Query psy3281
Match_columns 317
No_of_seqs 248 out of 1183
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 21:01:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3281.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3281hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0489|consensus 99.8 6.5E-21 1.4E-25 179.2 5.9 79 225-303 136-224 (261)
2 KOG0487|consensus 99.7 2.5E-18 5.5E-23 164.5 6.4 74 228-301 225-298 (308)
3 KOG0850|consensus 99.7 8.1E-18 1.8E-22 154.3 8.6 67 235-301 119-185 (245)
4 KOG0488|consensus 99.7 6.8E-18 1.5E-22 162.4 5.1 66 236-301 170-235 (309)
5 KOG0843|consensus 99.7 8E-17 1.7E-21 143.2 8.8 64 237-300 101-164 (197)
6 KOG2251|consensus 99.7 5.3E-17 1.2E-21 148.2 7.2 68 233-300 32-99 (228)
7 KOG0484|consensus 99.7 8.3E-18 1.8E-22 138.0 1.1 66 233-298 12-77 (125)
8 KOG0494|consensus 99.7 5.9E-17 1.3E-21 151.0 6.4 71 233-303 136-206 (332)
9 KOG0842|consensus 99.7 4.8E-17 1E-21 155.7 5.4 69 236-304 151-219 (307)
10 KOG0848|consensus 99.7 2.1E-17 4.6E-22 154.4 2.9 76 225-300 175-261 (317)
11 PF00046 Homeobox: Homeobox do 99.6 2.9E-16 6.2E-21 114.1 4.3 57 239-295 1-57 (57)
12 KOG0485|consensus 99.6 1.9E-16 4E-21 144.5 2.8 67 235-301 101-167 (268)
13 KOG0492|consensus 99.6 4.1E-16 8.9E-21 141.4 3.5 72 230-301 136-207 (246)
14 KOG3802|consensus 99.5 5.5E-15 1.2E-19 144.7 5.1 70 229-298 285-354 (398)
15 KOG0491|consensus 99.5 3.1E-15 6.6E-20 131.6 1.9 71 237-307 99-169 (194)
16 KOG0493|consensus 99.5 7E-15 1.5E-19 137.3 4.3 63 239-301 247-309 (342)
17 KOG0486|consensus 99.5 1.3E-14 2.8E-19 138.4 4.5 72 230-301 104-175 (351)
18 cd00086 homeodomain Homeodomai 99.5 2.3E-14 5E-19 103.7 4.6 58 239-296 1-58 (59)
19 smart00389 HOX Homeodomain. DN 99.5 2.2E-14 4.7E-19 103.3 4.3 56 239-294 1-56 (56)
20 TIGR01565 homeo_ZF_HD homeobox 99.5 2.8E-14 6.2E-19 106.1 4.9 53 238-290 1-57 (58)
21 KOG0844|consensus 99.5 1.2E-14 2.6E-19 138.2 2.4 65 236-300 179-243 (408)
22 COG5576 Homeodomain-containing 99.5 7E-14 1.5E-18 122.9 5.8 66 236-301 49-114 (156)
23 KOG0483|consensus 99.4 8.7E-14 1.9E-18 126.4 3.3 63 238-300 50-112 (198)
24 KOG0847|consensus 99.3 1.2E-12 2.7E-17 119.9 3.3 64 235-298 164-227 (288)
25 KOG4577|consensus 99.3 2.4E-12 5.3E-17 121.9 4.5 65 237-301 166-230 (383)
26 KOG0490|consensus 99.2 5.3E-12 1.1E-16 114.0 4.9 64 235-298 57-120 (235)
27 KOG1168|consensus 99.1 3.4E-11 7.5E-16 114.2 2.7 65 236-300 307-371 (385)
28 KOG0849|consensus 99.0 1.4E-10 3E-15 113.8 4.8 71 229-299 167-237 (354)
29 KOG0775|consensus 98.9 1.6E-09 3.5E-14 102.2 5.8 55 244-298 182-236 (304)
30 KOG0774|consensus 98.6 2.3E-08 5.1E-13 94.0 3.2 59 238-296 188-249 (334)
31 KOG2252|consensus 98.4 4.1E-07 8.8E-12 92.9 6.0 58 237-294 419-476 (558)
32 PF05920 Homeobox_KN: Homeobox 98.4 1.2E-07 2.7E-12 65.5 1.3 34 259-292 7-40 (40)
33 KOG1146|consensus 98.0 5.4E-06 1.2E-10 91.6 4.8 77 237-313 902-978 (1406)
34 KOG0490|consensus 98.0 8.1E-06 1.8E-10 73.7 4.9 64 235-298 150-213 (235)
35 KOG0773|consensus 96.8 0.00074 1.6E-08 65.6 2.9 60 237-296 238-300 (342)
36 PF11569 Homez: Homeodomain le 96.8 0.00058 1.3E-08 50.7 1.6 43 250-292 10-52 (56)
37 KOG3623|consensus 96.1 0.0062 1.3E-07 64.9 4.7 52 250-301 568-619 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 95.2 0.028 6E-07 40.9 3.8 47 239-290 1-47 (53)
39 PF04545 Sigma70_r4: Sigma-70, 88.9 0.42 9.1E-06 33.5 2.8 47 244-295 4-50 (50)
40 cd00569 HTH_Hin_like Helix-tur 83.6 2 4.2E-05 25.7 3.5 38 244-286 5-42 (42)
41 cd06171 Sigma70_r4 Sigma70, re 83.1 0.85 1.8E-05 30.5 1.8 44 244-292 10-53 (55)
42 PF01527 HTH_Tnp_1: Transposas 81.1 0.85 1.8E-05 34.2 1.3 44 240-287 2-45 (76)
43 KOG3755|consensus 77.4 1.4 3.1E-05 46.7 2.0 73 231-303 640-716 (769)
44 PRK03975 tfx putative transcri 75.9 3.3 7.1E-05 36.2 3.6 51 242-298 4-54 (141)
45 PF09607 BrkDBD: Brinker DNA-b 74.3 4 8.6E-05 30.7 3.2 46 241-287 2-47 (58)
46 PF04967 HTH_10: HTH DNA bindi 73.1 3.9 8.4E-05 30.0 2.8 42 245-286 1-44 (53)
47 PF13388 DUF4106: Protein of u 72.7 15 0.00033 36.2 7.6 31 238-268 256-286 (422)
48 KOG1146|consensus 71.6 3.9 8.5E-05 46.9 3.7 65 238-302 444-508 (1406)
49 PRK11924 RNA polymerase sigma 71.5 2.9 6.3E-05 35.4 2.2 36 264-299 140-175 (179)
50 PRK09646 RNA polymerase sigma 71.0 4.5 9.8E-05 35.7 3.4 48 245-297 143-190 (194)
51 PRK05602 RNA polymerase sigma 70.4 3.6 7.8E-05 35.8 2.6 40 264-303 143-182 (186)
52 KOG3623|consensus 70.3 3.4 7.5E-05 44.9 2.8 64 239-302 627-690 (1007)
53 PF00196 GerE: Bacterial regul 69.9 3.7 8.1E-05 29.5 2.2 46 244-295 3-48 (58)
54 PF08281 Sigma70_r4_2: Sigma-7 69.7 2.6 5.6E-05 29.7 1.3 43 245-292 11-53 (54)
55 PRK09644 RNA polymerase sigma 69.5 5 0.00011 34.2 3.3 40 263-302 122-161 (165)
56 smart00421 HTH_LUXR helix_turn 68.5 5.5 0.00012 27.1 2.7 44 244-293 3-46 (58)
57 TIGR03879 near_KaiC_dom probab 68.2 1.8 3.8E-05 33.9 0.1 37 253-289 20-56 (73)
58 PRK04217 hypothetical protein; 67.5 6.1 0.00013 33.2 3.2 51 243-298 41-91 (110)
59 PRK06759 RNA polymerase factor 67.3 6.3 0.00014 32.9 3.4 46 245-295 107-152 (154)
60 PRK12516 RNA polymerase sigma 65.8 5.4 0.00012 35.3 2.8 38 264-301 131-168 (187)
61 TIGR02937 sigma70-ECF RNA poly 65.8 4.9 0.00011 32.3 2.3 46 245-295 111-156 (158)
62 PRK10072 putative transcriptio 65.5 6.5 0.00014 32.1 2.9 41 244-291 32-72 (96)
63 PF13936 HTH_38: Helix-turn-he 65.0 4.1 8.9E-05 28.2 1.5 40 243-287 3-42 (44)
64 PRK09652 RNA polymerase sigma 65.0 4.7 0.0001 34.2 2.2 49 244-297 128-176 (182)
65 PRK12514 RNA polymerase sigma 64.5 5.3 0.00012 34.5 2.5 34 263-296 143-176 (179)
66 PRK12512 RNA polymerase sigma 61.3 8 0.00017 33.5 3.0 51 244-299 131-181 (184)
67 PRK12519 RNA polymerase sigma 61.0 4.6 0.0001 35.3 1.4 35 262-296 154-188 (194)
68 PF10668 Phage_terminase: Phag 60.6 4 8.7E-05 30.8 0.8 20 267-286 24-43 (60)
69 PRK09642 RNA polymerase sigma 60.4 9.9 0.00021 32.1 3.3 34 265-298 122-155 (160)
70 KOG3755|consensus 59.2 2.5 5.4E-05 44.9 -0.7 46 254-299 708-760 (769)
71 PRK09480 slmA division inhibit 59.0 8.7 0.00019 33.1 2.8 41 250-291 16-56 (194)
72 KOG1819|consensus 58.9 5 0.00011 42.0 1.4 16 244-259 676-691 (990)
73 TIGR02985 Sig70_bacteroi1 RNA 58.9 7.1 0.00015 32.3 2.1 46 245-295 114-159 (161)
74 PRK10403 transcriptional regul 58.1 6.8 0.00015 33.1 2.0 49 243-297 152-200 (215)
75 PRK09413 IS2 repressor TnpA; R 58.0 11 0.00023 31.5 3.1 43 241-287 9-51 (121)
76 PRK12526 RNA polymerase sigma 57.7 12 0.00026 33.5 3.5 37 262-298 166-202 (206)
77 PRK06986 fliA flagellar biosyn 57.6 8.3 0.00018 35.3 2.5 49 245-298 185-233 (236)
78 KOG0773|consensus 57.2 8.3 0.00018 37.5 2.6 44 258-301 117-160 (342)
79 cd06170 LuxR_C_like C-terminal 56.5 8.7 0.00019 26.3 2.0 37 246-288 2-38 (57)
80 COG3413 Predicted DNA binding 56.0 10 0.00022 34.5 2.9 49 244-294 155-205 (215)
81 TIGR02948 SigW_bacill RNA poly 55.3 9.1 0.0002 33.0 2.3 48 245-297 137-184 (187)
82 TIGR02943 Sig70_famx1 RNA poly 55.1 12 0.00027 32.9 3.1 53 245-302 132-184 (188)
83 PRK09648 RNA polymerase sigma 54.8 11 0.00025 32.7 2.9 48 244-296 139-186 (189)
84 PRK09647 RNA polymerase sigma 53.8 9.8 0.00021 34.2 2.3 38 265-302 154-191 (203)
85 TIGR02939 RpoE_Sigma70 RNA pol 53.7 6.8 0.00015 33.8 1.2 36 262-297 151-186 (190)
86 PRK06811 RNA polymerase factor 53.5 15 0.00033 32.1 3.5 49 245-298 132-180 (189)
87 TIGR02989 Sig-70_gvs1 RNA poly 52.8 14 0.00031 30.9 3.0 34 262-295 124-157 (159)
88 PRK12540 RNA polymerase sigma 52.3 14 0.00031 32.5 3.1 39 263-301 125-163 (182)
89 PRK12530 RNA polymerase sigma 52.3 13 0.00029 32.7 2.9 49 245-298 135-183 (189)
90 PRK00118 putative DNA-binding 51.8 12 0.00026 31.0 2.4 47 245-296 18-64 (104)
91 PRK09639 RNA polymerase sigma 51.8 14 0.0003 31.2 2.9 48 245-298 113-160 (166)
92 TIGR02983 SigE-fam_strep RNA p 51.3 13 0.00028 31.4 2.5 33 265-297 126-158 (162)
93 PRK09047 RNA polymerase factor 51.2 18 0.00039 30.3 3.4 49 245-298 107-155 (161)
94 TIGR00721 tfx DNA-binding prot 51.0 19 0.00042 31.3 3.6 48 242-295 4-51 (137)
95 PRK12520 RNA polymerase sigma 50.9 18 0.00039 31.6 3.5 37 265-301 147-183 (191)
96 PRK13919 putative RNA polymera 50.9 13 0.00028 32.2 2.5 47 245-296 136-182 (186)
97 TIGR02999 Sig-70_X6 RNA polyme 50.7 17 0.00037 31.2 3.3 32 265-296 150-181 (183)
98 smart00027 EH Eps15 homology d 50.6 20 0.00043 28.2 3.3 44 244-287 3-51 (96)
99 cd04761 HTH_MerR-SF Helix-Turn 50.5 7.4 0.00016 26.4 0.8 23 268-290 3-25 (49)
100 PHA02955 hypothetical protein; 49.9 18 0.0004 33.8 3.5 45 246-290 59-104 (213)
101 TIGR02959 SigZ RNA polymerase 49.9 17 0.00038 31.3 3.2 50 244-298 100-149 (170)
102 PRK09645 RNA polymerase sigma 49.6 21 0.00045 30.5 3.6 49 245-298 119-167 (173)
103 PRK12546 RNA polymerase sigma 49.3 11 0.00023 33.5 1.8 38 263-300 127-164 (188)
104 COG4367 Uncharacterized protei 49.3 16 0.00035 29.8 2.6 40 244-283 2-41 (97)
105 PRK12532 RNA polymerase sigma 49.2 20 0.00043 31.5 3.5 37 265-301 152-188 (195)
106 PRK12541 RNA polymerase sigma 49.2 16 0.00035 30.9 2.8 34 263-296 126-159 (161)
107 PRK12535 RNA polymerase sigma 49.2 22 0.00047 31.7 3.8 42 264-305 148-189 (196)
108 PF13443 HTH_26: Cro/C1-type H 48.9 7.6 0.00016 27.9 0.7 27 267-293 12-38 (63)
109 PRK12515 RNA polymerase sigma 48.8 18 0.0004 31.5 3.2 51 244-299 131-181 (189)
110 PRK12533 RNA polymerase sigma 48.6 19 0.00042 32.8 3.4 39 263-301 148-186 (216)
111 PRK12537 RNA polymerase sigma 48.6 21 0.00046 31.0 3.5 34 263-296 147-180 (182)
112 PRK12513 RNA polymerase sigma 48.1 8.3 0.00018 33.8 0.9 37 262-298 152-188 (194)
113 TIGR02859 spore_sigH RNA polym 48.1 6.4 0.00014 34.3 0.2 34 262-295 162-195 (198)
114 TIGR03541 reg_near_HchA LuxR f 48.0 13 0.00028 34.2 2.2 51 242-298 169-219 (232)
115 PRK08301 sporulation sigma fac 47.2 17 0.00037 33.0 2.9 52 244-296 178-229 (234)
116 PRK15369 two component system 47.2 17 0.00038 30.2 2.7 45 244-294 149-193 (211)
117 PRK07408 RNA polymerase sigma 47.1 16 0.00034 34.1 2.7 50 244-298 203-252 (256)
118 PRK10360 DNA-binding transcrip 47.1 14 0.0003 31.2 2.1 45 244-294 137-181 (196)
119 PRK06930 positive control sigm 47.0 20 0.00044 31.9 3.2 52 244-300 114-165 (170)
120 PRK12538 RNA polymerase sigma 46.8 15 0.00033 33.9 2.4 36 263-298 185-220 (233)
121 PRK05657 RNA polymerase sigma 46.7 18 0.0004 35.2 3.1 55 244-299 262-316 (325)
122 PF08280 HTH_Mga: M protein tr 46.3 18 0.0004 26.3 2.4 36 247-286 5-40 (59)
123 PRK08583 RNA polymerase sigma 46.3 16 0.00035 33.8 2.6 48 244-296 205-252 (257)
124 TIGR02479 FliA_WhiG RNA polyme 45.4 17 0.00037 32.9 2.5 47 244-295 175-221 (224)
125 PRK12518 RNA polymerase sigma 45.4 8.8 0.00019 32.8 0.6 38 262-299 133-170 (175)
126 PF13551 HTH_29: Winged helix- 45.4 40 0.00086 26.4 4.4 48 240-287 53-109 (112)
127 PRK12524 RNA polymerase sigma 45.3 31 0.00068 30.3 4.2 35 264-298 151-185 (196)
128 PRK09643 RNA polymerase sigma 45.2 29 0.00062 30.6 3.9 40 263-302 148-187 (192)
129 cd04762 HTH_MerR-trunc Helix-T 45.2 8.5 0.00018 25.4 0.4 25 268-292 3-27 (49)
130 TIGR02952 Sig70_famx2 RNA poly 45.1 20 0.00043 30.2 2.8 33 263-295 136-168 (170)
131 PRK08295 RNA polymerase factor 44.9 24 0.00051 31.1 3.3 37 263-299 168-204 (208)
132 PRK07670 RNA polymerase sigma 44.8 18 0.00039 33.5 2.6 47 245-296 202-248 (251)
133 TIGR02954 Sig70_famx3 RNA poly 44.5 22 0.00048 30.2 3.0 33 264-296 134-166 (169)
134 PRK12545 RNA polymerase sigma 44.2 23 0.0005 31.5 3.2 37 264-300 154-190 (201)
135 PF02796 HTH_7: Helix-turn-hel 44.0 20 0.00043 24.7 2.1 39 244-287 5-43 (45)
136 COG2944 Predicted transcriptio 43.8 19 0.0004 30.1 2.3 41 244-291 43-83 (104)
137 PRK07037 extracytoplasmic-func 43.3 26 0.00057 29.5 3.2 32 265-296 125-156 (163)
138 PRK06704 RNA polymerase factor 43.3 21 0.00045 33.3 2.8 34 266-299 133-166 (228)
139 PRK09641 RNA polymerase sigma 43.2 17 0.00037 31.2 2.1 35 263-297 150-184 (187)
140 PRK09935 transcriptional regul 42.7 18 0.0004 30.6 2.2 46 243-294 148-193 (210)
141 KOG1819|consensus 42.5 12 0.00027 39.2 1.3 8 240-247 647-654 (990)
142 PRK09637 RNA polymerase sigma 42.4 13 0.00027 32.7 1.2 36 263-298 120-155 (181)
143 PRK12547 RNA polymerase sigma 41.8 31 0.00067 29.4 3.5 34 264-297 127-160 (164)
144 PF06056 Terminase_5: Putative 41.8 7.9 0.00017 28.7 -0.2 23 265-287 13-35 (58)
145 TIGR03020 EpsA transcriptional 41.6 23 0.0005 33.5 2.8 50 243-298 189-238 (247)
146 PRK12536 RNA polymerase sigma 41.5 22 0.00048 30.8 2.6 35 263-297 143-177 (181)
147 PRK12539 RNA polymerase sigma 41.2 24 0.00052 30.7 2.7 34 264-297 146-179 (184)
148 cd00131 PAX Paired Box domain 41.1 57 0.0012 27.6 4.9 46 244-289 75-127 (128)
149 TIGR02941 Sigma_B RNA polymera 41.0 22 0.00047 32.9 2.6 48 244-296 205-252 (255)
150 PF13384 HTH_23: Homeodomain-l 40.8 12 0.00027 25.7 0.7 24 265-288 17-40 (50)
151 PRK10651 transcriptional regul 40.7 25 0.00053 29.7 2.7 47 244-296 155-201 (216)
152 PRK06424 transcription factor; 40.3 30 0.00066 30.2 3.2 24 268-291 100-123 (144)
153 PRK12534 RNA polymerase sigma 40.3 26 0.00056 30.4 2.8 34 263-296 151-184 (187)
154 TIGR02393 RpoD_Cterm RNA polym 40.1 25 0.00053 32.3 2.8 53 244-297 176-228 (238)
155 PRK11923 algU RNA polymerase s 39.9 13 0.00029 32.4 0.9 37 262-298 151-187 (193)
156 TIGR02980 SigBFG RNA polymeras 39.3 23 0.00049 32.0 2.3 47 244-295 178-224 (227)
157 PF12824 MRP-L20: Mitochondria 39.1 1.5E+02 0.0032 26.5 7.4 44 241-286 82-125 (164)
158 TIGR02950 SigM_subfam RNA poly 39.1 12 0.00027 31.0 0.6 34 262-295 118-151 (154)
159 PRK10100 DNA-binding transcrip 38.7 29 0.00063 31.7 2.9 48 244-297 155-202 (216)
160 PRK09638 RNA polymerase sigma 38.4 15 0.00032 31.5 0.9 35 262-296 139-173 (176)
161 PF13518 HTH_28: Helix-turn-he 38.2 16 0.00034 25.0 0.9 24 267-290 14-37 (52)
162 PF13411 MerR_1: MerR HTH fami 38.0 17 0.00036 26.5 1.1 21 268-288 3-23 (69)
163 PRK12522 RNA polymerase sigma 38.0 34 0.00074 29.3 3.1 36 262-297 132-167 (173)
164 TIGR03001 Sig-70_gmx1 RNA poly 37.9 28 0.0006 32.5 2.7 37 264-300 176-212 (244)
165 COG2963 Transposase and inacti 37.6 46 0.00099 27.0 3.7 42 242-287 5-47 (116)
166 TIGR03070 couple_hipB transcri 37.3 17 0.00036 25.0 0.9 23 268-290 18-40 (58)
167 PRK12543 RNA polymerase sigma 37.2 36 0.00078 29.4 3.2 36 263-298 131-166 (179)
168 PRK12511 RNA polymerase sigma 37.0 38 0.00082 29.8 3.3 49 245-298 112-160 (182)
169 PRK09649 RNA polymerase sigma 37.0 15 0.00033 32.2 0.8 33 263-295 144-176 (185)
170 PF01381 HTH_3: Helix-turn-hel 36.7 16 0.00034 25.4 0.7 23 268-290 12-34 (55)
171 cd01392 HTH_LacI Helix-turn-he 36.2 13 0.00028 25.6 0.2 21 270-290 2-22 (52)
172 PRK12527 RNA polymerase sigma 36.2 44 0.00096 28.1 3.5 36 263-298 119-154 (159)
173 PRK07122 RNA polymerase sigma 36.2 28 0.0006 32.8 2.5 48 244-296 215-262 (264)
174 PRK12544 RNA polymerase sigma 35.8 37 0.0008 30.6 3.1 34 266-299 165-198 (206)
175 PRK12531 RNA polymerase sigma 35.7 42 0.00092 29.4 3.5 34 263-296 155-188 (194)
176 PF13730 HTH_36: Helix-turn-he 35.7 23 0.0005 24.8 1.4 42 245-287 3-47 (55)
177 PF07638 Sigma70_ECF: ECF sigm 35.6 17 0.00036 32.2 0.8 33 264-296 150-182 (185)
178 PRK15008 HTH-type transcriptio 35.4 27 0.00058 31.1 2.2 41 250-291 24-64 (212)
179 PRK12529 RNA polymerase sigma 35.1 41 0.0009 29.1 3.3 31 265-295 143-173 (178)
180 PRK12542 RNA polymerase sigma 34.9 18 0.0004 31.4 1.0 35 263-297 136-170 (185)
181 PF15063 TC1: Thyroid cancer p 34.7 50 0.0011 26.3 3.2 40 241-280 30-69 (79)
182 TIGR02947 SigH_actino RNA poly 34.6 17 0.00036 31.9 0.7 38 262-299 144-181 (193)
183 PRK05803 sporulation sigma fac 34.5 34 0.00073 31.2 2.7 52 244-296 175-226 (233)
184 PRK12523 RNA polymerase sigma 34.5 44 0.00095 28.6 3.3 34 263-296 133-166 (172)
185 PF00376 MerR: MerR family reg 34.1 19 0.00041 24.3 0.7 20 268-287 2-21 (38)
186 PRK06288 RNA polymerase sigma 34.0 26 0.00057 32.8 1.9 49 244-297 212-260 (268)
187 PF08279 HTH_11: HTH domain; 33.6 43 0.00093 23.4 2.6 34 250-286 3-36 (55)
188 cd04763 HTH_MlrA-like Helix-Tu 33.5 19 0.00041 26.5 0.7 21 268-288 3-23 (68)
189 PF13565 HTH_32: Homeodomain-l 33.4 1.3E+02 0.0028 22.2 5.3 40 246-285 32-76 (77)
190 PRK09651 RNA polymerase sigma 33.4 25 0.00053 30.3 1.5 34 262-295 132-165 (172)
191 PRK07500 rpoH2 RNA polymerase 33.0 37 0.00081 32.4 2.8 52 244-298 227-278 (289)
192 PRK08215 sporulation sigma fac 32.4 36 0.00077 31.6 2.5 47 244-295 209-255 (258)
193 PRK09390 fixJ response regulat 32.3 32 0.00069 28.4 2.0 47 245-297 142-188 (202)
194 TIGR02392 rpoH_proteo alternat 32.2 39 0.00085 31.7 2.8 50 244-296 218-267 (270)
195 TIGR02394 rpoS_proteo RNA poly 32.0 46 0.001 31.4 3.3 54 244-298 222-275 (285)
196 TIGR02957 SigX4 RNA polymerase 31.7 45 0.00098 31.5 3.1 31 266-296 125-155 (281)
197 cd04764 HTH_MlrA-like_sg1 Heli 31.7 21 0.00046 26.1 0.7 21 268-288 3-23 (67)
198 TIGR01764 excise DNA binding d 31.6 23 0.0005 23.4 0.9 24 268-291 4-27 (49)
199 PRK11511 DNA-binding transcrip 31.5 40 0.00088 28.1 2.5 26 264-289 24-49 (127)
200 PRK05911 RNA polymerase sigma 31.4 35 0.00076 31.9 2.3 48 244-296 205-252 (257)
201 PF04936 DUF658: Protein of un 31.4 18 0.00039 32.7 0.3 36 266-301 15-50 (186)
202 TIGR02960 SigX5 RNA polymerase 30.8 60 0.0013 30.7 3.8 33 266-298 159-191 (324)
203 TIGR02885 spore_sigF RNA polym 30.8 44 0.00096 30.2 2.8 47 244-295 183-229 (231)
204 PRK09636 RNA polymerase sigma 30.7 48 0.001 31.3 3.1 32 266-297 132-163 (293)
205 TIGR02984 Sig-70_plancto1 RNA 30.6 41 0.00088 28.9 2.4 47 244-295 140-186 (189)
206 TIGR02846 spore_sigmaK RNA pol 30.6 51 0.0011 30.0 3.2 51 244-295 174-224 (227)
207 TIGR02835 spore_sigmaE RNA pol 30.4 51 0.0011 30.1 3.1 53 244-297 178-230 (234)
208 PRK09415 RNA polymerase factor 30.1 24 0.00052 30.6 0.9 33 264-296 142-174 (179)
209 cd00093 HTH_XRE Helix-turn-hel 29.9 27 0.00059 22.5 1.0 23 268-290 15-37 (58)
210 PRK09975 DNA-binding transcrip 29.6 33 0.00071 30.1 1.7 41 250-291 17-57 (213)
211 PRK11922 RNA polymerase sigma 29.6 25 0.00055 32.0 1.0 38 262-299 162-199 (231)
212 TIGR02607 antidote_HigA addict 28.6 29 0.00063 25.8 1.0 23 268-290 21-43 (78)
213 PF07022 Phage_CI_repr: Bacter 28.4 23 0.00049 26.4 0.4 21 268-288 15-36 (66)
214 PRK12525 RNA polymerase sigma 28.3 61 0.0013 27.7 3.1 32 263-294 132-163 (168)
215 PHA01976 helix-turn-helix prot 28.2 30 0.00065 25.0 1.0 23 268-290 18-40 (67)
216 PRK09640 RNA polymerase sigma 28.1 29 0.00063 30.3 1.1 36 262-297 147-182 (188)
217 cd01104 HTH_MlrA-CarA Helix-Tu 27.7 29 0.00063 25.1 0.9 20 268-287 3-22 (68)
218 PRK05572 sporulation sigma fac 27.1 49 0.0011 30.6 2.5 48 243-295 201-248 (252)
219 COG1595 RpoE DNA-directed RNA 27.0 34 0.00075 29.7 1.4 38 263-300 141-178 (182)
220 smart00530 HTH_XRE Helix-turn- 26.6 34 0.00074 21.8 1.0 23 268-290 13-35 (56)
221 PRK09726 antitoxin HipB; Provi 26.6 80 0.0017 24.6 3.3 22 268-289 28-49 (88)
222 PRK09958 DNA-binding transcrip 26.4 54 0.0012 27.7 2.4 45 243-293 142-186 (204)
223 PRK06596 RNA polymerase factor 26.3 57 0.0012 31.1 2.8 50 244-296 230-279 (284)
224 PRK11552 putative DNA-binding 26.3 52 0.0011 29.9 2.5 42 250-293 19-60 (225)
225 PRK12528 RNA polymerase sigma 26.0 69 0.0015 26.9 3.0 30 263-292 127-156 (161)
226 PTZ00183 centrin; Provisional 25.6 1.5E+02 0.0033 24.3 5.0 41 237-277 3-48 (158)
227 PRK10430 DNA-binding transcrip 25.5 71 0.0015 28.7 3.2 45 244-289 158-202 (239)
228 PHA00542 putative Cro-like pro 25.4 85 0.0018 24.4 3.2 23 267-289 33-55 (82)
229 PRK12517 RNA polymerase sigma 24.8 73 0.0016 28.0 3.1 39 263-301 142-180 (188)
230 PRK15411 rcsA colanic acid cap 24.8 27 0.00058 31.5 0.2 45 244-294 137-181 (207)
231 COG1905 NuoE NADH:ubiquinone o 24.7 84 0.0018 28.1 3.4 38 246-283 24-61 (160)
232 PRK10188 DNA-binding transcrip 24.5 80 0.0017 29.3 3.4 51 242-298 177-227 (240)
233 PF12728 HTH_17: Helix-turn-he 24.3 36 0.00078 23.5 0.8 24 268-291 4-27 (51)
234 PF01710 HTH_Tnp_IS630: Transp 24.2 74 0.0016 26.3 2.8 37 246-287 4-40 (119)
235 PLN03162 golden-2 like transcr 24.1 72 0.0016 32.5 3.1 61 237-297 232-294 (526)
236 KOG1151|consensus 24.1 2.1E+02 0.0045 30.5 6.4 38 76-113 5-44 (775)
237 smart00595 MADF subfamily of S 24.0 29 0.00063 26.6 0.3 34 268-301 30-63 (89)
238 PRK10668 DNA-binding transcrip 23.8 46 0.00099 29.3 1.6 43 248-291 15-57 (215)
239 COG1309 AcrR Transcriptional r 23.6 90 0.0019 24.9 3.2 33 257-290 25-57 (201)
240 PF13412 HTH_24: Winged helix- 23.2 75 0.0016 21.6 2.2 37 246-286 2-38 (48)
241 TIGR03613 RutR pyrimidine util 23.1 44 0.00096 29.0 1.3 40 250-290 14-53 (202)
242 TIGR03830 CxxCG_CxxCG_HTH puta 22.8 66 0.0014 26.2 2.2 43 241-290 61-103 (127)
243 PF13542 HTH_Tnp_ISL3: Helix-t 22.4 1.1E+02 0.0025 20.9 3.1 21 267-287 29-49 (52)
244 TIGR01557 myb_SHAQKYF myb-like 22.3 1E+02 0.0022 22.7 2.9 51 240-290 1-54 (57)
245 PRK14996 TetR family transcrip 21.7 86 0.0019 27.1 2.8 41 250-291 14-54 (192)
246 smart00422 HTH_MERR helix_turn 21.7 45 0.00097 24.2 0.9 20 268-287 3-22 (70)
247 PF13443 HTH_26: Cro/C1-type H 21.7 90 0.0019 22.2 2.5 34 252-285 26-60 (63)
248 PRK13870 transcriptional regul 21.7 86 0.0019 29.0 3.0 51 242-298 171-221 (234)
249 PRK13890 conjugal transfer pro 21.1 76 0.0016 26.6 2.3 19 262-280 44-62 (120)
250 PF13933 HRXXH: Putative pepti 21.0 1.4E+02 0.0031 28.6 4.2 62 227-289 33-94 (245)
251 PRK05988 formate dehydrogenase 20.9 1.1E+02 0.0024 26.9 3.4 36 248-283 24-59 (156)
252 cd01106 HTH_TipAL-Mta Helix-Tu 20.8 46 0.001 26.7 0.9 23 268-290 3-25 (103)
253 PF00424 REV: REV protein (ant 20.7 85 0.0018 25.7 2.3 35 250-298 14-48 (91)
254 PRK07539 NADH dehydrogenase su 20.3 1.1E+02 0.0024 26.5 3.3 36 248-283 23-58 (154)
255 TIGR01958 nuoE_fam NADH-quinon 20.3 1.1E+02 0.0025 26.3 3.3 36 248-283 17-52 (148)
256 PRK07405 RNA polymerase sigma 20.2 90 0.002 30.3 2.9 52 244-296 256-307 (317)
No 1
>KOG0489|consensus
Probab=99.82 E-value=6.5e-21 Score=179.20 Aligned_cols=79 Identities=73% Similarity=1.201 Sum_probs=73.2
Q ss_pred CCCCCcchhccc----------ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhh
Q psy3281 225 PSPLYPWMRSQF----------ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294 (317)
Q Consensus 225 ~s~~~P~~~s~~----------krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~K 294 (317)
+..+++||+... +.||.||.||..||.+||++|..|+|+++..|.|||..|+|+|++|||||||||+|||
T Consensus 136 ~~~~~p~~~~~~~~~~~~~~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~K 215 (261)
T KOG0489|consen 136 SNQIYPWMKSTANYLSSSETGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWK 215 (261)
T ss_pred ccccccchhhhhcccccccccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHH
Confidence 347899999864 5789999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcccCCC
Q psy3281 295 KENKSKDGG 303 (317)
Q Consensus 295 K~~k~k~~~ 303 (317)
|.++.+...
T Consensus 216 k~~k~~~~~ 224 (261)
T KOG0489|consen 216 KENKAKSSQ 224 (261)
T ss_pred Hhhcccccc
Confidence 998877754
No 2
>KOG0487|consensus
Probab=99.73 E-value=2.5e-18 Score=164.52 Aligned_cols=74 Identities=53% Similarity=0.790 Sum_probs=67.1
Q ss_pred CCcchhcccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281 228 LYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301 (317)
Q Consensus 228 ~~P~~~s~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~ 301 (317)
..+|...-++.||||.-+|+.|+.+||++|..|.|++++.|.||++.|+|+++||||||||||.|+||.++...
T Consensus 225 ~~~~~~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 225 HLPNASSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred CCcccccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence 44566666677889999999999999999999999999999999999999999999999999999999987444
No 3
>KOG0850|consensus
Probab=99.73 E-value=8.1e-18 Score=154.33 Aligned_cols=67 Identities=39% Similarity=0.611 Sum_probs=62.9
Q ss_pred ccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281 235 QFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301 (317)
Q Consensus 235 ~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~ 301 (317)
.+|.||.||.|+..||..|.+.|+++.|+...||.+||..|||+.++|||||||||.|.||..|.+.
T Consensus 119 ~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~ 185 (245)
T KOG0850|consen 119 GKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGS 185 (245)
T ss_pred cccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCC
Confidence 3466788999999999999999999999999999999999999999999999999999999999555
No 4
>KOG0488|consensus
Probab=99.71 E-value=6.8e-18 Score=162.42 Aligned_cols=66 Identities=42% Similarity=0.765 Sum_probs=61.7
Q ss_pred cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281 236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301 (317)
Q Consensus 236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~ 301 (317)
+|+||.||.||..||..||+.|++.+|++..+|++||..|||+..|||+||||||+||||......
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~ 235 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGG 235 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhh
Confidence 577788999999999999999999999999999999999999999999999999999999766533
No 5
>KOG0843|consensus
Probab=99.68 E-value=8e-17 Score=143.23 Aligned_cols=64 Identities=41% Similarity=0.654 Sum_probs=60.9
Q ss_pred ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhccc
Q psy3281 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK 300 (317)
Q Consensus 237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k 300 (317)
+.||.||.||.+||..||..|+.+.|....||+.||..|+|++.+|||||||||.|.||+...+
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 6688999999999999999999999999999999999999999999999999999999987763
No 6
>KOG2251|consensus
Probab=99.68 E-value=5.3e-17 Score=148.23 Aligned_cols=68 Identities=32% Similarity=0.510 Sum_probs=63.7
Q ss_pred hcccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhccc
Q psy3281 233 RSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK 300 (317)
Q Consensus 233 ~s~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k 300 (317)
...+|.||+||+|+..||++||..|.++.||++..|++||.+|+|.+.+|+|||+|||+|+|+..+..
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 44567789999999999999999999999999999999999999999999999999999999988764
No 7
>KOG0484|consensus
Probab=99.67 E-value=8.3e-18 Score=137.96 Aligned_cols=66 Identities=38% Similarity=0.579 Sum_probs=62.4
Q ss_pred hcccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 233 RSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 233 ~s~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
.+++|.||.||.||..||.+||+.|..+.||++-.|++||.++.|++.+|+|||||||+|.||.++
T Consensus 12 ~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 12 TEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred hHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 456678899999999999999999999999999999999999999999999999999999999765
No 8
>KOG0494|consensus
Probab=99.67 E-value=5.9e-17 Score=150.95 Aligned_cols=71 Identities=38% Similarity=0.601 Sum_probs=64.2
Q ss_pred hcccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCCC
Q psy3281 233 RSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGG 303 (317)
Q Consensus 233 ~s~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~~ 303 (317)
++++|+|+.||.||..|+++||+.|++..||+...|+.||.++.|.|.+|+|||||||+||||++|....+
T Consensus 136 kkk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~s 206 (332)
T KOG0494|consen 136 KKKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGS 206 (332)
T ss_pred ccccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcc
Confidence 33445555699999999999999999999999999999999999999999999999999999999987654
No 9
>KOG0842|consensus
Probab=99.67 E-value=4.8e-17 Score=155.70 Aligned_cols=69 Identities=39% Similarity=0.624 Sum_probs=63.9
Q ss_pred cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCCCC
Q psy3281 236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGGS 304 (317)
Q Consensus 236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~~~ 304 (317)
.+|||.|..||..|+.+||+.|+..+|++..||+.||..|.||++||||||||||-|.||..+.+...+
T Consensus 151 ~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~ 219 (307)
T KOG0842|consen 151 RKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA 219 (307)
T ss_pred ccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence 466778889999999999999999999999999999999999999999999999999999988887433
No 10
>KOG0848|consensus
Probab=99.66 E-value=2.1e-17 Score=154.44 Aligned_cols=76 Identities=54% Similarity=0.838 Sum_probs=66.9
Q ss_pred CCCCCcchhccc-----------ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhh
Q psy3281 225 PSPLYPWMRSQF-----------ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 293 (317)
Q Consensus 225 ~s~~~P~~~s~~-----------krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~ 293 (317)
....+.||++.- .+.|-|.++|+.|..+||++|..++|+++..+.|||..|||+|++|||||||||+|+
T Consensus 175 R~s~~dwmrkpa~~~~g~~~KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKE 254 (317)
T KOG0848|consen 175 RRSPYDWMRKPAQPGTGQNVKTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKE 254 (317)
T ss_pred CCChhhhhhcccccCCCCCceeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHH
Confidence 345678887631 223568899999999999999999999999999999999999999999999999999
Q ss_pred hhhhccc
Q psy3281 294 KKENKSK 300 (317)
Q Consensus 294 KK~~k~k 300 (317)
||.+|++
T Consensus 255 RK~nKKk 261 (317)
T KOG0848|consen 255 RKDNKKK 261 (317)
T ss_pred HHHHHHH
Confidence 9998887
No 11
>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=99.62 E-value=2.9e-16 Score=114.11 Aligned_cols=57 Identities=51% Similarity=0.674 Sum_probs=55.4
Q ss_pred CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
||+|+.||.+|+.+|+.+|..+.||+..++++||..|||+..+|++||+|||.++||
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 578999999999999999999999999999999999999999999999999999986
No 12
>KOG0485|consensus
Probab=99.61 E-value=1.9e-16 Score=144.53 Aligned_cols=67 Identities=42% Similarity=0.740 Sum_probs=62.2
Q ss_pred ccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281 235 QFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301 (317)
Q Consensus 235 ~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~ 301 (317)
..+|||.||+|+..|+..||..|+..+|++..||..||++|.|+|.||||||||||.||||......
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ 167 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADL 167 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhh
Confidence 3477899999999999999999999999999999999999999999999999999999999765444
No 13
>KOG0492|consensus
Probab=99.60 E-value=4.1e-16 Score=141.44 Aligned_cols=72 Identities=38% Similarity=0.558 Sum_probs=65.4
Q ss_pred cchhcccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281 230 PWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301 (317)
Q Consensus 230 P~~~s~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~ 301 (317)
..+++.+..|+.||-||..||..||+.|....|++++||.+++..|.|++.+|||||||||+|.||.+..+.
T Consensus 136 C~LrKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~ 207 (246)
T KOG0492|consen 136 CTLRKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAEL 207 (246)
T ss_pred chhcccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHH
Confidence 345666777889999999999999999999999999999999999999999999999999999999766544
No 14
>KOG3802|consensus
Probab=99.53 E-value=5.5e-15 Score=144.75 Aligned_cols=70 Identities=27% Similarity=0.333 Sum_probs=64.5
Q ss_pred CcchhcccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 229 YPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 229 ~P~~~s~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
...+....+|||+||.|....+..||++|.+|+.|+..|+..||++|+|.+++|+|||+|||.|+||...
T Consensus 285 ~e~i~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 285 IEKIGAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred HHHhhccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 3344445588899999999999999999999999999999999999999999999999999999999888
No 15
>KOG0491|consensus
Probab=99.52 E-value=3.1e-15 Score=131.62 Aligned_cols=71 Identities=42% Similarity=0.706 Sum_probs=65.0
Q ss_pred ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCCCCCCC
Q psy3281 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGGSDAG 307 (317)
Q Consensus 237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~~~s~~ 307 (317)
+++|.|++|+..|+..||+.|++.+|++..||.|||..|+|++++||.||||||+|.||..++....++.+
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~nS~~ 169 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPKNSNG 169 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCCCCCc
Confidence 56778999999999999999999999999999999999999999999999999999999988887554443
No 16
>KOG0493|consensus
Probab=99.52 E-value=7e-15 Score=137.33 Aligned_cols=63 Identities=54% Similarity=0.763 Sum_probs=58.6
Q ss_pred CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301 (317)
Q Consensus 239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~ 301 (317)
||.||.||.+||..|+.+|..|+|+++..|.+||.+|+|.|.+|||||||+|+|.||.--.+.
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn 309 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKN 309 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCC
Confidence 578999999999999999999999999999999999999999999999999999998654443
No 17
>KOG0486|consensus
Probab=99.50 E-value=1.3e-14 Score=138.39 Aligned_cols=72 Identities=38% Similarity=0.631 Sum_probs=65.9
Q ss_pred cchhcccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281 230 PWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301 (317)
Q Consensus 230 P~~~s~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~ 301 (317)
+.+++.+|+||.||.|+..||.+||..|.+|+||+-+.|+|||..++|+|.+|++||+|||+||||+++...
T Consensus 104 ~~~kki~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 104 PNKKKISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred cccchhhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 344555578899999999999999999999999999999999999999999999999999999999887665
No 18
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.49 E-value=2.3e-14 Score=103.67 Aligned_cols=58 Identities=55% Similarity=0.788 Sum_probs=54.8
Q ss_pred CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
++.|+.|+.+++.+||.+|..++||+..++++||..|||++++|++||+|||.+.|+.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 3667899999999999999999999999999999999999999999999999998874
No 19
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.49 E-value=2.2e-14 Score=103.27 Aligned_cols=56 Identities=55% Similarity=0.880 Sum_probs=52.8
Q ss_pred CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhh
Q psy3281 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294 (317)
Q Consensus 239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~K 294 (317)
++.|+.|+.+++.+|+.+|..+.||+..++++||..|||+.++|++||+|||.+.|
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 35678899999999999999999999999999999999999999999999999864
No 20
>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=99.49 E-value=2.8e-14 Score=106.14 Aligned_cols=53 Identities=21% Similarity=0.358 Sum_probs=51.0
Q ss_pred cCCCCcccCHHHHHHHHHHhhhCCC----CCHHHHHHHHHHcCCCcccchhhcccch
Q psy3281 238 RKRGRQTYTRYQTLELEKEFHFNRY----LTRRRRIEIAHALCLTERQIKIWFQNRR 290 (317)
Q Consensus 238 rRR~Rt~fT~~Ql~~LE~~F~~n~y----Ps~~er~eLA~~LgLse~qVkiWFQNRR 290 (317)
+||.||.||.+|+..||++|+.+.| |+..++++||..|||++++|+|||+|.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 4789999999999999999999999 9999999999999999999999999965
No 21
>KOG0844|consensus
Probab=99.47 E-value=1.2e-14 Score=138.21 Aligned_cols=65 Identities=48% Similarity=0.671 Sum_probs=60.7
Q ss_pred cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhccc
Q psy3281 236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK 300 (317)
Q Consensus 236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k 300 (317)
..-||-||.||.|||..||++|-+..|.++..|.|||..|+|.|..||+||||||+|+||.+..-
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlam 243 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAM 243 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhc
Confidence 35579999999999999999999999999999999999999999999999999999999976643
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.46 E-value=7e-14 Score=122.86 Aligned_cols=66 Identities=35% Similarity=0.515 Sum_probs=61.0
Q ss_pred cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281 236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301 (317)
Q Consensus 236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~ 301 (317)
...+++|++.|.+|+.+|++.|++++||+..+|.+|+..|+|+++.|+|||||||++.|+....+.
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~ 114 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKV 114 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccch
Confidence 355778889999999999999999999999999999999999999999999999999999877644
No 23
>KOG0483|consensus
Probab=99.41 E-value=8.7e-14 Score=126.43 Aligned_cols=63 Identities=37% Similarity=0.592 Sum_probs=58.1
Q ss_pred cCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhccc
Q psy3281 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK 300 (317)
Q Consensus 238 rRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k 300 (317)
.++++.+|+.+|+..||+.|+.+.++..+++..||+.|||.+++|+|||||||+|||.++...
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~ 112 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEK 112 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhh
Confidence 456677899999999999999999999999999999999999999999999999999876543
No 24
>KOG0847|consensus
Probab=99.29 E-value=1.2e-12 Score=119.90 Aligned_cols=64 Identities=42% Similarity=0.776 Sum_probs=59.8
Q ss_pred ccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 235 QFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 235 ~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
..+++..|.+|+..||..||+.|+..+|+-.++|.+||..+|+++.+|+|||||||.||||+..
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 4467778999999999999999999999999999999999999999999999999999999744
No 25
>KOG4577|consensus
Probab=99.28 E-value=2.4e-12 Score=121.89 Aligned_cols=65 Identities=31% Similarity=0.419 Sum_probs=61.2
Q ss_pred ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301 (317)
Q Consensus 237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~ 301 (317)
..||.||+||+.||+.|+.+|+..+.|.+-.|+.|+.++||..++|+|||||||+|+||.+|...
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcc
Confidence 45899999999999999999999999999999999999999999999999999999999887543
No 26
>KOG0490|consensus
Probab=99.25 E-value=5.3e-12 Score=113.99 Aligned_cols=64 Identities=33% Similarity=0.420 Sum_probs=60.9
Q ss_pred ccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 235 QFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 235 ~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
..++||.|+.|+..++++||+.|+++.||+...|+.||..++|++..|++||+|||+||++.++
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 4577899999999999999999999999999999999999999999999999999999999874
No 27
>KOG1168|consensus
Probab=99.10 E-value=3.4e-11 Score=114.22 Aligned_cols=65 Identities=28% Similarity=0.384 Sum_probs=60.6
Q ss_pred cccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhccc
Q psy3281 236 FERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK 300 (317)
Q Consensus 236 ~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k 300 (317)
..|||+||.+..-+.+.||.+|...+.|+.+.+..||++|+|.+.+|++||+|.|.|.||++...
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa 371 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSA 371 (385)
T ss_pred cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhh
Confidence 36789999999999999999999999999999999999999999999999999999999966544
No 28
>KOG0849|consensus
Probab=99.05 E-value=1.4e-10 Score=113.84 Aligned_cols=71 Identities=30% Similarity=0.507 Sum_probs=63.5
Q ss_pred CcchhcccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281 229 YPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS 299 (317)
Q Consensus 229 ~P~~~s~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~ 299 (317)
.+.....++.+|+||+|+.+|++.||+.|+++.||++..|++||.+++|++..|.+||+|||+|+||....
T Consensus 167 ~p~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 167 PPGYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred cccccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 33344455677889999999999999999999999999999999999999999999999999999998843
No 29
>KOG0775|consensus
Probab=98.91 E-value=1.6e-09 Score=102.22 Aligned_cols=55 Identities=27% Similarity=0.386 Sum_probs=49.7
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
.|...-..+|.++|..++||+.+++.+||+++||+..||-+||+|||.|+|-...
T Consensus 182 CFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~a 236 (304)
T KOG0775|consen 182 CFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAA 236 (304)
T ss_pred ehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhccc
Confidence 4666678899999999999999999999999999999999999999999994433
No 30
>KOG0774|consensus
Probab=98.60 E-value=2.3e-08 Score=94.01 Aligned_cols=59 Identities=29% Similarity=0.523 Sum_probs=55.3
Q ss_pred cCCCCcccCHHHHHHHHHHhh---hCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 238 RKRGRQTYTRYQTLELEKEFH---FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 238 rRR~Rt~fT~~Ql~~LE~~F~---~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
.||+|+.|++...++|..+|- .|+||+.+++++||++++++..+|..||.|+|-+.||.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 478899999999999999995 57899999999999999999999999999999999985
No 31
>KOG2252|consensus
Probab=98.39 E-value=4.1e-07 Score=92.91 Aligned_cols=58 Identities=24% Similarity=0.282 Sum_probs=54.2
Q ss_pred ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhh
Q psy3281 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294 (317)
Q Consensus 237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~K 294 (317)
..||.|.+||..|++.|..+|+.+++|+.+..+.|+..|+|....|.+||-|-|+|.+
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSL 476 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence 3477899999999999999999999999999999999999999999999999988853
No 32
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.37 E-value=1.2e-07 Score=65.55 Aligned_cols=34 Identities=32% Similarity=0.589 Sum_probs=29.1
Q ss_pred hCCCCCHHHHHHHHHHcCCCcccchhhcccchhh
Q psy3281 259 FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 292 (317)
Q Consensus 259 ~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK 292 (317)
.++||+.+|+++||+++||+.++|..||-|.|.|
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 4789999999999999999999999999999875
No 33
>KOG1146|consensus
Probab=98.00 E-value=5.4e-06 Score=91.59 Aligned_cols=77 Identities=25% Similarity=0.339 Sum_probs=66.9
Q ss_pred ccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCCCCCCCCCCCCC
Q psy3281 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGGSDAGSDITPA 313 (317)
Q Consensus 237 krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~~~s~~s~~sp~ 313 (317)
.+|+.|+.++..+|++|..+|..-.++..++.|.|.+.++|..+.|.+||+|.|.|.||........++.+...++-
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~~~~ss~~~s~sp~ 978 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNGTAASSTGGSSSPL 978 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhccccccccccccCcc
Confidence 56789999999999999999999999999999999999999999999999999999999888664444444444443
No 34
>KOG0490|consensus
Probab=97.98 E-value=8.1e-06 Score=73.70 Aligned_cols=64 Identities=34% Similarity=0.494 Sum_probs=59.4
Q ss_pred ccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 235 QFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 235 ~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
..+.++.|+.|+..++..|+..|..+.+|+...++.|+..+|++++.|.+||+|+|.+.|+...
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 3466788999999999999999999999999999999999999999999999999999998655
No 35
>KOG0773|consensus
Probab=96.83 E-value=0.00074 Score=65.62 Aligned_cols=60 Identities=18% Similarity=0.270 Sum_probs=50.8
Q ss_pred ccCCCCcccCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 237 ERKRGRQTYTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 237 krRR~Rt~fT~~Ql~~LE~~F~~---n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
.++|.+..|.+....+|+.++.. .+||+..++..||+++||+..+|.+||-|.|.|..+.
T Consensus 238 ~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p 300 (342)
T KOG0773|consen 238 SKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKP 300 (342)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCc
Confidence 34566678999999999988432 4699999999999999999999999999999876653
No 36
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.83 E-value=0.00058 Score=50.72 Aligned_cols=43 Identities=19% Similarity=0.302 Sum_probs=31.5
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhh
Q psy3281 250 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 292 (317)
Q Consensus 250 l~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK 292 (317)
+..|+++|...+++...+...|..+.+|+..+|+.||-.|+.+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 4569999999999999999999999999999999999766543
No 37
>KOG3623|consensus
Probab=96.14 E-value=0.0062 Score=64.87 Aligned_cols=52 Identities=19% Similarity=0.270 Sum_probs=47.6
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281 250 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301 (317)
Q Consensus 250 l~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~ 301 (317)
+.+|+.+|..|.+|+.+|...||..+||+.+.|+.||.+++++++..++.-.
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps 619 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPS 619 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCcc
Confidence 7889999999999999999999999999999999999999999888765433
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=95.20 E-value=0.028 Score=40.89 Aligned_cols=47 Identities=21% Similarity=0.344 Sum_probs=35.5
Q ss_pred CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccch
Q psy3281 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR 290 (317)
Q Consensus 239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRR 290 (317)
||+|..+|-++...+-..++... ...+||.++|++..+|..|..|+.
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 57889999999887777777666 477899999999999999998853
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=88.92 E-value=0.42 Score=33.51 Aligned_cols=47 Identities=13% Similarity=0.146 Sum_probs=35.6
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
.+++.+..+|...| .......++|+.+|++...|+.+...-..|.|+
T Consensus 4 ~L~~~er~vi~~~y-----~~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRY-----FEGLTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHH-----TST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh-----cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 46788999999888 233457889999999999999998766666553
No 40
>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=83.57 E-value=2 Score=25.72 Aligned_cols=38 Identities=18% Similarity=0.117 Sum_probs=27.1
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhc
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWF 286 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWF 286 (317)
.++.+....+...|.. .. ...++|+.++++...|..|+
T Consensus 5 ~~~~~~~~~i~~~~~~-~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAA-GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHc-CC----CHHHHHHHHCCCHHHHHHhC
Confidence 4566666666666653 22 46688999999999998884
No 41
>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=83.11 E-value=0.85 Score=30.53 Aligned_cols=44 Identities=14% Similarity=0.096 Sum_probs=32.4
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 292 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK 292 (317)
.++..+..+|+..|. ......++|+.+|++...|+.|...-+.+
T Consensus 10 ~l~~~~~~~~~~~~~-----~~~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFG-----EGLSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 456777777776653 22456788999999999999998665544
No 42
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=81.07 E-value=0.85 Score=34.16 Aligned_cols=44 Identities=18% Similarity=0.310 Sum_probs=28.9
Q ss_pred CCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcc
Q psy3281 240 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 287 (317)
Q Consensus 240 R~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQ 287 (317)
++|+.||.++...+-..+. .......+||+++||+...|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~----~~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYL----ESGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHH----HHHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHH----HCCCceEeeecccccccccccHHHH
Confidence 4677899998776666552 2235678899999999999999964
No 43
>KOG3755|consensus
Probab=77.44 E-value=1.4 Score=46.66 Aligned_cols=73 Identities=19% Similarity=0.188 Sum_probs=60.5
Q ss_pred chhcccccCCCCcccCHHHHHHHHHHhhhCC-CCCHHH---HHHHHHHcCCCcccchhhcccchhhhhhhhcccCCC
Q psy3281 231 WMRSQFERKRGRQTYTRYQTLELEKEFHFNR-YLTRRR---RIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGG 303 (317)
Q Consensus 231 ~~~s~~krRR~Rt~fT~~Ql~~LE~~F~~n~-yPs~~e---r~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~~ 303 (317)
++.....++|+|+.++.+.+.+|..+..... ||+.+. ...|+..+++.++.|...|+|.|...|+..+.+..+
T Consensus 640 f~~~n~~~p~~~~~isge~~~~~qs~i~~~gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~~~w~~k~~s 716 (769)
T KOG3755|consen 640 FYLKNWHKPRKRTKISGEALGILQSFITDVGLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVKHHWKLKTRS 716 (769)
T ss_pred HHHHhccCccccceecccchHHHHHHHHHhccCchhhcccccchhhhhhcccHHHHHHhhhcceeecchhheecccC
Confidence 3455566789999999999999998876544 898888 889999999999999999999998888766665543
No 44
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=75.94 E-value=3.3 Score=36.23 Aligned_cols=51 Identities=18% Similarity=0.058 Sum_probs=39.7
Q ss_pred CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 242 Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
...++..++.+|+..+ ......+||+.||++...|+.|..+.|.|.|+...
T Consensus 4 ~~~Lt~rqreVL~lr~------~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 4 ESFLTERQIEVLRLRE------RGLTQQEIADILGTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred ccCCCHHHHHHHHHHH------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4568899999997732 22346789999999999999999988887776543
No 45
>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=74.30 E-value=4 Score=30.70 Aligned_cols=46 Identities=20% Similarity=0.325 Sum_probs=23.4
Q ss_pred CCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcc
Q psy3281 241 GRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 287 (317)
Q Consensus 241 ~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQ 287 (317)
.|..|+.........+|.....--...|. -|.++|++++.|+.|.+
T Consensus 2 ~rrsy~~~FKL~Vv~~a~~~~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 2 SRRSYTAEFKLKVVEYAEKDNNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp ------HHHHHHHHHHHHH-TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred CccccChHHHHHHHHHHHHccchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 35567777644444444433332223343 49999999999999974
No 46
>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=73.13 E-value=3.9 Score=30.00 Aligned_cols=42 Identities=17% Similarity=0.211 Sum_probs=33.6
Q ss_pred cCHHHHHHHHHHhhhCCC--CCHHHHHHHHHHcCCCcccchhhc
Q psy3281 245 YTRYQTLELEKEFHFNRY--LTRRRRIEIAHALCLTERQIKIWF 286 (317)
Q Consensus 245 fT~~Ql~~LE~~F~~n~y--Ps~~er~eLA~~LgLse~qVkiWF 286 (317)
+|+.|+++|+.+|+..=| |-.....+||++||+++..|..-+
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 578899999999986653 556677899999999998776544
No 47
>PF13388 DUF4106: Protein of unknown function (DUF4106)
Probab=72.73 E-value=15 Score=36.18 Aligned_cols=31 Identities=19% Similarity=0.223 Sum_probs=20.0
Q ss_pred cCCCCcccCHHHHHHHHHHhhhCCCCCHHHH
Q psy3281 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRR 268 (317)
Q Consensus 238 rRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er 268 (317)
-||.|..-..++|..|++.|-....++..+|
T Consensus 256 HKrSreqgnqeflkmLke~~g~~d~~dfsdr 286 (422)
T PF13388_consen 256 HKRSREQGNQEFLKMLKENYGYPDTLDFSDR 286 (422)
T ss_pred hhhhhhhhhHHHHHHHHhccCCCCccchhHH
Confidence 3566777788888888877654444444444
No 48
>KOG1146|consensus
Probab=71.60 E-value=3.9 Score=46.86 Aligned_cols=65 Identities=14% Similarity=-0.026 Sum_probs=55.4
Q ss_pred cCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCC
Q psy3281 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDG 302 (317)
Q Consensus 238 rRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~ 302 (317)
.+-.|++++..++.+|..+|+...++.-.+...++..|++-.+.+-.||++++.++.+...+...
T Consensus 444 ~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~ar 508 (1406)
T KOG1146|consen 444 PLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLAR 508 (1406)
T ss_pred hhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccc
Confidence 34467888999999999999999999999999999999999999888998888888775554443
No 49
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=71.53 E-value=2.9 Score=35.39 Aligned_cols=36 Identities=17% Similarity=0.096 Sum_probs=29.0
Q ss_pred CHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281 264 TRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS 299 (317)
Q Consensus 264 s~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~ 299 (317)
......+||+.+|+++..|+.|+..-|.|.|+.-..
T Consensus 140 ~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~ 175 (179)
T PRK11924 140 EGLSYREIAEILGVPVGTVKSRLRRARQLLRECLEA 175 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 344568899999999999999998888887765443
No 50
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=71.05 E-value=4.5 Score=35.68 Aligned_cols=48 Identities=13% Similarity=0.111 Sum_probs=34.1
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297 (317)
Q Consensus 245 fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~ 297 (317)
++..+..+|...| ......++||+.||++...|++|+..-|.+.|+.-
T Consensus 143 L~~~~r~vl~l~~-----~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 143 LTDTQRESVTLAY-----YGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 4455555554332 33356788999999999999999987777777654
No 51
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=70.35 E-value=3.6 Score=35.83 Aligned_cols=40 Identities=13% Similarity=0.141 Sum_probs=31.2
Q ss_pred CHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCCC
Q psy3281 264 TRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGG 303 (317)
Q Consensus 264 s~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~~ 303 (317)
.....++||+.||++...|+.+...-|.+.|+.......+
T Consensus 143 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~ 182 (186)
T PRK05602 143 QGLSNIEAAAVMDISVDALESLLARGRRALRAQLADLPGS 182 (186)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 3345678999999999999999988888877766555443
No 52
>KOG3623|consensus
Probab=70.26 E-value=3.4 Score=44.86 Aligned_cols=64 Identities=11% Similarity=0.069 Sum_probs=52.3
Q ss_pred CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCC
Q psy3281 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDG 302 (317)
Q Consensus 239 RR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~ 302 (317)
-|.|+.+..++-..|..+++.+-.++..+...++.+|-..+.+|.+||.+|+...++.......
T Consensus 627 ~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl~lts 690 (1007)
T KOG3623|consen 627 VKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPLFLTS 690 (1007)
T ss_pred ccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCcccccc
Confidence 3556777777788889999988888888888888888899999999999999998877665543
No 53
>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=69.94 E-value=3.7 Score=29.51 Aligned_cols=46 Identities=20% Similarity=0.055 Sum_probs=34.3
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
.||..++.+|+....- ....++|..++++++.|+.+..+=+.|.+-
T Consensus 3 ~LT~~E~~vl~~l~~G------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG------MSNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp SS-HHHHHHHHHHHTT------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred ccCHHHHHHHHHHHhc------CCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 5788888888766432 347789999999999999998877766553
No 54
>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=69.73 E-value=2.6 Score=29.67 Aligned_cols=43 Identities=23% Similarity=0.225 Sum_probs=27.7
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhh
Q psy3281 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 292 (317)
Q Consensus 245 fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK 292 (317)
+++.+..++... |.......++|+.+|+++..|+.|...-|.+
T Consensus 11 L~~~~r~i~~l~-----~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 11 LPERQREIFLLR-----YFQGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp S-HHHHHHHHHH-----HTS---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHH-----HHHCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 455555555544 3444567899999999999999999755443
No 55
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=69.48 E-value=5 Score=34.21 Aligned_cols=40 Identities=20% Similarity=0.076 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCC
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDG 302 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~ 302 (317)
......++||..||+++..|++|...-|.|.|+.-+...+
T Consensus 122 ~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~~~ 161 (165)
T PRK09644 122 VHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEEKS 161 (165)
T ss_pred HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 3445678899999999999999999888888876655444
No 56
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=68.51 E-value=5.5 Score=27.09 Aligned_cols=44 Identities=23% Similarity=0.157 Sum_probs=31.1
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 293 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~ 293 (317)
.++..+..++...+. . ....+||+.++++...|+.|...-+.|.
T Consensus 3 ~l~~~e~~i~~~~~~--g----~s~~eia~~l~is~~tv~~~~~~~~~kl 46 (58)
T smart00421 3 SLTPREREVLRLLAE--G----LTNKEIAERLGISEKTVKTHLSNIMRKL 46 (58)
T ss_pred CCCHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 367777777765432 2 2568899999999999999987544443
No 57
>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=68.21 E-value=1.8 Score=33.93 Aligned_cols=37 Identities=22% Similarity=0.216 Sum_probs=29.1
Q ss_pred HHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccc
Q psy3281 253 LEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 289 (317)
Q Consensus 253 LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNR 289 (317)
.+..|....+.......+||+.+|+++..|+.|+.+.
T Consensus 20 ~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~ 56 (73)
T TIGR03879 20 AEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGE 56 (73)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcC
Confidence 3445666666666678899999999999999999753
No 58
>PRK04217 hypothetical protein; Provisional
Probab=67.47 E-value=6.1 Score=33.15 Aligned_cols=51 Identities=10% Similarity=-0.141 Sum_probs=38.5
Q ss_pred cccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 243 QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 243 t~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
..++.+++.+|...|...- ..++||+.+|++...|+..+...|.+.|....
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L~ 91 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQMLV 91 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3567888877776654322 57789999999999999999877777766543
No 59
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=67.26 E-value=6.3 Score=32.90 Aligned_cols=46 Identities=15% Similarity=0.146 Sum_probs=32.3
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 245 fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
++..+..++...| ......++||+.+|+++..|+.|...-|.|.|+
T Consensus 107 L~~~~r~ii~l~~-----~~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 107 LDEKEKYIIFERF-----FVGKTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred CCHHHHHHHHHHH-----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 4444545444333 334557899999999999999998876666654
No 60
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=65.82 E-value=5.4 Score=35.30 Aligned_cols=38 Identities=13% Similarity=-0.018 Sum_probs=30.3
Q ss_pred CHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281 264 TRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301 (317)
Q Consensus 264 s~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~ 301 (317)
......+||+.||+++..|+++...-|.+.|+..+...
T Consensus 131 ~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~ 168 (187)
T PRK12516 131 SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG 168 (187)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 34456789999999999999999888888877655443
No 61
>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=65.82 E-value=4.9 Score=32.28 Aligned_cols=46 Identities=20% Similarity=0.189 Sum_probs=32.2
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 245 fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
++..+..+|...| .......+||+.+|++++.|+.|...-+.|.|+
T Consensus 111 L~~~~~~ii~~~~-----~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRY-----LEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHH-----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4555555554432 233457789999999999999998877666654
No 62
>PRK10072 putative transcriptional regulator; Provisional
Probab=65.49 E-value=6.5 Score=32.13 Aligned_cols=41 Identities=20% Similarity=0.176 Sum_probs=30.2
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 291 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRa 291 (317)
..+...+..|.+.... ...+||+.+|++...|..|...+|.
T Consensus 32 ~~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 3466667766544322 2678999999999999999988764
No 63
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=65.00 E-value=4.1 Score=28.23 Aligned_cols=40 Identities=15% Similarity=0.073 Sum_probs=21.1
Q ss_pred cccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcc
Q psy3281 243 QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 287 (317)
Q Consensus 243 t~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQ 287 (317)
..||.++...++..++.. ....+||+.||++...|..|.+
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 467888888888776532 4566799999999999988864
No 64
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=64.98 E-value=4.7 Score=34.21 Aligned_cols=49 Identities=8% Similarity=-0.058 Sum_probs=35.4
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~ 297 (317)
.++..+..+|...|- ......+||..||+++..|+.|...-|.|.|+.-
T Consensus 128 ~L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREI-----EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 466666666665432 3345678999999999999999987676666543
No 65
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=64.52 E-value=5.3 Score=34.45 Aligned_cols=34 Identities=15% Similarity=0.256 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
......++||..||+++..|++++..-|.+.|+.
T Consensus 143 ~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 143 LEGLSYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred HcCCCHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 3344578899999999999999998777777664
No 66
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=61.26 E-value=8 Score=33.52 Aligned_cols=51 Identities=14% Similarity=0.074 Sum_probs=36.6
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS 299 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~ 299 (317)
.++..+..+|...| ......++||..||++...|+.++..-|.+.|+.-..
T Consensus 131 ~L~~~~r~v~~l~~-----~~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~~ 181 (184)
T PRK12512 131 TLPPRQRDVVQSIS-----VEGASIKETAAKLSMSEGAVRVALHRGLAALAAKFRS 181 (184)
T ss_pred hCCHHHHHHHHHHH-----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 34555555555543 3344578899999999999999998888887765443
No 67
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=61.02 E-value=4.6 Score=35.31 Aligned_cols=35 Identities=20% Similarity=0.212 Sum_probs=28.8
Q ss_pred CCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 262 YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 262 yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
|.......+||..+|++...|+.|+..-|.|.|+.
T Consensus 154 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 154 YYEGLSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred hhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 34556678899999999999999998777777764
No 68
>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=60.61 E-value=4 Score=30.78 Aligned_cols=20 Identities=30% Similarity=0.529 Sum_probs=17.5
Q ss_pred HHHHHHHHcCCCcccchhhc
Q psy3281 267 RRIEIAHALCLTERQIKIWF 286 (317)
Q Consensus 267 er~eLA~~LgLse~qVkiWF 286 (317)
...+||++||+++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 35678999999999999994
No 69
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=60.36 E-value=9.9 Score=32.08 Aligned_cols=34 Identities=21% Similarity=0.127 Sum_probs=27.7
Q ss_pred HHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 265 RRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 265 ~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
....++||+.||+++..|++++..-|.+.|+..+
T Consensus 122 g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (160)
T PRK09642 122 EKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWK 155 (160)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 3456789999999999999999888877776543
No 70
>KOG3755|consensus
Probab=59.17 E-value=2.5 Score=44.93 Aligned_cols=46 Identities=17% Similarity=0.155 Sum_probs=29.8
Q ss_pred HHHhhhCCCCCHHHHHHHHHHcC-------CCcccchhhcccchhhhhhhhcc
Q psy3281 254 EKEFHFNRYLTRRRRIEIAHALC-------LTERQIKIWFQNRRMKWKKENKS 299 (317)
Q Consensus 254 E~~F~~n~yPs~~er~eLA~~Lg-------Lse~qVkiWFQNRRaK~KK~~k~ 299 (317)
+-+|.++..++.....+.-+++. ...+.|+.||+|||.++|+.+..
T Consensus 708 ~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~~ 760 (769)
T KOG3755|consen 708 HHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKMS 760 (769)
T ss_pred hhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhcc
Confidence 44455666555544444333332 46688999999999999886544
No 71
>PRK09480 slmA division inhibitor protein; Provisional
Probab=59.04 E-value=8.7 Score=33.06 Aligned_cols=41 Identities=12% Similarity=0.099 Sum_probs=31.8
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchh
Q psy3281 250 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 291 (317)
Q Consensus 250 l~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRa 291 (317)
++.....|...+. ......+||++.|+++..+-.+|.|+..
T Consensus 16 l~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 16 LQALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 3333444555556 7788999999999999999999999763
No 72
>KOG1819|consensus
Probab=58.90 E-value=5 Score=42.02 Aligned_cols=16 Identities=13% Similarity=0.135 Sum_probs=7.5
Q ss_pred ccCHHHHHHHHHHhhh
Q psy3281 244 TYTRYQTLELEKEFHF 259 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~ 259 (317)
.|..+-..+|+..|..
T Consensus 676 nfasdirkilksvflm 691 (990)
T KOG1819|consen 676 NFASDIRKILKSVFLM 691 (990)
T ss_pred hhHHHHHHHHHHHHhh
Confidence 3444444455555543
No 73
>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=58.89 E-value=7.1 Score=32.30 Aligned_cols=46 Identities=11% Similarity=0.072 Sum_probs=31.2
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 245 fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
++..+..+|...| .......+||+.+|+++..|+.+...-|.|.|+
T Consensus 114 L~~~~r~il~l~~-----~~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 114 LPEQCRKIFILSR-----FEGKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 3444444444433 333456789999999999999998776666654
No 74
>PRK10403 transcriptional regulator NarP; Provisional
Probab=58.08 E-value=6.8 Score=33.07 Aligned_cols=49 Identities=18% Similarity=0.134 Sum_probs=37.5
Q ss_pred cccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281 243 QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297 (317)
Q Consensus 243 t~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~ 297 (317)
..+|..+.++|+...+. ..+++||+.++++++.|+++..|=|.|....+
T Consensus 152 ~~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~ 200 (215)
T PRK10403 152 SVLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLNVRS 200 (215)
T ss_pred ccCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCC
Confidence 35888888888765432 44678899999999999999988777765443
No 75
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=58.03 E-value=11 Score=31.47 Aligned_cols=43 Identities=12% Similarity=0.133 Sum_probs=29.1
Q ss_pred CCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcc
Q psy3281 241 GRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 287 (317)
Q Consensus 241 ~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQ 287 (317)
+|.+|+.+.....-.....+. ....+||+++||+...|..|.+
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g----~sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPG----MTVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCC----CCHHHHHHHHCcCHHHHHHHHH
Confidence 355678887554433332232 3456789999999999999954
No 76
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=57.65 E-value=12 Score=33.47 Aligned_cols=37 Identities=16% Similarity=0.156 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 262 YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 262 yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
|......++||..||+++..|++++.+-|.+.|+..+
T Consensus 166 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 202 (206)
T PRK12526 166 YFQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMG 202 (206)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 3444567889999999999999999877777776543
No 77
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=57.58 E-value=8.3 Score=35.27 Aligned_cols=49 Identities=12% Similarity=0.095 Sum_probs=36.4
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 245 fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
++..+..+|...| .......+||..+|++...|+.+...-|.+.|+.-+
T Consensus 185 L~~~~r~vl~l~~-----~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~ 233 (236)
T PRK06986 185 LPEREQLVLSLYY-----QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLG 233 (236)
T ss_pred CCHHHHHHHHhHh-----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 4555666665544 333457899999999999999999988888877543
No 78
>KOG0773|consensus
Probab=57.17 E-value=8.3 Score=37.51 Aligned_cols=44 Identities=34% Similarity=0.435 Sum_probs=37.9
Q ss_pred hhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281 258 HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301 (317)
Q Consensus 258 ~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~ 301 (317)
+++.|++..+...|+....|+..+|.+||-|.|.+.++..+...
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~ 160 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTW 160 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCC
Confidence 45789999999999999999999999999999998887655443
No 79
>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=56.50 E-value=8.7 Score=26.26 Aligned_cols=37 Identities=24% Similarity=0.261 Sum_probs=25.9
Q ss_pred CHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhccc
Q psy3281 246 TRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN 288 (317)
Q Consensus 246 T~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQN 288 (317)
+..+..++...+ . .....++|+.++++.+.|+.|...
T Consensus 2 ~~~e~~i~~~~~--~----~~s~~eia~~l~~s~~tv~~~~~~ 38 (57)
T cd06170 2 TPREREVLRLLA--E----GKTNKEIADILGISEKTVKTHLRN 38 (57)
T ss_pred CHHHHHHHHHHH--c----CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 445555555433 2 235678899999999999999863
No 80
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=56.01 E-value=10 Score=34.47 Aligned_cols=49 Identities=20% Similarity=0.236 Sum_probs=37.8
Q ss_pred ccCHHHHHHHHHHhhhCC--CCCHHHHHHHHHHcCCCcccchhhcccchhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNR--YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~--yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~K 294 (317)
.+|+.|+++|..+|+..= +|-.....+||++||+++..+.- .=||+..|
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~e--hLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSE--HLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHH--HHHHHHHH
Confidence 699999999999998654 46777778999999999977543 33444444
No 81
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=55.30 E-value=9.1 Score=32.96 Aligned_cols=48 Identities=17% Similarity=0.153 Sum_probs=33.7
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297 (317)
Q Consensus 245 fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~ 297 (317)
++..+..+|+.. |......+++|+.||+++..|++++..-|.|.|+.-
T Consensus 137 L~~~~r~v~~l~-----~~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 137 LPPKYRMVIVLK-----YMEDLSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred CCHHHhHHhhhH-----HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 444444444432 234456788999999999999999987777777643
No 82
>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=55.07 E-value=12 Score=32.90 Aligned_cols=53 Identities=8% Similarity=-0.041 Sum_probs=37.1
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCC
Q psy3281 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDG 302 (317)
Q Consensus 245 fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~ 302 (317)
++..+..+|... |......++||..||++...|+.+...-|.+.|+..+....
T Consensus 132 L~~~~r~v~~l~-----~~~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~~~ 184 (188)
T TIGR02943 132 LPEQTARVFMMR-----EVLGFESDEICQELEISTSNCHVLLYRARLSLRACLSINWF 184 (188)
T ss_pred CCHHHHHHHHHH-----HHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 344444444433 33345678999999999999999998888888776655443
No 83
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=54.77 E-value=11 Score=32.74 Aligned_cols=48 Identities=17% Similarity=0.058 Sum_probs=33.4
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
.++..+..+++..| ......++||..||++...|+.+...-|.+.|+.
T Consensus 139 ~L~~~~r~i~~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 139 TLPEKQREILILRV-----VVGLSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred hCCHHHHHHHHHHH-----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34555555555433 3335578999999999999999987766666653
No 84
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=53.82 E-value=9.8 Score=34.24 Aligned_cols=38 Identities=13% Similarity=0.082 Sum_probs=30.7
Q ss_pred HHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCC
Q psy3281 265 RRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDG 302 (317)
Q Consensus 265 ~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~ 302 (317)
....++||+.||+++..|+.+...-|.+.|+..+....
T Consensus 154 g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~~~ 191 (203)
T PRK09647 154 GLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAHAP 191 (203)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhch
Confidence 34567899999999999999999888888876655443
No 85
>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=53.71 E-value=6.8 Score=33.85 Aligned_cols=36 Identities=11% Similarity=-0.058 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281 262 YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297 (317)
Q Consensus 262 yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~ 297 (317)
|......++||..||+++..|++|...-|.+.|+.-
T Consensus 151 ~~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 151 ELEGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 345556789999999999999999987777766644
No 86
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=53.50 E-value=15 Score=32.14 Aligned_cols=49 Identities=22% Similarity=0.243 Sum_probs=33.2
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 245 fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
++..+..+|...| ......++||+.+|++...|+.....-|.+.|+...
T Consensus 132 L~~~~r~i~~l~~-----~~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 132 LEKLDREIFIRRY-----LLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred CCHHHHHHHHHHH-----HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence 4444444444332 233457889999999999999998777777666443
No 87
>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=52.80 E-value=14 Score=30.86 Aligned_cols=34 Identities=15% Similarity=0.130 Sum_probs=26.1
Q ss_pred CCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 262 YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 262 yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
+......++||+.+||+...|+++...-|.|.|.
T Consensus 124 ~~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 124 YQRGVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 3444567889999999999999988766666554
No 88
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=52.33 E-value=14 Score=32.46 Aligned_cols=39 Identities=13% Similarity=-0.097 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~ 301 (317)
......++||+.||+++..|+.....-|.+.|+......
T Consensus 125 ~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~ 163 (182)
T PRK12540 125 ASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDG 163 (182)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 344557889999999999999999888888777666544
No 89
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=52.28 E-value=13 Score=32.68 Aligned_cols=49 Identities=6% Similarity=0.020 Sum_probs=34.4
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 245 fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
++..+..+|...| ......++||..||+++..|+++...-|.+.|+...
T Consensus 135 Lp~~~R~v~~L~~-----~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 183 (189)
T PRK12530 135 LPAQQARVFMMRE-----YLELSSEQICQECDISTSNLHVLLYRARLQLQACLS 183 (189)
T ss_pred CCHHHHHHHhHHH-----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444432 233457889999999999999999888887776544
No 90
>PRK00118 putative DNA-binding protein; Validated
Probab=51.81 E-value=12 Score=31.04 Aligned_cols=47 Identities=13% Similarity=-0.026 Sum_probs=34.0
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 245 fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
++..+..++...|.. .....+||+.+|+++..|+.|+...|.+.|+.
T Consensus 18 L~ekqRevl~L~y~e-----g~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 18 LTEKQRNYMELYYLD-----DYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 455566666544432 34467799999999999999998777777664
No 91
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=51.79 E-value=14 Score=31.20 Aligned_cols=48 Identities=23% Similarity=0.219 Sum_probs=34.2
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 245 fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
++..+..+|...| .....++||..+|++...|+.+...-|.+.|+..+
T Consensus 113 L~~~~r~il~l~~------~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 113 MTERDRTVLLLRF------SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred CCHHHHHHHHHHH------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4444545554443 33456789999999999999999877777776544
No 92
>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=51.32 E-value=13 Score=31.40 Aligned_cols=33 Identities=12% Similarity=0.126 Sum_probs=27.1
Q ss_pred HHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281 265 RRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297 (317)
Q Consensus 265 ~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~ 297 (317)
....++||..+|++...|+.+...-|.+.|+..
T Consensus 126 g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 126 DLSEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 455788999999999999999987777777643
No 93
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=51.21 E-value=18 Score=30.31 Aligned_cols=49 Identities=14% Similarity=0.051 Sum_probs=33.4
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 245 fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
++..+..+|.-.| ......++||..||++...|+++...-|.+.|+.-+
T Consensus 107 Lp~~~r~v~~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 155 (161)
T PRK09047 107 LPARQREAFLLRY-----WEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALE 155 (161)
T ss_pred CCHHHHHHHHHHH-----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4444444444432 233446889999999999999998877777776544
No 94
>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=50.97 E-value=19 Score=31.30 Aligned_cols=48 Identities=21% Similarity=0.069 Sum_probs=37.9
Q ss_pred CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 242 Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
.+.++..++.+|+..+ . ....++||+.||++...|+.|-.+-|.|.|+
T Consensus 4 ~~~Lte~qr~VL~Lr~--~----GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE--K----GLSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH--c----CCCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 4678899999998742 2 2356789999999999999998877777775
No 95
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=50.92 E-value=18 Score=31.63 Aligned_cols=37 Identities=16% Similarity=0.121 Sum_probs=30.7
Q ss_pred HHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281 265 RRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301 (317)
Q Consensus 265 ~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~ 301 (317)
.....+||..||+++..|++....-|.+.|+.....+
T Consensus 147 g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 147 ELETEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3457889999999999999999888888887666555
No 96
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=50.89 E-value=13 Score=32.21 Aligned_cols=47 Identities=17% Similarity=0.082 Sum_probs=32.0
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 245 fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
++..+..+|... |......++||..+|++...|+.+...-|.+.|+.
T Consensus 136 L~~~~r~vl~l~-----~~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 136 LSPEERRVIEVL-----YYQGYTHREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred CCHHHHHHHHHH-----HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 444444444433 23344578899999999999999987766666654
No 97
>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=50.66 E-value=17 Score=31.23 Aligned_cols=32 Identities=22% Similarity=0.115 Sum_probs=26.4
Q ss_pred HHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 265 RRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 265 ~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
....++||..||+++..|++.+..-|.+.|+.
T Consensus 150 g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 150 GLTVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 34577899999999999999998777777653
No 98
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=50.58 E-value=20 Score=28.25 Aligned_cols=44 Identities=11% Similarity=0.074 Sum_probs=35.8
Q ss_pred ccCHHHHHHHHHHhhh-----CCCCCHHHHHHHHHHcCCCcccchhhcc
Q psy3281 244 TYTRYQTLELEKEFHF-----NRYLTRRRRIEIAHALCLTERQIKIWFQ 287 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~-----n~yPs~~er~eLA~~LgLse~qVkiWFQ 287 (317)
.++.+++..|...|.. +.+.+..+..++-..+++++..|+.+|.
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 4678899999999864 3478888888887888999888888874
No 99
>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=50.53 E-value=7.4 Score=26.38 Aligned_cols=23 Identities=9% Similarity=0.018 Sum_probs=19.2
Q ss_pred HHHHHHHcCCCcccchhhcccch
Q psy3281 268 RIEIAHALCLTERQIKIWFQNRR 290 (317)
Q Consensus 268 r~eLA~~LgLse~qVkiWFQNRR 290 (317)
..++|+.+|++++.|+.|.++-.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 46789999999999999975543
No 100
>PHA02955 hypothetical protein; Provisional
Probab=49.95 E-value=18 Score=33.76 Aligned_cols=45 Identities=11% Similarity=0.002 Sum_probs=36.1
Q ss_pred CHHHHHHHHHHhhhC-CCCCHHHHHHHHHHcCCCcccchhhcccch
Q psy3281 246 TRYQTLELEKEFHFN-RYLTRRRRIEIAHALCLTERQIKIWFQNRR 290 (317)
Q Consensus 246 T~~Ql~~LE~~F~~n-~yPs~~er~eLA~~LgLse~qVkiWFQNRR 290 (317)
...++..|.+.|.+. ..++.++|.+++++||+....|..||.+.-
T Consensus 59 a~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~ 104 (213)
T PHA02955 59 EEKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDL 104 (213)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchh
Confidence 345677777777765 578889999999999999988899998743
No 101
>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=49.91 E-value=17 Score=31.28 Aligned_cols=50 Identities=22% Similarity=0.067 Sum_probs=35.3
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
.++..+..+|...| ......++||..||+++..|+.+...-|.+.|+..+
T Consensus 100 ~L~~~~r~v~~l~~-----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTE-----LEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHH-----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 34455555554433 333457889999999999999999887877777654
No 102
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=49.61 E-value=21 Score=30.52 Aligned_cols=49 Identities=12% Similarity=0.102 Sum_probs=33.7
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 245 fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
++..+..+|...| ......++||+.||+++..|+.+...-|.+.|+.-+
T Consensus 119 L~~~~r~vl~L~~-----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 167 (173)
T PRK09645 119 LSPEHRAVLVRSY-----YRGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQ 167 (173)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 4444444444432 233457889999999999999998877777776544
No 103
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=49.28 E-value=11 Score=33.54 Aligned_cols=38 Identities=11% Similarity=-0.042 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhccc
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK 300 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k 300 (317)
......+++|..||++...|++++..-|.+.|+.-...
T Consensus 127 ~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~~ 164 (188)
T PRK12546 127 ASGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQLE 164 (188)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 34455788999999999999999998888887765443
No 104
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.27 E-value=16 Score=29.83 Aligned_cols=40 Identities=28% Similarity=0.204 Sum_probs=30.7
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccch
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIK 283 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVk 283 (317)
.++++|+.+-.+.|..|--.+....+++|.+|++++..|.
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHH
Confidence 3567777777777777777777788899999999886654
No 105
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=49.23 E-value=20 Score=31.49 Aligned_cols=37 Identities=11% Similarity=-0.009 Sum_probs=29.9
Q ss_pred HHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281 265 RRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301 (317)
Q Consensus 265 ~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~ 301 (317)
....++||+.||++...|+.+...-|.+.|+.-..+.
T Consensus 152 g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~ 188 (195)
T PRK12532 152 GFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKW 188 (195)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3456889999999999999999888888887655443
No 106
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=49.21 E-value=16 Score=30.87 Aligned_cols=34 Identities=24% Similarity=0.099 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
......++||..+|++...|+++...-|.|.|+.
T Consensus 126 ~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 126 YYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 3344578899999999999999988777776654
No 107
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=49.15 E-value=22 Score=31.72 Aligned_cols=42 Identities=10% Similarity=0.009 Sum_probs=31.7
Q ss_pred CHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCCCCC
Q psy3281 264 TRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGGSD 305 (317)
Q Consensus 264 s~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~~~s 305 (317)
.....++||+.||+++..|+++...-|.+.|+.-.....++.
T Consensus 148 ~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~~ 189 (196)
T PRK12535 148 LGYTYEEAAKIADVRVGTIRSRVARARADLIAATATGQASAE 189 (196)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccccchhh
Confidence 334578899999999999999998777777776555544433
No 108
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=48.93 E-value=7.6 Score=27.93 Aligned_cols=27 Identities=4% Similarity=0.083 Sum_probs=18.4
Q ss_pred HHHHHHHHcCCCcccchhhcccchhhh
Q psy3281 267 RRIEIAHALCLTERQIKIWFQNRRMKW 293 (317)
Q Consensus 267 er~eLA~~LgLse~qVkiWFQNRRaK~ 293 (317)
...+||+.+|++...|..||.+++.+.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~ 38 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNP 38 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT----
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccc
Confidence 467899999999999999999874443
No 109
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=48.75 E-value=18 Score=31.49 Aligned_cols=51 Identities=12% Similarity=0.117 Sum_probs=35.8
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS 299 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~ 299 (317)
.++..+..+|+..| ......++||+.+|+++..|++.+.+-|.+.|+.-+.
T Consensus 131 ~L~~~~r~vl~l~~-----~~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 181 (189)
T PRK12515 131 KLSPAHREIIDLVY-----YHEKSVEEVGEIVGIPESTVKTRMFYARKKLAELLKA 181 (189)
T ss_pred hCCHHHHHHHHHHH-----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555554432 3334578899999999999999998888777775443
No 110
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=48.58 E-value=19 Score=32.84 Aligned_cols=39 Identities=13% Similarity=-0.014 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~ 301 (317)
......++||..||+++..|+.+...-|.|.|+....+.
T Consensus 148 ~eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~~ 186 (216)
T PRK12533 148 LEDMSYREIAAIADVPVGTVMSRLARARRRLAALLGGAS 186 (216)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccc
Confidence 334457889999999999999999888888777654443
No 111
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=48.56 E-value=21 Score=30.98 Aligned_cols=34 Identities=18% Similarity=0.241 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
......++||+.+|++...|++|...-|.+.|+.
T Consensus 147 ~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 147 VDGCSHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred HcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 3445578899999999999999988777666653
No 112
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=48.10 E-value=8.3 Score=33.76 Aligned_cols=37 Identities=16% Similarity=0.007 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 262 YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 262 yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
|......++||+.+|++...|+.+..+-|.+.|+.-+
T Consensus 152 ~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 188 (194)
T PRK12513 152 EHGDLELEEIAELTGVPEETVKSRLRYALQKLRELLA 188 (194)
T ss_pred hccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4555668899999999999999998888887777554
No 113
>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=48.09 E-value=6.4 Score=34.30 Aligned_cols=34 Identities=29% Similarity=0.273 Sum_probs=27.3
Q ss_pred CCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 262 YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 262 yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
|.......+||..||++...|++++..-|.|.|+
T Consensus 162 ~~~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 162 YLDGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4455667899999999999999988766666664
No 114
>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=48.03 E-value=13 Score=34.25 Aligned_cols=51 Identities=20% Similarity=0.205 Sum_probs=39.9
Q ss_pred CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 242 Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
...+|..++++|.-.. ......+||..|+++++.|+.+..|-+.|.+-.++
T Consensus 169 ~~~Lt~re~evl~~~a------~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~ 219 (232)
T TIGR03541 169 AGVLSEREREVLAWTA------LGRRQADIAAILGISERTVENHLRSARRKLGVATT 219 (232)
T ss_pred hccCCHHHHHHHHHHH------CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCH
Confidence 4468999999997643 22456789999999999999999988887765443
No 115
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=47.20 E-value=17 Score=32.99 Aligned_cols=52 Identities=19% Similarity=0.172 Sum_probs=35.9
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
.++..+..++...|-.. +......++||..+|++...|+.+...-|.|.|+.
T Consensus 178 ~Lp~~~R~v~~L~y~l~-~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 178 KLSDREKQIMELRFGLN-GGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred hCCHHHHHHHHHHhccC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35566666665554211 13344578899999999999999988777777764
No 116
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=47.15 E-value=17 Score=30.20 Aligned_cols=45 Identities=18% Similarity=0.143 Sum_probs=34.4
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~K 294 (317)
.+|..+..+|+. +..+ + ..+++|+.++++++.|+.|.+|=|.|..
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 478888888876 3322 2 3678899999999999999988776654
No 117
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=47.12 E-value=16 Score=34.15 Aligned_cols=50 Identities=16% Similarity=0.033 Sum_probs=37.1
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
.++..+..+|...|- ......+||..+|++...|+.+...-+.|.|+..+
T Consensus 203 ~L~~~~r~vl~l~y~-----~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~ 252 (256)
T PRK07408 203 QLEERTREVLEFVFL-----HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQ 252 (256)
T ss_pred cCCHHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 456666666666553 34567889999999999999999877777776543
No 118
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=47.07 E-value=14 Score=31.21 Aligned_cols=45 Identities=22% Similarity=0.094 Sum_probs=35.3
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~K 294 (317)
.+|..+.++|+..++- ..+++||..++++++.|+....+=|.|..
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 5788888888766542 35788999999999999998877666654
No 119
>PRK06930 positive control sigma-like factor; Validated
Probab=47.01 E-value=20 Score=31.86 Aligned_cols=52 Identities=12% Similarity=-0.003 Sum_probs=37.0
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhccc
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK 300 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k 300 (317)
.++..+..+|...| .......+||..||++...|+.++.+-|.|.++..+..
T Consensus 114 ~L~~rer~V~~L~~-----~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~ 165 (170)
T PRK06930 114 VLTEREKEVYLMHR-----GYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQINES 165 (170)
T ss_pred hCCHHHHHHHHHHH-----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 35555555555433 22334678999999999999999998888887765543
No 120
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=46.79 E-value=15 Score=33.92 Aligned_cols=36 Identities=14% Similarity=0.095 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
......++||+.||+++..|+++...-|.|.|+..+
T Consensus 185 ~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 185 HENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 344557889999999999999999888888877554
No 121
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=46.68 E-value=18 Score=35.25 Aligned_cols=55 Identities=11% Similarity=0.082 Sum_probs=42.9
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS 299 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~ 299 (317)
.++..+..+|+..|-.. +......++||..||++...|+.+...-|.|.|+.-..
T Consensus 262 ~L~~~~R~vl~lrygL~-~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~ 316 (325)
T PRK05657 262 ELNDKQREVLARRFGLL-GYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQT 316 (325)
T ss_pred cCCHHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 57888888888776332 23445678999999999999999999888888876544
No 122
>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=46.30 E-value=18 Score=26.33 Aligned_cols=36 Identities=33% Similarity=0.400 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhc
Q psy3281 247 RYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWF 286 (317)
Q Consensus 247 ~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWF 286 (317)
..++.+|+-.++ +...+.. +||..|+++++.|+.-.
T Consensus 5 ~rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i 40 (59)
T PF08280_consen 5 KRQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDI 40 (59)
T ss_dssp HHHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHH
Confidence 357788888888 6666644 89999999999998654
No 123
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=46.27 E-value=16 Score=33.77 Aligned_cols=48 Identities=8% Similarity=0.089 Sum_probs=36.0
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
.++..+..+|...|- ......+||+.|||+...|+.|...-|.|.|+.
T Consensus 205 ~L~~~~r~vl~l~~~-----~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFI-----ENLSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHh-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 466777777776553 233468899999999999999988777776654
No 124
>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=45.44 E-value=17 Score=32.87 Aligned_cols=47 Identities=19% Similarity=0.177 Sum_probs=35.3
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
.++..+..+|...|- .....++||..+|++...|+.|...-+.+.|+
T Consensus 175 ~L~~~~r~il~l~y~-----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 175 SLSEREQLVLSLYYY-----EELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred hCCHHHHHHHHHHHh-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 456777777776653 23356899999999999999998777766665
No 125
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=45.44 E-value=8.8 Score=32.83 Aligned_cols=38 Identities=21% Similarity=0.122 Sum_probs=31.0
Q ss_pred CCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281 262 YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS 299 (317)
Q Consensus 262 yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~ 299 (317)
|......++||..+|+++..|++.+..-|.|.|+..+.
T Consensus 133 ~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~ 170 (175)
T PRK12518 133 DLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQ 170 (175)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 45555678999999999999999998888887776543
No 126
>PF13551 HTH_29: Winged helix-turn helix
Probab=45.41 E-value=40 Score=26.39 Aligned_cols=48 Identities=17% Similarity=0.158 Sum_probs=31.8
Q ss_pred CCCcccCHHHHHHHHHHhhhCC-----CCCHHHHHH-H-HHHc--CCCcccchhhcc
Q psy3281 240 RGRQTYTRYQTLELEKEFHFNR-----YLTRRRRIE-I-AHAL--CLTERQIKIWFQ 287 (317)
Q Consensus 240 R~Rt~fT~~Ql~~LE~~F~~n~-----yPs~~er~e-L-A~~L--gLse~qVkiWFQ 287 (317)
+.+..++.++...|.+.+..++ ..+..+..+ | .+.+ .++...|..|+.
T Consensus 53 ~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 53 RPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 3344489999999999998776 344444444 3 3333 467788888874
No 127
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=45.33 E-value=31 Score=30.33 Aligned_cols=35 Identities=9% Similarity=-0.034 Sum_probs=28.7
Q ss_pred CHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 264 TRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 264 s~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
.....++||+.||++...|+.++..-|.+.|+...
T Consensus 151 ~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 185 (196)
T PRK12524 151 EGLSNPEIAEVMEIGVEAVESLTARGKRALAALLA 185 (196)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 34457889999999999999999888888777544
No 128
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=45.24 E-value=29 Score=30.60 Aligned_cols=40 Identities=13% Similarity=0.048 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccCC
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDG 302 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~~ 302 (317)
......++||..+|++...|++=+..-|.+.|+.-+...+
T Consensus 148 ~~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l~~~~~ 187 (192)
T PRK09643 148 MQGYSVADAARMLGVAEGTVKSRCARGRARLAELLGYLRA 187 (192)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3444577899999999999987665556666665544443
No 129
>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=45.19 E-value=8.5 Score=25.42 Aligned_cols=25 Identities=20% Similarity=0.457 Sum_probs=20.8
Q ss_pred HHHHHHHcCCCcccchhhcccchhh
Q psy3281 268 RIEIAHALCLTERQIKIWFQNRRMK 292 (317)
Q Consensus 268 r~eLA~~LgLse~qVkiWFQNRRaK 292 (317)
..++|+.||++.+.|..|.++.+..
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~~ 27 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKLK 27 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 4678999999999999998776543
No 130
>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=45.13 E-value=20 Score=30.22 Aligned_cols=33 Identities=24% Similarity=0.087 Sum_probs=25.3
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
......++||+.||+++..|+.....-|.|.|+
T Consensus 136 ~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 136 GQNLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344557889999999999999988666665554
No 131
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=44.92 E-value=24 Score=31.05 Aligned_cols=37 Identities=24% Similarity=0.167 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS 299 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~ 299 (317)
.......+||..+|++...|++.+..-|.+.|+.-..
T Consensus 168 ~e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~~ 204 (208)
T PRK08295 168 LDGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYLEN 204 (208)
T ss_pred HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 3445678899999999999999888777777765443
No 132
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=44.77 E-value=18 Score=33.48 Aligned_cols=47 Identities=19% Similarity=0.167 Sum_probs=34.7
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 245 fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
++..+..+|...| ......++||..||++...|+.++..-|.+.|+.
T Consensus 202 L~~~~r~vl~l~~-----~~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 202 LSEKEQLVISLFY-----KEELTLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred CCHHHHHHHHHHH-----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4566666666544 3344578899999999999999998777777653
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=44.46 E-value=22 Score=30.25 Aligned_cols=33 Identities=24% Similarity=0.234 Sum_probs=26.6
Q ss_pred CHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 264 TRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 264 s~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
.....++||..||+++..|+++...-|.+.|+.
T Consensus 134 ~g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 134 HDLTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 345578899999999999999988777776654
No 134
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=44.17 E-value=23 Score=31.48 Aligned_cols=37 Identities=16% Similarity=0.143 Sum_probs=29.6
Q ss_pred CHHHHHHHHHHcCCCcccchhhcccchhhhhhhhccc
Q psy3281 264 TRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK 300 (317)
Q Consensus 264 s~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k 300 (317)
.....++||..||+++..|++....-|.+.|+.-+..
T Consensus 154 eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~ 190 (201)
T PRK12545 154 LDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEK 190 (201)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3345788999999999999999988888887765433
No 135
>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=43.99 E-value=20 Score=24.72 Aligned_cols=39 Identities=13% Similarity=0.189 Sum_probs=25.3
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcc
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 287 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQ 287 (317)
.++.++++.+.+.+... ....+||+.+|++...|..|+.
T Consensus 5 ~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHHC
T ss_pred CCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHHh
Confidence 45565555555555443 3467899999999999987763
No 136
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=43.79 E-value=19 Score=30.13 Aligned_cols=41 Identities=15% Similarity=0.281 Sum_probs=33.5
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 291 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRa 291 (317)
.++..+++.|.+.+..+ ...+|..||++...|+.|=++|+.
T Consensus 43 ~ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 43 TLSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 37888888888776543 467899999999999999998863
No 137
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=43.25 E-value=26 Score=29.49 Aligned_cols=32 Identities=13% Similarity=0.223 Sum_probs=25.7
Q ss_pred HHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 265 RRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 265 ~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
....++||+.+|++...|+.+...-|.+.|+.
T Consensus 125 ~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 125 GETQKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34578899999999999999877666666654
No 138
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=43.25 E-value=21 Score=33.26 Aligned_cols=34 Identities=18% Similarity=0.186 Sum_probs=28.2
Q ss_pred HHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281 266 RRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS 299 (317)
Q Consensus 266 ~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~ 299 (317)
...++||+.+|+++..|+.+...-|.+.|+....
T Consensus 133 ~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~ 166 (228)
T PRK06704 133 YSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE 166 (228)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 4568899999999999999998888887776544
No 139
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=43.21 E-value=17 Score=31.24 Aligned_cols=35 Identities=20% Similarity=0.172 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~ 297 (317)
......++||..||++...|+.+..+-|.|.|+.-
T Consensus 150 ~~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T PRK09641 150 IEDLSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34556788999999999999999887777777643
No 140
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=42.71 E-value=18 Score=30.55 Aligned_cols=46 Identities=17% Similarity=0.042 Sum_probs=35.4
Q ss_pred cccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhh
Q psy3281 243 QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294 (317)
Q Consensus 243 t~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~K 294 (317)
..+|..+..+|+..++- ..+++||.+|+++.+.|+.+..+=|.|..
T Consensus 148 ~~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 148 TVLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred ccCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 34788888888654332 55788999999999999999887776654
No 141
>KOG1819|consensus
Probab=42.46 E-value=12 Score=39.22 Aligned_cols=8 Identities=25% Similarity=0.559 Sum_probs=3.5
Q ss_pred CCCcccCH
Q psy3281 240 RGRQTYTR 247 (317)
Q Consensus 240 R~Rt~fT~ 247 (317)
|.|-+|..
T Consensus 647 ~arlkfks 654 (990)
T KOG1819|consen 647 RARLKFKS 654 (990)
T ss_pred hhhhcccc
Confidence 44444443
No 142
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=42.38 E-value=13 Score=32.68 Aligned_cols=36 Identities=31% Similarity=0.216 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
......++||..+|+++..|+.++..-|.+.|+.-.
T Consensus 120 ~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (181)
T PRK09637 120 LEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLE 155 (181)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 444567889999999999999999877777776544
No 143
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=41.81 E-value=31 Score=29.41 Aligned_cols=34 Identities=12% Similarity=-0.064 Sum_probs=27.2
Q ss_pred CHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281 264 TRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297 (317)
Q Consensus 264 s~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~ 297 (317)
.....++||..||+++..|+++...-|.+.|+..
T Consensus 127 ~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 127 SGFSYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4455788999999999999999987777766543
No 144
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=41.77 E-value=7.9 Score=28.72 Aligned_cols=23 Identities=22% Similarity=0.266 Sum_probs=19.3
Q ss_pred HHHHHHHHHHcCCCcccchhhcc
Q psy3281 265 RRRRIEIAHALCLTERQIKIWFQ 287 (317)
Q Consensus 265 ~~er~eLA~~LgLse~qVkiWFQ 287 (317)
.-...+||+.|||+.+.|..|-.
T Consensus 13 G~~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 13 GWSIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CCCHHHHHHHHCCChHHHHHHHH
Confidence 34567899999999999999963
No 145
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=41.59 E-value=23 Score=33.51 Aligned_cols=50 Identities=20% Similarity=0.090 Sum_probs=38.5
Q ss_pred cccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 243 QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 243 t~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
..+|..+.++|+-.. . .....+||+.|+++++.|+.+..|-+.|.+-.++
T Consensus 189 ~~LT~RE~evl~l~a--~----G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~nr 238 (247)
T TIGR03020 189 GLITAREAEILAWVR--D----GKTNEEIAAILGISSLTVKNHLQHIFKKLDVRNR 238 (247)
T ss_pred cCCCHHHHHHHHHHH--C----CCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCCH
Confidence 468899999998543 2 2446788999999999999999888777665443
No 146
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=41.48 E-value=22 Score=30.83 Aligned_cols=35 Identities=17% Similarity=0.081 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~ 297 (317)
......++||+.||+++..|++.+..-|.|.|+.-
T Consensus 143 ~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 143 LEGLSVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 44456788999999999999999987777777643
No 147
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=41.19 E-value=24 Score=30.71 Aligned_cols=34 Identities=12% Similarity=-0.027 Sum_probs=27.4
Q ss_pred CHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281 264 TRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297 (317)
Q Consensus 264 s~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~ 297 (317)
.....++||+.||++...|+.+...-|.+.|+..
T Consensus 146 ~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 146 EGLSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred cCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4456788999999999999999977777766643
No 148
>cd00131 PAX Paired Box domain
Probab=41.11 E-value=57 Score=27.59 Aligned_cols=46 Identities=11% Similarity=-0.091 Sum_probs=31.2
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCC-------Ccccchhhcccc
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCL-------TERQIKIWFQNR 289 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgL-------se~qVkiWFQNR 289 (317)
..+......|+.....++..+..|..++...-|+ +...|-.||+++
T Consensus 75 ~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 75 VATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred cCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 4466666777777788888888877654224455 777787777653
No 149
>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=40.97 E-value=22 Score=32.88 Aligned_cols=48 Identities=13% Similarity=0.100 Sum_probs=36.3
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
.++..+..+|...|... ....+||+.+|++...|+.|...-+.|.|+.
T Consensus 205 ~L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred cCCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 56777777777765322 3467899999999999999988777776653
No 150
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=40.78 E-value=12 Score=25.66 Aligned_cols=24 Identities=21% Similarity=0.328 Sum_probs=17.8
Q ss_pred HHHHHHHHHHcCCCcccchhhccc
Q psy3281 265 RRRRIEIAHALCLTERQIKIWFQN 288 (317)
Q Consensus 265 ~~er~eLA~~LgLse~qVkiWFQN 288 (317)
.....++|+.||++...|..|.+.
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 355778999999999999999754
No 151
>PRK10651 transcriptional regulator NarL; Provisional
Probab=40.68 E-value=25 Score=29.73 Aligned_cols=47 Identities=21% Similarity=0.061 Sum_probs=35.9
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
.+|..+.++|+...+- ...++||++++++++.|++..+|=|.|..-.
T Consensus 155 ~Lt~rE~~vl~~l~~g------~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~ 201 (216)
T PRK10651 155 QLTPRERDILKLIAQG------LPNKMIARRLDITESTVKVHVKHMLKKMKLK 201 (216)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 4888898888765421 2356789999999999999998877776543
No 152
>PRK06424 transcription factor; Provisional
Probab=40.34 E-value=30 Score=30.24 Aligned_cols=24 Identities=8% Similarity=0.068 Sum_probs=21.4
Q ss_pred HHHHHHHcCCCcccchhhcccchh
Q psy3281 268 RIEIAHALCLTERQIKIWFQNRRM 291 (317)
Q Consensus 268 r~eLA~~LgLse~qVkiWFQNRRa 291 (317)
.++||+.+|++...|..|..+++.
T Consensus 100 Q~eLA~~iGvs~stIskiE~G~~~ 123 (144)
T PRK06424 100 QADLAAKIFERKNVIASIERGDLL 123 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 568999999999999999988764
No 153
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=40.26 E-value=26 Score=30.38 Aligned_cols=34 Identities=18% Similarity=0.117 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
......++||..||+++..|++....-|.|.|+.
T Consensus 151 ~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 151 FEGITYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred HcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 3445678899999999999998877666666653
No 154
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=40.15 E-value=25 Score=32.30 Aligned_cols=53 Identities=13% Similarity=0.088 Sum_probs=39.7
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~ 297 (317)
.++..+..+|...|-...+ .....++||..||++...|+.+...-+.|.|...
T Consensus 176 ~L~~~er~vl~l~ygl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~ 228 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRHPS 228 (238)
T ss_pred hCCHHHHHHHHHHhCCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhH
Confidence 5677778888877743222 2345788999999999999999988888877653
No 155
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=39.93 E-value=13 Score=32.36 Aligned_cols=37 Identities=11% Similarity=-0.000 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 262 YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 262 yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
|......++||+.||++++.|+++...-|.+.|+.-+
T Consensus 151 ~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 151 EFDGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3444557889999999999999999888888777543
No 156
>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=39.32 E-value=23 Score=32.00 Aligned_cols=47 Identities=15% Similarity=0.197 Sum_probs=35.8
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
.++..+..+|...|- ......+||+.+|++...|+.|...-+.|.|+
T Consensus 178 ~L~~~~r~vl~l~y~-----~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFF-----EDKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 567777777776653 23457889999999999999998776666664
No 157
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=39.08 E-value=1.5e+02 Score=26.52 Aligned_cols=44 Identities=9% Similarity=-0.023 Sum_probs=34.3
Q ss_pred CCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhc
Q psy3281 241 GRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWF 286 (317)
Q Consensus 241 ~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWF 286 (317)
++..+|.+++.++.+.-.. -|..-.+..||+++||+..-|.+-.
T Consensus 82 k~y~Lt~e~i~Eir~LR~~--DP~~wTr~~LAkkF~~S~~fV~~v~ 125 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAE--DPEKWTRKKLAKKFNCSPLFVSMVA 125 (164)
T ss_pred ccccCCHHHHHHHHHHHHc--CchHhhHHHHHHHhCCCHHHHHHhc
Confidence 4467999999998877544 4566778999999999987777644
No 158
>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=39.05 E-value=12 Score=31.03 Aligned_cols=34 Identities=26% Similarity=0.175 Sum_probs=28.0
Q ss_pred CCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 262 YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 262 yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
|......++||..+|+++..|+++...-|.|.|+
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4555678899999999999999998877777665
No 159
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=38.66 E-value=29 Score=31.75 Aligned_cols=48 Identities=25% Similarity=0.151 Sum_probs=37.5
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~ 297 (317)
.+|..++++|+.... . ....+||++|+++++.|+.+..+-..|..-++
T Consensus 155 ~Lt~rE~~Vl~l~~~--G----~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~n 202 (216)
T PRK10100 155 LLTHREKEILNKLRI--G----ASNNEIARSLFISENTVKTHLYNLFKKIAVKN 202 (216)
T ss_pred CCCHHHHHHHHHHHc--C----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC
Confidence 478889999987654 2 33678899999999999999988777665443
No 160
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=38.37 E-value=15 Score=31.49 Aligned_cols=35 Identities=23% Similarity=0.163 Sum_probs=28.2
Q ss_pred CCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 262 YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 262 yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
|......++||+.||++.+.|+.+..+-|.+.|+.
T Consensus 139 ~~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 139 HYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred hhcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 44556778999999999999999987777766654
No 161
>PF13518 HTH_28: Helix-turn-helix domain
Probab=38.18 E-value=16 Score=25.02 Aligned_cols=24 Identities=21% Similarity=0.404 Sum_probs=20.0
Q ss_pred HHHHHHHHcCCCcccchhhcccch
Q psy3281 267 RRIEIAHALCLTERQIKIWFQNRR 290 (317)
Q Consensus 267 er~eLA~~LgLse~qVkiWFQNRR 290 (317)
...++|+++||+..+|..|.+.-+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 456799999999999999986544
No 162
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=38.05 E-value=17 Score=26.52 Aligned_cols=21 Identities=14% Similarity=0.256 Sum_probs=18.1
Q ss_pred HHHHHHHcCCCcccchhhccc
Q psy3281 268 RIEIAHALCLTERQIKIWFQN 288 (317)
Q Consensus 268 r~eLA~~LgLse~qVkiWFQN 288 (317)
..++|+.+|++.+.|+.|-..
T Consensus 3 i~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 468999999999999999643
No 163
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=37.96 E-value=34 Score=29.29 Aligned_cols=36 Identities=11% Similarity=0.181 Sum_probs=28.3
Q ss_pred CCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281 262 YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297 (317)
Q Consensus 262 yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~ 297 (317)
|......+++|+.||+++..|+.+...-|.+.|+..
T Consensus 132 ~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 167 (173)
T PRK12522 132 YYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHL 167 (173)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 344456788999999999999999887777776643
No 164
>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=37.89 E-value=28 Score=32.53 Aligned_cols=37 Identities=8% Similarity=0.171 Sum_probs=30.2
Q ss_pred CHHHHHHHHHHcCCCcccchhhcccchhhhhhhhccc
Q psy3281 264 TRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK 300 (317)
Q Consensus 264 s~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k 300 (317)
.....++||..||+++..|+++...-|.+.|+.-++.
T Consensus 176 eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~ 212 (244)
T TIGR03001 176 DGLSMDRIGAMYQVHRSTVSRWVAQARERLLERTRRR 212 (244)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445788999999999999999998888877765443
No 165
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=37.59 E-value=46 Score=27.01 Aligned_cols=42 Identities=19% Similarity=0.221 Sum_probs=32.2
Q ss_pred CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCC-Ccccchhhcc
Q psy3281 242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCL-TERQIKIWFQ 287 (317)
Q Consensus 242 Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgL-se~qVkiWFQ 287 (317)
|.+|+.+....+-..+....+ ...+||.++|+ ....+..|-.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHH
Confidence 778999987666666554443 57789999996 9999888854
No 166
>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=37.29 E-value=17 Score=25.03 Aligned_cols=23 Identities=13% Similarity=0.059 Sum_probs=20.5
Q ss_pred HHHHHHHcCCCcccchhhcccch
Q psy3281 268 RIEIAHALCLTERQIKIWFQNRR 290 (317)
Q Consensus 268 r~eLA~~LgLse~qVkiWFQNRR 290 (317)
..+||..+|++...|..|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 57899999999999999997764
No 167
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=37.23 E-value=36 Score=29.43 Aligned_cols=36 Identities=19% Similarity=0.205 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
......++||+.||+++..|++....-|.+.|+.-.
T Consensus 131 ~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 166 (179)
T PRK12543 131 LHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ 166 (179)
T ss_pred HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 344457889999999999999999888888877543
No 168
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=37.03 E-value=38 Score=29.79 Aligned_cols=49 Identities=12% Similarity=-0.000 Sum_probs=34.0
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 245 fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
++..+..+|+..| ......++||..||++...|+++...-|.+.|+...
T Consensus 112 Lp~~~R~v~~L~~-----~eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 112 LPEEQRAALHLVA-----IEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4444444444432 233457889999999999999999877777776554
No 169
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=37.02 E-value=15 Score=32.17 Aligned_cols=33 Identities=12% Similarity=-0.063 Sum_probs=26.1
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
......++||..||+++..|+++...-|.+.|+
T Consensus 144 ~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 144 LLGLSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 344457889999999999999998766666665
No 170
>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=36.69 E-value=16 Score=25.40 Aligned_cols=23 Identities=22% Similarity=0.280 Sum_probs=19.6
Q ss_pred HHHHHHHcCCCcccchhhcccch
Q psy3281 268 RIEIAHALCLTERQIKIWFQNRR 290 (317)
Q Consensus 268 r~eLA~~LgLse~qVkiWFQNRR 290 (317)
..+||+.+|++...|..|+.++|
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 47899999999999999998855
No 171
>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=36.24 E-value=13 Score=25.57 Aligned_cols=21 Identities=14% Similarity=0.205 Sum_probs=19.3
Q ss_pred HHHHHcCCCcccchhhcccch
Q psy3281 270 EIAHALCLTERQIKIWFQNRR 290 (317)
Q Consensus 270 eLA~~LgLse~qVkiWFQNRR 290 (317)
+||+.+|++...|..|+.+++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 689999999999999999884
No 172
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=36.23 E-value=44 Score=28.09 Aligned_cols=36 Identities=14% Similarity=0.135 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
......++||..||+++..|+.....-|.+.|+.-.
T Consensus 119 ~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~ 154 (159)
T PRK12527 119 LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR 154 (159)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 334457889999999999999988877777666543
No 173
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=36.18 E-value=28 Score=32.82 Aligned_cols=48 Identities=8% Similarity=0.164 Sum_probs=36.2
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
.++..+..+|+..|- ......+||..||++...|+.|...-+.|.|+.
T Consensus 215 ~L~~rer~vl~l~y~-----~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 262 (264)
T PRK07122 215 ALPERERTVLVLRFF-----ESMTQTQIAERVGISQMHVSRLLAKTLARLRDQ 262 (264)
T ss_pred cCCHHHHHHHHHHhc-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 466677777776653 334568999999999999999988777776653
No 174
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=35.78 E-value=37 Score=30.56 Aligned_cols=34 Identities=18% Similarity=0.295 Sum_probs=28.4
Q ss_pred HHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281 266 RRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS 299 (317)
Q Consensus 266 ~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~ 299 (317)
....+||+.+|++...|+++...-|.+.|+..+.
T Consensus 165 ~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~ 198 (206)
T PRK12544 165 LETNEICHAVDLSVSNLNVLLYRARLRLRECLEN 198 (206)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 4468899999999999999998888888876543
No 175
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=35.74 E-value=42 Score=29.45 Aligned_cols=34 Identities=12% Similarity=0.095 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
......++||..||++...|++.+.+-|.+.|+.
T Consensus 155 ~eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 155 LEELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 3344578899999999999999887666666654
No 176
>PF13730 HTH_36: Helix-turn-helix domain
Probab=35.70 E-value=23 Score=24.81 Aligned_cols=42 Identities=12% Similarity=0.044 Sum_probs=27.8
Q ss_pred cCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHcCCCcccchhhcc
Q psy3281 245 YTRYQTLELEKEFHF---NRYLTRRRRIEIAHALCLTERQIKIWFQ 287 (317)
Q Consensus 245 fT~~Ql~~LE~~F~~---n~yPs~~er~eLA~~LgLse~qVkiWFQ 287 (317)
++...+.++...+.. +.. .....+.||+.+|++.+.|..++.
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~-~~pS~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGG-CFPSQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCC-CCcCHHHHHHHHCcCHHHHHHHHH
Confidence 455555555544332 223 334578899999999999998874
No 177
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=35.61 E-value=17 Score=32.20 Aligned_cols=33 Identities=24% Similarity=0.305 Sum_probs=26.4
Q ss_pred CHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 264 TRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 264 s~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
.....++||+.||++++.|+..+..-|.+.++.
T Consensus 150 ~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~~~ 182 (185)
T PF07638_consen 150 EGLSVEEIAERLGISERTVRRRLRRARAWLRRE 182 (185)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 444678899999999999999888877665554
No 178
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=35.41 E-value=27 Score=31.11 Aligned_cols=41 Identities=12% Similarity=0.149 Sum_probs=30.9
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchh
Q psy3281 250 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 291 (317)
Q Consensus 250 l~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRa 291 (317)
++.-...|....|-. ....+||++.|++...|...|.||..
T Consensus 24 L~AA~~lf~e~Gy~~-~s~~dIA~~aGvs~gtiY~hF~sKe~ 64 (212)
T PRK15008 24 LSAALDTFSQFGFHG-TRLEQIAELAGVSKTNLLYYFPSKEA 64 (212)
T ss_pred HHHHHHHHHHhCccc-CCHHHHHHHhCcCHHHHHHHCCCHHH
Confidence 334444477777654 34678899999999999999999864
No 179
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=35.12 E-value=41 Score=29.14 Aligned_cols=31 Identities=16% Similarity=0.218 Sum_probs=25.1
Q ss_pred HHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 265 RRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 265 ~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
....++||+.||+++..|+..+.+-+.+.+.
T Consensus 143 g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 143 GMKQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3457889999999999999999876666654
No 180
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=34.88 E-value=18 Score=31.38 Aligned_cols=35 Identities=17% Similarity=0.221 Sum_probs=27.4
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~ 297 (317)
......++||..+|+++..|++....-|.+.|+.-
T Consensus 136 ~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 136 FYNLTYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 33455788999999999999999877777766643
No 181
>PF15063 TC1: Thyroid cancer protein 1
Probab=34.66 E-value=50 Score=26.27 Aligned_cols=40 Identities=10% Similarity=0.094 Sum_probs=31.8
Q ss_pred CCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcc
Q psy3281 241 GRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTER 280 (317)
Q Consensus 241 ~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~ 280 (317)
.-..|..-.+..|.+.|+...-...+||..|.-.+.-..+
T Consensus 30 saNIFe~vn~~qlqrLF~~sGD~kAEeRA~iI~~~~~d~e 69 (79)
T PF15063_consen 30 SANIFENVNLDQLQRLFQKSGDKKAEERARIIWECAQDPE 69 (79)
T ss_pred hhhhhhccCHHHHHHHHHHccchhHHHHHHHHHhhCCCHH
Confidence 3456888889999999999999999999988666654443
No 182
>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=34.57 E-value=17 Score=31.86 Aligned_cols=38 Identities=13% Similarity=0.038 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281 262 YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS 299 (317)
Q Consensus 262 yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~ 299 (317)
|.......+||..||+++..|+++...-|.+.|+.-..
T Consensus 144 ~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 181 (193)
T TIGR02947 144 DVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD 181 (193)
T ss_pred hhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 45556678999999999999999999888888776543
No 183
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=34.52 E-value=34 Score=31.24 Aligned_cols=52 Identities=17% Similarity=0.137 Sum_probs=34.4
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
.++..+..++...|-... ......++||..+|++...|+.|-...|.|.|+.
T Consensus 175 ~Lp~~~R~i~~l~y~~~~-~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGN-GKEKTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred hCCHHHHHHHHHHhCCCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456666666666542111 2334578899999999999999866556665554
No 184
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=34.49 E-value=44 Score=28.63 Aligned_cols=34 Identities=15% Similarity=0.164 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
......++||+.||+++..|+++..+-|.+.+..
T Consensus 133 ~~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 133 LDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3445578899999999999999997777666553
No 185
>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=34.06 E-value=19 Score=24.34 Aligned_cols=20 Identities=20% Similarity=0.295 Sum_probs=16.2
Q ss_pred HHHHHHHcCCCcccchhhcc
Q psy3281 268 RIEIAHALCLTERQIKIWFQ 287 (317)
Q Consensus 268 r~eLA~~LgLse~qVkiWFQ 287 (317)
+.++|+.+|++.+.|+.|=.
T Consensus 2 i~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 45789999999999999953
No 186
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=34.02 E-value=26 Score=32.77 Aligned_cols=49 Identities=16% Similarity=0.104 Sum_probs=36.1
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~ 297 (317)
.++..+..+|...|- ......+||..+|++...|+.+..+-+.+.|+..
T Consensus 212 ~L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 260 (268)
T PRK06288 212 TLPEREKKVLILYYY-----EDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260 (268)
T ss_pred hCCHHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 456666666666553 3345788999999999999999887777777653
No 187
>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=33.56 E-value=43 Score=23.37 Aligned_cols=34 Identities=21% Similarity=0.160 Sum_probs=22.0
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhc
Q psy3281 250 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWF 286 (317)
Q Consensus 250 l~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWF 286 (317)
..+|+..++...+.+ ..+||+.|+++.+.|+.-.
T Consensus 3 ~~il~~L~~~~~~it---~~eLa~~l~vS~rTi~~~i 36 (55)
T PF08279_consen 3 KQILKLLLESKEPIT---AKELAEELGVSRRTIRRDI 36 (55)
T ss_dssp HHHHHHHHHTTTSBE---HHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHcCCCcC---HHHHHHHhCCCHHHHHHHH
Confidence 345555445555544 5689999999999887544
No 188
>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=33.52 E-value=19 Score=26.50 Aligned_cols=21 Identities=14% Similarity=0.235 Sum_probs=18.2
Q ss_pred HHHHHHHcCCCcccchhhccc
Q psy3281 268 RIEIAHALCLTERQIKIWFQN 288 (317)
Q Consensus 268 r~eLA~~LgLse~qVkiWFQN 288 (317)
..++|+.+|++.+.|+.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 467899999999999999753
No 189
>PF13565 HTH_32: Homeodomain-like domain
Probab=33.38 E-value=1.3e+02 Score=22.21 Aligned_cols=40 Identities=10% Similarity=0.005 Sum_probs=28.0
Q ss_pred CHHHHHHHHHHhhhCCCCCHHHHHH-HHHHcCC----Ccccchhh
Q psy3281 246 TRYQTLELEKEFHFNRYLTRRRRIE-IAHALCL----TERQIKIW 285 (317)
Q Consensus 246 T~~Ql~~LE~~F~~n~yPs~~er~e-LA~~LgL----se~qVkiW 285 (317)
+.++...|.+.+..++..+..+..+ |...+|+ +.+.|..|
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 6777788888888888777777754 6777664 44555443
No 190
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=33.36 E-value=25 Score=30.33 Aligned_cols=34 Identities=21% Similarity=0.158 Sum_probs=26.3
Q ss_pred CCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 262 YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 262 yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
|......++||+.||++...|+++...-+.+.++
T Consensus 132 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 132 QLDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred hccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3444567899999999999999998766655554
No 191
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=33.01 E-value=37 Score=32.43 Aligned_cols=52 Identities=6% Similarity=-0.030 Sum_probs=40.0
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
.++..+..+|...|- +-.....++||+.||++...|+.+...-+.|.|+..+
T Consensus 227 ~L~~rer~vl~lr~~---~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~ 278 (289)
T PRK07500 227 TLNERELRIIRERRL---REDGATLEALGEELGISKERVRQIEARALEKLRRALL 278 (289)
T ss_pred cCCHHHHHHHHHHhc---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 577788888877762 1234467899999999999999999888888776544
No 192
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=32.41 E-value=36 Score=31.63 Aligned_cols=47 Identities=15% Similarity=0.227 Sum_probs=35.7
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
.++..+..+|+..|-. .....+||+.+|++...|+.+..+-+.|.|+
T Consensus 209 ~L~~~er~vi~~~~~~-----~~t~~eIA~~lgis~~~V~~~~~~al~kLr~ 255 (258)
T PRK08215 209 KLNDREKLILNLRFFQ-----GKTQMEVAEEIGISQAQVSRLEKAALKHMRK 255 (258)
T ss_pred cCCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5778888888887732 2357889999999999999887666666554
No 193
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=32.26 E-value=32 Score=28.44 Aligned_cols=47 Identities=13% Similarity=0.106 Sum_probs=31.4
Q ss_pred cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297 (317)
Q Consensus 245 fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~ 297 (317)
++..+..+|+..+.. ..-+++|..+++++..|+++-.+-|.|.++.+
T Consensus 142 l~~~e~~vl~~~~~~------~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~ 188 (202)
T PRK09390 142 LSERERQVMDGLVAG------LSNKVIARDLDISPRTVEVYRANVMTKMQAGS 188 (202)
T ss_pred hhhhHHHHHHHHHcc------CchHHHHHHcCCCHHHHHHHHHHHHHHHcccc
Confidence 555555666543321 12566899999999999998877676665443
No 194
>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=32.18 E-value=39 Score=31.71 Aligned_cols=50 Identities=14% Similarity=0.050 Sum_probs=38.0
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
.++..+..+|...|-. -......+||+.||++...|+.+..+-..|.|+.
T Consensus 218 ~L~~rer~vl~l~y~~---~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~ 267 (270)
T TIGR02392 218 SLDARSRRIIEARWLD---DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAA 267 (270)
T ss_pred cCCHHHHHHHHHHhcC---CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4677788888877732 1123467999999999999999988887777764
No 195
>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=31.99 E-value=46 Score=31.45 Aligned_cols=54 Identities=15% Similarity=0.081 Sum_probs=39.1
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
.++..+..+|...|-.. +.......+||..||++...|+.+...-|.|.|+.-.
T Consensus 222 ~Lp~~~R~Vl~l~ygL~-~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~ 275 (285)
T TIGR02394 222 ELNERQREVLARRFGLL-GYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILE 275 (285)
T ss_pred cCCHHHHHHHHHHhCCC-CCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 56777777777665111 1233457889999999999999999888888777544
No 196
>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=31.70 E-value=45 Score=31.46 Aligned_cols=31 Identities=16% Similarity=0.079 Sum_probs=26.0
Q ss_pred HHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 266 RRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 266 ~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
...++||+.||+++..|+.++..-|.+.|+.
T Consensus 125 ~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 125 YPYEEIASIVGKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 4467899999999999999998777777764
No 197
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=31.69 E-value=21 Score=26.10 Aligned_cols=21 Identities=5% Similarity=0.210 Sum_probs=18.3
Q ss_pred HHHHHHHcCCCcccchhhccc
Q psy3281 268 RIEIAHALCLTERQIKIWFQN 288 (317)
Q Consensus 268 r~eLA~~LgLse~qVkiWFQN 288 (317)
..++|+.+|++.+.|+.|.++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 467899999999999999764
No 198
>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=31.57 E-value=23 Score=23.43 Aligned_cols=24 Identities=13% Similarity=0.115 Sum_probs=19.8
Q ss_pred HHHHHHHcCCCcccchhhcccchh
Q psy3281 268 RIEIAHALCLTERQIKIWFQNRRM 291 (317)
Q Consensus 268 r~eLA~~LgLse~qVkiWFQNRRa 291 (317)
..++|+.||++.+.|..|.++.+-
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~i 27 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGEL 27 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCCC
Confidence 567899999999999999866543
No 199
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=31.51 E-value=40 Score=28.06 Aligned_cols=26 Identities=4% Similarity=0.096 Sum_probs=21.3
Q ss_pred CHHHHHHHHHHcCCCcccchhhcccc
Q psy3281 264 TRRRRIEIAHALCLTERQIKIWFQNR 289 (317)
Q Consensus 264 s~~er~eLA~~LgLse~qVkiWFQNR 289 (317)
.....++||+.+||+++.+..||+..
T Consensus 24 ~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 24 SPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 33567889999999999999888754
No 200
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=31.45 E-value=35 Score=31.93 Aligned_cols=48 Identities=10% Similarity=0.087 Sum_probs=35.5
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
.++..+..+|...|- ......+||..||++...|+.+...-+.|.|+.
T Consensus 205 ~L~~~er~vi~l~y~-----e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 205 ALEEKERKVMALYYY-----EELVLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred cCCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456666666666653 334578899999999999999987777666654
No 201
>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=31.38 E-value=18 Score=32.74 Aligned_cols=36 Identities=17% Similarity=0.289 Sum_probs=30.6
Q ss_pred HHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281 266 RRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301 (317)
Q Consensus 266 ~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~ 301 (317)
..+++|+.-++++...|-+|..|-+...++..+.+-
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~yKh 50 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAKPKYKH 50 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccccchhhH
Confidence 457889999999999999999999988887766443
No 202
>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=30.83 E-value=60 Score=30.74 Aligned_cols=33 Identities=18% Similarity=0.143 Sum_probs=27.2
Q ss_pred HHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 266 RRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 266 ~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
...++||+.||+++..|+..+..-|.+.|+..+
T Consensus 159 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 159 WRAAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 446889999999999999998877777776544
No 203
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=30.76 E-value=44 Score=30.25 Aligned_cols=47 Identities=13% Similarity=0.151 Sum_probs=33.8
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
.++..+..+|...|- ......+||..||++...|..+-..-..|.|+
T Consensus 183 ~L~~~e~~i~~~~~~-----~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~ 229 (231)
T TIGR02885 183 KLDERERQIIMLRYF-----KDKTQTEVANMLGISQVQVSRLEKKVLKKMKE 229 (231)
T ss_pred cCCHHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 567777777776653 23457899999999999998886555554443
No 204
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=30.67 E-value=48 Score=31.32 Aligned_cols=32 Identities=16% Similarity=0.013 Sum_probs=26.6
Q ss_pred HHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281 266 RRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297 (317)
Q Consensus 266 ~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~ 297 (317)
...++||+.||+++..|+..+..-|.+.|+..
T Consensus 132 ~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~ 163 (293)
T PRK09636 132 VPFDEIASTLGRSPAACRQLASRARKHVRAAR 163 (293)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 45678999999999999999987777777643
No 205
>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=30.62 E-value=41 Score=28.85 Aligned_cols=47 Identities=9% Similarity=0.044 Sum_probs=32.1
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
.++..+..++...| ......++||..||++...|+.=...-|.|.|+
T Consensus 140 ~L~~~~r~vi~l~~-----~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 140 KLPEDYREVILLRH-----LEGLSFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred cCCHHHHHHHHHHH-----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 34555555555433 344567889999999999999876666666554
No 206
>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=30.57 E-value=51 Score=29.95 Aligned_cols=51 Identities=18% Similarity=0.156 Sum_probs=32.7
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
.++..+..+|...|-.+. ......++||+.+|+++..|+.+...-|.|.|+
T Consensus 174 ~L~~~~r~il~l~y~~~~-~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 174 VLDGREREVIEMRYGLGD-GRRKTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred hCCHHHHHHHHHHHcCCC-CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 455555555555442110 123457889999999999998887655666554
No 207
>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=30.39 E-value=51 Score=30.14 Aligned_cols=53 Identities=19% Similarity=0.140 Sum_probs=34.9
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~ 297 (317)
.++..+..++...|-... ......++||+.+|+++..|+++...-|.+.|+..
T Consensus 178 ~Lp~~~R~ii~L~~~l~~-~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l 230 (234)
T TIGR02835 178 KLNDREKKIMELRFGLVG-GTEKTQKEVADMLGISQSYISRLEKRILKRLKKEI 230 (234)
T ss_pred hCCHHHHHHHHHHHccCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 455555555555442100 12345778999999999999999877777776643
No 208
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=30.13 E-value=24 Score=30.61 Aligned_cols=33 Identities=21% Similarity=0.185 Sum_probs=26.5
Q ss_pred CHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 264 TRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 264 s~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
.....++||+.||++...|+.+...-|.+.|+.
T Consensus 142 ~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~ 174 (179)
T PRK09415 142 EELSIKEIAEVTGVNENTVKTRLKKAKELLKKG 174 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 334568899999999999999988777776654
No 209
>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=29.91 E-value=27 Score=22.51 Aligned_cols=23 Identities=22% Similarity=0.257 Sum_probs=19.8
Q ss_pred HHHHHHHcCCCcccchhhcccch
Q psy3281 268 RIEIAHALCLTERQIKIWFQNRR 290 (317)
Q Consensus 268 r~eLA~~LgLse~qVkiWFQNRR 290 (317)
...||+.+++++..|..|..+++
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45789999999999999998763
No 210
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=29.60 E-value=33 Score=30.11 Aligned_cols=41 Identities=20% Similarity=0.157 Sum_probs=31.1
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchh
Q psy3281 250 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 291 (317)
Q Consensus 250 l~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRa 291 (317)
++...+.|....|-. ....+||++.|+++..+-.+|.+|..
T Consensus 17 l~aa~~lf~~~G~~~-~ti~~Ia~~agvsk~t~Y~~F~sKe~ 57 (213)
T PRK09975 17 IETAIAQFALRGVSN-TTLNDIADAANVTRGAIYWHFENKTQ 57 (213)
T ss_pred HHHHHHHHHHcCccc-CCHHHHHHHcCCCHHHHHHHcCCHHH
Confidence 444445566666654 44778899999999999999999865
No 211
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=29.56 E-value=25 Score=32.01 Aligned_cols=38 Identities=21% Similarity=0.184 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcc
Q psy3281 262 YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS 299 (317)
Q Consensus 262 yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~ 299 (317)
|......++||+.||++...|++....-|.|.|+..+.
T Consensus 162 ~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~ 199 (231)
T PRK11922 162 VVEELSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199 (231)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 45566788999999999999999998888888876654
No 212
>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=28.59 E-value=29 Score=25.81 Aligned_cols=23 Identities=22% Similarity=0.265 Sum_probs=20.2
Q ss_pred HHHHHHHcCCCcccchhhcccch
Q psy3281 268 RIEIAHALCLTERQIKIWFQNRR 290 (317)
Q Consensus 268 r~eLA~~LgLse~qVkiWFQNRR 290 (317)
..+||+.+|++...|..|+.++|
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46899999999999999998765
No 213
>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=28.37 E-value=23 Score=26.39 Aligned_cols=21 Identities=19% Similarity=0.419 Sum_probs=15.1
Q ss_pred HHHHHHHcCCCcccch-hhccc
Q psy3281 268 RIEIAHALCLTERQIK-IWFQN 288 (317)
Q Consensus 268 r~eLA~~LgLse~qVk-iWFQN 288 (317)
..+||+.||++...|. .|+..
T Consensus 15 ~~~lA~~lgis~st~s~~~~~r 36 (66)
T PF07022_consen 15 DKELAERLGISKSTLSNNWKKR 36 (66)
T ss_dssp CHHHHCCTT--HHHHH-HHHHS
T ss_pred HHHHHHHhCcCHHHhhHHHHhC
Confidence 5678889999999888 88753
No 214
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=28.32 E-value=61 Score=27.68 Aligned_cols=32 Identities=16% Similarity=0.108 Sum_probs=24.4
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhh
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~K 294 (317)
......++||..||+++..|+.+..+-+.+.+
T Consensus 132 ~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 163 (168)
T PRK12525 132 LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCY 163 (168)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 33345788999999999999998866655544
No 215
>PHA01976 helix-turn-helix protein
Probab=28.25 E-value=30 Score=25.05 Aligned_cols=23 Identities=13% Similarity=0.125 Sum_probs=20.1
Q ss_pred HHHHHHHcCCCcccchhhcccch
Q psy3281 268 RIEIAHALCLTERQIKIWFQNRR 290 (317)
Q Consensus 268 r~eLA~~LgLse~qVkiWFQNRR 290 (317)
..+||+.+|++...|..|...++
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 56899999999999999997654
No 216
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=28.14 E-value=29 Score=30.29 Aligned_cols=36 Identities=14% Similarity=0.184 Sum_probs=28.8
Q ss_pred CCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281 262 YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297 (317)
Q Consensus 262 yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~ 297 (317)
|......++||..||++...|++|...-|.+.|+..
T Consensus 147 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 147 FVAELEFQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 344456789999999999999999987777777643
No 217
>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=27.66 E-value=29 Score=25.15 Aligned_cols=20 Identities=10% Similarity=0.230 Sum_probs=17.8
Q ss_pred HHHHHHHcCCCcccchhhcc
Q psy3281 268 RIEIAHALCLTERQIKIWFQ 287 (317)
Q Consensus 268 r~eLA~~LgLse~qVkiWFQ 287 (317)
..++|+.+|++.+.|+.|.+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999975
No 218
>PRK05572 sporulation sigma factor SigF; Validated
Probab=27.07 E-value=49 Score=30.58 Aligned_cols=48 Identities=13% Similarity=0.158 Sum_probs=36.4
Q ss_pred cccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhh
Q psy3281 243 QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295 (317)
Q Consensus 243 t~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK 295 (317)
..++..+..+|...|. ......+||+.+|++...|+.|-..-..|.|+
T Consensus 201 ~~L~~~~~~v~~l~~~-----~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~ 248 (252)
T PRK05572 201 RELDERERLIVYLRYF-----KDKTQSEVAKRLGISQVQVSRLEKKILKQMKE 248 (252)
T ss_pred HcCCHHHHHHHHHHHh-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3577888888877763 23457889999999999999987766666654
No 219
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=27.00 E-value=34 Score=29.69 Aligned_cols=38 Identities=21% Similarity=0.214 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhccc
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK 300 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k 300 (317)
.....-+++|..+|++...|+.|...-|.|.|+.....
T Consensus 141 ~~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~~~ 178 (182)
T COG1595 141 LEGLSYEEIAEILGISVGTVKSRLHRARKKLREQLEEA 178 (182)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 44445678999999999999999988888877765443
No 220
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=26.63 E-value=34 Score=21.83 Aligned_cols=23 Identities=17% Similarity=0.239 Sum_probs=19.7
Q ss_pred HHHHHHHcCCCcccchhhcccch
Q psy3281 268 RIEIAHALCLTERQIKIWFQNRR 290 (317)
Q Consensus 268 r~eLA~~LgLse~qVkiWFQNRR 290 (317)
..+||+.+|++...|..|..+++
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~~ 35 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGKR 35 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 55889999999999999987664
No 221
>PRK09726 antitoxin HipB; Provisional
Probab=26.59 E-value=80 Score=24.60 Aligned_cols=22 Identities=18% Similarity=0.276 Sum_probs=14.7
Q ss_pred HHHHHHHcCCCcccchhhcccc
Q psy3281 268 RIEIAHALCLTERQIKIWFQNR 289 (317)
Q Consensus 268 r~eLA~~LgLse~qVkiWFQNR 289 (317)
.++||+.+|++...|..|..++
T Consensus 28 q~elA~~~gvs~~tis~~e~g~ 49 (88)
T PRK09726 28 QSELAKKIGIKQATISNFENNP 49 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHCCC
Confidence 4566777777777777776654
No 222
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=26.35 E-value=54 Score=27.74 Aligned_cols=45 Identities=7% Similarity=0.114 Sum_probs=34.9
Q ss_pred cccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhh
Q psy3281 243 QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 293 (317)
Q Consensus 243 t~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~ 293 (317)
..+|..+.++|+..++-. .+++||..++++++.|+.--.+=|.|.
T Consensus 142 ~~lt~~E~~vl~~l~~g~------~~~~I~~~l~~s~~tv~~~~~~l~~Kl 186 (204)
T PRK09958 142 DSLSKQEISVMRYILDGK------DNNDIAEKMFISNKTVSTYKSRLMEKL 186 (204)
T ss_pred ccCCHHHHHHHHHHHcCC------CHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 358888888888777533 377899999999999998776655554
No 223
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=26.31 E-value=57 Score=31.06 Aligned_cols=50 Identities=12% Similarity=0.076 Sum_probs=36.4
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
.++..+..+|...|-.. ......+||+.||++..+|+.+-..-..|.|+.
T Consensus 230 ~L~~rEr~VL~lry~~~---~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~ 279 (284)
T PRK06596 230 GLDERSRDIIEARWLDD---DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAA 279 (284)
T ss_pred cCCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46777777887776321 234467999999999999999877666666654
No 224
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=26.27 E-value=52 Score=29.85 Aligned_cols=42 Identities=12% Similarity=0.052 Sum_probs=33.6
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhh
Q psy3281 250 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 293 (317)
Q Consensus 250 l~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~ 293 (317)
++.-...|....|- ....+||++.|+++..|..+|.+|..-.
T Consensus 19 l~aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L~ 60 (225)
T PRK11552 19 IAAALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDLY 60 (225)
T ss_pred HHHHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHHH
Confidence 44445558888877 5688999999999999999999987543
No 225
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=26.01 E-value=69 Score=26.94 Aligned_cols=30 Identities=20% Similarity=0.237 Sum_probs=22.7
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhh
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMK 292 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK 292 (317)
......++||+.||++...|+++...-+.+
T Consensus 127 ~~g~s~~EIA~~l~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 127 VDGLGYGEIATELGISLATVKRYLNKAAMR 156 (161)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 334456789999999999999987655444
No 226
>PTZ00183 centrin; Provisional
Probab=25.61 E-value=1.5e+02 Score=24.26 Aligned_cols=41 Identities=17% Similarity=0.247 Sum_probs=31.8
Q ss_pred ccCCCCcccCHHHHHHHHHHhhh-----CCCCCHHHHHHHHHHcCC
Q psy3281 237 ERKRGRQTYTRYQTLELEKEFHF-----NRYLTRRRRIEIAHALCL 277 (317)
Q Consensus 237 krRR~Rt~fT~~Ql~~LE~~F~~-----n~yPs~~er~eLA~~LgL 277 (317)
+++-.+..++..++..|+++|.. +.+.+..+...+.+.+|+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~g~ 48 (158)
T PTZ00183 3 KRRSERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGF 48 (158)
T ss_pred ccccccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHhCC
Confidence 34456778999999999999863 457888888887777775
No 227
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=25.47 E-value=71 Score=28.68 Aligned_cols=45 Identities=11% Similarity=-0.054 Sum_probs=32.6
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccc
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 289 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNR 289 (317)
.+|..++.+|..+...+ +-....-++||++|+++++.|+..+.+-
T Consensus 158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~~~~~~~ 202 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCRKYLIWL 202 (239)
T ss_pred CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHHHHHHHH
Confidence 46777777776655433 3344566889999999999999988654
No 228
>PHA00542 putative Cro-like protein
Probab=25.41 E-value=85 Score=24.39 Aligned_cols=23 Identities=22% Similarity=0.241 Sum_probs=20.2
Q ss_pred HHHHHHHHcCCCcccchhhcccc
Q psy3281 267 RRIEIAHALCLTERQIKIWFQNR 289 (317)
Q Consensus 267 er~eLA~~LgLse~qVkiWFQNR 289 (317)
...+||+.+|++...|..|...+
T Consensus 33 Tq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 33 SQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCC
Confidence 45679999999999999999776
No 229
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=24.85 E-value=73 Score=27.99 Aligned_cols=39 Identities=21% Similarity=0.162 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281 263 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301 (317)
Q Consensus 263 Ps~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~ 301 (317)
......++||..||+++..|+++...-|.+.|+..+...
T Consensus 142 ~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 180 (188)
T PRK12517 142 IGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKPD 180 (188)
T ss_pred HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334457889999999999999999877777777655433
No 230
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=24.78 E-value=27 Score=31.53 Aligned_cols=45 Identities=16% Similarity=0.195 Sum_probs=33.0
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~K 294 (317)
.+|+.++++|...- ....-++||++|+++++.|+.-..|=..|.+
T Consensus 137 ~LT~RE~eVL~lla------~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 137 SLSRTESSMLRMWM------AGQGTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred cCCHHHHHHHHHHH------cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 38999999996543 2234578999999999999987765444443
No 231
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=24.74 E-value=84 Score=28.15 Aligned_cols=38 Identities=16% Similarity=0.024 Sum_probs=33.4
Q ss_pred CHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccch
Q psy3281 246 TRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIK 283 (317)
Q Consensus 246 T~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVk 283 (317)
.+.-+.+|...++...|.+...+..+|..|||+...|.
T Consensus 24 rsAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v~ 61 (160)
T COG1905 24 RSALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARVY 61 (160)
T ss_pred hhHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHhe
Confidence 45678889999999999999999999999999987765
No 232
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=24.47 E-value=80 Score=29.33 Aligned_cols=51 Identities=20% Similarity=0.283 Sum_probs=38.3
Q ss_pred CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 242 Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
+..+|..++++|.-..+ ...-.+||..|+++++.|+.=..|-+.|..-.++
T Consensus 177 ~~~LT~rE~evl~~~a~------G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~~nr 227 (240)
T PRK10188 177 EMNFSKREKEILKWTAE------GKTSAEIAMILSISENTVNFHQKNMQKKFNAPNK 227 (240)
T ss_pred CCCCCHHHHHHHHHHHc------CCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCH
Confidence 45789999999875532 2345789999999999999988887777654433
No 233
>PF12728 HTH_17: Helix-turn-helix domain
Probab=24.30 E-value=36 Score=23.48 Aligned_cols=24 Identities=17% Similarity=0.376 Sum_probs=19.6
Q ss_pred HHHHHHHcCCCcccchhhcccchh
Q psy3281 268 RIEIAHALCLTERQIKIWFQNRRM 291 (317)
Q Consensus 268 r~eLA~~LgLse~qVkiWFQNRRa 291 (317)
..++|+.||++...|..|.++.+-
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g~i 27 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQGKI 27 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 467889999999999999866544
No 234
>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=24.22 E-value=74 Score=26.35 Aligned_cols=37 Identities=8% Similarity=0.102 Sum_probs=25.6
Q ss_pred CHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcc
Q psy3281 246 TRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 287 (317)
Q Consensus 246 T~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQ 287 (317)
+-+-...+..+|+... .+.++|..++++...|..||+
T Consensus 4 S~DlR~rVl~~~~~g~-----s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 4 SLDLRQRVLAYIEKGK-----SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred CHHHHHHHHHHHHccc-----hHHHHHHHhCcHHHHHHHHHH
Confidence 3344444445555432 456789999999999999998
No 235
>PLN03162 golden-2 like transcription factor; Provisional
Probab=24.14 E-value=72 Score=32.52 Aligned_cols=61 Identities=16% Similarity=0.168 Sum_probs=41.4
Q ss_pred ccCCCCcccCHHH-HHHHHHHhhhCC-CCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhh
Q psy3281 237 ERKRGRQTYTRYQ-TLELEKEFHFNR-YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297 (317)
Q Consensus 237 krRR~Rt~fT~~Q-l~~LE~~F~~n~-yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~ 297 (317)
.+||.|.++|.+- .+.++.+..... .-+...+.+|-..-||+...|+.-+|--|...|+..
T Consensus 232 g~KKpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l~ 294 (526)
T PLN03162 232 GKKKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHLA 294 (526)
T ss_pred CCCCCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhccccc
Confidence 3567888999885 555566665552 234444556666678999999999888777666543
No 236
>KOG1151|consensus
Probab=24.09 E-value=2.1e+02 Score=30.48 Aligned_cols=38 Identities=29% Similarity=0.432 Sum_probs=17.3
Q ss_pred ccccchhhhhhcccCCCCCCCC--CCCCCCCCCCCCCCCC
Q psy3281 76 DRMDIRNAAYYGAHEGGMEQYP--RPDSPSMGHMGPQNGH 113 (317)
Q Consensus 76 ~~~~~~~~~~~~~~~~~~~~~~--~~~s~~~~~~~~~~~~ 113 (317)
+-++.|+..|...--.|...+. -..+||.+-.++.||-
T Consensus 5 hsldprrqellearftGv~qfmpqnsshpst~~k~p~N~e 44 (775)
T KOG1151|consen 5 HSLDPRRQELLEARFTGVTQFMPQNSSHPSTQQKPPQNGE 44 (775)
T ss_pred ccCCchhHHHHhhccccccccCCCCCCCCcccccCCCCCc
Confidence 3455566555554322222111 2234555556665654
No 237
>smart00595 MADF subfamily of SANT domain.
Probab=23.98 E-value=29 Score=26.62 Aligned_cols=34 Identities=29% Similarity=0.347 Sum_probs=28.1
Q ss_pred HHHHHHHcCCCcccchhhcccchhhhhhhhcccC
Q psy3281 268 RIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301 (317)
Q Consensus 268 r~eLA~~LgLse~qVkiWFQNRRaK~KK~~k~k~ 301 (317)
-.+||.+|+.+...|+.-+.|=|.+.++..+...
T Consensus 30 W~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~~ 63 (89)
T smart00595 30 WEEIAEELGLSVEECKKRWKNLRDRYRRELKRLQ 63 (89)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3568999999999999999999998888765543
No 238
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=23.83 E-value=46 Score=29.31 Aligned_cols=43 Identities=19% Similarity=0.064 Sum_probs=33.5
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchh
Q psy3281 248 YQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 291 (317)
Q Consensus 248 ~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRa 291 (317)
.-+..-...|.+..|-.. ...+||++.|+++..+-.+|.||..
T Consensus 15 ~Il~AA~~lf~e~G~~~~-t~~~Ia~~agvs~~tlY~~F~sKe~ 57 (215)
T PRK10668 15 HILDAALRLFSQQGVSAT-SLADIAKAAGVTRGAIYWHFKNKSD 57 (215)
T ss_pred HHHHHHHHHHHHcCcccC-CHHHHHHHhCCChHHHHHHCCCHHH
Confidence 345555666888887653 4778899999999999999999864
No 239
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=23.64 E-value=90 Score=24.90 Aligned_cols=33 Identities=21% Similarity=0.251 Sum_probs=25.4
Q ss_pred hhhCCCCCHHHHHHHHHHcCCCcccchhhcccch
Q psy3281 257 FHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR 290 (317)
Q Consensus 257 F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRR 290 (317)
|....|-. ....+||+++|++...+..+|.|+-
T Consensus 25 ~~~~G~~~-~t~~~Ia~~agvs~~~~Y~~f~~K~ 57 (201)
T COG1309 25 FAEKGYAA-TTVDEIAKAAGVSKGTLYRHFPSKE 57 (201)
T ss_pred HHHcCcCC-CCHHHHHHHhCCCcchhHHHcCCHH
Confidence 44445543 3467789999999999999999974
No 240
>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=23.20 E-value=75 Score=21.61 Aligned_cols=37 Identities=16% Similarity=0.177 Sum_probs=23.8
Q ss_pred CHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhc
Q psy3281 246 TRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWF 286 (317)
Q Consensus 246 T~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWF 286 (317)
+..+..+|+..++ ++.. .+.+||+.+|++...|..-+
T Consensus 2 ~~~~~~Il~~l~~-~~~~---t~~ela~~~~is~~tv~~~l 38 (48)
T PF13412_consen 2 DETQRKILNYLRE-NPRI---TQKELAEKLGISRSTVNRYL 38 (48)
T ss_dssp -HHHHHHHHHHHH-CTTS----HHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHHHHH-cCCC---CHHHHHHHhCCCHHHHHHHH
Confidence 3456677766555 4444 46788999999998886544
No 241
>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=23.10 E-value=44 Score=29.00 Aligned_cols=40 Identities=10% Similarity=0.107 Sum_probs=30.1
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccch
Q psy3281 250 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR 290 (317)
Q Consensus 250 l~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRR 290 (317)
+..-...|.+..|-. ....+||++.|++...|-..|.||-
T Consensus 14 l~aA~~lf~e~G~~~-~s~~~IA~~agvs~~~lY~hF~sKe 53 (202)
T TIGR03613 14 LSAALDTFSRFGFHG-TSLEQIAELAGVSKTNLLYYFPSKD 53 (202)
T ss_pred HHHHHHHHHHhCccc-CCHHHHHHHhCCCHHHHHHHcCCHH
Confidence 333444566677544 4477889999999999999999984
No 242
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=22.80 E-value=66 Score=26.16 Aligned_cols=43 Identities=12% Similarity=-0.003 Sum_probs=27.8
Q ss_pred CCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccch
Q psy3281 241 GRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR 290 (317)
Q Consensus 241 ~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRR 290 (317)
....++...+..|...... ...+||+.+|++...|..|...++
T Consensus 61 ~~~~~~~~~i~~~r~~~gl-------tq~~lA~~lg~~~~tis~~e~g~~ 103 (127)
T TIGR03830 61 VDGLLTPPEIRRIRKKLGL-------SQREAAELLGGGVNAFSRYERGEV 103 (127)
T ss_pred ccCCcCHHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHCCCC
Confidence 3344555555555443321 245789999999999999987665
No 243
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=22.42 E-value=1.1e+02 Score=20.87 Aligned_cols=21 Identities=14% Similarity=0.218 Sum_probs=18.5
Q ss_pred HHHHHHHHcCCCcccchhhcc
Q psy3281 267 RRIEIAHALCLTERQIKIWFQ 287 (317)
Q Consensus 267 er~eLA~~LgLse~qVkiWFQ 287 (317)
....+|+.+|++...|+.+|.
T Consensus 29 s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 29 SFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 467899999999999999885
No 244
>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=22.31 E-value=1e+02 Score=22.74 Aligned_cols=51 Identities=18% Similarity=0.089 Sum_probs=28.5
Q ss_pred CCCcccCHHHHHHHHHHhhhCCCCCH---HHHHHHHHHcCCCcccchhhcccch
Q psy3281 240 RGRQTYTRYQTLELEKEFHFNRYLTR---RRRIEIAHALCLTERQIKIWFQNRR 290 (317)
Q Consensus 240 R~Rt~fT~~Ql~~LE~~F~~n~yPs~---~er~eLA~~LgLse~qVkiWFQNRR 290 (317)
++|..+|.+.-..+...++.-...+. ..+.++-...+|+..+|+.=.|.-|
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 35677888875555555555454444 4333433334567777776555433
No 245
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=21.71 E-value=86 Score=27.14 Aligned_cols=41 Identities=10% Similarity=-0.018 Sum_probs=32.0
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchh
Q psy3281 250 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 291 (317)
Q Consensus 250 l~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRa 291 (317)
+....+.|....|- .....+||++.|+++..|-.+|.||..
T Consensus 14 l~aA~~lf~e~G~~-~tSi~~Ia~~aGvsk~~lY~~F~sK~~ 54 (192)
T PRK14996 14 LQAAMRVALAEGFA-AMTVRRIASEAQVAAGQVHHHFSSAGE 54 (192)
T ss_pred HHHHHHHHHhcChh-hccHHHHHHHhCCCcHHHHHHcCCHHH
Confidence 44445557777774 345788999999999999999999865
No 246
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=21.68 E-value=45 Score=24.16 Aligned_cols=20 Identities=15% Similarity=0.185 Sum_probs=17.4
Q ss_pred HHHHHHHcCCCcccchhhcc
Q psy3281 268 RIEIAHALCLTERQIKIWFQ 287 (317)
Q Consensus 268 r~eLA~~LgLse~qVkiWFQ 287 (317)
..++|+.+|++++.|+.|..
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999964
No 247
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=21.68 E-value=90 Score=22.18 Aligned_cols=34 Identities=15% Similarity=0.083 Sum_probs=21.0
Q ss_pred HHHHHhhhC-CCCCHHHHHHHHHHcCCCcccchhh
Q psy3281 252 ELEKEFHFN-RYLTRRRRIEIAHALCLTERQIKIW 285 (317)
Q Consensus 252 ~LE~~F~~n-~yPs~~er~eLA~~LgLse~qVkiW 285 (317)
.|.+++... ..++......||..|+++...+-.|
T Consensus 26 tl~~~~~~~~~~~~~~~l~~ia~~l~~~~~el~~~ 60 (63)
T PF13443_consen 26 TLSRILNGKPSNPSLDTLEKIAKALNCSPEELFEY 60 (63)
T ss_dssp HHHHHHTTT-----HHHHHHHHHHHT--HHHCTEC
T ss_pred HHHHHHhcccccccHHHHHHHHHHcCCCHHHHhhc
Confidence 355556554 4799999999999999998876544
No 248
>PRK13870 transcriptional regulator TraR; Provisional
Probab=21.68 E-value=86 Score=29.03 Aligned_cols=51 Identities=10% Similarity=0.036 Sum_probs=37.3
Q ss_pred CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 242 Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
+..+|..++++|.=.- ....-.+||..|||+++.|+.-++|-|.|..-.++
T Consensus 171 ~~~LT~RE~E~L~W~A------~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga~nr 221 (234)
T PRK13870 171 AAWLDPKEATYLRWIA------VGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSK 221 (234)
T ss_pred cCCCCHHHHHHHHHHH------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCH
Confidence 3468888888885221 12345688999999999999999998888654433
No 249
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=21.08 E-value=76 Score=26.58 Aligned_cols=19 Identities=21% Similarity=-0.046 Sum_probs=12.7
Q ss_pred CCCHHHHHHHHHHcCCCcc
Q psy3281 262 YLTRRRRIEIAHALCLTER 280 (317)
Q Consensus 262 yPs~~er~eLA~~LgLse~ 280 (317)
.|+.+....||..|+++..
T Consensus 44 ~ps~~~l~kIa~aL~v~~~ 62 (120)
T PRK13890 44 NPSLKVMEAIADALETPLP 62 (120)
T ss_pred CCCHHHHHHHHHHHCCCHH
Confidence 5677777777777766654
No 250
>PF13933 HRXXH: Putative peptidase family
Probab=20.96 E-value=1.4e+02 Score=28.57 Aligned_cols=62 Identities=11% Similarity=0.093 Sum_probs=40.3
Q ss_pred CCCcchhcccccCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccc
Q psy3281 227 PLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 289 (317)
Q Consensus 227 ~~~P~~~s~~krRR~Rt~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNR 289 (317)
..+.|.....+.-..-..-...++..|++.|.....+....|..|. +.|-...-.+.||-|+
T Consensus 33 ~~~~~~~~~~~~fpih~SCN~T~r~qL~~al~ea~~lA~~AkdhlL-r~G~~s~~f~kyFGn~ 94 (245)
T PF13933_consen 33 TSYDWSAGWVPVFPIHSSCNATQRRQLNSALDEAVELAAHAKDHLL-RWGNSSEFFRKYFGNG 94 (245)
T ss_pred CcCccccCcccCCccccchhHHHHHHHHHHHHHHHHHHHHHHHHHh-ccCCccHHHHHhcCCC
Confidence 3444444333333344456778899999999887777777666653 4455556689999994
No 251
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=20.88 E-value=1.1e+02 Score=26.91 Aligned_cols=36 Identities=19% Similarity=0.056 Sum_probs=29.3
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccch
Q psy3281 248 YQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIK 283 (317)
Q Consensus 248 ~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVk 283 (317)
.-+.+|...=+...|++.+..+.||+.|||+...|.
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 446666666566789999999999999999998776
No 252
>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=20.78 E-value=46 Score=26.67 Aligned_cols=23 Identities=13% Similarity=0.043 Sum_probs=19.4
Q ss_pred HHHHHHHcCCCcccchhhcccch
Q psy3281 268 RIEIAHALCLTERQIKIWFQNRR 290 (317)
Q Consensus 268 r~eLA~~LgLse~qVkiWFQNRR 290 (317)
..++|+.+|++.+.|+.|..+-.
T Consensus 3 i~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 46789999999999999986544
No 253
>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=20.68 E-value=85 Score=25.70 Aligned_cols=35 Identities=20% Similarity=0.386 Sum_probs=18.1
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhhhc
Q psy3281 250 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298 (317)
Q Consensus 250 l~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~~k 298 (317)
+.+++-.|+.|+||+.+--.. | -+|||.+||+...
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~ 48 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQR 48 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHH
Confidence 344455588899997442111 1 1588888887654
No 254
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=20.34 E-value=1.1e+02 Score=26.55 Aligned_cols=36 Identities=8% Similarity=0.011 Sum_probs=28.8
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccch
Q psy3281 248 YQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIK 283 (317)
Q Consensus 248 ~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVk 283 (317)
.-+.+|...=+...|.+.+....+|+.|+|+...|.
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 345556555566789999999999999999998876
No 255
>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=20.28 E-value=1.1e+02 Score=26.30 Aligned_cols=36 Identities=11% Similarity=-0.017 Sum_probs=28.2
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccch
Q psy3281 248 YQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIK 283 (317)
Q Consensus 248 ~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVk 283 (317)
.-+.+|...=+...|.+.+..+.+|+.|||+...|.
T Consensus 17 ~li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 17 AIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 345555555555679999999999999999987765
No 256
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=20.21 E-value=90 Score=30.31 Aligned_cols=52 Identities=13% Similarity=0.108 Sum_probs=38.9
Q ss_pred ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCCcccchhhcccchhhhhhh
Q psy3281 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296 (317)
Q Consensus 244 ~fT~~Ql~~LE~~F~~n~yPs~~er~eLA~~LgLse~qVkiWFQNRRaK~KK~ 296 (317)
.++..+..+|...|-.... .....++||..|||+...|+.....-+.|.|+.
T Consensus 256 ~L~~rer~Vi~lr~gl~~~-~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~ 307 (317)
T PRK07405 256 DLTPQQKEVIALRFGLEDG-QPLTLAKIGERLNISRERVRQIEREALSKLRKR 307 (317)
T ss_pred cCCHHHHHHHHHHhhcCCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4677777788777754322 224578999999999999999988777777763
Done!