Query 041521
Match_columns 524
No_of_seqs 259 out of 1690
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 08:01:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041521.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041521hhsearch_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 1.5E-39 3.2E-44 334.6 10.5 297 200-514 7-321 (326)
2 PF13359 DDE_Tnp_4: DDE superf 100.0 1.1E-36 2.4E-41 282.4 0.2 152 311-468 1-158 (158)
3 PF04827 Plant_tran: Plant tra 100.0 1.4E-31 3E-36 251.3 1.9 185 281-473 2-200 (205)
4 PF13612 DDE_Tnp_1_3: Transpos 98.7 1.7E-09 3.8E-14 100.7 0.2 131 304-447 3-150 (155)
5 PF13613 HTH_Tnp_4: Helix-turn 98.7 7.5E-09 1.6E-13 79.2 1.6 50 229-278 2-51 (53)
6 PF01609 DDE_Tnp_1: Transposas 97.5 3.3E-06 7E-11 79.9 -5.2 151 306-469 4-213 (213)
7 PF13586 DDE_Tnp_1_2: Transpos 95.8 0.002 4.3E-08 54.2 -0.7 50 416-466 35-84 (88)
8 PF04218 CENP-B_N: CENP-B N-te 93.9 0.019 4.1E-07 43.9 0.3 42 227-269 4-45 (53)
9 PF04545 Sigma70_r4: Sigma-70, 93.0 0.055 1.2E-06 40.3 1.6 45 229-274 4-48 (50)
10 PF02796 HTH_7: Helix-turn-hel 92.8 0.025 5.4E-07 41.6 -0.5 40 229-269 5-44 (45)
11 PF13936 HTH_38: Helix-turn-he 92.7 0.028 6E-07 41.2 -0.3 41 228-269 3-43 (44)
12 PF13518 HTH_28: Helix-turn-he 89.0 0.14 3E-06 38.1 0.3 37 235-272 2-38 (52)
13 PF13384 HTH_23: Homeodomain-l 88.7 0.074 1.6E-06 39.5 -1.3 37 234-271 6-42 (50)
14 PF12116 SpoIIID: Stage III sp 88.6 0.1 2.2E-06 43.2 -0.7 43 236-278 9-51 (82)
15 PF08281 Sigma70_r4_2: Sigma-7 87.5 0.28 6E-06 36.9 1.2 43 229-272 10-52 (54)
16 smart00351 PAX Paired Box doma 87.0 0.28 6.1E-06 44.1 1.1 44 228-272 16-59 (125)
17 PF13340 DUF4096: Putative tra 86.7 0.94 2E-05 36.9 4.0 46 226-272 21-66 (75)
18 PF02209 VHP: Villin headpiece 86.3 0.47 1E-05 33.5 1.7 22 192-213 2-23 (36)
19 PF13011 LZ_Tnp_IS481: leucine 85.5 0.4 8.7E-06 40.3 1.2 47 225-271 4-50 (85)
20 PF00872 Transposase_mut: Tran 84.5 0.71 1.5E-05 49.4 2.9 129 242-409 110-248 (381)
21 cd00569 HTH_Hin_like Helix-tur 84.5 0.4 8.7E-06 31.4 0.7 38 229-267 5-42 (42)
22 cd00131 PAX Paired Box domain 84.3 0.49 1.1E-05 42.8 1.4 45 227-272 15-59 (128)
23 smart00153 VHP Villin headpiec 83.8 0.82 1.8E-05 32.2 2.0 21 192-212 2-22 (36)
24 smart00421 HTH_LUXR helix_turn 83.7 0.57 1.2E-05 34.6 1.3 44 229-274 3-46 (58)
25 COG3415 Transposase and inacti 82.0 0.42 9.2E-06 43.9 -0.1 43 230-272 5-47 (138)
26 PRK09413 IS2 repressor TnpA; R 81.6 0.75 1.6E-05 41.0 1.4 46 227-272 10-55 (121)
27 PF05225 HTH_psq: helix-turn-h 81.4 0.36 7.7E-06 35.6 -0.6 37 233-269 2-39 (45)
28 PRK04217 hypothetical protein; 81.2 0.81 1.8E-05 40.4 1.4 50 228-278 41-90 (110)
29 PRK09639 RNA polymerase sigma 80.3 0.92 2E-05 41.8 1.6 48 229-278 112-159 (166)
30 cd06171 Sigma70_r4 Sigma70, re 80.1 0.85 1.8E-05 33.0 1.0 43 229-272 10-52 (55)
31 PRK00118 putative DNA-binding 78.7 1.1 2.4E-05 39.2 1.4 48 229-277 17-64 (104)
32 PF01527 HTH_Tnp_1: Transposas 78.5 0.4 8.8E-06 38.5 -1.3 45 227-271 4-48 (76)
33 cd06571 Bac_DnaA_C C-terminal 77.4 1.5 3.4E-05 36.9 2.0 49 228-276 26-75 (90)
34 PRK07037 extracytoplasmic-func 77.1 1.3 2.7E-05 40.8 1.4 49 229-278 109-157 (163)
35 TIGR02531 yecD_yerC TrpR-relat 75.9 1.2 2.7E-05 37.7 1.0 31 237-267 41-71 (88)
36 PRK12529 RNA polymerase sigma 75.7 1.5 3.3E-05 41.3 1.6 48 229-277 127-174 (178)
37 TIGR02985 Sig70_bacteroi1 RNA 75.5 1.5 3.3E-05 39.6 1.5 47 229-276 113-159 (161)
38 PRK09047 RNA polymerase factor 75.4 1.4 3.1E-05 40.2 1.3 50 229-279 106-155 (161)
39 TIGR02937 sigma70-ECF RNA poly 75.3 1.6 3.5E-05 38.4 1.6 47 229-276 110-156 (158)
40 TIGR02952 Sig70_famx2 RNA poly 75.1 1.6 3.4E-05 40.2 1.6 47 229-276 122-168 (170)
41 cd06170 LuxR_C_like C-terminal 74.7 1.5 3.2E-05 32.5 1.0 42 231-274 2-43 (57)
42 PRK09652 RNA polymerase sigma 74.0 1.5 3.2E-05 40.6 1.1 49 229-278 128-176 (182)
43 PRK08301 sporulation sigma fac 74.0 1.7 3.7E-05 42.8 1.6 50 229-278 178-230 (234)
44 PRK09638 RNA polymerase sigma 74.0 1.5 3.3E-05 40.8 1.1 48 229-277 126-173 (176)
45 TIGR02392 rpoH_proteo alternat 73.6 1.9 4.1E-05 43.8 1.8 49 229-277 218-267 (270)
46 TIGR02950 SigM_subfam RNA poly 73.3 1.3 2.8E-05 40.2 0.4 47 229-276 105-151 (154)
47 TIGR03879 near_KaiC_dom probab 72.9 1.1 2.5E-05 36.6 -0.0 41 229-269 15-55 (73)
48 PRK12547 RNA polymerase sigma 72.8 1.9 4.1E-05 39.9 1.5 49 229-278 112-160 (164)
49 PRK12515 RNA polymerase sigma 72.1 1.9 4.1E-05 40.9 1.3 49 229-278 131-179 (189)
50 PRK12530 RNA polymerase sigma 72.1 1.8 3.9E-05 41.2 1.2 49 229-278 134-182 (189)
51 PRK12514 RNA polymerase sigma 71.6 2.2 4.7E-05 40.0 1.6 48 229-277 129-176 (179)
52 PRK12532 RNA polymerase sigma 71.5 1.8 3.8E-05 41.3 0.9 50 229-279 136-185 (195)
53 PF13542 HTH_Tnp_ISL3: Helix-t 71.3 1 2.2E-05 33.5 -0.6 29 242-270 23-51 (52)
54 PRK05803 sporulation sigma fac 70.9 2.3 4.9E-05 42.0 1.6 49 229-277 175-226 (233)
55 TIGR02846 spore_sigmaK RNA pol 70.9 2.5 5.3E-05 41.6 1.9 50 229-278 174-226 (227)
56 PRK12533 RNA polymerase sigma 70.6 2.2 4.7E-05 41.9 1.4 49 229-278 134-182 (216)
57 PRK06596 RNA polymerase factor 70.1 2.5 5.5E-05 43.3 1.8 49 229-277 230-279 (284)
58 PRK12519 RNA polymerase sigma 69.7 2.4 5.3E-05 40.1 1.5 48 229-277 141-188 (194)
59 PRK12516 RNA polymerase sigma 69.5 2.4 5.2E-05 40.4 1.4 49 229-278 116-164 (187)
60 PRK07408 RNA polymerase sigma 69.3 2.5 5.4E-05 42.5 1.5 49 229-278 203-251 (256)
61 PRK11924 RNA polymerase sigma 69.2 2.2 4.8E-05 39.3 1.1 49 229-278 125-173 (179)
62 PRK12512 RNA polymerase sigma 68.7 2.6 5.7E-05 39.6 1.5 49 229-278 131-179 (184)
63 PRK12537 RNA polymerase sigma 68.5 2.8 6E-05 39.5 1.6 48 229-277 133-180 (182)
64 PRK12520 RNA polymerase sigma 68.3 2.3 5.1E-05 40.3 1.0 50 229-279 131-180 (191)
65 TIGR02989 Sig-70_gvs1 RNA poly 68.0 2.9 6.2E-05 38.1 1.5 47 229-276 111-157 (159)
66 PF00356 LacI: Bacterial regul 68.0 1.2 2.6E-05 33.1 -0.8 21 249-269 2-22 (46)
67 PRK12524 RNA polymerase sigma 67.9 2.6 5.7E-05 40.2 1.3 49 229-278 136-184 (196)
68 TIGR02999 Sig-70_X6 RNA polyme 67.6 2.9 6.3E-05 39.1 1.5 48 229-277 134-181 (183)
69 PRK12511 RNA polymerase sigma 67.5 2.8 6E-05 39.8 1.4 49 229-278 111-159 (182)
70 PRK05911 RNA polymerase sigma 67.5 2.8 6E-05 42.3 1.4 49 229-278 205-253 (257)
71 PRK12534 RNA polymerase sigma 67.4 3.1 6.8E-05 39.2 1.7 48 229-277 137-184 (187)
72 PRK09641 RNA polymerase sigma 67.1 2.7 5.9E-05 39.3 1.2 48 229-277 136-183 (187)
73 PRK09415 RNA polymerase factor 66.9 2.9 6.2E-05 39.3 1.3 49 229-278 127-175 (179)
74 TIGR02393 RpoD_Cterm RNA polym 66.8 2.5 5.3E-05 42.0 0.9 48 229-276 176-226 (238)
75 PRK03975 tfx putative transcri 66.6 3.1 6.6E-05 38.4 1.4 46 228-275 5-50 (141)
76 TIGR02984 Sig-70_plancto1 RNA 66.5 3.2 6.9E-05 38.9 1.5 48 229-277 140-187 (189)
77 PRK09645 RNA polymerase sigma 66.3 3.5 7.6E-05 38.3 1.8 49 229-278 118-166 (173)
78 TIGR02960 SigX5 RNA polymerase 65.9 5 0.00011 41.3 3.0 50 229-279 142-191 (324)
79 TIGR00721 tfx DNA-binding prot 65.8 3.1 6.8E-05 38.2 1.3 47 228-276 5-51 (137)
80 PRK05572 sporulation sigma fac 65.7 3.3 7.2E-05 41.4 1.6 48 229-277 202-249 (252)
81 PRK12540 RNA polymerase sigma 65.4 3.2 6.8E-05 39.4 1.3 50 229-279 111-160 (182)
82 PRK08583 RNA polymerase sigma 65.4 3.5 7.5E-05 41.3 1.6 49 229-278 205-253 (257)
83 TIGR02980 SigBFG RNA polymeras 65.4 3.3 7.2E-05 40.5 1.5 47 229-276 178-224 (227)
84 PRK05602 RNA polymerase sigma 65.3 3.3 7.1E-05 39.0 1.4 49 229-278 128-176 (186)
85 PRK12531 RNA polymerase sigma 65.3 3.2 7E-05 39.5 1.3 49 229-278 141-189 (194)
86 PRK12544 RNA polymerase sigma 65.1 2.6 5.7E-05 40.9 0.7 49 229-278 148-196 (206)
87 TIGR01321 TrpR trp operon repr 64.9 2.7 5.9E-05 36.1 0.6 38 230-267 33-76 (94)
88 TIGR02983 SigE-fam_strep RNA p 64.7 3.4 7.4E-05 37.8 1.3 48 229-277 110-157 (162)
89 TIGR02394 rpoS_proteo RNA poly 64.7 3.4 7.4E-05 42.2 1.5 50 229-278 222-274 (285)
90 PRK07500 rpoH2 RNA polymerase 64.5 3.7 8.1E-05 42.2 1.7 50 229-278 227-277 (289)
91 TIGR02885 spore_sigF RNA polym 64.4 3.6 7.8E-05 40.4 1.5 47 229-276 183-229 (231)
92 TIGR03001 Sig-70_gmx1 RNA poly 64.3 2.4 5.3E-05 42.4 0.3 50 229-279 161-210 (244)
93 PRK12528 RNA polymerase sigma 64.0 3.5 7.6E-05 37.8 1.3 46 229-275 113-158 (161)
94 PRK12523 RNA polymerase sigma 64.0 3.7 8E-05 38.2 1.4 49 229-278 119-167 (172)
95 PRK09642 RNA polymerase sigma 63.9 3.6 7.7E-05 37.7 1.3 49 229-278 106-154 (160)
96 TIGR02844 spore_III_D sporulat 63.8 1.9 4.2E-05 35.9 -0.4 22 247-268 20-41 (80)
97 COG1595 RpoE DNA-directed RNA 63.8 3.7 8.1E-05 38.7 1.5 49 229-278 127-175 (182)
98 PF01710 HTH_Tnp_IS630: Transp 63.7 6.1 0.00013 35.1 2.7 77 192-270 19-95 (119)
99 PRK12539 RNA polymerase sigma 63.6 3.8 8.3E-05 38.6 1.5 49 229-278 131-179 (184)
100 PRK06704 RNA polymerase factor 63.4 4.9 0.00011 40.0 2.3 70 229-300 116-186 (228)
101 TIGR02835 spore_sigmaE RNA pol 63.3 4.1 8.9E-05 40.3 1.7 49 229-277 178-229 (234)
102 PRK12546 RNA polymerase sigma 63.2 4 8.8E-05 39.0 1.6 49 229-278 113-161 (188)
103 PF13730 HTH_36: Helix-turn-he 62.6 3 6.4E-05 31.4 0.4 39 234-272 8-51 (55)
104 TIGR02939 RpoE_Sigma70 RNA pol 62.5 3.9 8.5E-05 38.3 1.3 49 229-278 138-186 (190)
105 TIGR02948 SigW_bacill RNA poly 61.9 4.1 9E-05 38.1 1.4 49 229-278 136-184 (187)
106 PRK08215 sporulation sigma fac 61.7 4.3 9.4E-05 40.7 1.6 47 229-276 209-255 (258)
107 PRK10402 DNA-binding transcrip 61.4 5.6 0.00012 38.9 2.2 105 192-297 109-220 (226)
108 TIGR03697 NtcA_cyano global ni 61.2 2.5 5.5E-05 39.6 -0.2 100 191-291 72-188 (193)
109 TIGR02954 Sig70_famx3 RNA poly 61.0 4.6 0.0001 37.3 1.5 48 229-277 119-166 (169)
110 PRK12536 RNA polymerase sigma 60.8 4.5 9.7E-05 38.0 1.4 49 229-278 129-177 (181)
111 PHA00675 hypothetical protein 60.8 4.2 9E-05 33.5 1.0 40 229-268 22-61 (78)
112 TIGR02850 spore_sigG RNA polym 60.6 5 0.00011 40.2 1.8 47 229-276 206-252 (254)
113 PF04967 HTH_10: HTH DNA bindi 60.3 3.6 7.9E-05 31.5 0.6 29 246-274 23-51 (53)
114 PRK06986 fliA flagellar biosyn 60.2 4.9 0.00011 39.7 1.6 49 229-278 184-232 (236)
115 PHA00542 putative Cro-like pro 59.9 3.2 7E-05 34.4 0.2 51 238-300 23-73 (82)
116 PRK09643 RNA polymerase sigma 59.5 4.9 0.00011 38.3 1.4 48 229-277 134-181 (192)
117 TIGR02941 Sigma_B RNA polymera 58.7 5.4 0.00012 39.9 1.6 48 229-277 205-252 (255)
118 TIGR02947 SigH_actino RNA poly 58.5 4.5 9.8E-05 38.4 1.0 49 229-278 131-179 (193)
119 PF12802 MarR_2: MarR family; 58.4 3.5 7.7E-05 31.5 0.2 26 247-272 22-47 (62)
120 PF09339 HTH_IclR: IclR helix- 58.4 3.3 7.1E-05 31.0 0.0 27 246-272 18-44 (52)
121 PF13751 DDE_Tnp_1_6: Transpos 58.2 3.5 7.5E-05 36.4 0.2 49 422-471 74-123 (125)
122 PRK12543 RNA polymerase sigma 58.1 5.1 0.00011 37.6 1.3 49 229-278 117-165 (179)
123 TIGR02943 Sig70_famx1 RNA poly 58.1 4.4 9.4E-05 38.6 0.8 49 229-278 131-179 (188)
124 PRK11753 DNA-binding transcrip 58.0 4.3 9.3E-05 38.7 0.8 81 192-272 99-194 (211)
125 PRK12545 RNA polymerase sigma 57.9 4.6 0.0001 38.8 1.0 49 229-278 139-187 (201)
126 PRK09637 RNA polymerase sigma 57.8 5.6 0.00012 37.6 1.5 49 229-278 106-154 (181)
127 TIGR02997 Sig70-cyanoRpoD RNA 57.6 5.1 0.00011 41.2 1.3 44 229-272 249-295 (298)
128 PRK06930 positive control sigm 57.3 5.3 0.00012 37.9 1.2 49 229-278 114-162 (170)
129 PRK07670 RNA polymerase sigma 57.0 6.1 0.00013 39.4 1.7 48 229-277 201-248 (251)
130 PRK09649 RNA polymerase sigma 57.0 6.3 0.00014 37.3 1.7 47 229-276 130-176 (185)
131 cd00092 HTH_CRP helix_turn_hel 56.8 3.3 7.1E-05 32.0 -0.2 27 246-272 25-51 (67)
132 PRK07122 RNA polymerase sigma 56.6 6.3 0.00014 39.9 1.8 47 229-276 215-261 (264)
133 PRK12525 RNA polymerase sigma 56.6 6 0.00013 36.7 1.5 48 229-277 118-165 (168)
134 PF13412 HTH_24: Winged helix- 56.2 4.7 0.0001 29.5 0.5 28 245-272 16-43 (48)
135 PF00196 GerE: Bacterial regul 56.0 3.1 6.8E-05 31.8 -0.4 43 230-274 4-46 (58)
136 PRK11923 algU RNA polymerase s 55.9 5.7 0.00012 37.6 1.2 49 229-278 138-186 (193)
137 PRK06811 RNA polymerase factor 55.9 6.1 0.00013 37.5 1.4 47 229-276 131-177 (189)
138 PRK08295 RNA polymerase factor 55.7 5.9 0.00013 37.8 1.3 48 229-278 155-202 (208)
139 cd08330 CARD_ASC_NALP1 Caspase 55.6 15 0.00033 30.5 3.6 61 63-123 16-79 (82)
140 PRK06759 RNA polymerase factor 55.2 6.1 0.00013 35.8 1.2 45 229-274 106-150 (154)
141 PF01371 Trp_repressor: Trp re 55.1 4 8.6E-05 34.6 -0.0 34 233-266 36-69 (87)
142 COG1191 FliA DNA-directed RNA 55.1 6.4 0.00014 39.7 1.5 49 229-278 196-244 (247)
143 COG5421 Transposase [DNA repli 54.9 20 0.00044 39.3 5.3 58 339-399 152-210 (480)
144 PRK07405 RNA polymerase sigma 54.8 6.9 0.00015 40.8 1.7 48 229-276 256-306 (317)
145 PRK09644 RNA polymerase sigma 54.4 5.7 0.00012 36.6 1.0 49 229-278 108-156 (165)
146 PRK15320 transcriptional activ 54.3 4.9 0.00011 39.2 0.4 45 228-274 163-207 (251)
147 PRK11922 RNA polymerase sigma 54.0 5.9 0.00013 39.0 1.0 49 229-278 149-197 (231)
148 TIGR02479 FliA_WhiG RNA polyme 53.9 7.4 0.00016 38.0 1.7 47 229-276 175-221 (224)
149 PRK06030 hypothetical protein; 53.5 7.1 0.00015 35.3 1.3 46 228-273 51-96 (124)
150 PF13551 HTH_29: Winged helix- 53.4 4.2 9.1E-05 34.7 -0.1 34 239-272 4-38 (112)
151 PRK03573 transcriptional regul 53.1 14 0.00029 33.5 3.2 44 229-272 28-72 (144)
152 PRK09648 RNA polymerase sigma 53.1 7.2 0.00016 36.8 1.4 48 229-277 139-186 (189)
153 PF01022 HTH_5: Bacterial regu 52.9 4.5 9.8E-05 29.7 -0.0 28 245-272 14-41 (47)
154 TIGR02959 SigZ RNA polymerase 51.6 7.7 0.00017 36.1 1.4 49 229-278 100-148 (170)
155 PF08299 Bac_DnaA_C: Bacterial 51.5 4.4 9.6E-05 32.6 -0.3 41 230-270 29-70 (70)
156 PRK12518 RNA polymerase sigma 51.3 6.4 0.00014 36.5 0.8 49 229-278 120-168 (175)
157 PRK01381 Trp operon repressor; 51.3 8.2 0.00018 33.5 1.3 24 244-267 53-76 (99)
158 PRK12538 RNA polymerase sigma 51.3 7.1 0.00015 38.7 1.1 49 229-278 171-219 (233)
159 PRK13919 putative RNA polymera 51.2 8.2 0.00018 36.2 1.5 49 229-278 135-183 (186)
160 PRK12542 RNA polymerase sigma 50.6 8 0.00017 36.4 1.3 49 229-278 122-170 (185)
161 smart00342 HTH_ARAC helix_turn 50.6 15 0.00032 28.9 2.7 71 194-271 4-76 (84)
162 PRK09646 RNA polymerase sigma 50.4 8.8 0.00019 36.5 1.5 49 229-278 142-190 (194)
163 PRK15418 transcriptional regul 50.3 6.8 0.00015 40.9 0.8 69 238-310 21-89 (318)
164 TIGR03209 P21_Cbot clostridium 50.2 6.3 0.00014 35.3 0.5 36 229-265 107-142 (142)
165 PRK12513 RNA polymerase sigma 49.8 7.5 0.00016 36.8 1.0 49 229-278 139-187 (194)
166 PRK12541 RNA polymerase sigma 49.5 8.8 0.00019 35.1 1.4 47 229-276 112-158 (161)
167 PRK12526 RNA polymerase sigma 49.0 8.8 0.00019 37.0 1.3 49 229-278 153-201 (206)
168 PRK09392 ftrB transcriptional 49.0 8.3 0.00018 37.6 1.2 101 192-293 107-219 (236)
169 PF07374 DUF1492: Protein of u 48.7 7.7 0.00017 33.4 0.8 41 231-272 57-97 (100)
170 COG2963 Transposase and inacti 47.6 8.5 0.00018 33.6 0.9 46 227-272 5-51 (116)
171 PF01325 Fe_dep_repress: Iron 47.4 6.8 0.00015 30.6 0.2 39 234-272 7-48 (60)
172 PRK12527 RNA polymerase sigma 47.0 10 0.00022 34.6 1.3 49 229-278 105-153 (159)
173 TIGR02859 spore_sigH RNA polym 46.3 9.8 0.00021 35.9 1.2 41 234-276 155-195 (198)
174 PF13545 HTH_Crp_2: Crp-like h 46.3 5.6 0.00012 31.7 -0.4 27 246-272 28-54 (76)
175 PRK12535 RNA polymerase sigma 46.1 11 0.00024 36.1 1.6 49 229-278 133-181 (196)
176 PRK05657 RNA polymerase sigma 45.7 12 0.00025 39.3 1.7 50 229-278 262-314 (325)
177 smart00346 HTH_ICLR helix_turn 45.7 7.9 0.00017 31.9 0.4 38 235-272 6-46 (91)
178 COG2390 DeoR Transcriptional r 45.6 9.2 0.0002 40.1 0.9 67 240-310 20-86 (321)
179 PRK11161 fumarate/nitrate redu 44.9 7.5 0.00016 37.9 0.1 80 192-271 114-209 (235)
180 PF01047 MarR: MarR family; I 44.7 6.7 0.00015 29.7 -0.2 28 245-272 16-43 (59)
181 PRK06288 RNA polymerase sigma 44.6 11 0.00023 38.1 1.2 48 229-277 212-259 (268)
182 PRK12517 RNA polymerase sigma 44.6 11 0.00023 35.9 1.2 49 229-278 128-176 (188)
183 PRK07406 RNA polymerase sigma 44.4 12 0.00025 40.1 1.5 48 229-276 311-361 (373)
184 PRK12427 flagellar biosynthesi 44.0 12 0.00026 37.0 1.5 45 229-274 183-227 (231)
185 PF01710 HTH_Tnp_IS630: Transp 43.7 5.5 0.00012 35.3 -0.9 37 230-269 5-41 (119)
186 PRK13870 transcriptional regul 43.7 20 0.00043 35.7 2.9 46 228-275 172-217 (234)
187 PRK13918 CRP/FNR family transc 43.7 9.3 0.0002 36.1 0.6 64 230-294 119-197 (202)
188 PF08279 HTH_11: HTH domain; 43.3 9 0.00019 28.7 0.3 27 247-273 16-42 (55)
189 PRK12522 RNA polymerase sigma 43.2 13 0.00028 34.5 1.5 49 229-278 119-167 (173)
190 PRK09640 RNA polymerase sigma 43.2 8.9 0.00019 36.2 0.4 49 229-278 134-182 (188)
191 TIGR01636 phage_rinA phage tra 42.7 15 0.00033 33.3 1.8 50 229-278 82-132 (134)
192 PRK09210 RNA polymerase sigma 42.2 13 0.00029 39.5 1.5 47 229-275 305-354 (367)
193 PRK15201 fimbriae regulatory p 41.2 19 0.00041 34.7 2.2 45 228-274 132-176 (198)
194 PRK09651 RNA polymerase sigma 40.5 15 0.00032 34.2 1.4 46 229-275 119-164 (172)
195 COG2739 Uncharacterized protei 40.4 12 0.00026 32.5 0.7 43 233-276 21-63 (105)
196 PRK05949 RNA polymerase sigma 40.4 16 0.00035 38.3 1.8 48 229-276 266-316 (327)
197 smart00550 Zalpha Z-DNA-bindin 40.2 13 0.00029 29.6 0.9 40 231-270 6-46 (68)
198 TIGR02337 HpaR homoprotocatech 39.6 25 0.00053 30.7 2.6 43 229-272 25-68 (118)
199 PRK09636 RNA polymerase sigma 39.6 24 0.00052 36.0 2.9 49 229-278 115-163 (293)
200 PRK09391 fixK transcriptional 39.4 11 0.00025 36.8 0.5 81 192-272 113-205 (230)
201 PRK07598 RNA polymerase sigma 39.3 15 0.00032 39.9 1.4 47 229-275 350-399 (415)
202 PF07638 Sigma70_ECF: ECF sigm 39.0 16 0.00034 34.8 1.4 46 230-276 136-181 (185)
203 smart00418 HTH_ARSR helix_turn 38.8 13 0.00029 27.5 0.7 28 244-271 8-35 (66)
204 PF13463 HTH_27: Winged helix 37.7 10 0.00022 29.4 -0.2 28 245-272 17-44 (68)
205 smart00419 HTH_CRP helix_turn_ 36.9 11 0.00024 26.9 -0.1 28 245-272 7-34 (48)
206 smart00345 HTH_GNTR helix_turn 36.7 12 0.00025 27.9 -0.0 25 248-272 22-46 (60)
207 PRK09647 RNA polymerase sigma 36.3 18 0.00038 35.0 1.2 49 229-278 138-186 (203)
208 PRK15411 rcsA colanic acid cap 35.8 14 0.0003 35.8 0.4 44 229-274 137-180 (207)
209 PF12840 HTH_20: Helix-turn-he 35.7 10 0.00022 29.2 -0.4 30 243-272 21-50 (61)
210 TIGR02957 SigX4 RNA polymerase 35.3 34 0.00073 34.8 3.2 48 229-277 108-155 (281)
211 TIGR01610 phage_O_Nterm phage 35.2 17 0.00036 31.0 0.8 28 244-271 45-72 (95)
212 PRK07921 RNA polymerase sigma 34.8 20 0.00044 37.5 1.5 48 229-276 262-312 (324)
213 PF01381 HTH_3: Helix-turn-hel 34.3 9.9 0.00021 28.2 -0.7 42 244-298 7-48 (55)
214 PF13560 HTH_31: Helix-turn-he 34.3 8.8 0.00019 29.8 -1.0 28 241-268 9-36 (64)
215 PRK05901 RNA polymerase sigma 34.2 21 0.00046 39.8 1.5 48 229-276 447-497 (509)
216 PF00165 HTH_AraC: Bacterial r 33.9 11 0.00023 26.8 -0.5 29 243-271 5-33 (42)
217 PRK09635 sigI RNA polymerase s 33.2 36 0.00078 35.0 3.0 48 229-277 118-165 (290)
218 PRK09191 two-component respons 33.1 32 0.0007 33.6 2.5 52 229-281 88-139 (261)
219 PRK00149 dnaA chromosomal repl 32.0 30 0.00064 37.7 2.2 50 226-275 382-432 (450)
220 PF04297 UPF0122: Putative hel 31.6 24 0.00052 30.7 1.1 45 231-276 19-63 (101)
221 PF04552 Sigma54_DBD: Sigma-54 31.6 16 0.00034 34.5 0.0 23 246-268 49-71 (160)
222 TIGR03541 reg_near_HchA LuxR f 31.5 36 0.00077 33.7 2.5 46 228-275 170-215 (232)
223 PRK09492 treR trehalose repres 31.3 16 0.00035 36.8 0.0 23 247-269 5-27 (315)
224 PRK08241 RNA polymerase factor 31.2 23 0.0005 36.8 1.2 47 229-276 153-199 (339)
225 cd07377 WHTH_GntR Winged helix 31.1 34 0.00074 25.8 1.9 25 248-272 27-51 (66)
226 cd00090 HTH_ARSR Arsenical Res 30.9 22 0.00049 27.1 0.8 26 245-270 19-44 (78)
227 PRK14088 dnaA chromosomal repl 30.6 28 0.0006 38.0 1.7 48 227-274 368-415 (440)
228 TIGR02404 trehalos_R_Bsub treh 30.0 35 0.00076 33.4 2.2 21 251-271 29-49 (233)
229 PRK13413 mpi multiple promoter 29.9 14 0.00031 35.5 -0.6 29 241-269 167-195 (200)
230 TIGR02405 trehalos_R_Ecol treh 29.9 14 0.0003 37.4 -0.7 21 248-268 3-23 (311)
231 PF13551 HTH_29: Winged helix- 29.7 74 0.0016 26.8 3.9 77 193-269 14-110 (112)
232 PF14942 Muted: Organelle biog 29.5 69 0.0015 29.7 3.9 39 77-115 104-142 (145)
233 PRK10163 DNA-binding transcrip 29.5 26 0.00056 35.5 1.2 45 228-272 19-66 (271)
234 PF00126 HTH_1: Bacterial regu 29.4 20 0.00043 27.6 0.2 31 247-277 14-44 (60)
235 PHA00738 putative HTH transcri 28.8 16 0.00034 32.2 -0.4 31 242-272 20-52 (108)
236 PF12964 DUF3853: Protein of u 28.6 18 0.00039 31.2 -0.2 65 201-276 11-77 (96)
237 smart00354 HTH_LACI helix_turn 28.4 14 0.00031 29.4 -0.7 21 248-268 2-22 (70)
238 cd01392 HTH_LacI Helix-turn-he 28.3 15 0.00034 26.9 -0.5 18 251-268 2-19 (52)
239 PRK14987 gluconate operon tran 28.1 17 0.00038 37.0 -0.4 22 248-269 7-28 (331)
240 PF00392 GntR: Bacterial regul 28.1 35 0.00076 26.4 1.5 23 249-271 27-49 (64)
241 PRK14086 dnaA chromosomal repl 28.1 36 0.00079 38.8 2.1 50 227-276 550-599 (617)
242 PF02001 DUF134: Protein of un 28.0 26 0.00057 30.8 0.8 31 245-275 56-86 (106)
243 PF11662 DUF3263: Protein of u 27.8 65 0.0014 26.7 3.0 35 180-217 14-48 (77)
244 PRK11512 DNA-binding transcrip 27.6 32 0.0007 31.1 1.3 43 229-272 37-80 (144)
245 PRK10188 DNA-binding transcrip 27.5 52 0.0011 32.8 2.9 45 228-274 178-222 (240)
246 PRK13719 conjugal transfer tra 27.0 23 0.00051 35.0 0.3 44 229-274 143-186 (217)
247 PRK09526 lacI lac repressor; R 26.7 17 0.00038 37.1 -0.7 23 247-269 6-28 (342)
248 PRK10339 DNA-binding transcrip 26.5 20 0.00044 36.5 -0.2 22 248-269 3-24 (327)
249 smart00420 HTH_DEOR helix_turn 26.4 24 0.00051 25.4 0.2 27 246-272 14-40 (53)
250 PF13701 DDE_Tnp_1_4: Transpos 26.2 1.7E+02 0.0037 32.1 6.8 87 305-399 140-229 (448)
251 PF01978 TrmB: Sugar-specific 25.9 16 0.00035 28.7 -0.9 27 246-272 22-48 (68)
252 COG3293 Transposase and inacti 25.9 13 0.00028 32.8 -1.5 88 346-448 3-101 (124)
253 PRK10014 DNA-binding transcrip 25.8 18 0.00039 37.0 -0.8 23 247-269 7-29 (342)
254 PRK10840 transcriptional regul 25.6 24 0.00053 33.7 0.2 43 228-272 149-191 (216)
255 TIGR02431 pcaR_pcaU beta-ketoa 25.4 27 0.00058 34.7 0.4 44 230-273 5-51 (248)
256 PF03333 PapB: Adhesin biosynt 25.3 48 0.001 28.3 1.9 55 202-270 22-77 (91)
257 PRK09483 response regulator; P 25.2 25 0.00053 33.0 0.1 43 228-272 147-189 (217)
258 PRK08558 adenine phosphoribosy 25.2 22 0.00048 35.6 -0.2 36 233-268 10-45 (238)
259 COG3413 Predicted DNA binding 24.9 40 0.00086 32.9 1.5 50 227-276 153-208 (215)
260 PRK00215 LexA repressor; Valid 24.6 32 0.0007 33.1 0.8 27 246-272 23-50 (205)
261 PF00325 Crp: Bacterial regula 24.5 18 0.00039 24.8 -0.7 23 248-270 4-26 (32)
262 PRK10401 DNA-binding transcrip 24.3 21 0.00044 36.8 -0.7 22 248-269 3-24 (346)
263 PF05344 DUF746: Domain of Unk 24.1 39 0.00084 27.1 1.0 42 235-276 2-43 (65)
264 PRK11303 DNA-binding transcrip 24.1 21 0.00045 36.3 -0.7 22 248-269 2-23 (328)
265 smart00347 HTH_MARR helix_turn 24.1 44 0.00095 27.3 1.4 27 246-272 24-50 (101)
266 PRK05658 RNA polymerase sigma 24.1 44 0.00095 38.2 1.8 47 229-275 556-605 (619)
267 PRK14999 histidine utilization 23.7 49 0.0011 32.6 1.9 48 208-271 14-61 (241)
268 PF10654 DUF2481: Protein of u 23.7 20 0.00044 31.8 -0.7 26 245-270 79-104 (126)
269 cd04762 HTH_MerR-trunc Helix-T 23.6 21 0.00045 25.2 -0.6 22 248-269 2-23 (49)
270 TIGR02325 C_P_lyase_phnF phosp 23.5 56 0.0012 31.9 2.3 49 207-271 9-57 (238)
271 TIGR02018 his_ut_repres histid 23.3 55 0.0012 32.0 2.2 22 250-271 29-50 (230)
272 PRK09764 DNA-binding transcrip 23.2 57 0.0012 32.2 2.3 48 208-271 7-54 (240)
273 PRK10703 DNA-binding transcrip 22.9 23 0.0005 36.2 -0.6 22 248-269 3-24 (341)
274 COG2188 PhnF Transcriptional r 22.7 59 0.0013 32.2 2.3 50 206-271 7-56 (236)
275 PRK10079 phosphonate metabolis 22.5 54 0.0012 32.3 2.0 48 207-271 13-60 (241)
276 PRK10423 transcriptional repre 22.5 25 0.00053 35.7 -0.5 19 250-268 2-20 (327)
277 COG2771 CsgD DNA-binding HTH d 22.3 32 0.0007 26.0 0.3 34 239-272 12-45 (65)
278 PF09862 DUF2089: Protein of u 22.1 38 0.00082 30.1 0.7 46 229-275 33-78 (113)
279 TIGR01764 excise DNA binding d 21.9 23 0.00051 25.1 -0.6 22 248-269 3-24 (49)
280 TIGR00122 birA_repr_reg BirA b 21.8 26 0.00057 27.5 -0.3 24 247-270 14-37 (69)
281 PRK11402 DNA-binding transcrip 21.7 63 0.0014 31.8 2.3 49 207-271 10-58 (241)
282 COG2197 CitB Response regulato 21.6 34 0.00074 33.3 0.3 44 229-274 148-191 (211)
283 PF13744 HTH_37: Helix-turn-he 21.6 23 0.0005 29.0 -0.8 25 244-268 29-53 (80)
284 COG2522 Predicted transcriptio 21.4 30 0.00065 31.1 -0.1 24 246-269 22-45 (119)
285 PRK11475 DNA-binding transcrip 21.4 32 0.0007 33.5 0.1 42 229-272 134-175 (207)
286 TIGR02395 rpoN_sigma RNA polym 21.3 35 0.00076 37.2 0.4 32 246-288 318-349 (429)
287 PRK12422 chromosomal replicati 21.1 55 0.0012 35.9 1.8 49 226-274 377-425 (445)
288 cd00131 PAX Paired Box domain 21.1 1.7E+02 0.0037 26.3 4.7 79 190-268 32-125 (128)
289 PRK14087 dnaA chromosomal repl 21.0 57 0.0012 35.8 1.9 49 227-275 382-431 (450)
290 TIGR03020 EpsA transcriptional 21.0 48 0.001 33.4 1.3 46 227-274 188-233 (247)
291 PF13404 HTH_AsnC-type: AsnC-t 20.9 26 0.00056 25.3 -0.5 24 246-269 17-40 (42)
292 TIGR01889 Staph_reg_Sar staphy 20.6 55 0.0012 28.3 1.4 27 246-272 43-69 (109)
293 COG1508 RpoN DNA-directed RNA 20.5 27 0.00059 38.1 -0.7 31 247-288 331-361 (444)
294 TIGR02417 fruct_sucro_rep D-fr 20.5 28 0.0006 35.4 -0.6 21 249-269 2-22 (327)
295 PRK14161 heat shock protein Gr 20.4 1.3E+02 0.0028 28.9 4.0 49 55-104 4-56 (178)
296 PRK10870 transcriptional repre 20.4 47 0.001 31.5 1.0 44 229-272 52-97 (176)
297 TIGR03070 couple_hipB transcri 20.4 27 0.00058 25.7 -0.6 24 244-267 13-36 (58)
298 PRK10100 DNA-binding transcrip 20.4 37 0.0008 33.3 0.3 44 229-274 155-198 (216)
299 PF04703 FaeA: FaeA-like prote 20.3 27 0.00058 27.6 -0.6 36 234-269 3-38 (62)
300 PRK09834 DNA-binding transcrip 20.2 36 0.00078 34.2 0.2 43 230-272 7-52 (263)
301 PF13309 HTH_22: HTH domain 20.1 26 0.00056 27.7 -0.7 40 229-268 20-64 (64)
302 smart00344 HTH_ASNC helix_turn 20.1 48 0.001 28.2 0.9 27 246-272 17-43 (108)
No 1
>KOG4585 consensus Predicted transposase [Replication, recombination and repair]
Probab=100.00 E-value=1.5e-39 Score=334.59 Aligned_cols=297 Identities=38% Similarity=0.616 Sum_probs=238.4
Q ss_pred HcCCCHHHHHHHHHHhhccccccC--CCCCCCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 200 DFRMSKATFEMICEELESTVMKKN--TMLRDAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 200 ~fRmSr~tF~~Lv~~L~~~i~~~~--t~~r~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.|++++.+|+.++........... ......+++..+++++|+.++++.+.+.++..||...+|+ ++......
T Consensus 7 ~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~i~~~fg~~~~~~------~~~~~~~~ 80 (326)
T KOG4585|consen 7 EFRKSYTTFDKICSLVQSLNVVKNSGFMLSSLLPADTLVAVALWRLKTGESLRTVEKKFGLGQSTC------KFLEEKED 80 (326)
T ss_pred HHHHHHHHHHHHhhhhhhhhhhcccchhhhccccHHhhhhhhhccccccchHHHHHHHcCCcchhh------hHHHhhhc
Confidence 788999999999998765433222 1222333388899999999999999999999999999998 34444445
Q ss_pred cccccccCcchHHHHHHHhhhccccCCCccccCCcceeeeEecCCCccccccccccccccCCCCccccccccccCCCcee
Q 041521 278 LMPKFLQWPDELKMKQIKEEFQGISGIPNVGGSMYTTHIPIIAPKISVASYFNKRHTERNQKTSYSITVQGVVDTKGVFT 357 (524)
Q Consensus 278 L~~~~I~~P~~ee~~~i~~~F~~~~gfP~~vGaIDgThIpI~~P~~~~~~y~n~~~~~rn~K~~~Si~vq~v~D~~g~fi 357 (524)
+++.++.||....+..+.+.|+. +|+|+|+||+||+++..|....+.|+|+ .++.++|+|||++++|+
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 68999999998888889899877 9999999999999999999988888763 67888999999999999
Q ss_pred eecCCCCCCCCChHHHHhHHHHhhhhccccc-----------eEEEEcccCCCCccccccccccCCcccchhhccccccc
Q 041521 358 DVCIGWPGSMPDDQVLERSALFQRADRGLLK-----------DVWIVGNSGYPLMDWVMVPYTQKNLTWTQHAFNEKIGD 426 (524)
Q Consensus 358 ~v~~g~pGS~hDs~V~~~S~L~~~l~~~~~~-----------g~~lLGD~gYpl~~~LmtPy~~~~lt~~q~~FN~~ls~ 426 (524)
+|++||||+.||+.|++.+.+......+.+. ..+++|+.+||+.+++|+||.++.++..++.||.+|+.
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 9999999999999999999988766544442 45666667777777788888887778899999999999
Q ss_pred chhhhhhcccccccccccccccccccCCCccceehhhHHHHhhhhhcCCCCCCCCCcCCCCCCC-----CCCCcccChhH
Q 041521 427 IQAVAKDAFARLKGRWACLQKRTEVKLQDLPVVLGACCVLHNICEMRNEVMDPQLKFDLFDDEM-----IPDNSVRSMAS 501 (524)
Q Consensus 427 ~R~~VE~aFG~LK~RFriL~~~~~~~~~~~~~iI~AccvLHNi~~~~~~~~~~~~~~~~~dd~~-----~p~~~~~~~~~ 501 (524)
+|.++|++||+||+||+||+........+.+.||.|||+|||||++..+..+++...+..++.. .........-+
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 9999999999999999999998667788999999999999999999877543322222223322 11111223346
Q ss_pred HHHHHHHHHHHhh
Q 041521 502 AQARDHIAHNLLH 514 (524)
Q Consensus 502 ~~~Rd~ia~~l~~ 514 (524)
..+||.|+..||.
T Consensus 309 ~~~r~~l~~~l~~ 321 (326)
T KOG4585|consen 309 EKIRDNLLSELWN 321 (326)
T ss_pred HHHHHHHHHHHHh
Confidence 7788999988864
No 2
>PF13359 DDE_Tnp_4: DDE superfamily endonuclease
Probab=100.00 E-value=1.1e-36 Score=282.36 Aligned_cols=152 Identities=33% Similarity=0.665 Sum_probs=138.7
Q ss_pred CcceeeeEecCCCc--cccccccccccccCCCCccccccccccCCCceeeecCCCCCCCCChHHHHhHHHHhhhhccccc
Q 041521 311 MYTTHIPIIAPKIS--VASYFNKRHTERNQKTSYSITVQGVVDTKGVFTDVCIGWPGSMPDDQVLERSALFQRADRGLLK 388 (524)
Q Consensus 311 IDgThIpI~~P~~~--~~~y~n~~~~~rn~K~~~Si~vq~v~D~~g~fi~v~~g~pGS~hDs~V~~~S~L~~~l~~~~~~ 388 (524)
||||||+|.+|... ...+| +++|+.|++++|+|||++|+|++|+++||||+||++||++|++...++..++.
T Consensus 1 iDgt~v~i~~P~~~~~~~~~y------~~~k~~~~~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~s~~~~~l~~~~~~ 74 (158)
T PF13359_consen 1 IDGTHVPIQRPSDKEEQREFY------SGKKKNHSLKVQIVCDPDGRIIYVSVGWPGSVHDSTIFRQSGLLDRLEQAFPP 74 (158)
T ss_pred CccEEEEEEeCCccccccccc------cCCCCcceEeEEEEEeccceeEeeecccccccccccccccccccceeeccccc
Confidence 79999999999872 23333 45799999999999999999999999999999999999999999887633667
Q ss_pred eEEEEcccCCCCccccccccc---cCCcccchhhcccccccchhhhhhccccccccccccccccccc-CCCccceehhhH
Q 041521 389 DVWIVGNSGYPLMDWVMVPYT---QKNLTWTQHAFNEKIGDIQAVAKDAFARLKGRWACLQKRTEVK-LQDLPVVLGACC 464 (524)
Q Consensus 389 g~~lLGD~gYpl~~~LmtPy~---~~~lt~~q~~FN~~ls~~R~~VE~aFG~LK~RFriL~~~~~~~-~~~~~~iI~Acc 464 (524)
++|+|||+|||+.+++|+||+ +..++..|+.||++|+++|++||++||+||+||+||...++.+ ++.+..+|.|||
T Consensus 75 ~~~~l~D~gy~~~~~~~~P~~~~~~~~l~~~e~~~N~~~s~~R~~vE~~~~~lK~rf~~l~~~~~~~~~~~~~~ii~~~~ 154 (158)
T PF13359_consen 75 GEYLLGDSGYPLSPYLLTPYKKPKGRELTPEEKEFNRRHSSARIIVERAFGRLKSRFRILRGRLRLSRPEKAPQIILACC 154 (158)
T ss_pred CccccccccccccccccccccccccccccccccchhccccceeeeeHHHHHHHHHhcccCCcccCCCcHhHHHHHHheeE
Confidence 899999999999999999996 5578999999999999999999999999999999999888888 899999999999
Q ss_pred HHHh
Q 041521 465 VLHN 468 (524)
Q Consensus 465 vLHN 468 (524)
+|||
T Consensus 155 ~LhN 158 (158)
T PF13359_consen 155 VLHN 158 (158)
T ss_pred EEEC
Confidence 9999
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=99.96 E-value=1.4e-31 Score=251.33 Aligned_cols=185 Identities=21% Similarity=0.294 Sum_probs=166.5
Q ss_pred ccccCcchHHHHHHHhhhccccCCCccccCCcceeeeEe-cCCCccccccccccccccCCCCccccccccccCCCceeee
Q 041521 281 KFLQWPDELKMKQIKEEFQGISGIPNVGGSMYTTHIPII-APKISVASYFNKRHTERNQKTSYSITVQGVVDTKGVFTDV 359 (524)
Q Consensus 281 ~~I~~P~~ee~~~i~~~F~~~~gfP~~vGaIDgThIpI~-~P~~~~~~y~n~~~~~rn~K~~~Si~vq~v~D~~g~fi~v 359 (524)
+|++-|+.++++.+.+.+ +..||||.+|+|||+|+.+. +|......|.. ++++..++.+++|++.+.+|+++
T Consensus 2 ~YLr~P~~~d~~rll~~~-e~rGFpGmlGSIDCmHw~WkncP~aw~g~~~~------G~~g~pTiiLEaVAs~dlwIWha 74 (205)
T PF04827_consen 2 EYLRRPTNEDLERLLQIG-EARGFPGMLGSIDCMHWEWKNCPTAWKGQYTR------GKEGVPTIILEAVASHDLWIWHA 74 (205)
T ss_pred cccCCCChhHHHHHHHhh-hhcCCCccccceeEEEeehhcchHHhhhcccC------CCCCCCeehhhhhhccchhhhhe
Confidence 588999999999999666 56899999999999999999 78777677753 46899999999999999999999
Q ss_pred cCCCCCCCCChHHHHhHHHHhhhhccccc------------eEEEEcccCCCCccccccccccCCcccchhhcccccccc
Q 041521 360 CIGWPGSMPDDQVLERSALFQRADRGLLK------------DVWIVGNSGYPLMDWVMVPYTQKNLTWTQHAFNEKIGDI 427 (524)
Q Consensus 360 ~~g~pGS~hDs~V~~~S~L~~~l~~~~~~------------g~~lLGD~gYpl~~~LmtPy~~~~lt~~q~~FN~~ls~~ 427 (524)
..|.|||.+|..|+..|+|+..+..|..+ -.|+|+|..||-...++...+.|. +.+++.|.++..++
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 99999999999999999999988766321 368999999999999999999886 67899999999999
Q ss_pred hhhhhhccccccccccccccccc-ccCCCccceehhhHHHHhhhhhc
Q 041521 428 QAVAKDAFARLKGRWACLQKRTE-VKLQDLPVVLGACCVLHNICEMR 473 (524)
Q Consensus 428 R~~VE~aFG~LK~RFriL~~~~~-~~~~~~~~iI~AccvLHNi~~~~ 473 (524)
|.-||+|||+|++||+|++.+.+ .+.+++..|+.||++||||+++.
T Consensus 154 RKDVErAFGVLQaRfaIi~~p~r~w~~~~l~~Im~aCiILHNMIvED 200 (205)
T PF04827_consen 154 RKDVERAFGVLQARFAIIRGPARLWDREDLANIMRACIILHNMIVED 200 (205)
T ss_pred HHHHHHHHHHHHHHHHHhcCchhccCHHHHHHHHHHHHHhhheeEec
Confidence 99999999999999999999866 67789999999999999999863
No 4
>PF13612 DDE_Tnp_1_3: Transposase DDE domain
Probab=98.74 E-value=1.7e-09 Score=100.73 Aligned_cols=131 Identities=16% Similarity=0.183 Sum_probs=97.0
Q ss_pred CCccccCCcceeeeEecCCCcc-------ccccccccccccCCCCccccccccccCCCceeeecCCCCCCCCChHHHHhH
Q 041521 304 IPNVGGSMYTTHIPIIAPKISV-------ASYFNKRHTERNQKTSYSITVQGVVDTKGVFTDVCIGWPGSMPDDQVLERS 376 (524)
Q Consensus 304 fP~~vGaIDgThIpI~~P~~~~-------~~y~n~~~~~rn~K~~~Si~vq~v~D~~g~fi~v~~g~pGS~hDs~V~~~S 376 (524)
-+..+.+||.|.||++.|.... .++++ |...+-+|++++.++|+..|.++.+.+. ||++||..++.
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 QCTGIYIIDSFPIPVCHNIRIKRHKVFKGLAYRG----YCAMGWFYGFKLHLLVNDSGEIVAFTLT-PANVHDRKVLE-- 75 (155)
T ss_pred CccEEEEEecCChhHhCccchhhhccccCccccc----eeccceeEeeeeeeEEccCCcEEEEEEc-ccccccccccc--
Confidence 4567889999999999776421 22222 2233457999999999999999998774 99999999884
Q ss_pred HHHhhhhccccceEEEEcccCCCCcc----------ccccccccCCcccchhhcccccccchhhhhhccccccccccccc
Q 041521 377 ALFQRADRGLLKDVWIVGNSGYPLMD----------WVMVPYTQKNLTWTQHAFNEKIGDIQAVAKDAFARLKGRWACLQ 446 (524)
Q Consensus 377 ~L~~~l~~~~~~g~~lLGD~gYpl~~----------~LmtPy~~~~lt~~q~~FN~~ls~~R~~VE~aFG~LK~RFriL~ 446 (524)
.+. ..+ ...|+||.||-... .|+||.+...-......+++.+.+.|.+||-.|+.||+.|.+=+
T Consensus 76 ~l~----~~~--~g~l~gDkGYis~~L~~~L~~~gI~L~t~~RkNmk~~~~~~~~~~l~~~R~~IETvfs~Lk~~~~ie~ 149 (155)
T PF13612_consen 76 ELS----ENL--KGKLFGDKGYISKELKDELKEQGIKLITPRRKNMKNKLMPLFDKLLLRKRRIIETVFSQLKNQFNIEH 149 (155)
T ss_pred ccc----ccc--ccceecchhhhcchHHhhhhhceEEEeccccccccccccchhhhhhhheeeEeehHHHHHHHhhceEe
Confidence 222 222 34799999996433 47899986532233456788999999999999999999888755
Q ss_pred c
Q 041521 447 K 447 (524)
Q Consensus 447 ~ 447 (524)
.
T Consensus 150 ~ 150 (155)
T PF13612_consen 150 S 150 (155)
T ss_pred e
Confidence 3
No 5
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=98.67 E-value=7.5e-09 Score=79.18 Aligned_cols=50 Identities=18% Similarity=0.298 Sum_probs=47.9
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.++++++++++|.||+.|.++.++|..||||+|||++++++++++++..+
T Consensus 2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l 51 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVL 51 (53)
T ss_pred CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhc
Confidence 57999999999999999999999999999999999999999999998865
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=97.54 E-value=3.3e-06 Score=79.94 Aligned_cols=151 Identities=17% Similarity=0.161 Sum_probs=81.4
Q ss_pred ccccCCcceeeeEecCCCccccccccccccccCCCCccccccccc-cCCCceeeecCCCCCCCCChHHHHhHHHHhhhhc
Q 041521 306 NVGGSMYTTHIPIIAPKISVASYFNKRHTERNQKTSYSITVQGVV-DTKGVFTDVCIGWPGSMPDDQVLERSALFQRADR 384 (524)
Q Consensus 306 ~~vGaIDgThIpI~~P~~~~~~y~n~~~~~rn~K~~~Si~vq~v~-D~~g~fi~v~~g~pGS~hDs~V~~~S~L~~~l~~ 384 (524)
..+-+||+|+|+.. +......++ .+++.....+++++| +..|.++.+.+. +|+++|...+.. +.+. .
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 35678999999998 111112222 223556667899988 566777777777 999999998885 3333 2
Q ss_pred cccceEEEEcccCCCCccc----------cccccccCCcc----------------------------------cchhhc
Q 041521 385 GLLKDVWIVGNSGYPLMDW----------VMVPYTQKNLT----------------------------------WTQHAF 420 (524)
Q Consensus 385 ~~~~g~~lLGD~gYpl~~~----------LmtPy~~~~lt----------------------------------~~q~~F 420 (524)
....+.++++|+||.-.+. .+.|.+..... ..+...
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 2345789999999975542 23444322100 111111
Q ss_pred ccc--------------cccchhhhhhcccccccccccccccccccCCCccceehhhHHHHhh
Q 041521 421 NEK--------------IGDIQAVAKDAFARLKGRWACLQKRTEVKLQDLPVVLGACCVLHNI 469 (524)
Q Consensus 421 N~~--------------ls~~R~~VE~aFG~LK~RFriL~~~~~~~~~~~~~iI~AccvLHNi 469 (524)
... +.+.|-.||+.|..||+.|. |..........+...+.+|++-.|+
T Consensus 152 ~~~~~~~~~~~~~~~~~~Y~~Rw~IE~~f~~lK~~~~-l~~~~~~~~~~~~~~~~~~~la~nl 213 (213)
T PF01609_consen 152 GYFLVTNITTLPRDTAALYRRRWQIERFFRELKQFLG-LERLRVRSPERIEAHLFLTLLAYNL 213 (213)
T ss_dssp TTS---EEEEEESS--SHHHCGGHHHHHHHHHTTTTT-GGGS--SSHHHHHHHHHHHHHH---
T ss_pred cccccccccccccccceeecccchhhHHHHHHHhcCC-CchhcccCHHHHHHHHHHHHhhCcC
Confidence 222 77889999999999998655 3222223344555556666665553
No 7
>PF13586 DDE_Tnp_1_2: Transposase DDE domain
Probab=95.76 E-value=0.002 Score=54.20 Aligned_cols=50 Identities=22% Similarity=0.335 Sum_probs=37.9
Q ss_pred chhhcccccccchhhhhhcccccccccccccccccccCCCccceehhhHHH
Q 041521 416 TQHAFNEKIGDIQAVAKDAFARLKGRWACLQKRTEVKLQDLPVVLGACCVL 466 (524)
Q Consensus 416 ~q~~FN~~ls~~R~~VE~aFG~LK~RFriL~~~~~~~~~~~~~iI~AccvL 466 (524)
.+..+...+...|.+||++|+-|| +|+.|....+.........|.-+|++
T Consensus 35 ~~~~~d~~~~~~Rw~VEr~f~wlk-~~Rrl~~ryek~~~s~~~~v~la~~~ 84 (88)
T PF13586_consen 35 RPRKFDFRLYKRRWVVERTFAWLK-RFRRLATRYEKLASSFLAFVHLACIV 84 (88)
T ss_pred ccCccchhhhccceehhhhhHHHH-HcCccccccccCHHHHHHHHHHHHHH
Confidence 467788899999999999999999 69999887776555544444444443
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=93.86 E-value=0.019 Score=43.93 Aligned_cols=42 Identities=24% Similarity=0.540 Sum_probs=31.5
Q ss_pred CCCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhh
Q 041521 227 RDAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 227 r~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~ 269 (524)
|..++.++++.+ +..+-.|.+..+||..|||+.|||+.++..
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 568899999887 556788999999999999999999988653
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=92.96 E-value=0.055 Score=40.34 Aligned_cols=45 Identities=20% Similarity=0.390 Sum_probs=37.4
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHH
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAI 274 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI 274 (524)
.+|++++-.+.++| -.|.++.++|..+|+|.+||+++..+...-|
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 57899999998888 6788999999999999999999988766544
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=92.79 E-value=0.025 Score=41.59 Aligned_cols=40 Identities=18% Similarity=0.252 Sum_probs=29.5
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~ 269 (524)
.++.+ ++.-++..+..|.+..+||..||||++||.|++.+
T Consensus 5 ~~~~~-~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 5 KLSKE-QIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLNK 44 (45)
T ss_dssp SSSHC-CHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHCC
T ss_pred CCCHH-HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 34443 56666778899999999999999999999998753
No 11
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=92.73 E-value=0.028 Score=41.22 Aligned_cols=41 Identities=22% Similarity=0.329 Sum_probs=22.7
Q ss_pred CCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhh
Q 041521 228 DAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 228 ~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~ 269 (524)
..++.+++..+.-+ +..|.+++.||..+|+|+|||++.+.+
T Consensus 3 ~~Lt~~eR~~I~~l-~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEAL-LEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHH-HCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHH-HHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 35677777776643 689999999999999999999998764
No 12
>PF13518 HTH_28: Helix-turn-helix domain
Probab=88.96 E-value=0.14 Score=38.06 Aligned_cols=37 Identities=24% Similarity=0.439 Sum_probs=30.2
Q ss_pred hhhhhhhccccCCCccchhhccCccccceehhhhhhHH
Q 041521 235 RVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 235 rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
++.+...++ .|.++..++..||||.+||.+++..+-.
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 455666666 6779999999999999999998877654
No 13
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=88.75 E-value=0.074 Score=39.46 Aligned_cols=37 Identities=24% Similarity=0.391 Sum_probs=22.2
Q ss_pred hhhhhhhhccccCCCccchhhccCccccceehhhhhhH
Q 041521 234 QRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVC 271 (524)
Q Consensus 234 ~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~ 271 (524)
.++.+ |..+..|.+.+.++..+|||.+||++++.++.
T Consensus 6 ~R~~i-i~l~~~G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 6 RRAQI-IRLLREGWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp ----H-HHHHHHT--HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHHHH-HHHHHCCCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 34443 33344499999999999999999999988753
No 14
>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=88.56 E-value=0.1 Score=43.15 Aligned_cols=43 Identities=30% Similarity=0.394 Sum_probs=30.9
Q ss_pred hhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 236 VAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 236 L~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
+-++-+.+.+..+.+..|..||||+||||+=+.+=+..|...|
T Consensus 9 i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~L 51 (82)
T PF12116_consen 9 IEIANYIIETKATVRQAAKVFGVSKSTVHKDVTERLPKINPEL 51 (82)
T ss_dssp HHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-HHH
T ss_pred HHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHH
Confidence 4456677889999999999999999999998887666666544
No 15
>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=87.49 E-value=0.28 Score=36.95 Aligned_cols=43 Identities=19% Similarity=0.274 Sum_probs=31.0
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHH
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
.+|+.++.++.|.|+ .|.++.++|..+|+|.+||...+.+...
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 578888888777665 6899999999999999999888776543
No 16
>smart00351 PAX Paired Box domain.
Probab=86.95 E-value=0.28 Score=44.09 Aligned_cols=44 Identities=11% Similarity=0.146 Sum_probs=37.5
Q ss_pred CCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHH
Q 041521 228 DAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 228 ~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
.+++.+.+.-+.+.+. .|.+.+.||..||||.+||++++.++-.
T Consensus 16 ~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 16 RPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4688888888877664 8999999999999999999999888643
No 17
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)
Probab=86.71 E-value=0.94 Score=36.86 Aligned_cols=46 Identities=26% Similarity=0.313 Sum_probs=40.1
Q ss_pred CCCCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHH
Q 041521 226 LRDAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 226 ~r~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
++..++..+-|-..|+.|.+|+..+.|-..|| +.+||++.+.+...
T Consensus 21 ~~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg-~~~tv~~~f~rW~~ 66 (75)
T PF13340_consen 21 GRPRIDLREVLNAILYVLRTGCPWRDLPEDFG-PWSTVYRRFRRWSR 66 (75)
T ss_pred CCCccchHHHHhcccccceecceecccchhcc-CcCcHHHHHHHHHH
Confidence 45678888989999999999999999999999 88899888877543
No 18
>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=86.33 E-value=0.47 Score=33.46 Aligned_cols=22 Identities=27% Similarity=0.498 Sum_probs=17.3
Q ss_pred CCHhhHHHHcCCCHHHHHHHHH
Q 041521 192 FPEEEFWRDFRMSKATFEMICE 213 (524)
Q Consensus 192 ~~d~~F~~~fRmSr~tF~~Lv~ 213 (524)
++|++|...|+|+++.|..|-.
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 5799999999999999998744
No 19
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=85.51 E-value=0.4 Score=40.35 Aligned_cols=47 Identities=17% Similarity=0.209 Sum_probs=41.7
Q ss_pred CCCCCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhH
Q 041521 225 MLRDAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVC 271 (524)
Q Consensus 225 ~~r~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~ 271 (524)
.....+++..++.++-..+..|.+...++..||||..|+++++.++-
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 34568999999999999999999999999999999999999877653
No 20
>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=84.55 E-value=0.71 Score=49.36 Aligned_cols=129 Identities=13% Similarity=0.156 Sum_probs=73.1
Q ss_pred ccccCCCccchhhc----cC---ccccceehhhhhhHHHHHhhcccccccCcchHHHHHHHhhhccccCCCccccCCcce
Q 041521 242 RLATGEPLRVVSKR----FG---LGISTCHKLVLEVCSAIKTVLMPKFLQWPDELKMKQIKEEFQGISGIPNVGGSMYTT 314 (524)
Q Consensus 242 ~LatG~s~~~la~~----Fg---iS~STvsriv~~v~~aI~~~L~~~~I~~P~~ee~~~i~~~F~~~~gfP~~vGaIDgT 314 (524)
.++.|.+.++++.. +| +|++|||+++.++...+... ..+ ...+.|-++-.|||+
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 LYLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVEAW-RNR------------------PLESEPYPYLWIDGT 170 (381)
T ss_pred hhccccccccccchhhhhhcccccCchhhhhhhhhhhhhHHHH-hhh------------------ccccccccceeeeee
Confidence 35566666655543 45 89999999887765544331 110 111233357789999
Q ss_pred eeeEecCCCccccccccccccccCCCCccccccccccCCCc--eeeecCCCCCCCCChHHHHhHHHHhhh-hccccceEE
Q 041521 315 HIPIIAPKISVASYFNKRHTERNQKTSYSITVQGVVDTKGV--FTDVCIGWPGSMPDDQVLERSALFQRA-DRGLLKDVW 391 (524)
Q Consensus 315 hIpI~~P~~~~~~y~n~~~~~rn~K~~~Si~vq~v~D~~g~--fi~v~~g~pGS~hDs~V~~~S~L~~~l-~~~~~~g~~ 391 (524)
|+.+..-. .-..-++.+-.-+|.+|+ ++.+.++ ..-....|. .+...| ++|+.....
T Consensus 171 ~~kvr~~~---------------~~~~~~~~v~iGi~~dG~r~vLg~~~~---~~Es~~~W~--~~l~~L~~RGl~~~~l 230 (381)
T PF00872_consen 171 YFKVREDG---------------RVVKKAVYVAIGIDEDGRREVLGFWVG---DRESAASWR--EFLQDLKERGLKDILL 230 (381)
T ss_pred eccccccc---------------ccccchhhhhhhhhcccccceeeeecc---cCCccCEee--ecchhhhhccccccce
Confidence 99986210 011123444455677775 6665554 322333344 333344 567767788
Q ss_pred EEcccCCCCccccccccc
Q 041521 392 IVGNSGYPLMDWVMVPYT 409 (524)
Q Consensus 392 lLGD~gYpl~~~LmtPy~ 409 (524)
+++|.+=.+..-+-.-|+
T Consensus 231 vv~Dg~~gl~~ai~~~fp 248 (381)
T PF00872_consen 231 VVSDGHKGLKEAIREVFP 248 (381)
T ss_pred eecccccccccccccccc
Confidence 999977666666555554
No 21
>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=84.48 E-value=0.4 Score=31.40 Aligned_cols=38 Identities=24% Similarity=0.327 Sum_probs=27.6
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLV 267 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv 267 (524)
.++.+++..+... +..|.++..++..||++.+|+++++
T Consensus 5 ~~~~~~~~~i~~~-~~~~~s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRL-LAAGESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHhC
Confidence 4555555444433 4577899999999999999998763
No 22
>cd00131 PAX Paired Box domain
Probab=84.34 E-value=0.49 Score=42.77 Aligned_cols=45 Identities=11% Similarity=0.134 Sum_probs=37.9
Q ss_pred CCCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHH
Q 041521 227 RDAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 227 r~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
..++|.+.+.-|.+.+ ..|.+.+.+|.+||||.+||.+++.++-.
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 3578888887777665 68999999999999999999999887654
No 23
>smart00153 VHP Villin headpiece domain.
Probab=83.85 E-value=0.82 Score=32.23 Aligned_cols=21 Identities=24% Similarity=0.455 Sum_probs=18.9
Q ss_pred CCHhhHHHHcCCCHHHHHHHH
Q 041521 192 FPEEEFWRDFRMSKATFEMIC 212 (524)
Q Consensus 192 ~~d~~F~~~fRmSr~tF~~Lv 212 (524)
++|++|...|+||++.|..|=
T Consensus 2 LsdeeF~~vfgmsr~eF~~LP 22 (36)
T smart00153 2 LSDEDFEEVFGMTREEFYKLP 22 (36)
T ss_pred CCHHHHHHHHCCCHHHHHhCc
Confidence 579999999999999999873
No 24
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=83.67 E-value=0.57 Score=34.63 Aligned_cols=44 Identities=18% Similarity=0.323 Sum_probs=34.1
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHH
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAI 274 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI 274 (524)
.++..++-.+. ++..|.++.+++..+|+|.+||.+++.++...+
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 357899999999999999999999988876544
No 25
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=81.96 E-value=0.42 Score=43.87 Aligned_cols=43 Identities=28% Similarity=0.265 Sum_probs=37.2
Q ss_pred CChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHH
Q 041521 230 IPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 230 l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
.+.+.+.+++..++..|.+.+.+|.+||||.+||.+++.+.=+
T Consensus 5 ~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e 47 (138)
T COG3415 5 FSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRE 47 (138)
T ss_pred hhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhcc
Confidence 4556777888899999999999999999999999999887643
No 26
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=81.61 E-value=0.75 Score=41.02 Aligned_cols=46 Identities=13% Similarity=0.224 Sum_probs=41.6
Q ss_pred CCCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHH
Q 041521 227 RDAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 227 r~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
++..+.+.++-++...+..|.++.+++..||||.+|+++++.++-.
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 4678999999999999999999999999999999999999888643
No 27
>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=81.38 E-value=0.36 Score=35.64 Aligned_cols=37 Identities=16% Similarity=0.297 Sum_probs=27.2
Q ss_pred hhhhhhhhhccccC-CCccchhhccCccccceehhhhh
Q 041521 233 RQRVAVCVWRLATG-EPLRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 233 e~rL~i~L~~LatG-~s~~~la~~FgiS~STvsriv~~ 269 (524)
++.+..+|-.+..| .+++..+..|||+.+|+++.++.
T Consensus 2 ee~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 2 EEDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp HHHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 45666677777788 99999999999999999877653
No 28
>PRK04217 hypothetical protein; Provisional
Probab=81.18 E-value=0.81 Score=40.41 Aligned_cols=50 Identities=14% Similarity=0.100 Sum_probs=39.4
Q ss_pred CCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 228 DAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 228 ~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
..++.+++-++.|+ .-.|.++.+||..+|||.+||.+++.+....|.+.+
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 46777787555443 347889999999999999999999998877776644
No 29
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=80.33 E-value=0.92 Score=41.77 Aligned_cols=48 Identities=10% Similarity=0.231 Sum_probs=41.9
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|++++-++.|.+ .|.++.+||..+|+|.+||...+.+....|...+
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 57888998888877 9999999999999999999999888877776643
No 30
>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=80.11 E-value=0.85 Score=32.95 Aligned_cols=43 Identities=16% Similarity=0.236 Sum_probs=33.3
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHH
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
.+++.++-++.+.++ .|.++.+++..+|++.+||.+++.+...
T Consensus 10 ~l~~~~~~~~~~~~~-~~~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFG-EGLSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 355666665555554 8899999999999999999998877543
No 31
>PRK00118 putative DNA-binding protein; Validated
Probab=78.66 E-value=1.1 Score=39.23 Aligned_cols=48 Identities=8% Similarity=0.120 Sum_probs=38.8
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|..++-++.|+ ...|.++..||..+|+|.+||++.+.+....+.+.
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 5677777776555 45699999999999999999999998877766654
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=78.49 E-value=0.4 Score=38.50 Aligned_cols=45 Identities=18% Similarity=0.201 Sum_probs=37.1
Q ss_pred CCCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhH
Q 041521 227 RDAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVC 271 (524)
Q Consensus 227 r~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~ 271 (524)
+...|++.++-+.-.+|..|.+..+++..+||+.+|+++++.+..
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 457789999999888899999999999999999999999998876
No 33
>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=77.42 E-value=1.5 Score=36.90 Aligned_cols=49 Identities=22% Similarity=0.307 Sum_probs=41.7
Q ss_pred CCCChhhhhhhhhhccccCCCccchhhccC-ccccceehhhhhhHHHHHh
Q 041521 228 DAIPVRQRVAVCVWRLATGEPLRVVSKRFG-LGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 228 ~~l~~e~rL~i~L~~LatG~s~~~la~~Fg-iS~STvsriv~~v~~aI~~ 276 (524)
+.+...-++++.|..--+|.++.+||..|| .+.|||+..+.++-..+..
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 456677788888888888999999999999 9999999998888776643
No 34
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=77.12 E-value=1.3 Score=40.78 Aligned_cols=49 Identities=20% Similarity=0.429 Sum_probs=40.5
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|++++-.+.|.++. |.++.+||..+|+|.+||...+.+....|...+
T Consensus 109 ~L~~~~r~v~~l~~~~-~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 109 ELPARTRYAFEMYRLH-GETQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5788888888777665 999999999999999999988887777666544
No 35
>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=75.89 E-value=1.2 Score=37.67 Aligned_cols=31 Identities=13% Similarity=0.131 Sum_probs=26.5
Q ss_pred hhhhhccccCCCccchhhccCccccceehhh
Q 041521 237 AVCVWRLATGEPLRVVSKRFGLGISTCHKLV 267 (524)
Q Consensus 237 ~i~L~~LatG~s~~~la~~FgiS~STvsriv 267 (524)
...+.+++.|.+...|+..+|||.+||+|+.
T Consensus 41 ~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 41 LQVAKMLKQGKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 3445668899999999999999999999854
No 36
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=75.73 E-value=1.5 Score=41.26 Aligned_cols=48 Identities=13% Similarity=0.226 Sum_probs=41.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|++++.++.|.++ .|.++.+||..+|+|.+||...+.+-+..+.+.
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 588999999988877 899999999999999999988888766666553
No 37
>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=75.49 E-value=1.5 Score=39.58 Aligned_cols=47 Identities=13% Similarity=0.347 Sum_probs=38.8
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+|++++-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+
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 467888888888776 69999999999999999999888876665543
No 38
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=75.36 E-value=1.4 Score=40.18 Aligned_cols=50 Identities=16% Similarity=0.172 Sum_probs=42.6
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhcc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVLM 279 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L~ 279 (524)
.+|+.++-++.|.++ .|.++..||..+|+|.+||...+.+....|...+.
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 578888888877765 69999999999999999999999988888776553
No 39
>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=75.31 E-value=1.6 Score=38.42 Aligned_cols=47 Identities=15% Similarity=0.367 Sum_probs=37.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+|+.++-.+.+.++ .|.++.+||..+|+|.+||++...++...|.+
T Consensus 110 ~L~~~~~~ii~~~~~-~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYL-EGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 456667766665554 69999999999999999999998887766543
No 40
>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=75.15 E-value=1.6 Score=40.21 Aligned_cols=47 Identities=11% Similarity=0.142 Sum_probs=40.0
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+|+.++.++.|.++ .|.++.+||..+|+|.+||...+.+....|..
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 678999999988776 59999999999999999999888877666543
No 41
>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=74.70 E-value=1.5 Score=32.52 Aligned_cols=42 Identities=17% Similarity=0.309 Sum_probs=31.6
Q ss_pred ChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHH
Q 041521 231 PVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAI 274 (524)
Q Consensus 231 ~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI 274 (524)
+..++-++.+ +..|.++.++|..+|+|.+||.+.+.++...+
T Consensus 2 ~~~e~~i~~~--~~~~~s~~eia~~l~~s~~tv~~~~~~~~~~l 43 (57)
T cd06170 2 TPREREVLRL--LAEGKTNKEIADILGISEKTVKTHLRNIMRKL 43 (57)
T ss_pred CHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 3344443333 45899999999999999999999988776544
No 42
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=74.03 E-value=1.5 Score=40.63 Aligned_cols=49 Identities=18% Similarity=0.355 Sum_probs=40.4
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|++++.++.|.++ .|.++.+||..+|+|.+||...+.+...-|...+
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 578888888877776 7899999999999999999988887766665543
No 43
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=74.02 E-value=1.7 Score=42.79 Aligned_cols=50 Identities=12% Similarity=0.147 Sum_probs=42.9
Q ss_pred CCChhhhhhhhhhcc---ccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRL---ATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~L---atG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|+++ -.|.++.+||..+|+|.+||...+.+....|.+.+
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 678899999988874 58999999999999999999998888877776543
No 44
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=73.96 E-value=1.5 Score=40.77 Aligned_cols=48 Identities=13% Similarity=0.097 Sum_probs=40.6
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|+.++.++.|.++ .|.++.+||..+|+|.+||...+.+....|...
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 578888888888777 699999999999999999988888777666553
No 45
>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=73.57 E-value=1.9 Score=43.75 Aligned_cols=49 Identities=12% Similarity=0.226 Sum_probs=42.0
Q ss_pred CCChhhhhhhhhhccc-cCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLA-TGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~La-tG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|.+++..+.|+|+. .|.++..||..+|||..+|+++..+.+.-|...
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 5788999999999874 489999999999999999999988877766543
No 46
>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=73.25 E-value=1.3 Score=40.19 Aligned_cols=47 Identities=9% Similarity=0.223 Sum_probs=38.9
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+.+....|.+
T Consensus 105 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 105 RLPENYRTVLILREF-KEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hCCHhheeeeeehhh-ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 467777777777766 79999999999999999999888887776654
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=72.95 E-value=1.1 Score=36.61 Aligned_cols=41 Identities=12% Similarity=0.114 Sum_probs=36.0
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~ 269 (524)
.+|+..+.+..|.+.-.|.++.+||...|+|.+||...+..
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 57788888888888889999999999999999999887664
No 48
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=72.83 E-value=1.9 Score=39.89 Aligned_cols=49 Identities=16% Similarity=0.193 Sum_probs=42.4
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+.+....|...+
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 578888888888777 8999999999999999999998888887776654
No 49
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=72.12 E-value=1.9 Score=40.85 Aligned_cols=49 Identities=12% Similarity=0.133 Sum_probs=41.9
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|++++-++.|.++ .|.++.+||..+|+|.+||...+.+....|...+
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 678889988888877 8999999999999999999988888777666543
No 50
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=72.11 E-value=1.8 Score=41.18 Aligned_cols=49 Identities=12% Similarity=0.183 Sum_probs=42.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|.++- |.++.+||..+|+|.+||...+.+....|.+.+
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 5788899988888876 999999999999999999988888777776644
No 51
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=71.64 E-value=2.2 Score=39.95 Aligned_cols=48 Identities=13% Similarity=0.149 Sum_probs=40.7
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|++++-.+.|.++ .|.++.+||..+|+|..||...+.+....|.+.
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 578888888888876 789999999999999999988888877766553
No 52
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=71.46 E-value=1.8 Score=41.29 Aligned_cols=50 Identities=12% Similarity=0.235 Sum_probs=42.7
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhcc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVLM 279 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L~ 279 (524)
.+|+.++-++.|.++ .|.++..||..+|+|.+||...+.+....|.+.+.
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 578888888877776 79999999999999999999999888888777653
No 53
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=71.31 E-value=1 Score=33.53 Aligned_cols=29 Identities=17% Similarity=0.311 Sum_probs=23.9
Q ss_pred ccccCCCccchhhccCccccceehhhhhh
Q 041521 242 RLATGEPLRVVSKRFGLGISTCHKLVLEV 270 (524)
Q Consensus 242 ~LatG~s~~~la~~FgiS~STvsriv~~v 270 (524)
.|..+.++.++|..+|+|.+||.+++.+.
T Consensus 23 ~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 23 LLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 33444589999999999999999998764
No 54
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=70.95 E-value=2.3 Score=42.03 Aligned_cols=49 Identities=10% Similarity=0.118 Sum_probs=41.4
Q ss_pred CCChhhhhhhhhhcc---ccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRL---ATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~L---atG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|+.++..+.|.|+ -.|.++.+||..+|+|.+||.+..++....|...
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 689999999999886 4678999999999999999988877766666553
No 55
>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=70.94 E-value=2.5 Score=41.64 Aligned_cols=50 Identities=14% Similarity=0.135 Sum_probs=42.9
Q ss_pred CCChhhhhhhhhhcc---ccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRL---ATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~L---atG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-.+.|+++ -.|.++.+||...|++.+||.+.+++....|...|
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 578899999999876 48999999999999999999998888877776543
No 56
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=70.62 E-value=2.2 Score=41.91 Aligned_cols=49 Identities=14% Similarity=0.216 Sum_probs=42.6
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|+|+ .|.++.+|+..+|||.+||...+++....|...|
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 578888888888877 6999999999999999999999988877777655
No 57
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=70.06 E-value=2.5 Score=43.27 Aligned_cols=49 Identities=12% Similarity=0.230 Sum_probs=42.1
Q ss_pred CCChhhhhhhhhhccc-cCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLA-TGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~La-tG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|..++..+.++|+. .+.++.+||..+|||.++|+++..+.+.-|...
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 5788899999998875 689999999999999999999988877766553
No 58
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=69.66 E-value=2.4 Score=40.14 Aligned_cols=48 Identities=17% Similarity=0.244 Sum_probs=40.0
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|++++-++.|.++. |.++.+||..+|+|.+||...+.+....|...
T Consensus 141 ~L~~~~~~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 141 QLPESQRQVLELAYYE-GLSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred hCCHHHhhhhhhhhhc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 5678888877777665 99999999999999999998888877766654
No 59
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=69.52 E-value=2.4 Score=40.40 Aligned_cols=49 Identities=18% Similarity=0.238 Sum_probs=42.1
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+.+....|...+
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 578888888888777 8999999999999999999988888887777654
No 60
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=69.28 E-value=2.5 Score=42.52 Aligned_cols=49 Identities=18% Similarity=0.201 Sum_probs=42.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++..+.|+|+ .|.++..||..+|+|.++|++...+....|...+
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 578888888888886 5999999999999999999999998887776644
No 61
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=69.21 E-value=2.2 Score=39.28 Aligned_cols=49 Identities=20% Similarity=0.360 Sum_probs=40.6
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-.+.|.++ .|.++.+||..+|+|.+||.+.+.+....|...+
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 467778877777776 6999999999999999999999888777766544
No 62
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=68.69 E-value=2.6 Score=39.57 Aligned_cols=49 Identities=14% Similarity=0.248 Sum_probs=42.0
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|++++-.+.|.++. |.++.+||..+|+|.+||...+.+....|...+
T Consensus 131 ~L~~~~r~v~~l~~~~-g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVE-GASIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 5788888888887665 999999999999999999999988888777655
No 63
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=68.48 E-value=2.8 Score=39.51 Aligned_cols=48 Identities=13% Similarity=0.197 Sum_probs=40.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|++++.++.|. +-.|.++.+||..+|+|.+||...+.+....|...
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 5788888777776 46899999999999999999999888887776553
No 64
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=68.30 E-value=2.3 Score=40.29 Aligned_cols=50 Identities=8% Similarity=0.109 Sum_probs=42.0
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhcc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVLM 279 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L~ 279 (524)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+.+....|.+.+.
T Consensus 131 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (191)
T PRK12520 131 RLPPRTGRVFMMREW-LELETEEICQELQITATNAWVLLYRARMRLRECLD 180 (191)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 578888888877765 57999999999999999999888888887776553
No 65
>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=68.04 E-value=2.9 Score=38.06 Aligned_cols=47 Identities=17% Similarity=0.292 Sum_probs=39.3
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+|++++-.+.|.++ .|.++.+||..+|+|.+||...+.+.-..|.+
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 578888888888665 79999999999999999999888877665543
No 66
>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=67.98 E-value=1.2 Score=33.11 Aligned_cols=21 Identities=14% Similarity=0.339 Sum_probs=18.5
Q ss_pred ccchhhccCccccceehhhhh
Q 041521 249 LRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 249 ~~~la~~FgiS~STvsriv~~ 269 (524)
..+||...|+|.+||+++++.
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 578999999999999998764
No 67
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=67.88 E-value=2.6 Score=40.20 Aligned_cols=49 Identities=24% Similarity=0.378 Sum_probs=42.0
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|++++-++.|.++ .|.++.+||..+|+|.+||...+.+....|...+
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 578889988888777 8999999999999999999999888777776543
No 68
>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=67.61 E-value=2.9 Score=39.11 Aligned_cols=48 Identities=13% Similarity=0.108 Sum_probs=39.8
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+.+....|...
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 478888887777655 689999999999999999999888877766553
No 69
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=67.55 E-value=2.8 Score=39.83 Aligned_cols=49 Identities=18% Similarity=0.264 Sum_probs=41.5
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|+++ .|.++.+||..+|+|.+||...+.+....|...+
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 578889988888877 5999999999999999999988888777666543
No 70
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=67.49 E-value=2.8 Score=42.28 Aligned_cols=49 Identities=14% Similarity=0.257 Sum_probs=42.1
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++..+.|+|+ .|.++.+||..+|+|.++|+++..+....|...+
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 578889988888875 6899999999999999999999888877776543
No 71
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=67.38 E-value=3.1 Score=39.17 Aligned_cols=48 Identities=10% Similarity=0.066 Sum_probs=39.7
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+++....|...
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 567888877777654 899999999999999999999888877766654
No 72
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=67.06 E-value=2.7 Score=39.32 Aligned_cols=48 Identities=15% Similarity=0.243 Sum_probs=40.4
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|++++-++.|.++ .|.++.+||..+|+|.+||...+.+....|...
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 578888888888777 799999999999999999988888777666553
No 73
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=66.90 E-value=2.9 Score=39.32 Aligned_cols=49 Identities=12% Similarity=0.262 Sum_probs=41.3
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++.++.|.++. |.++.+||..+|+|.+||...+.+....|...+
T Consensus 127 ~L~~~~r~v~~l~~~~-g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 127 SLPIKYREVIYLFYYE-ELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred hCCHHHhhHhHhHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5788888888887775 999999999999999999988888777666543
No 74
>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=66.81 E-value=2.5 Score=41.96 Aligned_cols=48 Identities=13% Similarity=0.165 Sum_probs=41.5
Q ss_pred CCChhhhhhhhhhcc---ccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWRL---ATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~L---atG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+|+.++..+.|+|. ..|.++..||..+|||.++|+++..+...-|..
T Consensus 176 ~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~ 226 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRH 226 (238)
T ss_pred hCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 578899999999884 578999999999999999999998887776654
No 75
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=66.55 E-value=3.1 Score=38.43 Aligned_cols=46 Identities=11% Similarity=0.108 Sum_probs=37.4
Q ss_pred CCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHH
Q 041521 228 DAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIK 275 (524)
Q Consensus 228 ~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~ 275 (524)
..+++.++-.+.| ...|.++.+||..+|+|.+||+.+......-|.
T Consensus 5 ~~Lt~rqreVL~l--r~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr 50 (141)
T PRK03975 5 SFLTERQIEVLRL--RERGLTQQEIADILGTSRANVSSIEKRARENIE 50 (141)
T ss_pred cCCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4678888877777 369999999999999999999998877555443
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=66.46 E-value=3.2 Score=38.89 Aligned_cols=48 Identities=15% Similarity=0.237 Sum_probs=40.3
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|+.++-++.|.++ .|.++..||..+|+|.+||...+.+....|...
T Consensus 140 ~L~~~~r~vi~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~ 187 (189)
T TIGR02984 140 KLPEDYREVILLRHL-EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQI 187 (189)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 578888888877776 899999999999999999999888877766543
No 77
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=66.34 E-value=3.5 Score=38.25 Aligned_cols=49 Identities=12% Similarity=0.137 Sum_probs=40.8
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+.+....|...|
T Consensus 118 ~L~~~~r~vl~L~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 118 QLSPEHRAVLVRSYY-RGWSTAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 578888887777665 5999999999999999999888888777776654
No 78
>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=65.91 E-value=5 Score=41.34 Aligned_cols=50 Identities=14% Similarity=0.182 Sum_probs=43.6
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhcc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVLM 279 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L~ 279 (524)
.+|+.++.++.|.++ .|.++.+||..+|+|.+||...+.+....|.+.+.
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 578888888888776 78999999999999999999999998888877653
No 79
>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=65.80 E-value=3.1 Score=38.19 Aligned_cols=47 Identities=11% Similarity=0.095 Sum_probs=38.5
Q ss_pred CCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 228 DAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 228 ~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
..++..++-.+.|+ ..|.++.++|..+|+|++||+++.++...-|..
T Consensus 5 ~~Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 5 TFLTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred CCCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 35777787777773 799999999999999999999988877666643
No 80
>PRK05572 sporulation sigma factor SigF; Validated
Probab=65.72 E-value=3.3 Score=41.38 Aligned_cols=48 Identities=19% Similarity=0.306 Sum_probs=41.8
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|+.++.++.|+|+ .|.++..||..+|+|.++|+++..+.+..|...
T Consensus 202 ~L~~~~~~v~~l~~~-~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~ 249 (252)
T PRK05572 202 ELDERERLIVYLRYF-KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEK 249 (252)
T ss_pred cCCHHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 578889988888775 689999999999999999999999888877654
No 81
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=65.43 E-value=3.2 Score=39.39 Aligned_cols=50 Identities=20% Similarity=0.216 Sum_probs=42.7
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhcc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVLM 279 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L~ 279 (524)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+.+....|.+.|.
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 567888888888765 89999999999999999999998888888877653
No 82
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=65.37 E-value=3.5 Score=41.31 Aligned_cols=49 Identities=8% Similarity=0.163 Sum_probs=41.6
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|+|+ .|.++.+||..+|||.+||.+...+....|...+
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 578888888877765 7999999999999999999999998888776544
No 83
>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=65.36 E-value=3.3 Score=40.47 Aligned_cols=47 Identities=15% Similarity=0.318 Sum_probs=40.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+|+.++-++.|+|+ .|.++.+||..+|+|.+||.+.+.+....|..
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 578888888888765 68999999999999999999999988877654
No 84
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=65.33 E-value=3.3 Score=39.02 Aligned_cols=49 Identities=20% Similarity=0.259 Sum_probs=41.7
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|++++-++.|.++. |.++.+||..+|+|..||...+.+....|...|
T Consensus 128 ~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 128 ALPERQREAIVLQYYQ-GLSNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred hCCHHHHHHhhHHHhc-CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 5688888888888764 999999999999999999998888777776654
No 85
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=65.29 E-value=3.2 Score=39.54 Aligned_cols=49 Identities=16% Similarity=0.229 Sum_probs=41.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|++++-++.|.++ .|.++.+||..+|+|.+||...+.+....|...+
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 578888888887776 8999999999999999999888887777666544
No 86
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=65.13 E-value=2.6 Score=40.89 Aligned_cols=49 Identities=10% Similarity=0.177 Sum_probs=42.3
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|++++.++.|.++- |.++.+||..+|++.+||...+.+....|.+.+
T Consensus 148 ~L~~~~r~v~~L~~~~-g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 148 GLPAKYARVFMMREFI-ELETNEICHAVDLSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5788899888887764 999999999999999999999888888877655
No 87
>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=64.94 E-value=2.7 Score=36.09 Aligned_cols=38 Identities=16% Similarity=0.192 Sum_probs=29.1
Q ss_pred CChhhhhhhhhhc------cccCCCccchhhccCccccceehhh
Q 041521 230 IPVRQRVAVCVWR------LATGEPLRVVSKRFGLGISTCHKLV 267 (524)
Q Consensus 230 l~~e~rL~i~L~~------LatG~s~~~la~~FgiS~STvsriv 267 (524)
++++++-++..++ +..|.+++.|+...|||.+||+|+=
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 5566665555543 3467999999999999999998863
No 88
>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=64.72 E-value=3.4 Score=37.82 Aligned_cols=48 Identities=17% Similarity=0.295 Sum_probs=40.4
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|++++.++.|.+ -.|.++.+||..+|+|.+||...+.+....|...
T Consensus 110 ~L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 110 RLPARQRAVVVLRY-YEDLSEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred hCCHHHHHHhhhHH-HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 57788888777766 5699999999999999999999988887777654
No 89
>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=64.68 E-value=3.4 Score=42.18 Aligned_cols=50 Identities=20% Similarity=0.266 Sum_probs=44.0
Q ss_pred CCChhhhhhhhhhc-c--ccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWR-L--ATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~-L--atG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.+|..+.|+| | -.|.++..||..+|+|.+||.....+....|...|
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 68999999999987 4 57899999999999999999999999888777655
No 90
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=64.54 E-value=3.7 Score=42.16 Aligned_cols=50 Identities=14% Similarity=0.287 Sum_probs=43.7
Q ss_pred CCChhhhhhhhhhcc-ccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRL-ATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~L-atG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++..+.|+|+ ..|.++.+||..+|||.++|+++..+...-|...|
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 578999999999886 47899999999999999999999998888777654
No 91
>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=64.37 E-value=3.6 Score=40.41 Aligned_cols=47 Identities=15% Similarity=0.232 Sum_probs=39.7
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+|+.++..+.++|+ .|.++..||..+|+|.++|+++.++...-|..
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 578888888877664 68899999999999999999998888776654
No 92
>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=64.27 E-value=2.4 Score=42.44 Aligned_cols=50 Identities=14% Similarity=0.152 Sum_probs=42.9
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhcc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVLM 279 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L~ 279 (524)
.+|+.++-++.|.++ .|.++.+||..+|||.+||...+.+....|...+.
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 578888888888776 89999999999999999999999888887776543
No 93
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=64.02 E-value=3.5 Score=37.82 Aligned_cols=46 Identities=11% Similarity=0.216 Sum_probs=37.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHH
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIK 275 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~ 275 (524)
.+|++++-++.|.++ .|.++.+||..+|+|.+||...+.+....+.
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 578888887766655 7999999999999999999888777655543
No 94
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=64.00 E-value=3.7 Score=38.23 Aligned_cols=49 Identities=18% Similarity=0.262 Sum_probs=40.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|++++-++.|.++ .|.++.+||..+|+|.+||...+.+....+...|
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 578888888888776 5999999999999999999888887766665443
No 95
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=63.94 E-value=3.6 Score=37.67 Aligned_cols=49 Identities=12% Similarity=0.083 Sum_probs=39.8
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|.+ -.|.++.+||..+|+|.+||...+.+....|...|
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 47788777666655 47999999999999999999888888777776654
No 96
>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=63.82 E-value=1.9 Score=35.88 Aligned_cols=22 Identities=41% Similarity=0.496 Sum_probs=19.4
Q ss_pred CCccchhhccCccccceehhhh
Q 041521 247 EPLRVVSKRFGLGISTCHKLVL 268 (524)
Q Consensus 247 ~s~~~la~~FgiS~STvsriv~ 268 (524)
.+..+|+..||||.+||++.++
T Consensus 20 ~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 20 ATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred CCHHHHHHHhCCCHHHHHHHhc
Confidence 5678999999999999999765
No 97
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=63.81 E-value=3.7 Score=38.66 Aligned_cols=49 Identities=20% Similarity=0.337 Sum_probs=41.8
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|++++-++.|.++ .|.+|.++|...||+.+||...+.+....+...+
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 578888888877666 6899999999999999999999988887777654
No 98
>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=63.68 E-value=6.1 Score=35.05 Aligned_cols=77 Identities=17% Similarity=0.143 Sum_probs=47.1
Q ss_pred CCHhhHHHHcCCCHHHHHHHHHHhhccccccCCCCCCCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhh
Q 041521 192 FPEEEFWRDFRMSKATFEMICEELESTVMKKNTMLRDAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEV 270 (524)
Q Consensus 192 ~~d~~F~~~fRmSr~tF~~Lv~~L~~~i~~~~t~~r~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v 270 (524)
.+-.+--..|++|+.|....+.....--......++..++. +. +..+.--....++.+++..||||.+||++.+.++
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 KSIREAAKRFGVSRNTVYRWLKRKETGDLEPKPRGRKKIDR-DE-LKALVEENPDATLRELAERLGVSPSTIWRALKRL 95 (119)
T ss_pred chHHHHHHHhCcHHHHHHHHHHhcccccccccccccccccH-HH-HHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHc
Confidence 35566778899999999888773332111111111224432 22 2222222345778899999999999998877653
No 99
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=63.64 E-value=3.8 Score=38.60 Aligned_cols=49 Identities=20% Similarity=0.300 Sum_probs=42.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+.+....|...+
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 578888888888777 4999999999999999999999988888777654
No 100
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=63.35 E-value=4.9 Score=39.96 Aligned_cols=70 Identities=10% Similarity=0.063 Sum_probs=50.3
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhccccccc-CcchHHHHHHHhhhcc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVLMPKFLQ-WPDELKMKQIKEEFQG 300 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L~~~~I~-~P~~ee~~~i~~~F~~ 300 (524)
.+|+.++.++.|.++ .|.++.+||...|+|.+||...+.+....|...+. +... .+...+...+...|..
T Consensus 116 ~Lp~~~R~v~lL~~~-eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~-~~~~~~~~~~~~~~~~~~~~~ 186 (228)
T PRK06704 116 SLNVQQSAILLLKDV-FQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSE-EGIEIVEFTDDMEVVVTSIRE 186 (228)
T ss_pred hCCHHHhhHhhhHHh-hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH-hcCCCCCccccHHHHHHHHHh
Confidence 578888887777665 48999999999999999999888888887776553 3222 2233355555666644
No 101
>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=63.34 E-value=4.1 Score=40.26 Aligned_cols=49 Identities=14% Similarity=0.136 Sum_probs=42.1
Q ss_pred CCChhhhhhhhhhcc---ccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRL---ATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~L---atG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|+.++..+.|+++ -.|.++.+||...|+|.+||...+.+....|.+.
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 689999999999885 3789999999999999999988888777766553
No 102
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=63.17 E-value=4 Score=38.95 Aligned_cols=49 Identities=16% Similarity=0.231 Sum_probs=42.8
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|++++-++.|+++ .|.++.+||..+|+|.+||...+.+....|...+
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 578889988888887 8999999999999999999998888887776654
No 103
>PF13730 HTH_36: Helix-turn-helix domain
Probab=62.63 E-value=3 Score=31.37 Aligned_cols=39 Identities=18% Similarity=0.265 Sum_probs=28.1
Q ss_pred hhhhhhhhcccc--C---CCccchhhccCccccceehhhhhhHH
Q 041521 234 QRVAVCVWRLAT--G---EPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 234 ~rL~i~L~~Lat--G---~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
..|.+.|..++. + .++..|++..|+|..||.+.+.+..+
T Consensus 8 ~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 8 KLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred HHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 345555655552 2 26789999999999999999887543
No 104
>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=62.48 E-value=3.9 Score=38.35 Aligned_cols=49 Identities=20% Similarity=0.297 Sum_probs=40.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|++++-.+.|.++ .|.++..||..+|++.+||...+.+....|.+.+
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 467777777767665 8999999999999999999988888777776654
No 105
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=61.85 E-value=4.1 Score=38.09 Aligned_cols=49 Identities=18% Similarity=0.295 Sum_probs=40.9
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+.+....|...+
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 578888888877766 6999999999999999999998888777666543
No 106
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=61.71 E-value=4.3 Score=40.69 Aligned_cols=47 Identities=11% Similarity=0.230 Sum_probs=40.0
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+|+.++..+.++|+ .|.++.++|..+|+|.++|+++..+....|..
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 578888888888775 68899999999999999999998887776654
No 107
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=61.40 E-value=5.6 Score=38.86 Aligned_cols=105 Identities=10% Similarity=0.127 Sum_probs=64.4
Q ss_pred CCHhhHHHHcCCCHHHHHHHHHHhhccccc--cCCCCCCCCChhhhhhhhhhccccC----CCccchhhccCccccceeh
Q 041521 192 FPEEEFWRDFRMSKATFEMICEELESTVMK--KNTMLRDAIPVRQRVAVCVWRLATG----EPLRVVSKRFGLGISTCHK 265 (524)
Q Consensus 192 ~~d~~F~~~fRmSr~tF~~Lv~~L~~~i~~--~~t~~r~~l~~e~rL~i~L~~LatG----~s~~~la~~FgiS~STvsr 265 (524)
++-+.|...+.-++..-..++..+...+.. .........++++||+-+|..++.+ .+..+||...|+++.|++|
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 455666666655555444444444432110 0001112458999999999876543 3568999999999999999
Q ss_pred hhhhhHHH-HHhhcccccccCcchHHHHHHHhh
Q 041521 266 LVLEVCSA-IKTVLMPKFLQWPDELKMKQIKEE 297 (524)
Q Consensus 266 iv~~v~~a-I~~~L~~~~I~~P~~ee~~~i~~~ 297 (524)
.+.++.+- +.. .....|.-++.+.+..++..
T Consensus 189 ~L~~L~~~G~I~-~~~~~i~I~d~~~L~~~~~~ 220 (226)
T PRK10402 189 VLAQFIQDGYLK-KSKRGYLIKNRKQLSGLALE 220 (226)
T ss_pred HHHHHHHCCCEE-eeCCEEEEeCHHHHHHHHHH
Confidence 99998763 333 23445666666666555444
No 108
>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=61.17 E-value=2.5 Score=39.62 Aligned_cols=100 Identities=11% Similarity=0.135 Sum_probs=63.3
Q ss_pred CCCHhhHHHHcCCCHHHHHHHHHHhhccccccCC--CCCCCCChhhhhhhhhhcccc--------------CCCccchhh
Q 041521 191 DFPEEEFWRDFRMSKATFEMICEELESTVMKKNT--MLRDAIPVRQRVAVCVWRLAT--------------GEPLRVVSK 254 (524)
Q Consensus 191 ~~~d~~F~~~fRmSr~tF~~Lv~~L~~~i~~~~t--~~r~~l~~e~rL~i~L~~Lat--------------G~s~~~la~ 254 (524)
.++-+.|...+.-++..-..++..+...+..... ..-...++++||+-+|..|+. ..+..+||.
T Consensus 72 ~i~~~~~~~l~~~~p~l~~~~~~~l~~~l~~~~~~~~~l~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~ 151 (193)
T TIGR03697 72 AVPIEQVEKAIEEDPDLSMLLLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAE 151 (193)
T ss_pred EeeHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHH
Confidence 3567788887777777666666655543322100 001245789999999877642 246789999
Q ss_pred ccCccccceehhhhhhHHH-HHhhcccccccCcchHHH
Q 041521 255 RFGLGISTCHKLVLEVCSA-IKTVLMPKFLQWPDELKM 291 (524)
Q Consensus 255 ~FgiS~STvsriv~~v~~a-I~~~L~~~~I~~P~~ee~ 291 (524)
..|+++.||+|+++++... +.+ .....|..++.+.+
T Consensus 152 ~lG~tretvsR~l~~l~~~g~I~-~~~~~i~I~d~~~L 188 (193)
T TIGR03697 152 AIGSTRVTITRLLGDLRKKKLIS-IHKKKITVHDPIAL 188 (193)
T ss_pred HhCCcHHHHHHHHHHHHHCCCEE-ecCCEEEEeCHHHH
Confidence 9999999999999887653 222 12334555544433
No 109
>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=61.02 E-value=4.6 Score=37.33 Aligned_cols=48 Identities=6% Similarity=0.075 Sum_probs=39.3
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|+.++-++.|.++. |.++.+||..+|+|.+||...+.+....|...
T Consensus 119 ~L~~~~r~i~~l~~~~-g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 119 TLNDKYQTAIILRYYH-DLTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred hCCHHHhHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5677888777676665 89999999999999999998888877776654
No 110
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=60.81 E-value=4.5 Score=38.05 Aligned_cols=49 Identities=18% Similarity=0.220 Sum_probs=39.5
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++.++.|.+ -.|.++.+||..+|+|.+||...+.+....|...+
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 56777787665554 57999999999999999999999888777776644
No 111
>PHA00675 hypothetical protein
Probab=60.77 E-value=4.2 Score=33.55 Aligned_cols=40 Identities=10% Similarity=0.108 Sum_probs=28.8
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVL 268 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~ 268 (524)
.|...+--.|-...-..|.++..||..||||+|||..|.+
T Consensus 22 KLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 22 KLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred ccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHc
Confidence 4444444444443336788999999999999999987754
No 112
>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=60.60 E-value=5 Score=40.22 Aligned_cols=47 Identities=11% Similarity=0.232 Sum_probs=40.0
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+++.++..+.++|+ .|.++.+||..+|+|.++|+++..+.+.-|..
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 578888988888775 68899999999999999999998887766543
No 113
>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=60.33 E-value=3.6 Score=31.52 Aligned_cols=29 Identities=14% Similarity=0.188 Sum_probs=24.5
Q ss_pred CCCccchhhccCccccceehhhhhhHHHH
Q 041521 246 GEPLRVVSKRFGLGISTCHKLVLEVCSAI 274 (524)
Q Consensus 246 G~s~~~la~~FgiS~STvsriv~~v~~aI 274 (524)
+.+..+||..+|||++|++..+++...-|
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae~kl 51 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAERKL 51 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 56788999999999999999988765544
No 114
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=60.22 E-value=4.9 Score=39.65 Aligned_cols=49 Identities=12% Similarity=0.297 Sum_probs=41.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-.+.|.|+ .|.++..||..+|+|.+||...+.+....|...|
T Consensus 184 ~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 184 SLPEREQLVLSLYYQ-EELNLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred hCCHHHHHHHHhHhc-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888877764 7899999999999999999999888887776644
No 115
>PHA00542 putative Cro-like protein
Probab=59.85 E-value=3.2 Score=34.44 Aligned_cols=51 Identities=6% Similarity=0.020 Sum_probs=35.5
Q ss_pred hhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhcccccccCcchHHHHHHHhhhcc
Q 041521 238 VCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVLMPKFLQWPDELKMKQIKEEFQG 300 (524)
Q Consensus 238 i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L~~~~I~~P~~ee~~~i~~~F~~ 300 (524)
+...+...|.+..++|...|||++||+++.+.- ...|+.+.+..+++.+.+
T Consensus 23 l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~------------~~~p~~~~l~ki~~~~~~ 73 (82)
T PHA00542 23 LVCALIRAGWSQEQIADATDVSQPTICRIYSGR------------HKDPRYSVVEKLRHLVLN 73 (82)
T ss_pred HHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCC------------CCCCCHHHHHHHHHHHHH
Confidence 334457789999999999999999999885421 123555555666555544
No 116
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=59.49 E-value=4.9 Score=38.32 Aligned_cols=48 Identities=17% Similarity=0.266 Sum_probs=39.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|++++.++.|.++ .|.++.+||..+|+|.+||...+.+....|.+.
T Consensus 134 ~Lp~~~r~i~~l~~~-~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~ 181 (192)
T PRK09643 134 RLPVEQRAALVAVDM-QGYSVADAARMLGVAEGTVKSRCARGRARLAEL 181 (192)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 478888887777666 789999999999999999988777766666554
No 117
>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=58.70 E-value=5.4 Score=39.86 Aligned_cols=48 Identities=13% Similarity=0.162 Sum_probs=40.7
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|+.++-.+.|+++ .|.++.+||..+|+|.+||.+.+.+....|...
T Consensus 205 ~L~~~~r~ii~l~~~-~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 205 ILSEREKSIIHCTFE-ENLSQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred cCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 578888888878765 689999999999999999999988887776553
No 118
>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=58.50 E-value=4.5 Score=38.38 Aligned_cols=49 Identities=18% Similarity=0.217 Sum_probs=39.9
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|.+ -.|.++.+||..+|+|.+||...+.+....|...|
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 56777887777755 46899999999999999999988888777776644
No 119
>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=58.43 E-value=3.5 Score=31.45 Aligned_cols=26 Identities=19% Similarity=0.293 Sum_probs=21.5
Q ss_pred CCccchhhccCccccceehhhhhhHH
Q 041521 247 EPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 247 ~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
.+..+|+..++++++|+++++.+...
T Consensus 22 ~t~~~la~~l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 22 LTQSELAERLGISKSTVSRIVKRLEK 47 (62)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 57889999999999999999887544
No 120
>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=58.41 E-value=3.3 Score=31.03 Aligned_cols=27 Identities=26% Similarity=0.400 Sum_probs=21.8
Q ss_pred CCCccchhhccCccccceehhhhhhHH
Q 041521 246 GEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 246 G~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
+.+..+|+...|+++||++|++...+.
T Consensus 18 ~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 18 PLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp CEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 456889999999999999999877554
No 121
>PF13751 DDE_Tnp_1_6: Transposase DDE domain
Probab=58.21 E-value=3.5 Score=36.44 Aligned_cols=49 Identities=10% Similarity=0.116 Sum_probs=32.6
Q ss_pred cccccchh-hhhhcccccccccccccccccccCCCccceehhhHHHHhhhh
Q 041521 422 EKIGDIQA-VAKDAFARLKGRWACLQKRTEVKLQDLPVVLGACCVLHNICE 471 (524)
Q Consensus 422 ~~ls~~R~-~VE~aFG~LK~RFriL~~~~~~~~~~~~~iI~AccvLHNi~~ 471 (524)
..+.+.|. .||..||.||. +--|..........+..-+.-.|+-|||-.
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 34566777 99999999995 444444333445555555666677889854
No 122
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=58.12 E-value=5.1 Score=37.60 Aligned_cols=49 Identities=10% Similarity=0.163 Sum_probs=39.9
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+.+....|...|
T Consensus 117 ~Lp~~~r~i~~l~~~-e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 117 KLPYKLRQVIILRYL-HDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred hCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 578888877777544 6889999999999999999888888777766544
No 123
>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=58.06 E-value=4.4 Score=38.56 Aligned_cols=49 Identities=14% Similarity=0.310 Sum_probs=40.5
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+.+....|.+.+
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 577788877777655 5999999999999999999888888877776654
No 124
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=57.97 E-value=4.3 Score=38.71 Aligned_cols=81 Identities=9% Similarity=0.102 Sum_probs=51.5
Q ss_pred CCHhhHHHHcCCCHHHHHHHHHHhhccccccC--CCCCCCCChhhhhhhhhhcccc-------------CCCccchhhcc
Q 041521 192 FPEEEFWRDFRMSKATFEMICEELESTVMKKN--TMLRDAIPVRQRVAVCVWRLAT-------------GEPLRVVSKRF 256 (524)
Q Consensus 192 ~~d~~F~~~fRmSr~tF~~Lv~~L~~~i~~~~--t~~r~~l~~e~rL~i~L~~Lat-------------G~s~~~la~~F 256 (524)
++.+.|.+.+.-.++....+...+...+.... ...-...++.+|++-+|..|+. ..+..+||...
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 46677777766666555555544443221110 0012346888999988877753 12347899999
Q ss_pred CccccceehhhhhhHH
Q 041521 257 GLGISTCHKLVLEVCS 272 (524)
Q Consensus 257 giS~STvsriv~~v~~ 272 (524)
|++..|++|+++++..
T Consensus 179 G~tr~tvsR~l~~l~~ 194 (211)
T PRK11753 179 GCSREMVGRVLKMLED 194 (211)
T ss_pred CCCHHHHHHHHHHHHH
Confidence 9999999999887543
No 125
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=57.91 E-value=4.6 Score=38.80 Aligned_cols=49 Identities=12% Similarity=0.232 Sum_probs=41.0
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+.+....|...|
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 578888888887764 6889999999999999999988888777776654
No 126
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=57.79 E-value=5.6 Score=37.60 Aligned_cols=49 Identities=20% Similarity=0.295 Sum_probs=39.7
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|++++.++.|.+ -.|.++.+||..+|+|.+||...+.+....|...+
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 56788887777765 47999999999999999999888888777666543
No 127
>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=57.59 E-value=5.1 Score=41.21 Aligned_cols=44 Identities=11% Similarity=0.133 Sum_probs=38.2
Q ss_pred CCChhhhhhhhhhcc---ccCCCccchhhccCccccceehhhhhhHH
Q 041521 229 AIPVRQRVAVCVWRL---ATGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 229 ~l~~e~rL~i~L~~L---atG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
.+|+.++..+.|+|. ..+.++.+||..+|||..+|..+..+...
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 588999999999885 67899999999999999999988776544
No 128
>PRK06930 positive control sigma-like factor; Validated
Probab=57.30 E-value=5.3 Score=37.90 Aligned_cols=49 Identities=10% Similarity=0.145 Sum_probs=39.4
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|. +..|.++.+||..+|+|.+||...+.+....|...+
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 4677776655554 578999999999999999999999888877776644
No 129
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=57.04 E-value=6.1 Score=39.43 Aligned_cols=48 Identities=8% Similarity=0.186 Sum_probs=40.5
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|+.++-.+.|+++ .|.++.+||..+|+|.+||...+.+....|...
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 899999999999999999998888877766553
No 130
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=56.95 E-value=6.3 Score=37.31 Aligned_cols=47 Identities=19% Similarity=0.167 Sum_probs=39.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+|++++-++.|.++ .|.++.+||..+|+|.+||...+.+....|.+
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 678888888777665 68889999999999999999888887776654
No 131
>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=56.77 E-value=3.3 Score=32.00 Aligned_cols=27 Identities=15% Similarity=0.142 Sum_probs=22.7
Q ss_pred CCCccchhhccCccccceehhhhhhHH
Q 041521 246 GEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 246 G~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
..+..+|+..+|++.+||++++.....
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 357789999999999999998887654
No 132
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=56.63 E-value=6.3 Score=39.89 Aligned_cols=47 Identities=15% Similarity=0.336 Sum_probs=39.9
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+|+.++-.+.|+|+ .|.++..||..+|+|.++|++++.+....|..
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 577888888888775 69999999999999999999998887776654
No 133
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=56.57 E-value=6 Score=36.68 Aligned_cols=48 Identities=17% Similarity=0.272 Sum_probs=39.9
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|+.++.++.|.+ -.|.++.+||..+|+|.+||...+.+....+...
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 67888888777765 5799999999999999999998888777766543
No 134
>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=56.17 E-value=4.7 Score=29.47 Aligned_cols=28 Identities=11% Similarity=0.245 Sum_probs=22.3
Q ss_pred cCCCccchhhccCccccceehhhhhhHH
Q 041521 245 TGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 245 tG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
.+.+..+++..+|+|.+||++++.+..+
T Consensus 16 ~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 16 PRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4478899999999999999999887654
No 135
>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=56.04 E-value=3.1 Score=31.78 Aligned_cols=43 Identities=14% Similarity=0.217 Sum_probs=32.3
Q ss_pred CChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHH
Q 041521 230 IPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAI 274 (524)
Q Consensus 230 l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI 274 (524)
++..+. -.|..++.|.+..+||...|||.+||..++..+..-+
T Consensus 4 LT~~E~--~vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 4 LTEREL--EVLRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp S-HHHH--HHHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred cCHHHH--HHHHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHh
Confidence 444443 2567889999999999999999999988877765543
No 136
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=55.90 E-value=5.7 Score=37.56 Aligned_cols=49 Identities=16% Similarity=0.261 Sum_probs=41.0
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|++++-.+.|.++ .|.++.+||..+|++..||...+.+....|...+
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 578888888888776 8999999999999999999988888777766543
No 137
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=55.89 E-value=6.1 Score=37.46 Aligned_cols=47 Identities=17% Similarity=0.192 Sum_probs=40.3
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+|++++-.+.|+++ .|.++.+||..+|+|.+||...+.+....|..
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 678899988888876 68999999999999999999888877666654
No 138
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=55.75 E-value=5.9 Score=37.81 Aligned_cols=48 Identities=8% Similarity=0.189 Sum_probs=39.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.| ++ .|.++.+||..+|+|.+||...+.+.-..|...+
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 467778877777 55 7999999999999999999988888777666544
No 139
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=55.63 E-value=15 Score=30.50 Aligned_cols=61 Identities=13% Similarity=0.092 Sum_probs=52.5
Q ss_pred cHHHHHHHhhc---ccHHHHHHHHHHhhhhhhhhhhhhhhcchhhhhhhHHHHhhhhhccccch
Q 041521 63 AWSDILTSLIL---LDEEEKREQQQYSIHSHQDKLLVDDNHKRKEQAMNDYFHQLQDHYTDLDV 123 (524)
Q Consensus 63 ~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 123 (524)
.+..||-.|+. |.+++.+++....+...+...||+.=-++-..+-.-|++-|++.++.|-+
T Consensus 16 ~v~~ilD~L~~~~Vit~e~~~~I~a~~T~~~kar~Lld~l~~kG~~A~~~F~~~L~e~~p~L~~ 79 (82)
T cd08330 16 NVDPILDKLHGKKVITQEQYSEVRAEKTNQEKMRKLFSFVRSWGASCKDIFYQILREEEPYLVE 79 (82)
T ss_pred hHHHHHHHHHHCCCCCHHHHHHHHcCCCcHHHHHHHHHHHHccCHHHHHHHHHHHHHhChHHHh
Confidence 56777888876 99999999999999999999999888888888999999999988877643
No 140
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=55.19 E-value=6.1 Score=35.75 Aligned_cols=45 Identities=2% Similarity=0.067 Sum_probs=37.4
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHH
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAI 274 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI 274 (524)
.+|+.++-++.|.|+ .|.++.+||..+|+|.+||...+.+....|
T Consensus 106 ~L~~~~r~ii~l~~~-~~~s~~EIA~~l~is~~tV~~~~~ra~~~L 150 (154)
T PRK06759 106 VLDEKEKYIIFERFF-VGKTMGEIALETEMTYYQVRWIYRQALEKM 150 (154)
T ss_pred hCCHHHHHHHHHHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 578888888877765 588999999999999999998887766554
No 141
>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=55.09 E-value=4 Score=34.58 Aligned_cols=34 Identities=26% Similarity=0.368 Sum_probs=27.5
Q ss_pred hhhhhhhhhccccCCCccchhhccCccccceehh
Q 041521 233 RQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKL 266 (524)
Q Consensus 233 e~rL~i~L~~LatG~s~~~la~~FgiS~STvsri 266 (524)
.+|+.++=-.|..|.+|+.|+...|+|..||+|+
T Consensus 36 ~~R~~va~~lL~~g~syreIa~~tgvS~aTItRv 69 (87)
T PF01371_consen 36 AQRWQVAKELLDEGKSYREIAEETGVSIATITRV 69 (87)
T ss_dssp HHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHH
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHH
Confidence 3455555446789999999999999999998875
No 142
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=55.07 E-value=6.4 Score=39.70 Aligned_cols=49 Identities=12% Similarity=0.272 Sum_probs=42.1
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.++-.+|+.+.|+| --+.++..+|...|||.|.||++..+.+..|...|
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 57788899999888 46789999999999999999999999888776644
No 143
>COG5421 Transposase [DNA replication, recombination, and repair]
Probab=54.89 E-value=20 Score=39.29 Aligned_cols=58 Identities=22% Similarity=0.385 Sum_probs=41.9
Q ss_pred CCCccccccccccCCCceeeecCCCCCCCCChHHHHhHHHHhhh-hccccceEEEEcccCCC
Q 041521 339 KTSYSITVQGVVDTKGVFTDVCIGWPGSMPDDQVLERSALFQRA-DRGLLKDVWIVGNSGYP 399 (524)
Q Consensus 339 K~~~Si~vq~v~D~~g~fi~v~~g~pGS~hDs~V~~~S~L~~~l-~~~~~~g~~lLGD~gYp 399 (524)
..-.-|++..+++..|--+.+.+ ++|+.+|...+-. ..+.+ ..+...+.++++|+|+-
T Consensus 152 ~dl~QI~vsMi~~~~gIPl~~~v-~~Gni~D~~~~~~--ti~kl~~~l~~~~~~~V~Dkgf~ 210 (480)
T COG5421 152 LDLPQINVSMIVNQKGIPLFVRV-YSGNISDKNTLIK--TIQKLKSVLVKDEVYLVADKGFN 210 (480)
T ss_pred CCcceeEEEEEEcCCCCceEEEc-cCCCccchHHHHH--HHHHHHHhcccceEEEEEccccc
Confidence 44567888889988866665555 7999999987774 34444 33444458999999995
No 144
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=54.80 E-value=6.9 Score=40.78 Aligned_cols=48 Identities=10% Similarity=0.162 Sum_probs=41.6
Q ss_pred CCChhhhhhhhhhcc---ccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWRL---ATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~L---atG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+|+.++..+.|+|. ..+.++.+||..+|||..+|..+..+...-|..
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 589999999999886 477899999999999999999998887776654
No 145
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=54.43 E-value=5.7 Score=36.58 Aligned_cols=49 Identities=14% Similarity=0.208 Sum_probs=39.4
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|++ -.|.++.+||..+|+|.+||...+.+....|...+
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 56777777666554 47899999999999999999988888877776644
No 146
>PRK15320 transcriptional activator SprB; Provisional
Probab=54.28 E-value=4.9 Score=39.25 Aligned_cols=45 Identities=22% Similarity=0.337 Sum_probs=36.4
Q ss_pred CCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHH
Q 041521 228 DAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAI 274 (524)
Q Consensus 228 ~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI 274 (524)
+.++..+. -.|..|+.|.+.++||+.+++|.+||+.+..++..-+
T Consensus 163 ~~LSdREI--EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKL 207 (251)
T PRK15320 163 PGVTQAKY--ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRL 207 (251)
T ss_pred CCCCHHHH--HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHc
Confidence 34454444 5678899999999999999999999999988776654
No 147
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=53.99 E-value=5.9 Score=39.00 Aligned_cols=49 Identities=14% Similarity=0.175 Sum_probs=39.6
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|++++-++.|+++ .|.++.+||..+|+|.+||...+.+....|...+
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 467777877766665 4999999999999999999988888777666544
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=53.93 E-value=7.4 Score=38.04 Aligned_cols=47 Identities=11% Similarity=0.271 Sum_probs=39.4
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+|+.++-.+.|+|+ .|.++.+||..+|+|.+||.+.+.+....|..
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 578888888888774 78899999999999999999888887776654
No 149
>PRK06030 hypothetical protein; Provisional
Probab=53.46 E-value=7.1 Score=35.26 Aligned_cols=46 Identities=20% Similarity=0.234 Sum_probs=39.5
Q ss_pred CCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHH
Q 041521 228 DAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSA 273 (524)
Q Consensus 228 ~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~a 273 (524)
..+...-+++|.|.+--+|.++..||..||.+.|||...++.+-+.
T Consensus 51 k~i~~aRqIAMYL~r~~~~~sl~~IG~~FGRDHSTV~haikkIe~~ 96 (124)
T PRK06030 51 REVSRIRQIAMYVAHVSLGWPMNEVALAFGRDRTTVGHACHTVEDL 96 (124)
T ss_pred cccchHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHHHHHHH
Confidence 5677778999999999999999999999999999998877755443
No 150
>PF13551 HTH_29: Winged helix-turn helix
Probab=53.44 E-value=4.2 Score=34.65 Aligned_cols=34 Identities=18% Similarity=0.292 Sum_probs=29.4
Q ss_pred hhhccccCCC-ccchhhccCccccceehhhhhhHH
Q 041521 239 CVWRLATGEP-LRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 239 ~L~~LatG~s-~~~la~~FgiS~STvsriv~~v~~ 272 (524)
+|..++.|.+ ...++..+|+|..||++++..+..
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 4566888995 999999999999999999998754
No 151
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=53.15 E-value=14 Score=33.47 Aligned_cols=44 Identities=7% Similarity=0.085 Sum_probs=30.5
Q ss_pred CCChhh-hhhhhhhccccCCCccchhhccCccccceehhhhhhHH
Q 041521 229 AIPVRQ-RVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 229 ~l~~e~-rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
.+++.+ .++..|+...-|.+..+|++.++++++||++++.+...
T Consensus 28 glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~ 72 (144)
T PRK03573 28 ELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEE 72 (144)
T ss_pred CCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHH
Confidence 344444 34444444444567899999999999999988877544
No 152
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=53.12 E-value=7.2 Score=36.79 Aligned_cols=48 Identities=10% Similarity=0.144 Sum_probs=38.7
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|+.++-++.|.++. |.++.+||..+|+|.+||...+.+....|...
T Consensus 139 ~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 139 TLPEKQREILILRVVV-GLSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5778888777776664 89999999999999999988888776666543
No 153
>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=52.87 E-value=4.5 Score=29.67 Aligned_cols=28 Identities=14% Similarity=0.166 Sum_probs=22.4
Q ss_pred cCCCccchhhccCccccceehhhhhhHH
Q 041521 245 TGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 245 tG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
...+..+|++.+|++++||++.+....+
T Consensus 14 ~~~~~~el~~~l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 14 GPLTVSELAEELGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCchhhHHHhccccchHHHHHHHHHHH
Confidence 4577889999999999999998876543
No 154
>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=51.61 E-value=7.7 Score=36.10 Aligned_cols=49 Identities=22% Similarity=0.336 Sum_probs=39.8
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++.++.|.++ .|.++.+||..+|+|.+||...+.+....|...+
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 577888877777664 7899999999999999999988888777666543
No 155
>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=51.46 E-value=4.4 Score=32.61 Aligned_cols=41 Identities=27% Similarity=0.310 Sum_probs=29.7
Q ss_pred CChhhhhhhhhhccccCCCccchhhccC-ccccceehhhhhh
Q 041521 230 IPVRQRVAVCVWRLATGEPLRVVSKRFG-LGISTCHKLVLEV 270 (524)
Q Consensus 230 l~~e~rL~i~L~~LatG~s~~~la~~Fg-iS~STvsriv~~v 270 (524)
+.-.-++++.|.+=-+|.++.+||..|| .+.|||...+++|
T Consensus 29 i~~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHstV~~a~~ki 70 (70)
T PF08299_consen 29 IVEARQVAMYLARELTGLSLSEIGRYFGGRDHSTVIHAIRKI 70 (70)
T ss_dssp HHHHHHHHHHHHHHHS---HHHHHHHCTSSTHHHHHHHHHHH
T ss_pred hcchHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHHhC
Confidence 4445567787777778999999999999 9999997766553
No 156
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=51.33 E-value=6.4 Score=36.46 Aligned_cols=49 Identities=8% Similarity=0.252 Sum_probs=39.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|.+ -.|.++.+||..+|+|.+||...+.+....|...+
T Consensus 120 ~L~~~~r~vl~l~~-~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 120 TLSLEHRAVLVLHD-LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred hCCHHHeeeeeehH-hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46777776666655 46888999999999999999998888877777654
No 157
>PRK01381 Trp operon repressor; Provisional
Probab=51.29 E-value=8.2 Score=33.48 Aligned_cols=24 Identities=21% Similarity=0.306 Sum_probs=20.7
Q ss_pred ccCCCccchhhccCccccceehhh
Q 041521 244 ATGEPLRVVSKRFGLGISTCHKLV 267 (524)
Q Consensus 244 atG~s~~~la~~FgiS~STvsriv 267 (524)
..+.+|+.|+...|||.+||+|.-
T Consensus 53 ~g~~sQREIa~~lGvSiaTITRgs 76 (99)
T PRK01381 53 RGELSQREIKQELGVGIATITRGS 76 (99)
T ss_pred cCCcCHHHHHHHhCCceeeehhhH
Confidence 335899999999999999998763
No 158
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=51.27 E-value=7.1 Score=38.74 Aligned_cols=49 Identities=14% Similarity=0.214 Sum_probs=40.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|++ -.|.++.+||..+|+|.+||...+.+....|...+
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 56778887776665 47999999999999999999988888877776644
No 159
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=51.23 E-value=8.2 Score=36.18 Aligned_cols=49 Identities=24% Similarity=0.278 Sum_probs=40.9
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++..+.|+++ .|.++.+||..+|+|.+||...+++....|...+
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 478888888877764 6899999999999999999998888777776543
No 160
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=50.62 E-value=8 Score=36.40 Aligned_cols=49 Identities=8% Similarity=0.076 Sum_probs=39.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+.+....|...+
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 567777776666554 6899999999999999999988888777776544
No 161
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=50.59 E-value=15 Score=28.86 Aligned_cols=71 Identities=13% Similarity=0.107 Sum_probs=49.2
Q ss_pred HhhHHHHcCCCHHHHHHHHHHhhccccccCCCCCCCCChhhhhhhhhhccccC-CCccchhhccCc-cccceehhhhhhH
Q 041521 194 EEEFWRDFRMSKATFEMICEELESTVMKKNTMLRDAIPVRQRVAVCVWRLATG-EPLRVVSKRFGL-GISTCHKLVLEVC 271 (524)
Q Consensus 194 d~~F~~~fRmSr~tF~~Lv~~L~~~i~~~~t~~r~~l~~e~rL~i~L~~LatG-~s~~~la~~Fgi-S~STvsriv~~v~ 271 (524)
=+++-..++++...|..++......-. ...-...++.-++.+|..+ .+..+++..+|+ +.++.++.|.+..
T Consensus 4 ~~~la~~~~~s~~~l~~~f~~~~~~s~-------~~~~~~~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk~~~ 76 (84)
T smart00342 4 LEDLAEALGMSPRHLQRLFKKETGTTP-------KQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLF 76 (84)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHhCcCH-------HHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 356778889999988888765432100 0111234566666666665 799999999999 9999999887653
No 162
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=50.38 E-value=8.8 Score=36.51 Aligned_cols=49 Identities=20% Similarity=0.228 Sum_probs=39.8
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|.+ -.|.++.+||...|+|.+||...+.+....|...+
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 57888887776665 46899999999999999999888888777766543
No 163
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=50.31 E-value=6.8 Score=40.89 Aligned_cols=69 Identities=9% Similarity=0.086 Sum_probs=46.8
Q ss_pred hhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhcccccccCcchHHHHHHHhhhccccCCCccccC
Q 041521 238 VCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVLMPKFLQWPDELKMKQIKEEFQGISGIPNVGGS 310 (524)
Q Consensus 238 i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L~~~~I~~P~~ee~~~i~~~F~~~~gfP~~vGa 310 (524)
++=+|+-.|.++.+||.++|+|+++|+|++.+.-+. -+-..-|.-|.. ....+.+.+++++|+..|+-+
T Consensus 21 vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~---GiV~I~I~~~~~-~~~~Le~~L~~~fgLk~~iVv 89 (318)
T PRK15418 21 IAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQS---GIIRVQINSRFE-GCLELENALRQHFSLQHIRVL 89 (318)
T ss_pred HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHc---CcEEEEEeCCCc-cHHHHHHHHHHHhCCCEEEEE
Confidence 455677789999999999999999999998874321 122233444532 333455666677788887644
No 164
>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=50.17 E-value=6.3 Score=35.34 Aligned_cols=36 Identities=11% Similarity=0.150 Sum_probs=30.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceeh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHK 265 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsr 265 (524)
.+|+.+|-++.|.++ .|.++.+||..+|+|.+||.+
T Consensus 107 ~Lp~~~r~v~~l~~~-~~~s~~EIA~~l~is~~tV~~ 142 (142)
T TIGR03209 107 ILPNKQKKIIYMKFF-EDMKEIDIAKKLHISRQSVYK 142 (142)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHhhcC
Confidence 578888887777555 789999999999999999853
No 165
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=49.85 E-value=7.5 Score=36.84 Aligned_cols=49 Identities=14% Similarity=0.162 Sum_probs=38.5
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++.++.|++ -.|.++.+||...|+|.+||...+.+....|...+
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 46777777666654 57999999999999999999888777776666543
No 166
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=49.51 E-value=8.8 Score=35.12 Aligned_cols=47 Identities=13% Similarity=0.223 Sum_probs=38.3
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+|+.++.++.|.++ .|.++..||..+|+|.+||...+.+....|.+
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 678888887777655 68899999999999999998887777665543
No 167
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=49.01 E-value=8.8 Score=37.02 Aligned_cols=49 Identities=10% Similarity=0.117 Sum_probs=39.8
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|++++.++.|.++ .|.++.+||..+|+|.+||...+.+....|...+
T Consensus 153 ~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYF-QELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 578888888766654 6899999999999999999888887777666543
No 168
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=48.97 E-value=8.3 Score=37.64 Aligned_cols=101 Identities=11% Similarity=0.062 Sum_probs=61.6
Q ss_pred CCHhhHHHHcCCCHHHHHHHHHHhhcccccc--CCCCCCCCChhhhhhhhhhccccC----------CCccchhhccCcc
Q 041521 192 FPEEEFWRDFRMSKATFEMICEELESTVMKK--NTMLRDAIPVRQRVAVCVWRLATG----------EPLRVVSKRFGLG 259 (524)
Q Consensus 192 ~~d~~F~~~fRmSr~tF~~Lv~~L~~~i~~~--~t~~r~~l~~e~rL~i~L~~LatG----------~s~~~la~~FgiS 259 (524)
++.+.|...+.=++.--..++..+...+... ........++++|++-+|..++.. .+..+||...|++
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 4556777766666655444444443321110 000112458999999999877642 2236799999999
Q ss_pred ccceehhhhhhHHHHHhhcccccccCcchHHHHH
Q 041521 260 ISTCHKLVLEVCSAIKTVLMPKFLQWPDELKMKQ 293 (524)
Q Consensus 260 ~STvsriv~~v~~aI~~~L~~~~I~~P~~ee~~~ 293 (524)
..||+|+++++...=.. +....|..++.+.+..
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 99999999887654332 3344566666665544
No 169
>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=48.66 E-value=7.7 Score=33.41 Aligned_cols=41 Identities=5% Similarity=0.084 Sum_probs=34.6
Q ss_pred ChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHH
Q 041521 231 PVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 231 ~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
.++++..+.++|+ .+.++.+++...++|++|++++-.+.+.
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 4677888888888 6888999999999999999988766544
No 170
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=47.58 E-value=8.5 Score=33.63 Aligned_cols=46 Identities=15% Similarity=0.291 Sum_probs=40.4
Q ss_pred CCCCChhhhhhhhhhccccCCCccchhhccCc-cccceehhhhhhHH
Q 041521 227 RDAIPVRQRVAVCVWRLATGEPLRVVSKRFGL-GISTCHKLVLEVCS 272 (524)
Q Consensus 227 r~~l~~e~rL~i~L~~LatG~s~~~la~~Fgi-S~STvsriv~~v~~ 272 (524)
++..|.+.|+-++-.++..|.++..||..||| +.+++++++.+.-.
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 99999888776544
No 171
>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=47.40 E-value=6.8 Score=30.61 Aligned_cols=39 Identities=10% Similarity=0.267 Sum_probs=26.6
Q ss_pred hhhhhhhhccc---cCCCccchhhccCccccceehhhhhhHH
Q 041521 234 QRVAVCVWRLA---TGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 234 ~rL~i~L~~La---tG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
+.-+-+++.|. ...+..+||..+|||++||+..+.+...
T Consensus 7 e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~ 48 (60)
T PF01325_consen 7 EDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAE 48 (60)
T ss_dssp HHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHH
Confidence 33444455554 4456679999999999999988776543
No 172
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=46.97 E-value=10 Score=34.63 Aligned_cols=49 Identities=12% Similarity=0.212 Sum_probs=39.8
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|++++-++.|. .-.|.++.+||..+|+|.+||...+.+....|...+
T Consensus 105 ~L~~~~r~v~~l~-~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 105 ELPPACRDSFLLR-KLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4777877766665 457999999999999999999998888877776644
No 173
>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=46.34 E-value=9.8 Score=35.94 Aligned_cols=41 Identities=7% Similarity=0.114 Sum_probs=31.1
Q ss_pred hhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 234 QRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 234 ~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+.++ +.++ .|.++.+||..+|+|.+||...+++....|..
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 34443 4554 89999999999999999998777776665543
No 174
>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=46.27 E-value=5.6 Score=31.68 Aligned_cols=27 Identities=7% Similarity=0.145 Sum_probs=23.0
Q ss_pred CCCccchhhccCccccceehhhhhhHH
Q 041521 246 GEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 246 G~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
+.+..+||...|+|..||+++++++.+
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 356789999999999999999887654
No 175
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=46.13 E-value=11 Score=36.09 Aligned_cols=49 Identities=16% Similarity=0.186 Sum_probs=40.7
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+.+....|.+.|
T Consensus 133 ~Lp~~~r~v~~l~~~-~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l 181 (196)
T PRK12535 133 ALPPERREALILTQV-LGYTYEEAAKIADVRVGTIRSRVARARADLIAAT 181 (196)
T ss_pred cCCHHHHHHhhhHHH-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 477788877777655 6788999999999999999998888888777755
No 176
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=45.69 E-value=12 Score=39.25 Aligned_cols=50 Identities=18% Similarity=0.278 Sum_probs=43.0
Q ss_pred CCChhhhhhhhhhc-c--ccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWR-L--ATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~-L--atG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++..+.++| | -.|.++..||...||+.+||..++.+....|...|
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 68899999998776 4 46899999999999999999999998888777654
No 177
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=45.66 E-value=7.9 Score=31.85 Aligned_cols=38 Identities=32% Similarity=0.418 Sum_probs=27.9
Q ss_pred hhhhhhhcccc---CCCccchhhccCccccceehhhhhhHH
Q 041521 235 RVAVCVWRLAT---GEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 235 rL~i~L~~Lat---G~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
+..-.|.+|+. +.+..+|+..+|++++||++++.....
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 33334444442 477889999999999999999887654
No 178
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=45.58 E-value=9.2 Score=40.10 Aligned_cols=67 Identities=12% Similarity=0.162 Sum_probs=45.0
Q ss_pred hhccccCCCccchhhccCccccceehhhhhhHHHHHhhcccccccCcchHHHHHHHhhhccccCCCccccC
Q 041521 240 VWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVLMPKFLQWPDELKMKQIKEEFQGISGIPNVGGS 310 (524)
Q Consensus 240 L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L~~~~I~~P~~ee~~~i~~~F~~~~gfP~~vGa 310 (524)
=.|+..|.++.+||+++|||+.+|+|.+.+--. +-+-...|..|.. ..-.+.+..++++|++.|+-+
T Consensus 20 ~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~---~GiV~I~i~~~~~-~~~~Le~~L~~~fgL~~a~VV 86 (321)
T COG2390 20 WLYYVEGLTQSEIAERLGISRATVSRLLAKARE---EGIVKISINSPVE-GCLELEQQLKERFGLKEAIVV 86 (321)
T ss_pred HHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH---CCeEEEEeCCCCc-chHHHHHHHHHhcCCCeEEEE
Confidence 356778999999999999999999998776322 2222334553332 233355666667788877654
No 179
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=44.88 E-value=7.5 Score=37.88 Aligned_cols=80 Identities=14% Similarity=0.118 Sum_probs=49.0
Q ss_pred CCHhhHHHHcCCCHHHHHHHHHHhhcccccc--CCCCCCCCChhhhhhhhhhcccc--------------CCCccchhhc
Q 041521 192 FPEEEFWRDFRMSKATFEMICEELESTVMKK--NTMLRDAIPVRQRVAVCVWRLAT--------------GEPLRVVSKR 255 (524)
Q Consensus 192 ~~d~~F~~~fRmSr~tF~~Lv~~L~~~i~~~--~t~~r~~l~~e~rL~i~L~~Lat--------------G~s~~~la~~ 255 (524)
++-+.|.+.+.=.++.-..++..+...+... ....-...++++|++-+|..|+. ..+..+||..
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 3455666665555544333444433221100 00001245789999999988762 2456799999
Q ss_pred cCccccceehhhhhhH
Q 041521 256 FGLGISTCHKLVLEVC 271 (524)
Q Consensus 256 FgiS~STvsriv~~v~ 271 (524)
.|++..||+|++.++-
T Consensus 194 lG~sr~tvsR~l~~l~ 209 (235)
T PRK11161 194 LGLTVETISRLLGRFQ 209 (235)
T ss_pred hCCcHHHHHHHHHHHH
Confidence 9999999999987654
No 180
>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=44.67 E-value=6.7 Score=29.70 Aligned_cols=28 Identities=14% Similarity=0.306 Sum_probs=22.3
Q ss_pred cCCCccchhhccCccccceehhhhhhHH
Q 041521 245 TGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 245 tG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
.|.+..+|+..++++++++++++.....
T Consensus 16 ~~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 16 GGITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 3578889999999999999988876543
No 181
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=44.65 E-value=11 Score=38.12 Aligned_cols=48 Identities=15% Similarity=0.287 Sum_probs=39.7
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|+.++-++.|+|+ .|.++.+||..+|+|.+||.+.+.+....|...
T Consensus 212 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 212 TLPEREKKVLILYYY-EDLTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 578888888877764 689999999999999999998887776666554
No 182
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=44.60 E-value=11 Score=35.87 Aligned_cols=49 Identities=12% Similarity=0.101 Sum_probs=39.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+..+-++.|.+ -.|.++.+||..+|+|.+||...+.+....|...+
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 56777777665554 46999999999999999999998888877776654
No 183
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=44.35 E-value=12 Score=40.12 Aligned_cols=48 Identities=8% Similarity=0.126 Sum_probs=40.3
Q ss_pred CCChhhhhhhhhhcc---ccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWRL---ATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~L---atG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+|+.++..+.|+|+ ..+.++..||..+|||+.+|.++..+...-|..
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 488889999999886 346899999999999999999998887766543
No 184
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=44.03 E-value=12 Score=37.02 Aligned_cols=45 Identities=11% Similarity=0.185 Sum_probs=37.6
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHH
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAI 274 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI 274 (524)
.+|+.++-.+.|+|+ .|.++..||..+|+|.++|+++......-|
T Consensus 183 ~L~~~er~vi~l~~~-~~~t~~EIA~~lgis~~~V~q~~~~~~~kL 227 (231)
T PRK12427 183 QLDEREQLILHLYYQ-HEMSLKEIALVLDLTEARICQLNKKIAQKI 227 (231)
T ss_pred cCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 577888888888774 689999999999999999998877766544
No 185
>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=43.75 E-value=5.5 Score=35.34 Aligned_cols=37 Identities=30% Similarity=0.499 Sum_probs=28.8
Q ss_pred CChhhhhhhhhhccccCCCccchhhccCccccceehhhhh
Q 041521 230 IPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 230 l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~ 269 (524)
++..++|+ .++..|.+.+.++..|+||.+||.+++..
T Consensus 5 ~DlR~rVl---~~~~~g~s~~eaa~~F~VS~~Tv~~W~k~ 41 (119)
T PF01710_consen 5 LDLRQRVL---AYIEKGKSIREAAKRFGVSRNTVYRWLKR 41 (119)
T ss_pred HHHHHHHH---HHHHccchHHHHHHHhCcHHHHHHHHHHh
Confidence 34445543 46677889999999999999999988773
No 186
>PRK13870 transcriptional regulator TraR; Provisional
Probab=43.69 E-value=20 Score=35.68 Aligned_cols=46 Identities=9% Similarity=0.152 Sum_probs=38.7
Q ss_pred CCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHH
Q 041521 228 DAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIK 275 (524)
Q Consensus 228 ~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~ 275 (524)
..++++|+ =+|.+.+.|.+..+||...|||.+||..+++.+..-|.
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 57889999999999999999999999988887766443
No 187
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=43.68 E-value=9.3 Score=36.15 Aligned_cols=64 Identities=14% Similarity=0.094 Sum_probs=44.4
Q ss_pred CChhhhhhhhhhcccc--------------CCCccchhhccCccccceehhhhhhHHH-HHhhcccccccCcchHHHHHH
Q 041521 230 IPVRQRVAVCVWRLAT--------------GEPLRVVSKRFGLGISTCHKLVLEVCSA-IKTVLMPKFLQWPDELKMKQI 294 (524)
Q Consensus 230 l~~e~rL~i~L~~Lat--------------G~s~~~la~~FgiS~STvsriv~~v~~a-I~~~L~~~~I~~P~~ee~~~i 294 (524)
.++++||+-+|..|+. ..+..+||...|+++.||+|++.++.+. +.. .....|..++.+.+..+
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 2356799999999999999999987652 222 23345666655555444
No 188
>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=43.29 E-value=9 Score=28.67 Aligned_cols=27 Identities=11% Similarity=0.140 Sum_probs=21.7
Q ss_pred CCccchhhccCccccceehhhhhhHHH
Q 041521 247 EPLRVVSKRFGLGISTCHKLVLEVCSA 273 (524)
Q Consensus 247 ~s~~~la~~FgiS~STvsriv~~v~~a 273 (524)
.+..+||+.+|||..||.+.+...-..
T Consensus 16 it~~eLa~~l~vS~rTi~~~i~~L~~~ 42 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIRRDIKELREW 42 (55)
T ss_dssp BEHHHHHHHCTS-HHHHHHHHHHHHHT
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 677899999999999999988776443
No 189
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=43.21 E-value=13 Score=34.48 Aligned_cols=49 Identities=10% Similarity=0.050 Sum_probs=37.8
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|++.+-+ ++.++-.|.++.++|...|+|.+||...+.+....|...+
T Consensus 119 ~L~~~~r~i-~~l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 167 (173)
T PRK12522 119 LLNEKYKTV-LVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHL 167 (173)
T ss_pred hCCHHHHHH-HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 355655543 4445557999999999999999999999888888777644
No 190
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=43.20 E-value=8.9 Score=36.22 Aligned_cols=49 Identities=6% Similarity=0.100 Sum_probs=36.8
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|++++=++.|.++ .|.++.+||..+|+|.+||...+.+....|...+
T Consensus 134 ~L~~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 134 HVNPIDREILVLRFV-AELEFQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred hcChhheeeeeeHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 455566555555444 7889999999999999999888887777666543
No 191
>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=42.74 E-value=15 Score=33.26 Aligned_cols=50 Identities=16% Similarity=0.114 Sum_probs=39.5
Q ss_pred CCChhhhhhhhhhcccc-CCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLAT-GEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~Lat-G~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.++.+++-.+-++|+.. ..++..||..+|+|++|+++.-..++..+...|
T Consensus 82 ~Ld~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~l 132 (134)
T TIGR01636 82 EADEQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEEL 132 (134)
T ss_pred hCCHHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 36777888888888743 348999999999999999998887777666543
No 192
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=42.23 E-value=13 Score=39.48 Aligned_cols=47 Identities=13% Similarity=0.152 Sum_probs=38.7
Q ss_pred CCChhhhhhhhhhcc-c--cCCCccchhhccCccccceehhhhhhHHHHH
Q 041521 229 AIPVRQRVAVCVWRL-A--TGEPLRVVSKRFGLGISTCHKLVLEVCSAIK 275 (524)
Q Consensus 229 ~l~~e~rL~i~L~~L-a--tG~s~~~la~~FgiS~STvsriv~~v~~aI~ 275 (524)
.+|+.++..+.|+|. . .+.++..||..||||...|+++-.+.+.-|.
T Consensus 305 ~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr 354 (367)
T PRK09210 305 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 354 (367)
T ss_pred hCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 588889999999885 3 5589999999999999999998776655444
No 193
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=41.17 E-value=19 Score=34.69 Aligned_cols=45 Identities=16% Similarity=0.160 Sum_probs=36.1
Q ss_pred CCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHH
Q 041521 228 DAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAI 274 (524)
Q Consensus 228 ~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI 274 (524)
..+++.|+ =.|..++.|.+..+||...++|.+||..++..+..-+
T Consensus 132 ~~LSpREr--EVLrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKL 176 (198)
T PRK15201 132 RHFSVTER--HLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKL 176 (198)
T ss_pred CCCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 34777765 4567789999999999999999999988877665543
No 194
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=40.47 E-value=15 Score=34.22 Aligned_cols=46 Identities=15% Similarity=0.250 Sum_probs=35.1
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHH
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIK 275 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~ 275 (524)
.+|++++-++.| ..-.|.++.+||..+|+|.+||...+.+....+.
T Consensus 119 ~L~~~~r~i~~l-~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 119 GLNGKTREAFLL-SQLDGLTYSEIAHKLGVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred hCCHHHhHHhhh-hhccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 466777755544 4457889999999999999999888777665554
No 195
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.37 E-value=12 Score=32.49 Aligned_cols=43 Identities=7% Similarity=0.116 Sum_probs=34.4
Q ss_pred hhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 233 RQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 233 e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.++--+-|+| .-.-|+..||+.|+||+++|+..|.+++..+.+
T Consensus 21 KQ~~Y~~lyy-~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~ 63 (105)
T COG2739 21 KQKNYLELYY-LDDLSLSEIAEEFNVSRQAIYDNIKRTEKILED 63 (105)
T ss_pred HHHHHHHHHH-HhhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 3444555544 467789999999999999999999999988765
No 196
>PRK05949 RNA polymerase sigma factor; Validated
Probab=40.36 E-value=16 Score=38.27 Aligned_cols=48 Identities=17% Similarity=0.220 Sum_probs=40.3
Q ss_pred CCChhhhhhhhhhc-cc--cCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWR-LA--TGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~-La--tG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+|+.++-.+.|+| |. .+.++.+||..+|+|..+|..+..+....|..
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 47888998898887 43 56899999999999999999998887766654
No 197
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=40.25 E-value=13 Score=29.56 Aligned_cols=40 Identities=8% Similarity=0.181 Sum_probs=30.5
Q ss_pred Chhhhhhhhhhcccc-CCCccchhhccCccccceehhhhhh
Q 041521 231 PVRQRVAVCVWRLAT-GEPLRVVSKRFGLGISTCHKLVLEV 270 (524)
Q Consensus 231 ~~e~rL~i~L~~Lat-G~s~~~la~~FgiS~STvsriv~~v 270 (524)
+.+++++.+|..-.. |.+..+|+..+|+++++|++++...
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L 46 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSL 46 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 456677777765544 4788999999999999988876643
No 198
>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=39.63 E-value=25 Score=30.69 Aligned_cols=43 Identities=5% Similarity=0.001 Sum_probs=29.2
Q ss_pred CCChhh-hhhhhhhccccCCCccchhhccCccccceehhhhhhHH
Q 041521 229 AIPVRQ-RVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 229 ~l~~e~-rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
.+++.+ .++.+|. -..+.+..+|+...|++++|+++.+.+...
T Consensus 25 ~lt~~q~~iL~~l~-~~~~~t~~ela~~~~~~~~tvs~~l~~Le~ 68 (118)
T TIGR02337 25 GLTEQQWRILRILA-EQGSMEFTQLANQACILRPSLTGILARLER 68 (118)
T ss_pred CCCHHHHHHHHHHH-HcCCcCHHHHHHHhCCCchhHHHHHHHHHH
Confidence 344444 3333333 234677899999999999999988877544
No 199
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=39.62 E-value=24 Score=36.01 Aligned_cols=49 Identities=14% Similarity=0.314 Sum_probs=40.7
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++.++.|.++ .|.++.+||..+|+|.+||...+.+.-..|.+.+
T Consensus 115 ~L~~~~R~v~~L~~~-~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~ 163 (293)
T PRK09636 115 RLSPLERAAFLLHDV-FGVPFDEIASTLGRSPAACRQLASRARKHVRAAR 163 (293)
T ss_pred hCCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 578888877766554 5899999999999999999999998888777643
No 200
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=39.37 E-value=11 Score=36.84 Aligned_cols=81 Identities=11% Similarity=0.115 Sum_probs=51.9
Q ss_pred CCHhhHHHHcCCCHHHHHHHHHHhhcccccc-C-CCCCCCCChhhhhhhhhhcccc----------CCCccchhhccCcc
Q 041521 192 FPEEEFWRDFRMSKATFEMICEELESTVMKK-N-TMLRDAIPVRQRVAVCVWRLAT----------GEPLRVVSKRFGLG 259 (524)
Q Consensus 192 ~~d~~F~~~fRmSr~tF~~Lv~~L~~~i~~~-~-t~~r~~l~~e~rL~i~L~~Lat----------G~s~~~la~~FgiS 259 (524)
++-+.|...+.-+++....++..+...+... . ...-...++++||+-+|..++. ..+..+||...|++
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 4556666666666655555555444322110 0 0001246899999999988753 23557999999999
Q ss_pred ccceehhhhhhHH
Q 041521 260 ISTCHKLVLEVCS 272 (524)
Q Consensus 260 ~STvsriv~~v~~ 272 (524)
+.|++|++.++-+
T Consensus 193 retlsR~L~~L~~ 205 (230)
T PRK09391 193 IETVSRALSQLQD 205 (230)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999887543
No 201
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=39.34 E-value=15 Score=39.90 Aligned_cols=47 Identities=9% Similarity=0.124 Sum_probs=39.2
Q ss_pred CCChhhhhhhhhhcc---ccCCCccchhhccCccccceehhhhhhHHHHH
Q 041521 229 AIPVRQRVAVCVWRL---ATGEPLRVVSKRFGLGISTCHKLVLEVCSAIK 275 (524)
Q Consensus 229 ~l~~e~rL~i~L~~L---atG~s~~~la~~FgiS~STvsriv~~v~~aI~ 275 (524)
.+|+.++-.+.|+|. ..+.++.+||..+|+|.++|.++.++....|.
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 588889988988885 35689999999999999999998887666554
No 202
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=39.03 E-value=16 Score=34.76 Aligned_cols=46 Identities=17% Similarity=0.274 Sum_probs=35.1
Q ss_pred CChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 230 IPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 230 l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
+++++.=.+.|+++ .|.++.+||...|||.+||.+-....-..+..
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 56666666667655 78999999999999999999887665544433
No 203
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=38.84 E-value=13 Score=27.52 Aligned_cols=28 Identities=14% Similarity=0.078 Sum_probs=23.0
Q ss_pred ccCCCccchhhccCccccceehhhhhhH
Q 041521 244 ATGEPLRVVSKRFGLGISTCHKLVLEVC 271 (524)
Q Consensus 244 atG~s~~~la~~FgiS~STvsriv~~v~ 271 (524)
..+.+..+++..+|+|.+|+++.+....
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~ 35 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLR 35 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4456788999999999999998887654
No 204
>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=37.72 E-value=10 Score=29.40 Aligned_cols=28 Identities=14% Similarity=0.245 Sum_probs=21.1
Q ss_pred cCCCccchhhccCccccceehhhhhhHH
Q 041521 245 TGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 245 tG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
.+.+..+|+..++++++++++.+.+.+.
T Consensus 17 ~~~t~~~l~~~~~~~~~~vs~~i~~L~~ 44 (68)
T PF13463_consen 17 GPMTQSDLAERLGISKSTVSRIIKKLEE 44 (68)
T ss_dssp S-BEHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3466789999999999999998887655
No 205
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=36.88 E-value=11 Score=26.88 Aligned_cols=28 Identities=11% Similarity=0.086 Sum_probs=22.7
Q ss_pred cCCCccchhhccCccccceehhhhhhHH
Q 041521 245 TGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 245 tG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
-..+..++++.+|++.+|+++++.....
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3456789999999999999988776544
No 206
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=36.66 E-value=12 Score=27.90 Aligned_cols=25 Identities=12% Similarity=0.234 Sum_probs=20.4
Q ss_pred CccchhhccCccccceehhhhhhHH
Q 041521 248 PLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 248 s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
+..++++.||+|.+||.+.+.....
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~ 46 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEA 46 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5678999999999999888776543
No 207
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=36.29 E-value=18 Score=34.99 Aligned_cols=49 Identities=16% Similarity=0.299 Sum_probs=39.3
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVL 278 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L 278 (524)
.+|+.++-.+.|.+ -.|.++.+||..+|+|.+||...+.+....|...+
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 46777776665654 57999999999999999999998888877776654
No 208
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=35.79 E-value=14 Score=35.83 Aligned_cols=44 Identities=9% Similarity=0.080 Sum_probs=36.2
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHH
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAI 274 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI 274 (524)
.+++.|+ =.|..++.|.+..+||...++|.+||..++..++.-+
T Consensus 137 ~LT~RE~--eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~~KL 180 (207)
T PRK15411 137 SLSRTES--SMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKI 180 (207)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 3666665 4577899999999999999999999998887766544
No 209
>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=35.65 E-value=10 Score=29.24 Aligned_cols=30 Identities=10% Similarity=0.086 Sum_probs=24.6
Q ss_pred cccCCCccchhhccCccccceehhhhhhHH
Q 041521 243 LATGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 243 LatG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
-..+.+..+|+..+|++.+|+++.+....+
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 466788899999999999999999887654
No 210
>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=35.35 E-value=34 Score=34.79 Aligned_cols=48 Identities=13% Similarity=0.230 Sum_probs=40.1
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+++.-..|.+.
T Consensus 108 ~L~~~~R~v~~L~~~-~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 108 RLSPLERAVFVLREV-FDYPYEEIASIVGKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 578888877766554 589999999999999999999999888877764
No 211
>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=35.23 E-value=17 Score=30.97 Aligned_cols=28 Identities=11% Similarity=0.150 Sum_probs=22.9
Q ss_pred ccCCCccchhhccCccccceehhhhhhH
Q 041521 244 ATGEPLRVVSKRFGLGISTCHKLVLEVC 271 (524)
Q Consensus 244 atG~s~~~la~~FgiS~STvsriv~~v~ 271 (524)
.-+.+..+||...|++++||+|.+.++.
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le 72 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKSLA 72 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4456788999999999999998877643
No 212
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=34.77 E-value=20 Score=37.51 Aligned_cols=48 Identities=19% Similarity=0.260 Sum_probs=39.3
Q ss_pred CCChhhhhhhhhhcc---ccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWRL---ATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~L---atG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.++..++..+.++|. ..+.++.+||..+|||+..|+++-.+.+.-|..
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 478888888889884 245799999999999999999998877666544
No 213
>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=34.30 E-value=9.9 Score=28.24 Aligned_cols=42 Identities=17% Similarity=0.275 Sum_probs=30.2
Q ss_pred ccCCCccchhhccCccccceehhhhhhHHHHHhhcccccccCcchHHHHHHHhhh
Q 041521 244 ATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVLMPKFLQWPDELKMKQIKEEF 298 (524)
Q Consensus 244 atG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L~~~~I~~P~~ee~~~i~~~F 298 (524)
..|.++.++|...|+|++|++++.+. -+.|+.+.+..++..|
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~g-------------~~~~~~~~~~~ia~~l 48 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIENG-------------KRNPSLDTLKKIAKAL 48 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHTT-------------SSTSBHHHHHHHHHHH
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhcC-------------CCCCCHHHHHHHHHHH
Confidence 57889999999999999999988553 2346666666666655
No 214
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=34.28 E-value=8.8 Score=29.80 Aligned_cols=28 Identities=21% Similarity=0.294 Sum_probs=21.6
Q ss_pred hccccCCCccchhhccCccccceehhhh
Q 041521 241 WRLATGEPLRVVSKRFGLGISTCHKLVL 268 (524)
Q Consensus 241 ~~LatG~s~~~la~~FgiS~STvsriv~ 268 (524)
++-+.|.++.+++...|+|.+|++++-+
T Consensus 9 ~R~~~gls~~~lA~~~g~s~s~v~~iE~ 36 (64)
T PF13560_consen 9 LRERAGLSQAQLADRLGVSQSTVSRIER 36 (64)
T ss_dssp HHHCHTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 4456799999999999999999988743
No 215
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=34.18 E-value=21 Score=39.80 Aligned_cols=48 Identities=6% Similarity=0.120 Sum_probs=40.6
Q ss_pred CCChhhhhhhhhhcc---ccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWRL---ATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~L---atG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.++..++..+.++|. ..+.++..||..||||+..|+++-.+.+.-|..
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 588889999999884 467999999999999999999998877666554
No 216
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=33.93 E-value=11 Score=26.78 Aligned_cols=29 Identities=17% Similarity=0.178 Sum_probs=21.3
Q ss_pred cccCCCccchhhccCccccceehhhhhhH
Q 041521 243 LATGEPLRVVSKRFGLGISTCHKLVLEVC 271 (524)
Q Consensus 243 LatG~s~~~la~~FgiS~STvsriv~~v~ 271 (524)
|.++.+..+||..+|+|.++.+|.+.+.+
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 45677888999999999999999888753
No 217
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=33.23 E-value=36 Score=34.97 Aligned_cols=48 Identities=21% Similarity=0.358 Sum_probs=39.4
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.+|+.++.++.|+++ .|.++.+||...|+|.+||...+.+....|...
T Consensus 118 ~L~p~~R~vf~L~~~-~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~ 165 (290)
T PRK09635 118 RLGPAERVVFVLHEI-FGLPYQQIATTIGSQASTCRQLAHRARRKINES 165 (290)
T ss_pred hCCHHHHHHhhHHHH-hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 567788877766544 599999999999999999999998887777663
No 218
>PRK09191 two-component response regulator; Provisional
Probab=33.08 E-value=32 Score=33.58 Aligned_cols=52 Identities=13% Similarity=0.176 Sum_probs=41.0
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHhhcccc
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVLMPK 281 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~~L~~~ 281 (524)
.+|+.++-.+.|.++ .|.++.++|...|+|.+||...+.+....+...+...
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 467777776666654 6888999999999999999999888888777655433
No 219
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=32.05 E-value=30 Score=37.75 Aligned_cols=50 Identities=16% Similarity=0.189 Sum_probs=42.3
Q ss_pred CCCCCChhhhhhhhhhccccCCCccchhhcc-CccccceehhhhhhHHHHH
Q 041521 226 LRDAIPVRQRVAVCVWRLATGEPLRVVSKRF-GLGISTCHKLVLEVCSAIK 275 (524)
Q Consensus 226 ~r~~l~~e~rL~i~L~~LatG~s~~~la~~F-giS~STvsriv~~v~~aI~ 275 (524)
+.+.+...-+++|.|.+=-+|.++.+||..| |.+.|||...++++-..+.
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 3456777778999998888999999999999 5999999998888777554
No 220
>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=31.63 E-value=24 Score=30.75 Aligned_cols=45 Identities=9% Similarity=0.118 Sum_probs=31.9
Q ss_pred ChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 231 PVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 231 ~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
+..++-.+- .|+-...|+..||..+|||+.+|+..+++....|..
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 344554444 566688999999999999999999999998887765
No 221
>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=31.59 E-value=16 Score=34.49 Aligned_cols=23 Identities=22% Similarity=0.280 Sum_probs=0.0
Q ss_pred CCCccchhhccCccccceehhhh
Q 041521 246 GEPLRVVSKRFGLGISTCHKLVL 268 (524)
Q Consensus 246 G~s~~~la~~FgiS~STvsriv~ 268 (524)
+.++.+||+..|++.|||||++.
T Consensus 49 PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 49 PLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp -----------------------
T ss_pred CCCHHHHHHHhCCCHhHHHHHHc
Confidence 45788999999999999999854
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=31.53 E-value=36 Score=33.65 Aligned_cols=46 Identities=13% Similarity=0.163 Sum_probs=37.4
Q ss_pred CCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHH
Q 041521 228 DAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIK 275 (524)
Q Consensus 228 ~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~ 275 (524)
..+++.++=++.+ .+.|.++.+||..+|+|.+||...+.+...-+.
T Consensus 170 ~~Lt~re~evl~~--~a~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~ 215 (232)
T TIGR03541 170 GVLSEREREVLAW--TALGRRQADIAAILGISERTVENHLRSARRKLG 215 (232)
T ss_pred ccCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence 4688877755554 589999999999999999999988887766543
No 223
>PRK09492 treR trehalose repressor; Provisional
Probab=31.32 E-value=16 Score=36.84 Aligned_cols=23 Identities=17% Similarity=0.340 Sum_probs=20.5
Q ss_pred CCccchhhccCccccceehhhhh
Q 041521 247 EPLRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 247 ~s~~~la~~FgiS~STvsriv~~ 269 (524)
.+.++||+..|||.+||||+++.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCC
Confidence 46789999999999999999874
No 224
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=31.20 E-value=23 Score=36.79 Aligned_cols=47 Identities=13% Similarity=0.219 Sum_probs=39.8
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+|+.++-++.|++ -.|.++.+||..+|+|.+||...+.+....|.+
T Consensus 153 ~Lp~~~R~v~~L~~-~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 153 HLPPRQRAVLILRD-VLGWSAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred hCCHHHhhhhhhHH-hhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 57788887777765 478999999999999999999998888887776
No 225
>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=31.07 E-value=34 Score=25.81 Aligned_cols=25 Identities=16% Similarity=0.282 Sum_probs=20.2
Q ss_pred CccchhhccCccccceehhhhhhHH
Q 041521 248 PLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 248 s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
+..+|+..||+|.+||++.+....+
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~ 51 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA 51 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4668999999999999887776543
No 226
>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=30.90 E-value=22 Score=27.07 Aligned_cols=26 Identities=19% Similarity=0.286 Sum_probs=21.8
Q ss_pred cCCCccchhhccCccccceehhhhhh
Q 041521 245 TGEPLRVVSKRFGLGISTCHKLVLEV 270 (524)
Q Consensus 245 tG~s~~~la~~FgiS~STvsriv~~v 270 (524)
.+.+..+++..+|++.+|+++.+..+
T Consensus 19 ~~~~~~ei~~~~~i~~~~i~~~l~~L 44 (78)
T cd00090 19 GPLTVSELAERLGLSQSTVSRHLKKL 44 (78)
T ss_pred CCcCHHHHHHHHCcCHhHHHHHHHHH
Confidence 34888999999999999998887764
No 227
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=30.64 E-value=28 Score=38.04 Aligned_cols=48 Identities=17% Similarity=0.236 Sum_probs=40.9
Q ss_pred CCCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHH
Q 041521 227 RDAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAI 274 (524)
Q Consensus 227 r~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI 274 (524)
.+.+...-+++|.|.+=-+|.++..||..||.+.|||...++++-..+
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 346667778888888878899999999999999999999988887755
No 228
>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=30.01 E-value=35 Score=33.41 Aligned_cols=21 Identities=14% Similarity=0.186 Sum_probs=17.1
Q ss_pred chhhccCccccceehhhhhhH
Q 041521 251 VVSKRFGLGISTCHKLVLEVC 271 (524)
Q Consensus 251 ~la~~FgiS~STvsriv~~v~ 271 (524)
+|+..||||+.||.+.+....
T Consensus 29 eLa~~~gVSR~TVR~Al~~L~ 49 (233)
T TIGR02404 29 ELMDQYGASRETVRKALNLLT 49 (233)
T ss_pred HHHHHHCCCHHHHHHHHHHHH
Confidence 578899999999988776543
No 229
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=29.93 E-value=14 Score=35.50 Aligned_cols=29 Identities=14% Similarity=0.287 Sum_probs=25.1
Q ss_pred hccccCCCccchhhccCccccceehhhhh
Q 041521 241 WRLATGEPLRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 241 ~~LatG~s~~~la~~FgiS~STvsriv~~ 269 (524)
.++..|.++..++..+|||.+|++|++..
T Consensus 167 ~~~~~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 167 KLLDKGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 34678999999999999999999998763
No 230
>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=29.89 E-value=14 Score=37.45 Aligned_cols=21 Identities=19% Similarity=0.411 Sum_probs=19.1
Q ss_pred CccchhhccCccccceehhhh
Q 041521 248 PLRVVSKRFGLGISTCHKLVL 268 (524)
Q Consensus 248 s~~~la~~FgiS~STvsriv~ 268 (524)
+..+||...|||++||||+++
T Consensus 3 ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 3 TIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred cHHHHHHHhCCCHHHHHHHhC
Confidence 567999999999999999986
No 231
>PF13551 HTH_29: Winged helix-turn helix
Probab=29.70 E-value=74 Score=26.79 Aligned_cols=77 Identities=16% Similarity=0.098 Sum_probs=43.7
Q ss_pred CHhhHHHHcCCCHHHHHHHHHHhhccc----cc-cCCCCCCC--CChhhhhhhhhhccccC------CCccchhhc----
Q 041521 193 PEEEFWRDFRMSKATFEMICEELESTV----MK-KNTMLRDA--IPVRQRVAVCVWRLATG------EPLRVVSKR---- 255 (524)
Q Consensus 193 ~d~~F~~~fRmSr~tF~~Lv~~L~~~i----~~-~~t~~r~~--l~~e~rL~i~L~~LatG------~s~~~la~~---- 255 (524)
+..+.-+.+++++.|+...+......- .. ....++.. ++++++-.+.=+..... -+...|+..
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~ 93 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEE 93 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHh
Confidence 378899999999999999988766532 11 11122322 56665543322222221 233444442
Q ss_pred -c--Cccccceehhhhh
Q 041521 256 -F--GLGISTCHKLVLE 269 (524)
Q Consensus 256 -F--giS~STvsriv~~ 269 (524)
+ .+|.+||.+++++
T Consensus 94 ~~~~~~s~~ti~r~L~~ 110 (112)
T PF13551_consen 94 EFGIDVSPSTIRRILKR 110 (112)
T ss_pred ccCccCCHHHHHHHHHH
Confidence 2 4567778777654
No 232
>PF14942 Muted: Organelle biogenesis, Muted-like protein
Probab=29.50 E-value=69 Score=29.73 Aligned_cols=39 Identities=21% Similarity=0.474 Sum_probs=25.8
Q ss_pred HHHHHHHHHhhhhhhhhhhhhhhcchhhhhhhHHHHhhh
Q 041521 77 EEKREQQQYSIHSHQDKLLVDDNHKRKEQAMNDYFHQLQ 115 (524)
Q Consensus 77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 (524)
+.+++-++...+.+..++-++..|+++.+-..+.|++|+
T Consensus 104 ~~~~~we~f~~e~~~~~~~vdee~~~~~~~l~e~Y~~~~ 142 (145)
T PF14942_consen 104 QRKQEWEEFMKEQQQKKQRVDEEFREKEERLKEQYSEME 142 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 334444455555666777777778877777777777774
No 233
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=29.45 E-value=26 Score=35.51 Aligned_cols=45 Identities=16% Similarity=0.152 Sum_probs=36.0
Q ss_pred CCCChhhhhhhhhhcccc---CCCccchhhccCccccceehhhhhhHH
Q 041521 228 DAIPVRQRVAVCVWRLAT---GEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 228 ~~l~~e~rL~i~L~~Lat---G~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
..+++-++.+-.|..|+. +.+..+|+...|+++||++|++...+.
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 346667777777777763 467899999999999999999887765
No 234
>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=29.38 E-value=20 Score=27.56 Aligned_cols=31 Identities=6% Similarity=0.220 Sum_probs=25.9
Q ss_pred CCccchhhccCccccceehhhhhhHHHHHhh
Q 041521 247 EPLRVVSKRFGLGISTCHKLVLEVCSAIKTV 277 (524)
Q Consensus 247 ~s~~~la~~FgiS~STvsriv~~v~~aI~~~ 277 (524)
.++...|...++|+++|++.+.++-..+-..
T Consensus 14 gs~~~AA~~l~is~~~vs~~i~~LE~~lg~~ 44 (60)
T PF00126_consen 14 GSISAAAEELGISQSAVSRQIKQLEEELGVP 44 (60)
T ss_dssp SSHHHHHHHCTSSHHHHHHHHHHHHHHHTS-
T ss_pred CCHHHHHHHhhccchHHHHHHHHHHHHhCCe
Confidence 3788999999999999999999887766543
No 235
>PHA00738 putative HTH transcription regulator
Probab=28.82 E-value=16 Score=32.20 Aligned_cols=31 Identities=13% Similarity=0.093 Sum_probs=24.1
Q ss_pred ccccC--CCccchhhccCccccceehhhhhhHH
Q 041521 242 RLATG--EPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 242 ~LatG--~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
+|+.| .+-.+|+..|++|++|||+.+.-.-.
T Consensus 20 lL~~~e~~~V~eLae~l~lSQptVS~HLKvLre 52 (108)
T PHA00738 20 LIAENYILSASLISHTLLLSYTTVLRHLKILNE 52 (108)
T ss_pred HHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHH
Confidence 34553 67789999999999999998765433
No 236
>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=28.56 E-value=18 Score=31.18 Aligned_cols=65 Identities=18% Similarity=0.275 Sum_probs=37.4
Q ss_pred cCCCHHHHHHHHHHhhccccccCCCCCCCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhh--hHHHHHh
Q 041521 201 FRMSKATFEMICEELESTVMKKNTMLRDAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLE--VCSAIKT 276 (524)
Q Consensus 201 fRmSr~tF~~Lv~~L~~~i~~~~t~~r~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~--v~~aI~~ 276 (524)
.-|+-+.|-.|.......-... +. ......+.+. -+ .+..||..||+|.||++|+... .=.||..
T Consensus 11 ~qmTg~ell~L~~~~~~~~~~~-~~-~~~~~~~~~y-------vy--G~~GlAklfgcSv~Ta~RiK~sG~id~AI~Q 77 (96)
T PF12964_consen 11 WQMTGEELLFLLKEGKTNSEKQ-TS-QKAKKDEKKY-------VY--GLKGLAKLFGCSVPTANRIKKSGKIDPAITQ 77 (96)
T ss_pred HHhhHHHHHHHHHHHhcCCCcc-CC-ccccCcccce-------ee--hHHHHHHHhCCCchhHHHHHhcCCccHHHHH
Confidence 3477777777777663322111 11 1222233321 12 3678999999999999998754 2245544
No 237
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=28.37 E-value=14 Score=29.39 Aligned_cols=21 Identities=14% Similarity=0.300 Sum_probs=17.8
Q ss_pred CccchhhccCccccceehhhh
Q 041521 248 PLRVVSKRFGLGISTCHKLVL 268 (524)
Q Consensus 248 s~~~la~~FgiS~STvsriv~ 268 (524)
+.++|+...|||.+||+++++
T Consensus 2 t~~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHC
Confidence 456899999999999998754
No 238
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=28.34 E-value=15 Score=26.85 Aligned_cols=18 Identities=11% Similarity=0.366 Sum_probs=15.7
Q ss_pred chhhccCccccceehhhh
Q 041521 251 VVSKRFGLGISTCHKLVL 268 (524)
Q Consensus 251 ~la~~FgiS~STvsriv~ 268 (524)
+++...|||.+||+++++
T Consensus 2 ~lA~~~gvs~~tvs~~l~ 19 (52)
T cd01392 2 DIARAAGVSVATVSRVLN 19 (52)
T ss_pred cHHHHHCcCHHHHHHHHc
Confidence 688999999999998765
No 239
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=28.13 E-value=17 Score=37.01 Aligned_cols=22 Identities=23% Similarity=0.333 Sum_probs=19.6
Q ss_pred CccchhhccCccccceehhhhh
Q 041521 248 PLRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 248 s~~~la~~FgiS~STvsriv~~ 269 (524)
+..+||...|||.+||||+++.
T Consensus 7 ti~dIA~~agVS~~TVSrvLn~ 28 (331)
T PRK14987 7 VLQDVADRVGVTKMTVSRFLRN 28 (331)
T ss_pred cHHHHHHHhCCCHHHhhhhhCC
Confidence 5679999999999999999754
No 240
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=28.13 E-value=35 Score=26.45 Aligned_cols=23 Identities=17% Similarity=0.345 Sum_probs=17.1
Q ss_pred ccchhhccCccccceehhhhhhH
Q 041521 249 LRVVSKRFGLGISTCHKLVLEVC 271 (524)
Q Consensus 249 ~~~la~~FgiS~STvsriv~~v~ 271 (524)
...|+..||+|.+||.+.+...+
T Consensus 27 ~~~la~~~~vsr~tvr~al~~L~ 49 (64)
T PF00392_consen 27 ERELAERYGVSRTTVREALRRLE 49 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHhccCCcHHHHHHHHHH
Confidence 35789999999999887766543
No 241
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=28.10 E-value=36 Score=38.83 Aligned_cols=50 Identities=14% Similarity=0.199 Sum_probs=42.2
Q ss_pred CCCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 227 RDAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 227 r~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
.+.+...-+|+|.|.+=-++.++..||..||.+.|||...++++-..|.+
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 34566677899999888899999999999999999999888887776543
No 242
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=28.00 E-value=26 Score=30.76 Aligned_cols=31 Identities=16% Similarity=0.274 Sum_probs=24.3
Q ss_pred cCCCccchhhccCccccceehhhhhhHHHHH
Q 041521 245 TGEPLRVVSKRFGLGISTCHKLVLEVCSAIK 275 (524)
Q Consensus 245 tG~s~~~la~~FgiS~STvsriv~~v~~aI~ 275 (524)
.|.++.+.|...|||++|+++++...-.-|.
T Consensus 56 egl~QeeaA~~MgVSR~T~~ril~~ARkKiA 86 (106)
T PF02001_consen 56 EGLSQEEAAERMGVSRPTFQRILESARKKIA 86 (106)
T ss_pred cCCCHHHHHHHcCCcHHHHHHHHHHHHHHHH
Confidence 3577889999999999999999876444333
No 243
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=27.77 E-value=65 Score=26.70 Aligned_cols=35 Identities=20% Similarity=0.452 Sum_probs=28.7
Q ss_pred CcccccccCCCCCCHhhHHHHcCCCHHHHHHHHHHhhc
Q 041521 180 SKDWWDERNHPDFPEEEFWRDFRMSKATFEMICEELES 217 (524)
Q Consensus 180 ~~~w~~r~~~~~~~d~~F~~~fRmSr~tF~~Lv~~L~~ 217 (524)
++.||.. ..-.++..+..||||+..|..+++.|-.
T Consensus 14 E~~ww~~---~GaKe~aIre~fGls~~rYyq~Ln~LiD 48 (77)
T PF11662_consen 14 ERRWWRH---GGAKEEAIREEFGLSPTRYYQRLNALID 48 (77)
T ss_pred HHHhCcC---CCCcHHHHHHHHCCCHHHHHHHHHHHhC
Confidence 3568875 5678999999999999999988887754
No 244
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=27.61 E-value=32 Score=31.13 Aligned_cols=43 Identities=12% Similarity=0.098 Sum_probs=30.7
Q ss_pred CCChhhh-hhhhhhccccCCCccchhhccCccccceehhhhhhHH
Q 041521 229 AIPVRQR-VAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 229 ~l~~e~r-L~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
.+++.+- ++..|+ -..|.+..+|+..++++++|+++.+.....
T Consensus 37 glt~~q~~vL~~l~-~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~ 80 (144)
T PRK11512 37 DITAAQFKVLCSIR-CAACITPVELKKVLSVDLGALTRMLDRLVC 80 (144)
T ss_pred CCCHHHHHHHHHHH-HcCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4555443 444443 345688999999999999999998877543
No 245
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=27.54 E-value=52 Score=32.80 Aligned_cols=45 Identities=9% Similarity=0.028 Sum_probs=36.6
Q ss_pred CCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHH
Q 041521 228 DAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAI 274 (524)
Q Consensus 228 ~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI 274 (524)
..+++.|+ -+|.+++.|.+..+||...+||..||..++..+..-+
T Consensus 178 ~~LT~rE~--evl~~~a~G~t~~eIa~~l~is~~TV~~h~~~~~~KL 222 (240)
T PRK10188 178 MNFSKREK--EILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKF 222 (240)
T ss_pred CCCCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 36777776 4566779999999999999999999988887765544
No 246
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=27.01 E-value=23 Score=35.02 Aligned_cols=44 Identities=7% Similarity=0.092 Sum_probs=35.4
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHH
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAI 274 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI 274 (524)
.+++.++ -.|..++.|.+..+||...++|.+||..++..+..-+
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 4566789999999999999999999998887765543
No 247
>PRK09526 lacI lac repressor; Reviewed
Probab=26.74 E-value=17 Score=37.10 Aligned_cols=23 Identities=17% Similarity=0.236 Sum_probs=20.3
Q ss_pred CCccchhhccCccccceehhhhh
Q 041521 247 EPLRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 247 ~s~~~la~~FgiS~STvsriv~~ 269 (524)
.+..+||...|||.+||||+++.
T Consensus 6 ~ti~dIA~~aGVS~~TVSrvLn~ 28 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRVLNQ 28 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHhcC
Confidence 36789999999999999999873
No 248
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=26.46 E-value=20 Score=36.50 Aligned_cols=22 Identities=14% Similarity=0.381 Sum_probs=19.5
Q ss_pred CccchhhccCccccceehhhhh
Q 041521 248 PLRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 248 s~~~la~~FgiS~STvsriv~~ 269 (524)
+..+||...|||++||||+++.
T Consensus 3 ti~dIA~~agVS~~TVSrvln~ 24 (327)
T PRK10339 3 TLKDIAIEAGVSLATVSRVLND 24 (327)
T ss_pred CHHHHHHHhCCCHHhhhhhhcC
Confidence 5679999999999999998764
No 249
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=26.40 E-value=24 Score=25.40 Aligned_cols=27 Identities=7% Similarity=0.076 Sum_probs=22.1
Q ss_pred CCCccchhhccCccccceehhhhhhHH
Q 041521 246 GEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 246 G~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
+.+..+++..|+++.+|+++.+..+..
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~~ 40 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLEE 40 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 456778999999999999988876544
No 250
>PF13701 DDE_Tnp_1_4: Transposase DDE domain group 1
Probab=26.18 E-value=1.7e+02 Score=32.12 Aligned_cols=87 Identities=11% Similarity=0.142 Sum_probs=47.1
Q ss_pred CccccCCcceeeeEecCCCccccccccccccccCCCCccccccccccCCCceeeecCCCCCCCCChHHHHh--HHHHhhh
Q 041521 305 PNVGGSMYTTHIPIIAPKISVASYFNKRHTERNQKTSYSITVQGVVDTKGVFTDVCIGWPGSMPDDQVLER--SALFQRA 382 (524)
Q Consensus 305 P~~vGaIDgThIpI~~P~~~~~~y~n~~~~~rn~K~~~Si~vq~v~D~~g~fi~v~~g~pGS~hDs~V~~~--S~L~~~l 382 (524)
..++-=||.|+.++. ...+...||. |.+.++++.+. +.....|.++.+. =-||++|-+.=... ..+...+
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 KEIVLDIDSTVDDVH--GEQEGAVFNT---YYGEDGYHPLV--AFDGQTGYLLAAE-LRPGNVHSAKGAAEFLKRVLRRL 211 (448)
T ss_pred ceEEEecccccccch--hhcccccccc---cCCCcccccce--eccCCCCceEEEE-ccCCCCChHHHHHHHHHHHHHHH
Confidence 346667899986654 2233344543 23344555442 2334578888764 45999987753221 0122333
Q ss_pred hccccc-eEEEEcccCCC
Q 041521 383 DRGLLK-DVWIVGNSGYP 399 (524)
Q Consensus 383 ~~~~~~-g~~lLGD~gYp 399 (524)
.+..+. .-.+=||+||-
T Consensus 212 r~~~~~~~ILvR~DSgF~ 229 (448)
T PF13701_consen 212 RQRWPDTRILVRGDSGFA 229 (448)
T ss_pred hhhCccceEEEEecCccC
Confidence 333332 34688999993
No 251
>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=25.94 E-value=16 Score=28.69 Aligned_cols=27 Identities=11% Similarity=0.174 Sum_probs=22.6
Q ss_pred CCCccchhhccCccccceehhhhhhHH
Q 041521 246 GEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 246 G~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
+.+..+|+...|+++++|++++.....
T Consensus 22 ~~t~~eIa~~l~i~~~~v~~~L~~L~~ 48 (68)
T PF01978_consen 22 PATAEEIAEELGISRSTVYRALKSLEE 48 (68)
T ss_dssp HEEHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 467789999999999999988877544
No 252
>COG3293 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.87 E-value=13 Score=32.83 Aligned_cols=88 Identities=14% Similarity=0.195 Sum_probs=55.6
Q ss_pred ccccccCCCceeeecCCC-----CCCCCChHHHHhHHHHhhhhccccceEEEEcccCCCCccccccccccCC----ccc-
Q 041521 346 VQGVVDTKGVFTDVCIGW-----PGSMPDDQVLERSALFQRADRGLLKDVWIVGNSGYPLMDWVMVPYTQKN----LTW- 415 (524)
Q Consensus 346 vq~v~D~~g~fi~v~~g~-----pGS~hDs~V~~~S~L~~~l~~~~~~g~~lLGD~gYpl~~~LmtPy~~~~----lt~- 415 (524)
.+.++|..|+++....+- +...++.. + ..+ .-++.|.+|...+|-+-|-..+. ...
T Consensus 3 ~~~l~D~~~~~i~~~lp~~~~~~~~~~~~~~---~----~~v-------~~~i~~~~~~g~~wr~~p~~~~~~~~~~~~~ 68 (124)
T COG3293 3 LHALVDAEWRPVEPLLPPAKYGGPPGVTLLR---D----REV-------LNGIADLLYTGCAWRALPADFPPATTVIPYR 68 (124)
T ss_pred cccccccccceeeccCCCcccCCCCCCcccc---c----HHH-------HHHHHHHhccchHHHHhHHHhCCCceEeCCC
Confidence 567899999998776651 11111111 0 011 11567888887777665543321 111
Q ss_pred -chhhcccccccchhhhhhccccccccccccccc
Q 041521 416 -TQHAFNEKIGDIQAVAKDAFARLKGRWACLQKR 448 (524)
Q Consensus 416 -~q~~FN~~ls~~R~~VE~aFG~LK~RFriL~~~ 448 (524)
.+.-++..+...|..+|+.|+.+| .|+.+...
T Consensus 69 ~~~~~~~~g~~~~~~~~~~~f~~~~-~~r~~~~~ 101 (124)
T COG3293 69 RFRRWFKRGLWKRRNLVERTFGRLK-QFRRTATR 101 (124)
T ss_pred cchhhHHHHHHHHHHHHHHHHHHHh-cccceecc
Confidence 257778889999999999999888 47776654
No 253
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=25.79 E-value=18 Score=36.98 Aligned_cols=23 Identities=17% Similarity=0.182 Sum_probs=20.6
Q ss_pred CCccchhhccCccccceehhhhh
Q 041521 247 EPLRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 247 ~s~~~la~~FgiS~STvsriv~~ 269 (524)
.+.++||...|||.+||||+++.
T Consensus 7 ~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 7 ITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHHCC
Confidence 46889999999999999999865
No 254
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=25.62 E-value=24 Score=33.65 Aligned_cols=43 Identities=12% Similarity=0.116 Sum_probs=35.9
Q ss_pred CCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHH
Q 041521 228 DAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 228 ~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
..+++.|+ -.|..++.|.+..+||...++|.+||..++..+..
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 35888876 56778899999999999999999999888766544
No 255
>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=25.36 E-value=27 Score=34.72 Aligned_cols=44 Identities=14% Similarity=0.171 Sum_probs=32.6
Q ss_pred CChhhhhhhhhhccc---cCCCccchhhccCccccceehhhhhhHHH
Q 041521 230 IPVRQRVAVCVWRLA---TGEPLRVVSKRFGLGISTCHKLVLEVCSA 273 (524)
Q Consensus 230 l~~e~rL~i~L~~La---tG~s~~~la~~FgiS~STvsriv~~v~~a 273 (524)
+.+-++.+-.|..|+ .+.+..+|+...|+++||++|++...+..
T Consensus 5 v~sl~ral~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~ 51 (248)
T TIGR02431 5 VASLARGLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVEL 51 (248)
T ss_pred HHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 334455555566665 35788999999999999999998876543
No 256
>PF03333 PapB: Adhesin biosynthesis transcription regulatory protein; InterPro: IPR004356 P pili, or fimbriae, are ~68A in diameter and 1 micron in length, the bulk of which is a fibre composed of the main structural protein PapA []. At its tip, the pilus is terminated by a fibrillum consisting of repeating units of the PapE protein. This, in turn, is topped by the adhesins, PapF and PapG, both of which are needed for receptor binding. The tip fibrillum is anchored to the main PapA fibre by the PapK pilus-adaptor protein. PapH, an outer membrane protein, then anchors the entire rod in the bacterial envelope []. A cytoplasmic chaperone (PapD) assists in assembling the monomers of the macromolecule in the membrane. All of the functional pap genes are arranged in a cluster (operon) on the Escherichia coli genome. It is believed that selective pressure exerted by the host's urinal and intestinal tract isoreceptors forced the spread of this operon to other strains via lateral transfer []. PapB, encoded within the cluster, acts as a transcriptional regulator of the functional pap genes and is located in the bacterial cytoplasm []. Its mechanism involves differential binding to separate sites in the cluster, suggesting that this protein is both an activator and repressor of pilus-adhesion transcription. The protein shares similarity with other E. coli fimbrial- adhesion transcription regulators, such as AfaA, DaaA and FanB. ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 3M8J_A.
Probab=25.32 E-value=48 Score=28.34 Aligned_cols=55 Identities=16% Similarity=0.230 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHhhccccccCCCCCCCCChhhhhhhhh-hccccCCCccchhhccCccccceehhhhhh
Q 041521 202 RMSKATFEMICEELESTVMKKNTMLRDAIPVRQRVAVCV-WRLATGEPLRVVSKRFGLGISTCHKLVLEV 270 (524)
Q Consensus 202 RmSr~tF~~Lv~~L~~~i~~~~t~~r~~l~~e~rL~i~L-~~LatG~s~~~la~~FgiS~STvsriv~~v 270 (524)
.|+.+.|..|++.-. +..+ ++..+| -+|-.|.+-..++.++||+++-.++.+.++
T Consensus 22 ~vs~e~F~lLl~ls~-------------IrS~-kiI~AL~dyLV~G~srkeac~~~gV~~syfs~~L~rL 77 (91)
T PF03333_consen 22 KVSEEHFWLLLELSS-------------IRSE-KIIAALRDYLVDGLSRKEACERHGVNQSYFSRALNRL 77 (91)
T ss_dssp -S-HHHHHHHHHHS-----------------H-HHHHHHHHHHTT---HHHHHHHTT--HHHHHHHHHHH
T ss_pred CcCHHHHHHHHHHCC-------------CCcH-HHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHH
Confidence 366777777766422 2223 344444 678899999999999999999988876654
No 257
>PRK09483 response regulator; Provisional
Probab=25.21 E-value=25 Score=32.96 Aligned_cols=43 Identities=14% Similarity=0.251 Sum_probs=34.1
Q ss_pred CCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHH
Q 041521 228 DAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 228 ~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
..+++.++-.+ ..++.|.+..+||..+++|.+||..++..+..
T Consensus 147 ~~Lt~rE~~vl--~~~~~G~~~~~Ia~~l~is~~TV~~~~~~i~~ 189 (217)
T PRK09483 147 ASLSERELQIM--LMITKGQKVNEISEQLNLSPKTVNSYRYRMFS 189 (217)
T ss_pred cccCHHHHHHH--HHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 35777776544 45789999999999999999999888776544
No 258
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=25.21 E-value=22 Score=35.56 Aligned_cols=36 Identities=19% Similarity=0.114 Sum_probs=30.3
Q ss_pred hhhhhhhhhccccCCCccchhhccCccccceehhhh
Q 041521 233 RQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVL 268 (524)
Q Consensus 233 e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~ 268 (524)
..++.-.|+.|..--+|++|+..+|++.|.++|+++
T Consensus 10 ~~~~v~~lr~lk~~~ty~el~~~~g~p~~~l~RYv~ 45 (238)
T PRK08558 10 QLRAVRVLRSLKKTYTYEELSSITGLPESVLNRYVN 45 (238)
T ss_pred HHHHHHHHHHHhcccCHHHHHHHHCCCHHHHHHHHc
Confidence 345556678888888999999999999999999976
No 259
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=24.88 E-value=40 Score=32.91 Aligned_cols=50 Identities=14% Similarity=0.149 Sum_probs=35.5
Q ss_pred CCCCChhhhhhhhh----hccc--cCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 227 RDAIPVRQRVAVCV----WRLA--TGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 227 r~~l~~e~rL~i~L----~~La--tG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
...++..|+-++.+ -|+- ...+..+||+.||||+||++.++++...-|..
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 34677777544333 3343 35778899999999999999998887665544
No 260
>PRK00215 LexA repressor; Validated
Probab=24.56 E-value=32 Score=33.08 Aligned_cols=27 Identities=19% Similarity=0.246 Sum_probs=22.6
Q ss_pred CCCccchhhccCc-cccceehhhhhhHH
Q 041521 246 GEPLRVVSKRFGL-GISTCHKLVLEVCS 272 (524)
Q Consensus 246 G~s~~~la~~Fgi-S~STvsriv~~v~~ 272 (524)
+.++.+|+..+|+ +++|+++++.....
T Consensus 23 ~~s~~ela~~~~~~~~~tv~~~l~~L~~ 50 (205)
T PRK00215 23 PPSRREIADALGLRSPSAVHEHLKALER 50 (205)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 3478899999999 99999998876544
No 261
>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=24.47 E-value=18 Score=24.82 Aligned_cols=23 Identities=13% Similarity=0.280 Sum_probs=18.4
Q ss_pred CccchhhccCccccceehhhhhh
Q 041521 248 PLRVVSKRFGLGISTCHKLVLEV 270 (524)
Q Consensus 248 s~~~la~~FgiS~STvsriv~~v 270 (524)
+..+||+..|++.-||+|++.++
T Consensus 4 tr~diA~~lG~t~ETVSR~l~~l 26 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRILKKL 26 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHHHHH
Confidence 45789999999999999998764
No 262
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=24.26 E-value=21 Score=36.79 Aligned_cols=22 Identities=18% Similarity=0.465 Sum_probs=19.6
Q ss_pred CccchhhccCccccceehhhhh
Q 041521 248 PLRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 248 s~~~la~~FgiS~STvsriv~~ 269 (524)
+..+||...|||.+||||+++.
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn~ 24 (346)
T PRK10401 3 TIRDVARQAGVSVATVSRVLNN 24 (346)
T ss_pred CHHHHHHHhCCCHHHHHHHHCC
Confidence 5789999999999999999863
No 263
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=24.12 E-value=39 Score=27.09 Aligned_cols=42 Identities=12% Similarity=0.109 Sum_probs=36.8
Q ss_pred hhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHHh
Q 041521 235 RVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIKT 276 (524)
Q Consensus 235 rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~~ 276 (524)
++-.++.+|+...+..+.++..|+...+|.+.+..+-..+..
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 445678889999999999999999999999999998888775
No 264
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=24.10 E-value=21 Score=36.26 Aligned_cols=22 Identities=14% Similarity=0.203 Sum_probs=19.4
Q ss_pred CccchhhccCccccceehhhhh
Q 041521 248 PLRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 248 s~~~la~~FgiS~STvsriv~~ 269 (524)
+.++||...|||.+||||+++.
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 4679999999999999998764
No 265
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=24.06 E-value=44 Score=27.33 Aligned_cols=27 Identities=19% Similarity=0.257 Sum_probs=23.0
Q ss_pred CCCccchhhccCccccceehhhhhhHH
Q 041521 246 GEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 246 G~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
+.+..+++..++++++++++.+.+...
T Consensus 24 ~~~~~~la~~~~~s~~~i~~~l~~L~~ 50 (101)
T smart00347 24 PLSVSELAKRLGVSPSTVTRVLDRLEK 50 (101)
T ss_pred CcCHHHHHHHHCCCchhHHHHHHHHHH
Confidence 467889999999999999998887655
No 266
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=24.05 E-value=44 Score=38.19 Aligned_cols=47 Identities=13% Similarity=0.165 Sum_probs=38.6
Q ss_pred CCChhhhhhhhhhcc---ccCCCccchhhccCccccceehhhhhhHHHHH
Q 041521 229 AIPVRQRVAVCVWRL---ATGEPLRVVSKRFGLGISTCHKLVLEVCSAIK 275 (524)
Q Consensus 229 ~l~~e~rL~i~L~~L---atG~s~~~la~~FgiS~STvsriv~~v~~aI~ 275 (524)
.+|..++..+.++|. ..+.++..||..||||+..|+++-.+.+.-|.
T Consensus 556 ~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr 605 (619)
T PRK05658 556 SLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605 (619)
T ss_pred cCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence 478888888888885 36788999999999999999998777665544
No 267
>PRK14999 histidine utilization repressor; Provisional
Probab=23.73 E-value=49 Score=32.65 Aligned_cols=48 Identities=15% Similarity=0.268 Sum_probs=30.3
Q ss_pred HHHHHHHhhccccccCCCCCCCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhH
Q 041521 208 FEMICEELESTVMKKNTMLRDAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVC 271 (524)
Q Consensus 208 F~~Lv~~L~~~i~~~~t~~r~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~ 271 (524)
...|.+.|...|....-.....+|.|. +|++.||||+.||.+.+....
T Consensus 14 y~qi~~~i~~~I~~g~~~~G~~LPsE~----------------eLa~~~gVSR~TVR~Al~~L~ 61 (241)
T PRK14999 14 YETVKQDICKKIAGGVWQPHDRIPSEA----------------ELVAQYGFSRMTINRALRELT 61 (241)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCCCHH----------------HHHHHHCCCHHHHHHHHHHHH
Confidence 455556666555432222234566554 688999999999988776643
No 268
>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=23.67 E-value=20 Score=31.77 Aligned_cols=26 Identities=15% Similarity=0.203 Sum_probs=22.2
Q ss_pred cCCCccchhhccCccccceehhhhhh
Q 041521 245 TGEPLRVVSKRFGLGISTCHKLVLEV 270 (524)
Q Consensus 245 tG~s~~~la~~FgiS~STvsriv~~v 270 (524)
.|.+...||+.|+||+||+..+..+.
T Consensus 79 AGlt~~aIAd~F~iS~s~~~nft~~n 104 (126)
T PF10654_consen 79 AGLTCYAIADYFKISKSTVFNFTQNN 104 (126)
T ss_pred cCCChHHHHHHHhHHHHHHHHHHHHh
Confidence 47889999999999999998876554
No 269
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=23.64 E-value=21 Score=25.17 Aligned_cols=22 Identities=23% Similarity=0.285 Sum_probs=18.1
Q ss_pred CccchhhccCccccceehhhhh
Q 041521 248 PLRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 248 s~~~la~~FgiS~STvsriv~~ 269 (524)
+..+++..+|||.+|+.+++.+
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 3567899999999999888665
No 270
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=23.54 E-value=56 Score=31.90 Aligned_cols=49 Identities=16% Similarity=0.373 Sum_probs=31.3
Q ss_pred HHHHHHHHhhccccccCCCCCCCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhH
Q 041521 207 TFEMICEELESTVMKKNTMLRDAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVC 271 (524)
Q Consensus 207 tF~~Lv~~L~~~i~~~~t~~r~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~ 271 (524)
-+..|.+.|...|....-.....+|.|. +|+..||||+.||.+.+....
T Consensus 9 ~y~~i~~~l~~~I~~g~~~~G~~LPsE~----------------eLa~~~~VSR~TvR~Al~~L~ 57 (238)
T TIGR02325 9 LWRQIADKIEQEIAAGHLRAGDYLPAEM----------------QLAERFGVNRHTVRRAIAALV 57 (238)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCcCHH----------------HHHHHHCCCHHHHHHHHHHHH
Confidence 3555666666655432222234566554 688999999999988766543
No 271
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=23.28 E-value=55 Score=31.99 Aligned_cols=22 Identities=14% Similarity=0.261 Sum_probs=17.5
Q ss_pred cchhhccCccccceehhhhhhH
Q 041521 250 RVVSKRFGLGISTCHKLVLEVC 271 (524)
Q Consensus 250 ~~la~~FgiS~STvsriv~~v~ 271 (524)
++|+..||||+.||.+.+....
T Consensus 29 ~eLa~~~~VSR~TVR~Al~~L~ 50 (230)
T TIGR02018 29 HELVAQYGCSRMTVNRALRELT 50 (230)
T ss_pred HHHHHHHCCCHHHHHHHHHHHH
Confidence 3678999999999988776543
No 272
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=23.22 E-value=57 Score=32.18 Aligned_cols=48 Identities=15% Similarity=0.376 Sum_probs=30.5
Q ss_pred HHHHHHHhhccccccCCCCCCCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhH
Q 041521 208 FEMICEELESTVMKKNTMLRDAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVC 271 (524)
Q Consensus 208 F~~Lv~~L~~~i~~~~t~~r~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~ 271 (524)
...|.+.|...|....-.....+|.|. +|+..||||+.||.+.+....
T Consensus 7 y~qi~~~L~~~I~~g~~~~G~~LPsE~----------------eL~~~~~VSR~TvR~Al~~L~ 54 (240)
T PRK09764 7 YRQIADRIREQIARGELKPGDALPTES----------------ALQTEFGVSRVTVRQALRQLV 54 (240)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCCCHH----------------HHHHHHCCCHHHHHHHHHHHH
Confidence 455666666555432222234566554 688999999999988776643
No 273
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=22.90 E-value=23 Score=36.19 Aligned_cols=22 Identities=23% Similarity=0.433 Sum_probs=19.8
Q ss_pred CccchhhccCccccceehhhhh
Q 041521 248 PLRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 248 s~~~la~~FgiS~STvsriv~~ 269 (524)
+..+||...|||++||||+++.
T Consensus 3 Ti~dIA~~agVS~~TVSrvLn~ 24 (341)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINK 24 (341)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 5779999999999999999874
No 274
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=22.67 E-value=59 Score=32.20 Aligned_cols=50 Identities=18% Similarity=0.351 Sum_probs=34.4
Q ss_pred HHHHHHHHHhhccccccCCCCCCCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhH
Q 041521 206 ATFEMICEELESTVMKKNTMLRDAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVC 271 (524)
Q Consensus 206 ~tF~~Lv~~L~~~i~~~~t~~r~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~ 271 (524)
+-+..|.+.|...|..........+|.|. +|+..||||+-||.+.+....
T Consensus 7 plY~qI~~~i~~~I~~G~~~~G~~LPsE~----------------eLa~~f~VSR~TvRkAL~~L~ 56 (236)
T COG2188 7 PLYQQIAEDIRQRIESGELPPGDKLPSER----------------ELAEQFGVSRMTVRKALDELV 56 (236)
T ss_pred ccHHHHHHHHHHHHHhCCCCCCCCCCCHH----------------HHHHHHCCcHHHHHHHHHHHH
Confidence 34566777777666543333345677664 688999999999988877654
No 275
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=22.53 E-value=54 Score=32.35 Aligned_cols=48 Identities=17% Similarity=0.322 Sum_probs=31.6
Q ss_pred HHHHHHHHhhccccccCCCCCCCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhH
Q 041521 207 TFEMICEELESTVMKKNTMLRDAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVC 271 (524)
Q Consensus 207 tF~~Lv~~L~~~i~~~~t~~r~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~ 271 (524)
-+..|.+.|...|.. .-.-...+|.|. .|+..||||+.||.+.+....
T Consensus 13 ~Y~qi~~~L~~~I~~-~~~~G~~LPsE~----------------eLa~~~~VSR~TVR~Al~~L~ 60 (241)
T PRK10079 13 RYQEIAAKLEQELRQ-HYRCGDYLPAEQ----------------QLAARYEVNRHTLRRAIDQLV 60 (241)
T ss_pred HHHHHHHHHHHHHhc-ccCCCCcCCCHH----------------HHHHHHCCCHHHHHHHHHHHH
Confidence 356666666665542 222234566554 688999999999988776643
No 276
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=22.45 E-value=25 Score=35.66 Aligned_cols=19 Identities=21% Similarity=0.312 Sum_probs=17.5
Q ss_pred cchhhccCccccceehhhh
Q 041521 250 RVVSKRFGLGISTCHKLVL 268 (524)
Q Consensus 250 ~~la~~FgiS~STvsriv~ 268 (524)
++||...|||.+||||+++
T Consensus 2 ~dIA~~agVS~~TVSrvLn 20 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVIN 20 (327)
T ss_pred hhHHHHhCCcHHHHHHHhC
Confidence 5899999999999999986
No 277
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=22.27 E-value=32 Score=25.96 Aligned_cols=34 Identities=12% Similarity=0.248 Sum_probs=28.4
Q ss_pred hhhccccCCCccchhhccCccccceehhhhhhHH
Q 041521 239 CVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 239 ~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
.+.+++.|.+...++...++|..||......+..
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 4567788999999999999999999877766544
No 278
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=22.10 E-value=38 Score=30.15 Aligned_cols=46 Identities=11% Similarity=0.165 Sum_probs=34.9
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHHH
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAIK 275 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI~ 275 (524)
.++.+++-++-+ |+.+..++.+++..+|||-+||..-+.+++.+|-
T Consensus 33 ~L~~E~~~Fi~~-Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg 78 (113)
T PF09862_consen 33 RLSPEQLEFIKL-FIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLG 78 (113)
T ss_pred cCCHHHHHHHHH-HHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhC
Confidence 456666555544 4445557999999999999999988888887764
No 279
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=21.90 E-value=23 Score=25.06 Aligned_cols=22 Identities=18% Similarity=0.335 Sum_probs=18.0
Q ss_pred CccchhhccCccccceehhhhh
Q 041521 248 PLRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 248 s~~~la~~FgiS~STvsriv~~ 269 (524)
+..+++..+|||.+|+.+.+.+
T Consensus 3 t~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHHc
Confidence 4568899999999999887654
No 280
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=21.80 E-value=26 Score=27.54 Aligned_cols=24 Identities=8% Similarity=0.152 Sum_probs=20.3
Q ss_pred CCccchhhccCccccceehhhhhh
Q 041521 247 EPLRVVSKRFGLGISTCHKLVLEV 270 (524)
Q Consensus 247 ~s~~~la~~FgiS~STvsriv~~v 270 (524)
.+...|+..||+|.+||++.+...
T Consensus 14 ~~~~eLa~~l~vS~~tv~~~l~~L 37 (69)
T TIGR00122 14 FSGEKLGEALGMSRTAVNKHIQTL 37 (69)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHH
Confidence 447789999999999999887764
No 281
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=21.73 E-value=63 Score=31.79 Aligned_cols=49 Identities=10% Similarity=0.215 Sum_probs=32.2
Q ss_pred HHHHHHHHhhccccccCCCCCCCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhH
Q 041521 207 TFEMICEELESTVMKKNTMLRDAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVC 271 (524)
Q Consensus 207 tF~~Lv~~L~~~i~~~~t~~r~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~ 271 (524)
.+..|.+.|...|....-.....+|.|. +|+..||||+.||.+.+....
T Consensus 10 ~y~qI~~~i~~~I~~G~~~~g~kLPsE~----------------eLa~~~~VSR~TvR~Al~~L~ 58 (241)
T PRK11402 10 LYATVRQRLLDDIAQGVYQAGQQIPTEN----------------ELCTQYNVSRITIRKAISDLV 58 (241)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCcCHH----------------HHHHHHCCCHHHHHHHHHHHH
Confidence 4556666666655443222235677665 578899999999988766543
No 282
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=21.56 E-value=34 Score=33.31 Aligned_cols=44 Identities=16% Similarity=0.197 Sum_probs=35.7
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHH
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAI 274 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI 274 (524)
.+++++. -.|..|+.|.+-.+||+..++|.+||..++.....-|
T Consensus 148 ~LT~RE~--eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 148 LLTPREL--EVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHc
Confidence 4666665 5577899999999999999999999998877655433
No 283
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=21.55 E-value=23 Score=29.01 Aligned_cols=25 Identities=16% Similarity=0.270 Sum_probs=19.4
Q ss_pred ccCCCccchhhccCccccceehhhh
Q 041521 244 ATGEPLRVVSKRFGLGISTCHKLVL 268 (524)
Q Consensus 244 atG~s~~~la~~FgiS~STvsriv~ 268 (524)
+.|.++.++|...|+++++|+++.+
T Consensus 29 ~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 29 ERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp CCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HcCCCHHHHHHHHCCChhHHHHHHc
Confidence 4678999999999999999998864
No 284
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=21.40 E-value=30 Score=31.07 Aligned_cols=24 Identities=17% Similarity=0.217 Sum_probs=22.2
Q ss_pred CCCccchhhccCccccceehhhhh
Q 041521 246 GEPLRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 246 G~s~~~la~~FgiS~STvsriv~~ 269 (524)
|.++..+|+..|++++.||+++..
T Consensus 22 G~Sq~~iA~LLGltqaAVS~Yls~ 45 (119)
T COG2522 22 GLSQYRIAKLLGLTQAAVSQYLSG 45 (119)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHcc
Confidence 999999999999999999999754
No 285
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=21.38 E-value=32 Score=33.48 Aligned_cols=42 Identities=14% Similarity=0.203 Sum_probs=34.4
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHH
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
.+++.|+ =.|..++.|.+.++||...++|..||..++..+..
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 4676665 45677899999999999999999999888776544
No 286
>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=21.30 E-value=35 Score=37.23 Aligned_cols=32 Identities=34% Similarity=0.409 Sum_probs=26.2
Q ss_pred CCCccchhhccCccccceehhhhhhHHHHHhhcccccccCcch
Q 041521 246 GEPLRVVSKRFGLGISTCHKLVLEVCSAIKTVLMPKFLQWPDE 288 (524)
Q Consensus 246 G~s~~~la~~FgiS~STvsriv~~v~~aI~~~L~~~~I~~P~~ 288 (524)
+.++++||+..|++.|||||+++ .+|+..|..
T Consensus 318 PLtlkdiA~~lglheSTVSRav~-----------~Kyi~tp~G 349 (429)
T TIGR02395 318 PLTLREVAEELGLHESTISRAIN-----------NKYLQTPRG 349 (429)
T ss_pred CCcHHHHHHHhCCCccchhhhhc-----------CceEecCCc
Confidence 46789999999999999999854 577777743
No 287
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=21.12 E-value=55 Score=35.87 Aligned_cols=49 Identities=12% Similarity=0.104 Sum_probs=41.6
Q ss_pred CCCCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHH
Q 041521 226 LRDAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAI 274 (524)
Q Consensus 226 ~r~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI 274 (524)
+.+.+...-+++|.|.+=-++.++..||..||...|||...++.+-..+
T Consensus 377 R~~~i~~~Rqiamyl~r~~t~~s~~~IG~~fgrdHsTV~~a~~ki~~~~ 425 (445)
T PRK12422 377 QSREYVLPRQVAMYLCRQKLSLSYVKIGDVFSRDHSTVISSIRAISQKL 425 (445)
T ss_pred CCcccccHHHHHHHHHHHhcCCCHHHHHHHhCCChHHHHHHHHHHHHHH
Confidence 4456777778999998888999999999999999999988877776655
No 288
>cd00131 PAX Paired Box domain
Probab=21.07 E-value=1.7e+02 Score=26.29 Aligned_cols=79 Identities=11% Similarity=0.112 Sum_probs=46.9
Q ss_pred CCCCHhhHHHHcCCCHHHHHHHHHHhhcc--ccccCCC-CCCC-CChh-hhhhhhhhccccCCCccchhhcc---Cc---
Q 041521 190 PDFPEEEFWRDFRMSKATFEMICEELEST--VMKKNTM-LRDA-IPVR-QRVAVCVWRLATGEPLRVVSKRF---GL--- 258 (524)
Q Consensus 190 ~~~~d~~F~~~fRmSr~tF~~Lv~~L~~~--i~~~~t~-~r~~-l~~e-~rL~i~L~~LatG~s~~~la~~F---gi--- 258 (524)
..++..+.-+.|++++.+...++...... +...... .++. +..+ ....+.+..-.-..+..+|++.+ |+
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 45788899999999999999999877753 2221121 2222 2222 22223232222335566666553 55
Q ss_pred ----cccceehhhh
Q 041521 259 ----GISTCHKLVL 268 (524)
Q Consensus 259 ----S~STvsriv~ 268 (524)
|.|||+|++.
T Consensus 112 ~~~~s~stI~R~L~ 125 (128)
T cd00131 112 SNVPSVSSINRILR 125 (128)
T ss_pred CCCCCHHHHHHHHH
Confidence 8889888754
No 289
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=21.04 E-value=57 Score=35.76 Aligned_cols=49 Identities=14% Similarity=0.199 Sum_probs=41.7
Q ss_pred CCCCChhhhhhhhhhccccCCCccchhhccC-ccccceehhhhhhHHHHH
Q 041521 227 RDAIPVRQRVAVCVWRLATGEPLRVVSKRFG-LGISTCHKLVLEVCSAIK 275 (524)
Q Consensus 227 r~~l~~e~rL~i~L~~LatG~s~~~la~~Fg-iS~STvsriv~~v~~aI~ 275 (524)
.+.+...-+++|.|.+=-++.++..||..|| .+.|||...+.++-..+.
T Consensus 382 ~~~i~~~RqiamyL~r~~t~~sl~~IG~~FggrdHsTV~~a~~ki~~~~~ 431 (450)
T PRK14087 382 SKSIVTARHIAMYLTKEILNHTLAQIGEEFGGRDHTTVINAERKIEKMLK 431 (450)
T ss_pred CccccHHHHHHHHHHHHHcCCCHHHHHHHhCCCChHHHHHHHHHHHHHHH
Confidence 4567777899999999889999999999997 999999888887766554
No 290
>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=21.02 E-value=48 Score=33.40 Aligned_cols=46 Identities=11% Similarity=0.195 Sum_probs=37.0
Q ss_pred CCCCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHH
Q 041521 227 RDAIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAI 274 (524)
Q Consensus 227 r~~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI 274 (524)
...+++.++=.+.| ++.|.++.+||..+|||..||...+..+..-+
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 57999999999999999999988877765543
No 291
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=20.86 E-value=26 Score=25.35 Aligned_cols=24 Identities=17% Similarity=0.268 Sum_probs=18.1
Q ss_pred CCCccchhhccCccccceehhhhh
Q 041521 246 GEPLRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 246 G~s~~~la~~FgiS~STvsriv~~ 269 (524)
-.+|..||...|+|.+||.+-+.+
T Consensus 17 r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 17 RRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CccHHHHHHHHCcCHHHHHHHHHH
Confidence 367899999999999999876554
No 292
>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=20.57 E-value=55 Score=28.26 Aligned_cols=27 Identities=15% Similarity=0.148 Sum_probs=23.5
Q ss_pred CCCccchhhccCccccceehhhhhhHH
Q 041521 246 GEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 246 G~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
+.+..+|+...+++++||++++.....
T Consensus 43 ~~t~~eL~~~l~~~~stvs~~i~~Le~ 69 (109)
T TIGR01889 43 KLTLKEIIKEILIKQSALVKIIKKLSK 69 (109)
T ss_pred cCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 588999999999999999998887544
No 293
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=20.54 E-value=27 Score=38.14 Aligned_cols=31 Identities=29% Similarity=0.365 Sum_probs=25.3
Q ss_pred CCccchhhccCccccceehhhhhhHHHHHhhcccccccCcch
Q 041521 247 EPLRVVSKRFGLGISTCHKLVLEVCSAIKTVLMPKFLQWPDE 288 (524)
Q Consensus 247 ~s~~~la~~FgiS~STvsriv~~v~~aI~~~L~~~~I~~P~~ 288 (524)
..+++||+..|++.|||||++. .+|+.-|..
T Consensus 331 L~LrdvA~~i~~HESTISRai~-----------nKy~~tprG 361 (444)
T COG1508 331 LVLRDVADEIGMHESTISRAIT-----------NKYLATPRG 361 (444)
T ss_pred ccHHHHHHHhCccHHHHHHHHh-----------cccccCCcc
Confidence 5669999999999999999854 567777754
No 294
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=20.51 E-value=28 Score=35.38 Aligned_cols=21 Identities=19% Similarity=0.221 Sum_probs=18.5
Q ss_pred ccchhhccCccccceehhhhh
Q 041521 249 LRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 249 ~~~la~~FgiS~STvsriv~~ 269 (524)
.++||..-|||.+||||+++.
T Consensus 2 i~dIA~~aGVS~~TVSrvLn~ 22 (327)
T TIGR02417 2 LSDIAKLAGVSKTTASYVING 22 (327)
T ss_pred HHHHHHHhCCCHHHHHHHHcC
Confidence 568999999999999999764
No 295
>PRK14161 heat shock protein GrpE; Provisional
Probab=20.42 E-value=1.3e+02 Score=28.90 Aligned_cols=49 Identities=14% Similarity=0.174 Sum_probs=29.3
Q ss_pred cccccchhcHHHHHHHhhcccHHHHHHHHHHhh----hhhhhhhhhhhhcchhh
Q 041521 55 DDVLNKSAAWSDILTSLILLDEEEKREQQQYSI----HSHQDKLLVDDNHKRKE 104 (524)
Q Consensus 55 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~ 104 (524)
|...|+..++.+|+..++.-.+++-++.++... ...+..+-| .|.+|+.
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~ei~~l~~e~~elkd~~lR~~Aef-eN~rkR~ 56 (178)
T PRK14161 4 DNIENNEQTINDIAEEIVETANPEITALKAEIEELKDKLIRTTAEI-DNTRKRL 56 (178)
T ss_pred ccccccHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHH
Confidence 445778889999999888877776444333333 233344444 4444443
No 296
>PRK10870 transcriptional repressor MprA; Provisional
Probab=20.39 E-value=47 Score=31.46 Aligned_cols=44 Identities=9% Similarity=0.006 Sum_probs=29.8
Q ss_pred CCChhh-hhhhhhhcccc-CCCccchhhccCccccceehhhhhhHH
Q 041521 229 AIPVRQ-RVAVCVWRLAT-GEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 229 ~l~~e~-rL~i~L~~Lat-G~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
.+++.+ .++..|+.... +.+..+|+..++++++|+++++.+...
T Consensus 52 gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~ 97 (176)
T PRK10870 52 GINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEK 97 (176)
T ss_pred CCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 344443 44444544333 356789999999999999998877543
No 297
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=20.35 E-value=27 Score=25.69 Aligned_cols=24 Identities=17% Similarity=0.198 Sum_probs=20.9
Q ss_pred ccCCCccchhhccCccccceehhh
Q 041521 244 ATGEPLRVVSKRFGLGISTCHKLV 267 (524)
Q Consensus 244 atG~s~~~la~~FgiS~STvsriv 267 (524)
..|.++.+++...|+|++|++++.
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e 36 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVE 36 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 457889999999999999998874
No 298
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=20.35 E-value=37 Score=33.27 Aligned_cols=44 Identities=11% Similarity=0.195 Sum_probs=34.3
Q ss_pred CCChhhhhhhhhhccccCCCccchhhccCccccceehhhhhhHHHH
Q 041521 229 AIPVRQRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLEVCSAI 274 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~v~~aI 274 (524)
.+++.++= .|..++.|.++.+||..+++|..||..++...+.-+
T Consensus 155 ~Lt~rE~~--Vl~l~~~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl 198 (216)
T PRK10100 155 LLTHREKE--ILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKI 198 (216)
T ss_pred CCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 36666653 345567799999999999999999998887766544
No 299
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=20.32 E-value=27 Score=27.64 Aligned_cols=36 Identities=11% Similarity=0.148 Sum_probs=25.6
Q ss_pred hhhhhhhhccccCCCccchhhccCccccceehhhhh
Q 041521 234 QRVAVCVWRLATGEPLRVVSKRFGLGISTCHKLVLE 269 (524)
Q Consensus 234 ~rL~i~L~~LatG~s~~~la~~FgiS~STvsriv~~ 269 (524)
++++-+|.....+.+-++||+.+|+|..++.+++..
T Consensus 3 e~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~ 38 (62)
T PF04703_consen 3 EKILEYIKEQNGPLKTREIADALGLSIYQARYYLEK 38 (62)
T ss_dssp HCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 344555555567778889999999999999887654
No 300
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=20.18 E-value=36 Score=34.21 Aligned_cols=43 Identities=16% Similarity=0.214 Sum_probs=32.8
Q ss_pred CChhhhhhhhhhcccc---CCCccchhhccCccccceehhhhhhHH
Q 041521 230 IPVRQRVAVCVWRLAT---GEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 230 l~~e~rL~i~L~~Lat---G~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
+++-++.+-.|..|+. +.+..+|+..+|+++||++|++.....
T Consensus 7 v~sl~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~ 52 (263)
T PRK09834 7 VRGLSRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQE 52 (263)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4445566666666653 368999999999999999999887654
No 301
>PF13309 HTH_22: HTH domain
Probab=20.10 E-value=26 Score=27.68 Aligned_cols=40 Identities=10% Similarity=0.228 Sum_probs=26.8
Q ss_pred CCChhhhhhhhhhccccCC-----CccchhhccCccccceehhhh
Q 041521 229 AIPVRQRVAVCVWRLATGE-----PLRVVSKRFGLGISTCHKLVL 268 (524)
Q Consensus 229 ~l~~e~rL~i~L~~LatG~-----s~~~la~~FgiS~STvsriv~ 268 (524)
.++.++++-+.-..-..|. .-..+|..+|||+.||+++++
T Consensus 20 ~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YLr 64 (64)
T PF13309_consen 20 RLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYLR 64 (64)
T ss_pred hCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHcC
Confidence 4555666555443334443 346899999999999998863
No 302
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=20.09 E-value=48 Score=28.19 Aligned_cols=27 Identities=30% Similarity=0.316 Sum_probs=23.0
Q ss_pred CCCccchhhccCccccceehhhhhhHH
Q 041521 246 GEPLRVVSKRFGLGISTCHKLVLEVCS 272 (524)
Q Consensus 246 G~s~~~la~~FgiS~STvsriv~~v~~ 272 (524)
..++.+++..+|+|.+||.+.+.+...
T Consensus 17 ~~~~~~la~~l~~s~~tv~~~l~~L~~ 43 (108)
T smart00344 17 RISLAELAKKVGLSPSTVHNRVKRLEE 43 (108)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 478999999999999999988776544
Done!