Query psy5909
Match_columns 130
No_of_seqs 119 out of 1422
Neff 8.1
Searched_HMMs 46136
Date Fri Aug 16 21:21:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5909.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5909hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0484|consensus 99.9 2E-23 4.3E-28 134.8 1.8 65 49-113 13-77 (125)
2 KOG0489|consensus 99.9 6E-23 1.3E-27 154.6 4.6 68 51-118 157-224 (261)
3 KOG0488|consensus 99.9 2.8E-22 6.1E-27 153.8 6.0 68 47-114 166-233 (309)
4 KOG0842|consensus 99.9 1.7E-21 3.7E-26 148.0 8.4 76 47-122 147-222 (307)
5 KOG0850|consensus 99.9 1.7E-21 3.6E-26 141.6 7.9 76 47-122 116-191 (245)
6 KOG0487|consensus 99.9 1.1E-21 2.4E-26 149.1 7.2 69 48-116 230-298 (308)
7 KOG0494|consensus 99.8 1.9E-20 4.2E-25 138.2 6.7 63 52-114 140-202 (332)
8 KOG0848|consensus 99.8 2.3E-21 4.9E-26 143.6 1.7 70 49-118 195-264 (317)
9 KOG2251|consensus 99.8 3.8E-20 8.3E-25 133.8 6.5 67 48-114 32-98 (228)
10 KOG0485|consensus 99.8 5.8E-20 1.3E-24 132.7 6.9 66 48-113 99-164 (268)
11 KOG0492|consensus 99.8 3.1E-20 6.7E-25 133.2 4.3 65 53-117 144-208 (246)
12 KOG0843|consensus 99.8 5.5E-20 1.2E-24 129.3 4.4 64 51-114 100-163 (197)
13 KOG0844|consensus 99.7 1.5E-18 3.1E-23 130.9 4.7 65 48-112 176-240 (408)
14 PF00046 Homeobox: Homeobox do 99.7 2.3E-18 4.9E-23 101.5 3.9 57 54-110 1-57 (57)
15 KOG0491|consensus 99.7 1.8E-18 3.9E-23 120.2 1.5 68 52-119 99-166 (194)
16 TIGR01565 homeo_ZF_HD homeobox 99.7 6.3E-17 1.4E-21 95.4 5.4 53 53-105 1-57 (58)
17 KOG0493|consensus 99.7 3.9E-17 8.5E-22 120.9 5.3 59 54-112 247-305 (342)
18 KOG0486|consensus 99.6 1.9E-16 4E-21 119.8 5.1 64 50-113 109-172 (351)
19 COG5576 Homeodomain-containing 99.6 3.2E-16 6.9E-21 109.7 5.5 64 51-114 49-112 (156)
20 KOG3802|consensus 99.6 2.6E-16 5.6E-21 122.4 4.9 62 52-113 293-354 (398)
21 KOG4577|consensus 99.6 4.9E-16 1.1E-20 116.6 4.2 67 51-117 165-231 (383)
22 smart00389 HOX Homeodomain. DN 99.6 7.7E-16 1.7E-20 90.0 4.0 54 55-108 2-55 (56)
23 cd00086 homeodomain Homeodomai 99.6 1.9E-15 4.2E-20 89.0 4.4 56 55-110 2-57 (59)
24 KOG0483|consensus 99.5 2.2E-15 4.7E-20 108.9 2.8 57 56-112 53-109 (198)
25 KOG0847|consensus 99.5 4.8E-15 1E-19 107.6 2.2 65 50-114 164-228 (288)
26 KOG0490|consensus 99.5 1.5E-14 3.2E-19 106.4 4.7 64 50-113 57-120 (235)
27 KOG0849|consensus 99.4 9.1E-13 2E-17 103.2 5.7 68 45-112 168-235 (354)
28 KOG1168|consensus 99.3 2.4E-12 5.1E-17 97.0 2.9 63 50-112 306-368 (385)
29 KOG0775|consensus 98.6 3.8E-08 8.2E-13 73.9 3.9 50 60-109 183-232 (304)
30 KOG2252|consensus 98.6 8.9E-08 1.9E-12 77.7 5.8 56 52-107 419-474 (558)
31 KOG0490|consensus 98.5 1.4E-07 3.1E-12 69.2 3.5 67 47-113 147-213 (235)
32 KOG0774|consensus 98.4 1.7E-07 3.6E-12 70.1 3.3 60 53-112 188-250 (334)
33 PF05920 Homeobox_KN: Homeobox 98.4 7.5E-08 1.6E-12 52.7 0.7 34 74-107 7-40 (40)
34 KOG1146|consensus 98.2 1.6E-06 3.5E-11 76.4 5.3 63 51-113 901-963 (1406)
35 PF11569 Homez: Homeodomain le 97.1 0.0002 4.3E-09 41.7 0.8 42 65-106 10-51 (56)
36 KOG3623|consensus 96.9 0.0012 2.6E-08 56.0 3.9 52 65-116 568-619 (1007)
37 KOG0773|consensus 95.7 0.014 3.1E-07 45.5 3.8 56 53-108 239-297 (342)
38 PF04218 CENP-B_N: CENP-B N-te 94.1 0.086 1.9E-06 30.2 3.3 46 54-104 1-46 (53)
39 KOG1146|consensus 82.2 2.7 5.8E-05 38.6 4.9 66 47-112 699-764 (1406)
40 PF04967 HTH_10: HTH DNA bindi 76.4 2.8 6E-05 24.0 2.2 38 60-97 1-40 (53)
41 PF04545 Sigma70_r4: Sigma-70, 71.0 4 8.7E-05 22.4 2.0 43 59-106 4-46 (50)
42 PF08281 Sigma70_r4_2: Sigma-7 70.6 3.9 8.4E-05 22.7 1.9 41 60-105 11-51 (54)
43 PRK03975 tfx putative transcri 69.5 5.7 0.00012 27.5 2.9 50 57-112 4-53 (141)
44 PF01527 HTH_Tnp_1: Transposas 68.0 5.7 0.00012 23.5 2.4 44 55-102 2-45 (76)
45 PRK12526 RNA polymerase sigma 66.2 7.3 0.00016 27.9 3.0 32 82-113 171-202 (206)
46 PF10668 Phage_terminase: Phag 65.0 2 4.3E-05 25.4 -0.1 20 82-101 24-43 (60)
47 cd06171 Sigma70_r4 Sigma70, re 62.4 6.8 0.00015 20.7 1.8 42 59-105 10-51 (55)
48 PRK09646 RNA polymerase sigma 57.2 16 0.00034 25.8 3.4 49 59-112 142-190 (194)
49 PRK09642 RNA polymerase sigma 57.1 15 0.00032 24.9 3.2 32 82-113 124-155 (160)
50 PRK12512 RNA polymerase sigma 55.2 15 0.00034 25.4 3.1 50 59-113 131-180 (184)
51 PRK11924 RNA polymerase sigma 54.6 15 0.00033 25.0 2.9 32 82-113 143-174 (179)
52 PRK12530 RNA polymerase sigma 54.1 13 0.00028 26.2 2.6 49 60-113 135-183 (189)
53 COG3413 Predicted DNA binding 53.2 15 0.00033 26.6 2.8 47 59-107 155-203 (215)
54 PRK06759 RNA polymerase factor 50.8 15 0.00033 24.5 2.4 45 59-108 106-150 (154)
55 PRK12515 RNA polymerase sigma 50.6 21 0.00045 25.0 3.1 51 59-114 131-181 (189)
56 PRK12532 RNA polymerase sigma 50.5 21 0.00047 25.0 3.2 38 82-119 154-191 (195)
57 PRK09644 RNA polymerase sigma 50.4 18 0.00038 24.7 2.7 32 82-113 126-157 (165)
58 PRK09047 RNA polymerase factor 50.2 23 0.0005 23.8 3.2 50 60-114 107-156 (161)
59 PRK07037 extracytoplasmic-func 49.3 23 0.0005 23.9 3.1 32 82-113 127-158 (163)
60 PRK09652 RNA polymerase sigma 49.3 19 0.00041 24.6 2.7 48 59-111 128-175 (182)
61 cd00569 HTH_Hin_like Helix-tur 49.0 28 0.00061 16.1 2.8 36 60-100 6-41 (42)
62 PF09607 BrkDBD: Brinker DNA-b 47.8 19 0.00041 21.1 2.1 17 86-102 31-47 (58)
63 PRK12519 RNA polymerase sigma 47.7 17 0.00036 25.5 2.3 31 82-112 159-189 (194)
64 PRK12514 RNA polymerase sigma 47.5 27 0.00059 24.1 3.3 30 82-111 147-176 (179)
65 TIGR02943 Sig70_famx1 RNA poly 47.2 22 0.00047 25.0 2.8 53 60-117 132-184 (188)
66 TIGR02959 SigZ RNA polymerase 47.0 23 0.0005 24.4 2.8 50 59-113 100-149 (170)
67 cd04761 HTH_MerR-SF Helix-Turn 46.1 6.1 0.00013 21.2 -0.2 21 83-103 3-23 (49)
68 PRK09648 RNA polymerase sigma 46.0 23 0.0005 24.7 2.8 47 59-110 139-185 (189)
69 PRK00118 putative DNA-binding 45.8 26 0.00056 22.9 2.7 48 59-111 17-64 (104)
70 PRK10072 putative transcriptio 45.6 15 0.00033 23.6 1.6 41 59-106 32-72 (96)
71 KOG3755|consensus 45.5 7.3 0.00016 33.2 0.1 21 92-112 738-758 (769)
72 TIGR02948 SigW_bacill RNA poly 45.3 22 0.00047 24.6 2.5 48 59-111 136-183 (187)
73 PRK12547 RNA polymerase sigma 45.2 27 0.00058 23.8 2.9 48 60-112 113-160 (164)
74 TIGR03879 near_KaiC_dom probab 45.2 3.9 8.5E-05 25.1 -1.1 33 71-103 23-55 (73)
75 PRK05602 RNA polymerase sigma 44.7 25 0.00054 24.5 2.8 32 82-113 146-177 (186)
76 TIGR02989 Sig-70_gvs1 RNA poly 44.0 24 0.00053 23.6 2.6 44 59-107 111-154 (159)
77 TIGR02985 Sig70_bacteroi1 RNA 42.2 28 0.00061 23.1 2.6 28 82-109 131-158 (161)
78 PRK06930 positive control sigm 41.6 30 0.00064 24.5 2.7 50 59-113 114-163 (170)
79 PF00196 GerE: Bacterial regul 41.5 19 0.00042 20.2 1.5 43 59-107 3-45 (58)
80 PRK12541 RNA polymerase sigma 41.4 24 0.00052 23.9 2.2 46 60-110 113-158 (161)
81 PF06056 Terminase_5: Putative 41.4 3.8 8.3E-05 23.8 -1.6 20 82-101 15-34 (58)
82 TIGR02983 SigE-fam_strep RNA p 41.0 34 0.00074 23.0 2.9 31 82-112 128-158 (162)
83 TIGR02937 sigma70-ECF RNA poly 41.0 29 0.00064 22.4 2.5 45 60-109 111-155 (158)
84 PRK12520 RNA polymerase sigma 40.7 33 0.00072 24.0 2.9 52 60-116 132-183 (191)
85 PF08280 HTH_Mga: M protein tr 40.6 26 0.00056 20.0 1.9 33 63-99 6-38 (59)
86 TIGR02999 Sig-70_X6 RNA polyme 40.6 31 0.00067 23.8 2.7 46 60-110 135-180 (183)
87 PRK12537 RNA polymerase sigma 40.2 41 0.00089 23.3 3.3 29 82-110 151-179 (182)
88 PRK09645 RNA polymerase sigma 39.9 42 0.0009 22.9 3.3 49 60-113 119-167 (173)
89 TIGR02939 RpoE_Sigma70 RNA pol 39.6 24 0.00051 24.5 2.0 31 82-112 156-186 (190)
90 PRK04217 hypothetical protein; 39.5 38 0.00082 22.3 2.8 51 57-112 40-90 (110)
91 PRK12531 RNA polymerase sigma 39.4 41 0.0009 23.6 3.2 33 82-114 159-191 (194)
92 TIGR02954 Sig70_famx3 RNA poly 38.5 40 0.00087 22.9 3.0 46 60-110 120-165 (169)
93 PF13936 HTH_38: Helix-turn-he 38.2 17 0.00037 19.6 0.9 38 58-100 3-40 (44)
94 PRK12546 RNA polymerase sigma 38.1 33 0.00071 24.3 2.5 32 82-113 131-162 (188)
95 PF13518 HTH_28: Helix-turn-he 38.0 13 0.00029 20.1 0.4 24 82-105 14-37 (52)
96 KOG3623|consensus 37.9 31 0.00067 30.4 2.7 53 57-109 630-682 (1007)
97 PRK09647 RNA polymerase sigma 37.9 39 0.00083 24.2 2.9 33 82-114 156-188 (203)
98 PRK09637 RNA polymerase sigma 37.8 37 0.00081 23.7 2.8 32 82-113 124-155 (181)
99 PRK09639 RNA polymerase sigma 37.7 37 0.00079 22.9 2.7 48 59-112 112-159 (166)
100 PRK12545 RNA polymerase sigma 37.6 37 0.0008 24.1 2.8 35 82-116 157-191 (201)
101 PRK06986 fliA flagellar biosyn 37.6 35 0.00075 24.9 2.7 48 60-112 185-232 (236)
102 PRK09413 IS2 repressor TnpA; R 37.4 49 0.0011 21.8 3.2 43 57-103 10-52 (121)
103 PRK12544 RNA polymerase sigma 37.3 38 0.00082 24.3 2.8 53 60-117 149-201 (206)
104 PRK12538 RNA polymerase sigma 37.1 28 0.0006 25.7 2.1 32 82-113 189-220 (233)
105 PF12824 MRP-L20: Mitochondria 36.9 68 0.0015 22.7 3.9 44 56-101 82-125 (164)
106 PRK13919 putative RNA polymera 36.5 48 0.001 22.9 3.2 46 60-110 136-181 (186)
107 PF13411 MerR_1: MerR HTH fami 36.1 10 0.00022 22.0 -0.4 19 84-102 4-22 (69)
108 COG4367 Uncharacterized protei 35.8 41 0.00089 21.5 2.4 38 60-97 3-40 (97)
109 PRK12543 RNA polymerase sigma 34.7 48 0.001 22.9 2.9 31 82-112 135-165 (179)
110 PRK12535 RNA polymerase sigma 34.5 48 0.001 23.6 2.9 34 82-115 151-184 (196)
111 PRK12516 RNA polymerase sigma 34.5 47 0.001 23.4 2.9 35 82-116 134-168 (187)
112 PRK12518 RNA polymerase sigma 33.1 25 0.00053 24.1 1.2 32 82-113 138-169 (175)
113 COG2944 Predicted transcriptio 33.1 33 0.00071 22.5 1.7 40 59-105 43-82 (104)
114 PF00376 MerR: MerR family reg 32.9 10 0.00023 19.9 -0.5 18 84-101 3-20 (38)
115 PRK06811 RNA polymerase factor 32.7 51 0.0011 23.0 2.8 47 60-111 132-178 (189)
116 PRK12536 RNA polymerase sigma 32.4 53 0.0012 22.7 2.9 31 82-112 147-177 (181)
117 COG1905 NuoE NADH:ubiquinone o 32.3 75 0.0016 22.5 3.5 37 62-98 25-61 (160)
118 PRK12529 RNA polymerase sigma 32.2 51 0.0011 22.8 2.7 47 59-110 127-173 (178)
119 PRK12524 RNA polymerase sigma 31.8 52 0.0011 23.1 2.7 32 82-113 154-185 (196)
120 PRK11923 algU RNA polymerase s 31.7 48 0.001 23.1 2.5 32 82-113 156-187 (193)
121 cd04764 HTH_MlrA-like_sg1 Heli 31.3 14 0.00031 21.4 -0.2 20 84-103 4-23 (67)
122 cd02413 40S_S3_KH K homology R 31.2 46 0.00099 20.5 2.1 21 82-102 55-75 (81)
123 PRK12533 RNA polymerase sigma 31.2 47 0.001 24.2 2.5 35 82-116 152-186 (216)
124 PF08880 QLQ: QLQ; InterPro: 31.2 51 0.0011 17.3 1.9 14 59-72 2-15 (37)
125 PRK12523 RNA polymerase sigma 31.0 61 0.0013 22.2 2.9 47 60-111 120-166 (172)
126 PRK12542 RNA polymerase sigma 30.8 54 0.0012 22.7 2.7 48 60-112 123-170 (185)
127 PRK08583 RNA polymerase sigma 29.6 62 0.0013 23.9 2.9 48 59-111 205-252 (257)
128 cd04763 HTH_MlrA-like Helix-Tu 29.4 15 0.00033 21.4 -0.3 19 84-102 4-22 (68)
129 PRK12522 RNA polymerase sigma 29.4 71 0.0015 21.8 3.0 31 82-112 137-167 (173)
130 PRK09641 RNA polymerase sigma 29.3 57 0.0012 22.4 2.6 30 82-111 154-183 (187)
131 PRK12539 RNA polymerase sigma 28.6 78 0.0017 21.9 3.2 48 60-112 132-179 (184)
132 KOG0773|consensus 28.3 49 0.0011 25.8 2.2 39 73-111 117-155 (342)
133 smart00421 HTH_LUXR helix_turn 27.6 73 0.0016 16.8 2.4 40 59-104 3-42 (58)
134 TIGR00721 tfx DNA-binding prot 27.4 71 0.0015 21.9 2.7 48 57-110 4-51 (137)
135 PRK12511 RNA polymerase sigma 27.1 75 0.0016 22.2 2.9 49 60-113 112-160 (182)
136 PF09301 DUF1970: Domain of un 26.7 16 0.00034 23.3 -0.6 11 97-107 19-29 (117)
137 TIGR02479 FliA_WhiG RNA polyme 26.7 66 0.0014 23.2 2.6 46 59-109 175-220 (224)
138 TIGR02952 Sig70_famx2 RNA poly 26.5 70 0.0015 21.5 2.6 43 60-107 123-165 (170)
139 TIGR02980 SigBFG RNA polymeras 26.5 70 0.0015 23.1 2.7 45 59-108 178-222 (227)
140 PRK07408 RNA polymerase sigma 26.2 73 0.0016 23.7 2.8 48 60-112 204-251 (256)
141 PRK09649 RNA polymerase sigma 26.0 65 0.0014 22.5 2.4 29 82-110 148-176 (185)
142 PRK12513 RNA polymerase sigma 26.0 29 0.00062 24.3 0.5 33 81-113 156-188 (194)
143 TIGR03001 Sig-70_gmx1 RNA poly 25.9 75 0.0016 23.6 2.8 31 82-112 179-209 (244)
144 PF11516 DUF3220: Protein of u 25.6 17 0.00036 22.8 -0.6 10 95-104 31-40 (106)
145 PRK05657 RNA polymerase sigma 25.3 69 0.0015 25.0 2.6 55 59-114 262-316 (325)
146 cd04762 HTH_MerR-trunc Helix-T 25.3 24 0.00052 18.3 0.0 23 83-105 3-25 (49)
147 PF06505 XylR_N: Activator of 24.9 28 0.00062 22.6 0.3 21 86-106 2-22 (103)
148 PRK12527 RNA polymerase sigma 24.9 1E+02 0.0022 20.7 3.1 32 82-113 123-154 (159)
149 TIGR02947 SigH_actino RNA poly 24.6 40 0.00087 23.6 1.1 33 81-113 148-180 (193)
150 TIGR02941 Sigma_B RNA polymera 24.5 70 0.0015 23.6 2.4 47 59-110 205-251 (255)
151 cd01796 DDI1_N DNA damage indu 24.0 43 0.00093 19.8 1.0 26 82-107 25-50 (71)
152 cd01769 UBL Ubiquitin-like dom 23.8 71 0.0015 17.8 1.9 25 82-106 23-47 (69)
153 PF13384 HTH_23: Homeodomain-l 23.7 21 0.00046 19.2 -0.4 23 81-103 18-40 (50)
154 PTZ00044 ubiquitin; Provisiona 23.7 56 0.0012 19.2 1.5 26 82-107 26-51 (76)
155 PRK07670 RNA polymerase sigma 23.6 81 0.0017 23.3 2.6 46 60-110 202-247 (251)
156 cd01793 Fubi Fubi ubiquitin-li 23.2 46 0.00099 19.7 1.0 27 82-108 24-50 (74)
157 PRK12528 RNA polymerase sigma 22.9 88 0.0019 21.0 2.5 42 60-106 114-155 (161)
158 cd01798 parkin_N amino-termina 22.7 47 0.001 19.3 1.0 26 82-107 24-49 (70)
159 PRK12540 RNA polymerase sigma 22.6 1E+02 0.0022 21.5 2.9 35 82-116 129-163 (182)
160 cd01392 HTH_LacI Helix-turn-he 22.4 19 0.0004 19.5 -0.8 21 85-105 2-22 (52)
161 PRK12534 RNA polymerase sigma 22.4 1.3E+02 0.0029 20.7 3.5 29 82-110 155-183 (187)
162 PRK08301 sporulation sigma fac 22.4 80 0.0017 22.9 2.3 52 59-111 178-229 (234)
163 PRK08295 RNA polymerase factor 22.3 91 0.002 21.9 2.6 32 81-112 171-202 (208)
164 TIGR02960 SigX5 RNA polymerase 22.1 1.3E+02 0.0027 22.9 3.5 32 82-113 160-191 (324)
165 TIGR03629 arch_S13P archaeal r 22.0 81 0.0017 21.8 2.1 16 59-74 51-66 (144)
166 PTZ00352 60S ribosomal protein 21.8 33 0.0007 25.4 0.2 11 95-105 18-29 (212)
167 PF08279 HTH_11: HTH domain; 21.8 78 0.0017 17.3 1.7 17 82-98 17-33 (55)
168 cd01763 Sumo Small ubiquitin-r 21.7 89 0.0019 19.2 2.2 25 83-107 38-62 (87)
169 COG2963 Transposase and inacti 21.3 1.3E+02 0.0028 19.3 3.0 41 57-101 5-46 (116)
170 PRK09480 slmA division inhibit 21.3 73 0.0016 21.9 1.9 34 71-105 22-55 (194)
171 TIGR02957 SigX4 RNA polymerase 21.1 93 0.002 23.5 2.5 46 60-110 109-154 (281)
172 PRK05988 formate dehydrogenase 20.9 1.4E+02 0.003 20.8 3.2 35 64-98 25-59 (156)
173 PRK06288 RNA polymerase sigma 20.9 1.1E+02 0.0023 22.9 2.8 48 59-111 212-259 (268)
174 cd01797 NIRF_N amino-terminal 20.6 60 0.0013 19.6 1.2 27 82-108 28-54 (78)
175 cd01104 HTH_MlrA-CarA Helix-Tu 20.5 34 0.00074 19.6 0.0 19 84-102 4-22 (68)
176 PF13443 HTH_26: Cro/C1-type H 20.4 29 0.00064 19.6 -0.3 23 82-104 12-34 (63)
177 PRK06704 RNA polymerase factor 20.4 1.2E+02 0.0026 22.4 3.0 33 82-114 134-166 (228)
178 PF01710 HTH_Tnp_IS630: Transp 20.4 94 0.002 20.3 2.2 21 82-102 20-40 (119)
179 PF08452 DNAP_B_exo_N: DNA pol 20.1 34 0.00073 15.9 -0.0 9 98-106 6-14 (22)
No 1
>KOG0484|consensus
Probab=99.87 E-value=2e-23 Score=134.81 Aligned_cols=65 Identities=48% Similarity=0.691 Sum_probs=61.1
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 49 DKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 49 ~~~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
-.+++||.||.||..||.+||+.|...+||++..|++||.++.|++.+|||||||||+|.||..+
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 46778999999999999999999999999999999999999999999999999999999887653
No 2
>KOG0489|consensus
Probab=99.87 E-value=6e-23 Score=154.64 Aligned_cols=68 Identities=29% Similarity=0.289 Sum_probs=63.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhccCCC
Q psy5909 51 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEFNIRV 118 (130)
Q Consensus 51 ~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~~~~~ 118 (130)
.+.||.||.||.+|+.+||+.|..++|+++..|.+||..|.|+++|||||||||||||||..+.....
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 45788999999999999999999999999999999999999999999999999999999888776655
No 3
>KOG0488|consensus
Probab=99.86 E-value=2.8e-22 Score=153.82 Aligned_cols=68 Identities=32% Similarity=0.357 Sum_probs=63.4
Q ss_pred CCccCCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhc
Q psy5909 47 PVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEF 114 (130)
Q Consensus 47 ~~~~~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~ 114 (130)
....+|.|+.||.||..||.+||+.|++++|++...|.+||..|||+..||++||||||+|||+....
T Consensus 166 ~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 166 RSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred cCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 34457888899999999999999999999999999999999999999999999999999999998765
No 4
>KOG0842|consensus
Probab=99.85 E-value=1.7e-21 Score=148.04 Aligned_cols=76 Identities=24% Similarity=0.211 Sum_probs=67.4
Q ss_pred CCccCCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhccCCCCCCC
Q psy5909 47 PVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEFNIRVPEPS 122 (130)
Q Consensus 47 ~~~~~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~~~~~~~~~ 122 (130)
....+++||.|..|+..|..+||+.|.+++|++..+|+.||..|.|++.||||||||||-|.||......+.....
T Consensus 147 ~t~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~~ 222 (307)
T KOG0842|consen 147 QTGKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALLL 222 (307)
T ss_pred ccccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcccC
Confidence 4446778888999999999999999999999999999999999999999999999999999888877666654333
No 5
>KOG0850|consensus
Probab=99.85 E-value=1.7e-21 Score=141.56 Aligned_cols=76 Identities=25% Similarity=0.230 Sum_probs=67.6
Q ss_pred CCccCCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhccCCCCCCC
Q psy5909 47 PVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEFNIRVPEPS 122 (130)
Q Consensus 47 ~~~~~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~~~~~~~~~ 122 (130)
..+.+|.|+.||.|+..||..|.+.|++++|+-..+|.+||+.|||+..||||||||||.|.||.++.+....++.
T Consensus 116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~~e~~ 191 (245)
T KOG0850|consen 116 NGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSGPVEGD 191 (245)
T ss_pred CCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCCccccC
Confidence 3456677888999999999999999999999999999999999999999999999999999999998655554443
No 6
>KOG0487|consensus
Probab=99.85 E-value=1.1e-21 Score=149.10 Aligned_cols=69 Identities=26% Similarity=0.188 Sum_probs=63.3
Q ss_pred CccCCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhccC
Q psy5909 48 VDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEFNI 116 (130)
Q Consensus 48 ~~~~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~~~ 116 (130)
...++.|++|..+|..|+.+||+.|..|.|++...|.+|++.|+|+++||+|||||||||.||..+.+.
T Consensus 230 ~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 230 SSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred ccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence 445778889999999999999999999999999999999999999999999999999999999875433
No 7
>KOG0494|consensus
Probab=99.82 E-value=1.9e-20 Score=138.23 Aligned_cols=63 Identities=48% Similarity=0.607 Sum_probs=58.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhc
Q psy5909 52 KHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEF 114 (130)
Q Consensus 52 ~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~ 114 (130)
++|+.||.||..|+.+||..|++.+||+...|+.||.++.|++.+|+|||||||+||||..+.
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence 444459999999999999999999999999999999999999999999999999999886553
No 8
>KOG0848|consensus
Probab=99.82 E-value=2.3e-21 Score=143.57 Aligned_cols=70 Identities=24% Similarity=0.248 Sum_probs=63.3
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhccCCC
Q psy5909 49 DKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEFNIRV 118 (130)
Q Consensus 49 ~~~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~~~~~ 118 (130)
+-+.+-+.|.++|+.|+.+||++|.-++|+++..+.+||..|+|+++||||||||||+|+||.++.+.+.
T Consensus 195 KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~~~ 264 (317)
T KOG0848|consen 195 KTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKRLQ 264 (317)
T ss_pred eeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHHHH
Confidence 4455667799999999999999999999999999999999999999999999999999999988766433
No 9
>KOG2251|consensus
Probab=99.81 E-value=3.8e-20 Score=133.83 Aligned_cols=67 Identities=46% Similarity=0.582 Sum_probs=63.8
Q ss_pred CccCCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhc
Q psy5909 48 VDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEF 114 (130)
Q Consensus 48 ~~~~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~ 114 (130)
...++.||.||.|+..|+.+||..|.+.+||++.+|++||.+|+|.+.+|||||.|||+|+|+..+.
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 5678899999999999999999999999999999999999999999999999999999999888765
No 10
>KOG0485|consensus
Probab=99.81 E-value=5.8e-20 Score=132.69 Aligned_cols=66 Identities=23% Similarity=0.286 Sum_probs=62.2
Q ss_pred CccCCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 48 VDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 48 ~~~~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
.+..++++.||+|+..|+..||..|...+|++..+|..||.+|.|++.||||||||||.|||+...
T Consensus 99 ~g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 99 LGDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred ccccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 456688899999999999999999999999999999999999999999999999999999998764
No 11
>KOG0492|consensus
Probab=99.80 E-value=3.1e-20 Score=133.24 Aligned_cols=65 Identities=29% Similarity=0.350 Sum_probs=60.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhccCC
Q psy5909 53 HRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEFNIR 117 (130)
Q Consensus 53 ~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~~~~ 117 (130)
.|+.||.||..||..||+.|.+.+|+++.+|.+++..|.|++.||+|||||||+|.||.++.+..
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~E 208 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELE 208 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHH
Confidence 56679999999999999999999999999999999999999999999999999999988765443
No 12
>KOG0843|consensus
Probab=99.79 E-value=5.5e-20 Score=129.32 Aligned_cols=64 Identities=30% Similarity=0.277 Sum_probs=60.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhc
Q psy5909 51 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEF 114 (130)
Q Consensus 51 ~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~ 114 (130)
.+.+|.||.||.+|+..||..|..++|....+|+.||..|+|++.||+|||||||.|.||....
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 3788999999999999999999999999999999999999999999999999999998887655
No 13
>KOG0844|consensus
Probab=99.74 E-value=1.5e-18 Score=130.92 Aligned_cols=65 Identities=29% Similarity=0.336 Sum_probs=61.3
Q ss_pred CccCCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 48 VDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 48 ~~~~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
+...+.||.||.||.+||..||+.|.+..|.++..|.+||..|+|++..|||||||||||.||++
T Consensus 176 sa~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQR 240 (408)
T KOG0844|consen 176 SADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQR 240 (408)
T ss_pred CccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhh
Confidence 45677899999999999999999999999999999999999999999999999999999998765
No 14
>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=99.73 E-value=2.3e-18 Score=101.48 Aligned_cols=57 Identities=37% Similarity=0.425 Sum_probs=54.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhh
Q psy5909 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQ 110 (130)
Q Consensus 54 rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~ 110 (130)
|+.|+.||..|+..|+..|..++||+..+++.||..+||+..+|++||+|+|.++|+
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 467899999999999999999999999999999999999999999999999999875
No 15
>KOG0491|consensus
Probab=99.71 E-value=1.8e-18 Score=120.19 Aligned_cols=68 Identities=28% Similarity=0.311 Sum_probs=63.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhccCCCC
Q psy5909 52 KHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEFNIRVP 119 (130)
Q Consensus 52 ~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~~~~~~ 119 (130)
++++.||+|+..|+..|+..|+.++|++..+|.+||..|+|++.||+.||||||||.||+.+.+....
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~n 166 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPKN 166 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 45677999999999999999999999999999999999999999999999999999999998887544
No 16
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.68 E-value=6.3e-17 Score=95.45 Aligned_cols=53 Identities=17% Similarity=0.122 Sum_probs=50.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhCC----CCHHHHHHHHHHhCCCCCccceechhhh
Q psy5909 53 HRRNRTTFTTYQLHELERAFEKSHY----PDVYSREELAMKVNLPEVRVQAVGMLYY 105 (130)
Q Consensus 53 ~rr~Rt~~t~~q~~~L~~~F~~~~~----p~~~~r~~La~~l~l~~~~VqvWFqNrR 105 (130)
++|.||.||.+|+..|+..|....| |+...+.+||..|||++.+|||||||-+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 3788999999999999999999999 9999999999999999999999999954
No 17
>KOG0493|consensus
Probab=99.68 E-value=3.9e-17 Score=120.94 Aligned_cols=59 Identities=27% Similarity=0.328 Sum_probs=55.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 54 rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
+|.||.||.+||..|+..|+.++|++...|.+||.+|+|.+.||+|||||+|+|.||-.
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 46799999999999999999999999999999999999999999999999999987754
No 18
>KOG0486|consensus
Probab=99.64 E-value=1.9e-16 Score=119.82 Aligned_cols=64 Identities=39% Similarity=0.493 Sum_probs=60.3
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 50 KKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 50 ~~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
-.|+||.||.||..|+.+||..|+++.||++..|++||.-.+|++.+|+|||.|||+||||..+
T Consensus 109 i~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrEr 172 (351)
T KOG0486|consen 109 ISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRER 172 (351)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhh
Confidence 3478899999999999999999999999999999999999999999999999999999988654
No 19
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.64 E-value=3.2e-16 Score=109.70 Aligned_cols=64 Identities=28% Similarity=0.268 Sum_probs=58.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhc
Q psy5909 51 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEF 114 (130)
Q Consensus 51 ~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~ 114 (130)
+..++.|++.|..|+.+|+..|..++||+...|..|+..|+|+++-|||||||||++.|+....
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 3456778889999999999999999999999999999999999999999999999998776654
No 20
>KOG3802|consensus
Probab=99.63 E-value=2.6e-16 Score=122.44 Aligned_cols=62 Identities=19% Similarity=0.137 Sum_probs=59.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 52 KHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 52 ~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
++|++||.|....+..||.+|.+|+.|+..+...||.+|+|.+.+|+|||||||.|+||...
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 77889999999999999999999999999999999999999999999999999999988665
No 21
>KOG4577|consensus
Probab=99.61 E-value=4.9e-16 Score=116.58 Aligned_cols=67 Identities=28% Similarity=0.194 Sum_probs=62.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhccCC
Q psy5909 51 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEFNIR 117 (130)
Q Consensus 51 ~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~~~~ 117 (130)
...+|.||.||..||..|+..|...+.|....|+.|+..+||.-++|||||||||+|+|+.++-.++
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcch
Confidence 3458899999999999999999999999999999999999999999999999999999999876665
No 22
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.60 E-value=7.7e-16 Score=90.03 Aligned_cols=54 Identities=43% Similarity=0.497 Sum_probs=51.4
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHH
Q psy5909 55 RNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVE 108 (130)
Q Consensus 55 r~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~ 108 (130)
+.|+.|+..++..|+..|..++||+..++..||..+||+..+|+.||+|+|.+.
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~ 55 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKW 55 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhcc
Confidence 567889999999999999999999999999999999999999999999999875
No 23
>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=99.58 E-value=1.9e-15 Score=89.03 Aligned_cols=56 Identities=41% Similarity=0.463 Sum_probs=53.0
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhh
Q psy5909 55 RNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQ 110 (130)
Q Consensus 55 r~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~ 110 (130)
+.|+.|+..++..|+..|..++||+..++..||..+||+..+|++||+|+|.+.++
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 46789999999999999999999999999999999999999999999999998765
No 24
>KOG0483|consensus
Probab=99.55 E-value=2.2e-15 Score=108.93 Aligned_cols=57 Identities=18% Similarity=0.117 Sum_probs=52.7
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 56 NRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 56 ~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
+..+|+.+|...|+..|....++....+..||..|||.++||.|||||||++||..+
T Consensus 53 kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq 109 (198)
T KOG0483|consen 53 KKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ 109 (198)
T ss_pred ccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence 344699999999999999999999999999999999999999999999999997643
No 25
>KOG0847|consensus
Probab=99.51 E-value=4.8e-15 Score=107.56 Aligned_cols=65 Identities=26% Similarity=0.297 Sum_probs=59.3
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhc
Q psy5909 50 KKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEF 114 (130)
Q Consensus 50 ~~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~ 114 (130)
..+++..|..|+..||..|+..|.+.+|+-...|.+||..+|+++.+|+|||||||.||||....
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa 228 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA 228 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence 35566678899999999999999999999999999999999999999999999999999886543
No 26
>KOG0490|consensus
Probab=99.51 E-value=1.5e-14 Score=106.42 Aligned_cols=64 Identities=39% Similarity=0.373 Sum_probs=60.5
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 50 KKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 50 ~~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
..++|+.|+.|+..|+.+|++.|...+||+...++.||..+++++..|+|||||||+||++..+
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 5678999999999999999999999999999999999999999999999999999999987653
No 27
>KOG0849|consensus
Probab=99.36 E-value=9.1e-13 Score=103.23 Aligned_cols=68 Identities=35% Similarity=0.433 Sum_probs=62.6
Q ss_pred CCCCccCCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 45 LSPVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 45 ~~~~~~~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
......++.+|.||.|+..|+..|+..|..++||++..|+.||.++++++..|+|||+|||+++++..
T Consensus 168 p~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 168 PGYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 33455667788899999999999999999999999999999999999999999999999999998877
No 28
>KOG1168|consensus
Probab=99.26 E-value=2.4e-12 Score=96.97 Aligned_cols=63 Identities=17% Similarity=0.099 Sum_probs=58.1
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 50 KKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 50 ~~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
...++|+||.|.....+.||++|..++.|+......+|.+|+|.+.+|+|||||.|.|.||.+
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 445788999999999999999999999999999999999999999999999999999987744
No 29
>KOG0775|consensus
Probab=98.61 E-value=3.8e-08 Score=73.85 Aligned_cols=50 Identities=18% Similarity=0.118 Sum_probs=44.9
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHh
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVEL 109 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~ 109 (130)
|...-+..|...|..++||+..++.+||..+||+..||-.||.|||.+.|
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 34444568888999999999999999999999999999999999999876
No 30
>KOG2252|consensus
Probab=98.59 E-value=8.9e-08 Score=77.73 Aligned_cols=56 Identities=21% Similarity=0.240 Sum_probs=52.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhH
Q psy5909 52 KHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSV 107 (130)
Q Consensus 52 ~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k 107 (130)
..++.|.+||..|...|...|+.+++|+..+.+.|+.+|+|....|..||.|-|.+
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRR 474 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRR 474 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhh
Confidence 34667999999999999999999999999999999999999999999999998865
No 31
>KOG0490|consensus
Probab=98.46 E-value=1.4e-07 Score=69.19 Aligned_cols=67 Identities=34% Similarity=0.313 Sum_probs=60.4
Q ss_pred CCccCCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 47 PVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 47 ~~~~~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
.....+.++.|+.+...|+..|...|....+|+...+..|+..++++...|+|||||+|.+.++...
T Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 147 GPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 3445567888999999999999999999999999999999999999999999999999999876544
No 32
>KOG0774|consensus
Probab=98.44 E-value=1.7e-07 Score=70.15 Aligned_cols=60 Identities=23% Similarity=0.233 Sum_probs=54.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHH---hhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 53 HRRNRTTFTTYQLHELERAFE---KSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 53 ~rr~Rt~~t~~q~~~L~~~F~---~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
.+|+|..|+..-..+|...|. .++||+..++++||.++|++..||-.||-|+|.+.+|..
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence 357788899999999999996 488999999999999999999999999999998877765
No 33
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.41 E-value=7.5e-08 Score=52.69 Aligned_cols=34 Identities=21% Similarity=0.217 Sum_probs=28.7
Q ss_pred hhCCCCHHHHHHHHHHhCCCCCccceechhhhhH
Q psy5909 74 KSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSV 107 (130)
Q Consensus 74 ~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k 107 (130)
.++||+..++..|+..+||+..||..||-|.|.+
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4789999999999999999999999999998864
No 34
>KOG1146|consensus
Probab=98.23 E-value=1.6e-06 Score=76.35 Aligned_cols=63 Identities=19% Similarity=0.140 Sum_probs=58.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 51 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 51 ~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
-.+|..|+.++..|+..|...|....|+.....+.|...+++++++|+|||||-|.|.++...
T Consensus 901 ~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 901 MGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 345678999999999999999999999999999999999999999999999999999877655
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.08 E-value=0.0002 Score=41.75 Aligned_cols=42 Identities=17% Similarity=0.061 Sum_probs=31.1
Q ss_pred HHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhh
Q psy5909 65 LHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYS 106 (130)
Q Consensus 65 ~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~ 106 (130)
+..|+.+|...+++.......|..+.+|+..||+-||-.++.
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 566999999999999999999999999999999999966543
No 36
>KOG3623|consensus
Probab=96.86 E-value=0.0012 Score=55.99 Aligned_cols=52 Identities=17% Similarity=0.015 Sum_probs=46.4
Q ss_pred HHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhccC
Q psy5909 65 LHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEFNI 116 (130)
Q Consensus 65 ~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~~~ 116 (130)
+..|+.+|..+.+|+..+...+|.++||+...|++||+++++++....+...
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps 619 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPS 619 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCcc
Confidence 6789999999999999999999999999999999999999999876554333
No 37
>KOG0773|consensus
Probab=95.65 E-value=0.014 Score=45.55 Aligned_cols=56 Identities=14% Similarity=0.028 Sum_probs=44.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHh---hCCCCHHHHHHHHHHhCCCCCccceechhhhhHH
Q psy5909 53 HRRNRTTFTTYQLHELERAFEK---SHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVE 108 (130)
Q Consensus 53 ~rr~Rt~~t~~q~~~L~~~F~~---~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~ 108 (130)
..+.+..+.......|+.-... .+||+...+..|+.++||+..||-.||-|.|.+.
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~ 297 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRL 297 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhccccc
Confidence 3444557777777777754322 5799999999999999999999999999999763
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=94.09 E-value=0.086 Score=30.20 Aligned_cols=46 Identities=17% Similarity=0.270 Sum_probs=34.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhh
Q psy5909 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLY 104 (130)
Q Consensus 54 rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNr 104 (130)
++.|..+|-.+...+-..+.... ....||..+|++..+|.-|..|+
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 46788999999888888777765 57789999999999999999774
No 39
>KOG1146|consensus
Probab=82.22 E-value=2.7 Score=38.65 Aligned_cols=66 Identities=12% Similarity=-0.044 Sum_probs=58.3
Q ss_pred CCccCCCCCCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 47 PVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 47 ~~~~~~~rr~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
.+..-+.++.+..+-..++..|-+.|..+.-|+..++.-|......+.+++++||+|-|.+.++..
T Consensus 699 ~~~~~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 699 ESLSPRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred CCCCcccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 344455677888999999999999999999999999999999999999999999999999887765
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=76.41 E-value=2.8 Score=24.05 Aligned_cols=38 Identities=29% Similarity=0.381 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHHhhCC--CCHHHHHHHHHHhCCCCCcc
Q psy5909 60 FTTYQLHELERAFEKSHY--PDVYSREELAMKVNLPEVRV 97 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~--p~~~~r~~La~~l~l~~~~V 97 (130)
+|..|+..|...+...-| |-...-.+||..+|++..-|
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHH
Confidence 578899999999887654 55667888999999998653
No 41
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=71.00 E-value=4 Score=22.42 Aligned_cols=43 Identities=9% Similarity=0.125 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhh
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYS 106 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~ 106 (130)
.+++.+..+|...|... ..-.++|..+|++...|+.+...-..
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~ 46 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALK 46 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 46778888888888333 24678999999999988766644333
No 42
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=70.55 E-value=3.9 Score=22.73 Aligned_cols=41 Identities=15% Similarity=-0.023 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhh
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYY 105 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR 105 (130)
+++.+...+...|.. ...-.++|..+|++...|+.|.+.-|
T Consensus 11 L~~~~r~i~~l~~~~-----g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRYFQ-----GMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHH-----CcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 445555555544433 34678899999999999999985544
No 43
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=69.50 E-value=5.7 Score=27.45 Aligned_cols=50 Identities=14% Similarity=0.090 Sum_probs=37.9
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 57 RTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 57 Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
...+++.|+.+|.. +... ....++|..+|++...|..|..+.+.|.++.+
T Consensus 4 ~~~Lt~rqreVL~l-r~~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 4 ESFLTERQIEVLRL-RERG-----LTQQEIADILGTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred ccCCCHHHHHHHHH-HHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35788999999877 3222 25668999999999999999988777655543
No 44
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=68.04 E-value=5.7 Score=23.53 Aligned_cols=44 Identities=16% Similarity=0.119 Sum_probs=27.7
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceech
Q psy5909 55 RNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGM 102 (130)
Q Consensus 55 r~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFq 102 (130)
+.|..||.++...+-..+.... .....+|..+|++...+.-|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g----~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG----ESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH----CHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC----CceEeeecccccccccccHHHH
Confidence 3567899998887766662222 3677899999999998888863
No 45
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=66.17 E-value=7.3 Score=27.93 Aligned_cols=32 Identities=25% Similarity=0.209 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
.-.++|..+|++...|+++...-+.+-++...
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 202 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLKVQMG 202 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 56789999999999999998777776665543
No 46
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=65.04 E-value=2 Score=25.38 Aligned_cols=20 Identities=15% Similarity=0.260 Sum_probs=17.3
Q ss_pred HHHHHHHHhCCCCCccceec
Q psy5909 82 SREELAMKVNLPEVRVQAVG 101 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWF 101 (130)
.-..||.+||+++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 34578999999999999995
No 47
>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=62.43 E-value=6.8 Score=20.74 Aligned_cols=42 Identities=14% Similarity=0.075 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhh
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYY 105 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR 105 (130)
.++..+...+...|... ..-..+|..+|++...|..|...-+
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 35666666676655322 2456789999999999988875543
No 48
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=57.16 E-value=16 Score=25.81 Aligned_cols=49 Identities=14% Similarity=0.024 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
.++..+..+|...|... ..-.++|..+|++...|+.+...-|.+-++..
T Consensus 142 ~L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 35555555555444333 25678999999999999999977666655543
No 49
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=57.06 E-value=15 Score=24.87 Aligned_cols=32 Identities=13% Similarity=-0.013 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
.-.++|..+|++...|+..+..-|.+-++..+
T Consensus 124 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (160)
T PRK09642 124 SYQEIALQEKIEVKTVEMKLYRARKWIKKHWK 155 (160)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 45689999999999999999777776655544
No 50
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=55.19 E-value=15 Score=25.45 Aligned_cols=50 Identities=16% Similarity=0.036 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
.++..+...|...|... ..-.++|..+|++...|+.++..-|.+-+....
T Consensus 131 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG-----ASIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 34555555555544332 256689999999999999999877777655443
No 51
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=54.59 E-value=15 Score=24.96 Aligned_cols=32 Identities=19% Similarity=0.057 Sum_probs=26.1
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
.-.++|..+|++...|+.|...-|.+.++...
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45689999999999999999877777666544
No 52
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=54.11 E-value=13 Score=26.17 Aligned_cols=49 Identities=6% Similarity=-0.055 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
++..+..++...|... ..-.++|..+|++...|+++...-|.+-++...
T Consensus 135 Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 183 (189)
T PRK12530 135 LPAQQARVFMMREYLE-----LSSEQICQECDISTSNLHVLLYRARLQLQACLS 183 (189)
T ss_pred CCHHHHHHHhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4444555554443332 246689999999999999999777766665554
No 53
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=53.18 E-value=15 Score=26.64 Aligned_cols=47 Identities=23% Similarity=0.274 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHHhhC--CCCHHHHHHHHHHhCCCCCccceechhhhhH
Q psy5909 59 TFTTYQLHELERAFEKSH--YPDVYSREELAMKVNLPEVRVQAVGMLYYSV 107 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~--~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k 107 (130)
.+|..|+..|..+|...- ||-.....+||..+|+++.- +|..=||+.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst--~~ehLRrAe 203 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST--LSEHLRRAE 203 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH--HHHHHHHHH
Confidence 699999999999998765 46667788899999999875 344444443
No 54
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=50.76 E-value=15 Score=24.52 Aligned_cols=45 Identities=9% Similarity=-0.015 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHH
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVE 108 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~ 108 (130)
.+++.+...+...|... ..-.++|..+|++...|+.|...-+.+-
T Consensus 106 ~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~L 150 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKM 150 (154)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 34555555555444333 3567899999999999999986655544
No 55
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=50.55 E-value=21 Score=25.01 Aligned_cols=51 Identities=14% Similarity=0.109 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhc
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEF 114 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~ 114 (130)
.++..+...|...|... ..-.++|..+|++...|++-+..-|.+.++....
T Consensus 131 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 181 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE-----KSVEEVGEIVGIPESTVKTRMFYARKKLAELLKA 181 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 35555555555443322 2456789999999999999998878777665543
No 56
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=50.50 E-value=21 Score=25.04 Aligned_cols=38 Identities=8% Similarity=-0.026 Sum_probs=29.5
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhhccCCCC
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIEFNIRVP 119 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~~~~~~ 119 (130)
.-.++|..+|++...|+.....-|.+-++.....+...
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~ 191 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWFNQ 191 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence 45789999999999999999887877777665544443
No 57
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=50.44 E-value=18 Score=24.70 Aligned_cols=32 Identities=13% Similarity=-0.113 Sum_probs=26.1
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
...++|..+|++...|++|.+.-|.+-++...
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999877777665544
No 58
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=50.23 E-value=23 Score=23.77 Aligned_cols=50 Identities=12% Similarity=-0.007 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhc
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEF 114 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~ 114 (130)
++..+..++...|... ..-.++|..+|++...|++....-|.+-++....
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 156 (161)
T PRK09047 107 LPARQREAFLLRYWED-----MDVAETAAAMGCSEGSVKTHCSRATHALAKALEA 156 (161)
T ss_pred CCHHHHHHHHHHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 4455555554443322 2356899999999999999887766666555443
No 59
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=49.34 E-value=23 Score=23.92 Aligned_cols=32 Identities=6% Similarity=0.001 Sum_probs=24.5
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
...++|..+|++...|+.....-+.+-++...
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~ 158 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALVHCRKCLD 158 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 46789999999999999887666666555443
No 60
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=49.29 E-value=19 Score=24.56 Aligned_cols=48 Identities=13% Similarity=-0.048 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhh
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQD 111 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~ 111 (130)
.+++.+...|...|... ..-.++|..+|++...|+.|...-+.+-++.
T Consensus 128 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45666666665554322 2456789999999999999987655555443
No 61
>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=49.01 E-value=28 Score=16.10 Aligned_cols=36 Identities=19% Similarity=0.237 Sum_probs=22.7
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCcccee
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAV 100 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvW 100 (130)
++..+...+...+... + ....++..++++...|.-|
T Consensus 6 ~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHh
Confidence 5566666565555432 2 4557788889887776655
No 62
>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=47.79 E-value=19 Score=21.08 Aligned_cols=17 Identities=24% Similarity=0.163 Sum_probs=14.1
Q ss_pred HHHHhCCCCCccceech
Q psy5909 86 LAMKVNLPEVRVQAVGM 102 (130)
Q Consensus 86 La~~l~l~~~~VqvWFq 102 (130)
.|.++|+..++|+-|-+
T Consensus 31 aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 31 AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp HHHHTTS-HHHHHHHHT
T ss_pred HHHHhCccHHHHHHHHH
Confidence 49999999999999974
No 63
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=47.71 E-value=17 Score=25.51 Aligned_cols=31 Identities=19% Similarity=0.115 Sum_probs=25.3
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
.-.++|..+|++...|+.|+..-|.+-++..
T Consensus 159 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 159 SQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4668999999999999999977777665543
No 64
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=47.51 E-value=27 Score=24.08 Aligned_cols=30 Identities=17% Similarity=-0.027 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQD 111 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~ 111 (130)
.-.++|..+|++...|+++...-|.+-|+.
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 467899999999999999987766665443
No 65
>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=47.16 E-value=22 Score=25.03 Aligned_cols=53 Identities=4% Similarity=-0.050 Sum_probs=35.5
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhccCC
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEFNIR 117 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~~~~ 117 (130)
++..+...|...|... ..-.++|..+|++...|+.....-|.+-++.....+.
T Consensus 132 L~~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~~~ 184 (188)
T TIGR02943 132 LPEQTARVFMMREVLG-----FESDEICQELEISTSNCHVLLYRARLSLRACLSINWF 184 (188)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4444545554443332 2467899999999999999987777777666654443
No 66
>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=46.98 E-value=23 Score=24.42 Aligned_cols=50 Identities=12% Similarity=-0.027 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
.++..+...|...|... ..-.++|..+|++...|+.+...-|.+.++...
T Consensus 100 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35555555555544333 246789999999999999999777777666554
No 67
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=46.07 E-value=6.1 Score=21.18 Aligned_cols=21 Identities=14% Similarity=0.074 Sum_probs=17.3
Q ss_pred HHHHHHHhCCCCCccceechh
Q psy5909 83 REELAMKVNLPEVRVQAVGML 103 (130)
Q Consensus 83 r~~La~~l~l~~~~VqvWFqN 103 (130)
..++|..+|++...|+.|.++
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 356899999999999999744
No 68
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=45.99 E-value=23 Score=24.70 Aligned_cols=47 Identities=19% Similarity=-0.046 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhh
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQ 110 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~ 110 (130)
.++..+...+...|... ..-.++|..+|++...|+.+...-|.+-++
T Consensus 139 ~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 139 TLPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45555555555544433 256789999999999999988666655544
No 69
>PRK00118 putative DNA-binding protein; Validated
Probab=45.80 E-value=26 Score=22.88 Aligned_cols=48 Identities=17% Similarity=-0.028 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhh
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQD 111 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~ 111 (130)
.++..|...+...|.... .-.++|..+|++...|..|...-|.+-++.
T Consensus 17 ~L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 17 LLTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 345666666655554432 456799999999999999987766655443
No 70
>PRK10072 putative transcriptional regulator; Provisional
Probab=45.55 E-value=15 Score=23.56 Aligned_cols=41 Identities=10% Similarity=0.050 Sum_probs=29.4
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhh
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYS 106 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~ 106 (130)
..+...+..|..... . ...+||..+|++...|.-|.+.+|.
T Consensus 32 ~~~~~eik~LR~~~g----l---TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTG----L---KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcC----C---CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 446666666643221 1 3678999999999999999988774
No 71
>KOG3755|consensus
Probab=45.46 E-value=7.3 Score=33.21 Aligned_cols=21 Identities=14% Similarity=-0.183 Sum_probs=0.0
Q ss_pred CCCCccceechhhhhHHhhhh
Q psy5909 92 LPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 92 l~~~~VqvWFqNrR~k~~~~~ 112 (130)
.....|+.||.|||.++++.+
T Consensus 738 ~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 738 FESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred hhhcchHHHHHHHHHHHhhhh
No 72
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=45.35 E-value=22 Score=24.58 Aligned_cols=48 Identities=10% Similarity=-0.029 Sum_probs=31.5
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhh
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQD 111 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~ 111 (130)
.+++.+...|...|.. ...-.++|..+|++...|+.+++.-|.+-+..
T Consensus 136 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME-----DLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3444454454443322 23466789999999999999997766665543
No 73
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=45.20 E-value=27 Score=23.85 Aligned_cols=48 Identities=8% Similarity=-0.092 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
++..+...+...|... ..-.++|..+|++...|+.+...-|.+-+...
T Consensus 113 L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 113 LSADQREAIILIGASG-----FSYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4444444444433322 24668999999999999999977766665543
No 74
>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=45.16 E-value=3.9 Score=25.07 Aligned_cols=33 Identities=15% Similarity=-0.055 Sum_probs=24.2
Q ss_pred HHHhhCCCCHHHHHHHHHHhCCCCCccceechh
Q psy5909 71 AFEKSHYPDVYSREELAMKVNLPEVRVQAVGML 103 (130)
Q Consensus 71 ~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqN 103 (130)
.|....|.......++|..+|++...|+.|+.+
T Consensus 23 af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 23 AAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 344444444446778999999999999999854
No 75
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=44.73 E-value=25 Score=24.48 Aligned_cols=32 Identities=9% Similarity=-0.044 Sum_probs=25.8
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
.-.++|..+|++...|+.+...-|.+-++...
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999777777666544
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=44.00 E-value=24 Score=23.62 Aligned_cols=44 Identities=14% Similarity=0.002 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhH
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSV 107 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k 107 (130)
.++..+...+...|... ..-.++|..+|++...|+++...-|.+
T Consensus 111 ~L~~~~r~v~~l~~~~g-----~~~~eIA~~l~is~~tv~~~l~Rar~~ 154 (159)
T TIGR02989 111 KLPERQRELLQLRYQRG-----VSLTALAEQLGRTVNAVYKALSRLRVR 154 (159)
T ss_pred HCCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 35555555555544332 356789999999999999887544444
No 77
>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=42.15 E-value=28 Score=23.09 Aligned_cols=28 Identities=14% Similarity=-0.056 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVEL 109 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~ 109 (130)
...++|..+|++...|+.+...-+.|.+
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4567899999999999988866555544
No 78
>PRK06930 positive control sigma-like factor; Validated
Probab=41.64 E-value=30 Score=24.46 Aligned_cols=50 Identities=16% Similarity=-0.018 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
.++..+..+|...|.... .-.++|..+|++...|+.+...-+.|-++...
T Consensus 114 ~L~~rer~V~~L~~~eg~-----s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 114 VLTEREKEVYLMHRGYGL-----SYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 466666666665443332 45678999999999999999877777665544
No 79
>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=41.51 E-value=19 Score=20.23 Aligned_cols=43 Identities=19% Similarity=0.169 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhH
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSV 107 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k 107 (130)
.||..++.+|.....-. ...++|..+++++..|..+..+=+.|
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 57788888776654433 46788999999999999887665544
No 80
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=41.43 E-value=24 Score=23.90 Aligned_cols=46 Identities=13% Similarity=-0.086 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhh
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQ 110 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~ 110 (130)
++..|...|...|... ..-.++|..+|++...|+.+...-|.+-++
T Consensus 113 L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 113 LPLERRNVLLLRDYYG-----FSYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CCHHHHHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4444444444433222 245678999999999999988766665543
No 81
>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=41.36 E-value=3.8 Score=23.83 Aligned_cols=20 Identities=25% Similarity=0.317 Sum_probs=17.6
Q ss_pred HHHHHHHHhCCCCCccceec
Q psy5909 82 SREELAMKVNLPEVRVQAVG 101 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWF 101 (130)
...++|..||++...|.-|-
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~ 34 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWK 34 (58)
T ss_pred CHHHHHHHHCCChHHHHHHH
Confidence 45679999999999999997
No 82
>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=41.03 E-value=34 Score=23.04 Aligned_cols=31 Identities=10% Similarity=-0.056 Sum_probs=24.6
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
.-.++|..+|++...|+.+...-|.+-++..
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 4567899999999999999877776665543
No 83
>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=41.00 E-value=29 Score=22.37 Aligned_cols=45 Identities=11% Similarity=-0.088 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHh
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVEL 109 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~ 109 (130)
++..+...|...|.. ...-.++|..+|++...|..|...-+.|-+
T Consensus 111 L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 111 LPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred CCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 455555555444322 224568999999999999988866555443
No 84
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=40.71 E-value=33 Score=23.98 Aligned_cols=52 Identities=4% Similarity=-0.098 Sum_probs=36.4
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhccC
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEFNI 116 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~~~ 116 (130)
++..+..++...|... ..-.++|..+|++...|++....-|.+-++.....+
T Consensus 132 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 132 LPPRTGRVFMMREWLE-----LETEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555554443322 245689999999999999999888877777776665
No 85
>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=40.64 E-value=26 Score=20.05 Aligned_cols=33 Identities=30% Similarity=0.396 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccce
Q psy5909 63 YQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQA 99 (130)
Q Consensus 63 ~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~Vqv 99 (130)
-|+..|+-.+. +...+.. +||..+|++.+.|+-
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~ 38 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKN 38 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHH
Confidence 35666776677 6666554 899999999987763
No 86
>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=40.61 E-value=31 Score=23.78 Aligned_cols=46 Identities=15% Similarity=0.013 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhh
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQ 110 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~ 110 (130)
++..+..++...|... ..-.++|..+|++...|++....-|.+-++
T Consensus 135 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG-----LTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4444555444443332 246689999999999999998776665544
No 87
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=40.23 E-value=41 Score=23.32 Aligned_cols=29 Identities=21% Similarity=0.085 Sum_probs=22.9
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQ 110 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~ 110 (130)
.-.++|..+|++...|++|...-+.+-++
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 46688999999999999998666655443
No 88
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=39.85 E-value=42 Score=22.92 Aligned_cols=49 Identities=14% Similarity=0.204 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
++..+..+|...|... ..-.++|..+|++...|+.....-|.+-++...
T Consensus 119 L~~~~r~vl~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 167 (173)
T PRK09645 119 LSPEHRAVLVRSYYRG-----WSTAQIAADLGIPEGTVKSRLHYALRALRLALQ 167 (173)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 4455555555443332 245689999999999999988666666555443
No 89
>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=39.61 E-value=24 Score=24.47 Aligned_cols=31 Identities=16% Similarity=0.051 Sum_probs=24.3
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
.-.++|..+|++...|+++...-|.+-++..
T Consensus 156 s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 156 SYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 4578999999999999999966666655543
No 90
>PRK04217 hypothetical protein; Provisional
Probab=39.46 E-value=38 Score=22.34 Aligned_cols=51 Identities=12% Similarity=-0.040 Sum_probs=37.1
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 57 RTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 57 Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
-..++..+...+...|...- ...++|..+|++...|+..+..-+.+-+...
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 34678888777765554332 5667999999999999988877776655544
No 91
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=39.35 E-value=41 Score=23.61 Aligned_cols=33 Identities=12% Similarity=0.086 Sum_probs=25.0
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhhc
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIEF 114 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~ 114 (130)
.-.++|..+|++...|++-...-|.+-++....
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~~ 191 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMDA 191 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhhh
Confidence 456889999999999988886666666555443
No 92
>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=38.48 E-value=40 Score=22.94 Aligned_cols=46 Identities=13% Similarity=0.026 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhh
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQ 110 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~ 110 (130)
++..+...+...|... ..-.++|..+|++...|+.+...-|.+-++
T Consensus 120 L~~~~r~i~~l~~~~g-----~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 120 LNDKYQTAIILRYYHD-----LTIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CCHHHhHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4444444454443332 246678999999999999888665555444
No 93
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=38.21 E-value=17 Score=19.56 Aligned_cols=38 Identities=18% Similarity=0.239 Sum_probs=17.3
Q ss_pred CCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCcccee
Q psy5909 58 TTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAV 100 (130)
Q Consensus 58 t~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvW 100 (130)
..+|..+...++..+... ....++|..+|.+...|.-+
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~re 40 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRE 40 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHH
Confidence 457788888888765433 35667999999988766544
No 94
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=38.05 E-value=33 Score=24.26 Aligned_cols=32 Identities=16% Similarity=-0.040 Sum_probs=26.2
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
.-.++|..+|++...|++++..-|.+-++...
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 45688999999999999999887777666554
No 95
>PF13518 HTH_28: Helix-turn-helix domain
Probab=38.03 E-value=13 Score=20.08 Aligned_cols=24 Identities=21% Similarity=0.116 Sum_probs=19.4
Q ss_pred HHHHHHHHhCCCCCccceechhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYY 105 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR 105 (130)
...++|..+|++..+|.-|.+.-+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 345689999999999999985544
No 96
>KOG3623|consensus
Probab=37.92 E-value=31 Score=30.38 Aligned_cols=53 Identities=15% Similarity=0.089 Sum_probs=31.8
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHh
Q psy5909 57 RTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVEL 109 (130)
Q Consensus 57 Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~ 109 (130)
++.+...+-..|..++..+.-+.-..-..++..|-.-+.+|.|||++|+..-+
T Consensus 630 ~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstps 682 (1007)
T KOG3623|consen 630 RSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPS 682 (1007)
T ss_pred cCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCC
Confidence 34444444455555555544443333333445566778889999999987543
No 97
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=37.89 E-value=39 Score=24.24 Aligned_cols=33 Identities=15% Similarity=-0.066 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhhc
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIEF 114 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~ 114 (130)
.-.++|..+|++...|+.+...-|.+-++....
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~ 188 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQLRAALAA 188 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999998777777665543
No 98
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=37.78 E-value=37 Score=23.71 Aligned_cols=32 Identities=19% Similarity=0.019 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
.-.++|..+|++...|+..+..-|.+.++...
T Consensus 124 ~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (181)
T PRK09637 124 SQKEIAEKLGLSLSGAKSRVQRGRVKLKELLE 155 (181)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999777776665544
No 99
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=37.68 E-value=37 Score=22.95 Aligned_cols=48 Identities=19% Similarity=0.058 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
.++..+...|...| .. ..-.++|..+|++...|+.+...-|.+.++..
T Consensus 112 ~L~~~~r~il~l~~-~g-----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 112 KMTERDRTVLLLRF-SG-----YSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35555555665555 22 24667899999999999999977666665544
No 100
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=37.62 E-value=37 Score=24.14 Aligned_cols=35 Identities=3% Similarity=-0.093 Sum_probs=27.5
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhhccC
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIEFNI 116 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~~~ 116 (130)
.-.++|..+|++...|++....-|.+-++.....+
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~ 191 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRTCLSEKG 191 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45689999999999999999877777766654333
No 101
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=37.56 E-value=35 Score=24.94 Aligned_cols=48 Identities=10% Similarity=0.093 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
++..+..+|...|.. ...-.++|..+|++...|+.+...-+.+-++..
T Consensus 185 L~~~~r~vl~l~~~~-----g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 185 LPEREQLVLSLYYQE-----ELNLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred CCHHHHHHHHhHhcc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 344444455444422 235678999999999999999987777766544
No 102
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=37.39 E-value=49 Score=21.75 Aligned_cols=43 Identities=9% Similarity=-0.070 Sum_probs=29.0
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechh
Q psy5909 57 RTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGML 103 (130)
Q Consensus 57 Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqN 103 (130)
|..|+.++....-.....+.+ ....+|..+|++...|.-|.+.
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHHH
Confidence 456888876554444333332 3456799999999999999643
No 103
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=37.33 E-value=38 Score=24.34 Aligned_cols=53 Identities=8% Similarity=-0.135 Sum_probs=35.0
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhccCC
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEFNIR 117 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~~~~ 117 (130)
++..+...+...|.... .-.++|..+|++...|++....-|.+-++.....+.
T Consensus 149 L~~~~r~v~~L~~~~g~-----s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~~ 201 (206)
T PRK12544 149 LPAKYARVFMMREFIEL-----ETNEICHAVDLSVSNLNVLLYRARLRLRECLENKWF 201 (206)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 44444444444433321 356899999999999999998777777666554443
No 104
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=37.13 E-value=28 Score=25.66 Aligned_cols=32 Identities=13% Similarity=-0.049 Sum_probs=26.3
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
.-.++|..+|++...|++....-|.+-++...
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999887777666554
No 105
>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=36.95 E-value=68 Score=22.67 Aligned_cols=44 Identities=25% Similarity=0.411 Sum_probs=35.1
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceec
Q psy5909 56 NRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVG 101 (130)
Q Consensus 56 ~Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWF 101 (130)
....+|.+++.++...-..+ |..+.+..||.++|++..-|-+-.
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 34789999999998876555 677889999999999887666544
No 106
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=36.52 E-value=48 Score=22.91 Aligned_cols=46 Identities=15% Similarity=0.143 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhh
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQ 110 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~ 110 (130)
++..+...|...|... ..-.++|..+|++...|+.+...-|.+-+.
T Consensus 136 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 136 LSPEERRVIEVLYYQG-----YTHREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4444444444333222 245688999999999999888666655544
No 107
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=36.06 E-value=10 Score=22.02 Aligned_cols=19 Identities=11% Similarity=0.102 Sum_probs=16.3
Q ss_pred HHHHHHhCCCCCccceech
Q psy5909 84 EELAMKVNLPEVRVQAVGM 102 (130)
Q Consensus 84 ~~La~~l~l~~~~VqvWFq 102 (130)
.++|..+|++...|+.|=.
T Consensus 4 ~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999953
No 108
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.80 E-value=41 Score=21.47 Aligned_cols=38 Identities=21% Similarity=0.242 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCcc
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRV 97 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~V 97 (130)
+.++|+..-...|+.+--.+....+++|..|+.++.-|
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~l 40 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKL 40 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHH
Confidence 56677776666676666666667788898888776433
No 109
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=34.72 E-value=48 Score=22.92 Aligned_cols=31 Identities=23% Similarity=0.093 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
.-.++|..+|++...|++....-|.+-++..
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4568999999999999999877777665544
No 110
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=34.52 E-value=48 Score=23.55 Aligned_cols=34 Identities=9% Similarity=-0.083 Sum_probs=26.8
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhhcc
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIEFN 115 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~~ 115 (130)
.-.++|..+|++...|+++...-|.+-++.....
T Consensus 151 s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~ 184 (196)
T PRK12535 151 TYEEAAKIADVRVGTIRSRVARARADLIAATATG 184 (196)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 4568999999999999999977777766655443
No 111
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=34.49 E-value=47 Score=23.38 Aligned_cols=35 Identities=9% Similarity=-0.159 Sum_probs=27.6
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhhccC
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIEFNI 116 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~~~ 116 (130)
.-.++|..||++...|+++...-|.+-++.....+
T Consensus 134 s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~ 168 (187)
T PRK12516 134 AYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG 168 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 45678999999999999999887777666655433
No 112
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=33.14 E-value=25 Score=24.10 Aligned_cols=32 Identities=16% Similarity=0.110 Sum_probs=26.7
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
.-.++|..+|++...|+..+..-|.+-++..+
T Consensus 138 s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 138 PQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999887777766554
No 113
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=33.06 E-value=33 Score=22.50 Aligned_cols=40 Identities=10% Similarity=0.057 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhh
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYY 105 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR 105 (130)
.+++..+..+...+.-. ...+|+.||++...|+-|=|+|+
T Consensus 43 ~ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~ 82 (104)
T COG2944 43 TLSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRK 82 (104)
T ss_pred CCCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCc
Confidence 37888888888766544 45689999999999999999987
No 114
>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=32.91 E-value=10 Score=19.91 Aligned_cols=18 Identities=11% Similarity=0.084 Sum_probs=13.8
Q ss_pred HHHHHHhCCCCCccceec
Q psy5909 84 EELAMKVNLPEVRVQAVG 101 (130)
Q Consensus 84 ~~La~~l~l~~~~VqvWF 101 (130)
-++|..+|++...|+.|=
T Consensus 3 ~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHH
Confidence 367899999999888774
No 115
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=32.71 E-value=51 Score=23.02 Aligned_cols=47 Identities=13% Similarity=0.019 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhh
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQD 111 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~ 111 (130)
++..+...+...|... ....++|..+|++...|+...+.-|.+-+++
T Consensus 132 L~~~~r~i~~l~~~~g-----~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 132 LEKLDREIFIRRYLLG-----EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred CCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 4455545554433222 3467899999999999988876666655443
No 116
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=32.45 E-value=53 Score=22.71 Aligned_cols=31 Identities=23% Similarity=-0.010 Sum_probs=24.8
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
.-.++|..+|++...|++....-|.+-++..
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 4678999999999999999977776665543
No 117
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=32.34 E-value=75 Score=22.45 Aligned_cols=37 Identities=24% Similarity=0.201 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccc
Q psy5909 62 TYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98 (130)
Q Consensus 62 ~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~Vq 98 (130)
..-+..|...+.+.-|.+......+|..|+++...|.
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 4456778888888889999999999999999987553
No 118
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=32.16 E-value=51 Score=22.82 Aligned_cols=47 Identities=13% Similarity=0.067 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhh
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQ 110 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~ 110 (130)
.++..|..++.-.|... ..-.++|..+|++...|+.....-+.+.+.
T Consensus 127 ~Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG-----MKQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35556666555544333 246689999999999999998766666544
No 119
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=31.76 E-value=52 Score=23.14 Aligned_cols=32 Identities=13% Similarity=-0.010 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
.-.++|..+|++...|+.++.--|.+-++...
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 185 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKRALAALLA 185 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999777766655543
No 120
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=31.74 E-value=48 Score=23.11 Aligned_cols=32 Identities=16% Similarity=0.065 Sum_probs=25.6
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
.-.++|..+|++...|+...+.-|.+-++..+
T Consensus 156 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 156 SYEDIASVMQCPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45789999999999999998777777665543
No 121
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=31.33 E-value=14 Score=21.41 Aligned_cols=20 Identities=5% Similarity=0.012 Sum_probs=16.9
Q ss_pred HHHHHHhCCCCCccceechh
Q psy5909 84 EELAMKVNLPEVRVQAVGML 103 (130)
Q Consensus 84 ~~La~~l~l~~~~VqvWFqN 103 (130)
.++|..+|++...++.|-++
T Consensus 4 ~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 4 KEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHCcCHHHHHHHHHh
Confidence 46899999999999999754
No 122
>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=31.20 E-value=46 Score=20.55 Aligned_cols=21 Identities=19% Similarity=0.207 Sum_probs=17.6
Q ss_pred HHHHHHHHhCCCCCccceech
Q psy5909 82 SREELAMKVNLPEVRVQAVGM 102 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFq 102 (130)
.+..|...++|..-++.||+.
T Consensus 55 L~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 55 LTSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHHHHhCCCCCeEEEEEE
Confidence 355688888999999999984
No 123
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=31.20 E-value=47 Score=24.17 Aligned_cols=35 Identities=14% Similarity=-0.115 Sum_probs=27.6
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhhccC
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIEFNI 116 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~~~ 116 (130)
.-.++|..+|++...|+.+...-|.+-++......
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~~ 186 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLARARRRLAALLGGAS 186 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccc
Confidence 45678999999999999999877777766654443
No 124
>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=31.19 E-value=51 Score=17.33 Aligned_cols=14 Identities=43% Similarity=0.562 Sum_probs=11.7
Q ss_pred CCCHHHHHHHHHHH
Q psy5909 59 TFTTYQLHELERAF 72 (130)
Q Consensus 59 ~~t~~q~~~L~~~F 72 (130)
.||..|+..|+.-.
T Consensus 2 ~FT~~Ql~~L~~Qi 15 (37)
T PF08880_consen 2 PFTPAQLQELRAQI 15 (37)
T ss_pred CCCHHHHHHHHHHH
Confidence 69999999998753
No 125
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=31.01 E-value=61 Score=22.18 Aligned_cols=47 Identities=9% Similarity=-0.038 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhh
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQD 111 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~ 111 (130)
++..+..++...|... ..-.++|..+|++...|+++...-+.+.+..
T Consensus 120 Lp~~~r~v~~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 120 LSSKARAAFLYNRLDG-----MGHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4444444444433222 2456789999999999999997766665443
No 126
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=30.81 E-value=54 Score=22.72 Aligned_cols=48 Identities=8% Similarity=-0.033 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
+++.+..++...|... ..-.++|..+|++...|+.....-|.+-++..
T Consensus 123 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 123 LNESNRQVFKYKVFYN-----LTYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4444444444433222 24568999999999999998877666665544
No 127
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=29.61 E-value=62 Score=23.93 Aligned_cols=48 Identities=8% Similarity=0.126 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhh
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQD 111 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~ 111 (130)
.++..+..+|...|... ..-.++|..+|++...|+.|...-+.+-++.
T Consensus 205 ~L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN-----LSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHhCC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35566666666554322 2457899999999999998886666555443
No 128
>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=29.45 E-value=15 Score=21.36 Aligned_cols=19 Identities=16% Similarity=0.114 Sum_probs=16.5
Q ss_pred HHHHHHhCCCCCccceech
Q psy5909 84 EELAMKVNLPEVRVQAVGM 102 (130)
Q Consensus 84 ~~La~~l~l~~~~VqvWFq 102 (130)
.++|..+|++...++.|.+
T Consensus 4 ~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 4 GEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4789999999999999974
No 129
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=29.39 E-value=71 Score=21.83 Aligned_cols=31 Identities=16% Similarity=0.044 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
.-.++|..+|++...|++....-|.+-++..
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 167 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMREHL 167 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999876666655443
No 130
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=29.34 E-value=57 Score=22.42 Aligned_cols=30 Identities=17% Similarity=0.027 Sum_probs=23.7
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQD 111 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~ 111 (130)
.-.++|..+|++...|+.....-|.+-++.
T Consensus 154 s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 154 SLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 466789999999999988887766665554
No 131
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=28.56 E-value=78 Score=21.93 Aligned_cols=48 Identities=13% Similarity=-0.056 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
++..+...+.-.|.. ...-.++|..+|++...|+.+...-|.+-++..
T Consensus 132 L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 132 LPEKMRLAIQAVKLE-----GLSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred CCHHHHHHHHHHHHc-----CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 444554444433322 235668999999999999999866666555443
No 132
>KOG0773|consensus
Probab=28.27 E-value=49 Score=25.76 Aligned_cols=39 Identities=15% Similarity=0.045 Sum_probs=32.6
Q ss_pred HhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhh
Q psy5909 73 EKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQD 111 (130)
Q Consensus 73 ~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~ 111 (130)
..+.|++......|+....|+..+|.+||-|-|.+..+.
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~ 155 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKE 155 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhc
Confidence 358899999999999999999999999998888665443
No 133
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=27.60 E-value=73 Score=16.81 Aligned_cols=40 Identities=15% Similarity=0.137 Sum_probs=27.3
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhh
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLY 104 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNr 104 (130)
.++..+...+...+ .. ....++|..++++...|..|...-
T Consensus 3 ~l~~~e~~i~~~~~-~g-----~s~~eia~~l~is~~tv~~~~~~~ 42 (58)
T smart00421 3 SLTPREREVLRLLA-EG-----LTNKEIAERLGISEKTVKTHLSNI 42 (58)
T ss_pred CCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 35677777665432 22 145678999999999998887543
No 134
>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=27.36 E-value=71 Score=21.91 Aligned_cols=48 Identities=25% Similarity=0.236 Sum_probs=35.4
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhh
Q psy5909 57 RTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQ 110 (130)
Q Consensus 57 Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~ 110 (130)
.+.++..|+..|... ... ....++|..+|++...|..+-..-+.|-++
T Consensus 4 ~~~Lte~qr~VL~Lr-~~G-----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELR-EKG-----LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHH-HcC-----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 357888999888773 222 256789999999999988888666655543
No 135
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=27.11 E-value=75 Score=22.22 Aligned_cols=49 Identities=14% Similarity=-0.086 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
++..+...|...|... ..-.++|..+|++...|+++...-|.+-++...
T Consensus 112 Lp~~~R~v~~L~~~eg-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 112 LPEEQRAALHLVAIEG-----LSYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4444444444433322 246688999999999999998666666555443
No 136
>PF09301 DUF1970: Domain of unknown function (DUF1970); InterPro: IPR015380 This entry is represented by Bacteriophage PRD1, P16; it is a family of uncharacterised viral proteins.; PDB: 1W8X_P.
Probab=26.69 E-value=16 Score=23.26 Aligned_cols=11 Identities=0% Similarity=-0.511 Sum_probs=7.8
Q ss_pred cceechhhhhH
Q psy5909 97 VQAVGMLYYSV 107 (130)
Q Consensus 97 VqvWFqNrR~k 107 (130)
|.+||.||-+-
T Consensus 19 iwlwfrnrpaa 29 (117)
T PF09301_consen 19 IWLWFRNRPAA 29 (117)
T ss_dssp HHHHHHHTT-S
T ss_pred HHHHHccChHH
Confidence 57899998753
No 137
>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=26.65 E-value=66 Score=23.22 Aligned_cols=46 Identities=13% Similarity=0.096 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHh
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVEL 109 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~ 109 (130)
.++..+...|...|... ....++|..+|++...|+.+...-+.+-+
T Consensus 175 ~L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr 220 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKKLR 220 (224)
T ss_pred hCCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 35666666666655333 24678999999999999888755555443
No 138
>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=26.48 E-value=70 Score=21.52 Aligned_cols=43 Identities=19% Similarity=0.142 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhH
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSV 107 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k 107 (130)
+++.+..+|...|... ..-.++|..+|++...|+....--|.+
T Consensus 123 L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tv~~~l~ra~~~ 165 (170)
T TIGR02952 123 LTPKQQHVIALRFGQN-----LPIAEVARILGKTEGAVKILQFRAIKK 165 (170)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 4455555554433322 245678999999999988776433333
No 139
>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=26.47 E-value=70 Score=23.05 Aligned_cols=45 Identities=11% Similarity=0.085 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHH
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVE 108 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~ 108 (130)
.++..+...|...|... ..-.++|..+|++...|+.|...-+.+-
T Consensus 178 ~L~~~~r~vl~l~y~~~-----~s~~eIA~~lgis~~~v~~~~~ra~~~L 222 (227)
T TIGR02980 178 ALPERERRILLLRFFED-----KTQSEIAERLGISQMHVSRLLRRALKKL 222 (227)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 46666666666655332 2467899999999999998885544443
No 140
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=26.18 E-value=73 Score=23.72 Aligned_cols=48 Identities=15% Similarity=0.038 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
++..+..+|...|.. ...-.++|..+|++...|+.+..--+.|-++..
T Consensus 204 L~~~~r~vl~l~y~~-----~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 204 LEERTREVLEFVFLH-----DLTQKEAAERLGISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred CCHHHHHHHHHHHHC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 455555555555533 235678999999999999998866666655543
No 141
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=26.00 E-value=65 Score=22.49 Aligned_cols=29 Identities=14% Similarity=-0.019 Sum_probs=22.9
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQ 110 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~ 110 (130)
.-.++|..+|++...|+++...-|.+-++
T Consensus 148 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45689999999999999998666655544
No 142
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=25.97 E-value=29 Score=24.33 Aligned_cols=33 Identities=18% Similarity=0.076 Sum_probs=25.9
Q ss_pred HHHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 81 YSREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 81 ~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
..-.++|..+|++...|+.+...-|.+-++...
T Consensus 156 ~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 188 (194)
T PRK12513 156 LELEEIAELTGVPEETVKSRLRYALQKLRELLA 188 (194)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999888777766655544
No 143
>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=25.91 E-value=75 Score=23.61 Aligned_cols=31 Identities=10% Similarity=-0.048 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
.-.++|..+|++...|+++...-|.+-++..
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4668999999999999999988776654443
No 144
>PF11516 DUF3220: Protein of unknown function (DUF3120); InterPro: IPR021597 This family of proteins with unknown function appears to be restricted to Bordetella. ; PDB: 2JPF_A.
Probab=25.62 E-value=17 Score=22.77 Aligned_cols=10 Identities=10% Similarity=-0.287 Sum_probs=8.0
Q ss_pred Cccceechhh
Q psy5909 95 VRVQAVGMLY 104 (130)
Q Consensus 95 ~~VqvWFqNr 104 (130)
..|+||.||-
T Consensus 31 gdvkvwmqnl 40 (106)
T PF11516_consen 31 GDVKVWMQNL 40 (106)
T ss_dssp HHHHHHHHHH
T ss_pred ccHHHHHHHH
Confidence 3689999984
No 145
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=25.33 E-value=69 Score=24.96 Aligned_cols=55 Identities=16% Similarity=0.120 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhhhhc
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQDIEF 114 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~ 114 (130)
.++..+..+|...|-.. |.......++|..+|++...|+.+...-+.+-|+....
T Consensus 262 ~L~~~~R~vl~lrygL~-~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~ 316 (325)
T PRK05657 262 ELNDKQREVLARRFGLL-GYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQT 316 (325)
T ss_pred cCCHHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 46677777777665222 22334567899999999999999998888777766554
No 146
>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=25.25 E-value=24 Score=18.28 Aligned_cols=23 Identities=9% Similarity=-0.129 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCCCccceechhhh
Q psy5909 83 REELAMKVNLPEVRVQAVGMLYY 105 (130)
Q Consensus 83 r~~La~~l~l~~~~VqvWFqNrR 105 (130)
..++|..+|++...|.-|.++-.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCC
Confidence 35789999999999998886544
No 147
>PF06505 XylR_N: Activator of aromatic catabolism; InterPro: IPR010523 This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators in several proteobacteria, including activators of phenol degradation such as XylR. It is found adjacent to IPR004096 from INTERPRO.
Probab=24.90 E-value=28 Score=22.64 Aligned_cols=21 Identities=5% Similarity=-0.314 Sum_probs=16.9
Q ss_pred HHHHhCCCCCccceechhhhh
Q psy5909 86 LAMKVNLPEVRVQAVGMLYYS 106 (130)
Q Consensus 86 La~~l~l~~~~VqvWFqNrR~ 106 (130)
|...|-..+..=+|||.++|+
T Consensus 2 L~~~L~F~p~~G~Iwl~~~Rm 22 (103)
T PF06505_consen 2 LRELLRFSPEDGRIWLNGQRM 22 (103)
T ss_pred hHHheeEeCCCCeEEECCEEE
Confidence 456677778888999999995
No 148
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=24.88 E-value=1e+02 Score=20.65 Aligned_cols=32 Identities=9% Similarity=0.013 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
...++|..+|++...|+.....-+.+.++...
T Consensus 123 s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~ 154 (159)
T PRK12527 123 SHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR 154 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45788999999999999888766665555443
No 149
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=24.55 E-value=40 Score=23.57 Aligned_cols=33 Identities=12% Similarity=-0.027 Sum_probs=27.1
Q ss_pred HHHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 81 YSREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 81 ~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
..-.++|..+|++...|+++...-|.+-++...
T Consensus 148 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 148 FAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999999888877666554
No 150
>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=24.55 E-value=70 Score=23.61 Aligned_cols=47 Identities=13% Similarity=0.176 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhh
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQ 110 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~ 110 (130)
.++..+..+|...|... ..-.++|..+|++...|+.+...-+.+-|+
T Consensus 205 ~L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred cCCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45666666666655332 245789999999999998888666655443
No 151
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=24.02 E-value=43 Score=19.76 Aligned_cols=26 Identities=12% Similarity=-0.052 Sum_probs=21.0
Q ss_pred HHHHHHHHhCCCCCccceechhhhhH
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSV 107 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k 107 (130)
.+..++...|++..+.++||..+-..
T Consensus 25 lK~~I~~~~gip~~~q~Li~~Gk~L~ 50 (71)
T cd01796 25 FKALCEAESGIPASQQQLIYNGRELV 50 (71)
T ss_pred HHHHHHHHhCCCHHHeEEEECCeEcc
Confidence 45677888899999999999876553
No 152
>cd01769 UBL Ubiquitin-like domain of UBL. UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
Probab=23.84 E-value=71 Score=17.83 Aligned_cols=25 Identities=12% Similarity=0.061 Sum_probs=19.3
Q ss_pred HHHHHHHHhCCCCCccceechhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYS 106 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~ 106 (130)
.+..++..++++...+++||..+-.
T Consensus 23 lK~~i~~~~~~~~~~~~l~~~g~~l 47 (69)
T cd01769 23 LKAKIAAKEGVPPEQQRLIYAGKIL 47 (69)
T ss_pred HHHHHHHHHCcChHHEEEEECCcCC
Confidence 4566788889999889999976543
No 153
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=23.72 E-value=21 Score=19.23 Aligned_cols=23 Identities=17% Similarity=0.124 Sum_probs=16.7
Q ss_pred HHHHHHHHHhCCCCCccceechh
Q psy5909 81 YSREELAMKVNLPEVRVQAVGML 103 (130)
Q Consensus 81 ~~r~~La~~l~l~~~~VqvWFqN 103 (130)
....++|..+|++...|.-|...
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 35668899999999999999743
No 154
>PTZ00044 ubiquitin; Provisional
Probab=23.68 E-value=56 Score=19.18 Aligned_cols=26 Identities=8% Similarity=-0.078 Sum_probs=21.6
Q ss_pred HHHHHHHHhCCCCCccceechhhhhH
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSV 107 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k 107 (130)
.+..|+...|++..+.++||..+...
T Consensus 26 lK~~i~~~~gi~~~~q~L~~~g~~L~ 51 (76)
T PTZ00044 26 VKMALQEKEGIDVKQIRLIYSGKQMS 51 (76)
T ss_pred HHHHHHHHHCCCHHHeEEEECCEEcc
Confidence 46678889999999999999887654
No 155
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=23.64 E-value=81 Score=23.28 Aligned_cols=46 Identities=9% Similarity=0.074 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhh
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQ 110 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~ 110 (130)
+...+..++...|.. ...-.++|..+|++...|+.++..-|.+-|+
T Consensus 202 L~~~~r~vl~l~~~~-----~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 202 LSEKEQLVISLFYKE-----ELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred CCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 455555555544432 2246789999999999999888665555443
No 156
>cd01793 Fubi Fubi ubiquitin-like protein. Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.
Probab=23.17 E-value=46 Score=19.68 Aligned_cols=27 Identities=4% Similarity=-0.256 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHH
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVE 108 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~ 108 (130)
.+..++...|++..+.++||..+..+.
T Consensus 24 lK~~i~~~~gip~~~q~Li~~Gk~L~D 50 (74)
T cd01793 24 IKAHVAGLEGIDVEDQVLLLAGVPLED 50 (74)
T ss_pred HHHHHHhhhCCCHHHEEEEECCeECCC
Confidence 466788889999999999998877653
No 157
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=22.92 E-value=88 Score=21.02 Aligned_cols=42 Identities=10% Similarity=-0.050 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhh
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYS 106 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~ 106 (130)
++..+...+...|... ..-.++|..+|++...|+++...-+.
T Consensus 114 L~~~~r~v~~L~~~~g-----~s~~EIA~~l~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 114 LPPLVKRAFLLAQVDG-----LGYGEIATELGISLATVKRYLNKAAM 155 (161)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4444555554443332 24567899999999999988754443
No 158
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=22.68 E-value=47 Score=19.29 Aligned_cols=26 Identities=12% Similarity=0.022 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCCCCccceechhhhhH
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSV 107 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k 107 (130)
.+..++...|++..+.++||..+...
T Consensus 24 lK~~i~~~~gi~~~~q~Li~~G~~L~ 49 (70)
T cd01798 24 LKEVVAKRQGVPPDQLRVIFAGKELR 49 (70)
T ss_pred HHHHHHHHHCCCHHHeEEEECCeECC
Confidence 46678899999999999999887754
No 159
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=22.57 E-value=1e+02 Score=21.51 Aligned_cols=35 Identities=11% Similarity=-0.185 Sum_probs=27.1
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhhccC
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIEFNI 116 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~~~ 116 (130)
.-.++|..+|++...|+.....-|.+-++......
T Consensus 129 s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~ 163 (182)
T PRK12540 129 SYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDG 163 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 45689999999999999998777777666655433
No 160
>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=22.43 E-value=19 Score=19.53 Aligned_cols=21 Identities=14% Similarity=-0.050 Sum_probs=18.4
Q ss_pred HHHHHhCCCCCccceechhhh
Q psy5909 85 ELAMKVNLPEVRVQAVGMLYY 105 (130)
Q Consensus 85 ~La~~l~l~~~~VqvWFqNrR 105 (130)
+||..+|++...|--|+.++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 578999999999999998874
No 161
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=22.43 E-value=1.3e+02 Score=20.66 Aligned_cols=29 Identities=21% Similarity=0.036 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQ 110 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~ 110 (130)
.-.++|..+|++...|+.-...-|.+-+.
T Consensus 155 s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 155 TYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred CHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 45678999999999988777555554433
No 162
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=22.37 E-value=80 Score=22.90 Aligned_cols=52 Identities=8% Similarity=0.066 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhh
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQD 111 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~ 111 (130)
.++..+..++...|.. .+.....-.++|..+|++...|+.+...-|.+-|+.
T Consensus 178 ~Lp~~~R~v~~L~y~l-~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 178 KLSDREKQIMELRFGL-NGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred hCCHHHHHHHHHHhcc-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3455555555544411 002223466889999999999998887666665543
No 163
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=22.32 E-value=91 Score=21.86 Aligned_cols=32 Identities=13% Similarity=-0.065 Sum_probs=24.4
Q ss_pred HHHHHHHHHhCCCCCccceechhhhhHHhhhh
Q psy5909 81 YSREELAMKVNLPEVRVQAVGMLYYSVELQDI 112 (130)
Q Consensus 81 ~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~ 112 (130)
..-.++|..+|++...|++.+..-|.+-++..
T Consensus 171 ~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 171 KSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35667899999999999988876666655543
No 164
>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=22.12 E-value=1.3e+02 Score=22.91 Aligned_cols=32 Identities=9% Similarity=-0.177 Sum_probs=24.5
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIE 113 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~ 113 (130)
.-.++|..+|++...|+.....-|.+-++...
T Consensus 160 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 160 RAAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 35678999999999999988766666555443
No 165
>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=21.96 E-value=81 Score=21.82 Aligned_cols=16 Identities=25% Similarity=0.385 Sum_probs=9.7
Q ss_pred CCCHHHHHHHHHHHHh
Q psy5909 59 TFTTYQLHELERAFEK 74 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~ 74 (130)
.++.+|+..|......
T Consensus 51 ~Lt~~qi~~l~~~i~~ 66 (144)
T TIGR03629 51 YLDDEEIEKLEEAVEN 66 (144)
T ss_pred cCCHHHHHHHHHHHHh
Confidence 4667777766655443
No 166
>PTZ00352 60S ribosomal protein L13; Provisional
Probab=21.80 E-value=33 Score=25.36 Aligned_cols=11 Identities=9% Similarity=-0.463 Sum_probs=7.6
Q ss_pred Cccceec-hhhh
Q psy5909 95 VRVQAVG-MLYY 105 (130)
Q Consensus 95 ~~VqvWF-qNrR 105 (130)
+.|++|| |.-|
T Consensus 18 ~~VktwFnQp~r 29 (212)
T PTZ00352 18 RFVKTWYNQPGR 29 (212)
T ss_pred hhcccccCchHH
Confidence 4689999 4444
No 167
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=21.80 E-value=78 Score=17.26 Aligned_cols=17 Identities=18% Similarity=0.364 Sum_probs=12.6
Q ss_pred HHHHHHHHhCCCCCccc
Q psy5909 82 SREELAMKVNLPEVRVQ 98 (130)
Q Consensus 82 ~r~~La~~l~l~~~~Vq 98 (130)
...+||..++++.+.|+
T Consensus 17 t~~eLa~~l~vS~rTi~ 33 (55)
T PF08279_consen 17 TAKELAEELGVSRRTIR 33 (55)
T ss_dssp EHHHHHHHCTS-HHHHH
T ss_pred CHHHHHHHhCCCHHHHH
Confidence 45689999999987765
No 168
>cd01763 Sumo Small ubiquitin-related modifier (SUMO). Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.
Probab=21.73 E-value=89 Score=19.20 Aligned_cols=25 Identities=12% Similarity=-0.164 Sum_probs=20.2
Q ss_pred HHHHHHHhCCCCCccceechhhhhH
Q psy5909 83 REELAMKVNLPEVRVQAVGMLYYSV 107 (130)
Q Consensus 83 r~~La~~l~l~~~~VqvWFqNrR~k 107 (130)
...++...|++..+++.+|..++..
T Consensus 38 ~~~y~~~~gi~~~~~rf~f~G~~L~ 62 (87)
T cd01763 38 MEAYCQRQGLSMNSVRFLFDGQRIR 62 (87)
T ss_pred HHHHHHHhCCCccceEEEECCeECC
Confidence 3455777899999999999988865
No 169
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.33 E-value=1.3e+02 Score=19.28 Aligned_cols=41 Identities=10% Similarity=0.088 Sum_probs=30.1
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCC-CCCccceec
Q psy5909 57 RTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNL-PEVRVQAVG 101 (130)
Q Consensus 57 Rt~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l-~~~~VqvWF 101 (130)
|..|+.+....+-..+....+ ....+|..+|+ ...++..|-
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~ 46 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWR 46 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHH
Confidence 677898887776666655544 46678999996 888777665
No 170
>PRK09480 slmA division inhibitor protein; Provisional
Probab=21.30 E-value=73 Score=21.86 Aligned_cols=34 Identities=15% Similarity=0.040 Sum_probs=28.4
Q ss_pred HHHhhCCCCHHHHHHHHHHhCCCCCccceechhhh
Q psy5909 71 AFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYY 105 (130)
Q Consensus 71 ~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR 105 (130)
.|..... .......||...|++...+-.+|.|+-
T Consensus 22 l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~ 55 (194)
T PRK09480 22 MLESPPG-ERITTAKLAARVGVSEAALYRHFPSKA 55 (194)
T ss_pred HHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHH
Confidence 3555556 777888999999999999999999876
No 171
>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=21.08 E-value=93 Score=23.45 Aligned_cols=46 Identities=13% Similarity=-0.044 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhh
Q psy5909 60 FTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQ 110 (130)
Q Consensus 60 ~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~ 110 (130)
+++.|...|.-.+... ..-.++|..+|++...|+..++.-|.+-+.
T Consensus 109 L~~~~R~v~~L~~~~g-----~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~ 154 (281)
T TIGR02957 109 LSPLERAVFVLREVFD-----YPYEEIASIVGKSEANCRQLVSRARRHLDA 154 (281)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4455555444433222 235678999999999999999777766544
No 172
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=20.91 E-value=1.4e+02 Score=20.78 Aligned_cols=35 Identities=20% Similarity=0.138 Sum_probs=26.2
Q ss_pred HHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccc
Q psy5909 64 QLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98 (130)
Q Consensus 64 q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~Vq 98 (130)
-+..|...=....|.+......+|..+|++...|.
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 34455544455679999999999999999887654
No 173
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=20.90 E-value=1.1e+02 Score=22.91 Aligned_cols=48 Identities=10% Similarity=0.050 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHhCCCCCccceechhhhhHHhhh
Q psy5909 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGMLYYSVELQD 111 (130)
Q Consensus 59 ~~t~~q~~~L~~~F~~~~~p~~~~r~~La~~l~l~~~~VqvWFqNrR~k~~~~ 111 (130)
.++..+...|...|... ..-.++|..+|++...|+.....-+.+-++.
T Consensus 212 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 212 TLPEREKKVLILYYYED-----LTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 35555555565555332 2467899999999999987776655554443
No 174
>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF. NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.
Probab=20.58 E-value=60 Score=19.64 Aligned_cols=27 Identities=11% Similarity=-0.109 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHH
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVE 108 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~ 108 (130)
.+..++...|++..+.++||..+..+.
T Consensus 28 lK~~i~~~~gi~~~~QrLi~~Gk~L~D 54 (78)
T cd01797 28 LREKIQELFNVEPECQRLFYRGKQMED 54 (78)
T ss_pred HHHHHHHHhCCCHHHeEEEeCCEECCC
Confidence 466778888999999999998877654
No 175
>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=20.49 E-value=34 Score=19.58 Aligned_cols=19 Identities=11% Similarity=-0.011 Sum_probs=16.1
Q ss_pred HHHHHHhCCCCCccceech
Q psy5909 84 EELAMKVNLPEVRVQAVGM 102 (130)
Q Consensus 84 ~~La~~l~l~~~~VqvWFq 102 (130)
.++|..+|++...++.|-+
T Consensus 4 ~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 4 GAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4689999999999998874
No 176
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=20.43 E-value=29 Score=19.55 Aligned_cols=23 Identities=13% Similarity=0.133 Sum_probs=17.8
Q ss_pred HHHHHHHHhCCCCCccceechhh
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLY 104 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNr 104 (130)
....||..+|++...|.-|+.++
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhcc
Confidence 46679999999999999999876
No 177
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=20.41 E-value=1.2e+02 Score=22.37 Aligned_cols=33 Identities=18% Similarity=-0.058 Sum_probs=26.2
Q ss_pred HHHHHHHHhCCCCCccceechhhhhHHhhhhhc
Q psy5909 82 SREELAMKVNLPEVRVQAVGMLYYSVELQDIEF 114 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFqNrR~k~~~~~~~ 114 (130)
.-.++|..+|++...|+.+...-|.+-++....
T Consensus 134 S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~ 166 (228)
T PRK06704 134 SIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE 166 (228)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 456899999999999999997777766665543
No 178
>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=20.40 E-value=94 Score=20.33 Aligned_cols=21 Identities=19% Similarity=-0.002 Sum_probs=18.3
Q ss_pred HHHHHHHHhCCCCCccceech
Q psy5909 82 SREELAMKVNLPEVRVQAVGM 102 (130)
Q Consensus 82 ~r~~La~~l~l~~~~VqvWFq 102 (130)
...++|..++++...|.-||+
T Consensus 20 s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 20 SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred hHHHHHHHhCcHHHHHHHHHH
Confidence 456689999999999999997
No 179
>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=20.15 E-value=34 Score=15.85 Aligned_cols=9 Identities=0% Similarity=-0.725 Sum_probs=6.5
Q ss_pred ceechhhhh
Q psy5909 98 QAVGMLYYS 106 (130)
Q Consensus 98 qvWFqNrR~ 106 (130)
-.||.||.-
T Consensus 6 iNWFE~~ge 14 (22)
T PF08452_consen 6 INWFESRGE 14 (22)
T ss_pred eehhhhCCc
Confidence 369988763
Done!