Query 016336
Match_columns 391
No_of_seqs 250 out of 1780
Neff 8.3
Searched_HMMs 46136
Date Fri Mar 29 05:56:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016336.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016336hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4585 Predicted transposase 100.0 3.6E-42 7.9E-47 327.8 14.6 313 59-389 7-323 (326)
2 PF04827 Plant_tran: Plant tra 100.0 3.6E-37 7.8E-42 264.5 9.5 199 143-345 2-201 (205)
3 PF13359 DDE_Tnp_4: DDE superf 100.0 1.4E-37 3.1E-42 270.1 3.7 154 173-339 1-158 (158)
4 PF13613 HTH_Tnp_4: Helix-turn 99.0 2.2E-10 4.7E-15 80.2 3.1 51 92-142 2-52 (53)
5 PF13612 DDE_Tnp_1_3: Transpos 98.8 1.3E-09 2.8E-14 93.5 2.3 128 167-316 4-149 (155)
6 PF13586 DDE_Tnp_1_2: Transpos 97.4 7.1E-05 1.5E-09 58.1 1.7 52 285-337 34-85 (88)
7 PF01609 DDE_Tnp_1: Transposas 97.1 8.9E-06 1.9E-10 72.7 -7.7 151 168-340 4-213 (213)
8 PF13936 HTH_38: Helix-turn-he 96.0 0.0015 3.1E-08 43.6 -0.4 41 91-132 3-43 (44)
9 PF02796 HTH_7: Helix-turn-hel 95.9 0.0014 3E-08 44.0 -0.8 40 91-131 4-43 (45)
10 PF04545 Sigma70_r4: Sigma-70, 95.9 0.0064 1.4E-07 41.6 2.4 45 92-137 4-48 (50)
11 PF04218 CENP-B_N: CENP-B N-te 95.6 0.0063 1.4E-07 42.3 1.4 42 90-132 4-45 (53)
12 smart00351 PAX Paired Box doma 94.5 0.024 5.2E-07 47.0 2.2 46 89-135 14-59 (125)
13 PF13384 HTH_23: Homeodomain-l 94.2 0.0091 2E-07 40.7 -0.9 37 97-134 6-42 (50)
14 PF13518 HTH_28: Helix-turn-he 93.9 0.02 4.3E-07 39.2 0.5 37 98-135 2-38 (52)
15 cd00131 PAX Paired Box domain 93.8 0.04 8.6E-07 45.8 2.1 46 89-135 14-59 (128)
16 PF13011 LZ_Tnp_IS481: leucine 93.6 0.047 1E-06 41.6 2.1 47 89-135 5-51 (85)
17 PF08281 Sigma70_r4_2: Sigma-7 93.0 0.061 1.3E-06 37.2 1.8 43 92-135 10-52 (54)
18 PF05225 HTH_psq: helix-turn-h 92.8 0.034 7.4E-07 37.2 0.2 36 96-131 2-38 (45)
19 cd06571 Bac_DnaA_C C-terminal 92.2 0.13 2.8E-06 39.9 2.8 51 89-139 24-75 (90)
20 PRK00118 putative DNA-binding 91.9 0.14 3.1E-06 40.8 2.8 49 91-140 16-64 (104)
21 cd00569 HTH_Hin_like Helix-tur 91.7 0.11 2.3E-06 32.0 1.5 39 91-130 4-42 (42)
22 PF02209 VHP: Villin headpiece 91.7 0.12 2.6E-06 32.7 1.6 26 51-76 2-27 (36)
23 COG3415 Transposase and inacti 91.5 0.078 1.7E-06 44.5 0.9 45 91-135 3-47 (138)
24 PF12116 SpoIIID: Stage III sp 91.1 0.071 1.5E-06 39.8 0.2 41 98-138 8-48 (82)
25 PRK04217 hypothetical protein; 91.1 0.17 3.7E-06 40.7 2.5 49 91-140 41-89 (110)
26 PRK09413 IS2 repressor TnpA; R 90.9 0.14 3.1E-06 42.0 1.9 46 90-135 10-55 (121)
27 smart00421 HTH_LUXR helix_turn 90.7 0.17 3.7E-06 34.7 1.9 44 92-137 3-46 (58)
28 smart00153 VHP Villin headpiec 90.5 0.2 4.3E-06 31.8 1.8 21 52-72 3-23 (36)
29 cd06171 Sigma70_r4 Sigma70, re 90.3 0.16 3.5E-06 34.2 1.5 43 92-135 10-52 (55)
30 TIGR01321 TrpR trp operon repr 89.5 0.22 4.8E-06 38.8 1.8 38 93-130 33-76 (94)
31 PRK12529 RNA polymerase sigma 89.4 0.28 6.1E-06 42.9 2.7 49 92-141 127-175 (178)
32 PF01527 HTH_Tnp_1: Transposas 89.2 0.088 1.9E-06 39.1 -0.6 45 90-134 4-48 (76)
33 PF13340 DUF4096: Putative tra 89.1 0.55 1.2E-05 35.0 3.7 45 90-135 22-66 (75)
34 PRK06030 hypothetical protein; 88.5 0.4 8.7E-06 39.5 2.7 47 91-137 51-97 (124)
35 PRK09639 RNA polymerase sigma 88.4 0.28 6.1E-06 42.1 2.0 48 92-141 112-159 (166)
36 TIGR00721 tfx DNA-binding prot 87.9 0.57 1.2E-05 39.3 3.4 46 91-138 5-50 (137)
37 TIGR02985 Sig70_bacteroi1 RNA 87.5 0.45 9.7E-06 40.3 2.6 47 92-139 113-159 (161)
38 PRK09652 RNA polymerase sigma 87.4 0.33 7.2E-06 42.1 1.8 49 92-141 128-176 (182)
39 TIGR02531 yecD_yerC TrpR-relat 87.4 0.2 4.4E-06 38.7 0.4 34 96-130 38-71 (88)
40 TIGR03879 near_KaiC_dom probab 87.4 0.26 5.6E-06 36.5 0.9 41 92-132 15-55 (73)
41 PRK05911 RNA polymerase sigma 87.0 0.41 8.8E-06 44.8 2.2 50 92-142 205-254 (257)
42 PRK12519 RNA polymerase sigma 86.8 0.32 6.9E-06 43.1 1.3 49 92-141 141-189 (194)
43 PHA00675 hypothetical protein 86.7 0.36 7.9E-06 35.8 1.3 40 92-131 22-61 (78)
44 PRK07037 extracytoplasmic-func 86.2 0.51 1.1E-05 40.4 2.3 49 92-141 109-157 (163)
45 cd06170 LuxR_C_like C-terminal 86.2 0.53 1.2E-05 32.2 2.0 42 94-137 2-43 (57)
46 TIGR02960 SigX5 RNA polymerase 86.1 0.92 2E-05 43.7 4.3 71 92-163 142-216 (324)
47 PF08299 Bac_DnaA_C: Bacterial 86.1 0.19 4.1E-06 37.0 -0.4 43 91-133 27-70 (70)
48 PRK08301 sporulation sigma fac 86.1 0.5 1.1E-05 43.4 2.3 50 92-141 178-230 (234)
49 TIGR02952 Sig70_famx2 RNA poly 85.7 0.59 1.3E-05 40.2 2.5 47 92-139 122-168 (170)
50 PF13542 HTH_Tnp_ISL3: Helix-t 85.4 0.23 5E-06 33.9 -0.2 31 103-133 21-51 (52)
51 TIGR02937 sigma70-ECF RNA poly 85.4 0.59 1.3E-05 38.8 2.2 47 92-139 110-156 (158)
52 TIGR02392 rpoH_proteo alternat 85.3 0.58 1.3E-05 44.1 2.4 49 92-140 218-267 (270)
53 PRK05803 sporulation sigma fac 84.8 0.61 1.3E-05 42.8 2.2 49 92-140 175-226 (233)
54 PRK12514 RNA polymerase sigma 84.7 0.83 1.8E-05 39.8 2.9 48 92-140 129-176 (179)
55 PRK09638 RNA polymerase sigma 84.5 0.39 8.4E-06 41.7 0.8 48 92-140 126-173 (176)
56 PRK06596 RNA polymerase factor 84.0 0.72 1.6E-05 43.8 2.4 49 92-140 230-279 (284)
57 PRK09641 RNA polymerase sigma 83.6 0.7 1.5E-05 40.4 2.0 48 92-140 136-183 (187)
58 PRK12547 RNA polymerase sigma 83.5 0.83 1.8E-05 39.3 2.4 48 92-140 112-159 (164)
59 PRK12530 RNA polymerase sigma 83.2 0.66 1.4E-05 41.0 1.7 48 92-140 134-181 (189)
60 PHA00542 putative Cro-like pro 83.2 1.1 2.4E-05 34.0 2.7 52 101-163 23-74 (82)
61 PRK09415 RNA polymerase factor 82.9 0.78 1.7E-05 40.1 2.0 49 92-141 127-175 (179)
62 PRK11924 RNA polymerase sigma 82.5 0.91 2E-05 39.2 2.3 48 92-140 125-172 (179)
63 PRK12511 RNA polymerase sigma 82.5 0.88 1.9E-05 40.1 2.2 48 92-140 111-158 (182)
64 PRK07408 RNA polymerase sigma 82.5 0.92 2E-05 42.3 2.4 48 92-140 203-250 (256)
65 PRK12524 RNA polymerase sigma 82.4 0.92 2E-05 40.3 2.3 48 92-140 136-183 (196)
66 PRK12533 RNA polymerase sigma 82.1 0.89 1.9E-05 41.3 2.1 49 92-141 134-182 (216)
67 TIGR02989 Sig-70_gvs1 RNA poly 82.0 1 2.2E-05 38.2 2.4 47 92-139 111-157 (159)
68 TIGR02939 RpoE_Sigma70 RNA pol 81.9 0.81 1.8E-05 40.2 1.7 50 92-142 138-187 (190)
69 PRK12516 RNA polymerase sigma 81.8 1 2.2E-05 39.8 2.3 49 92-141 116-164 (187)
70 PRK12534 RNA polymerase sigma 81.8 1.3 2.8E-05 38.9 3.0 48 92-140 137-184 (187)
71 PRK11923 algU RNA polymerase s 81.7 0.81 1.8E-05 40.4 1.7 51 92-143 138-188 (193)
72 PRK12515 RNA polymerase sigma 81.5 0.97 2.1E-05 39.8 2.1 48 92-140 131-178 (189)
73 PF04967 HTH_10: HTH DNA bindi 81.4 1.3 2.8E-05 30.7 2.2 29 109-137 23-51 (53)
74 PRK12537 RNA polymerase sigma 81.3 1.2 2.7E-05 38.9 2.7 48 92-140 133-180 (182)
75 PRK03975 tfx putative transcri 81.3 1.1 2.4E-05 37.8 2.2 46 91-138 5-50 (141)
76 PRK05572 sporulation sigma fac 81.1 1.1 2.5E-05 41.5 2.5 48 92-140 202-249 (252)
77 PRK09047 RNA polymerase factor 81.1 1 2.2E-05 38.3 2.0 49 92-141 106-154 (161)
78 PRK05602 RNA polymerase sigma 81.0 1 2.2E-05 39.6 2.0 49 92-141 128-176 (186)
79 PRK15320 transcriptional activ 80.9 0.71 1.5E-05 40.9 0.9 46 91-138 163-208 (251)
80 TIGR02983 SigE-fam_strep RNA p 80.9 1.1 2.4E-05 38.2 2.2 48 92-140 110-157 (162)
81 PRK06704 RNA polymerase factor 80.8 1.6 3.5E-05 40.0 3.3 70 92-162 116-186 (228)
82 TIGR02999 Sig-70_X6 RNA polyme 80.4 1.3 2.9E-05 38.6 2.6 47 93-140 135-181 (183)
83 PRK12512 RNA polymerase sigma 80.4 1.3 2.7E-05 38.8 2.4 49 92-141 131-179 (184)
84 PRK07500 rpoH2 RNA polymerase 80.3 1.1 2.5E-05 42.6 2.3 50 92-141 227-277 (289)
85 PRK13919 putative RNA polymera 80.3 1.4 3.1E-05 38.5 2.7 49 92-141 135-183 (186)
86 PRK12531 RNA polymerase sigma 80.3 1.3 2.8E-05 39.3 2.4 48 92-140 141-188 (194)
87 TIGR02984 Sig-70_plancto1 RNA 80.2 1.3 2.9E-05 38.7 2.5 48 92-140 140-187 (189)
88 TIGR02846 spore_sigmaK RNA pol 80.2 1.3 2.8E-05 40.5 2.5 49 92-140 174-225 (227)
89 TIGR02393 RpoD_Cterm RNA polym 80.0 1.1 2.4E-05 41.3 2.0 48 92-139 176-226 (238)
90 PF13730 HTH_36: Helix-turn-he 80.0 0.91 2E-05 31.3 1.1 39 96-134 7-50 (55)
91 TIGR02950 SigM_subfam RNA poly 79.9 0.47 1E-05 40.1 -0.5 48 92-140 105-152 (154)
92 COG2739 Uncharacterized protei 79.3 1.2 2.6E-05 34.9 1.6 45 94-139 19-63 (105)
93 PRK12532 RNA polymerase sigma 79.1 1.3 2.8E-05 39.3 2.1 49 92-141 136-184 (195)
94 PRK10402 DNA-binding transcrip 79.1 1.4 3.1E-05 40.0 2.5 68 92-159 148-220 (226)
95 TIGR02954 Sig70_famx3 RNA poly 79.0 1.6 3.4E-05 37.6 2.6 48 92-140 119-166 (169)
96 TIGR02980 SigBFG RNA polymeras 79.0 1.5 3.2E-05 40.0 2.5 47 92-139 178-224 (227)
97 TIGR02885 spore_sigF RNA polym 78.9 1.5 3.3E-05 40.0 2.5 47 92-139 183-229 (231)
98 PRK08583 RNA polymerase sigma 78.9 1.5 3.2E-05 40.9 2.5 48 92-140 205-252 (257)
99 PRK09645 RNA polymerase sigma 78.8 1.6 3.6E-05 37.6 2.6 49 92-141 118-166 (173)
100 TIGR02844 spore_III_D sporulat 78.7 0.8 1.7E-05 34.7 0.5 36 96-131 5-41 (80)
101 PRK09642 RNA polymerase sigma 78.7 1.5 3.3E-05 37.3 2.3 49 92-141 106-154 (160)
102 PF00356 LacI: Bacterial regul 78.4 0.33 7.1E-06 32.6 -1.5 21 112-132 2-22 (46)
103 TIGR02948 SigW_bacill RNA poly 78.4 1.4 3E-05 38.5 2.1 49 92-141 136-184 (187)
104 PRK12523 RNA polymerase sigma 78.3 1.6 3.5E-05 37.8 2.4 47 92-139 119-165 (172)
105 TIGR03001 Sig-70_gmx1 RNA poly 78.3 1.5 3.2E-05 40.7 2.3 49 92-141 161-209 (244)
106 TIGR02835 spore_sigmaE RNA pol 78.3 1.6 3.4E-05 40.1 2.4 49 92-140 178-229 (234)
107 PRK12528 RNA polymerase sigma 78.2 1.5 3.3E-05 37.4 2.2 46 92-138 113-158 (161)
108 PRK09643 RNA polymerase sigma 78.2 1.5 3.2E-05 38.9 2.1 48 92-140 134-181 (192)
109 PRK08215 sporulation sigma fac 78.2 1.6 3.5E-05 40.7 2.6 47 92-139 209-255 (258)
110 PRK12540 RNA polymerase sigma 78.1 1.6 3.4E-05 38.4 2.3 49 92-141 111-159 (182)
111 PF01325 Fe_dep_repress: Iron 77.7 1.2 2.5E-05 31.7 1.1 41 95-135 5-48 (60)
112 PRK12539 RNA polymerase sigma 77.7 1.7 3.6E-05 38.2 2.3 49 92-141 131-179 (184)
113 PRK12544 RNA polymerase sigma 77.7 1.6 3.5E-05 39.2 2.3 49 92-141 148-196 (206)
114 PF00872 Transposase_mut: Tran 77.5 2.4 5.1E-05 42.1 3.6 87 105-219 110-205 (381)
115 PF07374 DUF1492: Protein of u 77.4 1.4 3E-05 34.9 1.6 80 52-137 20-99 (100)
116 PRK09637 RNA polymerase sigma 77.3 1.7 3.7E-05 38.1 2.3 48 92-140 106-153 (181)
117 TIGR02957 SigX4 RNA polymerase 77.2 3.3 7.3E-05 39.1 4.4 67 92-161 108-174 (281)
118 PF01371 Trp_repressor: Trp re 77.1 1.2 2.5E-05 34.4 1.0 35 96-130 36-70 (87)
119 PRK06811 RNA polymerase factor 77.1 1.7 3.7E-05 38.3 2.2 47 92-139 131-177 (189)
120 TIGR02394 rpoS_proteo RNA poly 76.9 1.7 3.6E-05 41.3 2.3 51 91-141 221-274 (285)
121 PF12802 MarR_2: MarR family; 76.9 1.2 2.6E-05 31.3 1.0 26 110-135 22-47 (62)
122 PRK12522 RNA polymerase sigma 76.9 1.7 3.6E-05 37.7 2.1 52 93-145 120-171 (173)
123 PRK12536 RNA polymerase sigma 76.7 1.8 3.9E-05 37.8 2.3 48 92-140 129-176 (181)
124 PRK06986 fliA flagellar biosyn 76.7 1.7 3.8E-05 39.8 2.2 49 92-141 184-232 (236)
125 PRK11753 DNA-binding transcrip 76.7 1.5 3.3E-05 39.0 1.9 81 52-134 100-193 (211)
126 PF13551 HTH_29: Winged helix- 76.6 0.91 2E-05 36.1 0.3 35 101-135 3-38 (112)
127 PRK12546 RNA polymerase sigma 76.4 1.8 3.8E-05 38.4 2.1 49 92-141 113-161 (188)
128 PRK06930 positive control sigm 76.3 1.7 3.6E-05 38.0 1.9 49 92-141 114-162 (170)
129 COG1595 RpoE DNA-directed RNA 76.3 1.6 3.5E-05 38.2 1.9 49 92-141 127-175 (182)
130 PRK01381 Trp operon repressor; 76.3 1.8 3.8E-05 34.1 1.8 38 93-130 33-76 (99)
131 TIGR02997 Sig70-cyanoRpoD RNA 76.3 1.5 3.2E-05 41.9 1.7 45 92-136 249-296 (298)
132 PF01047 MarR: MarR family; I 76.1 1.1 2.5E-05 31.2 0.7 38 97-134 5-42 (59)
133 PRK12535 RNA polymerase sigma 76.0 2 4.4E-05 38.2 2.4 53 92-145 133-185 (196)
134 PF01710 HTH_Tnp_IS630: Transp 76.0 2.5 5.4E-05 34.5 2.8 75 52-132 20-94 (119)
135 COG1191 FliA DNA-directed RNA 75.9 1.9 4E-05 40.1 2.2 49 92-141 196-244 (247)
136 TIGR03697 NtcA_cyano global ni 75.8 1.2 2.5E-05 39.2 0.8 98 52-151 74-186 (193)
137 TIGR02850 spore_sigG RNA polym 75.8 2 4.4E-05 39.9 2.5 47 92-139 206-252 (254)
138 cd00092 HTH_CRP helix_turn_hel 75.7 0.99 2.1E-05 32.2 0.3 26 110-135 26-51 (67)
139 PRK06759 RNA polymerase factor 75.6 1.9 4.1E-05 36.4 2.0 46 92-138 106-151 (154)
140 PF00196 GerE: Bacterial regul 75.4 0.89 1.9E-05 31.8 -0.0 43 93-137 4-46 (58)
141 TIGR02941 Sigma_B RNA polymera 75.4 2.1 4.5E-05 39.8 2.4 47 92-139 205-251 (255)
142 PRK12520 RNA polymerase sigma 75.0 2.1 4.6E-05 37.7 2.3 49 92-141 131-179 (191)
143 PRK12545 RNA polymerase sigma 74.9 2.1 4.6E-05 38.2 2.3 49 92-141 139-187 (201)
144 PF01022 HTH_5: Bacterial regu 74.7 1 2.2E-05 30.1 0.1 37 98-134 4-40 (47)
145 PRK07405 RNA polymerase sigma 74.7 2.2 4.8E-05 41.2 2.5 48 92-139 256-306 (317)
146 PRK14086 dnaA chromosomal repl 74.3 2.7 5.9E-05 44.1 3.1 51 89-139 549-599 (617)
147 TIGR02943 Sig70_famx1 RNA poly 74.2 2.2 4.8E-05 37.6 2.2 49 92-141 131-179 (188)
148 PRK12525 RNA polymerase sigma 74.1 2.4 5.3E-05 36.5 2.4 48 92-140 118-165 (168)
149 COG2963 Transposase and inacti 73.9 2.4 5.2E-05 34.3 2.1 47 90-136 5-52 (116)
150 PRK09636 RNA polymerase sigma 73.9 4.8 0.0001 38.3 4.5 68 92-162 115-182 (293)
151 PRK07122 RNA polymerase sigma 73.8 2.3 5E-05 39.9 2.3 47 92-139 215-261 (264)
152 PRK08241 RNA polymerase factor 73.8 2.9 6.2E-05 40.6 3.1 73 92-165 153-228 (339)
153 PRK12542 RNA polymerase sigma 73.6 2.5 5.4E-05 37.0 2.4 50 92-142 122-171 (185)
154 PRK07670 RNA polymerase sigma 73.3 2.6 5.6E-05 39.1 2.5 48 92-140 201-248 (251)
155 PF04297 UPF0122: Putative hel 73.3 2.2 4.7E-05 33.8 1.6 46 93-139 18-63 (101)
156 PF13412 HTH_24: Winged helix- 72.9 2.1 4.5E-05 28.6 1.3 29 107-135 15-43 (48)
157 PRK09649 RNA polymerase sigma 72.7 2.4 5.2E-05 37.3 2.0 47 92-139 130-176 (185)
158 PRK09644 RNA polymerase sigma 72.7 2.2 4.8E-05 36.6 1.8 49 92-141 108-156 (165)
159 PRK12543 RNA polymerase sigma 72.6 2.6 5.7E-05 36.7 2.3 48 92-140 117-164 (179)
160 PRK08295 RNA polymerase factor 72.2 2.5 5.4E-05 37.7 2.1 48 92-141 155-202 (208)
161 TIGR02479 FliA_WhiG RNA polyme 72.2 3 6.6E-05 37.9 2.6 48 92-140 175-222 (224)
162 PRK12527 RNA polymerase sigma 72.2 2.8 6.1E-05 35.6 2.3 49 92-141 105-153 (159)
163 PRK15418 transcriptional regul 71.7 3.3 7.1E-05 40.0 2.9 68 101-172 21-89 (318)
164 PRK09648 RNA polymerase sigma 71.6 3 6.5E-05 36.6 2.4 48 92-140 139-186 (189)
165 PRK00149 dnaA chromosomal repl 71.5 3.6 7.7E-05 41.8 3.2 50 89-138 382-432 (450)
166 PRK12526 RNA polymerase sigma 71.4 3 6.4E-05 37.4 2.4 48 92-140 153-200 (206)
167 PRK12541 RNA polymerase sigma 71.1 2.8 6.1E-05 35.7 2.1 47 92-139 112-158 (161)
168 TIGR02959 SigZ RNA polymerase 70.9 3.2 7E-05 35.9 2.4 48 92-140 100-147 (170)
169 smart00342 HTH_ARAC helix_turn 70.8 6.8 0.00015 28.6 3.9 72 52-134 3-76 (84)
170 TIGR02947 SigH_actino RNA poly 70.8 1.4 3.1E-05 38.9 0.1 49 92-141 131-179 (193)
171 PRK14088 dnaA chromosomal repl 70.5 3.3 7.2E-05 41.9 2.7 49 89-137 367-415 (440)
172 PRK09646 RNA polymerase sigma 69.9 3.9 8.5E-05 36.1 2.8 48 92-140 142-189 (194)
173 PRK09635 sigI RNA polymerase s 69.9 6.1 0.00013 37.6 4.2 67 92-161 118-184 (290)
174 PRK07406 RNA polymerase sigma 69.8 3 6.5E-05 41.2 2.1 48 92-139 311-361 (373)
175 TIGR01636 phage_rinA phage tra 69.6 3.9 8.5E-05 34.1 2.5 49 92-140 82-131 (134)
176 PF01710 HTH_Tnp_IS630: Transp 69.5 1.2 2.6E-05 36.4 -0.6 29 104-132 13-41 (119)
177 PRK12538 RNA polymerase sigma 69.3 2.9 6.2E-05 38.5 1.8 48 92-140 171-218 (233)
178 PRK11922 RNA polymerase sigma 67.8 1.8 4E-05 39.5 0.2 49 92-141 149-197 (231)
179 PRK12427 flagellar biosynthesi 67.4 4 8.6E-05 37.5 2.3 46 92-138 183-228 (231)
180 PRK09210 RNA polymerase sigma 67.0 3.5 7.6E-05 40.7 2.0 47 92-138 305-354 (367)
181 PRK14087 dnaA chromosomal repl 66.5 5.2 0.00011 40.7 3.1 73 66-138 357-431 (450)
182 PF00292 PAX: 'Paired box' dom 66.4 3.8 8.1E-05 33.8 1.7 46 88-135 13-59 (125)
183 PRK15201 fimbriae regulatory p 66.0 2.5 5.5E-05 36.9 0.7 45 91-137 132-176 (198)
184 PRK09651 RNA polymerase sigma 65.9 3.5 7.5E-05 35.7 1.6 48 92-140 119-166 (172)
185 PF08279 HTH_11: HTH domain; 65.9 2.5 5.4E-05 29.0 0.5 25 109-133 15-39 (55)
186 TIGR03209 P21_Cbot clostridium 65.9 3.3 7.1E-05 34.5 1.4 35 92-127 107-141 (142)
187 PRK06288 RNA polymerase sigma 65.8 4.4 9.5E-05 38.0 2.3 48 92-140 212-259 (268)
188 PF07638 Sigma70_ECF: ECF sigm 65.7 4.9 0.00011 35.4 2.5 46 93-139 136-181 (185)
189 PRK09392 ftrB transcriptional 65.4 4 8.6E-05 37.2 1.9 66 91-156 145-220 (236)
190 smart00346 HTH_ICLR helix_turn 65.3 3.5 7.5E-05 31.4 1.3 39 97-135 5-46 (91)
191 PRK07598 RNA polymerase sigma 64.6 4.3 9.3E-05 40.6 2.1 47 92-138 350-399 (415)
192 COG2390 DeoR Transcriptional r 64.1 4.7 0.0001 38.9 2.2 68 102-173 19-87 (321)
193 PRK13918 CRP/FNR family transc 63.9 3 6.4E-05 36.9 0.7 66 92-157 118-198 (202)
194 PF13545 HTH_Crp_2: Crp-like h 63.8 2.2 4.8E-05 31.3 -0.1 27 109-135 28-54 (76)
195 TIGR02859 spore_sigH RNA polym 63.6 4.4 9.6E-05 35.7 1.8 41 97-139 155-195 (198)
196 PRK05657 RNA polymerase sigma 63.4 5.1 0.00011 38.9 2.3 50 92-141 262-314 (325)
197 PRK12517 RNA polymerase sigma 63.1 5.4 0.00012 35.1 2.3 49 92-141 128-176 (188)
198 PRK12422 chromosomal replicati 63.0 6 0.00013 40.1 2.9 72 66-137 353-425 (445)
199 PRK05949 RNA polymerase sigma 63.0 5.3 0.00012 38.7 2.4 48 92-139 266-316 (327)
200 TIGR02337 HpaR homoprotocatech 62.2 13 0.00028 29.9 4.3 43 93-135 26-68 (118)
201 PRK09391 fixK transcriptional 62.1 5.7 0.00012 36.2 2.3 81 53-135 115-205 (230)
202 smart00550 Zalpha Z-DNA-bindin 62.1 4.6 0.0001 29.4 1.4 39 94-132 6-45 (68)
203 PRK12518 RNA polymerase sigma 61.6 2.5 5.4E-05 36.5 -0.2 48 93-141 121-168 (175)
204 PRK15411 rcsA colanic acid cap 61.3 3.7 7.9E-05 37.0 0.9 45 92-138 137-181 (207)
205 PF00325 Crp: Bacterial regula 61.2 1.6 3.5E-05 26.8 -1.0 24 111-134 4-27 (32)
206 PF00126 HTH_1: Bacterial regu 61.2 3.9 8.5E-05 28.8 0.8 28 111-138 15-42 (60)
207 PF09339 HTH_IclR: IclR helix- 61.0 1.8 3.9E-05 29.6 -0.9 25 110-134 19-43 (52)
208 PF06056 Terminase_5: Putative 60.8 4 8.7E-05 28.8 0.8 33 98-132 4-36 (58)
209 TIGR01610 phage_O_Nterm phage 60.8 4.2 9.2E-05 31.7 1.0 28 107-134 45-72 (95)
210 PF13551 HTH_29: Winged helix- 60.2 19 0.00041 28.2 4.8 80 52-132 14-110 (112)
211 PRK07921 RNA polymerase sigma 60.1 6 0.00013 38.3 2.2 48 92-139 262-312 (324)
212 PRK12513 RNA polymerase sigma 60.1 3.2 7E-05 36.6 0.3 48 92-140 139-186 (194)
213 PF02001 DUF134: Protein of un 59.6 7.2 0.00016 31.2 2.2 46 92-138 41-86 (106)
214 PRK03573 transcriptional regul 59.4 5.5 0.00012 33.4 1.6 43 93-135 29-72 (144)
215 COG0593 DnaA ATPase involved i 59.3 7.9 0.00017 38.6 2.9 51 89-139 345-395 (408)
216 PF01381 HTH_3: Helix-turn-hel 59.1 1.9 4E-05 29.6 -1.2 44 105-160 5-48 (55)
217 PRK05901 RNA polymerase sigma 58.9 6.2 0.00014 40.6 2.1 48 92-139 447-497 (509)
218 PF13701 DDE_Tnp_1_4: Transpos 58.6 31 0.00068 35.0 7.1 59 167-229 140-199 (448)
219 PRK09640 RNA polymerase sigma 58.3 2.3 5E-05 37.4 -1.0 48 93-141 135-182 (188)
220 PF13560 HTH_31: Helix-turn-he 57.3 2.3 5E-05 30.3 -0.9 29 102-130 7-35 (64)
221 PF13463 HTH_27: Winged helix 56.8 3.6 7.8E-05 29.4 0.0 34 102-135 8-44 (68)
222 PRK09647 RNA polymerase sigma 56.7 7.1 0.00015 35.0 1.9 48 92-140 138-185 (203)
223 cd00090 HTH_ARSR Arsenical Res 56.4 6.5 0.00014 28.0 1.4 27 107-133 18-44 (78)
224 PRK13870 transcriptional regul 56.2 4.5 9.7E-05 37.2 0.5 46 91-138 172-217 (234)
225 COG2522 Predicted transcriptio 56.1 4.9 0.00011 32.8 0.7 31 99-131 14-44 (119)
226 PF10654 DUF2481: Protein of u 56.0 3.3 7.2E-05 33.1 -0.3 31 108-138 79-109 (126)
227 PRK11161 fumarate/nitrate redu 54.8 7.7 0.00017 35.2 1.9 43 92-134 153-209 (235)
228 PF13751 DDE_Tnp_1_6: Transpos 54.5 4 8.8E-05 33.3 -0.0 49 291-341 73-122 (125)
229 PF05344 DUF746: Domain of Unk 54.5 6.1 0.00013 28.5 0.8 43 98-140 2-44 (65)
230 PRK13719 conjugal transfer tra 52.8 5.9 0.00013 35.9 0.7 44 92-137 143-186 (217)
231 PHA02591 hypothetical protein; 52.7 4.1 9E-05 30.3 -0.2 36 97-132 47-82 (83)
232 PRK11512 DNA-binding transcrip 52.5 11 0.00024 31.6 2.4 44 92-135 37-80 (144)
233 PF12840 HTH_20: Helix-turn-he 52.2 4.2 9.1E-05 28.7 -0.3 30 106-135 21-50 (61)
234 smart00419 HTH_CRP helix_turn_ 52.2 3.7 8E-05 26.9 -0.5 27 109-135 8-34 (48)
235 smart00760 Bac_DnaA_C Bacteria 52.1 8.9 0.00019 27.0 1.4 32 89-120 25-56 (60)
236 smart00345 HTH_GNTR helix_turn 51.4 3.8 8.2E-05 28.1 -0.6 24 111-134 22-45 (60)
237 PF12964 DUF3853: Protein of u 51.0 4 8.7E-05 31.7 -0.5 34 111-144 47-82 (96)
238 smart00352 POU Found in Pit-Oc 50.9 3.6 7.8E-05 30.6 -0.8 28 104-131 19-52 (75)
239 smart00418 HTH_ARSR helix_turn 50.4 5.8 0.00013 27.3 0.2 29 107-135 8-36 (66)
240 KOG0930 Guanine nucleotide exc 50.2 82 0.0018 29.7 7.6 83 97-180 94-189 (395)
241 PRK09191 two-component respons 50.1 16 0.00036 33.3 3.3 50 92-142 88-137 (261)
242 PHA00738 putative HTH transcri 49.9 4.6 0.0001 32.2 -0.4 37 98-135 14-52 (108)
243 COG2197 CitB Response regulato 49.5 7.2 0.00016 35.2 0.8 44 92-137 148-191 (211)
244 PRK13413 mpi multiple promoter 48.8 5.4 0.00012 35.6 -0.2 29 103-131 166-194 (200)
245 PF09862 DUF2089: Protein of u 48.6 12 0.00025 30.3 1.7 46 92-138 33-78 (113)
246 PRK10840 transcriptional regul 48.4 7.1 0.00015 34.8 0.6 45 91-137 149-193 (216)
247 TIGR02431 pcaR_pcaU beta-ketoa 48.3 32 0.00069 31.7 4.9 87 93-179 5-110 (248)
248 smart00347 HTH_MARR helix_turn 48.0 15 0.00033 27.9 2.3 44 92-135 7-50 (101)
249 cd01392 HTH_LacI Helix-turn-he 47.2 4.6 9.9E-05 27.2 -0.7 18 114-131 2-19 (52)
250 PF04552 Sigma54_DBD: Sigma-54 46.1 6.7 0.00015 33.9 0.0 23 109-131 49-71 (160)
251 COG2771 CsgD DNA-binding HTH d 46.0 9 0.0002 26.8 0.7 37 101-137 11-47 (65)
252 smart00344 HTH_ASNC helix_turn 45.4 14 0.00031 29.1 1.8 38 97-135 6-43 (108)
253 smart00420 HTH_DEOR helix_turn 45.2 13 0.00028 24.6 1.4 27 109-135 14-40 (53)
254 PRK11475 DNA-binding transcrip 44.9 8.5 0.00018 34.7 0.5 44 92-137 134-177 (207)
255 PRK10163 DNA-binding transcrip 44.8 48 0.001 31.1 5.6 44 92-135 20-66 (271)
256 TIGR03541 reg_near_HchA LuxR f 44.6 14 0.00031 33.8 1.9 46 91-138 170-215 (232)
257 PF05269 Phage_CII: Bacterioph 44.4 8.1 0.00018 30.0 0.2 29 111-139 25-53 (91)
258 PF01978 TrmB: Sugar-specific 44.2 6.2 0.00013 28.4 -0.4 38 96-134 10-47 (68)
259 PF03333 PapB: Adhesin biosynt 44.0 23 0.00049 27.5 2.6 55 61-133 22-77 (91)
260 PRK10188 DNA-binding transcrip 43.7 9.6 0.00021 35.2 0.6 45 91-137 178-222 (240)
261 cd00131 PAX Paired Box domain 43.5 59 0.0013 26.8 5.3 81 50-131 33-125 (128)
262 PRK10100 DNA-binding transcrip 43.5 9.9 0.00022 34.5 0.7 45 92-138 155-199 (216)
263 TIGR03070 couple_hipB transcri 43.3 7.8 0.00017 26.3 -0.0 26 105-130 11-36 (58)
264 PHA01976 helix-turn-helix prot 43.1 7.2 0.00016 27.8 -0.2 44 105-160 11-54 (67)
265 TIGR01889 Staph_reg_Sar staphy 43.0 17 0.00037 28.9 1.9 28 108-135 42-69 (109)
266 PRK05658 RNA polymerase sigma 42.6 15 0.00033 38.9 2.0 47 92-138 556-605 (619)
267 PRK12682 transcriptional regul 42.4 14 0.00031 35.0 1.6 43 97-139 4-46 (309)
268 smart00354 HTH_LACI helix_turn 42.1 4.8 0.0001 29.4 -1.3 20 111-130 2-21 (70)
269 TIGR03020 EpsA transcriptional 41.7 17 0.00036 33.8 1.9 45 91-137 189-233 (247)
270 PF13404 HTH_AsnC-type: AsnC-t 41.6 13 0.00029 24.2 0.9 25 108-132 16-40 (42)
271 PRK09483 response regulator; P 41.6 10 0.00022 33.3 0.5 44 92-137 148-191 (217)
272 PRK08558 adenine phosphoribosy 41.5 24 0.00051 32.6 2.9 39 93-131 7-45 (238)
273 TIGR00180 parB_part ParB-like 41.4 13 0.00027 32.9 1.0 40 91-130 101-141 (187)
274 PF13744 HTH_37: Helix-turn-he 41.3 4.9 0.00011 30.2 -1.4 35 97-131 17-53 (80)
275 PRK09492 treR trehalose repres 40.9 7.3 0.00016 36.8 -0.6 23 110-132 5-27 (315)
276 TIGR02405 trehalos_R_Ecol treh 39.8 9.8 0.00021 36.1 0.0 21 111-131 3-23 (311)
277 PF13309 HTH_22: HTH domain 39.7 19 0.00041 25.9 1.5 41 91-131 19-64 (64)
278 COG5606 Uncharacterized conser 39.1 8.7 0.00019 29.3 -0.3 61 63-132 2-64 (91)
279 PRK10141 DNA-binding transcrip 38.7 12 0.00025 30.6 0.3 44 93-136 13-57 (117)
280 COG3413 Predicted DNA binding 37.8 12 0.00026 33.8 0.3 51 90-140 153-209 (215)
281 PF10668 Phage_terminase: Phag 37.7 8.8 0.00019 27.3 -0.5 25 105-129 16-42 (60)
282 PRK14987 gluconate operon tran 37.6 7.9 0.00017 37.0 -1.0 22 111-132 7-28 (331)
283 PF00165 HTH_AraC: Bacterial r 37.5 6.1 0.00013 25.5 -1.2 28 106-133 5-32 (42)
284 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 37.5 14 0.00031 25.2 0.5 41 90-131 2-42 (50)
285 PF05263 DUF722: Protein of un 37.1 18 0.00038 30.1 1.2 46 92-137 81-127 (130)
286 TIGR03830 CxxCG_CxxCG_HTH puta 36.9 28 0.0006 28.2 2.4 57 63-130 43-99 (127)
287 PRK12683 transcriptional regul 36.6 20 0.00044 34.0 1.7 43 97-139 4-46 (309)
288 PRK15092 DNA-binding transcrip 36.6 14 0.0003 35.4 0.5 51 89-139 5-55 (310)
289 PF05043 Mga: Mga helix-turn-h 36.2 13 0.00029 28.0 0.3 34 106-139 27-60 (87)
290 PF13443 HTH_26: Cro/C1-type H 36.2 14 0.0003 25.9 0.4 43 107-160 8-50 (63)
291 PRK10014 DNA-binding transcrip 36.0 7.7 0.00017 37.2 -1.4 23 110-132 7-29 (342)
292 cd04762 HTH_MerR-trunc Helix-T 35.3 7 0.00015 25.4 -1.3 22 111-132 2-23 (49)
293 PRK00215 LexA repressor; Valid 35.1 23 0.00051 31.5 1.7 27 109-135 23-50 (205)
294 PRK09834 DNA-binding transcrip 34.9 21 0.00045 33.3 1.4 44 92-135 6-52 (263)
295 COG4496 Uncharacterized protei 34.7 26 0.00056 26.9 1.6 31 103-134 50-80 (100)
296 PRK12679 cbl transcriptional r 34.5 24 0.00052 33.6 1.8 43 97-139 4-46 (316)
297 PRK11233 nitrogen assimilation 33.9 24 0.00051 33.4 1.7 40 99-139 6-45 (305)
298 PRK09526 lacI lac repressor; R 33.7 9 0.00019 36.7 -1.3 22 111-132 7-28 (342)
299 PRK10339 DNA-binding transcrip 33.4 11 0.00023 36.1 -0.9 22 111-132 3-24 (327)
300 PRK10423 transcriptional repre 33.3 10 0.00022 36.0 -1.0 19 113-131 2-20 (327)
301 PRK10651 transcriptional regul 32.9 17 0.00038 31.5 0.5 44 92-137 155-198 (216)
302 COG1508 RpoN DNA-directed RNA 32.7 11 0.00024 37.9 -0.8 36 105-150 320-361 (444)
303 PRK11179 DNA-binding transcrip 32.6 33 0.00072 29.1 2.2 43 92-134 6-48 (153)
304 cd07377 WHTH_GntR Winged helix 32.3 12 0.00025 26.2 -0.6 24 111-134 27-50 (66)
305 PRK10870 transcriptional repre 31.9 23 0.00049 31.0 1.1 43 92-134 52-96 (176)
306 PRK11303 DNA-binding transcrip 31.9 11 0.00023 36.0 -1.1 22 111-132 2-23 (328)
307 PRK10703 DNA-binding transcrip 31.8 10 0.00023 36.3 -1.2 22 111-132 3-24 (341)
308 PRK10360 DNA-binding transcrip 31.6 20 0.00042 30.9 0.6 44 92-137 137-180 (196)
309 PRK11050 manganese transport r 31.3 25 0.00055 29.9 1.3 28 108-135 50-77 (152)
310 COG3677 Transposase and inacti 31.2 29 0.00063 28.8 1.5 44 96-139 76-119 (129)
311 PF09607 BrkDBD: Brinker DNA-b 31.1 23 0.00051 24.9 0.8 41 90-130 3-46 (58)
312 PRK04140 hypothetical protein; 31.0 24 0.00051 34.1 1.1 81 61-160 97-178 (317)
313 PRK12684 transcriptional regul 30.9 32 0.00068 32.7 2.0 43 97-139 4-46 (313)
314 PF04703 FaeA: FaeA-like prote 30.9 14 0.0003 26.5 -0.4 36 97-132 3-38 (62)
315 PF12728 HTH_17: Helix-turn-he 30.4 9.7 0.00021 25.6 -1.2 21 111-131 3-23 (51)
316 COG3179 Predicted chitinase [G 30.3 48 0.001 29.3 2.8 70 51-130 4-74 (206)
317 PRK10401 DNA-binding transcrip 30.1 18 0.00038 34.8 0.1 21 111-131 3-23 (346)
318 COG3355 Predicted transcriptio 30.0 25 0.00055 29.0 1.0 27 110-136 43-69 (126)
319 PRK13777 transcriptional regul 29.9 40 0.00087 29.8 2.3 41 92-132 42-82 (185)
320 TIGR01764 excise DNA binding d 29.9 10 0.00022 24.7 -1.2 21 111-131 3-23 (49)
321 TIGR00637 ModE_repress ModE mo 29.8 19 0.00041 28.3 0.2 35 105-139 12-46 (99)
322 TIGR02607 antidote_HigA addict 29.7 25 0.00054 25.7 0.8 36 94-130 4-39 (78)
323 PF07750 GcrA: GcrA cell cycle 29.5 29 0.00063 30.0 1.3 37 96-132 5-42 (162)
324 smart00529 HTH_DTXR Helix-turn 28.9 18 0.00039 27.7 -0.1 24 112-135 2-25 (96)
325 TIGR00122 birA_repr_reg BirA b 28.9 23 0.00051 25.4 0.5 24 110-133 14-37 (69)
326 PF08220 HTH_DeoR: DeoR-like h 28.6 27 0.00058 24.3 0.8 23 110-132 15-37 (57)
327 TIGR02395 rpoN_sigma RNA polym 28.6 18 0.00039 36.5 -0.1 22 110-131 319-340 (429)
328 smart00351 PAX Paired Box doma 28.5 1.3E+02 0.0028 24.6 5.0 31 51-81 34-64 (125)
329 PRK09958 DNA-binding transcrip 28.4 24 0.00053 30.5 0.7 44 92-137 143-186 (204)
330 COG4974 XerD Site-specific rec 28.2 99 0.0021 29.5 4.6 79 53-140 210-292 (300)
331 PRK10403 transcriptional regul 28.0 24 0.00052 30.5 0.6 44 92-137 153-196 (215)
332 PF00392 GntR: Bacterial regul 27.7 13 0.00028 26.4 -1.0 21 113-133 28-48 (64)
333 PRK10072 putative transcriptio 27.7 13 0.00028 29.2 -1.1 27 105-131 42-68 (96)
334 COG3293 Transposase and inacti 27.6 38 0.00083 27.5 1.7 56 262-318 40-101 (124)
335 PF13693 HTH_35: Winged helix- 27.5 9.3 0.0002 28.7 -1.8 27 107-133 13-39 (78)
336 TIGR02417 fruct_sucro_rep D-fr 27.1 14 0.00031 35.1 -1.1 21 112-132 2-22 (327)
337 PRK15369 two component system 26.9 26 0.00057 29.9 0.6 43 93-137 150-192 (211)
338 TIGR01481 ccpA catabolite cont 26.9 14 0.00031 35.0 -1.1 22 111-132 3-24 (329)
339 TIGR02702 SufR_cyano iron-sulf 26.9 36 0.00078 30.4 1.5 37 96-133 3-39 (203)
340 TIGR01884 cas_HTH CRISPR locus 26.3 45 0.00097 29.7 2.0 33 101-133 147-181 (203)
341 COG5421 Transposase [DNA repli 26.2 1.3E+02 0.0029 30.5 5.4 56 199-269 155-210 (480)
342 PRK10079 phosphonate metabolis 26.2 40 0.00086 30.9 1.7 47 67-134 14-60 (241)
343 TIGR03454 partition_RepB plasm 26.1 32 0.0007 33.3 1.1 44 88-131 156-199 (325)
344 PRK09906 DNA-binding transcrip 25.8 38 0.00083 31.6 1.6 40 100-139 6-45 (296)
345 PRK10727 DNA-binding transcrip 25.7 16 0.00035 35.1 -1.1 21 111-131 3-23 (343)
346 PRK11169 leucine-responsive tr 25.2 33 0.00072 29.5 0.9 45 91-135 10-54 (164)
347 PRK11013 DNA-binding transcrip 25.1 39 0.00084 32.0 1.5 41 98-139 8-48 (309)
348 PRK15090 DNA-binding transcrip 25.1 43 0.00094 31.0 1.8 45 91-135 8-54 (257)
349 PRK09726 antitoxin HipB; Provi 24.4 22 0.00048 27.1 -0.3 44 105-160 21-64 (88)
350 PRK11569 transcriptional repre 24.2 45 0.00098 31.3 1.7 44 92-135 23-69 (274)
351 PRK12681 cysB transcriptional 24.2 44 0.00096 32.0 1.7 42 98-139 5-46 (324)
352 COG1414 IclR Transcriptional r 23.9 47 0.001 30.7 1.7 37 99-135 6-45 (246)
353 PRK11151 DNA-binding transcrip 23.8 46 0.001 31.3 1.7 41 98-139 5-45 (305)
354 PF14493 HTH_40: Helix-turn-he 23.8 38 0.00081 26.0 0.9 61 100-162 4-64 (91)
355 COG1846 MarR Transcriptional r 23.6 46 0.00099 26.2 1.4 23 113-135 40-62 (126)
356 PRK05932 RNA polymerase factor 23.5 25 0.00055 35.8 -0.2 21 110-130 344-364 (455)
357 PF07022 Phage_CI_repr: Bacter 23.3 22 0.00048 25.5 -0.5 21 111-131 14-35 (66)
358 PRK12680 transcriptional regul 23.3 49 0.0011 31.8 1.8 41 99-139 6-46 (327)
359 PF07453 NUMOD1: NUMOD1 domain 23.2 16 0.00035 22.8 -1.1 23 108-130 15-37 (37)
360 PRK09791 putative DNA-binding 22.9 47 0.001 31.2 1.6 42 97-139 8-49 (302)
361 PRK12469 RNA polymerase factor 22.9 26 0.00055 35.9 -0.3 31 110-150 370-400 (481)
362 COG1609 PurR Transcriptional r 22.5 20 0.00043 34.8 -1.1 22 111-132 2-23 (333)
363 PRK09706 transcriptional repre 22.1 27 0.00058 28.9 -0.2 44 105-160 14-57 (135)
364 PF14549 P22_Cro: DNA-binding 22.1 14 0.0003 26.3 -1.7 20 110-129 10-29 (60)
365 PRK13832 plasmid partitioning 22.0 43 0.00093 34.4 1.1 40 90-129 99-138 (520)
366 PF13610 DDE_Tnp_IS240: DDE do 22.0 66 0.0014 26.8 2.1 44 297-343 95-138 (140)
367 TIGR03418 chol_sulf_TF putativ 21.9 47 0.001 30.9 1.4 40 98-138 5-44 (291)
368 PF00382 TFIIB: Transcription 21.9 91 0.002 22.4 2.6 65 55-126 3-71 (71)
369 PRK10094 DNA-binding transcrip 21.6 47 0.001 31.5 1.3 41 98-139 6-46 (308)
370 TIGR03734 PRTRC_parB PRTRC sys 21.6 44 0.00095 34.8 1.1 41 90-130 89-130 (554)
371 TIGR01637 phage_arpU phage tra 21.2 85 0.0018 25.7 2.6 49 92-140 79-128 (132)
372 COG1342 Predicted DNA-binding 21.1 69 0.0015 25.0 1.8 41 92-133 33-73 (99)
373 COG4941 Predicted RNA polymera 20.9 84 0.0018 30.6 2.7 61 91-153 119-179 (415)
374 PF00440 TetR_N: Bacterial reg 20.9 27 0.00058 23.0 -0.4 24 109-132 16-39 (47)
375 COG4565 CitB Response regulato 20.5 63 0.0014 29.3 1.7 24 110-133 174-197 (224)
376 TIGR02944 suf_reg_Xantho FeS a 20.4 42 0.0009 27.5 0.6 25 110-134 26-50 (130)
No 1
>KOG4585 consensus Predicted transposase [Replication, recombination and repair]
Probab=100.00 E-value=3.6e-42 Score=327.82 Aligned_cols=313 Identities=36% Similarity=0.578 Sum_probs=254.1
Q ss_pred hcCCCHHHHHHHHHHhhhccccccCCcccCCCCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHH
Q 016336 59 VFKISRRTFDYICSLVEEKMVVKTGGFSFTSGKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 59 ~frms~~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~ 138 (391)
.|++++.+|++|+.............+....+ +++...+++.|+.++++.+...++..||...+|+ .+...+.
T Consensus 7 ~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~v~~~~~~~~~~~~~~~i~~~fg~~~~~~-----~~~~~~~ 79 (326)
T KOG4585|consen 7 EFRKSYTTFDKICSLVQSLNVVKNSGFMLSSL--LPADTLVAVALWRLKTGESLRTVEKKFGLGQSTC-----KFLEEKE 79 (326)
T ss_pred HHHHHHHHHHHHhhhhhhhhhhcccchhhhcc--ccHHhhhhhhhccccccchHHHHHHHcCCcchhh-----hHHHhhh
Confidence 78999999999999876654443322222222 2289999999999999999999999999999999 6667777
Q ss_pred HhccccccCCCHHHHHHHHHHHhHhhCCCccceeeeeeEEEeecCCCCCccccccCCCCcceeEEEEeeCCCcceeeccc
Q 016336 139 QKGLQHLQWPSETEMAEIKSKFEKIQGLPNCCGVIDTTHILMCLPSSDPTNNLWLDHMKNHSMVLQAIVDPEMRFRDIVT 218 (391)
Q Consensus 139 ~~~~~~i~~P~~~~~~~i~~~f~~~~~fp~~~GaIDgthi~i~~p~~~~~~~~y~~~k~~~s~~~q~v~d~~~~f~~v~~ 218 (391)
..+++++.||....+.++.+.|+. +|+|+|+||+|||++..|+. ....|.|+ .+++++|+|||.+++|++|.+
T Consensus 80 ~~~~~~~~~p~~~~~~~i~~~~~~---~~~~~g~~d~~hi~~~~~~~--~~~~~~n~--~~~~Nvlav~n~d~~f~~v~v 152 (326)
T KOG4585|consen 80 DLAPHFLKWPSRRILYEIRERFES---LPNCVGAIDTTHIPIRVPPK--SGSVYFNK--EQSKNLLAVCNFDMRFIYVDV 152 (326)
T ss_pred cccchhhcCchhhhhhhhcccccc---ccchhccccccccceecCcc--cccccccc--ccchhhhheecCCceEEEEEc
Confidence 788999999998888889888876 99999999999999996654 45677777 889999999999999999999
Q ss_pred CCCCCCCcHHHHhhChhhHHhhhccccCCccccc-CCCCccceEEeeCCCCCCCCcccccCCCCCCCchhhhhhhchhhh
Q 016336 219 GWPGKMEDRLIFRSSNFYKLCEEGKRLNGKILEL-SGGSEIREYIIGDSGYPFLPYLVTPYKGQELPELGSEFNRRHSAS 297 (391)
Q Consensus 219 g~pGs~~D~~v~~~S~l~~~~~~g~~l~~~~~~~-~~g~~~~~~llgD~gYpl~~~l~~P~~~~~~~~~~~~fN~~ls~~ 297 (391)
|||||+||+.|++.+.+.+....+..+ ++.+ ..|-+.+.+++|+.+||+.+++|+|+.++..+..++.||.+|+.+
T Consensus 153 g~~Gs~~D~kvl~~~~~~~~~~~~~~~---k~yl~d~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~elFN~rh~~~ 229 (326)
T KOG4585|consen 153 GWPGSAHDTKVLQDSLLYKRNFPHPPL---KYYLVDSGYPLRPGLLGPIGFPLYSLLMFPYGGPQPTNSQELFNKRHSSL 229 (326)
T ss_pred cCCCCccHHHHHHhhcccccccccCCc---cccccccCcccccccccccccccchhhhcccCCCCCCchHHHHhhhhhhH
Confidence 999999999999999998776665433 3333 345577889999999999999999999887899999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhhccccCCCCCchhHHHHHHHHHHchhcccCCccCCCCCCCCCCCCC--cc-cccccccChhH
Q 016336 298 HLVAQRALARLKDKWKIIQGVMWRPDKHKLPRIILVCCLLHNIVIDLEDEMQDEIPLLHDHDSG--YH-QQVCETADMEG 374 (391)
Q Consensus 298 R~~vE~afg~Lk~rfriL~~~~~~~~~~~~~~ii~acc~LHN~~~~~~d~~~~~~~~~~~~~~~--~~-~~~~~~~~~~~ 374 (391)
|.++|++||++|.||+||... +..+..+.+.||.|||+||||+++.++...++...+..++.+ .. ..........+
T Consensus 230 r~v~e~~fg~lk~rw~il~~~-~~~~~~~~~~iV~a~caLHN~~~~~~~~~~~~~~~e~~~d~~~~~~~~~~~~~~~~~~ 308 (326)
T KOG4585|consen 230 RSVAERAFGVLKAKWRILQRR-EKYDLKKLPKIVTACCALHNIIRDSDEEDPDDPKWEKFDDYGENVAHLRYAPQQRDYM 308 (326)
T ss_pred HHHHHHHHHHhhhhhHHHhhc-ccccccchHHHHHHHHHHHHHHHhhcccccccccccccccccccchhcccchhHHHHH
Confidence 999999999999999999998 667788999999999999999999987554443222222222 01 11122345567
Q ss_pred HHHHHHHHHHhccCC
Q 016336 375 EYLRDKLSLYLSGKL 389 (391)
Q Consensus 375 ~~~Rd~l~~~~~~~~ 389 (391)
...|+.|+.-+.+..
T Consensus 309 ~~~r~~l~~~l~~~~ 323 (326)
T KOG4585|consen 309 EKIRDNLLSELWNGT 323 (326)
T ss_pred HHHHHHHHHHHHhcc
Confidence 888999988876654
No 2
>PF04827 Plant_tran: Plant transposon protein; InterPro: IPR006912 This entry represents a putative Harbinger transposase-derived nuclease, which is thought to have nuclease activity. However it does not have transposase activity [, ]. ; GO: 0016788 hydrolase activity, acting on ester bonds
Probab=100.00 E-value=3.6e-37 Score=264.51 Aligned_cols=199 Identities=20% Similarity=0.314 Sum_probs=173.0
Q ss_pred ccccCCCHHHHHHHHHHHhHhhCCCccceeeeeeEEEeecCCCCCccccccCCCCcceeEEEEeeCCCcceeecccCCCC
Q 016336 143 QHLQWPSETEMAEIKSKFEKIQGLPNCCGVIDTTHILMCLPSSDPTNNLWLDHMKNHSMVLQAIVDPEMRFRDIVTGWPG 222 (391)
Q Consensus 143 ~~i~~P~~~~~~~i~~~f~~~~~fp~~~GaIDgthi~i~~p~~~~~~~~y~~~k~~~s~~~q~v~d~~~~f~~v~~g~pG 222 (391)
+|++-|+.++++++.+.++ ..||||.+|+|||+|+.++.+|..-.+....++++..++.++||++.|.+|+++..|.||
T Consensus 2 ~YLr~P~~~d~~rll~~~e-~rGFpGmlGSIDCmHw~WkncP~aw~g~~~~G~~g~pTiiLEaVAs~dlwIWhaffG~~G 80 (205)
T PF04827_consen 2 EYLRRPTNEDLERLLQIGE-ARGFPGMLGSIDCMHWEWKNCPTAWKGQYTRGKEGVPTIILEAVASHDLWIWHAFFGMPG 80 (205)
T ss_pred cccCCCChhHHHHHHHhhh-hcCCCccccceeEEEeehhcchHHhhhcccCCCCCCCeehhhhhhccchhhhheeeccCC
Confidence 5889999999999997654 569999999999999999988765445444489999999999999999999999999999
Q ss_pred CCCcHHHHhhChhhHHhhhccccCCcccccCCCCcc-ceEEeeCCCCCCCCcccccCCCCCCCchhhhhhhchhhhHHHH
Q 016336 223 KMEDRLIFRSSNFYKLCEEGKRLNGKILELSGGSEI-REYIIGDSGYPFLPYLVTPYKGQELPELGSEFNRRHSASHLVA 301 (391)
Q Consensus 223 s~~D~~v~~~S~l~~~~~~g~~l~~~~~~~~~g~~~-~~~llgD~gYpl~~~l~~P~~~~~~~~~~~~fN~~ls~~R~~v 301 (391)
|.+|..|+..|+++..+.+|+... -.+.+. |.+. -.|+|+|..||-+..++.+++ .+.+++++.|.++++++|..|
T Consensus 81 S~NDiNVL~~Splf~~~~~G~ap~-v~f~VN-g~~Y~~gYYLaDGiYP~watfvktI~-~p~~~k~k~fa~~QE~~RKDV 157 (205)
T PF04827_consen 81 SNNDINVLDRSPLFDDLLQGQAPR-VQFTVN-GHEYNMGYYLADGIYPEWATFVKTIS-LPQGEKRKLFAKHQESARKDV 157 (205)
T ss_pred cccccccccccHHHHHHhcCcCCc-eEEEec-CeecccceeeccCcCcchHhHhhhcc-hhhchhhHHHHHhCHHHHHHH
Confidence 999999999999999998885421 112222 3221 348999999999999999999 578889999999999999999
Q ss_pred HHHHHHHHHHHHHhhccccCCCCCchhHHHHHHHHHHchhcccC
Q 016336 302 QRALARLKDKWKIIQGVMWRPDKHKLPRIILVCCLLHNIVIDLE 345 (391)
Q Consensus 302 E~afg~Lk~rfriL~~~~~~~~~~~~~~ii~acc~LHN~~~~~~ 345 (391)
|+|||+|++||+|++.+....+.+.+..|+.||++||||+++.+
T Consensus 158 ErAFGVLQaRfaIi~~p~r~w~~~~l~~Im~aCiILHNMIvEDE 201 (205)
T PF04827_consen 158 ERAFGVLQARFAIIRGPARLWDREDLANIMRACIILHNMIVEDE 201 (205)
T ss_pred HHHHHHHHHHHHHhcCchhccCHHHHHHHHHHHHHhhheeEecc
Confidence 99999999999999999777788899999999999999999775
No 3
>PF13359 DDE_Tnp_4: DDE superfamily endonuclease
Probab=100.00 E-value=1.4e-37 Score=270.14 Aligned_cols=154 Identities=43% Similarity=0.835 Sum_probs=136.5
Q ss_pred eeeeEEEeecCCC-CCccccccCCCCcceeEEEEeeCCCcceeecccCCCCCCCcHHHHhhChhhHHhhhccccCCcccc
Q 016336 173 IDTTHILMCLPSS-DPTNNLWLDHMKNHSMVLQAIVDPEMRFRDIVTGWPGKMEDRLIFRSSNFYKLCEEGKRLNGKILE 251 (391)
Q Consensus 173 IDgthi~i~~p~~-~~~~~~y~~~k~~~s~~~q~v~d~~~~f~~v~~g~pGs~~D~~v~~~S~l~~~~~~g~~l~~~~~~ 251 (391)
||||||+|++|.. ......|+++|+.|++++|++||++|+|++++.+||||+||+.+|++|++...++..
T Consensus 1 iDgt~v~i~~P~~~~~~~~~y~~~k~~~~~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~s~~~~~l~~~--------- 71 (158)
T PF13359_consen 1 IDGTHVPIQRPSDKEEQREFYSGKKKNHSLKVQIVCDPDGRIIYVSVGWPGSVHDSTIFRQSGLLDRLEQA--------- 71 (158)
T ss_pred CccEEEEEEeCCccccccccccCCCCcceEeEEEEEeccceeEeeecccccccccccccccccccceeecc---------
Confidence 7999999998874 235678999999999999999999999999999999999999999999988765521
Q ss_pred cCCCCccceEEeeCCCCCCCCcccccCC---CCCCCchhhhhhhchhhhHHHHHHHHHHHHHHHHHhhccccCCCCCchh
Q 016336 252 LSGGSEIREYIIGDSGYPFLPYLVTPYK---GQELPELGSEFNRRHSASHLVAQRALARLKDKWKIIQGVMWRPDKHKLP 328 (391)
Q Consensus 252 ~~~g~~~~~~llgD~gYpl~~~l~~P~~---~~~~~~~~~~fN~~ls~~R~~vE~afg~Lk~rfriL~~~~~~~~~~~~~ 328 (391)
+++ ++++|||.|||+.+++|+||+ +.+++.+++.||++|+++|.+||++||+||+||+||+..+.....+++.
T Consensus 72 ~~~----~~~~l~D~gy~~~~~~~~P~~~~~~~~l~~~e~~~N~~~s~~R~~vE~~~~~lK~rf~~l~~~~~~~~~~~~~ 147 (158)
T PF13359_consen 72 FPP----GEYLLGDSGYPLSPYLLTPYKKPKGRELTPEEKEFNRRHSSARIIVERAFGRLKSRFRILRGRLRLSRPEKAP 147 (158)
T ss_pred ccc----CccccccccccccccccccccccccccccccccchhccccceeeeeHHHHHHHHHhcccCCcccCCCcHhHHH
Confidence 222 489999999999999999995 5678999999999999999999999999999999998776432278999
Q ss_pred HHHHHHHHHHc
Q 016336 329 RIILVCCLLHN 339 (391)
Q Consensus 329 ~ii~acc~LHN 339 (391)
.+|.|||+|||
T Consensus 148 ~ii~~~~~LhN 158 (158)
T PF13359_consen 148 QIILACCVLHN 158 (158)
T ss_pred HHHheeEEEEC
Confidence 99999999999
No 4
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=99.01 E-value=2.2e-10 Score=80.23 Aligned_cols=51 Identities=24% Similarity=0.289 Sum_probs=48.1
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhcc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGL 142 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~ 142 (391)
.+++++|++++|.||++|.++.++|..||||+|||+++++++++.|+..++
T Consensus 2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l~ 52 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVLK 52 (53)
T ss_pred CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhcC
Confidence 479999999999999999999999999999999999999999999987653
No 5
>PF13612 DDE_Tnp_1_3: Transposase DDE domain
Probab=98.83 E-value=1.3e-09 Score=93.47 Aligned_cols=128 Identities=17% Similarity=0.219 Sum_probs=93.5
Q ss_pred CccceeeeeeEEEeecCCCCCcc-----cc---ccCCCCcceeEEEEeeCCCcceeecccCCCCCCCcHHHHhhChhhHH
Q 016336 167 PNCCGVIDTTHILMCLPSSDPTN-----NL---WLDHMKNHSMVLQAIVDPEMRFRDIVTGWPGKMEDRLIFRSSNFYKL 238 (391)
Q Consensus 167 p~~~GaIDgthi~i~~p~~~~~~-----~~---y~~~k~~~s~~~q~v~d~~~~f~~v~~g~pGs~~D~~v~~~S~l~~~ 238 (391)
+..+.+||++-|+++.+...... .. |+..+-+|++++.++|+..|.++.+.. .||++||..++..- .
T Consensus 4 ~~~i~~iDS~Pi~vC~~~R~~r~k~~~~~a~~G~~a~~~fyGfKlHllv~~~G~i~~~~l-T~an~~D~~~~~~l--~-- 78 (155)
T PF13612_consen 4 CTGIYIIDSFPIPVCHNIRIKRHKVFKGLAYRGYCAMGWFYGFKLHLLVNDSGEIVAFTL-TPANVHDRKVLEEL--S-- 78 (155)
T ss_pred ccEEEEEecCChhHhCccchhhhccccCccccceeccceeEeeeeeeEEccCCcEEEEEE-cccccccccccccc--c--
Confidence 56788999999999976422111 12 333445689999999999999998755 49999999988311 0
Q ss_pred hhhccccCCcccccCCCCccceEEeeCCCCCCCC----------cccccCCCCCCCchhhhhhhchhhhHHHHHHHHHHH
Q 016336 239 CEEGKRLNGKILELSGGSEIREYIIGDSGYPFLP----------YLVTPYKGQELPELGSEFNRRHSASHLVAQRALARL 308 (391)
Q Consensus 239 ~~~g~~l~~~~~~~~~g~~~~~~llgD~gYpl~~----------~l~~P~~~~~~~~~~~~fN~~ls~~R~~vE~afg~L 308 (391)
. + +...++||.||-... .|+||.+.+--......+++.+.+.|..||..|+.|
T Consensus 79 --~-------------~--~~g~l~gDkGYis~~L~~~L~~~gI~L~t~~RkNmk~~~~~~~~~~l~~~R~~IETvfs~L 141 (155)
T PF13612_consen 79 --E-------------N--LKGKLFGDKGYISKELKDELKEQGIKLITPRRKNMKNKLMPLFDKLLLRKRRIIETVFSQL 141 (155)
T ss_pred --c-------------c--cccceecchhhhcchHHhhhhhceEEEeccccccccccccchhhhhhhheeeEeehHHHHH
Confidence 0 0 123799999995322 589999853323344568889999999999999999
Q ss_pred HHHHHHhh
Q 016336 309 KDKWKIIQ 316 (391)
Q Consensus 309 k~rfriL~ 316 (391)
|+.|.+=+
T Consensus 142 k~~~~ie~ 149 (155)
T PF13612_consen 142 KNQFNIEH 149 (155)
T ss_pred HHhhceEe
Confidence 99887654
No 6
>PF13586 DDE_Tnp_1_2: Transposase DDE domain
Probab=97.40 E-value=7.1e-05 Score=58.08 Aligned_cols=52 Identities=19% Similarity=0.263 Sum_probs=39.0
Q ss_pred chhhhhhhchhhhHHHHHHHHHHHHHHHHHhhccccCCCCCchhHHHHHHHHH
Q 016336 285 ELGSEFNRRHSASHLVAQRALARLKDKWKIIQGVMWRPDKHKLPRIILVCCLL 337 (391)
Q Consensus 285 ~~~~~fN~~ls~~R~~vE~afg~Lk~rfriL~~~~~~~~~~~~~~ii~acc~L 337 (391)
.....+...+...|.+||++|+.||. |+.|.....+........+.+||+++
T Consensus 34 ~~~~~~d~~~~~~Rw~VEr~f~wlk~-~Rrl~~ryek~~~s~~~~v~la~~~i 85 (88)
T PF13586_consen 34 RRPRKFDFRLYKRRWVVERTFAWLKR-FRRLATRYEKLASSFLAFVHLACIVI 85 (88)
T ss_pred cccCccchhhhccceehhhhhHHHHH-cCccccccccCHHHHHHHHHHHHHHH
Confidence 34678889999999999999999998 89998876544444555555555543
No 7
>PF01609 DDE_Tnp_1: Transposase DDE domain; InterPro: IPR002559 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS4 transposase. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 3ECP_A 4DM0_A 1MUS_A 1MUH_A 1MM8_A 1B7E_A.
Probab=97.06 E-value=8.9e-06 Score=72.67 Aligned_cols=151 Identities=14% Similarity=0.118 Sum_probs=81.5
Q ss_pred ccceeeeeeEEEeecCCCCCccccccCCCCcceeEEEEee-CCCcceeecccCCCCCCCcHHHHhhChhhHHhhhccccC
Q 016336 168 NCCGVIDTTHILMCLPSSDPTNNLWLDHMKNHSMVLQAIV-DPEMRFRDIVTGWPGKMEDRLIFRSSNFYKLCEEGKRLN 246 (391)
Q Consensus 168 ~~~GaIDgthi~i~~p~~~~~~~~y~~~k~~~s~~~q~v~-d~~~~f~~v~~g~pGs~~D~~v~~~S~l~~~~~~g~~l~ 246 (391)
..+-+||+|+|+.. +.. .....+.+++....+++++++ +..+.++.+... +|+.+|...+.. + ++...
T Consensus 4 ~~~~~iD~T~i~~~-~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~d~~~~~~--l---l~~~~--- 72 (213)
T PF01609_consen 4 RRVVAIDGTTIRTP-HDK-SARRYKKGKKRGFGYKLHLAVDDNSGLPLSVKVT-PGNVHDSKALPE--L---LERKP--- 72 (213)
T ss_dssp EEEEEEETTT--EE-EEE-EE-B-SSGGGHSSHGGHHHHHHHHHGGGGGGEEE-EEEGG-HHHHHH--H---HTT-----
T ss_pred CeEEEEECcEEEee-cch-hhhcccCCCCcCCCEeEEEEEeecccceeeeecc-ccccceeecccc--c---ccccc---
Confidence 45778999999987 111 111223344555667888888 566667777776 999999998875 2 22100
Q ss_pred CcccccCCCCccceEEeeCCCCCCCC----------cccccCCCCCCC--------------------------------
Q 016336 247 GKILELSGGSEIREYIIGDSGYPFLP----------YLVTPYKGQELP-------------------------------- 284 (391)
Q Consensus 247 ~~~~~~~~g~~~~~~llgD~gYpl~~----------~l~~P~~~~~~~-------------------------------- 284 (391)
...+.++++|+||...+ ..+.|.+.....
T Consensus 73 ---------~~~~~~vv~D~gy~s~~~~~~l~~~~~~~vi~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 143 (213)
T PF01609_consen 73 ---------GRKPDLVVADRGYDSAENLEALKERGIHFVIRLKKNRKKKIQKIENKFWKSFDRRSARKKPKQKSKRVRVV 143 (213)
T ss_dssp ------------EEEEEE-S--BBTTHHHHHHTS---EEEEE--EEEE-TTS-EEEE--EEEEEEEEEEETGGGEEEEEE
T ss_pred ---------cccccceeecccccceeccccccccccccccccccccccccccchhhcccccccccccccccccccccccc
Confidence 01146899999996443 124444422110
Q ss_pred --chhhhhhhc--------------hhhhHHHHHHHHHHHHHHHHHhhccccCCCCCchhHHHHHHHHHHch
Q 016336 285 --ELGSEFNRR--------------HSASHLVAQRALARLKDKWKIIQGVMWRPDKHKLPRIILVCCLLHNI 340 (391)
Q Consensus 285 --~~~~~fN~~--------------ls~~R~~vE~afg~Lk~rfriL~~~~~~~~~~~~~~ii~acc~LHN~ 340 (391)
......... +.+.|..||+.|..||+.|. |... .......+...+.+|++-.|+
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~~Y~~Rw~IE~~f~~lK~~~~-l~~~-~~~~~~~~~~~~~~~~la~nl 213 (213)
T PF01609_consen 144 IRKEQKKKGYFLVTNITTLPRDTAALYRRRWQIERFFRELKQFLG-LERL-RVRSPERIEAHLFLTLLAYNL 213 (213)
T ss_dssp EEEECS--TTS---EEEEEESS--SHHHCGGHHHHHHHHHTTTTT-GGGS---SSHHHHHHHHHHHHHH---
T ss_pred cccccccccccccccccccccccceeecccchhhHHHHHHHhcCC-Cchh-cccCHHHHHHHHHHHHhhCcC
Confidence 111111222 88999999999999999544 3332 223445666777777777764
No 8
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=96.01 E-value=0.0015 Score=43.64 Aligned_cols=41 Identities=34% Similarity=0.352 Sum_probs=23.1
Q ss_pred CccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhH
Q 016336 91 KHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
+.++.+++..|.-+ +..|.+++.||..+|+|+|||++.+.+
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 45788888877744 689999999999999999999998764
No 9
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=95.93 E-value=0.0014 Score=43.99 Aligned_cols=40 Identities=25% Similarity=0.218 Sum_probs=30.3
Q ss_pred CccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhh
Q 016336 91 KHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~ 131 (391)
+.++.+ ++.-++..++.|.+..+||..||||++||.+++.
T Consensus 4 ~~~~~~-~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 4 PKLSKE-QIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSSHC-CHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred CCCCHH-HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 344444 6777788889999999999999999999999875
No 10
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=95.87 E-value=0.0064 Score=41.59 Aligned_cols=45 Identities=29% Similarity=0.399 Sum_probs=38.6
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
.++++++-.+.++| -.|.++.++|..+|+|.+||+++..+.+.-|
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 58899999999999 6788999999999999999999988877655
No 11
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=95.56 E-value=0.0063 Score=42.32 Aligned_cols=42 Identities=31% Similarity=0.442 Sum_probs=31.0
Q ss_pred CCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhH
Q 016336 90 GKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 90 ~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
+..+++++++.+.-. +-.|.+..+||..|||++|||+.|+..
T Consensus 4 R~~LTl~eK~~iI~~-~e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 4 RKSLTLEEKLEIIKR-LEEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp SSS--HHHHHHHHHH-HHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred CccCCHHHHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 467899999887654 678889999999999999999988653
No 12
>smart00351 PAX Paired Box domain.
Probab=94.51 E-value=0.024 Score=46.97 Aligned_cols=46 Identities=22% Similarity=0.260 Sum_probs=40.2
Q ss_pred CCCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHH
Q 016336 89 SGKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 89 ~~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
.+.+++.+.+.-+.+.+. .|.+...+|..||||++||++++.++-+
T Consensus 14 ~~~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 14 NGRPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCCCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 457799999988887775 8999999999999999999999988754
No 13
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=94.17 E-value=0.0091 Score=40.71 Aligned_cols=37 Identities=24% Similarity=0.196 Sum_probs=22.4
Q ss_pred HHHHHHHHHhcCCCCccccccccCCcccccchhhhHHH
Q 016336 97 DQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFV 134 (391)
Q Consensus 97 ~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~ 134 (391)
.++.+...+. .|.+...+|..||||++||++++.++.
T Consensus 6 ~R~~ii~l~~-~G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 6 RRAQIIRLLR-EGWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp ----HHHHHH-HT--HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 3444444444 499999999999999999999988764
No 14
>PF13518 HTH_28: Helix-turn-helix domain
Probab=93.94 E-value=0.02 Score=39.19 Aligned_cols=37 Identities=30% Similarity=0.382 Sum_probs=30.7
Q ss_pred HHHHHHHHhcCCCCccccccccCCcccccchhhhHHHH
Q 016336 98 QVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 98 ~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
++.+...++ .|.++..+|..||||.+||.+++..+-.
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 455666677 6779999999999999999998877654
No 15
>cd00131 PAX Paired Box domain
Probab=93.77 E-value=0.04 Score=45.84 Aligned_cols=46 Identities=24% Similarity=0.234 Sum_probs=40.4
Q ss_pred CCCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHH
Q 016336 89 SGKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 89 ~~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
.+.++|.+.+.-|.+.+ ..|.+.+.+|..||||++||++++.++-+
T Consensus 14 m~~~lS~d~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e 59 (128)
T cd00131 14 NGRPLPDSIRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILNRYYE 59 (128)
T ss_pred CCCcCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 46889999988888776 58999999999999999999999888765
No 16
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=93.63 E-value=0.047 Score=41.63 Aligned_cols=47 Identities=15% Similarity=0.201 Sum_probs=43.1
Q ss_pred CCCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHH
Q 016336 89 SGKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 89 ~~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
.+-.+++..++.++-..+..|.+...++..||||..|+++++.++-.
T Consensus 5 ~nA~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra 51 (85)
T PF13011_consen 5 KNARLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRA 51 (85)
T ss_pred CCCCCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34679999999999999999999999999999999999999988764
No 17
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=93.02 E-value=0.061 Score=37.17 Aligned_cols=43 Identities=28% Similarity=0.313 Sum_probs=32.2
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
.+|+.++-++.|+|+ .|.++.++|..+|+|.+||...+.+...
T Consensus 10 ~L~~~~r~i~~l~~~-~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 10 QLPERQREIFLLRYF-QGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp CS-HHHHHHHHHHHT-S---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHH-HCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 478888888888777 6889999999999999999988776554
No 18
>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=92.77 E-value=0.034 Score=37.20 Aligned_cols=36 Identities=17% Similarity=0.269 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhcCC-CCccccccccCCcccccchhhh
Q 016336 96 RDQVAIALRRLSSG-DSLMSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 96 e~~l~i~L~~L~~g-~~~~~l~~~Fgvs~sTvs~~~~ 131 (391)
++.+..+|..+..| .+++..|..|||++||+++.++
T Consensus 2 ee~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~ 38 (45)
T PF05225_consen 2 EEDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLR 38 (45)
T ss_dssp HHHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHc
Confidence 67788888888899 9999999999999999987654
No 19
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=92.15 E-value=0.13 Score=39.88 Aligned_cols=51 Identities=33% Similarity=0.436 Sum_probs=45.2
Q ss_pred CCCccCHHHHHHHHHHHhcCCCCccccccccC-CcccccchhhhHHHHHHHH
Q 016336 89 SGKHLSFRDQVAIALRRLSSGDSLMSIGDSCG-LHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 89 ~~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fg-vs~sTvs~~~~~~~~~l~~ 139 (391)
+.+.+...-++++.|..--+|.++.+||..|| .+.|||+..+.++-..+.+
T Consensus 24 R~~~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 24 RKKEIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred CCcCcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 44578888999999999999999999999999 9999999999888877753
No 20
>PRK00118 putative DNA-binding protein; Validated
Probab=91.95 E-value=0.14 Score=40.81 Aligned_cols=49 Identities=18% Similarity=0.138 Sum_probs=40.2
Q ss_pred CccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 91 KHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
+.++..++-++.|+++ .|.++..||..+|+|++||++.+.+....+.+.
T Consensus 16 ~~L~ekqRevl~L~y~-eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 16 SLLTEKQRNYMELYYL-DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred ccCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5577777777766544 599999999999999999999999887777654
No 21
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=91.70 E-value=0.11 Score=31.97 Aligned_cols=39 Identities=21% Similarity=0.236 Sum_probs=28.8
Q ss_pred CccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhh
Q 016336 91 KHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVT 130 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~ 130 (391)
..++.+++..+... +..|.+...++..||++++|+++++
T Consensus 4 ~~~~~~~~~~i~~~-~~~~~s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRL-LAAGESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHhC
Confidence 44566655555444 4577899999999999999998763
No 22
>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=91.66 E-value=0.12 Score=32.73 Aligned_cols=26 Identities=23% Similarity=0.346 Sum_probs=19.0
Q ss_pred CChhHHHhhcCCCHHHHHHHHHHhhh
Q 016336 51 KGLDKFKSVFKISRRTFDYICSLVEE 76 (391)
Q Consensus 51 ~~~~~F~~~frms~~tF~~L~~~l~~ 76 (391)
.+|++|...|+|+++.|..|-..=+.
T Consensus 2 Lsd~dF~~vFgm~~~eF~~lP~WKq~ 27 (36)
T PF02209_consen 2 LSDEDFEKVFGMSREEFYKLPKWKQN 27 (36)
T ss_dssp S-HHHHHHHHSS-HHHHHHS-HHHHH
T ss_pred cCHHHHHHHHCCCHHHHHHChHHHHH
Confidence 36899999999999999987654433
No 23
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=91.51 E-value=0.078 Score=44.50 Aligned_cols=45 Identities=22% Similarity=0.141 Sum_probs=40.0
Q ss_pred CccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHH
Q 016336 91 KHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
.+.+.+.+-+++..++..|.|.+.+|..||||.|||.+++.++-+
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 345678889999999999999999999999999999999988754
No 24
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=91.08 E-value=0.071 Score=39.80 Aligned_cols=41 Identities=15% Similarity=0.144 Sum_probs=29.6
Q ss_pred HHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHH
Q 016336 98 QVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 98 ~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~ 138 (391)
.+-++-+.+.+..+-+..|..||||+|||++-+.+=+..|.
T Consensus 8 ~i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in 48 (82)
T PF12116_consen 8 VIEIANYIIETKATVRQAAKVFGVSKSTVHKDVTERLPKIN 48 (82)
T ss_dssp HHHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-
T ss_pred HHHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcC
Confidence 35667888999999999999999999999987766555554
No 25
>PRK04217 hypothetical protein; Provisional
Probab=91.07 E-value=0.17 Score=40.74 Aligned_cols=49 Identities=16% Similarity=0.166 Sum_probs=39.3
Q ss_pred CccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 91 KHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
..++.+++-++.|++ -.|.++.+||..+|||.+||.+++.+....|.+.
T Consensus 41 ~~Lt~eereai~l~~-~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~ 89 (110)
T PRK04217 41 IFMTYEEFEALRLVD-YEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQM 89 (110)
T ss_pred ccCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 457888875554443 4788999999999999999999999888777654
No 26
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=90.94 E-value=0.14 Score=42.03 Aligned_cols=46 Identities=13% Similarity=0.229 Sum_probs=42.1
Q ss_pred CCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHH
Q 016336 90 GKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 90 ~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
++..+.+.++.++...+..|.+..++|..||||.+|+++++.++-.
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 4678999999999999999999999999999999999999888753
No 27
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=90.65 E-value=0.17 Score=34.71 Aligned_cols=44 Identities=20% Similarity=0.307 Sum_probs=34.4
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
.++..++-++.+ +..|.++.++|..+|+|.+||.+++.+....|
T Consensus 3 ~l~~~e~~i~~~--~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl 46 (58)
T smart00421 3 SLTPREREVLRL--LAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46 (58)
T ss_pred CCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 356666554433 57899999999999999999999988776655
No 28
>smart00153 VHP Villin headpiece domain.
Probab=90.51 E-value=0.2 Score=31.75 Aligned_cols=21 Identities=24% Similarity=0.414 Sum_probs=18.8
Q ss_pred ChhHHHhhcCCCHHHHHHHHH
Q 016336 52 GLDKFKSVFKISRRTFDYICS 72 (391)
Q Consensus 52 ~~~~F~~~frms~~tF~~L~~ 72 (391)
+|++|...|+|+++.|..|=.
T Consensus 3 sdeeF~~vfgmsr~eF~~LP~ 23 (36)
T smart00153 3 SDEDFEEVFGMTREEFYKLPL 23 (36)
T ss_pred CHHHHHHHHCCCHHHHHhCcH
Confidence 689999999999999998754
No 29
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=90.33 E-value=0.16 Score=34.16 Aligned_cols=43 Identities=33% Similarity=0.319 Sum_probs=34.5
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
.+++.++-++.+.++ .|.++.+++..+|+|.+||.+++.+...
T Consensus 10 ~l~~~~~~~~~~~~~-~~~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFG-EGLSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 356666666666664 8899999999999999999998877654
No 30
>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=89.49 E-value=0.22 Score=38.78 Aligned_cols=38 Identities=18% Similarity=0.223 Sum_probs=29.6
Q ss_pred cCHHHHHHHHHH------HhcCCCCccccccccCCcccccchhh
Q 016336 93 LSFRDQVAIALR------RLSSGDSLMSIGDSCGLHHSTVSQVT 130 (391)
Q Consensus 93 l~~e~~l~i~L~------~L~~g~~~~~l~~~Fgvs~sTvs~~~ 130 (391)
+++.++-++.++ .+..+.+|+.|+...|||++||+|+-
T Consensus 33 LTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~s 76 (94)
T TIGR01321 33 LTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGS 76 (94)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHH
Confidence 556666666555 34568999999999999999999853
No 31
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=89.38 E-value=0.28 Score=42.93 Aligned_cols=49 Identities=16% Similarity=0.068 Sum_probs=43.0
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|++++.++.|+++ .|.++.+||..+|+|.+||...+.+.+..+.+.+
T Consensus 127 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~ 175 (178)
T PRK12529 127 TLRPRVKQAFLMATL-DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLM 175 (178)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 488999999999988 8999999999999999999998888777776553
No 32
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=89.23 E-value=0.088 Score=39.10 Aligned_cols=45 Identities=18% Similarity=0.214 Sum_probs=37.6
Q ss_pred CCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHH
Q 016336 90 GKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFV 134 (391)
Q Consensus 90 ~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~ 134 (391)
++..|++.++.+.-.++..|.+..+++..+||+.+|+++++.++.
T Consensus 4 r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 4 RRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp S----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence 467899999999999999999999999999999999999998886
No 33
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)
Probab=89.07 E-value=0.55 Score=34.97 Aligned_cols=45 Identities=20% Similarity=0.264 Sum_probs=39.6
Q ss_pred CCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHH
Q 016336 90 GKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 90 ~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
++..+..+-|-..|+.|.+|+.++.|-..|| +.+||++.+.+...
T Consensus 22 ~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg-~~~tv~~~f~rW~~ 66 (75)
T PF13340_consen 22 RPRIDLREVLNAILYVLRTGCPWRDLPEDFG-PWSTVYRRFRRWSR 66 (75)
T ss_pred CCccchHHHHhcccccceecceecccchhcc-CcCcHHHHHHHHHH
Confidence 4568889999999999999999999999999 88999988777654
No 34
>PRK06030 hypothetical protein; Provisional
Probab=88.46 E-value=0.4 Score=39.50 Aligned_cols=47 Identities=17% Similarity=0.193 Sum_probs=41.1
Q ss_pred CccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 91 KHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
+.+...-|++|.|.+--++.++.+||..||.+.|||+..++.+-..+
T Consensus 51 k~i~~aRqIAMYL~r~~~~~sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 51 REVSRIRQIAMYVAHVSLGWPMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred cccchHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence 56888999999999999999999999999999999998877554433
No 35
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=88.39 E-value=0.28 Score=42.11 Aligned_cols=48 Identities=25% Similarity=0.313 Sum_probs=42.4
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|+.++-++.|++ .|.++..||..+|+|.+||...+.+....|...+
T Consensus 112 ~L~~~~r~il~l~~--~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 112 KMTERDRTVLLLRF--SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47888999999988 9999999999999999999999988888776543
No 36
>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=87.92 E-value=0.57 Score=39.30 Aligned_cols=46 Identities=26% Similarity=0.284 Sum_probs=38.5
Q ss_pred CccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHH
Q 016336 91 KHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~ 138 (391)
..++..++-.+.|+ ..|.++..+|..+|+|++||+++..+....|.
T Consensus 5 ~~Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr 50 (137)
T TIGR00721 5 TFLTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRAMENIE 50 (137)
T ss_pred CCCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhHHHHHH
Confidence 45777788777774 69999999999999999999998887766664
No 37
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=87.47 E-value=0.45 Score=40.30 Aligned_cols=47 Identities=19% Similarity=0.265 Sum_probs=40.4
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+++.++-++.|+++ .|.++.+||..+|+|.+||.....+....|.+
T Consensus 113 ~L~~~~r~il~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRF-EGKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 367888888889877 69999999999999999999998887776643
No 38
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=87.41 E-value=0.33 Score=42.10 Aligned_cols=49 Identities=31% Similarity=0.288 Sum_probs=41.7
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+++.++.++.|+++ .|.++.+||..+|+|.+||...+.+...-|.+.+
T Consensus 128 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREI-EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888877 7889999999999999999998888777776543
No 39
>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=87.40 E-value=0.2 Score=38.66 Aligned_cols=34 Identities=21% Similarity=0.315 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhcCCCCccccccccCCcccccchhh
Q 016336 96 RDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVT 130 (391)
Q Consensus 96 e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~ 130 (391)
.++ ...+.+++.|.++..||..+|||++||+++.
T Consensus 38 s~R-~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 38 AQR-LQVAKMLKQGKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred hHH-HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 345 5566678999999999999999999999944
No 40
>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=87.38 E-value=0.26 Score=36.54 Aligned_cols=41 Identities=22% Similarity=0.197 Sum_probs=36.2
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
.+++..+.+..|.+.-.|.++.+||..+|+|.+||..++..
T Consensus 15 ~l~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 15 WVDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred cCCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 47788888888888889999999999999999999987654
No 41
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=86.96 E-value=0.41 Score=44.79 Aligned_cols=50 Identities=22% Similarity=0.196 Sum_probs=43.2
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhcc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGL 142 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~ 142 (391)
.+++.++..+.|+|+ .|.++..||..+|+|.+||+++..+....|-..+.
T Consensus 205 ~L~~~er~vi~l~y~-e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l~ 254 (257)
T PRK05911 205 ALEEKERKVMALYYY-EELVLKEIGKILGVSESRVSQIHSKALLKLRATLS 254 (257)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 488888999999886 68999999999999999999999988887765543
No 42
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=86.83 E-value=0.32 Score=43.11 Aligned_cols=49 Identities=16% Similarity=0.106 Sum_probs=42.1
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|++++-++.|+++. |.++.+||..+|+|.+||...+.+....|.+.+
T Consensus 141 ~L~~~~~~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 141 QLPESQRQVLELAYYE-GLSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred hCCHHHhhhhhhhhhc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788888888888775 899999999999999999999988888776544
No 43
>PHA00675 hypothetical protein
Probab=86.72 E-value=0.36 Score=35.77 Aligned_cols=40 Identities=10% Similarity=0.087 Sum_probs=30.4
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~ 131 (391)
.|+..+--.|-..+-..|.++..||..||||+|||+.|.+
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 4555555555554447889999999999999999998753
No 44
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=86.24 E-value=0.51 Score=40.39 Aligned_cols=49 Identities=18% Similarity=0.209 Sum_probs=41.5
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.++++++-++.|+++. |.++.+||..+|+|.+||...+.+....|...+
T Consensus 109 ~L~~~~r~v~~l~~~~-~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 109 ELPARTRYAFEMYRLH-GETQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788888888888765 999999999999999999998888877776543
No 45
>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=86.23 E-value=0.53 Score=32.20 Aligned_cols=42 Identities=21% Similarity=0.343 Sum_probs=31.9
Q ss_pred CHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 94 SFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 94 ~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
+..++-++.+ +..|.++.++|..+++|.+||...+.+....+
T Consensus 2 ~~~e~~i~~~--~~~~~s~~eia~~l~~s~~tv~~~~~~~~~~l 43 (57)
T cd06170 2 TPREREVLRL--LAEGKTNKEIADILGISEKTVKTHLRNIMRKL 43 (57)
T ss_pred CHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 3344444333 45899999999999999999999988776654
No 46
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=86.09 E-value=0.92 Score=43.68 Aligned_cols=71 Identities=17% Similarity=0.238 Sum_probs=53.0
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhcccc----ccCCCHHHHHHHHHHHhHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGLQH----LQWPSETEMAEIKSKFEKI 163 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~~~----i~~P~~~~~~~i~~~f~~~ 163 (391)
.+|+.++.++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.+... ..-|...+..++.+.|...
T Consensus 142 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~~~~~~~~~~~~~v~~~~~a 216 (324)
T TIGR02960 142 YLPPRQRAVLLLRDV-LGWRAAETAELLGTSTASVNSALQRARATLDEVGPSARDDQLAQPPSPEEQDLLERYIAA 216 (324)
T ss_pred hCCHHHhhHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHH
Confidence 478889999999887 8899999999999999999999999999998766533 1122333444555555443
No 47
>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=86.06 E-value=0.19 Score=37.01 Aligned_cols=43 Identities=35% Similarity=0.380 Sum_probs=33.5
Q ss_pred CccCHHHHHHHHHHHhcCCCCccccccccC-CcccccchhhhHH
Q 016336 91 KHLSFRDQVAIALRRLSSGDSLMSIGDSCG-LHHSTVSQVTWRF 133 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fg-vs~sTvs~~~~~~ 133 (391)
+.+.-.-++++.|.+--++.++.+||..|| .++|||...++++
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 445567789999999999999999999999 9999998766553
No 48
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=86.05 E-value=0.5 Score=43.36 Aligned_cols=50 Identities=20% Similarity=0.296 Sum_probs=43.3
Q ss_pred ccCHHHHHHHHHHHh---cCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRL---SSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L---~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|+.++-++.|+|. -.|.++.+||..+|||.+||.....+....|-+.+
T Consensus 178 ~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l 230 (234)
T PRK08301 178 KLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEI 230 (234)
T ss_pred hCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478889999999884 68999999999999999999999888888776543
No 49
>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=85.74 E-value=0.59 Score=40.19 Aligned_cols=47 Identities=19% Similarity=0.242 Sum_probs=41.3
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+|+.++.++.|+|+ .|.++.+||..+|+|.+||...+.+....|.+
T Consensus 122 ~L~~~~r~vl~l~~~-~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 122 ILTPKQQHVIALRFG-QNLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred hCCHHHHHHHHHHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 588999999999877 58999999999999999999988888777654
No 50
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=85.42 E-value=0.23 Score=33.90 Aligned_cols=31 Identities=26% Similarity=0.390 Sum_probs=25.0
Q ss_pred HHHhcCCCCccccccccCCcccccchhhhHH
Q 016336 103 LRRLSSGDSLMSIGDSCGLHHSTVSQVTWRF 133 (391)
Q Consensus 103 L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~ 133 (391)
+..|....++.++|..+|||.+||.+++.+.
T Consensus 21 ~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 21 LKLLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3344444699999999999999999998764
No 51
>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=85.42 E-value=0.59 Score=38.82 Aligned_cols=47 Identities=26% Similarity=0.314 Sum_probs=38.8
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+++.++-++.+.++ .|.++.+||..+|+|.+||++...+....|.+
T Consensus 110 ~L~~~~~~ii~~~~~-~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYL-EGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 467777777777666 69999999999999999999999888776643
No 52
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=85.32 E-value=0.58 Score=44.07 Aligned_cols=49 Identities=16% Similarity=0.243 Sum_probs=42.8
Q ss_pred ccCHHHHHHHHHHHhc-CCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLS-SGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~-~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.++..++..+.|+|+. .|.++..||..+|||+++|+++..+.+.-|...
T Consensus 218 ~L~~rer~vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~ 267 (270)
T TIGR02392 218 SLDARSRRIIEARWLDDDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAA 267 (270)
T ss_pred cCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4889999999999974 478999999999999999999998888777543
No 53
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=84.78 E-value=0.61 Score=42.80 Aligned_cols=49 Identities=20% Similarity=0.255 Sum_probs=42.4
Q ss_pred ccCHHHHHHHHHHHh---cCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRL---SSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L---~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+|+.++.++.|+|+ -.|.++..||..+|+|.+||.+...+....|...
T Consensus 175 ~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred hCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 589999999999886 4778999999999999999999888877776553
No 54
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=84.70 E-value=0.83 Score=39.82 Aligned_cols=48 Identities=15% Similarity=0.099 Sum_probs=41.8
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.++++.+-.+.|+++ .|.++..||..+|+|.+||...+.+....|.+.
T Consensus 129 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 129 ELEKDRAAAVRRAYL-EGLSYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 478888988888887 789999999999999999999888888777654
No 55
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=84.52 E-value=0.39 Score=41.72 Aligned_cols=48 Identities=13% Similarity=0.169 Sum_probs=42.0
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+|+.++.++.|+++ .|.++.+||..+|+|.+||...+.+....|...
T Consensus 126 ~L~~~~r~v~~l~~~-~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 126 KLDPEFRAPVILKHY-YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred cCCHHHhheeeehhh-cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 478888999999887 699999999999999999999888888777654
No 56
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=84.01 E-value=0.72 Score=43.79 Aligned_cols=49 Identities=18% Similarity=0.250 Sum_probs=43.0
Q ss_pred ccCHHHHHHHHHHHhc-CCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLS-SGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~-~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.++..++..+.++|+. .+.++..||..+|||+++|+++..+.+.-|-..
T Consensus 230 ~L~~rEr~VL~lry~~~~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~ 279 (284)
T PRK06596 230 GLDERSRDIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAMKKLKAA 279 (284)
T ss_pred cCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4888999999999975 588999999999999999999998888777543
No 57
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=83.60 E-value=0.7 Score=40.45 Aligned_cols=48 Identities=25% Similarity=0.236 Sum_probs=41.8
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.++..++-++.|.++ .|.++.++|..+|||.+||...+.+....|...
T Consensus 136 ~L~~~~r~il~l~~~-~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 136 QLPEKYRTVIVLKYI-EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHHHHhhhHHh-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 478888888888887 799999999999999999999988888777654
No 58
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=83.47 E-value=0.83 Score=39.29 Aligned_cols=48 Identities=25% Similarity=0.206 Sum_probs=42.5
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+|+.++-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.
T Consensus 112 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 112 LLSADQREAIILIGA-SGFSYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 478888988999888 899999999999999999999998888877654
No 59
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=83.21 E-value=0.66 Score=41.02 Aligned_cols=48 Identities=17% Similarity=0.219 Sum_probs=42.2
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+|+..+-++.|+++. |.++.+||..+|+|.+||...+.+....|.+.
T Consensus 134 ~Lp~~~R~v~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 134 HLPAQQARVFMMREYL-ELSSEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred hCCHHHHHHHhHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4788899999999876 99999999999999999998888888777654
No 60
>PHA00542 putative Cro-like protein
Probab=83.16 E-value=1.1 Score=34.02 Aligned_cols=52 Identities=12% Similarity=0.144 Sum_probs=38.4
Q ss_pred HHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhccccccCCCHHHHHHHHHHHhHh
Q 016336 101 IALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGLQHLQWPSETEMAEIKSKFEKI 163 (391)
Q Consensus 101 i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~~~i~~P~~~~~~~i~~~f~~~ 163 (391)
+...+...|.++.++|...|||++||+++.+.- ..-|+.+.+..+++.+.+.
T Consensus 23 l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~-----------~~~p~~~~l~ki~~~~~~~ 74 (82)
T PHA00542 23 LVCALIRAGWSQEQIADATDVSQPTICRIYSGR-----------HKDPRYSVVEKLRHLVLNL 74 (82)
T ss_pred HHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCC-----------CCCCCHHHHHHHHHHHHHh
Confidence 344557889999999999999999999975321 1346666777777766654
No 61
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=82.90 E-value=0.78 Score=40.13 Aligned_cols=49 Identities=18% Similarity=0.150 Sum_probs=42.5
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|+.++-++.|+++. |.++..+|..+|+|.+||...+.+....|.+.+
T Consensus 127 ~L~~~~r~v~~l~~~~-g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 127 SLPIKYREVIYLFYYE-ELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred hCCHHHhhHhHhHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788888999998886 999999999999999999999888888776543
No 62
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=82.53 E-value=0.91 Score=39.17 Aligned_cols=48 Identities=21% Similarity=0.230 Sum_probs=41.0
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+|+.++-++.|+++ .|.++.+||..+|+|.+||.+.+.+....|.+.
T Consensus 125 ~L~~~~r~i~~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 125 ALPVKQREVFLLRYV-EGLSYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred hCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 377888888888877 699999999999999999999998887777554
No 63
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=82.52 E-value=0.88 Score=40.05 Aligned_cols=48 Identities=19% Similarity=0.134 Sum_probs=41.7
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+|+..+-++.|+++ .|.++.+||..+|+|.+||...+.+....|...
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 478889999999888 599999999999999999999888877776543
No 64
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=82.45 E-value=0.92 Score=42.34 Aligned_cols=48 Identities=15% Similarity=0.149 Sum_probs=42.3
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+++.++..+.|+|+ .|.++..||..+|+|.+||++...+....|...
T Consensus 203 ~L~~~~r~vl~l~y~-~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 203 QLEERTREVLEFVFL-HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred cCCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 478889999999986 589999999999999999999999888877654
No 65
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=82.37 E-value=0.92 Score=40.30 Aligned_cols=48 Identities=25% Similarity=0.232 Sum_probs=42.2
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+++.++-++.|+++ .|.++..||..+|+|.+||...+.+....|...
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 136 ALPERQRQAVVLRHI-EGLSNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 478888988888888 899999999999999999999998888877653
No 66
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=82.13 E-value=0.89 Score=41.32 Aligned_cols=49 Identities=18% Similarity=0.088 Sum_probs=42.7
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+++..+-++.|+|+ .|.++.+||..+|||.+||...+++....|.+.+
T Consensus 134 ~Lp~~~R~v~~L~y~-eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 134 KLPVEYREVLVLREL-EDMSYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCHHHHhHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888999999888 6999999999999999999999988887776543
No 67
>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=81.98 E-value=1 Score=38.19 Aligned_cols=47 Identities=21% Similarity=0.259 Sum_probs=40.6
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+|+.++-++.|+++ .|.++.+||..+|+|.+||...+.+.-..|.+
T Consensus 111 ~L~~~~r~v~~l~~~-~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 111 KLPERQRELLQLRYQ-RGVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 478888888888776 79999999999999999999988887776643
No 68
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=81.90 E-value=0.81 Score=40.16 Aligned_cols=50 Identities=28% Similarity=0.188 Sum_probs=42.2
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhcc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGL 142 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~ 142 (391)
.++++.+-++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+.
T Consensus 138 ~L~~~~r~v~~l~~~-~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l~ 187 (190)
T TIGR02939 138 ALPEDLRTAITLREL-EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRLR 187 (190)
T ss_pred cCCHHHhhhhhhhhh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 467778887777776 89999999999999999999999888888876543
No 69
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=81.83 E-value=1 Score=39.82 Aligned_cols=49 Identities=20% Similarity=0.183 Sum_probs=42.8
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|+..+-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.+
T Consensus 116 ~Lp~~~r~i~~L~~~-~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 116 QLPDDQREAIILVGA-SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888887 8999999999999999999999888888776644
No 70
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=81.81 E-value=1.3 Score=38.91 Aligned_cols=48 Identities=13% Similarity=0.011 Sum_probs=40.5
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+++.++-++.|+++ .|.++.+||..+|+|.+||...+++....|...
T Consensus 137 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 137 ELEPPRSELIRTAFF-EGITYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 467777777777765 899999999999999999999998888777654
No 71
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=81.75 E-value=0.81 Score=40.42 Aligned_cols=51 Identities=24% Similarity=0.204 Sum_probs=43.4
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhccc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGLQ 143 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~~ 143 (391)
.++++++-++.|+++ .|.++.+||..+|+|..||...+.+....|-+.+..
T Consensus 138 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~ 188 (193)
T PRK11923 138 QLPEDLRTALTLREF-DGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQP 188 (193)
T ss_pred hCCHHHhHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 478888888888876 899999999999999999999998888887665443
No 72
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=81.53 E-value=0.97 Score=39.83 Aligned_cols=48 Identities=21% Similarity=0.230 Sum_probs=42.3
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.++++++-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.
T Consensus 131 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 131 KLSPAHREIIDLVYY-HEKSVEEVGEIVGIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 578888999999888 899999999999999999999888887777654
No 73
>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=81.44 E-value=1.3 Score=30.72 Aligned_cols=29 Identities=24% Similarity=0.275 Sum_probs=23.9
Q ss_pred CCCccccccccCCcccccchhhhHHHHHH
Q 016336 109 GDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 109 g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
..+..+||..+|||++|++..+++...-|
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae~kl 51 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAERKL 51 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 35666899999999999999988876654
No 74
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=81.33 E-value=1.2 Score=38.90 Aligned_cols=48 Identities=21% Similarity=0.118 Sum_probs=40.5
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+|+..+.++.|++ -.|.++.+||..+|||.+||...+.+....|.+.
T Consensus 133 ~L~~~~r~i~~l~~-~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 133 QLEPARRNCILHAY-VDGCSHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 47778887777774 5899999999999999999999999888877653
No 75
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=81.33 E-value=1.1 Score=37.84 Aligned_cols=46 Identities=28% Similarity=0.323 Sum_probs=37.9
Q ss_pred CccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHH
Q 016336 91 KHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~ 138 (391)
..+++.++-.+.|+ ..|.++.++|..+|+|++||+.+..+....|.
T Consensus 5 ~~Lt~rqreVL~lr--~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr 50 (141)
T PRK03975 5 SFLTERQIEVLRLR--ERGLTQQEIADILGTSRANVSSIEKRARENIE 50 (141)
T ss_pred cCCCHHHHHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 45788888888773 69999999999999999999998877655443
No 76
>PRK05572 sporulation sigma factor SigF; Validated
Probab=81.12 E-value=1.1 Score=41.53 Aligned_cols=48 Identities=19% Similarity=0.377 Sum_probs=42.4
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.++..++.++.|+|+ .|.++..||..+|+|.+||+++..+.+..|...
T Consensus 202 ~L~~~~~~v~~l~~~-~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~ 249 (252)
T PRK05572 202 ELDERERLIVYLRYF-KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEK 249 (252)
T ss_pred cCCHHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 588899999999886 689999999999999999999999988877654
No 77
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=81.11 E-value=1 Score=38.33 Aligned_cols=49 Identities=18% Similarity=0.171 Sum_probs=42.6
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|+..+-++.|+++ .|.++..||..+|+|.+||...+.+....|...+
T Consensus 106 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 106 KLPARQREAFLLRYW-EDMDVAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred hCCHHHHHHHHHHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888876 5999999999999999999999999888886543
No 78
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=80.96 E-value=1 Score=39.57 Aligned_cols=49 Identities=18% Similarity=0.129 Sum_probs=42.5
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|+.++-++.|+++. |.++.+||..+|+|..||...+.+....|...+
T Consensus 128 ~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 128 ALPERQREAIVLQYYQ-GLSNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred hCCHHHHHHhhHHHhc-CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 4788899899998875 999999999999999999999988888776543
No 79
>PRK15320 transcriptional activator SprB; Provisional
Probab=80.93 E-value=0.71 Score=40.94 Aligned_cols=46 Identities=22% Similarity=0.206 Sum_probs=38.0
Q ss_pred CccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHH
Q 016336 91 KHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~ 138 (391)
+.++..|. -.|..|+.|.+..+||+.|++|.+||+.+..+...-+.
T Consensus 163 ~~LSdREI--EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLg 208 (251)
T PRK15320 163 PGVTQAKY--ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLG 208 (251)
T ss_pred CCCCHHHH--HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence 34555554 67889999999999999999999999999888776654
No 80
>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=80.89 E-value=1.1 Score=38.25 Aligned_cols=48 Identities=19% Similarity=0.230 Sum_probs=41.2
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+++.++.++.|.+ -.|.++.+||..+|+|.+||...+.+....|.+.
T Consensus 110 ~L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 110 RLPARQRAVVVLRY-YEDLSEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred hCCHHHHHHhhhHH-HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 36778888888877 4699999999999999999999999988887654
No 81
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=80.83 E-value=1.6 Score=40.02 Aligned_cols=70 Identities=11% Similarity=0.227 Sum_probs=52.8
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhccccccCC-CHHHHHHHHHHHhH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGLQHLQWP-SETEMAEIKSKFEK 162 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~~~i~~P-~~~~~~~i~~~f~~ 162 (391)
.+++.++.++.|.++- |.++.+||..+|+|.+||...+.+....|.+.+.+...-+ ...+...+...|.+
T Consensus 116 ~Lp~~~R~v~lL~~~e-g~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~~~~~~~~~~~~~~~~~~~~~ 186 (228)
T PRK06704 116 SLNVQQSAILLLKDVF-QYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEEGIEIVEFTDDMEVVVTSIRE 186 (228)
T ss_pred hCCHHHhhHhhhHHhh-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcCCCCCccccHHHHHHHHHh
Confidence 4788888888887764 8999999999999999999999999988877665433322 22356666666643
No 82
>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=80.45 E-value=1.3 Score=38.55 Aligned_cols=47 Identities=17% Similarity=0.150 Sum_probs=40.0
Q ss_pred cCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 93 LSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 93 l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
+|+..+-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.
T Consensus 135 Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 135 VDPRQAEVVELRFF-AGLTVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 78888887777766 689999999999999999999988888777543
No 83
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=80.40 E-value=1.3 Score=38.83 Aligned_cols=49 Identities=16% Similarity=0.148 Sum_probs=42.4
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|+.++-++.|+|+. |.++.+||..+|+|.+||...+.+....|.+.+
T Consensus 131 ~L~~~~r~v~~l~~~~-g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVE-GASIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 4788888888887776 999999999999999999999999888887654
No 84
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=80.34 E-value=1.1 Score=42.57 Aligned_cols=50 Identities=28% Similarity=0.418 Sum_probs=44.1
Q ss_pred ccCHHHHHHHHHHHh-cCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRL-SSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L-~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+++.++.++.|+|+ ..|.++..||..+|||++||+++..+.+.-|...+
T Consensus 227 ~L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l 277 (289)
T PRK07500 227 TLNERELRIIRERRLREDGATLEALGEELGISKERVRQIEARALEKLRRAL 277 (289)
T ss_pred cCCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 489999999999986 36899999999999999999999999888886543
No 85
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=80.29 E-value=1.4 Score=38.54 Aligned_cols=49 Identities=16% Similarity=0.125 Sum_probs=41.9
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|..++-++.|+++ .|.++..||..+|+|.+||...+++....|.+.+
T Consensus 135 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 135 ALSPEERRVIEVLYY-QGYTHREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 378888888888875 6899999999999999999999998888776543
No 86
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=80.29 E-value=1.3 Score=39.32 Aligned_cols=48 Identities=13% Similarity=0.056 Sum_probs=41.4
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+|++.+-++.|+++ .|.++..||..+|||.+||...+.+....|...
T Consensus 141 ~Lp~~~r~v~~l~~~-eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 141 RLPKAQRDVLQAVYL-EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 478888888888877 899999999999999999998888887777654
No 87
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=80.21 E-value=1.3 Score=38.69 Aligned_cols=48 Identities=23% Similarity=0.206 Sum_probs=41.2
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+++.++-++.|+++ .|.++..||..+|||.+||...+.+....|.+.
T Consensus 140 ~L~~~~r~vi~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~ 187 (189)
T TIGR02984 140 KLPEDYREVILLRHL-EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQI 187 (189)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 478888888888776 899999999999999999999988888777543
No 88
>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=80.18 E-value=1.3 Score=40.51 Aligned_cols=49 Identities=20% Similarity=0.211 Sum_probs=42.6
Q ss_pred ccCHHHHHHHHHHHh---cCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRL---SSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L---~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+++.++-++.|+|+ -.|.++..||..+|+|.+||.+..++....|.+.
T Consensus 174 ~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~ 225 (227)
T TIGR02846 174 VLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKE 225 (227)
T ss_pred hCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 478889999999886 4899999999999999999999988888777653
No 89
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=80.01 E-value=1.1 Score=41.26 Aligned_cols=48 Identities=13% Similarity=0.271 Sum_probs=41.9
Q ss_pred ccCHHHHHHHHHHHh---cCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRL---SSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L---~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+++.++..+.|+|. ..+.++..||..+|||.++|+++..+.+.-|-.
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 478899999999985 578899999999999999999998888777654
No 90
>PF13730 HTH_36: Helix-turn-helix domain
Probab=80.01 E-value=0.91 Score=31.29 Aligned_cols=39 Identities=18% Similarity=0.238 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhcC--CC---CccccccccCCcccccchhhhHHH
Q 016336 96 RDQVAIALRRLSS--GD---SLMSIGDSCGLHHSTVSQVTWRFV 134 (391)
Q Consensus 96 e~~l~i~L~~L~~--g~---~~~~l~~~Fgvs~sTvs~~~~~~~ 134 (391)
+..|.+.|..++. +. |+..|+...|+|+.||++.+.+..
T Consensus 7 ~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~ 50 (55)
T PF13730_consen 7 AKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELE 50 (55)
T ss_pred HHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4556667777762 22 668899999999999999876654
No 91
>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=79.88 E-value=0.47 Score=40.10 Aligned_cols=48 Identities=17% Similarity=0.176 Sum_probs=40.4
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+.+....|.+.
T Consensus 105 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 105 RLPENYRTVLILREF-KEFSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred hCCHhheeeeeehhh-ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 367777777777777 799999999999999999999888887777543
No 92
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.30 E-value=1.2 Score=34.91 Aligned_cols=45 Identities=16% Similarity=0.163 Sum_probs=35.5
Q ss_pred CHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 94 SFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 94 ~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
+-.++--+-|+|+ -..|+..||+.|+||+++|+..+.+++..+..
T Consensus 19 T~KQ~~Y~~lyy~-dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~ 63 (105)
T COG2739 19 TKKQKNYLELYYL-DDLSLSEIAEEFNVSRQAIYDNIKRTEKILED 63 (105)
T ss_pred hHHHHHHHHHHHH-hhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 3344555556554 56799999999999999999999999988754
No 93
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=79.14 E-value=1.3 Score=39.26 Aligned_cols=49 Identities=22% Similarity=0.264 Sum_probs=42.3
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+++..+-++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 136 NLPENTARVFTLKEI-LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred hCCHHHHHHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888877 7999999999999999999999988888886643
No 94
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=79.11 E-value=1.4 Score=40.00 Aligned_cols=68 Identities=9% Similarity=0.162 Sum_probs=49.2
Q ss_pred ccCHHHHHHHHHHHhcCC----CCccccccccCCcccccchhhhHHHH-HHHHhccccccCCCHHHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSG----DSLMSIGDSCGLHHSTVSQVTWRFVE-AMEQKGLQHLQWPSETEMAEIKSK 159 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g----~~~~~l~~~Fgvs~sTvs~~~~~~~~-~l~~~~~~~i~~P~~~~~~~i~~~ 159 (391)
..+++++|+-+|..++.+ .+..+||..+|+++.||+|.+.++.+ .+.+.....|.-++.+.+.+++.+
T Consensus 148 ~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~~~i~I~d~~~L~~~~~~ 220 (226)
T PRK10402 148 SFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSKRGYLIKNRKQLSGLALE 220 (226)
T ss_pred cChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeCCEEEEeCHHHHHHHHHH
Confidence 458999999999877543 35578999999999999999888876 244443445666666666655443
No 95
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=79.05 E-value=1.6 Score=37.63 Aligned_cols=48 Identities=21% Similarity=0.234 Sum_probs=40.6
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.++..++-++.|.++. |.++.++|..+|+|.+||...+.+....|...
T Consensus 119 ~L~~~~r~i~~l~~~~-g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 119 TLNDKYQTAIILRYYH-DLTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred hCCHHHhHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4777788777777775 89999999999999999999998888877654
No 96
>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=79.02 E-value=1.5 Score=39.97 Aligned_cols=47 Identities=19% Similarity=0.317 Sum_probs=40.9
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+|+.++-++.|+|+ .|.++.+||..+|+|.+||++...+....|..
T Consensus 178 ~L~~~~r~vl~l~y~-~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFF-EDKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 478888888888876 68899999999999999999999988887754
No 97
>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=78.94 E-value=1.5 Score=40.05 Aligned_cols=47 Identities=19% Similarity=0.359 Sum_probs=40.5
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.++..++.++.|+|+ .|.++..||..+|+|+++|+++..+...-|.+
T Consensus 183 ~L~~~e~~i~~~~~~-~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~ 229 (231)
T TIGR02885 183 KLDERERQIIMLRYF-KDKTQTEVANMLGISQVQVSRLEKKVLKKMKE 229 (231)
T ss_pred cCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 578888888888775 68899999999999999999999888877654
No 98
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=78.88 E-value=1.5 Score=40.86 Aligned_cols=48 Identities=19% Similarity=0.245 Sum_probs=41.6
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+++.++-++.|+|+ .|.++..||..+|||.+||.+..++....|...
T Consensus 205 ~L~~~~r~vl~l~~~-~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFI-ENLSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHh-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 478888888888876 799999999999999999999999888877553
No 99
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=78.81 E-value=1.6 Score=37.64 Aligned_cols=49 Identities=18% Similarity=0.125 Sum_probs=41.5
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|+..+-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.+
T Consensus 118 ~L~~~~r~vl~L~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 118 QLSPEHRAVLVRSYY-RGWSTAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 478888888888776 4999999999999999999988888888776543
No 100
>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=78.73 E-value=0.8 Score=34.65 Aligned_cols=36 Identities=14% Similarity=0.119 Sum_probs=26.1
Q ss_pred HHHHHHHHHHhcCC-CCccccccccCCcccccchhhh
Q 016336 96 RDQVAIALRRLSSG-DSLMSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 96 e~~l~i~L~~L~~g-~~~~~l~~~Fgvs~sTvs~~~~ 131 (391)
++++...+-+|..| .+..+++..||||.+|||+.+.
T Consensus 5 ~~R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 5 EERVLEIGKYIVETKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhc
Confidence 44555555555553 4667899999999999999764
No 101
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=78.70 E-value=1.5 Score=37.33 Aligned_cols=49 Identities=14% Similarity=0.042 Sum_probs=40.6
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|+..+-++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 106 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 106 ELPENYRDVVLAHYL-EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred hCCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 377777777777765 7899999999999999999998888887776543
No 102
>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=78.45 E-value=0.33 Score=32.60 Aligned_cols=21 Identities=33% Similarity=0.397 Sum_probs=17.7
Q ss_pred ccccccccCCcccccchhhhH
Q 016336 112 LMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 112 ~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
..+||...|||.+|||++++.
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 457899999999999997754
No 103
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=78.44 E-value=1.4 Score=38.52 Aligned_cols=49 Identities=24% Similarity=0.200 Sum_probs=41.9
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|+.++-++.|.++ .|.++..+|..+|+|.+||...+.+....|...+
T Consensus 136 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 136 ALPPKYRMVIVLKYM-EDLSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 478888888888777 6899999999999999999999988887776543
No 104
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=78.32 E-value=1.6 Score=37.75 Aligned_cols=47 Identities=23% Similarity=0.198 Sum_probs=40.2
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+|+..+-++.|+++ .|.++.+||..+|+|.+||...+.+.+..+..
T Consensus 119 ~Lp~~~r~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 119 KLSSKARAAFLYNRL-DGMGHAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 478888888888887 58999999999999999999988887776654
No 105
>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=78.29 E-value=1.5 Score=40.71 Aligned_cols=49 Identities=29% Similarity=0.290 Sum_probs=42.8
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|...+-++.|+++ .|.++.+||..+|||.+||...+.+....|.+.+
T Consensus 161 ~Lp~~~R~v~~L~~~-eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 161 ALSERERHLLRLHFV-DGLSMDRIGAMYQVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888887 8899999999999999999999998888776543
No 106
>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=78.27 E-value=1.6 Score=40.13 Aligned_cols=49 Identities=18% Similarity=0.323 Sum_probs=42.6
Q ss_pred ccCHHHHHHHHHHHh---cCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRL---SSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L---~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+|+.++.++.|+++ -.|.++..||...|+|.+||.....+....|-+.
T Consensus 178 ~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~ 229 (234)
T TIGR02835 178 KLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKE 229 (234)
T ss_pred hCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 589999999999985 3789999999999999999999888877777553
No 107
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=78.23 E-value=1.5 Score=37.39 Aligned_cols=46 Identities=17% Similarity=0.075 Sum_probs=38.2
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~ 138 (391)
.+|+.++-++.|+++ .|.++.+||..+|+|.+||...+.+....+.
T Consensus 113 ~L~~~~r~v~~L~~~-~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 113 GLPPLVKRAFLLAQV-DGLGYGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 477788887777766 6899999999999999999988887766553
No 108
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=78.21 E-value=1.5 Score=38.93 Aligned_cols=48 Identities=17% Similarity=0.174 Sum_probs=40.3
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+|++.+.++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.
T Consensus 134 ~Lp~~~r~i~~l~~~-~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~ 181 (192)
T PRK09643 134 RLPVEQRAALVAVDM-QGYSVADAARMLGVAEGTVKSRCARGRARLAEL 181 (192)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 378888888888777 789999999999999999988887777666543
No 109
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=78.21 E-value=1.6 Score=40.66 Aligned_cols=47 Identities=21% Similarity=0.429 Sum_probs=40.7
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.++..++..+.|+|+ .|.++..+|..+|+|.+||+++..+.+..|..
T Consensus 209 ~L~~~er~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~ 255 (258)
T PRK08215 209 KLNDREKLILNLRFF-QGKTQMEVAEEIGISQAQVSRLEKAALKHMRK 255 (258)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 478888888888875 68899999999999999999999888777654
No 110
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=78.05 E-value=1.6 Score=38.43 Aligned_cols=49 Identities=20% Similarity=0.141 Sum_probs=42.6
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+++..+-++.|+++ .|.++.+||..+|+|.+||...+.+....|-+.+
T Consensus 111 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l 159 (182)
T PRK12540 111 KLPQDQREALILVGA-SGFSYEDAAAICGCAVGTIKSRVNRARSKLSALL 159 (182)
T ss_pred hCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888876 8999999999999999999999988888886654
No 111
>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=77.75 E-value=1.2 Score=31.73 Aligned_cols=41 Identities=22% Similarity=0.242 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHhc---CCCCccccccccCCcccccchhhhHHHH
Q 016336 95 FRDQVAIALRRLS---SGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 95 ~e~~l~i~L~~L~---~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
..+.-+-+++.|. ...+-.+||..+|||++||+.++.+...
T Consensus 5 ~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~ 48 (60)
T PF01325_consen 5 SEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAE 48 (60)
T ss_dssp HHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHH
Confidence 3455566666666 4456678999999999999988776543
No 112
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=77.68 E-value=1.7 Score=38.19 Aligned_cols=49 Identities=22% Similarity=0.228 Sum_probs=42.7
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|+..+-++.|.++ .|.++.+||..+|+|.+||...+.+....|.+.+
T Consensus 131 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 131 RLPEKMRLAIQAVKL-EGLSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred hCCHHHHHHHHHHHH-cCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888888 4999999999999999999999999888886643
No 113
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=77.66 E-value=1.6 Score=39.23 Aligned_cols=49 Identities=12% Similarity=0.054 Sum_probs=42.7
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+++..+-++.|+++. |.++.+||..+|+|.+||...+.+....|.+.+
T Consensus 148 ~L~~~~r~v~~L~~~~-g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 148 GLPAKYARVFMMREFI-ELETNEICHAVDLSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4788899988888875 999999999999999999999988888886643
No 114
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=77.54 E-value=2.4 Score=42.12 Aligned_cols=87 Identities=21% Similarity=0.164 Sum_probs=51.1
Q ss_pred HhcCCCCcccccc----ccC---CcccccchhhhHHHHHHHHhccccccCCCHHHHHHHHHHHhHhhCCCccceeeeeeE
Q 016336 105 RLSSGDSLMSIGD----SCG---LHHSTVSQVTWRFVEAMEQKGLQHLQWPSETEMAEIKSKFEKIQGLPNCCGVIDTTH 177 (391)
Q Consensus 105 ~L~~g~~~~~l~~----~Fg---vs~sTvs~~~~~~~~~l~~~~~~~i~~P~~~~~~~i~~~f~~~~~fp~~~GaIDgth 177 (391)
.+..|.|.++++. ..| +|++|||+++.++.+.+...... ...+.|=++-.|||+|
T Consensus 110 ly~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~~w~~R------------------~L~~~~y~~l~iD~~~ 171 (381)
T PF00872_consen 110 LYLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVEAWRNR------------------PLESEPYPYLWIDGTY 171 (381)
T ss_pred hhccccccccccchhhhhhcccccCchhhhhhhhhhhhhHHHHhhh------------------ccccccccceeeeeee
Confidence 3677888888775 445 99999999887776655432111 0112223477899999
Q ss_pred EEeecCCCCCccccccCCCCcceeEEEEeeCCCcc--eeecccC
Q 016336 178 ILMCLPSSDPTNNLWLDHMKNHSMVLQAIVDPEMR--FRDIVTG 219 (391)
Q Consensus 178 i~i~~p~~~~~~~~y~~~k~~~s~~~q~v~d~~~~--f~~v~~g 219 (391)
+.+..- +. -..-++.+-+.+|.+|+ ++.+.++
T Consensus 172 ~kvr~~-----~~-----~~~~~~~v~iGi~~dG~r~vLg~~~~ 205 (381)
T PF00872_consen 172 FKVRED-----GR-----VVKKAVYVAIGIDEDGRREVLGFWVG 205 (381)
T ss_pred cccccc-----cc-----cccchhhhhhhhhcccccceeeeecc
Confidence 988621 10 01112333344677775 6666554
No 115
>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=77.40 E-value=1.4 Score=34.86 Aligned_cols=80 Identities=13% Similarity=0.199 Sum_probs=50.9
Q ss_pred ChhHHHhhcCCCHHHHHHHHHHhhhccccccCCcccCCCCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhh
Q 016336 52 GLDKFKSVFKISRRTFDYICSLVEEKMVVKTGGFSFTSGKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 52 ~~~~F~~~frms~~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~ 131 (391)
.++.......+...-=..+..++......... + ..--.+.++..+.++|+ .+.++..++..+++|++|+.++-.
T Consensus 20 ~ed~~v~~i~~~e~I~~~i~~li~~k~ei~~~--I---~~l~d~~~r~iL~~~Yi-~~~~~~~I~~~l~~S~~t~yr~~~ 93 (100)
T PF07374_consen 20 QEDKIVKIIDLKEEIEREIDELIKEKLEIRRA--I---NKLEDPDERLILRMRYI-NKLTWEQIAEELNISRRTYYRIHK 93 (100)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--H---HHccChhHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45556666555444333344443333222110 0 12235788999999999 578999999999999999999877
Q ss_pred HHHHHH
Q 016336 132 RFVEAM 137 (391)
Q Consensus 132 ~~~~~l 137 (391)
+.+..|
T Consensus 94 ~Al~~L 99 (100)
T PF07374_consen 94 KALKEL 99 (100)
T ss_pred HHHHhc
Confidence 665543
No 116
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=77.31 E-value=1.7 Score=38.10 Aligned_cols=48 Identities=23% Similarity=0.158 Sum_probs=40.1
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+++.++.++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.
T Consensus 106 ~L~~~~r~i~~l~~~-~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (181)
T PRK09637 106 ALPEKYAEALRLTEL-EGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKEL 153 (181)
T ss_pred hCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 478888888878765 789999999999999999999888877777654
No 117
>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=77.24 E-value=3.3 Score=39.11 Aligned_cols=67 Identities=16% Similarity=0.185 Sum_probs=50.0
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhccccccCCCHHHHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGLQHLQWPSETEMAEIKSKFE 161 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~~~i~~P~~~~~~~i~~~f~ 161 (391)
.+|+.++-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+..+..- +..++..++.+.|-
T Consensus 108 ~L~~~~R~v~~L~~~-~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~~~~--~~~~~~~~~~~~f~ 174 (281)
T TIGR02957 108 RLSPLERAVFVLREV-FDYPYEEIASIVGKSEANCRQLVSRARRHLDARRPRFE--VSREESRQLLERFV 174 (281)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCCCC--CChHHHHHHHHHHH
Confidence 478888888777765 58899999999999999999999999998877544321 22234455556564
No 118
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=77.12 E-value=1.2 Score=34.37 Aligned_cols=35 Identities=23% Similarity=0.388 Sum_probs=28.8
Q ss_pred HHHHHHHHHHhcCCCCccccccccCCcccccchhh
Q 016336 96 RDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVT 130 (391)
Q Consensus 96 e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~ 130 (391)
..++-++=-.|..|.+|+.|+...|+|..||+|+-
T Consensus 36 ~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvs 70 (87)
T PF01371_consen 36 AQRWQVAKELLDEGKSYREIAEETGVSIATITRVS 70 (87)
T ss_dssp HHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHH
Confidence 45555555578899999999999999999999843
No 119
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=77.08 E-value=1.7 Score=38.32 Aligned_cols=47 Identities=21% Similarity=0.251 Sum_probs=41.4
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+|+.++-++.|+++ .|.++.+||..+|+|.+||...+.+....|..
T Consensus 131 ~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 131 DLEKLDREIFIRRYL-LGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred hCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 488899999999887 68999999999999999999988888777754
No 120
>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=76.93 E-value=1.7 Score=41.28 Aligned_cols=51 Identities=20% Similarity=0.228 Sum_probs=44.4
Q ss_pred CccCHHHHHHHHHHH-h--cCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 91 KHLSFRDQVAIALRR-L--SSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~-L--~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
..+|..++..+.|+| | -.|.++..||..+|+|.+||.....+....|...+
T Consensus 221 ~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l 274 (285)
T TIGR02394 221 AELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL 274 (285)
T ss_pred HcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 358999999999998 4 57899999999999999999999999888886644
No 121
>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=76.90 E-value=1.2 Score=31.32 Aligned_cols=26 Identities=23% Similarity=0.337 Sum_probs=21.1
Q ss_pred CCccccccccCCcccccchhhhHHHH
Q 016336 110 DSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 110 ~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
.+..+|+..++++++||++++.+...
T Consensus 22 ~t~~~la~~l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 22 LTQSELAERLGISKSTVSRIVKRLEK 47 (62)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 58889999999999999998766543
No 122
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=76.88 E-value=1.7 Score=37.68 Aligned_cols=52 Identities=12% Similarity=-0.005 Sum_probs=40.3
Q ss_pred cCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhccccc
Q 016336 93 LSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGLQHL 145 (391)
Q Consensus 93 l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~~~i 145 (391)
+|+..+-++.|. +-.|.++..+|..+|+|.+||...+.+....|...+..+|
T Consensus 120 L~~~~r~i~~l~-~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~~ 171 (173)
T PRK12522 120 LNEKYKTVLVLY-YYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEGFV 171 (173)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 566666544444 4479999999999999999999999998888876655443
No 123
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=76.73 E-value=1.8 Score=37.80 Aligned_cols=48 Identities=27% Similarity=0.302 Sum_probs=39.8
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+|+.++.++.|+++ .|.++.+||..+|+|.+||...+.+....|...
T Consensus 129 ~L~~~~r~v~~l~~~-~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 129 QLPDRQRLPIVHVKL-EGLSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467777777666664 789999999999999999999998888877654
No 124
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=76.67 E-value=1.7 Score=39.85 Aligned_cols=49 Identities=24% Similarity=0.304 Sum_probs=41.7
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+++.++-++.|+|+ .|.++..||..+|+|.+||...+.+....|...+
T Consensus 184 ~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 184 SLPEREQLVLSLYYQ-EELNLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred hCCHHHHHHHHhHhc-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 468888888888775 7899999999999999999999988888876543
No 125
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=76.67 E-value=1.5 Score=39.03 Aligned_cols=81 Identities=14% Similarity=0.183 Sum_probs=48.1
Q ss_pred ChhHHHhhcCCCHHHHHHHHHHhhhccccccCCcccCCCCccCHHHHHHHHHHHhcC-------------CCCccccccc
Q 016336 52 GLDKFKSVFKISRRTFDYICSLVEEKMVVKTGGFSFTSGKHLSFRDQVAIALRRLSS-------------GDSLMSIGDS 118 (391)
Q Consensus 52 ~~~~F~~~frms~~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~e~~l~i~L~~L~~-------------g~~~~~l~~~ 118 (391)
+-+.|...+.-.++-...+...+...+....... ..-...++.++++-+|..|+. ..+..+||..
T Consensus 100 ~~~~~~~l~~~~p~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~ 177 (211)
T PRK11753 100 SYKKFRQLIQVNPDILMALSAQMARRLQNTSRKV--GDLAFLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRI 177 (211)
T ss_pred cHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHH--HHHHhcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHH
Confidence 3455655555555444444444433332211100 011357889999999887754 1234678999
Q ss_pred cCCcccccchhhhHHH
Q 016336 119 CGLHHSTVSQVTWRFV 134 (391)
Q Consensus 119 Fgvs~sTvs~~~~~~~ 134 (391)
.|+++.||||+++++.
T Consensus 178 lG~tr~tvsR~l~~l~ 193 (211)
T PRK11753 178 VGCSREMVGRVLKMLE 193 (211)
T ss_pred hCCCHHHHHHHHHHHH
Confidence 9999999999876654
No 126
>PF13551 HTH_29: Winged helix-turn helix
Probab=76.55 E-value=0.91 Score=36.05 Aligned_cols=35 Identities=29% Similarity=0.306 Sum_probs=30.3
Q ss_pred HHHHHhcCCCC-ccccccccCCcccccchhhhHHHH
Q 016336 101 IALRRLSSGDS-LMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 101 i~L~~L~~g~~-~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
.+|..++.|.+ ...+|..+|||.+||++++.++..
T Consensus 3 ~~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~ 38 (112)
T PF13551_consen 3 QILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYRE 38 (112)
T ss_pred HHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHc
Confidence 35667889996 999999999999999999998754
No 127
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=76.43 E-value=1.8 Score=38.37 Aligned_cols=49 Identities=22% Similarity=0.195 Sum_probs=43.5
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|+.++-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.+
T Consensus 113 ~Lp~~~r~v~~L~~~-~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 113 QLPDEQREALILVGA-SGFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred hCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478899999999888 8999999999999999999999988888886644
No 128
>PRK06930 positive control sigma-like factor; Validated
Probab=76.34 E-value=1.7 Score=38.02 Aligned_cols=49 Identities=20% Similarity=0.177 Sum_probs=39.8
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+++.++-++.|+ +..|.++.+||..+|+|.+||...+.+....|...+
T Consensus 114 ~L~~rer~V~~L~-~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l 162 (170)
T PRK06930 114 VLTEREKEVYLMH-RGYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQI 162 (170)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4677766666665 478999999999999999999999988888776543
No 129
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=76.33 E-value=1.6 Score=38.17 Aligned_cols=49 Identities=27% Similarity=0.270 Sum_probs=42.3
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|++.+-++.|+++ .|.+|.++|..+|||.+||...+++....|.+.+
T Consensus 127 ~Lp~~~R~~~~l~~~-~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l 175 (182)
T COG1595 127 RLPPRQREAFLLRYL-EGLSYEEIAEILGISVGTVKSRLHRARKKLREQL 175 (182)
T ss_pred hCCHHHhHHhhhHhh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888877 6899999999999999999999988888876654
No 130
>PRK01381 Trp operon repressor; Provisional
Probab=76.31 E-value=1.8 Score=34.07 Aligned_cols=38 Identities=21% Similarity=0.215 Sum_probs=27.1
Q ss_pred cCHHHHHHHHHH------HhcCCCCccccccccCCcccccchhh
Q 016336 93 LSFRDQVAIALR------RLSSGDSLMSIGDSCGLHHSTVSQVT 130 (391)
Q Consensus 93 l~~e~~l~i~L~------~L~~g~~~~~l~~~Fgvs~sTvs~~~ 130 (391)
+++.++=+++.+ .+..+.+|+.|+...|||.+||+|.-
T Consensus 33 lTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgs 76 (99)
T PRK01381 33 LTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITRGS 76 (99)
T ss_pred CCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhH
Confidence 344454444443 34445899999999999999999843
No 131
>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=76.29 E-value=1.5 Score=41.94 Aligned_cols=45 Identities=22% Similarity=0.252 Sum_probs=39.2
Q ss_pred ccCHHHHHHHHHHHh---cCCCCccccccccCCcccccchhhhHHHHH
Q 016336 92 HLSFRDQVAIALRRL---SSGDSLMSIGDSCGLHHSTVSQVTWRFVEA 136 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L---~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~ 136 (391)
.+++.++..+.|+|. ..+.++..||..+|||++||.++..+...-
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 489999999999985 678999999999999999999988776543
No 132
>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=76.12 E-value=1.1 Score=31.17 Aligned_cols=38 Identities=16% Similarity=0.228 Sum_probs=26.0
Q ss_pred HHHHHHHHHhcCCCCccccccccCCcccccchhhhHHH
Q 016336 97 DQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFV 134 (391)
Q Consensus 97 ~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~ 134 (391)
+-.++..-+=..+.+..+|+..++++++|+++++.+..
T Consensus 5 q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~ 42 (59)
T PF01047_consen 5 QFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLE 42 (59)
T ss_dssp HHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHH
Confidence 33333333344457888999999999999998876644
No 133
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=76.03 E-value=2 Score=38.23 Aligned_cols=53 Identities=11% Similarity=0.043 Sum_probs=44.2
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhccccc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGLQHL 145 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~~~i 145 (391)
.+|+..+-++.|.++ .|.++..||..+|+|.+||...+.+....|.+.+..+.
T Consensus 133 ~Lp~~~r~v~~l~~~-~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 185 (196)
T PRK12535 133 ALPPERREALILTQV-LGYTYEEAAKIADVRVGTIRSRVARARADLIAATATGQ 185 (196)
T ss_pred cCCHHHHHHhhhHHH-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcccc
Confidence 367777878777766 57889999999999999999999999998887766544
No 134
>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=76.02 E-value=2.5 Score=34.51 Aligned_cols=75 Identities=17% Similarity=0.127 Sum_probs=46.9
Q ss_pred ChhHHHhhcCCCHHHHHHHHHHhhhccccccCCcccCCCCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhh
Q 016336 52 GLDKFKSVFKISRRTFDYICSLVEEKMVVKTGGFSFTSGKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 52 ~~~~F~~~frms~~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~ 131 (391)
+-.+=-..|++++.|....+..... ....+. . ..+..++ ...+..+.--....++.+++..||||.+|+++.++
T Consensus 20 s~~eaa~~F~VS~~Tv~~W~k~~~~-G~~~~k-~--r~~~Kid--~~~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lk 93 (119)
T PF01710_consen 20 SIREAAKRFGVSRNTVYRWLKRKET-GDLEPK-P--RGRKKID--RDELKALVEENPDATLRELAERLGVSPSTIWRALK 93 (119)
T ss_pred hHHHHHHHhCcHHHHHHHHHHhccc-cccccc-c--ccccccc--HHHHHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHH
Confidence 3445567899999998888883332 222221 1 1112443 23344444445667788999999999999987665
Q ss_pred H
Q 016336 132 R 132 (391)
Q Consensus 132 ~ 132 (391)
+
T Consensus 94 r 94 (119)
T PF01710_consen 94 R 94 (119)
T ss_pred H
Confidence 4
No 135
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=75.87 E-value=1.9 Score=40.06 Aligned_cols=49 Identities=18% Similarity=0.283 Sum_probs=42.3
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.++-.+|+.+.|+| -.+.++..+|...|||+|+||++..+.+..|...+
T Consensus 196 ~L~EREk~Vl~l~y-~eelt~kEI~~~LgISes~VSql~kkai~kLr~~l 244 (247)
T COG1191 196 PLPEREKLVLVLRY-KEELTQKEIAEVLGISESRVSRLHKKAIKKLRKEL 244 (247)
T ss_pred ccCHHHHHHHHHHH-HhccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHh
Confidence 46778899999999 46789999999999999999999999888886543
No 136
>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=75.80 E-value=1.2 Score=39.18 Aligned_cols=98 Identities=7% Similarity=0.034 Sum_probs=56.6
Q ss_pred ChhHHHhhcCCCHHHHHHHHHHhhhccccccCCcccCCCCccCHHHHHHHHHHHhcC--------------CCCcccccc
Q 016336 52 GLDKFKSVFKISRRTFDYICSLVEEKMVVKTGGFSFTSGKHLSFRDQVAIALRRLSS--------------GDSLMSIGD 117 (391)
Q Consensus 52 ~~~~F~~~frms~~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~e~~l~i~L~~L~~--------------g~~~~~l~~ 117 (391)
+-+.|...+.-++.--..++..+...+....... ..-...+++++|+-+|..|+. ..+..+||.
T Consensus 74 ~~~~~~~l~~~~p~l~~~~~~~l~~~l~~~~~~~--~~l~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~ 151 (193)
T TIGR03697 74 PIEQVEKAIEEDPDLSMLLLQGLSSRILQTEMMI--ETLAHRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAE 151 (193)
T ss_pred eHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHH--HHHHhCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHH
Confidence 3445555555555444444444443322211000 001245889999999987643 246788999
Q ss_pred ccCCcccccchhhhHHHHH-HHHhccccccCCCHH
Q 016336 118 SCGLHHSTVSQVTWRFVEA-MEQKGLQHLQWPSET 151 (391)
Q Consensus 118 ~Fgvs~sTvs~~~~~~~~~-l~~~~~~~i~~P~~~ 151 (391)
..|+++.||+|++.++... +.+.-...|..++.+
T Consensus 152 ~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~d~~ 186 (193)
T TIGR03697 152 AIGSTRVTITRLLGDLRKKKLISIHKKKITVHDPI 186 (193)
T ss_pred HhCCcHHHHHHHHHHHHHCCCEEecCCEEEEeCHH
Confidence 9999999999988877652 333223345555544
No 137
>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=75.78 E-value=2 Score=39.91 Aligned_cols=47 Identities=19% Similarity=0.423 Sum_probs=40.6
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+++.++.++.|+|+ .|.++..||..+|+|+++|+++..+.+.-|..
T Consensus 206 ~L~~rer~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~ 252 (254)
T TIGR02850 206 RLNEREKMILNMRFF-EGKTQMEVAEEIGISQAQVSRLEKAALKHMRK 252 (254)
T ss_pred cCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 578889999999885 58899999999999999999998888776643
No 138
>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=75.67 E-value=0.99 Score=32.22 Aligned_cols=26 Identities=31% Similarity=0.262 Sum_probs=21.6
Q ss_pred CCccccccccCCcccccchhhhHHHH
Q 016336 110 DSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 110 ~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
.+..+++..+|+|++||++++.....
T Consensus 26 ~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 26 LTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 57778999999999999988766554
No 139
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=75.60 E-value=1.9 Score=36.39 Aligned_cols=46 Identities=17% Similarity=0.146 Sum_probs=38.8
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~ 138 (391)
.+|+.++-++.|.|+ .|.++.+||..+|+|.+||...+.+....|-
T Consensus 106 ~L~~~~r~ii~l~~~-~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 106 VLDEKEKYIIFERFF-VGKTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred hCCHHHHHHHHHHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 478888888888876 5889999999999999999998888776653
No 140
>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=75.45 E-value=0.89 Score=31.85 Aligned_cols=43 Identities=28% Similarity=0.373 Sum_probs=32.9
Q ss_pred cCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 93 LSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 93 l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
++..|.- .|..++.|.+...+|...|||.+||.........-+
T Consensus 4 LT~~E~~--vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 4 LTERELE--VLRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp S-HHHHH--HHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred cCHHHHH--HHHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHh
Confidence 4444433 677899999999999999999999998877766544
No 141
>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=75.43 E-value=2.1 Score=39.83 Aligned_cols=47 Identities=19% Similarity=0.211 Sum_probs=41.1
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+++.++-.+.|+++ .|.++..||..+|+|.+||++...+....|..
T Consensus 205 ~L~~~~r~ii~l~~~-~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 205 ILSEREKSIIHCTFE-ENLSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred cCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 478888888888875 68999999999999999999999888877754
No 142
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=75.04 E-value=2.1 Score=37.72 Aligned_cols=49 Identities=10% Similarity=0.005 Sum_probs=41.7
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|+..+-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.+
T Consensus 131 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 131 RLPPRTGRVFMMREW-LELETEEICQELQITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888876 4799999999999999999998888888776543
No 143
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=74.94 E-value=2.1 Score=38.19 Aligned_cols=49 Identities=14% Similarity=0.068 Sum_probs=41.4
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|+..+-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.+
T Consensus 139 ~Lp~~~r~v~~L~~~-eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 139 HLPEQIGRVFMMREF-LDFEIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888875 6889999999999999999988888877776543
No 144
>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=74.71 E-value=1 Score=30.14 Aligned_cols=37 Identities=19% Similarity=0.162 Sum_probs=25.5
Q ss_pred HHHHHHHHhcCCCCccccccccCCcccccchhhhHHH
Q 016336 98 QVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFV 134 (391)
Q Consensus 98 ~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~ 134 (391)
++-|.........+..+|+..+|+|++||++.+....
T Consensus 4 R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~ 40 (47)
T PF01022_consen 4 RLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLR 40 (47)
T ss_dssp HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHH
Confidence 4444333344456778999999999999999876543
No 145
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=74.70 E-value=2.2 Score=41.20 Aligned_cols=48 Identities=21% Similarity=0.269 Sum_probs=42.5
Q ss_pred ccCHHHHHHHHHHHh---cCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRL---SSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L---~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+++.++..+.|+|. ..+.++..||..+|||+++|.++..+.+.-|..
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 488999999999996 577899999999999999999999888877754
No 146
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=74.26 E-value=2.7 Score=44.09 Aligned_cols=51 Identities=27% Similarity=0.304 Sum_probs=45.5
Q ss_pred CCCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 89 SGKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 89 ~~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
+++.+...-+++|.|.+--++.++..||..||.++|||...++++-..|.+
T Consensus 549 R~~~i~~aRqiAMYL~r~lt~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~~ 599 (617)
T PRK14086 549 RSRVLVTARQIAMYLCRELTDLSLPKIGQQFGRDHTTVMHADRKIRALMAE 599 (617)
T ss_pred CCcccchHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHh
Confidence 445778889999999999999999999999999999999999888887754
No 147
>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=74.25 E-value=2.2 Score=37.60 Aligned_cols=49 Identities=14% Similarity=0.100 Sum_probs=41.1
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+++..+-++.|+|+- |.++..||..+|+|.+||...+.+....|.+.+
T Consensus 131 ~L~~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l 179 (188)
T TIGR02943 131 HLPEQTARVFMMREVL-GFESDEICQELEISTSNCHVLLYRARLSLRACL 179 (188)
T ss_pred hCCHHHHHHHHHHHHh-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 3677888888887764 999999999999999999998888888776543
No 148
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=74.13 E-value=2.4 Score=36.50 Aligned_cols=48 Identities=21% Similarity=0.231 Sum_probs=40.4
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+|+..+.++.|++ -.|.++..||..+|+|.+||...+.+....+...
T Consensus 118 ~L~~~~r~v~~L~~-~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 165 (168)
T PRK12525 118 GLSGKARAAFLMSQ-LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQG 165 (168)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 47888888888876 5789999999999999999999888877776543
No 149
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=73.93 E-value=2.4 Score=34.26 Aligned_cols=47 Identities=13% Similarity=0.181 Sum_probs=41.5
Q ss_pred CCccCHHHHHHHHHHHhcCCCCccccccccCC-cccccchhhhHHHHH
Q 016336 90 GKHLSFRDQVAIALRRLSSGDSLMSIGDSCGL-HHSTVSQVTWRFVEA 136 (391)
Q Consensus 90 ~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgv-s~sTvs~~~~~~~~~ 136 (391)
.+..|.|.++-++-.++..|.++..+|..||| +.+++++++.++...
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~ 52 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKG 52 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHc
Confidence 46789999999999999999999999999996 999999887776553
No 150
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=73.86 E-value=4.8 Score=38.26 Aligned_cols=68 Identities=21% Similarity=0.178 Sum_probs=49.9
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhccccccCCCHHHHHHHHHHHhH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGLQHLQWPSETEMAEIKSKFEK 162 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~~~i~~P~~~~~~~i~~~f~~ 162 (391)
.+|+.++-++.|+++ .|.+|.+||..+|+|.+||...+.+....|.+..+..- +..++..++...|..
T Consensus 115 ~L~~~~R~v~~L~~~-~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~~~~--~~~~~~~~~v~~f~~ 182 (293)
T PRK09636 115 RLSPLERAAFLLHDV-FGVPFDEIASTLGRSPAACRQLASRARKHVRAARPRFP--VSDEEGAELVEAFFA 182 (293)
T ss_pred hCCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCCCC--CCchHHHHHHHHHHH
Confidence 478888887777766 48999999999999999999999999888887654322 222233445555543
No 151
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=73.79 E-value=2.3 Score=39.87 Aligned_cols=47 Identities=17% Similarity=0.297 Sum_probs=40.9
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+++.++-++.|+|+ .|.++..||..+|||.+||+++..+....|..
T Consensus 215 ~L~~rer~vl~l~y~-~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 215 ALPERERTVLVLRFF-ESMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred cCCHHHHHHHHHHhc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 478888888888886 69999999999999999999998888777654
No 152
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=73.78 E-value=2.9 Score=40.59 Aligned_cols=73 Identities=18% Similarity=0.256 Sum_probs=52.5
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhcccc---ccCCCHHHHHHHHHHHhHhhC
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGLQH---LQWPSETEMAEIKSKFEKIQG 165 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~~~---i~~P~~~~~~~i~~~f~~~~~ 165 (391)
.+|+.++-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+..+.. ..-|..++..++...|...++
T Consensus 153 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~~~v~~~~~A~~ 228 (339)
T PRK08241 153 HLPPRQRAVLILRDV-LGWSAAEVAELLDTSVAAVNSALQRARATLAERGPSAADTLREPDDPEERALLARYVAAFE 228 (339)
T ss_pred hCCHHHhhhhhhHHh-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhcCCCcccccCCCCChHHHHHHHHHHHHHh
Confidence 477888888888765 7899999999999999999999999998887743321 112333455566666654433
No 153
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=73.56 E-value=2.5 Score=37.03 Aligned_cols=50 Identities=10% Similarity=0.052 Sum_probs=41.1
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhcc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGL 142 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~ 142 (391)
.+|+..+-++.|.++ .|.++..||..+|+|.+||...+.+....|...+.
T Consensus 122 ~L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 171 (185)
T PRK12542 122 ELNESNRQVFKYKVF-YNLTYQEISSVMGITEANVRKQFERARKRVQNMIG 171 (185)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHc
Confidence 477777777777665 68999999999999999999999888888866543
No 154
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=73.34 E-value=2.6 Score=39.12 Aligned_cols=48 Identities=25% Similarity=0.277 Sum_probs=41.3
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+++.++-++.|+|+ .|.++..||..+|+|.+||...+.+....|-..
T Consensus 201 ~L~~~~r~vl~l~~~-~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 201 QLSEKEQLVISLFYK-EELTLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 478888888888885 889999999999999999999988887777543
No 155
>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=73.30 E-value=2.2 Score=33.83 Aligned_cols=46 Identities=17% Similarity=0.201 Sum_probs=32.6
Q ss_pred cCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 93 LSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 93 l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
++..++-.+- .|+-...|+..||..+|||+.+|+..+++....|..
T Consensus 18 LT~kQ~~~l~-lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~ 63 (101)
T PF04297_consen 18 LTEKQREILE-LYYEEDLSLSEIAEELGISRQAVYDSIKRAEKKLEE 63 (101)
T ss_dssp S-HHHHHHHH-HHCTS---HHHHHHHCTS-HHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHH-HHHccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4444444444 566789999999999999999999999999888854
No 156
>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=72.89 E-value=2.1 Score=28.58 Aligned_cols=29 Identities=17% Similarity=0.239 Sum_probs=22.8
Q ss_pred cCCCCccccccccCCcccccchhhhHHHH
Q 016336 107 SSGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 107 ~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
..+.+..++|..+|+|.+||++++.+..+
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 45588999999999999999998877654
No 157
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=72.74 E-value=2.4 Score=37.27 Aligned_cols=47 Identities=23% Similarity=0.266 Sum_probs=40.1
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+|+..+-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+
T Consensus 130 ~Lp~~~r~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 130 DLTTDQREALLLTQL-LGLSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred hCCHHHhHHhhhHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 478888888888776 68899999999999999999988888877764
No 158
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=72.72 E-value=2.2 Score=36.58 Aligned_cols=49 Identities=14% Similarity=0.035 Sum_probs=40.2
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|+..+-++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 108 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 108 TLPVIEAQAILLCDV-HELTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred hCCHHHHHHHHhHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 477777777777655 7899999999999999999999888888776543
No 159
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=72.64 E-value=2.6 Score=36.70 Aligned_cols=48 Identities=23% Similarity=0.219 Sum_probs=39.7
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+.+....|.+.
T Consensus 117 ~Lp~~~r~i~~l~~~-e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 164 (179)
T PRK12543 117 KLPYKLRQVIILRYL-HDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQK 164 (179)
T ss_pred hCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 478888878877655 678999999999999999998888887777554
No 160
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=72.19 E-value=2.5 Score=37.66 Aligned_cols=48 Identities=21% Similarity=0.232 Sum_probs=39.8
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+++.++-++.| ++ .|.++.+||..+|+|.+||...+.+....|.+.+
T Consensus 155 ~L~~~~r~vl~l-~~-e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 155 LLSELEKEVLEL-YL-DGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred hCCHHHHHHHHH-HH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 367778888888 65 7999999999999999999988888777776543
No 161
>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=72.19 E-value=3 Score=37.86 Aligned_cols=48 Identities=31% Similarity=0.396 Sum_probs=40.9
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+++.++-++.|+|+ .|.++.+||..+|+|.+||.+...+....|-..
T Consensus 175 ~L~~~~r~il~l~y~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 175 SLSEREQLVLSLYYY-EELNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred hCCHHHHHHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 478888888888875 788999999999999999999888887776543
No 162
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=72.16 E-value=2.8 Score=35.65 Aligned_cols=49 Identities=18% Similarity=0.149 Sum_probs=40.1
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|++++-++.|.+ -.|.++.+||..+|+|.+||...+.+....|...+
T Consensus 105 ~L~~~~r~v~~l~~-~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 105 ELPPACRDSFLLRK-LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 37777777777765 57899999999999999999998888888776543
No 163
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=71.72 E-value=3.3 Score=40.05 Aligned_cols=68 Identities=18% Similarity=0.130 Sum_probs=47.3
Q ss_pred HHHHHhcCCCCccccccccCCcccccchhhhHHHH-HHHHhccccccCCCHHHHHHHHHHHhHhhCCCcccee
Q 016336 101 IALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVE-AMEQKGLQHLQWPSETEMAEIKSKFEKIQGLPNCCGV 172 (391)
Q Consensus 101 i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~-~l~~~~~~~i~~P~~~~~~~i~~~f~~~~~fp~~~Ga 172 (391)
++=.|+-.|.++.+||..+|+|+++|||++.+.-+ -|. .-.|.-|.. ...++.+.+.+++|+..|+-+
T Consensus 21 vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV---~I~I~~~~~-~~~~Le~~L~~~fgLk~~iVv 89 (318)
T PRK15418 21 IAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGII---RVQINSRFE-GCLELENALRQHFSLQHIRVL 89 (318)
T ss_pred HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcE---EEEEeCCCc-cHHHHHHHHHHHhCCCEEEEE
Confidence 56667789999999999999999999998866433 121 223444532 334466667777788877654
No 164
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=71.63 E-value=3 Score=36.63 Aligned_cols=48 Identities=17% Similarity=0.214 Sum_probs=40.0
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+|+.++-++.|+|+. |.++..||..+|+|.+||...+.+....|-..
T Consensus 139 ~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 139 TLPEKQREILILRVVV-GLSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4777788778777775 89999999999999999999888877776543
No 165
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=71.52 E-value=3.6 Score=41.78 Aligned_cols=50 Identities=24% Similarity=0.321 Sum_probs=44.6
Q ss_pred CCCccCHHHHHHHHHHHhcCCCCcccccccc-CCcccccchhhhHHHHHHH
Q 016336 89 SGKHLSFRDQVAIALRRLSSGDSLMSIGDSC-GLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 89 ~~~~l~~e~~l~i~L~~L~~g~~~~~l~~~F-gvs~sTvs~~~~~~~~~l~ 138 (391)
+.+.+...-|+||.|.+--++.++.+||..| |.++|||+..++++-..+.
T Consensus 382 R~~~~~~aR~iamyl~~~~~~~s~~~Ig~~fg~rdhstV~~a~~~i~~~~~ 432 (450)
T PRK00149 382 RTRNIARPRQIAMYLAKELTDLSLPEIGRAFGGRDHTTVLHAVRKIEKLLE 432 (450)
T ss_pred CCcccChHHHHHHHHHHHhcCCCHHHHHHHcCCCCHhHHHHHHHHHHHHHH
Confidence 4567888999999999999999999999999 5999999999888877664
No 166
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=71.45 E-value=3 Score=37.41 Aligned_cols=48 Identities=10% Similarity=-0.000 Sum_probs=39.8
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+|++++.++.|.++ .|.++..||..+|+|.+||...+.+....|.+.
T Consensus 153 ~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 153 KLPEAQQTVVKGVYF-QELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 477788888777665 689999999999999999998888887777654
No 167
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=71.08 E-value=2.8 Score=35.70 Aligned_cols=47 Identities=21% Similarity=0.208 Sum_probs=39.7
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+|+..+.++.|+++ .|.++..||..+|+|.+||...+.+....|.+
T Consensus 112 ~L~~~~r~v~~l~~~-~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 112 SLPLERRNVLLLRDY-YGFSYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HCCHHHHHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 478888888888766 68899999999999999999988888776654
No 168
>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=70.91 E-value=3.2 Score=35.87 Aligned_cols=48 Identities=25% Similarity=0.190 Sum_probs=40.1
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+|+.++.++.|.++ .|.++..||..+|+|.+||...+.+....|...
T Consensus 100 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 147 (170)
T TIGR02959 100 ELPDEYREAIRLTEL-EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKEL 147 (170)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 478888888888775 789999999999999999999888877766543
No 169
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=70.82 E-value=6.8 Score=28.62 Aligned_cols=72 Identities=17% Similarity=0.146 Sum_probs=51.1
Q ss_pred ChhHHHhhcCCCHHHHHHHHHHhhhccccccCCcccCCCCccCHHHHHHHHHHHhcCC-CCccccccccCC-cccccchh
Q 016336 52 GLDKFKSVFKISRRTFDYICSLVEEKMVVKTGGFSFTSGKHLSFRDQVAIALRRLSSG-DSLMSIGDSCGL-HHSTVSQV 129 (391)
Q Consensus 52 ~~~~F~~~frms~~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~e~~l~i~L~~L~~g-~~~~~l~~~Fgv-s~sTvs~~ 129 (391)
+-++.-..++++...|..++........ ...-...++.-++.+|..+ .+..++|..+|. |.++.++.
T Consensus 3 ~~~~la~~~~~s~~~l~~~f~~~~~~s~-----------~~~~~~~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~ 71 (84)
T smart00342 3 TLEDLAEALGMSPRHLQRLFKKETGTTP-----------KQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRA 71 (84)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHhCcCH-----------HHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHH
Confidence 3456778889999998888765432110 1122245677777787776 789999999999 99999998
Q ss_pred hhHHH
Q 016336 130 TWRFV 134 (391)
Q Consensus 130 ~~~~~ 134 (391)
+.+..
T Consensus 72 Fk~~~ 76 (84)
T smart00342 72 FKKLF 76 (84)
T ss_pred HHHHH
Confidence 86653
No 170
>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=70.77 E-value=1.4 Score=38.90 Aligned_cols=49 Identities=18% Similarity=0.092 Sum_probs=40.3
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|+..+-++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 131 ~Lp~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 131 GLPEEFRQAVYLADV-EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred hCCHHHhhheeehhh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 467777877777665 6899999999999999999998888887776543
No 171
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=70.52 E-value=3.3 Score=41.93 Aligned_cols=49 Identities=12% Similarity=0.204 Sum_probs=43.9
Q ss_pred CCCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 89 SGKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 89 ~~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
+.+.+...-|++|.|.+=-++.++..||..||.++|||+..+.++-..+
T Consensus 367 R~~~i~~aR~iamyl~r~~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 367 RNVKALLARRIGMYVAKNYLGSSLRTIAEKFNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred CCccccHHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 4567888899999999999999999999999999999999988887765
No 172
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=69.89 E-value=3.9 Score=36.14 Aligned_cols=48 Identities=10% Similarity=0.074 Sum_probs=39.9
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+|..++-++.|+++ .|.++.+||..+|+|.+||...+.+....|...
T Consensus 142 ~L~~~~r~vl~l~~~-~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 142 ALTDTQRESVTLAYY-GGLTYREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 477777777777665 679999999999999999999888888777654
No 173
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=69.87 E-value=6.1 Score=37.62 Aligned_cols=67 Identities=16% Similarity=0.215 Sum_probs=49.2
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhccccccCCCHHHHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGLQHLQWPSETEMAEIKSKFE 161 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~~~i~~P~~~~~~~i~~~f~ 161 (391)
.+++.++-++.|+++ .|.+|.+||..+|+|.+||...+.+....|.+..+.+- +...+..++.+.|-
T Consensus 118 ~L~p~~R~vf~L~~~-~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~~~~~--~~~~~~~~~~~~f~ 184 (290)
T PRK09635 118 RLGPAERVVFVLHEI-FGLPYQQIATTIGSQASTCRQLAHRARRKINESRIAAS--VEPAQHRVVTRAFI 184 (290)
T ss_pred hCCHHHHHHhhHHHH-hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhCCCCC--CChHHHHHHHHHHH
Confidence 467777777777665 59999999999999999999999998888876544221 23334455666664
No 174
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=69.79 E-value=3 Score=41.24 Aligned_cols=48 Identities=19% Similarity=0.257 Sum_probs=41.2
Q ss_pred ccCHHHHHHHHHHHh---cCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRL---SSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L---~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+++.++..+.|+|+ ..+.++..||..+|||+.+|+++..+.+.-|-.
T Consensus 311 ~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~ 361 (373)
T PRK07406 311 TLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRH 361 (373)
T ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 488999999999886 346899999999999999999998888776643
No 175
>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=69.62 E-value=3.9 Score=34.13 Aligned_cols=49 Identities=14% Similarity=0.150 Sum_probs=40.0
Q ss_pred ccCHHHHHHHHHHHhcC-CCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSS-GDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~-g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.++.+++-.+.++|+.. ..++..||..+|+|++|++++-.+++..+.+.
T Consensus 82 ~Ld~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~ 131 (134)
T TIGR01636 82 EADEQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEE 131 (134)
T ss_pred hCCHHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 37888999999988743 34899999999999999999887777766543
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=69.48 E-value=1.2 Score=36.43 Aligned_cols=29 Identities=21% Similarity=0.266 Sum_probs=25.5
Q ss_pred HHhcCCCCccccccccCCcccccchhhhH
Q 016336 104 RRLSSGDSLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 104 ~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
.++..|.+.+.++..|+||.+||.+++.+
T Consensus 13 ~~~~~g~s~~eaa~~F~VS~~Tv~~W~k~ 41 (119)
T PF01710_consen 13 AYIEKGKSIREAAKRFGVSRNTVYRWLKR 41 (119)
T ss_pred HHHHccchHHHHHHHhCcHHHHHHHHHHh
Confidence 46777889999999999999999998763
No 177
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=69.25 E-value=2.9 Score=38.46 Aligned_cols=48 Identities=15% Similarity=0.084 Sum_probs=40.0
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+|..++-++.|+++ .|.++..||..+|+|.+||...+.+....|.+.
T Consensus 171 ~Lp~~~R~v~~L~~~-eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~ 218 (233)
T PRK12538 171 RLPEQQRIAVILSYH-ENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDL 218 (233)
T ss_pred hCCHHHHHHhhhHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 367777777777665 789999999999999999999998888877654
No 178
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=67.83 E-value=1.8 Score=39.54 Aligned_cols=49 Identities=18% Similarity=0.108 Sum_probs=40.6
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.++..++-++.|+++. |.++.+||..+|+|.+||...+.+....|-+.+
T Consensus 149 ~L~~~~r~i~~l~~~~-g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 149 ALPDAFRAVFVLRVVE-ELSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred hCCHHHhhhheeehhc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3677778777777654 999999999999999999998888887776544
No 179
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=67.42 E-value=4 Score=37.47 Aligned_cols=46 Identities=20% Similarity=0.229 Sum_probs=39.2
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~ 138 (391)
.++..++-.+.|+|+ .|.++..+|..+|||+++|+++..+...-|-
T Consensus 183 ~L~~~er~vi~l~~~-~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr 228 (231)
T PRK12427 183 QLDEREQLILHLYYQ-HEMSLKEIALVLDLTEARICQLNKKIAQKIK 228 (231)
T ss_pred cCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 478888888888884 6899999999999999999998877776553
No 180
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=67.04 E-value=3.5 Score=40.68 Aligned_cols=47 Identities=17% Similarity=0.293 Sum_probs=39.6
Q ss_pred ccCHHHHHHHHHHHh-c--CCCCccccccccCCcccccchhhhHHHHHHH
Q 016336 92 HLSFRDQVAIALRRL-S--SGDSLMSIGDSCGLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L-~--~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~ 138 (391)
.++..++..+.|+|. . .+.++..||..||||+++|+++-.+.+.-|-
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 488899999999985 3 5589999999999999999998777766554
No 181
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=66.48 E-value=5.2 Score=40.68 Aligned_cols=73 Identities=19% Similarity=0.280 Sum_probs=53.9
Q ss_pred HHHHHHHHhhhccccccCCcc-cCCCCccCHHHHHHHHHHHhcCCCCccccccccC-CcccccchhhhHHHHHHH
Q 016336 66 TFDYICSLVEEKMVVKTGGFS-FTSGKHLSFRDQVAIALRRLSSGDSLMSIGDSCG-LHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 66 tF~~L~~~l~~~~~~~~~~~~-~~~~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fg-vs~sTvs~~~~~~~~~l~ 138 (391)
+.+.|.+.+...+......+. ..+.+.+...-|+||.|.+=-++.++..||..|| .++|||...++++-..+.
T Consensus 357 t~~~I~~~Va~~~~i~~~dl~s~~R~~~i~~~RqiamyL~r~~t~~sl~~IG~~FggrdHsTV~~a~~ki~~~~~ 431 (450)
T PRK14087 357 NVKKIKEVVSEKYGISVNAIDGKARSKSIVTARHIAMYLTKEILNHTLAQIGEEFGGRDHTTVINAERKIEKMLK 431 (450)
T ss_pred CHHHHHHHHHHHcCCCHHHHhCCCCCccccHHHHHHHHHHHHHcCCCHHHHHHHhCCCChHHHHHHHHHHHHHHH
Confidence 455566655555443221111 1244578889999999999999999999999997 999999988888877664
No 182
>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=66.41 E-value=3.8 Score=33.79 Aligned_cols=46 Identities=24% Similarity=0.295 Sum_probs=33.9
Q ss_pred CCCCccCHHHHHHHH-HHHhcCCCCccccccccCCcccccchhhhHHHH
Q 016336 88 TSGKHLSFRDQVAIA-LRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 88 ~~~~~l~~e~~l~i~-L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
.+|++++.+.+.-|. |. ..|.+-.+|+..+.||++.|++++.++-+
T Consensus 13 ~nGrPLp~~~R~rIvela--~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~e 59 (125)
T PF00292_consen 13 INGRPLPNELRQRIVELA--KEGVRPCDISRQLRVSHGCVSKILSRYRE 59 (125)
T ss_dssp ETTSSS-HHHHHHHHHHH--HTT--HHHHHHHHT--HHHHHHHHHHHHH
T ss_pred eCCccCcHHHHHHHHHHh--hhcCCHHHHHHHHccchhHHHHHHHHHHH
Confidence 368999999887776 44 36999999999999999999999887743
No 183
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=65.99 E-value=2.5 Score=36.91 Aligned_cols=45 Identities=16% Similarity=0.275 Sum_probs=36.6
Q ss_pred CccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 91 KHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
..+|+.|. =.|..++.|.+..+||...++|.+||..++.++..-+
T Consensus 132 ~~LSpREr--EVLrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKL 176 (198)
T PRK15201 132 RHFSVTER--HLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKL 176 (198)
T ss_pred CCCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 34776554 4677899999999999999999999998887766655
No 184
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=65.94 E-value=3.5 Score=35.72 Aligned_cols=48 Identities=19% Similarity=0.125 Sum_probs=37.2
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.++++.+-++.|.+ -.|.++..||..+|+|.+||...+.+....+...
T Consensus 119 ~L~~~~r~i~~l~~-~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~ 166 (172)
T PRK09651 119 GLNGKTREAFLLSQ-LDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLF 166 (172)
T ss_pred hCCHHHhHHhhhhh-ccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 36666665555544 4788999999999999999999888877766543
No 185
>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=65.90 E-value=2.5 Score=29.01 Aligned_cols=25 Identities=8% Similarity=0.126 Sum_probs=19.7
Q ss_pred CCCccccccccCCcccccchhhhHH
Q 016336 109 GDSLMSIGDSCGLHHSTVSQVTWRF 133 (391)
Q Consensus 109 g~~~~~l~~~Fgvs~sTvs~~~~~~ 133 (391)
+.+...+|..|+||+.||.+.+...
T Consensus 15 ~it~~eLa~~l~vS~rTi~~~i~~L 39 (55)
T PF08279_consen 15 PITAKELAEELGVSRRTIRRDIKEL 39 (55)
T ss_dssp SBEHHHHHHHCTS-HHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 3577789999999999999877554
No 186
>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=65.86 E-value=3.3 Score=34.48 Aligned_cols=35 Identities=11% Similarity=0.135 Sum_probs=30.4
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVS 127 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs 127 (391)
.+|+..+-++.|+++ .|.++.+||..+|+|.+||.
T Consensus 107 ~Lp~~~r~v~~l~~~-~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 107 ILPNKQKKIIYMKFF-EDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHhhc
Confidence 478888888888666 78899999999999999986
No 187
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=65.81 E-value=4.4 Score=37.99 Aligned_cols=48 Identities=25% Similarity=0.297 Sum_probs=40.5
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+++.++-++.|+|+ .|.++..||..+|+|.+||.+...+....|...
T Consensus 212 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 212 TLPEREKKVLILYYY-EDLTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 478888888888875 689999999999999999998888777766543
No 188
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=65.67 E-value=4.9 Score=35.41 Aligned_cols=46 Identities=24% Similarity=0.293 Sum_probs=34.2
Q ss_pred cCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 93 LSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 93 l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
+++++.=.+.|+++ .|.++..||...|||.+||.+-....-..|..
T Consensus 136 l~~~~~~~v~l~~~-~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 136 LDPRQRRVVELRFF-EGLSVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred cCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 44455555566555 78999999999999999999977666555543
No 189
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=65.42 E-value=4 Score=37.21 Aligned_cols=66 Identities=12% Similarity=0.010 Sum_probs=45.5
Q ss_pred CccCHHHHHHHHHHHhcCC----------CCccccccccCCcccccchhhhHHHHHHHHhccccccCCCHHHHHHH
Q 016336 91 KHLSFRDQVAIALRRLSSG----------DSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGLQHLQWPSETEMAEI 156 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g----------~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~~~i~~P~~~~~~~i 156 (391)
...+++++++-+|..++.. .+..+||...|+++.||+|++.++.+.=...-...|..++.+.+.++
T Consensus 145 ~~~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~lG~tretvsR~l~~L~~~gl~~~~~~i~I~d~~~L~~~ 220 (236)
T PRK09392 145 KLRSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYLGMTPENLSRAFAALASHGVHVDGSAVTITDPAGLARF 220 (236)
T ss_pred hcCCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHhCCChhHHHHHHHHHHhCCeEeeCCEEEEcCHHHHHHh
Confidence 3468999999999887652 12356999999999999999887654211222346666766655443
No 190
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=65.27 E-value=3.5 Score=31.41 Aligned_cols=39 Identities=26% Similarity=0.362 Sum_probs=28.4
Q ss_pred HHHHHHHHHhcC---CCCccccccccCCcccccchhhhHHHH
Q 016336 97 DQVAIALRRLSS---GDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 97 ~~l~i~L~~L~~---g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
++..-.|.+|+. +.+..+++..+|++++||++++.....
T Consensus 5 ~r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 5 ERGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 344445555543 467889999999999999998866543
No 191
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=64.57 E-value=4.3 Score=40.64 Aligned_cols=47 Identities=23% Similarity=0.294 Sum_probs=40.3
Q ss_pred ccCHHHHHHHHHHHh---cCCCCccccccccCCcccccchhhhHHHHHHH
Q 016336 92 HLSFRDQVAIALRRL---SSGDSLMSIGDSCGLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L---~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~ 138 (391)
.+++.++-.+.|+|. ..+.++..||..+|+|.+||.++.++....|.
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 488899999999985 35689999999999999999999888776664
No 192
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=64.12 E-value=4.7 Score=38.94 Aligned_cols=68 Identities=21% Similarity=0.194 Sum_probs=44.5
Q ss_pred HHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH-hccccccCCCHHHHHHHHHHHhHhhCCCccceee
Q 016336 102 ALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ-KGLQHLQWPSETEMAEIKSKFEKIQGLPNCCGVI 173 (391)
Q Consensus 102 ~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~-~~~~~i~~P~~~~~~~i~~~f~~~~~fp~~~GaI 173 (391)
+=.|+-.|.++++||..+|||+.||+|++.+.-. + ...-.|..|.. ..-++.+...+++|++.|+-+-
T Consensus 19 A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~---~GiV~I~i~~~~~-~~~~Le~~L~~~fgL~~a~VVp 87 (321)
T COG2390 19 AWLYYVEGLTQSEIAERLGISRATVSRLLAKARE---EGIVKISINSPVE-GCLELEQQLKERFGLKEAIVVP 87 (321)
T ss_pred HHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH---CCeEEEEeCCCCc-chHHHHHHHHHhcCCCeEEEEc
Confidence 4457788999999999999999999998755322 1 11223443333 2333555566666888776543
No 193
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=63.87 E-value=3 Score=36.92 Aligned_cols=66 Identities=18% Similarity=0.226 Sum_probs=46.2
Q ss_pred ccCHHHHHHHHHHHhcC--------------CCCccccccccCCcccccchhhhHHHH-HHHHhccccccCCCHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSS--------------GDSLMSIGDSCGLHHSTVSQVTWRFVE-AMEQKGLQHLQWPSETEMAEI 156 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~--------------g~~~~~l~~~Fgvs~sTvs~~~~~~~~-~l~~~~~~~i~~P~~~~~~~i 156 (391)
..+++++|+-+|..|+. ..++.+||...|+++.||||++.++.+ -+.+.....|..++.+.+.++
T Consensus 118 ~~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~d~~~L~~~ 197 (202)
T PRK13918 118 GQRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRETVTKVIGELSREGYIRSGYGKIQLLDLKGLEEL 197 (202)
T ss_pred hCchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcCCCEEEEECHHHHHHH
Confidence 35788999999887664 135678899999999999999888765 233333345666666555544
Q ss_pred H
Q 016336 157 K 157 (391)
Q Consensus 157 ~ 157 (391)
+
T Consensus 198 ~ 198 (202)
T PRK13918 198 A 198 (202)
T ss_pred H
Confidence 3
No 194
>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=63.82 E-value=2.2 Score=31.35 Aligned_cols=27 Identities=26% Similarity=0.291 Sum_probs=21.9
Q ss_pred CCCccccccccCCcccccchhhhHHHH
Q 016336 109 GDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 109 g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
..+..++|...|+|+.||++++.++.+
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~ 54 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKD 54 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 356778999999999999998776654
No 195
>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=63.62 E-value=4.4 Score=35.68 Aligned_cols=41 Identities=17% Similarity=0.214 Sum_probs=31.9
Q ss_pred HHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 97 DQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 97 ~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+.++ +.++ .|.++.+||..+|+|.+||...+++....|..
T Consensus 155 ~~~i~-~~~~-~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 155 EWKVL-QSYL-DGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred HHHHH-HHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34443 4555 89999999999999999998877777666643
No 196
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=63.36 E-value=5.1 Score=38.86 Aligned_cols=50 Identities=18% Similarity=0.221 Sum_probs=43.0
Q ss_pred ccCHHHHHHHHHHH-h--cCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRR-L--SSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~-L--~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+++.++.++.++| | -.|.++..||..+|||.+||..+..+....|...+
T Consensus 262 ~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 58889999999887 4 46889999999999999999999999888886543
No 197
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=63.06 E-value=5.4 Score=35.15 Aligned_cols=49 Identities=18% Similarity=0.156 Sum_probs=40.0
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
.+|...+-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.+
T Consensus 128 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 128 KLDPEYREPLLLQVI-GGFSGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred hCCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 367777776666655 5999999999999999999999888888776654
No 198
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=63.03 E-value=6 Score=40.12 Aligned_cols=72 Identities=24% Similarity=0.182 Sum_probs=52.5
Q ss_pred HHHHHHHHhhhccccccCCcc-cCCCCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 66 TFDYICSLVEEKMVVKTGGFS-FTSGKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 66 tF~~L~~~l~~~~~~~~~~~~-~~~~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
+.+.|...+...+........ ..+.+.+...-|+||.|.+=-++.|+.+||..||..+|||..-++++-+.+
T Consensus 353 t~~~I~~~Va~~~~v~~~dl~s~~R~~~i~~~Rqiamyl~r~~t~~s~~~IG~~fgrdHsTV~~a~~ki~~~~ 425 (445)
T PRK12422 353 TPSKIIRAVAQYYGVSPESILGRSQSREYVLPRQVAMYLCRQKLSLSYVKIGDVFSRDHSTVISSIRAISQKL 425 (445)
T ss_pred CHHHHHHHHHHHhCCCHHHHhcCCCCcccccHHHHHHHHHHHhcCCCHHHHHHHhCCChHHHHHHHHHHHHHH
Confidence 345555555444332221111 224567888899999999999999999999999999999998888877766
No 199
>PRK05949 RNA polymerase sigma factor; Validated
Probab=62.97 E-value=5.3 Score=38.74 Aligned_cols=48 Identities=19% Similarity=0.259 Sum_probs=41.4
Q ss_pred ccCHHHHHHHHHHHh-c--CCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRL-S--SGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L-~--~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+++.++-.+.|+|. . .+.++..||..+|||+++|.++..+....|..
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 488899999999984 3 56899999999999999999999888877754
No 200
>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=62.20 E-value=13 Score=29.89 Aligned_cols=43 Identities=5% Similarity=0.087 Sum_probs=29.3
Q ss_pred cCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHH
Q 016336 93 LSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 93 l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
+++.+-.++....-..+.+..+|+..++++++|+++.+.+...
T Consensus 26 lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~ 68 (118)
T TIGR02337 26 LTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLER 68 (118)
T ss_pred CCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHH
Confidence 4554433332223345677889999999999999988766554
No 201
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=62.14 E-value=5.7 Score=36.22 Aligned_cols=81 Identities=16% Similarity=0.057 Sum_probs=48.7
Q ss_pred hhHHHhhcCCCHHHHHHHHHHhhhccccccCCcccCCCCccCHHHHHHHHHHHhcC----------CCCccccccccCCc
Q 016336 53 LDKFKSVFKISRRTFDYICSLVEEKMVVKTGGFSFTSGKHLSFRDQVAIALRRLSS----------GDSLMSIGDSCGLH 122 (391)
Q Consensus 53 ~~~F~~~frms~~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~e~~l~i~L~~L~~----------g~~~~~l~~~Fgvs 122 (391)
-+.|...+.-+++....++..+...+....... ..-...+++++|+-+|..++. ..+..+||...|++
T Consensus 115 ~~~f~~l~~~~p~l~~~l~~~l~~~l~~~~~~~--~~l~~~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGis 192 (230)
T PRK09391 115 RRSLEQAAATDVDVARALLSLTAGGLRHAQDHM--LLLGRKTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLT 192 (230)
T ss_pred HHHHHHHHhhChHHHHHHHHHHHHHHHHHHHHH--HHHcCCCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCC
Confidence 345555555455444444444443322110000 001236899999999988754 13557899999999
Q ss_pred ccccchhhhHHHH
Q 016336 123 HSTVSQVTWRFVE 135 (391)
Q Consensus 123 ~sTvs~~~~~~~~ 135 (391)
+.|+||++.++-+
T Consensus 193 retlsR~L~~L~~ 205 (230)
T PRK09391 193 IETVSRALSQLQD 205 (230)
T ss_pred HHHHHHHHHHHHH
Confidence 9999998776553
No 202
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=62.09 E-value=4.6 Score=29.36 Aligned_cols=39 Identities=15% Similarity=0.318 Sum_probs=30.6
Q ss_pred CHHHHHHHHHHHhcC-CCCccccccccCCcccccchhhhH
Q 016336 94 SFRDQVAIALRRLSS-GDSLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 94 ~~e~~l~i~L~~L~~-g~~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
+.+++++.+|..-+. +.+..+|+..+|++.++|++++..
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~ 45 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYS 45 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 456777777776655 588899999999999998876544
No 203
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=61.55 E-value=2.5 Score=36.53 Aligned_cols=48 Identities=15% Similarity=0.126 Sum_probs=38.4
Q ss_pred cCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 93 LSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 93 l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
+|..++-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.+
T Consensus 121 L~~~~r~vl~l~~~-~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 121 LSLEHRAVLVLHDL-EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred CCHHHeeeeeehHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 56666666666554 6788999999999999999999988888776643
No 204
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=61.32 E-value=3.7 Score=36.95 Aligned_cols=45 Identities=22% Similarity=0.265 Sum_probs=37.3
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~ 138 (391)
.+++.|+ =.|.+++.|.+..+||...++|.+||..+..+...-|.
T Consensus 137 ~LT~RE~--eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 137 SLSRTES--SMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 3676664 56788999999999999999999999998877766553
No 205
>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=61.18 E-value=1.6 Score=26.83 Aligned_cols=24 Identities=29% Similarity=0.368 Sum_probs=18.8
Q ss_pred CccccccccCCcccccchhhhHHH
Q 016336 111 SLMSIGDSCGLHHSTVSQVTWRFV 134 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs~~~~~~~ 134 (391)
+..+||...|+++.||||++.++-
T Consensus 4 tr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHHHHHH
Confidence 456899999999999999887653
No 206
>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=61.16 E-value=3.9 Score=28.76 Aligned_cols=28 Identities=21% Similarity=0.331 Sum_probs=24.1
Q ss_pred CccccccccCCcccccchhhhHHHHHHH
Q 016336 111 SLMSIGDSCGLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs~~~~~~~~~l~ 138 (391)
++...|..+++|+++|++.+.+.-..+.
T Consensus 15 s~~~AA~~l~is~~~vs~~i~~LE~~lg 42 (60)
T PF00126_consen 15 SISAAAEELGISQSAVSRQIKQLEEELG 42 (60)
T ss_dssp SHHHHHHHCTSSHHHHHHHHHHHHHHHT
T ss_pred CHHHHHHHhhccchHHHHHHHHHHHHhC
Confidence 8899999999999999998877766554
No 207
>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=60.98 E-value=1.8 Score=29.57 Aligned_cols=25 Identities=32% Similarity=0.356 Sum_probs=19.7
Q ss_pred CCccccccccCCcccccchhhhHHH
Q 016336 110 DSLMSIGDSCGLHHSTVSQVTWRFV 134 (391)
Q Consensus 110 ~~~~~l~~~Fgvs~sTvs~~~~~~~ 134 (391)
.+..+|+...|+++||+++++...+
T Consensus 19 ~t~~eia~~~gl~~stv~r~L~tL~ 43 (52)
T PF09339_consen 19 LTLSEIARALGLPKSTVHRLLQTLV 43 (52)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4578899999999999999876544
No 208
>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=60.82 E-value=4 Score=28.79 Aligned_cols=33 Identities=30% Similarity=0.243 Sum_probs=26.7
Q ss_pred HHHHHHHHhcCCCCccccccccCCcccccchhhhH
Q 016336 98 QVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 98 ~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
..|..|+. .|-+...||..+|++.+||+.+..+
T Consensus 4 ~~A~~LY~--~G~~~~eIA~~Lg~~~~TV~~W~~r 36 (58)
T PF06056_consen 4 EQARSLYL--QGWSIKEIAEELGVPRSTVYSWKDR 36 (58)
T ss_pred HHHHHHHH--cCCCHHHHHHHHCCChHHHHHHHHh
Confidence 44566664 5999999999999999999987644
No 209
>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=60.81 E-value=4.2 Score=31.71 Aligned_cols=28 Identities=18% Similarity=0.201 Sum_probs=22.4
Q ss_pred cCCCCccccccccCCcccccchhhhHHH
Q 016336 107 SSGDSLMSIGDSCGLHHSTVSQVTWRFV 134 (391)
Q Consensus 107 ~~g~~~~~l~~~Fgvs~sTvs~~~~~~~ 134 (391)
.-..+..+||...|++++||++++.+..
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le 72 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKSLA 72 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3456788899999999999998776543
No 210
>PF13551 HTH_29: Winged helix-turn helix
Probab=60.21 E-value=19 Score=28.21 Aligned_cols=80 Identities=16% Similarity=0.107 Sum_probs=44.6
Q ss_pred ChhHHHhhcCCCHHHHHHHHHHhhhccc--cccCCcccCCCCc-cCHHHHHHHHHHHhcCCC-------Cccccccc---
Q 016336 52 GLDKFKSVFKISRRTFDYICSLVEEKMV--VKTGGFSFTSGKH-LSFRDQVAIALRRLSSGD-------SLMSIGDS--- 118 (391)
Q Consensus 52 ~~~~F~~~frms~~tF~~L~~~l~~~~~--~~~~~~~~~~~~~-l~~e~~l~i~L~~L~~g~-------~~~~l~~~--- 118 (391)
+..+.-..+++++.|+...+........ ..+...+.++... +++++.- ..+.++.... +...|+..
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~-~l~~~~~~~p~~g~~~~t~~~l~~~l~~ 92 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRA-QLIELLRENPPEGRSRWTLEELAEWLIE 92 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHH-HHHHHHHHCCCCCCCcccHHHHHHHHHH
Confidence 4778889999999999999988776541 1110111122233 5655444 3333333322 23344432
Q ss_pred ----cCCcccccchhhhH
Q 016336 119 ----CGLHHSTVSQVTWR 132 (391)
Q Consensus 119 ----Fgvs~sTvs~~~~~ 132 (391)
..+|.+||++++++
T Consensus 93 ~~~~~~~s~~ti~r~L~~ 110 (112)
T PF13551_consen 93 EEFGIDVSPSTIRRILKR 110 (112)
T ss_pred hccCccCCHHHHHHHHHH
Confidence 25677777777654
No 211
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=60.13 E-value=6 Score=38.33 Aligned_cols=48 Identities=27% Similarity=0.329 Sum_probs=40.5
Q ss_pred ccCHHHHHHHHHHHh---cCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRL---SSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L---~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.++..++..+.++|. ....++..||..||||++.|+++-.+.+.-|..
T Consensus 262 ~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~ 312 (324)
T PRK07921 262 TLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRN 312 (324)
T ss_pred hCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 488899999999885 245799999999999999999998887776653
No 212
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=60.10 E-value=3.2 Score=36.59 Aligned_cols=48 Identities=17% Similarity=0.167 Sum_probs=38.9
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+++.++-++.|++ -.|.++.+||..+|+|.+||...+.+....|.+.
T Consensus 139 ~L~~~~r~i~~l~~-~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 139 TLPDEQREVFLLRE-HGDLELEEIAELTGVPEETVKSRLRYALQKLREL 186 (194)
T ss_pred hCCHhHhhheeeeh-ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 36777777777665 5789999999999999999998888887777654
No 213
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=59.60 E-value=7.2 Score=31.16 Aligned_cols=46 Identities=17% Similarity=0.167 Sum_probs=35.8
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~ 138 (391)
.+++++-=+|-|..+ .|.++.+.|...|||++|+++++...-.-|.
T Consensus 41 ~L~~dElEAiRL~D~-egl~QeeaA~~MgVSR~T~~ril~~ARkKiA 86 (106)
T PF02001_consen 41 VLTVDELEAIRLVDY-EGLSQEEAAERMGVSRPTFQRILESARKKIA 86 (106)
T ss_pred EeeHHHHHHHHHHHH-cCCCHHHHHHHcCCcHHHHHHHHHHHHHHHH
Confidence 467777777777666 4689999999999999999998876544443
No 214
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=59.42 E-value=5.5 Score=33.38 Aligned_cols=43 Identities=12% Similarity=0.224 Sum_probs=29.7
Q ss_pred cCHHH-HHHHHHHHhcCCCCccccccccCCcccccchhhhHHHH
Q 016336 93 LSFRD-QVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 93 l~~e~-~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
+++.+ .++..|.....+.+..+|+..++++++||++++.+...
T Consensus 29 lt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~ 72 (144)
T PRK03573 29 LTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEE 72 (144)
T ss_pred CCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHH
Confidence 44444 34444444444567889999999999999988766543
No 215
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=59.30 E-value=7.9 Score=38.63 Aligned_cols=51 Identities=25% Similarity=0.334 Sum_probs=44.7
Q ss_pred CCCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 89 SGKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 89 ~~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
+.+.+...-|+||.|.+--+..|+..||..||..++||.-.++++...+.+
T Consensus 345 R~~~i~~~RqiamyL~r~lt~~Slp~IG~~FgrdHtTV~~a~~kI~~~~~~ 395 (408)
T COG0593 345 RTRNIVRPRQIAMYLARELTNLSLPEIGKAFGRDHTTVLHAVRKIEQLIEE 395 (408)
T ss_pred cccccchHHHHHHHHHHHHccCcHHHHHHHhCCCccHHHHHHHHHHHHHhc
Confidence 456788888999999999999999999999999999999888887776653
No 216
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=59.12 E-value=1.9 Score=29.55 Aligned_cols=44 Identities=23% Similarity=0.311 Sum_probs=31.9
Q ss_pred HhcCCCCccccccccCCcccccchhhhHHHHHHHHhccccccCCCHHHHHHHHHHH
Q 016336 105 RLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGLQHLQWPSETEMAEIKSKF 160 (391)
Q Consensus 105 ~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~~~i~~P~~~~~~~i~~~f 160 (391)
+...|.++.++|...|+|++|++++.+. -..|+.+.+..++..|
T Consensus 5 r~~~gls~~~la~~~gis~~~i~~~~~g------------~~~~~~~~~~~ia~~l 48 (55)
T PF01381_consen 5 RKEKGLSQKELAEKLGISRSTISRIENG------------KRNPSLDTLKKIAKAL 48 (55)
T ss_dssp HHHTTS-HHHHHHHHTS-HHHHHHHHTT------------SSTSBHHHHHHHHHHH
T ss_pred HHHcCCCHHHHHHHhCCCcchhHHHhcC------------CCCCCHHHHHHHHHHH
Confidence 3467899999999999999999997643 2456766666776655
No 217
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=58.91 E-value=6.2 Score=40.60 Aligned_cols=48 Identities=21% Similarity=0.295 Sum_probs=41.7
Q ss_pred ccCHHHHHHHHHHHh---cCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 92 HLSFRDQVAIALRRL---SSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L---~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.++..++..|.|+|. ..+.++..||..||||++.|+++-.+.+.-|..
T Consensus 447 ~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~ 497 (509)
T PRK05901 447 TLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRH 497 (509)
T ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 488899999999995 467899999999999999999998888777654
No 218
>PF13701 DDE_Tnp_1_4: Transposase DDE domain group 1
Probab=58.55 E-value=31 Score=35.02 Aligned_cols=59 Identities=8% Similarity=-0.058 Sum_probs=38.4
Q ss_pred CccceeeeeeEEEeecCCCCCccccccCCCCcceeEEEEee-CCCcceeecccCCCCCCCcHHH
Q 016336 167 PNCCGVIDTTHILMCLPSSDPTNNLWLDHMKNHSMVLQAIV-DPEMRFRDIVTGWPGKMEDRLI 229 (391)
Q Consensus 167 p~~~GaIDgthi~i~~p~~~~~~~~y~~~k~~~s~~~q~v~-d~~~~f~~v~~g~pGs~~D~~v 229 (391)
..++-=||+|+.++. +...+..|..|++.+++.=+++- ...|.++.+ .-.||+.|.+.-
T Consensus 140 ~~i~LDiD~T~~~~~---G~Qe~~~~n~y~g~~gY~PL~~f~g~~G~~l~a-~LRpGn~~sa~g 199 (448)
T PF13701_consen 140 KEIVLDIDSTVDDVH---GEQEGAVFNTYYGEDGYHPLVAFDGQTGYLLAA-ELRPGNVHSAKG 199 (448)
T ss_pred ceEEEecccccccch---hhcccccccccCCCcccccceeccCCCCceEEE-EccCCCCChHHH
Confidence 447777899987665 22334456667776666644444 457888876 456999987654
No 219
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=58.33 E-value=2.3 Score=37.38 Aligned_cols=48 Identities=17% Similarity=0.116 Sum_probs=36.9
Q ss_pred cCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhc
Q 016336 93 LSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKG 141 (391)
Q Consensus 93 l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~ 141 (391)
+|..++=++.|.++ .|.++..||..+|||.+||...+.+....|-+.+
T Consensus 135 L~~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 135 VNPIDREILVLRFV-AELEFQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred cChhheeeeeeHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 44555545555544 7889999999999999999998888888776543
No 220
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=57.35 E-value=2.3 Score=30.31 Aligned_cols=29 Identities=31% Similarity=0.358 Sum_probs=22.3
Q ss_pred HHHHhcCCCCccccccccCCcccccchhh
Q 016336 102 ALRRLSSGDSLMSIGDSCGLHHSTVSQVT 130 (391)
Q Consensus 102 ~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~ 130 (391)
-..+-+.|.++.++|...|+|.||++++-
T Consensus 7 r~~R~~~gls~~~lA~~~g~s~s~v~~iE 35 (64)
T PF13560_consen 7 RRLRERAGLSQAQLADRLGVSQSTVSRIE 35 (64)
T ss_dssp HHHHHCHTS-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 33456678999999999999999999863
No 221
>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=56.75 E-value=3.6 Score=29.38 Aligned_cols=34 Identities=26% Similarity=0.388 Sum_probs=23.1
Q ss_pred HHHHhc---CCCCccccccccCCcccccchhhhHHHH
Q 016336 102 ALRRLS---SGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 102 ~L~~L~---~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
.|++++ ...+..+|+..++++++|+++.+.+.++
T Consensus 8 vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~ 44 (68)
T PF13463_consen 8 VLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEE 44 (68)
T ss_dssp HHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred HHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 355555 3456678999999999999988766554
No 222
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=56.70 E-value=7.1 Score=34.97 Aligned_cols=48 Identities=21% Similarity=0.156 Sum_probs=39.2
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.+++..+-++.|++ -.|.++..||..+|+|.+||...+.+....|.+.
T Consensus 138 ~L~~~~r~v~~L~~-~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~ 185 (203)
T PRK09647 138 SLPPEFRAAVVLCD-IEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAA 185 (203)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 36776776666665 5789999999999999999999998888777654
No 223
>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=56.36 E-value=6.5 Score=28.00 Aligned_cols=27 Identities=22% Similarity=0.282 Sum_probs=21.9
Q ss_pred cCCCCccccccccCCcccccchhhhHH
Q 016336 107 SSGDSLMSIGDSCGLHHSTVSQVTWRF 133 (391)
Q Consensus 107 ~~g~~~~~l~~~Fgvs~sTvs~~~~~~ 133 (391)
..+.+..+++..+|++.+|+++.+...
T Consensus 18 ~~~~~~~ei~~~~~i~~~~i~~~l~~L 44 (78)
T cd00090 18 EGPLTVSELAERLGLSQSTVSRHLKKL 44 (78)
T ss_pred HCCcCHHHHHHHHCcCHhHHHHHHHHH
Confidence 334888899999999999998877654
No 224
>PRK13870 transcriptional regulator TraR; Provisional
Probab=56.22 E-value=4.5 Score=37.24 Aligned_cols=46 Identities=17% Similarity=0.274 Sum_probs=38.1
Q ss_pred CccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHH
Q 016336 91 KHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~ 138 (391)
..+|+.|+ =+|.|++.|.+..+||...|||.+||.-.+.....-|.
T Consensus 172 ~~LT~RE~--E~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~na~~KLg 217 (234)
T PRK13870 172 AWLDPKEA--TYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFD 217 (234)
T ss_pred CCCCHHHH--HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 35676553 56899999999999999999999999998887776553
No 225
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=56.10 E-value=4.9 Score=32.80 Aligned_cols=31 Identities=32% Similarity=0.231 Sum_probs=25.0
Q ss_pred HHHHHHHhcCCCCccccccccCCcccccchhhh
Q 016336 99 VAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 99 l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~ 131 (391)
||.-|.-- |.++..+|...|+|++.||+++.
T Consensus 14 lA~~L~ee--G~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 14 LAKELIEE--GLSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred HHHHHHHc--CCcHHHHHHHhCCCHHHHHHHHc
Confidence 44444444 99999999999999999999864
No 226
>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=55.98 E-value=3.3 Score=33.10 Aligned_cols=31 Identities=23% Similarity=0.141 Sum_probs=25.2
Q ss_pred CCCCccccccccCCcccccchhhhHHHHHHH
Q 016336 108 SGDSLMSIGDSCGLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 108 ~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~ 138 (391)
-|.+...||+.|+||+||+..++.+.-..-+
T Consensus 79 AGlt~~aIAd~F~iS~s~~~nft~~n~~eYy 109 (126)
T PF10654_consen 79 AGLTCYAIADYFKISKSTVFNFTQNNKKEYY 109 (126)
T ss_pred cCCChHHHHHHHhHHHHHHHHHHHHhHHHHH
Confidence 3889999999999999999988766544433
No 227
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=54.76 E-value=7.7 Score=35.21 Aligned_cols=43 Identities=26% Similarity=0.282 Sum_probs=35.0
Q ss_pred ccCHHHHHHHHHHHhcC--------------CCCccccccccCCcccccchhhhHHH
Q 016336 92 HLSFRDQVAIALRRLSS--------------GDSLMSIGDSCGLHHSTVSQVTWRFV 134 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~--------------g~~~~~l~~~Fgvs~sTvs~~~~~~~ 134 (391)
..+++++++-+|..|+. ..++.+||...|+++.||+|++.++-
T Consensus 153 ~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~ 209 (235)
T PRK11161 153 KKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQ 209 (235)
T ss_pred CCCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCCcHHHHHHHHHHHH
Confidence 46889999999998763 24567899999999999999876554
No 228
>PF13751 DDE_Tnp_1_6: Transposase DDE domain
Probab=54.53 E-value=4 Score=33.27 Aligned_cols=49 Identities=10% Similarity=0.123 Sum_probs=34.6
Q ss_pred hhchhhhHH-HHHHHHHHHHHHHHHhhccccCCCCCchhHHHHHHHHHHchh
Q 016336 291 NRRHSASHL-VAQRALARLKDKWKIIQGVMWRPDKHKLPRIILVCCLLHNIV 341 (391)
Q Consensus 291 N~~ls~~R~-~vE~afg~Lk~rfriL~~~~~~~~~~~~~~ii~acc~LHN~~ 341 (391)
...+.+.|. .||..||.||. +--|.....+ ...++..-+...|+-|||-
T Consensus 73 ~k~~y~~R~~~VE~~fg~~K~-~~g~~r~~~r-G~~kv~~~~~l~a~a~Nl~ 122 (125)
T PF13751_consen 73 GKELYKQRSIKVEGVFGTIKR-NHGLRRFRYR-GLEKVRIEFLLAAIAYNLK 122 (125)
T ss_pred hhhhhheeecccccccccchh-ccCCcccccc-chhhhHHHHHHHHHHHHHH
Confidence 346677777 99999999997 4444444333 4556667777778889985
No 229
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=54.47 E-value=6.1 Score=28.49 Aligned_cols=43 Identities=23% Similarity=0.165 Sum_probs=37.7
Q ss_pred HHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 98 QVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 98 ~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
++-.+..+|+...+..+.++..|+...+|.+++..|-..+.++
T Consensus 2 ~~~~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~L 44 (65)
T PF05344_consen 2 KARAFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQL 44 (65)
T ss_pred cHHHHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHHc
Confidence 3456788999999999999999999999999999998888754
No 230
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=52.77 E-value=5.9 Score=35.87 Aligned_cols=44 Identities=9% Similarity=-0.039 Sum_probs=35.4
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
.+++.++ -.|..++.|.+..+||..+++|.+||..++.++..-+
T Consensus 143 ~LS~RE~--eVL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KL 186 (217)
T PRK13719 143 KVTKYQN--DVFILYSFGFSHEYIAQLLNITVGSSKNKISEILKFF 186 (217)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 4565543 4566789999999999999999999999887776655
No 231
>PHA02591 hypothetical protein; Provisional
Probab=52.65 E-value=4.1 Score=30.33 Aligned_cols=36 Identities=14% Similarity=0.139 Sum_probs=28.9
Q ss_pred HHHHHHHHHhcCCCCccccccccCCcccccchhhhH
Q 016336 97 DQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 97 ~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
+-+-++=.....|.+...||...|+++.||+++++.
T Consensus 47 d~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 47 DLISVTHELARKGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred hHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 444455555677999999999999999999998754
No 232
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=52.47 E-value=11 Score=31.55 Aligned_cols=44 Identities=7% Similarity=0.050 Sum_probs=31.4
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
.+++.+-.++...+-..+.+...|+..++++++|+++++.+...
T Consensus 37 glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~ 80 (144)
T PRK11512 37 DITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVC 80 (144)
T ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 46665543333333455688999999999999999998876554
No 233
>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=52.25 E-value=4.2 Score=28.69 Aligned_cols=30 Identities=20% Similarity=0.224 Sum_probs=24.1
Q ss_pred hcCCCCccccccccCCcccccchhhhHHHH
Q 016336 106 LSSGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 106 L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
-..+.+..+|+..+|++++|+++.+....+
T Consensus 21 ~~~~~t~~ela~~l~~~~~t~s~hL~~L~~ 50 (61)
T PF12840_consen 21 SNGPMTVSELAEELGISQSTVSYHLKKLEE 50 (61)
T ss_dssp HCSTBEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 577788899999999999999998765443
No 234
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=52.23 E-value=3.7 Score=26.94 Aligned_cols=27 Identities=26% Similarity=0.229 Sum_probs=21.7
Q ss_pred CCCccccccccCCcccccchhhhHHHH
Q 016336 109 GDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 109 g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
..+..+++..+|+|++|+++++.....
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 456778999999999999887766543
No 235
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=52.14 E-value=8.9 Score=27.00 Aligned_cols=32 Identities=28% Similarity=0.346 Sum_probs=28.3
Q ss_pred CCCccCHHHHHHHHHHHhcCCCCccccccccC
Q 016336 89 SGKHLSFRDQVAIALRRLSSGDSLMSIGDSCG 120 (391)
Q Consensus 89 ~~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fg 120 (391)
+.+.+...-+++|.|..--+|.++.+||..||
T Consensus 25 R~~~~~~aR~iamyla~~~~~~sl~~Ig~~fg 56 (60)
T smart00760 25 RKREIVLARQIAMYLARELTDLSLPEIGKIFG 56 (60)
T ss_pred CCcchhHHHHHHHHHHHHHHCCCHHHHHHHhC
Confidence 34667888899999999999999999999998
No 236
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=51.43 E-value=3.8 Score=28.15 Aligned_cols=24 Identities=21% Similarity=0.246 Sum_probs=19.2
Q ss_pred CccccccccCCcccccchhhhHHH
Q 016336 111 SLMSIGDSCGLHHSTVSQVTWRFV 134 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs~~~~~~~ 134 (391)
+..+++..||+|++||.+.+....
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~ 45 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLE 45 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 566789999999999988765543
No 237
>PF12964 DUF3853: Protein of unknown function (DUF3853); InterPro: IPR024363 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences [].
Probab=51.01 E-value=4 Score=31.74 Aligned_cols=34 Identities=18% Similarity=0.186 Sum_probs=24.1
Q ss_pred CccccccccCCcccccchhhhH--HHHHHHHhcccc
Q 016336 111 SLMSIGDSCGLHHSTVSQVTWR--FVEAMEQKGLQH 144 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs~~~~~--~~~~l~~~~~~~ 144 (391)
.+.-||..||+|.+|++|+... .=.||....+.+
T Consensus 47 G~~GlAklfgcSv~Ta~RiK~sG~id~AI~Q~Gr~I 82 (96)
T PF12964_consen 47 GLKGLAKLFGCSVPTANRIKKSGKIDPAITQIGRKI 82 (96)
T ss_pred hHHHHHHHhCCCchhHHHHHhcCCccHHHHHcCCEE
Confidence 3567899999999999998754 224565554443
No 238
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=50.90 E-value=3.6 Score=30.60 Aligned_cols=28 Identities=21% Similarity=0.382 Sum_probs=23.5
Q ss_pred HHhcCCCCccccccccC------Ccccccchhhh
Q 016336 104 RRLSSGDSLMSIGDSCG------LHHSTVSQVTW 131 (391)
Q Consensus 104 ~~L~~g~~~~~l~~~Fg------vs~sTvs~~~~ 131 (391)
.+...|.++.++|...| +|++|||++-.
T Consensus 19 ~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 19 RRIKLGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 46677999999999999 59999999643
No 239
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=50.42 E-value=5.8 Score=27.34 Aligned_cols=29 Identities=24% Similarity=0.258 Sum_probs=23.1
Q ss_pred cCCCCccccccccCCcccccchhhhHHHH
Q 016336 107 SSGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 107 ~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
....+..+++..+|+|.+|+++++.+...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 44567788999999999999988766543
No 240
>KOG0930 consensus Guanine nucleotide exchange factor Cytohesin, contains PH and Sec7 domains [Intracellular trafficking, secretion, and vesicular transport]
Probab=50.19 E-value=82 Score=29.67 Aligned_cols=83 Identities=25% Similarity=0.274 Sum_probs=55.0
Q ss_pred HHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHH-------HHHhccccc---cCCCHH-HHHHHHHHHhHhhC
Q 016336 97 DQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEA-------MEQKGLQHL---QWPSET-EMAEIKSKFEKIQG 165 (391)
Q Consensus 97 ~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~-------l~~~~~~~i---~~P~~~-~~~~i~~~f~~~~~ 165 (391)
+.+|.+| |-+.|.+-..|+...|=-..---.+++.|+.. |...+++|+ +.|... ...++.+.|...+.
T Consensus 94 q~iA~fl-ykGEGLnKtaIG~yLGer~~~nl~vL~aFv~~Hef~dlnlVqALRQfLwSFRLPGEaQKIdRmmEaFA~rYc 172 (395)
T KOG0930|consen 94 EDIARFL-YKGEGLNKTAIGDYLGERDEFNLQVLHAFVDLHEFTDLNLVQALRQFLWSFRLPGEAQKIDRMMEAFAQRYC 172 (395)
T ss_pred HHHHHHH-HhcCCcchhhHhhhhccCchhHHHHHHHHHHHHHhccchHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHh
Confidence 4555555 45677888888888877666555555555442 222333443 567665 67788999987654
Q ss_pred --CCccceeeeeeEEEe
Q 016336 166 --LPNCCGVIDTTHILM 180 (391)
Q Consensus 166 --fp~~~GaIDgthi~i 180 (391)
-|++.+..|.+|+--
T Consensus 173 lcNPgvfqstDtcyvls 189 (395)
T KOG0930|consen 173 LCNPGVFQSTDTCYVLS 189 (395)
T ss_pred ccCCcccccCceeeeee
Confidence 499999999998753
No 241
>PRK09191 two-component response regulator; Provisional
Probab=50.07 E-value=16 Score=33.33 Aligned_cols=50 Identities=14% Similarity=0.075 Sum_probs=41.6
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhcc
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGL 142 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~ 142 (391)
.+++..+-++.|.++ .|.++..+|...|+|.+||...+.+....+.+...
T Consensus 88 ~L~~~~r~v~~l~~~-~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~ 137 (261)
T PRK09191 88 GLTPLPRQAFLLTAL-EGFSVEEAAEILGVDPAEAEALLDDARAEIARQVA 137 (261)
T ss_pred hCCHHHhHHHHHHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCC
Confidence 467777777777765 67899999999999999999999998888876554
No 242
>PHA00738 putative HTH transcription regulator
Probab=49.87 E-value=4.6 Score=32.22 Aligned_cols=37 Identities=19% Similarity=-0.016 Sum_probs=25.7
Q ss_pred HHHHHHHHhcCC--CCccccccccCCcccccchhhhHHHH
Q 016336 98 QVAIALRRLSSG--DSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 98 ~l~i~L~~L~~g--~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
++.|..+ |+.+ .+-.+|+..|++|++|||+.+.-.-+
T Consensus 14 Rr~IL~l-L~~~e~~~V~eLae~l~lSQptVS~HLKvLre 52 (108)
T PHA00738 14 RRKILEL-IAENYILSASLISHTLLLSYTTVLRHLKILNE 52 (108)
T ss_pred HHHHHHH-HHHcCCccHHHHHHhhCCCHHHHHHHHHHHHH
Confidence 4444333 4443 56778999999999999998755443
No 243
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=49.49 E-value=7.2 Score=35.18 Aligned_cols=44 Identities=25% Similarity=0.252 Sum_probs=35.6
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
.++..+ .-.|..|+.|.+...||...++|.+||..++.....-|
T Consensus 148 ~LT~RE--~eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 148 LLTPRE--LEVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCCHHH--HHHHHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHc
Confidence 356555 45677899999999999999999999999887765544
No 244
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=48.75 E-value=5.4 Score=35.58 Aligned_cols=29 Identities=21% Similarity=0.275 Sum_probs=25.5
Q ss_pred HHHhcCCCCccccccccCCcccccchhhh
Q 016336 103 LRRLSSGDSLMSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 103 L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~ 131 (391)
..++..|.++..++..+|||++||.++..
T Consensus 166 ~~~~~~g~s~~~iak~lgis~~Tv~r~~k 194 (200)
T PRK13413 166 KKLLDKGTSKSEIARKLGVSRTTLARFLK 194 (200)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34568899999999999999999999875
No 245
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=48.62 E-value=12 Score=30.35 Aligned_cols=46 Identities=15% Similarity=0.148 Sum_probs=35.9
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~ 138 (391)
.++.+++ .....|+.+..+...++..+|||=.||..-+.+++.+|.
T Consensus 33 ~L~~E~~-~Fi~~Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg 78 (113)
T PF09862_consen 33 RLSPEQL-EFIKLFIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLG 78 (113)
T ss_pred cCCHHHH-HHHHHHHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhC
Confidence 3555554 444556666669999999999999999999988888885
No 246
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=48.42 E-value=7.1 Score=34.84 Aligned_cols=45 Identities=20% Similarity=0.169 Sum_probs=37.2
Q ss_pred CccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 91 KHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
..+++.|+ -.|..++.|.+..+||...++|.+||..+..+...-|
T Consensus 149 ~~Lt~rE~--evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl 193 (216)
T PRK10840 149 KRLSPKES--EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKL 193 (216)
T ss_pred ccCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 35888775 6778889999999999999999999998876665544
No 247
>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=48.33 E-value=32 Score=31.67 Aligned_cols=87 Identities=11% Similarity=0.171 Sum_probs=51.9
Q ss_pred cCHHHHHHHHHHHhcC---CCCccccccccCCcccccchhhhHHHHH--HHHhccccc--------------cCCCHHHH
Q 016336 93 LSFRDQVAIALRRLSS---GDSLMSIGDSCGLHHSTVSQVTWRFVEA--MEQKGLQHL--------------QWPSETEM 153 (391)
Q Consensus 93 l~~e~~l~i~L~~L~~---g~~~~~l~~~Fgvs~sTvs~~~~~~~~~--l~~~~~~~i--------------~~P~~~~~ 153 (391)
+.+-++.+-.|..++. +.+..+|+...|+++||++|++...+.. +......|. ..+-.+..
T Consensus 5 v~sl~ral~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~~~~~Y~lG~~~~~lg~~~~~~~~l~~~a 84 (248)
T TIGR02431 5 VASLARGLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTSDGRLFWLTPRVLRLGYAYLSSAPLPKVA 84 (248)
T ss_pred HHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCEEEecHHHHHHHHHHHhcCchHHHH
Confidence 4455666666776654 4688899999999999999988776542 111111111 00111122
Q ss_pred HHHHHHHhHhhCCCccceeeeeeEEE
Q 016336 154 AEIKSKFEKIQGLPNCCGVIDTTHIL 179 (391)
Q Consensus 154 ~~i~~~f~~~~~fp~~~GaIDgthi~ 179 (391)
..+.+......+..-.+++.||.++-
T Consensus 85 ~p~l~~L~~~~g~tv~L~v~~g~~~v 110 (248)
T TIGR02431 85 QPLLERLSAQTHESCSVAVLDGDEIV 110 (248)
T ss_pred HHHHHHHHHHHCCeEEEEEEeCCEEE
Confidence 33445555556777777777777653
No 248
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=47.96 E-value=15 Score=27.94 Aligned_cols=44 Identities=18% Similarity=0.150 Sum_probs=30.6
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
.++..+..++.+.....+.+...++..++++++|+++.+.+...
T Consensus 7 ~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~ 50 (101)
T smart00347 7 GLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEK 50 (101)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHH
Confidence 34444444443333344578889999999999999998877665
No 249
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=47.18 E-value=4.6 Score=27.19 Aligned_cols=18 Identities=33% Similarity=0.403 Sum_probs=15.4
Q ss_pred ccccccCCcccccchhhh
Q 016336 114 SIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 114 ~l~~~Fgvs~sTvs~~~~ 131 (391)
+++...|||++||+++++
T Consensus 2 ~lA~~~gvs~~tvs~~l~ 19 (52)
T cd01392 2 DIARAAGVSVATVSRVLN 19 (52)
T ss_pred cHHHHHCcCHHHHHHHHc
Confidence 578899999999998764
No 250
>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=46.12 E-value=6.7 Score=33.87 Aligned_cols=23 Identities=39% Similarity=0.452 Sum_probs=0.0
Q ss_pred CCCccccccccCCcccccchhhh
Q 016336 109 GDSLMSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 109 g~~~~~l~~~Fgvs~sTvs~~~~ 131 (391)
...+.++|...|++.|||||++.
T Consensus 49 PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 49 PLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp -----------------------
T ss_pred CCCHHHHHHHhCCCHhHHHHHHc
Confidence 35778999999999999999764
No 251
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=45.96 E-value=9 Score=26.77 Aligned_cols=37 Identities=22% Similarity=0.236 Sum_probs=30.1
Q ss_pred HHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 101 IALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 101 i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
-.+.+++.|.+...++..+++|..||......+..-+
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 3466788899999999999999999998776665433
No 252
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=45.43 E-value=14 Score=29.06 Aligned_cols=38 Identities=26% Similarity=0.316 Sum_probs=27.1
Q ss_pred HHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHH
Q 016336 97 DQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 97 ~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
.+++..|.. ....++..++..+|+|++|+++.+.+...
T Consensus 6 ~~il~~L~~-~~~~~~~~la~~l~~s~~tv~~~l~~L~~ 43 (108)
T smart00344 6 RKILEELQK-DARISLAELAKKVGLSPSTVHNRVKRLEE 43 (108)
T ss_pred HHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 344444443 34578999999999999999987765543
No 253
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=45.20 E-value=13 Score=24.57 Aligned_cols=27 Identities=15% Similarity=0.166 Sum_probs=21.6
Q ss_pred CCCccccccccCCcccccchhhhHHHH
Q 016336 109 GDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 109 g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
+.+..+++..|++|++|+++.+..+..
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~~ 40 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLEE 40 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 467778899999999999988766543
No 254
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=44.93 E-value=8.5 Score=34.67 Aligned_cols=44 Identities=20% Similarity=0.244 Sum_probs=35.2
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
.+++.|+ =.|..++.|.+..+||...++|..||..+..+...-|
T Consensus 134 ~LT~RE~--eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KL 177 (207)
T PRK11475 134 MLSPTER--EILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKL 177 (207)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 3666554 4677889999999999999999999998876665544
No 255
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=44.77 E-value=48 Score=31.09 Aligned_cols=44 Identities=16% Similarity=0.028 Sum_probs=34.9
Q ss_pred ccCHHHHHHHHHHHhcC---CCCccccccccCCcccccchhhhHHHH
Q 016336 92 HLSFRDQVAIALRRLSS---GDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~---g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
.++.-++.+-.|..++. +.+..+|+...|+++||+++++...+.
T Consensus 20 ~~~sl~r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~ 66 (271)
T PRK10163 20 GAQALERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQA 66 (271)
T ss_pred cchHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 46677777777777764 457889999999999999998876655
No 256
>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=44.58 E-value=14 Score=33.78 Aligned_cols=46 Identities=20% Similarity=0.165 Sum_probs=38.0
Q ss_pred CccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHH
Q 016336 91 KHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~ 138 (391)
..+++.++=++.+ ++.|.++.+||..+|||.+||...+.+...-|.
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 4688877766666 589999999999999999999998888766553
No 257
>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=44.39 E-value=8.1 Score=29.96 Aligned_cols=29 Identities=24% Similarity=0.402 Sum_probs=22.7
Q ss_pred CccccccccCCcccccchhhhHHHHHHHH
Q 016336 111 SLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+..+|...||+.|||||+-..++.-+..
T Consensus 25 gq~~vA~~~Gv~eStISR~k~~~~~~~a~ 53 (91)
T PF05269_consen 25 GQKKVAEAMGVDESTISRWKNDFIEKMAM 53 (91)
T ss_dssp HHHHHHHHHTSSTTTHHHHHHHHHHHHHH
T ss_pred hhHHHHHHhCCCHHHHHHHHhhHHHHHHH
Confidence 56789999999999999987665554443
No 258
>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=44.24 E-value=6.2 Score=28.43 Aligned_cols=38 Identities=21% Similarity=0.214 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHH
Q 016336 96 RDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFV 134 (391)
Q Consensus 96 e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~ 134 (391)
|.++..+|. -..+.+..+|+...|++++||++++.+..
T Consensus 10 E~~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~ 47 (68)
T PF01978_consen 10 EAKVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLE 47 (68)
T ss_dssp HHHHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHH
T ss_pred HHHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 444555554 23446777999999999999998776543
No 259
>PF03333 PapB: Adhesin biosynthesis transcription regulatory protein; InterPro: IPR004356 P pili, or fimbriae, are ~68A in diameter and 1 micron in length, the bulk of which is a fibre composed of the main structural protein PapA []. At its tip, the pilus is terminated by a fibrillum consisting of repeating units of the PapE protein. This, in turn, is topped by the adhesins, PapF and PapG, both of which are needed for receptor binding. The tip fibrillum is anchored to the main PapA fibre by the PapK pilus-adaptor protein. PapH, an outer membrane protein, then anchors the entire rod in the bacterial envelope []. A cytoplasmic chaperone (PapD) assists in assembling the monomers of the macromolecule in the membrane. All of the functional pap genes are arranged in a cluster (operon) on the Escherichia coli genome. It is believed that selective pressure exerted by the host's urinal and intestinal tract isoreceptors forced the spread of this operon to other strains via lateral transfer []. PapB, encoded within the cluster, acts as a transcriptional regulator of the functional pap genes and is located in the bacterial cytoplasm []. Its mechanism involves differential binding to separate sites in the cluster, suggesting that this protein is both an activator and repressor of pilus-adhesion transcription. The protein shares similarity with other E. coli fimbrial- adhesion transcription regulators, such as AfaA, DaaA and FanB. ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 3M8J_A.
Probab=44.04 E-value=23 Score=27.51 Aligned_cols=55 Identities=24% Similarity=0.260 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHhhhccccccCCcccCCCCccCHHHHHHHHH-HHhcCCCCccccccccCCcccccchhhhHH
Q 016336 61 KISRRTFDYICSLVEEKMVVKTGGFSFTSGKHLSFRDQVAIAL-RRLSSGDSLMSIGDSCGLHHSTVSQVTWRF 133 (391)
Q Consensus 61 rms~~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~e~~l~i~L-~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~ 133 (391)
.|+.+.|.-|+++- ++..+ ++..+| -+|-.|.+-..++..+||++|-.|+.+.+.
T Consensus 22 ~vs~e~F~lLl~ls-----------------~IrS~-kiI~AL~dyLV~G~srkeac~~~gV~~syfs~~L~rL 77 (91)
T PF03333_consen 22 KVSEEHFWLLLELS-----------------SIRSE-KIIAALRDYLVDGLSRKEACERHGVNQSYFSRALNRL 77 (91)
T ss_dssp -S-HHHHHHHHHHS---------------------H-HHHHHHHHHHTT---HHHHHHHTT--HHHHHHHHHHH
T ss_pred CcCHHHHHHHHHHC-----------------CCCcH-HHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHH
Confidence 56777788877762 23333 444455 489999999999999999999998876554
No 260
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=43.71 E-value=9.6 Score=35.16 Aligned_cols=45 Identities=16% Similarity=0.165 Sum_probs=36.2
Q ss_pred CccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 91 KHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
..+++.|+= .|.+++.|.+..+||...+||..||...+..+..-|
T Consensus 178 ~~LT~rE~e--vl~~~a~G~t~~eIa~~l~is~~TV~~h~~~~~~KL 222 (240)
T PRK10188 178 MNFSKREKE--ILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKF 222 (240)
T ss_pred CCCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 357776654 456679999999999999999999998887766655
No 261
>cd00131 PAX Paired Box domain
Probab=43.54 E-value=59 Score=26.80 Aligned_cols=81 Identities=12% Similarity=0.054 Sum_probs=48.2
Q ss_pred CCChhHHHhhcCCCHHHHHHHHHHhhhccccccCCcccCCCCc-cCHH-HHHHHHHHHhcCCCCcccccccc---CC---
Q 016336 50 LKGLDKFKSVFKISRRTFDYICSLVEEKMVVKTGGFSFTSGKH-LSFR-DQVAIALRRLSSGDSLMSIGDSC---GL--- 121 (391)
Q Consensus 50 ~~~~~~F~~~frms~~tF~~L~~~l~~~~~~~~~~~~~~~~~~-l~~e-~~l~i~L~~L~~g~~~~~l~~~F---gv--- 121 (391)
-.+..+--..|++++.|...++..........+... .+.++. +..+ ...++.+..-.-..+...+++.+ ||
T Consensus 33 G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~-gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~ 111 (128)
T cd00131 33 GIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAI-GGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDK 111 (128)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCC-CCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCccc
Confidence 346777889999999999999998887654433211 122222 3333 33334343333344555555542 55
Q ss_pred ----cccccchhhh
Q 016336 122 ----HHSTVSQVTW 131 (391)
Q Consensus 122 ----s~sTvs~~~~ 131 (391)
|.||+++++.
T Consensus 112 ~~~~s~stI~R~L~ 125 (128)
T cd00131 112 SNVPSVSSINRILR 125 (128)
T ss_pred CCCCCHHHHHHHHH
Confidence 8999888754
No 262
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=43.51 E-value=9.9 Score=34.46 Aligned_cols=45 Identities=22% Similarity=0.285 Sum_probs=34.6
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~ 138 (391)
.+++.++= .|..++.|.++.+||..+++|.+||..++.+...-+.
T Consensus 155 ~Lt~rE~~--Vl~l~~~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 155 LLTHREKE--ILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 36665543 4455666999999999999999999998877766553
No 263
>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=43.30 E-value=7.8 Score=26.32 Aligned_cols=26 Identities=19% Similarity=0.259 Sum_probs=22.2
Q ss_pred HhcCCCCccccccccCCcccccchhh
Q 016336 105 RLSSGDSLMSIGDSCGLHHSTVSQVT 130 (391)
Q Consensus 105 ~L~~g~~~~~l~~~Fgvs~sTvs~~~ 130 (391)
+-..|.++.++|...|+|++|++++.
T Consensus 11 r~~~gltq~~lA~~~gvs~~~vs~~e 36 (58)
T TIGR03070 11 RKALGLTQADLADLAGVGLRFIRDVE 36 (58)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 44568899999999999999999864
No 264
>PHA01976 helix-turn-helix protein
Probab=43.13 E-value=7.2 Score=27.81 Aligned_cols=44 Identities=14% Similarity=0.191 Sum_probs=32.4
Q ss_pred HhcCCCCccccccccCCcccccchhhhHHHHHHHHhccccccCCCHHHHHHHHHHH
Q 016336 105 RLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGLQHLQWPSETEMAEIKSKF 160 (391)
Q Consensus 105 ~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~~~i~~P~~~~~~~i~~~f 160 (391)
+...|.++.++|...|||++||+++-+. -.-|+.+.+..+++.|
T Consensus 11 R~~~glt~~~lA~~~gvs~~~v~~~e~g------------~~~p~~~~l~~ia~~l 54 (67)
T PHA01976 11 RNARAWSAPELSRRAGVRHSLIYDFEAD------------KRLPNLKTLLRLADAL 54 (67)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHcC------------CCCCCHHHHHHHHHHH
Confidence 5567889999999999999999986421 1246666666666655
No 265
>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=43.02 E-value=17 Score=28.90 Aligned_cols=28 Identities=11% Similarity=0.096 Sum_probs=23.7
Q ss_pred CCCCccccccccCCcccccchhhhHHHH
Q 016336 108 SGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 108 ~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
.+.+..+|+..++++++||++++.+...
T Consensus 42 ~~~t~~eL~~~l~~~~stvs~~i~~Le~ 69 (109)
T TIGR01889 42 GKLTLKEIIKEILIKQSALVKIIKKLSK 69 (109)
T ss_pred CcCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3588999999999999999998876654
No 266
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=42.56 E-value=15 Score=38.90 Aligned_cols=47 Identities=13% Similarity=0.271 Sum_probs=39.6
Q ss_pred ccCHHHHHHHHHHHh---cCCCCccccccccCCcccccchhhhHHHHHHH
Q 016336 92 HLSFRDQVAIALRRL---SSGDSLMSIGDSCGLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L---~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~ 138 (391)
.++..++..+.++|. ..+.++..||..||||++.|+++-.+.+.-|-
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 478899999999995 46678999999999999999998777666553
No 267
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=42.38 E-value=14 Score=34.97 Aligned_cols=43 Identities=12% Similarity=0.097 Sum_probs=36.0
Q ss_pred HHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 97 DQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 97 ~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+|-.++....+|.+++..|...+||+||||+.+.+.-..+..
T Consensus 4 ~~L~~F~~v~~~~~s~s~AA~~L~isq~avSr~I~~LE~~lg~ 46 (309)
T PRK12682 4 QQLRFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGI 46 (309)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCccHHHHHHHHHHHHHhCC
Confidence 4566666667788899999999999999999999988887754
No 268
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=42.14 E-value=4.8 Score=29.37 Aligned_cols=20 Identities=25% Similarity=0.446 Sum_probs=16.8
Q ss_pred CccccccccCCcccccchhh
Q 016336 111 SLMSIGDSCGLHHSTVSQVT 130 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs~~~ 130 (391)
+..+|+...|||.+|||+++
T Consensus 2 t~~~iA~~~gvS~~TVSr~l 21 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVL 21 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 35678889999999999965
No 269
>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=41.70 E-value=17 Score=33.82 Aligned_cols=45 Identities=16% Similarity=0.207 Sum_probs=37.3
Q ss_pred CccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 91 KHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
..+++.++=.+.| ++.|.++.+||..+|||..||...+.+...-+
T Consensus 189 ~~LT~RE~evl~l--~a~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL 233 (247)
T TIGR03020 189 GLITAREAEILAW--VRDGKTNEEIAAILGISSLTVKNHLQHIFKKL 233 (247)
T ss_pred cCCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHh
Confidence 4688887777665 57999999999999999999998887776544
No 270
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=41.58 E-value=13 Score=24.18 Aligned_cols=25 Identities=28% Similarity=0.351 Sum_probs=18.6
Q ss_pred CCCCccccccccCCcccccchhhhH
Q 016336 108 SGDSLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 108 ~g~~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
.-.+|.+||...|+|.+||.+-+.+
T Consensus 16 ~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 16 GRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHH
Confidence 4568899999999999999875543
No 271
>PRK09483 response regulator; Provisional
Probab=41.57 E-value=10 Score=33.31 Aligned_cols=44 Identities=20% Similarity=0.333 Sum_probs=34.9
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
.++..+.=.+ ..++.|.+..+||..+++|.+||..++.+...-|
T Consensus 148 ~Lt~rE~~vl--~~~~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 148 SLSERELQIM--LMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKL 191 (217)
T ss_pred ccCHHHHHHH--HHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 4777665443 5678999999999999999999998877765544
No 272
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=41.52 E-value=24 Score=32.61 Aligned_cols=39 Identities=15% Similarity=0.190 Sum_probs=33.1
Q ss_pred cCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhh
Q 016336 93 LSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 93 l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~ 131 (391)
+-...++.-.|+.|+..-+|.+|+..+|++.|.++|+++
T Consensus 7 ~~~~~~~v~~lr~lk~~~ty~el~~~~g~p~~~l~RYv~ 45 (238)
T PRK08558 7 VRLQLRAVRVLRSLKKTYTYEELSSITGLPESVLNRYVN 45 (238)
T ss_pred HHHHHHHHHHHHHHhcccCHHHHHHHHCCCHHHHHHHHc
Confidence 334456677899999999999999999999999999874
No 273
>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=41.42 E-value=13 Score=32.89 Aligned_cols=40 Identities=13% Similarity=0.126 Sum_probs=30.6
Q ss_pred CccCHHHHHHHHHHHhc-CCCCccccccccCCcccccchhh
Q 016336 91 KHLSFRDQVAIALRRLS-SGDSLMSIGDSCGLHHSTVSQVT 130 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~-~g~~~~~l~~~Fgvs~sTvs~~~ 130 (391)
..+++-++...+...+. .|.+...||..+|+|+++|++++
T Consensus 101 ~~lt~~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l 141 (187)
T TIGR00180 101 EDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLL 141 (187)
T ss_pred cCCCHHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHH
Confidence 46777776555545443 68899999999999999999864
No 274
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=41.26 E-value=4.9 Score=30.20 Aligned_cols=35 Identities=20% Similarity=0.309 Sum_probs=23.6
Q ss_pred HHHHHHHHH--hcCCCCccccccccCCcccccchhhh
Q 016336 97 DQVAIALRR--LSSGDSLMSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 97 ~~l~i~L~~--L~~g~~~~~l~~~Fgvs~sTvs~~~~ 131 (391)
.+++..|.. =..|.++.++|...|+++++||++.+
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 344444443 34678999999999999999999763
No 275
>PRK09492 treR trehalose repressor; Provisional
Probab=40.88 E-value=7.3 Score=36.85 Aligned_cols=23 Identities=30% Similarity=0.289 Sum_probs=20.0
Q ss_pred CCccccccccCCcccccchhhhH
Q 016336 110 DSLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 110 ~~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
.+..+||...|||.+|||++++.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCC
Confidence 36679999999999999998864
No 276
>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=39.78 E-value=9.8 Score=36.07 Aligned_cols=21 Identities=33% Similarity=0.381 Sum_probs=18.6
Q ss_pred CccccccccCCcccccchhhh
Q 016336 111 SLMSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs~~~~ 131 (391)
+..+||..+|||++|||++++
T Consensus 3 ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 3 TIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred cHHHHHHHhCCCHHHHHHHhC
Confidence 456899999999999999885
No 277
>PF13309 HTH_22: HTH domain
Probab=39.74 E-value=19 Score=25.85 Aligned_cols=41 Identities=20% Similarity=0.208 Sum_probs=30.5
Q ss_pred CccCHHHHHHHHHHHhcCCCCc-----cccccccCCcccccchhhh
Q 016336 91 KHLSFRDQVAIALRRLSSGDSL-----MSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g~~~-----~~l~~~Fgvs~sTvs~~~~ 131 (391)
..++.++++.+.-..-..|... ..+|..+|||+.||+++++
T Consensus 19 ~~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YLr 64 (64)
T PF13309_consen 19 SRLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYLR 64 (64)
T ss_pred hhCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHcC
Confidence 4577788887766666666443 4588899999999998763
No 278
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=39.08 E-value=8.7 Score=29.34 Aligned_cols=61 Identities=18% Similarity=0.232 Sum_probs=38.8
Q ss_pred CHHHHHHHHHHhhhccccccCCcccCCCCccCHHHH--HHHHHHHhcCCCCccccccccCCcccccchhhhH
Q 016336 63 SRRTFDYICSLVEEKMVVKTGGFSFTSGKHLSFRDQ--VAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 63 s~~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~e~~--l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
+-++|..+.+.+.+..... ..+-...+ ..+.+|.=-.+.++..++..+||++|.||...+-
T Consensus 2 ~~~vF~s~~~~~~D~~e~a---------~~m~ir~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~g 64 (91)
T COG5606 2 SNEVFTSVWDAIEDTPEAA---------ENMKIRSALMMAIKQWIEQAALSQAQIAELLGVTQPRVSDLARG 64 (91)
T ss_pred CCchhhhHHHHHhccHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHhc
Confidence 4456777776666543211 12223333 4445555556789999999999999999976543
No 279
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=38.75 E-value=12 Score=30.58 Aligned_cols=44 Identities=16% Similarity=0.073 Sum_probs=30.3
Q ss_pred cCHHHHHHHHHHHhcC-CCCccccccccCCcccccchhhhHHHHH
Q 016336 93 LSFRDQVAIALRRLSS-GDSLMSIGDSCGLHHSTVSQVTWRFVEA 136 (391)
Q Consensus 93 l~~e~~l~i~L~~L~~-g~~~~~l~~~Fgvs~sTvs~~~~~~~~~ 136 (391)
++-+.++.|....... ..+..+|+..++++++|||+.+....++
T Consensus 13 LadptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~A 57 (117)
T PRK10141 13 LSDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRES 57 (117)
T ss_pred hCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3334555555444433 3567789999999999999988766554
No 280
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=37.76 E-value=12 Score=33.78 Aligned_cols=51 Identities=20% Similarity=0.224 Sum_probs=35.0
Q ss_pred CCccCHHHHHHHHHH-HhcC-----CCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 90 GKHLSFRDQVAIALR-RLSS-----GDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 90 ~~~l~~e~~l~i~L~-~L~~-----g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
...++..+.-++.+- .++. ..+..+||..||||+||++.++++...-|.+.
T Consensus 153 ~~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~~ 209 (215)
T COG3413 153 KNDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIEA 209 (215)
T ss_pred cccCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 345777665444333 3333 34566799999999999999998887766543
No 281
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=37.73 E-value=8.8 Score=27.29 Aligned_cols=25 Identities=24% Similarity=0.238 Sum_probs=20.2
Q ss_pred HhcC--CCCccccccccCCcccccchh
Q 016336 105 RLSS--GDSLMSIGDSCGLHHSTVSQV 129 (391)
Q Consensus 105 ~L~~--g~~~~~l~~~Fgvs~sTvs~~ 129 (391)
|+.+ ...+.+||..+|||.+||+.+
T Consensus 16 y~~~~g~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 16 YKESNGKIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred HHHhCCCccHHHHHHHHCCCHHHHHHH
Confidence 4444 367889999999999999874
No 282
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=37.63 E-value=7.9 Score=36.98 Aligned_cols=22 Identities=27% Similarity=0.380 Sum_probs=19.0
Q ss_pred CccccccccCCcccccchhhhH
Q 016336 111 SLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
+..+||...|||.+|||++++.
T Consensus 7 ti~dIA~~agVS~~TVSrvLn~ 28 (331)
T PRK14987 7 VLQDVADRVGVTKMTVSRFLRN 28 (331)
T ss_pred cHHHHHHHhCCCHHHhhhhhCC
Confidence 5679999999999999998753
No 283
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=37.51 E-value=6.1 Score=25.45 Aligned_cols=28 Identities=21% Similarity=0.210 Sum_probs=19.8
Q ss_pred hcCCCCccccccccCCcccccchhhhHH
Q 016336 106 LSSGDSLMSIGDSCGLHHSTVSQVTWRF 133 (391)
Q Consensus 106 L~~g~~~~~l~~~Fgvs~sTvs~~~~~~ 133 (391)
|.++.+..++|..+|+|+++.++.+.+.
T Consensus 5 ~~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 5 LQQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp T-SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4556677889999999999999887664
No 284
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=37.46 E-value=14 Score=25.21 Aligned_cols=41 Identities=24% Similarity=0.251 Sum_probs=24.8
Q ss_pred CCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhh
Q 016336 90 GKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 90 ~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~ 131 (391)
|..++..||--+-++ ...|.+...++...|.|+..|.+++.
T Consensus 2 G~~Lt~~Eqaqid~m-~qlG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 2 GKTLTDAEQAQIDVM-HQLGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp S----HHHHHHHHHH-HHTT--HHHHHHHHT--HHHHHHHHH
T ss_pred CCcCCHHHHHHHHHH-HHhchhHHHHHHHhCccHHHHHHHhc
Confidence 567888777666543 34588999999999999998888654
No 285
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=37.12 E-value=18 Score=30.11 Aligned_cols=46 Identities=17% Similarity=0.141 Sum_probs=38.1
Q ss_pred ccCHHHHHHHHHHHhcC-CCCccccccccCCcccccchhhhHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSS-GDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~-g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
.+..+++-.+-|+|-.. +.++..||..+++|.+|+.++..+|-+.|
T Consensus 81 ~l~de~k~Ii~lry~~r~~~TW~~IA~~l~i~erta~r~~~~fK~~i 127 (130)
T PF05263_consen 81 TLIDEEKRIIKLRYDRRSRRTWYQIAQKLHISERTARRWRDRFKNDI 127 (130)
T ss_pred hhCHHHHHHHHHHHcccccchHHHHHHHhCccHHHHHHHHHHHHHHh
Confidence 35667777888888877 79999999999999999999887775544
No 286
>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=36.93 E-value=28 Score=28.22 Aligned_cols=57 Identities=12% Similarity=-0.045 Sum_probs=36.2
Q ss_pred CHHHHHHHHHHhhhccccccCCcccCCCCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhh
Q 016336 63 SRRTFDYICSLVEEKMVVKTGGFSFTSGKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVT 130 (391)
Q Consensus 63 s~~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~ 130 (391)
+.+.-..+...+...+.... ..+++.+ +.-.+...|.++.++|..+|+|++|++++-
T Consensus 43 ~~e~~~~~~~~i~~~~~~~~--------~~~~~~~---i~~~r~~~gltq~~lA~~lg~~~~tis~~e 99 (127)
T TIGR03830 43 DPEESKRNSAALADFYRKVD--------GLLTPPE---IRRIRKKLGLSQREAAELLGGGVNAFSRYE 99 (127)
T ss_pred cHHHHHHHHHHHHHHHHHcc--------CCcCHHH---HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 44444555555555443321 2233322 333456679999999999999999999864
No 287
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=36.64 E-value=20 Score=34.04 Aligned_cols=43 Identities=14% Similarity=0.115 Sum_probs=36.3
Q ss_pred HHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 97 DQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 97 ~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+|-.++....+|.|+...|...++|+++||+.+.+.-..+..
T Consensus 4 ~~L~~F~~v~~~~~S~s~AA~~L~isQpavS~~I~~LE~~lg~ 46 (309)
T PRK12683 4 QQLRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGV 46 (309)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhCC
Confidence 4566677777788899999999999999999999888877754
No 288
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=36.58 E-value=14 Score=35.37 Aligned_cols=51 Identities=10% Similarity=0.092 Sum_probs=40.8
Q ss_pred CCCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 89 SGKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 89 ~~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
++..+..+-+.+-.+.-++...++...|...+||++|||+.+.+.-..+..
T Consensus 5 ~~~~~~m~l~~L~~F~~v~e~gs~s~AA~~L~iSQpavS~~I~~LE~~lG~ 55 (310)
T PRK15092 5 NRPIINLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGK 55 (310)
T ss_pred hhhhhcCCHHHHHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCc
Confidence 344555556666777777888899999999999999999999888887744
No 289
>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=36.22 E-value=13 Score=28.04 Aligned_cols=34 Identities=9% Similarity=0.049 Sum_probs=26.4
Q ss_pred hcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 106 LSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 106 L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
...+.+..++++.+.||+||+.+.+.++-..|..
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 5677888999999999999999988887777653
No 290
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=36.21 E-value=14 Score=25.88 Aligned_cols=43 Identities=19% Similarity=0.225 Sum_probs=25.5
Q ss_pred cCCCCccccccccCCcccccchhhhHHHHHHHHhccccccCCCHHHHHHHHHHH
Q 016336 107 SSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGLQHLQWPSETEMAEIKSKF 160 (391)
Q Consensus 107 ~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~~~i~~P~~~~~~~i~~~f 160 (391)
..|.+..+++..-|+|++|++++++.- ...|+.+.+..++..|
T Consensus 8 ~~~it~~~La~~~gis~~tl~~~~~~~-----------~~~~~~~~l~~ia~~l 50 (63)
T PF13443_consen 8 ERGITQKDLARKTGISRSTLSRILNGK-----------PSNPSLDTLEKIAKAL 50 (63)
T ss_dssp HTT--HHHHHHHHT--HHHHHHHHTTT----------------HHHHHHHHHHH
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHhcc-----------cccccHHHHHHHHHHc
Confidence 356788899999999999999977532 2345555666676655
No 291
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=35.97 E-value=7.7 Score=37.20 Aligned_cols=23 Identities=26% Similarity=0.199 Sum_probs=20.1
Q ss_pred CCccccccccCCcccccchhhhH
Q 016336 110 DSLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 110 ~~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
.+..+||..+|||.+|||++++.
T Consensus 7 ~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 7 ITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHHCC
Confidence 46789999999999999998764
No 292
>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=35.29 E-value=7 Score=25.40 Aligned_cols=22 Identities=14% Similarity=0.108 Sum_probs=17.6
Q ss_pred CccccccccCCcccccchhhhH
Q 016336 111 SLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
+..+++..+|||.+|+.+++.+
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 3457888999999999987654
No 293
>PRK00215 LexA repressor; Validated
Probab=35.06 E-value=23 Score=31.52 Aligned_cols=27 Identities=26% Similarity=0.188 Sum_probs=22.2
Q ss_pred CCCccccccccCC-cccccchhhhHHHH
Q 016336 109 GDSLMSIGDSCGL-HHSTVSQVTWRFVE 135 (391)
Q Consensus 109 g~~~~~l~~~Fgv-s~sTvs~~~~~~~~ 135 (391)
+.++.+|+..+|+ +++|+++++.....
T Consensus 23 ~~s~~ela~~~~~~~~~tv~~~l~~L~~ 50 (205)
T PRK00215 23 PPSRREIADALGLRSPSAVHEHLKALER 50 (205)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 3477799999999 99999998766554
No 294
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=34.88 E-value=21 Score=33.33 Aligned_cols=44 Identities=23% Similarity=0.306 Sum_probs=33.9
Q ss_pred ccCHHHHHHHHHHHhcC---CCCccccccccCCcccccchhhhHHHH
Q 016336 92 HLSFRDQVAIALRRLSS---GDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~---g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
.+..-++.+-.|..|+. +.+..+|+..+|+++||++|++.....
T Consensus 6 ~v~sl~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~ 52 (263)
T PRK09834 6 TVRGLSRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQE 52 (263)
T ss_pred hHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45556677777777754 367889999999999999998877654
No 295
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.67 E-value=26 Score=26.90 Aligned_cols=31 Identities=29% Similarity=0.423 Sum_probs=25.9
Q ss_pred HHHhcCCCCccccccccCCcccccchhhhHHH
Q 016336 103 LRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFV 134 (391)
Q Consensus 103 L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~ 134 (391)
-..|..|.+|++|...-|.|-.|+||+ .+++
T Consensus 50 a~mL~eg~tY~~I~~eTGaStaTIsRV-kRcl 80 (100)
T COG4496 50 AKMLKEGRTYRDIEDETGASTATISRV-KRCL 80 (100)
T ss_pred HHHHHcCCCcchhhhccCcchhhHHHH-HHHH
Confidence 356789999999999999999999984 3443
No 296
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=34.50 E-value=24 Score=33.62 Aligned_cols=43 Identities=14% Similarity=0.088 Sum_probs=36.0
Q ss_pred HHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 97 DQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 97 ~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
++|-.++.-..+|.++...|...+||++|||+.+.+.-..+..
T Consensus 4 ~~l~~f~~v~~~~~s~s~AA~~L~iSQ~avSr~I~~LE~~lg~ 46 (316)
T PRK12679 4 QQLKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGI 46 (316)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhcCCchHHHHHHHHHHHHhCC
Confidence 3566666666777899999999999999999999998888754
No 297
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=33.92 E-value=24 Score=33.41 Aligned_cols=40 Identities=13% Similarity=0.139 Sum_probs=30.8
Q ss_pred HHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 99 VAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 99 l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
|-.++. ++...++...|...|||+||||+.+.+.-..+..
T Consensus 6 L~~F~~-v~~~~S~s~AA~~L~isQ~avS~~I~~LE~~lg~ 45 (305)
T PRK11233 6 LKYFVK-IVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQ 45 (305)
T ss_pred HHHHHH-HHHcCCHHHHHHHhCCCchHHHHHHHHHHHHhCC
Confidence 334444 4444599999999999999999999888877744
No 298
>PRK09526 lacI lac repressor; Reviewed
Probab=33.72 E-value=9 Score=36.73 Aligned_cols=22 Identities=27% Similarity=0.357 Sum_probs=19.3
Q ss_pred CccccccccCCcccccchhhhH
Q 016336 111 SLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
+..+||...|||.+|||++++.
T Consensus 7 ti~dIA~~aGVS~~TVSrvLn~ 28 (342)
T PRK09526 7 TLYDVARYAGVSYQTVSRVLNQ 28 (342)
T ss_pred cHHHHHHHhCCCHHHHHHHhcC
Confidence 5679999999999999998763
No 299
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=33.40 E-value=11 Score=36.08 Aligned_cols=22 Identities=32% Similarity=0.323 Sum_probs=18.7
Q ss_pred CccccccccCCcccccchhhhH
Q 016336 111 SLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
+..+||...|||++|||++++.
T Consensus 3 ti~dIA~~agVS~~TVSrvln~ 24 (327)
T PRK10339 3 TLKDIAIEAGVSLATVSRVLND 24 (327)
T ss_pred CHHHHHHHhCCCHHhhhhhhcC
Confidence 4568999999999999998753
No 300
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=33.29 E-value=10 Score=36.00 Aligned_cols=19 Identities=32% Similarity=0.342 Sum_probs=17.1
Q ss_pred cccccccCCcccccchhhh
Q 016336 113 MSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 113 ~~l~~~Fgvs~sTvs~~~~ 131 (391)
.+||...|||.+||||+++
T Consensus 2 ~dIA~~agVS~~TVSrvLn 20 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVIN 20 (327)
T ss_pred hhHHHHhCCcHHHHHHHhC
Confidence 4789999999999999875
No 301
>PRK10651 transcriptional regulator NarL; Provisional
Probab=32.87 E-value=17 Score=31.51 Aligned_cols=44 Identities=20% Similarity=0.220 Sum_probs=35.1
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
.+++.+. =.|.+|+.|.+...++..+++|..||..++.+...-|
T Consensus 155 ~Lt~rE~--~vl~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl 198 (216)
T PRK10651 155 QLTPRER--DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKM 198 (216)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 3676554 4456688999999999999999999998887766554
No 302
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=32.73 E-value=11 Score=37.85 Aligned_cols=36 Identities=28% Similarity=0.351 Sum_probs=27.5
Q ss_pred HhcCC------CCccccccccCCcccccchhhhHHHHHHHHhccccccCCCH
Q 016336 105 RLSSG------DSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGLQHLQWPSE 150 (391)
Q Consensus 105 ~L~~g------~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~~~i~~P~~ 150 (391)
||.+| ...+++|+.+|++.|||||++. ..|+.-|..
T Consensus 320 Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai~----------nKy~~tprG 361 (444)
T COG1508 320 FFEGGEEALKPLVLRDVADEIGMHESTISRAIT----------NKYLATPRG 361 (444)
T ss_pred HHhCCcccCCcccHHHHHHHhCccHHHHHHHHh----------cccccCCcc
Confidence 55666 6668999999999999999763 346666654
No 303
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=32.58 E-value=33 Score=29.10 Aligned_cols=43 Identities=7% Similarity=0.064 Sum_probs=31.6
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFV 134 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~ 134 (391)
.++..++-.+.+..-..-.++..||...|+|++||.+-+.+..
T Consensus 6 ~lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~ 48 (153)
T PRK11179 6 QIDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMK 48 (153)
T ss_pred ccCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4555555555555555668999999999999999988665544
No 304
>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=32.26 E-value=12 Score=26.19 Aligned_cols=24 Identities=17% Similarity=0.252 Sum_probs=19.0
Q ss_pred CccccccccCCcccccchhhhHHH
Q 016336 111 SLMSIGDSCGLHHSTVSQVTWRFV 134 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs~~~~~~~ 134 (391)
+..+|+..||+|++||++.+.+..
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~ 50 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELE 50 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 456889999999999988765543
No 305
>PRK10870 transcriptional repressor MprA; Provisional
Probab=31.89 E-value=23 Score=31.00 Aligned_cols=43 Identities=7% Similarity=0.020 Sum_probs=28.1
Q ss_pred ccCHHH-HHHHHHHHhcC-CCCccccccccCCcccccchhhhHHH
Q 016336 92 HLSFRD-QVAIALRRLSS-GDSLMSIGDSCGLHHSTVSQVTWRFV 134 (391)
Q Consensus 92 ~l~~e~-~l~i~L~~L~~-g~~~~~l~~~Fgvs~sTvs~~~~~~~ 134 (391)
.+++.+ .+++.|+.... +.+..+|+..++++++|+++++.+..
T Consensus 52 gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe 96 (176)
T PRK10870 52 GINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELE 96 (176)
T ss_pred CCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 355543 33334433222 35678999999999999998876654
No 306
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=31.87 E-value=11 Score=35.98 Aligned_cols=22 Identities=27% Similarity=0.237 Sum_probs=18.7
Q ss_pred CccccccccCCcccccchhhhH
Q 016336 111 SLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
+..+||...|||.+|||++++.
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 3568999999999999998754
No 307
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=31.85 E-value=10 Score=36.29 Aligned_cols=22 Identities=23% Similarity=0.431 Sum_probs=19.1
Q ss_pred CccccccccCCcccccchhhhH
Q 016336 111 SLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
+..+||...|||.+|||++++.
T Consensus 3 Ti~dIA~~agVS~~TVSrvLn~ 24 (341)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINK 24 (341)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 4668999999999999998764
No 308
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=31.60 E-value=20 Score=30.87 Aligned_cols=44 Identities=23% Similarity=0.314 Sum_probs=34.1
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
.+++.+. -.|..|+.|.+...++..+++|.+||..++.++..-+
T Consensus 137 ~Lt~~E~--~il~~l~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 137 PLTKRER--QVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKL 180 (196)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 4555544 4456688899999999999999999988887766544
No 309
>PRK11050 manganese transport regulator MntR; Provisional
Probab=31.25 E-value=25 Score=29.87 Aligned_cols=28 Identities=18% Similarity=0.292 Sum_probs=23.5
Q ss_pred CCCCccccccccCCcccccchhhhHHHH
Q 016336 108 SGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 108 ~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
.+.+..+++..++|+++||++.+.+...
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~ 77 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLAR 77 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4568889999999999999998766554
No 310
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=31.23 E-value=29 Score=28.80 Aligned_cols=44 Identities=20% Similarity=0.176 Sum_probs=37.7
Q ss_pred HHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 96 RDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 96 e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+...-+..++.+|.+.++++...||+.+|+.++..++...+..
T Consensus 76 ~~~~~~~~~~~~~~~~i~~~a~~l~i~~~~~~r~~~r~~~~~~~ 119 (129)
T COG3677 76 YKIKLQAVTLYMLGLGIRDIARTLGISINTVNRWSKRFGSRVEG 119 (129)
T ss_pred hHHHHHHHHHHHcCCCcccHHHHhcccHHHHHHHHHhhcchhhc
Confidence 56666677777888999999999999999999999998887764
No 311
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=31.06 E-value=23 Score=24.93 Aligned_cols=41 Identities=2% Similarity=-0.001 Sum_probs=27.8
Q ss_pred CCccCHHHHHHHHHHHhcCCC---CccccccccCCcccccchhh
Q 016336 90 GKHLSFRDQVAIALRRLSSGD---SLMSIGDSCGLHHSTVSQVT 130 (391)
Q Consensus 90 ~~~l~~e~~l~i~L~~L~~g~---~~~~l~~~Fgvs~sTvs~~~ 130 (391)
++..+++-+|-+.-++..++. +|+..|..|||++..|.++.
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~ 46 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWR 46 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHH
T ss_pred ccccChHHHHHHHHHHHHccchhhhHHHHHHHhCccHHHHHHHH
Confidence 356788888888888888876 55999999999998887754
No 312
>PRK04140 hypothetical protein; Provisional
Probab=31.01 E-value=24 Score=34.10 Aligned_cols=81 Identities=16% Similarity=0.092 Sum_probs=52.3
Q ss_pred CCCHHH-HHHHHHHhhhccccccCCcccCCCCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 61 KISRRT-FDYICSLVEEKMVVKTGGFSFTSGKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 61 rms~~t-F~~L~~~l~~~~~~~~~~~~~~~~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
-|+.+| |+++++-..|..-..+ .|-.+......+ --.+-..|.++.++|...|+|++|+++|-+-
T Consensus 97 ~~~~~tl~~~~~~g~~p~v~~~~------Gg~~v~i~GerL-k~lRe~~GlSq~eLA~~lGVSr~tIskyE~G------- 162 (317)
T PRK04140 97 ALSPDTLYDDFVEGEPPLIYAAP------GGFYVKIDGDVL-REAREELGLSLGELASELGVSRRTISKYENG------- 162 (317)
T ss_pred eecHHHHHHHHhCCCCceEEEcC------CCeeehhhHHHH-HHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC-------
Confidence 457888 8888877666443221 233343332222 3346788999999999999999999986531
Q ss_pred hccccccCCCHHHHHHHHHHH
Q 016336 140 KGLQHLQWPSETEMAEIKSKF 160 (391)
Q Consensus 140 ~~~~~i~~P~~~~~~~i~~~f 160 (391)
-.-|+.+.+..+++.|
T Consensus 163 -----~~~Ps~e~~~kLa~~L 178 (317)
T PRK04140 163 -----GMNASIEVAIKLEEIL 178 (317)
T ss_pred -----CCCCCHHHHHHHHHHh
Confidence 1236666666666655
No 313
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=30.94 E-value=32 Score=32.74 Aligned_cols=43 Identities=9% Similarity=0.068 Sum_probs=35.3
Q ss_pred HHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 97 DQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 97 ~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+|-+++....+|.|+...|...++|++|||+.+.+.-..+..
T Consensus 4 ~~L~~f~~v~~~g~S~s~AA~~L~isQpavS~~ik~LE~~lg~ 46 (313)
T PRK12684 4 HQLRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGV 46 (313)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhcCCChHHHHHHHHHHHHhCC
Confidence 3555566666667799999999999999999999998888754
No 314
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=30.88 E-value=14 Score=26.49 Aligned_cols=36 Identities=11% Similarity=0.075 Sum_probs=25.9
Q ss_pred HHHHHHHHHhcCCCCccccccccCCcccccchhhhH
Q 016336 97 DQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 97 ~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
+++.-+|.....+.+=++||+.+|+|..++..++..
T Consensus 3 e~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~ 38 (62)
T PF04703_consen 3 EKILEYIKEQNGPLKTREIADALGLSIYQARYYLEK 38 (62)
T ss_dssp HCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 445556666677778889999999999999876533
No 315
>PF12728 HTH_17: Helix-turn-helix domain
Probab=30.41 E-value=9.7 Score=25.56 Aligned_cols=21 Identities=19% Similarity=0.218 Sum_probs=17.0
Q ss_pred CccccccccCCcccccchhhh
Q 016336 111 SLMSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs~~~~ 131 (391)
+..++|..+|||.+|+.++++
T Consensus 3 t~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 445788899999999988764
No 316
>COG3179 Predicted chitinase [General function prediction only]
Probab=30.32 E-value=48 Score=29.25 Aligned_cols=70 Identities=9% Similarity=0.107 Sum_probs=57.4
Q ss_pred CChhHHHhhcCCCHHHHHHHHHHhhhccccccCCcccCCCCccCHHHHHHHHHHHhcCCCC-ccccccccCCcccccchh
Q 016336 51 KGLDKFKSVFKISRRTFDYICSLVEEKMVVKTGGFSFTSGKHLSFRDQVAIALRRLSSGDS-LMSIGDSCGLHHSTVSQV 129 (391)
Q Consensus 51 ~~~~~F~~~frms~~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~e~~l~i~L~~L~~g~~-~~~l~~~Fgvs~sTvs~~ 129 (391)
.++.+|.+.|...+..|-..+-.|.+.+.. ..++...+++++|--+.|-.. +..+.+.|+-|..++.+.
T Consensus 4 i~e~~~~ki~p~a~k~~~~v~~al~~~l~~----------~gi~~p~r~AmFlAQ~~HESggf~rl~EnlnYSaq~L~~t 73 (206)
T COG3179 4 ITEVDLRKIFPKARKEFVDVIVALQPALDE----------AGITTPLRQAMFLAQVMHESGGFTRLDENLNYSAQGLLQT 73 (206)
T ss_pred hhHHHHHHhcchhhhhhHHHHHHHHHHHHH----------hcCCCHHHHHHHHHHHhhhcCCceeehhhcchHHHHHHHh
Confidence 467899999999999988888888877654 457778999999999999876 888888888887776664
Q ss_pred h
Q 016336 130 T 130 (391)
Q Consensus 130 ~ 130 (391)
+
T Consensus 74 f 74 (206)
T COG3179 74 F 74 (206)
T ss_pred c
Confidence 4
No 317
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=30.10 E-value=18 Score=34.85 Aligned_cols=21 Identities=24% Similarity=0.359 Sum_probs=18.7
Q ss_pred CccccccccCCcccccchhhh
Q 016336 111 SLMSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs~~~~ 131 (391)
+..+||...|||.+|||++++
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (346)
T PRK10401 3 TIRDVARQAGVSVATVSRVLN 23 (346)
T ss_pred CHHHHHHHhCCCHHHHHHHHC
Confidence 467899999999999999876
No 318
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=30.01 E-value=25 Score=28.98 Aligned_cols=27 Identities=19% Similarity=0.133 Sum_probs=22.4
Q ss_pred CCccccccccCCcccccchhhhHHHHH
Q 016336 110 DSLMSIGDSCGLHHSTVSQVTWRFVEA 136 (391)
Q Consensus 110 ~~~~~l~~~Fgvs~sTvs~~~~~~~~~ 136 (391)
.+-.+||...++++|||++.+.+.+.+
T Consensus 43 ~tvdelae~lnr~rStv~rsl~~L~~~ 69 (126)
T COG3355 43 LTVDELAEILNRSRSTVYRSLQNLLEA 69 (126)
T ss_pred cCHHHHHHHHCccHHHHHHHHHHHHHc
Confidence 344589999999999999998887763
No 319
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=29.89 E-value=40 Score=29.80 Aligned_cols=41 Identities=17% Similarity=0.170 Sum_probs=29.7
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
.+++.+-..+...+-..|.++.+||...+++++|+++++.+
T Consensus 42 gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~r 82 (185)
T PRK13777 42 DLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKK 82 (185)
T ss_pred CCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHH
Confidence 46665554444444456789999999999999998886644
No 320
>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=29.87 E-value=10 Score=24.74 Aligned_cols=21 Identities=14% Similarity=0.251 Sum_probs=16.7
Q ss_pred CccccccccCCcccccchhhh
Q 016336 111 SLMSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs~~~~ 131 (391)
+..+++..+|||++|+.+++.
T Consensus 3 t~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 445788899999999988764
No 321
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=29.77 E-value=19 Score=28.31 Aligned_cols=35 Identities=6% Similarity=0.057 Sum_probs=28.1
Q ss_pred HhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 105 RLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 105 ~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
-+....|++..|...|||++||++.+.+.-..+..
T Consensus 12 av~~~gSis~AA~~L~iS~stvs~~I~~LE~~lg~ 46 (99)
T TIGR00637 12 AIARMGSISQAAKDAGISYKSAWDYIRAMNNLSGE 46 (99)
T ss_pred HHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 34445688899999999999999998887776644
No 322
>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=29.72 E-value=25 Score=25.74 Aligned_cols=36 Identities=17% Similarity=0.158 Sum_probs=26.4
Q ss_pred CHHHHHHHHHHHhcCCCCccccccccCCcccccchhh
Q 016336 94 SFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVT 130 (391)
Q Consensus 94 ~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~ 130 (391)
++.+++.-. .+-..|.+..++|...|+|++||+++.
T Consensus 4 ~~g~~i~~~-~~~~~~~t~~~lA~~~gis~~tis~~~ 39 (78)
T TIGR02607 4 HPGEILREE-FLEPLGLSIRALAKALGVSRSTLSRIV 39 (78)
T ss_pred CHHHHHHHH-HHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 444553312 245678899999999999999999865
No 323
>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=29.46 E-value=29 Score=30.02 Aligned_cols=37 Identities=19% Similarity=0.197 Sum_probs=30.2
Q ss_pred HHHHHHHHHHhcCCCCccccccccC-CcccccchhhhH
Q 016336 96 RDQVAIALRRLSSGDSLMSIGDSCG-LHHSTVSQVTWR 132 (391)
Q Consensus 96 e~~l~i~L~~L~~g~~~~~l~~~Fg-vs~sTvs~~~~~ 132 (391)
++++...-..++.|.|...||..+| ||+.+|.-.+++
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 4566666667799999999999999 999998766655
No 324
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=28.94 E-value=18 Score=27.73 Aligned_cols=24 Identities=17% Similarity=0.213 Sum_probs=19.5
Q ss_pred ccccccccCCcccccchhhhHHHH
Q 016336 112 LMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 112 ~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
..+++..+|++++|+++.+.+...
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~ 25 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEK 25 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHH
Confidence 357889999999999998766554
No 325
>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=28.89 E-value=23 Score=25.42 Aligned_cols=24 Identities=17% Similarity=0.242 Sum_probs=19.4
Q ss_pred CCccccccccCCcccccchhhhHH
Q 016336 110 DSLMSIGDSCGLHHSTVSQVTWRF 133 (391)
Q Consensus 110 ~~~~~l~~~Fgvs~sTvs~~~~~~ 133 (391)
.+...++..||+|++||++.+...
T Consensus 14 ~~~~eLa~~l~vS~~tv~~~l~~L 37 (69)
T TIGR00122 14 FSGEKLGEALGMSRTAVNKHIQTL 37 (69)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHH
Confidence 346688999999999999877554
No 326
>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=28.65 E-value=27 Score=24.30 Aligned_cols=23 Identities=13% Similarity=0.209 Sum_probs=18.3
Q ss_pred CCccccccccCCcccccchhhhH
Q 016336 110 DSLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 110 ~~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
.+..+++..||||..|+.+-+..
T Consensus 15 ~s~~ela~~~~VS~~TiRRDl~~ 37 (57)
T PF08220_consen 15 VSVKELAEEFGVSEMTIRRDLNK 37 (57)
T ss_pred EEHHHHHHHHCcCHHHHHHHHHH
Confidence 45568999999999999886543
No 327
>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=28.61 E-value=18 Score=36.52 Aligned_cols=22 Identities=32% Similarity=0.447 Sum_probs=19.2
Q ss_pred CCccccccccCCcccccchhhh
Q 016336 110 DSLMSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 110 ~~~~~l~~~Fgvs~sTvs~~~~ 131 (391)
..+.++|...|++.|||||++.
T Consensus 319 LtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 319 LTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred CcHHHHHHHhCCCccchhhhhc
Confidence 4678899999999999999763
No 328
>smart00351 PAX Paired Box domain.
Probab=28.48 E-value=1.3e+02 Score=24.60 Aligned_cols=31 Identities=10% Similarity=-0.044 Sum_probs=24.6
Q ss_pred CChhHHHhhcCCCHHHHHHHHHHhhhccccc
Q 016336 51 KGLDKFKSVFKISRRTFDYICSLVEEKMVVK 81 (391)
Q Consensus 51 ~~~~~F~~~frms~~tF~~L~~~l~~~~~~~ 81 (391)
.+..+.-..|++++.|...++..........
T Consensus 34 ~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~ 64 (125)
T smart00351 34 VRPCDISRQLCVSHGCVSKILGRYYETGSIR 64 (125)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcC
Confidence 4567788899999999999999877664443
No 329
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=28.41 E-value=24 Score=30.50 Aligned_cols=44 Identities=23% Similarity=0.277 Sum_probs=35.3
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
.++..+. -.|..|+.|.+..+|+..+++|.+||..++.+...-|
T Consensus 143 ~lt~~E~--~vl~~l~~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl 186 (204)
T PRK09958 143 SLSKQEI--SVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKL 186 (204)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 4666554 4777788999999999999999999998877766544
No 330
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=28.22 E-value=99 Score=29.49 Aligned_cols=79 Identities=19% Similarity=0.095 Sum_probs=54.8
Q ss_pred hhHHHhhc--CCCHHHHHHHHHHhhhccccccCCcccCCCCccCH-HHHHHHHHHHhcCCCCccccccccCCc-ccccch
Q 016336 53 LDKFKSVF--KISRRTFDYICSLVEEKMVVKTGGFSFTSGKHLSF-RDQVAIALRRLSSGDSLMSIGDSCGLH-HSTVSQ 128 (391)
Q Consensus 53 ~~~F~~~f--rms~~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~-e~~l~i~L~~L~~g~~~~~l~~~Fgvs-~sTvs~ 128 (391)
+--|.+.- +||+..|-+++..+...-.. . ..+|| -.+=+.+.+.|.+|...+.++...|.+ -||...
T Consensus 210 ~~LF~n~~g~~ltrq~~w~~lk~~a~~Agi--------~-~~isPH~LRHsFATHLL~~GADlRvVQeLLGHadisTTQI 280 (300)
T COG4974 210 DALFPNQRGGGLTRQGFWKRLKDYAERAGI--------D-KKISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQI 280 (300)
T ss_pred CeeeecCCCCCCCHHHHHHHHHHHHHHhCC--------C-CCcCchhhHHHHHHHHHhCCccHHHHHHHhCccccchhHH
Confidence 44454443 68999999999876544322 1 34554 457788889999999999999999985 666666
Q ss_pred hhhHHHHHHHHh
Q 016336 129 VTWRFVEAMEQK 140 (391)
Q Consensus 129 ~~~~~~~~l~~~ 140 (391)
+++-..+.|.+.
T Consensus 281 YTHV~~e~L~~~ 292 (300)
T COG4974 281 YTHVTKERLRDL 292 (300)
T ss_pred HHHHHHHHHHHH
Confidence 665554555443
No 331
>PRK10403 transcriptional regulator NarP; Provisional
Probab=27.98 E-value=24 Score=30.49 Aligned_cols=44 Identities=20% Similarity=0.205 Sum_probs=35.0
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
.++..+.- .|.+++.|.++..++...++|..||..++.+...-|
T Consensus 153 ~Lt~~e~~--vl~~~~~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl 196 (215)
T PRK10403 153 VLTERELD--VLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKL 196 (215)
T ss_pred cCCHHHHH--HHHHHHCCCCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 36665543 466788999999999999999999998887776655
No 332
>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=27.68 E-value=13 Score=26.38 Aligned_cols=21 Identities=19% Similarity=0.404 Sum_probs=15.3
Q ss_pred cccccccCCcccccchhhhHH
Q 016336 113 MSIGDSCGLHHSTVSQVTWRF 133 (391)
Q Consensus 113 ~~l~~~Fgvs~sTvs~~~~~~ 133 (391)
..++..||||++||.+.+...
T Consensus 28 ~~la~~~~vsr~tvr~al~~L 48 (64)
T PF00392_consen 28 RELAERYGVSRTTVREALRRL 48 (64)
T ss_dssp HHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHhccCCcHHHHHHHHH
Confidence 477889999999988765443
No 333
>PRK10072 putative transcriptional regulator; Provisional
Probab=27.67 E-value=13 Score=29.15 Aligned_cols=27 Identities=15% Similarity=0.151 Sum_probs=23.1
Q ss_pred HhcCCCCccccccccCCcccccchhhh
Q 016336 105 RLSSGDSLMSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 105 ~L~~g~~~~~l~~~Fgvs~sTvs~~~~ 131 (391)
+-..|.++..+|..+|||.+||++|..
T Consensus 42 R~~~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 42 RKGTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 345699999999999999999998753
No 334
>COG3293 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=27.60 E-value=38 Score=27.45 Aligned_cols=56 Identities=18% Similarity=0.144 Sum_probs=36.5
Q ss_pred EeeCCCCCCCCcccccCCCCC------CCchhhhhhhchhhhHHHHHHHHHHHHHHHHHhhcc
Q 016336 262 IIGDSGYPFLPYLVTPYKGQE------LPELGSEFNRRHSASHLVAQRALARLKDKWKIIQGV 318 (391)
Q Consensus 262 llgD~gYpl~~~l~~P~~~~~------~~~~~~~fN~~ls~~R~~vE~afg~Lk~rfriL~~~ 318 (391)
.+.|.+|...+|-+-|-.-.+ ....+.-++..+...|..+|+.|+.+|. |+.+...
T Consensus 40 ~i~~~~~~g~~wr~~p~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~f~~~~~-~r~~~~~ 101 (124)
T COG3293 40 GIADLLYTGCAWRALPADFPPATTVIPYRRFRRWFKRGLWKRRNLVERTFGRLKQ-FRRTATR 101 (124)
T ss_pred HHHHHhccchHHHHhHHHhCCCceEeCCCcchhhHHHHHHHHHHHHHHHHHHHhc-ccceecc
Confidence 556666765555443332111 1113577889999999999999998886 7666544
No 335
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=27.47 E-value=9.3 Score=28.73 Aligned_cols=27 Identities=30% Similarity=0.396 Sum_probs=19.9
Q ss_pred cCCCCccccccccCCcccccchhhhHH
Q 016336 107 SSGDSLMSIGDSCGLHHSTVSQVTWRF 133 (391)
Q Consensus 107 ~~g~~~~~l~~~Fgvs~sTvs~~~~~~ 133 (391)
.-|.+++.|+...|++.+|++..+.+-
T Consensus 13 krG~sL~~lsr~~Gl~~~tl~nal~r~ 39 (78)
T PF13693_consen 13 KRGTSLAALSREAGLSSSTLRNALRRP 39 (78)
T ss_dssp TTS--HHHHHHHHSS-HHHHHHTTTSS
T ss_pred HcCCCHHHHHHHcCCCHHHHHHHHcCC
Confidence 358899999999999999998876553
No 336
>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=27.13 E-value=14 Score=35.08 Aligned_cols=21 Identities=29% Similarity=0.289 Sum_probs=17.9
Q ss_pred ccccccccCCcccccchhhhH
Q 016336 112 LMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 112 ~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
..+||...|||.+|||++++.
T Consensus 2 i~dIA~~aGVS~~TVSrvLn~ 22 (327)
T TIGR02417 2 LSDIAKLAGVSKTTASYVING 22 (327)
T ss_pred HHHHHHHhCCCHHHHHHHHcC
Confidence 357899999999999998754
No 337
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=26.95 E-value=26 Score=29.94 Aligned_cols=43 Identities=16% Similarity=0.271 Sum_probs=33.2
Q ss_pred cCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHH
Q 016336 93 LSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAM 137 (391)
Q Consensus 93 l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l 137 (391)
+++.+.=. |.++..|.+...++...++|..||..++.+...-+
T Consensus 150 lt~~e~~v--l~l~~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl 192 (211)
T PRK15369 150 LTPRERQI--LKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKL 192 (211)
T ss_pred CCHHHHHH--HHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 55544333 44578999999999999999999998887765554
No 338
>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=26.91 E-value=14 Score=35.04 Aligned_cols=22 Identities=23% Similarity=0.380 Sum_probs=18.6
Q ss_pred CccccccccCCcccccchhhhH
Q 016336 111 SLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
+..+||..-|||.+|||++++.
T Consensus 3 ti~dIA~~agvS~~TVSrvLn~ 24 (329)
T TIGR01481 3 TIYDVAREAGVSMATVSRVVNG 24 (329)
T ss_pred cHHHHHHHhCCCHHHHHHHhCC
Confidence 4568999999999999998653
No 339
>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=26.88 E-value=36 Score=30.38 Aligned_cols=37 Identities=5% Similarity=0.136 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhcCCCCccccccccCCcccccchhhhHH
Q 016336 96 RDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRF 133 (391)
Q Consensus 96 e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~ 133 (391)
..+++..|..- .+.+..+|+..+|++.+||++.+.+.
T Consensus 3 r~~IL~~L~~~-~~~t~~eLA~~lgis~~tV~~~L~~L 39 (203)
T TIGR02702 3 KEDILSYLLKQ-GQATAAALAEALAISPQAVRRHLKDL 39 (203)
T ss_pred HHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34555556543 44788899999999999999876443
No 340
>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=26.32 E-value=45 Score=29.75 Aligned_cols=33 Identities=24% Similarity=0.242 Sum_probs=24.8
Q ss_pred HHHHHhcC--CCCccccccccCCcccccchhhhHH
Q 016336 101 IALRRLSS--GDSLMSIGDSCGLHHSTVSQVTWRF 133 (391)
Q Consensus 101 i~L~~L~~--g~~~~~l~~~Fgvs~sTvs~~~~~~ 133 (391)
..|.+|.. +.+..+++..+|+|++|+++.+.+.
T Consensus 147 ~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~L 181 (203)
T TIGR01884 147 KVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLREL 181 (203)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 33455543 4589999999999999999877553
No 341
>COG5421 Transposase [DNA replication, recombination, and repair]
Probab=26.25 E-value=1.3e+02 Score=30.54 Aligned_cols=56 Identities=13% Similarity=0.168 Sum_probs=36.7
Q ss_pred ceeEEEEeeCCCcceeecccCCCCCCCcHHHHhhChhhHHhhhccccCCcccccCCCCccceEEeeCCCCC
Q 016336 199 HSMVLQAIVDPEMRFRDIVTGWPGKMEDRLIFRSSNFYKLCEEGKRLNGKILELSGGSEIREYIIGDSGYP 269 (391)
Q Consensus 199 ~s~~~q~v~d~~~~f~~v~~g~pGs~~D~~v~~~S~l~~~~~~g~~l~~~~~~~~~g~~~~~~llgD~gYp 269 (391)
.-+++..+++..|--+.+. -++|+.+|...+... .+.+.+. +..-+.|+++|+||-
T Consensus 155 ~QI~vsMi~~~~gIPl~~~-v~~Gni~D~~~~~~t--i~kl~~~------------l~~~~~~~V~Dkgf~ 210 (480)
T COG5421 155 PQINVSMIVNQKGIPLFVR-VYSGNISDKNTLIKT--IQKLKSV------------LVKDEVYLVADKGFN 210 (480)
T ss_pred ceeEEEEEEcCCCCceEEE-ccCCCccchHHHHHH--HHHHHHh------------cccceEEEEEccccc
Confidence 4778888898886555554 479999999887532 2322221 111136999999993
No 342
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=26.17 E-value=40 Score=30.87 Aligned_cols=47 Identities=13% Similarity=0.273 Sum_probs=31.5
Q ss_pred HHHHHHHhhhccccccCCcccCCCCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHH
Q 016336 67 FDYICSLVEEKMVVKTGGFSFTSGKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFV 134 (391)
Q Consensus 67 F~~L~~~l~~~~~~~~~~~~~~~~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~ 134 (391)
+..|.+.|+..+.. .| ..|..+|.|. .|+..||||+.||.+.+....
T Consensus 14 Y~qi~~~L~~~I~~---~~--~~G~~LPsE~----------------eLa~~~~VSR~TVR~Al~~L~ 60 (241)
T PRK10079 14 YQEIAAKLEQELRQ---HY--RCGDYLPAEQ----------------QLAARYEVNRHTLRRAIDQLV 60 (241)
T ss_pred HHHHHHHHHHHHhc---cc--CCCCcCCCHH----------------HHHHHHCCCHHHHHHHHHHHH
Confidence 56666666666532 12 2466788664 678899999999988665543
No 343
>TIGR03454 partition_RepB plasmid partitioning protein RepB. Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently.
Probab=26.13 E-value=32 Score=33.32 Aligned_cols=44 Identities=18% Similarity=0.206 Sum_probs=35.3
Q ss_pred CCCCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhh
Q 016336 88 TSGKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 88 ~~~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~ 131 (391)
..+..+|.-++...+...+..|.+...++..+|+++++||+++.
T Consensus 156 ~~R~dLS~iE~A~~~~~L~~~G~~~~~ia~~Lg~~ks~vSr~ls 199 (325)
T TIGR03454 156 SARRDLSFIERALFAQRLEDRGFDRDTIMAALSVDKTELSRMIS 199 (325)
T ss_pred hcccCCCHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34567888777666666677888888999999999999999764
No 344
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=25.84 E-value=38 Score=31.59 Aligned_cols=40 Identities=5% Similarity=-0.026 Sum_probs=31.8
Q ss_pred HHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 100 AIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 100 ~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
+-++..++...+++..|...++|+||||+.+.+.-+.+..
T Consensus 6 L~~f~~v~~~gs~s~AA~~L~isQ~avSr~i~~LE~~lg~ 45 (296)
T PRK09906 6 LRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGV 45 (296)
T ss_pred HHHHHHHHhhCCHHHHHHHhCCCCcHHHHHHHHHHHHhCC
Confidence 3344555556699999999999999999999888877643
No 345
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=25.70 E-value=16 Score=35.11 Aligned_cols=21 Identities=24% Similarity=0.338 Sum_probs=18.2
Q ss_pred CccccccccCCcccccchhhh
Q 016336 111 SLMSIGDSCGLHHSTVSQVTW 131 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs~~~~ 131 (391)
+..+||..-|||.+|||++++
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVIN 23 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhC
Confidence 456899999999999999875
No 346
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=25.17 E-value=33 Score=29.48 Aligned_cols=45 Identities=16% Similarity=0.116 Sum_probs=32.6
Q ss_pred CccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHH
Q 016336 91 KHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
..++..++-.+.+..-..-.++.+||...|+|++||.+-+.+..+
T Consensus 10 ~~lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~ 54 (164)
T PRK11169 10 KDLDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLER 54 (164)
T ss_pred hhHHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 345555555555555566688999999999999999886655443
No 347
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=25.12 E-value=39 Score=31.99 Aligned_cols=41 Identities=20% Similarity=0.175 Sum_probs=31.3
Q ss_pred HHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 98 QVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 98 ~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
+|-+++....+ .|+...|+..+|++||||+.+++.-+.+..
T Consensus 8 ~L~~f~av~~~-gS~s~AAe~L~isqsavS~~Ik~LE~~lg~ 48 (309)
T PRK11013 8 HIEIFHAVMTA-GSLTEAARLLHTSQPTVSRELARFEKVIGL 48 (309)
T ss_pred HHHHHHHHHHh-CcHHHHHHHHCCCcHHHHHHHHHHHHHhCc
Confidence 44444444444 489999999999999999999888877644
No 348
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=25.11 E-value=43 Score=30.99 Aligned_cols=45 Identities=16% Similarity=0.058 Sum_probs=33.9
Q ss_pred CccCHHHHHHHHHHHhcCC--CCccccccccCCcccccchhhhHHHH
Q 016336 91 KHLSFRDQVAIALRRLSSG--DSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g--~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
..++.-++.+-.|..|+.. .+..+|+...|+++||+++++...+.
T Consensus 8 ~~v~sl~r~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~ 54 (257)
T PRK15090 8 DSVSSVLKVFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKT 54 (257)
T ss_pred cccHHHHHHHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4466666777777776654 46778999999999999998776554
No 349
>PRK09726 antitoxin HipB; Provisional
Probab=24.40 E-value=22 Score=27.07 Aligned_cols=44 Identities=16% Similarity=0.195 Sum_probs=32.4
Q ss_pred HhcCCCCccccccccCCcccccchhhhHHHHHHHHhccccccCCCHHHHHHHHHHH
Q 016336 105 RLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGLQHLQWPSETEMAEIKSKF 160 (391)
Q Consensus 105 ~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~~~i~~P~~~~~~~i~~~f 160 (391)
+-..|.++..+|...|||++||+++.+. -.-|+.+.+..+++.|
T Consensus 21 R~~~gltq~elA~~~gvs~~tis~~e~g------------~~~ps~~~l~~ia~~l 64 (88)
T PRK09726 21 RQQNGWTQSELAKKIGIKQATISNFENN------------PDNTTLTTFFKILQSL 64 (88)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHCC------------CCCCCHHHHHHHHHHc
Confidence 4466889999999999999999986532 1236666667777655
No 350
>PRK11569 transcriptional repressor IclR; Provisional
Probab=24.17 E-value=45 Score=31.28 Aligned_cols=44 Identities=14% Similarity=0.163 Sum_probs=34.2
Q ss_pred ccCHHHHHHHHHHHhcC---CCCccccccccCCcccccchhhhHHHH
Q 016336 92 HLSFRDQVAIALRRLSS---GDSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~---g~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
.+..-++.+-.|..|+. +.+..+|+...|+++||++|++...+.
T Consensus 23 ~v~sl~ral~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~ 69 (274)
T PRK11569 23 QVQSLTRGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQ 69 (274)
T ss_pred CccHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 35566777777777764 468889999999999999998776554
No 351
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=24.16 E-value=44 Score=32.00 Aligned_cols=42 Identities=5% Similarity=0.045 Sum_probs=33.6
Q ss_pred HHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 98 QVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 98 ~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
+|-.++.-..+|.|++..|...++|++|||+.+.+.-..+..
T Consensus 5 ~L~~f~avae~g~S~s~AA~~L~iSQpavS~~I~~LE~~lG~ 46 (324)
T PRK12681 5 QLRYIVEVVNHNLNVSATAEGLYTSQPGISKQVRMLEDELGI 46 (324)
T ss_pred HHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhCC
Confidence 444555555567799999999999999999999888887754
No 352
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=23.95 E-value=47 Score=30.72 Aligned_cols=37 Identities=30% Similarity=0.315 Sum_probs=26.2
Q ss_pred HHHHHHHhc-CC--CCccccccccCCcccccchhhhHHHH
Q 016336 99 VAIALRRLS-SG--DSLMSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 99 l~i~L~~L~-~g--~~~~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
-+-.|..|+ .+ .+..+|+...|+++||++|++....+
T Consensus 6 al~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~ 45 (246)
T COG1414 6 ALAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVE 45 (246)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 334444444 22 35889999999999999998766544
No 353
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=23.85 E-value=46 Score=31.29 Aligned_cols=41 Identities=12% Similarity=0.207 Sum_probs=32.0
Q ss_pred HHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 98 QVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 98 ~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
+|-+++....+| |+...|+..+|+++|||+.+++.-..+..
T Consensus 5 ~L~~f~~v~~~g-S~s~AA~~L~itQpavS~~i~~LE~~lg~ 45 (305)
T PRK11151 5 DLEYLVALAEHR-HFRRAADSCHVSQPTLSGQIRKLEDELGV 45 (305)
T ss_pred HHHHHHHHHHhC-CHHHHHHHhCCCchHHHHHHHHHHHHhCc
Confidence 344455555555 99999999999999999999888777643
No 354
>PF14493 HTH_40: Helix-turn-helix domain
Probab=23.75 E-value=38 Score=25.97 Aligned_cols=61 Identities=26% Similarity=0.275 Sum_probs=42.0
Q ss_pred HHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhccccccCCCHHHHHHHHHHHhH
Q 016336 100 AIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGLQHLQWPSETEMAEIKSKFEK 162 (391)
Q Consensus 100 ~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~~~i~~P~~~~~~~i~~~f~~ 162 (391)
.+++..+..|.+..+||..-|++.+||...+-+.+..=... ++-.+-+.++.+.+.+.+.+
T Consensus 4 ~~T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~--~~~~~l~~e~~~~I~~~~~~ 64 (91)
T PF14493_consen 4 QITYELFQKGLSIEEIAKIRGLKESTIYGHLAELIESGEPL--DIEELLSEEEIKQIEDAIEK 64 (91)
T ss_pred HHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCC--CHHHhCCHHHHHHHHHHHHH
Confidence 46778888999999999999999999998776655442211 12233345566667666643
No 355
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=23.61 E-value=46 Score=26.15 Aligned_cols=23 Identities=26% Similarity=0.440 Sum_probs=19.7
Q ss_pred cccccccCCcccccchhhhHHHH
Q 016336 113 MSIGDSCGLHHSTVSQVTWRFVE 135 (391)
Q Consensus 113 ~~l~~~Fgvs~sTvs~~~~~~~~ 135 (391)
.+++...+++++||++++.+...
T Consensus 40 ~~la~~l~i~~~~vt~~l~~Le~ 62 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRLED 62 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH
Confidence 89999999999999998766543
No 356
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=23.50 E-value=25 Score=35.77 Aligned_cols=21 Identities=38% Similarity=0.539 Sum_probs=18.8
Q ss_pred CCccccccccCCcccccchhh
Q 016336 110 DSLMSIGDSCGLHHSTVSQVT 130 (391)
Q Consensus 110 ~~~~~l~~~Fgvs~sTvs~~~ 130 (391)
..+.+||...|++.|||||++
T Consensus 344 LtlkdvAe~lglheSTVSRav 364 (455)
T PRK05932 344 LVLKDIAEELGMHESTISRAT 364 (455)
T ss_pred ccHHHHHHHhCCCccchhhhh
Confidence 467889999999999999976
No 357
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=23.34 E-value=22 Score=25.53 Aligned_cols=21 Identities=24% Similarity=0.232 Sum_probs=15.0
Q ss_pred CccccccccCCcccccc-hhhh
Q 016336 111 SLMSIGDSCGLHHSTVS-QVTW 131 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs-~~~~ 131 (391)
+..++|..+|||++|++ .+..
T Consensus 14 ~~~~lA~~lgis~st~s~~~~~ 35 (66)
T PF07022_consen 14 SDKELAERLGISKSTLSNNWKK 35 (66)
T ss_dssp SCHHHHCCTT--HHHHH-HHHH
T ss_pred CHHHHHHHhCcCHHHhhHHHHh
Confidence 44589999999999999 5543
No 358
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=23.31 E-value=49 Score=31.79 Aligned_cols=41 Identities=2% Similarity=-0.043 Sum_probs=31.6
Q ss_pred HHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 99 VAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 99 l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
|-+++....++.|++..|...+||+||||+.+.+.-+.+..
T Consensus 6 L~~F~~vae~~gS~s~AA~~L~isQpavS~~I~~LE~~lG~ 46 (327)
T PRK12680 6 LRYLVAIADAELNITLAAARVHATQPGLSKQLKQLEDELGF 46 (327)
T ss_pred HHHHHHHHHccCCHHHHHHHhcCCchHHHHHHHHHHHHhCC
Confidence 33333333346799999999999999999999988887754
No 359
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=23.22 E-value=16 Score=22.82 Aligned_cols=23 Identities=35% Similarity=0.371 Sum_probs=18.1
Q ss_pred CCCCccccccccCCcccccchhh
Q 016336 108 SGDSLMSIGDSCGLHHSTVSQVT 130 (391)
Q Consensus 108 ~g~~~~~l~~~Fgvs~sTvs~~~ 130 (391)
...|.++.+..+|++++|+++++
T Consensus 15 ~F~Si~eAa~~l~i~~~~I~~~l 37 (37)
T PF07453_consen 15 SFDSIREAARYLGISHSTISKYL 37 (37)
T ss_pred EEcCHHHHHHHhCCCHHHHHHhC
Confidence 44567778889999999988753
No 360
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=22.90 E-value=47 Score=31.15 Aligned_cols=42 Identities=7% Similarity=0.118 Sum_probs=31.8
Q ss_pred HHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 97 DQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 97 ~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
.+|-+++....+ .++...|+..++|++|||+.+.+.-..+..
T Consensus 8 ~~L~~f~~v~~~-gs~s~AA~~L~isQ~avS~~i~~LE~~lG~ 49 (302)
T PRK09791 8 HQIRAFVEVARQ-GSIRGASRMLNMSQPALTKSIQELEEGLAA 49 (302)
T ss_pred HHHHHHHHHHHc-CCHHHHHHHhCCChHHHHHHHHHHHHHhCC
Confidence 344444444444 499999999999999999999888887744
No 361
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=22.85 E-value=26 Score=35.93 Aligned_cols=31 Identities=29% Similarity=0.344 Sum_probs=24.1
Q ss_pred CCccccccccCCcccccchhhhHHHHHHHHhccccccCCCH
Q 016336 110 DSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGLQHLQWPSE 150 (391)
Q Consensus 110 ~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~~~i~~P~~ 150 (391)
..+++||...|++.|||||++. ..|+.-|..
T Consensus 370 LtlkdVAe~lglHeSTVSRa~~----------~KY~~tp~G 400 (481)
T PRK12469 370 LVLRDVAEELGLHESTISRATG----------NKYMATPRG 400 (481)
T ss_pred CcHHHHHHHhCCCcchhhHHhc----------CceeecCCc
Confidence 4668899999999999999763 346666653
No 362
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=22.55 E-value=20 Score=34.77 Aligned_cols=22 Identities=23% Similarity=0.348 Sum_probs=18.2
Q ss_pred CccccccccCCcccccchhhhH
Q 016336 111 SLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 111 ~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
+..++|..-|||.+||||+++.
T Consensus 2 TikDVA~~AGVS~sTVSrvln~ 23 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLNG 23 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 3468899999999999997653
No 363
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=22.15 E-value=27 Score=28.93 Aligned_cols=44 Identities=16% Similarity=0.136 Sum_probs=31.8
Q ss_pred HhcCCCCccccccccCCcccccchhhhHHHHHHHHhccccccCCCHHHHHHHHHHH
Q 016336 105 RLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGLQHLQWPSETEMAEIKSKF 160 (391)
Q Consensus 105 ~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~~~i~~P~~~~~~~i~~~f 160 (391)
+-..|.++..+|...|||++||+++.+.. .-|+.+.+..+++.|
T Consensus 14 R~~~gltq~~lA~~~gvs~~~is~~E~g~------------~~p~~~~l~~la~~l 57 (135)
T PRK09706 14 RKQLKLSQRSLAKAVKVSHVSISQWERDE------------TEPTGKNLFALAKAL 57 (135)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHcCC------------CCCCHHHHHHHHHHH
Confidence 44568889999999999999999864321 236666666666655
No 364
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=22.13 E-value=14 Score=26.29 Aligned_cols=20 Identities=20% Similarity=0.245 Sum_probs=16.6
Q ss_pred CCccccccccCCcccccchh
Q 016336 110 DSLMSIGDSCGLHHSTVSQV 129 (391)
Q Consensus 110 ~~~~~l~~~Fgvs~sTvs~~ 129 (391)
.+...+|..+|||+++|+++
T Consensus 10 G~~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 10 GGQSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp SSHHHHHHHHTS-HHHHHHH
T ss_pred CCHHHHHHHHCCCHHHHHHh
Confidence 36678999999999999998
No 365
>PRK13832 plasmid partitioning protein; Provisional
Probab=22.05 E-value=43 Score=34.39 Aligned_cols=40 Identities=18% Similarity=0.078 Sum_probs=35.8
Q ss_pred CCccCHHHHHHHHHHHhcCCCCccccccccCCcccccchh
Q 016336 90 GKHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQV 129 (391)
Q Consensus 90 ~~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~ 129 (391)
+..+++-++...+-..+..|.+...|+..||+|+++|++.
T Consensus 99 RedL~PiEea~AfkrLie~G~T~EeIA~~lG~S~~~V~rl 138 (520)
T PRK13832 99 REPLNPVDQWRAIERLVALGWTEEAIAVALALPVRQIRKL 138 (520)
T ss_pred cCCCCHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHH
Confidence 4678888888888888899999999999999999999984
No 366
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=22.01 E-value=66 Score=26.77 Aligned_cols=44 Identities=14% Similarity=0.076 Sum_probs=35.3
Q ss_pred hHHHHHHHHHHHHHHHHHhhccccCCCCCchhHHHHHHHHHHchhcc
Q 016336 297 SHLVAQRALARLKDKWKIIQGVMWRPDKHKLPRIILVCCLLHNIVID 343 (391)
Q Consensus 297 ~R~~vE~afg~Lk~rfriL~~~~~~~~~~~~~~ii~acc~LHN~~~~ 343 (391)
.++.||+-+..+|.|.+...+. .+.+.+..++..-.+.||+...
T Consensus 95 ~nN~iE~~h~~~K~r~r~~~gF---ks~~~A~~~l~~~~~~~n~~r~ 138 (140)
T PF13610_consen 95 LNNRIERDHRTIKRRTRPMNGF---KSFRSAQRTLSGFEAYHNFRRP 138 (140)
T ss_pred hhChhhHhhhhhhhhcccccCc---CCHHHHHHHHHHHHHHHHHhCC
Confidence 4688999999999988776654 3456778899999999999753
No 367
>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=21.93 E-value=47 Score=30.89 Aligned_cols=40 Identities=18% Similarity=0.127 Sum_probs=30.3
Q ss_pred HHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHH
Q 016336 98 QVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAME 138 (391)
Q Consensus 98 ~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~ 138 (391)
+|-.++.... ..+++..|...+||+||||+.+.+.-..+.
T Consensus 5 ~L~~f~~v~~-~gs~s~AA~~L~itqpavS~~Ik~LE~~lg 44 (291)
T TIGR03418 5 ALRVFESAAR-LASFTAAARELGSTQPAVSQQVKRLEEELG 44 (291)
T ss_pred HHHHHHHHHH-hCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3334444444 449999999999999999999988877663
No 368
>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=21.92 E-value=91 Score=22.41 Aligned_cols=65 Identities=14% Similarity=0.132 Sum_probs=35.0
Q ss_pred HHHhhcCCCHHHHHHHHHHhhhccccccCCcccCCCCccCHHH----HHHHHHHHhcCCCCccccccccCCccccc
Q 016336 55 KFKSVFKISRRTFDYICSLVEEKMVVKTGGFSFTSGKHLSFRD----QVAIALRRLSSGDSLMSIGDSCGLHHSTV 126 (391)
Q Consensus 55 ~F~~~frms~~tF~~L~~~l~~~~~~~~~~~~~~~~~~l~~e~----~l~i~L~~L~~g~~~~~l~~~Fgvs~sTv 126 (391)
.|-..++++...-+.=..+++.-....- ..| -++.. .|.++-+.....-++.+++..+||+..|+
T Consensus 3 r~~~~L~L~~~v~~~A~~i~~~~~~~~~-----~~G--r~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 3 RICSKLGLPEDVRERAKEIYKKAQERGL-----LKG--RSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHTT--HHHHHHHHHHHHHHHHTTT-----STT--S-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred HHHhHcCCCHHHHHHHHHHHHHHHHcCC-----ccc--CCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 4556677777655554444443222111 112 22333 34444455666788889999999998764
No 369
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=21.64 E-value=47 Score=31.48 Aligned_cols=41 Identities=10% Similarity=0.010 Sum_probs=30.9
Q ss_pred HHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHH
Q 016336 98 QVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQ 139 (391)
Q Consensus 98 ~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~ 139 (391)
+|-+++. ++...++...|...++|++|||+.+.+.-..+..
T Consensus 6 ~L~~f~~-v~e~gs~s~AA~~L~iSQpavS~~I~~LE~~lg~ 46 (308)
T PRK10094 6 TLRTFIA-VAETGSFSKAAERLCKTTATISYRIKLLEENTGV 46 (308)
T ss_pred HHHHHHH-HHHhCCHHHHHHHhcCCHHHHHHHHHHHHHHhCC
Confidence 3443443 3444599999999999999999999888777644
No 370
>TIGR03734 PRTRC_parB PRTRC system ParB family protein. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family the member related to ParB, and is designated PRTRC system ParB family protein.
Probab=21.56 E-value=44 Score=34.82 Aligned_cols=41 Identities=15% Similarity=0.105 Sum_probs=34.3
Q ss_pred CCccCHHHHHHHHHHHhcCCC-CccccccccCCcccccchhh
Q 016336 90 GKHLSFRDQVAIALRRLSSGD-SLMSIGDSCGLHHSTVSQVT 130 (391)
Q Consensus 90 ~~~l~~e~~l~i~L~~L~~g~-~~~~l~~~Fgvs~sTvs~~~ 130 (391)
+..+++-++...+...+..|. +...|+..||+|+++|++.+
T Consensus 89 RedLtP~EeA~A~~rLl~~g~~t~eeIA~~lG~S~~~V~rrL 130 (554)
T TIGR03734 89 RADMSPAEEAEAAARLLGRCKGDREEAARRLGWSPATLDRRL 130 (554)
T ss_pred cCCCCHHHHHHHHHHHhhhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 367888888877777777776 88899999999999999864
No 371
>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family. This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.
Probab=21.22 E-value=85 Score=25.73 Aligned_cols=49 Identities=12% Similarity=0.015 Sum_probs=38.3
Q ss_pred ccCHHHHHHHHHHHhc-CCCCccccccccCCcccccchhhhHHHHHHHHh
Q 016336 92 HLSFRDQVAIALRRLS-SGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQK 140 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~-~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~ 140 (391)
.++..++-.+...|+. .+.+...++..+|+|++++.++-++.+..+...
T Consensus 79 ~l~~~~r~Il~~~Yl~~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~ 128 (132)
T TIGR01637 79 QLDEISRQILYDKYLEPDQKYDYQIMMELGYSHRQYYRIKKRALLRFATL 128 (132)
T ss_pred hCCHHHHHHHHHHHcCccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHH
Confidence 3677888888889886 356778899999999999998776666555443
No 372
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=21.12 E-value=69 Score=25.04 Aligned_cols=41 Identities=15% Similarity=0.092 Sum_probs=30.7
Q ss_pred ccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHH
Q 016336 92 HLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRF 133 (391)
Q Consensus 92 ~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~ 133 (391)
.+++++-=|+-|.-+ .|.++.+.|...|||++|+.+.++..
T Consensus 33 ~lt~eElEAlRLvD~-~~l~QeeAA~rMgISr~Tfwr~l~sA 73 (99)
T COG1342 33 ILTIEELEALRLVDY-EGLTQEEAALRMGISRQTFWRLLTSA 73 (99)
T ss_pred eecHHHHHHHHHHhH-hhccHHHHHHHhcccHHHHHHHHHHH
Confidence 466666666666544 47788899999999999988876543
No 373
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=20.91 E-value=84 Score=30.60 Aligned_cols=61 Identities=20% Similarity=0.286 Sum_probs=45.7
Q ss_pred CccCHHHHHHHHHHHhcCCCCccccccccCCcccccchhhhHHHHHHHHhccccccCCCHHHH
Q 016336 91 KHLSFRDQVAIALRRLSSGDSLMSIGDSCGLHHSTVSQVTWRFVEAMEQKGLQHLQWPSETEM 153 (391)
Q Consensus 91 ~~l~~e~~l~i~L~~L~~g~~~~~l~~~Fgvs~sTvs~~~~~~~~~l~~~~~~~i~~P~~~~~ 153 (391)
+.++++.|++++|+.+ +|.+-.+|+..|=|+.+|+-+-+.+--..|.+-.-.| .-|...++
T Consensus 119 Pal~~~~riALtLR~v-~GLs~~eIArAFLv~e~am~QRivRAK~ri~~agiPf-evP~~~e~ 179 (415)
T COG4941 119 PALPPEQRIALTLRLV-GGLSTAEIARAFLVPEAAMAQRIVRAKARIREAGIPF-EVPGPQEL 179 (415)
T ss_pred CCCChhhHHHHHHHHH-cCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHhcCCCC-cCCChhhH
Confidence 6799999999999876 6899999999999999999876666666665543222 23555443
No 374
>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=20.88 E-value=27 Score=23.03 Aligned_cols=24 Identities=13% Similarity=0.110 Sum_probs=19.8
Q ss_pred CCCccccccccCCcccccchhhhH
Q 016336 109 GDSLMSIGDSCGLHHSTVSQVTWR 132 (391)
Q Consensus 109 g~~~~~l~~~Fgvs~sTvs~~~~~ 132 (391)
+.+.++|+...|+|++++++++..
T Consensus 16 ~~s~~~Ia~~~gvs~~~~y~~f~~ 39 (47)
T PF00440_consen 16 AVSIRDIARRAGVSKGSFYRYFPS 39 (47)
T ss_dssp TSSHHHHHHHHTSCHHHHHHHCSS
T ss_pred hCCHHHHHHHHccchhhHHHHcCC
Confidence 567889999999999999886543
No 375
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=20.46 E-value=63 Score=29.31 Aligned_cols=24 Identities=8% Similarity=0.065 Sum_probs=18.6
Q ss_pred CCccccccccCCcccccchhhhHH
Q 016336 110 DSLMSIGDSCGLHHSTVSQVTWRF 133 (391)
Q Consensus 110 ~~~~~l~~~Fgvs~sTvs~~~~~~ 133 (391)
.+-.++|...|+|+.|+.|++...
T Consensus 174 ~Taeela~~~giSRvTaRRYLeyl 197 (224)
T COG4565 174 LTAEELAQALGISRVTARRYLEYL 197 (224)
T ss_pred cCHHHHHHHhCccHHHHHHHHHHH
Confidence 344478999999999999987443
No 376
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=20.39 E-value=42 Score=27.48 Aligned_cols=25 Identities=28% Similarity=0.353 Sum_probs=20.0
Q ss_pred CCccccccccCCcccccchhhhHHH
Q 016336 110 DSLMSIGDSCGLHHSTVSQVTWRFV 134 (391)
Q Consensus 110 ~~~~~l~~~Fgvs~sTvs~~~~~~~ 134 (391)
.+..+|+..+|+|+++|++++....
T Consensus 26 ~s~~eia~~l~is~~~v~~~l~~L~ 50 (130)
T TIGR02944 26 YSAAEIAEQTGLNAPTVSKILKQLS 50 (130)
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4677889999999999988765543
Done!