Query psy12003
Match_columns 61
No_of_seqs 126 out of 1034
Neff 7.5
Searched_HMMs 46136
Date Fri Aug 16 16:13:11 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12003.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12003hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0489|consensus 99.7 1.9E-17 4.1E-22 106.2 1.4 35 4-38 190-224 (261)
2 KOG0487|consensus 99.6 7.9E-17 1.7E-21 105.5 1.2 32 4-35 266-297 (308)
3 KOG0848|consensus 99.6 1.8E-16 4E-21 102.4 1.4 32 4-35 230-261 (317)
4 KOG0850|consensus 99.6 5E-16 1.1E-20 98.4 2.6 36 2-37 151-186 (245)
5 KOG0488|consensus 99.6 4.7E-16 1E-20 102.0 2.2 31 4-34 203-233 (309)
6 KOG0844|consensus 99.6 8.3E-17 1.8E-21 105.8 -1.7 34 4-37 212-245 (408)
7 KOG0842|consensus 99.6 1.1E-15 2.3E-20 100.2 2.6 40 2-41 182-221 (307)
8 KOG0485|consensus 99.5 2.7E-15 5.7E-20 95.0 0.3 32 2-33 133-164 (268)
9 KOG0484|consensus 99.5 2.4E-15 5.2E-20 86.1 -0.3 32 4-35 48-79 (125)
10 KOG0843|consensus 99.5 9.7E-15 2.1E-19 90.0 0.8 33 2-34 131-163 (197)
11 KOG0492|consensus 99.5 1.3E-14 2.8E-19 91.3 1.3 33 2-34 173-205 (246)
12 KOG0491|consensus 99.4 2E-14 4.4E-19 87.8 1.1 35 2-36 129-163 (194)
13 KOG0483|consensus 99.4 2.7E-14 5.8E-19 89.1 -0.9 32 2-33 79-110 (198)
14 KOG2251|consensus 99.4 1.8E-13 3.9E-18 86.3 2.7 32 4-35 68-99 (228)
15 KOG0494|consensus 99.3 1.9E-13 4.1E-18 88.5 0.6 32 6-37 174-205 (332)
16 KOG0847|consensus 99.3 7.9E-13 1.7E-17 84.1 0.4 32 2-33 196-227 (288)
17 KOG4577|consensus 99.2 7.4E-12 1.6E-16 82.2 1.2 34 4-37 198-231 (383)
18 PF00046 Homeobox: Homeobox do 99.2 1.2E-12 2.7E-17 66.5 -2.3 29 2-30 29-57 (57)
19 KOG0493|consensus 99.1 1.8E-11 3.8E-16 79.5 -0.3 30 4-33 277-306 (342)
20 KOG0486|consensus 99.1 7.4E-11 1.6E-15 77.8 2.3 33 4-36 143-175 (351)
21 KOG3802|consensus 99.0 1.6E-10 3.4E-15 77.9 1.9 32 2-33 323-354 (398)
22 cd00086 homeodomain Homeodomai 99.0 2E-11 4.3E-16 61.8 -2.0 30 2-31 29-58 (59)
23 COG5576 Homeodomain-containing 99.0 1.4E-10 3E-15 70.2 0.7 32 3-34 81-112 (156)
24 KOG0490|consensus 98.9 5.4E-10 1.2E-14 69.1 2.8 30 4-33 91-120 (235)
25 smart00389 HOX Homeodomain. DN 98.9 5.3E-11 1.1E-15 59.9 -2.6 28 2-29 29-56 (56)
26 TIGR01565 homeo_ZF_HD homeobox 98.8 7.3E-10 1.6E-14 57.5 0.1 24 2-25 34-57 (58)
27 KOG0849|consensus 98.5 6.7E-08 1.5E-12 64.6 1.5 30 4-33 207-236 (354)
28 KOG0775|consensus 98.2 6.7E-07 1.5E-11 58.5 2.2 31 3-33 206-236 (304)
29 KOG1168|consensus 98.2 7.8E-07 1.7E-11 58.9 1.6 34 2-35 338-371 (385)
30 PF05920 Homeobox_KN: Homeobox 97.8 8.9E-07 1.9E-11 42.7 -2.9 26 2-27 15-40 (40)
31 KOG0490|consensus 97.4 5.1E-05 1.1E-09 46.8 0.8 30 4-33 184-213 (235)
32 KOG0774|consensus 96.5 0.0024 5.3E-08 42.1 2.5 30 3-32 221-250 (334)
33 KOG1146|consensus 95.9 0.0059 1.3E-07 47.0 2.2 34 2-35 932-965 (1406)
34 PF10668 Phage_terminase: Phag 94.5 0.0048 1E-07 32.1 -1.2 28 1-30 23-50 (60)
35 KOG3623|consensus 94.1 0.012 2.6E-07 43.5 -0.3 33 2-34 585-617 (1007)
36 PF11569 Homez: Homeodomain le 93.9 0.0049 1.1E-07 31.7 -2.0 24 2-25 27-50 (56)
37 KOG0773|consensus 92.1 0.051 1.1E-06 35.9 0.3 28 5-32 274-301 (342)
38 cd04761 HTH_MerR-SF Helix-Turn 89.9 0.035 7.5E-07 26.4 -1.6 24 1-24 1-24 (49)
39 PF13411 MerR_1: MerR HTH fami 87.5 0.058 1.3E-06 27.5 -1.8 21 1-21 1-21 (69)
40 COG5484 Uncharacterized conser 86.3 0.1 2.2E-06 34.3 -1.5 27 1-29 20-46 (279)
41 PF06056 Terminase_5: Putative 85.9 0.11 2.3E-06 26.6 -1.3 28 2-31 15-42 (58)
42 cd04762 HTH_MerR-trunc Helix-T 85.6 0.094 2E-06 24.4 -1.5 26 1-26 1-26 (49)
43 KOG2252|consensus 83.1 0.18 4E-06 36.0 -1.5 25 4-28 451-475 (558)
44 TIGR03879 near_KaiC_dom probab 82.0 0.19 4.1E-06 27.0 -1.4 23 1-23 33-55 (73)
45 PF08281 Sigma70_r4_2: Sigma-7 81.9 0.13 2.7E-06 25.1 -2.0 22 2-23 28-49 (54)
46 cd04763 HTH_MlrA-like Helix-Tu 80.9 0.19 4.1E-06 25.7 -1.6 22 1-22 1-22 (68)
47 cd04764 HTH_MlrA-like_sg1 Heli 80.4 0.24 5.1E-06 25.2 -1.3 22 1-22 1-22 (67)
48 cd06171 Sigma70_r4 Sigma70, re 79.0 0.14 3.1E-06 23.8 -2.3 22 2-23 28-49 (55)
49 PF13518 HTH_28: Helix-turn-he 78.7 0.25 5.3E-06 23.6 -1.5 20 3-22 15-34 (52)
50 TIGR01764 excise DNA binding d 77.8 0.29 6.4E-06 22.7 -1.4 25 1-25 2-26 (49)
51 PRK10072 putative transcriptio 77.5 0.41 8.8E-06 26.9 -1.0 25 3-27 49-73 (96)
52 PRK06759 RNA polymerase factor 76.5 0.39 8.4E-06 27.6 -1.4 26 1-26 123-148 (154)
53 PRK09646 RNA polymerase sigma 76.1 0.59 1.3E-05 28.2 -0.7 29 2-30 160-188 (194)
54 cd04780 HTH_MerR-like_sg5 Heli 76.0 0.39 8.6E-06 26.6 -1.4 21 1-21 1-21 (95)
55 PF08280 HTH_Mga: M protein tr 75.8 0.43 9.4E-06 24.1 -1.1 17 2-18 21-37 (59)
56 TIGR02985 Sig70_bacteroi1 RNA 75.5 0.5 1.1E-05 26.9 -1.1 26 2-27 131-156 (161)
57 PF13443 HTH_26: Cro/C1-type H 75.3 0.23 5E-06 24.8 -2.3 27 2-28 12-38 (63)
58 PF04218 CENP-B_N: CENP-B N-te 74.8 0.26 5.7E-06 24.6 -2.1 23 3-25 25-47 (53)
59 PRK12526 RNA polymerase sigma 74.6 0.59 1.3E-05 28.6 -1.0 30 2-31 171-200 (206)
60 TIGR02939 RpoE_Sigma70 RNA pol 74.4 0.55 1.2E-05 27.8 -1.1 29 2-30 156-184 (190)
61 TIGR02947 SigH_actino RNA poly 74.2 0.67 1.4E-05 27.8 -0.8 32 1-32 148-179 (193)
62 TIGR02937 sigma70-ECF RNA poly 74.0 0.59 1.3E-05 25.9 -1.0 26 2-27 128-153 (158)
63 PRK12519 RNA polymerase sigma 73.9 0.68 1.5E-05 27.7 -0.8 29 2-30 159-187 (194)
64 PRK09644 RNA polymerase sigma 73.8 0.58 1.3E-05 27.4 -1.1 30 2-31 126-155 (165)
65 PRK12514 RNA polymerase sigma 73.5 0.76 1.6E-05 27.2 -0.7 29 2-30 147-175 (179)
66 PRK09642 RNA polymerase sigma 73.2 0.66 1.4E-05 26.9 -1.0 29 2-30 124-152 (160)
67 smart00422 HTH_MERR helix_turn 73.1 0.49 1.1E-05 23.9 -1.4 21 1-21 1-21 (70)
68 PF04545 Sigma70_r4: Sigma-70, 71.9 0.34 7.4E-06 23.3 -2.1 19 2-20 22-40 (50)
69 PRK09652 RNA polymerase sigma 71.1 0.74 1.6E-05 26.8 -1.1 28 2-29 146-173 (182)
70 PRK12530 RNA polymerase sigma 71.0 0.79 1.7E-05 27.6 -1.0 30 1-30 151-180 (189)
71 PRK12547 RNA polymerase sigma 70.7 0.84 1.8E-05 26.8 -0.9 29 1-29 129-157 (164)
72 PRK09639 RNA polymerase sigma 70.3 0.82 1.8E-05 26.5 -1.0 31 1-31 128-158 (166)
73 cd04774 HTH_YfmP Helix-Turn-He 69.7 0.69 1.5E-05 25.6 -1.4 22 1-22 1-22 (96)
74 TIGR02999 Sig-70_X6 RNA polyme 69.6 0.89 1.9E-05 26.9 -1.0 28 2-29 152-179 (183)
75 PRK12518 RNA polymerase sigma 69.3 1.2 2.5E-05 26.2 -0.5 31 2-32 138-168 (175)
76 TIGR02983 SigE-fam_strep RNA p 68.7 1 2.2E-05 26.1 -0.9 30 1-30 127-156 (162)
77 PF08765 Mor: Mor transcriptio 68.6 0.63 1.4E-05 26.2 -1.7 18 1-18 73-90 (108)
78 PRK12515 RNA polymerase sigma 68.6 1.2 2.6E-05 26.7 -0.6 33 1-33 148-180 (189)
79 PF13384 HTH_23: Homeodomain-l 68.6 0.38 8.3E-06 23.0 -2.3 20 3-22 20-39 (50)
80 PF13404 HTH_AsnC-type: AsnC-t 68.3 0.57 1.2E-05 22.3 -1.6 16 3-18 20-35 (42)
81 PHA03273 envelope glycoprotein 68.2 2.5 5.5E-05 30.0 0.9 20 8-28 114-133 (486)
82 PRK11924 RNA polymerase sigma 68.1 1.3 2.8E-05 25.7 -0.5 29 2-30 143-171 (179)
83 PRK00118 putative DNA-binding 67.9 1 2.2E-05 25.6 -0.9 31 1-31 34-64 (104)
84 TIGR02989 Sig-70_gvs1 RNA poly 67.1 0.92 2E-05 26.1 -1.3 21 2-22 129-149 (159)
85 cd04788 HTH_NolA-AlbR Helix-Tu 66.8 0.86 1.9E-05 25.1 -1.4 22 1-22 1-22 (96)
86 PRK09047 RNA polymerase factor 66.7 1.1 2.3E-05 25.8 -1.0 28 2-29 124-151 (161)
87 TIGR02948 SigW_bacill RNA poly 66.7 1.2 2.5E-05 26.3 -0.9 29 2-30 154-182 (187)
88 cd01104 HTH_MlrA-CarA Helix-Tu 66.6 0.82 1.8E-05 23.0 -1.4 21 2-22 2-22 (68)
89 cd01392 HTH_LacI Helix-turn-he 66.5 0.74 1.6E-05 22.0 -1.5 21 5-25 2-22 (52)
90 PF08279 HTH_11: HTH domain; 66.2 0.95 2.1E-05 22.0 -1.1 16 3-18 18-33 (55)
91 PRK12538 RNA polymerase sigma 65.5 1.1 2.4E-05 28.2 -1.2 32 1-32 188-219 (233)
92 PRK12535 RNA polymerase sigma 65.5 1.8 3.8E-05 26.4 -0.3 32 2-33 151-182 (196)
93 PRK09637 RNA polymerase sigma 65.3 1.2 2.7E-05 26.7 -1.0 30 1-30 123-152 (181)
94 PRK05602 RNA polymerase sigma 65.2 1.3 2.7E-05 26.4 -0.9 30 2-31 146-175 (186)
95 PRK09648 RNA polymerase sigma 65.0 1.2 2.7E-05 26.5 -1.0 22 2-23 157-178 (189)
96 PRK12536 RNA polymerase sigma 65.0 1.2 2.6E-05 26.5 -1.0 29 2-30 147-175 (181)
97 PRK12520 RNA polymerase sigma 64.6 2 4.4E-05 25.7 -0.1 32 2-33 149-180 (191)
98 PRK12543 RNA polymerase sigma 64.5 1.3 2.7E-05 26.4 -1.0 30 2-31 135-164 (179)
99 TIGR02959 SigZ RNA polymerase 64.2 1.3 2.8E-05 26.2 -1.0 31 2-32 118-148 (170)
100 cd04767 HTH_HspR-like_MBC Heli 63.8 1.1 2.3E-05 26.2 -1.4 24 1-24 2-25 (120)
101 TIGR02950 SigM_subfam RNA poly 63.6 1.3 2.8E-05 25.3 -1.1 21 2-22 123-143 (154)
102 cd04773 HTH_TioE_rpt2 Second H 63.4 1 2.3E-05 25.3 -1.5 22 1-22 1-22 (108)
103 TIGR03070 couple_hipB transcri 63.2 1.4 3E-05 21.0 -0.9 23 3-25 18-40 (58)
104 PF12728 HTH_17: Helix-turn-he 63.0 0.98 2.1E-05 21.7 -1.4 25 1-25 2-26 (51)
105 cd00592 HTH_MerR-like Helix-Tu 62.8 1.1 2.5E-05 24.3 -1.3 22 1-22 1-22 (100)
106 PF01381 HTH_3: Helix-turn-hel 62.8 0.67 1.5E-05 22.3 -2.1 24 2-25 11-34 (55)
107 PRK09645 RNA polymerase sigma 62.8 1.6 3.4E-05 25.6 -0.8 29 1-29 135-163 (173)
108 TIGR02607 antidote_HigA addict 62.4 1.3 2.9E-05 22.8 -1.1 24 2-25 20-43 (78)
109 PF00376 MerR: MerR family reg 62.4 0.58 1.3E-05 21.8 -2.2 18 3-20 2-19 (38)
110 cd01106 HTH_TipAL-Mta Helix-Tu 62.4 1.1 2.4E-05 24.7 -1.4 24 1-24 1-24 (103)
111 PRK12532 RNA polymerase sigma 62.4 1.5 3.3E-05 26.3 -1.0 31 1-31 153-183 (195)
112 PRK12516 RNA polymerase sigma 62.2 1.5 3.4E-05 26.4 -1.0 32 1-32 133-164 (187)
113 TIGR02952 Sig70_famx2 RNA poly 61.7 1.4 3E-05 25.5 -1.2 21 1-21 139-159 (170)
114 TIGR02954 Sig70_famx3 RNA poly 61.2 1.8 3.9E-05 25.3 -0.8 21 2-22 137-157 (169)
115 cd00093 HTH_XRE Helix-turn-hel 60.8 1.3 2.9E-05 20.0 -1.2 23 3-25 15-37 (58)
116 PRK12512 RNA polymerase sigma 60.7 1.8 3.9E-05 25.7 -0.9 30 2-31 149-178 (184)
117 KOG3755|consensus 60.7 2.4 5.2E-05 31.3 -0.3 21 13-33 739-759 (769)
118 PRK11923 algU RNA polymerase s 60.4 1.6 3.5E-05 26.1 -1.1 30 2-31 156-185 (193)
119 PRK06986 fliA flagellar biosyn 60.3 1.7 3.7E-05 27.1 -1.0 29 2-30 202-230 (236)
120 PRK12537 RNA polymerase sigma 60.3 2 4.4E-05 25.5 -0.7 24 2-25 151-174 (182)
121 PRK12542 RNA polymerase sigma 60.0 1.8 3.9E-05 25.8 -1.0 29 2-30 140-168 (185)
122 PRK13182 racA polar chromosome 59.5 1.5 3.2E-05 27.1 -1.4 23 1-23 1-23 (175)
123 PRK12529 RNA polymerase sigma 59.4 1.7 3.7E-05 25.9 -1.1 27 2-28 145-171 (178)
124 cd04766 HTH_HspR Helix-Turn-He 58.8 1.4 3E-05 23.9 -1.4 22 1-22 2-23 (91)
125 PRK08301 sporulation sigma fac 58.8 1.9 4.1E-05 26.8 -1.0 29 2-30 200-228 (234)
126 PRK12533 RNA polymerase sigma 58.5 3.6 7.9E-05 25.6 0.2 31 2-32 152-182 (216)
127 PRK09640 RNA polymerase sigma 58.4 1.9 4.1E-05 25.8 -1.0 29 2-30 152-180 (188)
128 smart00530 HTH_XRE Helix-turn- 58.1 1.7 3.6E-05 19.5 -1.1 23 3-25 13-35 (56)
129 PRK12513 RNA polymerase sigma 57.9 2 4.4E-05 25.7 -1.0 30 2-31 157-186 (194)
130 smart00421 HTH_LUXR helix_turn 57.4 1.2 2.7E-05 20.9 -1.7 21 2-22 20-40 (58)
131 cd08313 Death_TNFR1 Death doma 57.1 2.3 5.1E-05 23.0 -0.7 15 4-18 15-29 (80)
132 TIGR02044 CueR Cu(I)-responsiv 57.1 1.7 3.6E-05 25.0 -1.4 22 1-22 1-22 (127)
133 cd01105 HTH_GlnR-like Helix-Tu 56.8 1.6 3.5E-05 23.6 -1.4 20 1-20 2-21 (88)
134 PRK12541 RNA polymerase sigma 56.7 1.6 3.5E-05 25.3 -1.5 28 2-29 130-157 (161)
135 TIGR02859 spore_sigH RNA polym 56.5 2 4.4E-05 25.6 -1.1 21 2-22 167-187 (198)
136 PF06505 XylR_N: Activator of 56.5 3.4 7.4E-05 23.4 -0.1 22 5-26 1-22 (103)
137 PRK03975 tfx putative transcri 56.5 2 4.2E-05 25.7 -1.2 32 2-33 23-54 (141)
138 PRK12523 RNA polymerase sigma 56.4 2 4.3E-05 25.3 -1.2 28 2-29 137-164 (172)
139 PRK06930 positive control sigm 56.3 2 4.3E-05 26.1 -1.2 30 2-31 132-161 (170)
140 PF05331 DUF742: Protein of un 56.3 4.2 9E-05 23.5 0.2 18 3-20 58-75 (114)
141 cd01279 HTH_HspR-like Helix-Tu 56.0 1.6 3.4E-05 24.1 -1.5 22 1-22 2-23 (98)
142 PRK12522 RNA polymerase sigma 55.7 2.6 5.6E-05 24.8 -0.8 28 2-29 137-164 (173)
143 cd04789 HTH_Cfa Helix-Turn-Hel 55.6 1.8 3.9E-05 24.0 -1.4 22 1-22 2-23 (102)
144 PRK08295 RNA polymerase factor 55.2 2.3 5E-05 25.6 -1.0 29 2-30 172-200 (208)
145 cd01282 HTH_MerR-like_sg3 Heli 55.1 1.9 4.1E-05 24.3 -1.3 22 1-22 1-22 (112)
146 PRK12539 RNA polymerase sigma 55.0 2.4 5.3E-05 25.2 -0.9 29 2-30 149-177 (184)
147 cd01109 HTH_YyaN Helix-Turn-He 55.0 2 4.3E-05 24.1 -1.3 21 1-21 1-21 (113)
148 PRK09647 RNA polymerase sigma 54.9 3.1 6.6E-05 25.6 -0.5 30 2-31 156-185 (203)
149 cd04786 HTH_MerR-like_sg7 Heli 54.8 2 4.3E-05 25.1 -1.3 20 1-20 1-20 (131)
150 TIGR02943 Sig70_famx1 RNA poly 54.6 2.5 5.4E-05 25.5 -1.0 31 1-31 148-178 (188)
151 PRK12524 RNA polymerase sigma 54.4 2.4 5.1E-05 25.6 -1.1 30 2-31 154-183 (196)
152 TIGR03001 Sig-70_gmx1 RNA poly 54.4 2.9 6.2E-05 26.6 -0.7 31 2-32 179-209 (244)
153 PRK12545 RNA polymerase sigma 54.4 3.9 8.5E-05 24.8 -0.1 30 2-31 157-186 (201)
154 cd04779 HTH_MerR-like_sg4 Heli 54.3 1.9 4.2E-05 25.3 -1.4 24 1-24 1-24 (134)
155 PRK12546 RNA polymerase sigma 54.0 2.6 5.6E-05 25.5 -1.0 30 2-31 131-160 (188)
156 PRK10227 DNA-binding transcrip 53.9 2.1 4.5E-05 25.1 -1.3 20 1-20 1-20 (135)
157 PRK12511 RNA polymerase sigma 53.7 2.8 6E-05 25.3 -0.9 31 1-31 128-158 (182)
158 PRK09649 RNA polymerase sigma 53.5 2.3 5E-05 25.5 -1.2 21 2-22 148-168 (185)
159 PF07638 Sigma70_ECF: ECF sigm 53.4 2.5 5.3E-05 25.6 -1.1 24 2-25 153-176 (185)
160 PF04967 HTH_10: HTH DNA bindi 53.3 2.7 5.9E-05 21.1 -0.8 17 2-18 25-41 (53)
161 TIGR02054 MerD mercuric resist 52.7 2.2 4.8E-05 24.7 -1.3 22 1-22 4-25 (120)
162 PF07022 Phage_CI_repr: Bacter 52.5 2.5 5.5E-05 21.6 -1.0 22 4-25 16-38 (66)
163 PRK07037 extracytoplasmic-func 52.4 2.7 5.8E-05 24.3 -1.0 21 2-22 127-147 (163)
164 PRK12531 RNA polymerase sigma 52.3 3 6.4E-05 25.1 -0.9 26 2-27 159-184 (194)
165 TIGR03826 YvyF flagellar opero 51.8 2.3 4.9E-05 25.4 -1.4 25 2-26 48-72 (137)
166 cd06170 LuxR_C_like C-terminal 51.8 2.3 4.9E-05 20.1 -1.2 21 2-22 17-37 (57)
167 cd04775 HTH_Cfa-like Helix-Tur 51.8 2.2 4.9E-05 23.6 -1.4 21 2-22 3-23 (102)
168 PRK13919 putative RNA polymera 51.8 3.1 6.6E-05 24.7 -0.9 21 2-22 153-173 (186)
169 PRK06811 RNA polymerase factor 51.8 2.6 5.7E-05 25.2 -1.2 29 2-30 149-177 (189)
170 smart00354 HTH_LACI helix_turn 51.8 2.4 5.1E-05 21.9 -1.2 24 2-25 2-25 (70)
171 PRK09638 RNA polymerase sigma 51.6 3.2 7E-05 24.3 -0.8 21 2-22 144-164 (176)
172 PF13551 HTH_29: Winged helix- 51.5 1.6 3.4E-05 23.7 -2.0 21 2-22 14-34 (112)
173 TIGR02047 CadR-PbrR Cd(II)/Pb( 51.4 2.4 5.1E-05 24.5 -1.4 22 1-22 1-22 (127)
174 cd08306 Death_FADD Fas-associa 51.4 3.5 7.6E-05 22.3 -0.6 18 4-21 17-34 (86)
175 cd01110 HTH_SoxR Helix-Turn-He 51.1 2.4 5.2E-05 24.9 -1.4 22 1-22 2-23 (139)
176 PF02796 HTH_7: Helix-turn-hel 50.3 2.9 6.3E-05 19.8 -0.9 18 2-19 23-40 (45)
177 PF04552 Sigma54_DBD: Sigma-54 49.9 5.4 0.00012 24.2 0.0 18 1-18 50-67 (160)
178 COG2197 CitB Response regulato 49.8 3 6.4E-05 25.9 -1.2 17 4-20 167-183 (211)
179 PF08220 HTH_DeoR: DeoR-like h 49.5 3 6.6E-05 20.8 -1.0 17 2-18 16-32 (57)
180 cd02413 40S_S3_KH K homology R 49.4 7.1 0.00015 21.0 0.4 18 5-22 58-75 (81)
181 COG1595 RpoE DNA-directed RNA 48.9 3 6.6E-05 24.8 -1.2 31 3-33 146-176 (182)
182 PF13936 HTH_38: Helix-turn-he 48.6 2.9 6.3E-05 19.8 -1.1 19 2-20 22-40 (44)
183 PRK11922 RNA polymerase sigma 48.6 3.4 7.4E-05 25.7 -1.0 31 2-32 167-197 (231)
184 PHA01976 helix-turn-helix prot 48.4 3.1 6.7E-05 20.8 -1.1 23 3-25 18-40 (67)
185 PRK12540 RNA polymerase sigma 48.3 3.6 7.8E-05 24.7 -1.0 29 2-30 129-157 (182)
186 PRK11511 DNA-binding transcrip 48.1 2.2 4.8E-05 24.4 -1.8 23 2-24 27-49 (127)
187 PRK08583 RNA polymerase sigma 48.0 3.6 7.8E-05 26.0 -1.0 28 2-29 223-250 (257)
188 PRK04217 hypothetical protein; 47.9 3.2 6.9E-05 23.8 -1.2 30 2-31 60-89 (110)
189 TIGR01950 SoxR redox-sensitive 47.7 2.9 6.3E-05 24.7 -1.4 22 1-22 2-23 (142)
190 PRK09641 RNA polymerase sigma 47.7 3.6 7.7E-05 24.2 -1.0 29 2-30 154-182 (187)
191 cd01107 HTH_BmrR Helix-Turn-He 47.6 3.1 6.7E-05 23.2 -1.2 22 1-22 1-22 (108)
192 TIGR02980 SigBFG RNA polymeras 47.5 3.4 7.3E-05 25.5 -1.2 22 1-22 195-216 (227)
193 PF13542 HTH_Tnp_ISL3: Helix-t 47.4 2.5 5.3E-05 20.2 -1.5 19 3-21 30-48 (52)
194 PRK12525 RNA polymerase sigma 47.4 3.1 6.7E-05 24.4 -1.3 22 2-23 136-157 (168)
195 TIGR02835 spore_sigmaE RNA pol 47.3 3.7 7.9E-05 25.7 -1.1 21 2-22 200-220 (234)
196 PRK09636 RNA polymerase sigma 47.1 3.4 7.5E-05 26.6 -1.2 30 1-30 132-161 (293)
197 PF06322 Phage_NinH: Phage Nin 46.8 3.8 8.3E-05 21.5 -0.8 18 2-19 18-35 (64)
198 PF01418 HTH_6: Helix-turn-hel 46.5 3.9 8.4E-05 21.5 -0.9 18 1-18 35-52 (77)
199 cd04765 HTH_MlrA-like_sg2 Heli 46.5 3 6.5E-05 23.1 -1.4 21 2-22 2-22 (99)
200 PF01710 HTH_Tnp_IS630: Transp 46.4 2.7 5.9E-05 23.9 -1.6 21 2-22 20-40 (119)
201 cd04787 HTH_HMRTR_unk Helix-Tu 46.2 3.2 7E-05 24.0 -1.3 20 1-20 1-20 (133)
202 cd01108 HTH_CueR Helix-Turn-He 46.1 3.3 7.2E-05 23.8 -1.3 22 1-22 1-22 (127)
203 PRK09413 IS2 repressor TnpA; R 46.0 3.3 7.1E-05 23.6 -1.3 20 2-21 31-50 (121)
204 PF07498 Rho_N: Rho terminatio 45.9 9.5 0.00021 18.0 0.5 13 2-14 9-21 (43)
205 PRK11179 DNA-binding transcrip 45.8 3.7 8E-05 24.2 -1.2 16 3-18 26-41 (153)
206 PRK07670 RNA polymerase sigma 45.4 4 8.8E-05 25.7 -1.1 28 2-29 219-246 (251)
207 PRK06704 RNA polymerase factor 45.3 4 8.6E-05 25.9 -1.1 30 2-31 134-163 (228)
208 PF00356 LacI: Bacterial regul 45.2 2.7 5.9E-05 20.4 -1.5 22 3-24 2-23 (46)
209 COG0789 SoxR Predicted transcr 45.1 3.8 8.2E-05 22.9 -1.1 20 1-20 1-20 (124)
210 PRK12544 RNA polymerase sigma 44.9 4.2 9.2E-05 25.0 -1.0 30 2-31 166-195 (206)
211 PF01527 HTH_Tnp_1: Transposas 44.9 1.9 4.2E-05 22.0 -2.2 19 2-20 25-43 (76)
212 cd04784 HTH_CadR-PbrR Helix-Tu 44.7 3.5 7.5E-05 23.6 -1.4 21 1-21 1-21 (127)
213 cd04768 HTH_BmrR-like Helix-Tu 44.6 3.5 7.7E-05 22.6 -1.3 22 2-23 2-23 (96)
214 PF07813 LTXXQ: LTXXQ motif fa 44.4 4 8.6E-05 21.7 -1.1 18 3-20 6-23 (100)
215 PF08452 DNAP_B_exo_N: DNA pol 43.6 7.6 0.00016 16.2 -0.0 8 19-26 7-14 (22)
216 cd04769 HTH_MerR2 Helix-Turn-H 43.4 3.7 8.1E-05 23.2 -1.3 22 1-22 1-22 (116)
217 cd08315 Death_TRAILR_DR4_DR5 D 43.1 5.3 0.00011 22.2 -0.7 16 3-18 22-37 (96)
218 TIGR02960 SigX5 RNA polymerase 43.1 4.6 9.9E-05 26.1 -1.1 28 2-29 160-187 (324)
219 cd04781 HTH_MerR-like_sg6 Heli 43.0 3.8 8.3E-05 23.3 -1.4 22 1-22 1-22 (120)
220 PF13223 DUF4031: Protein of u 42.7 6.9 0.00015 21.5 -0.3 18 2-23 25-42 (83)
221 PF04936 DUF658: Protein of un 42.6 2.5 5.4E-05 26.3 -2.3 31 3-33 17-47 (186)
222 TIGR02043 ZntR Zn(II)-responsi 42.5 3.9 8.5E-05 23.7 -1.4 22 1-22 2-23 (131)
223 PF06971 Put_DNA-bind_N: Putat 42.4 2.2 4.8E-05 21.2 -2.1 15 4-18 32-46 (50)
224 PRK09651 RNA polymerase sigma 42.3 4.9 0.00011 23.7 -1.0 21 2-22 137-157 (172)
225 PF09012 FeoC: FeoC like trans 42.3 3.8 8.3E-05 21.0 -1.3 17 2-18 16-32 (69)
226 cd04770 HTH_HMRTR Helix-Turn-H 42.2 4 8.7E-05 23.1 -1.3 21 1-21 1-21 (123)
227 PRK12527 RNA polymerase sigma 42.0 5 0.00011 23.1 -1.0 21 2-22 123-143 (159)
228 PF11388 DotA: Phagosome traff 42.0 39 0.00085 19.2 2.7 18 16-33 31-48 (105)
229 cd04777 HTH_MerR-like_sg1 Heli 41.9 4 8.7E-05 22.6 -1.3 20 1-20 1-20 (107)
230 PRK12534 RNA polymerase sigma 41.4 6.7 0.00015 23.2 -0.5 21 2-22 155-175 (187)
231 TIGR02957 SigX4 RNA polymerase 41.3 4.7 0.0001 25.9 -1.3 29 2-30 126-154 (281)
232 PRK07408 RNA polymerase sigma 40.9 5 0.00011 25.5 -1.2 29 1-29 220-248 (256)
233 COG4189 Predicted transcriptio 40.6 9.5 0.00021 25.3 0.1 18 1-18 38-55 (308)
234 PRK12528 RNA polymerase sigma 40.4 4.5 9.8E-05 23.4 -1.3 21 2-22 131-151 (161)
235 PRK07122 RNA polymerase sigma 40.3 5.3 0.00011 25.7 -1.2 28 1-28 232-259 (264)
236 cd04785 HTH_CadR-PbrR-like Hel 40.3 4.4 9.6E-05 23.2 -1.4 22 1-22 1-22 (126)
237 cd08316 Death_FAS_TNFRSF6 Deat 39.9 6.8 0.00015 21.9 -0.6 16 3-18 23-38 (97)
238 TIGR02394 rpoS_proteo RNA poly 39.8 5.6 0.00012 25.6 -1.1 30 2-31 244-273 (285)
239 TIGR02479 FliA_WhiG RNA polyme 39.8 5.7 0.00012 24.5 -1.0 22 2-23 193-214 (224)
240 PRK09514 zntR zinc-responsive 39.8 4.5 9.8E-05 23.7 -1.4 22 1-22 2-23 (140)
241 cd00569 HTH_Hin_like Helix-tur 39.6 4.5 9.6E-05 16.4 -1.2 18 3-20 24-41 (42)
242 PRK05657 RNA polymerase sigma 39.5 5.6 0.00012 26.4 -1.1 31 2-32 284-314 (325)
243 cd04782 HTH_BltR Helix-Turn-He 39.5 4.6 9.9E-05 22.1 -1.4 21 2-22 2-22 (97)
244 PRK15411 rcsA colanic acid cap 39.2 6.6 0.00014 24.2 -0.8 18 3-20 155-172 (207)
245 PRK09706 transcriptional repre 39.0 5.7 0.00012 22.8 -1.1 25 3-27 21-45 (135)
246 PRK13890 conjugal transfer pro 38.6 5.4 0.00012 22.9 -1.2 24 2-25 20-43 (120)
247 PRK09415 RNA polymerase factor 38.4 5.7 0.00012 23.6 -1.2 21 2-22 145-165 (179)
248 cd08318 Death_NMPP84 Death dom 38.3 6.3 0.00014 21.3 -0.9 16 4-19 22-37 (86)
249 cd08779 Death_PIDD Death Domai 38.1 7.9 0.00017 21.0 -0.5 22 4-25 17-39 (86)
250 PRK09726 antitoxin HipB; Provi 38.0 5.6 0.00012 21.3 -1.1 23 3-25 28-50 (88)
251 PF00196 GerE: Bacterial regul 37.8 1.6 3.5E-05 21.5 -3.1 24 2-25 20-43 (58)
252 PF14493 HTH_40: Helix-turn-he 37.4 11 0.00024 20.3 -0.0 18 1-18 14-31 (91)
253 cd08784 Death_DRs Death Domain 37.2 7.1 0.00015 20.8 -0.8 22 4-25 15-37 (79)
254 cd04783 HTH_MerR1 Helix-Turn-H 37.2 5.2 0.00011 22.8 -1.4 20 1-20 1-20 (126)
255 KOG4580|consensus 37.2 13 0.00029 21.5 0.3 12 17-28 10-21 (112)
256 PRK11169 leucine-responsive tr 37.1 6.7 0.00014 23.4 -1.0 16 3-18 31-46 (164)
257 TIGR02941 Sigma_B RNA polymera 36.9 6.3 0.00014 24.8 -1.2 26 2-27 223-248 (255)
258 COG2452 Predicted site-specifi 36.9 6 0.00013 25.0 -1.2 27 1-27 2-28 (193)
259 TIGR02984 Sig-70_plancto1 RNA 36.4 6 0.00013 23.2 -1.3 20 1-20 157-176 (189)
260 PF09607 BrkDBD: Brinker DNA-b 36.0 3.5 7.6E-05 21.3 -2.0 17 6-22 31-47 (58)
261 COG1309 AcrR Transcriptional r 36.0 10 0.00023 20.9 -0.2 23 3-25 35-57 (201)
262 COG5264 VTC1 Vacuolar transpor 35.8 15 0.00031 21.8 0.3 12 17-28 25-36 (126)
263 PRK12517 RNA polymerase sigma 35.6 7.5 0.00016 23.4 -1.0 29 2-30 146-174 (188)
264 PRK13749 transcriptional regul 35.4 6 0.00013 23.0 -1.3 20 1-20 4-23 (121)
265 COG3747 Phage terminase, small 35.4 9.5 0.00021 23.4 -0.5 15 1-15 119-133 (160)
266 PRK09643 RNA polymerase sigma 35.2 7.6 0.00016 23.4 -1.0 18 2-19 152-169 (192)
267 COG3655 Predicted transcriptio 35.1 6.8 0.00015 21.1 -1.0 19 1-19 16-34 (73)
268 PRK06288 RNA polymerase sigma 34.6 7.8 0.00017 24.7 -1.0 30 2-31 230-259 (268)
269 TIGR02051 MerR Hg(II)-responsi 34.3 5.6 0.00012 22.8 -1.6 18 3-20 2-19 (124)
270 COG1522 Lrp Transcriptional re 34.2 10 0.00022 21.7 -0.5 17 2-18 24-40 (154)
271 KOG4752|consensus 33.9 27 0.00059 14.8 0.9 7 25-31 2-8 (26)
272 cd08804 Death_ank2 Death domai 33.9 8.4 0.00018 20.8 -0.8 15 4-18 19-33 (84)
273 cd08317 Death_ank Death domain 33.9 8.3 0.00018 20.6 -0.9 16 4-19 19-34 (84)
274 PRK08241 RNA polymerase factor 33.8 7 0.00015 25.5 -1.4 22 1-22 170-191 (339)
275 cd01111 HTH_MerD Helix-Turn-He 33.6 6.6 0.00014 22.1 -1.3 21 2-22 2-22 (107)
276 PRK10100 DNA-binding transcrip 33.5 5.4 0.00012 24.9 -1.8 26 3-28 173-198 (216)
277 COG2944 Predicted transcriptio 32.8 5.7 0.00012 22.7 -1.7 22 5-26 62-83 (104)
278 smart00342 HTH_ARAC helix_turn 32.7 9 0.00019 19.0 -0.8 20 2-21 3-22 (84)
279 PF00424 REV: REV protein (ant 32.6 24 0.00051 19.8 0.8 13 22-34 37-49 (91)
280 cd04776 HTH_GnyR Helix-Turn-He 32.1 7.2 0.00016 22.2 -1.4 20 1-20 1-20 (118)
281 TIGR02393 RpoD_Cterm RNA polym 31.8 8 0.00017 24.2 -1.3 30 2-31 198-227 (238)
282 TIGR02846 spore_sigmaK RNA pol 31.7 8.9 0.00019 23.8 -1.1 20 2-21 196-215 (227)
283 cd08319 Death_RAIDD Death doma 31.6 9.4 0.0002 20.7 -0.9 20 4-23 17-36 (83)
284 TIGR03541 reg_near_HchA LuxR f 31.6 5.4 0.00012 25.0 -2.1 27 3-29 189-215 (232)
285 cd08777 Death_RIP1 Death Domai 31.2 9.6 0.00021 20.7 -0.9 16 4-19 17-32 (86)
286 PF13560 HTH_31: Helix-turn-he 31.1 4.6 0.0001 20.1 -2.1 24 3-26 17-40 (64)
287 PRK15002 redox-sensitivie tran 31.0 7.8 0.00017 23.3 -1.4 22 1-22 12-33 (154)
288 cd04772 HTH_TioE_rpt1 First He 30.9 6.9 0.00015 21.6 -1.5 20 2-21 2-21 (99)
289 PRK13752 putative transcriptio 30.8 7.6 0.00017 23.0 -1.4 20 1-20 8-27 (144)
290 PF06032 DUF917: Protein of un 30.7 23 0.0005 24.0 0.7 12 13-24 267-278 (353)
291 PRK10046 dpiA two-component re 30.7 9.5 0.0002 23.3 -1.1 16 3-18 180-195 (225)
292 COG5566 Uncharacterized conser 30.7 11 0.00025 22.5 -0.7 19 1-19 103-121 (137)
293 TIGR02885 spore_sigF RNA polym 30.6 8.7 0.00019 23.7 -1.3 20 1-20 200-219 (231)
294 PRK05803 sporulation sigma fac 30.5 9.3 0.0002 23.8 -1.1 20 2-21 197-216 (233)
295 PRK10651 transcriptional regul 30.4 6.9 0.00015 22.7 -1.7 25 3-27 173-197 (216)
296 PF04391 DUF533: Protein of un 30.4 11 0.00024 23.5 -0.8 16 3-18 166-181 (188)
297 PF09339 HTH_IclR: IclR helix- 30.3 4.8 0.0001 19.4 -2.0 17 2-18 20-36 (52)
298 TIGR03020 EpsA transcriptional 30.3 6 0.00013 25.5 -2.1 26 3-28 208-233 (247)
299 PF11516 DUF3220: Protein of u 30.3 7.4 0.00016 21.6 -1.4 12 14-25 30-41 (106)
300 PF05344 DUF746: Domain of Unk 29.8 7.7 0.00017 20.5 -1.4 20 3-22 16-35 (65)
301 PRK05911 RNA polymerase sigma 29.7 10 0.00022 24.2 -1.1 21 2-22 223-243 (257)
302 cd01763 Sumo Small ubiquitin-r 29.4 27 0.00058 18.6 0.7 24 5-28 40-63 (87)
303 PHA02535 P terminase ATPase su 29.3 9.9 0.00021 27.7 -1.3 27 3-31 21-47 (581)
304 cd01793 Fubi Fubi ubiquitin-li 29.3 25 0.00054 18.0 0.5 23 5-27 27-49 (74)
305 PRK15369 two component system 29.2 7.6 0.00016 22.2 -1.6 24 3-26 167-190 (211)
306 cd01670 Death Death Domain: a 29.0 9.4 0.0002 19.5 -1.1 21 4-24 14-34 (79)
307 PHA03236 DNA packaging protein 28.9 30 0.00066 20.5 0.9 23 2-24 23-46 (127)
308 PRK10840 transcriptional regul 28.9 10 0.00022 22.8 -1.2 16 4-19 169-184 (216)
309 PRK15482 transcriptional regul 28.7 17 0.00037 23.2 -0.2 18 1-18 35-52 (285)
310 PF12844 HTH_19: Helix-turn-he 28.7 5.1 0.00011 19.8 -2.2 24 2-25 14-37 (64)
311 PF14354 Lar_restr_allev: Rest 28.6 12 0.00026 18.5 -0.7 8 17-26 54-61 (61)
312 PRK10403 transcriptional regul 28.4 7.6 0.00016 22.4 -1.7 24 4-27 172-195 (215)
313 PF09292 Neil1-DNA_bind: Endon 28.3 22 0.00049 16.8 0.2 6 18-23 27-32 (39)
314 PF01978 TrmB: Sugar-specific 28.3 6.2 0.00014 19.9 -1.9 17 2-18 24-40 (68)
315 TIGR02395 rpoN_sigma RNA polym 28.0 25 0.00055 24.5 0.5 18 1-18 319-336 (429)
316 PRK10430 DNA-binding transcrip 27.7 14 0.00031 22.6 -0.7 20 3-22 181-200 (239)
317 cd01798 parkin_N amino-termina 27.6 22 0.00047 17.9 0.1 22 5-26 27-48 (70)
318 PRK15043 transcriptional regul 27.4 10 0.00022 24.6 -1.4 21 1-21 4-24 (243)
319 PRK11475 DNA-binding transcrip 27.3 9.4 0.0002 23.7 -1.5 17 3-19 152-168 (207)
320 PF13412 HTH_24: Winged helix- 27.2 7.3 0.00016 18.2 -1.6 16 3-18 20-35 (48)
321 cd04778 HTH_MerR-like_sg2 Heli 26.9 11 0.00023 24.0 -1.4 20 1-20 2-21 (219)
322 PRK11557 putative DNA-binding 26.7 20 0.00043 22.7 -0.2 18 1-18 31-48 (278)
323 PF00440 TetR_N: Bacterial reg 26.7 5.8 0.00013 18.7 -2.1 23 2-24 18-40 (47)
324 TIGR00122 birA_repr_reg BirA b 26.7 11 0.00024 19.0 -1.1 16 3-18 16-31 (69)
325 PF04760 IF2_N: Translation in 26.6 7.3 0.00016 19.0 -1.7 15 3-17 6-20 (54)
326 PRK11337 DNA-binding transcrip 26.5 21 0.00045 22.9 -0.1 18 1-18 47-64 (292)
327 PRK11302 DNA-binding transcrip 26.3 19 0.00042 22.7 -0.2 18 1-18 35-52 (284)
328 PRK05572 sporulation sigma fac 26.0 13 0.00027 23.5 -1.2 20 1-20 219-238 (252)
329 PF04293 SpoVR: SpoVR like pro 25.8 31 0.00066 24.3 0.6 21 2-22 14-34 (426)
330 cd01796 DDI1_N DNA damage indu 25.7 29 0.00063 17.7 0.4 23 5-27 28-50 (71)
331 TIGR03613 RutR pyrimidine util 25.6 13 0.00029 22.0 -1.0 23 3-25 31-53 (202)
332 cd01803 Ubiquitin Ubiquitin. U 25.6 26 0.00057 17.5 0.2 21 5-25 29-49 (76)
333 PRK13870 transcriptional regul 25.5 8.4 0.00018 24.3 -2.0 24 4-27 192-215 (234)
334 PF14549 P22_Cro: DNA-binding 25.4 7.8 0.00017 19.9 -1.8 27 3-31 12-38 (60)
335 TIGR02612 mob_myst_A mobile my 25.4 13 0.00029 22.3 -1.0 24 2-25 40-63 (150)
336 smart00550 Zalpha Z-DNA-bindin 25.4 15 0.00033 18.8 -0.7 16 3-18 25-40 (68)
337 PRK09975 DNA-binding transcrip 25.3 15 0.00033 21.9 -0.8 24 3-26 34-57 (213)
338 PF05119 Terminase_4: Phage te 25.1 23 0.00049 19.0 -0.1 14 2-15 72-85 (100)
339 PRK06424 transcription factor; 24.8 14 0.0003 22.1 -1.1 25 3-27 100-124 (144)
340 PRK05932 RNA polymerase factor 24.8 31 0.00066 24.3 0.5 18 1-18 344-361 (455)
341 cd01769 UBL Ubiquitin-like dom 24.5 30 0.00065 16.7 0.3 20 5-24 26-45 (69)
342 PRK09635 sigI RNA polymerase s 24.1 13 0.00029 24.2 -1.3 26 2-27 136-161 (290)
343 PF13730 HTH_36: Helix-turn-he 24.0 12 0.00026 17.9 -1.2 18 3-20 28-45 (55)
344 PF08784 RPA_C: Replication pr 23.9 11 0.00023 20.6 -1.6 17 2-18 67-83 (102)
345 cd08805 Death_ank1 Death domai 23.6 18 0.00039 19.7 -0.7 15 4-18 19-33 (84)
346 PF04539 Sigma70_r3: Sigma-70 23.6 8.9 0.00019 19.7 -1.9 17 3-19 23-39 (78)
347 PF08671 SinI: Anti-repressor 23.3 9.7 0.00021 17.0 -1.5 19 2-20 7-25 (30)
348 PTZ00044 ubiquitin; Provisiona 23.3 28 0.0006 17.7 0.0 23 5-27 29-51 (76)
349 PF11976 Rad60-SLD: Ubiquitin- 23.2 27 0.00058 17.5 -0.0 24 4-27 28-52 (72)
350 PRK09191 two-component respons 23.0 17 0.00037 22.2 -0.9 21 2-22 106-126 (261)
351 COG1737 RpiR Transcriptional r 23.0 20 0.00044 23.2 -0.6 17 2-18 38-54 (281)
352 smart00344 HTH_ASNC helix_turn 22.9 18 0.0004 19.5 -0.8 16 3-18 20-35 (108)
353 TIGR02392 rpoH_proteo alternat 22.8 16 0.00034 23.4 -1.2 21 2-22 238-258 (270)
354 TIGR03624 putative hydrolase. 22.4 19 0.00041 24.5 -0.9 30 2-31 140-169 (345)
355 PRK06596 RNA polymerase factor 22.4 18 0.00039 23.5 -1.0 19 2-20 250-268 (284)
356 PF12793 SgrR_N: Sugar transpo 22.4 19 0.00042 20.5 -0.7 17 2-18 21-37 (115)
357 PRK07500 rpoH2 RNA polymerase 22.3 17 0.00036 23.7 -1.1 28 2-29 247-274 (289)
358 COG1318 Predicted transcriptio 22.3 18 0.00039 22.7 -0.9 19 2-20 63-81 (182)
359 PRK13719 conjugal transfer tra 22.3 20 0.00044 23.0 -0.7 17 3-19 161-177 (217)
360 PRK10360 DNA-binding transcrip 22.0 13 0.00028 21.4 -1.6 25 3-27 155-179 (196)
361 cd04790 HTH_Cfa-like_unk Helix 21.9 15 0.00032 22.3 -1.4 19 2-20 3-21 (172)
362 COG3149 PulM Type II secretory 21.9 37 0.00081 21.3 0.4 14 10-23 122-135 (181)
363 PF09301 DUF1970: Domain of un 21.7 18 0.00039 20.3 -0.9 11 17-27 19-29 (117)
364 PRK05863 sulfur carrier protei 21.6 96 0.0021 15.5 1.9 29 2-30 17-48 (65)
365 cd00419 Ferrochelatase_C Ferro 21.6 40 0.00088 19.6 0.5 21 5-25 49-69 (135)
366 PRK15201 fimbriae regulatory p 21.6 21 0.00045 22.7 -0.8 17 3-19 151-167 (198)
367 smart00420 HTH_DEOR helix_turn 21.5 19 0.00041 16.4 -0.8 18 2-19 16-33 (53)
368 PRK09943 DNA-binding transcrip 21.4 18 0.00038 21.8 -1.1 22 3-24 23-44 (185)
369 PF04046 PSP: PSP; InterPro: 21.3 27 0.00058 17.3 -0.2 19 4-22 7-25 (48)
370 cd01806 Nedd8 Nebb8-like ubiq 21.3 48 0.001 16.5 0.7 22 5-26 29-50 (76)
371 PRK09935 transcriptional regul 21.2 14 0.0003 21.4 -1.6 25 3-27 167-191 (210)
372 PRK10281 hypothetical protein; 21.0 31 0.00068 22.6 -0.1 16 2-17 34-49 (299)
373 TIGR03883 DUF2342_F420 unchara 21.0 21 0.00046 24.3 -0.8 30 2-31 144-173 (346)
374 TIGR02997 Sig70-cyanoRpoD RNA 21.0 20 0.00044 23.3 -1.0 19 2-20 271-289 (298)
375 COG3413 Predicted DNA binding 20.9 23 0.00049 21.9 -0.7 26 2-29 180-205 (215)
376 cd08311 Death_p75NR Death doma 20.9 18 0.0004 19.3 -1.0 17 4-20 19-35 (77)
377 PHA00542 putative Cro-like pro 20.9 15 0.00033 19.5 -1.3 23 2-24 33-55 (82)
378 PF00531 Death: Death domain; 20.8 14 0.00031 18.8 -1.4 17 4-20 16-32 (83)
379 PF13693 HTH_35: Winged helix- 20.8 18 0.0004 19.5 -1.0 26 2-27 17-42 (78)
380 PRK11303 DNA-binding transcrip 20.8 24 0.00052 22.4 -0.6 24 1-24 1-24 (328)
381 PF09862 DUF2089: Protein of u 20.7 22 0.00049 20.6 -0.7 17 2-18 51-67 (113)
382 PRK10668 DNA-binding transcrip 20.7 21 0.00046 21.4 -0.8 24 3-26 34-57 (215)
383 COG0384 Predicted epimerase, P 20.6 33 0.00073 22.8 0.0 15 2-16 35-49 (291)
384 cd08803 Death_ank3 Death domai 20.5 24 0.00052 19.1 -0.6 16 4-19 19-34 (84)
385 PF12840 HTH_20: Helix-turn-he 20.4 11 0.00025 18.6 -1.8 16 2-17 26-41 (61)
386 PRK08215 sporulation sigma fac 20.4 19 0.00041 22.8 -1.1 19 2-20 227-245 (258)
387 PF15599 Imm38: Immunity prote 20.4 49 0.0011 19.0 0.7 21 2-22 6-26 (124)
388 PF10846 DUF2722: Protein of u 20.2 31 0.00067 24.1 -0.2 21 1-21 88-108 (416)
389 PF02567 PhzC-PhzF: Phenazine 20.2 21 0.00046 22.6 -1.0 14 2-15 27-40 (281)
No 1
>KOG0489|consensus
Probab=99.66 E-value=1.9e-17 Score=106.23 Aligned_cols=35 Identities=60% Similarity=0.880 Sum_probs=31.7
Q ss_pred hhhhcCCCCCccceeeccccchhHHHHHhhhhccC
Q psy12003 4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHKMASMN 38 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~~~ 38 (61)
.|||..|+|+|+|||||||||||||||..+.....
T Consensus 190 iEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 190 IEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred HHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 48999999999999999999999999998866654
No 2
>KOG0487|consensus
Probab=99.62 E-value=7.9e-17 Score=105.49 Aligned_cols=32 Identities=53% Similarity=0.674 Sum_probs=29.3
Q ss_pred hhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003 4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA 35 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~ 35 (61)
.|||+.|||||+||||||||||+|.||..+..
T Consensus 266 ~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 266 LELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred HHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 48999999999999999999999999998633
No 3
>KOG0848|consensus
Probab=99.60 E-value=1.8e-16 Score=102.39 Aligned_cols=32 Identities=44% Similarity=0.577 Sum_probs=29.3
Q ss_pred hhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003 4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA 35 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~ 35 (61)
.|||..|+|+|+||||||||||||.||..+.+
T Consensus 230 SELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 230 SELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred HHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 58999999999999999999999999986654
No 4
>KOG0850|consensus
Probab=99.59 E-value=5e-16 Score=98.38 Aligned_cols=36 Identities=42% Similarity=0.473 Sum_probs=32.3
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHhhhhcc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMASM 37 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~~ 37 (61)
|=+|||+.||||.+||||||||||.|.||..+.+..
T Consensus 151 ERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~ 186 (245)
T KOG0850|consen 151 ERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSG 186 (245)
T ss_pred HHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCC
Confidence 568999999999999999999999999999885443
No 5
>KOG0488|consensus
Probab=99.59 E-value=4.7e-16 Score=101.97 Aligned_cols=31 Identities=39% Similarity=0.678 Sum_probs=29.0
Q ss_pred hhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003 4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHKM 34 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~ 34 (61)
++||+.||||++|||+||||||+||||+...
T Consensus 203 ~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 203 IELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred HHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 6899999999999999999999999999654
No 6
>KOG0844|consensus
Probab=99.58 E-value=8.3e-17 Score=105.79 Aligned_cols=34 Identities=35% Similarity=0.453 Sum_probs=30.3
Q ss_pred hhhhcCCCCCccceeeccccchhHHHHHhhhhcc
Q psy12003 4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHKMASM 37 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~~ 37 (61)
-|||.+|||+|++|||||||||+|.|||.....+
T Consensus 212 cELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaW 245 (408)
T KOG0844|consen 212 CELAAALNLPETTIKVWFQNRRMKDKRQRLAMAW 245 (408)
T ss_pred hhHHHhhCCCcceeehhhhhchhhhhhhhhhccC
Confidence 3899999999999999999999999999765444
No 7
>KOG0842|consensus
Probab=99.57 E-value=1.1e-15 Score=100.19 Aligned_cols=40 Identities=35% Similarity=0.474 Sum_probs=34.6
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHhhhhccCccC
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMASMNVIP 41 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~~~~~~ 41 (61)
|=.+||..|+||++||||||||||.|.||++..+......
T Consensus 182 ERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~ 221 (307)
T KOG0842|consen 182 EREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALL 221 (307)
T ss_pred hHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhccc
Confidence 3468999999999999999999999999998877665533
No 8
>KOG0485|consensus
Probab=99.50 E-value=2.7e-15 Score=94.96 Aligned_cols=32 Identities=44% Similarity=0.659 Sum_probs=28.9
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK 33 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~ 33 (61)
|=+.||++|.|||+||||||||||.||||+-.
T Consensus 133 eRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 133 ERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred HHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 44679999999999999999999999999944
No 9
>KOG0484|consensus
Probab=99.50 E-value=2.4e-15 Score=86.15 Aligned_cols=32 Identities=34% Similarity=0.551 Sum_probs=29.4
Q ss_pred hhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003 4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA 35 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~ 35 (61)
.|||.+++|||.+|||||||||+|.||+++..
T Consensus 48 EEiA~kidLTEARVQVWFQNRRAKfRKQEr~a 79 (125)
T KOG0484|consen 48 EEIALKIDLTEARVQVWFQNRRAKFRKQERAA 79 (125)
T ss_pred HHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHH
Confidence 58999999999999999999999999997743
No 10
>KOG0843|consensus
Probab=99.47 E-value=9.7e-15 Score=89.96 Aligned_cols=33 Identities=33% Similarity=0.490 Sum_probs=29.9
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM 34 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~ 34 (61)
|=.+||+.|+|+|+||||||||||.|.||....
T Consensus 131 eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 131 ERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred HHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 446899999999999999999999999998664
No 11
>KOG0492|consensus
Probab=99.47 E-value=1.3e-14 Score=91.25 Aligned_cols=33 Identities=39% Similarity=0.488 Sum_probs=30.0
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM 34 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~ 34 (61)
|=+|++..|.|||+||||||||||+|.||.+..
T Consensus 173 EraefSsSL~LTeTqVKIWFQNRRAKaKRlQea 205 (246)
T KOG0492|consen 173 ERAEFSSSLELTETQVKIWFQNRRAKAKRLQEA 205 (246)
T ss_pred HHHhhhhhhhhhhhheehhhhhhhHHHHHHHHH
Confidence 457899999999999999999999999998663
No 12
>KOG0491|consensus
Probab=99.45 E-value=2e-14 Score=87.76 Aligned_cols=35 Identities=40% Similarity=0.545 Sum_probs=32.2
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHhhhhc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMAS 36 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~ 36 (61)
|+.|||..|+|+|+|||.||||||+|.||+.+...
T Consensus 129 e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 129 ERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred HHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 67899999999999999999999999999987544
No 13
>KOG0483|consensus
Probab=99.39 E-value=2.7e-14 Score=89.07 Aligned_cols=32 Identities=31% Similarity=0.590 Sum_probs=28.7
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK 33 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~ 33 (61)
+...||..|||.++||.||||||||+||.++.
T Consensus 79 ~K~~LAk~LgL~pRQVavWFQNRRARwK~kql 110 (198)
T KOG0483|consen 79 RKKKLAKELGLQPRQVAVWFQNRRARWKTKQL 110 (198)
T ss_pred HHHHHHHhhCCChhHHHHHHhhccccccchhh
Confidence 34689999999999999999999999998843
No 14
>KOG2251|consensus
Probab=99.39 E-value=1.8e-13 Score=86.32 Aligned_cols=32 Identities=22% Similarity=0.437 Sum_probs=29.8
Q ss_pred hhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003 4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA 35 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~ 35 (61)
.|||.+|||+|.+|||||+|||+|+|++++..
T Consensus 68 EelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 68 EELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred HHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 58999999999999999999999999998864
No 15
>KOG0494|consensus
Probab=99.34 E-value=1.9e-13 Score=88.48 Aligned_cols=32 Identities=38% Similarity=0.642 Sum_probs=28.7
Q ss_pred hhcCCCCCccceeeccccchhHHHHHhhhhcc
Q psy12003 6 DKNPPRGTERQIKIWFQNRRMKWKKEHKMASM 37 (61)
Q Consensus 6 LA~~l~Lte~~VqvWFqNrRak~kr~~~~~~~ 37 (61)
||.++.|+|.+|+|||||||+||||.++.-..
T Consensus 174 la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~ 205 (332)
T KOG0494|consen 174 LADKTELPEDRIQVWFQNRRAKWRKTEKRWGG 205 (332)
T ss_pred HhhhccCchhhhhHHhhhhhHHhhhhhhhcCc
Confidence 68899999999999999999999999886443
No 16
>KOG0847|consensus
Probab=99.27 E-value=7.9e-13 Score=84.07 Aligned_cols=32 Identities=44% Similarity=0.783 Sum_probs=29.4
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK 33 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~ 33 (61)
|-++||..+|++|.+|+|||||||.||||+..
T Consensus 196 ~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 196 DRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred hHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 45789999999999999999999999999854
No 17
>KOG4577|consensus
Probab=99.17 E-value=7.4e-12 Score=82.19 Aligned_cols=34 Identities=32% Similarity=0.385 Sum_probs=29.8
Q ss_pred hhhhcCCCCCccceeeccccchhHHHHHhhhhcc
Q psy12003 4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHKMASM 37 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~~ 37 (61)
..|+.++||+.++|||||||||||.||..+..+.
T Consensus 198 EQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T KOG4577|consen 198 EQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T ss_pred HHhhhccCcceeehhhhhhhhhHHHHhhhhhcch
Confidence 3689999999999999999999999999775443
No 18
>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=99.16 E-value=1.2e-12 Score=66.48 Aligned_cols=29 Identities=48% Similarity=0.486 Sum_probs=27.3
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
++.+||..|||++.+|++||+|||.++|+
T Consensus 29 ~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 29 EREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp HHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred ccccccccccccccccccCHHHhHHHhCc
Confidence 57899999999999999999999999986
No 19
>KOG0493|consensus
Probab=99.07 E-value=1.8e-11 Score=79.53 Aligned_cols=30 Identities=43% Similarity=0.509 Sum_probs=27.3
Q ss_pred hhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003 4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHK 33 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~ 33 (61)
.+||.+|+|.|.||||||||+|+|.||--.
T Consensus 277 Q~La~ELgLNEsQIKIWFQNKRAKiKKsTg 306 (342)
T KOG0493|consen 277 QELAQELGLNESQIKIWFQNKRAKIKKSTG 306 (342)
T ss_pred HHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence 479999999999999999999999998644
No 20
>KOG0486|consensus
Probab=99.06 E-value=7.4e-11 Score=77.81 Aligned_cols=33 Identities=30% Similarity=0.585 Sum_probs=30.0
Q ss_pred hhhhcCCCCCccceeeccccchhHHHHHhhhhc
Q psy12003 4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHKMAS 36 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~ 36 (61)
.|||..++|||.+|+|||.|||+||||.++...
T Consensus 143 EEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 143 EEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 488999999999999999999999999987544
No 21
>KOG3802|consensus
Probab=99.00 E-value=1.6e-10 Score=77.89 Aligned_cols=32 Identities=22% Similarity=0.376 Sum_probs=30.8
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK 33 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~ 33 (61)
||.+||.+|+|...+|+|||+|||.|.||...
T Consensus 323 EIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 323 EITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred HHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 89999999999999999999999999999876
No 22
>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=98.99 E-value=2e-11 Score=61.79 Aligned_cols=30 Identities=47% Similarity=0.593 Sum_probs=27.7
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
++.+||..+||++.+|++||+|||.+.++.
T Consensus 29 ~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 29 EREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred HHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 678999999999999999999999998763
No 23
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.97 E-value=1.4e-10 Score=70.21 Aligned_cols=32 Identities=28% Similarity=0.395 Sum_probs=28.8
Q ss_pred hhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM 34 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~ 34 (61)
-.+|+..||++++-|||||||||++.|+....
T Consensus 81 r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 81 RIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred HHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 35799999999999999999999999998654
No 24
>KOG0490|consensus
Probab=98.94 E-value=5.4e-10 Score=69.11 Aligned_cols=30 Identities=37% Similarity=0.512 Sum_probs=27.9
Q ss_pred hhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003 4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHK 33 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~ 33 (61)
.+||..++++|.+|||||||||+||+++..
T Consensus 91 ~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 91 ECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred HHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 368999999999999999999999999875
No 25
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=98.89 E-value=5.3e-11 Score=59.90 Aligned_cols=28 Identities=46% Similarity=0.741 Sum_probs=25.6
Q ss_pred chhhhhcCCCCCccceeeccccchhHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWK 29 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k 29 (61)
++.+||..+||+..+|+.||+|||++.+
T Consensus 29 ~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 29 EREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred HHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 5789999999999999999999998753
No 26
>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=98.82 E-value=7.3e-10 Score=57.47 Aligned_cols=24 Identities=17% Similarity=0.311 Sum_probs=22.1
Q ss_pred chhhhhcCCCCCccceeeccccch
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
+..+||..|||++.+|||||||.+
T Consensus 34 ~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 34 EVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred HHHHHHHHhCCCHHHeeeecccCC
Confidence 578999999999999999999975
No 27
>KOG0849|consensus
Probab=98.46 E-value=6.7e-08 Score=64.60 Aligned_cols=30 Identities=33% Similarity=0.769 Sum_probs=28.3
Q ss_pred hhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003 4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHK 33 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~ 33 (61)
.+||.+++|+|.+|+|||+|||++|+|+..
T Consensus 207 e~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 207 ETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred HHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 579999999999999999999999999984
No 28
>KOG0775|consensus
Probab=98.23 E-value=6.7e-07 Score=58.47 Aligned_cols=31 Identities=23% Similarity=0.258 Sum_probs=27.2
Q ss_pred hhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRRMKWKKEHK 33 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~ 33 (61)
=-|||.++||+.+||-.||+|||.+.|-...
T Consensus 206 KReLA~aTgLt~tQVsNWFKNRRQRDRa~~a 236 (304)
T KOG0775|consen 206 KRELAEATGLTITQVSNWFKNRRQRDRAAAA 236 (304)
T ss_pred HHHHHHHhCCchhhhhhhhhhhhhhhhhccc
Confidence 3589999999999999999999999985433
No 29
>KOG1168|consensus
Probab=98.17 E-value=7.8e-07 Score=58.88 Aligned_cols=34 Identities=21% Similarity=0.358 Sum_probs=30.4
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA 35 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~ 35 (61)
.|+-+|.+|+|...+|+|||+|.|.|.||.....
T Consensus 338 kIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa 371 (385)
T KOG1168|consen 338 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSA 371 (385)
T ss_pred HHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhh
Confidence 4788999999999999999999999999976543
No 30
>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=97.75 E-value=8.9e-07 Score=42.70 Aligned_cols=26 Identities=23% Similarity=0.311 Sum_probs=22.6
Q ss_pred chhhhhcCCCCCccceeeccccchhH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMK 27 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak 27 (61)
|..+||..+||+..||..||-|.|.+
T Consensus 15 ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 15 EKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 56789999999999999999998864
No 31
>KOG0490|consensus
Probab=97.41 E-value=5.1e-05 Score=46.84 Aligned_cols=30 Identities=37% Similarity=0.609 Sum_probs=27.5
Q ss_pred hhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003 4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHK 33 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~ 33 (61)
.+|+..+++++..|+|||||+|++.++...
T Consensus 184 ~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 184 EQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred HHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 578999999999999999999999998765
No 32
>KOG0774|consensus
Probab=96.46 E-value=0.0024 Score=42.06 Aligned_cols=30 Identities=27% Similarity=0.386 Sum_probs=27.6
Q ss_pred hhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRRMKWKKEH 32 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrRak~kr~~ 32 (61)
=.|||.+.|++-.||-.||.|.|-++||..
T Consensus 221 K~eLAkqCnItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 221 KEELAKQCNITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHHHHHHcCceehhhccccccceeehhhhh
Confidence 368999999999999999999999999873
No 33
>KOG1146|consensus
Probab=95.86 E-value=0.0059 Score=46.96 Aligned_cols=34 Identities=32% Similarity=0.389 Sum_probs=29.2
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA 35 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~ 35 (61)
++..|-..++|+.+.|+|||||-|+|.++.....
T Consensus 932 ~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 932 ECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred HHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence 4667788899999999999999999999986633
No 34
>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=94.54 E-value=0.0048 Score=32.12 Aligned_cols=28 Identities=25% Similarity=0.471 Sum_probs=21.6
Q ss_pred CchhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
|.+.+||.+||+++.+|+.| -.+.+|..
T Consensus 23 i~lkdIA~~Lgvs~~tIr~W--K~~dkW~~ 50 (60)
T PF10668_consen 23 IKLKDIAEKLGVSESTIRKW--KSRDKWDE 50 (60)
T ss_pred ccHHHHHHHHCCCHHHHHHH--hhhcchhh
Confidence 45789999999999999998 33444544
No 35
>KOG3623|consensus
Probab=94.14 E-value=0.012 Score=43.46 Aligned_cols=33 Identities=12% Similarity=0.152 Sum_probs=29.5
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM 34 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~ 34 (61)
||..+|.+.||+...|++||++++++...-++.
T Consensus 585 elskia~qvglp~~vvk~wfE~~~a~e~sv~rs 617 (1007)
T KOG3623|consen 585 ELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERS 617 (1007)
T ss_pred HHHHHHHHhcccHHHHHHHHHhhhhhhhhhccC
Confidence 688899999999999999999999998876653
No 36
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=93.87 E-value=0.0049 Score=31.72 Aligned_cols=24 Identities=25% Similarity=0.403 Sum_probs=18.8
Q ss_pred chhhhhcCCCCCccceeeccccch
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
.|-+|..+.+|+..+|+.||-.|.
T Consensus 27 DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 27 DLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp HHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHCCCHHHHHHHHHHhc
Confidence 477899999999999999997553
No 37
>KOG0773|consensus
Probab=92.06 E-value=0.051 Score=35.90 Aligned_cols=28 Identities=21% Similarity=0.264 Sum_probs=24.3
Q ss_pred hhhcCCCCCccceeeccccchhHHHHHh
Q psy12003 5 RDKNPPRGTERQIKIWFQNRRMKWKKEH 32 (61)
Q Consensus 5 eLA~~l~Lte~~VqvWFqNrRak~kr~~ 32 (61)
.||.++||+-.+|-.||-|.|-+..+..
T Consensus 274 ~La~~TGLs~~Qv~NWFINaR~R~w~p~ 301 (342)
T KOG0773|consen 274 MLAKQTGLSRPQVSNWFINARVRLWKPM 301 (342)
T ss_pred ccchhcCCCcccCCchhhhcccccCCch
Confidence 5899999999999999999988765543
No 38
>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=89.94 E-value=0.035 Score=26.43 Aligned_cols=24 Identities=0% Similarity=-0.101 Sum_probs=20.2
Q ss_pred CchhhhhcCCCCCccceeeccccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNR 24 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNr 24 (61)
|-+.|+|..+|+++.+|+.|.++.
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCC
Confidence 457899999999999999996543
No 39
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=87.48 E-value=0.058 Score=27.50 Aligned_cols=21 Identities=0% Similarity=-0.064 Sum_probs=18.6
Q ss_pred CchhhhhcCCCCCccceeecc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWF 21 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWF 21 (61)
|.+.|+|..+|++..+|+.|-
T Consensus 1 yti~eva~~~gvs~~tlr~y~ 21 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYE 21 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHH
T ss_pred CcHHHHHHHHCcCHHHHHHHH
Confidence 467899999999999999983
No 40
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=86.28 E-value=0.1 Score=34.30 Aligned_cols=27 Identities=30% Similarity=0.464 Sum_probs=23.8
Q ss_pred CchhhhhcCCCCCccceeeccccchhHHH
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRMKWK 29 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~k 29 (61)
|-+.+||.++|+++.+|+-| -||..|.
T Consensus 20 mk~~dIAeklGvspntiksW--Krr~gWs 46 (279)
T COG5484 20 MKLKDIAEKLGVSPNTIKSW--KRRDGWS 46 (279)
T ss_pred ccHHHHHHHhCCChHHHHHH--HHhcCCC
Confidence 66899999999999999999 5688883
No 41
>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=85.86 E-value=0.11 Score=26.64 Aligned_cols=28 Identities=14% Similarity=0.284 Sum_probs=21.7
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
-+.|+|..||++..+|.-|-+ |.+|...
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~--r~~W~~~ 42 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD--RYKWDEL 42 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH--hhCcccc
Confidence 468999999999999999943 5555443
No 42
>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=85.57 E-value=0.094 Score=24.37 Aligned_cols=26 Identities=4% Similarity=0.216 Sum_probs=21.4
Q ss_pred CchhhhhcCCCCCccceeeccccchh
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRM 26 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRa 26 (61)
+.+.|+|..+|++..+|.-|.++...
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 45789999999999999999775543
No 43
>KOG2252|consensus
Probab=83.10 E-value=0.18 Score=36.05 Aligned_cols=25 Identities=12% Similarity=-0.028 Sum_probs=21.9
Q ss_pred hhhhcCCCCCccceeeccccchhHH
Q psy12003 4 LRDKNPPRGTERQIKIWFQNRRMKW 28 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvWFqNrRak~ 28 (61)
.-|+.+|||.-++|..||-|-|.+.
T Consensus 451 ~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 451 ETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred HHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 3579999999999999999987764
No 44
>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=82.04 E-value=0.19 Score=27.04 Aligned_cols=23 Identities=9% Similarity=0.029 Sum_probs=19.8
Q ss_pred CchhhhhcCCCCCccceeecccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQN 23 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqN 23 (61)
|...|+|..+|+|+..|+.|+.+
T Consensus 33 lS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 33 KTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred CCHHHHHHHHCcCHHHHHHHHhc
Confidence 34679999999999999998774
No 45
>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=81.88 E-value=0.13 Score=25.14 Aligned_cols=22 Identities=9% Similarity=-0.037 Sum_probs=17.4
Q ss_pred chhhhhcCCCCCccceeecccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQN 23 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqN 23 (61)
...|+|..+|+++..|+.|.+.
T Consensus 28 s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 28 SYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp -HHHHHHHCTS-HHHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 4679999999999999988763
No 46
>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=80.88 E-value=0.19 Score=25.74 Aligned_cols=22 Identities=5% Similarity=0.007 Sum_probs=19.1
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
+.+.|+|+.+|++..+++-|.+
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 3578999999999999998855
No 47
>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=80.41 E-value=0.24 Score=25.24 Aligned_cols=22 Identities=0% Similarity=-0.047 Sum_probs=19.1
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
+.+.|+|..+|++..+++-|-+
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~ 22 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEK 22 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4578999999999999998855
No 48
>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=79.02 E-value=0.14 Score=23.80 Aligned_cols=22 Identities=0% Similarity=-0.114 Sum_probs=17.8
Q ss_pred chhhhhcCCCCCccceeecccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQN 23 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqN 23 (61)
...++|..+|+++.+|..|...
T Consensus 28 ~~~~ia~~~~~s~~~i~~~~~~ 49 (55)
T cd06171 28 SYEEIAEILGISRSTVRQRLHR 49 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 4578899999999999877654
No 49
>PF13518 HTH_28: Helix-turn-helix domain
Probab=78.71 E-value=0.25 Score=23.64 Aligned_cols=20 Identities=5% Similarity=0.057 Sum_probs=17.8
Q ss_pred hhhhhcCCCCCccceeeccc
Q psy12003 3 LLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFq 22 (61)
+.++|..+|++..+|.-|.+
T Consensus 15 ~~~~a~~~gis~~tv~~w~~ 34 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIK 34 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHH
Confidence 57899999999999999965
No 50
>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=77.76 E-value=0.29 Score=22.74 Aligned_cols=25 Identities=0% Similarity=-0.051 Sum_probs=20.4
Q ss_pred CchhhhhcCCCCCccceeeccccch
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
|.+.|+|..+|++.++|.-|.++.+
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcCC
Confidence 4678999999999999988875543
No 51
>PRK10072 putative transcriptional regulator; Provisional
Probab=77.55 E-value=0.41 Score=26.86 Aligned_cols=25 Identities=12% Similarity=-0.016 Sum_probs=21.7
Q ss_pred hhhhhcCCCCCccceeeccccchhH
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRRMK 27 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrRak 27 (61)
-.+||..+|++...|.-|.+.+|..
T Consensus 49 Q~elA~~lGvS~~TVs~WE~G~r~P 73 (96)
T PRK10072 49 IDDFARVLGVSVAMVKEWESRRVKP 73 (96)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 4689999999999999999988754
No 52
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=76.47 E-value=0.39 Score=27.61 Aligned_cols=26 Identities=8% Similarity=-0.092 Sum_probs=20.5
Q ss_pred CchhhhhcCCCCCccceeeccccchh
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRM 26 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRa 26 (61)
+.+.|+|..+|+++.+|+.+...-+.
T Consensus 123 ~s~~EIA~~l~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 123 KTMGEIALETEMTYYQVRWIYRQALE 148 (154)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35789999999999999987654333
No 53
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=76.07 E-value=0.59 Score=28.20 Aligned_cols=29 Identities=3% Similarity=-0.004 Sum_probs=22.5
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
...|+|..||+++..|+++...-|.+-|+
T Consensus 160 s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 160 TYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred CHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 46799999999999999887655544444
No 54
>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=76.02 E-value=0.39 Score=26.55 Aligned_cols=21 Identities=14% Similarity=0.151 Sum_probs=18.7
Q ss_pred CchhhhhcCCCCCccceeecc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWF 21 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWF 21 (61)
|.|.|+|..+|++..+|+-|=
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye 21 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYL 21 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 678999999999999998873
No 55
>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=75.81 E-value=0.43 Score=24.07 Aligned_cols=17 Identities=29% Similarity=0.180 Sum_probs=14.1
Q ss_pred chhhhhcCCCCCcccee
Q psy12003 2 NLLRDKNPPRGTERQIK 18 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~Vq 18 (61)
.+.|||..+|+|+++|+
T Consensus 21 ~~~ela~~l~~S~rti~ 37 (59)
T PF08280_consen 21 TLKELAKKLNISERTIK 37 (59)
T ss_dssp BHHHHHHHCTS-HHHHH
T ss_pred cHHHHHHHHCCCHHHHH
Confidence 57899999999999886
No 56
>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=75.48 E-value=0.5 Score=26.92 Aligned_cols=26 Identities=0% Similarity=-0.104 Sum_probs=20.0
Q ss_pred chhhhhcCCCCCccceeeccccchhH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMK 27 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak 27 (61)
.+.|+|..+|+++..|+.+...=+.|
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKE 156 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 46799999999999999765543333
No 57
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=75.28 E-value=0.23 Score=24.80 Aligned_cols=27 Identities=0% Similarity=-0.168 Sum_probs=18.4
Q ss_pred chhhhhcCCCCCccceeeccccchhHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKW 28 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~ 28 (61)
...+||..+|+++.+|.-|+.++....
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~ 38 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNP 38 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT----
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccc
Confidence 457899999999999999999884333
No 58
>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=74.76 E-value=0.26 Score=24.56 Aligned_cols=23 Identities=4% Similarity=-0.068 Sum_probs=17.9
Q ss_pred hhhhhcCCCCCccceeeccccch
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
..+||..+|++.++|.-|..|+.
T Consensus 25 ~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 25 KRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp HHHHHHHHT--CCHHHHHHHCHH
T ss_pred HHHHHHHhCCCHHHHHHHHHhHH
Confidence 46899999999999999988753
No 59
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=74.61 E-value=0.59 Score=28.59 Aligned_cols=30 Identities=10% Similarity=-0.100 Sum_probs=23.3
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
...|+|..+|+++..|+++...-+.+-++.
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467999999999999998876555555544
No 60
>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=74.37 E-value=0.55 Score=27.82 Aligned_cols=29 Identities=3% Similarity=-0.200 Sum_probs=22.0
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
...|+|..+|+++..|+++...-|.+-|+
T Consensus 156 s~~EIA~~lgis~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 156 SYEDIARIMDCPVGTVRSRIFRAREAIAI 184 (190)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 46899999999999999887544444443
No 61
>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=74.20 E-value=0.67 Score=27.85 Aligned_cols=32 Identities=6% Similarity=-0.037 Sum_probs=24.9
Q ss_pred CchhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRMKWKKEH 32 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~ 32 (61)
|...|+|..||+++..|++...-=|.+-|+.-
T Consensus 148 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 148 FAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35689999999999999998775555555543
No 62
>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=73.96 E-value=0.59 Score=25.90 Aligned_cols=26 Identities=12% Similarity=-0.047 Sum_probs=20.1
Q ss_pred chhhhhcCCCCCccceeeccccchhH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMK 27 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak 27 (61)
.+.|+|..+|+++..|..+...-+.|
T Consensus 128 s~~eIA~~l~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 128 SYKEIAEILGISVGTVKRRLKRARKK 153 (158)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 56899999999999998766544333
No 63
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=73.87 E-value=0.68 Score=27.74 Aligned_cols=29 Identities=7% Similarity=-0.094 Sum_probs=22.9
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
...|+|..+|+++..|+.++..-|.+-++
T Consensus 159 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 159 SQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 46799999999999999988655554444
No 64
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=73.84 E-value=0.58 Score=27.38 Aligned_cols=30 Identities=10% Similarity=-0.097 Sum_probs=23.7
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
...|+|..+|+++..|+++.+-=|.+-|+.
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 155 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKAL 155 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 568999999999999999877555555544
No 65
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=73.50 E-value=0.76 Score=27.18 Aligned_cols=29 Identities=7% Similarity=0.198 Sum_probs=22.2
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
-..|+|..+|+++..|++..+.-|.+-|+
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 46799999999999999877644444443
No 66
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=73.25 E-value=0.66 Score=26.89 Aligned_cols=29 Identities=10% Similarity=-0.016 Sum_probs=22.1
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
-..|+|..+|+++..|++...--|.+-|+
T Consensus 124 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 124 SYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46799999999999999876644444444
No 67
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=73.14 E-value=0.49 Score=23.90 Aligned_cols=21 Identities=5% Similarity=-0.004 Sum_probs=18.2
Q ss_pred CchhhhhcCCCCCccceeecc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWF 21 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWF 21 (61)
|-+.|+|+.+|+++.+|+-|-
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~ 21 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYE 21 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 457899999999999999884
No 68
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=71.91 E-value=0.34 Score=23.33 Aligned_cols=19 Identities=5% Similarity=-0.113 Sum_probs=16.2
Q ss_pred chhhhhcCCCCCccceeec
Q psy12003 2 NLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvW 20 (61)
.+.|+|..+|+++.+|+.+
T Consensus 22 t~~eIa~~lg~s~~~V~~~ 40 (50)
T PF04545_consen 22 TLEEIAERLGISRSTVRRI 40 (50)
T ss_dssp SHHHHHHHHTSCHHHHHHH
T ss_pred CHHHHHHHHCCcHHHHHHH
Confidence 4689999999999999754
No 69
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=71.10 E-value=0.74 Score=26.81 Aligned_cols=28 Identities=4% Similarity=-0.135 Sum_probs=21.5
Q ss_pred chhhhhcCCCCCccceeeccccchhHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWK 29 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k 29 (61)
.+.|+|..+|+++.+|+.+...=+.+-+
T Consensus 146 s~~eIA~~lgis~~tV~~~l~ra~~~Lr 173 (182)
T PRK09652 146 SYEEIAEIMGCPIGTVRSRIFRAREALR 173 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4678999999999999988774343333
No 70
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=71.02 E-value=0.79 Score=27.63 Aligned_cols=30 Identities=3% Similarity=0.037 Sum_probs=22.4
Q ss_pred CchhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
+...|+|..+|+++..|+++..-=|.+-|+
T Consensus 151 ~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 151 LSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 346899999999999999886644444443
No 71
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=70.65 E-value=0.84 Score=26.76 Aligned_cols=29 Identities=10% Similarity=-0.029 Sum_probs=21.7
Q ss_pred CchhhhhcCCCCCccceeeccccchhHHH
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRMKWK 29 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~k 29 (61)
+...|+|..+|+++..|++...-=|.+-|
T Consensus 129 ~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 157 (164)
T PRK12547 129 FSYEDAAAICGCAVGTIKSRVSRARNRLQ 157 (164)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 35789999999999999987654343333
No 72
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=70.35 E-value=0.82 Score=26.55 Aligned_cols=31 Identities=10% Similarity=0.030 Sum_probs=23.4
Q ss_pred CchhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
+...|+|..+|+++..|+.....-|.+.|+.
T Consensus 128 ~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 128 YSYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3568999999999999998875545554443
No 73
>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=69.72 E-value=0.69 Score=25.59 Aligned_cols=22 Identities=14% Similarity=0.052 Sum_probs=19.6
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
|.|.|+|..+|++..+|+-|.+
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~ 22 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEE 22 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5688999999999999999954
No 74
>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=69.56 E-value=0.89 Score=26.86 Aligned_cols=28 Identities=7% Similarity=-0.122 Sum_probs=21.2
Q ss_pred chhhhhcCCCCCccceeeccccchhHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWK 29 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k 29 (61)
-..|+|..||+++.+|++....-|.+-+
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~~Lr 179 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARAWLA 179 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4679999999999999987664444433
No 75
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=69.31 E-value=1.2 Score=26.18 Aligned_cols=31 Identities=10% Similarity=-0.160 Sum_probs=24.0
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEH 32 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~ 32 (61)
-..|+|..+|+|+..|++.+..-|.+-++.-
T Consensus 138 s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 138 PQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3578999999999999988765565555543
No 76
>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=68.72 E-value=1 Score=26.14 Aligned_cols=30 Identities=3% Similarity=-0.023 Sum_probs=22.5
Q ss_pred CchhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
+...|+|..+|+++..|+.+...-|.+-++
T Consensus 127 ~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 127 LSEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 346789999999999999876655544444
No 77
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=68.63 E-value=0.63 Score=26.20 Aligned_cols=18 Identities=33% Similarity=0.174 Sum_probs=13.3
Q ss_pred CchhhhhcCCCCCcccee
Q psy12003 1 MNLLRDKNPPRGTERQIK 18 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~Vq 18 (61)
+++.+||.+.|||+++|.
T Consensus 73 ~n~~eLA~kyglS~r~I~ 90 (108)
T PF08765_consen 73 MNVRELARKYGLSERQIY 90 (108)
T ss_dssp S-HHHHHHHHT--HHHHH
T ss_pred CCHHHHHHHHCcCHHHHH
Confidence 578999999999998885
No 78
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=68.61 E-value=1.2 Score=26.66 Aligned_cols=33 Identities=15% Similarity=-0.042 Sum_probs=25.0
Q ss_pred CchhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK 33 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~ 33 (61)
+.+.|+|..+|+++..|++-...=|.+.++.-.
T Consensus 148 ~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 148 KSVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 356899999999999999877655666555433
No 79
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=68.58 E-value=0.38 Score=22.99 Aligned_cols=20 Identities=5% Similarity=0.121 Sum_probs=16.6
Q ss_pred hhhhhcCCCCCccceeeccc
Q psy12003 3 LLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFq 22 (61)
..++|..+|++..+|.-|.+
T Consensus 20 ~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 20 IREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 56899999999999999855
No 80
>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=68.32 E-value=0.57 Score=22.32 Aligned_cols=16 Identities=6% Similarity=-0.035 Sum_probs=12.9
Q ss_pred hhhhhcCCCCCcccee
Q psy12003 3 LLRDKNPPRGTERQIK 18 (61)
Q Consensus 3 ~~eLA~~l~Lte~~Vq 18 (61)
..+||..+||++..|.
T Consensus 20 ~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 20 YAELAEELGLSESTVR 35 (42)
T ss_dssp HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHCcCHHHHH
Confidence 5789999999998884
No 81
>PHA03273 envelope glycoprotein C; Provisional
Probab=68.18 E-value=2.5 Score=29.97 Aligned_cols=20 Identities=15% Similarity=0.316 Sum_probs=15.1
Q ss_pred cCCCCCccceeeccccchhHH
Q psy12003 8 NPPRGTERQIKIWFQNRRMKW 28 (61)
Q Consensus 8 ~~l~Lte~~VqvWFqNrRak~ 28 (61)
...++++.+++|||| ||.+-
T Consensus 114 ~~~~~~~~RLeiWf~-~r~rf 133 (486)
T PHA03273 114 VGVNYSEYRLEIYLN-QRTPF 133 (486)
T ss_pred CCCCCcceEEEEEEc-ccccc
Confidence 456777899999999 55553
No 82
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=68.12 E-value=1.3 Score=25.68 Aligned_cols=29 Identities=7% Similarity=-0.058 Sum_probs=22.6
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
...|+|..+|+++..|..+..-=|.+.|+
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46799999999999999887655555444
No 83
>PRK00118 putative DNA-binding protein; Validated
Probab=67.87 E-value=1 Score=25.65 Aligned_cols=31 Identities=3% Similarity=-0.161 Sum_probs=24.6
Q ss_pred CchhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
+-..|+|..+|+++.+|..+...-|.+.+..
T Consensus 34 ~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 34 YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3468999999999999998887666665554
No 84
>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=67.12 E-value=0.92 Score=26.10 Aligned_cols=21 Identities=10% Similarity=-0.105 Sum_probs=17.9
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
.+.|+|..+|+|+.+|+++..
T Consensus 129 ~~~eIA~~l~is~~tv~~~l~ 149 (159)
T TIGR02989 129 SLTALAEQLGRTVNAVYKALS 149 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHH
Confidence 467999999999999997644
No 85
>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=66.84 E-value=0.86 Score=25.06 Aligned_cols=22 Identities=5% Similarity=-0.079 Sum_probs=19.6
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
|-|.|+|+.+|++..+++-|-+
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~ 22 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDH 22 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 6788999999999999998854
No 86
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=66.70 E-value=1.1 Score=25.85 Aligned_cols=28 Identities=7% Similarity=0.035 Sum_probs=20.9
Q ss_pred chhhhhcCCCCCccceeeccccchhHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWK 29 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k 29 (61)
...|+|..||+++..|++...--|.+-|
T Consensus 124 s~~EIA~~lgis~~tV~~~l~ra~~~Lr 151 (161)
T PRK09047 124 DVAETAAAMGCSEGSVKTHCSRATHALA 151 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4679999999999999976553333333
No 87
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=66.66 E-value=1.2 Score=26.35 Aligned_cols=29 Identities=14% Similarity=0.015 Sum_probs=22.2
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
...|+|..+|+++..|++.++.-|.+-+.
T Consensus 154 s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 154 SLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46789999999999999887654444443
No 88
>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=66.55 E-value=0.82 Score=23.01 Aligned_cols=21 Identities=5% Similarity=0.097 Sum_probs=18.2
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
-+.|+|..+|++..+++-|-+
T Consensus 2 s~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467999999999999998854
No 89
>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=66.50 E-value=0.74 Score=21.97 Aligned_cols=21 Identities=0% Similarity=-0.089 Sum_probs=19.1
Q ss_pred hhhcCCCCCccceeeccccch
Q psy12003 5 RDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 5 eLA~~l~Lte~~VqvWFqNrR 25 (61)
+||..+|++..+|--|+.++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 689999999999999999983
No 90
>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=66.24 E-value=0.95 Score=21.98 Aligned_cols=16 Identities=13% Similarity=-0.002 Sum_probs=13.0
Q ss_pred hhhhhcCCCCCcccee
Q psy12003 3 LLRDKNPPRGTERQIK 18 (61)
Q Consensus 3 ~~eLA~~l~Lte~~Vq 18 (61)
+.+||..+++|.++|+
T Consensus 18 ~~eLa~~l~vS~rTi~ 33 (55)
T PF08279_consen 18 AKELAEELGVSRRTIR 33 (55)
T ss_dssp HHHHHHHCTS-HHHHH
T ss_pred HHHHHHHhCCCHHHHH
Confidence 5789999999999885
No 91
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=65.52 E-value=1.1 Score=28.19 Aligned_cols=32 Identities=9% Similarity=-0.032 Sum_probs=24.6
Q ss_pred CchhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRMKWKKEH 32 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~ 32 (61)
+...|+|..+|+++..|++..+.-|.+-|+.-
T Consensus 188 ~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 188 MSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 34689999999999999988775555555543
No 92
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=65.47 E-value=1.8 Score=26.40 Aligned_cols=32 Identities=6% Similarity=-0.073 Sum_probs=24.0
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK 33 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~ 33 (61)
...|+|..+|+++..|+++...-|.+-|+.-.
T Consensus 151 s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 151 TYEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 46799999999999999887655555554433
No 93
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=65.27 E-value=1.2 Score=26.70 Aligned_cols=30 Identities=17% Similarity=0.009 Sum_probs=22.6
Q ss_pred CchhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
+.+.|+|..+|+++..|+..+..=|.+.++
T Consensus 123 ~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (181)
T PRK09637 123 LSQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152 (181)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 457899999999999999877644444443
No 94
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=65.16 E-value=1.3 Score=26.43 Aligned_cols=30 Identities=3% Similarity=-0.012 Sum_probs=23.0
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
...|+|..+|++..+|+.....-|.+-|+.
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 175 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQ 175 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 467999999999999998876555554443
No 95
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=65.04 E-value=1.2 Score=26.55 Aligned_cols=22 Identities=5% Similarity=0.013 Sum_probs=18.6
Q ss_pred chhhhhcCCCCCccceeecccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQN 23 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqN 23 (61)
.+.|+|..+|+++..|+.....
T Consensus 157 s~~EIA~~lgis~~tV~~~l~R 178 (189)
T PRK09648 157 SAEETAEAVGSTPGAVRVAQHR 178 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4689999999999999987643
No 96
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=65.00 E-value=1.2 Score=26.47 Aligned_cols=29 Identities=7% Similarity=0.011 Sum_probs=23.0
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
...|+|..+|+++..|++....-|.+.|+
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46799999999999999887655555554
No 97
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=64.60 E-value=2 Score=25.69 Aligned_cols=32 Identities=9% Similarity=-0.027 Sum_probs=24.0
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK 33 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~ 33 (61)
...|+|..+|+++..|++....-|.+-|+.-.
T Consensus 149 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (191)
T PRK12520 149 ETEEICQELQITATNAWVLLYRARMRLRECLD 180 (191)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46799999999999999876655555555433
No 98
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=64.49 E-value=1.3 Score=26.37 Aligned_cols=30 Identities=7% Similarity=-0.100 Sum_probs=24.6
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
...|+|..+|+++..|++-...-+.+-|+.
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 164 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQK 164 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467999999999999998877666666665
No 99
>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=64.19 E-value=1.3 Score=26.18 Aligned_cols=31 Identities=16% Similarity=-0.098 Sum_probs=23.7
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEH 32 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~ 32 (61)
.+.|+|..+|+++..|+...+--|.+.+..-
T Consensus 118 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5689999999999999988765555555543
No 100
>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=63.77 E-value=1.1 Score=26.16 Aligned_cols=24 Identities=8% Similarity=0.074 Sum_probs=20.4
Q ss_pred CchhhhhcCCCCCccceeeccccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNR 24 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNr 24 (61)
|.|.++|..+|++..+++.|-+..
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE~~G 25 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWERHG 25 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCC
Confidence 568899999999999999996543
No 101
>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=63.62 E-value=1.3 Score=25.32 Aligned_cols=21 Identities=5% Similarity=-0.201 Sum_probs=17.9
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
...|+|..+|+++.+|++...
T Consensus 123 s~~eIA~~lgis~~tv~~~l~ 143 (154)
T TIGR02950 123 SYKEIAELLNLSLAKVKSNLF 143 (154)
T ss_pred cHHHHHHHHCCCHHHHHHHHH
Confidence 467899999999999997755
No 102
>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=63.35 E-value=1 Score=25.26 Aligned_cols=22 Identities=9% Similarity=0.093 Sum_probs=19.4
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
|-+.|+|..+|++..+|+-|-+
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~ 22 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEK 22 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5688999999999999998854
No 103
>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=63.24 E-value=1.4 Score=21.03 Aligned_cols=23 Identities=9% Similarity=-0.201 Sum_probs=19.7
Q ss_pred hhhhhcCCCCCccceeeccccch
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
..+||..+|++...|.-|..+++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 56899999999999999987764
No 104
>PF12728 HTH_17: Helix-turn-helix domain
Probab=63.02 E-value=0.98 Score=21.67 Aligned_cols=25 Identities=4% Similarity=0.174 Sum_probs=20.0
Q ss_pred CchhhhhcCCCCCccceeeccccch
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
+.+.|+|.-||++..+|.-|.+...
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g~ 26 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQGK 26 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 3567899999999999998876543
No 105
>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=62.85 E-value=1.1 Score=24.32 Aligned_cols=22 Identities=5% Similarity=-0.017 Sum_probs=19.0
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
|.+.|+|..+|+++.+|+-|-+
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~ 22 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEE 22 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5678999999999999998844
No 106
>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=62.82 E-value=0.67 Score=22.35 Aligned_cols=24 Identities=8% Similarity=-0.110 Sum_probs=18.8
Q ss_pred chhhhhcCCCCCccceeeccccch
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
...+||..+|++...|.-|..+++
T Consensus 11 s~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 11 SQKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CHHHHHHHhCCCcchhHHHhcCCC
Confidence 457899999999999998888755
No 107
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=62.80 E-value=1.6 Score=25.62 Aligned_cols=29 Identities=7% Similarity=-0.107 Sum_probs=21.0
Q ss_pred CchhhhhcCCCCCccceeeccccchhHHH
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRMKWK 29 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~k 29 (61)
+...|+|..||+++..|+....--|.+-|
T Consensus 135 ~s~~EIA~~lgis~~tV~~~l~ra~~~Lr 163 (173)
T PRK09645 135 WSTAQIAADLGIPEGTVKSRLHYALRALR 163 (173)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 35689999999999999976543333333
No 108
>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=62.44 E-value=1.3 Score=22.75 Aligned_cols=24 Identities=8% Similarity=0.030 Sum_probs=20.5
Q ss_pred chhhhhcCCCCCccceeeccccch
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
-..+||..+|++...|--|..+++
T Consensus 20 t~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 20 SIRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCC
Confidence 357899999999999999988765
No 109
>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=62.44 E-value=0.58 Score=21.84 Aligned_cols=18 Identities=6% Similarity=0.039 Sum_probs=14.6
Q ss_pred hhhhhcCCCCCccceeec
Q psy12003 3 LLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvW 20 (61)
|-|+|..+|++..+|+-|
T Consensus 2 i~e~A~~~gvs~~tlR~y 19 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYY 19 (38)
T ss_dssp HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHH
Confidence 568899999999999877
No 110
>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=62.39 E-value=1.1 Score=24.74 Aligned_cols=24 Identities=4% Similarity=-0.086 Sum_probs=20.0
Q ss_pred CchhhhhcCCCCCccceeeccccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNR 24 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNr 24 (61)
+.+.|+|..+|++..+++-|..+.
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~~G 24 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEIG 24 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCC
Confidence 457899999999999999886643
No 111
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=62.35 E-value=1.5 Score=26.30 Aligned_cols=31 Identities=3% Similarity=-0.111 Sum_probs=23.7
Q ss_pred CchhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
|...|+|..+|+++..|+.....-|.+-|+.
T Consensus 153 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 183 (195)
T PRK12532 153 FSSDEIQQMCGISTSNYHTIMHRARESLRQC 183 (195)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3467999999999999998776555555554
No 112
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=62.17 E-value=1.5 Score=26.43 Aligned_cols=32 Identities=9% Similarity=-0.037 Sum_probs=24.1
Q ss_pred CchhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRMKWKKEH 32 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~ 32 (61)
+...|+|..||+++..|++....-|.+-++.-
T Consensus 133 ~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 133 FAYEEAAEICGCAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34679999999999999988765555555443
No 113
>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=61.66 E-value=1.4 Score=25.55 Aligned_cols=21 Identities=19% Similarity=0.094 Sum_probs=17.5
Q ss_pred CchhhhhcCCCCCccceeecc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWF 21 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWF 21 (61)
+...|+|..||+++..|+...
T Consensus 139 ~s~~eIA~~l~is~~tv~~~l 159 (170)
T TIGR02952 139 LPIAEVARILGKTEGAVKILQ 159 (170)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 356899999999999998654
No 114
>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=61.18 E-value=1.8 Score=25.32 Aligned_cols=21 Identities=10% Similarity=0.145 Sum_probs=17.7
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
-..|+|..+|+|+..|++...
T Consensus 137 s~~eiA~~lgis~~tv~~~l~ 157 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLH 157 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 467999999999999987654
No 115
>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=60.79 E-value=1.3 Score=20.02 Aligned_cols=23 Identities=9% Similarity=-0.120 Sum_probs=19.3
Q ss_pred hhhhhcCCCCCccceeeccccch
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
..++|..+++++..|.-|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 56889999999999998888763
No 116
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=60.71 E-value=1.8 Score=25.68 Aligned_cols=30 Identities=3% Similarity=0.034 Sum_probs=23.3
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
...|+|..+|++..+|+..+..-|.+-|..
T Consensus 149 s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12512 149 SIKETAAKLSMSEGAVRVALHRGLAALAAK 178 (184)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 467999999999999998877555555543
No 117
>KOG3755|consensus
Probab=60.69 E-value=2.4 Score=31.25 Aligned_cols=21 Identities=24% Similarity=0.575 Sum_probs=17.3
Q ss_pred CccceeeccccchhHHHHHhh
Q psy12003 13 TERQIKIWFQNRRMKWKKEHK 33 (61)
Q Consensus 13 te~~VqvWFqNrRak~kr~~~ 33 (61)
.+.-|+.||.|||++.++...
T Consensus 739 ~~kn~~~~fk~~~ee~~~~k~ 759 (769)
T KOG3755|consen 739 ESKNVQFWFKVRREEEKRLKM 759 (769)
T ss_pred hhcchHHHHHHHHHHHhhhhc
Confidence 455788999999999998654
No 118
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=60.38 E-value=1.6 Score=26.07 Aligned_cols=30 Identities=7% Similarity=-0.089 Sum_probs=23.0
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
...|+|..+|+++..|++..+--|.+-|+.
T Consensus 156 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 185 (193)
T PRK11923 156 SYEDIASVMQCPVGTVRSRIFRAREAIDKA 185 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 367999999999999998776555555554
No 119
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=60.34 E-value=1.7 Score=27.10 Aligned_cols=29 Identities=10% Similarity=-0.008 Sum_probs=23.3
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
-+.|+|..+|+++..|+.+...-+.+-|+
T Consensus 202 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 202 NLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46799999999999999887765555554
No 120
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=60.32 E-value=2 Score=25.53 Aligned_cols=24 Identities=8% Similarity=0.105 Sum_probs=19.2
Q ss_pred chhhhhcCCCCCccceeeccccch
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
-..|+|..+|+++..|+++...=+
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~ 174 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSL 174 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHH
Confidence 357899999999999998765333
No 121
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=60.00 E-value=1.8 Score=25.80 Aligned_cols=29 Identities=14% Similarity=0.095 Sum_probs=21.5
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
...|+|..+|+++..|++....-|.+-++
T Consensus 140 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 168 (185)
T PRK12542 140 TYQEISSVMGITEANVRKQFERARKRVQN 168 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46799999999999999866544444333
No 122
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=59.51 E-value=1.5 Score=27.06 Aligned_cols=23 Identities=9% Similarity=0.161 Sum_probs=20.3
Q ss_pred CchhhhhcCCCCCccceeecccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQN 23 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqN 23 (61)
|.+.|+|..+|++..+|+-|...
T Consensus 1 mti~evA~~lGVS~~TLRrw~k~ 23 (175)
T PRK13182 1 MKTPFVAKKLGVSPKTVQRWVKQ 23 (175)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 67899999999999999988653
No 123
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=59.40 E-value=1.7 Score=25.86 Aligned_cols=27 Identities=4% Similarity=-0.085 Sum_probs=21.0
Q ss_pred chhhhhcCCCCCccceeeccccchhHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKW 28 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~ 28 (61)
...|+|..||+++..|+.....-+.+.
T Consensus 145 s~~EIA~~lgis~~tVk~~l~rAl~~~ 171 (178)
T PRK12529 145 KQKDIAQALDIALPTVKKYIHQAYVTC 171 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 467999999999999998766444443
No 124
>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=58.84 E-value=1.4 Score=23.86 Aligned_cols=22 Identities=0% Similarity=0.015 Sum_probs=18.8
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
+-+-++|..+|++..+|+-|-+
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~ 23 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYER 23 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH
Confidence 3578999999999999999954
No 125
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=58.81 E-value=1.9 Score=26.80 Aligned_cols=29 Identities=10% Similarity=-0.132 Sum_probs=21.3
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
-..|+|..+|+++.+|+.+...=+.+-|+
T Consensus 200 s~~EIA~~lgis~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 200 TQKEVADMLGISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46799999999999998775544444433
No 126
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=58.54 E-value=3.6 Score=25.63 Aligned_cols=31 Identities=3% Similarity=-0.156 Sum_probs=23.9
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEH 32 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~ 32 (61)
-..|+|..||+++..|++....-|.+-++.-
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4679999999999999988775555555543
No 127
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=58.43 E-value=1.9 Score=25.78 Aligned_cols=29 Identities=7% Similarity=-0.015 Sum_probs=22.0
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
-..|+|..+|+++..|+++...-+.+-|.
T Consensus 152 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 180 (188)
T PRK09640 152 EFQEIADIMHMGLSATKMRYKRALDKLRE 180 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46799999999999999886644444443
No 128
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=58.09 E-value=1.7 Score=19.50 Aligned_cols=23 Identities=4% Similarity=-0.138 Sum_probs=19.4
Q ss_pred hhhhhcCCCCCccceeeccccch
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
..+||..+++++..|.-|..+++
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~~ 35 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGKR 35 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 56899999999999988877664
No 129
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=57.95 E-value=2 Score=25.71 Aligned_cols=30 Identities=13% Similarity=0.020 Sum_probs=22.2
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
-..|+|..+|++...|+.....=|.+-|+.
T Consensus 157 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 157 ELEEIAELTGVPEETVKSRLRYALQKLREL 186 (194)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 367999999999999997665545444443
No 130
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=57.39 E-value=1.2 Score=20.89 Aligned_cols=21 Identities=10% Similarity=-0.018 Sum_probs=17.3
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
...|+|..++++..+|..+.+
T Consensus 20 s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 20 TNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 457899999999999987655
No 131
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation a
Probab=57.13 E-value=2.3 Score=23.05 Aligned_cols=15 Identities=7% Similarity=-0.104 Sum_probs=13.3
Q ss_pred hhhhcCCCCCcccee
Q psy12003 4 LRDKNPPRGTERQIK 18 (61)
Q Consensus 4 ~eLA~~l~Lte~~Vq 18 (61)
.++|++|||+|..|.
T Consensus 15 k~~~R~LGlse~~Id 29 (80)
T cd08313 15 KEFVRRLGLSDNEIE 29 (80)
T ss_pred HHHHHHcCCCHHHHH
Confidence 578999999999887
No 132
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=57.07 E-value=1.7 Score=25.00 Aligned_cols=22 Identities=14% Similarity=0.141 Sum_probs=19.2
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
|.|-|+|..+|+|..+++-|-+
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~ 22 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIRYYEE 22 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 6788999999999999998744
No 133
>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=56.83 E-value=1.6 Score=23.61 Aligned_cols=20 Identities=15% Similarity=0.345 Sum_probs=17.7
Q ss_pred CchhhhhcCCCCCccceeec
Q psy12003 1 MNLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvW 20 (61)
+-+.|+|..+|++..+++-|
T Consensus 2 ~ti~evA~~~gvs~~tLR~y 21 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYW 21 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHH
Confidence 35789999999999999988
No 134
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=56.71 E-value=1.6 Score=25.29 Aligned_cols=28 Identities=14% Similarity=0.009 Sum_probs=20.9
Q ss_pred chhhhhcCCCCCccceeeccccchhHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWK 29 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k 29 (61)
...|+|..+|+++..|++....-|.+-+
T Consensus 130 s~~eIA~~lgis~~tv~~~l~Rar~~L~ 157 (161)
T PRK12541 130 SYKEIAEMTGLSLAKVKIELHRGRKETK 157 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4578999999999999987654444433
No 135
>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=56.55 E-value=2 Score=25.58 Aligned_cols=21 Identities=10% Similarity=-0.100 Sum_probs=17.6
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
-+.|+|..+|+++.+|++.+.
T Consensus 167 s~~eIA~~l~~s~~tV~~~l~ 187 (198)
T TIGR02859 167 SYQEIACDLNRHVKSIDNALQ 187 (198)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 367899999999999987655
No 136
>PF06505 XylR_N: Activator of aromatic catabolism; InterPro: IPR010523 This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators in several proteobacteria, including activators of phenol degradation such as XylR. It is found adjacent to IPR004096 from INTERPRO.
Probab=56.53 E-value=3.4 Score=23.43 Aligned_cols=22 Identities=23% Similarity=0.403 Sum_probs=18.0
Q ss_pred hhhcCCCCCccceeeccccchh
Q psy12003 5 RDKNPPRGTERQIKIWFQNRRM 26 (61)
Q Consensus 5 eLA~~l~Lte~~VqvWFqNrRa 26 (61)
+|+..|..++..=+|||.++|+
T Consensus 1 DL~~~L~F~p~~G~Iwl~~~Rm 22 (103)
T PF06505_consen 1 DLRELLRFSPEDGRIWLNGQRM 22 (103)
T ss_pred ChHHheeEeCCCCeEEECCEEE
Confidence 3666778888889999999986
No 137
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=56.46 E-value=2 Score=25.75 Aligned_cols=32 Identities=6% Similarity=-0.044 Sum_probs=25.7
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK 33 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~ 33 (61)
-..|+|..||++...|..|-+.-+.|.++...
T Consensus 23 Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 23 TQQEIADILGTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35789999999999999998877776666543
No 138
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=56.45 E-value=2 Score=25.32 Aligned_cols=28 Identities=0% Similarity=-0.095 Sum_probs=21.6
Q ss_pred chhhhhcCCCCCccceeeccccchhHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWK 29 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k 29 (61)
...|+|..+|+++..|++....-+.+.+
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ra~~~~~ 164 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQGLRQCY 164 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4579999999999999988764444443
No 139
>PRK06930 positive control sigma-like factor; Validated
Probab=56.31 E-value=2 Score=26.13 Aligned_cols=30 Identities=3% Similarity=-0.027 Sum_probs=23.8
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
-..|+|..+|+++.+|+.+...-+.|-++.
T Consensus 132 s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~ 161 (170)
T PRK06930 132 SYSEIADYLNIKKSTVQSMIERAEKKIARQ 161 (170)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999877666655554
No 140
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=56.28 E-value=4.2 Score=23.54 Aligned_cols=18 Identities=0% Similarity=-0.165 Sum_probs=16.2
Q ss_pred hhhhhcCCCCCccceeec
Q psy12003 3 LLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvW 20 (61)
++|+|..++|+-..|+|-
T Consensus 58 VAEiAA~L~lPlgVvrVL 75 (114)
T PF05331_consen 58 VAEIAARLGLPLGVVRVL 75 (114)
T ss_pred HHHHHHhhCCCchhhhhh
Confidence 789999999999999874
No 141
>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=56.04 E-value=1.6 Score=24.13 Aligned_cols=22 Identities=0% Similarity=-0.026 Sum_probs=19.1
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
+.|.|+|..+|++..+++-|-+
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~ 23 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDR 23 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH
Confidence 4688999999999999998844
No 142
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=55.73 E-value=2.6 Score=24.79 Aligned_cols=28 Identities=4% Similarity=-0.072 Sum_probs=21.1
Q ss_pred chhhhhcCCCCCccceeeccccchhHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWK 29 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k 29 (61)
...|+|..+|+++..|++....-|.+-+
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 164 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMR 164 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4679999999999999987654444433
No 143
>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=55.57 E-value=1.8 Score=24.04 Aligned_cols=22 Identities=0% Similarity=-0.066 Sum_probs=18.6
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
|-+-|+|+.+|++..+++-|-+
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~ 23 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEK 23 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4578999999999999998744
No 144
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=55.18 E-value=2.3 Score=25.57 Aligned_cols=29 Identities=14% Similarity=0.032 Sum_probs=21.4
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
...|+|..+|+++..|++-...-|.+-++
T Consensus 172 s~~EIA~~lgis~~tV~~~l~rar~~Lr~ 200 (208)
T PRK08295 172 SYQEIAEELNRHVKSIDNALQRVKRKLEK 200 (208)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35789999999999998765544444444
No 145
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). 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=55.09 E-value=1.9 Score=24.29 Aligned_cols=22 Identities=9% Similarity=0.075 Sum_probs=19.3
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
|-|-|+|..+|+|..+++-|-+
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~ 22 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEE 22 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 5688999999999999998854
No 146
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=54.98 E-value=2.4 Score=25.22 Aligned_cols=29 Identities=7% Similarity=0.032 Sum_probs=21.7
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
...|+|..+|++...|+.....-+.+-|+
T Consensus 149 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 149 SVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 46799999999999999876544444433
No 147
>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=54.98 E-value=2 Score=24.13 Aligned_cols=21 Identities=0% Similarity=-0.009 Sum_probs=18.3
Q ss_pred CchhhhhcCCCCCccceeecc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWF 21 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWF 21 (61)
|-|-|+|..+|++..+++-|-
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye 21 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYE 21 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 457899999999999999883
No 148
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=54.92 E-value=3.1 Score=25.58 Aligned_cols=30 Identities=3% Similarity=-0.058 Sum_probs=23.1
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
...|+|..||+++..|+++..-=|.+-++.
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~ 185 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQLRAA 185 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467999999999999998876555554443
No 149
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. 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 su
Probab=54.81 E-value=2 Score=25.10 Aligned_cols=20 Identities=10% Similarity=0.152 Sum_probs=18.2
Q ss_pred CchhhhhcCCCCCccceeec
Q psy12003 1 MNLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvW 20 (61)
|-|-|+|..+|+|..+++-|
T Consensus 1 m~Ige~a~~~gvs~~tLRyY 20 (131)
T cd04786 1 MKIGELAKRSGMAASRIRFY 20 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHH
Confidence 67889999999999999887
No 150
>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=54.55 E-value=2.5 Score=25.46 Aligned_cols=31 Identities=3% Similarity=-0.062 Sum_probs=22.7
Q ss_pred CchhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
+...|+|..+|+++..|++...--|.+-|+.
T Consensus 148 ~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 148 FESDEICQELEISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3578999999999999987665444444443
No 151
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=54.41 E-value=2.4 Score=25.58 Aligned_cols=30 Identities=0% Similarity=-0.257 Sum_probs=23.2
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
...|+|..+|+++.+|+.+..--|.+-|+.
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467999999999999998877555555444
No 152
>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=54.39 E-value=2.9 Score=26.64 Aligned_cols=31 Identities=10% Similarity=0.117 Sum_probs=25.1
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEH 32 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~ 32 (61)
-..|+|..+|+++..|+++...-|.+-|+.-
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4679999999999999998886666665553
No 153
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=54.37 E-value=3.9 Score=24.85 Aligned_cols=30 Identities=7% Similarity=-0.028 Sum_probs=22.6
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
-..|+|..+|+++..|++....-|.+-|+.
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 186 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRTC 186 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467999999999999998766444444443
No 154
>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=54.28 E-value=1.9 Score=25.33 Aligned_cols=24 Identities=8% Similarity=0.007 Sum_probs=20.4
Q ss_pred CchhhhhcCCCCCccceeeccccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNR 24 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNr 24 (61)
|-|-|+|..+|++..+|+-|.+..
T Consensus 1 y~I~e~a~~~gvs~~TLR~Ye~~G 24 (134)
T cd04779 1 YRIGQLAHLAGVSKRTIDYYTNLG 24 (134)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCC
Confidence 457899999999999999997644
No 155
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=53.97 E-value=2.6 Score=25.55 Aligned_cols=30 Identities=7% Similarity=-0.090 Sum_probs=23.8
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
...|+|..+|+|+..|++..+-=|.+-|+.
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~ 160 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAEL 160 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999887656555554
No 156
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=53.94 E-value=2.1 Score=25.14 Aligned_cols=20 Identities=20% Similarity=0.253 Sum_probs=18.0
Q ss_pred CchhhhhcCCCCCccceeec
Q psy12003 1 MNLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvW 20 (61)
|-|-|+|..+|++..+|+-|
T Consensus 1 m~Ige~a~~~gvs~~tlRyY 20 (135)
T PRK10227 1 MNISDVAKITGLTSKAIRFY 20 (135)
T ss_pred CCHHHHHHHHCcCHHHHHHH
Confidence 67889999999999999877
No 157
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=53.69 E-value=2.8 Score=25.25 Aligned_cols=31 Identities=3% Similarity=-0.134 Sum_probs=22.7
Q ss_pred CchhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
+...|+|..+|+++..|++...--|.+-++.
T Consensus 128 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 158 (182)
T PRK12511 128 LSYQEAAAVLGIPIGTLMSRIGRARAALRAF 158 (182)
T ss_pred CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 3567999999999999998765444444443
No 158
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=53.50 E-value=2.3 Score=25.51 Aligned_cols=21 Identities=5% Similarity=-0.141 Sum_probs=18.1
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
...|+|..+|+++..|++...
T Consensus 148 s~~EIA~~lgis~~tVk~~l~ 168 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVA 168 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 467999999999999998764
No 159
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=53.38 E-value=2.5 Score=25.59 Aligned_cols=24 Identities=13% Similarity=0.111 Sum_probs=18.5
Q ss_pred chhhhhcCCCCCccceeeccccch
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
...|+|..+|+++.+|+-.++.=|
T Consensus 153 s~~EIA~~lgiS~~tV~r~l~~aR 176 (185)
T PF07638_consen 153 SVEEIAERLGISERTVRRRLRRAR 176 (185)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 467999999999999985444334
No 160
>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=53.31 E-value=2.7 Score=21.11 Aligned_cols=17 Identities=6% Similarity=-0.076 Sum_probs=13.9
Q ss_pred chhhhhcCCCCCcccee
Q psy12003 2 NLLRDKNPPRGTERQIK 18 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~Vq 18 (61)
.+.|||..||++...+-
T Consensus 25 tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 25 TLEELAEELGISKSTVS 41 (53)
T ss_pred CHHHHHHHhCCCHHHHH
Confidence 47899999999987663
No 161
>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=52.72 E-value=2.2 Score=24.70 Aligned_cols=22 Identities=5% Similarity=0.043 Sum_probs=18.7
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
|-|-|||..+|++..+|+.|-+
T Consensus 4 ~tI~elA~~~gvs~~tlR~Ye~ 25 (120)
T TIGR02054 4 YTISRLAEDAGVSVHVVRDYLL 25 (120)
T ss_pred CcHHHHHHHHCcCHHHHHHHHH
Confidence 3678999999999999998843
No 162
>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=52.52 E-value=2.5 Score=21.63 Aligned_cols=22 Identities=5% Similarity=0.006 Sum_probs=16.6
Q ss_pred hhhhcCCCCCcccee-eccccch
Q psy12003 4 LRDKNPPRGTERQIK-IWFQNRR 25 (61)
Q Consensus 4 ~eLA~~l~Lte~~Vq-vWFqNrR 25 (61)
.+||..+|++...|. .|.....
T Consensus 16 ~~lA~~lgis~st~s~~~~~r~~ 38 (66)
T PF07022_consen 16 KELAERLGISKSTLSNNWKKRGS 38 (66)
T ss_dssp HHHHCCTT--HHHHH-HHHHSSS
T ss_pred HHHHHHhCcCHHHhhHHHHhCCC
Confidence 589999999999999 8876444
No 163
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=52.43 E-value=2.7 Score=24.31 Aligned_cols=21 Identities=0% Similarity=-0.138 Sum_probs=17.7
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
-..|+|..+|+++.+|+....
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ 147 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIR 147 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 467999999999999997644
No 164
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=52.35 E-value=3 Score=25.11 Aligned_cols=26 Identities=8% Similarity=-0.227 Sum_probs=19.5
Q ss_pred chhhhhcCCCCCccceeeccccchhH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMK 27 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak 27 (61)
...|+|..+|++...|++-...-|.+
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~ 184 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEK 184 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHH
Confidence 46799999999999998665433333
No 165
>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=51.84 E-value=2.3 Score=25.39 Aligned_cols=25 Identities=12% Similarity=0.146 Sum_probs=20.6
Q ss_pred chhhhhcCCCCCccceeeccccchh
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRM 26 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRa 26 (61)
.+.|+|..||+++..|.-|....|-
T Consensus 48 ti~eV~e~tgVs~~~I~~~IreGRL 72 (137)
T TIGR03826 48 TVSEIVEETGVSEKLILKFIREGRL 72 (137)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCCe
Confidence 5789999999999999988665443
No 166
>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=51.83 E-value=2.3 Score=20.06 Aligned_cols=21 Identities=10% Similarity=-0.004 Sum_probs=17.4
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
...++|..+++++.+|..|..
T Consensus 17 s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 17 TNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 456889999999999987754
No 167
>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=51.81 E-value=2.2 Score=23.61 Aligned_cols=21 Identities=0% Similarity=-0.137 Sum_probs=17.9
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
-|-|+|..+|+|..+++-|-+
T Consensus 3 ~i~eva~~~gvs~~tLR~ye~ 23 (102)
T cd04775 3 TIGQMSRKFGVSRSTLLYYES 23 (102)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 578999999999999988743
No 168
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=51.79 E-value=3.1 Score=24.65 Aligned_cols=21 Identities=5% Similarity=-0.217 Sum_probs=17.7
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
-..|+|..+|+++..|+.+..
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ 173 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRAR 173 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 457899999999999987655
No 169
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=51.79 E-value=2.6 Score=25.23 Aligned_cols=29 Identities=17% Similarity=0.050 Sum_probs=21.1
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
-..|+|..+|+++..|+...+--|.+-|+
T Consensus 149 s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 149 KIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46799999999999998765544444443
No 170
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=51.76 E-value=2.4 Score=21.87 Aligned_cols=24 Identities=0% Similarity=-0.076 Sum_probs=20.8
Q ss_pred chhhhhcCCCCCccceeeccccch
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
.+.+||+.+|++..+|--.+.+++
T Consensus 2 t~~~iA~~~gvS~~TVSr~ln~~~ 25 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLNGNG 25 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCC
Confidence 578999999999999988888764
No 171
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=51.65 E-value=3.2 Score=24.28 Aligned_cols=21 Identities=10% Similarity=-0.113 Sum_probs=17.7
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
...|+|..+|+++..|+.+..
T Consensus 144 s~~eIA~~l~is~~~V~~~l~ 164 (176)
T PRK09638 144 TYEEIAKMLNIPEGTVKSRVH 164 (176)
T ss_pred CHHHHHHHHCCChhHHHHHHH
Confidence 467899999999999987654
No 172
>PF13551 HTH_29: Winged helix-turn helix
Probab=51.46 E-value=1.6 Score=23.69 Aligned_cols=21 Identities=10% Similarity=0.205 Sum_probs=18.4
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
.+.++|..+|++..+|.-|.+
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~ 34 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLK 34 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 378999999999999998865
No 173
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=51.41 E-value=2.4 Score=24.47 Aligned_cols=22 Identities=9% Similarity=0.075 Sum_probs=19.2
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
|-|-|+|..+|+|..+|+-|-+
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~ 22 (127)
T TIGR02047 1 MKIGELAQKTGVSVETIRFYEK 22 (127)
T ss_pred CcHHHHHHHHCcCHHHHHHHHH
Confidence 6688999999999999998854
No 174
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=51.36 E-value=3.5 Score=22.34 Aligned_cols=18 Identities=11% Similarity=-0.141 Sum_probs=14.8
Q ss_pred hhhhcCCCCCccceeecc
Q psy12003 4 LRDKNPPRGTERQIKIWF 21 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvWF 21 (61)
-+||+.||+|+..|.---
T Consensus 17 k~laR~LGlse~~Id~i~ 34 (86)
T cd08306 17 RKLARKLGLSETKIESIE 34 (86)
T ss_pred HHHHHHcCCCHHHHHHHH
Confidence 579999999999988433
No 175
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=51.08 E-value=2.4 Score=24.92 Aligned_cols=22 Identities=5% Similarity=-0.000 Sum_probs=18.7
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
|-|-|+|+.+|++..+|+-|-+
T Consensus 2 ~~I~EvA~~~Gvs~~tLRyYE~ 23 (139)
T cd01110 2 LSVGEVAKRSGVAVSALHFYEQ 23 (139)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4678999999999999998844
No 176
>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=50.25 E-value=2.9 Score=19.81 Aligned_cols=18 Identities=0% Similarity=-0.154 Sum_probs=13.2
Q ss_pred chhhhhcCCCCCccceee
Q psy12003 2 NLLRDKNPPRGTERQIKI 19 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~Vqv 19 (61)
-+.++|..+|++.++|.-
T Consensus 23 si~~IA~~~gvsr~TvyR 40 (45)
T PF02796_consen 23 SIAEIAKQFGVSRSTVYR 40 (45)
T ss_dssp -HHHHHHHTTS-HHHHHH
T ss_pred CHHHHHHHHCcCHHHHHH
Confidence 478899999999888753
No 177
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=49.89 E-value=5.4 Score=24.22 Aligned_cols=18 Identities=6% Similarity=-0.001 Sum_probs=0.0
Q ss_pred CchhhhhcCCCCCcccee
Q psy12003 1 MNLLRDKNPPRGTERQIK 18 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~Vq 18 (61)
|-|.++|..|||.+.+|-
T Consensus 50 Lt~~~iA~~lgl~~STVS 67 (160)
T PF04552_consen 50 LTMKDIADELGLHESTVS 67 (160)
T ss_dssp ------------------
T ss_pred CCHHHHHHHhCCCHhHHH
Confidence 357899999999999995
No 178
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=49.85 E-value=3 Score=25.89 Aligned_cols=17 Identities=12% Similarity=0.018 Sum_probs=14.8
Q ss_pred hhhhcCCCCCccceeec
Q psy12003 4 LRDKNPPRGTERQIKIW 20 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvW 20 (61)
.|+|.+|+++|.+|++-
T Consensus 167 keIA~~L~iS~~TVk~h 183 (211)
T COG2197 167 KEIAEELNLSEKTVKTH 183 (211)
T ss_pred HHHHHHHCCCHhHHHHH
Confidence 58899999999999853
No 179
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=49.51 E-value=3 Score=20.76 Aligned_cols=17 Identities=12% Similarity=-0.017 Sum_probs=14.5
Q ss_pred chhhhhcCCCCCcccee
Q psy12003 2 NLLRDKNPPRGTERQIK 18 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~Vq 18 (61)
.+.|||..+++|+.+|+
T Consensus 16 s~~ela~~~~VS~~TiR 32 (57)
T PF08220_consen 16 SVKELAEEFGVSEMTIR 32 (57)
T ss_pred EHHHHHHHHCcCHHHHH
Confidence 36789999999999885
No 180
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=49.42 E-value=7.1 Score=21.04 Aligned_cols=18 Identities=6% Similarity=0.023 Sum_probs=15.2
Q ss_pred hhhcCCCCCccceeeccc
Q psy12003 5 RDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 5 eLA~~l~Lte~~VqvWFq 22 (61)
+|...++|.+-+|.||+.
T Consensus 58 ~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 58 LVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHhCCCCCeEEEEEE
Confidence 457778999999999986
No 181
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=48.86 E-value=3 Score=24.82 Aligned_cols=31 Identities=10% Similarity=-0.008 Sum_probs=24.6
Q ss_pred hhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRRMKWKKEHK 33 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~ 33 (61)
..|+|..+|++..+|+.+..--|.+.++...
T Consensus 146 ~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 146 YEEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 5789999999999999988766666665543
No 182
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=48.63 E-value=2.9 Score=19.81 Aligned_cols=19 Identities=0% Similarity=-0.146 Sum_probs=12.5
Q ss_pred chhhhhcCCCCCccceeec
Q psy12003 2 NLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvW 20 (61)
-+.++|..+|.+..+|--+
T Consensus 22 s~~~IA~~lg~s~sTV~re 40 (44)
T PF13936_consen 22 SIREIAKRLGRSRSTVSRE 40 (44)
T ss_dssp -HHHHHHHTT--HHHHHHH
T ss_pred CHHHHHHHHCcCcHHHHHH
Confidence 3678999999998887533
No 183
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=48.58 E-value=3.4 Score=25.69 Aligned_cols=31 Identities=10% Similarity=0.074 Sum_probs=23.7
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEH 32 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~ 32 (61)
...|+|..+|+++.+|++-..--|.|.|+.-
T Consensus 167 s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 167 SVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4679999999999999987665555555544
No 184
>PHA01976 helix-turn-helix protein
Probab=48.41 E-value=3.1 Score=20.78 Aligned_cols=23 Identities=9% Similarity=-0.084 Sum_probs=19.4
Q ss_pred hhhhhcCCCCCccceeeccccch
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
..+||..+|++...|.-|-..++
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46899999999999998877654
No 185
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=48.31 E-value=3.6 Score=24.71 Aligned_cols=29 Identities=14% Similarity=-0.048 Sum_probs=21.1
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
...|+|..||+++..|++...-=|.+-++
T Consensus 129 s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~ 157 (182)
T PRK12540 129 SYEDAAAICGCAVGTIKSRVNRARSKLSA 157 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46799999999999999765533333333
No 186
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=48.07 E-value=2.2 Score=24.40 Aligned_cols=23 Identities=9% Similarity=0.151 Sum_probs=19.1
Q ss_pred chhhhhcCCCCCccceeeccccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNR 24 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNr 24 (61)
.|.+||..+|++++.+.-+|+.-
T Consensus 27 sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 27 SLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHH
Confidence 47899999999999988777654
No 187
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=47.97 E-value=3.6 Score=25.96 Aligned_cols=28 Identities=4% Similarity=-0.093 Sum_probs=21.1
Q ss_pred chhhhhcCCCCCccceeeccccchhHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWK 29 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k 29 (61)
.+.|+|..+|+++.+|+.+...=+.|-|
T Consensus 223 s~~eIA~~l~is~~tV~~~~~ra~~kLr 250 (257)
T PRK08583 223 SQKETGERLGISQMHVSRLQRQAIKKLR 250 (257)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4679999999999999887654444433
No 188
>PRK04217 hypothetical protein; Provisional
Probab=47.89 E-value=3.2 Score=23.84 Aligned_cols=30 Identities=7% Similarity=-0.129 Sum_probs=22.7
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
.+.|+|..+|++..+|...+..-+.+-+..
T Consensus 60 S~~EIAk~LGIS~sTV~r~L~RArkkLre~ 89 (110)
T PRK04217 60 TQEEAGKRMGVSRGTVWRALTSARKKVAQM 89 (110)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467999999999999997776555554443
No 189
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=47.68 E-value=2.9 Score=24.73 Aligned_cols=22 Identities=0% Similarity=-0.061 Sum_probs=19.1
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
|.|-|+|..+|+|..+++-|-+
T Consensus 2 ~~IgevA~~~Gvs~~tLRyYE~ 23 (142)
T TIGR01950 2 LTVGELAKRSGVAVSALHFYES 23 (142)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5688999999999999998855
No 190
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=47.65 E-value=3.6 Score=24.23 Aligned_cols=29 Identities=14% Similarity=0.015 Sum_probs=21.1
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
...|+|..+|++...|+.....=|.+-++
T Consensus 154 s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 154 SLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35789999999999998765544444443
No 191
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares 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=47.64 E-value=3.1 Score=23.23 Aligned_cols=22 Identities=0% Similarity=-0.028 Sum_probs=18.9
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
|.+-|+|+.+|++..+++-|-.
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~ 22 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDK 22 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4578999999999999998844
No 192
>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=47.51 E-value=3.4 Score=25.49 Aligned_cols=22 Identities=0% Similarity=-0.147 Sum_probs=18.7
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
+.+.|+|..+|++...|+.+..
T Consensus 195 ~s~~eIA~~lgis~~~v~~~~~ 216 (227)
T TIGR02980 195 KTQSEIAERLGISQMHVSRLLR 216 (227)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 3578999999999999988754
No 193
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=47.44 E-value=2.5 Score=20.19 Aligned_cols=19 Identities=5% Similarity=-0.083 Sum_probs=15.6
Q ss_pred hhhhhcCCCCCccceeecc
Q psy12003 3 LLRDKNPPRGTERQIKIWF 21 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWF 21 (61)
+.++|+.+|++..+|+-.|
T Consensus 30 ~~~vA~~~~vs~~TV~ri~ 48 (52)
T PF13542_consen 30 FKDVARELGVSWSTVRRIF 48 (52)
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 5678999999999987655
No 194
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=47.37 E-value=3.1 Score=24.42 Aligned_cols=22 Identities=5% Similarity=-0.012 Sum_probs=18.1
Q ss_pred chhhhhcCCCCCccceeecccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQN 23 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqN 23 (61)
...|+|..||+++.+|+.+..+
T Consensus 136 s~~EIA~~l~is~~tV~~~l~r 157 (168)
T PRK12525 136 TYVEIGERLGVSLSRIHQYMVE 157 (168)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4679999999999999876543
No 195
>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=47.33 E-value=3.7 Score=25.65 Aligned_cols=21 Identities=5% Similarity=-0.222 Sum_probs=17.8
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
...|+|..+|+++.+|+.+.+
T Consensus 200 s~~EIA~~Lgis~~tV~~~l~ 220 (234)
T TIGR02835 200 TQKEVADMLGISQSYISRLEK 220 (234)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 467999999999999987654
No 196
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=47.12 E-value=3.4 Score=26.59 Aligned_cols=30 Identities=3% Similarity=-0.086 Sum_probs=22.7
Q ss_pred CchhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
+...|+|..+|+++..|+...+.-|.+-+.
T Consensus 132 ~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~ 161 (293)
T PRK09636 132 VPFDEIASTLGRSPAACRQLASRARKHVRA 161 (293)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 356899999999999999877644444444
No 197
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=46.76 E-value=3.8 Score=21.47 Aligned_cols=18 Identities=6% Similarity=-0.069 Sum_probs=15.2
Q ss_pred chhhhhcCCCCCccceee
Q psy12003 2 NLLRDKNPPRGTERQIKI 19 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~Vqv 19 (61)
|++|+|+.|++...+|+-
T Consensus 18 nqtEvaR~l~c~R~TVrK 35 (64)
T PF06322_consen 18 NQTEVARRLGCNRATVRK 35 (64)
T ss_pred cHHHHHHHhcccHHHHHH
Confidence 678999999999888863
No 198
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=46.48 E-value=3.9 Score=21.49 Aligned_cols=18 Identities=11% Similarity=0.027 Sum_probs=12.7
Q ss_pred CchhhhhcCCCCCcccee
Q psy12003 1 MNLLRDKNPPRGTERQIK 18 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~Vq 18 (61)
+.+.|||..+++++..|=
T Consensus 35 ~si~elA~~~~vS~sti~ 52 (77)
T PF01418_consen 35 MSISELAEKAGVSPSTIV 52 (77)
T ss_dssp --HHHHHHHCTS-HHHHH
T ss_pred ccHHHHHHHcCCCHHHHH
Confidence 357899999999988773
No 199
>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=46.47 E-value=3 Score=23.13 Aligned_cols=21 Identities=5% Similarity=0.015 Sum_probs=18.2
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
-+.|+|..+|+++.+++-|-+
T Consensus 2 ti~EvA~~~gVs~~tLR~ye~ 22 (99)
T cd04765 2 SIGEVAEILGLPPHVLRYWET 22 (99)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 478999999999999998854
No 200
>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=46.40 E-value=2.7 Score=23.92 Aligned_cols=21 Identities=5% Similarity=0.184 Sum_probs=18.8
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
.+.+.|...+++..+|.-|++
T Consensus 20 s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 20 SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred hHHHHHHHhCcHHHHHHHHHH
Confidence 367899999999999999988
No 201
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal 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. This subgroup lacks one of the c
Probab=46.20 E-value=3.2 Score=24.00 Aligned_cols=20 Identities=15% Similarity=0.227 Sum_probs=17.9
Q ss_pred CchhhhhcCCCCCccceeec
Q psy12003 1 MNLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvW 20 (61)
|-|-|+|..+|++..+|+-|
T Consensus 1 m~IgE~A~~~gvs~~TLRyY 20 (133)
T cd04787 1 MKVKELANAAGVTPDTVRFY 20 (133)
T ss_pred CCHHHHHHHHCcCHHHHHHH
Confidence 67889999999999999877
No 202
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins 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 winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. 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=46.12 E-value=3.3 Score=23.78 Aligned_cols=22 Identities=14% Similarity=0.161 Sum_probs=18.7
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
|-|-|+|..+|++..+++-|-+
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~ 22 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEE 22 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5678999999999999988744
No 203
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=45.97 E-value=3.3 Score=23.61 Aligned_cols=20 Identities=10% Similarity=0.099 Sum_probs=17.5
Q ss_pred chhhhhcCCCCCccceeecc
Q psy12003 2 NLLRDKNPPRGTERQIKIWF 21 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWF 21 (61)
.+.++|.++|+++.+|-.|.
T Consensus 31 sv~evA~e~gIs~~tl~~W~ 50 (121)
T PRK09413 31 TVSLVARQHGVAASQLFLWR 50 (121)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999999883
No 204
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=45.90 E-value=9.5 Score=18.04 Aligned_cols=13 Identities=8% Similarity=-0.240 Sum_probs=10.0
Q ss_pred chhhhhcCCCCCc
Q psy12003 2 NLLRDKNPPRGTE 14 (61)
Q Consensus 2 ~~~eLA~~l~Lte 14 (61)
||.++|..+|++.
T Consensus 9 eL~~iAk~lgI~~ 21 (43)
T PF07498_consen 9 ELREIAKELGIEG 21 (43)
T ss_dssp HHHHHHHCTT-TT
T ss_pred HHHHHHHHcCCCC
Confidence 6888999999873
No 205
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=45.79 E-value=3.7 Score=24.17 Aligned_cols=16 Identities=6% Similarity=-0.166 Sum_probs=14.0
Q ss_pred hhhhhcCCCCCcccee
Q psy12003 3 LLRDKNPPRGTERQIK 18 (61)
Q Consensus 3 ~~eLA~~l~Lte~~Vq 18 (61)
..|||+++|+++.+|.
T Consensus 26 ~~eiA~~lglS~~tV~ 41 (153)
T PRK11179 26 YAELAKQFGVSPGTIH 41 (153)
T ss_pred HHHHHHHHCcCHHHHH
Confidence 4689999999999985
No 206
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=45.42 E-value=4 Score=25.72 Aligned_cols=28 Identities=14% Similarity=-0.001 Sum_probs=20.9
Q ss_pred chhhhhcCCCCCccceeeccccchhHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWK 29 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k 29 (61)
-+.|+|..+|+|+.+|+..+..-+.+-|
T Consensus 219 s~~EIA~~lgis~~tV~~~~~ra~~~Lr 246 (251)
T PRK07670 219 TLTEIGQVLNLSTSRISQIHSKALFKLK 246 (251)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4679999999999999877654444333
No 207
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=45.35 E-value=4 Score=25.94 Aligned_cols=30 Identities=13% Similarity=0.024 Sum_probs=22.6
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
...|+|..+|+++..|++...--|.+-|..
T Consensus 134 S~~EIAe~LgiS~~tVksrL~Rark~Lr~~ 163 (228)
T PRK06704 134 SIADIAKVCSVSEGAVKASLFRSRNRLKTV 163 (228)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 468999999999999998766444444443
No 208
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. 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, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=45.19 E-value=2.7 Score=20.38 Aligned_cols=22 Identities=0% Similarity=-0.074 Sum_probs=18.0
Q ss_pred hhhhhcCCCCCccceeeccccc
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNR 24 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNr 24 (61)
|.++|+.+|++..+|---|.++
T Consensus 2 i~dIA~~agvS~~TVSr~ln~~ 23 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLNGP 23 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHTTC
T ss_pred HHHHHHHHCcCHHHHHHHHhCC
Confidence 6789999999999987666664
No 209
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=45.13 E-value=3.8 Score=22.87 Aligned_cols=20 Identities=5% Similarity=0.086 Sum_probs=16.9
Q ss_pred CchhhhhcCCCCCccceeec
Q psy12003 1 MNLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvW 20 (61)
|-|-|+|..+|++..+++-|
T Consensus 1 ~~I~eva~~~gvs~~tLRyY 20 (124)
T COG0789 1 YTIGEVAKLTGVSVRTLRFY 20 (124)
T ss_pred CcHHHHHHHhCCCHHHHHHH
Confidence 45778999999999999877
No 210
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=44.92 E-value=4.2 Score=25.00 Aligned_cols=30 Identities=3% Similarity=0.024 Sum_probs=23.0
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
...|+|..+|+++..|++..+-=|.+-|+.
T Consensus 166 s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~ 195 (206)
T PRK12544 166 ETNEICHAVDLSVSNLNVLLYRARLRLREC 195 (206)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 468999999999999998766555554444
No 211
>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=44.87 E-value=1.9 Score=22.02 Aligned_cols=19 Identities=5% Similarity=0.034 Sum_probs=15.6
Q ss_pred chhhhhcCCCCCccceeec
Q psy12003 2 NLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvW 20 (61)
.+.++|.+.|+++.++.-|
T Consensus 25 sv~~va~~~gi~~~~l~~W 43 (76)
T PF01527_consen 25 SVSEVAREYGISPSTLYNW 43 (76)
T ss_dssp HHHHHHHHHTS-HHHHHHH
T ss_pred ceEeeecccccccccccHH
Confidence 4678999999999999877
No 212
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are 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 have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. 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=44.67 E-value=3.5 Score=23.58 Aligned_cols=21 Identities=10% Similarity=0.050 Sum_probs=18.0
Q ss_pred CchhhhhcCCCCCccceeecc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWF 21 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWF 21 (61)
|-|-|+|..+|+|..+|+-|-
T Consensus 1 m~IgevA~~~gvs~~tLRyYe 21 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYYE 21 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 568899999999999998773
No 213
>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=44.62 E-value=3.5 Score=22.55 Aligned_cols=22 Identities=5% Similarity=-0.097 Sum_probs=18.9
Q ss_pred chhhhhcCCCCCccceeecccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQN 23 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqN 23 (61)
-|-|+|..+|++..+++-|-+.
T Consensus 2 ti~eva~~~gvs~~tLRyye~~ 23 (96)
T cd04768 2 TIGEFAKLAGVSIRTLRHYDDI 23 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 4779999999999999998653
No 214
>PF07813 LTXXQ: LTXXQ motif family protein; InterPro: IPR012899 This five residue motif is found in a number of bacterial proteins bearing similarity to the protein CpxP (P32158 from SWISSPROT). This is a periplasmic protein that aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH []. Another member of this family, Spy (P77754 from SWISSPROT) is also a periplasmic protein that may be involved in the response to stress []. The homology between CpxP and Spy may indicate that these two proteins are functionally related []. The motif is found repeated twice in many members of this entry. ; GO: 0042597 periplasmic space; PDB: 3ITF_B 3QZC_B 3OEO_D 3O39_A.
Probab=44.42 E-value=4 Score=21.71 Aligned_cols=18 Identities=28% Similarity=0.272 Sum_probs=12.0
Q ss_pred hhhhhcCCCCCccceeec
Q psy12003 3 LLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvW 20 (61)
+..|...|+||+.|.+-|
T Consensus 6 ~~~l~~~L~LT~eQ~~~~ 23 (100)
T PF07813_consen 6 IDRLKEELNLTDEQKAKW 23 (100)
T ss_dssp --STTTTS--THHHHHHH
T ss_pred HHHHHhhCCCCHHHHHHH
Confidence 567889999999988866
No 215
>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=43.64 E-value=7.6 Score=16.16 Aligned_cols=8 Identities=38% Similarity=0.945 Sum_probs=6.4
Q ss_pred eccccchh
Q psy12003 19 IWFQNRRM 26 (61)
Q Consensus 19 vWFqNrRa 26 (61)
.||.||+.
T Consensus 7 NWFE~~ge 14 (22)
T PF08452_consen 7 NWFESRGE 14 (22)
T ss_pred ehhhhCCc
Confidence 69999874
No 216
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. 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 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=43.38 E-value=3.7 Score=23.15 Aligned_cols=22 Identities=14% Similarity=0.113 Sum_probs=18.9
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
|-|-|+|..+|+|..+++-|-+
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~ 22 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEE 22 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5688999999999999988744
No 217
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=43.13 E-value=5.3 Score=22.20 Aligned_cols=16 Identities=19% Similarity=-0.006 Sum_probs=13.6
Q ss_pred hhhhhcCCCCCcccee
Q psy12003 3 LLRDKNPPRGTERQIK 18 (61)
Q Consensus 3 ~~eLA~~l~Lte~~Vq 18 (61)
..+||+.|||++..|.
T Consensus 22 Wk~laR~LGLse~~I~ 37 (96)
T cd08315 22 WNRLMRQLGLSENEID 37 (96)
T ss_pred HHHHHHHcCCCHHHHH
Confidence 3579999999999886
No 218
>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=43.11 E-value=4.6 Score=26.09 Aligned_cols=28 Identities=7% Similarity=0.001 Sum_probs=20.7
Q ss_pred chhhhhcCCCCCccceeeccccchhHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWK 29 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k 29 (61)
...|+|..||+++..|+....-=|.+-|
T Consensus 160 s~~EIA~~lgis~~tV~~~l~Rar~~Lr 187 (324)
T TIGR02960 160 RAAETAELLGTSTASVNSALQRARATLD 187 (324)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4679999999999999976553333333
No 219
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. 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, an
Probab=42.99 E-value=3.8 Score=23.26 Aligned_cols=22 Identities=0% Similarity=0.084 Sum_probs=18.4
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
|-|-|+|..+|+|..+|+-|-+
T Consensus 1 m~IgevA~~~gvs~~tlRyYe~ 22 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEE 22 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5678999999999999987733
No 220
>PF13223 DUF4031: Protein of unknown function (DUF4031)
Probab=42.67 E-value=6.9 Score=21.52 Aligned_cols=18 Identities=22% Similarity=0.218 Sum_probs=15.2
Q ss_pred chhhhhcCCCCCccceeecccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQN 23 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqN 23 (61)
||-+.|.++||.. -|||.
T Consensus 25 ELHafA~riGv~r----r~fq~ 42 (83)
T PF13223_consen 25 ELHAFAARIGVPR----RWFQR 42 (83)
T ss_pred HHHHHHHHcCCCH----HHHcC
Confidence 6778899999985 69997
No 221
>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=42.62 E-value=2.5 Score=26.32 Aligned_cols=31 Identities=10% Similarity=0.168 Sum_probs=26.6
Q ss_pred hhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRRMKWKKEHK 33 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~ 33 (61)
+-|||.-++++.++|-+|..|.+...+...+
T Consensus 17 ~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~ 47 (186)
T PF04936_consen 17 IDELADYFDVSRTSVSVWIKNGKDPKRAKPK 47 (186)
T ss_pred HHHHHHHHccCHHHHHHHHHcCCCcccccch
Confidence 5689999999999999999999888776644
No 222
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=42.54 E-value=3.9 Score=23.65 Aligned_cols=22 Identities=5% Similarity=-0.022 Sum_probs=18.9
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
|-|-|+|+.+|++..+++-|-+
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~ 23 (131)
T TIGR02043 2 FQIGELAKLCGVTSDTLRFYEK 23 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4578999999999999998855
No 223
>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=42.42 E-value=2.2 Score=21.21 Aligned_cols=15 Identities=13% Similarity=-0.048 Sum_probs=11.5
Q ss_pred hhhhcCCCCCcccee
Q psy12003 4 LRDKNPPRGTERQIK 18 (61)
Q Consensus 4 ~eLA~~l~Lte~~Vq 18 (61)
.+||..+|++..||+
T Consensus 32 ~~La~~~gi~~~qVR 46 (50)
T PF06971_consen 32 QELAEALGITPAQVR 46 (50)
T ss_dssp HHHHHHHTS-HHHHH
T ss_pred HHHHHHHCCCHHHhc
Confidence 478889999998884
No 224
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=42.28 E-value=4.9 Score=23.68 Aligned_cols=21 Identities=5% Similarity=-0.054 Sum_probs=17.8
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
...|+|..+|+++..|++...
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ 157 (172)
T PRK09651 137 TYSEIAHKLGVSVSSVKKYVA 157 (172)
T ss_pred CHHHHHHHhCCCHHHHHHHHH
Confidence 357999999999999997754
No 225
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=42.28 E-value=3.8 Score=21.01 Aligned_cols=17 Identities=6% Similarity=-0.082 Sum_probs=13.1
Q ss_pred chhhhhcCCCCCcccee
Q psy12003 2 NLLRDKNPPRGTERQIK 18 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~Vq 18 (61)
.+.+||..+++++..|.
T Consensus 16 S~~eLa~~~~~s~~~ve 32 (69)
T PF09012_consen 16 SLAELAREFGISPEAVE 32 (69)
T ss_dssp EHHHHHHHTT--HHHHH
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 47899999999999887
No 226
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal 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=42.22 E-value=4 Score=23.07 Aligned_cols=21 Identities=10% Similarity=0.058 Sum_probs=17.8
Q ss_pred CchhhhhcCCCCCccceeecc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWF 21 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWF 21 (61)
|-|-|+|..+|++..+++-|-
T Consensus 1 ~~I~eva~~~gvs~~tLRyYe 21 (123)
T cd04770 1 MKIGELAKAAGVSPDTIRYYE 21 (123)
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 567899999999999998773
No 227
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=42.04 E-value=5 Score=23.14 Aligned_cols=21 Identities=0% Similarity=-0.192 Sum_probs=17.8
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
-..|+|..+|+++..|+.-..
T Consensus 123 s~~eIA~~lgis~~tv~~~l~ 143 (159)
T PRK12527 123 SHQQIAEHLGISRSLVEKHIV 143 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHH
Confidence 467999999999999987655
No 228
>PF11388 DotA: Phagosome trafficking protein DotA; InterPro: IPR021528 DotA is essential for intracellular growth in Legionella []. DotA is thought to play an important role in regulating initial phagosome trafficking decisions either upon or immediately after macrophage uptake [].
Probab=41.96 E-value=39 Score=19.21 Aligned_cols=18 Identities=28% Similarity=0.481 Sum_probs=12.4
Q ss_pred ceeeccccchhHHHHHhh
Q psy12003 16 QIKIWFQNRRMKWKKEHK 33 (61)
Q Consensus 16 ~VqvWFqNrRak~kr~~~ 33 (61)
-+=+||||.-.|--.-+.
T Consensus 31 ~LC~WF~~~s~~l~qiqs 48 (105)
T PF11388_consen 31 LLCTWFQNKSDKLVQIQS 48 (105)
T ss_pred HHHHHHccCCchhhhhhH
Confidence 344899999887654443
No 229
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), 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=41.90 E-value=4 Score=22.62 Aligned_cols=20 Identities=10% Similarity=0.062 Sum_probs=17.1
Q ss_pred CchhhhhcCCCCCccceeec
Q psy12003 1 MNLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvW 20 (61)
|-|-|+|..+|+|..+|+-|
T Consensus 1 m~Ige~a~~~gvs~~tlRyY 20 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHY 20 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHH
Confidence 56889999999999988765
No 230
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=41.38 E-value=6.7 Score=23.23 Aligned_cols=21 Identities=10% Similarity=0.142 Sum_probs=17.0
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
...|+|..||+++..|++-..
T Consensus 155 s~~eIA~~lgis~~~v~~~l~ 175 (187)
T PRK12534 155 TYEELAARTDTPIGTVKSWIR 175 (187)
T ss_pred CHHHHHHHhCCChhHHHHHHH
Confidence 467999999999999985433
No 231
>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=41.31 E-value=4.7 Score=25.94 Aligned_cols=29 Identities=7% Similarity=-0.065 Sum_probs=22.5
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
...|+|..+|+++..|+..++-=|.+-+.
T Consensus 126 s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~ 154 (281)
T TIGR02957 126 PYEEIASIVGKSEANCRQLVSRARRHLDA 154 (281)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 46799999999999999887654544443
No 232
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=40.93 E-value=5 Score=25.52 Aligned_cols=29 Identities=3% Similarity=-0.113 Sum_probs=21.3
Q ss_pred CchhhhhcCCCCCccceeeccccchhHHH
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRMKWK 29 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~k 29 (61)
+.+.|+|..+|+++.+|+.+..-=+.|.|
T Consensus 220 ~s~~eIA~~lgvs~~~V~~~~~ra~~kLr 248 (256)
T PRK07408 220 LTQKEAAERLGISPVTVSRRVKKGLDQLK 248 (256)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 35789999999999999877553333333
No 233
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=40.63 E-value=9.5 Score=25.31 Aligned_cols=18 Identities=6% Similarity=-0.010 Sum_probs=15.4
Q ss_pred CchhhhhcCCCCCcccee
Q psy12003 1 MNLLRDKNPPRGTERQIK 18 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~Vq 18 (61)
||+.|+|..+||+...+-
T Consensus 38 lNvneiAe~lgLpqst~s 55 (308)
T COG4189 38 LNVNEIAEALGLPQSTMS 55 (308)
T ss_pred CCHHHHHHHhCCchhhhh
Confidence 688999999999988664
No 234
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=40.40 E-value=4.5 Score=23.39 Aligned_cols=21 Identities=5% Similarity=-0.105 Sum_probs=17.6
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
...|+|..+|++..+|++...
T Consensus 131 s~~EIA~~l~is~~tV~~~l~ 151 (161)
T PRK12528 131 GYGEIATELGISLATVKRYLN 151 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 467999999999999987654
No 235
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=40.29 E-value=5.3 Score=25.66 Aligned_cols=28 Identities=4% Similarity=-0.042 Sum_probs=20.8
Q ss_pred CchhhhhcCCCCCccceeeccccchhHH
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRMKW 28 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~ 28 (61)
+.+.|+|..+|++..+|+.+...-+.|.
T Consensus 232 ~t~~EIA~~lgis~~~V~~~~~ral~kL 259 (264)
T PRK07122 232 MTQTQIAERVGISQMHVSRLLAKTLARL 259 (264)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 4578999999999999987655433333
No 236
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are 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 have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. 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=40.26 E-value=4.4 Score=23.21 Aligned_cols=22 Identities=5% Similarity=-0.017 Sum_probs=18.4
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
|.|-|+|..+|++..+++-|-+
T Consensus 1 ~~I~e~a~~~gvs~~tlR~Ye~ 22 (126)
T cd04785 1 LSIGELARRTGVNVETIRYYES 22 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5678999999999999987743
No 237
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=39.88 E-value=6.8 Score=21.94 Aligned_cols=16 Identities=13% Similarity=0.025 Sum_probs=13.7
Q ss_pred hhhhhcCCCCCcccee
Q psy12003 3 LLRDKNPPRGTERQIK 18 (61)
Q Consensus 3 ~~eLA~~l~Lte~~Vq 18 (61)
.-++|+++||||..|.
T Consensus 23 wK~faR~lglse~~Id 38 (97)
T cd08316 23 VKKFVRKSGLSEPKID 38 (97)
T ss_pred HHHHHHHcCCCHHHHH
Confidence 4578999999999886
No 238
>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=39.79 E-value=5.6 Score=25.63 Aligned_cols=30 Identities=10% Similarity=-0.047 Sum_probs=22.4
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
-+.|+|..||+++.+|+.....-+.+-|+.
T Consensus 244 s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~ 273 (285)
T TIGR02394 244 TLEEVAAEVGLTRERVRQIQVEALKKLRRI 273 (285)
T ss_pred cHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467999999999999998765444444443
No 239
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=39.79 E-value=5.7 Score=24.49 Aligned_cols=22 Identities=18% Similarity=0.007 Sum_probs=18.0
Q ss_pred chhhhhcCCCCCccceeecccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQN 23 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqN 23 (61)
-+.|+|..+|++..+|+.+...
T Consensus 193 s~~eIA~~lgis~~tV~~~~~r 214 (224)
T TIGR02479 193 NLKEIGEVLGLTESRVSQIHSQ 214 (224)
T ss_pred CHHHHHHHhCCCHHHHHHHHHH
Confidence 4679999999999999876543
No 240
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=39.78 E-value=4.5 Score=23.72 Aligned_cols=22 Identities=5% Similarity=0.007 Sum_probs=18.6
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
|-|-|+|..+|++..+|+-|-+
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~ 23 (140)
T PRK09514 2 YRIGELAKLAEVTPDTLRFYEK 23 (140)
T ss_pred CcHHHHHHHHCcCHHHHHHHHH
Confidence 4578999999999999998854
No 241
>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=39.62 E-value=4.5 Score=16.41 Aligned_cols=18 Identities=0% Similarity=-0.114 Sum_probs=11.1
Q ss_pred hhhhhcCCCCCccceeec
Q psy12003 3 LLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvW 20 (61)
+.++|..++++...|.-|
T Consensus 24 ~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 24 VAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HHHHHHHHCCCHHHHHHh
Confidence 346677777776665544
No 242
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=39.50 E-value=5.6 Score=26.42 Aligned_cols=31 Identities=6% Similarity=-0.100 Sum_probs=24.0
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEH 32 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~ 32 (61)
-+.|+|..+|++..+|+.+...-+.|-|+.-
T Consensus 284 s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 284 TLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4689999999999999988765555555543
No 243
>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=39.49 E-value=4.6 Score=22.15 Aligned_cols=21 Identities=0% Similarity=-0.270 Sum_probs=18.1
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
-|-|+|..+|++..+++-|.+
T Consensus 2 ~i~eva~~~gvs~~tlR~ye~ 22 (97)
T cd04782 2 TTGEFAKLCGISKQTLFHYDK 22 (97)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467999999999999998854
No 244
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=39.18 E-value=6.6 Score=24.16 Aligned_cols=18 Identities=0% Similarity=-0.032 Sum_probs=15.4
Q ss_pred hhhhhcCCCCCccceeec
Q psy12003 3 LLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvW 20 (61)
-.|+|.+|++++++|+.-
T Consensus 155 nkeIA~~L~iS~~TVk~h 172 (207)
T PRK15411 155 TIQISDQMNIKAKTVSSH 172 (207)
T ss_pred HHHHHHHcCCCHHHHHHH
Confidence 368999999999999853
No 245
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=38.98 E-value=5.7 Score=22.84 Aligned_cols=25 Identities=8% Similarity=0.058 Sum_probs=21.5
Q ss_pred hhhhhcCCCCCccceeeccccchhH
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRRMK 27 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrRak 27 (61)
..+||..+|++...|.-|..+++..
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~~p 45 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDETEP 45 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 4689999999999999999988643
No 246
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=38.63 E-value=5.4 Score=22.89 Aligned_cols=24 Identities=0% Similarity=-0.224 Sum_probs=20.4
Q ss_pred chhhhhcCCCCCccceeeccccch
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
...|||..+|++...|--|.++++
T Consensus 20 sq~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 20 TKKELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCCC
Confidence 356899999999999998988876
No 247
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=38.38 E-value=5.7 Score=23.56 Aligned_cols=21 Identities=10% Similarity=0.077 Sum_probs=17.7
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
-..|+|..+|+++..|+....
T Consensus 145 s~~EIA~~l~is~~tv~~~l~ 165 (179)
T PRK09415 145 SIKEIAEVTGVNENTVKTRLK 165 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 357899999999999987655
No 248
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=38.33 E-value=6.3 Score=21.29 Aligned_cols=16 Identities=6% Similarity=-0.018 Sum_probs=13.5
Q ss_pred hhhhcCCCCCccceee
Q psy12003 4 LRDKNPPRGTERQIKI 19 (61)
Q Consensus 4 ~eLA~~l~Lte~~Vqv 19 (61)
-+||+.||+++..|.-
T Consensus 22 k~Lar~LGls~~dI~~ 37 (86)
T cd08318 22 KTLAPHLEMKDKEIRA 37 (86)
T ss_pred HHHHHHcCCCHHHHHH
Confidence 4789999999998863
No 249
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=38.07 E-value=7.9 Score=20.97 Aligned_cols=22 Identities=18% Similarity=0.080 Sum_probs=15.8
Q ss_pred hhhhcCCCCCcccee-eccccch
Q psy12003 4 LRDKNPPRGTERQIK-IWFQNRR 25 (61)
Q Consensus 4 ~eLA~~l~Lte~~Vq-vWFqNrR 25 (61)
-+||+.|||++..|. |=.+|++
T Consensus 17 k~lar~LGlse~~Id~Ie~~~~~ 39 (86)
T cd08779 17 QAIGLHLGLSYRELQRIKYNNRD 39 (86)
T ss_pred HHHHHHcCCCHHHHHHHHHHCcc
Confidence 368999999999887 3344443
No 250
>PRK09726 antitoxin HipB; Provisional
Probab=37.99 E-value=5.6 Score=21.32 Aligned_cols=23 Identities=9% Similarity=-0.143 Sum_probs=20.0
Q ss_pred hhhhhcCCCCCccceeeccccch
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
..+||..+|++...|.-|..+++
T Consensus 28 q~elA~~~gvs~~tis~~e~g~~ 50 (88)
T PRK09726 28 QSELAKKIGIKQATISNFENNPD 50 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHCCCC
Confidence 57899999999999999988764
No 251
>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=37.80 E-value=1.6 Score=21.53 Aligned_cols=24 Identities=8% Similarity=-0.128 Sum_probs=17.8
Q ss_pred chhhhhcCCCCCccceeeccccch
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
...|+|..+++++.+|.....+=+
T Consensus 20 ~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 20 SNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp -HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred CcchhHHhcCcchhhHHHHHHHHH
Confidence 456889999999999987654433
No 252
>PF14493 HTH_40: Helix-turn-helix domain
Probab=37.45 E-value=11 Score=20.28 Aligned_cols=18 Identities=11% Similarity=-0.049 Sum_probs=14.9
Q ss_pred CchhhhhcCCCCCcccee
Q psy12003 1 MNLLRDKNPPRGTERQIK 18 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~Vq 18 (61)
|.|.|+|..-+|++.+|.
T Consensus 14 ~si~eIA~~R~L~~sTI~ 31 (91)
T PF14493_consen 14 LSIEEIAKIRGLKESTIY 31 (91)
T ss_pred CCHHHHHHHcCCCHHHHH
Confidence 457889999999998885
No 253
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=37.24 E-value=7.1 Score=20.76 Aligned_cols=22 Identities=18% Similarity=0.098 Sum_probs=15.9
Q ss_pred hhhhcCCCCCccceee-ccccch
Q psy12003 4 LRDKNPPRGTERQIKI-WFQNRR 25 (61)
Q Consensus 4 ~eLA~~l~Lte~~Vqv-WFqNrR 25 (61)
.+||+.|||++..|.. =-.|++
T Consensus 15 k~laR~LGls~~~I~~ie~~~~~ 37 (79)
T cd08784 15 KRFFRKLGLSDNEIKVAELDNPQ 37 (79)
T ss_pred HHHHHHcCCCHHHHHHHHHcCCc
Confidence 4789999999998873 334444
No 254
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. 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=37.23 E-value=5.2 Score=22.83 Aligned_cols=20 Identities=5% Similarity=0.067 Sum_probs=17.2
Q ss_pred CchhhhhcCCCCCccceeec
Q psy12003 1 MNLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvW 20 (61)
|-|-|+|..+|++..+|+-|
T Consensus 1 m~I~e~a~~~gvs~~tlR~Y 20 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYY 20 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHH
Confidence 56789999999999999776
No 255
>KOG4580|consensus
Probab=37.20 E-value=13 Score=21.48 Aligned_cols=12 Identities=42% Similarity=0.805 Sum_probs=9.5
Q ss_pred eeeccccchhHH
Q psy12003 17 IKIWFQNRRMKW 28 (61)
Q Consensus 17 VqvWFqNrRak~ 28 (61)
-||||-|.|.--
T Consensus 10 pKV~fANERTFl 21 (112)
T KOG4580|consen 10 PKVWFANERTFL 21 (112)
T ss_pred ceeeeechHHHH
Confidence 479999999753
No 256
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=37.11 E-value=6.7 Score=23.36 Aligned_cols=16 Identities=0% Similarity=-0.301 Sum_probs=13.9
Q ss_pred hhhhhcCCCCCcccee
Q psy12003 3 LLRDKNPPRGTERQIK 18 (61)
Q Consensus 3 ~~eLA~~l~Lte~~Vq 18 (61)
..|||+++||++..|.
T Consensus 31 ~~eiA~~lglS~~tv~ 46 (164)
T PRK11169 31 NVELSKRVGLSPTPCL 46 (164)
T ss_pred HHHHHHHHCcCHHHHH
Confidence 5789999999999884
No 257
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=36.95 E-value=6.3 Score=24.82 Aligned_cols=26 Identities=4% Similarity=-0.126 Sum_probs=19.5
Q ss_pred chhhhhcCCCCCccceeeccccchhH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMK 27 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak 27 (61)
-+.|+|..+|+++.+|+.+...=+.+
T Consensus 223 s~~eIA~~lgis~~~V~~~~~ra~~~ 248 (255)
T TIGR02941 223 SQKETGERLGISQMHVSRLQRQAISK 248 (255)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 46799999999999998765433333
No 258
>COG2452 Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]
Probab=36.87 E-value=6 Score=24.99 Aligned_cols=27 Identities=4% Similarity=0.101 Sum_probs=23.5
Q ss_pred CchhhhhcCCCCCccceeeccccchhH
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNRRMK 27 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNrRak 27 (61)
|++.|-|..+|++..+...||...+-+
T Consensus 2 m~~~e~~~~lgis~~Tl~rw~r~G~i~ 28 (193)
T COG2452 2 LRPKEACQLLGISYSTLLRWIREGKIR 28 (193)
T ss_pred CCHHHHHHHhCcCHHHHHHHHHcCccc
Confidence 788999999999999999999876544
No 259
>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=36.40 E-value=6 Score=23.25 Aligned_cols=20 Identities=5% Similarity=0.115 Sum_probs=16.4
Q ss_pred CchhhhhcCCCCCccceeec
Q psy12003 1 MNLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvW 20 (61)
+...|+|..+|+++..|+.=
T Consensus 157 ~s~~eIA~~lgis~~~v~~~ 176 (189)
T TIGR02984 157 LSFAEVAERMDRSEGAVSML 176 (189)
T ss_pred CCHHHHHHHHCcCHHHHHHH
Confidence 34679999999999999753
No 260
>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=36.05 E-value=3.5 Score=21.28 Aligned_cols=17 Identities=18% Similarity=0.348 Sum_probs=13.2
Q ss_pred hhcCCCCCccceeeccc
Q psy12003 6 DKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 6 LA~~l~Lte~~VqvWFq 22 (61)
-|++.|+++.+|+-|.+
T Consensus 31 aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 31 AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp HHHHTTS-HHHHHHHHT
T ss_pred HHHHhCccHHHHHHHHH
Confidence 47888999999998854
No 261
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=36.05 E-value=10 Score=20.87 Aligned_cols=23 Identities=4% Similarity=0.019 Sum_probs=20.4
Q ss_pred hhhhhcCCCCCccceeeccccch
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
+.+||.++|++...+--.|.|+-
T Consensus 35 ~~~Ia~~agvs~~~~Y~~f~~K~ 57 (201)
T COG1309 35 VDEIAKAAGVSKGTLYRHFPSKE 57 (201)
T ss_pred HHHHHHHhCCCcchhHHHcCCHH
Confidence 57899999999999999999874
No 262
>COG5264 VTC1 Vacuolar transporter chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=35.82 E-value=15 Score=21.80 Aligned_cols=12 Identities=42% Similarity=0.805 Sum_probs=9.5
Q ss_pred eeeccccchhHH
Q psy12003 17 IKIWFQNRRMKW 28 (61)
Q Consensus 17 VqvWFqNrRak~ 28 (61)
-||||-|.|.--
T Consensus 25 pKv~fAnERTfl 36 (126)
T COG5264 25 PKVWFANERTFL 36 (126)
T ss_pred ceeeeechHHHH
Confidence 469999999753
No 263
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=35.56 E-value=7.5 Score=23.39 Aligned_cols=29 Identities=7% Similarity=-0.118 Sum_probs=21.2
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr 30 (61)
...|+|..||+++..|+++..--|.+-++
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (188)
T PRK12517 146 SGEEIAEILDLNKNTVMTRLFRARNQLKE 174 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35799999999999999875533433333
No 264
>PRK13749 transcriptional regulator MerD; Provisional
Probab=35.41 E-value=6 Score=22.98 Aligned_cols=20 Identities=5% Similarity=-0.047 Sum_probs=17.0
Q ss_pred CchhhhhcCCCCCccceeec
Q psy12003 1 MNLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvW 20 (61)
|-|-|+|..+|+|..+|+-|
T Consensus 4 ~tIgelA~~~gvS~~tiR~Y 23 (121)
T PRK13749 4 YTVSRLALDAGVSVHIVRDY 23 (121)
T ss_pred CcHHHHHHHHCCCHHHHHHH
Confidence 35789999999999999865
No 265
>COG3747 Phage terminase, small subunit [DNA replication, recombination, and repair]
Probab=35.38 E-value=9.5 Score=23.36 Aligned_cols=15 Identities=27% Similarity=0.067 Sum_probs=12.8
Q ss_pred CchhhhhcCCCCCcc
Q psy12003 1 MNLLRDKNPPRGTER 15 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~ 15 (61)
++|..||..|||++.
T Consensus 119 ~~l~klaSeLGltP~ 133 (160)
T COG3747 119 RNLLKLASELGLTPS 133 (160)
T ss_pred HHHHHHHHHhCCChH
Confidence 468999999999974
No 266
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=35.17 E-value=7.6 Score=23.36 Aligned_cols=18 Identities=11% Similarity=-0.007 Sum_probs=15.7
Q ss_pred chhhhhcCCCCCccceee
Q psy12003 2 NLLRDKNPPRGTERQIKI 19 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~Vqv 19 (61)
...|+|..+|+++.+|++
T Consensus 152 s~~EIA~~lg~s~~tV~~ 169 (192)
T PRK09643 152 SVADAARMLGVAEGTVKS 169 (192)
T ss_pred CHHHHHHHHCcCHHHHHH
Confidence 467999999999999975
No 267
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=35.08 E-value=6.8 Score=21.06 Aligned_cols=19 Identities=11% Similarity=0.010 Sum_probs=15.6
Q ss_pred CchhhhhcCCCCCccceee
Q psy12003 1 MNLLRDKNPPRGTERQIKI 19 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~Vqv 19 (61)
++..|||..+|+++..+.+
T Consensus 16 ~~~~eLa~~igis~~~ls~ 34 (73)
T COG3655 16 ISLKELAEAIGISEANLSK 34 (73)
T ss_pred hhHHHHHHHHcccHHHHHH
Confidence 3578999999999988763
No 268
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=34.56 E-value=7.8 Score=24.70 Aligned_cols=30 Identities=13% Similarity=0.051 Sum_probs=21.9
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
-+.|+|..+|+++.+|+.....-+.+-|+.
T Consensus 230 s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 230 TLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467999999999999986655444444443
No 269
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=34.31 E-value=5.6 Score=22.76 Aligned_cols=18 Identities=6% Similarity=0.014 Sum_probs=15.9
Q ss_pred hhhhhcCCCCCccceeec
Q psy12003 3 LLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvW 20 (61)
|-|+|..+|++..+|+-|
T Consensus 2 I~e~a~~~gvs~~tlR~Y 19 (124)
T TIGR02051 2 IGELAKAAGVNVETIRYY 19 (124)
T ss_pred HHHHHHHHCcCHHHHHHH
Confidence 568999999999999887
No 270
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=34.15 E-value=10 Score=21.74 Aligned_cols=17 Identities=0% Similarity=-0.246 Sum_probs=14.4
Q ss_pred chhhhhcCCCCCcccee
Q psy12003 2 NLLRDKNPPRGTERQIK 18 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~Vq 18 (61)
-+.|||.++|+++..|.
T Consensus 24 ~~~eia~~lglS~~~v~ 40 (154)
T COG1522 24 SNAELAERVGLSPSTVL 40 (154)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 36799999999998884
No 271
>KOG4752|consensus
Probab=33.88 E-value=27 Score=14.82 Aligned_cols=7 Identities=57% Similarity=1.355 Sum_probs=3.7
Q ss_pred hhHHHHH
Q psy12003 25 RMKWKKE 31 (61)
Q Consensus 25 Rak~kr~ 31 (61)
|+||++.
T Consensus 2 r~kwrkk 8 (26)
T KOG4752|consen 2 RAKWRKK 8 (26)
T ss_pred chHHHHH
Confidence 4555554
No 272
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=33.87 E-value=8.4 Score=20.79 Aligned_cols=15 Identities=27% Similarity=0.014 Sum_probs=13.0
Q ss_pred hhhhcCCCCCcccee
Q psy12003 4 LRDKNPPRGTERQIK 18 (61)
Q Consensus 4 ~eLA~~l~Lte~~Vq 18 (61)
.+||+.||+++..|.
T Consensus 19 k~LAr~Lg~se~dI~ 33 (84)
T cd08804 19 TELARELDFTEEQIH 33 (84)
T ss_pred HHHHHHcCCCHHHHH
Confidence 578999999999876
No 273
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=33.86 E-value=8.3 Score=20.56 Aligned_cols=16 Identities=13% Similarity=0.025 Sum_probs=13.5
Q ss_pred hhhhcCCCCCccceee
Q psy12003 4 LRDKNPPRGTERQIKI 19 (61)
Q Consensus 4 ~eLA~~l~Lte~~Vqv 19 (61)
.+||+.||+++..|..
T Consensus 19 ~~LAr~Lg~~~~dI~~ 34 (84)
T cd08317 19 PQLARELGVSETDIDL 34 (84)
T ss_pred HHHHHHcCCCHHHHHH
Confidence 5799999999987774
No 274
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=33.82 E-value=7 Score=25.52 Aligned_cols=22 Identities=5% Similarity=-0.126 Sum_probs=18.2
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
|...|+|..||+++..|+.-..
T Consensus 170 ~s~~EIA~~lgis~~tVk~~l~ 191 (339)
T PRK08241 170 WSAAEVAELLDTSVAAVNSALQ 191 (339)
T ss_pred CCHHHHHHHhCCCHHHHHHHHH
Confidence 3467999999999999987654
No 275
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which 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 N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=33.58 E-value=6.6 Score=22.06 Aligned_cols=21 Identities=0% Similarity=-0.064 Sum_probs=17.9
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
-|-|+|..+|++..+|+-|-+
T Consensus 2 ~Ige~A~~~gvs~~tlR~ye~ 22 (107)
T cd01111 2 SISQLALDAGVSVHIVRDYLL 22 (107)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999998844
No 276
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=33.51 E-value=5.4 Score=24.88 Aligned_cols=26 Identities=15% Similarity=-0.127 Sum_probs=20.1
Q ss_pred hhhhhcCCCCCccceeeccccchhHH
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRRMKW 28 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrRak~ 28 (61)
-.|+|..|++++.+|+.+..+=..|.
T Consensus 173 ~~eIA~~L~iS~~TVk~~~~~i~~Kl 198 (216)
T PRK10100 173 NNEIARSLFISENTVKTHLYNLFKKI 198 (216)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 36889999999999998766554443
No 277
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=32.82 E-value=5.7 Score=22.73 Aligned_cols=22 Identities=14% Similarity=0.096 Sum_probs=18.9
Q ss_pred hhhcCCCCCccceeeccccchh
Q psy12003 5 RDKNPPRGTERQIKIWFQNRRM 26 (61)
Q Consensus 5 eLA~~l~Lte~~VqvWFqNrRa 26 (61)
+.|+.||++..+|+-|=|+|+.
T Consensus 62 vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 62 VFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred HHHHHHCCCHHHHHHHHcCCcC
Confidence 5688899999999999888764
No 278
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=32.75 E-value=9 Score=19.03 Aligned_cols=20 Identities=15% Similarity=0.110 Sum_probs=15.8
Q ss_pred chhhhhcCCCCCccceeecc
Q psy12003 2 NLLRDKNPPRGTERQIKIWF 21 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWF 21 (61)
.|.+||..+|+++..+.--|
T Consensus 3 ~~~~la~~~~~s~~~l~~~f 22 (84)
T smart00342 3 TLEDLAEALGMSPRHLQRLF 22 (84)
T ss_pred CHHHHHHHhCCCHHHHHHHH
Confidence 47889999999998876444
No 279
>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=32.64 E-value=24 Score=19.78 Aligned_cols=13 Identities=31% Similarity=0.910 Sum_probs=10.0
Q ss_pred ccchhHHHHHhhh
Q psy12003 22 QNRRMKWKKEHKM 34 (61)
Q Consensus 22 qNrRak~kr~~~~ 34 (61)
.|||.+|++.+..
T Consensus 37 RnRRRRWR~rq~Q 49 (91)
T PF00424_consen 37 RNRRRRWRARQRQ 49 (91)
T ss_dssp HHHHHHHHHHHHH
T ss_pred cchhhhHHHHHHH
Confidence 5889999988653
No 280
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. 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=32.07 E-value=7.2 Score=22.20 Aligned_cols=20 Identities=10% Similarity=0.114 Sum_probs=17.0
Q ss_pred CchhhhhcCCCCCccceeec
Q psy12003 1 MNLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvW 20 (61)
+-|-|+|..+|+|..+++-|
T Consensus 1 ~~Igeva~~~gvs~~tlRyY 20 (118)
T cd04776 1 YTISELAREFDVTPRTLRFY 20 (118)
T ss_pred CCHHHHHHHHCcCHHHHHHH
Confidence 35778999999999999877
No 281
>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=31.84 E-value=8 Score=24.18 Aligned_cols=30 Identities=13% Similarity=-0.027 Sum_probs=22.6
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
.+.|+|..+|++..+|+-..+.=..|.|..
T Consensus 198 t~~EIA~~lgis~~~V~q~~~~al~kLr~~ 227 (238)
T TIGR02393 198 TLEEVGKEFNVTRERIRQIESKALRKLRHP 227 (238)
T ss_pred cHHHHHHHHCCCHHHHHHHHHHHHHHHhhh
Confidence 478999999999999987765555554443
No 282
>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=31.68 E-value=8.9 Score=23.79 Aligned_cols=20 Identities=0% Similarity=-0.356 Sum_probs=16.7
Q ss_pred chhhhhcCCCCCccceeecc
Q psy12003 2 NLLRDKNPPRGTERQIKIWF 21 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWF 21 (61)
.+.|+|..+|+++.+|+.+.
T Consensus 196 S~~EIAe~lgis~~tV~~~~ 215 (227)
T TIGR02846 196 TQREIAKILGISRSYVSRIE 215 (227)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 46899999999999997653
No 283
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=31.60 E-value=9.4 Score=20.75 Aligned_cols=20 Identities=10% Similarity=-0.215 Sum_probs=15.9
Q ss_pred hhhhcCCCCCccceeecccc
Q psy12003 4 LRDKNPPRGTERQIKIWFQN 23 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvWFqN 23 (61)
..||+.||||+..|...-.+
T Consensus 17 ~~Lar~Lgls~~~I~~i~~~ 36 (83)
T cd08319 17 EQVLLDLGLSQTDIYRCKEN 36 (83)
T ss_pred HHHHHHcCCCHHHHHHHHHh
Confidence 36899999999988866555
No 284
>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=31.56 E-value=5.4 Score=25.00 Aligned_cols=27 Identities=15% Similarity=0.011 Sum_probs=21.4
Q ss_pred hhhhhcCCCCCccceeeccccchhHHH
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRRMKWK 29 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrRak~k 29 (61)
..|+|..|++++.+|+....|=+.|-+
T Consensus 189 ~~eIa~~l~is~~Tv~~~l~~~~~kl~ 215 (232)
T TIGR03541 189 QADIAAILGISERTVENHLRSARRKLG 215 (232)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence 468899999999999988776655544
No 285
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=31.17 E-value=9.6 Score=20.71 Aligned_cols=16 Identities=25% Similarity=0.009 Sum_probs=13.9
Q ss_pred hhhhcCCCCCccceee
Q psy12003 4 LRDKNPPRGTERQIKI 19 (61)
Q Consensus 4 ~eLA~~l~Lte~~Vqv 19 (61)
.+||+.||+++..|..
T Consensus 17 k~lar~LG~s~~eI~~ 32 (86)
T cd08777 17 KRCARKLGFTESEIEE 32 (86)
T ss_pred HHHHHHcCCCHHHHHH
Confidence 4789999999999885
No 286
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=31.14 E-value=4.6 Score=20.15 Aligned_cols=24 Identities=8% Similarity=-0.053 Sum_probs=19.5
Q ss_pred hhhhhcCCCCCccceeeccccchh
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRRM 26 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrRa 26 (61)
..++|..+|++...|.-|-.+++.
T Consensus 17 ~~~lA~~~g~s~s~v~~iE~G~~~ 40 (64)
T PF13560_consen 17 QAQLADRLGVSQSTVSRIERGRRP 40 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSSS
T ss_pred HHHHHHHHCcCHHHHHHHHCCCCC
Confidence 468899999999999988888874
No 287
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=30.98 E-value=7.8 Score=23.30 Aligned_cols=22 Identities=0% Similarity=-0.106 Sum_probs=18.1
Q ss_pred CchhhhhcCCCCCccceeeccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFq 22 (61)
|-|-|+|..+|++..+|+-|-+
T Consensus 12 ~~IgevAk~~gvs~~TlRyYE~ 33 (154)
T PRK15002 12 LTPGEVAKRSGVAVSALHFYES 33 (154)
T ss_pred ccHHHHHHHHCcCHHHHHHHHH
Confidence 4577899999999999987754
No 288
>cd04772 HTH_TioE_rpt1 First 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 contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=30.90 E-value=6.9 Score=21.56 Aligned_cols=20 Identities=0% Similarity=-0.091 Sum_probs=17.1
Q ss_pred chhhhhcCCCCCccceeecc
Q psy12003 2 NLLRDKNPPRGTERQIKIWF 21 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWF 21 (61)
.+.|+|..+|++..+++-|-
T Consensus 2 ~i~e~A~~~gvs~~tlR~Ye 21 (99)
T cd04772 2 RTVDLARAIGLSPQTVRNYE 21 (99)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 36789999999999998873
No 289
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=30.79 E-value=7.6 Score=22.99 Aligned_cols=20 Identities=5% Similarity=0.047 Sum_probs=16.7
Q ss_pred CchhhhhcCCCCCccceeec
Q psy12003 1 MNLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvW 20 (61)
|.|-|+|..+|+|..+++-|
T Consensus 8 ~~IgevAk~~Gvs~~TLRyY 27 (144)
T PRK13752 8 LTIGVFAKAAGVNVETIRFY 27 (144)
T ss_pred ccHHHHHHHHCcCHHHHHHH
Confidence 35778999999999998876
No 290
>PF06032 DUF917: Protein of unknown function (DUF917); InterPro: IPR010318 This family consists of hypothetical bacterial and archaeal proteins of unknown function.; PDB: 2O3I_B.
Probab=30.71 E-value=23 Score=24.03 Aligned_cols=12 Identities=42% Similarity=0.642 Sum_probs=10.1
Q ss_pred Cccceeeccccc
Q psy12003 13 TERQIKIWFQNR 24 (61)
Q Consensus 13 te~~VqvWFqNr 24 (61)
.++.++|||||.
T Consensus 267 ~~~~~~i~fqNE 278 (353)
T PF06032_consen 267 KGRTLRIEFQNE 278 (353)
T ss_dssp TTEEEEEEESSS
T ss_pred CCCEEEEEEEcC
Confidence 567899999996
No 291
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=30.68 E-value=9.5 Score=23.26 Aligned_cols=16 Identities=0% Similarity=-0.203 Sum_probs=14.1
Q ss_pred hhhhhcCCCCCcccee
Q psy12003 3 LLRDKNPPRGTERQIK 18 (61)
Q Consensus 3 ~~eLA~~l~Lte~~Vq 18 (61)
..|+|.+|++++.+|+
T Consensus 180 ~~eIa~~l~iS~~Tv~ 195 (225)
T PRK10046 180 AETVAQALTISRTTAR 195 (225)
T ss_pred HHHHHHHhCccHHHHH
Confidence 3579999999999997
No 292
>COG5566 Uncharacterized conserved protein [Function unknown]
Probab=30.65 E-value=11 Score=22.46 Aligned_cols=19 Identities=21% Similarity=0.067 Sum_probs=16.5
Q ss_pred CchhhhhcCCCCCccceee
Q psy12003 1 MNLLRDKNPPRGTERQIKI 19 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~Vqv 19 (61)
|++.|||.+-.||+..|-.
T Consensus 103 ~n~~eLaKkYrlS~~~Iy~ 121 (137)
T COG5566 103 SNYVELAKKYRLSENHIYR 121 (137)
T ss_pred ccHHHHHHHhcccHHHHHH
Confidence 5889999999999988753
No 293
>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=30.60 E-value=8.7 Score=23.74 Aligned_cols=20 Identities=10% Similarity=-0.149 Sum_probs=16.8
Q ss_pred CchhhhhcCCCCCccceeec
Q psy12003 1 MNLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvW 20 (61)
+.+.|+|..+|++..+|..+
T Consensus 200 ~t~~eIA~~lgis~~~V~~~ 219 (231)
T TIGR02885 200 KTQTEVANMLGISQVQVSRL 219 (231)
T ss_pred CCHHHHHHHHCcCHHHHHHH
Confidence 45789999999999998754
No 294
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=30.54 E-value=9.3 Score=23.76 Aligned_cols=20 Identities=0% Similarity=-0.308 Sum_probs=16.6
Q ss_pred chhhhhcCCCCCccceeecc
Q psy12003 2 NLLRDKNPPRGTERQIKIWF 21 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWF 21 (61)
.+.|+|..+|+|+.+|+.+-
T Consensus 197 S~~EIA~~lgis~~tV~~~~ 216 (233)
T PRK05803 197 TQREIAKALGISRSYVSRIE 216 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 36789999999999997653
No 295
>PRK10651 transcriptional regulator NarL; Provisional
Probab=30.44 E-value=6.9 Score=22.65 Aligned_cols=25 Identities=16% Similarity=-0.044 Sum_probs=19.1
Q ss_pred hhhhhcCCCCCccceeeccccchhH
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRRMK 27 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrRak 27 (61)
..++|+.+++++.+|++..++=+.|
T Consensus 173 ~~~ia~~l~is~~tV~~~~~~l~~K 197 (216)
T PRK10651 173 NKMIARRLDITESTVKVHVKHMLKK 197 (216)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 3578899999999998776655544
No 296
>PF04391 DUF533: Protein of unknown function (DUF533); InterPro: IPR007486 Some family members may be secreted or integral membrane proteins.
Probab=30.39 E-value=11 Score=23.53 Aligned_cols=16 Identities=6% Similarity=-0.213 Sum_probs=13.3
Q ss_pred hhhhhcCCCCCcccee
Q psy12003 3 LLRDKNPPRGTERQIK 18 (61)
Q Consensus 3 ~~eLA~~l~Lte~~Vq 18 (61)
|.+||..|+|++..|.
T Consensus 166 L~~LA~aL~L~~~lv~ 181 (188)
T PF04391_consen 166 LDELAQALGLDPDLVA 181 (188)
T ss_pred HHHHHHHhCcCHHHHH
Confidence 6789999999987663
No 297
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 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 subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=30.34 E-value=4.8 Score=19.42 Aligned_cols=17 Identities=6% Similarity=-0.070 Sum_probs=12.2
Q ss_pred chhhhhcCCCCCcccee
Q psy12003 2 NLLRDKNPPRGTERQIK 18 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~Vq 18 (61)
-+.|||+.+|++...|.
T Consensus 20 t~~eia~~~gl~~stv~ 36 (52)
T PF09339_consen 20 TLSEIARALGLPKSTVH 36 (52)
T ss_dssp EHHHHHHHHTS-HHHHH
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 36789999998877653
No 298
>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=30.29 E-value=6 Score=25.53 Aligned_cols=26 Identities=12% Similarity=-0.211 Sum_probs=20.4
Q ss_pred hhhhhcCCCCCccceeeccccchhHH
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRRMKW 28 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrRak~ 28 (61)
-.|+|..|++++.+|+...+|=+.|-
T Consensus 208 ~~eIA~~L~IS~~TVk~hl~~i~~KL 233 (247)
T TIGR03020 208 NEEIAAILGISSLTVKNHLQHIFKKL 233 (247)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHh
Confidence 35889999999999998776655443
No 299
>PF11516 DUF3220: Protein of unknown function (DUF3120); InterPro: IPR021597 This family of proteins with unknown function appears to be restricted to Bordetella. ; PDB: 2JPF_A.
Probab=30.26 E-value=7.4 Score=21.59 Aligned_cols=12 Identities=33% Similarity=0.875 Sum_probs=8.8
Q ss_pred ccceeeccccch
Q psy12003 14 ERQIKIWFQNRR 25 (61)
Q Consensus 14 e~~VqvWFqNrR 25 (61)
...|+||.||--
T Consensus 30 qgdvkvwmqnle 41 (106)
T PF11516_consen 30 QGDVKVWMQNLE 41 (106)
T ss_dssp -HHHHHHHHHHH
T ss_pred cccHHHHHHHHH
Confidence 346899999953
No 300
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=29.78 E-value=7.7 Score=20.45 Aligned_cols=20 Identities=5% Similarity=0.268 Sum_probs=17.2
Q ss_pred hhhhhcCCCCCccceeeccc
Q psy12003 3 LLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFq 22 (61)
+++.|..+|+++..|.-|-.
T Consensus 16 ~~~Aa~~lG~~~~~v~~wv~ 35 (65)
T PF05344_consen 16 VAQAADRLGTDPGTVRRWVR 35 (65)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 67889999999999998854
No 301
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=29.66 E-value=10 Score=24.20 Aligned_cols=21 Identities=10% Similarity=-0.111 Sum_probs=17.5
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
.+.|+|..+|+++.+|+....
T Consensus 223 t~~EIA~~lgis~~~V~~~~~ 243 (257)
T PRK05911 223 VLKEIGKILGVSESRVSQIHS 243 (257)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 478999999999999986543
No 302
>cd01763 Sumo Small ubiquitin-related modifier (SUMO). Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.
Probab=29.39 E-value=27 Score=18.63 Aligned_cols=24 Identities=8% Similarity=0.122 Sum_probs=19.3
Q ss_pred hhhcCCCCCccceeeccccchhHH
Q psy12003 5 RDKNPPRGTERQIKIWFQNRRMKW 28 (61)
Q Consensus 5 eLA~~l~Lte~~VqvWFqNrRak~ 28 (61)
..+.+-|++..+++.+|..++-..
T Consensus 40 ~y~~~~gi~~~~~rf~f~G~~L~~ 63 (87)
T cd01763 40 AYCQRQGLSMNSVRFLFDGQRIRD 63 (87)
T ss_pred HHHHHhCCCccceEEEECCeECCC
Confidence 456777999999999999887653
No 303
>PHA02535 P terminase ATPase subunit; Provisional
Probab=29.34 E-value=9.9 Score=27.69 Aligned_cols=27 Identities=19% Similarity=0.313 Sum_probs=22.3
Q ss_pred hhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
+.|+|..||+++++|.-| -+|.+|...
T Consensus 21 v~eIA~~LGv~~~Tl~~W--~kr~~w~~~ 47 (581)
T PHA02535 21 VAEIAEELGLKSRTIYSW--KERDGWRDL 47 (581)
T ss_pred HHHHHHHhCCChhHHHHH--hcccccccc
Confidence 678999999999999999 556666654
No 304
>cd01793 Fubi Fubi ubiquitin-like protein. Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.
Probab=29.34 E-value=25 Score=17.97 Aligned_cols=23 Identities=0% Similarity=-0.133 Sum_probs=18.5
Q ss_pred hhhcCCCCCccceeeccccchhH
Q psy12003 5 RDKNPPRGTERQIKIWFQNRRMK 27 (61)
Q Consensus 5 eLA~~l~Lte~~VqvWFqNrRak 27 (61)
.++...|++..+.+++|.++..+
T Consensus 27 ~i~~~~gip~~~q~Li~~Gk~L~ 49 (74)
T cd01793 27 HVAGLEGIDVEDQVLLLAGVPLE 49 (74)
T ss_pred HHHhhhCCCHHHEEEEECCeECC
Confidence 45777889999999999987654
No 305
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=29.23 E-value=7.6 Score=22.16 Aligned_cols=24 Identities=4% Similarity=-0.242 Sum_probs=18.4
Q ss_pred hhhhhcCCCCCccceeeccccchh
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRRM 26 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrRa 26 (61)
..++|..+++++.+|+.+.++=+.
T Consensus 167 ~~~Ia~~l~~s~~tv~~~~~~~~~ 190 (211)
T PRK15369 167 NRDIAEQLSISIKTVETHRLNMMR 190 (211)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHH
Confidence 457888999999999987665333
No 306
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=28.97 E-value=9.4 Score=19.50 Aligned_cols=21 Identities=5% Similarity=-0.089 Sum_probs=15.9
Q ss_pred hhhhcCCCCCccceeeccccc
Q psy12003 4 LRDKNPPRGTERQIKIWFQNR 24 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvWFqNr 24 (61)
.+||..||+++..|...=.+.
T Consensus 14 ~~la~~Lgl~~~~I~~i~~~~ 34 (79)
T cd01670 14 KKLARKLGLSDGEIDQIEEDN 34 (79)
T ss_pred HHHHHHhCCCHHHHHHHHHhC
Confidence 468999999999888654444
No 307
>PHA03236 DNA packaging protein UL33; Provisional
Probab=28.90 E-value=30 Score=20.50 Aligned_cols=23 Identities=22% Similarity=0.309 Sum_probs=14.7
Q ss_pred chhhhhcCC-CCCccceeeccccc
Q psy12003 2 NLLRDKNPP-RGTERQIKIWFQNR 24 (61)
Q Consensus 2 ~~~eLA~~l-~Lte~~VqvWFqNr 24 (61)
.|-+|..+. .-++....|||.+=
T Consensus 23 ~ld~L~~~Y~~~~~~~~~iwFE~l 46 (127)
T PHA03236 23 DLDALEEKYLIDDDFQYRIWFEYL 46 (127)
T ss_pred CHHHHHHHhccCCccceeeeeccc
Confidence 344555554 33667889999864
No 308
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=28.89 E-value=10 Score=22.80 Aligned_cols=16 Identities=6% Similarity=-0.083 Sum_probs=14.3
Q ss_pred hhhhcCCCCCccceee
Q psy12003 4 LRDKNPPRGTERQIKI 19 (61)
Q Consensus 4 ~eLA~~l~Lte~~Vqv 19 (61)
.|+|.+|++++++|+.
T Consensus 169 ~eIA~~l~iS~~TV~~ 184 (216)
T PRK10840 169 TEIAKKLNRSIKTISS 184 (216)
T ss_pred HHHHHHHCCCHHHHHH
Confidence 5889999999999984
No 309
>PRK15482 transcriptional regulator MurR; Provisional
Probab=28.69 E-value=17 Score=23.21 Aligned_cols=18 Identities=6% Similarity=-0.075 Sum_probs=15.0
Q ss_pred CchhhhhcCCCCCcccee
Q psy12003 1 MNLLRDKNPPRGTERQIK 18 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~Vq 18 (61)
|-+.|||.++++++.+|-
T Consensus 35 ~si~elA~~~~vS~aTv~ 52 (285)
T PRK15482 35 VSSRKMAKQLGISQSSIV 52 (285)
T ss_pred cCHHHHHHHhCCCHHHHH
Confidence 457899999999999874
No 310
>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=28.68 E-value=5.1 Score=19.78 Aligned_cols=24 Identities=8% Similarity=-0.121 Sum_probs=18.0
Q ss_pred chhhhhcCCCCCccceeeccccch
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
.+.++|..++++..+|.-|-.+++
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 456788899999888888887766
No 311
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=28.64 E-value=12 Score=18.47 Aligned_cols=8 Identities=63% Similarity=1.294 Sum_probs=3.8
Q ss_pred eeeccccchh
Q psy12003 17 IKIWFQNRRM 26 (61)
Q Consensus 17 VqvWFqNrRa 26 (61)
|..| |||+
T Consensus 54 i~~W--N~Ra 61 (61)
T PF14354_consen 54 IEAW--NRRA 61 (61)
T ss_pred HHHH--cCCC
Confidence 3345 5553
No 312
>PRK10403 transcriptional regulator NarP; Provisional
Probab=28.44 E-value=7.6 Score=22.41 Aligned_cols=24 Identities=17% Similarity=0.091 Sum_probs=18.1
Q ss_pred hhhhcCCCCCccceeeccccchhH
Q psy12003 4 LRDKNPPRGTERQIKIWFQNRRMK 27 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvWFqNrRak 27 (61)
.++|..+++++++|++...|=+.|
T Consensus 172 ~~ia~~l~~s~~tv~~~~~~i~~k 195 (215)
T PRK10403 172 KQIASVLNISEQTVKVHIRNLLRK 195 (215)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHH
Confidence 468889999999998776654444
No 313
>PF09292 Neil1-DNA_bind: Endonuclease VIII-like 1, DNA bind; InterPro: IPR015371 This domain is predominantly found in Endonuclease VIII-like 1 proteins and adopts a glucocorticoid receptor-like fold. Structural analysis reveals a zincless finger motif that is required for glycosylase activity []. ; PDB: 1TDH_A.
Probab=28.30 E-value=22 Score=16.80 Aligned_cols=6 Identities=67% Similarity=1.575 Sum_probs=4.5
Q ss_pred eecccc
Q psy12003 18 KIWFQN 23 (61)
Q Consensus 18 qvWFqN 23 (61)
.||||.
T Consensus 27 TiWFqG 32 (39)
T PF09292_consen 27 TIWFQG 32 (39)
T ss_dssp EEEESS
T ss_pred EEEeeC
Confidence 389984
No 314
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=28.26 E-value=6.2 Score=19.89 Aligned_cols=17 Identities=0% Similarity=-0.232 Sum_probs=13.7
Q ss_pred chhhhhcCCCCCcccee
Q psy12003 2 NLLRDKNPPRGTERQIK 18 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~Vq 18 (61)
...|||..+|++..+|.
T Consensus 24 t~~eIa~~l~i~~~~v~ 40 (68)
T PF01978_consen 24 TAEEIAEELGISRSTVY 40 (68)
T ss_dssp EHHHHHHHHTSSHHHHH
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 35789999999988875
No 315
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. 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 sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=28.04 E-value=25 Score=24.45 Aligned_cols=18 Identities=17% Similarity=0.041 Sum_probs=16.0
Q ss_pred CchhhhhcCCCCCcccee
Q psy12003 1 MNLLRDKNPPRGTERQIK 18 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~Vq 18 (61)
|.|.++|..+||.|.+|-
T Consensus 319 LtlkdiA~~lglheSTVS 336 (429)
T TIGR02395 319 LTLREVAEELGLHESTIS 336 (429)
T ss_pred CcHHHHHHHhCCCccchh
Confidence 568899999999999994
No 316
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=27.66 E-value=14 Score=22.65 Aligned_cols=20 Identities=5% Similarity=-0.120 Sum_probs=16.1
Q ss_pred hhhhhcCCCCCccceeeccc
Q psy12003 3 LLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFq 22 (61)
..|+|.++++++.+|+.-+.
T Consensus 181 ~~eIA~~l~iS~~Tv~~~~~ 200 (239)
T PRK10430 181 TDELANAVNISRVSCRKYLI 200 (239)
T ss_pred HHHHHHHhCchHHHHHHHHH
Confidence 45799999999999986543
No 317
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=27.64 E-value=22 Score=17.92 Aligned_cols=22 Identities=9% Similarity=0.184 Sum_probs=17.9
Q ss_pred hhhcCCCCCccceeeccccchh
Q psy12003 5 RDKNPPRGTERQIKIWFQNRRM 26 (61)
Q Consensus 5 eLA~~l~Lte~~VqvWFqNrRa 26 (61)
.|+...|++..+.+++|.++..
T Consensus 27 ~i~~~~gi~~~~q~Li~~G~~L 48 (70)
T cd01798 27 VVAKRQGVPPDQLRVIFAGKEL 48 (70)
T ss_pred HHHHHHCCCHHHeEEEECCeEC
Confidence 4577888999999999987764
No 318
>PRK15043 transcriptional regulator MirA; Provisional
Probab=27.41 E-value=10 Score=24.61 Aligned_cols=21 Identities=5% Similarity=-0.047 Sum_probs=18.5
Q ss_pred CchhhhhcCCCCCccceeecc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWF 21 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWF 21 (61)
|.|.|+|+.+|++..+++.|-
T Consensus 4 ytIgeVA~~~GVs~~TLR~wE 24 (243)
T PRK15043 4 YTIGEVALLCDINPVTLRAWQ 24 (243)
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 468899999999999999984
No 319
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=27.35 E-value=9.4 Score=23.69 Aligned_cols=17 Identities=6% Similarity=0.042 Sum_probs=14.7
Q ss_pred hhhhhcCCCCCccceee
Q psy12003 3 LLRDKNPPRGTERQIKI 19 (61)
Q Consensus 3 ~~eLA~~l~Lte~~Vqv 19 (61)
-.|+|.+|++++.+|+.
T Consensus 152 nkeIA~~L~iS~~TV~~ 168 (207)
T PRK11475 152 MPQIAEQLERNIKTIRA 168 (207)
T ss_pred HHHHHHHHCCCHHHHHH
Confidence 35889999999999985
No 320
>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=27.18 E-value=7.3 Score=18.24 Aligned_cols=16 Identities=0% Similarity=-0.197 Sum_probs=12.0
Q ss_pred hhhhhcCCCCCcccee
Q psy12003 3 LLRDKNPPRGTERQIK 18 (61)
Q Consensus 3 ~~eLA~~l~Lte~~Vq 18 (61)
..|||..+|++...|.
T Consensus 20 ~~ela~~~~is~~tv~ 35 (48)
T PF13412_consen 20 QKELAEKLGISRSTVN 35 (48)
T ss_dssp HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHhCCCHHHHH
Confidence 4688999999988774
No 321
>cd04778 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). 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=26.89 E-value=11 Score=23.98 Aligned_cols=20 Identities=10% Similarity=0.137 Sum_probs=17.1
Q ss_pred CchhhhhcCCCCCccceeec
Q psy12003 1 MNLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvW 20 (61)
+-|-|||+.+|+|..+|+.|
T Consensus 2 y~i~elA~~~Gvs~~tIR~Y 21 (219)
T cd04778 2 YRIDDLARAAGTTVRNVRAY 21 (219)
T ss_pred CCHHHHHHHHCcCHHHHHHH
Confidence 35789999999999999877
No 322
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=26.73 E-value=20 Score=22.73 Aligned_cols=18 Identities=6% Similarity=0.021 Sum_probs=14.9
Q ss_pred CchhhhhcCCCCCcccee
Q psy12003 1 MNLLRDKNPPRGTERQIK 18 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~Vq 18 (61)
|-+.|||.++++++.+|=
T Consensus 31 ~si~elA~~~~vS~aTv~ 48 (278)
T PRK11557 31 LSSQQLANEAGVSQSSVV 48 (278)
T ss_pred cCHHHHHHHhCCCHHHHH
Confidence 457899999999999874
No 323
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=26.70 E-value=5.8 Score=18.69 Aligned_cols=23 Identities=4% Similarity=0.079 Sum_probs=17.4
Q ss_pred chhhhhcCCCCCccceeeccccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNR 24 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNr 24 (61)
-+.+||+++|++...+---|.|+
T Consensus 18 s~~~Ia~~~gvs~~~~y~~f~~k 40 (47)
T PF00440_consen 18 SIRDIARRAGVSKGSFYRYFPSK 40 (47)
T ss_dssp SHHHHHHHHTSCHHHHHHHCSSH
T ss_pred CHHHHHHHHccchhhHHHHcCCH
Confidence 36788888888888777666664
No 324
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=26.65 E-value=11 Score=19.00 Aligned_cols=16 Identities=0% Similarity=-0.201 Sum_probs=13.5
Q ss_pred hhhhhcCCCCCcccee
Q psy12003 3 LLRDKNPPRGTERQIK 18 (61)
Q Consensus 3 ~~eLA~~l~Lte~~Vq 18 (61)
..|||..++++...|.
T Consensus 16 ~~eLa~~l~vS~~tv~ 31 (69)
T TIGR00122 16 GEKLGEALGMSRTAVN 31 (69)
T ss_pred HHHHHHHHCCCHHHHH
Confidence 5689999999998875
No 325
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=26.62 E-value=7.3 Score=18.97 Aligned_cols=15 Identities=7% Similarity=-0.040 Sum_probs=11.6
Q ss_pred hhhhhcCCCCCccce
Q psy12003 3 LLRDKNPPRGTERQI 17 (61)
Q Consensus 3 ~~eLA~~l~Lte~~V 17 (61)
+-|||..+|++...|
T Consensus 6 V~elAk~l~v~~~~i 20 (54)
T PF04760_consen 6 VSELAKELGVPSKEI 20 (54)
T ss_dssp TTHHHHHHSSSHHHH
T ss_pred HHHHHHHHCcCHHHH
Confidence 568888888887655
No 326
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=26.46 E-value=21 Score=22.86 Aligned_cols=18 Identities=17% Similarity=-0.047 Sum_probs=15.0
Q ss_pred CchhhhhcCCCCCcccee
Q psy12003 1 MNLLRDKNPPRGTERQIK 18 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~Vq 18 (61)
|-+.+||.++++++.+|-
T Consensus 47 ~si~~lA~~~~vS~aTi~ 64 (292)
T PRK11337 47 TALKDIAEALAVSEAMIV 64 (292)
T ss_pred cCHHHHHHHhCCChHHHH
Confidence 457899999999999874
No 327
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=26.26 E-value=19 Score=22.71 Aligned_cols=18 Identities=6% Similarity=0.008 Sum_probs=14.8
Q ss_pred CchhhhhcCCCCCcccee
Q psy12003 1 MNLLRDKNPPRGTERQIK 18 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~Vq 18 (61)
|-+.+||.++++++.+|-
T Consensus 35 ~si~~lA~~~~vS~aTv~ 52 (284)
T PRK11302 35 SSIATLAKMANVSEPTVN 52 (284)
T ss_pred cCHHHHHHHhCCCHHHHH
Confidence 457889999999998874
No 328
>PRK05572 sporulation sigma factor SigF; Validated
Probab=26.03 E-value=13 Score=23.50 Aligned_cols=20 Identities=5% Similarity=-0.187 Sum_probs=16.9
Q ss_pred CchhhhhcCCCCCccceeec
Q psy12003 1 MNLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvW 20 (61)
|.+.|+|..+|++..+|..+
T Consensus 219 ~s~~eIA~~lgis~~~V~~~ 238 (252)
T PRK05572 219 KTQSEVAKRLGISQVQVSRL 238 (252)
T ss_pred CCHHHHHHHHCcCHHHHHHH
Confidence 35789999999999999765
No 329
>PF04293 SpoVR: SpoVR like protein; InterPro: IPR007390 One of the family members P37875 from SWISSPROT is Bacillus subtilis stage V sporulation protein R, which is involved in spore cortex formation []. Little is known about cortex biosynthesis, except that it depends on several sigma E controlled genes, including spoVR [].
Probab=25.84 E-value=31 Score=24.32 Aligned_cols=21 Identities=0% Similarity=-0.249 Sum_probs=18.1
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
+|.++|+.+||+.-.++.|.-
T Consensus 14 ~i~~~A~~~GLd~yp~~fEiv 34 (426)
T PF04293_consen 14 EIEEIARELGLDFYPVQFEIV 34 (426)
T ss_pred HHHHHHHHcCCCCCCceEEEe
Confidence 688999999999999987754
No 330
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=25.66 E-value=29 Score=17.71 Aligned_cols=23 Identities=9% Similarity=0.082 Sum_probs=17.9
Q ss_pred hhhcCCCCCccceeeccccchhH
Q psy12003 5 RDKNPPRGTERQIKIWFQNRRMK 27 (61)
Q Consensus 5 eLA~~l~Lte~~VqvWFqNrRak 27 (61)
.++...|++..+.+++|..+-..
T Consensus 28 ~I~~~~gip~~~q~Li~~Gk~L~ 50 (71)
T cd01796 28 LCEAESGIPASQQQLIYNGRELV 50 (71)
T ss_pred HHHHHhCCCHHHeEEEECCeEcc
Confidence 45777899999999999876543
No 331
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=25.65 E-value=13 Score=22.01 Aligned_cols=23 Identities=9% Similarity=0.154 Sum_probs=20.0
Q ss_pred hhhhhcCCCCCccceeeccccch
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
|.+||++.|++...+--.|.|+-
T Consensus 31 ~~~IA~~agvs~~~lY~hF~sKe 53 (202)
T TIGR03613 31 LEQIAELAGVSKTNLLYYFPSKD 53 (202)
T ss_pred HHHHHHHhCCCHHHHHHHcCCHH
Confidence 67899999999999999998874
No 332
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=25.56 E-value=26 Score=17.52 Aligned_cols=21 Identities=10% Similarity=0.180 Sum_probs=16.0
Q ss_pred hhhcCCCCCccceeeccccch
Q psy12003 5 RDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 5 eLA~~l~Lte~~VqvWFqNrR 25 (61)
.|+..++++....++||.++-
T Consensus 29 ~i~~~~g~~~~~q~L~~~g~~ 49 (76)
T cd01803 29 KIQDKEGIPPDQQRLIFAGKQ 49 (76)
T ss_pred HHHHHhCCCHHHeEEEECCEE
Confidence 456777888889999987553
No 333
>PRK13870 transcriptional regulator TraR; Provisional
Probab=25.51 E-value=8.4 Score=24.34 Aligned_cols=24 Identities=0% Similarity=-0.057 Sum_probs=19.1
Q ss_pred hhhhcCCCCCccceeeccccchhH
Q psy12003 4 LRDKNPPRGTERQIKIWFQNRRMK 27 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvWFqNrRak 27 (61)
-|+|..||++|.+|..=.+|=+.|
T Consensus 192 ~EIa~ILgISe~TV~~Hl~na~~K 215 (234)
T PRK13870 192 EEIADVEGVKYNSVRVKLREAMKR 215 (234)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHH
Confidence 478999999999998766665554
No 334
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=25.39 E-value=7.8 Score=19.86 Aligned_cols=27 Identities=7% Similarity=0.182 Sum_probs=19.0
Q ss_pred hhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
..+||+.||++...|--| ..+-..++.
T Consensus 12 ~~~lAkalGVs~~aVs~W--~~~IP~~ra 38 (60)
T PF14549_consen 12 QSKLAKALGVSPQAVSQW--GERIPAERA 38 (60)
T ss_dssp HHHHHHHHTS-HHHHHHH--HTS--HHHH
T ss_pred HHHHHHHHCCCHHHHHHh--cCccCHHHH
Confidence 468999999999999999 455555554
No 335
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=25.39 E-value=13 Score=22.29 Aligned_cols=24 Identities=4% Similarity=-0.139 Sum_probs=20.2
Q ss_pred chhhhhcCCCCCccceeeccccch
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrR 25 (61)
-..+||..+|++...|.-|..+..
T Consensus 40 Tq~eLAerlGVS~~tIs~iE~G~~ 63 (150)
T TIGR02612 40 SGAQLAGRLGVTPQRVEALEKSEL 63 (150)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCC
Confidence 457899999999999999987754
No 336
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=25.36 E-value=15 Score=18.82 Aligned_cols=16 Identities=6% Similarity=0.038 Sum_probs=13.2
Q ss_pred hhhhhcCCCCCcccee
Q psy12003 3 LLRDKNPPRGTERQIK 18 (61)
Q Consensus 3 ~~eLA~~l~Lte~~Vq 18 (61)
..|||..+|++...|.
T Consensus 25 a~eLa~~lgl~~~~v~ 40 (68)
T smart00550 25 ALQLAKNLGLPKKEVN 40 (68)
T ss_pred HHHHHHHHCCCHHHHH
Confidence 5689999999988773
No 337
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=25.28 E-value=15 Score=21.95 Aligned_cols=24 Identities=21% Similarity=0.159 Sum_probs=21.2
Q ss_pred hhhhhcCCCCCccceeeccccchh
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRRM 26 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrRa 26 (61)
|.++|.+.|++...+--.|.++-.
T Consensus 34 i~~Ia~~agvsk~t~Y~~F~sKe~ 57 (213)
T PRK09975 34 LNDIADAANVTRGAIYWHFENKTQ 57 (213)
T ss_pred HHHHHHHcCCCHHHHHHHcCCHHH
Confidence 678999999999999999998855
No 338
>PF05119 Terminase_4: Phage terminase, small subunit; InterPro: IPR006448 This entry is represented by Streptococcus phage 7201, Orf21. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This group of sequences describe the distinct family of phage (and integrated prophage) putative terminase small subunit sequnces. Members tend to be encoded by the gene adjacent to the phage terminase large subunit gene.
Probab=25.12 E-value=23 Score=18.97 Aligned_cols=14 Identities=7% Similarity=-0.216 Sum_probs=11.5
Q ss_pred chhhhhcCCCCCcc
Q psy12003 2 NLLRDKNPPRGTER 15 (61)
Q Consensus 2 ~~~eLA~~l~Lte~ 15 (61)
+|..|+.+||||+.
T Consensus 72 ~~~~l~~~lGLtP~ 85 (100)
T PF05119_consen 72 QMRSLASELGLTPA 85 (100)
T ss_pred HHHHHHHHcCCCHH
Confidence 46788999999974
No 339
>PRK06424 transcription factor; Provisional
Probab=24.82 E-value=14 Score=22.11 Aligned_cols=25 Identities=4% Similarity=-0.230 Sum_probs=21.1
Q ss_pred hhhhhcCCCCCccceeeccccchhH
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRRMK 27 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrRak 27 (61)
..+||..+|++...|.-|..+++..
T Consensus 100 Q~eLA~~iGvs~stIskiE~G~~~P 124 (144)
T PRK06424 100 QADLAAKIFERKNVIASIERGDLLP 124 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCCC
Confidence 4689999999999999998877653
No 340
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=24.79 E-value=31 Score=24.25 Aligned_cols=18 Identities=17% Similarity=-0.020 Sum_probs=15.9
Q ss_pred CchhhhhcCCCCCcccee
Q psy12003 1 MNLLRDKNPPRGTERQIK 18 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~Vq 18 (61)
|-|.++|..+||.|.+|-
T Consensus 344 LtlkdvAe~lglheSTVS 361 (455)
T PRK05932 344 LVLKDIAEELGMHESTIS 361 (455)
T ss_pred ccHHHHHHHhCCCccchh
Confidence 468899999999999994
No 341
>cd01769 UBL Ubiquitin-like domain of UBL. UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
Probab=24.46 E-value=30 Score=16.67 Aligned_cols=20 Identities=5% Similarity=0.091 Sum_probs=15.4
Q ss_pred hhhcCCCCCccceeeccccc
Q psy12003 5 RDKNPPRGTERQIKIWFQNR 24 (61)
Q Consensus 5 eLA~~l~Lte~~VqvWFqNr 24 (61)
.++..++++...++++|..+
T Consensus 26 ~i~~~~~~~~~~~~l~~~g~ 45 (69)
T cd01769 26 KIAAKEGVPPEQQRLIYAGK 45 (69)
T ss_pred HHHHHHCcChHHEEEEECCc
Confidence 35667788888899988764
No 342
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=24.13 E-value=13 Score=24.18 Aligned_cols=26 Identities=8% Similarity=-0.051 Sum_probs=20.3
Q ss_pred chhhhhcCCCCCccceeeccccchhH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMK 27 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak 27 (61)
...|+|..+|+|+..|+...+-=|.+
T Consensus 136 s~~EIA~~Lgis~~tVr~~l~RAr~~ 161 (290)
T PRK09635 136 PYQQIATTIGSQASTCRQLAHRARRK 161 (290)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 46799999999999999876533333
No 343
>PF13730 HTH_36: Helix-turn-helix domain
Probab=24.00 E-value=12 Score=17.87 Aligned_cols=18 Identities=6% Similarity=-0.188 Sum_probs=14.0
Q ss_pred hhhhhcCCCCCccceeec
Q psy12003 3 LLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvW 20 (61)
+..||..+|++.++|+-+
T Consensus 28 ~~~la~~~g~s~~Tv~~~ 45 (55)
T PF13730_consen 28 QETLAKDLGVSRRTVQRA 45 (55)
T ss_pred HHHHHHHHCcCHHHHHHH
Confidence 467888899998888644
No 344
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=23.94 E-value=11 Score=20.63 Aligned_cols=17 Identities=6% Similarity=0.038 Sum_probs=12.5
Q ss_pred chhhhhcCCCCCcccee
Q psy12003 2 NLLRDKNPPRGTERQIK 18 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~Vq 18 (61)
.+.+||++|++++..|+
T Consensus 67 ~v~~I~~~l~~~~~~v~ 83 (102)
T PF08784_consen 67 HVDEIAQQLGMSENEVR 83 (102)
T ss_dssp EHHHHHHHSTS-HHHHH
T ss_pred cHHHHHHHhCcCHHHHH
Confidence 36788888899888775
No 345
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=23.57 E-value=18 Score=19.69 Aligned_cols=15 Identities=7% Similarity=-0.124 Sum_probs=11.8
Q ss_pred hhhhcCCCCCcccee
Q psy12003 4 LRDKNPPRGTERQIK 18 (61)
Q Consensus 4 ~eLA~~l~Lte~~Vq 18 (61)
.+||.+|+++++.|.
T Consensus 19 ~~Lar~L~vs~~dI~ 33 (84)
T cd08805 19 AELARELQFSVEDIN 33 (84)
T ss_pred HHHHHHcCCCHHHHH
Confidence 468999999997664
No 346
>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=23.55 E-value=8.9 Score=19.69 Aligned_cols=17 Identities=0% Similarity=-0.255 Sum_probs=13.2
Q ss_pred hhhhhcCCCCCccceee
Q psy12003 3 LLRDKNPPRGTERQIKI 19 (61)
Q Consensus 3 ~~eLA~~l~Lte~~Vqv 19 (61)
..|||..||++...|+-
T Consensus 23 ~eEiA~~lgis~~~v~~ 39 (78)
T PF04539_consen 23 DEEIAEELGISVEEVRE 39 (78)
T ss_dssp HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHcccHHHHHH
Confidence 46899999999988863
No 347
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=23.34 E-value=9.7 Score=17.01 Aligned_cols=19 Identities=11% Similarity=0.359 Sum_probs=12.9
Q ss_pred chhhhhcCCCCCccceeec
Q psy12003 2 NLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvW 20 (61)
+|..-|...|||..+|+-.
T Consensus 7 ~Li~eA~~~Gls~eeir~F 25 (30)
T PF08671_consen 7 ELIKEAKESGLSKEEIREF 25 (30)
T ss_dssp HHHHHHHHTT--HHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHH
Confidence 5677799999998887644
No 348
>PTZ00044 ubiquitin; Provisional
Probab=23.31 E-value=28 Score=17.66 Aligned_cols=23 Identities=13% Similarity=0.244 Sum_probs=18.1
Q ss_pred hhhcCCCCCccceeeccccchhH
Q psy12003 5 RDKNPPRGTERQIKIWFQNRRMK 27 (61)
Q Consensus 5 eLA~~l~Lte~~VqvWFqNrRak 27 (61)
.|+...|++....+++|..+-..
T Consensus 29 ~i~~~~gi~~~~q~L~~~g~~L~ 51 (76)
T PTZ00044 29 ALQEKEGIDVKQIRLIYSGKQMS 51 (76)
T ss_pred HHHHHHCCCHHHeEEEECCEEcc
Confidence 35777899999999999877643
No 349
>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins. SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair []. Unlike ubiquitin, they are not involved in protein degradation. This entry also contains the C-terminal Rad60 DNA repair protein SUMO-like domain.; PDB: 3RD2_A 2JXX_A 3RCZ_A 3GOE_A 3A4S_D 3A4R_B 2IO1_D 1U4A_A 2K1F_A 1WZ0_A ....
Probab=23.20 E-value=27 Score=17.50 Aligned_cols=24 Identities=13% Similarity=0.216 Sum_probs=17.7
Q ss_pred hhhhcCCCCCc-cceeeccccchhH
Q psy12003 4 LRDKNPPRGTE-RQIKIWFQNRRMK 27 (61)
Q Consensus 4 ~eLA~~l~Lte-~~VqvWFqNrRak 27 (61)
...+.+.+++. ..++.+|...+..
T Consensus 28 ~~~~~~~~i~~~~~~~l~fdG~~L~ 52 (72)
T PF11976_consen 28 EKYCEKKGIPPEESIRLIFDGKRLD 52 (72)
T ss_dssp HHHHHHHTTTT-TTEEEEETTEEE-
T ss_pred HHHHHhhCCCccceEEEEECCEEcC
Confidence 34567778888 8999999876653
No 350
>PRK09191 two-component response regulator; Provisional
Probab=23.04 E-value=17 Score=22.22 Aligned_cols=21 Identities=0% Similarity=-0.097 Sum_probs=17.3
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
...|+|..+|+++..|+.-..
T Consensus 106 s~~eIA~~l~~s~~tV~~~l~ 126 (261)
T PRK09191 106 SVEEAAEILGVDPAEAEALLD 126 (261)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 467899999999999986553
No 351
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=22.98 E-value=20 Score=23.15 Aligned_cols=17 Identities=0% Similarity=-0.070 Sum_probs=14.3
Q ss_pred chhhhhcCCCCCcccee
Q psy12003 2 NLLRDKNPPRGTERQIK 18 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~Vq 18 (61)
-+.|||..+|+++.+|=
T Consensus 38 si~elA~~a~VS~aTv~ 54 (281)
T COG1737 38 SIAELAERAGVSPATVV 54 (281)
T ss_pred HHHHHHHHhCCCHHHHH
Confidence 47899999999998874
No 352
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=22.88 E-value=18 Score=19.55 Aligned_cols=16 Identities=6% Similarity=-0.074 Sum_probs=13.3
Q ss_pred hhhhhcCCCCCcccee
Q psy12003 3 LLRDKNPPRGTERQIK 18 (61)
Q Consensus 3 ~~eLA~~l~Lte~~Vq 18 (61)
..+||..+|+++..|.
T Consensus 20 ~~~la~~l~~s~~tv~ 35 (108)
T smart00344 20 LAELAKKVGLSPSTVH 35 (108)
T ss_pred HHHHHHHHCcCHHHHH
Confidence 4688999999998884
No 353
>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=22.79 E-value=16 Score=23.40 Aligned_cols=21 Identities=10% Similarity=-0.081 Sum_probs=16.6
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
-+.|+|..+|+|..+|+-...
T Consensus 238 t~~eIA~~lgvS~~~V~q~~~ 258 (270)
T TIGR02392 238 TLQELAAEYGVSAERIRQIEK 258 (270)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 468999999999999974433
No 354
>TIGR03624 putative hydrolase. Members of this protein family have a phylogenetic distribution skewed toward the Actinobacteria (high GC Gram-positive bacteria), but with a few members occuring in the Archaea and Chloroflexi. The function is unknown.
Probab=22.43 E-value=19 Score=24.54 Aligned_cols=30 Identities=7% Similarity=0.279 Sum_probs=24.6
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
||.+.++.|++++..|.+|..-|=+=+.++
T Consensus 140 NI~~~~~~L~v~~~d~rlwlalhE~aH~~l 169 (345)
T TIGR03624 140 NIVAVERGLGVPPDDFRLWVALHEVTHRRQ 169 (345)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence 789999999999999999988775444443
No 355
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=22.43 E-value=18 Score=23.46 Aligned_cols=19 Identities=5% Similarity=-0.064 Sum_probs=16.0
Q ss_pred chhhhhcCCCCCccceeec
Q psy12003 2 NLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvW 20 (61)
.+.|+|..+|+|..+|+-.
T Consensus 250 Tl~EIA~~lgvS~~rVrqi 268 (284)
T PRK06596 250 TLQELAAEYGVSAERVRQI 268 (284)
T ss_pred CHHHHHHHHCCCHHHHHHH
Confidence 4689999999999999743
No 356
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=22.39 E-value=19 Score=20.54 Aligned_cols=17 Identities=12% Similarity=-0.060 Sum_probs=13.8
Q ss_pred chhhhhcCCCCCcccee
Q psy12003 2 NLLRDKNPPRGTERQIK 18 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~Vq 18 (61)
-|.|||..+.+|++.++
T Consensus 21 tl~elA~~l~cS~Rn~r 37 (115)
T PF12793_consen 21 TLDELAELLFCSRRNAR 37 (115)
T ss_pred eHHHHHHHhCCCHHHHH
Confidence 37789999999988775
No 357
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=22.32 E-value=17 Score=23.68 Aligned_cols=28 Identities=7% Similarity=-0.093 Sum_probs=20.5
Q ss_pred chhhhhcCCCCCccceeeccccchhHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWK 29 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k 29 (61)
.+.|+|..+|+|..+|+-.-..=+.|-|
T Consensus 247 t~~EIa~~lgvs~~~V~q~~~~Al~kLr 274 (289)
T PRK07500 247 TLEALGEELGISKERVRQIEARALEKLR 274 (289)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4789999999999999866443333333
No 358
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=22.30 E-value=18 Score=22.67 Aligned_cols=19 Identities=11% Similarity=0.060 Sum_probs=15.5
Q ss_pred chhhhhcCCCCCccceeec
Q psy12003 2 NLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvW 20 (61)
-+-|+|..+|.||.+|+--
T Consensus 63 Ti~EIAeelG~TeqTir~h 81 (182)
T COG1318 63 TISEIAEELGRTEQTVRNH 81 (182)
T ss_pred cHHHHHHHhCCCHHHHHHH
Confidence 4678999999999999743
No 359
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=22.26 E-value=20 Score=22.99 Aligned_cols=17 Identities=12% Similarity=-0.396 Sum_probs=14.9
Q ss_pred hhhhhcCCCCCccceee
Q psy12003 3 LLRDKNPPRGTERQIKI 19 (61)
Q Consensus 3 ~~eLA~~l~Lte~~Vqv 19 (61)
-.|+|.+|++++++|+.
T Consensus 161 nkEIA~~L~IS~~TVk~ 177 (217)
T PRK13719 161 HEYIAQLLNITVGSSKN 177 (217)
T ss_pred HHHHHHHhCCCHHHHHH
Confidence 46899999999999974
No 360
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=22.01 E-value=13 Score=21.40 Aligned_cols=25 Identities=8% Similarity=-0.066 Sum_probs=18.0
Q ss_pred hhhhhcCCCCCccceeeccccchhH
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRRMK 27 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrRak 27 (61)
..++|..+++++++|++..++=|.|
T Consensus 155 ~~~Ia~~l~~s~~tv~~~~~~l~~K 179 (196)
T PRK10360 155 VKEIAAELGLSPKTVHVHRANLMEK 179 (196)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 4578889999999998765544433
No 361
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, 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 domain
Probab=21.95 E-value=15 Score=22.30 Aligned_cols=19 Identities=0% Similarity=-0.085 Sum_probs=16.6
Q ss_pred chhhhhcCCCCCccceeec
Q psy12003 2 NLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvW 20 (61)
-|-|+|..+|+|..+|+-|
T Consensus 3 ~I~evA~~~gvs~~tLRyY 21 (172)
T cd04790 3 TISQLARQFGLSRSTLLYY 21 (172)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 4779999999999999877
No 362
>COG3149 PulM Type II secretory pathway, component PulM [Intracellular trafficking and secretion]
Probab=21.87 E-value=37 Score=21.26 Aligned_cols=14 Identities=14% Similarity=0.517 Sum_probs=10.4
Q ss_pred CCCCccceeecccc
Q psy12003 10 PRGTERQIKIWFQN 23 (61)
Q Consensus 10 l~Lte~~VqvWFqN 23 (61)
+...+..|||||+-
T Consensus 122 l~~~ge~vQV~i~p 135 (181)
T COG3149 122 LDNRGEAVQVWIQP 135 (181)
T ss_pred ecCCCceEEEEecc
Confidence 34467789999984
No 363
>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=21.70 E-value=18 Score=20.35 Aligned_cols=11 Identities=45% Similarity=0.984 Sum_probs=7.0
Q ss_pred eeeccccchhH
Q psy12003 17 IKIWFQNRRMK 27 (61)
Q Consensus 17 VqvWFqNrRak 27 (61)
|=+||.||-+-
T Consensus 19 iwlwfrnrpaa 29 (117)
T PF09301_consen 19 IWLWFRNRPAA 29 (117)
T ss_dssp HHHHHHHTT-S
T ss_pred HHHHHccChHH
Confidence 34699998653
No 364
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=21.64 E-value=96 Score=15.54 Aligned_cols=29 Identities=14% Similarity=0.139 Sum_probs=23.2
Q ss_pred chhhhhcCCCCCccceeeccccc---hhHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNR---RMKWKK 30 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNr---Rak~kr 30 (61)
-|.+|-..+++++..|-|..-+. |..|..
T Consensus 17 tl~~ll~~l~~~~~~vav~~N~~iv~r~~~~~ 48 (65)
T PRK05863 17 TVAALLDSLGFPEKGIAVAVDWSVLPRSDWAT 48 (65)
T ss_pred cHHHHHHHcCCCCCcEEEEECCcCcChhHhhh
Confidence 37788889999999999998775 666653
No 365
>cd00419 Ferrochelatase_C Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is ubiquitous in nature and widely distributed in bacteria and eukaryotes. Recently, some archaeal members have been identified. The oligomeric state of these enzymes varies depending on the presence of a dimerization motif at the C-terminus.
Probab=21.61 E-value=40 Score=19.56 Aligned_cols=21 Identities=10% Similarity=-0.088 Sum_probs=16.5
Q ss_pred hhhcCCCCCccceeeccccch
Q psy12003 5 RDKNPPRGTERQIKIWFQNRR 25 (61)
Q Consensus 5 eLA~~l~Lte~~VqvWFqNrR 25 (61)
.|+..++++..++.+-||+|-
T Consensus 49 ~v~~~l~~~~~~~~~~fqS~~ 69 (135)
T cd00419 49 LVAERLGLPFDEYELAYQSRF 69 (135)
T ss_pred HHHHHhCCCCCCEEEEecCCC
Confidence 356778877888999999864
No 366
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=21.60 E-value=21 Score=22.68 Aligned_cols=17 Identities=24% Similarity=0.030 Sum_probs=15.0
Q ss_pred hhhhhcCCCCCccceee
Q psy12003 3 LLRDKNPPRGTERQIKI 19 (61)
Q Consensus 3 ~~eLA~~l~Lte~~Vqv 19 (61)
..|+|..|++++++|+.
T Consensus 151 nKEIAe~L~IS~rTVkt 167 (198)
T PRK15201 151 LSETAALLSLSEEQTKS 167 (198)
T ss_pred HHHHHHHhCCCHHHHHH
Confidence 56899999999999974
No 367
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=21.52 E-value=19 Score=16.41 Aligned_cols=18 Identities=11% Similarity=-0.079 Sum_probs=13.3
Q ss_pred chhhhhcCCCCCccceee
Q psy12003 2 NLLRDKNPPRGTERQIKI 19 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~Vqv 19 (61)
.+.+||..++++...|.-
T Consensus 16 s~~~l~~~l~~s~~tv~~ 33 (53)
T smart00420 16 SVEELAELLGVSEMTIRR 33 (53)
T ss_pred CHHHHHHHHCCCHHHHHH
Confidence 356788888888887753
No 368
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=21.37 E-value=18 Score=21.77 Aligned_cols=22 Identities=18% Similarity=0.028 Sum_probs=12.0
Q ss_pred hhhhhcCCCCCccceeeccccc
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNR 24 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNr 24 (61)
+.+||..+|++...|.-|.+++
T Consensus 23 ~~elA~~~gis~~~is~~E~g~ 44 (185)
T PRK09943 23 QRRAAELSGLTHSAISTIEQDK 44 (185)
T ss_pred HHHHHHHHCCCHHHHHHHHcCC
Confidence 3455555555555555555444
No 369
>PF04046 PSP: PSP; InterPro: IPR006568 PSP is a proline-rich domain of unknown function found in spliceosome associated proteins.
Probab=21.34 E-value=27 Score=17.28 Aligned_cols=19 Identities=11% Similarity=0.055 Sum_probs=16.1
Q ss_pred hhhhcCCCCCccceeeccc
Q psy12003 4 LRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvWFq 22 (61)
.||=.+|||.+.+.--|+.
T Consensus 7 ~~LR~ALg~~~~~~PPwl~ 25 (48)
T PF04046_consen 7 DELREALGMQENDPPPWLY 25 (48)
T ss_pred HHHHHHcCCCCCCCChHHH
Confidence 3677789999999999986
No 370
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=21.32 E-value=48 Score=16.53 Aligned_cols=22 Identities=14% Similarity=0.261 Sum_probs=17.1
Q ss_pred hhhcCCCCCccceeeccccchh
Q psy12003 5 RDKNPPRGTERQIKIWFQNRRM 26 (61)
Q Consensus 5 eLA~~l~Lte~~VqvWFqNrRa 26 (61)
.|+...+++....+++|..+..
T Consensus 29 ~i~~~~g~~~~~qrL~~~g~~L 50 (76)
T cd01806 29 RVEEKEGIPPQQQRLIYSGKQM 50 (76)
T ss_pred HHhHhhCCChhhEEEEECCeEc
Confidence 4567779999999999986654
No 371
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=21.16 E-value=14 Score=21.36 Aligned_cols=25 Identities=8% Similarity=-0.169 Sum_probs=18.3
Q ss_pred hhhhhcCCCCCccceeeccccchhH
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRRMK 27 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrRak 27 (61)
..|+|..+++++++|+++..+=|.|
T Consensus 167 ~~eIa~~l~~s~~tv~~~~~~~~~k 191 (210)
T PRK09935 167 NKEIADQLLLSNKTVSAHKSNIYGK 191 (210)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 4578889999999998775544443
No 372
>PRK10281 hypothetical protein; Provisional
Probab=20.99 E-value=31 Score=22.64 Aligned_cols=16 Identities=6% Similarity=-0.047 Sum_probs=12.3
Q ss_pred chhhhhcCCCCCccce
Q psy12003 2 NLLRDKNPPRGTERQI 17 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~V 17 (61)
+|..+|+++|++|+.-
T Consensus 34 ~Mq~IAre~n~SETaF 49 (299)
T PRK10281 34 QMQLIARELNHSETAF 49 (299)
T ss_pred HHHHHHHHhCCceEEE
Confidence 5678899999988643
No 373
>TIGR03883 DUF2342_F420 uncharacterized protein, coenzyme F420 biosynthesis associated. protein whose crystal structure has been determined (PDB:3CMN_A). This has been annotated as a putative hydrolase, but the support for that assertion is untraceable. There is no cofactor present in the structure.
Probab=20.99 E-value=21 Score=24.33 Aligned_cols=30 Identities=7% Similarity=0.227 Sum_probs=24.4
Q ss_pred chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE 31 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~ 31 (61)
||.+.++.|++++..+.+|..-|=+=+.++
T Consensus 144 NI~~~~~~L~v~~~d~rlwlalhE~aH~~~ 173 (346)
T TIGR03883 144 NIVAVERELGVDPHDFRLWVCLHEVTHRVQ 173 (346)
T ss_pred hHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence 789999999999999999988775444443
No 374
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=20.96 E-value=20 Score=23.28 Aligned_cols=19 Identities=5% Similarity=-0.038 Sum_probs=16.1
Q ss_pred chhhhhcCCCCCccceeec
Q psy12003 2 NLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvW 20 (61)
-+.|+|..+|+|..+|+..
T Consensus 271 Tl~EIa~~lgiS~erVrq~ 289 (298)
T TIGR02997 271 TLAEIGRRLNLSRERVRQI 289 (298)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 4789999999999999743
No 375
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=20.94 E-value=23 Score=21.94 Aligned_cols=26 Identities=15% Similarity=0.026 Sum_probs=17.6
Q ss_pred chhhhhcCCCCCccceeeccccchhHHH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMKWK 29 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k 29 (61)
.|.+||..+|++...+. ..=|||..|
T Consensus 180 ~l~dLA~~lGISkst~~--ehLRrAe~K 205 (215)
T COG3413 180 SLKDLAKELGISKSTLS--EHLRRAERK 205 (215)
T ss_pred CHHHHHHHhCCCHHHHH--HHHHHHHHH
Confidence 47899999999987653 333444433
No 376
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptor
Probab=20.94 E-value=18 Score=19.29 Aligned_cols=17 Identities=6% Similarity=-0.074 Sum_probs=14.3
Q ss_pred hhhhcCCCCCccceeec
Q psy12003 4 LRDKNPPRGTERQIKIW 20 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvW 20 (61)
..||.+||+++..|..+
T Consensus 19 ~~LA~~LG~~~~~I~~i 35 (77)
T cd08311 19 RSLAGELGYEDEAIDTF 35 (77)
T ss_pred HHHHHHcCCCHHHHHHH
Confidence 36899999999988865
No 377
>PHA00542 putative Cro-like protein
Probab=20.90 E-value=15 Score=19.50 Aligned_cols=23 Identities=9% Similarity=0.039 Sum_probs=19.6
Q ss_pred chhhhhcCCCCCccceeeccccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNR 24 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNr 24 (61)
...+||..+|++...|--|..++
T Consensus 33 Tq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 33 SQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCC
Confidence 35789999999999999888776
No 378
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=20.78 E-value=14 Score=18.83 Aligned_cols=17 Identities=18% Similarity=-0.048 Sum_probs=12.8
Q ss_pred hhhhcCCCCCccceeec
Q psy12003 4 LRDKNPPRGTERQIKIW 20 (61)
Q Consensus 4 ~eLA~~l~Lte~~VqvW 20 (61)
-.||..||+++..|+..
T Consensus 16 k~La~~Lg~~~~~i~~i 32 (83)
T PF00531_consen 16 KRLARKLGLSESEIENI 32 (83)
T ss_dssp HHHHHHTTS-HHHHHHH
T ss_pred HHHHHHhCcCHHHHHHH
Confidence 46899999999988744
No 379
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=20.76 E-value=18 Score=19.54 Aligned_cols=26 Identities=8% Similarity=-0.041 Sum_probs=18.7
Q ss_pred chhhhhcCCCCCccceeeccccchhH
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQNRRMK 27 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFqNrRak 27 (61)
.|++||.+.||+...+..=+...-.|
T Consensus 17 sL~~lsr~~Gl~~~tl~nal~r~~pk 42 (78)
T PF13693_consen 17 SLAALSREAGLSSSTLRNALRRPWPK 42 (78)
T ss_dssp -HHHHHHHHSS-HHHHHHTTTSS-HH
T ss_pred CHHHHHHHcCCCHHHHHHHHcCCChH
Confidence 57899999999999999777655433
No 380
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=20.76 E-value=24 Score=22.35 Aligned_cols=24 Identities=8% Similarity=-0.028 Sum_probs=19.7
Q ss_pred CchhhhhcCCCCCccceeeccccc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWFQNR 24 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWFqNr 24 (61)
|-|.++|+.+|++-.+|---+-|+
T Consensus 1 ~ti~dIA~~aGVS~~TVSrvLn~~ 24 (328)
T PRK11303 1 MKLDEIARLAGVSRTTASYVINGK 24 (328)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCC
Confidence 568899999999999888767665
No 381
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=20.69 E-value=22 Score=20.55 Aligned_cols=17 Identities=12% Similarity=0.012 Sum_probs=15.1
Q ss_pred chhhhhcCCCCCcccee
Q psy12003 2 NLLRDKNPPRGTERQIK 18 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~Vq 18 (61)
+|-|+|+.+|+++-+|+
T Consensus 51 nlKe~e~~lgiSYPTvR 67 (113)
T PF09862_consen 51 NLKEMEKELGISYPTVR 67 (113)
T ss_pred CHHHHHHHHCCCcHHHH
Confidence 67899999999999986
No 382
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=20.66 E-value=21 Score=21.38 Aligned_cols=24 Identities=21% Similarity=0.116 Sum_probs=21.1
Q ss_pred hhhhhcCCCCCccceeeccccchh
Q psy12003 3 LLRDKNPPRGTERQIKIWFQNRRM 26 (61)
Q Consensus 3 ~~eLA~~l~Lte~~VqvWFqNrRa 26 (61)
|.+||.+.|++...+--.|.|+..
T Consensus 34 ~~~Ia~~agvs~~tlY~~F~sKe~ 57 (215)
T PRK10668 34 LADIAKAAGVTRGAIYWHFKNKSD 57 (215)
T ss_pred HHHHHHHhCCChHHHHHHCCCHHH
Confidence 678999999999999999998854
No 383
>COG0384 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]
Probab=20.58 E-value=33 Score=22.78 Aligned_cols=15 Identities=7% Similarity=-0.137 Sum_probs=12.0
Q ss_pred chhhhhcCCCCCccc
Q psy12003 2 NLLRDKNPPRGTERQ 16 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~ 16 (61)
+|..+|+++|++|+.
T Consensus 35 ~MQ~IA~e~n~SET~ 49 (291)
T COG0384 35 QMQAIAREFNLSETA 49 (291)
T ss_pred HHHHHHHHhCCceeE
Confidence 467888899998874
No 384
>cd08803 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=20.51 E-value=24 Score=19.13 Aligned_cols=16 Identities=6% Similarity=-0.180 Sum_probs=12.8
Q ss_pred hhhhcCCCCCccceee
Q psy12003 4 LRDKNPPRGTERQIKI 19 (61)
Q Consensus 4 ~eLA~~l~Lte~~Vqv 19 (61)
.+||..||+++..|..
T Consensus 19 ~~LA~eLg~s~~dI~~ 34 (84)
T cd08803 19 TELARELNFSVDEINQ 34 (84)
T ss_pred HHHHHHcCCCHHHHHH
Confidence 4689999999987763
No 385
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=20.45 E-value=11 Score=18.58 Aligned_cols=16 Identities=0% Similarity=-0.103 Sum_probs=11.0
Q ss_pred chhhhhcCCCCCccce
Q psy12003 2 NLLRDKNPPRGTERQI 17 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~V 17 (61)
.+.|||..+|++...|
T Consensus 26 t~~ela~~l~~~~~t~ 41 (61)
T PF12840_consen 26 TVSELAEELGISQSTV 41 (61)
T ss_dssp EHHHHHHHHTS-HHHH
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4568888888887665
No 386
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=20.44 E-value=19 Score=22.76 Aligned_cols=19 Identities=5% Similarity=-0.059 Sum_probs=15.8
Q ss_pred chhhhhcCCCCCccceeec
Q psy12003 2 NLLRDKNPPRGTERQIKIW 20 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvW 20 (61)
-+.|+|..+|++..+|...
T Consensus 227 t~~eIA~~lgis~~~V~~~ 245 (258)
T PRK08215 227 TQMEVAEEIGISQAQVSRL 245 (258)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 4678999999999998754
No 387
>PF15599 Imm38: Immunity protein 38
Probab=20.43 E-value=49 Score=19.05 Aligned_cols=21 Identities=5% Similarity=0.172 Sum_probs=16.2
Q ss_pred chhhhhcCCCCCccceeeccc
Q psy12003 2 NLLRDKNPPRGTERQIKIWFQ 22 (61)
Q Consensus 2 ~~~eLA~~l~Lte~~VqvWFq 22 (61)
+|.+|+.++|.++..+..-+.
T Consensus 6 ~i~~l~~k~g~~~~~~~~~~~ 26 (124)
T PF15599_consen 6 EIDELARKIGAPDNEYPLFFR 26 (124)
T ss_pred HHHHHHHHhCCCccccccccc
Confidence 578899999998877765544
No 388
>PF10846 DUF2722: Protein of unknown function (DUF2722); InterPro: IPR021216 This eukaryotic family of proteins has no known function.
Probab=20.18 E-value=31 Score=24.12 Aligned_cols=21 Identities=24% Similarity=0.294 Sum_probs=19.8
Q ss_pred CchhhhhcCCCCCccceeecc
Q psy12003 1 MNLLRDKNPPRGTERQIKIWF 21 (61)
Q Consensus 1 ~~~~eLA~~l~Lte~~VqvWF 21 (61)
+||+++|.+.|++...|-.-|
T Consensus 88 lelLr~Al~~gIPp~lIP~LF 108 (416)
T PF10846_consen 88 LELLRTALQAGIPPNLIPLLF 108 (416)
T ss_pred HHHHHHHHHcCCChhhcceee
Confidence 589999999999999999999
No 389
>PF02567 PhzC-PhzF: Phenazine biosynthesis-like protein; InterPro: IPR003719 Five genes, phzF, phzA, phzB, phzC and phzD, encode enzymes for phenazine biosynthesis in the biological control bacterium Pseudomonas chlororaphis (also known as Pseudomonas aureofaciens). Protein PhzF is similar to 3-deoxy-D-arabino-heptulosonate-7-phosphate synthases of solanaceous plants. PhzC is responsible for the conversion of phenazine-I-carboxylic acid to 2-hydroxy-phenazine-I-carboxylic acid [].; GO: 0003824 catalytic activity, 0009058 biosynthetic process; PDB: 1U0K_A 1QYA_B 1QY9_D 1SDJ_A 1U1X_A 1U1W_B 1T6K_A 1XUA_A 1XUB_A 1U1V_A ....
Probab=20.16 E-value=21 Score=22.59 Aligned_cols=14 Identities=7% Similarity=-0.142 Sum_probs=11.1
Q ss_pred chhhhhcCCCCCcc
Q psy12003 2 NLLRDKNPPRGTER 15 (61)
Q Consensus 2 ~~~eLA~~l~Lte~ 15 (61)
+|..||+++|++|+
T Consensus 27 ~mq~iA~e~n~sET 40 (281)
T PF02567_consen 27 QMQAIAREFNLSET 40 (281)
T ss_dssp HHHHHHHHHTSSEE
T ss_pred HHHHHHHHcCCCee
Confidence 46778888888886
Done!