Query 046385
Match_columns 218
No_of_seqs 163 out of 362
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 11:34:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046385.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046385hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13613 HTH_Tnp_4: Helix-turn 98.8 7.3E-09 1.6E-13 69.8 4.2 48 90-137 2-49 (53)
2 KOG4585 Predicted transposase 98.7 2.7E-08 5.9E-13 90.2 5.5 146 64-217 7-217 (326)
3 PF13936 HTH_38: Helix-turn-he 96.2 0.0026 5.6E-08 41.0 1.5 41 89-130 3-43 (44)
4 PF12116 SpoIIID: Stage III sp 96.0 0.0049 1.1E-07 45.0 2.2 45 97-141 9-54 (82)
5 PF04545 Sigma70_r4: Sigma-70, 96.0 0.01 2.2E-07 38.7 3.6 45 90-135 4-48 (50)
6 PF04218 CENP-B_N: CENP-B N-te 95.0 0.034 7.4E-07 37.2 3.6 41 89-130 5-45 (53)
7 PF02796 HTH_7: Helix-turn-hel 94.1 0.012 2.7E-07 37.9 -0.2 34 96-129 10-43 (45)
8 COG3415 Transposase and inacti 93.9 0.052 1.1E-06 43.6 2.9 45 89-133 3-47 (138)
9 smart00351 PAX Paired Box doma 93.7 0.084 1.8E-06 41.3 3.7 45 88-133 15-59 (125)
10 smart00421 HTH_LUXR helix_turn 93.5 0.1 2.3E-06 33.5 3.4 44 91-136 4-47 (58)
11 cd00131 PAX Paired Box domain 93.2 0.11 2.4E-06 40.9 3.7 47 87-134 14-60 (128)
12 PF13384 HTH_23: Homeodomain-l 93.0 0.035 7.6E-07 35.9 0.5 34 98-131 8-41 (50)
13 PRK11753 DNA-binding transcrip 92.7 0.085 1.8E-06 43.5 2.6 58 89-146 137-208 (211)
14 PF13518 HTH_28: Helix-turn-he 92.5 0.13 2.9E-06 33.2 2.7 37 96-133 2-38 (52)
15 TIGR02531 yecD_yerC TrpR-relat 92.0 0.17 3.7E-06 37.6 3.1 35 93-128 37-71 (88)
16 PF05225 HTH_psq: helix-turn-h 91.8 0.17 3.6E-06 32.8 2.5 37 94-130 2-39 (45)
17 PRK10402 DNA-binding transcrip 91.3 0.34 7.4E-06 40.9 4.7 56 91-146 149-209 (226)
18 TIGR03697 NtcA_cyano global ni 91.3 0.43 9.4E-06 38.6 5.1 57 90-146 112-183 (193)
19 TIGR01321 TrpR trp operon repr 91.3 0.19 4.1E-06 37.9 2.7 39 91-129 33-77 (94)
20 cd06170 LuxR_C_like C-terminal 91.1 0.31 6.8E-06 31.4 3.4 42 93-136 3-44 (57)
21 PRK01381 Trp operon repressor; 90.3 0.25 5.4E-06 37.6 2.6 39 91-129 33-77 (99)
22 cd06171 Sigma70_r4 Sigma70, re 90.2 0.39 8.4E-06 30.1 3.1 43 91-134 11-53 (55)
23 PRK04217 hypothetical protein; 89.6 0.45 9.7E-06 36.8 3.6 48 89-137 41-88 (110)
24 cd06571 Bac_DnaA_C C-terminal 89.3 0.63 1.4E-05 34.2 4.1 48 89-136 26-74 (90)
25 PF13542 HTH_Tnp_ISL3: Helix-t 88.5 0.43 9.3E-06 30.9 2.4 32 100-131 19-51 (52)
26 PRK11161 fumarate/nitrate redu 88.2 0.73 1.6E-05 38.8 4.3 57 90-146 153-224 (235)
27 TIGR02937 sigma70-ECF RNA poly 88.1 0.62 1.3E-05 35.3 3.5 46 90-136 110-155 (158)
28 PRK09639 RNA polymerase sigma 88.0 0.72 1.6E-05 36.5 4.0 47 90-138 112-158 (166)
29 PRK09391 fixK transcriptional 88.0 0.97 2.1E-05 38.3 5.0 45 90-134 152-206 (230)
30 cd00092 HTH_CRP helix_turn_hel 87.3 0.54 1.2E-05 31.6 2.4 41 94-134 2-52 (67)
31 PF08281 Sigma70_r4_2: Sigma-7 86.8 0.94 2E-05 29.5 3.3 44 90-134 10-53 (54)
32 PRK09652 RNA polymerase sigma 86.7 0.97 2.1E-05 35.9 4.0 47 90-137 128-174 (182)
33 cd00569 HTH_Hin_like Helix-tur 86.7 0.55 1.2E-05 26.4 1.9 37 91-128 6-42 (42)
34 PRK09392 ftrB transcriptional 86.5 1.4 3E-05 37.1 5.0 45 90-134 146-200 (236)
35 PRK15320 transcriptional activ 86.4 0.58 1.3E-05 40.2 2.6 38 99-136 171-208 (251)
36 PF01371 Trp_repressor: Trp re 86.4 0.82 1.8E-05 33.9 3.1 36 94-129 36-71 (87)
37 PRK00118 putative DNA-binding 86.1 1.2 2.7E-05 34.0 4.1 45 91-136 18-62 (104)
38 PRK05911 RNA polymerase sigma 86.0 1.1 2.3E-05 39.1 4.2 48 90-138 205-252 (257)
39 TIGR00721 tfx DNA-binding prot 85.9 0.92 2E-05 36.4 3.4 45 90-136 6-50 (137)
40 PRK09047 RNA polymerase factor 85.8 1.4 3E-05 34.7 4.4 53 90-143 106-159 (161)
41 PF01022 HTH_5: Bacterial regu 85.2 0.81 1.7E-05 29.4 2.3 39 96-134 4-42 (47)
42 TIGR02985 Sig70_bacteroi1 RNA 85.1 1.2 2.6E-05 34.6 3.8 46 90-136 113-158 (161)
43 PRK12529 RNA polymerase sigma 85.1 1.3 2.8E-05 36.0 4.0 47 90-137 127-173 (178)
44 PRK06030 hypothetical protein; 85.1 1.8 3.8E-05 34.2 4.6 46 89-134 51-96 (124)
45 PF13730 HTH_36: Helix-turn-he 84.9 1.3 2.8E-05 29.0 3.3 40 94-133 7-51 (55)
46 TIGR02392 rpoH_proteo alternat 84.8 0.97 2.1E-05 39.6 3.4 47 90-136 218-265 (270)
47 PF00196 GerE: Bacterial regul 84.7 0.82 1.8E-05 30.5 2.3 44 91-136 4-47 (58)
48 TIGR02844 spore_III_D sporulat 84.5 0.68 1.5E-05 33.8 1.9 37 94-130 5-42 (80)
49 PRK08301 sporulation sigma fac 84.2 1.4 3E-05 37.4 4.0 48 90-137 178-228 (234)
50 TIGR02393 RpoD_Cterm RNA polym 83.8 1.1 2.5E-05 38.3 3.3 48 90-137 176-226 (238)
51 PRK07408 RNA polymerase sigma 82.9 1.6 3.5E-05 38.0 3.9 46 90-136 203-248 (256)
52 PRK12519 RNA polymerase sigma 82.8 1.5 3.2E-05 35.9 3.5 47 90-137 141-187 (194)
53 PRK05803 sporulation sigma fac 82.1 1.5 3.2E-05 37.4 3.4 48 90-137 175-225 (233)
54 PF08299 Bac_DnaA_C: Bacterial 82.1 1.2 2.7E-05 31.2 2.4 43 89-131 27-70 (70)
55 PRK06596 RNA polymerase factor 82.0 1.5 3.2E-05 38.9 3.4 47 90-136 230-277 (284)
56 PF13011 LZ_Tnp_IS481: leucine 81.9 1.6 3.5E-05 32.3 3.0 44 90-133 8-51 (85)
57 PRK09413 IS2 repressor TnpA; R 81.6 1.6 3.6E-05 33.7 3.2 45 89-133 11-55 (121)
58 PRK12524 RNA polymerase sigma 81.6 1.9 4E-05 35.6 3.7 47 90-137 136-182 (196)
59 PRK12514 RNA polymerase sigma 81.6 2.2 4.8E-05 34.4 4.0 46 90-136 129-174 (179)
60 PF12840 HTH_20: Helix-turn-he 81.1 1.2 2.7E-05 30.0 2.1 41 94-134 10-51 (61)
61 PRK12532 RNA polymerase sigma 80.9 2.8 6.1E-05 34.3 4.5 54 90-144 136-190 (195)
62 PF00356 LacI: Bacterial regul 80.8 0.48 1E-05 30.9 -0.1 21 110-130 2-22 (46)
63 PRK07037 extracytoplasmic-func 80.8 2.1 4.6E-05 33.7 3.7 47 90-137 109-155 (163)
64 PRK11923 algU RNA polymerase s 80.6 2.3 5E-05 34.7 3.9 53 90-143 138-190 (193)
65 TIGR02997 Sig70-cyanoRpoD RNA 80.4 1.6 3.4E-05 38.8 3.1 45 90-134 249-296 (298)
66 PF13340 DUF4096: Putative tra 80.3 2.7 5.9E-05 29.7 3.7 66 68-134 2-67 (75)
67 PRK03975 tfx putative transcri 80.2 2.6 5.7E-05 34.0 3.9 45 90-136 6-50 (141)
68 PRK08583 RNA polymerase sigma 79.8 2.5 5.4E-05 36.5 4.0 46 90-136 205-250 (257)
69 PRK13918 CRP/FNR family transc 79.7 1.9 4.2E-05 35.2 3.2 57 90-146 118-189 (202)
70 smart00153 VHP Villin headpiec 79.7 0.7 1.5E-05 28.7 0.4 22 57-78 3-24 (36)
71 PRK15411 rcsA colanic acid cap 79.5 1.5 3.3E-05 36.8 2.5 44 91-136 138-181 (207)
72 PRK07500 rpoH2 RNA polymerase 79.4 2 4.4E-05 38.1 3.4 48 90-137 227-275 (289)
73 TIGR02952 Sig70_famx2 RNA poly 79.3 2.5 5.4E-05 33.4 3.6 46 90-136 122-167 (170)
74 PF02209 VHP: Villin headpiece 79.2 0.6 1.3E-05 29.0 -0.0 24 57-80 3-26 (36)
75 PRK05572 sporulation sigma fac 79.1 2.3 5E-05 36.7 3.6 47 90-137 202-248 (252)
76 PF13545 HTH_Crp_2: Crp-like h 79.0 2 4.4E-05 29.7 2.6 26 109-134 30-55 (76)
77 PRK15201 fimbriae regulatory p 79.0 2.8 6.1E-05 35.4 3.9 48 87-136 130-177 (198)
78 PF12802 MarR_2: MarR family; 78.9 2.6 5.6E-05 27.9 3.1 27 108-134 22-48 (62)
79 PF00325 Crp: Bacterial regula 78.7 0.89 1.9E-05 27.5 0.6 23 109-131 4-26 (32)
80 PHA00675 hypothetical protein 78.4 2.6 5.6E-05 30.6 3.0 40 90-129 22-61 (78)
81 PF04967 HTH_10: HTH DNA bindi 78.2 1.5 3.2E-05 29.5 1.6 30 107-136 23-52 (53)
82 PRK12530 RNA polymerase sigma 78.1 3.1 6.7E-05 34.1 3.9 47 90-137 134-180 (189)
83 TIGR02983 SigE-fam_strep RNA p 78.1 2.6 5.7E-05 33.2 3.4 47 90-137 110-156 (162)
84 PRK12544 RNA polymerase sigma 77.9 3.3 7.2E-05 34.7 4.1 47 90-137 148-194 (206)
85 PRK12515 RNA polymerase sigma 77.8 3.6 7.8E-05 33.5 4.2 47 90-137 131-177 (189)
86 TIGR03879 near_KaiC_dom probab 77.7 2.4 5.2E-05 30.5 2.7 45 90-134 15-59 (73)
87 PRK08215 sporulation sigma fac 77.7 2.7 5.9E-05 36.4 3.6 46 90-136 209-254 (258)
88 TIGR02980 SigBFG RNA polymeras 77.6 2.9 6.2E-05 35.3 3.7 46 90-136 178-223 (227)
89 PRK09415 RNA polymerase factor 77.5 3 6.5E-05 33.8 3.7 47 90-137 127-173 (179)
90 TIGR02835 spore_sigmaE RNA pol 77.4 2.7 5.9E-05 35.8 3.5 47 90-136 178-227 (234)
91 PF13412 HTH_24: Winged helix- 77.4 3.2 7E-05 26.4 3.0 27 107-133 17-43 (48)
92 TIGR02846 spore_sigmaK RNA pol 77.4 2.7 5.9E-05 35.7 3.5 47 90-136 174-223 (227)
93 TIGR02885 spore_sigF RNA polym 77.2 2.9 6.3E-05 35.4 3.6 46 90-136 183-228 (231)
94 PRK07405 RNA polymerase sigma 77.1 2.7 5.8E-05 37.9 3.5 48 90-137 256-306 (317)
95 PRK06930 positive control sigm 76.9 3.6 7.8E-05 33.9 4.0 47 90-137 114-160 (170)
96 PRK12516 RNA polymerase sigma 76.9 3.8 8.2E-05 33.7 4.1 47 90-137 116-162 (187)
97 COG2771 CsgD DNA-binding HTH d 76.9 2.1 4.5E-05 28.3 2.1 37 99-135 11-47 (65)
98 PRK12547 RNA polymerase sigma 76.7 3.8 8.3E-05 32.6 4.0 46 90-136 112-157 (164)
99 TIGR03001 Sig-70_gmx1 RNA poly 76.5 3.5 7.6E-05 35.7 4.0 53 90-143 161-214 (244)
100 COG2197 CitB Response regulato 76.5 2.9 6.4E-05 35.3 3.4 44 91-136 149-192 (211)
101 PRK11924 RNA polymerase sigma 76.3 3.4 7.4E-05 32.6 3.6 46 90-136 125-170 (179)
102 PRK12511 RNA polymerase sigma 75.8 5.4 0.00012 32.6 4.8 48 90-138 111-158 (182)
103 PF01527 HTH_Tnp_1: Transposas 75.7 2.2 4.7E-05 29.6 2.0 43 90-132 6-48 (76)
104 PRK09641 RNA polymerase sigma 75.6 3.3 7.1E-05 33.3 3.4 46 90-136 136-181 (187)
105 PRK12534 RNA polymerase sigma 75.5 4.4 9.6E-05 32.8 4.1 47 90-137 137-183 (187)
106 TIGR02850 spore_sigG RNA polym 75.5 3.3 7.2E-05 35.8 3.6 46 90-136 206-251 (254)
107 PF00126 HTH_1: Bacterial regu 75.2 4 8.7E-05 27.4 3.2 40 96-136 3-42 (60)
108 PRK10840 transcriptional regul 75.1 2.2 4.8E-05 35.2 2.3 45 90-136 150-194 (216)
109 PRK09638 RNA polymerase sigma 75.1 1.8 4E-05 34.6 1.7 46 90-136 126-171 (176)
110 TIGR02394 rpoS_proteo RNA poly 74.9 3.6 7.8E-05 36.2 3.7 48 90-137 222-272 (285)
111 PRK12533 RNA polymerase sigma 74.9 3.3 7.1E-05 35.2 3.3 47 90-137 134-180 (216)
112 PRK12537 RNA polymerase sigma 74.5 4.6 0.0001 32.7 4.0 46 90-136 133-178 (182)
113 PRK06811 RNA polymerase factor 74.4 4.3 9.4E-05 33.1 3.8 46 90-136 131-176 (189)
114 TIGR02984 Sig-70_plancto1 RNA 74.2 4.7 0.0001 32.4 4.0 47 90-137 140-186 (189)
115 TIGR02941 Sigma_B RNA polymera 74.1 3.9 8.4E-05 35.3 3.6 46 90-136 205-250 (255)
116 TIGR02989 Sig-70_gvs1 RNA poly 73.9 4.6 9.9E-05 31.6 3.7 46 90-136 111-156 (159)
117 PRK12512 RNA polymerase sigma 72.9 4.8 0.0001 32.5 3.7 46 90-136 131-176 (184)
118 PRK12531 RNA polymerase sigma 72.9 5 0.00011 32.9 3.8 46 90-136 141-186 (194)
119 PRK12540 RNA polymerase sigma 72.8 4.6 0.0001 33.0 3.6 47 90-137 111-157 (182)
120 smart00346 HTH_ICLR helix_turn 72.6 5 0.00011 28.5 3.4 37 98-134 8-47 (91)
121 PRK12522 RNA polymerase sigma 72.5 5.2 0.00011 32.0 3.8 52 91-143 120-171 (173)
122 PF08279 HTH_11: HTH domain; 72.4 4 8.7E-05 26.6 2.6 27 108-134 16-42 (55)
123 TIGR02950 SigM_subfam RNA poly 72.3 1.8 3.9E-05 33.7 1.0 47 90-137 105-151 (154)
124 PRK07406 RNA polymerase sigma 72.3 4.1 9E-05 37.8 3.5 47 90-136 311-360 (373)
125 PRK12520 RNA polymerase sigma 72.1 6.9 0.00015 31.9 4.5 53 90-143 131-184 (191)
126 PRK06759 RNA polymerase factor 72.0 5.1 0.00011 31.2 3.6 45 90-135 106-150 (154)
127 PF01325 Fe_dep_repress: Iron 71.7 5.9 0.00013 27.0 3.4 42 92-133 4-48 (60)
128 PRK05602 RNA polymerase sigma 71.6 5.6 0.00012 32.2 3.8 46 90-136 128-173 (186)
129 PRK09492 treR trehalose repres 71.1 1.9 4.1E-05 37.5 0.9 23 108-130 5-27 (315)
130 PF01047 MarR: MarR family; I 70.9 5.7 0.00012 26.0 3.1 29 105-133 15-43 (59)
131 PF13551 HTH_29: Winged helix- 70.8 8.4 0.00018 28.2 4.4 73 58-130 15-110 (112)
132 PRK11475 DNA-binding transcrip 70.6 3.2 7E-05 35.1 2.2 44 91-136 135-178 (207)
133 PRK09483 response regulator; P 70.5 3.2 7E-05 33.4 2.2 44 90-135 148-191 (217)
134 PF12964 DUF3853: Protein of u 70.3 3.2 6.9E-05 31.4 1.9 59 63-129 9-67 (96)
135 TIGR02939 RpoE_Sigma70 RNA pol 70.3 5.2 0.00011 32.2 3.4 47 90-137 138-184 (190)
136 TIGR03541 reg_near_HchA LuxR f 70.3 11 0.00023 32.3 5.4 46 89-136 170-215 (232)
137 TIGR02948 SigW_bacill RNA poly 70.1 5.2 0.00011 32.1 3.3 47 90-137 136-182 (187)
138 PRK12523 RNA polymerase sigma 69.8 6.1 0.00013 31.6 3.7 46 90-136 119-164 (172)
139 TIGR02337 HpaR homoprotocatech 69.7 12 0.00027 28.1 5.2 29 106-134 41-69 (118)
140 PRK12539 RNA polymerase sigma 69.5 6 0.00013 32.1 3.6 47 90-137 131-177 (184)
141 PRK12546 RNA polymerase sigma 69.4 5.5 0.00012 32.8 3.4 47 90-137 113-159 (188)
142 PRK09643 RNA polymerase sigma 69.4 7.4 0.00016 31.9 4.1 47 90-137 134-180 (192)
143 PRK07122 RNA polymerase sigma 69.2 5.5 0.00012 34.9 3.5 46 90-136 215-260 (264)
144 PRK09210 RNA polymerase sigma 69.2 5 0.00011 36.9 3.4 47 90-136 305-354 (367)
145 PRK09645 RNA polymerase sigma 69.0 8.5 0.00018 30.6 4.3 47 90-137 118-164 (173)
146 PRK12427 flagellar biosynthesi 68.9 6.1 0.00013 33.8 3.6 45 90-135 183-227 (231)
147 PRK05949 RNA polymerase sigma 68.6 5.4 0.00012 36.2 3.4 48 90-137 266-316 (327)
148 PF13551 HTH_29: Winged helix- 68.5 4.4 9.4E-05 29.7 2.4 35 100-134 4-39 (112)
149 PRK06986 fliA flagellar biosyn 68.4 6.9 0.00015 33.3 3.9 47 90-137 184-230 (236)
150 smart00342 HTH_ARAC helix_turn 68.4 12 0.00026 25.3 4.5 69 60-132 6-76 (84)
151 PRK07670 RNA polymerase sigma 67.9 6.4 0.00014 33.9 3.6 46 90-136 201-246 (251)
152 PRK07598 RNA polymerase sigma 67.9 5.9 0.00013 37.4 3.6 47 90-136 350-399 (415)
153 PRK13870 transcriptional regul 67.8 12 0.00027 32.1 5.3 45 90-136 173-217 (234)
154 TIGR02954 Sig70_famx3 RNA poly 67.8 8.3 0.00018 30.6 4.0 47 90-137 119-165 (169)
155 PF07374 DUF1492: Protein of u 67.7 6.6 0.00014 29.4 3.2 43 92-135 57-99 (100)
156 PHA00738 putative HTH transcri 67.7 5.3 0.00011 30.8 2.7 38 96-134 14-53 (108)
157 PF13560 HTH_31: Helix-turn-he 66.1 3.7 8E-05 27.7 1.4 26 104-129 11-36 (64)
158 TIGR02479 FliA_WhiG RNA polyme 65.9 7.7 0.00017 32.6 3.7 46 90-136 175-220 (224)
159 PF09339 HTH_IclR: IclR helix- 65.9 5.8 0.00013 25.8 2.3 26 108-133 19-44 (52)
160 COG3179 Predicted chitinase [G 65.5 3.7 7.9E-05 34.8 1.5 69 58-129 6-75 (206)
161 TIGR02859 spore_sigH RNA polym 65.3 7.2 0.00016 31.7 3.3 42 94-136 153-194 (198)
162 PRK13919 putative RNA polymera 65.2 8.9 0.00019 30.9 3.8 46 90-136 135-180 (186)
163 PRK06704 RNA polymerase factor 64.9 10 0.00022 32.7 4.3 53 90-143 116-168 (228)
164 PRK13719 conjugal transfer tra 64.5 7.8 0.00017 33.5 3.4 45 90-136 143-187 (217)
165 PRK06288 RNA polymerase sigma 64.1 8.5 0.00018 33.5 3.7 46 90-136 212-257 (268)
166 PRK09648 RNA polymerase sigma 63.9 9.1 0.0002 31.0 3.6 46 90-136 139-184 (189)
167 PRK10360 DNA-binding transcrip 63.8 6.2 0.00013 31.2 2.5 45 90-136 137-181 (196)
168 PRK12525 RNA polymerase sigma 63.8 9.4 0.0002 30.4 3.6 47 90-137 118-164 (168)
169 PF01710 HTH_Tnp_IS630: Transp 63.8 13 0.00028 28.6 4.2 68 59-130 22-94 (119)
170 PRK09651 RNA polymerase sigma 63.7 8 0.00017 31.0 3.2 47 91-138 120-166 (172)
171 PF13463 HTH_27: Winged helix 63.4 6.7 0.00014 26.3 2.3 35 100-134 8-45 (68)
172 TIGR02960 SigX5 RNA polymerase 63.1 7.8 0.00017 34.3 3.3 48 90-138 142-189 (324)
173 PRK10651 transcriptional regul 62.9 6.1 0.00013 31.4 2.4 45 90-136 155-199 (216)
174 PRK10100 DNA-binding transcrip 62.0 6.4 0.00014 33.4 2.4 45 90-136 155-199 (216)
175 TIGR03020 EpsA transcriptional 61.8 9.4 0.0002 33.4 3.5 45 90-136 190-234 (247)
176 PF01710 HTH_Tnp_IS630: Transp 61.8 4.6 0.0001 31.1 1.4 28 102-129 13-40 (119)
177 PRK07921 RNA polymerase sigma 61.8 9.4 0.0002 34.7 3.6 47 90-136 262-311 (324)
178 TIGR02999 Sig-70_X6 RNA polyme 61.7 9.5 0.00021 30.6 3.3 45 91-136 135-179 (183)
179 PRK12527 RNA polymerase sigma 61.7 12 0.00025 29.4 3.8 47 90-137 105-151 (159)
180 PRK12528 RNA polymerase sigma 61.7 9.9 0.00021 29.9 3.3 46 90-136 113-158 (161)
181 COG1508 RpoN DNA-directed RNA 61.6 8.9 0.00019 36.5 3.5 32 108-149 331-362 (444)
182 TIGR02943 Sig70_famx1 RNA poly 61.5 13 0.00028 30.4 4.1 47 90-137 131-177 (188)
183 PHA00542 putative Cro-like pro 61.4 6.2 0.00013 28.5 1.9 31 100-130 24-54 (82)
184 smart00345 HTH_GNTR helix_turn 61.2 4.7 0.0001 26.0 1.2 25 109-133 22-46 (60)
185 PRK14088 dnaA chromosomal repl 61.1 9.7 0.00021 36.0 3.7 48 88-135 368-415 (440)
186 PRK08295 RNA polymerase factor 61.1 13 0.00028 30.4 4.1 45 90-136 155-199 (208)
187 PRK11922 RNA polymerase sigma 60.9 6.6 0.00014 33.3 2.3 48 90-138 149-196 (231)
188 PRK14086 dnaA chromosomal repl 60.2 13 0.00029 36.9 4.5 49 88-136 550-598 (617)
189 TIGR02395 rpoN_sigma RNA polym 60.0 8.9 0.00019 36.3 3.2 33 107-149 318-350 (429)
190 smart00418 HTH_ARSR helix_turn 59.9 7.2 0.00016 25.0 1.9 29 105-133 8-36 (66)
191 PRK00149 dnaA chromosomal repl 59.8 14 0.0003 34.7 4.5 48 89-136 384-432 (450)
192 PRK10141 DNA-binding transcrip 59.4 8.9 0.00019 29.8 2.6 43 92-134 14-57 (117)
193 PRK05932 RNA polymerase factor 59.0 9.2 0.0002 36.5 3.1 33 107-149 343-375 (455)
194 cd07377 WHTH_GntR Winged helix 58.8 15 0.00032 24.0 3.4 25 109-133 27-51 (66)
195 PRK09958 DNA-binding transcrip 58.4 8.7 0.00019 30.5 2.5 45 90-136 143-187 (204)
196 PRK10403 transcriptional regul 58.2 12 0.00025 29.6 3.2 45 90-136 153-197 (215)
197 TIGR02405 trehalos_R_Ecol treh 57.4 3.8 8.2E-05 35.7 0.3 21 109-129 3-23 (311)
198 PF04297 UPF0122: Putative hel 57.3 14 0.0003 28.2 3.3 45 93-137 19-63 (101)
199 PRK12536 RNA polymerase sigma 57.2 12 0.00027 30.1 3.3 47 90-137 129-175 (181)
200 cd00090 HTH_ARSR Arsenical Res 57.1 15 0.00031 24.2 3.1 28 105-132 18-45 (78)
201 PRK15369 two component system 56.9 14 0.00029 28.9 3.4 44 91-136 150-193 (211)
202 PRK05657 RNA polymerase sigma 56.4 12 0.00027 33.8 3.4 48 90-137 262-312 (325)
203 PRK09642 RNA polymerase sigma 56.2 16 0.00035 28.6 3.7 47 90-137 106-152 (160)
204 smart00550 Zalpha Z-DNA-bindin 55.8 12 0.00027 25.9 2.6 41 92-132 6-47 (68)
205 COG2739 Uncharacterized protei 55.6 17 0.00036 27.9 3.4 40 97-136 23-62 (105)
206 PRK10401 DNA-binding transcrip 54.8 7 0.00015 34.5 1.5 21 109-129 3-23 (346)
207 smart00419 HTH_CRP helix_turn_ 54.7 7.3 0.00016 24.1 1.2 28 107-134 8-35 (48)
208 PRK09649 RNA polymerase sigma 54.7 13 0.00029 30.2 3.1 47 90-137 130-176 (185)
209 PRK05901 RNA polymerase sigma 54.6 14 0.0003 35.9 3.6 47 90-136 447-496 (509)
210 PRK10703 DNA-binding transcrip 54.5 5.7 0.00012 34.9 0.9 22 109-130 3-24 (341)
211 TIGR02959 SigZ RNA polymerase 54.4 18 0.0004 28.9 3.8 52 90-142 100-151 (170)
212 PRK12545 RNA polymerase sigma 54.2 18 0.00039 29.9 3.8 53 90-143 139-192 (201)
213 PF00165 HTH_AraC: Bacterial r 54.0 5.2 0.00011 24.7 0.4 29 104-132 5-33 (42)
214 PF02001 DUF134: Protein of un 54.0 22 0.00047 27.3 3.9 47 89-136 40-86 (106)
215 PRK03573 transcriptional regul 53.9 14 0.00031 28.7 3.0 29 106-134 45-73 (144)
216 COG1595 RpoE DNA-directed RNA 53.6 16 0.00034 29.6 3.3 47 90-137 127-173 (182)
217 PRK12683 transcriptional regul 53.4 16 0.00035 32.0 3.6 42 95-136 4-45 (309)
218 PRK12538 RNA polymerase sigma 53.2 17 0.00036 31.2 3.6 47 90-137 171-217 (233)
219 PRK14087 dnaA chromosomal repl 53.1 21 0.00046 33.8 4.6 49 88-136 382-431 (450)
220 PRK12679 cbl transcriptional r 53.0 13 0.00028 32.7 3.0 42 95-136 4-45 (316)
221 PRK09646 RNA polymerase sigma 52.9 18 0.00039 29.6 3.6 47 90-137 142-188 (194)
222 PF11776 DUF3315: Domain of un 52.8 5.7 0.00012 26.4 0.5 18 198-215 8-25 (52)
223 PRK10014 DNA-binding transcrip 52.8 5 0.00011 35.2 0.3 24 107-130 6-29 (342)
224 PF01381 HTH_3: Helix-turn-hel 52.7 4.7 0.0001 26.0 0.1 26 105-130 7-32 (55)
225 PRK09637 RNA polymerase sigma 52.5 21 0.00045 29.0 3.9 51 90-141 106-156 (181)
226 PRK10188 DNA-binding transcrip 51.8 17 0.00036 31.4 3.4 45 90-136 179-223 (240)
227 PRK09644 RNA polymerase sigma 51.7 19 0.0004 28.5 3.4 47 90-137 108-154 (165)
228 PRK12682 transcriptional regul 51.6 18 0.00039 31.5 3.6 42 95-136 4-45 (309)
229 cd01392 HTH_LacI Helix-turn-he 51.4 5 0.00011 25.6 0.0 19 112-130 2-20 (52)
230 PRK12541 RNA polymerase sigma 51.3 18 0.00038 28.4 3.2 48 90-138 112-159 (161)
231 PRK14987 gluconate operon tran 51.1 5 0.00011 35.2 -0.1 23 108-130 6-28 (331)
232 smart00347 HTH_MARR helix_turn 50.8 26 0.00056 24.7 3.8 28 107-134 24-51 (101)
233 COG2973 TrpR Trp operon repres 50.6 16 0.00034 27.8 2.6 38 90-127 37-80 (103)
234 PRK09640 RNA polymerase sigma 50.4 8.5 0.00018 31.3 1.3 46 91-137 135-180 (188)
235 PRK12535 RNA polymerase sigma 50.3 20 0.00043 29.7 3.5 51 91-142 134-184 (196)
236 smart00354 HTH_LACI helix_turn 50.0 5.5 0.00012 27.6 0.0 22 109-130 2-23 (70)
237 PRK12513 RNA polymerase sigma 49.9 9.5 0.00021 31.1 1.5 47 90-137 139-185 (194)
238 PRK12469 RNA polymerase factor 49.6 17 0.00037 35.0 3.3 33 107-149 369-401 (481)
239 PRK13413 mpi multiple promoter 49.2 8.9 0.00019 31.9 1.2 28 103-130 168-195 (200)
240 PF13309 HTH_22: HTH domain 48.8 20 0.00044 24.6 2.8 39 90-128 20-63 (64)
241 PRK12542 RNA polymerase sigma 48.8 22 0.00049 28.6 3.5 47 90-137 122-168 (185)
242 PRK09526 lacI lac repressor; R 48.5 6 0.00013 34.7 0.0 22 108-129 6-27 (342)
243 PF09182 PuR_N: Bacterial puri 47.8 20 0.00044 25.5 2.6 39 95-133 4-49 (70)
244 PRK12543 RNA polymerase sigma 47.7 26 0.00056 28.2 3.7 46 90-136 117-162 (179)
245 PRK09647 RNA polymerase sigma 47.6 26 0.00057 29.2 3.8 47 90-137 138-184 (203)
246 COG1191 FliA DNA-directed RNA 47.3 23 0.0005 31.1 3.6 46 90-136 196-241 (247)
247 TIGR01610 phage_O_Nterm phage 47.3 19 0.00042 26.5 2.6 55 64-134 20-74 (95)
248 COG4974 XerD Site-specific rec 47.1 81 0.0018 28.6 7.0 67 65-134 219-287 (300)
249 COG5606 Uncharacterized conser 47.0 14 0.0003 27.6 1.8 62 68-129 2-63 (91)
250 TIGR01889 Staph_reg_Sar staphy 46.5 50 0.0011 24.6 4.9 38 107-150 43-81 (109)
251 PRK11233 nitrogen assimilation 46.1 25 0.00053 30.6 3.6 36 96-132 5-40 (305)
252 PRK11303 DNA-binding transcrip 45.6 7.3 0.00016 33.9 0.2 22 109-130 2-23 (328)
253 TIGR01636 phage_rinA phage tra 45.5 29 0.00063 27.2 3.6 46 91-136 83-129 (134)
254 PF08220 HTH_DeoR: DeoR-like h 45.4 9.5 0.00021 25.5 0.7 25 108-132 15-39 (57)
255 PF05732 RepL: Firmicute plasm 44.9 16 0.00035 30.0 2.1 39 96-134 57-102 (165)
256 PRK10339 DNA-binding transcrip 44.3 7.7 0.00017 34.0 0.1 22 109-130 3-24 (327)
257 COG2826 Tra8 Transposase and i 44.3 21 0.00046 32.4 2.9 39 90-129 7-45 (318)
258 PRK12517 RNA polymerase sigma 43.9 31 0.00067 28.2 3.7 47 90-137 128-174 (188)
259 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 43.9 24 0.00052 23.4 2.4 40 90-130 4-43 (50)
260 PF06056 Terminase_5: Putative 43.9 24 0.00053 23.9 2.5 32 96-129 4-35 (58)
261 PRK12422 chromosomal replicati 43.9 34 0.00074 32.4 4.4 48 88-135 378-425 (445)
262 PRK09834 DNA-binding transcrip 43.3 28 0.00061 30.2 3.5 47 88-134 4-53 (263)
263 PRK04841 transcriptional regul 42.8 25 0.00054 35.3 3.5 45 90-136 838-882 (903)
264 PF00440 TetR_N: Bacterial reg 42.7 23 0.0005 22.3 2.2 34 98-131 7-40 (47)
265 PRK12526 RNA polymerase sigma 42.5 34 0.00074 28.3 3.8 46 90-136 153-198 (206)
266 PF01978 TrmB: Sugar-specific 42.4 22 0.00048 24.1 2.2 29 106-134 21-49 (68)
267 PRK10423 transcriptional repre 42.2 8.5 0.00019 33.4 0.1 19 111-129 2-20 (327)
268 TIGR00122 birA_repr_reg BirA b 42.2 20 0.00042 24.5 1.9 25 109-133 15-39 (69)
269 PRK11511 DNA-binding transcrip 42.1 27 0.00059 26.9 2.9 28 104-131 22-49 (127)
270 PRK12684 transcriptional regul 42.1 34 0.00073 30.0 3.8 42 95-136 4-45 (313)
271 PF07638 Sigma70_ECF: ECF sigm 41.7 27 0.00059 28.6 3.0 42 91-133 136-177 (185)
272 PRK11512 DNA-binding transcrip 40.9 31 0.00067 26.9 3.1 30 105-134 52-81 (144)
273 PRK00215 LexA repressor; Valid 40.6 36 0.00079 28.2 3.6 29 106-134 22-51 (205)
274 PF10654 DUF2481: Protein of u 40.2 12 0.00026 29.3 0.6 38 89-130 66-103 (126)
275 COG3413 Predicted DNA binding 40.2 20 0.00043 30.2 2.0 48 90-137 155-208 (215)
276 COG3139 Uncharacterized protei 39.8 93 0.002 23.0 5.1 42 66-108 9-54 (90)
277 TIGR02417 fruct_sucro_rep D-fr 39.5 10 0.00022 33.0 0.1 21 110-130 2-22 (327)
278 TIGR02947 SigH_actino RNA poly 38.4 22 0.00048 28.9 1.9 48 90-138 131-178 (193)
279 PRK11151 DNA-binding transcrip 38.1 30 0.00066 29.9 2.9 35 96-131 5-39 (305)
280 COG0664 Crp cAMP-binding prote 37.9 39 0.00085 26.8 3.4 45 90-134 140-198 (214)
281 PF04552 Sigma54_DBD: Sigma-54 37.8 11 0.00023 31.0 0.0 31 108-148 50-80 (160)
282 TIGR01481 ccpA catabolite cont 37.8 11 0.00024 32.7 0.1 22 109-130 3-24 (329)
283 PRK15418 transcriptional regul 37.8 23 0.00049 32.1 2.1 67 101-173 23-92 (318)
284 PRK09935 transcriptional regul 37.3 33 0.00071 27.1 2.8 45 90-136 149-193 (210)
285 PRK11050 manganese transport r 36.9 38 0.00082 27.1 3.1 29 106-134 50-78 (152)
286 TIGR00637 ModE_repress ModE mo 36.2 40 0.00086 25.2 2.9 37 100-136 9-45 (99)
287 PRK09636 RNA polymerase sigma 35.9 45 0.00098 29.2 3.6 48 90-138 115-162 (293)
288 PF05344 DUF746: Domain of Unk 35.8 42 0.0009 23.6 2.7 44 96-139 2-45 (65)
289 PF01418 HTH_6: Helix-turn-hel 35.8 41 0.00089 23.6 2.8 25 106-130 33-57 (77)
290 smart00420 HTH_DEOR helix_turn 35.6 24 0.00051 21.9 1.4 27 108-134 15-41 (53)
291 PRK10430 DNA-binding transcrip 35.6 38 0.00081 28.4 3.0 32 105-136 176-207 (239)
292 TIGR02702 SufR_cyano iron-sulf 35.5 37 0.00081 28.3 2.9 40 94-134 3-42 (203)
293 PRK05658 RNA polymerase sigma 34.5 38 0.00082 33.4 3.2 47 90-136 556-605 (619)
294 PRK10727 DNA-binding transcrip 34.5 14 0.00029 32.6 0.1 21 109-129 3-23 (343)
295 PRK12681 cysB transcriptional 34.3 38 0.00081 30.0 2.9 41 96-136 5-45 (324)
296 PRK02287 hypothetical protein; 34.2 36 0.00077 28.4 2.5 44 90-134 106-149 (171)
297 PRK09390 fixJ response regulat 34.2 51 0.0011 25.4 3.4 34 103-136 152-185 (202)
298 PRK10434 srlR DNA-bindng trans 33.9 38 0.00083 29.4 2.8 39 93-131 3-43 (256)
299 TIGR02607 antidote_HigA addict 33.8 38 0.00083 23.2 2.3 38 91-129 3-40 (78)
300 PRK11242 DNA-binding transcrip 33.7 41 0.0009 28.6 3.0 35 96-131 5-39 (296)
301 TIGR03070 couple_hipB transcri 33.6 17 0.00036 23.1 0.4 26 104-129 12-37 (58)
302 TIGR01884 cas_HTH CRISPR locus 33.2 50 0.0011 27.5 3.3 27 107-133 157-183 (203)
303 PF07453 NUMOD1: NUMOD1 domain 33.1 15 0.00033 22.1 0.1 21 108-128 17-37 (37)
304 COG2963 Transposase and inacti 33.1 56 0.0012 24.5 3.3 46 89-134 6-52 (116)
305 PRK09906 DNA-binding transcrip 33.0 52 0.0011 28.1 3.5 33 100-132 8-40 (296)
306 TIGR02957 SigX4 RNA polymerase 32.9 56 0.0012 28.6 3.7 48 90-138 108-155 (281)
307 PRK11013 DNA-binding transcrip 32.8 39 0.00085 29.4 2.7 35 96-131 8-42 (309)
308 PRK13501 transcriptional activ 32.8 1E+02 0.0022 26.7 5.3 44 104-147 189-241 (290)
309 PRK13509 transcriptional repre 32.7 41 0.00089 29.2 2.8 38 94-131 4-43 (251)
310 PF05043 Mga: Mga helix-turn-h 32.5 39 0.00084 24.0 2.2 34 104-137 27-60 (87)
311 PRK09940 transcriptional regul 32.4 88 0.0019 27.5 4.8 87 44-130 83-173 (253)
312 PRK06474 hypothetical protein; 32.3 44 0.00094 27.6 2.8 40 95-134 12-54 (178)
313 cd04762 HTH_MerR-trunc Helix-T 32.2 18 0.00039 22.0 0.3 22 109-130 2-23 (49)
314 TIGR03830 CxxCG_CxxCG_HTH puta 32.0 63 0.0014 24.3 3.5 59 67-129 42-100 (127)
315 PRK12518 RNA polymerase sigma 31.9 26 0.00056 27.8 1.3 46 91-137 121-166 (175)
316 PRK09801 transcriptional activ 31.7 57 0.0012 28.6 3.6 40 95-135 9-48 (310)
317 TIGR03418 chol_sulf_TF putativ 31.4 53 0.0012 28.0 3.3 36 96-132 5-40 (291)
318 smart00529 HTH_DTXR Helix-turn 31.2 25 0.00054 25.2 1.0 25 110-134 2-26 (96)
319 TIGR00180 parB_part ParB-like 31.0 46 0.001 27.4 2.7 81 43-129 59-142 (187)
320 COG1609 PurR Transcriptional r 31.0 18 0.00038 32.6 0.2 21 109-129 2-22 (333)
321 TIGR01764 excise DNA binding d 31.0 19 0.0004 22.1 0.3 21 109-129 3-23 (49)
322 PF05269 Phage_CII: Bacterioph 30.8 43 0.00094 25.0 2.2 24 109-132 25-48 (91)
323 COG0593 DnaA ATPase involved i 30.6 81 0.0018 29.8 4.5 50 87-136 345-394 (408)
324 PRK10094 DNA-binding transcrip 30.3 44 0.00095 29.2 2.6 36 95-131 5-40 (308)
325 PF13744 HTH_37: Helix-turn-he 30.1 18 0.00039 25.7 0.1 35 95-129 17-53 (80)
326 COG1342 Predicted DNA-binding 29.8 84 0.0018 23.9 3.6 46 90-136 33-78 (99)
327 PF04827 Plant_tran: Plant tra 29.6 15 0.00033 31.4 -0.4 37 141-179 2-39 (205)
328 smart00497 IENR1 Intron encode 29.5 24 0.00052 22.4 0.6 22 108-129 18-39 (53)
329 smart00344 HTH_ASNC helix_turn 29.2 77 0.0017 23.1 3.5 28 107-134 17-44 (108)
330 PF00292 PAX: 'Paired box' dom 29.1 60 0.0013 25.6 2.9 55 86-143 13-68 (125)
331 PRK08241 RNA polymerase factor 29.1 67 0.0014 28.6 3.6 50 90-140 153-202 (339)
332 PHA02591 hypothetical protein; 29.0 43 0.00092 24.5 1.9 29 102-130 54-82 (83)
333 PRK12680 transcriptional regul 28.8 70 0.0015 28.4 3.7 41 96-136 5-45 (327)
334 PF11198 DUF2857: Protein of u 28.6 1.5E+02 0.0033 24.5 5.4 51 65-126 56-106 (180)
335 PRK10163 DNA-binding transcrip 28.5 76 0.0016 27.7 3.8 45 90-134 20-67 (271)
336 KOG1567 Ribonucleotide reducta 28.3 59 0.0013 29.5 3.0 39 11-50 267-305 (344)
337 PRK10046 dpiA two-component re 28.1 33 0.00072 28.5 1.4 29 101-129 168-199 (225)
338 smart00760 Bac_DnaA_C Bacteria 28.0 64 0.0014 21.5 2.6 31 88-118 26-56 (60)
339 PRK09791 putative DNA-binding 27.9 71 0.0015 27.5 3.5 40 96-136 9-48 (302)
340 PRK10870 transcriptional repre 27.9 48 0.001 27.2 2.3 27 108-134 72-98 (176)
341 TIGR00498 lexA SOS regulatory 27.7 67 0.0015 26.4 3.2 27 107-133 25-52 (199)
342 TIGR03209 P21_Cbot clostridium 27.7 37 0.0008 26.0 1.5 35 90-125 107-141 (142)
343 PF04703 FaeA: FaeA-like prote 27.6 36 0.00079 23.5 1.3 37 95-131 3-39 (62)
344 COG1846 MarR Transcriptional r 27.5 78 0.0017 22.8 3.2 24 111-134 40-63 (126)
345 PF01726 LexA_DNA_bind: LexA D 27.4 26 0.00056 24.2 0.5 23 108-130 26-49 (65)
346 PRK13348 chromosome replicatio 27.3 55 0.0012 28.0 2.7 38 97-135 7-44 (294)
347 PRK13503 transcriptional activ 26.8 1.9E+02 0.004 24.6 5.9 27 105-131 185-211 (278)
348 PF13443 HTH_26: Cro/C1-type H 26.8 20 0.00044 23.7 -0.1 26 105-130 8-33 (63)
349 PRK11569 transcriptional repre 26.7 84 0.0018 27.4 3.8 46 89-134 22-70 (274)
350 TIGR02431 pcaR_pcaU beta-ketoa 26.5 81 0.0017 26.9 3.6 44 91-134 5-51 (248)
351 PF07750 GcrA: GcrA cell cycle 26.5 57 0.0012 26.7 2.5 37 94-130 5-42 (162)
352 COG4496 Uncharacterized protei 26.3 76 0.0016 23.9 2.8 27 102-128 51-77 (100)
353 CHL00180 rbcR LysR transcripti 26.3 79 0.0017 27.4 3.5 39 97-136 10-48 (305)
354 PF08535 KorB: KorB domain; I 25.9 27 0.00058 25.5 0.4 24 106-129 2-25 (93)
355 PHA01976 helix-turn-helix prot 25.9 29 0.00062 23.2 0.5 26 104-129 12-37 (67)
356 smart00352 POU Found in Pit-Oc 25.9 76 0.0017 22.9 2.7 27 103-129 20-52 (75)
357 PRK11564 stationary phase indu 25.7 1.1E+02 0.0024 28.3 4.6 49 87-135 7-58 (426)
358 PF13305 WHG: WHG domain; PDB: 25.6 1.5E+02 0.0034 19.8 4.3 15 94-108 58-72 (81)
359 TIGR03298 argP transcriptional 25.4 65 0.0014 27.5 2.8 38 97-135 6-43 (292)
360 PF04034 DUF367: Domain of unk 25.2 65 0.0014 25.6 2.5 44 90-134 65-108 (127)
361 PF09862 DUF2089: Protein of u 25.1 1.1E+02 0.0024 23.8 3.7 47 90-137 33-79 (113)
362 PF12162 STAT1_TAZ2bind: STAT1 24.9 67 0.0014 18.0 1.7 17 63-79 6-22 (23)
363 PRK10906 DNA-binding transcrip 24.7 83 0.0018 27.3 3.3 40 95-134 5-46 (252)
364 PRK15421 DNA-binding transcrip 24.6 82 0.0018 27.7 3.3 35 96-131 6-40 (317)
365 COG2390 DeoR Transcriptional r 24.0 52 0.0011 30.0 2.0 65 102-172 21-88 (321)
366 PRK09986 DNA-binding transcrip 24.0 1E+02 0.0022 26.1 3.8 37 96-133 11-47 (294)
367 PF13972 TetR: Bacterial trans 23.6 1.9E+02 0.0041 22.4 5.0 76 59-136 57-134 (146)
368 TIGR03384 betaine_BetI transcr 23.6 54 0.0012 25.9 1.8 33 97-129 18-50 (189)
369 COG3398 Uncharacterized protei 23.5 1.7E+02 0.0037 25.6 4.9 72 60-131 120-212 (240)
370 PF00392 GntR: Bacterial regul 23.4 42 0.0009 22.5 1.0 45 70-131 4-48 (64)
371 PRK10837 putative DNA-binding 23.1 92 0.002 26.4 3.3 36 100-135 10-45 (290)
372 PF14393 DUF4422: Domain of un 22.9 79 0.0017 27.5 2.8 32 50-81 156-187 (231)
373 PF07900 DUF1670: Protein of u 22.8 2.4E+02 0.0052 24.5 5.6 74 61-136 111-192 (220)
374 PF01498 HTH_Tnp_Tc3_2: Transp 22.8 36 0.00077 23.3 0.5 24 108-131 14-42 (72)
375 PRK11074 putative DNA-binding 22.6 77 0.0017 27.4 2.7 37 96-133 6-42 (300)
376 PRK15090 DNA-binding transcrip 22.6 1.1E+02 0.0025 26.2 3.8 47 88-134 7-55 (257)
377 PRK10219 DNA-binding transcrip 22.5 95 0.002 22.7 2.8 23 109-131 23-45 (107)
378 PRK10082 cell density-dependen 22.4 96 0.0021 26.8 3.3 29 103-131 21-49 (303)
379 PF00382 TFIIB: Transcription 22.3 1.6E+02 0.0035 20.0 3.8 64 61-124 4-71 (71)
380 COG2186 FadR Transcriptional r 22.1 1.2E+02 0.0025 26.2 3.7 50 67-137 11-60 (241)
381 PRK13756 tetracycline represso 22.0 1E+02 0.0022 25.9 3.3 31 106-136 23-56 (205)
382 PRK10572 DNA-binding transcrip 21.9 2.1E+02 0.0046 24.6 5.4 29 104-132 196-224 (290)
383 PF12728 HTH_17: Helix-turn-he 21.9 34 0.00074 21.7 0.3 21 109-129 3-23 (51)
384 PRK09508 leuO leucine transcri 21.8 93 0.002 27.1 3.1 34 99-132 28-61 (314)
385 TIGR02404 trehalos_R_Bsub treh 21.3 1.3E+02 0.0029 25.2 3.9 44 72-132 6-49 (233)
386 PF02954 HTH_8: Bacterial regu 21.1 1.1E+02 0.0023 18.9 2.4 26 105-130 16-41 (42)
387 PRK13500 transcriptional activ 20.9 2.2E+02 0.0048 25.1 5.4 65 67-131 177-246 (312)
388 TIGR03339 phn_lysR aminoethylp 20.9 88 0.0019 26.2 2.7 31 101-131 5-35 (279)
389 PRK04424 fatty acid biosynthes 20.9 1E+02 0.0022 25.5 3.0 42 93-134 5-48 (185)
390 PRK12423 LexA repressor; Provi 20.7 86 0.0019 26.1 2.6 27 108-134 26-53 (202)
391 PRK00423 tfb transcription ini 20.6 2.6E+02 0.0056 25.1 5.7 77 60-136 131-211 (310)
392 PRK15092 DNA-binding transcrip 20.5 91 0.002 27.4 2.8 38 96-133 14-51 (310)
393 PRK09635 sigI RNA polymerase s 20.3 1.2E+02 0.0026 26.9 3.5 48 90-138 118-165 (290)
394 COG2909 MalT ATP-dependent tra 20.3 44 0.00095 34.5 0.8 65 59-135 810-874 (894)
395 PRK03902 manganese transport t 20.0 1.5E+02 0.0033 23.0 3.7 41 94-134 7-49 (142)
No 1
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=98.78 E-value=7.3e-09 Score=69.76 Aligned_cols=48 Identities=29% Similarity=0.451 Sum_probs=45.9
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|.++|+.++|.++.+|.++.+++.+||+|.+||||+|+++++.+..
T Consensus 2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~ 49 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQ 49 (53)
T ss_pred CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHH
Confidence 478999999999999999999999999999999999999999999874
No 2
>KOG4585 consensus Predicted transposase [Replication, recombination and repair]
Probab=98.67 E-value=2.7e-08 Score=90.15 Aligned_cols=146 Identities=17% Similarity=0.182 Sum_probs=113.9
Q ss_pred ccccCHHHHHHHHHHHHhcCccCCC-----ccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhh
Q 046385 64 LMRMDKNGFISLCQLFKEKGWLSDS-----KHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKF 138 (218)
Q Consensus 64 ~fRM~~~~F~~L~~~L~~~~~~~~T-----~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L 138 (218)
.|++++.+|..++...........+ ..+++.++++++++.++++.+.+.++..|++..+|+ .++.+...+
T Consensus 7 ~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~i~~~fg~~~~~~-----~~~~~~~~~ 81 (326)
T KOG4585|consen 7 EFRKSYTTFDKICSLVQSLNVVKNSGFMLSSLLPADTLVAVALWRLKTGESLRTVEKKFGLGQSTC-----KFLEEKEDL 81 (326)
T ss_pred HHHHHHHHHHHHhhhhhhhhhhcccchhhhccccHHhhhhhhhccccccchHHHHHHHcCCcchhh-----hHHHhhhcc
Confidence 8899999999999987754322222 133399999999999999999999999999999999 566666689
Q ss_pred hhhhcCCCCCCCCcccccCcccccCCCCCccccCCccccccCC-------------------------------------
Q 046385 139 SKEMITPPSFTDNSRGIRNTRLRQIFKRSPVVPLNLQKMSRMP------------------------------------- 181 (218)
Q Consensus 139 ~~~~Ik~P~~~~~~~~i~n~~~~p~Fk~ci~vp~~~~v~~r~p------------------------------------- 181 (218)
++++++.|+... ...+.. ++.- |++|.|+.|++|+..+.|
T Consensus 82 ~~~~~~~p~~~~-~~~i~~-~~~~-~~~~~g~~d~~hi~~~~~~~~~~~~~n~~~~~Nvlav~n~d~~f~~v~vg~~Gs~ 158 (326)
T KOG4585|consen 82 APHFLKWPSRRI-LYEIRE-RFES-LPNCVGAIDTTHIPIRVPPKSGSVYFNKEQSKNLLAVCNFDMRFIYVDVGWPGSA 158 (326)
T ss_pred cchhhcCchhhh-hhhhcc-cccc-ccchhccccccccceecCccccccccccccchhhhheecCCceEEEEEccCCCCc
Confidence 999999998432 233332 3322 899999999999842110
Q ss_pred ----------------------ccccc-ccccccccccccCCCccCccccccCCCCCCC
Q 046385 182 ----------------------QFLTD-QMGKSKGHHQDFGGSRCPINDIVGTGLGPSR 217 (218)
Q Consensus 182 ----------------------~~~~~-~~g~~dG~hip~r~~ryh~~~~~~~~~~p~~ 217 (218)
-++++ +|.+++|...|++-+.||...+..+|..|.+
T Consensus 159 ~D~kvl~~~~~~~~~~~~~~~k~yl~d~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~ 217 (326)
T KOG4585|consen 159 HDTKVLQDSLLYKRNFPHPPLKYYLVDSGYPLRPGLLGPIGFPLYSLLMFPYGGPQPTN 217 (326)
T ss_pred cHHHHHHhhcccccccccCCccccccccCcccccccccccccccchhhhcccCCCCCCc
Confidence 03445 7889999999999999999999999998865
No 3
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=96.19 E-value=0.0026 Score=41.04 Aligned_cols=41 Identities=32% Similarity=0.371 Sum_probs=23.5
Q ss_pred ccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHH
Q 046385 89 KHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 89 ~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~e 130 (218)
.+++.+|+..|.-+ +..|.|++.|+..+++|.+||++.++.
T Consensus 3 ~~Lt~~eR~~I~~l-~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEAL-LEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHH-HCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHH-HHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 35788888888755 689999999999999999999998764
No 4
>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=95.98 E-value=0.0049 Score=44.99 Aligned_cols=45 Identities=22% Similarity=0.262 Sum_probs=34.0
Q ss_pred HHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH-hhhhh
Q 046385 97 MAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM-KFSKE 141 (218)
Q Consensus 97 laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~-~L~~~ 141 (218)
+.+.-|++-++++.|.++..||+|+|||++-+.+=|..|. .|+.+
T Consensus 9 i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~La~e 54 (82)
T PF12116_consen 9 IEIANYIIETKATVRQAAKVFGVSKSTVHKDVTERLPKINPELARE 54 (82)
T ss_dssp HHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-HHHHHH
T ss_pred HHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHHHHH
Confidence 4567799999999999999999999999999988888776 56544
No 5
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=95.97 E-value=0.01 Score=38.72 Aligned_cols=45 Identities=24% Similarity=0.204 Sum_probs=38.4
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAM 135 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI 135 (218)
.+|.+|+-.+.+++ ..+.++..++..+++|.+||+++.++.++-|
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 46889999998888 7888999999999999999999999887764
No 6
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=95.01 E-value=0.034 Score=37.24 Aligned_cols=41 Identities=29% Similarity=0.322 Sum_probs=30.3
Q ss_pred ccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHH
Q 046385 89 KHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 89 ~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~e 130 (218)
..+|.+|++.|--. +-.|.+.++++..||++.+||+.++..
T Consensus 5 ~~LTl~eK~~iI~~-~e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 5 KSLTLEEKLEIIKR-LEEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp SS--HHHHHHHHHH-HHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred ccCCHHHHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 46899999998665 566679999999999999999998763
No 7
>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=94.13 E-value=0.012 Score=37.90 Aligned_cols=34 Identities=21% Similarity=0.194 Sum_probs=25.7
Q ss_pred HHHHHHHHHhcCccchhhhhcccccccchhHHHH
Q 046385 96 KMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 96 ~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
++.-.+..+..|.+..+|+..|++|++||.|+++
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 3445566678889999999999999999999875
No 8
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=93.90 E-value=0.052 Score=43.63 Aligned_cols=45 Identities=20% Similarity=0.145 Sum_probs=40.2
Q ss_pred ccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHH
Q 046385 89 KHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLS 133 (218)
Q Consensus 89 ~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~ 133 (218)
++-+.+++.++|-.++..|.|.|.++.+|++|.+||.+.+++-=+
T Consensus 3 k~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e 47 (138)
T COG3415 3 KPFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRE 47 (138)
T ss_pred chhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhcc
Confidence 345778999999999999999999999999999999999887644
No 9
>smart00351 PAX Paired Box domain.
Probab=93.68 E-value=0.084 Score=41.34 Aligned_cols=45 Identities=16% Similarity=0.132 Sum_probs=39.3
Q ss_pred CccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHH
Q 046385 88 SKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLS 133 (218)
Q Consensus 88 T~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~ 133 (218)
.++.|.+++..|.+.+. .|.+.+.++.+|++|.+||+++++..-+
T Consensus 15 ~~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 15 GRPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 35789999999887775 7899999999999999999999998644
No 10
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=93.53 E-value=0.1 Score=33.52 Aligned_cols=44 Identities=23% Similarity=0.317 Sum_probs=35.4
Q ss_pred chHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 91 LTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 91 isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
++..|+- ++.+ +..|.++..++..+++|.+||.++.++++..+.
T Consensus 4 l~~~e~~-i~~~-~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 4 LTPRERE-VLRL-LAEGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCHHHHH-HHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 4566655 4333 578999999999999999999999999877664
No 11
>cd00131 PAX Paired Box domain
Probab=93.20 E-value=0.11 Score=40.91 Aligned_cols=47 Identities=11% Similarity=0.135 Sum_probs=40.9
Q ss_pred CCccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHH
Q 046385 87 DSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 87 ~T~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
..++.|.+++..|.+.+ ..|.+.+.++.+|++|.+||+++++..-+.
T Consensus 14 m~~~lS~d~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~ 60 (128)
T cd00131 14 NGRPLPDSIRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILNRYYET 60 (128)
T ss_pred CCCcCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHc
Confidence 44688999999998775 689999999999999999999999987653
No 12
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=93.05 E-value=0.035 Score=35.93 Aligned_cols=34 Identities=24% Similarity=0.206 Sum_probs=23.1
Q ss_pred HHHHHHHhcCccchhhhhcccccccchhHHHHHH
Q 046385 98 AMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEV 131 (218)
Q Consensus 98 aifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eV 131 (218)
+-.+..+..|.+.+.++..+++|.+||+++++..
T Consensus 8 ~~ii~l~~~G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 8 AQIIRLLREGWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp --HHHHHHHT--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 3345555559999999999999999999998764
No 13
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=92.75 E-value=0.085 Score=43.52 Aligned_cols=58 Identities=16% Similarity=0.151 Sum_probs=42.3
Q ss_pred ccchHHHHHHHHHHHHhcC-------------ccchhhhhcccccccchhHHHHHHHHH-HHhhhhhhcCCC
Q 046385 89 KHLTVEEKMAMFLFTISHN-------------LRNRFIKIRFQHSGHTVHRYFHEVLSA-MMKFSKEMITPP 146 (218)
Q Consensus 89 ~~isveE~laifL~~la~~-------------~s~r~i~~~F~~S~sTVsr~f~eVl~A-I~~L~~~~Ik~P 146 (218)
...++.+|++-+|..++.. .+...++...|.+.+||||++++..+. ++......|..|
T Consensus 137 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~~~~i~i~ 208 (211)
T PRK11753 137 AFLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKMLEDQGLISAHGKTIVVY 208 (211)
T ss_pred HhcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecCCEEEEe
Confidence 3568999999999887641 234789999999999999999987766 334434434433
No 14
>PF13518 HTH_28: Helix-turn-helix domain
Probab=92.50 E-value=0.13 Score=33.15 Aligned_cols=37 Identities=19% Similarity=0.202 Sum_probs=31.0
Q ss_pred HHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHH
Q 046385 96 KMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLS 133 (218)
Q Consensus 96 ~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~ 133 (218)
++.+.+.++ .|.|.+.++..|++|.+||.+.+.....
T Consensus 2 r~~iv~~~~-~g~s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 2 RLQIVELYL-EGESVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHH-cCCCHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 456666666 5679999999999999999999887765
No 15
>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=92.04 E-value=0.17 Score=37.58 Aligned_cols=35 Identities=11% Similarity=0.020 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHhcCccchhhhhcccccccchhHHH
Q 046385 93 VEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYF 128 (218)
Q Consensus 93 veE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f 128 (218)
..+| ...+..++.|.+++.++..+++|.+||+|+.
T Consensus 37 Ls~R-~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 37 LAQR-LQVAKMLKQGKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred hhHH-HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 4555 4445568899999999999999999999954
No 16
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=91.83 E-value=0.17 Score=32.82 Aligned_cols=37 Identities=14% Similarity=0.204 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHhcC-ccchhhhhcccccccchhHHHHH
Q 046385 94 EEKMAMFLFTISHN-LRNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 94 eE~laifL~~la~~-~s~r~i~~~F~~S~sTVsr~f~e 130 (218)
||.+.-.|--+-.| .|++.++..|+++.+|+++.++.
T Consensus 2 ee~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 2 EEDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp HHHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 56666777666677 99999999999999999987653
No 17
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=91.32 E-value=0.34 Score=40.93 Aligned_cols=56 Identities=13% Similarity=0.115 Sum_probs=42.6
Q ss_pred chHHHHHHHHHHHHhcC----ccchhhhhcccccccchhHHHHHHHHH-HHhhhhhhcCCC
Q 046385 91 LTVEEKMAMFLFTISHN----LRNRFIKIRFQHSGHTVHRYFHEVLSA-MMKFSKEMITPP 146 (218)
Q Consensus 91 isveE~laifL~~la~~----~s~r~i~~~F~~S~sTVsr~f~eVl~A-I~~L~~~~Ik~P 146 (218)
.++++|+|-||..++.+ .+..+++...|.|++|+||.+.+..+. ++......|..+
T Consensus 149 ~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~~~i~I~ 209 (226)
T PRK10402 149 FPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSKRGYLIK 209 (226)
T ss_pred ChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeCCEEEEe
Confidence 48999999999876543 355899999999999999999988775 444444444444
No 18
>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=91.28 E-value=0.43 Score=38.60 Aligned_cols=57 Identities=18% Similarity=0.314 Sum_probs=42.6
Q ss_pred cchHHHHHHHHHHHHhc--------------CccchhhhhcccccccchhHHHHHHHHH-HHhhhhhhcCCC
Q 046385 90 HLTVEEKMAMFLFTISH--------------NLRNRFIKIRFQHSGHTVHRYFHEVLSA-MMKFSKEMITPP 146 (218)
Q Consensus 90 ~isveE~laifL~~la~--------------~~s~r~i~~~F~~S~sTVsr~f~eVl~A-I~~L~~~~Ik~P 146 (218)
.-++++||+-+|..++. ..+..++++..|.|++||||.+++.-+. ++.....-|..+
T Consensus 112 ~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~ 183 (193)
T TIGR03697 112 HRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKKKLISIHKKKITVH 183 (193)
T ss_pred hCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCCEEEEe
Confidence 45899999999987653 1367899999999999999999987766 444444444433
No 19
>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=91.25 E-value=0.19 Score=37.87 Aligned_cols=39 Identities=23% Similarity=0.117 Sum_probs=31.6
Q ss_pred chHHHHHHHHHHH------HhcCccchhhhhcccccccchhHHHH
Q 046385 91 LTVEEKMAMFLFT------ISHNLRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 91 isveE~laifL~~------la~~~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
.+++|+-++.+++ +..+.++|.|+...|+|.+||+|.=+
T Consensus 33 LTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn 77 (94)
T TIGR01321 33 LTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSN 77 (94)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHh
Confidence 5777777777763 35679999999999999999998643
No 20
>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=91.10 E-value=0.31 Score=31.37 Aligned_cols=42 Identities=14% Similarity=0.174 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 93 VEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 93 veE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
..++. ++.. +..|.++++++..+++|.+||.++++++...+.
T Consensus 3 ~~e~~-i~~~-~~~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~ 44 (57)
T cd06170 3 PRERE-VLRL-LAEGKTNKEIADILGISEKTVKTHLRNIMRKLG 44 (57)
T ss_pred HHHHH-HHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 34444 3333 468999999999999999999999998877654
No 21
>PRK01381 Trp operon repressor; Provisional
Probab=90.28 E-value=0.25 Score=37.58 Aligned_cols=39 Identities=26% Similarity=0.163 Sum_probs=30.6
Q ss_pred chHHHHHHHHHHH-----Hhc-CccchhhhhcccccccchhHHHH
Q 046385 91 LTVEEKMAMFLFT-----ISH-NLRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 91 isveE~laifL~~-----la~-~~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
+++.|+-++..++ |-. +.|+|.|+...|+|.+||+|.=+
T Consensus 33 lTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn 77 (99)
T PRK01381 33 LTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITRGSN 77 (99)
T ss_pred CCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHH
Confidence 5777777777764 234 48999999999999999998643
No 22
>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=90.19 E-value=0.39 Score=30.06 Aligned_cols=43 Identities=23% Similarity=0.210 Sum_probs=33.1
Q ss_pred chHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHH
Q 046385 91 LTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 91 isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
++.+++.++-+++ ..|.++.+++..+++|..||.++++.....
T Consensus 11 l~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 11 LPEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred CCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 4555555554444 478899999999999999999999887543
No 23
>PRK04217 hypothetical protein; Provisional
Probab=89.65 E-value=0.45 Score=36.82 Aligned_cols=48 Identities=23% Similarity=0.104 Sum_probs=39.1
Q ss_pred ccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 89 KHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 89 ~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
..++.+++.++.|+ .-.+.++.+|+..+++|.+||.+++++..+.|-.
T Consensus 41 ~~Lt~eereai~l~-~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 41 IFMTYEEFEALRLV-DYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred ccCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 47788887554444 4478899999999999999999999998888763
No 24
>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=89.33 E-value=0.63 Score=34.18 Aligned_cols=48 Identities=19% Similarity=0.194 Sum_probs=43.0
Q ss_pred ccchHHHHHHHHHHHHhcCccchhhhhccc-ccccchhHHHHHHHHHHH
Q 046385 89 KHLTVEEKMAMFLFTISHNLRNRFIKIRFQ-HSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 89 ~~isveE~laifL~~la~~~s~r~i~~~F~-~S~sTVsr~f~eVl~AI~ 136 (218)
+.+...-+++|+|-.--.|.|+..++..|+ ++.+||+.-++.|-+.+-
T Consensus 26 ~~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~ 74 (90)
T cd06571 26 KEIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLE 74 (90)
T ss_pred cCcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHH
Confidence 478888899999999999999999999999 999999999888877654
No 25
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=88.48 E-value=0.43 Score=30.95 Aligned_cols=32 Identities=16% Similarity=0.208 Sum_probs=25.3
Q ss_pred HHHHHhcC-ccchhhhhcccccccchhHHHHHH
Q 046385 100 FLFTISHN-LRNRFIKIRFQHSGHTVHRYFHEV 131 (218)
Q Consensus 100 fL~~la~~-~s~r~i~~~F~~S~sTVsr~f~eV 131 (218)
.+..+... .++..++..+++|-+||.|+|++.
T Consensus 19 ~i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 19 YILKLLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 33334444 499999999999999999999864
No 26
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=88.21 E-value=0.73 Score=38.76 Aligned_cols=57 Identities=19% Similarity=0.290 Sum_probs=41.5
Q ss_pred cchHHHHHHHHHHHHhc--------------CccchhhhhcccccccchhHHHHHHHHH-HHhhhhhhcCCC
Q 046385 90 HLTVEEKMAMFLFTISH--------------NLRNRFIKIRFQHSGHTVHRYFHEVLSA-MMKFSKEMITPP 146 (218)
Q Consensus 90 ~isveE~laifL~~la~--------------~~s~r~i~~~F~~S~sTVsr~f~eVl~A-I~~L~~~~Ik~P 146 (218)
.-++++|++-+|..++. .-+..++++..|+|.+||||.+.+.-+. ++.+....|..+
T Consensus 153 ~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~~~~i~i~ 224 (235)
T PRK11161 153 KKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQKSGMLAVKGKYITIE 224 (235)
T ss_pred CCCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCCEEEEc
Confidence 35889999999998763 1356799999999999999998765444 334444444443
No 27
>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=88.10 E-value=0.62 Score=35.27 Aligned_cols=46 Identities=20% Similarity=0.148 Sum_probs=38.6
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..++-.+.++++ .|.++..++..+++|.+||++...++...|-
T Consensus 110 ~L~~~~~~ii~~~~~-~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 110 KLPEREREVLVLRYL-EGLSYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred hCCHHHHHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 467777777766655 6899999999999999999999999887764
No 28
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=88.03 E-value=0.72 Score=36.55 Aligned_cols=47 Identities=11% Similarity=0.095 Sum_probs=41.6
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKF 138 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L 138 (218)
.+|..++.++.|++ .|.++..|+..+|+|.+||...++.....+-..
T Consensus 112 ~L~~~~r~il~l~~--~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 112 KMTERDRTVLLLRF--SGYSYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred cCCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46888888888887 999999999999999999999999998887643
No 29
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=88.02 E-value=0.97 Score=38.35 Aligned_cols=45 Identities=22% Similarity=0.259 Sum_probs=36.8
Q ss_pred cchHHHHHHHHHHHHhcC----------ccchhhhhcccccccchhHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHN----------LRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 90 ~isveE~laifL~~la~~----------~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
..++++|++-+|..++.. .+..++++..|++++|+||.+++.-+.
T Consensus 152 ~~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~L~~L~~~ 206 (230)
T PRK09391 152 RKTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLQDR 206 (230)
T ss_pred CCCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 458999999999887541 345799999999999999999876554
No 30
>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=87.28 E-value=0.54 Score=31.61 Aligned_cols=41 Identities=27% Similarity=0.331 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHhc----------CccchhhhhcccccccchhHHHHHHHHH
Q 046385 94 EEKMAMFLFTISH----------NLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 94 eE~laifL~~la~----------~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
++|++-+|..++. ..+..+++..+++|.+||++++....+.
T Consensus 2 ~~ria~~l~~l~~~~~~~~~~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~ 52 (67)
T cd00092 2 KERLASFLLNLSLRYGAGDLVQLPLTRQEIADYLGLTRETVSRTLKELEEE 52 (67)
T ss_pred chHHHHHHHHHHHHcCCCccccCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3556666655432 2567899999999999999999877664
No 31
>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=86.84 E-value=0.94 Score=29.54 Aligned_cols=44 Identities=16% Similarity=0.092 Sum_probs=30.8
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.+|..++..+.|++ -.|.++..++..+++|.+||.+.++.....
T Consensus 10 ~L~~~~r~i~~l~~-~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLRY-FQGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHHH-TS---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHH-HHCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 46777776666554 467899999999999999999998877654
No 32
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=86.69 E-value=0.97 Score=35.94 Aligned_cols=47 Identities=21% Similarity=0.082 Sum_probs=39.6
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..++..+-|+++ .|.+++.++..+|+|.+||....+....-|-.
T Consensus 128 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 128 SLPEELRTAITLREI-EGLSYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 467888877777765 78899999999999999999999988777664
No 33
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=86.65 E-value=0.55 Score=26.40 Aligned_cols=37 Identities=24% Similarity=0.165 Sum_probs=26.6
Q ss_pred chHHHHHHHHHHHHhcCccchhhhhcccccccchhHHH
Q 046385 91 LTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYF 128 (218)
Q Consensus 91 isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f 128 (218)
.+.+++..+... +-.+.+...++..|++|.+||++++
T Consensus 6 ~~~~~~~~i~~~-~~~~~s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRL-LAAGESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHhC
Confidence 344444444433 4467799999999999999998763
No 34
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=86.47 E-value=1.4 Score=37.15 Aligned_cols=45 Identities=18% Similarity=0.248 Sum_probs=36.1
Q ss_pred cchHHHHHHHHHHHHhcC----------ccchhhhhcccccccchhHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHN----------LRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 90 ~isveE~laifL~~la~~----------~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.-++++|+|-||..++.. .+..+++...|++.+||||.+++.-+.
T Consensus 146 ~~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~lG~tretvsR~l~~L~~~ 200 (236)
T PRK09392 146 LRSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYLGMTPENLSRAFAALASH 200 (236)
T ss_pred cCCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHhCCChhHHHHHHHHHHhC
Confidence 458999999999987653 223679999999999999999885544
No 35
>PRK15320 transcriptional activator SprB; Provisional
Probab=86.42 E-value=0.58 Score=40.23 Aligned_cols=38 Identities=18% Similarity=0.182 Sum_probs=34.4
Q ss_pred HHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 99 MFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 99 ifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
--|..||.|.|++.|++.++.|.+|||.+..+.++.+-
T Consensus 171 EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLg 208 (251)
T PRK15320 171 ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLG 208 (251)
T ss_pred HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence 55778999999999999999999999999999888754
No 36
>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=86.35 E-value=0.82 Score=33.90 Aligned_cols=36 Identities=14% Similarity=-0.033 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHhcCccchhhhhcccccccchhHHHH
Q 046385 94 EEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 94 eE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
..|+.|+=-.|-.|.+||.|+...|+|..||+|.=+
T Consensus 36 ~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr 71 (87)
T PF01371_consen 36 AQRWQVAKELLDEGKSYREIAEETGVSIATITRVSR 71 (87)
T ss_dssp HHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 334444444677899999999999999999998644
No 37
>PRK00118 putative DNA-binding protein; Validated
Probab=86.08 E-value=1.2 Score=34.01 Aligned_cols=45 Identities=18% Similarity=0.116 Sum_probs=35.9
Q ss_pred chHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 91 LTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 91 isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
++..++.++-|+ ...|.|+..|+..+|+|.+||++.+++....+-
T Consensus 18 L~ekqRevl~L~-y~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr 62 (104)
T PRK00118 18 LTEKQRNYMELY-YLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLE 62 (104)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 466666666555 556999999999999999999999988766655
No 38
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=85.95 E-value=1.1 Score=39.09 Aligned_cols=48 Identities=19% Similarity=0.130 Sum_probs=41.4
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKF 138 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L 138 (218)
.++..|+..+.|+++ .+.++..|+..+|+|.+||+++.++.+..+-..
T Consensus 205 ~L~~~er~vi~l~y~-e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 205 ALEEKERKVMALYYY-EELVLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467888888888875 789999999999999999999999988887643
No 39
>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=85.92 E-value=0.92 Score=36.40 Aligned_cols=45 Identities=13% Similarity=0.113 Sum_probs=36.8
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..|+-.+.|+ ..|.++..++..++.|.+||+++.+...+.+-
T Consensus 6 ~Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr 50 (137)
T TIGR00721 6 FLTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRAMENIE 50 (137)
T ss_pred CCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhHHHHHH
Confidence 4566777677664 79999999999999999999988887766654
No 40
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=85.75 E-value=1.4 Score=34.68 Aligned_cols=53 Identities=13% Similarity=0.095 Sum_probs=42.4
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH-hhhhhhc
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM-KFSKEMI 143 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~-~L~~~~I 143 (218)
.+|..++-++.|+++ .|.++..|+...|+|..||....+.....+- .|....+
T Consensus 106 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~ 159 (161)
T PRK09047 106 KLPARQREAFLLRYW-EDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKGI 159 (161)
T ss_pred hCCHHHHHHHHHHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcCc
Confidence 467777777776654 6899999999999999999999999998887 3544433
No 41
>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=85.18 E-value=0.81 Score=29.39 Aligned_cols=39 Identities=13% Similarity=0.104 Sum_probs=27.8
Q ss_pred HHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHH
Q 046385 96 KMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 96 ~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
|+.|.....-...+..+++..++.|.+|||+++..-.++
T Consensus 4 R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~~ 42 (47)
T PF01022_consen 4 RLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLREA 42 (47)
T ss_dssp HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHHC
Confidence 444544444455666999999999999999999876543
No 42
>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=85.12 E-value=1.2 Score=34.56 Aligned_cols=46 Identities=15% Similarity=0.087 Sum_probs=39.4
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++..++-++.|+++ .|.++..|+..+|+|.+||....+.....+-
T Consensus 113 ~L~~~~r~il~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 113 KLPEQCRKIFILSRF-EGKSYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 467888888888776 6899999999999999999999888776653
No 43
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=85.09 E-value=1.3 Score=36.03 Aligned_cols=47 Identities=19% Similarity=0.315 Sum_probs=40.3
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|.+++.++-|+++ .|.|+..|+..+|+|.+||...++.-+..+..
T Consensus 127 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 127 TLRPRVKQAFLMATL-DGMKQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 567788888888777 88999999999999999999999987777764
No 44
>PRK06030 hypothetical protein; Provisional
Probab=85.05 E-value=1.8 Score=34.20 Aligned_cols=46 Identities=17% Similarity=0.234 Sum_probs=40.5
Q ss_pred ccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHH
Q 046385 89 KHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 89 ~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
+.+...-|+||+|-.--++.|+..|+..||++.+||+.-++.|=+.
T Consensus 51 k~i~~aRqIAMYL~r~~~~~sl~~IG~~FGRDHSTV~haikkIe~~ 96 (124)
T PRK06030 51 REVSRIRQIAMYVAHVSLGWPMNEVALAFGRDRTTVGHACHTVEDL 96 (124)
T ss_pred cccchHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHHHHHHH
Confidence 4688889999999999999999999999999999999887755443
No 45
>PF13730 HTH_36: Helix-turn-helix domain
Probab=84.93 E-value=1.3 Score=28.96 Aligned_cols=40 Identities=15% Similarity=0.174 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHhc--Cc---cchhhhhcccccccchhHHHHHHHH
Q 046385 94 EEKMAMFLFTISH--NL---RNRFIKIRFQHSGHTVHRYFHEVLS 133 (218)
Q Consensus 94 eE~laifL~~la~--~~---s~r~i~~~F~~S~sTVsr~f~eVl~ 133 (218)
+..|.++|...+. +. |+..++...++|..||.+.+++-.+
T Consensus 7 ~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 7 AKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred HHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4445555555542 22 6799999999999999999987543
No 46
>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=84.78 E-value=0.97 Score=39.59 Aligned_cols=47 Identities=6% Similarity=0.083 Sum_probs=41.4
Q ss_pred cchHHHHHHHHHHHHh-cCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTIS-HNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la-~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..||..+-|+++. .+.+++.|+..+++|.+||+++.++.+.-+-
T Consensus 218 ~L~~rer~vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr 265 (270)
T TIGR02392 218 SLDARSRRIIEARWLDDDKLTLQELAAEYGVSAERIRQIEKNAMKKLK 265 (270)
T ss_pred cCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4788899999999873 4789999999999999999999998888765
No 47
>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=84.74 E-value=0.82 Score=30.49 Aligned_cols=44 Identities=20% Similarity=0.181 Sum_probs=35.1
Q ss_pred chHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 91 LTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 91 isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
+|..|. -.|..++.|.+...++...++|.+||..+...+..-+-
T Consensus 4 LT~~E~--~vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 4 LTEREL--EVLRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp S-HHHH--HHHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred cCHHHH--HHHHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 344443 36788999999999999999999999999999887754
No 48
>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=84.51 E-value=0.68 Score=33.79 Aligned_cols=37 Identities=27% Similarity=0.147 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHhc-CccchhhhhcccccccchhHHHHH
Q 046385 94 EEKMAMFLFTISH-NLRNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 94 eE~laifL~~la~-~~s~r~i~~~F~~S~sTVsr~f~e 130 (218)
++|+..-+-+|.. ..+..+++..||+|.+||||.+++
T Consensus 5 ~~R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 5 EERVLEIGKYIVETKATVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhcC
Confidence 4455555544444 345589999999999999998864
No 49
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=84.25 E-value=1.4 Score=37.45 Aligned_cols=48 Identities=17% Similarity=0.084 Sum_probs=41.6
Q ss_pred cchHHHHHHHHHHHH---hcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTI---SHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~l---a~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..+|-.+-|++. -.|.|+..|+..+|+|.+||.+..+..+..+-.
T Consensus 178 ~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 178 KLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred hCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 577888888888774 589999999999999999999999988888764
No 50
>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=83.80 E-value=1.1 Score=38.26 Aligned_cols=48 Identities=10% Similarity=0.054 Sum_probs=42.5
Q ss_pred cchHHHHHHHHHHHH---hcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTI---SHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~l---a~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.++..|+..+.|++. ..+.++..|+..+|+|.++|+++.++.+.-+-.
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 568889999999885 578999999999999999999999998888763
No 51
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=82.92 E-value=1.6 Score=37.96 Aligned_cols=46 Identities=20% Similarity=0.208 Sum_probs=41.0
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++..++..+.|+++ .|.++..++..+|+|.+||++..++.+..+-
T Consensus 203 ~L~~~~r~vl~l~y~-~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr 248 (256)
T PRK07408 203 QLEERTREVLEFVFL-HDLTQKEAAERLGISPVTVSRRVKKGLDQLK 248 (256)
T ss_pred cCCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 568888888888885 5899999999999999999999999888876
No 52
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=82.76 E-value=1.5 Score=35.89 Aligned_cols=47 Identities=17% Similarity=0.075 Sum_probs=38.7
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|.+++.++-|+++. |.++..|+..+|+|.+||...++.....|-.
T Consensus 141 ~L~~~~~~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 141 QLPESQRQVLELAYYE-GLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred hCCHHHhhhhhhhhhc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4566676666666554 8999999999999999999999998888774
No 53
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=82.11 E-value=1.5 Score=37.38 Aligned_cols=48 Identities=21% Similarity=0.090 Sum_probs=41.3
Q ss_pred cchHHHHHHHHHHHH---hcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTI---SHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~l---a~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..+|..+-|+++ -.|.|++.++..+|+|.+||++..+..+..+-.
T Consensus 175 ~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~ 225 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFK 225 (233)
T ss_pred hCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 578899999999875 477899999999999999999998887777653
No 54
>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=82.11 E-value=1.2 Score=31.23 Aligned_cols=43 Identities=19% Similarity=0.197 Sum_probs=34.0
Q ss_pred ccchHHHHHHHHHHHHhcCccchhhhhccc-ccccchhHHHHHH
Q 046385 89 KHLTVEEKMAMFLFTISHNLRNRFIKIRFQ-HSGHTVHRYFHEV 131 (218)
Q Consensus 89 ~~isveE~laifL~~la~~~s~r~i~~~F~-~S~sTVsr~f~eV 131 (218)
+.+.-.-++||+|-.--++.|+.+++..|+ +..+||..-++.|
T Consensus 27 ~~i~~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHstV~~a~~ki 70 (70)
T PF08299_consen 27 RKIVEARQVAMYLARELTGLSLSEIGRYFGGRDHSTVIHAIRKI 70 (70)
T ss_dssp HHHHHHHHHHHHHHHHHS---HHHHHHHCTSSTHHHHHHHHHHH
T ss_pred hhhcchHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHHhC
Confidence 356677889999988888999999999999 9999998877654
No 55
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=82.04 E-value=1.5 Score=38.91 Aligned_cols=47 Identities=6% Similarity=0.010 Sum_probs=41.0
Q ss_pred cchHHHHHHHHHHHHh-cCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTIS-HNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la-~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++..|+..+-++|+. .+.++..|+..+|+|.++|+++-+..+.-+-
T Consensus 230 ~L~~rEr~VL~lry~~~~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR 277 (284)
T PRK06596 230 GLDERSRDIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAMKKLK 277 (284)
T ss_pred cCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4788899999998874 6889999999999999999999998877654
No 56
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=81.93 E-value=1.6 Score=32.30 Aligned_cols=44 Identities=11% Similarity=0.142 Sum_probs=40.7
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLS 133 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~ 133 (218)
.+++.-++.+.-.++..|.+...++..||+|..|+++.+...-.
T Consensus 8 ~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra 51 (85)
T PF13011_consen 8 RLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRA 51 (85)
T ss_pred CCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 68899999999999999999999999999999999999987754
No 57
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=81.63 E-value=1.6 Score=33.68 Aligned_cols=45 Identities=9% Similarity=0.149 Sum_probs=41.3
Q ss_pred ccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHH
Q 046385 89 KHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLS 133 (218)
Q Consensus 89 ~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~ 133 (218)
+.-|.|.++.+....+..|.+.+.++..|++|.+|+++..++...
T Consensus 11 r~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 11 RRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 567899999999999999999999999999999999999998764
No 58
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=81.58 E-value=1.9 Score=35.57 Aligned_cols=47 Identities=19% Similarity=0.109 Sum_probs=41.0
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..+|-++-|+++ .|.++..|+..+++|..||...++.....+-.
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~ 182 (196)
T PRK12524 136 ALPERQRQAVVLRHI-EGLSNPEIAEVMEIGVEAVESLTARGKRALAA 182 (196)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 567888877777776 89999999999999999999999998888763
No 59
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=81.56 E-value=2.2 Score=34.36 Aligned_cols=46 Identities=13% Similarity=0.128 Sum_probs=39.8
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|.+++..+.|+++ .|.|+..|+..+|+|..||...++.....+-
T Consensus 129 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 129 ELEKDRAAAVRRAYL-EGLSYKELAERHDVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence 567788878888865 7899999999999999999999998888765
No 60
>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=81.13 E-value=1.2 Score=29.96 Aligned_cols=41 Identities=10% Similarity=0.062 Sum_probs=32.0
Q ss_pred HHHHHHHHHH-HhcCccchhhhhcccccccchhHHHHHHHHH
Q 046385 94 EEKMAMFLFT-ISHNLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 94 eE~laifL~~-la~~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
..++.|.-+. ...+.+...++..++++.+|+|++++.-.++
T Consensus 10 p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~a 51 (61)
T PF12840_consen 10 PTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEA 51 (61)
T ss_dssp HHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3455565555 6777888999999999999999999887665
No 61
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=80.86 E-value=2.8 Score=34.31 Aligned_cols=54 Identities=13% Similarity=0.087 Sum_probs=43.9
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH-hhhhhhcC
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM-KFSKEMIT 144 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~-~L~~~~Ik 144 (218)
.+|...+.++.|+++ .|.++..|+..+|+|..||...++.....|- .|...++.
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~ 190 (195)
T PRK12532 136 NLPENTARVFTLKEI-LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWFN 190 (195)
T ss_pred hCCHHHHHHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 467777777777665 7889999999999999999999999999987 45555543
No 62
>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=80.84 E-value=0.48 Score=30.87 Aligned_cols=21 Identities=24% Similarity=0.070 Sum_probs=18.4
Q ss_pred chhhhhcccccccchhHHHHH
Q 046385 110 NRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 110 ~r~i~~~F~~S~sTVsr~f~e 130 (218)
..+++..-|+|.+||||.++.
T Consensus 2 i~dIA~~agvS~~TVSr~ln~ 22 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLNG 22 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHTT
T ss_pred HHHHHHHHCcCHHHHHHHHhC
Confidence 468899999999999998873
No 63
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=80.77 E-value=2.1 Score=33.75 Aligned_cols=47 Identities=15% Similarity=0.159 Sum_probs=38.3
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|.+++..+.|+++. |.|+..|+..+|+|.+||.+.+...+.-+-.
T Consensus 109 ~L~~~~r~v~~l~~~~-~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 109 ELPARTRYAFEMYRLH-GETQKDIARELGVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4677777777676655 8999999999999999999998887777653
No 64
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=80.63 E-value=2.3 Score=34.67 Aligned_cols=53 Identities=19% Similarity=0.121 Sum_probs=43.1
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhhhhhhc
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEMI 143 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L~~~~I 143 (218)
.+|.+++..+.|+++ .|.++..|+..+++|..||...++.....|-..-+.++
T Consensus 138 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~~ 190 (193)
T PRK11923 138 QLPEDLRTALTLREF-DGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQPLL 190 (193)
T ss_pred hCCHHHhHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 467788777777665 78999999999999999999999999888875444444
No 65
>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=80.40 E-value=1.6 Score=38.84 Aligned_cols=45 Identities=22% Similarity=0.098 Sum_probs=40.0
Q ss_pred cchHHHHHHHHHHHH---hcCccchhhhhcccccccchhHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTI---SHNLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 90 ~isveE~laifL~~l---a~~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.+|..|+..+.|++. ..+.++..|+..+|+|.+||..+.+..+..
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 578899999999886 688999999999999999999998887764
No 66
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)
Probab=80.25 E-value=2.7 Score=29.66 Aligned_cols=66 Identities=14% Similarity=0.148 Sum_probs=48.2
Q ss_pred CHHHHHHHHHHHHhcCccCCCccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHH
Q 046385 68 DKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 68 ~~~~F~~L~~~L~~~~~~~~T~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
+-+.+..+-.+|.+.........++..+-+--.||.+.+|+.-|.+-..|+ +.+||++.|.+=.++
T Consensus 2 sD~~W~~i~p~lp~~~~~~~~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg-~~~tv~~~f~rW~~~ 67 (75)
T PF13340_consen 2 SDEEWALIEPLLPPRKPRGGRPRIDLREVLNAILYVLRTGCPWRDLPEDFG-PWSTVYRRFRRWSRS 67 (75)
T ss_pred CHHHHHHHHhhCCCCCCCCCCCccchHHHHhcccccceecceecccchhcc-CcCcHHHHHHHHHHc
Confidence 344455555555443322222467788888888999999999999999999 899999999876554
No 67
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=80.16 E-value=2.6 Score=33.98 Aligned_cols=45 Identities=16% Similarity=0.025 Sum_probs=36.6
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..++-.+.|+ ..|.++..++..+++|.+||+++.+..++.+-
T Consensus 6 ~Lt~rqreVL~lr--~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr 50 (141)
T PRK03975 6 FLTERQIEVLRLR--ERGLTQQEIADILGTSRANVSSIEKRARENIE 50 (141)
T ss_pred CCCHHHHHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4567777776663 69999999999999999999998887666543
No 68
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=79.76 E-value=2.5 Score=36.50 Aligned_cols=46 Identities=22% Similarity=0.155 Sum_probs=39.5
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..++-.+-|+++ .|.|+..|+..+++|.+||++..+..+..|-
T Consensus 205 ~L~~~~r~vl~l~~~-~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr 250 (257)
T PRK08583 205 VLSDREKSIIQCTFI-ENLSQKETGERLGISQMHVSRLQRQAIKKLR 250 (257)
T ss_pred hCCHHHHHHHHHHHh-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 467778777777664 7899999999999999999999999988876
No 69
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=79.74 E-value=1.9 Score=35.15 Aligned_cols=57 Identities=12% Similarity=0.111 Sum_probs=42.1
Q ss_pred cchHHHHHHHHHHHHhcC--------------ccchhhhhcccccccchhHHHHHHHHH-HHhhhhhhcCCC
Q 046385 90 HLTVEEKMAMFLFTISHN--------------LRNRFIKIRFQHSGHTVHRYFHEVLSA-MMKFSKEMITPP 146 (218)
Q Consensus 90 ~isveE~laifL~~la~~--------------~s~r~i~~~F~~S~sTVsr~f~eVl~A-I~~L~~~~Ik~P 146 (218)
..++++|||-+|..++.. .+..++++..|.+++||||.+++..+. ++......|..+
T Consensus 118 ~~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~ 189 (202)
T PRK13918 118 GQRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRETVTKVIGELSREGYIRSGYGKIQLL 189 (202)
T ss_pred hCchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcCCCEEEEE
Confidence 457899999999877641 246799999999999999999998775 334443444443
No 70
>smart00153 VHP Villin headpiece domain.
Probab=79.71 E-value=0.7 Score=28.67 Aligned_cols=22 Identities=18% Similarity=0.123 Sum_probs=19.4
Q ss_pred CcccchhccccCHHHHHHHHHH
Q 046385 57 SPIFCYDLMRMDKNGFISLCQL 78 (218)
Q Consensus 57 ~~~~~~~~fRM~~~~F~~L~~~ 78 (218)
++++|...|+|+++.|..|=..
T Consensus 3 sdeeF~~vfgmsr~eF~~LP~W 24 (36)
T smart00153 3 SDEDFEEVFGMTREEFYKLPLW 24 (36)
T ss_pred CHHHHHHHHCCCHHHHHhCcHh
Confidence 6789999999999999988654
No 71
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=79.54 E-value=1.5 Score=36.80 Aligned_cols=44 Identities=14% Similarity=0.009 Sum_probs=38.3
Q ss_pred chHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 91 LTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 91 isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
+|..|+ =-|..++.|.++++|+...++|..||..+...++.-+-
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 666664 56788999999999999999999999999999988765
No 72
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=79.35 E-value=2 Score=38.12 Aligned_cols=48 Identities=10% Similarity=0.003 Sum_probs=42.8
Q ss_pred cchHHHHHHHHHHHH-hcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTI-SHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~l-a~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.++..||..+-|+++ ..+.++..|+..+++|.+||+++.++.+..|-.
T Consensus 227 ~L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~ 275 (289)
T PRK07500 227 TLNERELRIIRERRLREDGATLEALGEELGISKERVRQIEARALEKLRR 275 (289)
T ss_pred cCCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 578899999999885 378999999999999999999999999988773
No 73
>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=79.26 E-value=2.5 Score=33.41 Aligned_cols=46 Identities=13% Similarity=0.033 Sum_probs=39.7
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|+.++..+.|+++ .|.++..|+..+++|.+||....+.....+-
T Consensus 122 ~L~~~~r~vl~l~~~-~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr 167 (170)
T TIGR02952 122 ILTPKQQHVIALRFG-QNLPIAEVARILGKTEGAVKILQFRAIKKLA 167 (170)
T ss_pred hCCHHHHHHHHHHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 578888888888766 5899999999999999999999988877764
No 74
>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=79.25 E-value=0.6 Score=29.02 Aligned_cols=24 Identities=17% Similarity=0.108 Sum_probs=18.3
Q ss_pred CcccchhccccCHHHHHHHHHHHH
Q 046385 57 SPIFCYDLMRMDKNGFISLCQLFK 80 (218)
Q Consensus 57 ~~~~~~~~fRM~~~~F~~L~~~L~ 80 (218)
++++|...|+|+++.|..|-..=+
T Consensus 3 sd~dF~~vFgm~~~eF~~lP~WKq 26 (36)
T PF02209_consen 3 SDEDFEKVFGMSREEFYKLPKWKQ 26 (36)
T ss_dssp -HHHHHHHHSS-HHHHHHS-HHHH
T ss_pred CHHHHHHHHCCCHHHHHHChHHHH
Confidence 678999999999999999876544
No 75
>PRK05572 sporulation sigma factor SigF; Validated
Probab=79.12 E-value=2.3 Score=36.67 Aligned_cols=47 Identities=19% Similarity=0.251 Sum_probs=41.3
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..++..+-|+++ .|.++..|+..+|+|.+||+++.+..+..|-.
T Consensus 202 ~L~~~~~~v~~l~~~-~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~ 248 (252)
T PRK05572 202 ELDERERLIVYLRYF-KDKTQSEVAKRLGISQVQVSRLEKKILKQMKE 248 (252)
T ss_pred cCCHHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 578888888888775 68999999999999999999999999988763
No 76
>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=78.99 E-value=2 Score=29.68 Aligned_cols=26 Identities=19% Similarity=0.112 Sum_probs=22.3
Q ss_pred cchhhhhcccccccchhHHHHHHHHH
Q 046385 109 RNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 109 s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
+..++++..|.|.+||+|.+++.-+.
T Consensus 30 t~~~iA~~~g~sr~tv~r~l~~l~~~ 55 (76)
T PF13545_consen 30 TQEEIADMLGVSRETVSRILKRLKDE 55 (76)
T ss_dssp SHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 45689999999999999999887665
No 77
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=78.95 E-value=2.8 Score=35.40 Aligned_cols=48 Identities=13% Similarity=0.176 Sum_probs=40.8
Q ss_pred CCccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 87 DSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 87 ~T~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.|..+|..|+ -.|..+|.|.+++.|+...++|.+||..+...+++-+-
T Consensus 130 ~~~~LSpREr--EVLrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKLg 177 (198)
T PRK15201 130 TTRHFSVTER--HLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLH 177 (198)
T ss_pred CCCCCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3456787775 56778999999999999999999999999999888764
No 78
>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=78.94 E-value=2.6 Score=27.90 Aligned_cols=27 Identities=22% Similarity=0.175 Sum_probs=22.6
Q ss_pred ccchhhhhcccccccchhHHHHHHHHH
Q 046385 108 LRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 108 ~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.+..+++..++++++||++.++...+.
T Consensus 22 ~t~~~la~~l~~~~~~vs~~v~~L~~~ 48 (62)
T PF12802_consen 22 LTQSELAERLGISKSTVSRIVKRLEKK 48 (62)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 588999999999999999999876554
No 79
>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=78.72 E-value=0.89 Score=27.49 Aligned_cols=23 Identities=17% Similarity=0.153 Sum_probs=18.5
Q ss_pred cchhhhhcccccccchhHHHHHH
Q 046385 109 RNRFIKIRFQHSGHTVHRYFHEV 131 (218)
Q Consensus 109 s~r~i~~~F~~S~sTVsr~f~eV 131 (218)
+.+++++..|.+.+||||.+.+.
T Consensus 4 tr~diA~~lG~t~ETVSR~l~~l 26 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRILKKL 26 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHHHHH
Confidence 45789999999999999998764
No 80
>PHA00675 hypothetical protein
Probab=78.37 E-value=2.6 Score=30.62 Aligned_cols=40 Identities=13% Similarity=0.137 Sum_probs=32.9
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
.++..+-..|.......|.|+..++..|++|.+||+.|-+
T Consensus 22 KLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 22 KLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred ccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHc
Confidence 5666676677777767788999999999999999987754
No 81
>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=78.18 E-value=1.5 Score=29.52 Aligned_cols=30 Identities=10% Similarity=0.059 Sum_probs=25.5
Q ss_pred CccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 107 NLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 107 ~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
..+..+++..+++|++|++.+++...+-|+
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae~kli 52 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAERKLI 52 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence 456678999999999999999998877654
No 82
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=78.11 E-value=3.1 Score=34.11 Aligned_cols=47 Identities=13% Similarity=0.122 Sum_probs=40.3
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|...|.++.|+++. |.|+..|+..+|+|.+||...++.....+-.
T Consensus 134 ~Lp~~~R~v~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 134 HLPAQQARVFMMREYL-ELSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred hCCHHHHHHHhHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4677788888887766 9999999999999999999999988888763
No 83
>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=78.09 E-value=2.6 Score=33.19 Aligned_cols=47 Identities=15% Similarity=0.152 Sum_probs=38.6
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..++..+-|++ -.|.++..|+..+|+|.+||....+.....|-.
T Consensus 110 ~L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 110 RLPARQRAVVVLRY-YEDLSEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred hCCHHHHHHhhhHH-HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 35667766666665 669999999999999999999999998888763
No 84
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=77.92 E-value=3.3 Score=34.72 Aligned_cols=47 Identities=9% Similarity=-0.006 Sum_probs=40.0
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|...+.++.|+++. |.+++.|+..+|+|..||...+++....|-.
T Consensus 148 ~L~~~~r~v~~L~~~~-g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~ 194 (206)
T PRK12544 148 GLPAKYARVFMMREFI-ELETNEICHAVDLSVSNLNVLLYRARLRLRE 194 (206)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4677777777776654 8999999999999999999999999998874
No 85
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=77.80 E-value=3.6 Score=33.53 Aligned_cols=47 Identities=11% Similarity=0.005 Sum_probs=40.9
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|.+++-++-|+++ .|.++..|+..+++|..||...++.....+-.
T Consensus 131 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 131 KLSPAHREIIDLVYY-HEKSVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 567888877778777 89999999999999999999999998888764
No 86
>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=77.71 E-value=2.4 Score=30.47 Aligned_cols=45 Identities=13% Similarity=-0.001 Sum_probs=36.4
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.++..++.+..|...-.|.|++.|+...++|.+||..+++.--++
T Consensus 15 ~l~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~ 59 (73)
T TIGR03879 15 WVDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGETKA 59 (73)
T ss_pred cCCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCccc
Confidence 456677777777666689999999999999999999998864433
No 87
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=77.68 E-value=2.7 Score=36.37 Aligned_cols=46 Identities=20% Similarity=0.106 Sum_probs=39.6
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++..++..+.++++ .|.++..++..+|+|.+||+++.+..+..|-
T Consensus 209 ~L~~~er~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~~al~kLr 254 (258)
T PRK08215 209 KLNDREKLILNLRFF-QGKTQMEVAEEIGISQAQVSRLEKAALKHMR 254 (258)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 467788888888774 6889999999999999999999999887765
No 88
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=77.63 E-value=2.9 Score=35.26 Aligned_cols=46 Identities=20% Similarity=0.195 Sum_probs=39.5
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..++-.+-|+++ .|.++..|+..+++|.+||++..+.++..+-
T Consensus 178 ~L~~~~r~vl~l~y~-~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr 223 (227)
T TIGR02980 178 ALPERERRILLLRFF-EDKTQSEIAERLGISQMHVSRLLRRALKKLR 223 (227)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 467788877777664 6889999999999999999999999988765
No 89
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=77.52 E-value=3 Score=33.77 Aligned_cols=47 Identities=17% Similarity=0.201 Sum_probs=39.8
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..+|.++.|+++. |.|+..++..+++|.+||...++.....|-.
T Consensus 127 ~L~~~~r~v~~l~~~~-g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 127 SLPIKYREVIYLFYYE-ELSIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred hCCHHHhhHhHhHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4677777777776665 8999999999999999999999998888764
No 90
>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=77.40 E-value=2.7 Score=35.82 Aligned_cols=47 Identities=17% Similarity=0.057 Sum_probs=41.7
Q ss_pred cchHHHHHHHHHHHH---hcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTI---SHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~l---a~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..+|..+.|+++ ..|.|+..|+...|+|..||.+..+..+..+-
T Consensus 178 ~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR 227 (234)
T TIGR02835 178 KLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLK 227 (234)
T ss_pred hCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 578999999999885 48899999999999999999999888877765
No 91
>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=77.37 E-value=3.2 Score=26.37 Aligned_cols=27 Identities=19% Similarity=0.337 Sum_probs=22.4
Q ss_pred CccchhhhhcccccccchhHHHHHHHH
Q 046385 107 NLRNRFIKIRFQHSGHTVHRYFHEVLS 133 (218)
Q Consensus 107 ~~s~r~i~~~F~~S~sTVsr~f~eVl~ 133 (218)
+.+.++++...++|.+||++++++..+
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 478899999999999999999998765
No 92
>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=77.36 E-value=2.7 Score=35.67 Aligned_cols=47 Identities=17% Similarity=0.017 Sum_probs=41.4
Q ss_pred cchHHHHHHHHHHHH---hcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTI---SHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~l---a~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..+|..+-|+++ ..+.|+..|+...++|.+||++..+..+..|-
T Consensus 174 ~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr 223 (227)
T TIGR02846 174 VLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLY 223 (227)
T ss_pred hCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 467888888888876 48899999999999999999999999888875
No 93
>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=77.24 E-value=2.9 Score=35.37 Aligned_cols=46 Identities=20% Similarity=0.125 Sum_probs=39.1
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++..++..+-|++ ..|.++..++..+|+|.+||+++-+.++.-|-
T Consensus 183 ~L~~~e~~i~~~~~-~~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr 228 (231)
T TIGR02885 183 KLDERERQIIMLRY-FKDKTQTEVANMLGISQVQVSRLEKKVLKKMK 228 (231)
T ss_pred cCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 56778887777776 46889999999999999999999999887764
No 94
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=77.13 E-value=2.7 Score=37.93 Aligned_cols=48 Identities=27% Similarity=0.167 Sum_probs=42.5
Q ss_pred cchHHHHHHHHHHHH---hcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTI---SHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~l---a~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.++..||..+.|++. ..+.++..|+..+|+|.+||..+.+..+..|-.
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 578899999999986 578999999999999999999999988887763
No 95
>PRK06930 positive control sigma-like factor; Validated
Probab=76.90 E-value=3.6 Score=33.91 Aligned_cols=47 Identities=17% Similarity=0.101 Sum_probs=38.6
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..++-.+.| ....|.++..++..+++|.+||..+++.....+-.
T Consensus 114 ~L~~rer~V~~L-~~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 114 VLTEREKEVYLM-HRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred hCCHHHHHHHHH-HHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 466666555444 45899999999999999999999999999888763
No 96
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=76.90 E-value=3.8 Score=33.70 Aligned_cols=47 Identities=9% Similarity=0.043 Sum_probs=40.5
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..++.++.|+++ .|.++..|+..+++|.+||...++.....|-.
T Consensus 116 ~Lp~~~r~i~~L~~~-~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~ 162 (187)
T PRK12516 116 QLPDDQREAIILVGA-SGFAYEEAAEICGCAVGTIKSRVNRARQRLQE 162 (187)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 467778777777766 89999999999999999999999998888764
No 97
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=76.85 E-value=2.1 Score=28.32 Aligned_cols=37 Identities=16% Similarity=0.154 Sum_probs=32.2
Q ss_pred HHHHHHhcCccchhhhhcccccccchhHHHHHHHHHH
Q 046385 99 MFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAM 135 (218)
Q Consensus 99 ifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI 135 (218)
.-+..++.|.++..++...++|..||..+...+..-+
T Consensus 11 ~v~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl 47 (65)
T COG2771 11 EILRLVAQGKSNKEIARILGISEETVKTHLRNIYRKL 47 (65)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4567788999999999999999999999998886554
No 98
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=76.70 E-value=3.8 Score=32.62 Aligned_cols=46 Identities=9% Similarity=0.058 Sum_probs=40.0
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..++-++-|+++ .|.|+..|+..+++|..||...+++....|-
T Consensus 112 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 157 (164)
T PRK12547 112 LLSADQREAIILIGA-SGFSYEDAAAICGCAVGTIKSRVSRARNRLQ 157 (164)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 467778777777766 8999999999999999999999999888876
No 99
>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=76.46 E-value=3.5 Score=35.75 Aligned_cols=53 Identities=17% Similarity=0.248 Sum_probs=42.2
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH-hhhhhhc
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM-KFSKEMI 143 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~-~L~~~~I 143 (218)
.+|...|-++.|+++ .|.|+..|+..+++|.+||...++.....+- .+.++..
T Consensus 161 ~Lp~~~R~v~~L~~~-eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~~ 214 (244)
T TIGR03001 161 ALSERERHLLRLHFV-DGLSMDRIGAMYQVHRSTVSRWVAQARERLLERTRRRLA 214 (244)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456667767777665 8899999999999999999999999999887 3444433
No 100
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=76.45 E-value=2.9 Score=35.30 Aligned_cols=44 Identities=25% Similarity=0.237 Sum_probs=37.7
Q ss_pred chHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 91 LTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 91 isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
+|..| .--|..++.|.++..|++.-++|..||+.|+..++.-+-
T Consensus 149 LT~RE--~eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~ 192 (211)
T COG2197 149 LTPRE--LEVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLG 192 (211)
T ss_pred CCHHH--HHHHHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHcC
Confidence 45555 456789999999999999999999999999999887754
No 101
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=76.30 E-value=3.4 Score=32.64 Aligned_cols=46 Identities=17% Similarity=0.138 Sum_probs=38.4
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..++-.+-|.++ .|.++..|+..+|+|.+||.+.++.....+-
T Consensus 125 ~L~~~~r~i~~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 125 ALPVKQREVFLLRYV-EGLSYREIAEILGVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred hCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 467777776666665 6899999999999999999999999887775
No 102
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=75.82 E-value=5.4 Score=32.64 Aligned_cols=48 Identities=19% Similarity=0.168 Sum_probs=40.8
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKF 138 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L 138 (218)
.+|...+-++.|+++ .|.|+..|+..+++|.+||...++.....|-.+
T Consensus 111 ~Lp~~~R~v~~L~~~-eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 158 (182)
T PRK12511 111 DLPEEQRAALHLVAI-EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAF 158 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 467788877777766 699999999999999999999999888887643
No 103
>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=75.69 E-value=2.2 Score=29.55 Aligned_cols=43 Identities=9% Similarity=-0.025 Sum_probs=36.2
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVL 132 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl 132 (218)
.-|.+.++.+.-.++..|.+..+++..+|++.+|+++...+..
T Consensus 6 ~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 6 RYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp ---HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence 4578888888888889999999999999999999999999887
No 104
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=75.61 E-value=3.3 Score=33.31 Aligned_cols=46 Identities=20% Similarity=0.129 Sum_probs=39.2
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..++.++.|.++ .|.++..++..+|+|.+||....+.+...+-
T Consensus 136 ~L~~~~r~il~l~~~-~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr 181 (187)
T PRK09641 136 QLPEKYRTVIVLKYI-EDLSLKEISEILDLPVGTVKTRIHRGREALR 181 (187)
T ss_pred hCCHHHHHHhhhHHh-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 467778877777766 7999999999999999999999888877765
No 105
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=75.55 E-value=4.4 Score=32.80 Aligned_cols=47 Identities=11% Similarity=0.020 Sum_probs=38.5
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..++-.+.|++ -.|.++..|+..+|+|.+||....+.....|-.
T Consensus 137 ~L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 137 ELEPPRSELIRTAF-FEGITYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 45666666666665 489999999999999999999999988877653
No 106
>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=75.54 E-value=3.3 Score=35.80 Aligned_cols=46 Identities=20% Similarity=0.109 Sum_probs=39.7
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++..++..+-++++ .+.++..++..+|+|.+||+++.++++.-+-
T Consensus 206 ~L~~rer~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~ral~kLr 251 (254)
T TIGR02850 206 RLNEREKMILNMRFF-EGKTQMEVAEEIGISQAQVSRLEKAALKHMR 251 (254)
T ss_pred cCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 567888888888875 6889999999999999999999998887654
No 107
>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=75.25 E-value=4 Score=27.36 Aligned_cols=40 Identities=13% Similarity=0.095 Sum_probs=31.9
Q ss_pred HHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 96 KMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 96 ~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
++-+|+-..-+| ++..++...++|.+|||+.+++.-+.+-
T Consensus 3 ~l~~f~~v~~~g-s~~~AA~~l~is~~~vs~~i~~LE~~lg 42 (60)
T PF00126_consen 3 QLRYFLAVAETG-SISAAAEELGISQSAVSRQIKQLEEELG 42 (60)
T ss_dssp HHHHHHHHHHHS-SHHHHHHHCTSSHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHhC-CHHHHHHHhhccchHHHHHHHHHHHHhC
Confidence 445555555555 9999999999999999999998877654
No 108
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=75.12 E-value=2.2 Score=35.17 Aligned_cols=45 Identities=13% Similarity=0.079 Sum_probs=38.8
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..|+ --|..++.|.|+.+|+...++|..||..|..+++.-+-
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 4777775 56788899999999999999999999999998887764
No 109
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=75.06 E-value=1.8 Score=34.59 Aligned_cols=46 Identities=15% Similarity=0.076 Sum_probs=39.0
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..++.++.|+++ .|.++.+|+..+++|.+||...++.....+-
T Consensus 126 ~L~~~~r~v~~l~~~-~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~ 171 (176)
T PRK09638 126 KLDPEFRAPVILKHY-YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLR 171 (176)
T ss_pred cCCHHHhheeeehhh-cCCCHHHHHHHHCCChhHHHHHHHHHHHHHH
Confidence 467777777777665 6999999999999999999999888887765
No 110
>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=74.94 E-value=3.6 Score=36.24 Aligned_cols=48 Identities=8% Similarity=0.023 Sum_probs=42.7
Q ss_pred cchHHHHHHHHHHH-H--hcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFT-I--SHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~-l--a~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..+|..+.|++ | -.|.|++.|+...|+|.+||+...+..+..|-.
T Consensus 222 ~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~ 272 (285)
T TIGR02394 222 ELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRR 272 (285)
T ss_pred cCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 57889999999987 3 578999999999999999999999998888863
No 111
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=74.88 E-value=3.3 Score=35.20 Aligned_cols=47 Identities=17% Similarity=0.119 Sum_probs=40.6
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|...+..+.|+++ .|.++..|+..+|+|.+||...++.....|-.
T Consensus 134 ~Lp~~~R~v~~L~y~-eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~ 180 (216)
T PRK12533 134 KLPVEYREVLVLREL-EDMSYREIAAIADVPVGTVMSRLARARRRLAA 180 (216)
T ss_pred cCCHHHHhHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 567778888888777 69999999999999999999999988888763
No 112
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=74.49 E-value=4.6 Score=32.72 Aligned_cols=46 Identities=15% Similarity=0.139 Sum_probs=37.8
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|...|..+.|+ .-.|.++.+|+..+|+|.+||....+.....|-
T Consensus 133 ~L~~~~r~i~~l~-~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 133 QLEPARRNCILHA-YVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHHCCChhhHHHHHHHHHHHHH
Confidence 4566666555555 678899999999999999999999999888765
No 113
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=74.38 E-value=4.3 Score=33.15 Aligned_cols=46 Identities=4% Similarity=-0.019 Sum_probs=39.7
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|.+++-.+.|+++ .|.|+..|+..+++|..||..........|-
T Consensus 131 ~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr 176 (189)
T PRK06811 131 DLEKLDREIFIRRYL-LGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQ 176 (189)
T ss_pred hCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 578888888888775 6899999999999999999999888877764
No 114
>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=74.20 E-value=4.7 Score=32.36 Aligned_cols=47 Identities=15% Similarity=0.173 Sum_probs=39.2
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|+.++-.+-|+++ .|.++..|+...|+|.+||....+.....+-.
T Consensus 140 ~L~~~~r~vi~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 140 KLPEDYREVILLRHL-EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 467777777766555 89999999999999999999999998887653
No 115
>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=74.09 E-value=3.9 Score=35.26 Aligned_cols=46 Identities=22% Similarity=0.169 Sum_probs=39.4
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..+|..+-|++ ..|.++..++..+++|.+||++..++.+..+-
T Consensus 205 ~L~~~~r~ii~l~~-~~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr 250 (255)
T TIGR02941 205 ILSEREKSIIHCTF-EENLSQKETGERLGISQMHVSRLQRQAISKLK 250 (255)
T ss_pred cCCHHHHHHHHHHH-cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 56788887777776 47899999999999999999999999888765
No 116
>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=73.87 E-value=4.6 Score=31.57 Aligned_cols=46 Identities=7% Similarity=0.035 Sum_probs=38.7
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..++-.+-|+++ .|.++..|+..+|+|.+||...++.....|-
T Consensus 111 ~L~~~~r~v~~l~~~-~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 111 KLPERQRELLQLRYQ-RGVSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred HCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 467888777777655 7899999999999999999999888877654
No 117
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=72.90 E-value=4.8 Score=32.48 Aligned_cols=46 Identities=13% Similarity=0.136 Sum_probs=38.2
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..++-.+-|+++. |.++..|+..+++|..||...++.....+-
T Consensus 131 ~L~~~~r~v~~l~~~~-g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr 176 (184)
T PRK12512 131 TLPPRQRDVVQSISVE-GASIKETAAKLSMSEGAVRVALHRGLAALA 176 (184)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4566676666665555 899999999999999999999999988876
No 118
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=72.85 E-value=5 Score=32.93 Aligned_cols=46 Identities=11% Similarity=0.109 Sum_probs=38.5
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|.+.+-.+.|+++ .|.++..|+..+|+|.+||...++.....+-
T Consensus 141 ~Lp~~~r~v~~l~~~-eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr 186 (194)
T PRK12531 141 RLPKAQRDVLQAVYL-EELPHQQVAEMFDIPLGTVKSRLRLAVEKLR 186 (194)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHH
Confidence 456777777766666 8899999999999999999999888887776
No 119
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=72.81 E-value=4.6 Score=33.04 Aligned_cols=47 Identities=11% Similarity=0.064 Sum_probs=39.8
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|...+.++.|+++ .|.|+..|+..+++|.+||...++...+.|-.
T Consensus 111 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~ 157 (182)
T PRK12540 111 KLPQDQREALILVGA-SGFSYEDAAAICGCAVGTIKSRVNRARSKLSA 157 (182)
T ss_pred hCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 457777777777664 89999999999999999999999999888863
No 120
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=72.56 E-value=5 Score=28.55 Aligned_cols=37 Identities=19% Similarity=0.187 Sum_probs=27.7
Q ss_pred HHHHHHHhc---CccchhhhhcccccccchhHHHHHHHHH
Q 046385 98 AMFLFTISH---NLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 98 aifL~~la~---~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.-.|..++. +.+..+++...++|.+||+|++....+.
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~ 47 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQEL 47 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 333444443 3678999999999999999999876554
No 121
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=72.53 E-value=5.2 Score=32.03 Aligned_cols=52 Identities=10% Similarity=0.045 Sum_probs=40.9
Q ss_pred chHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhhhhhhc
Q 046385 91 LTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEMI 143 (218)
Q Consensus 91 isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L~~~~I 143 (218)
+|...+ .+|+...-.|.++..++...|+|.+||...++.....+-....++|
T Consensus 120 L~~~~r-~i~~l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~~ 171 (173)
T PRK12522 120 LNEKYK-TVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEGFV 171 (173)
T ss_pred CCHHHH-HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 445444 4555555678999999999999999999999999999886555554
No 122
>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=72.42 E-value=4 Score=26.56 Aligned_cols=27 Identities=15% Similarity=0.144 Sum_probs=21.6
Q ss_pred ccchhhhhcccccccchhHHHHHHHHH
Q 046385 108 LRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 108 ~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.+-..+++.+++|..||.+.+.+.-+.
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 566789999999999999999876443
No 123
>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=72.32 E-value=1.8 Score=33.70 Aligned_cols=47 Identities=13% Similarity=0.096 Sum_probs=38.5
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..++-++.|.++ .|.++..|+..+|+|..||....+.....+-.
T Consensus 105 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 105 RLPENYRTVLILREF-KEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hCCHhheeeeeehhh-ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 356677766666666 79999999999999999999999888877653
No 124
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=72.31 E-value=4.1 Score=37.82 Aligned_cols=47 Identities=13% Similarity=0.015 Sum_probs=41.1
Q ss_pred cchHHHHHHHHHHHH---hcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTI---SHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~l---a~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++..|+..+-|++. +.+.++..|+..+|+|.++|+++-...+.-|-
T Consensus 311 ~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR 360 (373)
T PRK07406 311 TLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 360 (373)
T ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHh
Confidence 478899999999886 35689999999999999999999998888765
No 125
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=72.15 E-value=6.9 Score=31.89 Aligned_cols=53 Identities=8% Similarity=-0.006 Sum_probs=42.3
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH-hhhhhhc
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM-KFSKEMI 143 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~-~L~~~~I 143 (218)
.+|...|.++-|+++ .|.|+..|+..+|+|.+||...++.....|- .|.++..
T Consensus 131 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~ 184 (191)
T PRK12520 131 RLPPRTGRVFMMREW-LELETEEICQELQITATNAWVLLYRARMRLRECLDLHWF 184 (191)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 356777777766654 4689999999999999999999999999887 4555543
No 126
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=72.00 E-value=5.1 Score=31.16 Aligned_cols=45 Identities=18% Similarity=0.121 Sum_probs=36.6
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAM 135 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI 135 (218)
.+|..++..+.|+++ .|.|+..|+...|+|.+||....+.....|
T Consensus 106 ~L~~~~r~ii~l~~~-~~~s~~EIA~~l~is~~tV~~~~~ra~~~L 150 (154)
T PRK06759 106 VLDEKEKYIIFERFF-VGKTMGEIALETEMTYYQVRWIYRQALEKM 150 (154)
T ss_pred hCCHHHHHHHHHHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 456777766666654 578999999999999999999998877665
No 127
>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=71.66 E-value=5.9 Score=26.97 Aligned_cols=42 Identities=21% Similarity=0.247 Sum_probs=31.5
Q ss_pred hHHHHHHHHHHHHh---cCccchhhhhcccccccchhHHHHHHHH
Q 046385 92 TVEEKMAMFLFTIS---HNLRNRFIKIRFQHSGHTVHRYFHEVLS 133 (218)
Q Consensus 92 sveE~laifL~~la---~~~s~r~i~~~F~~S~sTVsr~f~eVl~ 133 (218)
+.+|.-.-++|.+. ...+..+++..+++|.+||+..+++.-+
T Consensus 4 ~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~ 48 (60)
T PF01325_consen 4 ESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAE 48 (60)
T ss_dssp CHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHH
Confidence 34555666777776 5677789999999999999988876544
No 128
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=71.58 E-value=5.6 Score=32.23 Aligned_cols=46 Identities=15% Similarity=0.057 Sum_probs=38.9
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..++-.+-|+++. |.++..|+..+|+|..||....+.....|-
T Consensus 128 ~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr 173 (186)
T PRK05602 128 ALPERQREAIVLQYYQ-GLSNIEAAAVMDISVDALESLLARGRRALR 173 (186)
T ss_pred hCCHHHHHHhhHHHhc-CCCHHHHHHHhCcCHHHHHHHHHHHHHHHH
Confidence 4577777777777654 899999999999999999999998887766
No 129
>PRK09492 treR trehalose repressor; Provisional
Probab=71.09 E-value=1.9 Score=37.46 Aligned_cols=23 Identities=22% Similarity=0.073 Sum_probs=20.8
Q ss_pred ccchhhhhcccccccchhHHHHH
Q 046385 108 LRNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 108 ~s~r~i~~~F~~S~sTVsr~f~e 130 (218)
.+.++|+...|+|.+||||.++.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCC
Confidence 46789999999999999999984
No 130
>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=70.94 E-value=5.7 Score=26.04 Aligned_cols=29 Identities=14% Similarity=0.140 Sum_probs=23.2
Q ss_pred hcCccchhhhhcccccccchhHHHHHHHH
Q 046385 105 SHNLRNRFIKIRFQHSGHTVHRYFHEVLS 133 (218)
Q Consensus 105 a~~~s~r~i~~~F~~S~sTVsr~f~eVl~ 133 (218)
..+.+..+++..++++.+|++++++...+
T Consensus 15 ~~~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 15 NGGITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp HSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 34478899999999999999999887654
No 131
>PF13551 HTH_29: Winged helix-turn helix
Probab=70.83 E-value=8.4 Score=28.17 Aligned_cols=73 Identities=11% Similarity=0.103 Sum_probs=44.1
Q ss_pred cccchhccccCHHHHHHHHHHHHhcC--ccCC-C----c--c-chHHHHHHHHHHHHhcC------ccchhhhhc-----
Q 046385 58 PIFCYDLMRMDKNGFISLCQLFKEKG--WLSD-S----K--H-LTVEEKMAMFLFTISHN------LRNRFIKIR----- 116 (218)
Q Consensus 58 ~~~~~~~fRM~~~~F~~L~~~L~~~~--~~~~-T----~--~-isveE~laifL~~la~~------~s~r~i~~~----- 116 (218)
..+.-..+++++.|+...+......+ .+.+ . + . ++.++.-.+.=+...+. .+...++..
T Consensus 15 ~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~ 94 (112)
T PF13551_consen 15 IAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEE 94 (112)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhc
Confidence 56677788889999888888877655 2222 1 1 2 55555443333333332 334555542
Q ss_pred --ccccccchhHHHHH
Q 046385 117 --FQHSGHTVHRYFHE 130 (218)
Q Consensus 117 --F~~S~sTVsr~f~e 130 (218)
-.+|.+||.+++++
T Consensus 95 ~~~~~s~~ti~r~L~~ 110 (112)
T PF13551_consen 95 FGIDVSPSTIRRILKR 110 (112)
T ss_pred cCccCCHHHHHHHHHH
Confidence 26788999998875
No 132
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=70.60 E-value=3.2 Score=35.08 Aligned_cols=44 Identities=18% Similarity=0.147 Sum_probs=37.1
Q ss_pred chHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 91 LTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 91 isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
+|..|+ =-|..++.|.++++|+...++|..||..|...+++-+-
T Consensus 135 LT~RE~--eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KLg 178 (207)
T PRK11475 135 LSPTER--EILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLG 178 (207)
T ss_pred CCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 555554 45778899999999999999999999999998877653
No 133
>PRK09483 response regulator; Provisional
Probab=70.48 E-value=3.2 Score=33.43 Aligned_cols=44 Identities=20% Similarity=0.246 Sum_probs=36.8
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAM 135 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI 135 (218)
.+|..|+-. |..++.|.+++.++..+++|..||..+.+.+..-+
T Consensus 148 ~Lt~rE~~v--l~~~~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 148 SLSERELQI--MLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKL 191 (217)
T ss_pred ccCHHHHHH--HHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 467777544 45679999999999999999999999999887765
No 134
>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=70.27 E-value=3.2 Score=31.37 Aligned_cols=59 Identities=17% Similarity=0.083 Sum_probs=37.9
Q ss_pred hccccCHHHHHHHHHHHHhcCccCCCccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHH
Q 046385 63 DLMRMDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 63 ~~fRM~~~~F~~L~~~L~~~~~~~~T~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
..+-|+-+.|..|.+........+....-...++-.+ | -+.-++..|+.|.+|++|+-.
T Consensus 9 Pv~qmTg~ell~L~~~~~~~~~~~~~~~~~~~~~~yv--y------G~~GlAklfgcSv~Ta~RiK~ 67 (96)
T PF12964_consen 9 PVWQMTGEELLFLLKEGKTNSEKQTSQKAKKDEKKYV--Y------GLKGLAKLFGCSVPTANRIKK 67 (96)
T ss_pred HHHHhhHHHHHHHHHHHhcCCCccCCccccCccccee--e------hHHHHHHHhCCCchhHHHHHh
Confidence 4667899999999988755443222222222222111 1 146788999999999999875
No 135
>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=70.26 E-value=5.2 Score=32.20 Aligned_cols=47 Identities=17% Similarity=0.076 Sum_probs=38.1
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|.+++-.+-|+++ .|.++..|+..+|+|..||...++.....|-.
T Consensus 138 ~L~~~~r~v~~l~~~-~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 138 ALPEDLRTAITLREL-EGLSYEDIARIMDCPVGTVRSRIFRAREAIAI 184 (190)
T ss_pred cCCHHHhhhhhhhhh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 345666665556554 88999999999999999999999988888764
No 136
>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=70.25 E-value=11 Score=32.27 Aligned_cols=46 Identities=15% Similarity=0.055 Sum_probs=38.7
Q ss_pred ccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 89 KHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 89 ~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
..+|..|+-.+.+ .+.|.++.+++..+++|..||..++.+++..+.
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 3678877655554 589999999999999999999999999987764
No 137
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=70.08 E-value=5.2 Score=32.12 Aligned_cols=47 Identities=21% Similarity=0.159 Sum_probs=39.4
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|+.++-++-|+++ .|.++..++..+|+|.+||...++.....+-.
T Consensus 136 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 136 ALPPKYRMVIVLKYM-EDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred hCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 467778777777655 68999999999999999999999988887763
No 138
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=69.85 E-value=6.1 Score=31.62 Aligned_cols=46 Identities=17% Similarity=0.231 Sum_probs=37.5
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|.+.+..+.|+++ .|.++..|+..+++|.+||...++..+..+-
T Consensus 119 ~Lp~~~r~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~ 164 (172)
T PRK12523 119 KLSSKARAAFLYNRL-DGMGHAEIAERLGVSVSRVRQYLAQGLRQCY 164 (172)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 456677777776665 5899999999999999999999888777664
No 139
>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=69.65 E-value=12 Score=28.13 Aligned_cols=29 Identities=0% Similarity=-0.133 Sum_probs=24.4
Q ss_pred cCccchhhhhcccccccchhHHHHHHHHH
Q 046385 106 HNLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 106 ~~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.+.+...++...+++++||++.+++..+.
T Consensus 41 ~~~t~~ela~~~~~~~~tvs~~l~~Le~~ 69 (118)
T TIGR02337 41 GSMEFTQLANQACILRPSLTGILARLERD 69 (118)
T ss_pred CCcCHHHHHHHhCCCchhHHHHHHHHHHC
Confidence 45678899999999999999988876654
No 140
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=69.45 E-value=6 Score=32.10 Aligned_cols=47 Identities=19% Similarity=0.148 Sum_probs=39.5
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..++-.+-|+++ .|-++..|+..+++|..||....+.....|-.
T Consensus 131 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 131 RLPEKMRLAIQAVKL-EGLSVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred hCCHHHHHHHHHHHH-cCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 456777766767666 59999999999999999999999999888763
No 141
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=69.43 E-value=5.5 Score=32.83 Aligned_cols=47 Identities=13% Similarity=0.048 Sum_probs=41.3
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|++++-++.|+++ .|.++..|+..+|+|..||-..++.....|-.
T Consensus 113 ~Lp~~~r~v~~L~~~-~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~ 159 (188)
T PRK12546 113 QLPDEQREALILVGA-SGFSYEEAAEMCGVAVGTVKSRANRARARLAE 159 (188)
T ss_pred hCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 568888888888877 89999999999999999999999998888763
No 142
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=69.38 E-value=7.4 Score=31.94 Aligned_cols=47 Identities=13% Similarity=0.076 Sum_probs=37.8
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|.+.+..+-|+++ .|.++..|+..+++|.+||-..++.....|-.
T Consensus 134 ~Lp~~~r~i~~l~~~-~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~ 180 (192)
T PRK09643 134 RLPVEQRAALVAVDM-QGYSVADAARMLGVAEGTVKSRCARGRARLAE 180 (192)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 467777766666655 78999999999999999999888877777653
No 143
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=69.23 E-value=5.5 Score=34.89 Aligned_cols=46 Identities=20% Similarity=0.218 Sum_probs=39.2
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++..++..+-|+++ .+.++..|+..+++|.+||+++.+..+.-+-
T Consensus 215 ~L~~rer~vl~l~y~-~~~t~~EIA~~lgis~~~V~~~~~ral~kLr 260 (264)
T PRK07122 215 ALPERERTVLVLRFF-ESMTQTQIAERVGISQMHVSRLLAKTLARLR 260 (264)
T ss_pred cCCHHHHHHHHHHhc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 467778878888774 6899999999999999999999998887764
No 144
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=69.18 E-value=5 Score=36.93 Aligned_cols=47 Identities=13% Similarity=0.009 Sum_probs=39.9
Q ss_pred cchHHHHHHHHHHHH---hcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTI---SHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~l---a~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++..|+..+-|||. +.+.++..|+..|++|.++|+++-.+.+.-+-
T Consensus 305 ~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr 354 (367)
T PRK09210 305 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 354 (367)
T ss_pred hCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 578888889999885 35689999999999999999999887777654
No 145
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=68.97 E-value=8.5 Score=30.63 Aligned_cols=47 Identities=17% Similarity=0.132 Sum_probs=38.9
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|...+..+-|+++ .|.++..|+...|+|.+||...++.....+-.
T Consensus 118 ~L~~~~r~vl~L~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 118 QLSPEHRAVLVRSYY-RGWSTAQIAADLGIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 467777776666654 58999999999999999999999988888763
No 146
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=68.87 E-value=6.1 Score=33.85 Aligned_cols=45 Identities=11% Similarity=0.279 Sum_probs=38.3
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAM 135 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI 135 (218)
.++..+|..+.|++ ..|.++..++..+|+|.++|+++-+..+.-+
T Consensus 183 ~L~~~er~vi~l~~-~~~~t~~EIA~~lgis~~~V~q~~~~~~~kL 227 (231)
T PRK12427 183 QLDEREQLILHLYY-QHEMSLKEIALVLDLTEARICQLNKKIAQKI 227 (231)
T ss_pred cCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 56777888888877 5789999999999999999999988887765
No 147
>PRK05949 RNA polymerase sigma factor; Validated
Probab=68.64 E-value=5.4 Score=36.22 Aligned_cols=48 Identities=19% Similarity=0.186 Sum_probs=41.4
Q ss_pred cchHHHHHHHHHHHH---hcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTI---SHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~l---a~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.++..||..+-|++. +.+.++..|+..+|+|.+||..+.+..+..+-.
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 468888888888874 467899999999999999999999998888764
No 148
>PF13551 HTH_29: Winged helix-turn helix
Probab=68.49 E-value=4.4 Score=29.75 Aligned_cols=35 Identities=20% Similarity=0.231 Sum_probs=30.2
Q ss_pred HHHHHhcCcc-chhhhhcccccccchhHHHHHHHHH
Q 046385 100 FLFTISHNLR-NRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 100 fL~~la~~~s-~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.|..++.|.+ ...++..+++|..||+++++...+-
T Consensus 4 ~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~ 39 (112)
T PF13551_consen 4 ILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREG 39 (112)
T ss_pred HHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcc
Confidence 4566888886 9999999999999999999987654
No 149
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=68.42 E-value=6.9 Score=33.28 Aligned_cols=47 Identities=15% Similarity=0.199 Sum_probs=39.7
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..+|-.+.|++ -.|.|+..|+..+|+|.+||...++..+..|-.
T Consensus 184 ~L~~~~r~vl~l~~-~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 184 SLPEREQLVLSLYY-QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred hCCHHHHHHHHhHh-ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45777777777766 478899999999999999999999999888763
No 150
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=68.40 E-value=12 Score=25.26 Aligned_cols=69 Identities=13% Similarity=0.092 Sum_probs=47.0
Q ss_pred cchhccccCHHHHHHHHHHHHhcCccCCCccchHHHHHHHHHHHHhcC-ccchhhhhcccc-cccchhHHHHHHH
Q 046385 60 FCYDLMRMDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHN-LRNRFIKIRFQH-SGHTVHRYFHEVL 132 (218)
Q Consensus 60 ~~~~~fRM~~~~F~~L~~~L~~~~~~~~T~~isveE~laifL~~la~~-~s~r~i~~~F~~-S~sTVsr~f~eVl 132 (218)
+.-..+.++...|..++....... . ...-...++.-++..+..+ .+..+++...|. |.++.+|.|++..
T Consensus 6 ~la~~~~~s~~~l~~~f~~~~~~s---~-~~~~~~~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk~~~ 76 (84)
T smart00342 6 DLAEALGMSPRHLQRLFKKETGTT---P-KQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLF 76 (84)
T ss_pred HHHHHhCCCHHHHHHHHHHHhCcC---H-HHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 344577888888888776543211 1 1122345566666666555 788999999999 9999999998764
No 151
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=67.87 E-value=6.4 Score=33.87 Aligned_cols=46 Identities=17% Similarity=0.191 Sum_probs=39.2
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..+|..+-|+++ .|.++..|+..+++|.+||...+++.+..+-
T Consensus 201 ~L~~~~r~vl~l~~~-~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr 246 (251)
T PRK07670 201 QLSEKEQLVISLFYK-EELTLTEIGQVLNLSTSRISQIHSKALFKLK 246 (251)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 457778888877764 8899999999999999999999998887765
No 152
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=67.85 E-value=5.9 Score=37.40 Aligned_cols=47 Identities=17% Similarity=0.075 Sum_probs=40.6
Q ss_pred cchHHHHHHHHHHHH---hcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTI---SHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~l---a~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++..++..+-|++. +.+.++..|+..+++|.+||..+.+..+..+-
T Consensus 350 ~L~~reR~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~KLR 399 (415)
T PRK07598 350 DLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLR 399 (415)
T ss_pred hCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHh
Confidence 478888888888885 46789999999999999999999998877765
No 153
>PRK13870 transcriptional regulator TraR; Provisional
Probab=67.83 E-value=12 Score=32.14 Aligned_cols=45 Identities=18% Similarity=0.023 Sum_probs=39.4
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..| .=.|.++|.|.+..+|+...++|.+||..|++.+.+.+-
T Consensus 173 ~LT~RE--~E~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~na~~KLg 217 (234)
T PRK13870 173 WLDPKE--ATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFD 217 (234)
T ss_pred CCCHHH--HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 566666 468999999999999999999999999999999877654
No 154
>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=67.76 E-value=8.3 Score=30.64 Aligned_cols=47 Identities=23% Similarity=0.267 Sum_probs=37.4
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..++-++-|.++. |.++..++..+|+|.+||....+.....+-.
T Consensus 119 ~L~~~~r~i~~l~~~~-g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 119 TLNDKYQTAIILRYYH-DLTIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred hCCHHHhHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4566666555555554 8999999999999999999999988887753
No 155
>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=67.72 E-value=6.6 Score=29.35 Aligned_cols=43 Identities=19% Similarity=0.203 Sum_probs=36.5
Q ss_pred hHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHH
Q 046385 92 TVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAM 135 (218)
Q Consensus 92 sveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI 135 (218)
.+++|..+.++++ .+.+..+++...++|..|+.|+=++.+..+
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 4678888888888 678889999999999999999988777653
No 156
>PHA00738 putative HTH transcription regulator
Probab=67.69 E-value=5.3 Score=30.85 Aligned_cols=38 Identities=21% Similarity=0.197 Sum_probs=28.9
Q ss_pred HHHHHHHHHhcC--ccchhhhhcccccccchhHHHHHHHHH
Q 046385 96 KMAMFLFTISHN--LRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 96 ~laifL~~la~~--~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
|+.|..+ |+.+ .+-..++..|++|++|||+|....-+|
T Consensus 14 Rr~IL~l-L~~~e~~~V~eLae~l~lSQptVS~HLKvLreA 53 (108)
T PHA00738 14 RRKILEL-IAENYILSASLISHTLLLSYTTVLRHLKILNEQ 53 (108)
T ss_pred HHHHHHH-HHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHC
Confidence 4555444 4443 566789999999999999999877666
No 157
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=66.12 E-value=3.7 Score=27.73 Aligned_cols=26 Identities=23% Similarity=0.101 Sum_probs=20.8
Q ss_pred HhcCccchhhhhcccccccchhHHHH
Q 046385 104 ISHNLRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 104 la~~~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
-..|.|..+++...++|.+||+++-+
T Consensus 11 ~~~gls~~~lA~~~g~s~s~v~~iE~ 36 (64)
T PF13560_consen 11 ERAGLSQAQLADRLGVSQSTVSRIER 36 (64)
T ss_dssp HCHTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 36789999999999999999998754
No 158
>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=65.88 E-value=7.7 Score=32.63 Aligned_cols=46 Identities=15% Similarity=0.193 Sum_probs=39.1
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..++-.+-|++ -.+.|+..++..+++|.+||.+..+..+..+-
T Consensus 175 ~L~~~~r~il~l~y-~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr 220 (224)
T TIGR02479 175 SLSEREQLVLSLYY-YEELNLKEIGEVLGLTESRVSQIHSQALKKLR 220 (224)
T ss_pred hCCHHHHHHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 46778887777776 46789999999999999999999998888765
No 159
>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=65.87 E-value=5.8 Score=25.78 Aligned_cols=26 Identities=23% Similarity=0.245 Sum_probs=20.9
Q ss_pred ccchhhhhcccccccchhHHHHHHHH
Q 046385 108 LRNRFIKIRFQHSGHTVHRYFHEVLS 133 (218)
Q Consensus 108 ~s~r~i~~~F~~S~sTVsr~f~eVl~ 133 (218)
.+..+++...+.+++|++|+.....+
T Consensus 19 ~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 19 LTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 35789999999999999998876544
No 160
>COG3179 Predicted chitinase [General function prediction only]
Probab=65.49 E-value=3.7 Score=34.85 Aligned_cols=69 Identities=14% Similarity=0.183 Sum_probs=54.8
Q ss_pred cccchhccccCHHHHHHHHHHHHhcCccCCCccchHHHHHHHHHHHHhcCcc-chhhhhcccccccchhHHHH
Q 046385 58 PIFCYDLMRMDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHNLR-NRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 58 ~~~~~~~fRM~~~~F~~L~~~L~~~~~~~~T~~isveE~laifL~~la~~~s-~r~i~~~F~~S~sTVsr~f~ 129 (218)
..++...|+..+..|-...-.|.+.+ +...|+.-+++||||--++|-+. ++.+.+.+..|-++.++.|.
T Consensus 6 e~~~~ki~p~a~k~~~~v~~al~~~l---~~~gi~~p~r~AmFlAQ~~HESggf~rl~EnlnYSaq~L~~tf~ 75 (206)
T COG3179 6 EVDLRKIFPKARKEFVDVIVALQPAL---DEAGITTPLRQAMFLAQVMHESGGFTRLDENLNYSAQGLLQTFP 75 (206)
T ss_pred HHHHHHhcchhhhhhHHHHHHHHHHH---HHhcCCCHHHHHHHHHHHhhhcCCceeehhhcchHHHHHHHhcc
Confidence 45667777878777776666666544 45578889999999999999988 89999999999888777665
No 161
>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=65.32 E-value=7.2 Score=31.68 Aligned_cols=42 Identities=5% Similarity=0.044 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 94 EEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 94 eE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
+.+..+++.++ .|.++..|+..+++|.+||...++.....+-
T Consensus 153 ~~~~~i~~~~~-~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~ 194 (198)
T TIGR02859 153 DLEWKVLQSYL-DGKSYQEIACDLNRHVKSIDNALQRVKRKLE 194 (198)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 33344555554 8999999999999999999988888777654
No 162
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=65.21 E-value=8.9 Score=30.90 Aligned_cols=46 Identities=15% Similarity=0.077 Sum_probs=38.3
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..++..+.|++ -.|.++..|+..+|+|.+||....+.....+-
T Consensus 135 ~L~~~~r~vl~l~~-~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr 180 (186)
T PRK13919 135 ALSPEERRVIEVLY-YQGYTHREAAQLLGLPLGTLKTRARRALSRLK 180 (186)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 46777777666665 56889999999999999999999999888875
No 163
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=64.89 E-value=10 Score=32.66 Aligned_cols=53 Identities=17% Similarity=0.117 Sum_probs=42.4
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhhhhhhc
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEMI 143 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L~~~~I 143 (218)
.+|..+|.++.|+++ .|.|++.|+...|+|.+||...++...+.+-....+..
T Consensus 116 ~Lp~~~R~v~lL~~~-eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~~~ 168 (228)
T PRK06704 116 SLNVQQSAILLLKDV-FQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEEGI 168 (228)
T ss_pred hCCHHHhhHhhhHHh-hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 467777777777654 47999999999999999999999999998875544433
No 164
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=64.46 E-value=7.8 Score=33.47 Aligned_cols=45 Identities=11% Similarity=0.110 Sum_probs=38.2
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..| .-.|..+|.|.++..++...++|..||..++..+++.+-
T Consensus 143 ~LS~RE--~eVL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLg 187 (217)
T PRK13719 143 KVTKYQ--NDVFILYSFGFSHEYIAQLLNITVGSSKNKISEILKFFG 187 (217)
T ss_pred CCCHHH--HHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 455555 356778899999999999999999999999999988764
No 165
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=64.13 E-value=8.5 Score=33.51 Aligned_cols=46 Identities=13% Similarity=0.169 Sum_probs=38.5
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..+|..+.|++ -.|.++..|+..+++|.+||.+..++.+..|-
T Consensus 212 ~L~~~~r~vl~l~~-~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr 257 (268)
T PRK06288 212 TLPEREKKVLILYY-YEDLTLKEIGKVLGVTESRISQLHTKAVLQLR 257 (268)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 56777887777776 46899999999999999999988887777665
No 166
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=63.94 E-value=9.1 Score=31.03 Aligned_cols=46 Identities=13% Similarity=0.109 Sum_probs=36.5
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..+|-++-|+++. |.++..|+..+|+|..||....+..+..|-
T Consensus 139 ~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 184 (189)
T PRK09648 139 TLPEKQREILILRVVV-GLSAEETAEAVGSTPGAVRVAQHRALARLR 184 (189)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4566666666665554 899999999999999999999888777765
No 167
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=63.81 E-value=6.2 Score=31.19 Aligned_cols=45 Identities=18% Similarity=0.155 Sum_probs=36.6
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++..|. -.|+.++.|.++..++..++.|..||..++..+.+-+-
T Consensus 137 ~Lt~~E~--~il~~l~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRER--QVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3555553 45677889999999999999999999999999887653
No 168
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=63.81 E-value=9.4 Score=30.44 Aligned_cols=47 Identities=19% Similarity=0.210 Sum_probs=38.6
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..++.++-|+ .-.|.++..|+..+++|..||.......+..+..
T Consensus 118 ~L~~~~r~v~~L~-~~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 118 GLSGKARAAFLMS-QLEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4666666655555 5788999999999999999999999999888763
No 169
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=63.79 E-value=13 Score=28.58 Aligned_cols=68 Identities=12% Similarity=0.104 Sum_probs=36.8
Q ss_pred ccchhccccCHHHHHHHHHHHHhcCccCCC---c-cchHHHHHHHHHHHHhc-CccchhhhhcccccccchhHHHHH
Q 046385 59 IFCYDLMRMDKNGFISLCQLFKEKGWLSDS---K-HLTVEEKMAMFLFTISH-NLRNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 59 ~~~~~~fRM~~~~F~~L~~~L~~~~~~~~T---~-~isveE~laifL~~la~-~~s~r~i~~~F~~S~sTVsr~f~e 130 (218)
.+--..|.+++.|....+...+ .+.+... . .|.. +.|.- ++-.+ ..+...++..|++|.+||++.++.
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 REAAKRFGVSRNTVYRWLKRKE-TGDLEPKPRGRKKIDR-DELKA--LVEENPDATLRELAERLGVSPSTIWRALKR 94 (119)
T ss_pred HHHHHHhCcHHHHHHHHHHhcc-cccccccccccccccH-HHHHH--HHHHCCCcCHHHHHHHcCCCHHHHHHHHHH
Confidence 3444567777777777766222 2211111 1 3322 22211 12222 344478889999999999887764
No 170
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=63.66 E-value=8 Score=31.04 Aligned_cols=47 Identities=19% Similarity=0.265 Sum_probs=37.6
Q ss_pred chHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhh
Q 046385 91 LTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKF 138 (218)
Q Consensus 91 isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L 138 (218)
+|.+.+ .+|+...-.|.++..|+..+|+|..||...++..+..+...
T Consensus 120 L~~~~r-~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~ 166 (172)
T PRK09651 120 LNGKTR-EAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLF 166 (172)
T ss_pred CCHHHh-HHhhhhhccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 445444 45566667789999999999999999999999998887643
No 171
>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=63.39 E-value=6.7 Score=26.28 Aligned_cols=35 Identities=17% Similarity=0.165 Sum_probs=25.4
Q ss_pred HHHHHh---cCccchhhhhcccccccchhHHHHHHHHH
Q 046385 100 FLFTIS---HNLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 100 fL~~la---~~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.|+.++ ...+..+++..++++++|||+.+++.++.
T Consensus 8 vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~ 45 (68)
T PF13463_consen 8 VLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEK 45 (68)
T ss_dssp HHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred HHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 355555 44666899999999999999999887765
No 172
>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=63.08 E-value=7.8 Score=34.28 Aligned_cols=48 Identities=10% Similarity=0.098 Sum_probs=40.4
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKF 138 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L 138 (218)
.+|..+|.++-|+++ .|.++..|+...++|.+||...+++....|-..
T Consensus 142 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 189 (324)
T TIGR02960 142 YLPPRQRAVLLLRDV-LGWRAAETAELLGTSTASVNSALQRARATLDEV 189 (324)
T ss_pred hCCHHHhhHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 467777777777665 788999999999999999999999998888743
No 173
>PRK10651 transcriptional regulator NarL; Provisional
Probab=62.94 E-value=6.1 Score=31.38 Aligned_cols=45 Identities=29% Similarity=0.347 Sum_probs=37.1
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++..|. -.|..++.|.+++.++...++|..||..++.+....+.
T Consensus 155 ~Lt~rE~--~vl~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 155 QLTPRER--DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 3666664 45566889999999999999999999999999877654
No 174
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=62.02 E-value=6.4 Score=33.43 Aligned_cols=45 Identities=22% Similarity=0.152 Sum_probs=36.5
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..|+ --|..++.|.++.+++...++|..||..+..+.+..+.
T Consensus 155 ~Lt~rE~--~Vl~l~~~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 155 LLTHREK--EILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3666554 34556677999999999999999999999999887764
No 175
>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=61.82 E-value=9.4 Score=33.42 Aligned_cols=45 Identities=16% Similarity=0.139 Sum_probs=38.7
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..|+-.+.| ++.|.++..|+...++|..||..+++.++.-+-
T Consensus 190 ~LT~RE~evl~l--~a~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~ 234 (247)
T TIGR03020 190 LITAREAEILAW--VRDGKTNEEIAAILGISSLTVKNHLQHIFKKLD 234 (247)
T ss_pred CCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHhC
Confidence 678888766665 589999999999999999999999999877654
No 176
>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=61.82 E-value=4.6 Score=31.08 Aligned_cols=28 Identities=29% Similarity=0.235 Sum_probs=24.6
Q ss_pred HHHhcCccchhhhhcccccccchhHHHH
Q 046385 102 FTISHNLRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 102 ~~la~~~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
-++-.|.|.+.++.+|++|.+||.+.+.
T Consensus 13 ~~~~~g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 13 AYIEKGKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred HHHHccchHHHHHHHhCcHHHHHHHHHH
Confidence 4555677999999999999999999988
No 177
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=61.79 E-value=9.4 Score=34.67 Aligned_cols=47 Identities=21% Similarity=0.077 Sum_probs=40.5
Q ss_pred cchHHHHHHHHHHHH---hcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTI---SHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~l---a~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++..|+..+.++|. +...++..|+..||+|.+.|+++-.+.+.-|-
T Consensus 262 ~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr 311 (324)
T PRK07921 262 TLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLR 311 (324)
T ss_pred hCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 468888999999885 35689999999999999999999998887765
No 178
>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=61.71 E-value=9.5 Score=30.59 Aligned_cols=45 Identities=16% Similarity=-0.017 Sum_probs=36.1
Q ss_pred chHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 91 LTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 91 isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
+|...+.++.|+ .-.|.|+..|+...|+|.+||...++.....+-
T Consensus 135 Lp~~~r~v~~l~-~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr 179 (183)
T TIGR02999 135 VDPRQAEVVELR-FFAGLTVEEIAELLGVSVRTVERDWRFARAWLA 179 (183)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 566666555444 556889999999999999999999998887765
No 179
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=61.66 E-value=12 Score=29.45 Aligned_cols=47 Identities=13% Similarity=0.077 Sum_probs=37.6
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|.+++-.+-| ..-.|.++.+++..+|+|.+||...+.....++-.
T Consensus 105 ~L~~~~r~v~~l-~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~ 151 (159)
T PRK12527 105 ELPPACRDSFLL-RKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRV 151 (159)
T ss_pred hCCHHHHHHHHH-HHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 356666554444 45788999999999999999999999988888763
No 180
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=61.66 E-value=9.9 Score=29.92 Aligned_cols=46 Identities=24% Similarity=0.135 Sum_probs=36.1
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|.++|.++.|+ .-.|.++..|+..+++|.+||...++.....+-
T Consensus 113 ~L~~~~r~v~~L~-~~~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 113 GLPPLVKRAFLLA-QVDGLGYGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HCCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4566666555554 557889999999999999999999988877654
No 181
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=61.64 E-value=8.9 Score=36.55 Aligned_cols=32 Identities=16% Similarity=0.115 Sum_probs=27.2
Q ss_pred ccchhhhhcccccccchhHHHHHHHHHHHhhhhhhcCCCCCC
Q 046385 108 LRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEMITPPSFT 149 (218)
Q Consensus 108 ~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L~~~~Ik~P~~~ 149 (218)
...+++++..+++.|||||.+. .+|+..|.+.
T Consensus 331 L~LrdvA~~i~~HESTISRai~----------nKy~~tprG~ 362 (444)
T COG1508 331 LVLRDVADEIGMHESTISRAIT----------NKYLATPRGL 362 (444)
T ss_pred ccHHHHHHHhCccHHHHHHHHh----------cccccCCcce
Confidence 4458999999999999999876 6899888754
No 182
>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=61.53 E-value=13 Score=30.42 Aligned_cols=47 Identities=11% Similarity=0.113 Sum_probs=37.7
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|...+.++-|+++ .|.++..|+..+|+|.+||...+......|-.
T Consensus 131 ~L~~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~ 177 (188)
T TIGR02943 131 HLPEQTARVFMMREV-LGFESDEICQELEISTSNCHVLLYRARLSLRA 177 (188)
T ss_pred hCCHHHHHHHHHHHH-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 356666665555544 58999999999999999999999998888764
No 183
>PHA00542 putative Cro-like protein
Probab=61.39 E-value=6.2 Score=28.47 Aligned_cols=31 Identities=16% Similarity=0.050 Sum_probs=26.4
Q ss_pred HHHHHhcCccchhhhhcccccccchhHHHHH
Q 046385 100 FLFTISHNLRNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 100 fL~~la~~~s~r~i~~~F~~S~sTVsr~f~e 130 (218)
.......|.+...++...++|.+||+++.+.
T Consensus 24 ~~~l~~~glTq~elA~~lgIs~~tIsr~e~g 54 (82)
T PHA00542 24 VCALIRAGWSQEQIADATDVSQPTICRIYSG 54 (82)
T ss_pred HHHHHHCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 3445788999999999999999999998753
No 184
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=61.20 E-value=4.7 Score=25.98 Aligned_cols=25 Identities=16% Similarity=0.155 Sum_probs=20.5
Q ss_pred cchhhhhcccccccchhHHHHHHHH
Q 046385 109 RNRFIKIRFQHSGHTVHRYFHEVLS 133 (218)
Q Consensus 109 s~r~i~~~F~~S~sTVsr~f~eVl~ 133 (218)
+.++++..|++|.+||.+.+..-.+
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~ 46 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEA 46 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5677899999999999888876544
No 185
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=61.12 E-value=9.7 Score=35.95 Aligned_cols=48 Identities=15% Similarity=0.166 Sum_probs=42.8
Q ss_pred CccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHH
Q 046385 88 SKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAM 135 (218)
Q Consensus 88 T~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI 135 (218)
++.+...-++||+|-.=-++.|+..++..||++.+||+.-++.|=+.+
T Consensus 368 ~~~i~~aR~iamyl~r~~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 368 NVKALLARRIGMYVAKNYLGSSLRTIAEKFNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred CccccHHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 357888899999998888899999999999999999999998887765
No 186
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=61.08 E-value=13 Score=30.43 Aligned_cols=45 Identities=13% Similarity=0.093 Sum_probs=37.5
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..++..+.| ++ .|.+++.|+...|+|.+||...++.....+-
T Consensus 155 ~L~~~~r~vl~l-~~-e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr 199 (208)
T PRK08295 155 LLSELEKEVLEL-YL-DGKSYQEIAEELNRHVKSIDNALQRVKRKLE 199 (208)
T ss_pred hCCHHHHHHHHH-HH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 346777777777 44 7999999999999999999999998888766
No 187
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=60.86 E-value=6.6 Score=33.32 Aligned_cols=48 Identities=13% Similarity=0.059 Sum_probs=39.2
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKF 138 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L 138 (218)
.+|..++-++.|+++ .|.++..|+..+|+|.+||...++.....+-..
T Consensus 149 ~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~ 196 (231)
T PRK11922 149 ALPDAFRAVFVLRVV-EELSVEETAQALGLPEETVKTRLHRARRLLRES 196 (231)
T ss_pred hCCHHHhhhheeehh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 466777766666554 489999999999999999999999988887743
No 188
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=60.24 E-value=13 Score=36.88 Aligned_cols=49 Identities=22% Similarity=0.222 Sum_probs=43.4
Q ss_pred CccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 88 SKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 88 T~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
++.+...-++||+|-.--++.|+..|+..||++.+||..-++.|-+.|-
T Consensus 550 ~~~i~~aRqiAMYL~r~lt~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~ 598 (617)
T PRK14086 550 SRVLVTARQIAMYLCRELTDLSLPKIGQQFGRDHTTVMHADRKIRALMA 598 (617)
T ss_pred CcccchHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHHHHH
Confidence 3478888999999999999999999999999999999998888877554
No 189
>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=60.04 E-value=8.9 Score=36.27 Aligned_cols=33 Identities=15% Similarity=0.164 Sum_probs=28.4
Q ss_pred CccchhhhhcccccccchhHHHHHHHHHHHhhhhhhcCCCCCC
Q 046385 107 NLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEMITPPSFT 149 (218)
Q Consensus 107 ~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L~~~~Ik~P~~~ 149 (218)
..+.++|++..|++.|||||.+. .+||..|.+-
T Consensus 318 PLtlkdiA~~lglheSTVSRav~----------~Kyi~tp~Gi 350 (429)
T TIGR02395 318 PLTLREVAEELGLHESTISRAIN----------NKYLQTPRGV 350 (429)
T ss_pred CCcHHHHHHHhCCCccchhhhhc----------CceEecCCce
Confidence 46778999999999999999876 7999888654
No 190
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=59.88 E-value=7.2 Score=24.98 Aligned_cols=29 Identities=14% Similarity=-0.017 Sum_probs=23.7
Q ss_pred hcCccchhhhhcccccccchhHHHHHHHH
Q 046385 105 SHNLRNRFIKIRFQHSGHTVHRYFHEVLS 133 (218)
Q Consensus 105 a~~~s~r~i~~~F~~S~sTVsr~f~eVl~ 133 (218)
....+..+++..+++|..|+++++++..+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 44567789999999999999999887554
No 191
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=59.80 E-value=14 Score=34.72 Aligned_cols=48 Identities=17% Similarity=0.179 Sum_probs=42.8
Q ss_pred ccchHHHHHHHHHHHHhcCccchhhhhcc-cccccchhHHHHHHHHHHH
Q 046385 89 KHLTVEEKMAMFLFTISHNLRNRFIKIRF-QHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 89 ~~isveE~laifL~~la~~~s~r~i~~~F-~~S~sTVsr~f~eVl~AI~ 136 (218)
+.+...-++||+|-.--++.|+..|+..| +++.+||+.-++.|-+-+-
T Consensus 384 ~~~~~aR~iamyl~~~~~~~s~~~Ig~~fg~rdhstV~~a~~~i~~~~~ 432 (450)
T PRK00149 384 RNIARPRQIAMYLAKELTDLSLPEIGRAFGGRDHTTVLHAVRKIEKLLE 432 (450)
T ss_pred cccChHHHHHHHHHHHhcCCCHHHHHHHcCCCCHhHHHHHHHHHHHHHH
Confidence 58888999999999999999999999999 6999999998888876553
No 192
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=59.42 E-value=8.9 Score=29.82 Aligned_cols=43 Identities=12% Similarity=0.115 Sum_probs=32.4
Q ss_pred hHHHHHHHHHHHHhc-CccchhhhhcccccccchhHHHHHHHHH
Q 046385 92 TVEEKMAMFLFTISH-NLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 92 sveE~laifL~~la~-~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
+-.-|+.|+.....+ ..+...++..+++|++|||+|+...-+|
T Consensus 14 adptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~A 57 (117)
T PRK10141 14 SDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRES 57 (117)
T ss_pred CCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 344566776655443 4567899999999999999999877666
No 193
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=58.96 E-value=9.2 Score=36.46 Aligned_cols=33 Identities=15% Similarity=0.084 Sum_probs=28.4
Q ss_pred CccchhhhhcccccccchhHHHHHHHHHHHhhhhhhcCCCCCC
Q 046385 107 NLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEMITPPSFT 149 (218)
Q Consensus 107 ~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L~~~~Ik~P~~~ 149 (218)
..+.++|++..|++.|||||.+. .+||..|.+-
T Consensus 343 PLtlkdvAe~lglheSTVSRav~----------~Kyv~tp~Gi 375 (455)
T PRK05932 343 PLVLKDIAEELGMHESTISRATT----------NKYMATPRGI 375 (455)
T ss_pred CccHHHHHHHhCCCccchhhhhc----------CceeecCCce
Confidence 46779999999999999999876 7999888654
No 194
>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=58.81 E-value=15 Score=24.02 Aligned_cols=25 Identities=20% Similarity=0.169 Sum_probs=19.9
Q ss_pred cchhhhhcccccccchhHHHHHHHH
Q 046385 109 RNRFIKIRFQHSGHTVHRYFHEVLS 133 (218)
Q Consensus 109 s~r~i~~~F~~S~sTVsr~f~eVl~ 133 (218)
+.++++..|++|.+||++.+....+
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~ 51 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA 51 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4567889999999999877776554
No 195
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=58.37 E-value=8.7 Score=30.51 Aligned_cols=45 Identities=20% Similarity=0.166 Sum_probs=37.6
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++..|. -.|..++.|.++.+++...++|..||..++....+-+-
T Consensus 143 ~lt~~E~--~vl~~l~~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~ 187 (204)
T PRK09958 143 SLSKQEI--SVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLE 187 (204)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 4666664 47788888999999999999999999999998887753
No 196
>PRK10403 transcriptional regulator NarP; Provisional
Probab=58.24 E-value=12 Score=29.63 Aligned_cols=45 Identities=24% Similarity=0.239 Sum_probs=37.0
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++..|.- .|..++.|.++..++...++|..||..++..+++.+.
T Consensus 153 ~Lt~~e~~--vl~~~~~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 153 VLTERELD--VLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred cCCHHHHH--HHHHHHCCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 35665543 4667789999999999999999999999999988754
No 197
>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=57.35 E-value=3.8 Score=35.71 Aligned_cols=21 Identities=19% Similarity=0.010 Sum_probs=19.2
Q ss_pred cchhhhhcccccccchhHHHH
Q 046385 109 RNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 109 s~r~i~~~F~~S~sTVsr~f~ 129 (218)
+.++|+...|+|.+||||.++
T Consensus 3 ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 3 TIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred cHHHHHHHhCCCHHHHHHHhC
Confidence 567999999999999999996
No 198
>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=57.25 E-value=14 Score=28.19 Aligned_cols=45 Identities=11% Similarity=0.064 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 93 VEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 93 veE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+.|--++-.+.-...|...||..+++|+..|+-.++++...+..
T Consensus 19 T~kQ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~ 63 (101)
T PF04297_consen 19 TEKQREILELYYEEDLSLSEIAEELGISRQAVYDSIKRAEKKLEE 63 (101)
T ss_dssp -HHHHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 455566677778889999999999999999999999998877763
No 199
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=57.19 E-value=12 Score=30.13 Aligned_cols=47 Identities=15% Similarity=0.050 Sum_probs=37.6
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..++.++.|+ .-.|.|+..|+..+++|.+||...++.....|-.
T Consensus 129 ~L~~~~r~v~~l~-~~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 129 QLPDRQRLPIVHV-KLEGLSVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred HCCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4566666655554 4578899999999999999999999998888763
No 200
>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=57.13 E-value=15 Score=24.15 Aligned_cols=28 Identities=21% Similarity=0.132 Sum_probs=23.0
Q ss_pred hcCccchhhhhcccccccchhHHHHHHH
Q 046385 105 SHNLRNRFIKIRFQHSGHTVHRYFHEVL 132 (218)
Q Consensus 105 a~~~s~r~i~~~F~~S~sTVsr~f~eVl 132 (218)
.++.+..+++..+++|..||++.++...
T Consensus 18 ~~~~~~~ei~~~~~i~~~~i~~~l~~L~ 45 (78)
T cd00090 18 EGPLTVSELAERLGLSQSTVSRHLKKLE 45 (78)
T ss_pred HCCcCHHHHHHHHCcCHhHHHHHHHHHH
Confidence 3347889999999999999998887743
No 201
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=56.87 E-value=14 Score=28.88 Aligned_cols=44 Identities=25% Similarity=0.177 Sum_probs=34.6
Q ss_pred chHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 91 LTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 91 isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
++..|+-. |..++.|.+++.++...++|..||..++.+..+.+-
T Consensus 150 lt~~e~~v--l~l~~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 150 LTPRERQI--LKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCHHHHHH--HHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 44444333 444789999999999999999999999998877654
No 202
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=56.44 E-value=12 Score=33.80 Aligned_cols=48 Identities=8% Similarity=0.002 Sum_probs=41.8
Q ss_pred cchHHHHHHHHHHH-H--hcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFT-I--SHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~-l--a~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..+|..+.++| | -.|.++..|+...++|.+||..+.++-+..|-.
T Consensus 262 ~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~ 312 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLRE 312 (325)
T ss_pred cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 57888888888876 3 578999999999999999999999999888773
No 203
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=56.20 E-value=16 Score=28.61 Aligned_cols=47 Identities=11% Similarity=-0.024 Sum_probs=37.9
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|...+-++.|++ -.|.|+..|+..+|+|.+||...++.....|-.
T Consensus 106 ~Lp~~~r~v~~l~~-~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 106 ELPENYRDVVLAHY-LEEKSYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred hCCHHHHHHHHHHH-HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35666666655554 578899999999999999999999988888763
No 204
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=55.76 E-value=12 Score=25.88 Aligned_cols=41 Identities=17% Similarity=0.160 Sum_probs=31.9
Q ss_pred hHHHHHHHHHHHHhc-CccchhhhhcccccccchhHHHHHHH
Q 046385 92 TVEEKMAMFLFTISH-NLRNRFIKIRFQHSGHTVHRYFHEVL 132 (218)
Q Consensus 92 sveE~laifL~~la~-~~s~r~i~~~F~~S~sTVsr~f~eVl 132 (218)
+.++++..+|.--+. +.+-.+++...+++++||+|++...-
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~ 47 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLE 47 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467777777776655 47889999999999999987766543
No 205
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.64 E-value=17 Score=27.88 Aligned_cols=40 Identities=10% Similarity=0.022 Sum_probs=32.3
Q ss_pred HHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 97 MAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 97 laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.--+=-+....-|...||+.|++|++.|+-.+++++..+.
T Consensus 23 ~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~ 62 (105)
T COG2739 23 KNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIKRTEKILE 62 (105)
T ss_pred HHHHHHHHHhhccHHHHHHHhCccHHHHHHHHHHHHHHHH
Confidence 3333344566789999999999999999999999987765
No 206
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=54.82 E-value=7 Score=34.53 Aligned_cols=21 Identities=24% Similarity=0.070 Sum_probs=19.3
Q ss_pred cchhhhhcccccccchhHHHH
Q 046385 109 RNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 109 s~r~i~~~F~~S~sTVsr~f~ 129 (218)
+.++|+...|+|.+||||.++
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (346)
T PRK10401 3 TIRDVARQAGVSVATVSRVLN 23 (346)
T ss_pred CHHHHHHHhCCCHHHHHHHHC
Confidence 568999999999999999987
No 207
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=54.75 E-value=7.3 Score=24.06 Aligned_cols=28 Identities=18% Similarity=0.122 Sum_probs=23.0
Q ss_pred CccchhhhhcccccccchhHHHHHHHHH
Q 046385 107 NLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 107 ~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
..+..+++..+++|.+|+++++.+..+.
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~ 35 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKE 35 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3566789999999999999988876653
No 208
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=54.72 E-value=13 Score=30.24 Aligned_cols=47 Identities=15% Similarity=0.082 Sum_probs=36.5
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|...|.++-|+ .-.|.++..|+..+++|.+||....+.....+-.
T Consensus 130 ~Lp~~~r~v~~L~-~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 130 DLTTDQREALLLT-QLLGLSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred hCCHHHhHHhhhH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4556655555554 4567899999999999999999999988887653
No 209
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=54.62 E-value=14 Score=35.88 Aligned_cols=47 Identities=9% Similarity=-0.034 Sum_probs=41.5
Q ss_pred cchHHHHHHHHHHHH---hcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTI---SHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~l---a~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++..||..|-+||. ..+.++..|+..||+|++.|+++-...+.-|-
T Consensus 447 ~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR 496 (509)
T PRK05901 447 TLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLR 496 (509)
T ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 478889999999985 56799999999999999999999998887765
No 210
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=54.48 E-value=5.7 Score=34.88 Aligned_cols=22 Identities=18% Similarity=0.072 Sum_probs=19.9
Q ss_pred cchhhhhcccccccchhHHHHH
Q 046385 109 RNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 109 s~r~i~~~F~~S~sTVsr~f~e 130 (218)
+.++|+...|+|.+||||.++.
T Consensus 3 Ti~dIA~~agVS~~TVSrvLn~ 24 (341)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINK 24 (341)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 5679999999999999999885
No 211
>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=54.36 E-value=18 Score=28.87 Aligned_cols=52 Identities=13% Similarity=0.027 Sum_probs=40.9
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhhhhhh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEM 142 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L~~~~ 142 (218)
.+|..++.++-|++ -.|.+++.|+..+++|..||....+.....+-......
T Consensus 100 ~L~~~~r~v~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 151 (170)
T TIGR02959 100 ELPDEYREAIRLTE-LEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLETC 151 (170)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 46676666555554 67899999999999999999999999988887544444
No 212
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=54.19 E-value=18 Score=29.91 Aligned_cols=53 Identities=8% Similarity=0.049 Sum_probs=40.7
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh-hhhhhc
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK-FSKEMI 143 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~-L~~~~I 143 (218)
.+|...|.++-|++ -.|.|+..|+..+|+|.+||...++.....|-. |.....
T Consensus 139 ~Lp~~~r~v~~L~~-~eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~ 192 (201)
T PRK12545 139 HLPEQIGRVFMMRE-FLDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKGL 192 (201)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 45666666666654 577899999999999999999999988888763 433333
No 213
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=54.00 E-value=5.2 Score=24.73 Aligned_cols=29 Identities=17% Similarity=0.110 Sum_probs=21.4
Q ss_pred HhcCccchhhhhcccccccchhHHHHHHH
Q 046385 104 ISHNLRNRFIKIRFQHSGHTVHRYFHEVL 132 (218)
Q Consensus 104 la~~~s~r~i~~~F~~S~sTVsr~f~eVl 132 (218)
++++.+..+++...+.|.+..+|.|++.+
T Consensus 5 ~~~~~~l~~iA~~~g~S~~~f~r~Fk~~~ 33 (42)
T PF00165_consen 5 LQQKLTLEDIAEQAGFSPSYFSRLFKKET 33 (42)
T ss_dssp T-SS--HHHHHHHHTS-HHHHHHHHHHHT
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 35667778999999999999999998764
No 214
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=53.97 E-value=22 Score=27.33 Aligned_cols=47 Identities=23% Similarity=0.176 Sum_probs=37.5
Q ss_pred ccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 89 KHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 89 ~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
-.++++|=-||=|--+ .|.++...+.+.++|++|++|++++.-.-|.
T Consensus 40 V~L~~dElEAiRL~D~-egl~QeeaA~~MgVSR~T~~ril~~ARkKiA 86 (106)
T PF02001_consen 40 VVLTVDELEAIRLVDY-EGLSQEEAAERMGVSRPTFQRILESARKKIA 86 (106)
T ss_pred EEeeHHHHHHHHHHHH-cCCCHHHHHHHcCCcHHHHHHHHHHHHHHHH
Confidence 4678888777776544 4588999999999999999999987655554
No 215
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=53.93 E-value=14 Score=28.71 Aligned_cols=29 Identities=3% Similarity=-0.040 Sum_probs=24.2
Q ss_pred cCccchhhhhcccccccchhHHHHHHHHH
Q 046385 106 HNLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 106 ~~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.+.+..+++..++++++||++.+....+.
T Consensus 45 ~~~t~~eLa~~l~~~~~tvt~~v~~Le~~ 73 (144)
T PRK03573 45 PEQSQIQLAKAIGIEQPSLVRTLDQLEEK 73 (144)
T ss_pred CCCCHHHHHHHhCCChhhHHHHHHHHHHC
Confidence 34678899999999999999988876554
No 216
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=53.58 E-value=16 Score=29.59 Aligned_cols=47 Identities=19% Similarity=0.114 Sum_probs=38.1
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|++++-++.|++ -.|.||..++...++|.+||...++.....+-.
T Consensus 127 ~Lp~~~R~~~~l~~-~~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~ 173 (182)
T COG1595 127 RLPPRQREAFLLRY-LEGLSYEEIAEILGISVGTVKSRLHRARKKLRE 173 (182)
T ss_pred hCCHHHhHHhhhHh-hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45666665555554 468999999999999999999999999988774
No 217
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=53.36 E-value=16 Score=31.98 Aligned_cols=42 Identities=7% Similarity=0.105 Sum_probs=34.7
Q ss_pred HHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 95 EKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 95 E~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
++|-.|+..+-+|.|+..++...++|++|||+.+.+.=+.+-
T Consensus 4 ~~L~~F~~v~~~~~S~s~AA~~L~isQpavS~~I~~LE~~lg 45 (309)
T PRK12683 4 QQLRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELG 45 (309)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhC
Confidence 467788888888889999999999999999988877665554
No 218
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=53.24 E-value=17 Score=31.18 Aligned_cols=47 Identities=15% Similarity=0.165 Sum_probs=38.0
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..+|..+.|++ -.|.|+..|+..+|+|.+||...++.....+-.
T Consensus 171 ~Lp~~~R~v~~L~~-~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~ 217 (233)
T PRK12538 171 RLPEQQRIAVILSY-HENMSNGEIAEVMDTTVAAVESLLKRGRQQLRD 217 (233)
T ss_pred hCCHHHHHHhhhHH-hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35666666555554 578899999999999999999999998888764
No 219
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=53.10 E-value=21 Score=33.80 Aligned_cols=49 Identities=20% Similarity=0.146 Sum_probs=42.9
Q ss_pred CccchHHHHHHHHHHHHhcCccchhhhhccc-ccccchhHHHHHHHHHHH
Q 046385 88 SKHLTVEEKMAMFLFTISHNLRNRFIKIRFQ-HSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 88 T~~isveE~laifL~~la~~~s~r~i~~~F~-~S~sTVsr~f~eVl~AI~ 136 (218)
++.|...-|+||+|--=-++.|+..|+..|| ++.+||..-++.|-+.+-
T Consensus 382 ~~~i~~~RqiamyL~r~~t~~sl~~IG~~FggrdHsTV~~a~~ki~~~~~ 431 (450)
T PRK14087 382 SKSIVTARHIAMYLTKEILNHTLAQIGEEFGGRDHTTVINAERKIEKMLK 431 (450)
T ss_pred CccccHHHHHHHHHHHHHcCCCHHHHHHHhCCCChHHHHHHHHHHHHHHH
Confidence 4578889999999999999999999999997 999999988887766553
No 220
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=53.04 E-value=13 Score=32.65 Aligned_cols=42 Identities=10% Similarity=0.051 Sum_probs=34.9
Q ss_pred HHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 95 EKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 95 E~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
+++-.|+....++.|+..++..-++|.+|||+.+++.=+.+-
T Consensus 4 ~~l~~f~~v~~~~~s~s~AA~~L~iSQ~avSr~I~~LE~~lg 45 (316)
T PRK12679 4 QQLKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELG 45 (316)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhcCCchHHHHHHHHHHHHhC
Confidence 457778888888889999999999999999998887666554
No 221
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=52.92 E-value=18 Score=29.57 Aligned_cols=47 Identities=19% Similarity=0.111 Sum_probs=38.0
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..++..+-|+ .-.|.++..|+...|+|.+||...++..+..|-.
T Consensus 142 ~L~~~~r~vl~l~-~~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 142 ALTDTQRESVTLA-YYGGLTYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 4666666655555 4667999999999999999999999998888763
No 222
>PF11776 DUF3315: Domain of unknown function (DUF3315); InterPro: IPR024572 This is a bacterial family of uncharacterised proteins, which include YohN from Escherichia coli K12.; PDB: 2L1S_A.
Probab=52.81 E-value=5.7 Score=26.43 Aligned_cols=18 Identities=22% Similarity=0.359 Sum_probs=11.3
Q ss_pred cCCCccCccccccCCCCC
Q 046385 198 FGGSRCPINDIVGTGLGP 215 (218)
Q Consensus 198 ~r~~ryh~~~~~~~~~~p 215 (218)
|++.+|.++||+.-||++
T Consensus 8 yr~~~y~V~D~~~~~L~~ 25 (52)
T PF11776_consen 8 YRSRRYVVDDWRRYGLPA 25 (52)
T ss_dssp GTSGGGEE---TTSS---
T ss_pred HcCCCeEECCHHHCCCCc
Confidence 899999999999999864
No 223
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=52.80 E-value=5 Score=35.19 Aligned_cols=24 Identities=13% Similarity=-0.020 Sum_probs=21.3
Q ss_pred CccchhhhhcccccccchhHHHHH
Q 046385 107 NLRNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 107 ~~s~r~i~~~F~~S~sTVsr~f~e 130 (218)
..+.++|+..+|+|.+||||.++.
T Consensus 6 ~~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 6 KITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHCC
Confidence 357789999999999999999876
No 224
>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=52.65 E-value=4.7 Score=25.99 Aligned_cols=26 Identities=15% Similarity=0.163 Sum_probs=21.6
Q ss_pred hcCccchhhhhcccccccchhHHHHH
Q 046385 105 SHNLRNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 105 a~~~s~r~i~~~F~~S~sTVsr~f~e 130 (218)
..|.++++++...++|.+||+++.+.
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhcC
Confidence 67889999999999999999998875
No 225
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=52.51 E-value=21 Score=29.03 Aligned_cols=51 Identities=12% Similarity=-0.005 Sum_probs=40.2
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhhhhh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKE 141 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L~~~ 141 (218)
.+|.+++..+.|++ -.|-++..|+..+++|..||...+......+-.....
T Consensus 106 ~L~~~~r~i~~l~~-~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 106 ALPEKYAEALRLTE-LEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred hCCHHHHHHHHHHH-hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 46777766665554 5788999999999999999999999998887754333
No 226
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=51.84 E-value=17 Score=31.39 Aligned_cols=45 Identities=16% Similarity=0.060 Sum_probs=38.2
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..|+ -.|.+++.|.++.+|+...++|..||..++..+.+-+-
T Consensus 179 ~LT~rE~--evl~~~a~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~ 223 (240)
T PRK10188 179 NFSKREK--EILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFN 223 (240)
T ss_pred CCCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 5676664 56677799999999999999999999999999887654
No 227
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=51.68 E-value=19 Score=28.51 Aligned_cols=47 Identities=17% Similarity=0.056 Sum_probs=38.0
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..++.++.|+ .-.|.++..|+..+|+|..||...++.+...|-.
T Consensus 108 ~L~~~~r~v~~l~-~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 154 (165)
T PRK09644 108 TLPVIEAQAILLC-DVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKA 154 (165)
T ss_pred hCCHHHHHHHHhH-HHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4566666655544 5678899999999999999999999999888764
No 228
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=51.60 E-value=18 Score=31.52 Aligned_cols=42 Identities=12% Similarity=0.071 Sum_probs=34.2
Q ss_pred HHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 95 EKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 95 E~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|-.|+-...+|.|++.++...++|.+||||.+++.=+.+-
T Consensus 4 ~~L~~F~~v~~~~~s~s~AA~~L~isq~avSr~I~~LE~~lg 45 (309)
T PRK12682 4 QQLRFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELG 45 (309)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCccHHHHHHHHHHHHHhC
Confidence 356667766677789999999999999999999888766654
No 229
>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=51.40 E-value=5 Score=25.61 Aligned_cols=19 Identities=26% Similarity=0.013 Sum_probs=16.1
Q ss_pred hhhhcccccccchhHHHHH
Q 046385 112 FIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 112 ~i~~~F~~S~sTVsr~f~e 130 (218)
+++..-|+|.+|||++++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g 20 (52)
T cd01392 2 DIARAAGVSVATVSRVLNG 20 (52)
T ss_pred cHHHHHCcCHHHHHHHHcC
Confidence 5778889999999998764
No 230
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=51.32 E-value=18 Score=28.44 Aligned_cols=48 Identities=15% Similarity=0.001 Sum_probs=37.4
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKF 138 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L 138 (218)
.+|...+.++-|+ .-.|.++..++..+|+|..||...++.....|-++
T Consensus 112 ~L~~~~r~v~~l~-~~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 112 SLPLERRNVLLLR-DYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HCCHHHHHHhhhH-HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 4566666655554 45678999999999999999999998888776543
No 231
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=51.05 E-value=5 Score=35.18 Aligned_cols=23 Identities=17% Similarity=0.125 Sum_probs=19.8
Q ss_pred ccchhhhhcccccccchhHHHHH
Q 046385 108 LRNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 108 ~s~r~i~~~F~~S~sTVsr~f~e 130 (218)
.+.++|+...|+|.+||||.++.
T Consensus 6 ~ti~dIA~~agVS~~TVSrvLn~ 28 (331)
T PRK14987 6 PVLQDVADRVGVTKMTVSRFLRN 28 (331)
T ss_pred CcHHHHHHHhCCCHHHhhhhhCC
Confidence 35689999999999999998853
No 232
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=50.78 E-value=26 Score=24.68 Aligned_cols=28 Identities=21% Similarity=0.141 Sum_probs=24.2
Q ss_pred CccchhhhhcccccccchhHHHHHHHHH
Q 046385 107 NLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 107 ~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
+.+...++..+++|..||++.+++..+.
T Consensus 24 ~~~~~~la~~~~~s~~~i~~~l~~L~~~ 51 (101)
T smart00347 24 PLSVSELAKRLGVSPSTVTRVLDRLEKK 51 (101)
T ss_pred CcCHHHHHHHHCCCchhHHHHHHHHHHC
Confidence 4678899999999999999999887765
No 233
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=50.56 E-value=16 Score=27.82 Aligned_cols=38 Identities=26% Similarity=0.169 Sum_probs=30.3
Q ss_pred cchHHHHHHHHHHH------HhcCccchhhhhcccccccchhHH
Q 046385 90 HLTVEEKMAMFLFT------ISHNLRNRFIKIRFQHSGHTVHRY 127 (218)
Q Consensus 90 ~isveE~laifL~~------la~~~s~r~i~~~F~~S~sTVsr~ 127 (218)
-+++.|+-++..++ |-.+.|.|.++...|+|..||.|=
T Consensus 37 lLTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRG 80 (103)
T COG2973 37 LLTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATITRG 80 (103)
T ss_pred HcCHhHHHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhccc
Confidence 35666666666653 678899999999999999999874
No 234
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=50.44 E-value=8.5 Score=31.29 Aligned_cols=46 Identities=7% Similarity=0.099 Sum_probs=35.2
Q ss_pred chHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 91 LTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 91 isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
+|.+++- +|+...-.|.|+..|+..+++|.+||...++.....|-.
T Consensus 135 L~~~~r~-v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 180 (188)
T PRK09640 135 VNPIDRE-ILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLRE 180 (188)
T ss_pred cChhhee-eeeeHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3444443 344444578899999999999999999999988888764
No 235
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=50.33 E-value=20 Score=29.67 Aligned_cols=51 Identities=10% Similarity=-0.023 Sum_probs=39.7
Q ss_pred chHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhhhhhh
Q 046385 91 LTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEM 142 (218)
Q Consensus 91 isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L~~~~ 142 (218)
+|...+-++.|++ -.|.+++.|+..+++|..||...++.....|-.+..++
T Consensus 134 Lp~~~r~v~~l~~-~~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~ 184 (196)
T PRK12535 134 LPPERREALILTQ-VLGYTYEEAAKIADVRVGTIRSRVARARADLIAATATG 184 (196)
T ss_pred CCHHHHHHhhhHH-HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 5666666665554 45678999999999999999999999999887554443
No 236
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=49.96 E-value=5.5 Score=27.63 Aligned_cols=22 Identities=18% Similarity=0.002 Sum_probs=17.7
Q ss_pred cchhhhhcccccccchhHHHHH
Q 046385 109 RNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 109 s~r~i~~~F~~S~sTVsr~f~e 130 (218)
+.++++..-|+|.+||||+++.
T Consensus 2 t~~~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLNG 23 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHCC
Confidence 3567888889999999997753
No 237
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=49.92 E-value=9.5 Score=31.08 Aligned_cols=47 Identities=17% Similarity=0.082 Sum_probs=36.6
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|..++..+-|+ .-.|.++..|+...|+|.+||...++.....|-.
T Consensus 139 ~L~~~~r~i~~l~-~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 185 (194)
T PRK12513 139 TLPDEQREVFLLR-EHGDLELEEIAELTGVPEETVKSRLRYALQKLRE 185 (194)
T ss_pred hCCHhHhhheeee-hccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3556666555554 3678899999999999999999888888877663
No 238
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=49.57 E-value=17 Score=34.98 Aligned_cols=33 Identities=18% Similarity=0.109 Sum_probs=28.3
Q ss_pred CccchhhhhcccccccchhHHHHHHHHHHHhhhhhhcCCCCCC
Q 046385 107 NLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEMITPPSFT 149 (218)
Q Consensus 107 ~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L~~~~Ik~P~~~ 149 (218)
....++|++..|++.|||||.+. .+||..|.+-
T Consensus 369 PLtlkdVAe~lglHeSTVSRa~~----------~KY~~tp~Gi 401 (481)
T PRK12469 369 PLVLRDVAEELGLHESTISRATG----------NKYMATPRGT 401 (481)
T ss_pred CCcHHHHHHHhCCCcchhhHHhc----------CceeecCCce
Confidence 35678999999999999999876 7999988654
No 239
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=49.20 E-value=8.9 Score=31.86 Aligned_cols=28 Identities=14% Similarity=0.214 Sum_probs=24.8
Q ss_pred HHhcCccchhhhhcccccccchhHHHHH
Q 046385 103 TISHNLRNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 103 ~la~~~s~r~i~~~F~~S~sTVsr~f~e 130 (218)
.+..|.|++.++..+++|.+||.|+.++
T Consensus 168 ~~~~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 168 LLDKGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 3577899999999999999999999863
No 240
>PF13309 HTH_22: HTH domain
Probab=48.80 E-value=20 Score=24.60 Aligned_cols=39 Identities=23% Similarity=0.248 Sum_probs=25.5
Q ss_pred cchHHHHHHHHHHHHhcC-----ccchhhhhcccccccchhHHH
Q 046385 90 HLTVEEKMAMFLFTISHN-----LRNRFIKIRFQHSGHTVHRYF 128 (218)
Q Consensus 90 ~isveE~laifL~~la~~-----~s~r~i~~~F~~S~sTVsr~f 128 (218)
.++.+|++.+.-.--..| .+-..++..+++|+.||.+++
T Consensus 20 ~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 20 RLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred hCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHc
Confidence 445555555543333333 233578999999999999986
No 241
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=48.79 E-value=22 Score=28.64 Aligned_cols=47 Identities=13% Similarity=0.122 Sum_probs=36.3
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|...+-.+-| ..-.|.|+..|+..+++|.+||...++.....+-.
T Consensus 122 ~L~~~~r~i~~l-~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 168 (185)
T PRK12542 122 ELNESNRQVFKY-KVFYNLTYQEISSVMGITEANVRKQFERARKRVQN 168 (185)
T ss_pred hCCHHHHHHHHH-HHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 355555555444 44567999999999999999999999888887764
No 242
>PRK09526 lacI lac repressor; Reviewed
Probab=48.47 E-value=6 Score=34.71 Aligned_cols=22 Identities=18% Similarity=-0.037 Sum_probs=19.8
Q ss_pred ccchhhhhcccccccchhHHHH
Q 046385 108 LRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 108 ~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
.+.++|+...|+|.+||||.++
T Consensus 6 ~ti~dIA~~aGVS~~TVSrvLn 27 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRVLN 27 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHhc
Confidence 3678999999999999999987
No 243
>PF09182 PuR_N: Bacterial purine repressor, N-terminal; InterPro: IPR015265 The N-terminal domain of the bacterial purine repressor PuR is a winged-helix domain, a subdivision of the HTH structural family. It consists of a canonical arrangement of secondary structures: a1-b1-a2-T-a3-b2-W-b3, where a2-T-a3 is the HTH motif, a3 is the recognition helix, and W is the wing. The domain allows for recognition of a conserved CGAA sequence in the centre of a DNA PurBox, resulting in binding to the major groove of DNA []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1O57_B 1P4A_D.
Probab=47.80 E-value=20 Score=25.54 Aligned_cols=39 Identities=13% Similarity=0.271 Sum_probs=22.5
Q ss_pred HHHHHHHHHHhcC----ccchhhhhcccccccchhH---HHHHHHH
Q 046385 95 EKMAMFLFTISHN----LRNRFIKIRFQHSGHTVHR---YFHEVLS 133 (218)
Q Consensus 95 E~laifL~~la~~----~s~r~i~~~F~~S~sTVsr---~f~eVl~ 133 (218)
|||.....+|..+ -+....+++|+.++||||- +++++++
T Consensus 4 eRlv~it~~L~~~P~~lisL~~Fae~f~~AKSsISEDl~iik~~~~ 49 (70)
T PF09182_consen 4 ERLVAITKYLLENPNKLISLTYFAERFGAAKSSISEDLSIIKETFE 49 (70)
T ss_dssp HHHHHHHHHHHTSTT--EEHHHHHHHHT--HHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHcCCcceEcHHHHHHHhcccccchHHHHHHHHHHHH
Confidence 4444444444333 3457889999999999995 4444443
No 244
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=47.68 E-value=26 Score=28.17 Aligned_cols=46 Identities=20% Similarity=0.171 Sum_probs=37.2
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..+|-++-|. .-.|.|+..|+..+|+|..||...+++.+..+-
T Consensus 117 ~Lp~~~r~i~~l~-~~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr 162 (179)
T PRK12543 117 KLPYKLRQVIILR-YLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLR 162 (179)
T ss_pred hCCHHHHHHHHHH-HHccCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4677777666664 446779999999999999999999888877765
No 245
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=47.61 E-value=26 Score=29.18 Aligned_cols=47 Identities=19% Similarity=0.060 Sum_probs=37.2
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|...+-.+.|+ .-.|.++..|+..+|+|.+||...++.....|-.
T Consensus 138 ~L~~~~r~v~~L~-~~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~ 184 (203)
T PRK09647 138 SLPPEFRAAVVLC-DIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRA 184 (203)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4555555444444 4778999999999999999999999998888764
No 246
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=47.35 E-value=23 Score=31.10 Aligned_cols=46 Identities=20% Similarity=0.217 Sum_probs=40.2
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++-.||+.+-||| -.+.+...++..-|+|.+.|||+..+.+..|-
T Consensus 196 ~L~EREk~Vl~l~y-~eelt~kEI~~~LgISes~VSql~kkai~kLr 241 (247)
T COG1191 196 PLPEREKLVLVLRY-KEELTQKEIAEVLGISESRVSRLHKKAIKKLR 241 (247)
T ss_pred ccCHHHHHHHHHHH-HhccCHHHHHHHhCccHHHHHHHHHHHHHHHH
Confidence 56777889999988 56678899999999999999999999888775
No 247
>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=47.27 E-value=19 Score=26.52 Aligned_cols=55 Identities=9% Similarity=-0.027 Sum_probs=35.6
Q ss_pred ccccCHHHHHHHHHHHHhcCccCCCccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHH
Q 046385 64 LMRMDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 64 ~fRM~~~~F~~L~~~L~~~~~~~~T~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.+.++...+..|+.+.+...+.+. .....+.+.++...+.|++||||.+++.-+.
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~----------------~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~ 74 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNK----------------KQDRVTATVIAELTGLSRTHVSDAIKSLARR 74 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccc----------------cCCccCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 556677777766666542211110 2334566788999999999999988876543
No 248
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=47.05 E-value=81 Score=28.61 Aligned_cols=67 Identities=12% Similarity=0.221 Sum_probs=50.1
Q ss_pred cccCHHHHHHHHHHHHhcCccCCCccchH-HHHHHHHHHHHhcCccchhhhhcccccc-cchhHHHHHHHHH
Q 046385 65 MRMDKNGFISLCQLFKEKGWLSDSKHLTV-EEKMAMFLFTISHNLRNRFIKIRFQHSG-HTVHRYFHEVLSA 134 (218)
Q Consensus 65 fRM~~~~F~~L~~~L~~~~~~~~T~~isv-eE~laifL~~la~~~s~r~i~~~F~~S~-sTVsr~f~eVl~A 134 (218)
-+|++..|-.+++.....-+.. .+||+ .-|=+.+-+.|-+|+..|+||..-||+- ||. .|-..|++.
T Consensus 219 ~~ltrq~~w~~lk~~a~~Agi~--~~isPH~LRHsFATHLL~~GADlRvVQeLLGHadisTT-QIYTHV~~e 287 (300)
T COG4974 219 GGLTRQGFWKRLKDYAERAGID--KKISPHTLRHSFATHLLENGADLRVVQELLGHADISTT-QIYTHVTKE 287 (300)
T ss_pred CCCCHHHHHHHHHHHHHHhCCC--CCcCchhhHHHHHHHHHhCCccHHHHHHHhCccccchh-HHHHHHHHH
Confidence 4799999999999988765444 34444 3566788889999999999999999995 554 444445443
No 249
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=47.00 E-value=14 Score=27.57 Aligned_cols=62 Identities=11% Similarity=0.058 Sum_probs=42.1
Q ss_pred CHHHHHHHHHHHHhcCccCCCccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHH
Q 046385 68 DKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 68 ~~~~F~~L~~~L~~~~~~~~T~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
+-++|..+=+.+.....-.++..+-.+--.+|.+|+=-.+.+.+.++..++++++.||-..+
T Consensus 2 ~~~vF~s~~~~~~D~~e~a~~m~ir~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~ 63 (91)
T COG5606 2 SNEVFTSVWDAIEDTPEAAENMKIRSALMMAIKQWIEQAALSQAQIAELLGVTQPRVSDLAR 63 (91)
T ss_pred CCchhhhHHHHHhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHh
Confidence 44566665555433222222234555555677888889999999999999999999996544
No 250
>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=46.47 E-value=50 Score=24.63 Aligned_cols=38 Identities=11% Similarity=0.057 Sum_probs=29.3
Q ss_pred CccchhhhhcccccccchhHHHHHHHHHHHhhhhhhcC-CCCCCC
Q 046385 107 NLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEMIT-PPSFTD 150 (218)
Q Consensus 107 ~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L~~~~Ik-~P~~~~ 150 (218)
+.+...++...+++++|||+.++...+. .||. .|+.++
T Consensus 43 ~~t~~eL~~~l~~~~stvs~~i~~Le~k------g~I~r~~~~~D 81 (109)
T TIGR01889 43 KLTLKEIIKEILIKQSALVKIIKKLSKK------GYLSKERSEDD 81 (109)
T ss_pred cCcHHHHHHHHCCCHHHHHHHHHHHHHC------CCEeccCCccc
Confidence 4788999999999999999998876554 6664 455443
No 251
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=46.09 E-value=25 Score=30.63 Aligned_cols=36 Identities=6% Similarity=-0.045 Sum_probs=27.0
Q ss_pred HHHHHHHHHhcCccchhhhhcccccccchhHHHHHHH
Q 046385 96 KMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVL 132 (218)
Q Consensus 96 ~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl 132 (218)
+|..|+. ++...|++.++...++|++|||+.+.+.=
T Consensus 5 ~L~~F~~-v~~~~S~s~AA~~L~isQ~avS~~I~~LE 40 (305)
T PRK11233 5 RLKYFVK-IVDIGSLTQAAEVLHIAQPALSQQVATLE 40 (305)
T ss_pred HHHHHHH-HHHcCCHHHHHHHhCCCchHHHHHHHHHH
Confidence 3455554 44445999999999999999998776543
No 252
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=45.55 E-value=7.3 Score=33.92 Aligned_cols=22 Identities=14% Similarity=-0.133 Sum_probs=19.3
Q ss_pred cchhhhhcccccccchhHHHHH
Q 046385 109 RNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 109 s~r~i~~~F~~S~sTVsr~f~e 130 (218)
+.++|+..-|+|.+||||.++.
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 4578999999999999998876
No 253
>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=45.47 E-value=29 Score=27.23 Aligned_cols=46 Identities=11% Similarity=0.061 Sum_probs=36.8
Q ss_pred chHHHHHHHHHHHHh-cCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 91 LTVEEKMAMFLFTIS-HNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 91 isveE~laifL~~la-~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
++.+++-.|-++++- ...+...++..+++|.+|++|.=+..+..+-
T Consensus 83 Ld~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla 129 (134)
T TIGR01636 83 ADEQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVA 129 (134)
T ss_pred CCHHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 466788888887763 3348899999999999999999887777654
No 254
>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=45.41 E-value=9.5 Score=25.49 Aligned_cols=25 Identities=16% Similarity=0.187 Sum_probs=20.2
Q ss_pred ccchhhhhcccccccchhHHHHHHH
Q 046385 108 LRNRFIKIRFQHSGHTVHRYFHEVL 132 (218)
Q Consensus 108 ~s~r~i~~~F~~S~sTVsr~f~eVl 132 (218)
.+...++..|++|..||.|-+.+.-
T Consensus 15 ~s~~ela~~~~VS~~TiRRDl~~L~ 39 (57)
T PF08220_consen 15 VSVKELAEEFGVSEMTIRRDLNKLE 39 (57)
T ss_pred EEHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4556789999999999998887543
No 255
>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=44.94 E-value=16 Score=30.00 Aligned_cols=39 Identities=15% Similarity=0.226 Sum_probs=30.0
Q ss_pred HHHHHHHHHhcC-------ccchhhhhcccccccchhHHHHHHHHH
Q 046385 96 KMAMFLFTISHN-------LRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 96 ~laifL~~la~~-------~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
++.|..|++.+- .+++.++..+++|..||+|.|.+..++
T Consensus 57 ~~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e~ 102 (165)
T PF05732_consen 57 AFRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVSRAIKELEEK 102 (165)
T ss_pred HHHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHHHHHHHHHhC
Confidence 455555655433 467899999999999999999987776
No 256
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=44.34 E-value=7.7 Score=33.97 Aligned_cols=22 Identities=27% Similarity=0.152 Sum_probs=19.4
Q ss_pred cchhhhhcccccccchhHHHHH
Q 046385 109 RNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 109 s~r~i~~~F~~S~sTVsr~f~e 130 (218)
+.++|+...|+|.+||||.++.
T Consensus 3 ti~dIA~~agVS~~TVSrvln~ 24 (327)
T PRK10339 3 TLKDIAIEAGVSLATVSRVLND 24 (327)
T ss_pred CHHHHHHHhCCCHHhhhhhhcC
Confidence 5678999999999999999874
No 257
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=44.33 E-value=21 Score=32.42 Aligned_cols=39 Identities=21% Similarity=0.255 Sum_probs=32.9
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
+++.+|+.-|-= .+..|.|.|.|+...+++.|||||=++
T Consensus 7 hLT~~eR~~I~~-l~~~~~S~reIA~~LgRh~sTIsRElk 45 (318)
T COG2826 7 HLTLFERYEIER-LLKAKMSIREIAKQLNRHHSTISRELK 45 (318)
T ss_pred hCCHHHHHHHHH-HHHcCCCHHHHHHHhCCCcchhhHHHh
Confidence 788888877754 458899999999999999999998543
No 258
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=43.93 E-value=31 Score=28.17 Aligned_cols=47 Identities=13% Similarity=0.119 Sum_probs=36.6
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.+|...+.++.|+ .-.|.++..|+...|+|.+||...++.....+-.
T Consensus 128 ~Lp~~~r~v~~l~-~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (188)
T PRK12517 128 KLDPEYREPLLLQ-VIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKE 174 (188)
T ss_pred hCCHHHHHHHHHH-HHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3455555544444 5568999999999999999999999988888764
No 259
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=43.88 E-value=24 Score=23.44 Aligned_cols=40 Identities=23% Similarity=0.258 Sum_probs=25.3
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~e 130 (218)
.++..||--|- -+..-|.|.+.++-..++|+..|.+++++
T Consensus 4 ~Lt~~Eqaqid-~m~qlG~s~~~isr~i~RSr~~Ir~yl~d 43 (50)
T PF11427_consen 4 TLTDAEQAQID-VMHQLGMSLREISRRIGRSRTCIRRYLKD 43 (50)
T ss_dssp ---HHHHHHHH-HHHHTT--HHHHHHHHT--HHHHHHHHHS
T ss_pred cCCHHHHHHHH-HHHHhchhHHHHHHHhCccHHHHHHHhcC
Confidence 46677765444 34567889999999999999999888763
No 260
>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=43.87 E-value=24 Score=23.90 Aligned_cols=32 Identities=16% Similarity=0.073 Sum_probs=27.3
Q ss_pred HHHHHHHHHhcCccchhhhhcccccccchhHHHH
Q 046385 96 KMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 96 ~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
+.|..||. .|.+...|+...+++.+||+....
T Consensus 4 ~~A~~LY~--~G~~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 4 EQARSLYL--QGWSIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred HHHHHHHH--cCCCHHHHHHHHCCChHHHHHHHH
Confidence 46778886 689999999999999999987654
No 261
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=43.86 E-value=34 Score=32.44 Aligned_cols=48 Identities=19% Similarity=0.209 Sum_probs=42.3
Q ss_pred CccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHH
Q 046385 88 SKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAM 135 (218)
Q Consensus 88 T~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI 135 (218)
++.|...-|+||+|--==++.|+..|+..||+..+||..-++.|=+.+
T Consensus 378 ~~~i~~~Rqiamyl~r~~t~~s~~~IG~~fgrdHsTV~~a~~ki~~~~ 425 (445)
T PRK12422 378 SREYVLPRQVAMYLCRQKLSLSYVKIGDVFSRDHSTVISSIRAISQKL 425 (445)
T ss_pred CcccccHHHHHHHHHHHhcCCCHHHHHHHhCCChHHHHHHHHHHHHHH
Confidence 458888999999999999999999999999999999988777776655
No 262
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=43.34 E-value=28 Score=30.17 Aligned_cols=47 Identities=13% Similarity=0.055 Sum_probs=34.6
Q ss_pred CccchHHHHHHHHHHHHhc---CccchhhhhcccccccchhHHHHHHHHH
Q 046385 88 SKHLTVEEKMAMFLFTISH---NLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 88 T~~isveE~laifL~~la~---~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
+..+.+-++..--|..++. +.+..+++...+++++|++|+++...+.
T Consensus 4 ~~~v~sl~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~ 53 (263)
T PRK09834 4 YKTVRGLSRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEE 53 (263)
T ss_pred chhHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3445555666666666653 2578999999999999999998876554
No 263
>PRK04841 transcriptional regulator MalT; Provisional
Probab=42.81 E-value=25 Score=35.35 Aligned_cols=45 Identities=18% Similarity=0.103 Sum_probs=37.0
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|..|.- -|..++.|.|++.|+....+|.+||..|++++...+-
T Consensus 838 ~lt~~e~~--v~~~~~~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~ 882 (903)
T PRK04841 838 PLTQREWQ--VLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLG 882 (903)
T ss_pred CCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 46666643 3455999999999999999999999999999877654
No 264
>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=42.71 E-value=23 Score=22.31 Aligned_cols=34 Identities=24% Similarity=0.140 Sum_probs=27.2
Q ss_pred HHHHHHHhcCccchhhhhcccccccchhHHHHHH
Q 046385 98 AMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEV 131 (218)
Q Consensus 98 aifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eV 131 (218)
-+|...--.+.+.+.++.+-++|++++.++|..-
T Consensus 7 ~l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~f~~k 40 (47)
T PF00440_consen 7 ELFAEKGYEAVSIRDIARRAGVSKGSFYRYFPSK 40 (47)
T ss_dssp HHHHHHHTTTSSHHHHHHHHTSCHHHHHHHCSSH
T ss_pred HHHHHhCHHhCCHHHHHHHHccchhhHHHHcCCH
Confidence 3444455567889999999999999999998754
No 265
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=42.52 E-value=34 Score=28.30 Aligned_cols=46 Identities=11% Similarity=0.062 Sum_probs=36.6
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|.+++.++.|+ .-.|.++..|+..+++|..||...++.....+-
T Consensus 153 ~L~~~~r~vl~l~-~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 198 (206)
T PRK12526 153 KLPEAQQTVVKGV-YFQELSQEQLAQQLNVPLGTVKSRLRLALAKLK 198 (206)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3566666665554 457899999999999999999998888877765
No 266
>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=42.36 E-value=22 Score=24.09 Aligned_cols=29 Identities=17% Similarity=0.019 Sum_probs=23.3
Q ss_pred cCccchhhhhcccccccchhHHHHHHHHH
Q 046385 106 HNLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 106 ~~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
...+-.+++...++|++||++.++.-.+.
T Consensus 21 ~~~t~~eIa~~l~i~~~~v~~~L~~L~~~ 49 (68)
T PF01978_consen 21 GPATAEEIAEELGISRSTVYRALKSLEEK 49 (68)
T ss_dssp CHEEHHHHHHHHTSSHHHHHHHHHHHHHT
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 33566899999999999999888776553
No 267
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=42.24 E-value=8.5 Score=33.41 Aligned_cols=19 Identities=16% Similarity=-0.010 Sum_probs=17.2
Q ss_pred hhhhhcccccccchhHHHH
Q 046385 111 RFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 111 r~i~~~F~~S~sTVsr~f~ 129 (218)
++|+...|+|.+||||.++
T Consensus 2 ~dIA~~agVS~~TVSrvLn 20 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVIN 20 (327)
T ss_pred hhHHHHhCCcHHHHHHHhC
Confidence 5789999999999999886
No 268
>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=42.16 E-value=20 Score=24.50 Aligned_cols=25 Identities=8% Similarity=0.054 Sum_probs=21.1
Q ss_pred cchhhhhcccccccchhHHHHHHHH
Q 046385 109 RNRFIKIRFQHSGHTVHRYFHEVLS 133 (218)
Q Consensus 109 s~r~i~~~F~~S~sTVsr~f~eVl~ 133 (218)
+...++..|++|.+||++.+...-+
T Consensus 15 ~~~eLa~~l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 15 SGEKLGEALGMSRTAVNKHIQTLRE 39 (69)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3578899999999999999987644
No 269
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=42.14 E-value=27 Score=26.90 Aligned_cols=28 Identities=18% Similarity=0.161 Sum_probs=22.2
Q ss_pred HhcCccchhhhhcccccccchhHHHHHH
Q 046385 104 ISHNLRNRFIKIRFQHSGHTVHRYFHEV 131 (218)
Q Consensus 104 la~~~s~r~i~~~F~~S~sTVsr~f~eV 131 (218)
+....+..+++..+++|..|++|.|++.
T Consensus 22 ~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 22 LESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred cCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3445566778888999999999998887
No 270
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=42.13 E-value=34 Score=29.99 Aligned_cols=42 Identities=10% Similarity=0.029 Sum_probs=33.7
Q ss_pred HHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 95 EKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 95 E~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+|-+|+...-+|.|+..++..-++|++|||+.+++.=+.+-
T Consensus 4 ~~L~~f~~v~~~g~S~s~AA~~L~isQpavS~~ik~LE~~lg 45 (313)
T PRK12684 4 HQLRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELG 45 (313)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhcCCChHHHHHHHHHHHHhC
Confidence 356667666677779999999999999999998888766665
No 271
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=41.68 E-value=27 Score=28.57 Aligned_cols=42 Identities=21% Similarity=0.156 Sum_probs=31.9
Q ss_pred chHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHH
Q 046385 91 LTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLS 133 (218)
Q Consensus 91 isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~ 133 (218)
+++++.-.+.|+++ .|.|+..|+...|+|..||.|-....-.
T Consensus 136 l~~~~~~~v~l~~~-~Gls~~EIA~~lgiS~~tV~r~l~~aR~ 177 (185)
T PF07638_consen 136 LDPRQRRVVELRFF-EGLSVEEIAERLGISERTVRRRLRRARA 177 (185)
T ss_pred cCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34455555555555 7889999999999999999998776543
No 272
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=40.92 E-value=31 Score=26.93 Aligned_cols=30 Identities=7% Similarity=0.044 Sum_probs=24.9
Q ss_pred hcCccchhhhhcccccccchhHHHHHHHHH
Q 046385 105 SHNLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 105 a~~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
..+.+...++..++++++||++.++.-.+.
T Consensus 52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~ 81 (144)
T PRK11512 52 AACITPVELKKVLSVDLGALTRMLDRLVCK 81 (144)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 345788999999999999999998875543
No 273
>PRK00215 LexA repressor; Validated
Probab=40.57 E-value=36 Score=28.17 Aligned_cols=29 Identities=17% Similarity=0.041 Sum_probs=24.5
Q ss_pred cCccchhhhhcccc-cccchhHHHHHHHHH
Q 046385 106 HNLRNRFIKIRFQH-SGHTVHRYFHEVLSA 134 (218)
Q Consensus 106 ~~~s~r~i~~~F~~-S~sTVsr~f~eVl~A 134 (218)
...+.++++..+++ |++|+++++....+.
T Consensus 22 ~~~s~~ela~~~~~~~~~tv~~~l~~L~~~ 51 (205)
T PRK00215 22 YPPSRREIADALGLRSPSAVHEHLKALERK 51 (205)
T ss_pred CCCCHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 34578899999999 999999998877655
No 274
>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=40.21 E-value=12 Score=29.30 Aligned_cols=38 Identities=24% Similarity=0.263 Sum_probs=27.5
Q ss_pred ccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHH
Q 046385 89 KHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 89 ~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~e 130 (218)
..|++.| |.-.=-.|.+...+++.|++|+|||..+..+
T Consensus 66 e~iti~E----fi~LR~AGlt~~aIAd~F~iS~s~~~nft~~ 103 (126)
T PF10654_consen 66 EEITIRE----FIELRHAGLTCYAIADYFKISKSTVFNFTQN 103 (126)
T ss_pred hHhhHHH----HHHHHhcCCChHHHHHHHhHHHHHHHHHHHH
Confidence 3455555 3333356889999999999999999876543
No 275
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=40.19 E-value=20 Score=30.20 Aligned_cols=48 Identities=10% Similarity=0.056 Sum_probs=36.2
Q ss_pred cchHHHHHHHHHHH------HhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFT------ISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~------la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.++..|.-++-+-+ .-...+-++++..||+|++|++.++++..+-|+.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~ 208 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIE 208 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 46666665555432 2345777899999999999999999998887763
No 276
>COG3139 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.76 E-value=93 Score=22.97 Aligned_cols=42 Identities=29% Similarity=0.340 Sum_probs=32.8
Q ss_pred ccCHHHHHHHHHHHHhcCccCCCccchHHHHH----HHHHHHHhcCc
Q 046385 66 RMDKNGFISLCQLFKEKGWLSDSKHLTVEEKM----AMFLFTISHNL 108 (218)
Q Consensus 66 RM~~~~F~~L~~~L~~~~~~~~T~~isveE~l----aifL~~la~~~ 108 (218)
-|+++.+-.|...+. -++.+|..+++.|.+- |+.||-.-||.
T Consensus 9 ~mtPEiYQrL~~AvE-lGKWPdG~~LtqeQke~clQaVmlwqarhN~ 54 (90)
T COG3139 9 SMTPEIYQRLSTAVE-LGKWPDGVALTQEQKENCLQAVMLWQARHNT 54 (90)
T ss_pred hcCHHHHHHHHHHHH-hcCCCCCCcCCHHHHHHHHHHHHHHHHhcCC
Confidence 488999999988764 4557899999988763 67788888774
No 277
>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=39.45 E-value=10 Score=33.01 Aligned_cols=21 Identities=14% Similarity=-0.187 Sum_probs=18.2
Q ss_pred chhhhhcccccccchhHHHHH
Q 046385 110 NRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 110 ~r~i~~~F~~S~sTVsr~f~e 130 (218)
.++|+..-|+|.+||||.++.
T Consensus 2 i~dIA~~aGVS~~TVSrvLn~ 22 (327)
T TIGR02417 2 LSDIAKLAGVSKTTASYVING 22 (327)
T ss_pred HHHHHHHhCCCHHHHHHHHcC
Confidence 468899999999999999865
No 278
>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=38.42 E-value=22 Score=28.90 Aligned_cols=48 Identities=19% Similarity=0.085 Sum_probs=38.3
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKF 138 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L 138 (218)
.+|...+.++.|++ -.|.|+..|+...|+|.+||...++.....|-..
T Consensus 131 ~Lp~~~r~i~~L~~-~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 178 (193)
T TIGR02947 131 GLPEEFRQAVYLAD-VEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQ 178 (193)
T ss_pred hCCHHHhhheeehh-hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35566666666654 5678999999999999999999999998887743
No 279
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=38.10 E-value=30 Score=29.87 Aligned_cols=35 Identities=11% Similarity=0.072 Sum_probs=27.4
Q ss_pred HHHHHHHHHhcCccchhhhhcccccccchhHHHHHH
Q 046385 96 KMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEV 131 (218)
Q Consensus 96 ~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eV 131 (218)
++-+|+...-+| |+..++..-++|++|||+.+++.
T Consensus 5 ~L~~f~~v~~~g-S~s~AA~~L~itQpavS~~i~~L 39 (305)
T PRK11151 5 DLEYLVALAEHR-HFRRAADSCHVSQPTLSGQIRKL 39 (305)
T ss_pred HHHHHHHHHHhC-CHHHHHHHhCCCchHHHHHHHHH
Confidence 455666666555 99999999999999999877654
No 280
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=37.90 E-value=39 Score=26.81 Aligned_cols=45 Identities=27% Similarity=0.363 Sum_probs=37.2
Q ss_pred cchHHHHHHHHHHHHhc--------------CccchhhhhcccccccchhHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISH--------------NLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 90 ~isveE~laifL~~la~--------------~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.-+++++++.+|..++. ..+...++...+.+.+|++|.+.+.-+.
T Consensus 140 ~~~~~~r~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~ia~~~g~~~~~vsr~l~~l~~~ 198 (214)
T COG0664 140 RKDVEERLARFLLNLGRRLGIATEDGILIPLPLTHKDLAEYLGLSRETVSRILKELRKD 198 (214)
T ss_pred hccHHHHHHHHHHHHhhccCCCCCCCcEEeccCCHHHHHHHhCCchhhHHHHHHHHHhC
Confidence 55899999999999885 3566788888899999999999876553
No 281
>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=37.79 E-value=11 Score=30.96 Aligned_cols=31 Identities=23% Similarity=0.162 Sum_probs=0.0
Q ss_pred ccchhhhhcccccccchhHHHHHHHHHHHhhhhhhcCCCCC
Q 046385 108 LRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEMITPPSF 148 (218)
Q Consensus 108 ~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L~~~~Ik~P~~ 148 (218)
.+++++++.-+++.|||||.+. .+|+..|.+
T Consensus 50 Lt~~~iA~~lgl~~STVSRav~----------~Ky~~t~~G 80 (160)
T PF04552_consen 50 LTMKDIADELGLHESTVSRAVK----------NKYIQTPRG 80 (160)
T ss_dssp -----------------------------------------
T ss_pred CCHHHHHHHhCCCHhHHHHHHc----------CceeecCCe
Confidence 5678999999999999999887 577777765
No 282
>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=37.78 E-value=11 Score=32.74 Aligned_cols=22 Identities=18% Similarity=-0.091 Sum_probs=19.1
Q ss_pred cchhhhhcccccccchhHHHHH
Q 046385 109 RNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 109 s~r~i~~~F~~S~sTVsr~f~e 130 (218)
+.++|+..-|+|.+||||.++.
T Consensus 3 ti~dIA~~agvS~~TVSrvLn~ 24 (329)
T TIGR01481 3 TIYDVAREAGVSMATVSRVVNG 24 (329)
T ss_pred cHHHHHHHhCCCHHHHHHHhCC
Confidence 5678999999999999998764
No 283
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=37.75 E-value=23 Score=32.07 Aligned_cols=67 Identities=13% Similarity=0.177 Sum_probs=43.7
Q ss_pred HHHHhcCccchhhhhcccccccchhHHHHHHHHH-HHhhhhhhcCCCCCC--CCcccccCcccccCCCCCccccCC
Q 046385 101 LFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSA-MMKFSKEMITPPSFT--DNSRGIRNTRLRQIFKRSPVVPLN 173 (218)
Q Consensus 101 L~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~A-I~~L~~~~Ik~P~~~--~~~~~i~n~~~~p~Fk~ci~vp~~ 173 (218)
=.|.-.|.++.+|+.++++|+.||||.+.+.-+. |+.+. |+.|... +..+.+ ..+|. .++|+.+|+.
T Consensus 23 ~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~---I~~~~~~~~~Le~~L-~~~fg--Lk~~iVvp~~ 92 (318)
T PRK15418 23 WFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQ---INSRFEGCLELENAL-RQHFS--LQHIRVLPAL 92 (318)
T ss_pred HHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEE---EeCCCccHHHHHHHH-HHHhC--CCEEEEEeCC
Confidence 3455678899999999999999999999987665 44321 3334321 111222 23553 7888888764
No 284
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=37.26 E-value=33 Score=27.06 Aligned_cols=45 Identities=20% Similarity=0.141 Sum_probs=36.8
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++..| .-.|..++.|.++..++...++|..||..++.+....+.
T Consensus 149 ~lt~re--~~vl~~l~~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 149 VLSNRE--VTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred cCCHHH--HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 344444 456678999999999999999999999999998877653
No 285
>PRK11050 manganese transport regulator MntR; Provisional
Probab=36.85 E-value=38 Score=27.09 Aligned_cols=29 Identities=21% Similarity=0.169 Sum_probs=25.1
Q ss_pred cCccchhhhhcccccccchhHHHHHHHHH
Q 046385 106 HNLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 106 ~~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.+.+.+.++..+++|.+||++.+.+.-..
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~~ 78 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLARD 78 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 46788999999999999999998877664
No 286
>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=36.23 E-value=40 Score=25.17 Aligned_cols=37 Identities=11% Similarity=-0.091 Sum_probs=30.2
Q ss_pred HHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 100 FLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 100 fL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+.-++...|++..+...++|.+|||+.+++.=+.+-
T Consensus 9 ~~~av~~~gSis~AA~~L~iS~stvs~~I~~LE~~lg 45 (99)
T TIGR00637 9 LLKAIARMGSISQAAKDAGISYKSAWDYIRAMNNLSG 45 (99)
T ss_pred HHHHHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 3444566679999999999999999999998776654
No 287
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=35.86 E-value=45 Score=29.24 Aligned_cols=48 Identities=13% Similarity=0.030 Sum_probs=37.5
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKF 138 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L 138 (218)
.+|+.+|.++-| ..-.|.||..|+..+++|.+||...++.....|-..
T Consensus 115 ~L~~~~R~v~~L-~~~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~ 162 (293)
T PRK09636 115 RLSPLERAAFLL-HDVFGVPFDEIASTLGRSPAACRQLASRARKHVRAA 162 (293)
T ss_pred hCCHHHHHHHHH-HHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 456666655444 445579999999999999999999999887777643
No 288
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=35.80 E-value=42 Score=23.61 Aligned_cols=44 Identities=16% Similarity=0.203 Sum_probs=38.8
Q ss_pred HHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhhh
Q 046385 96 KMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFS 139 (218)
Q Consensus 96 ~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L~ 139 (218)
++--|...|+...+..++++.-|+...||.+.+..+-.=+..|.
T Consensus 2 ~~~~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~LD 45 (65)
T PF05344_consen 2 KARAFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQLD 45 (65)
T ss_pred cHHHHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHHcC
Confidence 45568899999999999999999999999999998888777775
No 289
>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=35.76 E-value=41 Score=23.63 Aligned_cols=25 Identities=12% Similarity=0.052 Sum_probs=18.8
Q ss_pred cCccchhhhhcccccccchhHHHHH
Q 046385 106 HNLRNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 106 ~~~s~r~i~~~F~~S~sTVsr~f~e 130 (218)
...+.++++..-++|.+||.|..+.
T Consensus 33 ~~~si~elA~~~~vS~sti~Rf~kk 57 (77)
T PF01418_consen 33 AFMSISELAEKAGVSPSTIVRFCKK 57 (77)
T ss_dssp CT--HHHHHHHCTS-HHHHHHHHHH
T ss_pred HHccHHHHHHHcCCCHHHHHHHHHH
Confidence 3567789999999999999998654
No 290
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=35.63 E-value=24 Score=21.86 Aligned_cols=27 Identities=11% Similarity=0.052 Sum_probs=22.0
Q ss_pred ccchhhhhcccccccchhHHHHHHHHH
Q 046385 108 LRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 108 ~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.+..+++..|++|.+||++.+....+.
T Consensus 15 ~s~~~l~~~l~~s~~tv~~~l~~L~~~ 41 (53)
T smart00420 15 VSVEELAELLGVSEMTIRRDLNKLEEQ 41 (53)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 566788999999999999998775543
No 291
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=35.56 E-value=38 Score=28.37 Aligned_cols=32 Identities=6% Similarity=0.090 Sum_probs=29.0
Q ss_pred hcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 105 SHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 105 a~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
+.|.++..|+...++|..||..|+....++.+
T Consensus 176 ~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~ 207 (239)
T PRK10430 176 DYEFSTDELANAVNISRVSCRKYLIWLVNCHI 207 (239)
T ss_pred CCCcCHHHHHHHhCchHHHHHHHHHHHHhCCE
Confidence 58999999999999999999999998887754
No 292
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=35.49 E-value=37 Score=28.28 Aligned_cols=40 Identities=13% Similarity=0.190 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHH
Q 046385 94 EEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 94 eE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.+++...|+.- .+.+..+++..+++|..||++++.+..+.
T Consensus 3 r~~IL~~L~~~-~~~t~~eLA~~lgis~~tV~~~L~~Le~~ 42 (203)
T TIGR02702 3 KEDILSYLLKQ-GQATAAALAEALAISPQAVRRHLKDLETE 42 (203)
T ss_pred HHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34455555543 34788999999999999999998876655
No 293
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=34.51 E-value=38 Score=33.42 Aligned_cols=47 Identities=11% Similarity=0.053 Sum_probs=39.6
Q ss_pred cchHHHHHHHHHHHH---hcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTI---SHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~l---a~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++..|+.-+-+||. ..+.++..++..|++|++.|+++=...+.-|-
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 467888888888885 46788899999999999999999888777654
No 294
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=34.49 E-value=14 Score=32.62 Aligned_cols=21 Identities=19% Similarity=-0.036 Sum_probs=18.5
Q ss_pred cchhhhhcccccccchhHHHH
Q 046385 109 RNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 109 s~r~i~~~F~~S~sTVsr~f~ 129 (218)
+.++|+..-|+|.+||||.++
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVIN 23 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhC
Confidence 467899999999999999875
No 295
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=34.25 E-value=38 Score=30.04 Aligned_cols=41 Identities=10% Similarity=0.096 Sum_probs=31.0
Q ss_pred HHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 96 KMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 96 ~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
+|-.|+...-+|.|++.++...++|++|||+.+.+.=+.+-
T Consensus 5 ~L~~f~avae~g~S~s~AA~~L~iSQpavS~~I~~LE~~lG 45 (324)
T PRK12681 5 QLRYIVEVVNHNLNVSATAEGLYTSQPGISKQVRMLEDELG 45 (324)
T ss_pred HHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhC
Confidence 45556655556679999999999999999988777655543
No 296
>PRK02287 hypothetical protein; Provisional
Probab=34.24 E-value=36 Score=28.39 Aligned_cols=44 Identities=20% Similarity=0.233 Sum_probs=36.8
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.+|.-|.+|.+||++|-...-..+-..|..+.+-+ ...+|.|++
T Consensus 106 kLs~vEAlAaaLyI~G~~~~A~~ll~~F~WG~~Fl-~lN~elLe~ 149 (171)
T PRK02287 106 KLSSVEALAAALYILGFKEEAEKILSKFKWGHTFL-ELNKEPLEA 149 (171)
T ss_pred cccHHHHHHHHHHHcCCHHHHHHHHhhCCChHHHH-HHHHHHHHH
Confidence 78999999999999999999999999998875443 666666665
No 297
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=34.24 E-value=51 Score=25.40 Aligned_cols=34 Identities=26% Similarity=0.326 Sum_probs=29.1
Q ss_pred HHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 103 TISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 103 ~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.+..|.+++.++..+++|..||..++.+....+-
T Consensus 152 ~~~~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~ 185 (202)
T PRK09390 152 GLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQ 185 (202)
T ss_pred HHHccCchHHHHHHcCCCHHHHHHHHHHHHHHHc
Confidence 4667889999999999999999999988777653
No 298
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=33.87 E-value=38 Score=29.44 Aligned_cols=39 Identities=13% Similarity=0.140 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHhcCc--cchhhhhcccccccchhHHHHHH
Q 046385 93 VEEKMAMFLFTISHNL--RNRFIKIRFQHSGHTVHRYFHEV 131 (218)
Q Consensus 93 veE~laifL~~la~~~--s~r~i~~~F~~S~sTVsr~f~eV 131 (218)
.+||...-|-.|..+. +..+++..|++|.+||.|-+.+.
T Consensus 3 ~~eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~L 43 (256)
T PRK10434 3 PRQRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVIL 43 (256)
T ss_pred HHHHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHH
Confidence 4566666666666543 55789999999999999998873
No 299
>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=33.80 E-value=38 Score=23.21 Aligned_cols=38 Identities=18% Similarity=0.073 Sum_probs=28.1
Q ss_pred chHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHH
Q 046385 91 LTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 91 isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
.++.+++... +.-..|.+..+++..-|+|.+||+++.+
T Consensus 3 ~~~g~~i~~~-~~~~~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 3 AHPGEILREE-FLEPLGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred CCHHHHHHHH-HHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 4556654422 2356778889999999999999999765
No 300
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=33.75 E-value=41 Score=28.65 Aligned_cols=35 Identities=11% Similarity=0.069 Sum_probs=25.4
Q ss_pred HHHHHHHHHhcCccchhhhhcccccccchhHHHHHH
Q 046385 96 KMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEV 131 (218)
Q Consensus 96 ~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eV 131 (218)
+|-+|+... ...|++.++..-++|.+|||+.+++.
T Consensus 5 ~L~~f~~v~-~~gs~s~AA~~L~isqsavS~~i~~L 39 (296)
T PRK11242 5 HIRYFLAVA-EHGNFTRAAEALHVSQPTLSQQIRQL 39 (296)
T ss_pred HHHHHHHHH-HhCCHHHHHHHcCCCchHHHHHHHHH
Confidence 344444444 44589999999999999999776554
No 301
>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=33.61 E-value=17 Score=23.12 Aligned_cols=26 Identities=4% Similarity=-0.228 Sum_probs=22.2
Q ss_pred HhcCccchhhhhcccccccchhHHHH
Q 046385 104 ISHNLRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 104 la~~~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
-..|.+..+++..-++|.+|||++.+
T Consensus 12 ~~~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 12 KALGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 35678889999999999999999864
No 302
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=33.23 E-value=50 Score=27.50 Aligned_cols=27 Identities=19% Similarity=0.158 Sum_probs=23.1
Q ss_pred CccchhhhhcccccccchhHHHHHHHH
Q 046385 107 NLRNRFIKIRFQHSGHTVHRYFHEVLS 133 (218)
Q Consensus 107 ~~s~r~i~~~F~~S~sTVsr~f~eVl~ 133 (218)
+.+..+++..+++|.+|+++++.+..+
T Consensus 157 ~~s~~eia~~l~is~stv~r~L~~Le~ 183 (203)
T TIGR01884 157 EKSVKNIAKKLGKSLSTISRHLRELEK 183 (203)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 458899999999999999999887443
No 303
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=33.09 E-value=15 Score=22.11 Aligned_cols=21 Identities=19% Similarity=0.093 Sum_probs=17.3
Q ss_pred ccchhhhhcccccccchhHHH
Q 046385 108 LRNRFIKIRFQHSGHTVHRYF 128 (218)
Q Consensus 108 ~s~r~i~~~F~~S~sTVsr~f 128 (218)
.|.+.++..++++.+||++++
T Consensus 17 ~Si~eAa~~l~i~~~~I~~~l 37 (37)
T PF07453_consen 17 DSIREAARYLGISHSTISKYL 37 (37)
T ss_pred cCHHHHHHHhCCCHHHHHHhC
Confidence 466788899999999998763
No 304
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=33.07 E-value=56 Score=24.49 Aligned_cols=46 Identities=11% Similarity=0.067 Sum_probs=39.1
Q ss_pred ccchHHHHHHHHHHHHhcCccchhhhhcccc-cccchhHHHHHHHHH
Q 046385 89 KHLTVEEKMAMFLFTISHNLRNRFIKIRFQH-SGHTVHRYFHEVLSA 134 (218)
Q Consensus 89 ~~isveE~laifL~~la~~~s~r~i~~~F~~-S~sTVsr~f~eVl~A 134 (218)
+.-|.|.++.+.-.++-.|.++..++..|++ +.++..+...+.-+.
T Consensus 6 r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~ 52 (116)
T COG2963 6 KKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKG 52 (116)
T ss_pred ccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHc
Confidence 3568899999999999999999999999995 999999877765553
No 305
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=33.05 E-value=52 Score=28.13 Aligned_cols=33 Identities=3% Similarity=0.183 Sum_probs=25.9
Q ss_pred HHHHHhcCccchhhhhcccccccchhHHHHHHH
Q 046385 100 FLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVL 132 (218)
Q Consensus 100 fL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl 132 (218)
.+..++...|++.++...++|.+||||.+++.=
T Consensus 8 ~f~~v~~~gs~s~AA~~L~isQ~avSr~i~~LE 40 (296)
T PRK09906 8 YFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLE 40 (296)
T ss_pred HHHHHHhhCCHHHHHHHhCCCCcHHHHHHHHHH
Confidence 445566666999999999999999998766543
No 306
>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=32.86 E-value=56 Score=28.58 Aligned_cols=48 Identities=10% Similarity=-0.011 Sum_probs=38.1
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKF 138 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L 138 (218)
.+|+.++.++.|+ .-.|.++..|+..+++|..||...++.....|-..
T Consensus 108 ~L~~~~R~v~~L~-~~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 108 RLSPLERAVFVLR-EVFDYPYEEIASIVGKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 4566776555454 45688999999999999999999999988887653
No 307
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=32.78 E-value=39 Score=29.40 Aligned_cols=35 Identities=14% Similarity=0.064 Sum_probs=25.5
Q ss_pred HHHHHHHHHhcCccchhhhhcccccccchhHHHHHH
Q 046385 96 KMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEV 131 (218)
Q Consensus 96 ~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eV 131 (218)
++-+|+-..-+ .|+..++...++|.+|||+.+++.
T Consensus 8 ~L~~f~av~~~-gS~s~AAe~L~isqsavS~~Ik~L 42 (309)
T PRK11013 8 HIEIFHAVMTA-GSLTEAARLLHTSQPTVSRELARF 42 (309)
T ss_pred HHHHHHHHHHh-CcHHHHHHHHCCCcHHHHHHHHHH
Confidence 45555554444 488999999999999999776654
No 308
>PRK13501 transcriptional activator RhaR; Provisional
Probab=32.77 E-value=1e+02 Score=26.74 Aligned_cols=44 Identities=7% Similarity=0.084 Sum_probs=32.1
Q ss_pred HhcCccchhhhhcccccccchhHHHHHHHH--------HH-HhhhhhhcCCCC
Q 046385 104 ISHNLRNRFIKIRFQHSGHTVHRYFHEVLS--------AM-MKFSKEMITPPS 147 (218)
Q Consensus 104 la~~~s~r~i~~~F~~S~sTVsr~f~eVl~--------AI-~~L~~~~Ik~P~ 147 (218)
++...+..+++..+++|.++++|.|++... .+ +..+++.+.-++
T Consensus 189 ~~e~~sl~~lA~~~~lS~~~l~r~Fk~~~G~T~~qyi~~~Ri~~A~~LL~~t~ 241 (290)
T PRK13501 189 LGAYFDMADFCHKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSE 241 (290)
T ss_pred hccCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCC
Confidence 456677789999999999999999988732 22 245667776554
No 309
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=32.66 E-value=41 Score=29.16 Aligned_cols=38 Identities=13% Similarity=0.148 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHhcC--ccchhhhhcccccccchhHHHHHH
Q 046385 94 EEKMAMFLFTISHN--LRNRFIKIRFQHSGHTVHRYFHEV 131 (218)
Q Consensus 94 eE~laifL~~la~~--~s~r~i~~~F~~S~sTVsr~f~eV 131 (218)
+||...-|.+|..+ .+..+++..|++|.+||.|.+++.
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~L 43 (251)
T PRK13509 4 AQRHQILLELLAQLGFVTVEKVIERLGISPATARRDINKL 43 (251)
T ss_pred HHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 45555555555443 344789999999999999998884
No 310
>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=32.51 E-value=39 Score=23.97 Aligned_cols=34 Identities=12% Similarity=-0.002 Sum_probs=25.9
Q ss_pred HhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 104 ISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 104 la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
...+.+..++++.+.+|.+|+.+.++++=+.+-.
T Consensus 27 ~~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~~ 60 (87)
T PF05043_consen 27 NNEYVSIEDLAEELFISRSTIYRDIKKLNKYLKK 60 (87)
T ss_dssp H-SEEEHHHHHHHHT--HHHHHHHHHHHHHHHHC
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3566778999999999999999999988777653
No 311
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=32.35 E-value=88 Score=27.52 Aligned_cols=87 Identities=10% Similarity=0.006 Sum_probs=53.9
Q ss_pred ccHHHHHHHHHhCCcccchhccccCHHHHHHHHHHHHhcCcc---CCCccchHHHHHHHH-HHHHhcCccchhhhhcccc
Q 046385 44 LTGSLYIQELLNGSPIFCYDLMRMDKNGFISLCQLFKEKGWL---SDSKHLTVEEKMAMF-LFTISHNLRNRFIKIRFQH 119 (218)
Q Consensus 44 l~G~~~v~ell~~~~~~~~~~fRM~~~~F~~L~~~L~~~~~~---~~T~~isveE~laif-L~~la~~~s~r~i~~~F~~ 119 (218)
..-..|+..++..-..+-...-++..-.|..|+..+...... ......+..+++.-. ..-++...+..+++..++.
T Consensus 83 ~~~~~~L~~ll~~l~~e~~~~~~l~~~ll~~lL~~l~~~~~~~~~l~~~~~~~~~kv~~~I~~~~~~~~tl~~LA~~~gm 162 (253)
T PRK09940 83 NVPTGLLNEMIAYLNSEERNHHNFSELLLFSCLSIFAACKGFITLLTNGVLSVSGKVRNIVNMKLAHPWKLKDICDCLYI 162 (253)
T ss_pred CCCHHHHHHHHHHHHhcchhhhHHHHHHHHHHHHHHHhCccHHHhhccccccHHHHHHHHHHHhhcCCCCHHHHHHHHCc
Confidence 455667666554211122122288888888888877643211 111223333333333 3456777889999999999
Q ss_pred cccchhHHHHH
Q 046385 120 SGHTVHRYFHE 130 (218)
Q Consensus 120 S~sTVsr~f~e 130 (218)
|.++.+|.|++
T Consensus 163 S~s~l~R~FK~ 173 (253)
T PRK09940 163 SESLLKKKLKQ 173 (253)
T ss_pred CHHHHHHHHHH
Confidence 99999999987
No 312
>PRK06474 hypothetical protein; Provisional
Probab=32.27 E-value=44 Score=27.61 Aligned_cols=40 Identities=10% Similarity=0.115 Sum_probs=27.3
Q ss_pred HHHHHHHHHHhcC--ccchhhhhcc-cccccchhHHHHHHHHH
Q 046385 95 EKMAMFLFTISHN--LRNRFIKIRF-QHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 95 E~laifL~~la~~--~s~r~i~~~F-~~S~sTVsr~f~eVl~A 134 (218)
.|+.|.-....++ .+-.++.... ++|++||+|+++...++
T Consensus 12 ~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~ 54 (178)
T PRK06474 12 VRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDS 54 (178)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHC
Confidence 3444444444433 4556666666 79999999999988777
No 313
>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=32.19 E-value=18 Score=21.97 Aligned_cols=22 Identities=18% Similarity=0.160 Sum_probs=17.8
Q ss_pred cchhhhhcccccccchhHHHHH
Q 046385 109 RNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 109 s~r~i~~~F~~S~sTVsr~f~e 130 (218)
+...++..+++|.+|+.+.+.+
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 3467888999999999888773
No 314
>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=32.02 E-value=63 Score=24.31 Aligned_cols=59 Identities=15% Similarity=0.013 Sum_probs=36.4
Q ss_pred cCHHHHHHHHHHHHhcCccCCCccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHH
Q 046385 67 MDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 67 M~~~~F~~L~~~L~~~~~~~~T~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
.+.+.-..+...+...+...+.. +++.+ + --..-..|.+.+.++..+|+|.+||+++-+
T Consensus 42 ~~~e~~~~~~~~i~~~~~~~~~~-~~~~~-i--~~~r~~~gltq~~lA~~lg~~~~tis~~e~ 100 (127)
T TIGR03830 42 LDPEESKRNSAALADFYRKVDGL-LTPPE-I--RRIRKKLGLSQREAAELLGGGVNAFSRYER 100 (127)
T ss_pred EcHHHHHHHHHHHHHHHHHccCC-cCHHH-H--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 44455555555555444333332 22322 2 222345688999999999999999999755
No 315
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=31.94 E-value=26 Score=27.77 Aligned_cols=46 Identities=17% Similarity=0.145 Sum_probs=35.4
Q ss_pred chHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 91 LTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 91 isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
+|..++-.+.|+ .-.|.+++.|+..+|+|..||...++.+...+-.
T Consensus 121 L~~~~r~vl~l~-~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~ 166 (175)
T PRK12518 121 LSLEHRAVLVLH-DLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRK 166 (175)
T ss_pred CCHHHeeeeeeh-HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 445555444443 3567789999999999999999999999888763
No 316
>PRK09801 transcriptional activator TtdR; Provisional
Probab=31.75 E-value=57 Score=28.55 Aligned_cols=40 Identities=8% Similarity=0.079 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHH
Q 046385 95 EKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAM 135 (218)
Q Consensus 95 E~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI 135 (218)
.+|-.|+. ++...|++.++...++|++|||+.+++.=+.+
T Consensus 9 ~~L~~F~~-v~~~gs~t~AA~~L~iSQpavS~~I~~LE~~L 48 (310)
T PRK09801 9 KDLQVLVE-IVHSGSFSAAAATLGQTPAFVTKRIQILENTL 48 (310)
T ss_pred HHHHHHHH-HHHcCCHHHHHHHhCcCHHHHHHHHHHHHHHh
Confidence 44555554 44555889999999999999998776654443
No 317
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=31.38 E-value=53 Score=28.00 Aligned_cols=36 Identities=6% Similarity=-0.033 Sum_probs=25.5
Q ss_pred HHHHHHHHHhcCccchhhhhcccccccchhHHHHHHH
Q 046385 96 KMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVL 132 (218)
Q Consensus 96 ~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl 132 (218)
+|-.|+...-+ .|+..++...++|.+|||+.+++.=
T Consensus 5 ~L~~f~~v~~~-gs~s~AA~~L~itqpavS~~Ik~LE 40 (291)
T TIGR03418 5 ALRVFESAARL-ASFTAAARELGSTQPAVSQQVKRLE 40 (291)
T ss_pred HHHHHHHHHHh-CCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 34445444444 4899999999999999997766543
No 318
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=31.22 E-value=25 Score=25.21 Aligned_cols=25 Identities=20% Similarity=0.158 Sum_probs=21.3
Q ss_pred chhhhhcccccccchhHHHHHHHHH
Q 046385 110 NRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 110 ~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.+.++..+++|++||++.+....+.
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~ 26 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKD 26 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHC
Confidence 4678999999999999998877664
No 319
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=31.02 E-value=46 Score=27.41 Aligned_cols=81 Identities=10% Similarity=0.071 Sum_probs=47.5
Q ss_pred cccHHHHHHHHHh-C-CcccchhccccCHHHHHHHHHHHHhcCccCCCccchHHHHHHHHHHHHh-cCccchhhhhcccc
Q 046385 43 SLTGSLYIQELLN-G-SPIFCYDLMRMDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTIS-HNLRNRFIKIRFQH 119 (218)
Q Consensus 43 ~l~G~~~v~ell~-~-~~~~~~~~fRM~~~~F~~L~~~L~~~~~~~~T~~isveE~laifL~~la-~~~s~r~i~~~F~~ 119 (218)
+..|+..+.-... | .+-.|.- .-++.+.. .... +.++.. ...+++-|+-..+...+. .|.+...++..+|+
T Consensus 59 ii~G~rR~~A~~~lg~~~ip~~v-~~~~~~~~-~~~~-l~eN~~---r~~lt~~e~a~~~~~l~~~~g~s~~~iA~~lg~ 132 (187)
T TIGR00180 59 IIAGERRWRAAKLAGLKTIPAIV-RELDDEQM-LADA-LIENIQ---REDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGK 132 (187)
T ss_pred EEcCHHHHHHHHHcCCCceeEEE-ecCCHHHH-HHHH-HHHHhC---ccCCCHHHHHHHHHHHHHHhCCCHHHHHHHHCc
Confidence 5678888766554 3 3433431 22444332 2222 223221 235666665444444443 57888999999999
Q ss_pred cccchhHHHH
Q 046385 120 SGHTVHRYFH 129 (218)
Q Consensus 120 S~sTVsr~f~ 129 (218)
|.++|+++..
T Consensus 133 s~~~V~r~l~ 142 (187)
T TIGR00180 133 SRAHITNLLR 142 (187)
T ss_pred CHHHHHHHHH
Confidence 9999998764
No 320
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=30.99 E-value=18 Score=32.58 Aligned_cols=21 Identities=19% Similarity=0.020 Sum_probs=18.1
Q ss_pred cchhhhhcccccccchhHHHH
Q 046385 109 RNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 109 s~r~i~~~F~~S~sTVsr~f~ 129 (218)
+..+++..-|+|.+||||.++
T Consensus 2 TikDVA~~AGVS~sTVSrvln 22 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLN 22 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHc
Confidence 457889999999999999875
No 321
>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=30.96 E-value=19 Score=22.05 Aligned_cols=21 Identities=24% Similarity=0.070 Sum_probs=16.7
Q ss_pred cchhhhhcccccccchhHHHH
Q 046385 109 RNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 109 s~r~i~~~F~~S~sTVsr~f~ 129 (218)
+..+++..+++|.+||.+.++
T Consensus 3 t~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 346788899999999887764
No 322
>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=30.75 E-value=43 Score=25.02 Aligned_cols=24 Identities=8% Similarity=0.200 Sum_probs=19.8
Q ss_pred cchhhhhcccccccchhHHHHHHH
Q 046385 109 RNRFIKIRFQHSGHTVHRYFHEVL 132 (218)
Q Consensus 109 s~r~i~~~F~~S~sTVsr~f~eVl 132 (218)
..+.+++.-|++.|||||.-.+.+
T Consensus 25 gq~~vA~~~Gv~eStISR~k~~~~ 48 (91)
T PF05269_consen 25 GQKKVAEAMGVDESTISRWKNDFI 48 (91)
T ss_dssp HHHHHHHHHTSSTTTHHHHHHHHH
T ss_pred hhHHHHHHhCCCHHHHHHHHhhHH
Confidence 458899999999999999765543
No 323
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=30.62 E-value=81 Score=29.82 Aligned_cols=50 Identities=18% Similarity=0.185 Sum_probs=43.8
Q ss_pred CCccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 87 DSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 87 ~T~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++.|.---|+||+|-.-=++.|+-.|+..||+..+||..-++.|-+-+-
T Consensus 345 R~~~i~~~RqiamyL~r~lt~~Slp~IG~~FgrdHtTV~~a~~kI~~~~~ 394 (408)
T COG0593 345 RTRNIVRPRQIAMYLARELTNLSLPEIGKAFGRDHTTVLHAVRKIEQLIE 394 (408)
T ss_pred cccccchHHHHHHHHHHHHccCcHHHHHHHhCCCccHHHHHHHHHHHHHh
Confidence 44688889999999999999999999999999999999888877766654
No 324
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=30.29 E-value=44 Score=29.23 Aligned_cols=36 Identities=11% Similarity=0.092 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhcCccchhhhhcccccccchhHHHHHH
Q 046385 95 EKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEV 131 (218)
Q Consensus 95 E~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eV 131 (218)
++|-+|+. ++...|+..++...++|++|||+.+.+.
T Consensus 5 ~~L~~f~~-v~e~gs~s~AA~~L~iSQpavS~~I~~L 40 (308)
T PRK10094 5 ETLRTFIA-VAETGSFSKAAERLCKTTATISYRIKLL 40 (308)
T ss_pred HHHHHHHH-HHHhCCHHHHHHHhcCCHHHHHHHHHHH
Confidence 34555554 4445599999999999999999876654
No 325
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=30.07 E-value=18 Score=25.74 Aligned_cols=35 Identities=14% Similarity=0.116 Sum_probs=24.2
Q ss_pred HHHHHHH--HHHhcCccchhhhhcccccccchhHHHH
Q 046385 95 EKMAMFL--FTISHNLRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 95 E~laifL--~~la~~~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
..++..| ..=..+.++++++...|+|.++||++.+
T Consensus 17 ~~l~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 17 AQLMAAIRELREERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp HHHHHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence 3344444 3447789999999999999999999874
No 326
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=29.80 E-value=84 Score=23.87 Aligned_cols=46 Identities=24% Similarity=0.231 Sum_probs=35.6
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
.++++|--|+=|--+ .+.++...+.+.|+|+.|+.+.++....-|.
T Consensus 33 ~lt~eElEAlRLvD~-~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA 78 (99)
T COG1342 33 ILTIEELEALRLVDY-EGLTQEEAALRMGISRQTFWRLLTSARKKVA 78 (99)
T ss_pred eecHHHHHHHHHHhH-hhccHHHHHHHhcccHHHHHHHHHHHHHHHH
Confidence 677777777666443 4678889999999999999999887655554
No 327
>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=29.63 E-value=15 Score=31.41 Aligned_cols=37 Identities=14% Similarity=0.013 Sum_probs=27.7
Q ss_pred hhcCCCCCCCCccccc-CcccccCCCCCccccCCcccccc
Q 046385 141 EMITPPSFTDNSRGIR-NTRLRQIFKRSPVVPLNLQKMSR 179 (218)
Q Consensus 141 ~~Ik~P~~~~~~~~i~-n~~~~p~Fk~ci~vp~~~~v~~r 179 (218)
+|+..|+.++..+.++ ++ ...|++.+|.+||+|..+.
T Consensus 2 ~YLr~P~~~d~~rll~~~e--~rGFpGmlGSIDCmHw~Wk 39 (205)
T PF04827_consen 2 EYLRRPTNEDLERLLQIGE--ARGFPGMLGSIDCMHWEWK 39 (205)
T ss_pred cccCCCChhHHHHHHHhhh--hcCCCccccceeEEEeehh
Confidence 6888999877655443 11 1379999999999998765
No 328
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=29.52 E-value=24 Score=22.44 Aligned_cols=22 Identities=14% Similarity=0.125 Sum_probs=18.4
Q ss_pred ccchhhhhcccccccchhHHHH
Q 046385 108 LRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 108 ~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
.|.+.++..++++.+||+++.+
T Consensus 18 ~S~~eAa~~lg~~~~~I~~~~~ 39 (53)
T smart00497 18 SSIREAAKYLGISHSSISKYLN 39 (53)
T ss_pred cCHHHHHHHhCCCHHHHHHHHh
Confidence 4667888999999999998876
No 329
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=29.16 E-value=77 Score=23.13 Aligned_cols=28 Identities=14% Similarity=0.082 Sum_probs=24.4
Q ss_pred CccchhhhhcccccccchhHHHHHHHHH
Q 046385 107 NLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 107 ~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
..++..++..+++|.+||++.+....+.
T Consensus 17 ~~~~~~la~~l~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 17 RISLAELAKKVGLSPSTVHNRVKRLEEE 44 (108)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4788999999999999999998877664
No 330
>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=29.13 E-value=60 Score=25.64 Aligned_cols=55 Identities=15% Similarity=0.101 Sum_probs=34.4
Q ss_pred CCCccchHHHHHHHH-HHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhhhhhhc
Q 046385 86 SDSKHLTVEEKMAMF-LFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEMI 143 (218)
Q Consensus 86 ~~T~~isveE~laif-L~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L~~~~I 143 (218)
.+.+++|.+.+.-|- |+ -.|.+-.+++.++++|.+.||+++...-+. -.+.+.-|
T Consensus 13 ~nGrPLp~~~R~rIvela--~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~eT-Gsi~Pg~i 68 (125)
T PF00292_consen 13 INGRPLPNELRQRIVELA--KEGVRPCDISRQLRVSHGCVSKILSRYRET-GSIRPGPI 68 (125)
T ss_dssp ETTSSS-HHHHHHHHHHH--HTT--HHHHHHHHT--HHHHHHHHHHHHHH-S-SS----
T ss_pred eCCccCcHHHHHHHHHHh--hhcCCHHHHHHHHccchhHHHHHHHHHHHh-cccCcccc
Confidence 456788888888776 44 358899999999999999999999877332 24444444
No 331
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=29.08 E-value=67 Score=28.62 Aligned_cols=50 Identities=10% Similarity=0.091 Sum_probs=39.6
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhhhh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSK 140 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L~~ 140 (218)
.+|..+|..+.|++ -.|.++..|+..+++|..||...+++....|-...+
T Consensus 153 ~Lp~~~R~v~~L~~-~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~ 202 (339)
T PRK08241 153 HLPPRQRAVLILRD-VLGWSAAEVAELLDTSVAAVNSALQRARATLAERGP 202 (339)
T ss_pred hCCHHHhhhhhhHH-hhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhcCC
Confidence 35666666666654 567899999999999999999999998888776433
No 332
>PHA02591 hypothetical protein; Provisional
Probab=28.99 E-value=43 Score=24.53 Aligned_cols=29 Identities=17% Similarity=0.103 Sum_probs=25.0
Q ss_pred HHHhcCccchhhhhcccccccchhHHHHH
Q 046385 102 FTISHNLRNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 102 ~~la~~~s~r~i~~~F~~S~sTVsr~f~e 130 (218)
.....|.|...|+..-|+|.+||+++.+.
T Consensus 54 eL~eqGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 54 ELARKGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 34567889999999999999999999875
No 333
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=28.78 E-value=70 Score=28.37 Aligned_cols=41 Identities=5% Similarity=0.122 Sum_probs=30.3
Q ss_pred HHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 96 KMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 96 ~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
+|-+|+...=++.|++.++...++|.+|||+.+++.=+.+-
T Consensus 5 ~L~~F~~vae~~gS~s~AA~~L~isQpavS~~I~~LE~~lG 45 (327)
T PRK12680 5 QLRYLVAIADAELNITLAAARVHATQPGLSKQLKQLEDELG 45 (327)
T ss_pred HHHHHHHHHHccCCHHHHHHHhcCCchHHHHHHHHHHHHhC
Confidence 34455444434578999999999999999988887766654
No 334
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=28.56 E-value=1.5e+02 Score=24.54 Aligned_cols=51 Identities=8% Similarity=0.098 Sum_probs=35.9
Q ss_pred cccCHHHHHHHHHHHHhcCccCCCccchHHHHHHHHHHHHhcCccchhhhhcccccccchhH
Q 046385 65 MRMDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHR 126 (218)
Q Consensus 65 fRM~~~~F~~L~~~L~~~~~~~~T~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr 126 (218)
+.++.+.|..++...+. .+++....=+.|..|+|...++..||.|..-|+.
T Consensus 56 i~in~~~l~~~L~~~~~-----------~~~~~~~idr~L~lGAS~~mm~~~FGls~~ev~~ 106 (180)
T PF11198_consen 56 ISINHDVLWRLLEQARR-----------EQQEQQLIDRALRLGASIEMMQRLFGLSSAEVAA 106 (180)
T ss_pred eeeCHHHHHHHHHHHHH-----------HHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHH
Confidence 55666666666655442 2233455568899999999999999999877753
No 335
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=28.53 E-value=76 Score=27.67 Aligned_cols=45 Identities=13% Similarity=0.056 Sum_probs=34.5
Q ss_pred cchHHHHHHHHHHHHhc---CccchhhhhcccccccchhHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISH---NLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 90 ~isveE~laifL~~la~---~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.+++-+|..--|..++. +.+...++...+++++|++|+++...+.
T Consensus 20 ~~~sl~r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~ 67 (271)
T PRK10163 20 GAQALERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAA 67 (271)
T ss_pred cchHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 46666666666666764 3578999999999999999988866554
No 336
>KOG1567 consensus Ribonucleotide reductase, beta subunit [Nucleotide transport and metabolism]
Probab=28.27 E-value=59 Score=29.52 Aligned_cols=39 Identities=18% Similarity=0.125 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCcccccceeccccHHHHH
Q 046385 11 KIGVRRILRKQLIMLVKKLLKGSTKRQRVSTSSLTGSLYI 50 (218)
Q Consensus 11 ~~~~~~~~~~~~~~~v~~~~~~~~~r~~~~ts~l~G~~~v 50 (218)
.||||.-|-+|+|.+||..++..-....|++.. .-..|+
T Consensus 267 liGMN~~lM~qYIEFVADrLL~~lG~~K~Yn~~-NPFdfM 305 (344)
T KOG1567|consen 267 LIGMNCDLMSQYIEFVADRLLVELGNEKYYNAE-NPFDFM 305 (344)
T ss_pred hhccCHHHHHHHHHHHHHHHHHHhCccceecCC-CchHHH
Confidence 589999999999999999999765554444432 334444
No 337
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=28.12 E-value=33 Score=28.47 Aligned_cols=29 Identities=14% Similarity=0.119 Sum_probs=24.9
Q ss_pred HHHHhc---CccchhhhhcccccccchhHHHH
Q 046385 101 LFTISH---NLRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 101 L~~la~---~~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
|..++. |.+++.|+...++|..||.+|+.
T Consensus 168 l~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~ 199 (225)
T PRK10046 168 RKLFKEPGVQHTAETVAQALTISRTTARRYLE 199 (225)
T ss_pred HHHHHcCCCCcCHHHHHHHhCccHHHHHHHHH
Confidence 555666 47999999999999999999985
No 338
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=27.98 E-value=64 Score=21.49 Aligned_cols=31 Identities=19% Similarity=0.249 Sum_probs=27.6
Q ss_pred CccchHHHHHHHHHHHHhcCccchhhhhccc
Q 046385 88 SKHLTVEEKMAMFLFTISHNLRNRFIKIRFQ 118 (218)
Q Consensus 88 T~~isveE~laifL~~la~~~s~r~i~~~F~ 118 (218)
++.++..-++||+|-.--.|.|+.+++..|+
T Consensus 26 ~~~~~~aR~iamyla~~~~~~sl~~Ig~~fg 56 (60)
T smart00760 26 KREIVLARQIAMYLARELTDLSLPEIGKIFG 56 (60)
T ss_pred CcchhHHHHHHHHHHHHHHCCCHHHHHHHhC
Confidence 4578888999999998889999999999997
No 339
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=27.92 E-value=71 Score=27.50 Aligned_cols=40 Identities=10% Similarity=0.137 Sum_probs=29.0
Q ss_pred HHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 96 KMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 96 ~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
+|-+|+ .++...|++.++..-++|.+|||+.+++.=+.+-
T Consensus 9 ~L~~f~-~v~~~gs~s~AA~~L~isQ~avS~~i~~LE~~lG 48 (302)
T PRK09791 9 QIRAFV-EVARQGSIRGASRMLNMSQPALTKSIQELEEGLA 48 (302)
T ss_pred HHHHHH-HHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhC
Confidence 344444 4445559999999999999999988777655443
No 340
>PRK10870 transcriptional repressor MprA; Provisional
Probab=27.86 E-value=48 Score=27.16 Aligned_cols=27 Identities=11% Similarity=0.085 Sum_probs=23.2
Q ss_pred ccchhhhhcccccccchhHHHHHHHHH
Q 046385 108 LRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 108 ~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.+..+++..++++++||++.+++-.+.
T Consensus 72 it~~eLa~~l~l~~~tvsr~v~rLe~k 98 (176)
T PRK10870 72 IQPSELSCALGSSRTNATRIADELEKR 98 (176)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 566899999999999999998876554
No 341
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=27.73 E-value=67 Score=26.40 Aligned_cols=27 Identities=7% Similarity=-0.107 Sum_probs=22.0
Q ss_pred Cccchhhhhccccc-ccchhHHHHHHHH
Q 046385 107 NLRNRFIKIRFQHS-GHTVHRYFHEVLS 133 (218)
Q Consensus 107 ~~s~r~i~~~F~~S-~sTVsr~f~eVl~ 133 (218)
..+.+.++..+++| .+||++++..--+
T Consensus 25 ~~~~~ela~~~~~~s~~tv~~~l~~L~~ 52 (199)
T TIGR00498 25 PPSIREIARAVGLRSPSAAEEHLKALER 52 (199)
T ss_pred CCcHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 46788999999998 9999988765433
No 342
>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=27.71 E-value=37 Score=26.01 Aligned_cols=35 Identities=14% Similarity=0.205 Sum_probs=27.4
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVH 125 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVs 125 (218)
.+|...|-++.|+ .=.|.|+..|+...|+|.+||.
T Consensus 107 ~Lp~~~r~v~~l~-~~~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 107 ILPNKQKKIIYMK-FFEDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHhhc
Confidence 4566666666664 4567899999999999999985
No 343
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=27.57 E-value=36 Score=23.48 Aligned_cols=37 Identities=19% Similarity=0.193 Sum_probs=26.3
Q ss_pred HHHHHHHHHHhcCccchhhhhcccccccchhHHHHHH
Q 046385 95 EKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEV 131 (218)
Q Consensus 95 E~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eV 131 (218)
|++.-||-...++.+=+++++.+++|..|+.++....
T Consensus 3 e~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~L 39 (62)
T PF04703_consen 3 EKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKL 39 (62)
T ss_dssp HCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 3445556666677788999999999999998776643
No 344
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=27.53 E-value=78 Score=22.80 Aligned_cols=24 Identities=17% Similarity=0.196 Sum_probs=21.4
Q ss_pred hhhhhcccccccchhHHHHHHHHH
Q 046385 111 RFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 111 r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
..++...+++++||++.++...+.
T Consensus 40 ~~la~~l~i~~~~vt~~l~~Le~~ 63 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRLEDK 63 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHC
Confidence 899999999999999998876654
No 345
>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=27.42 E-value=26 Score=24.25 Aligned_cols=23 Identities=22% Similarity=0.096 Sum_probs=17.5
Q ss_pred ccchhhhhccccc-ccchhHHHHH
Q 046385 108 LRNRFIKIRFQHS-GHTVHRYFHE 130 (218)
Q Consensus 108 ~s~r~i~~~F~~S-~sTVsr~f~e 130 (218)
-|.|.++..||++ .+||++++..
T Consensus 26 Pt~rEIa~~~g~~S~~tv~~~L~~ 49 (65)
T PF01726_consen 26 PTVREIAEALGLKSTSTVQRHLKA 49 (65)
T ss_dssp --HHHHHHHHTSSSHHHHHHHHHH
T ss_pred CCHHHHHHHhCCCChHHHHHHHHH
Confidence 4679999999986 8888877654
No 346
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=27.35 E-value=55 Score=28.04 Aligned_cols=38 Identities=5% Similarity=0.047 Sum_probs=27.6
Q ss_pred HHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHH
Q 046385 97 MAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAM 135 (218)
Q Consensus 97 laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI 135 (218)
|-.| ..++...|+..++...++|++|||+.+++.=+.+
T Consensus 7 L~~f-~~v~~~gs~t~AA~~L~iSQ~avS~~i~~LE~~l 44 (294)
T PRK13348 7 LEAL-AAVVETGSFERAARRLHVTPSAVSQRIKALEESL 44 (294)
T ss_pred HHHH-HHHHHcCCHHHHHHHhCCCchHHHHHHHHHHHHh
Confidence 3344 4445556999999999999999998877654443
No 347
>PRK13503 transcriptional activator RhaS; Provisional
Probab=26.80 E-value=1.9e+02 Score=24.55 Aligned_cols=27 Identities=19% Similarity=0.235 Sum_probs=23.9
Q ss_pred hcCccchhhhhcccccccchhHHHHHH
Q 046385 105 SHNLRNRFIKIRFQHSGHTVHRYFHEV 131 (218)
Q Consensus 105 a~~~s~r~i~~~F~~S~sTVsr~f~eV 131 (218)
....+..+++..+++|.++.+|.|+++
T Consensus 185 ~~~~tl~~lA~~~~lS~~~l~r~Fk~~ 211 (278)
T PRK13503 185 AEEVNWEALADQFSLSLRTLHRQLKQQ 211 (278)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 455677899999999999999999987
No 348
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=26.78 E-value=20 Score=23.66 Aligned_cols=26 Identities=12% Similarity=0.149 Sum_probs=17.7
Q ss_pred hcCccchhhhhcccccccchhHHHHH
Q 046385 105 SHNLRNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 105 a~~~s~r~i~~~F~~S~sTVsr~f~e 130 (218)
..|-+...++..-|+|.+|++++++.
T Consensus 8 ~~~it~~~La~~~gis~~tl~~~~~~ 33 (63)
T PF13443_consen 8 ERGITQKDLARKTGISRSTLSRILNG 33 (63)
T ss_dssp HTT--HHHHHHHHT--HHHHHHHHTT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 45667788888999999999988764
No 349
>PRK11569 transcriptional repressor IclR; Provisional
Probab=26.73 E-value=84 Score=27.39 Aligned_cols=46 Identities=11% Similarity=0.045 Sum_probs=34.0
Q ss_pred ccchHHHHHHHHHHHHhc---CccchhhhhcccccccchhHHHHHHHHH
Q 046385 89 KHLTVEEKMAMFLFTISH---NLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 89 ~~isveE~laifL~~la~---~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
..+.+-++..--|..++. +.+..+++..-+.+++|++|+++...+.
T Consensus 22 ~~v~sl~ral~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~ 70 (274)
T PRK11569 22 GQVQSLTRGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQ 70 (274)
T ss_pred cCccHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 345555665556666654 3688999999999999999988876544
No 350
>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=26.47 E-value=81 Score=26.91 Aligned_cols=44 Identities=5% Similarity=0.004 Sum_probs=31.5
Q ss_pred chHHHHHHHHHHHHhc---CccchhhhhcccccccchhHHHHHHHHH
Q 046385 91 LTVEEKMAMFLFTISH---NLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 91 isveE~laifL~~la~---~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
+.+-+|..--|..++. +.+..+++..-+.+++|++|+.....+.
T Consensus 5 v~sl~ral~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~ 51 (248)
T TIGR02431 5 VASLARGLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVEL 51 (248)
T ss_pred HHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4444555555555553 4678999999999999999988876544
No 351
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=26.46 E-value=57 Score=26.71 Aligned_cols=37 Identities=16% Similarity=0.108 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHhcCccchhhhhccc-ccccchhHHHHH
Q 046385 94 EEKMAMFLFTISHNLRNRFIKIRFQ-HSGHTVHRYFHE 130 (218)
Q Consensus 94 eE~laifL~~la~~~s~r~i~~~F~-~S~sTVsr~f~e 130 (218)
+|++...--..+.|.|..+|+..+| +|++.|--++|.
T Consensus 5 de~~~~L~~lw~~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 5 DERVERLRKLWAEGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 4566655556689999999999999 999998877776
No 352
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.29 E-value=76 Score=23.87 Aligned_cols=27 Identities=19% Similarity=0.002 Sum_probs=24.1
Q ss_pred HHHhcCccchhhhhcccccccchhHHH
Q 046385 102 FTISHNLRNRFIKIRFQHSGHTVHRYF 128 (218)
Q Consensus 102 ~~la~~~s~r~i~~~F~~S~sTVsr~f 128 (218)
.+|-.|..|++|...-|.|..||||.-
T Consensus 51 ~mL~eg~tY~~I~~eTGaStaTIsRVk 77 (100)
T COG4496 51 KMLKEGRTYRDIEDETGASTATISRVK 77 (100)
T ss_pred HHHHcCCCcchhhhccCcchhhHHHHH
Confidence 567789999999999999999999864
No 353
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=26.28 E-value=79 Score=27.36 Aligned_cols=39 Identities=8% Similarity=-0.034 Sum_probs=28.5
Q ss_pred HHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHH
Q 046385 97 MAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 97 laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~ 136 (218)
+-+|+. ++...|+..++...++|.++||+.+++.=+.+.
T Consensus 10 L~~f~~-v~e~gs~s~AA~~L~isqpavS~~i~~LE~~lg 48 (305)
T CHL00180 10 LRILKA-IATEGSFKKAAESLYISQPAVSLQIKNLEKQLN 48 (305)
T ss_pred HHHHHH-HHHcCCHHHHHHHhcCCChHHHHHHHHHHHHhC
Confidence 444444 444558999999999999999988877655543
No 354
>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=25.93 E-value=27 Score=25.49 Aligned_cols=24 Identities=17% Similarity=0.063 Sum_probs=17.6
Q ss_pred cCccchhhhhcccccccchhHHHH
Q 046385 106 HNLRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 106 ~~~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
.|.+...|+.+.|.|.+.||++..
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~l~ 25 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSRSWVSNHLA 25 (93)
T ss_dssp TT--HHHHHHHTT--HHHHHHHHG
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 578899999999999999998753
No 355
>PHA01976 helix-turn-helix protein
Probab=25.86 E-value=29 Score=23.19 Aligned_cols=26 Identities=4% Similarity=-0.120 Sum_probs=22.1
Q ss_pred HhcCccchhhhhcccccccchhHHHH
Q 046385 104 ISHNLRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 104 la~~~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
-..|.+..+++...++|.+||+++-+
T Consensus 12 ~~~glt~~~lA~~~gvs~~~v~~~e~ 37 (67)
T PHA01976 12 NARAWSAPELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 45678889999999999999998754
No 356
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=25.86 E-value=76 Score=22.89 Aligned_cols=27 Identities=15% Similarity=0.189 Sum_probs=22.4
Q ss_pred HHhcCccchhhhhccc------ccccchhHHHH
Q 046385 103 TISHNLRNRFIKIRFQ------HSGHTVHRYFH 129 (218)
Q Consensus 103 ~la~~~s~r~i~~~F~------~S~sTVsr~f~ 129 (218)
-..-|.++.+++...+ +|++||||+-.
T Consensus 20 R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 20 RIKLGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HHHcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 3566888999999999 59999999754
No 357
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=25.72 E-value=1.1e+02 Score=28.25 Aligned_cols=49 Identities=8% Similarity=0.030 Sum_probs=33.6
Q ss_pred CCccchHHHHHHHHHHHHhcC---ccchhhhhcccccccchhHHHHHHHHHH
Q 046385 87 DSKHLTVEEKMAMFLFTISHN---LRNRFIKIRFQHSGHTVHRYFHEVLSAM 135 (218)
Q Consensus 87 ~T~~isveE~laifL~~la~~---~s~r~i~~~F~~S~sTVsr~f~eVl~AI 135 (218)
.....+.+||...-+..|-.. .+..++++.+.+|++|+.+-++++=..+
T Consensus 7 ~~~~~s~~ER~~~il~~LL~~~~~v~l~~Lae~l~VSrsTi~~DLk~l~~~L 58 (426)
T PRK11564 7 PPSVLSAPQRRCQILLMLFQPGLTVTLETFSQLNGVDDDTARQDIAETGREI 58 (426)
T ss_pred CCcCCCHHHHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 334567777765444433232 4558999999999999999877775544
No 358
>PF13305 WHG: WHG domain; PDB: 1ZK8_B 3ON2_B 3CJD_B.
Probab=25.65 E-value=1.5e+02 Score=19.84 Aligned_cols=15 Identities=27% Similarity=0.530 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHhcCc
Q 046385 94 EEKMAMFLFTISHNL 108 (218)
Q Consensus 94 eE~laifL~~la~~~ 108 (218)
-..++..+|...||.
T Consensus 58 ~~~~~~~~wa~~HG~ 72 (81)
T PF13305_consen 58 AREIALALWAAVHGL 72 (81)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 345777888877773
No 359
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=25.36 E-value=65 Score=27.54 Aligned_cols=38 Identities=5% Similarity=0.025 Sum_probs=27.1
Q ss_pred HHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHH
Q 046385 97 MAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAM 135 (218)
Q Consensus 97 laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI 135 (218)
+-.|+ .++...|++.++...++|.+|||+.+++.=+-+
T Consensus 6 l~~f~-~v~~~~s~t~AA~~L~isQpavS~~I~~LE~~l 43 (292)
T TIGR03298 6 LAALA-AVVEEGSFERAAAALSVTPSAVSQRIKALEERL 43 (292)
T ss_pred HHHHH-HHHHcCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 33444 344455899999999999999998877654443
No 360
>PF04034 DUF367: Domain of unknown function (DUF367); InterPro: IPR007177 This domain is found in a family of proteins of unknown function. It appears to be found in eukaryotes and archaebacteria, and occurs associated with a potential metal-binding region in RNase L inhibitor, RLI (IPR007209 from INTERPRO).
Probab=25.25 E-value=65 Score=25.57 Aligned_cols=44 Identities=18% Similarity=0.262 Sum_probs=35.9
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHH
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.+|.-|.+|-+||++|-...-..+-..|..+.+-+ ...++.|++
T Consensus 65 kLscvEAlAAaLyI~G~~~~A~~lL~~FkWG~~F~-~LN~elLe~ 108 (127)
T PF04034_consen 65 KLSCVEALAAALYILGFKEQAEELLSKFKWGHTFL-ELNKELLEA 108 (127)
T ss_pred cccHHHHHHHHHHHcCCHHHHHHHHhcCCCcHHHH-HHHHHHHHH
Confidence 68999999999999999999999999998876443 555555554
No 361
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=25.14 E-value=1.1e+02 Score=23.75 Aligned_cols=47 Identities=15% Similarity=0.096 Sum_probs=35.5
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
.++.|++-.+-+++.++ -+...++..+++|=.||-.-+++++++|--
T Consensus 33 ~L~~E~~~Fi~~Fi~~r-GnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 33 RLSPEQLEFIKLFIKNR-GNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred cCCHHHHHHHHHHHHhc-CCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 45556654444444444 478999999999999999999999998753
No 362
>PF12162 STAT1_TAZ2bind: STAT1 TAZ2 binding domain; InterPro: IPR022752 This entry represents the C-terminal domain of STAT1, which selectively binds the TAZ2 domain of CRB (CREB-binding protein) []. This group of eukaryotic proteins is approximately 20 amino acids in length, and is found in association with PF02865 from PFAM, PF00017 from PFAM, PF01017 from PFAM, PF02864 from PFAM. By binding to CRB, it becomes a transcriptional activator and can initiate transcription of certain genes. ; GO: 0003700 sequence-specific DNA binding transcription factor activity; PDB: 2KA6_B.
Probab=24.89 E-value=67 Score=17.98 Aligned_cols=17 Identities=18% Similarity=0.429 Sum_probs=10.9
Q ss_pred hccccCHHHHHHHHHHH
Q 046385 63 DLMRMDKNGFISLCQLF 79 (218)
Q Consensus 63 ~~fRM~~~~F~~L~~~L 79 (218)
+++=||++.|..|...+
T Consensus 6 nmmPMSPddy~~l~~~V 22 (23)
T PF12162_consen 6 NMMPMSPDDYDELERMV 22 (23)
T ss_dssp S---S-HHHHHHHHHHH
T ss_pred cccCCCHHHHHHHHHhh
Confidence 57789999999998764
No 363
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=24.69 E-value=83 Score=27.33 Aligned_cols=40 Identities=10% Similarity=0.159 Sum_probs=27.0
Q ss_pred HHHHHHHHHHhcCc--cchhhhhcccccccchhHHHHHHHHH
Q 046385 95 EKMAMFLFTISHNL--RNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 95 E~laifL~~la~~~--s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
||..--|.+|.... +..+++..|++|.+||.|-+.+.-+.
T Consensus 5 ~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~ 46 (252)
T PRK10906 5 QRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQ 46 (252)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 44444444444443 44678999999999999987765553
No 364
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=24.63 E-value=82 Score=27.71 Aligned_cols=35 Identities=3% Similarity=0.056 Sum_probs=25.5
Q ss_pred HHHHHHHHHhcCccchhhhhcccccccchhHHHHHH
Q 046385 96 KMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEV 131 (218)
Q Consensus 96 ~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eV 131 (218)
+|-.|+-..-+| |++.++...++|.+|||+.+++.
T Consensus 6 ~L~~f~av~~~g-s~s~AA~~L~iSqpaVS~~Ik~L 40 (317)
T PRK15421 6 HLKTLQALRNCG-SLAAAAATLHQTQSALSHQFSDL 40 (317)
T ss_pred HHHHHHHHHHcC-CHHHHHHHhCCCHHHHHHHHHHH
Confidence 355555555555 88999999999999999766544
No 365
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=24.03 E-value=52 Score=30.01 Aligned_cols=65 Identities=23% Similarity=0.262 Sum_probs=42.9
Q ss_pred HHHhcCccchhhhhcccccccchhHHHHHHHHH-HHhhhhhhcCCCCCCCC--cccccCcccccCCCCCccccC
Q 046385 102 FTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSA-MMKFSKEMITPPSFTDN--SRGIRNTRLRQIFKRSPVVPL 172 (218)
Q Consensus 102 ~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~A-I~~L~~~~Ik~P~~~~~--~~~i~n~~~~p~Fk~ci~vp~ 172 (218)
.+.-.|.+.++|+.+.++|+.||||.+.+--+- |+++ .|+.|..... .+.+. .+|. -+.|+.||+
T Consensus 21 lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I---~i~~~~~~~~~Le~~L~-~~fg--L~~a~VVp~ 88 (321)
T COG2390 21 LYYVEGLTQSEIAERLGISRATVSRLLAKAREEGIVKI---SINSPVEGCLELEQQLK-ERFG--LKEAIVVPS 88 (321)
T ss_pred HHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEE---EeCCCCcchHHHHHHHH-HhcC--CCeEEEEcC
Confidence 356789999999999999999999998865443 3332 3443332211 12222 3554 788998884
No 366
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=23.97 E-value=1e+02 Score=26.13 Aligned_cols=37 Identities=16% Similarity=0.099 Sum_probs=25.1
Q ss_pred HHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHH
Q 046385 96 KMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLS 133 (218)
Q Consensus 96 ~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~ 133 (218)
++-+|+-..-+ .|+..++...++|.+|||+.+++.=+
T Consensus 11 ~l~~f~~v~~~-gs~t~AA~~L~itq~avS~~i~~LE~ 47 (294)
T PRK09986 11 LLRYFLAVAEE-LHFGRAAARLNISQPPLSIHIKELED 47 (294)
T ss_pred HHHHHHHHHHh-cCHHHHHHHhCCCCCHHHHHHHHHHH
Confidence 44455554444 48888888888888888876655433
No 367
>PF13972 TetR: Bacterial transcriptional repressor; PDB: 3RH2_A 3NNR_A.
Probab=23.59 E-value=1.9e+02 Score=22.38 Aligned_cols=76 Identities=16% Similarity=0.022 Sum_probs=46.2
Q ss_pred ccchhccccCHHHHHHHHHHHHhcCccCCCccchHHHHHHHHHHHHhcCcc-chhhhhccc-ccccchhHHHHHHHHHHH
Q 046385 59 IFCYDLMRMDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHNLR-NRFIKIRFQ-HSGHTVHRYFHEVLSAMM 136 (218)
Q Consensus 59 ~~~~~~fRM~~~~F~~L~~~L~~~~~~~~T~~isveE~laifL~~la~~~s-~r~i~~~F~-~S~sTVsr~f~eVl~AI~ 136 (218)
..+.+....-...+..+++.|...+.++.+ -.--+.|+-.+|.+++..- +..+...=. ...+++.+.+..|+..+.
T Consensus 57 ~~~~~~~~~~~~~~~~l~~~l~~~g~l~~~--~~~~~~La~~i~lv~t~Wl~~~~~~~~~~~~~~~~~~~gv~qv~~L~~ 134 (146)
T PF13972_consen 57 KRYRQLQQRRREQLRQLLQSLIEAGILRID--DEELQALADNIWLVSTFWLSFLETQHPRDKLTEEDIRRGVYQVLSLLR 134 (146)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHTTSB-----GHHHHHHHHHHHHHHHCHHHHHHHHSS-----HHCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCC--HHHHHHHHHHHHHHHHHHHhHHHHhCccccchHHHHHHHHHHHHHHHH
Confidence 455566667788889999999988766633 2233378888898888743 333332222 556677777766666554
No 368
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=23.59 E-value=54 Score=25.89 Aligned_cols=33 Identities=18% Similarity=0.056 Sum_probs=26.8
Q ss_pred HHHHHHHHhcCccchhhhhcccccccchhHHHH
Q 046385 97 MAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 97 laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~ 129 (218)
..+|...--++.|.++|+..-|+|+.|+.+||.
T Consensus 18 ~~lf~~~G~~~~s~~~IA~~agvsk~~ly~~F~ 50 (189)
T TIGR03384 18 IESIGERGSLDVTIAQIARRAGVSSGIISHYFG 50 (189)
T ss_pred HHHHHhcCcccCCHHHHHHHhCCCHHHHHHHcC
Confidence 344555555778999999999999999999984
No 369
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.53 E-value=1.7e+02 Score=25.64 Aligned_cols=72 Identities=11% Similarity=0.089 Sum_probs=49.1
Q ss_pred cchhccccCHHHHHHHHHHHHhcCccCCC----------ccchH----------HHHHHHHHHHHhcC-ccchhhhhccc
Q 046385 60 FCYDLMRMDKNGFISLCQLFKEKGWLSDS----------KHLTV----------EEKMAMFLFTISHN-LRNRFIKIRFQ 118 (218)
Q Consensus 60 ~~~~~fRM~~~~F~~L~~~L~~~~~~~~T----------~~isv----------eE~laifL~~la~~-~s~r~i~~~F~ 118 (218)
+...++-|.++|-..-+..|......... ..++- +.+-+|+..+.-.+ ...+.++..-+
T Consensus 120 El~~nl~i~R~TlRyhlriLe~~~li~a~~~~g~~~yfpa~~t~~~~e~~~Lkn~~~k~I~~eiq~~~~~t~~~ia~~l~ 199 (240)
T COG3398 120 ELRANLYINRSTLRYHLRILESNPLIEAGRVGGALRYFPADMTYGEAEVLSLKNETSKAIIYEIQENKCNTNLLIAYELN 199 (240)
T ss_pred HHHHhcCCChHHHHHHHHHHHhCcchhhhccCCceEEccCCCCcccchHHHhhchhHHHHHHHHhcCCcchHHHHHHHcC
Confidence 34467889999999999998865432211 02221 22356777777555 77899999999
Q ss_pred ccccchhHHHHHH
Q 046385 119 HSGHTVHRYFHEV 131 (218)
Q Consensus 119 ~S~sTVsr~f~eV 131 (218)
.|..||+=+..+.
T Consensus 200 ls~aTV~~~lk~l 212 (240)
T COG3398 200 LSVATVAYHLKKL 212 (240)
T ss_pred ccHHHHHHHHHHH
Confidence 9999998776643
No 370
>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=23.41 E-value=42 Score=22.48 Aligned_cols=45 Identities=22% Similarity=0.206 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHhcCccCCCccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHH
Q 046385 70 NGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEV 131 (218)
Q Consensus 70 ~~F~~L~~~L~~~~~~~~T~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eV 131 (218)
..+..|.+.|.... ++....+|.+ +.++..|++|..||.+-++..
T Consensus 4 ~i~~~l~~~I~~g~-~~~g~~lps~----------------~~la~~~~vsr~tvr~al~~L 48 (64)
T PF00392_consen 4 QIYDQLRQAILSGR-LPPGDRLPSE----------------RELAERYGVSRTTVREALRRL 48 (64)
T ss_dssp HHHHHHHHHHHTTS-S-TTSBE--H----------------HHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCC-CCCCCEeCCH----------------HHHHHHhccCCcHHHHHHHHH
Confidence 34555666665443 2333344444 456788999999996655543
No 371
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=23.13 E-value=92 Score=26.38 Aligned_cols=36 Identities=6% Similarity=0.042 Sum_probs=25.9
Q ss_pred HHHHHhcCccchhhhhcccccccchhHHHHHHHHHH
Q 046385 100 FLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAM 135 (218)
Q Consensus 100 fL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI 135 (218)
.+..++...+++.++..-++|++|||+.+++.=+.+
T Consensus 10 ~f~~v~e~~s~t~AA~~L~isqpavS~~I~~LE~~l 45 (290)
T PRK10837 10 VFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQL 45 (290)
T ss_pred HHHHHHHcCCHHHHHHHhCCCccHHHHHHHHHHHHh
Confidence 344455566889999999999999998776654433
No 372
>PF14393 DUF4422: Domain of unknown function (DUF4422)
Probab=22.95 E-value=79 Score=27.48 Aligned_cols=32 Identities=22% Similarity=0.597 Sum_probs=27.3
Q ss_pred HHHHHhCCcccchhccccCHHHHHHHHHHHHh
Q 046385 50 IQELLNGSPIFCYDLMRMDKNGFISLCQLFKE 81 (218)
Q Consensus 50 v~ell~~~~~~~~~~fRM~~~~F~~L~~~L~~ 81 (218)
.++++.++...+.+||=|.++.|.+-|+.|=+
T Consensus 156 ~~~~~~~~~~~~~NMfImkkelF~~Yc~wLF~ 187 (231)
T PF14393_consen 156 FDKVMNGTSAYFYNMFIMKKELFDEYCEWLFD 187 (231)
T ss_pred HHHHHhCCCceeeeeeEcchHHHHHHHHHHHH
Confidence 45677788899999999999999999988753
No 373
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=22.82 E-value=2.4e+02 Score=24.51 Aligned_cols=74 Identities=16% Similarity=0.225 Sum_probs=54.1
Q ss_pred chhccccCHHHHHHHHHHHHhc-CccCCCc-------cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHH
Q 046385 61 CYDLMRMDKNGFISLCQLFKEK-GWLSDSK-------HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVL 132 (218)
Q Consensus 61 ~~~~fRM~~~~F~~L~~~L~~~-~~~~~T~-------~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl 132 (218)
.--.|..|+.|..+.+..++.+ +..-+|+ +--...+.++-+| =.|-...+++-+-.||.+.|.|++..+.
T Consensus 111 la~LL~~S~~TI~~~i~~yq~e~g~vvPtrG~i~DiGp~~tHK~~ii~~~--l~g~~~~eiar~t~HS~~av~rYi~~F~ 188 (220)
T PF07900_consen 111 LAMLLGISPRTISKDIKEYQKEHGVVVPTRGTIHDIGPGVTHKKIIIRLY--LKGKPTPEIARRTNHSPEAVDRYIKDFK 188 (220)
T ss_pred HHHHHCCCHHHHHHHHHHHHHHcCceeccCCcccccCCcchHHHHHHHHH--HcCCCHHHHHHHhccCHHHHHHHHHhhH
Confidence 3356789999999999999876 4444442 2223344444443 3378899999999999999999999988
Q ss_pred HHHH
Q 046385 133 SAMM 136 (218)
Q Consensus 133 ~AI~ 136 (218)
.+.+
T Consensus 189 rV~~ 192 (220)
T PF07900_consen 189 RVLM 192 (220)
T ss_pred HhHH
Confidence 8865
No 374
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. 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, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=22.77 E-value=36 Score=23.28 Aligned_cols=24 Identities=25% Similarity=0.303 Sum_probs=13.9
Q ss_pred ccchhhhhcc-----cccccchhHHHHHH
Q 046385 108 LRNRFIKIRF-----QHSGHTVHRYFHEV 131 (218)
Q Consensus 108 ~s~r~i~~~F-----~~S~sTVsr~f~eV 131 (218)
.+.++++..+ .+|.+||.+.+++.
T Consensus 14 ~s~~~i~~~l~~~~~~vS~~TI~r~L~~~ 42 (72)
T PF01498_consen 14 ISAREIAQELQEAGISVSKSTIRRRLREA 42 (72)
T ss_dssp --HHHHHHHT---T--S-HHHHHHHHHHT
T ss_pred CCHHHHHHHHHHccCCcCHHHHHHHHHHc
Confidence 3445555544 88889998888763
No 375
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=22.64 E-value=77 Score=27.36 Aligned_cols=37 Identities=3% Similarity=-0.035 Sum_probs=26.4
Q ss_pred HHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHH
Q 046385 96 KMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLS 133 (218)
Q Consensus 96 ~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~ 133 (218)
+|-+| ..++...|++.++...++|++|||+.+.+.=+
T Consensus 6 ~L~~f-~~v~e~~s~s~AA~~L~isQpavS~~I~~LE~ 42 (300)
T PRK11074 6 SLEVV-DAVARTGSFSAAAQELHRVPSAVSYTVRQLEE 42 (300)
T ss_pred HHHHH-HHHHHhCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34344 44555569999999999999999987665433
No 376
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=22.60 E-value=1.1e+02 Score=26.17 Aligned_cols=47 Identities=15% Similarity=0.147 Sum_probs=34.5
Q ss_pred CccchHHHHHHHHHHHHhcC--ccchhhhhcccccccchhHHHHHHHHH
Q 046385 88 SKHLTVEEKMAMFLFTISHN--LRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 88 T~~isveE~laifL~~la~~--~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
...+++-++..--|..++.. .+...++..-+.+++|++|+++..++.
T Consensus 7 ~~~v~sl~r~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~ 55 (257)
T PRK15090 7 PDSVSSVLKVFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTL 55 (257)
T ss_pred ccccHHHHHHHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34566666666666666544 467899999999999999988765543
No 377
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=22.47 E-value=95 Score=22.70 Aligned_cols=23 Identities=17% Similarity=0.167 Sum_probs=17.2
Q ss_pred cchhhhhcccccccchhHHHHHH
Q 046385 109 RNRFIKIRFQHSGHTVHRYFHEV 131 (218)
Q Consensus 109 s~r~i~~~F~~S~sTVsr~f~eV 131 (218)
+..+++..+++|..+.+|.|++.
T Consensus 23 ~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 23 NIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Confidence 44556777888888888888876
No 378
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=22.36 E-value=96 Score=26.79 Aligned_cols=29 Identities=10% Similarity=0.009 Sum_probs=20.6
Q ss_pred HHhcCccchhhhhcccccccchhHHHHHH
Q 046385 103 TISHNLRNRFIKIRFQHSGHTVHRYFHEV 131 (218)
Q Consensus 103 ~la~~~s~r~i~~~F~~S~sTVsr~f~eV 131 (218)
.++...|++.++...++|.+|||+.+.+.
T Consensus 21 av~e~gS~t~AA~~L~iSQpavS~~I~~L 49 (303)
T PRK10082 21 TLEKCRNFSQAAVSRNVSQPAFSRRIRAL 49 (303)
T ss_pred HHHhcCCHHHHHHHhCCChHHHHHHHHHH
Confidence 34445578888888888888888655443
No 379
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=22.26 E-value=1.6e+02 Score=19.97 Aligned_cols=64 Identities=11% Similarity=-0.051 Sum_probs=31.2
Q ss_pred chhccccCHHHHHHHHHHHHhcCccCCCccchHHHHHHHHHH----HHhcCccchhhhhcccccccch
Q 046385 61 CYDLMRMDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLF----TISHNLRNRFIKIRFQHSGHTV 124 (218)
Q Consensus 61 ~~~~fRM~~~~F~~L~~~L~~~~~~~~T~~isveE~laifL~----~la~~~s~r~i~~~F~~S~sTV 124 (218)
+.+.+.++.++-..=.++++.-....-...-+++--.|-.|| ..+..-+.+++++..++|..||
T Consensus 4 ~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 4 ICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred HHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 344555665544443333332111111122223333344444 4566677789999999888775
No 380
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=22.08 E-value=1.2e+02 Score=26.17 Aligned_cols=50 Identities=22% Similarity=0.213 Sum_probs=32.2
Q ss_pred cCHHHHHHHHHHHHhcCccCCCccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385 67 MDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK 137 (218)
Q Consensus 67 M~~~~F~~L~~~L~~~~~~~~T~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~ 137 (218)
....+...|-+.+.... ++....+|.| |.++..||+|++|| +|.+.++-.
T Consensus 11 l~~~v~~~i~~~I~~g~-~~~G~~LP~E----------------reLae~fgVSR~~v----REAl~~L~a 60 (241)
T COG2186 11 LADEVAEQIGALIVSGE-LPPGDRLPSE----------------RELAERFGVSRTVV----REALKRLEA 60 (241)
T ss_pred hHHHHHHHHHHHHHcCC-CCCCCCCCCH----------------HHHHHHHCCCcHHH----HHHHHHHHH
Confidence 44555666666665444 4444455555 46778999999988 677766653
No 381
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=22.04 E-value=1e+02 Score=25.85 Aligned_cols=31 Identities=16% Similarity=0.180 Sum_probs=25.4
Q ss_pred cCccchhhhhcccccccchhHHHH---HHHHHHH
Q 046385 106 HNLRNRFIKIRFQHSGHTVHRYFH---EVLSAMM 136 (218)
Q Consensus 106 ~~~s~r~i~~~F~~S~sTVsr~f~---eVl~AI~ 136 (218)
.+.|.|.++.+-|+|+.|+.+||. +.+.+++
T Consensus 23 ~~lsmr~lA~~lgv~~~slY~hf~~K~~Ll~~~~ 56 (205)
T PRK13756 23 EGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALA 56 (205)
T ss_pred ccCCHHHHHHHhCCCchHHHHHcCCHHHHHHHHH
Confidence 357899999999999999999985 4555555
No 382
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=21.92 E-value=2.1e+02 Score=24.57 Aligned_cols=29 Identities=10% Similarity=0.139 Sum_probs=24.7
Q ss_pred HhcCccchhhhhcccccccchhHHHHHHH
Q 046385 104 ISHNLRNRFIKIRFQHSGHTVHRYFHEVL 132 (218)
Q Consensus 104 la~~~s~r~i~~~F~~S~sTVsr~f~eVl 132 (218)
++...+..+++..+++|.++.+|.|++.+
T Consensus 196 ~~~~isl~~lA~~~~lS~~~l~r~Fk~~~ 224 (290)
T PRK10572 196 LASEFDIESVAQHVCLSPSRLAHLFRQQL 224 (290)
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 34556778999999999999999999973
No 383
>PF12728 HTH_17: Helix-turn-helix domain
Probab=21.86 E-value=34 Score=21.69 Aligned_cols=21 Identities=19% Similarity=0.069 Sum_probs=16.7
Q ss_pred cchhhhhcccccccchhHHHH
Q 046385 109 RNRFIKIRFQHSGHTVHRYFH 129 (218)
Q Consensus 109 s~r~i~~~F~~S~sTVsr~f~ 129 (218)
+..+++..+++|.+||.+.++
T Consensus 3 t~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 346788889999999987774
No 384
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=21.84 E-value=93 Score=27.07 Aligned_cols=34 Identities=6% Similarity=-0.077 Sum_probs=25.5
Q ss_pred HHHHHHhcCccchhhhhcccccccchhHHHHHHH
Q 046385 99 MFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVL 132 (218)
Q Consensus 99 ifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl 132 (218)
-.+..++...|++.++...++|.+|||+.+.+.=
T Consensus 28 ~~f~avae~gs~s~AA~~L~isQpavS~~I~~LE 61 (314)
T PRK09508 28 TVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLK 61 (314)
T ss_pred HHHHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3445556666799999999999999998766543
No 385
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=21.31 E-value=1.3e+02 Score=25.15 Aligned_cols=44 Identities=16% Similarity=0.189 Sum_probs=27.5
Q ss_pred HHHHHHHHHhcCccCCCccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHH
Q 046385 72 FISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVL 132 (218)
Q Consensus 72 F~~L~~~L~~~~~~~~T~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl 132 (218)
...|.+.+... .++....+|.|.. ++..|++|+.||-+-+.+..
T Consensus 6 ~~~l~~~I~~g-~~~~G~~LPsE~e----------------La~~~gVSR~TVR~Al~~L~ 49 (233)
T TIGR02404 6 YQDLEQKITHG-QYKEGDYLPSEHE----------------LMDQYGASRETVRKALNLLT 49 (233)
T ss_pred HHHHHHHHHhC-CCCCCCCCcCHHH----------------HHHHHCCCHHHHHHHHHHHH
Confidence 34444555433 2455556877764 55789999999966555443
No 386
>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=21.05 E-value=1.1e+02 Score=18.93 Aligned_cols=26 Identities=12% Similarity=-0.095 Sum_probs=18.9
Q ss_pred hcCccchhhhhcccccccchhHHHHH
Q 046385 105 SHNLRNRFIKIRFQHSGHTVHRYFHE 130 (218)
Q Consensus 105 a~~~s~r~i~~~F~~S~sTVsr~f~e 130 (218)
.++.....++...|+|++|+.+.+.+
T Consensus 16 ~~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 16 RCGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HTTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HhCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 34446688999999999999987753
No 387
>PRK13500 transcriptional activator RhaR; Provisional
Probab=20.89 E-value=2.2e+02 Score=25.06 Aligned_cols=65 Identities=15% Similarity=0.128 Sum_probs=39.8
Q ss_pred cCHHHHHHHHHHHHhcCccCCC-ccchHHHHHHHHHHHH----hcCccchhhhhcccccccchhHHHHHH
Q 046385 67 MDKNGFISLCQLFKEKGWLSDS-KHLTVEEKMAMFLFTI----SHNLRNRFIKIRFQHSGHTVHRYFHEV 131 (218)
Q Consensus 67 M~~~~F~~L~~~L~~~~~~~~T-~~isveE~laifL~~l----a~~~s~r~i~~~F~~S~sTVsr~f~eV 131 (218)
|....|..|+..|......... ...+..+++.-++.++ +...+...++..+++|..+.+|.|++.
T Consensus 177 l~~~ll~~Ll~~l~r~~~~~~~~~~~~~~~~l~~i~~yI~~~~~e~isl~~lA~~~~iS~~~L~r~FK~~ 246 (312)
T PRK13500 177 MAELLFGQLVMLLNRHRYTSDSLPPTSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQ 246 (312)
T ss_pred HHHHHHHHHHHHHHHhhhcccCCCCcchHHHHHHHHHHHHHcccCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4456677777766543211111 1112233444444444 334666899999999999999999987
No 388
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=20.87 E-value=88 Score=26.17 Aligned_cols=31 Identities=13% Similarity=0.021 Sum_probs=23.6
Q ss_pred HHHHhcCccchhhhhcccccccchhHHHHHH
Q 046385 101 LFTISHNLRNRFIKIRFQHSGHTVHRYFHEV 131 (218)
Q Consensus 101 L~~la~~~s~r~i~~~F~~S~sTVsr~f~eV 131 (218)
+..++...|+..++...++|++|||+.+++.
T Consensus 5 f~~v~~~gs~~~AA~~L~isqsavS~~i~~L 35 (279)
T TIGR03339 5 FHAVARCGSFTRAAERLGLSQPTVTDQVRKL 35 (279)
T ss_pred hHHHHhcCCHHHHHHHhcCCchHHHHHHHHH
Confidence 3445666688999999999999999766554
No 389
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=20.86 E-value=1e+02 Score=25.48 Aligned_cols=42 Identities=17% Similarity=0.082 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHhcC--ccchhhhhcccccccchhHHHHHHHHH
Q 046385 93 VEEKMAMFLFTISHN--LRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 93 veE~laifL~~la~~--~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
.++|...-|-.|..+ .+..+++..|++|.+||-|=+.+..+.
T Consensus 5 ~~~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~ 48 (185)
T PRK04424 5 KKERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIP 48 (185)
T ss_pred HHHHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcc
Confidence 345555555555444 344789999999999999988766443
No 390
>PRK12423 LexA repressor; Provisional
Probab=20.73 E-value=86 Score=26.14 Aligned_cols=27 Identities=15% Similarity=0.039 Sum_probs=21.3
Q ss_pred ccchhhhhccc-ccccchhHHHHHHHHH
Q 046385 108 LRNRFIKIRFQ-HSGHTVHRYFHEVLSA 134 (218)
Q Consensus 108 ~s~r~i~~~F~-~S~sTVsr~f~eVl~A 134 (218)
-|.+.++..|+ +|.+||+.++...-++
T Consensus 26 Ps~~eia~~~g~~s~~~v~~~l~~L~~~ 53 (202)
T PRK12423 26 PSLAEIAQAFGFASRSVARKHVQALAEA 53 (202)
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 47899999999 6999999776655443
No 391
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=20.57 E-value=2.6e+02 Score=25.07 Aligned_cols=77 Identities=9% Similarity=-0.004 Sum_probs=52.8
Q ss_pred cchhccccCHHHHHHHHHHHHhcCccCCCccchHHHHHHHHHHHH----hcCccchhhhhcccccccchhHHHHHHHHHH
Q 046385 60 FCYDLMRMDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTI----SHNLRNRFIKIRFQHSGHTVHRYFHEVLSAM 135 (218)
Q Consensus 60 ~~~~~fRM~~~~F~~L~~~L~~~~~~~~T~~isveE~laifL~~l----a~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI 135 (218)
+.-+.+++.+.+-..-+.+++.-......+.-+.+--+|..||+. +..-+.++++...+++...|.+.++.+++.+
T Consensus 131 ~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L 210 (310)
T PRK00423 131 RIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLREL 210 (310)
T ss_pred HHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 345577777777766666666443333344555555566666654 5567778999999999999999888888776
Q ss_pred H
Q 046385 136 M 136 (218)
Q Consensus 136 ~ 136 (218)
-
T Consensus 211 ~ 211 (310)
T PRK00423 211 N 211 (310)
T ss_pred C
Confidence 3
No 392
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=20.54 E-value=91 Score=27.41 Aligned_cols=38 Identities=3% Similarity=-0.039 Sum_probs=28.6
Q ss_pred HHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHH
Q 046385 96 KMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLS 133 (218)
Q Consensus 96 ~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~ 133 (218)
+..-.+..++...|+..++...++|.+|||+.+++.=+
T Consensus 14 ~~L~~F~~v~e~gs~s~AA~~L~iSQpavS~~I~~LE~ 51 (310)
T PRK15092 14 DLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQ 51 (310)
T ss_pred HHHHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHH
Confidence 34445566777778999999999999999987665433
No 393
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=20.34 E-value=1.2e+02 Score=26.88 Aligned_cols=48 Identities=13% Similarity=0.134 Sum_probs=37.2
Q ss_pred cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHhh
Q 046385 90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKF 138 (218)
Q Consensus 90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~L 138 (218)
.+|+.++.++ +.....|.++..|+...++|..||...++.....|-..
T Consensus 118 ~L~p~~R~vf-~L~~~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~ 165 (290)
T PRK09635 118 RLGPAERVVF-VLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKINES 165 (290)
T ss_pred hCCHHHHHHh-hHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 4566665444 44455689999999999999999999998887776643
No 394
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=20.33 E-value=44 Score=34.55 Aligned_cols=65 Identities=18% Similarity=0.127 Sum_probs=44.4
Q ss_pred ccchhccccCHHHHHHHHHHHHhcCccCCCccchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHH
Q 046385 59 IFCYDLMRMDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAM 135 (218)
Q Consensus 59 ~~~~~~fRM~~~~F~~L~~~L~~~~~~~~T~~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI 135 (218)
.+|+.+.+.++..+..+.+.+ ++|-.| --.|--+++|.|+++|+..-.+|..||..|++..-.-+
T Consensus 810 ~~~~~f~~~~~~~~~~~~~e~----------~Ls~RE--~eVL~Lia~G~SN~eIa~~L~isl~TVKtH~rniy~KL 874 (894)
T COG2909 810 TQRQKFIHLDEEFVEGLLNEL----------PLSQRE--LEVLGLIAQGLSNEEIAQELFISLTTVKTHIRNIYQKL 874 (894)
T ss_pred HHHHHhccCChhhcccccccc----------CccHHH--HHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 444444445555444444311 244444 45677889999999999999999999999998875543
No 395
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=20.05 E-value=1.5e+02 Score=22.97 Aligned_cols=41 Identities=12% Similarity=0.107 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHhc--CccchhhhhcccccccchhHHHHHHHHH
Q 046385 94 EEKMAMFLFTISH--NLRNRFIKIRFQHSGHTVHRYFHEVLSA 134 (218)
Q Consensus 94 eE~laifL~~la~--~~s~r~i~~~F~~S~sTVsr~f~eVl~A 134 (218)
|+-|..++..+.. ..+..+++..+++|.+||++.+....+.
T Consensus 7 edyL~~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~ 49 (142)
T PRK03902 7 EDYIEQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKD 49 (142)
T ss_pred HHHHHHHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHC
Confidence 3334444444432 2355689999999999999998775554
Done!