Query psy15107
Match_columns 135
No_of_seqs 186 out of 1468
Neff 7.7
Searched_HMMs 46136
Date Fri Aug 16 20:48:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15107.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15107hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0842|consensus 99.9 2.1E-21 4.6E-26 151.4 8.9 66 64-129 149-214 (307)
2 KOG0488|consensus 99.8 4.5E-21 9.7E-26 150.9 8.9 68 63-130 167-234 (309)
3 KOG0484|consensus 99.8 2.8E-22 6E-27 133.1 1.8 65 64-128 13-77 (125)
4 KOG0850|consensus 99.8 6E-21 1.3E-25 142.4 8.4 69 60-128 114-182 (245)
5 KOG2251|consensus 99.8 5E-21 1.1E-25 142.1 7.4 90 37-128 3-97 (228)
6 KOG0489|consensus 99.8 1.4E-21 3.1E-26 150.8 4.1 66 66-131 157-222 (261)
7 KOG0843|consensus 99.8 7.7E-21 1.7E-25 137.2 4.8 65 65-129 99-163 (197)
8 KOG0487|consensus 99.8 6.2E-21 1.4E-25 148.8 4.6 64 65-128 232-295 (308)
9 KOG0485|consensus 99.8 2.3E-20 5.1E-25 138.4 7.3 65 65-129 101-165 (268)
10 KOG0492|consensus 99.8 5.6E-20 1.2E-24 135.5 5.9 65 64-128 140-204 (246)
11 KOG0494|consensus 99.8 1.3E-19 2.7E-24 137.6 6.7 67 62-128 134-201 (332)
12 KOG0848|consensus 99.8 8.2E-19 1.8E-23 133.5 5.7 68 63-130 194-261 (317)
13 PF00046 Homeobox: Homeobox do 99.8 7.2E-19 1.6E-23 106.0 4.3 57 69-125 1-57 (57)
14 KOG0844|consensus 99.7 1.5E-18 3.2E-23 134.3 3.6 68 62-129 175-242 (408)
15 KOG0493|consensus 99.7 2.3E-16 4.9E-21 120.1 9.3 64 68-131 246-309 (342)
16 KOG0491|consensus 99.7 7.9E-18 1.7E-22 120.2 0.4 63 67-129 99-161 (194)
17 TIGR01565 homeo_ZF_HD homeobox 99.7 1E-16 2.2E-21 97.0 4.9 53 68-120 1-57 (58)
18 KOG3802|consensus 99.7 6.5E-17 1.4E-21 129.0 3.8 63 66-128 292-354 (398)
19 smart00389 HOX Homeodomain. DN 99.6 1E-16 2.2E-21 96.0 3.6 56 69-124 1-56 (56)
20 cd00086 homeodomain Homeodomai 99.6 2.2E-16 4.8E-21 95.2 4.4 57 70-126 2-58 (59)
21 KOG0486|consensus 99.6 1.5E-16 3.3E-21 123.4 4.0 65 66-130 110-174 (351)
22 COG5576 Homeodomain-containing 99.6 5.7E-16 1.2E-20 111.2 6.0 65 65-129 48-112 (156)
23 KOG4577|consensus 99.6 1.1E-15 2.4E-20 117.8 4.6 65 65-129 164-228 (383)
24 KOG0483|consensus 99.6 1.5E-15 3.2E-20 112.6 2.7 57 73-129 55-111 (198)
25 KOG0847|consensus 99.5 1.1E-14 2.5E-19 108.4 2.3 65 64-128 163-227 (288)
26 KOG0490|consensus 99.5 3.9E-14 8.5E-19 106.4 4.1 64 65-128 57-120 (235)
27 KOG1168|consensus 99.3 9E-13 2E-17 101.8 3.0 64 66-129 307-370 (385)
28 KOG0849|consensus 99.3 7.1E-12 1.5E-16 100.6 6.3 64 64-127 172-235 (354)
29 KOG0775|consensus 99.0 1.7E-10 3.7E-15 88.6 4.2 54 75-128 183-236 (304)
30 KOG2252|consensus 98.7 2E-08 4.3E-13 83.5 4.5 60 64-123 416-475 (558)
31 PF05920 Homeobox_KN: Homeobox 98.6 1.6E-08 3.4E-13 56.8 0.9 34 89-122 7-40 (40)
32 KOG0774|consensus 98.6 3.8E-08 8.2E-13 75.5 2.9 61 68-128 188-251 (334)
33 KOG0490|consensus 98.5 1.5E-07 3.4E-12 70.5 4.5 65 64-128 149-213 (235)
34 KOG1146|consensus 98.1 5.3E-06 1.2E-10 75.0 5.3 63 67-129 902-964 (1406)
35 PF11569 Homez: Homeodomain le 97.4 6E-05 1.3E-09 45.1 0.7 43 80-122 10-52 (56)
36 KOG0773|consensus 97.0 0.00071 1.5E-08 54.0 3.4 57 68-124 239-298 (342)
37 KOG3623|consensus 96.0 0.0058 1.3E-07 53.3 3.1 49 80-128 568-616 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 95.1 0.033 7.2E-07 32.8 3.2 46 69-119 1-46 (53)
39 PF04545 Sigma70_r4: Sigma-70, 85.0 0.98 2.1E-05 25.6 2.4 44 74-122 4-47 (50)
40 PF04967 HTH_10: HTH DNA bindi 84.7 0.88 1.9E-05 26.8 2.1 48 75-124 1-50 (53)
41 PF08281 Sigma70_r4_2: Sigma-7 79.2 2.3 5.1E-05 24.2 2.6 42 75-121 11-52 (54)
42 cd06171 Sigma70_r4 Sigma70, re 78.5 1.8 3.8E-05 23.7 1.8 43 74-121 10-52 (55)
43 PRK03975 tfx putative transcri 78.0 3.1 6.6E-05 29.5 3.3 49 73-127 5-53 (141)
44 COG3413 Predicted DNA binding 75.3 3.4 7.4E-05 30.8 3.1 54 74-129 155-210 (215)
45 PF10668 Phage_terminase: Phag 75.0 1 2.2E-05 27.3 0.2 20 97-116 24-43 (60)
46 PF01527 HTH_Tnp_1: Transposas 74.2 2.8 6.2E-05 25.5 2.1 46 70-120 2-48 (76)
47 KOG3755|consensus 74.2 2.7 5.8E-05 36.5 2.5 49 83-131 707-762 (769)
48 KOG1146|consensus 72.3 8.3 0.00018 36.4 5.3 64 64-127 701-764 (1406)
49 cd00569 HTH_Hin_like Helix-tur 71.8 6.1 0.00013 19.2 2.8 37 75-116 6-42 (42)
50 PRK12512 RNA polymerase sigma 69.1 7.6 0.00017 27.6 3.6 35 97-131 149-183 (184)
51 PRK06759 RNA polymerase factor 66.8 6.3 0.00014 27.0 2.7 45 75-124 107-151 (154)
52 PRK09646 RNA polymerase sigma 66.3 9 0.0002 27.7 3.6 32 96-127 159-190 (194)
53 PRK04217 hypothetical protein; 65.3 16 0.00034 24.8 4.3 51 72-127 40-90 (110)
54 PF13936 HTH_38: Helix-turn-he 63.7 3.5 7.6E-05 23.0 0.8 39 73-116 3-41 (44)
55 PF06056 Terminase_5: Putative 63.5 1.1 2.3E-05 26.9 -1.5 22 96-117 14-35 (58)
56 PRK12526 RNA polymerase sigma 61.9 10 0.00022 27.7 3.2 32 96-127 170-201 (206)
57 TIGR03879 near_KaiC_dom probab 61.6 1.3 2.9E-05 27.9 -1.4 35 84-118 21-55 (73)
58 PF13518 HTH_28: Helix-turn-he 60.9 4.3 9.2E-05 22.7 0.8 25 97-121 14-38 (52)
59 PF00196 GerE: Bacterial regul 60.6 8 0.00017 22.4 2.0 43 74-122 3-45 (58)
60 PF09607 BrkDBD: Brinker DNA-b 60.5 7.8 0.00017 23.3 1.9 44 72-117 3-47 (58)
61 PRK00118 putative DNA-binding 60.0 10 0.00022 25.4 2.6 48 75-127 18-65 (104)
62 TIGR02948 SigW_bacill RNA poly 59.6 12 0.00026 26.5 3.1 32 96-127 153-184 (187)
63 PRK09652 RNA polymerase sigma 59.2 9.3 0.0002 26.7 2.5 48 75-127 129-176 (182)
64 PRK12514 RNA polymerase sigma 58.4 16 0.00034 25.8 3.6 30 97-126 147-176 (179)
65 COG4367 Uncharacterized protei 58.4 8.6 0.00019 25.2 2.0 39 75-113 3-41 (97)
66 PRK11924 RNA polymerase sigma 57.0 15 0.00032 25.5 3.2 30 97-126 143-172 (179)
67 PRK09642 RNA polymerase sigma 56.9 15 0.00032 25.4 3.2 31 97-127 124-154 (160)
68 PRK12519 RNA polymerase sigma 56.9 8.6 0.00019 27.6 2.0 32 95-126 157-188 (194)
69 cd04761 HTH_MerR-SF Helix-Turn 56.0 3.8 8.2E-05 22.6 0.0 21 98-118 3-23 (49)
70 TIGR02937 sigma70-ECF RNA poly 55.8 14 0.00031 24.4 2.9 28 97-124 128-155 (158)
71 PRK05602 RNA polymerase sigma 55.8 15 0.00033 26.1 3.2 33 97-129 146-178 (186)
72 PRK09637 RNA polymerase sigma 54.7 15 0.00033 26.3 3.0 32 97-128 124-155 (181)
73 PRK12537 RNA polymerase sigma 53.4 23 0.00049 25.2 3.8 29 97-125 151-179 (182)
74 smart00421 HTH_LUXR helix_turn 53.4 21 0.00046 19.6 3.0 40 74-119 3-42 (58)
75 TIGR02999 Sig-70_X6 RNA polyme 52.9 18 0.00039 25.5 3.2 29 97-125 152-180 (183)
76 TIGR02989 Sig-70_gvs1 RNA poly 52.1 17 0.00037 24.9 2.9 44 75-123 112-155 (159)
77 PRK09648 RNA polymerase sigma 52.1 19 0.0004 25.7 3.1 46 75-125 140-185 (189)
78 TIGR02959 SigZ RNA polymerase 52.1 19 0.00042 25.3 3.2 48 75-127 101-148 (170)
79 PRK06811 RNA polymerase factor 51.8 21 0.00045 25.6 3.4 34 97-130 149-182 (189)
80 PF13384 HTH_23: Homeodomain-l 51.7 4.3 9.3E-05 22.7 -0.2 25 96-120 18-42 (50)
81 PRK12523 RNA polymerase sigma 51.5 25 0.00054 24.7 3.7 34 97-130 137-170 (172)
82 PRK09644 RNA polymerase sigma 51.4 18 0.0004 25.2 3.0 30 97-126 126-155 (165)
83 PRK12516 RNA polymerase sigma 51.3 22 0.00048 25.6 3.4 32 97-128 134-165 (187)
84 PRK09413 IS2 repressor TnpA; R 50.2 25 0.00054 23.7 3.4 44 72-120 10-54 (121)
85 PRK12546 RNA polymerase sigma 50.1 23 0.00051 25.6 3.4 32 97-128 131-162 (188)
86 PRK12541 RNA polymerase sigma 49.9 17 0.00038 25.1 2.6 30 97-126 130-159 (161)
87 TIGR02939 RpoE_Sigma70 RNA pol 48.9 16 0.00036 25.8 2.4 34 94-127 153-186 (190)
88 PRK12530 RNA polymerase sigma 48.9 22 0.00047 25.6 3.1 29 97-125 152-180 (189)
89 PF08280 HTH_Mga: M protein tr 48.8 14 0.00031 21.7 1.7 35 78-116 6-40 (59)
90 TIGR02985 Sig70_bacteroi1 RNA 48.2 23 0.00051 24.0 3.0 28 97-124 131-158 (161)
91 KOG3623|consensus 47.4 6.6 0.00014 35.1 0.1 66 68-133 626-691 (1007)
92 PRK12540 RNA polymerase sigma 47.1 27 0.00059 25.0 3.4 33 97-129 129-161 (182)
93 PF02796 HTH_7: Helix-turn-hel 47.0 14 0.0003 20.5 1.4 37 75-116 6-42 (45)
94 PRK12515 RNA polymerase sigma 46.9 26 0.00057 25.0 3.3 30 97-126 149-178 (189)
95 PRK10072 putative transcriptio 46.8 6.3 0.00014 26.0 -0.1 40 74-120 32-71 (96)
96 TIGR02983 SigE-fam_strep RNA p 46.7 26 0.00056 24.2 3.1 30 97-126 128-157 (162)
97 PRK06930 positive control sigm 46.2 26 0.00056 25.3 3.1 48 74-126 114-161 (170)
98 PRK09639 RNA polymerase sigma 45.9 25 0.00053 24.3 2.9 47 75-127 113-159 (166)
99 PRK09047 RNA polymerase factor 45.9 28 0.00061 23.8 3.2 29 97-125 124-152 (161)
100 PF13411 MerR_1: MerR HTH fami 45.7 7.6 0.00016 23.1 0.2 19 98-116 3-21 (69)
101 PRK12542 RNA polymerase sigma 45.3 19 0.0004 25.7 2.2 32 97-128 140-171 (185)
102 PRK09643 RNA polymerase sigma 45.0 29 0.00063 25.0 3.3 36 97-132 152-187 (192)
103 PF13551 HTH_29: Winged helix- 44.2 31 0.00066 22.1 3.0 48 70-117 53-109 (112)
104 PRK07037 extracytoplasmic-func 44.0 32 0.00069 23.7 3.2 29 97-125 127-155 (163)
105 PRK12547 RNA polymerase sigma 43.9 31 0.00066 24.1 3.1 30 97-126 130-159 (164)
106 PRK12538 RNA polymerase sigma 43.5 23 0.0005 26.7 2.6 31 97-127 189-219 (233)
107 PRK06986 fliA flagellar biosyn 43.0 28 0.00062 26.0 3.0 31 96-126 201-231 (236)
108 TIGR02952 Sig70_famx2 RNA poly 42.9 31 0.00068 23.8 3.1 29 96-124 139-167 (170)
109 cd04762 HTH_MerR-trunc Helix-T 42.8 8.4 0.00018 20.7 0.1 22 98-119 3-24 (49)
110 TIGR02954 Sig70_famx3 RNA poly 42.4 36 0.00078 23.7 3.3 29 97-125 137-165 (169)
111 PRK12532 RNA polymerase sigma 42.4 31 0.00068 24.7 3.1 30 97-126 154-183 (195)
112 PRK12543 RNA polymerase sigma 42.2 34 0.00074 24.2 3.2 32 97-128 135-166 (179)
113 PRK09645 RNA polymerase sigma 41.6 40 0.00086 23.5 3.5 29 97-125 136-164 (173)
114 PRK11923 algU RNA polymerase s 41.5 29 0.00062 24.8 2.7 33 95-127 154-186 (193)
115 PRK12524 RNA polymerase sigma 41.3 34 0.00073 24.6 3.1 31 97-127 154-184 (196)
116 KOG0773|consensus 41.2 23 0.00049 28.2 2.3 39 88-126 117-155 (342)
117 PRK12536 RNA polymerase sigma 41.0 39 0.00084 23.9 3.4 31 96-126 146-176 (181)
118 PRK13919 putative RNA polymera 40.8 45 0.00098 23.5 3.7 29 97-125 153-181 (186)
119 TIGR00721 tfx DNA-binding prot 40.4 44 0.00095 23.5 3.4 47 73-125 5-51 (137)
120 cd06170 LuxR_C_like C-terminal 40.0 43 0.00093 18.3 2.9 36 76-117 2-37 (57)
121 COG1905 NuoE NADH:ubiquinone o 39.9 39 0.00084 24.5 3.1 37 77-113 25-61 (160)
122 TIGR02479 FliA_WhiG RNA polyme 39.9 36 0.00078 25.1 3.1 46 75-125 176-221 (224)
123 PRK12529 RNA polymerase sigma 39.5 39 0.00084 24.0 3.2 30 97-126 145-174 (178)
124 PF12824 MRP-L20: Mitochondria 39.3 63 0.0014 23.4 4.2 44 71-116 82-125 (164)
125 PRK08583 RNA polymerase sigma 39.1 37 0.00081 25.7 3.2 47 75-126 206-252 (257)
126 PRK12539 RNA polymerase sigma 38.9 43 0.00092 23.8 3.3 30 96-125 148-177 (184)
127 PRK13870 transcriptional regul 38.4 12 0.00027 28.3 0.4 43 74-122 173-215 (234)
128 PRK09480 slmA division inhibit 38.3 23 0.00051 24.9 1.9 38 82-120 18-55 (194)
129 PRK12511 RNA polymerase sigma 38.3 43 0.00092 24.0 3.2 30 97-126 129-158 (182)
130 PRK10403 transcriptional regul 38.3 24 0.00052 24.6 1.9 43 74-122 153-195 (215)
131 PHA02955 hypothetical protein; 37.7 50 0.0011 25.0 3.5 45 77-121 60-105 (213)
132 PRK05657 RNA polymerase sigma 37.2 36 0.00078 27.1 2.9 53 74-127 262-314 (325)
133 cd04763 HTH_MlrA-like Helix-Tu 37.0 12 0.00026 22.3 0.1 20 98-117 3-22 (68)
134 PRK10360 DNA-binding transcrip 37.0 27 0.00058 24.3 1.9 43 74-122 137-179 (196)
135 PRK12535 RNA polymerase sigma 36.7 50 0.0011 23.9 3.4 33 97-129 151-183 (196)
136 PRK09651 RNA polymerase sigma 36.5 37 0.00081 23.9 2.7 31 96-126 136-166 (172)
137 TIGR02980 SigBFG RNA polymeras 36.3 44 0.00095 24.6 3.1 46 74-124 178-223 (227)
138 PRK12518 RNA polymerase sigma 36.2 23 0.00051 24.7 1.5 37 92-128 133-169 (175)
139 COG2944 Predicted transcriptio 36.1 29 0.00064 23.3 1.9 39 75-120 44-82 (104)
140 TIGR02941 Sigma_B RNA polymera 36.1 44 0.00095 25.2 3.1 46 75-125 206-251 (255)
141 cd04764 HTH_MlrA-like_sg1 Heli 36.0 13 0.00029 22.1 0.2 21 98-118 3-23 (67)
142 PRK07670 RNA polymerase sigma 35.9 44 0.00095 25.3 3.1 46 75-125 202-247 (251)
143 PRK12545 RNA polymerase sigma 35.8 49 0.0011 24.0 3.3 30 97-126 157-186 (201)
144 PF00376 MerR: MerR family reg 35.7 11 0.00025 20.3 -0.1 18 98-115 2-19 (38)
145 PRK09641 RNA polymerase sigma 35.7 46 0.001 23.4 3.0 32 95-126 152-183 (187)
146 PRK12531 RNA polymerase sigma 35.6 52 0.0011 23.6 3.3 29 97-125 159-187 (194)
147 PF08279 HTH_11: HTH domain; 34.9 31 0.00067 19.4 1.7 32 80-114 3-34 (55)
148 PRK09647 RNA polymerase sigma 34.9 52 0.0011 24.1 3.3 29 97-125 156-184 (203)
149 TIGR02943 Sig70_famx1 RNA poly 34.7 51 0.0011 23.6 3.2 30 97-126 149-178 (188)
150 PRK12533 RNA polymerase sigma 34.5 44 0.00094 24.9 2.8 31 97-127 152-182 (216)
151 PRK12520 RNA polymerase sigma 34.2 52 0.0011 23.5 3.1 30 97-126 149-178 (191)
152 cd02413 40S_S3_KH K homology R 33.7 31 0.00067 21.8 1.7 20 98-117 56-75 (81)
153 PRK09649 RNA polymerase sigma 33.5 46 0.001 23.7 2.8 29 97-125 148-176 (185)
154 TIGR03001 Sig-70_gmx1 RNA poly 32.7 54 0.0012 24.9 3.1 29 97-125 179-207 (244)
155 PRK12528 RNA polymerase sigma 32.6 52 0.0011 22.6 2.9 26 97-122 131-156 (161)
156 PRK08301 sporulation sigma fac 32.6 45 0.00097 24.8 2.6 51 75-126 179-229 (234)
157 PRK09935 transcriptional regul 32.2 35 0.00075 23.8 1.9 44 73-122 148-191 (210)
158 PRK15369 two component system 32.1 44 0.00096 22.9 2.4 43 74-122 149-191 (211)
159 cd01104 HTH_MlrA-CarA Helix-Tu 32.0 16 0.00035 21.5 0.1 20 98-117 3-22 (68)
160 PRK12522 RNA polymerase sigma 31.8 56 0.0012 22.8 2.9 30 97-126 137-166 (173)
161 TIGR02950 SigM_subfam RNA poly 31.7 19 0.00042 24.5 0.5 34 92-125 118-151 (154)
162 PRK05988 formate dehydrogenase 31.7 58 0.0013 23.2 3.0 35 79-113 25-59 (156)
163 TIGR02947 SigH_actino RNA poly 31.6 31 0.00066 24.7 1.5 37 92-128 144-180 (193)
164 PRK12525 RNA polymerase sigma 31.2 57 0.0012 22.8 2.9 28 97-124 136-163 (168)
165 PRK12544 RNA polymerase sigma 30.9 63 0.0014 23.7 3.2 30 97-126 166-195 (206)
166 PRK07408 RNA polymerase sigma 30.3 61 0.0013 24.7 3.1 47 75-126 204-250 (256)
167 PRK06288 RNA polymerase sigma 30.0 64 0.0014 24.6 3.2 46 75-125 213-258 (268)
168 PRK10651 transcriptional regul 29.9 60 0.0013 22.5 2.9 43 74-122 155-197 (216)
169 PF01710 HTH_Tnp_IS630: Transp 29.9 49 0.0011 22.2 2.2 37 76-117 4-40 (119)
170 TIGR01958 nuoE_fam NADH-quinon 29.8 64 0.0014 22.6 2.9 35 79-113 18-52 (148)
171 PRK10100 DNA-binding transcrip 29.8 60 0.0013 24.2 2.9 43 74-122 155-197 (216)
172 PRK07539 NADH dehydrogenase su 29.7 63 0.0014 22.8 2.9 35 79-113 24-58 (154)
173 PRK08295 RNA polymerase factor 29.7 64 0.0014 23.2 3.0 32 95-126 170-201 (208)
174 PRK12513 RNA polymerase sigma 29.6 27 0.00059 25.0 1.0 35 93-127 153-187 (194)
175 TIGR03020 EpsA transcriptional 29.5 61 0.0013 24.9 2.9 46 72-123 188-233 (247)
176 PRK09640 RNA polymerase sigma 29.4 26 0.00056 25.0 0.9 34 94-127 149-182 (188)
177 smart00027 EH Eps15 homology d 29.4 65 0.0014 20.4 2.7 44 74-117 3-51 (96)
178 TIGR02859 spore_sigH RNA polym 29.3 16 0.00035 26.1 -0.3 33 92-124 162-194 (198)
179 TIGR02957 SigX4 RNA polymerase 28.6 83 0.0018 24.2 3.6 29 98-126 127-155 (281)
180 PF13565 HTH_32: Homeodomain-l 28.4 1.4E+02 0.003 17.8 5.1 33 76-108 32-65 (77)
181 PF01257 2Fe-2S_thioredx: Thio 28.4 48 0.001 23.1 2.1 34 80-113 16-49 (145)
182 PF07638 Sigma70_ECF: ECF sigm 28.2 72 0.0016 22.9 3.0 29 97-125 153-181 (185)
183 PRK12534 RNA polymerase sigma 28.2 1E+02 0.0022 21.7 3.8 29 96-124 154-182 (187)
184 COG2963 Transposase and inacti 27.7 78 0.0017 20.8 2.9 43 72-118 5-48 (116)
185 PRK07122 RNA polymerase sigma 27.6 69 0.0015 24.6 3.0 46 75-125 216-261 (264)
186 TIGR02393 RpoD_Cterm RNA polym 26.9 72 0.0016 23.8 2.9 51 74-125 176-226 (238)
187 PRK07571 bidirectional hydroge 26.5 80 0.0017 22.9 2.9 34 80-113 39-72 (169)
188 PRK09636 RNA polymerase sigma 26.2 74 0.0016 24.6 2.9 31 97-127 133-163 (293)
189 PRK12527 RNA polymerase sigma 26.1 93 0.002 21.3 3.2 28 97-124 123-150 (159)
190 PF01381 HTH_3: Helix-turn-hel 26.0 18 0.00038 20.3 -0.5 23 98-120 12-34 (55)
191 PRK05803 sporulation sigma fac 25.9 82 0.0018 23.4 3.1 49 75-124 176-224 (233)
192 cd01392 HTH_LacI Helix-turn-he 25.7 14 0.00031 20.5 -0.9 20 100-119 2-21 (52)
193 TIGR03070 couple_hipB transcri 25.4 22 0.00048 19.8 -0.1 23 98-120 18-40 (58)
194 TIGR02885 spore_sigF RNA polym 25.3 83 0.0018 23.2 3.0 39 74-117 183-221 (231)
195 TIGR01764 excise DNA binding d 25.1 25 0.00054 18.8 0.1 21 98-118 4-24 (49)
196 PRK09415 RNA polymerase factor 25.1 78 0.0017 22.3 2.7 29 97-125 145-173 (179)
197 PRK08215 sporulation sigma fac 24.9 88 0.0019 23.7 3.1 43 74-121 209-251 (258)
198 PTZ00183 centrin; Provisional 24.8 2.2E+02 0.0047 19.0 5.2 41 67-107 3-48 (158)
199 TIGR03541 reg_near_HchA LuxR f 24.4 49 0.0011 24.8 1.6 45 73-123 170-214 (232)
200 KOG3862|consensus 24.1 90 0.0019 24.8 3.0 26 72-97 223-248 (327)
201 smart00422 HTH_MERR helix_turn 23.9 28 0.00061 20.5 0.2 19 98-116 3-21 (70)
202 TIGR02392 rpoH_proteo alternat 23.3 82 0.0018 24.1 2.7 50 74-126 218-267 (270)
203 PF08880 QLQ: QLQ; InterPro: 23.3 81 0.0018 17.0 1.9 14 74-87 2-15 (37)
204 PRK11511 DNA-binding transcrip 23.3 19 0.00042 24.4 -0.8 25 94-118 24-48 (127)
205 PRK05911 RNA polymerase sigma 23.3 1E+02 0.0022 23.5 3.1 47 75-126 206-252 (257)
206 PRK07500 rpoH2 RNA polymerase 23.2 78 0.0017 24.7 2.6 51 74-127 227-277 (289)
207 TIGR02960 SigX5 RNA polymerase 22.9 94 0.002 24.1 3.0 32 97-128 160-191 (324)
208 PRK11922 RNA polymerase sigma 22.8 55 0.0012 24.3 1.6 36 92-127 162-197 (231)
209 PF08452 DNAP_B_exo_N: DNA pol 22.7 27 0.00059 16.6 -0.1 8 113-120 6-13 (22)
210 TIGR02394 rpoS_proteo RNA poly 22.2 1.1E+02 0.0024 23.6 3.3 52 74-126 222-273 (285)
211 PRK10430 DNA-binding transcrip 22.2 67 0.0014 23.7 1.9 44 74-118 158-201 (239)
212 PRK09638 RNA polymerase sigma 22.2 40 0.00087 23.5 0.7 34 92-125 139-172 (176)
213 PRK12517 RNA polymerase sigma 21.8 1.2E+02 0.0027 21.6 3.2 29 97-125 146-174 (188)
214 PF13412 HTH_24: Winged helix- 21.7 72 0.0016 17.4 1.6 35 76-114 2-36 (48)
215 PF06971 Put_DNA-bind_N: Putat 21.7 31 0.00066 19.9 -0.0 16 98-113 31-46 (50)
216 PRK05572 sporulation sigma fac 21.6 1.2E+02 0.0026 22.9 3.3 46 74-124 202-247 (252)
217 PRK00215 LexA repressor; Valid 21.5 52 0.0011 24.0 1.2 41 75-117 2-46 (205)
218 TIGR03629 arch_S13P archaeal r 21.5 79 0.0017 22.4 2.1 15 74-88 51-65 (144)
219 PF05263 DUF722: Protein of un 21.4 87 0.0019 21.8 2.2 22 99-120 103-124 (130)
220 PF12728 HTH_17: Helix-turn-he 21.4 32 0.00069 19.1 0.0 21 98-118 4-24 (51)
221 TIGR02984 Sig-70_plancto1 RNA 21.2 1.2E+02 0.0027 21.1 3.1 30 95-124 156-185 (189)
222 cd00093 HTH_XRE Helix-turn-hel 21.2 29 0.00063 18.2 -0.2 22 98-119 15-36 (58)
223 PF00424 REV: REV protein (ant 21.1 1.5E+02 0.0032 19.5 3.1 17 80-96 14-30 (91)
224 PF07750 GcrA: GcrA cell cycle 21.1 1.4E+02 0.003 21.5 3.3 32 75-111 3-35 (162)
225 PF03444 HrcA_DNA-bdg: Winged 20.9 1.4E+02 0.003 19.0 2.9 38 75-114 2-42 (78)
226 PRK10188 DNA-binding transcrip 20.8 1.3E+02 0.0028 22.7 3.3 44 73-122 178-221 (240)
227 PHA01976 helix-turn-helix prot 20.6 32 0.00069 20.1 -0.1 22 98-119 18-39 (67)
228 PF01726 LexA_DNA_bind: LexA D 20.3 1.7E+02 0.0037 17.5 3.2 38 74-113 3-44 (65)
229 PRK13558 bacterio-opsin activa 20.2 81 0.0017 27.1 2.3 40 73-112 606-647 (665)
230 COG1595 RpoE DNA-directed RNA 20.0 59 0.0013 23.0 1.2 32 97-128 145-176 (182)
No 1
>KOG0842|consensus
Probab=99.85 E-value=2.1e-21 Score=151.37 Aligned_cols=66 Identities=26% Similarity=0.315 Sum_probs=62.3
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhcC
Q psy15107 64 NHRKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKIN 129 (135)
Q Consensus 64 ~~~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~ 129 (135)
..+++||.|..|+..|+.+||+.|.+++|++..+|++||..|.|+++||||||||||-|.||.+..
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~d 214 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKD 214 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhh
Confidence 466788888999999999999999999999999999999999999999999999999999998874
No 2
>KOG0488|consensus
Probab=99.84 E-value=4.5e-21 Score=150.90 Aligned_cols=68 Identities=25% Similarity=0.290 Sum_probs=63.8
Q ss_pred CCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhcCC
Q psy15107 63 GNHRKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKINL 130 (135)
Q Consensus 63 ~~~~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~~ 130 (135)
+..+|.|+.||+||..|+..||+.|++++|++..+|.+||..|||+..||++||||||+|+||.....
T Consensus 167 ~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g 234 (309)
T KOG0488|consen 167 STPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEG 234 (309)
T ss_pred CCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhh
Confidence 35588899999999999999999999999999999999999999999999999999999999987653
No 3
>KOG0484|consensus
Probab=99.84 E-value=2.8e-22 Score=133.12 Aligned_cols=65 Identities=51% Similarity=0.653 Sum_probs=61.7
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 64 NHRKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 64 ~~~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
..+|+||.||.||..||.+||+.|...+||++..|++||.+++|++..|||||||||+|.++.+.
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 56789999999999999999999999999999999999999999999999999999999988753
No 4
>KOG0850|consensus
Probab=99.84 E-value=6e-21 Score=142.37 Aligned_cols=69 Identities=28% Similarity=0.371 Sum_probs=66.2
Q ss_pred CCCCCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 60 IPSGNHRKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 60 ~~~~~~~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
..+++.+|.|+.||.|+.-||..|.+.|++++|+-..+|.+||..|||+.+||||||||||.|.||+..
T Consensus 114 ~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 114 RPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred ccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 357789999999999999999999999999999999999999999999999999999999999999987
No 5
>KOG2251|consensus
Probab=99.84 E-value=5e-21 Score=142.10 Aligned_cols=90 Identities=57% Similarity=0.843 Sum_probs=74.6
Q ss_pred CCCCCCCCCCCCC---CCCCC--CCCCCCCCCCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCC
Q psy15107 37 KSAPYGVNGIGLS---MDSLH--SSLGYIPSGNHRKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESR 111 (135)
Q Consensus 37 ~~~~~s~~~~~~~---~~~~~--~~~~~~~~~~~~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~ 111 (135)
+.+++++++++.. .|..| ..... ....+|.||+||.|+..|+++||.+|.+.+||+...|++||.+|+|++.+
T Consensus 3 ~~~~~~~~~~~fa~p~~d~~h~~~~vP~--~~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSr 80 (228)
T KOG2251|consen 3 NQPPYAVNGLAFAAPYMDLLHPKPGVPY--SSGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESR 80 (228)
T ss_pred CCCCCCcCccccccccccccccCCCCCc--CccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhh
Confidence 3456666664443 45555 33333 24678899999999999999999999999999999999999999999999
Q ss_pred ccccchhhhHHHHHHhc
Q psy15107 112 VQGYPDIFMREEVALKI 128 (135)
Q Consensus 112 V~vWFqNRR~k~k~~~~ 128 (135)
|||||.|||+|+|+.+.
T Consensus 81 VqVWFKNRRAK~r~qq~ 97 (228)
T KOG2251|consen 81 VQVWFKNRRAKCRRQQQ 97 (228)
T ss_pred hhhhhccccchhhHhhh
Confidence 99999999999998876
No 6
>KOG0489|consensus
Probab=99.84 E-value=1.4e-21 Score=150.77 Aligned_cols=66 Identities=29% Similarity=0.228 Sum_probs=62.2
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhcCCC
Q psy15107 66 RKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKINLP 131 (135)
Q Consensus 66 ~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~~~ 131 (135)
.+.||.||.||..|+.+||+.|..++|++...|.+||..|.|+|+||||||||||+|+||.+....
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~ 222 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS 222 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence 457999999999999999999999999999999999999999999999999999999998877544
No 7
>KOG0843|consensus
Probab=99.82 E-value=7.7e-21 Score=137.24 Aligned_cols=65 Identities=25% Similarity=0.272 Sum_probs=61.7
Q ss_pred CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhcC
Q psy15107 65 HRKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKIN 129 (135)
Q Consensus 65 ~~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~ 129 (135)
..+.+|.||.|+.+|+..||..|+.++|....+|++||..|+|++.||+|||||||.|.||++.+
T Consensus 99 ~~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 99 SMRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred ccCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 33789999999999999999999999999999999999999999999999999999999998764
No 8
>KOG0487|consensus
Probab=99.82 E-value=6.2e-21 Score=148.83 Aligned_cols=64 Identities=25% Similarity=0.217 Sum_probs=61.3
Q ss_pred CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 65 HRKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 65 ~~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
.+..||+|..||+.|+.+||+.|..|.|++...|.+|++.|+|+++||+|||||||+|+||+..
T Consensus 232 ~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 232 ARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred ccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 4678888999999999999999999999999999999999999999999999999999999984
No 9
>KOG0485|consensus
Probab=99.82 E-value=2.3e-20 Score=138.36 Aligned_cols=65 Identities=26% Similarity=0.275 Sum_probs=61.3
Q ss_pred CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhcC
Q psy15107 65 HRKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKIN 129 (135)
Q Consensus 65 ~~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~ 129 (135)
+.++||.||+|+..|+..||..|+..+|++..+|..||.+|.|+|+||+|||||||.|+||....
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa 165 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA 165 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence 44678899999999999999999999999999999999999999999999999999999998763
No 10
>KOG0492|consensus
Probab=99.80 E-value=5.6e-20 Score=135.47 Aligned_cols=65 Identities=29% Similarity=0.373 Sum_probs=62.0
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 64 NHRKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 64 ~~~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
+.+..|++||.||..||..||+.|.+.+|+++.+|.+++..|.|+++||+|||||||+|.||.+.
T Consensus 140 Khk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe 204 (246)
T KOG0492|consen 140 KHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE 204 (246)
T ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence 56677899999999999999999999999999999999999999999999999999999999875
No 11
>KOG0494|consensus
Probab=99.79 E-value=1.3e-19 Score=137.55 Aligned_cols=67 Identities=36% Similarity=0.507 Sum_probs=60.6
Q ss_pred CCCCCCCCCC-CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 62 SGNHRKQRRE-RTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 62 ~~~~~k~rr~-Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
..+.+++||. ||.||..|+..||+.|++.+||+...|+-||.++.|+|.+|+|||||||+|+||.+.
T Consensus 134 ~~kkk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek 201 (332)
T KOG0494|consen 134 NAKKKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEK 201 (332)
T ss_pred ccccccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhh
Confidence 3344545555 999999999999999999999999999999999999999999999999999998765
No 12
>KOG0848|consensus
Probab=99.76 E-value=8.2e-19 Score=133.51 Aligned_cols=68 Identities=24% Similarity=0.204 Sum_probs=62.7
Q ss_pred CCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhcCC
Q psy15107 63 GNHRKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKINL 130 (135)
Q Consensus 63 ~~~~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~~ 130 (135)
++.+.+-|.|.+||..|..+||+.|..++|.++..+.+||.-|+|+|+||||||||||+||||.+.+.
T Consensus 194 ~KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 194 VKTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ceeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 35666778899999999999999999999999999999999999999999999999999999987643
No 13
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.76 E-value=7.2e-19 Score=106.03 Aligned_cols=57 Identities=39% Similarity=0.553 Sum_probs=55.1
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 69 RRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 69 rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
|+.|+.|+.+|+.+||..|..++||+..+++.||..+||+..+|++||+|||.++|+
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 578899999999999999999999999999999999999999999999999999986
No 14
>KOG0844|consensus
Probab=99.73 E-value=1.5e-18 Score=134.33 Aligned_cols=68 Identities=28% Similarity=0.355 Sum_probs=63.6
Q ss_pred CCCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhcC
Q psy15107 62 SGNHRKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKIN 129 (135)
Q Consensus 62 ~~~~~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~ 129 (135)
...+.+.||.||.||.+|+..||+.|.+..|.+...|.+||..|+|+|..|+|||||||+|+||....
T Consensus 175 ~sa~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 175 NSADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred cCccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 34566789999999999999999999999999999999999999999999999999999999998763
No 15
>KOG0493|consensus
Probab=99.68 E-value=2.3e-16 Score=120.05 Aligned_cols=64 Identities=27% Similarity=0.280 Sum_probs=59.1
Q ss_pred CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhcCCC
Q psy15107 68 QRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKINLP 131 (135)
Q Consensus 68 ~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~~~ 131 (135)
.||+||.||.+||..|...|+.++|+....|.+||.+|+|.|.||+|||||+|+|-|+.....+
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn 309 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKN 309 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCC
Confidence 3578999999999999999999999999999999999999999999999999999998765443
No 16
>KOG0491|consensus
Probab=99.67 E-value=7.9e-18 Score=120.16 Aligned_cols=63 Identities=29% Similarity=0.381 Sum_probs=60.0
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhcC
Q psy15107 67 KQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKIN 129 (135)
Q Consensus 67 k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~ 129 (135)
++++.||+|+..|+..||+.|+.++|++..++.+||..|+|++.||+.||||||+|.||.+.+
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~ 161 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRN 161 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhc
Confidence 467789999999999999999999999999999999999999999999999999999998874
No 17
>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=99.66 E-value=1e-16 Score=97.03 Aligned_cols=53 Identities=17% Similarity=0.155 Sum_probs=50.7
Q ss_pred CCCCCCcCCHHHHHHHHHhhhhcCC----CCHHHHHHHHHHcCCCcCCccccchhhh
Q psy15107 68 QRRERTTFTRAQLDVLESLFGKTRY----PDIFMREEVALKINLPESRVQGYPDIFM 120 (135)
Q Consensus 68 ~rr~Rt~~t~~ql~~Le~~F~~~~~----p~~~~r~~La~~l~l~~~~V~vWFqNRR 120 (135)
++|.||.||.+|+..||..|+.++| |+..++++||..+||++.+|+|||||.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 3789999999999999999999999 9999999999999999999999999964
No 18
>KOG3802|consensus
Probab=99.65 E-value=6.5e-17 Score=129.02 Aligned_cols=63 Identities=19% Similarity=0.156 Sum_probs=60.7
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 66 RKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 66 ~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
.++||+||.|.......||+.|.+|+.|+..++..||.+|+|.+.+|+|||||||+|+||+..
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 378899999999999999999999999999999999999999999999999999999999876
No 19
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.65 E-value=1e-16 Score=95.98 Aligned_cols=56 Identities=39% Similarity=0.459 Sum_probs=52.3
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHH
Q psy15107 69 RRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEV 124 (135)
Q Consensus 69 rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k 124 (135)
++.|+.|+.+|+.+|+..|..++||+..++..||..+||+..+|++||+|||.+++
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 35677899999999999999999999999999999999999999999999998753
No 20
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.64 E-value=2.2e-16 Score=95.19 Aligned_cols=57 Identities=35% Similarity=0.383 Sum_probs=53.9
Q ss_pred CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 70 RERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 70 r~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
+.|+.++..++.+||.+|..++||+..++..||.++||++.+|++||+|||.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 567789999999999999999999999999999999999999999999999998763
No 21
>KOG0486|consensus
Probab=99.63 E-value=1.5e-16 Score=123.43 Aligned_cols=65 Identities=42% Similarity=0.508 Sum_probs=62.0
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhcCC
Q psy15107 66 RKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKINL 130 (135)
Q Consensus 66 ~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~~ 130 (135)
.|+||.||+|+..|+.+||..|++++||+...|++||...+|+|.+|+|||.|||+|+++.+.+-
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~ 174 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQ 174 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhH
Confidence 37889999999999999999999999999999999999999999999999999999999988754
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.63 E-value=5.7e-16 Score=111.18 Aligned_cols=65 Identities=26% Similarity=0.296 Sum_probs=58.9
Q ss_pred CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhcC
Q psy15107 65 HRKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKIN 129 (135)
Q Consensus 65 ~~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~ 129 (135)
....++.|++.+..|+.+|++.|+.++||+...|..|+..|+|+++.|||||||||++.|+....
T Consensus 48 s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 48 SSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 34456677778999999999999999999999999999999999999999999999999987653
No 23
>KOG4577|consensus
Probab=99.59 E-value=1.1e-15 Score=117.78 Aligned_cols=65 Identities=26% Similarity=0.310 Sum_probs=61.4
Q ss_pred CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhcC
Q psy15107 65 HRKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKIN 129 (135)
Q Consensus 65 ~~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~ 129 (135)
+...||+||.+|..||+.|...|...+.|....|++|+.++||.-+.|||||||||+|+||.+..
T Consensus 164 d~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T KOG4577|consen 164 DASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T ss_pred ccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence 34578999999999999999999999999999999999999999999999999999999999864
No 24
>KOG0483|consensus
Probab=99.56 E-value=1.5e-15 Score=112.64 Aligned_cols=57 Identities=14% Similarity=0.123 Sum_probs=54.1
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhcC
Q psy15107 73 TTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKIN 129 (135)
Q Consensus 73 t~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~ 129 (135)
.+|+.+|+..||+.|+...++....+..||.+|||.++||.|||||||+++|..+.+
T Consensus 55 ~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE 111 (198)
T KOG0483|consen 55 RRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLE 111 (198)
T ss_pred ccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence 458999999999999999999999999999999999999999999999999988764
No 25
>KOG0847|consensus
Probab=99.48 E-value=1.1e-14 Score=108.43 Aligned_cols=65 Identities=25% Similarity=0.250 Sum_probs=60.8
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 64 NHRKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 64 ~~~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
++.+++..|.+|+..|+..||+.|+..+|+-..++.+||..+|+++.||+|||||||.|+|++-.
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 45677788899999999999999999999999999999999999999999999999999998765
No 26
>KOG0490|consensus
Probab=99.46 E-value=3.9e-14 Score=106.41 Aligned_cols=64 Identities=31% Similarity=0.263 Sum_probs=60.8
Q ss_pred CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 65 HRKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 65 ~~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
..++++.|+.|+..|+++||+.|+..+||+...++.||..+++++..|+|||||||+|+++.+.
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 5678999999999999999999999999999999999999999999999999999999998764
No 27
>KOG1168|consensus
Probab=99.31 E-value=9e-13 Score=101.83 Aligned_cols=64 Identities=19% Similarity=0.204 Sum_probs=59.9
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhcC
Q psy15107 66 RKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKIN 129 (135)
Q Consensus 66 ~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~ 129 (135)
..+||+||.+...+...||.+|..++.|+.+.+..||++|+|.+..|+|||+|.|+|.||++..
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~S 370 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRS 370 (385)
T ss_pred cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhh
Confidence 3467889999999999999999999999999999999999999999999999999999998763
No 28
>KOG0849|consensus
Probab=99.27 E-value=7.1e-12 Score=100.64 Aligned_cols=64 Identities=39% Similarity=0.500 Sum_probs=60.5
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 64 NHRKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 64 ~~~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
..++.++.||.|+..|+..||+.|+.++||++..|++||.++++++..|+|||+|||++.+|..
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 4667788899999999999999999999999999999999999999999999999999998876
No 29
>KOG0775|consensus
Probab=99.05 E-value=1.7e-10 Score=88.58 Aligned_cols=54 Identities=17% Similarity=0.204 Sum_probs=48.4
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
|...-...|..+|..++||+..++.+||+++||+..||-+||.|||+++|....
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~a 236 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAA 236 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhccc
Confidence 334446799999999999999999999999999999999999999999996655
No 30
>KOG2252|consensus
Probab=98.68 E-value=2e-08 Score=83.50 Aligned_cols=60 Identities=23% Similarity=0.319 Sum_probs=55.6
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHH
Q psy15107 64 NHRKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREE 123 (135)
Q Consensus 64 ~~~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~ 123 (135)
+.-+.||+|.+||..|...|..+|+.+++|+.+..+.|+.+|+|....|.+||.|-|++.
T Consensus 416 ~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 416 KMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 445678889999999999999999999999999999999999999999999999977764
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=98.58 E-value=1.6e-08 Score=56.83 Aligned_cols=34 Identities=21% Similarity=0.260 Sum_probs=28.8
Q ss_pred hcCCCCHHHHHHHHHHcCCCcCCccccchhhhHH
Q psy15107 89 KTRYPDIFMREEVALKINLPESRVQGYPDIFMRE 122 (135)
Q Consensus 89 ~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k 122 (135)
.++||+..+++.||.++||+..||..||-|.|.+
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 3789999999999999999999999999998864
No 32
>KOG0774|consensus
Probab=98.57 E-value=3.8e-08 Score=75.47 Aligned_cols=61 Identities=23% Similarity=0.269 Sum_probs=54.6
Q ss_pred CCCCCCcCCHHHHHHHHHhhhh---cCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 68 QRRERTTFTRAQLDVLESLFGK---TRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 68 ~rr~Rt~~t~~ql~~Le~~F~~---~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
.+|+|..|+..-.++|..+|.. ++||+..++++||++++++..||-.||.|.|-+.|+--.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~ 251 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMG 251 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhh
Confidence 4677888999999999999954 799999999999999999999999999999988776443
No 33
>KOG0490|consensus
Probab=98.49 E-value=1.5e-07 Score=70.50 Aligned_cols=65 Identities=37% Similarity=0.398 Sum_probs=60.2
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 64 NHRKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 64 ~~~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
...+.++.|+.+...|+..|+..|...++|+...++.|+..+++++..|++||||+|.+.++.+.
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 45667888999999999999999999999999999999999999999999999999999998644
No 34
>KOG1146|consensus
Probab=98.07 E-value=5.3e-06 Score=75.03 Aligned_cols=63 Identities=22% Similarity=0.257 Sum_probs=59.2
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhcC
Q psy15107 67 KQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKIN 129 (135)
Q Consensus 67 k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~ 129 (135)
.+++.|++++..||.+|..+|....||...+.+.|-..+++..+.|++||||-|.|.|+...+
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n 964 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLN 964 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhc
Confidence 467889999999999999999999999999999999999999999999999999999988764
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.37 E-value=6e-05 Score=45.09 Aligned_cols=43 Identities=19% Similarity=0.145 Sum_probs=31.7
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHH
Q psy15107 80 LDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMRE 122 (135)
Q Consensus 80 l~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k 122 (135)
+..|+++|...+++.......|..+.+|+..||+.||-.|+.+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 4569999999999999999999999999999999999877654
No 36
>KOG0773|consensus
Probab=96.97 E-value=0.00071 Score=54.04 Aligned_cols=57 Identities=12% Similarity=0.097 Sum_probs=48.2
Q ss_pred CCCCCCcCCHHHHHHHHHhhhh---cCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHH
Q psy15107 68 QRRERTTFTRAQLDVLESLFGK---TRYPDIFMREEVALKINLPESRVQGYPDIFMREEV 124 (135)
Q Consensus 68 ~rr~Rt~~t~~ql~~Le~~F~~---~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k 124 (135)
..+.+..+......+|+.+... .+||+..++..||.++||+..||-+||-|.|.+..
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w 298 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLW 298 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccC
Confidence 4555667899999999988533 57999999999999999999999999999887643
No 37
>KOG3623|consensus
Probab=96.00 E-value=0.0058 Score=53.30 Aligned_cols=49 Identities=16% Similarity=0.228 Sum_probs=45.7
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 80 LDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 80 l~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
...|..+|..+..|+..+...+|.+.||+...|+.||++++.++...+.
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 6788889999999999999999999999999999999999999887764
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=95.08 E-value=0.033 Score=32.76 Aligned_cols=46 Identities=13% Similarity=0.143 Sum_probs=34.0
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhh
Q psy15107 69 RRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIF 119 (135)
Q Consensus 69 rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNR 119 (135)
++.|..+|-++...+-..++... ....||..+|++..+|..|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 46788899988777777777765 46789999999999999999875
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=85.02 E-value=0.98 Score=25.61 Aligned_cols=44 Identities=14% Similarity=0.222 Sum_probs=32.0
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHH
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMRE 122 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k 122 (135)
.+++.+..+|...|... ....++|..+|++...|+.+...-..|
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKK 47 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHH
Confidence 46788899999988433 356789999999999988776544333
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=84.74 E-value=0.88 Score=26.83 Aligned_cols=48 Identities=21% Similarity=0.314 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHhhhhcCC--CCHHHHHHHHHHcCCCcCCccccchhhhHHHH
Q psy15107 75 FTRAQLDVLESLFGKTRY--PDIFMREEVALKINLPESRVQGYPDIFMREEV 124 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~--p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k 124 (135)
+|+.|..+|...++..-| |-.....+||.+||++...|. ..=||+..|
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~--~~LRrae~k 50 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVS--EHLRRAERK 50 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHH--HHHHHHHHH
Confidence 578899999999987644 656678899999999987543 233444443
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=79.24 E-value=2.3 Score=24.23 Aligned_cols=42 Identities=14% Similarity=0.080 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhH
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMR 121 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~ 121 (135)
+++.+..++.-.|. ......++|..+|+++..|+.|.+.-|.
T Consensus 11 L~~~~r~i~~l~~~-----~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 11 LPERQREIFLLRYF-----QGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S-HHHHHHHHHHHT-----S---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH-----HCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 45556566655443 3346789999999999999999865443
No 42
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=78.47 E-value=1.8 Score=23.75 Aligned_cols=43 Identities=19% Similarity=0.261 Sum_probs=31.0
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhH
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMR 121 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~ 121 (135)
.++..+..+++..|... ....++|..+|++...|..|...-+.
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 35667777777766432 34667899999999999998765443
No 43
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=78.05 E-value=3.1 Score=29.49 Aligned_cols=49 Identities=14% Similarity=0.155 Sum_probs=37.9
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 73 TTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 73 t~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
..+++.|..+|+.. ... ....++|..||++...|..|-+..+.|-++..
T Consensus 5 ~~Lt~rqreVL~lr-~~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 5 SFLTERQIEVLRLR-ERG-----LTQQEIADILGTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred cCCCHHHHHHHHHH-HcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46889999999773 222 35678999999999999999988777766543
No 44
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=75.25 E-value=3.4 Score=30.78 Aligned_cols=54 Identities=19% Similarity=0.230 Sum_probs=42.8
Q ss_pred cCCHHHHHHHHHhhhhcC--CCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhcC
Q psy15107 74 TFTRAQLDVLESLFGKTR--YPDIFMREEVALKINLPESRVQGYPDIFMREEVALKIN 129 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~--~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~ 129 (135)
.+|..|+++|...|...= ||-.....+||+++|+++.. ++..=||+..|-+..-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst--~~ehLRrAe~Kl~~~~ 210 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST--LSEHLRRAERKLIEAY 210 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH--HHHHHHHHHHHHHHHh
Confidence 699999999999998764 46667788999999999875 5555677777766543
No 45
>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=75.01 E-value=1 Score=27.29 Aligned_cols=20 Identities=20% Similarity=0.404 Sum_probs=17.5
Q ss_pred HHHHHHHHcCCCcCCccccc
Q psy15107 97 MREEVALKINLPESRVQGYP 116 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWF 116 (135)
...+||.+||+++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 45678999999999999994
No 46
>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=74.24 E-value=2.8 Score=25.49 Aligned_cols=46 Identities=13% Similarity=0.106 Sum_probs=28.8
Q ss_pred CCCCcCCHHHHHHHHHhh-hhcCCCCHHHHHHHHHHcCCCcCCccccchhhh
Q psy15107 70 RERTTFTRAQLDVLESLF-GKTRYPDIFMREEVALKINLPESRVQGYPDIFM 120 (135)
Q Consensus 70 r~Rt~~t~~ql~~Le~~F-~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR 120 (135)
+.|..|+.++...+-..+ ... .....+|.++||+..++..|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHHHHHHh
Confidence 345678998776665554 332 4678899999999999999965443
No 47
>KOG3755|consensus
Probab=74.22 E-value=2.7 Score=36.55 Aligned_cols=49 Identities=20% Similarity=0.019 Sum_probs=35.0
Q ss_pred HHHhhhhcCCCCHHHHHHHHHHcC-------CCcCCccccchhhhHHHHHHhcCCC
Q psy15107 83 LESLFGKTRYPDIFMREEVALKIN-------LPESRVQGYPDIFMREEVALKINLP 131 (135)
Q Consensus 83 Le~~F~~~~~p~~~~r~~La~~l~-------l~~~~V~vWFqNRR~k~k~~~~~~~ 131 (135)
-+.+|.+++.+......+..+.+. .....|+.||.|||.++|+.+-+-+
T Consensus 707 ~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~~~d 762 (769)
T KOG3755|consen 707 KHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKMSYD 762 (769)
T ss_pred chhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhccCC
Confidence 356677777777766655544443 3456799999999999999887643
No 48
>KOG1146|consensus
Probab=72.34 E-value=8.3 Score=36.43 Aligned_cols=64 Identities=8% Similarity=-0.014 Sum_probs=56.1
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 64 NHRKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 64 ~~~k~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
-....++.+..+-.+++.+|-.+|-.+.-|+...+..|......+.+++.+||+|-+.+.++..
T Consensus 701 ~~~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 701 LSPRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred CCcccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 3445677788888899999999999999999999999999999999999999999888777654
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=71.80 E-value=6.1 Score=19.16 Aligned_cols=37 Identities=19% Similarity=0.298 Sum_probs=24.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccc
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYP 116 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWF 116 (135)
++.++...+...+.... ...++|..++++...|..|.
T Consensus 6 ~~~~~~~~i~~~~~~~~-----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAAGE-----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHhC
Confidence 55666666666665332 45678899999888777763
No 50
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=69.10 E-value=7.6 Score=27.62 Aligned_cols=35 Identities=20% Similarity=0.054 Sum_probs=28.9
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHHhcCCC
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVALKINLP 131 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~~~ 131 (135)
.-.+||..+|++...|+.++..-|.+-|....+-|
T Consensus 149 s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~~~~ 183 (184)
T PRK12512 149 SIKETAAKLSMSEGAVRVALHRGLAALAAKFRSEP 183 (184)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCC
Confidence 45789999999999999999888888777665544
No 51
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=66.75 E-value=6.3 Score=27.04 Aligned_cols=45 Identities=11% Similarity=-0.032 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHH
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEV 124 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k 124 (135)
+++.+..++.-.|-. .....++|..+|++...|+.|...-+.+-|
T Consensus 107 L~~~~r~ii~l~~~~-----~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 107 LDEKEKYIIFERFFV-----GKTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred CCHHHHHHHHHHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 444455555444322 234688999999999999998766555544
No 52
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=66.33 E-value=9 Score=27.65 Aligned_cols=32 Identities=16% Similarity=0.013 Sum_probs=25.3
Q ss_pred HHHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 96 FMREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 96 ~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
....++|..||++...|+++...-|.+-|+..
T Consensus 159 ~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 159 LTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 34678999999999999999877666665543
No 53
>PRK04217 hypothetical protein; Provisional
Probab=65.32 E-value=16 Score=24.78 Aligned_cols=51 Identities=10% Similarity=0.039 Sum_probs=38.3
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 72 RTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 72 Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
-..++.++..++...|.... ...+||+.+|++...|+..+..-+.+-+...
T Consensus 40 ~~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 34578888888877765443 5678999999999999988877666665543
No 54
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=63.66 E-value=3.5 Score=22.96 Aligned_cols=39 Identities=18% Similarity=0.224 Sum_probs=19.8
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccc
Q psy15107 73 TTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYP 116 (135)
Q Consensus 73 t~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWF 116 (135)
..+|.++...++..++.. ....+||..||.+...|..+.
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHH
Confidence 457888888888887644 356679999999988876654
No 55
>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=63.48 E-value=1.1 Score=26.86 Aligned_cols=22 Identities=27% Similarity=0.513 Sum_probs=18.8
Q ss_pred HHHHHHHHHcCCCcCCccccch
Q psy15107 96 FMREEVALKINLPESRVQGYPD 117 (135)
Q Consensus 96 ~~r~~La~~l~l~~~~V~vWFq 117 (135)
....+||..||++...|..|-+
T Consensus 14 ~~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 14 WSIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CCHHHHHHHHCCChHHHHHHHH
Confidence 3567899999999999999954
No 56
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=61.91 E-value=10 Score=27.73 Aligned_cols=32 Identities=16% Similarity=0.234 Sum_probs=25.1
Q ss_pred HHHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 96 FMREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 96 ~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
....++|..+|+++..|+++...-+.+.++..
T Consensus 170 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 170 LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999998877666665543
No 57
>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=61.56 E-value=1.3 Score=27.85 Aligned_cols=35 Identities=17% Similarity=0.018 Sum_probs=26.1
Q ss_pred HHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchh
Q psy15107 84 ESLFGKTRYPDIFMREEVALKINLPESRVQGYPDI 118 (135)
Q Consensus 84 e~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqN 118 (135)
+..|...+|.......+||..+|+++..|+.|+.+
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 33454444445556789999999999999999864
No 58
>PF13518 HTH_28: Helix-turn-helix domain
Probab=60.86 E-value=4.3 Score=22.69 Aligned_cols=25 Identities=16% Similarity=0.218 Sum_probs=20.7
Q ss_pred HHHHHHHHcCCCcCCccccchhhhH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMR 121 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~ 121 (135)
...++|.++|++..+|..|.+..+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 3556899999999999999876554
No 59
>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=60.64 E-value=8 Score=22.44 Aligned_cols=43 Identities=23% Similarity=0.351 Sum_probs=31.9
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHH
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMRE 122 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k 122 (135)
.+|..++.+|.-...-. ...++|..+++++..|..+..+=+.|
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHH
Confidence 47888888887766443 46789999999999999887665444
No 60
>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=60.47 E-value=7.8 Score=23.30 Aligned_cols=44 Identities=25% Similarity=0.259 Sum_probs=21.4
Q ss_pred CCcCCHHH-HHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccch
Q psy15107 72 RTTFTRAQ-LDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPD 117 (135)
Q Consensus 72 Rt~~t~~q-l~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFq 117 (135)
|..|+... |.+++- |.....--...|. .|.++|+++.+|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~-a~~~~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEY-AEKDNNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHH-HHH-TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHH-HHHccchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 34455544 334443 3333222222333 49999999999999964
No 61
>PRK00118 putative DNA-binding protein; Validated
Probab=60.04 E-value=10 Score=25.44 Aligned_cols=48 Identities=15% Similarity=0.104 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
++..|..++.-.|... ....+||..+|++...|..|...-|.+.+...
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 4566666665555443 24678999999999999999887666665543
No 62
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=59.65 E-value=12 Score=26.50 Aligned_cols=32 Identities=13% Similarity=-0.004 Sum_probs=25.7
Q ss_pred HHHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 96 FMREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 96 ~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
..-+++|..+|+++..|+++++.-|.+-+..-
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 45678999999999999999877777666543
No 63
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=59.16 E-value=9.3 Score=26.66 Aligned_cols=48 Identities=13% Similarity=-0.119 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
+++.+..+|.-.|-. .....++|..+|++...|+.|...-+.+-++.-
T Consensus 129 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 129 LPEELRTAITLREIE-----GLSYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 555555555554322 224568999999999999999886666655543
No 64
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=58.36 E-value=16 Score=25.81 Aligned_cols=30 Identities=10% Similarity=0.078 Sum_probs=24.2
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
..+++|..+|+++..|+++...-|.+-|..
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 467899999999999999887766665543
No 65
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.35 E-value=8.6 Score=25.16 Aligned_cols=39 Identities=15% Similarity=0.101 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCcc
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQ 113 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~ 113 (135)
++++|...-...|+.+--.+....+++|.+|++++-.|+
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 567777777777777766667778889999998875543
No 66
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=56.98 E-value=15 Score=25.54 Aligned_cols=30 Identities=13% Similarity=-0.006 Sum_probs=24.4
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
...++|..+|++...|+.|...-|.+.|+.
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999987766666544
No 67
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=56.93 E-value=15 Score=25.40 Aligned_cols=31 Identities=13% Similarity=-0.129 Sum_probs=24.7
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
.-.++|..+|+++..|++....-|.+-|+..
T Consensus 124 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 124 SYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3478999999999999999877666665543
No 68
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=56.93 E-value=8.6 Score=27.58 Aligned_cols=32 Identities=16% Similarity=0.169 Sum_probs=25.8
Q ss_pred HHHHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 95 IFMREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 95 ~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
.....++|..+|++...|+.|+..-|.+-++.
T Consensus 157 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 157 GLSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 34567899999999999999997777666654
No 69
>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=55.99 E-value=3.8 Score=22.60 Aligned_cols=21 Identities=24% Similarity=0.227 Sum_probs=17.5
Q ss_pred HHHHHHHcCCCcCCccccchh
Q psy15107 98 REEVALKINLPESRVQGYPDI 118 (135)
Q Consensus 98 r~~La~~l~l~~~~V~vWFqN 118 (135)
..++|+.+|++...|+.|.++
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999643
No 70
>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=55.80 E-value=14 Score=24.37 Aligned_cols=28 Identities=11% Similarity=0.001 Sum_probs=22.4
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEV 124 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k 124 (135)
...++|..+|+++..|+.+...-+.|-|
T Consensus 128 s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 128 SYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4578999999999999998876555544
No 71
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=55.80 E-value=15 Score=26.12 Aligned_cols=33 Identities=12% Similarity=-0.025 Sum_probs=26.4
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHHhcC
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVALKIN 129 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~ 129 (135)
...++|..+|++...|+.+...-|.+-++...+
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 178 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQLAD 178 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 457899999999999999987777776665543
No 72
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=54.71 E-value=15 Score=26.31 Aligned_cols=32 Identities=19% Similarity=0.010 Sum_probs=24.9
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
...++|..+|++...|+..+..-|.+.++...
T Consensus 124 ~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (181)
T PRK09637 124 SQKEIAEKLGLSLSGAKSRVQRGRVKLKELLE 155 (181)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999888766666555443
No 73
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=53.45 E-value=23 Score=25.22 Aligned_cols=29 Identities=14% Similarity=0.224 Sum_probs=23.2
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
...++|..+|++...|+++...-+.+-|.
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 46789999999999999988766655544
No 74
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=53.40 E-value=21 Score=19.56 Aligned_cols=40 Identities=20% Similarity=0.268 Sum_probs=28.4
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhh
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIF 119 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNR 119 (135)
.++..+..++...+. . ....++|..++++...|..|.+.-
T Consensus 3 ~l~~~e~~i~~~~~~-g-----~s~~eia~~l~is~~tv~~~~~~~ 42 (58)
T smart00421 3 SLTPREREVLRLLAE-G-----LTNKEIAERLGISEKTVKTHLSNI 42 (58)
T ss_pred CCCHHHHHHHHHHHc-C-----CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 357777777765432 2 245788999999999998887643
No 75
>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=52.92 E-value=18 Score=25.51 Aligned_cols=29 Identities=14% Similarity=-0.073 Sum_probs=23.4
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
..+++|..+|+++..|++....-|.+-++
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45789999999999999988766666554
No 76
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=52.15 E-value=17 Score=24.91 Aligned_cols=44 Identities=9% Similarity=-0.018 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHH
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREE 123 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~ 123 (135)
+++.+..++...| ......+++|..+|++...|+++...-|.+-
T Consensus 112 L~~~~r~v~~l~~-----~~g~~~~eIA~~l~is~~tv~~~l~Rar~~L 155 (159)
T TIGR02989 112 LPERQRELLQLRY-----QRGVSLTALAEQLGRTVNAVYKALSRLRVRL 155 (159)
T ss_pred CCHHHHHHHHHHH-----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 4444444444432 2333567899999999999998765444443
No 77
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=52.08 E-value=19 Score=25.74 Aligned_cols=46 Identities=15% Similarity=-0.010 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
+++.+..++.-.|-. ....+++|..+|++...|+.+...-+.+-|+
T Consensus 140 L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 140 LPEKQREILILRVVV-----GLSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 444455555444322 2346789999999999999887555554443
No 78
>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=52.05 E-value=19 Score=25.35 Aligned_cols=48 Identities=13% Similarity=0.023 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
+++.+..+|.-.|-.. ...+++|..+|+++..|+++.+.-|.+.+...
T Consensus 101 L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 101 LPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4444444444443222 34678999999999999998876665555443
No 79
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=51.81 E-value=21 Score=25.60 Aligned_cols=34 Identities=24% Similarity=0.194 Sum_probs=26.1
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHHhcCC
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVALKINL 130 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~~ 130 (135)
..+++|..+|++...|++..+.-|.+-|+.+.++
T Consensus 149 s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~~~ 182 (189)
T PRK06811 149 KIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKLNI 182 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHcccCc
Confidence 4578999999999999988776666666555443
No 80
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=51.69 E-value=4.3 Score=22.69 Aligned_cols=25 Identities=16% Similarity=0.287 Sum_probs=17.4
Q ss_pred HHHHHHHHHcCCCcCCccccchhhh
Q psy15107 96 FMREEVALKINLPESRVQGYPDIFM 120 (135)
Q Consensus 96 ~~r~~La~~l~l~~~~V~vWFqNRR 120 (135)
....++|..+|++...|..|.+..+
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT---
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 4567899999999999999976543
No 81
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=51.48 E-value=25 Score=24.71 Aligned_cols=34 Identities=21% Similarity=0.163 Sum_probs=27.4
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHHhcCC
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVALKINL 130 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~~ 130 (135)
.-.++|..+|++...|+++...-+.+.+.....-
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~~ 170 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQGLRQCYIALYGE 170 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcCC
Confidence 4578999999999999999988777777655443
No 82
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=51.36 E-value=18 Score=25.16 Aligned_cols=30 Identities=20% Similarity=-0.027 Sum_probs=24.5
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
..+++|..+|+++..|++|.+.-|.+-|+.
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 155 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKAL 155 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999987766665554
No 83
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=51.26 E-value=22 Score=25.63 Aligned_cols=32 Identities=9% Similarity=-0.077 Sum_probs=25.4
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
.-.++|..||+++..|++....-|.+-++...
T Consensus 134 s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 134 AYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45789999999999999998777766665443
No 84
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=50.23 E-value=25 Score=23.74 Aligned_cols=44 Identities=14% Similarity=0.098 Sum_probs=29.0
Q ss_pred CCcCCHHHHH-HHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhh
Q psy15107 72 RTTFTRAQLD-VLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFM 120 (135)
Q Consensus 72 Rt~~t~~ql~-~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR 120 (135)
|..|+.++.. ++...+... . ...++|.++|++..+|..|.+..+
T Consensus 10 rr~ys~EfK~~aV~~~~~~g-~----sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPG-M----TVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCC-C----CHHHHHHHHCcCHHHHHHHHHHHh
Confidence 3457777644 344444322 2 355789999999999999976543
No 85
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=50.08 E-value=23 Score=25.59 Aligned_cols=32 Identities=16% Similarity=-0.011 Sum_probs=26.1
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
...++|..+|++...|+++...-|.+-|+...
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 45789999999999999999877777665443
No 86
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=49.85 E-value=17 Score=25.12 Aligned_cols=30 Identities=17% Similarity=0.036 Sum_probs=22.9
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
...++|..+|++...|+.+...-|.+-++.
T Consensus 130 s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 130 SYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 457899999999999998876655555443
No 87
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=48.94 E-value=16 Score=25.81 Aligned_cols=34 Identities=12% Similarity=-0.034 Sum_probs=25.6
Q ss_pred CHHHHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 94 DIFMREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 94 ~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
....-.++|..+|+++..|+++...-|.+-|...
T Consensus 153 ~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 153 EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3345688999999999999998866666655443
No 88
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=48.91 E-value=22 Score=25.58 Aligned_cols=29 Identities=10% Similarity=-0.004 Sum_probs=23.4
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
.-.++|..+|+++..|+++...-|.+-|+
T Consensus 152 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 152 SSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45789999999999999998766665554
No 89
>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=48.83 E-value=14 Score=21.70 Aligned_cols=35 Identities=29% Similarity=0.425 Sum_probs=25.5
Q ss_pred HHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccc
Q psy15107 78 AQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYP 116 (135)
Q Consensus 78 ~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWF 116 (135)
.|+..|+-.+. +...+.. +||..++++++.|+.-.
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i 40 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDI 40 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHH
Confidence 57788888888 5555444 89999999998876543
No 90
>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=48.15 E-value=23 Score=23.97 Aligned_cols=28 Identities=14% Similarity=0.081 Sum_probs=21.2
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEV 124 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k 124 (135)
...++|..+|+++..|+.+...-+.|-|
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4578999999999999987655444443
No 91
>KOG3623|consensus
Probab=47.44 E-value=6.6 Score=35.10 Aligned_cols=66 Identities=11% Similarity=0.063 Sum_probs=45.9
Q ss_pred CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhcCCCCC
Q psy15107 68 QRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKINLPES 133 (135)
Q Consensus 68 ~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~~~~~ 133 (135)
.-+.++....++-..|...++.+-.+.-.+-..++..|-..+..|++||++|+...+.+...+-.+
T Consensus 626 p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl~ltss 691 (1007)
T KOG3623|consen 626 PVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPLFLTSS 691 (1007)
T ss_pred CccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCccccccc
Confidence 344456666666677777777666665555555566677788889999999998877766655443
No 92
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=47.15 E-value=27 Score=25.00 Aligned_cols=33 Identities=12% Similarity=-0.053 Sum_probs=25.7
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHHhcC
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVALKIN 129 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~ 129 (135)
.-+++|..||+++..|+.....-|.+-++....
T Consensus 129 s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~ 161 (182)
T PRK12540 129 SYEDAAAICGCAVGTIKSRVNRARSKLSALLYV 161 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 467899999999999999887666666655543
No 93
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=47.03 E-value=14 Score=20.49 Aligned_cols=37 Identities=19% Similarity=0.406 Sum_probs=24.6
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccc
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYP 116 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWF 116 (135)
++.++...+...+... ....+||+.+|++...|..++
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 5665666666666655 247789999999988776554
No 94
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=46.95 E-value=26 Score=24.98 Aligned_cols=30 Identities=27% Similarity=0.201 Sum_probs=23.5
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
...++|..+|+++..|++-...-|.+-++.
T Consensus 149 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 149 SVEEVGEIVGIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999998876666655544
No 95
>PRK10072 putative transcriptional regulator; Provisional
Probab=46.75 E-value=6.3 Score=26.01 Aligned_cols=40 Identities=13% Similarity=0.117 Sum_probs=28.7
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhh
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFM 120 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR 120 (135)
+.+...+..|...-.. ...+||..+|++...|..|.+.+|
T Consensus 32 ~~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 32 TTSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred cCChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCC
Confidence 3466666666443221 367899999999999999998765
No 96
>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=46.69 E-value=26 Score=24.18 Aligned_cols=30 Identities=13% Similarity=0.078 Sum_probs=24.2
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
.-.++|..+|++...|+.+...-|.+-++.
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999887766666554
No 97
>PRK06930 positive control sigma-like factor; Validated
Probab=46.18 E-value=26 Score=25.34 Aligned_cols=48 Identities=19% Similarity=0.120 Sum_probs=32.8
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
.+++.+..++.-.|... ..-.++|..+|++...|+.+...-+.|-++.
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~ 161 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIARQ 161 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 35555555555543222 2457899999999999999988766665543
No 98
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=45.88 E-value=25 Score=24.34 Aligned_cols=47 Identities=19% Similarity=0.108 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
++..+..+|.-.| ......+||..+|++...|+.+...-+.+-|...
T Consensus 113 L~~~~r~il~l~~------~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 113 MTERDRTVLLLRF------SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred CCHHHHHHHHHHH------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4444444544444 2234678999999999999999876666655543
No 99
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=45.86 E-value=28 Score=23.84 Aligned_cols=29 Identities=14% Similarity=-0.041 Sum_probs=22.7
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
...++|..||++...|++....-|.+.|.
T Consensus 124 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 124 DVAETAAAMGCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35789999999999999887665555544
No 100
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=45.69 E-value=7.6 Score=23.08 Aligned_cols=19 Identities=26% Similarity=0.308 Sum_probs=16.6
Q ss_pred HHHHHHHcCCCcCCccccc
Q psy15107 98 REEVALKINLPESRVQGYP 116 (135)
Q Consensus 98 r~~La~~l~l~~~~V~vWF 116 (135)
..++|+.+|++...|+.|=
T Consensus 3 i~eva~~~gvs~~tlr~y~ 21 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYE 21 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4578999999999999994
No 101
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=45.33 E-value=19 Score=25.69 Aligned_cols=32 Identities=9% Similarity=0.047 Sum_probs=24.9
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
..+++|..+|++...|++....-|.+-++...
T Consensus 140 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 171 (185)
T PRK12542 140 TYQEISSVMGITEANVRKQFERARKRVQNMIG 171 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHc
Confidence 45789999999999999987766666655443
No 102
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=45.03 E-value=29 Score=24.98 Aligned_cols=36 Identities=14% Similarity=-0.050 Sum_probs=24.4
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHHhcCCCC
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVALKINLPE 132 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~~~~ 132 (135)
.-.+||..+|++...|++=...-|.+.|+...++++
T Consensus 152 s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l~~~~~ 187 (192)
T PRK09643 152 SVADAARMLGVAEGTVKSRCARGRARLAELLGYLRA 187 (192)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 457899999999999876554445555554444443
No 103
>PF13551 HTH_29: Winged helix-turn helix
Probab=44.19 E-value=31 Score=22.10 Aligned_cols=48 Identities=15% Similarity=0.121 Sum_probs=28.1
Q ss_pred CCCCcCCHHHHHHHHHhhhhcCC-----CCHHHHHH-H-HHHc--CCCcCCccccch
Q psy15107 70 RERTTFTRAQLDVLESLFGKTRY-----PDIFMREE-V-ALKI--NLPESRVQGYPD 117 (135)
Q Consensus 70 r~Rt~~t~~ql~~Le~~F~~~~~-----p~~~~r~~-L-a~~l--~l~~~~V~vWFq 117 (135)
+.+..++.++...|...+...+. .+.....+ | .... .++...|..|++
T Consensus 53 ~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 53 RPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 33334899999999999987652 33333333 3 2222 455555666653
No 104
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=43.98 E-value=32 Score=23.73 Aligned_cols=29 Identities=7% Similarity=-0.009 Sum_probs=22.2
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
...++|..+|++...|+.....-+.+.++
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46789999999999999876555555444
No 105
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=43.88 E-value=31 Score=24.06 Aligned_cols=30 Identities=10% Similarity=-0.057 Sum_probs=23.7
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
..+++|..+|+++..|+++...-|.+-|..
T Consensus 130 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 130 SYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999887666655543
No 106
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=43.49 E-value=23 Score=26.65 Aligned_cols=31 Identities=13% Similarity=-0.006 Sum_probs=25.0
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
...+||..+|+++..|++..+.-|.+-|+..
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4578999999999999998877666666543
No 107
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=43.01 E-value=28 Score=25.95 Aligned_cols=31 Identities=19% Similarity=0.186 Sum_probs=25.5
Q ss_pred HHHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 96 FMREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 96 ~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
....++|..+|++...|+.+...-+.+-|+.
T Consensus 201 ~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 201 LNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3568899999999999999988777776654
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=42.87 E-value=31 Score=23.81 Aligned_cols=29 Identities=17% Similarity=0.021 Sum_probs=21.1
Q ss_pred HHHHHHHHHcCCCcCCccccchhhhHHHH
Q psy15107 96 FMREEVALKINLPESRVQGYPDIFMREEV 124 (135)
Q Consensus 96 ~~r~~La~~l~l~~~~V~vWFqNRR~k~k 124 (135)
....++|..||+++..|+....--|.+-|
T Consensus 139 ~s~~eIA~~l~is~~tv~~~l~ra~~~Lr 167 (170)
T TIGR02952 139 LPIAEVARILGKTEGAVKILQFRAIKKLA 167 (170)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 34578999999999998887644444433
No 109
>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=42.81 E-value=8.4 Score=20.68 Aligned_cols=22 Identities=14% Similarity=0.098 Sum_probs=18.1
Q ss_pred HHHHHHHcCCCcCCccccchhh
Q psy15107 98 REEVALKINLPESRVQGYPDIF 119 (135)
Q Consensus 98 r~~La~~l~l~~~~V~vWFqNR 119 (135)
..++|+.+|++...|..|.++-
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g 24 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 4578999999999999997653
No 110
>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=42.40 E-value=36 Score=23.68 Aligned_cols=29 Identities=24% Similarity=0.291 Sum_probs=22.2
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
...++|..+|++...|+++...-|.+-++
T Consensus 137 s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45789999999999999877655555443
No 111
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=42.38 E-value=31 Score=24.70 Aligned_cols=30 Identities=7% Similarity=-0.069 Sum_probs=23.8
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
.-.++|..+|++...|+.....-|.+-|+.
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 183 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQC 183 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999887666655543
No 112
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=42.21 E-value=34 Score=24.20 Aligned_cols=32 Identities=16% Similarity=0.185 Sum_probs=25.6
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
...++|..+|+++..|++....-+.+.|+...
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 166 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ 166 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45789999999999999988877777666443
No 113
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=41.61 E-value=40 Score=23.51 Aligned_cols=29 Identities=17% Similarity=0.259 Sum_probs=22.3
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
..+++|..||+++..|+.....-|.+-|+
T Consensus 136 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 136 STAQIAADLGIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45789999999999999877655555444
No 114
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=41.49 E-value=29 Score=24.79 Aligned_cols=33 Identities=12% Similarity=-0.088 Sum_probs=25.5
Q ss_pred HHHHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 95 IFMREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 95 ~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
...-.++|..+|+++..|++..+.-|.+-|+.-
T Consensus 154 g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 154 GLSYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 334578999999999999998877666666543
No 115
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=41.27 E-value=34 Score=24.64 Aligned_cols=31 Identities=19% Similarity=0.087 Sum_probs=25.3
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
.-++||..+|++...|+.+...-|.+-|+.-
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4578999999999999999987777766543
No 116
>KOG0773|consensus
Probab=41.20 E-value=23 Score=28.23 Aligned_cols=39 Identities=15% Similarity=0.079 Sum_probs=33.4
Q ss_pred hhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 88 GKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 88 ~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
..+.|+...+...++....++..+|.+||-|.|.+.+..
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~ 155 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKE 155 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhc
Confidence 448899999999999999999999999999987775543
No 117
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=40.99 E-value=39 Score=23.93 Aligned_cols=31 Identities=23% Similarity=0.015 Sum_probs=25.1
Q ss_pred HHHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 96 FMREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 96 ~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
....++|..+|++...|++....-|.+.|+.
T Consensus 146 ~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 146 LSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999987766666653
No 118
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=40.85 E-value=45 Score=23.54 Aligned_cols=29 Identities=14% Similarity=0.108 Sum_probs=22.2
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
.-.++|..+|++...|+.+...-|.+-+.
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45789999999999999887655555443
No 119
>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=40.36 E-value=44 Score=23.50 Aligned_cols=47 Identities=23% Similarity=0.218 Sum_probs=34.9
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 73 TTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 73 t~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
+.++..|..+|+-.. .. ....++|..+|++...|..+-..-+.|-+.
T Consensus 5 ~~Lte~qr~VL~Lr~-~G-----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 5 TFLTERQIKVLELRE-KG-----LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred CCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 567888998887742 22 257789999999999999887665555553
No 120
>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=40.00 E-value=43 Score=18.33 Aligned_cols=36 Identities=22% Similarity=0.170 Sum_probs=24.7
Q ss_pred CHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccch
Q psy15107 76 TRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPD 117 (135)
Q Consensus 76 t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFq 117 (135)
+..+..++.-.+. . ....++|..++++...|+.|..
T Consensus 2 ~~~e~~i~~~~~~-~-----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLAE-G-----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHHc-C-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 4455566654332 1 2457889999999999998875
No 121
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=39.87 E-value=39 Score=24.46 Aligned_cols=37 Identities=22% Similarity=0.192 Sum_probs=31.6
Q ss_pred HHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCcc
Q psy15107 77 RAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQ 113 (135)
Q Consensus 77 ~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~ 113 (135)
..-+..|...+++.-|.+....+.+|..|+++...|.
T Consensus 25 sAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v~ 61 (160)
T COG1905 25 SALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARVY 61 (160)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHhe
Confidence 4557788888888889999999999999999987653
No 122
>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=39.86 E-value=36 Score=25.14 Aligned_cols=46 Identities=20% Similarity=0.203 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
++..+..+|...|... ....++|..+|++...|+.+...-+.+-|+
T Consensus 176 L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 176 LSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 5566666666655332 246789999999999998887655555443
No 123
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=39.49 E-value=39 Score=23.95 Aligned_cols=30 Identities=13% Similarity=0.222 Sum_probs=23.9
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
.-+++|..||+++..|+.....-+.+.+..
T Consensus 145 s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 145 KQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 457899999999999999887666665443
No 124
>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=39.27 E-value=63 Score=23.39 Aligned_cols=44 Identities=18% Similarity=0.261 Sum_probs=34.9
Q ss_pred CCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccc
Q psy15107 71 ERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYP 116 (135)
Q Consensus 71 ~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWF 116 (135)
+..+++.+++.++.+.-..+ |....+..||+++|++..-|.+=.
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~ 125 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVA 125 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhc
Confidence 34689999999998877554 677889999999999887666533
No 125
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=39.15 E-value=37 Score=25.67 Aligned_cols=47 Identities=6% Similarity=0.188 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
+++.+..+|.-.|-.. ....++|..+|++...|+.|...-+.|-|..
T Consensus 206 L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 206 LSDREKSIIQCTFIEN-----LSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5556666665554322 2457899999999999999876666665543
No 126
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=38.92 E-value=43 Score=23.79 Aligned_cols=30 Identities=20% Similarity=0.102 Sum_probs=23.5
Q ss_pred HHHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 96 FMREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 96 ~~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
....++|..+|++...|+.+...-+.+.|+
T Consensus 148 ~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 148 LSVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 356789999999999999988665555554
No 127
>PRK13870 transcriptional regulator TraR; Provisional
Probab=38.36 E-value=12 Score=28.27 Aligned_cols=43 Identities=14% Similarity=-0.067 Sum_probs=29.6
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHH
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMRE 122 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k 122 (135)
.+|+.++++|.=. -....-.++|..||++++.|..-.+|-+.|
T Consensus 173 ~LT~RE~E~L~W~------A~GKT~~EIa~ILgISe~TV~~Hl~na~~K 215 (234)
T PRK13870 173 WLDPKEATYLRWI------AVGKTMEEIADVEGVKYNSVRVKLREAMKR 215 (234)
T ss_pred CCCHHHHHHHHHH------HcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 4666666666221 112244689999999999999988887766
No 128
>PRK09480 slmA division inhibitor protein; Provisional
Probab=38.34 E-value=23 Score=24.94 Aligned_cols=38 Identities=8% Similarity=0.067 Sum_probs=30.1
Q ss_pred HHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhh
Q psy15107 82 VLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFM 120 (135)
Q Consensus 82 ~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR 120 (135)
.....|...+. .......||++.|++...+..+|.|+-
T Consensus 18 aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~ 55 (194)
T PRK09480 18 ALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKA 55 (194)
T ss_pred HHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHH
Confidence 33344555556 788889999999999999999998854
No 129
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=38.34 E-value=43 Score=24.02 Aligned_cols=30 Identities=13% Similarity=0.028 Sum_probs=23.2
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
...++|..+|++...|+++...-|.+-++.
T Consensus 129 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 158 (182)
T PRK12511 129 SYQEAAAVLGIPIGTLMSRIGRARAALRAF 158 (182)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999876655555443
No 130
>PRK10403 transcriptional regulator NarP; Provisional
Probab=38.33 E-value=24 Score=24.59 Aligned_cols=43 Identities=26% Similarity=0.355 Sum_probs=32.7
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHH
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMRE 122 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k 122 (135)
.+|..+..+|+..... ....+||+.++++++.|++..++=+.|
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~k 195 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRK 195 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 5788888888765432 346788999999999999888765554
No 131
>PHA02955 hypothetical protein; Provisional
Probab=37.72 E-value=50 Score=25.05 Aligned_cols=45 Identities=11% Similarity=0.034 Sum_probs=34.1
Q ss_pred HHHHHHHHHhhhhc-CCCCHHHHHHHHHHcCCCcCCccccchhhhH
Q psy15107 77 RAQLDVLESLFGKT-RYPDIFMREEVALKINLPESRVQGYPDIFMR 121 (135)
Q Consensus 77 ~~ql~~Le~~F~~~-~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~ 121 (135)
..++..|-+.|.+. .-++..++.+++.+||+....|..||.+.=.
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~~ 105 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDLQ 105 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchhh
Confidence 34566666666554 5688889999999999999888999987443
No 132
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=37.15 E-value=36 Score=27.13 Aligned_cols=53 Identities=25% Similarity=0.207 Sum_probs=38.0
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
.++..+..+|+..|.- .|......++||..+|++...|+.+...-+.|-|+..
T Consensus 262 ~L~~~~R~vl~lrygL-~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGL-LGYEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhcc-CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4667777777766522 2233456789999999999999999887777766554
No 133
>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=37.02 E-value=12 Score=22.33 Aligned_cols=20 Identities=20% Similarity=0.243 Sum_probs=17.1
Q ss_pred HHHHHHHcCCCcCCccccch
Q psy15107 98 REEVALKINLPESRVQGYPD 117 (135)
Q Consensus 98 r~~La~~l~l~~~~V~vWFq 117 (135)
..++|+.+|++...++.|.+
T Consensus 3 i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999964
No 134
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=37.01 E-value=27 Score=24.28 Aligned_cols=43 Identities=21% Similarity=0.248 Sum_probs=32.7
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHH
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMRE 122 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k 122 (135)
.+|+.+..+|+-..+. ..++++|..++++++.|++..++=|.|
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~K 179 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEK 179 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 5788888888776543 257789999999999998887765554
No 135
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=36.70 E-value=50 Score=23.94 Aligned_cols=33 Identities=12% Similarity=0.021 Sum_probs=26.1
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHHhcC
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVALKIN 129 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~~ 129 (135)
.-.++|..+|++...|+++...-|.+-|+....
T Consensus 151 s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~ 183 (196)
T PRK12535 151 TYEEAAKIADVRVGTIRSRVARARADLIAATAT 183 (196)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 457899999999999999987767666665543
No 136
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=36.53 E-value=37 Score=23.85 Aligned_cols=31 Identities=19% Similarity=0.223 Sum_probs=23.7
Q ss_pred HHHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 96 FMREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 96 ~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
...++||..+|++...|+++...-+.+.+..
T Consensus 136 ~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~ 166 (172)
T PRK09651 136 LTYSEIAHKLGVSVSSVKKYVAKATEHCLLF 166 (172)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3468999999999999999886655554443
No 137
>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=36.28 E-value=44 Score=24.64 Aligned_cols=46 Identities=11% Similarity=0.091 Sum_probs=31.6
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHH
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEV 124 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k 124 (135)
.+++.+..++...|.. .....++|..+|++...|+.|...-+.+.|
T Consensus 178 ~L~~~~r~vl~l~y~~-----~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr 223 (227)
T TIGR02980 178 ALPERERRILLLRFFE-----DKTQSEIAERLGISQMHVSRLLRRALKKLR 223 (227)
T ss_pred cCCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 3566666666555432 235678999999999999998765555444
No 138
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=36.25 E-value=23 Score=24.73 Aligned_cols=37 Identities=16% Similarity=0.064 Sum_probs=28.3
Q ss_pred CCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 92 YPDIFMREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 92 ~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
|.....-+++|..+|++...|++.+..-|.+.++...
T Consensus 133 ~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 133 DLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3444456899999999999999998777776665543
No 139
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=36.06 E-value=29 Score=23.29 Aligned_cols=39 Identities=10% Similarity=0.169 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhh
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFM 120 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR 120 (135)
++..++..+.+.+.-. +...|..||++...|+.|=|+|+
T Consensus 44 ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~ 82 (104)
T COG2944 44 LSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRK 82 (104)
T ss_pred CCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCc
Confidence 7888888887776543 45789999999999999988875
No 140
>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=36.05 E-value=44 Score=25.24 Aligned_cols=46 Identities=7% Similarity=0.204 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
+++.+..++.-.|... ....++|..+|++...|+.+...-+.+-|.
T Consensus 206 L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 206 LSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred CCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5566666666555332 245789999999999999887666666554
No 141
>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=35.99 E-value=13 Score=22.05 Aligned_cols=21 Identities=19% Similarity=0.178 Sum_probs=17.4
Q ss_pred HHHHHHHcCCCcCCccccchh
Q psy15107 98 REEVALKINLPESRVQGYPDI 118 (135)
Q Consensus 98 r~~La~~l~l~~~~V~vWFqN 118 (135)
..++|+.+|++...++.|-++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 457899999999999999653
No 142
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=35.90 E-value=44 Score=25.27 Aligned_cols=46 Identities=13% Similarity=0.170 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
+++.+..++.-.|. ......++|..+|++...|+.++..-+.+-|.
T Consensus 202 L~~~~r~vl~l~~~-----~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 202 LSEKEQLVISLFYK-----EELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 34445555544432 22346789999999999999988766665554
No 143
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=35.82 E-value=49 Score=23.99 Aligned_cols=30 Identities=3% Similarity=-0.072 Sum_probs=23.6
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
.-.++|..+|+++..|++....-|.+-|+.
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 186 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRTC 186 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999877666655543
No 144
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=35.73 E-value=11 Score=20.28 Aligned_cols=18 Identities=22% Similarity=0.253 Sum_probs=14.3
Q ss_pred HHHHHHHcCCCcCCcccc
Q psy15107 98 REEVALKINLPESRVQGY 115 (135)
Q Consensus 98 r~~La~~l~l~~~~V~vW 115 (135)
+.++|+.+|++...|+.|
T Consensus 2 i~e~A~~~gvs~~tlR~y 19 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYY 19 (38)
T ss_dssp HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHH
Confidence 357899999999998888
No 145
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=35.72 E-value=46 Score=23.37 Aligned_cols=32 Identities=13% Similarity=-0.021 Sum_probs=24.2
Q ss_pred HHHHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 95 IFMREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 95 ~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
...-+++|..+|++...|++....-|.+-++.
T Consensus 152 ~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 152 DLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34567899999999999988876666665543
No 146
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=35.61 E-value=52 Score=23.62 Aligned_cols=29 Identities=14% Similarity=0.154 Sum_probs=21.8
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
.-+++|..+|++...|++-...-|.+-|+
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr~ 187 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLRH 187 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 45789999999999998876555554443
No 147
>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=34.95 E-value=31 Score=19.44 Aligned_cols=32 Identities=13% Similarity=0.213 Sum_probs=19.8
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccc
Q psy15107 80 LDVLESLFGKTRYPDIFMREEVALKINLPESRVQG 114 (135)
Q Consensus 80 l~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~v 114 (135)
..+|+-.++...+. ...+||.+|+++.+.|+.
T Consensus 3 ~~il~~L~~~~~~i---t~~eLa~~l~vS~rTi~~ 34 (55)
T PF08279_consen 3 KQILKLLLESKEPI---TAKELAEELGVSRRTIRR 34 (55)
T ss_dssp HHHHHHHHHTTTSB---EHHHHHHHCTS-HHHHHH
T ss_pred HHHHHHHHHcCCCc---CHHHHHHHhCCCHHHHHH
Confidence 44555544444443 456899999999987654
No 148
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=34.92 E-value=52 Score=24.09 Aligned_cols=29 Identities=17% Similarity=0.037 Sum_probs=23.3
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
.-.++|..||+++..|+++...-|.+-++
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~Lr~ 184 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQLRA 184 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45789999999999999988766665554
No 149
>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=34.72 E-value=51 Score=23.61 Aligned_cols=30 Identities=10% Similarity=-0.030 Sum_probs=22.9
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
..++||..+|++...|++....-|.+-|+.
T Consensus 149 s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 149 ESDEICQELEISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999998776655554443
No 150
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=34.47 E-value=44 Score=24.88 Aligned_cols=31 Identities=23% Similarity=0.118 Sum_probs=24.4
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
.-++||..||+++..|+++...-|.+-++..
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4578999999999999998876666655543
No 151
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=34.19 E-value=52 Score=23.45 Aligned_cols=30 Identities=7% Similarity=-0.093 Sum_probs=23.3
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
.-.+||..+|+++..|++....-|.+-|..
T Consensus 149 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (191)
T PRK12520 149 ETEEICQELQITATNAWVLLYRARMRLREC 178 (191)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999877655555443
No 152
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=33.71 E-value=31 Score=21.84 Aligned_cols=20 Identities=30% Similarity=0.512 Sum_probs=17.2
Q ss_pred HHHHHHHcCCCcCCccccch
Q psy15107 98 REEVALKINLPESRVQGYPD 117 (135)
Q Consensus 98 r~~La~~l~l~~~~V~vWFq 117 (135)
+..|...++|.+.++.+|+.
T Consensus 56 ~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 56 TSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHHHhCCCCCeEEEEEE
Confidence 55688889999999999985
No 153
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=33.45 E-value=46 Score=23.75 Aligned_cols=29 Identities=10% Similarity=-0.013 Sum_probs=22.2
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
.-++||..+|+++..|+++...-|.+-|+
T Consensus 148 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45789999999999999987555554443
No 154
>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=32.72 E-value=54 Score=24.94 Aligned_cols=29 Identities=7% Similarity=0.032 Sum_probs=23.6
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
..+++|..+|++...|+++...-|.+-|+
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~ 207 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLE 207 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45789999999999999999876665544
No 155
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=32.64 E-value=52 Score=22.63 Aligned_cols=26 Identities=15% Similarity=0.163 Sum_probs=20.3
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMRE 122 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k 122 (135)
.-.++|..+|++...|+++...-+.+
T Consensus 131 s~~EIA~~l~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 131 GYGEIATELGISLATVKRYLNKAAMR 156 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 45789999999999999887654443
No 156
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=32.59 E-value=45 Score=24.76 Aligned_cols=51 Identities=14% Similarity=0.163 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
+++.+..++.-.|.. .+.....-.++|..+|++...|+.+...-+.+-|+.
T Consensus 179 Lp~~~R~v~~L~y~l-~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 179 LSDREKQIMELRFGL-NGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred CCHHHHHHHHHHhcc-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 444555555444411 012334567899999999999999877666665544
No 157
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=32.24 E-value=35 Score=23.81 Aligned_cols=44 Identities=16% Similarity=0.243 Sum_probs=33.2
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHH
Q psy15107 73 TTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMRE 122 (135)
Q Consensus 73 t~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k 122 (135)
..++..+..+|+...+. ...+++|..++++.+.|+++.++=|.|
T Consensus 148 ~~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~k 191 (210)
T PRK09935 148 TVLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGK 191 (210)
T ss_pred ccCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 34788888888654433 457889999999999999987765555
No 158
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=32.15 E-value=44 Score=22.91 Aligned_cols=43 Identities=16% Similarity=0.258 Sum_probs=32.3
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHH
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMRE 122 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k 122 (135)
.+|..+..+|+- +..+ + ...++|..+++++..|+.+.++=+.|
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~k 191 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRK 191 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 488888888876 3333 2 25788999999999999998875555
No 159
>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=31.98 E-value=16 Score=21.49 Aligned_cols=20 Identities=10% Similarity=0.122 Sum_probs=16.8
Q ss_pred HHHHHHHcCCCcCCccccch
Q psy15107 98 REEVALKINLPESRVQGYPD 117 (135)
Q Consensus 98 r~~La~~l~l~~~~V~vWFq 117 (135)
..++|+.+|++...++.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999964
No 160
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=31.82 E-value=56 Score=22.82 Aligned_cols=30 Identities=13% Similarity=0.080 Sum_probs=23.3
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
.-+++|..+|++...|++....-|.+-++.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999876655555543
No 161
>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=31.71 E-value=19 Score=24.50 Aligned_cols=34 Identities=21% Similarity=0.047 Sum_probs=25.9
Q ss_pred CCCHHHHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 92 YPDIFMREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 92 ~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
|......+++|..+|+++..|+++...-|.+-++
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4455567899999999999999987665555543
No 162
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=31.70 E-value=58 Score=23.24 Aligned_cols=35 Identities=20% Similarity=0.206 Sum_probs=27.3
Q ss_pred HHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCcc
Q psy15107 79 QLDVLESLFGKTRYPDIFMREEVALKINLPESRVQ 113 (135)
Q Consensus 79 ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~ 113 (135)
-+..|...=+...|.+......+|..|+++..+|.
T Consensus 25 li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~ 59 (156)
T PRK05988 25 LLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVH 59 (156)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHH
Confidence 35555555555679999999999999999987754
No 163
>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=31.61 E-value=31 Score=24.73 Aligned_cols=37 Identities=14% Similarity=-0.010 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 92 YPDIFMREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 92 ~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
|.......+||..+|+++..|+++...-|.+.|+...
T Consensus 144 ~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 144 DVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred hhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3444456899999999999999998877777666543
No 164
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=31.24 E-value=57 Score=22.75 Aligned_cols=28 Identities=14% Similarity=0.125 Sum_probs=21.9
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEV 124 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k 124 (135)
.-+++|..||++...|+.+..+-+.+.+
T Consensus 136 s~~EIA~~l~is~~tV~~~l~ra~~~~~ 163 (168)
T PRK12525 136 TYVEIGERLGVSLSRIHQYMVEAFKCCY 163 (168)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4578999999999999988766555544
No 165
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=30.90 E-value=63 Score=23.68 Aligned_cols=30 Identities=10% Similarity=-0.069 Sum_probs=23.6
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
...++|..+|++...|++....-|.+-|+.
T Consensus 166 s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~ 195 (206)
T PRK12544 166 ETNEICHAVDLSVSNLNVLLYRARLRLREC 195 (206)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999887666655543
No 166
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=30.33 E-value=61 Score=24.66 Aligned_cols=47 Identities=17% Similarity=0.157 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
++..+..+|...|.. .....++|..+|++...|+.+...-+.|-|..
T Consensus 204 L~~~~r~vl~l~y~~-----~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 204 LEERTREVLEFVFLH-----DLTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred CCHHHHHHHHHHHHC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 445555555555532 33568899999999999999876655555543
No 167
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=30.00 E-value=64 Score=24.64 Aligned_cols=46 Identities=15% Similarity=0.132 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
+++.+..+|...|.. .....++|..+|++...|+.....-+.+-|+
T Consensus 213 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 258 (268)
T PRK06288 213 LPEREKKVLILYYYE-----DLTLKEIGKVLGVTESRISQLHTKAVLQLRA 258 (268)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 455555555555432 2346789999999999998877665555444
No 168
>PRK10651 transcriptional regulator NarL; Provisional
Probab=29.93 E-value=60 Score=22.54 Aligned_cols=43 Identities=16% Similarity=0.270 Sum_probs=32.8
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHH
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMRE 122 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k 122 (135)
.+|..+.++|+-..+. ....++|.++++++..|++..++=+.|
T Consensus 155 ~Lt~rE~~vl~~l~~g------~~~~~ia~~l~is~~tV~~~~~~l~~K 197 (216)
T PRK10651 155 QLTPRERDILKLIAQG------LPNKMIARRLDITESTVKVHVKHMLKK 197 (216)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 4899999888765532 135678999999999999988776555
No 169
>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=29.92 E-value=49 Score=22.23 Aligned_cols=37 Identities=11% Similarity=0.094 Sum_probs=25.5
Q ss_pred CHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccch
Q psy15107 76 TRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPD 117 (135)
Q Consensus 76 t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFq 117 (135)
+.+-....-..++... .+.++|..++++...|..||+
T Consensus 4 S~DlR~rVl~~~~~g~-----s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 4 SLDLRQRVLAYIEKGK-----SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred CHHHHHHHHHHHHccc-----hHHHHHHHhCcHHHHHHHHHH
Confidence 3333444444555433 456789999999999999998
No 170
>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=29.76 E-value=64 Score=22.61 Aligned_cols=35 Identities=14% Similarity=0.031 Sum_probs=26.5
Q ss_pred HHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCcc
Q psy15107 79 QLDVLESLFGKTRYPDIFMREEVALKINLPESRVQ 113 (135)
Q Consensus 79 ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~ 113 (135)
-+..|...=+...|.+....+.+|..|+++..+|.
T Consensus 18 li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 18 IMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 34455544455669999999999999999987654
No 171
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=29.76 E-value=60 Score=24.17 Aligned_cols=43 Identities=16% Similarity=0.170 Sum_probs=33.8
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHH
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMRE 122 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k 122 (135)
.+|+.+.++|+-..+- ..-.++|..|++++..|+.+..+-..|
T Consensus 155 ~Lt~rE~~Vl~l~~~G------~s~~eIA~~L~iS~~TVk~~~~~i~~K 197 (216)
T PRK10100 155 LLTHREKEILNKLRIG------ASNNEIARSLFISENTVKTHLYNLFKK 197 (216)
T ss_pred CCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 4899999999877652 235688999999999999988765444
No 172
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=29.71 E-value=63 Score=22.81 Aligned_cols=35 Identities=17% Similarity=0.131 Sum_probs=27.0
Q ss_pred HHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCcc
Q psy15107 79 QLDVLESLFGKTRYPDIFMREEVALKINLPESRVQ 113 (135)
Q Consensus 79 ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~ 113 (135)
-+.+|...=+...|.+......+|..++++..+|.
T Consensus 24 ll~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v~ 58 (154)
T PRK07539 24 VIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVE 58 (154)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 34555555555679999999999999999987764
No 173
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=29.65 E-value=64 Score=23.15 Aligned_cols=32 Identities=13% Similarity=-0.024 Sum_probs=24.5
Q ss_pred HHHHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 95 IFMREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 95 ~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
...-.++|..+|++...|++-...-|.+-++.
T Consensus 170 ~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 170 GKSYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34567899999999999998777666665543
No 174
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=29.63 E-value=27 Score=24.98 Aligned_cols=35 Identities=20% Similarity=0.136 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 93 PDIFMREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 93 p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
.......++|..+|++...|+.+...-|.+-|+..
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 153 HGDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34445689999999999999988877666666543
No 175
>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=29.49 E-value=61 Score=24.92 Aligned_cols=46 Identities=13% Similarity=0.127 Sum_probs=35.1
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHH
Q psy15107 72 RTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREE 123 (135)
Q Consensus 72 Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~ 123 (135)
...+|+.+.++|+-..+- ....++|..|++++..|+.+.+|=+.|-
T Consensus 188 ~~~LT~RE~evl~l~a~G------~s~~eIA~~L~IS~~TVk~hl~~i~~KL 233 (247)
T TIGR03020 188 AGLITAREAEILAWVRDG------KTNEEIAAILGISSLTVKNHLQHIFKKL 233 (247)
T ss_pred ccCCCHHHHHHHHHHHCC------CCHHHHHHHHCcCHHHHHHHHHHHHHHh
Confidence 346899999999864422 3467889999999999999988765553
No 176
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=29.45 E-value=26 Score=25.03 Aligned_cols=34 Identities=9% Similarity=-0.148 Sum_probs=26.2
Q ss_pred CHHHHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 94 DIFMREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 94 ~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
.....+++|..+|++...|+++...-+.+-|...
T Consensus 149 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 149 AELEFQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3345689999999999999999877666665543
No 177
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=29.36 E-value=65 Score=20.44 Aligned_cols=44 Identities=14% Similarity=0.128 Sum_probs=30.8
Q ss_pred cCCHHHHHHHHHhhhh-----cCCCCHHHHHHHHHHcCCCcCCccccch
Q psy15107 74 TFTRAQLDVLESLFGK-----TRYPDIFMREEVALKINLPESRVQGYPD 117 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~-----~~~p~~~~r~~La~~l~l~~~~V~vWFq 117 (135)
.++.+|+..|...|.. ..+.+..+...+-..+++++..|..+|.
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 4678888888888855 2356777777766667887777666654
No 178
>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=29.29 E-value=16 Score=26.08 Aligned_cols=33 Identities=18% Similarity=0.089 Sum_probs=24.5
Q ss_pred CCCHHHHHHHHHHcCCCcCCccccchhhhHHHH
Q psy15107 92 YPDIFMREEVALKINLPESRVQGYPDIFMREEV 124 (135)
Q Consensus 92 ~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k 124 (135)
|.......++|..+|++...|++.+..-|.+-|
T Consensus 162 ~~~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~ 194 (198)
T TIGR02859 162 YLDGKSYQEIACDLNRHVKSIDNALQRVKRKLE 194 (198)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 344456689999999999999987765555544
No 179
>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=28.62 E-value=83 Score=24.21 Aligned_cols=29 Identities=21% Similarity=0.070 Sum_probs=24.1
Q ss_pred HHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 98 REEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 98 r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
-.++|..+|+++..|+..++.-|.+-+..
T Consensus 127 ~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 127 YEEIASIVGKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 47899999999999999988777766654
No 180
>PF13565 HTH_32: Homeodomain-like domain
Probab=28.38 E-value=1.4e+02 Score=17.81 Aligned_cols=33 Identities=9% Similarity=-0.027 Sum_probs=23.4
Q ss_pred CHHHHHHHHHhhhhcCCCCHHHHHH-HHHHcCCC
Q psy15107 76 TRAQLDVLESLFGKTRYPDIFMREE-VALKINLP 108 (135)
Q Consensus 76 t~~ql~~Le~~F~~~~~p~~~~r~~-La~~l~l~ 108 (135)
+.++...|......++..+..+... |..++|+.
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~ 65 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGIS 65 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCC
Confidence 6777788888888887666665554 66666643
No 181
>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=28.35 E-value=48 Score=23.14 Aligned_cols=34 Identities=24% Similarity=0.281 Sum_probs=24.2
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCcc
Q psy15107 80 LDVLESLFGKTRYPDIFMREEVALKINLPESRVQ 113 (135)
Q Consensus 80 l~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~ 113 (135)
+..|...=+...|.+......+|+.|+|+..+|.
T Consensus 16 l~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~ 49 (145)
T PF01257_consen 16 LPILHEVQEEYGYIPEEALEEIAEALGIPPAEVY 49 (145)
T ss_dssp HHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHHH
Confidence 5556555555679999999999999999987764
No 182
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=28.20 E-value=72 Score=22.93 Aligned_cols=29 Identities=17% Similarity=0.021 Sum_probs=22.7
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
..+++|..+|+++..|+..++.-|.+-++
T Consensus 153 s~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 153 SVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45789999999999999877766655443
No 183
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=28.19 E-value=1e+02 Score=21.75 Aligned_cols=29 Identities=17% Similarity=0.171 Sum_probs=21.0
Q ss_pred HHHHHHHHHcCCCcCCccccchhhhHHHH
Q psy15107 96 FMREEVALKINLPESRVQGYPDIFMREEV 124 (135)
Q Consensus 96 ~~r~~La~~l~l~~~~V~vWFqNRR~k~k 124 (135)
..-+++|..||++...|++-...-|.+-|
T Consensus 154 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr 182 (187)
T PRK12534 154 ITYEELAARTDTPIGTVKSWIRRGLAKLK 182 (187)
T ss_pred CCHHHHHHHhCCChhHHHHHHHHHHHHHH
Confidence 34578999999999998876554444433
No 184
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=27.71 E-value=78 Score=20.81 Aligned_cols=43 Identities=12% Similarity=0.084 Sum_probs=30.7
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCC-CcCCccccchh
Q psy15107 72 RTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINL-PESRVQGYPDI 118 (135)
Q Consensus 72 Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l-~~~~V~vWFqN 118 (135)
|..|+.+....+-..+....+ ....+|.++|+ ...++..|-..
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~~ 48 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRIQ 48 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHHH
Confidence 667888876655555444433 56789999996 99999988643
No 185
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=27.56 E-value=69 Score=24.58 Aligned_cols=46 Identities=11% Similarity=0.104 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
++..+..+|.-.|.. .....++|..+|++...|+.+...-+.+-|.
T Consensus 216 L~~rer~vl~l~y~~-----~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 216 LPERERTVLVLRFFE-----SMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred CCHHHHHHHHHHhcC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 455555566655532 3356889999999999999887665555443
No 186
>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=26.88 E-value=72 Score=23.84 Aligned_cols=51 Identities=22% Similarity=0.233 Sum_probs=34.4
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
.++..+..+|...|.... .......++|..+|++...|+.....-..|-|.
T Consensus 176 ~L~~~er~vl~l~ygl~~-~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~ 226 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLD-GRPHTLEEVGKEFNVTRERIRQIESKALRKLRH 226 (238)
T ss_pred hCCHHHHHHHHHHhCCCC-CCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 356666677776663211 123357889999999999999887665555554
No 187
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=26.47 E-value=80 Score=22.94 Aligned_cols=34 Identities=29% Similarity=0.257 Sum_probs=25.7
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCcc
Q psy15107 80 LDVLESLFGKTRYPDIFMREEVALKINLPESRVQ 113 (135)
Q Consensus 80 l~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~ 113 (135)
+..|...=+...|.+....+.+|+.||++..+|.
T Consensus 39 i~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V~ 72 (169)
T PRK07571 39 IEVLHKAQELFGYLERDLLLYVARQLKLPLSRVY 72 (169)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHH
Confidence 4444444455679999999999999999987654
No 188
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=26.18 E-value=74 Score=24.57 Aligned_cols=31 Identities=10% Similarity=0.041 Sum_probs=24.9
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
..+++|..+|+++..|+...+.-|.+-+...
T Consensus 133 s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~ 163 (293)
T PRK09636 133 PFDEIASTLGRSPAACRQLASRARKHVRAAR 163 (293)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 3578999999999999999887776666543
No 189
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=26.08 E-value=93 Score=21.30 Aligned_cols=28 Identities=14% Similarity=0.077 Sum_probs=21.2
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEV 124 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k 124 (135)
..+++|..+|+++..|++....-+.+.+
T Consensus 123 s~~eIA~~lgis~~tv~~~l~ra~~~Lr 150 (159)
T PRK12527 123 SHQQIAEHLGISRSLVEKHIVNAMKHCR 150 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4578999999999999887665444444
No 190
>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=26.00 E-value=18 Score=20.33 Aligned_cols=23 Identities=17% Similarity=0.198 Sum_probs=18.5
Q ss_pred HHHHHHHcCCCcCCccccchhhh
Q psy15107 98 REEVALKINLPESRVQGYPDIFM 120 (135)
Q Consensus 98 r~~La~~l~l~~~~V~vWFqNRR 120 (135)
..+||+.+|++...|..|..+.+
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 47899999999999999987743
No 191
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=25.93 E-value=82 Score=23.43 Aligned_cols=49 Identities=14% Similarity=0.183 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHH
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEV 124 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k 124 (135)
+++.+..++...|--. .......+++|..+|++...|+.+-..-+.+.|
T Consensus 176 Lp~~~R~i~~l~y~~~-~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr 224 (233)
T PRK05803 176 LDEREKEVIEMRYGLG-NGKEKTQREIAKALGISRSYVSRIEKRALKKLF 224 (233)
T ss_pred CCHHHHHHHHHHhCCC-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4455555555544110 022345678999999999999887443333333
No 192
>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=25.67 E-value=14 Score=20.49 Aligned_cols=20 Identities=10% Similarity=0.002 Sum_probs=18.0
Q ss_pred HHHHHcCCCcCCccccchhh
Q psy15107 100 EVALKINLPESRVQGYPDIF 119 (135)
Q Consensus 100 ~La~~l~l~~~~V~vWFqNR 119 (135)
+||+.+|++...|..|+.+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 58999999999999999886
No 193
>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=25.40 E-value=22 Score=19.76 Aligned_cols=23 Identities=4% Similarity=-0.128 Sum_probs=19.5
Q ss_pred HHHHHHHcCCCcCCccccchhhh
Q psy15107 98 REEVALKINLPESRVQGYPDIFM 120 (135)
Q Consensus 98 r~~La~~l~l~~~~V~vWFqNRR 120 (135)
..+||..+|++...|..|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 57899999999999999986653
No 194
>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=25.28 E-value=83 Score=23.24 Aligned_cols=39 Identities=13% Similarity=0.129 Sum_probs=26.8
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccch
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPD 117 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFq 117 (135)
.++..+..++...|.. .....++|..+|++...|..+-.
T Consensus 183 ~L~~~e~~i~~~~~~~-----~~t~~eIA~~lgis~~~V~~~~~ 221 (231)
T TIGR02885 183 KLDERERQIIMLRYFK-----DKTQTEVANMLGISQVQVSRLEK 221 (231)
T ss_pred cCCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHH
Confidence 3556666666655532 23578899999999988876643
No 195
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=25.14 E-value=25 Score=18.80 Aligned_cols=21 Identities=19% Similarity=0.090 Sum_probs=16.5
Q ss_pred HHHHHHHcCCCcCCccccchh
Q psy15107 98 REEVALKINLPESRVQGYPDI 118 (135)
Q Consensus 98 r~~La~~l~l~~~~V~vWFqN 118 (135)
..++|+.||++...|..|.++
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHc
Confidence 457788999999888888644
No 196
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=25.11 E-value=78 Score=22.32 Aligned_cols=29 Identities=14% Similarity=-0.065 Sum_probs=22.7
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
..+++|..+|++...|+.+...-|.+-+.
T Consensus 145 s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 145 SIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45789999999999999887665555554
No 197
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=24.88 E-value=88 Score=23.70 Aligned_cols=43 Identities=16% Similarity=0.184 Sum_probs=30.3
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhH
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMR 121 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~ 121 (135)
.++..+..+++..|... ....++|..+|++...|...-.+-..
T Consensus 209 ~L~~~er~vi~~~~~~~-----~t~~eIA~~lgis~~~V~~~~~~al~ 251 (258)
T PRK08215 209 KLNDREKLILNLRFFQG-----KTQMEVAEEIGISQAQVSRLEKAALK 251 (258)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 46777777777777432 34678999999999988776544333
No 198
>PTZ00183 centrin; Provisional
Probab=24.82 E-value=2.2e+02 Score=18.99 Aligned_cols=41 Identities=20% Similarity=0.164 Sum_probs=30.2
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhh-----cCCCCHHHHHHHHHHcCC
Q psy15107 67 KQRRERTTFTRAQLDVLESLFGK-----TRYPDIFMREEVALKINL 107 (135)
Q Consensus 67 k~rr~Rt~~t~~ql~~Le~~F~~-----~~~p~~~~r~~La~~l~l 107 (135)
+.+-.+..++..++..++..|.. +.+.+..+...+...+++
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~g~ 48 (158)
T PTZ00183 3 KRRSERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGF 48 (158)
T ss_pred ccccccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHhCC
Confidence 44556778999999999999854 456777777776666664
No 199
>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=24.42 E-value=49 Score=24.78 Aligned_cols=45 Identities=13% Similarity=0.040 Sum_probs=33.8
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHH
Q psy15107 73 TTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREE 123 (135)
Q Consensus 73 t~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~ 123 (135)
..++..+.++|.-..+ ...-.++|..|++++..|+.+..|=+.|-
T Consensus 170 ~~Lt~re~evl~~~a~------G~t~~eIa~~l~is~~Tv~~~l~~~~~kl 214 (232)
T TIGR03541 170 GVLSEREREVLAWTAL------GRRQADIAAILGISERTVENHLRSARRKL 214 (232)
T ss_pred ccCCHHHHHHHHHHHC------CCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 4578888888866431 23457889999999999999988766654
No 200
>KOG3862|consensus
Probab=24.15 E-value=90 Score=24.80 Aligned_cols=26 Identities=27% Similarity=0.639 Sum_probs=22.0
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHH
Q psy15107 72 RTTFTRAQLDVLESLFGKTRYPDIFM 97 (135)
Q Consensus 72 Rt~~t~~ql~~Le~~F~~~~~p~~~~ 97 (135)
-..|+..+++.|+..|+..+|+....
T Consensus 223 ~d~ft~~~~~~ld~~~~r~~y~~~~~ 248 (327)
T KOG3862|consen 223 ADAFTQQHLEPLDRSFERPHYPLVYA 248 (327)
T ss_pred cccccccccccccceeeccccccccc
Confidence 44689999999999999999887753
No 201
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=23.87 E-value=28 Score=20.45 Aligned_cols=19 Identities=21% Similarity=0.144 Sum_probs=15.7
Q ss_pred HHHHHHHcCCCcCCccccc
Q psy15107 98 REEVALKINLPESRVQGYP 116 (135)
Q Consensus 98 r~~La~~l~l~~~~V~vWF 116 (135)
..++|+.+|+++..|+.|-
T Consensus 3 ~~eva~~~gvs~~tlr~~~ 21 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYE 21 (70)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 3578899999999998884
No 202
>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=23.33 E-value=82 Score=24.13 Aligned_cols=50 Identities=14% Similarity=0.190 Sum_probs=34.9
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
.++..+..+|...|.. -......++|..+|++...|+-...+-..|-|+.
T Consensus 218 ~L~~rer~vl~l~y~~---~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~ 267 (270)
T TIGR02392 218 SLDARSRRIIEARWLD---DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAA 267 (270)
T ss_pred cCCHHHHHHHHHHhcC---CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4667777777777632 1133567999999999999988776666665543
No 203
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=23.31 E-value=81 Score=16.98 Aligned_cols=14 Identities=43% Similarity=0.517 Sum_probs=11.7
Q ss_pred cCCHHHHHHHHHhh
Q psy15107 74 TFTRAQLDVLESLF 87 (135)
Q Consensus 74 ~~t~~ql~~Le~~F 87 (135)
.||..|+..|+.--
T Consensus 2 ~FT~~Ql~~L~~Qi 15 (37)
T PF08880_consen 2 PFTPAQLQELRAQI 15 (37)
T ss_pred CCCHHHHHHHHHHH
Confidence 58999999998753
No 204
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=23.29 E-value=19 Score=24.41 Aligned_cols=25 Identities=12% Similarity=0.014 Sum_probs=20.5
Q ss_pred CHHHHHHHHHHcCCCcCCccccchh
Q psy15107 94 DIFMREEVALKINLPESRVQGYPDI 118 (135)
Q Consensus 94 ~~~~r~~La~~l~l~~~~V~vWFqN 118 (135)
.....++||..+|+++..+..+|+.
T Consensus 24 ~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 24 SPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3456788999999999999888874
No 205
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=23.25 E-value=1e+02 Score=23.52 Aligned_cols=47 Identities=15% Similarity=0.159 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
+.+.+..+|...|.. .....+||..+|++...|+.+...-+.|-|+.
T Consensus 206 L~~~er~vi~l~y~e-----~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 206 LEEKERKVMALYYYE-----ELVLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred CCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 455555555555532 23567899999999999988766555554443
No 206
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=23.16 E-value=78 Score=24.66 Aligned_cols=51 Identities=12% Similarity=0.067 Sum_probs=36.4
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
.++..+..+|.-.|. +-......+||..+|++...|+.+-..-+.|-|...
T Consensus 227 ~L~~rer~vl~lr~~---~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l 277 (289)
T PRK07500 227 TLNERELRIIRERRL---REDGATLEALGEELGISKERVRQIEARALEKLRRAL 277 (289)
T ss_pred cCCHHHHHHHHHHhc---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 467777777777663 123346789999999999999988776666655443
No 207
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=22.85 E-value=94 Score=24.10 Aligned_cols=32 Identities=9% Similarity=-0.121 Sum_probs=25.0
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
.-.+||..||+++..|+.....-|.+-|+...
T Consensus 160 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 160 RAAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 35789999999999999988776666655443
No 208
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=22.85 E-value=55 Score=24.34 Aligned_cols=36 Identities=22% Similarity=0.079 Sum_probs=27.3
Q ss_pred CCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHHh
Q psy15107 92 YPDIFMREEVALKINLPESRVQGYPDIFMREEVALK 127 (135)
Q Consensus 92 ~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~ 127 (135)
|.......++|..+|++...|++....-|.|-|+..
T Consensus 162 ~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 162 VVEELSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 444456789999999999999988766666666544
No 209
>PF08452 DNAP_B_exo_N: DNA polymerase family B exonuclease domain, N-terminal; InterPro: IPR013660 This domain is found in viral DNA polymerases to the N terminus of DNA polymerase family B exonuclease domains (IPR006133 from INTERPRO). ; GO: 0003887 DNA-directed DNA polymerase activity
Probab=22.70 E-value=27 Score=16.63 Aligned_cols=8 Identities=0% Similarity=-0.288 Sum_probs=6.3
Q ss_pred cccchhhh
Q psy15107 113 QGYPDIFM 120 (135)
Q Consensus 113 ~vWFqNRR 120 (135)
-+||.+|.
T Consensus 6 iNWFE~~g 13 (22)
T PF08452_consen 6 INWFESRG 13 (22)
T ss_pred eehhhhCC
Confidence 47999876
No 210
>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=22.20 E-value=1.1e+02 Score=23.55 Aligned_cols=52 Identities=23% Similarity=0.211 Sum_probs=33.8
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHHHH
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVAL 126 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~~ 126 (135)
.++..+..+|.-.|.. .|.......+||..||++...|+.+...-+.+-|+.
T Consensus 222 ~Lp~~~R~Vl~l~ygL-~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~ 273 (285)
T TIGR02394 222 ELNERQREVLARRFGL-LGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRI 273 (285)
T ss_pred cCCHHHHHHHHHHhCC-CCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3555666666655411 112334567899999999999999876666655543
No 211
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=22.19 E-value=67 Score=23.66 Aligned_cols=44 Identities=18% Similarity=0.162 Sum_probs=31.2
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchh
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDI 118 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqN 118 (135)
.+|..++.+|...-..+ +-....-+++|.++++++..|+..+.+
T Consensus 158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~~~~~~ 201 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCRKYLIW 201 (239)
T ss_pred CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHHHHHHH
Confidence 46777776665554422 344456678999999999999987764
No 212
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=22.19 E-value=40 Score=23.52 Aligned_cols=34 Identities=21% Similarity=0.164 Sum_probs=25.2
Q ss_pred CCCHHHHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 92 YPDIFMREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 92 ~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
|......++||..+|++...|+.+...-|.+.++
T Consensus 139 ~~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 139 HYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred hhcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHH
Confidence 4444566899999999999998887655555444
No 213
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=21.80 E-value=1.2e+02 Score=21.63 Aligned_cols=29 Identities=17% Similarity=-0.007 Sum_probs=22.4
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHH
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVA 125 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~ 125 (135)
..+++|..||+++..|+++..--|.+.++
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (188)
T PRK12517 146 SGEEIAEILDLNKNTVMTRLFRARNQLKE 174 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45789999999999999887655555444
No 214
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=21.70 E-value=72 Score=17.36 Aligned_cols=35 Identities=23% Similarity=0.282 Sum_probs=21.6
Q ss_pred CHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccc
Q psy15107 76 TRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQG 114 (135)
Q Consensus 76 t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~v 114 (135)
+..+..+|.-..+. +. ....+||+.+|++...|..
T Consensus 2 ~~~~~~Il~~l~~~-~~---~t~~ela~~~~is~~tv~~ 36 (48)
T PF13412_consen 2 DETQRKILNYLREN-PR---ITQKELAEKLGISRSTVNR 36 (48)
T ss_dssp -HHHHHHHHHHHHC-TT---S-HHHHHHHHTS-HHHHHH
T ss_pred CHHHHHHHHHHHHc-CC---CCHHHHHHHhCCCHHHHHH
Confidence 34566777666653 22 3566889999999877643
No 215
>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=21.67 E-value=31 Score=19.95 Aligned_cols=16 Identities=19% Similarity=0.401 Sum_probs=12.3
Q ss_pred HHHHHHHcCCCcCCcc
Q psy15107 98 REEVALKINLPESRVQ 113 (135)
Q Consensus 98 r~~La~~l~l~~~~V~ 113 (135)
-.+||+.+|++..||+
T Consensus 31 S~~La~~~gi~~~qVR 46 (50)
T PF06971_consen 31 SQELAEALGITPAQVR 46 (50)
T ss_dssp HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHCCCHHHhc
Confidence 3578999999998875
No 216
>PRK05572 sporulation sigma factor SigF; Validated
Probab=21.63 E-value=1.2e+02 Score=22.85 Aligned_cols=46 Identities=11% Similarity=0.117 Sum_probs=31.1
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHHHH
Q psy15107 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEV 124 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k~k 124 (135)
.++..+..++...|.. .....+||..+|++...|..+-..-..|-|
T Consensus 202 ~L~~~~~~v~~l~~~~-----~~s~~eIA~~lgis~~~V~~~~~ral~kLr 247 (252)
T PRK05572 202 ELDERERLIVYLRYFK-----DKTQSEVAKRLGISQVQVSRLEKKILKQMK 247 (252)
T ss_pred cCCHHHHHHHHHHHhC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4666666677666633 235678999999999998777544444433
No 217
>PRK00215 LexA repressor; Validated
Probab=21.53 E-value=52 Score=23.98 Aligned_cols=41 Identities=29% Similarity=0.394 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHhhh---hcCCCCHHHHHHHHHHcCC-CcCCccccch
Q psy15107 75 FTRAQLDVLESLFG---KTRYPDIFMREEVALKINL-PESRVQGYPD 117 (135)
Q Consensus 75 ~t~~ql~~Le~~F~---~~~~p~~~~r~~La~~l~l-~~~~V~vWFq 117 (135)
+|..|..+|+...+ ...++ ....+||..+++ +...|..+.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~--~s~~ela~~~~~~~~~tv~~~l~ 46 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYP--PSRREIADALGLRSPSAVHEHLK 46 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCC--CCHHHHHHHhCCCChHHHHHHHH
Confidence 57888888887763 23332 245689999999 8877766654
No 218
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=21.46 E-value=79 Score=22.39 Aligned_cols=15 Identities=13% Similarity=0.251 Sum_probs=9.8
Q ss_pred cCCHHHHHHHHHhhh
Q psy15107 74 TFTRAQLDVLESLFG 88 (135)
Q Consensus 74 ~~t~~ql~~Le~~F~ 88 (135)
.++.+|+..|+...+
T Consensus 51 ~Lt~~qi~~l~~~i~ 65 (144)
T TIGR03629 51 YLDDEEIEKLEEAVE 65 (144)
T ss_pred cCCHHHHHHHHHHHH
Confidence 367777777766554
No 219
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.41 E-value=87 Score=21.84 Aligned_cols=22 Identities=23% Similarity=0.428 Sum_probs=17.5
Q ss_pred HHHHHHcCCCcCCccccchhhh
Q psy15107 99 EEVALKINLPESRVQGYPDIFM 120 (135)
Q Consensus 99 ~~La~~l~l~~~~V~vWFqNRR 120 (135)
..+|.++++++++++-|++.-+
T Consensus 103 ~~IA~~l~i~erta~r~~~~fK 124 (130)
T PF05263_consen 103 YQIAQKLHISERTARRWRDRFK 124 (130)
T ss_pred HHHHHHhCccHHHHHHHHHHHH
Confidence 4689999999999888876543
No 220
>PF12728 HTH_17: Helix-turn-helix domain
Probab=21.37 E-value=32 Score=19.12 Aligned_cols=21 Identities=19% Similarity=0.148 Sum_probs=16.5
Q ss_pred HHHHHHHcCCCcCCccccchh
Q psy15107 98 REEVALKINLPESRVQGYPDI 118 (135)
Q Consensus 98 r~~La~~l~l~~~~V~vWFqN 118 (135)
..++|+.||++...|..|.+.
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~ 24 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQ 24 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 357788899999888888744
No 221
>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=21.21 E-value=1.2e+02 Score=21.09 Aligned_cols=30 Identities=17% Similarity=-0.098 Sum_probs=20.9
Q ss_pred HHHHHHHHHHcCCCcCCccccchhhhHHHH
Q psy15107 95 IFMREEVALKINLPESRVQGYPDIFMREEV 124 (135)
Q Consensus 95 ~~~r~~La~~l~l~~~~V~vWFqNRR~k~k 124 (135)
.....++|..+|++...|++=...-|.+-|
T Consensus 156 g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr 185 (189)
T TIGR02984 156 GLSFAEVAERMDRSEGAVSMLWVRGLARLR 185 (189)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 335678999999999988875544444433
No 222
>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=21.20 E-value=29 Score=18.24 Aligned_cols=22 Identities=23% Similarity=0.253 Sum_probs=18.0
Q ss_pred HHHHHHHcCCCcCCccccchhh
Q psy15107 98 REEVALKINLPESRVQGYPDIF 119 (135)
Q Consensus 98 r~~La~~l~l~~~~V~vWFqNR 119 (135)
...+|..+++++..|..|..+.
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCC
Confidence 3578999999999998888764
No 223
>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=21.11 E-value=1.5e+02 Score=19.48 Aligned_cols=17 Identities=18% Similarity=0.471 Sum_probs=8.6
Q ss_pred HHHHHHhhhhcCCCCHH
Q psy15107 80 LDVLESLFGKTRYPDIF 96 (135)
Q Consensus 80 l~~Le~~F~~~~~p~~~ 96 (135)
+.+..-.|+.++||...
T Consensus 14 vRiIk~LyqsnPyP~~~ 30 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPE 30 (91)
T ss_dssp HHHHHHHHHTS-S--S-
T ss_pred HHHHHHHHccccCCCCC
Confidence 34455568889999754
No 224
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=21.10 E-value=1.4e+02 Score=21.47 Aligned_cols=32 Identities=13% Similarity=0.325 Sum_probs=23.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcC-CCcCC
Q psy15107 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKIN-LPESR 111 (135)
Q Consensus 75 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~-l~~~~ 111 (135)
+|.+.+..|.+.+.... ...+||.+|| ++..-
T Consensus 3 Wtde~~~~L~~lw~~G~-----SasqIA~~lg~vsRnA 35 (162)
T PF07750_consen 3 WTDERVERLRKLWAEGL-----SASQIARQLGGVSRNA 35 (162)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHhCCcchhh
Confidence 68899999999987653 3457788888 66543
No 225
>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=20.89 E-value=1.4e+02 Score=18.98 Aligned_cols=38 Identities=18% Similarity=0.271 Sum_probs=23.4
Q ss_pred CCHHHHHHHHHh---hhhcCCCCHHHHHHHHHHcCCCcCCccc
Q psy15107 75 FTRAQLDVLESL---FGKTRYPDIFMREEVALKINLPESRVQG 114 (135)
Q Consensus 75 ~t~~ql~~Le~~---F~~~~~p~~~~r~~La~~l~l~~~~V~v 114 (135)
+|..|..+|... |....-|-.. ..||+.++++...|++
T Consensus 2 Lt~rq~~IL~alV~~Y~~~~~PVgS--k~ia~~l~~s~aTIRN 42 (78)
T PF03444_consen 2 LTERQREILKALVELYIETGEPVGS--KTIAEELGRSPATIRN 42 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCcCH--HHHHHHHCCChHHHHH
Confidence 456666666655 6555555443 3567788888776653
No 226
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=20.78 E-value=1.3e+02 Score=22.70 Aligned_cols=44 Identities=14% Similarity=0.213 Sum_probs=31.4
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCcCCccccchhhhHH
Q psy15107 73 TTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMRE 122 (135)
Q Consensus 73 t~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNRR~k 122 (135)
..+|..++++|.-.-+- ..-.++|..|++++..|+.-.+|=+.|
T Consensus 178 ~~LT~rE~evl~~~a~G------~t~~eIa~~l~is~~TV~~h~~~~~~K 221 (240)
T PRK10188 178 MNFSKREKEILKWTAEG------KTSAEIAMILSISENTVNFHQKNMQKK 221 (240)
T ss_pred CCCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 35777777777544321 245689999999999999887776655
No 227
>PHA01976 helix-turn-helix protein
Probab=20.56 E-value=32 Score=20.15 Aligned_cols=22 Identities=9% Similarity=0.086 Sum_probs=18.6
Q ss_pred HHHHHHHcCCCcCCccccchhh
Q psy15107 98 REEVALKINLPESRVQGYPDIF 119 (135)
Q Consensus 98 r~~La~~l~l~~~~V~vWFqNR 119 (135)
..+||..+|++...|..|...+
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~ 39 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADK 39 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCC
Confidence 5689999999999999997654
No 228
>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=20.27 E-value=1.7e+02 Score=17.51 Aligned_cols=38 Identities=34% Similarity=0.461 Sum_probs=21.8
Q ss_pred cCCHHHHHHHHHh---hhhcCCCCHHHHHHHHHHcCCC-cCCcc
Q psy15107 74 TFTRAQLDVLESL---FGKTRYPDIFMREEVALKINLP-ESRVQ 113 (135)
Q Consensus 74 ~~t~~ql~~Le~~---F~~~~~p~~~~r~~La~~l~l~-~~~V~ 113 (135)
.+|..|.++|+-. ...+.||. ...+||..+|+. ...|+
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~G~~P--t~rEIa~~~g~~S~~tv~ 44 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEENGYPP--TVREIAEALGLKSTSTVQ 44 (65)
T ss_dssp ---HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSSSHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHcCCCC--CHHHHHHHhCCCChHHHH
Confidence 3677777777654 45567764 556889999987 44343
No 229
>PRK13558 bacterio-opsin activator; Provisional
Probab=20.24 E-value=81 Score=27.11 Aligned_cols=40 Identities=23% Similarity=0.326 Sum_probs=33.6
Q ss_pred CcCCHHHHHHHHHhhhhcCC--CCHHHHHHHHHHcCCCcCCc
Q psy15107 73 TTFTRAQLDVLESLFGKTRY--PDIFMREEVALKINLPESRV 112 (135)
Q Consensus 73 t~~t~~ql~~Le~~F~~~~~--p~~~~r~~La~~l~l~~~~V 112 (135)
..+|..|.+.|+..|+..-| |-....++||..||++...+
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~ 647 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTF 647 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 46999999999999988754 66667889999999998753
No 230
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=20.03 E-value=59 Score=23.04 Aligned_cols=32 Identities=13% Similarity=-0.027 Sum_probs=26.4
Q ss_pred HHHHHHHHcCCCcCCccccchhhhHHHHHHhc
Q psy15107 97 MREEVALKINLPESRVQGYPDIFMREEVALKI 128 (135)
Q Consensus 97 ~r~~La~~l~l~~~~V~vWFqNRR~k~k~~~~ 128 (135)
.-.++|..+|++...|+.+...-|.+.++...
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 45789999999999999999887777766543
Done!