Query psy17316
Match_columns 229
No_of_seqs 164 out of 312
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 18:53:11 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17316.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17316hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01710 HTH_Tnp_IS630: Transp 99.2 2.2E-10 4.7E-15 90.0 11.1 90 118-212 2-93 (119)
2 PF05225 HTH_psq: helix-turn-h 99.1 3E-10 6.5E-15 74.7 4.9 39 34-72 1-39 (45)
3 COG3415 Transposase and inacti 99.0 2.6E-09 5.7E-14 86.1 10.5 110 116-225 2-126 (138)
4 PF01710 HTH_Tnp_IS630: Transp 98.9 1.3E-08 2.9E-13 79.9 11.0 100 32-165 2-101 (119)
5 COG3415 Transposase and inacti 98.9 2.9E-08 6.3E-13 80.1 11.6 110 30-166 2-117 (138)
6 PF05225 HTH_psq: helix-turn-h 98.8 8E-09 1.7E-13 67.9 5.2 39 120-158 1-39 (45)
7 cd00131 PAX Paired Box domain 98.8 1.5E-07 3.4E-12 74.9 13.3 104 109-213 8-126 (128)
8 smart00351 PAX Paired Box doma 98.7 4.2E-07 9E-12 72.0 12.6 96 116-212 15-125 (125)
9 COG2963 Transposase and inacti 98.7 1.7E-07 3.7E-12 72.8 9.1 91 116-206 5-98 (116)
10 PF13551 HTH_29: Winged helix- 98.6 3.4E-07 7.4E-12 69.4 9.9 97 39-160 2-112 (112)
11 PF13551 HTH_29: Winged helix- 98.6 3.9E-07 8.4E-12 69.1 10.2 88 125-212 2-109 (112)
12 cd00131 PAX Paired Box domain 98.6 1.5E-06 3.3E-11 69.2 12.7 103 27-158 12-126 (128)
13 PF01527 HTH_Tnp_1: Transposas 98.6 4.7E-08 1E-12 69.9 3.4 47 28-74 2-48 (76)
14 PF01527 HTH_Tnp_1: Transposas 98.5 1E-07 2.3E-12 68.1 4.4 54 169-222 2-55 (76)
15 smart00351 PAX Paired Box doma 98.5 2.2E-06 4.9E-11 67.8 11.4 48 28-76 13-60 (125)
16 PRK09413 IS2 repressor TnpA; R 98.5 3.9E-07 8.5E-12 71.7 6.4 49 28-76 8-56 (121)
17 COG2963 Transposase and inacti 98.5 1.1E-06 2.4E-11 68.1 8.8 46 30-75 5-51 (116)
18 PF02796 HTH_7: Helix-turn-hel 98.4 3.4E-07 7.4E-12 59.9 4.2 43 114-157 1-43 (45)
19 PRK09413 IS2 repressor TnpA; R 98.4 6.8E-07 1.5E-11 70.3 6.3 45 170-214 9-53 (121)
20 PF13518 HTH_28: Helix-turn-he 98.4 5.8E-07 1.3E-11 59.5 5.0 42 123-165 1-45 (52)
21 PF13518 HTH_28: Helix-turn-he 98.4 3.9E-07 8.5E-12 60.4 3.8 43 38-81 2-44 (52)
22 PF13384 HTH_23: Homeodomain-l 98.3 3.7E-07 8.1E-12 60.4 3.0 46 34-80 3-48 (50)
23 PF04218 CENP-B_N: CENP-B N-te 98.3 2.2E-06 4.9E-11 58.1 5.3 44 28-72 2-45 (53)
24 PF02796 HTH_7: Helix-turn-hel 98.2 1.5E-06 3.2E-11 56.9 3.9 43 169-212 1-43 (45)
25 PF04218 CENP-B_N: CENP-B N-te 98.1 6.3E-06 1.4E-10 55.9 4.9 41 171-212 4-44 (53)
26 PF13936 HTH_38: Helix-turn-he 98.0 9.5E-06 2.1E-10 52.9 3.9 42 30-72 2-43 (44)
27 PF13384 HTH_23: Homeodomain-l 98.0 9.4E-06 2E-10 53.6 3.8 40 175-215 3-42 (50)
28 cd01104 HTH_MlrA-CarA Helix-Tu 97.8 0.00014 3E-09 50.7 7.6 64 50-144 1-66 (68)
29 PF06056 Terminase_5: Putative 97.8 5.1E-05 1.1E-09 52.4 5.2 43 122-165 1-43 (58)
30 PF09607 BrkDBD: Brinker DNA-b 97.7 6.5E-05 1.4E-09 51.8 5.0 43 170-212 2-47 (58)
31 cd01104 HTH_MlrA-CarA Helix-Tu 97.7 0.00028 6E-09 49.2 8.3 64 136-199 1-66 (68)
32 PF13936 HTH_38: Helix-turn-he 97.7 4.1E-05 9E-10 49.8 3.2 40 172-212 3-42 (44)
33 PF06056 Terminase_5: Putative 97.7 7.9E-05 1.7E-09 51.5 4.4 44 37-81 2-45 (58)
34 cd00569 HTH_Hin_like Helix-tur 97.6 0.00019 4.1E-09 42.2 5.4 41 170-211 2-42 (42)
35 cd04764 HTH_MlrA-like_sg1 Heli 97.6 0.00043 9.3E-09 48.4 8.0 66 50-145 1-66 (67)
36 PF13011 LZ_Tnp_IS481: leucine 97.6 0.00014 3.1E-09 54.0 5.7 49 30-78 6-54 (85)
37 cd00569 HTH_Hin_like Helix-tur 97.6 0.00024 5.3E-09 41.7 5.3 42 114-156 1-42 (42)
38 PF13411 MerR_1: MerR HTH fami 97.4 0.00034 7.4E-09 48.8 5.3 64 50-145 1-66 (69)
39 PF09862 DUF2089: Protein of u 97.4 0.0019 4.1E-08 50.5 9.7 77 117-200 32-112 (113)
40 PF13011 LZ_Tnp_IS481: leucine 97.3 0.00073 1.6E-08 50.2 6.3 40 173-212 8-47 (85)
41 cd04763 HTH_MlrA-like Helix-Tu 97.3 0.0019 4.2E-08 45.2 8.2 65 50-145 1-67 (68)
42 PRK13413 mpi multiple promoter 97.3 0.0012 2.6E-08 55.8 7.9 70 92-161 124-198 (200)
43 PF13411 MerR_1: MerR HTH fami 97.2 0.00076 1.7E-08 47.0 5.4 64 136-200 1-66 (69)
44 cd04763 HTH_MlrA-like Helix-Tu 97.2 0.0041 8.9E-08 43.5 8.6 65 136-200 1-67 (68)
45 PF13565 HTH_32: Homeodomain-l 97.2 0.0017 3.6E-08 46.3 6.6 60 151-211 1-77 (77)
46 cd04764 HTH_MlrA-like_sg1 Heli 97.1 0.0039 8.4E-08 43.4 8.1 64 136-200 1-66 (67)
47 cd04762 HTH_MerR-trunc Helix-T 97.1 0.0012 2.6E-08 42.1 4.9 27 50-76 1-27 (49)
48 smart00342 HTH_ARAC helix_turn 97.1 0.0025 5.5E-08 44.7 6.9 77 50-163 2-80 (84)
49 PHA02535 P terminase ATPase su 97.1 0.00084 1.8E-08 65.6 5.6 48 118-166 2-49 (581)
50 KOG4565|consensus 97.0 0.00024 5.3E-09 59.0 1.3 68 144-212 93-160 (206)
51 PF09607 BrkDBD: Brinker DNA-b 97.0 0.0011 2.4E-08 45.7 4.3 45 114-158 1-48 (58)
52 PF02954 HTH_8: Bacterial regu 97.0 0.0017 3.7E-08 41.7 4.6 33 41-73 10-42 (42)
53 PRK11511 DNA-binding transcrip 96.9 0.008 1.7E-07 47.4 8.9 88 37-163 13-104 (127)
54 PRK10219 DNA-binding transcrip 96.9 0.029 6.3E-07 42.4 11.6 86 39-163 11-100 (107)
55 PF09862 DUF2089: Protein of u 96.9 0.0075 1.6E-07 47.2 8.2 43 29-72 30-72 (113)
56 smart00422 HTH_MERR helix_turn 96.8 0.0091 2E-07 41.5 7.7 23 50-72 1-23 (70)
57 PF12116 SpoIIID: Stage III sp 96.8 0.002 4.2E-08 47.3 4.2 36 176-211 5-40 (82)
58 cd04788 HTH_NolA-AlbR Helix-Tu 96.8 0.014 3E-07 43.9 8.9 74 136-210 1-77 (96)
59 PHA00675 hypothetical protein 96.8 0.0037 7.9E-08 45.5 5.4 47 25-72 15-62 (78)
60 smart00342 HTH_ARAC helix_turn 96.8 0.0077 1.7E-07 42.2 7.1 69 136-212 2-73 (84)
61 PHA02535 P terminase ATPase su 96.8 0.0018 3.8E-08 63.4 4.8 43 32-75 2-44 (581)
62 KOG4565|consensus 96.7 0.00097 2.1E-08 55.4 2.5 48 27-74 116-163 (206)
63 cd01105 HTH_GlnR-like Helix-Tu 96.7 0.01 2.2E-07 44.0 7.4 65 136-201 2-69 (88)
64 cd04788 HTH_NolA-AlbR Helix-Tu 96.7 0.018 4E-07 43.3 8.9 70 50-150 1-72 (96)
65 cd01106 HTH_TipAL-Mta Helix-Tu 96.6 0.02 4.4E-07 43.4 9.1 69 136-205 1-72 (103)
66 smart00422 HTH_MERR helix_turn 96.6 0.017 3.6E-07 40.1 7.9 64 136-200 1-67 (70)
67 cd01105 HTH_GlnR-like Helix-Tu 96.6 0.013 2.8E-07 43.5 7.6 66 50-146 2-69 (88)
68 PF00292 PAX: 'Paired box' dom 96.6 0.014 2.9E-07 46.5 8.1 44 30-74 15-58 (125)
69 cd04765 HTH_MlrA-like_sg2 Heli 96.6 0.013 2.9E-07 44.5 7.8 71 136-206 1-74 (99)
70 cd04762 HTH_MerR-trunc Helix-T 96.6 0.0079 1.7E-07 38.2 5.4 47 136-183 1-47 (49)
71 PF01022 HTH_5: Bacterial regu 96.6 0.0046 1E-07 40.4 4.3 41 177-217 2-43 (47)
72 smart00421 HTH_LUXR helix_turn 96.6 0.0086 1.9E-07 39.1 5.7 37 174-212 4-40 (58)
73 cd04765 HTH_MlrA-like_sg2 Heli 96.5 0.014 3E-07 44.3 7.5 29 50-78 1-29 (99)
74 PRK13182 racA polar chromosome 96.5 0.0091 2E-07 50.1 6.9 27 50-76 1-27 (175)
75 PF10668 Phage_terminase: Phag 96.5 0.0041 8.8E-08 43.3 3.9 37 37-73 8-46 (60)
76 TIGR02531 yecD_yerC TrpR-relat 96.5 0.0056 1.2E-07 45.8 5.0 36 176-212 37-72 (88)
77 TIGR01764 excise DNA binding d 96.5 0.0038 8.2E-08 40.0 3.5 29 50-78 2-30 (49)
78 smart00421 HTH_LUXR helix_turn 96.5 0.0093 2E-07 38.9 5.5 40 32-73 3-42 (58)
79 COG2826 Tra8 Transposase and i 96.5 0.033 7.1E-07 50.5 10.5 106 32-157 7-115 (318)
80 cd04761 HTH_MerR-SF Helix-Turn 96.4 0.0066 1.4E-07 39.2 4.5 27 50-76 1-27 (49)
81 PF02954 HTH_8: Bacterial regu 96.4 0.0092 2E-07 38.2 5.0 35 178-212 6-40 (42)
82 cd04768 HTH_BmrR-like Helix-Tu 96.4 0.043 9.3E-07 41.2 9.3 70 50-150 1-72 (96)
83 PRK11511 DNA-binding transcrip 96.3 0.037 7.9E-07 43.6 8.9 81 132-220 22-104 (127)
84 PF13542 HTH_Tnp_ISL3: Helix-t 96.3 0.012 2.6E-07 38.8 5.1 44 29-73 8-51 (52)
85 PF02042 RWP-RK: RWP-RK domain 96.3 0.013 2.8E-07 39.7 5.2 39 32-76 4-42 (52)
86 PRK04217 hypothetical protein; 96.2 0.014 2.9E-07 45.5 5.9 45 27-72 37-81 (110)
87 cd04782 HTH_BltR Helix-Turn-He 96.2 0.059 1.3E-06 40.6 9.3 67 136-203 1-70 (97)
88 PF13565 HTH_32: Homeodomain-l 96.2 0.02 4.3E-07 40.7 6.4 42 113-155 26-76 (77)
89 cd04768 HTH_BmrR-like Helix-Tu 96.2 0.058 1.3E-06 40.5 9.2 74 136-210 1-77 (96)
90 cd04775 HTH_Cfa-like Helix-Tur 96.2 0.038 8.2E-07 42.0 8.1 67 136-203 2-70 (102)
91 COG1342 Predicted DNA-binding 96.2 0.0071 1.5E-07 45.8 3.9 37 175-212 35-71 (99)
92 cd01106 HTH_TipAL-Mta Helix-Tu 96.1 0.056 1.2E-06 40.9 9.0 69 50-149 1-71 (103)
93 PRK13413 mpi multiple promoter 96.1 0.011 2.4E-07 49.9 5.5 37 40-76 163-199 (200)
94 cd01109 HTH_YyaN Helix-Turn-He 96.1 0.038 8.1E-07 42.6 8.1 66 50-146 1-68 (113)
95 cd01282 HTH_MerR-like_sg3 Heli 96.1 0.043 9.2E-07 42.4 8.2 66 136-202 1-68 (112)
96 TIGR02531 yecD_yerC TrpR-relat 96.1 0.01 2.2E-07 44.4 4.5 32 40-71 41-72 (88)
97 PF12728 HTH_17: Helix-turn-he 96.1 0.0074 1.6E-07 39.7 3.4 29 50-78 2-30 (51)
98 PF10668 Phage_terminase: Phag 96.1 0.013 2.9E-07 40.7 4.8 41 123-163 8-50 (60)
99 cd00592 HTH_MerR-like Helix-Tu 96.1 0.051 1.1E-06 40.7 8.3 67 136-203 1-69 (100)
100 PF12840 HTH_20: Helix-turn-he 96.1 0.015 3.2E-07 39.9 4.9 40 177-216 10-51 (61)
101 cd01110 HTH_SoxR Helix-Turn-He 96.1 0.031 6.7E-07 45.0 7.5 66 49-146 1-68 (139)
102 PF13542 HTH_Tnp_ISL3: Helix-t 96.0 0.022 4.9E-07 37.4 5.6 42 170-212 8-49 (52)
103 PF13309 HTH_22: HTH domain 96.0 0.028 6.1E-07 39.4 6.3 40 173-212 20-64 (64)
104 cd01109 HTH_YyaN Helix-Turn-He 96.0 0.052 1.1E-06 41.8 8.3 65 136-201 1-68 (113)
105 PRK11608 pspF phage shock prot 96.0 0.01 2.2E-07 54.1 4.9 38 38-75 288-325 (326)
106 cd01282 HTH_MerR-like_sg3 Heli 96.0 0.044 9.6E-07 42.3 7.8 65 50-146 1-67 (112)
107 PRK15044 transcriptional regul 96.0 0.028 6E-07 50.9 7.6 87 39-163 198-286 (295)
108 PF07900 DUF1670: Protein of u 96.0 0.36 7.9E-06 41.9 14.0 113 44-210 99-217 (220)
109 PRK15186 AraC family transcrip 96.0 0.031 6.6E-07 50.4 7.8 86 40-163 188-275 (291)
110 cd00592 HTH_MerR-like Helix-Tu 96.0 0.051 1.1E-06 40.6 7.9 23 50-72 1-23 (100)
111 cd01110 HTH_SoxR Helix-Turn-He 95.9 0.041 8.8E-07 44.3 7.6 66 135-201 1-68 (139)
112 cd04775 HTH_Cfa-like Helix-Tur 95.9 0.054 1.2E-06 41.2 7.9 68 50-149 2-71 (102)
113 cd01107 HTH_BmrR Helix-Turn-He 95.9 0.054 1.2E-06 41.5 7.9 70 50-150 1-73 (108)
114 cd04790 HTH_Cfa-like_unk Helix 95.9 0.075 1.6E-06 44.3 9.3 71 136-207 2-75 (172)
115 TIGR01321 TrpR trp operon repr 95.9 0.016 3.4E-07 43.9 4.7 34 40-73 46-79 (94)
116 PRK01905 DNA-binding protein F 95.9 0.019 4.1E-07 41.6 5.0 37 39-75 40-76 (77)
117 PRK04217 hypothetical protein; 95.9 0.019 4.2E-07 44.7 5.3 40 172-212 41-80 (110)
118 PF08281 Sigma70_r4_2: Sigma-7 95.9 0.021 4.5E-07 37.9 4.8 34 39-72 16-49 (54)
119 cd01107 HTH_BmrR Helix-Turn-He 95.9 0.064 1.4E-06 41.1 8.1 69 136-205 1-73 (108)
120 TIGR01764 excise DNA binding d 95.8 0.012 2.5E-07 37.6 3.4 46 136-183 2-47 (49)
121 PRK10219 DNA-binding transcrip 95.8 0.074 1.6E-06 40.1 8.4 80 133-220 19-100 (107)
122 cd04785 HTH_CadR-PbrR-like Hel 95.8 0.058 1.2E-06 42.5 8.0 68 136-203 1-70 (126)
123 cd04780 HTH_MerR-like_sg5 Heli 95.8 0.051 1.1E-06 40.9 7.3 67 50-147 1-70 (95)
124 PRK13503 transcriptional activ 95.8 0.16 3.4E-06 44.2 11.3 80 46-164 184-267 (278)
125 cd04774 HTH_YfmP Helix-Turn-He 95.8 0.058 1.3E-06 40.7 7.4 70 136-206 1-73 (96)
126 cd04782 HTH_BltR Helix-Turn-He 95.7 0.15 3.4E-06 38.2 9.7 68 50-148 1-70 (97)
127 cd04780 HTH_MerR-like_sg5 Heli 95.7 0.068 1.5E-06 40.3 7.7 66 136-202 1-70 (95)
128 cd06171 Sigma70_r4 Sigma70, re 95.7 0.029 6.3E-07 35.8 5.0 40 32-72 10-49 (55)
129 TIGR01321 TrpR trp operon repr 95.7 0.022 4.7E-07 43.2 4.9 42 177-218 42-83 (94)
130 cd04789 HTH_Cfa Helix-Turn-Hel 95.7 0.076 1.6E-06 40.4 8.0 66 136-202 2-69 (102)
131 cd04761 HTH_MerR-SF Helix-Turn 95.7 0.028 6E-07 36.2 4.8 45 136-181 1-45 (49)
132 cd04773 HTH_TioE_rpt2 Second H 95.7 0.051 1.1E-06 41.8 7.0 26 50-76 1-26 (108)
133 cd04789 HTH_Cfa Helix-Turn-Hel 95.7 0.072 1.6E-06 40.5 7.8 65 50-146 2-68 (102)
134 cd04781 HTH_MerR-like_sg6 Heli 95.7 0.074 1.6E-06 41.5 8.0 67 136-203 1-69 (120)
135 cd04781 HTH_MerR-like_sg6 Heli 95.7 0.064 1.4E-06 41.9 7.6 67 50-148 1-69 (120)
136 PRK11361 acetoacetate metaboli 95.6 0.021 4.5E-07 53.5 5.5 39 38-76 419-457 (457)
137 PRK09978 DNA-binding transcrip 95.6 0.061 1.3E-06 48.2 8.2 88 37-163 146-236 (274)
138 PRK01381 Trp operon repressor; 95.6 0.015 3.2E-07 44.5 3.5 35 39-73 45-79 (99)
139 PF02001 DUF134: Protein of un 95.6 0.022 4.7E-07 44.1 4.5 35 178-212 45-79 (106)
140 cd01108 HTH_CueR Helix-Turn-He 95.5 0.065 1.4E-06 42.3 7.3 66 50-146 1-68 (127)
141 PRK15185 transcriptional regul 95.5 0.061 1.3E-06 49.0 8.0 87 39-163 212-300 (309)
142 cd01279 HTH_HspR-like Helix-Tu 95.5 0.091 2E-06 39.7 7.8 66 136-202 2-70 (98)
143 cd06170 LuxR_C_like C-terminal 95.5 0.041 8.9E-07 35.9 5.2 38 34-73 2-39 (57)
144 cd01111 HTH_MerD Helix-Turn-He 95.5 0.076 1.7E-06 40.8 7.4 66 50-146 1-68 (107)
145 cd04770 HTH_HMRTR Helix-Turn-H 95.5 0.1 2.2E-06 40.6 8.1 67 136-203 1-70 (123)
146 cd04773 HTH_TioE_rpt2 Second H 95.4 0.082 1.8E-06 40.6 7.4 66 136-202 1-69 (108)
147 cd04774 HTH_YfmP Helix-Turn-He 95.4 0.083 1.8E-06 39.8 7.3 26 50-76 1-26 (96)
148 PRK15115 response regulator Gl 95.4 0.022 4.8E-07 53.2 5.0 41 37-77 399-439 (444)
149 cd04767 HTH_HspR-like_MBC Heli 95.4 0.071 1.5E-06 42.1 7.0 66 50-148 2-70 (120)
150 TIGR02043 ZntR Zn(II)-responsi 95.4 0.091 2E-06 41.7 7.7 66 136-202 2-70 (131)
151 cd01108 HTH_CueR Helix-Turn-He 95.4 0.095 2.1E-06 41.3 7.7 65 136-201 1-68 (127)
152 PF12116 SpoIIID: Stage III sp 95.4 0.017 3.6E-07 42.4 3.0 40 33-72 3-42 (82)
153 TIGR02915 PEP_resp_reg putativ 95.3 0.025 5.4E-07 52.9 5.0 39 38-76 407-445 (445)
154 cd04783 HTH_MerR1 Helix-Turn-H 95.3 0.11 2.4E-06 40.8 7.9 67 136-203 1-70 (126)
155 cd06170 LuxR_C_like C-terminal 95.3 0.053 1.1E-06 35.4 5.2 32 180-212 6-37 (57)
156 PF12728 HTH_17: Helix-turn-he 95.3 0.027 6E-07 37.0 3.8 46 136-183 2-47 (51)
157 PRK13501 transcriptional activ 95.3 0.27 5.9E-06 43.4 11.3 88 38-163 181-271 (290)
158 cd04769 HTH_MerR2 Helix-Turn-H 95.3 0.12 2.5E-06 40.1 7.9 67 136-203 1-69 (116)
159 PRK13182 racA polar chromosome 95.3 0.07 1.5E-06 44.8 7.0 62 136-198 1-64 (175)
160 PRK15043 transcriptional regul 95.3 0.082 1.8E-06 46.6 7.7 68 136-203 4-73 (243)
161 COG3829 RocR Transcriptional r 95.2 0.025 5.4E-07 54.9 4.7 40 37-76 521-560 (560)
162 TIGR02043 ZntR Zn(II)-responsi 95.2 0.1 2.2E-06 41.5 7.5 66 50-146 2-69 (131)
163 cd01279 HTH_HspR-like Helix-Tu 95.2 0.1 2.2E-06 39.4 7.1 28 50-78 2-29 (98)
164 PF13613 HTH_Tnp_4: Helix-turn 95.2 0.05 1.1E-06 36.4 4.9 41 32-72 2-42 (53)
165 cd04785 HTH_CadR-PbrR-like Hel 95.2 0.11 2.5E-06 40.8 7.7 67 50-147 1-69 (126)
166 TIGR02044 CueR Cu(I)-responsiv 95.2 0.12 2.7E-06 40.6 7.9 65 136-201 1-68 (127)
167 PRK10923 glnG nitrogen regulat 95.2 0.03 6.5E-07 52.8 5.1 36 41-76 434-469 (469)
168 cd04770 HTH_HMRTR Helix-Turn-H 95.2 0.13 2.8E-06 40.1 7.9 67 50-147 1-69 (123)
169 cd04790 HTH_Cfa-like_unk Helix 95.2 0.21 4.6E-06 41.5 9.6 70 50-150 2-73 (172)
170 TIGR02044 CueR Cu(I)-responsiv 95.2 0.12 2.6E-06 40.7 7.7 66 50-146 1-68 (127)
171 PRK00430 fis global DNA-bindin 95.2 0.046 1E-06 41.3 5.1 33 43-75 62-94 (95)
172 PF04545 Sigma70_r4: Sigma-70, 95.2 0.059 1.3E-06 35.3 5.0 38 34-72 6-43 (50)
173 PRK10820 DNA-binding transcrip 95.1 0.031 6.6E-07 54.2 5.1 34 43-77 481-514 (520)
174 cd04783 HTH_MerR1 Helix-Turn-H 95.1 0.12 2.6E-06 40.6 7.6 68 50-148 1-70 (126)
175 PF07750 GcrA: GcrA cell cycle 95.1 0.034 7.4E-07 46.1 4.6 46 32-78 2-48 (162)
176 PF13412 HTH_24: Winged helix- 95.1 0.043 9.3E-07 35.6 4.2 35 39-73 6-41 (48)
177 cd04766 HTH_HspR Helix-Turn-He 95.1 0.13 2.8E-06 38.1 7.2 65 136-201 2-69 (91)
178 PHA00675 hypothetical protein 95.1 0.06 1.3E-06 39.2 5.1 41 172-212 21-61 (78)
179 cd04786 HTH_MerR-like_sg7 Heli 95.1 0.15 3.2E-06 40.7 8.0 66 136-202 1-69 (131)
180 cd04769 HTH_MerR2 Helix-Turn-H 95.1 0.13 2.8E-06 39.9 7.5 66 50-147 1-68 (116)
181 PRK09514 zntR zinc-responsive 95.0 0.12 2.6E-06 41.6 7.5 66 136-202 2-70 (140)
182 cd01111 HTH_MerD Helix-Turn-He 95.0 0.14 3.1E-06 39.3 7.6 66 136-202 1-69 (107)
183 PRK09393 ftrA transcriptional 95.0 0.098 2.1E-06 47.1 7.7 85 41-163 226-313 (322)
184 TIGR02297 HpaA 4-hydroxyphenyl 95.0 0.44 9.5E-06 41.7 11.7 87 39-163 192-281 (287)
185 PRK09514 zntR zinc-responsive 95.0 0.12 2.5E-06 41.7 7.3 67 50-147 2-70 (140)
186 PRK13502 transcriptional activ 95.0 0.27 5.8E-06 43.0 10.3 86 40-163 183-271 (282)
187 PRK11388 DNA-binding transcrip 95.0 0.038 8.3E-07 54.6 5.4 40 37-76 592-631 (638)
188 PRK00118 putative DNA-binding 95.0 0.043 9.4E-07 42.3 4.5 40 32-72 17-56 (104)
189 PF13404 HTH_AsnC-type: AsnC-t 94.9 0.061 1.3E-06 34.6 4.4 28 46-73 14-41 (42)
190 PF00292 PAX: 'Paired box' dom 94.9 0.12 2.7E-06 41.1 7.0 79 117-196 16-99 (125)
191 PHA00542 putative Cro-like pro 94.9 0.061 1.3E-06 39.4 5.0 44 171-215 13-56 (82)
192 PF13412 HTH_24: Winged helix- 94.9 0.092 2E-06 34.0 5.4 40 177-216 3-44 (48)
193 cd04767 HTH_HspR-like_MBC Heli 94.9 0.12 2.6E-06 40.8 6.9 64 136-201 2-68 (120)
194 PRK10572 DNA-binding transcrip 94.9 0.36 7.9E-06 42.4 10.8 87 39-164 189-279 (290)
195 cd04784 HTH_CadR-PbrR Helix-Tu 94.9 0.15 3.2E-06 40.1 7.4 66 50-146 1-68 (127)
196 PF08281 Sigma70_r4_2: Sigma-7 94.9 0.071 1.5E-06 35.3 4.8 36 177-212 13-48 (54)
197 PRK05022 anaerobic nitric oxid 94.8 0.048 1E-06 52.6 5.5 40 37-76 469-508 (509)
198 TIGR02047 CadR-PbrR Cd(II)/Pb( 94.8 0.16 3.6E-06 40.0 7.7 66 50-146 1-68 (127)
199 PF12833 HTH_18: Helix-turn-he 94.8 0.36 7.8E-06 34.3 8.8 71 55-163 1-75 (81)
200 cd06171 Sigma70_r4 Sigma70, re 94.8 0.093 2E-06 33.3 5.2 39 174-213 11-49 (55)
201 COG1342 Predicted DNA-binding 94.8 0.038 8.3E-07 41.9 3.7 38 34-72 35-72 (99)
202 PF04545 Sigma70_r4: Sigma-70, 94.8 0.095 2.1E-06 34.3 5.3 37 175-212 6-42 (50)
203 TIGR02047 CadR-PbrR Cd(II)/Pb( 94.8 0.2 4.4E-06 39.5 8.0 66 136-202 1-69 (127)
204 PHA02591 hypothetical protein; 94.8 0.053 1.1E-06 39.6 4.2 38 34-71 44-81 (83)
205 PRK15043 transcriptional regul 94.8 0.12 2.6E-06 45.6 7.2 30 49-78 3-32 (243)
206 COG0789 SoxR Predicted transcr 94.7 0.19 4.2E-06 38.7 7.7 69 136-204 1-71 (124)
207 PRK15121 right oriC-binding tr 94.7 0.5 1.1E-05 41.9 11.3 88 38-163 10-100 (289)
208 cd04766 HTH_HspR Helix-Turn-He 94.7 0.19 4E-06 37.2 7.2 65 50-146 2-69 (91)
209 TIGR02051 MerR Hg(II)-responsi 94.7 0.17 3.7E-06 39.8 7.3 67 137-204 1-70 (124)
210 PF01022 HTH_5: Bacterial regu 94.7 0.054 1.2E-06 35.2 3.7 38 36-73 2-39 (47)
211 PF02001 DUF134: Protein of un 94.6 0.059 1.3E-06 41.7 4.5 38 34-72 43-80 (106)
212 COG3284 AcoR Transcriptional a 94.6 0.048 1E-06 53.6 4.9 40 37-76 566-605 (606)
213 cd04786 HTH_MerR-like_sg7 Heli 94.6 0.19 4.2E-06 40.0 7.6 67 50-147 1-69 (131)
214 TIGR02844 spore_III_D sporulat 94.6 0.09 1.9E-06 38.6 5.2 39 174-212 3-41 (80)
215 TIGR01950 SoxR redox-sensitive 94.6 0.17 3.8E-06 40.9 7.4 65 136-201 2-68 (142)
216 COG2826 Tra8 Transposase and i 94.6 0.18 4E-06 45.7 8.1 84 128-212 16-115 (318)
217 cd04776 HTH_GnyR Helix-Turn-He 94.6 0.22 4.7E-06 38.9 7.7 65 50-147 1-67 (118)
218 PF13022 HTH_Tnp_1_2: Helix-tu 94.5 0.077 1.7E-06 43.0 5.0 42 31-72 9-57 (142)
219 COG2973 TrpR Trp operon repres 94.5 0.042 9.2E-07 41.8 3.3 32 38-69 49-80 (103)
220 cd04787 HTH_HMRTR_unk Helix-Tu 94.5 0.23 5.1E-06 39.4 7.9 67 136-203 1-70 (133)
221 PF01371 Trp_repressor: Trp re 94.5 0.068 1.5E-06 39.9 4.3 35 38-72 38-72 (87)
222 PRK13500 transcriptional activ 94.5 0.43 9.2E-06 42.9 10.4 88 39-164 212-302 (312)
223 PF13613 HTH_Tnp_4: Helix-turn 94.5 0.12 2.6E-06 34.6 5.2 38 175-212 4-41 (53)
224 PRK09940 transcriptional regul 94.5 0.28 6E-06 43.5 9.0 88 36-163 137-227 (253)
225 PRK00118 putative DNA-binding 94.4 0.086 1.9E-06 40.6 4.9 35 178-212 21-55 (104)
226 PF07750 GcrA: GcrA cell cycle 94.4 0.094 2E-06 43.5 5.5 39 173-212 2-41 (162)
227 cd04784 HTH_CadR-PbrR Helix-Tu 94.4 0.25 5.5E-06 38.8 7.8 66 136-202 1-69 (127)
228 cd04776 HTH_GnyR Helix-Turn-He 94.4 0.29 6.2E-06 38.2 7.9 65 136-202 1-67 (118)
229 TIGR01817 nifA Nif-specific re 94.3 0.068 1.5E-06 51.7 5.3 41 37-77 491-531 (534)
230 cd04779 HTH_MerR-like_sg4 Heli 94.3 0.24 5.3E-06 39.7 7.6 67 136-203 1-69 (134)
231 PRK15002 redox-sensitivie tran 94.3 0.19 4.2E-06 41.2 7.1 67 135-202 11-79 (154)
232 COG5484 Uncharacterized conser 94.3 0.067 1.5E-06 47.3 4.5 40 122-162 7-46 (279)
233 TIGR02054 MerD mercuric resist 94.3 0.23 5.1E-06 39.1 7.2 68 49-147 3-72 (120)
234 cd04779 HTH_MerR-like_sg4 Heli 94.2 0.22 4.8E-06 39.9 7.2 66 50-147 1-68 (134)
235 PF03683 UPF0175: Uncharacteri 94.2 0.12 2.6E-06 37.4 5.1 38 39-76 24-61 (76)
236 PRK10227 DNA-binding transcrip 94.2 0.28 6E-06 39.3 7.7 66 136-202 1-69 (135)
237 TIGR03879 near_KaiC_dom probab 94.2 0.097 2.1E-06 37.8 4.5 36 38-73 20-56 (73)
238 PF09824 ArsR: ArsR transcript 94.2 0.95 2.1E-05 37.4 10.7 108 34-159 15-145 (160)
239 TIGR01950 SoxR redox-sensitive 94.1 0.23 5.1E-06 40.1 7.2 66 49-146 1-68 (142)
240 TIGR02054 MerD mercuric resist 94.1 0.28 6.1E-06 38.6 7.5 66 136-202 4-72 (120)
241 PF06627 DUF1153: Protein of u 94.1 0.2 4.4E-06 37.4 6.2 57 28-84 28-84 (90)
242 PHA02943 hypothetical protein; 94.1 0.12 2.5E-06 42.6 5.4 42 176-217 10-52 (165)
243 PF12840 HTH_20: Helix-turn-he 94.1 0.082 1.8E-06 36.1 3.9 38 36-73 10-48 (61)
244 PHA00542 putative Cro-like pro 94.1 0.075 1.6E-06 38.9 3.9 30 42-71 24-53 (82)
245 cd04778 HTH_MerR-like_sg2 Heli 94.1 3.6 7.7E-05 35.7 15.6 153 50-208 2-165 (219)
246 PF08220 HTH_DeoR: DeoR-like h 94.1 0.12 2.7E-06 35.1 4.7 38 180-217 3-42 (57)
247 PRK11179 DNA-binding transcrip 94.1 0.087 1.9E-06 42.7 4.6 46 31-76 3-50 (153)
248 PF04297 UPF0122: Putative hel 94.0 0.082 1.8E-06 40.6 4.0 36 177-212 20-55 (101)
249 cd04787 HTH_HMRTR_unk Helix-Tu 94.0 0.3 6.4E-06 38.8 7.5 67 50-147 1-69 (133)
250 PRK15424 propionate catabolism 94.0 0.086 1.9E-06 51.5 5.1 40 37-76 498-537 (538)
251 PRK15429 formate hydrogenlyase 93.9 0.075 1.6E-06 53.1 4.7 40 37-76 642-684 (686)
252 PF03683 UPF0175: Uncharacteri 93.9 0.33 7.1E-06 35.0 6.8 49 124-181 23-71 (76)
253 PRK10371 DNA-binding transcrip 93.9 1.1 2.4E-05 40.2 11.8 78 47-163 205-286 (302)
254 TIGR03734 PRTRC_parB PRTRC sys 93.8 0.67 1.5E-05 45.5 10.9 93 29-141 88-181 (554)
255 PRK01381 Trp operon repressor; 93.7 0.062 1.4E-06 41.0 2.9 36 177-212 42-77 (99)
256 PF08822 DUF1804: Protein of u 93.7 0.15 3.3E-06 42.4 5.5 41 33-73 3-43 (165)
257 PF01978 TrmB: Sugar-specific 93.7 0.07 1.5E-06 37.1 3.0 39 36-74 9-47 (68)
258 COG0789 SoxR Predicted transcr 93.7 0.46 1E-05 36.5 7.9 69 50-149 1-71 (124)
259 PRK10227 DNA-binding transcrip 93.7 0.36 7.9E-06 38.6 7.5 66 50-146 1-68 (135)
260 PF01381 HTH_3: Helix-turn-hel 93.7 0.12 2.6E-06 34.1 4.0 30 184-213 3-32 (55)
261 PRK15002 redox-sensitivie tran 93.5 0.31 6.7E-06 40.0 7.0 66 49-146 11-78 (154)
262 PF00196 GerE: Bacterial regul 93.5 0.13 2.9E-06 34.6 4.0 31 181-212 10-40 (58)
263 PF04967 HTH_10: HTH DNA bindi 93.5 0.28 6.1E-06 33.2 5.5 39 34-72 2-46 (53)
264 PF13309 HTH_22: HTH domain 93.5 0.11 2.3E-06 36.4 3.6 42 30-71 18-64 (64)
265 PF04297 UPF0122: Putative hel 93.4 0.1 2.3E-06 40.0 3.8 34 39-72 23-56 (101)
266 cd04777 HTH_MerR-like_sg1 Heli 93.4 0.57 1.2E-05 35.6 7.9 65 50-147 1-67 (107)
267 PF03333 PapB: Adhesin biosynt 93.4 0.18 4E-06 37.9 4.9 43 31-73 35-77 (91)
268 TIGR02844 spore_III_D sporulat 93.4 0.16 3.5E-06 37.3 4.6 57 33-99 3-59 (80)
269 TIGR02051 MerR Hg(II)-responsi 93.4 0.38 8.1E-06 37.8 7.0 68 51-149 1-70 (124)
270 PF13556 HTH_30: PucR C-termin 93.3 0.14 3.1E-06 34.9 3.9 35 39-73 2-36 (59)
271 PF14493 HTH_40: Helix-turn-he 93.3 0.88 1.9E-05 33.6 8.5 78 125-208 4-87 (91)
272 PF01371 Trp_repressor: Trp re 93.3 0.2 4.4E-06 37.4 4.9 36 177-212 36-71 (87)
273 PRK15435 bifunctional DNA-bind 93.2 0.64 1.4E-05 43.1 9.3 87 38-163 87-177 (353)
274 TIGR03879 near_KaiC_dom probab 93.2 0.24 5.1E-06 35.8 5.1 37 176-212 17-54 (73)
275 COG2207 AraC AraC-type DNA-bin 93.2 2.5 5.4E-05 31.5 11.2 89 37-163 24-115 (127)
276 PRK15044 transcriptional regul 93.2 0.4 8.6E-06 43.5 7.7 82 132-220 205-286 (295)
277 PF01381 HTH_3: Helix-turn-hel 93.2 0.099 2.1E-06 34.5 2.9 27 46-72 6-32 (55)
278 PF06163 DUF977: Bacterial pro 93.0 0.34 7.3E-06 38.6 6.1 42 171-212 2-48 (127)
279 PRK15186 AraC family transcrip 93.0 0.45 9.7E-06 42.9 7.8 87 127-220 189-275 (291)
280 smart00420 HTH_DEOR helix_turn 93.0 0.28 6.2E-06 31.4 4.9 36 37-74 4-39 (53)
281 PHA01976 helix-turn-helix prot 93.0 0.37 7.9E-06 33.1 5.7 25 47-71 13-37 (67)
282 COG2204 AtoC Response regulato 93.0 0.15 3.3E-06 48.9 4.9 34 44-77 425-458 (464)
283 PRK13501 transcriptional activ 92.9 0.69 1.5E-05 40.8 8.8 79 125-211 182-262 (290)
284 PRK11169 leucine-responsive tr 92.9 0.19 4.1E-06 41.2 4.8 42 35-76 12-55 (164)
285 COG3311 AlpA Predicted transcr 92.9 0.37 7.9E-06 34.6 5.6 54 136-189 14-67 (70)
286 PRK13752 putative transcriptio 92.8 0.62 1.3E-05 37.7 7.7 67 135-202 7-76 (144)
287 COG3677 Transposase and inacti 92.8 0.15 3.4E-06 40.6 4.0 40 36-76 76-116 (129)
288 PF01978 TrmB: Sugar-specific 92.8 0.17 3.8E-06 35.1 3.8 32 181-212 12-44 (68)
289 PRK13749 transcriptional regul 92.7 0.84 1.8E-05 36.0 8.1 66 136-202 4-72 (121)
290 COG5484 Uncharacterized conser 92.7 0.15 3.2E-06 45.2 4.1 39 36-75 7-45 (279)
291 cd04777 HTH_MerR-like_sg1 Heli 92.6 0.92 2E-05 34.4 8.0 65 136-202 1-67 (107)
292 PF14493 HTH_40: Helix-turn-he 92.5 0.59 1.3E-05 34.6 6.6 59 38-99 3-62 (91)
293 PF13556 HTH_30: PucR C-termin 92.5 0.15 3.3E-06 34.8 3.2 43 180-222 2-46 (59)
294 PF00356 LacI: Bacterial regul 92.5 0.4 8.6E-06 31.4 5.0 38 51-99 1-38 (46)
295 PF08822 DUF1804: Protein of u 92.5 0.33 7.1E-06 40.4 5.6 40 119-158 3-42 (165)
296 PRK13752 putative transcriptio 92.5 0.64 1.4E-05 37.7 7.3 68 49-147 7-76 (144)
297 cd06571 Bac_DnaA_C C-terminal 92.5 0.85 1.8E-05 33.7 7.4 61 138-212 5-67 (90)
298 PF14549 P22_Cro: DNA-binding 92.5 0.53 1.2E-05 32.6 5.9 50 39-107 3-52 (60)
299 PF13443 HTH_26: Cro/C1-type H 92.4 0.13 2.7E-06 35.0 2.7 29 44-72 5-33 (63)
300 PRK15185 transcriptional regul 92.4 0.6 1.3E-05 42.6 7.8 79 134-220 221-300 (309)
301 TIGR01818 ntrC nitrogen regula 92.4 0.19 4E-06 47.3 4.7 34 40-73 430-463 (463)
302 PRK09726 antitoxin HipB; Provi 92.4 0.28 6.2E-06 36.0 4.7 41 31-71 6-47 (88)
303 cd04772 HTH_TioE_rpt1 First He 92.3 0.99 2.1E-05 34.0 7.8 59 137-197 2-63 (99)
304 PF13404 HTH_AsnC-type: AsnC-t 92.3 0.39 8.4E-06 30.8 4.7 31 182-212 8-39 (42)
305 TIGR02974 phageshock_pspF psp 92.3 0.2 4.4E-06 45.7 4.7 30 44-73 300-329 (329)
306 PF01418 HTH_6: Helix-turn-hel 92.3 0.17 3.7E-06 36.4 3.3 30 48-77 33-62 (77)
307 PRK06759 RNA polymerase factor 92.2 0.32 7E-06 38.4 5.3 40 32-72 106-145 (154)
308 PRK09863 putative frv operon r 92.2 2 4.3E-05 42.1 11.7 96 39-157 7-114 (584)
309 PRK15435 bifunctional DNA-bind 92.1 1 2.2E-05 41.7 9.1 91 123-221 86-178 (353)
310 PF03374 ANT: Phage antirepres 92.1 0.27 5.9E-06 37.4 4.5 41 38-78 11-53 (111)
311 PF13443 HTH_26: Cro/C1-type H 92.1 0.28 6.1E-06 33.2 4.1 32 183-214 3-34 (63)
312 PRK13502 transcriptional activ 92.1 0.79 1.7E-05 40.0 8.0 81 132-220 189-271 (282)
313 PF04936 DUF658: Protein of un 92.1 0.071 1.5E-06 44.2 1.2 96 45-157 10-110 (186)
314 PRK09685 DNA-binding transcrip 92.0 1 2.2E-05 39.7 8.7 86 39-163 203-294 (302)
315 PF09339 HTH_IclR: IclR helix- 92.0 0.18 3.8E-06 33.4 2.9 35 39-73 6-42 (52)
316 TIGR02989 Sig-70_gvs1 RNA poly 92.0 0.34 7.4E-06 38.4 5.2 41 31-72 110-150 (159)
317 PF08279 HTH_11: HTH domain; 91.9 0.39 8.5E-06 31.7 4.6 33 180-212 3-37 (55)
318 PF12844 HTH_19: Helix-turn-he 91.9 0.28 6E-06 33.4 3.9 26 46-71 9-34 (64)
319 PRK12537 RNA polymerase sigma 91.8 0.37 8E-06 39.6 5.3 26 47-72 147-172 (182)
320 PF05930 Phage_AlpA: Prophage 91.8 0.11 2.3E-06 34.6 1.6 29 50-78 4-32 (51)
321 PF07900 DUF1670: Protein of u 91.8 1.8 3.9E-05 37.6 9.6 82 128-212 97-185 (220)
322 smart00550 Zalpha Z-DNA-bindin 91.8 0.33 7.1E-06 34.2 4.3 31 47-77 18-50 (68)
323 PRK11608 pspF phage shock prot 91.8 0.28 6E-06 44.7 4.9 36 177-212 286-321 (326)
324 PRK09940 transcriptional regul 91.8 1.3 2.7E-05 39.4 8.9 81 123-211 138-218 (253)
325 PRK10365 transcriptional regul 91.8 0.21 4.6E-06 46.4 4.2 35 38-72 407-441 (441)
326 TIGR00122 birA_repr_reg BirA b 91.7 0.34 7.4E-06 33.8 4.3 34 40-73 4-37 (69)
327 PRK09393 ftrA transcriptional 91.7 0.83 1.8E-05 41.1 7.9 91 122-220 218-313 (322)
328 PRK10371 DNA-binding transcrip 91.7 1.1 2.5E-05 40.1 8.8 89 124-220 193-286 (302)
329 TIGR02297 HpaA 4-hydroxyphenyl 91.7 1.3 2.8E-05 38.7 9.0 81 133-221 200-282 (287)
330 PRK09652 RNA polymerase sigma 91.7 0.38 8.2E-06 38.7 5.2 26 47-72 142-167 (182)
331 TIGR02937 sigma70-ECF RNA poly 91.6 0.4 8.6E-06 36.7 4.9 40 32-72 110-149 (158)
332 smart00346 HTH_ICLR helix_turn 91.5 0.48 1E-05 34.3 5.1 37 38-74 7-45 (91)
333 PRK13503 transcriptional activ 91.5 1.3 2.8E-05 38.4 8.7 82 122-211 171-257 (278)
334 PF12833 HTH_18: Helix-turn-he 91.5 0.41 8.9E-06 33.9 4.6 62 141-210 1-65 (81)
335 PRK10572 DNA-binding transcrip 91.5 1.1 2.4E-05 39.4 8.3 81 132-220 196-278 (290)
336 PRK01905 DNA-binding protein F 91.4 0.52 1.1E-05 34.0 5.0 36 178-213 38-73 (77)
337 PF08279 HTH_11: HTH domain; 91.3 0.38 8.2E-06 31.8 4.0 35 40-74 4-40 (55)
338 COG2207 AraC AraC-type DNA-bin 91.3 2.4 5.1E-05 31.6 9.0 81 132-220 33-115 (127)
339 cd00090 HTH_ARSR Arsenical Res 91.3 0.5 1.1E-05 31.8 4.8 36 38-73 9-44 (78)
340 smart00418 HTH_ARSR helix_turn 91.3 0.37 8E-06 31.7 3.9 31 182-212 2-32 (66)
341 COG2944 Predicted transcriptio 91.3 0.71 1.5E-05 35.6 5.9 36 33-71 44-79 (104)
342 PRK13749 transcriptional regul 91.2 1.5 3.2E-05 34.7 7.8 68 49-147 3-72 (121)
343 TIGR00122 birA_repr_reg BirA b 91.2 0.55 1.2E-05 32.7 4.9 38 181-218 4-42 (69)
344 PF09339 HTH_IclR: IclR helix- 91.2 0.41 8.9E-06 31.6 4.0 39 178-216 4-45 (52)
345 PF00126 HTH_1: Bacterial regu 91.1 0.43 9.2E-06 32.5 4.2 33 40-73 5-37 (60)
346 PRK10072 putative transcriptio 91.1 0.44 9.6E-06 36.1 4.6 37 32-71 32-68 (96)
347 TIGR02329 propionate_PrpR prop 91.1 0.26 5.7E-06 48.0 4.3 34 39-72 493-526 (526)
348 PRK09978 DNA-binding transcrip 91.1 1.3 2.7E-05 39.8 8.2 83 122-212 142-228 (274)
349 cd04772 HTH_TioE_rpt1 First He 90.9 1.4 3.1E-05 33.1 7.3 23 51-73 2-24 (99)
350 PF05344 DUF746: Domain of Unk 90.8 0.39 8.4E-06 33.9 3.7 34 39-73 4-37 (65)
351 cd04778 HTH_MerR-like_sg2 Heli 90.7 1.4 3E-05 38.2 8.0 66 136-202 2-69 (219)
352 PRK09642 RNA polymerase sigma 90.7 0.42 9.1E-06 38.1 4.4 29 44-72 117-145 (160)
353 PRK15340 transcriptional regul 90.7 1 2.2E-05 39.0 7.1 78 47-163 123-204 (216)
354 COG2901 Fis Factor for inversi 90.6 0.5 1.1E-05 35.4 4.4 30 44-75 68-97 (98)
355 PF12298 Bot1p: Eukaryotic mit 90.6 1.1 2.3E-05 37.6 6.9 44 169-212 12-55 (172)
356 PRK06759 RNA polymerase factor 90.6 0.61 1.3E-05 36.8 5.3 36 176-212 109-144 (154)
357 PRK15418 transcriptional regul 90.6 0.46 1E-05 43.3 5.1 36 37-72 17-52 (318)
358 cd00090 HTH_ARSR Arsenical Res 90.5 0.8 1.7E-05 30.8 5.2 36 177-212 7-42 (78)
359 PRK12525 RNA polymerase sigma 90.5 0.63 1.4E-05 37.7 5.4 41 31-72 117-157 (168)
360 PRK10130 transcriptional regul 90.5 1.7 3.8E-05 40.1 8.9 86 40-164 247-339 (350)
361 COG2973 TrpR Trp operon repres 90.5 0.38 8.2E-06 36.7 3.7 36 177-212 47-82 (103)
362 COG2739 Uncharacterized protei 90.4 0.61 1.3E-05 35.8 4.8 34 179-212 22-55 (105)
363 TIGR02999 Sig-70_X6 RNA polyme 90.4 0.46 9.9E-06 38.7 4.6 31 42-72 143-173 (183)
364 PF13022 HTH_Tnp_1_2: Helix-tu 90.4 0.81 1.8E-05 37.1 5.7 25 134-158 33-57 (142)
365 PRK06288 RNA polymerase sigma 90.4 7.5 0.00016 34.1 12.5 33 125-157 218-250 (268)
366 PRK12547 RNA polymerase sigma 90.4 0.63 1.4E-05 37.5 5.3 26 47-72 126-151 (164)
367 PRK10072 putative transcriptio 90.4 0.54 1.2E-05 35.6 4.5 35 181-215 37-71 (96)
368 TIGR02989 Sig-70_gvs1 RNA poly 90.3 0.56 1.2E-05 37.1 4.8 34 179-212 116-149 (159)
369 PRK09642 RNA polymerase sigma 90.2 0.56 1.2E-05 37.4 4.8 34 179-212 111-144 (160)
370 PRK11924 RNA polymerase sigma 90.2 0.61 1.3E-05 37.3 5.0 39 33-72 126-164 (179)
371 PHA00738 putative HTH transcri 90.1 0.68 1.5E-05 35.9 4.9 41 177-217 12-54 (108)
372 PRK09639 RNA polymerase sigma 90.1 0.52 1.1E-05 37.7 4.5 39 32-72 112-150 (166)
373 PRK06986 fliA flagellar biosyn 90.1 9.2 0.0002 32.8 12.6 102 36-158 98-223 (236)
374 TIGR02952 Sig70_famx2 RNA poly 90.1 0.7 1.5E-05 36.9 5.3 25 48-72 137-161 (170)
375 COG2739 Uncharacterized protei 90.1 0.47 1E-05 36.4 3.9 33 40-72 24-56 (105)
376 PRK09646 RNA polymerase sigma 90.0 0.67 1.5E-05 38.5 5.3 40 32-72 142-181 (194)
377 TIGR02366 DHAK_reg probable di 90.0 0.46 9.9E-06 38.5 4.2 40 32-71 2-45 (176)
378 PRK15115 response regulator Gl 90.0 0.49 1.1E-05 44.2 4.9 35 178-212 399-433 (444)
379 PRK06474 hypothetical protein; 89.9 0.64 1.4E-05 38.9 5.0 37 176-212 10-49 (178)
380 TIGR02985 Sig70_bacteroi1 RNA 89.9 0.68 1.5E-05 36.3 5.0 32 41-72 121-152 (161)
381 PF00376 MerR: MerR family reg 89.9 0.23 4.9E-06 31.2 1.8 22 51-72 1-22 (38)
382 TIGR03070 couple_hipB transcri 89.8 0.58 1.3E-05 30.5 3.9 25 47-71 13-37 (58)
383 PF12759 HTH_Tnp_IS1: InsA C-t 89.8 0.57 1.2E-05 30.9 3.6 41 174-215 6-46 (46)
384 PF05930 Phage_AlpA: Prophage 89.8 0.22 4.8E-06 33.0 1.8 23 136-158 4-26 (51)
385 PF06627 DUF1153: Protein of u 89.8 0.79 1.7E-05 34.3 4.8 43 170-212 29-71 (90)
386 PRK12520 RNA polymerase sigma 89.8 0.74 1.6E-05 38.0 5.3 39 33-72 132-170 (191)
387 PRK09047 RNA polymerase factor 89.8 0.55 1.2E-05 37.3 4.4 26 47-72 120-145 (161)
388 TIGR02915 PEP_resp_reg putativ 89.8 0.52 1.1E-05 44.0 4.9 36 177-212 405-440 (445)
389 PHA02591 hypothetical protein; 89.7 0.79 1.7E-05 33.6 4.7 38 175-212 44-81 (83)
390 smart00418 HTH_ARSR helix_turn 89.7 0.53 1.1E-05 30.9 3.6 30 45-74 6-35 (66)
391 PRK09644 RNA polymerase sigma 89.7 0.68 1.5E-05 37.2 5.0 41 31-72 107-147 (165)
392 TIGR02607 antidote_HigA addict 89.7 1.4 2.9E-05 31.0 6.0 26 46-71 15-40 (78)
393 PRK13919 putative RNA polymera 89.7 0.77 1.7E-05 37.5 5.3 26 47-72 149-174 (186)
394 PRK12528 RNA polymerase sigma 89.7 0.6 1.3E-05 37.3 4.6 32 41-72 121-152 (161)
395 PF04703 FaeA: FaeA-like prote 89.6 0.52 1.1E-05 32.9 3.6 39 179-217 2-43 (62)
396 PRK09415 RNA polymerase factor 89.6 0.65 1.4E-05 38.0 4.8 26 47-72 141-166 (179)
397 smart00346 HTH_ICLR helix_turn 89.6 1 2.2E-05 32.5 5.4 36 177-212 5-42 (91)
398 PF00196 GerE: Bacterial regul 89.5 0.67 1.5E-05 31.1 4.0 38 33-72 4-41 (58)
399 TIGR02983 SigE-fam_strep RNA p 89.5 0.55 1.2E-05 37.4 4.2 26 47-72 124-149 (162)
400 PF07638 Sigma70_ECF: ECF sigm 89.5 0.69 1.5E-05 38.5 4.9 33 40-72 142-174 (185)
401 PRK12543 RNA polymerase sigma 89.4 0.81 1.8E-05 37.4 5.3 25 48-72 132-156 (179)
402 PRK12540 RNA polymerase sigma 89.4 0.96 2.1E-05 37.4 5.7 34 179-212 116-149 (182)
403 PRK12532 RNA polymerase sigma 89.4 0.75 1.6E-05 38.1 5.1 40 32-72 136-175 (195)
404 TIGR00637 ModE_repress ModE mo 89.4 0.73 1.6E-05 34.9 4.6 34 39-73 7-40 (99)
405 PRK10141 DNA-binding transcrip 89.4 0.91 2E-05 35.6 5.2 43 175-217 14-58 (117)
406 TIGR01818 ntrC nitrogen regula 89.4 0.6 1.3E-05 43.8 5.0 35 178-212 427-461 (463)
407 PRK15121 right oriC-binding tr 89.4 2 4.4E-05 38.0 8.1 70 133-210 19-90 (289)
408 PRK12539 RNA polymerase sigma 89.3 0.59 1.3E-05 38.4 4.3 40 32-72 131-170 (184)
409 TIGR03001 Sig-70_gmx1 RNA poly 89.3 0.87 1.9E-05 39.8 5.6 35 178-212 165-199 (244)
410 smart00420 HTH_DEOR helix_turn 89.2 1.2 2.6E-05 28.3 5.0 32 181-212 4-36 (53)
411 PRK10365 transcriptional regul 89.2 0.6 1.3E-05 43.4 4.9 37 176-212 404-440 (441)
412 PRK05602 RNA polymerase sigma 89.2 0.75 1.6E-05 37.7 5.0 39 33-72 129-167 (186)
413 PRK11361 acetoacetate metaboli 89.2 0.62 1.4E-05 43.6 5.0 36 177-212 417-452 (457)
414 PRK12527 RNA polymerase sigma 89.2 0.68 1.5E-05 36.9 4.6 26 47-72 119-144 (159)
415 PRK11179 DNA-binding transcrip 89.2 1.4 2.9E-05 35.7 6.3 37 181-217 13-51 (153)
416 PF01047 MarR: MarR family; I 89.2 0.84 1.8E-05 30.4 4.4 31 44-74 12-42 (59)
417 PRK12514 RNA polymerase sigma 89.2 0.87 1.9E-05 37.1 5.3 39 33-72 130-168 (179)
418 PRK13500 transcriptional activ 89.2 2.1 4.5E-05 38.5 8.1 79 134-220 221-301 (312)
419 PRK12511 RNA polymerase sigma 89.2 0.83 1.8E-05 37.8 5.2 40 32-72 111-150 (182)
420 PRK12528 RNA polymerase sigma 89.1 0.82 1.8E-05 36.5 5.0 34 179-212 118-151 (161)
421 PF02042 RWP-RK: RWP-RK domain 89.1 0.69 1.5E-05 31.2 3.7 28 135-162 15-42 (52)
422 COG1595 RpoE DNA-directed RNA 89.1 0.75 1.6E-05 37.8 4.8 35 177-212 131-165 (182)
423 COG1710 Uncharacterized protei 89.1 1 2.2E-05 35.6 5.2 44 168-212 88-131 (139)
424 PRK07037 extracytoplasmic-func 89.0 0.73 1.6E-05 36.8 4.6 26 47-72 123-148 (163)
425 COG3284 AcoR Transcriptional a 88.9 0.68 1.5E-05 45.8 5.1 39 124-162 567-605 (606)
426 PRK12536 RNA polymerase sigma 88.9 0.68 1.5E-05 37.9 4.5 27 46-72 142-168 (181)
427 COG3877 Uncharacterized protei 88.9 3.9 8.4E-05 31.8 8.1 38 34-72 43-80 (122)
428 PF14549 P22_Cro: DNA-binding 88.8 2.1 4.5E-05 29.7 6.1 51 124-194 2-52 (60)
429 PF00440 TetR_N: Bacterial reg 88.8 0.93 2E-05 29.2 4.2 24 48-71 15-38 (47)
430 PRK11388 DNA-binding transcrip 88.8 0.62 1.4E-05 46.0 4.9 38 175-212 589-626 (638)
431 PRK12529 RNA polymerase sigma 88.8 0.72 1.6E-05 37.8 4.6 31 42-72 136-166 (178)
432 PRK15340 transcriptional regul 88.8 2.9 6.2E-05 36.3 8.3 70 134-211 124-195 (216)
433 TIGR02329 propionate_PrpR prop 88.8 0.66 1.4E-05 45.3 4.9 35 178-212 491-525 (526)
434 PRK12530 RNA polymerase sigma 88.7 0.69 1.5E-05 38.3 4.4 26 47-72 148-173 (189)
435 TIGR02943 Sig70_famx1 RNA poly 88.7 0.95 2.1E-05 37.5 5.3 26 47-72 145-170 (188)
436 TIGR02937 sigma70-ECF RNA poly 88.7 0.99 2.2E-05 34.4 5.1 37 175-212 112-148 (158)
437 PRK11169 leucine-responsive tr 88.7 0.74 1.6E-05 37.7 4.5 38 180-217 17-56 (164)
438 PRK12519 RNA polymerase sigma 88.7 0.59 1.3E-05 38.6 4.0 26 47-72 155-180 (194)
439 PRK12529 RNA polymerase sigma 88.6 0.89 1.9E-05 37.3 5.0 35 178-212 131-165 (178)
440 smart00344 HTH_ASNC helix_turn 88.6 1.3 2.7E-05 33.3 5.4 29 47-75 15-43 (108)
441 PRK09644 RNA polymerase sigma 88.6 1 2.2E-05 36.2 5.2 37 175-212 110-146 (165)
442 PRK12516 RNA polymerase sigma 88.6 1.1 2.3E-05 37.3 5.4 35 178-212 120-154 (187)
443 PRK09637 RNA polymerase sigma 88.6 0.93 2E-05 37.4 5.1 40 32-72 106-145 (181)
444 PF00356 LacI: Bacterial regul 88.5 1.3 2.8E-05 29.0 4.7 42 137-190 1-42 (46)
445 TIGR02954 Sig70_famx3 RNA poly 88.5 0.73 1.6E-05 37.1 4.4 26 47-72 133-158 (169)
446 PRK10820 DNA-binding transcrip 88.5 0.89 1.9E-05 44.1 5.6 34 130-164 482-515 (520)
447 TIGR02999 Sig-70_X6 RNA polyme 88.5 0.9 2E-05 37.0 4.9 34 179-212 139-172 (183)
448 PRK09648 RNA polymerase sigma 88.5 0.78 1.7E-05 37.7 4.5 41 31-72 138-178 (189)
449 PRK12514 RNA polymerase sigma 88.5 1.1 2.3E-05 36.5 5.3 36 176-212 132-167 (179)
450 TIGR02974 phageshock_pspF psp 88.4 0.8 1.7E-05 41.8 5.0 35 178-212 293-327 (329)
451 PRK12541 RNA polymerase sigma 88.4 0.93 2E-05 36.2 4.8 39 33-72 113-151 (161)
452 TIGR02959 SigZ RNA polymerase 88.4 0.83 1.8E-05 37.1 4.6 40 32-72 100-139 (170)
453 PRK00430 fis global DNA-bindin 88.3 1.2 2.6E-05 33.6 5.1 36 178-213 56-91 (95)
454 COG3413 Predicted DNA binding 88.3 1.5 3.3E-05 37.4 6.3 43 30-72 153-201 (215)
455 PRK12533 RNA polymerase sigma 88.3 0.92 2E-05 38.9 5.0 25 48-72 149-173 (216)
456 COG1961 PinR Site-specific rec 88.3 1.4 3.1E-05 37.5 6.2 73 88-160 122-202 (222)
457 PRK09047 RNA polymerase factor 88.3 0.95 2.1E-05 35.9 4.8 35 178-212 110-144 (161)
458 PRK12547 RNA polymerase sigma 88.2 0.98 2.1E-05 36.4 4.9 34 179-212 117-150 (164)
459 PRK12519 RNA polymerase sigma 88.2 0.74 1.6E-05 38.0 4.3 35 178-212 145-179 (194)
460 PRK12523 RNA polymerase sigma 88.2 0.86 1.9E-05 37.0 4.6 32 41-72 127-158 (172)
461 PRK11050 manganese transport r 88.2 1.1 2.5E-05 36.3 5.3 47 31-77 31-79 (152)
462 PRK12542 RNA polymerase sigma 88.1 1.1 2.3E-05 36.8 5.2 26 47-72 136-161 (185)
463 PRK12524 RNA polymerase sigma 88.0 0.84 1.8E-05 38.0 4.5 26 47-72 150-175 (196)
464 COG1522 Lrp Transcriptional re 88.0 1.3 2.8E-05 35.2 5.4 30 46-75 19-48 (154)
465 PRK12526 RNA polymerase sigma 88.0 1.1 2.4E-05 37.7 5.3 26 47-72 167-192 (206)
466 PF12298 Bot1p: Eukaryotic mit 88.0 1.8 3.9E-05 36.3 6.4 46 31-76 15-60 (172)
467 PRK12537 RNA polymerase sigma 88.0 0.98 2.1E-05 37.0 4.8 32 181-212 140-171 (182)
468 PRK09648 RNA polymerase sigma 88.0 1 2.2E-05 37.0 4.9 38 34-73 7-44 (189)
469 PRK12530 RNA polymerase sigma 87.9 0.98 2.1E-05 37.4 4.8 34 179-212 139-172 (189)
470 PRK09645 RNA polymerase sigma 87.9 0.93 2E-05 36.6 4.6 31 42-72 127-157 (173)
471 COG1710 Uncharacterized protei 87.9 1.5 3.3E-05 34.7 5.4 45 113-158 88-132 (139)
472 PRK12527 RNA polymerase sigma 87.8 1.1 2.4E-05 35.7 4.9 36 177-212 108-143 (159)
473 TIGR02954 Sig70_famx3 RNA poly 87.8 0.95 2.1E-05 36.5 4.6 34 179-212 124-157 (169)
474 TIGR02983 SigE-fam_strep RNA p 87.8 0.99 2.1E-05 36.0 4.6 34 179-212 115-148 (162)
475 PRK08301 sporulation sigma fac 87.7 0.91 2E-05 38.9 4.6 26 47-72 196-221 (234)
476 PF00126 HTH_1: Bacterial regu 87.6 1.1 2.5E-05 30.3 4.2 33 179-212 3-35 (60)
477 PF08220 HTH_DeoR: DeoR-like h 87.6 1 2.2E-05 30.5 4.0 30 47-76 12-41 (57)
478 TIGR02947 SigH_actino RNA poly 87.6 0.56 1.2E-05 38.8 3.2 25 48-72 146-170 (193)
479 PF11198 DUF2857: Protein of u 87.5 15 0.00032 30.8 11.8 153 36-213 5-176 (180)
480 PRK12516 RNA polymerase sigma 87.5 0.94 2E-05 37.6 4.5 32 41-72 124-155 (187)
481 PRK10130 transcriptional regul 87.5 3.3 7.2E-05 38.3 8.5 83 121-211 239-329 (350)
482 PRK09685 DNA-binding transcrip 87.4 3.5 7.5E-05 36.3 8.4 78 135-220 214-294 (302)
483 PRK12522 RNA polymerase sigma 87.4 0.94 2E-05 36.7 4.4 26 47-72 133-158 (173)
484 COG1595 RpoE DNA-directed RNA 87.4 0.89 1.9E-05 37.3 4.2 26 47-72 141-166 (182)
485 PF04967 HTH_10: HTH DNA bindi 87.3 2.6 5.6E-05 28.5 5.7 24 135-158 23-46 (53)
486 PRK03975 tfx putative transcri 87.3 1.2 2.6E-05 36.1 4.9 40 31-72 5-44 (141)
487 TIGR02980 SigBFG RNA polymeras 87.3 1.3 2.8E-05 37.7 5.4 40 32-72 178-217 (227)
488 PF07638 Sigma70_ECF: ECF sigm 87.3 1.2 2.5E-05 37.1 5.0 35 178-212 139-173 (185)
489 PRK10783 mltD membrane-bound l 87.3 0.83 1.8E-05 43.8 4.5 81 130-213 347-433 (456)
490 PRK05602 RNA polymerase sigma 87.3 1.3 2.8E-05 36.3 5.2 32 181-212 135-166 (186)
491 PRK12542 RNA polymerase sigma 87.3 1.1 2.4E-05 36.8 4.7 34 179-212 127-160 (185)
492 PRK12512 RNA polymerase sigma 87.3 1 2.2E-05 36.9 4.5 25 48-72 146-170 (184)
493 PRK06811 RNA polymerase factor 87.3 1 2.2E-05 37.3 4.5 40 32-72 131-170 (189)
494 PF04703 FaeA: FaeA-like prote 87.2 0.72 1.6E-05 32.2 3.0 40 36-76 3-42 (62)
495 PRK12540 RNA polymerase sigma 87.2 1.3 2.8E-05 36.6 5.2 26 47-72 125-150 (182)
496 PRK10100 DNA-binding transcrip 87.2 9.6 0.00021 32.6 10.7 104 31-189 110-213 (216)
497 cd00093 HTH_XRE Helix-turn-hel 87.2 1.1 2.4E-05 27.7 3.8 25 47-71 10-34 (58)
498 smart00345 HTH_GNTR helix_turn 87.1 0.71 1.5E-05 30.2 2.9 28 49-76 19-47 (60)
499 PRK12525 RNA polymerase sigma 87.1 1.3 2.7E-05 35.9 4.9 36 176-212 121-156 (168)
500 TIGR00721 tfx DNA-binding prot 87.1 1.2 2.7E-05 35.9 4.8 38 33-72 7-44 (137)
No 1
>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=99.20 E-value=2.2e-10 Score=90.02 Aligned_cols=90 Identities=18% Similarity=0.378 Sum_probs=69.2
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh--CCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHH
Q psy17316 118 SWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE--GIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQR 195 (229)
Q Consensus 118 kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~--g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~e 195 (229)
.||.|++..+|..+..|+ |..+||..|+|+.+|+++|+++. |-....|. ..++.+.++..+.|+. +.+.++.|
T Consensus 2 aYS~DlR~rVl~~~~~g~-s~~eaa~~F~VS~~Tv~~W~k~~~~G~~~~k~r--~~~Kid~~~L~~~v~~--~pd~tl~E 76 (119)
T PF01710_consen 2 AYSLDLRQRVLAYIEKGK-SIREAAKRFGVSRNTVYRWLKRKETGDLEPKPR--GRKKIDRDELKALVEE--NPDATLRE 76 (119)
T ss_pred CCCHHHHHHHHHHHHccc-hHHHHHHHhCcHHHHHHHHHHhccccccccccc--ccccccHHHHHHHHHH--CCCcCHHH
Confidence 699999999999888877 99999999999999999999843 32211121 1115554444444443 36688999
Q ss_pred HHHHhCCChHHHHHHHH
Q psy17316 196 ASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 196 AA~~fgVp~~tv~~~vk 212 (229)
.|.+|||+.+||+..++
T Consensus 77 la~~l~Vs~~ti~~~Lk 93 (119)
T PF01710_consen 77 LAERLGVSPSTIWRALK 93 (119)
T ss_pred HHHHcCCCHHHHHHHHH
Confidence 99999999999999998
No 2
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=99.05 E-value=3e-10 Score=74.71 Aligned_cols=39 Identities=44% Similarity=0.753 Sum_probs=33.3
Q ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
|+|+|.+||++|.+|++|+++||+.||||++||+++++.
T Consensus 1 tee~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 1 TEEDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp -HHHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 689999999999999999999999999999999998874
No 3
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.03 E-value=2.6e-09 Score=86.13 Aligned_cols=110 Identities=24% Similarity=0.400 Sum_probs=86.3
Q ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh---CCcccC-CCCCCCCCCCHHHHHHHHHHHHhCCC
Q psy17316 116 TKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE---GIRLAQ-PFNASPTAWKPEDLEIALEGIRSGQT 191 (229)
Q Consensus 116 ~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~---g~k~~~-~~~~~~r~~t~e~r~eaV~~~~~~~~ 191 (229)
++.|+.+.+..++..+.-+++|.++||++|||+.+|+|+|++++ |..+.. +..+++++.+++++..+++.|..+..
T Consensus 2 ~k~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~w 81 (138)
T COG3415 2 AKPFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKDW 81 (138)
T ss_pred CchhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhcccc
Confidence 35677888888888888888899999999999999999999876 544221 24577889999999999999999988
Q ss_pred cHHHH----HHHhCCChH--HHHHHHH-----hhcCCCCCCCCCC
Q psy17316 192 TVQRA----SAEYGIPSG--TLYGRCK-----LSRSTPRPPPGNL 225 (229)
Q Consensus 192 s~~eA----A~~fgVp~~--tv~~~vk-----~~~~~~~~~~~~~ 225 (229)
+..+. ..+|||.|. .|+.+++ ...+-..|...|.
T Consensus 82 Tl~~~~~~l~~e~gv~y~~~~v~~~l~~~GlsykK~~~~~~~~~~ 126 (138)
T COG3415 82 TLKELVEELGLEFGVWYHASAVRRLLHELGLSYKKPRWTPAERDE 126 (138)
T ss_pred hHHHHHHHHhhhcCeEEeHHHHHHHHHHcCCCcCCCCCCccccCh
Confidence 87666 668999999 8999998 3344444444443
No 4
>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=98.93 E-value=1.3e-08 Score=79.88 Aligned_cols=100 Identities=12% Similarity=0.247 Sum_probs=72.1
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhh
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASK 111 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~ 111 (229)
.||.|-...+|..+.. |.|.++||+.|||+++||++|+++..........+.
T Consensus 2 aYS~DlR~rVl~~~~~-g~s~~eaa~~F~VS~~Tv~~W~k~~~~G~~~~k~r~--------------------------- 53 (119)
T PF01710_consen 2 AYSLDLRQRVLAYIEK-GKSIREAAKRFGVSRNTVYRWLKRKETGDLEPKPRG--------------------------- 53 (119)
T ss_pred CCCHHHHHHHHHHHHc-cchHHHHHHHhCcHHHHHHHHHHhcccccccccccc---------------------------
Confidence 4888989999976656 559999999999999999999996443221111110
Q ss_pred ccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccC
Q psy17316 112 AYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQ 165 (229)
Q Consensus 112 ~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~ 165 (229)
.. +.+.+.+.+-|+. +...++.++|..|||+.+||++.+++.|+..+.
T Consensus 54 ---~~-Kid~~~L~~~v~~--~pd~tl~Ela~~l~Vs~~ti~~~Lkrlg~t~KK 101 (119)
T PF01710_consen 54 ---RK-KIDRDELKALVEE--NPDATLRELAERLGVSPSTIWRALKRLGITRKK 101 (119)
T ss_pred ---cc-cccHHHHHHHHHH--CCCcCHHHHHHHcCCCHHHHHHHHHHcCchhcc
Confidence 01 2233333444444 456799999999999999999999999976653
No 5
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=98.89 E-value=2.9e-08 Score=80.09 Aligned_cols=110 Identities=16% Similarity=0.319 Sum_probs=84.5
Q ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhh
Q psy17316 30 TKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKA 109 (229)
Q Consensus 30 ~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~ 109 (229)
+..++.+....++..+.-+|||.++||++|||+.+|+++|++++.-.|.. +..+
T Consensus 2 ~k~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~-l~~~------------------------- 55 (138)
T COG3415 2 AKPFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRETGLD-LPPK------------------------- 55 (138)
T ss_pred CchhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhcccccc-ccCc-------------------------
Confidence 45778888888888888899999999999999999999999998766544 2210
Q ss_pred hhccCCCCCCCHHHHHHHHHHHHcCCCCHHHH----HHHhCCChH--HHHHHHHHhCCcccCC
Q psy17316 110 SKAYGPTKSWNEEILNVALDALRAGSISANKA----SKAYGIPSS--TLYKIARKEGIRLAQP 166 (229)
Q Consensus 110 ~~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~----a~k~gIp~s--TL~~~ik~~g~k~~~~ 166 (229)
...|++.+-+++.+...++.+.....++.++ ..+|||..+ .|++++++.|+....|
T Consensus 56 -~~~GrP~kl~~~q~~~l~e~~~~k~wTl~~~~~~l~~e~gv~y~~~~v~~~l~~~GlsykK~ 117 (138)
T COG3415 56 -PRKGRPRKLSEEQLEILLERLREKDWTLKELVEELGLEFGVWYHASAVRRLLHELGLSYKKP 117 (138)
T ss_pred -cCCCCCcccCHHHHHHHHHHHhcccchHHHHHHHHhhhcCeEEeHHHHHHHHHHcCCCcCCC
Confidence 1235666777777666666666666666666 568999986 5999999999888754
No 6
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=98.82 E-value=8e-09 Score=67.88 Aligned_cols=39 Identities=44% Similarity=0.652 Sum_probs=32.7
Q ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHH
Q psy17316 120 NEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARK 158 (229)
Q Consensus 120 s~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~ 158 (229)
++|.+++||++|.+|++|++++|++||||++||+++++.
T Consensus 1 tee~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 1 TEEDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp -HHHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 578899999999999999999999999999999988764
No 7
>cd00131 PAX Paired Box domain
Probab=98.81 E-value=1.5e-07 Score=74.89 Aligned_cols=104 Identities=10% Similarity=0.085 Sum_probs=74.9
Q ss_pred hhhccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh---CCcccCCCCC-CCCCCCHHHHHHHHH
Q psy17316 109 ASKAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE---GIRLAQPFNA-SPTAWKPEDLEIALE 184 (229)
Q Consensus 109 ~~~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~---g~k~~~~~~~-~~r~~t~e~r~eaV~ 184 (229)
.+..+-..+-||.+.+.++|.++.+|. |..+||++|||+.+|+++|++++ |--...+..+ +++..+++....+++
T Consensus 8 ~~~~~~m~~~lS~d~R~rIv~~~~~G~-s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~ 86 (128)
T cd00131 8 LGGVFVNGRPLPDSIRQRIVELAQSGI-RPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEI 86 (128)
T ss_pred CCccccCCCcCCHHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHH
Confidence 333333468899999999999998665 99999999999999999999875 3211122222 255556655555665
Q ss_pred HHHh-CCCcHHHHHHHh---CC-------ChHHHHHHHHh
Q psy17316 185 GIRS-GQTTVQRASAEY---GI-------PSGTLYGRCKL 213 (229)
Q Consensus 185 ~~~~-~~~s~~eAA~~f---gV-------p~~tv~~~vk~ 213 (229)
++.+ ...+..|.+..+ || |.+||.++++.
T Consensus 87 ~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~ 126 (128)
T cd00131 87 YKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN 126 (128)
T ss_pred HHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence 5555 457888888875 56 99999999874
No 8
>smart00351 PAX Paired Box domain.
Probab=98.70 E-value=4.2e-07 Score=72.04 Aligned_cols=96 Identities=9% Similarity=0.101 Sum_probs=70.0
Q ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh---CCcccCCCCC-CCCCCCHHHHHHHHHHHHh-CC
Q psy17316 116 TKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE---GIRLAQPFNA-SPTAWKPEDLEIALEGIRS-GQ 190 (229)
Q Consensus 116 ~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~---g~k~~~~~~~-~~r~~t~e~r~eaV~~~~~-~~ 190 (229)
...|+.+.+.++|.++.+|. |..+||++|||+.+|+++|++++ |.....|..+ +++..+++....|++.+.+ ..
T Consensus 15 ~~~~s~~~R~riv~~~~~G~-s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~ 93 (125)
T smart00351 15 GRPLPDEERQRIVELAQNGV-RPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPG 93 (125)
T ss_pred CCCCCHHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCC
Confidence 45699999999999998665 99999999999999999999876 4322222222 4566666556666666555 45
Q ss_pred CcHHHHHHHh---CC-------ChHHHHHHHH
Q psy17316 191 TTVQRASAEY---GI-------PSGTLYGRCK 212 (229)
Q Consensus 191 ~s~~eAA~~f---gV-------p~~tv~~~vk 212 (229)
.+..+++..+ || |.+|+.+|++
T Consensus 94 ~t~~el~~~L~~~gv~~~~~~Ps~sti~~~l~ 125 (125)
T smart00351 94 IFAWEIRDRLLSEGVCDKDNVPSVSSINRILR 125 (125)
T ss_pred CCHHHHHHHHHHcCCCcCCCCCChhhHHHhhC
Confidence 8888887655 33 7888888763
No 9
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=98.66 E-value=1.7e-07 Score=72.75 Aligned_cols=91 Identities=14% Similarity=0.157 Sum_probs=65.9
Q ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCC-ChHHHHHHHHHhCCc--ccCCCCCCCCCCCHHHHHHHHHHHHhCCCc
Q psy17316 116 TKSWNEEILNVALDALRAGSISANKASKAYGI-PSSTLYKIARKEGIR--LAQPFNASPTAWKPEDLEIALEGIRSGQTT 192 (229)
Q Consensus 116 ~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gI-p~sTL~~~ik~~g~k--~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s 192 (229)
+.+||+|||++||+++++++.|+.++|++||| +.++||+|++.+... ...+.....+.+++++..++++.+...+.+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~e~ 84 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKGGGLAFSGKGKTVSYDAEEILRLRKLAELREES 84 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHcccccccCccccCCcCHHHHHHHHHHHHHHHHH
Confidence 67899999999999999988899999999996 999999999865221 111111234577888888887744444455
Q ss_pred HHHHHHHhCCChHH
Q psy17316 193 VQRASAEYGIPSGT 206 (229)
Q Consensus 193 ~~eAA~~fgVp~~t 206 (229)
.......+.+....
T Consensus 85 ~il~~~~~~~~~~~ 98 (116)
T COG2963 85 DILKKAAFYLANAG 98 (116)
T ss_pred HHHHHHHHHHHhch
Confidence 55555555555543
No 10
>PF13551 HTH_29: Winged helix-turn helix
Probab=98.63 E-value=3.4e-07 Score=69.42 Aligned_cols=97 Identities=18% Similarity=0.230 Sum_probs=63.2
Q ss_pred HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCC
Q psy17316 39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKS 118 (229)
Q Consensus 39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~k 118 (229)
..+|.++.+|..++.+||+.+||++.|+++|+++|.-.|...... .....|.+.+
T Consensus 2 ~~~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~-------------------------~~~~~g~~~~ 56 (112)
T PF13551_consen 2 AQILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGGIEGLLP-------------------------RKPRGGRPRK 56 (112)
T ss_pred HHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHh-------------------------ccccCCCCCC
Confidence 356777777553599999999999999999999985544222110 0011223333
Q ss_pred -CCHHHHHHHHHHHHcC------CCCHHHHHHHh-------CCChHHHHHHHHHhC
Q psy17316 119 -WNEEILNVALDALRAG------SISANKASKAY-------GIPSSTLYKIARKEG 160 (229)
Q Consensus 119 -Ys~e~k~~AV~~~~~g------~~S~~~~a~k~-------gIp~sTL~~~ik~~g 160 (229)
.+++.....++.+.+. ..+...++... .++.+|+++|+++.|
T Consensus 57 ~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~~~G 112 (112)
T PF13551_consen 57 RLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILKRAG 112 (112)
T ss_pred CCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHHHCc
Confidence 5566666666666542 35677776643 678889999998765
No 11
>PF13551 HTH_29: Winged helix-turn helix
Probab=98.63 E-value=3.9e-07 Score=69.14 Aligned_cols=88 Identities=19% Similarity=0.233 Sum_probs=69.3
Q ss_pred HHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh---CCcccCC---CCCCCCC-CCHHHHHHHHHHHHhCC------C
Q psy17316 125 NVALDALRAGSISANKASKAYGIPSSTLYKIARKE---GIRLAQP---FNASPTA-WKPEDLEIALEGIRSGQ------T 191 (229)
Q Consensus 125 ~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~---g~k~~~~---~~~~~r~-~t~e~r~eaV~~~~~~~------~ 191 (229)
.+++.++.+|..+..+||+.+||+..|+++|++++ |+....+ ..++++. .+++.+..+++++.++. .
T Consensus 2 ~~~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~ 81 (112)
T PF13551_consen 2 AQILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRW 81 (112)
T ss_pred HHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcc
Confidence 46778888887449999999999999999999875 4322222 2344555 79999999999999863 6
Q ss_pred cHHHHHHHh-------CCChHHHHHHHH
Q psy17316 192 TVQRASAEY-------GIPSGTLYGRCK 212 (229)
Q Consensus 192 s~~eAA~~f-------gVp~~tv~~~vk 212 (229)
+..+++..+ .||.+||++|++
T Consensus 82 t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 82 TLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred cHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 788888755 899999999987
No 12
>cd00131 PAX Paired Box domain
Probab=98.58 E-value=1.5e-06 Score=69.17 Aligned_cols=103 Identities=11% Similarity=0.068 Sum_probs=69.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhh
Q psy17316 27 LTVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISA 106 (229)
Q Consensus 27 ~~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~ 106 (229)
-..-+.||.+....+|.++. +|+|.++||+++||+++|+++|+++|.-.|.-..++
T Consensus 12 ~~m~~~lS~d~R~rIv~~~~-~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~----------------------- 67 (128)
T cd00131 12 FVNGRPLPDSIRQRIVELAQ-SGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGA----------------------- 67 (128)
T ss_pred ccCCCcCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCC-----------------------
Confidence 34458899999999998886 578999999999999999999999985443211110
Q ss_pred hhhhhccCC-CCCCCHHHHHHHHHHH-HcCCCCHHHHHHHh---CC-------ChHHHHHHHHH
Q psy17316 107 NKASKAYGP-TKSWNEEILNVALDAL-RAGSISANKASKAY---GI-------PSSTLYKIARK 158 (229)
Q Consensus 107 ~~~~~~~G~-~~kYs~e~k~~AV~~~-~~g~~S~~~~a~k~---gI-------p~sTL~~~ik~ 158 (229)
..|. +.+.+++.....+..+ .+...++.++++.+ || +.+|+.++.++
T Consensus 68 -----~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~ 126 (128)
T cd00131 68 -----IGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN 126 (128)
T ss_pred -----CCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence 0011 2222332222222222 45667888888774 55 88999998764
No 13
>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=98.57 E-value=4.7e-08 Score=69.91 Aligned_cols=47 Identities=17% Similarity=0.251 Sum_probs=38.7
Q ss_pred CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316 28 TVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG 74 (229)
Q Consensus 28 ~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g 74 (229)
..++.||.|+++.+|..+..+|.|+.++|++|||+.+||++|++++.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence 35689999999999999988899999999999999999999999984
No 14
>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=98.54 E-value=1e-07 Score=68.11 Aligned_cols=54 Identities=26% Similarity=0.308 Sum_probs=40.0
Q ss_pred CCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhcCCCCCCC
Q psy17316 169 ASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSRSTPRPPP 222 (229)
Q Consensus 169 ~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~~~~~~~~ 222 (229)
.+.+.||+||+..||+.+..++.++.++|..|||+.+|||+|++..+.|....+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~~~~~~~~ 55 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYREGQSAFP 55 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH--STT-S
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHhcCCCCCC
Confidence 456899999999999999888899999999999999999999996555554444
No 15
>smart00351 PAX Paired Box domain.
Probab=98.49 E-value=2.2e-06 Score=67.84 Aligned_cols=48 Identities=8% Similarity=-0.009 Sum_probs=41.8
Q ss_pred CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 28 TVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 28 ~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
...+.|+.|....+|.++. +|+|..+||+++||+++|+++|+++|.-.
T Consensus 13 ~~~~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~r~~~~ 60 (125)
T smart00351 13 VNGRPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILGRYYET 60 (125)
T ss_pred cCCCCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHc
Confidence 3346799999999999887 57799999999999999999999998443
No 16
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=98.47 E-value=3.9e-07 Score=71.65 Aligned_cols=49 Identities=10% Similarity=0.104 Sum_probs=45.2
Q ss_pred CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 28 TVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 28 ~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
..+++||.|.+..+|..+.++|.|+.++|++|||+.+||++|+++|...
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~~ 56 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQEG 56 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhhc
Confidence 4578999999999999999999999999999999999999999998543
No 17
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=98.46 E-value=1.1e-06 Score=68.14 Aligned_cols=46 Identities=20% Similarity=0.268 Sum_probs=43.3
Q ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCC-ChhhHHHHHHHhCC
Q psy17316 30 TKTWTHEDMDAALEALRAGQMSLTKASVSYGI-PSTTLWQRAHRLGI 75 (229)
Q Consensus 30 ~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gI-p~sTL~~~i~~~gi 75 (229)
+++||.|+++++|+++.++|.|+.++|++||| +.++|++|++++.-
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~ 51 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQK 51 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 78999999999999999999999999999995 99999999998744
No 18
>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=98.42 E-value=3.4e-07 Score=59.89 Aligned_cols=43 Identities=21% Similarity=0.414 Sum_probs=37.4
Q ss_pred CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHH
Q psy17316 114 GPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIAR 157 (229)
Q Consensus 114 G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik 157 (229)
|++++++++...++++++.+| +|+.+||+.|||+++|||++.+
T Consensus 1 GRp~~~~~~~~~~i~~l~~~G-~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 1 GRPPKLSKEQIEEIKELYAEG-MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSSSSSHCCHHHHHHHHHTT---HHHHHHHTTS-HHHHHHHHC
T ss_pred CcCCCCCHHHHHHHHHHHHCC-CCHHHHHHHHCcCHHHHHHHHh
Confidence 688999999999999999999 6999999999999999999764
No 19
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=98.40 E-value=6.8e-07 Score=70.29 Aligned_cols=45 Identities=11% Similarity=0.044 Sum_probs=41.8
Q ss_pred CCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316 170 SPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLS 214 (229)
Q Consensus 170 ~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~ 214 (229)
+.+.||.||+.+||+.+..++.++.++|.+|||+++|||+|++..
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y 53 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQY 53 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 357899999999999999999999999999999999999999943
No 20
>PF13518 HTH_28: Helix-turn-helix domain
Probab=98.40 E-value=5.8e-07 Score=59.54 Aligned_cols=42 Identities=21% Similarity=0.383 Sum_probs=35.9
Q ss_pred HHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh---CCcccC
Q psy17316 123 ILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE---GIRLAQ 165 (229)
Q Consensus 123 ~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~---g~k~~~ 165 (229)
++.++|++|++|. |+.++|++|||+.+||++|++.+ |+..+.
T Consensus 1 ~r~~iv~~~~~g~-s~~~~a~~~gis~~tv~~w~~~y~~~G~~~l~ 45 (52)
T PF13518_consen 1 FRLQIVELYLEGE-SVREIAREFGISRSTVYRWIKRYREGGIEGLK 45 (52)
T ss_pred CHHHHHHHHHcCC-CHHHHHHHHCCCHhHHHHHHHHHHhcCHHHhc
Confidence 3688999999988 99999999999999999999865 554444
No 21
>PF13518 HTH_28: Helix-turn-helix domain
Probab=98.38 E-value=3.9e-07 Score=60.37 Aligned_cols=43 Identities=16% Similarity=0.202 Sum_probs=36.9
Q ss_pred HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCC
Q psy17316 38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKE 81 (229)
Q Consensus 38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~ 81 (229)
++++|+++.+|. |+.++|++|||+++||++|+++|...|+.++
T Consensus 2 r~~iv~~~~~g~-s~~~~a~~~gis~~tv~~w~~~y~~~G~~~l 44 (52)
T PF13518_consen 2 RLQIVELYLEGE-SVREIAREFGISRSTVYRWIKRYREGGIEGL 44 (52)
T ss_pred HHHHHHHHHcCC-CHHHHHHHHCCCHhHHHHHHHHHHhcCHHHh
Confidence 678999999866 9999999999999999999999866554443
No 22
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=98.34 E-value=3.7e-07 Score=60.37 Aligned_cols=46 Identities=15% Similarity=0.240 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCC
Q psy17316 34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKK 80 (229)
Q Consensus 34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~ 80 (229)
+.+.+..+|.++.+ |.|..+||+.+|||++|+++|+++|.-.|+.+
T Consensus 3 ~~~~R~~ii~l~~~-G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G~~g 48 (50)
T PF13384_consen 3 SEERRAQIIRLLRE-GWSIREIAKRLGVSRSTVYRWIKRYREEGLEG 48 (50)
T ss_dssp -------HHHHHHH-T--HHHHHHHHTS-HHHHHHHHT---------
T ss_pred chhHHHHHHHHHHC-CCCHHHHHHHHCcCHHHHHHHHHHcccccccc
Confidence 56778899999998 77999999999999999999999986555443
No 23
>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=98.25 E-value=2.2e-06 Score=58.09 Aligned_cols=44 Identities=18% Similarity=0.247 Sum_probs=35.2
Q ss_pred CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 28 TVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 28 ~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
..+..+|.++++++|+.+.+|. |..++|++|||+++||++|++.
T Consensus 2 rkR~~LTl~eK~~iI~~~e~g~-s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 2 RKRKSLTLEEKLEIIKRLEEGE-SKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp SSSSS--HHHHHHHHHHHHCTT--HHHHHHHHT--CCHHHHHHHC
T ss_pred CCCccCCHHHHHHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHHh
Confidence 4578899999999999997766 9999999999999999999984
No 24
>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=98.23 E-value=1.5e-06 Score=56.89 Aligned_cols=43 Identities=19% Similarity=0.359 Sum_probs=35.3
Q ss_pred CCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 169 ASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 169 ~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
+++++++++...+|++...+| +++.++|..||||.+|||++++
T Consensus 1 GRp~~~~~~~~~~i~~l~~~G-~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 1 GRPPKLSKEQIEEIKELYAEG-MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSSSSSHCCHHHHHHHHHTT---HHHHHHHTTS-HHHHHHHHC
T ss_pred CcCCCCCHHHHHHHHHHHHCC-CCHHHHHHHHCcCHHHHHHHHh
Confidence 357788888888999988888 9999999999999999999874
No 25
>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=98.09 E-value=6.3e-06 Score=55.89 Aligned_cols=41 Identities=15% Similarity=0.248 Sum_probs=33.8
Q ss_pred CCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 171 PTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 171 ~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
.+.+|.+++.+||+.+.+|. ++.++|..||||.+||++|++
T Consensus 4 R~~LTl~eK~~iI~~~e~g~-s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 4 RKSLTLEEKLEIIKRLEEGE-SKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp SSS--HHHHHHHHHHHHCTT--HHHHHHHHT--CCHHHHHHH
T ss_pred CccCCHHHHHHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHH
Confidence 45779999999999999996 899999999999999999998
No 26
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=97.98 E-value=9.5e-06 Score=52.86 Aligned_cols=42 Identities=19% Similarity=0.168 Sum_probs=23.3
Q ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 30 TKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 30 ~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
++.+|.+|...+-.. .+.|+|+++||+.+|++++||++++++
T Consensus 2 ~~~Lt~~eR~~I~~l-~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 2 YKHLTPEERNQIEAL-LEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ----------HHHHH-HCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred ccchhhhHHHHHHHH-HHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 467788888876644 566799999999999999999999987
No 27
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=97.97 E-value=9.4e-06 Score=53.55 Aligned_cols=40 Identities=20% Similarity=0.309 Sum_probs=26.2
Q ss_pred CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316 175 KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR 215 (229)
Q Consensus 175 t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~ 215 (229)
+.+.|.+||+.+.+| +|+.++|..||||.+|||+|++..+
T Consensus 3 ~~~~R~~ii~l~~~G-~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 3 SEERRAQIIRLLREG-WSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp -------HHHHHHHT---HHHHHHHHTS-HHHHHHHHT---
T ss_pred chhHHHHHHHHHHCC-CCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 356799999999995 9999999999999999999999544
No 28
>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=97.80 E-value=0.00014 Score=50.73 Aligned_cols=64 Identities=14% Similarity=0.229 Sum_probs=44.0
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
+|+.++|+.+||+.+||++|.+++|+..+..... ....|++++ ....
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~~g~~~~~r~~~-------------------------------~~r~yt~~~v~~l~~ 49 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERRYGLPAPQRTDG-------------------------------GHRLYSEADVARLRL 49 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhCCCCCCCcCCC-------------------------------CCeecCHHHHHHHHH
Confidence 4789999999999999999999887755422111 123444444 3444
Q ss_pred HHHHHcCCCCHHHHHHH
Q psy17316 128 LDALRAGSISANKASKA 144 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k 144 (229)
|..+.+-++|+.+|.+.
T Consensus 50 i~~l~~~g~~l~~i~~~ 66 (68)
T cd01104 50 IRRLTSEGVRISQAAAL 66 (68)
T ss_pred HHHHHHCCCCHHHHHHH
Confidence 55666667799888764
No 29
>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=97.79 E-value=5.1e-05 Score=52.44 Aligned_cols=43 Identities=21% Similarity=0.230 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccC
Q psy17316 122 EILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQ 165 (229)
Q Consensus 122 e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~ 165 (229)
|.+.+|..+|++|- ++.+||++.|||.+||+.|+.++++....
T Consensus 1 e~k~~A~~LY~~G~-~~~eIA~~Lg~~~~TV~~W~~r~~W~~~~ 43 (58)
T PF06056_consen 1 EVKEQARSLYLQGW-SIKEIAEELGVPRSTVYSWKDRYKWDELL 43 (58)
T ss_pred CHHHHHHHHHHcCC-CHHHHHHHHCCChHHHHHHHHhhCccccC
Confidence 35788999999976 99999999999999999999999887764
No 30
>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=97.74 E-value=6.5e-05 Score=51.77 Aligned_cols=43 Identities=12% Similarity=0.091 Sum_probs=32.0
Q ss_pred CCCCCCHHHHHHHHHHHHhCCC---cHHHHHHHhCCChHHHHHHHH
Q psy17316 170 SPTAWKPEDLEIALEGIRSGQT---TVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 170 ~~r~~t~e~r~eaV~~~~~~~~---s~~eAA~~fgVp~~tv~~~vk 212 (229)
..+.|+.+|+++||++-..+.. |++.||.+|||+..+|..|.+
T Consensus 2 ~rrsy~~~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 2 SRRSYTAEFKLKVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp ------HHHHHHHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHHT
T ss_pred CccccChHHHHHHHHHHHHccchhhhHHHHHHHhCccHHHHHHHHH
Confidence 4578999999999999988755 689999999999999999987
No 31
>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=97.73 E-value=0.00028 Score=49.15 Aligned_cols=64 Identities=16% Similarity=0.208 Sum_probs=46.5
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHH--HHHHHHHHHhCCCcHHHHHHH
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPED--LEIALEGIRSGQTTVQRASAE 199 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA~~ 199 (229)
+|+.++|+.+||+.+||++|.++.|........+..+.|++++ +...|..+.+-+++..++...
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~~g~~~~~r~~~~~r~yt~~~v~~l~~i~~l~~~g~~l~~i~~~ 66 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIRRLTSEGVRISQAAAL 66 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHH
Confidence 4789999999999999999998766533221123457888776 455566667777999888764
No 32
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=97.68 E-value=4.1e-05 Score=49.81 Aligned_cols=40 Identities=15% Similarity=0.218 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 172 TAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 172 r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
+.+|+++|..|..+..+| +|+.++|..+|++.+||+++++
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS----HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-CCHHHHHHHHCcCcHHHHHHHh
Confidence 456788999988776555 9999999999999999999987
No 33
>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=97.65 E-value=7.9e-05 Score=51.50 Aligned_cols=44 Identities=14% Similarity=0.138 Sum_probs=37.3
Q ss_pred HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCC
Q psy17316 37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKE 81 (229)
Q Consensus 37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~ 81 (229)
-+..|..+|.. |.++.+||+.+|||.+||+.|+.+++=....+.
T Consensus 2 ~k~~A~~LY~~-G~~~~eIA~~Lg~~~~TV~~W~~r~~W~~~~~~ 45 (58)
T PF06056_consen 2 VKEQARSLYLQ-GWSIKEIAEELGVPRSTVYSWKDRYKWDELLPI 45 (58)
T ss_pred HHHHHHHHHHc-CCCHHHHHHHHCCChHHHHHHHHhhCccccCch
Confidence 46788999987 779999999999999999999999976654443
No 34
>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=97.63 E-value=0.00019 Score=42.22 Aligned_cols=41 Identities=27% Similarity=0.438 Sum_probs=33.8
Q ss_pred CCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHH
Q psy17316 170 SPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRC 211 (229)
Q Consensus 170 ~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~v 211 (229)
+++.++.+++..+++.+.++ .++.++|..|||+.+|||+|+
T Consensus 2 r~~~~~~~~~~~i~~~~~~~-~s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 2 RPPKLTPEQIEEARRLLAAG-ESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCCcCCHHHHHHHHHHHHcC-CCHHHHHHHHCCCHHHHHHhC
Confidence 34567778888888876655 799999999999999999984
No 35
>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=97.63 E-value=0.00043 Score=48.36 Aligned_cols=66 Identities=15% Similarity=0.261 Sum_probs=44.8
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHHHHHHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEILNVALD 129 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~k~~AV~ 129 (229)
+|+.++|+.+||+.+||+.|.++.++..+......+-|++++.. ....|.
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~g~l~~~~~~~g~R~y~~~~l~------------------------------~l~~i~ 50 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKEFNLYIPRTENGRRYYTDEDIE------------------------------LLKKIK 50 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCCCCCCCCCCceeeCHHHHH------------------------------HHHHHH
Confidence 47899999999999999999998776644322222234444331 344566
Q ss_pred HHHcCCCCHHHHHHHh
Q psy17316 130 ALRAGSISANKASKAY 145 (229)
Q Consensus 130 ~~~~g~~S~~~~a~k~ 145 (229)
.+.+.++|+.+|....
T Consensus 51 ~l~~~g~~l~~i~~~l 66 (67)
T cd04764 51 TLLEKGLSIKEIKEIL 66 (67)
T ss_pred HHHHCCCCHHHHHHHh
Confidence 6666778999887643
No 36
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=97.62 E-value=0.00014 Score=53.99 Aligned_cols=49 Identities=10% Similarity=0.131 Sum_probs=43.0
Q ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316 30 TKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTP 78 (229)
Q Consensus 30 ~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~ 78 (229)
....|+.-.+..+..+.+++.++.++|.+|||++.|.++|+.+|-.+|.
T Consensus 6 nA~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G~ 54 (85)
T PF13011_consen 6 NARLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRAEGE 54 (85)
T ss_pred CCCCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHcCc
Confidence 3567888899999999999999999999999999999999999854443
No 37
>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=97.56 E-value=0.00024 Score=41.74 Aligned_cols=42 Identities=29% Similarity=0.415 Sum_probs=35.3
Q ss_pred CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHH
Q psy17316 114 GPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIA 156 (229)
Q Consensus 114 G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~i 156 (229)
|++..++.+.+..++..+.+|. |+.++++.+||+.+|+++|+
T Consensus 1 Gr~~~~~~~~~~~i~~~~~~~~-s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 1 GRPPKLTPEQIEEARRLLAAGE-SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCCCcCCHHHHHHHHHHHHcCC-CHHHHHHHHCCCHHHHHHhC
Confidence 4567778888777788877665 99999999999999999984
No 38
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=97.43 E-value=0.00034 Score=48.83 Aligned_cols=64 Identities=17% Similarity=0.217 Sum_probs=44.1
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
+|+.++|+.+|||.+||+.|.+...+..+..... ...|++++ ++..
T Consensus 1 yti~eva~~~gvs~~tlr~y~~~gll~~~~~~~g--------------------------------~r~y~~~dv~~l~~ 48 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYEREGLLPPPRDENG--------------------------------YRYYSEEDVERLRE 48 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHHHTTSSTTBESTTS--------------------------------SEEE-HHHHHHHHH
T ss_pred CcHHHHHHHHCcCHHHHHHHHHhcCcccccccCc--------------------------------eeeccHHHHHHHHH
Confidence 4789999999999999999999866544332211 23444444 3556
Q ss_pred HHHHHcCCCCHHHHHHHh
Q psy17316 128 LDALRAGSISANKASKAY 145 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~ 145 (229)
|..+.+.++|+.+|.+..
T Consensus 49 i~~l~~~G~sl~~I~~~l 66 (69)
T PF13411_consen 49 IKELRKQGMSLEEIKKLL 66 (69)
T ss_dssp HHHHHHTTTHHHHHHHHH
T ss_pred HHHHHHCcCCHHHHHHHH
Confidence 667777777988887653
No 39
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=97.41 E-value=0.0019 Score=50.49 Aligned_cols=77 Identities=16% Similarity=0.158 Sum_probs=58.1
Q ss_pred CCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHH----HhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCc
Q psy17316 117 KSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIAR----KEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTT 192 (229)
Q Consensus 117 ~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik----~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s 192 (229)
..-++|++.-+...+++.+ |++++++.+|||.+|++.++. +.|.... ...-...++.+|++.+.+|++|
T Consensus 32 ~~L~~E~~~Fi~~Fi~~rG-nlKe~e~~lgiSYPTvR~rLd~ii~~lg~~~~------~~~~~~~~~~~IL~~L~~GeIs 104 (113)
T PF09862_consen 32 ARLSPEQLEFIKLFIKNRG-NLKEMEKELGISYPTVRNRLDKIIEKLGYEED------EEEEEEDERKEILDKLEKGEIS 104 (113)
T ss_pred hcCCHHHHHHHHHHHHhcC-CHHHHHHHHCCCcHHHHHHHHHHHHHhCCCCC------cccccchhHHHHHHHHHcCCCC
Confidence 3456677766667777766 999999999999999888764 3454111 1223457799999999999999
Q ss_pred HHHHHHHh
Q psy17316 193 VQRASAEY 200 (229)
Q Consensus 193 ~~eAA~~f 200 (229)
+.+|....
T Consensus 105 ~eeA~~~L 112 (113)
T PF09862_consen 105 VEEALEIL 112 (113)
T ss_pred HHHHHHHh
Confidence 99998764
No 40
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=97.34 E-value=0.00073 Score=50.22 Aligned_cols=40 Identities=20% Similarity=0.229 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 173 AWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 173 ~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
..|+.-|...|+.|.+++.++.++|..||||..|++.|+.
T Consensus 8 ~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~ 47 (85)
T PF13011_consen 8 RLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLA 47 (85)
T ss_pred CCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHH
Confidence 4678889999999999999999999999999999999998
No 41
>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=97.32 E-value=0.0019 Score=45.21 Aligned_cols=65 Identities=14% Similarity=0.283 Sum_probs=45.1
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
+++.++|+.+||+.+||+.|.+..|+-.|.... |....|+.++ +...
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~~gl~~~~r~~-------------------------------~g~R~yt~~di~~l~~ 49 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWEREFGLLKPQRSD-------------------------------GGHRLFNDADIDRILE 49 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCCCCCCcCC-------------------------------CCCcccCHHHHHHHHH
Confidence 478899999999999999998887765432211 1134455555 3445
Q ss_pred HHHHHcCCCCHHHHHHHh
Q psy17316 128 LDALRAGSISANKASKAY 145 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~ 145 (229)
|..+.+.++|+.+|+...
T Consensus 50 i~~l~~~g~~l~~i~~~l 67 (68)
T cd04763 50 IKRWIDNGVQVSKVKKLL 67 (68)
T ss_pred HHHHHHcCCCHHHHHHHh
Confidence 666677778999988653
No 42
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=97.27 E-value=0.0012 Score=55.76 Aligned_cols=70 Identities=13% Similarity=0.197 Sum_probs=49.9
Q ss_pred HHHHHHHHhhcchhhhhhhhccCCCCCCCHHH-----HHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCC
Q psy17316 92 LNVALDALRAGSISANKASKAYGPTKSWNEEI-----LNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGI 161 (229)
Q Consensus 92 ~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~-----k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~ 161 (229)
++...+-..+|...+++.|++.|++..+.+.. ..+.|..+..++.|+.+||+.+|||++|+|++++..|+
T Consensus 124 r~~i~~R~~~g~~~~~~~G~~~Grp~g~~~~~~~~~~~~~~i~~~~~~g~s~~~iak~lgis~~Tv~r~~k~~~~ 198 (200)
T PRK13413 124 RNLISQRTKEALARKKAEGVTLGRPKGSTPKKYKLTGKEEKIKKLLDKGTSKSEIARKLGVSRTTLARFLKTRGL 198 (200)
T ss_pred HHHHHHHHHHHHHHHHHcCCccCCCCCCcchhhhcchhHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHhccc
Confidence 33334445568888888888889876655432 22344444455569999999999999999999987664
No 43
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=97.24 E-value=0.00076 Score=47.04 Aligned_cols=64 Identities=13% Similarity=0.153 Sum_probs=46.3
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHh
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEY 200 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~f 200 (229)
+++.++|+.+|||.+||+.|.+..-+..... .+..+.|+++ +++..|..+.+.+++..+|...+
T Consensus 1 yti~eva~~~gvs~~tlr~y~~~gll~~~~~-~~g~r~y~~~dv~~l~~i~~l~~~G~sl~~I~~~l 66 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYEREGLLPPPRD-ENGYRYYSEEDVERLREIKELRKQGMSLEEIKKLL 66 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHHHTTSSTTBES-TTSSEEE-HHHHHHHHHHHHHHHTTTHHHHHHHHH
T ss_pred CcHHHHHHHHCcCHHHHHHHHHhcCcccccc-cCceeeccHHHHHHHHHHHHHHHCcCCHHHHHHHH
Confidence 3788999999999999999998543333321 1234777766 56677888888889999988754
No 44
>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=97.18 E-value=0.0041 Score=43.51 Aligned_cols=65 Identities=12% Similarity=0.121 Sum_probs=46.2
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHh
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEY 200 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~f 200 (229)
+++.++|+++||+.+||+.|.++.|........+..|.|+.+ ++...|..+.+.+++..+++..+
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~~gl~~~~r~~~g~R~yt~~di~~l~~i~~l~~~g~~l~~i~~~l 67 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWEREFGLLKPQRSDGGHRLFNDADIDRILEIKRWIDNGVQVSKVKKLL 67 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCCCCCCcCCCCCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHh
Confidence 378899999999999999998865643221112345678766 45556667777889998888754
No 45
>PF13565 HTH_32: Homeodomain-like domain
Probab=97.17 E-value=0.0017 Score=46.29 Aligned_cols=60 Identities=22% Similarity=0.358 Sum_probs=43.1
Q ss_pred HHHHHHHHh---CCcccC-----CCCCCCCCCCHHHHHHHHHHHHhC-CCcHHHHHHH----hC--C--ChHHHHHHH
Q psy17316 151 TLYKIARKE---GIRLAQ-----PFNASPTAWKPEDLEIALEGIRSG-QTTVQRASAE----YG--I--PSGTLYGRC 211 (229)
Q Consensus 151 TL~~~ik~~---g~k~~~-----~~~~~~r~~t~e~r~eaV~~~~~~-~~s~~eAA~~----fg--V--p~~tv~~~v 211 (229)
|+++|++++ |...+. +..+++++ +++.+..|++.+.++ .++..+++.. || + |++|||+++
T Consensus 1 Tv~rw~~ry~~~G~~gL~~~~~~~~~Grp~~-~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~L 77 (77)
T PF13565_consen 1 TVYRWLKRYREEGLEGLKDRKRRPRPGRPRK-DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRIL 77 (77)
T ss_pred CHHHHHHHHHhhCchhhhcccccCCCCCCCC-cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHhC
Confidence 688999765 644332 33455566 677779999998887 6888888775 34 3 999999874
No 46
>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=97.14 E-value=0.0039 Score=43.44 Aligned_cols=64 Identities=11% Similarity=0.161 Sum_probs=46.0
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHH--HHHHHHHHHhCCCcHHHHHHHh
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPED--LEIALEGIRSGQTTVQRASAEY 200 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA~~f 200 (229)
+|+.++|+.+||+.+||+.|.++.++.... ..+..|.|+.++ +...+..+.+.+++..++....
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~g~l~~~~-~~~g~R~y~~~~l~~l~~i~~l~~~g~~l~~i~~~l 66 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKEFNLYIPR-TENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEIL 66 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCCCCCC-CCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 478899999999999999999875554322 123457787664 4555666667778888887654
No 47
>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=97.11 E-value=0.0012 Score=42.09 Aligned_cols=27 Identities=15% Similarity=0.244 Sum_probs=23.7
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
+|+.++|+.+||+++||++|+++..+.
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~~~ 27 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGKLK 27 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 588999999999999999999985443
No 48
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=97.10 E-value=0.0025 Score=44.72 Aligned_cols=77 Identities=21% Similarity=0.257 Sum_probs=57.0
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHHHHHHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEILNVALD 129 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~k~~AV~ 129 (229)
+|+.++|+++||+.++|.+.+++..-..+.. .+ ....+..|++
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~--------------~~-----------------------~~~r~~~a~~ 44 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKETGTTPKQ--------------YL-----------------------RDRRLERARR 44 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHhCcCHHH--------------HH-----------------------HHHHHHHHHH
Confidence 6899999999999999999998752211100 00 0123467788
Q ss_pred HHHcCCCCHHHHHHHhCC-ChHHHHHHHHHh-CCcc
Q psy17316 130 ALRAGSISANKASKAYGI-PSSTLYKIARKE-GIRL 163 (229)
Q Consensus 130 ~~~~g~~S~~~~a~k~gI-p~sTL~~~ik~~-g~k~ 163 (229)
.+.++.+++.++|..+|+ +.+.+.+..++. |...
T Consensus 45 ~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk~~~g~sp 80 (84)
T smart00342 45 LLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80 (84)
T ss_pred HHHcCCCCHHHHHHHhCCCChHHHHHHHHHHHCcCh
Confidence 888887899999999999 778899988765 6543
No 49
>PHA02535 P terminase ATPase subunit; Provisional
Probab=97.08 E-value=0.00084 Score=65.62 Aligned_cols=48 Identities=19% Similarity=0.374 Sum_probs=43.7
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCC
Q psy17316 118 SWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQP 166 (229)
Q Consensus 118 kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~ 166 (229)
.|++|+|.+|+.+|.+| .|+.+||+.+||+.+|||+|++++++....|
T Consensus 2 ~yt~EfK~~Av~Ly~~G-~sv~eIA~~LGv~~~Tl~~W~kr~~w~~~~~ 49 (581)
T PHA02535 2 AYDDDVRRAAKFLYWQG-WTVAEIAEELGLKSRTIYSWKERDGWRDLLP 49 (581)
T ss_pred CCCHHHHHHHHHHHHcC-CCHHHHHHHhCCChhHHHHHhccccccccCC
Confidence 69999999999999995 5999999999999999999999998877654
No 50
>KOG4565|consensus
Probab=97.05 E-value=0.00024 Score=58.96 Aligned_cols=68 Identities=26% Similarity=0.337 Sum_probs=53.0
Q ss_pred HhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 144 AYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 144 k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
-.|||..|--. ..+.+++..++..++.|.|+.|-+.|||..+..|+|++..|-..||||.+||-..||
T Consensus 93 ~tg~se~t~d~-~g~~~sKqpRkKRGrYRqYd~eileEAi~~VmsGkMsVskAqsiyGvPHSTLEYKVK 160 (206)
T KOG4565|consen 93 TTGISEKTQDM-HGNEESKQPRKKRGRYRQYDKEILEEAIRSVMSGKMSVSKAQSIYGVPHSTLEYKVK 160 (206)
T ss_pred CCCCCCccccc-cCCccccCccccccchhhhhHHHHHHHHHHHhcCceeeecccceeccccchhhhhhH
Confidence 35666655211 111344444455678899999999999999999999999999999999999999998
No 51
>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=97.04 E-value=0.0011 Score=45.70 Aligned_cols=45 Identities=11% Similarity=0.237 Sum_probs=30.9
Q ss_pred CCCCCCCHHHHHHHHHHHHcCC---CCHHHHHHHhCCChHHHHHHHHH
Q psy17316 114 GPTKSWNEEILNVALDALRAGS---ISANKASKAYGIPSSTLYKIARK 158 (229)
Q Consensus 114 G~~~kYs~e~k~~AV~~~~~g~---~S~~~~a~k~gIp~sTL~~~ik~ 158 (229)
|....|+.+||++||+.+.... .+++.++++|||++..+++|.+.
T Consensus 1 g~rrsy~~~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~kq 48 (58)
T PF09607_consen 1 GSRRSYTAEFKLKVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWRKQ 48 (58)
T ss_dssp -------HHHHHHHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHHTT
T ss_pred CCccccChHHHHHHHHHHHHccchhhhHHHHHHHhCccHHHHHHHHHH
Confidence 3456799999999999996543 37799999999999999999863
No 52
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=96.97 E-value=0.0017 Score=41.65 Aligned_cols=33 Identities=24% Similarity=0.332 Sum_probs=24.9
Q ss_pred HHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 41 ALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 41 AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
..+.+...+-++.++|+.+||+++||++++++|
T Consensus 10 i~~aL~~~~gn~~~aA~~Lgisr~tL~~klkk~ 42 (42)
T PF02954_consen 10 IRQALERCGGNVSKAARLLGISRRTLYRKLKKY 42 (42)
T ss_dssp HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHC
T ss_pred HHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHhC
Confidence 334454555589999999999999999999875
No 53
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=96.90 E-value=0.008 Score=47.37 Aligned_cols=88 Identities=15% Similarity=0.099 Sum_probs=63.9
Q ss_pred HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCC
Q psy17316 37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGP 115 (229)
Q Consensus 37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~ 115 (229)
.+...|+.-....+++.++|+.+|+++++|.++.++. |... .
T Consensus 13 ~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G~s~------------~------------------------- 55 (127)
T PRK11511 13 SILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSL------------G------------------------- 55 (127)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH------------H-------------------------
Confidence 3444554445567999999999999999999999975 5431 1
Q ss_pred CCCCCHHHH-HHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316 116 TKSWNEEIL-NVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL 163 (229)
Q Consensus 116 ~~kYs~e~k-~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~ 163 (229)
.|-...+ ..|.++++..+.++.+||...|-+... +.+..++. |..+
T Consensus 56 --~~l~~~Rl~~A~~~L~~t~~~i~eIA~~~Gf~s~s~F~r~Fkk~~G~tP 104 (127)
T PRK11511 56 --QYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPP 104 (127)
T ss_pred --HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence 1112233 456777777778999999999999866 88877755 7544
No 54
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=96.89 E-value=0.029 Score=42.40 Aligned_cols=86 Identities=12% Similarity=0.033 Sum_probs=62.6
Q ss_pred HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCC
Q psy17316 39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTK 117 (229)
Q Consensus 39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~ 117 (229)
...|+.-....+++.++|+.+|++.++|.+..++. |... ..
T Consensus 11 ~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~~g~s~------------~~-------------------------- 52 (107)
T PRK10219 11 IAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTL------------GD-------------------------- 52 (107)
T ss_pred HHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCH------------HH--------------------------
Confidence 34444434566899999999999999999999985 4431 11
Q ss_pred CCCHH-HHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316 118 SWNEE-ILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL 163 (229)
Q Consensus 118 kYs~e-~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~ 163 (229)
|-.. -+..|.+.+.++..|+.+||...|-+..+ +.+..+++ |..+
T Consensus 53 -~i~~~Rl~~a~~~L~~~~~~i~~iA~~~Gf~~~s~f~~~Fk~~~G~tP 100 (107)
T PRK10219 53 -YIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSRVFRRQFDRTP 100 (107)
T ss_pred -HHHHHHHHHHHHHHHccCCCHHHHHHHHCCCCHHHHHHHHHHHHCcCH
Confidence 1111 24667778888888999999999999977 88888765 6543
No 55
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=96.86 E-value=0.0075 Score=47.16 Aligned_cols=43 Identities=14% Similarity=0.162 Sum_probs=36.5
Q ss_pred CCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 29 VTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 29 ~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
.-...+.||+..+..-+++.| |++++++.|||+-.|++.++.+
T Consensus 30 ~~~~L~~E~~~Fi~~Fi~~rG-nlKe~e~~lgiSYPTvR~rLd~ 72 (113)
T PF09862_consen 30 WFARLSPEQLEFIKLFIKNRG-NLKEMEKELGISYPTVRNRLDK 72 (113)
T ss_pred hhhcCCHHHHHHHHHHHHhcC-CHHHHHHHHCCCcHHHHHHHHH
Confidence 346678899887777777766 9999999999999999998886
No 56
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=96.81 E-value=0.0091 Score=41.47 Aligned_cols=23 Identities=13% Similarity=0.117 Sum_probs=21.2
Q ss_pred CCHHHHHHHcCCChhhHHHHHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+|+.++|+.+||+.+||+.|.+.
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~~ 23 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERI 23 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 57899999999999999999875
No 57
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=96.81 E-value=0.002 Score=47.25 Aligned_cols=36 Identities=19% Similarity=0.218 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHH
Q psy17316 176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRC 211 (229)
Q Consensus 176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~v 211 (229)
++--+++.+++++++.++++||..||||.+||..-+
T Consensus 5 eeR~i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDv 40 (82)
T PF12116_consen 5 EERVIEIANYIIETKATVRQAAKVFGVSKSTVHKDV 40 (82)
T ss_dssp HHHHHHHHHHHHHH---HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHHcccHHHHHHHHHCCcHHHHHHHH
Confidence 456689999999999999999999999999999865
No 58
>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=96.78 E-value=0.014 Score=43.94 Aligned_cols=74 Identities=9% Similarity=0.039 Sum_probs=54.4
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCc-ccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHH
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIR-LAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGR 210 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k-~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~ 210 (229)
+++.++|+.+|||..||+.|.+ .|.- ......+..|.|+++ +++..|..+.+-+++..++...++.+...+...
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~-~Gll~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~eI~~~l~~~~~~~~~~ 77 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDH-IGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDGPDFDPLEL 77 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhCCChhHHHH
Confidence 4788999999999999999987 4532 221112346788766 566778888888899999999998765443333
No 59
>PHA00675 hypothetical protein
Probab=96.78 E-value=0.0037 Score=45.47 Aligned_cols=47 Identities=11% Similarity=0.072 Sum_probs=40.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 25 GSLTVTKTWTHEDMDAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 25 ~~~~~~~kyt~e~~~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
|...++.+.|+.+..++..++ .+|. |...+|++||||++||+.....
T Consensus 15 Ge~h~~AKLt~~qV~~IR~l~~r~G~-s~~~IA~~fGVsrstV~~I~~g 62 (78)
T PHA00675 15 GEDHPNAKLTDAEVERIRELHEVEGM-SYAVLAEKFEQSKGAIAKICRY 62 (78)
T ss_pred CCCCCCcccCHHHHHHHHHHHHhcCc-cHHHHHHHhCCCHHHHHHHHcc
Confidence 445668999999999999988 6755 9999999999999999987653
No 60
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=96.77 E-value=0.0077 Score=42.17 Aligned_cols=69 Identities=19% Similarity=0.295 Sum_probs=55.3
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCC-CHHHHHHHHHHHHhCCCcHHHHHHHhCC-ChHHHHHHHH
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAW-KPEDLEIALEGIRSGQTTVQRASAEYGI-PSGTLYGRCK 212 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~-t~e~r~eaV~~~~~~~~s~~eAA~~fgV-p~~tv~~~vk 212 (229)
.|+.++|+.+|++.++|++..+.. |.... .| .......|++++.++++++.++|..+|+ +.+.+.+..|
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~~~s~~--------~~~~~~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk 73 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKETGTTPK--------QYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFK 73 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHhCcCHH--------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 589999999999999999988865 43332 12 2233556888888888999999999999 9999988886
No 61
>PHA02535 P terminase ATPase subunit; Provisional
Probab=96.75 E-value=0.0018 Score=63.40 Aligned_cols=43 Identities=16% Similarity=0.193 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI 75 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi 75 (229)
.||+|.+.+|+.+|.+ |.|+.+||+++||+.+||++|+++++=
T Consensus 2 ~yt~EfK~~Av~Ly~~-G~sv~eIA~~LGv~~~Tl~~W~kr~~w 44 (581)
T PHA02535 2 AYDDDVRRAAKFLYWQ-GWTVAEIAEELGLKSRTIYSWKERDGW 44 (581)
T ss_pred CCCHHHHHHHHHHHHc-CCCHHHHHHHhCCChhHHHHHhccccc
Confidence 6999999999999999 889999999999999999999999863
No 62
>KOG4565|consensus
Probab=96.74 E-value=0.00097 Score=55.44 Aligned_cols=48 Identities=25% Similarity=0.440 Sum_probs=43.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316 27 LTVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG 74 (229)
Q Consensus 27 ~~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g 74 (229)
+..+++|..+.+.+||..+..|.||+..|.--||||++||--+++...
T Consensus 116 RGrYRqYd~eileEAi~~VmsGkMsVskAqsiyGvPHSTLEYKVKER~ 163 (206)
T KOG4565|consen 116 RGRYRQYDKEILEEAIRSVMSGKMSVSKAQSIYGVPHSTLEYKVKERN 163 (206)
T ss_pred ccchhhhhHHHHHHHHHHHhcCceeeecccceeccccchhhhhhHhhc
Confidence 334688999999999999999999999999999999999999998643
No 63
>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=96.67 E-value=0.01 Score=43.96 Aligned_cols=65 Identities=15% Similarity=0.168 Sum_probs=48.4
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCC-CCCCCCCHHH--HHHHHHHHHhCCCcHHHHHHHhC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFN-ASPTAWKPED--LEIALEGIRSGQTTVQRASAEYG 201 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~-~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA~~fg 201 (229)
+++.++|+.+||+.+||+.|.+. |.-...... +..|.|++++ ++..|..+.+.+++..++...+.
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~-Gll~p~r~~~~g~R~Ys~~dv~~l~~I~~Lr~~G~sl~~i~~~l~ 69 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEK-GLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLR 69 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCCCCceecCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 48899999999999999999774 532221111 2467887764 45778888888899999988765
No 64
>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=96.66 E-value=0.018 Score=43.26 Aligned_cols=70 Identities=19% Similarity=0.227 Sum_probs=48.9
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
|++.++|+.+|||..||+.|-+. |+-.|..... |....|++++ +...
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~~-Gll~p~~r~~------------------------------~gyR~Y~~~~l~~l~~ 49 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDHI-GLLSPSQRTE------------------------------GGHRLYDRADIRRLHQ 49 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCC------------------------------CCceeeCHHHHHHHHH
Confidence 68899999999999999999874 4433321111 1134455555 4566
Q ss_pred HHHHHcCCCCHHHHHHHhCCChH
Q psy17316 128 LDALRAGSISANKASKAYGIPSS 150 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~gIp~s 150 (229)
|..+.+-++|+.+|...++....
T Consensus 50 I~~lr~~G~~l~eI~~~l~~~~~ 72 (96)
T cd04788 50 IIALRRLGFSLREIGRALDGPDF 72 (96)
T ss_pred HHHHHHcCCCHHHHHHHHhCCCh
Confidence 77888888899999988876543
No 65
>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=96.64 E-value=0.02 Score=43.39 Aligned_cols=69 Identities=14% Similarity=0.136 Sum_probs=50.3
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCC-cccCCCCCCCCCCCHHHH--HHHHHHHHhCCCcHHHHHHHhCCChH
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGI-RLAQPFNASPTAWKPEDL--EIALEGIRSGQTTVQRASAEYGIPSG 205 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~-k~~~~~~~~~r~~t~e~r--~eaV~~~~~~~~s~~eAA~~fgVp~~ 205 (229)
+++.++|+.+||+.+||+.|.+. |. .......+..|.|++++. +..|..+.+.+++..++...+.....
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~~-Gll~~~~~~~~g~R~y~~~di~~l~~i~~lr~~g~~l~~i~~~~~~~~~ 72 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEI-GLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSE 72 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHcCcH
Confidence 47899999999999999999874 43 221111234577887654 45577888888999999998887653
No 66
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=96.62 E-value=0.017 Score=40.13 Aligned_cols=64 Identities=14% Similarity=0.135 Sum_probs=42.1
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCC-cccCCCCCCCCCCCHHHH--HHHHHHHHhCCCcHHHHHHHh
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGI-RLAQPFNASPTAWKPEDL--EIALEGIRSGQTTVQRASAEY 200 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~-k~~~~~~~~~r~~t~e~r--~eaV~~~~~~~~s~~eAA~~f 200 (229)
+|+.++|+.+||+.+||+.|.+ .|+ ..........+.|+.++. ...+..+.+.+++..++...+
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~-~gli~~~~~~~~g~r~y~~~dl~~l~~i~~lr~~g~~~~~i~~~l 67 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYER-IGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELL 67 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCCEecCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 4789999999999999999987 443 222111233567776644 444555555667777766544
No 67
>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=96.61 E-value=0.013 Score=43.45 Aligned_cols=66 Identities=11% Similarity=0.159 Sum_probs=45.8
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
+++.++|+.+||+.+||+.|-+. |.-.|..... |....|+.++ +...
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~-Gll~p~r~~~------------------------------~g~R~Ys~~dv~~l~~ 50 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEK-GLIKSIRSDG------------------------------GGQRKYSLADVDRLLV 50 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCC------------------------------CCceecCHHHHHHHHH
Confidence 68999999999999999999776 4332322111 0134455555 3556
Q ss_pred HHHHHcCCCCHHHHHHHhC
Q psy17316 128 LDALRAGSISANKASKAYG 146 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~g 146 (229)
|..+.+.++|+.+|.+...
T Consensus 51 I~~Lr~~G~sl~~i~~~l~ 69 (88)
T cd01105 51 IKELLDEGFTLAAAVEKLR 69 (88)
T ss_pred HHHHHHCCCCHHHHHHHHH
Confidence 7777777889999988765
No 68
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=96.61 E-value=0.014 Score=46.51 Aligned_cols=44 Identities=9% Similarity=0.030 Sum_probs=34.9
Q ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316 30 TKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG 74 (229)
Q Consensus 30 ~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g 74 (229)
-+.++.+....+|++..+ |++..+||+++.|+++.+.+++.+|.
T Consensus 15 GrPLp~~~R~rIvela~~-G~rp~~Isr~l~Vs~gcVsKIl~Ry~ 58 (125)
T PF00292_consen 15 GRPLPNELRQRIVELAKE-GVRPCDISRQLRVSHGCVSKILSRYR 58 (125)
T ss_dssp TSSS-HHHHHHHHHHHHT-T--HHHHHHHHT--HHHHHHHHHHHH
T ss_pred CccCcHHHHHHHHHHhhh-cCCHHHHHHHHccchhHHHHHHHHHH
Confidence 366788999999999876 77999999999999999999999983
No 69
>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=96.61 E-value=0.013 Score=44.46 Aligned_cols=71 Identities=13% Similarity=0.168 Sum_probs=49.0
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHH--HHHH-HhCCCcHHHHHHHhCCChHH
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIA--LEGI-RSGQTTVQRASAEYGIPSGT 206 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~ea--V~~~-~~~~~s~~eAA~~fgVp~~t 206 (229)
+++.++|+.+||+.+||+.|.+..|.-......+..|.|+.++...+ |+.| .+-+++..++....+-....
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~~gli~p~r~~~g~R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~~~~~ 74 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETEFPQLKPVKRAGGRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKEDGAA 74 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHcCCCCCcCCCCCCeeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhcccc
Confidence 37889999999999999999887553221111234678888765544 5554 55669998888877654443
No 70
>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=96.55 E-value=0.0079 Score=38.20 Aligned_cols=47 Identities=21% Similarity=0.359 Sum_probs=32.4
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHH
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIAL 183 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV 183 (229)
+|+.++|+.+||+.+||++|++.-.+.... ..+..+.|+.++..+.+
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~~~~~~-~~~~~~~~~~~ei~~~~ 47 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGKLKAIR-TPGGHRRFPEEDLERLL 47 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCCcee-CCCCceecCHHHHHHHH
Confidence 478999999999999999999854333221 12245567776665543
No 71
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=96.55 E-value=0.0046 Score=40.39 Aligned_cols=41 Identities=22% Similarity=0.229 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316 177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-LSRST 217 (229)
Q Consensus 177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~ 217 (229)
+.|.+|+..+.+|.+++.++|..+|+|+++|...++ +...|
T Consensus 2 ~~R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~~g 43 (47)
T PF01022_consen 2 PTRLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLREAG 43 (47)
T ss_dssp HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHHCc
Confidence 469999999999999999999999999999999988 44443
No 72
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=96.55 E-value=0.0086 Score=39.11 Aligned_cols=37 Identities=19% Similarity=0.227 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 174 WKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 174 ~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
.+++++. ++.++.. ++++.++|..+|||.+||+.+++
T Consensus 4 l~~~e~~-i~~~~~~-g~s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 4 LTPRERE-VLRLLAE-GLTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred CCHHHHH-HHHHHHc-CCCHHHHHHHHCCCHHHHHHHHH
Confidence 4555554 7777654 49999999999999999999987
No 73
>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=96.53 E-value=0.014 Score=44.34 Aligned_cols=29 Identities=17% Similarity=0.287 Sum_probs=24.7
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTP 78 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~ 78 (229)
+++.++|+.+||+.+||+.|-+.+|+-.|
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~~gli~p 29 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETEFPQLKP 29 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHcCCCCC
Confidence 47889999999999999999888775444
No 74
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=96.52 E-value=0.0091 Score=50.13 Aligned_cols=27 Identities=15% Similarity=0.247 Sum_probs=25.0
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
|++.++|+.+||+..||++|.+++++.
T Consensus 1 mti~evA~~lGVS~~TLRrw~k~g~L~ 27 (175)
T PRK13182 1 MKTPFVAKKLGVSPKTVQRWVKQLNLP 27 (175)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 578999999999999999999998875
No 75
>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=96.50 E-value=0.0041 Score=43.31 Aligned_cols=37 Identities=22% Similarity=0.398 Sum_probs=32.2
Q ss_pred HHHHHHHHHHc--CCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 37 DMDAALEALRA--GQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 37 ~~~~AI~~~~~--g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
+...|-+.|++ |++...+||.++||+.+||+.|-.+.
T Consensus 8 ~rdkA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~~d 46 (60)
T PF10668_consen 8 NRDKAFEIYKESNGKIKLKDIAEKLGVSESTIRKWKSRD 46 (60)
T ss_pred CHHHHHHHHHHhCCCccHHHHHHHHCCCHHHHHHHhhhc
Confidence 45677788874 88999999999999999999998874
No 76
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=96.49 E-value=0.0056 Score=45.81 Aligned_cols=36 Identities=17% Similarity=0.132 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
..+|.+|++++.+| +++.++|..+|||.+|||++.+
T Consensus 37 Ls~R~~I~~ll~~G-~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 37 LAQRLQVAKMLKQG-KTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred hhHHHHHHHHHHCC-CCHHHHHHHHCcCHHHHHHHHH
Confidence 34587777776666 8999999999999999999776
No 77
>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=96.48 E-value=0.0038 Score=39.96 Aligned_cols=29 Identities=14% Similarity=0.282 Sum_probs=25.0
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTP 78 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~ 78 (229)
+|+.++|+.+||+++||++|++...+...
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g~i~~~ 30 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEGELPAY 30 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcCCCCeE
Confidence 68999999999999999999987655543
No 78
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=96.46 E-value=0.0093 Score=38.93 Aligned_cols=40 Identities=15% Similarity=0.222 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
..++++.. ++..+. .|+|..+||+.+||+++|+++++++.
T Consensus 3 ~l~~~e~~-i~~~~~-~g~s~~eia~~l~is~~tv~~~~~~~ 42 (58)
T smart00421 3 SLTPRERE-VLRLLA-EGLTNKEIAERLGISEKTVKTHLSNI 42 (58)
T ss_pred CCCHHHHH-HHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45677765 676664 57899999999999999999998863
No 79
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=96.46 E-value=0.033 Score=50.46 Aligned_cols=106 Identities=16% Similarity=0.121 Sum_probs=68.2
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhh
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASK 111 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~ 111 (229)
..|.++..++ +.+..-++|.++||+++|..++||.+-+++.-... .|+.+.=++..+.++..
T Consensus 7 hLT~~eR~~I-~~l~~~~~S~reIA~~LgRh~sTIsRElkRn~~~~--------~Y~a~~A~~~~~~~rrr--------- 68 (318)
T COG2826 7 HLTLFERYEI-ERLLKAKMSIREIAKQLNRHHSTISRELKRNRTRD--------IYSAVKAQERYRMLRRR--------- 68 (318)
T ss_pred hCCHHHHHHH-HHHHHcCCCHHHHHHHhCCCcchhhHHHhcCCccc--------eeeHHHHHHHHHHhhcc---------
Confidence 4566776654 45556689999999999999999999999864432 24433333333211111
Q ss_pred ccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHH--HhC-CChHHHHHHHH
Q psy17316 112 AYGPTKSWNEEILNVALDALRAGSISANKASK--AYG-IPSSTLYKIAR 157 (229)
Q Consensus 112 ~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~--k~g-Ip~sTL~~~ik 157 (229)
.-+..+.+.+....+++.+.+ ..|..+|+- ..+ |+..|+|+|+-
T Consensus 69 -~~~k~~~~~eL~~~V~e~L~~-~wSPEQI~g~l~~~~i~~eTIYr~ly 115 (318)
T COG2826 69 -RIRKLKLNPELRELVLEKLKS-KWSPEQIIGRLKKSKISFETIYRWLY 115 (318)
T ss_pred -cCCcccCCHHHHHHHHHHHHh-hCCHHHHHHHHHhcccCHHHHHHHHh
Confidence 112445666666666666544 458888854 333 88999999973
No 80
>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=96.43 E-value=0.0066 Score=39.22 Aligned_cols=27 Identities=11% Similarity=0.049 Sum_probs=23.9
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
+|+.++|+.+||+..||++|.++..+.
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~l~ 27 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGLLS 27 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 588999999999999999999886554
No 81
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=96.42 E-value=0.0092 Score=38.20 Aligned_cols=35 Identities=23% Similarity=0.359 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
|+.-|.+.+...+-|..+||...|||++|||+.++
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~~klk 40 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLLGISRRTLYRKLK 40 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 57778888888888999999999999999999876
No 82
>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=96.38 E-value=0.043 Score=41.24 Aligned_cols=70 Identities=13% Similarity=0.089 Sum_probs=49.1
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
+++.++|+.+||+..||+.|-+. |+-.|.....+ ....|+.++ +...
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~-Gll~p~~~~~~------------------------------gyR~Y~~~~l~~l~~ 49 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDI-GLFKPAKIAEN------------------------------GYRYYSYAQLYQLQF 49 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCCC------------------------------CeeeCCHHHHHHHHH
Confidence 47899999999999999999987 55433221111 134455555 4566
Q ss_pred HHHHHcCCCCHHHHHHHhCCChH
Q psy17316 128 LDALRAGSISANKASKAYGIPSS 150 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~gIp~s 150 (229)
|..+.+-++|+.+|...+.-...
T Consensus 50 I~~lr~~G~~l~~I~~~l~~~~~ 72 (96)
T cd04768 50 ILFLRELGFSLAEIKELLDTEME 72 (96)
T ss_pred HHHHHHcCCCHHHHHHHHhcCcH
Confidence 77788878899999888876543
No 83
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=96.30 E-value=0.037 Score=43.57 Aligned_cols=81 Identities=17% Similarity=0.194 Sum_probs=62.1
Q ss_pred HcCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHHH-HHHHHHHhCCCcHHHHHHHhCCChHHHHH
Q psy17316 132 RAGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDLE-IALEGIRSGQTTVQRASAEYGIPSGTLYG 209 (229)
Q Consensus 132 ~~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r~-eaV~~~~~~~~s~~eAA~~fgVp~~tv~~ 209 (229)
.....++.++|+..|++.++|.++.++. |.... .|-.+.|+ .|.+.+...++++.++|...|-+-+.-..
T Consensus 22 ~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G~s~~--------~~l~~~Rl~~A~~~L~~t~~~i~eIA~~~Gf~s~s~F~ 93 (127)
T PRK11511 22 LESPLSLEKVSERSGYSKWHLQRMFKKETGHSLG--------QYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLT 93 (127)
T ss_pred cCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHH
Confidence 3455799999999999999999999976 75443 35445566 57888888889999999999988877776
Q ss_pred HHHhhcCCCCC
Q psy17316 210 RCKLSRSTPRP 220 (229)
Q Consensus 210 ~vk~~~~~~~~ 220 (229)
.+=....|-+|
T Consensus 94 r~Fkk~~G~tP 104 (127)
T PRK11511 94 RTFKNYFDVPP 104 (127)
T ss_pred HHHHHHHCcCH
Confidence 65444444444
No 84
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=96.27 E-value=0.012 Score=38.76 Aligned_cols=44 Identities=18% Similarity=0.117 Sum_probs=37.6
Q ss_pred CCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 29 VTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 29 ~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
.+..+|..-...+++++.+. .|+..+|+.+||+.+||++++.++
T Consensus 8 ~~~r~T~~~~~~i~~~~~~~-~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 8 RYCRITKRLEQYILKLLRES-RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred cCCcHHHHHHHHHHHHHhhc-CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 45677777778888888776 799999999999999999998764
No 85
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=96.25 E-value=0.013 Score=39.66 Aligned_cols=39 Identities=33% Similarity=0.541 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
..|.+++.... .+++.+||+++||+.++|.+..+++||.
T Consensus 4 ~lt~~~L~~~f------hlp~~eAA~~Lgv~~T~LKr~CR~~GI~ 42 (52)
T PF02042_consen 4 SLTLEDLSQYF------HLPIKEAAKELGVSVTTLKRRCRRLGIP 42 (52)
T ss_pred ccCHHHHHHHh------CCCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 44555555444 5899999999999999999999999985
No 86
>PRK04217 hypothetical protein; Provisional
Probab=96.23 E-value=0.014 Score=45.53 Aligned_cols=45 Identities=18% Similarity=0.247 Sum_probs=38.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 27 LTVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 27 ~~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
...-.+.+.+++ +++..+...++|+.+||+.+||+++||++.+++
T Consensus 37 ~~p~~~Lt~eer-eai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 37 PKPPIFMTYEEF-EALRLVDYEGLTQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred CCCcccCCHHHH-HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 334567788885 788777767999999999999999999999885
No 87
>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=96.22 E-value=0.059 Score=40.56 Aligned_cols=67 Identities=10% Similarity=0.057 Sum_probs=51.6
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCccc-CCCCCCCCCCCHHH--HHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLA-QPFNASPTAWKPED--LEIALEGIRSGQTTVQRASAEYGIP 203 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~-~~~~~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA~~fgVp 203 (229)
+++.++|+.+||+..||+.|.+ .|+-.. ....+..|.|+.++ ++..|..+.+-+++..++...+...
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~-~Gll~p~~~~~~gyR~Y~~~~~~~l~~I~~lr~~G~~l~eI~~~l~~~ 70 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDK-IGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDNR 70 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcC
Confidence 3788999999999999999987 564322 11123467888776 7888999999999999999877654
No 88
>PF13565 HTH_32: Homeodomain-like domain
Probab=96.22 E-value=0.02 Score=40.65 Aligned_cols=42 Identities=19% Similarity=0.379 Sum_probs=26.6
Q ss_pred cCCCCCCCHHHHHHHHHHHHcC-CCCHHHHHH----HhCC----ChHHHHHH
Q psy17316 113 YGPTKSWNEEILNVALDALRAG-SISANKASK----AYGI----PSSTLYKI 155 (229)
Q Consensus 113 ~G~~~kYs~e~k~~AV~~~~~g-~~S~~~~a~----k~gI----p~sTL~~~ 155 (229)
.|++.+ +++.....++.+.+. ..|..+++. +||| +.+|++++
T Consensus 26 ~Grp~~-~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 26 PGRPRK-DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred CCCCCC-cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 345555 555556666666655 467777755 3453 88889986
No 89
>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=96.21 E-value=0.058 Score=40.49 Aligned_cols=74 Identities=9% Similarity=-0.030 Sum_probs=55.0
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCC-CCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHH
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQP-FNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGR 210 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~-~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~ 210 (229)
+++.++|+.+||+..||+-|-+. |+-.... .....|.|+.+ .++..|..+.+-+++..++...+......+...
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~-Gll~p~~~~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~~~~~~~~~ 77 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDI-GLFKPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTEMEELTAM 77 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCcHHHHHH
Confidence 37899999999999999999985 6432211 12345778765 577888899998899999999888765444443
No 90
>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=96.16 E-value=0.038 Score=41.99 Aligned_cols=67 Identities=13% Similarity=0.178 Sum_probs=50.5
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIP 203 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp 203 (229)
+++.++|+.+|||.+||+-|.+. |+-.........|.|+++ +++..|..+.+-+++..+++..+..+
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~-Gll~~~r~~~g~R~Y~~~dl~~l~~I~~l~~~G~~l~ei~~~~~~~ 70 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESI-GLIPSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQP 70 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCCCCCCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHcCC
Confidence 58899999999999999999984 644222112345778765 56677778888889999999887665
No 91
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=96.16 E-value=0.0071 Score=45.80 Aligned_cols=37 Identities=22% Similarity=0.114 Sum_probs=33.6
Q ss_pred CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 175 KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 175 t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
+.| =.||+++|.-.+++..+||.+.|||++|+|+-++
T Consensus 35 t~e-ElEAlRLvD~~~l~QeeAA~rMgISr~Tfwr~l~ 71 (99)
T COG1342 35 TIE-ELEALRLVDYEGLTQEEAALRMGISRQTFWRLLT 71 (99)
T ss_pred cHH-HHHHHHHHhHhhccHHHHHHHhcccHHHHHHHHH
Confidence 444 4789999999999999999999999999999987
No 92
>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=96.15 E-value=0.056 Score=40.93 Aligned_cols=69 Identities=17% Similarity=0.178 Sum_probs=45.2
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHHH--HHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEIL--NVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~k--~~A 127 (229)
+++.++|+.+||+.+||+.|.+. |.-.|..... |....|++++. ...
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~~-Gll~~~~~~~------------------------------~g~R~y~~~di~~l~~ 49 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEI-GLLKPSRRTE------------------------------NGYRLYTEEDLERLQQ 49 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCC------------------------------CCceeeCHHHHHHHHH
Confidence 57899999999999999999775 4432211111 01234555553 344
Q ss_pred HHHHHcCCCCHHHHHHHhCCCh
Q psy17316 128 LDALRAGSISANKASKAYGIPS 149 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~gIp~ 149 (229)
|..+...++|+.+|........
T Consensus 50 i~~lr~~g~~l~~i~~~~~~~~ 71 (103)
T cd01106 50 ILFLKELGFSLKEIKELLKDPS 71 (103)
T ss_pred HHHHHHcCCCHHHHHHHHHcCc
Confidence 5666667789998888776664
No 93
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=96.14 E-value=0.011 Score=49.91 Aligned_cols=37 Identities=19% Similarity=0.216 Sum_probs=31.0
Q ss_pred HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
..|..+..+|+|+.+||+.+||+++||+++++..++.
T Consensus 163 ~~i~~~~~~g~s~~~iak~lgis~~Tv~r~~k~~~~~ 199 (200)
T PRK13413 163 EKIKKLLDKGTSKSEIARKLGVSRTTLARFLKTRGLR 199 (200)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHhcccC
Confidence 4555666778999999999999999999999977653
No 94
>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=96.13 E-value=0.038 Score=42.62 Aligned_cols=66 Identities=14% Similarity=0.145 Sum_probs=43.6
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
+++.++|+.+|||..||+.|-+..-+..+.... +....|++++ +...
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~gll~~~~r~~-------------------------------~gyR~Y~~~~l~~l~~ 49 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDE-------------------------------NGIRDFTEEDLEWLEF 49 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCC-------------------------------CCCccCCHHHHHHHHH
Confidence 578999999999999999998864332221111 0133455444 3556
Q ss_pred HHHHHcCCCCHHHHHHHhC
Q psy17316 128 LDALRAGSISANKASKAYG 146 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~g 146 (229)
|..+.+-++|+.+|..-+.
T Consensus 50 I~~lr~~G~sL~eI~~~l~ 68 (113)
T cd01109 50 IKCLRNTGMSIKDIKEYAE 68 (113)
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 6777776788888877554
No 95
>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=96.11 E-value=0.043 Score=42.42 Aligned_cols=66 Identities=8% Similarity=0.096 Sum_probs=50.0
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI 202 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV 202 (229)
+++.++|+.+|||.+||+.|-+ .|+-......+..|.|+++ .++..|..+.+-+++..++...+..
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~-~GLl~p~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~l~~ 68 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEE-QGLLVPERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPC 68 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH-CCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4788999999999999999988 4643222122346788765 6778888888888999999887654
No 96
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=96.10 E-value=0.01 Score=44.43 Aligned_cols=32 Identities=6% Similarity=0.087 Sum_probs=26.3
Q ss_pred HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316 40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAH 71 (229)
Q Consensus 40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~ 71 (229)
..|..++++|+|..+||+.+||+++||+++.+
T Consensus 41 ~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 41 LQVAKMLKQGKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 44445556678999999999999999999665
No 97
>PF12728 HTH_17: Helix-turn-helix domain
Probab=96.10 E-value=0.0074 Score=39.74 Aligned_cols=29 Identities=17% Similarity=0.260 Sum_probs=25.7
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTP 78 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~ 78 (229)
+|+.+||..+||+++||++|+++.++...
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g~i~~~ 30 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQGKIPPF 30 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCCeE
Confidence 68999999999999999999998766544
No 98
>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=96.10 E-value=0.013 Score=40.73 Aligned_cols=41 Identities=17% Similarity=0.268 Sum_probs=34.0
Q ss_pred HHHHHHHHHHc--CCCCHHHHHHHhCCChHHHHHHHHHhCCcc
Q psy17316 123 ILNVALDALRA--GSISANKASKAYGIPSSTLYKIARKEGIRL 163 (229)
Q Consensus 123 ~k~~AV~~~~~--g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~ 163 (229)
.+.+|-+.|++ |.+.+.+||.++||+.+|++.|-.+..+..
T Consensus 8 ~rdkA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~~dkW~~ 50 (60)
T PF10668_consen 8 NRDKAFEIYKESNGKIKLKDIAEKLGVSESTIRKWKSRDKWDE 50 (60)
T ss_pred CHHHHHHHHHHhCCCccHHHHHHHHCCCHHHHHHHhhhcchhh
Confidence 45677788874 779999999999999999999988766544
No 99
>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=96.07 E-value=0.051 Score=40.66 Aligned_cols=67 Identities=12% Similarity=0.118 Sum_probs=45.3
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHH--HHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPED--LEIALEGIRSGQTTVQRASAEYGIP 203 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA~~fgVp 203 (229)
+++.++|+.+||+.+||+.|.+ .|+-......+..+.|+.++ +...|..+...+++..+++..+.-.
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~-~Gll~~~~~~~g~r~y~~~dv~~l~~i~~l~~~g~~~~~i~~~l~~~ 69 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEE-KGLLPPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDAR 69 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCcCCCcCCCCCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 4789999999999999999988 45422111123456787664 4455556666668888887765543
No 100
>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=96.06 E-value=0.015 Score=39.93 Aligned_cols=40 Identities=25% Similarity=0.240 Sum_probs=34.7
Q ss_pred HHHHHHHHHH-HhCCCcHHHHHHHhCCChHHHHHHHH-hhcC
Q psy17316 177 EDLEIALEGI-RSGQTTVQRASAEYGIPSGTLYGRCK-LSRS 216 (229)
Q Consensus 177 e~r~eaV~~~-~~~~~s~~eAA~~fgVp~~tv~~~vk-~~~~ 216 (229)
..|.+|++++ ..+.++..++|..+|+|.+|++..++ +.+.
T Consensus 10 p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~a 51 (61)
T PF12840_consen 10 PTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEA 51 (61)
T ss_dssp HHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 5699999999 88999999999999999999999998 4433
No 101
>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=96.06 E-value=0.031 Score=45.01 Aligned_cols=66 Identities=11% Similarity=0.240 Sum_probs=46.9
Q ss_pred CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHH
Q psy17316 49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNV 126 (229)
Q Consensus 49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~ 126 (229)
.|++.++|+.+||+.+||+.|-+. |+-.|.... |....|++++ +..
T Consensus 1 ~~~I~EvA~~~Gvs~~tLRyYE~~-GLl~p~r~~-------------------------------~g~R~Y~~~dl~~l~ 48 (139)
T cd01110 1 ELSVGEVAKRSGVAVSALHFYEQK-GLIASWRNA-------------------------------GNQRRYPRDVLRRIA 48 (139)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHC-CCCCCCcCC-------------------------------CCCeEECHHHHHHHH
Confidence 479999999999999999999887 543231111 1234455555 466
Q ss_pred HHHHHHcCCCCHHHHHHHhC
Q psy17316 127 ALDALRAGSISANKASKAYG 146 (229)
Q Consensus 127 AV~~~~~g~~S~~~~a~k~g 146 (229)
.|..+.+-++|+.+|...+.
T Consensus 49 ~I~~lr~~G~sl~eI~~~l~ 68 (139)
T cd01110 49 FIKVAQRLGLSLAEIAEALA 68 (139)
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 67777888889999887653
No 102
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=96.05 E-value=0.022 Score=37.43 Aligned_cols=42 Identities=12% Similarity=0.072 Sum_probs=37.5
Q ss_pred CCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 170 SPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 170 ~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
.+..+|......|++.|... .|+.++|..+|||.+||+++.+
T Consensus 8 ~~~r~T~~~~~~i~~~~~~~-~s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 8 RYCRITKRLEQYILKLLRES-RSFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred cCCcHHHHHHHHHHHHHhhc-CCHHHHHHHHCCCHHHHHHHHH
Confidence 45567888899999999999 8999999999999999999875
No 103
>PF13309 HTH_22: HTH domain
Probab=96.04 E-value=0.028 Score=39.37 Aligned_cols=40 Identities=15% Similarity=0.230 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHhCC-----CcHHHHHHHhCCChHHHHHHHH
Q psy17316 173 AWKPEDLEIALEGIRSGQ-----TTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 173 ~~t~e~r~eaV~~~~~~~-----~s~~eAA~~fgVp~~tv~~~vk 212 (229)
..+.++|.++|+.+.+.+ -++..+|..+|||..|||+.++
T Consensus 20 ~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YLr 64 (64)
T PF13309_consen 20 RLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYLR 64 (64)
T ss_pred hCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHcC
Confidence 356789999999999865 3689999999999999999764
No 104
>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=96.01 E-value=0.052 Score=41.84 Aligned_cols=65 Identities=9% Similarity=0.137 Sum_probs=47.5
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCc-ccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIR-LAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYG 201 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k-~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fg 201 (229)
+++.++|+.+|||.+||+.|.+. |.- .........|.|+++ +++..|..+.+-+++..++...+.
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~-gll~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~ 68 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKE-GLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAE 68 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 47899999999999999999874 432 211112346788766 566667777877799999988765
No 105
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=95.99 E-value=0.01 Score=54.09 Aligned_cols=38 Identities=13% Similarity=0.176 Sum_probs=31.6
Q ss_pred HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316 38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI 75 (229)
Q Consensus 38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi 75 (229)
+..+++++...+....++|+.+||+++|||+++++|||
T Consensus 288 r~~I~~aL~~~~gn~~~aA~~LGIsR~tLyrklk~~gi 325 (326)
T PRK11608 288 KELLQRSLQQAKFNQKRAAELLGLTYHQLRALLKKHQI 325 (326)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHcCC
Confidence 33455566666668999999999999999999999987
No 106
>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=95.99 E-value=0.044 Score=42.33 Aligned_cols=65 Identities=12% Similarity=0.241 Sum_probs=45.0
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
|++.++|+.+|||.+||+.|-+. |+-.|... . +....|++++ ++..
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~~-GLl~p~r~-~------------------------------~g~R~Y~~~~~~~l~~ 48 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQ-GLLVPERS-A------------------------------NGYRDYDEAAVDRVRQ 48 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHC-CCCCCCcC-C------------------------------CCCeecCHHHHHHHHH
Confidence 68899999999999999999875 55433111 1 1234455554 4666
Q ss_pred HHHHHcCCCCHHHHHHHhC
Q psy17316 128 LDALRAGSISANKASKAYG 146 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~g 146 (229)
|..+.+-++|+.+|..-+.
T Consensus 49 I~~lr~~G~sl~eI~~~l~ 67 (112)
T cd01282 49 IRRLLAAGLTLEEIREFLP 67 (112)
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 7777777788888876553
No 107
>PRK15044 transcriptional regulator SirC; Provisional
Probab=95.98 E-value=0.028 Score=50.86 Aligned_cols=87 Identities=13% Similarity=0.142 Sum_probs=64.3
Q ss_pred HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCC
Q psy17316 39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKS 118 (229)
Q Consensus 39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~k 118 (229)
.+.|..-.....++.++|+++|+++++|.+..+..|.. +. +.
T Consensus 198 ~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~eg~T-~~----------~y--------------------------- 239 (295)
T PRK15044 198 YNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAAEEVS-FS----------KI--------------------------- 239 (295)
T ss_pred HHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHHcCCC-HH----------HH---------------------------
Confidence 44444444568999999999999999999999975321 10 11
Q ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316 119 WNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL 163 (229)
Q Consensus 119 Ys~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~ 163 (229)
|.+.-+..|.+++..+..++.+||.+.|-...+ ..+..|+. |..+
T Consensus 240 ~~~~RL~~A~~LL~~t~~sIseIA~~~GFss~S~FsRaFKk~fG~TP 286 (295)
T PRK15044 240 YLDARMNQAIKLLRMGAGNISQVATMCGYDTPSYFIAIFKRHFKITP 286 (295)
T ss_pred HHHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHHHHHCcCH
Confidence 122345788899999999999999999999977 77777754 6443
No 108
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=95.98 E-value=0.36 Score=41.87 Aligned_cols=113 Identities=10% Similarity=0.164 Sum_probs=83.0
Q ss_pred HHHc-CCCCHHHHHHHcCCChhhHHHHHHHh----CCCCCCCCC-CCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCC
Q psy17316 44 ALRA-GQMSLTKASVSYGIPSTTLWQRAHRL----GIHTPKKEG-PTKSWNEEILNVALDALRAGSISANKASKAYGPTK 117 (229)
Q Consensus 44 ~~~~-g~~S~~~aA~~~gIp~sTL~~~i~~~----gi~~~~~~~-~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~ 117 (229)
+|.+ |-++..++|.-+|++.+||++.++.| |...|..+. +. .|+
T Consensus 99 Ay~QgglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG~i~D----------------------------iGp-- 148 (220)
T PF07900_consen 99 AYDQGGLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTRGTIHD----------------------------IGP-- 148 (220)
T ss_pred HHHcCCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccCCcccc----------------------------cCC--
Confidence 4444 45899999999999999999999976 444443331 11 011
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHH
Q psy17316 118 SWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRAS 197 (229)
Q Consensus 118 kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA 197 (229)
+---|..+|+.|++|. +..+|++.+.=+...+-+.++. | +-|..|.+.+++..++|
T Consensus 149 --~~tHK~~ii~~~l~g~-~~~eiar~t~HS~~av~rYi~~---------------F------~rV~~l~~~~~~~~eia 204 (220)
T PF07900_consen 149 --GVTHKKIIIRLYLKGK-PTPEIARRTNHSPEAVDRYIKD---------------F------KRVLMLYEKGMSPEEIA 204 (220)
T ss_pred --cchHHHHHHHHHHcCC-CHHHHHHHhccCHHHHHHHHHh---------------h------HHhHHHHHcCCCHHHHH
Confidence 1122567789999986 9999999999999888887773 1 12667777889999999
Q ss_pred HHhCCChHHHHHH
Q psy17316 198 AEYGIPSGTLYGR 210 (229)
Q Consensus 198 ~~fgVp~~tv~~~ 210 (229)
.-.|+|..-|-..
T Consensus 205 ~~tg~S~~Lv~eY 217 (220)
T PF07900_consen 205 FITGMSERLVKEY 217 (220)
T ss_pred HHHCCCHHHHHHH
Confidence 9999998766543
No 109
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=95.97 E-value=0.031 Score=50.43 Aligned_cols=86 Identities=15% Similarity=0.139 Sum_probs=63.9
Q ss_pred HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCC
Q psy17316 40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSW 119 (229)
Q Consensus 40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kY 119 (229)
.+|..-.....++.++|+.+|++++||.+..++.|... .+. |
T Consensus 188 ~~I~~~~~~~~sl~~lA~~~gmS~stl~R~Fk~~g~s~-----------~~~---------------------------~ 229 (291)
T PRK15186 188 NIIISDISRKWALKDISDSLYMSCSTLKRKLKQENTSF-----------SEV---------------------------Y 229 (291)
T ss_pred HHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHHcCCCH-----------HHH---------------------------H
Confidence 44444345689999999999999999999999753221 111 1
Q ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316 120 NEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL 163 (229)
Q Consensus 120 s~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~ 163 (229)
..--+..|..++.++..++.+||.+.|-...+ +.+..|++ |...
T Consensus 230 ~~~Rl~~A~~lL~~~~~sI~~IA~~~GY~s~S~Fsr~FK~~~G~TP 275 (291)
T PRK15186 230 LNARMNKATKLLRNSEYNITRVAYMCGYDSASYFTCVFKKHFKTTP 275 (291)
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence 12235778888888888999999999999877 88888765 7544
No 110
>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=95.96 E-value=0.051 Score=40.64 Aligned_cols=23 Identities=13% Similarity=0.219 Sum_probs=21.3
Q ss_pred CCHHHHHHHcCCChhhHHHHHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+++.++|+.+||+.+||+.|.+.
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~~ 23 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEK 23 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 57899999999999999999885
No 111
>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=95.92 E-value=0.041 Score=44.29 Aligned_cols=66 Identities=11% Similarity=0.099 Sum_probs=50.1
Q ss_pred CCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhC
Q psy17316 135 SISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYG 201 (229)
Q Consensus 135 ~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fg 201 (229)
++++.++|+.+||+.+||+-|-+. |+-......+..|.|+++ +++..|..+.+-+++..++...+.
T Consensus 1 ~~~I~EvA~~~Gvs~~tLRyYE~~-GLl~p~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~ 68 (139)
T cd01110 1 ELSVGEVAKRSGVAVSALHFYEQK-GLIASWRNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALA 68 (139)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHC-CCCCCCcCCCCCeEECHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 368999999999999999999985 642221112345778765 677788888888899999998764
No 112
>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=95.91 E-value=0.054 Score=41.15 Aligned_cols=68 Identities=15% Similarity=0.237 Sum_probs=47.2
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
+++.++|+.+||+.+||+.|-+. |+-.|... .+ ....|++++ +...
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~-Gll~~~r~-~~------------------------------g~R~Y~~~dl~~l~~ 49 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESI-GLIPSARS-EA------------------------------NYRLYSEADLSRLEK 49 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCC-CC------------------------------CCeeeCHHHHHHHHH
Confidence 58899999999999999999987 55422111 11 123455555 3555
Q ss_pred HHHHHcCCCCHHHHHHHhCCCh
Q psy17316 128 LDALRAGSISANKASKAYGIPS 149 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~gIp~ 149 (229)
|..+.+-++|+.+|......+.
T Consensus 50 I~~l~~~G~~l~ei~~~~~~~~ 71 (102)
T cd04775 50 IVFLQAGGLPLEEIAGCLAQPH 71 (102)
T ss_pred HHHHHHCCCCHHHHHHHHcCCc
Confidence 6677777889999998776554
No 113
>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=95.91 E-value=0.054 Score=41.52 Aligned_cols=70 Identities=11% Similarity=0.111 Sum_probs=49.4
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCC-CCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGP-TKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNV 126 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~-~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~ 126 (229)
+++.++|+.+|||.+||+.|-+. |+-.|..... + ....|+++. ...
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~-GLi~p~~~~~~n------------------------------gyR~Y~~~~i~~l~ 49 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKI-GLLKPAYVDPDT------------------------------GYRYYSAEQLERLN 49 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc-CCCCCCcCCCCC------------------------------CccccCHHHHHHHH
Confidence 57899999999999999999997 6544422111 1 123444444 456
Q ss_pred HHHHHHcCCCCHHHHHHHhCCChH
Q psy17316 127 ALDALRAGSISANKASKAYGIPSS 150 (229)
Q Consensus 127 AV~~~~~g~~S~~~~a~k~gIp~s 150 (229)
.|..+.+-++|+.+|..-+.-...
T Consensus 50 ~I~~lr~~G~sl~~i~~l~~~~~~ 73 (108)
T cd01107 50 RIKYLRDLGFPLEEIKEILDADND 73 (108)
T ss_pred HHHHHHHcCCCHHHHHHHHhcCCH
Confidence 677888877899999887776654
No 114
>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=95.89 E-value=0.075 Score=44.27 Aligned_cols=71 Identities=13% Similarity=0.195 Sum_probs=55.2
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCc-ccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCChHHH
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIR-LAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIPSGTL 207 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k-~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv 207 (229)
+++.++|+.+|||.+||+.|-+ .|+- .........|.|+++ .++..|..+.+-+++..++...++.+...+
T Consensus 2 ~~I~evA~~~gvs~~tLRyYe~-~GLl~p~~r~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~~~~~~~ 75 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYER-IGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGDDA 75 (172)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCChhH
Confidence 5889999999999999999887 4532 221112356888877 788899999998899999999888665543
No 115
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=95.89 E-value=0.016 Score=43.95 Aligned_cols=34 Identities=21% Similarity=0.327 Sum_probs=28.4
Q ss_pred HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
..+..+.++++|+++||+.+||+++||.|+-+-.
T Consensus 46 ~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~l 79 (94)
T TIGR01321 46 RIVNELLNGNMSQREIASKLGVSIATITRGSNNL 79 (94)
T ss_pred HHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhhc
Confidence 3444556789999999999999999999998754
No 116
>PRK01905 DNA-binding protein Fis; Provisional
Probab=95.89 E-value=0.019 Score=41.60 Aligned_cols=37 Identities=16% Similarity=0.162 Sum_probs=30.5
Q ss_pred HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316 39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI 75 (229)
Q Consensus 39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi 75 (229)
..+++.+...+.++.++|+.+||+++||+++++++|+
T Consensus 40 ~~i~~aL~~~~gn~s~aAr~LGIsrstL~rklkk~gi 76 (77)
T PRK01905 40 PLLEVVMEQAGGNQSLAAEYLGINRNTLRKKLQQHGL 76 (77)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHhCC
Confidence 3344555556668999999999999999999999886
No 117
>PRK04217 hypothetical protein; Provisional
Probab=95.87 E-value=0.019 Score=44.67 Aligned_cols=40 Identities=20% Similarity=0.223 Sum_probs=35.1
Q ss_pred CCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 172 TAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 172 r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
...+++++ +|+..+..+++++.++|..+|||.+|||+.++
T Consensus 41 ~~Lt~eer-eai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~ 80 (110)
T PRK04217 41 IFMTYEEF-EALRLVDYEGLTQEEAGKRMGVSRGTVWRALT 80 (110)
T ss_pred ccCCHHHH-HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 45577776 88888887889999999999999999999987
No 118
>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=95.86 E-value=0.021 Score=37.91 Aligned_cols=34 Identities=21% Similarity=0.172 Sum_probs=24.7
Q ss_pred HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
..++..+.-.|+|..+||+.+||+.+|++.|+.+
T Consensus 16 r~i~~l~~~~g~s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 16 REIFLLRYFQGMSYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp HHHHHHHHTS---HHHHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 4455565566899999999999999999999886
No 119
>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=95.85 E-value=0.064 Score=41.12 Aligned_cols=69 Identities=7% Similarity=0.038 Sum_probs=52.5
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCC--CCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCChH
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPF--NASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIPSG 205 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~--~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp~~ 205 (229)
+++.++|+.+|||.+||+-|.+. |+-..... ....|.|+++ +++..|..+.+-+++..++...+.-...
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~-GLi~p~~~~~~ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l~~~~~~ 73 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKI-GLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADND 73 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc-CCCCCCcCCCCCCccccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCCH
Confidence 47889999999999999999985 64332211 1346788765 5677788888888999999998877654
No 120
>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=95.85 E-value=0.012 Score=37.62 Aligned_cols=46 Identities=15% Similarity=0.290 Sum_probs=31.7
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHH
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIAL 183 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV 183 (229)
+|+.++|+.+||+.+||++|++.-.++... .+....|+.++..+-+
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g~i~~~~--~g~~~~~~~~~l~~~~ 47 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEGELPAYR--VGRHYRIPREDVDEYL 47 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcCCCCeEE--eCCeEEEeHHHHHHHH
Confidence 589999999999999999999854333322 1334556665555443
No 121
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=95.84 E-value=0.074 Score=40.14 Aligned_cols=80 Identities=14% Similarity=0.165 Sum_probs=58.0
Q ss_pred cCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHH-HHHHHHHHhCCCcHHHHHHHhCCChHHHHHH
Q psy17316 133 AGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDL-EIALEGIRSGQTTVQRASAEYGIPSGTLYGR 210 (229)
Q Consensus 133 ~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r-~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~ 210 (229)
....++.++|+.+|++.++|.+..+++ |.... .|=...| ..|.+.+..+++++.++|...|-+-++-...
T Consensus 19 ~~~~~~~~lA~~~~~S~~~l~r~f~~~~g~s~~--------~~i~~~Rl~~a~~~L~~~~~~i~~iA~~~Gf~~~s~f~~ 90 (107)
T PRK10219 19 DQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLG--------DYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSR 90 (107)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHHccCCCHHHHHHHHCCCCHHHHHH
Confidence 344799999999999999999999886 65443 3433444 4566677777899999999999987776655
Q ss_pred HHhhcCCCCC
Q psy17316 211 CKLSRSTPRP 220 (229)
Q Consensus 211 vk~~~~~~~~ 220 (229)
+=...-|-+|
T Consensus 91 ~Fk~~~G~tP 100 (107)
T PRK10219 91 VFRRQFDRTP 100 (107)
T ss_pred HHHHHHCcCH
Confidence 4333334444
No 122
>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=95.83 E-value=0.058 Score=42.51 Aligned_cols=68 Identities=7% Similarity=0.014 Sum_probs=50.9
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIP 203 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp 203 (229)
+++.++|+.+||+.+||+-|-+.--+.......+..|.|+++ +++..|..+.+-+++..++...+...
T Consensus 1 ~~I~e~a~~~gvs~~tlR~Ye~~Gll~~~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~ 70 (126)
T cd04785 1 LSIGELARRTGVNVETIRYYESIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLALS 70 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHhhh
Confidence 478999999999999999988842232221112346788766 67788888888889999999988753
No 123
>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=95.82 E-value=0.051 Score=40.94 Aligned_cols=67 Identities=13% Similarity=0.185 Sum_probs=44.9
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
|++.++|+.+||+..||+.|.+..-+..+.....+ ...|+++. +...
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~GLl~p~~r~~~g-------------------------------~r~Y~~~dv~~l~~ 49 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGLLPEGRRLAPN-------------------------------QAEYSEAHVERLRL 49 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCcCCCCC-------------------------------CeecCHHHHHHHHH
Confidence 68899999999999999999997444332222111 23455544 3555
Q ss_pred HHHHHc-CCCCHHHHHHHhCC
Q psy17316 128 LDALRA-GSISANKASKAYGI 147 (229)
Q Consensus 128 V~~~~~-g~~S~~~~a~k~gI 147 (229)
|..+.. -++|+.+|...+..
T Consensus 50 I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 50 IRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred HHHHHHHcCCCHHHHHHHHHh
Confidence 666664 56799998887665
No 124
>PRK13503 transcriptional activator RhaS; Provisional
Probab=95.75 E-value=0.16 Score=44.19 Aligned_cols=80 Identities=16% Similarity=0.187 Sum_probs=61.2
Q ss_pred HcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHH-H
Q psy17316 46 RAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEE-I 123 (229)
Q Consensus 46 ~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e-~ 123 (229)
-...+|+.++|+.+|+++++|.+-.++. |.. +-. |=.+ -
T Consensus 184 ~~~~~tl~~lA~~~~lS~~~l~r~Fk~~~G~S------------~~~---------------------------yi~~~R 224 (278)
T PRK13503 184 FAEEVNWEALADQFSLSLRTLHRQLKQQTGLT------------PQR---------------------------YLNRLR 224 (278)
T ss_pred hcCCCCHHHHHHHHCCCHHHHHHHHHHHhCcC------------HHH---------------------------HHHHHH
Confidence 3468999999999999999999999874 443 111 1112 2
Q ss_pred HHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCccc
Q psy17316 124 LNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRLA 164 (229)
Q Consensus 124 k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~~ 164 (229)
+.+|.+++..+..|+.+||.+.|=+..+ ..+.-|++ |+.+.
T Consensus 225 l~~A~~LL~~~~~sI~eIA~~~GF~~~s~F~r~FKk~~G~TP~ 267 (278)
T PRK13503 225 LLKARHLLRHSDASVTDIAYRCGFGDSNHFSTLFRREFSWSPR 267 (278)
T ss_pred HHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCHH
Confidence 5788888888888999999999999987 88877765 76553
No 125
>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=95.75 E-value=0.058 Score=40.66 Aligned_cols=70 Identities=13% Similarity=0.096 Sum_probs=49.9
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHh-CCCcHHHHHHHhCCChHH
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRS-GQTTVQRASAEYGIPSGT 206 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~-~~~s~~eAA~~fgVp~~t 206 (229)
+++.++|+.+||+.+||+.|.+. |+-......+..|.|+++ +++..|..+.+ -+++..++....+...+.
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~-Gll~p~r~~~g~R~Y~~~dv~~l~~I~~L~~~~G~~l~ei~~~l~~~~~~ 73 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEI-GLVSPERSEGRYRLYSEEDLKRLERILRLREVLGFSLQEVTHFLERPLEP 73 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCcCCCCCEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHhccccc
Confidence 47889999999999999999873 643322122346678755 46666777777 678888888877765543
No 126
>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=95.74 E-value=0.15 Score=38.24 Aligned_cols=68 Identities=15% Similarity=0.109 Sum_probs=47.3
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
+++.++|+.+||+..||+.|-+. |+-.|.....+ ....|++++ ....
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~-Gll~p~~~~~~------------------------------gyR~Y~~~~~~~l~~ 49 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDKI-GLFKPEIVKEN------------------------------GYRYYTLEQFEQLDI 49 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCCC------------------------------CCccCCHHHHHHHHH
Confidence 47899999999999999999774 55433221111 134555555 4666
Q ss_pred HHHHHcCCCCHHHHHHHhCCC
Q psy17316 128 LDALRAGSISANKASKAYGIP 148 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~gIp 148 (229)
|..+..-++|+.+|..-+.-.
T Consensus 50 I~~lr~~G~~l~eI~~~l~~~ 70 (97)
T cd04782 50 ILLLKELGISLKEIKDYLDNR 70 (97)
T ss_pred HHHHHHcCCCHHHHHHHHhcC
Confidence 778888888999998866544
No 127
>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=95.73 E-value=0.068 Score=40.25 Aligned_cols=66 Identities=12% Similarity=0.230 Sum_probs=48.3
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCC-cccCCCCCCCCCCCHH--HHHHHHHHHHh-CCCcHHHHHHHhCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGI-RLAQPFNASPTAWKPE--DLEIALEGIRS-GQTTVQRASAEYGI 202 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~-k~~~~~~~~~r~~t~e--~r~eaV~~~~~-~~~s~~eAA~~fgV 202 (229)
+++.++|+++||+.+||+.|.+ .|+ ..........+.|+++ .++..|+.+.+ -+++..++...+..
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~-~GLl~p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLR-EGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 4789999999999999999998 443 2211111234667665 56777778876 57999999998876
No 128
>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=95.72 E-value=0.029 Score=35.75 Aligned_cols=40 Identities=23% Similarity=0.285 Sum_probs=30.4
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
..++++..... ++--.++|..+||+.+|++.+|+++|+++
T Consensus 10 ~l~~~~~~~~~-~~~~~~~~~~~ia~~~~~s~~~i~~~~~~ 49 (55)
T cd06171 10 KLPEREREVIL-LRFGEGLSYEEIAEILGISRSTVRQRLHR 49 (55)
T ss_pred hCCHHHHHHHH-HHHhcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34555544444 44345789999999999999999999886
No 129
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=95.72 E-value=0.022 Score=43.17 Aligned_cols=42 Identities=10% Similarity=0.155 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhcCCC
Q psy17316 177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSRSTP 218 (229)
Q Consensus 177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~~~~ 218 (229)
..|..++..+.++++|++++|.++|||.+||-++-+....++
T Consensus 42 ~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk~~~ 83 (94)
T TIGR01321 42 GDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNNLKTMD 83 (94)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhhcccCC
Confidence 357888888889999999999999999999999988554443
No 130
>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=95.71 E-value=0.076 Score=40.37 Aligned_cols=66 Identities=12% Similarity=0.136 Sum_probs=48.6
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI 202 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV 202 (229)
+++.++|+.+|||.+||+-|-+. |.-.........|.|+++ +++..|+.+.+-+++..++...+.-
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~-Gll~~~r~~~g~R~Y~~~~l~~l~~I~~l~~~G~~l~ei~~~l~~ 69 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKL-GLITGTRNANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQG 69 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCcCCCCCeeCCHHHHHHHHHHHHHHHCCCCHHHHHHHHcC
Confidence 58899999999999999999884 543222112346788766 5666777888877999998876643
No 131
>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=95.70 E-value=0.028 Score=36.21 Aligned_cols=45 Identities=22% Similarity=0.197 Sum_probs=31.5
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHH
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEI 181 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~e 181 (229)
+|+.++|+.+||+.+||+.|+++-.+.... ..+..+.|++++...
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~l~~~~-~~~~~~~y~~~~v~~ 45 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGLLSPAR-TEGGYRLYSDADLER 45 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCCCCCCc-CCCCCEEeCHHHHHH
Confidence 478999999999999999999854333211 123456788766544
No 132
>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=95.69 E-value=0.051 Score=41.76 Aligned_cols=26 Identities=23% Similarity=0.472 Sum_probs=22.8
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
|++.++|+.+|||..||+.|-+. |.-
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~-Gll 26 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKE-GLL 26 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCC
Confidence 68999999999999999999886 543
No 133
>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=95.68 E-value=0.072 Score=40.47 Aligned_cols=65 Identities=15% Similarity=0.232 Sum_probs=44.1
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
+++.++|+.+|||.+||+.|-+. |.-.|.... +....|++++ +...
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~-Gll~~~r~~-------------------------------~g~R~Y~~~~l~~l~~ 49 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKL-GLITGTRNA-------------------------------NGYRLYPDSDLQRLLL 49 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCcCC-------------------------------CCCeeCCHHHHHHHHH
Confidence 68899999999999999999886 543331111 1234455554 3456
Q ss_pred HHHHHcCCCCHHHHHHHhC
Q psy17316 128 LDALRAGSISANKASKAYG 146 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~g 146 (229)
|..+.+-++|+.+|...+.
T Consensus 50 I~~l~~~G~~l~ei~~~l~ 68 (102)
T cd04789 50 IQQLQAGGLSLKECLACLQ 68 (102)
T ss_pred HHHHHHCCCCHHHHHHHHc
Confidence 6777776788888866553
No 134
>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=95.68 E-value=0.074 Score=41.50 Aligned_cols=67 Identities=16% Similarity=0.196 Sum_probs=51.9
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIP 203 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp 203 (229)
+++.++|+++|||..||+-|-+. |.-......+..|.|+++ +++..|..+.+-+++..++...++-.
T Consensus 1 m~IgevA~~~gvs~~tlRyYe~~-GLl~p~~~~~gyR~Y~~~~l~~l~~I~~lr~~G~~L~eI~~~l~~~ 69 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEEK-GLIASIGRRGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHD 69 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 47899999999999999999884 543222122356788765 67788889999889999999988765
No 135
>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=95.66 E-value=0.064 Score=41.87 Aligned_cols=67 Identities=13% Similarity=0.257 Sum_probs=47.4
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
|++.++|+.+|||..||+.|-+. |+-.|.... |....|++++ ++..
T Consensus 1 m~IgevA~~~gvs~~tlRyYe~~-GLl~p~~~~-------------------------------~gyR~Y~~~~l~~l~~ 48 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEEK-GLIASIGRR-------------------------------GLRRQYDPQVLDRLAL 48 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCcCC-------------------------------CCceecCHHHHHHHHH
Confidence 68999999999999999999887 443231111 1234455555 4566
Q ss_pred HHHHHcCCCCHHHHHHHhCCC
Q psy17316 128 LDALRAGSISANKASKAYGIP 148 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~gIp 148 (229)
|..+..-++|+.+|.+-++-.
T Consensus 49 I~~lr~~G~~L~eI~~~l~~~ 69 (120)
T cd04781 49 IALGRAAGFSLDEIQAMLSHD 69 (120)
T ss_pred HHHHHHcCCCHHHHHHHHhcc
Confidence 778888788999998877654
No 136
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=95.61 E-value=0.021 Score=53.55 Aligned_cols=39 Identities=21% Similarity=0.319 Sum_probs=31.3
Q ss_pred HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
+..+.+++...+....++|+.+||+++|||+++++||+.
T Consensus 419 ~~~i~~al~~~~gn~~~aA~~LGisr~tL~rkl~~~~i~ 457 (457)
T PRK11361 419 KRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEYGID 457 (457)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHhCCC
Confidence 333444555555689999999999999999999999874
No 137
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=95.61 E-value=0.061 Score=48.22 Aligned_cols=88 Identities=11% Similarity=0.093 Sum_probs=63.6
Q ss_pred HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCC
Q psy17316 37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPT 116 (229)
Q Consensus 37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~ 116 (229)
.+...|+.-....+++.++|..+|+++++|.+..++.|.. +.
T Consensus 146 ~v~~yI~~~~~~~lsl~~lA~~~g~S~~~L~R~Fk~~G~S------------~~-------------------------- 187 (274)
T PRK09978 146 RVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETS------------YS-------------------------- 187 (274)
T ss_pred HHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHhcCCC------------HH--------------------------
Confidence 3345555445568999999999999999999999865321 11
Q ss_pred CCCCH-HHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316 117 KSWNE-EILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL 163 (229)
Q Consensus 117 ~kYs~-e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~ 163 (229)
.|-. .-+..|.+++..+..|+.+||...|-...+ +.+..|++ |+.+
T Consensus 188 -~yl~~~Rl~~A~~LL~~t~~sI~eIA~~~GF~s~S~Fsr~FKk~~G~TP 236 (274)
T PRK09978 188 -QLLTECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTP 236 (274)
T ss_pred -HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence 1111 224677888887888999999999999866 77777765 7544
No 138
>PRK01381 Trp operon repressor; Provisional
Probab=95.57 E-value=0.015 Score=44.48 Aligned_cols=35 Identities=20% Similarity=0.271 Sum_probs=29.8
Q ss_pred HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
..++..+..|++|+++||.++||+.+||.|=.+.+
T Consensus 45 ~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~L 79 (99)
T PRK01381 45 VRIVEELLRGELSQREIKQELGVGIATITRGSNSL 79 (99)
T ss_pred HHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHHh
Confidence 46677778999999999999999999999866643
No 139
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=95.56 E-value=0.022 Score=44.09 Aligned_cols=35 Identities=14% Similarity=0.084 Sum_probs=32.4
Q ss_pred HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
+=.||++++.-.++++.+||.+.|||++|+++.+.
T Consensus 45 dElEAiRL~D~egl~QeeaA~~MgVSR~T~~ril~ 79 (106)
T PF02001_consen 45 DELEAIRLVDYEGLSQEEAAERMGVSRPTFQRILE 79 (106)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHcCCcHHHHHHHHH
Confidence 34789999999999999999999999999999886
No 140
>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=95.55 E-value=0.065 Score=42.27 Aligned_cols=66 Identities=12% Similarity=0.085 Sum_probs=44.3
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
|++.++|+.+||+..||+.|-+..-+..+.... +....|++++ +...
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~GLl~~~~r~~-------------------------------~g~R~Y~~~~~~~l~~ 49 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSD-------------------------------NGYRVYNQRDIEELRF 49 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCC-------------------------------CCceecCHHHHHHHHH
Confidence 689999999999999999998873333221111 0133455444 4556
Q ss_pred HHHHHcCCCCHHHHHHHhC
Q psy17316 128 LDALRAGSISANKASKAYG 146 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~g 146 (229)
|..+..-++|+.+|..-+.
T Consensus 50 I~~lr~~G~sL~eI~~~l~ 68 (127)
T cd01108 50 IRRARDLGFSLEEIRELLA 68 (127)
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 6777777788888877654
No 141
>PRK15185 transcriptional regulator HilD; Provisional
Probab=95.53 E-value=0.061 Score=49.03 Aligned_cols=87 Identities=18% Similarity=0.165 Sum_probs=63.2
Q ss_pred HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCC
Q psy17316 39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKS 118 (229)
Q Consensus 39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~k 118 (229)
...|+.-.....|+.++|+.+|+++++|.++.+.+|... . +..
T Consensus 212 ~~~I~~n~~~~~SledLA~~lgmS~~tL~R~FK~~G~S~---~--------~yl-------------------------- 254 (309)
T PRK15185 212 YNIISSSPSRQWKLTDVADHIFMSTSTLKRKLAEEGTSF---S--------DIY-------------------------- 254 (309)
T ss_pred HHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHHcCCCH---H--------HHH--------------------------
Confidence 344443344678999999999999999999998654431 0 001
Q ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316 119 WNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL 163 (229)
Q Consensus 119 Ys~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~ 163 (229)
....+..|.+++..+..|+.+||...|-...+ +.+..|++ |..+
T Consensus 255 -~~~Ri~~A~~LL~~t~~sIseIA~~~GFss~S~FsR~FKk~~G~TP 300 (309)
T PRK15185 255 -LSARMNQAAKLLRIGNHNVNAVALKCGYDSTSYFIQCFKKYFKTTP 300 (309)
T ss_pred -HHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence 11235778888888889999999999998866 88888765 6443
No 142
>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=95.52 E-value=0.091 Score=39.66 Aligned_cols=66 Identities=15% Similarity=0.140 Sum_probs=46.9
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHH--HHHHHHHHHh-CCCcHHHHHHHhCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPED--LEIALEGIRS-GQTTVQRASAEYGI 202 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~--r~eaV~~~~~-~~~s~~eAA~~fgV 202 (229)
+++.++|+.+||+.+||+.|.+ .|+-......+..+.|+.++ ++..|..+.+ -+++..++...+..
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~-~Gli~p~r~~~g~R~Ys~~dv~~l~~I~~L~~~~G~~l~~i~~~l~l 70 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDR-LGLVSPARTNGGGRRYSNNDLELLRQVQRLSQDEGFNLAGIKRIIEL 70 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH-CCCCCCCcCCCCCeeECHHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 4789999999999999999987 56432211123457787664 4455556666 67999999887655
No 143
>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=95.52 E-value=0.041 Score=35.94 Aligned_cols=38 Identities=16% Similarity=0.174 Sum_probs=29.7
Q ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
++.+.. ++..+. +++|..+||+.+||+.+|++.++++.
T Consensus 2 ~~~e~~-i~~~~~-~~~s~~eia~~l~~s~~tv~~~~~~~ 39 (57)
T cd06170 2 TPRERE-VLRLLA-EGKTNKEIADILGISEKTVKTHLRNI 39 (57)
T ss_pred CHHHHH-HHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 344444 555554 67899999999999999999998863
No 144
>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=95.50 E-value=0.076 Score=40.84 Aligned_cols=66 Identities=12% Similarity=0.156 Sum_probs=44.1
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
+++.++|+.+||+..||+.|-+. |.-.|..... |....|++++ ++..
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~~-GLl~p~~r~~------------------------------~g~R~Y~~~~l~~l~~ 49 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLR-GLLHPVARTE------------------------------GGYGLFDDCALQRLRF 49 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCcCC------------------------------CCCeecCHHHHHHHHH
Confidence 47899999999999999999887 5433321111 1234455555 4556
Q ss_pred HHHHHcCCCCHHHHHHHhC
Q psy17316 128 LDALRAGSISANKASKAYG 146 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~g 146 (229)
|..+.+-++|+.+|.....
T Consensus 50 I~~lr~~G~~l~~I~~~l~ 68 (107)
T cd01111 50 VRAAFEAGIGLDELARLCR 68 (107)
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 7777777778888876553
No 145
>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=95.46 E-value=0.1 Score=40.63 Aligned_cols=67 Identities=10% Similarity=0.062 Sum_probs=49.7
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcc-cCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRL-AQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIP 203 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~-~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp 203 (229)
+++.++|+.+||+..||+-|-+ .|.-. .....+..|.|+++ .++..|..+.+-+++..++...++..
T Consensus 1 ~~I~eva~~~gvs~~tLRyYe~-~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~~~ 70 (123)
T cd04770 1 MKIGELAKAAGVSPDTIRYYER-IGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLR 70 (123)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCCCCCCCCccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhh
Confidence 4789999999999999988777 35322 11112346788765 56778888888889999999888653
No 146
>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=95.45 E-value=0.082 Score=40.59 Aligned_cols=66 Identities=14% Similarity=0.228 Sum_probs=46.7
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCC-CCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPF-NASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI 202 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~-~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV 202 (229)
+++.++|+.+|||..||+.|.+. |.-..... .+..|.|+++ .++..|..+.+-+++..++...+..
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~-Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~~ 69 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKE-GLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQ 69 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 47899999999999999999884 54222111 1345678766 4666777777777888888776653
No 147
>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=95.44 E-value=0.083 Score=39.82 Aligned_cols=26 Identities=15% Similarity=0.213 Sum_probs=22.6
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
+++.++|+.+||+.+||+.|.+. |+-
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~-Gll 26 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEI-GLV 26 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCC
Confidence 57899999999999999999875 544
No 148
>PRK15115 response regulator GlrR; Provisional
Probab=95.43 E-value=0.022 Score=53.24 Aligned_cols=41 Identities=15% Similarity=0.186 Sum_probs=32.6
Q ss_pred HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316 37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHT 77 (229)
Q Consensus 37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~ 77 (229)
++..+.+++...+....++|+.+||+++|||+++++||+..
T Consensus 399 E~~~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~~~~~~~ 439 (444)
T PRK15115 399 ELNYLRKLLQITKGNVTHAARMAGRNRTEFYKLLSRHELDA 439 (444)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhCCCc
Confidence 33444445555555899999999999999999999999963
No 149
>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=95.41 E-value=0.071 Score=42.12 Aligned_cols=66 Identities=9% Similarity=0.102 Sum_probs=44.8
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
+++.++|+.+||+.+||+.|-+. |+-.|.... ....|++++ +++.
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE~~-GLl~p~r~~--------------------------------G~R~Ys~~dv~rL~~ 48 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWERH-GLIKPARRN--------------------------------GQRLYSNNDLKRLRF 48 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCcCCC--------------------------------CcEEECHHHHHHHHH
Confidence 68999999999999999999997 443332211 234555555 3455
Q ss_pred HHHHHc-CCCCHHHHHHHhCCC
Q psy17316 128 LDALRA-GSISANKASKAYGIP 148 (229)
Q Consensus 128 V~~~~~-g~~S~~~~a~k~gIp 148 (229)
|..+.. .++++.+|.....+-
T Consensus 49 I~~L~~e~G~~l~eI~~~L~l~ 70 (120)
T cd04767 49 IKKLINEKGLNIAGVKQILSMY 70 (120)
T ss_pred HHHHHHHcCCCHHHHHHHHHhC
Confidence 666655 667888887765544
No 150
>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=95.39 E-value=0.091 Score=41.73 Aligned_cols=66 Identities=15% Similarity=0.104 Sum_probs=50.3
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCc-ccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIR-LAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI 202 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k-~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV 202 (229)
+++.++|+.+||+..||+-|-+. |+- .........|.|+++ +++..|..+.+-+++..++...+..
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~~-GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~ 70 (131)
T TIGR02043 2 FQIGELAKLCGVTSDTLRFYEKN-GLIKPAGRTDSGYRLYTDEDQKRLRFILKAKELGFTLDEIKELLSI 70 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 58899999999999999999985 532 221112346788755 6778888888888999999988764
No 151
>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=95.36 E-value=0.095 Score=41.31 Aligned_cols=65 Identities=8% Similarity=0.074 Sum_probs=49.0
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcc-cCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRL-AQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYG 201 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~-~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fg 201 (229)
+++.++|+++||+..||+-|-+. |.-. ........|.|+++ +++..|..+.+=+++..++...+.
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~-GLl~~~~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~ 68 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEEI-GLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLA 68 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 47899999999999999999884 5322 21112346778765 567778888888899999998775
No 152
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=95.35 E-value=0.017 Score=42.40 Aligned_cols=40 Identities=10% Similarity=0.243 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
|=++-.+++.+-+.+.+.+++++|+.||||+|||++=+..
T Consensus 3 yIeeR~i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvte 42 (82)
T PF12116_consen 3 YIEERVIEIANYIIETKATVRQAAKVFGVSKSTVHKDVTE 42 (82)
T ss_dssp THHHHHHHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHH
Confidence 3345556777777788999999999999999999987653
No 153
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).
Probab=95.34 E-value=0.025 Score=52.93 Aligned_cols=39 Identities=23% Similarity=0.334 Sum_probs=31.5
Q ss_pred HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
+..+.+++...+..+.++|+.+||+++|||+++++||+.
T Consensus 407 ~~~i~~al~~~~gn~~~aA~~Lgisr~tl~rkl~~~~i~ 445 (445)
T TIGR02915 407 REAVRKAIARVDGNIARAAELLGITRPTLYDLMKKHGIK 445 (445)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence 334445555556689999999999999999999999873
No 154
>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=95.32 E-value=0.11 Score=40.81 Aligned_cols=67 Identities=12% Similarity=0.091 Sum_probs=51.5
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcc-cCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRL-AQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIP 203 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~-~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp 203 (229)
+++.++|+.+||+..||+-|-+ .|.-. .....+..|.|+++ .++..|..+.+-+++..++...++..
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~-~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~ 70 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYYQR-RGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELD 70 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 4789999999999999988866 45322 22112356888877 66778888899889999999988765
No 155
>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=95.31 E-value=0.053 Score=35.40 Aligned_cols=32 Identities=16% Similarity=0.115 Sum_probs=27.2
Q ss_pred HHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 180 EIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 180 ~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
.+++..+. +++++.++|..++||..||+.+++
T Consensus 6 ~~i~~~~~-~~~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 6 REVLRLLA-EGKTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred HHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 33776655 559999999999999999999987
No 156
>PF12728 HTH_17: Helix-turn-helix domain
Probab=95.31 E-value=0.027 Score=36.96 Aligned_cols=46 Identities=24% Similarity=0.283 Sum_probs=31.0
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHH
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIAL 183 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV 183 (229)
+|+.++|+.+||+.+|+++|++.-.++... .++...|..++..+-+
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g~i~~~~--~g~~~~~~~~~l~~~~ 47 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQGKIPPFK--IGRKWRIPKSDLDRWL 47 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCCeEE--eCCEEEEeHHHHHHHH
Confidence 589999999999999999999865543331 2233445554444433
No 157
>PRK13501 transcriptional activator RhaR; Provisional
Probab=95.30 E-value=0.27 Score=43.37 Aligned_cols=88 Identities=16% Similarity=0.139 Sum_probs=66.4
Q ss_pred HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCC
Q psy17316 38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPT 116 (229)
Q Consensus 38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~ 116 (229)
+..+|+.-....+++.++|+.+|+++++|.+..++. |.. +-.. +
T Consensus 181 i~~~I~~~~~e~~sl~~lA~~~~lS~~~l~r~Fk~~~G~T------------~~qy---i-------------------- 225 (290)
T PRK13501 181 IMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMS------------ISHY---L-------------------- 225 (290)
T ss_pred HHHHHHHhhccCCCHHHHHHHHCcCHHHHHHHHHHHHCcC------------HHHH---H--------------------
Confidence 466666666678999999999999999999999974 332 1111 0
Q ss_pred CCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316 117 KSWNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL 163 (229)
Q Consensus 117 ~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~ 163 (229)
.+--+.+|.+++..+..|+.+||.+.|=+..+ ..+..|++ |...
T Consensus 226 ---~~~Ri~~A~~LL~~t~~sI~eIA~~~GF~~~s~F~r~FKk~~G~TP 271 (290)
T PRK13501 226 ---RQIRLCHAKCLLRGSEHRISDIAARCGFEDSNYFSAVFTREAGMTP 271 (290)
T ss_pred ---HHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence 01135788889999989999999999999877 77777765 6544
No 158
>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=95.28 E-value=0.12 Score=40.12 Aligned_cols=67 Identities=9% Similarity=0.079 Sum_probs=50.4
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIP 203 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp 203 (229)
+++.++|+.+|||..||+-|.+. |.-.........|.|+++ .++..|..+.+-+++..++...+...
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~~-GLi~p~~~~~~yR~Y~~~d~~~l~~I~~lr~~G~sl~eI~~~l~~~ 69 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEK-GLLPSPKRSGNYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGH 69 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 57899999999999999999884 542221112245778665 56778888999999999999887653
No 159
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=95.28 E-value=0.07 Score=44.79 Aligned_cols=62 Identities=11% Similarity=0.139 Sum_probs=44.8
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHH--HHHHHHHHHhCCCcHHHHHH
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPED--LEIALEGIRSGQTTVQRASA 198 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA~ 198 (229)
+++.++|+.+||+..||++|.+..++...+. .+..|.|++++ +++-|..+.+-+|+..++-.
T Consensus 1 mti~evA~~lGVS~~TLRrw~k~g~L~~~R~-~~G~R~y~~~dl~~L~~I~~l~~~Gm~i~~i~~ 64 (175)
T PRK13182 1 MKTPFVAKKLGVSPKTVQRWVKQLNLPCEKN-EYGHYIFTEEDLQLLEYVKSQIEEGQNMQDTQK 64 (175)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCCCCcC-CCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 4789999999999999999999888754321 23357787664 44455555566688888755
No 160
>PRK15043 transcriptional regulator MirA; Provisional
Probab=95.26 E-value=0.082 Score=46.61 Aligned_cols=68 Identities=12% Similarity=0.071 Sum_probs=52.0
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIP 203 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp 203 (229)
+++.++|+.+||+..||+.|.+++|.-......+..|-|+++ +++..|..+.+.+++..++...+.-.
T Consensus 4 ytIgeVA~~~GVs~~TLR~wErr~GLL~P~Rt~~G~R~Ys~~dv~rL~~I~~l~~~G~~i~eIk~ll~~~ 73 (243)
T PRK15043 4 YTIGEVALLCDINPVTLRAWQRRYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSNE 73 (243)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCCCCCccCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 589999999999999999999888854322122446778766 56666777788889999998877543
No 161
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=95.23 E-value=0.025 Score=54.92 Aligned_cols=40 Identities=28% Similarity=0.394 Sum_probs=30.8
Q ss_pred HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
++..+-+++...+-+...+|+.+||+++|||+|+++|++.
T Consensus 521 Ek~~I~~aL~~~~gn~~~aAk~LgIsrttL~rKlkk~~l~ 560 (560)
T COG3829 521 EKHLIREALERHGGNKSKAAKELGISRTTLYRKLKKYGLR 560 (560)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhcCC
Confidence 3333334444445589999999999999999999999863
No 162
>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=95.23 E-value=0.1 Score=41.45 Aligned_cols=66 Identities=11% Similarity=0.109 Sum_probs=45.7
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
+++.++|+.+||+..||+.|-+. |+-.|..... +....|++++ ++..
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~~-GLl~p~~r~~------------------------------~gyR~Y~~~~l~~l~~ 50 (131)
T TIGR02043 2 FQIGELAKLCGVTSDTLRFYEKN-GLIKPAGRTD------------------------------SGYRLYTDEDQKRLRF 50 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCcCC------------------------------CCceecCHHHHHHHHH
Confidence 68999999999999999999987 5433321111 0134455544 4566
Q ss_pred HHHHHcCCCCHHHHHHHhC
Q psy17316 128 LDALRAGSISANKASKAYG 146 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~g 146 (229)
|..+.+-++|+.+|..-+.
T Consensus 51 I~~lr~~G~sl~eI~~~l~ 69 (131)
T TIGR02043 51 ILKAKELGFTLDEIKELLS 69 (131)
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 7777777789998887665
No 163
>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=95.21 E-value=0.1 Score=39.42 Aligned_cols=28 Identities=29% Similarity=0.413 Sum_probs=23.4
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTP 78 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~ 78 (229)
+++.++|+.+||+.+||+.|.+ .|+-.|
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~-~Gli~p 29 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDR-LGLVSP 29 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH-CCCCCC
Confidence 5789999999999999999987 565433
No 164
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=95.21 E-value=0.05 Score=36.43 Aligned_cols=41 Identities=15% Similarity=0.132 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+.|.+|.+-.+-.+...+.+...+|..|||+++|+.++++.
T Consensus 2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~ 42 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHE 42 (53)
T ss_pred CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHH
Confidence 45667776666677777889999999999999999999886
No 165
>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=95.20 E-value=0.11 Score=40.80 Aligned_cols=67 Identities=10% Similarity=0.074 Sum_probs=45.7
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
|++.++|+.+||+..||+.|-+..-+..+.... |....|++++ +...
T Consensus 1 ~~I~e~a~~~gvs~~tlR~Ye~~Gll~~~~r~~-------------------------------~g~R~Y~~~~l~~l~~ 49 (126)
T cd04785 1 LSIGELARRTGVNVETIRYYESIGLLPEPARTA-------------------------------GGYRLYGAAHVERLRF 49 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCC-------------------------------CCccccCHHHHHHHHH
Confidence 688999999999999999998864443221111 1133455554 4556
Q ss_pred HHHHHcCCCCHHHHHHHhCC
Q psy17316 128 LDALRAGSISANKASKAYGI 147 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~gI 147 (229)
|..+..-++|+.+|..-+..
T Consensus 50 I~~lr~~G~sL~eI~~~l~~ 69 (126)
T cd04785 50 IRRARDLGFSLEEIRALLAL 69 (126)
T ss_pred HHHHHHCCCCHHHHHHHHhh
Confidence 77777777899988876654
No 166
>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=95.20 E-value=0.12 Score=40.63 Aligned_cols=65 Identities=9% Similarity=0.106 Sum_probs=48.9
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCc-ccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIR-LAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYG 201 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k-~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fg 201 (229)
+++.++|+.+||+..||+-|-+ .|.- ......+..|.|+++ .++..|..+..=+++..++...+.
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~-~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~ 68 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIRYYEE-KGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLN 68 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 5789999999999999999887 4432 221112346788766 567788888888899999998775
No 167
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=95.20 E-value=0.03 Score=52.83 Aligned_cols=36 Identities=28% Similarity=0.262 Sum_probs=29.8
Q ss_pred HHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 41 ALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 41 AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
+..++...+....++|+.+||+++|||+++++||++
T Consensus 434 i~~aL~~~~gn~~~aA~~Lgisr~tL~rkl~~~~i~ 469 (469)
T PRK10923 434 LTTALRHTQGHKQEAARLLGWGRNTLTRKLKELGME 469 (469)
T ss_pred HHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence 334555556689999999999999999999999874
No 168
>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=95.20 E-value=0.13 Score=40.07 Aligned_cols=67 Identities=12% Similarity=0.140 Sum_probs=44.7
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
|++.++|+.+||+..||+.|-+. |+-.|..... +....|+++. .+..
T Consensus 1 ~~I~eva~~~gvs~~tLRyYe~~-GLl~p~~r~~------------------------------~gyR~Y~~~~i~~l~~ 49 (123)
T cd04770 1 MKIGELAKAAGVSPDTIRYYERI-GLLPPPQRSE------------------------------NGYRLYGEADLARLRF 49 (123)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCCCC------------------------------CCCccCCHHHHHHHHH
Confidence 68899999999999999988775 4332211111 1134455554 4566
Q ss_pred HHHHHcCCCCHHHHHHHhCC
Q psy17316 128 LDALRAGSISANKASKAYGI 147 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~gI 147 (229)
|..+.+-++|+.+|..-+..
T Consensus 50 I~~lr~~G~sl~eI~~~l~~ 69 (123)
T cd04770 50 IRRAQALGFSLAEIRELLSL 69 (123)
T ss_pred HHHHHHCCCCHHHHHHHHHh
Confidence 77777778898888776653
No 169
>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=95.18 E-value=0.21 Score=41.54 Aligned_cols=70 Identities=14% Similarity=0.263 Sum_probs=49.5
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
+++.++|+.+||+..||+.|-+. |+-.|..... +....|++++ ++..
T Consensus 2 ~~I~evA~~~gvs~~tLRyYe~~-GLl~p~~r~~------------------------------~gyR~Y~~~dl~rL~~ 50 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYERI-GLLSPSARSE------------------------------SNYRLYGERDLERLEQ 50 (172)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCC------------------------------CCCccCCHHHHHHHHH
Confidence 58999999999999999999875 5443322111 1234566654 5667
Q ss_pred HHHHHcCCCCHHHHHHHhCCChH
Q psy17316 128 LDALRAGSISANKASKAYGIPSS 150 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~gIp~s 150 (229)
|..+.+-++|+.+|..-...+..
T Consensus 51 I~~lr~~G~sL~eI~~ll~~~~~ 73 (172)
T cd04790 51 ICAYRSAGVSLEDIRSLLQQPGD 73 (172)
T ss_pred HHHHHHcCCCHHHHHHHHhcCCh
Confidence 88888888899999887765543
No 170
>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=95.18 E-value=0.12 Score=40.74 Aligned_cols=66 Identities=12% Similarity=0.155 Sum_probs=44.4
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
|++.++|+.+||+..||+.|-+..-+..+.... +....|++++ +...
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~GLl~p~~r~~-------------------------------~gyR~Y~~~~l~~l~~ 49 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIRYYEEKGLIPPPLRSE-------------------------------GGYRTYTQQHLDELRL 49 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCC-------------------------------CCCeecCHHHHHHHHH
Confidence 689999999999999999998764333221111 1134455554 3556
Q ss_pred HHHHHcCCCCHHHHHHHhC
Q psy17316 128 LDALRAGSISANKASKAYG 146 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~g 146 (229)
|..+..-++|+.+|..-+.
T Consensus 50 I~~lr~~G~sL~eI~~~l~ 68 (127)
T TIGR02044 50 ISRARQVGFSLEECKELLN 68 (127)
T ss_pred HHHHHHCCCCHHHHHHHHH
Confidence 7777777788888877654
No 171
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=95.17 E-value=0.046 Score=41.35 Aligned_cols=33 Identities=21% Similarity=0.347 Sum_probs=27.7
Q ss_pred HHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316 43 EALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI 75 (229)
Q Consensus 43 ~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi 75 (229)
+.+...+..+.++|+.+||+++||+++++++|+
T Consensus 62 ~aL~~~~gn~s~AAr~LGIsRsTL~rKLkr~gi 94 (95)
T PRK00430 62 MVMQYTRGNQTRAALMLGINRGTLRKKLKKYGM 94 (95)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhCC
Confidence 344444558999999999999999999999986
No 172
>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=95.16 E-value=0.059 Score=35.30 Aligned_cols=38 Identities=13% Similarity=0.179 Sum_probs=28.4
Q ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
++++. .+|..+--.++|+.+||+.+|||.+|++++.++
T Consensus 6 ~~~er-~vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 6 PPRER-EVIRLRYFEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp -HHHH-HHHHHHHTST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred CHHHH-HHHHHHhcCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 44444 444455567899999999999999999999875
No 173
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=95.14 E-value=0.031 Score=54.19 Aligned_cols=34 Identities=18% Similarity=0.256 Sum_probs=29.2
Q ss_pred HHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316 43 EALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHT 77 (229)
Q Consensus 43 ~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~ 77 (229)
+++..++ +.+++|+++||+++|||+++++||+..
T Consensus 481 ~~l~~~~-~~~~aA~~LGisr~tL~rkl~~~gi~~ 514 (520)
T PRK10820 481 RLYRNYP-STRKLAKRLGVSHTAIANKLREYGLSQ 514 (520)
T ss_pred HHHHHCC-CHHHHHHHhCCCHHHHHHHHHHcCCCc
Confidence 3455555 899999999999999999999999963
No 174
>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=95.13 E-value=0.12 Score=40.56 Aligned_cols=68 Identities=10% Similarity=0.148 Sum_probs=45.5
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
|++.++|+.+||+..||+.|-+..-+..|.... |....|++++ +...
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~~GLl~~~~r~~-------------------------------~gyR~Y~~~~l~~l~~ 49 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYYQRRGLLPEPPRPE-------------------------------GGYRRYPEETVTRLRF 49 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCC-------------------------------CCCeecCHHHHHHHHH
Confidence 688999999999999999886653333221111 1234455554 3556
Q ss_pred HHHHHcCCCCHHHHHHHhCCC
Q psy17316 128 LDALRAGSISANKASKAYGIP 148 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~gIp 148 (229)
|..+.+-++|+.+|..-+...
T Consensus 50 I~~lr~~G~sL~eI~~~l~~~ 70 (126)
T cd04783 50 IKRAQELGFTLDEIAELLELD 70 (126)
T ss_pred HHHHHHcCCCHHHHHHHHhcc
Confidence 777777788998888776654
No 175
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=95.11 E-value=0.034 Score=46.06 Aligned_cols=46 Identities=24% Similarity=0.468 Sum_probs=37.6
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcC-CChhhHHHHHHHhCCCCC
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYG-IPSTTLWQRAHRLGIHTP 78 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~g-Ip~sTL~~~i~~~gi~~~ 78 (229)
.||+|.+...-++. ..|+|..+||+++| |++..|.-+++++|+.+.
T Consensus 2 ~Wtde~~~~L~~lw-~~G~SasqIA~~lg~vsRnAViGk~hRlgL~~~ 48 (162)
T PF07750_consen 2 SWTDERVERLRKLW-AEGLSASQIARQLGGVSRNAVIGKAHRLGLSGR 48 (162)
T ss_pred CCCHHHHHHHHHHH-HcCCCHHHHHHHhCCcchhhhhhhhhccccccc
Confidence 47877776555444 55889999999999 999999999999987654
No 176
>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=95.10 E-value=0.043 Score=35.60 Aligned_cols=35 Identities=20% Similarity=0.288 Sum_probs=26.2
Q ss_pred HHHHHHHH-cCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 39 DAALEALR-AGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 39 ~~AI~~~~-~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
.+++..+. ++++|+.++|+.+|++.+|+++.++++
T Consensus 6 ~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L 41 (48)
T PF13412_consen 6 RKILNYLRENPRITQKELAEKLGISRSTVNRYLKKL 41 (48)
T ss_dssp HHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 34444333 678999999999999999999999875
No 177
>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=95.08 E-value=0.13 Score=38.10 Aligned_cols=65 Identities=9% Similarity=0.066 Sum_probs=46.7
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHh-CCCcHHHHHHHhC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRS-GQTTVQRASAEYG 201 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~-~~~s~~eAA~~fg 201 (229)
+++.++|+.+||+.+||+.|.+ .|+-......+..+.|+++ ++...|..+.+ -+++..++...++
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~-~Gli~p~r~~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l~ 69 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYER-LGLLSPSRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGVKRILE 69 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH-CCCcCCCcCCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 4789999999999999999987 4543221112335667665 45666676666 6799999988776
No 178
>PHA00675 hypothetical protein
Probab=95.07 E-value=0.06 Score=39.20 Aligned_cols=41 Identities=10% Similarity=0.135 Sum_probs=31.7
Q ss_pred CCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 172 TAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 172 r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
-+.+..+-.+|-.....-++|+.++|.+||||++||+.+.+
T Consensus 21 AKLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 21 AKLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred cccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHc
Confidence 35666666666666624447999999999999999999876
No 179
>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=95.06 E-value=0.15 Score=40.67 Aligned_cols=66 Identities=11% Similarity=0.117 Sum_probs=50.1
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCC-cccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGI-RLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI 202 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~-k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV 202 (229)
+++.++|+.+||+..||+-|-+ .|. ..........|.|+++ .++..|..+..-++|..++...+..
T Consensus 1 m~Ige~a~~~gvs~~tLRyYE~-~GLl~p~~r~~~gyR~Y~~~~v~~l~~I~~lr~~GfsL~eI~~ll~~ 69 (131)
T cd04786 1 MKIGELAKRSGMAASRIRFYEA-EGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLPA 69 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 5789999999999999999987 443 2221112345778655 6788899999988999999998864
No 180
>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=95.05 E-value=0.13 Score=39.88 Aligned_cols=66 Identities=8% Similarity=0.108 Sum_probs=46.6
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
|++.++|+.+||+..||+.|-+. |+-.|..... ....|++++ +...
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~~-GLi~p~~~~~-------------------------------~yR~Y~~~d~~~l~~ 48 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEK-GLLPSPKRSG-------------------------------NYRVYDAQHVECLRF 48 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCCCC-------------------------------CceeeCHHHHHHHHH
Confidence 68999999999999999999887 4433321111 123455555 4666
Q ss_pred HHHHHcCCCCHHHHHHHhCC
Q psy17316 128 LDALRAGSISANKASKAYGI 147 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~gI 147 (229)
|..+..-++|+.+|..-+..
T Consensus 49 I~~lr~~G~sl~eI~~~l~~ 68 (116)
T cd04769 49 IKEARQLGFTLAELKAIFAG 68 (116)
T ss_pred HHHHHHcCCCHHHHHHHHhc
Confidence 78888888899998776544
No 181
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=95.05 E-value=0.12 Score=41.56 Aligned_cols=66 Identities=9% Similarity=0.034 Sum_probs=50.2
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCc-ccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIR-LAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI 202 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k-~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV 202 (229)
+++.++|+.+||+..||+.|.+. |+- .........|.|+++ +++..|..+.+-+++..++...++.
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~~-GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 70 (140)
T PRK09514 2 YRIGELAKLAEVTPDTLRFYEKQ-GLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSI 70 (140)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHC-CCCCCcccCCCCCeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 57899999999999999999884 542 211112346788766 5677788888888999999998864
No 182
>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=95.03 E-value=0.14 Score=39.32 Aligned_cols=66 Identities=5% Similarity=-0.047 Sum_probs=49.3
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCccc-CCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLA-QPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI 202 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~-~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV 202 (229)
+++.++|+.+||+..||+.|-+. |.-.. ....+..|.|+++ .++..|+.+.+-+++..++...+..
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~~-GLl~p~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~ 69 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLR-GLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRA 69 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 37889999999999999999884 64322 1112346778766 5677888888888999999887643
No 183
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=95.03 E-value=0.098 Score=47.09 Aligned_cols=85 Identities=18% Similarity=0.173 Sum_probs=62.0
Q ss_pred HHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCC
Q psy17316 41 ALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSW 119 (229)
Q Consensus 41 AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kY 119 (229)
.|+.-.+..+|+.++|+.+|++.++|.+..++. |... ... +
T Consensus 226 ~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~g~s~------------~~~--------------------------~ 267 (322)
T PRK09393 226 WMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTP------------AEW--------------------------L 267 (322)
T ss_pred HHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH------------HHH--------------------------H
Confidence 333333457999999999999999999999984 5531 111 0
Q ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316 120 NEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL 163 (229)
Q Consensus 120 s~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~ 163 (229)
..--+..|.+++.+...|+.+||...|-+..+ +.+..|++ |..+
T Consensus 268 ~~~Rl~~A~~lL~~~~~~i~~IA~~~Gf~~~s~F~r~Fk~~~G~tP 313 (322)
T PRK09393 268 LRERLARARDLLESSALSIDQIAERAGFGSEESLRHHFRRRAATSP 313 (322)
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence 11234678888888888999999999998855 88877765 6544
No 184
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=95.01 E-value=0.44 Score=41.65 Aligned_cols=87 Identities=18% Similarity=0.234 Sum_probs=63.0
Q ss_pred HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCC
Q psy17316 39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTK 117 (229)
Q Consensus 39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~ 117 (229)
...|++--...+|+.++|+.+|+++++|.+..++. |... -.. +
T Consensus 192 ~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~G~t~------------~~y---i--------------------- 235 (287)
T TIGR02297 192 NFLIEENYKQHLRLPEYADRLGISESRLNDICRRFSALSP------------KRL---I--------------------- 235 (287)
T ss_pred HHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHHHhCCCH------------HHH---H---------------------
Confidence 34444333457899999999999999999999983 4431 111 0
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316 118 SWNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL 163 (229)
Q Consensus 118 kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~ 163 (229)
..--+.+|..+++....|+.+||...|-+..+ ..+..|++ |..+
T Consensus 236 --~~~Rl~~A~~lL~~t~~sI~eIA~~~GF~s~s~Fsr~FKk~~G~tP 281 (287)
T TIGR02297 236 --IERVMQEARRLLLFTQHSINQIAYDLGYKDPAYFARFFQKETGLSP 281 (287)
T ss_pred --HHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence 01235777788887888999999999999966 88877765 7544
No 185
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=95.00 E-value=0.12 Score=41.66 Aligned_cols=67 Identities=9% Similarity=0.074 Sum_probs=45.6
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
+++.++|+.+||+..||+.|-+. |+-.|.....+ ....|++++ ++..
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~~-GLl~p~~r~~~------------------------------gyR~Y~~~~l~~l~~ 50 (140)
T PRK09514 2 YRIGELAKLAEVTPDTLRFYEKQ-GLMDPEVRTEG------------------------------GYRLYTEQDLQRLRF 50 (140)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHC-CCCCCcccCCC------------------------------CCeeeCHHHHHHHHH
Confidence 68899999999999999999887 54333211111 133455444 3555
Q ss_pred HHHHHcCCCCHHHHHHHhCC
Q psy17316 128 LDALRAGSISANKASKAYGI 147 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~gI 147 (229)
|..+..-++|+.+|..-++.
T Consensus 51 I~~lr~~G~sL~eI~~~l~~ 70 (140)
T PRK09514 51 IRRAKQLGFTLEEIRELLSI 70 (140)
T ss_pred HHHHHHcCCCHHHHHHHHHh
Confidence 66777777899998887653
No 186
>PRK13502 transcriptional activator RhaR; Provisional
Probab=94.99 E-value=0.27 Score=43.03 Aligned_cols=86 Identities=16% Similarity=0.140 Sum_probs=63.6
Q ss_pred HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCC
Q psy17316 40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKS 118 (229)
Q Consensus 40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~k 118 (229)
..|+.-....+++.++|..+||+++.|.+.++++ |... -.. +
T Consensus 183 ~~I~~~~~~~~~~~~lA~~~~iS~~~L~r~fk~~~G~t~------------~~y---i---------------------- 225 (282)
T PRK13502 183 TALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTI------------NQY---L---------------------- 225 (282)
T ss_pred HHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH------------HHH---H----------------------
Confidence 3333334557899999999999999999999983 5542 000 0
Q ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316 119 WNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL 163 (229)
Q Consensus 119 Ys~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~ 163 (229)
..--+.+|.+++.++..|+.+||.+.|-+..+ ..+..|++ |..+
T Consensus 226 -~~~Rl~~A~~lL~~t~~sI~eIA~~~GF~d~s~F~r~FKk~~G~tP 271 (282)
T PRK13502 226 -RQVRICHAQYLLQHSPLMISEISMQCGFEDSNYFSVVFTRETGMTP 271 (282)
T ss_pred -HHHHHHHHHHHHHcCCCCHHHHHHHcCCCCHHHHHHHHHHHHCcCH
Confidence 01235788889988889999999999999977 88877765 7544
No 187
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=94.99 E-value=0.038 Score=54.56 Aligned_cols=40 Identities=25% Similarity=0.455 Sum_probs=33.1
Q ss_pred HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
++..+++++...+..+.++|+.+||+++|||+++++||+.
T Consensus 592 E~~~i~~al~~~~gn~~~aA~~LGisR~TLyrklk~~~i~ 631 (638)
T PRK11388 592 EKEAIINAAQVCGGRIQEMAALLGIGRTTLWRKMKQHGID 631 (638)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHcCCC
Confidence 4455555666556689999999999999999999999985
No 188
>PRK00118 putative DNA-binding protein; Validated
Probab=94.98 E-value=0.043 Score=42.29 Aligned_cols=40 Identities=13% Similarity=0.253 Sum_probs=31.5
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
..++.+... +.....+++|+.+||+.+|||++||++++++
T Consensus 17 ~L~ekqRev-l~L~y~eg~S~~EIAe~lGIS~~TV~r~L~R 56 (104)
T PRK00118 17 LLTEKQRNY-MELYYLDDYSLGEIAEEFNVSRQAVYDNIKR 56 (104)
T ss_pred cCCHHHHHH-HHHHHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 345555544 4455566899999999999999999999986
No 189
>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=94.92 E-value=0.061 Score=34.57 Aligned_cols=28 Identities=25% Similarity=0.449 Sum_probs=23.0
Q ss_pred HcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 46 RAGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 46 ~~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
.++.+|+.++|+..|++.+|+++++++.
T Consensus 14 ~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 14 EDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp H-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 3689999999999999999999999874
No 190
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=94.91 E-value=0.12 Score=41.08 Aligned_cols=79 Identities=16% Similarity=0.169 Sum_probs=45.2
Q ss_pred CCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh---C-CcccCCCCCCCCCCCHHHHHHHHHHHHhCC-C
Q psy17316 117 KSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE---G-IRLAQPFNASPTAWKPEDLEIALEGIRSGQ-T 191 (229)
Q Consensus 117 ~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~---g-~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~-~ 191 (229)
.-++.+.+++.|++..+|. +..+||+++.|+.+.+.+|+.+| | +....-...+++..+++.-..|.++..++- +
T Consensus 16 rPLp~~~R~rIvela~~G~-rp~~Isr~l~Vs~gcVsKIl~Ry~eTGsi~Pg~iGGskprv~tp~v~~~I~~~k~enP~i 94 (125)
T PF00292_consen 16 RPLPNELRQRIVELAKEGV-RPCDISRQLRVSHGCVSKILSRYRETGSIRPGPIGGSKPRVATPEVVEKIEQYKRENPTI 94 (125)
T ss_dssp SSS-HHHHHHHHHHHHTT---HHHHHHHHT--HHHHHHHHHHHHHHS-SS----S----SSS-HCHHHHHHHHHHH-TTS
T ss_pred ccCcHHHHHHHHHHhhhcC-CHHHHHHHHccchhHHHHHHHHHHHhcccCcccccCCCCCCCChHHHHHHHHHHhcCCCc
Confidence 4577888899999998875 99999999999999999999866 3 221110123466666665555555555543 3
Q ss_pred cHHHH
Q psy17316 192 TVQRA 196 (229)
Q Consensus 192 s~~eA 196 (229)
-.+|+
T Consensus 95 fawEi 99 (125)
T PF00292_consen 95 FAWEI 99 (125)
T ss_dssp -HHHH
T ss_pred chHHH
Confidence 34443
No 191
>PHA00542 putative Cro-like protein
Probab=94.91 E-value=0.061 Score=39.38 Aligned_cols=44 Identities=7% Similarity=0.059 Sum_probs=34.9
Q ss_pred CCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316 171 PTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR 215 (229)
Q Consensus 171 ~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~ 215 (229)
+..++.+ ..+++..+...+++..++|..+||+.+||++|.++..
T Consensus 13 p~~~~~~-~~~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~~ 56 (82)
T PHA00542 13 PAAYTQR-PDELVCALIRAGWSQEQIADATDVSQPTICRIYSGRH 56 (82)
T ss_pred CcccCcC-HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCCC
Confidence 3444432 4466777888889999999999999999999998664
No 192
>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=94.89 E-value=0.092 Score=33.99 Aligned_cols=40 Identities=23% Similarity=0.247 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHhCC-CcHHHHHHHhCCChHHHHHHHH-hhcC
Q psy17316 177 EDLEIALEGIRSGQ-TTVQRASAEYGIPSGTLYGRCK-LSRS 216 (229)
Q Consensus 177 e~r~eaV~~~~~~~-~s~~eAA~~fgVp~~tv~~~vk-~~~~ 216 (229)
+...+|+..+.++. ++..++|..+|+|.+||...++ +.+.
T Consensus 3 ~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~ 44 (48)
T PF13412_consen 3 ETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEK 44 (48)
T ss_dssp HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 45678888888844 9999999999999999999998 4433
No 193
>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=94.88 E-value=0.12 Score=40.81 Aligned_cols=64 Identities=8% Similarity=0.042 Sum_probs=45.5
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHh-CCCcHHHHHHHhC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRS-GQTTVQRASAEYG 201 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~-~~~s~~eAA~~fg 201 (229)
+++.++|+++||+.+||+.|.++ |+-.... .+..|.|+++ .+++.|..+.+ -+++..++...+.
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE~~-GLl~p~r-~~G~R~Ys~~dv~rL~~I~~L~~e~G~~l~eI~~~L~ 68 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWERH-GLIKPAR-RNGQRLYSNNDLKRLRFIKKLINEKGLNIAGVKQILS 68 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCcC-CCCcEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 58899999999999999999985 4322221 2446778766 45666777766 6687777776543
No 194
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=94.87 E-value=0.36 Score=42.43 Aligned_cols=87 Identities=13% Similarity=0.184 Sum_probs=63.2
Q ss_pred HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCC
Q psy17316 39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTK 117 (229)
Q Consensus 39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~ 117 (229)
...|..-..+.+|+.++|+++|+++++|.+-.++. |... .+
T Consensus 189 ~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~~~G~tp-----------~~--------------------------- 230 (290)
T PRK10572 189 CQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISV-----------LR--------------------------- 230 (290)
T ss_pred HHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCH-----------HH---------------------------
Confidence 33443334578999999999999999999999985 5431 01
Q ss_pred CCCHH-HHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCccc
Q psy17316 118 SWNEE-ILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRLA 164 (229)
Q Consensus 118 kYs~e-~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~~ 164 (229)
|-.+ -+++|..++.....|+.+||...|-+... ..+.-|++ |..+.
T Consensus 231 -~l~~~Rl~~A~~lL~~t~~sI~eIA~~~GF~d~s~Fsr~FKk~~G~SP~ 279 (290)
T PRK10572 231 -WREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPS 279 (290)
T ss_pred -HHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCHH
Confidence 1112 25777888887888999999999999766 77777765 75443
No 195
>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=94.86 E-value=0.15 Score=40.11 Aligned_cols=66 Identities=14% Similarity=0.153 Sum_probs=45.0
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHHH--HHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEIL--NVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~k--~~A 127 (229)
|++.++|+.+||+..||+.|-+..-+..+.... +....|++++. ...
T Consensus 1 m~IgevA~~~gvs~~tLRyYe~~GLl~p~~r~~-------------------------------~gyR~Y~~~~l~~l~~ 49 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYYEKEGLLPAPARSA-------------------------------NNYRLYDEEHLERLLF 49 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCC-------------------------------CCCeecCHHHHHHHHH
Confidence 688999999999999999998864333221111 12345555553 456
Q ss_pred HHHHHcCCCCHHHHHHHhC
Q psy17316 128 LDALRAGSISANKASKAYG 146 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~g 146 (229)
|..+..-++|+.+|..-+.
T Consensus 50 I~~lr~~G~sL~eI~~~l~ 68 (127)
T cd04784 50 IRRCRSLDMSLDEIRTLLQ 68 (127)
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 7777776788888877654
No 196
>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=94.85 E-value=0.071 Score=35.27 Aligned_cols=36 Identities=14% Similarity=0.009 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
+...+++...--.++++.++|..+|||.++|+.++.
T Consensus 13 ~~~r~i~~l~~~~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 13 ERQREIFLLRYFQGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp HHHHHHHHHHHTS---HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHHCcCHHHHHHHHCcCHHHHHHHHH
Confidence 334555666555669999999999999999999986
No 197
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=94.84 E-value=0.048 Score=52.63 Aligned_cols=40 Identities=23% Similarity=0.255 Sum_probs=32.7
Q ss_pred HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
++..+++++...+..+..+|+.+||+++|||+++++|||.
T Consensus 469 Er~~I~~aL~~~~gn~~~aA~~LGisr~tL~rklk~~gi~ 508 (509)
T PRK05022 469 QRQLIRQALAQHQGNWAAAARALELDRANLHRLAKRLGLK 508 (509)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 3445555666666688999999999999999999999985
No 198
>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=94.84 E-value=0.16 Score=40.03 Aligned_cols=66 Identities=9% Similarity=0.071 Sum_probs=44.5
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
|++.++|+.+||+..||+.|-+..-+..+.... +....|++++ +...
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~~GLl~~~~r~~-------------------------------~gyR~Y~~~~l~~l~~ 49 (127)
T TIGR02047 1 MKIGELAQKTGVSVETIRFYEKQGLLPPPARTD-------------------------------NNYRVYTVGHVERLAF 49 (127)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCC-------------------------------CCCCcCCHHHHHHHHH
Confidence 678999999999999999998763333221111 1134455555 3556
Q ss_pred HHHHHcCCCCHHHHHHHhC
Q psy17316 128 LDALRAGSISANKASKAYG 146 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~g 146 (229)
|..+..-++|+.+|..-+.
T Consensus 50 I~~lr~lG~sL~eI~~~l~ 68 (127)
T TIGR02047 50 IRNCRTLDMSLAEIRQLLR 68 (127)
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 7777777788888877654
No 199
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=94.83 E-value=0.36 Score=34.25 Aligned_cols=71 Identities=18% Similarity=0.247 Sum_probs=46.9
Q ss_pred HHHHcCCChhhHHHHHHH-hCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHHHHHHHHHHH-
Q psy17316 55 ASVSYGIPSTTLWQRAHR-LGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEILNVALDALR- 132 (229)
Q Consensus 55 aA~~~gIp~sTL~~~i~~-~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~k~~AV~~~~- 132 (229)
+|+.+||+..+|.+.+++ .|... ... + ...-+..|.+++.
T Consensus 1 lA~~~~~s~~~l~~~f~~~~g~s~------------~~~---~-----------------------~~~R~~~a~~~L~~ 42 (81)
T PF12833_consen 1 LADELGMSERYLSRIFKKETGMSF------------KQY---L-----------------------RELRLQRAKELLRQ 42 (81)
T ss_dssp HHHHCTS-HHHHHHHHHHHHSS-H------------HHH---H-----------------------HHHHHHHHHHHHHH
T ss_pred ChHHhCcCHHHHHHHHHHHHCcCH------------HHH---H-----------------------HHHHHHHHHHHHHH
Confidence 589999999999999998 45431 111 0 0123466777775
Q ss_pred cCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316 133 AGSISANKASKAYGIPSST-LYKIARKE-GIRL 163 (229)
Q Consensus 133 ~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~ 163 (229)
+++.|+.+||.++|-+..+ +.+..++. |..+
T Consensus 43 ~~~~~i~~ia~~~Gf~~~~~f~~~fk~~~g~tP 75 (81)
T PF12833_consen 43 NTDLSIAEIAEECGFSSQSHFSRAFKRYFGMTP 75 (81)
T ss_dssp HTT--HHHHHHHTT-SSHHHHHHHHHHHHSS-H
T ss_pred hhcccHHHHHHHcCCCCHHHHHHHHHHHHCcCH
Confidence 4788999999999999877 88888765 6543
No 200
>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=94.83 E-value=0.093 Score=33.30 Aligned_cols=39 Identities=13% Similarity=0.041 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHh
Q psy17316 174 WKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKL 213 (229)
Q Consensus 174 ~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~ 213 (229)
.+++.+. ++...--.++++.++|..+|+|..||++|++.
T Consensus 11 l~~~~~~-~~~~~~~~~~~~~~ia~~~~~s~~~i~~~~~~ 49 (55)
T cd06171 11 LPERERE-VILLRFGEGLSYEEIAEILGISRSTVRQRLHR 49 (55)
T ss_pred CCHHHHH-HHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3444444 44444435599999999999999999999873
No 201
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=94.83 E-value=0.038 Score=41.87 Aligned_cols=38 Identities=24% Similarity=0.365 Sum_probs=32.4
Q ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
|.|+ ++||.++--.++++.+||.+.||++.|+|+-+..
T Consensus 35 t~eE-lEAlRLvD~~~l~QeeAA~rMgISr~Tfwr~l~s 72 (99)
T COG1342 35 TIEE-LEALRLVDYEGLTQEEAALRMGISRQTFWRLLTS 72 (99)
T ss_pred cHHH-HHHHHHHhHhhccHHHHHHHhcccHHHHHHHHHH
Confidence 4444 5788888778999999999999999999998874
No 202
>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=94.82 E-value=0.095 Score=34.27 Aligned_cols=37 Identities=16% Similarity=0.120 Sum_probs=27.8
Q ss_pred CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 175 KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 175 t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
+++++ +||...--+++|+.++|..+|||.++|..+.+
T Consensus 6 ~~~er-~vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 6 PPRER-EVIRLRYFEGLTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp -HHHH-HHHHHHHTST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred CHHHH-HHHHHHhcCCCCHHHHHHHHCCcHHHHHHHHH
Confidence 34444 45555556669999999999999999999876
No 203
>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=94.77 E-value=0.2 Score=39.52 Aligned_cols=66 Identities=6% Similarity=0.082 Sum_probs=49.2
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCc-ccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIR-LAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI 202 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k-~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV 202 (229)
+++.++|+.+|||..||+-|-+ .|.- ......+..|.|+++ +++..|..+.+=+++..++...+..
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~-~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~lG~sL~eI~~~l~~ 69 (127)
T TIGR02047 1 MKIGELAQKTGVSVETIRFYEK-QGLLPPPARTDNNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLRY 69 (127)
T ss_pred CcHHHHHHHHCcCHHHHHHHHH-CCCCCCCCcCCCCCCcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 4788999999999999999987 3432 211112346788766 4677788888878999999988764
No 204
>PHA02591 hypothetical protein; Provisional
Probab=94.77 E-value=0.053 Score=39.64 Aligned_cols=38 Identities=11% Similarity=0.200 Sum_probs=34.2
Q ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316 34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAH 71 (229)
Q Consensus 34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~ 71 (229)
++||.......+.+.|+|+.+||..+||+..++++.++
T Consensus 44 ~~dd~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 44 SEDDLISVTHELARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred ccchHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 77888888888888899999999999999999998875
No 205
>PRK15043 transcriptional regulator MirA; Provisional
Probab=94.75 E-value=0.12 Score=45.64 Aligned_cols=30 Identities=20% Similarity=0.335 Sum_probs=26.7
Q ss_pred CCCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316 49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTP 78 (229)
Q Consensus 49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~ 78 (229)
-+++.++|+.+||+..||+.|-+++|+-.|
T Consensus 3 ~ytIgeVA~~~GVs~~TLR~wErr~GLL~P 32 (243)
T PRK15043 3 LYTIGEVALLCDINPVTLRAWQRRYGLLKP 32 (243)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHhcCCCCC
Confidence 378999999999999999999999887654
No 206
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=94.72 E-value=0.19 Score=38.69 Aligned_cols=69 Identities=16% Similarity=0.148 Sum_probs=49.1
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCCh
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIPS 204 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp~ 204 (229)
+++.++|+.+||+..||+-|-+.--+.......+..|-|+++ .++.+|..+.+-+++..++-.......
T Consensus 1 ~~I~eva~~~gvs~~tLRyYE~~GLl~p~~~~~~gyR~Ys~~dl~~l~~I~~~r~~G~~L~~I~~~l~~~~ 71 (124)
T COG0789 1 YTIGEVAKLTGVSVRTLRFYERKGLLSPERRDEGGYRYYTPEDLELLQIIKTLRELGFSLAEIKELLDLLS 71 (124)
T ss_pred CcHHHHHHHhCCCHHHHHHHHHcCCCCCcccCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhccc
Confidence 478899999999999999998853333332222456788766 455667777766688888887766654
No 207
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=94.69 E-value=0.5 Score=41.92 Aligned_cols=88 Identities=19% Similarity=0.095 Sum_probs=61.9
Q ss_pred HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCC
Q psy17316 38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPT 116 (229)
Q Consensus 38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~ 116 (229)
++..|+.-....+|+.++|+..|+++.+|.|..+.. |... ...-..
T Consensus 10 ~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~~~g~s~------------~~yi~~--------------------- 56 (289)
T PRK15121 10 LLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAI------------GAYIRA--------------------- 56 (289)
T ss_pred HHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH------------HHHHHH---------------------
Confidence 344444444568999999999999999999999974 5532 111001
Q ss_pred CCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316 117 KSWNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL 163 (229)
Q Consensus 117 ~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~ 163 (229)
--+..|..++..++.++.+||..+|-.... +.+..|+. |+..
T Consensus 57 -----~Rl~~A~~~L~~~~~~i~~iA~~~Gf~s~~~f~r~Fk~~~g~sP 100 (289)
T PRK15121 57 -----RRLSKAAVALRLTSRPILDIALQYRFDSQQTFTRAFKKQFAQTP 100 (289)
T ss_pred -----HHHHHHHHHHHcCCCCHHHHHHHHCCCCHHHHHHHHHHHHCcCH
Confidence 124667777877778999999999997755 77777654 6443
No 208
>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=94.69 E-value=0.19 Score=37.23 Aligned_cols=65 Identities=14% Similarity=0.163 Sum_probs=42.6
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
+++.++|+.+||+.+||+.|.+. |+-.|..... ....|++++ +...
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~~-Gli~p~r~~~-------------------------------g~R~y~~~dv~~l~~ 49 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERL-GLLSPSRTDG-------------------------------GTRRYSERDIERLRR 49 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHC-CCcCCCcCCC-------------------------------CCeeECHHHHHHHHH
Confidence 57899999999999999999884 5543421111 123455444 3444
Q ss_pred HHHHHc-CCCCHHHHHHHhC
Q psy17316 128 LDALRA-GSISANKASKAYG 146 (229)
Q Consensus 128 V~~~~~-g~~S~~~~a~k~g 146 (229)
|..+.. -++++.+|..-+.
T Consensus 50 i~~L~~d~g~~l~~i~~~l~ 69 (91)
T cd04766 50 IQRLTQELGVNLAGVKRILE 69 (91)
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 555554 6678888877765
No 209
>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=94.68 E-value=0.17 Score=39.77 Aligned_cols=67 Identities=12% Similarity=0.126 Sum_probs=48.9
Q ss_pred CHHHHHHHhCCChHHHHHHHHHhCC-cccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCCh
Q psy17316 137 SANKASKAYGIPSSTLYKIARKEGI-RLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIPS 204 (229)
Q Consensus 137 S~~~~a~k~gIp~sTL~~~ik~~g~-k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp~ 204 (229)
++.++|+++||+..||+.|-+ .|+ .......+..|.|+++ +++..|..+..=+++..++...++...
T Consensus 1 ~I~e~a~~~gvs~~tlR~Ye~-~GLl~~~~r~~~g~R~Y~~~~l~~l~~I~~l~~~G~sl~eI~~~l~~~~ 70 (124)
T TIGR02051 1 TIGELAKAAGVNVETIRYYER-KGLLPEPDRPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLGLVD 70 (124)
T ss_pred CHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCCEeECHHHHHHHHHHHHHHHCCCCHHHHHHHHhccc
Confidence 468899999999999999876 343 2222112346777655 567778888888899999999887643
No 210
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=94.66 E-value=0.054 Score=35.24 Aligned_cols=38 Identities=16% Similarity=0.300 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
+.+.+++..+.+|.+++.++|+.+|++++|+.+.++..
T Consensus 2 ~~R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L 39 (47)
T PF01022_consen 2 PTRLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKL 39 (47)
T ss_dssp HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHH
Confidence 35678899999999999999999999999999988864
No 211
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=94.64 E-value=0.059 Score=41.70 Aligned_cols=38 Identities=16% Similarity=0.172 Sum_probs=32.0
Q ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+.|+ ++||.++--.++|+.++|.+.||+++|+++.+..
T Consensus 43 ~~dE-lEAiRL~D~egl~QeeaA~~MgVSR~T~~ril~~ 80 (106)
T PF02001_consen 43 TVDE-LEAIRLVDYEGLSQEEAAERMGVSRPTFQRILES 80 (106)
T ss_pred eHHH-HHHHHHHHHcCCCHHHHHHHcCCcHHHHHHHHHH
Confidence 4444 5778877777899999999999999999998874
No 212
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=94.64 E-value=0.048 Score=53.63 Aligned_cols=40 Identities=33% Similarity=0.485 Sum_probs=31.0
Q ss_pred HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
++...|.++...+--+.++|+.+|||++||||+++++||.
T Consensus 566 ~~~~l~~al~~~~~~is~aa~~lgi~R~T~yrklk~~gi~ 605 (606)
T COG3284 566 EKAALLAALQATNGNISEAARLLGISRSTLYRKLKRHGIS 605 (606)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence 3344444454445578899999999999999999999984
No 213
>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=94.63 E-value=0.19 Score=40.00 Aligned_cols=67 Identities=6% Similarity=0.098 Sum_probs=45.5
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
|++.++|+.+||+..||+.|-+..-+..+.... +....|++++ ++..
T Consensus 1 m~Ige~a~~~gvs~~tLRyYE~~GLl~p~~r~~-------------------------------~gyR~Y~~~~v~~l~~ 49 (131)
T cd04786 1 MKIGELAKRSGMAASRIRFYEAEGLLSSVERSA-------------------------------NGYRDYPPETVWVLEI 49 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCC-------------------------------CCCeecCHHHHHHHHH
Confidence 689999999999999999998764443221111 0133455544 3556
Q ss_pred HHHHHcCCCCHHHHHHHhCC
Q psy17316 128 LDALRAGSISANKASKAYGI 147 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~gI 147 (229)
|..+..-++|+.+|...+..
T Consensus 50 I~~lr~~GfsL~eI~~ll~~ 69 (131)
T cd04786 50 ISSAQQAGFSLDEIRQLLPA 69 (131)
T ss_pred HHHHHHcCCCHHHHHHHHhc
Confidence 77777777898888876643
No 214
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=94.59 E-value=0.09 Score=38.65 Aligned_cols=39 Identities=15% Similarity=0.173 Sum_probs=35.0
Q ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 174 WKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 174 ~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
|=++-+.+|++++..|..+..++|..||||.+||.+-++
T Consensus 3 ~~~~R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 3 YIEERVLEIGKYIVETKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred cHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhc
Confidence 446778899999999999999999999999999999774
No 215
>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=94.59 E-value=0.17 Score=40.85 Aligned_cols=65 Identities=11% Similarity=0.141 Sum_probs=49.6
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYG 201 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fg 201 (229)
+++.++|+.+|||..||+-|-+. |+-......+..|.|+++ +++..|..+.+-+++..++...+.
T Consensus 2 ~~IgevA~~~Gvs~~tLRyYE~~-GLl~~~r~~~g~R~Y~~~di~~l~~I~~lr~~G~sL~eI~~~l~ 68 (142)
T TIGR01950 2 LTVGELAKRSGVAVSALHFYESK-GLITSIRNSGNQRRYKRDVLRRVAVIKAAQRVGIPLATIGEALA 68 (142)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCccCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 68999999999999999999885 643222112335788766 457788888888899999998775
No 216
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=94.56 E-value=0.18 Score=45.69 Aligned_cols=84 Identities=18% Similarity=0.203 Sum_probs=58.0
Q ss_pred HHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcc--c-----------CCCCCCCCCCCHHHHHHHHHHHHhCCCcHH
Q psy17316 128 LDALRAGSISANKASKAYGIPSSTLYKIARKEGIRL--A-----------QPFNASPTAWKPEDLEIALEGIRSGQTTVQ 194 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~--~-----------~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~ 194 (229)
|+.+..-++|.++||++.|-..+|+++.+++.-... . +.....+-+.+++=+..|++.+.+ ..|..
T Consensus 16 I~~l~~~~~S~reIA~~LgRh~sTIsRElkRn~~~~~Y~a~~A~~~~~~~rrr~~~k~~~~~eL~~~V~e~L~~-~wSPE 94 (318)
T COG2826 16 IERLLKAKMSIREIAKQLNRHHSTISRELKRNRTRDIYSAVKAQERYRMLRRRRIRKLKLNPELRELVLEKLKS-KWSPE 94 (318)
T ss_pred HHHHHHcCCCHHHHHHHhCCCcchhhHHHhcCCccceeeHHHHHHHHHHhhcccCCcccCCHHHHHHHHHHHHh-hCCHH
Confidence 444555557999999999999999999987532111 0 001123446677766666666554 59999
Q ss_pred HHHHHh--C-CChHHHHHHHH
Q psy17316 195 RASAEY--G-IPSGTLYGRCK 212 (229)
Q Consensus 195 eAA~~f--g-Vp~~tv~~~vk 212 (229)
+++... + |+.+|+|+|+-
T Consensus 95 QI~g~l~~~~i~~eTIYr~ly 115 (318)
T COG2826 95 QIIGRLKKSKISFETIYRWLY 115 (318)
T ss_pred HHHHHHHhcccCHHHHHHHHh
Confidence 998743 4 89999999986
No 217
>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=94.56 E-value=0.22 Score=38.89 Aligned_cols=65 Identities=11% Similarity=0.209 Sum_probs=44.5
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
+++.++|+.+|||..||+-|=+. |+-.|....- ...|++++ +...
T Consensus 1 ~~Igeva~~~gvs~~tlRyYe~~-GLl~p~r~~g--------------------------------yR~Y~~~~l~~l~~ 47 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYEDK-GLLSPERRGQ--------------------------------TRVYSRRDRARLKL 47 (118)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCcCCCC--------------------------------ccccCHHHHHHHHH
Confidence 47899999999999999999886 5544422111 34455555 3455
Q ss_pred HHHHHcCCCCHHHHHHHhCC
Q psy17316 128 LDALRAGSISANKASKAYGI 147 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~gI 147 (229)
|..+.+-++|+.+|..-+..
T Consensus 48 I~~lr~~G~~L~~I~~~l~~ 67 (118)
T cd04776 48 ILRGKRLGFSLEEIRELLDL 67 (118)
T ss_pred HHHHHHCCCCHHHHHHHHHh
Confidence 66777777888888765543
No 218
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=94.51 E-value=0.077 Score=42.97 Aligned_cols=42 Identities=19% Similarity=0.209 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHHHH----HH---cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 31 KTWTHEDMDAALEA----LR---AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 31 ~kyt~e~~~~AI~~----~~---~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
.+.|.+++.+|.-. +. .+..|..+||++.||+++|||+|.++
T Consensus 9 ~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~ 57 (142)
T PF13022_consen 9 AKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQ 57 (142)
T ss_dssp TTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhc
Confidence 45666766544322 22 25688999999999999999999975
No 219
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=94.51 E-value=0.042 Score=41.77 Aligned_cols=32 Identities=19% Similarity=0.246 Sum_probs=28.9
Q ss_pred HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHH
Q psy17316 38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQR 69 (229)
Q Consensus 38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~ 69 (229)
...+|+++++|++|+++|+.++||+-+|+.|=
T Consensus 49 Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRG 80 (103)
T COG2973 49 RVRIVEELLRGELSQREIAQKLGVSIATITRG 80 (103)
T ss_pred HHHHHHHHHhccccHHHHHHHhCcchhhhccc
Confidence 35889999999999999999999999999763
No 220
>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=94.51 E-value=0.23 Score=39.38 Aligned_cols=67 Identities=9% Similarity=0.023 Sum_probs=50.0
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCC-CCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFN-ASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIP 203 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~-~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp 203 (229)
+++.++|+.+||+..||+-|-+ .|+-...... ...|.|+++ +++..|..+.+-+++..++...+...
T Consensus 1 m~IgE~A~~~gvs~~TLRyYE~-~GLl~p~r~~~~gyR~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~ 70 (133)
T cd04787 1 MKVKELANAAGVTPDTVRFYTR-IGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSHA 70 (133)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCcCCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhhh
Confidence 4788999999999999988765 4642222111 345778665 67788888999889999999988753
No 221
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=94.47 E-value=0.068 Score=39.93 Aligned_cols=35 Identities=11% Similarity=0.011 Sum_probs=28.7
Q ss_pred HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
..+++...+.+|+|+++||+.+||+.+||.|--+-
T Consensus 38 R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr~ 72 (87)
T PF01371_consen 38 RWQVAKELLDEGKSYREIAEETGVSIATITRVSRC 72 (87)
T ss_dssp HHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 34566646678999999999999999999987664
No 222
>PRK13500 transcriptional activator RhaR; Provisional
Probab=94.47 E-value=0.43 Score=42.90 Aligned_cols=88 Identities=17% Similarity=0.152 Sum_probs=63.7
Q ss_pred HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCC
Q psy17316 39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTK 117 (229)
Q Consensus 39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~ 117 (229)
...|++-....+++.++|+.+||++++|.+..++. |... -.. +
T Consensus 212 ~~yI~~~~~e~isl~~lA~~~~iS~~~L~r~FK~~tG~T~------------~~y---i--------------------- 255 (312)
T PRK13500 212 ITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTI------------NQY---L--------------------- 255 (312)
T ss_pred HHHHHHcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH------------HHH---H---------------------
Confidence 34444333447999999999999999999999985 5531 000 0
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCccc
Q psy17316 118 SWNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRLA 164 (229)
Q Consensus 118 kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~~ 164 (229)
.+--+.+|..++..+..|+.+||...|-+.++ ..+..|++ |+.++
T Consensus 256 --~~~RL~~A~~LL~~t~~sI~eIA~~~GF~d~s~Fsr~FKk~~G~TP~ 302 (312)
T PRK13500 256 --RQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMTPS 302 (312)
T ss_pred --HHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCHH
Confidence 01125788888888889999999999999977 77777765 75543
No 223
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=94.46 E-value=0.12 Score=34.59 Aligned_cols=38 Identities=18% Similarity=0.057 Sum_probs=28.3
Q ss_pred CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 175 KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 175 t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
+.+++.-++=.-.+.+.++.+.|..||||.+||.++++
T Consensus 4 s~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~ 41 (53)
T PF13613_consen 4 SLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFH 41 (53)
T ss_pred CHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHH
Confidence 34444444444444448899999999999999999887
No 224
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=94.46 E-value=0.28 Score=43.52 Aligned_cols=88 Identities=16% Similarity=0.103 Sum_probs=65.7
Q ss_pred HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCC
Q psy17316 36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGP 115 (229)
Q Consensus 36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~ 115 (229)
+....+|..-..+..++.++|...|+++++|.|..++.|.. +.
T Consensus 137 ~kv~~~I~~~~~~~~tl~~LA~~~gmS~s~l~R~FK~~G~T------------~~------------------------- 179 (253)
T PRK09940 137 GKVRNIVNMKLAHPWKLKDICDCLYISESLLKKKLKQEQTT------------FS------------------------- 179 (253)
T ss_pred HHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHcCCC------------HH-------------------------
Confidence 45577777777788999999999999999999999975421 10
Q ss_pred CCCCCHH-HHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316 116 TKSWNEE-ILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL 163 (229)
Q Consensus 116 ~~kYs~e-~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~ 163 (229)
.|-.+ -+..|.+++..+. |+.+||...|-...+ ..++.+++ |..+
T Consensus 180 --eyl~~~Rl~~A~~LL~~~~-sI~eIA~~~GF~s~S~Fsr~FKr~~G~TP 227 (253)
T PRK09940 180 --QILLDARMQHAKNLIRVEG-SVNKIAEQCGYASTSYFIYAFRKHFGNSP 227 (253)
T ss_pred --HHHHHHHHHHHHHHHccCC-CHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence 11112 2467777776654 999999999999977 88888765 7544
No 225
>PRK00118 putative DNA-binding protein; Validated
Probab=94.42 E-value=0.086 Score=40.64 Aligned_cols=35 Identities=11% Similarity=0.172 Sum_probs=30.0
Q ss_pred HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
.-.+++..+..+++|+.++|..+|||.+||++++.
T Consensus 21 kqRevl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~ 55 (104)
T PRK00118 21 KQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIK 55 (104)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 35566677777779999999999999999999986
No 226
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=94.41 E-value=0.094 Score=43.45 Aligned_cols=39 Identities=10% Similarity=0.340 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHHhCCCcHHHHHHHhC-CChHHHHHHHH
Q psy17316 173 AWKPEDLEIALEGIRSGQTTVQRASAEYG-IPSGTLYGRCK 212 (229)
Q Consensus 173 ~~t~e~r~eaV~~~~~~~~s~~eAA~~fg-Vp~~tv~~~vk 212 (229)
.||+ ++++.|..+...++|+.+||.++| ||++.|.+.+.
T Consensus 2 ~Wtd-e~~~~L~~lw~~G~SasqIA~~lg~vsRnAViGk~h 41 (162)
T PF07750_consen 2 SWTD-ERVERLRKLWAEGLSASQIARQLGGVSRNAVIGKAH 41 (162)
T ss_pred CCCH-HHHHHHHHHHHcCCCHHHHHHHhCCcchhhhhhhhh
Confidence 4774 588888999998899999999999 99999999998
No 227
>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=94.41 E-value=0.25 Score=38.76 Aligned_cols=66 Identities=12% Similarity=0.124 Sum_probs=48.6
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcc-cCCCCCCCCCCCHHH--HHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRL-AQPFNASPTAWKPED--LEIALEGIRSGQTTVQRASAEYGI 202 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~-~~~~~~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA~~fgV 202 (229)
+++.++|+.+||+..||+-|-+ .|.-. ........|.|++++ ++..|..+.+=+++..++...+..
T Consensus 1 m~IgevA~~~gvs~~tLRyYe~-~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYYEK-EGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQL 69 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 4788999999999999999887 44322 111123468888764 457777888877999999988764
No 228
>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=94.37 E-value=0.29 Score=38.23 Aligned_cols=65 Identities=8% Similarity=0.095 Sum_probs=49.2
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHH--HHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPED--LEIALEGIRSGQTTVQRASAEYGI 202 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA~~fgV 202 (229)
+++.++|+.+|||..||+-|-+. |+-.... ....|.|+++. ++..|..+.+-+++..++...+..
T Consensus 1 ~~Igeva~~~gvs~~tlRyYe~~-GLl~p~r-~~gyR~Y~~~~l~~l~~I~~lr~~G~~L~~I~~~l~~ 67 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYEDK-GLLSPER-RGQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDL 67 (118)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCcC-CCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 36889999999999999999884 6533221 22568888774 555578888888999999887765
No 229
>TIGR01817 nifA Nif-specific regulatory protein. This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.
Probab=94.34 E-value=0.068 Score=51.70 Aligned_cols=41 Identities=17% Similarity=0.210 Sum_probs=32.5
Q ss_pred HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316 37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHT 77 (229)
Q Consensus 37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~ 77 (229)
++..+++++...+-.+.++|+.+||+++|||+++++|||..
T Consensus 491 Er~~i~~aL~~~~gn~~~aA~~LGisr~tLy~klk~~gi~~ 531 (534)
T TIGR01817 491 ERERLIAALEQAGWVQAKAARLLGMTPRQVGYALRKLNIEM 531 (534)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHcCCCc
Confidence 34445555554455799999999999999999999999964
No 230
>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=94.32 E-value=0.24 Score=39.70 Aligned_cols=67 Identities=7% Similarity=0.090 Sum_probs=49.2
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIP 203 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp 203 (229)
+++.++|+.+||+..||+.|.+ .|.-.........|-|+++ +++..|..+.+-+++..++...+..-
T Consensus 1 y~I~e~a~~~gvs~~TLR~Ye~-~GLl~p~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~ 69 (134)
T cd04779 1 YRIGQLAHLAGVSKRTIDYYTN-LGLLTPERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEEV 69 (134)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCccCCCCCeeECHHHHHHHHHHHHHHHCCCCHHHHHHHHHhh
Confidence 3678999999999999999986 4532221112235667665 57788888888889999998877543
No 231
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=94.30 E-value=0.19 Score=41.24 Aligned_cols=67 Identities=10% Similarity=0.171 Sum_probs=49.8
Q ss_pred CCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316 135 SISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI 202 (229)
Q Consensus 135 ~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV 202 (229)
-+++.++|+.+||+..||+-|-+ .|.-.........|.|+++ +++..|..+.+=++|..++...+..
T Consensus 11 ~~~IgevAk~~gvs~~TlRyYE~-~GLi~~~r~~~g~R~Y~~~~i~~L~~I~~lr~lG~sL~eIk~ll~~ 79 (154)
T PRK15002 11 LLTPGEVAKRSGVAVSALHFYES-KGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGV 79 (154)
T ss_pred cccHHHHHHHHCcCHHHHHHHHH-CCCCCCccCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 47999999999999999999987 3432211112235777665 5777788888888999999998763
No 232
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=94.26 E-value=0.067 Score=47.32 Aligned_cols=40 Identities=15% Similarity=0.287 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCc
Q psy17316 122 EILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIR 162 (229)
Q Consensus 122 e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k 162 (229)
+.+..|-.+|+.| +-+.+||++|||+..|++.|.+++||.
T Consensus 7 ~~r~~Akk~yl~g-mk~~dIAeklGvspntiksWKrr~gWs 46 (279)
T COG5484 7 DKRIIAKKDYLKG-MKLKDIAEKLGVSPNTIKSWKRRDGWS 46 (279)
T ss_pred chHHHHHHHHHhh-ccHHHHHHHhCCChHHHHHHHHhcCCC
Confidence 4567888999999 699999999999999999999999984
No 233
>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=94.25 E-value=0.23 Score=39.08 Aligned_cols=68 Identities=9% Similarity=0.129 Sum_probs=47.5
Q ss_pred CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHH
Q psy17316 49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNV 126 (229)
Q Consensus 49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~ 126 (229)
.+++.++|+.+||+..||+.|-+. |+-.|.....+ ....|++++ +++
T Consensus 3 ~~tI~elA~~~gvs~~tlR~Ye~~-GLL~p~~r~~~------------------------------gyR~Y~~~~l~rL~ 51 (120)
T TIGR02054 3 AYTISRLAEDAGVSVHVVRDYLLR-GLLHPVRRTTS------------------------------GYGIFDDASLQRLR 51 (120)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCCC------------------------------CCeeCCHHHHHHHH
Confidence 479999999999999999999887 54333222111 234455554 466
Q ss_pred HHHHHHcCCCCHHHHHHHhCC
Q psy17316 127 ALDALRAGSISANKASKAYGI 147 (229)
Q Consensus 127 AV~~~~~g~~S~~~~a~k~gI 147 (229)
.|..+...++|+.+|..-...
T Consensus 52 ~I~~lr~~G~~L~eI~~ll~~ 72 (120)
T TIGR02054 52 FVRAAFEAGIGLGELARLCRA 72 (120)
T ss_pred HHHHHHHcCCCHHHHHHHHHh
Confidence 777878888899998776543
No 234
>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=94.23 E-value=0.22 Score=39.93 Aligned_cols=66 Identities=12% Similarity=0.181 Sum_probs=43.8
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
+++.++|+.+||+..||+.|-+. |.-.|..... ....|+++. +...
T Consensus 1 y~I~e~a~~~gvs~~TLR~Ye~~-GLl~p~r~~~-------------------------------g~R~Y~~~~l~~l~~ 48 (134)
T cd04779 1 YRIGQLAHLAGVSKRTIDYYTNL-GLLTPERSDS-------------------------------NYRYYDETALDRLQL 48 (134)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCccCCC-------------------------------CCeeECHHHHHHHHH
Confidence 47889999999999999999865 4432322110 123345444 4556
Q ss_pred HHHHHcCCCCHHHHHHHhCC
Q psy17316 128 LDALRAGSISANKASKAYGI 147 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~gI 147 (229)
|..+.+-++|+.+|......
T Consensus 49 I~~lr~~G~sL~eI~~~l~~ 68 (134)
T cd04779 49 IEHLKGQRLSLAEIKDQLEE 68 (134)
T ss_pred HHHHHHCCCCHHHHHHHHHh
Confidence 77777777888888776543
No 235
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=94.23 E-value=0.12 Score=37.35 Aligned_cols=38 Identities=24% Similarity=0.325 Sum_probs=36.3
Q ss_pred HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
..||..|..|.+|..+||+-.|+++..+..-+.++|+.
T Consensus 24 ~~Ai~lY~~g~iS~gkAAelag~s~~eF~~~L~~~gI~ 61 (76)
T PF03683_consen 24 ELAIKLYEEGKISLGKAAELAGMSRWEFLELLKERGIP 61 (76)
T ss_pred HHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHCCCC
Confidence 67899999999999999999999999999999999986
No 236
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=94.22 E-value=0.28 Score=39.30 Aligned_cols=66 Identities=11% Similarity=0.125 Sum_probs=48.9
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCc-ccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIR-LAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI 202 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k-~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV 202 (229)
+++.++|+.+||+..||+-|-+. |.- .........|-|+++ .++..|..+.+=+++..++...++.
T Consensus 1 m~Ige~a~~~gvs~~tlRyYE~~-GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~ 69 (135)
T PRK10227 1 MNISDVAKITGLTSKAIRFYEEK-GLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNL 69 (135)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCcccCCCCcccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 57899999999999999998873 432 211112346788765 5777888888877999999887764
No 237
>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=94.18 E-value=0.097 Score=37.84 Aligned_cols=36 Identities=14% Similarity=0.111 Sum_probs=28.3
Q ss_pred HHHHHHHHH-cCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 38 MDAALEALR-AGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 38 ~~~AI~~~~-~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
...|..... ..++|+.+||+.+|||.+|++.|+++.
T Consensus 20 ~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~ 56 (73)
T TIGR03879 20 AEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGE 56 (73)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcC
Confidence 334444433 468999999999999999999999963
No 238
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=94.17 E-value=0.95 Score=37.38 Aligned_cols=108 Identities=19% Similarity=0.260 Sum_probs=70.6
Q ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCC-----CCCCCCC-CCCCC-------------cHHHHHH
Q psy17316 34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI-----HTPKKEG-PTKSW-------------NEEILNV 94 (229)
Q Consensus 34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi-----~~~~~~~-~~k~~-------------s~e~~~~ 94 (229)
..+......+++..|=++..++...+|-..+-=-..+++-|. ..|.+.. +.|.| |=++..+
T Consensus 15 ~s~~~kkV~~~Ls~~W~T~~El~e~~G~d~~~~L~~LkK~gLiE~qWrmP~pG~kPeKEYhtsYs~vqaNFqcs~~DLsd 94 (160)
T PF09824_consen 15 NSEVYKKVYDELSKGWMTEEELEEKYGKDVRESLLILKKGGLIESQWRMPEPGEKPEKEYHTSYSKVQANFQCSMEDLSD 94 (160)
T ss_pred CCHHHHHHHHHHHhccCCHHHHHHHHCcCHHHHHHHHHHcCchhhccccCCCCCCchHHHHhhHhheeeeeEeeHHHHHH
Confidence 345556778888899999999999999887555556665442 1344442 32322 2222222
Q ss_pred HHHHHhhcchhhhhhhhccCCCCCCCHH-H---HHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh
Q psy17316 95 ALDALRAGSISANKASKAYGPTKSWNEE-I---LNVALDALRAGSISANKASKAYGIPSSTLYKIARKE 159 (229)
Q Consensus 95 a~~ll~~G~ls~~~~~~~~G~~~kYs~e-~---k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~ 159 (229)
.+. -..-+.| + ..+.++.+.+|..|+..+++++|++..-++-.+|+.
T Consensus 95 ii~------------------i~f~~deel~~~~e~i~~~v~~Gn~Sl~~lsr~l~~sp~firglAKRs 145 (160)
T PF09824_consen 95 IIY------------------IAFMSDEELRDYVEKIEKEVEAGNTSLSDLSRKLGISPVFIRGLAKRS 145 (160)
T ss_pred HHh------------------eeecCHHHHHHHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHhc
Confidence 221 0111112 2 355677888899999999999999999999988865
No 239
>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=94.14 E-value=0.23 Score=40.11 Aligned_cols=66 Identities=12% Similarity=0.268 Sum_probs=45.0
Q ss_pred CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHH
Q psy17316 49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNV 126 (229)
Q Consensus 49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~ 126 (229)
.|++.++|+.+||+..||+.|=+. |+-.|... . |....|++++ ++.
T Consensus 1 ~~~IgevA~~~Gvs~~tLRyYE~~-GLl~~~r~-~------------------------------~g~R~Y~~~di~~l~ 48 (142)
T TIGR01950 1 ELTVGELAKRSGVAVSALHFYESK-GLITSIRN-S------------------------------GNQRRYKRDVLRRVA 48 (142)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHC-CCCCCccC-C------------------------------CCCEEECHHHHHHHH
Confidence 378999999999999999999887 54333111 1 1134555555 355
Q ss_pred HHHHHHcCCCCHHHHHHHhC
Q psy17316 127 ALDALRAGSISANKASKAYG 146 (229)
Q Consensus 127 AV~~~~~g~~S~~~~a~k~g 146 (229)
.|..+.+-++|+.+|..-+.
T Consensus 49 ~I~~lr~~G~sL~eI~~~l~ 68 (142)
T TIGR01950 49 VIKAAQRVGIPLATIGEALA 68 (142)
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 56677777788888877654
No 240
>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=94.14 E-value=0.28 Score=38.63 Aligned_cols=66 Identities=3% Similarity=-0.023 Sum_probs=51.1
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCC-CCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQP-FNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI 202 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~-~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV 202 (229)
+++.++|+++||+..||+-|-+. |.-.... ..+..|.|+++ +++..|..+..-+++..++...++.
T Consensus 4 ~tI~elA~~~gvs~~tlR~Ye~~-GLL~p~~r~~~gyR~Y~~~~l~rL~~I~~lr~~G~~L~eI~~ll~~ 72 (120)
T TIGR02054 4 YTISRLAEDAGVSVHVVRDYLLR-GLLHPVRRTTSGYGIFDDASLQRLRFVRAAFEAGIGLGELARLCRA 72 (120)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCCCCCeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 68999999999999999998874 5432211 12346778766 6788899999999999999987764
No 241
>PF06627 DUF1153: Protein of unknown function (DUF1153); InterPro: IPR009534 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2OA4_A 2JRT_A.
Probab=94.14 E-value=0.2 Score=37.45 Aligned_cols=57 Identities=21% Similarity=0.341 Sum_probs=44.1
Q ss_pred CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCC
Q psy17316 28 TVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPT 84 (229)
Q Consensus 28 ~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~ 84 (229)
.-.+.|+.--+.+.|.+|..|-+|+.+|+++|+++..=+-.|.+...-.|..+++.|
T Consensus 28 ~~t~RWva~RKAaVV~aV~~Glis~~EA~~rY~Ls~eEf~~W~~av~rhge~aLraT 84 (90)
T PF06627_consen 28 PDTRRWVARRKAAVVRAVRGGLISVEEACRRYGLSEEEFESWQRAVDRHGENALRAT 84 (90)
T ss_dssp SS-S---HHHHHHHHHHHHCTTS-HHHHHHCTTSSHHHHHHHHHHCCT--TTSS-TC
T ss_pred cccccchhhHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhHHHHHHH
Confidence 346899999999999999999999999999999999999999999877776666543
No 242
>PHA02943 hypothetical protein; Provisional
Probab=94.13 E-value=0.12 Score=42.61 Aligned_cols=42 Identities=14% Similarity=0.181 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316 176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-LSRST 217 (229)
Q Consensus 176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~ 217 (229)
.+.+.+|++++..|..|..++|+.+|+|++++...++ +.+.|
T Consensus 10 ~~R~~eILE~Lk~G~~TtseIAkaLGlS~~qa~~~LyvLErEG 52 (165)
T PHA02943 10 HTRMIKTLRLLADGCKTTSRIANKLGVSHSMARNALYQLAKEG 52 (165)
T ss_pred HHHHHHHHHHHhcCCccHHHHHHHHCCCHHHHHHHHHHHHHcC
Confidence 3678999999988889999999999999999999998 66665
No 243
>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=94.13 E-value=0.082 Score=36.13 Aligned_cols=38 Identities=21% Similarity=0.288 Sum_probs=32.3
Q ss_pred HHHHHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 36 EDMDAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 36 e~~~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
.....++..+ .++.++..++|..+|||.+|+++.++.+
T Consensus 10 p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L 48 (61)
T PF12840_consen 10 PTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKL 48 (61)
T ss_dssp HHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4456777777 7899999999999999999999999975
No 244
>PHA00542 putative Cro-like protein
Probab=94.11 E-value=0.075 Score=38.87 Aligned_cols=30 Identities=13% Similarity=0.049 Sum_probs=26.6
Q ss_pred HHHHHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316 42 LEALRAGQMSLTKASVSYGIPSTTLWQRAH 71 (229)
Q Consensus 42 I~~~~~g~~S~~~aA~~~gIp~sTL~~~i~ 71 (229)
+..+...++|+.++|+.+||+++||++|..
T Consensus 24 ~~~l~~~glTq~elA~~lgIs~~tIsr~e~ 53 (82)
T PHA00542 24 VCALIRAGWSQEQIADATDVSQPTICRIYS 53 (82)
T ss_pred HHHHHHCCCCHHHHHHHHCcCHHHHHHHHc
Confidence 345567899999999999999999999987
No 245
>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=94.09 E-value=3.6 Score=35.66 Aligned_cols=153 Identities=11% Similarity=0.112 Sum_probs=86.0
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCC-CCCCCCCCCcHHHHHHH--HHHHhhcchhhhhhhhccCCCCC-CCHHHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTP-KKEGPTKSWNEEILNVA--LDALRAGSISANKASKAYGPTKS-WNEEILN 125 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~-~~~~~~k~~s~e~~~~a--~~ll~~G~ls~~~~~~~~G~~~k-Ys~e~k~ 125 (229)
+++.++|+..||+..||+.|-++ |+-.| .....+.-|+++..... +..+.+-..+-++|...+.-... -.-...+
T Consensus 2 y~i~elA~~~Gvs~~tIR~Ye~~-GLL~p~r~~~~~r~Y~~~~v~rL~~I~~l~~~G~~L~~I~~~l~~~~~g~~l~~~l 80 (219)
T cd04778 2 YRIDDLARAAGTTVRNVRAYQDR-GLLPPPRRRGRVAIYNDSHLARLRLINQLLERGYTLAHIAELLAAWEQGRDLGDVL 80 (219)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCcccCCCCcccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhhhcCCCHHHHH
Confidence 68999999999999999999988 54333 33233457887655332 22333333346666654322111 0111111
Q ss_pred HHHHHH-------HcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHHH
Q psy17316 126 VALDAL-------RAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASA 198 (229)
Q Consensus 126 ~AV~~~-------~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~ 198 (229)
...... ..+.+|..++++.+| +.++|.+|+. .|+-...+ ...+.++. ...+++..+...++....+..
T Consensus 81 ~~~~~~~~~~~~~~~~~~t~~eL~~~~G-~~~~l~~l~~-~Gll~pd~--~~~~~~~~-~~~~~~~~L~~~Gi~~~~i~~ 155 (219)
T cd04778 81 GLQAAIDGPWSTEEPGTALLAELQSEFG-DERALARAVA-LGLLEPDG--DRVLVPSP-RLLEALAELVDAGIPLRAVLD 155 (219)
T ss_pred hhhccccCCccCCCCCccCHHHHHHHHC-CHHHHHHHHH-CCCceeCC--CCCcccCH-HHHHHHHHHHHcCCCHHHHHH
Confidence 110110 123568999999999 8788999988 66433221 11233333 456666666666677776655
Q ss_pred HhCCChHHHH
Q psy17316 199 EYGIPSGTLY 208 (229)
Q Consensus 199 ~fgVp~~tv~ 208 (229)
+...=++.+-
T Consensus 156 ~lr~~r~~ad 165 (219)
T cd04778 156 LVAAVRRHAD 165 (219)
T ss_pred HHHHHHHHHH
Confidence 5544443333
No 246
>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=94.07 E-value=0.12 Score=35.06 Aligned_cols=38 Identities=21% Similarity=0.402 Sum_probs=30.6
Q ss_pred HHHHHHHHh-CCCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316 180 EIALEGIRS-GQTTVQRASAEYGIPSGTLYGRCK-LSRST 217 (229)
Q Consensus 180 ~eaV~~~~~-~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~ 217 (229)
..|++++.. +..++.++|..||||..|+++-++ +...|
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g 42 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQG 42 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 466777765 568999999999999999999887 44444
No 247
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=94.05 E-value=0.087 Score=42.70 Aligned_cols=46 Identities=15% Similarity=0.372 Sum_probs=33.9
Q ss_pred CCCCHHHH-HHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 31 KTWTHEDM-DAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 31 ~kyt~e~~-~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
.+++.|++ ...|+.+ .+|..|..++|+++|++++|+++++++..-.
T Consensus 3 ~~~~lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~ 50 (153)
T PRK11179 3 ENYQIDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQA 50 (153)
T ss_pred cccccCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34444555 3334433 5789999999999999999999999986433
No 248
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=94.02 E-value=0.082 Score=40.57 Aligned_cols=36 Identities=22% Similarity=0.269 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
+.-.+++++....++|+.|+|..+|||++.|+.+++
T Consensus 20 ~kQ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ik 55 (101)
T PF04297_consen 20 EKQREILELYYEEDLSLSEIAEELGISRQAVYDSIK 55 (101)
T ss_dssp HHHHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345678888889999999999999999999999998
No 249
>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=93.99 E-value=0.3 Score=38.79 Aligned_cols=67 Identities=12% Similarity=0.142 Sum_probs=45.9
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
|++.++|+.+||+..||+.|-+ .|+-.|.....+ ....|++++ +...
T Consensus 1 m~IgE~A~~~gvs~~TLRyYE~-~GLl~p~r~~~~------------------------------gyR~Y~~~~~~~l~~ 49 (133)
T cd04787 1 MKVKELANAAGVTPDTVRFYTR-IGLLRPTRDPVN------------------------------GYRLYSEKDLSRLRF 49 (133)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCcCCCC------------------------------CeeeCCHHHHHHHHH
Confidence 6889999999999999988854 455434221101 134555555 4566
Q ss_pred HHHHHcCCCCHHHHHHHhCC
Q psy17316 128 LDALRAGSISANKASKAYGI 147 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~gI 147 (229)
|..+.+-++|+.+|..-+..
T Consensus 50 I~~lr~~G~sL~eI~~~l~~ 69 (133)
T cd04787 50 ILSARQLGFSLKDIKEILSH 69 (133)
T ss_pred HHHHHHcCCCHHHHHHHHhh
Confidence 77888888899998776654
No 250
>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional
Probab=93.95 E-value=0.086 Score=51.50 Aligned_cols=40 Identities=28% Similarity=0.222 Sum_probs=31.6
Q ss_pred HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
++..+.+.+...+....++|+.+||+++|||+++++||..
T Consensus 498 Er~~I~~~L~~~~Gn~~~aA~~LGIsRtTL~RkLk~~g~~ 537 (538)
T PRK15424 498 LAATLQQALERFNGDKTAAANYLGISRTTLWRRLKAEAKA 537 (538)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence 4444445555556689999999999999999999999753
No 251
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=93.88 E-value=0.075 Score=53.06 Aligned_cols=40 Identities=28% Similarity=0.414 Sum_probs=30.7
Q ss_pred HHHHHHHHHHcCCCCH---HHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 37 DMDAALEALRAGQMSL---TKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 37 ~~~~AI~~~~~g~~S~---~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
++..+++++...+..+ ..+|+.+||+++|||+++++|||.
T Consensus 642 Er~~I~~aL~~~~gn~~~~~~aA~~LGi~R~tL~rklk~~gi~ 684 (686)
T PRK15429 642 EYQLIVRVLKETNGVVAGPKGAAQRLGLKRTTLLSRMKRLGID 684 (686)
T ss_pred HHHHHHHHHHHcCCCcccHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 4445555555544344 599999999999999999999985
No 252
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=93.87 E-value=0.33 Score=35.04 Aligned_cols=49 Identities=24% Similarity=0.411 Sum_probs=41.4
Q ss_pred HHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHH
Q psy17316 124 LNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEI 181 (229)
Q Consensus 124 k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~e 181 (229)
..-||.+|..|.+|+.++|+..|+++......++++|+. . .|+.++..+
T Consensus 23 ~~~Ai~lY~~g~iS~gkAAelag~s~~eF~~~L~~~gI~-~--------~~~~eel~~ 71 (76)
T PF03683_consen 23 EELAIKLYEEGKISLGKAAELAGMSRWEFLELLKERGIP-I--------NYDEEELEE 71 (76)
T ss_pred HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHCCCC-C--------CCCHHHHHH
Confidence 477899999999999999999999999999999988877 3 266665544
No 253
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=93.87 E-value=1.1 Score=40.15 Aligned_cols=78 Identities=13% Similarity=0.147 Sum_probs=58.9
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH-H
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI-L 124 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~-k 124 (229)
...+++.++|+.+||++++|.+..++. |... . .|-... +
T Consensus 205 ~~~~tl~~lA~~~~~S~~~l~r~Fk~~~G~t~------------~---------------------------~~l~~~Rl 245 (302)
T PRK10371 205 DQALTINDVAEHVKLNANYAMGIFQRVMQLTM------------K---------------------------QYITAMRI 245 (302)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHhCCCH------------H---------------------------HHHHHHHH
Confidence 357999999999999999999999984 4421 1 111222 4
Q ss_pred HHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316 125 NVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL 163 (229)
Q Consensus 125 ~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~ 163 (229)
..|..++.++..|+.+||...|-+..+ ..+-.|+. |..+
T Consensus 246 ~~A~~lL~~~~~si~eIA~~~Gf~~~s~F~r~Fk~~~G~tP 286 (302)
T PRK10371 246 NHVRALLSDTDKSILDIALTAGFRSSSRFYSTFGKYVGMSP 286 (302)
T ss_pred HHHHHHHhcCCCCHHHHHHHcCCCCHHHHHHHHHHHHCcCH
Confidence 678888888888999999999999977 66666654 6444
No 254
>TIGR03734 PRTRC_parB PRTRC system ParB family protein. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family the member related to ParB, and is designated PRTRC system ParB family protein.
Probab=93.83 E-value=0.67 Score=45.49 Aligned_cols=93 Identities=17% Similarity=0.097 Sum_probs=62.4
Q ss_pred CCCCCCHHHHHHHHHHHHc-CCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhh
Q psy17316 29 VTKTWTHEDMDAALEALRA-GQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISAN 107 (229)
Q Consensus 29 ~~~kyt~e~~~~AI~~~~~-g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~ 107 (229)
-+...++-|...++..+.. |..+..+||+++|+++++|+++++-.. . +|+ .+++|.+|.++-.
T Consensus 88 qRedLtP~EeA~A~~rLl~~g~~t~eeIA~~lG~S~~~V~rrLkL~~------L------~p~----ll~al~~g~Itl~ 151 (554)
T TIGR03734 88 QRADMSPAEEAEAAARLLGRCKGDREEAARRLGWSPATLDRRLALMN------C------TDE----VRQALIDRKILLG 151 (554)
T ss_pred ccCCCCHHHHHHHHHHHhhhcCCCHHHHHHHHCCCHHHHHHHHHHcC------C------CHH----HHHHHHcCCCChH
Confidence 3566777777777766655 444999999999999999999998421 2 333 5678888988777
Q ss_pred hhhhccCCCCCCCHHHHHHHHHHHHcCCCCHHHH
Q psy17316 108 KASKAYGPTKSWNEEILNVALDALRAGSISANKA 141 (229)
Q Consensus 108 ~~~~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~ 141 (229)
++-...+.+ .+.-.++++.+..+..++.+|
T Consensus 152 ~A~aLA~l~----~e~Q~~vl~~~~~~~~sv~~i 181 (554)
T TIGR03734 152 HAELLAGLP----KDKQDNVLTAILAEKPTVAEL 181 (554)
T ss_pred HHHHHhcCC----HHHHHHHHHHHHHcCCCHHHH
Confidence 766543332 444455566665554444433
No 255
>PRK01381 Trp operon repressor; Provisional
Probab=93.75 E-value=0.062 Score=41.04 Aligned_cols=36 Identities=14% Similarity=0.165 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
..|..|++.+.+|++|++++|.++|||..||-+=.+
T Consensus 42 ~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn 77 (99)
T PRK01381 42 GTRVRIVEELLRGELSQREIKQELGVGIATITRGSN 77 (99)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHH
Confidence 358889999999999999999999999999877655
No 256
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=93.74 E-value=0.15 Score=42.39 Aligned_cols=41 Identities=22% Similarity=0.237 Sum_probs=34.8
Q ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
+.+|.+..+=.+|..+++|+-.||..+|||.+|.++|-++-
T Consensus 3 h~~e~R~~~R~~YV~~~~sLe~aA~~~gVs~~TarrWK~~A 43 (165)
T PF08822_consen 3 HPQETRDAVRRAYVFDRLSLEQAAAKCGVSYATARRWKREA 43 (165)
T ss_pred CcHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 34556666667899899999999999999999999999864
No 257
>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=93.73 E-value=0.07 Score=37.15 Aligned_cols=39 Identities=18% Similarity=0.345 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316 36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG 74 (229)
Q Consensus 36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g 74 (229)
.+..-.+..+.+|.++..+||+..|||++++++.++.+.
T Consensus 9 ~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~ 47 (68)
T PF01978_consen 9 NEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLE 47 (68)
T ss_dssp HHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 333333334579999999999999999999999998763
No 258
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=93.71 E-value=0.46 Score=36.54 Aligned_cols=69 Identities=14% Similarity=0.162 Sum_probs=45.5
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
+++.++|+.+||+..||+.|-+...+..+.... |...-|++++ ++..
T Consensus 1 ~~I~eva~~~gvs~~tLRyYE~~GLl~p~~~~~-------------------------------~gyR~Ys~~dl~~l~~ 49 (124)
T COG0789 1 YTIGEVAKLTGVSVRTLRFYERKGLLSPERRDE-------------------------------GGYRYYTPEDLELLQI 49 (124)
T ss_pred CcHHHHHHHhCCCHHHHHHHHHcCCCCCcccCC-------------------------------CCceecCHHHHHHHHH
Confidence 578999999999999999998886555432221 1133444444 3444
Q ss_pred HHHHHcCCCCHHHHHHHhCCCh
Q psy17316 128 LDALRAGSISANKASKAYGIPS 149 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~gIp~ 149 (229)
|....+-++|+.+|-.-.....
T Consensus 50 I~~~r~~G~~L~~I~~~l~~~~ 71 (124)
T COG0789 50 IKTLRELGFSLAEIKELLDLLS 71 (124)
T ss_pred HHHHHHcCCCHHHHHHHHhccc
Confidence 5566655668888877665554
No 259
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=93.68 E-value=0.36 Score=38.62 Aligned_cols=66 Identities=9% Similarity=0.145 Sum_probs=43.4
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
|++.++|+.+||+..||+.|=+..-+..+... . +....|++++ ++..
T Consensus 1 m~Ige~a~~~gvs~~tlRyYE~~GLl~p~~r~-~------------------------------~gyR~Y~~~~l~~l~~ 49 (135)
T PRK10227 1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRS-E------------------------------NGYRTYTQQHLNELTL 49 (135)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCcccC-C------------------------------CCcccCCHHHHHHHHH
Confidence 68999999999999999999776433322111 1 1133455444 3556
Q ss_pred HHHHHcCCCCHHHHHHHhC
Q psy17316 128 LDALRAGSISANKASKAYG 146 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~g 146 (229)
|..+.+-++|+.+|..-++
T Consensus 50 I~~lr~~G~sl~eI~~~l~ 68 (135)
T PRK10227 50 LRQARQVGFNLEESGELVN 68 (135)
T ss_pred HHHHHHCCCCHHHHHHHHH
Confidence 6666666678888876654
No 260
>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=93.67 E-value=0.12 Score=34.05 Aligned_cols=30 Identities=13% Similarity=0.046 Sum_probs=25.0
Q ss_pred HHHHhCCCcHHHHHHHhCCChHHHHHHHHh
Q psy17316 184 EGIRSGQTTVQRASAEYGIPSGTLYGRCKL 213 (229)
Q Consensus 184 ~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~ 213 (229)
+.+.+.++|+.+.|...|||+++|.+|.++
T Consensus 3 ~~r~~~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 3 ELRKEKGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HHHHHTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHHcCCCHHHHHHHhCCCcchhHHHhcC
Confidence 455678899999999999999999999987
No 261
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=93.53 E-value=0.31 Score=40.02 Aligned_cols=66 Identities=11% Similarity=0.205 Sum_probs=45.9
Q ss_pred CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHH
Q psy17316 49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNV 126 (229)
Q Consensus 49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~ 126 (229)
-+++.++|+.+||+..||+.|-+.--+...+.. |....|+++. ++.
T Consensus 11 ~~~IgevAk~~gvs~~TlRyYE~~GLi~~~r~~--------------------------------~g~R~Y~~~~i~~L~ 58 (154)
T PRK15002 11 LLTPGEVAKRSGVAVSALHFYESKGLITSIRNS--------------------------------GNQRRYKRDVLRYVA 58 (154)
T ss_pred cccHHHHHHHHCcCHHHHHHHHHCCCCCCccCC--------------------------------CCCEEECHHHHHHHH
Confidence 489999999999999999999886333221111 1234555555 355
Q ss_pred HHHHHHcCCCCHHHHHHHhC
Q psy17316 127 ALDALRAGSISANKASKAYG 146 (229)
Q Consensus 127 AV~~~~~g~~S~~~~a~k~g 146 (229)
.|..+.+-++|+.+|..-+.
T Consensus 59 ~I~~lr~lG~sL~eIk~ll~ 78 (154)
T PRK15002 59 IIKIAQRIGIPLATIGEAFG 78 (154)
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 67777777789999888664
No 262
>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=93.49 E-value=0.13 Score=34.65 Aligned_cols=31 Identities=19% Similarity=0.267 Sum_probs=26.8
Q ss_pred HHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 181 IALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 181 eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
+++.++..| ++..++|..++||..||+.+.+
T Consensus 10 ~vl~~l~~G-~~~~eIA~~l~is~~tV~~~~~ 40 (58)
T PF00196_consen 10 EVLRLLAQG-MSNKEIAEELGISEKTVKSHRR 40 (58)
T ss_dssp HHHHHHHTT-S-HHHHHHHHTSHHHHHHHHHH
T ss_pred HHHHHHHhc-CCcchhHHhcCcchhhHHHHHH
Confidence 477777777 9999999999999999999886
No 263
>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=93.47 E-value=0.28 Score=33.20 Aligned_cols=39 Identities=21% Similarity=0.327 Sum_probs=30.3
Q ss_pred CHHHHHHHHHHHHcC------CCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 34 THEDMDAALEALRAG------QMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 34 t~e~~~~AI~~~~~g------~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
|+.++.....+|..| +.++.++|+++||+++|+...+++
T Consensus 2 T~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 2 TDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred CHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 444554445566554 689999999999999999999986
No 264
>PF13309 HTH_22: HTH domain
Probab=93.45 E-value=0.11 Score=36.40 Aligned_cols=42 Identities=12% Similarity=0.189 Sum_probs=35.3
Q ss_pred CCCCCHHHHHHHHHHHHcCC-----CCHHHHHHHcCCChhhHHHHHH
Q psy17316 30 TKTWTHEDMDAALEALRAGQ-----MSLTKASVSYGIPSTTLWQRAH 71 (229)
Q Consensus 30 ~~kyt~e~~~~AI~~~~~g~-----~S~~~aA~~~gIp~sTL~~~i~ 71 (229)
....+.+++.++|+.+.+.| -++..+|+.+||++.|||+.++
T Consensus 18 ~~~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YLr 64 (64)
T PF13309_consen 18 PSRLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYLR 64 (64)
T ss_pred hhhCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHcC
Confidence 35678899999999886644 5899999999999999998763
No 265
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=93.45 E-value=0.1 Score=39.98 Aligned_cols=34 Identities=21% Similarity=0.358 Sum_probs=27.6
Q ss_pred HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
..+++.|-..++|+.+||..+||++..+++++++
T Consensus 23 ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr 56 (101)
T PF04297_consen 23 REILELYYEEDLSLSEIAEELGISRQAVYDSIKR 56 (101)
T ss_dssp HHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4678899999999999999999999999999997
No 266
>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=93.43 E-value=0.57 Score=35.60 Aligned_cols=65 Identities=18% Similarity=0.180 Sum_probs=44.0
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA 127 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A 127 (229)
|++.++|+.+||+..||+.|-+. |+-.|.... ....|++++ +...
T Consensus 1 m~Ige~a~~~gvs~~tlRyYe~~-GLl~p~~~~--------------------------------g~r~Y~~~~~~~l~~ 47 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHYIDL-GLLIPEKKG--------------------------------GQYFFDEKCQDDLEF 47 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCcCCccCC--------------------------------CccccCHHHHHHHHH
Confidence 68899999999999999999775 433232211 122355444 3556
Q ss_pred HHHHHcCCCCHHHHHHHhCC
Q psy17316 128 LDALRAGSISANKASKAYGI 147 (229)
Q Consensus 128 V~~~~~g~~S~~~~a~k~gI 147 (229)
|..+.+=++|+.+|..-+..
T Consensus 48 I~~lr~~G~sL~eI~~~l~~ 67 (107)
T cd04777 48 ILELKGLGFSLIEIQKIFSY 67 (107)
T ss_pred HHHHHHCCCCHHHHHHHHHh
Confidence 67777767899888876654
No 267
>PF03333 PapB: Adhesin biosynthesis transcription regulatory protein; InterPro: IPR004356 P pili, or fimbriae, are ~68A in diameter and 1 micron in length, the bulk of which is a fibre composed of the main structural protein PapA []. At its tip, the pilus is terminated by a fibrillum consisting of repeating units of the PapE protein. This, in turn, is topped by the adhesins, PapF and PapG, both of which are needed for receptor binding. The tip fibrillum is anchored to the main PapA fibre by the PapK pilus-adaptor protein. PapH, an outer membrane protein, then anchors the entire rod in the bacterial envelope []. A cytoplasmic chaperone (PapD) assists in assembling the monomers of the macromolecule in the membrane. All of the functional pap genes are arranged in a cluster (operon) on the Escherichia coli genome. It is believed that selective pressure exerted by the host's urinal and intestinal tract isoreceptors forced the spread of this operon to other strains via lateral transfer []. PapB, encoded within the cluster, acts as a transcriptional regulator of the functional pap genes and is located in the bacterial cytoplasm []. Its mechanism involves differential binding to separate sites in the cluster, suggesting that this protein is both an activator and repressor of pilus-adhesion transcription. The protein shares similarity with other E. coli fimbrial- adhesion transcription regulators, such as AfaA, DaaA and FanB. ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 3M8J_A.
Probab=93.39 E-value=0.18 Score=37.94 Aligned_cols=43 Identities=21% Similarity=0.213 Sum_probs=31.3
Q ss_pred CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
++...+++..|+++++-.|.|.++||.+|||+.+-+...+.+.
T Consensus 35 s~IrS~kiI~AL~dyLV~G~srkeac~~~gV~~syfs~~L~rL 77 (91)
T PF03333_consen 35 SSIRSEKIIAALRDYLVDGLSRKEACERHGVNQSYFSRALNRL 77 (91)
T ss_dssp S----HHHHHHHHHHHTT---HHHHHHHTT--HHHHHHHHHHH
T ss_pred CCCCcHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHH
Confidence 4567789999999999999999999999999999999988864
No 268
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=93.39 E-value=0.16 Score=37.28 Aligned_cols=57 Identities=11% Similarity=0.176 Sum_probs=40.4
Q ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHH
Q psy17316 33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDAL 99 (229)
Q Consensus 33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll 99 (229)
|-++-..++++.+..|.+++.++|+.+||+.+|+++-+... +. ..+++.+....++.
T Consensus 3 ~~~~R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~~~----~~------~Vs~~Tr~rV~~aa 59 (80)
T TIGR02844 3 YIEERVLEIGKYIVETKATVRETAKVFGVSKSTVHKDVTER----LP------EINPELAEEVKEVL 59 (80)
T ss_pred cHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhcCC----CC------CCCHHHHHHHHHHH
Confidence 44555567777776799999999999999999999965310 01 13677776666544
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=93.38 E-value=0.38 Score=37.78 Aligned_cols=68 Identities=12% Similarity=0.148 Sum_probs=43.7
Q ss_pred CHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHHH
Q psy17316 51 SLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVAL 128 (229)
Q Consensus 51 S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~AV 128 (229)
++.++|+.+||+..||+.|-+..-+..+... . |....|++++ +...|
T Consensus 1 ~I~e~a~~~gvs~~tlR~Ye~~GLl~~~~r~-~------------------------------~g~R~Y~~~~l~~l~~I 49 (124)
T TIGR02051 1 TIGELAKAAGVNVETIRYYERKGLLPEPDRP-E------------------------------GGYRRYPEETVKRLRFI 49 (124)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCCCccC-C------------------------------CCCEeECHHHHHHHHHH
Confidence 5789999999999999999665333322111 1 1123444444 34556
Q ss_pred HHHHcCCCCHHHHHHHhCCCh
Q psy17316 129 DALRAGSISANKASKAYGIPS 149 (229)
Q Consensus 129 ~~~~~g~~S~~~~a~k~gIp~ 149 (229)
..+..-++|+.+|..-+....
T Consensus 50 ~~l~~~G~sl~eI~~~l~~~~ 70 (124)
T TIGR02051 50 KRAQELGFSLEEIGGLLGLVD 70 (124)
T ss_pred HHHHHCCCCHHHHHHHHhccc
Confidence 666777789999988776543
No 270
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=93.30 E-value=0.14 Score=34.91 Aligned_cols=35 Identities=20% Similarity=0.217 Sum_probs=28.3
Q ss_pred HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
.+.+..|.+.+.++.++|+.++|.+.||+.++++.
T Consensus 2 ~~TL~~yl~~~~n~~~tA~~L~iHrNTl~yRl~ki 36 (59)
T PF13556_consen 2 LETLRAYLENNGNISKTARALHIHRNTLRYRLKKI 36 (59)
T ss_dssp --HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred hhHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45677888888899999999999999999999984
No 271
>PF14493 HTH_40: Helix-turn-helix domain
Probab=93.29 E-value=0.88 Score=33.60 Aligned_cols=78 Identities=14% Similarity=0.165 Sum_probs=54.6
Q ss_pred HHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh---CCcccCCCCCCCCCCCHHHHHHHHHHHHhCC-CcHHHHHHHh
Q psy17316 125 NVALDALRAGSISANKASKAYGIPSSTLYKIARKE---GIRLAQPFNASPTAWKPEDLEIALEGIRSGQ-TTVQRASAEY 200 (229)
Q Consensus 125 ~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~---g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~-~s~~eAA~~f 200 (229)
+...+++.+|. |+.+||++-|+..+|++.++-+. |..... ..-.+.|+...|.+.+.+.+ .+++.+=..+
T Consensus 4 ~~T~~l~~~G~-si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~~-----~~~l~~e~~~~I~~~~~~~~~~~lk~i~e~l 77 (91)
T PF14493_consen 4 QITYELFQKGL-SIEEIAKIRGLKESTIYGHLAELIESGEPLDI-----EELLSEEEIKQIEDAIEKLGSEKLKPIKEAL 77 (91)
T ss_pred HHHHHHHHcCC-CHHHHHHHcCCCHHHHHHHHHHHHHhCCCCCH-----HHhCCHHHHHHHHHHHHHcCcccHHHHHHHC
Confidence 55677888775 99999999999999988887543 322211 12246677777777776533 5677777777
Q ss_pred C--CChHHHH
Q psy17316 201 G--IPSGTLY 208 (229)
Q Consensus 201 g--Vp~~tv~ 208 (229)
+ ++|..+.
T Consensus 78 ~~~~sy~~iR 87 (91)
T PF14493_consen 78 PGDYSYFEIR 87 (91)
T ss_pred CCCCCHHHHH
Confidence 7 8877764
No 272
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=93.26 E-value=0.2 Score=37.37 Aligned_cols=36 Identities=8% Similarity=0.072 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
..|.+|++.+..++++|++++..+|||-.|+-+--+
T Consensus 36 ~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr 71 (87)
T PF01371_consen 36 AQRWQVAKELLDEGKSYREIAEETGVSIATITRVSR 71 (87)
T ss_dssp HHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 358899996677779999999999999999977655
No 273
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=93.23 E-value=0.64 Score=43.06 Aligned_cols=87 Identities=18% Similarity=0.218 Sum_probs=59.9
Q ss_pred HHHHHHHHH-cCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCC
Q psy17316 38 MDAALEALR-AGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGP 115 (229)
Q Consensus 38 ~~~AI~~~~-~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~ 115 (229)
+..+++.+. +..+++.++|..+|++.++|.++.++. |.. +......+
T Consensus 87 i~~a~~~I~~~~~lsl~eLA~~lG~S~~~L~R~Fkk~~G~T------------P~~yl~~~------------------- 135 (353)
T PRK15435 87 ITHACRLLEQETPVTLEALADQVAMSPFHLHRLFKATTGMT------------PKAWQQAW------------------- 135 (353)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHCcC------------HHHHHHHH-------------------
Confidence 455655553 467999999999999999999999984 543 11111111
Q ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316 116 TKSWNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL 163 (229)
Q Consensus 116 ~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~ 163 (229)
-+..|.+++..+ .|+.+||...|-+..+ +++..++. |...
T Consensus 136 -------Rl~~A~~lL~~~-~sI~eIA~~~Gf~s~s~F~~~Fkk~~G~TP 177 (353)
T PRK15435 136 -------RARRLREALAKG-ESVTTSILNAGFPDSSSYYRKADETLGMTA 177 (353)
T ss_pred -------HHHHHHHHHhCC-CCHHHHHHHhCCCChHHHHHHHHHHHCcCc
Confidence 134555666554 6999999999998866 77777654 5433
No 274
>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=93.20 E-value=0.24 Score=35.84 Aligned_cols=37 Identities=22% Similarity=0.123 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHH-hCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 176 PEDLEIALEGIR-SGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 176 ~e~r~eaV~~~~-~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
++....|...+. ..++|+.|+|..+|||.+||..++.
T Consensus 17 ~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~ 54 (73)
T TIGR03879 17 DSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLK 54 (73)
T ss_pred CHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence 344555555554 4779999999999999999999988
No 275
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=93.19 E-value=2.5 Score=31.47 Aligned_cols=89 Identities=18% Similarity=0.209 Sum_probs=63.7
Q ss_pred HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH-hCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCC
Q psy17316 37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR-LGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGP 115 (229)
Q Consensus 37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~-~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~ 115 (229)
.+...|.....+++++.++|...|+++++|.+..++ .|.... +..
T Consensus 24 ~~~~~i~~~~~~~~~l~~la~~~g~S~~~l~r~f~~~~g~s~~-----------~~~----------------------- 69 (127)
T COG2207 24 RALDYIEENLAEPLTLEDLARRLGMSRRTLSRLFKKETGTSPS-----------QYL----------------------- 69 (127)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHH-----------HHH-----------------------
Confidence 555555555566789999999999999999999995 344310 000
Q ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316 116 TKSWNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL 163 (229)
Q Consensus 116 ~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~ 163 (229)
..-.+..|...+..+..++.+||...|-+... ..+..++. |..+
T Consensus 70 ----~~~Rl~~A~~lL~~~~~~i~~iA~~~Gf~~~s~F~~~Fk~~~g~tP 115 (127)
T COG2207 70 ----RQLRLEEARRLLRSTDLSITEIALRLGYSSPSHFSRAFKRLFGVTP 115 (127)
T ss_pred ----HHHHHHHHHHHHHcCCCCHHHHHHHhCcCCHHHHHHHHHHHhCCCh
Confidence 01235778888888888999999999999977 66655543 5433
No 276
>PRK15044 transcriptional regulator SirC; Provisional
Probab=93.19 E-value=0.4 Score=43.48 Aligned_cols=82 Identities=11% Similarity=0.126 Sum_probs=60.1
Q ss_pred HcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHH
Q psy17316 132 RAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRC 211 (229)
Q Consensus 132 ~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~v 211 (229)
.....++.++|++.|++.++|.+..+..|.... .-+....+..|.+.+..+++++.++|.+.|-+..+-...+
T Consensus 205 l~~~~SLeeLA~~lgmS~~tL~R~Fk~eg~T~~-------~y~~~~RL~~A~~LL~~t~~sIseIA~~~GFss~S~FsRa 277 (295)
T PRK15044 205 LTRKWSQAEVAGKLFMSVSSLKRKLAAEEVSFS-------KIYLDARMNQAIKLLRMGAGNISQVATMCGYDTPSYFIAI 277 (295)
T ss_pred cccCCCHHHHHHHhCCCHHHHHHHHHHcCCCHH-------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHH
Confidence 344579999999999999999999987652221 1233444567788888899999999999998888777665
Q ss_pred HhhcCCCCC
Q psy17316 212 KLSRSTPRP 220 (229)
Q Consensus 212 k~~~~~~~~ 220 (229)
=...-|-+|
T Consensus 278 FKk~fG~TP 286 (295)
T PRK15044 278 FKRHFKITP 286 (295)
T ss_pred HHHHHCcCH
Confidence 433334444
No 277
>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=93.16 E-value=0.099 Score=34.46 Aligned_cols=27 Identities=15% Similarity=0.212 Sum_probs=22.6
Q ss_pred HcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 46 RAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 46 ~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
...++|+.++|+..||+++||.+|...
T Consensus 6 ~~~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 6 KEKGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HHTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHcCCCHHHHHHHhCCCcchhHHHhcC
Confidence 467999999999999999999999883
No 278
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=93.04 E-value=0.34 Score=38.58 Aligned_cols=42 Identities=21% Similarity=0.295 Sum_probs=36.2
Q ss_pred CCCCCHHHHHHHHHHHHh-----CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 171 PTAWKPEDLEIALEGIRS-----GQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 171 ~r~~t~e~r~eaV~~~~~-----~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
.+.+|+|+|.++...|++ |.++..+++..+|+++.|+...++
T Consensus 2 a~~~T~eer~eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lr 48 (127)
T PF06163_consen 2 ARVFTPEEREELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLR 48 (127)
T ss_pred CCcCCHHHHHHHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHH
Confidence 367889998887666665 789999999999999999999988
No 279
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=93.04 E-value=0.45 Score=42.91 Aligned_cols=87 Identities=13% Similarity=0.140 Sum_probs=59.7
Q ss_pred HHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHH
Q psy17316 127 ALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGT 206 (229)
Q Consensus 127 AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~t 206 (229)
+|..-.....++.++|+.+|++.+||.+..++.|.... ..+..-.+..|.+++..+++++.++|...|-+-++
T Consensus 189 ~I~~~~~~~~sl~~lA~~~gmS~stl~R~Fk~~g~s~~-------~~~~~~Rl~~A~~lL~~~~~sI~~IA~~~GY~s~S 261 (291)
T PRK15186 189 IIISDISRKWALKDISDSLYMSCSTLKRKLKQENTSFS-------EVYLNARMNKATKLLRNSEYNITRVAYMCGYDSAS 261 (291)
T ss_pred HHHhCccCCCCHHHHHHHHCcCHHHHHHHHHHcCCCHH-------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHH
Confidence 33333445679999999999999999999987653222 11223345566777777789999999999987766
Q ss_pred HHHHHHhhcCCCCC
Q psy17316 207 LYGRCKLSRSTPRP 220 (229)
Q Consensus 207 v~~~vk~~~~~~~~ 220 (229)
-...+=...-|-+|
T Consensus 262 ~Fsr~FK~~~G~TP 275 (291)
T PRK15186 262 YFTCVFKKHFKTTP 275 (291)
T ss_pred HHHHHHHHHHCcCH
Confidence 66554333334444
No 280
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=92.98 E-value=0.28 Score=31.36 Aligned_cols=36 Identities=17% Similarity=0.323 Sum_probs=29.2
Q ss_pred HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316 37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG 74 (229)
Q Consensus 37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g 74 (229)
.++..+. .++.+++.++|+.+||+++|+++.+..+.
T Consensus 4 ~il~~l~--~~~~~s~~~l~~~l~~s~~tv~~~l~~L~ 39 (53)
T smart00420 4 QILELLA--QQGKVSVEELAELLGVSEMTIRRDLNKLE 39 (53)
T ss_pred HHHHHHH--HcCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3445543 36789999999999999999999998763
No 281
>PHA01976 helix-turn-helix protein
Probab=92.97 E-value=0.37 Score=33.08 Aligned_cols=25 Identities=16% Similarity=0.158 Sum_probs=23.0
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAH 71 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~ 71 (229)
.-++|+.++|+..||++++|.+|..
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~e~ 37 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 4689999999999999999999976
No 282
>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]
Probab=92.97 E-value=0.15 Score=48.93 Aligned_cols=34 Identities=26% Similarity=0.391 Sum_probs=28.9
Q ss_pred HHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316 44 ALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHT 77 (229)
Q Consensus 44 ~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~ 77 (229)
++...+-.+.++|+.+||+++|||+++++||+..
T Consensus 425 aL~~~~g~~~~aA~~LGi~R~tLy~Klk~~g~~~ 458 (464)
T COG2204 425 ALERTGGNKSEAAERLGISRKTLYRKLKEYGIDR 458 (464)
T ss_pred HHHHhCCCHHHHHHHHCCCHHHHHHHHHHhCCCc
Confidence 4444455899999999999999999999999875
No 283
>PRK13501 transcriptional activator RhaR; Provisional
Probab=92.93 E-value=0.69 Score=40.78 Aligned_cols=79 Identities=13% Similarity=0.174 Sum_probs=60.1
Q ss_pred HHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHH-HHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316 125 NVALDALRAGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPED-LEIALEGIRSGQTTVQRASAEYGI 202 (229)
Q Consensus 125 ~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~-r~eaV~~~~~~~~s~~eAA~~fgV 202 (229)
...|+.-....+++.++|+++|++.++|.+..+++ |.... .|=.+- ..+|-+++...++++.++|...|=
T Consensus 182 ~~~I~~~~~e~~sl~~lA~~~~lS~~~l~r~Fk~~~G~T~~--------qyi~~~Ri~~A~~LL~~t~~sI~eIA~~~GF 253 (290)
T PRK13501 182 MSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMSIS--------HYLRQIRLCHAKCLLRGSEHRISDIAARCGF 253 (290)
T ss_pred HHHHHHhhccCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCC
Confidence 44555555667899999999999999999999976 64443 232333 446777778888999999999999
Q ss_pred ChHHHHHHH
Q psy17316 203 PSGTLYGRC 211 (229)
Q Consensus 203 p~~tv~~~v 211 (229)
+..+-..++
T Consensus 254 ~~~s~F~r~ 262 (290)
T PRK13501 254 EDSNYFSAV 262 (290)
T ss_pred CCHHHHHHH
Confidence 877766654
No 284
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=92.90 E-value=0.19 Score=41.23 Aligned_cols=42 Identities=24% Similarity=0.369 Sum_probs=32.7
Q ss_pred HHHH-HHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 35 HEDM-DAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 35 ~e~~-~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
-|++ .++|+.+ .+|.+|..++|++.|++.+|++++++++.-.
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~ 55 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQ 55 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3444 3444444 5789999999999999999999999986433
No 285
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=92.89 E-value=0.37 Score=34.58 Aligned_cols=54 Identities=11% Similarity=0.336 Sum_probs=38.6
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSG 189 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~ 189 (229)
+.+.+++.++|++++|+|++++.-.......-.++---|.+.|-.+-++.++..
T Consensus 14 lrl~ev~~~~GlSrstiYr~i~~~~FPkpvklG~r~v~W~~SEI~~Wi~~~~~~ 67 (70)
T COG3311 14 LRLPEVAQLTGLSRSTIYRLIKDGTFPKPVKLGGRSVAWPESEIDEWIASRKAA 67 (70)
T ss_pred hhHHHHHHHHCccHHHHHHHHccCCCCCCeecCcccccccHHHHHHHHHHHHhc
Confidence 588999999999999999999854222211112234568888888888887765
No 286
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=92.84 E-value=0.62 Score=37.72 Aligned_cols=67 Identities=10% Similarity=0.062 Sum_probs=50.5
Q ss_pred CCCHHHHHHHhCCChHHHHHHHHHhCCcc-cCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316 135 SISANKASKAYGIPSSTLYKIARKEGIRL-AQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI 202 (229)
Q Consensus 135 ~~S~~~~a~k~gIp~sTL~~~ik~~g~k~-~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV 202 (229)
.+++.++|+.+||+..||+-|-+ .|.-. .....+..|-|+++ .++..|..+.+-+++..++...++.
T Consensus 7 ~~~IgevAk~~Gvs~~TLRyYE~-~GLl~p~~r~~~gyR~Y~~~~l~rl~~I~~lr~~G~sL~eI~~ll~~ 76 (144)
T PRK13752 7 NLTIGVFAKAAGVNVETIRFYQR-KGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLRL 76 (144)
T ss_pred cccHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 36999999999999999999876 45322 11112335788765 6778888888888999999998854
No 287
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=92.79 E-value=0.15 Score=40.63 Aligned_cols=40 Identities=18% Similarity=0.229 Sum_probs=32.5
Q ss_pred HHH-HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 36 EDM-DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 36 e~~-~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
.++ +.++ .+..++++++++|+..||+..++.+|+++++-.
T Consensus 76 ~~~~~~~~-~~~~~~~~i~~~a~~l~i~~~~~~r~~~r~~~~ 116 (129)
T COG3677 76 YKIKLQAV-TLYMLGLGIRDIARTLGISINTVNRWSKRFGSR 116 (129)
T ss_pred hHHHHHHH-HHHHcCCCcccHHHHhcccHHHHHHHHHhhcch
Confidence 444 5555 556778999999999999999999999997543
No 288
>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=92.78 E-value=0.17 Score=35.12 Aligned_cols=32 Identities=25% Similarity=0.429 Sum_probs=27.5
Q ss_pred HHHHHH-HhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 181 IALEGI-RSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 181 eaV~~~-~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
+|..++ ..|.++..++|...|||+++||+.++
T Consensus 12 ~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~ 44 (68)
T PF01978_consen 12 KVYLALLKNGPATAEEIAEELGISRSTVYRALK 44 (68)
T ss_dssp HHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHH
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 344444 58899999999999999999999998
No 289
>PRK13749 transcriptional regulator MerD; Provisional
Probab=92.75 E-value=0.84 Score=36.05 Aligned_cols=66 Identities=3% Similarity=-0.045 Sum_probs=49.4
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccC-CCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQ-PFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI 202 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~-~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV 202 (229)
+++.++|+++||+..||+-+-+. |.-... ...+..|.|+++ .++..|..|.+=++++.++...+++
T Consensus 4 ~tIgelA~~~gvS~~tiR~YE~~-GLl~p~~r~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~l 72 (121)
T PRK13749 4 YTVSRLALDAGVSVHIVRDYLLR-GLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCRA 72 (121)
T ss_pred CcHHHHHHHHCCCHHHHHHHHHC-CCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhh
Confidence 68999999999999999997763 532221 112456788766 5677788888888999999887766
No 290
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=92.74 E-value=0.15 Score=45.23 Aligned_cols=39 Identities=21% Similarity=0.230 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316 36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI 75 (229)
Q Consensus 36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi 75 (229)
+....|-.+|..| |-+.+||.+|||++.||+.|.++.|-
T Consensus 7 ~~r~~Akk~yl~g-mk~~dIAeklGvspntiksWKrr~gW 45 (279)
T COG5484 7 DKRIIAKKDYLKG-MKLKDIAEKLGVSPNTIKSWKRRDGW 45 (279)
T ss_pred chHHHHHHHHHhh-ccHHHHHHHhCCChHHHHHHHHhcCC
Confidence 4567788899995 99999999999999999999999876
No 291
>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=92.58 E-value=0.92 Score=34.45 Aligned_cols=65 Identities=9% Similarity=0.075 Sum_probs=47.4
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI 202 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV 202 (229)
+++.++|+++||+..||+-+-+ .|.-.... ....+.|+++ +++..|..+.+=++|..++...+..
T Consensus 1 m~Ige~a~~~gvs~~tlRyYe~-~GLl~p~~-~~g~r~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~ 67 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHYID-LGLLIPEK-KGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIFSY 67 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCcCCcc-CCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 4789999999999999998776 35322121 1234567655 5677788888877999999998865
No 292
>PF14493 HTH_40: Helix-turn-helix domain
Probab=92.53 E-value=0.59 Score=34.56 Aligned_cols=59 Identities=15% Similarity=0.153 Sum_probs=39.7
Q ss_pred HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCC-CCCCCCCCCcHHHHHHHHHHH
Q psy17316 38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTP-KKEGPTKSWNEEILNVALDAL 99 (229)
Q Consensus 38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~-~~~~~~k~~s~e~~~~a~~ll 99 (229)
....++.+.+ |+|+.+||+.-|+..+||...+-.+-..|+ ..... -.+++..+...+.+
T Consensus 3 ~~~T~~l~~~-G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~~~~--~l~~e~~~~I~~~~ 62 (91)
T PF14493_consen 3 AQITYELFQK-GLSIEEIAKIRGLKESTIYGHLAELIESGEPLDIEE--LLSEEEIKQIEDAI 62 (91)
T ss_pred HHHHHHHHHc-CCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCCHHH--hCCHHHHHHHHHHH
Confidence 3456677776 789999999999999999999998755443 22211 13555554444433
No 293
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=92.52 E-value=0.15 Score=34.82 Aligned_cols=43 Identities=14% Similarity=-0.002 Sum_probs=30.2
Q ss_pred HHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH--hhcCCCCCCC
Q psy17316 180 EIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK--LSRSTPRPPP 222 (229)
Q Consensus 180 ~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk--~~~~~~~~~~ 222 (229)
.+.++...+++.|+.+||...+|.++||+.+++ ..-.|..+.+
T Consensus 2 ~~TL~~yl~~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~dl~~ 46 (59)
T PF13556_consen 2 LETLRAYLENNGNISKTARALHIHRNTLRYRLKKIEELLGLDLDD 46 (59)
T ss_dssp --HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--TTS
T ss_pred hhHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCcCCCC
Confidence 356778888889999999999999999999998 3334444443
No 294
>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=92.51 E-value=0.4 Score=31.43 Aligned_cols=38 Identities=16% Similarity=0.160 Sum_probs=28.7
Q ss_pred CHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHH
Q psy17316 51 SLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDAL 99 (229)
Q Consensus 51 S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll 99 (229)
++++||+..||+.+|+.+-+..- . ..+++.++..++..
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~-----~------~vs~~tr~rI~~~a 38 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGP-----P------RVSEETRERILEAA 38 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTC-----S------SSTHHHHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHhCC-----C------CCCHHHHHHHHHHH
Confidence 57899999999999999998732 1 24677777666543
No 295
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=92.49 E-value=0.33 Score=40.43 Aligned_cols=40 Identities=18% Similarity=0.188 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHH
Q psy17316 119 WNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARK 158 (229)
Q Consensus 119 Ys~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~ 158 (229)
+++|.+..+=.+|..+.+|+..+|.++|||..|.++|-++
T Consensus 3 h~~e~R~~~R~~YV~~~~sLe~aA~~~gVs~~TarrWK~~ 42 (165)
T PF08822_consen 3 HPQETRDAVRRAYVFDRLSLEQAAAKCGVSYATARRWKRE 42 (165)
T ss_pred CcHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 4567777777899988889999999999999999999753
No 296
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=92.48 E-value=0.64 Score=37.66 Aligned_cols=68 Identities=10% Similarity=0.113 Sum_probs=46.5
Q ss_pred CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHH
Q psy17316 49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNV 126 (229)
Q Consensus 49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~ 126 (229)
.+++.++|+.+||+..||+-|=+..-+..+... . |...-|++++ +..
T Consensus 7 ~~~IgevAk~~Gvs~~TLRyYE~~GLl~p~~r~-~------------------------------~gyR~Y~~~~l~rl~ 55 (144)
T PRK13752 7 NLTIGVFAKAAGVNVETIRFYQRKGLLPEPDKP-Y------------------------------GSIRRYGEADVTRVR 55 (144)
T ss_pred cccHHHHHHHHCcCHHHHHHHHHCCCCCCCccC-C------------------------------CCCeecCHHHHHHHH
Confidence 489999999999999999999875323211111 0 1134455555 456
Q ss_pred HHHHHHcCCCCHHHHHHHhCC
Q psy17316 127 ALDALRAGSISANKASKAYGI 147 (229)
Q Consensus 127 AV~~~~~g~~S~~~~a~k~gI 147 (229)
.|..+..-++|+.+|..-...
T Consensus 56 ~I~~lr~~G~sL~eI~~ll~~ 76 (144)
T PRK13752 56 FVKSAQRLGFSLDEIAELLRL 76 (144)
T ss_pred HHHHHHHcCCCHHHHHHHHhc
Confidence 677777778899999887653
No 297
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=92.47 E-value=0.85 Score=33.70 Aligned_cols=61 Identities=13% Similarity=0.159 Sum_probs=45.4
Q ss_pred HHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhC-CCcHHHHHHHhC-CChHHHHHHHH
Q psy17316 138 ANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSG-QTTVQRASAEYG-IPSGTLYGRCK 212 (229)
Q Consensus 138 ~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~-~~s~~eAA~~fg-Vp~~tv~~~vk 212 (229)
+..+|+.|||+...|.. ..+.+... ..|.-++-.|... ++|+.+++..|| ..++||..-++
T Consensus 5 i~~Va~~~~v~~~~i~~-------------~~R~~~~~-~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ 67 (90)
T cd06571 5 IEAVAEYFGISVEDLRS-------------KSRKKEIA-LARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVR 67 (90)
T ss_pred HHHHHHHhCCCHHHHhc-------------CCCCcCcc-hHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHH
Confidence 34578899999877644 11222332 3577777777774 899999999999 99999998876
No 298
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=92.46 E-value=0.53 Score=32.65 Aligned_cols=50 Identities=12% Similarity=0.161 Sum_probs=32.3
Q ss_pred HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhh
Q psy17316 39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISAN 107 (229)
Q Consensus 39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~ 107 (229)
.+||+-+ | |+..+|+.+||++++|++| ... -|+.+--.+|.+.+|.+.+.
T Consensus 3 ~~aI~~~---G-~~~~lAkalGVs~~aVs~W--~~~-------------IP~~ra~~Ie~~T~G~l~~~ 52 (60)
T PF14549_consen 3 KDAIKYF---G-GQSKLAKALGVSPQAVSQW--GER-------------IPAERAYQIEKLTNGKLKCE 52 (60)
T ss_dssp HHHHHHH---S-SHHHHHHHHTS-HHHHHHH--HTS---------------HHHHHHHHHHTTTSS--H
T ss_pred HHHHHHH---C-CHHHHHHHHCCCHHHHHHh--cCc-------------cCHHHHHHHHHHhCCceeeC
Confidence 3455443 4 7899999999999999999 211 13445556777777876654
No 299
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=92.43 E-value=0.13 Score=34.99 Aligned_cols=29 Identities=14% Similarity=0.137 Sum_probs=21.8
Q ss_pred HHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 44 ALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 44 ~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
.+.+.++|+.++|+..||+++||++|+..
T Consensus 5 ~m~~~~it~~~La~~~gis~~tl~~~~~~ 33 (63)
T PF13443_consen 5 LMAERGITQKDLARKTGISRSTLSRILNG 33 (63)
T ss_dssp HHHHTT--HHHHHHHHT--HHHHHHHHTT
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 44567899999999999999999999983
No 300
>PRK15185 transcriptional regulator HilD; Provisional
Probab=92.42 E-value=0.6 Score=42.62 Aligned_cols=79 Identities=16% Similarity=0.204 Sum_probs=57.3
Q ss_pred CCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCC-CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 134 GSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAW-KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 134 g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~-t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
...|+.++|+..|++.++|.++.+.+|.... .| ..-....|.+++..++++..++|...|-+.++-...+=
T Consensus 221 ~~~SledLA~~lgmS~~tL~R~FK~~G~S~~--------~yl~~~Ri~~A~~LL~~t~~sIseIA~~~GFss~S~FsR~F 292 (309)
T PRK15185 221 RQWKLTDVADHIFMSTSTLKRKLAEEGTSFS--------DIYLSARMNQAAKLLRIGNHNVNAVALKCGYDSTSYFIQCF 292 (309)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHcCCCHH--------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHH
Confidence 4469999999999999999999986664432 22 23345566777778889999999999997766665553
Q ss_pred hhcCCCCC
Q psy17316 213 LSRSTPRP 220 (229)
Q Consensus 213 ~~~~~~~~ 220 (229)
...-|-+|
T Consensus 293 Kk~~G~TP 300 (309)
T PRK15185 293 KKYFKTTP 300 (309)
T ss_pred HHHHCcCH
Confidence 33334433
No 301
>TIGR01818 ntrC nitrogen regulation protein NR(I). This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.
Probab=92.39 E-value=0.19 Score=47.26 Aligned_cols=34 Identities=21% Similarity=0.136 Sum_probs=27.2
Q ss_pred HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
.+.+++...+..+.++|+.+||+++|||++++++
T Consensus 430 ~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~~~ 463 (463)
T TIGR01818 430 LLEAALQHTRGHKQEAAALLGWGRNTLTRKLKEL 463 (463)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHhC
Confidence 3444555556689999999999999999999864
No 302
>PRK09726 antitoxin HipB; Provisional
Probab=92.39 E-value=0.28 Score=36.04 Aligned_cols=41 Identities=12% Similarity=0.233 Sum_probs=34.4
Q ss_pred CCCCHHHHHHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316 31 KTWTHEDMDAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAH 71 (229)
Q Consensus 31 ~kyt~e~~~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~ 71 (229)
.-|+...+...|+.+ ...++|+.++|+..||+++||.+|.+
T Consensus 6 ~~~~~~~l~~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 6 KIYSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFEN 47 (88)
T ss_pred cccCHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 457788887666655 46789999999999999999999987
No 303
>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=92.34 E-value=0.99 Score=34.03 Aligned_cols=59 Identities=10% Similarity=0.072 Sum_probs=38.1
Q ss_pred CHHHHHHHhCCChHHHHHHHHHhCCccc-CCCCCCCCCCCHHH--HHHHHHHHHhCCCcHHHHH
Q psy17316 137 SANKASKAYGIPSSTLYKIARKEGIRLA-QPFNASPTAWKPED--LEIALEGIRSGQTTVQRAS 197 (229)
Q Consensus 137 S~~~~a~k~gIp~sTL~~~ik~~g~k~~-~~~~~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA 197 (229)
++.++|+.+||+..||+.|-+ .|.-.. .......|.|++++ ++..|+.+.. ++++.++.
T Consensus 2 ~i~e~A~~~gvs~~tlR~Ye~-~Gll~~~~r~~~g~R~Y~~~~v~~l~~I~~l~~-g~~l~~i~ 63 (99)
T cd04772 2 RTVDLARAIGLSPQTVRNYES-LGLIPPAERTANGYRIYTDKHIAALRAYRALLP-GYGYRVAQ 63 (99)
T ss_pred CHHHHHHHHCcCHHHHHHHHH-cCCCCCCCcCCCCCeecCHHHHHHHHHHHHHhh-CCCHHHHH
Confidence 678999999999999999977 453221 11123467787764 4445555543 46666653
No 304
>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=92.29 E-value=0.39 Score=30.78 Aligned_cols=31 Identities=19% Similarity=0.369 Sum_probs=23.3
Q ss_pred HHHHHH-hCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 182 ALEGIR-SGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 182 aV~~~~-~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
|++.+. ++..++.++|...|||.++|+.+++
T Consensus 8 Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~ 39 (42)
T PF13404_consen 8 ILRLLQEDGRRSYAELAEELGLSESTVRRRIR 39 (42)
T ss_dssp HHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHcCCccHHHHHHHHCcCHHHHHHHHH
Confidence 444433 4779999999999999999999987
No 305
>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF. Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH
Probab=92.29 E-value=0.2 Score=45.73 Aligned_cols=30 Identities=23% Similarity=0.214 Sum_probs=25.2
Q ss_pred HHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 44 ALRAGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 44 ~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
.+...+..+.++|+.+||+++|||+++++|
T Consensus 300 aL~~~~gn~~~aA~~LGisr~tL~rklkk~ 329 (329)
T TIGR02974 300 ALAEAQFNQRKAAELLGLTYHQLRGLLRKH 329 (329)
T ss_pred HHHHhCCCHHHHHHHhCCCHHHHHHHHHhC
Confidence 444445589999999999999999999875
No 306
>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=92.29 E-value=0.17 Score=36.38 Aligned_cols=30 Identities=20% Similarity=0.367 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316 48 GQMSLTKASVSYGIPSTTLWQRAHRLGIHT 77 (229)
Q Consensus 48 g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~ 77 (229)
..+|+.++|+..||+.+||.|-+++.|..|
T Consensus 33 ~~~si~elA~~~~vS~sti~Rf~kkLG~~g 62 (77)
T PF01418_consen 33 AFMSISELAEKAGVSPSTIVRFCKKLGFSG 62 (77)
T ss_dssp CT--HHHHHHHCTS-HHHHHHHHHHCTTTC
T ss_pred HHccHHHHHHHcCCCHHHHHHHHHHhCCCC
Confidence 579999999999999999999999999887
No 307
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=92.24 E-value=0.32 Score=38.41 Aligned_cols=40 Identities=3% Similarity=-0.022 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+.++.+..-.+..+.+ |+|+.+||..+|||.+||+.++.+
T Consensus 106 ~L~~~~r~ii~l~~~~-~~s~~EIA~~l~is~~tV~~~~~r 145 (154)
T PRK06759 106 VLDEKEKYIIFERFFV-GKTMGEIALETEMTYYQVRWIYRQ 145 (154)
T ss_pred hCCHHHHHHHHHHHhc-CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3444444444434445 789999999999999999999886
No 308
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=92.16 E-value=2 Score=42.07 Aligned_cols=96 Identities=13% Similarity=0.066 Sum_probs=59.2
Q ss_pred HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-------CCCCCCCCCCCCCC-----cHHHHHHHHHHHhhcchhh
Q psy17316 39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-------GIHTPKKEGPTKSW-----NEEILNVALDALRAGSISA 106 (229)
Q Consensus 39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-------gi~~~~~~~~~k~~-----s~e~~~~a~~ll~~G~ls~ 106 (229)
...++.+.++.+|..++|+.+||+..|+++-++.. |+..... .+.| +++.....+
T Consensus 7 ~~iL~~L~~~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~~i~~---~~Gy~l~~~~~~~~~~~~---------- 73 (584)
T PRK09863 7 LKIVDLLEQQDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIGSISG---SAKYHLEILNRRSLFQLL---------- 73 (584)
T ss_pred HHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchhheec---CCceEEEeCCHHHHHHHH----------
Confidence 34455556788999999999999999999987753 3321111 1123 222111111
Q ss_pred hhhhhccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHH
Q psy17316 107 NKASKAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIAR 157 (229)
Q Consensus 107 ~~~~~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik 157 (229)
...+++.+.-....+.+...++.++|.++.|+++||.+-++
T Consensus 74 ----------~~~~~e~~~il~~Ll~~~~~~~~~La~~l~vS~sTi~~dl~ 114 (584)
T PRK09863 74 ----------QKSDNEDRLLLLRLLLNTFTPMAQLASALNLSRTWVAERLP 114 (584)
T ss_pred ----------hcCCHHHHHHHHHHHHcCCccHHHHHHHhCCCHHHHHHHHH
Confidence 01123333333334456668999999999999999777654
No 309
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=92.11 E-value=1 Score=41.75 Aligned_cols=91 Identities=13% Similarity=0.143 Sum_probs=62.2
Q ss_pred HHHHHHHHHHc-CCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHh
Q psy17316 123 ILNVALDALRA-GSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASAEY 200 (229)
Q Consensus 123 ~k~~AV~~~~~-g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~f 200 (229)
.+.+|++.+.+ ..+++.++|..+|++.++|.++.+++ |.... .|-..-|.+.+...+..++++.++|...
T Consensus 86 ~i~~a~~~I~~~~~lsl~eLA~~lG~S~~~L~R~Fkk~~G~TP~--------~yl~~~Rl~~A~~lL~~~~sI~eIA~~~ 157 (353)
T PRK15435 86 KITHACRLLEQETPVTLEALADQVAMSPFHLHRLFKATTGMTPK--------AWQQAWRARRLREALAKGESVTTSILNA 157 (353)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHhCCCCHHHHHHHh
Confidence 35666666643 55799999999999999999999876 75443 2333345554444455669999999999
Q ss_pred CCChHHHHHHHHhhcCCCCCC
Q psy17316 201 GIPSGTLYGRCKLSRSTPRPP 221 (229)
Q Consensus 201 gVp~~tv~~~vk~~~~~~~~~ 221 (229)
|-+-++=....=...-|-+|.
T Consensus 158 Gf~s~s~F~~~Fkk~~G~TPs 178 (353)
T PRK15435 158 GFPDSSSYYRKADETLGMTAK 178 (353)
T ss_pred CCCChHHHHHHHHHHHCcCch
Confidence 987666555443344444444
No 310
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=92.11 E-value=0.27 Score=37.43 Aligned_cols=41 Identities=20% Similarity=0.217 Sum_probs=34.1
Q ss_pred HHHHHHHHH--cCCCCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316 38 MDAALEALR--AGQMSLTKASVSYGIPSTTLWQRAHRLGIHTP 78 (229)
Q Consensus 38 ~~~AI~~~~--~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~ 78 (229)
+.++.+.+. +|.++++++|+.+||++..|.+|++..|+-..
T Consensus 11 Ka~~~d~~~~~~~~~ti~~~AK~L~i~~~~l~~~Lr~~g~l~~ 53 (111)
T PF03374_consen 11 KAEFYDAFVDSDGLYTIREAAKLLGIGRNKLFQWLREKGWLYR 53 (111)
T ss_pred hhHHHHHHHcCCCCccHHHHHHHhCCCHHHHHHHHHhCCceEE
Confidence 356666665 47799999999999999999999999887643
No 311
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=92.10 E-value=0.28 Score=33.24 Aligned_cols=32 Identities=19% Similarity=0.052 Sum_probs=24.5
Q ss_pred HHHHHhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316 183 LEGIRSGQTTVQRASAEYGIPSGTLYGRCKLS 214 (229)
Q Consensus 183 V~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~ 214 (229)
=+.+.+.+++..+.|...|||++||++|+++.
T Consensus 3 ~~~m~~~~it~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 3 KELMAERGITQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp HHHHHHTT--HHHHHHHHT--HHHHHHHHTTT
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcc
Confidence 35677888999999999999999999999854
No 312
>PRK13502 transcriptional activator RhaR; Provisional
Probab=92.09 E-value=0.79 Score=40.04 Aligned_cols=81 Identities=10% Similarity=0.125 Sum_probs=59.5
Q ss_pred HcCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCC-CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHH
Q psy17316 132 RAGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAW-KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYG 209 (229)
Q Consensus 132 ~~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~-t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~ 209 (229)
....+++.++|..+||+.+.|.+..+++ |..... | ..--..+|.+++...++++.++|...|-+-.+-..
T Consensus 189 ~~~~~~~~~lA~~~~iS~~~L~r~fk~~~G~t~~~--------yi~~~Rl~~A~~lL~~t~~sI~eIA~~~GF~d~s~F~ 260 (282)
T PRK13502 189 LECPFALDAFCQQEQCSERVLRQQFRAQTGMTINQ--------YLRQVRICHAQYLLQHSPLMISEISMQCGFEDSNYFS 260 (282)
T ss_pred ccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHH--------HHHHHHHHHHHHHHHcCCCCHHHHHHHcCCCCHHHHH
Confidence 3445799999999999999999999975 755432 3 22335566777777889999999999999877766
Q ss_pred HHHhhcCCCCC
Q psy17316 210 RCKLSRSTPRP 220 (229)
Q Consensus 210 ~vk~~~~~~~~ 220 (229)
.+=.+.-|-+|
T Consensus 261 r~FKk~~G~tP 271 (282)
T PRK13502 261 VVFTRETGMTP 271 (282)
T ss_pred HHHHHHHCcCH
Confidence 65433334333
No 313
>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=92.06 E-value=0.071 Score=44.20 Aligned_cols=96 Identities=14% Similarity=0.198 Sum_probs=58.5
Q ss_pred HHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHH-HHHhhcchhhhhhhhccCCCCCCCHHH
Q psy17316 45 LRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVAL-DALRAGSISANKASKAYGPTKSWNEEI 123 (229)
Q Consensus 45 ~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~-~ll~~G~ls~~~~~~~~G~~~kYs~e~ 123 (229)
.+.+.-++.++|+.|+|++++++-|++. |+.. ...+.+|..+.++.-. +.+.++ .++-..+.
T Consensus 10 ~k~~tgt~~e~~~~~~VS~~sv~~WiKN-G~~~---~~a~~~yKhAvlN~E~t~e~~e~-------------~kke~kkl 72 (186)
T PF04936_consen 10 EKKATGTIDELADYFDVSRTSVSVWIKN-GKDP---KRAKPKYKHAVLNYEKTDELNEQ-------------KKKEEKKL 72 (186)
T ss_pred cccccccHHHHHHHHccCHHHHHHHHHc-CCCc---ccccchhhHHHhcccchhhhhhh-------------hcchhhhc
Confidence 3445568999999999999999999996 4432 2222233222211100 000000 12222233
Q ss_pred HHHHHHHHHcCC----CCHHHHHHHhCCChHHHHHHHH
Q psy17316 124 LNVALDALRAGS----ISANKASKAYGIPSSTLYKIAR 157 (229)
Q Consensus 124 k~~AV~~~~~g~----~S~~~~a~k~gIp~sTL~~~ik 157 (229)
...++..|..|. ++-.++|+.|+|-+-++|-|+.
T Consensus 73 p~sVy~~y~kG~~~~TGta~eisq~~~i~k~~Vy~yis 110 (186)
T PF04936_consen 73 PASVYDYYDKGIFIMTGTAREISQFFSIKKQNVYYYIS 110 (186)
T ss_pred cHHHHHHHhccccccCccHHHHHhhhccccccEEEEEe
Confidence 456677776665 4889999999999999888864
No 314
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=92.01 E-value=1 Score=39.74 Aligned_cols=86 Identities=14% Similarity=0.194 Sum_probs=57.3
Q ss_pred HHHHHHHHcC-CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCC
Q psy17316 39 DAALEALRAG-QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTK 117 (229)
Q Consensus 39 ~~AI~~~~~g-~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~ 117 (229)
...|++-... .+|+.++|..+||++.+|++-.++.|... .
T Consensus 203 ~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~G~T~---------------------------------------~ 243 (302)
T PRK09685 203 VALIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQGLVV---------------------------------------A 243 (302)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHcCCCH---------------------------------------H
Confidence 3444444333 48999999999999999999998754321 1
Q ss_pred CCCHHH-HHHHHHHHHc--CCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316 118 SWNEEI-LNVALDALRA--GSISANKASKAYGIPSST-LYKIARKE-GIRL 163 (229)
Q Consensus 118 kYs~e~-k~~AV~~~~~--g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~ 163 (229)
.|=.+. +..|.+++.. ...|+.+||...|-+... ..+..|++ |..+
T Consensus 244 ~yi~~~RL~~A~~lL~~~~~~~sI~eIA~~~GF~d~s~Fsr~Fkk~~G~sP 294 (302)
T PRK09685 244 QYIRNRRLDRCADDLRPAADDEKITSIAYKWGFSDSSHFSTAFKQRFGVSP 294 (302)
T ss_pred HHHHHHHHHHHHHHhhhhccCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence 111223 3445555522 246999999999999977 77766654 7544
No 315
>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=92.01 E-value=0.18 Score=33.40 Aligned_cols=35 Identities=29% Similarity=0.482 Sum_probs=26.7
Q ss_pred HHHHHHHH--cCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 39 DAALEALR--AGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 39 ~~AI~~~~--~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
+.+++.+. .+++++.+||++.|+|++|+++-+..+
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL 42 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTL 42 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 44555444 345789999999999999999999875
No 316
>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=91.99 E-value=0.34 Score=38.41 Aligned_cols=41 Identities=12% Similarity=0.149 Sum_probs=30.2
Q ss_pred CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
.+.++++..-++--+. +|+|+.+||..+|||.+|++.++++
T Consensus 110 ~~L~~~~r~v~~l~~~-~g~~~~eIA~~l~is~~tv~~~l~R 150 (159)
T TIGR02989 110 EKLPERQRELLQLRYQ-RGVSLTALAEQLGRTVNAVYKALSR 150 (159)
T ss_pred HHCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 3444444444443344 5889999999999999999999886
No 317
>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=91.92 E-value=0.39 Score=31.74 Aligned_cols=33 Identities=21% Similarity=0.237 Sum_probs=26.9
Q ss_pred HHHHHHHH-hCC-CcHHHHHHHhCCChHHHHHHHH
Q psy17316 180 EIALEGIR-SGQ-TTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 180 ~eaV~~~~-~~~-~s~~eAA~~fgVp~~tv~~~vk 212 (229)
..+++.+. +++ ++..+.|..|+||..||++.++
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~ 37 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIK 37 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHH
Confidence 46777773 333 8999999999999999999998
No 318
>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=91.87 E-value=0.28 Score=33.38 Aligned_cols=26 Identities=12% Similarity=0.185 Sum_probs=20.9
Q ss_pred HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316 46 RAGQMSLTKASVSYGIPSTTLWQRAH 71 (229)
Q Consensus 46 ~~g~~S~~~aA~~~gIp~sTL~~~i~ 71 (229)
.+.++|+.++|+..||++++|++|..
T Consensus 9 ~~~~lt~~~~a~~~~i~~~~i~~~e~ 34 (64)
T PF12844_consen 9 EEKGLTQKDLAEKLGISRSTISKIEN 34 (64)
T ss_dssp HHCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 35689999999999999999999987
No 319
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=91.84 E-value=0.37 Score=39.57 Aligned_cols=26 Identities=19% Similarity=0.165 Sum_probs=23.9
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
-.|+|+.+||..+|||.+||+.++.+
T Consensus 147 ~~~~s~~eIA~~lgis~~tV~~~l~r 172 (182)
T PRK12537 147 VDGCSHAEIAQRLGAPLGTVKAWIKR 172 (182)
T ss_pred HcCCCHHHHHHHHCCChhhHHHHHHH
Confidence 45889999999999999999999886
No 320
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=91.82 E-value=0.11 Score=34.57 Aligned_cols=29 Identities=10% Similarity=0.296 Sum_probs=21.2
Q ss_pred CCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316 50 MSLTKASVSYGIPSTTLWQRAHRLGIHTP 78 (229)
Q Consensus 50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~ 78 (229)
++..++++.+||+++||++|++.-...-|
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~g~FP~p 32 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKDGKFPKP 32 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHHHH---S
T ss_pred ccHHHHHHHHCCCHHHHHHHHhcccCCCC
Confidence 57889999999999999999997554433
No 321
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=91.80 E-value=1.8 Score=37.62 Aligned_cols=82 Identities=12% Similarity=0.099 Sum_probs=62.6
Q ss_pred HHHHHcCC-CCHHHHHHHhCCChHHHHHHHHHhC--CcccCCCCC----CCCCCCHHHHHHHHHHHHhCCCcHHHHHHHh
Q psy17316 128 LDALRAGS-ISANKASKAYGIPSSTLYKIARKEG--IRLAQPFNA----SPTAWKPEDLEIALEGIRSGQTTVQRASAEY 200 (229)
Q Consensus 128 V~~~~~g~-~S~~~~a~k~gIp~sTL~~~ik~~g--~k~~~~~~~----~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~f 200 (229)
=++|.+|. ++..+++..+|||.+|+++.++.+- .....|..+ .++..| -+..||+.+..| .++.++|...
T Consensus 97 ~EAy~QgglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG~i~DiGp~~t--HK~~ii~~~l~g-~~~~eiar~t 173 (220)
T PF07900_consen 97 NEAYDQGGLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTRGTIHDIGPGVT--HKKIIIRLYLKG-KPTPEIARRT 173 (220)
T ss_pred HHHHHcCCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccCCcccccCCcch--HHHHHHHHHHcC-CCHHHHHHHh
Confidence 35666666 7999999999999999999987541 122234322 123333 388899999998 8899999999
Q ss_pred CCChHHHHHHHH
Q psy17316 201 GIPSGTLYGRCK 212 (229)
Q Consensus 201 gVp~~tv~~~vk 212 (229)
.-|-..|-+.++
T Consensus 174 ~HS~~av~rYi~ 185 (220)
T PF07900_consen 174 NHSPEAVDRYIK 185 (220)
T ss_pred ccCHHHHHHHHH
Confidence 999999998887
No 322
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=91.79 E-value=0.33 Score=34.16 Aligned_cols=31 Identities=13% Similarity=0.202 Sum_probs=26.3
Q ss_pred cCC--CCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316 47 AGQ--MSLTKASVSYGIPSTTLWQRAHRLGIHT 77 (229)
Q Consensus 47 ~g~--~S~~~aA~~~gIp~sTL~~~i~~~gi~~ 77 (229)
.|+ ++..++|+.+||+++++++-+..+.-.|
T Consensus 18 ~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G 50 (68)
T smart00550 18 SGDETSTALQLAKNLGLPKKEVNRVLYSLEKKG 50 (68)
T ss_pred CCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 356 9999999999999999999998764443
No 323
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=91.79 E-value=0.28 Score=44.71 Aligned_cols=36 Identities=17% Similarity=0.236 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
-||..|++.+..++.|..+||+..|||++|+|+++|
T Consensus 286 ~Er~~I~~aL~~~~gn~~~aA~~LGIsR~tLyrklk 321 (326)
T PRK11608 286 QEKELLQRSLQQAKFNQKRAAELLGLTYHQLRALLK 321 (326)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 367778888888889999999999999999999988
No 324
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=91.77 E-value=1.3 Score=39.38 Aligned_cols=81 Identities=11% Similarity=0.059 Sum_probs=58.1
Q ss_pred HHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316 123 ILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGI 202 (229)
Q Consensus 123 ~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgV 202 (229)
.....|..-..+..++.++|+..|++.++|.+..++.|... ..|-.+.|.+....+...+.++.++|...|-
T Consensus 138 kv~~~I~~~~~~~~tl~~LA~~~gmS~s~l~R~FK~~G~T~--------~eyl~~~Rl~~A~~LL~~~~sI~eIA~~~GF 209 (253)
T PRK09940 138 KVRNIVNMKLAHPWKLKDICDCLYISESLLKKKLKQEQTTF--------SQILLDARMQHAKNLIRVEGSVNKIAEQCGY 209 (253)
T ss_pred HHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHcCCCH--------HHHHHHHHHHHHHHHHccCCCHHHHHHHhCC
Confidence 34555666666778999999999999999999998765322 2454445554444444445799999999988
Q ss_pred ChHHHHHHH
Q psy17316 203 PSGTLYGRC 211 (229)
Q Consensus 203 p~~tv~~~v 211 (229)
+..+=.+.+
T Consensus 210 ~s~S~Fsr~ 218 (253)
T PRK09940 210 ASTSYFIYA 218 (253)
T ss_pred CCHHHHHHH
Confidence 777766654
No 325
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=91.77 E-value=0.21 Score=46.45 Aligned_cols=35 Identities=29% Similarity=0.304 Sum_probs=27.6
Q ss_pred HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+..+.+++...+..+.++|+.+||+++|||+++++
T Consensus 407 ~~~i~~~l~~~~gn~~~aa~~Lgisr~tl~rk~~~ 441 (441)
T PRK10365 407 KEVILAALEKTGGNKTEAARQLGITRKTLLAKLSR 441 (441)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHhhC
Confidence 33444556555668999999999999999999874
No 326
>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=91.75 E-value=0.34 Score=33.76 Aligned_cols=34 Identities=21% Similarity=0.219 Sum_probs=29.4
Q ss_pred HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
..++.+.++.++..++|.++||+++|+++.++..
T Consensus 4 ~il~~L~~~~~~~~eLa~~l~vS~~tv~~~l~~L 37 (69)
T TIGR00122 4 RLLALLADNPFSGEKLGEALGMSRTAVNKHIQTL 37 (69)
T ss_pred HHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3455567889999999999999999999999876
No 327
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=91.74 E-value=0.83 Score=41.06 Aligned_cols=91 Identities=15% Similarity=0.191 Sum_probs=61.9
Q ss_pred HHHHHHHHHHHc---CCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHHH-HHHHHHHhCCCcHHHH
Q psy17316 122 EILNVALDALRA---GSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDLE-IALEGIRSGQTTVQRA 196 (229)
Q Consensus 122 e~k~~AV~~~~~---g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r~-eaV~~~~~~~~s~~eA 196 (229)
....++++.+.+ ..+|+.++|+.+|++.++|.+..++. |.... .|=.+.|+ .|.+.+...++++.++
T Consensus 218 ~~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~g~s~~--------~~~~~~Rl~~A~~lL~~~~~~i~~I 289 (322)
T PRK09393 218 DRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPA--------EWLLRERLARARDLLESSALSIDQI 289 (322)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHHcCCCCHHHH
Confidence 345555555544 34799999999999999999999976 75443 24333444 5566666778999999
Q ss_pred HHHhCCChHHHHHHHHhhcCCCCC
Q psy17316 197 SAEYGIPSGTLYGRCKLSRSTPRP 220 (229)
Q Consensus 197 A~~fgVp~~tv~~~vk~~~~~~~~ 220 (229)
|...|-+.++-....=...-|-+|
T Consensus 290 A~~~Gf~~~s~F~r~Fk~~~G~tP 313 (322)
T PRK09393 290 AERAGFGSEESLRHHFRRRAATSP 313 (322)
T ss_pred HHHhCCCCHHHHHHHHHHHHCcCH
Confidence 999998775555444333333333
No 328
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=91.74 E-value=1.1 Score=40.06 Aligned_cols=89 Identities=7% Similarity=0.038 Sum_probs=63.3
Q ss_pred HHHHHHHHHc---CCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHHH-HHHHHHHhCCCcHHHHHH
Q psy17316 124 LNVALDALRA---GSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDLE-IALEGIRSGQTTVQRASA 198 (229)
Q Consensus 124 k~~AV~~~~~---g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r~-eaV~~~~~~~~s~~eAA~ 198 (229)
..+++..+.+ ..+++.++|...|++.++|.+..++. |.... .|-.+-|+ .|.+.+..+++++.++|.
T Consensus 193 i~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~~~G~t~~--------~~l~~~Rl~~A~~lL~~~~~si~eIA~ 264 (302)
T PRK10371 193 VSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMK--------QYITAMRINHVRALLSDTDKSILDIAL 264 (302)
T ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHHhCCCHH--------HHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence 3444444433 35799999999999999999999875 64443 34445555 566777777899999999
Q ss_pred HhCCChHHHHHHHHhhcCCCCC
Q psy17316 199 EYGIPSGTLYGRCKLSRSTPRP 220 (229)
Q Consensus 199 ~fgVp~~tv~~~vk~~~~~~~~ 220 (229)
..|-+.++-...+=...-|-+|
T Consensus 265 ~~Gf~~~s~F~r~Fk~~~G~tP 286 (302)
T PRK10371 265 TAGFRSSSRFYSTFGKYVGMSP 286 (302)
T ss_pred HcCCCCHHHHHHHHHHHHCcCH
Confidence 9998888777765444444444
No 329
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=91.74 E-value=1.3 Score=38.66 Aligned_cols=81 Identities=14% Similarity=0.157 Sum_probs=59.7
Q ss_pred cCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCC-CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHH
Q psy17316 133 AGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAW-KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGR 210 (229)
Q Consensus 133 ~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~-t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~ 210 (229)
....|+.++|+++|++.++|.+..++. |.... .| ..--+.+|.+++...++++.++|...|-+.++-...
T Consensus 200 ~~~~sl~~lA~~~~~S~~~l~r~Fk~~~G~t~~--------~yi~~~Rl~~A~~lL~~t~~sI~eIA~~~GF~s~s~Fsr 271 (287)
T TIGR02297 200 KQHLRLPEYADRLGISESRLNDICRRFSALSPK--------RLIIERVMQEARRLLLFTQHSINQIAYDLGYKDPAYFAR 271 (287)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHhCCCHH--------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHH
Confidence 346799999999999999999999874 64432 23 222355566667778899999999999998887777
Q ss_pred HHhhcCCCCCC
Q psy17316 211 CKLSRSTPRPP 221 (229)
Q Consensus 211 vk~~~~~~~~~ 221 (229)
+=.+.-|-+|.
T Consensus 272 ~FKk~~G~tP~ 282 (287)
T TIGR02297 272 FFQKETGLSPS 282 (287)
T ss_pred HHHHHHCcCHH
Confidence 65444444443
No 330
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=91.70 E-value=0.38 Score=38.68 Aligned_cols=26 Identities=23% Similarity=0.277 Sum_probs=23.7
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
-.++|+.+||..+|||.+||+.++++
T Consensus 142 ~~~~s~~eIA~~lgis~~tV~~~l~r 167 (182)
T PRK09652 142 IEGLSYEEIAEIMGCPIGTVRSRIFR 167 (182)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 35889999999999999999999885
No 331
>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=91.56 E-value=0.4 Score=36.70 Aligned_cols=40 Identities=15% Similarity=0.133 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
..++.+..-. ..+.-+|+|..+||+.+|||++||++++++
T Consensus 110 ~L~~~~~~ii-~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~ 149 (158)
T TIGR02937 110 KLPEREREVL-VLRYLEGLSYKEIAEILGISVGTVKRRLKR 149 (158)
T ss_pred hCCHHHHHHH-hhHHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4455555433 333235789999999999999999999886
No 332
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=91.52 E-value=0.48 Score=34.27 Aligned_cols=37 Identities=24% Similarity=0.296 Sum_probs=29.9
Q ss_pred HHHHHHHHHc--CCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316 38 MDAALEALRA--GQMSLTKASVSYGIPSTTLWQRAHRLG 74 (229)
Q Consensus 38 ~~~AI~~~~~--g~~S~~~aA~~~gIp~sTL~~~i~~~g 74 (229)
.+.+++.+.. +.+++.++|+.+|||++|+++-+..+.
T Consensus 7 ~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~ 45 (91)
T smart00346 7 GLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQ 45 (91)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3455555543 579999999999999999999999763
No 333
>PRK13503 transcriptional activator RhaS; Provisional
Probab=91.52 E-value=1.3 Score=38.40 Aligned_cols=82 Identities=15% Similarity=0.165 Sum_probs=58.8
Q ss_pred HHHHHHHHHHH---cCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHHH-HHHHHHHhCCCcHHHH
Q psy17316 122 EILNVALDALR---AGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDLE-IALEGIRSGQTTVQRA 196 (229)
Q Consensus 122 e~k~~AV~~~~---~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r~-eaV~~~~~~~~s~~eA 196 (229)
+...++++.+. ....|+.++|+.+|++.++|.+-.|+. |.... .|=.+-|+ +|.+.+..+++++.++
T Consensus 171 ~~i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~~~G~S~~--------~yi~~~Rl~~A~~LL~~~~~sI~eI 242 (278)
T PRK13503 171 ARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQ--------RYLNRLRLLKARHLLRHSDASVTDI 242 (278)
T ss_pred HHHHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHHHhCcCHH--------HHHHHHHHHHHHHHHHcCCCCHHHH
Confidence 33444444443 346799999999999999999999876 64432 34334444 6666677778999999
Q ss_pred HHHhCCChHHHHHHH
Q psy17316 197 SAEYGIPSGTLYGRC 211 (229)
Q Consensus 197 A~~fgVp~~tv~~~v 211 (229)
|...|=+.++=...+
T Consensus 243 A~~~GF~~~s~F~r~ 257 (278)
T PRK13503 243 AYRCGFGDSNHFSTL 257 (278)
T ss_pred HHHhCCCCHHHHHHH
Confidence 999998887665554
No 334
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=91.51 E-value=0.41 Score=33.95 Aligned_cols=62 Identities=23% Similarity=0.327 Sum_probs=40.5
Q ss_pred HHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHHH-HHHHHHHh-CCCcHHHHHHHhCCChHHHHHH
Q psy17316 141 ASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDLE-IALEGIRS-GQTTVQRASAEYGIPSGTLYGR 210 (229)
Q Consensus 141 ~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r~-eaV~~~~~-~~~s~~eAA~~fgVp~~tv~~~ 210 (229)
+|+.+|++..+|.+..++. |.... .|-.+.|+ .|.+.+.+ ++++..++|..+|-+.++-...
T Consensus 1 lA~~~~~s~~~l~~~f~~~~g~s~~--------~~~~~~R~~~a~~~L~~~~~~~i~~ia~~~Gf~~~~~f~~ 65 (81)
T PF12833_consen 1 LADELGMSERYLSRIFKKETGMSFK--------QYLRELRLQRAKELLRQNTDLSIAEIAEECGFSSQSHFSR 65 (81)
T ss_dssp HHHHCTS-HHHHHHHHHHHHSS-HH--------HHHHHHHHHHHHHHHHHHTT--HHHHHHHTT-SSHHHHHH
T ss_pred ChHHhCcCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHHHhhcccHHHHHHHcCCCCHHHHHH
Confidence 5899999999999999874 75443 23334444 45555544 8899999999999986654443
No 335
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=91.51 E-value=1.1 Score=39.36 Aligned_cols=81 Identities=14% Similarity=0.229 Sum_probs=59.0
Q ss_pred HcCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHHH-HHHHHHHhCCCcHHHHHHHhCCChHHHHH
Q psy17316 132 RAGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDLE-IALEGIRSGQTTVQRASAEYGIPSGTLYG 209 (229)
Q Consensus 132 ~~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r~-eaV~~~~~~~~s~~eAA~~fgVp~~tv~~ 209 (229)
..+.+++.++|+++|++.++|.+..|+. |.... .|-.+.|+ +|.+.+...++++.++|...|-+.+.-.+
T Consensus 196 ~~~~isl~~lA~~~~lS~~~l~r~Fk~~~G~tp~--------~~l~~~Rl~~A~~lL~~t~~sI~eIA~~~GF~d~s~Fs 267 (290)
T PRK10572 196 LASEFDIESVAQHVCLSPSRLAHLFRQQLGISVL--------RWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFS 267 (290)
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHH
Confidence 3466899999999999999999999876 75443 34334444 45555666789999999999998777666
Q ss_pred HHHhhcCCCCC
Q psy17316 210 RCKLSRSTPRP 220 (229)
Q Consensus 210 ~vk~~~~~~~~ 220 (229)
++=.+.-|-+|
T Consensus 268 r~FKk~~G~SP 278 (290)
T PRK10572 268 RVFKKCTGASP 278 (290)
T ss_pred HHHHHHHCcCH
Confidence 65444444444
No 336
>PRK01905 DNA-binding protein Fis; Provisional
Probab=91.37 E-value=0.52 Score=34.02 Aligned_cols=36 Identities=14% Similarity=0.073 Sum_probs=31.2
Q ss_pred HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHh
Q psy17316 178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKL 213 (229)
Q Consensus 178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~ 213 (229)
++.-+++.+...+-+..+||...||+++|+|++++.
T Consensus 38 E~~~i~~aL~~~~gn~s~aAr~LGIsrstL~rklkk 73 (77)
T PRK01905 38 EKPLLEVVMEQAGGNQSLAAEYLGINRNTLRKKLQQ 73 (77)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 466677888888888999999999999999999873
No 337
>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=91.32 E-value=0.38 Score=31.81 Aligned_cols=35 Identities=14% Similarity=0.265 Sum_probs=26.0
Q ss_pred HHHHHH-Hc-CCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316 40 AALEAL-RA-GQMSLTKASVSYGIPSTTLWQRAHRLG 74 (229)
Q Consensus 40 ~AI~~~-~~-g~~S~~~aA~~~gIp~sTL~~~i~~~g 74 (229)
..+..+ .+ +.+|..++|+++||++.|+++-+....
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~ 40 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKELR 40 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 344444 23 349999999999999999999988753
No 338
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=91.32 E-value=2.4 Score=31.59 Aligned_cols=81 Identities=20% Similarity=0.271 Sum_probs=58.1
Q ss_pred HcCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCC-CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHH
Q psy17316 132 RAGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAW-KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYG 209 (229)
Q Consensus 132 ~~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~-t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~ 209 (229)
..+..++.++|..+|++.++|.+..++. |.... .| ..-.+..|.+++..++.++.++|...|-+-+.-..
T Consensus 33 ~~~~~~l~~la~~~g~S~~~l~r~f~~~~g~s~~--------~~~~~~Rl~~A~~lL~~~~~~i~~iA~~~Gf~~~s~F~ 104 (127)
T COG2207 33 LAEPLTLEDLARRLGMSRRTLSRLFKKETGTSPS--------QYLRQLRLEEARRLLRSTDLSITEIALRLGYSSPSHFS 104 (127)
T ss_pred hcCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHH--------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCcCCHHHHH
Confidence 3444799999999999999999998854 64432 12 23456777888888888999999999988877554
Q ss_pred HHHhhcCCCCC
Q psy17316 210 RCKLSRSTPRP 220 (229)
Q Consensus 210 ~vk~~~~~~~~ 220 (229)
..=...-|-+|
T Consensus 105 ~~Fk~~~g~tP 115 (127)
T COG2207 105 RAFKRLFGVTP 115 (127)
T ss_pred HHHHHHhCCCh
Confidence 44333333333
No 339
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=91.28 E-value=0.5 Score=31.85 Aligned_cols=36 Identities=17% Similarity=0.294 Sum_probs=29.1
Q ss_pred HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
....+..+..++++..++|+.+||+.+|+++.+...
T Consensus 9 ~~~il~~l~~~~~~~~ei~~~~~i~~~~i~~~l~~L 44 (78)
T cd00090 9 RLRILRLLLEGPLTVSELAERLGLSQSTVSRHLKKL 44 (78)
T ss_pred HHHHHHHHHHCCcCHHHHHHHHCcCHhHHHHHHHHH
Confidence 344455555556999999999999999999999875
No 340
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=91.26 E-value=0.37 Score=31.65 Aligned_cols=31 Identities=19% Similarity=0.230 Sum_probs=27.5
Q ss_pred HHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 182 ALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 182 aV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
|++.+..+..+..+++.+++||.++++..++
T Consensus 2 il~~l~~~~~~~~~i~~~l~is~~~v~~~l~ 32 (66)
T smart00418 2 ILKLLAEGELCVCELAEILGLSQSTVSHHLK 32 (66)
T ss_pred HHHHhhcCCccHHHHHHHHCCCHHHHHHHHH
Confidence 4566667789999999999999999999998
No 341
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=91.26 E-value=0.71 Score=35.61 Aligned_cols=36 Identities=14% Similarity=0.128 Sum_probs=27.7
Q ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316 33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAH 71 (229)
Q Consensus 33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~ 71 (229)
.+.+++.++=+. -++|+..+|+.+||+.+||++|=+
T Consensus 44 ls~~eIk~iRe~---~~lSQ~vFA~~L~vs~~Tv~~WEq 79 (104)
T COG2944 44 LSPTEIKAIREK---LGLSQPVFARYLGVSVSTVRKWEQ 79 (104)
T ss_pred CCHHHHHHHHHH---hCCCHHHHHHHHCCCHHHHHHHHc
Confidence 455554443333 489999999999999999999965
No 342
>PRK13749 transcriptional regulator MerD; Provisional
Probab=91.19 E-value=1.5 Score=34.66 Aligned_cols=68 Identities=10% Similarity=0.147 Sum_probs=45.6
Q ss_pred CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHH
Q psy17316 49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNV 126 (229)
Q Consensus 49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~ 126 (229)
.+++.++|+++||+..||+.+-+. |+-.|..... |....|+++. ++.
T Consensus 3 ~~tIgelA~~~gvS~~tiR~YE~~-GLl~p~~r~~------------------------------~gyR~Y~~~~l~rL~ 51 (121)
T PRK13749 3 AYTVSRLALDAGVSVHIVRDYLLR-GLLRPVACTT------------------------------GGYGLFDDAALQRLC 51 (121)
T ss_pred CCcHHHHHHHHCCCHHHHHHHHHC-CCCCCCCcCC------------------------------CCCccCCHHHHHHHH
Confidence 478999999999999999999776 4432221111 1234555555 456
Q ss_pred HHHHHHcCCCCHHHHHHHhCC
Q psy17316 127 ALDALRAGSISANKASKAYGI 147 (229)
Q Consensus 127 AV~~~~~g~~S~~~~a~k~gI 147 (229)
.|.....-++|+.+|..-..+
T Consensus 52 ~I~~~r~~G~sL~eI~~ll~l 72 (121)
T PRK13749 52 FVRAAFEAGIGLDALARLCRA 72 (121)
T ss_pred HHHHHHHcCCCHHHHHHHHhh
Confidence 677767777788888766555
No 343
>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=91.18 E-value=0.55 Score=32.68 Aligned_cols=38 Identities=8% Similarity=0.051 Sum_probs=31.1
Q ss_pred HHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH-hhcCCC
Q psy17316 181 IALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-LSRSTP 218 (229)
Q Consensus 181 eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~~ 218 (229)
.+++.+.++.++..+.|..||||.+||+..++ +...|-
T Consensus 4 ~il~~L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~ 42 (69)
T TIGR00122 4 RLLALLADNPFSGEKLGEALGMSRTAVNKHIQTLREWGV 42 (69)
T ss_pred HHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 46667778889999999999999999999998 434443
No 344
>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=91.16 E-value=0.41 Score=31.59 Aligned_cols=39 Identities=18% Similarity=0.221 Sum_probs=29.7
Q ss_pred HHHHHHHHHHhCC--CcHHHHHHHhCCChHHHHHHHH-hhcC
Q psy17316 178 DLEIALEGIRSGQ--TTVQRASAEYGIPSGTLYGRCK-LSRS 216 (229)
Q Consensus 178 ~r~eaV~~~~~~~--~s~~eAA~~fgVp~~tv~~~vk-~~~~ 216 (229)
.-..|++.+..++ ++..++|.+.|+|++|+++.++ +...
T Consensus 4 ral~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~ 45 (52)
T PF09339_consen 4 RALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEE 45 (52)
T ss_dssp HHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3456777777644 6899999999999999999988 4433
No 345
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 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, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=91.13 E-value=0.43 Score=32.45 Aligned_cols=33 Identities=18% Similarity=0.263 Sum_probs=26.8
Q ss_pred HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
+++..+.+.+ |+..||+.+||+.++|++.+++.
T Consensus 5 ~~f~~v~~~g-s~~~AA~~l~is~~~vs~~i~~L 37 (60)
T PF00126_consen 5 RYFLAVAETG-SISAAAEELGISQSAVSRQIKQL 37 (60)
T ss_dssp HHHHHHHHHS-SHHHHHHHCTSSHHHHHHHHHHH
T ss_pred HHHHHHHHhC-CHHHHHHHhhccchHHHHHHHHH
Confidence 3444555545 99999999999999999999974
No 346
>PRK10072 putative transcriptional regulator; Provisional
Probab=91.12 E-value=0.44 Score=36.13 Aligned_cols=37 Identities=5% Similarity=0.129 Sum_probs=29.4
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAH 71 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~ 71 (229)
..+..++...- ..-++|+.++|+.+||+.+||.+|..
T Consensus 32 ~~~~~eik~LR---~~~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 32 TTSFTEFEQLR---KGTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred cCChHHHHHHH---HHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 44666654443 34589999999999999999999977
No 347
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR. At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.
Probab=91.10 E-value=0.26 Score=47.99 Aligned_cols=34 Identities=32% Similarity=0.321 Sum_probs=27.3
Q ss_pred HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
..+.+.+...+....++|+.+||+++|||+++++
T Consensus 493 ~~I~~aL~~~~Gn~~~aA~~LGIsRtTL~Rklk~ 526 (526)
T TIGR02329 493 LAVRAALERFGGDRDAAAKALGISRTTLWRRLKA 526 (526)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhC
Confidence 3444455666668999999999999999999873
No 348
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=91.08 E-value=1.3 Score=39.85 Aligned_cols=83 Identities=16% Similarity=0.063 Sum_probs=59.2
Q ss_pred HHHHHHHHHH---HcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHH-HHHHHHHhCCCcHHHHH
Q psy17316 122 EILNVALDAL---RAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLE-IALEGIRSGQTTVQRAS 197 (229)
Q Consensus 122 e~k~~AV~~~---~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~-eaV~~~~~~~~s~~eAA 197 (229)
....++++.+ .....++.++|..+|++.++|.+..++.|... ..|=.+.|+ .|.+.+...++++.++|
T Consensus 142 ~~~~~v~~yI~~~~~~~lsl~~lA~~~g~S~~~L~R~Fk~~G~S~--------~~yl~~~Rl~~A~~LL~~t~~sI~eIA 213 (274)
T PRK09978 142 NMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETSY--------SQLLTECRMQRALQLIVIHGFSIKRVA 213 (274)
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHhcCCCH--------HHHHHHHHHHHHHHHHHcCCCCHHHHH
Confidence 3344444444 33557999999999999999999998755322 234334455 45666666889999999
Q ss_pred HHhCCChHHHHHHHH
Q psy17316 198 AEYGIPSGTLYGRCK 212 (229)
Q Consensus 198 ~~fgVp~~tv~~~vk 212 (229)
...|-+.++-.+.+=
T Consensus 214 ~~~GF~s~S~Fsr~F 228 (274)
T PRK09978 214 VSCGYHSVSYFIYVF 228 (274)
T ss_pred HHhCCCCHHHHHHHH
Confidence 999998877776653
No 349
>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=90.95 E-value=1.4 Score=33.15 Aligned_cols=23 Identities=9% Similarity=0.036 Sum_probs=20.6
Q ss_pred CHHHHHHHcCCChhhHHHHHHHh
Q psy17316 51 SLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 51 S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
++.++|+.+||+..||+.|-+.-
T Consensus 2 ~i~e~A~~~gvs~~tlR~Ye~~G 24 (99)
T cd04772 2 RTVDLARAIGLSPQTVRNYESLG 24 (99)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcC
Confidence 67899999999999999997753
No 350
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=90.77 E-value=0.39 Score=33.93 Aligned_cols=34 Identities=21% Similarity=0.235 Sum_probs=28.7
Q ss_pred HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
...| .++...+|..+||+++|+...++.+|+..+
T Consensus 4 ~~fI-rlLs~~~s~~~Aa~~lG~~~~~v~~wv~~f 37 (65)
T PF05344_consen 4 RAFI-RLLSQQISVAQAADRLGTDPGTVRRWVRMF 37 (65)
T ss_pred HHHH-HHhcccccHHHHHHHHCcCHHHHHHHHHHH
Confidence 3445 455778999999999999999999999975
No 351
>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=90.74 E-value=1.4 Score=38.22 Aligned_cols=66 Identities=6% Similarity=0.037 Sum_probs=49.4
Q ss_pred CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316 136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI 202 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV 202 (229)
+++.++|+.+||+..||+.|-++ |.-......+..+.|+++ +++..|..+..-+++..+|...+..
T Consensus 2 y~i~elA~~~Gvs~~tIR~Ye~~-GLL~p~r~~~~~r~Y~~~~v~rL~~I~~l~~~G~~L~~I~~~l~~ 69 (219)
T cd04778 2 YRIDDLARAAGTTVRNVRAYQDR-GLLPPPRRRGRVAIYNDSHLARLRLINQLLERGYTLAHIAELLAA 69 (219)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC-CCCCCcccCCCCcccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 58899999999999999998875 543221112234678765 6788888888777999999887765
No 352
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=90.67 E-value=0.42 Score=38.13 Aligned_cols=29 Identities=17% Similarity=0.054 Sum_probs=24.9
Q ss_pred HHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 44 ALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 44 ~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+..-.|+|+.+||+.+|||.+||+.++.+
T Consensus 117 l~~~~g~s~~EIA~~lgis~~tV~~~l~R 145 (160)
T PRK09642 117 AHYLEEKSYQEIALQEKIEVKTVEMKLYR 145 (160)
T ss_pred HHHHhCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 33345889999999999999999999886
No 353
>PRK15340 transcriptional regulator InvF; Provisional
Probab=90.66 E-value=1 Score=39.04 Aligned_cols=78 Identities=15% Similarity=0.181 Sum_probs=56.6
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH-H
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI-L 124 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~-k 124 (229)
....++.++|+.+|++.++|.|..+++ |... .. . + ... +
T Consensus 123 ~~~~sleeLA~~~gvS~r~f~RlFk~~~G~tp-k~-----------y---l------------------------~~~Rl 163 (216)
T PRK15340 123 TSGNTMRMLGEDYGVSYTHFRRLCSRALGGKA-KS-----------E---L------------------------RNWRM 163 (216)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH-HH-----------H---H------------------------HHHHH
Confidence 367899999999999999999999985 4431 00 0 0 111 2
Q ss_pred HHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316 125 NVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL 163 (229)
Q Consensus 125 ~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~ 163 (229)
.+|+..+.++..|+.+||..+|-.... +.+..+++ |..+
T Consensus 164 ~~all~L~~s~~sItdIA~~~GY~d~ShFsr~FKk~~G~TP 204 (216)
T PRK15340 164 AQSLLNSVEGHENITQLAVNHGYSSPSHFSSEIKELIGVSP 204 (216)
T ss_pred HHHHHhhhcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence 455666667788999999999998866 77777765 6544
No 354
>COG2901 Fis Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]
Probab=90.65 E-value=0.5 Score=35.43 Aligned_cols=30 Identities=27% Similarity=0.479 Sum_probs=25.2
Q ss_pred HHHcCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316 44 ALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI 75 (229)
Q Consensus 44 ~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi 75 (229)
.+..| .+..||..+||.|+||++++++||.
T Consensus 68 ~~~~g--NQtrAa~mLGinR~TLRKKLkqygl 97 (98)
T COG2901 68 QYTRG--NQTRAALMLGINRGTLRKKLKKYGL 97 (98)
T ss_pred HHhcc--cHHHHHHHHcccHHHHHHHHHHhCC
Confidence 44444 4788999999999999999999985
No 355
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=90.63 E-value=1.1 Score=37.62 Aligned_cols=44 Identities=20% Similarity=0.209 Sum_probs=40.1
Q ss_pred CCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 169 ASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 169 ~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
......+.+.|.+|.+.+..++++++++|.+|||..+.|.-.++
T Consensus 12 ~~~~~lse~~r~~Iy~~~~~~~~sv~~vS~~ygi~~~RV~AIvr 55 (172)
T PF12298_consen 12 RSNPVLSEELREQIYEDVMQDGKSVREVSQKYGIKIQRVEAIVR 55 (172)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 44556799999999999999999999999999999999999887
No 356
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=90.61 E-value=0.61 Score=36.79 Aligned_cols=36 Identities=14% Similarity=0.057 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
+.+|.-++.....| +|+.|+|..+|||.+||+.++.
T Consensus 109 ~~~r~ii~l~~~~~-~s~~EIA~~l~is~~tV~~~~~ 144 (154)
T PRK06759 109 EKEKYIIFERFFVG-KTMGEIALETEMTYYQVRWIYR 144 (154)
T ss_pred HHHHHHHHHHHhcC-CCHHHHHHHHCCCHHHHHHHHH
Confidence 34444444444555 9999999999999999999976
No 357
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=90.61 E-value=0.46 Score=43.31 Aligned_cols=36 Identities=3% Similarity=-0.041 Sum_probs=32.3
Q ss_pred HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
.+..+-.+|-..+|++.+||+++||+|+++.|-+.+
T Consensus 17 l~~~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~ 52 (318)
T PRK15418 17 LVARIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEK 52 (318)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 367788899999999999999999999999997775
No 358
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=90.55 E-value=0.8 Score=30.82 Aligned_cols=36 Identities=19% Similarity=0.170 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
+....++..+..+..+..+++..+++|..+++..++
T Consensus 7 ~~~~~il~~l~~~~~~~~ei~~~~~i~~~~i~~~l~ 42 (78)
T cd00090 7 PTRLRILRLLLEGPLTVSELAERLGLSQSTVSRHLK 42 (78)
T ss_pred hHHHHHHHHHHHCCcCHHHHHHHHCcCHhHHHHHHH
Confidence 457788888888879999999999999999999998
No 359
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=90.53 E-value=0.63 Score=37.65 Aligned_cols=41 Identities=10% Similarity=0.087 Sum_probs=30.5
Q ss_pred CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
.+.++.+..-.+ +..-.|+|+.+||..+|||.+|++.++++
T Consensus 117 ~~L~~~~r~v~~-L~~~eg~s~~EIA~~l~is~~tV~~~l~r 157 (168)
T PRK12525 117 DGLSGKARAAFL-MSQLEGLTYVEIGERLGVSLSRIHQYMVE 157 (168)
T ss_pred HhCCHHHHHHHH-HHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 445555544333 43345889999999999999999999876
No 360
>PRK10130 transcriptional regulator EutR; Provisional
Probab=90.50 E-value=1.7 Score=40.10 Aligned_cols=86 Identities=14% Similarity=0.134 Sum_probs=56.8
Q ss_pred HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCC
Q psy17316 40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKS 118 (229)
Q Consensus 40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~k 118 (229)
+.|++-.+..+++.++|+.+||++.+|.+-.++. |... ..
T Consensus 247 ~~i~~~~~~~ltv~~lA~~~gvS~r~L~r~Fk~~~G~sp---------------------------------------~~ 287 (350)
T PRK10130 247 EYVLENMSEPVTVLDLCNQLHVSRRTLQNAFHAILGIGP---------------------------------------NA 287 (350)
T ss_pred HHHHhhhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCH---------------------------------------HH
Confidence 3333334556999999999999999999999874 4431 11
Q ss_pred CCHHHHHHHH-HHHHc---CCCCHHHHHHHhCCChHH-HHHHHHHh-CCccc
Q psy17316 119 WNEEILNVAL-DALRA---GSISANKASKAYGIPSST-LYKIARKE-GIRLA 164 (229)
Q Consensus 119 Ys~e~k~~AV-~~~~~---g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~~ 164 (229)
|=...+++.+ .++.+ ...|+.+||.++|..... ..+..|+. |...+
T Consensus 288 ylr~~RL~~ar~lL~~~~~~~~sI~eIA~~~GF~~~s~Fs~~fk~~fG~tPs 339 (350)
T PRK10130 288 WLKRIRLNAVRRELISPWSQSTTVKDAAMQWGFWHLGQFATDYQQLFAEKPS 339 (350)
T ss_pred HHHHHHHHHHHHHHhccCCCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCcH
Confidence 1123334443 44443 356999999999998866 66665544 65443
No 361
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=90.49 E-value=0.38 Score=36.66 Aligned_cols=36 Identities=11% Similarity=0.171 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
..|+.||+.+.+|++|.+|++.++|||-.|+-+=.+
T Consensus 47 ~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGSN 82 (103)
T COG2973 47 GTRVRIVEELLRGELSQREIAQKLGVSIATITRGSN 82 (103)
T ss_pred HHHHHHHHHHHhccccHHHHHHHhCcchhhhccchh
Confidence 358899999999999999999999999988765433
No 362
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.44 E-value=0.61 Score=35.79 Aligned_cols=34 Identities=15% Similarity=0.219 Sum_probs=30.0
Q ss_pred HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
-.+.++.....++|..|+|..|+||+|.||..+|
T Consensus 22 Q~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIK 55 (105)
T COG2739 22 QKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIK 55 (105)
T ss_pred HHHHHHHHHHhhccHHHHHHHhCccHHHHHHHHH
Confidence 3456777778889999999999999999999988
No 363
>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=90.43 E-value=0.46 Score=38.72 Aligned_cols=31 Identities=10% Similarity=0.039 Sum_probs=26.0
Q ss_pred HHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 42 LEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 42 I~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+.+..-.|+|+.+||..+|||.+||+.++++
T Consensus 143 ~~l~~~~g~s~~EIA~~lgis~~tVk~~l~R 173 (183)
T TIGR02999 143 VELRFFAGLTVEEIAELLGVSVRTVERDWRF 173 (183)
T ss_pred HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 3344446899999999999999999999886
No 364
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=90.40 E-value=0.81 Score=37.13 Aligned_cols=25 Identities=24% Similarity=0.399 Sum_probs=19.5
Q ss_pred CCCCHHHHHHHhCCChHHHHHHHHH
Q psy17316 134 GSISANKASKAYGIPSSTLYKIARK 158 (229)
Q Consensus 134 g~~S~~~~a~k~gIp~sTL~~~ik~ 158 (229)
+..|..+||+..||+++|||+|-++
T Consensus 33 ~r~T~~eiAee~Gis~~tLYrWr~~ 57 (142)
T PF13022_consen 33 ERRTQAEIAEEVGISRSTLYRWRQQ 57 (142)
T ss_dssp --S-HHHHHHHHTS-HHHHHHHHHH
T ss_pred ccchHHHHHHHhCCCHHHHHHHHhc
Confidence 4579999999999999999999863
No 365
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=90.37 E-value=7.5 Score=34.11 Aligned_cols=33 Identities=12% Similarity=0.185 Sum_probs=24.5
Q ss_pred HHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHH
Q psy17316 125 NVALDALRAGSISANKASKAYGIPSSTLYKIAR 157 (229)
Q Consensus 125 ~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik 157 (229)
..++.+..-.++|+.+||..+|||..|+++++.
T Consensus 218 r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~~~ 250 (268)
T PRK06288 218 KKVLILYYYEDLTLKEIGKVLGVTESRISQLHT 250 (268)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 344444333345999999999999999887664
No 366
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=90.37 E-value=0.63 Score=37.51 Aligned_cols=26 Identities=27% Similarity=0.288 Sum_probs=23.9
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
-+|+|+.+||..+|||.+|++.++.+
T Consensus 126 ~~g~s~~eIA~~lgis~~tV~~~l~R 151 (164)
T PRK12547 126 ASGFSYEDAAAICGCAVGTIKSRVSR 151 (164)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 36889999999999999999999886
No 367
>PRK10072 putative transcriptional regulator; Provisional
Probab=90.36 E-value=0.54 Score=35.64 Aligned_cols=35 Identities=3% Similarity=-0.131 Sum_probs=28.9
Q ss_pred HHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316 181 IALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR 215 (229)
Q Consensus 181 eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~ 215 (229)
++-+.....+++..+.|..+|||.+||.+|-++.+
T Consensus 37 eik~LR~~~glTQ~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 37 EFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC
Confidence 34445567789999999999999999999988553
No 368
>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=90.25 E-value=0.56 Score=37.14 Aligned_cols=34 Identities=9% Similarity=0.054 Sum_probs=27.7
Q ss_pred HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
..+|+....-+++++.++|..+|||.+||+.++.
T Consensus 116 ~r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~ 149 (159)
T TIGR02989 116 QRELLQLRYQRGVSLTALAEQLGRTVNAVYKALS 149 (159)
T ss_pred HHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4455555455669999999999999999999976
No 369
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=90.22 E-value=0.56 Score=37.39 Aligned_cols=34 Identities=9% Similarity=-0.093 Sum_probs=28.1
Q ss_pred HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
..+|+....-.++|+.|+|..+|||.+||+.++.
T Consensus 111 ~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ 144 (160)
T PRK09642 111 YRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLY 144 (160)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4456666665669999999999999999999876
No 370
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=90.21 E-value=0.61 Score=37.35 Aligned_cols=39 Identities=18% Similarity=0.196 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
.++.+..-.+--+. .++|+.+||..+|||.+||++++++
T Consensus 126 L~~~~r~i~~l~~~-~~~~~~eIA~~lgis~~tv~~~~~r 164 (179)
T PRK11924 126 LPVKQREVFLLRYV-EGLSYREIAEILGVPVGTVKSRLRR 164 (179)
T ss_pred CCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 44444433332333 5889999999999999999999886
No 371
>PHA00738 putative HTH transcription regulator
Probab=90.10 E-value=0.68 Score=35.93 Aligned_cols=41 Identities=17% Similarity=-0.010 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHhC-CCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316 177 EDLEIALEGIRSG-QTTVQRASAEYGIPSGTLYGRCK-LSRST 217 (229)
Q Consensus 177 e~r~eaV~~~~~~-~~s~~eAA~~fgVp~~tv~~~vk-~~~~~ 217 (229)
.-|..||+++..| .+++.+++..|++|.++|-..++ +...|
T Consensus 12 ptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreAG 54 (108)
T PHA00738 12 ILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQG 54 (108)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCC
Confidence 4699999999997 59999999999999999999998 44444
No 372
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=90.10 E-value=0.52 Score=37.69 Aligned_cols=39 Identities=18% Similarity=0.142 Sum_probs=30.1
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+.++++. .++.+.. .|+|+.+||..+|||.+|++.++.+
T Consensus 112 ~L~~~~r-~il~l~~-~g~s~~eIA~~lgis~~tV~~~i~r 150 (166)
T PRK09639 112 KMTERDR-TVLLLRF-SGYSYKEIAEALGIKESSVGTTLAR 150 (166)
T ss_pred cCCHHHH-HHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3444444 3444555 7899999999999999999999886
No 373
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=90.10 E-value=9.2 Score=32.77 Aligned_cols=102 Identities=13% Similarity=0.080 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCC--------------CCCcHHH----------
Q psy17316 36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPT--------------KSWNEEI---------- 91 (229)
Q Consensus 36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~--------------k~~s~e~---------- 91 (229)
......+....+...+..++|..+||+...+......-....+...... ...+++.
T Consensus 98 ~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 (236)
T PRK06986 98 AQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDSILVTEDHQDEDPLQQLEDEELREA 177 (236)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcccccccCCCCCCHHHHHHHHHHHHH
Q ss_pred HHHHHHHHhhcchhhhhhhhccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHH
Q psy17316 92 LNVALDALRAGSISANKASKAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARK 158 (229)
Q Consensus 92 ~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~ 158 (229)
...+++.| ++.-..++.+..-.++|+.+||..+|||..|++.++++
T Consensus 178 l~~~l~~L---------------------~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~~~r 223 (236)
T PRK06986 178 LVEAIESL---------------------PEREQLVLSLYYQEELNLKEIGAVLGVSESRVSQIHSQ 223 (236)
T ss_pred HHHHHHhC---------------------CHHHHHHHHhHhccCCCHHHHHHHHCCCHHHHHHHHHH
No 374
>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=90.07 E-value=0.7 Score=36.94 Aligned_cols=25 Identities=8% Similarity=0.106 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 48 GQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 48 g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
.|+|+.+||+.+|||.+|++.++++
T Consensus 137 ~g~s~~eIA~~l~is~~tv~~~l~r 161 (170)
T TIGR02952 137 QNLPIAEVARILGKTEGAVKILQFR 161 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5889999999999999999999886
No 375
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.07 E-value=0.47 Score=36.38 Aligned_cols=33 Identities=15% Similarity=0.347 Sum_probs=30.3
Q ss_pred HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
..+++|-...+|+.+||..++|+++.|++-+++
T Consensus 24 ~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIKr 56 (105)
T COG2739 24 NYLELYYLDDLSLSEIAEEFNVSRQAIYDNIKR 56 (105)
T ss_pred HHHHHHHHhhccHHHHHHHhCccHHHHHHHHHH
Confidence 567788888999999999999999999999997
No 376
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=90.05 E-value=0.67 Score=38.47 Aligned_cols=40 Identities=15% Similarity=0.214 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+.++.++.-.+.-+. +|+|+.+||+.+|||.+||+.++++
T Consensus 142 ~L~~~~r~vl~l~~~-~~~s~~EIA~~Lgis~~tVk~~l~r 181 (194)
T PRK09646 142 ALTDTQRESVTLAYY-GGLTYREVAERLAVPLGTVKTRMRD 181 (194)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCChHhHHHHHHH
Confidence 344444433332333 5789999999999999999999886
No 377
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=90.04 E-value=0.46 Score=38.47 Aligned_cols=40 Identities=13% Similarity=0.223 Sum_probs=30.2
Q ss_pred CCCHHHHHHH-HHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316 32 TWTHEDMDAA-LEALRA---GQMSLTKASVSYGIPSTTLWQRAH 71 (229)
Q Consensus 32 kyt~e~~~~A-I~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~ 71 (229)
..|.+.+.+| ++++.+ ..+|+.+||++.||+|+|+|+...
T Consensus 2 ~~Tk~~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY~hF~ 45 (176)
T TIGR02366 2 IITKKKIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFYNHFQ 45 (176)
T ss_pred hHHHHHHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHHHHCC
Confidence 3566667666 444443 569999999999999999998644
No 378
>PRK15115 response regulator GlrR; Provisional
Probab=89.97 E-value=0.49 Score=44.21 Aligned_cols=35 Identities=14% Similarity=0.119 Sum_probs=32.4
Q ss_pred HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
||..|.+.+...+.|..+||+..|||++|+|+.+|
T Consensus 399 E~~~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~ 433 (444)
T PRK15115 399 ELNYLRKLLQITKGNVTHAARMAGRNRTEFYKLLS 433 (444)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 67788888888888999999999999999999998
No 379
>PRK06474 hypothetical protein; Provisional
Probab=89.87 E-value=0.64 Score=38.87 Aligned_cols=37 Identities=14% Similarity=0.060 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHhCC--CcHHHHHHHh-CCChHHHHHHHH
Q psy17316 176 PEDLEIALEGIRSGQ--TTVQRASAEY-GIPSGTLYGRCK 212 (229)
Q Consensus 176 ~e~r~eaV~~~~~~~--~s~~eAA~~f-gVp~~tv~~~vk 212 (229)
...|..|++.+..++ ++..+++..+ +||.+|||+.++
T Consensus 10 ~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~ 49 (178)
T PRK06474 10 HPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQ 49 (178)
T ss_pred CHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHH
Confidence 456999999998854 8999999999 899999999998
No 380
>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=89.87 E-value=0.68 Score=36.32 Aligned_cols=32 Identities=16% Similarity=0.077 Sum_probs=25.9
Q ss_pred HHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 41 ALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 41 AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
++.++.-.|+|+.+||+.+|||.+|++.++++
T Consensus 121 il~l~~~~~~~~~eIA~~lgis~~tv~~~~~r 152 (161)
T TIGR02985 121 IFILSRFEGKSYKEIAEELGISVKTVEYHISK 152 (161)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34442335889999999999999999999886
No 381
>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=89.86 E-value=0.23 Score=31.19 Aligned_cols=22 Identities=14% Similarity=0.222 Sum_probs=19.2
Q ss_pred CHHHHHHHcCCChhhHHHHHHH
Q psy17316 51 SLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 51 S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
|+.++|+.+||+..||+.|-+.
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~ 22 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYERE 22 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHT
T ss_pred CHHHHHHHHCCCHHHHHHHHHC
Confidence 4789999999999999999887
No 382
>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=89.80 E-value=0.58 Score=30.54 Aligned_cols=25 Identities=8% Similarity=-0.019 Sum_probs=23.2
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAH 71 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~ 71 (229)
.-++|+.++|+..||++++|.+|..
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 5689999999999999999999976
No 383
>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA.
Probab=89.80 E-value=0.57 Score=30.86 Aligned_cols=41 Identities=24% Similarity=0.191 Sum_probs=35.1
Q ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316 174 WKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR 215 (229)
Q Consensus 174 ~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~ 215 (229)
+.++-+..||+...+| .-.+++|+..+|+..||.+.+|.+|
T Consensus 6 ~kpgikeqIvema~nG-~GiRdtaRvL~I~~nTVlrtLK~sr 46 (46)
T PF12759_consen 6 RKPGIKEQIVEMAFNG-SGIRDTARVLKISINTVLRTLKNSR 46 (46)
T ss_pred cCccHHHHHHHHHhcC-CcchhhHhHhcchHHHHHHHHhcCC
Confidence 3466788999999988 7799999999999999999888543
No 384
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=89.79 E-value=0.22 Score=32.96 Aligned_cols=23 Identities=17% Similarity=0.553 Sum_probs=19.4
Q ss_pred CCHHHHHHHhCCChHHHHHHHHH
Q psy17316 136 ISANKASKAYGIPSSTLYKIARK 158 (229)
Q Consensus 136 ~S~~~~a~k~gIp~sTL~~~ik~ 158 (229)
++..++++.+||+++|+|++++.
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~ 26 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKD 26 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHH
T ss_pred ccHHHHHHHHCCCHHHHHHHHhc
Confidence 47899999999999999999984
No 385
>PF06627 DUF1153: Protein of unknown function (DUF1153); InterPro: IPR009534 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2OA4_A 2JRT_A.
Probab=89.79 E-value=0.79 Score=34.31 Aligned_cols=43 Identities=16% Similarity=0.387 Sum_probs=36.4
Q ss_pred CCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 170 SPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 170 ~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
..+.|...-+.++|..|+.|-++..||+..|++|-+=+-.|.+
T Consensus 29 ~t~RWva~RKAaVV~aV~~Glis~~EA~~rY~Ls~eEf~~W~~ 71 (90)
T PF06627_consen 29 DTRRWVARRKAAVVRAVRGGLISVEEACRRYGLSEEEFESWQR 71 (90)
T ss_dssp S-S---HHHHHHHHHHHHCTTS-HHHHHHCTTSSHHHHHHHHH
T ss_pred ccccchhhHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3568999999999999999999999999999999999999998
No 386
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=89.77 E-value=0.74 Score=38.01 Aligned_cols=39 Identities=10% Similarity=0.040 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
.++++..-.+-.+. .|+|+.+||..+|||.+||+.++.+
T Consensus 132 Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~R 170 (191)
T PRK12520 132 LPPRTGRVFMMREW-LELETEEICQELQITATNAWVLLYR 170 (191)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 33444333332333 4789999999999999999999885
No 387
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=89.76 E-value=0.55 Score=37.28 Aligned_cols=26 Identities=12% Similarity=0.233 Sum_probs=23.7
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
-.|+|+.+||..+|||.+|++.++.+
T Consensus 120 ~~g~s~~EIA~~lgis~~tV~~~l~r 145 (161)
T PRK09047 120 WEDMDVAETAAAMGCSEGSVKTHCSR 145 (161)
T ss_pred HhcCCHHHHHHHHCCCHHHHHHHHHH
Confidence 35889999999999999999999886
No 388
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).
Probab=89.75 E-value=0.52 Score=44.04 Aligned_cols=36 Identities=28% Similarity=0.324 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
-+|..|.+.+...+.|..+||+..|||++|+|++++
T Consensus 405 ~E~~~i~~al~~~~gn~~~aA~~Lgisr~tl~rkl~ 440 (445)
T TIGR02915 405 AEREAVRKAIARVDGNIARAAELLGITRPTLYDLMK 440 (445)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 367778888888889999999999999999999987
No 389
>PHA02591 hypothetical protein; Provisional
Probab=89.75 E-value=0.79 Score=33.58 Aligned_cols=38 Identities=13% Similarity=0.148 Sum_probs=34.3
Q ss_pred CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 175 KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 175 t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
++++...+.+.+.+-++|..++|...||+..+|...++
T Consensus 44 ~~dd~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 44 SEDDLISVTHELARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred ccchHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 67788889999999889999999999999999998765
No 390
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=89.73 E-value=0.53 Score=30.88 Aligned_cols=30 Identities=17% Similarity=0.365 Sum_probs=26.4
Q ss_pred HHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316 45 LRAGQMSLTKASVSYGIPSTTLWQRAHRLG 74 (229)
Q Consensus 45 ~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g 74 (229)
+..+.++..++++.+||+++|+++.++++.
T Consensus 6 l~~~~~~~~~i~~~l~is~~~v~~~l~~L~ 35 (66)
T smart00418 6 LAEGELCVCELAEILGLSQSTVSHHLKKLR 35 (66)
T ss_pred hhcCCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 337789999999999999999999999863
No 391
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=89.72 E-value=0.68 Score=37.22 Aligned_cols=41 Identities=15% Similarity=0.081 Sum_probs=30.8
Q ss_pred CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
...+++++.-.+-.+.+ |+|+.+||..+|||.+|++.++++
T Consensus 107 ~~L~~~~r~v~~l~~~~-g~s~~eIA~~lgis~~tv~~~l~R 147 (165)
T PRK09644 107 HTLPVIEAQAILLCDVH-ELTYEEAASVLDLKLNTYKSHLFR 147 (165)
T ss_pred HhCCHHHHHHHHhHHHh-cCCHHHHHHHHCCCHHHHHHHHHH
Confidence 44455555444434444 779999999999999999999886
No 392
>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=89.69 E-value=1.4 Score=31.02 Aligned_cols=26 Identities=15% Similarity=0.217 Sum_probs=23.8
Q ss_pred HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316 46 RAGQMSLTKASVSYGIPSTTLWQRAH 71 (229)
Q Consensus 46 ~~g~~S~~~aA~~~gIp~sTL~~~i~ 71 (229)
...++++.++|+..||+++||.+|..
T Consensus 15 ~~~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 15 EPLGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 45689999999999999999999976
No 393
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=89.68 E-value=0.77 Score=37.54 Aligned_cols=26 Identities=31% Similarity=0.326 Sum_probs=23.7
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
-.++|+.+||..+||+.+||+.++++
T Consensus 149 ~~~~s~~eIA~~lgis~~~V~~~l~r 174 (186)
T PRK13919 149 YQGYTHREAAQLLGLPLGTLKTRARR 174 (186)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 35889999999999999999999886
No 394
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=89.68 E-value=0.6 Score=37.32 Aligned_cols=32 Identities=13% Similarity=0.173 Sum_probs=26.6
Q ss_pred HHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 41 ALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 41 AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
++.+..-+|+|..+||..+|||.+|++.++++
T Consensus 121 v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~r 152 (161)
T PRK12528 121 AFLLAQVDGLGYGEIATELGISLATVKRYLNK 152 (161)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34344446899999999999999999999886
No 395
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=89.62 E-value=0.52 Score=32.94 Aligned_cols=39 Identities=18% Similarity=0.148 Sum_probs=29.7
Q ss_pred HHHHHHHHHh--CCCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316 179 LEIALEGIRS--GQTTVQRASAEYGIPSGTLYGRCK-LSRST 217 (229)
Q Consensus 179 r~eaV~~~~~--~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~ 217 (229)
+.+|++++.. +.++..++|..+||+..|++.++. +..+|
T Consensus 2 ke~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG 43 (62)
T PF04703_consen 2 KEKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEG 43 (62)
T ss_dssp HHCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCT
T ss_pred cHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 3456666666 779999999999999999999998 55444
No 396
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=89.61 E-value=0.65 Score=38.04 Aligned_cols=26 Identities=15% Similarity=0.263 Sum_probs=23.8
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
-+|+|+.+||..+|||.+|++.++.+
T Consensus 141 ~~g~s~~EIA~~l~is~~tv~~~l~R 166 (179)
T PRK09415 141 YEELSIKEIAEVTGVNENTVKTRLKK 166 (179)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 35889999999999999999999886
No 397
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=89.57 E-value=1 Score=32.45 Aligned_cols=36 Identities=17% Similarity=0.162 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHh--CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 177 EDLEIALEGIRS--GQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 177 e~r~eaV~~~~~--~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
+.-..|++++.. +.++..++|..+|||.+||++.++
T Consensus 5 ~r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~ 42 (91)
T smart00346 5 ERGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLN 42 (91)
T ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHH
Confidence 345678888766 469999999999999999999998
No 398
>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=89.48 E-value=0.67 Score=31.13 Aligned_cols=38 Identities=24% Similarity=0.329 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+|+.++. ++..+.. |+|..+||..+||+..||+.+++.
T Consensus 4 LT~~E~~-vl~~l~~-G~~~~eIA~~l~is~~tV~~~~~~ 41 (58)
T PF00196_consen 4 LTERELE-VLRLLAQ-GMSNKEIAEELGISEKTVKSHRRR 41 (58)
T ss_dssp S-HHHHH-HHHHHHT-TS-HHHHHHHHTSHHHHHHHHHHH
T ss_pred cCHHHHH-HHHHHHh-cCCcchhHHhcCcchhhHHHHHHH
Confidence 3444443 5555555 779999999999999999988775
No 399
>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=89.46 E-value=0.55 Score=37.45 Aligned_cols=26 Identities=23% Similarity=0.265 Sum_probs=24.0
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
-.|+|..+||..+|||.+||+.++.+
T Consensus 124 ~~g~s~~eIA~~lgis~~tV~~~l~r 149 (162)
T TIGR02983 124 YEDLSEAQVAEALGISVGTVKSRLSR 149 (162)
T ss_pred HhcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 45889999999999999999999886
No 400
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=89.46 E-value=0.69 Score=38.45 Aligned_cols=33 Identities=21% Similarity=0.247 Sum_probs=27.0
Q ss_pred HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+.|+...-+|+|..+||..+||+..|++++++.
T Consensus 142 ~~v~l~~~~Gls~~EIA~~lgiS~~tV~r~l~~ 174 (185)
T PF07638_consen 142 RVVELRFFEGLSVEEIAERLGISERTVRRRLRR 174 (185)
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 444444457999999999999999999998774
No 401
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=89.41 E-value=0.81 Score=37.40 Aligned_cols=25 Identities=24% Similarity=0.211 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 48 GQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 48 g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
.++|+.+||..+|||.+|++.++++
T Consensus 132 e~~s~~EIA~~lgis~~tV~~~l~r 156 (179)
T PRK12543 132 HDYSQEEIAQLLQIPIGTVKSRIHA 156 (179)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4789999999999999999999886
No 402
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=89.39 E-value=0.96 Score=37.39 Aligned_cols=34 Identities=24% Similarity=0.206 Sum_probs=26.9
Q ss_pred HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
-.+|+....-.++|+.|+|..+|||..||+..+.
T Consensus 116 ~R~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~ 149 (182)
T PRK12540 116 QREALILVGASGFSYEDAAAICGCAVGTIKSRVN 149 (182)
T ss_pred HHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4445555444559999999999999999999875
No 403
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=89.37 E-value=0.75 Score=38.10 Aligned_cols=40 Identities=13% Similarity=0.028 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+.++.+..-.+-.+. .|+|+.+||..+|||.+|++.++.+
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~R 175 (195)
T PRK12532 136 NLPENTARVFTLKEI-LGFSSDEIQQMCGISTSNYHTIMHR 175 (195)
T ss_pred hCCHHHHHHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 334444433332344 4889999999999999999999886
No 404
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=89.36 E-value=0.73 Score=34.91 Aligned_cols=34 Identities=24% Similarity=0.353 Sum_probs=28.4
Q ss_pred HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
+.++.++.+.+ |+..||+.+||+.+|+++.+++.
T Consensus 7 l~~~~av~~~g-Sis~AA~~L~iS~stvs~~I~~L 40 (99)
T TIGR00637 7 VALLKAIARMG-SISQAAKDAGISYKSAWDYIRAM 40 (99)
T ss_pred HHHHHHHHHhC-CHHHHHHHHCCCHHHHHHHHHHH
Confidence 44555666656 99999999999999999999985
No 405
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=89.36 E-value=0.91 Score=35.62 Aligned_cols=43 Identities=14% Similarity=0.025 Sum_probs=36.2
Q ss_pred CHHHHHHHHHHHHh-CCCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316 175 KPEDLEIALEGIRS-GQTTVQRASAEYGIPSGTLYGRCK-LSRST 217 (229)
Q Consensus 175 t~e~r~eaV~~~~~-~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~ 217 (229)
....|..|+..+.+ +++++.+++..+++|.+||-.+++ +.+.|
T Consensus 14 adptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~AG 58 (117)
T PRK10141 14 SDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRESG 58 (117)
T ss_pred CCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 34679999999976 689999999999999999999998 44333
No 406
>TIGR01818 ntrC nitrogen regulation protein NR(I). This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.
Probab=89.36 E-value=0.6 Score=43.82 Aligned_cols=35 Identities=20% Similarity=0.176 Sum_probs=31.2
Q ss_pred HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
||..|.+.+...+.|..+||+..|||++|+|+++|
T Consensus 427 E~~~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~ 461 (463)
T TIGR01818 427 ERPLLEAALQHTRGHKQEAAALLGWGRNTLTRKLK 461 (463)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 56677788888888999999999999999999987
No 407
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=89.36 E-value=2 Score=38.02 Aligned_cols=70 Identities=14% Similarity=0.217 Sum_probs=52.0
Q ss_pred cCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHH-HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHH
Q psy17316 133 AGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPED-LEIALEGIRSGQTTVQRASAEYGIPSGTLYGR 210 (229)
Q Consensus 133 ~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~-r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~ 210 (229)
...+++.++|+..|+|..+|.+..++. |..... |-..- +..|.+.+...+++..++|..+|-+-++-...
T Consensus 19 ~~~~~l~~lA~~~~~S~~~l~r~F~~~~g~s~~~--------yi~~~Rl~~A~~~L~~~~~~i~~iA~~~Gf~s~~~f~r 90 (289)
T PRK15121 19 DQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGA--------YIRARRLSKAAVALRLTSRPILDIALQYRFDSQQTFTR 90 (289)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHH--------HHHHHHHHHHHHHHHcCCCCHHHHHHHHCCCCHHHHHH
Confidence 445799999999999999999999876 755532 32222 45566777777899999999999855544443
No 408
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=89.27 E-value=0.59 Score=38.43 Aligned_cols=40 Identities=15% Similarity=0.130 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
..++.+..-.+..+. +|+|+.+||+.+|||.+||+.++.+
T Consensus 131 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~r 170 (184)
T PRK12539 131 RLPEKMRLAIQAVKL-EGLSVAEAATRSGMSESAVKVSVHR 170 (184)
T ss_pred hCCHHHHHHHHHHHH-cCCcHHHHHHHHCcCHHHHHHHHHH
Confidence 334444333332333 5889999999999999999999886
No 409
>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=89.27 E-value=0.87 Score=39.84 Aligned_cols=35 Identities=14% Similarity=0.025 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
...+|+..+.-+++||.|||..+|||.+||+.++.
T Consensus 165 ~~R~v~~L~~~eg~S~~EIA~~Lgis~~TVk~rl~ 199 (244)
T TIGR03001 165 RERHLLRLHFVDGLSMDRIGAMYQVHRSTVSRWVA 199 (244)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34556666666779999999999999999999885
No 410
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=89.25 E-value=1.2 Score=28.34 Aligned_cols=32 Identities=19% Similarity=0.245 Sum_probs=26.2
Q ss_pred HHHHHHHh-CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 181 IALEGIRS-GQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 181 eaV~~~~~-~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
.+++.+.. +.++..+++..|+||.+|+++.++
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~ 36 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLGVSEMTIRRDLN 36 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 34444444 569999999999999999999998
No 411
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=89.24 E-value=0.6 Score=43.39 Aligned_cols=37 Identities=19% Similarity=0.274 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
.-|+..|.+.+..++.+..+||+..|||++|+|+.+|
T Consensus 404 ~~e~~~i~~~l~~~~gn~~~aa~~Lgisr~tl~rk~~ 440 (441)
T PRK10365 404 EVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKLS 440 (441)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHhh
Confidence 3467778888888889999999999999999999876
No 412
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=89.23 E-value=0.75 Score=37.73 Aligned_cols=39 Identities=15% Similarity=0.072 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
.++++..-.+..+. .|+|+.+||+.+|||..||+.++++
T Consensus 129 L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~R 167 (186)
T PRK05602 129 LPERQREAIVLQYY-QGLSNIEAAAVMDISVDALESLLAR 167 (186)
T ss_pred CCHHHHHHhhHHHh-cCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 34443333333343 5889999999999999999999886
No 413
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=89.22 E-value=0.62 Score=43.57 Aligned_cols=36 Identities=17% Similarity=0.215 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
-++..|.+.+...+.|..+||+..|||++|+|++++
T Consensus 417 ~E~~~i~~al~~~~gn~~~aA~~LGisr~tL~rkl~ 452 (457)
T PRK11361 417 VEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQ 452 (457)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 367777777888788999999999999999999987
No 414
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=89.21 E-value=0.68 Score=36.94 Aligned_cols=26 Identities=12% Similarity=0.104 Sum_probs=23.8
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
-.++|+.+||..+|||.+|++.++.+
T Consensus 119 ~~~~s~~eIA~~lgis~~tv~~~l~r 144 (159)
T PRK12527 119 LEGLSHQQIAEHLGISRSLVEKHIVN 144 (159)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 35889999999999999999999885
No 415
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=89.21 E-value=1.4 Score=35.68 Aligned_cols=37 Identities=19% Similarity=0.399 Sum_probs=29.5
Q ss_pred HHHHHH-HhCCCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316 181 IALEGI-RSGQTTVQRASAEYGIPSGTLYGRCK-LSRST 217 (229)
Q Consensus 181 eaV~~~-~~~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~ 217 (229)
.|++.+ .+++.++.++|+..|+|.+||.++++ +..+|
T Consensus 13 ~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~G 51 (153)
T PRK11179 13 GILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAG 51 (153)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 444544 55789999999999999999999998 44444
No 416
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=89.21 E-value=0.84 Score=30.40 Aligned_cols=31 Identities=19% Similarity=0.298 Sum_probs=26.5
Q ss_pred HHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316 44 ALRAGQMSLTKASVSYGIPSTTLWQRAHRLG 74 (229)
Q Consensus 44 ~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g 74 (229)
...+|++++.++|+.++++++++.+.+++..
T Consensus 12 l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~ 42 (59)
T PF01047_consen 12 LYENGGITQSELAEKLGISRSTVTRIIKRLE 42 (59)
T ss_dssp HHHHSSEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHcCCCCHHHHHHHHCCChhHHHHHHHHHH
Confidence 3457889999999999999999999999863
No 417
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=89.19 E-value=0.87 Score=37.05 Aligned_cols=39 Identities=15% Similarity=0.153 Sum_probs=28.6
Q ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
.++++..-.+..+. .|+|+.+||..+|||.+||+.++.+
T Consensus 130 L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~R 168 (179)
T PRK12514 130 LEKDRAAAVRRAYL-EGLSYKELAERHDVPLNTMRTWLRR 168 (179)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCCChHHHHHHHHH
Confidence 34444333333344 4789999999999999999999886
No 418
>PRK13500 transcriptional activator RhaR; Provisional
Probab=89.16 E-value=2.1 Score=38.46 Aligned_cols=79 Identities=11% Similarity=0.155 Sum_probs=57.6
Q ss_pred CCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHH-HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHH
Q psy17316 134 GSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPED-LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRC 211 (229)
Q Consensus 134 g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~-r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~v 211 (229)
..+++.++|+++||+.++|.+..|+. |.... .|=.+. ..+|.+.+...++++.++|...|=+-++=.+.+
T Consensus 221 e~isl~~lA~~~~iS~~~L~r~FK~~tG~T~~--------~yi~~~RL~~A~~LL~~t~~sI~eIA~~~GF~d~s~Fsr~ 292 (312)
T PRK13500 221 SPFALDKFCDEASCSERVLRQQFRQQTGMTIN--------QYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVV 292 (312)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHH
Confidence 35799999999999999999999976 75443 232233 445566666678999999999999887776665
Q ss_pred HhhcCCCCC
Q psy17316 212 KLSRSTPRP 220 (229)
Q Consensus 212 k~~~~~~~~ 220 (229)
=.+.-|-+|
T Consensus 293 FKk~~G~TP 301 (312)
T PRK13500 293 FTRETGMTP 301 (312)
T ss_pred HHHHHCcCH
Confidence 444444433
No 419
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=89.15 E-value=0.83 Score=37.82 Aligned_cols=40 Identities=28% Similarity=0.263 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+.++.+..-.+-.+.+ |+|+.+||..+|||.+|++.++.+
T Consensus 111 ~Lp~~~R~v~~L~~~e-g~s~~EIA~~lgis~~tV~~~l~R 150 (182)
T PRK12511 111 DLPEEQRAALHLVAIE-GLSYQEAAAVLGIPIGTLMSRIGR 150 (182)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHhCcCHHHHHHHHHH
No 420
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=89.11 E-value=0.82 Score=36.54 Aligned_cols=34 Identities=15% Similarity=0.052 Sum_probs=27.7
Q ss_pred HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
..+|+....-+++++.++|..+|||.+||+.++.
T Consensus 118 ~r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ 151 (161)
T PRK12528 118 VKRAFLLAQVDGLGYGEIATELGISLATVKRYLN 151 (161)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4445555555559999999999999999999987
No 421
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=89.08 E-value=0.69 Score=31.24 Aligned_cols=28 Identities=29% Similarity=0.489 Sum_probs=25.7
Q ss_pred CCCHHHHHHHhCCChHHHHHHHHHhCCc
Q psy17316 135 SISANKASKAYGIPSSTLYKIARKEGIR 162 (229)
Q Consensus 135 ~~S~~~~a~k~gIp~sTL~~~ik~~g~k 162 (229)
++++.++|+..||+.++|.+.+++.||.
T Consensus 15 hlp~~eAA~~Lgv~~T~LKr~CR~~GI~ 42 (52)
T PF02042_consen 15 HLPIKEAAKELGVSVTTLKRRCRRLGIP 42 (52)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence 5799999999999999999999998874
No 422
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=89.08 E-value=0.75 Score=37.77 Aligned_cols=35 Identities=20% Similarity=0.163 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
+.|..++-... +++||.|||..+|||.+||.+++.
T Consensus 131 ~~R~~~~l~~~-~gls~~EIA~~l~i~~~tVks~l~ 165 (182)
T COG1595 131 RQREAFLLRYL-EGLSYEEIAEILGISVGTVKSRLH 165 (182)
T ss_pred HHhHHhhhHhh-cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 33433333333 559999999999999999999987
No 423
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=89.06 E-value=1 Score=35.62 Aligned_cols=44 Identities=30% Similarity=0.399 Sum_probs=36.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 168 NASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 168 ~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
.+++++|+...+.-|=+++.+| +..+++|+..|||--|||..++
T Consensus 88 rGrprkyd~~t~~~i~emlr~g-k~preIsk~lGIpirTvyY~l~ 131 (139)
T COG1710 88 RGRPRKYDRNTLLRIREMLRNG-KTPREISKDLGIPIRTVYYLLK 131 (139)
T ss_pred CCCCcccchhHHHHHHHHHHcC-CCHHHHHHhhCCchhhhHHHHH
Confidence 4678899876666665655555 8899999999999999999887
No 424
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=88.98 E-value=0.73 Score=36.79 Aligned_cols=26 Identities=8% Similarity=-0.016 Sum_probs=23.6
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
-.++|+.+||..+|||.+||+.++.+
T Consensus 123 ~~~~s~~EIA~~lgis~~tV~~~l~r 148 (163)
T PRK07037 123 LHGETQKDIARELGVSPTLVNFMIRD 148 (163)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 35889999999999999999999875
No 425
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=88.93 E-value=0.68 Score=45.76 Aligned_cols=39 Identities=33% Similarity=0.479 Sum_probs=31.1
Q ss_pred HHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCc
Q psy17316 124 LNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIR 162 (229)
Q Consensus 124 k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k 162 (229)
+..-+.++..-...+.++|+..|||++|||+.+|++|+.
T Consensus 567 ~~~l~~al~~~~~~is~aa~~lgi~R~T~yrklk~~gi~ 605 (606)
T COG3284 567 KAALLAALQATNGNISEAARLLGISRSTLYRKLKRHGIS 605 (606)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence 344455555545689999999999999999999999873
No 426
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=88.90 E-value=0.68 Score=37.93 Aligned_cols=27 Identities=15% Similarity=0.277 Sum_probs=24.3
Q ss_pred HcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 46 RAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 46 ~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
.-.|+|+.+||+.+|||.+||+.++.+
T Consensus 142 ~~~g~s~~EIA~~l~is~~tV~~~l~r 168 (181)
T PRK12536 142 KLEGLSVAETAQLTGLSESAVKVGIHR 168 (181)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 346889999999999999999999886
No 427
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=88.86 E-value=3.9 Score=31.76 Aligned_cols=38 Identities=16% Similarity=0.219 Sum_probs=29.0
Q ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
|.|++ +.++.+..-.-+++++-+.+|++-.||+-++..
T Consensus 43 t~d~L-eFv~lf~r~RGnlKEvEr~lg~sYptvR~kld~ 80 (122)
T COG3877 43 TSDQL-EFVELFLRCRGNLKEVERELGISYPTVRTKLDE 80 (122)
T ss_pred CHhHh-HHHHHHHHHccCHHHHHHHHCCccHHHHHHHHH
Confidence 55554 555566554559999999999999999987765
No 428
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=88.84 E-value=2.1 Score=29.67 Aligned_cols=51 Identities=18% Similarity=0.307 Sum_probs=34.6
Q ss_pred HHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHH
Q psy17316 124 LNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQ 194 (229)
Q Consensus 124 k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~ 194 (229)
+.+||..+ + |...+|+.+||+.+++++| . .. . |..|.--|+.+-+|.+.+.
T Consensus 2 k~~aI~~~---G-~~~~lAkalGVs~~aVs~W-~-~~----I----------P~~ra~~Ie~~T~G~l~~~ 52 (60)
T PF14549_consen 2 KKDAIKYF---G-GQSKLAKALGVSPQAVSQW-G-ER----I----------PAERAYQIEKLTNGKLKCE 52 (60)
T ss_dssp HHHHHHHH---S-SHHHHHHHHTS-HHHHHHH-H-TS----------------HHHHHHHHHHTTTSS--H
T ss_pred HHHHHHHH---C-CHHHHHHHHCCCHHHHHHh-c-Cc----c----------CHHHHHHHHHHhCCceeeC
Confidence 35667776 3 8999999999999999999 2 11 1 3457777777777776554
No 429
>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=88.83 E-value=0.93 Score=29.19 Aligned_cols=24 Identities=8% Similarity=0.207 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316 48 GQMSLTKASVSYGIPSTTLWQRAH 71 (229)
Q Consensus 48 g~~S~~~aA~~~gIp~sTL~~~i~ 71 (229)
.++|+++||++.||++++|++...
T Consensus 15 ~~~s~~~Ia~~~gvs~~~~y~~f~ 38 (47)
T PF00440_consen 15 EAVSIRDIARRAGVSKGSFYRYFP 38 (47)
T ss_dssp TTSSHHHHHHHHTSCHHHHHHHCS
T ss_pred HhCCHHHHHHHHccchhhHHHHcC
Confidence 578999999999999999998743
No 430
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=88.82 E-value=0.62 Score=46.04 Aligned_cols=38 Identities=21% Similarity=0.239 Sum_probs=34.5
Q ss_pred CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 175 KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 175 t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
.+-||..|.+.+...+-|..+||+..|||++|||+++|
T Consensus 589 ~~~E~~~i~~al~~~~gn~~~aA~~LGisR~TLyrklk 626 (638)
T PRK11388 589 AELEKEAIINAAQVCGGRIQEMAALLGIGRTTLWRKMK 626 (638)
T ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34578889999999889999999999999999999998
No 431
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=88.82 E-value=0.72 Score=37.80 Aligned_cols=31 Identities=13% Similarity=0.087 Sum_probs=25.7
Q ss_pred HHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 42 LEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 42 I~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+.+..-.|+|+.+||..+|||.+|++.++++
T Consensus 136 ~~L~~~~g~s~~EIA~~lgis~~tVk~~l~r 166 (178)
T PRK12529 136 FLMATLDGMKQKDIAQALDIALPTVKKYIHQ 166 (178)
T ss_pred HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3343346889999999999999999999885
No 432
>PRK15340 transcriptional regulator InvF; Provisional
Probab=88.77 E-value=2.9 Score=36.32 Aligned_cols=70 Identities=10% Similarity=0.149 Sum_probs=51.5
Q ss_pred CCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHH-HHHHHHHHhCCCcHHHHHHHhCCChHHHHHHH
Q psy17316 134 GSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDL-EIALEGIRSGQTTVQRASAEYGIPSGTLYGRC 211 (229)
Q Consensus 134 g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r-~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~v 211 (229)
...++.++|+.+|++.+++.+..+++ |..... |=...| .+++..+.+++.+..++|..+|-+.+.-....
T Consensus 124 ~~~sleeLA~~~gvS~r~f~RlFk~~~G~tpk~--------yl~~~Rl~~all~L~~s~~sItdIA~~~GY~d~ShFsr~ 195 (216)
T PRK15340 124 SGNTMRMLGEDYGVSYTHFRRLCSRALGGKAKS--------ELRNWRMAQSLLNSVEGHENITQLAVNHGYSSPSHFSSE 195 (216)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHH--------HHHHHHHHHHHHhhhcCCCCHHHHHHHhCCCCHHHHHHH
Confidence 45699999999999999999999876 754431 212223 35566666788999999999888666655544
No 433
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR. At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.
Probab=88.77 E-value=0.66 Score=45.26 Aligned_cols=35 Identities=20% Similarity=0.184 Sum_probs=31.7
Q ss_pred HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
++..|.+.+..++.|..+||+..|||++|||+++|
T Consensus 491 Er~~I~~aL~~~~Gn~~~aA~~LGIsRtTL~Rklk 525 (526)
T TIGR02329 491 EALAVRAALERFGGDRDAAAKALGISRTTLWRRLK 525 (526)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 57778888888889999999999999999999986
No 434
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=88.74 E-value=0.69 Score=38.34 Aligned_cols=26 Identities=15% Similarity=0.075 Sum_probs=23.8
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
-.|+|+.+||..+|||.+||+.++++
T Consensus 148 ~~g~s~~EIA~~lgis~~tVk~~l~R 173 (189)
T PRK12530 148 YLELSSEQICQECDISTSNLHVLLYR 173 (189)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 35899999999999999999999886
No 435
>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=88.74 E-value=0.95 Score=37.53 Aligned_cols=26 Identities=8% Similarity=-0.049 Sum_probs=23.5
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
-.|+|+.+||..+|||.+||+.++.+
T Consensus 145 ~~g~s~~EIA~~lgis~~tvk~rl~R 170 (188)
T TIGR02943 145 VLGFESDEICQELEISTSNCHVLLYR 170 (188)
T ss_pred HhCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 35889999999999999999999875
No 436
>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=88.71 E-value=0.99 Score=34.41 Aligned_cols=37 Identities=19% Similarity=0.089 Sum_probs=27.7
Q ss_pred CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 175 KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 175 t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
++.++ .++...--+++++.++|..+|||.++|+.+.+
T Consensus 112 ~~~~~-~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~ 148 (158)
T TIGR02937 112 PERER-EVLVLRYLEGLSYKEIAEILGISVGTVKRRLK 148 (158)
T ss_pred CHHHH-HHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34444 44444433459999999999999999999987
No 437
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=88.69 E-value=0.74 Score=37.69 Aligned_cols=38 Identities=18% Similarity=0.307 Sum_probs=30.5
Q ss_pred HHHHHHH-HhCCCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316 180 EIALEGI-RSGQTTVQRASAEYGIPSGTLYGRCK-LSRST 217 (229)
Q Consensus 180 ~eaV~~~-~~~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~ 217 (229)
.+|+..+ .++.+++.++|+..|+|.+||+++++ +.++|
T Consensus 17 ~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~G 56 (164)
T PRK11169 17 RNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQG 56 (164)
T ss_pred HHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 4555555 55789999999999999999999998 54444
No 438
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=88.65 E-value=0.59 Score=38.56 Aligned_cols=26 Identities=27% Similarity=0.326 Sum_probs=23.8
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
-.|+|+.+||..+|||.+||+.++++
T Consensus 155 ~~g~s~~EIA~~lgis~~tV~~~l~R 180 (194)
T PRK12519 155 YEGLSQSEIAKRLGIPLGTVKARARQ 180 (194)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 35889999999999999999999886
No 439
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=88.62 E-value=0.89 Score=37.26 Aligned_cols=35 Identities=9% Similarity=-0.057 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
...+|+....-.++|+.|||..+|||.+||..++.
T Consensus 131 ~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~ 165 (178)
T PRK12529 131 RVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34556666555669999999999999999999876
No 440
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=88.61 E-value=1.3 Score=33.26 Aligned_cols=29 Identities=24% Similarity=0.414 Sum_probs=26.1
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHRLGI 75 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~~gi 75 (229)
++.+|..++|+.+|++++|++++++++.-
T Consensus 15 ~~~~~~~~la~~l~~s~~tv~~~l~~L~~ 43 (108)
T smart00344 15 DARISLAELAKKVGLSPSTVHNRVKRLEE 43 (108)
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 57899999999999999999999998633
No 441
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=88.59 E-value=1 Score=36.23 Aligned_cols=37 Identities=11% Similarity=-0.078 Sum_probs=28.8
Q ss_pred CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 175 KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 175 t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
+++.|.-++-....| +++.++|..+|||..||+.++.
T Consensus 110 ~~~~r~v~~l~~~~g-~s~~eIA~~lgis~~tv~~~l~ 146 (165)
T PRK09644 110 PVIEAQAILLCDVHE-LTYEEAASVLDLKLNTYKSHLF 146 (165)
T ss_pred CHHHHHHHHhHHHhc-CCHHHHHHHHCCCHHHHHHHHH
Confidence 445555444455555 9999999999999999999976
No 442
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=88.56 E-value=1.1 Score=37.31 Aligned_cols=35 Identities=20% Similarity=0.209 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
...+|+.+..-+++++.|+|..+|||..||..++.
T Consensus 120 ~~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~ 154 (187)
T PRK12516 120 DQREAIILVGASGFAYEEAAEICGCAVGTIKSRVN 154 (187)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34556666555669999999999999999999875
No 443
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=88.56 E-value=0.93 Score=37.38 Aligned_cols=40 Identities=13% Similarity=0.072 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+.+++++.-.+..+. .|+|+.+||..+|||.+|++.++.+
T Consensus 106 ~L~~~~r~i~~l~~~-~g~~~~EIA~~lgis~~tV~~~l~R 145 (181)
T PRK09637 106 ALPEKYAEALRLTEL-EGLSQKEIAEKLGLSLSGAKSRVQR 145 (181)
T ss_pred hCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 344444443333333 5889999999999999999998875
No 444
>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=88.54 E-value=1.3 Score=28.99 Aligned_cols=42 Identities=17% Similarity=0.174 Sum_probs=33.1
Q ss_pred CHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCC
Q psy17316 137 SANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQ 190 (229)
Q Consensus 137 S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~ 190 (229)
++++||+..||+.+|+.+.+... ...+++-|..|.+.+.+-+
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~------------~~vs~~tr~rI~~~a~~lg 42 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGP------------PRVSEETRERILEAAEELG 42 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTC------------SSSTHHHHHHHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHhCC------------CCCCHHHHHHHHHHHHHHC
Confidence 57899999999999999977632 2466788888888877644
No 445
>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=88.53 E-value=0.73 Score=37.14 Aligned_cols=26 Identities=15% Similarity=0.212 Sum_probs=23.8
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
-+|+|..+||..+|||.+|++.++.+
T Consensus 133 ~~g~s~~eiA~~lgis~~tv~~~l~R 158 (169)
T TIGR02954 133 YHDLTIKEIAEVMNKPEGTVKTYLHR 158 (169)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 35889999999999999999999886
No 446
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=88.51 E-value=0.89 Score=44.12 Aligned_cols=34 Identities=21% Similarity=0.285 Sum_probs=28.4
Q ss_pred HHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCccc
Q psy17316 130 ALRAGSISANKASKAYGIPSSTLYKIARKEGIRLA 164 (229)
Q Consensus 130 ~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~ 164 (229)
++..+. +.+++|+..||+++|||+.+++||+...
T Consensus 482 ~l~~~~-~~~~aA~~LGisr~tL~rkl~~~gi~~~ 515 (520)
T PRK10820 482 LYRNYP-STRKLAKRLGVSHTAIANKLREYGLSQK 515 (520)
T ss_pred HHHHCC-CHHHHHHHhCCCHHHHHHHHHHcCCCcc
Confidence 344444 8999999999999999999999998643
No 447
>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=88.51 E-value=0.9 Score=36.96 Aligned_cols=34 Identities=15% Similarity=0.024 Sum_probs=27.2
Q ss_pred HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
-.+|+....-.++|+.|+|..+|||.+||+.++.
T Consensus 139 ~r~v~~l~~~~g~s~~EIA~~lgis~~tVk~~l~ 172 (183)
T TIGR02999 139 QAEVVELRFFAGLTVEEIAELLGVSVRTVERDWR 172 (183)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3445555544559999999999999999999886
No 448
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=88.47 E-value=0.78 Score=37.75 Aligned_cols=41 Identities=15% Similarity=0.102 Sum_probs=29.7
Q ss_pred CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
.+.++.+. ++|....-+|+|+.+||..+|||.+||+.++++
T Consensus 138 ~~L~~~~r-~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~R 178 (189)
T PRK09648 138 DTLPEKQR-EILILRVVVGLSAEETAEAVGSTPGAVRVAQHR 178 (189)
T ss_pred HhCCHHHH-HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34444443 344443345889999999999999999999886
No 449
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=88.47 E-value=1.1 Score=36.51 Aligned_cols=36 Identities=8% Similarity=0.120 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
++.+.-++.....| +|+.++|..+|||..||+.++.
T Consensus 132 ~~~r~i~~l~~~~g-~s~~eIA~~lgis~~tV~~~l~ 167 (179)
T PRK12514 132 KDRAAAVRRAYLEG-LSYKELAERHDVPLNTMRTWLR 167 (179)
T ss_pred HHHHHHHHHHHHcC-CCHHHHHHHHCCChHHHHHHHH
Confidence 44444444444545 9999999999999999999876
No 450
>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF. Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH
Probab=88.41 E-value=0.8 Score=41.85 Aligned_cols=35 Identities=17% Similarity=0.312 Sum_probs=30.5
Q ss_pred HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
|+.-|.+.+..++.|..+||+..|||++|+|+++|
T Consensus 293 E~~~I~~aL~~~~gn~~~aA~~LGisr~tL~rklk 327 (329)
T TIGR02974 293 EIELLQQALAEAQFNQRKAAELLGLTYHQLRGLLR 327 (329)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 56667777777888999999999999999999987
No 451
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=88.40 E-value=0.93 Score=36.22 Aligned_cols=39 Identities=15% Similarity=0.044 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
.++.+..-.+-.+. .|+|..+||..+|||.+|++.++.+
T Consensus 113 L~~~~r~v~~l~~~-~~~s~~eIA~~lgis~~tv~~~l~R 151 (161)
T PRK12541 113 LPLERRNVLLLRDY-YGFSYKEIAEMTGLSLAKVKIELHR 151 (161)
T ss_pred CCHHHHHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34444333332333 5889999999999999999999886
No 452
>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=88.36 E-value=0.83 Score=37.13 Aligned_cols=40 Identities=15% Similarity=0.141 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+.++++. .++.+..-.|+|+.+||..+|||.+|++.++.+
T Consensus 100 ~L~~~~r-~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~R 139 (170)
T TIGR02959 100 ELPDEYR-EAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQR 139 (170)
T ss_pred hCCHHHH-HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4444433 333343345889999999999999999998875
No 453
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=88.34 E-value=1.2 Score=33.64 Aligned_cols=36 Identities=22% Similarity=0.194 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHh
Q psy17316 178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKL 213 (229)
Q Consensus 178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~ 213 (229)
++.-+.+.+...+.+..+||...||+++|+|++++.
T Consensus 56 Er~~i~~aL~~~~gn~s~AAr~LGIsRsTL~rKLkr 91 (95)
T PRK00430 56 EAPLLDMVMQYTRGNQTRAALMLGINRGTLRKKLKK 91 (95)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 355566666667778999999999999999999873
No 454
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=88.32 E-value=1.5 Score=37.40 Aligned_cols=43 Identities=23% Similarity=0.353 Sum_probs=38.3
Q ss_pred CCCCCHHHHHHHHHHHHcC------CCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 30 TKTWTHEDMDAALEALRAG------QMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 30 ~~kyt~e~~~~AI~~~~~g------~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+...|+.|+.-...+|..| ..+..++|+++||+++|+.+.+++
T Consensus 153 ~~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRr 201 (215)
T COG3413 153 KNDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRR 201 (215)
T ss_pred cccCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHH
Confidence 3469999998888899876 589999999999999999999986
No 455
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=88.29 E-value=0.92 Score=38.87 Aligned_cols=25 Identities=24% Similarity=0.316 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 48 GQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 48 g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
.++|+.+||..+|||.+||+.++++
T Consensus 149 eg~s~~EIAe~LgiS~~tVk~~L~R 173 (216)
T PRK12533 149 EDMSYREIAAIADVPVGTVMSRLAR 173 (216)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5889999999999999999999886
No 456
>COG1961 PinR Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]
Probab=88.28 E-value=1.4 Score=37.49 Aligned_cols=73 Identities=30% Similarity=0.256 Sum_probs=51.5
Q ss_pred cHHHHHHHHHHHhhcchhhhhhhhccCCCC-------CC-CHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh
Q psy17316 88 NEEILNVALDALRAGSISANKASKAYGPTK-------SW-NEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE 159 (229)
Q Consensus 88 s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~-------kY-s~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~ 159 (229)
.+.+++...+=..+|...+++.++..|.+. .. .++....++..+..|..+...++..++|+.+|++++.++.
T Consensus 122 Ae~Er~~i~er~~~g~~~a~~~G~~~g~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~a~~~~i~~~t~~r~~~~~ 201 (222)
T COG1961 122 AEFERELISERTRAGIEAARKAGKEGGRPPGYKIKKGRKKAEEQAAAVRRLLADGLGSYSEIARALGISRSTVYRILNKL 201 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCcCCCCCccccccccccccchhHHHHHHHHHhccchHHHHHHHcCccHHHHHHhhhhh
Confidence 556666666666778888888888887652 22 3333444444444442699999999999999999998765
Q ss_pred C
Q psy17316 160 G 160 (229)
Q Consensus 160 g 160 (229)
.
T Consensus 202 ~ 202 (222)
T COG1961 202 K 202 (222)
T ss_pred h
Confidence 3
No 457
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=88.26 E-value=0.95 Score=35.89 Aligned_cols=35 Identities=17% Similarity=0.169 Sum_probs=28.2
Q ss_pred HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
...+|+.+..-.++++.|+|..+|||..||+.++.
T Consensus 110 ~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 110 RQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 34556666555559999999999999999999876
No 458
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=88.22 E-value=0.98 Score=36.37 Aligned_cols=34 Identities=24% Similarity=0.196 Sum_probs=27.2
Q ss_pred HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
-.+|+....-+++|+.|+|..+|||.+||+.++.
T Consensus 117 ~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ 150 (164)
T PRK12547 117 QREAIILIGASGFSYEDAAAICGCAVGTIKSRVS 150 (164)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3445555444669999999999999999999986
No 459
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=88.19 E-value=0.74 Score=37.97 Aligned_cols=35 Identities=23% Similarity=0.262 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
...+|+....-+++++.++|..+|||.+||+.++.
T Consensus 145 ~~~~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ 179 (194)
T PRK12519 145 SQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARAR 179 (194)
T ss_pred HHhhhhhhhhhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 34555555544559999999999999999999986
No 460
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=88.18 E-value=0.86 Score=36.95 Aligned_cols=32 Identities=16% Similarity=0.135 Sum_probs=26.0
Q ss_pred HHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 41 ALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 41 AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
++.+..-.|+|+.+||..+|||.+||+.++.+
T Consensus 127 v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~r 158 (172)
T PRK12523 127 AFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQ 158 (172)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 33333335889999999999999999999886
No 461
>PRK11050 manganese transport regulator MntR; Provisional
Probab=88.16 E-value=1.1 Score=36.27 Aligned_cols=47 Identities=17% Similarity=0.185 Sum_probs=36.3
Q ss_pred CCCCHHHHHHHHHHHH--cCCCCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316 31 KTWTHEDMDAALEALR--AGQMSLTKASVSYGIPSTTLWQRAHRLGIHT 77 (229)
Q Consensus 31 ~kyt~e~~~~AI~~~~--~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~ 77 (229)
.....++.+..|..+. .|++++.++|+.+||+++|+.++++++.-.+
T Consensus 31 ~~~~~e~~l~~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~G 79 (152)
T PRK11050 31 RRELIEDYVELIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDG 79 (152)
T ss_pred hHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 4555666666666443 3789999999999999999999999875444
No 462
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=88.13 E-value=1.1 Score=36.81 Aligned_cols=26 Identities=15% Similarity=0.221 Sum_probs=23.6
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
-.|+|+.+||..+|||.+||+.++.+
T Consensus 136 ~~g~s~~EIA~~lgis~~tVk~~l~R 161 (185)
T PRK12542 136 FYNLTYQEISSVMGITEANVRKQFER 161 (185)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 35889999999999999999999886
No 463
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=88.05 E-value=0.84 Score=37.95 Aligned_cols=26 Identities=12% Similarity=-0.010 Sum_probs=24.0
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
-.++|+.+||+.+|||.+||+.++++
T Consensus 150 ~~g~s~~eIA~~lgis~~tV~~~l~R 175 (196)
T PRK12524 150 IEGLSNPEIAEVMEIGVEAVESLTAR 175 (196)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 36889999999999999999999986
No 464
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=88.04 E-value=1.3 Score=35.18 Aligned_cols=30 Identities=20% Similarity=0.322 Sum_probs=26.8
Q ss_pred HcCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316 46 RAGQMSLTKASVSYGIPSTTLWQRAHRLGI 75 (229)
Q Consensus 46 ~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi 75 (229)
.++.+|+.++|++.|+|.+|++++++++.-
T Consensus 19 ~d~r~~~~eia~~lglS~~~v~~Ri~~L~~ 48 (154)
T COG1522 19 EDARISNAELAERVGLSPSTVLRRIKRLEE 48 (154)
T ss_pred HhCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 368899999999999999999999998633
No 465
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=87.98 E-value=1.1 Score=37.69 Aligned_cols=26 Identities=15% Similarity=0.164 Sum_probs=23.6
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
-.|+|+.+||..+|||.+||+.++++
T Consensus 167 ~~g~s~~EIA~~lgis~~tV~~~l~R 192 (206)
T PRK12526 167 FQELSQEQLAQQLNVPLGTVKSRLRL 192 (206)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 35889999999999999999999875
No 466
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=87.98 E-value=1.8 Score=36.29 Aligned_cols=46 Identities=17% Similarity=0.130 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
...|++.+..+++++.++++|++++|.+|||...+|.-.++-..++
T Consensus 15 ~~lse~~r~~Iy~~~~~~~~sv~~vS~~ygi~~~RV~AIvrLkeiE 60 (172)
T PF12298_consen 15 PVLSEELREQIYEDVMQDGKSVREVSQKYGIKIQRVEAIVRLKEIE 60 (172)
T ss_pred CcCCHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 3458999999999999999999999999999999998777755444
No 467
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=87.98 E-value=0.98 Score=37.01 Aligned_cols=32 Identities=16% Similarity=0.133 Sum_probs=26.2
Q ss_pred HHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 181 IALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 181 eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
+|+....-+++++.++|..+|||.+||+.++.
T Consensus 140 ~i~~l~~~~~~s~~eIA~~lgis~~tV~~~l~ 171 (182)
T PRK12537 140 NCILHAYVDGCSHAEIAQRLGAPLGTVKAWIK 171 (182)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCChhhHHHHHH
Confidence 44555444559999999999999999999886
No 468
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=87.96 E-value=1 Score=37.04 Aligned_cols=38 Identities=18% Similarity=0.121 Sum_probs=29.9
Q ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316 34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL 73 (229)
Q Consensus 34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~ 73 (229)
|++++...+..+.+| ....+..-|..-..-|++++..+
T Consensus 7 ~~~~~~~l~~~~~~g--d~~a~~~l~~~~~~~l~~~~~~~ 44 (189)
T PRK09648 7 TGEELDALVAEAVAG--DRRALREVLEIIRPLVVRYCRAR 44 (189)
T ss_pred CchHHHHHHHHHHcC--CHHHHHHHHHHHHHHHHHHHHHH
Confidence 778888888888876 46777777777788888888875
No 469
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=87.88 E-value=0.98 Score=37.42 Aligned_cols=34 Identities=9% Similarity=-0.093 Sum_probs=27.7
Q ss_pred HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
..+|+....-++++|.|+|..+|||.+||+.++.
T Consensus 139 ~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~ 172 (189)
T PRK12530 139 QARVFMMREYLELSSEQICQECDISTSNLHVLLY 172 (189)
T ss_pred HHHHHhHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4455555555569999999999999999999876
No 470
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=87.87 E-value=0.93 Score=36.60 Aligned_cols=31 Identities=26% Similarity=0.242 Sum_probs=25.5
Q ss_pred HHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 42 LEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 42 I~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+.+..-.|+|+.+||+.+|||.+|++.++++
T Consensus 127 l~L~~~~g~s~~EIA~~lgis~~tV~~~l~r 157 (173)
T PRK09645 127 LVRSYYRGWSTAQIAADLGIPEGTVKSRLHY 157 (173)
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3333345889999999999999999999886
No 471
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=87.85 E-value=1.5 Score=34.70 Aligned_cols=45 Identities=29% Similarity=0.506 Sum_probs=38.6
Q ss_pred cCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHH
Q psy17316 113 YGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARK 158 (229)
Q Consensus 113 ~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~ 158 (229)
-|++.+|+...++..-+...+|. +-++|++..|||-.|||=.+++
T Consensus 88 rGrprkyd~~t~~~i~emlr~gk-~preIsk~lGIpirTvyY~l~k 132 (139)
T COG1710 88 RGRPRKYDRNTLLRIREMLRNGK-TPREISKDLGIPIRTVYYLLKK 132 (139)
T ss_pred CCCCcccchhHHHHHHHHHHcCC-CHHHHHHhhCCchhhhHHHHHH
Confidence 37899999988888777777776 9999999999999998877664
No 472
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=87.85 E-value=1.1 Score=35.72 Aligned_cols=36 Identities=8% Similarity=-0.040 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
+...+|+..+--+++++.++|..+|||.+||+..+.
T Consensus 108 ~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ 143 (159)
T PRK12527 108 PACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIV 143 (159)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 345567777666679999999999999999999876
No 473
>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=87.80 E-value=0.95 Score=36.45 Aligned_cols=34 Identities=15% Similarity=0.082 Sum_probs=27.9
Q ss_pred HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
-.+|+....-+++++.++|..+|||.+||+.++.
T Consensus 124 ~r~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~ 157 (169)
T TIGR02954 124 YQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLH 157 (169)
T ss_pred HhHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3456655555669999999999999999999986
No 474
>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=87.80 E-value=0.99 Score=35.97 Aligned_cols=34 Identities=15% Similarity=0.109 Sum_probs=27.4
Q ss_pred HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
..+|+....-+++++.++|..+|||..||+.++.
T Consensus 115 ~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ 148 (162)
T TIGR02983 115 QRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLS 148 (162)
T ss_pred HHHHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHH
Confidence 4445555445569999999999999999999986
No 475
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=87.67 E-value=0.91 Score=38.86 Aligned_cols=26 Identities=12% Similarity=0.169 Sum_probs=23.7
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
-.++|+.+||..+|||.+||+.++++
T Consensus 196 ~eg~s~~EIA~~lgis~~tVk~~~~r 221 (234)
T PRK08301 196 GEEKTQKEVADMLGISQSYISRLEKR 221 (234)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 46899999999999999999998775
No 476
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 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, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=87.63 E-value=1.1 Score=30.29 Aligned_cols=33 Identities=15% Similarity=0.177 Sum_probs=27.3
Q ss_pred HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
..+++..+.+.+ |+..||..++|++++|...++
T Consensus 3 ~l~~f~~v~~~g-s~~~AA~~l~is~~~vs~~i~ 35 (60)
T PF00126_consen 3 QLRYFLAVAETG-SISAAAEELGISQSAVSRQIK 35 (60)
T ss_dssp HHHHHHHHHHHS-SHHHHHHHCTSSHHHHHHHHH
T ss_pred HHHHHHHHHHhC-CHHHHHHHhhccchHHHHHHH
Confidence 345666666663 799999999999999999998
No 477
>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=87.62 E-value=1 Score=30.46 Aligned_cols=30 Identities=17% Similarity=0.418 Sum_probs=26.1
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
+|.+|+.++|..|||+..|+++=+..+.-.
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~~L~~~ 41 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLNKLEKQ 41 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 688999999999999999999988865433
No 478
>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=87.57 E-value=0.56 Score=38.79 Aligned_cols=25 Identities=24% Similarity=0.361 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 48 GQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 48 g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
.|+|+.+||..+|||.+||+.++.+
T Consensus 146 ~g~s~~EIA~~lgis~~tVk~~l~R 170 (193)
T TIGR02947 146 EGFAYKEIAEIMGTPIGTVMSRLHR 170 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 6899999999999999999999886
No 479
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=87.54 E-value=15 Score=30.79 Aligned_cols=153 Identities=18% Similarity=0.213 Sum_probs=93.0
Q ss_pred HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh--CCC--CCCCCC-CCCCCcHHHHHHHHHHHhhcchhhhhhh
Q psy17316 36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL--GIH--TPKKEG-PTKSWNEEILNVALDALRAGSISANKAS 110 (229)
Q Consensus 36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~--gi~--~~~~~~-~~k~~s~e~~~~a~~ll~~G~ls~~~~~ 110 (229)
.-+..++.++++|. -.-++.+|.+.-.|..--+-- .+. ...... -....+.+....+++-.+.
T Consensus 5 avL~~~l~~l~~G~---~~~c~~lG~~~eel~~L~~ls~~~l~~L~~~~v~~~~i~in~~~l~~~L~~~~~--------- 72 (180)
T PF11198_consen 5 AVLTQALHDLKEGN---IRRCEALGFSPEELDALQQLSLDDLHYLANSSVSFVSISINHDVLWRLLEQARR--------- 72 (180)
T ss_pred HHHHHHHHHHHccc---HHHHHHcCCCHHHHHHHhCCCHHHHHHHhcCCcceeeeeeCHHHHHHHHHHHHH---------
Confidence 44578888998877 456777888877665422210 000 001111 1123455656555532210
Q ss_pred hccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHH---
Q psy17316 111 KAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIR--- 187 (229)
Q Consensus 111 ~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~--- 187 (229)
.++..+.+-.++..|. |..=+..-||++..-+..|=+-.|+... .++++.-++|+..+|-+.-.
T Consensus 73 ---------~~~~~~~idr~L~lGA-S~~mm~~~FGls~~ev~~rR~llgi~~~---~GR~~~~~ee~~~~iW~~W~~~~ 139 (180)
T PF11198_consen 73 ---------EQQEQQLIDRALRLGA-SIEMMQRLFGLSSAEVAARRRLLGIPVR---KGRPPALSEEEEAAIWRRWQQLM 139 (180)
T ss_pred ---------HHHHHHHHHHHHHcCC-CHHHHHHHHCCCHHHHHHHHHHhCCCCC---CCCCCCcCHHHHHHHHHHHHHHH
Confidence 1122344455666666 9999999999988776665555576553 35667777777777776654
Q ss_pred -hCCC------cHH----HHHHHhCCChHHHHHHHHh
Q psy17316 188 -SGQT------TVQ----RASAEYGIPSGTLYGRCKL 213 (229)
Q Consensus 188 -~~~~------s~~----eAA~~fgVp~~tv~~~vk~ 213 (229)
+++. .+- .+|...+||-++||+.++.
T Consensus 140 ~~~~~~~~~~~~~Le~~m~~Ae~~~isL~~iW~~i~~ 176 (180)
T PF11198_consen 140 KKRGVDNLDSPDALELMMLLAEETNISLTVIWSLIQE 176 (180)
T ss_pred hhcCCCCccchHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 2222 233 4999999999999998873
No 480
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=87.53 E-value=0.94 Score=37.61 Aligned_cols=32 Identities=22% Similarity=0.246 Sum_probs=26.1
Q ss_pred HHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 41 ALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 41 AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
++.+..-.|+|+.+||+.+|||.+||+.++.+
T Consensus 124 i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~R 155 (187)
T PRK12516 124 AIILVGASGFAYEEAAEICGCAVGTIKSRVNR 155 (187)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 33333346899999999999999999999886
No 481
>PRK10130 transcriptional regulator EutR; Provisional
Probab=87.51 E-value=3.3 Score=38.25 Aligned_cols=83 Identities=17% Similarity=0.132 Sum_probs=59.3
Q ss_pred HHHHHHHHHHHH---cCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHHHHHHHHHHh----CCCc
Q psy17316 121 EEILNVALDALR---AGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDLEIALEGIRS----GQTT 192 (229)
Q Consensus 121 ~e~k~~AV~~~~---~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r~eaV~~~~~----~~~s 192 (229)
.....+|.+.+. ...+++.++|+..||+..+|.+-.++. |.... .|=..-|++.++.... .+.+
T Consensus 239 ~~~v~~~~~~i~~~~~~~ltv~~lA~~~gvS~r~L~r~Fk~~~G~sp~--------~ylr~~RL~~ar~lL~~~~~~~~s 310 (350)
T PRK10130 239 RRLLSRAREYVLENMSEPVTVLDLCNQLHVSRRTLQNAFHAILGIGPN--------AWLKRIRLNAVRRELISPWSQSTT 310 (350)
T ss_pred HHHHHHHHHHHHhhhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHhccCCCCCC
Confidence 444555555543 344799999999999999999999875 64443 3444567777775554 3588
Q ss_pred HHHHHHHhCCChHHHHHHH
Q psy17316 193 VQRASAEYGIPSGTLYGRC 211 (229)
Q Consensus 193 ~~eAA~~fgVp~~tv~~~v 211 (229)
+.++|.++|.....-....
T Consensus 311 I~eIA~~~GF~~~s~Fs~~ 329 (350)
T PRK10130 311 VKDAAMQWGFWHLGQFATD 329 (350)
T ss_pred HHHHHHHhCCCCHHHHHHH
Confidence 9999999998776655543
No 482
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=87.44 E-value=3.5 Score=36.28 Aligned_cols=78 Identities=10% Similarity=0.180 Sum_probs=57.3
Q ss_pred CCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhC---CCcHHHHHHHhCCChHHHHHHH
Q psy17316 135 SISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSG---QTTVQRASAEYGIPSGTLYGRC 211 (229)
Q Consensus 135 ~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~---~~s~~eAA~~fgVp~~tv~~~v 211 (229)
.+|+.++|..+||+.++|++..++.|... ..|=.+.|++.....+.. +.++.++|...|-+-.+-.+.+
T Consensus 214 ~ls~~~lA~~~giS~r~L~r~Fk~~G~T~--------~~yi~~~RL~~A~~lL~~~~~~~sI~eIA~~~GF~d~s~Fsr~ 285 (302)
T PRK09685 214 ILRPEWIAGELGISVRSLYRLFAEQGLVV--------AQYIRNRRLDRCADDLRPAADDEKITSIAYKWGFSDSSHFSTA 285 (302)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHcCCCH--------HHHHHHHHHHHHHHHhhhhccCCCHHHHHHHhCCCCHHHHHHH
Confidence 37999999999999999999998766433 235455677666555542 5799999999999887777665
Q ss_pred HhhcCCCCC
Q psy17316 212 KLSRSTPRP 220 (229)
Q Consensus 212 k~~~~~~~~ 220 (229)
=.+.-|-+|
T Consensus 286 Fkk~~G~sP 294 (302)
T PRK09685 286 FKQRFGVSP 294 (302)
T ss_pred HHHHHCcCH
Confidence 444444444
No 483
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=87.43 E-value=0.94 Score=36.70 Aligned_cols=26 Identities=27% Similarity=0.155 Sum_probs=23.8
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
-.|+|+.+||..+|||.+||+.++.+
T Consensus 133 ~~~~s~~EIA~~lgis~~tV~~~l~R 158 (173)
T PRK12522 133 YEQYSYKEMSEILNIPIGTVKYRLNY 158 (173)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 35889999999999999999999886
No 484
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=87.38 E-value=0.89 Score=37.34 Aligned_cols=26 Identities=27% Similarity=0.307 Sum_probs=24.1
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
-.|+|+.+||..+|||.+||..++++
T Consensus 141 ~~gls~~EIA~~l~i~~~tVks~l~r 166 (182)
T COG1595 141 LEGLSYEEIAEILGISVGTVKSRLHR 166 (182)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 35899999999999999999999986
No 485
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=87.34 E-value=2.6 Score=28.51 Aligned_cols=24 Identities=25% Similarity=0.393 Sum_probs=21.0
Q ss_pred CCCHHHHHHHhCCChHHHHHHHHH
Q psy17316 135 SISANKASKAYGIPSSTLYKIARK 158 (229)
Q Consensus 135 ~~S~~~~a~k~gIp~sTL~~~ik~ 158 (229)
+.++.++|+.+||+.+|+..++++
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHH
Confidence 459999999999999998887764
No 486
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=87.34 E-value=1.2 Score=36.12 Aligned_cols=40 Identities=10% Similarity=0.097 Sum_probs=30.4
Q ss_pred CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+..|+.++ +++.++ ..|+|+.+||+.+|||++|+..|.++
T Consensus 5 ~~Lt~rqr-eVL~lr-~~GlTq~EIAe~LGiS~~tVs~ie~r 44 (141)
T PRK03975 5 SFLTERQI-EVLRLR-ERGLTQQEIADILGTSRANVSSIEKR 44 (141)
T ss_pred cCCCHHHH-HHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 33444444 445554 56899999999999999999999875
No 487
>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=87.33 E-value=1.3 Score=37.68 Aligned_cols=40 Identities=10% Similarity=0.098 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
..++.+..-.+..| -.++|+.+||+.+||+.+|+++++++
T Consensus 178 ~L~~~~r~vl~l~y-~~~~s~~eIA~~lgis~~~v~~~~~r 217 (227)
T TIGR02980 178 ALPERERRILLLRF-FEDKTQSEIAERLGISQMHVSRLLRR 217 (227)
T ss_pred cCCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34444443333333 35789999999999999999999875
No 488
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=87.33 E-value=1.2 Score=37.08 Aligned_cols=35 Identities=17% Similarity=0.107 Sum_probs=29.2
Q ss_pred HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
...++|+...-+++|+.|||..+|||-.||++.++
T Consensus 139 ~~~~~v~l~~~~Gls~~EIA~~lgiS~~tV~r~l~ 173 (185)
T PF07638_consen 139 RQRRVVELRFFEGLSVEEIAERLGISERTVRRRLR 173 (185)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34566666655679999999999999999999887
No 489
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=87.30 E-value=0.83 Score=43.79 Aligned_cols=81 Identities=9% Similarity=0.055 Sum_probs=48.1
Q ss_pred HHHcCCCCHHHHHHHhCCChHHHHHHHHHh------CCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316 130 ALRAGSISANKASKAYGIPSSTLYKIARKE------GIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIP 203 (229)
Q Consensus 130 ~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~------g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp 203 (229)
.|..|. |+..||++|||+...|.+|=... |-.+..|....... ... ....+.+...-+=|+..+|.+|||+
T Consensus 347 ~Vk~GD-TL~sIA~r~gvs~~~L~~~N~l~~~~L~~Gq~L~Ip~~~~~~~-~~~-~~~~~~Y~Vr~GDTL~sIA~kygVt 423 (456)
T PRK10783 347 KVRSGD-TLSGIASRLNVSTKDLQQWNNLRGSKLKVGQTLTIGAGSSAQR-LAN-NSDSITYRVRKGDSLSSIAKRHGVN 423 (456)
T ss_pred EECCCC-cHHHHHHHHCcCHHHHHHHcCCCcccCCCCCEEEecCCccccc-ccc-cccceeEEeCCCCCHHHHHHHhCCC
Confidence 345666 99999999999999999884211 21221121100000 000 0111223333335699999999999
Q ss_pred hHHHHHHHHh
Q psy17316 204 SGTLYGRCKL 213 (229)
Q Consensus 204 ~~tv~~~vk~ 213 (229)
-..|..|=.+
T Consensus 424 v~~L~~~N~l 433 (456)
T PRK10783 424 IKDVMRWNSD 433 (456)
T ss_pred HHHHHHhcCC
Confidence 9999988553
No 490
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=87.29 E-value=1.3 Score=36.30 Aligned_cols=32 Identities=16% Similarity=-0.094 Sum_probs=25.3
Q ss_pred HHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 181 IALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 181 eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
+|+....-+++++.++|..+|||..||+.++.
T Consensus 135 ~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ 166 (186)
T PRK05602 135 EAIVLQYYQGLSNIEAAAVMDISVDALESLLA 166 (186)
T ss_pred HHhhHHHhcCCCHHHHHHHhCcCHHHHHHHHH
Confidence 34444334559999999999999999999875
No 491
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=87.29 E-value=1.1 Score=36.78 Aligned_cols=34 Identities=15% Similarity=0.011 Sum_probs=27.9
Q ss_pred HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
..+|+....-.++|+.++|..+|||.+||+.++.
T Consensus 127 ~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~ 160 (185)
T PRK12542 127 NRQVFKYKVFYNLTYQEISSVMGITEANVRKQFE 160 (185)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4456666555569999999999999999999875
No 492
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=87.27 E-value=1 Score=36.86 Aligned_cols=25 Identities=12% Similarity=0.219 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 48 GQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 48 g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
.|+|+.+||..+|||.+||+.++.+
T Consensus 146 ~g~s~~eIA~~l~is~~tV~~~l~r 170 (184)
T PRK12512 146 EGASIKETAAKLSMSEGAVRVALHR 170 (184)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 5889999999999999999999886
No 493
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=87.26 E-value=1 Score=37.25 Aligned_cols=40 Identities=10% Similarity=0.111 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
+.++++..-.+--+. .|+|+.+||..+|||.+|++.++.+
T Consensus 131 ~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~~V~~~l~R 170 (189)
T PRK06811 131 DLEKLDREIFIRRYL-LGEKIEEIAKKLGLTRSAIDNRLSR 170 (189)
T ss_pred hCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHH
Confidence 444444333332233 5789999999999999999999886
No 494
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=87.24 E-value=0.72 Score=32.22 Aligned_cols=40 Identities=10% Similarity=0.112 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
|++++.|+.. ++.++-+++|+.+||++.++++++..+.-+
T Consensus 3 e~Il~~i~~~-~~p~~T~eiA~~~gls~~~aR~yL~~Le~e 42 (62)
T PF04703_consen 3 EKILEYIKEQ-NGPLKTREIADALGLSIYQARYYLEKLEKE 42 (62)
T ss_dssp HCHHHHHHHH-TS-EEHHHHHHHHTS-HHHHHHHHHHHHHC
T ss_pred HHHHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 5567777666 678999999999999999999999976433
No 495
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=87.22 E-value=1.3 Score=36.59 Aligned_cols=26 Identities=27% Similarity=0.306 Sum_probs=23.6
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
-.|+|+.+||..+|||.+|++.++++
T Consensus 125 ~~g~s~~EIA~~Lgis~~tV~~~l~R 150 (182)
T PRK12540 125 ASGFSYEDAAAICGCAVGTIKSRVNR 150 (182)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 35889999999999999999998885
No 496
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=87.18 E-value=9.6 Score=32.58 Aligned_cols=104 Identities=13% Similarity=0.046 Sum_probs=0.0
Q ss_pred CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhh
Q psy17316 31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKAS 110 (229)
Q Consensus 31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~ 110 (229)
+.-+.+++.+||+.+.+|+ .=+|+....+.+...+........ ....++-++
T Consensus 110 K~~~~~~L~~aI~~v~~G~---------~~~~~~~~~~l~~~~~~~~~~~~~-~~~Lt~rE~------------------ 161 (216)
T PRK10100 110 AMEDQERVVNGLQGVLRGE---------CYFTQKLASYLITHSGNYRYNSTE-SALLTHREK------------------ 161 (216)
T ss_pred CCCCHHHHHHHHHHHHcCC---------cccCHHHHHHHHHhhcccccCCCc-cCCCCHHHH------------------
Q ss_pred hccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhC
Q psy17316 111 KAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSG 189 (229)
Q Consensus 111 ~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~ 189 (229)
+++.++.+|. |.++||++.+||..|+..++.+.-.++.. ..|.+++.+..++
T Consensus 162 ---------------~Vl~l~~~G~-s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v-----------~nr~elv~~a~~~ 213 (216)
T PRK10100 162 ---------------EILNKLRIGA-SNNEIARSLFISENTVKTHLYNLFKKIAV-----------KNRTQAVSWANDN 213 (216)
T ss_pred ---------------HHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCC-----------CCHHHHHHHHHHh
No 497
>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=87.17 E-value=1.1 Score=27.74 Aligned_cols=25 Identities=8% Similarity=0.182 Sum_probs=23.0
Q ss_pred cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316 47 AGQMSLTKASVSYGIPSTTLWQRAH 71 (229)
Q Consensus 47 ~g~~S~~~aA~~~gIp~sTL~~~i~ 71 (229)
..++|..++|+.+|++..+|.+|..
T Consensus 10 ~~~~s~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 10 EKGLTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 4588999999999999999999977
No 498
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=87.13 E-value=0.71 Score=30.24 Aligned_cols=28 Identities=21% Similarity=0.325 Sum_probs=24.0
Q ss_pred CC-CHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316 49 QM-SLTKASVSYGIPSTTLWQRAHRLGIH 76 (229)
Q Consensus 49 ~~-S~~~aA~~~gIp~sTL~~~i~~~gi~ 76 (229)
.+ |.+++|+.+||+++|+++.++.+.-.
T Consensus 19 ~l~s~~~la~~~~vs~~tv~~~l~~L~~~ 47 (60)
T smart00345 19 KLPSERELAAQLGVSRTTVREALSRLEAE 47 (60)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 35 89999999999999999999876433
No 499
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=87.12 E-value=1.3 Score=35.88 Aligned_cols=36 Identities=8% Similarity=-0.066 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316 176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK 212 (229)
Q Consensus 176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk 212 (229)
+..| +|+.+..-+++++.|+|..+|||..||+.+++
T Consensus 121 ~~~r-~v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ 156 (168)
T PRK12525 121 GKAR-AAFLMSQLEGLTYVEIGERLGVSLSRIHQYMV 156 (168)
T ss_pred HHHH-HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4444 45555445559999999999999999999987
No 500
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=87.10 E-value=1.2 Score=35.89 Aligned_cols=38 Identities=13% Similarity=0.106 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316 33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR 72 (229)
Q Consensus 33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~ 72 (229)
.|+.++ .++.++ ..|+|+.+||+.+|++++|+.++.++
T Consensus 7 Lte~qr-~VL~Lr-~~GlTq~EIAe~LgiS~stV~~~e~r 44 (137)
T TIGR00721 7 LTERQI-KVLELR-EKGLSQKEIAKELKTTRANVSAIEKR 44 (137)
T ss_pred CCHHHH-HHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 344444 455554 57899999999999999999999886
Done!