Query psy17897
Match_columns 391
No_of_seqs 294 out of 1483
Neff 5.2
Searched_HMMs 46136
Date Fri Aug 16 16:55:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17897.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17897hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1168|consensus 100.0 8.7E-70 1.9E-74 520.7 18.8 300 5-390 54-372 (385)
2 KOG3802|consensus 100.0 1.1E-51 2.4E-56 411.4 19.6 157 227-387 198-354 (398)
3 PF00157 Pou: Pou domain - N-t 99.9 5.6E-26 1.2E-30 181.2 4.6 73 231-306 3-75 (75)
4 smart00352 POU Found in Pit-Oc 99.8 9.1E-21 2E-25 151.3 6.0 75 229-306 1-75 (75)
5 KOG0775|consensus 99.7 5.3E-16 1.2E-20 149.4 13.1 150 228-384 73-233 (304)
6 KOG0489|consensus 99.6 4.5E-17 9.8E-22 157.9 3.0 65 325-389 157-221 (261)
7 KOG2252|consensus 99.6 1.1E-15 2.3E-20 158.7 10.1 138 234-382 320-475 (558)
8 KOG0488|consensus 99.6 2.1E-16 4.6E-21 156.6 4.5 65 325-389 170-234 (309)
9 KOG0842|consensus 99.6 4.6E-16 9.9E-21 153.3 4.9 66 324-389 150-215 (307)
10 KOG4577|consensus 99.6 1.3E-15 2.7E-20 147.8 7.2 138 238-389 85-229 (383)
11 KOG0487|consensus 99.6 8.4E-16 1.8E-20 151.5 4.4 67 321-387 229-295 (308)
12 KOG0843|consensus 99.6 1.2E-15 2.7E-20 139.4 4.8 63 326-388 101-163 (197)
13 PF00046 Homeobox: Homeobox do 99.6 1.5E-15 3.3E-20 113.6 3.4 57 328-384 1-57 (57)
14 KOG0484|consensus 99.5 1.3E-15 2.8E-20 128.4 2.1 65 325-389 15-79 (125)
15 KOG0485|consensus 99.5 2.5E-15 5.3E-20 140.9 3.9 67 322-388 99-165 (268)
16 KOG2251|consensus 99.5 4.9E-15 1.1E-19 139.2 5.5 67 322-388 32-98 (228)
17 KOG0850|consensus 99.5 2E-14 4.2E-19 135.9 5.2 67 323-389 118-184 (245)
18 KOG0848|consensus 99.5 1.5E-14 3.2E-19 139.2 2.5 65 325-389 197-261 (317)
19 KOG0494|consensus 99.5 3.1E-14 6.8E-19 136.4 4.6 60 330-389 144-203 (332)
20 cd00086 homeodomain Homeodomai 99.4 1.2E-13 2.5E-18 103.0 4.2 58 328-385 1-58 (59)
21 KOG0492|consensus 99.4 1.3E-13 2.8E-18 128.7 4.9 63 326-388 143-205 (246)
22 smart00389 HOX Homeodomain. DN 99.4 1.2E-13 2.7E-18 102.3 3.8 56 328-383 1-56 (56)
23 TIGR01565 homeo_ZF_HD homeobox 99.4 1.8E-13 3.9E-18 104.8 4.5 53 327-379 1-57 (58)
24 KOG0844|consensus 99.3 2.6E-13 5.6E-18 132.6 2.1 64 325-388 179-242 (408)
25 COG5576 Homeodomain-containing 99.3 2.2E-12 4.8E-17 116.8 7.1 64 325-388 49-112 (156)
26 KOG0493|consensus 99.3 1.3E-12 2.8E-17 125.6 4.5 61 326-386 245-305 (342)
27 KOG0486|consensus 99.3 1E-12 2.2E-17 129.0 3.7 66 325-390 110-175 (351)
28 KOG0491|consensus 99.3 3.9E-13 8.5E-18 121.6 0.5 65 326-390 99-163 (194)
29 KOG0483|consensus 99.3 2.7E-12 5.8E-17 120.2 3.2 62 327-388 50-111 (198)
30 KOG0847|consensus 99.1 1.8E-11 3.8E-16 115.4 1.8 63 324-386 164-226 (288)
31 KOG0849|consensus 99.0 2.2E-10 4.7E-15 115.9 5.2 64 323-386 172-235 (354)
32 KOG0490|consensus 99.0 1.7E-10 3.7E-15 107.5 3.6 63 325-387 58-120 (235)
33 KOG0774|consensus 98.8 1.4E-09 3.1E-14 104.9 0.7 101 286-388 147-252 (334)
34 PF05920 Homeobox_KN: Homeobox 98.3 1.9E-07 4.2E-12 66.5 0.8 34 348-381 7-40 (40)
35 KOG0490|consensus 97.8 2.1E-05 4.5E-10 73.4 4.6 62 325-386 151-212 (235)
36 KOG1146|consensus 97.3 0.00015 3.2E-09 82.9 2.9 62 326-387 902-963 (1406)
37 KOG0773|consensus 96.5 0.0016 3.5E-08 65.3 2.5 59 327-385 239-300 (342)
38 PF11569 Homez: Homeodomain le 95.8 0.0026 5.6E-08 48.7 0.3 43 339-381 10-52 (56)
39 KOG3623|consensus 94.9 0.016 3.5E-07 63.5 2.7 48 339-386 568-615 (1007)
40 PF13560 HTH_31: Helix-turn-he 94.3 0.029 6.2E-07 42.8 2.1 40 239-287 1-40 (64)
41 PF04218 CENP-B_N: CENP-B N-te 94.3 0.058 1.3E-06 40.4 3.6 47 328-379 1-47 (53)
42 COG3620 Predicted transcriptio 92.9 0.13 2.7E-06 47.7 4.1 54 242-306 8-61 (187)
43 TIGR03070 couple_hipB transcri 92.3 0.091 2E-06 38.0 1.9 39 239-286 2-40 (58)
44 PHA01976 helix-turn-helix prot 91.5 0.14 3.1E-06 38.9 2.3 39 239-286 2-40 (67)
45 PF04814 HNF-1_N: Hepatocyte n 90.6 0.26 5.6E-06 46.1 3.4 56 240-306 119-174 (180)
46 KOG3623|consensus 89.9 0.29 6.3E-06 54.1 3.7 86 297-385 599-684 (1007)
47 TIGR00270 conserved hypothetic 88.3 0.46 1E-05 43.3 3.3 43 237-288 67-109 (154)
48 PRK06424 transcription factor; 88.2 0.75 1.6E-05 41.5 4.5 45 235-288 80-124 (144)
49 PRK09726 antitoxin HipB; Provi 87.5 0.83 1.8E-05 37.2 4.1 40 237-285 10-49 (88)
50 TIGR03830 CxxCG_CxxCG_HTH puta 86.7 0.91 2E-05 38.6 4.1 38 242-288 68-105 (127)
51 PF13744 HTH_37: Helix-turn-he 86.6 0.79 1.7E-05 36.7 3.4 40 239-287 18-57 (80)
52 cd00131 PAX Paired Box domain 84.3 3.5 7.5E-05 36.2 6.6 45 333-377 75-126 (128)
53 PRK09706 transcriptional repre 84.2 0.79 1.7E-05 40.0 2.5 42 238-288 4-45 (135)
54 TIGR01321 TrpR trp operon repr 83.2 2.5 5.5E-05 35.7 5.0 56 234-304 35-92 (94)
55 PRK10856 cytoskeletal protein 82.8 3.1 6.7E-05 42.3 6.5 47 233-288 8-54 (331)
56 PF01381 HTH_3: Helix-turn-hel 80.7 1 2.2E-05 32.7 1.6 36 244-288 1-36 (55)
57 PRK08359 transcription factor; 80.4 1.6 3.5E-05 40.7 3.2 46 235-289 81-126 (176)
58 PF12844 HTH_19: Helix-turn-he 80.1 2.1 4.5E-05 32.1 3.2 38 242-288 2-39 (64)
59 PRK09943 DNA-binding transcrip 79.7 1.7 3.7E-05 39.8 3.1 43 237-288 5-47 (185)
60 PRK10072 putative transcriptio 76.9 2 4.4E-05 36.2 2.5 38 243-289 37-74 (96)
61 PF13551 HTH_29: Winged helix- 76.7 6 0.00013 32.3 5.2 48 329-376 53-109 (112)
62 PF04545 Sigma70_r4: Sigma-70, 75.8 2.3 5E-05 30.7 2.2 47 333-384 4-50 (50)
63 PHA00542 putative Cro-like pro 74.9 4.2 9.1E-05 32.9 3.8 30 248-286 27-56 (82)
64 PF02376 CUT: CUT domain; Int 74.4 3 6.6E-05 34.5 2.9 62 236-308 10-78 (87)
65 PRK08154 anaerobic benzoate ca 74.2 4.5 9.8E-05 40.2 4.6 43 235-286 24-66 (309)
66 PRK13890 conjugal transfer pro 70.3 5.7 0.00012 34.5 3.8 39 239-286 5-43 (120)
67 cd06171 Sigma70_r4 Sigma70, re 70.2 3.4 7.4E-05 28.4 2.0 44 333-381 10-53 (55)
68 PF08281 Sigma70_r4_2: Sigma-7 70.0 3.6 7.7E-05 29.9 2.1 43 334-381 11-53 (54)
69 cd00569 HTH_Hin_like Helix-tur 68.7 5.9 0.00013 24.3 2.7 37 334-375 6-42 (42)
70 PF01527 HTH_Tnp_1: Transposas 65.9 1.9 4E-05 33.4 -0.2 46 329-378 2-47 (76)
71 PRK03975 tfx putative transcri 64.7 8.3 0.00018 34.8 3.8 51 331-387 4-54 (141)
72 TIGR02612 mob_myst_A mobile my 62.4 6.4 0.00014 35.8 2.6 34 244-286 30-63 (150)
73 smart00351 PAX Paired Box doma 61.0 41 0.0009 29.2 7.4 44 332-375 74-124 (125)
74 KOG3755|consensus 60.2 2.7 5.7E-05 46.0 -0.3 48 341-388 706-760 (769)
75 PRK09646 RNA polymerase sigma 59.9 9.3 0.0002 34.8 3.3 49 333-386 142-190 (194)
76 PF04967 HTH_10: HTH DNA bindi 59.6 7.3 0.00016 29.5 2.1 42 334-375 1-44 (53)
77 PRK06759 RNA polymerase factor 59.3 7 0.00015 33.8 2.3 47 333-384 106-152 (154)
78 PRK11924 RNA polymerase sigma 58.2 11 0.00023 33.0 3.3 33 356-388 143-175 (179)
79 PF00196 GerE: Bacterial regul 57.0 7.8 0.00017 28.8 1.9 46 333-384 3-48 (58)
80 COG1476 Predicted transcriptio 55.9 11 0.00024 30.1 2.7 38 243-289 5-42 (68)
81 PF13936 HTH_38: Helix-turn-he 55.6 5.3 0.00011 28.6 0.7 40 332-376 3-42 (44)
82 PRK00118 putative DNA-binding 55.4 13 0.00029 31.8 3.2 49 334-387 18-66 (104)
83 PRK09642 RNA polymerase sigma 54.7 13 0.00028 32.4 3.2 50 334-388 107-156 (160)
84 PF13565 HTH_32: Homeodomain-l 54.5 52 0.0011 25.3 6.3 40 335-374 32-76 (77)
85 TIGR02607 antidote_HigA addict 53.1 11 0.00024 29.1 2.2 33 244-285 9-42 (78)
86 PRK12526 RNA polymerase sigma 53.1 13 0.00029 34.3 3.1 32 356-387 171-202 (206)
87 PRK09652 RNA polymerase sigma 52.6 14 0.0003 32.4 3.0 50 333-387 128-177 (182)
88 PRK04140 hypothetical protein; 52.5 15 0.00032 37.4 3.6 43 242-293 129-173 (317)
89 cd00093 HTH_XRE Helix-turn-hel 52.2 19 0.00041 24.1 3.1 34 243-285 3-36 (58)
90 TIGR02937 sigma70-ECF RNA poly 51.9 14 0.0003 30.6 2.8 46 334-384 111-156 (158)
91 TIGR02948 SigW_bacill RNA poly 50.0 14 0.00031 32.8 2.7 32 355-386 153-184 (187)
92 PRK09639 RNA polymerase sigma 49.9 17 0.00036 31.8 3.2 49 334-388 113-161 (166)
93 PRK12514 RNA polymerase sigma 48.5 20 0.00042 32.0 3.4 30 356-385 147-176 (179)
94 PRK12512 RNA polymerase sigma 48.5 17 0.00038 32.5 3.1 49 334-387 132-180 (184)
95 PRK09480 slmA division inhibit 47.9 13 0.00029 33.0 2.2 40 340-380 17-56 (194)
96 TIGR02939 RpoE_Sigma70 RNA pol 47.6 14 0.00031 32.9 2.3 32 355-386 155-186 (190)
97 smart00421 HTH_LUXR helix_turn 47.1 19 0.00042 25.1 2.5 44 334-383 4-47 (58)
98 PRK12519 RNA polymerase sigma 46.6 15 0.00034 33.1 2.5 32 355-386 158-189 (194)
99 PRK09644 RNA polymerase sigma 46.3 18 0.00039 31.8 2.8 50 334-388 109-158 (165)
100 PRK04217 hypothetical protein; 46.2 22 0.00048 30.8 3.2 52 331-387 40-91 (110)
101 TIGR02985 Sig70_bacteroi1 RNA 46.0 19 0.0004 30.8 2.8 45 335-384 115-159 (161)
102 PRK12515 RNA polymerase sigma 45.8 22 0.00048 32.0 3.4 50 334-388 132-181 (189)
103 PF01371 Trp_repressor: Trp re 45.5 25 0.00054 29.3 3.3 39 234-281 29-69 (87)
104 PRK09648 RNA polymerase sigma 45.0 19 0.00042 32.4 2.8 48 333-385 139-186 (189)
105 PRK12537 RNA polymerase sigma 44.2 26 0.00056 31.5 3.5 30 356-385 151-180 (182)
106 TIGR02959 SigZ RNA polymerase 44.0 24 0.00052 31.4 3.2 50 333-387 100-149 (170)
107 TIGR02999 Sig-70_X6 RNA polyme 43.9 21 0.00046 31.7 2.9 47 334-385 135-181 (183)
108 PRK05602 RNA polymerase sigma 43.5 22 0.00048 31.9 3.0 32 356-387 146-177 (186)
109 PRK12541 RNA polymerase sigma 43.4 18 0.00039 31.6 2.3 48 334-386 113-160 (161)
110 TIGR02989 Sig-70_gvs1 RNA poly 43.2 21 0.00045 30.9 2.6 47 333-384 111-157 (159)
111 PRK12530 RNA polymerase sigma 42.3 24 0.00053 32.0 3.1 48 335-387 136-183 (189)
112 PF10668 Phage_terminase: Phag 42.1 9.1 0.0002 29.8 0.2 21 356-376 24-44 (60)
113 PRK06930 positive control sigm 40.5 28 0.0006 32.1 3.1 50 333-387 114-163 (170)
114 PRK12538 RNA polymerase sigma 39.9 22 0.00048 33.9 2.5 33 356-388 189-221 (233)
115 PF06056 Terminase_5: Putative 39.5 13 0.00028 28.5 0.6 21 356-376 15-35 (58)
116 KOG1146|consensus 39.3 23 0.00049 42.3 2.8 61 326-386 704-764 (1406)
117 PRK10072 putative transcriptio 38.2 23 0.0005 29.9 2.0 41 333-380 32-72 (96)
118 PRK12547 RNA polymerase sigma 37.9 29 0.00063 30.6 2.8 47 334-385 113-159 (164)
119 PF00292 PAX: 'Paired box' dom 37.7 10 0.00022 33.7 -0.2 32 227-258 77-113 (125)
120 PF09607 BrkDBD: Brinker DNA-b 37.3 22 0.00049 27.6 1.7 46 330-376 2-47 (58)
121 TIGR00721 tfx DNA-binding prot 37.3 41 0.00089 30.2 3.6 49 331-385 4-52 (137)
122 TIGR02954 Sig70_famx3 RNA poly 37.2 34 0.00073 30.1 3.1 30 356-385 137-166 (169)
123 PRK09047 RNA polymerase factor 37.2 34 0.00073 29.6 3.1 49 334-387 107-155 (161)
124 PRK12546 RNA polymerase sigma 37.1 30 0.00065 31.7 2.8 32 356-387 131-162 (188)
125 PRK07037 extracytoplasmic-func 37.0 32 0.00069 30.0 2.9 47 334-385 110-156 (163)
126 PRK12518 RNA polymerase sigma 36.9 21 0.00045 31.6 1.7 36 354-389 136-171 (175)
127 PRK12543 RNA polymerase sigma 36.8 36 0.00078 30.5 3.2 33 356-388 135-167 (179)
128 PRK12536 RNA polymerase sigma 36.7 31 0.00066 31.0 2.8 30 356-385 147-176 (181)
129 TIGR02983 SigE-fam_strep RNA p 36.7 30 0.00065 30.1 2.7 47 335-386 112-158 (162)
130 PRK06986 fliA flagellar biosyn 36.6 31 0.00066 32.6 2.9 47 335-386 186-232 (236)
131 COG3413 Predicted DNA binding 36.6 25 0.00055 33.0 2.3 49 333-383 155-205 (215)
132 PRK12524 RNA polymerase sigma 36.4 35 0.00076 31.1 3.1 32 356-387 154-185 (196)
133 PHA02591 hypothetical protein; 36.3 32 0.0007 28.4 2.5 26 247-281 54-79 (83)
134 PRK01381 Trp operon repressor; 36.3 77 0.0017 27.2 4.9 55 234-304 35-92 (99)
135 smart00530 HTH_XRE Helix-turn- 36.1 51 0.0011 21.7 3.3 33 245-286 3-35 (56)
136 PRK09637 RNA polymerase sigma 35.9 34 0.00074 30.9 3.0 31 356-386 124-154 (181)
137 PRK12532 RNA polymerase sigma 35.6 36 0.00078 30.8 3.1 32 356-387 154-185 (195)
138 PRK12539 RNA polymerase sigma 35.2 40 0.00086 30.3 3.3 50 333-387 131-180 (184)
139 PRK11923 algU RNA polymerase s 35.2 36 0.00077 30.7 3.0 32 356-387 156-187 (193)
140 PRK13919 putative RNA polymera 35.2 39 0.00084 30.2 3.2 30 356-385 153-182 (186)
141 PRK09413 IS2 repressor TnpA; R 35.0 28 0.00061 29.9 2.1 43 331-377 10-52 (121)
142 TIGR03879 near_KaiC_dom probab 34.9 6.6 0.00014 31.7 -1.7 25 355-379 33-57 (73)
143 PRK12520 RNA polymerase sigma 34.9 38 0.00083 30.5 3.1 49 334-387 132-180 (191)
144 PRK12542 RNA polymerase sigma 34.9 33 0.00072 30.8 2.7 32 356-387 140-171 (185)
145 TIGR02684 dnstrm_HI1420 probab 34.8 54 0.0012 27.2 3.7 39 239-288 32-70 (89)
146 KOG0773|consensus 34.8 23 0.00051 35.5 1.8 42 347-388 117-158 (342)
147 TIGR02952 Sig70_famx2 RNA poly 34.6 36 0.00077 29.7 2.8 29 356-384 140-168 (170)
148 PRK09647 RNA polymerase sigma 34.4 42 0.00091 31.2 3.3 32 356-387 156-187 (203)
149 PRK06811 RNA polymerase factor 34.3 35 0.00076 30.9 2.8 48 334-386 132-179 (189)
150 TIGR03001 Sig-70_gmx1 RNA poly 34.2 39 0.00084 32.6 3.2 33 356-388 179-211 (244)
151 PRK09645 RNA polymerase sigma 34.0 43 0.00092 29.5 3.2 32 356-387 136-167 (173)
152 PRK12516 RNA polymerase sigma 33.8 42 0.00091 30.6 3.2 32 356-387 134-165 (187)
153 cd04761 HTH_MerR-SF Helix-Turn 33.5 14 0.00031 25.8 0.1 22 357-378 3-24 (49)
154 PRK12531 RNA polymerase sigma 33.5 44 0.00095 30.4 3.3 33 356-388 159-191 (194)
155 PRK12513 RNA polymerase sigma 33.5 22 0.00047 32.2 1.3 35 353-387 154-188 (194)
156 TIGR02943 Sig70_famx1 RNA poly 33.2 42 0.0009 30.5 3.1 49 335-388 133-181 (188)
157 PRK15369 two component system 33.0 39 0.00085 29.0 2.8 45 333-383 149-193 (211)
158 PF13384 HTH_23: Homeodomain-l 32.7 14 0.0003 26.3 -0.2 23 355-377 18-40 (50)
159 COG4974 XerD Site-specific rec 32.7 1.6E+02 0.0035 29.9 7.3 94 234-345 31-126 (300)
160 PRK10403 transcriptional regul 32.5 23 0.00049 30.9 1.2 49 332-386 152-200 (215)
161 PF02796 HTH_7: Helix-turn-hel 32.2 27 0.00059 24.9 1.3 38 333-375 5-42 (45)
162 PRK12523 RNA polymerase sigma 32.1 43 0.00092 29.7 2.9 47 334-385 120-166 (172)
163 PRK12511 RNA polymerase sigma 31.9 48 0.001 30.1 3.3 49 334-387 112-160 (182)
164 PRK12522 RNA polymerase sigma 31.5 54 0.0012 29.0 3.5 32 356-387 137-168 (173)
165 PRK09641 RNA polymerase sigma 31.3 41 0.00089 29.8 2.7 32 355-386 153-184 (187)
166 COG2963 Transposase and inacti 31.1 53 0.0011 27.6 3.2 43 331-377 5-48 (116)
167 PRK12545 RNA polymerase sigma 30.7 51 0.0011 30.3 3.3 32 356-387 157-188 (201)
168 PRK08295 RNA polymerase factor 30.6 57 0.0012 29.6 3.5 33 355-387 171-203 (208)
169 cd06170 LuxR_C_like C-terminal 30.6 54 0.0012 23.0 2.7 42 335-382 2-43 (57)
170 TIGR02947 SigH_actino RNA poly 30.4 27 0.00059 31.6 1.4 32 355-386 148-179 (193)
171 PRK13355 bifunctional HTH-doma 30.3 38 0.00082 35.9 2.6 47 238-288 2-48 (517)
172 PRK12529 RNA polymerase sigma 30.0 47 0.001 29.8 2.8 48 333-385 127-174 (178)
173 PRK12535 RNA polymerase sigma 29.9 46 0.001 30.6 2.8 32 356-387 151-182 (196)
174 PRK08301 sporulation sigma fac 29.3 51 0.0011 30.9 3.1 53 334-387 179-231 (234)
175 TIGR02479 FliA_WhiG RNA polyme 29.0 48 0.001 30.9 2.8 47 334-385 176-222 (224)
176 PRK12533 RNA polymerase sigma 29.0 43 0.00093 31.6 2.5 31 356-386 152-182 (216)
177 PF13518 HTH_28: Helix-turn-he 29.0 26 0.00057 24.7 0.8 25 356-380 14-38 (52)
178 PRK06288 RNA polymerase sigma 28.8 53 0.0011 31.8 3.1 50 334-388 213-262 (268)
179 PRK08583 RNA polymerase sigma 28.6 49 0.0011 31.6 2.8 48 334-386 206-253 (257)
180 PF00424 REV: REV protein (ant 28.4 71 0.0015 27.0 3.4 35 340-388 15-49 (91)
181 PRK07670 RNA polymerase sigma 28.4 50 0.0011 31.5 2.9 46 335-385 203-248 (251)
182 PF13411 MerR_1: MerR HTH fami 28.3 20 0.00044 27.0 0.1 20 357-376 3-22 (69)
183 KOG3517|consensus 28.1 14 0.00031 36.6 -0.9 29 227-255 80-113 (334)
184 PRK12544 RNA polymerase sigma 28.1 58 0.0013 30.3 3.2 32 356-387 166-197 (206)
185 TIGR03020 EpsA transcriptional 27.9 45 0.00098 32.6 2.5 51 331-387 188-238 (247)
186 PRK09649 RNA polymerase sigma 27.8 47 0.001 30.0 2.4 29 356-384 148-176 (185)
187 PRK09651 RNA polymerase sigma 27.3 49 0.0011 29.4 2.4 30 356-385 137-166 (172)
188 TIGR02859 spore_sigH RNA polym 27.3 62 0.0013 29.0 3.1 31 354-384 165-195 (198)
189 PF00376 MerR: MerR family reg 27.1 20 0.00044 25.0 -0.1 19 357-375 2-20 (38)
190 TIGR02941 Sigma_B RNA polymera 27.0 53 0.0012 31.3 2.8 48 333-385 205-252 (255)
191 PF13443 HTH_26: Cro/C1-type H 26.8 20 0.00043 26.6 -0.2 25 356-380 12-36 (63)
192 PRK10651 transcriptional regul 26.6 47 0.001 28.9 2.2 46 333-384 155-200 (216)
193 TIGR02980 SigBFG RNA polymeras 26.5 56 0.0012 30.4 2.8 47 333-384 178-224 (227)
194 PF13413 HTH_25: Helix-turn-he 26.5 32 0.00069 26.5 0.9 37 244-289 2-38 (62)
195 PRK11242 DNA-binding transcrip 26.2 95 0.0021 29.4 4.3 70 233-307 2-77 (296)
196 PRK09390 fixJ response regulat 26.1 49 0.0011 28.3 2.1 47 334-386 142-188 (202)
197 PRK12534 RNA polymerase sigma 25.8 81 0.0018 28.2 3.6 30 356-385 155-184 (187)
198 PRK12528 RNA polymerase sigma 25.7 58 0.0013 28.4 2.6 45 334-383 114-158 (161)
199 cd04762 HTH_MerR-trunc Helix-T 25.6 17 0.00036 24.8 -0.7 24 357-380 3-26 (49)
200 PRK05803 sporulation sigma fac 25.4 67 0.0015 30.2 3.1 55 334-389 176-230 (233)
201 PRK12540 RNA polymerase sigma 25.3 70 0.0015 29.0 3.1 32 356-387 129-160 (182)
202 PRK11139 DNA-binding transcrip 24.8 1.2E+02 0.0027 28.8 4.9 76 229-309 3-84 (297)
203 PRK10360 DNA-binding transcrip 24.5 46 0.00099 29.0 1.7 45 333-383 137-181 (196)
204 PRK12525 RNA polymerase sigma 24.3 69 0.0015 28.3 2.8 47 333-384 118-164 (168)
205 TIGR03541 reg_near_HchA LuxR f 24.0 62 0.0013 30.7 2.6 51 331-387 169-219 (232)
206 COG1709 Predicted transcriptio 24.0 92 0.002 30.5 3.7 59 238-305 26-84 (241)
207 COG1426 Predicted transcriptio 23.8 1.4E+02 0.003 29.8 5.1 26 238-263 2-27 (284)
208 PRK09975 DNA-binding transcrip 23.2 48 0.001 30.1 1.6 40 340-380 18-57 (213)
209 TIGR02835 spore_sigmaE RNA pol 23.1 87 0.0019 29.6 3.4 53 334-387 179-231 (234)
210 PRK09935 transcriptional regul 22.9 53 0.0011 28.7 1.8 46 332-383 148-193 (210)
211 TIGR02957 SigX4 RNA polymerase 22.6 68 0.0015 31.3 2.6 30 356-385 126-155 (281)
212 COG2944 Predicted transcriptio 22.5 61 0.0013 28.0 2.0 39 334-379 44-82 (104)
213 PRK07408 RNA polymerase sigma 22.4 77 0.0017 30.6 2.9 49 334-387 204-252 (256)
214 PRK09415 RNA polymerase factor 22.3 72 0.0016 28.5 2.6 31 356-386 145-175 (179)
215 PF01710 HTH_Tnp_IS630: Transp 22.2 66 0.0014 27.6 2.2 33 339-376 8-40 (119)
216 PF02001 DUF134: Protein of un 22.1 68 0.0015 27.7 2.2 36 230-281 40-77 (106)
217 TIGR02950 SigM_subfam RNA poly 22.0 42 0.00091 28.8 0.9 33 352-384 119-151 (154)
218 cd04764 HTH_MlrA-like_sg1 Heli 21.8 34 0.00073 25.9 0.3 21 357-377 3-23 (67)
219 PRK10100 DNA-binding transcrip 21.8 70 0.0015 30.2 2.5 46 333-384 155-200 (216)
220 PRK11233 nitrogen assimilation 21.7 1.2E+02 0.0025 29.3 4.1 71 233-308 2-78 (305)
221 PRK09636 RNA polymerase sigma 21.7 71 0.0015 31.2 2.6 31 356-386 133-163 (293)
222 PRK11922 RNA polymerase sigma 21.3 54 0.0012 30.8 1.6 36 352-387 163-198 (231)
223 cd04763 HTH_MlrA-like Helix-Tu 21.3 33 0.00071 26.1 0.1 21 357-377 3-23 (68)
224 TIGR02393 RpoD_Cterm RNA polym 21.1 91 0.002 29.5 3.1 53 333-386 176-228 (238)
225 KOG3520|consensus 21.0 1E+02 0.0022 36.7 3.9 76 233-308 437-520 (1167)
226 PF09048 Cro: Cro; InterPro: 21.0 1E+02 0.0022 24.1 2.8 28 237-264 6-35 (59)
227 PRK09643 RNA polymerase sigma 21.0 1E+02 0.0022 28.0 3.3 31 356-386 152-182 (192)
228 PRK12517 RNA polymerase sigma 20.9 99 0.0021 28.1 3.2 32 356-387 146-177 (188)
229 PRK02866 cyanate hydratase; Va 20.7 1.5E+02 0.0032 27.2 4.1 51 239-298 5-57 (147)
230 CHL00180 rbcR LysR transcripti 20.7 1.5E+02 0.0032 28.5 4.5 38 229-266 2-44 (305)
231 PRK09640 RNA polymerase sigma 20.6 53 0.0012 29.6 1.3 33 355-387 151-183 (188)
232 PRK10216 DNA-binding transcrip 20.4 1.5E+02 0.0032 28.8 4.5 74 230-308 6-85 (319)
233 cd01392 HTH_LacI Helix-turn-he 20.4 40 0.00086 23.9 0.4 18 360-377 3-20 (52)
234 PRK11151 DNA-binding transcrip 20.3 1.3E+02 0.0027 28.9 3.9 34 233-266 2-40 (305)
No 1
>KOG1168|consensus
Probab=100.00 E-value=8.7e-70 Score=520.68 Aligned_cols=300 Identities=61% Similarity=0.835 Sum_probs=231.6
Q ss_pred ccCccccccchhhhhHHHHHhhhhhccc-cCCCCCCCCCCCCCccccc--cCCCCCCC---CC-------CCCCCCCCCC
Q psy17897 5 RYALLFSGLNDGLLSRAEALAAVDIGKH-SASSTPTLPTLKHDMMYHH--GMNGTHGG---PN-------GRPHQMSHHG 71 (391)
Q Consensus 5 ~~~~~f~g~~~~~~~~~~~~a~~~~~~~-~~~~~~~~~~~~~~~~~~~--~~~~~~~~---~~-------~~~~~~~~~~ 71 (391)
+++|||+|+||+||+||||||||||.|+ +++|.++.||||||++||| .+.|+.+. +. ++||+.+|..
T Consensus 54 ~~snifa~~deslLaRaealaavdi~~~qgk~~h~~pppfk~d~tyht~~~~~~ts~ts~vP~~~~a~~~~h~hh~~h~~ 133 (385)
T KOG1168|consen 54 RGSNIFAGTDESLLARAEALAAVDIPKSQGKQHHGDPPPFKPDATYHTMSVPPCTSQTSPVPLTHTASKMHHPHHHPHQM 133 (385)
T ss_pred cCCcccccccHHHHHHHHhhhheechhhcCcccCCCCCCCCCCCcccccccCCCCCCCCCcccccchhhccCcccChhhh
Confidence 5899999999999999999999999554 4566558889999999998 55555422 22 4555555554
Q ss_pred CCccccccccCCCCcccCCCCCCC--CCCCCCCCccccCCCccccccccccccCCCCCCcCCCCCCCCccccccccccCC
Q psy17897 72 MDGLEMLDSISSSMTTLTPMSDPT--PNPHQLHSSSMYGPSMNSMMTGHHHHHHHSGALPASHHHVATPSLLLFPQMSHH 149 (391)
Q Consensus 72 ~~~~~~~d~~~~~~~~~~p~~~~~--~~~~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 (391)
+| +.|++++-.++|+++.... |.+..
T Consensus 134 le---~~d~~~~ispsla~~~~~g~~P~~~~------------------------------------------------- 161 (385)
T KOG1168|consen 134 LE---YGDLLSHISPSLATNIYQGSEPFHAS------------------------------------------------- 161 (385)
T ss_pred cc---ccccccccCcchhhccccCCCCCCce-------------------------------------------------
Confidence 44 4444333335677665442 11100
Q ss_pred CCCCccccccccCcCccCCCCCCCCCCCcCCCCCCCCCcccccccccCCCCCCCCCCCCCCCCCCCCCCCCC----CCCC
Q psy17897 150 GMDGLEMLDSISSSMTTLTPMSDPTPNPHQLHSSSMYGPSMNSMMTGHHHHHHHSGALPASHHHGATHHPVM----PPGL 225 (391)
Q Consensus 150 ~~~g~~ml~~~~~~~~~~~~m~~~~~~~h~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~h~~~~~~~~~~~----~~~~ 225 (391)
+...+.++ ++|+. +.|.+...++..-+||+..++|+.+ +...
T Consensus 162 --------------------~~~~~hs~-------------~hm~~-~~h~~~~~~~~~m~hphs~~~h~~~~a~~a~~~ 207 (385)
T KOG1168|consen 162 --------------------VVGPTHSD-------------DHMTS-LQHVMAMQQAYGMTHPHSTTSHASSNARYAIAG 207 (385)
T ss_pred --------------------ecccCCCc-------------ccccc-ccchhhHHHHhccCCCCCCCCcchhhhccccCC
Confidence 01111111 11111 1111111112222344444444433 1122
Q ss_pred CCCCCCCCHHHHHHHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCChhhhhhhhHHHHHHHHHH
Q psy17897 226 QHPDTDTDPRELEAFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEA 305 (391)
Q Consensus 226 ~~pd~~~d~~eLe~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~knm~KLkPlL~kWLeea 305 (391)
.++|.++|.+|||.||++||||||+||+||+|||.||.+|++|||+.+||+||||||+|.||..||..|||+|+.||||+
T Consensus 208 ~~sD~dtDPReLEaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLTLSHNNMiALKPILqaWLEeA 287 (385)
T KOG1168|consen 208 PTSDMDTDPRELEAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLTLSHNNMIALKPILQAWLEEA 287 (385)
T ss_pred CCcccCCCHHHHHHHHHHHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeeeccccCcchhhhHHHHHHHHHH
Confidence 36799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhcCCCCCCCCCCCCCCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 306 EAQAKNKRRDPDAPSVLPAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 306 E~~~~~~~~~~~~~~~~~~~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
|...+++...++.+.+++...||||||++...+++.||++|..+++|+.+.|..||++|+|.+++|||||||+|+|.||+
T Consensus 288 E~a~keK~~~pd~~~l~~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 288 EAAMKEKDTKPDINELLPGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 367 (385)
T ss_pred HHHHHhhccCCchhhccCccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence 99999999999888899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Hhhhc
Q psy17897 386 KFAAQ 390 (391)
Q Consensus 386 ~k~aq 390 (391)
+.++-
T Consensus 368 ~~Sa~ 372 (385)
T KOG1168|consen 368 KRSAT 372 (385)
T ss_pred hhhhc
Confidence 88763
No 2
>KOG3802|consensus
Probab=100.00 E-value=1.1e-51 Score=411.35 Aligned_cols=157 Identities=50% Similarity=0.793 Sum_probs=141.8
Q ss_pred CCCCCCCHHHHHHHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCChhhhhhhhHHHHHHHHHHH
Q psy17897 227 HPDTDTDPRELEAFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAE 306 (391)
Q Consensus 227 ~pd~~~d~~eLe~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~knm~KLkPlL~kWLeeaE 306 (391)
.+|+..+++|||+||+.||+|||+|||||+|||.|||++| | ++|||+||||||+|||||||||||||+|+|||+|+|
T Consensus 198 ~~ed~~~leELEqFAK~FKqRRIkLGfTQaDVGlALG~ly--G-n~FSQTTIcRFEALqLSFKNMCKLKPLL~KWLeEAe 274 (398)
T KOG3802|consen 198 SDEDTPDLEELEQFAKTFKQRRIKLGFTQADVGLALGALY--G-NVFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAE 274 (398)
T ss_pred CcccccCHHHHHHHHHHHHhheeccccchhHHHHHHHhhh--C-cccchhhhhHhHhhccCHHHHhhhHHHHHHHHHHHh
Confidence 4677789999999999999999999999999999999999 4 689999999999999999999999999999999999
Q ss_pred HHhhhcCCCCCCCCCCCCCCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 307 AQAKNKRRDPDAPSVLPAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 307 ~~~~~~~~~~~~~~~~~~~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
..... ...+..+.+....|||||||+|+...+..||+.|.+|++|+.+||..||++|+|++++|||||||||+|+||..
T Consensus 275 s~~~~-~~~~~~e~i~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 275 SREST-GSPNSIEKIGAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred ccccc-CCCCCHHHhhccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 75222 22333344455568899999999999999999999999999999999999999999999999999999999987
Q ss_pred h
Q psy17897 387 F 387 (391)
Q Consensus 387 k 387 (391)
.
T Consensus 354 ~ 354 (398)
T KOG3802|consen 354 P 354 (398)
T ss_pred C
Confidence 6
No 3
>PF00157 Pou: Pou domain - N-terminal to homeobox domain; InterPro: IPR000327 POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain. The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [] and the development of an organism []. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [, ], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1). The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327 from INTERPRO), while the C-terminal subunit is a homeobox domain (IPR007103 from INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions []. The subdomains are connected by a flexible linker [, , ]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ]. This entry represents the POU-specific subunit of the POU domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3D1N_O 1AU7_A 3L1P_A 2XSD_C 1O4X_A 1HF0_B 1GT0_C 1POU_A 1CQT_B 1E3O_C ....
Probab=99.92 E-value=5.6e-26 Score=181.15 Aligned_cols=73 Identities=64% Similarity=0.941 Sum_probs=67.1
Q ss_pred CCCHHHHHHHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCChhhhhhhhHHHHHHHHHHH
Q psy17897 231 DTDPRELEAFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAE 306 (391)
Q Consensus 231 ~~d~~eLe~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~knm~KLkPlL~kWLeeaE 306 (391)
..+++||++||+.||+|||++||||++||.+++.+|+ ..|||+||||||++++|++|||||+|+|++||+++|
T Consensus 3 ~~~~~ele~Fa~~fk~rRi~LG~TQ~dVg~al~~~~G---~~~SQttI~RFE~L~LS~kn~~klkP~L~kWL~eaE 75 (75)
T PF00157_consen 3 TPDLKELEQFAKEFKQRRIKLGYTQADVGAALGRLYG---KEFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAE 75 (75)
T ss_dssp CHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHS---SGGSHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHHHhhhhcccCHHHHhHHHHHhcC---ccccchhhhhhHhcccCHHHHHHHHHHHHHHHHhcC
Confidence 4568999999999999999999999999999999994 469999999999999999999999999999999986
No 4
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=99.82 E-value=9.1e-21 Score=151.25 Aligned_cols=75 Identities=72% Similarity=1.062 Sum_probs=70.6
Q ss_pred CCCCCHHHHHHHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCChhhhhhhhHHHHHHHHHHH
Q psy17897 229 DTDTDPRELEAFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAE 306 (391)
Q Consensus 229 d~~~d~~eLe~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~knm~KLkPlL~kWLeeaE 306 (391)
|+..|++|||.|+..|+++|+++|+||.+||.+++.+|++ .+||++|||||++++|++|||||+|+|++||+++|
T Consensus 1 ~~~~~~~ele~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~---i~SQstISR~Es~~ls~~n~~kl~p~l~~wl~~~e 75 (75)
T smart00352 1 DEDTDPRELEAFAKTFKQRRIKLGFTQADVGLALGALYGP---DFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAE 75 (75)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHcCCCHHHHHHHhcccccC---cCCHHHHHHHHhcCccHHHHHHHHHHHHHHHHhcC
Confidence 4568899999999999999999999999999999999865 59999999999999999999999999999999875
No 5
>KOG0775|consensus
Probab=99.67 E-value=5.3e-16 Score=149.42 Aligned_cols=150 Identities=20% Similarity=0.232 Sum_probs=117.0
Q ss_pred CCCCCCHHHHHHHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCChhhhhhhhHHHHHHHHHHHH
Q psy17897 228 PDTDTDPRELEAFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEA 307 (391)
Q Consensus 228 pd~~~d~~eLe~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~knm~KLkPlL~kWLeeaE~ 307 (391)
.++.+|++.|.+|.|.+.....-++..-..+++|+..++. .-.....-.+|...++..+..+|..+ ||+.-..
T Consensus 73 L~q~Gd~erL~rFlwsLp~~~~~~~nEsvLkArA~vafH~----gnf~eLY~iLE~h~Fs~~~h~~LQ~l---Wl~AhY~ 145 (304)
T KOG0775|consen 73 LQQGGDIERLGRFLWSLPVCEELLKNESVLKARAVVAFHS----GNFRELYHILENHKFSPHNHPKLQAL---WLKAHYK 145 (304)
T ss_pred HHhccCHHHHHHHHHcCchHHHHhhhHHHHHHHHHHHHhc----ccHHHHHHHHHhccCChhhhHHHHHH---HHHHHHH
Confidence 3467999999999999998777677777788999887763 13345567799999999996665443 7777666
Q ss_pred HhhhcCCCCCCCCCCCCCCCCC--CCc---------ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccc
Q psy17897 308 QAKNKRRDPDAPSVLPAGEKKR--KRT---------SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFC 376 (391)
Q Consensus 308 ~~~~~~~~~~~~~~~~~~~kKR--kRT---------~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFq 376 (391)
+++..+..+-.+....+-|||- .|| +|.+.-+..|..+|.+|+||+..++.+||+++||+..||.+||+
T Consensus 146 EAek~RGR~LgaV~KYRvRrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFK 225 (304)
T KOG0775|consen 146 EAEKLRGRPLGAVDKYRVRRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFK 225 (304)
T ss_pred HHHHhcCCcCCccccceeeccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhh
Confidence 6655665555555544433332 355 67777789999999999999999999999999999999999999
Q ss_pred hhhhHHhh
Q psy17897 377 NQRQKQKR 384 (391)
Q Consensus 377 NRR~K~KR 384 (391)
|||+|+|-
T Consensus 226 NRRQRDRa 233 (304)
T KOG0775|consen 226 NRRQRDRA 233 (304)
T ss_pred hhhhhhhh
Confidence 99999983
No 6
>KOG0489|consensus
Probab=99.65 E-value=4.5e-17 Score=157.87 Aligned_cols=65 Identities=29% Similarity=0.445 Sum_probs=61.8
Q ss_pred CCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhhh
Q psy17897 325 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFAA 389 (391)
Q Consensus 325 ~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~a 389 (391)
.+.||.||.||..|+.+||+.|..|+|.++..|.+||..|+|+++||||||||||+||||.++..
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~ 221 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAK 221 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccc
Confidence 46789999999999999999999999999999999999999999999999999999999988754
No 7
>KOG2252|consensus
Probab=99.62 E-value=1.1e-15 Score=158.72 Aligned_cols=138 Identities=27% Similarity=0.421 Sum_probs=106.1
Q ss_pred HHHHHHHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhh----hccCCCChhhhhhhhH------HHHHHHH
Q psy17897 234 PRELEAFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICR----FESLTLSHNNMIALKP------ILQAWLE 303 (391)
Q Consensus 234 ~~eLe~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcR----fE~LqLS~knm~KLkP------lL~kWLe 303 (391)
+.+.|++.+..-.+||+..++.+.|++|+ |.|.++|| +.+|-..+|.|.|||. ++++||+
T Consensus 320 ~~d~eeldTkeia~rI~~eLk~~sIpQai----------FAervLcRSQGTLSDLLrnPKPW~klKsGRetFrRM~~WL~ 389 (558)
T KOG2252|consen 320 SGDDEELDTKEIAQRIKAELKRYSIPQAI----------FAERVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMANWLE 389 (558)
T ss_pred cCCcceecHHHHHHHHHHHHhhcCCcHHH----------HHHHHhhcccchHHHHhhCCCchhhhccccHHHHHHHHHhc
Confidence 34445545556667888777777777776 66666676 5677888899998886 7899999
Q ss_pred HHHHHh--------hhcCCCCCCCCCCCCCCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCcccccc
Q psy17897 304 EAEAQA--------KNKRRDPDAPSVLPAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWF 375 (391)
Q Consensus 304 eaE~~~--------~~~~~~~~~~~~~~~~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWF 375 (391)
+.+... ..+|..+ .+......+.||.|.+||+.|++.|..+|+.++||+.++++.|+.+|+|+..+|.+||
T Consensus 390 eP~~~r~m~~L~~~a~kRke~-ep~~d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfF 468 (558)
T KOG2252|consen 390 EPEFQRLMSALRKKACKRKEQ-EPTDDKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFF 468 (558)
T ss_pred CHHHHHHHHHHHHHHhhhccc-CCCccccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHH
Confidence 766432 1222222 2223344567888999999999999999999999999999999999999999999999
Q ss_pred chhhhHH
Q psy17897 376 CNQRQKQ 382 (391)
Q Consensus 376 qNRR~K~ 382 (391)
.|.|.|.
T Consensus 469 mNaRRRs 475 (558)
T KOG2252|consen 469 MNARRRS 475 (558)
T ss_pred Hhhhhhc
Confidence 9999885
No 8
>KOG0488|consensus
Probab=99.62 E-value=2.1e-16 Score=156.63 Aligned_cols=65 Identities=28% Similarity=0.369 Sum_probs=61.6
Q ss_pred CCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhhh
Q psy17897 325 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFAA 389 (391)
Q Consensus 325 ~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~a 389 (391)
+|+||.||.||..|+..||+.|++.+|.+..+|.+||..|||+..||++||||||+||||....+
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g 234 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEG 234 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhh
Confidence 57777899999999999999999999999999999999999999999999999999999987654
No 9
>KOG0842|consensus
Probab=99.60 E-value=4.6e-16 Score=153.30 Aligned_cols=66 Identities=27% Similarity=0.395 Sum_probs=61.7
Q ss_pred CCCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhhh
Q psy17897 324 AGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFAA 389 (391)
Q Consensus 324 ~~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~a 389 (391)
..+|||+|..|+..|+.+||+.|.+++|.+..||+.||..|+|+++||||||||||.|.||+.+..
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk 215 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDK 215 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhh
Confidence 357777899999999999999999999999999999999999999999999999999999987654
No 10
>KOG4577|consensus
Probab=99.60 E-value=1.3e-15 Score=147.76 Aligned_cols=138 Identities=25% Similarity=0.389 Sum_probs=108.2
Q ss_pred HHHHHHHhhh--hHhcCccchhhhh-hhhcCcCCCCcccccchhhhhccCCCChhh----hhhhhHHHHHHHHHHHHHhh
Q psy17897 238 EAFAERFKQR--RIKLGVTQADVGK-ALANLKLPGVGALSQSTICRFESLTLSHNN----MIALKPILQAWLEEAEAQAK 310 (391)
Q Consensus 238 e~Fa~~fkqr--RI~lGlTQ~~Vg~-ALg~l~~~G~~~fSQstIcRfE~LqLS~kn----m~KLkPlL~kWLeeaE~~~~ 310 (391)
|.|.++|-.+ -...||.-.+|-+ |-...| .+.+| .|-+++.+|...+ |..-|.++++-||++++...
T Consensus 85 edFfKrfGTKCsaC~~GIpPtqVVRkAqd~VY--Hl~CF----~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~ 158 (383)
T KOG4577|consen 85 EDFFKRFGTKCSACQEGIPPTQVVRKAQDFVY--HLHCF----ACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHC 158 (383)
T ss_pred HHHHHHhCCcchhhcCCCChHHHHHHhhccee--ehhhh----hhHhhhcccccCCeeEEeccceeehhhhHHHHHhccc
Confidence 4476666554 4557887776544 444333 44444 7888888887665 66778888989998886643
Q ss_pred hcCCCCCCCCCCCCCCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhhh
Q psy17897 311 NKRRDPDAPSVLPAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFAA 389 (391)
Q Consensus 311 ~~~~~~~~~~~~~~~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~a 389 (391)
+. .......||.||.||..|++.|...|...++|.+..|+.|+.++||+-++|+|||||||+|+||.+|.|
T Consensus 159 ~~--------l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T KOG4577|consen 159 NE--------LEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T ss_pred cc--------cccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence 31 222345788999999999999999999999999999999999999999999999999999999999865
No 11
>KOG0487|consensus
Probab=99.58 E-value=8.4e-16 Score=151.51 Aligned_cols=67 Identities=25% Similarity=0.400 Sum_probs=62.8
Q ss_pred CCCCCCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 321 VLPAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 321 ~~~~~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
....++-||||.-+|+.|+.+||+.|..|.|.+++.|.+|++.|+|+++||||||||||+|+||.++
T Consensus 229 ~~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 229 ASSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 4444678889999999999999999999999999999999999999999999999999999999985
No 12
>KOG0843|consensus
Probab=99.58 E-value=1.2e-15 Score=139.39 Aligned_cols=63 Identities=33% Similarity=0.485 Sum_probs=61.1
Q ss_pred CCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 326 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 326 ~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
+.||.||.|+.+|+..||..|+.|.|....+|+.||+.|+|++.||||||||||.|.||+..+
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 788999999999999999999999999999999999999999999999999999999998776
No 13
>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=99.56 E-value=1.5e-15 Score=113.55 Aligned_cols=57 Identities=40% Similarity=0.695 Sum_probs=55.4
Q ss_pred CCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhh
Q psy17897 328 KRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 384 (391)
Q Consensus 328 KRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR 384 (391)
||+|+.|+.+|+..|+.+|..++||+..++..||.++||+..+|++||+|||+++||
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 14
>KOG0484|consensus
Probab=99.55 E-value=1.3e-15 Score=128.45 Aligned_cols=65 Identities=34% Similarity=0.474 Sum_probs=61.5
Q ss_pred CCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhhh
Q psy17897 325 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFAA 389 (391)
Q Consensus 325 ~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~a 389 (391)
+++||-||.||..|+..||+.|.+..||+...|++||.++.|++..|+|||||||+|.||+.+.+
T Consensus 15 rKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a 79 (125)
T KOG0484|consen 15 RKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAA 79 (125)
T ss_pred HHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHH
Confidence 56788899999999999999999999999999999999999999999999999999999987754
No 15
>KOG0485|consensus
Probab=99.55 E-value=2.5e-15 Score=140.95 Aligned_cols=67 Identities=33% Similarity=0.458 Sum_probs=63.2
Q ss_pred CCCCCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 322 LPAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 322 ~~~~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
+...+|||.||+|+..|+..||..|+..+|.+..+|..||.+|.|++.|||+||||||.||||+...
T Consensus 99 ~g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa 165 (268)
T KOG0485|consen 99 LGDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA 165 (268)
T ss_pred ccccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence 4567899999999999999999999999999999999999999999999999999999999998653
No 16
>KOG2251|consensus
Probab=99.54 E-value=4.9e-15 Score=139.21 Aligned_cols=67 Identities=31% Similarity=0.426 Sum_probs=63.0
Q ss_pred CCCCCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 322 LPAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 322 ~~~~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
...+|.||.||.|+..|+.+||+.|.+..||+...+++||.+|+|.+.+|+|||+|||+|+|++++.
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 3446889999999999999999999999999999999999999999999999999999999998875
No 17
>KOG0850|consensus
Probab=99.49 E-value=2e-14 Score=135.88 Aligned_cols=67 Identities=24% Similarity=0.362 Sum_probs=62.2
Q ss_pred CCCCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhhh
Q psy17897 323 PAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFAA 389 (391)
Q Consensus 323 ~~~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~a 389 (391)
..+|.||.||.|+..|+..|.+.|++++|.-..||.+||..|||+-+||||||||||.|.||.+|..
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g 184 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQG 184 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcC
Confidence 3456677899999999999999999999999999999999999999999999999999999998843
No 18
>KOG0848|consensus
Probab=99.47 E-value=1.5e-14 Score=139.18 Aligned_cols=65 Identities=22% Similarity=0.349 Sum_probs=60.8
Q ss_pred CCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhhh
Q psy17897 325 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFAA 389 (391)
Q Consensus 325 ~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~a 389 (391)
+.|-|-|.++|+.|+.+||+.|..++|.++..+.+||.-|+|+++||||||||||+|+||.+|+.
T Consensus 197 RTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 197 RTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 34556789999999999999999999999999999999999999999999999999999998876
No 19
>KOG0494|consensus
Probab=99.47 E-value=3.1e-14 Score=136.44 Aligned_cols=60 Identities=25% Similarity=0.335 Sum_probs=57.6
Q ss_pred CCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhhh
Q psy17897 330 KRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFAA 389 (391)
Q Consensus 330 kRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~a 389 (391)
-||.||..|+..||+.|++..||+...|+.||.++.|.+++|+|||||||+||||.+++-
T Consensus 144 ~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 144 FRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred ccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence 389999999999999999999999999999999999999999999999999999998863
No 20
>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=99.42 E-value=1.2e-13 Score=102.95 Aligned_cols=58 Identities=38% Similarity=0.623 Sum_probs=54.8
Q ss_pred CCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 328 KRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 328 KRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
+++|+.|+..++..|+++|..++||+..++..||.++||++.+|++||+|||.+.|+.
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 3578899999999999999999999999999999999999999999999999998874
No 21
>KOG0492|consensus
Probab=99.42 E-value=1.3e-13 Score=128.71 Aligned_cols=63 Identities=29% Similarity=0.443 Sum_probs=58.9
Q ss_pred CCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 326 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 326 ~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
.-|+.||-||..|+..||+.|.+.+|.+.++|.+++..|.|++.||+|||||||+|.||.+..
T Consensus 143 ~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQea 205 (246)
T KOG0492|consen 143 PNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEA 205 (246)
T ss_pred CCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHH
Confidence 346679999999999999999999999999999999999999999999999999999997653
No 22
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.42 E-value=1.2e-13 Score=102.28 Aligned_cols=56 Identities=43% Similarity=0.639 Sum_probs=52.7
Q ss_pred CCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHh
Q psy17897 328 KRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQK 383 (391)
Q Consensus 328 KRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~K 383 (391)
++.|+.|+..++..|++.|..|+||+..++..||..+||+..+|++||+|||.+.|
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 45678899999999999999999999999999999999999999999999998864
No 23
>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=99.41 E-value=1.8e-13 Score=104.81 Aligned_cols=53 Identities=25% Similarity=0.508 Sum_probs=51.1
Q ss_pred CCCCCcccChHHHHHHHHHhhcCCC----CCHHHHHHHHHHhCCCCCccccccchhh
Q psy17897 327 KKRKRTSIAAPEKRSLEAYFAVQPR----PSGEKIAAIAEKLDLKKNVVRVWFCNQR 379 (391)
Q Consensus 327 kKRkRT~ft~~Ql~~LE~~F~~n~y----PS~~er~~LA~qLgLs~~qVrvWFqNRR 379 (391)
+||.||.||.+|+..||..|+.++| |+..++.+||..+||++++|+|||||.+
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 9999999999999999999999999975
No 24
>KOG0844|consensus
Probab=99.34 E-value=2.6e-13 Score=132.63 Aligned_cols=64 Identities=30% Similarity=0.472 Sum_probs=60.1
Q ss_pred CCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 325 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 325 ~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
..-||-||.||.+|+..||+.|-+..|.++..|.+||.+|||.+.+|||||||||+|+||++..
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 4567889999999999999999999999999999999999999999999999999999998753
No 25
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.33 E-value=2.2e-12 Score=116.76 Aligned_cols=64 Identities=27% Similarity=0.438 Sum_probs=59.1
Q ss_pred CCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 325 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 325 ~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
...+++|++-+..|+.+|++.|+.|+||+..++..|+..|+|+++.|++||||||++.|+....
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 4567778888999999999999999999999999999999999999999999999999987654
No 26
>KOG0493|consensus
Probab=99.31 E-value=1.3e-12 Score=125.59 Aligned_cols=61 Identities=30% Similarity=0.513 Sum_probs=57.8
Q ss_pred CCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 326 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 326 ~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
.-||.||.||.+|+..|...|+.|+|.+...|.+||.+|+|.+.||++||||+|+|.||..
T Consensus 245 eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 245 EEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred hhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 4477899999999999999999999999999999999999999999999999999999864
No 27
>KOG0486|consensus
Probab=99.31 E-value=1e-12 Score=128.99 Aligned_cols=66 Identities=30% Similarity=0.431 Sum_probs=62.1
Q ss_pred CCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhhhc
Q psy17897 325 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFAAQ 390 (391)
Q Consensus 325 ~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~aq 390 (391)
.|+||.||.|+..|+.+||..|++|.||+...|++||...+|++..|+|||+|||+||||+++-.+
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 478889999999999999999999999999999999999999999999999999999999876543
No 28
>KOG0491|consensus
Probab=99.30 E-value=3.9e-13 Score=121.64 Aligned_cols=65 Identities=29% Similarity=0.457 Sum_probs=60.9
Q ss_pred CCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhhhc
Q psy17897 326 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFAAQ 390 (391)
Q Consensus 326 ~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~aq 390 (391)
+++|.||+|+..|+..||+.|+..+|.+..++.+||..|+|++.||+.||||||+|.||..+..+
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 56778999999999999999999999999999999999999999999999999999999877543
No 29
>KOG0483|consensus
Probab=99.25 E-value=2.7e-12 Score=120.19 Aligned_cols=62 Identities=26% Similarity=0.434 Sum_probs=56.8
Q ss_pred CCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 327 KKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 327 kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
.++++.+|+.+|...||+.|+.+.+....++..||++|||.++||.|||||||+|||.++..
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE 111 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLE 111 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence 44556679999999999999999999999999999999999999999999999999987653
No 30
>KOG0847|consensus
Probab=99.12 E-value=1.8e-11 Score=115.41 Aligned_cols=63 Identities=27% Similarity=0.507 Sum_probs=59.1
Q ss_pred CCCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 324 AGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 324 ~~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
.+++|..|..|+..|+..||+.|++.+|+..+++.++|..+|+++.+|+|||||||.||||+.
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 356777899999999999999999999999999999999999999999999999999999864
No 31
>KOG0849|consensus
Probab=99.02 E-value=2.2e-10 Score=115.92 Aligned_cols=64 Identities=30% Similarity=0.444 Sum_probs=59.9
Q ss_pred CCCCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 323 PAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 323 ~~~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
..++.+|.||+|+..|+..||+.|+.++||....+++||+++++++..|+|||+|||.|++|..
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 3456677799999999999999999999999999999999999999999999999999999976
No 32
>KOG0490|consensus
Probab=99.01 E-value=1.7e-10 Score=107.48 Aligned_cols=63 Identities=24% Similarity=0.241 Sum_probs=59.8
Q ss_pred CCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 325 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 325 ~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
.++||.|+.|+..|+..||+.|++++||+...++.+|..+++++..|+|||||||+||++..+
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 467889999999999999999999999999999999999999999999999999999998763
No 33
>KOG0774|consensus
Probab=98.78 E-value=1.4e-09 Score=104.88 Aligned_cols=101 Identities=22% Similarity=0.326 Sum_probs=71.5
Q ss_pred CChhhhhhhhHHHHHHHHHHHHHhhhcCCCCCCCCCC--CCCCCCCCCcccChHHHHHHHHHhh---cCCCCCHHHHHHH
Q psy17897 286 LSHNNMIALKPILQAWLEEAEAQAKNKRRDPDAPSVL--PAGEKKRKRTSIAAPEKRSLEAYFA---VQPRPSGEKIAAI 360 (391)
Q Consensus 286 LS~knm~KLkPlL~kWLeeaE~~~~~~~~~~~~~~~~--~~~~kKRkRT~ft~~Ql~~LE~~F~---~n~yPS~~er~~L 360 (391)
+.++.+.++.-.+.+-++......+... +....++ ..-..+|||..|++....+|..+|- .|+||+.+.+++|
T Consensus 147 i~~ke~e~m~~~i~~kF~~iq~~lkqst--ce~vmiLr~r~ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eL 224 (334)
T KOG0774|consen 147 IMPKEIERMVQIISKKFSHIQMQLKQST--CEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEEL 224 (334)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHH
Confidence 4455566666666665554443322110 0000000 0113577889999999999999994 7899999999999
Q ss_pred HHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 361 AEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 361 A~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
|++||++..||.+||.|+|-+.||..-.
T Consensus 225 AkqCnItvsQvsnwfgnkrIrykK~~~k 252 (334)
T KOG0774|consen 225 AKQCNITVSQVSNWFGNKRIRYKKNMGK 252 (334)
T ss_pred HHHcCceehhhccccccceeehhhhhhh
Confidence 9999999999999999999999986443
No 34
>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=98.30 E-value=1.9e-07 Score=66.49 Aligned_cols=34 Identities=29% Similarity=0.608 Sum_probs=29.4
Q ss_pred cCCCCCHHHHHHHHHHhCCCCCccccccchhhhH
Q psy17897 348 VQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQK 381 (391)
Q Consensus 348 ~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K 381 (391)
.+|||+.+++..||+++||+..||.+||-|.|.|
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 5799999999999999999999999999999975
No 35
>KOG0490|consensus
Probab=97.81 E-value=2.1e-05 Score=73.36 Aligned_cols=62 Identities=31% Similarity=0.598 Sum_probs=58.2
Q ss_pred CCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 325 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 325 ~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
.+.++.|+.+...++..++..|..+++|+...+..|+..++++..+|++||+|+|.+.++.+
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred cccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 56777899999999999999999999999999999999999999999999999999998754
No 36
>KOG1146|consensus
Probab=97.27 E-value=0.00015 Score=82.92 Aligned_cols=62 Identities=27% Similarity=0.504 Sum_probs=58.3
Q ss_pred CCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 326 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 326 ~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
.+|+.|+.++..|++.+..+|....||..++++.+-..+++.+++|.|||+|.|+|.|+.+.
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 45678999999999999999999999999999999999999999999999999999998765
No 37
>KOG0773|consensus
Probab=96.46 E-value=0.0016 Score=65.28 Aligned_cols=59 Identities=24% Similarity=0.397 Sum_probs=49.6
Q ss_pred CCCCCcccChHHHHHHHHHhh---cCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 327 KKRKRTSIAAPEKRSLEAYFA---VQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 327 kKRkRT~ft~~Ql~~LE~~F~---~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
++|++..+....+.+|+.+.. ..+||+..++..||+++||+..||.+||-|.|.|..+-
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p 300 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKP 300 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCc
Confidence 455566888888888888743 35899999999999999999999999999999886653
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.83 E-value=0.0026 Score=48.69 Aligned_cols=43 Identities=23% Similarity=0.475 Sum_probs=31.6
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhH
Q psy17897 339 KRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQK 381 (391)
Q Consensus 339 l~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K 381 (391)
...|+++|...+.+...+...|..+.+|+..+|+.||--|+.+
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 4569999999999999999999999999999999999776554
No 39
>KOG3623|consensus
Probab=94.90 E-value=0.016 Score=63.49 Aligned_cols=48 Identities=29% Similarity=0.584 Sum_probs=45.1
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 339 KRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 339 l~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
...|..+|..|..|+.++...||.+.|+..++|++||.+++.+..+..
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 678999999999999999999999999999999999999999887655
No 40
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=94.29 E-value=0.029 Score=42.75 Aligned_cols=40 Identities=30% Similarity=0.458 Sum_probs=34.0
Q ss_pred HHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCC
Q psy17897 239 AFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLS 287 (391)
Q Consensus 239 ~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS 287 (391)
+|...++..|...|+||.+++..++ +|++++|++|.=...
T Consensus 1 ~lg~~lr~~R~~~gls~~~lA~~~g---------~s~s~v~~iE~G~~~ 40 (64)
T PF13560_consen 1 QLGRRLRRLRERAGLSQAQLADRLG---------VSQSTVSRIERGRRP 40 (64)
T ss_dssp HHHHHHHHHHHCHTS-HHHHHHHHT---------S-HHHHHHHHTTSSS
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHHC---------cCHHHHHHHHCCCCC
Confidence 5788899999999999999999996 899999999987764
No 41
>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=94.26 E-value=0.058 Score=40.43 Aligned_cols=47 Identities=23% Similarity=0.281 Sum_probs=35.9
Q ss_pred CCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhh
Q psy17897 328 KRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQR 379 (391)
Q Consensus 328 KRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR 379 (391)
||+|..+|-+++..+-..++... ....||+++|+...+|..|..|+.
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 57889999999888888887765 577899999999999999998853
No 42
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=92.91 E-value=0.13 Score=47.71 Aligned_cols=54 Identities=39% Similarity=0.570 Sum_probs=41.0
Q ss_pred HHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCChhhhhhhhHHHHHHHHHHH
Q psy17897 242 ERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAE 306 (391)
Q Consensus 242 ~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~knm~KLkPlL~kWLeeaE 306 (391)
+.+|.+|-.||+||.+.++..| .||++|.|+|+=.+.++ ..+++.++. .|+|++
T Consensus 8 edlrk~Rk~LGitQ~dLA~~aG---------VSQ~~IArlE~G~vdPr-lSt~k~Il~-aL~e~e 61 (187)
T COG3620 8 EDLRKRRKELGITQKDLARRAG---------VSQPYIARLEAGKVDPR-LSTVKRILE-ALEEAE 61 (187)
T ss_pred HHHHHHHHHcCCCHHHHHHHcC---------ccHHHHHHHhcCCCCcc-HHHHHHHHH-HHHHhh
Confidence 3467779999999999987764 89999999999988873 355555544 455555
No 43
>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=92.28 E-value=0.091 Score=38.05 Aligned_cols=39 Identities=26% Similarity=0.257 Sum_probs=33.6
Q ss_pred HHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCC
Q psy17897 239 AFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTL 286 (391)
Q Consensus 239 ~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqL 286 (391)
.|...++..|...|+||.+++..++ +++++++++|+-..
T Consensus 2 ~~~~~l~~~r~~~gltq~~lA~~~g---------vs~~~vs~~e~g~~ 40 (58)
T TIGR03070 2 QIGMLVRARRKALGLTQADLADLAG---------VGLRFIRDVENGKP 40 (58)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHCCCC
Confidence 4777888889999999999999985 89999999997654
No 44
>PHA01976 helix-turn-helix protein
Probab=91.50 E-value=0.14 Score=38.88 Aligned_cols=39 Identities=18% Similarity=0.238 Sum_probs=34.3
Q ss_pred HHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCC
Q psy17897 239 AFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTL 286 (391)
Q Consensus 239 ~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqL 286 (391)
.|.+.++..|...|+||.+++..++ +++++++++|+-..
T Consensus 2 ~~~~rl~~~R~~~glt~~~lA~~~g---------vs~~~v~~~e~g~~ 40 (67)
T PHA01976 2 SFAIQLIKARNARAWSAPELSRRAG---------VRHSLIYDFEADKR 40 (67)
T ss_pred cHHHHHHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHcCCC
Confidence 3788999999999999999999985 88999999997654
No 45
>PF04814 HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N terminus; InterPro: IPR006899 This domain consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerisation sequence [] and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2GYP_B 1IC8_B 2H8R_B 1G2Y_D 1F93_H 1G39_D 1G2Z_B 1JB6_B.
Probab=90.55 E-value=0.26 Score=46.12 Aligned_cols=56 Identities=16% Similarity=0.193 Sum_probs=34.8
Q ss_pred HHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCChhhhhhhhHHHHHHHHHHH
Q psy17897 240 FAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAE 306 (391)
Q Consensus 240 Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~knm~KLkPlL~kWLeeaE 306 (391)
-++++|...-...|+|..|+++.| ++|+.|+.|-......++.. |..|+.||....
T Consensus 119 VkeeIK~fl~~h~IsQ~~V~q~TG---------isQS~lSq~L~kGt~Mk~qK--R~alY~Wy~~~~ 174 (180)
T PF04814_consen 119 VKEEIKAFLQQHNISQREVVQVTG---------ISQSHLSQHLNKGTPMKEQK--RRALYRWYVRKK 174 (180)
T ss_dssp HHHHHHHHHHHCT--CHHHHHHHT-----------HHHHHHHHCTB----HHH--HHHHHHHHHHHC
T ss_pred HHHHHHHHHHHcCCcHHHHHHHhh---------hhHHHHHHHHHcCCCccHHH--HHHHHHHHHHHH
Confidence 344455444455779999999985 99999999976666666644 667899998643
No 46
>KOG3623|consensus
Probab=89.91 E-value=0.29 Score=54.12 Aligned_cols=86 Identities=27% Similarity=0.513 Sum_probs=62.6
Q ss_pred HHHHHHHHHHHHhhhcCCCCCCCCCCCCCCCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccc
Q psy17897 297 ILQAWLEEAEAQAKNKRRDPDAPSVLPAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFC 376 (391)
Q Consensus 297 lL~kWLeeaE~~~~~~~~~~~~~~~~~~~~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFq 376 (391)
+.++|+|+.+.......+.+..+.. .++-|-|+-+..++-..|...++.+-.++..+...++..|...+.+|.+||+
T Consensus 599 vvk~wfE~~~a~e~sv~rsps~psg---~~p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dh 675 (1007)
T KOG3623|consen 599 VVKAWFEDEEAEEMSVERSPSQPSG---ERPVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDH 675 (1007)
T ss_pred HHHHHHHhhhhhhhhhccCccCCCC---CCCccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhccc
Confidence 6788999887665444444443322 2444455666677777788888888888888777788888889999999999
Q ss_pred hhhhHHhhH
Q psy17897 377 NQRQKQKRM 385 (391)
Q Consensus 377 NRR~K~KR~ 385 (391)
+|+...+..
T Consensus 676 srsstpsp~ 684 (1007)
T KOG3623|consen 676 SRSSTPSPM 684 (1007)
T ss_pred CCCCCCCCC
Confidence 999876653
No 47
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=88.26 E-value=0.46 Score=43.28 Aligned_cols=43 Identities=21% Similarity=0.319 Sum_probs=37.4
Q ss_pred HHHHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCCh
Q psy17897 237 LEAFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSH 288 (391)
Q Consensus 237 Le~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~ 288 (391)
.+.|.+.++..|...|+||.+++..++ +++++|++||+-...+
T Consensus 67 ~~~~g~~Ir~~Re~~glSqeeLA~~lg---------vs~s~IsriE~G~~~P 109 (154)
T TIGR00270 67 VEDYGIIIRREREKRGWSQEQLAKKIQ---------EKESLIKKIENAEIEP 109 (154)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHCCCCCC
Confidence 356999999999999999999999985 8999999999866554
No 48
>PRK06424 transcription factor; Provisional
Probab=88.17 E-value=0.75 Score=41.53 Aligned_cols=45 Identities=27% Similarity=0.319 Sum_probs=39.3
Q ss_pred HHHHHHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCCh
Q psy17897 235 RELEAFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSH 288 (391)
Q Consensus 235 ~eLe~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~ 288 (391)
+.++.|+..++..|-..|+||.+++..++ +++++|.+||+-...+
T Consensus 80 ~~~~~~g~~Ir~lRe~~GLSQ~eLA~~iG---------vs~stIskiE~G~~~P 124 (144)
T PRK06424 80 DIVEDYAELVKNARERLSMSQADLAAKIF---------ERKNVIASIERGDLLP 124 (144)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHCCCCCC
Confidence 44577999999999999999999999985 7899999999877654
No 49
>PRK09726 antitoxin HipB; Provisional
Probab=87.53 E-value=0.83 Score=37.16 Aligned_cols=40 Identities=30% Similarity=0.403 Sum_probs=34.7
Q ss_pred HHHHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCC
Q psy17897 237 LEAFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLT 285 (391)
Q Consensus 237 Le~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~Lq 285 (391)
-++|...++..|...|+||.+++..++ ++++++.++|+-.
T Consensus 10 ~~~l~~~lk~~R~~~gltq~elA~~~g---------vs~~tis~~e~g~ 49 (88)
T PRK09726 10 PTQLANAMKLVRQQNGWTQSELAKKIG---------IKQATISNFENNP 49 (88)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHC---------cCHHHHHHHHCCC
Confidence 357888899999999999999999985 8899999998843
No 50
>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=86.73 E-value=0.91 Score=38.59 Aligned_cols=38 Identities=21% Similarity=0.340 Sum_probs=31.8
Q ss_pred HHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCCh
Q psy17897 242 ERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSH 288 (391)
Q Consensus 242 ~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~ 288 (391)
.+++..|.++|+||.+++..+| +++.++.+||+-...+
T Consensus 68 ~~i~~~r~~~gltq~~lA~~lg---------~~~~tis~~e~g~~~p 105 (127)
T TIGR03830 68 PEIRRIRKKLGLSQREAAELLG---------GGVNAFSRYERGEVRP 105 (127)
T ss_pred HHHHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHCCCCCC
Confidence 4667778889999999999985 8899999999887644
No 51
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=86.62 E-value=0.79 Score=36.75 Aligned_cols=40 Identities=25% Similarity=0.435 Sum_probs=30.4
Q ss_pred HHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCC
Q psy17897 239 AFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLS 287 (391)
Q Consensus 239 ~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS 287 (391)
++++.++..+-..|+||.+++..+| ++|+.|+++++-...
T Consensus 18 ~l~~~i~~~~~~~~ltQ~e~A~~lg---------isq~~vS~l~~g~~~ 57 (80)
T PF13744_consen 18 QLMAAIRELREERGLTQAELAERLG---------ISQPRVSRLENGKID 57 (80)
T ss_dssp HHHHHHHHHHHCCT--HHHHHHHHT---------S-HHHHHHHHTT-GC
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHC---------CChhHHHHHHcCccc
Confidence 3777888888889999999999996 899999999864433
No 52
>cd00131 PAX Paired Box domain
Probab=84.34 E-value=3.5 Score=36.19 Aligned_cols=45 Identities=11% Similarity=0.033 Sum_probs=29.7
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCC-------CCCccccccch
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDL-------KKNVVRVWFCN 377 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgL-------s~~qVrvWFqN 377 (391)
..+..+...++.+...++..+..++.+....-++ +..+|-.||++
T Consensus 75 ~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~ 126 (128)
T cd00131 75 VATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN 126 (128)
T ss_pred cCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence 3455566667777788888888877665223355 67777777765
No 53
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=84.22 E-value=0.79 Score=40.00 Aligned_cols=42 Identities=24% Similarity=0.379 Sum_probs=36.2
Q ss_pred HHHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCCh
Q psy17897 238 EAFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSH 288 (391)
Q Consensus 238 e~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~ 288 (391)
..|.+.++..|...|+||.+++..+| +++++|++||.-...+
T Consensus 4 ~~~g~rlk~~R~~~gltq~~lA~~~g---------vs~~~is~~E~g~~~p 45 (135)
T PRK09706 4 LTLGQRIRYRRKQLKLSQRSLAKAVK---------VSHVSISQWERDETEP 45 (135)
T ss_pred hhHHHHHHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHcCCCCC
Confidence 45788899999999999999999985 8899999999776444
No 54
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=83.18 E-value=2.5 Score=35.69 Aligned_cols=56 Identities=20% Similarity=0.325 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHhhhh--HhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCChhhhhhhhHHHHHHHHH
Q psy17897 234 PRELEAFAERFKQRR--IKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEE 304 (391)
Q Consensus 234 ~~eLe~Fa~~fkqrR--I~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~knm~KLkPlL~kWLee 304 (391)
.+|++.++.+++--+ +..|+||..|+..+| +|++||.|.++---. ..|-...|++.
T Consensus 35 p~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lG---------iS~atIsR~sn~lk~------~~~~~~~~l~~ 92 (94)
T TIGR01321 35 RSEREDLGDRIRIVNELLNGNMSQREIASKLG---------VSIATITRGSNNLKT------MDPNFKQFLRK 92 (94)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhC---------CChhhhhHHHhhccc------CCHHHHHHHHh
Confidence 355566555554433 346899999999985 899999998754321 23456677754
No 55
>PRK10856 cytoskeletal protein RodZ; Provisional
Probab=82.85 E-value=3.1 Score=42.30 Aligned_cols=47 Identities=34% Similarity=0.393 Sum_probs=39.1
Q ss_pred CHHHHHHHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCCh
Q psy17897 233 DPRELEAFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSH 288 (391)
Q Consensus 233 d~~eLe~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~ 288 (391)
+..+...+-..||+.|..+|+||.+++..++ +++++|..+|+-++..
T Consensus 8 ~~~~~~~~G~~Lr~aRe~~GlSq~~vA~~l~---------l~~~~I~~iE~g~~~~ 54 (331)
T PRK10856 8 DQNEALTTGERLRQAREQLGLTQQAVAERLC---------LKVSTVRDIEEDKAPA 54 (331)
T ss_pred chhHHHHHHHHHHHHHHHcCCCHHHHHHHHC---------CCHHHHHHHHCCCCCC
Confidence 3445556888999999999999999999985 7889999999877654
No 56
>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=80.71 E-value=1 Score=32.70 Aligned_cols=36 Identities=31% Similarity=0.433 Sum_probs=27.8
Q ss_pred HhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCCh
Q psy17897 244 FKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSH 288 (391)
Q Consensus 244 fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~ 288 (391)
+++.|...|+||.+++..++ ++++++.++|+-...+
T Consensus 1 ik~~r~~~gls~~~la~~~g---------is~~~i~~~~~g~~~~ 36 (55)
T PF01381_consen 1 IKELRKEKGLSQKELAEKLG---------ISRSTISRIENGKRNP 36 (55)
T ss_dssp HHHHHHHTTS-HHHHHHHHT---------S-HHHHHHHHTTSSTS
T ss_pred CHHHHHHcCCCHHHHHHHhC---------CCcchhHHHhcCCCCC
Confidence 45668899999999999995 8899999998775443
No 57
>PRK08359 transcription factor; Validated
Probab=80.40 E-value=1.6 Score=40.72 Aligned_cols=46 Identities=20% Similarity=0.267 Sum_probs=39.2
Q ss_pred HHHHHHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCChh
Q psy17897 235 RELEAFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHN 289 (391)
Q Consensus 235 ~eLe~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~k 289 (391)
+=++.|+..+++-|-..|+||.+++..++ +++++|.++|.=...+.
T Consensus 81 elv~dy~~rIkeaRe~kglSQeeLA~~lg---------vs~stI~~iE~G~~~Ps 126 (176)
T PRK08359 81 DIVEDYAERVYEAIQKSGLSYEELSHEVG---------LSVNDLRRIAHGEYEPT 126 (176)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHCCCcCCC
Confidence 33467999999999999999999999985 89999999987766553
No 58
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=80.08 E-value=2.1 Score=32.08 Aligned_cols=38 Identities=37% Similarity=0.489 Sum_probs=28.4
Q ss_pred HHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCCh
Q psy17897 242 ERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSH 288 (391)
Q Consensus 242 ~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~ 288 (391)
+.+|+.|...|+||.+++..++ ++.+++++||+=...+
T Consensus 2 ~~lk~~r~~~~lt~~~~a~~~~---------i~~~~i~~~e~g~~~~ 39 (64)
T PF12844_consen 2 ERLKELREEKGLTQKDLAEKLG---------ISRSTISKIENGKRKP 39 (64)
T ss_dssp HHHHHHHHHCT--HHHHHHHHT---------S-HHHHHHHHTTSS--
T ss_pred HHHHHHHHHcCCCHHHHHHHHC---------cCHHHHHHHHCCCcCC
Confidence 4678889999999999999985 7889999999776543
No 59
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=79.73 E-value=1.7 Score=39.76 Aligned_cols=43 Identities=23% Similarity=0.233 Sum_probs=36.7
Q ss_pred HHHHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCCh
Q psy17897 237 LEAFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSH 288 (391)
Q Consensus 237 Le~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~ 288 (391)
-..+.+.+|..|..+|+||.+++..++ +++++|+++|+-...+
T Consensus 5 ~~~~g~~l~~~R~~~glt~~elA~~~g---------is~~~is~~E~g~~~p 47 (185)
T PRK09943 5 GLAPGKRLSEIRQQQGLSQRRAAELSG---------LTHSAISTIEQDKVSP 47 (185)
T ss_pred hhHHHHHHHHHHHHcCCCHHHHHHHHC---------CCHHHHHHHHcCCCCC
Confidence 345888999999999999999999985 8999999999876544
No 60
>PRK10072 putative transcriptional regulator; Provisional
Probab=76.91 E-value=2 Score=36.18 Aligned_cols=38 Identities=24% Similarity=0.357 Sum_probs=31.3
Q ss_pred HHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCChh
Q psy17897 243 RFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHN 289 (391)
Q Consensus 243 ~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~k 289 (391)
+|++-|-.+|+||.+++..+| ++++||+.||.-...++
T Consensus 37 eik~LR~~~glTQ~elA~~lG---------vS~~TVs~WE~G~r~P~ 74 (96)
T PRK10072 37 EFEQLRKGTGLKIDDFARVLG---------VSVAMVKEWESRRVKPS 74 (96)
T ss_pred HHHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHcCCCCCC
Confidence 356668899999999999985 78999999998765553
No 61
>PF13551 HTH_29: Winged helix-turn helix
Probab=76.68 E-value=6 Score=32.25 Aligned_cols=48 Identities=21% Similarity=0.360 Sum_probs=32.0
Q ss_pred CCCcccChHHHHHHHHHhhcCC-----CCCHHHHHH-H-HHHh--CCCCCccccccc
Q psy17897 329 RKRTSIAAPEKRSLEAYFAVQP-----RPSGEKIAA-I-AEKL--DLKKNVVRVWFC 376 (391)
Q Consensus 329 RkRT~ft~~Ql~~LE~~F~~n~-----yPS~~er~~-L-A~qL--gLs~~qVrvWFq 376 (391)
+.+..+++++...|.+.+..++ ..+...+.+ | .+.. .++..+|+.|+.
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 3333489999999999998876 345555554 3 3333 467778887774
No 62
>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=75.79 E-value=2.3 Score=30.69 Aligned_cols=47 Identities=17% Similarity=0.298 Sum_probs=35.4
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhh
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 384 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR 384 (391)
.+++.++.++...|..+ ....+||+.+|++...|+.+...-..|.|+
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 46778889999988433 346789999999999999988766666553
No 63
>PHA00542 putative Cro-like protein
Probab=74.91 E-value=4.2 Score=32.89 Aligned_cols=30 Identities=37% Similarity=0.458 Sum_probs=25.9
Q ss_pred hHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCC
Q psy17897 248 RIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTL 286 (391)
Q Consensus 248 RI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqL 286 (391)
+...|+||.+++..+| +++++|+++++-..
T Consensus 27 l~~~glTq~elA~~lg---------Is~~tIsr~e~g~~ 56 (82)
T PHA00542 27 LIRAGWSQEQIADATD---------VSQPTICRIYSGRH 56 (82)
T ss_pred HHHCCCCHHHHHHHHC---------cCHHHHHHHHcCCC
Confidence 5667999999999986 89999999997763
No 64
>PF02376 CUT: CUT domain; InterPro: IPR003350 A class, also called ONECUT, of homeodomain proteins. The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain (IPR001356 from INTERPRO), often found downstream of the CUT domain. Proteins display two modes of DNA binding, which hinge on the homeodomain and on the linker that separates it from the cut domain, and two modes of transcriptional stimulation, which hinge on the homeodomain [].; GO: 0003677 DNA binding; PDB: 1WH6_A 2D5V_A 2CSF_A 1X2L_A 2O49_A 2O4A_A 1YSE_A 1S7E_A 1WIZ_A 1WH8_A.
Probab=74.45 E-value=3 Score=34.50 Aligned_cols=62 Identities=23% Similarity=0.297 Sum_probs=41.9
Q ss_pred HHHHHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCChhhhhhhhH-------HHHHHHHHHHHH
Q psy17897 236 ELEAFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKP-------ILQAWLEEAEAQ 308 (391)
Q Consensus 236 eLe~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~knm~KLkP-------lL~kWLeeaE~~ 308 (391)
+-++.+..+++..-..+++|..+|..+- ..||.++|.+-+ .++.+.+|++ .++.||+..+..
T Consensus 10 dT~~I~~~ik~~L~~~~IsQ~~Fa~~vL--------~rsqgtlsdlL~---~PKpW~~L~~~gre~y~RM~nWL~~~e~~ 78 (87)
T PF02376_consen 10 DTKEIARRIKEWLKRNNISQRVFAKKVL--------NRSQGTLSDLLR---KPKPWNKLKPKGREPYIRMYNWLSLPEEE 78 (87)
T ss_dssp -HHHHHHHHHHHHHHTT--HHHHHHHTT--------SS-HHHHHHHHH---SCCTTCHHHHHHHHHHHHHHHHHCSTHHH
T ss_pred CHHHHHHHHHHHHHHcCCCHHHHHHHHh--------ccChhHHHHHhC---CCCCHHHcCccccHHHHHHHHHhcCCHHH
Confidence 4566777888888888999999998873 288888887544 5566666663 577899776643
No 65
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=74.17 E-value=4.5 Score=40.25 Aligned_cols=43 Identities=23% Similarity=0.291 Sum_probs=36.6
Q ss_pred HHHHHHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCC
Q psy17897 235 RELEAFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTL 286 (391)
Q Consensus 235 ~eLe~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqL 286 (391)
+=+..|.+.++..|...|+||.+++..++ +|+++|.+||.-..
T Consensus 24 ~~~~~~g~rl~~~R~~~gltq~~lA~~~g---------vs~~~i~~~E~g~~ 66 (309)
T PRK08154 24 PFLAALGERVRTLRARRGMSRKVLAQASG---------VSERYLAQLESGQG 66 (309)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHC---------cCHHHHHHHHCCCC
Confidence 34566889999999999999999999885 88999999987653
No 66
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=70.30 E-value=5.7 Score=34.50 Aligned_cols=39 Identities=10% Similarity=0.043 Sum_probs=33.0
Q ss_pred HHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCC
Q psy17897 239 AFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTL 286 (391)
Q Consensus 239 ~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqL 286 (391)
-|...++..+...|+||.+++..+| +++++|.++|+-..
T Consensus 5 i~~~~l~~ll~~~Glsq~eLA~~~G---------is~~~is~iE~g~~ 43 (120)
T PRK13890 5 IFFTNVLRLLDERHMTKKELSERSG---------VSISFLSDLTTGKA 43 (120)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHC---------cCHHHHHHHHcCCC
Confidence 3777788888899999999999985 88999999997554
No 67
>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=70.25 E-value=3.4 Score=28.43 Aligned_cols=44 Identities=20% Similarity=0.252 Sum_probs=31.9
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhH
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQK 381 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K 381 (391)
.++..+...+...|... ....+||+.+|++..+|+.|....+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 35566777777776433 246678999999999999998765544
No 68
>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=70.00 E-value=3.6 Score=29.91 Aligned_cols=43 Identities=19% Similarity=0.237 Sum_probs=29.3
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhH
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQK 381 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K 381 (391)
+++.++..+...|..+ ....+||+.+|+++..|++|...-|.+
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 4566666776665443 357789999999999999999765554
No 69
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=68.66 E-value=5.9 Score=24.32 Aligned_cols=37 Identities=14% Similarity=0.314 Sum_probs=25.7
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCcccccc
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWF 375 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWF 375 (391)
++.+.+..+...|... + ...++|+.++++..+|..|.
T Consensus 6 ~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 5556666565566532 2 45678999999999998884
No 70
>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=65.85 E-value=1.9 Score=33.36 Aligned_cols=46 Identities=20% Similarity=0.273 Sum_probs=29.3
Q ss_pred CCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchh
Q psy17897 329 RKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQ 378 (391)
Q Consensus 329 RkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNR 378 (391)
++|..|+.+++..+-..+.. ....+..+|+++|++..++..|-.--
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~----~g~sv~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE----SGESVSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp -SS----HHHHHHHHHHHHH----HHCHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH----CCCceEeeecccccccccccHHHHHH
Confidence 46778999888766555521 23578899999999999999996433
No 71
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=64.71 E-value=8.3 Score=34.79 Aligned_cols=51 Identities=12% Similarity=0.012 Sum_probs=39.7
Q ss_pred CcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 331 RTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 331 RT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
...+++.|+.+|...+ +. ....+||+.+|++...|+.|-.+.+.|.|+...
T Consensus 4 ~~~Lt~rqreVL~lr~-~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 4 ESFLTERQIEVLRLRE-RG-----LTQQEIADILGTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred ccCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3567888999988743 22 246689999999999999999988888776543
No 72
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=62.44 E-value=6.4 Score=35.80 Aligned_cols=34 Identities=21% Similarity=0.331 Sum_probs=29.5
Q ss_pred HhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCC
Q psy17897 244 FKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTL 286 (391)
Q Consensus 244 fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqL 286 (391)
++..|..+|+||.+++..+| +++.+|+++|+-..
T Consensus 30 Ir~~R~~lGmTq~eLAerlG---------VS~~tIs~iE~G~~ 63 (150)
T TIGR02612 30 VRAIRKALGMSGAQLAGRLG---------VTPQRVEALEKSEL 63 (150)
T ss_pred HHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHcCCC
Confidence 56669999999999999985 89999999998753
No 73
>smart00351 PAX Paired Box domain.
Probab=61.01 E-value=41 Score=29.16 Aligned_cols=44 Identities=7% Similarity=-0.014 Sum_probs=27.1
Q ss_pred cccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCC-------CCCcccccc
Q psy17897 332 TSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDL-------KKNVVRVWF 375 (391)
Q Consensus 332 T~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgL-------s~~qVrvWF 375 (391)
...+..+...+++..+.++..+..++...-...|+ ...+|-.||
T Consensus 74 ~~~~~~~~~~I~~~~~~~p~~t~~el~~~L~~~gv~~~~~~Ps~sti~~~l 124 (125)
T smart00351 74 KVATPKVVKKIADYKQENPGIFAWEIRDRLLSEGVCDKDNVPSVSSINRIL 124 (125)
T ss_pred CccCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCCcCCCCCChhhHHHhh
Confidence 34455556667777788888888877654334444 445555554
No 74
>KOG3755|consensus
Probab=60.19 E-value=2.7 Score=45.99 Aligned_cols=48 Identities=21% Similarity=0.289 Sum_probs=36.5
Q ss_pred HHHHHhhcCCCCCHHHHHHHHHHhC-------CCCCccccccchhhhHHhhHHhh
Q psy17897 341 SLEAYFAVQPRPSGEKIAAIAEKLD-------LKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 341 ~LE~~F~~n~yPS~~er~~LA~qLg-------Ls~~qVrvWFqNRR~K~KR~~k~ 388 (391)
+-+.+|.++..++...+.+..+.+. .+.+.|+.||.|||.++||.+-+
T Consensus 706 v~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~~ 760 (769)
T KOG3755|consen 706 VKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKMS 760 (769)
T ss_pred cchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhcc
Confidence 3356677788888887777666664 35567999999999999997653
No 75
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=59.92 E-value=9.3 Score=34.81 Aligned_cols=49 Identities=10% Similarity=0.143 Sum_probs=35.3
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
.++..++.+|...|..+ ....+||+.+|++..+|+++...-|++.|+.-
T Consensus 142 ~L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 34555566665544332 34678999999999999999988888777654
No 76
>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=59.64 E-value=7.3 Score=29.50 Aligned_cols=42 Identities=19% Similarity=0.351 Sum_probs=33.5
Q ss_pred cChHHHHHHHHHhhcC--CCCCHHHHHHHHHHhCCCCCcccccc
Q psy17897 334 IAAPEKRSLEAYFAVQ--PRPSGEKIAAIAEKLDLKKNVVRVWF 375 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n--~yPS~~er~~LA~qLgLs~~qVrvWF 375 (391)
+|+.|+..|...|+.. .+|-.....+||+++|+++..|..-.
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 4788999999998765 34777788899999999998765444
No 77
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=59.30 E-value=7 Score=33.75 Aligned_cols=47 Identities=19% Similarity=0.204 Sum_probs=34.2
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhh
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 384 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR 384 (391)
.+++.++.++...|-.+ ....+||+.+|++..+|++|...-|.|.|+
T Consensus 106 ~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 34556666665554333 247789999999999999999877777665
No 78
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=58.24 E-value=11 Score=32.96 Aligned_cols=33 Identities=24% Similarity=0.168 Sum_probs=28.0
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
...+||+.+|+++.+|++|...-|.|.|+.-.+
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~ 175 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLRECLEA 175 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999999888888776544
No 79
>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=57.01 E-value=7.8 Score=28.77 Aligned_cols=46 Identities=20% Similarity=0.109 Sum_probs=35.3
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhh
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 384 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR 384 (391)
.||+.++.+|.....-. ...+||..+++++.+|+.+..|-+.|.+-
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 57888888887776543 46789999999999999999888877653
No 80
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=55.92 E-value=11 Score=30.07 Aligned_cols=38 Identities=29% Similarity=0.448 Sum_probs=30.6
Q ss_pred HHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCChh
Q psy17897 243 RFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHN 289 (391)
Q Consensus 243 ~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~k 289 (391)
++|+-|..+|+||.+.+..+| +|..||--+|+=...++
T Consensus 5 k~k~~R~~~~ltQ~elA~~vg---------VsRQTi~~iEkgky~Ps 42 (68)
T COG1476 5 KLKELRAELGLTQEELAKLVG---------VSRQTIIAIEKGKYNPS 42 (68)
T ss_pred HHHHHHHHhCcCHHHHHHHcC---------cCHHHHHHHHcCCCCch
Confidence 577779999999999999986 66677877887765553
No 81
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=55.59 E-value=5.3 Score=28.60 Aligned_cols=40 Identities=20% Similarity=0.266 Sum_probs=21.6
Q ss_pred cccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccc
Q psy17897 332 TSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFC 376 (391)
Q Consensus 332 T~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFq 376 (391)
..+|.+++..++..++.. ....+||+.+|.++.+|..|..
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 457788888888887644 3567899999999999988764
No 82
>PRK00118 putative DNA-binding protein; Validated
Probab=55.41 E-value=13 Score=31.84 Aligned_cols=49 Identities=12% Similarity=0.218 Sum_probs=36.3
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
++..++..+...|... ....+||+.+|+++.+|+.|....|.+.|+...
T Consensus 18 L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~ 66 (104)
T PRK00118 18 LTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEE 66 (104)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3556666766665543 246789999999999999999888877776543
No 83
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=54.67 E-value=13 Score=32.44 Aligned_cols=50 Identities=12% Similarity=0.084 Sum_probs=35.0
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
+++.++.++...|-.. ....+||+.+|++..+|+++...-|.+.|+.-+.
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (160)
T PRK09642 107 LPENYRDVVLAHYLEE-----KSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKE 156 (160)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 3444455554433222 2356899999999999999999888888876554
No 84
>PF13565 HTH_32: Homeodomain-like domain
Probab=54.54 E-value=52 Score=25.26 Aligned_cols=40 Identities=18% Similarity=0.302 Sum_probs=28.8
Q ss_pred ChHHHHHHHHHhhcCCCCCHHHHHH-HHHHhCC----CCCccccc
Q psy17897 335 AAPEKRSLEAYFAVQPRPSGEKIAA-IAEKLDL----KKNVVRVW 374 (391)
Q Consensus 335 t~~Ql~~LE~~F~~n~yPS~~er~~-LA~qLgL----s~~qVrvW 374 (391)
+.++...+.+.+..++.-+..++.. |++++|+ +..+|..|
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 6777788889999888888777776 5666664 55555544
No 85
>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=53.14 E-value=11 Score=29.13 Aligned_cols=33 Identities=27% Similarity=0.349 Sum_probs=26.5
Q ss_pred Hh-hhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCC
Q psy17897 244 FK-QRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLT 285 (391)
Q Consensus 244 fk-qrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~Lq 285 (391)
++ ..|-..|+||.+++..+| ++++++.++|+-.
T Consensus 9 i~~~~~~~~~~t~~~lA~~~g---------is~~tis~~~~g~ 42 (78)
T TIGR02607 9 LREEFLEPLGLSIRALAKALG---------VSRSTLSRIVNGR 42 (78)
T ss_pred HHHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHcCC
Confidence 44 447778999999999985 7889999988754
No 86
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=53.11 E-value=13 Score=34.32 Aligned_cols=32 Identities=16% Similarity=0.054 Sum_probs=27.5
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
...+||+.+|++..+|+++..+-|.+.|+.-+
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 202 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLKVQMG 202 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 46789999999999999999888888877654
No 87
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=52.58 E-value=14 Score=32.37 Aligned_cols=50 Identities=14% Similarity=0.052 Sum_probs=35.1
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
.+++.++.++...|-.. ....+||+.+|++..+|++|...-+.|.|+.-.
T Consensus 128 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 128 SLPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 34555566665544322 246689999999999999999877777776543
No 88
>PRK04140 hypothetical protein; Provisional
Probab=52.51 E-value=15 Score=37.40 Aligned_cols=43 Identities=23% Similarity=0.429 Sum_probs=32.9
Q ss_pred HHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCC--Chhhhhh
Q psy17897 242 ERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTL--SHNNMIA 293 (391)
Q Consensus 242 ~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqL--S~knm~K 293 (391)
+.+++.|-..|+||.+++..+| +|+.++.+||+-.. +...+.+
T Consensus 129 erLk~lRe~~GlSq~eLA~~lG---------VSr~tIskyE~G~~~Ps~e~~~k 173 (317)
T PRK04140 129 DVLREAREELGLSLGELASELG---------VSRRTISKYENGGMNASIEVAIK 173 (317)
T ss_pred HHHHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHcCCCCCCHHHHHH
Confidence 4455559999999999999985 89999999998544 3444444
No 89
>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=52.18 E-value=19 Score=24.15 Aligned_cols=34 Identities=38% Similarity=0.542 Sum_probs=25.7
Q ss_pred HHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCC
Q psy17897 243 RFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLT 285 (391)
Q Consensus 243 ~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~Lq 285 (391)
.++..+...|+++.+++..++ ++..+++.+++-.
T Consensus 3 ~l~~~~~~~~~s~~~~a~~~~---------~~~~~v~~~~~g~ 36 (58)
T cd00093 3 RLKELRKEKGLTQEELAEKLG---------VSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHHcCCCHHHHHHHHC---------CCHHHHHHHHcCC
Confidence 345556678999999999885 6777788877654
No 90
>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=51.93 E-value=14 Score=30.65 Aligned_cols=46 Identities=22% Similarity=0.278 Sum_probs=32.2
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhh
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 384 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR 384 (391)
+++.++..+...|-. .....+||+.+|+++..|+.|...-+.|.|+
T Consensus 111 L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 445555555544322 2246689999999999999999877777665
No 91
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=50.04 E-value=14 Score=32.84 Aligned_cols=32 Identities=22% Similarity=0.286 Sum_probs=27.0
Q ss_pred HHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 355 EKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 355 ~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
....+||+.+|++..+|+++++.-|.+.|+.-
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 35678999999999999999988888777654
No 92
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=49.91 E-value=17 Score=31.76 Aligned_cols=49 Identities=18% Similarity=0.238 Sum_probs=36.1
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
++..++.+|...| .. ....+||..+|++..+|+++...-|.+.|+.-.+
T Consensus 113 L~~~~r~il~l~~-~g-----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~ 161 (166)
T PRK09639 113 MTERDRTVLLLRF-SG-----YSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQ 161 (166)
T ss_pred CCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4455556665555 32 2467899999999999999998888888776544
No 93
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=48.48 E-value=20 Score=31.96 Aligned_cols=30 Identities=23% Similarity=0.412 Sum_probs=25.9
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
...+||+.+|+++.+|+++...-|.+.|+.
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 467899999999999999998888777764
No 94
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=48.48 E-value=17 Score=32.46 Aligned_cols=49 Identities=14% Similarity=0.113 Sum_probs=34.9
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
+++.++.++...|-.. ....+||..+|++..+|++++..-|.+.|+.-.
T Consensus 132 L~~~~r~v~~l~~~~g-----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 132 LPPRQRDVVQSISVEG-----ASIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 3444555555543322 246789999999999999999988888877654
No 95
>PRK09480 slmA division inhibitor protein; Provisional
Probab=47.94 E-value=13 Score=33.01 Aligned_cols=40 Identities=13% Similarity=0.241 Sum_probs=31.7
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhh
Q psy17897 340 RSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQ 380 (391)
Q Consensus 340 ~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~ 380 (391)
......|..++. ....+..||++.|+++.++..+|.|+..
T Consensus 17 ~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 17 QALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 334444655556 7888999999999999999999999763
No 96
>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=47.56 E-value=14 Score=32.92 Aligned_cols=32 Identities=19% Similarity=0.090 Sum_probs=26.8
Q ss_pred HHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 355 EKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 355 ~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
....+||+.+|++..+|+++...-|.+.|+.-
T Consensus 155 ~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 155 LSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 35678999999999999999987777777654
No 97
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=47.09 E-value=19 Score=25.13 Aligned_cols=44 Identities=20% Similarity=0.240 Sum_probs=31.1
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHh
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQK 383 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~K 383 (391)
++..++..+..++.. ....+||+.++++..+|+.|...-+.|.+
T Consensus 4 l~~~e~~i~~~~~~g------~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 4 LTPREREVLRLLAEG------LTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCHHHHHHHHHHHcC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 566677776554322 24578999999999999999876555543
No 98
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=46.57 E-value=15 Score=33.07 Aligned_cols=32 Identities=16% Similarity=0.135 Sum_probs=26.8
Q ss_pred HHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 355 EKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 355 ~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
....+||+.+|++..+|++|+..-|.+.|+.-
T Consensus 158 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 158 LSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999999988887777643
No 99
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=46.31 E-value=18 Score=31.83 Aligned_cols=50 Identities=18% Similarity=0.131 Sum_probs=35.0
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
++..++..+...|-. .....+||..+|++..+|++|...-|.+.|+.-+.
T Consensus 109 L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~ 158 (165)
T PRK09644 109 LPVIEAQAILLCDVH-----ELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158 (165)
T ss_pred CCHHHHHHHHhHHHh-----cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 445555555543221 12467899999999999999999888888776543
No 100
>PRK04217 hypothetical protein; Provisional
Probab=46.17 E-value=22 Score=30.78 Aligned_cols=52 Identities=12% Similarity=0.050 Sum_probs=39.6
Q ss_pred CcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 331 RTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 331 RT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
-..++.+++..+...|...- ...+||+.+|+++.+|+..+...+.+.|..-.
T Consensus 40 ~~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L~ 91 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQMLV 91 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 34567788877777764432 46789999999999999999888887776543
No 101
>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=46.03 E-value=19 Score=30.79 Aligned_cols=45 Identities=11% Similarity=0.105 Sum_probs=30.6
Q ss_pred ChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhh
Q psy17897 335 AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 384 (391)
Q Consensus 335 t~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR 384 (391)
+..+...+...|-.. ....+||+.+|+++.+|+++...-|.|.|+
T Consensus 115 ~~~~r~il~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 115 PEQCRKIFILSRFEG-----KSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 444455555433221 246679999999999999998777766664
No 102
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=45.80 E-value=22 Score=32.04 Aligned_cols=50 Identities=10% Similarity=0.262 Sum_probs=35.2
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
+++.++.+|+..|-.. ....+||..+|+++.+|++....-|.+.|+.-+.
T Consensus 132 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 181 (189)
T PRK12515 132 LSPAHREIIDLVYYHE-----KSVEEVGEIVGIPESTVKTRMFYARKKLAELLKA 181 (189)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 4445555554433222 2467899999999999999999888888876544
No 103
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=45.52 E-value=25 Score=29.26 Aligned_cols=39 Identities=31% Similarity=0.495 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHhhh--hHhcCccchhhhhhhhcCcCCCCcccccchhhhh
Q psy17897 234 PRELEAFAERFKQR--RIKLGVTQADVGKALANLKLPGVGALSQSTICRF 281 (391)
Q Consensus 234 ~~eLe~Fa~~fkqr--RI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRf 281 (391)
.+|++.++.++.-- .+.-|.||.+|...+| .|-.||+|.
T Consensus 29 ~~E~~~l~~R~~va~~lL~~g~syreIa~~tg---------vS~aTItRv 69 (87)
T PF01371_consen 29 PDELEALAQRWQVAKELLDEGKSYREIAEETG---------VSIATITRV 69 (87)
T ss_dssp HHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHT---------STHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhC---------CCHHHHHHH
Confidence 57888888887543 5778999999999986 788899985
No 104
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=45.03 E-value=19 Score=32.37 Aligned_cols=48 Identities=15% Similarity=0.086 Sum_probs=33.6
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
.+++.++.++...|-.. ....+||..+|++..+|+++...-|.+.|+.
T Consensus 139 ~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 139 TLPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34455555555543332 3477899999999999999997777776654
No 105
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=44.20 E-value=26 Score=31.49 Aligned_cols=30 Identities=20% Similarity=0.338 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
...+||+.+|++..+|++|...-|.+.|+.
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 467899999999999999998777776654
No 106
>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=44.01 E-value=24 Score=31.44 Aligned_cols=50 Identities=18% Similarity=0.093 Sum_probs=36.6
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
.+++.++.++...|... ....+||..+|++..+|+++...-|.+.|+.-+
T Consensus 100 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45556666666655433 246789999999999999999888877776543
No 107
>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=43.85 E-value=21 Score=31.73 Aligned_cols=47 Identities=17% Similarity=0.097 Sum_probs=32.9
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
+++.++.++...|-.. ....+||+.+|+++.+|++....-|.+.|+.
T Consensus 135 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG-----LTVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4444444444443322 2467899999999999999998888777664
No 108
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=43.48 E-value=22 Score=31.89 Aligned_cols=32 Identities=9% Similarity=0.113 Sum_probs=26.8
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
...+||+.+|++..+|+++...-|.+.|+.-.
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999888877777543
No 109
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=43.35 E-value=18 Score=31.61 Aligned_cols=48 Identities=19% Similarity=0.118 Sum_probs=33.4
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
++..++.++...|-.+ ....+||..+|++..+|+++...-|.+.|+.+
T Consensus 113 L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~~ 160 (161)
T PRK12541 113 LPLERRNVLLLRDYYG-----FSYKEIAEMTGLSLAKVKIELHRGRKETKSIK 160 (161)
T ss_pred CCHHHHHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhc
Confidence 4455555555443222 24678999999999999999988777777654
No 110
>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=43.19 E-value=21 Score=30.89 Aligned_cols=47 Identities=17% Similarity=0.228 Sum_probs=32.9
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhh
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 384 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR 384 (391)
.+++.++.++...|-.. ....+||+.+|++..+|+++...-|.+.|.
T Consensus 111 ~L~~~~r~v~~l~~~~g-----~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 111 KLPERQRELLQLRYQRG-----VSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HCCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 45666666666644322 357789999999999999988666665543
No 111
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=42.32 E-value=24 Score=32.01 Aligned_cols=48 Identities=13% Similarity=0.105 Sum_probs=33.6
Q ss_pred ChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 335 AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 335 t~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
+..++.++...|-.. ....+||..+|+++.+|+++...-|.+.|+.-.
T Consensus 136 p~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 183 (189)
T PRK12530 136 PAQQARVFMMREYLE-----LSSEQICQECDISTSNLHVLLYRARLQLQACLS 183 (189)
T ss_pred CHHHHHHHhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 444555554443322 246789999999999999999888877776543
No 112
>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=42.14 E-value=9.1 Score=29.82 Aligned_cols=21 Identities=38% Similarity=0.694 Sum_probs=17.9
Q ss_pred HHHHHHHHhCCCCCccccccc
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFC 376 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFq 376 (391)
...+||++||+++.+|+.|=.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh
Confidence 355789999999999999954
No 113
>PRK06930 positive control sigma-like factor; Validated
Probab=40.55 E-value=28 Score=32.05 Aligned_cols=50 Identities=20% Similarity=0.139 Sum_probs=37.7
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
.+++.++.++...|... ....+||..+|++..+|+++..+-|.|.++.-.
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46666777776654333 246789999999999999999988888877654
No 114
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=39.86 E-value=22 Score=33.87 Aligned_cols=33 Identities=21% Similarity=0.181 Sum_probs=28.0
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
...+||+.+|++..+|+++...-|.+.|+.-++
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~~ 221 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRDLLRR 221 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999999888888876543
No 115
>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=39.46 E-value=13 Score=28.48 Aligned_cols=21 Identities=33% Similarity=0.510 Sum_probs=18.5
Q ss_pred HHHHHHHHhCCCCCccccccc
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFC 376 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFq 376 (391)
...+||+.||++..+|..|-+
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH
Confidence 467899999999999999974
No 116
>KOG1146|consensus
Probab=39.28 E-value=23 Score=42.25 Aligned_cols=61 Identities=18% Similarity=0.277 Sum_probs=54.9
Q ss_pred CCCCCCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 326 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 326 ~kKRkRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
+-++-|..+-.++...|-++|-.+.-|+.+.+..|......+.+++.+||+|-|.|.++..
T Consensus 704 ~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 704 RDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred ccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 4566677887899999999999999999999999999999999999999999999988754
No 117
>PRK10072 putative transcriptional regulator; Provisional
Probab=38.17 E-value=23 Score=29.86 Aligned_cols=41 Identities=20% Similarity=0.254 Sum_probs=29.4
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhh
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQ 380 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~ 380 (391)
..+...+..|...... .+.++|+.+|++..+|+.|...+|.
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 3355556666543322 2678999999999999999988764
No 118
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=37.94 E-value=29 Score=30.59 Aligned_cols=47 Identities=9% Similarity=0.071 Sum_probs=32.5
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
+++.++.++...|... ....+||+.+|++..+|+++...-|.+.|..
T Consensus 113 L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 113 LSADQREAIILIGASG-----FSYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3444455444433222 2467899999999999999998777777654
No 119
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=37.74 E-value=10 Score=33.68 Aligned_cols=32 Identities=22% Similarity=0.292 Sum_probs=23.0
Q ss_pred CCCCCCCHHHHHH-----HHHHHhhhhHhcCccchhh
Q psy17897 227 HPDTDTDPRELEA-----FAERFKQRRIKLGVTQADV 258 (391)
Q Consensus 227 ~pd~~~d~~eLe~-----Fa~~fkqrRI~lGlTQ~~V 258 (391)
+|+...-++++++ |+|+++++.++.|+.+.+.
T Consensus 77 tp~v~~~I~~~k~enP~ifawEiR~~L~~~gvc~~~~ 113 (125)
T PF00292_consen 77 TPEVVEKIEQYKRENPTIFAWEIRDRLIADGVCDRSN 113 (125)
T ss_dssp -HCHHHHHHHHHHH-TTS-HHHHHHHHHHTTSS-TTT
T ss_pred ChHHHHHHHHHHhcCCCcchHHHHHHHHHcCCCCCCC
Confidence 5666666666665 9999999999999977654
No 120
>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=37.33 E-value=22 Score=27.58 Aligned_cols=46 Identities=26% Similarity=0.314 Sum_probs=22.5
Q ss_pred CCcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccc
Q psy17897 330 KRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFC 376 (391)
Q Consensus 330 kRT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFq 376 (391)
.|..|+...+...-.+|.....--...| ..|+++|+++.+|+-|-+
T Consensus 2 ~rrsy~~~FKL~Vv~~a~~~~nc~~~~R-Aaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 2 SRRSYTAEFKLKVVEYAEKDNNCKGNQR-AAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp ------HHHHHHHHHHHHH-TTTTT-HH-HHHHHTTS-HHHHHHHHT
T ss_pred CccccChHHHHHHHHHHHHccchhhhHH-HHHHHhCccHHHHHHHHH
Confidence 3556776655443444433322222223 359999999999999964
No 121
>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=37.25 E-value=41 Score=30.21 Aligned_cols=49 Identities=14% Similarity=0.060 Sum_probs=38.4
Q ss_pred CcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 331 RTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 331 RT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
.+.+++.|+.+|+..+ .. ....+||+.+|++...|+.|-..-|.|.|+.
T Consensus 4 ~~~Lte~qr~VL~Lr~-~G-----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~a 52 (137)
T TIGR00721 4 KTFLTERQIKVLELRE-KG-----LSQKEIAKELKTTRANVSAIEKRAMENIEKA 52 (137)
T ss_pred cCCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHHH
Confidence 4567888888887743 22 2467899999999999999998888887763
No 122
>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=37.24 E-value=34 Score=30.13 Aligned_cols=30 Identities=23% Similarity=0.357 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
...+||+.+|++..+|+++...-|.+.|+.
T Consensus 137 s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999998777777664
No 123
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=37.24 E-value=34 Score=29.59 Aligned_cols=49 Identities=8% Similarity=0.097 Sum_probs=34.4
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
++..++.++.-.|-.. ....+||..+|++..+|++....-|.+.|+.-.
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 155 (161)
T PRK09047 107 LPARQREAFLLRYWED-----MDVAETAAAMGCSEGSVKTHCSRATHALAKALE 155 (161)
T ss_pred CCHHHHHHHHHHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4455566655543222 136789999999999999999887777776543
No 124
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=37.14 E-value=30 Score=31.67 Aligned_cols=32 Identities=13% Similarity=0.056 Sum_probs=27.1
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
...+||..+|++..+|++++..-|.+.|+.-.
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 46789999999999999999988888776543
No 125
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=36.97 E-value=32 Score=29.95 Aligned_cols=47 Identities=17% Similarity=0.223 Sum_probs=31.8
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
+++.++.++...|-.. ....+||+.+|++..+|+.+...-|.+.|+.
T Consensus 110 L~~~~r~v~~l~~~~~-----~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 110 LPARTRYAFEMYRLHG-----ETQKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3445555555443222 2367899999999999999877666666654
No 126
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=36.86 E-value=21 Score=31.55 Aligned_cols=36 Identities=17% Similarity=0.192 Sum_probs=30.3
Q ss_pred HHHHHHHHHHhCCCCCccccccchhhhHHhhHHhhh
Q psy17897 354 GEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFAA 389 (391)
Q Consensus 354 ~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~a 389 (391)
.....+||+.+|++..+|++.+..-|.+.|+.-+..
T Consensus 136 g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~~ 171 (175)
T PRK12518 136 DLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQQ 171 (175)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 335778999999999999999999898888876543
No 127
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=36.82 E-value=36 Score=30.45 Aligned_cols=33 Identities=15% Similarity=0.142 Sum_probs=28.0
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
...+||+.+|++..+|++....-|++.|+.-.+
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 167 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQI 167 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999999888888875443
No 128
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=36.67 E-value=31 Score=30.96 Aligned_cols=30 Identities=17% Similarity=0.130 Sum_probs=26.1
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
...+||+.+|+++.+|++....-|.+.|+.
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999998888887764
No 129
>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=36.66 E-value=30 Score=30.08 Aligned_cols=47 Identities=13% Similarity=0.158 Sum_probs=33.0
Q ss_pred ChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 335 AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 335 t~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
+..++..+...|-. .....+||..+|++..+|+++-..-|.+.|+.-
T Consensus 112 ~~~~r~i~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 112 PARQRAVVVLRYYE-----DLSEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred CHHHHHHhhhHHHh-----cCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 34444455444322 234678999999999999999988888877654
No 130
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=36.59 E-value=31 Score=32.59 Aligned_cols=47 Identities=13% Similarity=0.179 Sum_probs=34.4
Q ss_pred ChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 335 AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 335 t~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
++.++.++...|... ....+||+.+|++...|+++...-|.+.|+.-
T Consensus 186 ~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 186 PEREQLVLSLYYQEE-----LNLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred CHHHHHHHHhHhccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 444555555544322 24678999999999999999998888887754
No 131
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=36.58 E-value=25 Score=33.00 Aligned_cols=49 Identities=14% Similarity=0.262 Sum_probs=38.4
Q ss_pred ccChHHHHHHHHHhhcC--CCCCHHHHHHHHHHhCCCCCccccccchhhhHHh
Q psy17897 333 SIAAPEKRSLEAYFAVQ--PRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQK 383 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n--~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~K 383 (391)
.+|+.|+..|...|... -||-.....+||+++|+++.++.. .=||+..|
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 79999999999999865 458888899999999999987543 33444433
No 132
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=36.43 E-value=35 Score=31.06 Aligned_cols=32 Identities=13% Similarity=0.124 Sum_probs=27.0
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
...+||+.+|++..+|++++..-|.+.|+.-.
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 185 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKRALAALLA 185 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46689999999999999999888888777543
No 133
>PHA02591 hypothetical protein; Provisional
Probab=36.29 E-value=32 Score=28.41 Aligned_cols=26 Identities=19% Similarity=0.339 Sum_probs=20.9
Q ss_pred hhHhcCccchhhhhhhhcCcCCCCcccccchhhhh
Q psy17897 247 RRIKLGVTQADVGKALANLKLPGVGALSQSTICRF 281 (391)
Q Consensus 247 rRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRf 281 (391)
+..++|+||..|+..|| ++|.++.++
T Consensus 54 eL~eqGlSqeqIA~~LG---------VsqetVrKY 79 (83)
T PHA02591 54 ELARKGFTVEKIASLLG---------VSVRKVRRY 79 (83)
T ss_pred HHHHcCCCHHHHHHHhC---------CCHHHHHHH
Confidence 36778999999999996 777777654
No 134
>PRK01381 Trp operon repressor; Provisional
Probab=36.27 E-value=77 Score=27.16 Aligned_cols=55 Identities=25% Similarity=0.450 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHhhhh-Hhc-CccchhhhhhhhcCcCCCCcccccchhhhhccCCCChhhhhh-hhHHHHHHHHH
Q psy17897 234 PRELEAFAERFKQRR-IKL-GVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIA-LKPILQAWLEE 304 (391)
Q Consensus 234 ~~eLe~Fa~~fkqrR-I~l-GlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~knm~K-LkPlL~kWLee 304 (391)
.+|++.++.+++--+ +.. +.||..|...+| +|-+||.|-.+ +.| .-+-.+.|++.
T Consensus 35 p~Er~al~~R~~I~~~L~~g~~sQREIa~~lG---------vSiaTITRgsn-------~Lk~~~~~~k~~l~~ 92 (99)
T PRK01381 35 PDEREALGTRVRIVEELLRGELSQREIKQELG---------VGIATITRGSN-------SLKTAPPEFKEWLEQ 92 (99)
T ss_pred HHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhC---------CceeeehhhHH-------HhccCCHHHHHHHHH
Confidence 356666666654443 223 599999999986 77788888532 222 23456677765
No 135
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=36.13 E-value=51 Score=21.73 Aligned_cols=33 Identities=33% Similarity=0.451 Sum_probs=25.0
Q ss_pred hhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCC
Q psy17897 245 KQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTL 286 (391)
Q Consensus 245 kqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqL 286 (391)
+..|-..++|+.+++..++ +++.+++.++.-..
T Consensus 3 ~~~~~~~~~s~~~la~~~~---------i~~~~i~~~~~~~~ 35 (56)
T smart00530 3 KELREEKGLTQEELAEKLG---------VSRSTLSRIENGKR 35 (56)
T ss_pred HHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHCCCC
Confidence 4446667899999998875 77788888877653
No 136
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=35.91 E-value=34 Score=30.95 Aligned_cols=31 Identities=29% Similarity=0.228 Sum_probs=25.8
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
...+||..+|+++.+|++.+..-|.+.|+.-
T Consensus 124 ~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 124 SQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999987777766543
No 137
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=35.61 E-value=36 Score=30.82 Aligned_cols=32 Identities=6% Similarity=0.044 Sum_probs=27.3
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
...+||+.+|++..+|+++...-|.+.|+.-.
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999988888777654
No 138
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=35.24 E-value=40 Score=30.32 Aligned_cols=50 Identities=12% Similarity=0.096 Sum_probs=34.8
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
.+++.++.+++..|-. .....+||+.+|++..+|+++...-|.+.|+.-.
T Consensus 131 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12539 131 RLPEKMRLAIQAVKLE-----GLSVAEAATRSGMSESAVKVSVHRGLKALAALIG 180 (184)
T ss_pred hCCHHHHHHHHHHHHc-----CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHh
Confidence 3445555555543322 2356789999999999999999887777776543
No 139
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=35.23 E-value=36 Score=30.67 Aligned_cols=32 Identities=16% Similarity=0.127 Sum_probs=27.9
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
...+||+.+|+++.+|++....-|.+-|+.-+
T Consensus 156 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 156 SYEDIASVMQCPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999988888887654
No 140
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=35.23 E-value=39 Score=30.18 Aligned_cols=30 Identities=13% Similarity=0.081 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
...+||+.+|++..+|+++...-|.+.|+.
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999988777776654
No 141
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=35.03 E-value=28 Score=29.91 Aligned_cols=43 Identities=12% Similarity=0.121 Sum_probs=28.8
Q ss_pred CcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccch
Q psy17897 331 RTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCN 377 (391)
Q Consensus 331 RT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqN 377 (391)
|..|+.+++...-.....+.+ ...++|+.+|++..+|..|..-
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHHH
Confidence 455777776544333333332 3567899999999999999643
No 142
>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=34.95 E-value=6.6 Score=31.73 Aligned_cols=25 Identities=24% Similarity=0.307 Sum_probs=21.2
Q ss_pred HHHHHHHHHhCCCCCccccccchhh
Q psy17897 355 EKIAAIAEKLDLKKNVVRVWFCNQR 379 (391)
Q Consensus 355 ~er~~LA~qLgLs~~qVrvWFqNRR 379 (391)
....+||+.+|+++.+|++|+.+..
T Consensus 33 lS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 33 KTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred CCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 3577899999999999999997543
No 143
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=34.95 E-value=38 Score=30.55 Aligned_cols=49 Identities=10% Similarity=0.088 Sum_probs=34.1
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
+++.++.++...|-.. ....+||+.+|++..+|++....-|.+.|+.-.
T Consensus 132 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (191)
T PRK12520 132 LPPRTGRVFMMREWLE-----LETEEICQELQITATNAWVLLYRARMRLRECLD 180 (191)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3445555555443222 236789999999999999999888888776543
No 144
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=34.95 E-value=33 Score=30.77 Aligned_cols=32 Identities=19% Similarity=0.224 Sum_probs=26.7
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
...+||+.+|++..+|++....-|.+.|+.-.
T Consensus 140 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 171 (185)
T PRK12542 140 TYQEISSVMGITEANVRKQFERARKRVQNMIG 171 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHc
Confidence 46789999999999999999888877776543
No 145
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=34.81 E-value=54 Score=27.16 Aligned_cols=39 Identities=18% Similarity=0.105 Sum_probs=29.7
Q ss_pred HHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCCh
Q psy17897 239 AFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSH 288 (391)
Q Consensus 239 ~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~ 288 (391)
.|...|++-|-..|+|| ++...| +++++|.++|+-..++
T Consensus 32 ~~~~~l~~~r~~~glSq--LAe~~G---------Is~stLs~iE~g~~~P 70 (89)
T TIGR02684 32 YIAHALGYIARARGMTQ--LARKTG---------LSRESLYKALSGKGNP 70 (89)
T ss_pred HHHHHHHHHHHHCChHH--HHHHHC---------CCHHHHHHHHcCCCCC
Confidence 36666777788889996 776664 8999999999776544
No 146
>KOG0773|consensus
Probab=34.75 E-value=23 Score=35.53 Aligned_cols=42 Identities=26% Similarity=0.364 Sum_probs=37.0
Q ss_pred hcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 347 AVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 347 ~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
+.++||+..+...++....++..+|.+||-|.|.+.+...+.
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~ 158 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKM 158 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCC
Confidence 468999999999999999999999999999999988775543
No 147
>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=34.60 E-value=36 Score=29.67 Aligned_cols=29 Identities=24% Similarity=0.273 Sum_probs=23.5
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKR 384 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR 384 (391)
...+||+.+|++..+|++...--|.+.|+
T Consensus 140 s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 140 PIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46789999999999999988666666554
No 148
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=34.38 E-value=42 Score=31.17 Aligned_cols=32 Identities=25% Similarity=0.232 Sum_probs=26.8
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
...+||+.+|++..+|+++...-|.+.|+.-+
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~ 187 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQLRAALA 187 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999888887776543
No 149
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=34.32 E-value=35 Score=30.87 Aligned_cols=48 Identities=23% Similarity=0.367 Sum_probs=33.2
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
+++.++..+...|-.. ....+||+.+|++..+|++..+.-|.+.|+.+
T Consensus 132 L~~~~r~i~~l~~~~g-----~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 132 LEKLDREIFIRRYLLG-----EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred CCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 4455555555433222 24678999999999999999887777776654
No 150
>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=34.22 E-value=39 Score=32.59 Aligned_cols=33 Identities=12% Similarity=0.290 Sum_probs=28.1
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
...+||..+|++..+|+++...-|.+.|+.-++
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~ 211 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLERTRR 211 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999999888887776544
No 151
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=34.03 E-value=43 Score=29.54 Aligned_cols=32 Identities=16% Similarity=0.122 Sum_probs=26.3
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
...+||+.+|++..+|++....-|.+.|+.-+
T Consensus 136 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 167 (173)
T PRK09645 136 STAQIAADLGIPEGTVKSRLHYALRALRLALQ 167 (173)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 46789999999999999999877777776543
No 152
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=33.76 E-value=42 Score=30.57 Aligned_cols=32 Identities=13% Similarity=0.077 Sum_probs=27.0
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
...+||+.||+++.+|+++...-|.+.|+.-+
T Consensus 134 s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 134 AYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46689999999999999999888888776544
No 153
>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=33.52 E-value=14 Score=25.78 Aligned_cols=22 Identities=14% Similarity=0.144 Sum_probs=18.6
Q ss_pred HHHHHHHhCCCCCccccccchh
Q psy17897 357 IAAIAEKLDLKKNVVRVWFCNQ 378 (391)
Q Consensus 357 r~~LA~qLgLs~~qVrvWFqNR 378 (391)
+.++|+.+|+++.+|+.|.++-
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4678999999999999996554
No 154
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=33.50 E-value=44 Score=30.37 Aligned_cols=33 Identities=18% Similarity=0.118 Sum_probs=26.9
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
...+||+.+|++..+|++....-|.+.|+.-.+
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~~ 191 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMDA 191 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhhh
Confidence 467899999999999999988877777765443
No 155
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=33.49 E-value=22 Score=32.16 Aligned_cols=35 Identities=17% Similarity=0.164 Sum_probs=28.4
Q ss_pred CHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 353 SGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 353 S~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
......+||+.+|++..+|+++..+-|.+.|+.-+
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 188 (194)
T PRK12513 154 GDLELEEIAELTGVPEETVKSRLRYALQKLRELLA 188 (194)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 33457789999999999999999888888776543
No 156
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=33.19 E-value=42 Score=30.52 Aligned_cols=49 Identities=10% Similarity=0.076 Sum_probs=34.6
Q ss_pred ChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 335 AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 335 t~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
+..++.++...|-.. ....+||+.+|++...|+++...-|.+.|+.-.+
T Consensus 133 ~~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~ 181 (188)
T TIGR02943 133 PEQTARVFMMREVLG-----FESDEICQELEISTSNCHVLLYRARLSLRACLSI 181 (188)
T ss_pred CHHHHHHHHHHHHhC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 344455554443222 2567899999999999999998888887776544
No 157
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=33.02 E-value=39 Score=29.02 Aligned_cols=45 Identities=20% Similarity=0.184 Sum_probs=35.1
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHh
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQK 383 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~K 383 (391)
.++..++..|+. +..+ + ...+||+.+++++.+|++|.+|-|.|..
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 478888888776 4433 2 2568899999999999999999888765
No 158
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=32.74 E-value=14 Score=26.33 Aligned_cols=23 Identities=26% Similarity=0.456 Sum_probs=17.5
Q ss_pred HHHHHHHHHhCCCCCccccccch
Q psy17897 355 EKIAAIAEKLDLKKNVVRVWFCN 377 (391)
Q Consensus 355 ~er~~LA~qLgLs~~qVrvWFqN 377 (391)
....+||+.+|++..+|..|.+.
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 35778999999999999999754
No 159
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=32.72 E-value=1.6e+02 Score=29.92 Aligned_cols=94 Identities=28% Similarity=0.334 Sum_probs=48.8
Q ss_pred HHHHHHHHHHHhhhhH--hcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCChhhhhhhhHHHHHHHHHHHHHhhh
Q psy17897 234 PRELEAFAERFKQRRI--KLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAQAKN 311 (391)
Q Consensus 234 ~~eLe~Fa~~fkqrRI--~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~knm~KLkPlL~kWLeeaE~~~~~ 311 (391)
-++|+.|..-+.++-| -..++-.++-.-+..+...| ++-+++.|. +..+|.+ .+|+... +
T Consensus 31 rrDL~~f~~~L~~~~~~~l~~~~~~di~~yl~~l~~~g---~s~~S~aR~---------lsalR~f-y~fl~~E-----~ 92 (300)
T COG4974 31 RRDLEDFREWLEERGITDLADATEADIREYLTELAEQG---LSATSIARA---------LSALRSF-YQFLIRE-----G 92 (300)
T ss_pred HHHHHHHHHHHHhcCCCChhhcCHHHHHHHHHHHHhCC---cChhhHHHH---------HHHHHHH-HHHHHHC-----C
Confidence 3677778777777755 23566666666555544322 555555442 2333333 3344321 2
Q ss_pred cCCCCCCCCCCCCCCCCCCCcccChHHHHHHHHH
Q psy17897 312 KRRDPDAPSVLPAGEKKRKRTSIAAPEKRSLEAY 345 (391)
Q Consensus 312 ~~~~~~~~~~~~~~~kKRkRT~ft~~Ql~~LE~~ 345 (391)
.+.+.........+..++--..++.+|+..|-..
T Consensus 93 ~~~~dP~~~l~~PK~~~~LPk~Ls~~eve~Ll~~ 126 (300)
T COG4974 93 LREDDPTRLLDSPKLPKRLPKFLSEEEVEALLEA 126 (300)
T ss_pred CcccCchhhhcCCCCCCcCCcccCHHHHHHHHhC
Confidence 2222222223333445555678888888777663
No 160
>PRK10403 transcriptional regulator NarP; Provisional
Probab=32.49 E-value=23 Score=30.91 Aligned_cols=49 Identities=18% Similarity=0.134 Sum_probs=37.4
Q ss_pred cccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 332 TSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 332 T~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
..++..+...|+...+. ....+||+.+++++++|+++.+|=|.|....+
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 35788888888765543 23568899999999999999999888765433
No 161
>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=32.16 E-value=27 Score=24.86 Aligned_cols=38 Identities=16% Similarity=0.342 Sum_probs=24.7
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCcccccc
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWF 375 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWF 375 (391)
.++.++...+.+.+... ..+.+||+.+|++..+|..|+
T Consensus 5 ~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 34554555555555543 357789999999999988766
No 162
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=32.12 E-value=43 Score=29.70 Aligned_cols=47 Identities=15% Similarity=0.102 Sum_probs=32.8
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
++..++.++...|-.. ....+||+.+|++..+|+++..+-+.+.+..
T Consensus 120 Lp~~~r~v~~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 120 LSSKARAAFLYNRLDG-----MGHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3445555555443222 2467899999999999999998888877654
No 163
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=31.94 E-value=48 Score=30.12 Aligned_cols=49 Identities=8% Similarity=0.034 Sum_probs=33.9
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
++..++.++...|-.. ....+||..+|++..+|+++...-|.+.|+...
T Consensus 112 Lp~~~R~v~~L~~~eg-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 112 LPEEQRAALHLVAIEG-----LSYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555533322 246789999999999999999877777766543
No 164
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=31.49 E-value=54 Score=29.00 Aligned_cols=32 Identities=9% Similarity=0.141 Sum_probs=26.9
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
...+||+.+|++..+|+++...-|.+.|+.-+
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 168 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMREHLE 168 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999888888776544
No 165
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=31.29 E-value=41 Score=29.82 Aligned_cols=32 Identities=22% Similarity=0.286 Sum_probs=26.7
Q ss_pred HHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 355 EKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 355 ~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
....+||+.+|++..+|+++...-|.|.|+.-
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T PRK09641 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999999988888777653
No 166
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=31.12 E-value=53 Score=27.56 Aligned_cols=43 Identities=12% Similarity=0.193 Sum_probs=33.3
Q ss_pred CcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCC-CCCccccccch
Q psy17897 331 RTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDL-KKNVVRVWFCN 377 (391)
Q Consensus 331 RT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgL-s~~qVrvWFqN 377 (391)
|..|+.+.+..+-+.+....+ .+..+|+++|+ ...++..|-..
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~~ 48 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRIQ 48 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHHH
Confidence 778999888776666655443 57889999996 99999988653
No 167
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=30.74 E-value=51 Score=30.26 Aligned_cols=32 Identities=22% Similarity=0.276 Sum_probs=27.0
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
...+||..+|++..+|++....-|.+.|+.-+
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999888888776543
No 168
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=30.65 E-value=57 Score=29.57 Aligned_cols=33 Identities=15% Similarity=0.135 Sum_probs=27.0
Q ss_pred HHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 355 EKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 355 ~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
....+||..+|++..+|++.+..-|.+.|+.-.
T Consensus 171 ~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~ 203 (208)
T PRK08295 171 KSYQEIAEELNRHVKSIDNALQRVKRKLEKYLE 203 (208)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999988888877776543
No 169
>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=30.59 E-value=54 Score=22.95 Aligned_cols=42 Identities=19% Similarity=0.220 Sum_probs=27.7
Q ss_pred ChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHH
Q psy17897 335 AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQ 382 (391)
Q Consensus 335 t~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~ 382 (391)
+..+...+..++. . ....+||+.++++..+|+.|...-+.+.
T Consensus 2 ~~~e~~i~~~~~~--~----~s~~eia~~l~~s~~tv~~~~~~~~~~l 43 (57)
T cd06170 2 TPREREVLRLLAE--G----KTNKEIADILGISEKTVKTHLRNIMRKL 43 (57)
T ss_pred CHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 3445555554432 1 2456889999999999999986544443
No 170
>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=30.43 E-value=27 Score=31.59 Aligned_cols=32 Identities=16% Similarity=0.099 Sum_probs=27.5
Q ss_pred HHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 355 EKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 355 ~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
....+||+.+|++..+|+++...-|.+.|+.-
T Consensus 148 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 148 FAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45778999999999999999988888877654
No 171
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=30.34 E-value=38 Score=35.90 Aligned_cols=47 Identities=32% Similarity=0.343 Sum_probs=37.1
Q ss_pred HHHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCCh
Q psy17897 238 EAFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSH 288 (391)
Q Consensus 238 e~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~ 288 (391)
+.|.+++++.|.+.|+||.+++..++.. | ..+++++|.+||+-...+
T Consensus 2 ~~~~~rL~~~r~~~g~tq~~la~~~~~~---g-~~vs~~~is~~e~g~~~p 48 (517)
T PRK13355 2 TTFAERLKQAMKARGLKQEDLVHAAEAR---G-VKLGKSHISQYVSGKTGP 48 (517)
T ss_pred chHHHHHHHHHHHCCCCHHHHHHHHHhc---c-CCcCHHHHHHHHCCCCCC
Confidence 3688889999999999999999987643 2 138999999999766433
No 172
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=29.95 E-value=47 Score=29.77 Aligned_cols=48 Identities=15% Similarity=0.099 Sum_probs=33.9
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
.+++.++.++.-.|-.. ....+||..+|+++.+|++...+-+.+.+..
T Consensus 127 ~Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG-----MKQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 34555666555544322 2467899999999999999998877776553
No 173
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=29.91 E-value=46 Score=30.59 Aligned_cols=32 Identities=13% Similarity=0.112 Sum_probs=26.7
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
...+||+.+|++..+|+++...-|.+.|+.-.
T Consensus 151 s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 151 TYEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 46789999999999999999887777776543
No 174
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=29.32 E-value=51 Score=30.92 Aligned_cols=53 Identities=13% Similarity=0.145 Sum_probs=34.5
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
+++.++.++...|.. .+-......+||..+|++..+|+++...-|.+.|+.-.
T Consensus 179 Lp~~~R~v~~L~y~l-~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~ 231 (234)
T PRK08301 179 LSDREKQIMELRFGL-NGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEIN 231 (234)
T ss_pred CCHHHHHHHHHHhcc-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 344555555554410 00122346789999999999999998888887776543
No 175
>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=29.05 E-value=48 Score=30.93 Aligned_cols=47 Identities=19% Similarity=0.253 Sum_probs=34.7
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
++..++..+...|-.. ....+||+.+|++..+|+.+...-+.+.|+.
T Consensus 176 L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 176 LSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4566667776665332 2467899999999999999998777776653
No 176
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=29.01 E-value=43 Score=31.60 Aligned_cols=31 Identities=16% Similarity=0.165 Sum_probs=26.1
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
...+||+.+|+++.+|+++...-|.+.|+.-
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999988887777653
No 177
>PF13518 HTH_28: Helix-turn-helix domain
Probab=28.98 E-value=26 Score=24.71 Aligned_cols=25 Identities=20% Similarity=0.484 Sum_probs=20.2
Q ss_pred HHHHHHHHhCCCCCccccccchhhh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQ 380 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~ 380 (391)
...++|+++|++..+|..|.+.-+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 3557999999999999999865443
No 178
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=28.76 E-value=53 Score=31.77 Aligned_cols=50 Identities=12% Similarity=0.159 Sum_probs=36.1
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
+++.++.++...|... ....+||..+|++..+|+....+-+.+.|+.-..
T Consensus 213 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 262 (268)
T PRK06288 213 LPEREKKVLILYYYED-----LTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAE 262 (268)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555666555332 2467899999999999999998888887776543
No 179
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=28.63 E-value=49 Score=31.63 Aligned_cols=48 Identities=15% Similarity=0.141 Sum_probs=34.9
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
+++.++.+|...|-.. ....+||+.+|++..+|+.|...-+.|.|+.-
T Consensus 206 L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l 253 (257)
T PRK08583 206 LSDREKSIIQCTFIEN-----LSQKETGERLGISQMHVSRLQRQAIKKLREAA 253 (257)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 4556666666655322 24578999999999999999988777777643
No 180
>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=28.45 E-value=71 Score=27.00 Aligned_cols=35 Identities=23% Similarity=0.348 Sum_probs=18.9
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhh
Q psy17897 340 RSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFA 388 (391)
Q Consensus 340 ~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~ 388 (391)
....-.|+.|+||+.+-... |+ .|||.+||+....
T Consensus 15 RiIk~LyqsnPyP~~~GTr~-aR-------------RnRRRRWR~rq~Q 49 (91)
T PF00424_consen 15 RIIKILYQSNPYPSPEGTRQ-AR-------------RNRRRRWRARQRQ 49 (91)
T ss_dssp HHHHHHHHTS-S--S-S-HH-HH-------------HHHHHHHHHHHHH
T ss_pred HHHHHHHccccCCCCCCccc-cc-------------cchhhhHHHHHHH
Confidence 34455588999997442111 11 5899999887654
No 181
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=28.43 E-value=50 Score=31.53 Aligned_cols=46 Identities=13% Similarity=0.230 Sum_probs=32.6
Q ss_pred ChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 335 AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 335 t~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
++.++.++...|.. .....+||..+|++..+|++++..-|.+.|+.
T Consensus 203 ~~~~r~vl~l~~~~-----~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 203 SEKEQLVISLFYKE-----ELTLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred CHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 44455555544422 22467899999999999999998888777664
No 182
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=28.29 E-value=20 Score=26.98 Aligned_cols=20 Identities=20% Similarity=0.300 Sum_probs=17.4
Q ss_pred HHHHHHHhCCCCCccccccc
Q psy17897 357 IAAIAEKLDLKKNVVRVWFC 376 (391)
Q Consensus 357 r~~LA~qLgLs~~qVrvWFq 376 (391)
+.++|+.+|++.++|+.|=.
T Consensus 3 i~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 56899999999999999943
No 183
>KOG3517|consensus
Probab=28.06 E-value=14 Score=36.56 Aligned_cols=29 Identities=24% Similarity=0.359 Sum_probs=24.2
Q ss_pred CCCCCCCHHHHHH-----HHHHHhhhhHhcCccc
Q psy17897 227 HPDTDTDPRELEA-----FAERFKQRRIKLGVTQ 255 (391)
Q Consensus 227 ~pd~~~d~~eLe~-----Fa~~fkqrRI~lGlTQ 255 (391)
+|.+..-+++|++ |||+++.|.+..|+..
T Consensus 80 TP~VV~~IR~~Kq~DPGIFAWEIRDRLlsdgiCD 113 (334)
T KOG3517|consen 80 TPKVVKYIRSLKQRDPGIFAWEIRDRLLSDGICD 113 (334)
T ss_pred ChhHHHHHHHhhccCCceeeehhhhhhhhccccc
Confidence 5666667888988 9999999999998854
No 184
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=28.05 E-value=58 Score=30.30 Aligned_cols=32 Identities=16% Similarity=0.202 Sum_probs=27.4
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
...+||+.+|++..+|+++...-|.+.|+.-+
T Consensus 166 s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~ 197 (206)
T PRK12544 166 ETNEICHAVDLSVSNLNVLLYRARLRLRECLE 197 (206)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35789999999999999999888888887654
No 185
>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=27.86 E-value=45 Score=32.58 Aligned_cols=51 Identities=18% Similarity=0.001 Sum_probs=39.6
Q ss_pred CcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 331 RTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 331 RT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
...+|+.++.+|+-..+- ....+||+.|++++.+|+++.+|-+.|.+-.++
T Consensus 188 ~~~LT~RE~evl~l~a~G------~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~nr 238 (247)
T TIGR03020 188 AGLITAREAEILAWVRDG------KTNEEIAAILGISSLTVKNHLQHIFKKLDVRNR 238 (247)
T ss_pred ccCCCHHHHHHHHHHHCC------CCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCCH
Confidence 446889999999865432 235678999999999999999998888765443
No 186
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=27.76 E-value=47 Score=30.03 Aligned_cols=29 Identities=14% Similarity=0.042 Sum_probs=24.4
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKR 384 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR 384 (391)
...+||+.+|++..+|+++...-|.+.|+
T Consensus 148 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 46789999999999999999777776665
No 187
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=27.27 E-value=49 Score=29.42 Aligned_cols=30 Identities=17% Similarity=0.240 Sum_probs=24.6
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
...+||+.+|++..+|+++...-+.+.+..
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~ 166 (172)
T PRK09651 137 TYSEIAHKLGVSVSSVKKYVAKATEHCLLF 166 (172)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 477899999999999999997666666543
No 188
>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=27.26 E-value=62 Score=29.04 Aligned_cols=31 Identities=16% Similarity=0.203 Sum_probs=25.0
Q ss_pred HHHHHHHHHHhCCCCCccccccchhhhHHhh
Q psy17897 354 GEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 384 (391)
Q Consensus 354 ~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR 384 (391)
.....+||+.+|++..+|++++..-|.+.|+
T Consensus 165 ~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 165 GKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3457789999999999999988776666654
No 189
>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=27.11 E-value=20 Score=25.03 Aligned_cols=19 Identities=21% Similarity=0.359 Sum_probs=15.8
Q ss_pred HHHHHHHhCCCCCcccccc
Q psy17897 357 IAAIAEKLDLKKNVVRVWF 375 (391)
Q Consensus 357 r~~LA~qLgLs~~qVrvWF 375 (391)
+.++|+.+|++.++|+.|=
T Consensus 2 i~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 5678999999999999994
No 190
>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=27.00 E-value=53 Score=31.34 Aligned_cols=48 Identities=17% Similarity=0.124 Sum_probs=35.0
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
.+++.++.++...|... ....+||..+|++..+|+.+...-+.|.|+.
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 34566666666665433 2457899999999999999998877777764
No 191
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=26.82 E-value=20 Score=26.60 Aligned_cols=25 Identities=8% Similarity=0.146 Sum_probs=18.3
Q ss_pred HHHHHHHHhCCCCCccccccchhhh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQ 380 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~ 380 (391)
.+..||+.+|++..+|..|+.++..
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~ 36 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPS 36 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT--
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccc
Confidence 4668999999999999999998743
No 192
>PRK10651 transcriptional regulator NarL; Provisional
Probab=26.62 E-value=47 Score=28.95 Aligned_cols=46 Identities=22% Similarity=0.218 Sum_probs=36.1
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhh
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 384 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR 384 (391)
.++..+...|+...+- + ...+||+++++++++|++..+|-|.|..-
T Consensus 155 ~Lt~rE~~vl~~l~~g--~----~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 155 QLTPRERDILKLIAQG--L----PNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred cCCHHHHHHHHHHHcC--C----CHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 4888888888775532 1 35678999999999999999998888654
No 193
>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=26.53 E-value=56 Score=30.42 Aligned_cols=47 Identities=21% Similarity=0.259 Sum_probs=34.4
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhh
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 384 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR 384 (391)
.+++.++..+...|... ....+||+.+|++..+|+.|...-+.|.|+
T Consensus 178 ~L~~~~r~vl~l~y~~~-----~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFFED-----KTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45666666666665332 247789999999999999998776666654
No 194
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=26.46 E-value=32 Score=26.47 Aligned_cols=37 Identities=19% Similarity=0.228 Sum_probs=26.5
Q ss_pred HhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCChh
Q psy17897 244 FKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHN 289 (391)
Q Consensus 244 fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~k 289 (391)
+++.|...|+|..+|+..+. ++..+|..+|.-++..-
T Consensus 2 Lr~~R~~~glsl~~va~~t~---------I~~~~l~aiE~~~~~~l 38 (62)
T PF13413_consen 2 LREAREAKGLSLEDVAEETK---------ISVSYLEAIENGDFDSL 38 (62)
T ss_dssp HHHHHHCTT--HHHHHHHCS-----------HHHHHHHHCT-GCCS
T ss_pred hHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHCcChhhC
Confidence 68899999999999998874 77888888888776653
No 195
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=26.20 E-value=95 Score=29.35 Aligned_cols=70 Identities=17% Similarity=0.176 Sum_probs=44.2
Q ss_pred CHHHHHHHHHHHhhhhHh-----cCccchhhhhhhhcCcCCCCcccccchhhhh-ccCCCChhhhhhhhHHHHHHHHHHH
Q psy17897 233 DPRELEAFAERFKQRRIK-----LGVTQADVGKALANLKLPGVGALSQSTICRF-ESLTLSHNNMIALKPILQAWLEEAE 306 (391)
Q Consensus 233 d~~eLe~Fa~~fkqrRI~-----lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRf-E~LqLS~knm~KLkPlL~kWLeeaE 306 (391)
++++|+-|....+.+-++ |++||.-|.+.+.++. ..+-...+-|- ..+.++. .-.++.+..++++++.+
T Consensus 2 ~l~~L~~f~~v~~~gs~s~AA~~L~isqsavS~~i~~LE----~~lg~~Lf~R~~~~~~lT~-~G~~l~~~~~~il~~~~ 76 (296)
T PRK11242 2 LLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLE----ESLGVQLFDRSGRTVRLTD-AGEVYLRYARRALQDLE 76 (296)
T ss_pred ChHHHHHHHHHHHhCCHHHHHHHcCCCchHHHHHHHHHH----HHhCCeeEeEcCCceeech-hHHHHHHHHHHHHHHHH
Confidence 468899999999998776 6999999999998766 33433333331 1122222 12345556666665554
Q ss_pred H
Q psy17897 307 A 307 (391)
Q Consensus 307 ~ 307 (391)
.
T Consensus 77 ~ 77 (296)
T PRK11242 77 A 77 (296)
T ss_pred H
Confidence 3
No 196
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=26.12 E-value=49 Score=28.27 Aligned_cols=47 Identities=21% Similarity=0.270 Sum_probs=33.7
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
++..+...|+..+... .-..||+.+++++.+|+++-++-|.|.+..+
T Consensus 142 l~~~e~~vl~~~~~~~------~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~ 188 (202)
T PRK09390 142 LSERERQVMDGLVAGL------SNKVIARDLDISPRTVEVYRANVMTKMQAGS 188 (202)
T ss_pred hhhhHHHHHHHHHccC------chHHHHHHcCCCHHHHHHHHHHHHHHHcccc
Confidence 5566666776544322 2456899999999999999988888766543
No 197
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=25.79 E-value=81 Score=28.18 Aligned_cols=30 Identities=20% Similarity=0.284 Sum_probs=24.4
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
...+||..+|++..+|++....-|.+.|+.
T Consensus 155 s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 155 TYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred CHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 467899999999999998887777666654
No 198
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=25.68 E-value=58 Score=28.38 Aligned_cols=45 Identities=13% Similarity=0.085 Sum_probs=30.6
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHh
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQK 383 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~K 383 (391)
+++.++.++...|-.. ....+||+.+|++..+|+++...-+++.+
T Consensus 114 L~~~~r~v~~L~~~~g-----~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 114 LPPLVKRAFLLAQVDG-----LGYGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4455566665544322 24678999999999999999876655543
No 199
>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=25.56 E-value=17 Score=24.77 Aligned_cols=24 Identities=21% Similarity=0.354 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCCCccccccchhhh
Q psy17897 357 IAAIAEKLDLKKNVVRVWFCNQRQ 380 (391)
Q Consensus 357 r~~LA~qLgLs~~qVrvWFqNRR~ 380 (391)
..++|+.+|+++.+|+.|..+.+-
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 467899999999999999766553
No 200
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=25.43 E-value=67 Score=30.25 Aligned_cols=55 Identities=16% Similarity=0.161 Sum_probs=34.2
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHhhh
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFAA 389 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k~a 389 (391)
+++.++.++...|-... -......+||..+|++..+|++|-...+.+.|+.-.++
T Consensus 176 Lp~~~R~i~~l~y~~~~-~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~~~ 230 (233)
T PRK05803 176 LDEREKEVIEMRYGLGN-GKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYRA 230 (233)
T ss_pred CCHHHHHHHHHHhCCCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 34445555555441100 12234678999999999999999766666666655544
No 201
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=25.27 E-value=70 Score=28.99 Aligned_cols=32 Identities=9% Similarity=0.079 Sum_probs=26.4
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
...+||+.+|++..+|++....-|.+.|+.-.
T Consensus 129 s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 129 SYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999877777766543
No 202
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=24.76 E-value=1.2e+02 Score=28.83 Aligned_cols=76 Identities=20% Similarity=0.142 Sum_probs=48.5
Q ss_pred CCCCCHHHHHHHHHHHhhhhHh-----cCccchhhhhhhhcCcCCCCcccccchhhhh-ccCCCChhhhhhhhHHHHHHH
Q psy17897 229 DTDTDPRELEAFAERFKQRRIK-----LGVTQADVGKALANLKLPGVGALSQSTICRF-ESLTLSHNNMIALKPILQAWL 302 (391)
Q Consensus 229 d~~~d~~eLe~Fa~~fkqrRI~-----lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRf-E~LqLS~knm~KLkPlL~kWL 302 (391)
|+..+++.|+-|....+...++ |++||..|.+.+..+. ..+-...+-|- -.+.++. .-..+.+..++++
T Consensus 3 ~~~~~l~~l~~f~~v~~~gs~s~AA~~L~isq~avS~~i~~LE----~~lg~~Lf~R~~r~l~lT~-~G~~l~~~~~~~l 77 (297)
T PRK11139 3 RRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALE----DFLGLKLFRRRNRSLLLTE-EGQRYFLDIREIF 77 (297)
T ss_pred CCCCchHHHHHHHHHHHhCCHHHHHHHhCCChHHHHHHHHHHH----HHhCchheEecCCceeECH-hHHHHHHHHHHHH
Confidence 4456889999999999988775 7999999999997665 22333222221 1122222 1334666777777
Q ss_pred HHHHHHh
Q psy17897 303 EEAEAQA 309 (391)
Q Consensus 303 eeaE~~~ 309 (391)
++.++..
T Consensus 78 ~~~~~~~ 84 (297)
T PRK11139 78 DQLAEAT 84 (297)
T ss_pred HHHHHHH
Confidence 7766543
No 203
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=24.48 E-value=46 Score=28.96 Aligned_cols=45 Identities=22% Similarity=0.212 Sum_probs=35.5
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHh
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQK 383 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~K 383 (391)
.+|+.+...|+..++- ..+.+||+.+++++++|++..+|=|.|..
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 5777888887776543 25778999999999999999988877754
No 204
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=24.35 E-value=69 Score=28.30 Aligned_cols=47 Identities=6% Similarity=0.064 Sum_probs=33.0
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhh
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 384 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR 384 (391)
.+++.++.++...|-.. ....+||+.+|++..+|+++..+-+.+.+.
T Consensus 118 ~L~~~~r~v~~L~~~eg-----~s~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 118 GLSGKARAAFLMSQLEG-----LTYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35566666666544332 246789999999999999998776666554
No 205
>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=23.98 E-value=62 Score=30.72 Aligned_cols=51 Identities=18% Similarity=0.113 Sum_probs=39.6
Q ss_pred CcccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 331 RTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 331 RT~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
...++..++++|.-...- ..-.+||..+++++++|+.+..|-+.|.+..++
T Consensus 169 ~~~Lt~re~evl~~~a~G------~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~ 219 (232)
T TIGR03541 169 AGVLSEREREVLAWTALG------RRQADIAAILGISERTVENHLRSARRKLGVATT 219 (232)
T ss_pred hccCCHHHHHHHHHHHCC------CCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCH
Confidence 346888899988775322 346688999999999999999999888765443
No 206
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=23.97 E-value=92 Score=30.51 Aligned_cols=59 Identities=24% Similarity=0.326 Sum_probs=41.6
Q ss_pred HHHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCChhhhhhhhHHHHHHHHHH
Q psy17897 238 EAFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPILQAWLEEA 305 (391)
Q Consensus 238 e~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~knm~KLkPlL~kWLeea 305 (391)
+.+.+.+|..|.-.++||.+++..|+ .|++.|+.+|.=..-+-...-+|-+.++.++-+
T Consensus 26 ~~pge~lrKWR~~F~vSQ~elA~~l~---------vSpSVISDYE~GRRk~Pg~~~vkk~V~ALIeID 84 (241)
T COG1709 26 EDPGETLRKWREIFNVSQTELARELG---------VSPSVISDYESGRRKSPGIAFVKKFVEALIEID 84 (241)
T ss_pred CChhHHHHHHHHHhCccHHHHHHHhC---------CCcceeehhhccCccCccHHHHHHHHHHHHhhh
Confidence 34667889999999999999999985 889999999876655333333344444444433
No 207
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]
Probab=23.76 E-value=1.4e+02 Score=29.84 Aligned_cols=26 Identities=27% Similarity=0.446 Sum_probs=22.5
Q ss_pred HHHHHHHhhhhHhcCccchhhhhhhh
Q psy17897 238 EAFAERFKQRRIKLGVTQADVGKALA 263 (391)
Q Consensus 238 e~Fa~~fkqrRI~lGlTQ~~Vg~ALg 263 (391)
+.+-..||+.|..+|+|+.+|...+.
T Consensus 2 ~~~Ge~Lr~~Re~~gLsL~dva~~t~ 27 (284)
T COG1426 2 KTLGERLRQAREEKGLSLEDVAARTK 27 (284)
T ss_pred ccHHHHHHHHHHHcCCCHHHHHHHhC
Confidence 34667899999999999999998874
No 208
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=23.25 E-value=48 Score=30.07 Aligned_cols=40 Identities=20% Similarity=0.300 Sum_probs=30.4
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhh
Q psy17897 340 RSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQ 380 (391)
Q Consensus 340 ~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~ 380 (391)
..-.+.|.+..|-. ..+.+||++.|+++.++-.+|.|+..
T Consensus 18 ~aa~~lf~~~G~~~-~ti~~Ia~~agvsk~t~Y~~F~sKe~ 57 (213)
T PRK09975 18 ETAIAQFALRGVSN-TTLNDIADAANVTRGAIYWHFENKTQ 57 (213)
T ss_pred HHHHHHHHHcCccc-CCHHHHHHHcCCCHHHHHHHcCCHHH
Confidence 34445566666544 34778999999999999999999865
No 209
>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=23.07 E-value=87 Score=29.56 Aligned_cols=53 Identities=13% Similarity=0.145 Sum_probs=34.1
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
+++.++.++...|-... -......+||+.+|++..+|+++...-|.+.|+.-+
T Consensus 179 Lp~~~R~ii~L~~~l~~-~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~ 231 (234)
T TIGR02835 179 LNDREKKIMELRFGLVG-GTEKTQKEVADMLGISQSYISRLEKRILKRLKKEIN 231 (234)
T ss_pred CCHHHHHHHHHHHccCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhh
Confidence 44455555554441000 111246789999999999999998877777776544
No 210
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=22.93 E-value=53 Score=28.67 Aligned_cols=46 Identities=22% Similarity=0.100 Sum_probs=35.6
Q ss_pred cccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHh
Q psy17897 332 TSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQK 383 (391)
Q Consensus 332 T~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~K 383 (391)
..++..+...|+...+. ....+||+.++++.++|+++.++-|.|..
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 34777777787654433 34778999999999999999998888754
No 211
>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=22.65 E-value=68 Score=31.29 Aligned_cols=30 Identities=13% Similarity=0.091 Sum_probs=25.8
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhH
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 385 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~ 385 (391)
...+||+.+|+++..|+.++..-|.+.|+.
T Consensus 126 s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 126 PYEEIASIVGKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 367899999999999999998888877764
No 212
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=22.46 E-value=61 Score=27.98 Aligned_cols=39 Identities=15% Similarity=0.339 Sum_probs=0.0
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhh
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQR 379 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR 379 (391)
++..++..+.+.+... +...|..||++..+|+.|=++|+
T Consensus 44 ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~ 82 (104)
T COG2944 44 LSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRK 82 (104)
T ss_pred CCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCc
No 213
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=22.39 E-value=77 Score=30.56 Aligned_cols=49 Identities=16% Similarity=0.127 Sum_probs=35.2
Q ss_pred cChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 334 IAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 334 ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
++..++.++...|.. .....+||..+|++..+|+.+...-+.|.|+.-+
T Consensus 204 L~~~~r~vl~l~y~~-----~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~ 252 (256)
T PRK07408 204 LEERTREVLEFVFLH-----DLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQ 252 (256)
T ss_pred CCHHHHHHHHHHHHC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 345555555555533 2356789999999999999999888877776543
No 214
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=22.32 E-value=72 Score=28.53 Aligned_cols=31 Identities=23% Similarity=0.257 Sum_probs=26.0
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
...+||..+|++..+|+.+...-|.+.|+.-
T Consensus 145 s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 145 SIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999988777777643
No 215
>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=22.16 E-value=66 Score=27.57 Aligned_cols=33 Identities=21% Similarity=0.439 Sum_probs=24.4
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccc
Q psy17897 339 KRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFC 376 (391)
Q Consensus 339 l~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFq 376 (391)
+...-.+++... .+.++|+.++++..+|..||+
T Consensus 8 R~rVl~~~~~g~-----s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 8 RQRVLAYIEKGK-----SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred HHHHHHHHHccc-----hHHHHHHHhCcHHHHHHHHHH
Confidence 333345555532 466789999999999999998
No 216
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=22.08 E-value=68 Score=27.73 Aligned_cols=36 Identities=28% Similarity=0.407 Sum_probs=27.8
Q ss_pred CCCCHHHHHHHHHHHhhhhHh--cCccchhhhhhhhcCcCCCCcccccchhhhh
Q psy17897 230 TDTDPRELEAFAERFKQRRIK--LGVTQADVGKALANLKLPGVGALSQSTICRF 281 (391)
Q Consensus 230 ~~~d~~eLe~Fa~~fkqrRI~--lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRf 281 (391)
+.-..+|+|.+ |+. .|++|.+.+..++ +|++|.+|.
T Consensus 40 V~L~~dElEAi-------RL~D~egl~QeeaA~~Mg---------VSR~T~~ri 77 (106)
T PF02001_consen 40 VVLTVDELEAI-------RLVDYEGLSQEEAAERMG---------VSRPTFQRI 77 (106)
T ss_pred EEeeHHHHHHH-------HHHHHcCCCHHHHHHHcC---------CcHHHHHHH
Confidence 34457889887 554 4999999999985 788888764
No 217
>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=21.97 E-value=42 Score=28.76 Aligned_cols=33 Identities=24% Similarity=0.196 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHHhCCCCCccccccchhhhHHhh
Q psy17897 352 PSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 384 (391)
Q Consensus 352 PS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR 384 (391)
.......+||+.+|+++.+|+++...-|.|.|+
T Consensus 119 ~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 119 FKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344467889999999999999999877777665
No 218
>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=21.85 E-value=34 Score=25.90 Aligned_cols=21 Identities=19% Similarity=0.343 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCCCccccccch
Q psy17897 357 IAAIAEKLDLKKNVVRVWFCN 377 (391)
Q Consensus 357 r~~LA~qLgLs~~qVrvWFqN 377 (391)
+.++|+.+|++..+++.|-.+
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 568899999999999999754
No 219
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=21.83 E-value=70 Score=30.23 Aligned_cols=46 Identities=22% Similarity=0.145 Sum_probs=36.9
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhh
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 384 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR 384 (391)
.+|+.++.+|+...+- ....+||+.|++++.+|+.+..|-..|..-
T Consensus 155 ~Lt~rE~~Vl~l~~~G------~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 155 LLTHREKEILNKLRIG------ASNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred CCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 4888999999887652 235688999999999999999887777654
No 220
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=21.73 E-value=1.2e+02 Score=29.30 Aligned_cols=71 Identities=21% Similarity=0.279 Sum_probs=44.1
Q ss_pred CHHHHHHHHHHHhhhhHh-----cCccchhhhhhhhcCcCCCCcccccchhhhhccCCCChhh-hhhhhHHHHHHHHHHH
Q psy17897 233 DPRELEAFAERFKQRRIK-----LGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNN-MIALKPILQAWLEEAE 306 (391)
Q Consensus 233 d~~eLe~Fa~~fkqrRI~-----lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~kn-m~KLkPlL~kWLeeaE 306 (391)
++++|+-|....+.+-++ ||+||.-|.+.+..+. ..+....+-| ....+.+.. -..+.+..+++++..+
T Consensus 2 ~l~~L~~F~~v~~~~S~s~AA~~L~isQ~avS~~I~~LE----~~lg~~LF~R-~~r~v~lT~~G~~l~~~a~~~l~~~~ 76 (305)
T PRK11233 2 NFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLE----GELNQQLLIR-TKRGVTPTEAGKILYTHARAILRQCE 76 (305)
T ss_pred CHHHHHHHHHHHHcCCHHHHHHHhCCCchHHHHHHHHHH----HHhCCceEEe-CCCCceECHhHHHHHHHHHHHHHHHH
Confidence 578899999988888776 6999999999987665 2233332222 112223222 2346666666666655
Q ss_pred HH
Q psy17897 307 AQ 308 (391)
Q Consensus 307 ~~ 308 (391)
+.
T Consensus 77 ~~ 78 (305)
T PRK11233 77 QA 78 (305)
T ss_pred HH
Confidence 43
No 221
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=21.68 E-value=71 Score=31.18 Aligned_cols=31 Identities=16% Similarity=0.193 Sum_probs=26.3
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
...+||+.+|+++..|++....-|.+.|+..
T Consensus 133 s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~ 163 (293)
T PRK09636 133 PFDEIASTLGRSPAACRQLASRARKHVRAAR 163 (293)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 4678999999999999999988888777643
No 222
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=21.28 E-value=54 Score=30.84 Aligned_cols=36 Identities=14% Similarity=0.148 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 352 PSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 352 PS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
.......+||+.+|++..+|++....-|.|.|+...
T Consensus 163 ~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~ 198 (231)
T PRK11922 163 VEELSVEETAQALGLPEETVKTRLHRARRLLRESLA 198 (231)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 344567889999999999999999888888877654
No 223
>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=21.27 E-value=33 Score=26.11 Aligned_cols=21 Identities=29% Similarity=0.469 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCCCccccccch
Q psy17897 357 IAAIAEKLDLKKNVVRVWFCN 377 (391)
Q Consensus 357 r~~LA~qLgLs~~qVrvWFqN 377 (391)
+.++|+.+|+++.+++.|...
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 568899999999999999753
No 224
>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=21.07 E-value=91 Score=29.52 Aligned_cols=53 Identities=8% Similarity=0.231 Sum_probs=38.5
Q ss_pred ccChHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 333 SIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 333 ~ft~~Ql~~LE~~F~~n~yPS~~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
.+++.++.+|...|-...+ ......+||..+|++...|+.+...-+.|.|...
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 3556677778777732111 1234778999999999999999988888888754
No 225
>KOG3520|consensus
Probab=21.03 E-value=1e+02 Score=36.65 Aligned_cols=76 Identities=22% Similarity=0.188 Sum_probs=46.8
Q ss_pred CHHHHHH----HHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCCCChhhhhhh----hHHHHHHHHH
Q psy17897 233 DPRELEA----FAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIAL----KPILQAWLEE 304 (391)
Q Consensus 233 d~~eLe~----Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~LqLS~knm~KL----kPlL~kWLee 304 (391)
+++||-+ |...+|+||..-.+--..||..|..+|.--....=+.+...||+.+-.--++.|. .+.+++|+.+
T Consensus 437 ~LdeL~eiH~~f~~~lk~rr~e~~~vI~~IGDlLl~~FsGe~ae~L~~~~a~FCs~q~~ALe~~K~k~~KD~rFq~fvkk 516 (1167)
T KOG3520|consen 437 CLDELIEIHSSFLQRLKERRKESLVVIKRIGDLLLDQFSGENAERLKKTYAQFCSRQSIALEQLKTKQAKDKRFQAFVKK 516 (1167)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHcCchHHHHHHHHHHHHhhccHHHHHHHHHHHhccHHHHHHHHH
Confidence 3555544 9999999999877755567877766542100111134445588776544344432 3477889999
Q ss_pred HHHH
Q psy17897 305 AEAQ 308 (391)
Q Consensus 305 aE~~ 308 (391)
+|.+
T Consensus 517 aeS~ 520 (1167)
T KOG3520|consen 517 AESN 520 (1167)
T ss_pred hhcc
Confidence 8865
No 226
>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth. Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor [] reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change []. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement []. This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 5CRO_A 2ECS_A 2OVG_A 6CRO_A 1D1L_A 2ORC_A 1D1M_B 3ORC_A 1ORC_A 2A63_A ....
Probab=21.00 E-value=1e+02 Score=24.07 Aligned_cols=28 Identities=36% Similarity=0.541 Sum_probs=22.5
Q ss_pred HHHHHHHHhhhhHh--cCccchhhhhhhhc
Q psy17897 237 LEAFAERFKQRRIK--LGVTQADVGKALAN 264 (391)
Q Consensus 237 Le~Fa~~fkqrRI~--lGlTQ~~Vg~ALg~ 264 (391)
|.+|+++.-|.... +|++|.-|.+|+..
T Consensus 6 L~eyv~~~GQ~kaA~~lGV~Q~AIsKAlr~ 35 (59)
T PF09048_consen 6 LAEYVKEHGQAKAARALGVTQSAISKALRA 35 (59)
T ss_dssp HHHHHHHHHHHHHHHHHTS-HHHHHHHHHC
T ss_pred HHHHHHHhChHHHHHHcCCcHHHHHHHHHc
Confidence 78899999887655 79999999999964
No 227
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=20.99 E-value=1e+02 Score=27.99 Aligned_cols=31 Identities=16% Similarity=0.236 Sum_probs=23.2
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHH
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 386 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~ 386 (391)
...+||..+|++..+|++=...-|.+.|+.-
T Consensus 152 s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l 182 (192)
T PRK09643 152 SVADAARMLGVAEGTVKSRCARGRARLAELL 182 (192)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999776655566655543
No 228
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=20.85 E-value=99 Score=28.11 Aligned_cols=32 Identities=34% Similarity=0.289 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 356 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 356 er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
...+||..+|++...|+++..--|.+.++.-+
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (188)
T PRK12517 146 SGEEIAEILDLNKNTVMTRLFRARNQLKEALE 177 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999877777776544
No 229
>PRK02866 cyanate hydratase; Validated
Probab=20.74 E-value=1.5e+02 Score=27.18 Aligned_cols=51 Identities=20% Similarity=0.234 Sum_probs=33.6
Q ss_pred HHHHHHhhhhHhcCccchhhhhhhhcCcCCCCcccccchhhhhccCC--CChhhhhhhhHHH
Q psy17897 239 AFAERFKQRRIKLGVTQADVGKALANLKLPGVGALSQSTICRFESLT--LSHNNMIALKPIL 298 (391)
Q Consensus 239 ~Fa~~fkqrRI~lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRfE~Lq--LS~knm~KLkPlL 298 (391)
+..+.+.+.|++.|+|+.+++.++| +|..++.-.+.-| ++...+.++..+|
T Consensus 5 ~~~e~Ll~AK~~kGLTw~~IA~~iG---------~S~v~vaaa~lGQ~~ls~e~A~kla~~L 57 (147)
T PRK02866 5 ELTEKILAAKKEKGLTWADIAEAIG---------LSEVWVTAALLGQMTLPAEEAEKVAELL 57 (147)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhC---------CCHHHHHHHHhCCCCCCHHHHHHHHHHh
Confidence 4466788889999999999999996 5555555544433 4444444444433
No 230
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=20.69 E-value=1.5e+02 Score=28.54 Aligned_cols=38 Identities=21% Similarity=0.222 Sum_probs=32.4
Q ss_pred CCCCCHHHHHHHHHHHhhhhHh-----cCccchhhhhhhhcCc
Q psy17897 229 DTDTDPRELEAFAERFKQRRIK-----LGVTQADVGKALANLK 266 (391)
Q Consensus 229 d~~~d~~eLe~Fa~~fkqrRI~-----lGlTQ~~Vg~ALg~l~ 266 (391)
|...+++.|+-|....+.+.++ +++||..|.+.+..+.
T Consensus 2 ~~~~~l~~L~~f~~v~e~gs~s~AA~~L~isqpavS~~i~~LE 44 (305)
T CHL00180 2 DLPFTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLE 44 (305)
T ss_pred CCcccHHHHHHHHHHHHcCCHHHHHHHhcCCChHHHHHHHHHH
Confidence 4567889999999999999877 6999999999997665
No 231
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=20.56 E-value=53 Score=29.59 Aligned_cols=33 Identities=9% Similarity=0.118 Sum_probs=27.7
Q ss_pred HHHHHHHHHhCCCCCccccccchhhhHHhhHHh
Q psy17897 355 EKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKF 387 (391)
Q Consensus 355 ~er~~LA~qLgLs~~qVrvWFqNRR~K~KR~~k 387 (391)
....+||..+|++..+|++|...-|.+.|+.-.
T Consensus 151 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 183 (188)
T PRK09640 151 LEFQEIADIMHMGLSATKMRYKRALDKLREKFA 183 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999999888888777544
No 232
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=20.44 E-value=1.5e+02 Score=28.77 Aligned_cols=74 Identities=20% Similarity=0.317 Sum_probs=46.4
Q ss_pred CCCCHHHHHHHHHHHhhhhHh-----cCccchhhhhhhhcCcCCCCcccccchhhhh-ccCCCChhhhhhhhHHHHHHHH
Q psy17897 230 TDTDPRELEAFAERFKQRRIK-----LGVTQADVGKALANLKLPGVGALSQSTICRF-ESLTLSHNNMIALKPILQAWLE 303 (391)
Q Consensus 230 ~~~d~~eLe~Fa~~fkqrRI~-----lGlTQ~~Vg~ALg~l~~~G~~~fSQstIcRf-E~LqLS~knm~KLkPlL~kWLe 303 (391)
.+-|++.|+-|....+..-++ +++||..|.+++..+. ..|.-...-|- -.+.++. .-..+.+.+..+++
T Consensus 6 ~~mdl~~L~~f~av~e~gs~t~AA~~L~iSQpavS~~I~~LE----~~lg~~LF~R~~r~~~lT~-~G~~l~~~~~~~~~ 80 (319)
T PRK10216 6 TTLDLNLLLCLQLLMQERSVTKAAKRMNVTPSAVSKSLAKLR----AWFDDPLFVNTPLGLSPTP-LMVSMEQNLAEWMQ 80 (319)
T ss_pred hhcCHHHHHHHHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHH----HHhCCceEEecCCCcccCH-HHHHHHHHHHHHHH
Confidence 345789999999999888776 6999999999997665 22322222221 1122222 12346677777776
Q ss_pred HHHHH
Q psy17897 304 EAEAQ 308 (391)
Q Consensus 304 eaE~~ 308 (391)
..+.-
T Consensus 81 ~~~~~ 85 (319)
T PRK10216 81 MGNQL 85 (319)
T ss_pred HHHHH
Confidence 55543
No 233
>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=20.44 E-value=40 Score=23.88 Aligned_cols=18 Identities=17% Similarity=0.084 Sum_probs=7.4
Q ss_pred HHHHhCCCCCccccccch
Q psy17897 360 IAEKLDLKKNVVRVWFCN 377 (391)
Q Consensus 360 LA~qLgLs~~qVrvWFqN 377 (391)
||+.+|++..+|..|+.+
T Consensus 3 lA~~~gvs~~tvs~~l~g 20 (52)
T cd01392 3 IARAAGVSVATVSRVLNG 20 (52)
T ss_pred HHHHHCcCHHHHHHHHcC
Confidence 344444444444444433
No 234
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=20.28 E-value=1.3e+02 Score=28.90 Aligned_cols=34 Identities=21% Similarity=0.349 Sum_probs=29.2
Q ss_pred CHHHHHHHHHHHhhhhHh-----cCccchhhhhhhhcCc
Q psy17897 233 DPRELEAFAERFKQRRIK-----LGVTQADVGKALANLK 266 (391)
Q Consensus 233 d~~eLe~Fa~~fkqrRI~-----lGlTQ~~Vg~ALg~l~ 266 (391)
+++.|+.|....+...++ |++||..|.+.+..++
T Consensus 2 ~l~~L~~f~~v~~~gS~s~AA~~L~itQpavS~~i~~LE 40 (305)
T PRK11151 2 NIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLE 40 (305)
T ss_pred CHHHHHHHHHHHHhCCHHHHHHHhCCCchHHHHHHHHHH
Confidence 478899999999998887 6999999999997665
Done!