Query psy4625
Match_columns 120
No_of_seqs 130 out of 1139
Neff 8.3
Searched_HMMs 46136
Date Fri Aug 16 21:36:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4625.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4625hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0493|consensus 99.8 1.6E-19 3.4E-24 130.4 8.0 106 1-106 231-336 (342)
2 KOG0850|consensus 99.8 4.9E-19 1.1E-23 125.7 6.2 70 12-81 118-187 (245)
3 KOG0488|consensus 99.8 9.3E-19 2E-23 131.1 7.5 73 5-77 161-233 (309)
4 KOG0484|consensus 99.8 3.6E-19 7.8E-24 112.4 3.8 66 12-77 13-78 (125)
5 KOG0489|consensus 99.8 1.2E-18 2.6E-23 128.1 6.4 70 12-81 155-224 (261)
6 PF00046 Homeobox: Homeobox do 99.8 4.4E-18 9.6E-23 97.9 7.3 57 17-73 1-57 (57)
7 KOG0843|consensus 99.7 5E-18 1.1E-22 116.7 5.5 64 15-78 101-164 (197)
8 KOG2251|consensus 99.7 7.3E-18 1.6E-22 119.1 5.3 68 11-78 32-99 (228)
9 KOG0842|consensus 99.7 4.8E-18 1E-22 126.1 4.1 75 13-87 150-224 (307)
10 KOG0485|consensus 99.7 1.9E-17 4.1E-22 116.9 4.9 66 12-77 100-165 (268)
11 KOG0494|consensus 99.7 3.7E-17 8.1E-22 118.1 5.9 67 15-81 140-206 (332)
12 KOG0487|consensus 99.7 2.2E-17 4.9E-22 122.6 2.9 64 14-77 233-296 (308)
13 cd00086 homeodomain Homeodomai 99.6 1.6E-15 3.4E-20 87.4 7.5 57 18-74 2-58 (59)
14 smart00389 HOX Homeodomain. DN 99.6 1.1E-15 2.4E-20 87.4 6.8 55 18-72 2-56 (56)
15 KOG0492|consensus 99.6 3.4E-16 7.3E-21 109.9 5.3 65 12-76 140-204 (246)
16 KOG0848|consensus 99.6 1.6E-16 3.6E-21 115.1 3.6 64 18-81 201-264 (317)
17 COG5576 Homeodomain-containing 99.6 2E-15 4.4E-20 103.1 7.5 70 11-80 46-115 (156)
18 TIGR01565 homeo_ZF_HD homeobox 99.6 7.2E-16 1.6E-20 88.9 3.5 52 17-68 2-57 (58)
19 KOG3802|consensus 99.6 3E-16 6.5E-21 119.1 1.4 64 13-76 291-354 (398)
20 KOG0847|consensus 99.5 4.5E-15 9.8E-20 105.2 4.1 66 12-77 163-228 (288)
21 KOG0491|consensus 99.5 3.2E-15 6.9E-20 101.6 2.8 66 16-81 100-165 (194)
22 KOG0483|consensus 99.5 1.4E-14 3.1E-19 102.2 4.9 58 18-75 52-109 (198)
23 KOG0486|consensus 99.5 2E-14 4.3E-19 106.3 2.8 65 15-79 111-175 (351)
24 KOG4577|consensus 99.5 1.5E-13 3.3E-18 100.8 6.3 66 12-77 163-228 (383)
25 KOG0844|consensus 99.4 1.2E-13 2.6E-18 102.0 1.3 65 12-76 177-241 (408)
26 KOG0775|consensus 99.3 7.4E-12 1.6E-16 91.3 5.8 54 23-76 183-236 (304)
27 KOG0490|consensus 99.2 3.7E-12 7.9E-17 91.4 2.5 64 13-76 57-120 (235)
28 KOG0849|consensus 99.2 5.7E-11 1.2E-15 90.8 6.9 66 12-77 172-237 (354)
29 KOG1168|consensus 99.2 3E-12 6.6E-17 94.1 -0.3 65 12-76 305-369 (385)
30 PF05920 Homeobox_KN: Homeobox 98.8 6.1E-09 1.3E-13 55.7 3.9 34 37-70 7-40 (40)
31 KOG0774|consensus 98.7 5.9E-09 1.3E-13 75.9 2.1 64 16-79 188-254 (334)
32 KOG2252|consensus 98.7 6.7E-08 1.4E-12 76.5 6.9 61 11-71 415-475 (558)
33 KOG0490|consensus 98.2 1.4E-06 3.1E-11 62.3 4.4 65 12-76 149-213 (235)
34 PF11569 Homez: Homeodomain le 97.8 3.3E-05 7.2E-10 44.0 3.6 42 28-69 10-51 (56)
35 KOG1146|consensus 97.7 4.2E-05 9.2E-10 66.1 4.0 62 15-76 902-963 (1406)
36 KOG3623|consensus 97.2 0.0022 4.8E-08 53.2 8.1 49 28-76 568-616 (1007)
37 KOG0773|consensus 96.8 0.0014 3E-08 50.0 3.3 58 16-73 239-299 (342)
38 PF04218 CENP-B_N: CENP-B N-te 95.7 0.055 1.2E-06 30.3 5.4 47 17-68 1-47 (53)
39 PF04545 Sigma70_r4: Sigma-70, 91.1 1.3 2.8E-05 23.9 5.4 46 22-72 4-49 (50)
40 PF04967 HTH_10: HTH DNA bindi 87.0 2.5 5.5E-05 23.7 4.6 42 23-64 1-44 (53)
41 PF01527 HTH_Tnp_1: Transposas 86.0 1.3 2.7E-05 25.9 3.3 45 19-67 3-47 (76)
42 cd06171 Sigma70_r4 Sigma70, re 83.4 3.3 7.2E-05 21.5 4.0 44 22-70 10-53 (55)
43 PF10668 Phage_terminase: Phag 82.5 1.3 2.9E-05 25.5 2.2 21 45-65 24-44 (60)
44 KOG1146|consensus 82.3 3.3 7.1E-05 37.2 5.3 60 16-75 705-764 (1406)
45 PF08281 Sigma70_r4_2: Sigma-7 78.7 8.4 0.00018 20.8 5.2 42 23-69 11-52 (54)
46 COG3413 Predicted DNA binding 78.3 7.1 0.00015 27.7 5.3 49 22-72 155-205 (215)
47 PF09607 BrkDBD: Brinker DNA-b 76.9 9.3 0.0002 21.9 4.4 44 20-65 3-47 (58)
48 PRK03975 tfx putative transcri 75.0 20 0.00044 24.1 6.5 50 20-75 4-53 (141)
49 cd04761 HTH_MerR-SF Helix-Turn 70.9 5.6 0.00012 20.8 2.5 21 46-66 3-23 (49)
50 PRK09413 IS2 repressor TnpA; R 70.5 17 0.00038 23.4 5.2 42 20-65 10-51 (121)
51 PF13518 HTH_28: Helix-turn-he 70.2 6.5 0.00014 20.9 2.7 24 45-68 14-37 (52)
52 KOG0773|consensus 69.5 9.4 0.0002 29.1 4.3 44 34-77 115-158 (342)
53 PRK06759 RNA polymerase factor 69.1 28 0.0006 22.7 6.1 29 45-73 124-152 (154)
54 cd00569 HTH_Hin_like Helix-tur 68.8 10 0.00023 17.4 4.9 38 22-64 5-42 (42)
55 TIGR03879 near_KaiC_dom probab 68.5 3.1 6.8E-05 24.9 1.2 35 32-66 21-55 (73)
56 PRK09646 RNA polymerase sigma 68.5 28 0.00062 23.9 6.3 31 45-75 160-190 (194)
57 TIGR02937 sigma70-ECF RNA poly 66.0 27 0.00059 22.0 5.5 29 45-73 128-156 (158)
58 PF13384 HTH_23: Homeodomain-l 65.3 6.9 0.00015 20.8 2.2 22 44-65 18-39 (50)
59 PF06056 Terminase_5: Putative 65.0 7.9 0.00017 22.0 2.4 20 46-65 16-35 (58)
60 PRK04217 hypothetical protein; 64.7 35 0.00076 22.0 6.1 50 21-75 41-90 (110)
61 PF00376 MerR: MerR family reg 64.4 8.8 0.00019 19.7 2.3 19 47-65 3-21 (38)
62 PRK12514 RNA polymerase sigma 64.4 19 0.00041 24.3 4.7 30 45-74 147-176 (179)
63 PRK09652 RNA polymerase sigma 63.9 32 0.0007 22.8 5.8 30 45-74 146-175 (182)
64 PF13936 HTH_38: Helix-turn-he 63.3 19 0.0004 19.0 3.6 40 21-65 3-42 (44)
65 PRK09642 RNA polymerase sigma 63.2 39 0.00084 22.2 6.0 30 46-75 125-154 (160)
66 PRK11924 RNA polymerase sigma 63.0 32 0.00069 22.8 5.6 30 45-74 143-172 (179)
67 PRK12526 RNA polymerase sigma 62.5 38 0.00083 23.6 6.1 31 45-75 171-201 (206)
68 PF13411 MerR_1: MerR HTH fami 62.4 9.3 0.0002 21.6 2.5 20 46-65 3-22 (69)
69 PRK00118 putative DNA-binding 62.3 38 0.00083 21.6 5.9 50 23-77 18-67 (104)
70 PRK12512 RNA polymerase sigma 62.3 38 0.00081 22.9 5.9 31 45-75 149-179 (184)
71 PRK12533 RNA polymerase sigma 60.6 58 0.0013 23.1 7.1 33 45-77 152-184 (216)
72 PRK10072 putative transcriptio 60.3 7.2 0.00016 24.5 1.8 24 46-69 49-72 (96)
73 PRK05602 RNA polymerase sigma 59.9 37 0.0008 23.0 5.5 33 45-77 146-178 (186)
74 TIGR02999 Sig-70_X6 RNA polyme 59.4 47 0.001 22.3 6.0 30 45-74 152-181 (183)
75 cd04763 HTH_MlrA-like Helix-Tu 58.9 13 0.00028 21.2 2.7 20 46-65 3-22 (68)
76 cd04762 HTH_MerR-trunc Helix-T 58.5 14 0.00031 18.8 2.6 22 46-67 3-24 (49)
77 COG4367 Uncharacterized protei 57.8 24 0.00053 22.0 3.8 40 23-62 3-42 (97)
78 TIGR02989 Sig-70_gvs1 RNA poly 57.6 49 0.0011 21.6 5.7 28 45-72 129-156 (159)
79 PRK12530 RNA polymerase sigma 57.4 50 0.0011 22.6 5.9 31 45-75 152-182 (189)
80 TIGR02959 SigZ RNA polymerase 57.3 52 0.0011 22.1 5.9 31 45-75 118-148 (170)
81 cd04764 HTH_MlrA-like_sg1 Heli 57.2 15 0.00034 20.7 2.8 21 46-66 3-23 (67)
82 PRK12519 RNA polymerase sigma 56.8 38 0.00083 23.1 5.2 31 44-74 158-188 (194)
83 PRK09639 RNA polymerase sigma 56.8 54 0.0012 21.6 5.8 31 45-75 129-159 (166)
84 PRK09648 RNA polymerase sigma 56.1 56 0.0012 22.2 5.9 30 45-74 157-186 (189)
85 PRK09047 RNA polymerase factor 55.9 55 0.0012 21.4 5.9 30 46-75 125-154 (161)
86 PRK09644 RNA polymerase sigma 55.7 53 0.0012 21.7 5.7 31 45-75 126-156 (165)
87 TIGR02939 RpoE_Sigma70 RNA pol 55.6 41 0.00088 22.7 5.2 32 44-75 155-186 (190)
88 PRK06986 fliA flagellar biosyn 53.7 35 0.00077 24.3 4.8 30 45-74 202-231 (236)
89 TIGR02948 SigW_bacill RNA poly 53.1 53 0.0012 22.0 5.4 31 44-74 153-183 (187)
90 PRK12515 RNA polymerase sigma 53.1 68 0.0015 21.8 6.0 31 45-75 149-179 (189)
91 PF13443 HTH_26: Cro/C1-type H 52.8 12 0.00026 20.7 1.8 23 45-67 12-34 (63)
92 PRK12537 RNA polymerase sigma 52.5 69 0.0015 21.6 5.9 29 45-73 151-179 (182)
93 PRK06930 positive control sigm 52.3 71 0.0015 22.0 5.9 48 23-75 115-162 (170)
94 TIGR02985 Sig70_bacteroi1 RNA 51.6 63 0.0014 20.8 5.9 29 45-73 131-159 (161)
95 COG2963 Transposase and inacti 51.5 56 0.0012 20.5 5.0 43 20-66 5-48 (116)
96 PRK09480 slmA division inhibit 50.9 19 0.00041 24.3 2.9 35 34-69 22-56 (194)
97 cd01104 HTH_MlrA-CarA Helix-Tu 50.8 21 0.00046 20.0 2.7 20 46-65 3-22 (68)
98 PF00196 GerE: Bacterial regul 50.7 41 0.00089 18.4 5.2 44 22-71 3-46 (58)
99 PF08280 HTH_Mga: M protein tr 50.6 43 0.00094 18.6 4.0 37 26-66 6-42 (59)
100 PRK12524 RNA polymerase sigma 50.2 76 0.0017 21.7 5.9 31 45-75 154-184 (196)
101 PRK12546 RNA polymerase sigma 49.8 69 0.0015 22.1 5.6 32 45-76 131-162 (188)
102 PRK08583 RNA polymerase sigma 49.4 46 0.001 24.0 4.8 47 23-74 206-252 (257)
103 cd01392 HTH_LacI Helix-turn-he 49.1 11 0.00023 20.0 1.2 20 48-67 2-21 (52)
104 PRK08301 sporulation sigma fac 49.1 60 0.0013 23.0 5.3 31 44-74 199-229 (234)
105 PRK12536 RNA polymerase sigma 48.9 81 0.0018 21.3 6.0 30 45-74 147-176 (181)
106 PF13730 HTH_36: Helix-turn-he 48.8 32 0.00069 18.5 3.1 43 23-66 3-48 (55)
107 PRK12532 RNA polymerase sigma 48.5 81 0.0017 21.5 5.8 32 45-76 154-185 (195)
108 TIGR02479 FliA_WhiG RNA polyme 48.1 51 0.0011 23.2 4.8 45 24-73 177-221 (224)
109 PRK05657 RNA polymerase sigma 48.1 64 0.0014 24.5 5.6 53 23-76 263-315 (325)
110 PRK12541 RNA polymerase sigma 48.1 76 0.0016 20.8 5.4 29 45-73 130-158 (161)
111 PRK09637 RNA polymerase sigma 48.1 80 0.0017 21.5 5.7 31 45-75 124-154 (181)
112 PRK12529 RNA polymerase sigma 47.3 87 0.0019 21.1 5.9 30 45-74 145-174 (178)
113 TIGR02941 Sigma_B RNA polymera 47.0 77 0.0017 22.8 5.7 46 23-73 206-251 (255)
114 PRK12538 RNA polymerase sigma 46.8 70 0.0015 23.0 5.4 32 45-76 189-220 (233)
115 PF00424 REV: REV protein (ant 46.4 16 0.00036 22.8 1.8 41 28-82 14-54 (91)
116 PF15063 TC1: Thyroid cancer p 46.4 47 0.001 20.1 3.6 37 22-58 33-69 (79)
117 PRK09647 RNA polymerase sigma 46.2 86 0.0019 21.9 5.7 32 46-77 157-188 (203)
118 PRK12535 RNA polymerase sigma 46.0 98 0.0021 21.4 6.1 35 45-79 151-185 (196)
119 PRK12518 RNA polymerase sigma 45.8 37 0.00081 22.6 3.7 33 44-76 137-169 (175)
120 TIGR02983 SigE-fam_strep RNA p 45.8 84 0.0018 20.6 5.7 30 45-74 128-157 (162)
121 PRK09649 RNA polymerase sigma 45.7 88 0.0019 21.3 5.6 29 45-73 148-176 (185)
122 PRK12543 RNA polymerase sigma 45.1 94 0.002 20.9 5.9 31 45-75 135-165 (179)
123 smart00421 HTH_LUXR helix_turn 44.2 47 0.001 17.2 5.3 42 22-69 3-44 (58)
124 PF14549 P22_Cro: DNA-binding 43.6 28 0.0006 19.9 2.3 18 46-63 12-29 (60)
125 TIGR02980 SigBFG RNA polymeras 43.4 64 0.0014 22.7 4.7 46 23-73 179-224 (227)
126 COG1905 NuoE NADH:ubiquinone o 43.2 57 0.0012 22.5 4.2 36 25-60 25-60 (160)
127 PRK12547 RNA polymerase sigma 43.2 97 0.0021 20.5 5.9 30 45-74 130-159 (164)
128 PRK06811 RNA polymerase factor 43.1 89 0.0019 21.3 5.3 30 45-74 149-178 (189)
129 smart00422 HTH_MERR helix_turn 43.0 28 0.0006 19.5 2.4 20 46-65 3-22 (70)
130 PF01381 HTH_3: Helix-turn-hel 43.0 18 0.00039 19.3 1.5 22 46-67 12-33 (55)
131 TIGR02950 SigM_subfam RNA poly 43.0 45 0.00098 21.6 3.7 31 43-73 121-151 (154)
132 PF01710 HTH_Tnp_IS630: Transp 42.9 83 0.0018 20.1 4.8 38 23-65 3-40 (119)
133 TIGR02954 Sig70_famx3 RNA poly 42.7 98 0.0021 20.5 5.8 30 45-74 137-166 (169)
134 TIGR02952 Sig70_famx2 RNA poly 42.6 96 0.0021 20.3 5.9 29 45-73 140-168 (170)
135 PRK13919 putative RNA polymera 42.4 1E+02 0.0023 20.7 6.0 30 45-74 153-182 (186)
136 PRK07670 RNA polymerase sigma 42.3 75 0.0016 22.9 5.0 30 45-74 219-248 (251)
137 PRK12539 RNA polymerase sigma 41.8 1.1E+02 0.0024 20.7 5.9 30 45-74 149-178 (184)
138 TIGR02393 RpoD_Cterm RNA polym 41.5 94 0.002 22.2 5.4 51 23-74 177-227 (238)
139 PRK12516 RNA polymerase sigma 41.5 1.1E+02 0.0025 20.8 5.9 31 46-76 135-165 (187)
140 PRK09645 RNA polymerase sigma 41.1 1.1E+02 0.0023 20.4 6.1 31 45-75 136-166 (173)
141 TIGR01764 excise DNA binding d 40.9 40 0.00086 17.1 2.6 22 46-67 4-25 (49)
142 PF02796 HTH_7: Helix-turn-hel 40.8 56 0.0012 17.1 3.9 38 22-64 5-42 (45)
143 PRK11511 DNA-binding transcrip 40.8 96 0.0021 20.0 4.9 26 42-67 24-49 (127)
144 PRK07408 RNA polymerase sigma 40.7 72 0.0016 23.2 4.7 32 44-75 220-251 (256)
145 PRK07122 RNA polymerase sigma 40.5 75 0.0016 23.3 4.8 46 23-73 216-261 (264)
146 TIGR03070 couple_hipB transcri 40.0 23 0.00049 18.8 1.6 22 46-67 18-39 (58)
147 PRK05988 formate dehydrogenase 39.7 80 0.0017 21.5 4.5 36 26-61 24-59 (156)
148 PRK06424 transcription factor; 39.6 38 0.00082 22.9 2.8 23 46-68 100-122 (144)
149 cd00093 HTH_XRE Helix-turn-hel 39.2 31 0.00066 17.3 2.0 22 46-67 15-36 (58)
150 TIGR02392 rpoH_proteo alternat 39.0 1E+02 0.0022 22.6 5.3 49 23-74 219-267 (270)
151 PRK12511 RNA polymerase sigma 39.0 1.2E+02 0.0027 20.6 5.7 32 45-76 129-160 (182)
152 TIGR03001 Sig-70_gmx1 RNA poly 38.9 1.4E+02 0.003 21.7 6.0 31 45-75 179-209 (244)
153 TIGR02859 spore_sigH RNA polym 38.5 56 0.0012 22.2 3.7 31 43-73 165-195 (198)
154 PRK11552 putative DNA-binding 38.4 37 0.0008 24.1 2.8 43 28-72 19-61 (225)
155 PRK12545 RNA polymerase sigma 38.2 1.3E+02 0.0029 20.7 5.9 31 45-75 157-187 (201)
156 TIGR02943 Sig70_famx1 RNA poly 38.1 1.3E+02 0.0028 20.5 6.0 32 45-76 149-180 (188)
157 PRK07037 extracytoplasmic-func 38.1 1.2E+02 0.0025 19.9 6.0 30 45-74 127-156 (163)
158 TIGR02947 SigH_actino RNA poly 37.9 59 0.0013 22.2 3.8 32 44-75 148-179 (193)
159 cd04774 HTH_YfmP Helix-Turn-He 37.8 41 0.00089 20.8 2.7 21 46-66 3-23 (96)
160 cd01106 HTH_TipAL-Mta Helix-Tu 37.7 39 0.00084 21.0 2.6 21 46-66 3-23 (103)
161 cd04766 HTH_HspR Helix-Turn-He 37.6 36 0.00078 20.6 2.4 20 46-65 4-23 (91)
162 cd06170 LuxR_C_like C-terminal 37.6 63 0.0014 16.8 4.4 22 45-66 17-38 (57)
163 cd01105 HTH_GlnR-like Helix-Tu 37.2 37 0.0008 20.6 2.3 19 46-64 4-22 (88)
164 PRK12513 RNA polymerase sigma 37.0 63 0.0014 22.0 3.8 33 43-75 155-187 (194)
165 PRK12520 RNA polymerase sigma 36.8 1.3E+02 0.0029 20.3 5.9 31 46-76 150-180 (191)
166 PRK07539 NADH dehydrogenase su 36.7 92 0.002 21.0 4.4 36 26-61 23-58 (154)
167 PRK12523 RNA polymerase sigma 36.5 1.3E+02 0.0028 20.0 6.0 30 45-74 137-166 (172)
168 cd04779 HTH_MerR-like_sg4 Heli 36.4 41 0.00089 22.3 2.6 22 46-67 3-24 (134)
169 PRK09638 RNA polymerase sigma 35.8 76 0.0016 21.1 4.0 31 44-74 143-173 (176)
170 PRK12544 RNA polymerase sigma 35.8 1.5E+02 0.0033 20.7 6.0 30 46-75 167-196 (206)
171 TIGR02394 rpoS_proteo RNA poly 35.7 1.6E+02 0.0034 21.7 5.9 52 23-75 223-274 (285)
172 PRK12534 RNA polymerase sigma 35.6 1.1E+02 0.0024 20.6 4.8 29 45-73 155-183 (187)
173 PRK06288 RNA polymerase sigma 35.3 94 0.002 22.7 4.6 47 23-74 213-259 (268)
174 PF01257 2Fe-2S_thioredx: Thio 35.1 81 0.0017 21.0 3.9 35 27-61 15-49 (145)
175 PF12728 HTH_17: Helix-turn-he 35.1 53 0.0011 17.3 2.5 22 46-67 4-25 (51)
176 PF08279 HTH_11: HTH domain; 34.8 52 0.0011 17.6 2.5 34 29-65 4-37 (55)
177 PRK12531 RNA polymerase sigma 34.7 1.5E+02 0.0032 20.2 6.0 30 45-74 159-188 (194)
178 TIGR02607 antidote_HigA addict 34.6 33 0.00072 19.7 1.8 23 46-68 21-43 (78)
179 PF04936 DUF658: Protein of un 34.5 26 0.00057 24.4 1.4 32 44-75 15-46 (186)
180 cd04768 HTH_BmrR-like Helix-Tu 34.3 51 0.0011 20.2 2.7 21 46-66 3-23 (96)
181 PRK12542 RNA polymerase sigma 34.1 1.5E+02 0.0032 20.0 6.4 34 45-78 140-173 (185)
182 TIGR01958 nuoE_fam NADH-quinon 34.0 1.1E+02 0.0024 20.4 4.4 35 26-60 17-51 (148)
183 TIGR02984 Sig-70_plancto1 RNA 33.9 1.2E+02 0.0027 20.2 4.8 29 45-73 158-186 (189)
184 PRK09651 RNA polymerase sigma 33.7 1.4E+02 0.0031 19.9 5.1 28 45-72 137-164 (172)
185 PRK05911 RNA polymerase sigma 33.6 1.1E+02 0.0024 22.3 4.8 30 45-74 223-252 (257)
186 PRK10403 transcriptional regul 33.6 1E+02 0.0023 20.3 4.4 44 22-71 153-196 (215)
187 PRK08295 RNA polymerase factor 33.5 76 0.0017 21.7 3.8 32 44-75 171-202 (208)
188 PRK09640 RNA polymerase sigma 33.2 80 0.0017 21.4 3.8 30 45-74 152-181 (188)
189 TIGR02957 SigX4 RNA polymerase 33.0 1.7E+02 0.0037 21.5 5.8 29 46-74 127-155 (281)
190 PHA01976 helix-turn-helix prot 32.6 53 0.0012 18.2 2.4 22 46-67 18-39 (67)
191 PRK12528 RNA polymerase sigma 32.6 1.5E+02 0.0031 19.4 5.7 25 46-70 132-156 (161)
192 PRK11923 algU RNA polymerase s 32.5 82 0.0018 21.4 3.8 31 45-75 156-186 (193)
193 PF01325 Fe_dep_repress: Iron 32.5 41 0.00089 18.9 1.9 41 24-64 3-43 (60)
194 PF13542 HTH_Tnp_ISL3: Helix-t 32.3 62 0.0013 17.0 2.6 21 45-65 29-49 (52)
195 PRK07571 bidirectional hydroge 32.1 1.3E+02 0.0029 20.8 4.7 33 28-60 39-71 (169)
196 PRK07500 rpoH2 RNA polymerase 32.1 1.4E+02 0.003 22.2 5.2 50 23-75 228-277 (289)
197 smart00530 HTH_XRE Helix-turn- 31.9 59 0.0013 16.0 2.4 22 46-67 13-34 (56)
198 TIGR02885 spore_sigF RNA polym 31.9 1.6E+02 0.0035 20.7 5.3 44 23-71 184-227 (231)
199 PF06971 Put_DNA-bind_N: Putat 31.9 43 0.00094 18.4 1.8 18 45-62 30-47 (50)
200 PRK09641 RNA polymerase sigma 31.7 87 0.0019 21.0 3.8 30 45-74 154-183 (187)
201 PRK14996 TetR family transcrip 31.5 68 0.0015 21.7 3.2 41 29-70 15-55 (192)
202 PRK12522 RNA polymerase sigma 31.4 1.6E+02 0.0035 19.5 5.8 29 46-74 138-166 (173)
203 cd04780 HTH_MerR-like_sg5 Heli 31.4 52 0.0011 20.3 2.3 20 46-65 3-22 (95)
204 PRK08215 sporulation sigma fac 31.3 1.3E+02 0.0029 21.7 4.9 47 22-73 209-255 (258)
205 PRK09415 RNA polymerase factor 30.8 1.7E+02 0.0037 19.6 5.3 30 45-74 145-174 (179)
206 PF04703 FaeA: FaeA-like prote 30.7 65 0.0014 18.5 2.5 22 45-66 17-38 (62)
207 PF12244 DUF3606: Protein of u 30.6 71 0.0015 17.9 2.6 19 43-61 20-38 (57)
208 PRK05572 sporulation sigma fac 30.3 1.4E+02 0.003 21.5 4.8 46 23-73 203-248 (252)
209 TIGR02960 SigX5 RNA polymerase 30.2 1.8E+02 0.004 21.5 5.6 31 46-76 161-191 (324)
210 PRK05803 sporulation sigma fac 30.1 1.7E+02 0.0038 20.7 5.2 31 44-74 196-226 (233)
211 cd04782 HTH_BltR Helix-Turn-He 29.8 67 0.0015 19.7 2.7 21 46-66 3-23 (97)
212 COG5484 Uncharacterized conser 29.7 46 0.001 24.9 2.1 26 44-71 20-45 (279)
213 PRK12525 RNA polymerase sigma 29.5 1.7E+02 0.0037 19.3 5.8 28 45-72 136-163 (168)
214 PRK09636 RNA polymerase sigma 29.4 2.1E+02 0.0046 21.0 5.8 29 46-74 134-162 (293)
215 cd04775 HTH_Cfa-like Helix-Tur 29.4 58 0.0013 20.2 2.4 20 46-65 4-23 (102)
216 cd04788 HTH_NolA-AlbR Helix-Tu 29.0 71 0.0015 19.6 2.7 21 46-66 3-23 (96)
217 cd00592 HTH_MerR-like Helix-Tu 28.8 61 0.0013 19.7 2.4 20 46-65 3-22 (100)
218 PF01726 LexA_DNA_bind: LexA D 28.7 1.2E+02 0.0026 17.3 3.6 40 23-64 4-47 (65)
219 PF07022 Phage_CI_repr: Bacter 28.6 34 0.00074 19.5 1.1 20 46-65 15-35 (66)
220 cd04789 HTH_Cfa Helix-Turn-Hel 28.3 63 0.0014 20.1 2.4 21 46-66 4-24 (102)
221 TIGR02835 spore_sigmaE RNA pol 28.3 1.1E+02 0.0025 21.7 4.0 31 45-75 200-230 (234)
222 smart00027 EH Eps15 homology d 28.2 1.4E+02 0.0031 17.9 5.1 44 22-65 3-51 (96)
223 PHA02955 hypothetical protein; 28.1 68 0.0015 23.2 2.7 46 25-70 60-106 (213)
224 TIGR02054 MerD mercuric resist 28.0 63 0.0014 21.0 2.4 22 45-66 5-26 (120)
225 PF13551 HTH_29: Winged helix- 27.8 1.5E+02 0.0032 17.9 6.7 45 21-65 56-109 (112)
226 PRK10360 DNA-binding transcrip 27.8 1.6E+02 0.0034 19.3 4.5 44 22-71 137-180 (196)
227 cd04773 HTH_TioE_rpt2 Second H 27.7 75 0.0016 20.0 2.7 21 46-66 3-23 (108)
228 PF12793 SgrR_N: Sugar transpo 27.6 93 0.002 20.0 3.1 33 28-62 6-38 (115)
229 PRK09706 transcriptional repre 27.5 46 0.00099 21.7 1.7 23 46-68 21-43 (135)
230 PF14229 DUF4332: Domain of un 27.4 85 0.0018 20.3 2.9 26 40-65 26-51 (122)
231 COG1595 RpoE DNA-directed RNA 27.1 1.2E+02 0.0026 20.5 3.8 32 45-76 145-176 (182)
232 PF08671 SinI: Anti-repressor 26.9 91 0.002 15.3 2.7 20 46-65 8-27 (30)
233 TIGR03541 reg_near_HchA LuxR f 26.8 1.5E+02 0.0033 21.1 4.5 46 21-72 170-215 (232)
234 PRK06596 RNA polymerase factor 26.6 2.1E+02 0.0045 21.2 5.3 49 23-74 231-279 (284)
235 cd04765 HTH_MlrA-like_sg2 Heli 26.5 87 0.0019 19.4 2.8 21 46-66 3-23 (99)
236 PRK09975 DNA-binding transcrip 26.4 84 0.0018 21.6 3.0 42 28-70 17-58 (213)
237 PRK12540 RNA polymerase sigma 26.3 2.1E+02 0.0046 19.4 5.8 32 45-76 129-160 (182)
238 cd01109 HTH_YyaN Helix-Turn-He 26.3 70 0.0015 20.1 2.4 20 46-65 3-22 (113)
239 cd01107 HTH_BmrR Helix-Turn-He 26.2 71 0.0015 20.0 2.4 21 46-66 3-23 (108)
240 cd04767 HTH_HspR-like_MBC Heli 26.2 81 0.0018 20.6 2.7 21 46-66 4-24 (120)
241 PF07638 Sigma70_ECF: ECF sigm 26.1 2.2E+02 0.0048 19.4 5.8 29 45-73 153-181 (185)
242 COG0789 SoxR Predicted transcr 25.8 72 0.0016 20.1 2.4 20 46-65 3-22 (124)
243 KOG3755|consensus 25.7 42 0.00091 28.2 1.5 58 15-72 646-707 (769)
244 PF12802 MarR_2: MarR family; 25.4 1E+02 0.0023 16.6 2.8 38 23-62 3-40 (62)
245 cd01111 HTH_MerD Helix-Turn-He 25.0 91 0.002 19.7 2.7 21 46-66 3-23 (107)
246 PRK09935 transcriptional regul 24.8 1.9E+02 0.0041 19.1 4.5 44 22-71 149-192 (210)
247 PF13613 HTH_Tnp_4: Helix-turn 24.6 70 0.0015 17.3 1.9 21 46-66 22-42 (53)
248 TIGR01557 myb_SHAQKYF myb-like 24.6 1.4E+02 0.003 16.7 5.3 50 19-68 2-54 (57)
249 cd01279 HTH_HspR-like Helix-Tu 24.4 94 0.002 19.2 2.7 21 46-66 4-24 (98)
250 smart00595 MADF subfamily of S 24.4 1.6E+02 0.0035 17.3 3.7 31 47-77 31-61 (89)
251 PF00325 Crp: Bacterial regula 23.9 81 0.0017 15.6 1.8 20 45-64 4-23 (32)
252 PF07037 DUF1323: Putative tra 23.9 87 0.0019 20.6 2.4 20 46-65 3-22 (122)
253 PF01047 MarR: MarR family; I 23.8 1.3E+02 0.0028 16.1 3.9 39 23-65 1-39 (59)
254 PF07471 Phage_Nu1: Phage DNA 23.8 74 0.0016 22.0 2.2 21 46-66 5-25 (164)
255 PRK09744 DNA-binding transcrip 23.7 95 0.0021 18.7 2.4 18 46-63 13-30 (75)
256 PRK11922 RNA polymerase sigma 23.6 1.4E+02 0.003 21.1 3.8 35 41-75 163-197 (231)
257 TIGR01950 SoxR redox-sensitive 23.5 94 0.002 20.7 2.7 21 46-66 4-24 (142)
258 cd01282 HTH_MerR-like_sg3 Heli 23.4 87 0.0019 19.8 2.4 21 46-66 3-23 (112)
259 PF13565 HTH_32: Homeodomain-l 23.3 1.6E+02 0.0034 16.7 6.5 39 24-62 32-75 (77)
260 TIGR00721 tfx DNA-binding prot 23.3 2.4E+02 0.0052 18.9 6.4 49 20-74 4-52 (137)
261 TIGR03826 YvyF flagellar opero 23.3 1.4E+02 0.0029 20.1 3.4 27 44-70 47-73 (137)
262 PF13404 HTH_AsnC-type: AsnC-t 23.1 79 0.0017 16.4 1.8 17 45-61 19-35 (42)
263 PF12833 HTH_18: Helix-turn-he 22.7 81 0.0018 18.1 2.0 21 50-70 17-37 (81)
264 PRK13890 conjugal transfer pro 22.7 61 0.0013 20.9 1.6 23 46-68 21-43 (120)
265 PF00440 TetR_N: Bacterial reg 22.7 57 0.0012 17.0 1.2 33 35-68 9-41 (47)
266 PF13560 HTH_31: Helix-turn-he 22.7 62 0.0013 18.0 1.5 25 45-69 16-40 (64)
267 cd01110 HTH_SoxR Helix-Turn-He 22.6 86 0.0019 20.7 2.3 21 46-66 4-24 (139)
268 PF05269 Phage_CII: Bacterioph 22.6 1.7E+02 0.0036 18.3 3.4 29 45-73 25-53 (91)
269 PRK15369 two component system 22.6 2.3E+02 0.0049 18.4 5.8 45 22-72 149-193 (211)
270 PRK13182 racA polar chromosome 22.5 99 0.0021 21.5 2.7 21 46-66 3-23 (175)
271 PF04539 Sigma70_r3: Sigma-70 22.5 1.1E+02 0.0023 17.6 2.5 21 45-65 22-42 (78)
272 cd04776 HTH_GnyR Helix-Turn-He 22.4 91 0.002 20.0 2.4 20 46-65 3-22 (118)
273 PRK08241 RNA polymerase factor 22.4 2.5E+02 0.0054 21.0 5.1 29 45-73 171-199 (339)
274 cd04772 HTH_TioE_rpt1 First He 22.2 96 0.0021 19.2 2.4 21 46-66 3-23 (99)
275 PRK09514 zntR zinc-responsive 22.2 1E+02 0.0023 20.3 2.7 21 46-66 4-24 (140)
276 KOG0044|consensus 22.1 1.4E+02 0.0031 21.1 3.5 30 40-69 8-37 (193)
277 PF13022 HTH_Tnp_1_2: Helix-tu 22.0 1.5E+02 0.0032 20.1 3.3 25 43-67 34-59 (142)
278 cd04781 HTH_MerR-like_sg6 Heli 22.0 94 0.002 19.8 2.4 21 46-66 3-23 (120)
279 TIGR02051 MerR Hg(II)-responsi 21.8 92 0.002 20.1 2.3 19 46-64 2-20 (124)
280 COG2944 Predicted transcriptio 21.4 82 0.0018 20.2 1.9 39 23-68 44-82 (104)
281 PRK07405 RNA polymerase sigma 21.4 3.1E+02 0.0067 20.7 5.4 50 23-73 257-306 (317)
282 PF09301 DUF1970: Domain of un 21.2 54 0.0012 20.4 1.0 12 59-70 18-29 (117)
283 cd01108 HTH_CueR Helix-Turn-He 21.2 98 0.0021 20.0 2.4 22 46-67 3-24 (127)
284 PF05263 DUF722: Protein of un 21.0 2.6E+02 0.0057 18.5 4.5 20 47-66 103-122 (130)
285 TIGR02044 CueR Cu(I)-responsiv 20.9 99 0.0021 19.9 2.3 22 46-67 3-24 (127)
286 PRK10227 DNA-binding transcrip 20.8 1E+02 0.0022 20.3 2.4 21 46-66 3-23 (135)
287 TIGR02997 Sig70-cyanoRpoD RNA 20.7 2.9E+02 0.0063 20.5 5.1 44 23-67 250-293 (298)
288 TIGR02043 ZntR Zn(II)-responsi 20.7 1.2E+02 0.0026 19.8 2.7 21 46-66 4-24 (131)
289 TIGR03613 RutR pyrimidine util 20.7 1.2E+02 0.0025 20.6 2.8 38 32-70 18-55 (202)
290 PF01476 LysM: LysM domain; I 20.6 1.3E+02 0.0027 15.0 2.3 20 44-63 7-26 (44)
291 PF13412 HTH_24: Winged helix- 20.6 1.4E+02 0.0031 15.3 4.5 37 25-65 3-39 (48)
292 PRK13558 bacterio-opsin activa 20.6 1.4E+02 0.0031 24.5 3.6 42 21-62 606-649 (665)
293 PRK12527 RNA polymerase sigma 20.4 2.6E+02 0.0056 18.2 5.9 30 45-74 123-152 (159)
294 smart00351 PAX Paired Box doma 20.4 2.5E+02 0.0055 18.0 5.3 40 22-66 17-56 (125)
295 PF10078 DUF2316: Uncharacteri 20.3 93 0.002 19.3 1.9 32 28-63 12-43 (89)
296 PRK09726 antitoxin HipB; Provi 20.3 75 0.0016 19.0 1.6 22 46-67 28-49 (88)
297 PRK12517 RNA polymerase sigma 20.3 2.9E+02 0.0063 18.8 6.0 31 45-75 146-176 (188)
298 PLN03162 golden-2 like transcr 20.1 4.6E+02 0.01 21.0 6.3 59 15-73 232-292 (526)
299 PF12844 HTH_19: Helix-turn-he 20.1 76 0.0016 17.4 1.5 24 45-68 14-37 (64)
300 TIGR02846 spore_sigmaK RNA pol 20.1 3.2E+02 0.007 19.2 5.8 29 45-73 196-224 (227)
No 1
>KOG0493|consensus
Probab=99.80 E-value=1.6e-19 Score=130.41 Aligned_cols=106 Identities=70% Similarity=1.023 Sum_probs=92.1
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCCh
Q psy4625 1 PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNP 80 (120)
Q Consensus 1 ~~~~~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~ 80 (120)
|+.++++..+.....-+|.||.|+.+|+..|...|+.+.|.+...|..||.+|+|.+.||+|||||+|+|.||....+..
T Consensus 231 PR~Rk~kkkk~~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn~ 310 (342)
T KOG0493|consen 231 PRHRKPKKKKSSSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKNR 310 (342)
T ss_pred cccccccccCCccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCCc
Confidence 45555555555555667889999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHhhcCCCCCCCCCCCCchHHHh
Q psy4625 81 LALQLMAQGLYNHSTVPMSDEEMEME 106 (120)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~s~~~~~~~ 106 (120)
.+...+.++.+.+++.+....+..++
T Consensus 311 la~~lmaqglyNHst~~l~a~e~k~e 336 (342)
T KOG0493|consen 311 LALHLMAQGLYNHSTTHLMAQEAKVE 336 (342)
T ss_pred hhhhhhccccccCccchhhhhhhhhh
Confidence 99999999999999887655544443
No 2
>KOG0850|consensus
Probab=99.77 E-value=4.9e-19 Score=125.67 Aligned_cols=70 Identities=44% Similarity=0.692 Sum_probs=64.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCChh
Q psy4625 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNPL 81 (120)
Q Consensus 12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~~ 81 (120)
+.+|.|+.||.++.-||..|...|++++|..-.||.+||..|||+..||+|||||||.|.||..+.+...
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~ 187 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSGP 187 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCCc
Confidence 5667788999999999999999999999999999999999999999999999999999999998754433
No 3
>KOG0488|consensus
Probab=99.77 E-value=9.3e-19 Score=131.08 Aligned_cols=73 Identities=40% Similarity=0.657 Sum_probs=65.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625 5 RIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ 77 (120)
Q Consensus 5 ~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 77 (120)
.+.......+++|+.||.|+..|+..||..|+...|.+..+|+.||..|||+..||++||||||.|||+....
T Consensus 161 ~~~~~~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 161 NHPYQRSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred CCCcccCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 3444455567888899999999999999999999999999999999999999999999999999999998654
No 4
>KOG0484|consensus
Probab=99.76 E-value=3.6e-19 Score=112.44 Aligned_cols=66 Identities=38% Similarity=0.678 Sum_probs=62.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ 77 (120)
Q Consensus 12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 77 (120)
..++.||-||.|+..|+..|+..|...+||++..+++||..+.|++..|++||||||+|.||..+.
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~ 78 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERA 78 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence 456778889999999999999999999999999999999999999999999999999999998754
No 5
>KOG0489|consensus
Probab=99.76 E-value=1.2e-18 Score=128.10 Aligned_cols=70 Identities=51% Similarity=0.706 Sum_probs=64.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCChh
Q psy4625 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNPL 81 (120)
Q Consensus 12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~~ 81 (120)
..++.||.||.|+..|+..||+.|..+.|.+...|.+||..|.|+++||+|||||||.||||..+.....
T Consensus 155 ~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 155 TGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred ccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 3456788999999999999999999999999999999999999999999999999999999998766554
No 6
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.76 E-value=4.4e-18 Score=97.94 Aligned_cols=57 Identities=56% Similarity=0.814 Sum_probs=54.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 17 rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
|+.|+.|+.+|+.+|+.+|..++||+..++..||..+||+..+|.+||+|+|.++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 467899999999999999999999999999999999999999999999999999885
No 7
>KOG0843|consensus
Probab=99.73 E-value=5e-18 Score=116.68 Aligned_cols=64 Identities=44% Similarity=0.741 Sum_probs=60.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCC
Q psy4625 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQK 78 (120)
Q Consensus 15 ~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~ 78 (120)
+.+|.||.|+.+|+..||..|+.++|....+|..||..|+|++.||+|||||||.|.||.....
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 6788999999999999999999999999999999999999999999999999999999987653
No 8
>KOG2251|consensus
Probab=99.72 E-value=7.3e-18 Score=119.12 Aligned_cols=68 Identities=35% Similarity=0.621 Sum_probs=63.8
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCC
Q psy4625 11 DKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQK 78 (120)
Q Consensus 11 ~~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~ 78 (120)
.+.++.||+||.|+..|+.+|+..|.+.+||+...+++||.+++|.+.+|+|||+|||+|+|+.....
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 35678899999999999999999999999999999999999999999999999999999999987653
No 9
>KOG0842|consensus
Probab=99.71 E-value=4.8e-18 Score=126.12 Aligned_cols=75 Identities=39% Similarity=0.620 Sum_probs=66.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCChhhHHHhh
Q psy4625 13 RSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNPLALQLMA 87 (120)
Q Consensus 13 ~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~~~~~~~~ 87 (120)
..++||.|..|+..|+..||..|.+..|.+..||+.||..|.|++.||+|||||||-|.||....+.........
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~~~~ 224 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALLLAS 224 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcccCCC
Confidence 456777788999999999999999999999999999999999999999999999999999998776655444333
No 10
>KOG0485|consensus
Probab=99.70 E-value=1.9e-17 Score=116.91 Aligned_cols=66 Identities=41% Similarity=0.655 Sum_probs=62.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ 77 (120)
Q Consensus 12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 77 (120)
++.++|+.||+|+..|+..||..|+...|.+..+|..||..|.|++.||+|||||||.|||+....
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa 165 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA 165 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence 566888899999999999999999999999999999999999999999999999999999998643
No 11
>KOG0494|consensus
Probab=99.69 E-value=3.7e-17 Score=118.07 Aligned_cols=67 Identities=36% Similarity=0.531 Sum_probs=60.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCChh
Q psy4625 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNPL 81 (120)
Q Consensus 15 ~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~~ 81 (120)
++|+.||.|+..|+..||+.|+...||+...++.||..+.|.+.+|++||||||+||||........
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~s 206 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGS 206 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcc
Confidence 3444599999999999999999999999999999999999999999999999999999998664433
No 12
>KOG0487|consensus
Probab=99.67 E-value=2.2e-17 Score=122.63 Aligned_cols=64 Identities=39% Similarity=0.651 Sum_probs=60.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ 77 (120)
Q Consensus 14 ~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 77 (120)
+..||+|.-+|+.|+..||..|..|.|.+...|.+|+..|+|+++||+|||||||.|.||..+.
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re 296 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRE 296 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhh
Confidence 4567778899999999999999999999999999999999999999999999999999999853
No 13
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.64 E-value=1.6e-15 Score=87.39 Aligned_cols=57 Identities=56% Similarity=0.919 Sum_probs=53.5
Q ss_pred CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 18 r~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
+.+..++..++.+|+..|..++||+..++..||..+||+..+|++||+|+|.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 457789999999999999999999999999999999999999999999999998753
No 14
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.64 E-value=1.1e-15 Score=87.36 Aligned_cols=55 Identities=55% Similarity=0.888 Sum_probs=51.6
Q ss_pred CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHH
Q psy4625 18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72 (120)
Q Consensus 18 r~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k 72 (120)
+.|+.|+..++.+|+..|..++||+..++..||..+||+..+|++||+|+|.+.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 4577899999999999999999999999999999999999999999999998753
No 15
>KOG0492|consensus
Probab=99.63 E-value=3.4e-16 Score=109.89 Aligned_cols=65 Identities=43% Similarity=0.751 Sum_probs=60.3
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
+.+..|+.|+-|+..|+..||..|...+|.++.++.+++..|.|++.||+|||||||+|.||.+.
T Consensus 140 Khk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe 204 (246)
T KOG0492|consen 140 KHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE 204 (246)
T ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence 34456788999999999999999999999999999999999999999999999999999998864
No 16
>KOG0848|consensus
Probab=99.63 E-value=1.6e-16 Score=115.07 Aligned_cols=64 Identities=45% Similarity=0.718 Sum_probs=59.1
Q ss_pred CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCChh
Q psy4625 18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNPL 81 (120)
Q Consensus 18 r~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~~ 81 (120)
+-|.+++..|.-.||+.|..++|.++.-+.+||.-|||+++||+|||||||+|+||..+++..+
T Consensus 201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~~~ 264 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKRLQ 264 (317)
T ss_pred ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHHHH
Confidence 4477899999999999999999999999999999999999999999999999999998776433
No 17
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.61 E-value=2e-15 Score=103.12 Aligned_cols=70 Identities=39% Similarity=0.464 Sum_probs=63.3
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCCh
Q psy4625 11 DKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNP 80 (120)
Q Consensus 11 ~~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~ 80 (120)
.++...++.|.+.+..|+.+|+..|..++||+..++..|+..++|+++-|++||||+|++.|+....+..
T Consensus 46 ~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~~ 115 (156)
T COG5576 46 DGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVE 115 (156)
T ss_pred cCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccchh
Confidence 4566778888999999999999999999999999999999999999999999999999999988655433
No 18
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.60 E-value=7.2e-16 Score=88.86 Aligned_cols=52 Identities=25% Similarity=0.503 Sum_probs=50.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCC----CCHHHHHHHHHHhCCChhhHHHHHHHHH
Q psy4625 17 KRPRTAFSGEQLSRLKVEFTENRY----LTERRRQELANELGLNEAQIKIWFQNKR 68 (120)
Q Consensus 17 rr~R~~~~~~q~~~L~~~F~~~~~----p~~~~~~~La~~l~l~~~~V~~WFqNrR 68 (120)
+|.||.|+.+|+..|+.+|..++| |+..++..||..+||++.+|++||||.+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 678999999999999999999999 9999999999999999999999999964
No 19
>KOG3802|consensus
Probab=99.59 E-value=3e-16 Score=119.09 Aligned_cols=64 Identities=25% Similarity=0.447 Sum_probs=60.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 13 RSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 13 ~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
.+++||+||.|.......||.+|..|+.|+..++..||.+|+|.+.+|+|||||||+|.||...
T Consensus 291 ~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 291 QSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 3477888999999999999999999999999999999999999999999999999999999876
No 20
>KOG0847|consensus
Probab=99.54 E-value=4.5e-15 Score=105.15 Aligned_cols=66 Identities=36% Similarity=0.720 Sum_probs=62.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ 77 (120)
Q Consensus 12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 77 (120)
++++++..|..|+..|+..|+..|+..+|+-..++.+||..+||++.+|++||||||.||||+...
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa 228 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA 228 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence 667888889999999999999999999999999999999999999999999999999999998654
No 21
>KOG0491|consensus
Probab=99.54 E-value=3.2e-15 Score=101.64 Aligned_cols=66 Identities=48% Similarity=0.763 Sum_probs=60.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCChh
Q psy4625 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNPL 81 (120)
Q Consensus 16 ~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~~ 81 (120)
+++-|++|+..|+..|++.|+...|.+..++.+||..|+|++.||+.||||||.|.||..+..+..
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~ 165 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPK 165 (194)
T ss_pred hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCC
Confidence 356689999999999999999999999999999999999999999999999999999998776643
No 22
>KOG0483|consensus
Probab=99.52 E-value=1.4e-14 Score=102.20 Aligned_cols=58 Identities=34% Similarity=0.635 Sum_probs=54.5
Q ss_pred CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 18 r~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
.++.+|+.+|+..|+..|+...+..+..+..||.+|||.++||.+||||||++||..+
T Consensus 52 ~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq 109 (198)
T KOG0483|consen 52 GKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ 109 (198)
T ss_pred cccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence 4456799999999999999999999999999999999999999999999999999875
No 23
>KOG0486|consensus
Probab=99.47 E-value=2e-14 Score=106.32 Aligned_cols=65 Identities=38% Similarity=0.690 Sum_probs=61.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCC
Q psy4625 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKN 79 (120)
Q Consensus 15 ~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~ 79 (120)
++||.|+.|+..|+..||..|+++.||+...+++||.-++|++..|++||.|||+||||.++...
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 67888999999999999999999999999999999999999999999999999999999987655
No 24
>KOG4577|consensus
Probab=99.45 E-value=1.5e-13 Score=100.84 Aligned_cols=66 Identities=33% Similarity=0.590 Sum_probs=62.1
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ 77 (120)
Q Consensus 12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 77 (120)
+++..+|+||.++..|+..|..+|...+.|....|+.|+.++||.-++|++||||||+|+|+..+.
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence 567789999999999999999999999999999999999999999999999999999999987554
No 25
>KOG0844|consensus
Probab=99.37 E-value=1.2e-13 Score=102.05 Aligned_cols=65 Identities=45% Similarity=0.685 Sum_probs=59.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
.+.+-||-||.|+.+|+..||+.|-...|.+...|.+||.+|+|.+..|++||||||.|+|+...
T Consensus 177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 34455788999999999999999999999999999999999999999999999999999998754
No 26
>KOG0775|consensus
Probab=99.27 E-value=7.4e-12 Score=91.27 Aligned_cols=54 Identities=31% Similarity=0.561 Sum_probs=48.4
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
|...-..+|.+.|..++||++.++.+||.++||+..||-+||.|||+++|-...
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~a 236 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAA 236 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhccc
Confidence 445557799999999999999999999999999999999999999999994443
No 27
>KOG0490|consensus
Probab=99.23 E-value=3.7e-12 Score=91.36 Aligned_cols=64 Identities=30% Similarity=0.392 Sum_probs=60.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 13 RSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 13 ~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
..++++.|+.|+..|++.|+..|...+||+...++.||..+++++..|++||||+|+++++...
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 4567888999999999999999999999999999999999999999999999999999998764
No 28
>KOG0849|consensus
Probab=99.18 E-value=5.7e-11 Score=90.82 Aligned_cols=66 Identities=36% Similarity=0.585 Sum_probs=60.9
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ 77 (120)
Q Consensus 12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 77 (120)
...+.++.|+.|+..|+..|+..|+.++||++..++.||.++++++..|++||+|+|+++++....
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred ccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 445566778999999999999999999999999999999999999999999999999999998843
No 29
>KOG1168|consensus
Probab=99.18 E-value=3e-12 Score=94.12 Aligned_cols=65 Identities=23% Similarity=0.422 Sum_probs=59.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
..+.++|+||.+...+...||.+|...+.|+.+.+..||.+|.|.+.+|++||||.|+|.|+...
T Consensus 305 ~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 305 PGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred CccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence 35677888999999999999999999999999999999999999999999999999999988543
No 30
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.83 E-value=6.1e-09 Score=55.73 Aligned_cols=34 Identities=38% Similarity=0.715 Sum_probs=28.8
Q ss_pred hCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhH
Q psy4625 37 ENRYLTERRRQELANELGLNEAQIKIWFQNKRAK 70 (120)
Q Consensus 37 ~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k 70 (120)
.+|||+..++..||..+||+..||..||-|.|.+
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4799999999999999999999999999999864
No 31
>KOG0774|consensus
Probab=98.71 E-value=5.9e-09 Score=75.94 Aligned_cols=64 Identities=33% Similarity=0.546 Sum_probs=57.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHH---hCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCC
Q psy4625 16 EKRPRTAFSGEQLSRLKVEFT---ENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKN 79 (120)
Q Consensus 16 ~rr~R~~~~~~q~~~L~~~F~---~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~ 79 (120)
.+|+|..|++....+|..+|. .++||+...+++||.+++++..||..||.|+|-+++|......
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~~ 254 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKNQ 254 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhhh
Confidence 356788899999999999995 5889999999999999999999999999999999998765433
No 32
>KOG2252|consensus
Probab=98.67 E-value=6.7e-08 Score=76.54 Aligned_cols=61 Identities=26% Similarity=0.429 Sum_probs=56.0
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHH
Q psy4625 11 DKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71 (120)
Q Consensus 11 ~~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~ 71 (120)
...-..+|.|.+|+..|...|..+|+.+++|+..+.+.|+.+|+|....|.+||.|-|.+.
T Consensus 415 d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 415 DKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 3455667889999999999999999999999999999999999999999999999988774
No 33
>KOG0490|consensus
Probab=98.24 E-value=1.4e-06 Score=62.29 Aligned_cols=65 Identities=40% Similarity=0.673 Sum_probs=60.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
...+.++.++.+...++..|...|...++|+...+..|+..+|+....|++||+|+|.+.++...
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 44567788999999999999999999999999999999999999999999999999999988755
No 34
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.80 E-value=3.3e-05 Score=43.96 Aligned_cols=42 Identities=19% Similarity=0.413 Sum_probs=31.5
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHh
Q psy4625 28 LSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRA 69 (120)
Q Consensus 28 ~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~ 69 (120)
...|+.+|...+++.......|+.+.+|+..+|+.||-.+..
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 456999999999999999999999999999999999986644
No 35
>KOG1146|consensus
Probab=97.68 E-value=4.2e-05 Score=66.12 Aligned_cols=62 Identities=35% Similarity=0.429 Sum_probs=57.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 15 ~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
.++..|++++..|+..|..+|....+|...+.+.|...+++..+.|++||||-|++.++...
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 34567899999999999999999999999999999999999999999999999999988765
No 36
>KOG3623|consensus
Probab=97.20 E-value=0.0022 Score=53.20 Aligned_cols=49 Identities=27% Similarity=0.403 Sum_probs=45.4
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 28 LSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 28 ~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
+.+|..+|..|..|+..+...+|.+.||....|+.||.+++.......+
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~r 616 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVER 616 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhcc
Confidence 6789999999999999999999999999999999999999998777654
No 37
>KOG0773|consensus
Probab=96.75 E-value=0.0014 Score=49.97 Aligned_cols=58 Identities=28% Similarity=0.487 Sum_probs=46.5
Q ss_pred CCCCCCCCCHHHHHHHHHHH-H--hCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 16 EKRPRTAFSGEQLSRLKVEF-T--ENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 16 ~rr~R~~~~~~q~~~L~~~F-~--~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
..+.+..+......+|+... + ..+||+..++..||.++||+..||.+||-|.|.+.-+
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK 299 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCC
Confidence 33445578888888888663 3 2579999999999999999999999999999877443
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=95.71 E-value=0.055 Score=30.31 Aligned_cols=47 Identities=21% Similarity=0.420 Sum_probs=34.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHH
Q psy4625 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR 68 (120)
Q Consensus 17 rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR 68 (120)
++.|..++-++...+-..++.+. ....||..+|++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 45678899988777777787776 477889999999999999998854
No 39
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=91.11 E-value=1.3 Score=23.91 Aligned_cols=46 Identities=11% Similarity=0.309 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHH
Q psy4625 22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72 (120)
Q Consensus 22 ~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k 72 (120)
.+++.+..+|...|- ......++|..+|++...|+.+...-..+.|
T Consensus 4 ~L~~~er~vi~~~y~-----~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYF-----EGLTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHT-----ST-SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhc-----CCCCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 467888999999992 2234677899999999999998876555443
No 40
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=87.01 E-value=2.5 Score=23.65 Aligned_cols=42 Identities=21% Similarity=0.343 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHHHHhCCC--CCHHHHHHHHHHhCCChhhHHHHH
Q psy4625 23 FSGEQLSRLKVEFTENRY--LTERRRQELANELGLNEAQIKIWF 64 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~--p~~~~~~~La~~l~l~~~~V~~WF 64 (120)
++..|..+|...|...-| |-......||..+|++...|..-+
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~L 44 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHL 44 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHH
Confidence 467899999999988764 667778899999999987765433
No 41
>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=86.04 E-value=1.3 Score=25.89 Aligned_cols=45 Identities=22% Similarity=0.324 Sum_probs=29.0
Q ss_pred CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHH
Q psy4625 19 PRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNK 67 (120)
Q Consensus 19 ~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNr 67 (120)
.|..|+.++...+...+... ......+|..+|+++..+..|-.--
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~----g~sv~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLES----GESVSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp SS----HHHHHHHHHHHHHH----HCHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHC----CCceEeeecccccccccccHHHHHH
Confidence 46779998866665555222 2567788999999999999998543
No 42
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=83.43 E-value=3.3 Score=21.53 Aligned_cols=44 Identities=16% Similarity=0.292 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhH
Q psy4625 22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAK 70 (120)
Q Consensus 22 ~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k 70 (120)
.++..+..++...|... .....+|..+|++...|..|...-+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 35667777777776432 235667999999999999998755443
No 43
>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=82.55 E-value=1.3 Score=25.49 Aligned_cols=21 Identities=29% Similarity=0.725 Sum_probs=17.8
Q ss_pred HHHHHHHHhCCChhhHHHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFq 65 (120)
....||.+||+++.+|+.|=.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh
Confidence 456789999999999999953
No 44
>KOG1146|consensus
Probab=82.26 E-value=3.3 Score=37.21 Aligned_cols=60 Identities=15% Similarity=0.215 Sum_probs=54.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 16 ~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
.+..+..+-.++..+|-..|-.+.-|+......|......+.+.+.+||++-+.+.++..
T Consensus 705 ~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 705 DKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred cccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 355677788899999999999999999999999999999999999999999999988876
No 45
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=78.67 E-value=8.4 Score=20.80 Aligned_cols=42 Identities=19% Similarity=0.315 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHh
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRA 69 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~ 69 (120)
+++.+..++...|-.+ ....++|..+|++...|+.|.+.-+.
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 4555666665555443 45677899999999999999975544
No 46
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=78.31 E-value=7.1 Score=27.71 Aligned_cols=49 Identities=24% Similarity=0.392 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHHHHHhCC--CCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHH
Q psy4625 22 AFSGEQLSRLKVEFTENR--YLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72 (120)
Q Consensus 22 ~~~~~q~~~L~~~F~~~~--~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k 72 (120)
-+|..|+.+|..+|...= +|-......||.++|+++..+ |..=||+..|
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~--~ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTL--SEHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH--HHHHHHHHHH
Confidence 599999999999999876 577888999999999988654 4455555543
No 47
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=76.88 E-value=9.3 Score=21.86 Aligned_cols=44 Identities=16% Similarity=0.375 Sum_probs=22.2
Q ss_pred CCCCCHHH-HHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHH
Q psy4625 20 RTAFSGEQ-LSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 20 R~~~~~~q-~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFq 65 (120)
|..|+... +.+++.++..+.. -.. ...-|.++++.+.+|+-|.+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc-~~~-~RAaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNC-KGN-QRAAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTT-TT--HHHHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccch-hhh-HHHHHHHhCccHHHHHHHHH
Confidence 44566665 4444444433321 112 23348999999999999985
No 48
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=75.02 E-value=20 Score=24.13 Aligned_cols=50 Identities=24% Similarity=0.345 Sum_probs=38.4
Q ss_pred CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 20 R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
...+++.|..+|... . .. ....++|..+|++...|..|....+.+.++..
T Consensus 4 ~~~Lt~rqreVL~lr-~-~G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 4 ESFLTERQIEVLRLR-E-RG----LTQQEIADILGTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred ccCCCHHHHHHHHHH-H-cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 356888999998773 2 22 33567899999999999999998887776654
No 49
>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=70.86 E-value=5.6 Score=20.84 Aligned_cols=21 Identities=19% Similarity=0.270 Sum_probs=17.7
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
..++|..+|++...|+.|.+.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 356799999999999999754
No 50
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=70.46 E-value=17 Score=23.38 Aligned_cols=42 Identities=14% Similarity=0.192 Sum_probs=28.7
Q ss_pred CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHH
Q psy4625 20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 20 R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFq 65 (120)
|.+|+.++.......+..+.. ....+|..+|++...|..|..
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHH
Confidence 456888875544443333332 345679999999999999964
No 51
>PF13518 HTH_28: Helix-turn-helix domain
Probab=70.21 E-value=6.5 Score=20.86 Aligned_cols=24 Identities=25% Similarity=0.612 Sum_probs=19.4
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKR 68 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR 68 (120)
....+|..+|++..+|..|.+.-+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 345589999999999999996543
No 52
>KOG0773|consensus
Probab=69.50 E-value=9.4 Score=29.06 Aligned_cols=44 Identities=30% Similarity=0.385 Sum_probs=37.7
Q ss_pred HHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625 34 EFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ 77 (120)
Q Consensus 34 ~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 77 (120)
.-..++|++..+...++....|+..+|.+||-|.+.+.+.....
T Consensus 115 ~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~ 158 (342)
T KOG0773|consen 115 EHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKM 158 (342)
T ss_pred hhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCC
Confidence 34568899999999999999999999999999998887776544
No 53
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=69.09 E-value=28 Score=22.68 Aligned_cols=29 Identities=17% Similarity=0.250 Sum_probs=23.2
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
...++|..+|++...|+.|...-+.+.|+
T Consensus 124 s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 124 TMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 46778999999999999998766665543
No 54
>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=68.84 E-value=10 Score=17.39 Aligned_cols=38 Identities=16% Similarity=0.304 Sum_probs=25.6
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHH
Q psy4625 22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWF 64 (120)
Q Consensus 22 ~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF 64 (120)
.++..+...+...|... . ....+|..++++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 35566666666666532 2 45577889999998888873
No 55
>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=68.50 E-value=3.1 Score=24.91 Aligned_cols=35 Identities=20% Similarity=0.281 Sum_probs=25.5
Q ss_pred HHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHH
Q psy4625 32 KVEFTENRYLTERRRQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 32 ~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqN 66 (120)
+..|....+.......++|..+|++...|+.|+..
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 34454444444456778899999999999999864
No 56
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=68.47 E-value=28 Score=23.88 Aligned_cols=31 Identities=13% Similarity=0.261 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
...++|..+|++...|+.+...-|.+.++..
T Consensus 160 s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 160 TYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred CHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 4567799999999999999988777777654
No 57
>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=65.97 E-value=27 Score=22.01 Aligned_cols=29 Identities=24% Similarity=0.453 Sum_probs=23.3
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
....+|..+|+++..|..+...-+.+.++
T Consensus 128 s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 128 SYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45678999999999999999876666553
No 58
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=65.28 E-value=6.9 Score=20.77 Aligned_cols=22 Identities=23% Similarity=0.567 Sum_probs=16.9
Q ss_pred HHHHHHHHHhCCChhhHHHHHH
Q psy4625 44 RRRQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 44 ~~~~~La~~l~l~~~~V~~WFq 65 (120)
.....+|..+|++...|..|.+
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4466789999999999999975
No 59
>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=65.00 E-value=7.9 Score=21.96 Aligned_cols=20 Identities=30% Similarity=0.607 Sum_probs=17.5
Q ss_pred HHHHHHHhCCChhhHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFq 65 (120)
..++|..||++...|..|-+
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH
Confidence 45689999999999999985
No 60
>PRK04217 hypothetical protein; Provisional
Probab=64.74 E-value=35 Score=21.98 Aligned_cols=50 Identities=14% Similarity=0.203 Sum_probs=37.4
Q ss_pred CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 21 TAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 21 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
..++..+..++...|...- ...++|..+|++...|...+..-+.+.+...
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4577888877766664433 4667899999999999999987777766553
No 61
>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=64.38 E-value=8.8 Score=19.74 Aligned_cols=19 Identities=21% Similarity=0.413 Sum_probs=15.3
Q ss_pred HHHHHHhCCChhhHHHHHH
Q psy4625 47 QELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 47 ~~La~~l~l~~~~V~~WFq 65 (120)
.++|..+|++...|+.|=.
T Consensus 3 ~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHH
Confidence 4679999999999999964
No 62
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=64.35 E-value=19 Score=24.28 Aligned_cols=30 Identities=17% Similarity=0.407 Sum_probs=24.6
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
...++|..+|++...|+.++..-|.+.|+.
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 366789999999999999998777776654
No 63
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=63.89 E-value=32 Score=22.78 Aligned_cols=30 Identities=13% Similarity=0.237 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
....+|..+|++...|..|...-+.+.++.
T Consensus 146 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 146 SYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 355778999999999999998766666654
No 64
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=63.32 E-value=19 Score=18.96 Aligned_cols=40 Identities=13% Similarity=0.252 Sum_probs=20.3
Q ss_pred CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHH
Q psy4625 21 TAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 21 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFq 65 (120)
..++..+...++..+... .....||..+|++...|..+..
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 357777777777776533 3456689999999999988764
No 65
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=63.16 E-value=39 Score=22.22 Aligned_cols=30 Identities=23% Similarity=0.185 Sum_probs=24.8
Q ss_pred HHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 46 RQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
..++|..+|++...|+..+..-|.+.|+..
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 125 YQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 557799999999999999987777776654
No 66
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=63.05 E-value=32 Score=22.77 Aligned_cols=30 Identities=20% Similarity=0.362 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
....+|..+|++...|..|..--+.+.++.
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999998777776654
No 67
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=62.47 E-value=38 Score=23.58 Aligned_cols=31 Identities=23% Similarity=0.277 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
....+|..+|++...|+.++..-+.+.++..
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999987777766654
No 68
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=62.42 E-value=9.3 Score=21.63 Aligned_cols=20 Identities=20% Similarity=0.423 Sum_probs=17.1
Q ss_pred HHHHHHHhCCChhhHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFq 65 (120)
..++|..+|++...|+.|=.
T Consensus 3 i~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35689999999999999964
No 69
>PRK00118 putative DNA-binding protein; Validated
Probab=62.34 E-value=38 Score=21.58 Aligned_cols=50 Identities=8% Similarity=0.176 Sum_probs=35.6
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ 77 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 77 (120)
++..+..++...|.... ....+|..+|++...|..|...-+.+.+.....
T Consensus 18 L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~ 67 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEK 67 (104)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 45566666655554432 345689999999999999998877777765443
No 70
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=62.28 E-value=38 Score=22.90 Aligned_cols=31 Identities=16% Similarity=0.247 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
....+|..+|++...|+.++..-+.+.+...
T Consensus 149 s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 149 SIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 4567899999999999999988888777654
No 71
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=60.64 E-value=58 Score=23.12 Aligned_cols=33 Identities=12% Similarity=0.152 Sum_probs=27.1
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKASGQ 77 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 77 (120)
...++|..+|++...|+.+...-|.+.++....
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~ 184 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLARARRRLAALLGG 184 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcc
Confidence 456789999999999999998888887777543
No 72
>PRK10072 putative transcriptional regulator; Provisional
Probab=60.33 E-value=7.2 Score=24.52 Aligned_cols=24 Identities=25% Similarity=0.439 Sum_probs=20.6
Q ss_pred HHHHHHHhCCChhhHHHHHHHHHh
Q psy4625 46 RQELANELGLNEAQIKIWFQNKRA 69 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNrR~ 69 (120)
...||..+|++...|..|...+|.
T Consensus 49 Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 49 IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 567899999999999999987653
No 73
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=59.93 E-value=37 Score=23.03 Aligned_cols=33 Identities=9% Similarity=0.158 Sum_probs=26.9
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKASGQ 77 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 77 (120)
...++|..+|++...|+.+...-|.+.++....
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 178 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQLAD 178 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 356789999999999999998888887776543
No 74
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=59.40 E-value=47 Score=22.32 Aligned_cols=30 Identities=20% Similarity=0.246 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
...++|..+|++...|+.....-|.+.++.
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 356678999999999999998777776653
No 75
>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=58.88 E-value=13 Score=21.16 Aligned_cols=20 Identities=20% Similarity=0.355 Sum_probs=17.4
Q ss_pred HHHHHHHhCCChhhHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFq 65 (120)
..++|..+|++...++.|.+
T Consensus 3 i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35689999999999999975
No 76
>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=58.49 E-value=14 Score=18.78 Aligned_cols=22 Identities=23% Similarity=0.558 Sum_probs=18.5
Q ss_pred HHHHHHHhCCChhhHHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQNK 67 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNr 67 (120)
..++|..+|++...|..|....
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g 24 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 3567899999999999998753
No 77
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.82 E-value=24 Score=21.98 Aligned_cols=40 Identities=28% Similarity=0.309 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHH
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKI 62 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~ 62 (120)
+.++|...-...|+.+--.+....+.+|.+|+.++..|.-
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lek 42 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLEK 42 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHH
Confidence 5667777666666666666667788899999998866553
No 78
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=57.63 E-value=49 Score=21.57 Aligned_cols=28 Identities=18% Similarity=0.261 Sum_probs=21.9
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIK 72 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~k 72 (120)
...++|..+|++...|..+...-|.+.+
T Consensus 129 ~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 129 SLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4667899999999999998876555544
No 79
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=57.38 E-value=50 Score=22.59 Aligned_cols=31 Identities=6% Similarity=0.301 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
...++|..+|+++..|+.+...-|.+.|+..
T Consensus 152 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 152 SSEQICQECDISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999987777766543
No 80
>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=57.34 E-value=52 Score=22.07 Aligned_cols=31 Identities=35% Similarity=0.432 Sum_probs=25.0
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
...++|..+|++...|+.+...-|.+.+...
T Consensus 118 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999987777766654
No 81
>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=57.17 E-value=15 Score=20.73 Aligned_cols=21 Identities=10% Similarity=0.349 Sum_probs=17.7
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
..++|..+|++...++.|-+.
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 356899999999999999753
No 82
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=56.76 E-value=38 Score=23.08 Aligned_cols=31 Identities=19% Similarity=0.297 Sum_probs=25.0
Q ss_pred HHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 44 RRRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 44 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
....++|..+|++...|+.|+..-+.+.++.
T Consensus 158 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 158 LSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3466789999999999999998777776654
No 83
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=56.76 E-value=54 Score=21.58 Aligned_cols=31 Identities=23% Similarity=0.405 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
....+|..+|++...|+.+...-+.+.|+..
T Consensus 129 s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 129 SYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3566899999999999999987777766653
No 84
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=56.11 E-value=56 Score=22.18 Aligned_cols=30 Identities=13% Similarity=0.278 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
...++|..+|++...|+.+...-+.+.|+.
T Consensus 157 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 157 SAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 466789999999999999987766666553
No 85
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=55.90 E-value=55 Score=21.37 Aligned_cols=30 Identities=23% Similarity=0.268 Sum_probs=24.4
Q ss_pred HHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 46 RQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
..++|..+|++...|+.....-+.+.+...
T Consensus 125 ~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 125 VAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999887777766554
No 86
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=55.72 E-value=53 Score=21.74 Aligned_cols=31 Identities=23% Similarity=0.186 Sum_probs=25.3
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
...++|..+|++...|+.|.+.-|.+.++..
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4567889999999999999987777776653
No 87
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=55.57 E-value=41 Score=22.70 Aligned_cols=32 Identities=9% Similarity=0.064 Sum_probs=25.5
Q ss_pred HHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 44 RRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 44 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
..-.++|..+|++...|+++...-|.+.|+.-
T Consensus 155 ~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 155 LSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 34677899999999999999987777766543
No 88
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=53.71 E-value=35 Score=24.30 Aligned_cols=30 Identities=13% Similarity=0.314 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
...++|..+|++...|+.+...-+.+.++.
T Consensus 202 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 202 NLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467789999999999999998888777664
No 89
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=53.11 E-value=53 Score=22.04 Aligned_cols=31 Identities=19% Similarity=0.289 Sum_probs=24.9
Q ss_pred HHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 44 RRRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 44 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
.....+|..+|++...|+.+++.-|.+.+..
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3466789999999999999998777776654
No 90
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=53.07 E-value=68 Score=21.79 Aligned_cols=31 Identities=19% Similarity=0.300 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
....+|..+|++...|+.-+..-|.+.++..
T Consensus 149 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 149 SVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3566789999999999999988777777653
No 91
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=52.83 E-value=12 Score=20.75 Aligned_cols=23 Identities=17% Similarity=0.420 Sum_probs=17.8
Q ss_pred HHHHHHHHhCCChhhHHHHHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQNK 67 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNr 67 (120)
....||..+|++...|..|+.++
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhcc
Confidence 46678999999999999999866
No 92
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=52.51 E-value=69 Score=21.64 Aligned_cols=29 Identities=21% Similarity=0.491 Sum_probs=23.2
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
....+|..+|++...|+.|...-+.+.|.
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 35677899999999999999877666554
No 93
>PRK06930 positive control sigma-like factor; Validated
Probab=52.30 E-value=71 Score=21.98 Aligned_cols=48 Identities=10% Similarity=0.146 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
+++.+..++...|-.+ ..-..+|..+|++...|+.+...-+.+.++..
T Consensus 115 L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l 162 (170)
T PRK06930 115 LTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIARQI 162 (170)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4455555555443222 23556789999999999999988777766543
No 94
>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=51.59 E-value=63 Score=20.80 Aligned_cols=29 Identities=21% Similarity=0.421 Sum_probs=22.3
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
...++|..+|++...|+.+...-+.+.++
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35568899999999999988766665553
No 95
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=51.53 E-value=56 Score=20.53 Aligned_cols=43 Identities=21% Similarity=0.282 Sum_probs=33.3
Q ss_pred CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCC-ChhhHHHHHHH
Q psy4625 20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGL-NEAQIKIWFQN 66 (120)
Q Consensus 20 R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l-~~~~V~~WFqN 66 (120)
+..|+.+....+-..+....+ ....+|..+|+ ...++..|-..
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~~ 48 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRIQ 48 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHHH
Confidence 677999887776666666554 57788999996 99999988753
No 96
>PRK09480 slmA division inhibitor protein; Provisional
Probab=50.86 E-value=19 Score=24.33 Aligned_cols=35 Identities=20% Similarity=0.225 Sum_probs=28.9
Q ss_pred HHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHh
Q psy4625 34 EFTENRYLTERRRQELANELGLNEAQIKIWFQNKRA 69 (120)
Q Consensus 34 ~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~ 69 (120)
.|...+. .......||...|++...+..+|.|+-.
T Consensus 22 l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 22 MLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 3544545 7788999999999999999999999764
No 97
>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=50.78 E-value=21 Score=20.02 Aligned_cols=20 Identities=15% Similarity=0.368 Sum_probs=17.3
Q ss_pred HHHHHHHhCCChhhHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFq 65 (120)
..++|..+|++...++.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35689999999999999985
No 98
>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=50.69 E-value=41 Score=18.38 Aligned_cols=44 Identities=23% Similarity=0.342 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHH
Q psy4625 22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71 (120)
Q Consensus 22 ~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~ 71 (120)
.++..+..+|.....-. ...++|..+++++..|..+..+=+.|.
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHh
Confidence 46777777776544332 356789999999999999887766553
No 99
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=50.57 E-value=43 Score=18.61 Aligned_cols=37 Identities=32% Similarity=0.469 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHH
Q psy4625 26 EQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 26 ~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqN 66 (120)
.|+..|+-.+. +...+.. .||..+|++.+.|+.-..+
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i~~ 42 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDINE 42 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHHHH
Confidence 46777777777 6655544 7899999999999876643
No 100
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=50.16 E-value=76 Score=21.75 Aligned_cols=31 Identities=6% Similarity=0.108 Sum_probs=25.6
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
...++|..+|++...|+.++.--|.+.++..
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999988777777654
No 101
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=49.76 E-value=69 Score=22.06 Aligned_cols=32 Identities=19% Similarity=0.199 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
...++|..+|++...|+.++..-|.+.++...
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 35678999999999999999988888777654
No 102
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=49.42 E-value=46 Score=24.05 Aligned_cols=47 Identities=19% Similarity=0.350 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
+++.+..+|...|-. ......+|..+|++...|+.|...-+.+.|..
T Consensus 206 L~~~~r~vl~l~~~~-----g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 206 LSDREKSIIQCTFIE-----NLSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred CCHHHHHHHHHHHhC-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 344444455444422 22357789999999999999998777766654
No 103
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=49.11 E-value=11 Score=20.05 Aligned_cols=20 Identities=20% Similarity=0.356 Sum_probs=18.1
Q ss_pred HHHHHhCCChhhHHHHHHHH
Q psy4625 48 ELANELGLNEAQIKIWFQNK 67 (120)
Q Consensus 48 ~La~~l~l~~~~V~~WFqNr 67 (120)
.||..+|++...|..|+.+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 47999999999999999876
No 104
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=49.07 E-value=60 Score=23.00 Aligned_cols=31 Identities=23% Similarity=0.375 Sum_probs=24.6
Q ss_pred HHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 44 RRRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 44 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
....++|..+|++...|+.+...-+.+.|+.
T Consensus 199 ~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 199 KTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3466789999999999999987777766654
No 105
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=48.89 E-value=81 Score=21.26 Aligned_cols=30 Identities=20% Similarity=0.227 Sum_probs=24.8
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
...++|..+|++...|++....-|.+.++.
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999998877777664
No 106
>PF13730 HTH_36: Helix-turn-helix domain
Probab=48.78 E-value=32 Score=18.46 Aligned_cols=43 Identities=14% Similarity=0.064 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhCCChhhHHHHHHH
Q psy4625 23 FSGEQLSRLKVEFTE---NRYLTERRRQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WFqN 66 (120)
+++.+..++...+.. ... ..+....||..+|++.+.|+.+...
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~-~~pS~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGG-CFPSQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCC-CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 445554444444322 223 3345788999999999999988753
No 107
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=48.45 E-value=81 Score=21.53 Aligned_cols=32 Identities=9% Similarity=0.265 Sum_probs=26.1
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
...++|..+|++...|+.....-|.+.|+...
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999999887777776643
No 108
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=48.15 E-value=51 Score=23.23 Aligned_cols=45 Identities=22% Similarity=0.310 Sum_probs=29.7
Q ss_pred CHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 24 SGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 24 ~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
+..+..+|...|-. ......+|..+|++...|+.+...-+.+.++
T Consensus 177 ~~~~r~il~l~y~~-----~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 177 SEREQLVLSLYYYE-----ELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred CHHHHHHHHHHHhC-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 44444455444422 2245778999999999999988766666554
No 109
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=48.14 E-value=64 Score=24.55 Aligned_cols=53 Identities=13% Similarity=0.193 Sum_probs=37.7
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
++..+..+|...|.... ........+|..+|++...|+.+...-+.+.|+...
T Consensus 263 L~~~~R~vl~lrygL~~-~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~ 315 (325)
T PRK05657 263 LNDKQREVLARRFGLLG-YEAATLEDVAREIGLTRERVRQIQVEALRRLREILQ 315 (325)
T ss_pred CCHHHHHHHHHHhccCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45555666665553322 233456788999999999999999988888877653
No 110
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=48.08 E-value=76 Score=20.85 Aligned_cols=29 Identities=31% Similarity=0.405 Sum_probs=22.5
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
...++|..+|++...|+.+...-|.+.++
T Consensus 130 s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 130 SYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35677899999999999998766666553
No 111
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=48.07 E-value=80 Score=21.46 Aligned_cols=31 Identities=32% Similarity=0.425 Sum_probs=24.8
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
...++|..+|++...|+..+..-|.+.++..
T Consensus 124 ~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 124 SQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999987777766543
No 112
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=47.27 E-value=87 Score=21.13 Aligned_cols=30 Identities=10% Similarity=0.261 Sum_probs=23.5
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
...++|..+|++...|+.....-+.+.+..
T Consensus 145 s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 145 KQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 356789999999999999998766665543
No 113
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=46.97 E-value=77 Score=22.84 Aligned_cols=46 Identities=22% Similarity=0.367 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
+++.+..++...|-.. ....++|..+|++...|+.+...-+.+.|.
T Consensus 206 L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 206 LSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred CCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3445555555554322 235678999999999999998776666554
No 114
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=46.80 E-value=70 Score=22.96 Aligned_cols=32 Identities=13% Similarity=0.226 Sum_probs=26.4
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
...++|..+|++...|+.....-|.+.|+...
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999888888776643
No 115
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=46.43 E-value=16 Score=22.79 Aligned_cols=41 Identities=17% Similarity=0.294 Sum_probs=21.9
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCChhh
Q psy4625 28 LSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNPLA 82 (120)
Q Consensus 28 ~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~~~ 82 (120)
+.+..-.|+.++||...-... =-.|||.+|++...+-...+
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~--------------aRRnRRRRWR~rq~QI~~ls 54 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ--------------ARRNRRRRWRARQRQIRALS 54 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH--------------HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc--------------cccchhhhHHHHHHHHHHHH
Confidence 344455588999997441111 12588999998876544443
No 116
>PF15063 TC1: Thyroid cancer protein 1
Probab=46.42 E-value=47 Score=20.10 Aligned_cols=37 Identities=16% Similarity=0.204 Sum_probs=29.4
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChh
Q psy4625 22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEA 58 (120)
Q Consensus 22 ~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~ 58 (120)
.|....+..|...|+...-....++..+.-.+.-...
T Consensus 33 IFe~vn~~qlqrLF~~sGD~kAEeRA~iI~~~~~d~e 69 (79)
T PF15063_consen 33 IFENVNLDQLQRLFQKSGDKKAEERARIIWECAQDPE 69 (79)
T ss_pred hhhccCHHHHHHHHHHccchhHHHHHHHHHhhCCCHH
Confidence 4777778889999999999999999888766655443
No 117
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=46.22 E-value=86 Score=21.88 Aligned_cols=32 Identities=19% Similarity=0.363 Sum_probs=25.9
Q ss_pred HHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625 46 RQELANELGLNEAQIKIWFQNKRAKIKKASGQ 77 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 77 (120)
..++|..+|++...|+.+...-|.+.++....
T Consensus 157 ~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~ 188 (203)
T PRK09647 157 YEEIAATLGVKLGTVRSRIHRGRQQLRAALAA 188 (203)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 56678999999999999998877777765443
No 118
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=46.04 E-value=98 Score=21.39 Aligned_cols=35 Identities=17% Similarity=0.166 Sum_probs=27.7
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCC
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKASGQKN 79 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~ 79 (120)
.-.++|..+|++...|+.+...-|.+.++.-....
T Consensus 151 s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 185 (196)
T PRK12535 151 TYEEAAKIADVRVGTIRSRVARARADLIAATATGQ 185 (196)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcccc
Confidence 35678999999999999999887887777655443
No 119
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=45.78 E-value=37 Score=22.63 Aligned_cols=33 Identities=18% Similarity=0.216 Sum_probs=27.1
Q ss_pred HHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 44 RRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 44 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
.....+|..+|++...|+..+..-|.+.++...
T Consensus 137 ~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 137 LPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 346788999999999999999888887776543
No 120
>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=45.77 E-value=84 Score=20.55 Aligned_cols=30 Identities=17% Similarity=0.369 Sum_probs=24.5
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
...++|..+|++...|+.+...-+.+.++.
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 356678999999999999998777776654
No 121
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=45.74 E-value=88 Score=21.28 Aligned_cols=29 Identities=14% Similarity=0.097 Sum_probs=23.7
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
...++|..+|++...|+.+...-|.+.++
T Consensus 148 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35678999999999999999777776665
No 122
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=45.06 E-value=94 Score=20.90 Aligned_cols=31 Identities=16% Similarity=0.262 Sum_probs=25.6
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
...++|..+|++...|+.....-+.+.++..
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999988888877654
No 123
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=44.22 E-value=47 Score=17.20 Aligned_cols=42 Identities=21% Similarity=0.324 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHh
Q psy4625 22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRA 69 (120)
Q Consensus 22 ~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~ 69 (120)
.++..+..++...+ . . .....+|..+|++...|..|...-+.
T Consensus 3 ~l~~~e~~i~~~~~-~-g----~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 3 SLTPREREVLRLLA-E-G----LTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred CCCHHHHHHHHHHH-c-C----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35677777775533 2 2 24567899999999999998874433
No 124
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=43.60 E-value=28 Score=19.89 Aligned_cols=18 Identities=28% Similarity=0.704 Sum_probs=15.4
Q ss_pred HHHHHHHhCCChhhHHHH
Q psy4625 46 RQELANELGLNEAQIKIW 63 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~W 63 (120)
...||..||++..-|..|
T Consensus 12 ~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 12 QSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHh
Confidence 457899999999999999
No 125
>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=43.41 E-value=64 Score=22.71 Aligned_cols=46 Identities=17% Similarity=0.405 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
+++.+..++...|-. ......+|..+|++...|..|...-+.+.++
T Consensus 179 L~~~~r~vl~l~y~~-----~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 179 LPERERRILLLRFFE-----DKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred CCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 444555555554422 2346678999999999999998766555543
No 126
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=43.22 E-value=57 Score=22.51 Aligned_cols=36 Identities=19% Similarity=0.354 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhH
Q psy4625 25 GEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60 (120)
Q Consensus 25 ~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V 60 (120)
..-+.+|...+....|.+......+|..|||+...|
T Consensus 25 sAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v 60 (160)
T COG1905 25 SALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARV 60 (160)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHh
Confidence 455778888898888999999999999999998654
No 127
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=43.20 E-value=97 Score=20.50 Aligned_cols=30 Identities=17% Similarity=0.201 Sum_probs=24.1
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
...++|..+|++...|+.+...-|.+.+..
T Consensus 130 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 130 SYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999998777666544
No 128
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=43.10 E-value=89 Score=21.28 Aligned_cols=30 Identities=30% Similarity=0.505 Sum_probs=23.3
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
...++|..+|++...|+...+.-|.+.++.
T Consensus 149 s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 149 KIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 356789999999999999887666665554
No 129
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=43.01 E-value=28 Score=19.55 Aligned_cols=20 Identities=15% Similarity=0.243 Sum_probs=16.8
Q ss_pred HHHHHHHhCCChhhHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFq 65 (120)
..++|..+|++...|+.|-.
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35678999999999999964
No 130
>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=42.99 E-value=18 Score=19.35 Aligned_cols=22 Identities=32% Similarity=0.474 Sum_probs=18.0
Q ss_pred HHHHHHHhCCChhhHHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQNK 67 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNr 67 (120)
...||..+|++...|..|..+.
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~ 33 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGK 33 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTS
T ss_pred HHHHHHHhCCCcchhHHHhcCC
Confidence 4678999999999999999763
No 131
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=42.98 E-value=45 Score=21.60 Aligned_cols=31 Identities=32% Similarity=0.347 Sum_probs=24.7
Q ss_pred HHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 43 ERRRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 43 ~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
.....++|..+|++...|+++..--|.+.++
T Consensus 121 g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 121 EFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred cCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3457788999999999999998776666554
No 132
>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=42.91 E-value=83 Score=20.12 Aligned_cols=38 Identities=16% Similarity=0.366 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHH
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFq 65 (120)
++-+....+..+|.... ....+|..++++...|..||+
T Consensus 3 YS~DlR~rVl~~~~~g~-----s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 3 YSLDLRQRVLAYIEKGK-----SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred CCHHHHHHHHHHHHccc-----hHHHHHHHhCcHHHHHHHHHH
Confidence 44455555556666543 345578899999999999998
No 133
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=42.74 E-value=98 Score=20.46 Aligned_cols=30 Identities=23% Similarity=0.369 Sum_probs=23.4
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
...++|..+|++...|+.+..--|.+.++.
T Consensus 137 s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356779999999999999887666665553
No 134
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=42.63 E-value=96 Score=20.33 Aligned_cols=29 Identities=28% Similarity=0.284 Sum_probs=21.9
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
....+|..+|++...|+....--|.+.|+
T Consensus 140 s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 140 PIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45678899999999999888655555543
No 135
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=42.43 E-value=1e+02 Score=20.67 Aligned_cols=30 Identities=23% Similarity=0.310 Sum_probs=23.2
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
...++|..+|++...|+.+...-|.+.+..
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 356678999999999999987666665543
No 136
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=42.33 E-value=75 Score=22.89 Aligned_cols=30 Identities=23% Similarity=0.254 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
....+|..+|++...|+.++..-+.+.|..
T Consensus 219 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 219 TLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 457789999999999999998776666543
No 137
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=41.82 E-value=1.1e+02 Score=20.69 Aligned_cols=30 Identities=17% Similarity=0.228 Sum_probs=24.5
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
...++|..+|++...|+.+...-+.+.++.
T Consensus 149 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 149 SVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 466789999999999999998777776654
No 138
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=41.53 E-value=94 Score=22.19 Aligned_cols=51 Identities=10% Similarity=0.171 Sum_probs=35.6
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
++..+..+|...|....+ .......+|..+|++...|+.+...-..+.|..
T Consensus 177 L~~~er~vl~l~ygl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~ 227 (238)
T TIGR02393 177 LTERERKVLRMRYGLLDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRHP 227 (238)
T ss_pred CCHHHHHHHHHHhCCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhh
Confidence 455566666666643222 224577889999999999999988777776654
No 139
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=41.48 E-value=1.1e+02 Score=20.85 Aligned_cols=31 Identities=19% Similarity=0.197 Sum_probs=25.6
Q ss_pred HHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 46 RQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
-.++|..+|++...|+.+...-|.+.++...
T Consensus 135 ~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 135 YEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5567899999999999999888877776644
No 140
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=41.12 E-value=1.1e+02 Score=20.36 Aligned_cols=31 Identities=19% Similarity=0.325 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
...++|..+|++...|+.....-+.+.++..
T Consensus 136 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 136 STAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3567899999999999999877777766654
No 141
>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=40.92 E-value=40 Score=17.11 Aligned_cols=22 Identities=18% Similarity=0.256 Sum_probs=18.0
Q ss_pred HHHHHHHhCCChhhHHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQNK 67 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNr 67 (120)
..++|..+|++...|..|....
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcC
Confidence 4567889999999999998644
No 142
>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=40.78 E-value=56 Score=17.06 Aligned_cols=38 Identities=21% Similarity=0.420 Sum_probs=24.3
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHH
Q psy4625 22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWF 64 (120)
Q Consensus 22 ~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF 64 (120)
.++.++...+...+... .....+|..+|++...|.-++
T Consensus 5 ~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 35555555555555554 346778999999999888765
No 143
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=40.75 E-value=96 Score=19.95 Aligned_cols=26 Identities=8% Similarity=0.247 Sum_probs=21.1
Q ss_pred CHHHHHHHHHHhCCChhhHHHHHHHH
Q psy4625 42 TERRRQELANELGLNEAQIKIWFQNK 67 (120)
Q Consensus 42 ~~~~~~~La~~l~l~~~~V~~WFqNr 67 (120)
.......||..+||++..+.-+|+.-
T Consensus 24 ~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 24 SPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34567888999999999999988754
No 144
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=40.74 E-value=72 Score=23.19 Aligned_cols=32 Identities=19% Similarity=0.273 Sum_probs=25.5
Q ss_pred HHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 44 RRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 44 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
.....+|..+|++...|+.+..--+.+.+...
T Consensus 220 ~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 220 LTQKEAAERLGISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 34677899999999999999987777766553
No 145
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=40.53 E-value=75 Score=23.30 Aligned_cols=46 Identities=11% Similarity=0.322 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
++..+..+|...|- .......+|..+|++...|+.+...-+.+.+.
T Consensus 216 L~~rer~vl~l~y~-----~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 216 LPERERTVLVLRFF-----ESMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred CCHHHHHHHHHHhc-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 34444445555542 22345778999999999999998766666554
No 146
>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=39.98 E-value=23 Score=18.83 Aligned_cols=22 Identities=23% Similarity=0.185 Sum_probs=18.7
Q ss_pred HHHHHHHhCCChhhHHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQNK 67 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNr 67 (120)
...||..+|++...|..|...+
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~ 39 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGK 39 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 5678999999999999998654
No 147
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=39.71 E-value=80 Score=21.50 Aligned_cols=36 Identities=25% Similarity=0.291 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHH
Q psy4625 26 EQLSRLKVEFTENRYLTERRRQELANELGLNEAQIK 61 (120)
Q Consensus 26 ~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~ 61 (120)
.-+.+|...=....|.+......+|..+|++...|.
T Consensus 24 ~li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~ 59 (156)
T PRK05988 24 ALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVH 59 (156)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHH
Confidence 345666666667789999999999999999987643
No 148
>PRK06424 transcription factor; Provisional
Probab=39.56 E-value=38 Score=22.89 Aligned_cols=23 Identities=13% Similarity=0.033 Sum_probs=19.3
Q ss_pred HHHHHHHhCCChhhHHHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQNKR 68 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNrR 68 (120)
...||..+|++...|..|....+
T Consensus 100 Q~eLA~~iGvs~stIskiE~G~~ 122 (144)
T PRK06424 100 QADLAAKIFERKNVIASIERGDL 122 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 56789999999999999987654
No 149
>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=39.22 E-value=31 Score=17.33 Aligned_cols=22 Identities=32% Similarity=0.462 Sum_probs=18.2
Q ss_pred HHHHHHHhCCChhhHHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQNK 67 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNr 67 (120)
...+|..+|++...|..|..+.
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCC
Confidence 3578899999999999998754
No 150
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=39.01 E-value=1e+02 Score=22.61 Aligned_cols=49 Identities=22% Similarity=0.279 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
++..+..+|...|-. -.......+|..+|++...|......-..+.|+.
T Consensus 219 L~~rer~vl~l~y~~---~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~ 267 (270)
T TIGR02392 219 LDARSRRIIEARWLD---DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAA 267 (270)
T ss_pred CCHHHHHHHHHHhcC---CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 455566666666632 1123467889999999999999888777776653
No 151
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=38.96 E-value=1.2e+02 Score=20.58 Aligned_cols=32 Identities=22% Similarity=0.214 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
...++|..+|++...|+.+..--|.+.++...
T Consensus 129 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 129 SYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999999877777666543
No 152
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=38.91 E-value=1.4e+02 Score=21.67 Aligned_cols=31 Identities=6% Similarity=0.317 Sum_probs=26.0
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
...++|..+|++...|+.+...-|.+.++..
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3667899999999999999988887777654
No 153
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=38.50 E-value=56 Score=22.20 Aligned_cols=31 Identities=26% Similarity=0.297 Sum_probs=23.9
Q ss_pred HHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 43 ERRRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 43 ~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
......+|..+|++...|...+.--|.+.++
T Consensus 165 ~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 165 GKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3346778999999999999988766666554
No 154
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=38.44 E-value=37 Score=24.09 Aligned_cols=43 Identities=21% Similarity=0.286 Sum_probs=34.1
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHH
Q psy4625 28 LSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72 (120)
Q Consensus 28 ~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k 72 (120)
+..-...|....|- .....+|...|++...|..+|.++..-..
T Consensus 19 l~aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L~~ 61 (225)
T PRK11552 19 IAAALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDLYL 61 (225)
T ss_pred HHHHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHHHH
Confidence 33444558888877 67888999999999999999999876543
No 155
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=38.15 E-value=1.3e+02 Score=20.69 Aligned_cols=31 Identities=13% Similarity=0.334 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
...++|..+|++...|+.....-|.+.++..
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999987777777654
No 156
>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=38.07 E-value=1.3e+02 Score=20.52 Aligned_cols=32 Identities=13% Similarity=0.319 Sum_probs=25.3
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
....+|..+|++...|+.....-|.+.++...
T Consensus 149 s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~ 180 (188)
T TIGR02943 149 ESDEICQELEISTSNCHVLLYRARLSLRACLS 180 (188)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999998877777666543
No 157
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=38.06 E-value=1.2e+02 Score=19.91 Aligned_cols=30 Identities=17% Similarity=0.428 Sum_probs=23.3
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
...++|..+|++...|+....--+.+.++.
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999877666665554
No 158
>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=37.90 E-value=59 Score=22.16 Aligned_cols=32 Identities=16% Similarity=0.218 Sum_probs=26.5
Q ss_pred HHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 44 RRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 44 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
....++|..+|++...|+.+...-|.+.++..
T Consensus 148 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 148 FAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34677899999999999999988887777654
No 159
>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=37.76 E-value=41 Score=20.78 Aligned_cols=21 Identities=29% Similarity=0.445 Sum_probs=17.7
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
...+|..+|++...++.|...
T Consensus 3 I~e~a~~~gvs~~tLR~ye~~ 23 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYEEI 23 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 356899999999999999753
No 160
>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=37.72 E-value=39 Score=20.97 Aligned_cols=21 Identities=14% Similarity=0.153 Sum_probs=17.8
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
...+|..+|++...++.|...
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDEI 23 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 356799999999999999864
No 161
>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=37.64 E-value=36 Score=20.63 Aligned_cols=20 Identities=10% Similarity=0.218 Sum_probs=17.4
Q ss_pred HHHHHHHhCCChhhHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFq 65 (120)
...+|..+|++...|+.|-.
T Consensus 4 i~e~A~~~gvs~~tLr~ye~ 23 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYER 23 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45689999999999999974
No 162
>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=37.58 E-value=63 Score=16.77 Aligned_cols=22 Identities=32% Similarity=0.601 Sum_probs=18.4
Q ss_pred HHHHHHHHhCCChhhHHHHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqN 66 (120)
....+|..++++...|..|...
T Consensus 17 s~~eia~~l~~s~~tv~~~~~~ 38 (57)
T cd06170 17 TNKEIADILGISEKTVKTHLRN 38 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4567889999999999999863
No 163
>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=37.19 E-value=37 Score=20.56 Aligned_cols=19 Identities=21% Similarity=0.454 Sum_probs=16.5
Q ss_pred HHHHHHHhCCChhhHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWF 64 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WF 64 (120)
..++|..+|++...++.|-
T Consensus 4 i~evA~~~gvs~~tLR~ye 22 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWE 22 (88)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4568999999999999994
No 164
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=36.98 E-value=63 Score=22.01 Aligned_cols=33 Identities=18% Similarity=0.263 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 43 ERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 43 ~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
.....++|..+|++...|+.+...-|.+.++..
T Consensus 155 g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 155 DLELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 345678899999999999999887777766654
No 165
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=36.78 E-value=1.3e+02 Score=20.32 Aligned_cols=31 Identities=13% Similarity=0.329 Sum_probs=25.4
Q ss_pred HHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 46 RQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
-.++|..+|++...|++....-|.+.++...
T Consensus 150 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (191)
T PRK12520 150 TEEICQELQITATNAWVLLYRARMRLRECLD 180 (191)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5678999999999999999877777776543
No 166
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=36.69 E-value=92 Score=20.98 Aligned_cols=36 Identities=14% Similarity=0.337 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHH
Q psy4625 26 EQLSRLKVEFTENRYLTERRRQELANELGLNEAQIK 61 (120)
Q Consensus 26 ~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~ 61 (120)
.-+.+|...=....|.+......+|..++++...|.
T Consensus 23 ~ll~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v~ 58 (154)
T PRK07539 23 AVIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVE 58 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 345566666666789999999999999999987643
No 167
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=36.50 E-value=1.3e+02 Score=20.02 Aligned_cols=30 Identities=17% Similarity=0.320 Sum_probs=23.8
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
.-.++|..+|++...|+.+...-+.+.+..
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356679999999999999998777666543
No 168
>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=36.37 E-value=41 Score=22.29 Aligned_cols=22 Identities=18% Similarity=0.215 Sum_probs=18.5
Q ss_pred HHHHHHHhCCChhhHHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQNK 67 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNr 67 (120)
...+|..+|++...++.|...-
T Consensus 3 I~e~a~~~gvs~~TLR~Ye~~G 24 (134)
T cd04779 3 IGQLAHLAGVSKRTIDYYTNLG 24 (134)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3568999999999999999643
No 169
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=35.85 E-value=76 Score=21.11 Aligned_cols=31 Identities=19% Similarity=0.298 Sum_probs=25.1
Q ss_pred HHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 44 RRRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 44 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
.....+|..+|++...|+.+...-+.+.++.
T Consensus 143 ~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 143 YTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred CCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 4567789999999999999998777776654
No 170
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=35.84 E-value=1.5e+02 Score=20.66 Aligned_cols=30 Identities=10% Similarity=0.366 Sum_probs=25.2
Q ss_pred HHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 46 RQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
..++|..+|++...|+.....-|.+.++..
T Consensus 167 ~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 167 TNEICHAVDLSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999988787777654
No 171
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=35.73 E-value=1.6e+02 Score=21.72 Aligned_cols=52 Identities=17% Similarity=0.180 Sum_probs=33.6
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
++..+..+|...|... +.......++|..+|++...|+.+...-+.+.|+..
T Consensus 223 Lp~~~R~Vl~l~ygL~-~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l 274 (285)
T TIGR02394 223 LNERQREVLARRFGLL-GYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL 274 (285)
T ss_pred CCHHHHHHHHHHhCCC-CCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3344444554444111 122244677899999999999999988777777654
No 172
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=35.59 E-value=1.1e+02 Score=20.62 Aligned_cols=29 Identities=28% Similarity=0.387 Sum_probs=21.8
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
.-.++|..+|++...|+.....-|.+.+.
T Consensus 155 s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 155 TYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred CHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 45677899999999999877666655554
No 173
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=35.26 E-value=94 Score=22.66 Aligned_cols=47 Identities=15% Similarity=0.263 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
+++.+..+|...|-. ......+|..+|++...|+.....-+.+.|+.
T Consensus 213 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 213 LPEREKKVLILYYYE-----DLTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 344444444444422 23367789999999999998887766666654
No 174
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=35.08 E-value=81 Score=21.00 Aligned_cols=35 Identities=29% Similarity=0.383 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHH
Q psy4625 27 QLSRLKVEFTENRYLTERRRQELANELGLNEAQIK 61 (120)
Q Consensus 27 q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~ 61 (120)
-+.+|...=....|.+......+|..++|+..+|.
T Consensus 15 ll~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~ 49 (145)
T PF01257_consen 15 LLPILHEVQEEYGYIPEEALEEIAEALGIPPAEVY 49 (145)
T ss_dssp HHHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHHH
Confidence 35666666666779999999999999999987654
No 175
>PF12728 HTH_17: Helix-turn-helix domain
Probab=35.06 E-value=53 Score=17.31 Aligned_cols=22 Identities=23% Similarity=0.502 Sum_probs=17.9
Q ss_pred HHHHHHHhCCChhhHHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQNK 67 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNr 67 (120)
..++|..||++...|..|.+..
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 3567888999999999998654
No 176
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=34.81 E-value=52 Score=17.59 Aligned_cols=34 Identities=26% Similarity=0.312 Sum_probs=21.5
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHH
Q psy4625 29 SRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 29 ~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFq 65 (120)
.+|...+....+ .....||..++++.+.|..-..
T Consensus 4 ~il~~L~~~~~~---it~~eLa~~l~vS~rTi~~~i~ 37 (55)
T PF08279_consen 4 QILKLLLESKEP---ITAKELAEELGVSRRTIRRDIK 37 (55)
T ss_dssp HHHHHHHHTTTS---BEHHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHcCCC---cCHHHHHHHhCCCHHHHHHHHH
Confidence 344444444443 3466789999999998886554
No 177
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=34.67 E-value=1.5e+02 Score=20.22 Aligned_cols=30 Identities=13% Similarity=0.227 Sum_probs=23.6
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
.-.++|..+|++...|+.-...-+.+.++.
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 356678999999999999887777666654
No 178
>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=34.57 E-value=33 Score=19.73 Aligned_cols=23 Identities=22% Similarity=0.413 Sum_probs=19.3
Q ss_pred HHHHHHHhCCChhhHHHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQNKR 68 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNrR 68 (120)
...||..+|++...|..|+..++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46789999999999999996543
No 179
>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=34.50 E-value=26 Score=24.40 Aligned_cols=32 Identities=16% Similarity=0.423 Sum_probs=27.0
Q ss_pred HHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 44 RRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 44 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
..+.+|+.-++++..+|-.|..|-+...+...
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~ 46 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAKP 46 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccccc
Confidence 45778999999999999999999887766554
No 180
>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=34.33 E-value=51 Score=20.25 Aligned_cols=21 Identities=14% Similarity=0.135 Sum_probs=18.2
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
...+|..+|++...++.|.+.
T Consensus 3 i~eva~~~gvs~~tLRyye~~ 23 (96)
T cd04768 3 IGEFAKLAGVSIRTLRHYDDI 23 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456899999999999999964
No 181
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=34.07 E-value=1.5e+02 Score=19.99 Aligned_cols=34 Identities=24% Similarity=0.487 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCC
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKASGQK 78 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~ 78 (120)
...++|..+|++...|+.....-|.+.++.-...
T Consensus 140 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~ 173 (185)
T PRK12542 140 TYQEISSVMGITEANVRKQFERARKRVQNMIGGI 173 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence 3567899999999999999987777777655433
No 182
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=33.99 E-value=1.1e+02 Score=20.44 Aligned_cols=35 Identities=14% Similarity=0.248 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhH
Q psy4625 26 EQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60 (120)
Q Consensus 26 ~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V 60 (120)
.-+.+|...=....|.+......+|..+||+...|
T Consensus 17 ~li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v 51 (148)
T TIGR01958 17 AIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWV 51 (148)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHH
Confidence 34556655556667999999999999999998654
No 183
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=33.90 E-value=1.2e+02 Score=20.20 Aligned_cols=29 Identities=14% Similarity=0.314 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
....+|..+|++...|+.=...-|.+.++
T Consensus 158 s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 158 SFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45677889999999988776665655554
No 184
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=33.65 E-value=1.4e+02 Score=19.85 Aligned_cols=28 Identities=18% Similarity=0.334 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIK 72 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~k 72 (120)
...++|..+|++...|+++...-+.+.+
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 137 TYSEIAHKLGVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4667899999999999999876555544
No 185
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=33.62 E-value=1.1e+02 Score=22.26 Aligned_cols=30 Identities=17% Similarity=0.305 Sum_probs=23.7
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
...++|..+|++...|+.+...-+.+.|+.
T Consensus 223 t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 223 VLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467789999999999999887666665554
No 186
>PRK10403 transcriptional regulator NarP; Provisional
Probab=33.60 E-value=1e+02 Score=20.31 Aligned_cols=44 Identities=18% Similarity=0.282 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHH
Q psy4625 22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71 (120)
Q Consensus 22 ~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~ 71 (120)
.++..+..+|...... .....+|..++++++.|+...++=+.|.
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl 196 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKL 196 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 4788888888755432 3356778999999999999988766653
No 187
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=33.46 E-value=76 Score=21.75 Aligned_cols=32 Identities=28% Similarity=0.289 Sum_probs=25.3
Q ss_pred HHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 44 RRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 44 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
....++|..+|++...|++.+..-|.+.++..
T Consensus 171 ~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 171 KSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 44667899999999999998887777766653
No 188
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=33.16 E-value=80 Score=21.45 Aligned_cols=30 Identities=17% Similarity=0.312 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
...++|..+|++...|+.+...-+.+.++.
T Consensus 152 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 152 EFQEIADIMHMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467789999999999999998777776654
No 189
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=32.96 E-value=1.7e+02 Score=21.45 Aligned_cols=29 Identities=21% Similarity=0.312 Sum_probs=23.7
Q ss_pred HHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 46 RQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
-.++|..+|+++..|+..++.-|.+.+..
T Consensus 127 ~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 127 YEEIASIVGKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 45678899999999999998777776654
No 190
>PHA01976 helix-turn-helix protein
Probab=32.63 E-value=53 Score=18.24 Aligned_cols=22 Identities=23% Similarity=0.289 Sum_probs=18.5
Q ss_pred HHHHHHHhCCChhhHHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQNK 67 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNr 67 (120)
...||..+|++...|..|....
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~ 39 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADK 39 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCC
Confidence 5678999999999999998653
No 191
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=32.59 E-value=1.5e+02 Score=19.44 Aligned_cols=25 Identities=28% Similarity=0.487 Sum_probs=19.5
Q ss_pred HHHHHHHhCCChhhHHHHHHHHHhH
Q psy4625 46 RQELANELGLNEAQIKIWFQNKRAK 70 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNrR~k 70 (120)
-.++|..+|++...|+.+...-+.+
T Consensus 132 ~~EIA~~l~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 132 YGEIATELGISLATVKRYLNKAAMR 156 (161)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 5667889999999999988655444
No 192
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=32.53 E-value=82 Score=21.38 Aligned_cols=31 Identities=16% Similarity=0.191 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
...++|..+|++...|+.....-|.+-|+.-
T Consensus 156 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 156 SYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999987777766643
No 193
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=32.47 E-value=41 Score=18.94 Aligned_cols=41 Identities=15% Similarity=0.211 Sum_probs=29.2
Q ss_pred CHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHH
Q psy4625 24 SGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWF 64 (120)
Q Consensus 24 ~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF 64 (120)
+...-+.|+..|....--.......||..+++++..|..-+
T Consensus 3 t~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml 43 (60)
T PF01325_consen 3 TESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEML 43 (60)
T ss_dssp SCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHH
T ss_pred CcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHH
Confidence 44556788888877654445567788999999998887655
No 194
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=32.30 E-value=62 Score=17.01 Aligned_cols=21 Identities=24% Similarity=0.453 Sum_probs=17.8
Q ss_pred HHHHHHHHhCCChhhHHHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFq 65 (120)
....+|..+|++...|..+|.
T Consensus 29 s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 29 SFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 356789999999999999885
No 195
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=32.11 E-value=1.3e+02 Score=20.79 Aligned_cols=33 Identities=18% Similarity=0.128 Sum_probs=25.2
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhH
Q psy4625 28 LSRLKVEFTENRYLTERRRQELANELGLNEAQI 60 (120)
Q Consensus 28 ~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V 60 (120)
+.+|...=....|.+......+|..+||+...|
T Consensus 39 i~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V 71 (169)
T PRK07571 39 IEVLHKAQELFGYLERDLLLYVARQLKLPLSRV 71 (169)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHH
Confidence 445555445667999999999999999998654
No 196
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=32.10 E-value=1.4e+02 Score=22.21 Aligned_cols=50 Identities=14% Similarity=0.214 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
++..+..+|...|- +-.......+|..+|++...|+.+-..-..+.|...
T Consensus 228 L~~rer~vl~lr~~---~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l 277 (289)
T PRK07500 228 LNERELRIIRERRL---REDGATLEALGEELGISKERVRQIEARALEKLRRAL 277 (289)
T ss_pred CCHHHHHHHHHHhc---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 55556666666652 113345778899999999999999887777766543
No 197
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=31.93 E-value=59 Score=16.00 Aligned_cols=22 Identities=27% Similarity=0.444 Sum_probs=17.7
Q ss_pred HHHHHHHhCCChhhHHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQNK 67 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNr 67 (120)
...+|..+|++...|..|..++
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 4578899999999999887543
No 198
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=31.89 E-value=1.6e+02 Score=20.74 Aligned_cols=44 Identities=16% Similarity=0.320 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHH
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~ 71 (120)
++..+..++...|.. ......+|..+|++...|..+-..-..+.
T Consensus 184 L~~~e~~i~~~~~~~-----~~t~~eIA~~lgis~~~V~~~~~~al~~L 227 (231)
T TIGR02885 184 LDERERQIIMLRYFK-----DKTQTEVANMLGISQVQVSRLEKKVLKKM 227 (231)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 344455555555432 23577789999999999988765444443
No 199
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=31.87 E-value=43 Score=18.38 Aligned_cols=18 Identities=44% Similarity=0.656 Sum_probs=13.4
Q ss_pred HHHHHHHHhCCChhhHHH
Q psy4625 45 RRQELANELGLNEAQIKI 62 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~ 62 (120)
.-..||..+|++..||+-
T Consensus 30 SS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 30 SSQELAEALGITPAQVRK 47 (50)
T ss_dssp -HHHHHHHHTS-HHHHHH
T ss_pred CHHHHHHHHCCCHHHhcc
Confidence 356789999999999874
No 200
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=31.73 E-value=87 Score=20.96 Aligned_cols=30 Identities=20% Similarity=0.323 Sum_probs=24.1
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
....+|..+|++...|......-|.+.++.
T Consensus 154 s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 154 SLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999888777776654
No 201
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=31.52 E-value=68 Score=21.71 Aligned_cols=41 Identities=10% Similarity=0.079 Sum_probs=31.7
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhH
Q psy4625 29 SRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAK 70 (120)
Q Consensus 29 ~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k 70 (120)
..-...|....|.. .....+|...|++...+..+|.++..-
T Consensus 15 ~aA~~lf~e~G~~~-tSi~~Ia~~aGvsk~~lY~~F~sK~~L 55 (192)
T PRK14996 15 QAAMRVALAEGFAA-MTVRRIASEAQVAAGQVHHHFSSAGEL 55 (192)
T ss_pred HHHHHHHHhcChhh-ccHHHHHHHhCCCcHHHHHHcCCHHHH
Confidence 34444577777744 567888999999999999999987653
No 202
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=31.37 E-value=1.6e+02 Score=19.54 Aligned_cols=29 Identities=10% Similarity=0.275 Sum_probs=23.1
Q ss_pred HHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 46 RQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
-.++|..+|++...|+.....-+.+.++.
T Consensus 138 ~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 138 YKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 56679999999999999987666665554
No 203
>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=31.36 E-value=52 Score=20.31 Aligned_cols=20 Identities=30% Similarity=0.504 Sum_probs=17.2
Q ss_pred HHHHHHHhCCChhhHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFq 65 (120)
...+|..+|++...|+.|=.
T Consensus 3 I~eva~~~gvs~~tlR~Ye~ 22 (95)
T cd04780 3 MSELSKRSGVSVATIKYYLR 22 (95)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35689999999999999975
No 204
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=31.26 E-value=1.3e+02 Score=21.66 Aligned_cols=47 Identities=19% Similarity=0.360 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 22 ~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
.++..+..++...|-.. .....+|..+|++...|...-..-..+.++
T Consensus 209 ~L~~~er~vi~~~~~~~-----~t~~eIA~~lgis~~~V~~~~~~al~kLr~ 255 (258)
T PRK08215 209 KLNDREKLILNLRFFQG-----KTQMEVAEEIGISQAQVSRLEKAALKHMRK 255 (258)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35556666666666322 346678999999999998877655555443
No 205
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=30.75 E-value=1.7e+02 Score=19.65 Aligned_cols=30 Identities=27% Similarity=0.437 Sum_probs=23.6
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
....+|..+|++...|+.+..--|.+.+..
T Consensus 145 s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~ 174 (179)
T PRK09415 145 SIKEIAEVTGVNENTVKTRLKKAKELLKKG 174 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356788999999999999988767666543
No 206
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=30.70 E-value=65 Score=18.49 Aligned_cols=22 Identities=27% Similarity=0.578 Sum_probs=17.6
Q ss_pred HHHHHHHHhCCChhhHHHHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqN 66 (120)
...++|..+||+.-+++.|...
T Consensus 17 ~T~eiA~~~gls~~~aR~yL~~ 38 (62)
T PF04703_consen 17 KTREIADALGLSIYQARYYLEK 38 (62)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHH
T ss_pred CHHHHHHHhCCCHHHHHHHHHH
Confidence 3457899999999999999864
No 207
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=30.57 E-value=71 Score=17.89 Aligned_cols=19 Identities=21% Similarity=0.361 Sum_probs=12.8
Q ss_pred HHHHHHHHHHhCCChhhHH
Q psy4625 43 ERRRQELANELGLNEAQIK 61 (120)
Q Consensus 43 ~~~~~~La~~l~l~~~~V~ 61 (120)
..+...++..+|+++.+++
T Consensus 20 ~~ev~ywa~~~gvt~~~L~ 38 (57)
T PF12244_consen 20 PYEVRYWAKRFGVTEEQLR 38 (57)
T ss_pred HHHHHHHHHHHCcCHHHHH
Confidence 3556667777777776654
No 208
>PRK05572 sporulation sigma factor SigF; Validated
Probab=30.35 E-value=1.4e+02 Score=21.51 Aligned_cols=46 Identities=13% Similarity=0.291 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
++..+..++..+|.. ......+|..+|++...|..+-..-..+.++
T Consensus 203 L~~~~~~v~~l~~~~-----~~s~~eIA~~lgis~~~V~~~~~ral~kLr~ 248 (252)
T PRK05572 203 LDERERLIVYLRYFK-----DKTQSEVAKRLGISQVQVSRLEKKILKQMKE 248 (252)
T ss_pred CCHHHHHHHHHHHhC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 555556666665532 2346778999999999998887665555544
No 209
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=30.19 E-value=1.8e+02 Score=21.48 Aligned_cols=31 Identities=26% Similarity=0.307 Sum_probs=25.0
Q ss_pred HHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 46 RQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
..++|..+|++...|+.....-|.+.|+...
T Consensus 161 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 161 AAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 5678999999999999999877777666543
No 210
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=30.07 E-value=1.7e+02 Score=20.67 Aligned_cols=31 Identities=19% Similarity=0.313 Sum_probs=22.8
Q ss_pred HHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 44 RRRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 44 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
....++|..+|++...|..+-..-+.+.++.
T Consensus 196 ~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 196 KTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4567789999999999998865555554443
No 211
>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=29.77 E-value=67 Score=19.74 Aligned_cols=21 Identities=14% Similarity=0.164 Sum_probs=17.8
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
...+|..+|++...++.|...
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (97)
T cd04782 3 TGEFAKLCGISKQTLFHYDKI 23 (97)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 356899999999999999853
No 212
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=29.66 E-value=46 Score=24.88 Aligned_cols=26 Identities=27% Similarity=0.541 Sum_probs=21.1
Q ss_pred HHHHHHHHHhCCChhhHHHHHHHHHhHH
Q psy4625 44 RRRQELANELGLNEAQIKIWFQNKRAKI 71 (120)
Q Consensus 44 ~~~~~La~~l~l~~~~V~~WFqNrR~k~ 71 (120)
-...+||..+||++.+|+.|=+ |..|
T Consensus 20 mk~~dIAeklGvspntiksWKr--r~gW 45 (279)
T COG5484 20 MKLKDIAEKLGVSPNTIKSWKR--RDGW 45 (279)
T ss_pred ccHHHHHHHhCCChHHHHHHHH--hcCC
Confidence 4456789999999999999974 5555
No 213
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=29.51 E-value=1.7e+02 Score=19.34 Aligned_cols=28 Identities=14% Similarity=0.188 Sum_probs=21.9
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIK 72 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~k 72 (120)
.-.++|..+|++...|+.+...-+...+
T Consensus 136 s~~EIA~~l~is~~tV~~~l~ra~~~~~ 163 (168)
T PRK12525 136 TYVEIGERLGVSLSRIHQYMVEAFKCCY 163 (168)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3567899999999999998876665544
No 214
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=29.40 E-value=2.1e+02 Score=21.02 Aligned_cols=29 Identities=24% Similarity=0.321 Sum_probs=23.8
Q ss_pred HHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 46 RQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
..++|..+|++...|+...+.-|.+.+..
T Consensus 134 ~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~ 162 (293)
T PRK09636 134 FDEIASTLGRSPAACRQLASRARKHVRAA 162 (293)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 45678999999999999998777776654
No 215
>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=29.35 E-value=58 Score=20.22 Aligned_cols=20 Identities=5% Similarity=0.283 Sum_probs=17.4
Q ss_pred HHHHHHHhCCChhhHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFq 65 (120)
..++|..+|++...++.|-+
T Consensus 4 i~eva~~~gvs~~tLR~ye~ 23 (102)
T cd04775 4 IGQMSRKFGVSRSTLLYYES 23 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45689999999999999985
No 216
>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=28.98 E-value=71 Score=19.59 Aligned_cols=21 Identities=24% Similarity=0.227 Sum_probs=17.8
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
...+|..+|++...++.|-..
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (96)
T cd04788 3 IGELARRTGLSVRTLHHYDHI 23 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 356899999999999999853
No 217
>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=28.79 E-value=61 Score=19.72 Aligned_cols=20 Identities=20% Similarity=0.333 Sum_probs=16.9
Q ss_pred HHHHHHHhCCChhhHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFq 65 (120)
..++|..+|++...|+.|-.
T Consensus 3 ~~eva~~~gi~~~tlr~~~~ 22 (100)
T cd00592 3 IGEVAKLLGVSVRTLRYYEE 22 (100)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35678999999999999964
No 218
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=28.68 E-value=1.2e+02 Score=17.34 Aligned_cols=40 Identities=25% Similarity=0.382 Sum_probs=23.9
Q ss_pred CCHHHHHHH---HHHHHhCCCCCHHHHHHHHHHhCCC-hhhHHHHH
Q psy4625 23 FSGEQLSRL---KVEFTENRYLTERRRQELANELGLN-EAQIKIWF 64 (120)
Q Consensus 23 ~~~~q~~~L---~~~F~~~~~p~~~~~~~La~~l~l~-~~~V~~WF 64 (120)
++..|..+| ..+...+.||. ...+||..+|+. ...|..-.
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~P--t~rEIa~~~g~~S~~tv~~~L 47 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPP--TVREIAEALGLKSTSTVQRHL 47 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSSSHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHcCCCC--CHHHHHHHhCCCChHHHHHHH
Confidence 455565555 44566677763 567889999997 66666544
No 219
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=28.64 E-value=34 Score=19.51 Aligned_cols=20 Identities=30% Similarity=0.694 Sum_probs=15.2
Q ss_pred HHHHHHHhCCChhhHH-HHHH
Q psy4625 46 RQELANELGLNEAQIK-IWFQ 65 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~-~WFq 65 (120)
...||..+|++...|. .|..
T Consensus 15 ~~~lA~~lgis~st~s~~~~~ 35 (66)
T PF07022_consen 15 DKELAERLGISKSTLSNNWKK 35 (66)
T ss_dssp CHHHHCCTT--HHHHH-HHHH
T ss_pred HHHHHHHhCcCHHHhhHHHHh
Confidence 4578999999999999 8885
No 220
>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=28.30 E-value=63 Score=20.10 Aligned_cols=21 Identities=19% Similarity=0.306 Sum_probs=17.8
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
...+|..+|++...++.|-..
T Consensus 4 i~eva~~~gvs~~tlR~ye~~ 24 (102)
T cd04789 4 ISELAEKAGISRSTLLYYEKL 24 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456899999999999999864
No 221
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=28.29 E-value=1.1e+02 Score=21.68 Aligned_cols=31 Identities=23% Similarity=0.329 Sum_probs=24.4
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
...++|..+|++...|+.+...-+.+.|+..
T Consensus 200 s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l 230 (234)
T TIGR02835 200 TQKEVADMLGISQSYISRLEKRILKRLKKEI 230 (234)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 4567788999999999999877677766543
No 222
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=28.24 E-value=1.4e+02 Score=17.94 Aligned_cols=44 Identities=16% Similarity=0.223 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHHh-----CCCCCHHHHHHHHHHhCCChhhHHHHHH
Q psy4625 22 AFSGEQLSRLKVEFTE-----NRYLTERRRQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 22 ~~~~~q~~~L~~~F~~-----~~~p~~~~~~~La~~l~l~~~~V~~WFq 65 (120)
.++.+++..+...|.. ..+.+..+...+...+|++...|..+|.
T Consensus 3 ~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 3 AISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3677888899988865 2357777777766668888888887775
No 223
>PHA02955 hypothetical protein; Provisional
Probab=28.07 E-value=68 Score=23.22 Aligned_cols=46 Identities=17% Similarity=0.255 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHhC-CCCCHHHHHHHHHHhCCChhhHHHHHHHHHhH
Q psy4625 25 GEQLSRLKVEFTEN-RYLTERRRQELANELGLNEAQIKIWFQNKRAK 70 (120)
Q Consensus 25 ~~q~~~L~~~F~~~-~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k 70 (120)
..++..|.+.|... ...+..++..++.++|+....|..||.+.-.+
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~~q 106 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDLQL 106 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchhhh
Confidence 45677777777664 46777889999999999987788899775443
No 224
>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=28.00 E-value=63 Score=21.01 Aligned_cols=22 Identities=14% Similarity=0.285 Sum_probs=18.7
Q ss_pred HHHHHHHHhCCChhhHHHHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqN 66 (120)
.+..+|..+||+...|+.|-+.
T Consensus 5 tI~elA~~~gvs~~tlR~Ye~~ 26 (120)
T TIGR02054 5 TISRLAEDAGVSVHVVRDYLLR 26 (120)
T ss_pred cHHHHHHHHCcCHHHHHHHHHC
Confidence 3567899999999999999754
No 225
>PF13551 HTH_29: Winged helix-turn helix
Probab=27.77 E-value=1.5e+02 Score=17.94 Aligned_cols=45 Identities=24% Similarity=0.255 Sum_probs=30.6
Q ss_pred CCCCHHHHHHHHHHHHhCC-----CCCHHHHHH-H-HHHh--CCChhhHHHHHH
Q psy4625 21 TAFSGEQLSRLKVEFTENR-----YLTERRRQE-L-ANEL--GLNEAQIKIWFQ 65 (120)
Q Consensus 21 ~~~~~~q~~~L~~~F~~~~-----~p~~~~~~~-L-a~~l--~l~~~~V~~WFq 65 (120)
..++.++...|...+...+ ..+...... | .... .++...|..|++
T Consensus 56 ~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 56 KRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 3389999999999999876 344444444 3 3333 467778888875
No 226
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=27.76 E-value=1.6e+02 Score=19.34 Aligned_cols=44 Identities=18% Similarity=0.197 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHH
Q psy4625 22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71 (120)
Q Consensus 22 ~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~ 71 (120)
.+++.+..+|.....- .....+|..++++.+.|+...++=+.|.
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEKL 180 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 4777777777665542 2567788899999999998887665553
No 227
>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=27.74 E-value=75 Score=19.97 Aligned_cols=21 Identities=29% Similarity=0.526 Sum_probs=17.9
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
..++|..+|++...|+.|...
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (108)
T cd04773 3 IGELAHLLGVPPSTLRHWEKE 23 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456899999999999999764
No 228
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=27.65 E-value=93 Score=20.02 Aligned_cols=33 Identities=21% Similarity=0.118 Sum_probs=23.3
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHH
Q psy4625 28 LSRLKVEFTENRYLTERRRQELANELGLNEAQIKI 62 (120)
Q Consensus 28 ~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~ 62 (120)
...|...|. ..+......+||..+.++.+.++.
T Consensus 6 y~~L~~~~~--~~~~~vtl~elA~~l~cS~Rn~r~ 38 (115)
T PF12793_consen 6 YQRLWQHYG--GQPVEVTLDELAELLFCSRRNART 38 (115)
T ss_pred HHHHHHHcC--CCCcceeHHHHHHHhCCCHHHHHH
Confidence 344555555 456667788999999999976654
No 229
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=27.50 E-value=46 Score=21.69 Aligned_cols=23 Identities=17% Similarity=0.460 Sum_probs=20.1
Q ss_pred HHHHHHHhCCChhhHHHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQNKR 68 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNrR 68 (120)
...||..+|++...|..|..+++
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~ 43 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDET 43 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46789999999999999998764
No 230
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=27.41 E-value=85 Score=20.33 Aligned_cols=26 Identities=31% Similarity=0.475 Sum_probs=22.1
Q ss_pred CCCHHHHHHHHHHhCCChhhHHHHHH
Q psy4625 40 YLTERRRQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 40 ~p~~~~~~~La~~l~l~~~~V~~WFq 65 (120)
-++...+..||..+|++...|.-|-.
T Consensus 26 ~~~~~~r~~La~~~~i~~~~l~~w~~ 51 (122)
T PF14229_consen 26 GDTPLGRKALAKKLGISERNLLKWVN 51 (122)
T ss_pred CCCHHHHHHHHHhcCCCHHHHHHHHh
Confidence 35667788899999999999999964
No 231
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=27.06 E-value=1.2e+02 Score=20.51 Aligned_cols=32 Identities=22% Similarity=0.384 Sum_probs=26.0
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
.-.++|..+|++...|+.+..--|.+.+....
T Consensus 145 s~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 145 SYEEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 35667899999999999999888887776543
No 232
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=26.85 E-value=91 Score=15.26 Aligned_cols=20 Identities=25% Similarity=0.413 Sum_probs=13.9
Q ss_pred HHHHHHHhCCChhhHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFq 65 (120)
...-|...|++..+|+..+.
T Consensus 8 Li~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 8 LIKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 34458899999999998774
No 233
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=26.83 E-value=1.5e+02 Score=21.09 Aligned_cols=46 Identities=22% Similarity=0.304 Sum_probs=33.3
Q ss_pred CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHH
Q psy4625 21 TAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72 (120)
Q Consensus 21 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k 72 (120)
..++..+..+|.-.. .. ..-.++|..+|+++..|+.+..+-+.|..
T Consensus 170 ~~Lt~re~evl~~~a--~G----~t~~eIa~~l~is~~Tv~~~l~~~~~kl~ 215 (232)
T TIGR03541 170 GVLSEREREVLAWTA--LG----RRQADIAAILGISERTVENHLRSARRKLG 215 (232)
T ss_pred ccCCHHHHHHHHHHH--CC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence 357777777776643 11 33556788899999999999988776654
No 234
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=26.61 E-value=2.1e+02 Score=21.19 Aligned_cols=49 Identities=20% Similarity=0.325 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
++..+..+|...|-.. .......+|..+|++...|+.+-..-..+.|..
T Consensus 231 L~~rEr~VL~lry~~~---~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~ 279 (284)
T PRK06596 231 LDERSRDIIEARWLDD---DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAA 279 (284)
T ss_pred CCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4444555666656321 234467889999999999998776555555443
No 235
>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=26.48 E-value=87 Score=19.45 Aligned_cols=21 Identities=29% Similarity=0.469 Sum_probs=17.6
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
...+|..+|++...++.|-..
T Consensus 3 i~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 3 IGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred HHHHHHHHCcCHHHHHHHHHH
Confidence 346799999999999999754
No 236
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=26.37 E-value=84 Score=21.55 Aligned_cols=42 Identities=14% Similarity=0.205 Sum_probs=31.3
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhH
Q psy4625 28 LSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAK 70 (120)
Q Consensus 28 ~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k 70 (120)
++.....|....|.. .....||...|++...+..+|.++-.-
T Consensus 17 l~aa~~lf~~~G~~~-~ti~~Ia~~agvsk~t~Y~~F~sKe~L 58 (213)
T PRK09975 17 IETAIAQFALRGVSN-TTLNDIADAANVTRGAIYWHFENKTQL 58 (213)
T ss_pred HHHHHHHHHHcCccc-CCHHHHHHHcCCCHHHHHHHcCCHHHH
Confidence 334444576776655 457778999999999999999988653
No 237
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=26.31 E-value=2.1e+02 Score=19.37 Aligned_cols=32 Identities=19% Similarity=0.119 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKASG 76 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 76 (120)
...++|..+|++...|+.....-|.+.++...
T Consensus 129 s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 129 SYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999998877777666544
No 238
>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=26.30 E-value=70 Score=20.14 Aligned_cols=20 Identities=20% Similarity=0.424 Sum_probs=17.1
Q ss_pred HHHHHHHhCCChhhHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFq 65 (120)
...+|..+|++...++.|-+
T Consensus 3 i~e~a~~~gvs~~tlr~ye~ 22 (113)
T cd01109 3 IKEVAEKTGLSADTLRYYEK 22 (113)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45689999999999999965
No 239
>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=26.23 E-value=71 Score=20.03 Aligned_cols=21 Identities=14% Similarity=0.091 Sum_probs=17.9
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
...+|..+|++...++.|-..
T Consensus 3 i~eva~~~gis~~tlR~ye~~ 23 (108)
T cd01107 3 IGEFAKLSNLSIKALRYYDKI 23 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 456899999999999999863
No 240
>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=26.21 E-value=81 Score=20.59 Aligned_cols=21 Identities=19% Similarity=0.436 Sum_probs=18.1
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
...+|..+|++...++.|.+.
T Consensus 4 I~eVA~~~GVs~~TLR~wE~~ 24 (120)
T cd04767 4 IGVVAELLNIHPETLRIWERH 24 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456899999999999999864
No 241
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=26.06 E-value=2.2e+02 Score=19.43 Aligned_cols=29 Identities=24% Similarity=0.506 Sum_probs=22.7
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
...++|..+|+++..|+..++.-|...++
T Consensus 153 s~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 153 SVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 46678899999999999888777755444
No 242
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=25.76 E-value=72 Score=20.05 Aligned_cols=20 Identities=15% Similarity=0.270 Sum_probs=16.2
Q ss_pred HHHHHHHhCCChhhHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFq 65 (120)
...+|..+||+.+.++.|=.
T Consensus 3 I~eva~~~gvs~~tLRyYE~ 22 (124)
T COG0789 3 IGEVAKLTGVSVRTLRFYER 22 (124)
T ss_pred HHHHHHHhCCCHHHHHHHHH
Confidence 34678889999999999853
No 243
>KOG3755|consensus
Probab=25.70 E-value=42 Score=28.23 Aligned_cols=58 Identities=33% Similarity=0.457 Sum_probs=48.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhCC-CCCHHH---HHHHHHHhCCChhhHHHHHHHHHhHHH
Q psy4625 15 KEKRPRTAFSGEQLSRLKVEFTENR-YLTERR---RQELANELGLNEAQIKIWFQNKRAKIK 72 (120)
Q Consensus 15 ~~rr~R~~~~~~q~~~L~~~F~~~~-~p~~~~---~~~La~~l~l~~~~V~~WFqNrR~k~k 72 (120)
...+.|+.+..+.+.+|..+...-. ||+... ...|...+.+..+.+.-.|+|.|...+
T Consensus 646 ~~p~~~~~isge~~~~~qs~i~~~gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~ 707 (769)
T KOG3755|consen 646 HKPRKRTKISGEALGILQSFITDVGLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVK 707 (769)
T ss_pred cCccccceecccchHHHHHHHHHhccCchhhcccccchhhhhhcccHHHHHHhhhcceeecc
Confidence 4567788899999999988876544 888777 888999999999999999999887654
No 244
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=25.39 E-value=1e+02 Score=16.55 Aligned_cols=38 Identities=21% Similarity=0.260 Sum_probs=25.7
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHH
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKI 62 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~ 62 (120)
++..|..+|...+..... ......||..++++...|..
T Consensus 3 lt~~q~~vL~~l~~~~~~--~~t~~~la~~l~~~~~~vs~ 40 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGE--ELTQSELAERLGISKSTVSR 40 (62)
T ss_dssp STHHHHHHHHHHHHSTTS--GEEHHHHHHHHTS-HHHHHH
T ss_pred cCHHHHHHHHHHHHCCCC--CcCHHHHHHHHCcCHHHHHH
Confidence 567788888777666553 22466788999998876653
No 245
>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=24.99 E-value=91 Score=19.65 Aligned_cols=21 Identities=14% Similarity=0.254 Sum_probs=17.9
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
...+|..+|++...|+.|-..
T Consensus 3 Ige~A~~~gvs~~tlR~ye~~ 23 (107)
T cd01111 3 ISQLALDAGVSVHIVRDYLLR 23 (107)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 356899999999999999864
No 246
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=24.84 E-value=1.9e+02 Score=19.08 Aligned_cols=44 Identities=18% Similarity=0.254 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHH
Q psy4625 22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71 (120)
Q Consensus 22 ~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~ 71 (120)
.++..+..+|...... .....+|..++++.+.|+.+..+=|.|.
T Consensus 149 ~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl 192 (210)
T PRK09935 149 VLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGKL 192 (210)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 4677777777543322 4567788999999999999988766664
No 247
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=24.63 E-value=70 Score=17.29 Aligned_cols=21 Identities=24% Similarity=0.490 Sum_probs=17.6
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
-..||..+|++...|..||+.
T Consensus 22 ~~~La~~FgIs~stvsri~~~ 42 (53)
T PF13613_consen 22 FQDLAYRFGISQSTVSRIFHE 42 (53)
T ss_pred HhHHhhheeecHHHHHHHHHH
Confidence 456789999999999999875
No 248
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=24.60 E-value=1.4e+02 Score=16.69 Aligned_cols=50 Identities=22% Similarity=0.230 Sum_probs=30.2
Q ss_pred CCCCCCHHHHHHHHHHHHhCCCCC---HHHHHHHHHHhCCChhhHHHHHHHHH
Q psy4625 19 PRTAFSGEQLSRLKVEFTENRYLT---ERRRQELANELGLNEAQIKIWFQNKR 68 (120)
Q Consensus 19 ~R~~~~~~q~~~L~~~F~~~~~p~---~~~~~~La~~l~l~~~~V~~WFqNrR 68 (120)
+|..++.+.-..+...+......+ +..+..+....+|+..+|+.=.|--|
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 466788877666666655555533 34444444445677888887666433
No 249
>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=24.43 E-value=94 Score=19.15 Aligned_cols=21 Identities=14% Similarity=0.252 Sum_probs=17.5
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
...+|..+|++...++.|.+.
T Consensus 4 i~eva~~~gVs~~tLR~ye~~ 24 (98)
T cd01279 4 ISVAAELLGIHPQTLRVYDRL 24 (98)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456799999999999999653
No 250
>smart00595 MADF subfamily of SANT domain.
Probab=24.37 E-value=1.6e+02 Score=17.26 Aligned_cols=31 Identities=29% Similarity=0.491 Sum_probs=25.5
Q ss_pred HHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625 47 QELANELGLNEAQIKIWFQNKRAKIKKASGQ 77 (120)
Q Consensus 47 ~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 77 (120)
..||.++|.+...|+.-+.+=|...++....
T Consensus 31 ~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r 61 (89)
T smart00595 31 EEIAEELGLSVEECKKRWKNLRDRYRRELKR 61 (89)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 4478899999999999999999888877543
No 251
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 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. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=23.93 E-value=81 Score=15.63 Aligned_cols=20 Identities=30% Similarity=0.519 Sum_probs=14.3
Q ss_pred HHHHHHHHhCCChhhHHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWF 64 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WF 64 (120)
.+..||..+|++...|.-=|
T Consensus 4 tr~diA~~lG~t~ETVSR~l 23 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRIL 23 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHH
Confidence 46789999999988776444
No 252
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=23.88 E-value=87 Score=20.64 Aligned_cols=20 Identities=30% Similarity=0.559 Sum_probs=17.6
Q ss_pred HHHHHHHhCCChhhHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFq 65 (120)
-++||..+|++...|.-|-.
T Consensus 3 ~eELA~~tG~srQTINrWvR 22 (122)
T PF07037_consen 3 PEELAELTGYSRQTINRWVR 22 (122)
T ss_pred HHHHHHHhCccHHHHHHHHH
Confidence 36799999999999999984
No 253
>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=23.82 E-value=1.3e+02 Score=16.06 Aligned_cols=39 Identities=18% Similarity=0.386 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHH
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFq 65 (120)
++..|..+|...+...+ .....||..++++...|..+..
T Consensus 1 lt~~q~~iL~~l~~~~~----~~~~~la~~~~~~~~~~t~~i~ 39 (59)
T PF01047_consen 1 LTPSQFRILRILYENGG----ITQSELAEKLGISRSTVTRIIK 39 (59)
T ss_dssp STHHHHHHHHHHHHHSS----EEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHHcCC----CCHHHHHHHHCCChhHHHHHHH
Confidence 35678888888887766 3344889999999888877653
No 254
>PF07471 Phage_Nu1: Phage DNA packaging protein Nu1; InterPro: IPR010906 This entry is represented by the Bacteriophage lambda, Nu1, terminase small subunit. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA [].; PDB: 1J9I_A.
Probab=23.77 E-value=74 Score=21.95 Aligned_cols=21 Identities=33% Similarity=0.681 Sum_probs=15.6
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
+..||..+|+++..|.-|-.+
T Consensus 5 k~~lA~i~gvS~~ti~~W~~~ 25 (164)
T PF07471_consen 5 KKELAEIFGVSERTIDKWQRQ 25 (164)
T ss_dssp HHHHHHHTT--HHHHHHHTTT
T ss_pred HHHHHHHHCCCHHHHHHHHHC
Confidence 567899999999999999643
No 255
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=23.67 E-value=95 Score=18.67 Aligned_cols=18 Identities=33% Similarity=0.695 Sum_probs=16.3
Q ss_pred HHHHHHHhCCChhhHHHH
Q psy4625 46 RQELANELGLNEAQIKIW 63 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~W 63 (120)
...+|..+|++..-|..|
T Consensus 13 ~~kvA~aLGIs~~AVsQW 30 (75)
T PRK09744 13 KTKLANAAGVRLASVAAW 30 (75)
T ss_pred HHHHHHHHCCCHHHHHHH
Confidence 567899999999999999
No 256
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=23.59 E-value=1.4e+02 Score=21.15 Aligned_cols=35 Identities=26% Similarity=0.384 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 41 LTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 41 p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
.......++|..+|++...|+.....-|.+.|+..
T Consensus 163 ~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 163 VEELSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 33445778899999999999999987787777764
No 257
>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=23.50 E-value=94 Score=20.71 Aligned_cols=21 Identities=19% Similarity=0.300 Sum_probs=18.2
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
+.++|..+|++...++.|.+-
T Consensus 4 IgevA~~~Gvs~~tLRyYE~~ 24 (142)
T TIGR01950 4 VGELAKRSGVAVSALHFYESK 24 (142)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999864
No 258
>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=23.38 E-value=87 Score=19.78 Aligned_cols=21 Identities=19% Similarity=0.316 Sum_probs=17.9
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
...+|..+|++...++.|-+.
T Consensus 3 i~eva~~~gvs~~tlR~Ye~~ 23 (112)
T cd01282 3 IGELAARTGVSVRSLRYYEEQ 23 (112)
T ss_pred HHHHHHHHCCCHHHHHHHHHC
Confidence 456899999999999999864
No 259
>PF13565 HTH_32: Homeodomain-like domain
Probab=23.33 E-value=1.6e+02 Score=16.73 Aligned_cols=39 Identities=26% Similarity=0.319 Sum_probs=26.8
Q ss_pred CHHHHHHHHHHHHhCCCCCHHHHHH-HHHHhCC----ChhhHHH
Q psy4625 24 SGEQLSRLKVEFTENRYLTERRRQE-LANELGL----NEAQIKI 62 (120)
Q Consensus 24 ~~~q~~~L~~~F~~~~~p~~~~~~~-La~~l~l----~~~~V~~ 62 (120)
+.++...+...+..++..+..+... |...+|+ +...|.-
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R 75 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYR 75 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHH
Confidence 6777788888888888777776665 5666664 4444443
No 260
>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=23.33 E-value=2.4e+02 Score=18.87 Aligned_cols=49 Identities=22% Similarity=0.276 Sum_probs=36.6
Q ss_pred CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 20 R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
.+.++..|..+|...+ .. ....++|..+|++...|..+-..-+.+.++.
T Consensus 4 ~~~Lte~qr~VL~Lr~--~G----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~a 52 (137)
T TIGR00721 4 KTFLTERQIKVLELRE--KG----LSQKEIAKELKTTRANVSAIEKRAMENIEKA 52 (137)
T ss_pred cCCCCHHHHHHHHHHH--cC----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHHH
Confidence 3567888888887742 22 2467789999999999999988777776653
No 261
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=23.27 E-value=1.4e+02 Score=20.07 Aligned_cols=27 Identities=22% Similarity=0.356 Sum_probs=22.4
Q ss_pred HHHHHHHHHhCCChhhHHHHHHHHHhH
Q psy4625 44 RRRQELANELGLNEAQIKIWFQNKRAK 70 (120)
Q Consensus 44 ~~~~~La~~l~l~~~~V~~WFqNrR~k 70 (120)
+....++..+|++...|..|...-|..
T Consensus 47 ati~eV~e~tgVs~~~I~~~IreGRL~ 73 (137)
T TIGR03826 47 ATVSEIVEETGVSEKLILKFIREGRLQ 73 (137)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCee
Confidence 456778999999999999999776654
No 262
>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=23.15 E-value=79 Score=16.42 Aligned_cols=17 Identities=47% Similarity=0.751 Sum_probs=12.2
Q ss_pred HHHHHHHHhCCChhhHH
Q psy4625 45 RRQELANELGLNEAQIK 61 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~ 61 (120)
.-..||..+||+...|.
T Consensus 19 s~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 19 SYAELAEELGLSESTVR 35 (42)
T ss_dssp -HHHHHHHHTS-HHHHH
T ss_pred cHHHHHHHHCcCHHHHH
Confidence 34568999999998875
No 263
>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=22.73 E-value=81 Score=18.12 Aligned_cols=21 Identities=29% Similarity=0.227 Sum_probs=9.4
Q ss_pred HHHhCCChhhHHHHHHHHHhH
Q psy4625 50 ANELGLNEAQIKIWFQNKRAK 70 (120)
Q Consensus 50 a~~l~l~~~~V~~WFqNrR~k 70 (120)
...+|++..+...+.+-.+..
T Consensus 17 ~~~~g~s~~~~~~~~R~~~a~ 37 (81)
T PF12833_consen 17 KKETGMSFKQYLRELRLQRAK 37 (81)
T ss_dssp HHHHSS-HHHHHHHHHHHHHH
T ss_pred HHHHCcCHHHHHHHHHHHHHH
Confidence 344565555544444433333
No 264
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=22.70 E-value=61 Score=20.95 Aligned_cols=23 Identities=17% Similarity=0.240 Sum_probs=20.1
Q ss_pred HHHHHHHhCCChhhHHHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQNKR 68 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNrR 68 (120)
+..||..+|++...|..|.+++.
T Consensus 21 q~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 21 KKELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHcCCC
Confidence 56789999999999999998764
No 265
>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=22.69 E-value=57 Score=16.99 Aligned_cols=33 Identities=21% Similarity=0.438 Sum_probs=23.5
Q ss_pred HHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHH
Q psy4625 35 FTENRYLTERRRQELANELGLNEAQIKIWFQNKR 68 (120)
Q Consensus 35 F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR 68 (120)
|....|-. .....+|..+|++...+...|.++-
T Consensus 9 ~~~~G~~~-~s~~~Ia~~~gvs~~~~y~~f~~k~ 41 (47)
T PF00440_consen 9 FAEKGYEA-VSIRDIARRAGVSKGSFYRYFPSKD 41 (47)
T ss_dssp HHHHHTTT-SSHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred HHHhCHHh-CCHHHHHHHHccchhhHHHHcCCHH
Confidence 44444333 3467789999999999999887753
No 266
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=22.66 E-value=62 Score=17.95 Aligned_cols=25 Identities=20% Similarity=0.436 Sum_probs=19.1
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRA 69 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~ 69 (120)
....+|..+|++...|..|-..++.
T Consensus 16 s~~~lA~~~g~s~s~v~~iE~G~~~ 40 (64)
T PF13560_consen 16 SQAQLADRLGVSQSTVSRIERGRRP 40 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCCC
Confidence 4667899999999999998876653
No 267
>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=22.64 E-value=86 Score=20.75 Aligned_cols=21 Identities=19% Similarity=0.305 Sum_probs=18.1
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
+.++|..+|++...|+.|-+.
T Consensus 4 I~EvA~~~Gvs~~tLRyYE~~ 24 (139)
T cd01110 4 VGEVAKRSGVAVSALHFYEQK 24 (139)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999864
No 268
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=22.64 E-value=1.7e+02 Score=18.25 Aligned_cols=29 Identities=21% Similarity=0.462 Sum_probs=21.9
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
....+|...|+++.+|.-|..+-+.++-.
T Consensus 25 gq~~vA~~~Gv~eStISR~k~~~~~~~a~ 53 (91)
T PF05269_consen 25 GQKKVAEAMGVDESTISRWKNDFIEKMAM 53 (91)
T ss_dssp HHHHHHHHHTSSTTTHHHHHHHHHHHHHH
T ss_pred hhHHHHHHhCCCHHHHHHHHhhHHHHHHH
Confidence 34567999999999999998665544433
No 269
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=22.55 E-value=2.3e+02 Score=18.38 Aligned_cols=45 Identities=20% Similarity=0.331 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHH
Q psy4625 22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72 (120)
Q Consensus 22 ~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k 72 (120)
.++..+..+|.. +..+ + ....+|..++++...|+.+.++=+.|..
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 478888888766 3332 2 2567889999999999999987665543
No 270
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=22.51 E-value=99 Score=21.55 Aligned_cols=21 Identities=19% Similarity=0.525 Sum_probs=18.0
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
...+|..+|++...|+.|...
T Consensus 3 i~evA~~lGVS~~TLRrw~k~ 23 (175)
T PRK13182 3 TPFVAKKLGVSPKTVQRWVKQ 23 (175)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 356799999999999999964
No 271
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=22.49 E-value=1.1e+02 Score=17.61 Aligned_cols=21 Identities=29% Similarity=0.567 Sum_probs=16.3
Q ss_pred HHHHHHHHhCCChhhHHHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFq 65 (120)
....||..+||+...|...++
T Consensus 22 t~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 22 TDEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp BHHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHcccHHHHHHHHH
Confidence 356789999999999987774
No 272
>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=22.42 E-value=91 Score=19.97 Aligned_cols=20 Identities=20% Similarity=0.378 Sum_probs=16.5
Q ss_pred HHHHHHHhCCChhhHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFq 65 (120)
...+|..+|++...++.|=+
T Consensus 3 Igeva~~~gvs~~tlRyYe~ 22 (118)
T cd04776 3 ISELAREFDVTPRTLRFYED 22 (118)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35689999999999999853
No 273
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=22.40 E-value=2.5e+02 Score=21.03 Aligned_cols=29 Identities=24% Similarity=0.264 Sum_probs=23.5
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
...++|..+|++...|+.....-|.+.++
T Consensus 171 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 171 SAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 45678999999999999988766666665
No 274
>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=22.24 E-value=96 Score=19.16 Aligned_cols=21 Identities=19% Similarity=0.346 Sum_probs=17.3
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
...+|..+|++...++.|-+.
T Consensus 3 i~e~A~~~gvs~~tlR~Ye~~ 23 (99)
T cd04772 3 TVDLARAIGLSPQTVRNYESL 23 (99)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 356899999999999999653
No 275
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=22.16 E-value=1e+02 Score=20.34 Aligned_cols=21 Identities=14% Similarity=0.208 Sum_probs=18.1
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
...+|..+|++...|+.|...
T Consensus 4 I~e~a~~~gvs~~tlR~Ye~~ 24 (140)
T PRK09514 4 IGELAKLAEVTPDTLRFYEKQ 24 (140)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999864
No 276
>KOG0044|consensus
Probab=22.07 E-value=1.4e+02 Score=21.13 Aligned_cols=30 Identities=13% Similarity=0.403 Sum_probs=23.7
Q ss_pred CCCHHHHHHHHHHhCCChhhHHHHHHHHHh
Q psy4625 40 YLTERRRQELANELGLNEAQIKIWFQNKRA 69 (120)
Q Consensus 40 ~p~~~~~~~La~~l~l~~~~V~~WFqNrR~ 69 (120)
.......+.|...+..++..|+.|+.+=..
T Consensus 8 ~~~~~~~e~l~~~t~f~~~ei~~~Yr~Fk~ 37 (193)
T KOG0044|consen 8 KLQPESLEQLVQQTKFSKKEIQQWYRGFKN 37 (193)
T ss_pred cCCcHHHHHHHHhcCCCHHHHHHHHHHhcc
Confidence 345566788888999999999999987544
No 277
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=21.98 E-value=1.5e+02 Score=20.13 Aligned_cols=25 Identities=36% Similarity=0.695 Sum_probs=18.3
Q ss_pred HHHHHHHHHHhCCChhhHHHHHH-HH
Q psy4625 43 ERRRQELANELGLNEAQIKIWFQ-NK 67 (120)
Q Consensus 43 ~~~~~~La~~l~l~~~~V~~WFq-Nr 67 (120)
......+|..+|++...+.-|-+ |+
T Consensus 34 r~T~~eiAee~Gis~~tLYrWr~~~~ 59 (142)
T PF13022_consen 34 RRTQAEIAEEVGISRSTLYRWRQQNK 59 (142)
T ss_dssp -S-HHHHHHHHTS-HHHHHHHHHH-H
T ss_pred cchHHHHHHHhCCCHHHHHHHHhcCH
Confidence 45577899999999999999984 44
No 278
>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=21.96 E-value=94 Score=19.83 Aligned_cols=21 Identities=19% Similarity=0.373 Sum_probs=17.6
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
..++|..+|++...++.|-..
T Consensus 3 IgevA~~~gvs~~tlRyYe~~ 23 (120)
T cd04781 3 IAEVARQSGLPASTLRYYEEK 23 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456899999999999999853
No 279
>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=21.78 E-value=92 Score=20.06 Aligned_cols=19 Identities=32% Similarity=0.399 Sum_probs=16.0
Q ss_pred HHHHHHHhCCChhhHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWF 64 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WF 64 (120)
..++|..+|++...|+.|=
T Consensus 2 I~e~a~~~gvs~~tlR~Ye 20 (124)
T TIGR02051 2 IGELAKAAGVNVETIRYYE 20 (124)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 3568999999999999983
No 280
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=21.39 E-value=82 Score=20.16 Aligned_cols=39 Identities=15% Similarity=0.400 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHH
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR 68 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR 68 (120)
+++.++..+...+... ...+|..+|++...|+.|=++|+
T Consensus 44 ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~ 82 (104)
T COG2944 44 LSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRK 82 (104)
T ss_pred CCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCc
Confidence 5666666666555433 34578889999999999988764
No 281
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=21.38 E-value=3.1e+02 Score=20.72 Aligned_cols=50 Identities=10% Similarity=0.190 Sum_probs=34.5
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
++..+..+|...|..... ......++|..+|++...|+..-..-..+.|+
T Consensus 257 L~~rer~Vi~lr~gl~~~-~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~ 306 (317)
T PRK07405 257 LTPQQKEVIALRFGLEDG-QPLTLAKIGERLNISRERVRQIEREALSKLRK 306 (317)
T ss_pred CCHHHHHHHHHHhhcCCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 455555666666654322 22457788999999999999988777766665
No 282
>PF09301 DUF1970: Domain of unknown function (DUF1970); InterPro: IPR015380 This entry is represented by Bacteriophage PRD1, P16; it is a family of uncharacterised viral proteins.; PDB: 1W8X_P.
Probab=21.25 E-value=54 Score=20.38 Aligned_cols=12 Identities=42% Similarity=0.889 Sum_probs=8.1
Q ss_pred hHHHHHHHHHhH
Q psy4625 59 QIKIWFQNKRAK 70 (120)
Q Consensus 59 ~V~~WFqNrR~k 70 (120)
-|-.||+||-+.
T Consensus 18 liwlwfrnrpaa 29 (117)
T PF09301_consen 18 LIWLWFRNRPAA 29 (117)
T ss_dssp HHHHHHHHTT-S
T ss_pred HHHHHHccChHH
Confidence 466899997654
No 283
>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=21.23 E-value=98 Score=19.99 Aligned_cols=22 Identities=23% Similarity=0.187 Sum_probs=18.1
Q ss_pred HHHHHHHhCCChhhHHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQNK 67 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNr 67 (120)
..++|..+|++...++.|-+.-
T Consensus 3 I~e~a~~~gvs~~tlRyYe~~G 24 (127)
T cd01108 3 IGEAAKLTGLSAKMIRYYEEIG 24 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3568999999999999998643
No 284
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.01 E-value=2.6e+02 Score=18.52 Aligned_cols=20 Identities=20% Similarity=0.469 Sum_probs=15.4
Q ss_pred HHHHHHhCCChhhHHHHHHH
Q psy4625 47 QELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 47 ~~La~~l~l~~~~V~~WFqN 66 (120)
..+|..++++++++.-|+..
T Consensus 103 ~~IA~~l~i~erta~r~~~~ 122 (130)
T PF05263_consen 103 YQIAQKLHISERTARRWRDR 122 (130)
T ss_pred HHHHHHhCccHHHHHHHHHH
Confidence 34678888999988888764
No 285
>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=20.93 E-value=99 Score=19.94 Aligned_cols=22 Identities=18% Similarity=0.261 Sum_probs=18.2
Q ss_pred HHHHHHHhCCChhhHHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQNK 67 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNr 67 (120)
..++|..+|++...++.|-+.-
T Consensus 3 I~e~a~~~gvs~~tlRyYe~~G 24 (127)
T TIGR02044 3 IGQVAKLTGLSSKMIRYYEEKG 24 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4568999999999999998643
No 286
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=20.78 E-value=1e+02 Score=20.34 Aligned_cols=21 Identities=19% Similarity=0.360 Sum_probs=17.2
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
+.++|..+|++...|+.|=..
T Consensus 3 Ige~a~~~gvs~~tlRyYE~~ 23 (135)
T PRK10227 3 ISDVAKITGLTSKAIRFYEEK 23 (135)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456899999999999998643
No 287
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=20.71 E-value=2.9e+02 Score=20.52 Aligned_cols=44 Identities=11% Similarity=0.161 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHH
Q psy4625 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNK 67 (120)
Q Consensus 23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNr 67 (120)
+++.+..+|...|-...+ ......++|..+|++...|+..-..-
T Consensus 250 L~~rer~Vi~lr~gl~~~-~~~Tl~EIa~~lgiS~erVrq~~~rA 293 (298)
T TIGR02997 250 LTPRERQVLRLRFGLDGG-EPLTLAEIGRRLNLSRERVRQIEAKA 293 (298)
T ss_pred CCHHHHHHHHHHhccCCC-CCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 445555566665543222 22457788999999999998876543
No 288
>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=20.69 E-value=1.2e+02 Score=19.75 Aligned_cols=21 Identities=24% Similarity=0.381 Sum_probs=18.2
Q ss_pred HHHHHHHhCCChhhHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqN 66 (120)
...+|..+|++...++.|.+.
T Consensus 4 I~e~a~~~gvs~~tlR~Ye~~ 24 (131)
T TIGR02043 4 IGELAKLCGVTSDTLRFYEKN 24 (131)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456899999999999999965
No 289
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=20.67 E-value=1.2e+02 Score=20.63 Aligned_cols=38 Identities=16% Similarity=0.278 Sum_probs=28.9
Q ss_pred HHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhH
Q psy4625 32 KVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAK 70 (120)
Q Consensus 32 ~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k 70 (120)
...|....|-. .....||...|++...+...|.++-.-
T Consensus 18 ~~lf~e~G~~~-~s~~~IA~~agvs~~~lY~hF~sKe~L 55 (202)
T TIGR03613 18 LDTFSRFGFHG-TSLEQIAELAGVSKTNLLYYFPSKDAL 55 (202)
T ss_pred HHHHHHhCccc-CCHHHHHHHhCCCHHHHHHHcCCHHHH
Confidence 33466677544 557778999999999999999987543
No 290
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=20.65 E-value=1.3e+02 Score=15.00 Aligned_cols=20 Identities=10% Similarity=0.152 Sum_probs=13.3
Q ss_pred HHHHHHHHHhCCChhhHHHH
Q psy4625 44 RRRQELANELGLNEAQIKIW 63 (120)
Q Consensus 44 ~~~~~La~~l~l~~~~V~~W 63 (120)
.....||..++++...+..|
T Consensus 7 Dtl~~IA~~~~~~~~~l~~~ 26 (44)
T PF01476_consen 7 DTLWSIAKRYGISVDELMEL 26 (44)
T ss_dssp --HHHHHHHTTS-HHHHHHH
T ss_pred CcHHHHHhhhhhhHhHHHHh
Confidence 34667888899888877665
No 291
>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=20.61 E-value=1.4e+02 Score=15.31 Aligned_cols=37 Identities=22% Similarity=0.302 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHH
Q psy4625 25 GEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQ 65 (120)
Q Consensus 25 ~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFq 65 (120)
..+..+|...+. ++. .....||..+|++...|..-++
T Consensus 3 ~~~~~Il~~l~~-~~~---~t~~ela~~~~is~~tv~~~l~ 39 (48)
T PF13412_consen 3 ETQRKILNYLRE-NPR---ITQKELAEKLGISRSTVNRYLK 39 (48)
T ss_dssp HHHHHHHHHHHH-CTT---S-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHH-cCC---CCHHHHHHHhCCCHHHHHHHHH
Confidence 345566655555 333 4466789999999988876553
No 292
>PRK13558 bacterio-opsin activator; Provisional
Probab=20.55 E-value=1.4e+02 Score=24.53 Aligned_cols=42 Identities=17% Similarity=0.374 Sum_probs=35.6
Q ss_pred CCCCHHHHHHHHHHHHhCCC--CCHHHHHHHHHHhCCChhhHHH
Q psy4625 21 TAFSGEQLSRLKVEFTENRY--LTERRRQELANELGLNEAQIKI 62 (120)
Q Consensus 21 ~~~~~~q~~~L~~~F~~~~~--p~~~~~~~La~~l~l~~~~V~~ 62 (120)
..+|..|..+|+..|...-| |-......||..+|++...+..
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~ 649 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQ 649 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHH
Confidence 46999999999999998775 7677889999999999876553
No 293
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=20.39 E-value=2.6e+02 Score=18.16 Aligned_cols=30 Identities=17% Similarity=0.308 Sum_probs=23.0
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKA 74 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 74 (120)
....+|..+|++...|+.....-+.+.+..
T Consensus 123 s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 123 SHQQIAEHLGISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 356778999999999998887666665554
No 294
>smart00351 PAX Paired Box domain.
Probab=20.36 E-value=2.5e+02 Score=18.04 Aligned_cols=40 Identities=10% Similarity=0.152 Sum_probs=30.1
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHH
Q psy4625 22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQN 66 (120)
Q Consensus 22 ~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqN 66 (120)
.++.++...+...|.... ....+|..+|++...|..|.+-
T Consensus 17 ~~s~~~R~riv~~~~~G~-----s~~~iA~~~gvs~~tV~kwi~r 56 (125)
T smart00351 17 PLPDEERQRIVELAQNGV-----RPCDISRQLCVSHGCVSKILGR 56 (125)
T ss_pred CCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHH
Confidence 377777777777776332 3457899999999999999864
No 295
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=20.33 E-value=93 Score=19.33 Aligned_cols=32 Identities=16% Similarity=0.272 Sum_probs=21.9
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHH
Q psy4625 28 LSRLKVEFTENRYLTERRRQELANELGLNEAQIKIW 63 (120)
Q Consensus 28 ~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~W 63 (120)
...|.+.|....+. ...+|..|+++...|..=
T Consensus 12 ~~ELq~nf~~~~ls----~~~ia~dL~~s~~~le~v 43 (89)
T PF10078_consen 12 RQELQANFELSGLS----LEQIAADLGTSPEHLEQV 43 (89)
T ss_pred HHHHHHHHHHcCCC----HHHHHHHhCCCHHHHHHH
Confidence 34677778877754 556788888887766543
No 296
>PRK09726 antitoxin HipB; Provisional
Probab=20.32 E-value=75 Score=19.05 Aligned_cols=22 Identities=32% Similarity=0.542 Sum_probs=19.1
Q ss_pred HHHHHHHhCCChhhHHHHHHHH
Q psy4625 46 RQELANELGLNEAQIKIWFQNK 67 (120)
Q Consensus 46 ~~~La~~l~l~~~~V~~WFqNr 67 (120)
...||..+|++...|..|...+
T Consensus 28 q~elA~~~gvs~~tis~~e~g~ 49 (88)
T PRK09726 28 QSELAKKIGIKQATISNFENNP 49 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHCCC
Confidence 6678999999999999998754
No 297
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=20.32 E-value=2.9e+02 Score=18.76 Aligned_cols=31 Identities=26% Similarity=0.351 Sum_probs=24.8
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKKAS 75 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 75 (120)
...++|..+|++...|+.+..--|.+.++..
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 146 SGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999887777766654
No 298
>PLN03162 golden-2 like transcription factor; Provisional
Probab=20.10 E-value=4.6e+02 Score=20.98 Aligned_cols=59 Identities=15% Similarity=0.080 Sum_probs=40.6
Q ss_pred CCCCCCCCCCHHH-HHHHHHHHHhCC-CCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 15 KEKRPRTAFSGEQ-LSRLKVEFTENR-YLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 15 ~~rr~R~~~~~~q-~~~L~~~F~~~~-~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
..++.|-+++.+. ...++...+... .-.+..+..|...-||+...|+.-+|--|...++
T Consensus 232 g~KKpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~ 292 (526)
T PLN03162 232 GKKKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRH 292 (526)
T ss_pred CCCCCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhccc
Confidence 3556778898876 445555566652 3445556666667789999999999887776554
No 299
>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=20.07 E-value=76 Score=17.39 Aligned_cols=24 Identities=29% Similarity=0.488 Sum_probs=18.4
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKR 68 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR 68 (120)
....+|..+|++...|..|-.+++
T Consensus 14 t~~~~a~~~~i~~~~i~~~e~g~~ 37 (64)
T PF12844_consen 14 TQKDLAEKLGISRSTISKIENGKR 37 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCc
Confidence 466789999999999999987754
No 300
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=20.07 E-value=3.2e+02 Score=19.20 Aligned_cols=29 Identities=21% Similarity=0.283 Sum_probs=21.4
Q ss_pred HHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625 45 RRQELANELGLNEAQIKIWFQNKRAKIKK 73 (120)
Q Consensus 45 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 73 (120)
...++|..+|++...|..+...-+.+.++
T Consensus 196 S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 196 TQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46678999999999998876554555443
Done!