase sigma 49.8 62 0.0013 24.2 5.9 47 65-116 112-158 (182)
123 PRK09647 RNA polymerase sigma 49.7 47 0.001 25.4 5.2 50 64-118 138-187 (203)
124 cd06170 LuxR_C_like C-terminal 49.3 35 0.00077 19.5 3.6 36 66-107 2-37 (57)
125 PRK12531 RNA polymerase sigma 49.0 41 0.00088 25.3 4.8 47 64-115 141-187 (194)
126 TIGR02943 Sig70_famx1 RNA poly 48.7 55 0.0012 24.5 5.4 50 64-118 131-180 (188)
127 PRK12535 RNA polymerase sigma 48.6 40 0.00086 25.6 4.7 48 64-116 133-180 (196)
128 PRK09649 RNA polymerase sigma 48.4 36 0.00078 25.4 4.4 47 64-115 130-176 (185)
129 PRK12539 RNA polymerase sigma 48.3 43 0.00094 24.8 4.8 47 64-115 131-177 (184)
130 PRK12542 RNA polymerase sigma 47.6 42 0.00092 24.9 4.6 47 64-115 122-168 (185)
131 TIGR00721 tfx DNA-binding prot 47.5 87 0.0019 22.9 6.0 48 62-115 4-51 (137)
132 PRK12523 RNA polymerase sigma 47.4 48 0.001 24.3 4.8 47 64-115 119-165 (172)
133 cd01392 HTH_LacI Helix-turn-he 47.3 12 0.00026 21.7 1.3 21 90-110 2-22 (52)
134 PRK12518 RNA polymerase sigma 46.7 28 0.00061 25.4 3.5 32 86-117 137-168 (175)
135 smart00027 EH Eps15 homology d 46.3 50 0.0011 21.9 4.4 44 64-107 3-51 (96)
136 PRK11923 algU RNA polymerase s 46.2 49 0.0011 24.7 4.8 33 86-118 155-187 (193)
137 PRK12522 RNA polymerase sigma 45.9 55 0.0012 23.9 5.0 47 65-116 120-166 (173)
138 PRK08301 sporulation sigma fac 45.9 45 0.00097 25.9 4.7 52 64-116 178-229 (234)
139 PRK08583 RNA polymerase sigma 45.6 44 0.00096 26.4 4.7 47 64-115 205-251 (257)
140 TIGR02479 FliA_WhiG RNA polyme 45.6 44 0.00096 25.8 4.6 47 64-115 175-221 (224)
141 COG1905 NuoE NADH:ubiquinone o 45.4 42 0.00091 25.2 4.2 38 65-102 23-60 (160)
142 PRK05657 RNA polymerase sigma 44.9 48 0.001 27.6 4.9 54 63-117 261-314 (325)
143 TIGR02859 spore_sigH RNA polym 44.9 17 0.00038 27.1 2.1 32 84-115 164-195 (198)
144 PF01381 HTH_3: Helix-turn-hel 44.8 17 0.00037 21.3 1.7 23 88-110 12-34 (55)
145 cd01104 HTH_MlrA-CarA Helix-Tu 44.6 20 0.00043 22.0 2.1 20 88-107 3-22 (68)
146 PRK09641 RNA polymerase sigma 44.6 53 0.0012 24.1 4.8 47 65-116 137-183 (187)
147 TIGR02950 SigM_subfam RNA poly 44.5 29 0.00063 24.7 3.2 33 83-115 119-151 (154)
148 PRK12544 RNA polymerase sigma 44.3 61 0.0013 24.8 5.1 50 64-118 148-197 (206)
149 PRK12511 RNA polymerase sigma 44.0 59 0.0013 24.3 4.9 49 64-117 111-159 (182)
150 PRK12528 RNA polymerase sigma 43.8 50 0.0011 23.8 4.4 44 64-112 113-156 (161)
151 COG2963 Transposase and inacti 43.4 63 0.0014 22.2 4.7 42 62-107 5-47 (116)
152 TIGR02941 Sigma_B RNA polymera 43.3 45 0.00098 26.3 4.4 48 63-115 204-251 (255)
153 TIGR02980 SigBFG RNA polymeras 43.1 53 0.0011 25.3 4.7 47 63-114 177-223 (227)
154 PF04936 DUF658: Protein of un 42.7 13 0.00028 28.1 1.0 37 86-122 15-51 (186)
155 PRK08295 RNA polymerase factor 42.3 74 0.0016 23.9 5.3 46 65-116 156-201 (208)
156 KOG0773|consensus 42.1 31 0.00067 28.7 3.4 39 78-116 117-155 (342)
157 TIGR02947 SigH_actino RNA poly 41.8 33 0.00071 25.7 3.2 33 86-118 148-180 (193)
158 PF07638 Sigma70_ECF: ECF sigm 41.5 58 0.0013 24.4 4.6 46 65-115 136-181 (185)
159 TIGR03070 couple_hipB transcri 40.8 22 0.00048 20.6 1.8 23 88-110 18-40 (58)
160 PRK07670 RNA polymerase sigma 40.5 57 0.0012 25.8 4.6 47 64-115 201-247 (251)
161 PRK07408 RNA polymerase sigma 40.5 63 0.0014 25.7 4.8 48 64-116 203-250 (256)
162 PRK12517 RNA polymerase sigma 40.3 1.3E+02 0.0028 22.5 6.4 51 64-119 128-178 (188)
163 PRK09415 RNA polymerase factor 39.9 53 0.0012 24.3 4.1 47 64-115 127-173 (179)
164 PRK09651 RNA polymerase sigma 39.7 51 0.0011 24.2 4.0 47 64-115 119-165 (172)
165 PRK09643 RNA polymerase sigma 39.5 80 0.0017 23.7 5.1 45 65-114 135-179 (192)
166 PRK12525 RNA polymerase sigma 39.5 72 0.0016 23.2 4.7 47 63-114 117-163 (168)
167 TIGR02957 SigX4 RNA polymerase 39.2 58 0.0013 26.2 4.5 47 64-115 108-154 (281)
168 PF13551 HTH_29: Winged helix- 38.9 90 0.002 20.7 4.9 47 61-107 54-109 (112)
169 PHA02955 hypothetical protein; 38.9 49 0.0011 26.0 3.8 44 67-110 60-104 (213)
170 PRK07122 RNA polymerase sigma 38.6 54 0.0012 26.3 4.2 47 64-115 215-261 (264)
171 PRK06288 RNA polymerase sigma 38.4 68 0.0015 25.6 4.7 48 64-116 212-259 (268)
172 PRK09480 slmA division inhibit 38.4 39 0.00085 24.9 3.2 37 74-111 20-56 (194)
173 PRK10403 transcriptional regul 38.1 48 0.001 24.1 3.6 47 64-116 153-199 (215)
174 cd00093 HTH_XRE Helix-turn-hel 38.0 27 0.00058 19.2 1.8 23 88-110 15-37 (58)
175 PRK12513 RNA polymerase sigma 37.7 53 0.0011 24.5 3.8 33 85-117 155-187 (194)
176 TIGR02393 RpoD_Cterm RNA polym 37.5 67 0.0015 25.1 4.5 52 64-116 176-227 (238)
177 PRK09640 RNA polymerase sigma 36.4 45 0.00097 24.9 3.2 30 87-116 152-181 (188)
178 PF04297 UPF0122: Putative hel 36.4 1.2E+02 0.0025 21.1 4.9 45 64-113 17-61 (101)
179 PRK09636 RNA polymerase sigma 36.4 68 0.0015 25.9 4.5 47 64-115 115-161 (293)
180 PF00424 REV: REV protein (ant 36.3 70 0.0015 21.8 3.7 38 70-121 14-51 (91)
181 TIGR01764 excise DNA binding d 36.3 30 0.00065 19.2 1.8 23 88-110 4-26 (49)
182 PRK12527 RNA polymerase sigma 36.1 92 0.002 22.3 4.8 46 65-115 106-151 (159)
183 PRK10360 DNA-binding transcrip 35.8 57 0.0012 23.6 3.7 45 63-113 136-180 (196)
184 PRK12534 RNA polymerase sigma 35.8 89 0.0019 23.1 4.8 47 64-115 137-183 (187)
185 PF12824 MRP-L20: Mitochondria 35.6 1.9E+02 0.0041 21.7 6.9 50 61-112 82-131 (164)
186 smart00422 HTH_MERR helix_turn 35.0 34 0.00073 21.0 2.0 19 88-106 3-21 (70)
187 PRK15369 two component system 34.8 1E+02 0.0022 22.1 4.9 45 64-114 149-193 (211)
188 PRK09638 RNA polymerase sigma 34.7 50 0.0011 24.1 3.2 32 84-115 141-172 (176)
189 TIGR03541 reg_near_HchA LuxR f 34.5 43 0.00092 26.3 2.9 51 62-118 169-219 (232)
190 PRK05988 formate dehydrogenase 34.1 85 0.0018 23.3 4.3 35 68-102 24-58 (156)
191 TIGR02392 rpoH_proteo alternat 34.0 83 0.0018 25.2 4.6 49 64-115 218-266 (270)
192 PF12728 HTH_17: Helix-turn-he 33.9 38 0.00082 19.6 2.0 22 88-109 4-25 (51)
193 PF08279 HTH_11: HTH domain; 33.6 75 0.0016 18.5 3.3 34 70-106 3-36 (55)
194 PRK10651 transcriptional regul 33.4 94 0.002 22.6 4.6 46 64-115 155-200 (216)
195 PHA01976 helix-turn-helix prot 33.3 35 0.00076 20.8 1.8 23 88-110 18-40 (67)
196 TIGR02394 rpoS_proteo RNA poly 33.0 1.2E+02 0.0025 24.5 5.3 54 63-117 221-274 (285)
197 PRK10100 DNA-binding transcrip 32.9 72 0.0016 24.8 4.0 47 64-116 155-201 (216)
198 TIGR02960 SigX5 RNA polymerase 32.8 79 0.0017 25.7 4.4 47 64-115 142-188 (324)
199 PF06971 Put_DNA-bind_N: Putat 32.6 34 0.00073 20.5 1.6 17 88-104 31-47 (50)
200 TIGR03020 EpsA transcriptional 32.3 72 0.0016 25.6 3.9 49 62-116 188-236 (247)
201 TIGR02607 antidote_HigA addict 32.2 36 0.00078 21.4 1.8 23 88-110 21-43 (78)
202 PRK07500 rpoH2 RNA polymerase 32.2 90 0.002 25.4 4.6 51 63-116 226-276 (289)
203 TIGR02984 Sig-70_plancto1 RNA 32.2 87 0.0019 22.9 4.2 47 64-115 140-186 (189)
204 TIGR02846 spore_sigmaK RNA pol 32.1 1.4E+02 0.003 23.1 5.5 51 63-114 173-223 (227)
205 PRK09935 transcriptional regul 31.3 74 0.0016 23.1 3.7 46 63-114 148-193 (210)
206 PRK07539 NADH dehydrogenase su 31.2 99 0.0021 22.7 4.3 35 68-102 23-57 (154)
207 PRK08215 sporulation sigma fac 31.1 88 0.0019 24.8 4.3 46 64-114 209-254 (258)
208 PRK05803 sporulation sigma fac 30.9 1.4E+02 0.0031 23.1 5.4 51 64-115 175-225 (233)
209 cd01106 HTH_TipAL-Mta Helix-Tu 30.9 43 0.00094 22.7 2.1 21 88-108 3-23 (103)
210 PF14991 MLANA: Protein melan- 30.5 16 0.00035 25.9 -0.1 18 101-118 41-58 (118)
211 cd00131 PAX Paired Box domain 30.2 2E+02 0.0044 20.4 6.0 46 64-109 75-127 (128)
212 PRK05911 RNA polymerase sigma 30.1 1.1E+02 0.0024 24.3 4.7 48 64-116 205-252 (257)
213 PRK11511 DNA-binding transcrip 30.1 63 0.0014 22.7 3.0 25 85-109 25-49 (127)
214 KOG3623|consensus 30.0 22 0.00047 33.2 0.6 56 61-116 629-684 (1007)
215 PF01257 2Fe-2S_thioredx: Thio 29.9 99 0.0022 22.4 4.0 34 69-102 15-48 (145)
216 cd01105 HTH_GlnR-like Helix-Tu 29.8 44 0.00096 22.1 2.0 19 88-106 4-22 (88)
217 cd04774 HTH_YfmP Helix-Turn-He 29.7 46 0.001 22.4 2.1 20 88-107 3-22 (96)
218 TIGR01958 nuoE_fam NADH-quinon 29.6 1.1E+02 0.0024 22.3 4.3 35 68-102 17-51 (148)
219 TIGR02885 spore_sigF RNA polym 29.4 1.1E+02 0.0024 23.6 4.6 42 63-109 182-223 (231)
220 PF01710 HTH_Tnp_IS630: Transp 29.0 40 0.00086 23.6 1.7 21 87-107 20-40 (119)
221 PRK05572 sporulation sigma fac 28.8 1.1E+02 0.0025 24.0 4.6 47 63-114 201-247 (252)
222 smart00530 HTH_XRE Helix-turn- 28.7 46 0.001 18.0 1.8 23 88-110 13-35 (56)
223 PF14549 P22_Cro: DNA-binding 28.4 1E+02 0.0022 19.1 3.3 27 88-116 12-38 (60)
224 PRK07571 bidirectional hydroge 28.3 1.2E+02 0.0026 22.9 4.3 35 68-102 37-71 (169)
225 PF13542 HTH_Tnp_ISL3: Helix-t 28.3 57 0.0012 18.8 2.1 21 87-107 29-49 (52)
226 PF13730 HTH_36: Helix-turn-he 28.3 58 0.0013 19.0 2.2 42 65-107 3-47 (55)
227 cd04766 HTH_HspR Helix-Turn-He 28.1 50 0.0011 21.8 2.0 20 88-107 4-23 (91)
228 COG1595 RpoE DNA-directed RNA 27.9 83 0.0018 23.3 3.5 32 87-118 145-176 (182)
229 PRK06704 RNA polymerase factor 27.6 1.1E+02 0.0025 24.0 4.3 47 65-116 117-163 (228)
230 PHA03308 transcriptional regul 27.2 84 0.0018 29.7 3.8 48 26-73 1258-1309(1463)
231 TIGR01557 myb_SHAQKYF myb-like 27.1 1.5E+02 0.0033 18.0 4.6 51 61-111 2-55 (57)
232 COG5484 Uncharacterized conser 27.1 37 0.0008 27.6 1.4 31 82-114 16-46 (279)
233 cd04779 HTH_MerR-like_sg4 Heli 27.0 52 0.0011 23.8 2.1 21 88-108 3-23 (134)
234 PF00440 TetR_N: Bacterial reg 26.9 82 0.0018 17.9 2.6 35 75-110 7-41 (47)
235 PRK11552 putative DNA-binding 26.6 94 0.002 24.0 3.6 43 70-114 19-61 (225)
236 PF05703 Auxin_canalis: Auxin 26.4 1.5E+02 0.0034 23.8 4.8 19 98-116 99-117 (242)
237 PF12200 DUF3597: Domain of un 26.2 1E+02 0.0022 22.2 3.4 30 83-112 83-117 (127)
238 PRK11922 RNA polymerase sigma 26.2 54 0.0012 25.5 2.2 48 65-117 150-197 (231)
239 PRK09706 transcriptional repre 26.2 49 0.0011 23.5 1.8 24 88-111 21-44 (135)
240 TIGR02835 spore_sigmaE RNA pol 26.0 88 0.0019 24.4 3.4 53 63-116 177-229 (234)
241 cd04768 HTH_BmrR-like Helix-Tu 25.7 61 0.0013 21.7 2.1 21 88-108 3-23 (96)
242 PRK06596 RNA polymerase factor 25.4 1.3E+02 0.0029 24.3 4.4 50 63-115 229-278 (284)
243 PRK13558 bacterio-opsin activa 25.2 79 0.0017 28.5 3.3 42 63-104 606-649 (665)
244 TIGR03830 CxxCG_CxxCG_HTH puta 25.1 1E+02 0.0022 21.3 3.3 45 59-110 59-103 (127)
245 PRK08241 RNA polymerase factor 23.9 1.1E+02 0.0024 25.1 3.8 46 65-115 154-199 (339)
246 cd04780 HTH_MerR-like_sg5 Heli 23.8 66 0.0014 21.7 2.0 20 88-107 3-22 (95)
247 PRK13890 conjugal transfer pro 23.4 57 0.0012 23.0 1.7 23 88-110 21-43 (120)
248 PF10078 DUF2316: Uncharacteri 23.4 73 0.0016 21.5 2.1 32 70-105 12-43 (89)
249 PF08671 SinI: Anti-repressor 23.4 96 0.0021 16.5 2.2 19 89-107 9-27 (30)
250 PRK14996 TetR family transcrip 23.4 1.4E+02 0.003 22.0 4.0 42 70-112 14-55 (192)
251 PRK06424 transcription factor; 22.8 65 0.0014 23.7 1.9 24 88-111 100-123 (144)
252 cd04773 HTH_TioE_rpt2 Second H 22.8 73 0.0016 21.9 2.1 21 88-108 3-23 (108)
253 PRK10430 DNA-binding transcrip 22.8 1.3E+02 0.0028 23.1 3.8 45 64-109 158-202 (239)
254 PRK09975 DNA-binding transcrip 22.7 1.1E+02 0.0024 22.9 3.3 42 70-112 17-58 (213)
255 PF13560 HTH_31: Helix-turn-he 22.7 65 0.0014 19.5 1.7 25 87-111 16-40 (64)
256 PF09862 DUF2089: Protein of u 22.4 1.9E+02 0.0042 20.4 4.2 38 64-106 33-70 (113)
257 PRK13870 transcriptional regul 22.3 2.1E+02 0.0045 22.5 4.9 48 62-115 171-218 (234)
258 cd04767 HTH_HspR-like_MBC Heli 22.3 74 0.0016 22.7 2.1 21 88-108 4-24 (120)
259 PF03444 HrcA_DNA-bdg: Winged 22.0 2.4E+02 0.0053 18.5 4.4 39 65-105 2-43 (78)
260 cd04775 HTH_Cfa-like Helix-Tur 22.0 75 0.0016 21.5 2.0 20 88-107 4-23 (102)
261 PF13404 HTH_AsnC-type: AsnC-t 22.0 70 0.0015 18.2 1.6 17 88-104 20-36 (42)
262 cd04782 HTH_BltR Helix-Turn-He 21.9 79 0.0017 21.2 2.1 20 88-107 3-22 (97)
263 PF03457 HA: Helicase associat 21.9 1.3E+02 0.0028 18.5 3.0 42 69-116 11-52 (68)
264 PRK09635 sigI RNA polymerase s 21.7 1.6E+02 0.0035 23.9 4.3 47 64-115 118-164 (290)
265 PF04539 Sigma70_r3: Sigma-70 21.6 75 0.0016 20.0 1.9 21 87-107 22-42 (78)
266 cd04788 HTH_NolA-AlbR Helix-Tu 21.3 83 0.0018 21.1 2.1 20 88-107 3-22 (96)
267 PRK09390 fixJ response regulat 21.3 1.8E+02 0.0038 20.6 4.1 31 88-118 159-189 (202)
268 PF01726 LexA_DNA_bind: LexA D 21.2 1.9E+02 0.0041 18.0 3.6 38 65-104 4-45 (65)
269 PRK09726 antitoxin HipB; Provi 21.0 73 0.0016 20.9 1.7 23 88-110 28-50 (88)
270 PF11516 DUF3220: Protein of u 20.9 44 0.00094 22.2 0.6 11 100-110 31-41 (106)
271 cd00592 HTH_MerR-like Helix-Tu 20.8 83 0.0018 20.9 2.0 20 88-107 3-22 (100)
272 cd04765 HTH_MlrA-like_sg2 Heli 20.7 87 0.0019 21.2 2.1 21 88-108 3-23 (99)
273 cd04789 HTH_Cfa Helix-Turn-Hel 20.5 84 0.0018 21.3 2.0 20 88-107 4-23 (102)
274 cd01279 HTH_HspR-like Helix-Tu 20.5 87 0.0019 21.1 2.1 20 88-107 4-23 (98)
275 PF12844 HTH_19: Helix-turn-he 20.3 78 0.0017 19.0 1.7 24 87-110 14-37 (64)
276 PRK10188 DNA-binding transcrip 20.1 2.7E+02 0.0059 21.9 5.2 48 62-115 177-224 (240)
277 TIGR02054 MerD mercuric resist 20.0 87 0.0019 22.2 2.1 21 87-107 5-25 (120)
No 1
>KOG0484|consensus
Probab=99.86 E-value=1.7e-21 Score=133.47 Aligned_cols=70 Identities=53% Similarity=0.905 Sum_probs=66.1
Q ss_pred hhhhccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHHHHh
Q psy4868 54 LKRKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLRNQR 123 (169)
Q Consensus 54 ~~~k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~~~ 123 (169)
.++|+||-||.|+..||..||+.|...+||++-.|++||..+.|++..|+|||||||+|+||+++.....
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~ 82 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAK 82 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence 4788999999999999999999999999999999999999999999999999999999999998876553
No 2
>KOG0485|consensus
Probab=99.81 E-value=1.3e-19 Score=139.11 Aligned_cols=68 Identities=34% Similarity=0.630 Sum_probs=62.9
Q ss_pred hhhccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHHHH
Q psy4868 55 KRKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLRNQ 122 (169)
Q Consensus 55 ~~k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~~ 122 (169)
..++||.||+|+..|+..||..|+...|++..+|..||..|.|++.||+|||||||.||||+......
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~e 168 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLE 168 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhh
Confidence 45778899999999999999999999999999999999999999999999999999999998765443
No 3
>KOG0489|consensus
Probab=99.81 E-value=2.7e-20 Score=149.97 Aligned_cols=68 Identities=40% Similarity=0.684 Sum_probs=62.8
Q ss_pred hhccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHHHHh
Q psy4868 56 RKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLRNQR 123 (169)
Q Consensus 56 ~k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~~~ 123 (169)
.+.||.||.||..|+.+||..|..|.|++...|.+||..|.|+++||+||||||||||||..+.....
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 45789999999999999999999999999999999999999999999999999999999987755443
No 4
>KOG0850|consensus
Probab=99.81 E-value=1.9e-19 Score=139.37 Aligned_cols=65 Identities=32% Similarity=0.700 Sum_probs=61.8
Q ss_pred hhhhccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 54 LKRKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 54 ~~~k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
..+|.|+.||.|+.-||..|.+.|++++|+-..+|.+||..|||+..||+|||||||.|+||..+
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 35677788999999999999999999999999999999999999999999999999999999888
No 5
>KOG0488|consensus
Probab=99.80 E-value=2.2e-19 Score=147.34 Aligned_cols=67 Identities=40% Similarity=0.772 Sum_probs=63.2
Q ss_pred hhhccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHHH
Q psy4868 55 KRKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLRN 121 (169)
Q Consensus 55 ~~k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~ 121 (169)
.+|.|+.||.||..|+..||..|+...|++..+|.+||..|||+..||++||||||+||||......
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~ 235 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGG 235 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhh
Confidence 4788889999999999999999999999999999999999999999999999999999999877643
No 6
>KOG0842|consensus
Probab=99.79 E-value=1.1e-19 Score=147.64 Aligned_cols=71 Identities=32% Similarity=0.583 Sum_probs=65.1
Q ss_pred hhhccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHHHHhhc
Q psy4868 55 KRKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLRNQRQR 125 (169)
Q Consensus 55 ~~k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~~~~~ 125 (169)
++++||.|..|+..|+.+||+.|...+|++..+|+.||..|.||+.||||||||||.|.||+++.......
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~ 220 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEAL 220 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcc
Confidence 66778889999999999999999999999999999999999999999999999999999998886655433
No 7
>KOG0487|consensus
Probab=99.79 E-value=4.9e-20 Score=149.64 Aligned_cols=69 Identities=29% Similarity=0.463 Sum_probs=63.8
Q ss_pred hhhhhccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHHH
Q psy4868 53 RLKRKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLRN 121 (169)
Q Consensus 53 ~~~~k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~ 121 (169)
...+..||+|+.+|+.|+.+||+.|..|.|++.+.|.+|++.|+|+++||+|||||||+|+||..+...
T Consensus 230 ~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 230 SSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred ccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence 334778899999999999999999999999999999999999999999999999999999999887444
No 8
>KOG2251|consensus
Probab=99.76 E-value=2.6e-18 Score=132.39 Aligned_cols=67 Identities=55% Similarity=0.919 Sum_probs=64.3
Q ss_pred hhhhccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHH
Q psy4868 54 LKRKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLR 120 (169)
Q Consensus 54 ~~~k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~ 120 (169)
..+|.||.||.|+..|+.+||.+|.+.+||+...|++||.+|+|.+.+|+|||+|||+|+|++++.+
T Consensus 33 ~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 33 GPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred cchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 4789999999999999999999999999999999999999999999999999999999999988865
No 9
>KOG0843|consensus
Probab=99.76 E-value=7e-19 Score=131.65 Aligned_cols=65 Identities=37% Similarity=0.611 Sum_probs=61.4
Q ss_pred hhccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHH
Q psy4868 56 RKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLR 120 (169)
Q Consensus 56 ~k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~ 120 (169)
.+.||.||.|+.+|+..||..|+.++|....+|+.||..|+|++.||+|||||||.|.||.+...
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 47889999999999999999999999999999999999999999999999999999999876654
No 10
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.74 E-value=5.1e-18 Score=106.29 Aligned_cols=57 Identities=42% Similarity=0.762 Sum_probs=55.0
Q ss_pred cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 59 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
|+.|+.|+.+|+.+|+.+|..++||+..+++.||..|||+..+|++||+|+|.++||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 578999999999999999999999999999999999999999999999999999886
No 11
>KOG0492|consensus
Probab=99.72 E-value=6.2e-18 Score=129.14 Aligned_cols=74 Identities=28% Similarity=0.559 Sum_probs=66.5
Q ss_pred hhhhhccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHHHHhhcC
Q psy4868 53 RLKRKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLRNQRQRG 126 (169)
Q Consensus 53 ~~~~k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~~~~~~ 126 (169)
.+.+..|+.||.||..||..||+.|...+|+++.+|.+++..|.|++.||+|||||||+|.||.+......-..
T Consensus 139 rKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~Ek~km 212 (246)
T KOG0492|consen 139 RKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELEKLKM 212 (246)
T ss_pred cccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHHHhhh
Confidence 34566778899999999999999999999999999999999999999999999999999999998877664333
No 12
>KOG0494|consensus
Probab=99.71 E-value=1e-17 Score=131.84 Aligned_cols=65 Identities=60% Similarity=0.965 Sum_probs=60.1
Q ss_pred hccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHHH
Q psy4868 57 KLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLRN 121 (169)
Q Consensus 57 k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~ 121 (169)
|+|+.||.||..|+..||..|....||+...|+.||..+.|.+..|+|||||||+||||.++...
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg 204 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWG 204 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcC
Confidence 34445999999999999999999999999999999999999999999999999999999988654
No 13
>KOG0848|consensus
Probab=99.71 E-value=1.1e-17 Score=132.05 Aligned_cols=65 Identities=37% Similarity=0.660 Sum_probs=60.0
Q ss_pred hccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHHH
Q psy4868 57 KLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLRN 121 (169)
Q Consensus 57 k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~ 121 (169)
.+-|-|.++|..|..+||+.|..++|.++..+.+||..|+|+++||+|||||||+|+||..+...
T Consensus 198 TkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 198 TKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred cccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 34456889999999999999999999999999999999999999999999999999999888763
No 14
>KOG0491|consensus
Probab=99.69 E-value=2.7e-17 Score=121.51 Aligned_cols=68 Identities=35% Similarity=0.681 Sum_probs=62.1
Q ss_pred hhhhhccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHH
Q psy4868 53 RLKRKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLR 120 (169)
Q Consensus 53 ~~~~k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~ 120 (169)
...-++++.|++|+..|+..|++.|+...|++..++.+||..|+|++.||+.||||||+|-||+.+..
T Consensus 95 ~~~~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~ 162 (194)
T KOG0491|consen 95 RLHCRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNN 162 (194)
T ss_pred hHHHHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence 34556678899999999999999999999999999999999999999999999999999999877743
No 15
>KOG0493|consensus
Probab=99.67 E-value=6.8e-17 Score=127.29 Aligned_cols=59 Identities=39% Similarity=0.745 Sum_probs=56.2
Q ss_pred ccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 58 LQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 58 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
-||.||.|+.+||..|+..|+.++|++...|.+||.+|+|.+.||+|||||+|+|.||-
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 36789999999999999999999999999999999999999999999999999999874
No 16
>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=99.62 E-value=4.2e-16 Score=97.62 Aligned_cols=53 Identities=23% Similarity=0.425 Sum_probs=50.8
Q ss_pred ccCCCCCCCHHHHHHHHHHHHhcCC----CCHHHHHHHHHHhCCCchhHhhhhhhhH
Q psy4868 58 LQRNRTSFTNDQIDNLEKEFERTHY----PDVFARERLAAKIGLPEARIQVWFSNRR 110 (169)
Q Consensus 58 ~rr~Rt~~t~~q~~~Le~~F~~~~~----p~~~~~~~La~~l~l~~~qV~~WFqNrR 110 (169)
+||.||.|+.+|+..|+.+|..++| |+..++.+||..|||++.+|+|||||.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 3788999999999999999999999 9999999999999999999999999964
No 17
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.62 E-value=1.4e-15 Score=95.33 Aligned_cols=56 Identities=52% Similarity=0.943 Sum_probs=53.4
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 60 RNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 60 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
+.|..|+..++.+|+.+|..++||+..++..||..+||+..+|++||+|+|.+.++
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 56788999999999999999999999999999999999999999999999999875
No 18
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.61 E-value=1.1e-15 Score=95.13 Aligned_cols=54 Identities=59% Similarity=1.060 Sum_probs=51.5
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHH
Q psy4868 60 RNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKW 113 (169)
Q Consensus 60 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~ 113 (169)
+.|+.|+..|+.+|+..|..++||+..++..||..+||+..+|++||+|+|.+.
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~ 55 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKW 55 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhcc
Confidence 567889999999999999999999999999999999999999999999999875
No 19
>KOG0844|consensus
Probab=99.61 E-value=5.6e-16 Score=124.52 Aligned_cols=63 Identities=48% Similarity=0.728 Sum_probs=58.8
Q ss_pred hccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHH
Q psy4868 57 KLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKL 119 (169)
Q Consensus 57 k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~ 119 (169)
.-||.||.||.+||..||+.|-+-.|.+...|.+||..|+|.+..|+|||||||+|+||+...
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 357789999999999999999999999999999999999999999999999999999997653
No 20
>KOG0486|consensus
Probab=99.58 E-value=1.6e-15 Score=122.26 Aligned_cols=67 Identities=48% Similarity=0.863 Sum_probs=63.3
Q ss_pred hhhccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHHH
Q psy4868 55 KRKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLRN 121 (169)
Q Consensus 55 ~~k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~ 121 (169)
..|+||.|+.|+..|+..||..|.++.||+...|++||...+|++..|+|||.|||+||||+++-..
T Consensus 109 i~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 109 ISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 3478899999999999999999999999999999999999999999999999999999999888655
No 21
>KOG3802|consensus
Probab=99.57 E-value=1.4e-15 Score=126.24 Aligned_cols=64 Identities=28% Similarity=0.447 Sum_probs=60.0
Q ss_pred hhhccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 55 KRKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 55 ~~k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
..|+||+||.|....+..||.+|..|+.|+..++..||.+|+|...+|+|||||||+|.||...
T Consensus 291 ~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 291 QSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 3478889999999999999999999999999999999999999999999999999999998554
No 22
>KOG0483|consensus
Probab=99.56 E-value=1.9e-15 Score=116.47 Aligned_cols=60 Identities=32% Similarity=0.665 Sum_probs=55.2
Q ss_pred cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 59 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
.+++.+|+.+|+..||..|..+.++....+..||..|||.++||.|||||||++||.++.
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kql 110 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQL 110 (198)
T ss_pred ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhh
Confidence 344566999999999999999999999999999999999999999999999999997744
No 23
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.55 E-value=5.5e-15 Score=110.31 Aligned_cols=65 Identities=31% Similarity=0.585 Sum_probs=59.0
Q ss_pred hhccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHH
Q psy4868 56 RKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLR 120 (169)
Q Consensus 56 ~k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~ 120 (169)
...+++|++.+.+|+.+|+..|..++||+...+..|+..|+|+++-|++||||+|++.|+.....
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~ 113 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGK 113 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccc
Confidence 34467788899999999999999999999999999999999999999999999999999876643
No 24
>KOG0847|consensus
Probab=99.47 E-value=2.6e-14 Score=110.31 Aligned_cols=67 Identities=36% Similarity=0.703 Sum_probs=61.3
Q ss_pred hhccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHHHH
Q psy4868 56 RKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLRNQ 122 (169)
Q Consensus 56 ~k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~~ 122 (169)
.+++..|..|+-.|+..|+..|+...|+-..++.+||..+|+++.||+|||||||.||||+......
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEma 231 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMA 231 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchh
Confidence 4556678899999999999999999999999999999999999999999999999999998766544
No 25
>KOG4577|consensus
Probab=99.45 E-value=7.2e-14 Score=111.71 Aligned_cols=63 Identities=37% Similarity=0.587 Sum_probs=60.0
Q ss_pred ccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHH
Q psy4868 58 LQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLR 120 (169)
Q Consensus 58 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~ 120 (169)
.||.||.++..||..|+..|...+.|-...|+.|+.++||.-++|||||||||+|+||.++..
T Consensus 167 nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T KOG4577|consen 167 NKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T ss_pred cCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence 488999999999999999999999999999999999999999999999999999999987754
No 26
>KOG0490|consensus
Probab=99.32 E-value=6.6e-13 Score=104.49 Aligned_cols=64 Identities=47% Similarity=0.652 Sum_probs=61.3
Q ss_pred hhhccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 55 KRKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 55 ~~k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
..++++.|+.|+..|+.+|++.|...+||+...++.||..+++++..|++||||||+||++..+
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 6778899999999999999999999999999999999999999999999999999999998775
No 27
>KOG0775|consensus
Probab=99.21 E-value=6.9e-11 Score=94.08 Aligned_cols=48 Identities=27% Similarity=0.478 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHH
Q psy4868 67 NDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114 (169)
Q Consensus 67 ~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~k 114 (169)
..-..+|..+|..++||+..++.+||..+||+..||-+||+|||+++|
T Consensus 185 ekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 185 EKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred HhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 344679999999999999999999999999999999999999999998
No 28
>KOG0849|consensus
Probab=99.18 E-value=1.8e-11 Score=102.57 Aligned_cols=66 Identities=58% Similarity=1.025 Sum_probs=61.9
Q ss_pred hhhhhccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 53 RLKRKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 53 ~~~~k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
..+++.+|.|+.|+..|+..|+..|..++||+...|+.||.++++++..|++||+|||++++|...
T Consensus 171 ~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 171 ALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred cccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 346778888999999999999999999999999999999999999999999999999999999774
No 29
>KOG1168|consensus
Probab=99.14 E-value=1.2e-11 Score=99.15 Aligned_cols=62 Identities=29% Similarity=0.447 Sum_probs=57.6
Q ss_pred hccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 57 KLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 57 k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
-+||+||.+-......||.+|...+.|+.+.+..||.+|+|...+|+|||||.|+|.||...
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence 45788999999999999999999999999999999999999999999999999999888554
No 30
>KOG0774|consensus
Probab=98.98 E-value=1.1e-09 Score=86.75 Aligned_cols=63 Identities=24% Similarity=0.521 Sum_probs=56.7
Q ss_pred ccCCCCCCCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHH
Q psy4868 58 LQRNRTSFTNDQIDNLEKEFE---RTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLR 120 (169)
Q Consensus 58 ~rr~Rt~~t~~q~~~Le~~F~---~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~ 120 (169)
.+|+|..|++.-..+|..+|. .++||+...+++||.+++++..||-.||.|+|-+++|-....
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~ 253 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKN 253 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhh
Confidence 467788899999999999995 588999999999999999999999999999999999865543
No 31
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.70 E-value=1.7e-08 Score=58.67 Aligned_cols=34 Identities=35% Similarity=0.665 Sum_probs=28.8
Q ss_pred hcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHH
Q psy4868 79 RTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112 (169)
Q Consensus 79 ~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k 112 (169)
.++||+..++..||..+||+..||..||-|.|.+
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4789999999999999999999999999999864
No 32
>KOG2252|consensus
Probab=98.52 E-value=1.4e-07 Score=81.72 Aligned_cols=57 Identities=21% Similarity=0.331 Sum_probs=53.2
Q ss_pred hccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHH
Q psy4868 57 KLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKW 113 (169)
Q Consensus 57 k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~ 113 (169)
+.||.|.+|+..|+..|..+|+.+++|+....+.|+.+|+|....|.+||-|-|.+.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 346779999999999999999999999999999999999999999999999988764
No 33
>KOG0490|consensus
Probab=98.23 E-value=1e-06 Score=69.11 Aligned_cols=64 Identities=48% Similarity=0.764 Sum_probs=59.4
Q ss_pred hhhccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 55 KRKLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 55 ~~k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
..+.++.|+.+...|+..|...|....+|+...++.|+..+|++...|++||+|+|.+.++...
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 4566788999999999999999999999999999999999999999999999999999987655
No 34
>KOG1146|consensus
Probab=97.81 E-value=1.9e-05 Score=74.54 Aligned_cols=62 Identities=32% Similarity=0.465 Sum_probs=57.4
Q ss_pred hccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 57 KLQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 57 k~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
.+++.|++++..||.+|..+|....||...+.+.|...+++..+.|++||||-|.|.++...
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 34667999999999999999999999999999999999999999999999999999887655
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.54 E-value=7.8e-05 Score=46.10 Aligned_cols=41 Identities=20% Similarity=0.332 Sum_probs=31.1
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhH
Q psy4868 70 IDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRR 110 (169)
Q Consensus 70 ~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR 110 (169)
+..|+++|....++.......|..+.+|+..||+.||--++
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 45699999999999999999999999999999999996554
No 36
>KOG0773|consensus
Probab=96.89 E-value=0.00063 Score=56.86 Aligned_cols=64 Identities=19% Similarity=0.264 Sum_probs=52.1
Q ss_pred ccCCCCCCCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHHH
Q psy4868 58 LQRNRTSFTNDQIDNLEKEFE---RTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLRN 121 (169)
Q Consensus 58 ~rr~Rt~~t~~q~~~Le~~F~---~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~ 121 (169)
..|.+..+......+|+.+.. ..+||+..++..||.++||+..||.+||.|.|-+.-+-.....
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~~ 305 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIEEM 305 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHHHH
Confidence 445566888999999998743 2579999999999999999999999999999988766555433
No 37
>KOG3623|consensus
Probab=96.58 E-value=0.0065 Score=55.08 Aligned_cols=49 Identities=22% Similarity=0.404 Sum_probs=45.0
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 70 IDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 70 ~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
+.+|..+|..|..|+..+...+|.++||..+.|+.||+++++.....++
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~r 616 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVER 616 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhcc
Confidence 7889999999999999999999999999999999999999998766443
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=95.79 E-value=0.027 Score=34.37 Aligned_cols=47 Identities=19% Similarity=0.386 Sum_probs=35.4
Q ss_pred cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhH
Q psy4868 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRR 110 (169)
Q Consensus 59 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR 110 (169)
||+|..+|-++...+-..++... ....||..+|+...+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 46788999999888888887664 578899999999999999998853
No 39
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=90.31 E-value=0.97 Score=26.64 Aligned_cols=46 Identities=11% Similarity=0.265 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~k 114 (169)
.+++.+..+|...|... ....++|..+|++...|+.+...-..|.|
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 46788889999888322 34678999999999999998765554443
No 40
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=87.61 E-value=1.2 Score=27.23 Aligned_cols=41 Identities=22% Similarity=0.418 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHHHhcCC--CCHHHHHHHHHHhCCCchhHhhh
Q psy4868 65 FTNDQIDNLEKEFERTHY--PDVFARERLAAKIGLPEARIQVW 105 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~--p~~~~~~~La~~l~l~~~qV~~W 105 (169)
+|..|..+|...|...-| |-.....+||..||++...|..-
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~ 43 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEH 43 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHH
Confidence 578899999999997765 66667789999999999866543
No 41
>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=84.26 E-value=2.9 Score=24.79 Aligned_cols=42 Identities=12% Similarity=0.225 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRA 111 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~ 111 (169)
+++.+..++...|.. .....++|..+|++...|+.|.+.-|.
T Consensus 11 L~~~~r~i~~l~~~~-----g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 11 LPERQREIFLLRYFQ-----GMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHH-----CcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 455566666555443 346789999999999999999875444
No 42
>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=83.43 E-value=1 Score=28.67 Aligned_cols=44 Identities=14% Similarity=0.262 Sum_probs=28.3
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhh
Q psy4868 60 RNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 60 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFq 107 (169)
+.|..|+.++...+-..+... ......+|..+||++.+|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~----g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES----GESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH----HCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC----CCceEeeecccccccccccHHHH
Confidence 356779998877666655222 24578899999999999999963
No 43
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=81.49 E-value=6.9 Score=28.81 Aligned_cols=53 Identities=17% Similarity=0.224 Sum_probs=41.2
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHH
Q psy4868 62 RTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLR 120 (169)
Q Consensus 62 Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~ 120 (169)
...+++.|..+|...+ . . ....+||..||++...|..|..+.+.+.++....-
T Consensus 4 ~~~Lt~rqreVL~lr~-~-G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl 56 (141)
T PRK03975 4 ESFLTERQIEVLRLRE-R-G----LTQQEIADILGTSRANVSSIEKRARENIEKARETL 56 (141)
T ss_pred ccCCCHHHHHHHHHHH-c-C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3568899999997743 2 1 24678999999999999999998888877765544
No 44
>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=81.43 E-value=2.3 Score=24.29 Aligned_cols=43 Identities=12% Similarity=0.251 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k 112 (169)
++..+..++...|... .....+|..+|++...|..|...-+.+
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 5677777777766422 246778999999999999998655443
No 45
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=79.65 E-value=3.5 Score=32.05 Aligned_cols=49 Identities=20% Similarity=0.370 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHHhcCC--CCHHHHHHHHHHhCCCchhHhhhhhhhHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHY--PDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~--p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~k 114 (169)
.+|..|+.+|...|...-| |-.....+||.+||++... +|..=||+..|
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst--~~ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST--LSEHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH--HHHHHHHHHHH
Confidence 5999999999999997764 7777779999999999874 45555555533
No 46
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=79.36 E-value=1.6 Score=27.44 Aligned_cols=20 Identities=30% Similarity=0.625 Sum_probs=17.6
Q ss_pred HHHHHHHHhCCCchhHhhhh
Q psy4868 87 ARERLAAKIGLPEARIQVWF 106 (169)
Q Consensus 87 ~~~~La~~l~l~~~qV~~WF 106 (169)
...+||.+||+++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 45689999999999999994
No 47
>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=79.17 E-value=5.8 Score=24.69 Aligned_cols=45 Identities=18% Similarity=0.218 Sum_probs=22.8
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhh
Q psy4868 62 RTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 62 Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFq 107 (169)
|..|+.......-.+|....---...|. .|.++|+++.+|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 4456665544333444433322223344 49999999999999975
No 48
>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=74.82 E-value=1.7 Score=28.33 Aligned_cols=35 Identities=11% Similarity=0.111 Sum_probs=25.8
Q ss_pred HHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhh
Q psy4868 74 EKEFERTHYPDVFARERLAAKIGLPEARIQVWFSN 108 (169)
Q Consensus 74 e~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqN 108 (169)
+..|....|.......+||..+|++...|+.|+.+
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 33444444444455789999999999999999875
No 49
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=74.04 E-value=9.7 Score=19.19 Aligned_cols=37 Identities=14% Similarity=0.346 Sum_probs=25.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhh
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWF 106 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF 106 (169)
++..+...+...|... + ....+|..++++...|..|.
T Consensus 6 ~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 5566666666666532 2 45678899999999998884
No 50
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=73.26 E-value=11 Score=26.53 Aligned_cols=42 Identities=12% Similarity=0.166 Sum_probs=28.7
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhh
Q psy4868 62 RTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 62 Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFq 107 (169)
|..|+.++....-.....+.+ ...++|..+|++..+|..|.+
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHH
Confidence 456788775544333333332 366789999999999999954
No 51
>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=73.20 E-value=9 Score=23.10 Aligned_cols=45 Identities=16% Similarity=0.250 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~k 114 (169)
.||+.++.+|.....- ....++|..+++++..|..+..+=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG------MSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTT------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhc------CCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 4788888888776553 24788999999999999999877666643
No 52
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=72.21 E-value=8.6 Score=29.04 Aligned_cols=48 Identities=10% Similarity=0.254 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
.++..+..+|...|... ....+||..||++...|+++...-|.+.|+.
T Consensus 142 ~L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 46777777776655332 3467899999999999999997766666553
No 53
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=71.40 E-value=9.8 Score=29.12 Aligned_cols=49 Identities=14% Similarity=0.239 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~ 117 (169)
.+++.+..+|...|-.. ....+||..+|++...|++++..-+.+.++..
T Consensus 153 ~L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE-----LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35666667766544322 34688999999999999999877666665543
No 54
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=70.27 E-value=8.8 Score=27.49 Aligned_cols=47 Identities=9% Similarity=0.042 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.+..++...|-.. ....+||..+|++...|+.|...-+.+.|+
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 46677777776655433 347889999999999999998765555543
No 55
>KOG1146|consensus
Probab=69.80 E-value=5.1 Score=39.30 Aligned_cols=60 Identities=17% Similarity=0.265 Sum_probs=54.2
Q ss_pred ccCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHH
Q psy4868 58 LQRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117 (169)
Q Consensus 58 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~ 117 (169)
.++-+..+-.+++..|-.+|-.+.-|+...+..|......+.+++.+||+|-|.+.++..
T Consensus 705 ~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 705 DKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred cccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 456677888899999999999999999999999999999999999999999999988764
No 56
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=69.78 E-value=10 Score=27.74 Aligned_cols=48 Identities=15% Similarity=0.192 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
.+++.+..+|...|... ....++|..+|++...|+.|...-+.+.|+.
T Consensus 128 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 47788888887765422 2367899999999999999998666555543
No 57
>PRK04217 hypothetical protein; Provisional
Probab=68.73 E-value=17 Score=25.50 Aligned_cols=48 Identities=13% Similarity=0.144 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
.++.++..++...|.... ...+||..+|++...|...+..-+.+.+..
T Consensus 42 ~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~ 89 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQM 89 (110)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467888877776664332 467899999999999999987766666543
No 58
>PRK10072 putative transcriptional regulator; Provisional
Probab=68.27 E-value=8.3 Score=26.43 Aligned_cols=41 Identities=20% Similarity=0.289 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRA 111 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~ 111 (169)
+.+...+..|...... ...+||..+|++...|..|.+.+|.
T Consensus 32 ~~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 3456666666443222 2678999999999999999988764
No 59
>KOG3755|consensus
Probab=68.26 E-value=4.9 Score=36.37 Aligned_cols=45 Identities=18% Similarity=0.165 Sum_probs=29.9
Q ss_pred HHHHHhcCCCCHHHHHHHHHHhCC-------CchhHhhhhhhhHHHHHHHHH
Q psy4868 74 EKEFERTHYPDVFARERLAAKIGL-------PEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 74 e~~F~~~~~p~~~~~~~La~~l~l-------~~~qV~~WFqNrR~k~kk~~~ 118 (169)
+.+|..+..+......+.-..+.+ ..+.|+.||.|||.++++.+-
T Consensus 708 ~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~ 759 (769)
T KOG3755|consen 708 HHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKM 759 (769)
T ss_pred hhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhc
Confidence 445566666665555544444433 457799999999999987543
No 60
>PRK00118 putative DNA-binding protein; Validated
Probab=67.67 E-value=19 Score=25.00 Aligned_cols=48 Identities=10% Similarity=0.128 Sum_probs=35.1
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~ 117 (169)
++..|..++...|... ....+||..+|++...|..|...-|.+.|...
T Consensus 18 L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~ 65 (104)
T PRK00118 18 LTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYE 65 (104)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4566666666555442 24678999999999999999987777766543
No 61
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=67.67 E-value=6.7 Score=22.60 Aligned_cols=40 Identities=13% Similarity=0.287 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhh
Q psy4868 63 TSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 63 t~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFq 107 (169)
..++.++...++.++... .-..+||..||.+...|..|.+
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 457888888888776533 4467799999999999988764
No 62
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=66.52 E-value=17 Score=26.41 Aligned_cols=47 Identities=13% Similarity=0.221 Sum_probs=33.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
+++.+..+|...|... ....+||..+|++...|..|...-|.+.|+.
T Consensus 126 L~~~~r~i~~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 126 LPVKQREVFLLRYVEG-----LSYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CCHHHHHHhhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5666666666554332 3457899999999999999997766666543
No 63
>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=66.30 E-value=5.7 Score=22.74 Aligned_cols=21 Identities=14% Similarity=0.162 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCchhHhhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFSN 108 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqN 108 (169)
..++|..+|++...|+.|.+.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 467899999999999999643
No 64
>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=65.28 E-value=14 Score=25.67 Aligned_cols=47 Identities=13% Similarity=0.244 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.+..++...|-. .....+||..+|++...|..|...-+.+.|+
T Consensus 110 ~L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 3567777776555432 2346789999999999999998766655543
No 65
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=65.24 E-value=16 Score=27.04 Aligned_cols=46 Identities=15% Similarity=0.395 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
+++.+..+|...|-.. ....+||..+|++...|++++..-|.+.|+
T Consensus 130 L~~~~r~i~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 130 LEKDRAAAVRRAYLEG-----LSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 5556666565555322 236889999999999999998776666654
No 66
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=65.12 E-value=15 Score=27.28 Aligned_cols=49 Identities=16% Similarity=0.111 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~ 117 (169)
.+++.+..+|...|... ....+||..||++...|+.++..-|.+.|..-
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 46677777777765432 34678999999999999999987777766543
No 67
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=65.05 E-value=11 Score=28.27 Aligned_cols=47 Identities=17% Similarity=0.280 Sum_probs=33.7
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
+++.+..+|...|.. .....+||..+|++...|+.|+..-|.+.|+.
T Consensus 142 L~~~~~~v~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 142 LPESQRQVLELAYYE-----GLSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred CCHHHhhhhhhhhhc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 556666666554422 23468899999999999999997777666653
No 68
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=65.04 E-value=16 Score=26.36 Aligned_cols=48 Identities=6% Similarity=0.089 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
.+++.+..++...|-.. ....+||..+|++...|++++..-|.+.|+.
T Consensus 106 ~Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 106 ELPENYRDVVLAHYLEE-----KSYQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred hCCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 36666666666554332 2357899999999999999998766666654
No 69
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=65.02 E-value=25 Score=25.43 Aligned_cols=48 Identities=17% Similarity=0.317 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~ 117 (169)
.++..+..+|...| . . ....+||..+|++...|+.+...-|.+.|+.-
T Consensus 112 ~L~~~~r~il~l~~-~-g----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 112 KMTERDRTVLLLRF-S-G----YSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCHHHHHHHHHHH-c-C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46777777777766 3 2 24678999999999999999977666666543
No 70
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=65.00 E-value=19 Score=26.18 Aligned_cols=49 Identities=8% Similarity=-0.002 Sum_probs=34.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 63 TSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 63 t~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
..+++.+..+|...|-.. ....+||..+|++...|++|.+.-|.+.|+.
T Consensus 107 ~~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 155 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE-----LTYEEAASVLDLKLNTYKSHLFRGRKRLKAL 155 (165)
T ss_pred HhCCHHHHHHHHhHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 345666666665443322 3468899999999999999988666666554
No 71
>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=64.34 E-value=16 Score=26.00 Aligned_cols=47 Identities=9% Similarity=0.087 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.++..+..+|...|-. . ....+||..+|++...|+.+...-+.+.|+
T Consensus 113 ~L~~~~r~il~l~~~~-~----~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRFE-G----KSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHHc-C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 3566666676664432 2 246789999999999999988765555543
No 72
>PF13518 HTH_28: Helix-turn-helix domain
Probab=63.30 E-value=8.8 Score=22.21 Aligned_cols=23 Identities=13% Similarity=0.450 Sum_probs=19.2
Q ss_pred HHHHHHHHhCCCchhHhhhhhhh
Q psy4868 87 ARERLAAKIGLPEARIQVWFSNR 109 (169)
Q Consensus 87 ~~~~La~~l~l~~~qV~~WFqNr 109 (169)
...++|..+|++..+|..|.+.-
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y 36 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRY 36 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHH
Confidence 35679999999999999998643
No 73
>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=63.23 E-value=15 Score=26.32 Aligned_cols=47 Identities=19% Similarity=0.253 Sum_probs=33.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHH
Q psy4868 63 TSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114 (169)
Q Consensus 63 t~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~k 114 (169)
..+++.+..++...|-. .....+||..+|++...|+++...-|.+.+
T Consensus 110 ~~L~~~~r~v~~l~~~~-----g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 110 EKLPERQRELLQLRYQR-----GVSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred HHCCHHHHHHHHHHHhc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 34677777777765432 234788999999999999998765555443
No 74
>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=62.90 E-value=21 Score=26.33 Aligned_cols=49 Identities=12% Similarity=0.188 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~ 117 (169)
.+++.+..+|...|... ....+||..+|++...|+++...-|.+.++..
T Consensus 100 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46777777777665433 34688999999999999999876666655543
No 75
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=62.73 E-value=17 Score=27.08 Aligned_cols=48 Identities=17% Similarity=0.153 Sum_probs=35.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 63 TSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 63 t~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
..+++.+..++...|-.. ....+||..+|++...|+.+...-|.+.|+
T Consensus 138 ~~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 138 DTLPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred HhCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 456777777777665432 347889999999999999998666655554
No 76
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=62.42 E-value=14 Score=26.78 Aligned_cols=47 Identities=17% Similarity=0.186 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.|..+|.-.|... ....++|..+|++...|+++...-|.+.++
T Consensus 112 ~L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 112 SLPLERRNVLLLRDYYG-----FSYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HCCHHHHHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 46676766666654332 246789999999999999998766666554
No 77
>PRK06930 positive control sigma-like factor; Validated
Probab=61.42 E-value=24 Score=26.57 Aligned_cols=50 Identities=10% Similarity=0.107 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
.+++.+..+|...|... ....++|..+|++...|+.++..-+.+.++...
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46777777777654332 246789999999999999999877777766443
No 78
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=61.34 E-value=19 Score=26.52 Aligned_cols=46 Identities=17% Similarity=0.164 Sum_probs=34.3
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
+.+.+..++...|-.. ....++|..||++...|++....-|.+.|+
T Consensus 135 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG-----LTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 6666777776655432 246789999999999999999877766654
No 79
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=61.05 E-value=18 Score=26.75 Aligned_cols=48 Identities=8% Similarity=0.190 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
.+++.+..+|...|-. .....++|..+|++...|+++++.-|.+.|..
T Consensus 136 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME-----DLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4667777777664432 23467899999999999999998777666653
No 80
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=60.82 E-value=25 Score=26.37 Aligned_cols=49 Identities=8% Similarity=0.095 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~ 117 (169)
.+++.+..++...|-.. ....+||..+|+++..|+++...-|.+.|+..
T Consensus 134 ~Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 134 HLPAQQARVFMMREYLE-----LSSEQICQECDISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred hCCHHHHHHHhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35666667666655432 23678999999999999999877666666543
No 81
>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=60.76 E-value=16 Score=27.14 Aligned_cols=47 Identities=11% Similarity=0.081 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
+++.+..++...|. ....-.+||..+|++...|+++...-|.+.|+.
T Consensus 139 L~~~~r~v~~l~~~-----~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 139 LPEDLRTAITLREL-----EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred CCHHHhhhhhhhhh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 44555555544432 223468899999999999999987666665543
No 82
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=60.52 E-value=20 Score=21.82 Aligned_cols=36 Identities=22% Similarity=0.307 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhh
Q psy4868 68 DQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 68 ~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFq 107 (169)
.|+..|+-.|. +...+. .+||..+|++.+.|+.-..
T Consensus 6 rq~~Ll~~L~~-~~~~~~---~ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITL---KELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHH-HTSBBH---HHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcH---HHHHHHHCCCHHHHHHHHH
Confidence 57888888888 666654 4899999999999887653
No 83
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=60.48 E-value=26 Score=26.16 Aligned_cols=49 Identities=12% Similarity=0.212 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~ 117 (169)
.+++.+..+|...|... ....++|..+|++...|++.+..-|.+.++.-
T Consensus 131 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE-----KSVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 46777777776655432 34678999999999999999877777666543
No 84
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=60.38 E-value=18 Score=26.94 Aligned_cols=47 Identities=11% Similarity=0.190 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
+++.+..+|...|-. .....+||..+|++...|+.+...-|.+.|+.
T Consensus 129 L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 175 (186)
T PRK05602 129 LPERQREAIVLQYYQ-----GLSNIEAAAVMDISVDALESLLARGRRALRAQ 175 (186)
T ss_pred CCHHHHHHhhHHHhc-----CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 556666666554432 23467899999999999999987666666554
No 85
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=60.20 E-value=20 Score=26.84 Aligned_cols=49 Identities=14% Similarity=0.189 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~ 117 (169)
.+++.+..+|...|-.. ....+||..+|++...|+..+..-|.+.++.-
T Consensus 106 ~L~~~~r~i~~l~~~~g-----~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 106 ALPEKYAEALRLTELEG-----LSQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 35666666666554322 34688999999999999999976666655533
No 86
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=59.93 E-value=23 Score=25.42 Aligned_cols=47 Identities=13% Similarity=0.162 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.+..++.-.|-.. ....+||..||++...|++....-|.+.|+
T Consensus 106 ~Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 106 KLPARQREAFLLRYWED-----MDVAETAAAMGCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred hCCHHHHHHHHHHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46677777776654332 236789999999999999988766655554
No 87
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=59.29 E-value=8.9 Score=22.20 Aligned_cols=23 Identities=13% Similarity=0.559 Sum_probs=17.4
Q ss_pred HHHHHHHHHhCCCchhHhhhhhh
Q psy4868 86 FARERLAAKIGLPEARIQVWFSN 108 (169)
Q Consensus 86 ~~~~~La~~l~l~~~qV~~WFqN 108 (169)
....++|..||++...|..|.+.
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 34678999999999999999754
No 88
>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=58.73 E-value=22 Score=25.67 Aligned_cols=47 Identities=13% Similarity=0.198 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
+++.+..+|...|-. .....++|..+|++...|+++...-|.+.|+.
T Consensus 111 L~~~~r~i~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 111 LPARQRAVVVLRYYE-----DLSEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred CCHHHHHHhhhHHHh-----cCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 556666676665532 23467899999999999999987777766653
No 89
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=58.65 E-value=23 Score=26.33 Aligned_cols=47 Identities=11% Similarity=0.332 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.+..++...|-.+ ....++|..+|++...|++|...-+.+.|+
T Consensus 133 ~L~~~~r~i~~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 133 QLEPARRNCILHAYVDG-----CSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 35566666555554322 346789999999999999998766655544
No 90
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=58.38 E-value=33 Score=19.55 Aligned_cols=42 Identities=21% Similarity=0.317 Sum_probs=29.4
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRA 111 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~ 111 (169)
.++..+..++...+. . ....++|..+|++...|..|...-+.
T Consensus 3 ~l~~~e~~i~~~~~~--g----~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 3 SLTPREREVLRLLAE--G----LTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred CCCHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 356777777755332 2 24578999999999999998864433
No 91
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=57.95 E-value=20 Score=27.05 Aligned_cols=50 Identities=16% Similarity=0.133 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
.+++.+..+|...|-. .....++|..||++...|++++..-|.+.|+.-.
T Consensus 113 ~Lp~~~r~v~~L~~~~-----g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 113 QLPDEQREALILVGAS-----GFSYEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred hCCHHHhHHhhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 3566666666554332 2246789999999999999999877777766544
No 92
>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=57.74 E-value=3.7 Score=25.44 Aligned_cols=21 Identities=19% Similarity=0.613 Sum_probs=18.4
Q ss_pred HHHHHHHHhCCCchhHhhhhh
Q psy4868 87 ARERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 87 ~~~~La~~l~l~~~qV~~WFq 107 (169)
...+||..||++...|..|-+
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH
Confidence 367899999999999999964
No 93
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=56.94 E-value=35 Score=25.54 Aligned_cols=50 Identities=8% Similarity=0.147 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
.+.+.+..++...|-.. ....+||..+|++...|+.+...-|.+.|+.-.
T Consensus 136 ~L~~~~r~i~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 136 NLPENTARVFTLKEILG-----FSSDEIQQMCGISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred hCCHHHHHHhhhHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35666666666544322 236789999999999999999877777666543
No 94
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=56.68 E-value=10 Score=23.43 Aligned_cols=20 Identities=10% Similarity=0.270 Sum_probs=17.2
Q ss_pred HHHHHHHhCCCchhHhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFq 107 (169)
..++|..+|++...|+.|=.
T Consensus 3 i~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999953
No 95
>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=56.56 E-value=11 Score=21.16 Aligned_cols=19 Identities=11% Similarity=0.223 Sum_probs=15.4
Q ss_pred HHHHHHHhCCCchhHhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWF 106 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WF 106 (169)
+.++|..+|++...|+.|=
T Consensus 2 i~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 3578999999999999994
No 96
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=55.90 E-value=41 Score=24.83 Aligned_cols=52 Identities=12% Similarity=0.253 Sum_probs=37.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLR 120 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~ 120 (169)
.+++.+..++...|-.. ....+||..+|++...|++....-|.+.|+.-...
T Consensus 117 ~Lp~~~r~i~~l~~~e~-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~ 168 (179)
T PRK12543 117 KLPYKLRQVIILRYLHD-----YSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIE 168 (179)
T ss_pred hCCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 36666666666544322 34678999999999999999988888887755433
No 97
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=55.86 E-value=10 Score=23.00 Aligned_cols=26 Identities=15% Similarity=0.369 Sum_probs=18.5
Q ss_pred HHHHHHHHhCCCchhHhhhhhhhHHH
Q psy4868 87 ARERLAAKIGLPEARIQVWFSNRRAK 112 (169)
Q Consensus 87 ~~~~La~~l~l~~~qV~~WFqNrR~k 112 (169)
....||..+|++...|..||.++...
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~ 37 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSN 37 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT---
T ss_pred CHHHHHHHHCcCHHHHHHHHhccccc
Confidence 46789999999999999999987433
No 98
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=55.64 E-value=26 Score=26.35 Aligned_cols=48 Identities=4% Similarity=0.036 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
.+++.+..++.-.|... ....+||..+|++...|++++..-|.+.|+.
T Consensus 136 ~L~~~~r~i~~L~~~~g-----~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 136 ALPERQRQAVVLRHIEG-----LSNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 46666666666554322 2367899999999999999997666666553
No 99
>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=55.06 E-value=28 Score=25.39 Aligned_cols=47 Identities=9% Similarity=0.266 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+...+..++...|-.. ....++|..||++...|+++...-|.+.|+
T Consensus 119 ~L~~~~r~i~~l~~~~g-----~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD-----LTIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred hCCHHHhHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35566666666554432 346789999999999999988766666554
No 100
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=54.59 E-value=30 Score=25.68 Aligned_cols=47 Identities=13% Similarity=0.039 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
+++.+..++...|.. .....++|..+|++...|++....-|.+.|+.
T Consensus 130 L~~~~r~v~~l~~~~-----g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 130 LPDRQRLPIVHVKLE-----GLSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 455555544443322 23467899999999999999997777766653
No 101
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=54.32 E-value=30 Score=25.17 Aligned_cols=48 Identities=21% Similarity=0.151 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
.+++.+..++...|... ....+||..+|++...|+++...-|.+.|..
T Consensus 112 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 112 LLSADQREAIILIGASG-----FSYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 35666666666554322 3468899999999999999987666665543
No 102
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=54.05 E-value=32 Score=24.77 Aligned_cols=47 Identities=9% Similarity=0.114 Sum_probs=32.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.+..+|...|-.. ....++|..+|++...|+.+...-+.+.|+
T Consensus 109 ~L~~~~r~v~~l~~~~~-----~s~~EIA~~lgis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 109 ELPARTRYAFEMYRLHG-----ETQKDIARELGVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35666666776554332 236889999999999999987655555554
No 103
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=52.87 E-value=28 Score=27.39 Aligned_cols=49 Identities=10% Similarity=0.154 Sum_probs=34.3
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
++..+..+|...|... ....+||..||++...|+++...-|.+.|+...
T Consensus 172 Lp~~~R~v~~L~~~eg-----~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 172 LPEQQRIAVILSYHEN-----MSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred CCHHHHHHhhhHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4555555555444322 346889999999999999999877777766443
No 104
>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=52.66 E-value=14 Score=20.58 Aligned_cols=23 Identities=13% Similarity=0.462 Sum_probs=19.0
Q ss_pred HHHHHHHhCCCchhHhhhhhhhH
Q psy4868 88 RERLAAKIGLPEARIQVWFSNRR 110 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqNrR 110 (169)
..++|..||++...|..|.++..
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCC
Confidence 46789999999999999986543
No 105
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.48 E-value=27 Score=23.66 Aligned_cols=39 Identities=13% Similarity=0.261 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHh
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQ 103 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~ 103 (169)
+.++|...-...|+.+--.+....+++|..|++++..|.
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHH
Confidence 456666666666666655566678899999999875543
No 106
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=52.40 E-value=43 Score=25.39 Aligned_cols=50 Identities=10% Similarity=0.067 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
.+++.+..++...|-.. ....+||..+|++...|++....-|.+.|+.-.
T Consensus 139 ~Lp~~~r~v~~L~~~eg-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 139 HLPEQIGRVFMMREFLD-----FEIDDICTELTLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35666666666554322 246789999999999999998877776665443
No 107
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=52.25 E-value=28 Score=27.21 Aligned_cols=48 Identities=17% Similarity=0.259 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
.+.+.+..+|...|... ....+||..+|++...|+.+...-+.+.|+.
T Consensus 184 ~L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 184 SLPEREQLVLSLYYQEE-----LNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred hCCHHHHHHHHhHhccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35677777776665332 3468899999999999999998877777654
No 108
>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=52.04 E-value=33 Score=24.76 Aligned_cols=47 Identities=17% Similarity=0.203 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.+..+|...|-.. ....+||..||++...|++...--|.+.|+
T Consensus 122 ~L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQN-----LPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46677777776654332 346789999999999999987555544443
No 109
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=51.93 E-value=35 Score=25.31 Aligned_cols=47 Identities=2% Similarity=0.037 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.|..++.-.|-.. ....+||..||++...|+.....-+.+.+.
T Consensus 127 ~Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG-----MKQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46777777777655432 246789999999999999998866666543
No 110
>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=51.86 E-value=13 Score=23.05 Aligned_cols=20 Identities=15% Similarity=0.293 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhHhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFq 107 (169)
..++|..+|++...|+.|.+
T Consensus 3 i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999975
No 111
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=51.75 E-value=26 Score=24.44 Aligned_cols=40 Identities=13% Similarity=0.390 Sum_probs=33.8
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRA 111 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~ 111 (169)
+++..+..+...+... ....|..||++..-|+.|=|+|+.
T Consensus 44 ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 44 LSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 7888888888877653 567899999999999999998764
No 112
>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=51.71 E-value=27 Score=19.99 Aligned_cols=37 Identities=11% Similarity=0.431 Sum_probs=25.5
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhh
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWF 106 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF 106 (169)
++.+++..+...+... ....+||..+|++...|.-++
T Consensus 6 ~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 6 LSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 5565666666666654 347889999999999888776
No 113
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=51.58 E-value=36 Score=25.18 Aligned_cols=48 Identities=10% Similarity=0.254 Sum_probs=33.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 63 TSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 63 t~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
..++..+..+|...|-.. ....+||..+|++...|+++...-|.+.|.
T Consensus 134 ~~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 134 KALSPEERRVIEVLYYQG-----YTHREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred HhCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 346777777776554322 346789999999999999988665555443
No 114
>smart00595 MADF subfamily of SANT domain.
Probab=51.44 E-value=39 Score=21.93 Aligned_cols=34 Identities=29% Similarity=0.459 Sum_probs=29.0
Q ss_pred HHHHHHhCCCchhHhhhhhhhHHHHHHHHHHHHH
Q psy4868 89 ERLAAKIGLPEARIQVWFSNRRAKWRREEKLRNQ 122 (169)
Q Consensus 89 ~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~~ 122 (169)
..||..+|.+...|+.-+.|-|..+++..+....
T Consensus 31 ~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~~~ 64 (89)
T smart00595 31 EEIAEELGLSVEECKKRWKNLRDRYRRELKRLQN 64 (89)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5689999999999999999999999987665544
No 115
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=51.29 E-value=39 Score=25.38 Aligned_cols=49 Identities=18% Similarity=0.156 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
+++.+..++...|-.. ....+||..||++...|+++...-|.+.++...
T Consensus 117 Lp~~~r~i~~L~~~~g-----~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 117 LPDDQREAIILVGASG-----FAYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5566666665544322 236789999999999999998776666665433
No 116
>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=50.65 E-value=45 Score=26.49 Aligned_cols=52 Identities=13% Similarity=0.315 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLR 120 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~ 120 (169)
.+...+..++.-.|-.. ....+||..+|++...|+++...-|.+.|+.-..+
T Consensus 161 ~Lp~~~R~v~~L~~~eg-----~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~ 212 (244)
T TIGR03001 161 ALSERERHLLRLHFVDG-----LSMDRIGAMYQVHRSTVSRWVAQARERLLERTRRR 212 (244)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 35555655555554322 23678999999999999999988887777655433
No 117
>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=50.58 E-value=15 Score=22.72 Aligned_cols=20 Identities=10% Similarity=0.232 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhHhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFq 107 (169)
..++|..+|++...|+.|-+
T Consensus 3 i~evA~~~gvs~~tlR~~~~ 22 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEK 22 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999975
No 118
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=50.42 E-value=34 Score=25.57 Aligned_cols=47 Identities=19% Similarity=0.245 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.+..++...|-.. ....+||..+|++...|++..+.-|.+.|+
T Consensus 131 ~L~~~~r~i~~l~~~~g-----~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG-----EKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred hCCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46777777776655322 346789999999999999987655555444
No 119
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=50.15 E-value=34 Score=26.61 Aligned_cols=48 Identities=10% Similarity=0.085 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
.+.+.+..+|...|... ....+||..||++...|+++...-|.+.++.
T Consensus 134 ~Lp~~~R~v~~L~y~eg-----~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~ 181 (216)
T PRK12533 134 KLPVEYREVLVLRELED-----MSYREIAAIADVPVGTVMSRLARARRRLAAL 181 (216)
T ss_pred cCCHHHHhHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45666666666655432 2367899999999999999987666665554
No 120
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=50.10 E-value=39 Score=24.65 Aligned_cols=46 Identities=17% Similarity=0.369 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
+++.+..+|...|-.. ....+||..||++...|+.+...-|.+.|+
T Consensus 119 L~~~~r~vl~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 119 LSPEHRAVLVRSYYRG-----WSTAQIAADLGIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 6677777776655332 236789999999999999988665555554
No 121
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=50.03 E-value=60 Score=24.19 Aligned_cols=51 Identities=10% Similarity=0.046 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKL 119 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~ 119 (169)
.+++.+..++...|-.. ....+||..+|++...|++....-|.+.|+....
T Consensus 131 ~Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 181 (191)
T PRK12520 131 RLPPRTGRVFMMREWLE-----LETEEICQELQITATNAWVLLYRARMRLRECLDL 181 (191)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 36666766666554332 2367899999999999999988777776655443
No 122
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=49.81 E-value=62 Score=24.16 Aligned_cols=47 Identities=23% Similarity=0.150 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
+.+.+..++...|.. .....+||..||++...|+.....-|.+.|+.
T Consensus 112 Lp~~~R~v~~L~~~~-----g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~ 158 (182)
T PRK12540 112 LPQDQREALILVGAS-----GFSYEDAAAICGCAVGTIKSRVNRARSKLSAL 158 (182)
T ss_pred CCHHHHHHhhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 556666666555432 23467899999999999999886555555543
No 123
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=49.67 E-value=47 Score=25.42 Aligned_cols=50 Identities=14% Similarity=0.114 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
.+++.+..++...|... ....+||..||++...|+++...-|.+.++...
T Consensus 138 ~L~~~~r~v~~L~~~~g-----~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~ 187 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEG-----LSYEEIAATLGVKLGTVRSRIHRGRQQLRAALA 187 (203)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35566666555444222 246789999999999999999766666665433
No 124
>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=49.28 E-value=35 Score=19.51 Aligned_cols=36 Identities=14% Similarity=0.187 Sum_probs=24.7
Q ss_pred CHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhh
Q psy4868 66 TNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 66 t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFq 107 (169)
+..+..++...+ .. ....++|..++++...|..|..
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHH
Confidence 344555554433 12 2467889999999999999985
No 125
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=49.01 E-value=41 Score=25.27 Aligned_cols=47 Identities=15% Similarity=0.251 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.+..+|...|... ..-.++|..||++...|++.+..-|.+.|+
T Consensus 141 ~Lp~~~r~v~~l~~~eg-----~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~ 187 (194)
T PRK12531 141 RLPKAQRDVLQAVYLEE-----LPHQQVAEMFDIPLGTVKSRLRLAVEKLRH 187 (194)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 45666666776544322 246789999999999999888666665554
No 126
>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=48.68 E-value=55 Score=24.52 Aligned_cols=50 Identities=8% Similarity=0.102 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
.+.+.+..+|...|-.. ....+||..+|++...|+++...-|.+.|+...
T Consensus 131 ~L~~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~ 180 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG-----FESDEICQELEISTSNCHVLLYRARLSLRACLS 180 (188)
T ss_pred hCCHHHHHHHHHHHHhC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45666767776655432 346889999999999999988766666665443
No 127
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=48.57 E-value=40 Score=25.58 Aligned_cols=48 Identities=13% Similarity=0.077 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
.+++.+..++...|-.. ....+||..+|++...|+++...-|.+.|+.
T Consensus 133 ~Lp~~~r~v~~l~~~~g-----~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~ 180 (196)
T PRK12535 133 ALPPERREALILTQVLG-----YTYEEAAKIADVRVGTIRSRVARARADLIAA 180 (196)
T ss_pred cCCHHHHHHhhhHHHhC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 36666666665554332 2467899999999999999987666655543
No 128
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=48.43 E-value=36 Score=25.42 Aligned_cols=47 Identities=21% Similarity=0.147 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.|..++.-.|-.. ....+||..+|++...|+++...-|.+.|+
T Consensus 130 ~Lp~~~r~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 130 DLTTDQREALLLTQLLG-----LSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred hCCHHHhHHhhhHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35666666665544322 246789999999999999998665555544
No 129
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=48.28 E-value=43 Score=24.85 Aligned_cols=47 Identities=9% Similarity=0.044 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.+..++...|-. .....+||..+|++...|+.+...-|.+.|+
T Consensus 131 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 131 RLPEKMRLAIQAVKLE-----GLSVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred hCCHHHHHHHHHHHHc-----CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4677777777655432 2346889999999999999998766665554
No 130
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=47.56 E-value=42 Score=24.88 Aligned_cols=47 Identities=11% Similarity=0.258 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.+..++...|-.. ....+||..+|++...|++....-|.+.|+
T Consensus 122 ~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 168 (185)
T PRK12542 122 ELNESNRQVFKYKVFYN-----LTYQEISSVMGITEANVRKQFERARKRVQN 168 (185)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35666666666543322 246789999999999999988766666554
No 131
>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=47.46 E-value=87 Score=22.86 Aligned_cols=48 Identities=17% Similarity=0.189 Sum_probs=37.4
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 62 RTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 62 Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+.++..|..+|...+ .. ....++|..+|++...|..|-..-+.+.++
T Consensus 4 ~~~Lte~qr~VL~Lr~--~G----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE--KG----LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH--cC----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 3568888999987742 22 246789999999999999998877777765
No 132
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=47.45 E-value=48 Score=24.28 Aligned_cols=47 Identities=6% Similarity=0.161 Sum_probs=32.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+.+.+..++...|-.. ..-.+||..+|++...|+++...-+.+.+.
T Consensus 119 ~Lp~~~r~v~~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 119 KLSSKARAAFLYNRLDG-----MGHAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35566666665544322 346789999999999999999776666654
No 133
>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=47.27 E-value=12 Score=21.70 Aligned_cols=21 Identities=14% Similarity=0.256 Sum_probs=19.1
Q ss_pred HHHHHhCCCchhHhhhhhhhH
Q psy4868 90 RLAAKIGLPEARIQVWFSNRR 110 (169)
Q Consensus 90 ~La~~l~l~~~qV~~WFqNrR 110 (169)
+||..+|++...|..|+.++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999884
No 134
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=46.71 E-value=28 Score=25.42 Aligned_cols=32 Identities=13% Similarity=0.265 Sum_probs=26.2
Q ss_pred HHHHHHHHHhCCCchhHhhhhhhhHHHHHHHH
Q psy4868 86 FARERLAAKIGLPEARIQVWFSNRRAKWRREE 117 (169)
Q Consensus 86 ~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~ 117 (169)
....++|..+|++...|++.+..-|.+.++.-
T Consensus 137 ~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 137 LPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34688999999999999999987777766543
No 135
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=46.28 E-value=50 Score=21.90 Aligned_cols=44 Identities=14% Similarity=0.205 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHh-----cCCCCHHHHHHHHHHhCCCchhHhhhhh
Q psy4868 64 SFTNDQIDNLEKEFER-----THYPDVFARERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~-----~~~p~~~~~~~La~~l~l~~~qV~~WFq 107 (169)
.++.+++..|...|.. ..+.+..+...+...++++...|..+|.
T Consensus 3 ~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 3 AISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3678889999999864 3467788887777778998888888874
No 136
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=46.23 E-value=49 Score=24.65 Aligned_cols=33 Identities=12% Similarity=0.191 Sum_probs=26.5
Q ss_pred HHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 86 FARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 86 ~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
....++|..+|++...|++....-|.+.|+.-+
T Consensus 155 ~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 155 LSYEDIASVMQCPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 346889999999999999998877777666543
No 137
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=45.90 E-value=55 Score=23.91 Aligned_cols=47 Identities=6% Similarity=0.191 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
+++.+..++...|-. ...-.++|..+|++...|+++...-|.+.|+.
T Consensus 120 L~~~~r~i~~l~~~~-----~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 120 LNEKYKTVLVLYYYE-----QYSYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 444444444433322 23467899999999999999987666665543
No 138
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=45.87 E-value=45 Score=25.89 Aligned_cols=52 Identities=12% Similarity=0.181 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
.+++.+..++...|... +.......++|..+|++...|+.+...-|.+.|+.
T Consensus 178 ~Lp~~~R~v~~L~y~l~-~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 178 KLSDREKQIMELRFGLN-GGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred hCCHHHHHHHHHHhccC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46677777777665211 12223467899999999999999987666666553
No 139
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=45.61 E-value=44 Score=26.40 Aligned_cols=47 Identities=9% Similarity=0.239 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.+..+|...|-.. ....+||..+|++...|+.|...-+.+.|+
T Consensus 205 ~L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tV~~~~~ra~~kLr~ 251 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN-----LSQKETGERLGISQMHVSRLQRQAIKKLRE 251 (257)
T ss_pred hCCHHHHHHHHHHHhCC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 47777888887766432 235889999999999999998766666554
No 140
>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=45.55 E-value=44 Score=25.78 Aligned_cols=47 Identities=19% Similarity=0.241 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.+..+|...|... ....+||..+|++...|+.+...-+.+.|+
T Consensus 175 ~L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred hCCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 46788888888776432 246889999999999999988766555543
No 141
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=45.40 E-value=42 Score=25.25 Aligned_cols=38 Identities=26% Similarity=0.267 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARI 102 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV 102 (169)
....-+..|...+....|........+|..||++...|
T Consensus 23 ~rsAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v 60 (160)
T COG1905 23 KRSALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARV 60 (160)
T ss_pred chhHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHh
Confidence 34567889999999999999999999999999998665
No 142
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=44.92 E-value=48 Score=27.58 Aligned_cols=54 Identities=19% Similarity=0.205 Sum_probs=40.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHH
Q psy4868 63 TSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117 (169)
Q Consensus 63 t~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~ 117 (169)
..+++.+..+|...|.... .......+||..+|++...|+.+...-+.+.|+.-
T Consensus 261 ~~L~~~~R~vl~lrygL~~-~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 261 FELNDKQREVLARRFGLLG-YEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred HcCCHHHHHHHHHHhccCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3578888888888774322 23345789999999999999999887777766543
No 143
>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=44.90 E-value=17 Score=27.12 Aligned_cols=32 Identities=13% Similarity=0.111 Sum_probs=24.7
Q ss_pred CHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 84 DVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 84 ~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
......+||..+|++...|++++..-|.+.|+
T Consensus 164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 164 DGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34457899999999999999988765555543
No 144
>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=44.83 E-value=17 Score=21.26 Aligned_cols=23 Identities=26% Similarity=0.462 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCchhHhhhhhhhH
Q psy4868 88 RERLAAKIGLPEARIQVWFSNRR 110 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqNrR 110 (169)
..+||..+|++...|..|..+++
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 47899999999999999998854
No 145
>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=44.62 E-value=20 Score=21.99 Aligned_cols=20 Identities=15% Similarity=0.325 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhHhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFq 107 (169)
..++|..+|++...|+.|.+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999974
No 146
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=44.58 E-value=53 Score=24.12 Aligned_cols=47 Identities=9% Similarity=0.232 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
++..+..+|...|- ......++|..+|++...|+++...-|.+.|+.
T Consensus 137 L~~~~r~il~l~~~-----~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 137 LPEKYRTVIVLKYI-----EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHHHHhhhHHh-----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45555555544332 233468899999999999999887777666653
No 147
>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=44.54 E-value=29 Score=24.68 Aligned_cols=33 Identities=15% Similarity=0.252 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 83 PDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 83 p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.......+||..+|+++..|+++..--|.+.|+
T Consensus 119 ~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 119 FKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 334457889999999999999998766665554
No 148
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=44.28 E-value=61 Score=24.84 Aligned_cols=50 Identities=8% Similarity=0.074 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
.+++.+..++...|-.. ....+||..+|++...|+++...-|.+.|+.-.
T Consensus 148 ~L~~~~r~v~~L~~~~g-----~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~ 197 (206)
T PRK12544 148 GLPAKYARVFMMREFIE-----LETNEICHAVDLSVSNLNVLLYRARLRLRECLE 197 (206)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46677777776665432 236789999999999999998877777666443
No 149
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=43.98 E-value=59 Score=24.29 Aligned_cols=49 Identities=20% Similarity=0.229 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~ 117 (169)
.+++.+..+|...|-.. ....+||..+|++...|+++...-|.+.|+..
T Consensus 111 ~Lp~~~R~v~~L~~~eg-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 111 DLPEEQRAALHLVAIEG-----LSYQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 46677777776654432 23678999999999999999866665555433
No 150
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=43.76 E-value=50 Score=23.78 Aligned_cols=44 Identities=7% Similarity=0.117 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k 112 (169)
.+++.+..++...|-.. ..-.+||..+|++...|+++...-+.+
T Consensus 113 ~L~~~~r~v~~L~~~~g-----~s~~EIA~~l~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 113 GLPPLVKRAFLLAQVDG-----LGYGEIATELGISLATVKRYLNKAAMR 156 (161)
T ss_pred HCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 35666666666554332 246789999999999999988655444
No 151
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=43.36 E-value=63 Score=22.17 Aligned_cols=42 Identities=12% Similarity=0.211 Sum_probs=32.0
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCC-CchhHhhhhh
Q psy4868 62 RTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGL-PEARIQVWFS 107 (169)
Q Consensus 62 Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l-~~~qV~~WFq 107 (169)
|..|+.+....+-..+....+ ....||..+|+ ...++..|-+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHH
Confidence 677999887666666555444 47889999996 9999998853
No 152
>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=43.29 E-value=45 Score=26.31 Aligned_cols=48 Identities=8% Similarity=0.252 Sum_probs=36.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 63 TSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 63 t~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
..+++.+..+|...|... ....+||..+|++...|+.+...-+.+.|+
T Consensus 204 ~~L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 204 PILSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred HcCCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 357788888887776433 235789999999999999998766666554
No 153
>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=43.07 E-value=53 Score=25.31 Aligned_cols=47 Identities=13% Similarity=0.227 Sum_probs=35.0
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHH
Q psy4868 63 TSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114 (169)
Q Consensus 63 t~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~k 114 (169)
..+++.+..+|...|... ....+||..+|++...|..|...-+.+.|
T Consensus 177 ~~L~~~~r~vl~l~y~~~-----~s~~eIA~~lgis~~~v~~~~~ra~~~Lr 223 (227)
T TIGR02980 177 AALPERERRILLLRFFED-----KTQSEIAERLGISQMHVSRLLRRALKKLR 223 (227)
T ss_pred HcCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 357788888887776432 34778999999999999999865555544
No 154
>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=42.74 E-value=13 Score=28.13 Aligned_cols=37 Identities=19% Similarity=0.353 Sum_probs=31.1
Q ss_pred HHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHHHH
Q psy4868 86 FARERLAAKIGLPEARIQVWFSNRRAKWRREEKLRNQ 122 (169)
Q Consensus 86 ~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~~ 122 (169)
..+.+|+..++++..+|-+|..|-+...+........
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~yKhA 51 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAKPKYKHA 51 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccccchhhHH
Confidence 3578899999999999999999999988877665544
No 155
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=42.32 E-value=74 Score=23.88 Aligned_cols=46 Identities=11% Similarity=0.083 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
+++.+..+|..+|. .....+||..+|++...|++.+..-|.+.|+.
T Consensus 156 L~~~~r~vl~l~~e------~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 156 LSELEKEVLELYLD------GKSYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred CCHHHHHHHHHHHc------cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45555555544322 23467899999999999999887766666553
No 156
>KOG0773|consensus
Probab=42.08 E-value=31 Score=28.70 Aligned_cols=39 Identities=26% Similarity=0.527 Sum_probs=33.9
Q ss_pred HhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 78 ERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 78 ~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
..+.|+...+...|+....|+..+|.+||-|.|.+.+..
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~ 155 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKE 155 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhc
Confidence 457899999999999999999999999999988876654
No 157
>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=41.84 E-value=33 Score=25.70 Aligned_cols=33 Identities=21% Similarity=0.361 Sum_probs=26.7
Q ss_pred HHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 86 FARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 86 ~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
....+||..||++...|+++...-|.+.|+.-.
T Consensus 148 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 148 FAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999999877777665443
No 158
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=41.46 E-value=58 Score=24.44 Aligned_cols=46 Identities=24% Similarity=0.333 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
+.+.+..+++-.|-. ....++||..||+++..|+..++.-|.+.++
T Consensus 136 l~~~~~~~v~l~~~~-----Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 136 LDPRQRRVVELRFFE-----GLSVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred cCHHHHHHHHHHHHC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 445555555554332 2356889999999999999988877765554
No 159
>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=40.77 E-value=22 Score=20.63 Aligned_cols=23 Identities=17% Similarity=0.057 Sum_probs=20.2
Q ss_pred HHHHHHHhCCCchhHhhhhhhhH
Q psy4868 88 RERLAAKIGLPEARIQVWFSNRR 110 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqNrR 110 (169)
..+||..+|++...|..|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 57899999999999999997764
No 160
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=40.54 E-value=57 Score=25.75 Aligned_cols=47 Identities=11% Similarity=0.162 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+.+.+..++...|.. .....+||..+|++...|+.++..-+.+.|+
T Consensus 201 ~L~~~~r~vl~l~~~~-----~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 201 QLSEKEQLVISLFYKE-----ELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred cCCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3567777777765532 2346889999999999999998766666554
No 161
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=40.46 E-value=63 Score=25.70 Aligned_cols=48 Identities=10% Similarity=0.192 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
.+.+.+..+|...|.. .....+||..+|++...|+.+..--+.+.|+.
T Consensus 203 ~L~~~~r~vl~l~y~~-----~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 203 QLEERTREVLEFVFLH-----DLTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred cCCHHHHHHHHHHHHC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4677777787777753 23468899999999999999987666665543
No 162
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=40.27 E-value=1.3e+02 Score=22.47 Aligned_cols=51 Identities=12% Similarity=0.150 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKL 119 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~ 119 (169)
.+...+..++...|... ....++|..||++...|+++..--|.+.++.-..
T Consensus 128 ~Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 178 (188)
T PRK12517 128 KLDPEYREPLLLQVIGG-----FSGEEIAEILDLNKNTVMTRLFRARNQLKEALEK 178 (188)
T ss_pred hCCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 45566666655544332 3467899999999999999987666666655443
No 163
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=39.94 E-value=53 Score=24.26 Aligned_cols=47 Identities=9% Similarity=0.155 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.++..+..++...|-.. ....++|..+|++...|+.+..--|.+.|+
T Consensus 127 ~L~~~~r~v~~l~~~~g-----~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 127 SLPIKYREVIYLFYYEE-----LSIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred hCCHHHhhHhHhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46677767765554322 236789999999999999998766655554
No 164
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=39.67 E-value=51 Score=24.17 Aligned_cols=47 Identities=6% Similarity=0.109 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.+..++...|-. .....+||..+|++...|+++...-+.+++.
T Consensus 119 ~L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 119 GLNGKTREAFLLSQLD-----GLTYSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred hCCHHHhHHhhhhhcc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3556666665543322 2347889999999999999998655555443
No 165
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=39.54 E-value=80 Score=23.67 Aligned_cols=45 Identities=16% Similarity=0.184 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~k 114 (169)
+.+.+..+|...|-.. ....+||..+|++...|++=...-|.+.|
T Consensus 135 Lp~~~r~i~~l~~~~g-----~s~~EIA~~lg~s~~tV~~rl~rar~~Lr 179 (192)
T PRK09643 135 LPVEQRAALVAVDMQG-----YSVADAARMLGVAEGTVKSRCARGRARLA 179 (192)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 5666666666544332 34678999999999999775543333333
No 166
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=39.45 E-value=72 Score=23.23 Aligned_cols=47 Identities=6% Similarity=0.094 Sum_probs=33.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHH
Q psy4868 63 TSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114 (169)
Q Consensus 63 t~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~k 114 (169)
..+++.+..++.-.|-.. ..-.++|..||++...|+.+..+-+...+
T Consensus 117 ~~L~~~~r~v~~L~~~eg-----~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 163 (168)
T PRK12525 117 DGLSGKARAAFLMSQLEG-----LTYVEIGERLGVSLSRIHQYMVEAFKCCY 163 (168)
T ss_pred HhCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 446677777776654332 24678999999999999998866655544
No 167
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=39.21 E-value=58 Score=26.24 Aligned_cols=47 Identities=15% Similarity=0.101 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.|..+|.-.|-.. ..-.+||..+|+++..|+.+++.-|.+.+.
T Consensus 108 ~L~~~~R~v~~L~~~~g-----~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~ 154 (281)
T TIGR02957 108 RLSPLERAVFVLREVFD-----YPYEEIASIVGKSEANCRQLVSRARRHLDA 154 (281)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 46677777665543322 236789999999999999999877776654
No 168
>PF13551 HTH_29: Winged helix-turn helix
Probab=38.94 E-value=90 Score=20.69 Aligned_cols=47 Identities=11% Similarity=0.111 Sum_probs=30.6
Q ss_pred CCCCCCHHHHHHHHHHHHhcC-----CCCHHHHHH-H-HHHh--CCCchhHhhhhh
Q psy4868 61 NRTSFTNDQIDNLEKEFERTH-----YPDVFARER-L-AAKI--GLPEARIQVWFS 107 (169)
Q Consensus 61 ~Rt~~t~~q~~~Le~~F~~~~-----~p~~~~~~~-L-a~~l--~l~~~qV~~WFq 107 (169)
.+..+++++...|...+..++ ..+.....+ | .... .++...|..|++
T Consensus 54 ~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 54 PRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 333489999999999998776 233344433 3 2232 467788888874
No 169
>PHA02955 hypothetical protein; Provisional
Probab=38.92 E-value=49 Score=26.05 Aligned_cols=44 Identities=14% Similarity=0.056 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHhc-CCCCHHHHHHHHHHhCCCchhHhhhhhhhH
Q psy4868 67 NDQIDNLEKEFERT-HYPDVFARERLAAKIGLPEARIQVWFSNRR 110 (169)
Q Consensus 67 ~~q~~~Le~~F~~~-~~p~~~~~~~La~~l~l~~~qV~~WFqNrR 110 (169)
..++..|-..|... .-+...++.+++.+||+....|..||.+.-
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~ 104 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDL 104 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchh
Confidence 35666666666554 467788899999999999887899998744
No 170
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=38.64 E-value=54 Score=26.29 Aligned_cols=47 Identities=13% Similarity=0.301 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.+..+|...|.. .....+||..+|++...|+.+...-+.+.|+
T Consensus 215 ~L~~rer~vl~l~y~~-----~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 215 ALPERERTVLVLRFFE-----SMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred cCCHHHHHHHHHHhcC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4777888888877743 2346889999999999999998766666554
No 171
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=38.41 E-value=68 Score=25.62 Aligned_cols=48 Identities=13% Similarity=0.223 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
.+++.+..+|...|... ....+||..+|++...|+.....-+.+.|+.
T Consensus 212 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 212 TLPEREKKVLILYYYED-----LTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 46777777777766432 3468899999999999998887666666554
No 172
>PRK09480 slmA division inhibitor protein; Provisional
Probab=38.37 E-value=39 Score=24.88 Aligned_cols=37 Identities=22% Similarity=0.376 Sum_probs=29.7
Q ss_pred HHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHH
Q psy4868 74 EKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRA 111 (169)
Q Consensus 74 e~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~ 111 (169)
...|..... .......||...|++...+-.+|.|+-.
T Consensus 20 ~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 20 AQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 334555545 7778899999999999999999999774
No 173
>PRK10403 transcriptional regulator NarP; Provisional
Probab=38.10 E-value=48 Score=24.10 Aligned_cols=47 Identities=17% Similarity=0.290 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
.++..+..+|...... ....+||..++++++.|++..+|=+.|....
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~ 199 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLNVR 199 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 4788888888755432 2357889999999999999998877775443
No 174
>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=37.96 E-value=27 Score=19.24 Aligned_cols=23 Identities=30% Similarity=0.482 Sum_probs=19.5
Q ss_pred HHHHHHHhCCCchhHhhhhhhhH
Q psy4868 88 RERLAAKIGLPEARIQVWFSNRR 110 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqNrR 110 (169)
...+|..+|++...|..|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45789999999999999988763
No 175
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=37.75 E-value=53 Score=24.53 Aligned_cols=33 Identities=21% Similarity=0.246 Sum_probs=26.0
Q ss_pred HHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHH
Q psy4868 85 VFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117 (169)
Q Consensus 85 ~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~ 117 (169)
.....+||..+|++...|+++...-|.+.|+.-
T Consensus 155 g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 155 DLELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 345788999999999999999877776666543
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=37.46 E-value=67 Score=25.09 Aligned_cols=52 Identities=15% Similarity=0.141 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
.+++.+..+|...|....+ ......+||..+|++...|+.+...-..|.|..
T Consensus 176 ~L~~~er~vl~l~ygl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~ 227 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRHP 227 (238)
T ss_pred hCCHHHHHHHHHHhCCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhh
Confidence 5778888888888743222 223478899999999999999988777776654
No 177
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=36.44 E-value=45 Score=24.86 Aligned_cols=30 Identities=10% Similarity=0.155 Sum_probs=24.6
Q ss_pred HHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 87 ARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 87 ~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
...+||..+|++...|++|...-|.+.|+.
T Consensus 152 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 152 EFQEIADIMHMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 468899999999999999987666666553
No 178
>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=36.39 E-value=1.2e+02 Score=21.06 Aligned_cols=45 Identities=18% Similarity=0.257 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKW 113 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~ 113 (169)
.+|..|..+|+-+|..+ .-..+||..+|++..-|.-|.+.-+.+.
T Consensus 17 LLT~kQ~~~l~lyy~eD-----lSlsEIAe~~~iSRqaV~d~ikr~~~~L 61 (101)
T PF04297_consen 17 LLTEKQREILELYYEED-----LSLSEIAEELGISRQAVYDSIKRAEKKL 61 (101)
T ss_dssp GS-HHHHHHHHHHCTS--------HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred HCCHHHHHHHHHHHccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 47888888888776654 3467899999999999999986555443
No 179
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=36.35 E-value=68 Score=25.90 Aligned_cols=47 Identities=13% Similarity=0.029 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.|..++...|-.. ....+||..+|+++..|+..++.-|.+.++
T Consensus 115 ~L~~~~R~v~~L~~~~g-----~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~ 161 (293)
T PRK09636 115 RLSPLERAAFLLHDVFG-----VPFDEIASTLGRSPAACRQLASRARKHVRA 161 (293)
T ss_pred hCCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 36676666665544322 236789999999999999999877766665
No 180
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=36.34 E-value=70 Score=21.76 Aligned_cols=38 Identities=21% Similarity=0.450 Sum_probs=20.6
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHHHHH
Q psy4868 70 IDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLRN 121 (169)
Q Consensus 70 ~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~ 121 (169)
+.+.+-.|+.|+||...--.. | =.|||.+||+.+..-.
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~QI~ 51 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQRQIR 51 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHHHHH
Confidence 445566688899987331111 1 1588989988776543
No 181
>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=36.33 E-value=30 Score=19.24 Aligned_cols=23 Identities=13% Similarity=0.193 Sum_probs=18.6
Q ss_pred HHHHHHHhCCCchhHhhhhhhhH
Q psy4868 88 RERLAAKIGLPEARIQVWFSNRR 110 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqNrR 110 (169)
..++|..||++...|..|.+..+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 46789999999999999985543
No 182
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=36.10 E-value=92 Score=22.30 Aligned_cols=46 Identities=11% Similarity=0.166 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
+++.+..++...|-.. ....++|..+|++...|++....-+.+.+.
T Consensus 106 L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~ 151 (159)
T PRK12527 106 LPPACRDSFLLRKLEG-----LSHQQIAEHLGISRSLVEKHIVNAMKHCRV 151 (159)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 6666666666654322 346889999999999999988755555544
No 183
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=35.83 E-value=57 Score=23.61 Aligned_cols=45 Identities=24% Similarity=0.262 Sum_probs=34.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHH
Q psy4868 63 TSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKW 113 (169)
Q Consensus 63 t~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~ 113 (169)
..+++.+..+|...+.. + ...+||..++++.+.|++..++=|.|.
T Consensus 136 ~~Lt~~E~~il~~l~~g--~----~~~~Ia~~l~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 136 DPLTKRERQVAEKLAQG--M----AVKEIAAELGLSPKTVHVHRANLMEKL 180 (196)
T ss_pred cCCCHHHHHHHHHHHCC--C----CHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 35888888888766542 2 477889999999999999888776664
No 184
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=35.77 E-value=89 Score=23.06 Aligned_cols=47 Identities=19% Similarity=0.335 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+.+.+..++...|. ......+||..||++...|++....-|.+.|.
T Consensus 137 ~L~~~~r~i~~l~~~-----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 137 ELEPPRSELIRTAFF-----EGITYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred hCCHHHHHHHHHHHH-----cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 456666666666553 22346789999999999999877655555443
No 185
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=35.59 E-value=1.9e+02 Score=21.73 Aligned_cols=50 Identities=16% Similarity=0.307 Sum_probs=37.7
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHH
Q psy4868 61 NRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112 (169)
Q Consensus 61 ~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k 112 (169)
+...++++++..+...-..+ |..-.+..||.++|++..=|.+-..--..+
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~~~~e~ 131 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAPAPKEK 131 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcCCCHHH
Confidence 45789999999998876554 566778999999999987776655444433
No 186
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=34.98 E-value=34 Score=20.96 Aligned_cols=19 Identities=11% Similarity=0.135 Sum_probs=16.6
Q ss_pred HHHHHHHhCCCchhHhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWF 106 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WF 106 (169)
..++|..+|++...|+.|-
T Consensus 3 ~~eva~~~gvs~~tlr~~~ 21 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYE 21 (70)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4578999999999999995
No 187
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=34.80 E-value=1e+02 Score=22.05 Aligned_cols=45 Identities=13% Similarity=0.159 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~k 114 (169)
.+++.+..+|.- +..+ + ...++|..++++...|+.|.++=+.|..
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 488888888876 3322 2 2578899999999999999988766653
No 188
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=34.72 E-value=50 Score=24.07 Aligned_cols=32 Identities=16% Similarity=0.316 Sum_probs=25.1
Q ss_pred CHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 84 DVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 84 ~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
......+||..+|++...|+.+...-|.+.++
T Consensus 141 ~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 141 YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHH
Confidence 34457889999999999999998766666554
No 189
>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=34.47 E-value=43 Score=26.25 Aligned_cols=51 Identities=14% Similarity=0.126 Sum_probs=39.0
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 62 RTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 62 Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
...+++.+..+|.-... ...-.++|..||+++..|+.+..|-+.|..-..+
T Consensus 169 ~~~Lt~re~evl~~~a~------G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~ 219 (232)
T TIGR03541 169 AGVLSEREREVLAWTAL------GRRQADIAAILGISERTVENHLRSARRKLGVATT 219 (232)
T ss_pred hccCCHHHHHHHHHHHC------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCH
Confidence 44689999999877532 2346788999999999999999988877654433
No 190
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=34.08 E-value=85 Score=23.32 Aligned_cols=35 Identities=17% Similarity=0.108 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhH
Q psy4868 68 DQIDNLEKEFERTHYPDVFARERLAAKIGLPEARI 102 (169)
Q Consensus 68 ~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV 102 (169)
.-+.+|...=....|.+......+|..||++..+|
T Consensus 24 ~li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V 58 (156)
T PRK05988 24 ALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEV 58 (156)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHH
Confidence 44666666666778999999999999999998765
No 191
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=33.95 E-value=83 Score=25.19 Aligned_cols=49 Identities=22% Similarity=0.238 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.++..+..+|...|.. + ......+||..+|++...|+.+..+-..|.|+
T Consensus 218 ~L~~rer~vl~l~y~~--~-~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~ 266 (270)
T TIGR02392 218 SLDARSRRIIEARWLD--D-DKLTLQELAAEYGVSAERIRQIEKNAMKKLKA 266 (270)
T ss_pred cCCHHHHHHHHHHhcC--C-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5778888888888732 1 12346799999999999999988777666665
No 192
>PF12728 HTH_17: Helix-turn-helix domain
Probab=33.95 E-value=38 Score=19.56 Aligned_cols=22 Identities=14% Similarity=0.406 Sum_probs=18.2
Q ss_pred HHHHHHHhCCCchhHhhhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFSNR 109 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqNr 109 (169)
..++|..||++...|..|.+..
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 4578899999999999998654
No 193
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=33.56 E-value=75 Score=18.49 Aligned_cols=34 Identities=18% Similarity=0.161 Sum_probs=21.6
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhh
Q psy4868 70 IDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWF 106 (169)
Q Consensus 70 ~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF 106 (169)
..+|...+....+. ...+||..|+++.+.|+.-.
T Consensus 3 ~~il~~L~~~~~~i---t~~eLa~~l~vS~rTi~~~i 36 (55)
T PF08279_consen 3 KQILKLLLESKEPI---TAKELAEELGVSRRTIRRDI 36 (55)
T ss_dssp HHHHHHHHHTTTSB---EHHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHcCCCc---CHHHHHHHhCCCHHHHHHHH
Confidence 44555544544443 36789999999998876544
No 194
>PRK10651 transcriptional regulator NarL; Provisional
Probab=33.38 E-value=94 Score=22.58 Aligned_cols=46 Identities=15% Similarity=0.221 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.+..+|+..... ....++|..++++...|++..++=+.|..-
T Consensus 155 ~Lt~rE~~vl~~l~~g------~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 155 QLTPRERDILKLIAQG------LPNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 4889998888765432 135678999999999999999888777643
No 195
>PHA01976 helix-turn-helix protein
Probab=33.28 E-value=35 Score=20.82 Aligned_cols=23 Identities=17% Similarity=0.325 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCchhHhhhhhhhH
Q psy4868 88 RERLAAKIGLPEARIQVWFSNRR 110 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqNrR 110 (169)
..+||..+|++...|..|...++
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 56899999999999999987654
No 196
>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=33.00 E-value=1.2e+02 Score=24.55 Aligned_cols=54 Identities=22% Similarity=0.230 Sum_probs=38.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHH
Q psy4868 63 TSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117 (169)
Q Consensus 63 t~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~ 117 (169)
..+++.+..+|...|... |.......+||..||++...|+.+...-+.+.|+.-
T Consensus 221 ~~Lp~~~R~Vl~l~ygL~-~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l 274 (285)
T TIGR02394 221 AELNERQREVLARRFGLL-GYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL 274 (285)
T ss_pred HcCCHHHHHHHHHHhCCC-CCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 457788888888776211 122234788999999999999999876666665543
No 197
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=32.94 E-value=72 Score=24.77 Aligned_cols=47 Identities=15% Similarity=0.088 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
.+++.++.+|.....- ..-.++|..|++++..|+.+..+-..|..-.
T Consensus 155 ~Lt~rE~~Vl~l~~~G------~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~ 201 (216)
T PRK10100 155 LLTHREKEILNKLRIG------ASNNEIARSLFISENTVKTHLYNLFKKIAVK 201 (216)
T ss_pred CCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 4889999998877652 2357889999999999999998877766543
No 198
>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=32.79 E-value=79 Score=25.68 Aligned_cols=47 Identities=15% Similarity=0.050 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.+..++...|-.. ..-.+||..||++...|+.....-|.+.|+
T Consensus 142 ~Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 188 (324)
T TIGR02960 142 YLPPRQRAVLLLRDVLG-----WRAAETAELLGTSTASVNSALQRARATLDE 188 (324)
T ss_pred hCCHHHhhHhhhHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45566666665543322 236789999999999999988766655554
No 199
>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=32.60 E-value=34 Score=20.51 Aligned_cols=17 Identities=24% Similarity=0.520 Sum_probs=13.6
Q ss_pred HHHHHHHhCCCchhHhh
Q psy4868 88 RERLAAKIGLPEARIQV 104 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~ 104 (169)
-.+||..+|++..||+-
T Consensus 31 S~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 31 SQELAEALGITPAQVRK 47 (50)
T ss_dssp HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHCCCHHHhcc
Confidence 46899999999999974
No 200
>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=32.35 E-value=72 Score=25.58 Aligned_cols=49 Identities=14% Similarity=0.102 Sum_probs=37.6
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 62 RTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 62 Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
...+++.+..+|.-... . ....+||..|++++..|+.+.+|=+.|..-.
T Consensus 188 ~~~LT~RE~evl~l~a~--G----~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~ 236 (247)
T TIGR03020 188 AGLITAREAEILAWVRD--G----KTNEEIAAILGISSLTVKNHLQHIFKKLDVR 236 (247)
T ss_pred ccCCCHHHHHHHHHHHC--C----CCHHHHHHHHCcCHHHHHHHHHHHHHHhCCC
Confidence 34689999999986542 2 3467889999999999999998877775543
No 201
>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=32.23 E-value=36 Score=21.39 Aligned_cols=23 Identities=22% Similarity=0.377 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCchhHhhhhhhhH
Q psy4868 88 RERLAAKIGLPEARIQVWFSNRR 110 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqNrR 110 (169)
..+||..+|++...|..|+.+++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46899999999999999997664
No 202
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=32.20 E-value=90 Score=25.40 Aligned_cols=51 Identities=16% Similarity=0.231 Sum_probs=38.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 63 TSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 63 t~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
..+++.+..+|...|. +-......+||..+|++...|+.+-..-+.|.|..
T Consensus 226 ~~L~~rer~vl~lr~~---~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~ 276 (289)
T PRK07500 226 QTLNERELRIIRERRL---REDGATLEALGEELGISKERVRQIEARALEKLRRA 276 (289)
T ss_pred hcCCHHHHHHHHHHhc---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3578888888888773 12234578999999999999999987666666543
No 203
>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=32.20 E-value=87 Score=22.94 Aligned_cols=47 Identities=11% Similarity=0.179 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.+..++...|- ......+||..||++...|+.=...-|.+.|+
T Consensus 140 ~L~~~~r~vi~l~~~-----~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 140 KLPEDYREVILLRHL-----EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred cCCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 467777777766543 23346789999999999998877666655554
No 204
>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=32.11 E-value=1.4e+02 Score=23.09 Aligned_cols=51 Identities=8% Similarity=0.072 Sum_probs=33.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHH
Q psy4868 63 TSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114 (169)
Q Consensus 63 t~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~k 114 (169)
..+++.+..+|...|-...+ .....+++|..+|++...|..+...-+.+.|
T Consensus 173 ~~L~~~~r~il~l~y~~~~~-e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr 223 (227)
T TIGR02846 173 SVLDGREREVIEMRYGLGDG-RRKTQREIAKILGISRSYVSRIEKRALMKLY 223 (227)
T ss_pred HhCCHHHHHHHHHHHcCCCC-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 45777788888776631100 1123678999999999999887654454444
No 205
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=31.34 E-value=74 Score=23.15 Aligned_cols=46 Identities=17% Similarity=0.197 Sum_probs=34.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHH
Q psy4868 63 TSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114 (169)
Q Consensus 63 t~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~k 114 (169)
..++..+..+|...+.. ....+||..++++.+.|+++..+=|.|..
T Consensus 148 ~~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 148 TVLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred ccCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 35788888888654332 34788999999999999999887776643
No 206
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=31.22 E-value=99 Score=22.73 Aligned_cols=35 Identities=23% Similarity=0.237 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhH
Q psy4868 68 DQIDNLEKEFERTHYPDVFARERLAAKIGLPEARI 102 (169)
Q Consensus 68 ~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV 102 (169)
.-+.+|...=....|.+......+|..+|++..+|
T Consensus 23 ~ll~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v 57 (154)
T PRK07539 23 AVIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDV 57 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHH
Confidence 44566666666678999999999999999998765
No 207
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=31.12 E-value=88 Score=24.76 Aligned_cols=46 Identities=15% Similarity=0.173 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~k 114 (169)
.++..+..+|...|... ....+||..+|++...|..+-.+-..+.|
T Consensus 209 ~L~~~er~vi~~~~~~~-----~t~~eIA~~lgis~~~V~~~~~~al~kLr 254 (258)
T PRK08215 209 KLNDREKLILNLRFFQG-----KTQMEVAEEIGISQAQVSRLEKAALKHMR 254 (258)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 57888888888887432 34678999999999999887655444443
No 208
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=30.88 E-value=1.4e+02 Score=23.13 Aligned_cols=51 Identities=8% Similarity=0.111 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.+..++...|-... ......++||..+|++...|+.|-..-+.+.|+
T Consensus 175 ~Lp~~~R~i~~l~y~~~~-~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~ 225 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGN-GKEKTQREIAKALGISRSYVSRIEKRALKKLFK 225 (233)
T ss_pred hCCHHHHHHHHHHhCCCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 466777777776652111 122347889999999999998885444444444
No 209
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=30.86 E-value=43 Score=22.66 Aligned_cols=21 Identities=10% Similarity=0.077 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCchhHhhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFSN 108 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqN 108 (169)
..++|..+|++...|+.|..+
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDEI 23 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999754
No 210
>PF14991 MLANA: Protein melan-A; PDB: 2GTZ_F 2GT9_F 3MRO_P 2GUO_C 3MRQ_P 2GTW_C 3L6F_C 3MRP_P.
Probab=30.51 E-value=16 Score=25.91 Aligned_cols=18 Identities=22% Similarity=0.650 Sum_probs=0.0
Q ss_pred hHhhhhhhhHHHHHHHHH
Q psy4868 101 RIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 101 qV~~WFqNrR~k~kk~~~ 118 (169)
-+-.||+.||.-+|....
T Consensus 41 liGCWYckRRSGYk~L~~ 58 (118)
T PF14991_consen 41 LIGCWYCKRRSGYKTLRD 58 (118)
T ss_dssp ------------------
T ss_pred HHhheeeeecchhhhhhh
Confidence 467899999999997644
No 211
>cd00131 PAX Paired Box domain
Probab=30.20 E-value=2e+02 Score=20.38 Aligned_cols=46 Identities=11% Similarity=0.041 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCC-------CchhHhhhhhhh
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGL-------PEARIQVWFSNR 109 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l-------~~~qV~~WFqNr 109 (169)
..+..+...+......++..+..+..++...-|+ +...|--||+++
T Consensus 75 ~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 75 VATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred cCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 3466666667766778887777777554224355 777888777653
No 212
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=30.15 E-value=1.1e+02 Score=24.31 Aligned_cols=48 Identities=13% Similarity=0.207 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
.+.+.+..+|...|.. .....+||..+|++...|+.+...-+.+.|+.
T Consensus 205 ~L~~~er~vi~l~y~e-----~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 205 ALEEKERKVMALYYYE-----ELVLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred cCCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4677777777777643 23468899999999999999876655555543
No 213
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=30.08 E-value=63 Score=22.74 Aligned_cols=25 Identities=16% Similarity=0.337 Sum_probs=21.0
Q ss_pred HHHHHHHHHHhCCCchhHhhhhhhh
Q psy4868 85 VFARERLAAKIGLPEARIQVWFSNR 109 (169)
Q Consensus 85 ~~~~~~La~~l~l~~~qV~~WFqNr 109 (169)
.....+||..+|++...+..+|+.-
T Consensus 25 ~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 25 PLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3557889999999999999998765
No 214
>KOG3623|consensus
Probab=30.03 E-value=22 Score=33.21 Aligned_cols=56 Identities=14% Similarity=0.218 Sum_probs=41.1
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 61 NRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 61 ~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
.++.+..++-..|...+..+..+...+...++..|...+.+|.+||++|+..-+..
T Consensus 629 v~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~ 684 (1007)
T KOG3623|consen 629 VRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPM 684 (1007)
T ss_pred ccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCC
Confidence 34555566666777788777666666666667778888899999999999876554
No 215
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=29.85 E-value=99 Score=22.44 Aligned_cols=34 Identities=26% Similarity=0.319 Sum_probs=25.1
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhH
Q psy4868 69 QIDNLEKEFERTHYPDVFARERLAAKIGLPEARI 102 (169)
Q Consensus 69 q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV 102 (169)
-+..|...=....|.+......+|..|+|+..+|
T Consensus 15 ll~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v 48 (145)
T PF01257_consen 15 LLPILHEVQEEYGYIPEEALEEIAEALGIPPAEV 48 (145)
T ss_dssp HHHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHH
Confidence 4566666666778999999999999999998765
No 216
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=29.84 E-value=44 Score=22.05 Aligned_cols=19 Identities=11% Similarity=0.347 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCchhHhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWF 106 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WF 106 (169)
..++|..+|++...++.|-
T Consensus 4 i~evA~~~gvs~~tLR~ye 22 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWE 22 (88)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4578999999999999993
No 217
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=29.71 E-value=46 Score=22.44 Aligned_cols=20 Identities=15% Similarity=0.419 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCchhHhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFq 107 (169)
..++|..+|++...|+.|..
T Consensus 3 I~e~a~~~gvs~~tLR~ye~ 22 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYEE 22 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999964
No 218
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=29.64 E-value=1.1e+02 Score=22.28 Aligned_cols=35 Identities=17% Similarity=0.193 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhH
Q psy4868 68 DQIDNLEKEFERTHYPDVFARERLAAKIGLPEARI 102 (169)
Q Consensus 68 ~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV 102 (169)
.-+.+|...=....|.+......+|..||++..+|
T Consensus 17 ~li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v 51 (148)
T TIGR01958 17 AIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWV 51 (148)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHH
Confidence 44556655555667999999999999999998665
No 219
>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=29.42 E-value=1.1e+02 Score=23.56 Aligned_cols=42 Identities=5% Similarity=0.143 Sum_probs=31.0
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhh
Q psy4868 63 TSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNR 109 (169)
Q Consensus 63 t~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNr 109 (169)
..++..+..++...|... ....+||..+|++...|..+-..-
T Consensus 182 ~~L~~~e~~i~~~~~~~~-----~t~~eIA~~lgis~~~V~~~~~~a 223 (231)
T TIGR02885 182 SKLDERERQIIMLRYFKD-----KTQTEVANMLGISQVQVSRLEKKV 223 (231)
T ss_pred HcCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 357777788887776432 357889999999999998875433
No 220
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=28.98 E-value=40 Score=23.63 Aligned_cols=21 Identities=14% Similarity=0.452 Sum_probs=18.7
Q ss_pred HHHHHHHHhCCCchhHhhhhh
Q psy4868 87 ARERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 87 ~~~~La~~l~l~~~qV~~WFq 107 (169)
-..++|..++++...|..||+
T Consensus 20 s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 20 SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred hHHHHHHHhCcHHHHHHHHHH
Confidence 456789999999999999998
No 221
>PRK05572 sporulation sigma factor SigF; Validated
Probab=28.85 E-value=1.1e+02 Score=24.01 Aligned_cols=47 Identities=4% Similarity=0.101 Sum_probs=34.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHH
Q psy4868 63 TSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114 (169)
Q Consensus 63 t~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~k 114 (169)
..+++.+..+|...|... ....+||..+|++...|..|-..-..+.|
T Consensus 201 ~~L~~~~~~v~~l~~~~~-----~s~~eIA~~lgis~~~V~~~~~ral~kLr 247 (252)
T PRK05572 201 RELDERERLIVYLRYFKD-----KTQSEVAKRLGISQVQVSRLEKKILKQMK 247 (252)
T ss_pred HcCCHHHHHHHHHHHhCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 357888888888777432 34688999999999999888655444444
No 222
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=28.75 E-value=46 Score=18.01 Aligned_cols=23 Identities=26% Similarity=0.465 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCchhHhhhhhhhH
Q psy4868 88 RERLAAKIGLPEARIQVWFSNRR 110 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqNrR 110 (169)
...||..+|++...|..|..+++
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~~ 35 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGKR 35 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 45789999999999999987654
No 223
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=28.41 E-value=1e+02 Score=19.09 Aligned_cols=27 Identities=22% Similarity=0.518 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 88 RERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
...||..||++...|-.| ..+--..+.
T Consensus 12 ~~~lAkalGVs~~aVs~W--~~~IP~~ra 38 (60)
T PF14549_consen 12 QSKLAKALGVSPQAVSQW--GERIPAERA 38 (60)
T ss_dssp HHHHHHHHTS-HHHHHHH--HTS--HHHH
T ss_pred HHHHHHHHCCCHHHHHHh--cCccCHHHH
Confidence 457999999999999999 334433333
No 224
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=28.33 E-value=1.2e+02 Score=22.93 Aligned_cols=35 Identities=26% Similarity=0.226 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhH
Q psy4868 68 DQIDNLEKEFERTHYPDVFARERLAAKIGLPEARI 102 (169)
Q Consensus 68 ~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV 102 (169)
.-+.+|...=....|.+....+.+|..|||+..+|
T Consensus 37 ~li~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V 71 (169)
T PRK07571 37 ALIEVLHKAQELFGYLERDLLLYVARQLKLPLSRV 71 (169)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHH
Confidence 44556666656678999999999999999998665
No 225
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=28.31 E-value=57 Score=18.79 Aligned_cols=21 Identities=14% Similarity=0.321 Sum_probs=18.3
Q ss_pred HHHHHHHHhCCCchhHhhhhh
Q psy4868 87 ARERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 87 ~~~~La~~l~l~~~qV~~WFq 107 (169)
....+|..+|++...|+.+|.
T Consensus 29 s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 29 SFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 367899999999999999884
No 226
>PF13730 HTH_36: Helix-turn-helix domain
Probab=28.26 E-value=58 Score=19.00 Aligned_cols=42 Identities=12% Similarity=-0.032 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCchhHhhhhh
Q psy4868 65 FTNDQIDNLEKEFER---THYPDVFARERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~qV~~WFq 107 (169)
+++.++.++-..+.. +.. ...-...||..+|++.+.|+.+..
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~-~~pS~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGG-CFPSQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCC-CCcCHHHHHHHHCcCHHHHHHHHH
Confidence 455555555544432 222 222477899999999999988874
No 227
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=28.07 E-value=50 Score=21.83 Aligned_cols=20 Identities=10% Similarity=0.112 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhHhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFq 107 (169)
..++|..+|++...|+.|..
T Consensus 4 i~e~A~~~gvs~~tLr~ye~ 23 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYER 23 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999964
No 228
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=27.88 E-value=83 Score=23.26 Aligned_cols=32 Identities=19% Similarity=0.344 Sum_probs=26.1
Q ss_pred HHHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 87 ARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 87 ~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
.-.++|..+|++...|+.|..--|.+.++...
T Consensus 145 s~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 145 SYEEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 35788999999999999999877777765443
No 229
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=27.62 E-value=1.1e+02 Score=24.02 Aligned_cols=47 Identities=11% Similarity=0.066 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
+...+..++.-.|-.. ....+||..+|++...|+++...-|.+.|+.
T Consensus 117 Lp~~~R~v~lL~~~eg-----~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~ 163 (228)
T PRK06704 117 LNVQQSAILLLKDVFQ-----YSIADIAKVCSVSEGAVKASLFRSRNRLKTV 163 (228)
T ss_pred CCHHHhhHhhhHHhhC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4455555544433221 2367899999999999999987666665543
No 230
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=27.22 E-value=84 Score=29.66 Aligned_cols=48 Identities=19% Similarity=0.231 Sum_probs=25.9
Q ss_pred CCCCCCCCCCCCCCCCCCCCCcHHHH----HhhhhhccCCCCCCCHHHHHHH
Q psy4868 26 SDETCTTIGDNSNPGSNLEPEDDQAR----LRLKRKLQRNRTSFTNDQIDNL 73 (169)
Q Consensus 26 s~~~~~~~~~~s~~~s~~~~~~~~~~----~~~~~k~rr~Rt~~t~~q~~~L 73 (169)
+...|+++...+.+.++....++... ...-..+||.|..+.++|..+.
T Consensus 1258 sssscsssssss~ssss~ed~d~~~~~~dr~~~g~~KKRGRK~LPpe~Ka~~ 1309 (1463)
T PHA03308 1258 SSSSCSSSSSSSDSSSSEEDGDEKNEKEDRERAGGGKRRGRQRLPIRDRVYR 1309 (1463)
T ss_pred ccccccccCCCCCccccccccccccchhhhhcCCCccccCCCCCChHHhhhh
Confidence 34456555544444443333333222 2223456778889999987763
No 231
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=27.14 E-value=1.5e+02 Score=18.02 Aligned_cols=51 Identities=20% Similarity=0.211 Sum_probs=28.6
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCC---HHHHHHHHHHhCCCchhHhhhhhhhHH
Q psy4868 61 NRTSFTNDQIDNLEKEFERTHYPD---VFARERLAAKIGLPEARIQVWFSNRRA 111 (169)
Q Consensus 61 ~Rt~~t~~q~~~Le~~F~~~~~p~---~~~~~~La~~l~l~~~qV~~WFqNrR~ 111 (169)
.|...|.+.-..+..........+ +..+.++....+|+..||+.=.|--|.
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 456677765544444444444433 344444444456788888877665443
No 232
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=27.06 E-value=37 Score=27.61 Aligned_cols=31 Identities=29% Similarity=0.635 Sum_probs=23.8
Q ss_pred CCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHH
Q psy4868 82 YPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114 (169)
Q Consensus 82 ~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~k 114 (169)
|+....-.+||..||+++.+|+.|- ||-.|.
T Consensus 16 yl~gmk~~dIAeklGvspntiksWK--rr~gWs 46 (279)
T COG5484 16 YLKGMKLKDIAEKLGVSPNTIKSWK--RRDGWS 46 (279)
T ss_pred HHhhccHHHHHHHhCCChHHHHHHH--HhcCCC
Confidence 3333456789999999999999995 566663
No 233
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=27.01 E-value=52 Score=23.80 Aligned_cols=21 Identities=19% Similarity=0.221 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCchhHhhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFSN 108 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqN 108 (169)
+.++|..+|++...|+.|++.
T Consensus 3 I~e~a~~~gvs~~TLR~Ye~~ 23 (134)
T cd04779 3 IGQLAHLAGVSKRTIDYYTNL 23 (134)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999854
No 234
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=26.92 E-value=82 Score=17.89 Aligned_cols=35 Identities=17% Similarity=0.407 Sum_probs=25.1
Q ss_pred HHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhH
Q psy4868 75 KEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRR 110 (169)
Q Consensus 75 ~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR 110 (169)
..|....|-.. ....|+..+|++...+-..|.|+-
T Consensus 7 ~l~~~~G~~~~-s~~~Ia~~~gvs~~~~y~~f~~k~ 41 (47)
T PF00440_consen 7 ELFAEKGYEAV-SIRDIARRAGVSKGSFYRYFPSKD 41 (47)
T ss_dssp HHHHHHHTTTS-SHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred HHHHHhCHHhC-CHHHHHHHHccchhhHHHHcCCHH
Confidence 34444444332 367889999999999999998864
No 235
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=26.60 E-value=94 Score=24.05 Aligned_cols=43 Identities=19% Similarity=0.238 Sum_probs=34.6
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHH
Q psy4868 70 IDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114 (169)
Q Consensus 70 ~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~k 114 (169)
+..-...|....|- .....||...|++...|..+|.++..=+.
T Consensus 19 l~aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L~~ 61 (225)
T PRK11552 19 IAAALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDLYL 61 (225)
T ss_pred HHHHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHHHH
Confidence 34445558888887 56888999999999999999999887554
No 236
>PF05703 Auxin_canalis: Auxin canalisation; InterPro: IPR008546 This domain consists of several plant proteins of unknown function.
Probab=26.40 E-value=1.5e+02 Score=23.79 Aligned_cols=19 Identities=26% Similarity=0.532 Sum_probs=14.3
Q ss_pred CchhHhhhhhhhHHHHHHH
Q psy4868 98 PEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 98 ~~~qV~~WFqNrR~k~kk~ 116 (169)
....|..||+.++.|.|-.
T Consensus 99 ~~~~i~~w~~~~~~kkkee 117 (242)
T PF05703_consen 99 GGKTIGRWLKDRKEKKKEE 117 (242)
T ss_pred ccchHHHHHHHHHHHHHHH
Confidence 4678999999998864433
No 237
>PF12200 DUF3597: Domain of unknown function (DUF3597); InterPro: IPR022016 This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 126 and 281 amino acids in length. The function of this domain is unknown. The structure of this domain has been found to contain five helices with a long flexible loop between helices one and two. ; PDB: 2GQB_A.
Probab=26.22 E-value=1e+02 Score=22.25 Aligned_cols=30 Identities=23% Similarity=0.563 Sum_probs=20.6
Q ss_pred CCHHHHHHHHHHhCCCc-----hhHhhhhhhhHHH
Q psy4868 83 PDVFARERLAAKIGLPE-----ARIQVWFSNRRAK 112 (169)
Q Consensus 83 p~~~~~~~La~~l~l~~-----~qV~~WFqNrR~k 112 (169)
.+...|.+||.+||++. .+.-+|....-++
T Consensus 83 SSl~aRkeLA~eL~~~~~~~dsA~~NiwLhk~Vm~ 117 (127)
T PF12200_consen 83 SSLAARKELAKELGYTGDYNDSASMNIWLHKQVMQ 117 (127)
T ss_dssp -SHHHHHHHHHHHT---SS-HHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHH
Confidence 56789999999999876 6778898654443
No 238
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=26.17 E-value=54 Score=25.49 Aligned_cols=48 Identities=17% Similarity=0.218 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~~ 117 (169)
++..+..++... |.......+||..+|++...|++....-|.+.|+.-
T Consensus 150 L~~~~r~i~~l~-----~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 150 LPDAFRAVFVLR-----VVEELSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred CCHHHhhhheee-----hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 445555454332 333445789999999999999999877676666544
No 239
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=26.16 E-value=49 Score=23.53 Aligned_cols=24 Identities=17% Similarity=0.376 Sum_probs=21.2
Q ss_pred HHHHHHHhCCCchhHhhhhhhhHH
Q psy4868 88 RERLAAKIGLPEARIQVWFSNRRA 111 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqNrR~ 111 (169)
..+||..+|++...|..|..+++.
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~~ 44 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDETE 44 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 468999999999999999988764
No 240
>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=25.95 E-value=88 Score=24.36 Aligned_cols=53 Identities=11% Similarity=0.170 Sum_probs=35.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 63 TSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 63 t~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
..+++.+..++...|.... .......+||..+|++...|+++...-+.+.|+.
T Consensus 177 ~~Lp~~~R~ii~L~~~l~~-~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~ 229 (234)
T TIGR02835 177 AKLNDREKKIMELRFGLVG-GTEKTQKEVADMLGISQSYISRLEKRILKRLKKE 229 (234)
T ss_pred HhCCHHHHHHHHHHHccCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3467777777776652100 1123467899999999999999987666665553
No 241
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=25.69 E-value=61 Score=21.72 Aligned_cols=21 Identities=10% Similarity=0.053 Sum_probs=18.2
Q ss_pred HHHHHHHhCCCchhHhhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFSN 108 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqN 108 (169)
..++|..+|++...++.|.+.
T Consensus 3 i~eva~~~gvs~~tLRyye~~ 23 (96)
T cd04768 3 IGEFAKLAGVSIRTLRHYDDI 23 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999754
No 242
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=25.38 E-value=1.3e+02 Score=24.31 Aligned_cols=50 Identities=20% Similarity=0.243 Sum_probs=35.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 63 TSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 63 t~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
..++..+..+|...|... ......+||..+|++...|+.+-..-..|.|+
T Consensus 229 ~~L~~rEr~VL~lry~~~---~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~ 278 (284)
T PRK06596 229 EGLDERSRDIIEARWLDD---DKSTLQELAAEYGVSAERVRQIEKNAMKKLKA 278 (284)
T ss_pred hcCCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 357788888888887421 23346799999999999999886554444443
No 243
>PRK13558 bacterio-opsin activator; Provisional
Probab=25.17 E-value=79 Score=28.48 Aligned_cols=42 Identities=21% Similarity=0.442 Sum_probs=35.4
Q ss_pred CCCCHHHHHHHHHHHHhcCC--CCHHHHHHHHHHhCCCchhHhh
Q psy4868 63 TSFTNDQIDNLEKEFERTHY--PDVFARERLAAKIGLPEARIQV 104 (169)
Q Consensus 63 t~~t~~q~~~Le~~F~~~~~--p~~~~~~~La~~l~l~~~qV~~ 104 (169)
..+|..|...|+..|...-| |-.....+||..||++...+..
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~ 649 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQ 649 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHH
Confidence 36999999999999998775 7677779999999999876543
No 244
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=25.08 E-value=1e+02 Score=21.30 Aligned_cols=45 Identities=11% Similarity=0.112 Sum_probs=32.5
Q ss_pred cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhH
Q psy4868 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRR 110 (169)
Q Consensus 59 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR 110 (169)
++....++..++..+...... ...+||..+|++...|.-|-..+.
T Consensus 59 ~~~~~~~~~~~i~~~r~~~gl-------tq~~lA~~lg~~~~tis~~e~g~~ 103 (127)
T TIGR03830 59 RKVDGLLTPPEIRRIRKKLGL-------SQREAAELLGGGVNAFSRYERGEV 103 (127)
T ss_pred HHccCCcCHHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHCCCC
Confidence 344556777777777655433 256799999999999999987665
No 245
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=23.87 E-value=1.1e+02 Score=25.07 Aligned_cols=46 Identities=13% Similarity=0.035 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 65 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
++..+..+|...|-.. ....+||..||++...|+.....-|.+.|+
T Consensus 154 Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 154 LPPRQRAVLILRDVLG-----WSAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred CCHHHhhhhhhHHhhC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 5555555555443322 246789999999999999988665555554
No 246
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=23.83 E-value=66 Score=21.65 Aligned_cols=20 Identities=20% Similarity=0.399 Sum_probs=16.9
Q ss_pred HHHHHHHhCCCchhHhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFq 107 (169)
+.++|..+|++...|+.|=.
T Consensus 3 I~eva~~~gvs~~tlR~Ye~ 22 (95)
T cd04780 3 MSELSKRSGVSVATIKYYLR 22 (95)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999953
No 247
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=23.43 E-value=57 Score=23.01 Aligned_cols=23 Identities=9% Similarity=0.226 Sum_probs=21.0
Q ss_pred HHHHHHHhCCCchhHhhhhhhhH
Q psy4868 88 RERLAAKIGLPEARIQVWFSNRR 110 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqNrR 110 (169)
+.+||..+|++...|..|.++++
T Consensus 21 q~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 21 KKELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHcCCC
Confidence 67899999999999999999876
No 248
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=23.42 E-value=73 Score=21.55 Aligned_cols=32 Identities=22% Similarity=0.361 Sum_probs=23.2
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhh
Q psy4868 70 IDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVW 105 (169)
Q Consensus 70 ~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~W 105 (169)
...|...|....+. .+.+|..|+++...|..=
T Consensus 12 ~~ELq~nf~~~~ls----~~~ia~dL~~s~~~le~v 43 (89)
T PF10078_consen 12 RQELQANFELSGLS----LEQIAADLGTSPEHLEQV 43 (89)
T ss_pred HHHHHHHHHHcCCC----HHHHHHHhCCCHHHHHHH
Confidence 45688888877654 677889999888776543
No 249
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=23.41 E-value=96 Score=16.52 Aligned_cols=19 Identities=21% Similarity=0.363 Sum_probs=13.7
Q ss_pred HHHHHHhCCCchhHhhhhh
Q psy4868 89 ERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 89 ~~La~~l~l~~~qV~~WFq 107 (169)
..-|...||+..+|+..+.
T Consensus 9 i~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 9 IKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 3458999999999998774
No 250
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=23.41 E-value=1.4e+02 Score=22.02 Aligned_cols=42 Identities=10% Similarity=0.176 Sum_probs=32.4
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHH
Q psy4868 70 IDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112 (169)
Q Consensus 70 ~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k 112 (169)
+......|....|.. .....||...|++...|-.+|.++..=
T Consensus 14 l~aA~~lf~e~G~~~-tSi~~Ia~~aGvsk~~lY~~F~sK~~L 55 (192)
T PRK14996 14 LQAAMRVALAEGFAA-MTVRRIASEAQVAAGQVHHHFSSAGEL 55 (192)
T ss_pred HHHHHHHHHhcChhh-ccHHHHHHHhCCCcHHHHHHcCCHHHH
Confidence 344455677777753 457889999999999999999987763
No 251
>PRK06424 transcription factor; Provisional
Probab=22.80 E-value=65 Score=23.72 Aligned_cols=24 Identities=25% Similarity=0.014 Sum_probs=21.1
Q ss_pred HHHHHHHhCCCchhHhhhhhhhHH
Q psy4868 88 RERLAAKIGLPEARIQVWFSNRRA 111 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqNrR~ 111 (169)
..+||..+|++...|..|..+++.
T Consensus 100 Q~eLA~~iGvs~stIskiE~G~~~ 123 (144)
T PRK06424 100 QADLAAKIFERKNVIASIERGDLL 123 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 568999999999999999987764
No 252
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=22.77 E-value=73 Score=21.86 Aligned_cols=21 Identities=24% Similarity=0.532 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCchhHhhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFSN 108 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqN 108 (169)
..++|..+|++...|+.|.+.
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (108)
T cd04773 3 IGELAHLLGVPPSTLRHWEKE 23 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 467899999999999999643
No 253
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=22.75 E-value=1.3e+02 Score=23.13 Aligned_cols=45 Identities=11% Similarity=0.170 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhh
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNR 109 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNr 109 (169)
.++..++.+|..+...+ +-....-.+||..+++++..|+..+.+-
T Consensus 158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~~~~~~~ 202 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCRKYLIWL 202 (239)
T ss_pred CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHHHHHHHH
Confidence 36777766665554432 3333456789999999999999988653
No 254
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=22.68 E-value=1.1e+02 Score=22.92 Aligned_cols=42 Identities=14% Similarity=0.198 Sum_probs=31.8
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHH
Q psy4868 70 IDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112 (169)
Q Consensus 70 ~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k 112 (169)
+......|....|-.. ...+||...|++...+-.+|.++-.=
T Consensus 17 l~aa~~lf~~~G~~~~-ti~~Ia~~agvsk~t~Y~~F~sKe~L 58 (213)
T PRK09975 17 IETAIAQFALRGVSNT-TLNDIADAANVTRGAIYWHFENKTQL 58 (213)
T ss_pred HHHHHHHHHHcCcccC-CHHHHHHHcCCCHHHHHHHcCCHHHH
Confidence 3444555777766554 37788999999999999999998764
No 255
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=22.66 E-value=65 Score=19.54 Aligned_cols=25 Identities=20% Similarity=0.436 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCCchhHhhhhhhhHH
Q psy4868 87 ARERLAAKIGLPEARIQVWFSNRRA 111 (169)
Q Consensus 87 ~~~~La~~l~l~~~qV~~WFqNrR~ 111 (169)
....+|..+|++...|..|...++.
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 4678999999999999999988874
No 256
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=22.38 E-value=1.9e+02 Score=20.40 Aligned_cols=38 Identities=5% Similarity=0.218 Sum_probs=26.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhh
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWF 106 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF 106 (169)
.++.+|+..++.+..... -..+++..+|+++-.|+.-+
T Consensus 33 ~L~~E~~~Fi~~Fi~~rG-----nlKe~e~~lgiSYPTvR~rL 70 (113)
T PF09862_consen 33 RLSPEQLEFIKLFIKNRG-----NLKEMEKELGISYPTVRNRL 70 (113)
T ss_pred cCCHHHHHHHHHHHHhcC-----CHHHHHHHHCCCcHHHHHHH
Confidence 478889888887765432 35677888888887776544
No 257
>PRK13870 transcriptional regulator TraR; Provisional
Probab=22.34 E-value=2.1e+02 Score=22.48 Aligned_cols=48 Identities=10% Similarity=0.014 Sum_probs=35.7
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 62 RTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 62 Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
...+|+.++.+|.=.-. ...-.+||..||++++.|..-.+|-+.|.--
T Consensus 171 ~~~LT~RE~E~L~W~A~------GKT~~EIa~ILgISe~TV~~Hl~na~~KLga 218 (234)
T PRK13870 171 AAWLDPKEATYLRWIAV------GKTMEEIADVEGVKYNSVRVKLREAMKRFDV 218 (234)
T ss_pred cCCCCHHHHHHHHHHHc------CCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 34688888888853322 2335789999999999999999998877543
No 258
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=22.28 E-value=74 Score=22.66 Aligned_cols=21 Identities=10% Similarity=0.316 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCchhHhhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFSN 108 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqN 108 (169)
..++|..+|++...++.|.+.
T Consensus 4 I~eVA~~~GVs~~TLR~wE~~ 24 (120)
T cd04767 4 IGVVAELLNIHPETLRIWERH 24 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 467899999999999999653
No 259
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=22.03 E-value=2.4e+02 Score=18.53 Aligned_cols=39 Identities=23% Similarity=0.219 Sum_probs=25.9
Q ss_pred CCHHHHHHHHHH---HHhcCCCCHHHHHHHHHHhCCCchhHhhh
Q psy4868 65 FTNDQIDNLEKE---FERTHYPDVFARERLAAKIGLPEARIQVW 105 (169)
Q Consensus 65 ~t~~q~~~Le~~---F~~~~~p~~~~~~~La~~l~l~~~qV~~W 105 (169)
++..|..+|... |....-|-. -..||..+++++..|++=
T Consensus 2 Lt~rq~~IL~alV~~Y~~~~~PVg--Sk~ia~~l~~s~aTIRN~ 43 (78)
T PF03444_consen 2 LTERQREILKALVELYIETGEPVG--SKTIAEELGRSPATIRNE 43 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCcC--HHHHHHHHCCChHHHHHH
Confidence 456676666665 555555533 356788899999887663
No 260
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=22.03 E-value=75 Score=21.54 Aligned_cols=20 Identities=15% Similarity=0.308 Sum_probs=17.4
Q ss_pred HHHHHHHhCCCchhHhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFq 107 (169)
..++|..+|++...++.|-+
T Consensus 4 i~eva~~~gvs~~tLR~ye~ 23 (102)
T cd04775 4 IGQMSRKFGVSRSTLLYYES 23 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 56789999999999999964
No 261
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=21.99 E-value=70 Score=18.16 Aligned_cols=17 Identities=29% Similarity=0.532 Sum_probs=13.2
Q ss_pred HHHHHHHhCCCchhHhh
Q psy4868 88 RERLAAKIGLPEARIQV 104 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~ 104 (169)
-.+||..+||++..|..
T Consensus 20 ~~~la~~lglS~~~v~~ 36 (42)
T PF13404_consen 20 YAELAEELGLSESTVRR 36 (42)
T ss_dssp HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHCcCHHHHHH
Confidence 56899999999988754
No 262
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.92 E-value=79 Score=21.20 Aligned_cols=20 Identities=10% Similarity=0.147 Sum_probs=17.4
Q ss_pred HHHHHHHhCCCchhHhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFq 107 (169)
..++|..+|++...++.|.+
T Consensus 3 i~eva~~~gvs~~tlR~ye~ 22 (97)
T cd04782 3 TGEFAKLCGISKQTLFHYDK 22 (97)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999964
No 263
>PF03457 HA: Helicase associated domain; InterPro: IPR005114 This short domain is found in multiple copies in bacterial helicase proteins. The domain is predicted to contain 3 alpha helices. The function of this domain may be to bind nucleic acid.; PDB: 2KTA_A.
Probab=21.91 E-value=1.3e+02 Score=18.49 Aligned_cols=42 Identities=19% Similarity=0.249 Sum_probs=24.0
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHHH
Q psy4868 69 QIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116 (169)
Q Consensus 69 q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk~ 116 (169)
-+..|..+.....+.......... ...+..|..+.|.++++.
T Consensus 11 ~~~~l~~y~~~~G~~~vp~~~~~~------~~~Lg~Wl~~qR~~~r~g 52 (68)
T PF03457_consen 11 RYEALKAYKEEHGHLNVPRDYVTD------GFPLGQWLNNQRRKYRKG 52 (68)
T ss_dssp HHHHHHHHHHHHS--S-SS-----------SSHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHCCCCCCcccCcC------CCcHHHHHHHHHHHHHcC
Confidence 356666666666543322221111 466899999999998873
No 264
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=21.71 E-value=1.6e+02 Score=23.91 Aligned_cols=47 Identities=11% Similarity=0.014 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 64 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
.+++.|..++.-.+-.. ..-.++|..||+++..|+...+.-|.+.+.
T Consensus 118 ~L~p~~R~vf~L~~~~g-----~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~ 164 (290)
T PRK09635 118 RLGPAERVVFVLHEIFG-----LPYQQIATTIGSQASTCRQLAHRARRKINE 164 (290)
T ss_pred hCCHHHHHHhhHHHHhC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 35555555554332221 236789999999999999998766666554
No 265
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=21.62 E-value=75 Score=19.97 Aligned_cols=21 Identities=14% Similarity=0.414 Sum_probs=16.2
Q ss_pred HHHHHHHHhCCCchhHhhhhh
Q psy4868 87 ARERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 87 ~~~~La~~l~l~~~qV~~WFq 107 (169)
..++||..||++...|+..++
T Consensus 22 t~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 22 TDEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp BHHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHcccHHHHHHHHH
Confidence 467899999999998887663
No 266
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.31 E-value=83 Score=21.05 Aligned_cols=20 Identities=20% Similarity=0.248 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhHhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFq 107 (169)
..++|..+|++...|+.|.+
T Consensus 3 i~eva~~~gvs~~tlR~ye~ 22 (96)
T cd04788 3 IGELARRTGLSVRTLHHYDH 22 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999974
No 267
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=21.27 E-value=1.8e+02 Score=20.63 Aligned_cols=31 Identities=13% Similarity=0.224 Sum_probs=23.7
Q ss_pred HHHHHHHhCCCchhHhhhhhhhHHHHHHHHH
Q psy4868 88 RERLAAKIGLPEARIQVWFSNRRAKWRREEK 118 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 118 (169)
-..+|..++++...|+++-.+=|.|.+....
T Consensus 159 ~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~~ 189 (202)
T PRK09390 159 NKVIARDLDISPRTVEVYRANVMTKMQAGSL 189 (202)
T ss_pred hHHHHHHcCCCHHHHHHHHHHHHHHHccccH
Confidence 4567899999999999988877777554433
No 268
>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=21.15 E-value=1.9e+02 Score=18.01 Aligned_cols=38 Identities=29% Similarity=0.436 Sum_probs=23.3
Q ss_pred CCHHHHHHHH---HHHHhcCCCCHHHHHHHHHHhCCC-chhHhh
Q psy4868 65 FTNDQIDNLE---KEFERTHYPDVFARERLAAKIGLP-EARIQV 104 (169)
Q Consensus 65 ~t~~q~~~Le---~~F~~~~~p~~~~~~~La~~l~l~-~~qV~~ 104 (169)
+|..|..+|+ .+...+.|| +...+||..+|+. ...|+.
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~--Pt~rEIa~~~g~~S~~tv~~ 45 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYP--PTVREIAEALGLKSTSTVQR 45 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSSSHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHcCCC--CCHHHHHHHhCCCChHHHHH
Confidence 5666766655 445667787 3577899999997 655554
No 269
>PRK09726 antitoxin HipB; Provisional
Probab=21.04 E-value=73 Score=20.90 Aligned_cols=23 Identities=35% Similarity=0.482 Sum_probs=20.3
Q ss_pred HHHHHHHhCCCchhHhhhhhhhH
Q psy4868 88 RERLAAKIGLPEARIQVWFSNRR 110 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqNrR 110 (169)
..+||..+|++...|..|..+++
T Consensus 28 q~elA~~~gvs~~tis~~e~g~~ 50 (88)
T PRK09726 28 QSELAKKIGIKQATISNFENNPD 50 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHCCCC
Confidence 67899999999999999998754
No 270
>PF11516 DUF3220: Protein of unknown function (DUF3120); InterPro: IPR021597 This family of proteins with unknown function appears to be restricted to Bordetella. ; PDB: 2JPF_A.
Probab=20.89 E-value=44 Score=22.19 Aligned_cols=11 Identities=27% Similarity=0.794 Sum_probs=8.8
Q ss_pred hhHhhhhhhhH
Q psy4868 100 ARIQVWFSNRR 110 (169)
Q Consensus 100 ~qV~~WFqNrR 110 (169)
..|++|.||--
T Consensus 31 gdvkvwmqnle 41 (106)
T PF11516_consen 31 GDVKVWMQNLE 41 (106)
T ss_dssp HHHHHHHHHHH
T ss_pred ccHHHHHHHHH
Confidence 46999999953
No 271
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.77 E-value=83 Score=20.88 Aligned_cols=20 Identities=10% Similarity=0.192 Sum_probs=17.0
Q ss_pred HHHHHHHhCCCchhHhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFq 107 (169)
..++|..+|++...|+.|-+
T Consensus 3 ~~eva~~~gi~~~tlr~~~~ 22 (100)
T cd00592 3 IGEVAKLLGVSVRTLRYYEE 22 (100)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999953
No 272
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=20.67 E-value=87 Score=21.23 Aligned_cols=21 Identities=24% Similarity=0.523 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhHhhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFSN 108 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFqN 108 (169)
..++|..+|++...++.|-++
T Consensus 3 i~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 3 IGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred HHHHHHHHCcCHHHHHHHHHH
Confidence 457899999999999999643
No 273
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.53 E-value=84 Score=21.31 Aligned_cols=20 Identities=20% Similarity=0.310 Sum_probs=17.4
Q ss_pred HHHHHHHhCCCchhHhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFq 107 (169)
..++|..+|++...|+.|-+
T Consensus 4 i~eva~~~gvs~~tlR~ye~ 23 (102)
T cd04789 4 ISELAEKAGISRSTLLYYEK 23 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999964
No 274
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=20.46 E-value=87 Score=21.09 Aligned_cols=20 Identities=15% Similarity=0.205 Sum_probs=17.4
Q ss_pred HHHHHHHhCCCchhHhhhhh
Q psy4868 88 RERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 88 ~~~La~~l~l~~~qV~~WFq 107 (169)
..++|..+|++...++.|.+
T Consensus 4 i~eva~~~gVs~~tLR~ye~ 23 (98)
T cd01279 4 ISVAAELLGIHPQTLRVYDR 23 (98)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999964
No 275
>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=20.27 E-value=78 Score=18.97 Aligned_cols=24 Identities=25% Similarity=0.445 Sum_probs=19.5
Q ss_pred HHHHHHHHhCCCchhHhhhhhhhH
Q psy4868 87 ARERLAAKIGLPEARIQVWFSNRR 110 (169)
Q Consensus 87 ~~~~La~~l~l~~~qV~~WFqNrR 110 (169)
....+|..+|++..+|..|-.+++
T Consensus 14 t~~~~a~~~~i~~~~i~~~e~g~~ 37 (64)
T PF12844_consen 14 TQKDLAEKLGISRSTISKIENGKR 37 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCc
Confidence 367789999999999999998876
No 276
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=20.15 E-value=2.7e+02 Score=21.89 Aligned_cols=48 Identities=15% Similarity=0.216 Sum_probs=37.2
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhHhhhhhhhHHHHHH
Q psy4868 62 RTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115 (169)
Q Consensus 62 Rt~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WFqNrR~k~kk 115 (169)
...+|..++.+|.-...- ..-.+||..|++++..|+.-.+|=+.|..-
T Consensus 177 ~~~LT~rE~evl~~~a~G------~t~~eIa~~l~is~~TV~~h~~~~~~KL~~ 224 (240)
T PRK10188 177 EMNFSKREKEILKWTAEG------KTSAEIAMILSISENTVNFHQKNMQKKFNA 224 (240)
T ss_pred CCCCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 457899999998766332 245789999999999999998887777543
No 277
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=20.03 E-value=87 Score=22.21 Aligned_cols=21 Identities=19% Similarity=0.303 Sum_probs=18.2
Q ss_pred HHHHHHHHhCCCchhHhhhhh
Q psy4868 87 ARERLAAKIGLPEARIQVWFS 107 (169)
Q Consensus 87 ~~~~La~~l~l~~~qV~~WFq 107 (169)
.+.+||..+|++...|+.|-+
T Consensus 5 tI~elA~~~gvs~~tlR~Ye~ 25 (120)
T TIGR02054 5 TISRLAEDAGVSVHVVRDYLL 25 (120)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 367899999999999999964
Done!