Query psy2123
Match_columns 143
No_of_seqs 161 out of 1457
Neff 8.2
Searched_HMMs 46136
Date Fri Aug 16 16:39:14 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2123.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2123hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0489|consensus 99.9 1.2E-21 2.6E-26 150.2 9.4 86 2-92 139-224 (261)
2 KOG0850|consensus 99.9 3.7E-21 7.9E-26 141.8 11.3 79 14-92 109-187 (245)
3 KOG0484|consensus 99.8 2.2E-20 4.8E-25 122.2 7.9 75 24-98 14-88 (125)
4 KOG0848|consensus 99.8 4.7E-20 1E-24 138.5 6.3 83 3-89 179-261 (317)
5 KOG0843|consensus 99.8 9.8E-20 2.1E-24 129.8 6.8 87 2-88 71-163 (197)
6 KOG0488|consensus 99.8 1.6E-19 3.4E-24 141.0 7.9 69 21-89 166-234 (309)
7 KOG2251|consensus 99.8 1.4E-18 3.1E-23 127.5 9.9 70 20-89 30-99 (228)
8 KOG0487|consensus 99.8 3.7E-19 8.1E-24 137.6 4.9 65 25-89 233-297 (308)
9 PF00046 Homeobox: Homeobox do 99.8 3.3E-18 7.1E-23 102.3 7.2 57 28-84 1-57 (57)
10 KOG0842|consensus 99.8 6.7E-19 1.5E-23 136.1 4.8 66 24-89 150-215 (307)
11 KOG0485|consensus 99.8 7.2E-18 1.6E-22 123.6 9.5 64 25-88 102-165 (268)
12 KOG3802|consensus 99.7 1.1E-18 2.3E-23 137.8 5.4 84 4-87 268-354 (398)
13 KOG0492|consensus 99.7 5E-18 1.1E-22 123.6 6.8 65 25-89 142-206 (246)
14 KOG0494|consensus 99.7 7.4E-18 1.6E-22 126.4 6.7 63 27-89 141-203 (332)
15 KOG0493|consensus 99.7 7E-17 1.5E-21 121.3 6.9 59 27-85 246-304 (342)
16 smart00389 HOX Homeodomain. DN 99.7 4.3E-16 9.4E-21 92.5 6.5 55 29-83 2-56 (56)
17 KOG0491|consensus 99.6 2.2E-16 4.7E-21 111.3 5.8 64 27-90 100-163 (194)
18 cd00086 homeodomain Homeodomai 99.6 8.3E-16 1.8E-20 92.1 7.4 57 29-85 2-58 (59)
19 TIGR01565 homeo_ZF_HD homeobox 99.6 2.2E-16 4.7E-21 94.4 4.1 52 28-79 2-57 (58)
20 KOG0486|consensus 99.6 3.5E-16 7.6E-21 120.1 4.4 65 26-90 111-175 (351)
21 COG5576 Homeodomain-containing 99.6 2.9E-15 6.2E-20 106.5 6.4 64 25-88 49-112 (156)
22 KOG4577|consensus 99.6 1.6E-15 3.5E-20 115.4 4.4 63 27-89 167-229 (383)
23 KOG0844|consensus 99.6 1.1E-15 2.5E-20 117.0 2.1 64 25-88 179-242 (408)
24 KOG0483|consensus 99.5 8.6E-15 1.9E-19 107.5 4.7 58 29-86 52-109 (198)
25 KOG0847|consensus 99.4 3.3E-13 7.2E-18 99.4 6.4 63 26-88 166-228 (288)
26 KOG0775|consensus 99.4 1.3E-12 2.9E-17 98.8 9.3 63 25-87 165-236 (304)
27 KOG1168|consensus 99.4 7.5E-14 1.6E-18 106.4 0.8 85 4-88 282-370 (385)
28 KOG0490|consensus 99.3 2.1E-12 4.6E-17 96.7 4.1 64 24-87 57-120 (235)
29 KOG0849|consensus 99.3 3E-11 6.5E-16 96.4 10.0 67 22-88 171-237 (354)
30 KOG0774|consensus 99.1 9.9E-11 2.2E-15 88.4 5.5 63 27-89 188-253 (334)
31 KOG2252|consensus 98.9 9.3E-09 2E-13 84.6 9.0 57 26-82 419-475 (558)
32 PF05920 Homeobox_KN: Homeobox 98.8 4.9E-09 1.1E-13 58.1 3.8 34 48-81 7-40 (40)
33 KOG0490|consensus 98.3 7.9E-07 1.7E-11 66.5 4.8 66 22-87 148-213 (235)
34 KOG1146|consensus 98.1 4.9E-06 1.1E-10 74.7 5.4 61 27-87 903-963 (1406)
35 PF11569 Homez: Homeodomain le 97.6 9.4E-05 2E-09 43.6 3.5 42 39-80 10-51 (56)
36 KOG3623|consensus 97.0 0.0017 3.8E-08 55.9 5.6 49 39-87 568-616 (1007)
37 KOG0773|consensus 96.9 0.00051 1.1E-08 54.7 2.3 61 27-87 239-302 (342)
38 PF04218 CENP-B_N: CENP-B N-te 95.6 0.052 1.1E-06 31.6 5.1 47 28-79 1-47 (53)
39 PF04545 Sigma70_r4: Sigma-70, 91.6 0.9 1.9E-05 25.5 5.2 46 33-83 4-49 (50)
40 PF08281 Sigma70_r4_2: Sigma-7 86.8 3.2 6.9E-05 23.5 5.2 43 34-81 11-53 (54)
41 PF04967 HTH_10: HTH DNA bindi 86.6 3.1 6.7E-05 24.2 5.0 42 34-75 1-44 (53)
42 cd06171 Sigma70_r4 Sigma70, re 85.7 3 6.6E-05 22.6 4.7 43 34-81 11-53 (55)
43 KOG1146|consensus 83.6 2.2 4.7E-05 39.8 4.9 63 24-86 702-764 (1406)
44 PF13565 HTH_32: Homeodomain-l 83.0 6.2 0.00013 23.9 5.6 39 35-73 32-75 (77)
45 PF01527 HTH_Tnp_1: Transposas 81.7 1.5 3.2E-05 26.7 2.4 47 29-79 2-48 (76)
46 PF10668 Phage_terminase: Phag 81.5 1.5 3.2E-05 26.3 2.2 21 56-76 24-44 (60)
47 PRK03975 tfx putative transcri 80.7 9.2 0.0002 26.8 6.3 51 32-88 5-55 (141)
48 KOG3755|consensus 80.4 2.3 5E-05 36.6 3.7 20 67-86 739-758 (769)
49 PRK04217 hypothetical protein; 77.9 11 0.00024 25.3 5.8 50 32-86 41-90 (110)
50 PRK09646 RNA polymerase sigma 77.8 8.8 0.00019 27.6 5.8 31 56-86 160-190 (194)
51 PF00196 GerE: Bacterial regul 77.5 10 0.00022 21.8 5.0 46 33-84 3-48 (58)
52 PF13551 HTH_29: Winged helix- 77.5 8 0.00017 24.9 5.1 48 29-76 53-109 (112)
53 PRK12526 RNA polymerase sigma 76.9 11 0.00023 27.6 6.1 32 56-87 171-202 (206)
54 PF09607 BrkDBD: Brinker DNA-b 76.7 10 0.00023 22.5 4.7 45 31-77 3-48 (58)
55 PRK00118 putative DNA-binding 76.6 15 0.00033 24.3 6.1 49 34-87 18-66 (104)
56 PRK06759 RNA polymerase factor 76.3 9.9 0.00021 26.0 5.5 46 34-84 107-152 (154)
57 cd00569 HTH_Hin_like Helix-tur 75.0 7.9 0.00017 18.6 4.7 37 34-75 6-42 (42)
58 PRK09642 RNA polymerase sigma 74.3 15 0.00032 25.3 6.0 31 56-86 124-154 (160)
59 PRK11924 RNA polymerase sigma 73.7 15 0.00032 25.5 6.0 32 56-87 143-174 (179)
60 PRK09652 RNA polymerase sigma 73.3 13 0.00029 25.8 5.7 48 34-86 129-176 (182)
61 PRK12512 RNA polymerase sigma 73.0 15 0.00032 26.0 5.9 32 56-87 149-180 (184)
62 PRK09413 IS2 repressor TnpA; R 72.5 18 0.00038 24.3 5.8 42 31-77 10-52 (121)
63 PRK09644 RNA polymerase sigma 72.2 18 0.00039 25.1 6.1 32 56-87 126-157 (165)
64 cd04761 HTH_MerR-SF Helix-Turn 71.7 5 0.00011 21.9 2.5 21 57-77 3-23 (49)
65 COG3413 Predicted DNA binding 71.5 11 0.00024 27.9 5.0 47 33-81 155-203 (215)
66 PF06056 Terminase_5: Putative 71.3 4.5 9.8E-05 23.8 2.3 20 57-76 16-35 (58)
67 PF13518 HTH_28: Helix-turn-he 71.1 5.6 0.00012 22.0 2.7 24 56-79 14-37 (52)
68 PRK05602 RNA polymerase sigma 70.7 19 0.00041 25.5 6.0 33 56-88 146-178 (186)
69 PF13384 HTH_23: Homeodomain-l 70.2 5.2 0.00011 22.2 2.4 23 55-77 18-40 (50)
70 PF13936 HTH_38: Helix-turn-he 69.9 10 0.00022 20.8 3.5 40 32-76 3-42 (44)
71 PRK09643 RNA polymerase sigma 68.8 29 0.00063 24.9 6.7 33 56-88 152-184 (192)
72 PRK12515 RNA polymerase sigma 68.4 26 0.00056 24.9 6.3 33 56-88 149-181 (189)
73 TIGR02999 Sig-70_X6 RNA polyme 68.0 22 0.00047 25.0 5.8 29 56-84 152-180 (183)
74 PRK12519 RNA polymerase sigma 67.9 17 0.00037 25.9 5.3 32 55-86 158-189 (194)
75 PRK06930 positive control sigm 67.8 28 0.00061 25.0 6.3 50 34-88 115-164 (170)
76 TIGR02939 RpoE_Sigma70 RNA pol 67.7 16 0.00035 25.8 5.1 32 55-86 155-186 (190)
77 TIGR02959 SigZ RNA polymerase 67.5 25 0.00054 24.7 6.0 32 56-87 118-149 (170)
78 TIGR02989 Sig-70_gvs1 RNA poly 67.5 21 0.00046 24.4 5.6 29 55-83 128-156 (159)
79 PRK09639 RNA polymerase sigma 67.5 27 0.00059 24.1 6.1 32 56-87 129-160 (166)
80 PRK10072 putative transcriptio 67.5 5 0.00011 26.2 2.1 41 33-80 32-72 (96)
81 COG4367 Uncharacterized protei 67.3 13 0.00027 24.1 3.8 40 34-73 3-42 (97)
82 PRK12530 RNA polymerase sigma 67.0 25 0.00053 25.2 6.0 31 56-86 152-182 (189)
83 PRK09047 RNA polymerase factor 66.9 28 0.00061 23.8 6.1 30 57-86 125-154 (161)
84 PRK09648 RNA polymerase sigma 66.7 23 0.0005 25.1 5.8 30 56-85 157-186 (189)
85 TIGR03879 near_KaiC_dom probab 66.7 3.6 7.9E-05 25.6 1.3 24 55-78 33-56 (73)
86 TIGR02937 sigma70-ECF RNA poly 66.7 22 0.00048 23.4 5.5 46 34-84 111-156 (158)
87 PRK12514 RNA polymerase sigma 66.7 24 0.00051 24.8 5.8 30 56-85 147-176 (179)
88 KOG0773|consensus 66.5 9.4 0.0002 30.3 4.0 43 46-88 116-158 (342)
89 TIGR02948 SigW_bacill RNA poly 66.2 21 0.00045 25.1 5.5 32 55-86 153-184 (187)
90 smart00421 HTH_LUXR helix_turn 65.9 20 0.00043 19.6 5.0 42 34-81 4-45 (58)
91 TIGR02985 Sig70_bacteroi1 RNA 65.6 26 0.00057 23.6 5.7 29 56-84 131-159 (161)
92 PRK12516 RNA polymerase sigma 65.0 24 0.00052 25.3 5.6 33 56-88 134-166 (187)
93 PRK09647 RNA polymerase sigma 64.2 33 0.00071 25.0 6.3 33 56-88 156-188 (203)
94 PRK12541 RNA polymerase sigma 64.1 23 0.0005 24.4 5.2 30 56-85 130-159 (161)
95 PRK09637 RNA polymerase sigma 64.0 30 0.00064 24.7 5.9 33 56-88 124-156 (181)
96 PRK12537 RNA polymerase sigma 63.8 28 0.00062 24.6 5.8 29 56-84 151-179 (182)
97 PF08280 HTH_Mga: M protein tr 63.6 22 0.00048 20.7 4.3 37 37-77 6-42 (59)
98 TIGR02943 Sig70_famx1 RNA poly 63.1 38 0.00082 24.2 6.4 33 56-88 149-181 (188)
99 PRK12520 RNA polymerase sigma 62.2 48 0.001 23.6 6.8 34 56-89 149-182 (191)
100 PRK12543 RNA polymerase sigma 62.1 36 0.00077 24.0 6.0 33 56-88 135-167 (179)
101 PRK12538 RNA polymerase sigma 61.8 26 0.00057 26.2 5.5 32 56-87 189-220 (233)
102 cd04762 HTH_MerR-trunc Helix-T 61.6 11 0.00023 20.1 2.6 23 57-79 3-25 (49)
103 PRK12532 RNA polymerase sigma 61.5 43 0.00094 23.9 6.4 33 56-88 154-186 (195)
104 PRK12524 RNA polymerase sigma 61.4 45 0.00098 23.9 6.5 32 56-87 154-185 (196)
105 PRK12547 RNA polymerase sigma 61.0 38 0.00082 23.5 5.9 30 56-85 130-159 (164)
106 TIGR02983 SigE-fam_strep RNA p 60.9 33 0.00072 23.5 5.6 30 56-85 128-157 (162)
107 PRK12546 RNA polymerase sigma 60.7 32 0.00069 24.8 5.6 32 56-87 131-162 (188)
108 PRK09645 RNA polymerase sigma 60.4 43 0.00093 23.3 6.2 31 56-86 136-166 (173)
109 PRK12536 RNA polymerase sigma 60.3 37 0.0008 24.0 5.8 30 56-85 147-176 (181)
110 PRK12545 RNA polymerase sigma 60.2 42 0.0009 24.3 6.2 32 56-87 157-188 (201)
111 TIGR02947 SigH_actino RNA poly 59.8 19 0.00042 25.7 4.3 34 55-88 148-181 (193)
112 PRK12518 RNA polymerase sigma 59.5 17 0.00036 25.4 3.9 33 55-87 137-169 (175)
113 PRK13919 putative RNA polymera 59.2 40 0.00087 23.8 5.9 30 56-85 153-182 (186)
114 PRK12535 RNA polymerase sigma 59.2 48 0.001 24.0 6.3 33 56-88 151-183 (196)
115 PF00376 MerR: MerR family reg 59.2 11 0.00025 20.0 2.3 19 58-76 3-21 (38)
116 PRK07037 extracytoplasmic-func 59.1 43 0.00092 23.0 5.9 30 56-85 127-156 (163)
117 PRK06986 fliA flagellar biosyn 58.6 35 0.00075 25.4 5.6 31 56-86 202-232 (236)
118 PRK06811 RNA polymerase factor 58.6 44 0.00095 23.8 6.0 31 56-86 149-179 (189)
119 TIGR02952 Sig70_famx2 RNA poly 58.5 41 0.00088 23.2 5.7 29 56-84 140-168 (170)
120 PRK12533 RNA polymerase sigma 58.0 40 0.00087 24.9 5.8 31 56-86 152-182 (216)
121 TIGR02954 Sig70_famx3 RNA poly 57.3 42 0.0009 23.3 5.6 30 56-85 137-166 (169)
122 PRK12539 RNA polymerase sigma 57.3 47 0.001 23.5 6.0 30 56-85 149-178 (184)
123 PF13443 HTH_26: Cro/C1-type H 57.2 11 0.00024 21.8 2.2 25 56-80 12-36 (63)
124 TIGR03001 Sig-70_gmx1 RNA poly 57.0 45 0.00097 25.2 6.1 34 56-89 179-212 (244)
125 PF13411 MerR_1: MerR HTH fami 56.9 13 0.00028 21.9 2.5 20 57-76 3-22 (69)
126 PRK12522 RNA polymerase sigma 56.8 49 0.0011 23.1 5.9 32 56-87 137-168 (173)
127 PRK12531 RNA polymerase sigma 56.0 50 0.0011 23.6 6.0 30 56-85 159-188 (194)
128 PRK11923 algU RNA polymerase s 56.0 47 0.001 23.6 5.8 33 56-88 156-188 (193)
129 PRK12523 RNA polymerase sigma 55.9 51 0.0011 23.0 5.9 30 56-85 137-166 (172)
130 PRK09649 RNA polymerase sigma 55.5 42 0.00091 23.9 5.5 29 56-84 148-176 (185)
131 PRK09641 RNA polymerase sigma 55.5 47 0.001 23.3 5.7 32 55-86 153-184 (187)
132 PRK12529 RNA polymerase sigma 55.3 51 0.0011 23.2 5.8 29 56-84 145-173 (178)
133 PRK09480 slmA division inhibit 55.1 17 0.00037 25.6 3.3 37 43-80 20-56 (194)
134 smart00027 EH Eps15 homology d 54.5 48 0.001 20.9 5.1 44 33-76 3-51 (96)
135 PRK08583 RNA polymerase sigma 54.1 48 0.001 25.0 5.8 47 34-85 206-252 (257)
136 PRK12544 RNA polymerase sigma 54.0 58 0.0013 23.8 6.1 31 57-87 167-197 (206)
137 cd04763 HTH_MlrA-like Helix-Tu 53.5 16 0.00035 21.6 2.6 21 57-77 3-23 (68)
138 PRK12511 RNA polymerase sigma 52.8 59 0.0013 23.2 5.9 32 56-87 129-160 (182)
139 TIGR00721 tfx DNA-binding prot 52.6 77 0.0017 22.1 6.2 48 31-84 4-51 (137)
140 TIGR02950 SigM_subfam RNA poly 52.6 23 0.0005 24.0 3.6 32 53-84 120-151 (154)
141 PF00424 REV: REV protein (ant 52.4 20 0.00044 23.2 3.0 36 39-88 14-49 (91)
142 PRK12542 RNA polymerase sigma 52.4 58 0.0012 23.0 5.8 31 56-86 140-170 (185)
143 cd04764 HTH_MlrA-like_sg1 Heli 51.9 19 0.0004 21.2 2.6 21 57-77 3-23 (67)
144 COG2944 Predicted transcriptio 51.7 33 0.00071 22.8 3.9 40 34-80 44-83 (104)
145 PRK10403 transcriptional regul 51.2 34 0.00073 23.8 4.4 46 33-84 153-198 (215)
146 cd01392 HTH_LacI Helix-turn-he 50.9 11 0.00024 20.8 1.5 21 59-79 2-22 (52)
147 TIGR02479 FliA_WhiG RNA polyme 50.9 57 0.0012 24.0 5.7 46 34-84 176-221 (224)
148 cd06170 LuxR_C_like C-terminal 50.5 41 0.00089 18.3 4.9 39 35-79 2-40 (57)
149 PRK06288 RNA polymerase sigma 50.1 69 0.0015 24.4 6.2 49 34-87 213-261 (268)
150 TIGR02980 SigBFG RNA polymeras 50.1 62 0.0013 23.8 5.8 46 34-84 179-224 (227)
151 PRK07670 RNA polymerase sigma 49.9 59 0.0013 24.4 5.7 30 56-85 219-248 (251)
152 PRK08301 sporulation sigma fac 49.9 53 0.0012 24.3 5.4 30 56-85 200-229 (234)
153 COG3415 Transposase and inacti 49.8 47 0.001 23.2 4.7 76 3-84 39-116 (138)
154 cd01104 HTH_MlrA-CarA Helix-Tu 49.3 21 0.00046 20.8 2.6 20 57-76 3-22 (68)
155 PRK12513 RNA polymerase sigma 49.1 31 0.00067 24.6 3.9 33 54-86 155-187 (194)
156 TIGR01764 excise DNA binding d 48.9 20 0.00042 19.1 2.3 23 57-79 4-26 (49)
157 PRK05657 RNA polymerase sigma 48.8 58 0.0013 25.8 5.7 53 34-87 263-315 (325)
158 PF01381 HTH_3: Helix-turn-hel 48.8 16 0.00035 20.3 1.9 23 57-79 12-34 (55)
159 TIGR02941 Sigma_B RNA polymera 48.7 58 0.0013 24.5 5.5 46 34-84 206-251 (255)
160 PRK12540 RNA polymerase sigma 48.7 75 0.0016 22.6 5.9 33 56-88 129-161 (182)
161 PRK12528 RNA polymerase sigma 48.3 72 0.0016 21.9 5.6 27 56-82 131-157 (161)
162 PF08279 HTH_11: HTH domain; 47.5 49 0.0011 18.4 4.0 36 38-76 2-37 (55)
163 TIGR02859 spore_sigH RNA polym 47.4 30 0.00065 24.6 3.6 30 55-84 166-195 (198)
164 PF09301 DUF1970: Domain of un 47.2 8.2 0.00018 24.8 0.5 13 69-81 17-29 (117)
165 PRK10360 DNA-binding transcrip 47.1 43 0.00093 23.2 4.4 45 33-83 137-181 (196)
166 PRK12527 RNA polymerase sigma 47.1 91 0.002 21.3 6.2 31 56-86 123-153 (159)
167 PRK09640 RNA polymerase sigma 46.6 39 0.00084 24.0 4.1 32 55-86 151-182 (188)
168 PRK09651 RNA polymerase sigma 46.4 59 0.0013 22.7 5.0 29 56-84 137-165 (172)
169 PRK07408 RNA polymerase sigma 46.3 76 0.0016 24.1 5.8 47 34-85 204-250 (256)
170 PRK15369 two component system 46.1 79 0.0017 21.6 5.6 45 33-83 149-193 (211)
171 TIGR03070 couple_hipB transcri 45.5 21 0.00045 19.8 2.1 23 57-79 18-40 (58)
172 KOG3623|consensus 45.2 6.8 0.00015 34.7 -0.1 62 27-88 626-687 (1007)
173 PRK08295 RNA polymerase factor 44.5 39 0.00084 24.3 3.9 32 55-86 171-202 (208)
174 PRK12525 RNA polymerase sigma 44.0 91 0.002 21.6 5.6 29 56-84 136-164 (168)
175 TIGR03541 reg_near_HchA LuxR f 43.8 44 0.00095 25.0 4.1 50 32-87 170-219 (232)
176 smart00595 MADF subfamily of S 43.8 52 0.0011 20.3 3.9 32 58-89 31-62 (89)
177 TIGR02957 SigX4 RNA polymerase 43.7 77 0.0017 24.3 5.6 29 57-85 127-155 (281)
178 PRK09636 RNA polymerase sigma 43.5 80 0.0017 24.3 5.7 30 56-85 133-162 (293)
179 PF12728 HTH_17: Helix-turn-he 43.3 28 0.00061 19.2 2.4 22 57-78 4-25 (51)
180 PRK12534 RNA polymerase sigma 43.2 96 0.0021 21.8 5.7 29 56-84 155-183 (187)
181 cd00093 HTH_XRE Helix-turn-hel 43.1 25 0.00053 18.5 2.1 22 57-78 15-36 (58)
182 PRK05988 formate dehydrogenase 43.0 67 0.0015 22.7 4.7 36 37-72 24-59 (156)
183 PRK12517 RNA polymerase sigma 42.9 1.1E+02 0.0024 21.8 6.1 33 56-88 146-178 (188)
184 PRK06704 RNA polymerase factor 42.8 88 0.0019 23.5 5.6 32 56-87 134-165 (228)
185 PF02796 HTH_7: Helix-turn-hel 42.7 57 0.0012 17.7 3.7 37 34-75 6-42 (45)
186 PF04936 DUF658: Protein of un 42.6 16 0.00035 26.4 1.4 33 55-87 15-47 (186)
187 PRK09638 RNA polymerase sigma 42.2 41 0.0009 23.4 3.6 32 54-85 142-173 (176)
188 TIGR02960 SigX5 RNA polymerase 42.2 75 0.0016 24.6 5.4 32 56-87 160-191 (324)
189 PRK09415 RNA polymerase factor 41.4 98 0.0021 21.7 5.5 30 56-85 145-174 (179)
190 PRK07122 RNA polymerase sigma 40.7 64 0.0014 24.7 4.7 46 34-84 216-261 (264)
191 COG1905 NuoE NADH:ubiquinone o 40.5 64 0.0014 23.2 4.3 37 36-72 25-61 (160)
192 TIGR02393 RpoD_Cterm RNA polym 40.4 95 0.0021 23.1 5.5 51 34-85 177-227 (238)
193 PF04297 UPF0122: Putative hel 40.3 1.1E+02 0.0023 20.2 5.2 44 33-81 17-60 (101)
194 PF13730 HTH_36: Helix-turn-he 40.3 46 0.001 18.5 3.0 43 34-77 3-48 (55)
195 PHA02955 hypothetical protein; 40.0 38 0.00083 25.4 3.2 46 36-81 60-106 (213)
196 PRK09935 transcriptional regul 39.9 63 0.0014 22.4 4.3 46 32-83 148-193 (210)
197 TIGR02392 rpoH_proteo alternat 39.8 81 0.0018 24.1 5.1 49 34-85 219-267 (270)
198 PHA01976 helix-turn-helix prot 39.8 29 0.00062 20.2 2.1 23 57-79 18-40 (67)
199 TIGR03020 EpsA transcriptional 39.4 89 0.0019 23.9 5.2 50 31-86 188-237 (247)
200 PRK10100 DNA-binding transcrip 39.4 99 0.0022 22.9 5.4 46 33-84 155-200 (216)
201 PRK10651 transcriptional regul 39.1 1E+02 0.0022 21.3 5.4 45 33-83 155-199 (216)
202 COG1595 RpoE DNA-directed RNA 38.7 55 0.0012 23.1 3.8 32 56-87 145-176 (182)
203 PF01710 HTH_Tnp_IS630: Transp 38.5 30 0.00065 23.1 2.3 21 56-76 20-40 (119)
204 PF07638 Sigma70_ECF: ECF sigm 38.3 52 0.0011 23.6 3.7 30 56-85 153-182 (185)
205 PRK05911 RNA polymerase sigma 38.1 1.3E+02 0.0028 22.8 6.0 48 34-86 206-253 (257)
206 TIGR02607 antidote_HigA addict 38.0 31 0.00067 20.7 2.1 23 57-79 21-43 (78)
207 TIGR02885 spore_sigF RNA polym 37.8 1.2E+02 0.0026 22.3 5.7 45 34-83 184-228 (231)
208 smart00422 HTH_MERR helix_turn 37.8 35 0.00076 19.9 2.3 20 57-76 3-22 (70)
209 PRK11552 putative DNA-binding 37.5 52 0.0011 24.3 3.7 42 39-82 19-60 (225)
210 PRK07539 NADH dehydrogenase su 37.3 90 0.0019 21.9 4.7 36 37-72 23-58 (154)
211 PRK07571 bidirectional hydroge 37.2 92 0.002 22.4 4.7 35 38-72 38-72 (169)
212 TIGR02835 spore_sigmaE RNA pol 37.0 56 0.0012 24.3 3.8 30 56-85 200-229 (234)
213 PF14549 P22_Cro: DNA-binding 36.7 38 0.00083 20.0 2.3 18 57-74 12-29 (60)
214 TIGR02984 Sig-70_plancto1 RNA 36.6 1.4E+02 0.0031 20.7 5.8 29 56-84 158-186 (189)
215 TIGR01958 nuoE_fam NADH-quinon 36.3 96 0.0021 21.6 4.7 36 37-72 17-52 (148)
216 PF01257 2Fe-2S_thioredx: Thio 36.1 74 0.0016 22.1 4.0 35 38-72 15-49 (145)
217 cd01106 HTH_TipAL-Mta Helix-Tu 35.9 41 0.00089 21.7 2.6 21 57-77 3-23 (103)
218 PF13309 HTH_22: HTH domain 35.8 96 0.0021 18.3 4.1 42 34-75 21-63 (64)
219 PRK07500 rpoH2 RNA polymerase 35.7 1.1E+02 0.0023 23.8 5.2 51 34-87 228-278 (289)
220 PRK08215 sporulation sigma fac 35.7 1.3E+02 0.0028 22.7 5.7 47 33-84 209-255 (258)
221 PRK05803 sporulation sigma fac 35.5 1.1E+02 0.0025 22.6 5.2 31 55-85 196-226 (233)
222 TIGR02846 spore_sigmaK RNA pol 35.5 1.7E+02 0.0036 21.6 6.1 29 56-84 196-224 (227)
223 TIGR02394 rpoS_proteo RNA poly 34.6 1.6E+02 0.0034 22.7 6.0 53 34-87 223-275 (285)
224 PRK11922 RNA polymerase sigma 34.6 67 0.0015 23.8 3.9 37 52-88 163-199 (231)
225 PRK05572 sporulation sigma fac 34.0 1.4E+02 0.0031 22.4 5.6 47 33-84 202-248 (252)
226 smart00530 HTH_XRE Helix-turn- 33.2 42 0.00092 17.3 2.0 23 57-79 13-35 (56)
227 PRK11511 DNA-binding transcrip 31.7 1.4E+02 0.003 20.0 4.7 24 55-78 26-49 (127)
228 PRK14996 TetR family transcrip 31.7 85 0.0019 22.1 3.9 41 39-80 14-54 (192)
229 PRK06596 RNA polymerase factor 31.6 1.4E+02 0.003 23.1 5.3 49 34-85 231-279 (284)
230 PRK08241 RNA polymerase factor 31.2 1.2E+02 0.0026 23.8 5.0 29 56-84 171-199 (339)
231 PF00440 TetR_N: Bacterial reg 31.1 49 0.0011 18.0 2.0 25 56-80 18-42 (47)
232 PRK09706 transcriptional repre 30.8 43 0.00092 22.7 2.1 24 57-80 21-44 (135)
233 cd01105 HTH_GlnR-like Helix-Tu 30.7 51 0.0011 20.7 2.3 19 57-75 4-22 (88)
234 PRK09958 DNA-binding transcrip 30.3 1.4E+02 0.0031 20.6 4.9 44 33-82 143-186 (204)
235 cd04774 HTH_YfmP Helix-Turn-He 30.2 59 0.0013 20.9 2.6 20 57-76 3-22 (96)
236 PF13542 HTH_Tnp_ISL3: Helix-t 29.9 71 0.0015 17.5 2.6 21 56-76 29-49 (52)
237 cd04766 HTH_HspR Helix-Turn-He 29.7 54 0.0012 20.6 2.3 20 57-76 4-23 (91)
238 PRK09726 antitoxin HipB; Provi 28.7 1.5E+02 0.0033 18.4 4.6 43 34-79 8-50 (88)
239 PRK15008 HTH-type transcriptio 28.6 1.2E+02 0.0026 21.9 4.3 41 41-82 26-66 (212)
240 PRK15411 rcsA colanic acid cap 28.6 1.9E+02 0.0041 21.0 5.4 45 33-83 137-181 (207)
241 cd04779 HTH_MerR-like_sg4 Heli 28.2 62 0.0013 22.3 2.5 21 57-77 3-23 (134)
242 PF13560 HTH_31: Helix-turn-he 28.1 53 0.0012 19.0 1.9 25 56-80 16-40 (64)
243 PRK10188 DNA-binding transcrip 27.8 2.4E+02 0.0052 21.2 5.9 29 57-85 197-225 (240)
244 PF13022 HTH_Tnp_1_2: Helix-tu 27.8 94 0.002 21.9 3.3 23 54-76 34-56 (142)
245 cd00131 PAX Paired Box domain 27.5 2E+02 0.0043 19.5 7.1 45 33-77 75-126 (128)
246 PF10078 DUF2316: Uncharacteri 27.4 57 0.0012 21.1 2.0 31 39-73 12-42 (89)
247 PF06971 Put_DNA-bind_N: Putat 27.2 56 0.0012 18.6 1.8 18 56-73 30-47 (50)
248 PRK09390 fixJ response regulat 27.2 1.7E+02 0.0037 19.7 4.8 30 57-86 159-188 (202)
249 PF12200 DUF3597: Domain of un 26.7 1.3E+02 0.0029 20.7 3.8 30 52-81 83-117 (127)
250 PRK13890 conjugal transfer pro 26.7 54 0.0012 22.1 2.0 23 57-79 21-43 (120)
251 cd04780 HTH_MerR-like_sg5 Heli 26.4 67 0.0014 20.6 2.3 20 57-76 3-22 (95)
252 PF13404 HTH_AsnC-type: AsnC-t 26.3 61 0.0013 17.5 1.8 18 56-73 19-36 (42)
253 PF07022 Phage_CI_repr: Bacter 26.3 38 0.00083 20.1 1.1 22 57-78 15-37 (66)
254 cd04768 HTH_BmrR-like Helix-Tu 26.3 76 0.0017 20.2 2.6 21 57-77 3-23 (96)
255 PRK09635 sigI RNA polymerase s 25.9 2E+02 0.0044 22.3 5.3 28 57-84 137-164 (290)
256 COG2963 Transposase and inacti 25.8 1.9E+02 0.0042 18.7 5.7 43 31-77 5-48 (116)
257 PF13613 HTH_Tnp_4: Helix-turn 25.8 62 0.0013 18.2 1.9 21 57-77 22-42 (53)
258 PF12844 HTH_19: Helix-turn-he 25.8 62 0.0013 18.5 1.9 24 56-79 14-37 (64)
259 PRK10840 transcriptional regul 25.7 2.2E+02 0.0048 20.3 5.3 43 33-81 150-192 (216)
260 PRK10430 DNA-binding transcrip 25.6 1.5E+02 0.0032 21.8 4.4 45 33-78 158-202 (239)
261 PF14229 DUF4332: Domain of un 25.3 97 0.0021 20.9 3.0 26 51-76 26-51 (122)
262 cd04773 HTH_TioE_rpt2 Second H 25.2 79 0.0017 20.7 2.5 21 57-77 3-23 (108)
263 PF05263 DUF722: Protein of un 24.9 1.9E+02 0.0042 19.9 4.5 20 58-77 103-122 (130)
264 PF12802 MarR_2: MarR family; 24.9 98 0.0021 17.4 2.7 38 34-73 3-40 (62)
265 TIGR00993 3a0901s04IAP86 chlor 24.9 5.2E+02 0.011 23.4 8.6 13 33-45 415-427 (763)
266 PF03444 HrcA_DNA-bdg: Winged 24.7 1.9E+02 0.0041 18.2 4.6 38 34-73 2-42 (78)
267 PF08671 SinI: Anti-repressor 24.7 1.1E+02 0.0024 15.5 2.7 19 58-76 9-27 (30)
268 PRK09483 response regulator; P 24.5 1.5E+02 0.0033 20.7 4.2 45 32-82 147-191 (217)
269 PF07471 Phage_Nu1: Phage DNA 24.5 69 0.0015 23.0 2.3 21 57-77 5-25 (164)
270 TIGR03830 CxxCG_CxxCG_HTH puta 24.3 1.5E+02 0.0032 19.4 3.9 23 57-79 81-103 (127)
271 PRK13870 transcriptional regul 24.2 94 0.002 23.3 3.1 28 58-85 192-219 (234)
272 cd00592 HTH_MerR-like Helix-Tu 23.7 90 0.002 19.7 2.6 21 57-77 3-23 (100)
273 cd04782 HTH_BltR Helix-Turn-He 23.5 92 0.002 19.9 2.6 21 57-77 3-23 (97)
274 cd04775 HTH_Cfa-like Helix-Tur 23.3 82 0.0018 20.3 2.3 20 57-76 4-23 (102)
275 TIGR01557 myb_SHAQKYF myb-like 23.1 1.7E+02 0.0036 17.0 5.2 50 29-78 1-53 (57)
276 cd04767 HTH_HspR-like_MBC Heli 23.0 91 0.002 21.2 2.5 21 57-77 4-24 (120)
277 PF07037 DUF1323: Putative tra 23.0 85 0.0018 21.5 2.3 20 57-76 3-22 (122)
278 PF04703 FaeA: FaeA-like prote 22.9 97 0.0021 18.4 2.4 21 57-77 18-38 (62)
279 cd04765 HTH_MlrA-like_sg2 Heli 22.8 98 0.0021 20.0 2.6 21 57-77 3-23 (99)
280 TIGR03826 YvyF flagellar opero 22.8 82 0.0018 22.0 2.3 27 55-81 47-73 (137)
281 PRK00215 LexA repressor; Valid 22.7 1.4E+02 0.003 21.6 3.7 44 34-79 2-49 (205)
282 PRK11475 DNA-binding transcrip 22.6 2.9E+02 0.0062 20.2 5.4 43 33-81 134-176 (207)
283 cd04788 HTH_NolA-AlbR Helix-Tu 22.4 1E+02 0.0022 19.7 2.6 21 57-77 3-23 (96)
284 cd04789 HTH_Cfa Helix-Turn-Hel 22.1 91 0.002 20.2 2.3 21 57-77 4-24 (102)
285 cd01279 HTH_HspR-like Helix-Tu 22.0 1E+02 0.0022 19.8 2.5 21 57-77 4-24 (98)
286 TIGR02054 MerD mercuric resist 21.6 93 0.002 21.0 2.4 20 57-76 6-25 (120)
287 PF05269 Phage_CII: Bacterioph 21.4 1.4E+02 0.003 19.4 3.0 27 57-83 26-52 (91)
288 cd01109 HTH_YyaN Helix-Turn-He 21.4 93 0.002 20.4 2.3 20 57-76 3-22 (113)
289 KOG0044|consensus 21.3 1.4E+02 0.003 22.0 3.4 30 51-80 8-37 (193)
290 PRK09975 DNA-binding transcrip 21.2 1.4E+02 0.0031 21.2 3.5 41 39-80 17-57 (213)
291 PF04539 Sigma70_r3: Sigma-70 21.2 1E+02 0.0022 18.4 2.4 21 56-76 22-42 (78)
292 PF01047 MarR: MarR family; I 21.1 1.7E+02 0.0036 16.3 3.7 39 34-76 1-39 (59)
293 PF13412 HTH_24: Winged helix- 21.1 1.5E+02 0.0033 15.8 4.2 38 35-76 2-39 (48)
294 PF08452 DNAP_B_exo_N: DNA pol 21.0 29 0.00064 16.2 -0.1 8 72-79 6-13 (22)
295 PF09862 DUF2089: Protein of u 20.6 2.6E+02 0.0057 18.8 4.3 39 33-76 33-71 (113)
296 PRK07405 RNA polymerase sigma 20.5 2.8E+02 0.0061 21.8 5.2 51 34-85 257-307 (317)
297 COG0789 SoxR Predicted transcr 20.3 1E+02 0.0022 20.1 2.4 19 57-75 3-21 (124)
298 PF12244 DUF3606: Protein of u 20.2 1.4E+02 0.003 17.3 2.6 18 55-72 21-38 (57)
299 PRK13558 bacterio-opsin activa 20.0 2.3E+02 0.005 24.3 5.0 42 32-73 606-649 (665)
No 1
>KOG0489|consensus
Probab=99.86 E-value=1.2e-21 Score=150.19 Aligned_cols=86 Identities=33% Similarity=0.504 Sum_probs=71.6
Q ss_pred CcccccccccCCCCCCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123 2 EYDWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81 (143)
Q Consensus 2 ~~~w~~~~~~~~~~~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k 81 (143)
.|+||....... .......+.||.||.||..|+..||+.|..|+|.+...|.+||..|.|+++||+|||||||+|
T Consensus 139 ~~p~~~~~~~~~-----~~~~~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK 213 (261)
T KOG0489|consen 139 IYPWMKSTANYL-----SSSETGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMK 213 (261)
T ss_pred cccchhhhhccc-----ccccccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHH
Confidence 588888766431 111222346788999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhhhccc
Q psy2123 82 FRRNERNFISH 92 (143)
Q Consensus 82 ~rk~~~~~~~~ 92 (143)
|||.++.....
T Consensus 214 ~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 214 WKKENKAKSSQ 224 (261)
T ss_pred HHHhhcccccc
Confidence 99988765444
No 2
>KOG0850|consensus
Probab=99.86 E-value=3.7e-21 Score=141.80 Aligned_cols=79 Identities=34% Similarity=0.547 Sum_probs=71.4
Q ss_pred CCCCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhhccc
Q psy2123 14 EDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISH 92 (143)
Q Consensus 14 ~~~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~~~~ 92 (143)
|.++....++++|.||.||.++.-||..|+..|++++|+...||.+||..|||+.+||+|||||||.|.||..+.....
T Consensus 109 E~~e~~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~ 187 (245)
T KOG0850|consen 109 EPSERRPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSGP 187 (245)
T ss_pred CcceeccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCCc
Confidence 4455566778899999999999999999999999999999999999999999999999999999999999998854433
No 3
>KOG0484|consensus
Probab=99.83 E-value=2.2e-20 Score=122.15 Aligned_cols=75 Identities=60% Similarity=0.905 Sum_probs=67.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhhcccCCCCCC
Q psy2123 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHRNLDAP 98 (143)
Q Consensus 24 ~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~~~~~~~~~~ 98 (143)
++|.||-||.|+..||..||..|-...||++-.+++||..+.|++..|||||||||+|.||+++..........+
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~~~~~~~ 88 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAKMAAKSS 88 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHHhhhhcc
Confidence 456788999999999999999999999999999999999999999999999999999999999876655444433
No 4
>KOG0848|consensus
Probab=99.81 E-value=4.7e-20 Score=138.54 Aligned_cols=83 Identities=35% Similarity=0.568 Sum_probs=68.8
Q ss_pred cccccccccCCCCCCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHH
Q psy2123 3 YDWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKF 82 (143)
Q Consensus 3 ~~w~~~~~~~~~~~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~ 82 (143)
||||..---.+.+ ...+.+.+-|-|.++++.|..+||+.|.-++|++++.+.+||.-|||+++||+|||||||+|+
T Consensus 179 ~dwmrkpa~~~~g----~~~KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKE 254 (317)
T KOG0848|consen 179 YDWMRKPAQPGTG----QNVKTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKE 254 (317)
T ss_pred hhhhhcccccCCC----CCceeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHH
Confidence 7898753221111 223334455779999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhhh
Q psy2123 83 RRNERNF 89 (143)
Q Consensus 83 rk~~~~~ 89 (143)
||..++.
T Consensus 255 RK~nKKk 261 (317)
T KOG0848|consen 255 RKDNKKK 261 (317)
T ss_pred HHHHHHH
Confidence 9988876
No 5
>KOG0843|consensus
Probab=99.80 E-value=9.8e-20 Score=129.83 Aligned_cols=87 Identities=38% Similarity=0.698 Sum_probs=71.2
Q ss_pred CcccccccccC--CCCCCcc----cccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHH
Q psy2123 2 EYDWMLTLRCD--GEDDDYD----YERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWF 75 (143)
Q Consensus 2 ~~~w~~~~~~~--~~~~~~~----~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WF 75 (143)
+|+|+...... +.++... ..-...+.+|.||.|+.+|+..||..|+.++|....+|++||..|+|++.||+|||
T Consensus 71 ~~p~~~~~~~~~~~~~~~~~~~l~~~~~~~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWF 150 (197)
T KOG0843|consen 71 QYPWLIRIYSRHGGKDTMLEGFLLLPLRSMRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWF 150 (197)
T ss_pred cCCcceeeeecccccchhhhhhccccccccCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhh
Confidence 68898876532 3222211 12223367899999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHhhhh
Q psy2123 76 QNRRAKFRRNERN 88 (143)
Q Consensus 76 qNrR~k~rk~~~~ 88 (143)
||||.|.||....
T Consensus 151 QNRRtk~kr~~~e 163 (197)
T KOG0843|consen 151 QNRRTKHKRMQQE 163 (197)
T ss_pred hhhhHHHHHHHHH
Confidence 9999999987654
No 6
>KOG0488|consensus
Probab=99.80 E-value=1.6e-19 Score=141.03 Aligned_cols=69 Identities=42% Similarity=0.652 Sum_probs=63.9
Q ss_pred ccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123 21 ERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF 89 (143)
Q Consensus 21 ~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~ 89 (143)
...++|.|+.||+|+..|+..||..|++.+|.+..+|.+||..|||+..||++||||||+||||.....
T Consensus 166 ~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g 234 (309)
T KOG0488|consen 166 RSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEG 234 (309)
T ss_pred cCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhh
Confidence 344577888999999999999999999999999999999999999999999999999999999977663
No 7
>KOG2251|consensus
Probab=99.78 E-value=1.4e-18 Score=127.53 Aligned_cols=70 Identities=56% Similarity=0.904 Sum_probs=65.4
Q ss_pred cccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123 20 YERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF 89 (143)
Q Consensus 20 ~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~ 89 (143)
+....+|.||+||.|+-.|+++||..|.+.+||+...+++||.+|+|.+.+|+|||+|||+|+|+.++..
T Consensus 30 ~~~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 30 YSSGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred cCccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 4466788999999999999999999999999999999999999999999999999999999999987754
No 8
>KOG0487|consensus
Probab=99.76 E-value=3.7e-19 Score=137.56 Aligned_cols=65 Identities=35% Similarity=0.538 Sum_probs=61.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123 25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF 89 (143)
Q Consensus 25 ~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~ 89 (143)
++.||+|-.+|+.|+..||+.|..|.|++++.|.+|+..|+|+++||+|||||||+|+||..+..
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 56788899999999999999999999999999999999999999999999999999999988643
No 9
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.76 E-value=3.3e-18 Score=102.33 Aligned_cols=57 Identities=47% Similarity=0.778 Sum_probs=54.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 28 rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
|+.|+.|+.+|+.+|+..|..++||+..+++.||..+||+..+|++||+|+|+++||
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 467899999999999999999999999999999999999999999999999999886
No 10
>KOG0842|consensus
Probab=99.75 E-value=6.7e-19 Score=136.09 Aligned_cols=66 Identities=38% Similarity=0.628 Sum_probs=61.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF 89 (143)
Q Consensus 24 ~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~ 89 (143)
..++||.|..|+..|+.+||..|.+.+|++..||++||..|.|+.+||+|||||||-|.||.++..
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk 215 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDK 215 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhh
Confidence 456778899999999999999999999999999999999999999999999999999999987764
No 11
>KOG0485|consensus
Probab=99.75 E-value=7.2e-18 Score=123.56 Aligned_cols=64 Identities=36% Similarity=0.620 Sum_probs=60.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 25 ~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
.++||.||+|+..|+-.||..|+..+|.+..+|.-||.+|.|++.||+|||||||.||||+...
T Consensus 102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa 165 (268)
T KOG0485|consen 102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA 165 (268)
T ss_pred cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence 3577899999999999999999999999999999999999999999999999999999997654
No 12
>KOG3802|consensus
Probab=99.75 E-value=1.1e-18 Score=137.79 Aligned_cols=84 Identities=26% Similarity=0.428 Sum_probs=73.8
Q ss_pred ccccccccC---CCCCCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHH
Q psy2123 4 DWMLTLRCD---GEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRA 80 (143)
Q Consensus 4 ~w~~~~~~~---~~~~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~ 80 (143)
-|+++++.. ++-...+......|+||+||.|....+..||.+|.+|++|+..|+..||.+|+|.+.+|+|||||||+
T Consensus 268 KWLeEAes~~~~~~~~~~e~i~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQ 347 (398)
T KOG3802|consen 268 KWLEEAESRESTGSPNSIEKIGAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQ 347 (398)
T ss_pred HHHHHHhcccccCCCCCHHHhhccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeecccc
Confidence 499999852 34444555566668899999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhh
Q psy2123 81 KFRRNER 87 (143)
Q Consensus 81 k~rk~~~ 87 (143)
|+||...
T Consensus 348 keKR~~~ 354 (398)
T KOG3802|consen 348 KEKRITP 354 (398)
T ss_pred ccccCCC
Confidence 9999765
No 13
>KOG0492|consensus
Probab=99.74 E-value=5e-18 Score=123.57 Aligned_cols=65 Identities=38% Similarity=0.611 Sum_probs=60.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123 25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF 89 (143)
Q Consensus 25 ~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~ 89 (143)
+-.|+.||.|+..||..||..|...+|.++.++.+++..|.|+++||+|||||||+|.||.+...
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae 206 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAE 206 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHH
Confidence 33577899999999999999999999999999999999999999999999999999999977654
No 14
>KOG0494|consensus
Probab=99.73 E-value=7.4e-18 Score=126.36 Aligned_cols=63 Identities=56% Similarity=0.920 Sum_probs=58.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123 27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF 89 (143)
Q Consensus 27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~ 89 (143)
+|+.||.||..|+..||+.|+...||+...|+.||..++|.+.+|+|||||||+||||.++.-
T Consensus 141 RRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 141 RRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred cccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence 344599999999999999999999999999999999999999999999999999999988753
No 15
>KOG0493|consensus
Probab=99.68 E-value=7e-17 Score=121.29 Aligned_cols=59 Identities=37% Similarity=0.731 Sum_probs=56.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
-+|.||.|+.+||+.|...|+.|+|.+...|.+||.+|||.+.||+|||||+|+|.||.
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 36789999999999999999999999999999999999999999999999999999984
No 16
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.65 E-value=4.3e-16 Score=92.54 Aligned_cols=55 Identities=56% Similarity=0.898 Sum_probs=51.9
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123 29 RNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83 (143)
Q Consensus 29 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~r 83 (143)
+.|+.|+..++.+|+..|..++||+..++..||..+||+..+|++||+|+|.+.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 5678899999999999999999999999999999999999999999999998753
No 17
>KOG0491|consensus
Probab=99.65 E-value=2.2e-16 Score=111.31 Aligned_cols=64 Identities=47% Similarity=0.733 Sum_probs=60.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhhc
Q psy2123 27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFI 90 (143)
Q Consensus 27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~~ 90 (143)
++|-|++|+..|+..|++.|+..+|.+..++.+||..|+|++.||+.||||||+|.||..++..
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 5678999999999999999999999999999999999999999999999999999999887654
No 18
>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=99.65 E-value=8.3e-16 Score=92.07 Aligned_cols=57 Identities=54% Similarity=0.894 Sum_probs=53.8
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 29 RNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 29 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
+.|..++..++.+|+.+|..++||+..++..||.++||+..+|++||+|+|.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 467889999999999999999999999999999999999999999999999998763
No 19
>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=99.64 E-value=2.2e-16 Score=94.38 Aligned_cols=52 Identities=19% Similarity=0.418 Sum_probs=50.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCC----CCHHHHHHHHHHcCCChhHHHHHHhhHH
Q psy2123 28 RRNRTTFNSHQLNALEKVFERTHY----PDAFVREELAKKVCLSEARVQVWFQNRR 79 (143)
Q Consensus 28 rr~R~~~~~~q~~~L~~~f~~~~~----p~~~~~~~La~~lgl~~~~V~~WFqNrR 79 (143)
+|.||.|+.+|+..|+..|..++| |+..++++||..+||++.+|+|||||.+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 688999999999999999999999 9999999999999999999999999964
No 20
>KOG0486|consensus
Probab=99.62 E-value=3.5e-16 Score=120.07 Aligned_cols=65 Identities=57% Similarity=0.880 Sum_probs=62.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhhc
Q psy2123 26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFI 90 (143)
Q Consensus 26 ~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~~ 90 (143)
|+||.|+.|+..|+..||..|+++.||+...+++||..++|++..|+|||.|||+||||+++...
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 67899999999999999999999999999999999999999999999999999999999998765
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.59 E-value=2.9e-15 Score=106.53 Aligned_cols=64 Identities=33% Similarity=0.583 Sum_probs=58.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 25 ~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
...+++|++.+..|+.+|+..|..++||+...+..|+..|+|+++.|+|||||+|++.|+....
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 3456778889999999999999999999999999999999999999999999999999986654
No 22
>KOG4577|consensus
Probab=99.57 E-value=1.6e-15 Score=115.38 Aligned_cols=63 Identities=40% Similarity=0.627 Sum_probs=59.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123 27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF 89 (143)
Q Consensus 27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~ 89 (143)
.+|+||.|++.||+.|..+|+..+.|....|++|+.++||.-++|||||||||+|+||.++..
T Consensus 167 nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T KOG4577|consen 167 NKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T ss_pred cCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence 578999999999999999999999999999999999999999999999999999999877654
No 23
>KOG0844|consensus
Probab=99.56 E-value=1.1e-15 Score=117.02 Aligned_cols=64 Identities=42% Similarity=0.594 Sum_probs=59.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 25 ~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
...||-||.|+.+|+..||+.|-+..|.+...|.+||..|+|.+..|+|||||||+|+||+...
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 4568899999999999999999999999999999999999999999999999999999987643
No 24
>KOG0483|consensus
Probab=99.53 E-value=8.6e-15 Score=107.52 Aligned_cols=58 Identities=34% Similarity=0.583 Sum_probs=53.5
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 29 RNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 29 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
+++.+|+.+|+..||..|+.+.+.....+..||..|||..+||.||||||||+||.++
T Consensus 52 ~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq 109 (198)
T KOG0483|consen 52 GKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ 109 (198)
T ss_pred cccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence 3345699999999999999999999999999999999999999999999999999644
No 25
>KOG0847|consensus
Probab=99.42 E-value=3.3e-13 Score=99.38 Aligned_cols=63 Identities=40% Similarity=0.749 Sum_probs=58.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 26 ~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
+++..|..|+..|+..|+..|+..+|+-..++.+||..+|+++.+|+|||||||.||||+...
T Consensus 166 ~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa 228 (288)
T KOG0847|consen 166 QRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA 228 (288)
T ss_pred cccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence 345678889999999999999999999999999999999999999999999999999997654
No 26
>KOG0775|consensus
Probab=99.42 E-value=1.3e-12 Score=98.85 Aligned_cols=63 Identities=27% Similarity=0.415 Sum_probs=52.9
Q ss_pred CCCCCCCCCCCH---------HHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 25 PKPRRNRTTFNS---------HQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 25 ~~~rr~R~~~~~---------~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
+|-.-+||.+.. .-..+|.++|..++||+..++.+||+++||+..||-+||+|||+++|-...
T Consensus 165 rKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~a 236 (304)
T KOG0775|consen 165 RKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAA 236 (304)
T ss_pred ccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhccc
Confidence 344445776444 456799999999999999999999999999999999999999999995443
No 27
>KOG1168|consensus
Probab=99.38 E-value=7.5e-14 Score=106.44 Aligned_cols=85 Identities=25% Similarity=0.366 Sum_probs=68.6
Q ss_pred ccccccccCC----CCCCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHH
Q psy2123 4 DWMLTLRCDG----EDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRR 79 (143)
Q Consensus 4 ~w~~~~~~~~----~~~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR 79 (143)
-|+++++..- ...+...---...++|+||.+...+...||++|...+.|+.+.+..||++|+|.+.+|+|||||.|
T Consensus 282 aWLEeAE~a~keK~~~pd~~~l~~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQR 361 (385)
T KOG1168|consen 282 AWLEEAEAAMKEKDTKPDINELLPGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQR 361 (385)
T ss_pred HHHHHHHHHHHhhccCCchhhccCccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccH
Confidence 3888887321 222222222234467889999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhh
Q psy2123 80 AKFRRNERN 88 (143)
Q Consensus 80 ~k~rk~~~~ 88 (143)
+|.||....
T Consensus 362 QKQKRm~~S 370 (385)
T KOG1168|consen 362 QKQKRMKRS 370 (385)
T ss_pred HHHHHhhhh
Confidence 999997654
No 28
>KOG0490|consensus
Probab=99.29 E-value=2.1e-12 Score=96.73 Aligned_cols=64 Identities=50% Similarity=0.649 Sum_probs=60.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 24 ~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
..++++.|+.|+..|+++|+..|+...||+...++.||..+++++..|++||||||+|+++.++
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 4567889999999999999999999999999999999999999999999999999999998775
No 29
>KOG0849|consensus
Probab=99.28 E-value=3e-11 Score=96.38 Aligned_cols=67 Identities=58% Similarity=0.885 Sum_probs=61.6
Q ss_pred cCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 22 RRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 22 ~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
...++.+|.|+.|+..|+..|++.|+.++||+...+++||.++++++..|++||+|||++++|....
T Consensus 171 ~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 171 ALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred cccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 3455677889999999999999999999999999999999999999999999999999999998743
No 30
>KOG0774|consensus
Probab=99.12 E-value=9.9e-11 Score=88.35 Aligned_cols=63 Identities=30% Similarity=0.592 Sum_probs=56.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123 27 PRRNRTTFNSHQLNALEKVFE---RTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNF 89 (143)
Q Consensus 27 ~rr~R~~~~~~q~~~L~~~f~---~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~ 89 (143)
.+|+|..|+....++|+.+|. .++||+.+++++||.++|++..||.+||.|.|-+.+|.....
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~ 253 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKN 253 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhh
Confidence 356788899999999999994 788999999999999999999999999999999998865443
No 31
>KOG2252|consensus
Probab=98.89 E-value=9.3e-09 Score=84.64 Aligned_cols=57 Identities=21% Similarity=0.402 Sum_probs=53.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHH
Q psy2123 26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKF 82 (143)
Q Consensus 26 ~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~ 82 (143)
+.+|.|.+|++.|...|...|+.+++|+.++.+.|+.+|+|....|.+||.|-|.+.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 456779999999999999999999999999999999999999999999999998874
No 32
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.83 E-value=4.9e-09 Score=58.14 Aligned_cols=34 Identities=38% Similarity=0.655 Sum_probs=29.1
Q ss_pred hcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123 48 RTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81 (143)
Q Consensus 48 ~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k 81 (143)
.++||+.++++.||.++||+..||..||-|.|.+
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 5789999999999999999999999999999875
No 33
>KOG0490|consensus
Probab=98.33 E-value=7.9e-07 Score=66.51 Aligned_cols=66 Identities=56% Similarity=0.816 Sum_probs=60.2
Q ss_pred cCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 22 RRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 22 ~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
....+.++.|+.+...|+..|...|....+|+...++.|+..+|+....|++||+|+|++.++...
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 148 PSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 334567788999999999999999999999999999999999999999999999999999998654
No 34
>KOG1146|consensus
Probab=98.09 E-value=4.9e-06 Score=74.66 Aligned_cols=61 Identities=31% Similarity=0.439 Sum_probs=57.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
.++.|+.++..||.+|...|....+|..++.+.|...+++..++|++||||.|+|.++...
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 4678999999999999999999999999999999999999999999999999999998765
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.60 E-value=9.4e-05 Score=43.63 Aligned_cols=42 Identities=24% Similarity=0.363 Sum_probs=31.5
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHH
Q psy2123 39 LNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRA 80 (143)
Q Consensus 39 ~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~ 80 (143)
+..|+++|...+++.......|..+.+|+..+|+.||..+..
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 466999999999999999999999999999999999986644
No 36
>KOG3623|consensus
Probab=96.96 E-value=0.0017 Score=55.93 Aligned_cols=49 Identities=24% Similarity=0.348 Sum_probs=46.0
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 39 LNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 39 ~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
+..|..+|..|..|+..+...+|.+.||....|+.||.+++++....++
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~r 616 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVER 616 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhcc
Confidence 7889999999999999999999999999999999999999999887664
No 37
>KOG0773|consensus
Probab=96.95 E-value=0.00051 Score=54.68 Aligned_cols=61 Identities=23% Similarity=0.301 Sum_probs=49.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 27 PRRNRTTFNSHQLNALEKVFE---RTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 27 ~rr~R~~~~~~q~~~L~~~f~---~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
..|.+..+......+|+.+.. ..+||+..++..||.++||+..||.+||-|.|.+..+-..
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence 344455788888999998743 3479999999999999999999999999999988665443
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=95.57 E-value=0.052 Score=31.57 Aligned_cols=47 Identities=17% Similarity=0.337 Sum_probs=34.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHH
Q psy2123 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRR 79 (143)
Q Consensus 28 rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR 79 (143)
+|+|..++-++...+-..++... ....||..+|+...+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 46788899988777777777665 577899999999999999999854
No 39
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=91.57 E-value=0.9 Score=25.53 Aligned_cols=46 Identities=15% Similarity=0.262 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123 33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83 (143)
Q Consensus 33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~r 83 (143)
.+++.+..+|...|... ....++|..+|++...|+.+...-..|.|
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 36788899999998322 34678999999999999998876655544
No 40
>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=86.76 E-value=3.2 Score=23.45 Aligned_cols=43 Identities=19% Similarity=0.213 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k 81 (143)
+++.+..++...|-.. -...++|..+|++...|+.|.+.-|.+
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 4566666666655433 457789999999999999999865543
No 41
>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=86.65 E-value=3.1 Score=24.20 Aligned_cols=42 Identities=24% Similarity=0.388 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHHHhcCC--CCHHHHHHHHHHcCCChhHHHHHH
Q psy2123 34 FNSHQLNALEKVFERTHY--PDAFVREELAKKVCLSEARVQVWF 75 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~--p~~~~~~~La~~lgl~~~~V~~WF 75 (143)
+|+.|..+|..+|..--| |-......||..+|++...|..=.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~L 44 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHL 44 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHH
Confidence 478899999999975543 656677899999999998765533
No 42
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=85.70 E-value=3 Score=22.60 Aligned_cols=43 Identities=16% Similarity=0.203 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k 81 (143)
+++.+..++...|... .....+|..+|++...|..|...-+.+
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 5677777777776422 245678999999999999998765443
No 43
>KOG1146|consensus
Probab=83.56 E-value=2.2 Score=39.82 Aligned_cols=63 Identities=21% Similarity=0.348 Sum_probs=56.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 24 ~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
..+.+.-+..+-.+++.+|-.+|-.+.-|+...+.-|....+.+.+++.+||+|-+.+.++..
T Consensus 702 ~~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 702 SPRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred CcccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 344566788888899999999999999999999999999999999999999999999988754
No 44
>PF13565 HTH_32: Homeodomain-like domain
Probab=83.03 E-value=6.2 Score=23.88 Aligned_cols=39 Identities=15% Similarity=0.079 Sum_probs=26.8
Q ss_pred CHHHHHHHHHHHHhcCCCCHHHHHH-HHHHcCC----ChhHHHH
Q psy2123 35 NSHQLNALEKVFERTHYPDAFVREE-LAKKVCL----SEARVQV 73 (143)
Q Consensus 35 ~~~q~~~L~~~f~~~~~p~~~~~~~-La~~lgl----~~~~V~~ 73 (143)
+.++...|.+.+..++..+..+... |..++|+ +...|.-
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R 75 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYR 75 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHH
Confidence 6777788888888888777666655 5666664 4455543
No 45
>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=81.70 E-value=1.5 Score=26.65 Aligned_cols=47 Identities=15% Similarity=0.232 Sum_probs=29.0
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHH
Q psy2123 29 RNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRR 79 (143)
Q Consensus 29 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR 79 (143)
+.|..|++++...+-..+... ......+|.++||+...+..|-.--+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~----g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES----GESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH----HCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC----CCceEeeecccccccccccHHHHHHh
Confidence 346679998866665555222 24677899999999999999986433
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=81.52 E-value=1.5 Score=26.27 Aligned_cols=21 Identities=24% Similarity=0.507 Sum_probs=18.0
Q ss_pred HHHHHHHHcCCChhHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFq 76 (143)
....||.+||+++.+|+.|=.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh
Confidence 456789999999999999964
No 47
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=80.72 E-value=9.2 Score=26.83 Aligned_cols=51 Identities=16% Similarity=0.190 Sum_probs=39.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 32 TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 32 ~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
..+++.|..+|...+ .. ....++|..+|++...|..|..+.+.+.++....
T Consensus 5 ~~Lt~rqreVL~lr~--~G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRLRE--RG----LTQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 468899999997743 22 2356899999999999999999888877765443
No 48
>KOG3755|consensus
Probab=80.42 E-value=2.3 Score=36.64 Aligned_cols=20 Identities=35% Similarity=0.655 Sum_probs=15.1
Q ss_pred ChhHHHHHHhhHHHHHHHhh
Q psy2123 67 SEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 67 ~~~~V~~WFqNrR~k~rk~~ 86 (143)
....|+.||.|||.++++.+
T Consensus 739 ~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 739 ESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred hhcchHHHHHHHHHHHhhhh
Confidence 44568888888888888754
No 49
>PRK04217 hypothetical protein; Provisional
Probab=77.94 E-value=11 Score=25.26 Aligned_cols=50 Identities=20% Similarity=0.134 Sum_probs=38.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 32 TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 32 ~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
..++.++..++...|...- ...+||+.+|++...|+..+..-+.+.+...
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4578888888877764332 4678999999999999999887777766544
No 50
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=77.79 E-value=8.8 Score=27.62 Aligned_cols=31 Identities=13% Similarity=0.232 Sum_probs=25.8
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
...++|..+|++...|+.+...-|.+.++..
T Consensus 160 s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 160 TYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred CHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 4578899999999999999987777777654
No 51
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=77.48 E-value=10 Score=21.77 Aligned_cols=46 Identities=17% Similarity=0.236 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
.+++.++.+|.....-. ...++|..+|++...|..+..+-+.|..-
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 47888888887776433 46789999999999999998887776543
No 52
>PF13551 HTH_29: Winged helix-turn helix
Probab=77.47 E-value=8 Score=24.86 Aligned_cols=48 Identities=15% Similarity=0.118 Sum_probs=31.7
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCC-----CCHHHHHH-H-HHHc--CCChhHHHHHHh
Q psy2123 29 RNRTTFNSHQLNALEKVFERTHY-----PDAFVREE-L-AKKV--CLSEARVQVWFQ 76 (143)
Q Consensus 29 r~R~~~~~~q~~~L~~~f~~~~~-----p~~~~~~~-L-a~~l--gl~~~~V~~WFq 76 (143)
+.+..+++++...|.+.+..++. .+...... | .... .++...|..|++
T Consensus 53 ~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 53 RPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 33444899999999999987762 34444443 4 3333 467778888875
No 53
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=76.90 E-value=11 Score=27.60 Aligned_cols=32 Identities=19% Similarity=0.220 Sum_probs=26.0
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
...+||..+|++...|+.+...-+.+.++...
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 202 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLKVQMG 202 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 45788999999999999999877777766543
No 54
>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=76.67 E-value=10 Score=22.45 Aligned_cols=45 Identities=20% Similarity=0.305 Sum_probs=23.1
Q ss_pred CCCCCHHH-HHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhh
Q psy2123 31 RTTFNSHQ-LNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 31 R~~~~~~q-~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqN 77 (143)
|..|+... |.+++.++. +..--...| ..|.++|+..++|+-|.+-
T Consensus 3 rrsy~~~FKL~Vv~~a~~-~~nc~~~~R-Aaarkf~V~r~~Vr~W~kq 48 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEK-DNNCKGNQR-AAARKFNVSRRQVRKWRKQ 48 (58)
T ss_dssp -----HHHHHHHHHHHHH--TTTTT-HH-HHHHHTTS-HHHHHHHHTT
T ss_pred ccccChHHHHHHHHHHHH-ccchhhhHH-HHHHHhCccHHHHHHHHHH
Confidence 34566654 455554443 322222223 3489999999999999864
No 55
>PRK00118 putative DNA-binding protein; Validated
Probab=76.60 E-value=15 Score=24.32 Aligned_cols=49 Identities=16% Similarity=0.173 Sum_probs=35.7
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
++..|..++...|... ....+||..+|++...|..|....|.+.++...
T Consensus 18 L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~ 66 (104)
T PRK00118 18 LTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEE 66 (104)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4566666766655433 235679999999999999999887777776443
No 56
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=76.27 E-value=9.9 Score=25.96 Aligned_cols=46 Identities=13% Similarity=0.113 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
+++.+..++...|-.. ....+||..+|++...|+.+...-+.+.|+
T Consensus 107 L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 107 LDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 3444445544444222 346789999999999999998876666554
No 57
>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=75.03 E-value=7.9 Score=18.63 Aligned_cols=37 Identities=11% Similarity=0.285 Sum_probs=25.8
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHH
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWF 75 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WF 75 (143)
++..+...+...|... . ....+|..+|++...|..|.
T Consensus 6 ~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 5566666666666532 2 45678899999999988874
No 58
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=74.26 E-value=15 Score=25.33 Aligned_cols=31 Identities=13% Similarity=0.112 Sum_probs=25.5
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
...++|..+|++...|++.+..-|.+.|+..
T Consensus 124 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 124 SYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999987777776654
No 59
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=73.73 E-value=15 Score=25.47 Aligned_cols=32 Identities=16% Similarity=0.176 Sum_probs=26.2
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
...+||..+|++...|..|...-|.+.|+...
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45789999999999999999877777776543
No 60
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=73.34 E-value=13 Score=25.79 Aligned_cols=48 Identities=15% Similarity=0.067 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
+++.+..+|...|-. .....++|..+|++...|+.|...-+.+.++..
T Consensus 129 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 129 LPEELRTAITLREIE-----GLSYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 444455555444321 123567899999999999999987677666543
No 61
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=73.01 E-value=15 Score=26.04 Aligned_cols=32 Identities=28% Similarity=0.263 Sum_probs=26.5
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
...+||..+|++...|+.++..-|.+.++...
T Consensus 149 s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 149 SIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 45788999999999999999888887776543
No 62
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=72.51 E-value=18 Score=24.31 Aligned_cols=42 Identities=12% Similarity=0.263 Sum_probs=28.3
Q ss_pred CCCCCHHHHH-HHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhh
Q psy2123 31 RTTFNSHQLN-ALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 31 R~~~~~~q~~-~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqN 77 (143)
|..|+.++.. ++...+. +.. ....+|..+|++...|..|.+.
T Consensus 10 rr~ys~EfK~~aV~~~~~-~g~----sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFE-PGM----TVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCHHHHHHHHHHHHc-CCC----CHHHHHHHHCcCHHHHHHHHHH
Confidence 4457887744 4443333 332 3567899999999999999653
No 63
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=72.20 E-value=18 Score=25.09 Aligned_cols=32 Identities=16% Similarity=0.103 Sum_probs=26.5
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
..++||..+|++...|+.+.+.-|.+.++...
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46788999999999999999887777776544
No 64
>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=71.72 E-value=5 Score=21.90 Aligned_cols=21 Identities=24% Similarity=0.183 Sum_probs=17.8
Q ss_pred HHHHHHHcCCChhHHHHHHhh
Q psy2123 57 REELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqN 77 (143)
..++|..+|++...|+.|.++
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 357899999999999999754
No 65
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=71.50 E-value=11 Score=27.91 Aligned_cols=47 Identities=26% Similarity=0.422 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123 33 TFNSHQLNALEKVFERTH--YPDAFVREELAKKVCLSEARVQVWFQNRRAK 81 (143)
Q Consensus 33 ~~~~~q~~~L~~~f~~~~--~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k 81 (143)
.+|+.|+.+|..+|..-= +|-......||+++|+++..+.- +=||+.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~e--hLRrAe 203 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSE--HLRRAE 203 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHH--HHHHHH
Confidence 699999999999997544 46677778999999999986443 334444
No 66
>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=71.26 E-value=4.5 Score=23.85 Aligned_cols=20 Identities=20% Similarity=0.431 Sum_probs=18.0
Q ss_pred HHHHHHHcCCChhHHHHHHh
Q psy2123 57 REELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFq 76 (143)
..+||..||++...|..|-+
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH
Confidence 56799999999999999985
No 67
>PF13518 HTH_28: Helix-turn-helix domain
Probab=71.07 E-value=5.6 Score=22.00 Aligned_cols=24 Identities=25% Similarity=0.475 Sum_probs=19.7
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHH
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRR 79 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR 79 (143)
...++|.++|++..+|..|.+.-+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 345689999999999999997544
No 68
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=70.67 E-value=19 Score=25.54 Aligned_cols=33 Identities=15% Similarity=0.124 Sum_probs=26.9
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
...+||..+|++...|+.+...-|.+.++....
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 178 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQLAD 178 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 456789999999999999998877777775543
No 69
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=70.19 E-value=5.2 Score=22.15 Aligned_cols=23 Identities=26% Similarity=0.538 Sum_probs=17.3
Q ss_pred HHHHHHHHHcCCChhHHHHHHhh
Q psy2123 55 FVREELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 55 ~~~~~La~~lgl~~~~V~~WFqN 77 (143)
....++|..+|++...|..|.+.
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 34678899999999999999864
No 70
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=69.90 E-value=10 Score=20.79 Aligned_cols=40 Identities=20% Similarity=0.295 Sum_probs=20.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHh
Q psy2123 32 TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 32 ~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFq 76 (143)
..++.++...++..+... .-..+||..+|++...|..+.+
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 347778888888776532 3456799999999999988765
No 71
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=68.78 E-value=29 Score=24.89 Aligned_cols=33 Identities=15% Similarity=0.131 Sum_probs=23.6
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
...+||..+|++...|++=...-|.+.|+....
T Consensus 152 s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l~~ 184 (192)
T PRK09643 152 SVADAARMLGVAEGTVKSRCARGRARLAELLGY 184 (192)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 456789999999999987665555555555443
No 72
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=68.41 E-value=26 Score=24.94 Aligned_cols=33 Identities=21% Similarity=0.213 Sum_probs=26.6
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
...++|..+|++...|++-+..-|.+.++....
T Consensus 149 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 181 (189)
T PRK12515 149 SVEEVGEIVGIPESTVKTRMFYARKKLAELLKA 181 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999888777777765443
No 73
>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=67.99 E-value=22 Score=25.03 Aligned_cols=29 Identities=24% Similarity=0.170 Sum_probs=24.0
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
...++|..+|++...|++....-|.+.++
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 35678999999999999999877776665
No 74
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=67.93 E-value=17 Score=25.92 Aligned_cols=32 Identities=19% Similarity=0.224 Sum_probs=26.2
Q ss_pred HHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 55 FVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 55 ~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
....+||..+|++...|+.++..-|.+.++..
T Consensus 158 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 158 LSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 34678899999999999999987777776643
No 75
>PRK06930 positive control sigma-like factor; Validated
Probab=67.76 E-value=28 Score=24.96 Aligned_cols=50 Identities=12% Similarity=0.112 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
+++.+..++...|-.. ....++|..+|++...|+.+...-+.+.++....
T Consensus 115 L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~ 164 (170)
T PRK06930 115 LTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIARQINE 164 (170)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555554433222 2356789999999999999999888887765543
No 76
>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=67.74 E-value=16 Score=25.78 Aligned_cols=32 Identities=13% Similarity=0.077 Sum_probs=25.9
Q ss_pred HHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 55 FVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 55 ~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
....+||..+|++...|+++...-|.+.|+..
T Consensus 155 ~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 155 LSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 34678999999999999999987777766654
No 77
>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=67.52 E-value=25 Score=24.68 Aligned_cols=32 Identities=25% Similarity=0.283 Sum_probs=25.9
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
...+||..+|++...|+.+.+.-|.+.++...
T Consensus 118 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45788999999999999998877777766544
No 78
>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=67.50 E-value=21 Score=24.38 Aligned_cols=29 Identities=17% Similarity=0.153 Sum_probs=22.8
Q ss_pred HHHHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123 55 FVREELAKKVCLSEARVQVWFQNRRAKFR 83 (143)
Q Consensus 55 ~~~~~La~~lgl~~~~V~~WFqNrR~k~r 83 (143)
....++|..+|++...|+.+...-|.+.+
T Consensus 128 ~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 128 VSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 34678899999999999998776555544
No 79
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=67.49 E-value=27 Score=24.06 Aligned_cols=32 Identities=22% Similarity=0.318 Sum_probs=25.9
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
...+||..+|++...|+.+...-+.+.|+...
T Consensus 129 s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 129 SYKEIAEALGIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999877777776543
No 80
>PRK10072 putative transcriptional regulator; Provisional
Probab=67.46 E-value=5 Score=26.24 Aligned_cols=41 Identities=22% Similarity=0.221 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHH
Q psy2123 33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRA 80 (143)
Q Consensus 33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~ 80 (143)
..+...+..|...-.. ...+||..+|++...|..|...+|.
T Consensus 32 ~~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 3466666666544322 2678899999999999999988764
No 81
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=67.30 E-value=13 Score=24.10 Aligned_cols=40 Identities=15% Similarity=0.204 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHH
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQV 73 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~ 73 (143)
++++|...-.+.|+.+--.+....+++|..|++++..|+-
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lek 42 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLEK 42 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHH
Confidence 5677777766666666666666788899999998876553
No 82
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=67.00 E-value=25 Score=25.20 Aligned_cols=31 Identities=13% Similarity=0.240 Sum_probs=25.6
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
...++|..+|++...|+.+...-|.+.|+..
T Consensus 152 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 152 SSEQICQECDISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3678899999999999999987777766643
No 83
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=66.88 E-value=28 Score=23.80 Aligned_cols=30 Identities=17% Similarity=0.101 Sum_probs=24.4
Q ss_pred HHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 57 REELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
..++|..+|++...|++....-|.+.|+..
T Consensus 125 ~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 125 VAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 578899999999999998887776666544
No 84
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=66.74 E-value=23 Score=25.15 Aligned_cols=30 Identities=27% Similarity=0.231 Sum_probs=24.1
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
...+||..+|++...|+.+...-+.+.|+.
T Consensus 157 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 157 SAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467889999999999999987666666553
No 85
>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=66.73 E-value=3.6 Score=25.57 Aligned_cols=24 Identities=17% Similarity=0.224 Sum_probs=20.5
Q ss_pred HHHHHHHHHcCCChhHHHHHHhhH
Q psy2123 55 FVREELAKKVCLSEARVQVWFQNR 78 (143)
Q Consensus 55 ~~~~~La~~lgl~~~~V~~WFqNr 78 (143)
-...+||..+|++...|+.|+.+.
T Consensus 33 lS~kEIAe~LGIS~~TVk~~l~~~ 56 (73)
T TIGR03879 33 KTASEIAEELGRTEQTVRNHLKGE 56 (73)
T ss_pred CCHHHHHHHHCcCHHHHHHHHhcC
Confidence 356789999999999999999753
No 86
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=66.70 E-value=22 Score=23.41 Aligned_cols=46 Identities=17% Similarity=0.250 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
+++.+..++...|-. .....+||..+|++...|..+...-+.+.++
T Consensus 111 L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 344455554443321 2245688999999999999998876666554
No 87
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=66.68 E-value=24 Score=24.83 Aligned_cols=30 Identities=20% Similarity=0.357 Sum_probs=24.6
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
..++||..+|++...|+++...-|.+.|+.
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 367889999999999999988777766653
No 88
>KOG0773|consensus
Probab=66.46 E-value=9.4 Score=30.31 Aligned_cols=43 Identities=23% Similarity=0.431 Sum_probs=37.0
Q ss_pred HHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 46 FERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 46 f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
-..++|+++.+...|+....++..+|.+||-|.|.+.+...+.
T Consensus 116 ~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~ 158 (342)
T KOG0773|consen 116 HRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKM 158 (342)
T ss_pred hhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCC
Confidence 3568899999999999999999999999999999887765443
No 89
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=66.24 E-value=21 Score=25.13 Aligned_cols=32 Identities=16% Similarity=0.256 Sum_probs=25.9
Q ss_pred HHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 55 FVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 55 ~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
....++|..+|++...|+++++.-|.+.+...
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 34678899999999999999987777766543
No 90
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=65.87 E-value=20 Score=19.55 Aligned_cols=42 Identities=21% Similarity=0.308 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k 81 (143)
++..+..++...+. .+ ...++|..+|++...|..|.+.-+.+
T Consensus 4 l~~~e~~i~~~~~~--g~----s~~eia~~l~is~~tv~~~~~~~~~k 45 (58)
T smart00421 4 LTPREREVLRLLAE--GL----TNKEIAERLGISEKTVKTHLSNIMRK 45 (58)
T ss_pred CCHHHHHHHHHHHc--CC----CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 56777777755432 22 45788999999999999988754444
No 91
>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=65.62 E-value=26 Score=23.65 Aligned_cols=29 Identities=17% Similarity=0.283 Sum_probs=22.9
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
...+||..+|++...|+.+...-+.+.++
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45678999999999999988766666554
No 92
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=65.02 E-value=24 Score=25.30 Aligned_cols=33 Identities=12% Similarity=0.088 Sum_probs=27.0
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
...+||..+|++...|+.....-|.+.++....
T Consensus 134 s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~ 166 (187)
T PRK12516 134 AYEEAAEICGCAVGTIKSRVNRARQRLQEILQI 166 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 356789999999999999998888777776544
No 93
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=64.18 E-value=33 Score=25.05 Aligned_cols=33 Identities=18% Similarity=0.208 Sum_probs=26.6
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
...++|..+|++...|+++...-|.+.++....
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~ 188 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQLRAALAA 188 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999998777777765543
No 94
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=64.09 E-value=23 Score=24.40 Aligned_cols=30 Identities=23% Similarity=0.254 Sum_probs=24.0
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
...++|..+|++...|+.+...-|.+.++.
T Consensus 130 s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 130 SYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 357889999999999999988777666543
No 95
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=63.96 E-value=30 Score=24.67 Aligned_cols=33 Identities=24% Similarity=0.279 Sum_probs=26.4
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
...++|..+|++...|+..+..-|.+.++....
T Consensus 124 ~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 124 SQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999998777777765443
No 96
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=63.83 E-value=28 Score=24.60 Aligned_cols=29 Identities=17% Similarity=0.404 Sum_probs=23.7
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
...++|..+|++...|+++...-+.+.|+
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 45678999999999999998876666554
No 97
>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=63.57 E-value=22 Score=20.65 Aligned_cols=37 Identities=30% Similarity=0.357 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhh
Q psy2123 37 HQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 37 ~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqN 77 (143)
.|+..|+-.+. +...+.. +||..+|++.+.|+.-..+
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i~~ 42 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDINE 42 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHHHH
Confidence 57788888888 6666544 8999999999998876544
No 98
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=63.10 E-value=38 Score=24.22 Aligned_cols=33 Identities=15% Similarity=0.217 Sum_probs=26.8
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
...+||..+|++...|+.....-|.+.++....
T Consensus 149 s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~ 181 (188)
T TIGR02943 149 ESDEICQELEISTSNCHVLLYRARLSLRACLSI 181 (188)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999888777777765544
No 99
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=62.23 E-value=48 Score=23.56 Aligned_cols=34 Identities=15% Similarity=0.214 Sum_probs=27.6
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNERNF 89 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~ 89 (143)
...+||..+|++...|++....-|.+.++.....
T Consensus 149 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 182 (191)
T PRK12520 149 ETEEICQELQITATNAWVLLYRARMRLRECLDLH 182 (191)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3578899999999999999988888777765543
No 100
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=62.09 E-value=36 Score=24.01 Aligned_cols=33 Identities=21% Similarity=0.284 Sum_probs=27.0
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
...+||..+|++...|++....-+.+.|+....
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 167 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQI 167 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999998888887765443
No 101
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=61.82 E-value=26 Score=26.24 Aligned_cols=32 Identities=22% Similarity=0.239 Sum_probs=26.5
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
...+||..+|++...|++....-|.+.|+...
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45788999999999999999888877776544
No 102
>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=61.63 E-value=11 Score=20.07 Aligned_cols=23 Identities=17% Similarity=0.419 Sum_probs=19.2
Q ss_pred HHHHHHHcCCChhHHHHHHhhHH
Q psy2123 57 REELAKKVCLSEARVQVWFQNRR 79 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqNrR 79 (143)
..++|..+|++...|..|.++..
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCC
Confidence 35789999999999999987644
No 103
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=61.54 E-value=43 Score=23.89 Aligned_cols=33 Identities=12% Similarity=0.204 Sum_probs=27.0
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
...+||..+|++...|+.....-|.+.|+....
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 186 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQCLQI 186 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 357889999999999999998888777776543
No 104
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=61.36 E-value=45 Score=23.88 Aligned_cols=32 Identities=9% Similarity=0.032 Sum_probs=26.3
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
...+||..+|++...|+.++..-|.+.|+...
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 185 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKRALAALLA 185 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35788999999999999999877777776543
No 105
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=60.98 E-value=38 Score=23.50 Aligned_cols=30 Identities=10% Similarity=0.093 Sum_probs=24.6
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
...++|..+|++...|+++...-|.+.+..
T Consensus 130 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 130 SYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 467889999999999999998777766654
No 106
>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=60.91 E-value=33 Score=23.52 Aligned_cols=30 Identities=17% Similarity=0.230 Sum_probs=25.0
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
...++|..+|++...|+.+...-|.+.++.
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 457789999999999999998777777664
No 107
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=60.67 E-value=32 Score=24.77 Aligned_cols=32 Identities=19% Similarity=0.131 Sum_probs=26.5
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
...++|..+|++...|++++..-|.+.|+...
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 35788999999999999999988877776544
No 108
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=60.44 E-value=43 Score=23.27 Aligned_cols=31 Identities=13% Similarity=0.157 Sum_probs=24.8
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
...+||..+|++...|+.....-|.+.|+..
T Consensus 136 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 136 STAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3578899999999999998877776666543
No 109
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=60.25 E-value=37 Score=23.98 Aligned_cols=30 Identities=23% Similarity=0.155 Sum_probs=25.1
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
...++|..+|++...|++....-|.+.|+.
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999998777777664
No 110
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=60.15 E-value=42 Score=24.29 Aligned_cols=32 Identities=13% Similarity=0.266 Sum_probs=26.4
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
...+||..+|++...|++....-|.+.|+...
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45788999999999999998877777776554
No 111
>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=59.82 E-value=19 Score=25.72 Aligned_cols=34 Identities=18% Similarity=0.260 Sum_probs=28.2
Q ss_pred HHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 55 FVREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 55 ~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
....+||..+|++...|+++...-|.+.++....
T Consensus 148 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 181 (193)
T TIGR02947 148 FAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD 181 (193)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999999888887776544
No 112
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=59.52 E-value=17 Score=25.43 Aligned_cols=33 Identities=15% Similarity=0.231 Sum_probs=27.6
Q ss_pred HHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 55 FVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 55 ~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
...+++|..+|++...|++.+..-|.+.++...
T Consensus 137 ~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 137 LPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999999888888777554
No 113
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=59.19 E-value=40 Score=23.75 Aligned_cols=30 Identities=10% Similarity=0.135 Sum_probs=23.6
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
...++|..+|++...|+.+...-|.+.++.
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 457789999999999999887666665553
No 114
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=59.19 E-value=48 Score=23.96 Aligned_cols=33 Identities=18% Similarity=0.126 Sum_probs=26.2
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
...+||..+|++...|+++...-|.+.|+....
T Consensus 151 s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~ 183 (196)
T PRK12535 151 TYEEAAKIADVRVGTIRSRVARARADLIAATAT 183 (196)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 457889999999999999998777776665443
No 115
>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=59.17 E-value=11 Score=20.03 Aligned_cols=19 Identities=21% Similarity=0.256 Sum_probs=15.2
Q ss_pred HHHHHHcCCChhHHHHHHh
Q psy2123 58 EELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 58 ~~La~~lgl~~~~V~~WFq 76 (143)
.++|+.+|++.+.|+.|=+
T Consensus 3 ~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHH
Confidence 4689999999999999853
No 116
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=59.06 E-value=43 Score=23.00 Aligned_cols=30 Identities=13% Similarity=0.299 Sum_probs=23.6
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
...++|..+|++...|+.....-+.+.++.
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 367889999999999999877666665553
No 117
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=58.64 E-value=35 Score=25.41 Aligned_cols=31 Identities=19% Similarity=0.204 Sum_probs=26.2
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
...++|..+|++...|+.+...-+.+.|+..
T Consensus 202 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 202 NLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999988888777643
No 118
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=58.56 E-value=44 Score=23.79 Aligned_cols=31 Identities=29% Similarity=0.445 Sum_probs=24.7
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
...+||+.+|++...|++..+.-|.+.++..
T Consensus 149 s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 149 KIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 3578899999999999998877676666643
No 119
>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=58.51 E-value=41 Score=23.16 Aligned_cols=29 Identities=21% Similarity=0.177 Sum_probs=22.3
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
...++|..+|++...|+....--|.+.|+
T Consensus 140 s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 140 PIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45788999999999999887655555554
No 120
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=57.99 E-value=40 Score=24.95 Aligned_cols=31 Identities=13% Similarity=0.051 Sum_probs=25.6
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
...+||..+|++...|+.....-|.+.++..
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4578899999999999999987777777654
No 121
>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=57.34 E-value=42 Score=23.29 Aligned_cols=30 Identities=17% Similarity=0.327 Sum_probs=23.9
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
...++|..+|++...|++....-|.+.++.
T Consensus 137 s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457789999999999999887666666653
No 122
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=57.33 E-value=47 Score=23.47 Aligned_cols=30 Identities=20% Similarity=0.125 Sum_probs=24.6
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
...++|..+|++...|+.+...-+.+.++.
T Consensus 149 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 149 SVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467889999999999999997777766654
No 123
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=57.24 E-value=11 Score=21.76 Aligned_cols=25 Identities=16% Similarity=0.351 Sum_probs=18.2
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHH
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRA 80 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~ 80 (143)
....||..+|++...|..|+.++..
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~ 36 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPS 36 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT--
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccc
Confidence 3567899999999999999998743
No 124
>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=57.04 E-value=45 Score=25.25 Aligned_cols=34 Identities=12% Similarity=0.263 Sum_probs=28.1
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNERNF 89 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~ 89 (143)
...+||..+|++...|+.+...-|.+.++..+..
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~ 212 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLERTRRR 212 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4578899999999999999998888877765543
No 125
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=56.85 E-value=13 Score=21.87 Aligned_cols=20 Identities=20% Similarity=0.265 Sum_probs=17.2
Q ss_pred HHHHHHHcCCChhHHHHHHh
Q psy2123 57 REELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFq 76 (143)
..++|..+|++...|+.|=.
T Consensus 3 i~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999964
No 126
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=56.79 E-value=49 Score=23.08 Aligned_cols=32 Identities=9% Similarity=0.189 Sum_probs=25.7
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
...++|..+|++...|+.....-|.+.++..+
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 168 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMREHLE 168 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45778999999999999998877777666543
No 127
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=55.99 E-value=50 Score=23.59 Aligned_cols=30 Identities=13% Similarity=0.173 Sum_probs=23.8
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
...++|..+|++...|++-...-|.+.|+.
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 457889999999999998887666666553
No 128
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=55.97 E-value=47 Score=23.56 Aligned_cols=33 Identities=12% Similarity=0.095 Sum_probs=27.1
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
...++|..+|++...|++....-|.+.|+..+.
T Consensus 156 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~ 188 (193)
T PRK11923 156 SYEDIASVMQCPVGTVRSRIFRAREAIDKALQP 188 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999998888877776543
No 129
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=55.86 E-value=51 Score=22.97 Aligned_cols=30 Identities=17% Similarity=0.225 Sum_probs=24.5
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
...+||..+|++...|+++...-+.+.+..
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999998777776553
No 130
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=55.55 E-value=42 Score=23.89 Aligned_cols=29 Identities=7% Similarity=-0.008 Sum_probs=23.5
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
...+||..+|++...|+.....-|.+.|+
T Consensus 148 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35788999999999999988766666554
No 131
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=55.53 E-value=47 Score=23.26 Aligned_cols=32 Identities=16% Similarity=0.256 Sum_probs=25.4
Q ss_pred HHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 55 FVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 55 ~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
....++|..+|++...|++....-|.+.++..
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T PRK09641 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34578899999999999998887777766543
No 132
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=55.27 E-value=51 Score=23.24 Aligned_cols=29 Identities=7% Similarity=0.170 Sum_probs=23.7
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
..+++|..+|++...|+.....-+.+.+.
T Consensus 145 s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 145 KQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45788999999999999999876666554
No 133
>PRK09480 slmA division inhibitor protein; Provisional
Probab=55.06 E-value=17 Score=25.62 Aligned_cols=37 Identities=22% Similarity=0.304 Sum_probs=29.8
Q ss_pred HHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHH
Q psy2123 43 EKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRA 80 (143)
Q Consensus 43 ~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~ 80 (143)
...|..... .......||...|++...+..+|.|+..
T Consensus 20 ~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 20 AQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 334555545 7778899999999999999999999764
No 134
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=54.45 E-value=48 Score=20.93 Aligned_cols=44 Identities=9% Similarity=0.117 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHHh-----cCCCCHHHHHHHHHHcCCChhHHHHHHh
Q psy2123 33 TFNSHQLNALEKVFER-----THYPDAFVREELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 33 ~~~~~q~~~L~~~f~~-----~~~p~~~~~~~La~~lgl~~~~V~~WFq 76 (143)
.++.+++..|...|.. +.+.+..+...+-..+|++...|...|.
T Consensus 3 ~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 3 AISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3677888888888853 3467778777776778888888887774
No 135
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=54.11 E-value=48 Score=24.99 Aligned_cols=47 Identities=13% Similarity=0.241 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
+++.+..+|...|-. .....+||..+|++...|+.|...-+.+.|+.
T Consensus 206 L~~~~r~vl~l~~~~-----g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 206 LSDREKSIIQCTFIE-----NLSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred CCHHHHHHHHHHHhC-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 445555555554422 12357899999999999999988777776654
No 136
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=53.98 E-value=58 Score=23.79 Aligned_cols=31 Identities=23% Similarity=0.303 Sum_probs=26.1
Q ss_pred HHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 57 REELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
..+||..+|++...|+...+.-|.+.|+...
T Consensus 167 ~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~ 197 (206)
T PRK12544 167 TNEICHAVDLSVSNLNVLLYRARLRLRECLE 197 (206)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 5788999999999999999887877777554
No 137
>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=53.52 E-value=16 Score=21.60 Aligned_cols=21 Identities=14% Similarity=0.226 Sum_probs=17.8
Q ss_pred HHHHHHHcCCChhHHHHHHhh
Q psy2123 57 REELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqN 77 (143)
..++|+.+|++...++.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999753
No 138
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=52.82 E-value=59 Score=23.18 Aligned_cols=32 Identities=19% Similarity=0.146 Sum_probs=25.7
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
...+||..+|++...|+++...-|.+.++...
T Consensus 129 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 129 SYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45788999999999999998877777666544
No 139
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=52.61 E-value=77 Score=22.08 Aligned_cols=48 Identities=19% Similarity=0.228 Sum_probs=37.1
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 31 RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 31 R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
.+.++..|..+|.-.+ .. ....++|..+|++...|..+-..-+.+.++
T Consensus 4 ~~~Lte~qr~VL~Lr~--~G----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE--KG----LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH--cC----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 3568889999987742 22 246789999999999999998887777765
No 140
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=52.55 E-value=23 Score=24.03 Aligned_cols=32 Identities=25% Similarity=0.362 Sum_probs=25.3
Q ss_pred CHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 53 DAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 53 ~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
......++|..+|++...|+++...-|.+.++
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34456889999999999999998866666554
No 141
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=52.43 E-value=20 Score=23.21 Aligned_cols=36 Identities=22% Similarity=0.492 Sum_probs=19.9
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 39 LNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 39 ~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
+.+..-.|+.|+||...-... | =.|||.+|++.+..
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~Q 49 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQRQ 49 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHHH
Confidence 445566688999987432111 1 26888888887665
No 142
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=52.35 E-value=58 Score=23.01 Aligned_cols=31 Identities=19% Similarity=0.312 Sum_probs=24.8
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
...+||..+|++...|++....-|.+.++..
T Consensus 140 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 140 TYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4578899999999999998877777666543
No 143
>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=51.91 E-value=19 Score=21.21 Aligned_cols=21 Identities=5% Similarity=0.172 Sum_probs=17.8
Q ss_pred HHHHHHHcCCChhHHHHHHhh
Q psy2123 57 REELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqN 77 (143)
..++|..+|++...++.|-++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999764
No 144
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=51.73 E-value=33 Score=22.82 Aligned_cols=40 Identities=18% Similarity=0.371 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHH
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRA 80 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~ 80 (143)
+++.++..+.+.+... ...+|..||++...|+.|=|+|+.
T Consensus 44 ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 44 LSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 7888888888877543 456789999999999999998764
No 145
>PRK10403 transcriptional regulator NarP; Provisional
Probab=51.17 E-value=34 Score=23.82 Aligned_cols=46 Identities=20% Similarity=0.330 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
.++..+..+|...... ....+||..++++.+.|+...+|=+.|...
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~ 198 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLNV 198 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 5788888888765432 235678999999999999999888777543
No 146
>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=50.94 E-value=11 Score=20.80 Aligned_cols=21 Identities=19% Similarity=0.264 Sum_probs=18.9
Q ss_pred HHHHHcCCChhHHHHHHhhHH
Q psy2123 59 ELAKKVCLSEARVQVWFQNRR 79 (143)
Q Consensus 59 ~La~~lgl~~~~V~~WFqNrR 79 (143)
+||..+|++...|..|+.++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999883
No 147
>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=50.86 E-value=57 Score=23.96 Aligned_cols=46 Identities=17% Similarity=0.231 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
+++.+..+|...|-.. ....++|..+|++...|+.+...-+.+.|+
T Consensus 176 L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 176 LSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4455555555555322 245789999999999999988766666554
No 148
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=50.50 E-value=41 Score=18.31 Aligned_cols=39 Identities=18% Similarity=0.197 Sum_probs=26.2
Q ss_pred CHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHH
Q psy2123 35 NSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRR 79 (143)
Q Consensus 35 ~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR 79 (143)
+..+..++...+ .. ....++|..++++...|+.|...-+
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 345556664433 22 2457789999999999999987433
No 149
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=50.10 E-value=69 Score=24.38 Aligned_cols=49 Identities=12% Similarity=0.192 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
+.+.+..+|...|.. .....++|..+|++...|+.....-+.+.|+...
T Consensus 213 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~ 261 (268)
T PRK06288 213 LPEREKKVLILYYYE-----DLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLA 261 (268)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 444445555554432 2245788999999999999888877777766543
No 150
>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=50.07 E-value=62 Score=23.76 Aligned_cols=46 Identities=17% Similarity=0.223 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
+++.+..+|...|-. .....+||..+|++...|..|...-+.+.++
T Consensus 179 L~~~~r~vl~l~y~~-----~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 179 LPERERRILLLRFFE-----DKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred CCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 555555565555432 2346789999999999999998766666554
No 151
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=49.92 E-value=59 Score=24.44 Aligned_cols=30 Identities=17% Similarity=0.221 Sum_probs=24.4
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
...+||..+|++...|+..+..-+.+.|+.
T Consensus 219 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 219 TLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999998777766653
No 152
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=49.85 E-value=53 Score=24.28 Aligned_cols=30 Identities=10% Similarity=0.221 Sum_probs=24.8
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
...++|..+|++...|+.+...-+.+.|+.
T Consensus 200 s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 200 TQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467889999999999999988777776654
No 153
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=49.82 E-value=47 Score=23.19 Aligned_cols=76 Identities=17% Similarity=0.215 Sum_probs=43.1
Q ss_pred cccccccccCCCCCCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChh--HHHHHHhhHHH
Q psy2123 3 YDWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEA--RVQVWFQNRRA 80 (143)
Q Consensus 3 ~~w~~~~~~~~~~~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~--~V~~WFqNrR~ 80 (143)
|.|+.+-+..|..-..... ..++ ...+..|+.+|...-....+-.......|....|+... .|..+++..-.
T Consensus 39 y~wv~r~~e~G~~l~~~~~-----~GrP-~kl~~~q~~~l~e~~~~k~wTl~~~~~~l~~e~gv~y~~~~v~~~l~~~Gl 112 (138)
T COG3415 39 YRWVRRYRETGLDLPPKPR-----KGRP-RKLSEEQLEILLERLREKDWTLKELVEELGLEFGVWYHASAVRRLLHELGL 112 (138)
T ss_pred HHHHHHhccccccccCccC-----CCCC-cccCHHHHHHHHHHHhcccchHHHHHHHHhhhcCeEEeHHHHHHHHHHcCC
Confidence 6788876555544211111 1111 23788888888877665553334444556778887654 67777765444
Q ss_pred HHHH
Q psy2123 81 KFRR 84 (143)
Q Consensus 81 k~rk 84 (143)
.++|
T Consensus 113 sykK 116 (138)
T COG3415 113 SYKK 116 (138)
T ss_pred CcCC
Confidence 4443
No 154
>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=49.31 E-value=21 Score=20.84 Aligned_cols=20 Identities=15% Similarity=0.298 Sum_probs=17.4
Q ss_pred HHHHHHHcCCChhHHHHHHh
Q psy2123 57 REELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFq 76 (143)
..++|..+|++...++.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999985
No 155
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=49.07 E-value=31 Score=24.62 Aligned_cols=33 Identities=21% Similarity=0.190 Sum_probs=26.4
Q ss_pred HHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 54 AFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 54 ~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
.....++|..+|++...|+.+...-|.+.|+..
T Consensus 155 g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 155 DLELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 345678999999999999998887777766644
No 156
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=48.94 E-value=20 Score=19.12 Aligned_cols=23 Identities=22% Similarity=0.169 Sum_probs=18.7
Q ss_pred HHHHHHHcCCChhHHHHHHhhHH
Q psy2123 57 REELAKKVCLSEARVQVWFQNRR 79 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqNrR 79 (143)
..++|..+|++...|..|.++.+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 45778899999999999986543
No 157
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=48.82 E-value=58 Score=25.84 Aligned_cols=53 Identities=21% Similarity=0.229 Sum_probs=37.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
+++.+..+|...|... +......++||..+|++...|+.+...-+.+.|+...
T Consensus 263 L~~~~R~vl~lrygL~-~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~ 315 (325)
T PRK05657 263 LNDKQREVLARRFGLL-GYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQ 315 (325)
T ss_pred CCHHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 5555566666555221 2233456789999999999999999988888776553
No 158
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=48.80 E-value=16 Score=20.34 Aligned_cols=23 Identities=26% Similarity=0.397 Sum_probs=19.0
Q ss_pred HHHHHHHcCCChhHHHHHHhhHH
Q psy2123 57 REELAKKVCLSEARVQVWFQNRR 79 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqNrR 79 (143)
..+||..+|++...|..|..+++
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 36789999999999999998854
No 159
>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=48.70 E-value=58 Score=24.48 Aligned_cols=46 Identities=13% Similarity=0.284 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
+++.+..+|...|... ....+||..+|++...|+.+...-+.+.|+
T Consensus 206 L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 206 LSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred CCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4455555555555322 235789999999999999998877766665
No 160
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=48.67 E-value=75 Score=22.59 Aligned_cols=33 Identities=12% Similarity=0.014 Sum_probs=26.2
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
...+||..+|++...|+.....-|.+.++....
T Consensus 129 s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~ 161 (182)
T PRK12540 129 SYEDAAAICGCAVGTIKSRVNRARSKLSALLYV 161 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 457889999999999999988777776665443
No 161
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=48.27 E-value=72 Score=21.86 Aligned_cols=27 Identities=19% Similarity=0.235 Sum_probs=21.0
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHH
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKF 82 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~ 82 (143)
...+||..+|++...|+.+...-+.+.
T Consensus 131 s~~EIA~~l~is~~tV~~~l~ra~~~~ 157 (161)
T PRK12528 131 GYGEIATELGISLATVKRYLNKAAMRC 157 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 356789999999999999887554443
No 162
>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=47.52 E-value=49 Score=18.39 Aligned_cols=36 Identities=19% Similarity=0.205 Sum_probs=23.5
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHh
Q psy2123 38 QLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 38 q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFq 76 (143)
+..+|...+....+.+ ..+||..+|++.+.|+.-..
T Consensus 2 ~~~il~~L~~~~~~it---~~eLa~~l~vS~rTi~~~i~ 37 (55)
T PF08279_consen 2 QKQILKLLLESKEPIT---AKELAEELGVSRRTIRRDIK 37 (55)
T ss_dssp HHHHHHHHHHTTTSBE---HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHcCCCcC---HHHHHHHhCCCHHHHHHHHH
Confidence 3455555555555443 56789999999999876554
No 163
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=47.42 E-value=30 Score=24.61 Aligned_cols=30 Identities=13% Similarity=0.100 Sum_probs=23.7
Q ss_pred HHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 55 FVREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 55 ~~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
....+||..+|++...|++.+..-|.+.|+
T Consensus 166 ~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 166 KSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345788999999999999988766666554
No 164
>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=47.19 E-value=8.2 Score=24.83 Aligned_cols=13 Identities=38% Similarity=0.808 Sum_probs=8.9
Q ss_pred hHHHHHHhhHHHH
Q psy2123 69 ARVQVWFQNRRAK 81 (143)
Q Consensus 69 ~~V~~WFqNrR~k 81 (143)
--|-.||+||-+.
T Consensus 17 iliwlwfrnrpaa 29 (117)
T PF09301_consen 17 ILIWLWFRNRPAA 29 (117)
T ss_dssp HHHHHHHHHTT-S
T ss_pred HHHHHHHccChHH
Confidence 3467899998764
No 165
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=47.12 E-value=43 Score=23.17 Aligned_cols=45 Identities=22% Similarity=0.244 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123 33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83 (143)
Q Consensus 33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~r 83 (143)
.+++.+..+|.-.... ....+||..++++.+.|+...++-+.|..
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 5788888888776642 25778899999999999998888777644
No 166
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=47.05 E-value=91 Score=21.28 Aligned_cols=31 Identities=16% Similarity=0.197 Sum_probs=23.8
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
...++|..+|++...|+.....-+.+.++..
T Consensus 123 s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 123 SHQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 3577899999999999988876666665543
No 167
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=46.57 E-value=39 Score=24.02 Aligned_cols=32 Identities=13% Similarity=0.205 Sum_probs=26.3
Q ss_pred HHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 55 FVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 55 ~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
...++||..+|++...|+++...-+.+.|+..
T Consensus 151 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 151 LEFQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999999987777776644
No 168
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=46.42 E-value=59 Score=22.72 Aligned_cols=29 Identities=17% Similarity=0.190 Sum_probs=23.1
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
...+||..+|++...|+++...-+.+.+.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 137 TYSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 46789999999999999998765555444
No 169
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=46.29 E-value=76 Score=24.06 Aligned_cols=47 Identities=17% Similarity=0.265 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
+.+.+..+|...|-. .....+||..+|++...|+.+...-+.+.|+.
T Consensus 204 L~~~~r~vl~l~y~~-----~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 204 LEERTREVLEFVFLH-----DLTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred CCHHHHHHHHHHHHC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 344444444444432 23467899999999999999988777666654
No 170
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=46.12 E-value=79 Score=21.62 Aligned_cols=45 Identities=16% Similarity=0.237 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123 33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83 (143)
Q Consensus 33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~r 83 (143)
.++..+..+|.- +..+ + ...++|..++++...|+.+.++-+.|..
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 488888888876 3322 2 2568899999999999999998777654
No 171
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=45.47 E-value=21 Score=19.79 Aligned_cols=23 Identities=9% Similarity=0.014 Sum_probs=19.9
Q ss_pred HHHHHHHcCCChhHHHHHHhhHH
Q psy2123 57 REELAKKVCLSEARVQVWFQNRR 79 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqNrR 79 (143)
...||..+|++...|..|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 46789999999999999997764
No 172
>KOG3623|consensus
Probab=45.21 E-value=6.8 Score=34.73 Aligned_cols=62 Identities=16% Similarity=0.195 Sum_probs=46.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 27 ~rr~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
+.+-|+.+..++..-|..+|..+-.++-.+...++..|-..+.+|++||++|+...+.....
T Consensus 626 p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl~ 687 (1007)
T KOG3623|consen 626 PVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPLF 687 (1007)
T ss_pred CccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCccc
Confidence 34456667777777888888877777766666667777788889999999998877665443
No 173
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=44.50 E-value=39 Score=24.25 Aligned_cols=32 Identities=13% Similarity=0.099 Sum_probs=25.2
Q ss_pred HHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 55 FVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 55 ~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
....+||..+|++...|++-+..-|.+.++..
T Consensus 171 ~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 171 KSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45678899999999999988877777766543
No 174
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=44.04 E-value=91 Score=21.60 Aligned_cols=29 Identities=10% Similarity=0.159 Sum_probs=22.7
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
..+++|..+|++...|+.+..+-+.+.+.
T Consensus 136 s~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 136 TYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45788999999999999988766655543
No 175
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=43.80 E-value=44 Score=24.95 Aligned_cols=50 Identities=14% Similarity=0.122 Sum_probs=35.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 32 TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 32 ~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
..+++.++++|.-... . ..-.++|..+|++++.|+.+..|-+.|..-..+
T Consensus 170 ~~Lt~re~evl~~~a~--G----~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~ 219 (232)
T TIGR03541 170 GVLSEREREVLAWTAL--G----RRQADIAAILGISERTVENHLRSARRKLGVATT 219 (232)
T ss_pred ccCCHHHHHHHHHHHC--C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCH
Confidence 3567777777766431 1 234678899999999999999988887664433
No 176
>smart00595 MADF subfamily of SANT domain.
Probab=43.79 E-value=52 Score=20.31 Aligned_cols=32 Identities=28% Similarity=0.510 Sum_probs=27.3
Q ss_pred HHHHHHcCCChhHHHHHHhhHHHHHHHhhhhh
Q psy2123 58 EELAKKVCLSEARVQVWFQNRRAKFRRNERNF 89 (143)
Q Consensus 58 ~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~~ 89 (143)
.+||.++|.+...|+.-+.|-|...++..+..
T Consensus 31 ~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~ 62 (89)
T smart00595 31 EEIAEELGLSVEECKKRWKNLRDRYRRELKRL 62 (89)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 56799999999999999999999988876554
No 177
>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=43.72 E-value=77 Score=24.33 Aligned_cols=29 Identities=28% Similarity=0.252 Sum_probs=24.2
Q ss_pred HHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 57 REELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
..+||..+|++...|+..++.-|.+.+..
T Consensus 127 ~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 127 YEEIASIVGKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 56789999999999999998777776653
No 178
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=43.50 E-value=80 Score=24.32 Aligned_cols=30 Identities=20% Similarity=0.152 Sum_probs=24.7
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
...++|..+|++...|+...+.-|.+.++.
T Consensus 133 s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~ 162 (293)
T PRK09636 133 PFDEIASTLGRSPAACRQLASRARKHVRAA 162 (293)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 356789999999999999998777776654
No 179
>PF12728 HTH_17: Helix-turn-helix domain
Probab=43.32 E-value=28 Score=19.17 Aligned_cols=22 Identities=23% Similarity=0.385 Sum_probs=18.4
Q ss_pred HHHHHHHcCCChhHHHHHHhhH
Q psy2123 57 REELAKKVCLSEARVQVWFQNR 78 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqNr 78 (143)
..++|+.||++...|..|.+..
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 3577889999999999998654
No 180
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=43.22 E-value=96 Score=21.80 Aligned_cols=29 Identities=28% Similarity=0.403 Sum_probs=22.5
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
..+++|..+|++...|++-...-|.+.|.
T Consensus 155 s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 155 TYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred CHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 45788999999999998877766665554
No 181
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=43.10 E-value=25 Score=18.50 Aligned_cols=22 Identities=27% Similarity=0.365 Sum_probs=18.9
Q ss_pred HHHHHHHcCCChhHHHHHHhhH
Q psy2123 57 REELAKKVCLSEARVQVWFQNR 78 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqNr 78 (143)
...+|..+|++...|..|..+.
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCC
Confidence 3578999999999999998876
No 182
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=43.04 E-value=67 Score=22.75 Aligned_cols=36 Identities=22% Similarity=0.191 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHH
Q psy2123 37 HQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQ 72 (143)
Q Consensus 37 ~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~ 72 (143)
.-+.+|...=+...|.+......+|..+|++...|.
T Consensus 24 ~li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~ 59 (156)
T PRK05988 24 ALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVH 59 (156)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHH
Confidence 446667666677789999999999999999988765
No 183
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=42.85 E-value=1.1e+02 Score=21.76 Aligned_cols=33 Identities=18% Similarity=0.231 Sum_probs=26.7
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
...++|..+|++...|+++..--|.+.++..+.
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 178 (188)
T PRK12517 146 SGEEIAEILDLNKNTVMTRLFRARNQLKEALEK 178 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999988777777765544
No 184
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=42.82 E-value=88 Score=23.54 Aligned_cols=32 Identities=19% Similarity=0.260 Sum_probs=26.0
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
...+||+.+|++...|+.+...-|.+.++...
T Consensus 134 S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~ 165 (228)
T PRK06704 134 SIADIAKVCSVSEGAVKASLFRSRNRLKTVSE 165 (228)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35788999999999999999877777776543
No 185
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=42.70 E-value=57 Score=17.70 Aligned_cols=37 Identities=16% Similarity=0.381 Sum_probs=24.5
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHH
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWF 75 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WF 75 (143)
++.++.+.+...+..- ....+||..+|++...|.-++
T Consensus 6 ~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 6 LSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 5555556666666543 346789999999999988766
No 186
>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 This entry is represented by Bacteriophage r1t, Orf18. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.
Probab=42.58 E-value=16 Score=26.38 Aligned_cols=33 Identities=27% Similarity=0.378 Sum_probs=27.5
Q ss_pred HHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 55 FVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 55 ~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
..+.+|+.-++++..+|-.|..|-+...++..+
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~ 47 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAKPK 47 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccccch
Confidence 356788999999999999999999887766543
No 187
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=42.20 E-value=41 Score=23.40 Aligned_cols=32 Identities=22% Similarity=0.396 Sum_probs=25.4
Q ss_pred HHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 54 AFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 54 ~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
....++||..+|++...|+.+...-|.+.++.
T Consensus 142 g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 142 GYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred CCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 34567899999999999999887766666653
No 188
>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=42.16 E-value=75 Score=24.62 Aligned_cols=32 Identities=25% Similarity=0.141 Sum_probs=25.3
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
...+||..+|++...|+.....-|.+.|+...
T Consensus 160 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 160 RAAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 35788999999999999988877777666443
No 189
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=41.37 E-value=98 Score=21.74 Aligned_cols=30 Identities=13% Similarity=0.283 Sum_probs=24.0
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
...++|..+|++...|+.+...-|.+.++.
T Consensus 145 s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~ 174 (179)
T PRK09415 145 SIKEIAEVTGVNENTVKTRLKKAKELLKKG 174 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 357889999999999999888666666653
No 190
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=40.66 E-value=64 Score=24.67 Aligned_cols=46 Identities=17% Similarity=0.284 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
+.+.+..+|...|.. .....+||..+|++...|+.+...-+.+.|+
T Consensus 216 L~~rer~vl~l~y~~-----~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 216 LPERERTVLVLRFFE-----SMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred CCHHHHHHHHHHhcC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 445555556555532 2345789999999999999998877666665
No 191
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=40.51 E-value=64 Score=23.15 Aligned_cols=37 Identities=24% Similarity=0.188 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHH
Q psy2123 36 SHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQ 72 (143)
Q Consensus 36 ~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~ 72 (143)
..-+.+|...++...|........+|..||++...|.
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 4567788888999999999999999999999987654
No 192
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=40.39 E-value=95 Score=23.10 Aligned_cols=51 Identities=14% Similarity=0.164 Sum_probs=35.3
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
+++.+..+|...|....+ ......+||..+|++...|+.....-..|.|..
T Consensus 177 L~~~er~vl~l~ygl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~ 227 (238)
T TIGR02393 177 LTERERKVLRMRYGLLDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRHP 227 (238)
T ss_pred CCHHHHHHHHHHhCCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhh
Confidence 455566666666632211 223467899999999999999988777777754
No 193
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=40.29 E-value=1.1e+02 Score=20.22 Aligned_cols=44 Identities=20% Similarity=0.241 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123 33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81 (143)
Q Consensus 33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k 81 (143)
.+|..|..+|+-+|..+ --..+||..+|++..-|.-|.+.-+.+
T Consensus 17 LLT~kQ~~~l~lyy~eD-----lSlsEIAe~~~iSRqaV~d~ikr~~~~ 60 (101)
T PF04297_consen 17 LLTEKQREILELYYEED-----LSLSEIAEELGISRQAVYDSIKRAEKK 60 (101)
T ss_dssp GS-HHHHHHHHHHCTS--------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred HCCHHHHHHHHHHHccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 46788888888776544 356789999999999999998765544
No 194
>PF13730 HTH_36: Helix-turn-helix domain
Probab=40.26 E-value=46 Score=18.52 Aligned_cols=43 Identities=16% Similarity=-0.013 Sum_probs=27.1
Q ss_pred CCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHcCCChhHHHHHHhh
Q psy2123 34 FNSHQLNALEKVFER---THYPDAFVREELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~---~~~p~~~~~~~La~~lgl~~~~V~~WFqN 77 (143)
+++.+..++-..... +.. ...-...||..+|++.+.|+.+...
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~-~~pS~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGG-CFPSQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCC-CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 445555554444322 222 2224678999999999999888754
No 195
>PHA02955 hypothetical protein; Provisional
Probab=39.98 E-value=38 Score=25.44 Aligned_cols=46 Identities=9% Similarity=0.007 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHhc-CCCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123 36 SHQLNALEKVFERT-HYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81 (143)
Q Consensus 36 ~~q~~~L~~~f~~~-~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k 81 (143)
..++..|-+.|... ...+.+++.+++.++|+....|..||.+.-.+
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~~q 106 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDLQL 106 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchhhh
Confidence 45677777777655 46778889999999999988788999875444
No 196
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=39.94 E-value=63 Score=22.44 Aligned_cols=46 Identities=20% Similarity=0.275 Sum_probs=35.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123 32 TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83 (143)
Q Consensus 32 ~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~r 83 (143)
..++..+..+|....+. ...++||..++++.+.|+.+..+-|.|..
T Consensus 148 ~~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 148 TVLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred ccCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 45788888888654433 34678999999999999999988777643
No 197
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=39.77 E-value=81 Score=24.07 Aligned_cols=49 Identities=18% Similarity=0.254 Sum_probs=34.8
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
+++.+..+|...|-.. ......+||..+|++...|+....+-..|.|+.
T Consensus 219 L~~rer~vl~l~y~~~---~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~ 267 (270)
T TIGR02392 219 LDARSRRIIEARWLDD---DKLTLQELAAEYGVSAERIRQIEKNAMKKLKAA 267 (270)
T ss_pred CCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5566666776666321 122457899999999999999888777777653
No 198
>PHA01976 helix-turn-helix protein
Probab=39.76 E-value=29 Score=20.22 Aligned_cols=23 Identities=13% Similarity=0.286 Sum_probs=19.6
Q ss_pred HHHHHHHcCCChhHHHHHHhhHH
Q psy2123 57 REELAKKVCLSEARVQVWFQNRR 79 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqNrR 79 (143)
..+||..+|++...|..|...++
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46789999999999999987654
No 199
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=39.45 E-value=89 Score=23.89 Aligned_cols=50 Identities=18% Similarity=0.112 Sum_probs=38.0
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 31 RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 31 R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
...+++.+.++|.-.. .. ....+||..||+++..|+...+|-+.|..-..
T Consensus 188 ~~~LT~RE~evl~l~a--~G----~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~n 237 (247)
T TIGR03020 188 AGLITAREAEILAWVR--DG----KTNEEIAAILGISSLTVKNHLQHIFKKLDVRN 237 (247)
T ss_pred ccCCCHHHHHHHHHHH--CC----CCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCC
Confidence 3468999999998654 22 23567899999999999999998877765443
No 200
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=39.38 E-value=99 Score=22.86 Aligned_cols=46 Identities=20% Similarity=0.195 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
.+++.++.+|.-..+ .+ .-.++|..+++++..|+.+..+-..|..-
T Consensus 155 ~Lt~rE~~Vl~l~~~--G~----s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 155 LLTHREKEILNKLRI--GA----SNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred CCCHHHHHHHHHHHc--CC----CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 489999999988765 22 35678999999999999999887776553
No 201
>PRK10651 transcriptional regulator NarL; Provisional
Probab=39.14 E-value=1e+02 Score=21.32 Aligned_cols=45 Identities=13% Similarity=0.285 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123 33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83 (143)
Q Consensus 33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~r 83 (143)
.+++.+..+|+...+. + ...++|..++++...|++..++-+.|..
T Consensus 155 ~Lt~rE~~vl~~l~~g--~----~~~~ia~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 155 QLTPRERDILKLIAQG--L----PNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred cCCHHHHHHHHHHHcC--C----CHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 4889999998776532 1 2456788999999999999998877754
No 202
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=38.67 E-value=55 Score=23.14 Aligned_cols=32 Identities=25% Similarity=0.314 Sum_probs=26.5
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
.-.++|..+|++...|+.+...-|.+.++...
T Consensus 145 s~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 145 SYEEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 35678999999999999999988888776544
No 203
>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=38.55 E-value=30 Score=23.14 Aligned_cols=21 Identities=29% Similarity=0.431 Sum_probs=18.4
Q ss_pred HHHHHHHHcCCChhHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFq 76 (143)
...++|..++++...|..||+
T Consensus 20 s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 20 SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred hHHHHHHHhCcHHHHHHHHHH
Confidence 456678999999999999998
No 204
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=38.31 E-value=52 Score=23.58 Aligned_cols=30 Identities=33% Similarity=0.460 Sum_probs=23.9
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
..++||..+|++++.|+..++.-|.+.++.
T Consensus 153 s~~EIA~~lgiS~~tV~r~l~~aR~~l~~~ 182 (185)
T PF07638_consen 153 SVEEIAERLGISERTVRRRLRRARAWLRRE 182 (185)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999888777665543
No 205
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=38.11 E-value=1.3e+02 Score=22.82 Aligned_cols=48 Identities=19% Similarity=0.254 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
+.+.+..+|...|.. .....+||..+|++...|+.+...-+.+.|+..
T Consensus 206 L~~~er~vi~l~y~e-----~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 253 (257)
T PRK05911 206 LEEKERKVMALYYYE-----ELVLKEIGKILGVSESRVSQIHSKALLKLRATL 253 (257)
T ss_pred CCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 444445555555532 234578999999999999998876666666543
No 206
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=38.05 E-value=31 Score=20.70 Aligned_cols=23 Identities=26% Similarity=0.307 Sum_probs=19.8
Q ss_pred HHHHHHHcCCChhHHHHHHhhHH
Q psy2123 57 REELAKKVCLSEARVQVWFQNRR 79 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqNrR 79 (143)
...||..+|++...|..|..+++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 45799999999999999997764
No 207
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=37.80 E-value=1.2e+02 Score=22.32 Aligned_cols=45 Identities=11% Similarity=0.155 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~r 83 (143)
+.+.+..++...|... ....++|..+|++...|..+-..-..+.|
T Consensus 184 L~~~e~~i~~~~~~~~-----~t~~eIA~~lgis~~~V~~~~~~al~~Lr 228 (231)
T TIGR02885 184 LDERERQIIMLRYFKD-----KTQTEVANMLGISQVQVSRLEKKVLKKMK 228 (231)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4555555665555322 35678999999999998887654444443
No 208
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=37.76 E-value=35 Score=19.89 Aligned_cols=20 Identities=20% Similarity=0.152 Sum_probs=16.8
Q ss_pred HHHHHHHcCCChhHHHHHHh
Q psy2123 57 REELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFq 76 (143)
..++|..+|++...|+.|-.
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35689999999999999964
No 209
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=37.46 E-value=52 Score=24.30 Aligned_cols=42 Identities=12% Similarity=0.188 Sum_probs=33.6
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHH
Q psy2123 39 LNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKF 82 (143)
Q Consensus 39 ~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~ 82 (143)
+..-...|....|- .....||...|+++..|..+|.++..=.
T Consensus 19 l~aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L~ 60 (225)
T PRK11552 19 IAAALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDLY 60 (225)
T ss_pred HHHHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHHH
Confidence 34444558888877 5788899999999999999999987643
No 210
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=37.29 E-value=90 Score=21.90 Aligned_cols=36 Identities=19% Similarity=0.166 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHH
Q psy2123 37 HQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQ 72 (143)
Q Consensus 37 ~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~ 72 (143)
.-+.+|...=+...|.+.+....+|..+|++...|.
T Consensus 23 ~ll~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v~ 58 (154)
T PRK07539 23 AVIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVE 58 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 345566666667789999999999999999988765
No 211
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=37.19 E-value=92 Score=22.45 Aligned_cols=35 Identities=23% Similarity=0.181 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHH
Q psy2123 38 QLNALEKVFERTHYPDAFVREELAKKVCLSEARVQ 72 (143)
Q Consensus 38 q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~ 72 (143)
-+.+|...=+...|.+.+..+.+|+.+|++...|.
T Consensus 38 li~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V~ 72 (169)
T PRK07571 38 LIEVLHKAQELFGYLERDLLLYVARQLKLPLSRVY 72 (169)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHH
Confidence 34555555566789999999999999999987654
No 212
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=36.98 E-value=56 Score=24.30 Aligned_cols=30 Identities=10% Similarity=0.223 Sum_probs=24.3
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
...++|..+|++...|+++...-+.+.|+.
T Consensus 200 s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~ 229 (234)
T TIGR02835 200 TQKEVADMLGISQSYISRLEKRILKRLKKE 229 (234)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467889999999999999887766666654
No 213
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=36.68 E-value=38 Score=20.04 Aligned_cols=18 Identities=33% Similarity=0.573 Sum_probs=15.4
Q ss_pred HHHHHHHcCCChhHHHHH
Q psy2123 57 REELAKKVCLSEARVQVW 74 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~W 74 (143)
...||..||++...|..|
T Consensus 12 ~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 12 QSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHh
Confidence 357899999999999999
No 214
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=36.65 E-value=1.4e+02 Score=20.70 Aligned_cols=29 Identities=24% Similarity=0.305 Sum_probs=22.2
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
...+||..+|++...|+.=...-|.+.|+
T Consensus 158 s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 158 SFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45778999999999998876666665554
No 215
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=36.35 E-value=96 Score=21.56 Aligned_cols=36 Identities=14% Similarity=0.057 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHH
Q psy2123 37 HQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQ 72 (143)
Q Consensus 37 ~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~ 72 (143)
.-+.+|...=+...|.+.+....+|..+|++...|.
T Consensus 17 ~li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 17 AIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 345556555566679999999999999999987654
No 216
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=36.10 E-value=74 Score=22.07 Aligned_cols=35 Identities=29% Similarity=0.254 Sum_probs=25.9
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHH
Q psy2123 38 QLNALEKVFERTHYPDAFVREELAKKVCLSEARVQ 72 (143)
Q Consensus 38 q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~ 72 (143)
-+.+|...=+...|.+......+|..+|++..+|.
T Consensus 15 ll~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~ 49 (145)
T PF01257_consen 15 LLPILHEVQEEYGYIPEEALEEIAEALGIPPAEVY 49 (145)
T ss_dssp HHHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHHH
Confidence 45666666667789999999999999999988765
No 217
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=35.90 E-value=41 Score=21.72 Aligned_cols=21 Identities=19% Similarity=0.094 Sum_probs=17.9
Q ss_pred HHHHHHHcCCChhHHHHHHhh
Q psy2123 57 REELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqN 77 (143)
..++|+.+|++...++.|..+
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDEI 23 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 357899999999999999864
No 218
>PF13309 HTH_22: HTH domain
Probab=35.77 E-value=96 Score=18.34 Aligned_cols=42 Identities=17% Similarity=0.245 Sum_probs=31.1
Q ss_pred CCHHH-HHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHH
Q psy2123 34 FNSHQ-LNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWF 75 (143)
Q Consensus 34 ~~~~q-~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WF 75 (143)
++..+ +.++...+++--|--+.....+|+.||++...|....
T Consensus 21 l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 21 LSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred CCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHc
Confidence 44433 5666666666667778888999999999998887643
No 219
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=35.73 E-value=1.1e+02 Score=23.84 Aligned_cols=51 Identities=22% Similarity=0.212 Sum_probs=36.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
+.+.+..+|...|- +-......+||..+|++...|+..-..-+.|.|....
T Consensus 228 L~~rer~vl~lr~~---~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~ 278 (289)
T PRK07500 228 LNERELRIIRERRL---REDGATLEALGEELGISKERVRQIEARALEKLRRALL 278 (289)
T ss_pred CCHHHHHHHHHHhc---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 56666666666653 1123356889999999999999998877777765443
No 220
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=35.65 E-value=1.3e+02 Score=22.65 Aligned_cols=47 Identities=19% Similarity=0.213 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
.++..+..+|...|... ....++|..+|++...|...-.+-..+.|+
T Consensus 209 ~L~~~er~vi~~~~~~~-----~t~~eIA~~lgis~~~V~~~~~~al~kLr~ 255 (258)
T PRK08215 209 KLNDREKLILNLRFFQG-----KTQMEVAEEIGISQAQVSRLEKAALKHMRK 255 (258)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 46666777777776322 246789999999999998877655555443
No 221
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=35.52 E-value=1.1e+02 Score=22.58 Aligned_cols=31 Identities=19% Similarity=0.161 Sum_probs=23.2
Q ss_pred HHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 55 FVREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 55 ~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
...+++|..+|++...|+.+-..-+.+.|+.
T Consensus 196 ~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 196 KTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3467899999999999988865555555543
No 222
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=35.50 E-value=1.7e+02 Score=21.60 Aligned_cols=29 Identities=21% Similarity=0.193 Sum_probs=22.1
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
..+++|..+|++...|..+...-+.+.++
T Consensus 196 S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 196 TQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46788999999999998876655555544
No 223
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=34.60 E-value=1.6e+02 Score=22.68 Aligned_cols=53 Identities=26% Similarity=0.226 Sum_probs=33.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhh
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~ 87 (143)
+++.+..+|.-.|... +.......+||..+|++...|+.+...-+.+.|+...
T Consensus 223 Lp~~~R~Vl~l~ygL~-~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~ 275 (285)
T TIGR02394 223 LNERQREVLARRFGLL-GYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILE 275 (285)
T ss_pred CCHHHHHHHHHHhCCC-CCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4444445555444110 1222346788999999999999998877777766543
No 224
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=34.59 E-value=67 Score=23.77 Aligned_cols=37 Identities=22% Similarity=0.272 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHhhhh
Q psy2123 52 PDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88 (143)
Q Consensus 52 p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~~~~ 88 (143)
.......+||..+|++...|++....-|.+.|+....
T Consensus 163 ~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~ 199 (231)
T PRK11922 163 VEELSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199 (231)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 3444567899999999999999888777777776543
No 225
>PRK05572 sporulation sigma factor SigF; Validated
Probab=33.99 E-value=1.4e+02 Score=22.35 Aligned_cols=47 Identities=11% Similarity=0.145 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
.+++.+..++...|... ....+||..+|++...|..+-..-..+.|+
T Consensus 202 ~L~~~~~~v~~l~~~~~-----~s~~eIA~~lgis~~~V~~~~~ral~kLr~ 248 (252)
T PRK05572 202 ELDERERLIVYLRYFKD-----KTQSEVAKRLGISQVQVSRLEKKILKQMKE 248 (252)
T ss_pred cCCHHHHHHHHHHHhCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35566666666666322 345789999999999998877666666554
No 226
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=33.21 E-value=42 Score=17.32 Aligned_cols=23 Identities=30% Similarity=0.398 Sum_probs=18.9
Q ss_pred HHHHHHHcCCChhHHHHHHhhHH
Q psy2123 57 REELAKKVCLSEARVQVWFQNRR 79 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqNrR 79 (143)
...||..+|++...|..|-.+++
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~~ 35 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGKR 35 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 45788999999999999987653
No 227
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=31.72 E-value=1.4e+02 Score=19.99 Aligned_cols=24 Identities=17% Similarity=0.266 Sum_probs=20.1
Q ss_pred HHHHHHHHHcCCChhHHHHHHhhH
Q psy2123 55 FVREELAKKVCLSEARVQVWFQNR 78 (143)
Q Consensus 55 ~~~~~La~~lgl~~~~V~~WFqNr 78 (143)
.....||..+|++.+.+.-+|+..
T Consensus 26 ~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 26 LSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 456789999999999999888755
No 228
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=31.71 E-value=85 Score=22.14 Aligned_cols=41 Identities=17% Similarity=0.233 Sum_probs=31.3
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHH
Q psy2123 39 LNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRA 80 (143)
Q Consensus 39 ~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~ 80 (143)
+..-...|....|. ......||...|++...+..+|.++..
T Consensus 14 l~aA~~lf~e~G~~-~tSi~~Ia~~aGvsk~~lY~~F~sK~~ 54 (192)
T PRK14996 14 LQAAMRVALAEGFA-AMTVRRIASEAQVAAGQVHHHFSSAGE 54 (192)
T ss_pred HHHHHHHHHhcChh-hccHHHHHHHhCCCcHHHHHHcCCHHH
Confidence 33444557777774 345678899999999999999999866
No 229
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=31.59 E-value=1.4e+02 Score=23.10 Aligned_cols=49 Identities=20% Similarity=0.230 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
++..+..+|...|-.. ......+||..+|++...|+..-..-..|.|+.
T Consensus 231 L~~rEr~VL~lry~~~---~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~ 279 (284)
T PRK06596 231 LDERSRDIIEARWLDD---DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAA 279 (284)
T ss_pred CCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5555666666666321 123457899999999999998776666665554
No 230
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=31.15 E-value=1.2e+02 Score=23.75 Aligned_cols=29 Identities=28% Similarity=0.204 Sum_probs=23.7
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
...+||..+|++...|+.....-|.+.|+
T Consensus 171 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 171 SAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 45788999999999999988766666665
No 231
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=31.10 E-value=49 Score=17.96 Aligned_cols=25 Identities=12% Similarity=0.324 Sum_probs=20.8
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHH
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRA 80 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~ 80 (143)
....||.+.|++...+...|.|+-.
T Consensus 18 s~~~Ia~~~gvs~~~~y~~f~~k~~ 42 (47)
T PF00440_consen 18 SIRDIARRAGVSKGSFYRYFPSKDD 42 (47)
T ss_dssp SHHHHHHHHTSCHHHHHHHCSSHHH
T ss_pred CHHHHHHHHccchhhHHHHcCCHHH
Confidence 3567899999999999999988643
No 232
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=30.77 E-value=43 Score=22.74 Aligned_cols=24 Identities=25% Similarity=0.448 Sum_probs=20.8
Q ss_pred HHHHHHHcCCChhHHHHHHhhHHH
Q psy2123 57 REELAKKVCLSEARVQVWFQNRRA 80 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqNrR~ 80 (143)
...||..+|++...|..|..+++.
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~~ 44 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDETE 44 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 467899999999999999988753
No 233
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=30.70 E-value=51 Score=20.72 Aligned_cols=19 Identities=21% Similarity=0.340 Sum_probs=16.4
Q ss_pred HHHHHHHcCCChhHHHHHH
Q psy2123 57 REELAKKVCLSEARVQVWF 75 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WF 75 (143)
..++|..+|++...++.|-
T Consensus 4 i~evA~~~gvs~~tLR~ye 22 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWE 22 (88)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 3578999999999999994
No 234
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=30.34 E-value=1.4e+02 Score=20.61 Aligned_cols=44 Identities=11% Similarity=0.320 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHH
Q psy2123 33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKF 82 (143)
Q Consensus 33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~ 82 (143)
.++..+..+|...+... ..++||..++++.+.|+.--.+-|.|.
T Consensus 143 ~lt~~E~~vl~~l~~g~------~~~~I~~~l~~s~~tv~~~~~~l~~Kl 186 (204)
T PRK09958 143 SLSKQEISVMRYILDGK------DNNDIAEKMFISNKTVSTYKSRLMEKL 186 (204)
T ss_pred cCCHHHHHHHHHHHcCC------CHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 48888888888887543 367889999999999999887777664
No 235
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=30.21 E-value=59 Score=20.89 Aligned_cols=20 Identities=20% Similarity=0.404 Sum_probs=17.3
Q ss_pred HHHHHHHcCCChhHHHHHHh
Q psy2123 57 REELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFq 76 (143)
..++|..+|++...++.|..
T Consensus 3 I~e~a~~~gvs~~tLR~ye~ 22 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYEE 22 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999974
No 236
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=29.93 E-value=71 Score=17.46 Aligned_cols=21 Identities=19% Similarity=0.275 Sum_probs=18.0
Q ss_pred HHHHHHHHcCCChhHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFq 76 (143)
....+|..+|++...|...|.
T Consensus 29 s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 29 SFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 356789999999999998885
No 237
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=29.74 E-value=54 Score=20.62 Aligned_cols=20 Identities=5% Similarity=0.031 Sum_probs=17.4
Q ss_pred HHHHHHHcCCChhHHHHHHh
Q psy2123 57 REELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFq 76 (143)
..++|..+|++...|+.|-.
T Consensus 4 i~e~A~~~gvs~~tLr~ye~ 23 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYER 23 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999974
No 238
>PRK09726 antitoxin HipB; Provisional
Probab=28.66 E-value=1.5e+02 Score=18.41 Aligned_cols=43 Identities=23% Similarity=0.298 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHH
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRR 79 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR 79 (143)
+++.++...-..+......+ ..+||..+|++...|..|..+++
T Consensus 8 ~~~~~l~~~lk~~R~~~glt---q~elA~~~gvs~~tis~~e~g~~ 50 (88)
T PRK09726 8 YSPTQLANAMKLVRQQNGWT---QSELAKKIGIKQATISNFENNPD 50 (88)
T ss_pred cCHHHHHHHHHHHHHHcCCC---HHHHHHHHCcCHHHHHHHHCCCC
Confidence 44555543333333333333 56789999999999999998753
No 239
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=28.61 E-value=1.2e+02 Score=21.94 Aligned_cols=41 Identities=17% Similarity=0.285 Sum_probs=29.9
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHH
Q psy2123 41 ALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKF 82 (143)
Q Consensus 41 ~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~ 82 (143)
.-...|....|-. .....||...|++...|...|.|+..-.
T Consensus 26 AA~~lf~e~Gy~~-~s~~dIA~~aGvs~gtiY~hF~sKe~L~ 66 (212)
T PRK15008 26 AALDTFSQFGFHG-TRLEQIAELAGVSKTNLLYYFPSKEALY 66 (212)
T ss_pred HHHHHHHHhCccc-CCHHHHHHHhCcCHHHHHHHCCCHHHHH
Confidence 3334466666543 3456789999999999999999986543
No 240
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=28.56 E-value=1.9e+02 Score=21.02 Aligned_cols=45 Identities=9% Similarity=0.106 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123 33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83 (143)
Q Consensus 33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~r 83 (143)
.+++.++++|.-.-+ .+ .-.++|.+++++++.|+.-..+=..|..
T Consensus 137 ~LT~RE~eVL~lla~--G~----snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 137 SLSRTESSMLRMWMA--GQ----GTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred cCCHHHHHHHHHHHc--CC----CHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 489999999876643 22 2467899999999999998766555543
No 241
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=28.18 E-value=62 Score=22.31 Aligned_cols=21 Identities=14% Similarity=0.135 Sum_probs=18.2
Q ss_pred HHHHHHHcCCChhHHHHHHhh
Q psy2123 57 REELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqN 77 (143)
..++|..+|++.+.++.|.+.
T Consensus 3 I~e~a~~~gvs~~TLR~Ye~~ 23 (134)
T cd04779 3 IGQLAHLAGVSKRTIDYYTNL 23 (134)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 357899999999999999964
No 242
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=28.09 E-value=53 Score=18.99 Aligned_cols=25 Identities=24% Similarity=0.344 Sum_probs=20.1
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHHH
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRRA 80 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR~ 80 (143)
...++|..+|++...|..|-..++.
T Consensus 16 s~~~lA~~~g~s~s~v~~iE~G~~~ 40 (64)
T PF13560_consen 16 SQAQLADRLGVSQSTVSRIERGRRP 40 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCCC
Confidence 4567899999999999999988774
No 243
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=27.80 E-value=2.4e+02 Score=21.19 Aligned_cols=29 Identities=28% Similarity=0.342 Sum_probs=23.3
Q ss_pred HHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 57 REELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
-.++|..++++++.|+.-.+|-+.|..-.
T Consensus 197 ~~eIa~~l~is~~TV~~h~~~~~~KL~~~ 225 (240)
T PRK10188 197 SAEIAMILSISENTVNFHQKNMQKKFNAP 225 (240)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 35788999999999999888877775543
No 244
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=27.76 E-value=94 Score=21.88 Aligned_cols=23 Identities=26% Similarity=0.413 Sum_probs=17.8
Q ss_pred HHHHHHHHHHcCCChhHHHHHHh
Q psy2123 54 AFVREELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 54 ~~~~~~La~~lgl~~~~V~~WFq 76 (143)
.....+||..+|++...+.-|-+
T Consensus 34 r~T~~eiAee~Gis~~tLYrWr~ 56 (142)
T PF13022_consen 34 RRTQAEIAEEVGISRSTLYRWRQ 56 (142)
T ss_dssp -S-HHHHHHHHTS-HHHHHHHHH
T ss_pred cchHHHHHHHhCCCHHHHHHHHh
Confidence 44567899999999999999984
No 245
>cd00131 PAX Paired Box domain
Probab=27.52 E-value=2e+02 Score=19.45 Aligned_cols=45 Identities=9% Similarity=-0.017 Sum_probs=29.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCC-------ChhHHHHHHhh
Q psy2123 33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCL-------SEARVQVWFQN 77 (143)
Q Consensus 33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl-------~~~~V~~WFqN 77 (143)
..+..+...+...-..++..+..+..++...-|+ +...|--||++
T Consensus 75 ~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~ 126 (128)
T cd00131 75 VATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN 126 (128)
T ss_pred cCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence 3456666667766778888777766554224455 77778777765
No 246
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=27.39 E-value=57 Score=21.07 Aligned_cols=31 Identities=19% Similarity=0.235 Sum_probs=22.5
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHH
Q psy2123 39 LNALEKVFERTHYPDAFVREELAKKVCLSEARVQV 73 (143)
Q Consensus 39 ~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~ 73 (143)
...|.+.|....+. .+.+|..||++...|+.
T Consensus 12 ~~ELq~nf~~~~ls----~~~ia~dL~~s~~~le~ 42 (89)
T PF10078_consen 12 RQELQANFELSGLS----LEQIAADLGTSPEHLEQ 42 (89)
T ss_pred HHHHHHHHHHcCCC----HHHHHHHhCCCHHHHHH
Confidence 34677788777654 56788889888877654
No 247
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=27.23 E-value=56 Score=18.61 Aligned_cols=18 Identities=28% Similarity=0.409 Sum_probs=13.2
Q ss_pred HHHHHHHHcCCChhHHHH
Q psy2123 56 VREELAKKVCLSEARVQV 73 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~ 73 (143)
--.+||..+|++..||+-
T Consensus 30 SS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 30 SSQELAEALGITPAQVRK 47 (50)
T ss_dssp -HHHHHHHHTS-HHHHHH
T ss_pred CHHHHHHHHCCCHHHhcc
Confidence 346789999999999863
No 248
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=27.22 E-value=1.7e+02 Score=19.72 Aligned_cols=30 Identities=20% Similarity=0.296 Sum_probs=23.2
Q ss_pred HHHHHHHcCCChhHHHHHHhhHHHHHHHhh
Q psy2123 57 REELAKKVCLSEARVQVWFQNRRAKFRRNE 86 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqNrR~k~rk~~ 86 (143)
-..+|..+|++...|+++-.+-+.|.+...
T Consensus 159 ~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~ 188 (202)
T PRK09390 159 NKVIARDLDISPRTVEVYRANVMTKMQAGS 188 (202)
T ss_pred hHHHHHHcCCCHHHHHHHHHHHHHHHcccc
Confidence 455788899999999998888777765433
No 249
>PF12200 DUF3597: Domain of unknown function (DUF3597); InterPro: IPR022016 This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 126 and 281 amino acids in length. The function of this domain is unknown. The structure of this domain has been found to contain five helices with a long flexible loop between helices one and two. ; PDB: 2GQB_A.
Probab=26.72 E-value=1.3e+02 Score=20.72 Aligned_cols=30 Identities=23% Similarity=0.494 Sum_probs=20.3
Q ss_pred CCHHHHHHHHHHcCCCh-----hHHHHHHhhHHHH
Q psy2123 52 PDAFVREELAKKVCLSE-----ARVQVWFQNRRAK 81 (143)
Q Consensus 52 p~~~~~~~La~~lgl~~-----~~V~~WFqNrR~k 81 (143)
.+...|.+||.+||++. ...-+|.+..-++
T Consensus 83 SSl~aRkeLA~eL~~~~~~~dsA~~NiwLhk~Vm~ 117 (127)
T PF12200_consen 83 SSLAARKELAKELGYTGDYNDSASMNIWLHKQVMQ 117 (127)
T ss_dssp -SHHHHHHHHHHHT---SS-HHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHH
Confidence 56789999999999876 3577899855443
No 250
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=26.70 E-value=54 Score=22.06 Aligned_cols=23 Identities=13% Similarity=0.167 Sum_probs=20.6
Q ss_pred HHHHHHHcCCChhHHHHHHhhHH
Q psy2123 57 REELAKKVCLSEARVQVWFQNRR 79 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqNrR 79 (143)
+++||..+|++...|..|.++++
T Consensus 21 q~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 21 KKELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHcCCC
Confidence 56799999999999999999875
No 251
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=26.41 E-value=67 Score=20.60 Aligned_cols=20 Identities=25% Similarity=0.426 Sum_probs=17.1
Q ss_pred HHHHHHHcCCChhHHHHHHh
Q psy2123 57 REELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFq 76 (143)
..++|+.+|++...|+.|=.
T Consensus 3 I~eva~~~gvs~~tlR~Ye~ 22 (95)
T cd04780 3 MSELSKRSGVSVATIKYYLR 22 (95)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999874
No 252
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=26.32 E-value=61 Score=17.53 Aligned_cols=18 Identities=39% Similarity=0.427 Sum_probs=13.0
Q ss_pred HHHHHHHHcCCChhHHHH
Q psy2123 56 VREELAKKVCLSEARVQV 73 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~ 73 (143)
--.+||..+||+...|..
T Consensus 19 s~~~la~~lglS~~~v~~ 36 (42)
T PF13404_consen 19 SYAELAEELGLSESTVRR 36 (42)
T ss_dssp -HHHHHHHHTS-HHHHHH
T ss_pred cHHHHHHHHCcCHHHHHH
Confidence 356789999999988754
No 253
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=26.30 E-value=38 Score=20.06 Aligned_cols=22 Identities=23% Similarity=0.504 Sum_probs=16.5
Q ss_pred HHHHHHHcCCChhHHH-HHHhhH
Q psy2123 57 REELAKKVCLSEARVQ-VWFQNR 78 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~-~WFqNr 78 (143)
...||..+|++...|. .|....
T Consensus 15 ~~~lA~~lgis~st~s~~~~~r~ 37 (66)
T PF07022_consen 15 DKELAERLGISKSTLSNNWKKRG 37 (66)
T ss_dssp CHHHHCCTT--HHHHH-HHHHSS
T ss_pred HHHHHHHhCcCHHHhhHHHHhCC
Confidence 4578999999999999 898643
No 254
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=26.25 E-value=76 Score=20.24 Aligned_cols=21 Identities=19% Similarity=0.058 Sum_probs=18.1
Q ss_pred HHHHHHHcCCChhHHHHHHhh
Q psy2123 57 REELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqN 77 (143)
..++|..+|++...++.|.+.
T Consensus 3 i~eva~~~gvs~~tLRyye~~ 23 (96)
T cd04768 3 IGEFAKLAGVSIRTLRHYDDI 23 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 357899999999999999864
No 255
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=25.87 E-value=2e+02 Score=22.28 Aligned_cols=28 Identities=11% Similarity=0.169 Sum_probs=23.3
Q ss_pred HHHHHHHcCCChhHHHHHHhhHHHHHHH
Q psy2123 57 REELAKKVCLSEARVQVWFQNRRAKFRR 84 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqNrR~k~rk 84 (143)
..++|..+|++...|+...+.-|.+.+.
T Consensus 137 ~~EIA~~Lgis~~tVr~~l~RAr~~Lr~ 164 (290)
T PRK09635 137 YQQIATTIGSQASTCRQLAHRARRKINE 164 (290)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 5678999999999999999877766665
No 256
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.82 E-value=1.9e+02 Score=18.73 Aligned_cols=43 Identities=14% Similarity=0.213 Sum_probs=31.8
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCC-ChhHHHHHHhh
Q psy2123 31 RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCL-SEARVQVWFQN 77 (143)
Q Consensus 31 R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl-~~~~V~~WFqN 77 (143)
|..|+.+....+-+.+....+ ....+|..+|+ ...++..|-..
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~~ 48 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRIQ 48 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHHH
Confidence 667899887666665554443 56789999996 99998888753
No 257
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=25.82 E-value=62 Score=18.22 Aligned_cols=21 Identities=24% Similarity=0.363 Sum_probs=18.0
Q ss_pred HHHHHHHcCCChhHHHHHHhh
Q psy2123 57 REELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqN 77 (143)
.+.||..+|++...|..||+.
T Consensus 22 ~~~La~~FgIs~stvsri~~~ 42 (53)
T PF13613_consen 22 FQDLAYRFGISQSTVSRIFHE 42 (53)
T ss_pred HhHHhhheeecHHHHHHHHHH
Confidence 457899999999999999975
No 258
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=25.76 E-value=62 Score=18.50 Aligned_cols=24 Identities=21% Similarity=0.372 Sum_probs=19.3
Q ss_pred HHHHHHHHcCCChhHHHHHHhhHH
Q psy2123 56 VREELAKKVCLSEARVQVWFQNRR 79 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFqNrR 79 (143)
....+|..+|++...|..|-.+++
T Consensus 14 t~~~~a~~~~i~~~~i~~~e~g~~ 37 (64)
T PF12844_consen 14 TQKDLAEKLGISRSTISKIENGKR 37 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCc
Confidence 356789999999999999998866
No 259
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=25.69 E-value=2.2e+02 Score=20.25 Aligned_cols=43 Identities=21% Similarity=0.192 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123 33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81 (143)
Q Consensus 33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k 81 (143)
.+++.+.++|....+- ..-.++|..++++.+.|+.-..|=..|
T Consensus 150 ~Lt~rE~evl~~~~~G------~s~~eIA~~l~iS~~TV~~h~~~i~~K 192 (216)
T PRK10840 150 RLSPKESEVLRLFAEG------FLVTEIAKKLNRSIKTISSQKKSAMMK 192 (216)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 4899999999877632 235678999999999999877654444
No 260
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=25.58 E-value=1.5e+02 Score=21.76 Aligned_cols=45 Identities=18% Similarity=0.220 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhH
Q psy2123 33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNR 78 (143)
Q Consensus 33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNr 78 (143)
.+++.++.+|......+ +-....-.+||..+++++..|+..+.+-
T Consensus 158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~~~~~~~ 202 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCRKYLIWL 202 (239)
T ss_pred CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHHHHHHHH
Confidence 46777777776655433 2223356789999999999999988765
No 261
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=25.32 E-value=97 Score=20.87 Aligned_cols=26 Identities=31% Similarity=0.445 Sum_probs=21.7
Q ss_pred CCCHHHHHHHHHHcCCChhHHHHHHh
Q psy2123 51 YPDAFVREELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 51 ~p~~~~~~~La~~lgl~~~~V~~WFq 76 (143)
-.+...+..||..+|++.+.|.-|-.
T Consensus 26 ~~~~~~r~~La~~~~i~~~~l~~w~~ 51 (122)
T PF14229_consen 26 GDTPLGRKALAKKLGISERNLLKWVN 51 (122)
T ss_pred CCCHHHHHHHHHhcCCCHHHHHHHHh
Confidence 35567788899999999999999953
No 262
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=25.23 E-value=79 Score=20.68 Aligned_cols=21 Identities=19% Similarity=0.346 Sum_probs=17.8
Q ss_pred HHHHHHHcCCChhHHHHHHhh
Q psy2123 57 REELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqN 77 (143)
..++|+.+|++...|+.|.+.
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (108)
T cd04773 3 IGELAHLLGVPPSTLRHWEKE 23 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999754
No 263
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=24.91 E-value=1.9e+02 Score=19.94 Aligned_cols=20 Identities=25% Similarity=0.484 Sum_probs=15.4
Q ss_pred HHHHHHcCCChhHHHHHHhh
Q psy2123 58 EELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 58 ~~La~~lgl~~~~V~~WFqN 77 (143)
..+|..+++++++++-|++.
T Consensus 103 ~~IA~~l~i~erta~r~~~~ 122 (130)
T PF05263_consen 103 YQIAQKLHISERTARRWRDR 122 (130)
T ss_pred HHHHHHhCccHHHHHHHHHH
Confidence 45788888999988877653
No 264
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=24.90 E-value=98 Score=17.36 Aligned_cols=38 Identities=18% Similarity=0.282 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHH
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQV 73 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~ 73 (143)
++..|..+|...+..... .....+||..++++...|..
T Consensus 3 lt~~q~~vL~~l~~~~~~--~~t~~~la~~l~~~~~~vs~ 40 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGE--ELTQSELAERLGISKSTVSR 40 (62)
T ss_dssp STHHHHHHHHHHHHSTTS--GEEHHHHHHHHTS-HHHHHH
T ss_pred cCHHHHHHHHHHHHCCCC--CcCHHHHHHHHCcCHHHHHH
Confidence 677888888888765543 12456789999999877654
No 265
>TIGR00993 3a0901s04IAP86 chloroplast protein import component Toc86/159, G and M domains. The long precursor of the 86K protein originally described is proposed to have three domains. The N-terminal A-domain is acidic, repetitive, weakly conserved, readily removed by proteolysis during chloroplast isolation, and not required for protein translocation. The other domains are designated G (GTPase) and M (membrane anchor); this family includes most of the G domain and all of M.
Probab=24.85 E-value=5.2e+02 Score=23.37 Aligned_cols=13 Identities=23% Similarity=0.314 Sum_probs=8.9
Q ss_pred CCCHHHHHHHHHH
Q psy2123 33 TFNSHQLNALEKV 45 (143)
Q Consensus 33 ~~~~~q~~~L~~~ 45 (143)
.++..|++.|.+.
T Consensus 415 ~l~ksq~~kl~k~ 427 (763)
T TIGR00993 415 PLTKAQMAKLSKE 427 (763)
T ss_pred cccHHHHHHHhHH
Confidence 3667777777665
No 266
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=24.73 E-value=1.9e+02 Score=18.19 Aligned_cols=38 Identities=18% Similarity=0.236 Sum_probs=25.5
Q ss_pred CCHHHHHHHHHH---HHhcCCCCHHHHHHHHHHcCCChhHHHH
Q psy2123 34 FNSHQLNALEKV---FERTHYPDAFVREELAKKVCLSEARVQV 73 (143)
Q Consensus 34 ~~~~q~~~L~~~---f~~~~~p~~~~~~~La~~lgl~~~~V~~ 73 (143)
++..|..+|... |....-|-.. ..||+.++++...|++
T Consensus 2 Lt~rq~~IL~alV~~Y~~~~~PVgS--k~ia~~l~~s~aTIRN 42 (78)
T PF03444_consen 2 LTERQREILKALVELYIETGEPVGS--KTIAEELGRSPATIRN 42 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCcCH--HHHHHHHCCChHHHHH
Confidence 456666666554 7777666543 4677889999887766
No 267
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=24.71 E-value=1.1e+02 Score=15.51 Aligned_cols=19 Identities=21% Similarity=0.305 Sum_probs=13.5
Q ss_pred HHHHHHcCCChhHHHHHHh
Q psy2123 58 EELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 58 ~~La~~lgl~~~~V~~WFq 76 (143)
..-|...||+..+|+..+.
T Consensus 9 i~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 9 IKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 3448899999999998775
No 268
>PRK09483 response regulator; Provisional
Probab=24.55 E-value=1.5e+02 Score=20.71 Aligned_cols=45 Identities=13% Similarity=0.191 Sum_probs=32.7
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHH
Q psy2123 32 TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKF 82 (143)
Q Consensus 32 ~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~ 82 (143)
..+++.+..+|.... ..+. -.+||..++++.+.|+.--+|=+.|.
T Consensus 147 ~~Lt~rE~~vl~~~~--~G~~----~~~Ia~~l~is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 147 ASLSERELQIMLMIT--KGQK----VNEISEQLNLSPKTVNSYRYRMFSKL 191 (217)
T ss_pred cccCHHHHHHHHHHH--CCCC----HHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 358999999986543 2222 34889999999999998777666653
No 269
>PF07471 Phage_Nu1: Phage DNA packaging protein Nu1; InterPro: IPR010906 This entry is represented by the Bacteriophage lambda, Nu1, terminase small subunit. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA [].; PDB: 1J9I_A.
Probab=24.55 E-value=69 Score=22.99 Aligned_cols=21 Identities=29% Similarity=0.541 Sum_probs=15.5
Q ss_pred HHHHHHHcCCChhHHHHHHhh
Q psy2123 57 REELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqN 77 (143)
+.+||..+|++...|..|-.+
T Consensus 5 k~~lA~i~gvS~~ti~~W~~~ 25 (164)
T PF07471_consen 5 KKELAEIFGVSERTIDKWQRQ 25 (164)
T ss_dssp HHHHHHHTT--HHHHHHHTTT
T ss_pred HHHHHHHHCCCHHHHHHHHHC
Confidence 567899999999999998644
No 270
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=24.30 E-value=1.5e+02 Score=19.43 Aligned_cols=23 Identities=9% Similarity=-0.032 Sum_probs=17.7
Q ss_pred HHHHHHHcCCChhHHHHHHhhHH
Q psy2123 57 REELAKKVCLSEARVQVWFQNRR 79 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqNrR 79 (143)
..+||..+|++...|.-|-..+.
T Consensus 81 q~~lA~~lg~~~~tis~~e~g~~ 103 (127)
T TIGR03830 81 QREAAELLGGGVNAFSRYERGEV 103 (127)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 34678888888888888876654
No 271
>PRK13870 transcriptional regulator TraR; Provisional
Probab=24.19 E-value=94 Score=23.34 Aligned_cols=28 Identities=21% Similarity=0.242 Sum_probs=23.3
Q ss_pred HHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 58 EELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 58 ~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
.+||..||++++.|..-.+|-+.|.--.
T Consensus 192 ~EIa~ILgISe~TV~~Hl~na~~KLga~ 219 (234)
T PRK13870 192 EEIADVEGVKYNSVRVKLREAMKRFDVR 219 (234)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence 4678999999999999999988875543
No 272
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=23.67 E-value=90 Score=19.73 Aligned_cols=21 Identities=19% Similarity=0.188 Sum_probs=17.3
Q ss_pred HHHHHHHcCCChhHHHHHHhh
Q psy2123 57 REELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqN 77 (143)
..++|..+|++...|+.|-+.
T Consensus 3 ~~eva~~~gi~~~tlr~~~~~ 23 (100)
T cd00592 3 IGEVAKLLGVSVRTLRYYEEK 23 (100)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 356899999999999999643
No 273
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=23.47 E-value=92 Score=19.88 Aligned_cols=21 Identities=19% Similarity=0.120 Sum_probs=17.7
Q ss_pred HHHHHHHcCCChhHHHHHHhh
Q psy2123 57 REELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqN 77 (143)
..++|..+|++...++.|.+.
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (97)
T cd04782 3 TGEFAKLCGISKQTLFHYDKI 23 (97)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 357899999999999999753
No 274
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=23.28 E-value=82 Score=20.32 Aligned_cols=20 Identities=10% Similarity=0.189 Sum_probs=17.3
Q ss_pred HHHHHHHcCCChhHHHHHHh
Q psy2123 57 REELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFq 76 (143)
..++|..+|++...++.|-+
T Consensus 4 i~eva~~~gvs~~tLR~ye~ 23 (102)
T cd04775 4 IGQMSRKFGVSRSTLLYYES 23 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999975
No 275
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=23.11 E-value=1.7e+02 Score=17.02 Aligned_cols=50 Identities=12% Similarity=0.155 Sum_probs=28.9
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHH---cCCChhHHHHHHhhH
Q psy2123 29 RNRTTFNSHQLNALEKVFERTHYPDAFVREELAKK---VCLSEARVQVWFQNR 78 (143)
Q Consensus 29 r~R~~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~---lgl~~~~V~~WFqNr 78 (143)
++|..++++.-..+....+.-.....+.-..|+.. .+|+..+|+.=.|--
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy 53 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKY 53 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 35677888776666666665555444222334443 456777777655543
No 276
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=23.05 E-value=91 Score=21.18 Aligned_cols=21 Identities=10% Similarity=0.311 Sum_probs=17.9
Q ss_pred HHHHHHHcCCChhHHHHHHhh
Q psy2123 57 REELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqN 77 (143)
..++|..+|++...++.|.+.
T Consensus 4 I~eVA~~~GVs~~TLR~wE~~ 24 (120)
T cd04767 4 IGVVAELLNIHPETLRIWERH 24 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999764
No 277
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=23.05 E-value=85 Score=21.46 Aligned_cols=20 Identities=30% Similarity=0.494 Sum_probs=17.7
Q ss_pred HHHHHHHcCCChhHHHHHHh
Q psy2123 57 REELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFq 76 (143)
.++||..+|++...|--|.+
T Consensus 3 ~eELA~~tG~srQTINrWvR 22 (122)
T PF07037_consen 3 PEELAELTGYSRQTINRWVR 22 (122)
T ss_pred HHHHHHHhCccHHHHHHHHH
Confidence 36899999999999999985
No 278
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=22.91 E-value=97 Score=18.44 Aligned_cols=21 Identities=19% Similarity=0.332 Sum_probs=17.2
Q ss_pred HHHHHHHcCCChhHHHHHHhh
Q psy2123 57 REELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqN 77 (143)
..++|..+|++..+|+.|...
T Consensus 18 T~eiA~~~gls~~~aR~yL~~ 38 (62)
T PF04703_consen 18 TREIADALGLSIYQARYYLEK 38 (62)
T ss_dssp HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHhCCCHHHHHHHHHH
Confidence 458899999999999999864
No 279
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=22.81 E-value=98 Score=19.97 Aligned_cols=21 Identities=19% Similarity=0.287 Sum_probs=17.6
Q ss_pred HHHHHHHcCCChhHHHHHHhh
Q psy2123 57 REELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqN 77 (143)
..++|..+|++...++.|-++
T Consensus 3 i~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 3 IGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred HHHHHHHHCcCHHHHHHHHHH
Confidence 357899999999999999754
No 280
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=22.79 E-value=82 Score=21.97 Aligned_cols=27 Identities=15% Similarity=0.231 Sum_probs=22.0
Q ss_pred HHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123 55 FVREELAKKVCLSEARVQVWFQNRRAK 81 (143)
Q Consensus 55 ~~~~~La~~lgl~~~~V~~WFqNrR~k 81 (143)
+...+++..+|++..+|..|...-|-.
T Consensus 47 ati~eV~e~tgVs~~~I~~~IreGRL~ 73 (137)
T TIGR03826 47 ATVSEIVEETGVSEKLILKFIREGRLQ 73 (137)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCee
Confidence 346788999999999999999765543
No 281
>PRK00215 LexA repressor; Validated
Probab=22.66 E-value=1.4e+02 Score=21.64 Aligned_cols=44 Identities=25% Similarity=0.348 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHcCC-ChhHHHHHHhhHH
Q psy2123 34 FNSHQLNALEKVFE---RTHYPDAFVREELAKKVCL-SEARVQVWFQNRR 79 (143)
Q Consensus 34 ~~~~q~~~L~~~f~---~~~~p~~~~~~~La~~lgl-~~~~V~~WFqNrR 79 (143)
++..|..+|+...+ ....+ ....+||..+|+ +...|..+.+.-.
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~--~s~~ela~~~~~~~~~tv~~~l~~L~ 49 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYP--PSRREIADALGLRSPSAVHEHLKALE 49 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCC--CCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 56788888877653 33332 235689999999 8888888775433
No 282
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=22.57 E-value=2.9e+02 Score=20.24 Aligned_cols=43 Identities=9% Similarity=0.021 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHH
Q psy2123 33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81 (143)
Q Consensus 33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k 81 (143)
.+|+.+.++|....+-. .-.++|.+++++++.|+.--.|--.|
T Consensus 134 ~LT~RE~eVL~ll~~G~------snkeIA~~L~iS~~TV~~h~~~I~~K 176 (207)
T PRK11475 134 MLSPTEREILRFMSRGY------SMPQIAEQLERNIKTIRAHKFNVMSK 176 (207)
T ss_pred CCCHHHHHHHHHHHCCC------CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 48899999998776422 34678999999999999866554444
No 283
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=22.38 E-value=1e+02 Score=19.67 Aligned_cols=21 Identities=24% Similarity=0.203 Sum_probs=17.8
Q ss_pred HHHHHHHcCCChhHHHHHHhh
Q psy2123 57 REELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqN 77 (143)
..++|..+|++...++.|-+.
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (96)
T cd04788 3 IGELARRTGLSVRTLHHYDHI 23 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 357899999999999999853
No 284
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.09 E-value=91 Score=20.15 Aligned_cols=21 Identities=24% Similarity=0.230 Sum_probs=17.7
Q ss_pred HHHHHHHcCCChhHHHHHHhh
Q psy2123 57 REELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqN 77 (143)
..++|..+|++...++.|-+.
T Consensus 4 i~eva~~~gvs~~tlR~ye~~ 24 (102)
T cd04789 4 ISELAEKAGISRSTLLYYEKL 24 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999753
No 285
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=22.04 E-value=1e+02 Score=19.82 Aligned_cols=21 Identities=10% Similarity=0.042 Sum_probs=17.5
Q ss_pred HHHHHHHcCCChhHHHHHHhh
Q psy2123 57 REELAKKVCLSEARVQVWFQN 77 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqN 77 (143)
..++|+.+|++...++.|.+.
T Consensus 4 i~eva~~~gVs~~tLR~ye~~ 24 (98)
T cd01279 4 ISVAAELLGIHPQTLRVYDRL 24 (98)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456899999999999999653
No 286
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=21.57 E-value=93 Score=21.02 Aligned_cols=20 Identities=20% Similarity=0.172 Sum_probs=17.7
Q ss_pred HHHHHHHcCCChhHHHHHHh
Q psy2123 57 REELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFq 76 (143)
+.++|..+|++...|+.|-+
T Consensus 6 I~elA~~~gvs~~tlR~Ye~ 25 (120)
T TIGR02054 6 ISRLAEDAGVSVHVVRDYLL 25 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 56789999999999999975
No 287
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=21.44 E-value=1.4e+02 Score=19.35 Aligned_cols=27 Identities=15% Similarity=0.359 Sum_probs=21.2
Q ss_pred HHHHHHHcCCChhHHHHHHhhHHHHHH
Q psy2123 57 REELAKKVCLSEARVQVWFQNRRAKFR 83 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFqNrR~k~r 83 (143)
...+|..+|+++.+|.-|..+-+.+.-
T Consensus 26 q~~vA~~~Gv~eStISR~k~~~~~~~a 52 (91)
T PF05269_consen 26 QKKVAEAMGVDESTISRWKNDFIEKMA 52 (91)
T ss_dssp HHHHHHHHTSSTTTHHHHHHHHHHHHH
T ss_pred hHHHHHHhCCCHHHHHHHHhhHHHHHH
Confidence 456899999999999999876555443
No 288
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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=21.38 E-value=93 Score=20.36 Aligned_cols=20 Identities=25% Similarity=0.311 Sum_probs=17.0
Q ss_pred HHHHHHHcCCChhHHHHHHh
Q psy2123 57 REELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WFq 76 (143)
..++|..+|++.+.++.|-+
T Consensus 3 i~e~a~~~gvs~~tlr~ye~ 22 (113)
T cd01109 3 IKEVAEKTGLSADTLRYYEK 22 (113)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999964
No 289
>KOG0044|consensus
Probab=21.35 E-value=1.4e+02 Score=22.04 Aligned_cols=30 Identities=17% Similarity=0.328 Sum_probs=23.0
Q ss_pred CCCHHHHHHHHHHcCCChhHHHHHHhhHHH
Q psy2123 51 YPDAFVREELAKKVCLSEARVQVWFQNRRA 80 (143)
Q Consensus 51 ~p~~~~~~~La~~lgl~~~~V~~WFqNrR~ 80 (143)
.......+.|......+...|+.|++|=..
T Consensus 8 ~~~~~~~e~l~~~t~f~~~ei~~~Yr~Fk~ 37 (193)
T KOG0044|consen 8 KLQPESLEQLVQQTKFSKKEIQQWYRGFKN 37 (193)
T ss_pred cCCcHHHHHHHHhcCCCHHHHHHHHHHhcc
Confidence 344556777888899999999999987543
No 290
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=21.24 E-value=1.4e+02 Score=21.23 Aligned_cols=41 Identities=10% Similarity=0.184 Sum_probs=29.9
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHH
Q psy2123 39 LNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRA 80 (143)
Q Consensus 39 ~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~ 80 (143)
++...+.|....|-. .....||...|++...+..+|.++..
T Consensus 17 l~aa~~lf~~~G~~~-~ti~~Ia~~agvsk~t~Y~~F~sKe~ 57 (213)
T PRK09975 17 IETAIAQFALRGVSN-TTLNDIADAANVTRGAIYWHFENKTQ 57 (213)
T ss_pred HHHHHHHHHHcCccc-CCHHHHHHHcCCCHHHHHHHcCCHHH
Confidence 334444466665543 34677899999999999999999865
No 291
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=21.20 E-value=1e+02 Score=18.38 Aligned_cols=21 Identities=29% Similarity=0.395 Sum_probs=16.0
Q ss_pred HHHHHHHHcCCChhHHHHHHh
Q psy2123 56 VREELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 56 ~~~~La~~lgl~~~~V~~WFq 76 (143)
..++||..+|++...|+..++
T Consensus 22 t~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 22 TDEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp BHHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHcccHHHHHHHHH
Confidence 356789999999999887664
No 292
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=21.13 E-value=1.7e+02 Score=16.27 Aligned_cols=39 Identities=23% Similarity=0.336 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHh
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFq 76 (143)
++..|..+|...++..+ . ...+||..++++...|..+..
T Consensus 1 lt~~q~~iL~~l~~~~~-~---~~~~la~~~~~~~~~~t~~i~ 39 (59)
T PF01047_consen 1 LTPSQFRILRILYENGG-I---TQSELAEKLGISRSTVTRIIK 39 (59)
T ss_dssp STHHHHHHHHHHHHHSS-E---EHHHHHHHHTS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHHcCC-C---CHHHHHHHHCCChhHHHHHHH
Confidence 46678888888887655 2 334889999999988777664
No 293
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=21.10 E-value=1.5e+02 Score=15.82 Aligned_cols=38 Identities=24% Similarity=0.313 Sum_probs=24.2
Q ss_pred CHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHh
Q psy2123 35 NSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 35 ~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFq 76 (143)
+..+..+|...++ ++.. ...+||..+|++...|..-++
T Consensus 2 ~~~~~~Il~~l~~-~~~~---t~~ela~~~~is~~tv~~~l~ 39 (48)
T PF13412_consen 2 DETQRKILNYLRE-NPRI---TQKELAEKLGISRSTVNRYLK 39 (48)
T ss_dssp -HHHHHHHHHHHH-CTTS----HHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHHHHH-cCCC---CHHHHHHHhCCCHHHHHHHHH
Confidence 3456677766665 4444 466789999999988776543
No 294
>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=21.03 E-value=29 Score=16.21 Aligned_cols=8 Identities=38% Similarity=0.974 Sum_probs=5.9
Q ss_pred HHHHhhHH
Q psy2123 72 QVWFQNRR 79 (143)
Q Consensus 72 ~~WFqNrR 79 (143)
-+||-+|.
T Consensus 6 iNWFE~~g 13 (22)
T PF08452_consen 6 INWFESRG 13 (22)
T ss_pred eehhhhCC
Confidence 37998865
No 295
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=20.55 E-value=2.6e+02 Score=18.79 Aligned_cols=39 Identities=15% Similarity=0.220 Sum_probs=28.4
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHh
Q psy2123 33 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQ 76 (143)
Q Consensus 33 ~~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFq 76 (143)
.++++|+..++.+..... -..+++..+|+++-.|+.=+.
T Consensus 33 ~L~~E~~~Fi~~Fi~~rG-----nlKe~e~~lgiSYPTvR~rLd 71 (113)
T PF09862_consen 33 RLSPEQLEFIKLFIKNRG-----NLKEMEKELGISYPTVRNRLD 71 (113)
T ss_pred cCCHHHHHHHHHHHHhcC-----CHHHHHHHHCCCcHHHHHHHH
Confidence 478899998888765443 356778888988888776443
No 296
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=20.53 E-value=2.8e+02 Score=21.83 Aligned_cols=51 Identities=14% Similarity=0.234 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHcCCChhHHHHHHhhHHHHHHHh
Q psy2123 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85 (143)
Q Consensus 34 ~~~~q~~~L~~~f~~~~~p~~~~~~~La~~lgl~~~~V~~WFqNrR~k~rk~ 85 (143)
+.+.+..+|...|..... .....++||..+|++...|+..-..-..|.|+.
T Consensus 257 L~~rer~Vi~lr~gl~~~-~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~ 307 (317)
T PRK07405 257 LTPQQKEVIALRFGLEDG-QPLTLAKIGERLNISRERVRQIEREALSKLRKR 307 (317)
T ss_pred CCHHHHHHHHHHhhcCCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 455555566666643221 123467899999999999999887777776653
No 297
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=20.26 E-value=1e+02 Score=20.14 Aligned_cols=19 Identities=21% Similarity=0.153 Sum_probs=15.8
Q ss_pred HHHHHHHcCCChhHHHHHH
Q psy2123 57 REELAKKVCLSEARVQVWF 75 (143)
Q Consensus 57 ~~~La~~lgl~~~~V~~WF 75 (143)
..++|+.+||+.+.++.|=
T Consensus 3 I~eva~~~gvs~~tLRyYE 21 (124)
T COG0789 3 IGEVAKLTGVSVRTLRFYE 21 (124)
T ss_pred HHHHHHHhCCCHHHHHHHH
Confidence 3467889999999999884
No 298
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=20.18 E-value=1.4e+02 Score=17.31 Aligned_cols=18 Identities=17% Similarity=0.303 Sum_probs=11.2
Q ss_pred HHHHHHHHHcCCChhHHH
Q psy2123 55 FVREELAKKVCLSEARVQ 72 (143)
Q Consensus 55 ~~~~~La~~lgl~~~~V~ 72 (143)
.+...++..||++..+++
T Consensus 21 ~ev~ywa~~~gvt~~~L~ 38 (57)
T PF12244_consen 21 YEVRYWAKRFGVTEEQLR 38 (57)
T ss_pred HHHHHHHHHHCcCHHHHH
Confidence 345566777777766654
No 299
>PRK13558 bacterio-opsin activator; Provisional
Probab=20.02 E-value=2.3e+02 Score=24.32 Aligned_cols=42 Identities=26% Similarity=0.414 Sum_probs=34.5
Q ss_pred CCCCHHHHHHHHHHHHhcCC--CCHHHHHHHHHHcCCChhHHHH
Q psy2123 32 TTFNSHQLNALEKVFERTHY--PDAFVREELAKKVCLSEARVQV 73 (143)
Q Consensus 32 ~~~~~~q~~~L~~~f~~~~~--p~~~~~~~La~~lgl~~~~V~~ 73 (143)
..+|..|..+|+.+|..--| |-....++||..||++...+..
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~ 649 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQ 649 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHH
Confidence 36999999999999986554 6666778999999999987544
Done!