Query 046732
Match_columns 516
No_of_seqs 274 out of 1668
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 03:57:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046732.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046732hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4585 Predicted transposase 100.0 8.6E-40 1.9E-44 335.2 11.8 297 193-507 7-321 (326)
2 PF13359 DDE_Tnp_4: DDE superf 100.0 1.1E-36 2.3E-41 281.8 1.1 154 304-461 1-158 (158)
3 PF04827 Plant_tran: Plant tra 100.0 1.5E-31 3.2E-36 250.0 4.6 185 274-466 2-200 (205)
4 PF13612 DDE_Tnp_1_3: Transpos 98.8 7.1E-10 1.5E-14 102.9 1.1 135 297-440 3-150 (155)
5 PF13613 HTH_Tnp_4: Helix-turn 98.7 8.9E-09 1.9E-13 78.4 2.2 51 222-272 2-52 (53)
6 PF01609 DDE_Tnp_1: Transposas 97.7 2.3E-06 5.1E-11 80.8 -3.7 151 299-462 4-213 (213)
7 PF13586 DDE_Tnp_1_2: Transpos 96.6 0.00069 1.5E-08 56.8 0.4 73 385-458 1-83 (88)
8 PF04218 CENP-B_N: CENP-B N-te 94.5 0.014 3.1E-07 44.3 0.7 42 220-262 4-45 (53)
9 PF04545 Sigma70_r4: Sigma-70, 93.3 0.062 1.3E-06 39.9 2.2 45 222-267 4-48 (50)
10 PF02796 HTH_7: Helix-turn-hel 92.7 0.026 5.6E-07 41.3 -0.6 39 222-261 5-43 (45)
11 PF13936 HTH_38: Helix-turn-he 92.1 0.04 8.6E-07 40.2 -0.2 40 222-262 4-43 (44)
12 PF13340 DUF4096: Putative tra 90.2 0.34 7.3E-06 39.3 3.5 64 197-264 2-65 (75)
13 PF12116 SpoIIID: Stage III sp 90.1 0.089 1.9E-06 43.2 -0.0 44 229-272 9-52 (82)
14 PF08281 Sigma70_r4_2: Sigma-7 89.7 0.21 4.5E-06 37.5 1.8 43 222-265 10-52 (54)
15 PF13518 HTH_28: Helix-turn-he 89.5 0.13 2.8E-06 38.0 0.5 37 228-265 2-38 (52)
16 PF02209 VHP: Villin headpiece 88.9 0.27 5.9E-06 34.4 1.7 22 185-206 2-23 (36)
17 PF13384 HTH_23: Homeodomain-l 88.1 0.1 2.2E-06 38.5 -0.9 37 227-264 6-42 (50)
18 smart00153 VHP Villin headpiec 87.4 0.44 9.6E-06 33.4 2.0 21 185-205 2-22 (36)
19 smart00351 PAX Paired Box doma 86.7 0.36 7.9E-06 43.2 1.7 43 221-264 16-58 (125)
20 cd00569 HTH_Hin_like Helix-tur 86.3 0.42 9.1E-06 31.2 1.5 37 222-259 5-41 (42)
21 PF05225 HTH_psq: helix-turn-h 85.8 0.24 5.3E-06 36.3 0.1 36 226-261 2-38 (45)
22 PF13011 LZ_Tnp_IS481: leucine 85.3 0.53 1.1E-05 39.4 1.8 47 218-264 4-50 (85)
23 cd00131 PAX Paired Box domain 84.4 0.61 1.3E-05 42.0 2.0 45 220-265 15-59 (128)
24 PRK04217 hypothetical protein; 83.4 0.76 1.7E-05 40.4 2.1 50 221-271 41-90 (110)
25 PRK09413 IS2 repressor TnpA; R 83.3 0.77 1.7E-05 40.8 2.1 46 220-265 10-55 (121)
26 smart00421 HTH_LUXR helix_turn 83.0 0.76 1.7E-05 33.8 1.7 44 222-267 3-46 (58)
27 COG3415 Transposase and inacti 82.3 0.55 1.2E-05 42.9 0.8 43 222-264 4-46 (138)
28 PRK09639 RNA polymerase sigma 82.1 0.87 1.9E-05 41.8 2.1 48 222-271 112-159 (166)
29 cd06171 Sigma70_r4 Sigma70, re 81.3 0.91 2E-05 32.7 1.6 42 223-265 11-52 (55)
30 PF00872 Transposase_mut: Tran 81.2 1 2.2E-05 48.0 2.5 129 235-402 110-248 (381)
31 PRK00118 putative DNA-binding 80.5 1.1 2.4E-05 38.9 2.0 48 222-270 17-64 (104)
32 PF01527 HTH_Tnp_1: Transposas 79.4 0.48 1E-05 37.9 -0.6 45 220-264 4-48 (76)
33 PRK07037 extracytoplasmic-func 78.7 1.3 2.7E-05 40.6 1.9 49 222-271 109-157 (163)
34 PRK12515 RNA polymerase sigma 78.5 1.3 2.8E-05 41.9 2.0 49 222-271 131-179 (189)
35 PRK12529 RNA polymerase sigma 78.2 1.5 3.2E-05 41.2 2.3 48 222-270 127-174 (178)
36 TIGR02985 Sig70_bacteroi1 RNA 78.1 1.4 3.1E-05 39.6 2.1 47 222-269 113-159 (161)
37 TIGR02531 yecD_yerC TrpR-relat 77.9 1.2 2.5E-05 37.6 1.3 31 230-260 41-71 (88)
38 TIGR02952 Sig70_famx2 RNA poly 77.5 1.5 3.3E-05 40.2 2.1 47 222-269 122-168 (170)
39 PRK09652 RNA polymerase sigma 77.5 1.3 2.7E-05 41.0 1.6 49 222-271 128-176 (182)
40 PRK09047 RNA polymerase factor 77.2 1.5 3.2E-05 39.9 2.0 50 222-272 106-155 (161)
41 TIGR01321 TrpR trp operon repr 77.1 1.5 3.3E-05 37.4 1.8 38 223-260 33-76 (94)
42 TIGR02937 sigma70-ECF RNA poly 76.9 1.5 3.4E-05 38.5 1.9 46 223-269 111-156 (158)
43 TIGR00721 tfx DNA-binding prot 76.7 2.5 5.5E-05 38.6 3.3 71 221-293 5-85 (137)
44 PRK08301 sporulation sigma fac 76.7 1.6 3.4E-05 42.9 2.1 50 222-271 178-230 (234)
45 PRK12547 RNA polymerase sigma 76.2 1.7 3.7E-05 40.1 2.1 49 222-271 112-160 (164)
46 TIGR02960 SigX5 RNA polymerase 75.9 3 6.5E-05 42.9 4.0 50 222-272 142-191 (324)
47 TIGR03879 near_KaiC_dom probab 75.6 1.2 2.5E-05 36.3 0.7 41 222-262 15-55 (73)
48 cd06170 LuxR_C_like C-terminal 75.6 1.9 4.2E-05 31.7 1.9 43 224-268 2-44 (57)
49 cd06571 Bac_DnaA_C C-terminal 75.2 2.4 5.2E-05 35.6 2.5 49 221-269 26-75 (90)
50 PRK12532 RNA polymerase sigma 74.8 1.5 3.3E-05 41.6 1.4 50 222-272 136-185 (195)
51 TIGR02392 rpoH_proteo alternat 74.5 2 4.4E-05 43.3 2.3 49 222-270 218-267 (270)
52 PRK05803 sporulation sigma fac 74.5 2 4.2E-05 42.3 2.1 49 222-270 175-226 (233)
53 PRK12514 RNA polymerase sigma 74.4 2 4.4E-05 40.0 2.1 48 222-270 129-176 (179)
54 PRK12533 RNA polymerase sigma 74.1 1.8 4E-05 42.3 1.8 49 222-271 134-182 (216)
55 PRK12520 RNA polymerase sigma 73.9 1.8 4E-05 40.9 1.7 51 222-273 131-181 (191)
56 PRK12530 RNA polymerase sigma 73.7 1.9 4.2E-05 40.9 1.8 49 222-271 134-182 (189)
57 PRK09638 RNA polymerase sigma 72.9 1.5 3.2E-05 40.7 0.7 48 222-270 126-173 (176)
58 PRK11924 RNA polymerase sigma 72.8 1.9 4.1E-05 39.6 1.5 49 222-271 125-173 (179)
59 TIGR02999 Sig-70_X6 RNA polyme 72.8 2.4 5.1E-05 39.6 2.1 48 222-270 134-181 (183)
60 TIGR02989 Sig-70_gvs1 RNA poly 72.4 2.3 5.1E-05 38.5 2.0 47 222-269 111-157 (159)
61 PRK12516 RNA polymerase sigma 72.3 2.3 5E-05 40.4 1.9 49 222-271 116-164 (187)
62 PRK12528 RNA polymerase sigma 72.2 2.3 5.1E-05 38.9 1.9 46 222-268 113-158 (161)
63 PRK12524 RNA polymerase sigma 72.0 2.3 5E-05 40.4 1.9 49 222-271 136-184 (196)
64 PF13542 HTH_Tnp_ISL3: Helix-t 71.9 1.2 2.5E-05 33.0 -0.1 30 234-263 22-51 (52)
65 PRK12511 RNA polymerase sigma 71.8 2.4 5.1E-05 40.2 1.9 49 222-271 111-159 (182)
66 TIGR02846 spore_sigmaK RNA pol 71.8 2.7 5.8E-05 41.2 2.3 50 222-271 174-226 (227)
67 PRK03975 tfx putative transcri 71.1 3.7 8E-05 37.7 2.9 72 221-294 5-86 (141)
68 PRK12537 RNA polymerase sigma 71.0 2.7 5.8E-05 39.5 2.1 48 222-270 133-180 (182)
69 PRK06704 RNA polymerase factor 70.9 3 6.5E-05 41.3 2.5 89 222-314 116-209 (228)
70 PRK01381 Trp operon repressor; 70.5 3.8 8.3E-05 35.3 2.6 24 237-260 53-76 (99)
71 PRK06596 RNA polymerase factor 70.4 2.9 6.2E-05 42.7 2.3 49 222-270 230-279 (284)
72 PRK12512 RNA polymerase sigma 70.3 2.8 6.1E-05 39.2 2.0 50 222-272 131-180 (184)
73 PRK09642 RNA polymerase sigma 70.2 2.7 5.8E-05 38.4 1.8 49 222-271 106-154 (160)
74 TIGR02950 SigM_subfam RNA poly 70.1 1.3 2.9E-05 39.9 -0.2 46 223-269 106-151 (154)
75 PRK09415 RNA polymerase factor 69.9 2.6 5.6E-05 39.5 1.7 49 222-271 127-175 (179)
76 TIGR02984 Sig-70_plancto1 RNA 69.6 3.1 6.7E-05 38.9 2.2 47 222-269 140-186 (189)
77 TIGR03001 Sig-70_gmx1 RNA poly 69.5 2 4.4E-05 42.8 0.9 50 222-272 161-210 (244)
78 PRK12519 RNA polymerase sigma 69.5 2.6 5.7E-05 39.8 1.6 49 222-271 141-189 (194)
79 PRK09645 RNA polymerase sigma 69.3 3.4 7.5E-05 38.2 2.4 50 222-272 118-167 (173)
80 PRK05911 RNA polymerase sigma 69.3 2.9 6.3E-05 41.9 2.0 49 222-271 205-253 (257)
81 PRK07408 RNA polymerase sigma 69.3 3 6.6E-05 41.8 2.1 49 222-271 203-251 (256)
82 PRK12534 RNA polymerase sigma 69.0 3.4 7.3E-05 38.8 2.3 48 222-270 137-184 (187)
83 PRK12540 RNA polymerase sigma 68.9 2.9 6.3E-05 39.5 1.8 50 222-272 111-160 (182)
84 TIGR02983 SigE-fam_strep RNA p 68.8 2.9 6.4E-05 38.1 1.8 49 222-271 110-158 (162)
85 PRK09641 RNA polymerase sigma 68.7 2.8 6.1E-05 39.1 1.7 48 222-270 136-183 (187)
86 TIGR02393 RpoD_Cterm RNA polym 68.2 2.6 5.6E-05 41.7 1.4 49 222-270 176-227 (238)
87 PRK12544 RNA polymerase sigma 68.2 2.6 5.6E-05 40.8 1.3 49 222-271 148-196 (206)
88 TIGR02980 SigBFG RNA polymeras 67.8 3.4 7.4E-05 40.3 2.1 47 222-269 178-224 (227)
89 PRK05572 sporulation sigma fac 67.7 3.4 7.5E-05 41.1 2.2 49 222-271 202-250 (252)
90 PRK12525 RNA polymerase sigma 67.7 3.6 7.8E-05 38.1 2.1 48 222-270 118-165 (168)
91 PF13751 DDE_Tnp_1_6: Transpos 67.5 2.6 5.6E-05 37.2 1.1 49 415-464 74-123 (125)
92 PRK12523 RNA polymerase sigma 67.5 3.4 7.4E-05 38.3 1.9 49 222-271 119-167 (172)
93 PRK12531 RNA polymerase sigma 67.4 3.4 7.4E-05 39.2 2.0 49 222-271 141-189 (194)
94 PRK12536 RNA polymerase sigma 67.3 3.5 7.6E-05 38.6 2.0 49 222-271 129-177 (181)
95 PRK12546 RNA polymerase sigma 66.9 3.5 7.7E-05 39.2 2.0 49 222-271 113-161 (188)
96 PRK08583 RNA polymerase sigma 66.8 3.6 7.8E-05 41.0 2.1 49 222-271 205-253 (257)
97 TIGR02939 RpoE_Sigma70 RNA pol 66.6 3.1 6.8E-05 38.9 1.5 49 222-271 138-186 (190)
98 PRK13919 putative RNA polymera 66.3 4.1 8.8E-05 38.1 2.2 49 222-271 135-183 (186)
99 TIGR02885 spore_sigF RNA polym 66.0 3.9 8.6E-05 40.0 2.2 47 222-269 183-229 (231)
100 TIGR02394 rpoS_proteo RNA poly 65.9 3.9 8.5E-05 41.6 2.2 50 222-271 222-274 (285)
101 PRK09643 RNA polymerase sigma 65.8 3.7 8.1E-05 39.0 1.9 49 222-271 134-182 (192)
102 PRK07500 rpoH2 RNA polymerase 65.7 4 8.7E-05 41.8 2.2 50 222-271 227-277 (289)
103 PRK12539 RNA polymerase sigma 65.5 4 8.6E-05 38.4 2.0 49 222-271 131-179 (184)
104 PRK05602 RNA polymerase sigma 65.3 3.8 8.3E-05 38.5 1.8 49 222-271 128-176 (186)
105 TIGR02835 spore_sigmaE RNA pol 65.2 4.3 9.3E-05 40.0 2.2 49 222-270 178-229 (234)
106 COG1595 RpoE DNA-directed RNA 65.2 3.8 8.2E-05 38.5 1.8 49 222-271 127-175 (182)
107 PRK09649 RNA polymerase sigma 65.0 4.1 8.9E-05 38.4 2.0 47 222-269 130-176 (185)
108 PRK12545 RNA polymerase sigma 64.9 3.5 7.5E-05 39.5 1.5 49 222-271 139-187 (201)
109 TIGR02948 SigW_bacill RNA poly 64.5 3.8 8.3E-05 38.2 1.7 49 222-271 136-184 (187)
110 PRK09637 RNA polymerase sigma 64.5 4.3 9.2E-05 38.3 2.0 49 222-271 106-154 (181)
111 TIGR02954 Sig70_famx3 RNA poly 64.4 4.6 9.9E-05 37.2 2.1 49 222-271 119-167 (169)
112 PRK12543 RNA polymerase sigma 63.9 4.3 9.2E-05 38.0 1.9 49 222-271 117-165 (179)
113 PHA00675 hypothetical protein 63.7 3.7 8E-05 33.6 1.2 41 221-261 21-61 (78)
114 PRK08215 sporulation sigma fac 63.2 4.8 0.0001 40.2 2.2 47 222-269 209-255 (258)
115 PRK06986 fliA flagellar biosyn 63.0 4.7 0.0001 39.6 2.1 49 222-271 184-232 (236)
116 PF01371 Trp_repressor: Trp re 63.0 2.7 5.9E-05 35.4 0.3 33 227-259 37-69 (87)
117 PF01710 HTH_Tnp_IS630: Transp 62.9 7.3 0.00016 34.4 3.1 77 185-263 19-95 (119)
118 PHA00542 putative Cro-like pro 62.8 2.9 6.3E-05 34.5 0.4 53 230-294 22-74 (82)
119 TIGR02943 Sig70_famx1 RNA poly 62.1 4.1 8.9E-05 38.6 1.4 49 222-271 131-179 (188)
120 PRK06030 hypothetical protein; 61.2 8.9 0.00019 34.4 3.3 45 221-265 51-95 (124)
121 PRK09644 RNA polymerase sigma 61.2 4.5 9.8E-05 37.2 1.5 49 222-271 108-156 (165)
122 PRK12527 RNA polymerase sigma 61.1 5.2 0.00011 36.4 1.9 48 223-271 106-153 (159)
123 TIGR02941 Sigma_B RNA polymera 61.1 5.6 0.00012 39.6 2.2 47 222-269 205-251 (255)
124 PF13701 DDE_Tnp_1_4: Transpos 61.0 41 0.00088 36.8 9.0 87 298-392 140-229 (448)
125 TIGR02850 spore_sigG RNA polym 60.9 5.8 0.00013 39.6 2.3 47 222-269 206-252 (254)
126 PRK06811 RNA polymerase factor 60.9 5.4 0.00012 37.7 2.0 47 222-269 131-177 (189)
127 PRK06930 positive control sigm 60.5 5.4 0.00012 37.7 1.9 49 222-271 114-162 (170)
128 TIGR02947 SigH_actino RNA poly 60.5 3.5 7.7E-05 39.0 0.7 49 222-271 131-179 (193)
129 PF12802 MarR_2: MarR family; 60.5 4.4 9.6E-05 30.7 1.1 25 240-264 22-46 (62)
130 PRK08295 RNA polymerase factor 60.4 5.4 0.00012 38.0 1.9 48 222-271 155-202 (208)
131 PRK06759 RNA polymerase factor 60.4 5.5 0.00012 35.9 1.9 46 222-268 106-151 (154)
132 PRK07670 RNA polymerase sigma 59.9 6.1 0.00013 39.3 2.3 48 222-270 201-248 (251)
133 TIGR02844 spore_III_D sporulat 59.9 3.4 7.3E-05 34.2 0.3 35 227-261 6-41 (80)
134 TIGR03697 NtcA_cyano global ni 59.1 3.4 7.4E-05 38.6 0.3 101 183-284 71-188 (193)
135 PRK11923 algU RNA polymerase s 58.8 5.6 0.00012 37.5 1.7 49 222-271 138-186 (193)
136 TIGR02959 SigZ RNA polymerase 58.7 6.3 0.00014 36.6 2.0 49 222-271 100-148 (170)
137 PRK09646 RNA polymerase sigma 58.0 6.9 0.00015 37.1 2.2 49 222-271 142-190 (194)
138 PRK07122 RNA polymerase sigma 57.6 6.9 0.00015 39.5 2.2 47 222-269 215-261 (264)
139 PRK12542 RNA polymerase sigma 57.4 6.4 0.00014 36.9 1.8 49 222-271 122-170 (185)
140 PRK11753 DNA-binding transcrip 57.2 5.3 0.00011 38.0 1.2 80 185-264 99-193 (211)
141 TIGR02997 Sig70-cyanoRpoD RNA 57.1 6.2 0.00013 40.5 1.8 44 222-265 249-295 (298)
142 PRK12538 RNA polymerase sigma 57.0 5.7 0.00012 39.3 1.5 49 222-271 171-219 (233)
143 COG1191 FliA DNA-directed RNA 56.9 7 0.00015 39.3 2.1 49 222-271 196-244 (247)
144 PRK12526 RNA polymerase sigma 56.8 6.8 0.00015 37.7 2.0 49 222-271 153-201 (206)
145 TIGR03209 P21_Cbot clostridium 56.5 6.4 0.00014 35.2 1.6 35 222-257 107-141 (142)
146 PF07374 DUF1492: Protein of u 56.4 6 0.00013 33.9 1.3 41 224-265 57-97 (100)
147 PF13730 HTH_36: Helix-turn-he 56.3 5.5 0.00012 29.7 1.0 38 227-264 8-50 (55)
148 TIGR02479 FliA_WhiG RNA polyme 56.3 7.7 0.00017 37.8 2.2 47 222-269 175-221 (224)
149 COG5421 Transposase [DNA repli 56.2 18 0.0004 39.4 5.2 59 332-393 152-211 (480)
150 PF00196 GerE: Bacterial regul 56.2 3.5 7.6E-05 31.4 -0.1 43 223-267 4-46 (58)
151 PRK15320 transcriptional activ 55.9 4.7 0.0001 39.1 0.6 46 221-268 163-208 (251)
152 PRK12535 RNA polymerase sigma 55.5 7.6 0.00016 37.1 2.0 50 222-272 133-182 (196)
153 PF04967 HTH_10: HTH DNA bindi 55.2 4.5 9.6E-05 30.9 0.3 29 239-267 23-51 (53)
154 PRK10402 DNA-binding transcrip 55.0 8.9 0.00019 37.3 2.4 104 185-289 109-219 (226)
155 PF00356 LacI: Bacterial regul 55.0 2.6 5.5E-05 31.1 -1.0 21 242-262 2-22 (46)
156 PRK12522 RNA polymerase sigma 54.8 7.2 0.00016 36.1 1.7 48 223-271 120-167 (173)
157 PRK09648 RNA polymerase sigma 54.3 8.2 0.00018 36.3 2.0 48 222-270 139-186 (189)
158 PRK07405 RNA polymerase sigma 54.3 8.5 0.00018 40.0 2.3 48 222-269 256-306 (317)
159 PF13412 HTH_24: Winged helix- 53.8 6.9 0.00015 28.4 1.1 36 228-264 7-42 (48)
160 PRK12541 RNA polymerase sigma 53.2 8.3 0.00018 35.2 1.8 47 222-269 112-158 (161)
161 PF13551 HTH_29: Winged helix- 53.1 4.8 0.0001 34.2 0.2 34 232-265 4-38 (112)
162 PF09339 HTH_IclR: IclR helix- 52.6 4.5 9.8E-05 30.1 -0.0 37 228-264 4-43 (52)
163 cd00092 HTH_CRP helix_turn_hel 52.6 5 0.00011 30.8 0.2 27 239-265 25-51 (67)
164 PRK12518 RNA polymerase sigma 52.3 4.9 0.00011 37.2 0.1 50 222-272 120-169 (175)
165 PRK09636 RNA polymerase sigma 52.2 16 0.00035 37.1 4.0 68 222-293 115-182 (293)
166 PRK11922 RNA polymerase sigma 52.1 6.2 0.00013 38.7 0.8 49 222-271 149-197 (231)
167 PF01325 Fe_dep_repress: Iron 51.4 7.4 0.00016 30.2 1.0 40 225-264 5-47 (60)
168 PRK08241 RNA polymerase factor 51.4 11 0.00023 39.1 2.5 73 222-296 153-228 (339)
169 PF01047 MarR: MarR family; I 51.2 6.4 0.00014 29.7 0.6 28 237-264 15-42 (59)
170 smart00342 HTH_ARAC helix_turn 50.9 17 0.00037 28.4 3.1 71 187-264 4-76 (84)
171 TIGR02957 SigX4 RNA polymerase 50.4 18 0.0004 36.6 4.0 68 222-293 108-175 (281)
172 PF01022 HTH_5: Bacterial regu 50.3 6.6 0.00014 28.6 0.5 28 237-264 13-40 (47)
173 PRK12517 RNA polymerase sigma 48.9 10 0.00022 35.9 1.8 49 222-271 128-176 (188)
174 smart00346 HTH_ICLR helix_turn 48.8 8.3 0.00018 31.6 1.0 39 227-265 5-46 (91)
175 PRK05657 RNA polymerase sigma 48.7 12 0.00025 39.1 2.2 50 222-271 262-314 (325)
176 TIGR02859 spore_sigH RNA polym 48.6 9.9 0.00021 35.8 1.6 41 227-269 155-195 (198)
177 COG2963 Transposase and inacti 48.5 10 0.00022 33.0 1.5 46 220-265 5-51 (116)
178 PRK12513 RNA polymerase sigma 48.3 7.2 0.00016 36.8 0.6 49 222-271 139-187 (194)
179 PRK13870 transcriptional regul 47.8 19 0.00041 35.7 3.5 46 221-268 172-217 (234)
180 PRK15418 transcriptional regul 47.8 13 0.00027 38.8 2.3 69 231-303 21-89 (318)
181 PF08299 Bac_DnaA_C: Bacterial 47.3 6.7 0.00015 31.4 0.2 41 222-262 28-69 (70)
182 COG2390 DeoR Transcriptional r 47.1 12 0.00027 39.0 2.1 69 231-303 18-86 (321)
183 PRK06288 RNA polymerase sigma 46.6 12 0.00025 37.7 1.8 49 222-271 212-260 (268)
184 PRK09651 RNA polymerase sigma 45.0 12 0.00027 34.6 1.6 47 222-269 119-165 (172)
185 PF07638 Sigma70_ECF: ECF sigm 44.6 15 0.00032 34.9 2.1 46 223-269 136-181 (185)
186 PRK09635 sigI RNA polymerase s 44.1 24 0.00052 36.1 3.7 68 222-293 118-185 (290)
187 PRK12427 flagellar biosynthesi 44.1 15 0.00032 36.3 2.1 45 222-267 183-227 (231)
188 PRK07406 RNA polymerase sigma 43.7 14 0.00031 39.3 2.0 48 222-269 311-361 (373)
189 PRK09191 two-component respons 43.3 24 0.00053 34.3 3.5 52 222-274 88-139 (261)
190 TIGR01636 phage_rinA phage tra 43.0 18 0.0004 32.6 2.4 48 223-270 83-131 (134)
191 PRK09392 ftrB transcriptional 42.8 13 0.00029 36.1 1.5 101 185-286 107-219 (236)
192 PRK09210 RNA polymerase sigma 42.1 16 0.00034 38.8 2.0 48 222-269 305-355 (367)
193 PF08279 HTH_11: HTH domain; 41.7 12 0.00026 27.8 0.8 28 238-265 14-41 (55)
194 COG3293 Transposase and inacti 41.3 6.6 0.00014 34.6 -0.8 89 338-441 2-101 (124)
195 PRK09640 RNA polymerase sigma 41.1 8.2 0.00018 36.4 -0.3 48 223-271 135-182 (188)
196 PRK09647 RNA polymerase sigma 41.0 15 0.00033 35.3 1.6 49 222-271 138-186 (203)
197 PRK07598 RNA polymerase sigma 40.8 16 0.00036 39.4 1.9 47 222-268 350-399 (415)
198 COG2739 Uncharacterized protei 40.7 15 0.00032 31.8 1.2 42 227-269 22-63 (105)
199 PRK11161 fumarate/nitrate redu 40.6 12 0.00025 36.4 0.7 101 185-286 114-231 (235)
200 PRK05949 RNA polymerase sigma 40.3 19 0.00041 37.6 2.3 48 222-269 266-316 (327)
201 PRK03573 transcriptional regul 40.3 16 0.00034 32.9 1.5 42 223-264 29-71 (144)
202 PF01710 HTH_Tnp_IS630: Transp 40.0 7.3 0.00016 34.4 -0.8 38 222-262 4-41 (119)
203 PF13463 HTH_27: Winged helix 38.8 11 0.00024 29.1 0.2 33 233-265 9-44 (68)
204 smart00550 Zalpha Z-DNA-bindin 38.6 18 0.00038 28.7 1.3 39 224-262 6-45 (68)
205 PF13610 DDE_Tnp_IS240: DDE do 37.9 22 0.00049 32.1 2.1 116 339-465 20-138 (140)
206 PRK13918 CRP/FNR family transc 37.1 15 0.00034 34.5 1.0 64 223-287 119-197 (202)
207 TIGR01610 phage_O_Nterm phage 36.8 17 0.00037 30.7 1.1 28 236-263 44-71 (95)
208 PRK09391 fixK transcriptional 36.8 18 0.0004 35.3 1.4 80 185-264 113-204 (230)
209 PRK15411 rcsA colanic acid cap 35.9 15 0.00032 35.6 0.6 45 222-268 137-181 (207)
210 smart00418 HTH_ARSR helix_turn 34.9 16 0.00035 27.0 0.5 28 237-264 8-35 (66)
211 PRK15201 fimbriae regulatory p 34.7 15 0.00033 35.1 0.5 44 222-267 133-176 (198)
212 PF04921 XAP5: XAP5, circadian 34.3 57 0.0012 32.6 4.4 31 67-97 66-96 (239)
213 PF13545 HTH_Crp_2: Crp-like h 34.2 14 0.00031 29.1 0.2 27 239-265 28-54 (76)
214 PRK07921 RNA polymerase sigma 34.1 27 0.00058 36.5 2.2 48 222-269 262-312 (324)
215 PF04297 UPF0122: Putative hel 33.8 25 0.00055 30.4 1.6 45 224-269 19-63 (101)
216 PRK05901 RNA polymerase sigma 33.7 25 0.00055 39.0 2.0 48 222-269 447-497 (509)
217 PF12840 HTH_20: Helix-turn-he 33.6 14 0.00031 28.3 0.1 30 236-265 21-50 (61)
218 PF13551 HTH_29: Winged helix- 33.6 82 0.0018 26.4 4.9 25 186-210 14-38 (112)
219 TIGR02337 HpaR homoprotocatech 32.9 52 0.0011 28.5 3.5 41 223-264 26-67 (118)
220 PF01381 HTH_3: Helix-turn-hel 32.7 9.3 0.0002 28.3 -1.1 43 236-291 6-48 (55)
221 PF13560 HTH_31: Helix-turn-he 32.6 11 0.00024 29.0 -0.7 27 234-260 9-35 (64)
222 TIGR03541 reg_near_HchA LuxR f 31.8 41 0.00089 33.1 3.0 47 220-268 169-215 (232)
223 smart00419 HTH_CRP helix_turn_ 30.9 14 0.0003 26.3 -0.4 27 238-264 7-33 (48)
224 PRK10840 transcriptional regul 30.4 27 0.00059 33.2 1.4 43 221-265 149-191 (216)
225 PRK10163 DNA-binding transcrip 30.3 30 0.00064 34.9 1.8 45 221-265 19-66 (271)
226 smart00345 HTH_GNTR helix_turn 30.1 15 0.00033 27.1 -0.3 24 241-264 22-45 (60)
227 PF09862 DUF2089: Protein of u 29.9 28 0.0006 30.8 1.3 46 222-268 33-78 (113)
228 PRK10188 DNA-binding transcrip 29.7 54 0.0012 32.5 3.5 46 221-268 178-223 (240)
229 PRK14088 dnaA chromosomal repl 29.3 36 0.00079 37.0 2.3 48 220-267 368-415 (440)
230 PRK11512 DNA-binding transcrip 29.0 36 0.00078 30.7 1.9 42 222-264 37-79 (144)
231 cd00090 HTH_ARSR Arsenical Res 28.7 30 0.00064 26.3 1.1 26 238-263 19-44 (78)
232 PF00126 HTH_1: Bacterial regu 28.6 25 0.00054 26.8 0.7 30 240-269 14-43 (60)
233 PRK00149 dnaA chromosomal repl 28.1 44 0.00096 36.3 2.7 50 219-268 382-432 (450)
234 cd07377 WHTH_GntR Winged helix 27.9 46 0.001 24.9 2.1 23 241-263 27-49 (66)
235 PRK13413 mpi multiple promoter 27.8 18 0.0004 34.6 -0.3 28 234-261 167-194 (200)
236 TIGR02431 pcaR_pcaU beta-ketoa 27.5 28 0.0006 34.5 1.0 43 223-265 5-50 (248)
237 PF12964 DUF3853: Protein of u 27.1 18 0.00038 31.0 -0.4 65 194-269 11-77 (96)
238 PRK13719 conjugal transfer tra 27.1 25 0.00054 34.7 0.5 44 222-267 143-186 (217)
239 smart00347 HTH_MARR helix_turn 27.0 44 0.00096 27.2 2.0 28 238-265 23-50 (101)
240 PRK10870 transcriptional repre 26.8 67 0.0014 30.3 3.4 42 223-264 53-96 (176)
241 PF00165 HTH_AraC: Bacterial r 26.7 15 0.00033 25.9 -0.8 29 236-264 5-33 (42)
242 PRK08558 adenine phosphoribosy 26.4 35 0.00077 34.0 1.5 38 224-261 8-45 (238)
243 PF04552 Sigma54_DBD: Sigma-54 26.3 22 0.00048 33.3 0.0 22 239-260 49-70 (160)
244 PF02001 DUF134: Protein of un 25.8 43 0.00093 29.3 1.7 32 238-269 56-87 (106)
245 PLN03083 E3 UFM1-protein ligas 25.6 2.2E+02 0.0049 33.4 7.8 12 221-232 623-634 (803)
246 PHA00738 putative HTH transcri 25.5 20 0.00044 31.3 -0.3 32 234-265 19-52 (108)
247 PRK14086 dnaA chromosomal repl 25.4 50 0.0011 37.6 2.6 50 220-269 550-599 (617)
248 PRK09483 response regulator; P 25.4 26 0.00056 32.7 0.3 44 221-266 147-190 (217)
249 PF01978 TrmB: Sugar-specific 25.3 21 0.00045 27.9 -0.3 37 227-264 11-47 (68)
250 PF10654 DUF2481: Protein of u 24.9 17 0.00036 32.1 -1.0 26 238-263 79-104 (126)
251 TIGR02395 rpoN_sigma RNA polym 24.9 31 0.00067 37.5 0.8 31 239-280 318-348 (429)
252 PF05344 DUF746: Domain of Unk 24.6 41 0.00089 26.8 1.2 42 228-269 2-43 (65)
253 PRK09492 treR trehalose repres 24.0 25 0.00055 35.3 -0.1 23 240-262 5-27 (315)
254 COG0593 DnaA ATPase involved i 23.5 83 0.0018 34.0 3.7 50 219-268 345-394 (408)
255 COG2771 CsgD DNA-binding HTH d 23.5 32 0.0007 25.9 0.5 34 232-265 12-45 (65)
256 PRK05658 RNA polymerase sigma 23.3 50 0.0011 37.6 2.1 48 222-269 556-606 (619)
257 COG2197 CitB Response regulato 22.9 33 0.00072 33.3 0.5 43 222-266 148-190 (211)
258 TIGR03020 EpsA transcriptional 22.8 49 0.0011 33.2 1.7 46 220-267 188-233 (247)
259 smart00420 HTH_DEOR helix_turn 22.8 48 0.001 23.6 1.3 27 238-264 13-39 (53)
260 PRK00215 LexA repressor; Valid 22.3 45 0.00097 31.9 1.3 26 239-264 23-49 (205)
261 PRK11475 DNA-binding transcrip 22.3 32 0.0007 33.3 0.3 42 222-265 134-175 (207)
262 PRK09834 DNA-binding transcrip 22.3 37 0.00081 34.0 0.8 44 222-265 6-52 (263)
263 PRK10100 DNA-binding transcrip 22.1 35 0.00075 33.3 0.5 45 222-268 155-199 (216)
264 COG2522 Predicted transcriptio 21.9 35 0.00077 30.4 0.4 33 228-262 13-45 (119)
265 PRK05932 RNA polymerase factor 21.7 39 0.00084 37.1 0.8 32 238-280 342-373 (455)
266 COG3413 Predicted DNA binding 21.6 36 0.00078 33.1 0.5 50 220-269 153-208 (215)
267 PF00325 Crp: Bacterial regula 21.4 18 0.00038 24.7 -1.2 24 240-263 3-26 (32)
268 cd00131 PAX Paired Box domain 21.4 1.9E+02 0.004 25.9 5.0 79 183-261 32-125 (128)
269 TIGR01889 Staph_reg_Sar staphy 21.4 63 0.0014 27.8 1.9 27 238-264 42-68 (109)
270 smart00344 HTH_ASNC helix_turn 21.0 56 0.0012 27.7 1.5 37 227-264 6-42 (108)
271 TIGR02404 trehalos_R_Bsub treh 21.0 61 0.0013 31.6 2.0 19 244-262 29-47 (233)
272 TIGR02405 trehalos_R_Ecol treh 20.9 24 0.00052 35.6 -0.9 21 241-261 3-23 (311)
273 PRK12469 RNA polymerase factor 20.8 38 0.00083 37.4 0.5 31 239-280 369-399 (481)
274 PF14942 Muted: Organelle biog 20.7 1.1E+02 0.0024 28.2 3.4 28 83-110 115-142 (145)
275 PF06056 Terminase_5: Putative 20.7 45 0.00098 25.8 0.8 31 228-260 4-34 (58)
276 COG1508 RpoN DNA-directed RNA 20.6 27 0.00058 38.0 -0.7 30 240-280 331-360 (444)
277 PRK14987 gluconate operon tran 20.3 30 0.00066 35.1 -0.4 22 241-262 7-28 (331)
278 PF11662 DUF3263: Protein of u 20.3 1.2E+02 0.0027 24.9 3.2 34 174-210 15-48 (77)
No 1
>KOG4585 consensus Predicted transposase [Replication, recombination and repair]
Probab=100.00 E-value=8.6e-40 Score=335.19 Aligned_cols=297 Identities=36% Similarity=0.606 Sum_probs=238.5
Q ss_pred HcCCCHHHHHHHHHHhhccccccCC--CCCCCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhh
Q 046732 193 WFRMRRQTFDMICEELNSVIAKEDT--TLRNAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSV 270 (516)
Q Consensus 193 ~FRmsk~tF~~L~~~L~~~i~k~~t--~~r~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~ 270 (516)
.|++++.+|..|+............ .....+++..+++++|+.++++.+.+.++..||...+|+ ++......
T Consensus 7 ~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~i~~~fg~~~~~~------~~~~~~~~ 80 (326)
T KOG4585|consen 7 EFRKSYTTFDKICSLVQSLNVVKNSGFMLSSLLPADTLVAVALWRLKTGESLRTVEKKFGLGQSTC------KFLEEKED 80 (326)
T ss_pred HHHHHHHHHHHHhhhhhhhhhhcccchhhhccccHHhhhhhhhccccccchHHHHHHHcCCcchhh------hHHHhhhc
Confidence 7889999999999986653222221 122233388999999999999999999999999999998 33344445
Q ss_pred cccccccCCChhHHHhhHHHHHhhhCCCccccCCCceeeEEeCCCcccccccccccccccCCcccceeecceecCCCCee
Q 046732 271 LMPKYLQWPDDDALRKIKDEFEVISGIPNVVGSMYTTHVPIIAPKISVAAYFNKRHTERNQKTSYSITVQGVVNPNGAFT 350 (516)
Q Consensus 271 L~~~~I~~P~~ee~~~i~~~F~~~~gfP~~vGaIDgThIpI~~P~~~~~~y~n~~~~~~n~K~~~Si~vq~V~D~~g~fi 350 (516)
+++.++.||....+..+.+.|+. ||+|+|+||+|||++..|......|+|+ .++.++|+|||++++|+
T Consensus 81 ~~~~~~~~p~~~~~~~i~~~~~~---~~~~~g~~d~~hi~~~~~~~~~~~~~n~---------~~~~Nvlav~n~d~~f~ 148 (326)
T KOG4585|consen 81 LAPHFLKWPSRRILYEIRERFES---LPNCVGAIDTTHIPIRVPPKSGSVYFNK---------EQSKNLLAVCNFDMRFI 148 (326)
T ss_pred ccchhhcCchhhhhhhhcccccc---ccchhccccccccceecCcccccccccc---------ccchhhhheecCCceEE
Confidence 78999999998888888888876 9999999999999999999888888773 57888999999999999
Q ss_pred ccccCCCCCCCChhHhhhHHHHhhhhcCcc-----------eeEEEEeccCCCCcccccCccccCccccchhhhhhhhhh
Q 046732 351 DVCIGWPGSMPDDQVLEKSALYQRASGGLL-----------KGVWIVGGSGYPLMDWVLVPYTQQHLTWTQHAFNEKIGE 419 (516)
Q Consensus 351 ~v~~g~pGs~hDs~V~~~S~L~~~l~~~~~-----------~~~~llGD~gYpl~~~LltPy~~~~lt~~q~~FN~~~s~ 419 (516)
+|++||||++||+.|++.|.+........+ ...+++|+.+||+.+++|+||.++.++..++.||++|+.
T Consensus 149 ~v~vg~~Gs~~D~kvl~~~~~~~~~~~~~~~k~yl~d~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~elFN~rh~~ 228 (326)
T KOG4585|consen 149 YVDVGWPGSAHDTKVLQDSLLYKRNFPHPPLKYYLVDSGYPLRPGLLGPIGFPLYSLLMFPYGGPQPTNSQELFNKRHSS 228 (326)
T ss_pred EEEccCCCCccHHHHHHhhcccccccccCCccccccccCcccccccccccccccchhhhcccCCCCCCchHHHHhhhhhh
Confidence 999999999999999999988765543333 245677777788888888888888778899999999999
Q ss_pred hhhhhhhhhhhccccccccccccccCCCCcchhhhHHHHHhhhhhhcCCCCCcccccCCCCCCC-----CccccccChhH
Q 046732 420 IQRVSKDAFARLKGRWCCLQKRTEVKLQDLPVVLGACCVLHNICEMMNEELDPELAFDLVDDEM-----VPEVALRSVSS 494 (516)
Q Consensus 420 ~R~~VE~aFG~LK~RFriL~~~~~~~~~~~~~iI~AccvLHNi~~~~~~~~~~~~~~~~~dd~~-----~p~~~~~~~~~ 494 (516)
+|.++|++||+||.||+||+........+.+.||.|||+|||||++..+...+....+..+|.. .........-+
T Consensus 229 ~r~v~e~~fg~lk~rw~il~~~~~~~~~~~~~iV~a~caLHN~~~~~~~~~~~~~~~e~~~d~~~~~~~~~~~~~~~~~~ 308 (326)
T KOG4585|consen 229 LRSVAERAFGVLKAKWRILQRREKYDLKKLPKIVTACCALHNIIRDSDEEDPDDPKWEKFDDYGENVAHLRYAPQQRDYM 308 (326)
T ss_pred HHHHHHHHHHHhhhhhHHHhhcccccccchHHHHHHHHHHHHHHHhhcccccccccccccccccccchhcccchhHHHHH
Confidence 9999999999999999999988667788999999999999999998776543322222222221 11112223457
Q ss_pred HHHHHHHHHHHhh
Q 046732 495 MKTRDSIAHNLLH 507 (516)
Q Consensus 495 ~~~Rd~ia~~l~~ 507 (516)
..+||.|+..||.
T Consensus 309 ~~~r~~l~~~l~~ 321 (326)
T KOG4585|consen 309 EKIRDNLLSELWN 321 (326)
T ss_pred HHHHHHHHHHHHh
Confidence 7889999998864
No 2
>PF13359 DDE_Tnp_4: DDE superfamily endonuclease
Probab=100.00 E-value=1.1e-36 Score=281.80 Aligned_cols=154 Identities=35% Similarity=0.641 Sum_probs=138.3
Q ss_pred CCceeeEEeCCCcccccccccccccccCCcccceeecceecCCCCeeccccCCCCCCCChhHhhhHHHHhhhhcCcceeE
Q 046732 304 MYTTHVPIIAPKISVAAYFNKRHTERNQKTSYSITVQGVVNPNGAFTDVCIGWPGSMPDDQVLEKSALYQRASGGLLKGV 383 (516)
Q Consensus 304 IDgThIpI~~P~~~~~~y~n~~~~~~n~K~~~Si~vq~V~D~~g~fi~v~~g~pGs~hDs~V~~~S~L~~~l~~~~~~~~ 383 (516)
||||||||.+|.... .....|+|+|+.|++++|+|||++|+|++++++||||+||+.||++|.+...+...++.++
T Consensus 1 iDgt~v~i~~P~~~~----~~~~~y~~~k~~~~~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~s~~~~~l~~~~~~~~ 76 (158)
T PF13359_consen 1 IDGTHVPIQRPSDKE----EQREFYSGKKKNHSLKVQIVCDPDGRIIYVSVGWPGSVHDSTIFRQSGLLDRLEQAFPPGE 76 (158)
T ss_pred CccEEEEEEeCCccc----cccccccCCCCcceEeEEEEEeccceeEeeecccccccccccccccccccceeecccccCc
Confidence 799999999998621 1123346679999999999999999999999999999999999999998877653366789
Q ss_pred EEEeccCCCCcccccCccc---cCccccchhhhhhhhhhhhhhhhhhhhhccccccccccccccC-CCCcchhhhHHHHH
Q 046732 384 WIVGGSGYPLMDWVLVPYT---QQHLTWTQHAFNEKIGEIQRVSKDAFARLKGRWCCLQKRTEVK-LQDLPVVLGACCVL 459 (516)
Q Consensus 384 ~llGD~gYpl~~~LltPy~---~~~lt~~q~~FN~~~s~~R~~VE~aFG~LK~RFriL~~~~~~~-~~~~~~iI~AccvL 459 (516)
|+|||+|||+.+++|+||+ +..++..+..||++|+++|.+||++||+||+||+||+.+++.+ +..+..+|.|||+|
T Consensus 77 ~~l~D~gy~~~~~~~~P~~~~~~~~l~~~e~~~N~~~s~~R~~vE~~~~~lK~rf~~l~~~~~~~~~~~~~~ii~~~~~L 156 (158)
T PF13359_consen 77 YLLGDSGYPLSPYLLTPYKKPKGRELTPEEKEFNRRHSSARIIVERAFGRLKSRFRILRGRLRLSRPEKAPQIILACCVL 156 (158)
T ss_pred cccccccccccccccccccccccccccccccchhccccceeeeeHHHHHHHHHhcccCCcccCCCcHhHHHHHHheeEEE
Confidence 9999999999999999996 5568999999999999999999999999999999998888888 88999999999999
Q ss_pred hh
Q 046732 460 HN 461 (516)
Q Consensus 460 HN 461 (516)
||
T Consensus 157 hN 158 (158)
T PF13359_consen 157 HN 158 (158)
T ss_pred EC
Confidence 99
No 3
>PF04827 Plant_tran: Plant transposon protein; InterPro: IPR006912 This entry represents a putative Harbinger transposase-derived nuclease, which is thought to have nuclease activity. However it does not have transposase activity [, ]. ; GO: 0016788 hydrolase activity, acting on ester bonds
Probab=99.97 E-value=1.5e-31 Score=249.97 Aligned_cols=185 Identities=21% Similarity=0.311 Sum_probs=163.8
Q ss_pred ccccCCChhHHHhhHHHHHhhhCCCccccCCCceeeEEe-CCCcccccccccccccccCCcccceeecceecCCCCeecc
Q 046732 274 KYLQWPDDDALRKIKDEFEVISGIPNVVGSMYTTHVPII-APKISVAAYFNKRHTERNQKTSYSITVQGVVNPNGAFTDV 352 (516)
Q Consensus 274 ~~I~~P~~ee~~~i~~~F~~~~gfP~~vGaIDgThIpI~-~P~~~~~~y~n~~~~~~n~K~~~Si~vq~V~D~~g~fi~v 352 (516)
+|++-|+.++++++.+.+ +..|||+.+|+|||+|+.+. +|......|. +|+++..++.+++|++.+.+|+++
T Consensus 2 ~YLr~P~~~d~~rll~~~-e~rGFpGmlGSIDCmHw~WkncP~aw~g~~~------~G~~g~pTiiLEaVAs~dlwIWha 74 (205)
T PF04827_consen 2 EYLRRPTNEDLERLLQIG-EARGFPGMLGSIDCMHWEWKNCPTAWKGQYT------RGKEGVPTIILEAVASHDLWIWHA 74 (205)
T ss_pred cccCCCChhHHHHHHHhh-hhcCCCccccceeEEEeehhcchHHhhhccc------CCCCCCCeehhhhhhccchhhhhe
Confidence 578889999999998665 45899999999999999999 6666556554 457899999999999999999999
Q ss_pred ccCCCCCCCChhHhhhHHHHhhhhcCcce------------eEEEEeccCCCCcccccCccccCccccchhhhhhhhhhh
Q 046732 353 CIGWPGSMPDDQVLEKSALYQRASGGLLK------------GVWIVGGSGYPLMDWVLVPYTQQHLTWTQHAFNEKIGEI 420 (516)
Q Consensus 353 ~~g~pGs~hDs~V~~~S~L~~~l~~~~~~------------~~~llGD~gYpl~~~LltPy~~~~lt~~q~~FN~~~s~~ 420 (516)
..|.|||.+|..|+..|+|+..+..+..+ -.|.|+|..||-...++.+.+.|. +..++.|.++..++
T Consensus 75 ffG~~GS~NDiNVL~~Splf~~~~~G~ap~v~f~VNg~~Y~~gYYLaDGiYP~watfvktI~~p~-~~k~k~fa~~QE~~ 153 (205)
T PF04827_consen 75 FFGMPGSNNDINVLDRSPLFDDLLQGQAPRVQFTVNGHEYNMGYYLADGIYPEWATFVKTISLPQ-GEKRKLFAKHQESA 153 (205)
T ss_pred eeccCCcccccccccccHHHHHHhcCcCCceEEEecCeecccceeeccCcCcchHhHhhhcchhh-chhhHHHHHhCHHH
Confidence 99999999999999999999888665321 358999999999999999999876 66899999999999
Q ss_pred hhhhhhhhhhccccccccccccc-cCCCCcchhhhHHHHHhhhhhhc
Q 046732 421 QRVSKDAFARLKGRWCCLQKRTE-VKLQDLPVVLGACCVLHNICEMM 466 (516)
Q Consensus 421 R~~VE~aFG~LK~RFriL~~~~~-~~~~~~~~iI~AccvLHNi~~~~ 466 (516)
|.-||+|||+|++||+|++.+.+ ++.+.+..|+.||++||||+++.
T Consensus 154 RKDVErAFGVLQaRfaIi~~p~r~w~~~~l~~Im~aCiILHNMIvED 200 (205)
T PF04827_consen 154 RKDVERAFGVLQARFAIIRGPARLWDREDLANIMRACIILHNMIVED 200 (205)
T ss_pred HHHHHHHHHHHHHHHHHhcCchhccCHHHHHHHHHHHHHhhheeEec
Confidence 99999999999999999999865 57788999999999999999853
No 4
>PF13612 DDE_Tnp_1_3: Transposase DDE domain
Probab=98.84 E-value=7.1e-10 Score=102.90 Aligned_cols=135 Identities=16% Similarity=0.195 Sum_probs=97.1
Q ss_pred CCccccCCCceeeEEeCCCccc-ccccccc--cccccCCcccceeecceecCCCCeeccccCCCCCCCChhHhhhHHHHh
Q 046732 297 IPNVVGSMYTTHVPIIAPKISV-AAYFNKR--HTERNQKTSYSITVQGVVNPNGAFTDVCIGWPGSMPDDQVLEKSALYQ 373 (516)
Q Consensus 297 fP~~vGaIDgThIpI~~P~~~~-~~y~n~~--~~~~n~K~~~Si~vq~V~D~~g~fi~v~~g~pGs~hDs~V~~~S~L~~ 373 (516)
-+..+.+||.|.||++.|.... ...+... .-|+..+.+|++++.++|+..|.++.+.+. ||++||..++.
T Consensus 3 ~~~~i~~iDS~Pi~vC~~~R~~r~k~~~~~a~~G~~a~~~fyGfKlHllv~~~G~i~~~~lT-~an~~D~~~~~------ 75 (155)
T PF13612_consen 3 QCTGIYIIDSFPIPVCHNIRIKRHKVFKGLAYRGYCAMGWFYGFKLHLLVNDSGEIVAFTLT-PANVHDRKVLE------ 75 (155)
T ss_pred CccEEEEEecCChhHhCccchhhhccccCccccceeccceeEeeeeeeEEccCCcEEEEEEc-ccccccccccc------
Confidence 3556789999999999776321 1111110 012333567899999999999999988775 99999999884
Q ss_pred hhhcCcceeEEEEeccCCCCcc----------cccCccccCccccchhhhhhhhhhhhhhhhhhhhhcccccccccc
Q 046732 374 RASGGLLKGVWIVGGSGYPLMD----------WVLVPYTQQHLTWTQHAFNEKIGEIQRVSKDAFARLKGRWCCLQK 440 (516)
Q Consensus 374 ~l~~~~~~~~~llGD~gYpl~~----------~LltPy~~~~lt~~q~~FN~~~s~~R~~VE~aFG~LK~RFriL~~ 440 (516)
.+...+ ...|+||.||-... .|+||.+..--......+++.+.+.|.+||-+|+.||+.|.+=+.
T Consensus 76 ~l~~~~--~g~l~gDkGYis~~L~~~L~~~gI~L~t~~RkNmk~~~~~~~~~~l~~~R~~IETvfs~Lk~~~~ie~~ 150 (155)
T PF13612_consen 76 ELSENL--KGKLFGDKGYISKELKDELKEQGIKLITPRRKNMKNKLMPLFDKLLLRKRRIIETVFSQLKNQFNIEHS 150 (155)
T ss_pred cccccc--ccceecchhhhcchHHhhhhhceEEEeccccccccccccchhhhhhhheeeEeehHHHHHHHhhceEee
Confidence 222222 34799999997554 388998854222234567889999999999999999999887654
No 5
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=98.67 E-value=8.9e-09 Score=78.39 Aligned_cols=51 Identities=18% Similarity=0.284 Sum_probs=48.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhcc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLM 272 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~ 272 (516)
.++++++++++|.||+.|.++.++|..||||+|||++++++++++|+..+.
T Consensus 2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l~ 52 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVLK 52 (53)
T ss_pred CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhcC
Confidence 589999999999999999999999999999999999999999999998653
No 6
>PF01609 DDE_Tnp_1: Transposase DDE domain; InterPro: IPR002559 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS4 transposase. 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: 3ECP_A 4DM0_A 1MUS_A 1MUH_A 1MM8_A 1B7E_A.
Probab=97.70 E-value=2.3e-06 Score=80.81 Aligned_cols=151 Identities=16% Similarity=0.118 Sum_probs=81.7
Q ss_pred ccccCCCceeeEEeCCCcccccccccccccccCCcccceeeccee-cCCCCeeccccCCCCCCCChhHhhhHHHHhhhhc
Q 046732 299 NVVGSMYTTHVPIIAPKISVAAYFNKRHTERNQKTSYSITVQGVV-NPNGAFTDVCIGWPGSMPDDQVLEKSALYQRASG 377 (516)
Q Consensus 299 ~~vGaIDgThIpI~~P~~~~~~y~n~~~~~~n~K~~~Si~vq~V~-D~~g~fi~v~~g~pGs~hDs~V~~~S~L~~~l~~ 377 (516)
..+-+||+|+|+.. +......++ .+++.....++++++ +..|.++.+.+. +|+.+|...+.. +... .
T Consensus 4 ~~~~~iD~T~i~~~-~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~d~~~~~~--ll~~--~ 71 (213)
T PF01609_consen 4 RRVVAIDGTTIRTP-HDKSARRYK------KGKKRGFGYKLHLAVDDNSGLPLSVKVT-PGNVHDSKALPE--LLER--K 71 (213)
T ss_dssp EEEEEEETTT--EE-EEEEE-B-S------SGGGHSSHGGHHHHHHHHHGGGGGGEEE-EEEGG-HHHHHH--HHTT---
T ss_pred CeEEEEECcEEEee-cchhhhccc------CCCCcCCCEeEEEEEeecccceeeeecc-ccccceeecccc--cccc--c
Confidence 35668999999998 221112222 234556677999998 567778888887 999999998885 3222 2
Q ss_pred CcceeEEEEeccCCCCccc----------ccCccccCccc----------------------------------cchhhh
Q 046732 378 GLLKGVWIVGGSGYPLMDW----------VLVPYTQQHLT----------------------------------WTQHAF 413 (516)
Q Consensus 378 ~~~~~~~llGD~gYpl~~~----------LltPy~~~~lt----------------------------------~~q~~F 413 (516)
....+.++++|+||..... .+.|.+..... ......
T Consensus 72 ~~~~~~~vv~D~gy~s~~~~~~l~~~~~~~vi~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 151 (213)
T PF01609_consen 72 PGRKPDLVVADRGYDSAENLEALKERGIHFVIRLKKNRKKKIQKIENKFWKSFDRRSARKKPKQKSKRVRVVIRKEQKKK 151 (213)
T ss_dssp ----EEEEEE-S--BBTTHHHHHHTS---EEEEE--EEEE-TTS-EEEE--EEEEEEEEEEETGGGEEEEEEEEEECS--
T ss_pred ccccccceeecccccceeccccccccccccccccccccccccccchhhcccccccccccccccccccccccccccccccc
Confidence 2345789999999986652 23444322100 111112
Q ss_pred hhh--------------hhhhhhhhhhhhhhccccccccccccccCCCCcchhhhHHHHHhhh
Q 046732 414 NEK--------------IGEIQRVSKDAFARLKGRWCCLQKRTEVKLQDLPVVLGACCVLHNI 462 (516)
Q Consensus 414 N~~--------------~s~~R~~VE~aFG~LK~RFriL~~~~~~~~~~~~~iI~AccvLHNi 462 (516)
... +.+.|-.||+.|..||+.|..= .....+...+...+.+|++-.|+
T Consensus 152 ~~~~~~~~~~~~~~~~~~Y~~Rw~IE~~f~~lK~~~~l~-~~~~~~~~~~~~~~~~~~la~nl 213 (213)
T PF01609_consen 152 GYFLVTNITTLPRDTAALYRRRWQIERFFRELKQFLGLE-RLRVRSPERIEAHLFLTLLAYNL 213 (213)
T ss_dssp TTS---EEEEEESS--SHHHCGGHHHHHHHHHTTTTTGG-GS--SSHHHHHHHHHHHHHH---
T ss_pred cccccccccccccccceeecccchhhHHHHHHHhcCCCc-hhcccCHHHHHHHHHHHHhhCcC
Confidence 222 8889999999999999865532 21112334455556666665554
No 7
>PF13586 DDE_Tnp_1_2: Transposase DDE domain
Probab=96.55 E-value=0.00069 Score=56.77 Aligned_cols=73 Identities=19% Similarity=0.315 Sum_probs=47.6
Q ss_pred EEeccCCCCccc----------ccCccccCccccchhhhhhhhhhhhhhhhhhhhhccccccccccccccCCCCcchhhh
Q 046732 385 IVGGSGYPLMDW----------VLVPYTQQHLTWTQHAFNEKIGEIQRVSKDAFARLKGRWCCLQKRTEVKLQDLPVVLG 454 (516)
Q Consensus 385 llGD~gYpl~~~----------LltPy~~~~lt~~q~~FN~~~s~~R~~VE~aFG~LK~RFriL~~~~~~~~~~~~~iI~ 454 (516)
+++|.||-.... +..|-+.......+..+...+...|.+||++|+.|| +|+.|....+-.+......|.
T Consensus 1 v~aDkgYd~~~~r~~l~~~gi~~~i~~~~~~~~~~~~~~d~~~~~~Rw~VEr~f~wlk-~~Rrl~~ryek~~~s~~~~v~ 79 (88)
T PF13586_consen 1 VLADKGYDSRALREYLRERGIRPVIPKRGRRKKRRPRKFDFRLYKRRWVVERTFAWLK-RFRRLATRYEKLASSFLAFVH 79 (88)
T ss_pred CcccCCcCCHHHHHHHHHCCCEEecCCCCCccccccCccchhhhccceehhhhhHHHH-HcCccccccccCHHHHHHHHH
Confidence 468888865331 222222222113467888899999999999999999 599998877655555444443
Q ss_pred HHHH
Q 046732 455 ACCV 458 (516)
Q Consensus 455 Accv 458 (516)
-+|+
T Consensus 80 la~~ 83 (88)
T PF13586_consen 80 LACI 83 (88)
T ss_pred HHHH
Confidence 3343
No 8
>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=94.46 E-value=0.014 Score=44.35 Aligned_cols=42 Identities=26% Similarity=0.540 Sum_probs=31.4
Q ss_pred CCCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhh
Q 046732 220 RNAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLE 262 (516)
Q Consensus 220 r~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~ 262 (516)
|..+++++++-+ +.++-.|.+..+||..|||+.|||+.++..
T Consensus 4 R~~LTl~eK~~i-I~~~e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 4 RKSLTLEEKLEI-IKRLEEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp SSS--HHHHHHH-HHHHHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred CccCCHHHHHHH-HHHHHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 568999999988 456788889999999999999999887654
No 9
>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=93.28 E-value=0.062 Score=39.90 Aligned_cols=45 Identities=20% Similarity=0.391 Sum_probs=37.5
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHH
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAI 267 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL 267 (516)
.+|+.++-.+.++| -.|.++..+|..+|+|.+||+++..+.+.-|
T Consensus 4 ~L~~~er~vi~~~y-~~~~t~~eIa~~lg~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 4 QLPPREREVIRLRY-FEGLTLEEIAERLGISRSTVRRILKRALKKL 48 (50)
T ss_dssp TS-HHHHHHHHHHH-TST-SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh-cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence 58899999999888 6889999999999999999999887776544
No 10
>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=92.68 E-value=0.026 Score=41.31 Aligned_cols=39 Identities=18% Similarity=0.237 Sum_probs=29.1
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVL 261 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~ 261 (516)
.++.+ ++.-++..++.|.+...||..||||++||.+++.
T Consensus 5 ~~~~~-~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 5 KLSKE-QIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSHC-CHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred CCCHH-HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 34443 5666777889999999999999999999998864
No 11
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=92.05 E-value=0.04 Score=40.17 Aligned_cols=40 Identities=23% Similarity=0.306 Sum_probs=22.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLE 262 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~ 262 (516)
.++++++..+.- ++..|.+++.||..+|+|+|||++.+.+
T Consensus 4 ~Lt~~eR~~I~~-l~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 4 HLTPEERNQIEA-LLEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp --------HHHH-HHCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred chhhhHHHHHHH-HHHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 467777777664 4689999999999999999999887653
No 12
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)
Probab=90.16 E-value=0.34 Score=39.32 Aligned_cols=64 Identities=22% Similarity=0.254 Sum_probs=46.9
Q ss_pred CHHHHHHHHHHhhccccccCCCCCCCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhH
Q 046732 197 RRQTFDMICEELNSVIAKEDTTLRNAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 197 sk~tF~~L~~~L~~~i~k~~t~~r~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
|-+....|-..|.+. ....++..++..+-|-..|+.|.+|+.++.|-..|| +.+||++.+.+..
T Consensus 2 sD~~W~~i~p~lp~~---~~~~~~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg-~~~tv~~~f~rW~ 65 (75)
T PF13340_consen 2 SDEEWALIEPLLPPR---KPRGGRPRIDLREVLNAILYVLRTGCPWRDLPEDFG-PWSTVYRRFRRWS 65 (75)
T ss_pred CHHHHHHHHhhCCCC---CCCCCCCccchHHHHhcccccceecceecccchhcc-CcCcHHHHHHHHH
Confidence 444444454444431 122346678999999999999999999999999999 7888888776654
No 13
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=90.07 E-value=0.089 Score=43.18 Aligned_cols=44 Identities=30% Similarity=0.371 Sum_probs=32.0
Q ss_pred HHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhcc
Q 046732 229 VAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLM 272 (516)
Q Consensus 229 L~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~ 272 (516)
+-++-|.+.+..+.+..|..||||+||||+=+.+=+..|...|+
T Consensus 9 i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~La 52 (82)
T PF12116_consen 9 IEIANYIIETKATVRQAAKVFGVSKSTVHKDVTERLPKINPELA 52 (82)
T ss_dssp HHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-HHHH
T ss_pred HHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHHH
Confidence 55666788899999999999999999999988877776666553
No 14
>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=89.68 E-value=0.21 Score=37.48 Aligned_cols=43 Identities=19% Similarity=0.274 Sum_probs=30.8
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHH
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
.+|+.++.++.|.|+ .|.++.++|..+|+|.+||...+.+...
T Consensus 10 ~L~~~~r~i~~l~~~-~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 10 QLPERQREIFLLRYF-QGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp CS-HHHHHHHHHHHT-S---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHH-HCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 478888888877655 8999999999999999999877766543
No 15
>PF13518 HTH_28: Helix-turn-helix domain
Probab=89.52 E-value=0.13 Score=38.00 Aligned_cols=37 Identities=24% Similarity=0.421 Sum_probs=30.3
Q ss_pred HHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHH
Q 046732 228 RVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 228 kL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
++.++..++ .|.++..++..||||.+||.+++..+..
T Consensus 2 r~~iv~~~~-~g~s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 2 RLQIVELYL-EGESVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHH-cCCCHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 456667777 6779999999999999999888877654
No 16
>PF02209 VHP: Villin headpiece domain; InterPro: IPR003128 Villin is an F-actin bundling protein involved in the maintenance of the microvilli of the absorptive epithelia. The villin-type "headpiece" domain is a modular motif found at the extreme C terminus of larger "core" domains in over 25 cytoskeletal proteins in plants and animals, often in assocation with the Gelsolin repeat. Although the headpiece is classified as an F-actin-binding domain, it has been shown that not all headpiece domains are intrinsically F-actin-binding motifs, surface charge distribution may be an important element for F-actin recognition []. An autonomously folding, 35 residue, thermostable subdomain (HP36) of the full-length 76 amino acid residue villin headpiece, is the smallest known example of a cooperatively folded domain of a naturally occurring protein. The structure of HP36, as determined by NMR spectroscopy, consists of three short helices surrounding a tightly packed hydrophobic core []. ; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1ZV6_A 1QZP_A 1UND_A 2PPZ_A 3TJW_B 1YU8_X 2JM0_A 1WY4_A 3MYC_A 1YU5_X ....
Probab=88.90 E-value=0.27 Score=34.40 Aligned_cols=22 Identities=32% Similarity=0.581 Sum_probs=17.3
Q ss_pred CChhHHHHHcCCCHHHHHHHHH
Q 046732 185 YPEEEFKKWFRMRRQTFDMICE 206 (516)
Q Consensus 185 ~~d~~Fk~~FRmsk~tF~~L~~ 206 (516)
++|++|...|+|+++.|..|-.
T Consensus 2 Lsd~dF~~vFgm~~~eF~~lP~ 23 (36)
T PF02209_consen 2 LSDEDFEKVFGMSREEFYKLPK 23 (36)
T ss_dssp S-HHHHHHHHSS-HHHHHHS-H
T ss_pred cCHHHHHHHHCCCHHHHHHChH
Confidence 5799999999999999998754
No 17
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=88.05 E-value=0.1 Score=38.49 Aligned_cols=37 Identities=24% Similarity=0.345 Sum_probs=22.1
Q ss_pred hHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhH
Q 046732 227 QRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 227 ekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
.++.+. ..+..|.+.+.++..+|||.+||++++.++.
T Consensus 6 ~R~~ii-~l~~~G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 6 RRAQII-RLLREGWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp ----HH-HHHHHT--HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHHHHH-HHHHCCCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 344433 3344599999999999999999999887653
No 18
>smart00153 VHP Villin headpiece domain.
Probab=87.43 E-value=0.44 Score=33.36 Aligned_cols=21 Identities=29% Similarity=0.558 Sum_probs=19.0
Q ss_pred CChhHHHHHcCCCHHHHHHHH
Q 046732 185 YPEEEFKKWFRMRRQTFDMIC 205 (516)
Q Consensus 185 ~~d~~Fk~~FRmsk~tF~~L~ 205 (516)
++|++|...|+||++.|..|-
T Consensus 2 LsdeeF~~vfgmsr~eF~~LP 22 (36)
T smart00153 2 LSDEDFEEVFGMTREEFYKLP 22 (36)
T ss_pred CCHHHHHHHHCCCHHHHHhCc
Confidence 578999999999999998874
No 19
>smart00351 PAX Paired Box domain.
Probab=86.72 E-value=0.36 Score=43.19 Aligned_cols=43 Identities=12% Similarity=0.138 Sum_probs=37.2
Q ss_pred CCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhH
Q 046732 221 NAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 221 ~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
.+++.+.+.-+.+.+. .|.+.+.++..||||.+||++++.++-
T Consensus 16 ~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~r~~ 58 (125)
T smart00351 16 RPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILGRYY 58 (125)
T ss_pred CCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4588888888877765 899999999999999999999988764
No 20
>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=86.34 E-value=0.42 Score=31.21 Aligned_cols=37 Identities=24% Similarity=0.308 Sum_probs=27.4
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeeh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKL 259 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsri 259 (516)
.++.+.+..+... +..|.++..++..||++.+|++++
T Consensus 5 ~~~~~~~~~i~~~-~~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 5 KLTPEQIEEARRL-LAAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred cCCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHh
Confidence 4555555444443 457889999999999999998765
No 21
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=85.79 E-value=0.24 Score=36.29 Aligned_cols=36 Identities=19% Similarity=0.317 Sum_probs=27.1
Q ss_pred hhHHHHHHhhcccC-Ccchhhhhhcccccceeeehhh
Q 046732 226 RQRVAVCIWRLATG-EPLRLVSKRFGLGISTCHKLVL 261 (516)
Q Consensus 226 eekL~v~L~~La~G-~s~~~la~~Fgis~STvsrii~ 261 (516)
++.+..+|..+.+| .+++..+..|||++||+++.++
T Consensus 2 ee~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~ 38 (45)
T PF05225_consen 2 EEDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLR 38 (45)
T ss_dssp HHHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHc
Confidence 46677778777788 9999999999999999876554
No 22
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=85.31 E-value=0.53 Score=39.40 Aligned_cols=47 Identities=17% Similarity=0.214 Sum_probs=41.6
Q ss_pred CCCCCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhH
Q 046732 218 TLRNAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 218 ~~r~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
.....+++..++.++-..+..|.+...++..||||..|+++++.++-
T Consensus 4 H~nA~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryr 50 (85)
T PF13011_consen 4 HKNARLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYR 50 (85)
T ss_pred CCCCCCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 34567999999999999999999999999999999999988876653
No 23
>cd00131 PAX Paired Box domain
Probab=84.36 E-value=0.61 Score=41.97 Aligned_cols=45 Identities=11% Similarity=0.122 Sum_probs=37.8
Q ss_pred CCCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHH
Q 046732 220 RNAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 220 r~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
..++|.+.+.-|.+.+ ..|.+.+.++..||||.+||.+++.++-.
T Consensus 15 ~~~lS~d~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e 59 (128)
T cd00131 15 GRPLPDSIRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILNRYYE 59 (128)
T ss_pred CCcCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4578888887777665 69999999999999999999999887653
No 24
>PRK04217 hypothetical protein; Provisional
Probab=83.40 E-value=0.76 Score=40.38 Aligned_cols=50 Identities=14% Similarity=0.108 Sum_probs=39.6
Q ss_pred CCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 221 NAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 221 ~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
..++.+++-++.|+ ...|.++.+||..+|||.+||.+++.+....|...+
T Consensus 41 ~~Lt~eereai~l~-~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 41 IFMTYEEFEALRLV-DYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred ccCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 45777887555444 348889999999999999999999998877776654
No 25
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=83.29 E-value=0.77 Score=40.75 Aligned_cols=46 Identities=15% Similarity=0.239 Sum_probs=41.6
Q ss_pred CCCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHH
Q 046732 220 RNAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 220 r~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
+...+.+.++-++...+..|.++..++..|||+.+|+++++.++..
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 5678999999999999999999999999999999999999888653
No 26
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=83.00 E-value=0.76 Score=33.81 Aligned_cols=44 Identities=18% Similarity=0.317 Sum_probs=33.8
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHH
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAI 267 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL 267 (516)
.++..++-++. ++..|.++..++..+|+|.+||.+++.++...+
T Consensus 3 ~l~~~e~~i~~--~~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl 46 (58)
T smart00421 3 SLTPREREVLR--LLAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46 (58)
T ss_pred CCCHHHHHHHH--HHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 35666655333 357899999999999999999999888775544
No 27
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=82.34 E-value=0.55 Score=42.94 Aligned_cols=43 Identities=28% Similarity=0.252 Sum_probs=37.1
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhH
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
+.+...+.+++..++..|.+.+.++..||||.|||.+.+.+.-
T Consensus 4 ~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 4 PFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred hhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhc
Confidence 3455677888889999999999999999999999998887764
No 28
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=82.09 E-value=0.87 Score=41.79 Aligned_cols=48 Identities=13% Similarity=0.245 Sum_probs=41.7
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|++ .|.++..||..+|++.+||...+.+....|...|
T Consensus 112 ~L~~~~r~il~l~~--~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 112 KMTERDRTVLLLRF--SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47888998888877 9999999999999999999998888877776644
No 29
>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=81.34 E-value=0.91 Score=32.68 Aligned_cols=42 Identities=17% Similarity=0.245 Sum_probs=32.7
Q ss_pred CCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHH
Q 046732 223 IPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 223 l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
+|+.++-++.+.++ .|.++..++..+|++.+||.+++.....
T Consensus 11 l~~~~~~~~~~~~~-~~~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 11 LPEREREVILLRFG-EGLSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred CCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 56666666655554 8899999999999999999888776543
No 30
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. 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
Probab=81.18 E-value=1 Score=47.97 Aligned_cols=129 Identities=12% Similarity=0.122 Sum_probs=69.4
Q ss_pred hcccCCcchhhhhh----cc---cccceeeehhhhhHHHHHhhcccccccCCChhHHHhhHHHHHhhhCCCccccCCCce
Q 046732 235 RLATGEPLRLVSKR----FG---LGISTCHKLVLEVCTAIRSVLMPKYLQWPDDDALRKIKDEFEVISGIPNVVGSMYTT 307 (516)
Q Consensus 235 ~La~G~s~~~la~~----Fg---is~STvsrii~~v~~aL~~~L~~~~I~~P~~ee~~~i~~~F~~~~gfP~~vGaIDgT 307 (516)
.++.|.|.++++.. +| +|++|||+++..+...+.. +..+ ...+.|=++-.|||+
T Consensus 110 ly~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~~-w~~R------------------~L~~~~y~~l~iD~~ 170 (381)
T PF00872_consen 110 LYLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVEA-WRNR------------------PLESEPYPYLWIDGT 170 (381)
T ss_pred hhccccccccccchhhhhhcccccCchhhhhhhhhhhhhHHH-Hhhh------------------ccccccccceeeeee
Confidence 35566666665544 45 8999999987776544433 1110 001122246689999
Q ss_pred eeEEeCCCcccccccccccccccCCcccceeecceecCCCC--eeccccCCCCCCCChhHhhhHHHHhhh-hcCcceeEE
Q 046732 308 HVPIIAPKISVAAYFNKRHTERNQKTSYSITVQGVVNPNGA--FTDVCIGWPGSMPDDQVLEKSALYQRA-SGGLLKGVW 384 (516)
Q Consensus 308 hIpI~~P~~~~~~y~n~~~~~~n~K~~~Si~vq~V~D~~g~--fi~v~~g~pGs~hDs~V~~~S~L~~~l-~~~~~~~~~ 384 (516)
|+.+..-. . -..-++.+-+.+|.+|+ ++.+.++ ..-....|. .++..+ .+|+.....
T Consensus 171 ~~kvr~~~----~-----------~~~~~~~v~iGi~~dG~r~vLg~~~~---~~Es~~~W~--~~l~~L~~RGl~~~~l 230 (381)
T PF00872_consen 171 YFKVREDG----R-----------VVKKAVYVAIGIDEDGRREVLGFWVG---DRESAASWR--EFLQDLKERGLKDILL 230 (381)
T ss_pred eccccccc----c-----------cccchhhhhhhhhcccccceeeeecc---cCCccCEee--ecchhhhhccccccce
Confidence 99986211 0 11123445556677774 5665554 322333333 233333 456666678
Q ss_pred EEeccCCCCcccccCccc
Q 046732 385 IVGGSGYPLMDWVLVPYT 402 (516)
Q Consensus 385 llGD~gYpl~~~LltPy~ 402 (516)
+++|..=.+..-+-.-|+
T Consensus 231 vv~Dg~~gl~~ai~~~fp 248 (381)
T PF00872_consen 231 VVSDGHKGLKEAIREVFP 248 (381)
T ss_pred eecccccccccccccccc
Confidence 888855444444444443
No 31
>PRK00118 putative DNA-binding protein; Validated
Probab=80.46 E-value=1.1 Score=38.95 Aligned_cols=48 Identities=8% Similarity=0.119 Sum_probs=38.9
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSV 270 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~ 270 (516)
.+|..++-++.|+ +-.|.++..||..+|+|.+||++.+.+....+...
T Consensus 17 ~L~ekqRevl~L~-y~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 17 LLTEKQRNYMELY-YLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred cCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4677777776555 45699999999999999999999998877766664
No 32
>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=79.37 E-value=0.48 Score=37.90 Aligned_cols=45 Identities=18% Similarity=0.196 Sum_probs=37.1
Q ss_pred CCCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhH
Q 046732 220 RNAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 220 r~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
+...|++.++-++-.+|..|.+...++..+||+.+|+++++.+..
T Consensus 4 r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 4 RRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp S----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence 456899999999999999999999999999999999999888876
No 33
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=78.67 E-value=1.3 Score=40.64 Aligned_cols=49 Identities=22% Similarity=0.451 Sum_probs=40.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|.++ .|.++..+|..+|+|.+||...+.+....|...|
T Consensus 109 ~L~~~~r~v~~l~~~-~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 109 ELPARTRYAFEMYRL-HGETQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 468888888877765 4999999999999999999988877777666544
No 34
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=78.54 E-value=1.3 Score=41.90 Aligned_cols=49 Identities=12% Similarity=0.135 Sum_probs=41.9
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|+++ .|.++..||..+|+|.+||...+.+....|...+
T Consensus 131 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 131 KLSPAHREIIDLVYY-HEKSVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 478888988888877 9999999999999999999888888777666644
No 35
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=78.22 E-value=1.5 Score=41.22 Aligned_cols=48 Identities=15% Similarity=0.236 Sum_probs=41.5
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSV 270 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~ 270 (516)
.+|+.++.++.|.++ .|.++..||..+|+|.+||...+++.+..+.+.
T Consensus 127 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 127 TLRPRVKQAFLMATL-DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 478999999999877 999999999999999999988888776666553
No 36
>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=78.13 E-value=1.4 Score=39.62 Aligned_cols=47 Identities=15% Similarity=0.362 Sum_probs=38.9
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+|+.++-++.|+++ .|.++..||..+|+|.+||...+.+....|..
T Consensus 113 ~L~~~~r~il~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRF-EGKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 467788888888776 69999999999999999998888776665543
No 37
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=77.88 E-value=1.2 Score=37.65 Aligned_cols=31 Identities=13% Similarity=0.110 Sum_probs=26.6
Q ss_pred HHHHhhcccCCcchhhhhhcccccceeeehh
Q 046732 230 AVCIWRLATGEPLRLVSKRFGLGISTCHKLV 260 (516)
Q Consensus 230 ~v~L~~La~G~s~~~la~~Fgis~STvsrii 260 (516)
...+.+++.|.++..++..+|||++||+++.
T Consensus 41 ~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 41 LQVAKMLKQGKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 4455678999999999999999999998844
No 38
>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=77.52 E-value=1.5 Score=40.20 Aligned_cols=47 Identities=11% Similarity=0.142 Sum_probs=39.9
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+|+.++.++.|+|+ .|.++..||..+|+|.+||...+.+....|..
T Consensus 122 ~L~~~~r~vl~l~~~-~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 122 ILTPKQQHVIALRFG-QNLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred hCCHHHHHHHHHHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 578889999988776 69999999999999999998888777666543
No 39
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=77.52 E-value=1.3 Score=40.99 Aligned_cols=49 Identities=20% Similarity=0.371 Sum_probs=40.2
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++.++.|.++ .|.++..+|..+|+|.+||...+.+...-|...+
T Consensus 128 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREI-EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888776 7999999999999999999888877766665543
No 40
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=77.19 E-value=1.5 Score=39.93 Aligned_cols=50 Identities=16% Similarity=0.171 Sum_probs=42.8
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhcc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLM 272 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~ 272 (516)
.+|+.++-++.|.++ .|.++..||..+|+|.+||...+.+....|...|.
T Consensus 106 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 155 (161)
T PRK09047 106 KLPARQREAFLLRYW-EDMDVAETAAAMGCSEGSVKTHCSRATHALAKALE 155 (161)
T ss_pred hCCHHHHHHHHHHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 478888888888765 69999999999999999999999988888877654
No 41
>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=77.08 E-value=1.5 Score=37.41 Aligned_cols=38 Identities=16% Similarity=0.177 Sum_probs=29.3
Q ss_pred CCHhhHHHHHHhh------cccCCcchhhhhhcccccceeeehh
Q 046732 223 IPVRQRVAVCIWR------LATGEPLRLVSKRFGLGISTCHKLV 260 (516)
Q Consensus 223 l~~eekL~v~L~~------La~G~s~~~la~~Fgis~STvsrii 260 (516)
+++.++-++.+++ +..|.+|+.|+...|||.+||+|+-
T Consensus 33 LTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~s 76 (94)
T TIGR01321 33 LTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGS 76 (94)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHH
Confidence 5666666666653 3467999999999999999988753
No 42
>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=76.94 E-value=1.5 Score=38.49 Aligned_cols=46 Identities=17% Similarity=0.395 Sum_probs=36.5
Q ss_pred CCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 223 IPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 223 l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
+|+.++-++.+.++ .|.++.++|..+|+|.+||++...++...|..
T Consensus 111 L~~~~~~ii~~~~~-~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYL-EGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 56667766666554 79999999999999999999988887666543
No 43
>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=76.71 E-value=2.5 Score=38.58 Aligned_cols=71 Identities=13% Similarity=0.121 Sum_probs=50.7
Q ss_pred CCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh----------hcccccccCCChhHHHhhHHH
Q 046732 221 NAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS----------VLMPKYLQWPDDDALRKIKDE 290 (516)
Q Consensus 221 ~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~----------~L~~~~I~~P~~ee~~~i~~~ 290 (516)
..++..++-.+.|+ ..|.++..+|..+|+|++||+++..+....|.. ..+|..+..|...++-.+...
T Consensus 5 ~~Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~~~~a~~~~~~~~g~~~~~~~~~ 82 (137)
T TIGR00721 5 TFLTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVKFIKSPVRILCRRGDDLDEIPKR 82 (137)
T ss_pred CCCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHHHhcCCEEEEecCCCcHHHhHHH
Confidence 35778888777773 799999999999999999999888776655543 123555566665566555554
Q ss_pred HHh
Q 046732 291 FEV 293 (516)
Q Consensus 291 F~~ 293 (516)
.+.
T Consensus 83 v~~ 85 (137)
T TIGR00721 83 LFK 85 (137)
T ss_pred HHH
Confidence 444
No 44
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=76.66 E-value=1.6 Score=42.91 Aligned_cols=50 Identities=10% Similarity=0.145 Sum_probs=42.9
Q ss_pred CCCHhhHHHHHHhhc---ccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRL---ATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~L---a~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|+|+ -.|.++..+|..+|+|.+||...+++....|...|
T Consensus 178 ~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l 230 (234)
T PRK08301 178 KLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEI 230 (234)
T ss_pred hCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478889999999874 68999999999999999999988888877776644
No 45
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=76.17 E-value=1.7 Score=40.08 Aligned_cols=49 Identities=16% Similarity=0.192 Sum_probs=42.2
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+.+....|...|
T Consensus 112 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 112 LLSADQREAIILIGA-SGFSYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888777 9999999999999999999988888877777654
No 46
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=75.85 E-value=3 Score=42.87 Aligned_cols=50 Identities=14% Similarity=0.176 Sum_probs=43.8
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhcc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLM 272 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~ 272 (516)
.+|+.++.++.|.++ .|.+|..||..+|+|.+||...+.+....|...|.
T Consensus 142 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 142 YLPPRQRAVLLLRDV-LGWRAAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred hCCHHHhhHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 478888888888776 89999999999999999999999998888887664
No 47
>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=75.63 E-value=1.2 Score=36.30 Aligned_cols=41 Identities=12% Similarity=0.114 Sum_probs=35.6
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLE 262 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~ 262 (516)
.+|+..+.+..|.+.-.|.++..||...|+|.+||...++.
T Consensus 15 ~l~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 15 WVDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred cCCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 47888888888888889999999999999999998776654
No 48
>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=75.58 E-value=1.9 Score=31.69 Aligned_cols=43 Identities=16% Similarity=0.295 Sum_probs=31.8
Q ss_pred CHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHH
Q 046732 224 PVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIR 268 (516)
Q Consensus 224 ~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~ 268 (516)
+..++-++.+ +..|.++..++..+++|.+||...+.++...+.
T Consensus 2 ~~~e~~i~~~--~~~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~ 44 (57)
T cd06170 2 TPREREVLRL--LAEGKTNKEIADILGISEKTVKTHLRNIMRKLG 44 (57)
T ss_pred CHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 3444443333 468999999999999999999988877655443
No 49
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=75.19 E-value=2.4 Score=35.57 Aligned_cols=49 Identities=22% Similarity=0.304 Sum_probs=41.1
Q ss_pred CCCCHhhHHHHHHhhcccCCcchhhhhhcc-cccceeeehhhhhHHHHHh
Q 046732 221 NAIPVRQRVAVCIWRLATGEPLRLVSKRFG-LGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 221 ~~l~~eekL~v~L~~La~G~s~~~la~~Fg-is~STvsrii~~v~~aL~~ 269 (516)
..+...-++++-|..--+|.++..+|..|| .+.|||+..+..+-..+..
T Consensus 26 ~~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 26 KEIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred cCcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 366777788888888889999999999999 9999998888877665543
No 50
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=74.83 E-value=1.5 Score=41.58 Aligned_cols=50 Identities=14% Similarity=0.248 Sum_probs=42.9
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhcc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLM 272 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~ 272 (516)
.+|+.++-++.|+++ .|.++..||..+|+|.+||...+.+....|...|.
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 136 NLPENTARVFTLKEI-LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred hCCHHHHHHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 478888888888776 89999999999999999999999888888877654
No 51
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=74.53 E-value=2 Score=43.32 Aligned_cols=49 Identities=10% Similarity=0.213 Sum_probs=42.1
Q ss_pred CCCHhhHHHHHHhhcc-cCCcchhhhhhcccccceeeehhhhhHHHHHhh
Q 046732 222 AIPVRQRVAVCIWRLA-TGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSV 270 (516)
Q Consensus 222 ~l~~eekL~v~L~~La-~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~ 270 (516)
.+|..++..+.|+|+. .|.++..||..+|||..+|+++..+.+.-|...
T Consensus 218 ~L~~rer~vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~ 267 (270)
T TIGR02392 218 SLDARSRRIIEARWLDDDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAA 267 (270)
T ss_pred cCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4788899999999874 489999999999999999999988877766653
No 52
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=74.50 E-value=2 Score=42.33 Aligned_cols=49 Identities=10% Similarity=0.119 Sum_probs=41.5
Q ss_pred CCCHhhHHHHHHhhc---ccCCcchhhhhhcccccceeeehhhhhHHHHHhh
Q 046732 222 AIPVRQRVAVCIWRL---ATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSV 270 (516)
Q Consensus 222 ~l~~eekL~v~L~~L---a~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~ 270 (516)
.+|+.++..+.|.|+ -.|.++..+|..+|+|.+||.+..++....|...
T Consensus 175 ~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred hCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 588999999999886 4778999999999999999988877776666654
No 53
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=74.41 E-value=2 Score=40.03 Aligned_cols=48 Identities=15% Similarity=0.161 Sum_probs=40.5
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSV 270 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~ 270 (516)
.+|+.++-.+.|.++ .|.++..||..+|+|..||...+.+....|...
T Consensus 129 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 129 ELEKDRAAAVRRAYL-EGLSYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 478888888888876 889999999999999999988888877766654
No 54
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=74.10 E-value=1.8 Score=42.29 Aligned_cols=49 Identities=14% Similarity=0.219 Sum_probs=42.6
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++.++.|+|+ .|.+|..|+..+|||.+||...+++....|...|
T Consensus 134 ~Lp~~~R~v~~L~y~-eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 134 KLPVEYREVLVLREL-EDMSYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCHHHHhHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888877 6999999999999999999999988887777755
No 55
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=73.94 E-value=1.8 Score=40.89 Aligned_cols=51 Identities=10% Similarity=0.112 Sum_probs=42.5
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhccc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLMP 273 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~~ 273 (516)
.+|+.++-++.|.++ .|.+|..||..+|+|.+||...+.+....|...|..
T Consensus 131 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 181 (191)
T PRK12520 131 RLPPRTGRVFMMREW-LELETEEICQELQITATNAWVLLYRARMRLRECLDL 181 (191)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 478888888887765 689999999999999999999888888877776543
No 56
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=73.66 E-value=1.9 Score=40.87 Aligned_cols=49 Identities=12% Similarity=0.197 Sum_probs=42.0
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|+++- |.++..||..+|+|.+||...+.+....|...|
T Consensus 134 ~Lp~~~R~v~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 134 HLPAQQARVFMMREYL-ELSSEQICQECDISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred hCCHHHHHHHhHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788899999888765 999999999999999999888888877776644
No 57
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=72.87 E-value=1.5 Score=40.74 Aligned_cols=48 Identities=15% Similarity=0.112 Sum_probs=40.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSV 270 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~ 270 (516)
.+|+.++.++.|+++ .|.++.+||..+|+|.+||...+.+....|...
T Consensus 126 ~L~~~~r~v~~l~~~-~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 126 KLDPEFRAPVILKHY-YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred cCCHHHhheeeehhh-cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 478888888888776 799999999999999999988887777666553
No 58
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=72.84 E-value=1.9 Score=39.63 Aligned_cols=49 Identities=22% Similarity=0.375 Sum_probs=40.5
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|.++ .|.++..||..+|+|.+||.+.+.+....|...|
T Consensus 125 ~L~~~~r~i~~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 125 ALPVKQREVFLLRYV-EGLSYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred hCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 367778877777776 7999999999999999999999888777766544
No 59
>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=72.80 E-value=2.4 Score=39.62 Aligned_cols=48 Identities=13% Similarity=0.108 Sum_probs=39.8
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSV 270 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~ 270 (516)
.+|+.++-++.|.++ .|.++..+|..+|+|.+||...+.+....|...
T Consensus 134 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 134 QVDPRQAEVVELRFF-AGLTVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred cCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 378888887777655 899999999999999999998888877776653
No 60
>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=72.41 E-value=2.3 Score=38.54 Aligned_cols=47 Identities=19% Similarity=0.315 Sum_probs=39.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+|+.++-.+.|.++ .|.++..||..+|+|.+||...+++.-..|..
T Consensus 111 ~L~~~~r~v~~l~~~-~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 111 KLPERQRELLQLRYQ-RGVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 478888888888665 89999999999999999998888777666544
No 61
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=72.30 E-value=2.3 Score=40.39 Aligned_cols=49 Identities=18% Similarity=0.239 Sum_probs=42.1
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|.++ .|.++..||..+|+|.+||...+.+....|...|
T Consensus 116 ~Lp~~~r~i~~L~~~-~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 116 QLPDDQREAIILVGA-SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 368888888888776 9999999999999999999988888887777655
No 62
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=72.25 E-value=2.3 Score=38.86 Aligned_cols=46 Identities=11% Similarity=0.224 Sum_probs=37.5
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHH
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIR 268 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~ 268 (516)
.+|+.++.++.|.++ .|.++..||..+|+|.+||...+.+....+.
T Consensus 113 ~L~~~~r~v~~L~~~-~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 113 GLPPLVKRAFLLAQV-DGLGYGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 478888887777654 8999999999999999999888777665554
No 63
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=71.96 E-value=2.3 Score=40.44 Aligned_cols=49 Identities=24% Similarity=0.380 Sum_probs=42.1
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|+++ .|.++..||..+|+|.+||...+++....|...+
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 136 ALPERQRQAVVLRHI-EGLSNPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 578889988888877 8999999999999999999998888877776644
No 64
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=71.90 E-value=1.2 Score=33.03 Aligned_cols=30 Identities=17% Similarity=0.250 Sum_probs=24.3
Q ss_pred hhcccCCcchhhhhhcccccceeeehhhhh
Q 046732 234 WRLATGEPLRLVSKRFGLGISTCHKLVLEV 263 (516)
Q Consensus 234 ~~La~G~s~~~la~~Fgis~STvsrii~~v 263 (516)
..|....++..+|..+|+|.+||.+++.+.
T Consensus 22 ~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 22 KLLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 334444699999999999999999988764
No 65
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=71.82 E-value=2.4 Score=40.16 Aligned_cols=49 Identities=20% Similarity=0.278 Sum_probs=41.5
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|+++ .|.++..||..+|+|.+||...+.+....|...+
T Consensus 111 ~Lp~~~R~v~~L~~~-eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 111 DLPEEQRAALHLVAI-EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 478889998888877 6999999999999999999888887777666543
No 66
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=71.80 E-value=2.7 Score=41.24 Aligned_cols=50 Identities=14% Similarity=0.143 Sum_probs=42.6
Q ss_pred CCCHhhHHHHHHhhc---ccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRL---ATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~L---a~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|+|+ -.|.++..+|..+|++.+||.+.+++....|...|
T Consensus 174 ~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~~ 226 (227)
T TIGR02846 174 VLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKEL 226 (227)
T ss_pred hCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 478889999999886 48999999999999999999888888877776543
No 67
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=71.14 E-value=3.7 Score=37.71 Aligned_cols=72 Identities=14% Similarity=0.133 Sum_probs=50.2
Q ss_pred CCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhh---------c-ccccccCCChhHHHhhHHH
Q 046732 221 NAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSV---------L-MPKYLQWPDDDALRKIKDE 290 (516)
Q Consensus 221 ~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~---------L-~~~~I~~P~~ee~~~i~~~ 290 (516)
..+++.++-.+.| ...|.++..+|..+|+|++||+.+.......|... | +|..+..|...++-.+...
T Consensus 5 ~~Lt~rqreVL~l--r~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl~~~~~l~a~~~v~~~~G~d~~~ip~~ 82 (141)
T PRK03975 5 SFLTERQIEVLRL--RERGLTQQEIADILGTSRANVSSIEKRARENIEKARETLAFAETLNAPVRVTIPAGTDLFDIPKR 82 (141)
T ss_pred cCCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEEEecCCCcHHHhHHH
Confidence 4578888887777 36999999999999999999999887755444332 1 2445556665555555554
Q ss_pred HHhh
Q 046732 291 FEVI 294 (516)
Q Consensus 291 F~~~ 294 (516)
.+..
T Consensus 83 v~~~ 86 (141)
T PRK03975 83 IYKE 86 (141)
T ss_pred HHHH
Confidence 4443
No 68
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=71.04 E-value=2.7 Score=39.47 Aligned_cols=48 Identities=15% Similarity=0.205 Sum_probs=40.2
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSV 270 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~ 270 (516)
.+|+.++.++.|. +-.|.++.+||..+|+|.+||...+.+....|...
T Consensus 133 ~L~~~~r~i~~l~-~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 133 QLEPARRNCILHA-YVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 4788888877776 46899999999999999999999888887776653
No 69
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=70.90 E-value=3 Score=41.30 Aligned_cols=89 Identities=10% Similarity=0.141 Sum_probs=58.5
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhcccccccCC-ChhHHHhhHHHHHhhhCCCcc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLMPKYLQWP-DDDALRKIKDEFEVISGIPNV 300 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~~~~I~~P-~~ee~~~i~~~F~~~~gfP~~ 300 (516)
.+|+.++.++.|.++ .|.++..||...|+|.+||...+.+....|...+. +...-+ ...+...+...|.. +=|.+
T Consensus 116 ~Lp~~~R~v~lL~~~-eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~-~~~~~~~~~~~~~~~~~~~~~--~~~~~ 191 (228)
T PRK06704 116 SLNVQQSAILLLKDV-FQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSE-EGIEIVEFTDDMEVVVTSIRE--ERPEL 191 (228)
T ss_pred hCCHHHhhHhhhHHh-hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH-hcCCCCCccccHHHHHHHHHh--cCHHH
Confidence 478888887777665 58999999999999999999998888888877553 322222 23344555555543 23332
Q ss_pred c----cCCCceeeEEeCC
Q 046732 301 V----GSMYTTHVPIIAP 314 (516)
Q Consensus 301 v----GaIDgThIpI~~P 314 (516)
+ --|+.|+++..-|
T Consensus 192 ~~~~~~~~~~~~~~~~~~ 209 (228)
T PRK06704 192 LTKLLPTIDFTKLPSKQP 209 (228)
T ss_pred HHHHhccceeeecccccc
Confidence 2 2356666655444
No 70
>PRK01381 Trp operon repressor; Provisional
Probab=70.52 E-value=3.8 Score=35.29 Aligned_cols=24 Identities=21% Similarity=0.293 Sum_probs=20.5
Q ss_pred ccCCcchhhhhhcccccceeeehh
Q 046732 237 ATGEPLRLVSKRFGLGISTCHKLV 260 (516)
Q Consensus 237 a~G~s~~~la~~Fgis~STvsrii 260 (516)
..+.+|+.|+...|||.+||+|.-
T Consensus 53 ~g~~sQREIa~~lGvSiaTITRgs 76 (99)
T PRK01381 53 RGELSQREIKQELGVGIATITRGS 76 (99)
T ss_pred cCCcCHHHHHHHhCCceeeehhhH
Confidence 345899999999999999987753
No 71
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=70.42 E-value=2.9 Score=42.70 Aligned_cols=49 Identities=10% Similarity=0.218 Sum_probs=42.1
Q ss_pred CCCHhhHHHHHHhhcc-cCCcchhhhhhcccccceeeehhhhhHHHHHhh
Q 046732 222 AIPVRQRVAVCIWRLA-TGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSV 270 (516)
Q Consensus 222 ~l~~eekL~v~L~~La-~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~ 270 (516)
.+|..++..+.++|+. .+.++..||..+|||.++|+++..+.+.-|...
T Consensus 230 ~L~~rEr~VL~lry~~~~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~ 279 (284)
T PRK06596 230 GLDERSRDIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAMKKLKAA 279 (284)
T ss_pred cCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4788899999998875 689999999999999999999988877766553
No 72
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=70.25 E-value=2.8 Score=39.24 Aligned_cols=50 Identities=14% Similarity=0.219 Sum_probs=42.1
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhcc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLM 272 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~ 272 (516)
.+|+.++-.+.|.++. |.++..||..+|+|.+||...+.+....|...|.
T Consensus 131 ~L~~~~r~v~~l~~~~-g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 131 TLPPRQRDVVQSISVE-GASIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 4788888888887665 9999999999999999999998888887776553
No 73
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=70.16 E-value=2.7 Score=38.35 Aligned_cols=49 Identities=10% Similarity=0.068 Sum_probs=40.2
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|.+ -.|.++..||..+|+|.+||...+.+....|...|
T Consensus 106 ~Lp~~~r~v~~l~~-~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 106 ELPENYRDVVLAHY-LEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred hCCHHHHHHHHHHH-HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 37777777776655 48999999999999999999888888777776654
No 74
>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=70.06 E-value=1.3 Score=39.93 Aligned_cols=46 Identities=7% Similarity=0.229 Sum_probs=37.9
Q ss_pred CCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 223 IPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 223 l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
+|+.++-++.|.++ .|.++..||..+|+|.+||...+.+....|..
T Consensus 106 L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 106 LPENYRTVLILREF-KEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred CCHhheeeeeehhh-ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 66777777777666 79999999999999999998888877766655
No 75
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=69.94 E-value=2.6 Score=39.51 Aligned_cols=49 Identities=10% Similarity=0.257 Sum_probs=41.1
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++.++.|.++ .|.++..+|..+|+|.+||...+.+....|...+
T Consensus 127 ~L~~~~r~v~~l~~~-~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 127 SLPIKYREVIYLFYY-EELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred hCCHHHhhHhHhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888776 4999999999999999999888888777776644
No 76
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=69.65 E-value=3.1 Score=38.86 Aligned_cols=47 Identities=17% Similarity=0.233 Sum_probs=39.8
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+|+.++-++.|.++ .|.++..||..+|||.+||...+++....|..
T Consensus 140 ~L~~~~r~vi~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 140 KLPEDYREVILLRHL-EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 478888888877776 89999999999999999999888887776655
No 77
>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=69.52 E-value=2 Score=42.83 Aligned_cols=50 Identities=14% Similarity=0.157 Sum_probs=43.1
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhcc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLM 272 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~ 272 (516)
.+|+.++-++.|.++ .|.+|..||..+|||.+||...+.+....|...+.
T Consensus 161 ~Lp~~~R~v~~L~~~-eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~ 210 (244)
T TIGR03001 161 ALSERERHLLRLHFV-DGLSMDRIGAMYQVHRSTVSRWVAQARERLLERTR 210 (244)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 478888888888776 89999999999999999999999888888777554
No 78
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=69.50 E-value=2.6 Score=39.82 Aligned_cols=49 Identities=20% Similarity=0.287 Sum_probs=40.2
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|+++ .|.++..||..+|+|.+||...+.+....|...|
T Consensus 141 ~L~~~~~~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 141 QLPESQRQVLELAYY-EGLSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred hCCHHHhhhhhhhhh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 467788888877766 4999999999999999999988888777666543
No 79
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=69.35 E-value=3.4 Score=38.17 Aligned_cols=50 Identities=14% Similarity=0.132 Sum_probs=41.5
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhcc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLM 272 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~ 272 (516)
.+|+.++-++.|.++ .|.++..||..+|+|.+||...+++....|...|.
T Consensus 118 ~L~~~~r~vl~L~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 167 (173)
T PRK09645 118 QLSPEHRAVLVRSYY-RGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQ 167 (173)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 478888888777665 69999999999999999998888888777776553
No 80
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=69.34 E-value=2.9 Score=41.94 Aligned_cols=49 Identities=16% Similarity=0.280 Sum_probs=42.1
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++..+.|+|+ .|.++..||..+|+|.++|+++..+....|...|
T Consensus 205 ~L~~~er~vi~l~y~-e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 253 (257)
T PRK05911 205 ALEEKERKVMALYYY-EELVLKEIGKILGVSESRVSQIHSKALLKLRATL 253 (257)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 478889988888875 7899999999999999999999888877776644
No 81
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=69.27 E-value=3 Score=41.78 Aligned_cols=49 Identities=16% Similarity=0.194 Sum_probs=42.0
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++..+.|+|+ .|.++..||..+|+|.++|++...+....|...+
T Consensus 203 ~L~~~~r~vl~l~y~-~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 203 QLEERTREVLEFVFL-HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred cCCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 478888888888886 6999999999999999999999988887776644
No 82
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=69.02 E-value=3.4 Score=38.80 Aligned_cols=48 Identities=8% Similarity=0.052 Sum_probs=39.4
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSV 270 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~ 270 (516)
.+|+.++-++.|.++ .|.++..+|..+|+|.+||...+++....|...
T Consensus 137 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 137 ELEPPRSELIRTAFF-EGITYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 467778777777654 999999999999999999998888877766654
No 83
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=68.90 E-value=2.9 Score=39.49 Aligned_cols=50 Identities=18% Similarity=0.212 Sum_probs=42.7
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhcc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLM 272 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~ 272 (516)
.+|+.++-++.|.++ .|.++..||..+|+|.+||...+.+....|...|.
T Consensus 111 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 111 KLPQDQREALILVGA-SGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred hCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 367888888888765 99999999999999999999988888888877654
No 84
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=68.82 E-value=2.9 Score=38.12 Aligned_cols=49 Identities=20% Similarity=0.335 Sum_probs=40.9
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++.++.|.+ -.|.++..+|..+|+|.+||...+.+....|...+
T Consensus 110 ~L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 110 RLPARQRAVVVLRY-YEDLSEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred hCCHHHHHHhhhHH-HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 46788888877776 57999999999999999999998888877776643
No 85
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=68.73 E-value=2.8 Score=39.11 Aligned_cols=48 Identities=17% Similarity=0.256 Sum_probs=40.1
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSV 270 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~ 270 (516)
.+|+.++-++.|.++ .|.++..+|..+|+|.+||...+++....|...
T Consensus 136 ~L~~~~r~il~l~~~-~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 136 QLPEKYRTVIVLKYI-EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHHHHhhhHHh-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 468888888888776 799999999999999999988887777666553
No 86
>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=68.24 E-value=2.6 Score=41.66 Aligned_cols=49 Identities=14% Similarity=0.164 Sum_probs=42.0
Q ss_pred CCCHhhHHHHHHhhc---ccCCcchhhhhhcccccceeeehhhhhHHHHHhh
Q 046732 222 AIPVRQRVAVCIWRL---ATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSV 270 (516)
Q Consensus 222 ~l~~eekL~v~L~~L---a~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~ 270 (516)
.+|+.++..+.|+|. ..|.++..||..+|||.++|+++..+...-|...
T Consensus 176 ~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~ 227 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHP 227 (238)
T ss_pred hCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhh
Confidence 478889999999884 5789999999999999999999988877766653
No 87
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=68.18 E-value=2.6 Score=40.81 Aligned_cols=49 Identities=12% Similarity=0.199 Sum_probs=42.1
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++.++.|.++ .|.++..||..+|++.+||...+++....|...|
T Consensus 148 ~L~~~~r~v~~L~~~-~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 148 GLPAKYARVFMMREF-IELETNEICHAVDLSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 478888988888776 5999999999999999999998888888777755
No 88
>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=67.83 E-value=3.4 Score=40.25 Aligned_cols=47 Identities=17% Similarity=0.335 Sum_probs=40.1
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+|+.++-++.|+|+ .|.++..||..+|+|.+||...+.++...|..
T Consensus 178 ~L~~~~r~vl~l~y~-~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFF-EDKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 478888888888775 68999999999999999999998888776654
No 89
>PRK05572 sporulation sigma factor SigF; Validated
Probab=67.75 E-value=3.4 Score=41.13 Aligned_cols=49 Identities=18% Similarity=0.326 Sum_probs=42.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++.++.|+|+ .|.++..||..+|++.++|+++..+.+..|...|
T Consensus 202 ~L~~~~~~v~~l~~~-~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l 250 (252)
T PRK05572 202 ELDERERLIVYLRYF-KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKL 250 (252)
T ss_pred cCCHHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 478889999988775 6899999999999999999999988887776543
No 90
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=67.68 E-value=3.6 Score=38.05 Aligned_cols=48 Identities=17% Similarity=0.276 Sum_probs=39.9
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSV 270 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~ 270 (516)
.+|+..+.++.|.+ -.|.++..+|..+|+|.+||...+.+....+...
T Consensus 118 ~L~~~~r~v~~L~~-~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 165 (168)
T PRK12525 118 GLSGKARAAFLMSQ-LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQG 165 (168)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 57888888887765 6899999999999999999998887777666553
No 91
>PF13751 DDE_Tnp_1_6: Transposase DDE domain
Probab=67.51 E-value=2.6 Score=37.15 Aligned_cols=49 Identities=10% Similarity=0.101 Sum_probs=33.4
Q ss_pred hhhhhhhh-hhhhhhhhccccccccccccccCCCCcchhhhHHHHHhhhhh
Q 046732 415 EKIGEIQR-VSKDAFARLKGRWCCLQKRTEVKLQDLPVVLGACCVLHNICE 464 (516)
Q Consensus 415 ~~~s~~R~-~VE~aFG~LK~RFriL~~~~~~~~~~~~~iI~AccvLHNi~~ 464 (516)
..+.+.|. .||.+||.||. +--|.......+..+..-+...|+-|||-.
T Consensus 74 k~~y~~R~~~VE~~fg~~K~-~~g~~r~~~rG~~kv~~~~~l~a~a~Nl~r 123 (125)
T PF13751_consen 74 KELYKQRSIKVEGVFGTIKR-NHGLRRFRYRGLEKVRIEFLLAAIAYNLKR 123 (125)
T ss_pred hhhhheeecccccccccchh-ccCCccccccchhhhHHHHHHHHHHHHHHH
Confidence 34567777 99999999995 444444333345566666666678899854
No 92
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=67.47 E-value=3.4 Score=38.32 Aligned_cols=49 Identities=18% Similarity=0.252 Sum_probs=40.4
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|.++ .|.++..||..+|+|.+||...+.+....+...|
T Consensus 119 ~Lp~~~r~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l 167 (172)
T PRK12523 119 KLSSKARAAFLYNRL-DGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIAL 167 (172)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 478888888888776 6999999999999999999888877776665543
No 93
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=67.41 E-value=3.4 Score=39.21 Aligned_cols=49 Identities=18% Similarity=0.234 Sum_probs=40.9
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|+++ .|.++..||..+|+|.+||...+++....|...|
T Consensus 141 ~Lp~~~r~v~~l~~~-eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 141 RLPKAQRDVLQAVYL-EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 478888888888766 8999999999999999999888877777666544
No 94
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=67.30 E-value=3.5 Score=38.65 Aligned_cols=49 Identities=18% Similarity=0.215 Sum_probs=39.6
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++.++.|.+ -.|.++..||..+|+|.+||...+++....|...|
T Consensus 129 ~L~~~~r~v~~l~~-~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 129 QLPDRQRLPIVHVK-LEGLSVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred HCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 46777777665554 58999999999999999999998888877776644
No 95
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=66.87 E-value=3.5 Score=39.21 Aligned_cols=49 Identities=16% Similarity=0.229 Sum_probs=42.9
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|+++ .|.++..+|..+|+|.+||...+.+....|...+
T Consensus 113 ~Lp~~~r~v~~L~~~-~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 113 QLPDEQREALILVGA-SGFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred hCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478889988888887 9999999999999999999998888888777654
No 96
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=66.82 E-value=3.6 Score=41.04 Aligned_cols=49 Identities=10% Similarity=0.165 Sum_probs=41.8
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|+|+ .|.++..||..+|||.+||.+.+++....|...|
T Consensus 205 ~L~~~~r~vl~l~~~-~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l 253 (257)
T PRK08583 205 VLSDREKSIIQCTFI-ENLSQKETGERLGISQMHVSRLQRQAIKKLREAA 253 (257)
T ss_pred hCCHHHHHHHHHHHh-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 478888888888765 7999999999999999999999888888776644
No 97
>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=66.60 E-value=3.1 Score=38.90 Aligned_cols=49 Identities=20% Similarity=0.285 Sum_probs=40.2
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|.++ .|.++..||..+|++.+||...+++....|...|
T Consensus 138 ~L~~~~r~v~~l~~~-~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 138 ALPEDLRTAITLREL-EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCHHHhhhhhhhhh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 357777777777665 8999999999999999999888888877777654
No 98
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=66.29 E-value=4.1 Score=38.15 Aligned_cols=49 Identities=18% Similarity=0.264 Sum_probs=40.9
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++..+.|+++ .|.++..||..+|+|.+||...+++....|...|
T Consensus 135 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 135 ALSPEERRVIEVLYY-QGYTHREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 378888888887764 7999999999999999999988888877776544
No 99
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=65.97 E-value=3.9 Score=39.98 Aligned_cols=47 Identities=13% Similarity=0.231 Sum_probs=39.8
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+|+.++.++.++|+ .|.++..+|..+|+|.++|+++..+...-|..
T Consensus 183 ~L~~~e~~i~~~~~~-~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~ 229 (231)
T TIGR02885 183 KLDERERQIIMLRYF-KDKTQTEVANMLGISQVQVSRLEKKVLKKMKE 229 (231)
T ss_pred cCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 578888888888764 68899999999999999999998888776654
No 100
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=65.92 E-value=3.9 Score=41.57 Aligned_cols=50 Identities=22% Similarity=0.271 Sum_probs=44.0
Q ss_pred CCCHhhHHHHHHhh-c--ccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWR-L--ATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~-L--a~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++..+.|+| | -.|.++..||..+|+|.+||...+.+....|...|
T Consensus 222 ~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l 274 (285)
T TIGR02394 222 ELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL 274 (285)
T ss_pred cCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999999987 4 57899999999999999999999998888777755
No 101
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=65.77 E-value=3.7 Score=38.99 Aligned_cols=49 Identities=18% Similarity=0.271 Sum_probs=39.5
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++.++.|+++ .|.++..||..+|+|.+||...+.+....|...+
T Consensus 134 ~Lp~~~r~i~~l~~~-~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l 182 (192)
T PRK09643 134 RLPVEQRAALVAVDM-QGYSVADAARMLGVAEGTVKSRCARGRARLAELL 182 (192)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 378888888877766 8899999999999999999877777666665543
No 102
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=65.69 E-value=4 Score=41.78 Aligned_cols=50 Identities=16% Similarity=0.284 Sum_probs=43.7
Q ss_pred CCCHhhHHHHHHhhc-ccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRL-ATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~L-a~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++..+.|+|+ -.|.++..||..+|||.++|.++.++...-|...|
T Consensus 227 ~L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l 277 (289)
T PRK07500 227 TLNERELRIIRERRLREDGATLEALGEELGISKERVRQIEARALEKLRRAL 277 (289)
T ss_pred cCCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478899999999885 47899999999999999999999988888777654
No 103
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=65.51 E-value=4 Score=38.38 Aligned_cols=49 Identities=20% Similarity=0.290 Sum_probs=42.1
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|.++ .|.++..||..+|+|.+||...+++....|...+
T Consensus 131 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 131 RLPEKMRLAIQAVKL-EGLSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred hCCHHHHHHHHHHHH-cCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888777 5999999999999999999999988888777654
No 104
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=65.27 E-value=3.8 Score=38.46 Aligned_cols=49 Identities=22% Similarity=0.278 Sum_probs=41.5
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|.++ .|.++..||..+|+|..||...+++....|...|
T Consensus 128 ~L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 128 ALPERQREAIVLQYY-QGLSNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred hCCHHHHHHhhHHHh-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 468888888888776 5999999999999999999998888877776654
No 105
>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=65.16 E-value=4.3 Score=39.97 Aligned_cols=49 Identities=12% Similarity=0.133 Sum_probs=41.9
Q ss_pred CCCHhhHHHHHHhhc---ccCCcchhhhhhcccccceeeehhhhhHHHHHhh
Q 046732 222 AIPVRQRVAVCIWRL---ATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSV 270 (516)
Q Consensus 222 ~l~~eekL~v~L~~L---a~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~ 270 (516)
.+|+.++..+.|+++ -.|.++..||...|+|.+||...+.+....|...
T Consensus 178 ~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~ 229 (234)
T TIGR02835 178 KLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKE 229 (234)
T ss_pred hCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 589999999999885 3789999999999999999988887777766653
No 106
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=65.16 E-value=3.8 Score=38.48 Aligned_cols=49 Identities=22% Similarity=0.353 Sum_probs=41.7
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|.++ .|.+|..+|...||+.+||...+++....|...+
T Consensus 127 ~Lp~~~R~~~~l~~~-~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l 175 (182)
T COG1595 127 RLPPRQREAFLLRYL-EGLSYEEIAEILGISVGTVKSRLHRARKKLREQL 175 (182)
T ss_pred hCCHHHhHHhhhHhh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888877666 8999999999999999999999888887777654
No 107
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=64.97 E-value=4.1 Score=38.45 Aligned_cols=47 Identities=19% Similarity=0.166 Sum_probs=39.2
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+|+.++-++.|.++ .|.++..||..+|+|.+||...+.+....|..
T Consensus 130 ~Lp~~~r~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 130 DLTTDQREALLLTQL-LGLSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred hCCHHHhHHhhhHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 578888888877655 78889999999999999998888877776655
No 108
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=64.95 E-value=3.5 Score=39.54 Aligned_cols=49 Identities=14% Similarity=0.245 Sum_probs=41.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|.++ .|.+|..||..+|+|.+||...+.+....|...|
T Consensus 139 ~Lp~~~r~v~~L~~~-eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 139 HLPEQIGRVFMMREF-LDFEIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888764 7889999999999999999988888877777655
No 109
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=64.53 E-value=3.8 Score=38.19 Aligned_cols=49 Identities=20% Similarity=0.307 Sum_probs=40.9
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|.++ .|.++..+|..+|++.+||...+.+....|...|
T Consensus 136 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 136 ALPPKYRMVIVLKYM-EDLSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 478888888888766 6999999999999999999988888777766543
No 110
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=64.45 E-value=4.3 Score=38.28 Aligned_cols=49 Identities=18% Similarity=0.302 Sum_probs=39.7
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++.++.|.+ -.|.++..||..+|+|.+||...+.+....|...+
T Consensus 106 ~L~~~~r~i~~l~~-~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 106 ALPEKYAEALRLTE-LEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred hCCHHHHHHHHHHH-hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 46777887777765 48999999999999999999888877777666544
No 111
>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=64.36 E-value=4.6 Score=37.24 Aligned_cols=49 Identities=6% Similarity=0.101 Sum_probs=39.6
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|.++ .|.++..+|..+|+|.+||...+.+....|...+
T Consensus 119 ~L~~~~r~i~~l~~~-~g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l 167 (169)
T TIGR02954 119 TLNDKYQTAIILRYY-HDLTIKEIAEVMNKPEGTVKTYLHRALKKLKKRL 167 (169)
T ss_pred hCCHHHhHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 467778877777666 5899999999999999999988888777766543
No 112
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=63.88 E-value=4.3 Score=37.97 Aligned_cols=49 Identities=10% Similarity=0.144 Sum_probs=40.0
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|.+ -.|.++..||..+|+|.+||...+.+....|...|
T Consensus 117 ~Lp~~~r~i~~l~~-~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 117 KLPYKLRQVIILRY-LHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred hCCHHHHHHHHHHH-HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47888887777754 47889999999999999999888888777776654
No 113
>PHA00675 hypothetical protein
Probab=63.74 E-value=3.7 Score=33.63 Aligned_cols=41 Identities=7% Similarity=0.084 Sum_probs=29.2
Q ss_pred CCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhh
Q 046732 221 NAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVL 261 (516)
Q Consensus 221 ~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~ 261 (516)
..|...+--.+-...-..|.++..|+..||+|+|||..|.+
T Consensus 21 AKLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 21 AKLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred cccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHc
Confidence 34555444444433337889999999999999999876653
No 114
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=63.17 E-value=4.8 Score=40.24 Aligned_cols=47 Identities=13% Similarity=0.245 Sum_probs=40.0
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+|+.++..+.++|+ .|.++..+|..+|+|.++|+++..+...-|..
T Consensus 209 ~L~~~er~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~ 255 (258)
T PRK08215 209 KLNDREKLILNLRFF-QGKTQMEVAEEIGISQAQVSRLEKAALKHMRK 255 (258)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 478888888888775 68899999999999999999998887776654
No 115
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=63.03 E-value=4.7 Score=39.64 Aligned_cols=49 Identities=14% Similarity=0.325 Sum_probs=41.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-.+.|+| -.|.++..+|..+|+|.+||...+.+....|...|
T Consensus 184 ~L~~~~r~vl~l~~-~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 184 SLPEREQLVLSLYY-QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred hCCHHHHHHHHhHh-ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46888888887776 48899999999999999999999888887776644
No 116
>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=62.97 E-value=2.7 Score=35.36 Aligned_cols=33 Identities=27% Similarity=0.372 Sum_probs=27.2
Q ss_pred hHHHHHHhhcccCCcchhhhhhcccccceeeeh
Q 046732 227 QRVAVCIWRLATGEPLRLVSKRFGLGISTCHKL 259 (516)
Q Consensus 227 ekL~v~L~~La~G~s~~~la~~Fgis~STvsri 259 (516)
+++.|+=-.|..|.+|+.|+...|+|..||+|+
T Consensus 37 ~R~~va~~lL~~g~syreIa~~tgvS~aTItRv 69 (87)
T PF01371_consen 37 QRWQVAKELLDEGKSYREIAEETGVSIATITRV 69 (87)
T ss_dssp HHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHH
T ss_pred HHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHH
Confidence 455555447889999999999999999998764
No 117
>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=62.91 E-value=7.3 Score=34.41 Aligned_cols=77 Identities=17% Similarity=0.121 Sum_probs=47.1
Q ss_pred CChhHHHHHcCCCHHHHHHHHHHhhccccccCCCCCCCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhh
Q 046732 185 YPEEEFKKWFRMRRQTFDMICEELNSVIAKEDTTLRNAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEV 263 (516)
Q Consensus 185 ~~d~~Fk~~FRmsk~tF~~L~~~L~~~i~k~~t~~r~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v 263 (516)
.+-.+--..|++++.|....+.....--..+....+..++.+ . +..+.---...++..++..||||.+||++.+..+
T Consensus 19 ~s~~eaa~~F~VS~~Tv~~W~k~~~~G~~~~k~r~~~Kid~~-~-L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrl 95 (119)
T PF01710_consen 19 KSIREAAKRFGVSRNTVYRWLKRKETGDLEPKPRGRKKIDRD-E-LKALVEENPDATLRELAERLGVSPSTIWRALKRL 95 (119)
T ss_pred chHHHHHHHhCcHHHHHHHHHHhcccccccccccccccccHH-H-HHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHc
Confidence 355667788999999998887733221111122222255432 2 2333233455778899999999999988766553
No 118
>PHA00542 putative Cro-like protein
Probab=62.78 E-value=2.9 Score=34.54 Aligned_cols=53 Identities=8% Similarity=0.039 Sum_probs=37.2
Q ss_pred HHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhcccccccCCChhHHHhhHHHHHhh
Q 046732 230 AVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLMPKYLQWPDDDALRKIKDEFEVI 294 (516)
Q Consensus 230 ~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~~~~I~~P~~ee~~~i~~~F~~~ 294 (516)
.+...+...|.+...++...||+++||+++.+.- ..-|+.+.+..+++.+.+.
T Consensus 22 ~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~------------~~~p~~~~l~ki~~~~~~~ 74 (82)
T PHA00542 22 ELVCALIRAGWSQEQIADATDVSQPTICRIYSGR------------HKDPRYSVVEKLRHLVLNL 74 (82)
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCC------------CCCCCHHHHHHHHHHHHHh
Confidence 3444557889999999999999999988765321 1236666667777666543
No 119
>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=62.08 E-value=4.1 Score=38.59 Aligned_cols=49 Identities=16% Similarity=0.332 Sum_probs=40.6
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|.|+ .|.++..||..+|+|.+||...+.+....|...|
T Consensus 131 ~L~~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l 179 (188)
T TIGR02943 131 HLPEQTARVFMMREV-LGFESDEICQELEISTSNCHVLLYRARLSLRACL 179 (188)
T ss_pred hCCHHHHHHHHHHHH-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 467778887777655 5999999999999999999888888877777654
No 120
>PRK06030 hypothetical protein; Provisional
Probab=61.21 E-value=8.9 Score=34.44 Aligned_cols=45 Identities=18% Similarity=0.240 Sum_probs=38.5
Q ss_pred CCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHH
Q 046732 221 NAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 221 ~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
..+...-+++|-|.+--++.++..||..||.+.|||...+..+-.
T Consensus 51 k~i~~aRqIAMYL~r~~~~~sl~~IG~~FGRDHSTV~haikkIe~ 95 (124)
T PRK06030 51 REVSRIRQIAMYVAHVSLGWPMNEVALAFGRDRTTVGHACHTVED 95 (124)
T ss_pred cccchHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 567788899999999999999999999999999998776664443
No 121
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=61.18 E-value=4.5 Score=37.17 Aligned_cols=49 Identities=12% Similarity=0.209 Sum_probs=39.5
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|++ -.|.++..||..+|+|.+||...+.+....|...+
T Consensus 108 ~L~~~~r~v~~l~~-~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 108 TLPVIEAQAILLCD-VHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred hCCHHHHHHHHhHH-HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46777777666654 48999999999999999999888888877776654
No 122
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=61.06 E-value=5.2 Score=36.44 Aligned_cols=48 Identities=15% Similarity=0.263 Sum_probs=39.7
Q ss_pred CCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 223 IPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 223 l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
+|+.++-++.|.+ -.|.++.++|..+|+|.+||...+.+....|...+
T Consensus 106 L~~~~r~v~~l~~-~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 106 LPPACRDSFLLRK-LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 6777777776654 68999999999999999999998888877776644
No 123
>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=61.06 E-value=5.6 Score=39.61 Aligned_cols=47 Identities=9% Similarity=0.144 Sum_probs=40.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+|+.++-.+.|+|+ .|.++..+|..+|+|.+||...+++....|..
T Consensus 205 ~L~~~~r~ii~l~~~-~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 205 ILSEREKSIIHCTFE-ENLSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred cCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 578888888888775 78999999999999999999888887777665
No 124
>PF13701 DDE_Tnp_1_4: Transposase DDE domain group 1
Probab=61.02 E-value=41 Score=36.77 Aligned_cols=87 Identities=14% Similarity=0.156 Sum_probs=47.4
Q ss_pred CccccCCCceeeEEeCCCcccccccccccccccCCcccceeecceecCCCCeeccccCCCCCCCChhHhhh--HHHHhhh
Q 046732 298 PNVVGSMYTTHVPIIAPKISVAAYFNKRHTERNQKTSYSITVQGVVNPNGAFTDVCIGWPGSMPDDQVLEK--SALYQRA 375 (516)
Q Consensus 298 P~~vGaIDgThIpI~~P~~~~~~y~n~~~~~~n~K~~~Si~vq~V~D~~g~fi~v~~g~pGs~hDs~V~~~--S~L~~~l 375 (516)
..++-=||.|+.++.- ......||. |.+.++++.+. +.....|.++.+. -.||++|-+.=... ..+..++
T Consensus 140 ~~i~LDiD~T~~~~~G--~Qe~~~~n~---y~g~~gY~PL~--~f~g~~G~~l~a~-LRpGn~~sa~g~~~fL~~~l~~l 211 (448)
T PF13701_consen 140 KEIVLDIDSTVDDVHG--EQEGAVFNT---YYGEDGYHPLV--AFDGQTGYLLAAE-LRPGNVHSAKGAAEFLKRVLRRL 211 (448)
T ss_pred ceEEEecccccccchh--hcccccccc---cCCCcccccce--eccCCCCceEEEE-ccCCCCChHHHHHHHHHHHHHHH
Confidence 3477788999877663 223334543 33445555442 2224578888764 46999987643221 0112233
Q ss_pred hcCcce-eEEEEeccCCC
Q 046732 376 SGGLLK-GVWIVGGSGYP 392 (516)
Q Consensus 376 ~~~~~~-~~~llGD~gYp 392 (516)
....+. .-.+-||+||-
T Consensus 212 r~~~~~~~ILvR~DSgF~ 229 (448)
T PF13701_consen 212 RQRWPDTRILVRGDSGFA 229 (448)
T ss_pred hhhCccceEEEEecCccC
Confidence 333332 23466999994
No 125
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=60.95 E-value=5.8 Score=39.59 Aligned_cols=47 Identities=13% Similarity=0.246 Sum_probs=39.9
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+++.++.++.++|+ .|.++..+|..+|+|.++|+++..+.+.-|..
T Consensus 206 ~L~~rer~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~ 252 (254)
T TIGR02850 206 RLNEREKMILNMRFF-EGKTQMEVAEEIGISQAQVSRLEKAALKHMRK 252 (254)
T ss_pred cCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 578888988888875 68899999999999999999988887766543
No 126
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=60.88 E-value=5.4 Score=37.67 Aligned_cols=47 Identities=17% Similarity=0.183 Sum_probs=40.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+|+.++-++.|+++ .|.++..||..+|+|.+||...+.+....|..
T Consensus 131 ~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 131 DLEKLDREIFIRRYL-LGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred hCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 578899998888876 78999999999999999998888777666654
No 127
>PRK06930 positive control sigma-like factor; Validated
Probab=60.51 E-value=5.4 Score=37.69 Aligned_cols=49 Identities=10% Similarity=0.144 Sum_probs=39.5
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|+ +..|.++..+|..+|+|.+||...+.+....|...+
T Consensus 114 ~L~~rer~V~~L~-~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l 162 (170)
T PRK06930 114 VLTEREKEVYLMH-RGYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQI 162 (170)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3677777666554 479999999999999999999998888877776644
No 128
>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=60.50 E-value=3.5 Score=38.97 Aligned_cols=49 Identities=20% Similarity=0.231 Sum_probs=39.6
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|.+ -.|.++..||..+|+|.+||...+.+....|...|
T Consensus 131 ~Lp~~~r~i~~L~~-~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 131 GLPEEFRQAVYLAD-VEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred hCCHHHhhheeehh-hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46777777777754 48899999999999999999988888777776644
No 129
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=60.46 E-value=4.4 Score=30.75 Aligned_cols=25 Identities=20% Similarity=0.291 Sum_probs=20.9
Q ss_pred CcchhhhhhcccccceeeehhhhhH
Q 046732 240 EPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 240 ~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
.+..+|+..++++++|+++++..+.
T Consensus 22 ~t~~~la~~l~~~~~~vs~~v~~L~ 46 (62)
T PF12802_consen 22 LTQSELAERLGISKSTVSRIVKRLE 46 (62)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 6899999999999999988876654
No 130
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=60.39 E-value=5.4 Score=38.00 Aligned_cols=48 Identities=8% Similarity=0.184 Sum_probs=39.1
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.| ++ .|.++..||..+|+|.+||...+.+.-..|...+
T Consensus 155 ~L~~~~r~vl~l-~~-e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 155 LLSELEKEVLEL-YL-DGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred hCCHHHHHHHHH-HH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 357778877777 55 7999999999999999999888887777666644
No 131
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=60.38 E-value=5.5 Score=35.94 Aligned_cols=46 Identities=4% Similarity=0.085 Sum_probs=37.6
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHH
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIR 268 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~ 268 (516)
.+|+.++-++.|.|+ .|.++..||..+|+|.+||...+.+....|.
T Consensus 106 ~L~~~~r~ii~l~~~-~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 106 VLDEKEKYIIFERFF-VGKTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred hCCHHHHHHHHHHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 478888888877765 6899999999999999999888877665543
No 132
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=59.93 E-value=6.1 Score=39.31 Aligned_cols=48 Identities=6% Similarity=0.187 Sum_probs=40.5
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSV 270 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~ 270 (516)
.+|+.++-.+.|+|+ .|.++..+|..+|+|.+||...+.+....|...
T Consensus 201 ~L~~~~r~vl~l~~~-~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 201 QLSEKEQLVISLFYK-EELTLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 478888888888775 899999999999999999988888877766553
No 133
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=59.87 E-value=3.4 Score=34.25 Aligned_cols=35 Identities=31% Similarity=0.281 Sum_probs=25.2
Q ss_pred hHHHHHHhhccc-CCcchhhhhhcccccceeeehhh
Q 046732 227 QRVAVCIWRLAT-GEPLRLVSKRFGLGISTCHKLVL 261 (516)
Q Consensus 227 ekL~v~L~~La~-G~s~~~la~~Fgis~STvsrii~ 261 (516)
+++...+-+|.. -.+..+|+..||+|.+||++++.
T Consensus 6 ~R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 6 ERVLEIGKYIVETKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhc
Confidence 444445555544 35588999999999999999764
No 134
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=59.12 E-value=3.4 Score=38.64 Aligned_cols=101 Identities=16% Similarity=0.121 Sum_probs=63.3
Q ss_pred CCCChhHHHHHcCCCHHHHHHHHHHhhccccccCC--CCCCCCCHhhHHHHHHhhccc--------------CCcchhhh
Q 046732 183 PDYPEEEFKKWFRMRRQTFDMICEELNSVIAKEDT--TLRNAIPVRQRVAVCIWRLAT--------------GEPLRLVS 246 (516)
Q Consensus 183 ~~~~d~~Fk~~FRmsk~tF~~L~~~L~~~i~k~~t--~~r~~l~~eekL~v~L~~La~--------------G~s~~~la 246 (516)
..++-+.|...+.-.+..-..++..+...+..... ..-...++.++|+-+|..|+. ..+..+||
T Consensus 71 ~~i~~~~~~~l~~~~p~l~~~~~~~l~~~l~~~~~~~~~l~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA 150 (193)
T TIGR03697 71 LAVPIEQVEKAIEEDPDLSMLLLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIA 150 (193)
T ss_pred EEeeHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHH
Confidence 34566777777777766666666655443221100 011235788999999877642 24789999
Q ss_pred hhcccccceeeehhhhhHHH-HHhhcccccccCCChhHH
Q 046732 247 KRFGLGISTCHKLVLEVCTA-IRSVLMPKYLQWPDDDAL 284 (516)
Q Consensus 247 ~~Fgis~STvsrii~~v~~a-L~~~L~~~~I~~P~~ee~ 284 (516)
...|+++.||+|+++++... +.. +....|..++.+.+
T Consensus 151 ~~lG~tretvsR~l~~l~~~g~I~-~~~~~i~I~d~~~L 188 (193)
T TIGR03697 151 EAIGSTRVTITRLLGDLRKKKLIS-IHKKKITVHDPIAL 188 (193)
T ss_pred HHhCCcHHHHHHHHHHHHHCCCEE-ecCCEEEEeCHHHH
Confidence 99999999999998887643 333 23344555554433
No 135
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=58.78 E-value=5.6 Score=37.52 Aligned_cols=49 Identities=16% Similarity=0.253 Sum_probs=40.9
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|++++-++.|.++ .|.++..||..+|++..||...+.+....|...|
T Consensus 138 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 138 QLPEDLRTALTLREF-DGLSYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred hCCHHHhHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 367788888888765 8999999999999999999988888777776644
No 136
>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=58.68 E-value=6.3 Score=36.59 Aligned_cols=49 Identities=20% Similarity=0.335 Sum_probs=39.4
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++.++.|.++ .|.++..||..+|+|.+||...+.+....|...|
T Consensus 100 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 100 ELPDEYREAIRLTEL-EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 467778887777664 8999999999999999999888877766665543
No 137
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=58.01 E-value=6.9 Score=37.11 Aligned_cols=49 Identities=22% Similarity=0.253 Sum_probs=40.1
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|++ -.|.++..||..+|+|.+||...+.+....|...|
T Consensus 142 ~L~~~~r~vl~l~~-~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAY-YGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 47888888777665 47899999999999999999888888777776644
No 138
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=57.62 E-value=6.9 Score=39.47 Aligned_cols=47 Identities=17% Similarity=0.357 Sum_probs=39.6
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+|+.++-++.|+|+ .|.++..||..+|+|.++|++++.+....|..
T Consensus 215 ~L~~rer~vl~l~y~-~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 215 ALPERERTVLVLRFF-ESMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred cCCHHHHHHHHHHhc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 467788888888775 69999999999999999999988887766654
No 139
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=57.39 E-value=6.4 Score=36.92 Aligned_cols=49 Identities=8% Similarity=0.076 Sum_probs=39.4
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|.++ .|.++..||..+|+|.+||...+.+....|...|
T Consensus 122 ~L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 122 ELNESNRQVFKYKVF-YNLTYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 467777777666544 7899999999999999999988888777776644
No 140
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=57.15 E-value=5.3 Score=37.98 Aligned_cols=80 Identities=9% Similarity=0.130 Sum_probs=49.7
Q ss_pred CChhHHHHHcCCCHHHHHHHHHHhhcccccc--CCCCCCCCCHhhHHHHHHhhccc-------------CCcchhhhhhc
Q 046732 185 YPEEEFKKWFRMRRQTFDMICEELNSVIAKE--DTTLRNAIPVRQRVAVCIWRLAT-------------GEPLRLVSKRF 249 (516)
Q Consensus 185 ~~d~~Fk~~FRmsk~tF~~L~~~L~~~i~k~--~t~~r~~l~~eekL~v~L~~La~-------------G~s~~~la~~F 249 (516)
++-+.|...+.-.++....++..+...+... ....-...++.++++-+|..|+. ..+...||...
T Consensus 99 i~~~~~~~l~~~~p~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~l 178 (211)
T PRK11753 99 ISYKKFRQLIQVNPDILMALSAQMARRLQNTSRKVGDLAFLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRIV 178 (211)
T ss_pred EcHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHHh
Confidence 4556777776655555444444443322110 00112346888999988887753 23357899999
Q ss_pred ccccceeeehhhhhH
Q 046732 250 GLGISTCHKLVLEVC 264 (516)
Q Consensus 250 gis~STvsrii~~v~ 264 (516)
|+++.|++|+++++.
T Consensus 179 G~tr~tvsR~l~~l~ 193 (211)
T PRK11753 179 GCSREMVGRVLKMLE 193 (211)
T ss_pred CCCHHHHHHHHHHHH
Confidence 999999998877654
No 141
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=57.07 E-value=6.2 Score=40.46 Aligned_cols=44 Identities=11% Similarity=0.134 Sum_probs=37.9
Q ss_pred CCCHhhHHHHHHhhc---ccCCcchhhhhhcccccceeeehhhhhHH
Q 046732 222 AIPVRQRVAVCIWRL---ATGEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 222 ~l~~eekL~v~L~~L---a~G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
.+|+.++..+.|+|. ..+.++..||..+|||..+|..+..+...
T Consensus 249 ~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~ 295 (298)
T TIGR02997 249 ELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALR 295 (298)
T ss_pred cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 489999999999885 68899999999999999999887766544
No 142
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=57.02 E-value=5.7 Score=39.29 Aligned_cols=49 Identities=16% Similarity=0.230 Sum_probs=40.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|++ -.|.++..||..+|+|.+||...+++....|...|
T Consensus 171 ~Lp~~~R~v~~L~~-~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 171 RLPEQQRIAVILSY-HENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred hCCHHHHHHhhhHH-hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 46777887776665 48999999999999999999988888877776644
No 143
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=56.87 E-value=7 Score=39.26 Aligned_cols=49 Identities=14% Similarity=0.286 Sum_probs=42.7
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.++-.+|+.+.|+| -.+.++..+|...|||+|.||++..+.+..|...|
T Consensus 196 ~L~EREk~Vl~l~y-~eelt~kEI~~~LgISes~VSql~kkai~kLr~~l 244 (247)
T COG1191 196 PLPEREKLVLVLRY-KEELTQKEIAEVLGISESRVSRLHKKAIKKLRKEL 244 (247)
T ss_pred ccCHHHHHHHHHHH-HhccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHh
Confidence 57788899999988 47889999999999999999999999888777654
No 144
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=56.77 E-value=6.8 Score=37.65 Aligned_cols=49 Identities=8% Similarity=0.066 Sum_probs=39.8
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++.++.|.+ -.|.++..||..+|+|.+||...+++....|...+
T Consensus 153 ~L~~~~r~vl~l~~-~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVY-FQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47888888876655 48999999999999999999888877777666544
No 145
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=56.55 E-value=6.4 Score=35.15 Aligned_cols=35 Identities=9% Similarity=0.122 Sum_probs=29.8
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceee
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCH 257 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvs 257 (516)
.+|+.++-++.|.++ .|.++..||..+|+|.+||.
T Consensus 107 ~Lp~~~r~v~~l~~~-~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 107 ILPNKQKKIIYMKFF-EDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHhhc
Confidence 478888888877554 89999999999999999985
No 146
>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.
Probab=56.43 E-value=6 Score=33.91 Aligned_cols=41 Identities=5% Similarity=0.090 Sum_probs=34.4
Q ss_pred CHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHH
Q 046732 224 PVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 224 ~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
.+.++..+.++|+ .+.++..++..+++|++|++++-...+.
T Consensus 57 d~~~r~iL~~~Yi-~~~~~~~I~~~l~~S~~t~yr~~~~Al~ 97 (100)
T PF07374_consen 57 DPDERLILRMRYI-NKLTWEQIAEELNISRRTYYRIHKKALK 97 (100)
T ss_pred ChhHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4667888888888 6899999999999999999887766554
No 147
>PF13730 HTH_36: Helix-turn-helix domain
Probab=56.29 E-value=5.5 Score=29.72 Aligned_cols=38 Identities=18% Similarity=0.267 Sum_probs=27.5
Q ss_pred hHHHHHHhhccc--C---CcchhhhhhcccccceeeehhhhhH
Q 046732 227 QRVAVCIWRLAT--G---EPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 227 ekL~v~L~~La~--G---~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
..|.+.|..+++ + .++..|+...|+|+.||.+.+.+..
T Consensus 8 ~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~ 50 (55)
T PF13730_consen 8 KLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELE 50 (55)
T ss_pred HHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 445666666652 2 2679999999999999988876643
No 148
>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=56.26 E-value=7.7 Score=37.77 Aligned_cols=47 Identities=13% Similarity=0.289 Sum_probs=39.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+|+.++-++.|+|+ .|.++..+|..+|+|.+||.+.+.+....|..
T Consensus 175 ~L~~~~r~il~l~y~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 175 SLSEREQLVLSLYYY-EELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred hCCHHHHHHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 478888888888774 78899999999999999998888777766654
No 149
>COG5421 Transposase [DNA replication, recombination, and repair]
Probab=56.23 E-value=18 Score=39.44 Aligned_cols=59 Identities=24% Similarity=0.318 Sum_probs=41.5
Q ss_pred CcccceeecceecCCCCeeccccCCCCCCCChhHhhhHHHHhhhhcC-cceeEEEEeccCCCC
Q 046732 332 KTSYSITVQGVVNPNGAFTDVCIGWPGSMPDDQVLEKSALYQRASGG-LLKGVWIVGGSGYPL 393 (516)
Q Consensus 332 K~~~Si~vq~V~D~~g~fi~v~~g~pGs~hDs~V~~~S~L~~~l~~~-~~~~~~llGD~gYpl 393 (516)
..-.-+++..+++..|--+.+.+ ++|+.+|...+-. ..+.+... ...+.++++|+||--
T Consensus 152 ~dl~QI~vsMi~~~~gIPl~~~v-~~Gni~D~~~~~~--ti~kl~~~l~~~~~~~V~Dkgf~S 211 (480)
T COG5421 152 LDLPQINVSMIVNQKGIPLFVRV-YSGNISDKNTLIK--TIQKLKSVLVKDEVYLVADKGFNS 211 (480)
T ss_pred CCcceeEEEEEEcCCCCceEEEc-cCCCccchHHHHH--HHHHHHHhcccceEEEEEcccccc
Confidence 34556888889998876666655 7999999987764 34444333 333489999999953
No 150
>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=56.22 E-value=3.5 Score=31.35 Aligned_cols=43 Identities=14% Similarity=0.217 Sum_probs=31.8
Q ss_pred CCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHH
Q 046732 223 IPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAI 267 (516)
Q Consensus 223 l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL 267 (516)
++..+.- +|..++.|.+...+|...++|.+||...+..+..-+
T Consensus 4 LT~~E~~--vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 4 LTERELE--VLRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp S-HHHHH--HHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred cCHHHHH--HHHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHh
Confidence 4544543 567889999999999999999999987776655433
No 151
>PRK15320 transcriptional activator SprB; Provisional
Probab=55.88 E-value=4.7 Score=39.12 Aligned_cols=46 Identities=22% Similarity=0.322 Sum_probs=36.5
Q ss_pred CCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHH
Q 046732 221 NAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIR 268 (516)
Q Consensus 221 ~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~ 268 (516)
+.++..+. -.|..|+.|.+...|+..+++|.+||+.+..++..-+.
T Consensus 163 ~~LSdREI--EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLg 208 (251)
T PRK15320 163 PGVTQAKY--ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLG 208 (251)
T ss_pred CCCCHHHH--HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence 34444443 56788999999999999999999999998877765544
No 152
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=55.51 E-value=7.6 Score=37.15 Aligned_cols=50 Identities=16% Similarity=0.176 Sum_probs=41.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhcc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLM 272 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~ 272 (516)
.+|+.++-++.|.++ .|.++..||..+|+|.+||...+.+....|...|.
T Consensus 133 ~Lp~~~r~v~~l~~~-~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 133 ALPPERREALILTQV-LGYTYEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred cCCHHHHHHhhhHHH-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 367778877777654 78889999999999999999988888888877653
No 153
>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=55.24 E-value=4.5 Score=30.85 Aligned_cols=29 Identities=14% Similarity=0.178 Sum_probs=24.2
Q ss_pred CCcchhhhhhcccccceeeehhhhhHHHH
Q 046732 239 GEPLRLVSKRFGLGISTCHKLVLEVCTAI 267 (516)
Q Consensus 239 G~s~~~la~~Fgis~STvsrii~~v~~aL 267 (516)
..+..+||..+|||++|++..+++...-|
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae~kl 51 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAERKL 51 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 46788999999999999999888766544
No 154
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=55.01 E-value=8.9 Score=37.31 Aligned_cols=104 Identities=12% Similarity=0.129 Sum_probs=62.7
Q ss_pred CChhHHHHHcCCCHHHHHHHHHHhhccccc--cCCCCCCCCCHhhHHHHHHhhcccC----Ccchhhhhhcccccceeee
Q 046732 185 YPEEEFKKWFRMRRQTFDMICEELNSVIAK--EDTTLRNAIPVRQRVAVCIWRLATG----EPLRLVSKRFGLGISTCHK 258 (516)
Q Consensus 185 ~~d~~Fk~~FRmsk~tF~~L~~~L~~~i~k--~~t~~r~~l~~eekL~v~L~~La~G----~s~~~la~~Fgis~STvsr 258 (516)
++-+.|...+.-.+..-..++..+...+.. .........+++++|+-+|..++.+ .+..+||...|+++.|++|
T Consensus 109 i~~~~~~~ll~~~p~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR 188 (226)
T PRK10402 109 LPMKDCRPLLLNDALFLRKLCKFLSHKNYRNIVSLTQNQSFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLY 188 (226)
T ss_pred EEHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHhccChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHH
Confidence 444566666555554444444433322110 0001122358899999999876533 3568999999999999999
Q ss_pred hhhhhHHH-HHhhcccccccCCChhHHHhhHH
Q 046732 259 LVLEVCTA-IRSVLMPKYLQWPDDDALRKIKD 289 (516)
Q Consensus 259 ii~~v~~a-L~~~L~~~~I~~P~~ee~~~i~~ 289 (516)
++.++.+- +.. .....|..++.+.+.+++.
T Consensus 189 ~L~~L~~~G~I~-~~~~~i~I~d~~~L~~~~~ 219 (226)
T PRK10402 189 VLAQFIQDGYLK-KSKRGYLIKNRKQLSGLAL 219 (226)
T ss_pred HHHHHHHCCCEE-eeCCEEEEeCHHHHHHHHH
Confidence 99888753 433 2344566666666655544
No 155
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=54.99 E-value=2.6 Score=31.12 Aligned_cols=21 Identities=14% Similarity=0.322 Sum_probs=17.8
Q ss_pred chhhhhhcccccceeeehhhh
Q 046732 242 LRLVSKRFGLGISTCHKLVLE 262 (516)
Q Consensus 242 ~~~la~~Fgis~STvsrii~~ 262 (516)
..+||...|+|.+||+++++.
T Consensus 2 i~dIA~~agvS~~TVSr~ln~ 22 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLNG 22 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHTT
T ss_pred HHHHHHHHCcCHHHHHHHHhC
Confidence 468999999999999987644
No 156
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=54.76 E-value=7.2 Score=36.12 Aligned_cols=48 Identities=10% Similarity=0.068 Sum_probs=37.4
Q ss_pred CCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 223 IPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 223 l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
+|+..+-++. .++-.|.++..+|..+|+|.+||...+.+....|...|
T Consensus 120 L~~~~r~i~~-l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 167 (173)
T PRK12522 120 LNEKYKTVLV-LYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHL 167 (173)
T ss_pred CCHHHHHHHH-HHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 5555554443 44558999999999999999999998888888777644
No 157
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=54.31 E-value=8.2 Score=36.29 Aligned_cols=48 Identities=13% Similarity=0.158 Sum_probs=38.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSV 270 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~ 270 (516)
.+|+.++-++.|.|+ .|.++..||..+|+|.+||...+.+....|...
T Consensus 139 ~L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 139 TLPEKQREILILRVV-VGLSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467778777777655 489999999999999999988887777666543
No 158
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=54.28 E-value=8.5 Score=39.97 Aligned_cols=48 Identities=10% Similarity=0.175 Sum_probs=41.3
Q ss_pred CCCHhhHHHHHHhhc---ccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRL---ATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~L---a~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+|+.++..+.|+|. ..+.++..||..+|||..+|..+..+...-|..
T Consensus 256 ~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~ 306 (317)
T PRK07405 256 DLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK 306 (317)
T ss_pred cCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 489999999999986 477899999999999999999988777766654
No 159
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=53.78 E-value=6.9 Score=28.39 Aligned_cols=36 Identities=8% Similarity=0.210 Sum_probs=25.4
Q ss_pred HHHHHHhhcccCCcchhhhhhcccccceeeehhhhhH
Q 046732 228 RVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 228 kL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
+++-.|+- ..+.+..+++..+|+|.+||++++.++.
T Consensus 7 ~Il~~l~~-~~~~t~~ela~~~~is~~tv~~~l~~L~ 42 (48)
T PF13412_consen 7 KILNYLRE-NPRITQKELAEKLGISRSTVNRYLKKLE 42 (48)
T ss_dssp HHHHHHHH-CTTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHH-cCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 34444433 4558899999999999999998887764
No 160
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=53.16 E-value=8.3 Score=35.17 Aligned_cols=47 Identities=13% Similarity=0.225 Sum_probs=38.1
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+|+.++.++.|.++ .|.++..+|..+|+|.+||...+.+....|..
T Consensus 112 ~L~~~~r~v~~l~~~-~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 112 SLPLERRNVLLLRDY-YGFSYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HCCHHHHHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 578888888877654 78899999999999999988877776665543
No 161
>PF13551 HTH_29: Winged helix-turn helix
Probab=53.07 E-value=4.8 Score=34.17 Aligned_cols=34 Identities=18% Similarity=0.290 Sum_probs=29.4
Q ss_pred HHhhcccCCc-chhhhhhcccccceeeehhhhhHH
Q 046732 232 CIWRLATGEP-LRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 232 ~L~~La~G~s-~~~la~~Fgis~STvsrii~~v~~ 265 (516)
+|..++.|.+ ...++..+|+|.+||++++..+..
T Consensus 4 ~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~ 38 (112)
T PF13551_consen 4 ILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYRE 38 (112)
T ss_pred HHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHc
Confidence 4566889996 999999999999999999988653
No 162
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=52.60 E-value=4.5 Score=30.10 Aligned_cols=37 Identities=27% Similarity=0.316 Sum_probs=25.8
Q ss_pred HHHHHHhhcc---cCCcchhhhhhcccccceeeehhhhhH
Q 046732 228 RVAVCIWRLA---TGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 228 kL~v~L~~La---~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
+.+-.|..|+ .+.+..+|+...|+++||+++++...+
T Consensus 4 ral~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~ 43 (52)
T PF09339_consen 4 RALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLV 43 (52)
T ss_dssp HHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3344454554 344689999999999999998876654
No 163
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=52.57 E-value=5 Score=30.83 Aligned_cols=27 Identities=15% Similarity=0.127 Sum_probs=22.1
Q ss_pred CCcchhhhhhcccccceeeehhhhhHH
Q 046732 239 GEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 239 G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
..+..+|+..+|++++||++++..+..
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 357889999999999999888766543
No 164
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=52.31 E-value=4.9 Score=37.17 Aligned_cols=50 Identities=10% Similarity=0.254 Sum_probs=39.4
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhcc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLM 272 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~ 272 (516)
.+|+.++-++.|++ -.|.++.++|..+|+|.+||...+.+....|...|.
T Consensus 120 ~L~~~~r~vl~l~~-~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 120 TLSLEHRAVLVLHD-LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred hCCHHHeeeeeehH-hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 36666776666654 478889999999999999999888888877776553
No 165
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=52.25 E-value=16 Score=37.10 Aligned_cols=68 Identities=16% Similarity=0.349 Sum_probs=48.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhcccccccCCChhHHHhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLMPKYLQWPDDDALRKIKDEFEV 293 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~~~~I~~P~~ee~~~i~~~F~~ 293 (516)
.+|+.++.++.|+++ .|.+|..||..+|+|.+||...+++.-..|...+ +.+. +..++...+...|..
T Consensus 115 ~L~~~~R~v~~L~~~-~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~-~~~~--~~~~~~~~~v~~f~~ 182 (293)
T PRK09636 115 RLSPLERAAFLLHDV-FGVPFDEIASTLGRSPAACRQLASRARKHVRAAR-PRFP--VSDEEGAELVEAFFA 182 (293)
T ss_pred hCCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC-CCCC--CCchHHHHHHHHHHH
Confidence 378888887777654 6899999999999999999999988888877743 3221 222333445555544
No 166
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=52.06 E-value=6.2 Score=38.74 Aligned_cols=49 Identities=16% Similarity=0.191 Sum_probs=39.7
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|+++ .|.++..||..+|+|.+||...+.+....|...+
T Consensus 149 ~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 149 ALPDAFRAVFVLRVV-EELSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred hCCHHHhhhheeehh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 367777777766654 5999999999999999999888888777776654
No 167
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=51.44 E-value=7.4 Score=30.21 Aligned_cols=40 Identities=13% Similarity=0.253 Sum_probs=29.2
Q ss_pred HhhHHHHHHhhcc---cCCcchhhhhhcccccceeeehhhhhH
Q 046732 225 VRQRVAVCIWRLA---TGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 225 ~eekL~v~L~~La---~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
..+.-+-+++.|. ...+..+||..++++++||+..+.+..
T Consensus 5 ~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~ 47 (60)
T PF01325_consen 5 SEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA 47 (60)
T ss_dssp HHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH
Confidence 3455666677776 567788999999999999887766543
No 168
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=51.36 E-value=11 Score=39.15 Aligned_cols=73 Identities=15% Similarity=0.203 Sum_probs=51.1
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhcccccccC---CChhHHHhhHHHHHhhhC
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLMPKYLQW---PDDDALRKIKDEFEVISG 296 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~~~~I~~---P~~ee~~~i~~~F~~~~g 296 (516)
.+|+.++-++.|++ -.|.++..|+..+|+|.+||...+.+....|... .+....- |..++...+...|...++
T Consensus 153 ~Lp~~~R~v~~L~~-~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~-~~~~~~~~~~~~~~~~~~~v~~~~~A~~ 228 (339)
T PRK08241 153 HLPPRQRAVLILRD-VLGWSAAEVAELLDTSVAAVNSALQRARATLAER-GPSAADTLREPDDPEERALLARYVAAFE 228 (339)
T ss_pred hCCHHHhhhhhhHH-hhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhc-CCCcccccCCCCChHHHHHHHHHHHHHh
Confidence 46777888777765 5899999999999999999999988888877762 3332111 223455556666655443
No 169
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=51.21 E-value=6.4 Score=29.65 Aligned_cols=28 Identities=14% Similarity=0.291 Sum_probs=22.1
Q ss_pred ccCCcchhhhhhcccccceeeehhhhhH
Q 046732 237 ATGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 237 a~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
..|.+..+|+..++++++++++++....
T Consensus 15 ~~~~~~~~la~~~~~~~~~~t~~i~~L~ 42 (59)
T PF01047_consen 15 NGGITQSELAEKLGISRSTVTRIIKRLE 42 (59)
T ss_dssp HSSEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCChhHHHHHHHHHH
Confidence 4557899999999999999888776653
No 170
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=50.94 E-value=17 Score=28.40 Aligned_cols=71 Identities=11% Similarity=0.111 Sum_probs=49.3
Q ss_pred hhHHHHHcCCCHHHHHHHHHHhhccccccCCCCCCCCCHhhHHHHHHhhcccC-Ccchhhhhhccc-ccceeeehhhhhH
Q 046732 187 EEEFKKWFRMRRQTFDMICEELNSVIAKEDTTLRNAIPVRQRVAVCIWRLATG-EPLRLVSKRFGL-GISTCHKLVLEVC 264 (516)
Q Consensus 187 d~~Fk~~FRmsk~tF~~L~~~L~~~i~k~~t~~r~~l~~eekL~v~L~~La~G-~s~~~la~~Fgi-s~STvsrii~~v~ 264 (516)
=+++-..++++...|..++......-.+ ..-...++.-++.+|..+ .+..+++..+|+ +.++.++.|.+..
T Consensus 4 ~~~la~~~~~s~~~l~~~f~~~~~~s~~-------~~~~~~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk~~~ 76 (84)
T smart00342 4 LEDLAEALGMSPRHLQRLFKKETGTTPK-------QYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLF 76 (84)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHhCcCHH-------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 3567788999999988887754321000 111234566677777665 799999999999 9999888876653
No 171
>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=50.44 E-value=18 Score=36.61 Aligned_cols=68 Identities=13% Similarity=0.273 Sum_probs=48.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhcccccccCCChhHHHhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLMPKYLQWPDDDALRKIKDEFEV 293 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~~~~I~~P~~ee~~~i~~~F~~ 293 (516)
.+|+.++-++.|+++ .|.++.+|+..+|+|.+||...+++....|.+.. +.+. +..++...+.+.|-.
T Consensus 108 ~L~~~~R~v~~L~~~-~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~-~~~~--~~~~~~~~~~~~f~~ 175 (281)
T TIGR02957 108 RLSPLERAVFVLREV-FDYPYEEIASIVGKSEANCRQLVSRARRHLDARR-PRFE--VSREESRQLLERFVE 175 (281)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC-CCCC--CChHHHHHHHHHHHH
Confidence 467888887777554 6899999999999999999999988888877642 3321 122344455555543
No 172
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=50.32 E-value=6.6 Score=28.63 Aligned_cols=28 Identities=14% Similarity=0.153 Sum_probs=22.2
Q ss_pred ccCCcchhhhhhcccccceeeehhhhhH
Q 046732 237 ATGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 237 a~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
....+..+|+..+|++++||++.+....
T Consensus 13 ~~~~~~~el~~~l~~s~~~vs~hL~~L~ 40 (47)
T PF01022_consen 13 EGPLTVSELAEELGLSQSTVSHHLKKLR 40 (47)
T ss_dssp TSSEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred hCCCchhhHHHhccccchHHHHHHHHHH
Confidence 3567789999999999999998876543
No 173
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=48.93 E-value=10 Score=35.89 Aligned_cols=49 Identities=10% Similarity=0.098 Sum_probs=39.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+..+-++.|++ -.|.++..||..+|+|.+||...+.+....|...|
T Consensus 128 ~Lp~~~r~v~~l~~-~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 128 KLDPEYREPLLLQV-IGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred hCCHHHHHHHHHHH-HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46777777666554 47999999999999999999988888877777654
No 174
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=48.79 E-value=8.3 Score=31.60 Aligned_cols=39 Identities=31% Similarity=0.420 Sum_probs=29.1
Q ss_pred hHHHHHHhhccc---CCcchhhhhhcccccceeeehhhhhHH
Q 046732 227 QRVAVCIWRLAT---GEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 227 ekL~v~L~~La~---G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
.+....|.+|+. +.+..+++..+|++++||++++.....
T Consensus 5 ~r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 5 ERGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 444455555543 478999999999999999998877643
No 175
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=48.67 E-value=12 Score=39.15 Aligned_cols=50 Identities=20% Similarity=0.283 Sum_probs=43.2
Q ss_pred CCCHhhHHHHHHhh-c--ccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWR-L--ATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~-L--a~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++.++.++| | -.|.++..||..+||+.+||..++++....|...|
T Consensus 262 ~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 58899999998876 4 47899999999999999999999988888777655
No 176
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=48.56 E-value=9.9 Score=35.80 Aligned_cols=41 Identities=7% Similarity=0.097 Sum_probs=30.9
Q ss_pred hHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 227 QRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 227 ekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+.++ +.++ .|.++..||..+|+|.+||...+++....|..
T Consensus 155 ~~~i~-~~~~-~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 155 EWKVL-QSYL-DGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred HHHHH-HHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44444 4444 89999999999999999998777766655544
No 177
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=48.46 E-value=10 Score=33.04 Aligned_cols=46 Identities=15% Similarity=0.281 Sum_probs=39.8
Q ss_pred CCCCCHhhHHHHHHhhcccCCcchhhhhhccc-ccceeeehhhhhHH
Q 046732 220 RNAIPVRQRVAVCIWRLATGEPLRLVSKRFGL-GISTCHKLVLEVCT 265 (516)
Q Consensus 220 r~~l~~eekL~v~L~~La~G~s~~~la~~Fgi-s~STvsrii~~v~~ 265 (516)
+...|.+.++-++-.++..|.++..++..||| +.+++++.+.+.-.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~ 51 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQK 51 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 56789999999999999999999999999996 99998877665543
No 178
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=48.29 E-value=7.2 Score=36.85 Aligned_cols=49 Identities=16% Similarity=0.177 Sum_probs=38.4
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++.++.|++ -.|.++..||..+|+|.+||...+.+....|...|
T Consensus 139 ~L~~~~r~i~~l~~-~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 139 TLPDEQREVFLLRE-HGDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred hCCHhHhhheeeeh-ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 36777777666654 58999999999999999999888777776666544
No 179
>PRK13870 transcriptional regulator TraR; Provisional
Probab=47.78 E-value=19 Score=35.70 Aligned_cols=46 Identities=9% Similarity=0.147 Sum_probs=38.5
Q ss_pred CCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHH
Q 046732 221 NAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIR 268 (516)
Q Consensus 221 ~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~ 268 (516)
..+++.|+ =+|.|++.|.+..+||...|||.+||..++..+..-|.
T Consensus 172 ~~LT~RE~--E~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~na~~KLg 217 (234)
T PRK13870 172 AWLDPKEA--TYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFD 217 (234)
T ss_pred CCCCHHHH--HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 46777776 57889999999999999999999999888877765443
No 180
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=47.76 E-value=13 Score=38.78 Aligned_cols=69 Identities=7% Similarity=0.080 Sum_probs=46.0
Q ss_pred HHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhcccccccCCChhHHHhhHHHHHhhhCCCccccC
Q 046732 231 VCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLMPKYLQWPDDDALRKIKDEFEVISGIPNVVGS 303 (516)
Q Consensus 231 v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~~~~I~~P~~ee~~~i~~~F~~~~gfP~~vGa 303 (516)
++=+|+-.|.++.++|..+|+|+++|+|++.+.-+. -+-.--|.-|. .....+...+.+++|+..|+-+
T Consensus 21 vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~---GiV~I~I~~~~-~~~~~Le~~L~~~fgLk~~iVv 89 (318)
T PRK15418 21 IAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQS---GIIRVQINSRF-EGCLELENALRQHFSLQHIRVL 89 (318)
T ss_pred HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHc---CcEEEEEeCCC-ccHHHHHHHHHHHhCCCEEEEE
Confidence 666788899999999999999999999988764321 11122333343 2233455566666777776544
No 181
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=47.30 E-value=6.7 Score=31.39 Aligned_cols=41 Identities=27% Similarity=0.282 Sum_probs=29.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcc-cccceeeehhhh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFG-LGISTCHKLVLE 262 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fg-is~STvsrii~~ 262 (516)
.+.-.-++++.|.+--++.++.+||..|| .+.|||...+++
T Consensus 28 ~i~~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHstV~~a~~k 69 (70)
T PF08299_consen 28 KIVEARQVAMYLARELTGLSLSEIGRYFGGRDHSTVIHAIRK 69 (70)
T ss_dssp HHHHHHHHHHHHHHHHS---HHHHHHHCTSSTHHHHHHHHHH
T ss_pred hhcchHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHHh
Confidence 34445678887777778999999999999 999998665544
No 182
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=47.12 E-value=12 Score=38.96 Aligned_cols=69 Identities=10% Similarity=0.187 Sum_probs=43.9
Q ss_pred HHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhcccccccCCChhHHHhhHHHHHhhhCCCccccC
Q 046732 231 VCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLMPKYLQWPDDDALRKIKDEFEVISGIPNVVGS 303 (516)
Q Consensus 231 v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~~~~I~~P~~ee~~~i~~~F~~~~gfP~~vGa 303 (516)
++-.|+..|.++.+|+..+|||+.+|+|.+...-. +-+-.-.|..|. ...-.+.+...+.+|++.|+-+
T Consensus 18 ~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~---~GiV~I~i~~~~-~~~~~Le~~L~~~fgL~~a~VV 86 (321)
T COG2390 18 AAWLYYVEGLTQSEIAERLGISRATVSRLLAKARE---EGIVKISINSPV-EGCLELEQQLKERFGLKEAIVV 86 (321)
T ss_pred HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH---CCeEEEEeCCCC-cchHHHHHHHHHhcCCCeEEEE
Confidence 34467789999999999999999999988765321 112233344332 2223345555666677766544
No 183
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=46.62 E-value=12 Score=37.71 Aligned_cols=49 Identities=18% Similarity=0.331 Sum_probs=39.9
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-++.|+|+ .|.++..||..+|+|.+||.+.+.+....|...|
T Consensus 212 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 260 (268)
T PRK06288 212 TLPEREKKVLILYYY-EDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260 (268)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888764 7899999999999999999888777766665543
No 184
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=45.03 E-value=12 Score=34.64 Aligned_cols=47 Identities=15% Similarity=0.228 Sum_probs=35.4
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+|+.++-++.| .+-.|.+|..||..+|+|.+||...+.+....+..
T Consensus 119 ~L~~~~r~i~~l-~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 119 GLNGKTREAFLL-SQLDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred hCCHHHhHHhhh-hhccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 356667655554 44588899999999999999998887776655543
No 185
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=44.61 E-value=15 Score=34.87 Aligned_cols=46 Identities=20% Similarity=0.286 Sum_probs=34.6
Q ss_pred CCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 223 IPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 223 l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
+++.+.=.+.|+++ .|.++..||...|||.+||.+-+...-..|..
T Consensus 136 l~~~~~~~v~l~~~-~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 136 LDPRQRRVVELRFF-EGLSVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred cCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45566656666555 88999999999999999998877665544443
No 186
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=44.12 E-value=24 Score=36.10 Aligned_cols=68 Identities=18% Similarity=0.242 Sum_probs=47.7
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhcccccccCCChhHHHhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLMPKYLQWPDDDALRKIKDEFEV 293 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~~~~I~~P~~ee~~~i~~~F~~ 293 (516)
.+|+.++.++.|+++ .|.+|..|+...|+|.+||...+++....|... .+.+- |..++...+.+.|-.
T Consensus 118 ~L~p~~R~vf~L~~~-~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~-~~~~~--~~~~~~~~~~~~f~~ 185 (290)
T PRK09635 118 RLGPAERVVFVLHEI-FGLPYQQIATTIGSQASTCRQLAHRARRKINES-RIAAS--VEPAQHRVVTRAFIE 185 (290)
T ss_pred hCCHHHHHHhhHHHH-hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh-CCCCC--CChHHHHHHHHHHHH
Confidence 467778877766554 699999999999999999999998888777763 33322 223334455555543
No 187
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=44.09 E-value=15 Score=36.26 Aligned_cols=45 Identities=11% Similarity=0.194 Sum_probs=37.2
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHH
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAI 267 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL 267 (516)
.+|+.++-.+.|+| -.|.++..+|..+|+|.++|+++......-|
T Consensus 183 ~L~~~er~vi~l~~-~~~~t~~EIA~~lgis~~~V~q~~~~~~~kL 227 (231)
T PRK12427 183 QLDEREQLILHLYY-QHEMSLKEIALVLDLTEARICQLNKKIAQKI 227 (231)
T ss_pred cCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 47788888888877 4789999999999999999888877666544
No 188
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=43.74 E-value=14 Score=39.30 Aligned_cols=48 Identities=10% Similarity=0.142 Sum_probs=40.4
Q ss_pred CCCHhhHHHHHHhhc---ccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRL---ATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~L---a~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+|+.++..+.|+|+ ..+.++..||..+|||+.+|..+..+.+.-|..
T Consensus 311 ~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~ 361 (373)
T PRK07406 311 TLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRH 361 (373)
T ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 488999999999886 246899999999999999999988877766654
No 189
>PRK09191 two-component response regulator; Provisional
Probab=43.25 E-value=24 Score=34.34 Aligned_cols=52 Identities=13% Similarity=0.172 Sum_probs=41.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhcccc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLMPK 274 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~~~ 274 (516)
.+|+.++-.+.|.++ .|.+|..++...|+|.+||...+.+....+...+...
T Consensus 88 ~L~~~~r~v~~l~~~-~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~~~ 139 (261)
T PRK09191 88 GLTPLPRQAFLLTAL-EGFSVEEAAEILGVDPAEAEALLDDARAEIARQVATR 139 (261)
T ss_pred hCCHHHhHHHHHHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCCCe
Confidence 366777776766554 7889999999999999999999988888887655444
No 190
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=43.00 E-value=18 Score=32.59 Aligned_cols=48 Identities=15% Similarity=0.074 Sum_probs=37.9
Q ss_pred CCHhhHHHHHHhhcc-cCCcchhhhhhcccccceeeehhhhhHHHHHhh
Q 046732 223 IPVRQRVAVCIWRLA-TGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSV 270 (516)
Q Consensus 223 l~~eekL~v~L~~La-~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~ 270 (516)
++.+++-.+-++|+. ...++..|+..+|+|++|+++.-..++..|...
T Consensus 83 Ld~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~ 131 (134)
T TIGR01636 83 ADEQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEE 131 (134)
T ss_pred CCHHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 566788888888774 335899999999999999998877777666553
No 191
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=42.80 E-value=13 Score=36.06 Aligned_cols=101 Identities=10% Similarity=0.070 Sum_probs=60.7
Q ss_pred CChhHHHHHcCCCHHHHHHHHHHhhcccccc--CCCCCCCCCHhhHHHHHHhhcccC----------Ccchhhhhhcccc
Q 046732 185 YPEEEFKKWFRMRRQTFDMICEELNSVIAKE--DTTLRNAIPVRQRVAVCIWRLATG----------EPLRLVSKRFGLG 252 (516)
Q Consensus 185 ~~d~~Fk~~FRmsk~tF~~L~~~L~~~i~k~--~t~~r~~l~~eekL~v~L~~La~G----------~s~~~la~~Fgis 252 (516)
++-+.|...+.-++..-..++..+...+... ........++.++++-+|..++.. .+..+||...|++
T Consensus 107 i~~~~~~~l~~~~p~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~lG~t 186 (236)
T PRK09392 107 IPAELVREAMSEDPGFMRAVVFELAGCYRGLVKSLKNQKLRSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYLGMT 186 (236)
T ss_pred EeHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHhCCC
Confidence 4556676666655554444444443211100 000122458999999999877642 2246799999999
Q ss_pred cceeeehhhhhHHHHHhhcccccccCCChhHHHh
Q 046732 253 ISTCHKLVLEVCTAIRSVLMPKYLQWPDDDALRK 286 (516)
Q Consensus 253 ~STvsrii~~v~~aL~~~L~~~~I~~P~~ee~~~ 286 (516)
+.||+|+++++...=.. +....|..++.+.+..
T Consensus 187 retvsR~l~~L~~~gl~-~~~~~i~I~d~~~L~~ 219 (236)
T PRK09392 187 PENLSRAFAALASHGVH-VDGSAVTITDPAGLAR 219 (236)
T ss_pred hhHHHHHHHHHHhCCeE-eeCCEEEEcCHHHHHH
Confidence 99999998886543222 3345666676655544
No 192
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=42.05 E-value=16 Score=38.80 Aligned_cols=48 Identities=15% Similarity=0.162 Sum_probs=39.4
Q ss_pred CCCHhhHHHHHHhhc-c--cCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRL-A--TGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~L-a--~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+|+.++..+.|+|. . .+.++..||..||||+..|+++-.+.+.-|..
T Consensus 305 ~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~ 355 (367)
T PRK09210 305 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRH 355 (367)
T ss_pred hCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhC
Confidence 588899999999885 3 45899999999999999999887766655543
No 193
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=41.67 E-value=12 Score=27.79 Aligned_cols=28 Identities=11% Similarity=0.144 Sum_probs=21.6
Q ss_pred cCCcchhhhhhcccccceeeehhhhhHH
Q 046732 238 TGEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 238 ~G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
.+.+...||..|+||..||.+.+...-.
T Consensus 14 ~~it~~eLa~~l~vS~rTi~~~i~~L~~ 41 (55)
T PF08279_consen 14 EPITAKELAEELGVSRRTIRRDIKELRE 41 (55)
T ss_dssp TSBEHHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3468899999999999999887766533
No 194
>COG3293 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=41.32 E-value=6.6 Score=34.62 Aligned_cols=89 Identities=12% Similarity=0.156 Sum_probs=56.6
Q ss_pred eecceecCCCCeeccccCC-----CCCCCChhHhhhHHHHhhhhcCcceeEEEEeccCCCCcccccCccccCc----ccc
Q 046732 338 TVQGVVNPNGAFTDVCIGW-----PGSMPDDQVLEKSALYQRASGGLLKGVWIVGGSGYPLMDWVLVPYTQQH----LTW 408 (516)
Q Consensus 338 ~vq~V~D~~g~fi~v~~g~-----pGs~hDs~V~~~S~L~~~l~~~~~~~~~llGD~gYpl~~~LltPy~~~~----lt~ 408 (516)
+.++++|..|+++....+- +...+.. ++. .+ .-+|.|.+|...+|-+.|-..+. ...
T Consensus 2 ~~~~l~D~~~~~i~~~lp~~~~~~~~~~~~~---~~~----~v-------~~~i~~~~~~g~~wr~~p~~~~~~~~~~~~ 67 (124)
T COG3293 2 KLHALVDAEWRPVEPLLPPAKYGGPPGVTLL---RDR----EV-------LNGIADLLYTGCAWRALPADFPPATTVIPY 67 (124)
T ss_pred CcccccccccceeeccCCCcccCCCCCCccc---ccH----HH-------HHHHHHHhccchHHHHhHHHhCCCceEeCC
Confidence 3568999999988877761 1111111 100 00 01456778887777665543211 112
Q ss_pred --chhhhhhhhhhhhhhhhhhhhhccccccccccc
Q 046732 409 --TQHAFNEKIGEIQRVSKDAFARLKGRWCCLQKR 441 (516)
Q Consensus 409 --~q~~FN~~~s~~R~~VE~aFG~LK~RFriL~~~ 441 (516)
.+.-++..+...|..+|+.|+.+|. |+.+...
T Consensus 68 ~~~~~~~~~g~~~~~~~~~~~f~~~~~-~r~~~~~ 101 (124)
T COG3293 68 RRFRRWFKRGLWKRRNLVERTFGRLKQ-FRRTATR 101 (124)
T ss_pred CcchhhHHHHHHHHHHHHHHHHHHHhc-ccceecc
Confidence 2577888999999999999999994 8877654
No 195
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=41.11 E-value=8.2 Score=36.35 Aligned_cols=48 Identities=8% Similarity=0.121 Sum_probs=36.1
Q ss_pred CCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 223 IPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 223 l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
+|+.++=++.|.++ .|.++..||..+|+|.+||...+.+....|...+
T Consensus 135 L~~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 135 VNPIDREILVLRFV-AELEFQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred cChhheeeeeeHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45555544545444 8899999999999999999888888777666543
No 196
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=40.99 E-value=15 Score=35.31 Aligned_cols=49 Identities=18% Similarity=0.316 Sum_probs=39.1
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHhhc
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVL 271 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L 271 (516)
.+|+.++-.+.|.+ -.|.++..||..+|+|.+||...+.+....|...+
T Consensus 138 ~L~~~~r~v~~L~~-~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 138 SLPPEFRAAVVLCD-IEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 36676776666654 58999999999999999999988888777776654
No 197
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=40.78 E-value=16 Score=39.43 Aligned_cols=47 Identities=11% Similarity=0.137 Sum_probs=39.4
Q ss_pred CCCHhhHHHHHHhhc---ccCCcchhhhhhcccccceeeehhhhhHHHHH
Q 046732 222 AIPVRQRVAVCIWRL---ATGEPLRLVSKRFGLGISTCHKLVLEVCTAIR 268 (516)
Q Consensus 222 ~l~~eekL~v~L~~L---a~G~s~~~la~~Fgis~STvsrii~~v~~aL~ 268 (516)
.+|+.++-.+.|+|. ..+.++..||..+|+|.++|..+.++....|.
T Consensus 350 ~L~~reR~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~KLR 399 (415)
T PRK07598 350 DLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLR 399 (415)
T ss_pred hCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHh
Confidence 478889999999885 35689999999999999999988877766555
No 198
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.74 E-value=15 Score=31.83 Aligned_cols=42 Identities=7% Similarity=0.096 Sum_probs=34.8
Q ss_pred hHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 227 QRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 227 ekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
++--+-|+| ....|+..||+.|+||+++|+..|.+++..+..
T Consensus 22 Q~~Y~~lyy-~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~ 63 (105)
T COG2739 22 QKNYLELYY-LDDLSLSEIAEEFNVSRQAIYDNIKRTEKILED 63 (105)
T ss_pred HHHHHHHHH-HhhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 555555654 567789999999999999999999999888775
No 199
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=40.60 E-value=12 Score=36.38 Aligned_cols=101 Identities=18% Similarity=0.213 Sum_probs=56.8
Q ss_pred CChhHHHHHcCCCHHHHHHHHHHhhcccccc--CCCCCCCCCHhhHHHHHHhhccc--------------CCcchhhhhh
Q 046732 185 YPEEEFKKWFRMRRQTFDMICEELNSVIAKE--DTTLRNAIPVRQRVAVCIWRLAT--------------GEPLRLVSKR 248 (516)
Q Consensus 185 ~~d~~Fk~~FRmsk~tF~~L~~~L~~~i~k~--~t~~r~~l~~eekL~v~L~~La~--------------G~s~~~la~~ 248 (516)
+|-+.|...+.=.++.-..++..+...+... ....-...++++|++-+|..|+. ..+...||..
T Consensus 114 ip~~~f~~l~~~~p~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~ 193 (235)
T PRK11161 114 IPFETLDDLSGKMPKLRQQIMRLMSGEIKGDQEMILLLSKKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNY 193 (235)
T ss_pred EEHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHH
Confidence 4446666666555544344444333211100 00001235789999999988752 2467899999
Q ss_pred cccccceeeehhhhhHHH-HHhhcccccccCCChhHHHh
Q 046732 249 FGLGISTCHKLVLEVCTA-IRSVLMPKYLQWPDDDALRK 286 (516)
Q Consensus 249 Fgis~STvsrii~~v~~a-L~~~L~~~~I~~P~~ee~~~ 286 (516)
.|+++.|++|++.++-.. +.. +....|..++...+..
T Consensus 194 lG~sr~tvsR~l~~l~~~g~I~-~~~~~i~i~d~~~L~~ 231 (235)
T PRK11161 194 LGLTVETISRLLGRFQKSGMLA-VKGKYITIENNDALAQ 231 (235)
T ss_pred hCCcHHHHHHHHHHHHHCCCEE-ecCCEEEEcCHHHHHH
Confidence 999999999987665421 222 2334444454444433
No 200
>PRK05949 RNA polymerase sigma factor; Validated
Probab=40.34 E-value=19 Score=37.64 Aligned_cols=48 Identities=19% Similarity=0.234 Sum_probs=40.2
Q ss_pred CCCHhhHHHHHHhh-cc--cCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWR-LA--TGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~-La--~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+|+.++-.+.|+| |. .+.++..||..+|+|.++|..+..+....|..
T Consensus 266 ~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~ 316 (327)
T PRK05949 266 ELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR 316 (327)
T ss_pred hCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 47888999999987 43 56899999999999999999888877766654
No 201
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=40.33 E-value=16 Score=32.92 Aligned_cols=42 Identities=10% Similarity=0.094 Sum_probs=30.0
Q ss_pred CCHhh-HHHHHHhhcccCCcchhhhhhcccccceeeehhhhhH
Q 046732 223 IPVRQ-RVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 223 l~~ee-kL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
+++.+ .++..|+....+.+..+|+..++++++|+++++.+..
T Consensus 29 lt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le 71 (144)
T PRK03573 29 LTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLE 71 (144)
T ss_pred CCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHH
Confidence 44444 4455554444457889999999999999988776654
No 202
>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=39.99 E-value=7.3 Score=34.42 Aligned_cols=38 Identities=29% Similarity=0.488 Sum_probs=29.7
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhh
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLE 262 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~ 262 (516)
++...++|+ -++..|.+.+.++..|+||.+||.+++..
T Consensus 4 S~DlR~rVl---~~~~~g~s~~eaa~~F~VS~~Tv~~W~k~ 41 (119)
T PF01710_consen 4 SLDLRQRVL---AYIEKGKSIREAAKRFGVSRNTVYRWLKR 41 (119)
T ss_pred CHHHHHHHH---HHHHccchHHHHHHHhCcHHHHHHHHHHh
Confidence 345556654 46677899999999999999999887763
No 203
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=38.77 E-value=11 Score=29.06 Aligned_cols=33 Identities=18% Similarity=0.264 Sum_probs=23.1
Q ss_pred Hhhcc---cCCcchhhhhhcccccceeeehhhhhHH
Q 046732 233 IWRLA---TGEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 233 L~~La---~G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
|++++ .+.+..+|+..++++++++++.+.+.+.
T Consensus 9 L~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~ 44 (68)
T PF13463_consen 9 LRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEE 44 (68)
T ss_dssp HHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred HHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 44444 4567899999999999999988777653
No 204
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=38.60 E-value=18 Score=28.71 Aligned_cols=39 Identities=8% Similarity=0.178 Sum_probs=29.3
Q ss_pred CHhhHHHHHHhhccc-CCcchhhhhhcccccceeeehhhh
Q 046732 224 PVRQRVAVCIWRLAT-GEPLRLVSKRFGLGISTCHKLVLE 262 (516)
Q Consensus 224 ~~eekL~v~L~~La~-G~s~~~la~~Fgis~STvsrii~~ 262 (516)
+.+++++.+|..-.. +.+..+|+..+|++.++|++++..
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~ 45 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYS 45 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 455677777765544 488999999999999998766544
No 205
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=37.88 E-value=22 Score=32.07 Aligned_cols=116 Identities=15% Similarity=0.107 Sum_probs=61.1
Q ss_pred ecceecCCCCeeccccCCCCCCCChhHhhhHHHHhhhhcCc-ceeEEEEecc--CCCCcccccCccccCccccchhhhhh
Q 046732 339 VQGVVNPNGAFTDVCIGWPGSMPDDQVLEKSALYQRASGGL-LKGVWIVGGS--GYPLMDWVLVPYTQQHLTWTQHAFNE 415 (516)
Q Consensus 339 vq~V~D~~g~fi~v~~g~pGs~hDs~V~~~S~L~~~l~~~~-~~~~~llGD~--gYpl~~~LltPy~~~~lt~~q~~FN~ 415 (516)
+=.++|++|+++++.+.-.-...++.-| ...+.... ..+..++.|. +||.--.-+.|-.... ...+. .
T Consensus 20 l~~aiD~~~~~l~~~ls~~Rd~~aA~~F-----l~~~l~~~~~~p~~ivtDk~~aY~~A~~~l~~~~~~~-~~v~~---~ 90 (140)
T PF13610_consen 20 LWRAIDAEGNILDFYLSKRRDTAAAKRF-----LKRALKRHRGEPRVIVTDKLPAYPAAIKELNPEGRLH-DKVEH---R 90 (140)
T ss_pred EEEeecccccchhhhhhhhcccccceee-----ccccceeeccccceeecccCCccchhhhhcccccccc-cccce---e
Confidence 3468999999988877633333333222 12222222 3345677673 3443222222111000 00001 0
Q ss_pred hhhhhhhhhhhhhhhccccccccccccccCCCCcchhhhHHHHHhhhhhh
Q 046732 416 KIGEIQRVSKDAFARLKGRWCCLQKRTEVKLQDLPVVLGACCVLHNICEM 465 (516)
Q Consensus 416 ~~s~~R~~VE~aFG~LK~RFriL~~~~~~~~~~~~~iI~AccvLHNi~~~ 465 (516)
..--.++.||+-+..+|.|.+....- -+...+...+..-++.||+..-
T Consensus 91 ~~k~~nN~iE~~h~~~K~r~r~~~gF--ks~~~A~~~l~~~~~~~n~~r~ 138 (140)
T PF13610_consen 91 QRKYLNNRIERDHRTIKRRTRPMNGF--KSFRSAQRTLSGFEAYHNFRRP 138 (140)
T ss_pred echhhhChhhHhhhhhhhhcccccCc--CCHHHHHHHHHHHHHHHHHhCC
Confidence 11234788999999999887665432 1244555677788899999763
No 206
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=37.11 E-value=15 Score=34.51 Aligned_cols=64 Identities=16% Similarity=0.114 Sum_probs=45.1
Q ss_pred CCHhhHHHHHHhhccc--------------CCcchhhhhhcccccceeeehhhhhHHH-HHhhcccccccCCChhHHHhh
Q 046732 223 IPVRQRVAVCIWRLAT--------------GEPLRLVSKRFGLGISTCHKLVLEVCTA-IRSVLMPKYLQWPDDDALRKI 287 (516)
Q Consensus 223 l~~eekL~v~L~~La~--------------G~s~~~la~~Fgis~STvsrii~~v~~a-L~~~L~~~~I~~P~~ee~~~i 287 (516)
.++.++|+-.|..|+. ..+..+||...|+++.||+|++.++... +.. .....|..++.+.+..+
T Consensus 119 ~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~-~~~~~i~I~d~~~L~~~ 197 (202)
T PRK13918 119 QRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRETVTKVIGELSREGYIR-SGYGKIQLLDLKGLEEL 197 (202)
T ss_pred CchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHHHHHHHHHHHHCCCEE-cCCCEEEEECHHHHHHH
Confidence 4678999998876653 2357899999999999999999887642 333 23445666665555443
No 207
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=36.81 E-value=17 Score=30.72 Aligned_cols=28 Identities=7% Similarity=0.100 Sum_probs=22.4
Q ss_pred cccCCcchhhhhhcccccceeeehhhhh
Q 046732 236 LATGEPLRLVSKRFGLGISTCHKLVLEV 263 (516)
Q Consensus 236 La~G~s~~~la~~Fgis~STvsrii~~v 263 (516)
..-+.+...|+...|++++||++++.++
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~L 71 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSL 71 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3456778899999999999988776554
No 208
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=36.77 E-value=18 Score=35.27 Aligned_cols=80 Identities=11% Similarity=0.090 Sum_probs=50.2
Q ss_pred CChhHHHHHcCCCHHHHHHHHHHhhcccccc--CCCCCCCCCHhhHHHHHHhhccc----------CCcchhhhhhcccc
Q 046732 185 YPEEEFKKWFRMRRQTFDMICEELNSVIAKE--DTTLRNAIPVRQRVAVCIWRLAT----------GEPLRLVSKRFGLG 252 (516)
Q Consensus 185 ~~d~~Fk~~FRmsk~tF~~L~~~L~~~i~k~--~t~~r~~l~~eekL~v~L~~La~----------G~s~~~la~~Fgis 252 (516)
++-+.|...+.-.++....++..+...+... ....-...++++||+-+|..++. ..+..+||...|++
T Consensus 113 i~~~~f~~l~~~~p~l~~~l~~~l~~~l~~~~~~~~~l~~~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGis 192 (230)
T PRK09391 113 IKRRSLEQAAATDVDVARALLSLTAGGLRHAQDHMLLLGRKTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLT 192 (230)
T ss_pred EEHHHHHHHHhhChHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCC
Confidence 4456666666655555444444443322110 00111246899999999988753 23567999999999
Q ss_pred cceeeehhhhhH
Q 046732 253 ISTCHKLVLEVC 264 (516)
Q Consensus 253 ~STvsrii~~v~ 264 (516)
+.|++|++.++-
T Consensus 193 retlsR~L~~L~ 204 (230)
T PRK09391 193 IETVSRALSQLQ 204 (230)
T ss_pred HHHHHHHHHHHH
Confidence 999998887654
No 209
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=35.85 E-value=15 Score=35.56 Aligned_cols=45 Identities=9% Similarity=0.105 Sum_probs=36.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHH
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIR 268 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~ 268 (516)
.+++.|+ =.|.+++.|.+...+|...++|.+||..++..+..-|.
T Consensus 137 ~LT~RE~--eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 137 SLSRTES--SMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 3777776 45677899999999999999999999888876655443
No 210
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=34.88 E-value=16 Score=27.00 Aligned_cols=28 Identities=14% Similarity=0.068 Sum_probs=22.6
Q ss_pred ccCCcchhhhhhcccccceeeehhhhhH
Q 046732 237 ATGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 237 a~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
....+..+++..+++|.+|+++++....
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~ 35 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLR 35 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4557788999999999999888776654
No 211
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=34.74 E-value=15 Score=35.13 Aligned_cols=44 Identities=16% Similarity=0.166 Sum_probs=35.1
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHH
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAI 267 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL 267 (516)
.+++.++ =+|..++.|.+...+|...++|.+||..++..+..-+
T Consensus 133 ~LSpREr--EVLrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKL 176 (198)
T PRK15201 133 HFSVTER--HLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKL 176 (198)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 4777776 4566789999999999999999999887776654433
No 212
>PF04921 XAP5: XAP5, circadian clock regulator; InterPro: IPR007005 These proteins are found in a wide range of eukaryotes. Their function is uncertain though they are nuclear proteins, possibly with DNA-binding activity.; GO: 0005634 nucleus
Probab=34.35 E-value=57 Score=32.65 Aligned_cols=31 Identities=6% Similarity=0.134 Sum_probs=19.2
Q ss_pred hhhhhhhhcchHHHHHHhHHHHHHHhhhCcC
Q 046732 67 LLLEEQEKGDQDAQKKASAEEKSFFEANHRN 97 (516)
Q Consensus 67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 97 (516)
-|.|.+-++.+.+.-.+.++|+...++.-+.
T Consensus 66 fLpDk~Re~~E~~~Re~LRkE~~~~Qe~vK~ 96 (239)
T PF04921_consen 66 FLPDKEREEEEAQEREELRKEWLAKQEAVKA 96 (239)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 4556666666666666677777776554443
No 213
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=34.23 E-value=14 Score=29.13 Aligned_cols=27 Identities=7% Similarity=0.128 Sum_probs=22.3
Q ss_pred CCcchhhhhhcccccceeeehhhhhHH
Q 046732 239 GEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 239 G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
+.+..++|...|+|..||++++.++..
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~ 54 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKD 54 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 456889999999999999888877653
No 214
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=34.06 E-value=27 Score=36.46 Aligned_cols=48 Identities=19% Similarity=0.272 Sum_probs=39.4
Q ss_pred CCCHhhHHHHHHhhc-c--cCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRL-A--TGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~L-a--~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.++..++..+.++|. . .+.++..||..||||+..|+++-.+.+.-|..
T Consensus 262 ~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~ 312 (324)
T PRK07921 262 TLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRN 312 (324)
T ss_pred hCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 478888999999884 2 45799999999999999999988777666554
No 215
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=33.85 E-value=25 Score=30.43 Aligned_cols=45 Identities=9% Similarity=0.108 Sum_probs=32.3
Q ss_pred CHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 224 PVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 224 ~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
+..++-.+- .|+-...|+..||..+|||+.+|+..+.+....|..
T Consensus 19 T~kQ~~~l~-lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~ 63 (101)
T PF04297_consen 19 TEKQREILE-LYYEEDLSLSEIAEELGISRQAVYDSIKRAEKKLEE 63 (101)
T ss_dssp -HHHHHHHH-HHCTS---HHHHHHHCTS-HHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHH-HHHccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344555554 466789999999999999999999999998887765
No 216
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=33.66 E-value=25 Score=39.02 Aligned_cols=48 Identities=8% Similarity=0.134 Sum_probs=40.7
Q ss_pred CCCHhhHHHHHHhhc---ccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRL---ATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~L---a~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.|+..++..+.++|. ..+.++..||..||||++.|+++-.+.+.-|..
T Consensus 447 ~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~ 497 (509)
T PRK05901 447 TLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRH 497 (509)
T ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 488899999999984 467999999999999999999988777666654
No 217
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=33.62 E-value=14 Score=28.30 Aligned_cols=30 Identities=10% Similarity=0.072 Sum_probs=24.4
Q ss_pred cccCCcchhhhhhcccccceeeehhhhhHH
Q 046732 236 LATGEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 236 La~G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
-..+.+...|+..+|++.+|+++.+.....
T Consensus 21 ~~~~~t~~ela~~l~~~~~t~s~hL~~L~~ 50 (61)
T PF12840_consen 21 SNGPMTVSELAEELGISQSTVSYHLKKLEE 50 (61)
T ss_dssp HCSTBEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 467888999999999999999988766543
No 218
>PF13551 HTH_29: Winged helix-turn helix
Probab=33.58 E-value=82 Score=26.38 Aligned_cols=25 Identities=12% Similarity=0.124 Sum_probs=21.2
Q ss_pred ChhHHHHHcCCCHHHHHHHHHHhhc
Q 046732 186 PEEEFKKWFRMRRQTFDMICEELNS 210 (516)
Q Consensus 186 ~d~~Fk~~FRmsk~tF~~L~~~L~~ 210 (516)
+..++-..+++++.|+...+.....
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~ 38 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYRE 38 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHc
Confidence 4788999999999999988887654
No 219
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=32.93 E-value=52 Score=28.49 Aligned_cols=41 Identities=5% Similarity=0.006 Sum_probs=28.8
Q ss_pred CCHhh-HHHHHHhhcccCCcchhhhhhcccccceeeehhhhhH
Q 046732 223 IPVRQ-RVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 223 l~~ee-kL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
+++.+ .++.+|. -..+.+..+|+..++++++|+++.+.+..
T Consensus 26 lt~~q~~iL~~l~-~~~~~t~~ela~~~~~~~~tvs~~l~~Le 67 (118)
T TIGR02337 26 LTEQQWRILRILA-EQGSMEFTQLANQACILRPSLTGILARLE 67 (118)
T ss_pred CCHHHHHHHHHHH-HcCCcCHHHHHHHhCCCchhHHHHHHHHH
Confidence 44444 3444343 24567799999999999999988776654
No 220
>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=32.69 E-value=9.3 Score=28.26 Aligned_cols=43 Identities=21% Similarity=0.320 Sum_probs=30.3
Q ss_pred cccCCcchhhhhhcccccceeeehhhhhHHHHHhhcccccccCCChhHHHhhHHHH
Q 046732 236 LATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLMPKYLQWPDDDALRKIKDEF 291 (516)
Q Consensus 236 La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~~~~I~~P~~ee~~~i~~~F 291 (516)
...|.++.++|...|+|++|++++.+. ...|+.+.+..++..|
T Consensus 6 ~~~gls~~~la~~~gis~~~i~~~~~g-------------~~~~~~~~~~~ia~~l 48 (55)
T PF01381_consen 6 KEKGLSQKELAEKLGISRSTISRIENG-------------KRNPSLDTLKKIAKAL 48 (55)
T ss_dssp HHTTS-HHHHHHHHTS-HHHHHHHHTT-------------SSTSBHHHHHHHHHHH
T ss_pred HHcCCCHHHHHHHhCCCcchhHHHhcC-------------CCCCCHHHHHHHHHHH
Confidence 368899999999999999998876533 2346666666666655
No 221
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=32.59 E-value=11 Score=29.04 Aligned_cols=27 Identities=22% Similarity=0.331 Sum_probs=21.1
Q ss_pred hhcccCCcchhhhhhcccccceeeehh
Q 046732 234 WRLATGEPLRLVSKRFGLGISTCHKLV 260 (516)
Q Consensus 234 ~~La~G~s~~~la~~Fgis~STvsrii 260 (516)
++-+.|.++..++...|+|.||++++-
T Consensus 9 ~R~~~gls~~~lA~~~g~s~s~v~~iE 35 (64)
T PF13560_consen 9 LRERAGLSQAQLADRLGVSQSTVSRIE 35 (64)
T ss_dssp HHHCHTS-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 455689999999999999999987754
No 222
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=31.81 E-value=41 Score=33.07 Aligned_cols=47 Identities=13% Similarity=0.156 Sum_probs=37.5
Q ss_pred CCCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHH
Q 046732 220 RNAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIR 268 (516)
Q Consensus 220 r~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~ 268 (516)
...+++.++=++.+ ++.|.++.+++..+|+|.+||...+.+...-|.
T Consensus 169 ~~~Lt~re~evl~~--~a~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~ 215 (232)
T TIGR03541 169 AGVLSEREREVLAW--TALGRRQADIAAILGISERTVENHLRSARRKLG 215 (232)
T ss_pred hccCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence 34688877755554 589999999999999999999888877765544
No 223
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=30.91 E-value=14 Score=26.25 Aligned_cols=27 Identities=11% Similarity=0.076 Sum_probs=21.8
Q ss_pred cCCcchhhhhhcccccceeeehhhhhH
Q 046732 238 TGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 238 ~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
-..+..+++..+|++.+|+++++..+.
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~~L~ 33 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLKRLE 33 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 456778999999999999888776654
No 224
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=30.36 E-value=27 Score=33.21 Aligned_cols=43 Identities=12% Similarity=0.125 Sum_probs=35.5
Q ss_pred CCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHH
Q 046732 221 NAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 221 ~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
..+++.++ -.|..++.|.+...+|...++|.+||..++.....
T Consensus 149 ~~Lt~rE~--evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~~ 191 (216)
T PRK10840 149 KRLSPKES--EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMM 191 (216)
T ss_pred ccCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35888886 56778899999999999999999999877765544
No 225
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=30.30 E-value=30 Score=34.94 Aligned_cols=45 Identities=16% Similarity=0.149 Sum_probs=36.7
Q ss_pred CCCCHhhHHHHHHhhccc---CCcchhhhhhcccccceeeehhhhhHH
Q 046732 221 NAIPVRQRVAVCIWRLAT---GEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 221 ~~l~~eekL~v~L~~La~---G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
..++.-++.+-.|..|+. +.+..+|+...|+++||++|++...+.
T Consensus 19 ~~~~sl~r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~ 66 (271)
T PRK10163 19 KGAQALERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQA 66 (271)
T ss_pred ccchHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 457777888888888863 467899999999999999998877654
No 226
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=30.10 E-value=15 Score=27.09 Aligned_cols=24 Identities=13% Similarity=0.216 Sum_probs=19.1
Q ss_pred cchhhhhhcccccceeeehhhhhH
Q 046732 241 PLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 241 s~~~la~~Fgis~STvsrii~~v~ 264 (516)
+.++++..|++|++||.+.+....
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~ 45 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLE 45 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 567889999999999877665543
No 227
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=29.90 E-value=28 Score=30.82 Aligned_cols=46 Identities=11% Similarity=0.139 Sum_probs=35.4
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHH
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIR 268 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~ 268 (516)
.++.+++-++- .|+.+..+...++..+|||-+||..-+.+++.+|-
T Consensus 33 ~L~~E~~~Fi~-~Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg 78 (113)
T PF09862_consen 33 RLSPEQLEFIK-LFIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLG 78 (113)
T ss_pred cCCHHHHHHHH-HHHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhC
Confidence 46666665554 45556667999999999999999888888777765
No 228
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=29.66 E-value=54 Score=32.52 Aligned_cols=46 Identities=9% Similarity=0.036 Sum_probs=36.6
Q ss_pred CCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHH
Q 046732 221 NAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIR 268 (516)
Q Consensus 221 ~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~ 268 (516)
..+++.++ -+|.+++.|.+..++|...+||..||..++..+..-|.
T Consensus 178 ~~LT~rE~--evl~~~a~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~ 223 (240)
T PRK10188 178 MNFSKREK--EILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFN 223 (240)
T ss_pred CCCCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 45777776 45667799999999999999999999887776655443
No 229
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=29.32 E-value=36 Score=37.00 Aligned_cols=48 Identities=15% Similarity=0.226 Sum_probs=40.8
Q ss_pred CCCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHH
Q 046732 220 RNAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAI 267 (516)
Q Consensus 220 r~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL 267 (516)
...+...-+++|.|.+=-++.++..||..||.+.|||...+.++-..+
T Consensus 368 ~~~i~~aR~iamyl~r~~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 368 NVKALLARRIGMYVAKNYLGSSLRTIAEKFNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred CccccHHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 446777788999888888999999999999999999988887776654
No 230
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=29.05 E-value=36 Score=30.69 Aligned_cols=42 Identities=14% Similarity=0.099 Sum_probs=30.5
Q ss_pred CCCHhhH-HHHHHhhcccCCcchhhhhhcccccceeeehhhhhH
Q 046732 222 AIPVRQR-VAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 222 ~l~~eek-L~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
.+++.+- ++..|+ -..|.+...|+..++++++|+++++....
T Consensus 37 glt~~q~~vL~~l~-~~~~~t~~eLa~~l~i~~~tvsr~l~~Le 79 (144)
T PRK11512 37 DITAAQFKVLCSIR-CAACITPVELKKVLSVDLGALTRMLDRLV 79 (144)
T ss_pred CCCHHHHHHHHHHH-HcCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4555554 444443 35668899999999999999988876654
No 231
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=28.68 E-value=30 Score=26.28 Aligned_cols=26 Identities=19% Similarity=0.275 Sum_probs=21.3
Q ss_pred cCCcchhhhhhcccccceeeehhhhh
Q 046732 238 TGEPLRLVSKRFGLGISTCHKLVLEV 263 (516)
Q Consensus 238 ~G~s~~~la~~Fgis~STvsrii~~v 263 (516)
.+.+..+++..++++.+|+++.+..+
T Consensus 19 ~~~~~~ei~~~~~i~~~~i~~~l~~L 44 (78)
T cd00090 19 GPLTVSELAERLGLSQSTVSRHLKKL 44 (78)
T ss_pred CCcCHHHHHHHHCcCHhHHHHHHHHH
Confidence 34889999999999999987776554
No 232
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=28.64 E-value=25 Score=26.82 Aligned_cols=30 Identities=7% Similarity=0.220 Sum_probs=25.7
Q ss_pred CcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 240 EPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 240 ~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.++...|..+++|+|+|++.+.++-..+-.
T Consensus 14 gs~~~AA~~l~is~~~vs~~i~~LE~~lg~ 43 (60)
T PF00126_consen 14 GSISAAAEELGISQSAVSRQIKQLEEELGV 43 (60)
T ss_dssp SSHHHHHHHCTSSHHHHHHHHHHHHHHHTS
T ss_pred CCHHHHHHHhhccchHHHHHHHHHHHHhCC
Confidence 389999999999999999999887766654
No 233
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=28.10 E-value=44 Score=36.28 Aligned_cols=50 Identities=16% Similarity=0.189 Sum_probs=41.6
Q ss_pred CCCCCCHhhHHHHHHhhcccCCcchhhhhhc-ccccceeeehhhhhHHHHH
Q 046732 219 LRNAIPVRQRVAVCIWRLATGEPLRLVSKRF-GLGISTCHKLVLEVCTAIR 268 (516)
Q Consensus 219 ~r~~l~~eekL~v~L~~La~G~s~~~la~~F-gis~STvsrii~~v~~aL~ 268 (516)
+.+.+...-+++|-|.+--++.++..||..| |.+.|||...+..+-..+.
T Consensus 382 R~~~~~~aR~iamyl~~~~~~~s~~~Ig~~fg~rdhstV~~a~~~i~~~~~ 432 (450)
T PRK00149 382 RTRNIARPRQIAMYLAKELTDLSLPEIGRAFGGRDHTTVLHAVRKIEKLLE 432 (450)
T ss_pred CCcccChHHHHHHHHHHHhcCCCHHHHHHHcCCCCHhHHHHHHHHHHHHHH
Confidence 3456777889999998888999999999999 5999999888877766553
No 234
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=27.86 E-value=46 Score=24.95 Aligned_cols=23 Identities=17% Similarity=0.320 Sum_probs=18.2
Q ss_pred cchhhhhhcccccceeeehhhhh
Q 046732 241 PLRLVSKRFGLGISTCHKLVLEV 263 (516)
Q Consensus 241 s~~~la~~Fgis~STvsrii~~v 263 (516)
+..+|+..|++|.+||++.+...
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L 49 (66)
T cd07377 27 SERELAEELGVSRTTVREALREL 49 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Confidence 46689999999999987666554
No 235
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=27.75 E-value=18 Score=34.62 Aligned_cols=28 Identities=14% Similarity=0.287 Sum_probs=24.7
Q ss_pred hhcccCCcchhhhhhcccccceeeehhh
Q 046732 234 WRLATGEPLRLVSKRFGLGISTCHKLVL 261 (516)
Q Consensus 234 ~~La~G~s~~~la~~Fgis~STvsrii~ 261 (516)
.++..|.++..++..+|||.+|+++++.
T Consensus 167 ~~~~~g~s~~~iak~lgis~~Tv~r~~k 194 (200)
T PRK13413 167 KLLDKGTSKSEIARKLGVSRTTLARFLK 194 (200)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3467899999999999999999988875
No 236
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=27.45 E-value=28 Score=34.48 Aligned_cols=43 Identities=16% Similarity=0.180 Sum_probs=33.6
Q ss_pred CCHhhHHHHHHhhcc---cCCcchhhhhhcccccceeeehhhhhHH
Q 046732 223 IPVRQRVAVCIWRLA---TGEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 223 l~~eekL~v~L~~La---~G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
++.-++.+-.|..|+ .+.+..+|+...|+++||++|++...+.
T Consensus 5 v~sl~ral~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~ 50 (248)
T TIGR02431 5 VASLARGLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVE 50 (248)
T ss_pred HHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 455566677777775 3578999999999999999999877543
No 237
>PF12964 DUF3853: Protein of unknown function (DUF3853); InterPro: IPR024363 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences [].
Probab=27.13 E-value=18 Score=31.01 Aligned_cols=65 Identities=18% Similarity=0.275 Sum_probs=37.2
Q ss_pred cCCCHHHHHHHHHHhhccccccCCCCCCCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhh--hHHHHHh
Q 046732 194 FRMRRQTFDMICEELNSVIAKEDTTLRNAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLE--VCTAIRS 269 (516)
Q Consensus 194 FRmsk~tF~~L~~~L~~~i~k~~t~~r~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~--v~~aL~~ 269 (516)
+-|+=+.|-.|.......-... +. ......+.+ +.+ .+.-||..||+|.||++|+... .=.||..
T Consensus 11 ~qmTg~ell~L~~~~~~~~~~~-~~-~~~~~~~~~-------yvy--G~~GlAklfgcSv~Ta~RiK~sG~id~AI~Q 77 (96)
T PF12964_consen 11 WQMTGEELLFLLKEGKTNSEKQ-TS-QKAKKDEKK-------YVY--GLKGLAKLFGCSVPTANRIKKSGKIDPAITQ 77 (96)
T ss_pred HHhhHHHHHHHHHHHhcCCCcc-CC-ccccCcccc-------eee--hHHHHHHHhCCCchhHHHHHhcCCccHHHHH
Confidence 4477777777777663322111 11 122222322 122 3678999999999999998754 2244444
No 238
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=27.10 E-value=25 Score=34.67 Aligned_cols=44 Identities=7% Similarity=0.107 Sum_probs=34.8
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHH
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAI 267 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL 267 (516)
.+++.++ -.|..++.|.+...+|...++|.+||..++..+..-+
T Consensus 143 ~LS~RE~--eVL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KL 186 (217)
T PRK13719 143 KVTKYQN--DVFILYSFGFSHEYIAQLLNITVGSSKNKISEILKFF 186 (217)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 5666665 3466789999999999999999999988876665443
No 239
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=26.98 E-value=44 Score=27.20 Aligned_cols=28 Identities=18% Similarity=0.224 Sum_probs=23.2
Q ss_pred cCCcchhhhhhcccccceeeehhhhhHH
Q 046732 238 TGEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 238 ~G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
.+.+...++..++++++++++.+.....
T Consensus 23 ~~~~~~~la~~~~~s~~~i~~~l~~L~~ 50 (101)
T smart00347 23 GPLSVSELAKRLGVSPSTVTRVLDRLEK 50 (101)
T ss_pred CCcCHHHHHHHHCCCchhHHHHHHHHHH
Confidence 4568899999999999999888877654
No 240
>PRK10870 transcriptional repressor MprA; Provisional
Probab=26.77 E-value=67 Score=30.30 Aligned_cols=42 Identities=10% Similarity=0.002 Sum_probs=28.7
Q ss_pred CCHhh-HHHHHHhhccc-CCcchhhhhhcccccceeeehhhhhH
Q 046732 223 IPVRQ-RVAVCIWRLAT-GEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 223 l~~ee-kL~v~L~~La~-G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
+++.+ .++..|+.... +.+..+|+..++++++|+++++.+..
T Consensus 53 Lt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe 96 (176)
T PRK10870 53 INETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELE 96 (176)
T ss_pred CCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 44443 44445543333 45679999999999999988776654
No 241
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=26.67 E-value=15 Score=25.85 Aligned_cols=29 Identities=17% Similarity=0.165 Sum_probs=20.7
Q ss_pred cccCCcchhhhhhcccccceeeehhhhhH
Q 046732 236 LATGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 236 La~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
|.++.+..+||..+|+|.+..++++.+.+
T Consensus 5 ~~~~~~l~~iA~~~g~S~~~f~r~Fk~~~ 33 (42)
T PF00165_consen 5 LQQKLTLEDIAEQAGFSPSYFSRLFKKET 33 (42)
T ss_dssp T-SS--HHHHHHHHTS-HHHHHHHHHHHT
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45677888999999999999888887653
No 242
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=26.41 E-value=35 Score=33.98 Aligned_cols=38 Identities=18% Similarity=0.117 Sum_probs=31.6
Q ss_pred CHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhh
Q 046732 224 PVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVL 261 (516)
Q Consensus 224 ~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~ 261 (516)
-..-++.-.|+.|..--+|+.|+..+|++.|.++|+++
T Consensus 8 ~~~~~~v~~lr~lk~~~ty~el~~~~g~p~~~l~RYv~ 45 (238)
T PRK08558 8 RLQLRAVRVLRSLKKTYTYEELSSITGLPESVLNRYVN 45 (238)
T ss_pred HHHHHHHHHHHHHhcccCHHHHHHHHCCCHHHHHHHHc
Confidence 34455667788888889999999999999999988874
No 243
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=26.32 E-value=22 Score=33.34 Aligned_cols=22 Identities=23% Similarity=0.308 Sum_probs=0.0
Q ss_pred CCcchhhhhhcccccceeeehh
Q 046732 239 GEPLRLVSKRFGLGISTCHKLV 260 (516)
Q Consensus 239 G~s~~~la~~Fgis~STvsrii 260 (516)
+.++.++|...|++.|||||++
T Consensus 49 PLt~~~iA~~lgl~~STVSRav 70 (160)
T PF04552_consen 49 PLTMKDIADELGLHESTVSRAV 70 (160)
T ss_dssp ----------------------
T ss_pred CCCHHHHHHHhCCCHhHHHHHH
Confidence 4568899999999999999976
No 244
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=25.81 E-value=43 Score=29.28 Aligned_cols=32 Identities=16% Similarity=0.259 Sum_probs=25.3
Q ss_pred cCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 238 TGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 238 ~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.|.++...|...|||++|+++++...-.-|.+
T Consensus 56 egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~ 87 (106)
T PF02001_consen 56 EGLSQEEAAERMGVSRPTFQRILESARKKIAD 87 (106)
T ss_pred cCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHH
Confidence 46778899999999999999998765444444
No 245
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=25.58 E-value=2.2e+02 Score=33.42 Aligned_cols=12 Identities=17% Similarity=0.260 Sum_probs=6.1
Q ss_pred CCCCHhhHHHHH
Q 046732 221 NAIPVRQRVAVC 232 (516)
Q Consensus 221 ~~l~~eekL~v~ 232 (516)
..+++.+|..++
T Consensus 623 ~~l~~~~R~~~~ 634 (803)
T PLN03083 623 VLLSSAERTALA 634 (803)
T ss_pred ccCCHHHHHHHH
Confidence 345555555443
No 246
>PHA00738 putative HTH transcription regulator
Probab=25.50 E-value=20 Score=31.35 Aligned_cols=32 Identities=16% Similarity=0.065 Sum_probs=24.5
Q ss_pred hhcccC--CcchhhhhhcccccceeeehhhhhHH
Q 046732 234 WRLATG--EPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 234 ~~La~G--~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
.+|+.| .+..+|+..|++|++|||+.+.-.-.
T Consensus 19 ~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLre 52 (108)
T PHA00738 19 ELIAENYILSASLISHTLLLSYTTVLRHLKILNE 52 (108)
T ss_pred HHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHH
Confidence 344553 67889999999999999998755433
No 247
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=25.42 E-value=50 Score=37.56 Aligned_cols=50 Identities=14% Similarity=0.204 Sum_probs=41.3
Q ss_pred CCCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 220 RNAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 220 r~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
...+..--+|+|.|.+--++.++..||..||.+.|||...++.+-..|.+
T Consensus 550 ~~~i~~aRqiAMYL~r~lt~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~~ 599 (617)
T PRK14086 550 SRVLVTARQIAMYLCRELTDLSLPKIGQQFGRDHTTVMHADRKIRALMAE 599 (617)
T ss_pred CcccchHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHh
Confidence 34666778899999888899999999999999999988777776665543
No 248
>PRK09483 response regulator; Provisional
Probab=25.40 E-value=26 Score=32.69 Aligned_cols=44 Identities=11% Similarity=0.230 Sum_probs=34.3
Q ss_pred CCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHH
Q 046732 221 NAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTA 266 (516)
Q Consensus 221 ~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~a 266 (516)
..+++.++-.+ ..++.|.+...+|..+++|.+||..++.+...-
T Consensus 147 ~~Lt~rE~~vl--~~~~~G~~~~~Ia~~l~is~~TV~~~~~~i~~K 190 (217)
T PRK09483 147 ASLSERELQIM--LMITKGQKVNEISEQLNLSPKTVNSYRYRMFSK 190 (217)
T ss_pred cccCHHHHHHH--HHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 35777776554 457899999999999999999988777665443
No 249
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=25.26 E-value=21 Score=27.89 Aligned_cols=37 Identities=11% Similarity=0.159 Sum_probs=26.5
Q ss_pred hHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhH
Q 046732 227 QRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 227 ekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
.++..+|. -..+.+..+|+...|+++++|++++....
T Consensus 11 ~~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~ 47 (68)
T PF01978_consen 11 AKVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLE 47 (68)
T ss_dssp HHHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHH
T ss_pred HHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 34544443 23457789999999999999888776543
No 250
>PF10654 DUF2481: Protein of unknown function (DUF2481) ; InterPro: IPR018916 This entry is represented by Bacteriophage A500, Gp59. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=24.95 E-value=17 Score=32.09 Aligned_cols=26 Identities=15% Similarity=0.186 Sum_probs=21.8
Q ss_pred cCCcchhhhhhcccccceeeehhhhh
Q 046732 238 TGEPLRLVSKRFGLGISTCHKLVLEV 263 (516)
Q Consensus 238 ~G~s~~~la~~Fgis~STvsrii~~v 263 (516)
-|.+...+|+.|+||+||+.....+.
T Consensus 79 AGlt~~aIAd~F~iS~s~~~nft~~n 104 (126)
T PF10654_consen 79 AGLTCYAIADYFKISKSTVFNFTQNN 104 (126)
T ss_pred cCCChHHHHHHHhHHHHHHHHHHHHh
Confidence 57889999999999999987766443
No 251
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=24.88 E-value=31 Score=37.51 Aligned_cols=31 Identities=39% Similarity=0.459 Sum_probs=25.9
Q ss_pred CCcchhhhhhcccccceeeehhhhhHHHHHhhcccccccCCC
Q 046732 239 GEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLMPKYLQWPD 280 (516)
Q Consensus 239 G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~~~~I~~P~ 280 (516)
+.++++||...|++.|||||++ ..+|+..|.
T Consensus 318 PLtlkdiA~~lglheSTVSRav-----------~~Kyi~tp~ 348 (429)
T TIGR02395 318 PLTLREVAEELGLHESTISRAI-----------NNKYLQTPR 348 (429)
T ss_pred CCcHHHHHHHhCCCccchhhhh-----------cCceEecCC
Confidence 4678999999999999999975 567777775
No 252
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=24.64 E-value=41 Score=26.79 Aligned_cols=42 Identities=14% Similarity=0.114 Sum_probs=37.0
Q ss_pred HHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 228 RVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 228 kL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
++-.++.+|+...+..+.+...|+...+|.+.+..|-..+..
T Consensus 2 ~~~~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~ 43 (65)
T PF05344_consen 2 KARAFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQ 43 (65)
T ss_pred cHHHHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 345678899999999999999999999999999998888876
No 253
>PRK09492 treR trehalose repressor; Provisional
Probab=24.01 E-value=25 Score=35.32 Aligned_cols=23 Identities=17% Similarity=0.325 Sum_probs=20.4
Q ss_pred Ccchhhhhhcccccceeeehhhh
Q 046732 240 EPLRLVSKRFGLGISTCHKLVLE 262 (516)
Q Consensus 240 ~s~~~la~~Fgis~STvsrii~~ 262 (516)
.+.++||...|||.+|||++++.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCC
Confidence 46789999999999999999864
No 254
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=23.51 E-value=83 Score=34.01 Aligned_cols=50 Identities=22% Similarity=0.201 Sum_probs=40.5
Q ss_pred CCCCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHH
Q 046732 219 LRNAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIR 268 (516)
Q Consensus 219 ~r~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~ 268 (516)
+...+...-|++|.|.+--+..|+..||..||...|||...+..+...+.
T Consensus 345 R~~~i~~~RqiamyL~r~lt~~Slp~IG~~FgrdHtTV~~a~~kI~~~~~ 394 (408)
T COG0593 345 RTRNIVRPRQIAMYLARELTNLSLPEIGKAFGRDHTTVLHAVRKIEQLIE 394 (408)
T ss_pred cccccchHHHHHHHHHHHHccCcHHHHHHHhCCCccHHHHHHHHHHHHHh
Confidence 34567777899999999999999999999999999998666666555443
No 255
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=23.50 E-value=32 Score=25.85 Aligned_cols=34 Identities=12% Similarity=0.249 Sum_probs=27.9
Q ss_pred HHhhcccCCcchhhhhhcccccceeeehhhhhHH
Q 046732 232 CIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 232 ~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
.+.+++.|.+...++...++|..||......+..
T Consensus 12 v~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~~ 45 (65)
T COG2771 12 ILRLVAQGKSNKEIARILGISEETVKTHLRNIYR 45 (65)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4567789999999999999999998776665543
No 256
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=23.33 E-value=50 Score=37.57 Aligned_cols=48 Identities=15% Similarity=0.174 Sum_probs=39.1
Q ss_pred CCCHhhHHHHHHhhc---ccCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 222 AIPVRQRVAVCIWRL---ATGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 222 ~l~~eekL~v~L~~L---a~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
.+|..++..+.++|. ..+.++..||..||||++.|+++-...+.-|..
T Consensus 556 ~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~ 606 (619)
T PRK05658 556 SLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 606 (619)
T ss_pred cCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhc
Confidence 478888989999885 367889999999999999998887766655543
No 257
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=22.89 E-value=33 Score=33.29 Aligned_cols=43 Identities=16% Similarity=0.181 Sum_probs=34.8
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHH
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTA 266 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~a 266 (516)
.+++++. -.|..|+.|.+...||...++|.+||..++.....-
T Consensus 148 ~LT~RE~--eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~K 190 (211)
T COG2197 148 LLTPREL--EVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRK 190 (211)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHH
Confidence 4666665 456789999999999999999999998877665443
No 258
>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=22.82 E-value=49 Score=33.22 Aligned_cols=46 Identities=11% Similarity=0.196 Sum_probs=36.6
Q ss_pred CCCCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHH
Q 046732 220 RNAIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAI 267 (516)
Q Consensus 220 r~~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL 267 (516)
...+++.++=.+.| ++.|.++..||..++||..||...+..+..-+
T Consensus 188 ~~~LT~RE~evl~l--~a~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL 233 (247)
T TIGR03020 188 AGLITAREAEILAW--VRDGKTNEEIAAILGISSLTVKNHLQHIFKKL 233 (247)
T ss_pred ccCCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHh
Confidence 34688888766664 57999999999999999999988777665433
No 259
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=22.81 E-value=48 Score=23.59 Aligned_cols=27 Identities=7% Similarity=0.049 Sum_probs=21.8
Q ss_pred cCCcchhhhhhcccccceeeehhhhhH
Q 046732 238 TGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 238 ~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
.+.+..+++..|+++.+|+++.+..+.
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~ 39 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNKLE 39 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 346788899999999999988776553
No 260
>PRK00215 LexA repressor; Validated
Probab=22.33 E-value=45 Score=31.95 Aligned_cols=26 Identities=19% Similarity=0.247 Sum_probs=21.8
Q ss_pred CCcchhhhhhccc-ccceeeehhhhhH
Q 046732 239 GEPLRLVSKRFGL-GISTCHKLVLEVC 264 (516)
Q Consensus 239 G~s~~~la~~Fgi-s~STvsrii~~v~ 264 (516)
+.+..+|+..+|+ +++|+++++....
T Consensus 23 ~~s~~ela~~~~~~~~~tv~~~l~~L~ 49 (205)
T PRK00215 23 PPSRREIADALGLRSPSAVHEHLKALE 49 (205)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 3478899999999 9999998876654
No 261
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=22.26 E-value=32 Score=33.33 Aligned_cols=42 Identities=12% Similarity=0.204 Sum_probs=34.0
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHH
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
.+++.|+ =.|..++.|.+...||...++|..||..++..+..
T Consensus 134 ~LT~RE~--eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~ 175 (207)
T PRK11475 134 MLSPTER--EILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMS 175 (207)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4777776 45677899999999999999999999877766543
No 262
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=22.26 E-value=37 Score=34.00 Aligned_cols=44 Identities=18% Similarity=0.236 Sum_probs=34.1
Q ss_pred CCCHhhHHHHHHhhccc---CCcchhhhhhcccccceeeehhhhhHH
Q 046732 222 AIPVRQRVAVCIWRLAT---GEPLRLVSKRFGLGISTCHKLVLEVCT 265 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~---G~s~~~la~~Fgis~STvsrii~~v~~ 265 (516)
.++.-++.+-.|..|+. +.+..+|+..+|+++||++|++.....
T Consensus 6 ~v~sl~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~ 52 (263)
T PRK09834 6 TVRGLSRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQE 52 (263)
T ss_pred hHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 35556677777777753 368999999999999999998877543
No 263
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=22.06 E-value=35 Score=33.33 Aligned_cols=45 Identities=11% Similarity=0.187 Sum_probs=34.3
Q ss_pred CCCHhhHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhHHHHH
Q 046732 222 AIPVRQRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVCTAIR 268 (516)
Q Consensus 222 ~l~~eekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~~aL~ 268 (516)
.+++.++= .|..++.|.++.++|..+++|..||..++.+.+.-+.
T Consensus 155 ~Lt~rE~~--Vl~l~~~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 155 LLTHREKE--ILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 36766653 3455677999999999999999999888777655443
No 264
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=21.93 E-value=35 Score=30.44 Aligned_cols=33 Identities=15% Similarity=0.115 Sum_probs=26.0
Q ss_pred HHHHHHhhcccCCcchhhhhhcccccceeeehhhh
Q 046732 228 RVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLE 262 (516)
Q Consensus 228 kL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~ 262 (516)
.|+--|.-- |.++..+|...|++++.||+++..
T Consensus 13 ~lA~~L~ee--G~Sq~~iA~LLGltqaAVS~Yls~ 45 (119)
T COG2522 13 LLAKELIEE--GLSQYRIAKLLGLTQAAVSQYLSG 45 (119)
T ss_pred HHHHHHHHc--CCcHHHHHHHhCCCHHHHHHHHcc
Confidence 344444443 999999999999999999998754
No 265
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=21.65 E-value=39 Score=37.07 Aligned_cols=32 Identities=22% Similarity=0.319 Sum_probs=26.3
Q ss_pred cCCcchhhhhhcccccceeeehhhhhHHHHHhhcccccccCCC
Q 046732 238 TGEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLMPKYLQWPD 280 (516)
Q Consensus 238 ~G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~~~~I~~P~ 280 (516)
.+.++++||...|++.|||||++ ..+|+..|.
T Consensus 342 kPLtlkdvAe~lglheSTVSRav-----------~~Kyv~tp~ 373 (455)
T PRK05932 342 KPLVLKDIAEELGMHESTISRAT-----------TNKYMATPR 373 (455)
T ss_pred cCccHHHHHHHhCCCccchhhhh-----------cCceeecCC
Confidence 34678999999999999999975 577777775
No 266
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=21.64 E-value=36 Score=33.06 Aligned_cols=50 Identities=16% Similarity=0.161 Sum_probs=35.5
Q ss_pred CCCCCHhhHHHHHHh----hcc--cCCcchhhhhhcccccceeeehhhhhHHHHHh
Q 046732 220 RNAIPVRQRVAVCIW----RLA--TGEPLRLVSKRFGLGISTCHKLVLEVCTAIRS 269 (516)
Q Consensus 220 r~~l~~eekL~v~L~----~La--~G~s~~~la~~Fgis~STvsrii~~v~~aL~~ 269 (516)
...++..|.-++.+- |+- -..+..+||..||||+||++.++++...-|..
T Consensus 153 ~~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~ 208 (215)
T COG3413 153 KNDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIE 208 (215)
T ss_pred cccCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 346777775444442 222 34678999999999999999988887665554
No 267
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=21.44 E-value=18 Score=24.70 Aligned_cols=24 Identities=13% Similarity=0.225 Sum_probs=18.1
Q ss_pred Ccchhhhhhcccccceeeehhhhh
Q 046732 240 EPLRLVSKRFGLGISTCHKLVLEV 263 (516)
Q Consensus 240 ~s~~~la~~Fgis~STvsrii~~v 263 (516)
.+..++|+..|++..||+|++..+
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l 26 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKL 26 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHH
Confidence 356789999999999999987664
No 268
>cd00131 PAX Paired Box domain
Probab=21.39 E-value=1.9e+02 Score=25.88 Aligned_cols=79 Identities=9% Similarity=0.077 Sum_probs=46.2
Q ss_pred CCCChhHHHHHcCCCHHHHHHHHHHhhcc--cc-ccCCCCCCC-CCHh-hHHHHHHhhcccCCcchhhhhhc---cc---
Q 046732 183 PDYPEEEFKKWFRMRRQTFDMICEELNSV--IA-KEDTTLRNA-IPVR-QRVAVCIWRLATGEPLRLVSKRF---GL--- 251 (516)
Q Consensus 183 ~~~~d~~Fk~~FRmsk~tF~~L~~~L~~~--i~-k~~t~~r~~-l~~e-ekL~v~L~~La~G~s~~~la~~F---gi--- 251 (516)
..++..+.-..|++++.+...++...... +. ++....++. +.+. ...++.+..-.-..+...++..+ |+
T Consensus 32 ~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~ 111 (128)
T cd00131 32 SGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDK 111 (128)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCccc
Confidence 45788999999999999999998876642 22 111122232 2332 23233333323334566666553 55
Q ss_pred ----ccceeeehhh
Q 046732 252 ----GISTCHKLVL 261 (516)
Q Consensus 252 ----s~STvsrii~ 261 (516)
|.|||++++.
T Consensus 112 ~~~~s~stI~R~L~ 125 (128)
T cd00131 112 SNVPSVSSINRILR 125 (128)
T ss_pred CCCCCHHHHHHHHH
Confidence 8888877653
No 269
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=21.35 E-value=63 Score=27.77 Aligned_cols=27 Identities=15% Similarity=0.122 Sum_probs=23.2
Q ss_pred cCCcchhhhhhcccccceeeehhhhhH
Q 046732 238 TGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 238 ~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
.+.+...|+..++++++|+++++....
T Consensus 42 ~~~t~~eL~~~l~~~~stvs~~i~~Le 68 (109)
T TIGR01889 42 GKLTLKEIIKEILIKQSALVKIIKKLS 68 (109)
T ss_pred CcCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 458899999999999999988876654
No 270
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=21.05 E-value=56 Score=27.67 Aligned_cols=37 Identities=22% Similarity=0.260 Sum_probs=26.8
Q ss_pred hHHHHHHhhcccCCcchhhhhhcccccceeeehhhhhH
Q 046732 227 QRVAVCIWRLATGEPLRLVSKRFGLGISTCHKLVLEVC 264 (516)
Q Consensus 227 ekL~v~L~~La~G~s~~~la~~Fgis~STvsrii~~v~ 264 (516)
.+++..|.. ....++..++..+|++.+|+.+.+....
T Consensus 6 ~~il~~L~~-~~~~~~~~la~~l~~s~~tv~~~l~~L~ 42 (108)
T smart00344 6 RKILEELQK-DARISLAELAKKVGLSPSTVHNRVKRLE 42 (108)
T ss_pred HHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 344444443 2357899999999999999887776553
No 271
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=21.00 E-value=61 Score=31.57 Aligned_cols=19 Identities=16% Similarity=0.167 Sum_probs=14.6
Q ss_pred hhhhhcccccceeeehhhh
Q 046732 244 LVSKRFGLGISTCHKLVLE 262 (516)
Q Consensus 244 ~la~~Fgis~STvsrii~~ 262 (516)
.|+..||||+.||.+.+..
T Consensus 29 eLa~~~gVSR~TVR~Al~~ 47 (233)
T TIGR02404 29 ELMDQYGASRETVRKALNL 47 (233)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4678999999997665544
No 272
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=20.91 E-value=24 Score=35.60 Aligned_cols=21 Identities=19% Similarity=0.393 Sum_probs=18.9
Q ss_pred cchhhhhhcccccceeeehhh
Q 046732 241 PLRLVSKRFGLGISTCHKLVL 261 (516)
Q Consensus 241 s~~~la~~Fgis~STvsrii~ 261 (516)
+..+||...|||++|||++++
T Consensus 3 ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 3 TIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred cHHHHHHHhCCCHHHHHHHhC
Confidence 467999999999999999885
No 273
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=20.82 E-value=38 Score=37.38 Aligned_cols=31 Identities=32% Similarity=0.335 Sum_probs=26.1
Q ss_pred CCcchhhhhhcccccceeeehhhhhHHHHHhhcccccccCCC
Q 046732 239 GEPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLMPKYLQWPD 280 (516)
Q Consensus 239 G~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~~~~I~~P~ 280 (516)
+..+++||...|++.|||||++ ..+|+..|.
T Consensus 369 PLtlkdVAe~lglHeSTVSRa~-----------~~KY~~tp~ 399 (481)
T PRK12469 369 PLVLRDVAEELGLHESTISRAT-----------GNKYMATPR 399 (481)
T ss_pred CCcHHHHHHHhCCCcchhhHHh-----------cCceeecCC
Confidence 4578999999999999999875 577887775
No 274
>PF14942 Muted: Organelle biogenesis, Muted-like protein
Probab=20.74 E-value=1.1e+02 Score=28.25 Aligned_cols=28 Identities=21% Similarity=0.423 Sum_probs=15.3
Q ss_pred HhHHHHHHHhhhCcCchhhhHHHHHhHH
Q 046732 83 ASAEEKSFFEANHRNKKKTMLEYYSNIQ 110 (516)
Q Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 (516)
+..+.++.+++.|.+|+....++|+.|+
T Consensus 115 e~~~~~~~vdee~~~~~~~l~e~Y~~~~ 142 (145)
T PF14942_consen 115 EQQQKKQRVDEEFREKEERLKEQYSEME 142 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3444445555555666555555555554
No 275
>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=20.72 E-value=45 Score=25.76 Aligned_cols=31 Identities=16% Similarity=0.237 Sum_probs=24.6
Q ss_pred HHHHHHhhcccCCcchhhhhhcccccceeeehh
Q 046732 228 RVAVCIWRLATGEPLRLVSKRFGLGISTCHKLV 260 (516)
Q Consensus 228 kL~v~L~~La~G~s~~~la~~Fgis~STvsrii 260 (516)
..+..||. .|-+...||...|++.+||+...
T Consensus 4 ~~A~~LY~--~G~~~~eIA~~Lg~~~~TV~~W~ 34 (58)
T PF06056_consen 4 EQARSLYL--QGWSIKEIAEELGVPRSTVYSWK 34 (58)
T ss_pred HHHHHHHH--cCCCHHHHHHHHCCChHHHHHHH
Confidence 34555654 69999999999999999987655
No 276
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=20.59 E-value=27 Score=38.05 Aligned_cols=30 Identities=33% Similarity=0.411 Sum_probs=24.8
Q ss_pred CcchhhhhhcccccceeeehhhhhHHHHHhhcccccccCCC
Q 046732 240 EPLRLVSKRFGLGISTCHKLVLEVCTAIRSVLMPKYLQWPD 280 (516)
Q Consensus 240 ~s~~~la~~Fgis~STvsrii~~v~~aL~~~L~~~~I~~P~ 280 (516)
...++||+.+|++.|||||++ ..+|+.-|.
T Consensus 331 L~LrdvA~~i~~HESTISRai-----------~nKy~~tpr 360 (444)
T COG1508 331 LVLRDVADEIGMHESTISRAI-----------TNKYLATPR 360 (444)
T ss_pred ccHHHHHHHhCccHHHHHHHH-----------hcccccCCc
Confidence 667999999999999999865 467777775
No 277
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=20.33 E-value=30 Score=35.11 Aligned_cols=22 Identities=23% Similarity=0.317 Sum_probs=19.4
Q ss_pred cchhhhhhcccccceeeehhhh
Q 046732 241 PLRLVSKRFGLGISTCHKLVLE 262 (516)
Q Consensus 241 s~~~la~~Fgis~STvsrii~~ 262 (516)
+..+||...|||.+||||+++.
T Consensus 7 ti~dIA~~agVS~~TVSrvLn~ 28 (331)
T PRK14987 7 VLQDVADRVGVTKMTVSRFLRN 28 (331)
T ss_pred cHHHHHHHhCCCHHHhhhhhCC
Confidence 5679999999999999998854
No 278
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=20.27 E-value=1.2e+02 Score=24.94 Aligned_cols=34 Identities=18% Similarity=0.409 Sum_probs=27.2
Q ss_pred chhhhccCCCCCChhHHHHHcCCCHHHHHHHHHHhhc
Q 046732 174 KAWWDECNRPDYPEEEFKKWFRMRRQTFDMICEELNS 210 (516)
Q Consensus 174 ~~~~~~~~~~~~~d~~Fk~~FRmsk~tF~~L~~~L~~ 210 (516)
+.||.. ..-.++..+..|+||...|..+++.|-.
T Consensus 15 ~~ww~~---~GaKe~aIre~fGls~~rYyq~Ln~LiD 48 (77)
T PF11662_consen 15 RRWWRH---GGAKEEAIREEFGLSPTRYYQRLNALID 48 (77)
T ss_pred HHhCcC---CCCcHHHHHHHHCCCHHHHHHHHHHHhC
Confidence 457774 4567899999999999999888887643
Done!