Query 015432
Match_columns 407
No_of_seqs 244 out of 1765
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 06:15:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015432.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015432hhsearch_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 2.5E-41 5.4E-46 325.7 12.8 313 74-405 7-323 (326)
2 PF13359 DDE_Tnp_4: DDE superf 100.0 3.7E-37 8E-42 270.3 4.9 154 189-355 1-158 (158)
3 PF04827 Plant_tran: Plant tra 100.0 2.5E-36 5.5E-41 262.3 8.9 200 158-362 2-202 (205)
4 PF13613 HTH_Tnp_4: Helix-turn 98.9 1.5E-10 3.3E-15 82.0 -0.7 51 107-157 2-52 (53)
5 PF13612 DDE_Tnp_1_3: Transpos 98.9 1.7E-09 3.7E-14 93.8 4.0 130 182-333 3-150 (155)
6 PF01609 DDE_Tnp_1: Transposas 97.2 9.1E-06 2E-10 73.3 -6.5 150 184-356 4-213 (213)
7 PF13586 DDE_Tnp_1_2: Transpos 97.0 0.00028 6E-09 55.3 1.6 74 278-352 1-84 (88)
8 PF02796 HTH_7: Helix-turn-hel 95.1 0.0021 4.5E-08 43.6 -2.3 34 113-146 10-43 (45)
9 PF13936 HTH_38: Helix-turn-he 95.1 0.0027 5.9E-08 42.8 -1.8 41 106-147 3-43 (44)
10 PF04545 Sigma70_r4: Sigma-70, 94.3 0.0085 1.9E-07 41.4 -0.7 45 107-152 4-48 (50)
11 PF04218 CENP-B_N: CENP-B N-te 93.6 0.0087 1.9E-07 42.1 -1.9 42 105-147 4-45 (53)
12 smart00351 PAX Paired Box doma 92.6 0.023 5.1E-07 47.5 -1.0 46 104-150 14-59 (125)
13 PF02209 VHP: Villin headpiece 92.4 0.081 1.8E-06 33.9 1.5 25 66-90 2-26 (36)
14 PF13384 HTH_23: Homeodomain-l 92.2 0.0099 2.1E-07 41.0 -3.2 28 122-149 15-42 (50)
15 PF13518 HTH_28: Helix-turn-he 92.2 0.022 4.7E-07 39.4 -1.5 34 116-150 5-38 (52)
16 cd00131 PAX Paired Box domain 91.7 0.036 7.7E-07 46.7 -1.0 46 104-150 14-59 (128)
17 smart00153 VHP Villin headpiec 91.5 0.13 2.9E-06 32.9 1.8 22 66-87 2-23 (36)
18 PF08281 Sigma70_r4_2: Sigma-7 91.2 0.034 7.4E-07 38.9 -1.4 44 107-151 10-53 (54)
19 cd06571 Bac_DnaA_C C-terminal 90.8 0.075 1.6E-06 41.7 0.2 51 104-154 24-75 (90)
20 PF13011 LZ_Tnp_IS481: leucine 90.5 0.051 1.1E-06 42.0 -1.1 53 104-156 5-61 (85)
21 COG3415 Transposase and inacti 88.5 0.056 1.2E-06 45.9 -2.3 44 107-150 4-47 (138)
22 PRK09638 RNA polymerase sigma 88.4 0.35 7.5E-06 42.5 2.5 48 107-155 126-173 (176)
23 PF12116 SpoIIID: Stage III sp 88.2 0.063 1.4E-06 40.6 -1.9 35 119-153 14-48 (82)
24 PF13340 DUF4096: Putative tra 87.6 0.76 1.6E-05 34.6 3.6 46 104-150 21-66 (75)
25 PRK09413 IS2 repressor TnpA; R 87.0 0.12 2.7E-06 42.9 -1.1 47 104-150 9-55 (121)
26 TIGR02950 SigM_subfam RNA poly 86.9 0.45 9.7E-06 40.7 2.3 48 107-155 105-152 (154)
27 PF05225 HTH_psq: helix-turn-h 86.7 0.05 1.1E-06 36.9 -3.0 34 113-146 4-38 (45)
28 smart00421 HTH_LUXR helix_turn 86.4 0.18 3.9E-06 35.0 -0.4 43 108-152 4-46 (58)
29 PRK12519 RNA polymerase sigma 85.8 0.3 6.6E-06 43.7 0.7 50 107-157 141-190 (194)
30 PRK00118 putative DNA-binding 85.6 0.18 3.8E-06 40.7 -0.9 50 106-156 16-65 (104)
31 cd06171 Sigma70_r4 Sigma70, re 85.6 0.18 3.9E-06 34.3 -0.7 43 108-151 11-53 (55)
32 cd00569 HTH_Hin_like Helix-tur 85.2 0.1 2.3E-06 32.3 -2.0 37 108-145 6-42 (42)
33 PRK04217 hypothetical protein; 84.6 0.22 4.9E-06 40.6 -0.7 50 106-156 41-90 (110)
34 PRK06030 hypothetical protein; 84.3 0.3 6.4E-06 40.8 -0.1 47 106-152 51-97 (124)
35 PRK09639 RNA polymerase sigma 84.2 0.25 5.3E-06 42.9 -0.6 48 107-156 112-159 (166)
36 PF00356 LacI: Bacterial regul 84.1 0.24 5.2E-06 33.7 -0.6 20 127-146 2-21 (46)
37 TIGR02392 rpoH_proteo alternat 83.5 0.59 1.3E-05 44.5 1.6 49 107-155 218-267 (270)
38 PF01527 HTH_Tnp_1: Transposas 83.3 0.069 1.5E-06 40.1 -4.0 45 105-149 4-48 (76)
39 PF13542 HTH_Tnp_ISL3: Helix-t 82.9 0.21 4.5E-06 34.6 -1.4 25 124-148 27-51 (52)
40 TIGR02960 SigX5 RNA polymerase 82.7 0.87 1.9E-05 44.3 2.4 72 107-180 142-217 (324)
41 PRK09652 RNA polymerase sigma 82.2 0.34 7.4E-06 42.5 -0.6 49 107-156 128-176 (182)
42 PRK12529 RNA polymerase sigma 82.1 0.33 7.2E-06 42.9 -0.7 48 107-155 127-174 (178)
43 TIGR02531 yecD_yerC TrpR-relat 82.1 0.24 5.3E-06 38.7 -1.4 31 115-145 41-71 (88)
44 TIGR02939 RpoE_Sigma70 RNA pol 81.6 0.65 1.4E-05 41.2 1.0 50 107-157 138-187 (190)
45 PRK08301 sporulation sigma fac 81.0 0.42 9E-06 44.3 -0.5 51 107-157 178-231 (234)
46 PRK05911 RNA polymerase sigma 81.0 0.58 1.3E-05 44.2 0.5 50 107-157 205-254 (257)
47 PF04967 HTH_10: HTH DNA bindi 80.8 0.83 1.8E-05 32.1 1.1 29 124-152 23-51 (53)
48 PRK06704 RNA polymerase factor 80.8 1 2.2E-05 41.9 2.0 71 107-178 116-186 (228)
49 TIGR02985 Sig70_bacteroi1 RNA 80.5 0.41 8.9E-06 41.0 -0.7 46 108-154 114-159 (161)
50 TIGR02937 sigma70-ECF RNA poly 80.5 0.6 1.3E-05 39.1 0.4 47 107-154 110-156 (158)
51 TIGR02947 SigH_actino RNA poly 80.4 0.98 2.1E-05 40.4 1.7 49 107-156 131-179 (193)
52 PHA00675 hypothetical protein 80.1 0.52 1.1E-05 35.4 -0.1 25 122-146 37-61 (78)
53 cd06170 LuxR_C_like C-terminal 79.7 0.43 9.3E-06 33.1 -0.7 33 121-153 12-44 (57)
54 PRK12513 RNA polymerase sigma 79.6 2.1 4.6E-05 38.2 3.7 49 107-156 139-187 (194)
55 PRK12533 RNA polymerase sigma 79.0 0.71 1.5E-05 42.4 0.4 49 107-156 134-182 (216)
56 PRK11922 RNA polymerase sigma 78.9 1.8 3.9E-05 40.0 3.1 49 108-157 150-198 (231)
57 TIGR02952 Sig70_famx2 RNA poly 78.7 0.52 1.1E-05 41.0 -0.6 47 107-154 122-168 (170)
58 COG2739 Uncharacterized protei 78.7 0.87 1.9E-05 36.1 0.7 39 115-154 25-63 (105)
59 PRK09641 RNA polymerase sigma 78.6 0.66 1.4E-05 41.0 0.1 49 107-156 136-184 (187)
60 TIGR03879 near_KaiC_dom probab 78.4 0.21 4.6E-06 37.5 -2.7 40 108-147 16-55 (73)
61 PRK06596 RNA polymerase factor 78.1 0.96 2.1E-05 43.4 1.0 49 107-155 230-279 (284)
62 PRK09415 RNA polymerase factor 78.1 0.78 1.7E-05 40.6 0.3 49 107-156 127-175 (179)
63 TIGR00721 tfx DNA-binding prot 77.8 1.1 2.4E-05 38.0 1.2 47 106-154 5-51 (137)
64 PRK12530 RNA polymerase sigma 77.1 0.55 1.2E-05 42.0 -1.0 49 107-156 134-182 (189)
65 PRK07037 extracytoplasmic-func 77.0 0.59 1.3E-05 40.4 -0.8 49 107-156 109-157 (163)
66 PRK05803 sporulation sigma fac 77.0 0.68 1.5E-05 43.0 -0.4 49 107-155 175-226 (233)
67 PRK12514 RNA polymerase sigma 76.7 0.69 1.5E-05 40.7 -0.4 48 107-155 129-176 (179)
68 PRK11923 algU RNA polymerase s 76.6 0.73 1.6E-05 41.2 -0.3 52 107-159 138-189 (193)
69 PRK11924 RNA polymerase sigma 76.5 0.83 1.8E-05 39.8 0.0 48 108-156 126-173 (179)
70 PRK15320 transcriptional activ 76.4 0.81 1.8E-05 41.0 -0.0 38 116-153 171-208 (251)
71 PRK12518 RNA polymerase sigma 76.4 1.7 3.7E-05 38.0 2.0 49 107-156 120-168 (175)
72 TIGR01321 TrpR trp operon repr 75.7 1.1 2.3E-05 35.5 0.4 24 122-145 53-76 (94)
73 TIGR02999 Sig-70_X6 RNA polyme 75.7 0.71 1.5E-05 40.8 -0.6 47 108-155 135-181 (183)
74 PRK12511 RNA polymerase sigma 75.5 0.81 1.8E-05 40.7 -0.3 49 107-156 111-159 (182)
75 PRK12547 RNA polymerase sigma 75.4 0.72 1.6E-05 40.1 -0.6 49 107-156 112-160 (164)
76 PRK12516 RNA polymerase sigma 75.1 0.77 1.7E-05 41.0 -0.5 50 107-157 116-165 (187)
77 TIGR02948 SigW_bacill RNA poly 74.9 1.1 2.5E-05 39.5 0.5 49 107-156 136-184 (187)
78 TIGR02983 SigE-fam_strep RNA p 74.9 0.99 2.1E-05 39.0 0.1 48 108-156 111-158 (162)
79 TIGR02989 Sig-70_gvs1 RNA poly 74.9 0.75 1.6E-05 39.5 -0.7 47 107-154 111-157 (159)
80 PF00325 Crp: Bacterial regula 74.8 1.2 2.6E-05 27.7 0.4 25 125-149 3-27 (32)
81 PRK05602 RNA polymerase sigma 74.7 0.97 2.1E-05 40.1 0.0 50 107-157 128-177 (186)
82 COG1595 RpoE DNA-directed RNA 74.7 1.2 2.6E-05 39.5 0.6 49 108-157 128-176 (182)
83 PRK12532 RNA polymerase sigma 74.5 0.99 2.1E-05 40.4 0.0 49 107-156 136-184 (195)
84 PF12802 MarR_2: MarR family; 73.7 3.4 7.3E-05 29.3 2.7 25 125-149 22-46 (62)
85 PRK09640 RNA polymerase sigma 73.5 1.9 4E-05 38.4 1.5 48 108-156 135-182 (188)
86 PF08299 Bac_DnaA_C: Bacterial 73.5 0.17 3.7E-06 37.7 -4.4 42 107-148 28-70 (70)
87 PRK09047 RNA polymerase factor 73.3 0.73 1.6E-05 39.7 -1.2 50 107-157 106-155 (161)
88 PRK03975 tfx putative transcri 73.0 1.3 2.9E-05 37.7 0.4 46 106-153 5-50 (141)
89 TIGR02393 RpoD_Cterm RNA polym 73.0 1.5 3.2E-05 40.9 0.7 48 107-154 176-226 (238)
90 PRK12537 RNA polymerase sigma 73.0 0.99 2.1E-05 40.0 -0.4 48 107-155 133-180 (182)
91 PRK12524 RNA polymerase sigma 72.7 0.86 1.9E-05 40.9 -0.8 48 107-155 136-183 (196)
92 PRK07408 RNA polymerase sigma 72.7 0.93 2E-05 42.8 -0.6 49 107-156 203-251 (256)
93 PRK12538 RNA polymerase sigma 72.4 2.1 4.6E-05 39.8 1.7 48 108-156 172-219 (233)
94 PRK12546 RNA polymerase sigma 72.3 1.4 3E-05 39.5 0.4 50 107-157 113-162 (188)
95 PRK12535 RNA polymerase sigma 72.1 1.4 3E-05 39.7 0.4 53 107-160 133-185 (196)
96 PRK12540 RNA polymerase sigma 72.0 1.1 2.4E-05 39.9 -0.3 50 107-157 111-160 (182)
97 PRK12534 RNA polymerase sigma 72.0 1.1 2.4E-05 39.8 -0.3 47 108-155 138-184 (187)
98 PRK13919 putative RNA polymera 72.0 1 2.2E-05 39.9 -0.5 48 108-156 136-183 (186)
99 PRK07500 rpoH2 RNA polymerase 71.9 1.1 2.5E-05 43.0 -0.3 50 107-156 227-277 (289)
100 PF00196 GerE: Bacterial regul 71.9 0.68 1.5E-05 32.8 -1.4 37 117-153 11-47 (58)
101 PRK12515 RNA polymerase sigma 71.8 0.85 1.8E-05 40.6 -1.1 49 107-156 131-179 (189)
102 TIGR03001 Sig-70_gmx1 RNA poly 71.7 1.5 3.3E-05 41.0 0.6 49 107-156 161-209 (244)
103 PRK12522 RNA polymerase sigma 71.5 1.1 2.4E-05 39.2 -0.4 52 108-160 120-171 (173)
104 PRK15418 transcriptional regul 71.3 3.9 8.5E-05 39.9 3.3 64 119-187 24-88 (318)
105 PF13412 HTH_24: Winged helix- 71.3 1.8 3.9E-05 29.2 0.7 27 124-150 17-43 (48)
106 TIGR02846 spore_sigmaK RNA pol 71.3 1.2 2.5E-05 41.2 -0.3 49 107-155 174-225 (227)
107 PHA00542 putative Cro-like pro 71.0 1.7 3.8E-05 33.3 0.6 50 118-179 25-74 (82)
108 PRK05572 sporulation sigma fac 70.8 1.2 2.6E-05 41.9 -0.4 48 107-155 202-249 (252)
109 TIGR02394 rpoS_proteo RNA poly 70.6 2 4.3E-05 41.2 1.1 51 107-157 222-275 (285)
110 PF13551 HTH_29: Winged helix- 70.5 0.85 1.8E-05 36.6 -1.3 33 118-150 5-38 (112)
111 PRK12512 RNA polymerase sigma 70.5 1.1 2.4E-05 39.6 -0.7 49 107-156 131-179 (184)
112 PRK09637 RNA polymerase sigma 70.5 1.3 2.7E-05 39.4 -0.3 49 107-156 106-154 (181)
113 PRK12520 RNA polymerase sigma 70.2 1.8 3.8E-05 38.6 0.6 49 107-156 131-179 (191)
114 PRK12528 RNA polymerase sigma 70.1 1 2.2E-05 38.9 -0.9 46 107-153 113-158 (161)
115 PF13751 DDE_Tnp_1_6: Transpos 70.1 1.9 4.1E-05 35.7 0.7 49 307-357 73-122 (125)
116 PRK12531 RNA polymerase sigma 69.9 1.1 2.3E-05 40.2 -0.9 49 107-156 141-189 (194)
117 PRK09642 RNA polymerase sigma 69.8 1.1 2.4E-05 38.6 -0.8 49 107-156 106-154 (160)
118 PRK12539 RNA polymerase sigma 69.8 1.5 3.2E-05 38.9 -0.0 49 107-156 131-179 (184)
119 TIGR02954 Sig70_famx3 RNA poly 69.7 1.5 3.3E-05 38.1 0.0 49 107-156 119-167 (169)
120 PRK12525 RNA polymerase sigma 69.6 1.2 2.5E-05 39.0 -0.7 48 107-155 118-165 (168)
121 PRK12544 RNA polymerase sigma 69.6 1.8 3.9E-05 39.4 0.5 49 107-156 148-196 (206)
122 PRK09643 RNA polymerase sigma 69.3 1.2 2.7E-05 39.8 -0.6 48 108-156 135-182 (192)
123 PRK12541 RNA polymerase sigma 69.3 1.6 3.5E-05 37.6 0.1 47 107-154 112-158 (161)
124 TIGR02984 Sig-70_plancto1 RNA 68.9 1.3 2.7E-05 39.2 -0.6 48 107-155 140-187 (189)
125 PRK09649 RNA polymerase sigma 68.6 1.5 3.3E-05 38.9 -0.1 47 107-154 130-176 (185)
126 TIGR02980 SigBFG RNA polymeras 68.5 1.3 2.8E-05 40.8 -0.7 47 107-154 178-224 (227)
127 TIGR02835 spore_sigmaE RNA pol 68.5 1.4 3.1E-05 40.8 -0.4 50 107-156 178-230 (234)
128 PRK06986 fliA flagellar biosyn 68.4 1.6 3.5E-05 40.5 -0.0 48 108-156 185-232 (236)
129 PRK09651 RNA polymerase sigma 68.1 2.1 4.6E-05 37.5 0.7 48 107-155 119-166 (172)
130 PRK08583 RNA polymerase sigma 68.0 1.4 3E-05 41.5 -0.6 48 107-155 205-252 (257)
131 TIGR02885 spore_sigF RNA polym 67.9 1.4 2.9E-05 40.8 -0.7 47 107-154 183-229 (231)
132 PRK08241 RNA polymerase factor 67.5 4.4 9.6E-05 39.7 2.8 73 107-181 153-228 (339)
133 PRK09645 RNA polymerase sigma 67.3 1.4 3.1E-05 38.4 -0.6 49 107-156 118-166 (173)
134 PF09339 HTH_IclR: IclR helix- 67.1 2.3 4.9E-05 29.4 0.5 26 124-149 18-43 (52)
135 PRK08215 sporulation sigma fac 67.1 1.5 3.3E-05 41.3 -0.5 48 107-155 209-256 (258)
136 TIGR01636 phage_rinA phage tra 66.9 3.3 7E-05 35.0 1.5 48 108-155 83-131 (134)
137 TIGR02957 SigX4 RNA polymerase 66.8 3.7 8.1E-05 39.2 2.1 69 107-179 108-176 (281)
138 TIGR03697 NtcA_cyano global ni 66.7 0.85 1.8E-05 40.5 -2.3 99 66-166 73-186 (193)
139 PRK12536 RNA polymerase sigma 66.6 1.5 3.2E-05 38.8 -0.7 47 108-155 130-176 (181)
140 PF04297 UPF0122: Putative hel 66.4 3.1 6.8E-05 33.3 1.2 46 108-154 18-63 (101)
141 PRK12545 RNA polymerase sigma 66.0 1.6 3.5E-05 39.4 -0.5 49 107-156 139-187 (201)
142 TIGR02997 Sig70-cyanoRpoD RNA 66.0 1.5 3.2E-05 42.4 -0.8 45 107-151 249-296 (298)
143 PRK06759 RNA polymerase factor 65.9 1.3 2.9E-05 37.7 -1.1 46 107-153 106-151 (154)
144 PRK12523 RNA polymerase sigma 65.9 1.5 3.3E-05 38.4 -0.8 47 107-154 119-165 (172)
145 PRK14086 dnaA chromosomal repl 65.7 2.1 4.6E-05 45.3 0.2 51 104-154 549-599 (617)
146 PRK11753 DNA-binding transcrip 65.4 1.4 3.1E-05 39.7 -1.1 82 66-149 99-193 (211)
147 TIGR02844 spore_III_D sporulat 65.1 1.9 4E-05 33.1 -0.3 22 125-146 20-41 (80)
148 smart00419 HTH_CRP helix_turn_ 64.8 2.9 6.4E-05 27.7 0.7 27 124-150 8-34 (48)
149 PRK09644 RNA polymerase sigma 64.7 1.8 3.9E-05 37.6 -0.5 49 107-156 108-156 (165)
150 PRK12542 RNA polymerase sigma 64.5 1.9 4.2E-05 38.2 -0.4 50 107-157 122-171 (185)
151 PRK10402 DNA-binding transcrip 64.3 2.2 4.8E-05 39.2 0.0 67 107-174 148-219 (226)
152 PF13730 HTH_36: Helix-turn-he 64.3 2.9 6.3E-05 29.0 0.6 25 125-149 26-50 (55)
153 PRK01381 Trp operon repressor; 64.2 3.5 7.6E-05 32.8 1.1 23 123-145 54-76 (99)
154 PRK07122 RNA polymerase sigma 64.1 2.2 4.8E-05 40.4 -0.0 47 107-154 215-261 (264)
155 PRK12543 RNA polymerase sigma 64.0 1.7 3.6E-05 38.4 -0.9 49 107-156 117-165 (179)
156 smart00345 HTH_GNTR helix_turn 64.0 3 6.6E-05 29.0 0.7 24 126-149 22-45 (60)
157 TIGR02850 spore_sigG RNA polym 63.9 2 4.3E-05 40.4 -0.4 47 107-154 206-252 (254)
158 COG1191 FliA DNA-directed RNA 63.6 1.7 3.7E-05 40.8 -0.9 49 107-156 196-244 (247)
159 PRK07405 RNA polymerase sigma 63.6 2.1 4.5E-05 41.8 -0.3 48 107-154 256-306 (317)
160 TIGR02941 Sigma_B RNA polymera 63.4 2 4.3E-05 40.4 -0.5 48 107-155 205-252 (255)
161 PRK06930 positive control sigm 63.4 1.6 3.4E-05 38.6 -1.1 49 107-156 114-162 (170)
162 TIGR02943 Sig70_famx1 RNA poly 63.1 1.9 4E-05 38.5 -0.7 49 108-157 132-180 (188)
163 PF00872 Transposase_mut: Tran 63.1 7 0.00015 39.2 3.3 86 121-235 111-205 (381)
164 PF01710 HTH_Tnp_IS630: Transp 62.9 1.1 2.4E-05 37.0 -2.1 28 120-147 14-41 (119)
165 PRK00149 dnaA chromosomal repl 62.8 2.7 5.8E-05 43.1 0.3 74 81-154 358-433 (450)
166 PF01371 Trp_repressor: Trp re 62.7 2.7 5.8E-05 32.8 0.2 26 120-145 45-70 (87)
167 PRK06811 RNA polymerase factor 62.6 1.9 4.1E-05 38.4 -0.7 47 107-154 131-177 (189)
168 PRK09636 RNA polymerase sigma 62.1 3.7 8E-05 39.4 1.1 69 107-179 115-183 (293)
169 PRK07670 RNA polymerase sigma 61.9 2.2 4.9E-05 40.0 -0.4 48 107-155 201-248 (251)
170 PF02001 DUF134: Protein of un 61.9 4.9 0.00011 32.5 1.6 30 124-153 57-86 (106)
171 PRK12526 RNA polymerase sigma 61.6 2.1 4.5E-05 38.8 -0.7 47 108-155 154-200 (206)
172 PF05269 Phage_CII: Bacterioph 61.1 11 0.00024 29.6 3.3 29 126-154 25-53 (91)
173 PRK08295 RNA polymerase factor 60.6 2.4 5.1E-05 38.2 -0.5 47 108-156 156-202 (208)
174 PF01381 HTH_3: Helix-turn-hel 60.5 2.4 5.2E-05 29.3 -0.4 42 122-176 7-48 (55)
175 PRK12527 RNA polymerase sigma 60.4 2.1 4.5E-05 36.9 -0.9 48 108-156 106-153 (159)
176 PF10654 DUF2481: Protein of u 60.4 2.8 6E-05 34.0 -0.1 30 124-153 80-109 (126)
177 TIGR02479 FliA_WhiG RNA polyme 60.0 2.5 5.4E-05 38.8 -0.5 48 107-155 175-222 (224)
178 TIGR02959 SigZ RNA polymerase 60.0 2.2 4.8E-05 37.3 -0.8 49 107-156 100-148 (170)
179 PF07374 DUF1492: Protein of u 59.9 1.6 3.5E-05 34.9 -1.5 43 109-152 57-99 (100)
180 cd00092 HTH_CRP helix_turn_hel 59.6 4.4 9.6E-05 29.1 0.9 27 124-150 25-51 (67)
181 PRK14088 dnaA chromosomal repl 59.6 2.7 5.9E-05 43.0 -0.3 50 103-152 366-415 (440)
182 PRK09646 RNA polymerase sigma 59.2 2.5 5.4E-05 37.8 -0.6 49 107-156 142-190 (194)
183 PRK09210 RNA polymerase sigma 58.9 4.6 0.0001 40.3 1.2 46 108-153 306-354 (367)
184 PF01022 HTH_5: Bacterial regu 58.7 0.98 2.1E-05 30.6 -2.6 26 124-149 15-40 (47)
185 COG2963 Transposase and inacti 58.3 2.1 4.6E-05 34.9 -1.1 47 105-151 5-52 (116)
186 PRK15201 fimbriae regulatory p 58.2 2.6 5.6E-05 37.3 -0.7 45 107-153 133-177 (198)
187 PRK09647 RNA polymerase sigma 58.0 3.8 8.3E-05 37.1 0.4 48 108-156 139-186 (203)
188 PF12964 DUF3853: Protein of u 57.6 3.8 8.3E-05 32.3 0.3 34 127-160 48-83 (96)
189 PRK09635 sigI RNA polymerase s 57.4 7.6 0.00017 37.4 2.4 69 107-179 118-186 (290)
190 PF00165 HTH_AraC: Bacterial r 57.0 3.9 8.5E-05 26.7 0.2 28 121-148 5-32 (42)
191 PF01047 MarR: MarR family; I 56.9 1.2 2.5E-05 31.5 -2.6 26 124-149 17-42 (59)
192 PRK09648 RNA polymerase sigma 56.4 2.9 6.2E-05 37.1 -0.7 48 107-155 139-186 (189)
193 PF01325 Fe_dep_repress: Iron 55.9 5.6 0.00012 28.5 0.9 26 124-149 22-47 (60)
194 PRK14087 dnaA chromosomal repl 55.7 4 8.6E-05 41.9 0.1 74 81-154 357-432 (450)
195 PRK15411 rcsA colanic acid cap 55.4 3.2 7E-05 37.7 -0.5 44 108-153 138-181 (207)
196 smart00342 HTH_ARAC helix_turn 55.2 5.1 0.00011 29.6 0.6 70 69-149 5-76 (84)
197 PRK07406 RNA polymerase sigma 55.0 3.3 7.2E-05 41.4 -0.6 48 107-154 311-361 (373)
198 PRK07598 RNA polymerase sigma 54.5 6 0.00013 40.1 1.1 46 108-153 351-399 (415)
199 PF13560 HTH_31: Helix-turn-he 54.4 3.1 6.8E-05 29.9 -0.7 24 122-145 12-35 (64)
200 PF01710 HTH_Tnp_IS630: Transp 54.0 4.3 9.3E-05 33.5 0.0 73 69-147 22-94 (119)
201 PRK05901 RNA polymerase sigma 53.8 6.2 0.00013 41.0 1.2 48 107-154 447-497 (509)
202 COG2522 Predicted transcriptio 53.6 4.2 9.1E-05 33.6 -0.1 23 124-146 22-44 (119)
203 PF07638 Sigma70_ECF: ECF sigm 53.6 3.4 7.4E-05 36.8 -0.7 46 108-154 136-181 (185)
204 smart00420 HTH_DEOR helix_turn 53.4 6.6 0.00014 26.4 0.9 27 124-150 14-40 (53)
205 COG2390 DeoR Transcriptional r 53.2 12 0.00025 36.6 2.9 65 119-187 21-85 (321)
206 PRK11512 DNA-binding transcrip 53.0 18 0.00039 30.6 3.8 28 123-150 53-80 (144)
207 PHA02591 hypothetical protein; 52.7 4.7 0.0001 30.4 0.1 26 122-147 57-82 (83)
208 PRK13870 transcriptional regul 52.6 3.5 7.7E-05 38.3 -0.8 45 107-153 173-217 (234)
209 PRK13413 mpi multiple promoter 52.5 4.4 9.5E-05 36.6 -0.2 28 119-146 167-194 (200)
210 PRK12517 RNA polymerase sigma 52.3 3.5 7.7E-05 36.7 -0.8 48 108-156 129-176 (188)
211 PRK09492 treR trehalose repres 52.2 5.2 0.00011 38.3 0.3 23 125-147 5-27 (315)
212 smart00354 HTH_LACI helix_turn 51.4 4.1 8.9E-05 30.1 -0.4 20 126-145 2-21 (70)
213 PRK12422 chromosomal replicati 51.0 5.3 0.00012 40.9 0.2 73 81-153 353-426 (445)
214 cd01392 HTH_LacI Helix-turn-he 50.8 4.3 9.3E-05 27.7 -0.4 18 129-146 2-19 (52)
215 TIGR02859 spore_sigH RNA polym 50.5 3.7 8.1E-05 36.5 -1.0 37 117-154 159-195 (198)
216 PHA00738 putative HTH transcri 50.4 3.2 7E-05 33.5 -1.2 27 125-151 27-53 (108)
217 PF13545 HTH_Crp_2: Crp-like h 50.4 6.8 0.00015 29.0 0.6 27 124-150 28-54 (76)
218 PRK05657 RNA polymerase sigma 50.2 4.8 0.0001 39.4 -0.3 50 107-156 262-314 (325)
219 TIGR03209 P21_Cbot clostridium 50.1 2.2 4.7E-05 36.0 -2.4 36 107-143 107-142 (142)
220 PF08279 HTH_11: HTH domain; 50.0 7.9 0.00017 26.7 0.9 27 125-151 16-42 (55)
221 PF04552 Sigma54_DBD: Sigma-54 49.6 5.5 0.00012 34.8 0.0 23 124-146 49-71 (160)
222 PRK12427 flagellar biosynthesi 49.5 4.5 9.6E-05 37.5 -0.6 46 107-153 183-228 (231)
223 TIGR02405 trehalos_R_Ecol treh 49.4 4.8 0.00011 38.6 -0.4 21 126-146 3-23 (311)
224 PRK09391 fixK transcriptional 49.3 4 8.6E-05 37.6 -1.0 83 66-150 113-205 (230)
225 TIGR01889 Staph_reg_Sar staphy 49.3 25 0.00053 28.3 3.8 27 124-150 43-69 (109)
226 PRK05949 RNA polymerase sigma 49.1 5.4 0.00012 39.1 -0.2 48 107-154 266-316 (327)
227 cd04762 HTH_MerR-trunc Helix-T 49.0 5.3 0.00011 26.3 -0.2 22 126-147 2-23 (49)
228 smart00418 HTH_ARSR helix_turn 48.5 5.1 0.00011 27.9 -0.3 28 123-150 9-36 (66)
229 TIGR02337 HpaR homoprotocatech 48.5 10 0.00022 30.9 1.5 27 124-150 42-68 (118)
230 PF05344 DUF746: Domain of Unk 48.4 4.8 0.0001 29.4 -0.5 40 116-155 5-44 (65)
231 PRK09191 two-component respons 48.4 7.1 0.00015 36.2 0.5 50 108-158 89-138 (261)
232 PF12840 HTH_20: Helix-turn-he 47.9 7.3 0.00016 27.7 0.4 29 122-150 22-50 (61)
233 COG0593 DnaA ATPase involved i 47.2 6.2 0.00013 39.8 -0.1 52 103-154 344-395 (408)
234 PRK06288 RNA polymerase sigma 47.0 4.8 0.0001 38.1 -0.9 48 107-155 212-259 (268)
235 COG4565 CitB Response regulato 46.8 19 0.0004 33.0 2.9 45 75-148 153-197 (224)
236 PF00292 PAX: 'Paired box' dom 46.8 3.7 8.1E-05 34.2 -1.4 46 104-151 14-60 (125)
237 cd07377 WHTH_GntR Winged helix 46.5 8.8 0.00019 27.1 0.7 25 126-150 27-51 (66)
238 PRK13719 conjugal transfer tra 46.1 5.4 0.00012 36.5 -0.6 44 108-153 144-187 (217)
239 smart00550 Zalpha Z-DNA-bindin 45.8 3.7 8.1E-05 30.2 -1.4 24 124-147 22-45 (68)
240 PF13744 HTH_37: Helix-turn-he 45.6 5.8 0.00013 30.2 -0.4 23 123-145 30-52 (80)
241 PRK09392 ftrB transcriptional 44.9 5.9 0.00013 36.4 -0.6 60 107-166 146-215 (236)
242 PF08220 HTH_DeoR: DeoR-like h 44.8 9.7 0.00021 26.9 0.7 23 125-147 15-37 (57)
243 TIGR03070 couple_hipB transcri 44.8 7 0.00015 26.9 -0.1 23 123-145 14-36 (58)
244 PRK14987 gluconate operon tran 44.7 6.6 0.00014 37.9 -0.3 22 125-146 6-27 (331)
245 PF13463 HTH_27: Winged helix 44.5 4.2 9.2E-05 29.3 -1.3 27 124-150 18-44 (68)
246 PRK03573 transcriptional regul 44.5 5.7 0.00012 33.6 -0.7 27 124-150 46-72 (144)
247 PF13404 HTH_AsnC-type: AsnC-t 44.3 8.3 0.00018 25.5 0.2 24 124-147 17-40 (42)
248 PF00126 HTH_1: Bacterial regu 44.3 13 0.00028 26.4 1.3 30 125-154 14-43 (60)
249 smart00352 POU Found in Pit-Oc 44.2 5.7 0.00012 29.9 -0.6 25 122-146 22-52 (75)
250 PRK09526 lacI lac repressor; R 44.0 6.7 0.00014 38.0 -0.4 22 125-146 6-27 (342)
251 PRK10014 DNA-binding transcrip 43.7 6.6 0.00014 38.0 -0.5 23 125-147 7-29 (342)
252 COG3355 Predicted transcriptio 43.7 30 0.00065 28.9 3.5 72 70-171 18-98 (126)
253 TIGR02431 pcaR_pcaU beta-ketoa 43.3 40 0.00086 31.4 4.8 28 124-151 24-51 (248)
254 PF13309 HTH_22: HTH domain 43.2 5.3 0.00011 29.1 -0.9 21 125-145 43-63 (64)
255 PF12728 HTH_17: Helix-turn-he 43.0 7.5 0.00016 26.4 -0.1 21 126-146 3-23 (51)
256 PF06056 Terminase_5: Putative 42.9 10 0.00023 27.0 0.6 25 123-147 12-36 (58)
257 COG1508 RpoN DNA-directed RNA 42.8 7.1 0.00015 39.7 -0.4 31 125-165 331-361 (444)
258 PRK10339 DNA-binding transcrip 42.7 7.9 0.00017 37.4 -0.1 22 126-147 3-24 (327)
259 TIGR01764 excise DNA binding d 42.6 8.4 0.00018 25.4 0.0 21 126-146 3-23 (49)
260 TIGR01610 phage_O_Nterm phage 42.5 12 0.00026 29.5 0.9 54 73-149 19-72 (95)
261 PRK10840 transcriptional regul 42.3 6.4 0.00014 35.5 -0.8 45 107-153 150-194 (216)
262 PRK07921 RNA polymerase sigma 42.3 6.5 0.00014 38.5 -0.8 48 107-154 262-312 (324)
263 COG3413 Predicted DNA binding 42.0 15 0.00032 33.6 1.6 30 125-154 179-208 (215)
264 PRK11303 DNA-binding transcrip 41.9 8 0.00017 37.2 -0.2 22 126-147 2-23 (328)
265 PF13551 HTH_29: Winged helix- 41.5 18 0.00039 28.7 1.9 80 67-147 14-110 (112)
266 PRK11161 fumarate/nitrate redu 41.2 5.4 0.00012 36.6 -1.5 43 107-149 153-209 (235)
267 PF00392 GntR: Bacterial regul 41.1 11 0.00023 27.1 0.4 22 126-147 26-47 (64)
268 smart00346 HTH_ICLR helix_turn 41.1 13 0.00028 28.4 1.0 27 124-150 20-46 (91)
269 COG2197 CitB Response regulato 41.0 8.4 0.00018 35.1 -0.2 43 108-152 149-191 (211)
270 PRK10401 DNA-binding transcrip 40.9 7.9 0.00017 37.7 -0.4 21 126-146 3-23 (346)
271 PRK10163 DNA-binding transcrip 40.8 49 0.0011 31.3 5.0 27 124-150 40-66 (271)
272 PRK10703 DNA-binding transcrip 39.8 8.8 0.00019 37.2 -0.3 22 126-147 3-24 (341)
273 PHA01976 helix-turn-helix prot 39.8 9.4 0.0002 27.5 -0.1 24 122-145 13-36 (67)
274 cd00090 HTH_ARSR Arsenical Res 39.1 6 0.00013 28.5 -1.2 25 124-148 20-44 (78)
275 PRK10423 transcriptional repre 38.8 9 0.00019 36.8 -0.4 19 128-146 2-20 (327)
276 PRK10188 DNA-binding transcrip 38.7 8.1 0.00018 36.1 -0.7 45 107-153 179-223 (240)
277 TIGR03541 reg_near_HchA LuxR f 38.5 8.3 0.00018 35.7 -0.7 46 106-153 170-215 (232)
278 COG2771 CsgD DNA-binding HTH d 38.5 9.5 0.0002 27.0 -0.2 35 118-152 13-47 (65)
279 TIGR00122 birA_repr_reg BirA b 37.7 13 0.00028 27.2 0.4 24 125-148 14-37 (69)
280 PF13610 DDE_Tnp_IS240: DDE do 37.5 48 0.001 27.9 4.0 132 188-359 5-138 (140)
281 PRK11475 DNA-binding transcrip 37.5 9.5 0.00021 34.7 -0.4 43 108-152 135-177 (207)
282 PRK09483 response regulator; P 37.0 9.8 0.00021 33.8 -0.4 44 107-152 148-191 (217)
283 PRK10870 transcriptional repre 37.0 46 0.00099 29.4 3.9 26 124-149 71-96 (176)
284 COG5421 Transposase [DNA repli 36.5 47 0.001 34.1 4.2 56 215-285 155-210 (480)
285 PRK10100 DNA-binding transcrip 36.5 11 0.00023 34.6 -0.2 44 108-153 156-199 (216)
286 smart00529 HTH_DTXR Helix-turn 36.5 17 0.00038 28.1 1.0 24 127-150 2-25 (96)
287 TIGR02417 fruct_sucro_rep D-fr 36.2 11 0.00023 36.3 -0.3 21 127-147 2-22 (327)
288 TIGR02395 rpoN_sigma RNA polym 36.0 14 0.00031 37.6 0.5 32 124-165 318-349 (429)
289 TIGR01481 ccpA catabolite cont 35.4 11 0.00024 36.2 -0.3 21 126-146 3-23 (329)
290 smart00760 Bac_DnaA_C Bacteria 35.3 4.9 0.00011 28.7 -2.1 32 104-135 25-56 (60)
291 PF00440 TetR_N: Bacterial reg 35.2 12 0.00027 25.0 -0.0 23 124-146 16-38 (47)
292 PRK10727 DNA-binding transcrip 35.2 11 0.00025 36.5 -0.3 21 126-146 3-23 (343)
293 PF13443 HTH_26: Cro/C1-type H 33.9 10 0.00022 26.9 -0.6 24 123-146 9-32 (63)
294 PRK10072 putative transcriptio 33.9 14 0.0003 29.3 0.1 25 122-146 44-68 (96)
295 PF10668 Phage_terminase: Phag 32.3 16 0.00034 26.3 0.1 25 120-144 16-42 (60)
296 PRK05658 RNA polymerase sigma 32.2 22 0.00047 38.2 1.2 47 107-153 556-605 (619)
297 COG1609 PurR Transcriptional r 32.1 14 0.00031 36.1 -0.2 21 126-146 2-22 (333)
298 PF02954 HTH_8: Bacterial regu 31.2 18 0.0004 23.7 0.3 25 123-147 17-41 (42)
299 PRK12469 RNA polymerase factor 31.1 19 0.00041 37.2 0.5 33 124-166 369-401 (481)
300 PF05043 Mga: Mga helix-turn-h 30.9 22 0.00049 27.1 0.8 33 122-154 28-60 (87)
301 PRK05932 RNA polymerase factor 30.3 20 0.00043 36.9 0.5 32 124-165 343-374 (455)
302 PF07453 NUMOD1: NUMOD1 domain 30.2 16 0.00034 23.1 -0.1 24 122-145 14-37 (37)
303 COG1725 Predicted transcriptio 30.2 43 0.00094 27.9 2.4 58 73-150 4-61 (125)
304 PF09862 DUF2089: Protein of u 30.1 9.2 0.0002 31.3 -1.6 38 116-153 41-78 (113)
305 COG3293 Transposase and inacti 29.8 31 0.00067 28.3 1.5 57 277-334 39-101 (124)
306 PRK10219 DNA-binding transcrip 29.8 52 0.0011 26.1 2.8 25 125-149 22-46 (107)
307 TIGR00637 ModE_repress ModE mo 29.5 27 0.00059 27.8 1.0 33 123-155 15-47 (99)
308 TIGR03020 EpsA transcriptional 29.0 16 0.00034 34.3 -0.4 46 106-153 189-234 (247)
309 TIGR02607 antidote_HigA addict 28.4 18 0.0004 26.8 -0.1 24 122-145 16-39 (78)
310 PRK10360 DNA-binding transcrip 28.2 18 0.00038 31.5 -0.3 36 117-152 145-180 (196)
311 COG1342 Predicted DNA-binding 28.0 34 0.00074 27.0 1.3 26 123-148 48-73 (99)
312 PRK13777 transcriptional regul 27.9 88 0.0019 28.0 4.1 25 123-147 58-82 (185)
313 PRK12682 transcriptional regul 27.8 12 0.00027 35.8 -1.5 35 121-155 13-47 (309)
314 PF11044 TMEMspv1-c74-12: Plec 27.7 24 0.00052 23.6 0.3 8 5-12 33-40 (49)
315 PRK00215 LexA repressor; Valid 27.6 33 0.00071 30.9 1.4 26 125-150 24-50 (205)
316 smart00344 HTH_ASNC helix_turn 27.6 30 0.00064 27.5 1.0 27 124-150 17-43 (108)
317 PF04703 FaeA: FaeA-like prote 27.3 7.1 0.00015 28.3 -2.4 26 122-147 13-38 (62)
318 smart00347 HTH_MARR helix_turn 27.2 17 0.00037 28.0 -0.5 28 124-151 24-51 (101)
319 PF08765 Mor: Mor transcriptio 27.1 23 0.00049 28.6 0.2 29 124-152 72-100 (108)
320 PRK13918 CRP/FNR family transc 27.0 22 0.00047 31.6 0.1 64 108-172 119-197 (202)
321 PF13693 HTH_35: Winged helix- 26.9 11 0.00025 28.6 -1.4 24 123-146 14-37 (78)
322 PF01726 LexA_DNA_bind: LexA D 26.9 30 0.00065 25.2 0.8 23 124-146 25-48 (65)
323 cd00131 PAX Paired Box domain 26.9 38 0.00082 28.3 1.5 80 66-146 34-125 (128)
324 COG4941 Predicted RNA polymera 26.7 51 0.0011 32.4 2.5 60 105-166 118-177 (415)
325 PF05930 Phage_AlpA: Prophage 26.7 21 0.00045 24.5 -0.1 21 126-146 5-25 (51)
326 PF01978 TrmB: Sugar-specific 26.5 27 0.00058 25.3 0.5 25 125-149 23-47 (68)
327 PRK10651 transcriptional regul 26.1 19 0.00041 31.5 -0.4 43 108-152 156-198 (216)
328 PF01418 HTH_6: Helix-turn-hel 25.8 25 0.00054 26.4 0.2 23 124-146 34-56 (77)
329 PRK08558 adenine phosphoribosy 25.3 30 0.00065 32.3 0.7 33 114-146 13-45 (238)
330 PF14549 P22_Cro: DNA-binding 25.0 21 0.00045 25.7 -0.3 20 125-144 10-29 (60)
331 PRK09958 DNA-binding transcrip 24.9 19 0.00041 31.5 -0.7 43 108-152 144-186 (204)
332 PRK10403 transcriptional regul 24.9 21 0.00046 31.1 -0.4 44 108-153 154-197 (215)
333 PRK11050 manganese transport r 23.8 38 0.00083 29.1 1.0 28 123-150 50-77 (152)
334 PRK15090 DNA-binding transcrip 23.6 1.3E+02 0.0028 28.1 4.7 26 125-150 29-54 (257)
335 PF05732 RepL: Firmicute plasm 23.6 33 0.00072 30.1 0.6 25 126-150 77-101 (165)
336 TIGR03830 CxxCG_CxxCG_HTH puta 23.2 28 0.00061 28.5 0.1 26 120-145 74-99 (127)
337 PRK15369 two component system 23.1 25 0.00054 30.4 -0.3 36 118-153 158-193 (211)
338 PRK09726 antitoxin HipB; Provi 23.0 24 0.00052 27.2 -0.4 24 123-146 24-47 (88)
339 cd04761 HTH_MerR-SF Helix-Turn 23.0 25 0.00054 23.3 -0.2 22 126-147 2-23 (49)
340 PF01476 LysM: LysM domain; I 22.7 31 0.00068 22.3 0.2 24 120-143 2-25 (44)
341 KOG4620 Uncharacterized conser 22.5 1.4E+02 0.003 22.3 3.5 30 49-90 31-60 (80)
342 TIGR02404 trehalos_R_Bsub treh 22.4 37 0.00079 31.2 0.7 21 127-147 27-47 (233)
343 COG5566 Uncharacterized conser 22.3 39 0.00085 28.1 0.7 27 124-150 102-128 (137)
344 PRK10141 DNA-binding transcrip 22.3 40 0.00087 27.7 0.8 28 124-151 30-57 (117)
345 PRK12683 transcriptional regul 22.1 19 0.0004 34.7 -1.4 36 120-155 12-47 (309)
346 PRK09706 transcriptional repre 21.9 30 0.00065 29.0 0.0 23 123-145 17-39 (135)
347 PF13556 HTH_30: PucR C-termin 21.9 35 0.00077 24.1 0.4 35 119-153 7-41 (59)
348 cd01104 HTH_MlrA-CarA Helix-Tu 21.8 32 0.00068 24.7 0.1 22 126-147 2-23 (68)
349 PF07022 Phage_CI_repr: Bacter 21.4 26 0.00057 25.4 -0.4 20 126-145 14-34 (66)
350 PF03333 PapB: Adhesin biosynt 21.0 82 0.0018 24.7 2.3 30 120-149 49-78 (91)
351 PRK12679 cbl transcriptional r 20.9 22 0.00047 34.3 -1.2 36 121-156 13-48 (316)
352 TIGR00180 parB_part ParB-like 20.6 14 0.00031 32.9 -2.3 41 106-146 101-142 (187)
353 PF08535 KorB: KorB domain; I 20.5 32 0.00068 26.8 -0.1 23 123-145 2-24 (93)
354 PF05263 DUF722: Protein of un 20.3 20 0.00043 30.2 -1.4 45 108-152 82-127 (130)
355 smart00497 IENR1 Intron encode 20.2 35 0.00076 23.1 0.1 24 123-146 16-39 (53)
356 PF14493 HTH_40: Helix-turn-he 20.1 23 0.00051 27.5 -1.0 59 117-178 6-64 (91)
No 1
>KOG4585 consensus Predicted transposase [Replication, recombination and repair]
Probab=100.00 E-value=2.5e-41 Score=325.66 Aligned_cols=313 Identities=37% Similarity=0.602 Sum_probs=254.2
Q ss_pred hcCCCHHHHHHHHHHhhhhhhhhcCCCcCCCCCCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 74 VFKISRKTFDYICSLVKEDLAARQSNFSFSNGKPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 74 ~frmsr~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
.|++++.+|++|+.............+....... +...+++.|+.++++.+...++..||...+|+ .+...+.
T Consensus 7 ~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~v~~~~~~~~~~~~~~~i~~~fg~~~~~~-----~~~~~~~ 79 (326)
T KOG4585|consen 7 EFRKSYTTFDKICSLVQSLNVVKNSGFMLSSLLP--ADTLVAVALWRLKTGESLRTVEKKFGLGQSTC-----KFLEEKE 79 (326)
T ss_pred HHHHHHHHHHHHhhhhhhhhhhcccchhhhcccc--HHhhhhhhhccccccchHHHHHHHcCCcchhh-----hHHHhhh
Confidence 7899999999999987665554332222222222 89999999999999999999999999999999 6667777
Q ss_pred HhccccccCCChhhHHHHHHHHHHhhhCCcceeeeeeeeEEEeecCCCCCCcchhcCCCCcceeEEEeeeCCCcceeecc
Q 015432 154 ERGLHHLQWPSKETEMEDIKSKFEKIRGFRNCCGAIDITHIVMNIPAVDPANNVWYDREKNYSMILQGIVDPEMRFRDII 233 (407)
Q Consensus 154 ~~~~~~i~~P~~~~~~~~i~~~f~~~~~fp~~vGaIDgt~i~i~~P~~~~~~~~y~~~k~~~s~~~q~v~d~~grf~~v~ 233 (407)
..+.+++.||... .+..+.+.|+. +|+|+|+||+|||++..|+. ....|.|+ .+++++|+|||.+++|+++.
T Consensus 80 ~~~~~~~~~p~~~-~~~~i~~~~~~---~~~~~g~~d~~hi~~~~~~~--~~~~~~n~--~~~~Nvlav~n~d~~f~~v~ 151 (326)
T KOG4585|consen 80 DLAPHFLKWPSRR-ILYEIRERFES---LPNCVGAIDTTHIPIRVPPK--SGSVYFNK--EQSKNLLAVCNFDMRFIYVD 151 (326)
T ss_pred cccchhhcCchhh-hhhhhcccccc---ccchhccccccccceecCcc--cccccccc--ccchhhhheecCCceEEEEE
Confidence 7889999999977 78888888877 99999999999999998764 45677777 88899999999999999999
Q ss_pred ccCCCcccccccccccchhhhhhhcccCCCccccCCC-ccccceeeecCCCccCCccccccCCCCCCCchhhhhhhhhhh
Q 015432 234 AGWPGSLTDALVLRNSGFFKLTEEGKRLDGKSLQLSE-GIELREYIIGDTGFPLLPWLLTPYQGKGLSDIEAEYNKRHSA 312 (407)
Q Consensus 234 ~g~pGs~~D~~v~~~S~l~~~l~~g~~l~~~~~~~~~-g~~~~~~llgD~gYpl~~~l~tP~~~~~lt~~~~~fN~~ls~ 312 (407)
+||||+.||+.|+..+.+.+....+..+ +..+.+ |.+.+.+++|+.+||+.+++|+|+.++..+..++.||++|+.
T Consensus 152 vg~~Gs~~D~kvl~~~~~~~~~~~~~~~---k~yl~d~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~elFN~rh~~ 228 (326)
T KOG4585|consen 152 VGWPGSAHDTKVLQDSLLYKRNFPHPPL---KYYLVDSGYPLRPGLLGPIGFPLYSLLMFPYGGPQPTNSQELFNKRHSS 228 (326)
T ss_pred ccCCCCccHHHHHHhhcccccccccCCc---cccccccCcccccccccccccccchhhhcccCCCCCCchHHHHhhhhhh
Confidence 9999999999999999988776654332 333333 556788999999999999999999987778999999999999
Q ss_pred hhhHHHHHHHHHHhHHHhhcccccCCCCCchhHHHHHHHHHhhhhcccCccccCCCCCCCCCCCCc--cccc-ccccChh
Q 015432 313 TRMVAQMALARLKDVWRIIHGVMWMPDKNRLPRIVLVCCLLHNIVIDMEDEMLDELPLSYHHDSGY--HQQT-CESVDKT 389 (407)
Q Consensus 313 ~R~~vE~afg~LK~rfriL~~~~~~~~~~~~~~ii~accvLHN~~i~~~d~~~~~~~~~~~~d~~~--~~~~-~~~~~~~ 389 (407)
+|.++|++||+||+||+||... +..+..+.+.||.|||+|||+|++.+++..++......+|.+. .... ..+...-
T Consensus 229 ~r~v~e~~fg~lk~rw~il~~~-~~~~~~~~~~iV~a~caLHN~~~~~~~~~~~~~~~e~~~d~~~~~~~~~~~~~~~~~ 307 (326)
T KOG4585|consen 229 LRSVAERAFGVLKAKWRILQRR-EKYDLKKLPKIVTACCALHNIIRDSDEEDPDDPKWEKFDDYGENVAHLRYAPQQRDY 307 (326)
T ss_pred HHHHHHHHHHHhhhhhHHHhhc-ccccccchHHHHHHHHHHHHHHHhhcccccccccccccccccccchhcccchhHHHH
Confidence 9999999999999999999987 6678889999999999999999998876655543232233321 1111 2344556
Q ss_pred HHHHHHHHHHHhccCC
Q 015432 390 ASVMRDNLSLYLSGKL 405 (407)
Q Consensus 390 ~~~~Rd~l~~~l~~~~ 405 (407)
+...|+.|+..+....
T Consensus 308 ~~~~r~~l~~~l~~~~ 323 (326)
T KOG4585|consen 308 MEKIRDNLLSELWNGT 323 (326)
T ss_pred HHHHHHHHHHHHHhcc
Confidence 8888999988887654
No 2
>PF13359 DDE_Tnp_4: DDE superfamily endonuclease
Probab=100.00 E-value=3.7e-37 Score=270.28 Aligned_cols=154 Identities=38% Similarity=0.790 Sum_probs=136.7
Q ss_pred eeeeEEEeecCCCC-CCcchhcCCCCcceeEEEeeeCCCcceeeccccCCCcccccccccccchhhhhhhcccCCCcccc
Q 015432 189 IDITHIVMNIPAVD-PANNVWYDREKNYSMILQGIVDPEMRFRDIIAGWPGSLTDALVLRNSGFFKLTEEGKRLDGKSLQ 267 (407)
Q Consensus 189 IDgt~i~i~~P~~~-~~~~~y~~~k~~~s~~~q~v~d~~grf~~v~~g~pGs~~D~~v~~~S~l~~~l~~g~~l~~~~~~ 267 (407)
||||||+|++|... .....|+++|+.|++++|++||++|+|++++.+||||+||+.+|++|++...++..
T Consensus 1 iDgt~v~i~~P~~~~~~~~~y~~~k~~~~~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~s~~~~~l~~~--------- 71 (158)
T PF13359_consen 1 IDGTHVPIQRPSDKEEQREFYSGKKKNHSLKVQIVCDPDGRIIYVSVGWPGSVHDSTIFRQSGLLDRLEQA--------- 71 (158)
T ss_pred CccEEEEEEeCCccccccccccCCCCcceEeEEEEEeccceeEeeecccccccccccccccccccceeecc---------
Confidence 79999999998753 24578999999999999999999999999999999999999999999988766521
Q ss_pred CCCccccceeeecCCCccCCccccccCC---CCCCCchhhhhhhhhhhhhhHHHHHHHHHHhHHHhhcccccCCCCCchh
Q 015432 268 LSEGIELREYIIGDTGFPLLPWLLTPYQ---GKGLSDIEAEYNKRHSATRMVAQMALARLKDVWRIIHGVMWMPDKNRLP 344 (407)
Q Consensus 268 ~~~g~~~~~~llgD~gYpl~~~l~tP~~---~~~lt~~~~~fN~~ls~~R~~vE~afg~LK~rfriL~~~~~~~~~~~~~ 344 (407)
++ .++++|||+|||+.+++|+||+ +.+++.++..||++|+++|.+||++||+||+||+||+..+......++.
T Consensus 72 ~~----~~~~~l~D~gy~~~~~~~~P~~~~~~~~l~~~e~~~N~~~s~~R~~vE~~~~~lK~rf~~l~~~~~~~~~~~~~ 147 (158)
T PF13359_consen 72 FP----PGEYLLGDSGYPLSPYLLTPYKKPKGRELTPEEKEFNRRHSSARIIVERAFGRLKSRFRILRGRLRLSRPEKAP 147 (158)
T ss_pred cc----cCccccccccccccccccccccccccccccccccchhccccceeeeeHHHHHHHHHhcccCCcccCCCcHhHHH
Confidence 11 2489999999999999999995 5578999999999999999999999999999999998776433378999
Q ss_pred HHHHHHHHHhh
Q 015432 345 RIVLVCCLLHN 355 (407)
Q Consensus 345 ~ii~accvLHN 355 (407)
.+|.|||+|||
T Consensus 148 ~ii~~~~~LhN 158 (158)
T PF13359_consen 148 QIILACCVLHN 158 (158)
T ss_pred HHHheeEEEEC
Confidence 99999999999
No 3
>PF04827 Plant_tran: Plant transposon protein; InterPro: IPR006912 This entry represents a putative Harbinger transposase-derived nuclease, which is thought to have nuclease activity. However it does not have transposase activity [, ]. ; GO: 0016788 hydrolase activity, acting on ester bonds
Probab=100.00 E-value=2.5e-36 Score=262.29 Aligned_cols=200 Identities=22% Similarity=0.323 Sum_probs=172.4
Q ss_pred ccccCCChhhHHHHHHHHHHhhhCCcceeeeeeeeEEEeecCCCCCCcchhcCCCCcceeEEEeeeCCCcceeeccccCC
Q 015432 158 HHLQWPSKETEMEDIKSKFEKIRGFRNCCGAIDITHIVMNIPAVDPANNVWYDREKNYSMILQGIVDPEMRFRDIIAGWP 237 (407)
Q Consensus 158 ~~i~~P~~~~~~~~i~~~f~~~~~fp~~vGaIDgt~i~i~~P~~~~~~~~y~~~k~~~s~~~q~v~d~~grf~~v~~g~p 237 (407)
+|++-|+.+ +++++... .+..||||.+|+|||+|+.+..++....+....++++..++.++||++++.+|.++..|.|
T Consensus 2 ~YLr~P~~~-d~~rll~~-~e~rGFpGmlGSIDCmHw~WkncP~aw~g~~~~G~~g~pTiiLEaVAs~dlwIWhaffG~~ 79 (205)
T PF04827_consen 2 EYLRRPTNE-DLERLLQI-GEARGFPGMLGSIDCMHWEWKNCPTAWKGQYTRGKEGVPTIILEAVASHDLWIWHAFFGMP 79 (205)
T ss_pred cccCCCChh-HHHHHHHh-hhhcCCCccccceeEEEeehhcchHHhhhcccCCCCCCCeehhhhhhccchhhhheeeccC
Confidence 588999998 89998854 5667999999999999999997665444443349999999999999999999999999999
Q ss_pred CcccccccccccchhhhhhhcccCCCccccCCCccc-cceeeecCCCccCCccccccCCCCCCCchhhhhhhhhhhhhhH
Q 015432 238 GSLTDALVLRNSGFFKLTEEGKRLDGKSLQLSEGIE-LREYIIGDTGFPLLPWLLTPYQGKGLSDIEAEYNKRHSATRMV 316 (407)
Q Consensus 238 Gs~~D~~v~~~S~l~~~l~~g~~l~~~~~~~~~g~~-~~~~llgD~gYpl~~~l~tP~~~~~lt~~~~~fN~~ls~~R~~ 316 (407)
||.+|.+|+..|+++..+.+|+.. .-...+. |.+ --.|+|+|..||-+..++.+++. |.+.+++.|.++++++|..
T Consensus 80 GS~NDiNVL~~Splf~~~~~G~ap-~v~f~VN-g~~Y~~gYYLaDGiYP~watfvktI~~-p~~~k~k~fa~~QE~~RKD 156 (205)
T PF04827_consen 80 GSNNDINVLDRSPLFDDLLQGQAP-RVQFTVN-GHEYNMGYYLADGIYPEWATFVKTISL-PQGEKRKLFAKHQESARKD 156 (205)
T ss_pred CcccccccccccHHHHHHhcCcCC-ceEEEec-CeecccceeeccCcCcchHhHhhhcch-hhchhhHHHHHhCHHHHHH
Confidence 999999999999999999998631 1112222 222 13689999999999999999985 8889999999999999999
Q ss_pred HHHHHHHHHhHHHhhcccccCCCCCchhHHHHHHHHHhhhhcccCc
Q 015432 317 AQMALARLKDVWRIIHGVMWMPDKNRLPRIVLVCCLLHNIVIDMED 362 (407)
Q Consensus 317 vE~afg~LK~rfriL~~~~~~~~~~~~~~ii~accvLHN~~i~~~d 362 (407)
||+|||+|++||+|++.+....+.+.+..|+.||++||||+++++-
T Consensus 157 VErAFGVLQaRfaIi~~p~r~w~~~~l~~Im~aCiILHNMIvEDEr 202 (205)
T PF04827_consen 157 VERAFGVLQARFAIIRGPARLWDREDLANIMRACIILHNMIVEDER 202 (205)
T ss_pred HHHHHHHHHHHHHHhcCchhccCHHHHHHHHHHHHHhhheeEeccc
Confidence 9999999999999999998777888999999999999999998653
No 4
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=98.91 E-value=1.5e-10 Score=81.98 Aligned_cols=51 Identities=25% Similarity=0.277 Sum_probs=48.3
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhcc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGL 157 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~ 157 (407)
+++.++||+++|.||++|.++.++|..||||+|||++++++++++|...++
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 589999999999999999999999999999999999999999999987653
No 5
>PF13612 DDE_Tnp_1_3: Transposase DDE domain
Probab=98.86 E-value=1.7e-09 Score=93.80 Aligned_cols=130 Identities=18% Similarity=0.172 Sum_probs=95.6
Q ss_pred CcceeeeeeeeEEEeecCCCCCCcc--------hhcCCCCcceeEEEeeeCCCcceeeccccCCCcccccccccccchhh
Q 015432 182 FRNCCGAIDITHIVMNIPAVDPANN--------VWYDREKNYSMILQGIVDPEMRFRDIIAGWPGSLTDALVLRNSGFFK 253 (407)
Q Consensus 182 fp~~vGaIDgt~i~i~~P~~~~~~~--------~y~~~k~~~s~~~q~v~d~~grf~~v~~g~pGs~~D~~v~~~S~l~~ 253 (407)
-+..+.+||.|.|+++.+....... -|+..+-+|++++.++|+..|.++.+.. .||++||..++.. +..
T Consensus 3 ~~~~i~~iDS~Pi~vC~~~R~~r~k~~~~~a~~G~~a~~~fyGfKlHllv~~~G~i~~~~l-T~an~~D~~~~~~--l~~ 79 (155)
T PF13612_consen 3 QCTGIYIIDSFPIPVCHNIRIKRHKVFKGLAYRGYCAMGWFYGFKLHLLVNDSGEIVAFTL-TPANVHDRKVLEE--LSE 79 (155)
T ss_pred CccEEEEEecCChhHhCccchhhhccccCccccceeccceeEeeeeeeEEccCCcEEEEEE-ccccccccccccc--ccc
Confidence 4567889999999999765322111 1223334589999999999999998866 7999999998842 111
Q ss_pred hhhhcccCCCccccCCCccccceeeecCCCccCCc----------cccccCCCCCCCchhhhhhhhhhhhhhHHHHHHHH
Q 015432 254 LTEEGKRLDGKSLQLSEGIELREYIIGDTGFPLLP----------WLLTPYQGKGLSDIEAEYNKRHSATRMVAQMALAR 323 (407)
Q Consensus 254 ~l~~g~~l~~~~~~~~~g~~~~~~llgD~gYpl~~----------~l~tP~~~~~lt~~~~~fN~~ls~~R~~vE~afg~ 323 (407)
. ....++||.||-... .|+||.+.+--......+++.+.+.|..||-.|+.
T Consensus 80 ~-------------------~~g~l~gDkGYis~~L~~~L~~~gI~L~t~~RkNmk~~~~~~~~~~l~~~R~~IETvfs~ 140 (155)
T PF13612_consen 80 N-------------------LKGKLFGDKGYISKELKDELKEQGIKLITPRRKNMKNKLMPLFDKLLLRKRRIIETVFSQ 140 (155)
T ss_pred c-------------------cccceecchhhhcchHHhhhhhceEEEeccccccccccccchhhhhhhheeeEeehHHHH
Confidence 0 024799999996443 38899986433344566889999999999999999
Q ss_pred HHhHHHhhcc
Q 015432 324 LKDVWRIIHG 333 (407)
Q Consensus 324 LK~rfriL~~ 333 (407)
||+.|.|=+.
T Consensus 141 Lk~~~~ie~~ 150 (155)
T PF13612_consen 141 LKNQFNIEHS 150 (155)
T ss_pred HHHhhceEee
Confidence 9999887543
No 6
>PF01609 DDE_Tnp_1: Transposase DDE domain; InterPro: IPR002559 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS4 transposase. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 3ECP_A 4DM0_A 1MUS_A 1MUH_A 1MM8_A 1B7E_A.
Probab=97.19 E-value=9.1e-06 Score=73.30 Aligned_cols=150 Identities=14% Similarity=0.120 Sum_probs=81.5
Q ss_pred ceeeeeeeeEEEee-cCCCCCCcchhcCCCCcceeEEEeee-CCCcceeeccccCCCcccccccccccchhhhhhhcccC
Q 015432 184 NCCGAIDITHIVMN-IPAVDPANNVWYDREKNYSMILQGIV-DPEMRFRDIIAGWPGSLTDALVLRNSGFFKLTEEGKRL 261 (407)
Q Consensus 184 ~~vGaIDgt~i~i~-~P~~~~~~~~y~~~k~~~s~~~q~v~-d~~grf~~v~~g~pGs~~D~~v~~~S~l~~~l~~g~~l 261 (407)
..+-+||+|+|+.. .+ .....+.+++....+++++++ +..+.++.+.+. +|+.+|...+.. +.+. .
T Consensus 4 ~~~~~iD~T~i~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~d~~~~~~--ll~~---~--- 71 (213)
T PF01609_consen 4 RRVVAIDGTTIRTPHDK---SARRYKKGKKRGFGYKLHLAVDDNSGLPLSVKVT-PGNVHDSKALPE--LLER---K--- 71 (213)
T ss_dssp EEEEEEETTT--EEEEE---EE-B-SSGGGHSSHGGHHHHHHHHHGGGGGGEEE-EEEGG-HHHHHH--HHTT-------
T ss_pred CeEEEEECcEEEeecch---hhhcccCCCCcCCCEeEEEEEeecccceeeeecc-ccccceeecccc--cccc---c---
Confidence 35669999999988 21 111223344445667888888 456667777776 999999998875 2221 0
Q ss_pred CCccccCCCccccceeeecCCCccCCcc----------ccccCCCCCC--------------------------------
Q 015432 262 DGKSLQLSEGIELREYIIGDTGFPLLPW----------LLTPYQGKGL-------------------------------- 299 (407)
Q Consensus 262 ~~~~~~~~~g~~~~~~llgD~gYpl~~~----------l~tP~~~~~l-------------------------------- 299 (407)
. ...+.++++|+||..... .+.|.+....
T Consensus 72 -----~----~~~~~~vv~D~gy~s~~~~~~l~~~~~~~vi~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 142 (213)
T PF01609_consen 72 -----P----GRKPDLVVADRGYDSAENLEALKERGIHFVIRLKKNRKKKIQKIENKFWKSFDRRSARKKPKQKSKRVRV 142 (213)
T ss_dssp -------------EEEEEE-S--BBTTHHHHHHTS---EEEEE--EEEE-TTS-EEEE--EEEEEEEEEEETGGGEEEEE
T ss_pred -----c----cccccceeecccccceeccccccccccccccccccccccccccchhhccccccccccccccccccccccc
Confidence 0 011478999999975542 2333332110
Q ss_pred --Cchhhhhhhh--------------hhhhhhHHHHHHHHHHhHHHhhcccccCCCCCchhHHHHHHHHHhhh
Q 015432 300 --SDIEAEYNKR--------------HSATRMVAQMALARLKDVWRIIHGVMWMPDKNRLPRIVLVCCLLHNI 356 (407)
Q Consensus 300 --t~~~~~fN~~--------------ls~~R~~vE~afg~LK~rfriL~~~~~~~~~~~~~~ii~accvLHN~ 356 (407)
.......... +.+.|-.||+.|..||+.|..=+ .. ......+...+.++++-.|+
T Consensus 143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Y~~Rw~IE~~f~~lK~~~~l~~-~~-~~~~~~~~~~~~~~~la~nl 213 (213)
T PF01609_consen 143 VIRKEQKKKGYFLVTNITTLPRDTAALYRRRWQIERFFRELKQFLGLER-LR-VRSPERIEAHLFLTLLAYNL 213 (213)
T ss_dssp EEEEECS--TTS---EEEEEESS--SHHHCGGHHHHHHHHHTTTTTGGG-S---SSHHHHHHHHHHHHHH---
T ss_pred ccccccccccccccccccccccccceeecccchhhHHHHHHHhcCCCch-hc-ccCHHHHHHHHHHHHhhCcC
Confidence 0111112222 88999999999999998655333 21 23445666777777777664
No 7
>PF13586 DDE_Tnp_1_2: Transposase DDE domain
Probab=97.04 E-value=0.00028 Score=55.34 Aligned_cols=74 Identities=19% Similarity=0.261 Sum_probs=46.4
Q ss_pred eecCCCccCCc--------ccc--ccCCCCCCCchhhhhhhhhhhhhhHHHHHHHHHHhHHHhhcccccCCCCCchhHHH
Q 015432 278 IIGDTGFPLLP--------WLL--TPYQGKGLSDIEAEYNKRHSATRMVAQMALARLKDVWRIIHGVMWMPDKNRLPRIV 347 (407)
Q Consensus 278 llgD~gYpl~~--------~l~--tP~~~~~lt~~~~~fN~~ls~~R~~vE~afg~LK~rfriL~~~~~~~~~~~~~~ii 347 (407)
+++|+||.... .+. .|-.+.+.......+...+...|-+||++|+.|| +|+.|..............+.
T Consensus 1 v~aDkgYd~~~~r~~l~~~gi~~~i~~~~~~~~~~~~~~d~~~~~~Rw~VEr~f~wlk-~~Rrl~~ryek~~~s~~~~v~ 79 (88)
T PF13586_consen 1 VLADKGYDSRALREYLRERGIRPVIPKRGRRKKRRPRKFDFRLYKRRWVVERTFAWLK-RFRRLATRYEKLASSFLAFVH 79 (88)
T ss_pred CcccCCcCCHHHHHHHHHCCCEEecCCCCCccccccCccchhhhccceehhhhhHHHH-HcCccccccccCHHHHHHHHH
Confidence 57899997432 122 2222222224467888999999999999999999 689887765433333333444
Q ss_pred HHHHH
Q 015432 348 LVCCL 352 (407)
Q Consensus 348 ~accv 352 (407)
+||++
T Consensus 80 la~~~ 84 (88)
T PF13586_consen 80 LACIV 84 (88)
T ss_pred HHHHH
Confidence 44443
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=95.06 E-value=0.0021 Score=43.64 Aligned_cols=34 Identities=24% Similarity=0.253 Sum_probs=26.3
Q ss_pred ceeeEEEeccCCCcchhhhcccccccccchhhhH
Q 015432 113 MVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 113 ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~ 146 (407)
++.-++..+..|.+..+||..||||++||.|++.
T Consensus 10 ~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 10 QIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp CHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 5556666778899999999999999999999864
No 9
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=95.05 E-value=0.0027 Score=42.85 Aligned_cols=41 Identities=34% Similarity=0.404 Sum_probs=22.6
Q ss_pred CCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHH
Q 015432 106 KPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 106 ~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~ 147 (407)
+.|+.+++..|.- ++..|.+++.||..+|+|+|||++.+.+
T Consensus 3 ~~Lt~~eR~~I~~-l~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEA-LLEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHH-HHCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHH-HHHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 3466666666663 3678999999999999999999998865
No 10
>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=94.34 E-value=0.0085 Score=41.43 Aligned_cols=45 Identities=29% Similarity=0.461 Sum_probs=37.6
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESM 152 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al 152 (407)
.++++++-.+.++| -.+.++.+||..+|+|.+||+++..+.+.-|
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 47888888888888 5689999999999999999999988877655
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=93.55 E-value=0.0087 Score=42.11 Aligned_cols=42 Identities=36% Similarity=0.446 Sum_probs=29.4
Q ss_pred CCCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHH
Q 015432 105 GKPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 105 ~~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~ 147 (407)
+..+++++++.+.- ++-.|.+..+||..|||+.|||+.|+..
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 35677777777654 4677889999999999999999998753
No 12
>smart00351 PAX Paired Box domain.
Probab=92.63 E-value=0.023 Score=47.54 Aligned_cols=46 Identities=24% Similarity=0.302 Sum_probs=39.0
Q ss_pred CCCCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHH
Q 015432 104 NGKPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 104 ~~~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
.+++++.+.+.-+.+.+. .|.+...||..||||++||++++.++-+
T Consensus 14 ~~~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 14 NGRPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCCCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 346688888888877665 7999999999999999999999988754
No 13
>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=92.38 E-value=0.081 Score=33.89 Aligned_cols=25 Identities=28% Similarity=0.465 Sum_probs=18.4
Q ss_pred CChhHHHhhcCCCHHHHHHHHHHhh
Q 015432 66 KTSKNFESVFKISRKTFDYICSLVK 90 (407)
Q Consensus 66 ~~d~~F~~~frmsr~tF~~L~~~l~ 90 (407)
.+|++|...|+|+++.|..|=..=+
T Consensus 2 Lsd~dF~~vFgm~~~eF~~lP~WKq 26 (36)
T PF02209_consen 2 LSDEDFEKVFGMSREEFYKLPKWKQ 26 (36)
T ss_dssp S-HHHHHHHHSS-HHHHHHS-HHHH
T ss_pred cCHHHHHHHHCCCHHHHHHChHHHH
Confidence 3689999999999999998765433
No 14
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=92.17 E-value=0.0099 Score=41.00 Aligned_cols=28 Identities=29% Similarity=0.365 Sum_probs=20.3
Q ss_pred cCCCcchhhhcccccccccchhhhHHHH
Q 015432 122 SSGESLQIIGDLFGLNQSTVSQVTWRFV 149 (407)
Q Consensus 122 a~g~s~~~la~~Fgis~sTvsr~i~~~~ 149 (407)
..|.+...||..||||++||++++.++.
T Consensus 15 ~~G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 15 REGWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp HHT--HHHHHHHHTS-HHHHHHHHT---
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 3499999999999999999999987764
No 15
>PF13518 HTH_28: Helix-turn-helix domain
Probab=92.17 E-value=0.022 Score=39.45 Aligned_cols=34 Identities=38% Similarity=0.463 Sum_probs=27.6
Q ss_pred eEEEeccCCCcchhhhcccccccccchhhhHHHHH
Q 015432 116 IALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 116 i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
+...++ .|.++..+|..||||.+||.+++..+-.
T Consensus 5 iv~~~~-~g~s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 5 IVELYL-EGESVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHH-cCCCHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 344455 5779999999999999999999877654
No 16
>cd00131 PAX Paired Box domain
Probab=91.68 E-value=0.036 Score=46.65 Aligned_cols=46 Identities=26% Similarity=0.282 Sum_probs=39.3
Q ss_pred CCCCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHH
Q 015432 104 NGKPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 104 ~~~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
.++++|.+.+..|.+.+ ..|.+...||..||||++||++++.++-+
T Consensus 14 m~~~lS~d~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e 59 (128)
T cd00131 14 NGRPLPDSIRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILNRYYE 59 (128)
T ss_pred CCCcCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45778888877777665 68999999999999999999999988765
No 17
>smart00153 VHP Villin headpiece domain.
Probab=91.48 E-value=0.13 Score=32.94 Aligned_cols=22 Identities=27% Similarity=0.499 Sum_probs=19.0
Q ss_pred CChhHHHhhcCCCHHHHHHHHH
Q 015432 66 KTSKNFESVFKISRKTFDYICS 87 (407)
Q Consensus 66 ~~d~~F~~~frmsr~tF~~L~~ 87 (407)
.+|++|...|+|+|+.|..|=.
T Consensus 2 LsdeeF~~vfgmsr~eF~~LP~ 23 (36)
T smart00153 2 LSDEDFEEVFGMTREEFYKLPL 23 (36)
T ss_pred CCHHHHHHHHCCCHHHHHhCcH
Confidence 3689999999999999988643
No 18
>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=91.15 E-value=0.034 Score=38.94 Aligned_cols=44 Identities=25% Similarity=0.333 Sum_probs=32.3
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVES 151 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~a 151 (407)
.+|+.++.++.|.|+ .|.++.+||..+|+|.+||...+.+....
T Consensus 10 ~L~~~~r~i~~l~~~-~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLRYF-QGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHHHT-S---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHH-HCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 378888888888777 49999999999999999999988775543
No 19
>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=90.81 E-value=0.075 Score=41.72 Aligned_cols=51 Identities=33% Similarity=0.409 Sum_probs=45.4
Q ss_pred CCCCCChhcceeeEEEeccCCCcchhhhcccc-cccccchhhhHHHHHHHHH
Q 015432 104 NGKPLSPNDMVAIALRRLSSGESLQIIGDLFG-LNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 104 ~~~~l~~~~ql~i~L~~La~g~s~~~la~~Fg-is~sTvsr~i~~~~~al~~ 154 (407)
+.+.+...-++++.|..--+|.++.+||..|| .+.|||+..+.++-..+.+
T Consensus 24 R~~~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 24 RKKEIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred CCcCcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 44568888999999999889999999999999 9999999999998888764
No 20
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=90.45 E-value=0.051 Score=41.96 Aligned_cols=53 Identities=17% Similarity=0.315 Sum_probs=45.3
Q ss_pred CCCCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHH----HHHhc
Q 015432 104 NGKPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVES----MEERG 156 (407)
Q Consensus 104 ~~~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~a----l~~~~ 156 (407)
.+-.|++..++.++-..+..|.+...++..||||..|+++++.++-.. |.++.
T Consensus 5 ~nA~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G~~GL~DRS 61 (85)
T PF13011_consen 5 KNARLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRAEGEAGLQDRS 61 (85)
T ss_pred CCCCCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHcCcccccccC
Confidence 345689999999999999999999999999999999999999888643 55544
No 21
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=88.55 E-value=0.056 Score=45.87 Aligned_cols=44 Identities=25% Similarity=0.263 Sum_probs=37.1
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
+.+.+.+-+++..++..|.|.+.+|.+||||.|||.+++.++-+
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 34556666777778889999999999999999999999988764
No 22
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=88.36 E-value=0.35 Score=42.48 Aligned_cols=48 Identities=15% Similarity=0.286 Sum_probs=42.5
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.+|..++.++.|+++ .|.++.+||..+|+|.+||...+.+....|...
T Consensus 126 ~L~~~~r~v~~l~~~-~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 126 KLDPEFRAPVILKHY-YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred cCCHHHhheeeehhh-cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 388899999999887 699999999999999999999888888777654
No 23
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=88.24 E-value=0.063 Score=40.55 Aligned_cols=35 Identities=14% Similarity=0.258 Sum_probs=23.5
Q ss_pred EeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 119 RRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 119 ~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
+.+.+..+.+..|..||||+|||++-+.+=+..|.
T Consensus 14 yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in 48 (82)
T PF12116_consen 14 YIIETKATVRQAAKVFGVSKSTVHKDVTERLPKIN 48 (82)
T ss_dssp HHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-
T ss_pred HHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcC
Confidence 44566788899999999999999997665455444
No 24
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)
Probab=87.55 E-value=0.76 Score=34.63 Aligned_cols=46 Identities=20% Similarity=0.215 Sum_probs=40.6
Q ss_pred CCCCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHH
Q 015432 104 NGKPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 104 ~~~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
+....+..+.|-..|+.|.+|+..+.|-..|| +.+||++.+.+...
T Consensus 21 ~~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg-~~~tv~~~f~rW~~ 66 (75)
T PF13340_consen 21 GRPRIDLREVLNAILYVLRTGCPWRDLPEDFG-PWSTVYRRFRRWSR 66 (75)
T ss_pred CCCccchHHHHhcccccceecceecccchhcc-CcCcHHHHHHHHHH
Confidence 34568889999999999999999999999999 99999998877654
No 25
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=86.98 E-value=0.12 Score=42.89 Aligned_cols=47 Identities=13% Similarity=0.266 Sum_probs=42.2
Q ss_pred CCCCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHH
Q 015432 104 NGKPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 104 ~~~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
+++..+.+.++.++...+..|.++..+|..||||.+|+++++..+..
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 34678999999999999999999999999999999999999988754
No 26
>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=86.86 E-value=0.45 Score=40.66 Aligned_cols=48 Identities=21% Similarity=0.270 Sum_probs=41.4
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.+|..++-++.|.++ .|.++.+||..+|+|.+||...+.+....|.+.
T Consensus 105 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 105 RLPENYRTVLILREF-KEFSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred hCCHhheeeeeehhh-ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 378888888888887 699999999999999999999888887777653
No 27
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=86.69 E-value=0.05 Score=36.86 Aligned_cols=34 Identities=18% Similarity=0.280 Sum_probs=22.9
Q ss_pred ceeeEEEeccCC-CcchhhhcccccccccchhhhH
Q 015432 113 MVAIALRRLSSG-ESLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 113 ql~i~L~~La~g-~s~~~la~~Fgis~sTvsr~i~ 146 (407)
.+..+|..+..| .+++..|..|||++||+++.+.
T Consensus 4 ~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~ 38 (45)
T PF05225_consen 4 DLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLR 38 (45)
T ss_dssp HHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHH
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHc
Confidence 333444445566 8999999999999999997664
No 28
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=86.39 E-value=0.18 Score=34.96 Aligned_cols=43 Identities=19% Similarity=0.340 Sum_probs=32.6
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHH
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESM 152 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al 152 (407)
++..++-.+. ++..|.++.+||..+|+|.+||.+++.+....|
T Consensus 4 l~~~e~~i~~--~~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl 46 (58)
T smart00421 4 LTPREREVLR--LLAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46 (58)
T ss_pred CCHHHHHHHH--HHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4444444332 246899999999999999999999998876655
No 29
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=85.82 E-value=0.3 Score=43.70 Aligned_cols=50 Identities=18% Similarity=0.121 Sum_probs=42.9
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhcc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGL 157 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~ 157 (407)
.+|.+++-++.|+++. |.++..||..+|+|.+||...+.+....|...+.
T Consensus 141 ~L~~~~~~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 190 (194)
T PRK12519 141 QLPESQRQVLELAYYE-GLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQ 190 (194)
T ss_pred hCCHHHhhhhhhhhhc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3788888888888875 9999999999999999999999888887776543
No 30
>PRK00118 putative DNA-binding protein; Validated
Probab=85.60 E-value=0.18 Score=40.73 Aligned_cols=50 Identities=20% Similarity=0.167 Sum_probs=40.1
Q ss_pred CCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 106 KPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 106 ~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
..++..++-++.|+++ .|.++..||..+|+|++||++.+.+....|.+..
T Consensus 16 ~~L~ekqRevl~L~y~-eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~ 65 (104)
T PRK00118 16 SLLTEKQRNYMELYYL-DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYE 65 (104)
T ss_pred ccCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4467777777655544 5999999999999999999999998877776643
No 31
>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=85.58 E-value=0.18 Score=34.32 Aligned_cols=43 Identities=30% Similarity=0.376 Sum_probs=33.0
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHH
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVES 151 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~a 151 (407)
++..++-++.+.++ .|.++.+||..+|++.+||.+++.+...-
T Consensus 11 l~~~~~~~~~~~~~-~~~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 11 LPEREREVILLRFG-EGLSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred CCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 45555555555554 78999999999999999999998876543
No 32
>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=85.18 E-value=0.1 Score=32.33 Aligned_cols=37 Identities=27% Similarity=0.413 Sum_probs=25.8
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhh
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVT 145 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i 145 (407)
++.++...+... +..+.+...++..||++.+|+++++
T Consensus 6 ~~~~~~~~i~~~-~~~~~s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRL-LAAGESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHhC
Confidence 444444333332 3467799999999999999998763
No 33
>PRK04217 hypothetical protein; Provisional
Probab=84.58 E-value=0.22 Score=40.56 Aligned_cols=50 Identities=14% Similarity=0.110 Sum_probs=38.8
Q ss_pred CCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 106 KPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 106 ~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
..++.+++-++.|++ -.|.++.+||..+|||.+||++++.+....|.+.+
T Consensus 41 ~~Lt~eereai~l~~-~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 41 IFMTYEEFEALRLVD-YEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred ccCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 447777765544443 36889999999999999999999998877776543
No 34
>PRK06030 hypothetical protein; Provisional
Probab=84.27 E-value=0.3 Score=40.76 Aligned_cols=47 Identities=17% Similarity=0.232 Sum_probs=41.7
Q ss_pred CCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHH
Q 015432 106 KPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESM 152 (407)
Q Consensus 106 ~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al 152 (407)
+.+...-|++|.|.+--++.++..||..||.+.|||..-++.+-+.+
T Consensus 51 k~i~~aRqIAMYL~r~~~~~sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 51 REVSRIRQIAMYVAHVSLGWPMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred cccchHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence 56888999999999999999999999999999999998887666554
No 35
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=84.23 E-value=0.25 Score=42.94 Aligned_cols=48 Identities=23% Similarity=0.294 Sum_probs=42.6
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|..++-++.|++ .|.++..||..+|+|.+||...+.+....|...+
T Consensus 112 ~L~~~~r~il~l~~--~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 112 KMTERDRTVLLLRF--SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 38888999999977 8999999999999999999999988888877654
No 36
>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=84.13 E-value=0.24 Score=33.67 Aligned_cols=20 Identities=35% Similarity=0.346 Sum_probs=17.7
Q ss_pred chhhhcccccccccchhhhH
Q 015432 127 LQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 127 ~~~la~~Fgis~sTvsr~i~ 146 (407)
..+||...|||.+|||++++
T Consensus 2 i~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHh
Confidence 56899999999999999764
No 37
>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=83.51 E-value=0.59 Score=44.48 Aligned_cols=49 Identities=16% Similarity=0.259 Sum_probs=42.6
Q ss_pred CCChhcceeeEEEecc-CCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRLS-SGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La-~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.|+..++..+.|+|+. .+.++..||..+|||.++|+++..+.+.-|...
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 3899999999999974 478999999999999999999998887777653
No 38
>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=83.27 E-value=0.069 Score=40.15 Aligned_cols=45 Identities=22% Similarity=0.300 Sum_probs=36.4
Q ss_pred CCCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHH
Q 015432 105 GKPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFV 149 (407)
Q Consensus 105 ~~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~ 149 (407)
++..|++.++.++-.+|..|.+..+++..+||+.+|+++++..+.
T Consensus 4 r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 4 RRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp S----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence 356788888888888889999999999999999999999998887
No 39
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=82.90 E-value=0.21 Score=34.57 Aligned_cols=25 Identities=24% Similarity=0.357 Sum_probs=21.9
Q ss_pred CCcchhhhcccccccccchhhhHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRF 148 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~ 148 (407)
..++.+||..+|||.+||.+++.+.
T Consensus 27 ~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 27 SRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3577899999999999999998764
No 40
>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=82.67 E-value=0.87 Score=44.31 Aligned_cols=72 Identities=21% Similarity=0.279 Sum_probs=54.6
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhcccc--cc--CCChhhHHHHHHHHHHhhh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGLHH--LQ--WPSKETEMEDIKSKFEKIR 180 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~~~--i~--~P~~~~~~~~i~~~f~~~~ 180 (407)
.||+.++.++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+... -. -|..+ +...+.+.|...+
T Consensus 142 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~~~~~~~~-~~~~~v~~~~~a~ 217 (324)
T TIGR02960 142 YLPPRQRAVLLLRDV-LGWRAAETAELLGTSTASVNSALQRARATLDEVGPSARDDQLAQPPSP-EEQDLLERYIAAF 217 (324)
T ss_pred hCCHHHhhHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcccccccccCCCCCH-HHHHHHHHHHHHH
Confidence 488889999998887 7999999999999999999999999999998876543 11 12333 4555666665543
No 41
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=82.20 E-value=0.34 Score=42.47 Aligned_cols=49 Identities=27% Similarity=0.351 Sum_probs=41.4
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+++.++.++.|.++ .|.++.+||..+|+|.+||...+.+...-|.+.+
T Consensus 128 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREI-EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 378888888888776 6999999999999999999998888777776544
No 42
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=82.10 E-value=0.33 Score=42.94 Aligned_cols=48 Identities=17% Similarity=0.142 Sum_probs=41.9
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.||+.++.++.|+++ .|.++.+||..+|||.+||...+.+.+..+.+.
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 799999999999999999998888777666554
No 43
>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=82.09 E-value=0.24 Score=38.66 Aligned_cols=31 Identities=23% Similarity=0.269 Sum_probs=26.1
Q ss_pred eeEEEeccCCCcchhhhcccccccccchhhh
Q 015432 115 AIALRRLSSGESLQIIGDLFGLNQSTVSQVT 145 (407)
Q Consensus 115 ~i~L~~La~g~s~~~la~~Fgis~sTvsr~i 145 (407)
...+.+++.|.+...||..+|||++||+++.
T Consensus 41 ~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 41 LQVAKMLKQGKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 3344568899999999999999999999954
No 44
>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=81.62 E-value=0.65 Score=41.21 Aligned_cols=50 Identities=28% Similarity=0.268 Sum_probs=42.7
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhcc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGL 157 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~ 157 (407)
.++.+++-++.|+|+ .|.++..||..+|+|.+||...+.+....|.+.+.
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 377788887778776 79999999999999999999999988888877654
No 45
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=81.00 E-value=0.42 Score=44.33 Aligned_cols=51 Identities=20% Similarity=0.307 Sum_probs=43.5
Q ss_pred CCChhcceeeEEEec---cCCCcchhhhcccccccccchhhhHHHHHHHHHhcc
Q 015432 107 PLSPNDMVAIALRRL---SSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGL 157 (407)
Q Consensus 107 ~l~~~~ql~i~L~~L---a~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~ 157 (407)
.+|..++-++.|+|. -.|.++..||..+|||.+||.....+....|-+.+.
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 388888888888874 579999999999999999999999888888776543
No 46
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=80.95 E-value=0.58 Score=44.20 Aligned_cols=50 Identities=22% Similarity=0.272 Sum_probs=43.3
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhcc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGL 157 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~ 157 (407)
.+++.++..+.|+|+ .+.++..||..+|||.+||+++..+...-|...+.
T Consensus 205 ~L~~~er~vi~l~y~-e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l~ 254 (257)
T PRK05911 205 ALEEKERKVMALYYY-EELVLKEIGKILGVSESRVSQIHSKALLKLRATLS 254 (257)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 388899999998886 68999999999999999999999988887776543
No 47
>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=80.81 E-value=0.83 Score=32.05 Aligned_cols=29 Identities=24% Similarity=0.331 Sum_probs=24.5
Q ss_pred CCcchhhhcccccccccchhhhHHHHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVESM 152 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~al 152 (407)
..+..+||..+|||++|++..+++...-|
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae~kl 51 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAERKL 51 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 46678999999999999999998876554
No 48
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=80.78 E-value=1 Score=41.85 Aligned_cols=71 Identities=11% Similarity=0.161 Sum_probs=53.7
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhccccccCCChhhHHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGLHHLQWPSKETEMEDIKSKFEK 178 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~~~i~~P~~~~~~~~i~~~f~~ 178 (407)
.+|..++.++.|.++- |.++.+||..+|+|.+||...+.+....|.+.+......+....+...+...|.+
T Consensus 116 ~Lp~~~R~v~lL~~~e-g~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~~~~~~~~~~~~~~~~~~~~~ 186 (228)
T PRK06704 116 SLNVQQSAILLLKDVF-QYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEEGIEIVEFTDDMEVVVTSIRE 186 (228)
T ss_pred hCCHHHhhHhhhHHhh-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcCCCCCccccHHHHHHHHHh
Confidence 4788888888887754 8999999999999999999999999988887765544333223356666666654
No 49
>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=80.50 E-value=0.41 Score=40.96 Aligned_cols=46 Identities=20% Similarity=0.282 Sum_probs=39.6
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
++..++-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+
T Consensus 114 L~~~~r~il~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 114 LPEQCRKIFILSRF-EGKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 67788888888776 59999999999999999999998887776654
No 50
>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=80.50 E-value=0.6 Score=39.14 Aligned_cols=47 Identities=26% Similarity=0.370 Sum_probs=38.4
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.++..++-.+.+.++ .|.++.+||..+|+|.+||++...+....|.+
T Consensus 110 ~L~~~~~~ii~~~~~-~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYL-EGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 367777777666655 69999999999999999999999888776654
No 51
>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=80.41 E-value=0.98 Score=40.39 Aligned_cols=49 Identities=18% Similarity=0.152 Sum_probs=41.8
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|...+-++.|.++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 131 ~Lp~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 131 GLPEEFRQAVYLADV-EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred hCCHHHhhheeehhh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888776 5999999999999999999999888887776544
No 52
>PHA00675 hypothetical protein
Probab=80.12 E-value=0.52 Score=35.38 Aligned_cols=25 Identities=12% Similarity=0.368 Sum_probs=22.0
Q ss_pred cCCCcchhhhcccccccccchhhhH
Q 015432 122 SSGESLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 122 a~g~s~~~la~~Fgis~sTvsr~i~ 146 (407)
+.|.++..||..||||+|||+.|.+
T Consensus 37 r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 37 VEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred hcCccHHHHHHHhCCCHHHHHHHHc
Confidence 4588999999999999999998754
No 53
>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=79.75 E-value=0.43 Score=33.06 Aligned_cols=33 Identities=21% Similarity=0.435 Sum_probs=28.1
Q ss_pred ccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 121 LSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 121 La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
+..|.++.++|..+++|.+||.+.+.+....+.
T Consensus 12 ~~~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~ 44 (57)
T cd06170 12 LAEGKTNKEIADILGISEKTVKTHLRNIMRKLG 44 (57)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 357899999999999999999999987766553
No 54
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=79.55 E-value=2.1 Score=38.18 Aligned_cols=49 Identities=20% Similarity=0.202 Sum_probs=40.9
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|+.++.++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 139 ~L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 139 TLPDEQREVFLLREH-GDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred hCCHhHhhheeeehc-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 378888888888764 6999999999999999999988888777776543
No 55
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=79.00 E-value=0.71 Score=42.44 Aligned_cols=49 Identities=18% Similarity=0.078 Sum_probs=43.0
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|..++-++.|+|+ .|.++..||..+|||.+||...+.+....|.+.+
T Consensus 134 ~Lp~~~R~v~~L~y~-eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 134 KLPVEYREVLVLREL-EDMSYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCHHHHhHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 488889999999888 5999999999999999999999988888777654
No 56
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=78.88 E-value=1.8 Score=40.02 Aligned_cols=49 Identities=20% Similarity=0.148 Sum_probs=41.8
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhcc
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGL 157 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~ 157 (407)
+|..++-++.|+++. |.++..||..+|+|.+||...+.+....|.+.+.
T Consensus 150 L~~~~r~i~~l~~~~-g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~ 198 (231)
T PRK11922 150 LPDAFRAVFVLRVVE-ELSVEETAQALGLPEETVKTRLHRARRLLRESLA 198 (231)
T ss_pred CCHHHhhhheeehhc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 788888888887765 9999999999999999999988888877776543
No 57
>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=78.69 E-value=0.52 Score=40.97 Aligned_cols=47 Identities=19% Similarity=0.340 Sum_probs=41.3
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.+|+.++.++.|+|+ .|.++..||..+|||.+||...+.+....|.+
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 488999999999777 49999999999999999999998888777654
No 58
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=78.68 E-value=0.87 Score=36.09 Aligned_cols=39 Identities=18% Similarity=0.191 Sum_probs=32.1
Q ss_pred eeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 115 AIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 115 ~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
-+-|+| ....|+..||+.|+||+++|+..|.+++..|..
T Consensus 25 Y~~lyy-~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~ 63 (105)
T COG2739 25 YLELYY-LDDLSLSEIAEEFNVSRQAIYDNIKRTEKILED 63 (105)
T ss_pred HHHHHH-HhhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 333444 457889999999999999999999999998864
No 59
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=78.64 E-value=0.66 Score=41.03 Aligned_cols=49 Identities=22% Similarity=0.238 Sum_probs=42.1
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|..++-++.|.|+ .|.++..||..+|||.+||...+.+....|...+
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 378888888888877 6999999999999999999999888887776543
No 60
>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=78.38 E-value=0.21 Score=37.46 Aligned_cols=40 Identities=23% Similarity=0.214 Sum_probs=34.2
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHH
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~ 147 (407)
+|...+.+..|.+.-.|.++.+||..+|||.+||..++..
T Consensus 16 l~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 16 VDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred CCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 6777777777777778999999999999999999987654
No 61
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=78.13 E-value=0.96 Score=43.43 Aligned_cols=49 Identities=18% Similarity=0.256 Sum_probs=42.9
Q ss_pred CCChhcceeeEEEecc-CCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRLS-SGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La-~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.++..++..+.++|+. .+.++..||..+|||+++|+++..+.+.-|-..
T Consensus 230 ~L~~rEr~VL~lry~~~~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~ 279 (284)
T PRK06596 230 GLDERSRDIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAMKKLKAA 279 (284)
T ss_pred cCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4889999999999975 588999999999999999999998887777654
No 62
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=78.09 E-value=0.78 Score=40.57 Aligned_cols=49 Identities=20% Similarity=0.129 Sum_probs=42.7
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|..++-++.|.++. |.++..||..+|||.+||...+.+....|.+.+
T Consensus 127 ~L~~~~r~v~~l~~~~-g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 127 SLPIKYREVIYLFYYE-ELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred hCCHHHhhHhHhHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3888999999998875 999999999999999999999888887776543
No 63
>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=77.84 E-value=1.1 Score=38.01 Aligned_cols=47 Identities=21% Similarity=0.268 Sum_probs=38.2
Q ss_pred CCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 106 KPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 106 ~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
..++..++-.+.| +..|.++..||..+|+|++||+++..+...-|..
T Consensus 5 ~~Lte~qr~VL~L--r~~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 5 TFLTERQIKVLEL--REKGLSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred CCCCHHHHHHHHH--HHcCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 3467777777777 3699999999999999999999988887776653
No 64
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=77.09 E-value=0.55 Score=42.01 Aligned_cols=49 Identities=12% Similarity=0.079 Sum_probs=42.6
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|...+-++.|+++- |.++..||..+|+|.+||...+.+....|.+.+
T Consensus 134 ~Lp~~~R~v~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 134 HLPAQQARVFMMREYL-ELSSEQICQECDISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred hCCHHHHHHHhHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3888899999998876 999999999999999999998888887776543
No 65
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=77.00 E-value=0.59 Score=40.42 Aligned_cols=49 Identities=18% Similarity=0.188 Sum_probs=41.2
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|+.++-++.|.|+. |.++.+||..+|+|.+||...+.+...-|...+
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 3788888888887765 999999999999999999998888777776543
No 66
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=76.96 E-value=0.68 Score=42.95 Aligned_cols=49 Identities=18% Similarity=0.251 Sum_probs=41.9
Q ss_pred CCChhcceeeEEEec---cCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRL---SSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~L---a~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.+|+.++..+.|+|+ -.|.++..||..+|+|.+||.+...+....|...
T Consensus 175 ~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred hCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 489999999999886 4678999999999999999999888777766654
No 67
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=76.70 E-value=0.69 Score=40.75 Aligned_cols=48 Identities=17% Similarity=0.153 Sum_probs=41.7
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.+|.+++-.+.|.++ .|.++..||..+|+|.+||...+.+....|.+.
T Consensus 129 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 129 ELEKDRAAAVRRAYL-EGLSYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 388888888888876 789999999999999999999988888777654
No 68
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=76.56 E-value=0.73 Score=41.15 Aligned_cols=52 Identities=21% Similarity=0.221 Sum_probs=44.0
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhcccc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGLHH 159 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~~~ 159 (407)
.++.+++-++.|+++ .|.++..||..+|+|..||...+.+....|.+.+..+
T Consensus 138 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~ 189 (193)
T PRK11923 138 QLPEDLRTALTLREF-DGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQPL 189 (193)
T ss_pred hCCHHHhHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 378888888888876 6999999999999999999999988888887655433
No 69
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=76.49 E-value=0.83 Score=39.85 Aligned_cols=48 Identities=23% Similarity=0.239 Sum_probs=40.8
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
+|+.++-++.|.++ .|.++.+||..+|+|.+||.+.+.+....|.+.+
T Consensus 126 L~~~~r~i~~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 126 LPVKQREVFLLRYV-EGLSYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred CCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 77778887777776 6999999999999999999999988877776543
No 70
>PRK15320 transcriptional activator SprB; Provisional
Probab=76.43 E-value=0.81 Score=41.04 Aligned_cols=38 Identities=29% Similarity=0.283 Sum_probs=33.8
Q ss_pred eEEEeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 116 IALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 116 i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
-.|..|+.|.+...||+.|++|.+||+.+..+...-+.
T Consensus 171 EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLg 208 (251)
T PRK15320 171 ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLG 208 (251)
T ss_pred HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence 56778999999999999999999999999888777664
No 71
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=76.40 E-value=1.7 Score=38.00 Aligned_cols=49 Identities=14% Similarity=0.146 Sum_probs=41.6
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|..++-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.+
T Consensus 120 ~L~~~~r~vl~l~~~-~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 120 TLSLEHRAVLVLHDL-EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred hCCHHHeeeeeehHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 378888888888776 5889999999999999999999988888877654
No 72
>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=75.75 E-value=1.1 Score=35.45 Aligned_cols=24 Identities=17% Similarity=0.270 Sum_probs=21.2
Q ss_pred cCCCcchhhhcccccccccchhhh
Q 015432 122 SSGESLQIIGDLFGLNQSTVSQVT 145 (407)
Q Consensus 122 a~g~s~~~la~~Fgis~sTvsr~i 145 (407)
..+.+|+.|+...|||.+||+|+-
T Consensus 53 ~~~~tQrEIa~~lGiS~atIsR~s 76 (94)
T TIGR01321 53 NGNMSQREIASKLGVSIATITRGS 76 (94)
T ss_pred hCCCCHHHHHHHhCCChhhhhHHH
Confidence 357899999999999999999864
No 73
>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=75.74 E-value=0.71 Score=40.77 Aligned_cols=47 Identities=19% Similarity=0.299 Sum_probs=40.8
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
+|+.++-++.|+++ .|.++.+||..+|||.+||...+.+....|.+.
T Consensus 135 Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 135 VDPRQAEVVELRFF-AGLTVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 88888888888776 599999999999999999999998888877653
No 74
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=75.55 E-value=0.81 Score=40.73 Aligned_cols=49 Identities=18% Similarity=0.176 Sum_probs=41.9
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|...+-++.|+++ .|.++..||..+|||.+||...+.+....|...+
T Consensus 111 ~Lp~~~R~v~~L~~~-eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 111 DLPEEQRAALHLVAI-EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 388889999999888 5999999999999999999998888777776543
No 75
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=75.43 E-value=0.72 Score=40.10 Aligned_cols=49 Identities=24% Similarity=0.152 Sum_probs=42.6
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|+.++-++.|.++ .|.++.+||..+|||.+||...+.+....|.+.+
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 378888888888887 7999999999999999999999988888776543
No 76
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=75.07 E-value=0.77 Score=41.03 Aligned_cols=50 Identities=20% Similarity=0.158 Sum_probs=43.2
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhcc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGL 157 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~ 157 (407)
.||+.++-++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+.
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 378888888888877 79999999999999999999998888888776543
No 77
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=74.92 E-value=1.1 Score=39.48 Aligned_cols=49 Identities=24% Similarity=0.307 Sum_probs=42.2
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|+.++-++.|.++ .|.++..||..+|+|.+||...+.+....|...+
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 478888888888776 5999999999999999999999988888776644
No 78
>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=74.89 E-value=0.99 Score=38.96 Aligned_cols=48 Identities=19% Similarity=0.206 Sum_probs=41.3
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
+|..++.++.|.++ .|.++.+||..+|+|.+||...+.+....|.+.+
T Consensus 111 L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 111 LPARQRAVVVLRYY-EDLSEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred CCHHHHHHhhhHHH-hcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 77888888877774 5999999999999999999999999888887643
No 79
>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=74.85 E-value=0.75 Score=39.49 Aligned_cols=47 Identities=19% Similarity=0.256 Sum_probs=40.7
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.+|+.++-.+.|+++ .|.++..||..+|||.+||...+.+.-..|.+
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 388888888888776 79999999999999999999988887777654
No 80
>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=74.82 E-value=1.2 Score=27.75 Aligned_cols=25 Identities=32% Similarity=0.413 Sum_probs=19.3
Q ss_pred CcchhhhcccccccccchhhhHHHH
Q 015432 125 ESLQIIGDLFGLNQSTVSQVTWRFV 149 (407)
Q Consensus 125 ~s~~~la~~Fgis~sTvsr~i~~~~ 149 (407)
.+..+||+..|++..||||++.++-
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 3567999999999999999987653
No 81
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=74.74 E-value=0.97 Score=40.11 Aligned_cols=50 Identities=14% Similarity=0.096 Sum_probs=43.2
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhcc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGL 157 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~ 157 (407)
.+|..++-++.|.++. |.++..||..+|+|..||...+.+....|...+.
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 3788889888888875 9999999999999999999999888888776543
No 82
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=74.72 E-value=1.2 Score=39.50 Aligned_cols=49 Identities=29% Similarity=0.369 Sum_probs=43.0
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhcc
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGL 157 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~ 157 (407)
+|++++-++.|.++ .|.+|..||..+|||.+||...+.+....|.+.+.
T Consensus 128 Lp~~~R~~~~l~~~-~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 128 LPPRQREAFLLRYL-EGLSYEEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred CCHHHhHHhhhHhh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 88888988888887 59999999999999999999999888888876543
No 83
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=74.50 E-value=0.99 Score=40.43 Aligned_cols=49 Identities=22% Similarity=0.263 Sum_probs=42.6
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|..++-++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 136 NLPENTARVFTLKEI-LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred hCCHHHHHHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 378888888888777 6999999999999999999999988888887654
No 84
>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=73.74 E-value=3.4 Score=29.29 Aligned_cols=25 Identities=24% Similarity=0.380 Sum_probs=20.4
Q ss_pred CcchhhhcccccccccchhhhHHHH
Q 015432 125 ESLQIIGDLFGLNQSTVSQVTWRFV 149 (407)
Q Consensus 125 ~s~~~la~~Fgis~sTvsr~i~~~~ 149 (407)
.+..+|+..++++++||++++.+..
T Consensus 22 ~t~~~la~~l~~~~~~vs~~v~~L~ 46 (62)
T PF12802_consen 22 LTQSELAERLGISKSTVSRIVKRLE 46 (62)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4678999999999999999876654
No 85
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=73.52 E-value=1.9 Score=38.41 Aligned_cols=48 Identities=21% Similarity=0.261 Sum_probs=39.6
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
+|..++=++.|.++ .|.++..||..+|||.+||...+.+....|-+.+
T Consensus 135 L~~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 135 VNPIDREILVLRFV-AELEFQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred cChhheeeeeeHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 67776666666665 6899999999999999999999888888777644
No 86
>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=73.47 E-value=0.17 Score=37.74 Aligned_cols=42 Identities=33% Similarity=0.411 Sum_probs=31.8
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccc-cccccchhhhHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFG-LNQSTVSQVTWRF 148 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fg-is~sTvsr~i~~~ 148 (407)
.+.-.-++++.|.+-.++.++.+||..|| .+.|||...++++
T Consensus 28 ~i~~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHstV~~a~~ki 70 (70)
T PF08299_consen 28 KIVEARQVAMYLARELTGLSLSEIGRYFGGRDHSTVIHAIRKI 70 (70)
T ss_dssp HHHHHHHHHHHHHHHHS---HHHHHHHCTSSTHHHHHHHHHHH
T ss_pred hhcchHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHHhC
Confidence 35556788888888778999999999999 9999998776653
No 87
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=73.26 E-value=0.73 Score=39.68 Aligned_cols=50 Identities=14% Similarity=0.104 Sum_probs=43.4
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhcc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGL 157 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~ 157 (407)
.+|..++-++.|+|+ .|.++..||..+|||.+||...+.+....|...+.
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 488888888888876 59999999999999999999999998888876543
No 88
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=73.02 E-value=1.3 Score=37.74 Aligned_cols=46 Identities=26% Similarity=0.367 Sum_probs=37.4
Q ss_pred CCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 106 KPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 106 ~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
..+++.++-.+.| ...|.++..||..+|+|++||+.+..+...-|.
T Consensus 5 ~~Lt~rqreVL~l--r~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr 50 (141)
T PRK03975 5 SFLTERQIEVLRL--RERGLTQQEIADILGTSRANVSSIEKRARENIE 50 (141)
T ss_pred cCCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4477777777777 368999999999999999999999887666544
No 89
>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=72.98 E-value=1.5 Score=40.89 Aligned_cols=48 Identities=13% Similarity=0.293 Sum_probs=41.9
Q ss_pred CCChhcceeeEEEec---cCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRL---SSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 107 ~l~~~~ql~i~L~~L---a~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.++..++..+.|+|. ..+.++..||..+|||.++|+++..+.+.-|..
T Consensus 176 ~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~ 226 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRH 226 (238)
T ss_pred hCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 388899999999984 577899999999999999999998888777764
No 90
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=72.96 E-value=0.99 Score=39.98 Aligned_cols=48 Identities=23% Similarity=0.174 Sum_probs=40.8
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.+|+.++.++.|.+ -.|.++.+||..+|||.+||...+.+....|.+.
T Consensus 133 ~L~~~~r~i~~l~~-~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 133 QLEPARRNCILHAY-VDGCSHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 37888887777775 4799999999999999999999999888877653
No 91
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=72.75 E-value=0.86 Score=40.93 Aligned_cols=48 Identities=21% Similarity=0.258 Sum_probs=42.1
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.+|..++-++.|+++ .|.++..||..+|||.+||...+.+....|...
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 136 ALPERQRQAVVLRHI-EGLSNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 388888888888877 799999999999999999999998888777654
No 92
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=72.74 E-value=0.93 Score=42.77 Aligned_cols=49 Identities=12% Similarity=0.110 Sum_probs=42.4
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.++..++..+.|+|+ .|.++..||..+|+|.+||++...+...-|...+
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 5999999999999999999999998888776543
No 93
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=72.44 E-value=2.1 Score=39.77 Aligned_cols=48 Identities=15% Similarity=0.109 Sum_probs=41.3
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
||..++-++.|+|+ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 172 Lp~~~R~v~~L~~~-eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 172 LPEQQRIAVILSYH-ENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred CCHHHHHHhhhHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 78888888787775 5999999999999999999999988888887643
No 94
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=72.28 E-value=1.4 Score=39.48 Aligned_cols=50 Identities=22% Similarity=0.155 Sum_probs=44.1
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhcc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGL 157 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~ 157 (407)
.+|+.++-++.|+++ .|.++..||..+|||.+||...+.+....|.+.+.
T Consensus 113 ~Lp~~~r~v~~L~~~-~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 113 QLPDEQREALILVGA-SGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred hCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 488899999999888 79999999999999999999999888888876543
No 95
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=72.09 E-value=1.4 Score=39.72 Aligned_cols=53 Identities=13% Similarity=0.126 Sum_probs=44.9
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhccccc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGLHHL 160 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~~~i 160 (407)
.+|+..+-++.|.++ .|.++..||..+|+|.+||...+.+....|.+.+..+.
T Consensus 133 ~Lp~~~r~v~~l~~~-~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 185 (196)
T PRK12535 133 ALPPERREALILTQV-LGYTYEEAAKIADVRVGTIRSRVARARADLIAATATGQ 185 (196)
T ss_pred cCCHHHHHHhhhHHH-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcccc
Confidence 378888888888776 48999999999999999999999999988887766543
No 96
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=72.05 E-value=1.1 Score=39.85 Aligned_cols=50 Identities=18% Similarity=0.101 Sum_probs=43.3
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhcc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGL 157 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~ 157 (407)
.+|..++-++.|.++ .|.++.+||..+|+|.+||...+.+....|.+.+.
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 378888888888876 79999999999999999999999888888876554
No 97
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=72.03 E-value=1.1 Score=39.77 Aligned_cols=47 Identities=15% Similarity=0.078 Sum_probs=39.7
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
+|..++-++.|.++ .|.++..||..+|+|.+||...+.+....|...
T Consensus 138 L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 138 LEPPRSELIRTAFF-EGITYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 67777777777664 799999999999999999999998888777654
No 98
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=71.97 E-value=1 Score=39.86 Aligned_cols=48 Identities=23% Similarity=0.279 Sum_probs=41.8
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
+|..++.++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 136 L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 136 LSPEERRVIEVLYY-QGYTHREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 78888888888875 5999999999999999999999998888876644
No 99
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=71.91 E-value=1.1 Score=43.03 Aligned_cols=50 Identities=26% Similarity=0.468 Sum_probs=43.9
Q ss_pred CCChhcceeeEEEec-cCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRL-SSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~L-a~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.++..++..+.|+|+ ..|.++..||..+|||++||+++..+.+.-|...+
T Consensus 227 ~L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l 277 (289)
T PRK07500 227 TLNERELRIIRERRLREDGATLEALGEELGISKERVRQIEARALEKLRRAL 277 (289)
T ss_pred cCCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 389999999999886 36899999999999999999999999888887654
No 100
>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=71.89 E-value=0.68 Score=32.84 Aligned_cols=37 Identities=27% Similarity=0.416 Sum_probs=30.0
Q ss_pred EEEeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 117 ALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 117 ~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
+|..++.|.+...||...+||.+||..+..++..-|.
T Consensus 11 vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 11 VLRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp HHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 4566788999999999999999999998877666553
No 101
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=71.82 E-value=0.85 Score=40.65 Aligned_cols=49 Identities=24% Similarity=0.312 Sum_probs=42.5
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|.+++-++.|+++ .|.++.+||..+|+|.+||...+.+....|...+
T Consensus 131 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 131 KLSPAHREIIDLVYY-HEKSVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 488888888888887 7999999999999999999999888777776543
No 102
>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=71.73 E-value=1.5 Score=41.04 Aligned_cols=49 Identities=29% Similarity=0.358 Sum_probs=42.9
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|..++-++.|+++ .|.++..||..+|||.+||...+.+....|.+.+
T Consensus 161 ~Lp~~~R~v~~L~~~-eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 161 ALSERERHLLRLHFV-DGLSMDRIGAMYQVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 388888988888887 7999999999999999999999998888876643
No 103
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=71.50 E-value=1.1 Score=39.19 Aligned_cols=52 Identities=13% Similarity=0.054 Sum_probs=40.9
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhccccc
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGLHHL 160 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~~~i 160 (407)
+|+..+-++.|.|+ .|.++..||..+|+|.+||...+.+....|...+..+|
T Consensus 120 L~~~~r~i~~l~~~-~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~~ 171 (173)
T PRK12522 120 LNEKYKTVLVLYYY-EQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEGFV 171 (173)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 66666655555444 69999999999999999999999998888877665443
No 104
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=71.33 E-value=3.9 Score=39.94 Aligned_cols=64 Identities=13% Similarity=0.091 Sum_probs=44.9
Q ss_pred EeccCCCcchhhhcccccccccchhhhHHHHHH-HHHhccccccCCChhhHHHHHHHHHHhhhCCcceee
Q 015432 119 RRLSSGESLQIIGDLFGLNQSTVSQVTWRFVES-MEERGLHHLQWPSKETEMEDIKSKFEKIRGFRNCCG 187 (407)
Q Consensus 119 ~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~a-l~~~~~~~i~~P~~~~~~~~i~~~f~~~~~fp~~vG 187 (407)
.|+-.|.++.+||..+|||+++|+|++.+.-+. |. .-.|.-|.. ...++...+++.+|+..|+-
T Consensus 24 lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV---~I~I~~~~~--~~~~Le~~L~~~fgLk~~iV 88 (318)
T PRK15418 24 FYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGII---RVQINSRFE--GCLELENALRQHFSLQHIRV 88 (318)
T ss_pred HHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcE---EEEEeCCCc--cHHHHHHHHHHHhCCCEEEE
Confidence 345579999999999999999999987653321 11 223444543 35567777788888888873
No 105
>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=71.29 E-value=1.8 Score=29.25 Aligned_cols=27 Identities=19% Similarity=0.294 Sum_probs=21.7
Q ss_pred CCcchhhhcccccccccchhhhHHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
+.+..++|..+|+|.+||++++.+..+
T Consensus 17 ~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 17 RITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 577889999999999999999887653
No 106
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=71.27 E-value=1.2 Score=41.22 Aligned_cols=49 Identities=18% Similarity=0.257 Sum_probs=42.4
Q ss_pred CCChhcceeeEEEec---cCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRL---SSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~L---a~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.+|..++-++.|+|+ -.|.++..||..+|+|.+||.+...+....|...
T Consensus 174 ~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~ 225 (227)
T TIGR02846 174 VLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKE 225 (227)
T ss_pred hCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 388889999999886 4889999999999999999999988888777654
No 107
>PHA00542 putative Cro-like protein
Probab=70.99 E-value=1.7 Score=33.31 Aligned_cols=50 Identities=16% Similarity=0.177 Sum_probs=36.4
Q ss_pred EEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhccccccCCChhhHHHHHHHHHHhh
Q 015432 118 LRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGLHHLQWPSKETEMEDIKSKFEKI 179 (407)
Q Consensus 118 L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~~~i~~P~~~~~~~~i~~~f~~~ 179 (407)
..+...|.+...+|...|||++|++++.+. ...-|+.+ .+..+++.+.+.
T Consensus 25 ~~l~~~glTq~elA~~lgIs~~tIsr~e~g-----------~~~~p~~~-~l~ki~~~~~~~ 74 (82)
T PHA00542 25 CALIRAGWSQEQIADATDVSQPTICRIYSG-----------RHKDPRYS-VVEKLRHLVLNL 74 (82)
T ss_pred HHHHHCCCCHHHHHHHHCcCHHHHHHHHcC-----------CCCCCCHH-HHHHHHHHHHHh
Confidence 345678999999999999999999997532 11235555 677777776654
No 108
>PRK05572 sporulation sigma factor SigF; Validated
Probab=70.75 E-value=1.2 Score=41.89 Aligned_cols=48 Identities=19% Similarity=0.378 Sum_probs=42.0
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.+|..++.++.|+|+ .|.++..||..+|+|.+||+++..+.+.-|...
T Consensus 202 ~L~~~~~~v~~l~~~-~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~ 249 (252)
T PRK05572 202 ELDERERLIVYLRYF-KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEK 249 (252)
T ss_pred cCCHHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 488888988888876 589999999999999999999999988877654
No 109
>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=70.62 E-value=2 Score=41.23 Aligned_cols=51 Identities=18% Similarity=0.173 Sum_probs=44.3
Q ss_pred CCChhcceeeEEEe-c--cCCCcchhhhcccccccccchhhhHHHHHHHHHhcc
Q 015432 107 PLSPNDMVAIALRR-L--SSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGL 157 (407)
Q Consensus 107 ~l~~~~ql~i~L~~-L--a~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~ 157 (407)
.||..++..+.|+| | -.|.++..||..+|||.+||.+...+....|...+.
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 48999999999887 4 468999999999999999999999998888876553
No 110
>PF13551 HTH_29: Winged helix-turn helix
Probab=70.53 E-value=0.85 Score=36.62 Aligned_cols=33 Identities=30% Similarity=0.373 Sum_probs=28.2
Q ss_pred EEeccCCCc-chhhhcccccccccchhhhHHHHH
Q 015432 118 LRRLSSGES-LQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 118 L~~La~g~s-~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
|..++.|.+ ...+|..+|||.+||++++.++..
T Consensus 5 l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~ 38 (112)
T PF13551_consen 5 LLLLAEGVSTIAEIARRLGISRRTVYRWLKRYRE 38 (112)
T ss_pred HHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHc
Confidence 345678885 999999999999999999988754
No 111
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=70.50 E-value=1.1 Score=39.63 Aligned_cols=49 Identities=12% Similarity=0.193 Sum_probs=42.4
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|..++-.+.|+|+. |.++..||..+|+|.+||...+.+....|.+.+
T Consensus 131 ~L~~~~r~v~~l~~~~-g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVE-GASIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 3788888888887776 999999999999999999999998888887654
No 112
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=70.48 E-value=1.3 Score=39.40 Aligned_cols=49 Identities=24% Similarity=0.181 Sum_probs=41.0
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|+.++.++.|.++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 106 ~L~~~~r~i~~l~~~-~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 106 ALPEKYAEALRLTEL-EGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred hCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 378888888888765 6999999999999999999998888777776544
No 113
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=70.21 E-value=1.8 Score=38.62 Aligned_cols=49 Identities=12% Similarity=0.072 Sum_probs=41.8
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|+.++-++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 131 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 131 RLPPRTGRVFMMREW-LELETEEICQELQITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 388888888888876 4899999999999999999998888888776654
No 114
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=70.11 E-value=1 Score=38.87 Aligned_cols=46 Identities=20% Similarity=0.152 Sum_probs=39.1
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
.+|+.++-++.|.++ .|.++..||..+|+|.+||...+.+....|.
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 478888888888776 5999999999999999999988887766654
No 115
>PF13751 DDE_Tnp_1_6: Transposase DDE domain
Probab=70.10 E-value=1.9 Score=35.68 Aligned_cols=49 Identities=10% Similarity=0.090 Sum_probs=35.5
Q ss_pred hhhhhhhhh-HHHHHHHHHHhHHHhhcccccCCCCCchhHHHHHHHHHhhhh
Q 015432 307 NKRHSATRM-VAQMALARLKDVWRIIHGVMWMPDKNRLPRIVLVCCLLHNIV 357 (407)
Q Consensus 307 N~~ls~~R~-~vE~afg~LK~rfriL~~~~~~~~~~~~~~ii~accvLHN~~ 357 (407)
.+.+.+.|. .||..||.||. +--|..... ....++..-+...|+.|||-
T Consensus 73 ~k~~y~~R~~~VE~~fg~~K~-~~g~~r~~~-rG~~kv~~~~~l~a~a~Nl~ 122 (125)
T PF13751_consen 73 GKELYKQRSIKVEGVFGTIKR-NHGLRRFRY-RGLEKVRIEFLLAAIAYNLK 122 (125)
T ss_pred hhhhhheeecccccccccchh-ccCCccccc-cchhhhHHHHHHHHHHHHHH
Confidence 346677787 99999999994 444544432 35667777788888899985
No 116
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=69.91 E-value=1.1 Score=40.20 Aligned_cols=49 Identities=16% Similarity=0.119 Sum_probs=41.5
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|.+++-++.|+++ .|.++..||..+|||.+||...+.+....|...+
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 378888888888877 6999999999999999999888888777776543
No 117
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=69.81 E-value=1.1 Score=38.61 Aligned_cols=49 Identities=18% Similarity=0.059 Sum_probs=41.0
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|+.++-++.|.++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 106 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 106 ELPENYRDVVLAHYL-EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred hCCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 378888887777765 5999999999999999999998888877776654
No 118
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=69.78 E-value=1.5 Score=38.93 Aligned_cols=49 Identities=20% Similarity=0.173 Sum_probs=42.8
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|..++-++.|.++. |.++..||..+|+|.+||...+.+....|.+.+
T Consensus 131 ~L~~~~r~v~~l~~~~-g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 131 RLPEKMRLAIQAVKLE-GLSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred hCCHHHHHHHHHHHHc-CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3788888888888874 999999999999999999999999888887643
No 119
>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=69.68 E-value=1.5 Score=38.15 Aligned_cols=49 Identities=20% Similarity=0.259 Sum_probs=41.1
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|..++-++.|.++. |.++..||..+|||.+||...+.+....|.+.+
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 3777788777777775 999999999999999999999988888776543
No 120
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=69.64 E-value=1.2 Score=38.96 Aligned_cols=48 Identities=21% Similarity=0.239 Sum_probs=40.6
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.+|+.++.++.|+++ .|.++..||..+|+|.+||...+.+....+...
T Consensus 118 ~L~~~~r~v~~L~~~-eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 165 (168)
T PRK12525 118 GLSGKARAAFLMSQL-EGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQG 165 (168)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 388888888888764 699999999999999999999888877776553
No 121
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=69.59 E-value=1.8 Score=39.39 Aligned_cols=49 Identities=14% Similarity=0.078 Sum_probs=42.8
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|+.++-++.|+++- |.++..||..+|+|.+||...+.+....|.+.+
T Consensus 148 ~L~~~~r~v~~L~~~~-g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 148 GLPAKYARVFMMREFI-ELETNEICHAVDLSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3888899988888875 999999999999999999999988888887654
No 122
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=69.34 E-value=1.2 Score=39.82 Aligned_cols=48 Identities=19% Similarity=0.162 Sum_probs=40.2
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
+|+.++.++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 135 Lp~~~r~i~~l~~~-~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l 182 (192)
T PRK09643 135 LPVEQRAALVAVDM-QGYSVADAARMLGVAEGTVKSRCARGRARLAELL 182 (192)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 78888888888777 7999999999999999999888877776666543
No 123
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=69.33 E-value=1.6 Score=37.64 Aligned_cols=47 Identities=21% Similarity=0.196 Sum_probs=40.6
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.+|..++.++.|.++ .|.++..||..+|+|.+||...+.+....|.+
T Consensus 112 ~L~~~~r~v~~l~~~-~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 112 SLPLERRNVLLLRDY-YGFSYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HCCHHHHHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 488888988888776 49999999999999999999988888777654
No 124
>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=68.88 E-value=1.3 Score=39.22 Aligned_cols=48 Identities=21% Similarity=0.222 Sum_probs=40.7
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.+|+.++-++.|.++ .|.++..||..+|||.+||...+.+....|.+.
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 378888888878776 799999999999999999999988887777543
No 125
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=68.63 E-value=1.5 Score=38.94 Aligned_cols=47 Identities=19% Similarity=0.181 Sum_probs=40.9
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.+|+.++-++.|.++ .|.++..||..+|+|.+||...+.+....|.+
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 488888888888876 59999999999999999999998888777765
No 126
>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=68.54 E-value=1.3 Score=40.78 Aligned_cols=47 Identities=21% Similarity=0.337 Sum_probs=40.5
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.+|..++-++.|+|+ .|.++..||..+|+|.+||++...+....|..
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 378888888888775 58999999999999999999999988887764
No 127
>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=68.47 E-value=1.4 Score=40.79 Aligned_cols=50 Identities=18% Similarity=0.323 Sum_probs=42.7
Q ss_pred CCChhcceeeEEEec---cCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRL---SSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~L---a~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|..++..+.|+++ -.|.++..||...|||.+||.....+....|-+.+
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 489999999999885 37899999999999999999998888777776543
No 128
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=68.45 E-value=1.6 Score=40.47 Aligned_cols=48 Identities=23% Similarity=0.366 Sum_probs=41.4
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
+|+.++-.+.|+|+ .|.++..||..+|||.+||...+.+....|...+
T Consensus 185 L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 185 LPEREQLVLSLYYQ-EELNLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred CCHHHHHHHHhHhc-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 78888888888775 6899999999999999999999988888876654
No 129
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=68.15 E-value=2.1 Score=37.47 Aligned_cols=48 Identities=21% Similarity=0.171 Sum_probs=38.7
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.+|++++-++.|.++ .|.++..||..+|+|.+||...+.+....+...
T Consensus 119 ~L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~ 166 (172)
T PRK09651 119 GLNGKTREAFLLSQL-DGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLF 166 (172)
T ss_pred hCCHHHhHHhhhhhc-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 377777766666655 599999999999999999999888877776554
No 130
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=67.99 E-value=1.4 Score=41.54 Aligned_cols=48 Identities=21% Similarity=0.275 Sum_probs=41.1
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.+|+.++-++.|+|+ .|.++..||..+|||.+||.+...+....|...
T Consensus 205 ~L~~~~r~vl~l~~~-~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFI-ENLSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHh-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 378888888888775 699999999999999999999998888877654
No 131
>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=67.95 E-value=1.4 Score=40.79 Aligned_cols=47 Identities=21% Similarity=0.399 Sum_probs=40.0
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.++..++.++.|+|+ .|.++..||..+|||+++|+++..+...-|.+
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 478888888888765 68899999999999999999999888877754
No 132
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=67.48 E-value=4.4 Score=39.69 Aligned_cols=73 Identities=21% Similarity=0.293 Sum_probs=53.2
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhcccc---ccCCChhhHHHHHHHHHHhhhC
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGLHH---LQWPSKETEMEDIKSKFEKIRG 181 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~~~---i~~P~~~~~~~~i~~~f~~~~~ 181 (407)
.||..++-++.|+++ .|.++..||..+|+|.+||...+.+....|.+..+.. ..-|..+ +...+...|.+.++
T Consensus 153 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~~~~~~~~~~~~~-~~~~~v~~~~~A~~ 228 (339)
T PRK08241 153 HLPPRQRAVLILRDV-LGWSAAEVAELLDTSVAAVNSALQRARATLAERGPSAADTLREPDDP-EERALLARYVAAFE 228 (339)
T ss_pred hCCHHHhhhhhhHHh-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhcCCCcccccCCCCCh-HHHHHHHHHHHHHh
Confidence 378888888888775 5999999999999999999999999988888743221 1112223 55666666665543
No 133
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=67.31 E-value=1.4 Score=38.43 Aligned_cols=49 Identities=18% Similarity=0.155 Sum_probs=41.4
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|+.++-++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 118 ~L~~~~r~vl~L~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 118 QLSPEHRAVLVRSYY-RGWSTAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 378888888888776 4999999999999999999988888888777644
No 134
>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=67.08 E-value=2.3 Score=29.40 Aligned_cols=26 Identities=31% Similarity=0.350 Sum_probs=20.8
Q ss_pred CCcchhhhcccccccccchhhhHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFV 149 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~ 149 (407)
+.+..+|+...|+++||++|++....
T Consensus 18 ~~t~~eia~~~gl~~stv~r~L~tL~ 43 (52)
T PF09339_consen 18 PLTLSEIARALGLPKSTVHRLLQTLV 43 (52)
T ss_dssp CEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45688999999999999999876544
No 135
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=67.07 E-value=1.5 Score=41.32 Aligned_cols=48 Identities=19% Similarity=0.337 Sum_probs=40.5
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.++..++..+.|+|+ .|.++..||..+|||.+||+++..+...-|...
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 378888888888775 688999999999999999999998887777543
No 136
>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=66.85 E-value=3.3 Score=35.02 Aligned_cols=48 Identities=15% Similarity=0.124 Sum_probs=39.3
Q ss_pred CChhcceeeEEEeccC-CCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 108 LSPNDMVAIALRRLSS-GESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 108 l~~~~ql~i~L~~La~-g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
++.+++-.+-++|+.. ..++..||..+|+|++|+++.-.+++.-+...
T Consensus 83 Ld~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~ 131 (134)
T TIGR01636 83 ADEQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEE 131 (134)
T ss_pred CCHHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 6777888888888743 34899999999999999999988888777654
No 137
>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=66.84 E-value=3.7 Score=39.21 Aligned_cols=69 Identities=17% Similarity=0.263 Sum_probs=51.9
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhccccccCCChhhHHHHHHHHHHhh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGLHHLQWPSKETEMEDIKSKFEKI 179 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~~~i~~P~~~~~~~~i~~~f~~~ 179 (407)
.+|+.++-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+..+.. +...++...+.+.|...
T Consensus 108 ~L~~~~R~v~~L~~~-~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~~~---~~~~~~~~~~~~~f~~a 176 (281)
T TIGR02957 108 RLSPLERAVFVLREV-FDYPYEEIASIVGKSEANCRQLVSRARRHLDARRPRF---EVSREESRQLLERFVEA 176 (281)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCCC---CCChHHHHHHHHHHHHH
Confidence 478888888887765 4999999999999999999999999999988754422 12222455666666553
No 138
>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=66.68 E-value=0.85 Score=40.48 Aligned_cols=99 Identities=8% Similarity=-0.018 Sum_probs=58.4
Q ss_pred CChhHHHhhcCCCHHHHHHHHHHhhhhhhhhcCCCcCCCCCCCChhcceeeEEEeccC--------------CCcchhhh
Q 015432 66 KTSKNFESVFKISRKTFDYICSLVKEDLAARQSNFSFSNGKPLSPNDMVAIALRRLSS--------------GESLQIIG 131 (407)
Q Consensus 66 ~~d~~F~~~frmsr~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~~~ql~i~L~~La~--------------g~s~~~la 131 (407)
.+-+.|+..+.-++.--..++..+...+....... ..-...+++++|+-+|.+|+. ..+..+||
T Consensus 73 i~~~~~~~l~~~~p~l~~~~~~~l~~~l~~~~~~~--~~l~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA 150 (193)
T TIGR03697 73 VPIEQVEKAIEEDPDLSMLLLQGLSSRILQTEMMI--ETLAHRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIA 150 (193)
T ss_pred eeHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHH--HHHHhCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHH
Confidence 44556666655555544445554444333211100 011235788899988876632 24678999
Q ss_pred cccccccccchhhhHHHHHH-HHHhccccccCCChh
Q 015432 132 DLFGLNQSTVSQVTWRFVES-MEERGLHHLQWPSKE 166 (407)
Q Consensus 132 ~~Fgis~sTvsr~i~~~~~a-l~~~~~~~i~~P~~~ 166 (407)
...|+++.||+|+++++..- +.+.-...|..++.+
T Consensus 151 ~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~d~~ 186 (193)
T TIGR03697 151 EAIGSTRVTITRLLGDLRKKKLISIHKKKITVHDPI 186 (193)
T ss_pred HHhCCcHHHHHHHHHHHHHCCCEEecCCEEEEeCHH
Confidence 99999999999998877653 333333345555544
No 139
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=66.55 E-value=1.5 Score=38.77 Aligned_cols=47 Identities=23% Similarity=0.302 Sum_probs=39.4
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
+|..++.++.|+++ .|.++.+||..+|+|.+||...+.+....|...
T Consensus 130 L~~~~r~v~~l~~~-~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 130 LPDRQRLPIVHVKL-EGLSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 67777777666665 699999999999999999999998888777654
No 140
>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=66.42 E-value=3.1 Score=33.31 Aligned_cols=46 Identities=20% Similarity=0.224 Sum_probs=31.7
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
++-.++-.+- .|+-...|+..||..+|||+.+|+..+.+....|..
T Consensus 18 LT~kQ~~~l~-lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~ 63 (101)
T PF04297_consen 18 LTEKQREILE-LYYEEDLSLSEIAEELGISRQAVYDSIKRAEKKLEE 63 (101)
T ss_dssp S-HHHHHHHH-HHCTS---HHHHHHHCTS-HHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHH-HHHccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3333444444 445578999999999999999999999999888864
No 141
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=66.02 E-value=1.6 Score=39.39 Aligned_cols=49 Identities=12% Similarity=0.041 Sum_probs=42.0
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|+.++-++.|+|+ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 139 ~Lp~~~r~v~~L~~~-eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 139 HLPEQIGRVFMMREF-LDFEIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 388888888888876 5899999999999999999988888877776644
No 142
>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=65.95 E-value=1.5 Score=42.39 Aligned_cols=45 Identities=22% Similarity=0.294 Sum_probs=38.9
Q ss_pred CCChhcceeeEEEec---cCCCcchhhhcccccccccchhhhHHHHHH
Q 015432 107 PLSPNDMVAIALRRL---SSGESLQIIGDLFGLNQSTVSQVTWRFVES 151 (407)
Q Consensus 107 ~l~~~~ql~i~L~~L---a~g~s~~~la~~Fgis~sTvsr~i~~~~~a 151 (407)
.|+..++..+.|+|. ..+.++..||..+|||++||.++..+...-
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 388999999999985 578999999999999999999988776543
No 143
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=65.87 E-value=1.3 Score=37.72 Aligned_cols=46 Identities=17% Similarity=0.119 Sum_probs=38.8
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
.+|+.++-++.|.|+ .|.++.+||..+|+|.+||...+.+....|-
T Consensus 106 ~L~~~~r~ii~l~~~-~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 106 VLDEKEKYIIFERFF-VGKTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred hCCHHHHHHHHHHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 378888888888776 4899999999999999999998888766654
No 144
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=65.86 E-value=1.5 Score=38.37 Aligned_cols=47 Identities=23% Similarity=0.186 Sum_probs=39.9
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.+|..++-++.|+++ .|.++..||..+|+|.+||...+.+....+..
T Consensus 119 ~Lp~~~r~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 119 KLSSKARAAFLYNRL-DGMGHAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 378888888888876 59999999999999999999988877666654
No 145
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=65.70 E-value=2.1 Score=45.35 Aligned_cols=51 Identities=27% Similarity=0.335 Sum_probs=46.0
Q ss_pred CCCCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 104 NGKPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 104 ~~~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
+.+.+...-|++|.|.+=-++.++..||..||.+.|||...++++-..|.+
T Consensus 549 R~~~i~~aRqiAMYL~r~lt~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~~ 599 (617)
T PRK14086 549 RSRVLVTARQIAMYLCRELTDLSLPKIGQQFGRDHTTVMHADRKIRALMAE 599 (617)
T ss_pred CCcccchHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHh
Confidence 445688899999999999999999999999999999999999998887765
No 146
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=65.43 E-value=1.4 Score=39.68 Aligned_cols=82 Identities=16% Similarity=0.188 Sum_probs=47.2
Q ss_pred CChhHHHhhcCCCHHHHHHHHHHhhhhhhhhcCCCcCCCCCCCChhcceeeEEEeccC-------------CCcchhhhc
Q 015432 66 KTSKNFESVFKISRKTFDYICSLVKEDLAARQSNFSFSNGKPLSPNDMVAIALRRLSS-------------GESLQIIGD 132 (407)
Q Consensus 66 ~~d~~F~~~frmsr~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~~~ql~i~L~~La~-------------g~s~~~la~ 132 (407)
.+-+.|.+.+.-++.-...+...+...+....... ..-...++.++++-+|..|+. ..+..+||.
T Consensus 99 i~~~~~~~l~~~~p~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~ 176 (211)
T PRK11753 99 ISYKKFRQLIQVNPDILMALSAQMARRLQNTSRKV--GDLAFLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGR 176 (211)
T ss_pred EcHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHH--HHHHhcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHH
Confidence 34455555555444444444444433332211100 111346778888877766643 234578999
Q ss_pred ccccccccchhhhHHHH
Q 015432 133 LFGLNQSTVSQVTWRFV 149 (407)
Q Consensus 133 ~Fgis~sTvsr~i~~~~ 149 (407)
..|+++.|++|+++++.
T Consensus 177 ~lG~tr~tvsR~l~~l~ 193 (211)
T PRK11753 177 IVGCSREMVGRVLKMLE 193 (211)
T ss_pred HhCCCHHHHHHHHHHHH
Confidence 99999999999876644
No 147
>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=65.14 E-value=1.9 Score=33.07 Aligned_cols=22 Identities=23% Similarity=0.382 Sum_probs=18.8
Q ss_pred CcchhhhcccccccccchhhhH
Q 015432 125 ESLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 125 ~s~~~la~~Fgis~sTvsr~i~ 146 (407)
.+..+||..||||.+||++.+.
T Consensus 20 ~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 20 ATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred CCHHHHHHHhCCCHHHHHHHhc
Confidence 3567999999999999999763
No 148
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=64.85 E-value=2.9 Score=27.74 Aligned_cols=27 Identities=33% Similarity=0.393 Sum_probs=22.3
Q ss_pred CCcchhhhcccccccccchhhhHHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
..+..++|..+|+|++|+++++..+..
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 567889999999999999988766543
No 149
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=64.75 E-value=1.8 Score=37.57 Aligned_cols=49 Identities=14% Similarity=0.082 Sum_probs=41.0
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|+.++-++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 108 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 108 TLPVIEAQAILLCDV-HELTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred hCCHHHHHHHHhHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 378888887777665 6999999999999999999999988888776644
No 150
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=64.49 E-value=1.9 Score=38.18 Aligned_cols=50 Identities=12% Similarity=0.120 Sum_probs=41.6
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhcc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGL 157 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~ 157 (407)
.+|+.++-++.|.++ .|.++..||..+|+|.+||...+.+....|...+.
T Consensus 122 ~L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 171 (185)
T PRK12542 122 ELNESNRQVFKYKVF-YNLTYQEISSVMGITEANVRKQFERARKRVQNMIG 171 (185)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHc
Confidence 377777777777665 58999999999999999999998888888876543
No 151
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=64.33 E-value=2.2 Score=39.17 Aligned_cols=67 Identities=9% Similarity=0.167 Sum_probs=47.5
Q ss_pred CCChhcceeeEEEeccCC----CcchhhhcccccccccchhhhHHHHHH-HHHhccccccCCChhhHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSG----ESLQIIGDLFGLNQSTVSQVTWRFVES-MEERGLHHLQWPSKETEMEDIKS 174 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g----~s~~~la~~Fgis~sTvsr~i~~~~~a-l~~~~~~~i~~P~~~~~~~~i~~ 174 (407)
..+++++|+-+|..++.+ .+..+||..+|+++.|++|.+.++.+- +.+.....|..++.+ .+.+++.
T Consensus 148 ~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~~~i~I~d~~-~L~~~~~ 219 (226)
T PRK10402 148 SFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSKRGYLIKNRK-QLSGLAL 219 (226)
T ss_pred cChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeCCEEEEeCHH-HHHHHHH
Confidence 358899999998866533 356899999999999999998887763 334333455555555 5555543
No 152
>PF13730 HTH_36: Helix-turn-helix domain
Probab=64.28 E-value=2.9 Score=29.02 Aligned_cols=25 Identities=16% Similarity=0.238 Sum_probs=21.4
Q ss_pred CcchhhhcccccccccchhhhHHHH
Q 015432 125 ESLQIIGDLFGLNQSTVSQVTWRFV 149 (407)
Q Consensus 125 ~s~~~la~~Fgis~sTvsr~i~~~~ 149 (407)
.|+..||...|+|+.||.+++++..
T Consensus 26 pS~~~la~~~g~s~~Tv~~~i~~L~ 50 (55)
T PF13730_consen 26 PSQETLAKDLGVSRRTVQRAIKELE 50 (55)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3688999999999999999887654
No 153
>PRK01381 Trp operon repressor; Provisional
Probab=64.17 E-value=3.5 Score=32.81 Aligned_cols=23 Identities=17% Similarity=0.205 Sum_probs=20.2
Q ss_pred CCCcchhhhcccccccccchhhh
Q 015432 123 SGESLQIIGDLFGLNQSTVSQVT 145 (407)
Q Consensus 123 ~g~s~~~la~~Fgis~sTvsr~i 145 (407)
.+.+|+.|+...|||.+||+|.-
T Consensus 54 g~~sQREIa~~lGvSiaTITRgs 76 (99)
T PRK01381 54 GELSQREIKQELGVGIATITRGS 76 (99)
T ss_pred CCcCHHHHHHHhCCceeeehhhH
Confidence 35899999999999999999853
No 154
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=64.06 E-value=2.2 Score=40.44 Aligned_cols=47 Identities=17% Similarity=0.292 Sum_probs=40.9
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.++..++-++.|+|+ .|.++..||..+|||.+||+++..+...-|..
T Consensus 215 ~L~~rer~vl~l~y~-~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 215 ALPERERTVLVLRFF-ESMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred cCCHHHHHHHHHHhc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 378888888888886 59999999999999999999999888777654
No 155
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=63.98 E-value=1.7 Score=38.41 Aligned_cols=49 Identities=20% Similarity=0.178 Sum_probs=40.6
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|+.++-++.|.++ .|.++..||..+|||.+||...+.+....|.+.+
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 378888888887655 5899999999999999999998888877776543
No 156
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=63.95 E-value=3 Score=28.99 Aligned_cols=24 Identities=21% Similarity=0.301 Sum_probs=20.0
Q ss_pred cchhhhcccccccccchhhhHHHH
Q 015432 126 SLQIIGDLFGLNQSTVSQVTWRFV 149 (407)
Q Consensus 126 s~~~la~~Fgis~sTvsr~i~~~~ 149 (407)
+..++++.||+|++||++.+....
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~ 45 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLE 45 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 577899999999999998765543
No 157
>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=63.89 E-value=2 Score=40.40 Aligned_cols=47 Identities=17% Similarity=0.346 Sum_probs=40.2
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.++..++.++.|+|+ .|.++..||..+|+|+++|+++..+.+.-|..
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 478888888888875 58899999999999999999999888776653
No 158
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=63.58 E-value=1.7 Score=40.78 Aligned_cols=49 Identities=18% Similarity=0.364 Sum_probs=42.8
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.++-.+|+.+.|+|. .+.++..||...|||+|+|||+..+.+..|-..+
T Consensus 196 ~L~EREk~Vl~l~y~-eelt~kEI~~~LgISes~VSql~kkai~kLr~~l 244 (247)
T COG1191 196 PLPEREKLVLVLRYK-EELTQKEIAEVLGISESRVSRLHKKAIKKLRKEL 244 (247)
T ss_pred ccCHHHHHHHHHHHH-hccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHh
Confidence 477789999999984 5889999999999999999999999888887644
No 159
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=63.56 E-value=2.1 Score=41.83 Aligned_cols=48 Identities=23% Similarity=0.337 Sum_probs=42.3
Q ss_pred CCChhcceeeEEEec---cCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRL---SSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 107 ~l~~~~ql~i~L~~L---a~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.|+..++..+.|+|. ..+.++..||..+|||+++|.++..+...-|..
T Consensus 256 ~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~ 306 (317)
T PRK07405 256 DLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK 306 (317)
T ss_pred cCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 388999999999986 467899999999999999999999888877765
No 160
>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=63.41 E-value=2 Score=40.38 Aligned_cols=48 Identities=21% Similarity=0.226 Sum_probs=41.1
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.+|+.++-.+.|+|+ .|.++..||..+|||.+||++...+....|...
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 378888888888875 689999999999999999999998888777653
No 161
>PRK06930 positive control sigma-like factor; Validated
Probab=63.35 E-value=1.6 Score=38.60 Aligned_cols=49 Identities=20% Similarity=0.238 Sum_probs=39.7
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|+.++-++.|++ ..|.++..||..+|+|.+||...+.+....|...+
T Consensus 114 ~L~~rer~V~~L~~-~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l 162 (170)
T PRK06930 114 VLTEREKEVYLMHR-GYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQI 162 (170)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 36776666666654 67999999999999999999999988888776644
No 162
>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=63.11 E-value=1.9 Score=38.54 Aligned_cols=49 Identities=14% Similarity=0.096 Sum_probs=41.5
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhcc
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGL 157 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~ 157 (407)
+++.++-++.|+|+- |.++..||..+|+|.+||...+.+....|.+.+.
T Consensus 132 L~~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~ 180 (188)
T TIGR02943 132 LPEQTARVFMMREVL-GFESDEICQELEISTSNCHVLLYRARLSLRACLS 180 (188)
T ss_pred CCHHHHHHHHHHHHh-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 777788888787764 9999999999999999999998888888876543
No 163
>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=63.09 E-value=7 Score=39.19 Aligned_cols=86 Identities=22% Similarity=0.169 Sum_probs=48.8
Q ss_pred ccCCCcchhhhc----ccc---cccccchhhhHHHHHHHHHhccccccCCChhhHHHHHHHHHHhhhCCcceeeeeeeeE
Q 015432 121 LSSGESLQIIGD----LFG---LNQSTVSQVTWRFVESMEERGLHHLQWPSKETEMEDIKSKFEKIRGFRNCCGAIDITH 193 (407)
Q Consensus 121 La~g~s~~~la~----~Fg---is~sTvsr~i~~~~~al~~~~~~~i~~P~~~~~~~~i~~~f~~~~~fp~~vGaIDgt~ 193 (407)
+..|.|.++++. .+| +|++|||+++..+.+.+...... ...+.|-++-.|||++
T Consensus 111 y~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~~w~~R-------------------~L~~~~y~~l~iD~~~ 171 (381)
T PF00872_consen 111 YLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVEAWRNR-------------------PLESEPYPYLWIDGTY 171 (381)
T ss_pred hccccccccccchhhhhhcccccCchhhhhhhhhhhhhHHHHhhh-------------------ccccccccceeeeeee
Confidence 456777766654 456 89999999887776655432110 0111223455799999
Q ss_pred EEeecCCCCCCcchhcCCCCcceeEEEeeeCCCcc--eeecccc
Q 015432 194 IVMNIPAVDPANNVWYDREKNYSMILQGIVDPEMR--FRDIIAG 235 (407)
Q Consensus 194 i~i~~P~~~~~~~~y~~~k~~~s~~~q~v~d~~gr--f~~v~~g 235 (407)
+.+..-. .-...++.+-..+|.+|+ ++.+.++
T Consensus 172 ~kvr~~~----------~~~~~~~~v~iGi~~dG~r~vLg~~~~ 205 (381)
T PF00872_consen 172 FKVREDG----------RVVKKAVYVAIGIDEDGRREVLGFWVG 205 (381)
T ss_pred ccccccc----------ccccchhhhhhhhhcccccceeeeecc
Confidence 9887311 111122333344577775 6655554
No 164
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=62.90 E-value=1.1 Score=37.02 Aligned_cols=28 Identities=25% Similarity=0.387 Sum_probs=24.4
Q ss_pred eccCCCcchhhhcccccccccchhhhHH
Q 015432 120 RLSSGESLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 120 ~La~g~s~~~la~~Fgis~sTvsr~i~~ 147 (407)
+...|.+...+|..|+||.+||.+++.+
T Consensus 14 ~~~~g~s~~eaa~~F~VS~~Tv~~W~k~ 41 (119)
T PF01710_consen 14 YIEKGKSIREAAKRFGVSRNTVYRWLKR 41 (119)
T ss_pred HHHccchHHHHHHHhCcHHHHHHHHHHh
Confidence 5566889999999999999999998864
No 165
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=62.80 E-value=2.7 Score=43.13 Aligned_cols=74 Identities=26% Similarity=0.295 Sum_probs=53.7
Q ss_pred HHHHHHHHhhhhhhhhcCC-CcCCCCCCCChhcceeeEEEeccCCCcchhhhccc-ccccccchhhhHHHHHHHHH
Q 015432 81 TFDYICSLVKEDLAARQSN-FSFSNGKPLSPNDMVAIALRRLSSGESLQIIGDLF-GLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 81 tF~~L~~~l~~~~~~~~~~-~~~~~~~~l~~~~ql~i~L~~La~g~s~~~la~~F-gis~sTvsr~i~~~~~al~~ 154 (407)
+.+.|.+.+...+...... ....+.+.+...-|++|.|.+--++.++..||..| |.+.|||...++++-..+.+
T Consensus 358 ~~~~i~~~v~~~~~i~~~~l~~~~R~~~~~~aR~iamyl~~~~~~~s~~~Ig~~fg~rdhstV~~a~~~i~~~~~~ 433 (450)
T PRK00149 358 TIENIQKVVAEYYNIKVSDLKSKSRTRNIARPRQIAMYLAKELTDLSLPEIGRAFGGRDHTTVLHAVRKIEKLLEE 433 (450)
T ss_pred CHHHHHHHHHHHcCCCHHHHhCCCCCcccChHHHHHHHHHHHhcCCCHHHHHHHcCCCCHhHHHHHHHHHHHHHHh
Confidence 3445555554443321111 11234567888999999999999999999999999 59999999999998887753
No 166
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=62.75 E-value=2.7 Score=32.76 Aligned_cols=26 Identities=27% Similarity=0.456 Sum_probs=23.0
Q ss_pred eccCCCcchhhhcccccccccchhhh
Q 015432 120 RLSSGESLQIIGDLFGLNQSTVSQVT 145 (407)
Q Consensus 120 ~La~g~s~~~la~~Fgis~sTvsr~i 145 (407)
.|..|.+|+.|+...|+|..||+|+-
T Consensus 45 lL~~g~syreIa~~tgvS~aTItRvs 70 (87)
T PF01371_consen 45 LLDEGKSYREIAEETGVSIATITRVS 70 (87)
T ss_dssp HHHTTSSHHHHHHHHTSTHHHHHHHH
T ss_pred HHHCCCCHHHHHHHhCCCHHHHHHHH
Confidence 46679999999999999999999853
No 167
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=62.58 E-value=1.9 Score=38.41 Aligned_cols=47 Identities=23% Similarity=0.268 Sum_probs=41.5
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.+|+.++-++.|+|+ .|.++..||..+|+|.+||...+.+....|..
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 488899999998886 69999999999999999999998888777764
No 168
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=62.11 E-value=3.7 Score=39.44 Aligned_cols=69 Identities=20% Similarity=0.213 Sum_probs=51.5
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhccccccCCChhhHHHHHHHHHHhh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGLHHLQWPSKETEMEDIKSKFEKI 179 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~~~i~~P~~~~~~~~i~~~f~~~ 179 (407)
.+|+.++-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+..+..- +..+ +..++...|.+.
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--VSDE-EGAELVEAFFAA 183 (293)
T ss_pred hCCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCCCC--CCch-HHHHHHHHHHHH
Confidence 378888888877766 48999999999999999999999999888887654321 2222 345566666554
No 169
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=61.93 E-value=2.2 Score=39.96 Aligned_cols=48 Identities=23% Similarity=0.299 Sum_probs=41.1
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.+|+.++-.+.|+|+ .|.++..||..+|+|.+||...+.+....|...
T Consensus 201 ~L~~~~r~vl~l~~~-~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 201 QLSEKEQLVISLFYK-EELTLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 378888888888875 799999999999999999999988887777553
No 170
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=61.91 E-value=4.9 Score=32.50 Aligned_cols=30 Identities=13% Similarity=0.196 Sum_probs=24.4
Q ss_pred CCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
|.++.+.|...|||++|+++++...-.-|.
T Consensus 57 gl~QeeaA~~MgVSR~T~~ril~~ARkKiA 86 (106)
T PF02001_consen 57 GLSQEEAAERMGVSRPTFQRILESARKKIA 86 (106)
T ss_pred CCCHHHHHHHcCCcHHHHHHHHHHHHHHHH
Confidence 788899999999999999998865444443
No 171
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=61.59 E-value=2.1 Score=38.82 Aligned_cols=47 Identities=9% Similarity=0.032 Sum_probs=39.8
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
+|..++.++.|.|+ .|.++..||..+|+|.+||...+.+....|.+.
T Consensus 154 L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 154 LPEAQQTVVKGVYF-QELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 78888888777765 599999999999999999998888877777654
No 172
>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=61.12 E-value=11 Score=29.60 Aligned_cols=29 Identities=24% Similarity=0.443 Sum_probs=22.7
Q ss_pred cchhhhcccccccccchhhhHHHHHHHHH
Q 015432 126 SLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 126 s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.+..+|+..||+.|||||+-..++.-++.
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 45689999999999999987665554443
No 173
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=60.63 E-value=2.4 Score=38.21 Aligned_cols=47 Identities=21% Similarity=0.236 Sum_probs=39.2
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
++..++-++.| ++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 156 L~~~~r~vl~l-~~-e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 156 LSELEKEVLEL-YL-DGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred CCHHHHHHHHH-HH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 67777777777 65 6999999999999999999988888777776643
No 174
>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=60.51 E-value=2.4 Score=29.32 Aligned_cols=42 Identities=21% Similarity=0.374 Sum_probs=29.6
Q ss_pred cCCCcchhhhcccccccccchhhhHHHHHHHHHhccccccCCChhhHHHHHHHHH
Q 015432 122 SSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGLHHLQWPSKETEMEDIKSKF 176 (407)
Q Consensus 122 a~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~~~i~~P~~~~~~~~i~~~f 176 (407)
..|.++.++|...|+|++|++++.+. -..|+.+ .+..++..|
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~g------------~~~~~~~-~~~~ia~~l 48 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIENG------------KRNPSLD-TLKKIAKAL 48 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHTT------------SSTSBHH-HHHHHHHHH
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhcC------------CCCCCHH-HHHHHHHHH
Confidence 46889999999999999999997643 2446665 566666554
No 175
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=60.40 E-value=2.1 Score=36.85 Aligned_cols=48 Identities=25% Similarity=0.269 Sum_probs=40.4
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
+|++++-++.|.+ -.|.++.+||..+|+|.+||...+.+....|.+.+
T Consensus 106 L~~~~r~v~~l~~-~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 106 LPPACRDSFLLRK-LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 7888777777765 46999999999999999999999888888877654
No 176
>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=60.36 E-value=2.8 Score=33.96 Aligned_cols=30 Identities=27% Similarity=0.241 Sum_probs=24.8
Q ss_pred CCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
|.+...||+.|+||+||+..++.+.-.--.
T Consensus 80 Glt~~aIAd~F~iS~s~~~nft~~n~~eYy 109 (126)
T PF10654_consen 80 GLTCYAIADYFKISKSTVFNFTQNNKKEYY 109 (126)
T ss_pred CCChHHHHHHHhHHHHHHHHHHHHhHHHHH
Confidence 788899999999999999998866554443
No 177
>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=59.98 E-value=2.5 Score=38.81 Aligned_cols=48 Identities=25% Similarity=0.435 Sum_probs=40.7
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.+|..++-++.|+|+ .|.++.+||..+|+|.+||.+...+....|...
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 378888888888875 689999999999999999999888887777543
No 178
>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=59.98 E-value=2.2 Score=37.33 Aligned_cols=49 Identities=29% Similarity=0.205 Sum_probs=41.0
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.+|+.++.++.|.++ .|.++..||..+|+|.+||...+.+....|...+
T Consensus 100 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 100 ELPDEYREAIRLTEL-EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888776 5999999999999999999998888777776543
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=59.85 E-value=1.6 Score=34.88 Aligned_cols=43 Identities=9% Similarity=0.305 Sum_probs=36.3
Q ss_pred ChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHH
Q 015432 109 SPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESM 152 (407)
Q Consensus 109 ~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al 152 (407)
.+.++..+.++|+ .+.++..|+..+++|++|++++-.+.+..|
T Consensus 57 d~~~r~iL~~~Yi-~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 57 DPDERLILRMRYI-NKLTWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred ChhHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 5678888999999 689999999999999999999877655443
No 180
>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=59.63 E-value=4.4 Score=29.06 Aligned_cols=27 Identities=33% Similarity=0.345 Sum_probs=22.8
Q ss_pred CCcchhhhcccccccccchhhhHHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
..+..+||..+|+|++||++++.....
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 467889999999999999998776554
No 181
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=59.61 E-value=2.7 Score=42.97 Aligned_cols=50 Identities=16% Similarity=0.187 Sum_probs=44.4
Q ss_pred CCCCCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHH
Q 015432 103 SNGKPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESM 152 (407)
Q Consensus 103 ~~~~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al 152 (407)
.+.+.+...-|++|.|.+=-++.++..||..||.+.|||...+.++-..+
T Consensus 366 ~R~~~i~~aR~iamyl~r~~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 366 SRNVKALLARRIGMYVAKNYLGSSLRTIAEKFNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred CCCccccHHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 34556888999999999888999999999999999999999999888866
No 182
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=59.25 E-value=2.5 Score=37.80 Aligned_cols=49 Identities=10% Similarity=0.102 Sum_probs=40.8
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.||..++-++.|+|+ .|.++..||..+|+|.+||...+.+....|...+
T Consensus 142 ~L~~~~r~vl~l~~~-~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYY-GGLTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 378888887777765 5899999999999999999999888887776543
No 183
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=58.88 E-value=4.6 Score=40.26 Aligned_cols=46 Identities=17% Similarity=0.374 Sum_probs=39.3
Q ss_pred CChhcceeeEEEec-c--CCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 108 LSPNDMVAIALRRL-S--SGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 108 l~~~~ql~i~L~~L-a--~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
|+..++..+.|+|. . .+.++..||..||||++.|+++-.+.+.-|-
T Consensus 306 L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr 354 (367)
T PRK09210 306 LTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 354 (367)
T ss_pred CCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 89999999999885 3 4579999999999999999999877666654
No 184
>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=58.73 E-value=0.98 Score=30.60 Aligned_cols=26 Identities=27% Similarity=0.299 Sum_probs=20.8
Q ss_pred CCcchhhhcccccccccchhhhHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFV 149 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~ 149 (407)
..+..+|++.+|+|++||++.+....
T Consensus 15 ~~~~~el~~~l~~s~~~vs~hL~~L~ 40 (47)
T PF01022_consen 15 PLTVSELAEELGLSQSTVSHHLKKLR 40 (47)
T ss_dssp SEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCchhhHHHhccccchHHHHHHHHHH
Confidence 45678999999999999999886543
No 185
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=58.30 E-value=2.1 Score=34.95 Aligned_cols=47 Identities=15% Similarity=0.258 Sum_probs=40.7
Q ss_pred CCCCChhcceeeEEEeccCCCcchhhhccccc-ccccchhhhHHHHHH
Q 015432 105 GKPLSPNDMVAIALRRLSSGESLQIIGDLFGL-NQSTVSQVTWRFVES 151 (407)
Q Consensus 105 ~~~l~~~~ql~i~L~~La~g~s~~~la~~Fgi-s~sTvsr~i~~~~~a 151 (407)
.+..|.+.++-++-.++..|.++..||..||| +.++.++++..+...
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~ 52 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKG 52 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHc
Confidence 46688999999999999999999999999996 999999888776553
No 186
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=58.17 E-value=2.6 Score=37.31 Aligned_cols=45 Identities=16% Similarity=0.257 Sum_probs=35.7
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
.+|+.+. =+|..++.|.+..+||..+++|.+||..++.++..-|.
T Consensus 133 ~LSpREr--EVLrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKLg 177 (198)
T PRK15201 133 HFSVTER--HLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLH 177 (198)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3666444 34567899999999999999999999998877766553
No 187
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=58.04 E-value=3.8 Score=37.09 Aligned_cols=48 Identities=23% Similarity=0.244 Sum_probs=39.9
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
++...+-++.|.++ .|.++..||..+|||.+||...+.+....|.+.+
T Consensus 139 L~~~~r~v~~L~~~-~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 139 LPPEFRAAVVLCDI-EGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 67777776667664 6999999999999999999999988888777654
No 188
>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=57.61 E-value=3.8 Score=32.26 Aligned_cols=34 Identities=18% Similarity=0.307 Sum_probs=25.1
Q ss_pred chhhhcccccccccchhhhHH--HHHHHHHhccccc
Q 015432 127 LQIIGDLFGLNQSTVSQVTWR--FVESMEERGLHHL 160 (407)
Q Consensus 127 ~~~la~~Fgis~sTvsr~i~~--~~~al~~~~~~~i 160 (407)
+.-||..||+|.+|++|+... .-+||......+|
T Consensus 48 ~~GlAklfgcSv~Ta~RiK~sG~id~AI~Q~Gr~Ii 83 (96)
T PF12964_consen 48 LKGLAKLFGCSVPTANRIKKSGKIDPAITQIGRKII 83 (96)
T ss_pred HHHHHHHhCCCchhHHHHHhcCCccHHHHHcCCEEE
Confidence 578999999999999998752 3356666555443
No 189
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=57.44 E-value=7.6 Score=37.36 Aligned_cols=69 Identities=20% Similarity=0.270 Sum_probs=51.1
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhccccccCCChhhHHHHHHHHHHhh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGLHHLQWPSKETEMEDIKSKFEKI 179 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~~~i~~P~~~~~~~~i~~~f~~~ 179 (407)
.+|+.++-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+..+.. . +..+ +...+.+.|...
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-S-VEPA-QHRVVTRAFIEA 186 (290)
T ss_pred hCCHHHHHHhhHHHH-hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhCCCC-C-CChH-HHHHHHHHHHHH
Confidence 377888877777665 5999999999999999999999999888887654321 1 2223 455677666554
No 190
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=57.05 E-value=3.9 Score=26.73 Aligned_cols=28 Identities=21% Similarity=0.186 Sum_probs=20.7
Q ss_pred ccCCCcchhhhcccccccccchhhhHHH
Q 015432 121 LSSGESLQIIGDLFGLNQSTVSQVTWRF 148 (407)
Q Consensus 121 La~g~s~~~la~~Fgis~sTvsr~i~~~ 148 (407)
|.++.+..+||..+|+|.++.++.+.+.
T Consensus 5 ~~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 5 LQQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp T-SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4566788999999999999999988764
No 191
>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=56.91 E-value=1.2 Score=31.52 Aligned_cols=26 Identities=23% Similarity=0.436 Sum_probs=20.8
Q ss_pred CCcchhhhcccccccccchhhhHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFV 149 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~ 149 (407)
+.+..+|+..++++++|+++++++..
T Consensus 17 ~~~~~~la~~~~~~~~~~t~~i~~L~ 42 (59)
T PF01047_consen 17 GITQSELAEKLGISRSTVTRIIKRLE 42 (59)
T ss_dssp SEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCCChhHHHHHHHHHH
Confidence 56778999999999999998876543
No 192
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=56.41 E-value=2.9 Score=37.15 Aligned_cols=48 Identities=17% Similarity=0.214 Sum_probs=39.8
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.+|+.++-++.|.|+. |.++..||..+|+|.+||...+.+....|-..
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 3788787777777665 89999999999999999999888877776543
No 193
>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=55.85 E-value=5.6 Score=28.53 Aligned_cols=26 Identities=19% Similarity=0.282 Sum_probs=20.5
Q ss_pred CCcchhhhcccccccccchhhhHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFV 149 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~ 149 (407)
..+-.+||..++||++||+..+.+..
T Consensus 22 ~v~~~~iA~~L~vs~~tvt~ml~~L~ 47 (60)
T PF01325_consen 22 PVRTKDIAERLGVSPPTVTEMLKRLA 47 (60)
T ss_dssp SBBHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CccHHHHHHHHCCChHHHHHHHHHHH
Confidence 45567999999999999998877654
No 194
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=55.67 E-value=4 Score=41.93 Aligned_cols=74 Identities=18% Similarity=0.265 Sum_probs=55.3
Q ss_pred HHHHHHHHhhhhhhhhcCCC-cCCCCCCCChhcceeeEEEeccCCCcchhhhcccc-cccccchhhhHHHHHHHHH
Q 015432 81 TFDYICSLVKEDLAARQSNF-SFSNGKPLSPNDMVAIALRRLSSGESLQIIGDLFG-LNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 81 tF~~L~~~l~~~~~~~~~~~-~~~~~~~l~~~~ql~i~L~~La~g~s~~~la~~Fg-is~sTvsr~i~~~~~al~~ 154 (407)
+.+.|.+.|...+......+ ...+.+.+...-|+||.|.+=-++.++..||..|| .+.|||..-+.++-..+.+
T Consensus 357 t~~~I~~~Va~~~~i~~~dl~s~~R~~~i~~~RqiamyL~r~~t~~sl~~IG~~FggrdHsTV~~a~~ki~~~~~~ 432 (450)
T PRK14087 357 NVKKIKEVVSEKYGISVNAIDGKARSKSIVTARHIAMYLTKEILNHTLAQIGEEFGGRDHTTVINAERKIEKMLKK 432 (450)
T ss_pred CHHHHHHHHHHHcCCCHHHHhCCCCCccccHHHHHHHHHHHHHcCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHh
Confidence 55666666655544321111 12344568889999999999999999999999997 9999999988888887764
No 195
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=55.37 E-value=3.2 Score=37.70 Aligned_cols=44 Identities=23% Similarity=0.255 Sum_probs=35.9
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
+++.|. =.|.+++.|.+..+||...++|.+||..++.++..-|.
T Consensus 138 LT~RE~--eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 138 LSRTES--SMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred CCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 555444 34677899999999999999999999999887776664
No 196
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=55.20 E-value=5.1 Score=29.62 Aligned_cols=70 Identities=14% Similarity=0.119 Sum_probs=44.7
Q ss_pred hHHHhhcCCCHHHHHHHHHHhhhhhhhhcCCCcCCCCCCCChhcceeeEEEeccCC-Ccchhhhccccc-ccccchhhhH
Q 015432 69 KNFESVFKISRKTFDYICSLVKEDLAARQSNFSFSNGKPLSPNDMVAIALRRLSSG-ESLQIIGDLFGL-NQSTVSQVTW 146 (407)
Q Consensus 69 ~~F~~~frmsr~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~~~ql~i~L~~La~g-~s~~~la~~Fgi-s~sTvsr~i~ 146 (407)
++.-..++++...|..++......-.. ..-...++.-++.+|..+ .+..+||..+|+ |.++.++.+.
T Consensus 5 ~~la~~~~~s~~~l~~~f~~~~~~s~~-----------~~~~~~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk 73 (84)
T smart00342 5 EDLAEALGMSPRHLQRLFKKETGTTPK-----------QYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFK 73 (84)
T ss_pred HHHHHHhCCCHHHHHHHHHHHhCcCHH-----------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 456667788888777766543211000 011123344455555555 789999999999 9999999887
Q ss_pred HHH
Q 015432 147 RFV 149 (407)
Q Consensus 147 ~~~ 149 (407)
+..
T Consensus 74 ~~~ 76 (84)
T smart00342 74 KLF 76 (84)
T ss_pred HHH
Confidence 653
No 197
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=54.98 E-value=3.3 Score=41.38 Aligned_cols=48 Identities=21% Similarity=0.392 Sum_probs=41.1
Q ss_pred CCChhcceeeEEEec---cCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRL---SSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 107 ~l~~~~ql~i~L~~L---a~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.|+..++..+.|+|+ ..+.++..||..+|||+.+|+++..+.+.-|-.
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 388999999999886 246899999999999999999998887777754
No 198
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=54.54 E-value=6 Score=40.08 Aligned_cols=46 Identities=22% Similarity=0.275 Sum_probs=39.7
Q ss_pred CChhcceeeEEEec---cCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 108 LSPNDMVAIALRRL---SSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 108 l~~~~ql~i~L~~L---a~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
|++.++-.+.|+|. ..+.++..||..+|||.+||.++..+....|.
T Consensus 351 L~~reR~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~KLR 399 (415)
T PRK07598 351 LTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLR 399 (415)
T ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHh
Confidence 88899999999885 35689999999999999999999888776665
No 199
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=54.39 E-value=3.1 Score=29.95 Aligned_cols=24 Identities=38% Similarity=0.526 Sum_probs=19.6
Q ss_pred cCCCcchhhhcccccccccchhhh
Q 015432 122 SSGESLQIIGDLFGLNQSTVSQVT 145 (407)
Q Consensus 122 a~g~s~~~la~~Fgis~sTvsr~i 145 (407)
+.|.++..+|...|+|.||++++-
T Consensus 12 ~~gls~~~lA~~~g~s~s~v~~iE 35 (64)
T PF13560_consen 12 RAGLSQAQLADRLGVSQSTVSRIE 35 (64)
T ss_dssp CHTS-HHHHHHHHTS-HHHHHHHH
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHH
Confidence 468999999999999999999864
No 200
>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=53.96 E-value=4.3 Score=33.50 Aligned_cols=73 Identities=18% Similarity=0.144 Sum_probs=42.1
Q ss_pred hHHHhhcCCCHHHHHHHHHHhhhhhhhhcCCCcCCCCCCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHH
Q 015432 69 KNFESVFKISRKTFDYICSLVKEDLAARQSNFSFSNGKPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 69 ~~F~~~frmsr~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~ 147 (407)
.+=-..|++++.|....+..... ....+. ...+..+.. + .+..+.--....++..+|..||||.+|+++.+.+
T Consensus 22 ~eaa~~F~VS~~Tv~~W~k~~~~-G~~~~k---~r~~~Kid~-~-~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkr 94 (119)
T PF01710_consen 22 REAAKRFGVSRNTVYRWLKRKET-GDLEPK---PRGRKKIDR-D-ELKALVEENPDATLRELAERLGVSPSTIWRALKR 94 (119)
T ss_pred HHHHHHhCcHHHHHHHHHHhccc-cccccc---ccccccccH-H-HHHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHH
Confidence 44557899999998877773322 111111 111113432 2 2222222234566789999999999999876654
No 201
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=53.77 E-value=6.2 Score=41.04 Aligned_cols=48 Identities=19% Similarity=0.367 Sum_probs=41.7
Q ss_pred CCChhcceeeEEEec---cCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRL---SSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 107 ~l~~~~ql~i~L~~L---a~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.|+..++..|.|+|. ..+.++..||..||||++.|+++-.+.+.-|..
T Consensus 447 ~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~ 497 (509)
T PRK05901 447 TLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRH 497 (509)
T ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 388999999999995 457899999999999999999998887777754
No 202
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=53.64 E-value=4.2 Score=33.59 Aligned_cols=23 Identities=43% Similarity=0.427 Sum_probs=21.6
Q ss_pred CCcchhhhcccccccccchhhhH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~ 146 (407)
|.++..+|...|+|++.||+|+.
T Consensus 22 G~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 22 GLSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHc
Confidence 88999999999999999999974
No 203
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=53.59 E-value=3.4 Score=36.82 Aligned_cols=46 Identities=24% Similarity=0.357 Sum_probs=33.8
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
+++++.=.+.|+++ .|.++..||...|||.+||.+-+...-..|..
T Consensus 136 l~~~~~~~v~l~~~-~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 136 LDPRQRRVVELRFF-EGLSVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred cCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 34444444555555 69999999999999999999987766655544
No 204
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=53.38 E-value=6.6 Score=26.39 Aligned_cols=27 Identities=19% Similarity=0.336 Sum_probs=21.9
Q ss_pred CCcchhhhcccccccccchhhhHHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
+.+..+++..|+++.+|+++++..+..
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~~ 40 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLEE 40 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 356789999999999999998866544
No 205
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=53.17 E-value=12 Score=36.64 Aligned_cols=65 Identities=14% Similarity=0.171 Sum_probs=43.0
Q ss_pred EeccCCCcchhhhcccccccccchhhhHHHHHHHHHhccccccCCChhhHHHHHHHHHHhhhCCcceee
Q 015432 119 RRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGLHHLQWPSKETEMEDIKSKFEKIRGFRNCCG 187 (407)
Q Consensus 119 ~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~~~i~~P~~~~~~~~i~~~f~~~~~fp~~vG 187 (407)
.|+-.|.++.+||+.+|||+.||+|.+.+--+- -.-.-.|..|.. ..-++.+..++.+|++.|+-
T Consensus 21 lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~--GiV~I~i~~~~~--~~~~Le~~L~~~fgL~~a~V 85 (321)
T COG2390 21 LYYVEGLTQSEIAERLGISRATVSRLLAKAREE--GIVKISINSPVE--GCLELEQQLKERFGLKEAIV 85 (321)
T ss_pred HHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHC--CeEEEEeCCCCc--chHHHHHHHHHhcCCCeEEE
Confidence 355679999999999999999999987543211 011223443333 34456666777788888763
No 206
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=52.98 E-value=18 Score=30.58 Aligned_cols=28 Identities=7% Similarity=0.100 Sum_probs=23.7
Q ss_pred CCCcchhhhcccccccccchhhhHHHHH
Q 015432 123 SGESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 123 ~g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
.+.+...||..++++++|+++.+.+...
T Consensus 53 ~~~t~~eLa~~l~i~~~tvsr~l~~Le~ 80 (144)
T PRK11512 53 ACITPVELKKVLSVDLGALTRMLDRLVC 80 (144)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4678899999999999999998776544
No 207
>PHA02591 hypothetical protein; Provisional
Probab=52.70 E-value=4.7 Score=30.40 Aligned_cols=26 Identities=19% Similarity=0.284 Sum_probs=22.8
Q ss_pred cCCCcchhhhcccccccccchhhhHH
Q 015432 122 SSGESLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 122 a~g~s~~~la~~Fgis~sTvsr~i~~ 147 (407)
..|.+...||...|+++.||++++..
T Consensus 57 eqGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 57 RKGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 34899999999999999999998753
No 208
>PRK13870 transcriptional regulator TraR; Provisional
Probab=52.56 E-value=3.5 Score=38.33 Aligned_cols=45 Identities=20% Similarity=0.352 Sum_probs=37.3
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
.|++.++ =+|.|++.|.+..+||...|||++||.-++.+...-|.
T Consensus 173 ~LT~RE~--E~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~na~~KLg 217 (234)
T PRK13870 173 WLDPKEA--TYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFD 217 (234)
T ss_pred CCCHHHH--HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 4665544 35789999999999999999999999999888777664
No 209
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=52.52 E-value=4.4 Score=36.59 Aligned_cols=28 Identities=21% Similarity=0.332 Sum_probs=24.9
Q ss_pred EeccCCCcchhhhcccccccccchhhhH
Q 015432 119 RRLSSGESLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 119 ~~La~g~s~~~la~~Fgis~sTvsr~i~ 146 (407)
.++..|.++..||..+|||.+|+++++.
T Consensus 167 ~~~~~g~s~~~iak~lgis~~Tv~r~~k 194 (200)
T PRK13413 167 KLLDKGTSKSEIARKLGVSRTTLARFLK 194 (200)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3467899999999999999999999875
No 210
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=52.26 E-value=3.5 Score=36.73 Aligned_cols=48 Identities=25% Similarity=0.320 Sum_probs=39.8
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
||...+-++.|+++ .|.++..||..+|||.+||...+.+....|.+.+
T Consensus 129 Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 129 LDPEYREPLLLQVI-GGFSGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred CCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 67777776666655 5999999999999999999999988888877654
No 211
>PRK09492 treR trehalose repressor; Provisional
Probab=52.22 E-value=5.2 Score=38.28 Aligned_cols=23 Identities=35% Similarity=0.371 Sum_probs=20.5
Q ss_pred CcchhhhcccccccccchhhhHH
Q 015432 125 ESLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 125 ~s~~~la~~Fgis~sTvsr~i~~ 147 (407)
.+..+||...|||.+||||+++.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCC
Confidence 46789999999999999999863
No 212
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=51.37 E-value=4.1 Score=30.08 Aligned_cols=20 Identities=30% Similarity=0.511 Sum_probs=17.4
Q ss_pred cchhhhcccccccccchhhh
Q 015432 126 SLQIIGDLFGLNQSTVSQVT 145 (407)
Q Consensus 126 s~~~la~~Fgis~sTvsr~i 145 (407)
+..+||...|||.+|||+++
T Consensus 2 t~~~iA~~~gvS~~TVSr~l 21 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVL 21 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 45789999999999999965
No 213
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=50.96 E-value=5.3 Score=40.93 Aligned_cols=73 Identities=23% Similarity=0.193 Sum_probs=54.4
Q ss_pred HHHHHHHHhhhhhhhhcCCC-cCCCCCCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 81 TFDYICSLVKEDLAARQSNF-SFSNGKPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 81 tF~~L~~~l~~~~~~~~~~~-~~~~~~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
+.+.|.+.+..++......+ ...+.+.+...-|+||.|.+=-++.|+..||..||-..|||.--++++-+.|.
T Consensus 353 t~~~I~~~Va~~~~v~~~dl~s~~R~~~i~~~Rqiamyl~r~~t~~s~~~IG~~fgrdHsTV~~a~~ki~~~~~ 426 (445)
T PRK12422 353 TPSKIIRAVAQYYGVSPESILGRSQSREYVLPRQVAMYLCRQKLSLSYVKIGDVFSRDHSTVISSIRAISQKLE 426 (445)
T ss_pred CHHHHHHHHHHHhCCCHHHHhcCCCCcccccHHHHHHHHHHHhcCCCHHHHHHHhCCChHHHHHHHHHHHHHHH
Confidence 44556665555444321111 12345678889999999999999999999999999999999988888887774
No 214
>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=50.76 E-value=4.3 Score=27.66 Aligned_cols=18 Identities=33% Similarity=0.259 Sum_probs=15.7
Q ss_pred hhhcccccccccchhhhH
Q 015432 129 IIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 129 ~la~~Fgis~sTvsr~i~ 146 (407)
++|...|||.+||+++++
T Consensus 2 ~lA~~~gvs~~tvs~~l~ 19 (52)
T cd01392 2 DIARAAGVSVATVSRVLN 19 (52)
T ss_pred cHHHHHCcCHHHHHHHHc
Confidence 688999999999999763
No 215
>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=50.50 E-value=3.7 Score=36.55 Aligned_cols=37 Identities=19% Similarity=0.183 Sum_probs=30.0
Q ss_pred EEEeccCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 117 ALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 117 ~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.+.++ .|.++..||..+|+|.+||...+.+....|..
T Consensus 159 ~~~~~-~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 159 LQSYL-DGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred HHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34455 79999999999999999998877777666654
No 216
>PHA00738 putative HTH transcription regulator
Probab=50.44 E-value=3.2 Score=33.50 Aligned_cols=27 Identities=22% Similarity=0.085 Sum_probs=22.2
Q ss_pred CcchhhhcccccccccchhhhHHHHHH
Q 015432 125 ESLQIIGDLFGLNQSTVSQVTWRFVES 151 (407)
Q Consensus 125 ~s~~~la~~Fgis~sTvsr~i~~~~~a 151 (407)
.+..+|+..|++|++|||+.+.-.-+|
T Consensus 27 ~~V~eLae~l~lSQptVS~HLKvLreA 53 (108)
T PHA00738 27 LSASLISHTLLLSYTTVLRHLKILNEQ 53 (108)
T ss_pred ccHHHHHHhhCCCHHHHHHHHHHHHHC
Confidence 567899999999999999987655443
No 217
>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=50.41 E-value=6.8 Score=28.99 Aligned_cols=27 Identities=26% Similarity=0.435 Sum_probs=23.0
Q ss_pred CCcchhhhcccccccccchhhhHHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
..+..+||...|+|+.||++++.++.+
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 468899999999999999998776544
No 218
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=50.24 E-value=4.8 Score=39.42 Aligned_cols=50 Identities=20% Similarity=0.223 Sum_probs=42.2
Q ss_pred CCChhcceeeEEEe-c--cCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 107 PLSPNDMVAIALRR-L--SSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 107 ~l~~~~ql~i~L~~-L--a~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
.|+..++.++.++| | -.|.++..||..+|||.+||.++..+....|...+
T Consensus 262 ~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 48889999998765 3 36899999999999999999999988888877654
No 219
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=50.12 E-value=2.2 Score=35.98 Aligned_cols=36 Identities=11% Similarity=0.077 Sum_probs=31.1
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQ 143 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr 143 (407)
.||+..+-++.|+++ .|.++..||..+|+|.+||.+
T Consensus 107 ~Lp~~~r~v~~l~~~-~~~s~~EIA~~l~is~~tV~~ 142 (142)
T TIGR03209 107 ILPNKQKKIIYMKFF-EDMKEIDIAKKLHISRQSVYK 142 (142)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHhhcC
Confidence 488888888888766 599999999999999999863
No 220
>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=50.02 E-value=7.9 Score=26.75 Aligned_cols=27 Identities=11% Similarity=0.160 Sum_probs=21.1
Q ss_pred CcchhhhcccccccccchhhhHHHHHH
Q 015432 125 ESLQIIGDLFGLNQSTVSQVTWRFVES 151 (407)
Q Consensus 125 ~s~~~la~~Fgis~sTvsr~i~~~~~a 151 (407)
.+...+|+.|+||+.||.+.+...-..
T Consensus 16 it~~eLa~~l~vS~rTi~~~i~~L~~~ 42 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIRRDIKELREW 42 (55)
T ss_dssp BEHHHHHHHCTS-HHHHHHHHHHHHHT
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 567899999999999999987665443
No 221
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=49.62 E-value=5.5 Score=34.80 Aligned_cols=23 Identities=35% Similarity=0.406 Sum_probs=0.0
Q ss_pred CCcchhhhcccccccccchhhhH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~ 146 (407)
...+.+||+..|++.|||||++.
T Consensus 49 PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 49 PLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp -----------------------
T ss_pred CCCHHHHHHHhCCCHhHHHHHHc
Confidence 35678999999999999999763
No 222
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=49.54 E-value=4.5 Score=37.54 Aligned_cols=46 Identities=15% Similarity=0.256 Sum_probs=38.9
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
.++..++-.+.|+|+ .|.++..||..+|||+++|+++..+...-|-
T Consensus 183 ~L~~~er~vi~l~~~-~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr 228 (231)
T PRK12427 183 QLDEREQLILHLYYQ-HEMSLKEIALVLDLTEARICQLNKKIAQKIK 228 (231)
T ss_pred cCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 378888888888874 6899999999999999999998887776653
No 223
>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=49.40 E-value=4.8 Score=38.58 Aligned_cols=21 Identities=38% Similarity=0.453 Sum_probs=19.0
Q ss_pred cchhhhcccccccccchhhhH
Q 015432 126 SLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 126 s~~~la~~Fgis~sTvsr~i~ 146 (407)
+..+||..+|||++|||++++
T Consensus 3 ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 3 TIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred cHHHHHHHhCCCHHHHHHHhC
Confidence 467999999999999999985
No 224
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=49.32 E-value=4 Score=37.64 Aligned_cols=83 Identities=19% Similarity=0.133 Sum_probs=49.4
Q ss_pred CChhHHHhhcCCCHHHHHHHHHHhhhhhhhhcCCCcCCCCCCCChhcceeeEEEeccC----------CCcchhhhcccc
Q 015432 66 KTSKNFESVFKISRKTFDYICSLVKEDLAARQSNFSFSNGKPLSPNDMVAIALRRLSS----------GESLQIIGDLFG 135 (407)
Q Consensus 66 ~~d~~F~~~frmsr~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~~~ql~i~L~~La~----------g~s~~~la~~Fg 135 (407)
.+-+.|...+.-++.-...++..+...+....... ..-...+++++|+-+|..++. ..+..+||...|
T Consensus 113 i~~~~f~~l~~~~p~l~~~l~~~l~~~l~~~~~~~--~~l~~~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lG 190 (230)
T PRK09391 113 IKRRSLEQAAATDVDVARALLSLTAGGLRHAQDHM--LLLGRKTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLG 190 (230)
T ss_pred EEHHHHHHHHhhChHHHHHHHHHHHHHHHHHHHHH--HHHcCCCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHC
Confidence 34445555555444444444444443332111000 001236889999988887643 245679999999
Q ss_pred cccccchhhhHHHHH
Q 015432 136 LNQSTVSQVTWRFVE 150 (407)
Q Consensus 136 is~sTvsr~i~~~~~ 150 (407)
+++.|++|++.++.+
T Consensus 191 isretlsR~L~~L~~ 205 (230)
T PRK09391 191 LTIETVSRALSQLQD 205 (230)
T ss_pred CCHHHHHHHHHHHHH
Confidence 999999998876654
No 225
>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=49.27 E-value=25 Score=28.30 Aligned_cols=27 Identities=15% Similarity=0.119 Sum_probs=22.9
Q ss_pred CCcchhhhcccccccccchhhhHHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
+.+...|+..++++++||++++.+...
T Consensus 43 ~~t~~eL~~~l~~~~stvs~~i~~Le~ 69 (109)
T TIGR01889 43 KLTLKEIIKEILIKQSALVKIIKKLSK 69 (109)
T ss_pred cCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 577899999999999999998766544
No 226
>PRK05949 RNA polymerase sigma factor; Validated
Probab=49.07 E-value=5.4 Score=39.14 Aligned_cols=48 Identities=21% Similarity=0.321 Sum_probs=41.1
Q ss_pred CCChhcceeeEEEec-c--CCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRL-S--SGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 107 ~l~~~~ql~i~L~~L-a--~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.+++.++-.+.|+|. . .+.++..||..+|||+++|.++..+....|..
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 388889999999884 3 56899999999999999999999888777765
No 227
>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=48.99 E-value=5.3 Score=26.31 Aligned_cols=22 Identities=18% Similarity=0.284 Sum_probs=18.6
Q ss_pred cchhhhcccccccccchhhhHH
Q 015432 126 SLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 126 s~~~la~~Fgis~sTvsr~i~~ 147 (407)
+..++|..+|||.+|+.+++..
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 4568999999999999988764
No 228
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=48.55 E-value=5.1 Score=27.95 Aligned_cols=28 Identities=29% Similarity=0.354 Sum_probs=22.7
Q ss_pred CCCcchhhhcccccccccchhhhHHHHH
Q 015432 123 SGESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 123 ~g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
...+..+|+..+|+|.+|+++++.+...
T Consensus 9 ~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 9 GELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3467789999999999999988866543
No 229
>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=48.52 E-value=10 Score=30.90 Aligned_cols=27 Identities=4% Similarity=0.091 Sum_probs=22.5
Q ss_pred CCcchhhhcccccccccchhhhHHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
+.+..+|+..++++++|+++.+.+...
T Consensus 42 ~~t~~ela~~~~~~~~tvs~~l~~Le~ 68 (118)
T TIGR02337 42 SMEFTQLANQACILRPSLTGILARLER 68 (118)
T ss_pred CcCHHHHHHHhCCCchhHHHHHHHHHH
Confidence 566789999999999999988766554
No 230
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=48.42 E-value=4.8 Score=29.38 Aligned_cols=40 Identities=23% Similarity=0.193 Sum_probs=34.9
Q ss_pred eEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 116 IALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 116 i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.+..+|+...+..+.|+..|+...+|.+++..|-..+.+.
T Consensus 5 ~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~L 44 (65)
T PF05344_consen 5 AFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQL 44 (65)
T ss_pred HHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHHc
Confidence 4556788889999999999999999999999998888763
No 231
>PRK09191 two-component response regulator; Provisional
Probab=48.39 E-value=7.1 Score=36.17 Aligned_cols=50 Identities=16% Similarity=0.207 Sum_probs=41.6
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhccc
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGLH 158 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~~ 158 (407)
+|..++-++.|.++ .|.++..||...|+|.+||...+.+....+.+.+..
T Consensus 89 L~~~~r~v~~l~~~-~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~~ 138 (261)
T PRK09191 89 LTPLPRQAFLLTAL-EGFSVEEAAEILGVDPAEAEALLDDARAEIARQVAT 138 (261)
T ss_pred CCHHHhHHHHHHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCCC
Confidence 67777777777766 489999999999999999999999988888866543
No 232
>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=47.93 E-value=7.3 Score=27.75 Aligned_cols=29 Identities=24% Similarity=0.288 Sum_probs=23.0
Q ss_pred cCCCcchhhhcccccccccchhhhHHHHH
Q 015432 122 SSGESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 122 a~g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
..+.+..+|+..+|++.+|+++.+....+
T Consensus 22 ~~~~t~~ela~~l~~~~~t~s~hL~~L~~ 50 (61)
T PF12840_consen 22 NGPMTVSELAEELGISQSTVSYHLKKLEE 50 (61)
T ss_dssp CSTBEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45677899999999999999998766544
No 233
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=47.19 E-value=6.2 Score=39.82 Aligned_cols=52 Identities=27% Similarity=0.348 Sum_probs=46.0
Q ss_pred CCCCCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 103 SNGKPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 103 ~~~~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.+.+.+...-|++|.|.+--+..|+..||..||-..|||.-.+.++...+.+
T Consensus 344 ~R~~~i~~~RqiamyL~r~lt~~Slp~IG~~FgrdHtTV~~a~~kI~~~~~~ 395 (408)
T COG0593 344 SRTRNIVRPRQIAMYLARELTNLSLPEIGKAFGRDHTTVLHAVRKIEQLIEE 395 (408)
T ss_pred ccccccchHHHHHHHHHHHHccCcHHHHHHHhCCCccHHHHHHHHHHHHHhc
Confidence 4556788899999999999999999999999999999998888888877764
No 234
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=46.98 E-value=4.8 Score=38.15 Aligned_cols=48 Identities=21% Similarity=0.340 Sum_probs=40.2
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
.+|+.++-++.|+|+ .|.++..||..+|+|.+||.+...+....|...
T Consensus 212 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 212 TLPEREKKVLILYYY-EDLTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 378888888888875 589999999999999999998887777766554
No 235
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=46.83 E-value=19 Score=33.00 Aligned_cols=45 Identities=9% Similarity=0.107 Sum_probs=34.5
Q ss_pred cCCCHHHHHHHHHHhhhhhhhhcCCCcCCCCCCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHH
Q 015432 75 FKISRKTFDYICSLVKEDLAARQSNFSFSNGKPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRF 148 (407)
Q Consensus 75 frmsr~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~ 148 (407)
-|++..||+.+++.+. +... +-+-..+|+..|+|+.|+.||+...
T Consensus 153 kGi~~~Tl~~i~~~~~-~~~~----------------------------~~Taeela~~~giSRvTaRRYLeyl 197 (224)
T COG4565 153 KGLDELTLQKVREALK-EPDQ----------------------------ELTAEELAQALGISRVTARRYLEYL 197 (224)
T ss_pred CCcCHHHHHHHHHHHh-CcCC----------------------------ccCHHHHHHHhCccHHHHHHHHHHH
Confidence 4889999999999988 2111 2334689999999999999987543
No 236
>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=46.81 E-value=3.7 Score=34.19 Aligned_cols=46 Identities=26% Similarity=0.341 Sum_probs=32.8
Q ss_pred CCCCCChhcceeeE-EEeccCCCcchhhhcccccccccchhhhHHHHHH
Q 015432 104 NGKPLSPNDMVAIA-LRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVES 151 (407)
Q Consensus 104 ~~~~l~~~~ql~i~-L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~a 151 (407)
+|+++|.+.+.-|. |. ..|.+-.+|+..++||.+.|++++.++-+.
T Consensus 14 nGrPLp~~~R~rIvela--~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~eT 60 (125)
T PF00292_consen 14 NGRPLPNELRQRIVELA--KEGVRPCDISRQLRVSHGCVSKILSRYRET 60 (125)
T ss_dssp TTSSS-HHHHHHHHHHH--HTT--HHHHHHHHT--HHHHHHHHHHHHHH
T ss_pred CCccCcHHHHHHHHHHh--hhcCCHHHHHHHHccchhHHHHHHHHHHHh
Confidence 56788887777665 33 369999999999999999999999887543
No 237
>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=46.48 E-value=8.8 Score=27.15 Aligned_cols=25 Identities=16% Similarity=0.279 Sum_probs=20.3
Q ss_pred cchhhhcccccccccchhhhHHHHH
Q 015432 126 SLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 126 s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
+..+|+..|++|++||++.+.+..+
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~ 51 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA 51 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5779999999999999987665443
No 238
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=46.10 E-value=5.4 Score=36.53 Aligned_cols=44 Identities=11% Similarity=0.072 Sum_probs=34.2
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
+++.++ -+|..++.|.+..+||..+++|.+||..++.++..-+.
T Consensus 144 LS~RE~--eVL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLg 187 (217)
T PRK13719 144 VTKYQN--DVFILYSFGFSHEYIAQLLNITVGSSKNKISEILKFFG 187 (217)
T ss_pred CCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 444333 23556788999999999999999999999887776654
No 239
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=45.84 E-value=3.7 Score=30.22 Aligned_cols=24 Identities=17% Similarity=0.303 Sum_probs=20.1
Q ss_pred CCcchhhhcccccccccchhhhHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~ 147 (407)
+.+..+||..+|++.++|++++..
T Consensus 22 ~~ta~eLa~~lgl~~~~v~r~L~~ 45 (68)
T smart00550 22 TSTALQLAKNLGLPKKEVNRVLYS 45 (68)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHH
Confidence 367789999999999999887654
No 240
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=45.64 E-value=5.8 Score=30.16 Aligned_cols=23 Identities=22% Similarity=0.413 Sum_probs=18.2
Q ss_pred CCCcchhhhcccccccccchhhh
Q 015432 123 SGESLQIIGDLFGLNQSTVSQVT 145 (407)
Q Consensus 123 ~g~s~~~la~~Fgis~sTvsr~i 145 (407)
.|.++.++|...|+++++||++.
T Consensus 30 ~~ltQ~e~A~~lgisq~~vS~l~ 52 (80)
T PF13744_consen 30 RGLTQAELAERLGISQPRVSRLE 52 (80)
T ss_dssp CT--HHHHHHHHTS-HHHHHHHH
T ss_pred cCCCHHHHHHHHCCChhHHHHHH
Confidence 47889999999999999999976
No 241
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=44.91 E-value=5.9 Score=36.44 Aligned_cols=60 Identities=10% Similarity=0.031 Sum_probs=40.6
Q ss_pred CCChhcceeeEEEeccCC----------CcchhhhcccccccccchhhhHHHHHHHHHhccccccCCChh
Q 015432 107 PLSPNDMVAIALRRLSSG----------ESLQIIGDLFGLNQSTVSQVTWRFVESMEERGLHHLQWPSKE 166 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g----------~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~~~i~~P~~~ 166 (407)
..+++++++-+|..++.. .+..+||...|+++.||+|++.++.+-=...-...|..++.+
T Consensus 146 ~~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~lG~tretvsR~l~~L~~~gl~~~~~~i~I~d~~ 215 (236)
T PRK09392 146 LRSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYLGMTPENLSRAFAALASHGVHVDGSAVTITDPA 215 (236)
T ss_pred cCCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHhCCChhHHHHHHHHHHhCCeEeeCCEEEEcCHH
Confidence 468889998888766532 224679999999999999998775443112223355556555
No 242
>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=44.78 E-value=9.7 Score=26.89 Aligned_cols=23 Identities=17% Similarity=0.328 Sum_probs=19.0
Q ss_pred CcchhhhcccccccccchhhhHH
Q 015432 125 ESLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 125 ~s~~~la~~Fgis~sTvsr~i~~ 147 (407)
.+..+++..|+||..|+.+-+..
T Consensus 15 ~s~~ela~~~~VS~~TiRRDl~~ 37 (57)
T PF08220_consen 15 VSVKELAEEFGVSEMTIRRDLNK 37 (57)
T ss_pred EEHHHHHHHHCcCHHHHHHHHHH
Confidence 45678999999999999986654
No 243
>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=44.78 E-value=7 Score=26.90 Aligned_cols=23 Identities=22% Similarity=0.280 Sum_probs=20.6
Q ss_pred CCCcchhhhcccccccccchhhh
Q 015432 123 SGESLQIIGDLFGLNQSTVSQVT 145 (407)
Q Consensus 123 ~g~s~~~la~~Fgis~sTvsr~i 145 (407)
.|.++.++|...|+|++|++++.
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~e 36 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDVE 36 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Confidence 47889999999999999999875
No 244
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=44.74 E-value=6.6 Score=37.94 Aligned_cols=22 Identities=32% Similarity=0.356 Sum_probs=19.4
Q ss_pred CcchhhhcccccccccchhhhH
Q 015432 125 ESLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 125 ~s~~~la~~Fgis~sTvsr~i~ 146 (407)
.+..+||...|||.+||||+++
T Consensus 6 ~ti~dIA~~agVS~~TVSrvLn 27 (331)
T PRK14987 6 PVLQDVADRVGVTKMTVSRFLR 27 (331)
T ss_pred CcHHHHHHHhCCCHHHhhhhhC
Confidence 3678999999999999999874
No 245
>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=44.55 E-value=4.2 Score=29.33 Aligned_cols=27 Identities=22% Similarity=0.341 Sum_probs=19.7
Q ss_pred CCcchhhhcccccccccchhhhHHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
..+..+|+..++++++|+++.+++.++
T Consensus 18 ~~t~~~l~~~~~~~~~~vs~~i~~L~~ 44 (68)
T PF13463_consen 18 PMTQSDLAERLGISKSTVSRIIKKLEE 44 (68)
T ss_dssp -BEHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 456789999999999999988766544
No 246
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=44.48 E-value=5.7 Score=33.62 Aligned_cols=27 Identities=15% Similarity=0.214 Sum_probs=22.1
Q ss_pred CCcchhhhcccccccccchhhhHHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
+.+..+|+..++++++|+++++.+...
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~ 72 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQLEE 72 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHHHH
Confidence 456789999999999999988766544
No 247
>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=44.33 E-value=8.3 Score=25.51 Aligned_cols=24 Identities=29% Similarity=0.376 Sum_probs=18.3
Q ss_pred CCcchhhhcccccccccchhhhHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~ 147 (407)
-.+|..||...|+|.+||.+-+.+
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 357899999999999999876544
No 248
>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=44.29 E-value=13 Score=26.37 Aligned_cols=30 Identities=23% Similarity=0.313 Sum_probs=25.2
Q ss_pred CcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 125 ESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 125 ~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.++...|..++||+++|++.+.+.-..+..
T Consensus 14 gs~~~AA~~l~is~~~vs~~i~~LE~~lg~ 43 (60)
T PF00126_consen 14 GSISAAAEELGISQSAVSRQIKQLEEELGV 43 (60)
T ss_dssp SSHHHHHHHCTSSHHHHHHHHHHHHHHHTS
T ss_pred CCHHHHHHHhhccchHHHHHHHHHHHHhCC
Confidence 478889999999999999988877766653
No 249
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=44.19 E-value=5.7 Score=29.92 Aligned_cols=25 Identities=20% Similarity=0.274 Sum_probs=21.3
Q ss_pred cCCCcchhhhcccc------cccccchhhhH
Q 015432 122 SSGESLQIIGDLFG------LNQSTVSQVTW 146 (407)
Q Consensus 122 a~g~s~~~la~~Fg------is~sTvsr~i~ 146 (407)
..|.++.++|...| +|++||||+-.
T Consensus 22 ~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 22 KLGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 45889999999999 59999999654
No 250
>PRK09526 lacI lac repressor; Reviewed
Probab=43.99 E-value=6.7 Score=38.01 Aligned_cols=22 Identities=27% Similarity=0.229 Sum_probs=19.8
Q ss_pred CcchhhhcccccccccchhhhH
Q 015432 125 ESLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 125 ~s~~~la~~Fgis~sTvsr~i~ 146 (407)
.+..+||...|||.+||||+++
T Consensus 6 ~ti~dIA~~aGVS~~TVSrvLn 27 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRVLN 27 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHhc
Confidence 3678999999999999999886
No 251
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=43.72 E-value=6.6 Score=38.03 Aligned_cols=23 Identities=26% Similarity=0.138 Sum_probs=20.4
Q ss_pred CcchhhhcccccccccchhhhHH
Q 015432 125 ESLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 125 ~s~~~la~~Fgis~sTvsr~i~~ 147 (407)
.+..+||..+|||.+|||++++.
T Consensus 7 ~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 7 ITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHHCC
Confidence 46889999999999999998764
No 252
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=43.67 E-value=30 Score=28.92 Aligned_cols=72 Identities=18% Similarity=0.290 Sum_probs=50.9
Q ss_pred HHHhhcCCCHHHHHHHHHHhhhhhhhhcCCCcCCCCCCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHH
Q 015432 70 NFESVFKISRKTFDYICSLVKEDLAARQSNFSFSNGKPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFV 149 (407)
Q Consensus 70 ~F~~~frmsr~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~ 149 (407)
-.+..+|++...++-+..+|... .+.+..+||...++++|||++.+++.+
T Consensus 18 vl~c~~GLs~~Dv~v~~~LL~~~------------------------------~~~tvdelae~lnr~rStv~rsl~~L~ 67 (126)
T COG3355 18 VLKCVYGLSELDVEVYKALLEEN------------------------------GPLTVDELAEILNRSRSTVYRSLQNLL 67 (126)
T ss_pred HHHHHhCCcHHHHHHHHHHHhhc------------------------------CCcCHHHHHHHHCccHHHHHHHHHHHH
Confidence 44678999999998888888522 134557899999999999999998887
Q ss_pred HH-HHH-------h-ccccccCCChhhHHHH
Q 015432 150 ES-MEE-------R-GLHHLQWPSKETEMED 171 (407)
Q Consensus 150 ~a-l~~-------~-~~~~i~~P~~~~~~~~ 171 (407)
.+ |.. - ...|+.-|...+++.+
T Consensus 68 ~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k~ 98 (126)
T COG3355 68 EAGLVEREKVNLKGGGYYYLYKPIDPEEIKK 98 (126)
T ss_pred HcCCeeeeeeccCCCceeEEEecCCHHHHHH
Confidence 75 221 1 2346666665545543
No 253
>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=43.28 E-value=40 Score=31.37 Aligned_cols=28 Identities=18% Similarity=0.255 Sum_probs=24.0
Q ss_pred CCcchhhhcccccccccchhhhHHHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVES 151 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~a 151 (407)
+.+..+|+...|+++||++|++...+..
T Consensus 24 ~~~l~eia~~lglpksT~~RlL~tL~~~ 51 (248)
T TIGR02431 24 RLTLTDVAEATGLTRAAARRFLLTLVEL 51 (248)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 5678999999999999999998776553
No 254
>PF13309 HTH_22: HTH domain
Probab=43.16 E-value=5.3 Score=29.09 Aligned_cols=21 Identities=14% Similarity=0.403 Sum_probs=18.1
Q ss_pred Ccchhhhcccccccccchhhh
Q 015432 125 ESLQIIGDLFGLNQSTVSQVT 145 (407)
Q Consensus 125 ~s~~~la~~Fgis~sTvsr~i 145 (407)
.+...+|..+|||+.||++++
T Consensus 43 gav~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 43 GAVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred cHHHHHHHHHCCCHHHHHHHc
Confidence 445689999999999999986
No 255
>PF12728 HTH_17: Helix-turn-helix domain
Probab=43.00 E-value=7.5 Score=26.44 Aligned_cols=21 Identities=24% Similarity=0.401 Sum_probs=18.0
Q ss_pred cchhhhcccccccccchhhhH
Q 015432 126 SLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 126 s~~~la~~Fgis~sTvsr~i~ 146 (407)
+..++|+.+|||.+|+.++++
T Consensus 3 t~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999998774
No 256
>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=42.94 E-value=10 Score=27.01 Aligned_cols=25 Identities=32% Similarity=0.336 Sum_probs=22.3
Q ss_pred CCCcchhhhcccccccccchhhhHH
Q 015432 123 SGESLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 123 ~g~s~~~la~~Fgis~sTvsr~i~~ 147 (407)
.|-+...||..+|++.+||+.+..+
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~r 36 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKDR 36 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHh
Confidence 5899999999999999999987654
No 257
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=42.85 E-value=7.1 Score=39.65 Aligned_cols=31 Identities=26% Similarity=0.283 Sum_probs=24.3
Q ss_pred CcchhhhcccccccccchhhhHHHHHHHHHhccccccCCCh
Q 015432 125 ESLQIIGDLFGLNQSTVSQVTWRFVESMEERGLHHLQWPSK 165 (407)
Q Consensus 125 ~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~~~i~~P~~ 165 (407)
...++||+..|+++|||||++. ..|+.-|..
T Consensus 331 L~LrdvA~~i~~HESTISRai~----------nKy~~tprG 361 (444)
T COG1508 331 LVLRDVADEIGMHESTISRAIT----------NKYLATPRG 361 (444)
T ss_pred ccHHHHHHHhCccHHHHHHHHh----------cccccCCcc
Confidence 5568999999999999999873 346666654
No 258
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=42.69 E-value=7.9 Score=37.36 Aligned_cols=22 Identities=32% Similarity=0.235 Sum_probs=19.2
Q ss_pred cchhhhcccccccccchhhhHH
Q 015432 126 SLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 126 s~~~la~~Fgis~sTvsr~i~~ 147 (407)
+..+||...|||++||||+++.
T Consensus 3 ti~dIA~~agVS~~TVSrvln~ 24 (327)
T PRK10339 3 TLKDIAIEAGVSLATVSRVLND 24 (327)
T ss_pred CHHHHHHHhCCCHHhhhhhhcC
Confidence 4679999999999999998753
No 259
>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=42.56 E-value=8.4 Score=25.44 Aligned_cols=21 Identities=14% Similarity=0.381 Sum_probs=17.8
Q ss_pred cchhhhcccccccccchhhhH
Q 015432 126 SLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 126 s~~~la~~Fgis~sTvsr~i~ 146 (407)
+..++|..+|||.+|+.+++.
T Consensus 3 t~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 567899999999999988764
No 260
>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=42.53 E-value=12 Score=29.52 Aligned_cols=54 Identities=15% Similarity=0.263 Sum_probs=37.7
Q ss_pred hhcCCCHHHHHHHHHHhhhhhhhhcCCCcCCCCCCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHH
Q 015432 73 SVFKISRKTFDYICSLVKEDLAARQSNFSFSNGKPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFV 149 (407)
Q Consensus 73 ~~frmsr~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~ 149 (407)
..+.++...+..|+.+.+..... + ...-..+..+||...|++++||++.+.+..
T Consensus 19 ~~~~l~~r~~~vLl~L~~~~~G~---------~--------------~~~~~is~~eLa~~~g~sr~tVsr~L~~Le 72 (95)
T TIGR01610 19 PGADLSGREFRVLLAIIRLTYGW---------N--------------KKQDRVTATVIAELTGLSRTHVSDAIKSLA 72 (95)
T ss_pred HhCCCCHHHHHHHHHHHHHHhCc---------c--------------ccCCccCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 46778888888888775422110 0 033467788999999999999998765543
No 261
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=42.28 E-value=6.4 Score=35.52 Aligned_cols=45 Identities=20% Similarity=0.197 Sum_probs=36.6
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
.+++.++ -.|..++.|.+..+||...+||.+||..+..+...-|.
T Consensus 150 ~Lt~rE~--evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~ 194 (216)
T PRK10840 150 RLSPKES--EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLG 194 (216)
T ss_pred cCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 4777665 56777899999999999999999999998876655553
No 262
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=42.26 E-value=6.5 Score=38.51 Aligned_cols=48 Identities=27% Similarity=0.432 Sum_probs=40.4
Q ss_pred CCChhcceeeEEEec---cCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRL---SSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 107 ~l~~~~ql~i~L~~L---a~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.|+..++..+.++|. ....++..||..||||++.|+++-.+.+.-|..
T Consensus 262 ~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~ 312 (324)
T PRK07921 262 TLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRN 312 (324)
T ss_pred hCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 388889999999884 245789999999999999999998887777754
No 263
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=42.03 E-value=15 Score=33.61 Aligned_cols=30 Identities=27% Similarity=0.302 Sum_probs=25.4
Q ss_pred CcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 125 ESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 125 ~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
.+..+||..||||+||++.++++...-|.+
T Consensus 179 ~~l~dLA~~lGISkst~~ehLRrAe~Kl~~ 208 (215)
T COG3413 179 VSLKDLAKELGISKSTLSEHLRRAERKLIE 208 (215)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 567899999999999999999887666554
No 264
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=41.89 E-value=8 Score=37.20 Aligned_cols=22 Identities=32% Similarity=0.332 Sum_probs=19.2
Q ss_pred cchhhhcccccccccchhhhHH
Q 015432 126 SLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 126 s~~~la~~Fgis~sTvsr~i~~ 147 (407)
+..+||...|||.+||||+++.
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 4679999999999999998753
No 265
>PF13551 HTH_29: Winged helix-turn helix
Probab=41.49 E-value=18 Score=28.65 Aligned_cols=80 Identities=18% Similarity=0.141 Sum_probs=43.9
Q ss_pred ChhHHHhhcCCCHHHHHHHHHHhhhhhh--hhcCCCcCCCCCC-CChhcceeeEEEeccCC-------Ccchhhhcc---
Q 015432 67 TSKNFESVFKISRKTFDYICSLVKEDLA--ARQSNFSFSNGKP-LSPNDMVAIALRRLSSG-------ESLQIIGDL--- 133 (407)
Q Consensus 67 ~d~~F~~~frmsr~tF~~L~~~l~~~~~--~~~~~~~~~~~~~-l~~~~ql~i~L~~La~g-------~s~~~la~~--- 133 (407)
+..+.-..+++++.|+...+......-. ..+.....++... ++.++.-. .+-++... .+...|+..
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~-l~~~~~~~p~~g~~~~t~~~l~~~l~~ 92 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQ-LIELLRENPPEGRSRWTLEELAEWLIE 92 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHH-HHHHHHHCCCCCCCcccHHHHHHHHHH
Confidence 4678889999999999998887765441 1110111122222 55444332 22222222 233455442
Q ss_pred --c--ccccccchhhhHH
Q 015432 134 --F--GLNQSTVSQVTWR 147 (407)
Q Consensus 134 --F--gis~sTvsr~i~~ 147 (407)
+ .+|.+||++++.+
T Consensus 93 ~~~~~~~s~~ti~r~L~~ 110 (112)
T PF13551_consen 93 EEFGIDVSPSTIRRILKR 110 (112)
T ss_pred hccCccCCHHHHHHHHHH
Confidence 2 5678888887754
No 266
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=41.17 E-value=5.4 Score=36.61 Aligned_cols=43 Identities=26% Similarity=0.318 Sum_probs=34.5
Q ss_pred CCChhcceeeEEEeccC--------------CCcchhhhcccccccccchhhhHHHH
Q 015432 107 PLSPNDMVAIALRRLSS--------------GESLQIIGDLFGLNQSTVSQVTWRFV 149 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~--------------g~s~~~la~~Fgis~sTvsr~i~~~~ 149 (407)
..+++++++-+|..|+. ..+...||...|+++.||+|++.++.
T Consensus 153 ~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~ 209 (235)
T PRK11161 153 KKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQ 209 (235)
T ss_pred CCCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCCcHHHHHHHHHHHH
Confidence 36889999999987752 24678999999999999999876543
No 267
>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=41.14 E-value=11 Score=27.14 Aligned_cols=22 Identities=23% Similarity=0.436 Sum_probs=16.4
Q ss_pred cchhhhcccccccccchhhhHH
Q 015432 126 SLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 126 s~~~la~~Fgis~sTvsr~i~~ 147 (407)
+...|+..||||++||.+.+..
T Consensus 26 s~~~la~~~~vsr~tvr~al~~ 47 (64)
T PF00392_consen 26 SERELAERYGVSRTTVREALRR 47 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHH
T ss_pred CHHHHHHHhccCCcHHHHHHHH
Confidence 4578999999999999876544
No 268
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=41.09 E-value=13 Score=28.42 Aligned_cols=27 Identities=26% Similarity=0.398 Sum_probs=22.8
Q ss_pred CCcchhhhcccccccccchhhhHHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
+.+..+|+..+|++++||++++.....
T Consensus 20 ~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 20 GLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 467789999999999999998876644
No 269
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=41.04 E-value=8.4 Score=35.15 Aligned_cols=43 Identities=26% Similarity=0.393 Sum_probs=34.4
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHH
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESM 152 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al 152 (407)
++..+. -.|..|+.|.+...||...++|.+||..++.+...-|
T Consensus 149 LT~RE~--eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 149 LTPREL--EVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCHHHH--HHHHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHc
Confidence 555444 3467789999999999999999999999887765554
No 270
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=40.90 E-value=7.9 Score=37.67 Aligned_cols=21 Identities=24% Similarity=0.294 Sum_probs=19.1
Q ss_pred cchhhhcccccccccchhhhH
Q 015432 126 SLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 126 s~~~la~~Fgis~sTvsr~i~ 146 (407)
+..+||...|||.+||||+++
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (346)
T PRK10401 3 TIRDVARQAGVSVATVSRVLN 23 (346)
T ss_pred CHHHHHHHhCCCHHHHHHHHC
Confidence 568999999999999999885
No 271
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=40.76 E-value=49 Score=31.32 Aligned_cols=27 Identities=19% Similarity=0.014 Sum_probs=23.3
Q ss_pred CCcchhhhcccccccccchhhhHHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
+.+..+|+...|+++||++|++...+.
T Consensus 40 ~~tl~eIa~~lglpkStv~RlL~tL~~ 66 (271)
T PRK10163 40 SSSVSDISLNLDLPLSTTFRLLKVLQA 66 (271)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 456889999999999999998877665
No 272
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=39.79 E-value=8.8 Score=37.19 Aligned_cols=22 Identities=23% Similarity=0.359 Sum_probs=19.6
Q ss_pred cchhhhcccccccccchhhhHH
Q 015432 126 SLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 126 s~~~la~~Fgis~sTvsr~i~~ 147 (407)
+..+||...|||.+|||++++.
T Consensus 3 Ti~dIA~~agVS~~TVSrvLn~ 24 (341)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINK 24 (341)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 5679999999999999998864
No 273
>PHA01976 helix-turn-helix protein
Probab=39.77 E-value=9.4 Score=27.51 Aligned_cols=24 Identities=13% Similarity=0.093 Sum_probs=21.1
Q ss_pred cCCCcchhhhcccccccccchhhh
Q 015432 122 SSGESLQIIGDLFGLNQSTVSQVT 145 (407)
Q Consensus 122 a~g~s~~~la~~Fgis~sTvsr~i 145 (407)
..|.+..++|...|||++|++++.
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~e 36 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDFE 36 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 458889999999999999999864
No 274
>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=39.06 E-value=6 Score=28.51 Aligned_cols=25 Identities=28% Similarity=0.349 Sum_probs=20.9
Q ss_pred CCcchhhhcccccccccchhhhHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRF 148 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~ 148 (407)
+.+..+++..++++.+|+++.+...
T Consensus 20 ~~~~~ei~~~~~i~~~~i~~~l~~L 44 (78)
T cd00090 20 PLTVSELAERLGLSQSTVSRHLKKL 44 (78)
T ss_pred CcCHHHHHHHHCcCHhHHHHHHHHH
Confidence 3778899999999999998877664
No 275
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=38.80 E-value=9 Score=36.78 Aligned_cols=19 Identities=37% Similarity=0.399 Sum_probs=17.3
Q ss_pred hhhhcccccccccchhhhH
Q 015432 128 QIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 128 ~~la~~Fgis~sTvsr~i~ 146 (407)
.+||...|||.+||||+++
T Consensus 2 ~dIA~~agVS~~TVSrvLn 20 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVIN 20 (327)
T ss_pred hhHHHHhCCcHHHHHHHhC
Confidence 5899999999999999875
No 276
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=38.67 E-value=8.1 Score=36.06 Aligned_cols=45 Identities=13% Similarity=0.201 Sum_probs=36.0
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
.++..++= +|.+++.|.+..+||..++||..||..++.++..-|.
T Consensus 179 ~LT~rE~e--vl~~~a~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~ 223 (240)
T PRK10188 179 NFSKREKE--ILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFN 223 (240)
T ss_pred CCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 46665554 3556799999999999999999999998887766654
No 277
>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=38.49 E-value=8.3 Score=35.73 Aligned_cols=46 Identities=17% Similarity=0.193 Sum_probs=37.8
Q ss_pred CCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 106 KPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 106 ~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
..++..++=.+.+ .+.|.++.+||..+|||.+||..++.+...-|.
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 4577776666555 589999999999999999999999888766664
No 278
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=38.45 E-value=9.5 Score=26.97 Aligned_cols=35 Identities=23% Similarity=0.394 Sum_probs=28.4
Q ss_pred EEeccCCCcchhhhcccccccccchhhhHHHHHHH
Q 015432 118 LRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESM 152 (407)
Q Consensus 118 L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al 152 (407)
+.+++.|.+...+|..+++|..||.....++..-+
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 34567789999999999999999998877665444
No 279
>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=37.67 E-value=13 Score=27.17 Aligned_cols=24 Identities=17% Similarity=0.315 Sum_probs=20.0
Q ss_pred CcchhhhcccccccccchhhhHHH
Q 015432 125 ESLQIIGDLFGLNQSTVSQVTWRF 148 (407)
Q Consensus 125 ~s~~~la~~Fgis~sTvsr~i~~~ 148 (407)
.+...++..||||.+||++.+...
T Consensus 14 ~~~~eLa~~l~vS~~tv~~~l~~L 37 (69)
T TIGR00122 14 FSGEKLGEALGMSRTAVNKHIQTL 37 (69)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHH
Confidence 346789999999999999887664
No 280
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=37.55 E-value=48 Score=27.91 Aligned_cols=132 Identities=15% Similarity=0.046 Sum_probs=73.2
Q ss_pred eeeeeEEEeecCCCCCCcchhcCCCCcceeEEEeeeCCCcceeeccccCCCcccccccccccchhhhhhhcccCCCcccc
Q 015432 188 AIDITHIVMNIPAVDPANNVWYDREKNYSMILQGIVDPEMRFRDIIAGWPGSLTDALVLRNSGFFKLTEEGKRLDGKSLQ 267 (407)
Q Consensus 188 aIDgt~i~i~~P~~~~~~~~y~~~k~~~s~~~q~v~d~~grf~~v~~g~pGs~~D~~v~~~S~l~~~l~~g~~l~~~~~~ 267 (407)
.||-|-|.|.- + -.-+-.++|++|+++++.+.---...++.-|-.- .+... .
T Consensus 5 ~~DEt~iki~G----~------------~~yl~~aiD~~~~~l~~~ls~~Rd~~aA~~Fl~~----~l~~~---~----- 56 (140)
T PF13610_consen 5 HVDETYIKIKG----K------------WHYLWRAIDAEGNILDFYLSKRRDTAAAKRFLKR----ALKRH---R----- 56 (140)
T ss_pred EEeeEEEEECC----E------------EEEEEEeecccccchhhhhhhhcccccceeeccc----cceee---c-----
Confidence 57888888772 1 1124578899999888877544444443333221 11110 0
Q ss_pred CCCccccceeeecCCC--ccCCccccccCCCCCCCchhhhhhhhhhhhhhHHHHHHHHHHhHHHhhcccccCCCCCchhH
Q 015432 268 LSEGIELREYIIGDTG--FPLLPWLLTPYQGKGLSDIEAEYNKRHSATRMVAQMALARLKDVWRIIHGVMWMPDKNRLPR 345 (407)
Q Consensus 268 ~~~g~~~~~~llgD~g--Ypl~~~l~tP~~~~~lt~~~~~fN~~ls~~R~~vE~afg~LK~rfriL~~~~~~~~~~~~~~ 345 (407)
..+..|+.|.+ |+.--.-+.+-.... ..-+. ....-.+..||+-+..+|.|.+...+- .+...+..
T Consensus 57 -----~~p~~ivtDk~~aY~~A~~~l~~~~~~~-~~v~~---~~~k~~nN~iE~~h~~~K~r~r~~~gF---ks~~~A~~ 124 (140)
T PF13610_consen 57 -----GEPRVIVTDKLPAYPAAIKELNPEGRLH-DKVEH---RQRKYLNNRIERDHRTIKRRTRPMNGF---KSFRSAQR 124 (140)
T ss_pred -----cccceeecccCCccchhhhhcccccccc-cccce---eechhhhChhhHhhhhhhhhcccccCc---CCHHHHHH
Confidence 11356777753 443211111110000 00000 111134688999999999888766554 24567778
Q ss_pred HHHHHHHHhhhhcc
Q 015432 346 IVLVCCLLHNIVID 359 (407)
Q Consensus 346 ii~accvLHN~~i~ 359 (407)
++..-.+.||+...
T Consensus 125 ~l~~~~~~~n~~r~ 138 (140)
T PF13610_consen 125 TLSGFEAYHNFRRP 138 (140)
T ss_pred HHHHHHHHHHHhCC
Confidence 89999999998753
No 281
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=37.52 E-value=9.5 Score=34.73 Aligned_cols=43 Identities=26% Similarity=0.370 Sum_probs=33.6
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHH
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESM 152 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al 152 (407)
+++.++ =.|..++.|.+..+||...+||..||..+..+...-|
T Consensus 135 LT~RE~--eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KL 177 (207)
T PRK11475 135 LSPTER--EILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKL 177 (207)
T ss_pred CCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 554433 3466788999999999999999999999887765544
No 282
>PRK09483 response regulator; Provisional
Probab=36.99 E-value=9.8 Score=33.78 Aligned_cols=44 Identities=18% Similarity=0.401 Sum_probs=34.3
Q ss_pred CCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHH
Q 015432 107 PLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESM 152 (407)
Q Consensus 107 ~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al 152 (407)
.++..+.=.+ ..++.|.+...||..+++|.+||..++.+...-|
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 3666554443 4678999999999999999999999887766555
No 283
>PRK10870 transcriptional repressor MprA; Provisional
Probab=36.95 E-value=46 Score=29.38 Aligned_cols=26 Identities=4% Similarity=0.065 Sum_probs=21.4
Q ss_pred CCcchhhhcccccccccchhhhHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFV 149 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~ 149 (407)
+.+..+||..++++++|+++++.+..
T Consensus 71 ~it~~eLa~~l~l~~~tvsr~v~rLe 96 (176)
T PRK10870 71 SIQPSELSCALGSSRTNATRIADELE 96 (176)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 35678999999999999998776543
No 284
>COG5421 Transposase [DNA replication, recombination, and repair]
Probab=36.50 E-value=47 Score=34.05 Aligned_cols=56 Identities=16% Similarity=0.189 Sum_probs=37.0
Q ss_pred ceeEEEeeeCCCcceeeccccCCCcccccccccccchhhhhhhcccCCCccccCCCccccceeeecCCCcc
Q 015432 215 YSMILQGIVDPEMRFRDIIAGWPGSLTDALVLRNSGFFKLTEEGKRLDGKSLQLSEGIELREYIIGDTGFP 285 (407)
Q Consensus 215 ~s~~~q~v~d~~grf~~v~~g~pGs~~D~~v~~~S~l~~~l~~g~~l~~~~~~~~~g~~~~~~llgD~gYp 285 (407)
.-+++..+++..|--+.+.+ ++|+.+|...+-. ..+.+.+. +...+.|+++|+||-
T Consensus 155 ~QI~vsMi~~~~gIPl~~~v-~~Gni~D~~~~~~--ti~kl~~~------------l~~~~~~~V~Dkgf~ 210 (480)
T COG5421 155 PQINVSMIVNQKGIPLFVRV-YSGNISDKNTLIK--TIQKLKSV------------LVKDEVYLVADKGFN 210 (480)
T ss_pred ceeEEEEEEcCCCCceEEEc-cCCCccchHHHHH--HHHHHHHh------------cccceEEEEEccccc
Confidence 46788888888865555444 8999999987753 33333221 111137999999994
No 285
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=36.49 E-value=11 Score=34.59 Aligned_cols=44 Identities=18% Similarity=0.261 Sum_probs=33.7
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
++..++=. |..++.|.++.+||..+++|.+||..++.+...-+.
T Consensus 156 Lt~rE~~V--l~l~~~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 156 LTHREKEI--LNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCHHHHHH--HHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 55544333 445667999999999999999999999887766654
No 286
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=36.47 E-value=17 Score=28.12 Aligned_cols=24 Identities=17% Similarity=0.243 Sum_probs=20.2
Q ss_pred chhhhcccccccccchhhhHHHHH
Q 015432 127 LQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 127 ~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
+..+|..+||+++|+++.+.+...
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~ 25 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEK 25 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHH
Confidence 467899999999999998876655
No 287
>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=36.21 E-value=11 Score=36.33 Aligned_cols=21 Identities=33% Similarity=0.330 Sum_probs=18.3
Q ss_pred chhhhcccccccccchhhhHH
Q 015432 127 LQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 127 ~~~la~~Fgis~sTvsr~i~~ 147 (407)
..+||...|||.+||||+++.
T Consensus 2 i~dIA~~aGVS~~TVSrvLn~ 22 (327)
T TIGR02417 2 LSDIAKLAGVSKTTASYVING 22 (327)
T ss_pred HHHHHHHhCCCHHHHHHHHcC
Confidence 468999999999999998753
No 288
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=36.01 E-value=14 Score=37.63 Aligned_cols=32 Identities=28% Similarity=0.368 Sum_probs=25.3
Q ss_pred CCcchhhhcccccccccchhhhHHHHHHHHHhccccccCCCh
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVESMEERGLHHLQWPSK 165 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~~~i~~P~~ 165 (407)
...+.+||+..|++.|||||++ ...|+..|..
T Consensus 318 PLtlkdiA~~lglheSTVSRav----------~~Kyi~tp~G 349 (429)
T TIGR02395 318 PLTLREVAEELGLHESTISRAI----------NNKYLQTPRG 349 (429)
T ss_pred CCcHHHHHHHhCCCccchhhhh----------cCceEecCCc
Confidence 4668999999999999999976 3456666654
No 289
>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=35.38 E-value=11 Score=36.19 Aligned_cols=21 Identities=24% Similarity=0.253 Sum_probs=18.7
Q ss_pred cchhhhcccccccccchhhhH
Q 015432 126 SLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 126 s~~~la~~Fgis~sTvsr~i~ 146 (407)
+..+||...|||.+||||+++
T Consensus 3 ti~dIA~~agvS~~TVSrvLn 23 (329)
T TIGR01481 3 TIYDVAREAGVSMATVSRVVN 23 (329)
T ss_pred cHHHHHHHhCCCHHHHHHHhC
Confidence 467999999999999999875
No 290
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=35.32 E-value=4.9 Score=28.69 Aligned_cols=32 Identities=28% Similarity=0.396 Sum_probs=27.6
Q ss_pred CCCCCChhcceeeEEEeccCCCcchhhhcccc
Q 015432 104 NGKPLSPNDMVAIALRRLSSGESLQIIGDLFG 135 (407)
Q Consensus 104 ~~~~l~~~~ql~i~L~~La~g~s~~~la~~Fg 135 (407)
+.+.+...-+++|.|..--.|.++.+||..||
T Consensus 25 R~~~~~~aR~iamyla~~~~~~sl~~Ig~~fg 56 (60)
T smart00760 25 RKREIVLARQIAMYLARELTDLSLPEIGKIFG 56 (60)
T ss_pred CCcchhHHHHHHHHHHHHHHCCCHHHHHHHhC
Confidence 34568888899998888889999999999998
No 291
>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=35.24 E-value=12 Score=25.00 Aligned_cols=23 Identities=13% Similarity=0.076 Sum_probs=20.0
Q ss_pred CCcchhhhcccccccccchhhhH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~ 146 (407)
+.+.+.|+...|+|++++++++.
T Consensus 16 ~~s~~~Ia~~~gvs~~~~y~~f~ 38 (47)
T PF00440_consen 16 AVSIRDIARRAGVSKGSFYRYFP 38 (47)
T ss_dssp TSSHHHHHHHHTSCHHHHHHHCS
T ss_pred hCCHHHHHHHHccchhhHHHHcC
Confidence 56788999999999999998764
No 292
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=35.15 E-value=11 Score=36.50 Aligned_cols=21 Identities=29% Similarity=0.393 Sum_probs=18.8
Q ss_pred cchhhhcccccccccchhhhH
Q 015432 126 SLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 126 s~~~la~~Fgis~sTvsr~i~ 146 (407)
+..+||...|||.+||||+++
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVIN 23 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhC
Confidence 467999999999999999875
No 293
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=33.94 E-value=10 Score=26.90 Aligned_cols=24 Identities=21% Similarity=0.282 Sum_probs=17.6
Q ss_pred CCCcchhhhcccccccccchhhhH
Q 015432 123 SGESLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 123 ~g~s~~~la~~Fgis~sTvsr~i~ 146 (407)
.|.+...+|..-|||++|++++++
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~ 32 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILN 32 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHh
Confidence 467889999999999999999875
No 294
>PRK10072 putative transcriptional regulator; Provisional
Probab=33.88 E-value=14 Score=29.33 Aligned_cols=25 Identities=12% Similarity=0.244 Sum_probs=21.9
Q ss_pred cCCCcchhhhcccccccccchhhhH
Q 015432 122 SSGESLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 122 a~g~s~~~la~~Fgis~sTvsr~i~ 146 (407)
..|.++..+|..+|||.+||++|.+
T Consensus 44 ~~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 44 GTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 4588999999999999999998753
No 295
>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=32.32 E-value=16 Score=26.35 Aligned_cols=25 Identities=24% Similarity=0.303 Sum_probs=20.0
Q ss_pred eccCC--Ccchhhhcccccccccchhh
Q 015432 120 RLSSG--ESLQIIGDLFGLNQSTVSQV 144 (407)
Q Consensus 120 ~La~g--~s~~~la~~Fgis~sTvsr~ 144 (407)
|+.++ ..+.+||..+|||.+||+++
T Consensus 16 y~~~~g~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 16 YKESNGKIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred HHHhCCCccHHHHHHHHCCCHHHHHHH
Confidence 34444 56789999999999999875
No 296
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=32.21 E-value=22 Score=38.15 Aligned_cols=47 Identities=15% Similarity=0.385 Sum_probs=39.8
Q ss_pred CCChhcceeeEEEec---cCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 107 PLSPNDMVAIALRRL---SSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 107 ~l~~~~ql~i~L~~L---a~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
.|+..++..+.|+|. ..+.++..||..||||++.|+++-.+.+.-|-
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 388999999999885 36688999999999999999998877666654
No 297
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=32.06 E-value=14 Score=36.14 Aligned_cols=21 Identities=29% Similarity=0.442 Sum_probs=18.4
Q ss_pred cchhhhcccccccccchhhhH
Q 015432 126 SLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 126 s~~~la~~Fgis~sTvsr~i~ 146 (407)
+..+||...|||.+||||+++
T Consensus 2 TikDVA~~AGVS~sTVSrvln 22 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLN 22 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHc
Confidence 457899999999999999865
No 298
>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=31.22 E-value=18 Score=23.67 Aligned_cols=25 Identities=16% Similarity=0.319 Sum_probs=18.6
Q ss_pred CCCcchhhhcccccccccchhhhHH
Q 015432 123 SGESLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 123 ~g~s~~~la~~Fgis~sTvsr~i~~ 147 (407)
++.+....|...|||++|+++-+.+
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 4667789999999999999876543
No 299
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=31.07 E-value=19 Score=37.23 Aligned_cols=33 Identities=27% Similarity=0.372 Sum_probs=26.0
Q ss_pred CCcchhhhcccccccccchhhhHHHHHHHHHhccccccCCChh
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVESMEERGLHHLQWPSKE 166 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~~~i~~P~~~ 166 (407)
...+++||+..|++.|||||++ ...|+..|..-
T Consensus 369 PLtlkdVAe~lglHeSTVSRa~----------~~KY~~tp~Gi 401 (481)
T PRK12469 369 PLVLRDVAEELGLHESTISRAT----------GNKYMATPRGT 401 (481)
T ss_pred CCcHHHHHHHhCCCcchhhHHh----------cCceeecCCce
Confidence 4567999999999999999986 34567666553
No 300
>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=30.89 E-value=22 Score=27.10 Aligned_cols=33 Identities=9% Similarity=0.110 Sum_probs=25.9
Q ss_pred cCCCcchhhhcccccccccchhhhHHHHHHHHH
Q 015432 122 SSGESLQIIGDLFGLNQSTVSQVTWRFVESMEE 154 (407)
Q Consensus 122 a~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~ 154 (407)
..+.+..++|+.+.||+||+.+.+.++-..|..
T Consensus 28 ~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~~ 60 (87)
T PF05043_consen 28 NEYVSIEDLAEELFISRSTIYRDIKKLNKYLKK 60 (87)
T ss_dssp -SEEEHHHHHHHHT--HHHHHHHHHHHHHHHHC
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345678899999999999999999988888774
No 301
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=30.34 E-value=20 Score=36.91 Aligned_cols=32 Identities=25% Similarity=0.302 Sum_probs=25.3
Q ss_pred CCcchhhhcccccccccchhhhHHHHHHHHHhccccccCCCh
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVESMEERGLHHLQWPSK 165 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~~~i~~P~~ 165 (407)
...+.+||+..|++.|||||++ ...|+..|..
T Consensus 343 PLtlkdvAe~lglheSTVSRav----------~~Kyv~tp~G 374 (455)
T PRK05932 343 PLVLKDIAEELGMHESTISRAT----------TNKYMATPRG 374 (455)
T ss_pred CccHHHHHHHhCCCccchhhhh----------cCceeecCCc
Confidence 4568899999999999999976 3456666654
No 302
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=30.24 E-value=16 Score=23.13 Aligned_cols=24 Identities=25% Similarity=0.357 Sum_probs=19.4
Q ss_pred cCCCcchhhhcccccccccchhhh
Q 015432 122 SSGESLQIIGDLFGLNQSTVSQVT 145 (407)
Q Consensus 122 a~g~s~~~la~~Fgis~sTvsr~i 145 (407)
....|.++.+..+|++++|+++++
T Consensus 14 ~~F~Si~eAa~~l~i~~~~I~~~l 37 (37)
T PF07453_consen 14 KSFDSIREAARYLGISHSTISKYL 37 (37)
T ss_pred EEEcCHHHHHHHhCCCHHHHHHhC
Confidence 345678889999999999998763
No 303
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=30.21 E-value=43 Score=27.93 Aligned_cols=58 Identities=24% Similarity=0.394 Sum_probs=43.0
Q ss_pred hhcCCCHHHHHHHHHHhhhhhhhhcCCCcCCCCCCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHH
Q 015432 73 SVFKISRKTFDYICSLVKEDLAARQSNFSFSNGKPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 73 ~~frmsr~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
-.|..+++-|.+|++.|+..+... .+.+.++| .|.+.+|...||+.-||+|.....-.
T Consensus 4 i~f~s~~PIY~QI~~qIk~~I~~g----------~l~pGdkL----------PSvRelA~~~~VNpnTv~raY~eLE~ 61 (125)
T COG1725 4 IDFDSSKPIYEQIANQIKEQIASG----------ELKPGDKL----------PSVRELAKDLGVNPNTVQRAYQELER 61 (125)
T ss_pred cCcCCCCCHHHHHHHHHHHHHHhC----------CcCCCCCC----------CcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 356778889999999999887663 23333333 36789999999999999997766544
No 304
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=30.13 E-value=9.2 Score=31.29 Aligned_cols=38 Identities=13% Similarity=0.170 Sum_probs=31.4
Q ss_pred eEEEeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 116 IALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 116 i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
....++.+.++...++..+|||=+||..-+.+++.+|-
T Consensus 41 Fi~~Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg 78 (113)
T PF09862_consen 41 FIKLFIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLG 78 (113)
T ss_pred HHHHHHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhC
Confidence 33445556778999999999999999999998888885
No 305
>COG3293 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.84 E-value=31 Score=28.32 Aligned_cols=57 Identities=16% Similarity=0.135 Sum_probs=39.6
Q ss_pred eeecCCCccCCccccccCCCC------CCCchhhhhhhhhhhhhhHHHHHHHHHHhHHHhhccc
Q 015432 277 YIIGDTGFPLLPWLLTPYQGK------GLSDIEAEYNKRHSATRMVAQMALARLKDVWRIIHGV 334 (407)
Q Consensus 277 ~llgD~gYpl~~~l~tP~~~~------~lt~~~~~fN~~ls~~R~~vE~afg~LK~rfriL~~~ 334 (407)
-+|.|.+|...+|.+-|-.-. .....+.-++..+...|..+|+.|+.+| .|+.+...
T Consensus 39 ~~i~~~~~~g~~wr~~p~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~f~~~~-~~r~~~~~ 101 (124)
T COG3293 39 NGIADLLYTGCAWRALPADFPPATTVIPYRRFRRWFKRGLWKRRNLVERTFGRLK-QFRRTATR 101 (124)
T ss_pred HHHHHHhccchHHHHhHHHhCCCceEeCCCcchhhHHHHHHHHHHHHHHHHHHHh-cccceecc
Confidence 378888998887765443211 1111367888999999999999999888 46666543
No 306
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=29.76 E-value=52 Score=26.06 Aligned_cols=25 Identities=4% Similarity=0.123 Sum_probs=21.5
Q ss_pred CcchhhhcccccccccchhhhHHHH
Q 015432 125 ESLQIIGDLFGLNQSTVSQVTWRFV 149 (407)
Q Consensus 125 ~s~~~la~~Fgis~sTvsr~i~~~~ 149 (407)
.+..++|..+|+|.+++++.+.+..
T Consensus 22 ~~~~~lA~~~~~S~~~l~r~f~~~~ 46 (107)
T PRK10219 22 LNIDVVAKKSGYSKWYLQRMFRTVT 46 (107)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4567999999999999999988763
No 307
>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=29.50 E-value=27 Score=27.76 Aligned_cols=33 Identities=9% Similarity=-0.044 Sum_probs=27.5
Q ss_pred CCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 123 SGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 123 ~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
...|+...|...|||++|+++.+.+.-..+-..
T Consensus 15 ~~gSis~AA~~L~iS~stvs~~I~~LE~~lg~~ 47 (99)
T TIGR00637 15 RMGSISQAAKDAGISYKSAWDYIRAMNNLSGEP 47 (99)
T ss_pred HhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 356788899999999999999998887777643
No 308
>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=28.99 E-value=16 Score=34.33 Aligned_cols=46 Identities=13% Similarity=0.286 Sum_probs=37.2
Q ss_pred CCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 106 KPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 106 ~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
..++..++=.+.| ++.|.++.+||..++||..||..++.+...-+.
T Consensus 189 ~~LT~RE~evl~l--~a~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~ 234 (247)
T TIGR03020 189 GLITAREAEILAW--VRDGKTNEEIAAILGISSLTVKNHLQHIFKKLD 234 (247)
T ss_pred cCCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHhC
Confidence 3577777666665 679999999999999999999998877765553
No 309
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=28.41 E-value=18 Score=26.76 Aligned_cols=24 Identities=25% Similarity=0.508 Sum_probs=21.1
Q ss_pred cCCCcchhhhcccccccccchhhh
Q 015432 122 SSGESLQIIGDLFGLNQSTVSQVT 145 (407)
Q Consensus 122 a~g~s~~~la~~Fgis~sTvsr~i 145 (407)
..|.+..++|...|+|++|++++.
T Consensus 16 ~~~~t~~~lA~~~gis~~tis~~~ 39 (78)
T TIGR02607 16 PLGLSIRALAKALGVSRSTLSRIV 39 (78)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 457888999999999999999875
No 310
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=28.21 E-value=18 Score=31.49 Aligned_cols=36 Identities=22% Similarity=0.346 Sum_probs=30.2
Q ss_pred EEEeccCCCcchhhhcccccccccchhhhHHHHHHH
Q 015432 117 ALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESM 152 (407)
Q Consensus 117 ~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al 152 (407)
.|..|+.|.+...||..+++|.+||..++.++..-+
T Consensus 145 il~~l~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 145 VAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKL 180 (196)
T ss_pred HHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 355578899999999999999999998887776655
No 311
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=28.00 E-value=34 Score=27.01 Aligned_cols=26 Identities=12% Similarity=0.070 Sum_probs=21.6
Q ss_pred CCCcchhhhcccccccccchhhhHHH
Q 015432 123 SGESLQIIGDLFGLNQSTVSQVTWRF 148 (407)
Q Consensus 123 ~g~s~~~la~~Fgis~sTvsr~i~~~ 148 (407)
.+.++.+.|.+.|||+.|+.+.++.-
T Consensus 48 ~~l~QeeAA~rMgISr~Tfwr~l~sA 73 (99)
T COG1342 48 EGLTQEEAALRMGISRQTFWRLLTSA 73 (99)
T ss_pred hhccHHHHHHHhcccHHHHHHHHHHH
Confidence 36778899999999999998877543
No 312
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=27.95 E-value=88 Score=27.98 Aligned_cols=25 Identities=20% Similarity=0.185 Sum_probs=20.5
Q ss_pred CCCcchhhhcccccccccchhhhHH
Q 015432 123 SGESLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 123 ~g~s~~~la~~Fgis~sTvsr~i~~ 147 (407)
.|.++.+||...+++++|+++++.+
T Consensus 58 ~~itq~eLa~~l~l~~sTvtr~l~r 82 (185)
T PRK13777 58 KGASISEIAKFGVMHVSTAFNFSKK 82 (185)
T ss_pred CCcCHHHHHHHHCCCHhhHHHHHHH
Confidence 3678899999999999998876543
No 313
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=27.83 E-value=12 Score=35.77 Aligned_cols=35 Identities=14% Similarity=0.109 Sum_probs=29.9
Q ss_pred ccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 121 LSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 121 La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
..+|.++...|+..+||+||||+.+.+.-..|-..
T Consensus 13 ~~~~~s~s~AA~~L~isq~avSr~I~~LE~~lg~~ 47 (309)
T PRK12682 13 VRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIE 47 (309)
T ss_pred HHccCCHHHHHHHhcCccHHHHHHHHHHHHHhCCe
Confidence 34567999999999999999999999988887643
No 314
>PF11044 TMEMspv1-c74-12: Plectrovirus spv1-c74 ORF 12 transmembrane protein; InterPro: IPR022743 This is a group of proteins expressed by Plectroviruses. The Plectroviruses are single-stranded DNA viruses belonging to the Inoviridae. This entry represents putative transmembrane proteins of unknown function.
Probab=27.68 E-value=24 Score=23.55 Aligned_cols=8 Identities=63% Similarity=0.912 Sum_probs=3.2
Q ss_pred chhhhhhh
Q 015432 5 RGLKRRKK 12 (407)
Q Consensus 5 ~~~~~~~~ 12 (407)
||+||.||
T Consensus 33 rgKkk~KK 40 (49)
T PF11044_consen 33 RGKKKEKK 40 (49)
T ss_pred HhhhhhHH
Confidence 44444333
No 315
>PRK00215 LexA repressor; Validated
Probab=27.58 E-value=33 Score=30.89 Aligned_cols=26 Identities=27% Similarity=0.263 Sum_probs=21.9
Q ss_pred Ccchhhhccccc-ccccchhhhHHHHH
Q 015432 125 ESLQIIGDLFGL-NQSTVSQVTWRFVE 150 (407)
Q Consensus 125 ~s~~~la~~Fgi-s~sTvsr~i~~~~~ 150 (407)
.++.+||..+|+ +++|+++++.....
T Consensus 24 ~s~~ela~~~~~~~~~tv~~~l~~L~~ 50 (205)
T PRK00215 24 PSRREIADALGLRSPSAVHEHLKALER 50 (205)
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 478899999999 99999998766544
No 316
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=27.56 E-value=30 Score=27.49 Aligned_cols=27 Identities=33% Similarity=0.300 Sum_probs=22.6
Q ss_pred CCcchhhhcccccccccchhhhHHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
..++..++..+|+|++|+++.+.+...
T Consensus 17 ~~~~~~la~~l~~s~~tv~~~l~~L~~ 43 (108)
T smart00344 17 RISLAELAKKVGLSPSTVHNRVKRLEE 43 (108)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 467899999999999999987766544
No 317
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=27.25 E-value=7.1 Score=28.32 Aligned_cols=26 Identities=15% Similarity=0.084 Sum_probs=19.4
Q ss_pred cCCCcchhhhcccccccccchhhhHH
Q 015432 122 SSGESLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 122 a~g~s~~~la~~Fgis~sTvsr~i~~ 147 (407)
..+.+-++||+.+|+|..++.+++..
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~ 38 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEK 38 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 44566789999999999999887643
No 318
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=27.22 E-value=17 Score=27.98 Aligned_cols=28 Identities=25% Similarity=0.286 Sum_probs=23.0
Q ss_pred CCcchhhhcccccccccchhhhHHHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVES 151 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~a 151 (407)
+.+...|+..++++++|+++.+.+....
T Consensus 24 ~~~~~~la~~~~~s~~~i~~~l~~L~~~ 51 (101)
T smart00347 24 PLSVSELAKRLGVSPSTVTRVLDRLEKK 51 (101)
T ss_pred CcCHHHHHHHHCCCchhHHHHHHHHHHC
Confidence 3567889999999999999988776653
No 319
>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=27.07 E-value=23 Score=28.61 Aligned_cols=29 Identities=14% Similarity=0.321 Sum_probs=21.6
Q ss_pred CCcchhhhcccccccccchhhhHHHHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVESM 152 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~al 152 (407)
|.+...||..||+|..+|.+|+.+.-...
T Consensus 72 G~n~~eLA~kyglS~r~I~~Ii~~~~~~~ 100 (108)
T PF08765_consen 72 GMNVRELARKYGLSERQIYRIIKRVRRRE 100 (108)
T ss_dssp SS-HHHHHHHHT--HHHHHHHHHHHHH--
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 88899999999999999999998765543
No 320
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=27.04 E-value=22 Score=31.60 Aligned_cols=64 Identities=19% Similarity=0.204 Sum_probs=42.8
Q ss_pred CChhcceeeEEEeccC--------------CCcchhhhcccccccccchhhhHHHHHH-HHHhccccccCCChhhHHHHH
Q 015432 108 LSPNDMVAIALRRLSS--------------GESLQIIGDLFGLNQSTVSQVTWRFVES-MEERGLHHLQWPSKETEMEDI 172 (407)
Q Consensus 108 l~~~~ql~i~L~~La~--------------g~s~~~la~~Fgis~sTvsr~i~~~~~a-l~~~~~~~i~~P~~~~~~~~i 172 (407)
.++.++|+-+|..|+. ..++.+||...|+++.||+|++.++.+. +.+.....|..++.+ .+.++
T Consensus 119 ~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~d~~-~L~~~ 197 (202)
T PRK13918 119 QRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRETVTKVIGELSREGYIRSGYGKIQLLDLK-GLEEL 197 (202)
T ss_pred CchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcCCCEEEEECHH-HHHHH
Confidence 4567777777765542 2457899999999999999999887652 333333455556555 44444
No 321
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=26.94 E-value=11 Score=28.60 Aligned_cols=24 Identities=29% Similarity=0.351 Sum_probs=18.3
Q ss_pred CCCcchhhhcccccccccchhhhH
Q 015432 123 SGESLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 123 ~g~s~~~la~~Fgis~sTvsr~i~ 146 (407)
.|.++..|+..+|++.+|+...+.
T Consensus 14 rG~sL~~lsr~~Gl~~~tl~nal~ 37 (78)
T PF13693_consen 14 RGTSLAALSREAGLSSSTLRNALR 37 (78)
T ss_dssp TS--HHHHHHHHSS-HHHHHHTTT
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHc
Confidence 488999999999999999987664
No 322
>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=26.90 E-value=30 Score=25.24 Aligned_cols=23 Identities=26% Similarity=0.326 Sum_probs=16.8
Q ss_pred CCcchhhhcccccc-cccchhhhH
Q 015432 124 GESLQIIGDLFGLN-QSTVSQVTW 146 (407)
Q Consensus 124 g~s~~~la~~Fgis-~sTvsr~i~ 146 (407)
..++++|+..||++ .+||++++.
T Consensus 25 ~Pt~rEIa~~~g~~S~~tv~~~L~ 48 (65)
T PF01726_consen 25 PPTVREIAEALGLKSTSTVQRHLK 48 (65)
T ss_dssp ---HHHHHHHHTSSSHHHHHHHHH
T ss_pred CCCHHHHHHHhCCCChHHHHHHHH
Confidence 34678999999996 888887653
No 323
>cd00131 PAX Paired Box domain
Probab=26.86 E-value=38 Score=28.28 Aligned_cols=80 Identities=13% Similarity=0.075 Sum_probs=44.9
Q ss_pred CChhHHHhhcCCCHHHHHHHHHHhhhhhhhhcCCCcCCCCCC-CChh-cceeeEEEeccCCCcchhhhccc---cc----
Q 015432 66 KTSKNFESVFKISRKTFDYICSLVKEDLAARQSNFSFSNGKP-LSPN-DMVAIALRRLSSGESLQIIGDLF---GL---- 136 (407)
Q Consensus 66 ~~d~~F~~~frmsr~tF~~L~~~l~~~~~~~~~~~~~~~~~~-l~~~-~ql~i~L~~La~g~s~~~la~~F---gi---- 136 (407)
.+..+--..|++++.|...++......-...+- -..+.++. +..+ ....+.+..-.-..+...+++.+ ||
T Consensus 34 ~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk-~~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~ 112 (128)
T cd00131 34 IRPCDISRQLRVSHGCVSKILNRYYETGSIRPG-AIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKS 112 (128)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCC-CCCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccC
Confidence 466778899999999999999887764433221 11111122 2332 22222222222234455555542 55
Q ss_pred ---ccccchhhhH
Q 015432 137 ---NQSTVSQVTW 146 (407)
Q Consensus 137 ---s~sTvsr~i~ 146 (407)
|.||+++++.
T Consensus 113 ~~~s~stI~R~L~ 125 (128)
T cd00131 113 NVPSVSSINRILR 125 (128)
T ss_pred CCCCHHHHHHHHH
Confidence 8999988764
No 324
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=26.74 E-value=51 Score=32.41 Aligned_cols=60 Identities=23% Similarity=0.350 Sum_probs=46.4
Q ss_pred CCCCChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhccccccCCChh
Q 015432 105 GKPLSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGLHHLQWPSKE 166 (407)
Q Consensus 105 ~~~l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~~~i~~P~~~ 166 (407)
.+.++++.|++++|+.+ +|.+-..|+..|=|+.+|+-+-|.+--..|.+..-.| .-|...
T Consensus 118 HPal~~~~riALtLR~v-~GLs~~eIArAFLv~e~am~QRivRAK~ri~~agiPf-evP~~~ 177 (415)
T COG4941 118 HPALPPEQRIALTLRLV-GGLSTAEIARAFLVPEAAMAQRIVRAKARIREAGIPF-EVPGPQ 177 (415)
T ss_pred CCCCChhhHHHHHHHHH-cCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHhcCCCC-cCCChh
Confidence 36799999999999876 5999999999999999999877766666666543222 345554
No 325
>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=26.68 E-value=21 Score=24.48 Aligned_cols=21 Identities=19% Similarity=0.471 Sum_probs=16.3
Q ss_pred cchhhhcccccccccchhhhH
Q 015432 126 SLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 126 s~~~la~~Fgis~sTvsr~i~ 146 (407)
+..+++..+|+|++|+.+.+.
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 346889999999999998775
No 326
>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=26.46 E-value=27 Score=25.29 Aligned_cols=25 Identities=20% Similarity=0.274 Sum_probs=20.5
Q ss_pred CcchhhhcccccccccchhhhHHHH
Q 015432 125 ESLQIIGDLFGLNQSTVSQVTWRFV 149 (407)
Q Consensus 125 ~s~~~la~~Fgis~sTvsr~i~~~~ 149 (407)
.+..+|+...|++++||++++.+..
T Consensus 23 ~t~~eIa~~l~i~~~~v~~~L~~L~ 47 (68)
T PF01978_consen 23 ATAEEIAEELGISRSTVYRALKSLE 47 (68)
T ss_dssp EEHHHHHHHHTSSHHHHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4567999999999999998776543
No 327
>PRK10651 transcriptional regulator NarL; Provisional
Probab=26.12 E-value=19 Score=31.55 Aligned_cols=43 Identities=21% Similarity=0.339 Sum_probs=33.8
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHH
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESM 152 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al 152 (407)
++..+. =.|.+|+.|.+...||..+++|..||..++.+...-|
T Consensus 156 Lt~rE~--~vl~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl 198 (216)
T PRK10651 156 LTPRER--DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKM 198 (216)
T ss_pred CCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 555443 3345678999999999999999999999887776655
No 328
>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=25.82 E-value=25 Score=26.41 Aligned_cols=23 Identities=17% Similarity=0.153 Sum_probs=17.0
Q ss_pred CCcchhhhcccccccccchhhhH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~ 146 (407)
..+..+||...|||.+||.|..+
T Consensus 34 ~~si~elA~~~~vS~sti~Rf~k 56 (77)
T PF01418_consen 34 FMSISELAEKAGVSPSTIVRFCK 56 (77)
T ss_dssp T--HHHHHHHCTS-HHHHHHHHH
T ss_pred HccHHHHHHHcCCCHHHHHHHHH
Confidence 45678999999999999988654
No 329
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=25.25 E-value=30 Score=32.29 Aligned_cols=33 Identities=18% Similarity=0.251 Sum_probs=27.2
Q ss_pred eeeEEEeccCCCcchhhhcccccccccchhhhH
Q 015432 114 VAIALRRLSSGESLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 114 l~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~ 146 (407)
+.-.|+.|+..-+|.+++..+|++.|..+||++
T Consensus 13 ~v~~lr~lk~~~ty~el~~~~g~p~~~l~RYv~ 45 (238)
T PRK08558 13 AVRVLRSLKKTYTYEELSSITGLPESVLNRYVN 45 (238)
T ss_pred HHHHHHHHhcccCHHHHHHHHCCCHHHHHHHHc
Confidence 344566677777999999999999999999874
No 330
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=25.05 E-value=21 Score=25.71 Aligned_cols=20 Identities=20% Similarity=0.273 Sum_probs=16.8
Q ss_pred Ccchhhhcccccccccchhh
Q 015432 125 ESLQIIGDLFGLNQSTVSQV 144 (407)
Q Consensus 125 ~s~~~la~~Fgis~sTvsr~ 144 (407)
.+...+|..+|||+++|+++
T Consensus 10 G~~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 10 GGQSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp SSHHHHHHHHTS-HHHHHHH
T ss_pred CCHHHHHHHHCCCHHHHHHh
Confidence 46678999999999999998
No 331
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=24.94 E-value=19 Score=31.55 Aligned_cols=43 Identities=23% Similarity=0.339 Sum_probs=34.2
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHH
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESM 152 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al 152 (407)
++..+. -+|..|..|.+...|++.+++|.+||..++.+...-|
T Consensus 144 lt~~E~--~vl~~l~~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl 186 (204)
T PRK09958 144 LSKQEI--SVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKL 186 (204)
T ss_pred CCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 555443 3667778899999999999999999999887766655
No 332
>PRK10403 transcriptional regulator NarP; Provisional
Probab=24.91 E-value=21 Score=31.14 Aligned_cols=44 Identities=18% Similarity=0.337 Sum_probs=34.6
Q ss_pred CChhcceeeEEEeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 108 LSPNDMVAIALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 108 l~~~~ql~i~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
++..+.- .|.+++.|.+...|+...++|..||..++.+...-|.
T Consensus 154 Lt~~e~~--vl~~~~~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 154 LTERELD--VLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred CCHHHHH--HHHHHHCCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 5554443 3567788999999999999999999998888766653
No 333
>PRK11050 manganese transport regulator MntR; Provisional
Probab=23.78 E-value=38 Score=29.11 Aligned_cols=28 Identities=21% Similarity=0.257 Sum_probs=23.5
Q ss_pred CCCcchhhhcccccccccchhhhHHHHH
Q 015432 123 SGESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 123 ~g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
.+.+..+|+..++|+++||++.+.+...
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~ 77 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLAR 77 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3567889999999999999998876655
No 334
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=23.59 E-value=1.3e+02 Score=28.10 Aligned_cols=26 Identities=12% Similarity=0.065 Sum_probs=22.4
Q ss_pred CcchhhhcccccccccchhhhHHHHH
Q 015432 125 ESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 125 ~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
.+..+|+...|+++||++|++...+.
T Consensus 29 l~l~eia~~lgl~kstv~Rll~tL~~ 54 (257)
T PRK15090 29 IGITELSQRVMMSKSTVYRFLQTMKT 54 (257)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 56789999999999999998876554
No 335
>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=23.58 E-value=33 Score=30.08 Aligned_cols=25 Identities=24% Similarity=0.371 Sum_probs=21.1
Q ss_pred cchhhhcccccccccchhhhHHHHH
Q 015432 126 SLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 126 s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
++..||..+|+|++||++.+....+
T Consensus 77 t~~~ia~~l~iS~~Tv~r~ik~L~e 101 (165)
T PF05732_consen 77 TQKEIAEKLGISKPTVSRAIKELEE 101 (165)
T ss_pred eHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 5889999999999999998766544
No 336
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=23.22 E-value=28 Score=28.53 Aligned_cols=26 Identities=23% Similarity=0.225 Sum_probs=22.9
Q ss_pred eccCCCcchhhhcccccccccchhhh
Q 015432 120 RLSSGESLQIIGDLFGLNQSTVSQVT 145 (407)
Q Consensus 120 ~La~g~s~~~la~~Fgis~sTvsr~i 145 (407)
+-..|.++..+|..+|+|++|++++-
T Consensus 74 r~~~gltq~~lA~~lg~~~~tis~~e 99 (127)
T TIGR03830 74 RKKLGLSQREAAELLGGGVNAFSRYE 99 (127)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 45569999999999999999999874
No 337
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=23.15 E-value=25 Score=30.39 Aligned_cols=36 Identities=14% Similarity=0.295 Sum_probs=30.3
Q ss_pred EEeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 118 LRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 118 L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
|.++..|.+...||...++|..||..++.+...-|.
T Consensus 158 l~l~~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 158 LKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred HHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 445789999999999999999999998887666553
No 338
>PRK09726 antitoxin HipB; Provisional
Probab=23.03 E-value=24 Score=27.21 Aligned_cols=24 Identities=21% Similarity=0.310 Sum_probs=20.9
Q ss_pred CCCcchhhhcccccccccchhhhH
Q 015432 123 SGESLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 123 ~g~s~~~la~~Fgis~sTvsr~i~ 146 (407)
.|.++..+|...|||++|++++.+
T Consensus 24 ~gltq~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 24 NGWTQSELAKKIGIKQATISNFEN 47 (88)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHC
Confidence 478889999999999999998653
No 339
>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=23.02 E-value=25 Score=23.28 Aligned_cols=22 Identities=18% Similarity=0.225 Sum_probs=17.2
Q ss_pred cchhhhcccccccccchhhhHH
Q 015432 126 SLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 126 s~~~la~~Fgis~sTvsr~i~~ 147 (407)
+...+|..+||+.+|+..+..+
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHC
Confidence 3467899999999999887543
No 340
>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=22.70 E-value=31 Score=22.27 Aligned_cols=24 Identities=17% Similarity=0.441 Sum_probs=15.4
Q ss_pred eccCCCcchhhhcccccccccchh
Q 015432 120 RLSSGESLQIIGDLFGLNQSTVSQ 143 (407)
Q Consensus 120 ~La~g~s~~~la~~Fgis~sTvsr 143 (407)
....|+++..||.+||++.+.+.+
T Consensus 2 ~V~~gDtl~~IA~~~~~~~~~l~~ 25 (44)
T PF01476_consen 2 TVQPGDTLWSIAKRYGISVDELME 25 (44)
T ss_dssp EE-TT--HHHHHHHTTS-HHHHHH
T ss_pred EECcCCcHHHHHhhhhhhHhHHHH
Confidence 356789999999999888776544
No 341
>KOG4620 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.46 E-value=1.4e+02 Score=22.30 Aligned_cols=30 Identities=23% Similarity=0.409 Sum_probs=25.5
Q ss_pred chHHHhhhhcCCCCCCCCChhHHHhhcCCCHHHHHHHHHHhh
Q 015432 49 DWWDNFSRRISGPLFGSKTSKNFESVFKISRKTFDYICSLVK 90 (407)
Q Consensus 49 ~ww~~~~~r~~~~~~~~~~d~~F~~~frmsr~tF~~L~~~l~ 90 (407)
.-|..|+. ++|+++-+++|..|.+|--+++
T Consensus 31 ~~~m~fvh------------~EFrk~~~lpr~Df~~IEhLlR 60 (80)
T KOG4620|consen 31 RRWMAFVH------------AEFRKHAGLPRSDFLRIEHLLR 60 (80)
T ss_pred HHHHHHHH------------HHHHHhcCCcHhHHHHHHHHHH
Confidence 45777877 7999999999999999887775
No 342
>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=22.41 E-value=37 Score=31.19 Aligned_cols=21 Identities=19% Similarity=0.183 Sum_probs=16.8
Q ss_pred chhhhcccccccccchhhhHH
Q 015432 127 LQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 127 ~~~la~~Fgis~sTvsr~i~~ 147 (407)
...|+..||||+.||.+.+..
T Consensus 27 E~eLa~~~gVSR~TVR~Al~~ 47 (233)
T TIGR02404 27 EHELMDQYGASRETVRKALNL 47 (233)
T ss_pred HHHHHHHHCCCHHHHHHHHHH
Confidence 357889999999999875543
No 343
>COG5566 Uncharacterized conserved protein [Function unknown]
Probab=22.29 E-value=39 Score=28.08 Aligned_cols=27 Identities=15% Similarity=0.259 Sum_probs=24.1
Q ss_pred CCcchhhhcccccccccchhhhHHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVE 150 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~ 150 (407)
|.+|.+++..+.+|..+|.++++++..
T Consensus 102 G~n~~eLaKkYrlS~~~Iy~VIrr~~t 128 (137)
T COG5566 102 GSNYVELAKKYRLSENHIYRVIRRTHT 128 (137)
T ss_pred CccHHHHHHHhcccHHHHHHHHHHHHH
Confidence 888999999999999999999986644
No 344
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=22.27 E-value=40 Score=27.75 Aligned_cols=28 Identities=14% Similarity=0.000 Sum_probs=23.6
Q ss_pred CCcchhhhcccccccccchhhhHHHHHH
Q 015432 124 GESLQIIGDLFGLNQSTVSQVTWRFVES 151 (407)
Q Consensus 124 g~s~~~la~~Fgis~sTvsr~i~~~~~a 151 (407)
..+..+|+..++++++|||+.+....++
T Consensus 30 ~~~v~ela~~l~lsqstvS~HL~~L~~A 57 (117)
T PRK10141 30 ELCVCDLCTALDQSQPKISRHLALLRES 57 (117)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3567899999999999999998776665
No 345
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=22.08 E-value=19 Score=34.66 Aligned_cols=36 Identities=14% Similarity=0.100 Sum_probs=30.0
Q ss_pred eccCCCcchhhhcccccccccchhhhHHHHHHHHHh
Q 015432 120 RLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEER 155 (407)
Q Consensus 120 ~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~ 155 (407)
...+|.|+...|+.+++|+++||+.+.+.-..+-..
T Consensus 12 v~~~~~S~s~AA~~L~isQpavS~~I~~LE~~lg~~ 47 (309)
T PRK12683 12 AVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVE 47 (309)
T ss_pred HHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhCCe
Confidence 344567999999999999999999999888877643
No 346
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=21.93 E-value=30 Score=28.95 Aligned_cols=23 Identities=13% Similarity=0.084 Sum_probs=20.5
Q ss_pred CCCcchhhhcccccccccchhhh
Q 015432 123 SGESLQIIGDLFGLNQSTVSQVT 145 (407)
Q Consensus 123 ~g~s~~~la~~Fgis~sTvsr~i 145 (407)
.|.++..+|...|||++||+++.
T Consensus 17 ~gltq~~lA~~~gvs~~~is~~E 39 (135)
T PRK09706 17 LKLSQRSLAKAVKVSHVSISQWE 39 (135)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Confidence 47888999999999999999864
No 347
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=21.90 E-value=35 Score=24.10 Aligned_cols=35 Identities=9% Similarity=0.101 Sum_probs=27.7
Q ss_pred EeccCCCcchhhhcccccccccchhhhHHHHHHHH
Q 015432 119 RRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESME 153 (407)
Q Consensus 119 ~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~ 153 (407)
.||.++.+....|...+|++.|+..-+.++.+.+.
T Consensus 7 ~yl~~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g 41 (59)
T PF13556_consen 7 AYLENNGNISKTARALHIHRNTLRYRLKKIEELLG 41 (59)
T ss_dssp HHHHTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 36788999999999999999999887777766653
No 348
>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=21.84 E-value=32 Score=24.70 Aligned_cols=22 Identities=18% Similarity=0.327 Sum_probs=18.5
Q ss_pred cchhhhcccccccccchhhhHH
Q 015432 126 SLQIIGDLFGLNQSTVSQVTWR 147 (407)
Q Consensus 126 s~~~la~~Fgis~sTvsr~i~~ 147 (407)
+..++|..+||+.+|+.++..+
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 3468999999999999998754
No 349
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=21.38 E-value=26 Score=25.41 Aligned_cols=20 Identities=25% Similarity=0.360 Sum_probs=14.6
Q ss_pred cchhhhcccccccccch-hhh
Q 015432 126 SLQIIGDLFGLNQSTVS-QVT 145 (407)
Q Consensus 126 s~~~la~~Fgis~sTvs-r~i 145 (407)
+..++|+.+|||++|++ .+.
T Consensus 14 ~~~~lA~~lgis~st~s~~~~ 34 (66)
T PF07022_consen 14 SDKELAERLGISKSTLSNNWK 34 (66)
T ss_dssp SCHHHHCCTT--HHHHH-HHH
T ss_pred CHHHHHHHhCcCHHHhhHHHH
Confidence 34699999999999999 554
No 350
>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=20.97 E-value=82 Score=24.73 Aligned_cols=30 Identities=30% Similarity=0.231 Sum_probs=19.7
Q ss_pred eccCCCcchhhhcccccccccchhhhHHHH
Q 015432 120 RLSSGESLQIIGDLFGLNQSTVSQVTWRFV 149 (407)
Q Consensus 120 ~La~g~s~~~la~~Fgis~sTvsr~i~~~~ 149 (407)
||-.|.+-..++..+||++|-.++.+.+.-
T Consensus 49 yLV~G~srkeac~~~gV~~syfs~~L~rL~ 78 (91)
T PF03333_consen 49 YLVDGLSRKEACERHGVNQSYFSRALNRLN 78 (91)
T ss_dssp HHTT---HHHHHHHTT--HHHHHHHHHHHH
T ss_pred HHHcCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 344588899999999999999988776543
No 351
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=20.88 E-value=22 Score=34.26 Aligned_cols=36 Identities=14% Similarity=0.083 Sum_probs=30.2
Q ss_pred ccCCCcchhhhcccccccccchhhhHHHHHHHHHhc
Q 015432 121 LSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERG 156 (407)
Q Consensus 121 La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~ 156 (407)
..++.++...|+..+||+||||+.+.+.-..|-..+
T Consensus 13 ~~~~~s~s~AA~~L~iSQ~avSr~I~~LE~~lg~~L 48 (316)
T PRK12679 13 ARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEI 48 (316)
T ss_pred HHcCCCHHHHHHHhcCCchHHHHHHHHHHHHhCCEE
Confidence 345679999999999999999999999888876543
No 352
>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=20.65 E-value=14 Score=32.88 Aligned_cols=41 Identities=15% Similarity=0.178 Sum_probs=29.7
Q ss_pred CCCChhcceeeEEEecc-CCCcchhhhcccccccccchhhhH
Q 015432 106 KPLSPNDMVAIALRRLS-SGESLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 106 ~~l~~~~ql~i~L~~La-~g~s~~~la~~Fgis~sTvsr~i~ 146 (407)
..+++.++...+...+. .|.+...||..+|+|+++|++++.
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 45666665444433343 578999999999999999998763
No 353
>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=20.51 E-value=32 Score=26.83 Aligned_cols=23 Identities=26% Similarity=0.173 Sum_probs=17.1
Q ss_pred CCCcchhhhcccccccccchhhh
Q 015432 123 SGESLQIIGDLFGLNQSTVSQVT 145 (407)
Q Consensus 123 ~g~s~~~la~~Fgis~sTvsr~i 145 (407)
.|.+..+||..+|.|++.|++++
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~l 24 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSRSWVSNHL 24 (93)
T ss_dssp TT--HHHHHHHTT--HHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHH
Confidence 47889999999999999999875
No 354
>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=20.29 E-value=20 Score=30.18 Aligned_cols=45 Identities=18% Similarity=0.169 Sum_probs=35.0
Q ss_pred CChhcceeeEEEeccC-CCcchhhhcccccccccchhhhHHHHHHH
Q 015432 108 LSPNDMVAIALRRLSS-GESLQIIGDLFGLNQSTVSQVTWRFVESM 152 (407)
Q Consensus 108 l~~~~ql~i~L~~La~-g~s~~~la~~Fgis~sTvsr~i~~~~~al 152 (407)
+..+++-.+-|+|-.. +.++..||..+.||.+|+.++...|-..|
T Consensus 82 l~de~k~Ii~lry~~r~~~TW~~IA~~l~i~erta~r~~~~fK~~i 127 (130)
T PF05263_consen 82 LIDEEKRIIKLRYDRRSRRTWYQIAQKLHISERTARRWRDRFKNDI 127 (130)
T ss_pred hCHHHHHHHHHHHcccccchHHHHHHHhCccHHHHHHHHHHHHHHh
Confidence 3444555566777665 78999999999999999999988876654
No 355
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=20.16 E-value=35 Score=23.08 Aligned_cols=24 Identities=17% Similarity=0.241 Sum_probs=20.2
Q ss_pred CCCcchhhhcccccccccchhhhH
Q 015432 123 SGESLQIIGDLFGLNQSTVSQVTW 146 (407)
Q Consensus 123 ~g~s~~~la~~Fgis~sTvsr~i~ 146 (407)
.-.+..+.|..+|++.+++++++.
T Consensus 16 ~f~S~~eAa~~lg~~~~~I~~~~~ 39 (53)
T smart00497 16 EFSSIREAAKYLGISHSSISKYLN 39 (53)
T ss_pred EecCHHHHHHHhCCCHHHHHHHHh
Confidence 346788999999999999998764
No 356
>PF14493 HTH_40: Helix-turn-helix domain
Probab=20.07 E-value=23 Score=27.47 Aligned_cols=59 Identities=27% Similarity=0.316 Sum_probs=38.3
Q ss_pred EEEeccCCCcchhhhcccccccccchhhhHHHHHHHHHhccccccCCChhhHHHHHHHHHHh
Q 015432 117 ALRRLSSGESLQIIGDLFGLNQSTVSQVTWRFVESMEERGLHHLQWPSKETEMEDIKSKFEK 178 (407)
Q Consensus 117 ~L~~La~g~s~~~la~~Fgis~sTvsr~i~~~~~al~~~~~~~i~~P~~~~~~~~i~~~f~~ 178 (407)
++..+..|.+...||..-+++.|||..++-+.+..=... .+-.+-+.+ ....+...+.+
T Consensus 6 T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~--~~~~~l~~e-~~~~I~~~~~~ 64 (91)
T PF14493_consen 6 TYELFQKGLSIEEIAKIRGLKESTIYGHLAELIESGEPL--DIEELLSEE-EIKQIEDAIEK 64 (91)
T ss_pred HHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCC--CHHHhCCHH-HHHHHHHHHHH
Confidence 445566899999999999999999998876665542211 111222333 56666666543
Done!