Query 013572
Match_columns 440
No_of_seqs 305 out of 1661
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 05:12:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013572.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013572hhsearch_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-44 319.6 15.8 308 102-427 7-323 (326)
2 PF04827 Plant_tran: Plant tra 100.0 1.7E-35 3.7E-40 262.6 8.3 192 183-377 2-202 (205)
3 PF13359 DDE_Tnp_4: DDE superf 100.0 4.1E-35 8.8E-40 262.1 5.1 146 213-370 1-158 (158)
4 PF13613 HTH_Tnp_4: Helix-turn 98.9 2.3E-09 4.9E-14 77.6 3.7 51 132-182 2-52 (53)
5 PF13612 DDE_Tnp_1_3: Transpos 98.7 7.4E-09 1.6E-13 91.7 1.6 121 207-348 4-149 (155)
6 PF01609 DDE_Tnp_1: Transposas 96.9 3.1E-05 6.8E-10 71.0 -5.8 146 209-371 5-213 (213)
7 PF13586 DDE_Tnp_1_2: Transpos 96.8 0.0015 3.2E-08 52.2 4.2 51 320-370 36-86 (88)
8 PF02796 HTH_7: Helix-turn-hel 96.4 0.0017 3.7E-08 45.0 1.7 42 129-171 2-43 (45)
9 PF04545 Sigma70_r4: Sigma-70, 95.8 0.016 3.4E-07 40.9 4.4 45 132-177 4-48 (50)
10 PF13936 HTH_38: Helix-turn-he 95.6 0.008 1.7E-07 41.4 2.0 40 132-172 4-43 (44)
11 PF04218 CENP-B_N: CENP-B N-te 95.2 0.015 3.2E-07 41.9 2.5 42 130-172 4-45 (53)
12 PF13384 HTH_23: Homeodomain-l 93.8 0.023 5.1E-07 39.9 0.7 29 146-174 14-42 (50)
13 PF13518 HTH_28: Helix-turn-he 93.8 0.046 1E-06 38.6 2.3 37 138-175 2-38 (52)
14 PF08281 Sigma70_r4_2: Sigma-7 93.6 0.1 2.2E-06 37.3 3.8 43 132-175 10-52 (54)
15 PF13340 DUF4096: Putative tra 93.5 0.13 2.8E-06 39.7 4.5 60 115-175 7-66 (75)
16 smart00351 PAX Paired Box doma 93.1 0.12 2.6E-06 44.2 4.0 44 131-175 16-59 (125)
17 smart00421 HTH_LUXR helix_turn 93.0 0.2 4.3E-06 35.5 4.6 44 132-177 3-46 (58)
18 cd00569 HTH_Hin_like Helix-tur 92.9 0.097 2.1E-06 33.1 2.6 39 130-169 3-41 (42)
19 cd00131 PAX Paired Box domain 92.8 0.13 2.9E-06 44.1 4.0 44 131-175 16-59 (128)
20 PRK04217 hypothetical protein; 92.4 0.16 3.6E-06 42.3 3.7 50 131-181 41-90 (110)
21 COG3415 Transposase and inacti 91.6 0.13 2.9E-06 44.6 2.5 44 132-175 4-47 (138)
22 PF05225 HTH_psq: helix-turn-h 91.6 0.15 3.3E-06 35.3 2.3 37 136-172 2-39 (45)
23 PRK00118 putative DNA-binding 91.5 0.45 9.7E-06 39.2 5.3 50 132-182 17-66 (104)
24 PRK09413 IS2 repressor TnpA; R 91.4 0.24 5.2E-06 42.0 3.8 45 131-175 11-55 (121)
25 PF12116 SpoIIID: Stage III sp 91.3 0.13 2.8E-06 39.8 1.8 43 139-181 9-51 (82)
26 PRK09639 RNA polymerase sigma 90.7 0.41 8.9E-06 42.3 4.9 49 132-182 112-160 (166)
27 PF01527 HTH_Tnp_1: Transposas 90.4 0.17 3.6E-06 38.8 1.8 44 131-174 5-48 (76)
28 PF13011 LZ_Tnp_IS481: leucine 90.4 0.33 7.2E-06 38.4 3.4 45 131-175 7-51 (85)
29 PRK09652 RNA polymerase sigma 89.9 0.5 1.1E-05 42.2 4.8 50 132-182 128-177 (182)
30 cd06171 Sigma70_r4 Sigma70, re 89.7 0.53 1.1E-05 32.5 3.9 42 133-175 11-52 (55)
31 cd06170 LuxR_C_like C-terminal 89.3 0.66 1.4E-05 32.8 4.1 43 134-178 2-44 (57)
32 TIGR03879 near_KaiC_dom probab 89.2 0.32 6.9E-06 37.3 2.4 41 132-172 15-55 (73)
33 PRK12519 RNA polymerase sigma 88.8 0.69 1.5E-05 42.1 4.9 51 132-183 141-191 (194)
34 cd06571 Bac_DnaA_C C-terminal 88.5 0.78 1.7E-05 36.7 4.4 49 131-179 26-75 (90)
35 TIGR01321 TrpR trp operon repr 88.5 0.34 7.3E-06 39.1 2.2 39 133-171 33-77 (94)
36 PRK12529 RNA polymerase sigma 88.5 0.56 1.2E-05 42.3 4.0 48 132-180 127-174 (178)
37 PF02209 VHP: Villin headpiece 88.3 0.28 6E-06 32.2 1.4 22 95-116 3-24 (36)
38 PRK08301 sporulation sigma fac 88.2 0.75 1.6E-05 43.4 4.9 51 132-182 178-231 (234)
39 TIGR02960 SigX5 RNA polymerase 87.9 1 2.2E-05 44.7 5.9 73 132-205 142-218 (324)
40 PRK09638 RNA polymerase sigma 87.9 0.66 1.4E-05 41.5 4.1 49 132-181 126-174 (176)
41 PRK12530 RNA polymerase sigma 87.6 0.82 1.8E-05 41.7 4.6 50 132-182 134-183 (189)
42 PRK05911 RNA polymerase sigma 87.3 0.85 1.8E-05 44.0 4.7 51 132-183 205-255 (257)
43 smart00153 VHP Villin headpiec 87.2 0.43 9.3E-06 31.3 1.7 21 95-115 3-23 (36)
44 PRK05803 sporulation sigma fac 87.0 1 2.2E-05 42.6 5.0 50 132-181 175-227 (233)
45 TIGR02952 Sig70_famx2 RNA poly 86.7 0.92 2E-05 40.1 4.3 47 132-179 122-168 (170)
46 TIGR02950 SigM_subfam RNA poly 86.7 0.7 1.5E-05 40.2 3.5 47 133-180 106-152 (154)
47 PRK06704 RNA polymerase factor 86.6 1.2 2.6E-05 42.2 5.2 70 132-202 116-186 (228)
48 PF13542 HTH_Tnp_ISL3: Helix-t 86.6 0.5 1.1E-05 33.3 2.0 28 146-173 24-51 (52)
49 TIGR02531 yecD_yerC TrpR-relat 86.5 0.48 1E-05 37.8 2.1 31 140-170 41-71 (88)
50 PRK07037 extracytoplasmic-func 86.3 1.1 2.3E-05 39.5 4.5 49 132-181 109-157 (163)
51 TIGR02985 Sig70_bacteroi1 RNA 86.3 0.97 2.1E-05 39.3 4.2 46 132-178 113-158 (161)
52 TIGR02937 sigma70-ECF RNA poly 86.3 1.1 2.3E-05 38.3 4.4 46 133-179 111-156 (158)
53 PRK11923 algU RNA polymerase s 86.0 1.2 2.7E-05 40.4 4.9 53 132-185 138-190 (193)
54 TIGR02392 rpoH_proteo alternat 85.9 1.1 2.4E-05 43.4 4.8 49 132-180 218-267 (270)
55 PRK12533 RNA polymerase sigma 85.6 1.2 2.5E-05 41.9 4.5 50 132-182 134-183 (216)
56 PRK12547 RNA polymerase sigma 85.5 1.2 2.6E-05 39.5 4.3 49 132-181 112-160 (164)
57 PRK12511 RNA polymerase sigma 85.2 1.3 2.7E-05 40.3 4.5 50 132-182 111-160 (182)
58 PRK12516 RNA polymerase sigma 85.2 1.3 2.8E-05 40.4 4.5 50 132-182 116-165 (187)
59 PRK09415 RNA polymerase factor 85.0 1.3 2.7E-05 40.0 4.4 50 132-182 127-176 (179)
60 PRK12514 RNA polymerase sigma 84.9 1.3 2.7E-05 39.8 4.3 49 132-181 129-177 (179)
61 PRK12515 RNA polymerase sigma 84.8 1.3 2.9E-05 40.1 4.5 50 132-182 131-180 (189)
62 PRK11924 RNA polymerase sigma 84.6 1.5 3.2E-05 38.9 4.6 50 132-182 125-174 (179)
63 PRK12524 RNA polymerase sigma 84.6 1.4 3E-05 40.4 4.5 49 132-181 136-184 (196)
64 TIGR02939 RpoE_Sigma70 RNA pol 84.5 1.4 3.1E-05 39.7 4.6 50 132-182 138-187 (190)
65 PRK09641 RNA polymerase sigma 84.4 1.3 2.9E-05 39.8 4.3 49 132-181 136-184 (187)
66 PF04967 HTH_10: HTH DNA bindi 84.4 1.3 2.9E-05 31.8 3.3 30 149-178 23-52 (53)
67 PRK06596 RNA polymerase factor 84.2 1.6 3.4E-05 42.8 4.9 50 132-181 230-280 (284)
68 TIGR00721 tfx DNA-binding prot 84.2 1.5 3.2E-05 38.1 4.1 46 132-179 6-51 (137)
69 PRK03975 tfx putative transcri 84.1 2.1 4.5E-05 37.4 5.0 47 132-180 6-52 (141)
70 PRK09047 RNA polymerase factor 84.1 1.5 3.2E-05 38.5 4.3 50 132-182 106-155 (161)
71 TIGR02989 Sig-70_gvs1 RNA poly 83.9 1.4 3.1E-05 38.5 4.1 47 132-179 111-157 (159)
72 TIGR02846 spore_sigmaK RNA pol 83.7 1.6 3.6E-05 41.0 4.7 50 132-181 174-226 (227)
73 PRK12532 RNA polymerase sigma 83.6 1.7 3.7E-05 39.7 4.6 50 132-182 136-185 (195)
74 TIGR02983 SigE-fam_strep RNA p 83.5 1.5 3.3E-05 38.5 4.2 49 132-181 110-158 (162)
75 PRK12512 RNA polymerase sigma 83.4 1.5 3.3E-05 39.5 4.2 50 132-182 131-180 (184)
76 PRK12531 RNA polymerase sigma 83.3 1.6 3.5E-05 39.8 4.4 49 132-181 141-189 (194)
77 PRK05602 RNA polymerase sigma 83.3 1.7 3.7E-05 39.3 4.5 50 132-182 128-177 (186)
78 PRK12540 RNA polymerase sigma 83.1 1.8 3.8E-05 39.3 4.5 50 132-182 111-160 (182)
79 TIGR02999 Sig-70_X6 RNA polyme 82.8 1.8 3.9E-05 38.9 4.4 48 132-180 134-181 (183)
80 PRK07500 rpoH2 RNA polymerase 82.8 2 4.4E-05 42.1 5.1 51 132-182 227-278 (289)
81 TIGR02835 spore_sigmaE RNA pol 82.7 1.9 4.2E-05 40.8 4.7 50 132-181 178-230 (234)
82 PRK06930 positive control sigm 82.6 2 4.4E-05 38.7 4.6 50 132-182 114-163 (170)
83 PRK12537 RNA polymerase sigma 82.6 1.7 3.7E-05 39.2 4.1 48 132-180 133-180 (182)
84 PRK15320 transcriptional activ 82.4 1.5 3.2E-05 40.3 3.5 37 141-177 171-207 (251)
85 TIGR02948 SigW_bacill RNA poly 82.2 1.9 4.2E-05 38.7 4.4 49 132-181 136-184 (187)
86 PRK09643 RNA polymerase sigma 82.2 2.1 4.6E-05 39.0 4.7 49 132-181 134-182 (192)
87 COG2739 Uncharacterized protei 82.1 1.4 3E-05 35.8 2.9 41 137-178 22-62 (105)
88 PRK12523 RNA polymerase sigma 82.1 1.9 4.2E-05 38.4 4.3 49 132-181 119-167 (172)
89 TIGR03001 Sig-70_gmx1 RNA poly 82.0 1.9 4.2E-05 41.2 4.5 50 132-182 161-210 (244)
90 PRK12522 RNA polymerase sigma 82.0 2.2 4.8E-05 38.0 4.7 52 133-185 120-171 (173)
91 PRK05572 sporulation sigma fac 82.0 2 4.2E-05 41.2 4.6 49 132-181 202-250 (252)
92 PRK01381 Trp operon repressor; 81.9 0.94 2E-05 36.8 1.9 39 133-171 33-77 (99)
93 PHA00675 hypothetical protein 81.8 1 2.3E-05 34.6 2.0 39 133-171 23-61 (78)
94 PF00196 GerE: Bacterial regul 81.8 1.1 2.3E-05 32.5 2.1 43 133-177 4-46 (58)
95 PRK07408 RNA polymerase sigma 81.7 2 4.4E-05 41.3 4.5 49 132-181 203-251 (256)
96 PRK12534 RNA polymerase sigma 81.7 2 4.3E-05 38.8 4.3 49 132-181 137-185 (187)
97 PRK12546 RNA polymerase sigma 81.7 2.2 4.7E-05 38.9 4.6 49 132-181 113-161 (188)
98 PF00356 LacI: Bacterial regul 81.5 1 2.3E-05 31.3 1.8 21 152-172 2-22 (46)
99 PRK09642 RNA polymerase sigma 81.5 2.2 4.8E-05 37.4 4.4 50 132-182 106-155 (160)
100 PRK12544 RNA polymerase sigma 81.5 2.1 4.5E-05 39.7 4.4 50 132-182 148-197 (206)
101 TIGR02980 SigBFG RNA polymeras 81.4 2.1 4.5E-05 40.1 4.5 47 132-179 178-224 (227)
102 PRK12520 RNA polymerase sigma 81.3 2.6 5.6E-05 38.3 4.9 50 132-182 131-180 (191)
103 PRK11922 RNA polymerase sigma 81.2 2.6 5.6E-05 39.8 5.0 51 132-183 149-199 (231)
104 TIGR02393 RpoD_Cterm RNA polym 81.0 2.4 5.3E-05 40.2 4.8 49 132-180 176-227 (238)
105 PRK08583 RNA polymerase sigma 80.7 2.2 4.9E-05 40.9 4.5 49 132-181 205-253 (257)
106 TIGR02394 rpoS_proteo RNA poly 80.7 2.6 5.7E-05 41.1 5.0 51 132-182 222-275 (285)
107 PRK12539 RNA polymerase sigma 80.6 2.5 5.3E-05 38.2 4.5 49 132-181 131-179 (184)
108 PF13730 HTH_36: Helix-turn-he 80.6 2 4.4E-05 30.5 3.1 43 133-175 3-51 (55)
109 PRK09645 RNA polymerase sigma 80.5 2.4 5.3E-05 37.7 4.4 50 132-182 118-167 (173)
110 PRK09637 RNA polymerase sigma 80.5 2.8 6E-05 37.9 4.8 51 132-183 106-156 (181)
111 TIGR02984 Sig-70_plancto1 RNA 80.4 2.5 5.5E-05 38.0 4.5 48 132-180 140-187 (189)
112 COG1595 RpoE DNA-directed RNA 80.3 2.8 6E-05 37.8 4.7 50 132-182 127-176 (182)
113 TIGR02947 SigH_actino RNA poly 80.3 2.6 5.6E-05 38.4 4.5 50 132-182 131-180 (193)
114 PRK12528 RNA polymerase sigma 80.2 2.2 4.8E-05 37.5 4.0 46 132-178 113-158 (161)
115 TIGR02954 Sig70_famx3 RNA poly 79.7 2.5 5.4E-05 37.5 4.2 49 132-181 119-167 (169)
116 PRK06986 fliA flagellar biosyn 79.5 3 6.4E-05 39.5 4.8 50 132-182 184-233 (236)
117 TIGR02885 spore_sigF RNA polym 79.4 2.5 5.5E-05 39.7 4.3 47 132-179 183-229 (231)
118 PRK06030 hypothetical protein; 79.4 2.5 5.4E-05 36.0 3.7 47 131-177 51-97 (124)
119 PRK12545 RNA polymerase sigma 79.2 2.9 6.4E-05 38.4 4.6 50 132-182 139-188 (201)
120 TIGR02997 Sig70-cyanoRpoD RNA 78.8 2.4 5.2E-05 41.7 4.1 45 132-176 249-296 (298)
121 TIGR02943 Sig70_famx1 RNA poly 78.6 3 6.5E-05 37.9 4.4 50 132-182 131-180 (188)
122 PRK08215 sporulation sigma fac 78.5 3 6.4E-05 40.1 4.6 48 132-180 209-256 (258)
123 COG2963 Transposase and inacti 78.3 2.6 5.7E-05 35.1 3.6 46 131-176 6-52 (116)
124 PRK09644 RNA polymerase sigma 78.3 3.1 6.8E-05 36.7 4.3 50 132-182 108-157 (165)
125 PRK06811 RNA polymerase factor 78.2 2.9 6.2E-05 38.0 4.1 47 132-179 131-177 (189)
126 TIGR02959 SigZ RNA polymerase 78.0 3.5 7.6E-05 36.7 4.6 50 132-182 100-149 (170)
127 PRK08241 RNA polymerase factor 77.9 3.3 7.1E-05 41.4 4.8 77 132-209 153-232 (339)
128 PF12802 MarR_2: MarR family; 77.7 3 6.5E-05 30.2 3.4 26 150-175 22-47 (62)
129 TIGR02941 Sigma_B RNA polymera 77.6 3.4 7.3E-05 39.6 4.6 48 132-180 205-252 (255)
130 PRK12525 RNA polymerase sigma 77.6 3.3 7.1E-05 36.8 4.3 49 132-181 118-166 (168)
131 PRK12513 RNA polymerase sigma 77.6 3.7 7.9E-05 37.3 4.7 49 132-181 139-187 (194)
132 TIGR02850 spore_sigG RNA polym 77.5 3.3 7.2E-05 39.7 4.6 47 132-179 206-252 (254)
133 PRK12536 RNA polymerase sigma 77.4 3.2 6.9E-05 37.4 4.2 49 132-181 129-177 (181)
134 PRK06759 RNA polymerase factor 77.3 3.1 6.7E-05 36.1 4.0 45 132-177 106-150 (154)
135 PF01371 Trp_repressor: Trp re 77.3 2.4 5.3E-05 33.7 2.9 35 137-171 37-71 (87)
136 PRK07405 RNA polymerase sigma 77.2 3.9 8.6E-05 40.7 5.1 49 132-180 256-307 (317)
137 PF01022 HTH_5: Bacterial regu 77.1 2.7 5.9E-05 29.0 2.8 28 148-175 14-41 (47)
138 PF01710 HTH_Tnp_IS630: Transp 77.0 4.7 0.0001 34.0 4.8 74 96-172 21-94 (119)
139 PF13412 HTH_24: Winged helix- 76.9 3.6 7.9E-05 28.3 3.5 29 147-175 15-43 (48)
140 PF01325 Fe_dep_repress: Iron 76.9 3.2 7E-05 30.5 3.3 40 136-175 6-48 (60)
141 PRK07670 RNA polymerase sigma 76.5 3.9 8.4E-05 39.1 4.7 49 132-181 201-249 (251)
142 cd00092 HTH_CRP helix_turn_hel 76.3 2 4.4E-05 31.6 2.1 27 149-175 25-51 (67)
143 PRK13919 putative RNA polymera 76.1 3.7 7.9E-05 37.0 4.2 49 132-181 135-183 (186)
144 PF08299 Bac_DnaA_C: Bacterial 75.7 2 4.4E-05 32.6 2.0 41 133-173 29-70 (70)
145 PRK09640 RNA polymerase sigma 75.6 3 6.5E-05 37.8 3.5 49 133-182 135-183 (188)
146 PRK12538 RNA polymerase sigma 75.4 4.3 9.4E-05 38.4 4.7 50 132-182 171-220 (233)
147 PRK07122 RNA polymerase sigma 75.4 4.4 9.6E-05 39.2 4.8 48 132-180 215-262 (264)
148 PRK08295 RNA polymerase factor 75.3 4.8 0.0001 36.9 4.9 48 132-181 155-202 (208)
149 PRK12542 RNA polymerase sigma 75.3 4 8.6E-05 36.8 4.2 49 132-181 122-170 (185)
150 PRK12527 RNA polymerase sigma 75.2 4.6 9.9E-05 35.4 4.5 49 133-182 106-154 (159)
151 PRK09648 RNA polymerase sigma 75.1 4.2 9.1E-05 36.8 4.4 48 132-180 139-186 (189)
152 PRK12535 RNA polymerase sigma 75.1 4.1 8.8E-05 37.4 4.3 52 132-184 133-184 (196)
153 PRK10402 DNA-binding transcrip 75.0 2 4.3E-05 40.3 2.2 67 132-198 148-219 (226)
154 PF13551 HTH_29: Winged helix- 74.7 2.2 4.8E-05 34.8 2.2 34 142-175 4-38 (112)
155 PRK09649 RNA polymerase sigma 74.4 4.1 8.9E-05 36.9 4.1 47 132-179 130-176 (185)
156 PRK12541 RNA polymerase sigma 74.3 4.5 9.8E-05 35.5 4.2 46 132-178 112-157 (161)
157 PRK09636 RNA polymerase sigma 73.8 6.8 0.00015 38.3 5.8 69 132-203 115-183 (293)
158 PF09339 HTH_IclR: IclR helix- 73.3 4 8.6E-05 28.8 2.9 28 148-175 17-44 (52)
159 TIGR02957 SigX4 RNA polymerase 73.2 7.1 0.00015 38.0 5.7 68 132-202 108-175 (281)
160 PRK12543 RNA polymerase sigma 73.2 5.5 0.00012 35.7 4.6 49 132-181 117-165 (179)
161 PRK12526 RNA polymerase sigma 73.1 5 0.00011 37.0 4.4 49 132-181 153-201 (206)
162 smart00342 HTH_ARAC helix_turn 73.0 6.6 0.00014 29.6 4.4 72 96-175 4-77 (84)
163 PRK12518 RNA polymerase sigma 72.5 4.3 9.4E-05 36.1 3.7 50 132-182 120-169 (175)
164 PF01047 MarR: MarR family; I 71.7 4.5 9.7E-05 29.0 3.0 29 147-175 15-43 (59)
165 PRK05657 RNA polymerase sigma 71.6 6.5 0.00014 39.3 5.0 51 132-182 262-315 (325)
166 PF00872 Transposase_mut: Tran 71.4 5.5 0.00012 40.7 4.6 128 146-313 111-249 (381)
167 PF13751 DDE_Tnp_1_6: Transpos 71.3 2.2 4.7E-05 36.0 1.4 48 326-373 75-123 (125)
168 TIGR02479 FliA_WhiG RNA polyme 71.3 6 0.00013 37.0 4.5 48 132-180 175-222 (224)
169 PRK09651 RNA polymerase sigma 70.7 7.6 0.00016 34.6 4.9 47 132-179 119-165 (172)
170 PF01710 HTH_Tnp_IS630: Transp 70.4 2 4.4E-05 36.2 1.0 28 144-171 13-40 (119)
171 PRK12517 RNA polymerase sigma 70.4 6.5 0.00014 35.7 4.4 50 132-182 128-177 (188)
172 PRK12427 flagellar biosynthesi 70.3 6 0.00013 37.4 4.3 46 132-178 183-228 (231)
173 PHA00542 putative Cro-like pro 70.3 3.2 6.8E-05 32.6 2.0 50 143-203 25-74 (82)
174 PRK07406 RNA polymerase sigma 70.1 5.8 0.00013 40.4 4.4 48 132-179 311-361 (373)
175 PRK06288 RNA polymerase sigma 70.1 6.3 0.00014 38.0 4.5 49 132-181 212-260 (268)
176 PF00325 Crp: Bacterial regula 70.0 6 0.00013 25.2 2.8 24 151-174 4-27 (32)
177 PF04297 UPF0122: Putative hel 69.4 6.9 0.00015 32.1 3.8 44 134-178 19-62 (101)
178 PRK09635 sigI RNA polymerase s 69.3 9.1 0.0002 37.6 5.5 69 132-203 118-186 (290)
179 PF07374 DUF1492: Protein of u 69.0 5.9 0.00013 32.3 3.4 42 134-176 57-98 (100)
180 PF10654 DUF2481: Protein of u 68.7 5.8 0.00013 32.9 3.2 34 148-181 79-112 (126)
181 PRK13870 transcriptional regul 68.4 3.6 7.8E-05 39.0 2.3 46 131-178 172-217 (234)
182 PRK09647 RNA polymerase sigma 68.3 7.7 0.00017 35.8 4.5 50 132-182 138-187 (203)
183 PRK07598 RNA polymerase sigma 67.7 6.8 0.00015 40.5 4.3 47 132-178 350-399 (415)
184 PRK09646 RNA polymerase sigma 67.6 7.6 0.00017 35.3 4.3 49 132-181 142-190 (194)
185 TIGR02859 spore_sigH RNA polym 67.6 6.1 0.00013 35.8 3.6 41 137-179 155-195 (198)
186 COG1191 FliA DNA-directed RNA 67.5 7.4 0.00016 37.3 4.2 96 82-181 118-244 (247)
187 PRK15201 fimbriae regulatory p 67.3 4.5 9.7E-05 36.6 2.5 44 132-177 133-176 (198)
188 PRK15418 transcriptional regul 67.3 4.8 0.0001 40.1 3.1 69 141-212 21-89 (318)
189 PRK05949 RNA polymerase sigma 67.3 8.2 0.00018 38.6 4.7 48 132-179 266-316 (327)
190 smart00345 HTH_GNTR helix_turn 67.3 6 0.00013 28.0 2.8 25 151-175 22-46 (60)
191 PRK09210 RNA polymerase sigma 66.7 7.5 0.00016 39.5 4.4 47 132-178 305-354 (367)
192 TIGR01636 phage_rinA phage tra 66.6 9.9 0.00021 32.7 4.5 49 133-181 83-132 (134)
193 PF02001 DUF134: Protein of un 66.3 8.5 0.00018 31.8 3.8 48 133-181 42-89 (106)
194 PF08279 HTH_11: HTH domain; 66.2 7 0.00015 27.6 3.0 27 149-175 15-41 (55)
195 smart00419 HTH_CRP helix_turn_ 65.7 7.2 0.00016 26.3 2.9 28 148-175 7-34 (48)
196 PRK15411 rcsA colanic acid cap 65.4 4.7 0.0001 37.4 2.4 45 132-178 137-181 (207)
197 PF07638 Sigma70_ECF: ECF sigm 65.1 9.2 0.0002 34.7 4.3 47 133-180 136-182 (185)
198 PF13551 HTH_29: Winged helix- 64.7 27 0.00058 28.2 6.7 78 95-172 14-110 (112)
199 PRK11753 DNA-binding transcrip 64.6 4.4 9.5E-05 37.1 2.1 44 132-175 138-194 (211)
200 PRK03573 transcriptional regul 64.2 5.9 0.00013 34.2 2.7 44 132-175 28-72 (144)
201 TIGR03209 P21_Cbot clostridium 64.0 3.5 7.6E-05 35.4 1.2 35 132-167 107-141 (142)
202 PF00165 HTH_AraC: Bacterial r 63.2 7.4 0.00016 26.0 2.5 30 146-175 5-34 (42)
203 smart00346 HTH_ICLR helix_turn 62.8 7.8 0.00017 30.3 3.0 27 149-175 20-46 (91)
204 COG3316 Transposase and inacti 62.6 20 0.00043 33.5 5.9 96 141-265 17-117 (215)
205 PRK10840 transcriptional regul 61.7 8.5 0.00019 35.3 3.5 45 131-177 149-193 (216)
206 TIGR03697 NtcA_cyano global ni 61.5 6.9 0.00015 35.2 2.7 83 94-176 73-170 (193)
207 TIGR03541 reg_near_HchA LuxR f 61.3 12 0.00026 35.3 4.4 46 131-178 170-215 (232)
208 TIGR02844 spore_III_D sporulat 60.5 6 0.00013 31.0 1.8 22 150-171 20-41 (80)
209 PF12840 HTH_20: Helix-turn-he 60.0 9.2 0.0002 27.8 2.7 30 146-175 21-50 (61)
210 PF01381 HTH_3: Helix-turn-hel 59.6 7 0.00015 27.5 2.0 42 147-200 7-48 (55)
211 COG2771 CsgD DNA-binding HTH d 59.5 8.8 0.00019 27.7 2.6 35 143-177 13-47 (65)
212 TIGR01610 phage_O_Nterm phage 59.4 10 0.00023 30.5 3.2 29 147-175 45-73 (95)
213 smart00418 HTH_ARSR helix_turn 58.5 12 0.00025 26.6 3.1 29 147-175 8-36 (66)
214 TIGR03020 EpsA transcriptional 58.4 14 0.00031 35.3 4.4 45 131-177 189-233 (247)
215 PRK13413 mpi multiple promoter 58.4 6.6 0.00014 36.1 2.1 29 144-172 167-195 (200)
216 COG3413 Predicted DNA binding 58.2 12 0.00026 34.9 3.8 50 132-181 155-210 (215)
217 PRK07921 RNA polymerase sigma 58.2 13 0.00028 37.1 4.3 49 132-180 262-313 (324)
218 PRK13719 conjugal transfer tra 58.2 8 0.00017 36.2 2.5 45 132-178 143-187 (217)
219 PRK14088 dnaA chromosomal repl 57.1 14 0.0003 38.6 4.4 49 129-177 367-415 (440)
220 PRK14086 dnaA chromosomal repl 56.8 14 0.00031 40.1 4.5 50 130-179 550-599 (617)
221 PF12964 DUF3853: Protein of u 55.9 8 0.00017 31.2 1.8 58 103-172 11-68 (96)
222 smart00550 Zalpha Z-DNA-bindin 55.8 16 0.00035 27.4 3.5 40 134-173 6-46 (68)
223 PRK05901 RNA polymerase sigma 55.5 15 0.00033 39.0 4.3 49 132-180 447-498 (509)
224 PF06056 Terminase_5: Putative 55.0 13 0.00028 27.2 2.7 32 139-172 5-36 (58)
225 PRK00149 dnaA chromosomal repl 54.8 17 0.00036 38.0 4.6 50 129-178 382-432 (450)
226 smart00420 HTH_DEOR helix_turn 54.4 15 0.00034 25.0 3.0 27 149-175 14-40 (53)
227 PRK10188 DNA-binding transcrip 54.1 9.6 0.00021 36.3 2.4 46 131-178 178-223 (240)
228 PF05344 DUF746: Domain of Unk 54.0 17 0.00037 27.2 3.1 42 139-180 3-44 (65)
229 cd04762 HTH_MerR-trunc Helix-T 53.1 11 0.00024 25.3 2.0 22 151-172 2-23 (49)
230 COG2390 DeoR Transcriptional r 53.1 12 0.00026 37.3 3.0 69 142-213 19-87 (321)
231 PRK09483 response regulator; P 52.4 10 0.00022 34.3 2.3 44 132-177 148-191 (217)
232 PF13560 HTH_31: Helix-turn-he 51.5 8 0.00017 28.4 1.2 27 144-170 9-35 (64)
233 PRK11475 DNA-binding transcrip 51.4 11 0.00024 35.0 2.4 44 132-177 134-177 (207)
234 PF13545 HTH_Crp_2: Crp-like h 51.2 17 0.00036 27.4 3.0 27 149-175 28-54 (76)
235 PF00126 HTH_1: Bacterial regu 50.9 16 0.00034 26.5 2.6 31 149-179 13-43 (60)
236 PF01978 TrmB: Sugar-specific 50.8 13 0.00029 27.5 2.3 39 136-175 10-48 (68)
237 COG2197 CitB Response regulato 50.6 11 0.00023 35.2 2.1 44 132-177 148-191 (211)
238 PF00392 GntR: Bacterial regul 50.6 17 0.00036 26.7 2.8 24 151-174 26-49 (64)
239 PHA00738 putative HTH transcri 50.5 8.7 0.00019 31.8 1.3 31 146-176 21-53 (108)
240 PRK10100 DNA-binding transcrip 50.3 12 0.00027 34.9 2.5 45 132-178 155-199 (216)
241 PRK13918 CRP/FNR family transc 50.3 13 0.00029 33.7 2.7 63 133-195 119-196 (202)
242 TIGR01764 excise DNA binding d 50.1 13 0.00028 25.1 2.0 21 151-171 3-23 (49)
243 cd00090 HTH_ARSR Arsenical Res 50.0 18 0.00039 26.4 3.0 26 149-174 20-45 (78)
244 PF13610 DDE_Tnp_IS240: DDE do 49.9 64 0.0014 27.7 6.8 131 212-374 5-138 (140)
245 cd07377 WHTH_GntR Winged helix 48.4 19 0.00042 25.8 2.8 25 151-175 27-51 (66)
246 TIGR02337 HpaR homoprotocatech 48.2 31 0.00067 28.6 4.4 29 147-175 40-68 (118)
247 PRK09191 two-component respons 48.1 29 0.00063 32.6 4.8 50 132-182 88-137 (261)
248 PF13463 HTH_27: Winged helix 48.0 27 0.00059 25.5 3.6 28 148-175 17-44 (68)
249 cd01392 HTH_LacI Helix-turn-he 47.6 11 0.00024 26.1 1.4 19 154-172 2-20 (52)
250 PRK11161 fumarate/nitrate redu 47.1 16 0.00034 34.1 2.7 43 133-175 154-210 (235)
251 PF13404 HTH_AsnC-type: AsnC-t 46.9 20 0.00044 24.2 2.5 24 149-172 17-40 (42)
252 PRK09391 fixK transcriptional 46.8 17 0.00037 34.1 2.9 43 133-175 153-205 (230)
253 PF08220 HTH_DeoR: DeoR-like h 46.7 22 0.00047 25.7 2.8 24 150-173 15-38 (57)
254 PRK11512 DNA-binding transcrip 46.6 28 0.00061 30.0 4.0 44 132-175 37-80 (144)
255 PF09607 BrkDBD: Brinker DNA-b 46.4 14 0.00031 26.9 1.7 41 130-170 3-46 (58)
256 smart00354 HTH_LACI helix_turn 46.2 14 0.0003 27.8 1.7 21 151-171 2-22 (70)
257 PF09862 DUF2089: Protein of u 45.2 23 0.00051 29.6 3.1 45 133-178 34-78 (113)
258 PF11198 DUF2857: Protein of u 45.0 89 0.0019 28.4 7.2 78 94-175 88-179 (180)
259 TIGR02431 pcaR_pcaU beta-ketoa 45.0 67 0.0014 30.4 6.7 43 133-175 5-50 (248)
260 PRK14087 dnaA chromosomal repl 44.9 28 0.0006 36.5 4.4 50 129-178 381-431 (450)
261 PF12728 HTH_17: Helix-turn-he 44.4 17 0.00037 25.2 1.9 21 151-171 3-23 (51)
262 PRK12422 chromosomal replicati 44.3 27 0.00059 36.5 4.2 49 129-177 377-425 (445)
263 PRK10360 DNA-binding transcrip 44.1 18 0.00038 32.1 2.5 44 132-177 137-180 (196)
264 TIGR02404 trehalos_R_Bsub treh 43.9 29 0.00064 32.5 4.0 22 153-174 28-49 (233)
265 TIGR02405 trehalos_R_Ecol treh 43.8 26 0.00056 34.1 3.8 21 151-171 3-23 (311)
266 PF04703 FaeA: FaeA-like prote 43.5 21 0.00044 26.5 2.2 35 139-173 5-39 (62)
267 smart00347 HTH_MARR helix_turn 43.1 33 0.00072 26.8 3.7 28 148-175 23-50 (101)
268 PRK09492 treR trehalose repres 42.8 30 0.00065 33.5 4.1 23 150-172 5-27 (315)
269 PRK10079 phosphonate metabolis 42.7 28 0.00062 32.8 3.7 49 109-175 13-61 (241)
270 PF05043 Mga: Mga helix-turn-h 42.4 29 0.00062 27.1 3.2 33 146-178 27-59 (87)
271 PRK09392 ftrB transcriptional 41.9 27 0.00058 32.6 3.4 63 132-194 146-218 (236)
272 PRK05658 RNA polymerase sigma 41.7 34 0.00074 37.4 4.6 47 132-178 556-605 (619)
273 PF08765 Mor: Mor transcriptio 41.6 24 0.00052 29.1 2.6 30 147-176 70-99 (108)
274 PRK10403 transcriptional regul 41.1 19 0.00042 32.0 2.2 44 132-177 153-196 (215)
275 PF05269 Phage_CII: Bacterioph 40.7 36 0.00077 27.4 3.4 29 151-179 25-53 (91)
276 PF13309 HTH_22: HTH domain 40.3 15 0.00033 27.3 1.1 39 132-170 20-63 (64)
277 TIGR00122 birA_repr_reg BirA b 40.2 27 0.00058 26.0 2.5 25 150-174 14-38 (69)
278 TIGR03070 couple_hipB transcri 39.9 22 0.00048 24.8 1.9 24 147-170 13-36 (58)
279 PF13744 HTH_37: Helix-turn-he 39.9 21 0.00045 27.6 1.9 25 147-171 29-53 (80)
280 PRK09958 DNA-binding transcrip 39.9 21 0.00046 31.8 2.3 44 132-177 143-186 (204)
281 PRK10651 transcriptional regul 39.6 20 0.00044 32.0 2.1 44 132-177 155-198 (216)
282 PF00292 PAX: 'Paired box' dom 39.6 39 0.00084 28.8 3.6 41 132-174 17-58 (125)
283 PF13443 HTH_26: Cro/C1-type H 39.6 20 0.00043 25.9 1.7 43 147-200 8-50 (63)
284 COG2188 PhnF Transcriptional r 39.5 33 0.00071 32.4 3.6 50 108-175 7-57 (236)
285 PRK10014 DNA-binding transcrip 38.9 20 0.00043 35.3 2.1 23 150-172 7-29 (342)
286 TIGR02325 C_P_lyase_phnF phosp 38.7 41 0.00089 31.5 4.1 48 109-174 9-57 (238)
287 PHA02591 hypothetical protein; 38.1 27 0.00059 27.0 2.2 27 146-172 56-82 (83)
288 PRK15369 two component system 37.9 46 0.001 29.2 4.2 44 132-177 149-192 (211)
289 PRK09764 DNA-binding transcrip 37.6 44 0.00094 31.5 4.1 23 153-175 33-55 (240)
290 TIGR01889 Staph_reg_Sar staphy 37.3 52 0.0011 26.9 4.1 28 148-175 42-69 (109)
291 PRK14999 histidine utilization 37.3 44 0.00096 31.5 4.1 22 153-174 40-61 (241)
292 smart00344 HTH_ASNC helix_turn 37.2 43 0.00094 27.1 3.6 27 149-175 17-43 (108)
293 PF05263 DUF722: Protein of un 37.1 39 0.00084 29.0 3.3 46 133-178 82-128 (130)
294 PRK09526 lacI lac repressor; R 37.1 19 0.00042 35.4 1.7 23 150-172 6-28 (342)
295 PF03333 PapB: Adhesin biosynt 37.0 84 0.0018 25.2 4.9 58 104-175 22-79 (91)
296 PRK08558 adenine phosphoribosy 37.0 31 0.00068 32.8 3.0 37 135-171 9-45 (238)
297 COG1342 Predicted DNA-binding 36.5 50 0.0011 26.7 3.5 48 133-181 34-81 (99)
298 PRK14987 gluconate operon tran 35.3 19 0.0004 35.4 1.2 22 151-172 7-28 (331)
299 PF00440 TetR_N: Bacterial reg 35.0 29 0.00064 23.7 1.9 25 148-172 15-39 (47)
300 COG0593 DnaA ATPase involved i 35.0 45 0.00098 34.4 3.9 50 129-178 345-394 (408)
301 COG5566 Uncharacterized conser 34.6 36 0.00078 28.9 2.6 27 149-175 102-128 (137)
302 PHA01976 helix-turn-helix prot 34.5 31 0.00066 25.3 2.0 44 145-200 11-54 (67)
303 PRK11303 DNA-binding transcrip 34.4 24 0.00051 34.5 1.8 22 151-172 2-23 (328)
304 PRK10401 DNA-binding transcrip 34.1 46 0.00099 32.9 3.9 21 151-171 3-23 (346)
305 PRK10703 DNA-binding transcrip 33.9 24 0.00051 34.8 1.8 22 151-172 3-24 (341)
306 PRK00215 LexA repressor; Valid 33.7 41 0.00088 30.9 3.2 27 149-175 23-50 (205)
307 PRK10141 DNA-binding transcrip 33.6 34 0.00073 28.8 2.3 28 149-176 30-57 (117)
308 smart00529 HTH_DTXR Helix-turn 33.2 42 0.00091 26.4 2.8 24 152-175 2-25 (96)
309 PF05930 Phage_AlpA: Prophage 32.9 39 0.00085 23.6 2.3 21 151-171 5-25 (51)
310 PF01726 LexA_DNA_bind: LexA D 32.4 57 0.0012 24.3 3.2 25 149-173 25-50 (65)
311 smart00352 POU Found in Pit-Oc 32.4 26 0.00056 27.1 1.3 28 144-171 19-52 (75)
312 PF01418 HTH_6: Helix-turn-hel 32.4 36 0.00078 26.1 2.2 24 149-172 34-57 (77)
313 PRK10339 DNA-binding transcrip 32.1 23 0.00049 34.7 1.3 22 151-172 3-24 (327)
314 PRK10870 transcriptional repre 32.0 59 0.0013 29.3 3.8 44 132-175 52-97 (176)
315 COG3080 FrdD Fumarate reductas 31.9 46 0.001 27.4 2.7 24 4-27 52-75 (118)
316 TIGR00180 parB_part ParB-like 31.7 43 0.00093 30.4 2.9 41 131-171 101-142 (187)
317 PRK10423 transcriptional repre 31.6 25 0.00055 34.3 1.5 19 153-171 2-20 (327)
318 PF00382 TFIIB: Transcription 31.2 42 0.00091 25.1 2.3 65 98-166 3-71 (71)
319 PRK00423 tfb transcription ini 30.8 86 0.0019 31.0 5.1 76 98-177 225-304 (310)
320 PRK10163 DNA-binding transcrip 30.3 53 0.0011 31.7 3.4 44 132-175 20-66 (271)
321 TIGR02417 fruct_sucro_rep D-fr 29.9 30 0.00066 33.8 1.7 21 152-172 2-22 (327)
322 COG4565 CitB Response regulato 29.2 1.2E+02 0.0025 28.5 5.2 28 147-174 171-198 (224)
323 PF02954 HTH_8: Bacterial regu 28.6 64 0.0014 21.5 2.6 25 148-172 17-41 (42)
324 PRK12682 transcriptional regul 28.5 50 0.0011 32.1 3.0 43 139-181 6-48 (309)
325 TIGR02702 SufR_cyano iron-sulf 28.5 68 0.0015 29.5 3.7 38 136-174 3-40 (203)
326 PRK10072 putative transcriptio 28.4 45 0.00098 27.0 2.2 26 146-171 43-68 (96)
327 PRK09935 transcriptional regul 28.2 41 0.00088 29.9 2.2 44 132-177 149-192 (210)
328 PF07453 NUMOD1: NUMOD1 domain 28.2 38 0.00082 21.9 1.4 22 148-169 15-36 (37)
329 COG2522 Predicted transcriptio 28.1 46 0.001 28.1 2.2 33 138-172 13-45 (119)
330 cd04761 HTH_MerR-SF Helix-Turn 28.0 45 0.00097 22.5 1.8 20 152-171 3-22 (49)
331 PF14493 HTH_40: Helix-turn-he 28.0 49 0.0011 26.2 2.3 59 141-201 5-63 (91)
332 TIGR01481 ccpA catabolite cont 27.9 34 0.00073 33.4 1.6 22 151-172 3-24 (329)
333 PF10668 Phage_terminase: Phag 27.8 52 0.0011 24.2 2.2 21 149-169 22-42 (60)
334 COG5421 Transposase [DNA repli 27.8 86 0.0019 32.8 4.5 58 231-302 153-210 (480)
335 cd01104 HTH_MlrA-CarA Helix-Tu 27.7 51 0.0011 24.1 2.3 22 151-172 2-23 (68)
336 PF04552 Sigma54_DBD: Sigma-54 27.0 21 0.00045 31.8 0.0 24 149-172 49-72 (160)
337 PRK10727 DNA-binding transcrip 26.8 35 0.00077 33.6 1.6 22 151-172 3-24 (343)
338 COG4941 Predicted RNA polymera 26.8 1.4E+02 0.003 30.1 5.5 47 131-178 119-165 (415)
339 PRK09834 DNA-binding transcrip 26.6 52 0.0011 31.6 2.7 43 133-175 7-52 (263)
340 PF08769 Spo0A_C: Sporulation 26.6 79 0.0017 26.1 3.3 34 148-181 39-72 (106)
341 cd00131 PAX Paired Box domain 26.6 2.1E+02 0.0045 24.3 6.1 78 95-172 35-126 (128)
342 COG3355 Predicted transcriptio 26.2 73 0.0016 27.2 3.1 52 98-176 18-69 (126)
343 TIGR00637 ModE_repress ModE mo 25.4 62 0.0013 26.2 2.5 36 146-181 13-48 (99)
344 COG1609 PurR Transcriptional r 25.4 43 0.00093 33.4 1.9 22 151-172 2-23 (333)
345 PF05732 RepL: Firmicute plasm 25.4 61 0.0013 29.0 2.7 26 150-175 76-101 (165)
346 TIGR02607 antidote_HigA addict 25.0 54 0.0012 24.6 2.0 38 133-171 3-40 (78)
347 PRK12683 transcriptional regul 24.9 62 0.0014 31.6 2.9 44 138-181 5-48 (309)
348 COG1725 Predicted transcriptio 24.8 50 0.0011 28.2 1.9 59 100-175 3-61 (125)
349 PF01476 LysM: LysM domain; I 24.7 67 0.0015 21.1 2.2 23 146-168 3-25 (44)
350 TIGR02944 suf_reg_Xantho FeS a 24.4 47 0.001 28.1 1.7 26 150-175 26-51 (130)
351 PRK09390 fixJ response regulat 24.2 86 0.0019 27.2 3.5 44 133-178 142-185 (202)
352 PRK11050 manganese transport r 24.2 84 0.0018 27.5 3.3 28 148-175 50-77 (152)
353 TIGR03384 betaine_BetI transcr 24.0 64 0.0014 28.5 2.6 34 148-181 27-60 (189)
354 PF06530 Phage_antitermQ: Phag 23.8 87 0.0019 26.5 3.2 40 137-176 66-105 (125)
355 TIGR01884 cas_HTH CRISPR locus 23.6 99 0.0021 28.4 3.8 26 149-174 157-182 (203)
356 TIGR02018 his_ut_repres histid 23.2 71 0.0015 29.8 2.8 22 153-174 29-50 (230)
357 PRK13777 transcriptional regul 23.0 1.1E+02 0.0023 28.1 3.8 42 132-173 42-83 (185)
358 PRK15090 DNA-binding transcrip 22.8 88 0.0019 29.8 3.4 44 132-175 9-54 (257)
359 smart00497 IENR1 Intron encode 22.8 72 0.0016 22.0 2.2 25 148-172 16-40 (53)
360 PRK04140 hypothetical protein; 22.7 85 0.0018 31.3 3.3 81 103-200 96-178 (317)
361 PF12298 Bot1p: Eukaryotic mit 22.0 95 0.0021 28.0 3.2 42 130-171 14-55 (172)
362 COG1846 MarR Transcriptional r 21.9 94 0.002 25.0 3.1 23 153-175 40-62 (126)
363 PRK12679 cbl transcriptional r 21.9 80 0.0017 30.9 3.1 43 139-181 6-48 (316)
364 PRK09726 antitoxin HipB; Provi 21.9 62 0.0013 25.4 1.8 43 146-200 22-64 (88)
365 PF08535 KorB: KorB domain; I 21.6 63 0.0014 25.7 1.8 24 148-171 2-25 (93)
366 PRK11569 transcriptional repre 21.6 96 0.0021 30.0 3.4 43 133-175 24-69 (274)
367 PF14549 P22_Cro: DNA-binding 21.4 74 0.0016 23.4 2.0 19 151-169 11-29 (60)
368 smart00760 Bac_DnaA_C Bacteria 21.3 56 0.0012 23.6 1.3 30 131-160 27-56 (60)
369 COG1508 RpoN DNA-directed RNA 21.2 82 0.0018 32.8 2.9 31 150-190 331-361 (444)
370 PRK10430 DNA-binding transcrip 21.2 87 0.0019 29.2 3.0 32 146-177 175-206 (239)
371 PRK10219 DNA-binding transcrip 20.9 1.1E+02 0.0024 24.7 3.2 26 150-175 22-47 (107)
372 KOG0930 Guanine nucleotide exc 20.4 3.6E+02 0.0079 26.3 6.8 82 137-219 94-188 (395)
373 COG2944 Predicted transcriptio 20.0 74 0.0016 26.2 1.9 24 146-169 54-77 (104)
374 PF13411 MerR_1: MerR HTH fami 20.0 75 0.0016 23.2 1.9 23 152-174 3-25 (69)
No 1
>KOG4585 consensus Predicted transposase [Replication, recombination and repair]
Probab=100.00 E-value=1.5e-39 Score=319.62 Aligned_cols=308 Identities=26% Similarity=0.360 Sum_probs=244.3
Q ss_pred hcCCCHHHHHHHHHHhcccccccCCCCC-CCCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHh
Q 013572 102 SFKMSSSTFRWLSGLLEPLLDCRDPVGL-PLNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTN 180 (440)
Q Consensus 102 ~fRms~~tF~~L~~~L~~~l~~~~~~~r-~~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~ 180 (440)
.|++++.+|..++............... ...+++..+++++++.++++.+.+.++..||...+|+ .+.......
T Consensus 7 ~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~i~~~fg~~~~~~-----~~~~~~~~~ 81 (326)
T KOG4585|consen 7 EFRKSYTTFDKICSLVQSLNVVKNSGFMLSSLLPADTLVAVALWRLKTGESLRTVEKKFGLGQSTC-----KFLEEKEDL 81 (326)
T ss_pred HHHHHHHHHHHHhhhhhhhhhhcccchhhhccccHHhhhhhhhccccccchHHHHHHHcCCcchhh-----hHHHhhhcc
Confidence 7889999999999876544322221111 1122389999999999999999999999999999998 445555566
Q ss_pred hhhhhcCCChhhHHHHHHHHHhhhCCCCccccccceEEEEeecCCC-----CCCCCCCcEEEEeecCCCceEEeeecCCC
Q 013572 181 FRFWVAFPGPEELGLISKSFEELTGLPNCCGVIDCTRFKIIKIDGS-----NSSKDEDSIAVQIVVDSSSRMLSIVAGIR 255 (440)
Q Consensus 181 l~~~I~~P~~~~~~~~~~~f~~~~~fP~ciGaIDgthi~i~~p~~~-----n~k~~~~si~~q~v~D~~~rf~~v~~g~p 255 (440)
+..+++||....+..+...|+. ||+|+|+||+||+++..|+.. |+ .++.|+|+|||++++|++|++|||
T Consensus 82 ~~~~~~~p~~~~~~~i~~~~~~---~~~~~g~~d~~hi~~~~~~~~~~~~~n~---~~~~Nvlav~n~d~~f~~v~vg~~ 155 (326)
T KOG4585|consen 82 APHFLKWPSRRILYEIRERFES---LPNCVGAIDTTHIPIRVPPKSGSVYFNK---EQSKNLLAVCNFDMRFIYVDVGWP 155 (326)
T ss_pred cchhhcCchhhhhhhhcccccc---ccchhccccccccceecCcccccccccc---ccchhhhheecCCceEEEEEccCC
Confidence 7899999998888888888875 999999999999999988633 33 688999999999999999999999
Q ss_pred CCCCChhhhhcccccccccccccCCCCCccc--CCcccceEEEecCCCCCCCCcccccCCCCCCCcchhhhhhhhhhHHH
Q 013572 256 GDKGDSRVLKSSTLYKDIEEKKLLNSSPICV--NGVAVDQYLIGDGGYPLLPWLMVPFVDANPGSSEENFNAAHNLMRVP 333 (440)
Q Consensus 256 Gs~~D~~v~~~S~l~~~l~~~~l~~~~~~~l--~g~~~~~~llgD~~Ypl~~~lm~P~~~~~l~~~~~~FN~~ls~~R~~ 333 (440)
|++||+.|++.+.+.+....+... +..+ .|.+...+++|+.+||+.+|+|+||.++.++..++.||.+|+.+|.+
T Consensus 156 Gs~~D~kvl~~~~~~~~~~~~~~~---k~yl~d~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~elFN~rh~~~r~v 232 (326)
T KOG4585|consen 156 GSAHDTKVLQDSLLYKRNFPHPPL---KYYLVDSGYPLRPGLLGPIGFPLYSLLMFPYGGPQPTNSQELFNKRHSSLRSV 232 (326)
T ss_pred CCccHHHHHHhhcccccccccCCc---cccccccCcccccccccccccccchhhhcccCCCCCCchHHHHhhhhhhHHHH
Confidence 999999999999998877554322 2223 46688999999999999999999999988889999999999999999
Q ss_pred HHHHHHhhc-ccccccCCccCChhhHHHHHHHHHHHHhhhccCCCCCCcccccCCCcCCCccccccCccccccccchhhH
Q 013572 334 ALKAIASLK-NWGVLSRPIDEDFKTAVALIGACSILHNALLMREDFSGLFEELGDYSLHDESSQYYSDASLEENSTEKKA 412 (440)
Q Consensus 334 vE~afg~LK-rfriL~~~~~~~~~~~~~ii~accvLHN~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~a 412 (440)
+|++||+|| ||+||.+....+..+..+||.|||+|||+|++.++.+...+.+ +..+...... .......+.++.+
T Consensus 233 ~e~~fg~lk~rw~il~~~~~~~~~~~~~iV~a~caLHN~~~~~~~~~~~~~~~---e~~~d~~~~~-~~~~~~~~~~~~~ 308 (326)
T KOG4585|consen 233 AERAFGVLKAKWRILQRREKYDLKKLPKIVTACCALHNIIRDSDEEDPDDPKW---EKFDDYGENV-AHLRYAPQQRDYM 308 (326)
T ss_pred HHHHHHHhhhhhHHHhhcccccccchHHHHHHHHHHHHHHHhhcccccccccc---cccccccccc-hhcccchhHHHHH
Confidence 999999999 7999999866778899999999999999999877653322212 2222111000 0111124446778
Q ss_pred HHHHHHHHHHHHhhc
Q 013572 413 SAIRSALATRARVQH 427 (440)
Q Consensus 413 ~~~Rd~la~~~~~~~ 427 (440)
+.+|+.|+..+++..
T Consensus 309 ~~~r~~l~~~l~~~~ 323 (326)
T KOG4585|consen 309 EKIRDNLLSELWNGT 323 (326)
T ss_pred HHHHHHHHHHHHhcc
Confidence 999999999988753
No 2
>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=100.00 E-value=1.7e-35 Score=262.61 Aligned_cols=192 Identities=22% Similarity=0.352 Sum_probs=168.1
Q ss_pred hhhcCCChhhHHHHHHHHHhhhCCCCccccccceEEEEeecC------CCCCCCCCCcEEEEeecCCCceEEeeecCCCC
Q 013572 183 FWVAFPGPEELGLISKSFEELTGLPNCCGVIDCTRFKIIKID------GSNSSKDEDSIAVQIVVDSSSRMLSIVAGIRG 256 (440)
Q Consensus 183 ~~I~~P~~~~~~~~~~~f~~~~~fP~ciGaIDgthi~i~~p~------~~n~k~~~~si~~q~v~D~~~rf~~v~~g~pG 256 (440)
+|++-|+.++.+++++.++. .||||.+|+|||+|+.++..+ +..+|++.+++.++||++++.+|+++..|.||
T Consensus 2 ~YLr~P~~~d~~rll~~~e~-rGFpGmlGSIDCmHw~WkncP~aw~g~~~~G~~g~pTiiLEaVAs~dlwIWhaffG~~G 80 (205)
T PF04827_consen 2 EYLRRPTNEDLERLLQIGEA-RGFPGMLGSIDCMHWEWKNCPTAWKGQYTRGKEGVPTIILEAVASHDLWIWHAFFGMPG 80 (205)
T ss_pred cccCCCChhHHHHHHHhhhh-cCCCccccceeEEEeehhcchHHhhhcccCCCCCCCeehhhhhhccchhhhheeeccCC
Confidence 47889999999999977755 599999999999999999743 22477789999999999999999999999999
Q ss_pred CCCChhhhhcccccccccccccCCCCCcccCCcc-cceEEEecCCCCCCCCcccccCCCCCCCcchhhhhhhhhhHHHHH
Q 013572 257 DKGDSRVLKSSTLYKDIEEKKLLNSSPICVNGVA-VDQYLIGDGGYPLLPWLMVPFVDANPGSSEENFNAAHNLMRVPAL 335 (440)
Q Consensus 257 s~~D~~v~~~S~l~~~l~~~~l~~~~~~~l~g~~-~~~~llgD~~Ypl~~~lm~P~~~~~l~~~~~~FN~~ls~~R~~vE 335 (440)
|.+|.+|+..|+++..+.+|.. +.-...++|.+ .-.|+|+|..||-+..++++.+.|. +.+++.|.++.+++|+.||
T Consensus 81 S~NDiNVL~~Splf~~~~~G~a-p~v~f~VNg~~Y~~gYYLaDGiYP~watfvktI~~p~-~~k~k~fa~~QE~~RKDVE 158 (205)
T PF04827_consen 81 SNNDINVLDRSPLFDDLLQGQA-PRVQFTVNGHEYNMGYYLADGIYPEWATFVKTISLPQ-GEKRKLFAKHQESARKDVE 158 (205)
T ss_pred cccccccccccHHHHHHhcCcC-CceEEEecCeecccceeeccCcCcchHhHhhhcchhh-chhhHHHHHhCHHHHHHHH
Confidence 9999999999999999988863 11123457764 3568899999999999999999876 5789999999999999999
Q ss_pred HHHHhhc-ccccccCCccC-ChhhHHHHHHHHHHHHhhhccCCC
Q 013572 336 KAIASLK-NWGVLSRPIDE-DFKTAVALIGACSILHNALLMRED 377 (440)
Q Consensus 336 ~afg~LK-rfriL~~~~~~-~~~~~~~ii~accvLHN~~~~~~~ 377 (440)
||||+|+ ||+|++.|.+. +.+.+..|+.||+|||||+++.+.
T Consensus 159 rAFGVLQaRfaIi~~p~r~w~~~~l~~Im~aCiILHNMIvEDEr 202 (205)
T PF04827_consen 159 RAFGVLQARFAIIRGPARLWDREDLANIMRACIILHNMIVEDER 202 (205)
T ss_pred HHHHHHHHHHHHhcCchhccCHHHHHHHHHHHHHhhheeEeccc
Confidence 9999999 89999999875 889999999999999999997443
No 3
>PF13359 DDE_Tnp_4: DDE superfamily endonuclease
Probab=100.00 E-value=4.1e-35 Score=262.08 Aligned_cols=146 Identities=32% Similarity=0.551 Sum_probs=132.7
Q ss_pred ccceEEEEeecCC-------CCCCCCCCcEEEEeecCCCceEEeeecCCCCCCCChhhhhcccccccccccccCCCCCcc
Q 013572 213 IDCTRFKIIKIDG-------SNSSKDEDSIAVQIVVDSSSRMLSIVAGIRGDKGDSRVLKSSTLYKDIEEKKLLNSSPIC 285 (440)
Q Consensus 213 IDgthi~i~~p~~-------~n~k~~~~si~~q~v~D~~~rf~~v~~g~pGs~~D~~v~~~S~l~~~l~~~~l~~~~~~~ 285 (440)
||||||+|.+|.. ++++++.+++++|++||++|+|++++++||||+||+.+|++|.+...++.. .
T Consensus 1 iDgt~v~i~~P~~~~~~~~~y~~~k~~~~~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~s~~~~~l~~~--~------ 72 (158)
T PF13359_consen 1 IDGTHVPIQRPSDKEEQREFYSGKKKNHSLKVQIVCDPDGRIIYVSVGWPGSVHDSTIFRQSGLLDRLEQA--F------ 72 (158)
T ss_pred CccEEEEEEeCCccccccccccCCCCcceEeEEEEEeccceeEeeecccccccccccccccccccceeecc--c------
Confidence 7999999999974 244556899999999999999999999999999999999999998887522 1
Q ss_pred cCCcccceEEEecCCCCCCCCcccccC---CCCCCCcchhhhhhhhhhHHHHHHHHHhhc-ccccccCCccCC-hhhHHH
Q 013572 286 VNGVAVDQYLIGDGGYPLLPWLMVPFV---DANPGSSEENFNAAHNLMRVPALKAIASLK-NWGVLSRPIDED-FKTAVA 360 (440)
Q Consensus 286 l~g~~~~~~llgD~~Ypl~~~lm~P~~---~~~l~~~~~~FN~~ls~~R~~vE~afg~LK-rfriL~~~~~~~-~~~~~~ 360 (440)
+.++++|||.|||+.+++|+||+ +..++.+|+.||++|+++|.+||++||+|| ||++|..+++.+ ++.+..
T Consensus 73 ----~~~~~~l~D~gy~~~~~~~~P~~~~~~~~l~~~e~~~N~~~s~~R~~vE~~~~~lK~rf~~l~~~~~~~~~~~~~~ 148 (158)
T PF13359_consen 73 ----PPGEYLLGDSGYPLSPYLLTPYKKPKGRELTPEEKEFNRRHSSARIIVERAFGRLKSRFRILRGRLRLSRPEKAPQ 148 (158)
T ss_pred ----ccCccccccccccccccccccccccccccccccccchhccccceeeeeHHHHHHHHHhcccCCcccCCCcHhHHHH
Confidence 23789999999999999999996 467889999999999999999999999999 899999899988 999999
Q ss_pred HHHHHHHHHh
Q 013572 361 LIGACSILHN 370 (440)
Q Consensus 361 ii~accvLHN 370 (440)
+|.|||+|||
T Consensus 149 ii~~~~~LhN 158 (158)
T PF13359_consen 149 IILACCVLHN 158 (158)
T ss_pred HHheeEEEEC
Confidence 9999999999
No 4
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=98.85 E-value=2.3e-09 Score=77.56 Aligned_cols=51 Identities=22% Similarity=0.294 Sum_probs=48.2
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+++++|+.++|.||++|.++.++|..||||+|||++++++++++++..++
T Consensus 2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l~ 52 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVLK 52 (53)
T ss_pred CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhcC
Confidence 479999999999999999999999999999999999999999999987653
No 5
>PF13612 DDE_Tnp_1_3: Transposase DDE domain
Probab=98.66 E-value=7.4e-09 Score=91.74 Aligned_cols=121 Identities=17% Similarity=0.153 Sum_probs=91.1
Q ss_pred CCccccccceEEEEeecC--------------CCCCCCCCCcEEEEeecCCCceEEeeecCCCCCCCChhhhhccccccc
Q 013572 207 PNCCGVIDCTRFKIIKID--------------GSNSSKDEDSIAVQIVVDSSSRMLSIVAGIRGDKGDSRVLKSSTLYKD 272 (440)
Q Consensus 207 P~ciGaIDgthi~i~~p~--------------~~n~k~~~~si~~q~v~D~~~rf~~v~~g~pGs~~D~~v~~~S~l~~~ 272 (440)
+..+.+||.+-||++.+. +++..+++|++++.++|+..|.++.+.. .||++||..++.. +...
T Consensus 4 ~~~i~~iDS~Pi~vC~~~R~~r~k~~~~~a~~G~~a~~~fyGfKlHllv~~~G~i~~~~l-T~an~~D~~~~~~--l~~~ 80 (155)
T PF13612_consen 4 CTGIYIIDSFPIPVCHNIRIKRHKVFKGLAYRGYCAMGWFYGFKLHLLVNDSGEIVAFTL-TPANVHDRKVLEE--LSEN 80 (155)
T ss_pred ccEEEEEecCChhHhCccchhhhccccCccccceeccceeEeeeeeeEEccCCcEEEEEE-ccccccccccccc--cccc
Confidence 556889999999999863 1133467999999999999999998766 7999999988832 1111
Q ss_pred ccccccCCCCCcccCCcccceEEEecCCCCCCC----------CcccccCCCCCCCcchhhhhhhhhhHHHHHHHHHhhc
Q 013572 273 IEEKKLLNSSPICVNGVAVDQYLIGDGGYPLLP----------WLMVPFVDANPGSSEENFNAAHNLMRVPALKAIASLK 342 (440)
Q Consensus 273 l~~~~l~~~~~~~l~g~~~~~~llgD~~Ypl~~----------~lm~P~~~~~l~~~~~~FN~~ls~~R~~vE~afg~LK 342 (440)
....++||.||--.. .|+||.+...-......+++.+.+.|..||-+|+.||
T Consensus 81 ------------------~~g~l~gDkGYis~~L~~~L~~~gI~L~t~~RkNmk~~~~~~~~~~l~~~R~~IETvfs~Lk 142 (155)
T PF13612_consen 81 ------------------LKGKLFGDKGYISKELKDELKEQGIKLITPRRKNMKNKLMPLFDKLLLRKRRIIETVFSQLK 142 (155)
T ss_pred ------------------cccceecchhhhcchHHhhhhhceEEEeccccccccccccchhhhhhhheeeEeehHHHHHH
Confidence 133799999996432 4788888632222345688899999999999999999
Q ss_pred -cccccc
Q 013572 343 -NWGVLS 348 (440)
Q Consensus 343 -rfriL~ 348 (440)
.|.+=.
T Consensus 143 ~~~~ie~ 149 (155)
T PF13612_consen 143 NQFNIEH 149 (155)
T ss_pred HhhceEe
Confidence 587644
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=96.90 E-value=3.1e-05 Score=71.00 Aligned_cols=146 Identities=17% Similarity=0.100 Sum_probs=82.1
Q ss_pred ccccccceEEEEe-e---cCCCCCCCCCCcEEEEeecC-CCceEEeeecCCCCCCCChhhhhcccccccccccccCCCCC
Q 013572 209 CCGVIDCTRFKII-K---IDGSNSSKDEDSIAVQIVVD-SSSRMLSIVAGIRGDKGDSRVLKSSTLYKDIEEKKLLNSSP 283 (440)
Q Consensus 209 ciGaIDgthi~i~-~---p~~~n~k~~~~si~~q~v~D-~~~rf~~v~~g~pGs~~D~~v~~~S~l~~~l~~~~l~~~~~ 283 (440)
.+-+||+|+|+.. . ..+.++++.....++++++| ..+.++.+.+. +|+.+|...+.. +.+. ..
T Consensus 5 ~~~~iD~T~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~d~~~~~~--ll~~----~~----- 72 (213)
T PF01609_consen 5 RVVAIDGTTIRTPHDKSARRYKKGKKRGFGYKLHLAVDDNSGLPLSVKVT-PGNVHDSKALPE--LLER----KP----- 72 (213)
T ss_dssp EEEEEETTT--EEEEEEE-B-SSGGGHSSHGGHHHHHHHHHGGGGGGEEE-EEEGG-HHHHHH--HHTT-----------
T ss_pred eEEEEECcEEEeecchhhhcccCCCCcCCCEeEEEEEeecccceeeeecc-ccccceeecccc--cccc----cc-----
Confidence 4678999999998 2 22333334466778999985 56667777776 999999998876 2222 00
Q ss_pred cccCCcccceEEEecCCCCCCC----------CcccccCCCCCC----------------------------------Cc
Q 013572 284 ICVNGVAVDQYLIGDGGYPLLP----------WLMVPFVDANPG----------------------------------SS 319 (440)
Q Consensus 284 ~~l~g~~~~~~llgD~~Ypl~~----------~lm~P~~~~~l~----------------------------------~~ 319 (440)
...+.++++|+||.-.+ ..+.|.+..... ..
T Consensus 73 -----~~~~~~vv~D~gy~s~~~~~~l~~~~~~~vi~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 147 (213)
T PF01609_consen 73 -----GRKPDLVVADRGYDSAENLEALKERGIHFVIRLKKNRKKKIQKIENKFWKSFDRRSARKKPKQKSKRVRVVIRKE 147 (213)
T ss_dssp --------EEEEEE-S--BBTTHHHHHHTS---EEEEE--EEEE-TTS-EEEE--EEEEEEEEEEETGGGEEEEEEEEEE
T ss_pred -----cccccceeecccccceeccccccccccccccccccccccccccchhhcccccccccccccccccccccccccccc
Confidence 01277999999997443 123344431000 00
Q ss_pred chhhhhh--------------hhhhHHHHHHHHHhhcccccccCCccCChhhHHHHHHHHHHHHhh
Q 013572 320 EENFNAA--------------HNLMRVPALKAIASLKNWGVLSRPIDEDFKTAVALIGACSILHNA 371 (440)
Q Consensus 320 ~~~FN~~--------------ls~~R~~vE~afg~LKrfriL~~~~~~~~~~~~~ii~accvLHN~ 371 (440)
++..... +.+.|-.||+.|..||.+--+.+....+.+.+...+.+|++-.|+
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~Y~~Rw~IE~~f~~lK~~~~l~~~~~~~~~~~~~~~~~~~la~nl 213 (213)
T PF01609_consen 148 QKKKGYFLVTNITTLPRDTAALYRRRWQIERFFRELKQFLGLERLRVRSPERIEAHLFLTLLAYNL 213 (213)
T ss_dssp CS--TTS---EEEEEESS--SHHHCGGHHHHHHHHHTTTTTGGGS--SSHHHHHHHHHHHHHH---
T ss_pred cccccccccccccccccccceeecccchhhHHHHHHHhcCCCchhcccCHHHHHHHHHHHHhhCcC
Confidence 1111222 778899999999999964234443344678888888888887774
No 7
>PF13586 DDE_Tnp_1_2: Transposase DDE domain
Probab=96.83 E-value=0.0015 Score=52.24 Aligned_cols=51 Identities=16% Similarity=0.110 Sum_probs=41.8
Q ss_pred chhhhhhhhhhHHHHHHHHHhhcccccccCCccCChhhHHHHHHHHHHHHh
Q 013572 320 EENFNAAHNLMRVPALKAIASLKNWGVLSRPIDEDFKTAVALIGACSILHN 370 (440)
Q Consensus 320 ~~~FN~~ls~~R~~vE~afg~LKrfriL~~~~~~~~~~~~~ii~accvLHN 370 (440)
...+...+.+.|-+||++|+.||+|+.|....+..+.....+|.-+|++=+
T Consensus 36 ~~~~d~~~~~~Rw~VEr~f~wlk~~Rrl~~ryek~~~s~~~~v~la~~~i~ 86 (88)
T PF13586_consen 36 PRKFDFRLYKRRWVVERTFAWLKRFRRLATRYEKLASSFLAFVHLACIVIW 86 (88)
T ss_pred cCccchhhhccceehhhhhHHHHHcCccccccccCHHHHHHHHHHHHHHHH
Confidence 567788899999999999999999999999888777777766666665543
No 8
>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=96.41 E-value=0.0017 Score=45.01 Aligned_cols=42 Identities=24% Similarity=0.248 Sum_probs=31.1
Q ss_pred CCCCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHH
Q 013572 129 LPLNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 129 r~~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~ 171 (440)
||+.++.+ ++.-.+..++.|.+..+||..||||++||++++.
T Consensus 2 Rp~~~~~~-~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 2 RPPKLSKE-QIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSSSSHC-CHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred cCCCCCHH-HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 45556655 5566666789999999999999999999999864
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=95.83 E-value=0.016 Score=40.93 Aligned_cols=45 Identities=31% Similarity=0.323 Sum_probs=38.3
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
.+|++++-.+.++| -.|.++.++|..+|+|.+||+++.++...-|
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 58999999999988 6789999999999999999999988877654
No 10
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=95.61 E-value=0.008 Score=41.44 Aligned_cols=40 Identities=28% Similarity=0.322 Sum_probs=23.1
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
.++++++..+.-+ +..|.+.+.||..+|+|++||++.+++
T Consensus 4 ~Lt~~eR~~I~~l-~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 4 HLTPEERNQIEAL-LEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp --------HHHHH-HCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred chhhhHHHHHHHH-HHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 4777888777643 689999999999999999999998764
No 11
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=95.24 E-value=0.015 Score=41.85 Aligned_cols=42 Identities=29% Similarity=0.354 Sum_probs=31.0
Q ss_pred CCCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHH
Q 013572 130 PLNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 130 ~~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
+..++.++++.+.- ++-.|.+..+||..|||+.|||+.|++.
T Consensus 4 R~~LTl~eK~~iI~-~~e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 4 RKSLTLEEKLEIIK-RLEEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp SSS--HHHHHHHHH-HHHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred CccCCHHHHHHHHH-HHHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 35789999998764 4778889999999999999999998764
No 12
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=93.84 E-value=0.023 Score=39.93 Aligned_cols=29 Identities=31% Similarity=0.345 Sum_probs=20.7
Q ss_pred ccCCCchhhhhhhhccChhhHHHHHHHHH
Q 013572 146 LVNGSTYSEIATRFEVTESVTRFCVKQLC 174 (440)
Q Consensus 146 La~g~s~~~la~~Fgvs~sTv~~~v~~v~ 174 (440)
+..|.+.+++|..+|||++||+++++++.
T Consensus 14 ~~~G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 14 LREGWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp HHHT--HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 33499999999999999999999988764
No 13
>PF13518 HTH_28: Helix-turn-helix domain
Probab=93.83 E-value=0.046 Score=38.57 Aligned_cols=37 Identities=30% Similarity=0.373 Sum_probs=30.0
Q ss_pred HHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 138 RLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 138 ~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
++.+...++ .|.++..+|..||||.+||.++++.+-.
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 445555566 6779999999999999999999887654
No 14
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=93.62 E-value=0.1 Score=37.27 Aligned_cols=43 Identities=23% Similarity=0.280 Sum_probs=31.9
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.+|+.++-.+.|.|+ .|.++.++|..+|+|.+||...+.+...
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 478888888887766 5899999999999999999988776654
No 15
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)
Probab=93.53 E-value=0.13 Score=39.72 Aligned_cols=60 Identities=25% Similarity=0.335 Sum_probs=46.6
Q ss_pred HHhcccccccCCCCCCCCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 115 GLLEPLLDCRDPVGLPLNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 115 ~~L~~~l~~~~~~~r~~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
+.|+|.+......+++..++..+-+-..|+.+.+|+..+.+-..|| +.+||++.+++..+
T Consensus 7 ~~i~p~lp~~~~~~~~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg-~~~tv~~~f~rW~~ 66 (75)
T PF13340_consen 7 ALIEPLLPPRKPRGGRPRIDLREVLNAILYVLRTGCPWRDLPEDFG-PWSTVYRRFRRWSR 66 (75)
T ss_pred HHHHhhCCCCCCCCCCCccchHHHHhcccccceecceecccchhcc-CcCcHHHHHHHHHH
Confidence 3444444434444445678888889999999999999999999999 89999988887764
No 16
>smart00351 PAX Paired Box domain.
Probab=93.09 E-value=0.12 Score=44.21 Aligned_cols=44 Identities=16% Similarity=0.141 Sum_probs=37.9
Q ss_pred CCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 131 LNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 131 ~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.++|.+++.-+.+.+. .|.+..++|..||||++||+++++++-+
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 4588899888887664 8999999999999999999999888743
No 17
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=92.97 E-value=0.2 Score=35.46 Aligned_cols=44 Identities=30% Similarity=0.407 Sum_probs=35.1
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
.+++.++-.+.+ +..|.++.++|..+|+|.+||.+++.+....+
T Consensus 3 ~l~~~e~~i~~~--~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl 46 (58)
T smart00421 3 SLTPREREVLRL--LAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46 (58)
T ss_pred CCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 366666654433 57899999999999999999999999876655
No 18
>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=92.94 E-value=0.097 Score=33.11 Aligned_cols=39 Identities=26% Similarity=0.285 Sum_probs=29.3
Q ss_pred CCCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHH
Q 013572 130 PLNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFC 169 (440)
Q Consensus 130 ~~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~ 169 (440)
+..++.+.+..+... +..|.+..+++..||++.+|++++
T Consensus 3 ~~~~~~~~~~~i~~~-~~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 3 PPKLTPEQIEEARRL-LAAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCcCCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHh
Confidence 345666665555443 457889999999999999999876
No 19
>cd00131 PAX Paired Box domain
Probab=92.84 E-value=0.13 Score=44.10 Aligned_cols=44 Identities=16% Similarity=0.187 Sum_probs=38.1
Q ss_pred CCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 131 LNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 131 ~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.++|.+.+.-|.+.+ +.|.+.+++|..||||.+||+++++++-+
T Consensus 16 ~~lS~d~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e 59 (128)
T cd00131 16 RPLPDSIRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILNRYYE 59 (128)
T ss_pred CcCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 478888888887665 68999999999999999999999887764
No 20
>PRK04217 hypothetical protein; Provisional
Probab=92.36 E-value=0.16 Score=42.25 Aligned_cols=50 Identities=12% Similarity=0.106 Sum_probs=40.9
Q ss_pred CCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 131 LNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 131 ~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
..++.+++-++.++ ...|.++.+||..+|||.+||.+.+++....|.+.+
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 45888887555444 347889999999999999999999999888877665
No 21
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=91.64 E-value=0.13 Score=44.58 Aligned_cols=44 Identities=25% Similarity=0.214 Sum_probs=38.7
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
+.+.+.+..++-.++..|.|.+.+|..||||.+||.++++++-+
T Consensus 4 ~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e 47 (138)
T COG3415 4 PFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRE 47 (138)
T ss_pred hhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhcc
Confidence 34567888889999999999999999999999999999887653
No 22
>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=91.63 E-value=0.15 Score=35.28 Aligned_cols=37 Identities=19% Similarity=0.241 Sum_probs=27.3
Q ss_pred HHHHhhheeeccCC-CchhhhhhhhccChhhHHHHHHH
Q 013572 136 DIRLGIGLFRLVNG-STYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 136 e~~L~i~L~~La~g-~s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
++.+..++-.+..| .+++..|..|||+++|+++.++.
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 45666677777778 99999999999999999876653
No 23
>PRK00118 putative DNA-binding protein; Validated
Probab=91.46 E-value=0.45 Score=39.24 Aligned_cols=50 Identities=20% Similarity=0.225 Sum_probs=40.6
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+.++-++.++ ...|.++.+||..+|+|++||++.+++....+.+.+.
T Consensus 17 ~L~ekqRevl~L~-y~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~ 66 (104)
T PRK00118 17 LLTEKQRNYMELY-YLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEE 66 (104)
T ss_pred cCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4677777777555 4569999999999999999999999988877766553
No 24
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=91.35 E-value=0.24 Score=42.00 Aligned_cols=45 Identities=20% Similarity=0.096 Sum_probs=41.5
Q ss_pred CCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 131 LNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 131 ~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
...+.+.++.+....+..|.++.++|..||||.+|++++++++..
T Consensus 11 r~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 11 RRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 468999999999999999999999999999999999999998754
No 25
>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=91.31 E-value=0.13 Score=39.82 Aligned_cols=43 Identities=16% Similarity=0.170 Sum_probs=29.7
Q ss_pred HhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 139 LGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 139 L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
+-++=+.+.+..+.+..|..||||+|||++=+.+=+..|...+
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 4456677889999999999999999999988776665555443
No 26
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=90.71 E-value=0.41 Score=42.32 Aligned_cols=49 Identities=18% Similarity=0.202 Sum_probs=43.5
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|++++-++.|++ .|.++.+||..+|+|.+||...+.+....|...+.
T Consensus 112 ~L~~~~r~il~l~~--~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 112 KMTERDRTVLLLRF--SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred cCCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 47889999999977 99999999999999999999999988888776654
No 27
>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=90.43 E-value=0.17 Score=38.81 Aligned_cols=44 Identities=23% Similarity=0.190 Sum_probs=37.2
Q ss_pred CCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHH
Q 013572 131 LNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLC 174 (440)
Q Consensus 131 ~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~ 174 (440)
...|++.+..+.-.++..|.+..+++..+||+.+|+++++++..
T Consensus 5 ~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 5 RRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp ----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence 56899999999988899999999999999999999999999887
No 28
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=90.38 E-value=0.33 Score=38.36 Aligned_cols=45 Identities=16% Similarity=0.097 Sum_probs=41.1
Q ss_pred CCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 131 LNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 131 ~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
..+++.-++.++-..+..|.+...++..||||..|+++++.++-.
T Consensus 7 A~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra 51 (85)
T PF13011_consen 7 ARLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRA 51 (85)
T ss_pred CCCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 468999999999999999999999999999999999999887654
No 29
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=89.88 E-value=0.5 Score=42.15 Aligned_cols=50 Identities=22% Similarity=0.317 Sum_probs=42.7
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|++++..+.|.++ .|.++.+||..+|+|.+||...+++....|.+.+.
T Consensus 128 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 128 SLPEELRTAITLREI-EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 478888888888776 78999999999999999999998888777766654
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=89.74 E-value=0.53 Score=32.52 Aligned_cols=42 Identities=26% Similarity=0.219 Sum_probs=34.0
Q ss_pred CCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 133 LSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 133 is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
++++++-++-+.++ .|.++.+++..+|++.+|+.+++.+...
T Consensus 11 l~~~~~~~~~~~~~-~~~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 11 LPEREREVILLRFG-EGLSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred CCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 56666666666654 8899999999999999999999887654
No 31
>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=89.25 E-value=0.66 Score=32.76 Aligned_cols=43 Identities=26% Similarity=0.346 Sum_probs=32.7
Q ss_pred CHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 134 SADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 134 s~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
+..++-.+.+ +..|.++.++|..+++|.+||...+++....+.
T Consensus 2 ~~~e~~i~~~--~~~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~ 44 (57)
T cd06170 2 TPREREVLRL--LAEGKTNKEIADILGISEKTVKTHLRNIMRKLG 44 (57)
T ss_pred CHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 3344443333 468999999999999999999999988766543
No 32
>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=89.16 E-value=0.32 Score=37.35 Aligned_cols=41 Identities=29% Similarity=0.206 Sum_probs=36.6
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
.+|+..+.+..|.+.-.|.++.+||...|+|.+||..+++.
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 47888888888888889999999999999999999988664
No 33
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=88.80 E-value=0.69 Score=42.13 Aligned_cols=51 Identities=22% Similarity=0.122 Sum_probs=43.0
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRF 183 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~ 183 (440)
.+|++++-++.|+++. |.++.+||..+|+|.+||...+++....|-+.+..
T Consensus 141 ~L~~~~~~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~ 191 (194)
T PRK12519 141 QLPESQRQVLELAYYE-GLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQD 191 (194)
T ss_pred hCCHHHhhhhhhhhhc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4788888888887765 99999999999999999999999888877766543
No 34
>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=88.50 E-value=0.78 Score=36.65 Aligned_cols=49 Identities=18% Similarity=0.255 Sum_probs=43.1
Q ss_pred CCCCHHHHHhhheeeccCCCchhhhhhhhc-cChhhHHHHHHHHHHHHHH
Q 013572 131 LNLSADIRLGIGLFRLVNGSTYSEIATRFE-VTESVTRFCVKQLCRVLCT 179 (440)
Q Consensus 131 ~~is~e~~L~i~L~~La~g~s~~~la~~Fg-vs~sTv~~~v~~v~~~i~~ 179 (440)
..+...-++++.|..--+|.++.+||..|| .+.|||+..++++-+.+-+
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 457778899999988889999999999999 9999999999888876653
No 35
>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=88.49 E-value=0.34 Score=39.08 Aligned_cols=39 Identities=21% Similarity=0.154 Sum_probs=32.0
Q ss_pred CCHHHHHhhheee------ccCCCchhhhhhhhccChhhHHHHHH
Q 013572 133 LSADIRLGIGLFR------LVNGSTYSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 133 is~e~~L~i~L~~------La~g~s~~~la~~Fgvs~sTv~~~v~ 171 (440)
++|+++-++..+| +..|.++++|+...|||.+||+|+-+
T Consensus 33 LTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn 77 (94)
T TIGR01321 33 LTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSN 77 (94)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHh
Confidence 6778888887765 34679999999999999999998643
No 36
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=88.49 E-value=0.56 Score=42.31 Aligned_cols=48 Identities=13% Similarity=0.192 Sum_probs=41.9
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTN 180 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~ 180 (440)
.+|++++.++.|+++ .|.++.+||..+|+|.+||...+++-...+.+.
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 489999999999888 899999999999999999998888777666554
No 37
>PF02209 VHP: Villin headpiece domain; InterPro: IPR003128 Villin is an F-actin bundling protein involved in the maintenance of the microvilli of the absorptive epithelia. The villin-type "headpiece" domain is a modular motif found at the extreme C terminus of larger "core" domains in over 25 cytoskeletal proteins in plants and animals, often in assocation with the Gelsolin repeat. Although the headpiece is classified as an F-actin-binding domain, it has been shown that not all headpiece domains are intrinsically F-actin-binding motifs, surface charge distribution may be an important element for F-actin recognition []. An autonomously folding, 35 residue, thermostable subdomain (HP36) of the full-length 76 amino acid residue villin headpiece, is the smallest known example of a cooperatively folded domain of a naturally occurring protein. The structure of HP36, as determined by NMR spectroscopy, consists of three short helices surrounding a tightly packed hydrophobic core []. ; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1ZV6_A 1QZP_A 1UND_A 2PPZ_A 3TJW_B 1YU8_X 2JM0_A 1WY4_A 3MYC_A 1YU5_X ....
Probab=88.29 E-value=0.28 Score=32.21 Aligned_cols=22 Identities=27% Similarity=0.368 Sum_probs=17.0
Q ss_pred ChhHHHhhcCCCHHHHHHHHHH
Q 013572 95 LPDSFRNSFKMSSSTFRWLSGL 116 (440)
Q Consensus 95 ~~~~F~~~fRms~~tF~~L~~~ 116 (440)
+|++|...|+|+++.|..|=..
T Consensus 3 sd~dF~~vFgm~~~eF~~lP~W 24 (36)
T PF02209_consen 3 SDEDFEKVFGMSREEFYKLPKW 24 (36)
T ss_dssp -HHHHHHHHSS-HHHHHHS-HH
T ss_pred CHHHHHHHHCCCHHHHHHChHH
Confidence 5899999999999999987543
No 38
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=88.18 E-value=0.75 Score=43.44 Aligned_cols=51 Identities=18% Similarity=0.082 Sum_probs=44.1
Q ss_pred CCCHHHHHhhheeec---cCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRL---VNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+.++-.+.|+|. -.|.++.+||..+|+|.+||....++....|-+.+.
T Consensus 178 ~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~ 231 (234)
T PRK08301 178 KLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEIN 231 (234)
T ss_pred hCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 488899999999874 689999999999999999999998888887766553
No 39
>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=87.93 E-value=1 Score=44.67 Aligned_cols=73 Identities=12% Similarity=-0.051 Sum_probs=55.4
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhhhh-c---CCChhhHHHHHHHHHhhhC
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRFWV-A---FPGPEELGLISKSFEELTG 205 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~~I-~---~P~~~~~~~~~~~f~~~~~ 205 (440)
.+|+.++.++.|+++ .|.+|.+||..+|+|.+||...+.+....|.+.++..- . -|.+++...+...|...++
T Consensus 142 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~~~~~~~~~~~~~v~~~~~a~~ 218 (324)
T TIGR02960 142 YLPPRQRAVLLLRDV-LGWRAAETAELLGTSTASVNSALQRARATLDEVGPSARDDQLAQPPSPEEQDLLERYIAAFE 218 (324)
T ss_pred hCCHHHhhHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHHH
Confidence 478888988888876 79999999999999999999999999998888776331 1 2333455566666655443
No 40
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=87.93 E-value=0.66 Score=41.49 Aligned_cols=49 Identities=24% Similarity=0.331 Sum_probs=41.8
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+.++.++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.+
T Consensus 126 ~L~~~~r~v~~l~~~-~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~l 174 (176)
T PRK09638 126 KLDPEFRAPVILKHY-YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEW 174 (176)
T ss_pred cCCHHHhheeeehhh-cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHHh
Confidence 478888888888887 6999999999999999999988888877766543
No 41
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=87.60 E-value=0.82 Score=41.67 Aligned_cols=50 Identities=10% Similarity=0.031 Sum_probs=43.7
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+..+-++.|+++. |.++.+||..+|+|.+||...+++....|.+.+.
T Consensus 134 ~Lp~~~R~v~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 183 (189)
T PRK12530 134 HLPAQQARVFMMREYL-ELSSEQICQECDISTSNLHVLLYRARLQLQACLS 183 (189)
T ss_pred hCCHHHHHHHhHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4888999999998876 9999999999999999999998888887776653
No 42
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=87.34 E-value=0.85 Score=43.95 Aligned_cols=51 Identities=18% Similarity=0.111 Sum_probs=43.2
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRF 183 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~ 183 (440)
.+|+.++..+.|+|+ .|.++.+||..+|+|.+||+++.++....|-..+..
T Consensus 205 ~L~~~er~vi~l~y~-e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l~~ 255 (257)
T PRK05911 205 ALEEKERKVMALYYY-EELVLKEIGKILGVSESRVSQIHSKALLKLRATLSA 255 (257)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 378888888888875 689999999999999999999999988877766543
No 43
>smart00153 VHP Villin headpiece domain.
Probab=87.15 E-value=0.43 Score=31.35 Aligned_cols=21 Identities=24% Similarity=0.335 Sum_probs=18.5
Q ss_pred ChhHHHhhcCCCHHHHHHHHH
Q 013572 95 LPDSFRNSFKMSSSTFRWLSG 115 (440)
Q Consensus 95 ~~~~F~~~fRms~~tF~~L~~ 115 (440)
+|++|...|+|+++.|..|=.
T Consensus 3 sdeeF~~vfgmsr~eF~~LP~ 23 (36)
T smart00153 3 SDEDFEEVFGMTREEFYKLPL 23 (36)
T ss_pred CHHHHHHHHCCCHHHHHhCcH
Confidence 589999999999999998743
No 44
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=87.03 E-value=1 Score=42.63 Aligned_cols=50 Identities=18% Similarity=0.062 Sum_probs=43.2
Q ss_pred CCCHHHHHhhheeec---cCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRL---VNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+.++..+.|+|+ -.|.++.+||..+|+|.+||.+..++....|...+
T Consensus 175 ~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l 227 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKEL 227 (233)
T ss_pred hCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 489999999999886 46789999999999999999998888777766554
No 45
>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=86.75 E-value=0.92 Score=40.13 Aligned_cols=47 Identities=17% Similarity=0.070 Sum_probs=40.6
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCT 179 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~ 179 (440)
.+|+.++.++.|+|+ .|.++.+||..+|+|.+||...+++....|-+
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 488899999999776 59999999999999999999988887766543
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=86.73 E-value=0.7 Score=40.22 Aligned_cols=47 Identities=17% Similarity=0.133 Sum_probs=39.3
Q ss_pred CCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHh
Q 013572 133 LSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTN 180 (440)
Q Consensus 133 is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~ 180 (440)
+|+.++-++.|.++ .|.++.+||..+|+|.+||...+++....|.+.
T Consensus 106 L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 106 LPENYRTVLILREF-KEFSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred CCHhheeeeeehhh-ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 67777777777766 799999999999999999999888887776553
No 47
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=86.58 E-value=1.2 Score=42.16 Aligned_cols=70 Identities=14% Similarity=0.062 Sum_probs=53.2
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhhhhcCC-ChhhHHHHHHHHHh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRFWVAFP-GPEELGLISKSFEE 202 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~~I~~P-~~~~~~~~~~~f~~ 202 (440)
.+|+.++.++.|+++ .|.++.+||...|+|.+||...+.+..+.|.+.+.+....+ ...+.......|.+
T Consensus 116 ~Lp~~~R~v~lL~~~-eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~~~~~~~~~~~~~~~~~~~~~ 186 (228)
T PRK06704 116 SLNVQQSAILLLKDV-FQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEEGIEIVEFTDDMEVVVTSIRE 186 (228)
T ss_pred hCCHHHhhHhhhHHh-hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcCCCCCccccHHHHHHHHHh
Confidence 478888887777665 48999999999999999999999999998888776543333 22456666666654
No 48
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=86.57 E-value=0.5 Score=33.28 Aligned_cols=28 Identities=18% Similarity=0.296 Sum_probs=23.6
Q ss_pred ccCCCchhhhhhhhccChhhHHHHHHHH
Q 013572 146 LVNGSTYSEIATRFEVTESVTRFCVKQL 173 (440)
Q Consensus 146 La~g~s~~~la~~Fgvs~sTv~~~v~~v 173 (440)
+..+.++.++|..+|+|.+||.+++.+.
T Consensus 24 ~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 24 LRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3444589999999999999999998764
No 49
>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=86.52 E-value=0.48 Score=37.84 Aligned_cols=31 Identities=19% Similarity=0.088 Sum_probs=26.4
Q ss_pred hhheeeccCCCchhhhhhhhccChhhHHHHH
Q 013572 140 GIGLFRLVNGSTYSEIATRFEVTESVTRFCV 170 (440)
Q Consensus 140 ~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v 170 (440)
...+.+++.|.+..+||..+|||++||+++.
T Consensus 41 ~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 41 LQVAKMLKQGKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 3445568899999999999999999999954
No 50
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=86.35 E-value=1.1 Score=39.55 Aligned_cols=49 Identities=22% Similarity=0.380 Sum_probs=41.4
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|++++-.+.|+++. |.++.+||..+|+|.+||...+.+....|...+
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 4788888888887765 999999999999999999998888777766554
No 51
>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=86.35 E-value=0.97 Score=39.32 Aligned_cols=46 Identities=22% Similarity=0.346 Sum_probs=39.0
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
.+|+.++-.+.|+++ .|.++.+||..+|+|.+||....++....|-
T Consensus 113 ~L~~~~r~il~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 113 KLPEQCRKIFILSRF-EGKSYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 377888888888776 6999999999999999999988888766554
No 52
>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=86.32 E-value=1.1 Score=38.28 Aligned_cols=46 Identities=24% Similarity=0.235 Sum_probs=37.1
Q ss_pred CCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHH
Q 013572 133 LSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCT 179 (440)
Q Consensus 133 is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~ 179 (440)
+|+.++-.+.+.++ .|.++.+||..+|+|.+||++...+....|-+
T Consensus 111 L~~~~~~ii~~~~~-~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYL-EGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 56677766666554 69999999999999999999999887766543
No 53
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=86.02 E-value=1.2 Score=40.41 Aligned_cols=53 Identities=17% Similarity=0.293 Sum_probs=45.1
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRFWV 185 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~~I 185 (440)
.+|++++-.+.|+++ .|.++.+||..+|+|..||...+.+....|-..+..++
T Consensus 138 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~~ 190 (193)
T PRK11923 138 QLPEDLRTALTLREF-DGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQPLL 190 (193)
T ss_pred hCCHHHhHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 478888888888776 79999999999999999999999998888877765543
No 54
>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=85.89 E-value=1.1 Score=43.41 Aligned_cols=49 Identities=24% Similarity=0.163 Sum_probs=42.2
Q ss_pred CCCHHHHHhhheeecc-CCCchhhhhhhhccChhhHHHHHHHHHHHHHHh
Q 013572 132 NLSADIRLGIGLFRLV-NGSTYSEIATRFEVTESVTRFCVKQLCRVLCTN 180 (440)
Q Consensus 132 ~is~e~~L~i~L~~La-~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~ 180 (440)
.+|+.++..+.|+|+. .|.++.+||..+|||..+|+++.++...-|-..
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 4888999999999874 489999999999999999999988887766544
No 55
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=85.62 E-value=1.2 Score=41.86 Aligned_cols=50 Identities=22% Similarity=0.192 Sum_probs=43.7
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+..+-++.|+|+ .|.+|.+||..+|||.+||...+++....|.+.+.
T Consensus 134 ~Lp~~~R~v~~L~y~-eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~ 183 (216)
T PRK12533 134 KLPVEYREVLVLREL-EDMSYREIAAIADVPVGTVMSRLARARRRLAALLG 183 (216)
T ss_pred cCCHHHHhHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHc
Confidence 478888888888877 69999999999999999999999988888777663
No 56
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=85.47 E-value=1.2 Score=39.51 Aligned_cols=49 Identities=24% Similarity=0.171 Sum_probs=42.8
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+..+-++.|+++ .|.++.+||..+|+|.+||...+.+....|-+.+
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 478888888888877 8999999999999999999999888888776654
No 57
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=85.22 E-value=1.3 Score=40.28 Aligned_cols=50 Identities=16% Similarity=0.184 Sum_probs=42.9
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+..+-++.|+++ .|.++.+||..+|+|.+||...+.+....|...+.
T Consensus 111 ~Lp~~~R~v~~L~~~-eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 111 DLPEEQRAALHLVAI-EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 488899998988887 59999999999999999999988888777765553
No 58
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=85.16 E-value=1.3 Score=40.41 Aligned_cols=50 Identities=22% Similarity=0.175 Sum_probs=43.9
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+.++-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.+.
T Consensus 116 ~Lp~~~r~i~~L~~~-~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 116 QLPDDQREAIILVGA-SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 478888888888877 89999999999999999999999988888877664
No 59
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=84.96 E-value=1.3 Score=39.96 Aligned_cols=50 Identities=24% Similarity=0.192 Sum_probs=42.5
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+.++-++.|.++. |.++.+||..+|+|.+||...+.+....|.+.+.
T Consensus 127 ~L~~~~r~v~~l~~~~-g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~ 176 (179)
T PRK09415 127 SLPIKYREVIYLFYYE-ELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLE 176 (179)
T ss_pred hCCHHHhhHhHhHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 3788888888888776 9999999999999999999988888877766543
No 60
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=84.93 E-value=1.3 Score=39.81 Aligned_cols=49 Identities=22% Similarity=0.268 Sum_probs=41.7
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|++.+-.+.|+++ .|.+|.+||..+|+|..||...+++....|.+.+
T Consensus 129 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 177 (179)
T PRK12514 129 ELEKDRAAAVRRAYL-EGLSYKELAERHDVPLNTMRTWLRRSLLKLRECL 177 (179)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCChHHHHHHHHHHHHHHHHHh
Confidence 478889988888876 7899999999999999999988888877765543
No 61
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=84.76 E-value=1.3 Score=40.12 Aligned_cols=50 Identities=18% Similarity=0.144 Sum_probs=43.7
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|++++-++.|+++ .|.++.+||..+|+|.+||...+.+....|...+.
T Consensus 131 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 131 KLSPAHREIIDLVYY-HEKSVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 478899988888887 89999999999999999999998888887776653
No 62
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=84.63 E-value=1.5 Score=38.94 Aligned_cols=50 Identities=20% Similarity=0.201 Sum_probs=42.1
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+.++-.+.|.++ .|.++.+||..+|+|.+||.+.+++....|-+.+.
T Consensus 125 ~L~~~~r~i~~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 125 ALPVKQREVFLLRYV-EGLSYREIAEILGVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred hCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 377788887777776 69999999999999999999999998887766553
No 63
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=84.57 E-value=1.4 Score=40.37 Aligned_cols=49 Identities=20% Similarity=0.191 Sum_probs=42.9
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|++++-++.|+++ .|.++.+||..+|+|.+||...+++....|-..+
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 478899988888877 8999999999999999999999998888776654
No 64
>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=84.51 E-value=1.4 Score=39.68 Aligned_cols=50 Identities=24% Similarity=0.373 Sum_probs=41.9
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|++.+-.+.|+++ .|.++.+||..+|++.+||...+++....|.+.++
T Consensus 138 ~L~~~~r~v~~l~~~-~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l~ 187 (190)
T TIGR02939 138 ALPEDLRTAITLREL-EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRLR 187 (190)
T ss_pred cCCHHHhhhhhhhhh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 367777777777765 89999999999999999999998888887776654
No 65
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=84.45 E-value=1.3 Score=39.78 Aligned_cols=49 Identities=14% Similarity=0.146 Sum_probs=41.7
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|++++-++.|.++ .|.++.+||..+|+|.+||...+++....|...+
T Consensus 136 ~L~~~~r~il~l~~~-~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T PRK09641 136 QLPEKYRTVIVLKYI-EDLSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHHHHhhhHHh-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888777 7999999999999999999998888877766554
No 66
>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=84.39 E-value=1.3 Score=31.76 Aligned_cols=30 Identities=20% Similarity=0.230 Sum_probs=25.7
Q ss_pred CCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 149 GSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 149 g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
+.+..+||..+|||++|++..+++..+-|.
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae~kli 52 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAERKLI 52 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence 567789999999999999999988776554
No 67
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=84.25 E-value=1.6 Score=42.80 Aligned_cols=50 Identities=24% Similarity=0.168 Sum_probs=42.9
Q ss_pred CCCHHHHHhhheeecc-CCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLV-NGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La-~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.++..++..+.++|+. .+.++.+||..+|||.++|+++.++...-|-..+
T Consensus 230 ~L~~rEr~VL~lry~~~~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l 280 (284)
T PRK06596 230 GLDERSRDIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAI 280 (284)
T ss_pred cCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788899999998875 6899999999999999999999988887765544
No 68
>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=84.20 E-value=1.5 Score=38.09 Aligned_cols=46 Identities=17% Similarity=0.069 Sum_probs=39.4
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCT 179 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~ 179 (440)
.++..++-.+.|+ +.|.++.++|..+|+|++||+.+.++..+.|-.
T Consensus 6 ~Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 6 FLTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred CCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 4778888777773 799999999999999999999998888777653
No 69
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=84.13 E-value=2.1 Score=37.38 Aligned_cols=47 Identities=17% Similarity=0.016 Sum_probs=39.5
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTN 180 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~ 180 (440)
.+++.++-.+.| ...|.++.++|..+|+|++||+.+.+...+.|...
T Consensus 6 ~Lt~rqreVL~l--r~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~ 52 (141)
T PRK03975 6 FLTERQIEVLRL--RERGLTQQEIADILGTSRANVSSIEKRARENIEKA 52 (141)
T ss_pred CCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 488888888877 36999999999999999999999988877665443
No 70
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=84.12 E-value=1.5 Score=38.45 Aligned_cols=50 Identities=16% Similarity=0.132 Sum_probs=43.5
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+.++-++.|+++ .|.++.+||...|+|.+||...+.+....|.+.+.
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 488888888888776 59999999999999999999999998888877664
No 71
>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=83.94 E-value=1.4 Score=38.48 Aligned_cols=47 Identities=17% Similarity=0.104 Sum_probs=40.2
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCT 179 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~ 179 (440)
.+|+.++-.+.|+++ .|.++.+||..+|+|.+||...+++.-..|.+
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 488888988888765 79999999999999999999888887776643
No 72
>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=83.73 E-value=1.6 Score=41.00 Aligned_cols=50 Identities=20% Similarity=0.038 Sum_probs=43.2
Q ss_pred CCCHHHHHhhheeec---cCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRL---VNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+.++-.+.|+|+ -.|.++.+||...|+|.+||.+..++....|.+.+
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 488899999999886 48999999999999999999999888887776543
No 73
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=83.64 E-value=1.7 Score=39.67 Aligned_cols=50 Identities=16% Similarity=0.106 Sum_probs=43.7
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+..+-++.|+++ .|.++.+||..+|+|.+||...+++....|.+.+.
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 136 NLPENTARVFTLKEI-LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred hCCHHHHHHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 478888888888776 79999999999999999999999998888877764
No 74
>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=83.51 E-value=1.5 Score=38.50 Aligned_cols=49 Identities=12% Similarity=0.063 Sum_probs=41.2
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|++.+..+.|.+ -.|.++.+||..+|+|.+||...+.+....|-..+
T Consensus 110 ~L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 110 RLPARQRAVVVLRY-YEDLSEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred hCCHHHHHHhhhHH-HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 47888888877777 56999999999999999999999888887766544
No 75
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=83.39 E-value=1.5 Score=39.51 Aligned_cols=50 Identities=20% Similarity=0.323 Sum_probs=43.0
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|++++-.+.|+|+. |.++.+||..+|+|.+||...+++....|.+.+.
T Consensus 131 ~L~~~~r~v~~l~~~~-g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 131 TLPPRQRDVVQSISVE-GASIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 4788888888887776 9999999999999999999999998888776653
No 76
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=83.30 E-value=1.6 Score=39.82 Aligned_cols=49 Identities=12% Similarity=0.114 Sum_probs=42.3
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|++.+-++.|+++ .|.++.+||..+|+|.+||..-+++..+.|...+
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 478889988888877 7999999999999999999988888887776655
No 77
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=83.28 E-value=1.7 Score=39.30 Aligned_cols=50 Identities=18% Similarity=0.120 Sum_probs=43.1
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|++++-.+.|+++. |.++.+||..+|+|..||...+++....|...+.
T Consensus 128 ~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 128 ALPERQREAIVLQYYQ-GLSNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred hCCHHHHHHhhHHHhc-CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4788888888888764 9999999999999999999999888887776653
No 78
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=83.08 E-value=1.8 Score=39.31 Aligned_cols=50 Identities=18% Similarity=0.162 Sum_probs=43.6
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+..+-++.|+++ .|.++.+||..+|+|.+||...+++..+.|-+.+.
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 478888888888775 89999999999999999999999998888877764
No 79
>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=82.77 E-value=1.8 Score=38.86 Aligned_cols=48 Identities=17% Similarity=0.031 Sum_probs=40.5
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTN 180 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~ 180 (440)
.+|+..+-++.|+++ .|.++.+||..+|+|.+||...+++....|.+.
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 388888887777766 589999999999999999999988887776554
No 80
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=82.75 E-value=2 Score=42.12 Aligned_cols=51 Identities=16% Similarity=0.107 Sum_probs=44.6
Q ss_pred CCCHHHHHhhheeec-cCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRL-VNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~L-a~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+.++..+.|+|+ ..|.++.+||..+|||.+||+++.++....|...+.
T Consensus 227 ~L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~ 278 (289)
T PRK07500 227 TLNERELRIIRERRLREDGATLEALGEELGISKERVRQIEARALEKLRRALL 278 (289)
T ss_pred cCCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 488899999999885 478999999999999999999999999888776653
No 81
>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=82.73 E-value=1.9 Score=40.76 Aligned_cols=50 Identities=16% Similarity=0.064 Sum_probs=43.2
Q ss_pred CCCHHHHHhhheeec---cCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRL---VNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+.++..+.|+++ -.|.++.+||...|+|.+||....++....|-+.+
T Consensus 178 ~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l 230 (234)
T TIGR02835 178 KLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKEI 230 (234)
T ss_pred hCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 489999999999985 37899999999999999999998888777766544
No 82
>PRK06930 positive control sigma-like factor; Validated
Probab=82.61 E-value=2 Score=38.67 Aligned_cols=50 Identities=16% Similarity=0.181 Sum_probs=41.4
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+.++-.+.|+ +..|.++.+||..+|+|.+||...+.+....|...+.
T Consensus 114 ~L~~rer~V~~L~-~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 114 VLTEREKEVYLMH-RGYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4777777666665 4789999999999999999999999998888776654
No 83
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=82.55 E-value=1.7 Score=39.21 Aligned_cols=48 Identities=23% Similarity=0.212 Sum_probs=40.6
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTN 180 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~ 180 (440)
.+|+..+..+.|+ .-.|.++.+||..+|+|.+||...+++....|-+.
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 4788888877777 46799999999999999999999988888776554
No 84
>PRK15320 transcriptional activator SprB; Provisional
Probab=82.41 E-value=1.5 Score=40.29 Aligned_cols=37 Identities=22% Similarity=0.241 Sum_probs=32.7
Q ss_pred hheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 141 IGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 141 i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
-.|..|+.|.+.++||..+++|.+||+.+..+..+.+
T Consensus 171 EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKL 207 (251)
T PRK15320 171 ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRL 207 (251)
T ss_pred HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHc
Confidence 4567899999999999999999999999988877655
No 85
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=82.20 E-value=1.9 Score=38.72 Aligned_cols=49 Identities=14% Similarity=0.169 Sum_probs=41.9
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+.++-++.|+++ .|.++.+||..+|+|.+||...+++....|...+
T Consensus 136 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 136 ALPPKYRMVIVLKYM-EDLSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 478888888888766 6999999999999999999999888887776654
No 86
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=82.18 E-value=2.1 Score=39.05 Aligned_cols=49 Identities=14% Similarity=0.152 Sum_probs=40.6
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|++.+..+.|+++ .|.++.+||..+|+|.+||..-+.+....|-+.+
T Consensus 134 ~Lp~~~r~i~~l~~~-~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l 182 (192)
T PRK09643 134 RLPVEQRAALVAVDM-QGYSVADAARMLGVAEGTVKSRCARGRARLAELL 182 (192)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 378888888877766 7899999999999999999888877777666554
No 87
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=82.15 E-value=1.4 Score=35.77 Aligned_cols=41 Identities=22% Similarity=0.238 Sum_probs=33.4
Q ss_pred HHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 137 IRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 137 ~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
++--+-| |+...-|+.+||..|+||++.|+..+++++..+.
T Consensus 22 Q~~Y~~l-yy~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~ 62 (105)
T COG2739 22 QKNYLEL-YYLDDLSLSEIAEEFNVSRQAIYDNIKRTEKILE 62 (105)
T ss_pred HHHHHHH-HHHhhccHHHHHHHhCccHHHHHHHHHHHHHHHH
Confidence 3334444 4556889999999999999999999999998875
No 88
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=82.11 E-value=1.9 Score=38.39 Aligned_cols=49 Identities=31% Similarity=0.276 Sum_probs=41.3
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|++.+-++.|+++ .|.++.+||..+|+|.+||...+++-...+...+
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 478888888888876 5999999999999999999998888777665544
No 89
>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=82.04 E-value=1.9 Score=41.19 Aligned_cols=50 Identities=24% Similarity=0.214 Sum_probs=44.0
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+..+-++.|+++ .|.+|.+||..+|||.+||...+++....|.+.+.
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 478888988888777 79999999999999999999999999888877663
No 90
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=82.03 E-value=2.2 Score=38.04 Aligned_cols=52 Identities=10% Similarity=0.187 Sum_probs=42.1
Q ss_pred CCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhhhh
Q 013572 133 LSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRFWV 185 (440)
Q Consensus 133 is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~~I 185 (440)
+|++.+-.+.| ++-.|.++.+||...|+|.+||...+.+....|.+.++.+|
T Consensus 120 L~~~~r~i~~l-~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~~ 171 (173)
T PRK12522 120 LNEKYKTVLVL-YYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEGFV 171 (173)
T ss_pred CCHHHHHHHHH-HHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 66666654444 44579999999999999999999999999998888776554
No 91
>PRK05572 sporulation sigma factor SigF; Validated
Probab=82.03 E-value=2 Score=41.19 Aligned_cols=49 Identities=20% Similarity=0.224 Sum_probs=42.7
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+.++..+.++|+ .|.++.+||..+|+|.+||+++.++....|...+
T Consensus 202 ~L~~~~~~v~~l~~~-~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l 250 (252)
T PRK05572 202 ELDERERLIVYLRYF-KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKL 250 (252)
T ss_pred cCCHHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 488899999988775 6899999999999999999999999888776544
No 92
>PRK01381 Trp operon repressor; Provisional
Probab=81.94 E-value=0.94 Score=36.82 Aligned_cols=39 Identities=21% Similarity=0.166 Sum_probs=30.3
Q ss_pred CCHHHHHhhheee-----ccC-CCchhhhhhhhccChhhHHHHHH
Q 013572 133 LSADIRLGIGLFR-----LVN-GSTYSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 133 is~e~~L~i~L~~-----La~-g~s~~~la~~Fgvs~sTv~~~v~ 171 (440)
++|.++-+++.++ |.. +.++++|+...|||.+||+|.-+
T Consensus 33 lTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn 77 (99)
T PRK01381 33 LTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITRGSN 77 (99)
T ss_pred CCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHH
Confidence 6677777776655 334 48999999999999999987633
No 93
>PHA00675 hypothetical protein
Probab=81.84 E-value=1 Score=34.59 Aligned_cols=39 Identities=21% Similarity=0.272 Sum_probs=27.9
Q ss_pred CCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHH
Q 013572 133 LSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 133 is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~ 171 (440)
|...+--.|-..+-..|.++..||..||||++||..|.+
T Consensus 23 Lt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 23 LTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred cCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHc
Confidence 444443344333336788999999999999999988744
No 94
>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=81.78 E-value=1.1 Score=32.49 Aligned_cols=43 Identities=21% Similarity=0.238 Sum_probs=33.1
Q ss_pred CCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 133 LSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 133 is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
+++.+.- .|..++.|.+..+||...+||.+||..+...+.+-+
T Consensus 4 LT~~E~~--vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 4 LTERELE--VLRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp S-HHHHH--HHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred cCHHHHH--HHHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHh
Confidence 4444443 466789999999999999999999999888777654
No 95
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=81.71 E-value=2 Score=41.28 Aligned_cols=49 Identities=20% Similarity=0.116 Sum_probs=42.2
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+.++..+.|+|+ .|.++.+||..+|+|.+||++..++....|-..+
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 378888888888886 5999999999999999999999998888776554
No 96
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=81.68 E-value=2 Score=38.82 Aligned_cols=49 Identities=18% Similarity=0.150 Sum_probs=40.6
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+.++-.+.|+++ .|.++.+||..+|+|.+||...+++....|-..+
T Consensus 137 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 185 (187)
T PRK12534 137 ELEPPRSELIRTAFF-EGITYEELAARTDTPIGTVKSWIRRGLAKLKACL 185 (187)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Confidence 477788877777764 8999999999999999999999888877766544
No 97
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=81.68 E-value=2.2 Score=38.94 Aligned_cols=49 Identities=18% Similarity=0.167 Sum_probs=43.4
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|++++-++.|+++ .|.++.+||..+|+|.+||...+.+....|-+.+
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 488899999999888 8999999999999999999999888888776655
No 98
>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=81.50 E-value=1 Score=31.25 Aligned_cols=21 Identities=19% Similarity=0.194 Sum_probs=18.1
Q ss_pred hhhhhhhhccChhhHHHHHHH
Q 013572 152 YSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 152 ~~~la~~Fgvs~sTv~~~v~~ 172 (440)
..+||...|||.+||+++++.
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 578999999999999987653
No 99
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=81.49 E-value=2.2 Score=37.39 Aligned_cols=50 Identities=14% Similarity=0.181 Sum_probs=41.4
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+..+-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.+.
T Consensus 106 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (160)
T PRK09642 106 ELPENYRDVVLAHYL-EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWK 155 (160)
T ss_pred hCCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 378888877777664 69999999999999999999988888887776653
No 100
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=81.49 E-value=2.1 Score=39.71 Aligned_cols=50 Identities=12% Similarity=0.032 Sum_probs=43.8
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|++.+-++.|+++. |.++.+||..+|+|.+||...+++..+.|.+.+.
T Consensus 148 ~L~~~~r~v~~L~~~~-g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~ 197 (206)
T PRK12544 148 GLPAKYARVFMMREFI-ELETNEICHAVDLSVSNLNVLLYRARLRLRECLE 197 (206)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4888999988888765 9999999999999999999999988888877664
No 101
>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=81.37 E-value=2.1 Score=40.14 Aligned_cols=47 Identities=21% Similarity=0.151 Sum_probs=40.5
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCT 179 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~ 179 (440)
.+|+.++-.+.++|+ .|.++.+||..+|+|.+||+...++....|-.
T Consensus 178 ~L~~~~r~vl~l~y~-~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFF-EDKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 478888888888775 68999999999999999999999988877654
No 102
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=81.29 E-value=2.6 Score=38.29 Aligned_cols=50 Identities=10% Similarity=-0.017 Sum_probs=43.4
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+..+-++.|+++ .|.+|.+||..+|+|.+||...+.+..+.|.+.+.
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 488888988888776 58999999999999999999999988888877764
No 103
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=81.20 E-value=2.6 Score=39.75 Aligned_cols=51 Identities=16% Similarity=0.129 Sum_probs=42.4
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRF 183 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~ 183 (440)
.+|++++-.+.|+++ .|.++.+||..+|+|.+||...+++....|-+.+..
T Consensus 149 ~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~ 199 (231)
T PRK11922 149 ALPDAFRAVFVLRVV-EELSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199 (231)
T ss_pred hCCHHHhhhheeehh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 477788877777665 499999999999999999999998888887776643
No 104
>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=80.99 E-value=2.4 Score=40.17 Aligned_cols=49 Identities=20% Similarity=0.114 Sum_probs=42.4
Q ss_pred CCCHHHHHhhheeec---cCCCchhhhhhhhccChhhHHHHHHHHHHHHHHh
Q 013572 132 NLSADIRLGIGLFRL---VNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTN 180 (440)
Q Consensus 132 ~is~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~ 180 (440)
.+|+.++..+.|+|. ..|.++.+||..+|||.++|+++..+...-|-..
T Consensus 176 ~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~ 227 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHP 227 (238)
T ss_pred hCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhh
Confidence 478899999999884 5789999999999999999999988888776544
No 105
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=80.72 E-value=2.2 Score=40.86 Aligned_cols=49 Identities=14% Similarity=0.028 Sum_probs=42.0
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+.++-++.|+|+ .|.++.+||..+|||.+||.+..++....|-..+
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 478888888888775 7999999999999999999999998888776544
No 106
>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=80.70 E-value=2.6 Score=41.13 Aligned_cols=51 Identities=18% Similarity=0.095 Sum_probs=44.9
Q ss_pred CCCHHHHHhhheee-c--cCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFR-L--VNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~-L--a~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+.+|..+.|+| | -.|.++.+||...|+|.+||....++....|...+.
T Consensus 222 ~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~ 275 (285)
T TIGR02394 222 ELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILE 275 (285)
T ss_pred cCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 58999999999987 4 578999999999999999999999998888777664
No 107
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=80.57 E-value=2.5 Score=38.21 Aligned_cols=49 Identities=29% Similarity=0.400 Sum_probs=42.9
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+..+-++-|.++ .|.++.+||..+|+|.+||...+++....|.+.+
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 478888888888887 4999999999999999999999999888877654
No 108
>PF13730 HTH_36: Helix-turn-helix domain
Probab=80.56 E-value=2 Score=30.52 Aligned_cols=43 Identities=21% Similarity=0.237 Sum_probs=29.9
Q ss_pred CCH-HHHHhhheeeccC--CC---chhhhhhhhccChhhHHHHHHHHHH
Q 013572 133 LSA-DIRLGIGLFRLVN--GS---TYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 133 is~-e~~L~i~L~~La~--g~---s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
+++ +..|.+.|..++. +. |+..++...|+|+.||.+.+++..+
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 444 3334455555542 22 6789999999999999999887653
No 109
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=80.55 E-value=2.4 Score=37.67 Aligned_cols=50 Identities=18% Similarity=0.175 Sum_probs=41.9
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+..+-++.|+++ .|.++.+||..+|+|.+||...+++....|.+.+.
T Consensus 118 ~L~~~~r~vl~L~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 167 (173)
T PRK09645 118 QLSPEHRAVLVRSYY-RGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQ 167 (173)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 478888888887765 49999999999999999999888888877776553
No 110
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=80.46 E-value=2.8 Score=37.91 Aligned_cols=51 Identities=20% Similarity=0.115 Sum_probs=42.2
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRF 183 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~ 183 (440)
.+|++++..+.|+++ .|.++.+||..+|+|.+||...+.+....|.+.+..
T Consensus 106 ~L~~~~r~i~~l~~~-~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 106 ALPEKYAEALRLTEL-EGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred hCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 377788887777754 799999999999999999999988888877766543
No 111
>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=80.43 E-value=2.5 Score=37.99 Aligned_cols=48 Identities=25% Similarity=0.245 Sum_probs=40.5
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTN 180 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~ 180 (440)
.+|+.++-++.|.++ .|.++.+||...|+|.+||...+++....|-+.
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 478888888877776 899999999999999999999888887766543
No 112
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=80.27 E-value=2.8 Score=37.83 Aligned_cols=50 Identities=20% Similarity=0.238 Sum_probs=43.3
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|++++-++.|.++ .|.+|.++|...|||.+||...+++....+.+.+.
T Consensus 127 ~Lp~~~R~~~~l~~~-~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 127 RLPPRQREAFLLRYL-EGLSYEEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred hCCHHHhHHhhhHhh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 488888888888777 59999999999999999999999988888776653
No 113
>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=80.26 E-value=2.6 Score=38.37 Aligned_cols=50 Identities=20% Similarity=0.200 Sum_probs=41.5
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+..+-++.|++ -.|.++.+||...|+|.+||...+.+....|.+.+.
T Consensus 131 ~Lp~~~r~i~~L~~-~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 131 GLPEEFRQAVYLAD-VEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred hCCHHHhhheeehh-hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 37778887777765 468999999999999999999998888887776654
No 114
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=80.23 E-value=2.2 Score=37.48 Aligned_cols=46 Identities=17% Similarity=0.250 Sum_probs=38.3
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
.+|++++-++.|+++ .|.++.+||..+|+|.+||...+++..+.+.
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 478888887777655 6999999999999999999988887766553
No 115
>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=79.74 E-value=2.5 Score=37.49 Aligned_cols=49 Identities=18% Similarity=0.142 Sum_probs=40.2
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+.++-++.|.++. |.++.++|..+|+|.+||...+.+....|...+
T Consensus 119 ~L~~~~r~i~~l~~~~-g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l 167 (169)
T TIGR02954 119 TLNDKYQTAIILRYYH-DLTIKEIAEVMNKPEGTVKTYLHRALKKLKKRL 167 (169)
T ss_pred hCCHHHhHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 3777888777776665 999999999999999999998888887766544
No 116
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=79.53 E-value=3 Score=39.47 Aligned_cols=50 Identities=20% Similarity=0.186 Sum_probs=42.3
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+.++-.+.|+|+ .|.++.+||..+|+|.+||...+++....|.+.+.
T Consensus 184 ~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~ 233 (236)
T PRK06986 184 SLPEREQLVLSLYYQ-EELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLG 233 (236)
T ss_pred hCCHHHHHHHHhHhc-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 378888888888774 78999999999999999999999988887766553
No 117
>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=79.43 E-value=2.5 Score=39.74 Aligned_cols=47 Identities=17% Similarity=0.128 Sum_probs=39.9
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCT 179 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~ 179 (440)
.+|+.++..+.++|+ .|.++.+||..+|+|.++|+++.++...-|-.
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 478888888888764 68899999999999999999999888876654
No 118
>PRK06030 hypothetical protein; Provisional
Probab=79.36 E-value=2.5 Score=36.04 Aligned_cols=47 Identities=11% Similarity=0.091 Sum_probs=41.3
Q ss_pred CCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 131 LNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 131 ~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
..+...-|++|.|.+--+|.++.+||..||.+.|||..-++.+-+.+
T Consensus 51 k~i~~aRqIAMYL~r~~~~~sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 51 REVSRIRQIAMYVAHVSLGWPMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred cccchHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence 46788899999999999999999999999999999998888666544
No 119
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=79.16 E-value=2.9 Score=38.41 Aligned_cols=50 Identities=14% Similarity=0.072 Sum_probs=42.9
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+..+-++.|+++ .|.+|.+||..+|+|.+||...+.+....|.+.+.
T Consensus 139 ~Lp~~~r~v~~L~~~-eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 139 HLPEQIGRVFMMREF-LDFEIDDICTELTLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 488888988888765 68899999999999999999988888888777663
No 120
>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=78.80 E-value=2.4 Score=41.73 Aligned_cols=45 Identities=20% Similarity=0.105 Sum_probs=39.3
Q ss_pred CCCHHHHHhhheeec---cCCCchhhhhhhhccChhhHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRL---VNGSTYSEIATRFEVTESVTRFCVKQLCRV 176 (440)
Q Consensus 132 ~is~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTv~~~v~~v~~~ 176 (440)
.+|+.++..+.|+|. ..+.++.+||..+|||+++|..+.++....
T Consensus 249 ~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~k 296 (298)
T TIGR02997 249 ELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRK 296 (298)
T ss_pred cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 488999999999985 678999999999999999999988776553
No 121
>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=78.65 E-value=3 Score=37.91 Aligned_cols=50 Identities=14% Similarity=0.087 Sum_probs=42.1
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+..+-++.|+|+ .|.++.+||..+|+|.+||...+.+..+.|.+.+.
T Consensus 131 ~L~~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~ 180 (188)
T TIGR02943 131 HLPEQTARVFMMREV-LGFESDEICQELEISTSNCHVLLYRARLSLRACLS 180 (188)
T ss_pred hCCHHHHHHHHHHHH-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 377888887777766 49999999999999999999998888887776664
No 122
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=78.55 E-value=3 Score=40.09 Aligned_cols=48 Identities=17% Similarity=0.163 Sum_probs=40.4
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTN 180 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~ 180 (440)
.+++.++..+.++|+ .|.++.++|..+|+|.+||+++.++....|-..
T Consensus 209 ~L~~~er~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~~ 256 (258)
T PRK08215 209 KLNDREKLILNLRFF-QGKTQMEVAEEIGISQAQVSRLEKAALKHMRKY 256 (258)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 478888888888775 688999999999999999999988877766543
No 123
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=78.29 E-value=2.6 Score=35.10 Aligned_cols=46 Identities=24% Similarity=0.227 Sum_probs=41.2
Q ss_pred CCCCHHHHHhhheeeccCCCchhhhhhhhcc-ChhhHHHHHHHHHHH
Q 013572 131 LNLSADIRLGIGLFRLVNGSTYSEIATRFEV-TESVTRFCVKQLCRV 176 (440)
Q Consensus 131 ~~is~e~~L~i~L~~La~g~s~~~la~~Fgv-s~sTv~~~v~~v~~~ 176 (440)
...|.|.|+.+.-.++..|.++..+|..||| +.++.++++.++-..
T Consensus 6 r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~ 52 (116)
T COG2963 6 KKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKG 52 (116)
T ss_pred ccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHc
Confidence 4689999999999999999999999999996 999999988877653
No 124
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=78.27 E-value=3.1 Score=36.70 Aligned_cols=50 Identities=18% Similarity=0.103 Sum_probs=40.8
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|++.+-++.|++ -.|.++.+||..+|+|.+||...+++....|-..+.
T Consensus 108 ~L~~~~r~v~~l~~-~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 108 TLPVIEAQAILLCD-VHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred hCCHHHHHHHHhHH-HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46777777666654 468999999999999999999999988888776653
No 125
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=78.18 E-value=2.9 Score=37.99 Aligned_cols=47 Identities=21% Similarity=0.049 Sum_probs=40.6
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCT 179 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~ 179 (440)
.+|++++-.+.|+++ .|.++.+||..+|+|.+||...+.+....|-.
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 488999999998886 69999999999999999999888877766543
No 126
>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=78.01 E-value=3.5 Score=36.72 Aligned_cols=50 Identities=24% Similarity=0.247 Sum_probs=42.0
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+.++.++.|.++ .|.++.+||..+|+|.+||...+.+....|-..+.
T Consensus 100 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTEL-EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 478888888887765 68999999999999999999998888877766654
No 127
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=77.86 E-value=3.3 Score=41.40 Aligned_cols=77 Identities=13% Similarity=0.037 Sum_probs=55.0
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhhhhc---CCChhhHHHHHHHHHhhhCCCC
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRFWVA---FPGPEELGLISKSFEELTGLPN 208 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~~I~---~P~~~~~~~~~~~f~~~~~fP~ 208 (440)
.+|+.+|-++.|++ -.|.++.+||..+|+|.+||...+.+....|.+..+.... -|..++.+++...|...++=.+
T Consensus 153 ~Lp~~~R~v~~L~~-~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~~~v~~~~~A~~~gD 231 (339)
T PRK08241 153 HLPPRQRAVLILRD-VLGWSAAEVAELLDTSVAAVNSALQRARATLAERGPSAADTLREPDDPEERALLARYVAAFEAYD 231 (339)
T ss_pred hCCHHHhhhhhhHH-hhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhcCCCcccccCCCCChHHHHHHHHHHHHHhcCC
Confidence 47788888777765 4689999999999999999999999888888774332111 1233566677777766554334
Q ss_pred c
Q 013572 209 C 209 (440)
Q Consensus 209 c 209 (440)
.
T Consensus 232 ~ 232 (339)
T PRK08241 232 V 232 (339)
T ss_pred H
Confidence 3
No 128
>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=77.71 E-value=3 Score=30.21 Aligned_cols=26 Identities=35% Similarity=0.396 Sum_probs=21.9
Q ss_pred CchhhhhhhhccChhhHHHHHHHHHH
Q 013572 150 STYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 150 ~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.+..+|+..++++++|+++++++..+
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 58899999999999999998887654
No 129
>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=77.64 E-value=3.4 Score=39.58 Aligned_cols=48 Identities=15% Similarity=-0.023 Sum_probs=41.0
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTN 180 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~ 180 (440)
.+|+.++-.+.|+|+ .|.++.+||..+|+|.+||+...++....|-..
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 488889988888875 689999999999999999999988887766543
No 130
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=77.61 E-value=3.3 Score=36.79 Aligned_cols=49 Identities=24% Similarity=0.316 Sum_probs=41.1
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+..+.++.|++ -.|.++.+||..+|+|.+||...+.+....+.+.+
T Consensus 118 ~L~~~~r~v~~L~~-~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~ 166 (168)
T PRK12525 118 GLSGKARAAFLMSQ-LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGF 166 (168)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhh
Confidence 48888888888875 57999999999999999999988888777765543
No 131
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=77.58 E-value=3.7 Score=37.35 Aligned_cols=49 Identities=18% Similarity=0.061 Sum_probs=39.8
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+..+-.+.|++ -.|.++.+||...|+|.+||...+.+..+.|-+.+
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 36777777666665 57999999999999999999988888877776655
No 132
>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=77.52 E-value=3.3 Score=39.65 Aligned_cols=47 Identities=13% Similarity=0.159 Sum_probs=40.1
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCT 179 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~ 179 (440)
.+++.++..+.++|+ .|.++.+||..+|+|.++|+++.++...-|..
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 478888888888775 68899999999999999999998888776543
No 133
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=77.42 E-value=3.2 Score=37.38 Aligned_cols=49 Identities=20% Similarity=0.268 Sum_probs=40.1
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+.++.++.|++ -.|.++.+||..+|+|.+||...+++....|...+
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 46777787666655 47999999999999999999999988887776654
No 134
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=77.35 E-value=3.1 Score=36.10 Aligned_cols=45 Identities=24% Similarity=0.120 Sum_probs=38.2
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
.+|+.++-.+.|+|+ .|.++.+||...|+|.+||...+.+....|
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 478888888888776 589999999999999999998888776654
No 135
>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=77.29 E-value=2.4 Score=33.73 Aligned_cols=35 Identities=23% Similarity=0.217 Sum_probs=27.2
Q ss_pred HHHhhheeeccCCCchhhhhhhhccChhhHHHHHH
Q 013572 137 IRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 137 ~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~ 171 (440)
+|+.++=-.|..|.+|++|+...|+|..||+|.-+
T Consensus 37 ~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr 71 (87)
T PF01371_consen 37 QRWQVAKELLDEGKSYREIAEETGVSIATITRVSR 71 (87)
T ss_dssp HHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHH
T ss_pred HHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 33444433577999999999999999999998644
No 136
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=77.19 E-value=3.9 Score=40.67 Aligned_cols=49 Identities=16% Similarity=0.112 Sum_probs=42.9
Q ss_pred CCCHHHHHhhheeec---cCCCchhhhhhhhccChhhHHHHHHHHHHHHHHh
Q 013572 132 NLSADIRLGIGLFRL---VNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTN 180 (440)
Q Consensus 132 ~is~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~ 180 (440)
.+|+.++..+.|+|. ..+.++.+||..+|||+++|..+..+....|-..
T Consensus 256 ~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~ 307 (317)
T PRK07405 256 DLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR 307 (317)
T ss_pred cCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 488999999999986 5778999999999999999999988888777653
No 137
>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=77.06 E-value=2.7 Score=28.99 Aligned_cols=28 Identities=25% Similarity=0.298 Sum_probs=22.8
Q ss_pred CCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 148 NGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 148 ~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
...+..+++..+|++++||+++++...+
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 5677889999999999999999876543
No 138
>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=77.03 E-value=4.7 Score=33.97 Aligned_cols=74 Identities=19% Similarity=0.060 Sum_probs=45.1
Q ss_pred hhHHHhhcCCCHHHHHHHHHHhcccccccCCCCCCCCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHH
Q 013572 96 PDSFRNSFKMSSSTFRWLSGLLEPLLDCRDPVGLPLNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 96 ~~~F~~~fRms~~tF~~L~~~L~~~l~~~~~~~r~~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
-.+=-..|++++.|....+..-+.--....+.+++ .+.. +. ...+.---.+.+..+++..||||.+|+++.+++
T Consensus 21 ~~eaa~~F~VS~~Tv~~W~k~~~~G~~~~k~r~~~-Kid~-~~-L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkr 94 (119)
T PF01710_consen 21 IREAAKRFGVSRNTVYRWLKRKETGDLEPKPRGRK-KIDR-DE-LKALVEENPDATLRELAERLGVSPSTIWRALKR 94 (119)
T ss_pred HHHHHHHhCcHHHHHHHHHHhcccccccccccccc-cccH-HH-HHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHH
Confidence 34455688999999888887433211112223322 4432 22 222222345667789999999999999877654
No 139
>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=76.92 E-value=3.6 Score=28.32 Aligned_cols=29 Identities=21% Similarity=0.224 Sum_probs=22.9
Q ss_pred cCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 147 VNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 147 a~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
..+.+..++|..+|+|.+||++++++..+
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34578899999999999999999887654
No 140
>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=76.88 E-value=3.2 Score=30.48 Aligned_cols=40 Identities=18% Similarity=0.226 Sum_probs=28.1
Q ss_pred HHHHhhheeecc---CCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 136 DIRLGIGLFRLV---NGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 136 e~~L~i~L~~La---~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.+...-+++.|. ...+-.+||..++||++||+..+++..+
T Consensus 6 ~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~ 48 (60)
T PF01325_consen 6 EEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAE 48 (60)
T ss_dssp HHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHH
Confidence 344444555554 4566789999999999999998877653
No 141
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=76.54 E-value=3.9 Score=39.11 Aligned_cols=49 Identities=22% Similarity=0.142 Sum_probs=41.3
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+.++-.+.|+|+ .|.++.+||..+|+|.+||...+++....|-..+
T Consensus 201 ~L~~~~r~vl~l~~~-~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 249 (251)
T PRK07670 201 QLSEKEQLVISLFYK-EELTLTEIGQVLNLSTSRISQIHSKALFKLKKLL 249 (251)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 378888888888875 8999999999999999999998888777665443
No 142
>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=76.25 E-value=2 Score=31.57 Aligned_cols=27 Identities=26% Similarity=0.196 Sum_probs=23.1
Q ss_pred CCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 149 GSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 149 g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
..+..+++..+|++++||++++....+
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 357889999999999999998877665
No 143
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=76.12 E-value=3.7 Score=36.98 Aligned_cols=49 Identities=18% Similarity=0.118 Sum_probs=41.4
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+.++-.+.|+++ .|.++.+||..+|+|.+||...+++....|-+.+
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 378888888888775 6999999999999999999999888877776554
No 144
>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=75.73 E-value=2 Score=32.57 Aligned_cols=41 Identities=20% Similarity=0.298 Sum_probs=31.7
Q ss_pred CCHHHHHhhheeeccCCCchhhhhhhhc-cChhhHHHHHHHH
Q 013572 133 LSADIRLGIGLFRLVNGSTYSEIATRFE-VTESVTRFCVKQL 173 (440)
Q Consensus 133 is~e~~L~i~L~~La~g~s~~~la~~Fg-vs~sTv~~~v~~v 173 (440)
+.-.-++++.|.+--+|.++.+|+..|| .+.|||..-++++
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 4456778888888888999999999999 9999998776654
No 145
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=75.55 E-value=3 Score=37.80 Aligned_cols=49 Identities=20% Similarity=0.109 Sum_probs=38.0
Q ss_pred CCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 133 LSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 133 is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
+|++++=++.|+++ .|.++.+||..+|+|.+||...+++....|-+.+.
T Consensus 135 L~~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 183 (188)
T PRK09640 135 VNPIDREILVLRFV-AELEFQEIADIMHMGLSATKMRYKRALDKLREKFA 183 (188)
T ss_pred cChhheeeeeeHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 55555554555444 78999999999999999999998888887776654
No 146
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=75.42 E-value=4.3 Score=38.43 Aligned_cols=50 Identities=20% Similarity=0.160 Sum_probs=41.5
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+.++-++.|+|+ .|.++.+||..+|+|.+||...+++....|.+.+.
T Consensus 171 ~Lp~~~R~v~~L~~~-eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 171 RLPEQQRIAVILSYH-ENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred hCCHHHHHHhhhHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 377788877777664 69999999999999999999999988887776653
No 147
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=75.37 E-value=4.4 Score=39.16 Aligned_cols=48 Identities=17% Similarity=0.089 Sum_probs=40.3
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTN 180 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~ 180 (440)
.+|+.++-.+.|+|+ .|.++.+||..+|+|.+||+++.++....|-..
T Consensus 215 ~L~~rer~vl~l~y~-~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 262 (264)
T PRK07122 215 ALPERERTVLVLRFF-ESMTQTQIAERVGISQMHVSRLLAKTLARLRDQ 262 (264)
T ss_pred cCCHHHHHHHHHHhc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 377788888888875 699999999999999999999988887766543
No 148
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=75.35 E-value=4.8 Score=36.90 Aligned_cols=48 Identities=23% Similarity=0.230 Sum_probs=40.4
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+.++-.+.| ++ .|.++.+||...|+|.+||...+++....|.+.+
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 367788888888 55 7999999999999999999988888777766655
No 149
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=75.28 E-value=4 Score=36.84 Aligned_cols=49 Identities=18% Similarity=0.153 Sum_probs=40.6
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+..+-++.|.++ .|.++.+||..+|+|.+||...+.+....|...+
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 477787777776655 6899999999999999999998888888776655
No 150
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=75.21 E-value=4.6 Score=35.36 Aligned_cols=49 Identities=16% Similarity=0.202 Sum_probs=41.1
Q ss_pred CCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 133 LSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 133 is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
+|++.+-.+.|++ -.|.++.+||..+|+|.+||...+.+....|.+.+.
T Consensus 106 L~~~~r~v~~l~~-~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~ 154 (159)
T PRK12527 106 LPPACRDSFLLRK-LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR 154 (159)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 7778777777754 679999999999999999999998888888776653
No 151
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=75.10 E-value=4.2 Score=36.77 Aligned_cols=48 Identities=21% Similarity=0.117 Sum_probs=39.4
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTN 180 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~ 180 (440)
.+|+.++-++.|+|+. |.++.+||..+|+|.+||...+++....|-..
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 4788888877777665 89999999999999999998888877666543
No 152
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=75.06 E-value=4.1 Score=37.41 Aligned_cols=52 Identities=23% Similarity=0.121 Sum_probs=43.5
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRFW 184 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~~ 184 (440)
.+|+..+-++.|+++ .|.++.+||..+|+|.+||...+++....|.+.+..+
T Consensus 133 ~Lp~~~r~v~~l~~~-~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~ 184 (196)
T PRK12535 133 ALPPERREALILTQV-LGYTYEEAAKIADVRVGTIRSRVARARADLIAATATG 184 (196)
T ss_pred cCCHHHHHHhhhHHH-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 377788887777765 5888999999999999999999999888888777544
No 153
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=75.03 E-value=2 Score=40.26 Aligned_cols=67 Identities=10% Similarity=0.073 Sum_probs=48.9
Q ss_pred CCCHHHHHhhheeeccCC----CchhhhhhhhccChhhHHHHHHHHHHH-HHHhhhhhhcCCChhhHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNG----STYSEIATRFEVTESVTRFCVKQLCRV-LCTNFRFWVAFPGPEELGLISK 198 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g----~s~~~la~~Fgvs~sTv~~~v~~v~~~-i~~~l~~~I~~P~~~~~~~~~~ 198 (440)
..++++|++-+|..++.+ .+..++|...|+++.|++|.++++.+- +.+.-+..|..++.+.+.+.+.
T Consensus 148 ~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~~~i~I~d~~~L~~~~~ 219 (226)
T PRK10402 148 SFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSKRGYLIKNRKQLSGLAL 219 (226)
T ss_pred cChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeCCEEEEeCHHHHHHHHH
Confidence 358899999999876543 356899999999999999999998873 3333344566666655555443
No 154
>PF13551 HTH_29: Winged helix-turn helix
Probab=74.66 E-value=2.2 Score=34.78 Aligned_cols=34 Identities=24% Similarity=0.305 Sum_probs=29.3
Q ss_pred heeeccCCCc-hhhhhhhhccChhhHHHHHHHHHH
Q 013572 142 GLFRLVNGST-YSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 142 ~L~~La~g~s-~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.|..++.|.+ ..++|..+|+|..||+++++.+..
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 3455788996 999999999999999999998764
No 155
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=74.41 E-value=4.1 Score=36.86 Aligned_cols=47 Identities=23% Similarity=0.244 Sum_probs=39.6
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCT 179 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~ 179 (440)
.+|++.+-++.|+++ .|.++.+||..+|+|.+||...+++....|.+
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 478888888887766 58899999999999999999888887776654
No 156
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=74.33 E-value=4.5 Score=35.46 Aligned_cols=46 Identities=17% Similarity=0.099 Sum_probs=38.6
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
.+|+..+.++.|+++ .|.++.+||..+|+|.+||...+++....|.
T Consensus 112 ~L~~~~r~v~~l~~~-~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~ 157 (161)
T PRK12541 112 SLPLERRNVLLLRDY-YGFSYKEIAEMTGLSLAKVKIELHRGRKETK 157 (161)
T ss_pred HCCHHHHHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 488888888877765 5899999999999999999988887776654
No 157
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=73.82 E-value=6.8 Score=38.33 Aligned_cols=69 Identities=17% Similarity=0.122 Sum_probs=50.3
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhhhhcCCChhhHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRFWVAFPGPEELGLISKSFEEL 203 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~~I~~P~~~~~~~~~~~f~~~ 203 (440)
.+|++++-++.|+++ .|.+|.+||..+|+|.+||...+++-...|.+..+..- +..++-.++...|...
T Consensus 115 ~L~~~~R~v~~L~~~-~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~~~~--~~~~~~~~~v~~f~~A 183 (293)
T PRK09636 115 RLSPLERAAFLLHDV-FGVPFDEIASTLGRSPAACRQLASRARKHVRAARPRFP--VSDEEGAELVEAFFAA 183 (293)
T ss_pred hCCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCCCC--CCchHHHHHHHHHHHH
Confidence 378888887777655 58999999999999999999999998888877654211 2223445566666544
No 158
>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=73.34 E-value=4 Score=28.80 Aligned_cols=28 Identities=25% Similarity=0.248 Sum_probs=22.5
Q ss_pred CCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 148 NGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 148 ~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.+.+..+|+...|++++|+++++...++
T Consensus 17 ~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 17 GPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp SCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3457899999999999999999877654
No 159
>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=73.20 E-value=7.1 Score=38.03 Aligned_cols=68 Identities=25% Similarity=0.130 Sum_probs=50.0
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhhhhcCCChhhHHHHHHHHHh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRFWVAFPGPEELGLISKSFEE 202 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~~I~~P~~~~~~~~~~~f~~ 202 (440)
.+|+.++-++.|+++ .|.+|.+||..+|+|.+||...+++....|.+..+.+- +..++.+++...|-.
T Consensus 108 ~L~~~~R~v~~L~~~-~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~~~~--~~~~~~~~~~~~f~~ 175 (281)
T TIGR02957 108 RLSPLERAVFVLREV-FDYPYEEIASIVGKSEANCRQLVSRARRHLDARRPRFE--VSREESRQLLERFVE 175 (281)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCCCC--CChHHHHHHHHHHHH
Confidence 478888887777654 58999999999999999999999998888876543211 222455566666654
No 160
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=73.19 E-value=5.5 Score=35.73 Aligned_cols=49 Identities=18% Similarity=0.129 Sum_probs=41.1
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+++....|-+.+
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 478888888877544 6889999999999999999998888887776655
No 161
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=73.06 E-value=5 Score=37.04 Aligned_cols=49 Identities=8% Similarity=0.051 Sum_probs=40.8
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|++++.++.|.++ .|.++.+||..+|+|.+||...+++....|.+.+
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 478888888777665 6899999999999999999988888777776554
No 162
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=72.97 E-value=6.6 Score=29.58 Aligned_cols=72 Identities=21% Similarity=0.143 Sum_probs=51.6
Q ss_pred hhHHHhhcCCCHHHHHHHHHHhcccccccCCCCCCCCCCHHHHHhhheeeccCC-Cchhhhhhhhcc-ChhhHHHHHHHH
Q 013572 96 PDSFRNSFKMSSSTFRWLSGLLEPLLDCRDPVGLPLNLSADIRLGIGLFRLVNG-STYSEIATRFEV-TESVTRFCVKQL 173 (440)
Q Consensus 96 ~~~F~~~fRms~~tF~~L~~~L~~~l~~~~~~~r~~~is~e~~L~i~L~~La~g-~s~~~la~~Fgv-s~sTv~~~v~~v 173 (440)
-++.-..++++...|..++......- + ...-...++.-++.++..+ .+..++|..+|+ +.++.++.|++.
T Consensus 4 ~~~la~~~~~s~~~l~~~f~~~~~~s----~----~~~~~~~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk~~ 75 (84)
T smart00342 4 LEDLAEALGMSPRHLQRLFKKETGTT----P----KQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKL 75 (84)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHhCcC----H----HHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 45677888999999999887643110 0 1122245666667777665 799999999999 999999998876
Q ss_pred HH
Q 013572 174 CR 175 (440)
Q Consensus 174 ~~ 175 (440)
..
T Consensus 76 ~g 77 (84)
T smart00342 76 FG 77 (84)
T ss_pred HC
Confidence 53
No 163
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=72.53 E-value=4.3 Score=36.05 Aligned_cols=50 Identities=20% Similarity=0.131 Sum_probs=40.1
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+.++-++.|+++ .|.++.+||..+|+|.+||...+++....|.+.+.
T Consensus 120 ~L~~~~r~vl~l~~~-~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 120 TLSLEHRAVLVLHDL-EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred hCCHHHeeeeeehHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 366677766666554 68889999999999999999999888888776653
No 164
>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=71.73 E-value=4.5 Score=29.04 Aligned_cols=29 Identities=28% Similarity=0.378 Sum_probs=23.1
Q ss_pred cCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 147 VNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 147 a~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
..|.+..+++..++++++|+++++++..+
T Consensus 15 ~~~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 15 NGGITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp HSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 34578899999999999999998776553
No 165
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=71.59 E-value=6.5 Score=39.30 Aligned_cols=51 Identities=18% Similarity=0.126 Sum_probs=43.9
Q ss_pred CCCHHHHHhhheee-c--cCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFR-L--VNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~-L--a~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+.++..+.++| | -.|.++..||...|||.+||..+.++-...|...+.
T Consensus 262 ~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~ 315 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQ 315 (325)
T ss_pred cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 48999999999766 3 468999999999999999999999998888776653
No 166
>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=71.36 E-value=5.5 Score=40.71 Aligned_cols=128 Identities=21% Similarity=0.250 Sum_probs=67.7
Q ss_pred ccCCCchhhhhh----hhc---cChhhHHHHHHHHHHHHHHhhhhhhcCCChhhHHHHHHHHHhh--hCCCCccccccce
Q 013572 146 LVNGSTYSEIAT----RFE---VTESVTRFCVKQLCRVLCTNFRFWVAFPGPEELGLISKSFEEL--TGLPNCCGVIDCT 216 (440)
Q Consensus 146 La~g~s~~~la~----~Fg---vs~sTv~~~v~~v~~~i~~~l~~~I~~P~~~~~~~~~~~f~~~--~~fP~ciGaIDgt 216 (440)
++.|.|.++++. .+| +|++||+++..++...+.. |..+ .+.|-++-.|||+
T Consensus 111 y~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~~--------------------w~~R~L~~~~y~~l~iD~~ 170 (381)
T PF00872_consen 111 YLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVEA--------------------WRNRPLESEPYPYLWIDGT 170 (381)
T ss_pred hccccccccccchhhhhhcccccCchhhhhhhhhhhhhHHH--------------------Hhhhccccccccceeeeee
Confidence 667777776554 345 8999999987766544322 2222 2233457789999
Q ss_pred EEEEeecCCCCCCCCCCcEEEEeecCCCce--EEeeecCCCCCCCChhhhhcccccccccccccCCCCCcccCCcccceE
Q 013572 217 RFKIIKIDGSNSSKDEDSIAVQIVVDSSSR--MLSIVAGIRGDKGDSRVLKSSTLYKDIEEKKLLNSSPICVNGVAVDQY 294 (440)
Q Consensus 217 hi~i~~p~~~n~k~~~~si~~q~v~D~~~r--f~~v~~g~pGs~~D~~v~~~S~l~~~l~~~~l~~~~~~~l~g~~~~~~ 294 (440)
|+.+..-.. -...++.+-.-+|.+|+ ++.+.++..- ....+. .+...|.+. |...+..
T Consensus 171 ~~kvr~~~~----~~~~~~~v~iGi~~dG~r~vLg~~~~~~E---s~~~W~--~~l~~L~~R-----------Gl~~~~l 230 (381)
T PF00872_consen 171 YFKVREDGR----VVKKAVYVAIGIDEDGRREVLGFWVGDRE---SAASWR--EFLQDLKER-----------GLKDILL 230 (381)
T ss_pred ecccccccc----cccchhhhhhhhhcccccceeeeecccCC---ccCEee--ecchhhhhc-----------cccccce
Confidence 999872211 01123333334556664 6666665221 122221 233333321 2222557
Q ss_pred EEecCCCCCCCCcccccCC
Q 013572 295 LIGDGGYPLLPWLMVPFVD 313 (440)
Q Consensus 295 llgD~~Ypl~~~lm~P~~~ 313 (440)
+++|+.=.+..-+-.-|+.
T Consensus 231 vv~Dg~~gl~~ai~~~fp~ 249 (381)
T PF00872_consen 231 VVSDGHKGLKEAIREVFPG 249 (381)
T ss_pred eeccccccccccccccccc
Confidence 7778765555555555543
No 167
>PF13751 DDE_Tnp_1_6: Transposase DDE domain
Probab=71.34 E-value=2.2 Score=36.01 Aligned_cols=48 Identities=13% Similarity=-0.083 Sum_probs=35.8
Q ss_pred hhhhhHH-HHHHHHHhhcccccccCCccCChhhHHHHHHHHHHHHhhhc
Q 013572 326 AHNLMRV-PALKAIASLKNWGVLSRPIDEDFKTAVALIGACSILHNALL 373 (440)
Q Consensus 326 ~ls~~R~-~vE~afg~LKrfriL~~~~~~~~~~~~~ii~accvLHN~~~ 373 (440)
.+.+.|. .||.+||.||++--+.+........+..-+.-.|+-||+-.
T Consensus 75 ~~y~~R~~~VE~~fg~~K~~~g~~r~~~rG~~kv~~~~~l~a~a~Nl~r 123 (125)
T PF13751_consen 75 ELYKQRSIKVEGVFGTIKRNHGLRRFRYRGLEKVRIEFLLAAIAYNLKR 123 (125)
T ss_pred hhhheeecccccccccchhccCCccccccchhhhHHHHHHHHHHHHHHH
Confidence 4556677 99999999997655555444567777777888888899853
No 168
>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=71.32 E-value=6 Score=37.02 Aligned_cols=48 Identities=23% Similarity=0.204 Sum_probs=40.1
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTN 180 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~ 180 (440)
.+|+.++-.+.|+|+ .|.++.+||..+|+|.+||.+..++....|-..
T Consensus 175 ~L~~~~r~il~l~y~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 175 SLSEREQLVLSLYYY-EELNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred hCCHHHHHHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 378888888888775 688999999999999999999888877766543
No 169
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=70.72 E-value=7.6 Score=34.59 Aligned_cols=47 Identities=28% Similarity=0.299 Sum_probs=36.8
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCT 179 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~ 179 (440)
.+|++.+-++.|.+ -.|.+|.+||..+|+|.+||...+++....+..
T Consensus 119 ~L~~~~r~i~~l~~-~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 119 GLNGKTREAFLLSQ-LDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred hCCHHHhHHhhhhh-ccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 36777776655544 468999999999999999999888877766544
No 170
>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=70.40 E-value=2 Score=36.22 Aligned_cols=28 Identities=25% Similarity=0.314 Sum_probs=24.9
Q ss_pred eeccCCCchhhhhhhhccChhhHHHHHH
Q 013572 144 FRLVNGSTYSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 144 ~~La~g~s~~~la~~Fgvs~sTv~~~v~ 171 (440)
-+...|.+.++++..|+||.+||.+++.
T Consensus 13 ~~~~~g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 13 AYIEKGKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred HHHHccchHHHHHHHhCcHHHHHHHHHH
Confidence 3667788999999999999999998876
No 171
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=70.39 E-value=6.5 Score=35.70 Aligned_cols=50 Identities=16% Similarity=0.132 Sum_probs=41.4
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+..+-++.|+++ .|.++.+||...|+|.+||...+.+....|.+.+.
T Consensus 128 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (188)
T PRK12517 128 KLDPEYREPLLLQVI-GGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALE 177 (188)
T ss_pred hCCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 377777776666544 69999999999999999999999988888877664
No 172
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=70.27 E-value=6 Score=37.41 Aligned_cols=46 Identities=20% Similarity=0.205 Sum_probs=38.0
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
.+++.++-.+.|+| ..|.++.++|..+|+|.++|+++.+.....|-
T Consensus 183 ~L~~~er~vi~l~~-~~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr 228 (231)
T PRK12427 183 QLDEREQLILHLYY-QHEMSLKEIALVLDLTEARICQLNKKIAQKIK 228 (231)
T ss_pred cCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 36777777777777 46899999999999999999999888776553
No 173
>PHA00542 putative Cro-like protein
Probab=70.26 E-value=3.2 Score=32.58 Aligned_cols=50 Identities=12% Similarity=-0.007 Sum_probs=36.0
Q ss_pred eeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhhhhcCCChhhHHHHHHHHHhh
Q 013572 143 LFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRFWVAFPGPEELGLISKSFEEL 203 (440)
Q Consensus 143 L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~~I~~P~~~~~~~~~~~f~~~ 203 (440)
..+...|.+..++|...|||++|++++.+.- ...|+.+.+..+++.+.+.
T Consensus 25 ~~l~~~glTq~elA~~lgIs~~tIsr~e~g~-----------~~~p~~~~l~ki~~~~~~~ 74 (82)
T PHA00542 25 CALIRAGWSQEQIADATDVSQPTICRIYSGR-----------HKDPRYSVVEKLRHLVLNL 74 (82)
T ss_pred HHHHHCCCCHHHHHHHHCcCHHHHHHHHcCC-----------CCCCCHHHHHHHHHHHHHh
Confidence 3457889999999999999999999875421 1245556666666666543
No 174
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=70.12 E-value=5.8 Score=40.43 Aligned_cols=48 Identities=27% Similarity=0.097 Sum_probs=41.1
Q ss_pred CCCHHHHHhhheeec---cCCCchhhhhhhhccChhhHHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRL---VNGSTYSEIATRFEVTESVTRFCVKQLCRVLCT 179 (440)
Q Consensus 132 ~is~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~ 179 (440)
.+++.++..+.++|+ ..+.++.+||..+|||+.+|+++..+...-|-.
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 478899999999886 346899999999999999999998888877654
No 175
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=70.09 E-value=6.3 Score=38.05 Aligned_cols=49 Identities=20% Similarity=0.127 Sum_probs=41.0
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+.++-.+.|+|+ .|.++.+||..+|+|.+||.+..++....|...+
T Consensus 212 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 260 (268)
T PRK06288 212 TLPEREKKVLILYYY-EDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260 (268)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888764 6899999999999999999988888777766555
No 176
>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=69.96 E-value=6 Score=25.24 Aligned_cols=24 Identities=25% Similarity=0.242 Sum_probs=19.5
Q ss_pred chhhhhhhhccChhhHHHHHHHHH
Q 013572 151 TYSEIATRFEVTESVTRFCVKQLC 174 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~v~~v~ 174 (440)
+-+++|...|.++.||+|++.++-
T Consensus 4 tr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHHHHHH
Confidence 567999999999999999987764
No 177
>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=69.42 E-value=6.9 Score=32.06 Aligned_cols=44 Identities=16% Similarity=0.128 Sum_probs=31.2
Q ss_pred CHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 134 SADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 134 s~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
+..++-.+- .|+-.+.|+.+||..+|||+.+|+..+++....|.
T Consensus 19 T~kQ~~~l~-lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~ 62 (101)
T PF04297_consen 19 TEKQREILE-LYYEEDLSLSEIAEELGISRQAVYDSIKRAEKKLE 62 (101)
T ss_dssp -HHHHHHHH-HHCTS---HHHHHHHCTS-HHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHH-HHHccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 334444444 56678999999999999999999999999888774
No 178
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=69.31 E-value=9.1 Score=37.56 Aligned_cols=69 Identities=20% Similarity=0.202 Sum_probs=49.3
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhhhhcCCChhhHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRFWVAFPGPEELGLISKSFEEL 203 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~~I~~P~~~~~~~~~~~f~~~ 203 (440)
.+|+.++-++.|+++ .|.+|.+||...|+|.+||...+++....|.+..+.+ -|..++.+++...|-..
T Consensus 118 ~L~p~~R~vf~L~~~-~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~~~~--~~~~~~~~~~~~~f~~a 186 (290)
T PRK09635 118 RLGPAERVVFVLHEI-FGLPYQQIATTIGSQASTCRQLAHRARRKINESRIAA--SVEPAQHRVVTRAFIEA 186 (290)
T ss_pred hCCHHHHHHhhHHHH-hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhCCCC--CCChHHHHHHHHHHHHH
Confidence 377777777766554 5999999999999999999999998888776644321 12334455666666443
No 179
>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=68.96 E-value=5.9 Score=32.29 Aligned_cols=42 Identities=19% Similarity=0.206 Sum_probs=35.4
Q ss_pred CHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHH
Q 013572 134 SADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRV 176 (440)
Q Consensus 134 s~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~ 176 (440)
.++++..+.++|+ .+.++.+++...++|++|++++-++.+..
T Consensus 57 d~~~r~iL~~~Yi-~~~~~~~I~~~l~~S~~t~yr~~~~Al~~ 98 (100)
T PF07374_consen 57 DPDERLILRMRYI-NKLTWEQIAEELNISRRTYYRIHKKALKE 98 (100)
T ss_pred ChhHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence 3578888888888 68889999999999999999987766543
No 180
>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=68.71 E-value=5.8 Score=32.88 Aligned_cols=34 Identities=21% Similarity=0.185 Sum_probs=27.5
Q ss_pred CCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 148 NGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 148 ~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.|.+...||+.|+||+||+..++.+.-.--+..+
T Consensus 79 AGlt~~aIAd~F~iS~s~~~nft~~n~~eYyr~F 112 (126)
T PF10654_consen 79 AGLTCYAIADYFKISKSTVFNFTQNNKKEYYRIF 112 (126)
T ss_pred cCCChHHHHHHHhHHHHHHHHHHHHhHHHHHHHh
Confidence 3889999999999999999998877665544444
No 181
>PRK13870 transcriptional regulator TraR; Provisional
Probab=68.41 E-value=3.6 Score=39.04 Aligned_cols=46 Identities=20% Similarity=0.079 Sum_probs=39.0
Q ss_pred CCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 131 LNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 131 ~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
..+++.|+= +|.|.|.|.+..+||...|||.+||..+++...+.|.
T Consensus 172 ~~LT~RE~E--~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~na~~KLg 217 (234)
T PRK13870 172 AWLDPKEAT--YLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFD 217 (234)
T ss_pred CCCCHHHHH--HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 357776654 5779999999999999999999999999988887654
No 182
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=68.34 E-value=7.7 Score=35.81 Aligned_cols=50 Identities=22% Similarity=0.325 Sum_probs=40.8
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+..+-.+.|++ -.|.++.+||..+|+|.+||...+.+....|.+.+.
T Consensus 138 ~L~~~~r~v~~L~~-~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~ 187 (203)
T PRK09647 138 SLPPEFRAAVVLCD-IEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALA 187 (203)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 36777777666665 579999999999999999999999888887776553
No 183
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=67.66 E-value=6.8 Score=40.49 Aligned_cols=47 Identities=15% Similarity=0.068 Sum_probs=40.5
Q ss_pred CCCHHHHHhhheeec---cCCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRL---VNGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 132 ~is~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
.+++.++-.+.|+|. ..+.++.+||..+|+|.++|..+.++....|-
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 488899999999885 35689999999999999999999888777654
No 184
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=67.60 E-value=7.6 Score=35.31 Aligned_cols=49 Identities=22% Similarity=0.227 Sum_probs=40.7
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.+|+.++-++.|++ -.|.++.+||...|+|.+||...+++....|...+
T Consensus 142 ~L~~~~r~vl~l~~-~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAY-YGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 47888888777665 46899999999999999999999888887776654
No 185
>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=67.58 E-value=6.1 Score=35.85 Aligned_cols=41 Identities=20% Similarity=0.170 Sum_probs=31.4
Q ss_pred HHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHH
Q 013572 137 IRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCT 179 (440)
Q Consensus 137 ~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~ 179 (440)
.+..+ +.++ .|.++.+||..+|+|.+||...+++..+.|-.
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 34433 4454 89999999999999999998877777665543
No 186
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=67.47 E-value=7.4 Score=37.30 Aligned_cols=96 Identities=15% Similarity=0.060 Sum_probs=65.1
Q ss_pred ccccCccccCCCCChhHHHhhcCCCHHHHHHHHHHhccc--------cccc-CC-----CCC-----------------C
Q 013572 82 RLGHGLSQLGFTQLPDSFRNSFKMSSSTFRWLSGLLEPL--------LDCR-DP-----VGL-----------------P 130 (440)
Q Consensus 82 ~l~~eL~~f~l~~~~~~F~~~fRms~~tF~~L~~~L~~~--------l~~~-~~-----~~r-----------------~ 130 (440)
.+..||.+ ..++.+--..++++.+............ .... +. ... -
T Consensus 118 ~l~~el~r---~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~ai 194 (247)
T COG1191 118 ELEQELGR---EPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDDVDDQIENPDDGVEKEELLEILKEAI 194 (247)
T ss_pred HHHHHhCC---CCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccchhhccccchhHHHHHHHHHHHHHHH
Confidence 45566664 4567788888999988655544443210 0000 00 000 0
Q ss_pred CCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 131 LNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 131 ~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
..++-.+|+.+.|+| -.+.+...+|...|||++.||++.++.+..|-..+
T Consensus 195 ~~L~EREk~Vl~l~y-~eelt~kEI~~~LgISes~VSql~kkai~kLr~~l 244 (247)
T COG1191 195 EPLPEREKLVLVLRY-KEELTQKEIAEVLGISESRVSRLHKKAIKKLRKEL 244 (247)
T ss_pred HccCHHHHHHHHHHH-HhccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHh
Confidence 146777888899888 46789999999999999999999999888776654
No 187
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=67.34 E-value=4.5 Score=36.60 Aligned_cols=44 Identities=25% Similarity=0.247 Sum_probs=36.6
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
.+|+.++= .|..++.|.+..+||...++|.+||..++..+.+-+
T Consensus 133 ~LSpRErE--VLrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKL 176 (198)
T PRK15201 133 HFSVTERH--LLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKL 176 (198)
T ss_pred CCCHHHHH--HHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 47776663 455689999999999999999999999888777654
No 188
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=67.34 E-value=4.8 Score=40.10 Aligned_cols=69 Identities=16% Similarity=0.068 Sum_probs=46.5
Q ss_pred hheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhhhhcCCChhhHHHHHHHHHhhhCCCCcccc
Q 013572 141 IGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRFWVAFPGPEELGLISKSFEELTGLPNCCGV 212 (440)
Q Consensus 141 i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~~I~~P~~~~~~~~~~~f~~~~~fP~ciGa 212 (440)
++=+|+-.|.+..+||..+|+|+++|+|.+.+--+. ...+-.|.-|.. ...++...+++++|+..|+-+
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 455677789999999999999999999987764431 011223555543 334455567777788777544
No 189
>PRK05949 RNA polymerase sigma factor; Validated
Probab=67.33 E-value=8.2 Score=38.62 Aligned_cols=48 Identities=15% Similarity=0.064 Sum_probs=41.3
Q ss_pred CCCHHHHHhhheeec---cCCCchhhhhhhhccChhhHHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRL---VNGSTYSEIATRFEVTESVTRFCVKQLCRVLCT 179 (440)
Q Consensus 132 ~is~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~ 179 (440)
.+|+.++-.+.|+|. ..+.++.+||..+|+|.++|..+..+....|-.
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 478899999999884 357899999999999999999998888877765
No 190
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=67.27 E-value=6 Score=28.01 Aligned_cols=25 Identities=20% Similarity=0.303 Sum_probs=21.0
Q ss_pred chhhhhhhhccChhhHHHHHHHHHH
Q 013572 151 TYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
+.++++..||+|++||++.+....+
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~ 46 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEA 46 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5778999999999999988776553
No 191
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=66.69 E-value=7.5 Score=39.53 Aligned_cols=47 Identities=21% Similarity=0.061 Sum_probs=39.5
Q ss_pred CCCHHHHHhhheeec-c--CCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRL-V--NGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 132 ~is~e~~L~i~L~~L-a--~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
.+|+.++..+.|+|. . .+.++..||..||||++.|+++-.+.+.-|-
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 478889999999885 3 5589999999999999999999777776554
No 192
>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=66.60 E-value=9.9 Score=32.73 Aligned_cols=49 Identities=10% Similarity=0.105 Sum_probs=39.8
Q ss_pred CCHHHHHhhheeeccC-CCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 133 LSADIRLGIGLFRLVN-GSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 133 is~e~~L~i~L~~La~-g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
++.+++-.+-++|+.. ..+...||..+|+|++|+++.-+.+...+...+
T Consensus 83 Ld~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~l 132 (134)
T TIGR01636 83 ADEQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEEL 132 (134)
T ss_pred CCHHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 6778888888888743 348999999999999999998887777666543
No 193
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=66.30 E-value=8.5 Score=31.83 Aligned_cols=48 Identities=19% Similarity=0.227 Sum_probs=33.9
Q ss_pred CCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 133 LSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 133 is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
+++++-=++-|..+ .|.++.+.|...|||++|+++++...-+.|.+.+
T Consensus 42 L~~dElEAiRL~D~-egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~AL 89 (106)
T PF02001_consen 42 LTVDELEAIRLVDY-EGLSQEEAAERMGVSRPTFQRILESARKKIADAL 89 (106)
T ss_pred eeHHHHHHHHHHHH-cCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHH
Confidence 34444434433333 3677889999999999999999888777666654
No 194
>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=66.19 E-value=7 Score=27.64 Aligned_cols=27 Identities=26% Similarity=0.252 Sum_probs=21.8
Q ss_pred CCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 149 GSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 149 g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
+.+..++|..++||+.||.+.+...-.
T Consensus 15 ~it~~eLa~~l~vS~rTi~~~i~~L~~ 41 (55)
T PF08279_consen 15 PITAKELAEELGVSRRTIRRDIKELRE 41 (55)
T ss_dssp SBEHHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 367889999999999999998877644
No 195
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=65.72 E-value=7.2 Score=26.33 Aligned_cols=28 Identities=25% Similarity=0.172 Sum_probs=23.4
Q ss_pred CCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 148 NGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 148 ~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
-..+..+++..+|+|++|+++++....+
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3567889999999999999998877654
No 196
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=65.37 E-value=4.7 Score=37.37 Aligned_cols=45 Identities=13% Similarity=0.079 Sum_probs=37.2
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
.+++.|+= .|..++.|.+..+||...++|..||..++..+++-+.
T Consensus 137 ~LT~RE~e--VL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 137 SLSRTESS--MLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred cCCHHHHH--HHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 37776663 4567899999999999999999999999888777654
No 197
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=65.08 E-value=9.2 Score=34.71 Aligned_cols=47 Identities=23% Similarity=0.248 Sum_probs=35.9
Q ss_pred CCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHh
Q 013572 133 LSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTN 180 (440)
Q Consensus 133 is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~ 180 (440)
+++++.=.+.|+++ .|.++.+||...|||..||.+-....-..+...
T Consensus 136 l~~~~~~~v~l~~~-~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~~~ 182 (185)
T PF07638_consen 136 LDPRQRRVVELRFF-EGLSVEEIAERLGISERTVRRRLRRARAWLRRE 182 (185)
T ss_pred cCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 55566666666655 789999999999999999998877665544433
No 198
>PF13551 HTH_29: Winged helix-turn helix
Probab=64.70 E-value=27 Score=28.21 Aligned_cols=78 Identities=22% Similarity=0.111 Sum_probs=48.2
Q ss_pred ChhHHHhhcCCCHHHHHHHHHHhcccc----cccCC-CCCCCC-CCHHHHHhhheeeccC------CCchhhhhhh----
Q 013572 95 LPDSFRNSFKMSSSTFRWLSGLLEPLL----DCRDP-VGLPLN-LSADIRLGIGLFRLVN------GSTYSEIATR---- 158 (440)
Q Consensus 95 ~~~~F~~~fRms~~tF~~L~~~L~~~l----~~~~~-~~r~~~-is~e~~L~i~L~~La~------g~s~~~la~~---- 158 (440)
+..+.-..+++++.|+...+....... ..+.+ .+++.. ++++++-.+.=+...+ ..+...++..
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 478889999999999999998766532 22112 233333 6766655443222222 1345566653
Q ss_pred ---hccChhhHHHHHHH
Q 013572 159 ---FEVTESVTRFCVKQ 172 (440)
Q Consensus 159 ---Fgvs~sTv~~~v~~ 172 (440)
..+|.+||++++++
T Consensus 94 ~~~~~~s~~ti~r~L~~ 110 (112)
T PF13551_consen 94 EFGIDVSPSTIRRILKR 110 (112)
T ss_pred ccCccCCHHHHHHHHHH
Confidence 26789999998775
No 199
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=64.58 E-value=4.4 Score=37.12 Aligned_cols=44 Identities=20% Similarity=0.150 Sum_probs=34.9
Q ss_pred CCCHHHHHhhheeeccC-------------CCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVN-------------GSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~-------------g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
..++.+|++-+|..++. ..+..+||...|+++.|++|+++++.+
T Consensus 138 ~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lG~tr~tvsR~l~~l~~ 194 (211)
T PRK11753 138 FLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKMLED 194 (211)
T ss_pred hcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 46789999988877653 233578999999999999999887664
No 200
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=64.24 E-value=5.9 Score=34.22 Aligned_cols=44 Identities=11% Similarity=0.059 Sum_probs=30.9
Q ss_pred CCCHHH-HHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 132 NLSADI-RLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 132 ~is~e~-~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
++++.+ .+...|+....|.+..+|+..++++++|+++.+.+..+
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 355544 33444444444567899999999999999988776654
No 201
>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=63.96 E-value=3.5 Score=35.38 Aligned_cols=35 Identities=11% Similarity=0.061 Sum_probs=30.3
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTR 167 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~ 167 (440)
.+|+..|-++.|+++ .|.++.+||..+|+|.+||.
T Consensus 107 ~Lp~~~r~v~~l~~~-~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 107 ILPNKQKKIIYMKFF-EDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHhhc
Confidence 488888888888655 68999999999999999985
No 202
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=63.21 E-value=7.4 Score=25.98 Aligned_cols=30 Identities=20% Similarity=0.066 Sum_probs=22.2
Q ss_pred ccCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 146 LVNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 146 La~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
+.++.+..+||..+|+|.++.++.+++.+.
T Consensus 5 ~~~~~~l~~iA~~~g~S~~~f~r~Fk~~~g 34 (42)
T PF00165_consen 5 LQQKLTLEDIAEQAGFSPSYFSRLFKKETG 34 (42)
T ss_dssp T-SS--HHHHHHHHTS-HHHHHHHHHHHTS
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHHHHHC
Confidence 456778899999999999999999887643
No 203
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=62.82 E-value=7.8 Score=30.34 Aligned_cols=27 Identities=26% Similarity=0.378 Sum_probs=23.7
Q ss_pred CCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 149 GSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 149 g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
+.+..+++..+|++++||++++....+
T Consensus 20 ~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 20 GLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 478889999999999999999887754
No 204
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=62.60 E-value=20 Score=33.53 Aligned_cols=96 Identities=13% Similarity=0.062 Sum_probs=62.8
Q ss_pred hheeeccCCCchhhhhhh-----hccChhhHHHHHHHHHHHHHHhhhhhhcCCChhhHHHHHHHHHhhhCCCCccccccc
Q 013572 141 IGLFRLVNGSTYSEIATR-----FEVTESVTRFCVKQLCRVLCTNFRFWVAFPGPEELGLISKSFEELTGLPNCCGVIDC 215 (440)
Q Consensus 141 i~L~~La~g~s~~~la~~-----Fgvs~sTv~~~v~~v~~~i~~~l~~~I~~P~~~~~~~~~~~f~~~~~fP~ciGaIDg 215 (440)
..=+||+.+.||+.++.. ..|+.+|+++++.+.-..+...++.. . .-++-.-.||-
T Consensus 17 ~V~~yl~~~Ls~r~v~e~l~~rgi~v~h~Ti~rwv~k~~~~~~~~~~~r----~---------------~~~~~~w~vDE 77 (215)
T COG3316 17 AVWLYLRYGLSLRDVEEMLAERGIEVDHETIHRWVQKYGPLLARRLKRR----K---------------RKAGDSWRVDE 77 (215)
T ss_pred HHHHHhhcchhhccHHHHHHHcCcchhHHHHHHHHHHHhHHHHHHhhhh----c---------------cccccceeeee
Confidence 334567779999988765 35568999999999888877665321 0 11233457888
Q ss_pred eEEEEeecCCCCCCCCCCcEEEEeecCCCceEEeeecCCCCCCCChhhhh
Q 013572 216 TRFKIIKIDGSNSSKDEDSIAVQIVVDSSSRMLSIVAGIRGDKGDSRVLK 265 (440)
Q Consensus 216 thi~i~~p~~~n~k~~~~si~~q~v~D~~~rf~~v~~g~pGs~~D~~v~~ 265 (440)
|-|.|...-.+ +=..||.+|..+++...-.-....+.-|-
T Consensus 78 t~ikv~gkw~y----------lyrAid~~g~~Ld~~L~~rRn~~aAk~Fl 117 (215)
T COG3316 78 TYIKVNGKWHY----------LYRAIDADGLTLDVWLSKRRNALAAKAFL 117 (215)
T ss_pred eEEeeccEeee----------hhhhhccCCCeEEEEEEcccCcHHHHHHH
Confidence 88888733222 23467888888888876555555555443
No 205
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=61.68 E-value=8.5 Score=35.35 Aligned_cols=45 Identities=20% Similarity=0.059 Sum_probs=37.5
Q ss_pred CCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 131 LNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 131 ~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
..+++.++ -.|..++.|.+..+||...++|.+||..++.+..+-+
T Consensus 149 ~~Lt~rE~--evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl 193 (216)
T PRK10840 149 KRLSPKES--EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKL 193 (216)
T ss_pred ccCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 35888776 4566789999999999999999999999887776654
No 206
>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=61.47 E-value=6.9 Score=35.17 Aligned_cols=83 Identities=12% Similarity=-0.049 Sum_probs=51.9
Q ss_pred CChhHHHhhcCCCHHHHHHHHHHhcccccccCCCC-CCCCCCHHHHHhhheeeccC--------------CCchhhhhhh
Q 013572 94 QLPDSFRNSFKMSSSTFRWLSGLLEPLLDCRDPVG-LPLNLSADIRLGIGLFRLVN--------------GSTYSEIATR 158 (440)
Q Consensus 94 ~~~~~F~~~fRms~~tF~~L~~~L~~~l~~~~~~~-r~~~is~e~~L~i~L~~La~--------------g~s~~~la~~ 158 (440)
.+-+.|...+.-++..-..++..+...+....... .-...++++|++-+|.+|+. ..+..+||..
T Consensus 73 i~~~~~~~l~~~~p~l~~~~~~~l~~~l~~~~~~~~~l~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~ 152 (193)
T TIGR03697 73 VPIEQVEKAIEEDPDLSMLLLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEA 152 (193)
T ss_pred eeHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHH
Confidence 34456666655555555555544443322110000 00135789999999877642 2468899999
Q ss_pred hccChhhHHHHHHHHHHH
Q 013572 159 FEVTESVTRFCVKQLCRV 176 (440)
Q Consensus 159 Fgvs~sTv~~~v~~v~~~ 176 (440)
.|+++.||+|+++++.+.
T Consensus 153 lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 153 IGSTRVTITRLLGDLRKK 170 (193)
T ss_pred hCCcHHHHHHHHHHHHHC
Confidence 999999999998887753
No 207
>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=61.26 E-value=12 Score=35.32 Aligned_cols=46 Identities=20% Similarity=0.133 Sum_probs=38.7
Q ss_pred CCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 131 LNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 131 ~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
..+|+.++=.+.+ .+.|.++.+||..+|+|.+||..++.+..+.+.
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 4588877766665 589999999999999999999999888877654
No 208
>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=60.47 E-value=6 Score=30.99 Aligned_cols=22 Identities=32% Similarity=0.273 Sum_probs=19.1
Q ss_pred CchhhhhhhhccChhhHHHHHH
Q 013572 150 STYSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 150 ~s~~~la~~Fgvs~sTv~~~v~ 171 (440)
.+..+++..||||.+||++.+.
T Consensus 20 ~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 20 ATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred CCHHHHHHHhCCCHHHHHHHhc
Confidence 4577999999999999999764
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=59.99 E-value=9.2 Score=27.83 Aligned_cols=30 Identities=23% Similarity=0.301 Sum_probs=25.1
Q ss_pred ccCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 146 LVNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 146 La~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
-..+.+..+++..+|++.+|++..++...+
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 467888999999999999999999877654
No 210
>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=59.62 E-value=7 Score=27.48 Aligned_cols=42 Identities=19% Similarity=0.248 Sum_probs=29.8
Q ss_pred cCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhhhhcCCChhhHHHHHHHH
Q 013572 147 VNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRFWVAFPGPEELGLISKSF 200 (440)
Q Consensus 147 a~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~~I~~P~~~~~~~~~~~f 200 (440)
..|.++.++|...|+|++|++++.+. -..|+.+.+..++..|
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 57889999999999999999987554 2345656666666555
No 211
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=59.48 E-value=8.8 Score=27.71 Aligned_cols=35 Identities=23% Similarity=0.371 Sum_probs=29.8
Q ss_pred eeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 143 LFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 143 L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
+.+++.|.+..+++...++|..||......+..-+
T Consensus 13 ~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl 47 (65)
T COG2771 13 LRLVAQGKSNKEIARILGISEETVKTHLRNIYRKL 47 (65)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 45678899999999999999999998887776544
No 212
>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=59.43 E-value=10 Score=30.47 Aligned_cols=29 Identities=21% Similarity=0.167 Sum_probs=23.5
Q ss_pred cCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 147 VNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 147 a~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.-+.+..+||...|++++||++.+++..+
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le~ 73 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKSLAR 73 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 44567889999999999999998776543
No 213
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=58.53 E-value=12 Score=26.56 Aligned_cols=29 Identities=17% Similarity=0.185 Sum_probs=24.0
Q ss_pred cCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 147 VNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 147 a~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
....+..+++..+|+|.+|+++.++...+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 44567889999999999999998877654
No 214
>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=58.42 E-value=14 Score=35.32 Aligned_cols=45 Identities=16% Similarity=0.172 Sum_probs=38.2
Q ss_pred CCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 131 LNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 131 ~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
..+|+.++=.+.+ ++.|.++.+||...+||..||..+++....-+
T Consensus 189 ~~LT~RE~evl~l--~a~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL 233 (247)
T TIGR03020 189 GLITAREAEILAW--VRDGKTNEEIAAILGISSLTVKNHLQHIFKKL 233 (247)
T ss_pred cCCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHh
Confidence 4588888777775 68999999999999999999999988876654
No 215
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=58.38 E-value=6.6 Score=36.12 Aligned_cols=29 Identities=28% Similarity=0.297 Sum_probs=25.4
Q ss_pred eeccCCCchhhhhhhhccChhhHHHHHHH
Q 013572 144 FRLVNGSTYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 144 ~~La~g~s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
.++..|.++..++..+|||++|++++.+.
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 216
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=58.24 E-value=12 Score=34.89 Aligned_cols=50 Identities=12% Similarity=0.129 Sum_probs=36.4
Q ss_pred CCCHHHHHhhhe----eec--cCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 132 NLSADIRLGIGL----FRL--VNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 132 ~is~e~~L~i~L----~~L--a~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
.++..+.-++.+ =|+ -...+..+||..||||+||++.++++..+-|.+.+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~~~ 210 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIEAY 210 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 477665544432 222 23577889999999999999999999888777654
No 217
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=58.18 E-value=13 Score=37.12 Aligned_cols=49 Identities=16% Similarity=0.076 Sum_probs=40.5
Q ss_pred CCCHHHHHhhheeec---cCCCchhhhhhhhccChhhHHHHHHHHHHHHHHh
Q 013572 132 NLSADIRLGIGLFRL---VNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTN 180 (440)
Q Consensus 132 ~is~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~ 180 (440)
.++..++..+.++|. ..+.++.+||..+|||++.|+++-.+.+.-|-..
T Consensus 262 ~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~ 313 (324)
T PRK07921 262 TLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNG 313 (324)
T ss_pred hCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Confidence 378888888999884 2457999999999999999999988887776543
No 218
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=58.16 E-value=8 Score=36.16 Aligned_cols=45 Identities=9% Similarity=0.053 Sum_probs=36.3
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
.+++.++-. |..++.|.+..+||...++|.+||..++..+.+.+.
T Consensus 143 ~LS~RE~eV--L~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLg 187 (217)
T PRK13719 143 KVTKYQNDV--FILYSFGFSHEYIAQLLNITVGSSKNKISEILKFFG 187 (217)
T ss_pred CCCHHHHHH--HHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 466665543 455899999999999999999999999888776553
No 219
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=57.06 E-value=14 Score=38.60 Aligned_cols=49 Identities=22% Similarity=0.233 Sum_probs=42.9
Q ss_pred CCCCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 129 LPLNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 129 r~~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
|...+...-+++|.|.+=-+|.++.+||..||.+.|||...++++-+.+
T Consensus 367 R~~~i~~aR~iamyl~r~~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 367 RNVKALLARRIGMYVAKNYLGSSLRTIAEKFNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred CCccccHHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 3456777888999998888999999999999999999999998888765
No 220
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=56.80 E-value=14 Score=40.09 Aligned_cols=50 Identities=10% Similarity=0.174 Sum_probs=44.0
Q ss_pred CCCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHH
Q 013572 130 PLNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCT 179 (440)
Q Consensus 130 ~~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~ 179 (440)
...+..--+++|.|.+=-++.++.+|+..||.+.|||...++++-+.|.+
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 34677788999999999999999999999999999999988888876654
No 221
>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=55.93 E-value=8 Score=31.17 Aligned_cols=58 Identities=10% Similarity=0.067 Sum_probs=35.0
Q ss_pred cCCCHHHHHHHHHHhcccccccCCCCCCCCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHH
Q 013572 103 FKMSSSTFRWLSGLLEPLLDCRDPVGLPLNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 103 fRms~~tF~~L~~~L~~~l~~~~~~~r~~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
+-|+-+.|..|.+.....-..+.+. .....+.+ +.+ .+..||..||+|.+|++||...
T Consensus 11 ~qmTg~ell~L~~~~~~~~~~~~~~---~~~~~~~~-------yvy--G~~GlAklfgcSv~Ta~RiK~s 68 (96)
T PF12964_consen 11 WQMTGEELLFLLKEGKTNSEKQTSQ---KAKKDEKK-------YVY--GLKGLAKLFGCSVPTANRIKKS 68 (96)
T ss_pred HHhhHHHHHHHHHHHhcCCCccCCc---cccCcccc-------eee--hHHHHHHHhCCCchhHHHHHhc
Confidence 4577788888887764332222110 11222222 222 3679999999999999998753
No 222
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=55.82 E-value=16 Score=27.36 Aligned_cols=40 Identities=15% Similarity=0.015 Sum_probs=30.3
Q ss_pred CHHHHHhhheeeccC-CCchhhhhhhhccChhhHHHHHHHH
Q 013572 134 SADIRLGIGLFRLVN-GSTYSEIATRFEVTESVTRFCVKQL 173 (440)
Q Consensus 134 s~e~~L~i~L~~La~-g~s~~~la~~Fgvs~sTv~~~v~~v 173 (440)
+.++++..+|..-+. |.+..+|+...|+++++|++++...
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 346667666665544 5788999999999999998876544
No 223
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=55.51 E-value=15 Score=39.02 Aligned_cols=49 Identities=22% Similarity=0.037 Sum_probs=41.8
Q ss_pred CCCHHHHHhhheeec---cCCCchhhhhhhhccChhhHHHHHHHHHHHHHHh
Q 013572 132 NLSADIRLGIGLFRL---VNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTN 180 (440)
Q Consensus 132 ~is~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~ 180 (440)
.++..++..+.++|. ..+.++.+||..||||++.|+++-.+.+.-|-..
T Consensus 447 ~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~ 498 (509)
T PRK05901 447 TLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHP 498 (509)
T ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 488899999999984 4679999999999999999999988887766543
No 224
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=54.96 E-value=13 Score=27.17 Aligned_cols=32 Identities=22% Similarity=0.220 Sum_probs=25.4
Q ss_pred HhhheeeccCCCchhhhhhhhccChhhHHHHHHH
Q 013572 139 LGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 139 L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
.|..|+. .|-+..+||...|++.+||+.+..+
T Consensus 5 ~A~~LY~--~G~~~~eIA~~Lg~~~~TV~~W~~r 36 (58)
T PF06056_consen 5 QARSLYL--QGWSIKEIAEELGVPRSTVYSWKDR 36 (58)
T ss_pred HHHHHHH--cCCCHHHHHHHHCCChHHHHHHHHh
Confidence 3445543 6999999999999999999987554
No 225
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=54.84 E-value=17 Score=38.04 Aligned_cols=50 Identities=14% Similarity=0.210 Sum_probs=43.8
Q ss_pred CCCCCCHHHHHhhheeeccCCCchhhhhhhh-ccChhhHHHHHHHHHHHHH
Q 013572 129 LPLNLSADIRLGIGLFRLVNGSTYSEIATRF-EVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 129 r~~~is~e~~L~i~L~~La~g~s~~~la~~F-gvs~sTv~~~v~~v~~~i~ 178 (440)
|...+...-+++|.|.+=-+|.++.+||..| |.+.|||...++++-+.+.
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 3456888899999999999999999999999 5999999999888887664
No 226
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=54.35 E-value=15 Score=25.00 Aligned_cols=27 Identities=22% Similarity=0.206 Sum_probs=22.5
Q ss_pred CCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 149 GSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 149 g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
+.+..+++..|+++.+|+++.+..+.+
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~~ 40 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLEE 40 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 456789999999999999998876654
No 227
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=54.10 E-value=9.6 Score=36.28 Aligned_cols=46 Identities=24% Similarity=0.279 Sum_probs=37.6
Q ss_pred CCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 131 LNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 131 ~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
..+++.++=. |.+++.|.+..+||...+||..||..++..+.+.+.
T Consensus 178 ~~LT~rE~ev--l~~~a~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~ 223 (240)
T PRK10188 178 MNFSKREKEI--LKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFN 223 (240)
T ss_pred CCCCHHHHHH--HHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3577777654 456799999999999999999999999888777653
No 228
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=54.03 E-value=17 Score=27.20 Aligned_cols=42 Identities=14% Similarity=0.038 Sum_probs=35.9
Q ss_pred HhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHh
Q 013572 139 LGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTN 180 (440)
Q Consensus 139 L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~ 180 (440)
+-.+..+|+...+..+.|+..|+...+|.+++..|-..+.+.
T Consensus 3 ~~~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~L 44 (65)
T PF05344_consen 3 ARAFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQL 44 (65)
T ss_pred HHHHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHHc
Confidence 445677889999999999999999999999999988876643
No 229
>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=53.15 E-value=11 Score=25.26 Aligned_cols=22 Identities=36% Similarity=0.288 Sum_probs=18.5
Q ss_pred chhhhhhhhccChhhHHHHHHH
Q 013572 151 TYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
+..+++..+|||.+|+.+++.+
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 4578999999999999988664
No 230
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=53.06 E-value=12 Score=37.34 Aligned_cols=69 Identities=19% Similarity=0.159 Sum_probs=44.1
Q ss_pred heeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhhhhcCCChhhHHHHHHHHHhhhCCCCccccc
Q 013572 142 GLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRFWVAFPGPEELGLISKSFEELTGLPNCCGVI 213 (440)
Q Consensus 142 ~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~~I~~P~~~~~~~~~~~f~~~~~fP~ciGaI 213 (440)
+=.|+..|.+..+||..+|||+.||++.+.+--+- -..+-.|..|.. ..-++....++++|++.|+-+-
T Consensus 19 A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~--GiV~I~i~~~~~-~~~~Le~~L~~~fgL~~a~VVp 87 (321)
T COG2390 19 AWLYYVEGLTQSEIAERLGISRATVSRLLAKAREE--GIVKISINSPVE-GCLELEQQLKERFGLKEAIVVP 87 (321)
T ss_pred HHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHC--CeEEEEeCCCCc-chHHHHHHHHHhcCCCeEEEEc
Confidence 34567889999999999999999999986654321 011223443333 3333555666777887774443
No 231
>PRK09483 response regulator; Provisional
Probab=52.45 E-value=10 Score=34.30 Aligned_cols=44 Identities=14% Similarity=0.178 Sum_probs=36.1
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
.+++.++-.+ ..++.|.+..+||..+++|.+||..++++..+-+
T Consensus 148 ~Lt~rE~~vl--~~~~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 148 SLSERELQIM--LMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKL 191 (217)
T ss_pred ccCHHHHHHH--HHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 4777666554 4578999999999999999999999888777654
No 232
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=51.52 E-value=8 Score=28.38 Aligned_cols=27 Identities=22% Similarity=0.276 Sum_probs=21.2
Q ss_pred eeccCCCchhhhhhhhccChhhHHHHH
Q 013572 144 FRLVNGSTYSEIATRFEVTESVTRFCV 170 (440)
Q Consensus 144 ~~La~g~s~~~la~~Fgvs~sTv~~~v 170 (440)
++-+.|.+..++|...|+|.+|++++-
T Consensus 9 ~R~~~gls~~~lA~~~g~s~s~v~~iE 35 (64)
T PF13560_consen 9 LRERAGLSQAQLADRLGVSQSTVSRIE 35 (64)
T ss_dssp HHHCHTS-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 345679999999999999999999863
No 233
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=51.36 E-value=11 Score=34.97 Aligned_cols=44 Identities=23% Similarity=0.118 Sum_probs=35.4
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
.+++.++= .|..++.|.+.++||...++|..||..+...+.+-+
T Consensus 134 ~LT~RE~e--VL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KL 177 (207)
T PRK11475 134 MLSPTERE--ILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKL 177 (207)
T ss_pred CCCHHHHH--HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 36665553 456689999999999999999999999888776654
No 234
>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=51.16 E-value=17 Score=27.38 Aligned_cols=27 Identities=26% Similarity=0.190 Sum_probs=23.4
Q ss_pred CCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 149 GSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 149 g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
+.+..++|...|+|+.||+++++++.+
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 456889999999999999999887765
No 235
>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=50.86 E-value=16 Score=26.52 Aligned_cols=31 Identities=23% Similarity=0.203 Sum_probs=26.2
Q ss_pred CCchhhhhhhhccChhhHHHHHHHHHHHHHH
Q 013572 149 GSTYSEIATRFEVTESVTRFCVKQLCRVLCT 179 (440)
Q Consensus 149 g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~ 179 (440)
-.++...|...++|++++++.+++.-+.+..
T Consensus 13 ~gs~~~AA~~l~is~~~vs~~i~~LE~~lg~ 43 (60)
T PF00126_consen 13 TGSISAAAEELGISQSAVSRQIKQLEEELGV 43 (60)
T ss_dssp HSSHHHHHHHCTSSHHHHHHHHHHHHHHHTS
T ss_pred hCCHHHHHHHhhccchHHHHHHHHHHHHhCC
Confidence 3489999999999999999998887776643
No 236
>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=50.83 E-value=13 Score=27.53 Aligned_cols=39 Identities=21% Similarity=0.246 Sum_probs=28.1
Q ss_pred HHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 136 DIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 136 e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
|.++..+|. -..+.+..+|+...|++++||+++++...+
T Consensus 10 E~~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~ 48 (68)
T PF01978_consen 10 EAKVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEE 48 (68)
T ss_dssp HHHHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred HHHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 344444443 234567889999999999999998877654
No 237
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=50.65 E-value=11 Score=35.17 Aligned_cols=44 Identities=25% Similarity=0.242 Sum_probs=35.9
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
.+++.+.- .|..++.|.+..+||...++|.+||..++....+-|
T Consensus 148 ~LT~RE~e--VL~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 148 LLTPRELE--VLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCCHHHHH--HHHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHc
Confidence 36665554 456799999999999999999999999988776654
No 238
>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=50.63 E-value=17 Score=26.68 Aligned_cols=24 Identities=25% Similarity=0.437 Sum_probs=18.0
Q ss_pred chhhhhhhhccChhhHHHHHHHHH
Q 013572 151 TYSEIATRFEVTESVTRFCVKQLC 174 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~v~~v~ 174 (440)
+..+++..||||++||.+.+...+
T Consensus 26 s~~~la~~~~vsr~tvr~al~~L~ 49 (64)
T PF00392_consen 26 SERELAERYGVSRTTVREALRRLE 49 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CHHHHHHHhccCCcHHHHHHHHHH
Confidence 346889999999999988766554
No 239
>PHA00738 putative HTH transcription regulator
Probab=50.54 E-value=8.7 Score=31.75 Aligned_cols=31 Identities=13% Similarity=0.048 Sum_probs=24.7
Q ss_pred ccCC--CchhhhhhhhccChhhHHHHHHHHHHH
Q 013572 146 LVNG--STYSEIATRFEVTESVTRFCVKQLCRV 176 (440)
Q Consensus 146 La~g--~s~~~la~~Fgvs~sTv~~~v~~v~~~ 176 (440)
|+.| .+-.+|+..|++|++|||++++-.-++
T Consensus 21 L~~~e~~~V~eLae~l~lSQptVS~HLKvLreA 53 (108)
T PHA00738 21 IAENYILSASLISHTLLLSYTTVLRHLKILNEQ 53 (108)
T ss_pred HHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHC
Confidence 4443 678899999999999999997765543
No 240
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=50.30 E-value=12 Score=34.88 Aligned_cols=45 Identities=18% Similarity=0.237 Sum_probs=35.3
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
.+++.++=.+. .++.|.++.+||...++|..||..++.+.+..+.
T Consensus 155 ~Lt~rE~~Vl~--l~~~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 155 LLTHREKEILN--KLRIGASNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCHHHHHHHH--HHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 36765554443 4667999999999999999999999888776553
No 241
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=50.27 E-value=13 Score=33.65 Aligned_cols=63 Identities=14% Similarity=0.065 Sum_probs=42.7
Q ss_pred CCHHHHHhhheeeccC--------------CCchhhhhhhhccChhhHHHHHHHHHHH-HHHhhhhhhcCCChhhHHH
Q 013572 133 LSADIRLGIGLFRLVN--------------GSTYSEIATRFEVTESVTRFCVKQLCRV-LCTNFRFWVAFPGPEELGL 195 (440)
Q Consensus 133 is~e~~L~i~L~~La~--------------g~s~~~la~~Fgvs~sTv~~~v~~v~~~-i~~~l~~~I~~P~~~~~~~ 195 (440)
.++++||+-+|..|+. ..+..+||...|+++.||+|+++++.+. +.+.-+..|..++.+.+.+
T Consensus 119 ~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~d~~~L~~ 196 (202)
T PRK13918 119 QRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRETVTKVIGELSREGYIRSGYGKIQLLDLKGLEE 196 (202)
T ss_pred CchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcCCCEEEEECHHHHHH
Confidence 4578899988876653 2357899999999999999999888752 2222223455555544443
No 242
>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=50.14 E-value=13 Score=25.05 Aligned_cols=21 Identities=19% Similarity=0.159 Sum_probs=17.8
Q ss_pred chhhhhhhhccChhhHHHHHH
Q 013572 151 TYSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~v~ 171 (440)
+..+++..+|||.+|+.++++
T Consensus 3 t~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 467899999999999988754
No 243
>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=50.04 E-value=18 Score=26.42 Aligned_cols=26 Identities=31% Similarity=0.316 Sum_probs=22.3
Q ss_pred CCchhhhhhhhccChhhHHHHHHHHH
Q 013572 149 GSTYSEIATRFEVTESVTRFCVKQLC 174 (440)
Q Consensus 149 g~s~~~la~~Fgvs~sTv~~~v~~v~ 174 (440)
+.+..+++..++++.+|+++.+....
T Consensus 20 ~~~~~ei~~~~~i~~~~i~~~l~~L~ 45 (78)
T cd00090 20 PLTVSELAERLGLSQSTVSRHLKKLE 45 (78)
T ss_pred CcCHHHHHHHHCcCHhHHHHHHHHHH
Confidence 38899999999999999998877654
No 244
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=49.89 E-value=64 Score=27.72 Aligned_cols=131 Identities=14% Similarity=0.154 Sum_probs=71.4
Q ss_pred cccceEEEEeecCCCCCCCCCCcEEEEeecCCCceEEeeecCCCCCCCChhhhhcccccccccccccCCCCCcccCCccc
Q 013572 212 VIDCTRFKIIKIDGSNSSKDEDSIAVQIVVDSSSRMLSIVAGIRGDKGDSRVLKSSTLYKDIEEKKLLNSSPICVNGVAV 291 (440)
Q Consensus 212 aIDgthi~i~~p~~~n~k~~~~si~~q~v~D~~~rf~~v~~g~pGs~~D~~v~~~S~l~~~l~~~~l~~~~~~~l~g~~~ 291 (440)
.+|=|-|.|. |+ ..=+=.+||++|+++++.+.-.-...++.-|-. +.+.... ..
T Consensus 5 ~~DEt~iki~------G~----~~yl~~aiD~~~~~l~~~ls~~Rd~~aA~~Fl~----~~l~~~~------------~~ 58 (140)
T PF13610_consen 5 HVDETYIKIK------GK----WHYLWRAIDAEGNILDFYLSKRRDTAAAKRFLK----RALKRHR------------GE 58 (140)
T ss_pred EEeeEEEEEC------CE----EEEEEEeecccccchhhhhhhhcccccceeecc----ccceeec------------cc
Confidence 5777888776 22 122457899999988888865444444443321 1121100 12
Q ss_pred ceEEEecC--CCCCCCCcccccCCCCCCCcchhhhhhhhhhHHHHHHHHHhhc-ccccccCCccCChhhHHHHHHHHHHH
Q 013572 292 DQYLIGDG--GYPLLPWLMVPFVDANPGSSEENFNAAHNLMRVPALKAIASLK-NWGVLSRPIDEDFKTAVALIGACSIL 368 (440)
Q Consensus 292 ~~~llgD~--~Ypl~~~lm~P~~~~~l~~~~~~FN~~ls~~R~~vE~afg~LK-rfriL~~~~~~~~~~~~~ii~accvL 368 (440)
|..++-|+ +||.--.-+.+-.. .....+... ..-.++.||+-+..+| +.+.... + .+.+.+...+.+-.+.
T Consensus 59 p~~ivtDk~~aY~~A~~~l~~~~~-~~~~v~~~~---~k~~nN~iE~~h~~~K~r~r~~~g-F-ks~~~A~~~l~~~~~~ 132 (140)
T PF13610_consen 59 PRVIVTDKLPAYPAAIKELNPEGR-LHDKVEHRQ---RKYLNNRIERDHRTIKRRTRPMNG-F-KSFRSAQRTLSGFEAY 132 (140)
T ss_pred cceeecccCCccchhhhhcccccc-cccccceee---chhhhChhhHhhhhhhhhcccccC-c-CCHHHHHHHHHHHHHH
Confidence 55677776 34422111111100 000001101 0123567999999998 4544332 2 3578888999999999
Q ss_pred Hhhhcc
Q 013572 369 HNALLM 374 (440)
Q Consensus 369 HN~~~~ 374 (440)
||+...
T Consensus 133 ~n~~r~ 138 (140)
T PF13610_consen 133 HNFRRP 138 (140)
T ss_pred HHHhCC
Confidence 999864
No 245
>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=48.41 E-value=19 Score=25.84 Aligned_cols=25 Identities=20% Similarity=0.316 Sum_probs=20.7
Q ss_pred chhhhhhhhccChhhHHHHHHHHHH
Q 013572 151 TYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
+.++++..|++|++||++.+....+
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~ 51 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA 51 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4678999999999999987776554
No 246
>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=48.24 E-value=31 Score=28.57 Aligned_cols=29 Identities=10% Similarity=0.122 Sum_probs=24.2
Q ss_pred cCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 147 VNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 147 a~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
..+.+..+|+...+++++|+++.+.+..+
T Consensus 40 ~~~~t~~ela~~~~~~~~tvs~~l~~Le~ 68 (118)
T TIGR02337 40 QGSMEFTQLANQACILRPSLTGILARLER 68 (118)
T ss_pred cCCcCHHHHHHHhCCCchhHHHHHHHHHH
Confidence 44667899999999999999988777654
No 247
>PRK09191 two-component response regulator; Provisional
Probab=48.06 E-value=29 Score=32.59 Aligned_cols=50 Identities=16% Similarity=0.096 Sum_probs=41.7
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhh
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFR 182 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~ 182 (440)
.+|+..+-.+.|.++ .|.+|.++|...|+|.+||...+.+....+...+.
T Consensus 88 ~L~~~~r~v~~l~~~-~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~ 137 (261)
T PRK09191 88 GLTPLPRQAFLLTAL-EGFSVEEAAEILGVDPAEAEALLDDARAEIARQVA 137 (261)
T ss_pred hCCHHHhHHHHHHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCC
Confidence 377777777777665 58899999999999999999999998888877665
No 248
>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=47.98 E-value=27 Score=25.49 Aligned_cols=28 Identities=25% Similarity=0.320 Sum_probs=21.3
Q ss_pred CCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 148 NGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 148 ~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
...+..+|+..++++++++++.+++.++
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 4566789999999999999998887765
No 249
>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=47.56 E-value=11 Score=26.08 Aligned_cols=19 Identities=16% Similarity=0.134 Sum_probs=16.1
Q ss_pred hhhhhhccChhhHHHHHHH
Q 013572 154 EIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 154 ~la~~Fgvs~sTv~~~v~~ 172 (440)
+++...|||.+||+++++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g 20 (52)
T cd01392 2 DIARAAGVSVATVSRVLNG 20 (52)
T ss_pred cHHHHHCcCHHHHHHHHcC
Confidence 6889999999999987553
No 250
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=47.14 E-value=16 Score=34.11 Aligned_cols=43 Identities=16% Similarity=0.182 Sum_probs=35.2
Q ss_pred CCHHHHHhhheeeccC--------------CCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 133 LSADIRLGIGLFRLVN--------------GSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 133 is~e~~L~i~L~~La~--------------g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.++++|++-+|..++. ..+..+||...|+++.|++|+++++-+
T Consensus 154 ~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~~ 210 (235)
T PRK11161 154 KNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQK 210 (235)
T ss_pred CCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 5789999999988753 246789999999999999998776553
No 251
>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=46.90 E-value=20 Score=24.21 Aligned_cols=24 Identities=25% Similarity=0.490 Sum_probs=18.1
Q ss_pred CCchhhhhhhhccChhhHHHHHHH
Q 013572 149 GSTYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 149 g~s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
-.+|.+||...|+|.+||.+=+.+
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 357899999999999999875543
No 252
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=46.79 E-value=17 Score=34.06 Aligned_cols=43 Identities=19% Similarity=0.111 Sum_probs=35.4
Q ss_pred CCHHHHHhhheeeccC----------CCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 133 LSADIRLGIGLFRLVN----------GSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 133 is~e~~L~i~L~~La~----------g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.++++|++-+|..++. ..+..+||...|+++.|++|+++++-+
T Consensus 153 ~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~L~~L~~ 205 (230)
T PRK09391 153 KTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLQD 205 (230)
T ss_pred CCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6889999999987743 235689999999999999998877654
No 253
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=46.70 E-value=22 Score=25.66 Aligned_cols=24 Identities=29% Similarity=0.386 Sum_probs=19.8
Q ss_pred CchhhhhhhhccChhhHHHHHHHH
Q 013572 150 STYSEIATRFEVTESVTRFCVKQL 173 (440)
Q Consensus 150 ~s~~~la~~Fgvs~sTv~~~v~~v 173 (440)
.+..+++..|+||..|+.+-+...
T Consensus 15 ~s~~ela~~~~VS~~TiRRDl~~L 38 (57)
T PF08220_consen 15 VSVKELAEEFGVSEMTIRRDLNKL 38 (57)
T ss_pred EEHHHHHHHHCcCHHHHHHHHHHH
Confidence 456799999999999999876653
No 254
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=46.59 E-value=28 Score=30.02 Aligned_cols=44 Identities=14% Similarity=0.024 Sum_probs=30.9
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.+++.+-..+...+-..|.+..+|+..++++++|+++.+.+..+
T Consensus 37 glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~ 80 (144)
T PRK11512 37 DITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVC 80 (144)
T ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45555443333223345678999999999999999998776553
No 255
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=46.41 E-value=14 Score=26.93 Aligned_cols=41 Identities=15% Similarity=0.198 Sum_probs=28.0
Q ss_pred CCCCCHHHHHhhheeeccCCC---chhhhhhhhccChhhHHHHH
Q 013572 130 PLNLSADIRLGIGLFRLVNGS---TYSEIATRFEVTESVTRFCV 170 (440)
Q Consensus 130 ~~~is~e~~L~i~L~~La~g~---s~~~la~~Fgvs~sTv~~~v 170 (440)
+...+++.+|-+.-++..++. .++..|..|+|++..|.++.
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~ 46 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWR 46 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHH
T ss_pred ccccChHHHHHHHHHHHHccchhhhHHHHHHHhCccHHHHHHHH
Confidence 356788889988888877776 56999999999998887664
No 256
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=46.16 E-value=14 Score=27.85 Aligned_cols=21 Identities=14% Similarity=0.177 Sum_probs=17.7
Q ss_pred chhhhhhhhccChhhHHHHHH
Q 013572 151 TYSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~v~ 171 (440)
+.++|+..-|||.+||+++++
T Consensus 2 t~~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHC
Confidence 357899999999999998653
No 257
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=45.23 E-value=23 Score=29.59 Aligned_cols=45 Identities=16% Similarity=0.207 Sum_probs=35.1
Q ss_pred CCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 133 LSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 133 is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
++.+ ++.....|+.+..+..+++..+|||=+||..-+.+++.+|-
T Consensus 34 L~~E-~~~Fi~~Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg 78 (113)
T PF09862_consen 34 LSPE-QLEFIKLFIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLG 78 (113)
T ss_pred CCHH-HHHHHHHHHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhC
Confidence 5544 44455556667778999999999999999988888887764
No 258
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=45.05 E-value=89 Score=28.35 Aligned_cols=78 Identities=18% Similarity=0.079 Sum_probs=54.9
Q ss_pred CChhHHHhhcCCCHHHHHHHHHHhcccccccCCCCCCCCCCHHHHHhhheeec----cCCC------chh----hhhhhh
Q 013572 94 QLPDSFRNSFKMSSSTFRWLSGLLEPLLDCRDPVGLPLNLSADIRLGIGLFRL----VNGS------TYS----EIATRF 159 (440)
Q Consensus 94 ~~~~~F~~~fRms~~tF~~L~~~L~~~l~~~~~~~r~~~is~e~~L~i~L~~L----a~g~------s~~----~la~~F 159 (440)
.+-+-..++||||...+-..=..++- ..+.||++.++.++..++--.|- ..+. .+- .+|+..
T Consensus 88 AS~~mm~~~FGls~~ev~~rR~llgi----~~~~GR~~~~~ee~~~~iW~~W~~~~~~~~~~~~~~~~~Le~~m~~Ae~~ 163 (180)
T PF11198_consen 88 ASIEMMQRLFGLSSAEVAARRRLLGI----PVRKGRPPALSEEEEAAIWRRWQQLMKKRGVDNLDSPDALELMMLLAEET 163 (180)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHhCC----CCCCCCCCCcCHHHHHHHHHHHHHHHhhcCCCCccchHHHHHHHHHHHHh
Confidence 56677888999999999888777752 33467767777777777765443 1221 122 388999
Q ss_pred ccChhhHHHHHHHHHH
Q 013572 160 EVTESVTRFCVKQLCR 175 (440)
Q Consensus 160 gvs~sTv~~~v~~v~~ 175 (440)
++|-++|...|+++++
T Consensus 164 ~isL~~iW~~i~~w~~ 179 (180)
T PF11198_consen 164 NISLTVIWSLIQEWER 179 (180)
T ss_pred CCCHHHHHHHHHHHHh
Confidence 9999998888877653
No 259
>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=45.04 E-value=67 Score=30.44 Aligned_cols=43 Identities=14% Similarity=0.032 Sum_probs=31.6
Q ss_pred CCHHHHHhhheeecc---CCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 133 LSADIRLGIGLFRLV---NGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 133 is~e~~L~i~L~~La---~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
+++-++..-.|..++ .+.+..+|+...|+++||+++++...+.
T Consensus 5 v~sl~ral~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~ 50 (248)
T TIGR02431 5 VASLARGLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVE 50 (248)
T ss_pred HHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 333444444455554 3578999999999999999999888764
No 260
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=44.95 E-value=28 Score=36.47 Aligned_cols=50 Identities=10% Similarity=0.135 Sum_probs=43.5
Q ss_pred CCCCCCHHHHHhhheeeccCCCchhhhhhhhc-cChhhHHHHHHHHHHHHH
Q 013572 129 LPLNLSADIRLGIGLFRLVNGSTYSEIATRFE-VTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 129 r~~~is~e~~L~i~L~~La~g~s~~~la~~Fg-vs~sTv~~~v~~v~~~i~ 178 (440)
|...+...-|+||.|.+=-++.|+.+||..|| .+.|||..-++++-+.+-
T Consensus 381 R~~~i~~~RqiamyL~r~~t~~sl~~IG~~FggrdHsTV~~a~~ki~~~~~ 431 (450)
T PRK14087 381 RSKSIVTARHIAMYLTKEILNHTLAQIGEEFGGRDHTTVINAERKIEKMLK 431 (450)
T ss_pred CCccccHHHHHHHHHHHHHcCCCHHHHHHHhCCCChHHHHHHHHHHHHHHH
Confidence 34568888999999999999999999999997 999999988887777654
No 261
>PF12728 HTH_17: Helix-turn-helix domain
Probab=44.36 E-value=17 Score=25.18 Aligned_cols=21 Identities=19% Similarity=0.202 Sum_probs=17.8
Q ss_pred chhhhhhhhccChhhHHHHHH
Q 013572 151 TYSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~v~ 171 (440)
+..+++..+|||.+|+.++++
T Consensus 3 t~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 457899999999999988764
No 262
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=44.26 E-value=27 Score=36.50 Aligned_cols=49 Identities=14% Similarity=0.148 Sum_probs=43.2
Q ss_pred CCCCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 129 LPLNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 129 r~~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
|...+...-|+||.|.+=-++.|+.+||..||...|||..-++.+-+.+
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 4456888899999999999999999999999999999988888777766
No 263
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=44.12 E-value=18 Score=32.07 Aligned_cols=44 Identities=20% Similarity=0.205 Sum_probs=34.6
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
.+++.+.- .|..|+.|.+..+++..+++|.+||..++.++.+-+
T Consensus 137 ~Lt~~E~~--il~~l~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 137 PLTKRERQ--VAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKL 180 (196)
T ss_pred CCCHHHHH--HHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 45555543 345588899999999999999999999888877654
No 264
>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=43.88 E-value=29 Score=32.47 Aligned_cols=22 Identities=14% Similarity=0.303 Sum_probs=17.9
Q ss_pred hhhhhhhccChhhHHHHHHHHH
Q 013572 153 SEIATRFEVTESVTRFCVKQLC 174 (440)
Q Consensus 153 ~~la~~Fgvs~sTv~~~v~~v~ 174 (440)
.+|+..||||+.||.+.+....
T Consensus 28 ~eLa~~~gVSR~TVR~Al~~L~ 49 (233)
T TIGR02404 28 HELMDQYGASRETVRKALNLLT 49 (233)
T ss_pred HHHHHHHCCCHHHHHHHHHHHH
Confidence 5678899999999998766554
No 265
>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=43.79 E-value=26 Score=34.11 Aligned_cols=21 Identities=24% Similarity=0.167 Sum_probs=19.0
Q ss_pred chhhhhhhhccChhhHHHHHH
Q 013572 151 TYSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~v~ 171 (440)
+..+||...|||++|||++++
T Consensus 3 ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 3 TIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred cHHHHHHHhCCCHHHHHHHhC
Confidence 467999999999999999985
No 266
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=43.51 E-value=21 Score=26.53 Aligned_cols=35 Identities=14% Similarity=0.085 Sum_probs=24.8
Q ss_pred HhhheeeccCCCchhhhhhhhccChhhHHHHHHHH
Q 013572 139 LGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQL 173 (440)
Q Consensus 139 L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v 173 (440)
+.-+|.....+.+-++||+.+|+|..++..++...
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~L 39 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKL 39 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 33444444677888999999999999999876543
No 267
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=43.07 E-value=33 Score=26.77 Aligned_cols=28 Identities=25% Similarity=0.297 Sum_probs=24.3
Q ss_pred CCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 148 NGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 148 ~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.+.+..+++..++++++|+++.+++..+
T Consensus 23 ~~~~~~~la~~~~~s~~~i~~~l~~L~~ 50 (101)
T smart00347 23 GPLSVSELAKRLGVSPSTVTRVLDRLEK 50 (101)
T ss_pred CCcCHHHHHHHHCCCchhHHHHHHHHHH
Confidence 3568889999999999999999888775
No 268
>PRK09492 treR trehalose repressor; Provisional
Probab=42.78 E-value=30 Score=33.55 Aligned_cols=23 Identities=22% Similarity=0.125 Sum_probs=20.4
Q ss_pred CchhhhhhhhccChhhHHHHHHH
Q 013572 150 STYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 150 ~s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
.+.++||+..|||.+|||++++.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCC
Confidence 46789999999999999999873
No 269
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=42.73 E-value=28 Score=32.82 Aligned_cols=49 Identities=27% Similarity=0.372 Sum_probs=31.9
Q ss_pred HHHHHHHHhcccccccCCCCCCCCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 109 TFRWLSGLLEPLLDCRDPVGLPLNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 109 tF~~L~~~L~~~l~~~~~~~r~~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
-+..|.+.|+..+...-..| ..||.| .+++..||||+.||.+.+.....
T Consensus 13 ~Y~qi~~~L~~~I~~~~~~G--~~LPsE----------------~eLa~~~~VSR~TVR~Al~~L~~ 61 (241)
T PRK10079 13 RYQEIAAKLEQELRQHYRCG--DYLPAE----------------QQLAARYEVNRHTLRRAIDQLVE 61 (241)
T ss_pred HHHHHHHHHHHHHhcccCCC--CcCCCH----------------HHHHHHHCCCHHHHHHHHHHHHH
Confidence 35666666666554211222 347766 57788999999999987766553
No 270
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=42.43 E-value=29 Score=27.05 Aligned_cols=33 Identities=15% Similarity=0.095 Sum_probs=26.1
Q ss_pred ccCCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 146 LVNGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 146 La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
...+.+..+++..+.||+||+.+.++++-+.+.
T Consensus 27 ~~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~ 59 (87)
T PF05043_consen 27 NNEYVSIEDLAEELFISRSTIYRDIKKLNKYLK 59 (87)
T ss_dssp H-SEEEHHHHHHHHT--HHHHHHHHHHHHHHHH
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 567788999999999999999999888877665
No 271
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=41.85 E-value=27 Score=32.61 Aligned_cols=63 Identities=16% Similarity=-0.017 Sum_probs=42.8
Q ss_pred CCCHHHHHhhheeeccCC----------CchhhhhhhhccChhhHHHHHHHHHHHHHHhhhhhhcCCChhhHH
Q 013572 132 NLSADIRLGIGLFRLVNG----------STYSEIATRFEVTESVTRFCVKQLCRVLCTNFRFWVAFPGPEELG 194 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g----------~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~~I~~P~~~~~~ 194 (440)
..++++|++-+|..++.. .+..+||...|+++.||+|+++++.+.=...-+..|..++.+.+.
T Consensus 146 ~~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~lG~tretvsR~l~~L~~~gl~~~~~~i~I~d~~~L~ 218 (236)
T PRK09392 146 LRSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYLGMTPENLSRAFAALASHGVHVDGSAVTITDPAGLA 218 (236)
T ss_pred cCCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHhCCChhHHHHHHHHHHhCCeEeeCCEEEEcCHHHHH
Confidence 368899999999876542 224689999999999999998886653221112345555554443
No 272
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=41.74 E-value=34 Score=37.36 Aligned_cols=47 Identities=19% Similarity=0.123 Sum_probs=39.4
Q ss_pred CCCHHHHHhhheeec---cCCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRL---VNGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 132 ~is~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
.+++.++..+.++|. ..+.++..||..||||++.|+++-.+.+.-|-
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 378888999999885 46788999999999999999998777776554
No 273
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=41.64 E-value=24 Score=29.11 Aligned_cols=30 Identities=23% Similarity=0.362 Sum_probs=22.2
Q ss_pred cCCCchhhhhhhhccChhhHHHHHHHHHHH
Q 013572 147 VNGSTYSEIATRFEVTESVTRFCVKQLCRV 176 (440)
Q Consensus 147 a~g~s~~~la~~Fgvs~sTv~~~v~~v~~~ 176 (440)
-.|.+..+||..||+|..+|++|+++.-..
T Consensus 70 f~G~n~~eLA~kyglS~r~I~~Ii~~~~~~ 99 (108)
T PF08765_consen 70 FNGMNVRELARKYGLSERQIYRIIKRVRRR 99 (108)
T ss_dssp --SS-HHHHHHHHT--HHHHHHHHHHHHH-
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 349999999999999999999999887654
No 274
>PRK10403 transcriptional regulator NarP; Provisional
Probab=41.07 E-value=19 Score=32.00 Aligned_cols=44 Identities=23% Similarity=0.312 Sum_probs=35.9
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
.+++.+.-. |.+++.|.++..|+...++|..||..++.+..+.+
T Consensus 153 ~Lt~~e~~v--l~~~~~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl 196 (215)
T PRK10403 153 VLTERELDV--LHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKL 196 (215)
T ss_pred cCCHHHHHH--HHHHHCCCCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 366655544 45678999999999999999999999988887765
No 275
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=40.72 E-value=36 Score=27.36 Aligned_cols=29 Identities=14% Similarity=0.124 Sum_probs=22.6
Q ss_pred chhhhhhhhccChhhHHHHHHHHHHHHHH
Q 013572 151 TYSEIATRFEVTESVTRFCVKQLCRVLCT 179 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~v~~v~~~i~~ 179 (440)
+...+|...||+.|||+|+-..+..-+..
T Consensus 25 gq~~vA~~~Gv~eStISR~k~~~~~~~a~ 53 (91)
T PF05269_consen 25 GQKKVAEAMGVDESTISRWKNDFIEKMAM 53 (91)
T ss_dssp HHHHHHHHHTSSTTTHHHHHHHHHHHHHH
T ss_pred hhHHHHHHhCCCHHHHHHHHhhHHHHHHH
Confidence 46789999999999999987665544433
No 276
>PF13309 HTH_22: HTH domain
Probab=40.26 E-value=15 Score=27.27 Aligned_cols=39 Identities=13% Similarity=0.123 Sum_probs=26.7
Q ss_pred CCCHHHHHhhheeeccCC-----CchhhhhhhhccChhhHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNG-----STYSEIATRFEVTESVTRFCV 170 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g-----~s~~~la~~Fgvs~sTv~~~v 170 (440)
.++.++++.+.-.--..| .+-..+|..+|||+.||++++
T Consensus 20 ~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 20 RLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred hCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHc
Confidence 355566665543322333 456789999999999999875
No 277
>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=40.22 E-value=27 Score=25.97 Aligned_cols=25 Identities=4% Similarity=0.097 Sum_probs=20.7
Q ss_pred CchhhhhhhhccChhhHHHHHHHHH
Q 013572 150 STYSEIATRFEVTESVTRFCVKQLC 174 (440)
Q Consensus 150 ~s~~~la~~Fgvs~sTv~~~v~~v~ 174 (440)
.+..+++..+|+|.+||++.+...-
T Consensus 14 ~~~~eLa~~l~vS~~tv~~~l~~L~ 38 (69)
T TIGR00122 14 FSGEKLGEALGMSRTAVNKHIQTLR 38 (69)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3477999999999999998877653
No 278
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=39.92 E-value=22 Score=24.79 Aligned_cols=24 Identities=21% Similarity=0.047 Sum_probs=21.1
Q ss_pred cCCCchhhhhhhhccChhhHHHHH
Q 013572 147 VNGSTYSEIATRFEVTESVTRFCV 170 (440)
Q Consensus 147 a~g~s~~~la~~Fgvs~sTv~~~v 170 (440)
..|.+..++|...|+|++|++++.
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e 36 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVE 36 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 458889999999999999999864
No 279
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=39.88 E-value=21 Score=27.65 Aligned_cols=25 Identities=20% Similarity=0.243 Sum_probs=19.5
Q ss_pred cCCCchhhhhhhhccChhhHHHHHH
Q 013572 147 VNGSTYSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 147 a~g~s~~~la~~Fgvs~sTv~~~v~ 171 (440)
+.|.+..++|...|+++++|+++.+
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 5688999999999999999998764
No 280
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=39.87 E-value=21 Score=31.78 Aligned_cols=44 Identities=16% Similarity=0.197 Sum_probs=35.8
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
.+++.+.- .|..|+.|.+..+|+...++|.+||..++.+..+-+
T Consensus 143 ~lt~~E~~--vl~~l~~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl 186 (204)
T PRK09958 143 SLSKQEIS--VMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKL 186 (204)
T ss_pred cCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 46666543 566778899999999999999999999988877665
No 281
>PRK10651 transcriptional regulator NarL; Provisional
Probab=39.63 E-value=20 Score=31.96 Aligned_cols=44 Identities=27% Similarity=0.338 Sum_probs=35.3
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
.+++.+.= .|.+++.|.+.+.|+...++|..||..++.+....+
T Consensus 155 ~Lt~rE~~--vl~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl 198 (216)
T PRK10651 155 QLTPRERD--ILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKM 198 (216)
T ss_pred cCCHHHHH--HHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 37776653 334588999999999999999999999988876654
No 282
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=39.62 E-value=39 Score=28.84 Aligned_cols=41 Identities=17% Similarity=0.234 Sum_probs=29.3
Q ss_pred CCCHHHHHhhh-eeeccCCCchhhhhhhhccChhhHHHHHHHHH
Q 013572 132 NLSADIRLGIG-LFRLVNGSTYSEIATRFEVTESVTRFCVKQLC 174 (440)
Q Consensus 132 ~is~e~~L~i~-L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~ 174 (440)
++|-+.+.-+. |. ..|.+-.+|+..++||.++|++++.++-
T Consensus 17 PLp~~~R~rIvela--~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~ 58 (125)
T PF00292_consen 17 PLPNELRQRIVELA--KEGVRPCDISRQLRVSHGCVSKILSRYR 58 (125)
T ss_dssp SS-HHHHHHHHHHH--HTT--HHHHHHHHT--HHHHHHHHHHHH
T ss_pred cCcHHHHHHHHHHh--hhcCCHHHHHHHHccchhHHHHHHHHHH
Confidence 67777776665 44 3699999999999999999999988774
No 283
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=39.60 E-value=20 Score=25.91 Aligned_cols=43 Identities=19% Similarity=0.230 Sum_probs=24.6
Q ss_pred cCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhhhhcCCChhhHHHHHHHH
Q 013572 147 VNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRFWVAFPGPEELGLISKSF 200 (440)
Q Consensus 147 a~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~~I~~P~~~~~~~~~~~f 200 (440)
..|.+..++|..-|++++|++++++.- ...|+.+.+..++..|
T Consensus 8 ~~~it~~~La~~~gis~~tl~~~~~~~-----------~~~~~~~~l~~ia~~l 50 (63)
T PF13443_consen 8 ERGITQKDLARKTGISRSTLSRILNGK-----------PSNPSLDTLEKIAKAL 50 (63)
T ss_dssp HTT--HHHHHHHHT--HHHHHHHHTTT----------------HHHHHHHHHHH
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHhcc-----------cccccHHHHHHHHHHc
Confidence 356788999999999999999876532 2233445555555554
No 284
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=39.47 E-value=33 Score=32.44 Aligned_cols=50 Identities=18% Similarity=0.388 Sum_probs=33.7
Q ss_pred HHHHHHHHHhcccccccC-CCCCCCCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 108 STFRWLSGLLEPLLDCRD-PVGLPLNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 108 ~tF~~L~~~L~~~l~~~~-~~~r~~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
+.+..|.+.|+..|.... +.| ..+|.| .+++..||||+.||.+.+.....
T Consensus 7 plY~qI~~~i~~~I~~G~~~~G--~~LPsE----------------~eLa~~f~VSR~TvRkAL~~L~~ 57 (236)
T COG2188 7 PLYQQIAEDIRQRIESGELPPG--DKLPSE----------------RELAEQFGVSRMTVRKALDELVE 57 (236)
T ss_pred ccHHHHHHHHHHHHHhCCCCCC--CCCCCH----------------HHHHHHHCCcHHHHHHHHHHHHH
Confidence 456667777766655321 222 357766 67789999999999987766553
No 285
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=38.87 E-value=20 Score=35.30 Aligned_cols=23 Identities=17% Similarity=0.160 Sum_probs=20.5
Q ss_pred CchhhhhhhhccChhhHHHHHHH
Q 013572 150 STYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 150 ~s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
.+.++||..+|||.+|||+.++.
T Consensus 7 ~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 7 ITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHHCC
Confidence 47889999999999999998764
No 286
>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=38.73 E-value=41 Score=31.46 Aligned_cols=48 Identities=23% Similarity=0.354 Sum_probs=30.6
Q ss_pred HHHHHHHHhcccccccC-CCCCCCCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHH
Q 013572 109 TFRWLSGLLEPLLDCRD-PVGLPLNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLC 174 (440)
Q Consensus 109 tF~~L~~~L~~~l~~~~-~~~r~~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~ 174 (440)
-+..|.+.|+..+.... +.| ..+|.| ++|+..||||+.||.+.+....
T Consensus 9 ~y~~i~~~l~~~I~~g~~~~G--~~LPsE----------------~eLa~~~~VSR~TvR~Al~~L~ 57 (238)
T TIGR02325 9 LWRQIADKIEQEIAAGHLRAG--DYLPAE----------------MQLAERFGVNRHTVRRAIAALV 57 (238)
T ss_pred HHHHHHHHHHHHHHcCCCCCC--CcCcCH----------------HHHHHHHCCCHHHHHHHHHHHH
Confidence 35566666655543221 222 346666 6778899999999998766554
No 287
>PHA02591 hypothetical protein; Provisional
Probab=38.12 E-value=27 Score=27.03 Aligned_cols=27 Identities=22% Similarity=0.204 Sum_probs=23.8
Q ss_pred ccCCCchhhhhhhhccChhhHHHHHHH
Q 013572 146 LVNGSTYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 146 La~g~s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
...|.+...||...|+++.+|+++++.
T Consensus 56 ~eqGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 56 ARKGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 456899999999999999999998763
No 288
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=37.91 E-value=46 Score=29.17 Aligned_cols=44 Identities=18% Similarity=0.186 Sum_probs=34.5
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
.+++.++=.+. +++.|.+.+++|...++|..||..++.+..+.+
T Consensus 149 ~lt~~e~~vl~--l~~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl 192 (211)
T PRK15369 149 LLTPRERQILK--LITEGYTNRDIAEQLSISIKTVETHRLNMMRKL 192 (211)
T ss_pred CCCHHHHHHHH--HHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 36665554443 478999999999999999999999888866654
No 289
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=37.63 E-value=44 Score=31.55 Aligned_cols=23 Identities=30% Similarity=0.471 Sum_probs=18.7
Q ss_pred hhhhhhhccChhhHHHHHHHHHH
Q 013572 153 SEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 153 ~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.+++..||||+.||.+.+.....
T Consensus 33 ~eL~~~~~VSR~TvR~Al~~L~~ 55 (240)
T PRK09764 33 SALQTEFGVSRVTVRQALRQLVE 55 (240)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH
Confidence 67789999999999987766553
No 290
>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=37.33 E-value=52 Score=26.93 Aligned_cols=28 Identities=21% Similarity=0.233 Sum_probs=23.9
Q ss_pred CCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 148 NGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 148 ~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.+.+..+++...+++++|+++.+....+
T Consensus 42 ~~~t~~eL~~~l~~~~stvs~~i~~Le~ 69 (109)
T TIGR01889 42 GKLTLKEIIKEILIKQSALVKIIKKLSK 69 (109)
T ss_pred CcCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3578899999999999999998877654
No 291
>PRK14999 histidine utilization repressor; Provisional
Probab=37.27 E-value=44 Score=31.48 Aligned_cols=22 Identities=9% Similarity=0.324 Sum_probs=18.5
Q ss_pred hhhhhhhccChhhHHHHHHHHH
Q 013572 153 SEIATRFEVTESVTRFCVKQLC 174 (440)
Q Consensus 153 ~~la~~Fgvs~sTv~~~v~~v~ 174 (440)
++|+..||||+.||.+.+....
T Consensus 40 ~eLa~~~gVSR~TVR~Al~~L~ 61 (241)
T PRK14999 40 AELVAQYGFSRMTINRALRELT 61 (241)
T ss_pred HHHHHHHCCCHHHHHHHHHHHH
Confidence 6788999999999998776654
No 292
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=37.21 E-value=43 Score=27.07 Aligned_cols=27 Identities=22% Similarity=0.255 Sum_probs=23.3
Q ss_pred CCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 149 GSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 149 g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
..++.+++..+|+|.+|+++.+.+..+
T Consensus 17 ~~~~~~la~~l~~s~~tv~~~l~~L~~ 43 (108)
T smart00344 17 RISLAELAKKVGLSPSTVHNRVKRLEE 43 (108)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 578999999999999999988776654
No 293
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=37.14 E-value=39 Score=29.04 Aligned_cols=46 Identities=17% Similarity=0.138 Sum_probs=37.6
Q ss_pred CCHHHHHhhheeeccC-CCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 133 LSADIRLGIGLFRLVN-GSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 133 is~e~~L~i~L~~La~-g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
+..+++-.+-|+|-.. +.++..||..+++|.+|+.++..+|-+.|.
T Consensus 82 l~de~k~Ii~lry~~r~~~TW~~IA~~l~i~erta~r~~~~fK~~i~ 128 (130)
T PF05263_consen 82 LIDEEKRIIKLRYDRRSRRTWYQIAQKLHISERTARRWRDRFKNDIY 128 (130)
T ss_pred hCHHHHHHHHHHHcccccchHHHHHHHhCccHHHHHHHHHHHHHHhc
Confidence 4556777778887766 899999999999999999999888766543
No 294
>PRK09526 lacI lac repressor; Reviewed
Probab=37.07 E-value=19 Score=35.37 Aligned_cols=23 Identities=17% Similarity=0.104 Sum_probs=20.1
Q ss_pred CchhhhhhhhccChhhHHHHHHH
Q 013572 150 STYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 150 ~s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
.+..+||...|||.+|||++++.
T Consensus 6 ~ti~dIA~~aGVS~~TVSrvLn~ 28 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRVLNQ 28 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHhcC
Confidence 36789999999999999998763
No 295
>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=37.05 E-value=84 Score=25.25 Aligned_cols=58 Identities=24% Similarity=0.236 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHhcccccccCCCCCCCCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 104 KMSSSTFRWLSGLLEPLLDCRDPVGLPLNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 104 Rms~~tF~~L~~~L~~~l~~~~~~~r~~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.|+.+.|.-|+++- +|..+.-++.-=-||-.|.+-.+++..+||+.+-.++.+.+.-.
T Consensus 22 ~vs~e~F~lLl~ls--------------~IrS~kiI~AL~dyLV~G~srkeac~~~gV~~syfs~~L~rL~~ 79 (91)
T PF03333_consen 22 KVSEEHFWLLLELS--------------SIRSEKIIAALRDYLVDGLSRKEACERHGVNQSYFSRALNRLNR 79 (91)
T ss_dssp -S-HHHHHHHHHHS------------------HHHHHHHHHHHTT---HHHHHHHTT--HHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHHHC--------------CCCcHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 47778888888762 13334333333357899999999999999999999887766543
No 296
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=37.03 E-value=31 Score=32.80 Aligned_cols=37 Identities=27% Similarity=0.204 Sum_probs=31.3
Q ss_pred HHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHH
Q 013572 135 ADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 135 ~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~ 171 (440)
...++.-.|+.|..--+|++++..+|++.|.++|+++
T Consensus 9 ~~~~~v~~lr~lk~~~ty~el~~~~g~p~~~l~RYv~ 45 (238)
T PRK08558 9 LQLRAVRVLRSLKKTYTYEELSSITGLPESVLNRYVN 45 (238)
T ss_pred HHHHHHHHHHHHhcccCHHHHHHHHCCCHHHHHHHHc
Confidence 3455566788888889999999999999999999865
No 297
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=36.54 E-value=50 Score=26.69 Aligned_cols=48 Identities=15% Similarity=0.155 Sum_probs=33.1
Q ss_pred CCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 133 LSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 133 is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
+++++-=++-|.-+ .|.++.+-|.+.|||++|+++.+..--.-+.+.+
T Consensus 34 lt~eElEAlRLvD~-~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aL 81 (99)
T COG1342 34 LTIEELEALRLVDY-EGLTQEEAALRMGISRQTFWRLLTSARKKVADAL 81 (99)
T ss_pred ecHHHHHHHHHHhH-hhccHHHHHHHhcccHHHHHHHHHHHHHHHHHHH
Confidence 44444444444333 3677889999999999999998877666555544
No 298
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=35.26 E-value=19 Score=35.39 Aligned_cols=22 Identities=18% Similarity=0.291 Sum_probs=19.3
Q ss_pred chhhhhhhhccChhhHHHHHHH
Q 013572 151 TYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
+..+||...|||.+|||++++.
T Consensus 7 ti~dIA~~agVS~~TVSrvLn~ 28 (331)
T PRK14987 7 VLQDVADRVGVTKMTVSRFLRN 28 (331)
T ss_pred cHHHHHHHhCCCHHHhhhhhCC
Confidence 5689999999999999998753
No 299
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=35.05 E-value=29 Score=23.65 Aligned_cols=25 Identities=16% Similarity=0.122 Sum_probs=20.7
Q ss_pred CCCchhhhhhhhccChhhHHHHHHH
Q 013572 148 NGSTYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 148 ~g~s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
.+.+.++|+...|+|++++++++..
T Consensus 15 ~~~s~~~Ia~~~gvs~~~~y~~f~~ 39 (47)
T PF00440_consen 15 EAVSIRDIARRAGVSKGSFYRYFPS 39 (47)
T ss_dssp TTSSHHHHHHHHTSCHHHHHHHCSS
T ss_pred HhCCHHHHHHHHccchhhHHHHcCC
Confidence 3577899999999999999877543
No 300
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=35.01 E-value=45 Score=34.42 Aligned_cols=50 Identities=14% Similarity=0.198 Sum_probs=43.2
Q ss_pred CCCCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 129 LPLNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 129 r~~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
|...+.-.-|++|.|.+--+..|+..||..||-..+||.-.++.+-+.+-
T Consensus 345 R~~~i~~~RqiamyL~r~lt~~Slp~IG~~FgrdHtTV~~a~~kI~~~~~ 394 (408)
T COG0593 345 RTRNIVRPRQIAMYLARELTNLSLPEIGKAFGRDHTTVLHAVRKIEQLIE 394 (408)
T ss_pred cccccchHHHHHHHHHHHHccCcHHHHHHHhCCCccHHHHHHHHHHHHHh
Confidence 34567888999999999999999999999999999999888777776654
No 301
>COG5566 Uncharacterized conserved protein [Function unknown]
Probab=34.63 E-value=36 Score=28.93 Aligned_cols=27 Identities=22% Similarity=0.469 Sum_probs=24.3
Q ss_pred CCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 149 GSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 149 g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
|..|.+++..+++|..+|+++++++..
T Consensus 102 G~n~~eLaKkYrlS~~~Iy~VIrr~~t 128 (137)
T COG5566 102 GSNYVELAKKYRLSENHIYRVIRRTHT 128 (137)
T ss_pred CccHHHHHHHhcccHHHHHHHHHHHHH
Confidence 889999999999999999999986543
No 302
>PHA01976 helix-turn-helix protein
Probab=34.48 E-value=31 Score=25.26 Aligned_cols=44 Identities=16% Similarity=0.137 Sum_probs=30.6
Q ss_pred eccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhhhhcCCChhhHHHHHHHH
Q 013572 145 RLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRFWVAFPGPEELGLISKSF 200 (440)
Q Consensus 145 ~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~~I~~P~~~~~~~~~~~f 200 (440)
+-..|.+..++|...|++++|++++-+. -..|+.+.+..+++.|
T Consensus 11 R~~~glt~~~lA~~~gvs~~~v~~~e~g------------~~~p~~~~l~~ia~~l 54 (67)
T PHA01976 11 RNARAWSAPELSRRAGVRHSLIYDFEAD------------KRLPNLKTLLRLADAL 54 (67)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHcC------------CCCCCHHHHHHHHHHH
Confidence 3456888999999999999999976432 1245555555555544
No 303
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=34.40 E-value=24 Score=34.52 Aligned_cols=22 Identities=18% Similarity=0.309 Sum_probs=19.3
Q ss_pred chhhhhhhhccChhhHHHHHHH
Q 013572 151 TYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
+.++||...|||.+|||++++.
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 4679999999999999998764
No 304
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=34.12 E-value=46 Score=32.87 Aligned_cols=21 Identities=14% Similarity=0.181 Sum_probs=19.2
Q ss_pred chhhhhhhhccChhhHHHHHH
Q 013572 151 TYSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~v~ 171 (440)
+..+||...|||.+|||++++
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (346)
T PRK10401 3 TIRDVARQAGVSVATVSRVLN 23 (346)
T ss_pred CHHHHHHHhCCCHHHHHHHHC
Confidence 578999999999999999986
No 305
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=33.94 E-value=24 Score=34.76 Aligned_cols=22 Identities=18% Similarity=0.353 Sum_probs=19.7
Q ss_pred chhhhhhhhccChhhHHHHHHH
Q 013572 151 TYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
+..+||...|||.+|||++++.
T Consensus 3 Ti~dIA~~agVS~~TVSrvLn~ 24 (341)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINK 24 (341)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 5789999999999999999874
No 306
>PRK00215 LexA repressor; Validated
Probab=33.71 E-value=41 Score=30.89 Aligned_cols=27 Identities=26% Similarity=0.247 Sum_probs=22.8
Q ss_pred CCchhhhhhhhcc-ChhhHHHHHHHHHH
Q 013572 149 GSTYSEIATRFEV-TESVTRFCVKQLCR 175 (440)
Q Consensus 149 g~s~~~la~~Fgv-s~sTv~~~v~~v~~ 175 (440)
+.+..+|+..+|+ +++|+++++....+
T Consensus 23 ~~s~~ela~~~~~~~~~tv~~~l~~L~~ 50 (205)
T PRK00215 23 PPSRREIADALGLRSPSAVHEHLKALER 50 (205)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 4478899999999 99999998776654
No 307
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=33.65 E-value=34 Score=28.84 Aligned_cols=28 Identities=7% Similarity=0.054 Sum_probs=24.1
Q ss_pred CCchhhhhhhhccChhhHHHHHHHHHHH
Q 013572 149 GSTYSEIATRFEVTESVTRFCVKQLCRV 176 (440)
Q Consensus 149 g~s~~~la~~Fgvs~sTv~~~v~~v~~~ 176 (440)
+.+..+++..++++++||+++++..-++
T Consensus 30 ~~~v~ela~~l~lsqstvS~HL~~L~~A 57 (117)
T PRK10141 30 ELCVCDLCTALDQSQPKISRHLALLRES 57 (117)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4578899999999999999998877654
No 308
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=33.17 E-value=42 Score=26.43 Aligned_cols=24 Identities=33% Similarity=0.405 Sum_probs=20.5
Q ss_pred hhhhhhhhccChhhHHHHHHHHHH
Q 013572 152 YSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 152 ~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
..+++..+|++++|+++.+.....
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~ 25 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEK 25 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHH
Confidence 468999999999999998877665
No 309
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=32.89 E-value=39 Score=23.61 Aligned_cols=21 Identities=24% Similarity=0.222 Sum_probs=16.5
Q ss_pred chhhhhhhhccChhhHHHHHH
Q 013572 151 TYSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~v~ 171 (440)
+..+++...|+|++|+++.++
T Consensus 5 ~~~ev~~~~g~s~~ti~~~~k 25 (51)
T PF05930_consen 5 RIKEVAELLGVSRSTIYRLIK 25 (51)
T ss_dssp -HHHHHHHHSS-HHHHHHHHH
T ss_pred cHHHHHHHHCCCHHHHHHHHh
Confidence 356889999999999998766
No 310
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=32.43 E-value=57 Score=24.30 Aligned_cols=25 Identities=28% Similarity=0.272 Sum_probs=18.4
Q ss_pred CCchhhhhhhhccC-hhhHHHHHHHH
Q 013572 149 GSTYSEIATRFEVT-ESVTRFCVKQL 173 (440)
Q Consensus 149 g~s~~~la~~Fgvs-~sTv~~~v~~v 173 (440)
.-++++|+..||++ .+||+.++...
T Consensus 25 ~Pt~rEIa~~~g~~S~~tv~~~L~~L 50 (65)
T PF01726_consen 25 PPTVREIAEALGLKSTSTVQRHLKAL 50 (65)
T ss_dssp ---HHHHHHHHTSSSHHHHHHHHHHH
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 45689999999996 89988876543
No 311
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=32.37 E-value=26 Score=27.07 Aligned_cols=28 Identities=11% Similarity=0.081 Sum_probs=22.8
Q ss_pred eeccCCCchhhhhhhhc------cChhhHHHHHH
Q 013572 144 FRLVNGSTYSEIATRFE------VTESVTRFCVK 171 (440)
Q Consensus 144 ~~La~g~s~~~la~~Fg------vs~sTv~~~v~ 171 (440)
++..-|.+..++|...| +|++||+++-+
T Consensus 19 ~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 19 RRIKLGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 34566888999999999 59999999744
No 312
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=32.36 E-value=36 Score=26.07 Aligned_cols=24 Identities=25% Similarity=0.133 Sum_probs=17.7
Q ss_pred CCchhhhhhhhccChhhHHHHHHH
Q 013572 149 GSTYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 149 g~s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
..+-.++|...|||.+||.|..+.
T Consensus 34 ~~si~elA~~~~vS~sti~Rf~kk 57 (77)
T PF01418_consen 34 FMSISELAEKAGVSPSTIVRFCKK 57 (77)
T ss_dssp T--HHHHHHHCTS-HHHHHHHHHH
T ss_pred HccHHHHHHHcCCCHHHHHHHHHH
Confidence 567789999999999999886543
No 313
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=32.14 E-value=23 Score=34.74 Aligned_cols=22 Identities=18% Similarity=0.179 Sum_probs=19.3
Q ss_pred chhhhhhhhccChhhHHHHHHH
Q 013572 151 TYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
+..+||...|||++|||++++.
T Consensus 3 ti~dIA~~agVS~~TVSrvln~ 24 (327)
T PRK10339 3 TLKDIAIEAGVSLATVSRVLND 24 (327)
T ss_pred CHHHHHHHhCCCHHhhhhhhcC
Confidence 5679999999999999998754
No 314
>PRK10870 transcriptional repressor MprA; Provisional
Probab=32.02 E-value=59 Score=29.27 Aligned_cols=44 Identities=14% Similarity=0.080 Sum_probs=29.6
Q ss_pred CCCHHH-HHhhheeeccC-CCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 132 NLSADI-RLGIGLFRLVN-GSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 132 ~is~e~-~L~i~L~~La~-g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
++++.+ .+...|+.... +.+..+|+..++++++|+++++.+..+
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 355443 34444443323 356789999999999999998776554
No 315
>COG3080 FrdD Fumarate reductase subunit D [Energy production and conversion]
Probab=31.92 E-value=46 Score=27.40 Aligned_cols=24 Identities=42% Similarity=0.758 Sum_probs=21.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHhcCC
Q 013572 4 QKLSAFLSSLVSQLFLLLLLLFPD 27 (440)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~ 27 (440)
..|+|..-|.|.++++++|+.+|=
T Consensus 52 e~llaf~~s~Igkl~llvl~vlpl 75 (118)
T COG3080 52 ERLLAFAQSPIGKLFLLVLIVLPL 75 (118)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHH
Confidence 358899999999999999999886
No 316
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=31.70 E-value=43 Score=30.43 Aligned_cols=41 Identities=12% Similarity=-0.049 Sum_probs=30.4
Q ss_pred CCCCHHHHHhhheeecc-CCCchhhhhhhhccChhhHHHHHH
Q 013572 131 LNLSADIRLGIGLFRLV-NGSTYSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 131 ~~is~e~~L~i~L~~La-~g~s~~~la~~Fgvs~sTv~~~v~ 171 (440)
..+++-++.......+. .|.+...||..+|+|+++|++++.
T Consensus 101 ~~lt~~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~ 142 (187)
T TIGR00180 101 EDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLR 142 (187)
T ss_pred cCCCHHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHH
Confidence 45676666544444343 688999999999999999998755
No 317
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=31.61 E-value=25 Score=34.25 Aligned_cols=19 Identities=16% Similarity=0.237 Sum_probs=17.4
Q ss_pred hhhhhhhccChhhHHHHHH
Q 013572 153 SEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 153 ~~la~~Fgvs~sTv~~~v~ 171 (440)
++||...|||.+|||++++
T Consensus 2 ~dIA~~agVS~~TVSrvLn 20 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVIN 20 (327)
T ss_pred hhHHHHhCCcHHHHHHHhC
Confidence 5899999999999999876
No 318
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=31.18 E-value=42 Score=25.10 Aligned_cols=65 Identities=12% Similarity=0.025 Sum_probs=37.1
Q ss_pred HHHhhcCCCHHHHHHHHHHhcccccccCCCCCCCCCCHHHHHhhhee----eccCCCchhhhhhhhccChhhH
Q 013572 98 SFRNSFKMSSSTFRWLSGLLEPLLDCRDPVGLPLNLSADIRLGIGLF----RLVNGSTYSEIATRFEVTESVT 166 (440)
Q Consensus 98 ~F~~~fRms~~tF~~L~~~L~~~l~~~~~~~r~~~is~e~~L~i~L~----~La~g~s~~~la~~Fgvs~sTv 166 (440)
.|-..++++.+.-+.=.+..+......-..|| ++..-.+.++| .....-+..+++...||+..|+
T Consensus 3 r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr----~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 3 RICSKLGLPEDVRERAKEIYKKAQERGLLKGR----SPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-----HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred HHHhHcCCCHHHHHHHHHHHHHHHHcCCcccC----CHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 45667777776554444444333332333343 44444444443 3566888999999999999875
No 319
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=30.80 E-value=86 Score=31.03 Aligned_cols=76 Identities=20% Similarity=0.143 Sum_probs=47.1
Q ss_pred HHHhhcCCCHHHHHHHHHHhcccccccCCCCCCCCCCHHHHHhhhee----eccCCCchhhhhhhhccChhhHHHHHHHH
Q 013572 98 SFRNSFKMSSSTFRWLSGLLEPLLDCRDPVGLPLNLSADIRLGIGLF----RLVNGSTYSEIATRFEVTESVTRFCVKQL 173 (440)
Q Consensus 98 ~F~~~fRms~~tF~~L~~~L~~~l~~~~~~~r~~~is~e~~L~i~L~----~La~g~s~~~la~~Fgvs~sTv~~~v~~v 173 (440)
.|...++++...-..-...++......-..|+ +|.--.+.++| ..+...++.+|+...||+..|+.+..++.
T Consensus 225 r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr----~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ykel 300 (310)
T PRK00423 225 RFASELGLSGEVQKKAIEILQKAKEKGLTSGK----GPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKEL 300 (310)
T ss_pred HHHHHcCCCHHHHHHHHHHHHHHHhcCcccCC----CHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHH
Confidence 45557788877655555554433222222333 33333333333 34556789999999999999999888887
Q ss_pred HHHH
Q 013572 174 CRVL 177 (440)
Q Consensus 174 ~~~i 177 (440)
...+
T Consensus 301 ~~~l 304 (310)
T PRK00423 301 AEKL 304 (310)
T ss_pred HHHh
Confidence 7654
No 320
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=30.34 E-value=53 Score=31.75 Aligned_cols=44 Identities=25% Similarity=0.042 Sum_probs=34.8
Q ss_pred CCCHHHHHhhheeeccC---CCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVN---GSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~---g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.++.-++..-.|..++. +.+..+|+...|+++||++++++..++
T Consensus 20 ~~~sl~r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~ 66 (271)
T PRK10163 20 GAQALERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQA 66 (271)
T ss_pred cchHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 46666666666666653 467899999999999999999888775
No 321
>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=29.86 E-value=30 Score=33.76 Aligned_cols=21 Identities=19% Similarity=0.352 Sum_probs=18.5
Q ss_pred hhhhhhhhccChhhHHHHHHH
Q 013572 152 YSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 152 ~~~la~~Fgvs~sTv~~~v~~ 172 (440)
..+||...|||.+|||++++.
T Consensus 2 i~dIA~~aGVS~~TVSrvLn~ 22 (327)
T TIGR02417 2 LSDIAKLAGVSKTTASYVING 22 (327)
T ss_pred HHHHHHHhCCCHHHHHHHHcC
Confidence 468999999999999998764
No 322
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=29.18 E-value=1.2e+02 Score=28.53 Aligned_cols=28 Identities=18% Similarity=0.189 Sum_probs=22.1
Q ss_pred cCCCchhhhhhhhccChhhHHHHHHHHH
Q 013572 147 VNGSTYSEIATRFEVTESVTRFCVKQLC 174 (440)
Q Consensus 147 a~g~s~~~la~~Fgvs~sTv~~~v~~v~ 174 (440)
..+-+-.++|+..|+|+.|++|++....
T Consensus 171 ~~~~Taeela~~~giSRvTaRRYLeyl~ 198 (224)
T COG4565 171 DQELTAEELAQALGISRVTARRYLEYLV 198 (224)
T ss_pred CCccCHHHHHHHhCccHHHHHHHHHHHH
Confidence 3455567899999999999999876544
No 323
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=28.59 E-value=64 Score=21.53 Aligned_cols=25 Identities=16% Similarity=0.143 Sum_probs=18.6
Q ss_pred CCCchhhhhhhhccChhhHHHHHHH
Q 013572 148 NGSTYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 148 ~g~s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
++......|...|||++|+++-+++
T Consensus 17 ~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 17 CGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp TTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 4566789999999999999876553
No 324
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=28.51 E-value=50 Score=32.12 Aligned_cols=43 Identities=12% Similarity=0.036 Sum_probs=34.6
Q ss_pred HhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 139 LGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 139 L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
|-.++.-..+|.++...|+..+||+|+|++.+++.-+.+-..+
T Consensus 6 L~~F~~v~~~~~s~s~AA~~L~isq~avSr~I~~LE~~lg~~L 48 (309)
T PRK12682 6 LRFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEI 48 (309)
T ss_pred HHHHHHHHHccCCHHHHHHHhcCccHHHHHHHHHHHHHhCCee
Confidence 3344444556779999999999999999999999998886544
No 325
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=28.45 E-value=68 Score=29.49 Aligned_cols=38 Identities=16% Similarity=0.152 Sum_probs=28.0
Q ss_pred HHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHH
Q 013572 136 DIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLC 174 (440)
Q Consensus 136 e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~ 174 (440)
..++...|+.- .+.+..+|+..+|++.+||++.+.+..
T Consensus 3 r~~IL~~L~~~-~~~t~~eLA~~lgis~~tV~~~L~~Le 40 (203)
T TIGR02702 3 KEDILSYLLKQ-GQATAAALAEALAISPQAVRRHLKDLE 40 (203)
T ss_pred HHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 34555555443 458889999999999999998866544
No 326
>PRK10072 putative transcriptional regulator; Provisional
Probab=28.41 E-value=45 Score=27.02 Aligned_cols=26 Identities=12% Similarity=0.083 Sum_probs=22.5
Q ss_pred ccCCCchhhhhhhhccChhhHHHHHH
Q 013572 146 LVNGSTYSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 146 La~g~s~~~la~~Fgvs~sTv~~~v~ 171 (440)
-..|.+...+|..+|||.+||++|..
T Consensus 43 ~~~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 43 KGTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 35689999999999999999998744
No 327
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=28.25 E-value=41 Score=29.89 Aligned_cols=44 Identities=23% Similarity=0.144 Sum_probs=35.4
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
++++.+.. .|.+|+.|.+..+++...++|..||..++.+..+.+
T Consensus 149 ~lt~re~~--vl~~l~~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl 192 (210)
T PRK09935 149 VLSNREVT--ILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKL 192 (210)
T ss_pred cCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 45555554 445799999999999999999999999888876655
No 328
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=28.22 E-value=38 Score=21.86 Aligned_cols=22 Identities=14% Similarity=0.060 Sum_probs=18.6
Q ss_pred CCCchhhhhhhhccChhhHHHH
Q 013572 148 NGSTYSEIATRFEVTESVTRFC 169 (440)
Q Consensus 148 ~g~s~~~la~~Fgvs~sTv~~~ 169 (440)
.-.|.++.+..+|++++|++++
T Consensus 15 ~F~Si~eAa~~l~i~~~~I~~~ 36 (37)
T PF07453_consen 15 SFDSIREAARYLGISHSTISKY 36 (37)
T ss_pred EEcCHHHHHHHhCCCHHHHHHh
Confidence 3467889999999999999875
No 329
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=28.13 E-value=46 Score=28.12 Aligned_cols=33 Identities=18% Similarity=0.155 Sum_probs=25.9
Q ss_pred HHhhheeeccCCCchhhhhhhhccChhhHHHHHHH
Q 013572 138 RLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 138 ~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
.||--|..- |.+...+|...|+|++.||++++.
T Consensus 13 ~lA~~L~ee--G~Sq~~iA~LLGltqaAVS~Yls~ 45 (119)
T COG2522 13 LLAKELIEE--GLSQYRIAKLLGLTQAAVSQYLSG 45 (119)
T ss_pred HHHHHHHHc--CCcHHHHHHHhCCCHHHHHHHHcc
Confidence 344444444 999999999999999999998754
No 330
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=27.96 E-value=45 Score=22.50 Aligned_cols=20 Identities=25% Similarity=0.315 Sum_probs=16.5
Q ss_pred hhhhhhhhccChhhHHHHHH
Q 013572 152 YSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 152 ~~~la~~Fgvs~sTv~~~v~ 171 (440)
-.++|..+||+.+|+..+..
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYER 22 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999987644
No 331
>PF14493 HTH_40: Helix-turn-helix domain
Probab=27.95 E-value=49 Score=26.19 Aligned_cols=59 Identities=20% Similarity=0.089 Sum_probs=39.2
Q ss_pred hheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhhhhcCCChhhHHHHHHHHH
Q 013572 141 IGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRFWVAFPGPEELGLISKSFE 201 (440)
Q Consensus 141 i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~~I~~P~~~~~~~~~~~f~ 201 (440)
.|+..+..|.+..+||..-|++.+||..++-+....=.. + .+-.+-+.++.+.+.+.+.
T Consensus 5 ~T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~-~-~~~~~l~~e~~~~I~~~~~ 63 (91)
T PF14493_consen 5 ITYELFQKGLSIEEIAKIRGLKESTIYGHLAELIESGEP-L-DIEELLSEEEIKQIEDAIE 63 (91)
T ss_pred HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCC-C-CHHHhCCHHHHHHHHHHHH
Confidence 566667789999999999999999999887776654221 1 1112223345556655553
No 332
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=27.88 E-value=34 Score=33.44 Aligned_cols=22 Identities=18% Similarity=0.138 Sum_probs=19.2
Q ss_pred chhhhhhhhccChhhHHHHHHH
Q 013572 151 TYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
+.++||+.-|||.+|||++++.
T Consensus 3 ti~dIA~~agvS~~TVSrvLn~ 24 (329)
T TIGR01481 3 TIYDVAREAGVSMATVSRVVNG 24 (329)
T ss_pred cHHHHHHHhCCCHHHHHHHhCC
Confidence 4679999999999999998754
No 333
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=27.85 E-value=52 Score=24.25 Aligned_cols=21 Identities=29% Similarity=0.330 Sum_probs=18.6
Q ss_pred CCchhhhhhhhccChhhHHHH
Q 013572 149 GSTYSEIATRFEVTESVTRFC 169 (440)
Q Consensus 149 g~s~~~la~~Fgvs~sTv~~~ 169 (440)
...+.+||...|||.+||+.+
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred CccHHHHHHHHCCCHHHHHHH
Confidence 467899999999999999865
No 334
>COG5421 Transposase [DNA replication, recombination, and repair]
Probab=27.77 E-value=86 Score=32.84 Aligned_cols=58 Identities=24% Similarity=0.398 Sum_probs=40.2
Q ss_pred CCCcEEEEeecCCCceEEeeecCCCCCCCChhhhhcccccccccccccCCCCCcccCCcccceEEEecCCCC
Q 013572 231 DEDSIAVQIVVDSSSRMLSIVAGIRGDKGDSRVLKSSTLYKDIEEKKLLNSSPICVNGVAVDQYLIGDGGYP 302 (440)
Q Consensus 231 ~~~si~~q~v~D~~~rf~~v~~g~pGs~~D~~v~~~S~l~~~l~~~~l~~~~~~~l~g~~~~~~llgD~~Yp 302 (440)
+-+-+++..+++..|--+.+.+ .+|+.+|...+-. ..+.+.+. + ...+.++++|.||-
T Consensus 153 dl~QI~vsMi~~~~gIPl~~~v-~~Gni~D~~~~~~--ti~kl~~~-l----------~~~~~~~V~Dkgf~ 210 (480)
T COG5421 153 DLPQINVSMIVNQKGIPLFVRV-YSGNISDKNTLIK--TIQKLKSV-L----------VKDEVYLVADKGFN 210 (480)
T ss_pred CcceeEEEEEEcCCCCceEEEc-cCCCccchHHHHH--HHHHHHHh-c----------ccceEEEEEccccc
Confidence 4677899999998866666655 8999999988743 34433221 1 11147999999994
No 335
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=27.67 E-value=51 Score=24.06 Aligned_cols=22 Identities=18% Similarity=0.147 Sum_probs=18.6
Q ss_pred chhhhhhhhccChhhHHHHHHH
Q 013572 151 TYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
+..++|..+||+.+|++++.++
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 3568999999999999988764
No 336
>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=27.02 E-value=21 Score=31.84 Aligned_cols=24 Identities=29% Similarity=0.295 Sum_probs=0.0
Q ss_pred CCchhhhhhhhccChhhHHHHHHH
Q 013572 149 GSTYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 149 g~s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
.....++|...|++.|||||.+..
T Consensus 49 PLt~~~iA~~lgl~~STVSRav~~ 72 (160)
T PF04552_consen 49 PLTMKDIADELGLHESTVSRAVKN 72 (160)
T ss_dssp ------------------------
T ss_pred CCCHHHHHHHhCCCHhHHHHHHcC
Confidence 346789999999999999998663
No 337
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=26.82 E-value=35 Score=33.63 Aligned_cols=22 Identities=14% Similarity=0.152 Sum_probs=19.2
Q ss_pred chhhhhhhhccChhhHHHHHHH
Q 013572 151 TYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
+..+||..-|||.+|||++++.
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn~ 24 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVINN 24 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhCC
Confidence 4689999999999999998753
No 338
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=26.82 E-value=1.4e+02 Score=30.10 Aligned_cols=47 Identities=21% Similarity=0.223 Sum_probs=36.9
Q ss_pred CCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 131 LNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 131 ~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
+.++++.|++++|+.+ .|.+-.+|+..|=|+.+|+-+=+-+--..|.
T Consensus 119 Pal~~~~riALtLR~v-~GLs~~eIArAFLv~e~am~QRivRAK~ri~ 165 (415)
T COG4941 119 PALPPEQRIALTLRLV-GGLSTAEIARAFLVPEAAMAQRIVRAKARIR 165 (415)
T ss_pred CCCChhhHHHHHHHHH-cCCcHHHHHHHHcCCcHHHHHHHHHHHHHHH
Confidence 5799999999999765 5999999999999999998544333333333
No 339
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=26.64 E-value=52 Score=31.60 Aligned_cols=43 Identities=19% Similarity=0.070 Sum_probs=32.1
Q ss_pred CCHHHHHhhheeeccC---CCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 133 LSADIRLGIGLFRLVN---GSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 133 is~e~~L~i~L~~La~---g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
+..-++..-.|..|+. +.+..+|+...|+++||+++++.....
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 4444555555666643 368999999999999999999887764
No 340
>PF08769 Spo0A_C: Sporulation initiation factor Spo0A C terminal; InterPro: IPR014879 The response regulator Spo0A is comprised of a phophoacceptor domain and a transcription activation domain. This domain corresponds to the transcription activation domain and forms an alpha helical structure comprising of 6 alpha helices. The structure contains a helix-turn-helix and binds DNA [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005509 calcium ion binding, 0006355 regulation of transcription, DNA-dependent, 0042173 regulation of sporulation resulting in formation of a cellular spore, 0005737 cytoplasm; PDB: 1FC3_C 1LQ1_D.
Probab=26.59 E-value=79 Score=26.08 Aligned_cols=34 Identities=21% Similarity=0.261 Sum_probs=29.0
Q ss_pred CCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 148 NGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 148 ~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
+..=|..||..|+.+.+.|-+.++.++++.|..-
T Consensus 39 tK~LYp~IA~k~~TT~s~VERaIR~aI~~~w~~g 72 (106)
T PF08769_consen 39 TKELYPDIAKKYGTTPSRVERAIRHAIEVAWTRG 72 (106)
T ss_dssp TTTHHHHHHHHTTS-HHHHHHHHHHHHHHHHHCS
T ss_pred hhhHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcC
Confidence 3455999999999999999999999999998754
No 341
>cd00131 PAX Paired Box domain
Probab=26.55 E-value=2.1e+02 Score=24.31 Aligned_cols=78 Identities=14% Similarity=0.074 Sum_probs=44.7
Q ss_pred ChhHHHhhcCCCHHHHHHHHHHhccccccc-CCC-CC-CCCCCHHH-HHhhheeeccCCCchhhhhhhh---cc------
Q 013572 95 LPDSFRNSFKMSSSTFRWLSGLLEPLLDCR-DPV-GL-PLNLSADI-RLGIGLFRLVNGSTYSEIATRF---EV------ 161 (440)
Q Consensus 95 ~~~~F~~~fRms~~tF~~L~~~L~~~l~~~-~~~-~r-~~~is~e~-~L~i~L~~La~g~s~~~la~~F---gv------ 161 (440)
+..+--..|++++.|...+++......... .+. ++ +..+.++. ...+.+..-.-..+..+++... |+
T Consensus 35 s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~ 114 (128)
T cd00131 35 RPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNV 114 (128)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCC
Confidence 556778899999999999998766432211 112 22 23333332 3233332323334455555552 55
Q ss_pred -ChhhHHHHHHH
Q 013572 162 -TESVTRFCVKQ 172 (440)
Q Consensus 162 -s~sTv~~~v~~ 172 (440)
|.||++++++.
T Consensus 115 ~s~stI~R~L~~ 126 (128)
T cd00131 115 PSVSSINRILRN 126 (128)
T ss_pred CCHHHHHHHHHh
Confidence 99999998653
No 342
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=26.15 E-value=73 Score=27.20 Aligned_cols=52 Identities=19% Similarity=0.185 Sum_probs=38.6
Q ss_pred HHHhhcCCCHHHHHHHHHHhcccccccCCCCCCCCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHH
Q 013572 98 SFRNSFKMSSSTFRWLSGLLEPLLDCRDPVGLPLNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRV 176 (440)
Q Consensus 98 ~F~~~fRms~~tF~~L~~~L~~~l~~~~~~~r~~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~ 176 (440)
-.+-.|+++...++-+..+|+.. .++ +-.+||...++++|||++.++....+
T Consensus 18 vl~c~~GLs~~Dv~v~~~LL~~~----------~~~-----------------tvdelae~lnr~rStv~rsl~~L~~~ 69 (126)
T COG3355 18 VLKCVYGLSELDVEVYKALLEEN----------GPL-----------------TVDELAEILNRSRSTVYRSLQNLLEA 69 (126)
T ss_pred HHHHHhCCcHHHHHHHHHHHhhc----------CCc-----------------CHHHHHHHHCccHHHHHHHHHHHHHc
Confidence 34457888888888888887421 122 34589999999999999998887753
No 343
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=25.43 E-value=62 Score=26.25 Aligned_cols=36 Identities=6% Similarity=0.037 Sum_probs=30.0
Q ss_pred ccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 146 LVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 146 La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
++...|+...|...|+|++|+++.+++.-+.+-..+
T Consensus 13 v~~~gSis~AA~~L~iS~stvs~~I~~LE~~lg~~L 48 (99)
T TIGR00637 13 IARMGSISQAAKDAGISYKSAWDYIRAMNNLSGEPL 48 (99)
T ss_pred HHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCCe
Confidence 445678999999999999999999999888776543
No 344
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=25.41 E-value=43 Score=33.42 Aligned_cols=22 Identities=14% Similarity=0.158 Sum_probs=18.9
Q ss_pred chhhhhhhhccChhhHHHHHHH
Q 013572 151 TYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
+..++|..-|||.+|||++++.
T Consensus 2 TikDVA~~AGVS~sTVSrvln~ 23 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLNG 23 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 4679999999999999998653
No 345
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=25.38 E-value=61 Score=29.01 Aligned_cols=26 Identities=23% Similarity=0.367 Sum_probs=22.3
Q ss_pred CchhhhhhhhccChhhHHHHHHHHHH
Q 013572 150 STYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 150 ~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.++.+++..+|+|++||++.++...+
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~ik~L~e 101 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRAIKELEE 101 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 46889999999999999998877654
No 346
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=25.01 E-value=54 Score=24.64 Aligned_cols=38 Identities=16% Similarity=0.024 Sum_probs=27.1
Q ss_pred CCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHH
Q 013572 133 LSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 133 is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~ 171 (440)
.++.+++.-.+ +-..|.+..++|...|+|++|++++.+
T Consensus 3 ~~~g~~i~~~~-~~~~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 3 AHPGEILREEF-LEPLGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred CCHHHHHHHHH-HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 34455543121 345788899999999999999998754
No 347
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=24.85 E-value=62 Score=31.56 Aligned_cols=44 Identities=18% Similarity=0.092 Sum_probs=35.4
Q ss_pred HHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 138 RLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 138 ~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
+|-.++.-..+|.|+...|+..++|+++||+.+++.-+.+-..+
T Consensus 5 ~L~~F~~v~~~~~S~s~AA~~L~isQpavS~~I~~LE~~lg~~L 48 (309)
T PRK12683 5 QLRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEI 48 (309)
T ss_pred HHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhCCee
Confidence 34444444556779999999999999999999999998886554
No 348
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=24.85 E-value=50 Score=28.18 Aligned_cols=59 Identities=17% Similarity=0.280 Sum_probs=42.1
Q ss_pred HhhcCCCHHHHHHHHHHhcccccccCCCCCCCCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 100 RNSFKMSSSTFRWLSGLLEPLLDCRDPVGLPLNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 100 ~~~fRms~~tF~~L~~~L~~~l~~~~~~~r~~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.-.|..+++-+..|.+.+...+.+. .+.+.++| -|-+++|...||...||+|..++.-+
T Consensus 3 ~i~f~s~~PIY~QI~~qIk~~I~~g-------~l~pGdkL----------PSvRelA~~~~VNpnTv~raY~eLE~ 61 (125)
T COG1725 3 RIDFDSSKPIYEQIANQIKEQIASG-------ELKPGDKL----------PSVRELAKDLGVNPNTVQRAYQELER 61 (125)
T ss_pred ccCcCCCCCHHHHHHHHHHHHHHhC-------CcCCCCCC----------CcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3456778888999999887766432 13333333 35688999999999999998777654
No 349
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=24.75 E-value=67 Score=21.10 Aligned_cols=23 Identities=22% Similarity=0.231 Sum_probs=15.7
Q ss_pred ccCCCchhhhhhhhccChhhHHH
Q 013572 146 LVNGSTYSEIATRFEVTESVTRF 168 (440)
Q Consensus 146 La~g~s~~~la~~Fgvs~sTv~~ 168 (440)
...|+++..||.+||++...+.+
T Consensus 3 V~~gDtl~~IA~~~~~~~~~l~~ 25 (44)
T PF01476_consen 3 VQPGDTLWSIAKRYGISVDELME 25 (44)
T ss_dssp E-TT--HHHHHHHTTS-HHHHHH
T ss_pred ECcCCcHHHHHhhhhhhHhHHHH
Confidence 46789999999999998877654
No 350
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=24.42 E-value=47 Score=28.08 Aligned_cols=26 Identities=23% Similarity=0.189 Sum_probs=21.9
Q ss_pred CchhhhhhhhccChhhHHHHHHHHHH
Q 013572 150 STYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 150 ~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.+..+|+..+|+|.++|++++....+
T Consensus 26 ~s~~eia~~l~is~~~v~~~l~~L~~ 51 (130)
T TIGR02944 26 YSAAEIAEQTGLNAPTVSKILKQLSL 51 (130)
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 47889999999999999988766554
No 351
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=24.24 E-value=86 Score=27.22 Aligned_cols=44 Identities=18% Similarity=0.204 Sum_probs=32.7
Q ss_pred CCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHH
Q 013572 133 LSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLC 178 (440)
Q Consensus 133 is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~ 178 (440)
+++.++-.+. .+..|.++..++..+|+|..||..++.+....+.
T Consensus 142 l~~~e~~vl~--~~~~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~ 185 (202)
T PRK09390 142 LSERERQVMD--GLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQ 185 (202)
T ss_pred hhhhHHHHHH--HHHccCchHHHHHHcCCCHHHHHHHHHHHHHHHc
Confidence 4444433333 3667889999999999999999988887776653
No 352
>PRK11050 manganese transport regulator MntR; Provisional
Probab=24.24 E-value=84 Score=27.52 Aligned_cols=28 Identities=25% Similarity=0.374 Sum_probs=23.9
Q ss_pred CCCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 148 NGSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 148 ~g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.+.+..+++..++++++||++.+.+...
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~ 77 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLAR 77 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4668899999999999999998777654
No 353
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=23.96 E-value=64 Score=28.49 Aligned_cols=34 Identities=18% Similarity=0.136 Sum_probs=26.8
Q ss_pred CCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 148 NGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 148 ~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
++.+.++|+...|||++|++.+|..--..+.+.+
T Consensus 27 ~~~s~~~IA~~agvsk~~ly~~F~sK~~L~~~~~ 60 (189)
T TIGR03384 27 LDVTIAQIARRAGVSSGIISHYFGGKQGLLEATM 60 (189)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHcCCHHHHHHHHH
Confidence 3678899999999999999998865555555444
No 354
>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent
Probab=23.84 E-value=87 Score=26.53 Aligned_cols=40 Identities=15% Similarity=0.165 Sum_probs=30.8
Q ss_pred HHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHH
Q 013572 137 IRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRV 176 (440)
Q Consensus 137 ~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~ 176 (440)
+...+.+.|+..|.|.+.||...++|..++.+....--..
T Consensus 66 ~~~~ll~~~Yv~g~s~r~IA~~~~~s~~~ir~~l~~ae~~ 105 (125)
T PF06530_consen 66 EEYDLLILYYVYGWSKRQIARKLKCSEGKIRKRLQRAEGF 105 (125)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHhhhh
Confidence 3455666667789999999999999999998766544433
No 355
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=23.62 E-value=99 Score=28.39 Aligned_cols=26 Identities=15% Similarity=0.158 Sum_probs=22.2
Q ss_pred CCchhhhhhhhccChhhHHHHHHHHH
Q 013572 149 GSTYSEIATRFEVTESVTRFCVKQLC 174 (440)
Q Consensus 149 g~s~~~la~~Fgvs~sTv~~~v~~v~ 174 (440)
+.+..+++..+++|++|+++.+....
T Consensus 157 ~~s~~eia~~l~is~stv~r~L~~Le 182 (203)
T TIGR01884 157 EKSVKNIAKKLGKSLSTISRHLRELE 182 (203)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45889999999999999998877644
No 356
>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=23.23 E-value=71 Score=29.80 Aligned_cols=22 Identities=9% Similarity=0.312 Sum_probs=17.9
Q ss_pred hhhhhhhccChhhHHHHHHHHH
Q 013572 153 SEIATRFEVTESVTRFCVKQLC 174 (440)
Q Consensus 153 ~~la~~Fgvs~sTv~~~v~~v~ 174 (440)
++++..||||+.||++.+....
T Consensus 29 ~eLa~~~~VSR~TVR~Al~~L~ 50 (230)
T TIGR02018 29 HELVAQYGCSRMTVNRALRELT 50 (230)
T ss_pred HHHHHHHCCCHHHHHHHHHHHH
Confidence 5678899999999998766554
No 357
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=22.98 E-value=1.1e+02 Score=28.05 Aligned_cols=42 Identities=21% Similarity=0.093 Sum_probs=28.6
Q ss_pred CCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQL 173 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v 173 (440)
.+++.+-..+...+-..|.+..+|+...++.++|+++++.+.
T Consensus 42 gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rL 83 (185)
T PRK13777 42 DLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKL 83 (185)
T ss_pred CCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHH
Confidence 355554443333333457889999999999999998876543
No 358
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=22.78 E-value=88 Score=29.82 Aligned_cols=44 Identities=14% Similarity=0.076 Sum_probs=32.0
Q ss_pred CCCHHHHHhhheeeccC--CCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 132 NLSADIRLGIGLFRLVN--GSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 132 ~is~e~~L~i~L~~La~--g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.++.-++..-.|..|+. +.+..+|+...|+++||+++++...+.
T Consensus 9 ~v~sl~r~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~ 54 (257)
T PRK15090 9 SVSSVLKVFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKT 54 (257)
T ss_pred ccHHHHHHHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 35555555555555543 357889999999999999999887664
No 359
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=22.77 E-value=72 Score=21.95 Aligned_cols=25 Identities=16% Similarity=0.101 Sum_probs=20.5
Q ss_pred CCCchhhhhhhhccChhhHHHHHHH
Q 013572 148 NGSTYSEIATRFEVTESVTRFCVKQ 172 (440)
Q Consensus 148 ~g~s~~~la~~Fgvs~sTv~~~v~~ 172 (440)
.-.|..+.++.+|++.++++++++.
T Consensus 16 ~f~S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 16 EFSSIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred EecCHHHHHHHhCCCHHHHHHHHhC
Confidence 3467889999999999999987653
No 360
>PRK04140 hypothetical protein; Provisional
Probab=22.75 E-value=85 Score=31.29 Aligned_cols=81 Identities=17% Similarity=0.085 Sum_probs=51.9
Q ss_pred cCCCHHH-HHHHHHHhcccccccCCCCCCCCCCHH-HHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHh
Q 013572 103 FKMSSST-FRWLSGLLEPLLDCRDPVGLPLNLSAD-IRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTN 180 (440)
Q Consensus 103 fRms~~t-F~~L~~~L~~~l~~~~~~~r~~~is~e-~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~ 180 (440)
.-|+.+| |+.+++-..|.+... +.| .-+... ++|- -.+-..|.+..++|...|+|++|+++|-+.
T Consensus 96 ~~~~~~tl~~~~~~g~~p~v~~~-~Gg--~~v~i~GerLk--~lRe~~GlSq~eLA~~lGVSr~tIskyE~G-------- 162 (317)
T PRK04140 96 PALSPDTLYDDFVEGEPPLIYAA-PGG--FYVKIDGDVLR--EAREELGLSLGELASELGVSRRTISKYENG-------- 162 (317)
T ss_pred eeecHHHHHHHHhCCCCceEEEc-CCC--eeehhhHHHHH--HHHHHcCCCHHHHHHHhCCCHHHHHHHHcC--------
Confidence 3478999 999998887865422 222 112222 2222 236678999999999999999999986431
Q ss_pred hhhhhcCCChhhHHHHHHHH
Q 013572 181 FRFWVAFPGPEELGLISKSF 200 (440)
Q Consensus 181 l~~~I~~P~~~~~~~~~~~f 200 (440)
-..|+.+.+..+++.|
T Consensus 163 ----~~~Ps~e~~~kLa~~L 178 (317)
T PRK04140 163 ----GMNASIEVAIKLEEIL 178 (317)
T ss_pred ----CCCCCHHHHHHHHHHh
Confidence 1345555555555554
No 361
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=21.96 E-value=95 Score=28.03 Aligned_cols=42 Identities=17% Similarity=0.199 Sum_probs=36.5
Q ss_pred CCCCCHHHHHhhheeeccCCCchhhhhhhhccChhhHHHHHH
Q 013572 130 PLNLSADIRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 130 ~~~is~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~ 171 (440)
...||-+.|-.|.-.+...|.+.+.||..|||+...|.-|++
T Consensus 14 ~~~lse~~r~~Iy~~~~~~~~sv~~vS~~ygi~~~RV~AIvr 55 (172)
T PF12298_consen 14 NPVLSEELREQIYEDVMQDGKSVREVSQKYGIKIQRVEAIVR 55 (172)
T ss_pred CCcCCHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 356888999888888889999999999999999999877655
No 362
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=21.95 E-value=94 Score=25.01 Aligned_cols=23 Identities=26% Similarity=0.312 Sum_probs=20.1
Q ss_pred hhhhhhhccChhhHHHHHHHHHH
Q 013572 153 SEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 153 ~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.+++...+++++|+++.+.+...
T Consensus 40 ~~la~~l~i~~~~vt~~l~~Le~ 62 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRLED 62 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH
Confidence 89999999999999998776654
No 363
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=21.94 E-value=80 Score=30.87 Aligned_cols=43 Identities=16% Similarity=0.052 Sum_probs=34.9
Q ss_pred HhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhh
Q 013572 139 LGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNF 181 (440)
Q Consensus 139 L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l 181 (440)
+-.++.-..+|.++...|+..++|+|||++.+++.-+.+...+
T Consensus 6 l~~f~~v~~~~~s~s~AA~~L~iSQ~avSr~I~~LE~~lg~~L 48 (316)
T PRK12679 6 LKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEI 48 (316)
T ss_pred HHHHHHHHHcCCCHHHHHHHhcCCchHHHHHHHHHHHHhCCEE
Confidence 4444444556779999999999999999999999999887654
No 364
>PRK09726 antitoxin HipB; Provisional
Probab=21.88 E-value=62 Score=25.41 Aligned_cols=43 Identities=19% Similarity=0.105 Sum_probs=30.4
Q ss_pred ccCCCchhhhhhhhccChhhHHHHHHHHHHHHHHhhhhhhcCCChhhHHHHHHHH
Q 013572 146 LVNGSTYSEIATRFEVTESVTRFCVKQLCRVLCTNFRFWVAFPGPEELGLISKSF 200 (440)
Q Consensus 146 La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~~I~~P~~~~~~~~~~~f 200 (440)
-+.|.+..++|...||+++|++++.+. -..|+.+.+..++..|
T Consensus 22 ~~~gltq~elA~~~gvs~~tis~~e~g------------~~~ps~~~l~~ia~~l 64 (88)
T PRK09726 22 QQNGWTQSELAKKIGIKQATISNFENN------------PDNTTLTTFFKILQSL 64 (88)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHCC------------CCCCCHHHHHHHHHHc
Confidence 356888999999999999999976442 1235555555665554
No 365
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=21.62 E-value=63 Score=25.66 Aligned_cols=24 Identities=29% Similarity=0.194 Sum_probs=17.4
Q ss_pred CCCchhhhhhhhccChhhHHHHHH
Q 013572 148 NGSTYSEIATRFEVTESVTRFCVK 171 (440)
Q Consensus 148 ~g~s~~~la~~Fgvs~sTv~~~v~ 171 (440)
.|.+..+||...|.|++.|++++.
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~l~ 25 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSRSWVSNHLA 25 (93)
T ss_dssp TT--HHHHHHHTT--HHHHHHHHG
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 588899999999999999998754
No 366
>PRK11569 transcriptional repressor IclR; Provisional
Probab=21.58 E-value=96 Score=29.96 Aligned_cols=43 Identities=14% Similarity=0.050 Sum_probs=33.0
Q ss_pred CCHHHHHhhheeeccC---CCchhhhhhhhccChhhHHHHHHHHHH
Q 013572 133 LSADIRLGIGLFRLVN---GSTYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 133 is~e~~L~i~L~~La~---g~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
+..-++..-.|..++. +.+..+|+...|+++||+++++...++
T Consensus 24 v~sl~ral~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~ 69 (274)
T PRK11569 24 VQSLTRGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQ 69 (274)
T ss_pred ccHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4555565555666653 468999999999999999999887664
No 367
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=21.36 E-value=74 Score=23.39 Aligned_cols=19 Identities=16% Similarity=0.132 Sum_probs=16.3
Q ss_pred chhhhhhhhccChhhHHHH
Q 013572 151 TYSEIATRFEVTESVTRFC 169 (440)
Q Consensus 151 s~~~la~~Fgvs~sTv~~~ 169 (440)
+...+|..+|||+++|+.+
T Consensus 11 ~~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHh
Confidence 5678999999999999988
No 368
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=21.25 E-value=56 Score=23.64 Aligned_cols=30 Identities=17% Similarity=0.198 Sum_probs=26.7
Q ss_pred CCCCHHHHHhhheeeccCCCchhhhhhhhc
Q 013572 131 LNLSADIRLGIGLFRLVNGSTYSEIATRFE 160 (440)
Q Consensus 131 ~~is~e~~L~i~L~~La~g~s~~~la~~Fg 160 (440)
..+...-++++.|..--+|.++.+||..||
T Consensus 27 ~~~~~aR~iamyla~~~~~~sl~~Ig~~fg 56 (60)
T smart00760 27 REIVLARQIAMYLARELTDLSLPEIGKIFG 56 (60)
T ss_pred cchhHHHHHHHHHHHHHHCCCHHHHHHHhC
Confidence 567778899999888888999999999998
No 369
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=21.25 E-value=82 Score=32.84 Aligned_cols=31 Identities=16% Similarity=0.236 Sum_probs=24.1
Q ss_pred CchhhhhhhhccChhhHHHHHHHHHHHHHHhhhhhhcCCCh
Q 013572 150 STYSEIATRFEVTESVTRFCVKQLCRVLCTNFRFWVAFPGP 190 (440)
Q Consensus 150 ~s~~~la~~Fgvs~sTv~~~v~~v~~~i~~~l~~~I~~P~~ 190 (440)
...++||...|++.|||||++.. .|+.-|..
T Consensus 331 L~LrdvA~~i~~HESTISRai~n----------Ky~~tprG 361 (444)
T COG1508 331 LVLRDVADEIGMHESTISRAITN----------KYLATPRG 361 (444)
T ss_pred ccHHHHHHHhCccHHHHHHHHhc----------ccccCCcc
Confidence 55699999999999999987542 45666654
No 370
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=21.16 E-value=87 Score=29.16 Aligned_cols=32 Identities=13% Similarity=0.035 Sum_probs=28.0
Q ss_pred ccCCCchhhhhhhhccChhhHHHHHHHHHHHH
Q 013572 146 LVNGSTYSEIATRFEVTESVTRFCVKQLCRVL 177 (440)
Q Consensus 146 La~g~s~~~la~~Fgvs~sTv~~~v~~v~~~i 177 (440)
++.|.+..+||..+++|..||..++....+..
T Consensus 175 ~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~ 206 (239)
T PRK10430 175 QDYEFSTDELANAVNISRVSCRKYLIWLVNCH 206 (239)
T ss_pred CCCCcCHHHHHHHhCchHHHHHHHHHHHHhCC
Confidence 57899999999999999999999988776543
No 371
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=20.89 E-value=1.1e+02 Score=24.66 Aligned_cols=26 Identities=4% Similarity=-0.010 Sum_probs=22.1
Q ss_pred CchhhhhhhhccChhhHHHHHHHHHH
Q 013572 150 STYSEIATRFEVTESVTRFCVKQLCR 175 (440)
Q Consensus 150 ~s~~~la~~Fgvs~sTv~~~v~~v~~ 175 (440)
.+..++|..+|+|.+++++.+++.+.
T Consensus 22 ~~~~~lA~~~~~S~~~l~r~f~~~~g 47 (107)
T PRK10219 22 LNIDVVAKKSGYSKWYLQRMFRTVTH 47 (107)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHC
Confidence 45678999999999999999998753
No 372
>KOG0930 consensus Guanine nucleotide exchange factor Cytohesin, contains PH and Sec7 domains [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.42 E-value=3.6e+02 Score=26.34 Aligned_cols=82 Identities=12% Similarity=0.143 Sum_probs=54.8
Q ss_pred HHHhhheeeccCCCchhhhhhhhccChhhHHHHHHHHHH-------HHHHhhhhh---hcCCCh-hhHHHHHHHHHhhh-
Q 013572 137 IRLGIGLFRLVNGSTYSEIATRFEVTESVTRFCVKQLCR-------VLCTNFRFW---VAFPGP-EELGLISKSFEELT- 204 (440)
Q Consensus 137 ~~L~i~L~~La~g~s~~~la~~Fgvs~sTv~~~v~~v~~-------~i~~~l~~~---I~~P~~-~~~~~~~~~f~~~~- 204 (440)
+.+|.+| |-+.|.+-..|+...|=-..-.-.+++.|++ -|...+++| .+.|.. +...++++.|..++
T Consensus 94 q~iA~fl-ykGEGLnKtaIG~yLGer~~~nl~vL~aFv~~Hef~dlnlVqALRQfLwSFRLPGEaQKIdRmmEaFA~rYc 172 (395)
T KOG0930|consen 94 EDIARFL-YKGEGLNKTAIGDYLGERDEFNLQVLHAFVDLHEFTDLNLVQALRQFLWSFRLPGEAQKIDRMMEAFAQRYC 172 (395)
T ss_pred HHHHHHH-HhcCCcchhhHhhhhccCchhHHHHHHHHHHHHHhccchHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHh
Confidence 3444444 3466777888888877666554444444443 134445544 356776 77889999999886
Q ss_pred -CCCCccccccceEEE
Q 013572 205 -GLPNCCGVIDCTRFK 219 (440)
Q Consensus 205 -~fP~ciGaIDgthi~ 219 (440)
.-||++|..|.+|+-
T Consensus 173 lcNPgvfqstDtcyvl 188 (395)
T KOG0930|consen 173 LCNPGVFQSTDTCYVL 188 (395)
T ss_pred ccCCcccccCceeeee
Confidence 468899999998875
No 373
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=20.05 E-value=74 Score=26.20 Aligned_cols=24 Identities=21% Similarity=0.051 Sum_probs=20.3
Q ss_pred ccCCCchhhhhhhhccChhhHHHH
Q 013572 146 LVNGSTYSEIATRFEVTESVTRFC 169 (440)
Q Consensus 146 La~g~s~~~la~~Fgvs~sTv~~~ 169 (440)
=+.|.+....|..+|+|.+||+.|
T Consensus 54 e~~~lSQ~vFA~~L~vs~~Tv~~W 77 (104)
T COG2944 54 EKLGLSQPVFARYLGVSVSTVRKW 77 (104)
T ss_pred HHhCCCHHHHHHHHCCCHHHHHHH
Confidence 456888899999999999999865
No 374
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=20.01 E-value=75 Score=23.23 Aligned_cols=23 Identities=22% Similarity=0.274 Sum_probs=18.9
Q ss_pred hhhhhhhhccChhhHHHHHHHHH
Q 013572 152 YSEIATRFEVTESVTRFCVKQLC 174 (440)
Q Consensus 152 ~~~la~~Fgvs~sTv~~~v~~v~ 174 (440)
..++|..+|||.+|+..+.++..
T Consensus 3 i~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHTTS
T ss_pred HHHHHHHHCcCHHHHHHHHHhcC
Confidence 46899999999999998866544
Done!