Query psy13113
Match_columns 286
No_of_seqs 167 out of 1441
Neff 9.0
Searched_HMMs 46136
Date Fri Aug 16 19:55:27 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13113.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13113hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13359 DDE_Tnp_4: DDE superf 100.0 1E-38 2.2E-43 256.6 2.6 152 92-243 1-158 (158)
2 KOG4585|consensus 100.0 3.5E-34 7.6E-39 252.0 15.3 256 15-283 41-317 (326)
3 PF04827 Plant_tran: Plant tra 100.0 5.7E-35 1.2E-39 231.9 9.1 185 63-251 2-203 (205)
4 PF13613 HTH_Tnp_4: Helix-turn 99.3 6.7E-12 1.5E-16 81.3 6.2 51 11-61 1-51 (53)
5 PF13612 DDE_Tnp_1_3: Transpos 99.3 2.2E-12 4.7E-17 102.1 3.6 124 89-221 7-149 (155)
6 PF01609 DDE_Tnp_1: Transposas 98.2 3.3E-08 7.3E-13 82.0 -5.9 149 89-244 6-213 (213)
7 PF13586 DDE_Tnp_1_2: Transpos 98.1 8.6E-07 1.9E-11 63.7 1.6 76 166-243 1-86 (88)
8 PF02796 HTH_7: Helix-turn-hel 97.3 0.00033 7.2E-09 43.4 3.6 43 8-51 1-43 (45)
9 PF04545 Sigma70_r4: Sigma-70, 97.1 0.0024 5.3E-08 40.3 6.0 46 11-57 3-48 (50)
10 PF13936 HTH_38: Helix-turn-he 97.0 0.0011 2.4E-08 40.8 3.4 41 11-52 3-43 (44)
11 PF13011 LZ_Tnp_IS481: leucine 96.8 0.0044 9.5E-08 43.6 6.0 49 7-55 3-51 (85)
12 PF04218 CENP-B_N: CENP-B N-te 96.7 0.003 6.5E-08 40.5 4.0 43 9-52 3-45 (53)
13 PF13384 HTH_23: Homeodomain-l 96.4 0.0037 8E-08 39.4 2.9 38 16-54 5-42 (50)
14 PF13518 HTH_28: Helix-turn-he 96.3 0.0083 1.8E-07 38.0 4.3 37 18-55 2-38 (52)
15 smart00351 PAX Paired Box doma 96.1 0.017 3.6E-07 44.3 6.0 46 9-55 14-59 (125)
16 PF05225 HTH_psq: helix-turn-h 96.1 0.014 3E-07 36.0 4.3 37 16-52 2-39 (45)
17 cd00569 HTH_Hin_like Helix-tur 95.9 0.021 4.6E-07 32.7 4.6 41 9-50 2-42 (42)
18 PF08281 Sigma70_r4_2: Sigma-7 95.8 0.032 6.9E-07 35.7 5.4 44 12-56 10-53 (54)
19 PRK09413 IS2 repressor TnpA; R 95.7 0.035 7.5E-07 42.2 5.9 48 8-55 8-55 (121)
20 PF01527 HTH_Tnp_1: Transposas 95.7 0.017 3.6E-07 39.8 3.8 46 9-54 3-48 (76)
21 cd00131 PAX Paired Box domain 95.6 0.035 7.5E-07 42.7 5.8 46 9-55 14-59 (128)
22 cd06571 Bac_DnaA_C C-terminal 95.5 0.066 1.4E-06 38.4 6.5 52 8-59 23-75 (90)
23 PF13340 DUF4096: Putative tra 95.4 0.014 3E-07 40.4 2.6 47 8-55 20-66 (75)
24 smart00421 HTH_LUXR helix_turn 95.1 0.088 1.9E-06 33.4 5.8 45 12-58 3-47 (58)
25 COG3415 Transposase and inacti 95.1 0.042 9.2E-07 42.6 4.9 44 12-55 4-47 (138)
26 cd06171 Sigma70_r4 Sigma70, re 95.1 0.069 1.5E-06 33.4 5.2 44 12-56 10-53 (55)
27 PF12116 SpoIIID: Stage III sp 95.1 0.038 8.3E-07 38.0 3.9 41 18-58 8-48 (82)
28 PRK00118 putative DNA-binding 94.8 0.1 2.2E-06 38.4 5.7 49 10-59 15-63 (104)
29 PF13542 HTH_Tnp_ISL3: Helix-t 94.6 0.056 1.2E-06 34.2 3.6 31 23-53 21-51 (52)
30 PRK04217 hypothetical protein; 94.5 0.15 3.3E-06 37.9 6.1 49 10-59 40-88 (110)
31 PRK09639 RNA polymerase sigma 94.3 0.12 2.5E-06 41.2 5.7 49 11-61 111-159 (166)
32 PRK12529 RNA polymerase sigma 94.1 0.16 3.5E-06 41.1 6.3 49 11-60 126-174 (178)
33 cd06170 LuxR_C_like C-terminal 94.0 0.2 4.4E-06 31.7 5.5 43 14-58 2-44 (57)
34 TIGR03879 near_KaiC_dom probab 93.8 0.16 3.4E-06 34.8 4.7 42 11-52 14-55 (73)
35 TIGR02531 yecD_yerC TrpR-relat 93.5 0.14 3.1E-06 36.5 4.2 32 20-51 41-72 (88)
36 PRK06030 hypothetical protein; 93.3 0.31 6.7E-06 37.1 6.1 48 10-57 50-97 (124)
37 PRK09652 RNA polymerase sigma 93.1 0.23 4.9E-06 39.9 5.6 48 12-60 128-175 (182)
38 TIGR02844 spore_III_D sporulat 93.1 0.18 3.8E-06 35.3 4.1 37 15-51 4-41 (80)
39 PHA00675 hypothetical protein 93.0 0.2 4.3E-06 34.3 4.1 41 11-51 21-61 (78)
40 PRK08301 sporulation sigma fac 92.8 0.27 5.9E-06 41.7 5.8 50 12-61 178-230 (234)
41 PRK05911 RNA polymerase sigma 92.7 0.3 6.5E-06 42.2 6.0 49 12-61 205-253 (257)
42 PF04967 HTH_10: HTH DNA bindi 92.7 0.42 9.1E-06 30.5 5.1 42 17-58 6-52 (53)
43 TIGR02985 Sig70_bacteroi1 RNA 92.7 0.38 8.2E-06 37.7 6.2 47 12-59 113-159 (161)
44 PRK03975 tfx putative transcri 92.6 0.79 1.7E-05 35.7 7.6 49 9-59 3-51 (141)
45 TIGR00721 tfx DNA-binding prot 92.6 0.45 9.8E-06 36.9 6.2 47 10-58 4-50 (137)
46 PHA00542 putative Cro-like pro 92.5 0.21 4.5E-06 35.1 3.9 32 20-51 22-53 (82)
47 PF13412 HTH_24: Winged helix- 92.4 0.41 8.8E-06 29.6 4.8 28 28-55 16-43 (48)
48 TIGR02952 Sig70_famx2 RNA poly 92.3 0.41 9E-06 38.0 6.1 47 12-59 122-168 (170)
49 PF07374 DUF1492: Protein of u 92.3 0.39 8.5E-06 35.1 5.3 43 14-57 57-99 (100)
50 PRK07037 extracytoplasmic-func 92.2 0.42 9.1E-06 37.8 5.9 47 12-59 109-155 (163)
51 TIGR02960 SigX5 RNA polymerase 92.2 0.62 1.4E-05 41.5 7.6 52 12-64 142-193 (324)
52 PRK09641 RNA polymerase sigma 92.2 0.38 8.2E-06 39.0 5.7 48 12-60 136-183 (187)
53 PF01325 Fe_dep_repress: Iron 92.2 0.53 1.1E-05 30.9 5.3 41 15-55 5-48 (60)
54 TIGR02937 sigma70-ECF RNA poly 92.1 0.42 9E-06 36.8 5.7 47 12-59 110-156 (158)
55 PRK09638 RNA polymerase sigma 92.1 0.2 4.2E-06 40.3 3.9 48 12-60 126-173 (176)
56 PRK12547 RNA polymerase sigma 92.0 0.47 1E-05 37.7 6.0 47 12-59 112-158 (164)
57 PRK15320 transcriptional activ 92.0 0.41 8.9E-06 39.3 5.5 46 12-59 164-209 (251)
58 TIGR02989 Sig-70_gvs1 RNA poly 92.0 0.46 1E-05 37.3 5.8 47 12-59 111-157 (159)
59 PRK12514 RNA polymerase sigma 92.0 0.47 1E-05 38.3 6.0 48 12-60 129-176 (179)
60 PRK12511 RNA polymerase sigma 91.9 0.44 9.5E-06 38.8 5.8 49 12-61 111-159 (182)
61 PRK12519 RNA polymerase sigma 91.9 0.3 6.4E-06 40.0 4.8 48 12-60 141-188 (194)
62 TIGR01321 TrpR trp operon repr 91.9 0.34 7.4E-06 34.8 4.4 40 13-52 33-78 (94)
63 PF12802 MarR_2: MarR family; 91.7 0.52 1.1E-05 30.7 5.0 26 30-55 22-47 (62)
64 PRK12524 RNA polymerase sigma 91.7 0.48 1E-05 38.9 5.9 47 12-59 136-182 (196)
65 PRK12530 RNA polymerase sigma 91.7 0.46 9.9E-06 38.9 5.7 47 12-59 134-180 (189)
66 PF01022 HTH_5: Bacterial regu 91.7 0.37 8E-06 29.8 3.9 39 17-55 3-41 (47)
67 PF13730 HTH_36: Helix-turn-he 91.6 0.51 1.1E-05 30.0 4.7 43 13-55 3-51 (55)
68 PF00356 LacI: Bacterial regul 91.6 0.14 3.1E-06 31.7 1.9 21 31-51 1-21 (46)
69 PF01047 MarR: MarR family; I 91.6 0.52 1.1E-05 30.4 4.9 41 15-55 3-43 (59)
70 PRK12515 RNA polymerase sigma 91.6 0.5 1.1E-05 38.5 5.8 47 12-59 131-177 (189)
71 PRK05803 sporulation sigma fac 91.6 0.45 9.7E-06 40.4 5.7 48 12-59 175-225 (233)
72 PRK09415 RNA polymerase factor 91.6 0.48 1E-05 38.3 5.6 48 12-60 127-174 (179)
73 PRK12533 RNA polymerase sigma 91.6 0.48 1E-05 39.8 5.8 48 12-60 134-181 (216)
74 PF08279 HTH_11: HTH domain; 91.5 0.5 1.1E-05 30.1 4.6 29 29-57 15-43 (55)
75 PF13551 HTH_29: Winged helix- 91.4 0.34 7.4E-06 35.6 4.3 35 21-55 3-38 (112)
76 COG2963 Transposase and inacti 91.4 0.6 1.3E-05 34.9 5.6 48 10-57 5-53 (116)
77 PRK12537 RNA polymerase sigma 91.4 0.58 1.3E-05 37.9 6.0 47 12-59 133-179 (182)
78 PRK12531 RNA polymerase sigma 91.3 0.59 1.3E-05 38.3 6.0 47 12-59 141-187 (194)
79 PRK15418 transcriptional regul 91.3 0.51 1.1E-05 42.2 5.9 69 19-91 19-89 (318)
80 TIGR02392 rpoH_proteo alternat 91.3 0.51 1.1E-05 41.1 5.9 48 12-59 218-266 (270)
81 PRK12512 RNA polymerase sigma 91.2 0.6 1.3E-05 37.8 5.9 48 12-60 131-178 (184)
82 PRK12516 RNA polymerase sigma 91.2 0.59 1.3E-05 38.2 5.8 48 12-60 116-163 (187)
83 TIGR02939 RpoE_Sigma70 RNA pol 91.1 0.51 1.1E-05 38.3 5.5 50 12-62 138-187 (190)
84 PRK09047 RNA polymerase factor 91.1 0.67 1.4E-05 36.5 5.9 48 12-60 106-153 (161)
85 PRK11924 RNA polymerase sigma 91.0 0.56 1.2E-05 37.5 5.5 47 12-59 125-171 (179)
86 PRK05602 RNA polymerase sigma 90.9 0.59 1.3E-05 38.0 5.6 48 12-60 128-175 (186)
87 PRK12534 RNA polymerase sigma 90.9 0.7 1.5E-05 37.5 6.0 48 12-60 137-184 (187)
88 TIGR02948 SigW_bacill RNA poly 90.9 0.55 1.2E-05 38.0 5.4 49 12-61 136-184 (187)
89 PRK09643 RNA polymerase sigma 90.8 0.63 1.4E-05 38.1 5.7 48 12-60 134-181 (192)
90 PF00196 GerE: Bacterial regul 90.7 0.53 1.1E-05 30.5 4.2 44 13-58 4-47 (58)
91 TIGR02950 SigM_subfam RNA poly 90.7 0.25 5.4E-06 38.7 3.1 47 12-59 105-151 (154)
92 PRK11923 algU RNA polymerase s 90.6 0.6 1.3E-05 38.1 5.4 51 12-63 138-188 (193)
93 PRK06596 RNA polymerase factor 90.6 0.58 1.3E-05 41.1 5.6 48 12-59 230-278 (284)
94 PRK07408 RNA polymerase sigma 90.5 0.72 1.6E-05 39.8 6.0 48 12-60 203-250 (256)
95 TIGR02983 SigE-fam_strep RNA p 90.4 0.78 1.7E-05 36.2 5.8 48 12-60 110-157 (162)
96 TIGR03001 Sig-70_gmx1 RNA poly 90.3 0.7 1.5E-05 39.6 5.8 47 12-59 161-207 (244)
97 PRK12546 RNA polymerase sigma 90.1 0.83 1.8E-05 37.4 5.8 49 12-61 113-161 (188)
98 cd00092 HTH_CRP helix_turn_hel 90.1 0.66 1.4E-05 30.6 4.3 40 16-55 2-51 (67)
99 TIGR02984 Sig-70_plancto1 RNA 90.0 0.98 2.1E-05 36.5 6.2 47 12-59 140-186 (189)
100 TIGR02980 SigBFG RNA polymeras 90.0 0.92 2E-05 38.2 6.2 47 12-59 178-224 (227)
101 PRK05572 sporulation sigma fac 90.0 0.88 1.9E-05 39.1 6.2 47 12-59 202-248 (252)
102 PF08299 Bac_DnaA_C: Bacterial 90.0 0.32 6.9E-06 33.0 2.7 42 12-53 28-70 (70)
103 PRK06811 RNA polymerase factor 90.0 0.85 1.8E-05 37.2 5.8 48 11-59 130-177 (189)
104 PRK12540 RNA polymerase sigma 89.9 0.88 1.9E-05 37.0 5.8 48 12-60 111-158 (182)
105 TIGR02954 Sig70_famx3 RNA poly 89.9 0.93 2E-05 36.1 5.9 48 12-60 119-166 (169)
106 TIGR02393 RpoD_Cterm RNA polym 89.8 0.75 1.6E-05 39.2 5.5 48 12-59 176-226 (238)
107 PRK12532 RNA polymerase sigma 89.8 0.87 1.9E-05 37.3 5.7 48 12-60 136-183 (195)
108 TIGR01636 phage_rinA phage tra 89.7 1.2 2.6E-05 34.4 6.1 48 12-59 82-130 (134)
109 TIGR02835 spore_sigmaE RNA pol 89.7 0.91 2E-05 38.5 6.0 49 12-60 178-229 (234)
110 PF01710 HTH_Tnp_IS630: Transp 89.7 0.35 7.6E-06 36.5 3.0 30 24-53 13-42 (119)
111 PRK06759 RNA polymerase factor 89.6 0.96 2.1E-05 35.3 5.7 46 12-58 106-151 (154)
112 PRK06704 RNA polymerase factor 89.6 1.5 3.2E-05 37.2 7.0 68 12-80 116-186 (228)
113 PRK12544 RNA polymerase sigma 89.6 1 2.2E-05 37.5 6.0 48 12-60 148-195 (206)
114 PRK08583 RNA polymerase sigma 89.5 1 2.2E-05 38.8 6.1 47 12-59 205-251 (257)
115 TIGR02885 spore_sigF RNA polym 89.4 1.1 2.4E-05 37.8 6.2 47 12-59 183-229 (231)
116 PRK08215 sporulation sigma fac 89.3 1.1 2.3E-05 38.7 6.2 47 12-59 209-255 (258)
117 PRK12523 RNA polymerase sigma 89.3 1.1 2.5E-05 35.8 6.0 47 12-59 119-165 (172)
118 PRK07500 rpoH2 RNA polymerase 89.3 0.86 1.9E-05 40.1 5.6 48 12-59 227-275 (289)
119 TIGR02957 SigX4 RNA polymerase 89.1 2.1 4.6E-05 37.4 7.9 67 12-79 108-174 (281)
120 PRK12539 RNA polymerase sigma 89.0 1.1 2.4E-05 36.3 5.8 49 11-60 130-178 (184)
121 PRK12528 RNA polymerase sigma 89.0 1.1 2.4E-05 35.4 5.6 46 12-58 113-158 (161)
122 PRK09645 RNA polymerase sigma 89.0 1.2 2.7E-05 35.5 6.0 47 12-59 118-164 (173)
123 PF01371 Trp_repressor: Trp re 89.0 0.97 2.1E-05 32.1 4.6 37 16-52 36-72 (87)
124 PRK12520 RNA polymerase sigma 88.9 1.1 2.4E-05 36.5 5.8 47 12-59 131-177 (191)
125 TIGR02999 Sig-70_X6 RNA polyme 88.8 1.4 2.9E-05 35.6 6.1 46 13-59 135-180 (183)
126 COG2739 Uncharacterized protei 88.7 1.6 3.4E-05 31.6 5.5 41 18-59 23-63 (105)
127 TIGR02943 Sig70_famx1 RNA poly 88.7 1.2 2.6E-05 36.3 5.8 48 12-60 131-178 (188)
128 TIGR02850 spore_sigG RNA polym 88.6 1.2 2.7E-05 38.2 6.1 48 11-59 205-252 (254)
129 TIGR02846 spore_sigmaK RNA pol 88.6 1.2 2.6E-05 37.6 5.9 49 11-59 173-224 (227)
130 PRK09637 RNA polymerase sigma 88.5 1.2 2.6E-05 36.2 5.6 48 12-60 106-153 (181)
131 PRK06930 positive control sigm 88.4 1.4 3.1E-05 35.5 5.8 47 12-59 114-160 (170)
132 PRK12522 RNA polymerase sigma 88.3 1.2 2.6E-05 35.6 5.5 52 13-65 120-171 (173)
133 TIGR02394 rpoS_proteo RNA poly 88.2 1.1 2.4E-05 39.2 5.6 49 12-60 222-273 (285)
134 PRK06986 fliA flagellar biosyn 88.1 1.3 2.8E-05 37.6 5.8 48 12-60 184-231 (236)
135 PRK09636 RNA polymerase sigma 88.0 2.7 5.8E-05 37.0 7.9 67 12-79 115-181 (293)
136 PF05344 DUF746: Domain of Unk 88.0 1.3 2.9E-05 29.4 4.4 43 18-60 2-44 (65)
137 PRK12525 RNA polymerase sigma 87.8 1.8 3.9E-05 34.5 6.2 47 12-59 118-164 (168)
138 PF09339 HTH_IclR: IclR helix- 87.8 1.2 2.6E-05 28.1 4.1 38 18-55 4-44 (52)
139 PRK07405 RNA polymerase sigma 87.8 1.3 2.8E-05 39.6 5.8 48 12-59 256-306 (317)
140 COG3293 Transposase and inacti 87.7 0.33 7.2E-06 36.8 1.7 97 120-225 2-103 (124)
141 COG1595 RpoE DNA-directed RNA 87.5 1.5 3.2E-05 35.6 5.5 48 12-60 127-174 (182)
142 PRK07670 RNA polymerase sigma 87.5 1.7 3.6E-05 37.3 6.1 47 12-59 201-247 (251)
143 PF00126 HTH_1: Bacterial regu 87.3 2.1 4.5E-05 27.8 5.2 39 20-59 5-43 (60)
144 COG1191 FliA DNA-directed RNA 87.1 1.6 3.5E-05 37.4 5.6 47 12-59 196-242 (247)
145 PRK09642 RNA polymerase sigma 87.0 2 4.3E-05 33.8 5.9 48 12-60 106-153 (160)
146 PF04297 UPF0122: Putative hel 87.0 2 4.3E-05 31.4 5.3 40 20-59 24-63 (101)
147 PRK09648 RNA polymerase sigma 87.0 1.8 3.8E-05 35.2 5.8 47 12-59 139-185 (189)
148 TIGR02941 Sigma_B RNA polymera 86.9 1.8 3.9E-05 37.2 6.0 47 12-59 205-251 (255)
149 smart00346 HTH_ICLR helix_turn 86.9 1.8 4E-05 30.4 5.2 40 16-55 4-46 (91)
150 PRK13919 putative RNA polymera 86.8 2.1 4.5E-05 34.7 6.1 47 12-59 135-181 (186)
151 PRK09649 RNA polymerase sigma 86.8 1.6 3.5E-05 35.5 5.4 47 12-59 130-176 (185)
152 PF13545 HTH_Crp_2: Crp-like h 86.8 1.5 3.3E-05 29.7 4.5 26 30-55 29-54 (76)
153 PRK12527 RNA polymerase sigma 86.7 2.1 4.5E-05 33.7 5.9 48 12-60 105-152 (159)
154 PRK08295 RNA polymerase factor 86.7 1.7 3.8E-05 35.8 5.7 47 12-60 155-201 (208)
155 PRK07122 RNA polymerase sigma 86.7 1.8 3.9E-05 37.5 6.0 47 12-59 215-261 (264)
156 PRK12542 RNA polymerase sigma 86.6 2.1 4.6E-05 34.7 6.0 50 12-62 122-171 (185)
157 PRK12536 RNA polymerase sigma 86.5 2 4.4E-05 34.7 5.8 47 12-59 129-175 (181)
158 PF00325 Crp: Bacterial regula 86.5 1.1 2.4E-05 25.4 2.9 25 30-54 3-27 (32)
159 TIGR02479 FliA_WhiG RNA polyme 86.4 2.2 4.8E-05 35.8 6.2 47 12-59 175-221 (224)
160 PF09862 DUF2089: Protein of u 86.3 2.1 4.5E-05 31.9 5.2 48 11-59 32-79 (113)
161 PRK09635 sigI RNA polymerase s 86.2 3.6 7.8E-05 36.2 7.7 67 13-80 119-185 (290)
162 smart00550 Zalpha Z-DNA-bindin 86.2 2 4.3E-05 28.9 4.7 41 14-54 6-47 (68)
163 PRK12541 RNA polymerase sigma 86.1 2 4.3E-05 33.9 5.5 47 12-59 112-158 (161)
164 PRK12543 RNA polymerase sigma 85.9 2.1 4.6E-05 34.5 5.7 48 12-60 117-164 (179)
165 PRK09644 RNA polymerase sigma 85.7 2.2 4.9E-05 33.8 5.7 48 12-60 108-155 (165)
166 PF13751 DDE_Tnp_1_6: Transpos 85.7 0.37 7.9E-06 36.5 1.0 48 196-245 73-122 (125)
167 PF13560 HTH_31: Helix-turn-he 85.4 1.3 2.8E-05 29.2 3.4 33 19-51 2-36 (64)
168 COG2390 DeoR Transcriptional r 85.4 3.2 7E-05 37.1 6.9 69 21-92 18-87 (321)
169 PF09607 BrkDBD: Brinker DNA-b 85.3 2.5 5.3E-05 27.4 4.5 44 8-51 1-47 (58)
170 PRK12535 RNA polymerase sigma 85.3 2.5 5.5E-05 34.7 5.9 52 12-64 133-184 (196)
171 PRK12526 RNA polymerase sigma 85.3 2.4 5.3E-05 35.1 5.9 47 12-59 153-199 (206)
172 PRK14088 dnaA chromosomal repl 85.1 2.5 5.3E-05 39.6 6.4 51 8-58 366-416 (440)
173 PF13610 DDE_Tnp_IS240: DDE do 84.9 1.5 3.3E-05 34.0 4.2 130 91-247 5-138 (140)
174 PRK05657 RNA polymerase sigma 84.9 2.3 5E-05 38.1 5.8 48 12-59 262-312 (325)
175 PRK12545 RNA polymerase sigma 84.8 2.6 5.6E-05 34.8 5.8 48 12-60 139-186 (201)
176 PRK11922 RNA polymerase sigma 84.8 1.2 2.6E-05 37.7 3.8 49 12-61 149-197 (231)
177 TIGR02959 SigZ RNA polymerase 84.8 2.9 6.4E-05 33.4 6.0 48 12-60 100-147 (170)
178 TIGR03697 NtcA_cyano global ni 84.7 2 4.4E-05 34.7 5.1 45 12-56 112-170 (193)
179 PRK12517 RNA polymerase sigma 84.6 2.6 5.7E-05 34.3 5.7 49 12-61 128-176 (188)
180 PRK15201 fimbriae regulatory p 84.3 2 4.3E-05 34.7 4.5 46 12-59 133-178 (198)
181 PRK07406 RNA polymerase sigma 84.3 2.4 5.2E-05 38.7 5.7 48 12-59 311-361 (373)
182 TIGR01610 phage_O_Nterm phage 84.1 2.2 4.8E-05 30.7 4.5 27 28-54 46-72 (95)
183 PRK03573 transcriptional regul 83.9 2.7 5.8E-05 32.6 5.2 43 12-54 28-71 (144)
184 cd00090 HTH_ARSR Arsenical Res 83.9 3.1 6.8E-05 27.5 5.0 29 26-54 17-45 (78)
185 PF01381 HTH_3: Helix-turn-hel 83.8 1.1 2.5E-05 28.2 2.6 28 25-52 5-32 (55)
186 PRK12427 flagellar biosynthesi 83.7 3 6.5E-05 35.3 5.8 46 12-58 183-228 (231)
187 PF13463 HTH_27: Winged helix 83.7 2 4.4E-05 28.3 3.9 35 22-56 8-45 (68)
188 PRK00149 dnaA chromosomal repl 83.6 3.3 7.2E-05 38.8 6.6 52 8-59 381-433 (450)
189 PRK07598 RNA polymerase sigma 83.6 2.6 5.7E-05 39.0 5.7 48 12-59 350-400 (415)
190 PRK09646 RNA polymerase sigma 83.5 3.4 7.3E-05 33.8 5.9 47 12-59 142-188 (194)
191 TIGR02859 spore_sigH RNA polym 83.5 3 6.4E-05 34.0 5.6 38 21-59 158-195 (198)
192 PRK12538 RNA polymerase sigma 83.4 2.4 5.3E-05 36.0 5.1 48 12-60 171-218 (233)
193 PF06056 Terminase_5: Putative 83.2 2.9 6.2E-05 27.2 4.2 32 19-52 5-36 (58)
194 PRK11512 DNA-binding transcrip 83.2 3.7 8.1E-05 31.9 5.8 46 10-55 35-80 (144)
195 smart00345 HTH_GNTR helix_turn 83.1 1.6 3.4E-05 27.8 3.1 25 31-55 22-46 (60)
196 PF07638 Sigma70_ECF: ECF sigm 83.1 4 8.6E-05 33.2 6.1 46 13-59 136-181 (185)
197 PRK13870 transcriptional regul 83.1 1.9 4E-05 36.7 4.3 47 11-59 172-218 (234)
198 PRK11753 DNA-binding transcrip 83.0 2.7 5.8E-05 34.6 5.2 45 11-55 137-194 (211)
199 PF00872 Transposase_mut: Tran 82.8 2.4 5.2E-05 38.9 5.2 120 26-176 111-241 (381)
200 PRK15411 rcsA colanic acid cap 82.8 2.2 4.7E-05 35.5 4.5 46 12-59 137-182 (207)
201 TIGR02947 SigH_actino RNA poly 82.6 1.5 3.3E-05 35.8 3.5 48 12-60 131-178 (193)
202 PRK14086 dnaA chromosomal repl 82.5 3.6 7.9E-05 40.0 6.4 52 8-59 548-599 (617)
203 PF01978 TrmB: Sugar-specific 82.5 2.3 4.9E-05 28.4 3.7 38 16-55 10-48 (68)
204 PRK09210 RNA polymerase sigma 82.3 2.9 6.3E-05 38.2 5.5 48 12-59 305-355 (367)
205 PRK08241 RNA polymerase factor 82.3 5.1 0.00011 35.9 7.1 49 13-62 154-202 (339)
206 PRK06288 RNA polymerase sigma 82.2 3.3 7.1E-05 35.9 5.6 47 12-59 212-258 (268)
207 PRK09640 RNA polymerase sigma 82.1 1.3 2.7E-05 36.1 2.8 46 14-60 136-181 (188)
208 PRK05949 RNA polymerase sigma 81.9 3.3 7.1E-05 37.2 5.6 48 12-59 266-316 (327)
209 smart00419 HTH_CRP helix_turn_ 81.6 2.1 4.6E-05 25.9 3.1 28 28-55 7-34 (48)
210 PF10668 Phage_terminase: Phag 81.5 2.3 4.9E-05 27.9 3.2 29 23-51 14-44 (60)
211 smart00418 HTH_ARSR helix_turn 81.5 2.5 5.5E-05 27.0 3.7 29 27-55 8-36 (66)
212 PRK09651 RNA polymerase sigma 81.4 3.3 7.1E-05 33.1 5.0 47 12-59 119-165 (172)
213 PF00165 HTH_AraC: Bacterial r 81.2 1.8 3.8E-05 25.8 2.6 29 26-54 5-33 (42)
214 PRK09647 RNA polymerase sigma 81.2 4.2 9.2E-05 33.6 5.7 48 12-60 138-185 (203)
215 PF05263 DUF722: Protein of un 81.2 3.7 8E-05 31.5 4.8 46 13-58 82-128 (130)
216 PRK10402 DNA-binding transcrip 81.1 3 6.4E-05 35.0 4.8 57 12-68 148-209 (226)
217 PF04703 FaeA: FaeA-like prote 81.0 2.6 5.6E-05 27.9 3.4 37 17-53 3-39 (62)
218 PHA02591 hypothetical protein; 81.0 3.5 7.5E-05 28.4 4.0 38 15-52 45-82 (83)
219 PF12840 HTH_20: Helix-turn-he 80.8 2.6 5.7E-05 27.4 3.5 30 26-55 21-50 (61)
220 PF13404 HTH_AsnC-type: AsnC-t 80.3 6.8 0.00015 23.6 4.9 26 28-53 16-41 (42)
221 smart00347 HTH_MARR helix_turn 80.2 5.8 0.00013 28.0 5.6 46 11-56 6-51 (101)
222 PRK10840 transcriptional regul 79.9 4.5 9.7E-05 33.4 5.5 46 11-58 149-194 (216)
223 PRK01381 Trp operon repressor; 79.9 2.3 5E-05 30.8 3.1 39 13-51 33-77 (99)
224 PF13309 HTH_22: HTH domain 79.9 3.2 7E-05 27.5 3.7 42 10-51 18-64 (64)
225 smart00344 HTH_ASNC helix_turn 79.3 6.2 0.00013 28.8 5.5 39 16-55 5-43 (108)
226 PRK12513 RNA polymerase sigma 79.2 2.5 5.5E-05 34.4 3.7 47 12-59 139-185 (194)
227 PF05043 Mga: Mga helix-turn-h 79.0 4.1 8.8E-05 28.6 4.3 34 26-59 27-60 (87)
228 PF13701 DDE_Tnp_1_4: Transpos 78.9 4.8 0.0001 37.8 5.9 152 10-173 52-229 (448)
229 PRK09391 fixK transcriptional 78.3 5.2 0.00011 33.7 5.5 45 12-56 152-206 (230)
230 smart00420 HTH_DEOR helix_turn 78.3 7.1 0.00015 23.9 4.9 27 29-55 14-40 (53)
231 PRK07921 RNA polymerase sigma 78.2 5.4 0.00012 35.7 5.7 48 12-59 262-312 (324)
232 PRK05901 RNA polymerase sigma 78.0 5.1 0.00011 38.2 5.7 48 12-59 447-497 (509)
233 PF08220 HTH_DeoR: DeoR-like h 78.0 5.5 0.00012 25.6 4.3 25 29-53 14-38 (57)
234 PRK13719 conjugal transfer tra 78.0 4.2 9E-05 34.1 4.5 46 11-58 142-187 (217)
235 PRK11161 fumarate/nitrate redu 77.6 5.3 0.00011 33.5 5.3 44 12-55 153-210 (235)
236 cd04762 HTH_MerR-trunc Helix-T 77.5 2.2 4.7E-05 25.8 2.2 22 31-52 2-23 (49)
237 PRK13918 CRP/FNR family transc 77.4 5.2 0.00011 32.6 5.1 57 12-68 118-189 (202)
238 TIGR00122 birA_repr_reg BirA b 77.0 6.3 0.00014 26.3 4.5 30 26-55 9-39 (69)
239 TIGR02337 HpaR homoprotocatech 76.8 6.2 0.00013 29.4 4.9 46 11-56 24-69 (118)
240 TIGR03541 reg_near_HchA LuxR f 76.7 8 0.00017 32.7 6.1 48 10-59 169-216 (232)
241 PRK14087 dnaA chromosomal repl 76.5 7.8 0.00017 36.4 6.5 52 8-59 380-432 (450)
242 PF00292 PAX: 'Paired box' dom 76.2 9.6 0.00021 29.0 5.7 45 9-55 14-59 (125)
243 PF02001 DUF134: Protein of un 75.8 11 0.00024 27.8 5.8 48 11-59 40-87 (106)
244 PRK12422 chromosomal replicati 75.8 7.1 0.00015 36.6 6.0 51 8-58 376-426 (445)
245 TIGR01764 excise DNA binding d 75.5 2.9 6.4E-05 25.3 2.4 23 30-52 2-24 (49)
246 PRK10188 DNA-binding transcrip 75.4 4.9 0.00011 34.3 4.5 47 11-59 178-224 (240)
247 PF12964 DUF3853: Protein of u 75.4 2.1 4.5E-05 30.7 1.8 33 32-64 48-82 (96)
248 smart00352 POU Found in Pit-Oc 75.0 3.7 8.1E-05 28.2 2.9 28 24-51 19-52 (75)
249 COG3316 Transposase and inacti 74.8 20 0.00043 30.0 7.7 186 12-246 8-199 (215)
250 PRK11475 DNA-binding transcrip 74.7 5.2 0.00011 33.3 4.4 45 12-58 134-178 (207)
251 COG2771 CsgD DNA-binding HTH d 74.7 8.1 0.00018 24.9 4.6 37 22-58 12-48 (65)
252 smart00354 HTH_LACI helix_turn 74.4 2.4 5.2E-05 28.6 1.9 21 31-51 2-22 (70)
253 PF05269 Phage_CII: Bacterioph 74.2 4.4 9.5E-05 29.0 3.2 32 30-61 24-55 (91)
254 TIGR01889 Staph_reg_Sar staphy 74.1 10 0.00022 27.9 5.4 45 12-56 22-70 (109)
255 PHA01976 helix-turn-helix prot 73.8 5 0.00011 26.4 3.4 27 25-51 11-37 (67)
256 PRK12518 RNA polymerase sigma 73.7 3.7 8E-05 32.8 3.2 33 28-60 135-167 (175)
257 PF12728 HTH_17: Helix-turn-he 73.6 3 6.5E-05 25.9 2.1 22 30-51 2-23 (51)
258 TIGR00637 ModE_repress ModE mo 73.5 7.1 0.00015 28.4 4.3 39 21-59 8-46 (99)
259 PRK11564 stationary phase indu 73.4 12 0.00027 34.6 7.0 50 10-59 8-60 (426)
260 TIGR03070 couple_hipB transcri 73.3 5.7 0.00012 24.9 3.5 27 25-51 11-37 (58)
261 PF00392 GntR: Bacterial regul 73.3 4.3 9.4E-05 26.6 2.9 24 31-54 26-49 (64)
262 PF13744 HTH_37: Helix-turn-he 73.1 6.7 0.00015 27.1 4.0 36 16-51 16-53 (80)
263 PRK10100 DNA-binding transcrip 72.8 6.5 0.00014 33.0 4.6 45 12-58 155-199 (216)
264 PRK09483 response regulator; P 72.8 5.8 0.00013 32.3 4.3 46 11-58 147-192 (217)
265 TIGR00180 parB_part ParB-like 72.8 8.3 0.00018 31.5 5.1 42 10-51 100-142 (187)
266 TIGR03020 EpsA transcriptional 72.3 11 0.00023 32.5 5.8 47 10-58 188-234 (247)
267 COG2197 CitB Response regulato 72.2 5.8 0.00013 33.1 4.1 45 12-58 148-192 (211)
268 PRK12682 transcriptional regul 71.9 7.2 0.00016 34.2 4.9 43 17-59 4-46 (309)
269 COG3413 Predicted DNA binding 71.8 5.5 0.00012 33.3 3.9 49 11-59 154-208 (215)
270 cd01392 HTH_LacI Helix-turn-he 71.4 2.4 5.2E-05 26.4 1.3 18 34-51 2-19 (52)
271 smart00342 HTH_ARAC helix_turn 71.3 12 0.00026 25.1 5.0 39 16-54 36-76 (84)
272 PRK00215 LexA repressor; Valid 70.9 9.2 0.0002 31.6 5.0 40 17-56 7-51 (205)
273 cd07377 WHTH_GntR Winged helix 70.3 5.8 0.00013 25.6 3.1 25 31-55 27-51 (66)
274 PHA00738 putative HTH transcri 70.0 12 0.00025 27.7 4.7 40 17-56 13-53 (108)
275 PRK11179 DNA-binding transcrip 69.8 15 0.00033 28.8 5.8 46 11-56 5-50 (153)
276 PRK10141 DNA-binding transcrip 69.7 11 0.00023 28.5 4.6 44 13-56 13-57 (117)
277 COG3355 Predicted transcriptio 69.5 11 0.00023 28.8 4.6 30 27-56 40-69 (126)
278 COG0593 DnaA ATPase involved i 69.4 12 0.00026 34.6 5.7 52 8-59 344-395 (408)
279 TIGR02405 trehalos_R_Ecol treh 68.9 3.1 6.7E-05 36.5 1.9 21 31-51 3-23 (311)
280 PRK11050 manganese transport r 68.6 11 0.00023 29.7 4.7 28 28-55 50-77 (152)
281 COG2522 Predicted transcriptio 68.0 11 0.00024 28.4 4.3 24 28-51 21-44 (119)
282 PRK09191 two-component respons 67.9 14 0.0003 31.3 5.7 48 12-60 88-135 (261)
283 PRK10072 putative transcriptio 67.8 5.1 0.00011 29.0 2.5 26 26-51 43-68 (96)
284 PRK13509 transcriptional repre 67.8 12 0.00027 32.1 5.3 40 16-55 4-45 (251)
285 PF08280 HTH_Mga: M protein tr 67.6 16 0.00034 23.6 4.6 40 18-58 9-48 (59)
286 PRK09392 ftrB transcriptional 67.1 11 0.00025 31.5 5.0 45 12-56 146-200 (236)
287 PRK09492 treR trehalose repres 66.8 3.6 7.7E-05 36.1 1.8 23 30-52 5-27 (315)
288 PRK12683 transcriptional regul 66.8 11 0.00023 33.2 4.9 43 17-59 4-46 (309)
289 PF10654 DUF2481: Protein of u 66.6 4.8 0.0001 29.8 2.1 36 23-58 73-109 (126)
290 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 66.4 17 0.00037 22.8 4.3 42 9-51 1-42 (50)
291 COG2512 Predicted membrane-ass 65.8 16 0.00036 31.5 5.6 46 9-54 189-235 (258)
292 PF09182 PuR_N: Bacterial puri 65.3 27 0.00059 23.6 5.3 42 17-58 4-49 (70)
293 PRK13777 transcriptional regul 65.1 18 0.0004 29.5 5.5 41 11-51 41-81 (185)
294 PF02954 HTH_8: Bacterial regu 64.6 22 0.00047 21.1 4.5 26 27-52 16-41 (42)
295 PRK11169 leucine-responsive tr 64.6 14 0.00031 29.4 4.7 44 13-56 12-55 (164)
296 PRK10014 DNA-binding transcrip 64.6 4.2 9.2E-05 36.1 1.9 23 30-52 7-29 (342)
297 TIGR02702 SufR_cyano iron-sulf 64.6 15 0.00032 30.4 5.0 37 15-52 2-38 (203)
298 PF13443 HTH_26: Cro/C1-type H 64.5 6.5 0.00014 25.5 2.3 26 27-52 8-33 (63)
299 PRK10870 transcriptional repre 64.5 16 0.00034 29.5 5.1 24 30-53 72-95 (176)
300 PRK05658 RNA polymerase sigma 64.4 13 0.00027 36.6 5.2 48 12-59 556-606 (619)
301 PF13556 HTH_30: PucR C-termin 64.3 16 0.00035 23.6 4.1 36 23-58 6-41 (59)
302 PRK10360 DNA-binding transcrip 64.1 13 0.00027 29.7 4.5 45 12-58 137-181 (196)
303 PRK09526 lacI lac repressor; R 64.1 4.4 9.6E-05 36.0 1.9 23 30-52 6-28 (342)
304 PRK12679 cbl transcriptional r 63.6 14 0.0003 32.7 5.0 43 17-59 4-46 (316)
305 PRK10651 transcriptional regul 63.5 12 0.00025 30.2 4.3 45 12-58 155-199 (216)
306 PRK04424 fatty acid biosynthes 63.3 16 0.00034 29.8 4.9 42 14-55 4-47 (185)
307 PRK10434 srlR DNA-bindng trans 63.1 16 0.00034 31.5 5.1 42 15-56 3-46 (256)
308 TIGR01884 cas_HTH CRISPR locus 63.0 21 0.00045 29.5 5.6 34 21-54 147-182 (203)
309 COG1476 Predicted transcriptio 62.3 9.7 0.00021 25.6 2.8 28 24-51 9-36 (68)
310 PRK08558 adenine phosphoribosy 62.1 9.5 0.00021 32.5 3.5 40 12-51 6-45 (238)
311 PF05930 Phage_AlpA: Prophage 62.0 8.5 0.00018 24.1 2.4 21 31-51 5-25 (51)
312 PRK11569 transcriptional repre 61.9 23 0.00051 30.7 6.0 46 11-56 22-70 (274)
313 PRK10163 DNA-binding transcrip 61.8 22 0.00048 30.8 5.9 45 12-56 20-67 (271)
314 PRK10401 DNA-binding transcrip 61.7 5.2 0.00011 35.7 1.9 21 31-51 3-23 (346)
315 PRK14987 gluconate operon tran 61.3 4.5 9.7E-05 35.8 1.4 23 30-52 6-28 (331)
316 PRK10403 transcriptional regul 61.2 14 0.0003 29.6 4.3 45 12-58 153-197 (215)
317 PF01710 HTH_Tnp_IS630: Transp 61.2 22 0.00048 26.6 5.0 34 20-53 62-95 (119)
318 smart00760 Bac_DnaA_C Bacteria 61.1 14 0.00029 24.0 3.4 33 8-40 24-56 (60)
319 PRK15092 DNA-binding transcrip 61.0 13 0.00028 32.8 4.3 51 9-59 5-55 (310)
320 PRK10703 DNA-binding transcrip 60.9 5.5 0.00012 35.3 2.0 22 31-52 3-24 (341)
321 PRK09834 DNA-binding transcrip 60.9 16 0.00036 31.4 4.8 45 12-56 6-53 (263)
322 TIGR02431 pcaR_pcaU beta-ketoa 60.8 18 0.00039 30.8 5.0 86 12-98 4-110 (248)
323 PRK09958 DNA-binding transcrip 60.7 15 0.00032 29.5 4.3 45 12-58 143-187 (204)
324 PRK11303 DNA-binding transcrip 60.6 5.8 0.00012 35.0 2.0 22 31-52 2-23 (328)
325 PF08765 Mor: Mor transcriptio 60.1 9.1 0.0002 28.2 2.7 30 28-57 71-100 (108)
326 smart00529 HTH_DTXR Helix-turn 59.9 10 0.00023 26.8 2.9 25 32-56 2-26 (96)
327 PRK10411 DNA-binding transcrip 59.8 18 0.00039 30.8 4.8 39 18-56 5-45 (240)
328 TIGR02944 suf_reg_Xantho FeS a 59.3 19 0.00041 27.3 4.5 35 19-53 11-49 (130)
329 TIGR03830 CxxCG_CxxCG_HTH puta 59.3 13 0.00027 28.0 3.4 28 24-51 73-100 (127)
330 PRK11233 nitrogen assimilation 59.1 16 0.00035 31.9 4.6 40 20-59 6-45 (305)
331 PRK10339 DNA-binding transcrip 59.0 5.3 0.00011 35.3 1.5 22 31-52 3-24 (327)
332 PF14493 HTH_40: Helix-turn-he 58.2 24 0.00052 24.9 4.5 37 20-56 4-40 (91)
333 TIGR02607 antidote_HigA addict 58.2 12 0.00025 25.4 2.8 27 25-51 14-40 (78)
334 PRK09802 DNA-binding transcrip 58.0 21 0.00046 31.0 5.0 45 11-55 11-57 (269)
335 PRK10423 transcriptional repre 57.8 5.9 0.00013 34.8 1.6 19 33-51 2-20 (327)
336 PRK14999 histidine utilization 57.8 35 0.00076 28.8 6.3 48 8-55 6-62 (241)
337 PRK10906 DNA-binding transcrip 57.8 23 0.0005 30.5 5.1 41 16-56 4-46 (252)
338 PF07022 Phage_CI_repr: Bacter 57.8 9 0.0002 25.4 2.1 23 30-52 13-36 (66)
339 PRK09726 antitoxin HipB; Provi 57.7 11 0.00025 26.5 2.8 35 17-51 11-47 (88)
340 PRK09906 DNA-binding transcrip 57.6 16 0.00035 31.6 4.3 42 18-59 4-45 (296)
341 PF04552 Sigma54_DBD: Sigma-54 57.3 3.5 7.5E-05 32.9 0.0 22 30-51 50-71 (160)
342 COG1414 IclR Transcriptional r 57.3 27 0.00057 29.9 5.4 40 17-56 4-46 (246)
343 PRK03902 manganese transport t 57.3 28 0.00061 26.9 5.2 39 16-54 7-47 (142)
344 PF07453 NUMOD1: NUMOD1 domain 57.1 8.2 0.00018 22.2 1.6 23 28-50 15-37 (37)
345 PRK10219 DNA-binding transcrip 56.9 28 0.0006 25.3 4.8 28 27-54 19-46 (107)
346 PF14549 P22_Cro: DNA-binding 56.9 10 0.00022 24.9 2.1 20 30-49 10-29 (60)
347 PF13022 HTH_Tnp_1_2: Helix-tu 56.8 20 0.00044 27.8 4.1 35 30-64 35-72 (142)
348 PF00440 TetR_N: Bacterial reg 56.8 9.5 0.00021 23.2 2.0 29 29-57 16-44 (47)
349 PRK15369 two component system 56.7 20 0.00044 28.4 4.5 45 12-58 149-193 (211)
350 cd04761 HTH_MerR-SF Helix-Turn 56.7 9.7 0.00021 23.1 2.0 22 31-52 2-23 (49)
351 COG1508 RpoN DNA-directed RNA 56.6 8.7 0.00019 35.7 2.4 22 30-51 331-352 (444)
352 PRK12684 transcriptional regul 56.5 20 0.00044 31.5 4.8 43 17-59 4-46 (313)
353 TIGR02684 dnstrm_HI1420 probab 56.5 16 0.00034 26.0 3.3 34 18-51 32-65 (89)
354 PF09012 FeoC: FeoC like trans 56.3 15 0.00033 24.5 3.1 30 22-51 5-36 (69)
355 TIGR03418 chol_sulf_TF putativ 55.9 19 0.00042 31.0 4.5 40 20-59 6-45 (291)
356 TIGR02417 fruct_sucro_rep D-fr 55.9 7.6 0.00016 34.2 1.9 22 31-52 1-22 (327)
357 PF08148 DSHCT: DSHCT (NUC185) 54.9 22 0.00048 28.8 4.4 52 18-69 103-156 (180)
358 COG1342 Predicted DNA-binding 54.9 20 0.00044 25.8 3.5 44 13-57 34-77 (99)
359 PF02650 HTH_WhiA: WhiA C-term 54.9 49 0.0011 23.3 5.5 43 12-55 37-82 (85)
360 PRK06424 transcription factor; 54.6 39 0.00084 26.4 5.5 33 19-51 85-119 (144)
361 PRK12681 cysB transcriptional 54.5 24 0.00052 31.3 5.0 43 17-59 4-46 (324)
362 COG2944 Predicted transcriptio 54.4 12 0.00025 27.5 2.3 24 26-49 54-77 (104)
363 PF08822 DUF1804: Protein of u 53.9 30 0.00065 27.7 4.8 40 13-52 3-42 (165)
364 TIGR01637 phage_arpU phage tra 53.7 47 0.001 25.2 5.8 48 12-59 79-127 (132)
365 TIGR01481 ccpA catabolite cont 53.6 8.4 0.00018 33.9 1.8 22 31-52 3-24 (329)
366 PF07037 DUF1323: Putative tra 53.5 13 0.00029 27.8 2.5 21 31-51 2-22 (122)
367 CHL00180 rbcR LysR transcripti 53.5 25 0.00055 30.6 4.9 41 19-59 9-49 (305)
368 COG1609 PurR Transcriptional r 53.3 9 0.0002 34.3 2.0 22 31-52 2-23 (333)
369 PRK09508 leuO leucine transcri 53.2 25 0.00054 30.9 4.8 43 17-59 24-66 (314)
370 PF05732 RepL: Firmicute plasm 53.1 13 0.00029 29.7 2.7 27 30-56 76-102 (165)
371 PRK10727 DNA-binding transcrip 52.9 8.6 0.00019 34.2 1.8 22 31-52 3-24 (343)
372 TIGR03454 partition_RepB plasm 52.7 50 0.0011 29.6 6.5 45 9-53 157-201 (325)
373 PRK09801 transcriptional activ 52.6 27 0.00058 30.8 4.9 45 14-59 6-50 (310)
374 cd01104 HTH_MlrA-CarA Helix-Tu 52.6 14 0.00031 24.2 2.4 22 31-52 2-23 (68)
375 PRK12680 transcriptional regul 52.4 27 0.00059 31.0 4.9 39 21-59 7-46 (327)
376 PRK15090 DNA-binding transcrip 52.1 39 0.00084 29.0 5.7 47 10-56 7-55 (257)
377 COG5421 Transposase [DNA repli 52.0 16 0.00034 34.3 3.3 54 117-173 155-210 (480)
378 PRK09706 transcriptional repre 52.0 19 0.00041 27.6 3.3 27 25-51 14-40 (135)
379 PF06530 Phage_antitermQ: Phag 51.7 40 0.00087 25.5 5.1 38 21-58 70-107 (125)
380 smart00530 HTH_XRE Helix-turn- 51.4 23 0.00051 20.9 3.2 26 26-51 7-32 (56)
381 TIGR02404 trehalos_R_Bsub treh 51.3 16 0.00034 30.8 3.1 23 31-53 26-48 (233)
382 PRK11013 DNA-binding transcrip 51.3 28 0.00061 30.4 4.8 41 18-59 8-48 (309)
383 PRK10341 DNA-binding transcrip 51.2 27 0.00059 30.6 4.7 44 16-59 8-51 (312)
384 PRK09791 putative DNA-binding 51.0 28 0.00061 30.3 4.7 42 18-59 8-49 (302)
385 COG3677 Transposase and inacti 50.3 26 0.00056 26.8 3.8 47 14-60 74-120 (129)
386 PRK11151 DNA-binding transcrip 50.3 30 0.00065 30.1 4.8 41 18-59 5-45 (305)
387 PRK13348 chromosome replicatio 50.2 28 0.00061 30.1 4.6 39 21-59 8-46 (294)
388 TIGR02424 TF_pcaQ pca operon t 50.2 28 0.00061 30.2 4.6 40 20-59 8-47 (300)
389 PRK11511 DNA-binding transcrip 49.9 39 0.00085 25.5 4.8 30 25-54 21-50 (127)
390 PRK01905 DNA-binding protein F 49.7 45 0.00098 22.8 4.7 29 24-52 45-73 (77)
391 cd00093 HTH_XRE Helix-turn-hel 49.3 29 0.00062 20.6 3.4 26 26-51 9-34 (58)
392 smart00497 IENR1 Intron encode 49.3 18 0.00038 22.4 2.4 25 28-52 16-40 (53)
393 PF03333 PapB: Adhesin biosynt 49.1 58 0.0013 23.3 5.1 39 16-54 40-78 (91)
394 PRK10837 putative DNA-binding 49.0 29 0.00062 29.9 4.5 42 18-59 6-47 (290)
395 cd07153 Fur_like Ferric uptake 49.0 44 0.00096 24.5 4.9 35 18-52 5-44 (116)
396 COG1522 Lrp Transcriptional re 49.0 58 0.0013 25.1 5.9 26 30-55 23-48 (154)
397 TIGR00498 lexA SOS regulatory 48.6 36 0.00079 27.8 4.8 40 16-55 8-52 (199)
398 PRK11886 bifunctional biotin-- 48.5 32 0.00069 30.6 4.7 38 18-55 5-44 (319)
399 COG4941 Predicted RNA polymera 48.0 52 0.0011 29.7 5.7 50 9-59 117-166 (415)
400 PF01418 HTH_6: Helix-turn-hel 47.6 20 0.00044 24.5 2.6 24 29-52 34-57 (77)
401 TIGR03734 PRTRC_parB PRTRC sys 47.5 37 0.0008 32.8 5.1 43 10-52 89-132 (554)
402 PRK03601 transcriptional regul 47.4 37 0.0008 29.2 4.9 41 19-59 5-45 (275)
403 TIGR03339 phn_lysR aminoethylp 47.2 25 0.00055 29.9 3.8 37 23-59 5-41 (279)
404 PRK15421 DNA-binding transcrip 46.7 42 0.00091 29.6 5.2 41 18-59 6-46 (317)
405 TIGR02036 dsdC D-serine deamin 46.6 43 0.00092 29.2 5.2 42 18-59 11-52 (302)
406 COG1846 MarR Transcriptional r 46.5 45 0.00097 24.2 4.7 23 33-55 40-62 (126)
407 COG5566 Uncharacterized conser 46.5 25 0.00054 26.7 3.0 28 28-55 101-128 (137)
408 PF01726 LexA_DNA_bind: LexA D 46.5 72 0.0016 21.1 5.1 25 29-53 25-50 (65)
409 PRK13832 plasmid partitioning 46.4 42 0.00091 32.0 5.2 43 9-51 98-140 (520)
410 PRK10094 DNA-binding transcrip 46.2 36 0.00078 29.8 4.7 38 22-59 9-46 (308)
411 TIGR02395 rpoN_sigma RNA polym 46.1 10 0.00023 35.3 1.2 22 30-51 319-340 (429)
412 TIGR02325 C_P_lyase_phnF phosp 46.0 21 0.00046 30.0 3.1 44 11-54 5-57 (238)
413 PRK10216 DNA-binding transcrip 46.0 37 0.00081 29.8 4.8 42 18-59 11-52 (319)
414 TIGR02018 his_ut_repres histid 45.8 21 0.00047 29.9 3.1 24 31-54 27-50 (230)
415 COG2378 Predicted transcriptio 45.7 41 0.00088 30.0 4.9 44 13-56 4-49 (311)
416 TIGR02612 mob_myst_A mobile my 45.7 23 0.00049 27.9 2.9 29 23-51 32-60 (150)
417 PRK09935 transcriptional regul 45.6 57 0.0012 26.0 5.5 45 12-58 149-193 (210)
418 PRK11242 DNA-binding transcrip 45.6 30 0.00066 29.8 4.1 38 22-59 8-45 (296)
419 PRK10079 phosphonate metabolis 45.5 22 0.00047 30.1 3.1 45 10-54 8-60 (241)
420 PRK11482 putative DNA-binding 45.4 39 0.00084 29.8 4.8 43 17-59 31-73 (317)
421 PF12298 Bot1p: Eukaryotic mit 45.3 62 0.0013 26.2 5.4 43 9-51 13-55 (172)
422 PRK10086 DNA-binding transcrip 45.2 39 0.00084 29.6 4.7 42 18-59 17-58 (311)
423 PRK10681 DNA-binding transcrip 45.2 42 0.00092 28.7 4.8 40 15-54 5-46 (252)
424 PF12844 HTH_19: Helix-turn-he 44.4 23 0.00051 22.8 2.5 26 26-51 9-34 (64)
425 PF13411 MerR_1: MerR HTH fami 44.1 18 0.00039 23.8 1.9 23 32-54 3-25 (69)
426 TIGR03209 P21_Cbot clostridium 44.1 28 0.00061 26.5 3.3 22 26-47 120-141 (142)
427 PF08535 KorB: KorB domain; I 43.7 21 0.00046 25.3 2.3 24 28-51 2-25 (93)
428 COG1654 BirA Biotin operon rep 43.3 66 0.0014 22.3 4.6 39 17-55 6-45 (79)
429 PF00376 MerR: MerR family reg 43.3 20 0.00042 21.0 1.7 19 33-51 3-21 (38)
430 PRK09764 DNA-binding transcrip 43.1 25 0.00054 29.8 3.1 42 13-54 4-54 (240)
431 PF13565 HTH_32: Homeodomain-l 43.0 67 0.0014 21.5 4.7 22 29-50 48-77 (77)
432 PRK10046 dpiA two-component re 42.9 35 0.00076 28.3 3.9 30 22-51 167-199 (225)
433 PRK10632 transcriptional regul 42.5 44 0.00094 29.3 4.6 39 21-59 8-46 (309)
434 TIGR03298 argP transcriptional 42.5 46 0.001 28.7 4.8 38 22-59 8-45 (292)
435 PRK00430 fis global DNA-bindin 42.5 62 0.0014 23.3 4.6 27 26-52 65-91 (95)
436 PRK10082 cell density-dependen 42.3 46 0.001 29.0 4.8 42 18-59 14-55 (303)
437 PRK11139 DNA-binding transcrip 42.2 45 0.00099 28.8 4.7 42 17-59 9-50 (297)
438 smart00342 HTH_ARAC helix_turn 42.1 33 0.00072 22.8 3.1 25 30-54 2-26 (84)
439 PRK11074 putative DNA-binding 41.7 49 0.0011 28.7 4.8 39 21-59 8-46 (300)
440 PRK04984 fatty acid metabolism 41.7 27 0.00059 29.4 3.1 23 31-53 33-55 (239)
441 PRK11062 nhaR transcriptional 41.2 49 0.0011 28.7 4.7 40 20-59 9-48 (296)
442 PRK09744 DNA-binding transcrip 41.0 24 0.00051 24.1 2.0 22 28-49 9-30 (75)
443 PF01316 Arg_repressor: Argini 40.9 86 0.0019 21.2 4.8 36 17-52 5-47 (70)
444 PRK14165 winged helix-turn-hel 40.4 45 0.00098 28.0 4.1 27 30-56 22-48 (217)
445 COG2188 PhnF Transcriptional r 40.1 29 0.00064 29.4 3.0 45 11-55 4-57 (236)
446 PRK05932 RNA polymerase factor 39.9 15 0.00032 34.6 1.2 22 30-51 344-365 (455)
447 PRK11402 DNA-binding transcrip 39.9 30 0.00065 29.3 3.1 44 11-54 6-58 (241)
448 PRK06474 hypothetical protein; 39.7 61 0.0013 26.2 4.7 39 15-53 10-51 (178)
449 PRK10430 DNA-binding transcrip 39.6 61 0.0013 27.1 4.9 31 27-57 176-206 (239)
450 PRK14997 LysR family transcrip 39.5 56 0.0012 28.3 4.9 38 22-59 9-46 (301)
451 PRK03635 chromosome replicatio 39.4 54 0.0012 28.4 4.7 38 22-59 9-46 (294)
452 TIGR00270 conserved hypothetic 39.2 33 0.00071 27.2 2.9 33 19-51 70-104 (154)
453 PRK09390 fixJ response regulat 38.9 67 0.0014 25.1 4.9 34 25-58 152-185 (202)
454 PRK12469 RNA polymerase factor 38.9 18 0.0004 34.2 1.7 22 30-51 370-391 (481)
455 PRK13698 plasmid-partitioning 38.5 51 0.0011 29.5 4.3 40 13-52 158-199 (323)
456 TIGR03338 phnR_burk phosphonat 38.3 32 0.0007 28.3 3.0 23 31-53 36-58 (212)
457 PF05584 Sulfolobus_pRN: Sulfo 38.2 1.1E+02 0.0024 20.9 4.9 40 13-54 4-43 (72)
458 PRK09943 DNA-binding transcrip 38.1 32 0.00069 27.8 2.8 26 26-51 17-42 (185)
459 COG2186 FadR Transcriptional r 38.0 29 0.00062 29.6 2.6 21 31-51 36-56 (241)
460 PF08769 Spo0A_C: Sporulation 37.6 54 0.0012 24.1 3.7 31 30-60 41-71 (106)
461 PRK10225 DNA-binding transcrip 37.4 34 0.00074 29.2 3.1 23 31-53 35-57 (257)
462 PRK09990 DNA-binding transcrip 37.2 35 0.00075 29.0 3.1 23 31-53 33-55 (251)
463 PF14502 HTH_41: Helix-turn-he 37.2 52 0.0011 20.5 2.9 23 31-53 8-30 (48)
464 PF07750 GcrA: GcrA cell cycle 37.2 43 0.00094 26.7 3.4 37 16-52 5-42 (162)
465 COG3311 AlpA Predicted transcr 36.9 27 0.00059 23.6 1.8 37 31-69 15-54 (70)
466 PRK10421 DNA-binding transcrip 36.6 36 0.00078 29.0 3.1 23 31-53 28-50 (253)
467 PF06322 Phage_NinH: Phage Nin 36.5 31 0.00067 22.6 1.9 26 26-51 13-38 (64)
468 COG1321 TroR Mn-dependent tran 36.3 82 0.0018 24.9 4.8 41 16-56 8-51 (154)
469 PF09048 Cro: Cro; InterPro: 36.3 36 0.00079 22.1 2.2 20 32-51 15-34 (59)
470 TIGR00738 rrf2_super rrf2 fami 36.0 61 0.0013 24.3 4.0 27 29-55 25-51 (132)
471 PF02082 Rrf2: Transcriptional 35.9 54 0.0012 22.6 3.3 33 22-54 13-50 (83)
472 TIGR02812 fadR_gamma fatty aci 35.8 38 0.00082 28.5 3.0 23 31-53 32-54 (235)
473 PRK03837 transcriptional regul 35.8 40 0.00086 28.4 3.2 22 31-52 39-60 (241)
474 PRK09464 pdhR transcriptional 35.7 38 0.00082 28.8 3.1 23 31-53 36-58 (254)
475 PRK13890 conjugal transfer pro 35.2 40 0.00087 25.3 2.8 25 27-51 16-40 (120)
476 PRK13558 bacterio-opsin activa 35.1 95 0.0021 30.5 6.1 49 11-59 606-660 (665)
477 PRK09986 DNA-binding transcrip 35.0 58 0.0013 28.0 4.2 41 18-59 11-51 (294)
478 PRK15183 Vi polysaccharide bio 34.5 64 0.0014 23.6 3.5 50 20-69 89-138 (143)
479 PRK00441 argR arginine repress 34.5 78 0.0017 24.8 4.4 35 18-52 5-46 (149)
480 PRK15340 transcriptional regul 33.9 55 0.0012 27.5 3.6 28 28-55 124-151 (216)
481 cd04764 HTH_MlrA-like_sg1 Heli 33.4 44 0.00095 21.9 2.5 21 32-52 3-23 (67)
482 PRK08359 transcription factor; 33.4 46 0.00099 27.0 2.9 32 19-50 86-119 (176)
483 PRK13503 transcriptional activ 33.4 84 0.0018 26.9 4.9 26 29-54 187-212 (278)
484 PRK15243 transcriptional regul 33.3 87 0.0019 27.5 5.0 41 18-59 8-48 (297)
485 COG1349 GlpR Transcriptional r 33.3 86 0.0019 26.9 4.9 41 16-56 4-46 (253)
486 PF13601 HTH_34: Winged helix 32.9 77 0.0017 21.9 3.7 29 28-56 13-41 (80)
487 PF01476 LysM: LysM domain; I 32.9 44 0.00095 19.5 2.2 22 27-48 4-25 (44)
488 PRK09954 putative kinase; Prov 32.8 97 0.0021 27.9 5.4 33 23-55 9-43 (362)
489 PRK11523 DNA-binding transcrip 32.6 45 0.00099 28.4 3.1 22 32-53 35-56 (253)
490 PRK09863 putative frv operon r 32.4 92 0.002 30.3 5.5 33 27-59 15-47 (584)
491 PF07180 DUF1401: Protein of u 32.4 87 0.0019 24.5 4.1 38 18-55 25-64 (146)
492 smart00422 HTH_MERR helix_turn 32.2 38 0.00083 22.1 2.0 21 31-51 2-22 (70)
493 TIGR02698 CopY_TcrY copper tra 32.0 1.3E+02 0.0029 22.8 5.2 39 16-55 6-48 (130)
494 COG2973 TrpR Trp operon repres 31.7 57 0.0012 23.6 2.8 32 18-49 49-80 (103)
495 PRK11414 colanic acid/biofilm 31.6 47 0.001 27.6 2.9 23 31-53 36-58 (221)
496 COG3093 VapI Plasmid maintenan 31.3 45 0.00098 24.5 2.3 50 29-78 23-76 (104)
497 PRK12423 LexA repressor; Provi 31.3 1.1E+02 0.0024 25.2 5.0 26 30-55 26-52 (202)
498 PRK03341 arginine repressor; P 31.3 97 0.0021 24.9 4.5 42 12-53 10-58 (168)
499 PRK13756 tetracycline represso 31.1 64 0.0014 26.7 3.6 43 11-53 2-48 (205)
500 COG0583 LysR Transcriptional r 31.0 82 0.0018 26.7 4.5 40 20-59 6-45 (297)
No 1
>PF13359 DDE_Tnp_4: DDE superfamily endonuclease
Probab=100.00 E-value=1e-38 Score=256.56 Aligned_cols=152 Identities=43% Similarity=0.690 Sum_probs=139.6
Q ss_pred eeeeEEEecCCCC--CCccccccCCCccccceeeecCCCccEEEeccCCCCccccccccccchhhhhcc-ccccceEEEc
Q psy13113 92 IDGTHVPIELPSI--ENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFD-RREIRGLLLG 168 (286)
Q Consensus 92 iDgt~i~i~~P~~--~~~~~y~~~k~~~s~~~q~vvd~~g~i~~~~~~~~Gs~~D~~~~~~s~l~~~l~-~~~~~~~llg 168 (286)
||||+|++++|.. .+...|+++|+.|++|+|++||++|+|++++.++||++||..+|++|++...++ ..+.++++||
T Consensus 1 iDgt~v~i~~P~~~~~~~~~y~~~k~~~~~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~s~~~~~l~~~~~~~~~~l~ 80 (158)
T PF13359_consen 1 IDGTHVPIQRPSDKEEQREFYSGKKKNHSLKVQIVCDPDGRIIYVSVGWPGSVHDSTIFRQSGLLDRLEQAFPPGEYLLG 80 (158)
T ss_pred CccEEEEEEeCCccccccccccCCCCcceEeEEEEEeccceeEeeecccccccccccccccccccceeecccccCccccc
Confidence 7999999999943 378899999999999999999999999999999999999999999999988876 2222789999
Q ss_pred cccCCCCCcccccccCC--CCCChhhHHhHHHHHHHHHHHHHHHHHHHhhhhhhhccccCC-ccchHHHHHHHHHHHh
Q psy13113 169 DIGYAQNEFTFTPVRNP--ITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQ-PTTCSHIITACAVLHN 243 (286)
Q Consensus 169 D~gY~~~~~l~~p~~~~--~~l~~~~~~~N~~~~~~R~~vE~~~~~lK~rf~~L~~~~~~~-~~~~~~ii~a~~~LhN 243 (286)
|+||++.+++++|++++ ..++++|+.||+.+++.|++||++||+||+||++|..+++.+ +..+.++|.+||+|||
T Consensus 81 D~gy~~~~~~~~P~~~~~~~~l~~~e~~~N~~~s~~R~~vE~~~~~lK~rf~~l~~~~~~~~~~~~~~ii~~~~~LhN 158 (158)
T PF13359_consen 81 DSGYPLSPYLLTPYKKPKGRELTPEEKEFNRRHSSARIIVERAFGRLKSRFRILRGRLRLSRPEKAPQIILACCVLHN 158 (158)
T ss_pred cccccccccccccccccccccccccccchhccccceeeeeHHHHHHHHHhcccCCcccCCCcHhHHHHHHheeEEEEC
Confidence 99999999999999843 348899999999999999999999999999999999899998 9999999999999999
No 2
>KOG4585|consensus
Probab=100.00 E-value=3.5e-34 Score=251.99 Aligned_cols=256 Identities=27% Similarity=0.432 Sum_probs=202.3
Q ss_pred HHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcccccCCch--hHHHHHHHhhhhcCCCCceEeee
Q psy13113 15 PVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPE--DLQTAKNQFSGIAGFPRVVVGCI 92 (286)
Q Consensus 15 ~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~~i~~P~--~~~~~~~~f~~~~~~p~~~~g~i 92 (286)
+.+++++.++.++++.+++.++..||...+|. .+...+...++.++.||. ....+...+++ +|+| +|++
T Consensus 41 ~~~~v~~~~~~~~~~~~~~~i~~~fg~~~~~~-----~~~~~~~~~~~~~~~~p~~~~~~~i~~~~~~---~~~~-~g~~ 111 (326)
T KOG4585|consen 41 ADTLVAVALWRLKTGESLRTVEKKFGLGQSTC-----KFLEEKEDLAPHFLKWPSRRILYEIRERFES---LPNC-VGAI 111 (326)
T ss_pred HHhhhhhhhccccccchHHHHHHHcCCcchhh-----hHHHhhhcccchhhcCchhhhhhhhcccccc---ccch-hccc
Confidence 88999999999999999999999999999998 555666678999999998 56666666665 9999 9999
Q ss_pred eeeEEEecCCCCCCccccccCCCccccceeeecCCCccEEEeccCCCCccccccccccchhhhhccccccceEEEcccc-
Q psy13113 93 DGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDRREIRGLLLGDIG- 171 (286)
Q Consensus 93 Dgt~i~i~~P~~~~~~~y~~~k~~~s~~~q~vvd~~g~i~~~~~~~~Gs~~D~~~~~~s~l~~~l~~~~~~~~llgD~g- 171 (286)
|+||+++..| ......|.++ .++.++|++||.+++|+++.+++||+.||..++..+.+......+....|.|.|.|
T Consensus 112 d~~hi~~~~~-~~~~~~~~n~--~~~~Nvlav~n~d~~f~~v~vg~~Gs~~D~kvl~~~~~~~~~~~~~~~k~yl~d~~~ 188 (326)
T KOG4585|consen 112 DTTHIPIRVP-PKSGSVYFNK--EQSKNLLAVCNFDMRFIYVDVGWPGSAHDTKVLQDSLLYKRNFPHPPLKYYLVDSGY 188 (326)
T ss_pred cccccceecC-cccccccccc--ccchhhhheecCCceEEEEEccCCCCccHHHHHHhhcccccccccCCccccccccCc
Confidence 9999999988 5555556665 78889999999999999999999999999999999887766554432244444555
Q ss_pred -----------CCCCCcccccccCCCCCChhhHHhHHHHHHHHHHHHHHHHHHHhhhhhhhccccCCccchHHHHHHHHH
Q psy13113 172 -----------YAQNEFTFTPVRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAV 240 (286)
Q Consensus 172 -----------Y~~~~~l~~p~~~~~~l~~~~~~~N~~~~~~R~~vE~~~~~lK~rf~~L~~~~~~~~~~~~~ii~a~~~ 240 (286)
|+..+++++|+..+. .+..+..||+.|+..|.++|++||.||.||++|.+....+.++..++|.+||+
T Consensus 189 ~~~~~~~g~~~~~~~~~~~~~~~~~~-~~~~~elFN~rh~~~r~v~e~~fg~lk~rw~il~~~~~~~~~~~~~iV~a~ca 267 (326)
T KOG4585|consen 189 PLRPGLLGPIGFPLYSLLMFPYGGPQ-PTNSQELFNKRHSSLRSVAERAFGVLKAKWRILQRREKYDLKKLPKIVTACCA 267 (326)
T ss_pred ccccccccccccccchhhhcccCCCC-CCchHHHHhhhhhhHHHHHHHHHHHhhhhhHHHhhcccccccchHHHHHHHHH
Confidence 445555566665554 35788899999999999999999999999999998767789999999999999
Q ss_pred HHhhhhhcCCCCCCCC--CCCCCc-cc---CC-CCcccHHHHHHHHHHHH
Q psy13113 241 LHNIAIARREAPPPEN--NELPVN-VH---IR-DADDNRLGAAVREAFIN 283 (286)
Q Consensus 241 LhN~~~~~~~~~~~~~--~~~~~~-~~---~~-~~~~~~~~~~~r~~~~~ 283 (286)
|||++.+..+.++++. +..+.. ++ .. .......+...|+.+..
T Consensus 268 LHN~~~~~~~~~~~~~~~e~~~d~~~~~~~~~~~~~~~~~~~~~r~~l~~ 317 (326)
T KOG4585|consen 268 LHNIIRDSDEEDPDDPKWEKFDDYGENVAHLRYAPQQRDYMEKIRDNLLS 317 (326)
T ss_pred HHHHHHhhcccccccccccccccccccchhcccchhHHHHHHHHHHHHHH
Confidence 9999999888654433 222221 11 11 22334566677777654
No 3
>PF04827 Plant_tran: Plant transposon protein; InterPro: IPR006912 This entry represents a putative Harbinger transposase-derived nuclease, which is thought to have nuclease activity. However it does not have transposase activity [, ]. ; GO: 0016788 hydrolase activity, acting on ester bonds
Probab=100.00 E-value=5.7e-35 Score=231.93 Aligned_cols=185 Identities=25% Similarity=0.422 Sum_probs=166.7
Q ss_pred cccCCch--hHHHHHHHhhhhcCCCCceEeeeeeeEEEec-CCCCCCccccccCCCccccceeeecCCCccEEEeccCCC
Q psy13113 63 QWIHFPE--DLQTAKNQFSGIAGFPRVVVGCIDGTHVPIE-LPSIENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASWP 139 (286)
Q Consensus 63 ~~i~~P~--~~~~~~~~f~~~~~~p~~~~g~iDgt~i~i~-~P~~~~~~~y~~~k~~~s~~~q~vvd~~g~i~~~~~~~~ 139 (286)
.|++-|+ +.+++. ...+..||||+ +|.|||+|+.+. +|..-.+.+.+|++|..|+.+++|++.+.+|+++..|.|
T Consensus 2 ~YLr~P~~~d~~rll-~~~e~rGFpGm-lGSIDCmHw~WkncP~aw~g~~~~G~~g~pTiiLEaVAs~dlwIWhaffG~~ 79 (205)
T PF04827_consen 2 EYLRRPTNEDLERLL-QIGEARGFPGM-LGSIDCMHWEWKNCPTAWKGQYTRGKEGVPTIILEAVASHDLWIWHAFFGMP 79 (205)
T ss_pred cccCCCChhHHHHHH-HhhhhcCCCcc-ccceeEEEeehhcchHHhhhcccCCCCCCCeehhhhhhccchhhhheeeccC
Confidence 4778888 778887 44566799999 999999999999 674444566669999999999999999999999999999
Q ss_pred Cccccccccccchhhhhcccccc-------------ceEEEccccCCCCCcccccccCCCCCChhhHHhHHHHHHHHHHH
Q psy13113 140 GSTHDSRIFQNSRVYSRFDRREI-------------RGLLLGDIGYAQNEFTFTPVRNPITPTPSQVAYNAAQIRTRNSV 206 (286)
Q Consensus 140 Gs~~D~~~~~~s~l~~~l~~~~~-------------~~~llgD~gY~~~~~l~~p~~~~~~l~~~~~~~N~~~~~~R~~v 206 (286)
||.||..++..|+++..+.++.. -.|.|+|..||....++.+++.|.. .+++.|.+...++|.-|
T Consensus 80 GS~NDiNVL~~Splf~~~~~G~ap~v~f~VNg~~Y~~gYYLaDGiYP~watfvktI~~p~~--~k~k~fa~~QE~~RKDV 157 (205)
T PF04827_consen 80 GSNNDINVLDRSPLFDDLLQGQAPRVQFTVNGHEYNMGYYLADGIYPEWATFVKTISLPQG--EKRKLFAKHQESARKDV 157 (205)
T ss_pred CcccccccccccHHHHHHhcCcCCceEEEecCeecccceeeccCcCcchHhHhhhcchhhc--hhhHHHHHhCHHHHHHH
Confidence 99999999999999999887743 4589999999999999999999976 89999999999999999
Q ss_pred HHHHHHHHhhhhhhhccccC-CccchHHHHHHHHHHHhhhhhcCCC
Q psy13113 207 ERLFGVLKRRFACLRKKLAN-QPTTCSHIITACAVLHNIAIARREA 251 (286)
Q Consensus 207 E~~~~~lK~rf~~L~~~~~~-~~~~~~~ii~a~~~LhN~~~~~~~~ 251 (286)
|++||.|++||+|++.+.+. +.+.+..|+.||++||||+++++..
T Consensus 158 ErAFGVLQaRfaIi~~p~r~w~~~~l~~Im~aCiILHNMIvEDEr~ 203 (205)
T PF04827_consen 158 ERAFGVLQARFAIIRGPARLWDREDLANIMRACIILHNMIVEDERD 203 (205)
T ss_pred HHHHHHHHHHHHHhcCchhccCHHHHHHHHHHHHHhhheeEecccc
Confidence 99999999999999998887 8899999999999999999987653
No 4
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=99.30 E-value=6.7e-12 Score=81.25 Aligned_cols=51 Identities=24% Similarity=0.068 Sum_probs=48.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhc
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCH 61 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~ 61 (286)
+++++++|++++|.||++|.+++++|..||||+|||+++++++++.|+...
T Consensus 1 ~kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l 51 (53)
T PF13613_consen 1 RKLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVL 51 (53)
T ss_pred CCCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhc
Confidence 468999999999999999999999999999999999999999999998754
No 5
>PF13612 DDE_Tnp_1_3: Transposase DDE domain
Probab=99.28 E-value=2.2e-12 Score=102.14 Aligned_cols=124 Identities=23% Similarity=0.395 Sum_probs=94.3
Q ss_pred EeeeeeeEEEecCCCCCC---------ccccccCCCccccceeeecCCCccEEEeccCCCCccccccccccchhhhhccc
Q psy13113 89 VGCIDGTHVPIELPSIEN---------GEHYRNRKHFYSINVQVIGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDR 159 (286)
Q Consensus 89 ~g~iDgt~i~i~~P~~~~---------~~~y~~~k~~~s~~~q~vvd~~g~i~~~~~~~~Gs~~D~~~~~~s~l~~~l~~ 159 (286)
+.+||++.+|++.+.... .-.|+..+-+|++|++++|+..|.++.+... ||+.||..++.. +...+
T Consensus 7 i~~iDS~Pi~vC~~~R~~r~k~~~~~a~~G~~a~~~fyGfKlHllv~~~G~i~~~~lT-~an~~D~~~~~~--l~~~~-- 81 (155)
T PF13612_consen 7 IYIIDSFPIPVCHNIRIKRHKVFKGLAYRGYCAMGWFYGFKLHLLVNDSGEIVAFTLT-PANVHDRKVLEE--LSENL-- 81 (155)
T ss_pred EEEEecCChhHhCccchhhhccccCccccceeccceeEeeeeeeEEccCCcEEEEEEc-cccccccccccc--ccccc--
Confidence 889999999999763221 1234555556999999999999999998776 999999998854 22222
Q ss_pred cccceEEEccccCCCCC----------cccccccCCCCCChhhHHhHHHHHHHHHHHHHHHHHHHhhhhhhh
Q psy13113 160 REIRGLLLGDIGYAQNE----------FTFTPVRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLR 221 (286)
Q Consensus 160 ~~~~~~llgD~gY~~~~----------~l~~p~~~~~~l~~~~~~~N~~~~~~R~~vE~~~~~lK~rf~~L~ 221 (286)
...++||+||-... .++||.+++.. ......+++.+.+.|..||.+|+.||+.|.+=.
T Consensus 82 ---~g~l~gDkGYis~~L~~~L~~~gI~L~t~~RkNmk-~~~~~~~~~~l~~~R~~IETvfs~Lk~~~~ie~ 149 (155)
T PF13612_consen 82 ---KGKLFGDKGYISKELKDELKEQGIKLITPRRKNMK-NKLMPLFDKLLLRKRRIIETVFSQLKNQFNIEH 149 (155)
T ss_pred ---ccceecchhhhcchHHhhhhhceEEEecccccccc-ccccchhhhhhhheeeEeehHHHHHHHhhceEe
Confidence 34899999996432 36899887653 123356788999999999999999999887654
No 6
>PF01609 DDE_Tnp_1: Transposase DDE domain; InterPro: IPR002559 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS4 transposase. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 3ECP_A 4DM0_A 1MUS_A 1MUH_A 1MM8_A 1B7E_A.
Probab=98.19 E-value=3.3e-08 Score=81.99 Aligned_cols=149 Identities=20% Similarity=0.252 Sum_probs=85.6
Q ss_pred EeeeeeeEEEecCCCCCCccccccCCCccccceeeecC-CCccEEEeccCCCCccccccccccchhhhhccccccceEEE
Q psy13113 89 VGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGG-PNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDRREIRGLLL 167 (286)
Q Consensus 89 ~g~iDgt~i~i~~P~~~~~~~y~~~k~~~s~~~q~vvd-~~g~i~~~~~~~~Gs~~D~~~~~~s~l~~~l~~~~~~~~ll 167 (286)
+.+||+|.++.. +.......+.+++...+++.++++| ..|.++.+... +|+.+|...+.. +.+. .....+..++
T Consensus 6 ~~~iD~T~i~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~d~~~~~~--ll~~-~~~~~~~~vv 80 (213)
T PF01609_consen 6 VVAIDGTTIRTP-HDKSARRYKKGKKRGFGYKLHLAVDDNSGLPLSVKVT-PGNVHDSKALPE--LLER-KPGRKPDLVV 80 (213)
T ss_dssp EEEEETTT--EE-EEEEE-B-SSGGGHSSHGGHHHHHHHHHGGGGGGEEE-EEEGG-HHHHHH--HHTT------EEEEE
T ss_pred EEEEECcEEEee-cchhhhcccCCCCcCCCEeEEEEEeecccceeeeecc-ccccceeecccc--cccc-ccccccccee
Confidence 779999999998 2112223445556667889999994 67777777777 999999988876 3333 1122277999
Q ss_pred ccccCCCCCc----------ccccccCCCCC---------------------------------ChhhHHhHHH------
Q psy13113 168 GDIGYAQNEF----------TFTPVRNPITP---------------------------------TPSQVAYNAA------ 198 (286)
Q Consensus 168 gD~gY~~~~~----------l~~p~~~~~~l---------------------------------~~~~~~~N~~------ 198 (286)
+|+||...+. .+.|.+..... ....+.....
T Consensus 81 ~D~gy~s~~~~~~l~~~~~~~vi~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (213)
T PF01609_consen 81 ADRGYDSAENLEALKERGIHFVIRLKKNRKKKIQKIENKFWKSFDRRSARKKPKQKSKRVRVVIRKEQKKKGYFLVTNIT 160 (213)
T ss_dssp E-S--BBTTHHHHHHTS---EEEEE--EEEE-TTS-EEEE--EEEEEEEEEEETGGGEEEEEEEEEECS--TTS---EEE
T ss_pred ecccccceeccccccccccccccccccccccccccchhhccccccccccccccccccccccccccccccccccccccccc
Confidence 9999976542 13343322210 0011111122
Q ss_pred --------HHHHHHHHHHHHHHHHhhhhhhhccccC-CccchHHHHHHHHHHHhh
Q psy13113 199 --------QIRTRNSVERLFGVLKRRFACLRKKLAN-QPTTCSHIITACAVLHNI 244 (286)
Q Consensus 199 --------~~~~R~~vE~~~~~lK~rf~~L~~~~~~-~~~~~~~ii~a~~~LhN~ 244 (286)
+.+.|..||+.|..+|+.|. +. .++. +...+...+.++++-.|+
T Consensus 161 ~~~~~~~~~Y~~Rw~IE~~f~~lK~~~~-l~-~~~~~~~~~~~~~~~~~~la~nl 213 (213)
T PF01609_consen 161 TLPRDTAALYRRRWQIERFFRELKQFLG-LE-RLRVRSPERIEAHLFLTLLAYNL 213 (213)
T ss_dssp EEESS--SHHHCGGHHHHHHHHHTTTTT-GG-GS--SSHHHHHHHHHHHHHH---
T ss_pred ccccccceeecccchhhHHHHHHHhcCC-Cc-hhcccCHHHHHHHHHHHHhhCcC
Confidence 89999999999999999544 33 2444 667777777777777764
No 7
>PF13586 DDE_Tnp_1_2: Transposase DDE domain
Probab=98.15 E-value=8.6e-07 Score=63.68 Aligned_cols=76 Identities=21% Similarity=0.316 Sum_probs=54.6
Q ss_pred EEccccCCCCCc--------c--cccccCCCCCChhhHHhHHHHHHHHHHHHHHHHHHHhhhhhhhccccCCccchHHHH
Q psy13113 166 LLGDIGYAQNEF--------T--FTPVRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHII 235 (286)
Q Consensus 166 llgD~gY~~~~~--------l--~~p~~~~~~l~~~~~~~N~~~~~~R~~vE~~~~~lK~rf~~L~~~~~~~~~~~~~ii 235 (286)
++||+||..... + ..|.+..... .....+...+.+.|.+||++|++||. |+.|...+.........++
T Consensus 1 v~aDkgYd~~~~r~~l~~~gi~~~i~~~~~~~~-~~~~~~d~~~~~~Rw~VEr~f~wlk~-~Rrl~~ryek~~~s~~~~v 78 (88)
T PF13586_consen 1 VLADKGYDSRALREYLRERGIRPVIPKRGRRKK-RRPRKFDFRLYKRRWVVERTFAWLKR-FRRLATRYEKLASSFLAFV 78 (88)
T ss_pred CcccCCcCCHHHHHHHHHCCCEEecCCCCCccc-cccCccchhhhccceehhhhhHHHHH-cCccccccccCHHHHHHHH
Confidence 579999976321 1 2222222111 33667889999999999999999999 9999988888777777777
Q ss_pred HHHHHHHh
Q psy13113 236 TACAVLHN 243 (286)
Q Consensus 236 ~a~~~LhN 243 (286)
..+|++-+
T Consensus 79 ~la~~~i~ 86 (88)
T PF13586_consen 79 HLACIVIW 86 (88)
T ss_pred HHHHHHHH
Confidence 76666654
No 8
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=97.31 E-value=0.00033 Score=43.38 Aligned_cols=43 Identities=21% Similarity=0.245 Sum_probs=32.9
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
||+..++.+ ++.-++..+..|.+..++|..||||++||+++++
T Consensus 1 GRp~~~~~~-~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 1 GRPPKLSKE-QIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSSSSSHC-CHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred CcCCCCCHH-HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 455666665 5667777889999999999999999999999875
No 9
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=97.08 E-value=0.0024 Score=40.34 Aligned_cols=46 Identities=22% Similarity=0.249 Sum_probs=39.0
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHH
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEEL 57 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l 57 (286)
..+|++++-.+.++| -.+.++.++|..+|+|.+||+++.++.+.-|
T Consensus 3 ~~L~~~er~vi~~~y-~~~~t~~eIa~~lg~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 3 DQLPPREREVIRLRY-FEGLTLEEIAERLGISRSTVRRILKRALKKL 48 (50)
T ss_dssp CTS-HHHHHHHHHHH-TST-SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred hhCCHHHHHHHHHHh-cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence 368999999999999 6678999999999999999999999887655
No 10
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=96.95 E-value=0.0011 Score=40.80 Aligned_cols=41 Identities=15% Similarity=0.017 Sum_probs=23.4
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
..|+.+++..+.-+ +..|.+.+.+|..+|+|++||++.+++
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 46778888777644 689999999999999999999998875
No 11
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=96.84 E-value=0.0044 Score=43.60 Aligned_cols=49 Identities=16% Similarity=0.148 Sum_probs=44.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 7 DARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 7 ~~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
+.++..|++..++.++-..+..|.+...+|..||||..|+++|+.++-.
T Consensus 3 ~H~nA~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra 51 (85)
T PF13011_consen 3 SHKNARLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRA 51 (85)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4577889999999999999999999999999999999999999987653
No 12
>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=96.69 E-value=0.003 Score=40.54 Aligned_cols=43 Identities=19% Similarity=0.189 Sum_probs=32.2
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113 9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
.+..+++++++-+.-. +-.|.+..++|..|||+.||++.|++.
T Consensus 3 kR~~LTl~eK~~iI~~-~e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 3 KRKSLTLEEKLEIIKR-LEEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp SSSS--HHHHHHHHHH-HHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred CCccCCHHHHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 4678999999887655 677789999999999999999998864
No 13
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=96.37 E-value=0.0037 Score=39.42 Aligned_cols=38 Identities=13% Similarity=0.089 Sum_probs=22.7
Q ss_pred HHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113 16 VVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 16 ~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
+.++.+...+. .|.+..++|..+|||++||++|++++.
T Consensus 5 ~~R~~ii~l~~-~G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 5 ERRAQIIRLLR-EGWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp -----HHHHHH-HT--HHHHHHHHTS-HHHHHHHHT---
T ss_pred hHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 34444444444 499999999999999999999998764
No 14
>PF13518 HTH_28: Helix-turn-helix domain
Probab=96.30 E-value=0.0083 Score=37.98 Aligned_cols=37 Identities=24% Similarity=0.300 Sum_probs=31.2
Q ss_pred HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
++.+...++ .|.+...+|..||||.+||++|++....
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 456667777 5679999999999999999999988765
No 15
>smart00351 PAX Paired Box domain.
Probab=96.14 E-value=0.017 Score=44.25 Aligned_cols=46 Identities=13% Similarity=0.045 Sum_probs=39.6
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
....+|.+.+.-+.+.+. .|.+..++|..||||.+||++|++++.+
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 345689998888887775 7899999999999999999999998754
No 16
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=96.09 E-value=0.014 Score=36.04 Aligned_cols=37 Identities=14% Similarity=0.064 Sum_probs=29.8
Q ss_pred HHHHHHHHHHhhcC-CChHhhhhhccccHhHHHHHHHH
Q psy13113 16 VVKLLAVLRFYATG-NFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 16 ~~~l~~~L~~L~~~-~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
++++..+|..+..| .+++..|..|||+++|+++.++.
T Consensus 2 ee~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 2 EEDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp HHHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 67888888889998 89999999999999999987653
No 17
>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=95.91 E-value=0.021 Score=32.70 Aligned_cols=41 Identities=22% Similarity=0.116 Sum_probs=31.1
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHH
Q psy13113 9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLV 50 (286)
Q Consensus 9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~ 50 (286)
++..++.+++..+... +..+.+..+++..||+|.+|+++++
T Consensus 2 r~~~~~~~~~~~i~~~-~~~~~s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 2 RPPKLTPEQIEEARRL-LAAGESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCCcCCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHhC
Confidence 4556777666555444 4577799999999999999999863
No 18
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=95.81 E-value=0.032 Score=35.66 Aligned_cols=44 Identities=18% Similarity=0.271 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
.+|+.++-++.|.|+ .|.++.++|..+|+|.+||...+.+....
T Consensus 10 ~L~~~~r~i~~l~~~-~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLRYF-QGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHHHT-S---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHH-HCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 578888888888777 56899999999999999999998876654
No 19
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=95.67 E-value=0.035 Score=42.20 Aligned_cols=48 Identities=13% Similarity=0.078 Sum_probs=43.7
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
.++...+.+.++-++...+..|.+..++|..||||.+|+++|++.+..
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 346779999999999999999999999999999999999999998753
No 20
>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=95.65 E-value=0.017 Score=39.80 Aligned_cols=46 Identities=24% Similarity=0.203 Sum_probs=38.8
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113 9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
++...|++.++-++-.++..|.+..+++..+||+.+|+++|++...
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp SS----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence 5678899999999999999999999999999999999999999887
No 21
>cd00131 PAX Paired Box domain
Probab=95.63 E-value=0.035 Score=42.67 Aligned_cols=46 Identities=13% Similarity=0.117 Sum_probs=39.6
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
...++|.+.+.-+.+.+ ..|.+.+.+|..||||.+||++|++++.+
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 45778888888887765 68999999999999999999999987765
No 22
>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=95.47 E-value=0.066 Score=38.35 Aligned_cols=52 Identities=19% Similarity=0.064 Sum_probs=46.7
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhcc-ccHhHHHHHHHHHHHHHHh
Q psy13113 8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHD-ISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fg-vs~stv~~~~~~v~~~l~~ 59 (286)
++...+....++++.|..--+|.++.++|..|| .+.|||+..++++...+..
T Consensus 23 ~R~~~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 23 SRKKEIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred CCCcCcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 455578889999999999999999999999999 9999999999999988864
No 23
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)
Probab=95.40 E-value=0.014 Score=40.37 Aligned_cols=47 Identities=21% Similarity=0.024 Sum_probs=41.5
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
+++...+..+-+-..|+.|++|+++++|...|| +.+||++.+++...
T Consensus 20 ~~~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg-~~~tv~~~f~rW~~ 66 (75)
T PF13340_consen 20 GGRPRIDLREVLNAILYVLRTGCPWRDLPEDFG-PWSTVYRRFRRWSR 66 (75)
T ss_pred CCCCccchHHHHhcccccceecceecccchhcc-CcCcHHHHHHHHHH
Confidence 345678999999999999999999999999999 88899999887754
No 24
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=95.15 E-value=0.088 Score=33.45 Aligned_cols=45 Identities=18% Similarity=0.198 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
.++..++-++.+ +..|.+..++|..+|+|.+||.+++.+....|.
T Consensus 3 ~l~~~e~~i~~~--~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 3 SLTPREREVLRL--LAEGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 466666654433 578899999999999999999999998876664
No 25
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=95.14 E-value=0.042 Score=42.55 Aligned_cols=44 Identities=20% Similarity=0.112 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
..+.+.+-+++..++..|.+.+.+|..||||.+|+.+++++.-+
T Consensus 4 ~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e 47 (138)
T COG3415 4 PFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRE 47 (138)
T ss_pred hhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhcc
Confidence 45667888889999999999999999999999999999998764
No 26
>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=95.12 E-value=0.069 Score=33.35 Aligned_cols=44 Identities=18% Similarity=0.157 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
.++++++-++.+.++ .+.++.++|..+|+|.+|+.+++.+....
T Consensus 10 ~l~~~~~~~~~~~~~-~~~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFG-EGLSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 467777777777665 77899999999999999999999876543
No 27
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=95.08 E-value=0.038 Score=38.02 Aligned_cols=41 Identities=12% Similarity=0.050 Sum_probs=28.4
Q ss_pred HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
.+-++=+.+.+..+-+..|..||||+|||++=+.+=+..+.
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 35566777889999999999999999999987665444444
No 28
>PRK00118 putative DNA-binding protein; Validated
Probab=94.75 E-value=0.1 Score=38.44 Aligned_cols=49 Identities=8% Similarity=0.117 Sum_probs=40.2
Q ss_pred CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+.++..++-++.|++. .+.++..+|..+|+|.+||++.+++....|.+
T Consensus 15 ~~~L~ekqRevl~L~y~-eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 15 GSLLTEKQRNYMELYYL-DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred hccCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35677777777766544 58999999999999999999999988877775
No 29
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=94.57 E-value=0.056 Score=34.20 Aligned_cols=31 Identities=19% Similarity=0.187 Sum_probs=25.5
Q ss_pred HHHhhcCCChHhhhhhccccHhHHHHHHHHH
Q psy13113 23 LRFYATGNFQIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 23 L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v 53 (286)
+..|....++.++|..+|||.+||.+++++.
T Consensus 21 ~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 21 LKLLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3444455699999999999999999999864
No 30
>PRK04217 hypothetical protein; Provisional
Probab=94.45 E-value=0.15 Score=37.89 Aligned_cols=49 Identities=14% Similarity=0.070 Sum_probs=38.5
Q ss_pred CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
...++.+++-++.|+ .-.+.++.++|..+|||.+||++.+++....|.+
T Consensus 40 ~~~Lt~eereai~l~-~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 40 PIFMTYEEFEALRLV-DYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred cccCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 455777776444443 3377899999999999999999999988877765
No 31
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=94.30 E-value=0.12 Score=41.21 Aligned_cols=49 Identities=16% Similarity=0.219 Sum_probs=43.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhc
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCH 61 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~ 61 (286)
..+|++++-++.|.+ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus 111 ~~L~~~~r~il~l~~--~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 111 AKMTERDRTVLLLRF--SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred HcCCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 358889999999988 9999999999999999999999999888887643
No 32
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=94.10 E-value=0.16 Score=41.13 Aligned_cols=49 Identities=18% Similarity=0.102 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
..||++++.++.|.++ .|.++.++|..+|+|.+||...+++.+..+.+.
T Consensus 126 ~~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 126 DTLRPRVKQAFLMATL-DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 3578888889999888 789999999999999999999988877777653
No 33
>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=94.05 E-value=0.2 Score=31.72 Aligned_cols=43 Identities=21% Similarity=0.276 Sum_probs=33.7
Q ss_pred CHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 14 SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 14 ~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
+..++-++.+ +..|.+..++|..+++|.+|+...++++...+.
T Consensus 2 ~~~e~~i~~~--~~~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~ 44 (57)
T cd06170 2 TPREREVLRL--LAEGKTNKEIADILGISEKTVKTHLRNIMRKLG 44 (57)
T ss_pred CHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 4445554433 458899999999999999999999998876654
No 34
>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=93.85 E-value=0.16 Score=34.78 Aligned_cols=42 Identities=10% Similarity=0.033 Sum_probs=37.4
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
..+|...+.+..|.+.-.+.++.++|...|+|.+||..+++.
T Consensus 14 ~~l~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 14 TWVDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred hcCCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 457888888888888889999999999999999999988764
No 35
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=93.51 E-value=0.14 Score=36.47 Aligned_cols=32 Identities=28% Similarity=0.295 Sum_probs=27.5
Q ss_pred HHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 20 LAVLRFYATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 20 ~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
...+.++..|.+..++|..+|+|.+|++++.+
T Consensus 41 ~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 41 LQVAKMLKQGKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 45566788999999999999999999999553
No 36
>PRK06030 hypothetical protein; Provisional
Probab=93.35 E-value=0.31 Score=37.11 Aligned_cols=48 Identities=8% Similarity=-0.057 Sum_probs=43.4
Q ss_pred CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHH
Q psy13113 10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEEL 57 (286)
Q Consensus 10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l 57 (286)
+..+...-|++|.|.+--++.++.+++..||.+.|||.-.++.+-+.+
T Consensus 50 rk~i~~aRqIAMYL~r~~~~~sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 50 RREVSRIRQIAMYVAHVSLGWPMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred CcccchHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence 367889999999999999999999999999999999999999777655
No 37
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=93.14 E-value=0.23 Score=39.91 Aligned_cols=48 Identities=13% Similarity=0.027 Sum_probs=40.7
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++.++.|.++ .|.+++++|..+|+|.+||...+.+...-|-..
T Consensus 128 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREI-EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 577888888888776 678999999999999999999988887777653
No 38
>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=93.12 E-value=0.18 Score=35.27 Aligned_cols=37 Identities=14% Similarity=0.182 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHhhcC-CChHhhhhhccccHhHHHHHHH
Q psy13113 15 PVVKLLAVLRFYATG-NFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 15 ~~~~l~~~L~~L~~~-~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
.++++...+-+|..+ .+..++|..||||.+||++.++
T Consensus 4 ~~~R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 4 IEERVLEIGKYIVETKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhc
Confidence 356677777777764 3888999999999999999775
No 39
>PHA00675 hypothetical protein
Probab=92.98 E-value=0.2 Score=34.26 Aligned_cols=41 Identities=7% Similarity=-0.100 Sum_probs=29.6
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
..|...+--.+-..+-+.|.++..||..||||++||+.|.+
T Consensus 21 AKLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 21 AKLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred cccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHc
Confidence 34444444444433337888999999999999999998765
No 40
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=92.82 E-value=0.27 Score=41.69 Aligned_cols=50 Identities=32% Similarity=0.250 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHHHHh---hcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhc
Q psy13113 12 IHSPVVKLLAVLRFY---ATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCH 61 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~ 61 (286)
.+|+.++-++.|+|. -.|.++.++|..+|+|.+||....++....|-...
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 477778888888774 57899999999999999999999998888876543
No 41
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=92.71 E-value=0.3 Score=42.18 Aligned_cols=49 Identities=12% Similarity=0.116 Sum_probs=42.5
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhc
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCH 61 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~ 61 (286)
.+|+.++..+.|+|+ .+.++.++|..+|+|.++|+...++....|-..+
T Consensus 205 ~L~~~er~vi~l~y~-e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 253 (257)
T PRK05911 205 ALEEKERKVMALYYY-EELVLKEIGKILGVSESRVSQIHSKALLKLRATL 253 (257)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 588888888888886 6789999999999999999999999888877643
No 42
>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=92.70 E-value=0.42 Score=30.53 Aligned_cols=42 Identities=14% Similarity=0.040 Sum_probs=31.5
Q ss_pred HHHHHHHHHhhcC-----CChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 17 VKLLAVLRFYATG-----NFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 17 ~~l~~~L~~L~~~-----~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
..++.+-+.++.. .+..+||..+|||++|+++.+++...-|.
T Consensus 6 ~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~kli 52 (53)
T PF04967_consen 6 REILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAERKLI 52 (53)
T ss_pred HHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence 4445555555543 47788999999999999999998876553
No 43
>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=92.69 E-value=0.38 Score=37.67 Aligned_cols=47 Identities=19% Similarity=0.176 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.|+++ .|.++.++|..+|+|.+||...+++....|-+
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 467788888888776 68899999999999999999999887776643
No 44
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=92.61 E-value=0.79 Score=35.71 Aligned_cols=49 Identities=14% Similarity=0.107 Sum_probs=40.7
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
....+++.++-.+.| ...|.++.++|..+|+|++||+.+.++....|..
T Consensus 3 ~~~~Lt~rqreVL~l--r~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 3 MESFLTERQIEVLRL--RERGLTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred cccCCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 346688888888877 3699999999999999999999999887766553
No 45
>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=92.59 E-value=0.45 Score=36.86 Aligned_cols=47 Identities=11% Similarity=0.097 Sum_probs=39.7
Q ss_pred CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
...++..++-.+.|+ ..|.++.++|..+|+|++||+.+.++...-|.
T Consensus 4 ~~~Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr 50 (137)
T TIGR00721 4 KTFLTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRAMENIE 50 (137)
T ss_pred cCCCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhHHHHHH
Confidence 356788888777773 69999999999999999999999888777765
No 46
>PHA00542 putative Cro-like protein
Probab=92.47 E-value=0.21 Score=35.09 Aligned_cols=32 Identities=34% Similarity=0.404 Sum_probs=27.1
Q ss_pred HHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 20 LAVLRFYATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 20 ~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
-+...+...|.++.++|...|||++|++++.+
T Consensus 22 ~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~ 53 (82)
T PHA00542 22 ELVCALIRAGWSQEQIADATDVSQPTICRIYS 53 (82)
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHc
Confidence 33445678899999999999999999999875
No 47
>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=92.45 E-value=0.41 Score=29.62 Aligned_cols=28 Identities=29% Similarity=0.272 Sum_probs=22.6
Q ss_pred cCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 28 TGNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 28 ~~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
.+.+..++|..+|+|.+|+++++++..+
T Consensus 16 ~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 16 PRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3479999999999999999999987754
No 48
>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=92.34 E-value=0.41 Score=38.04 Aligned_cols=47 Identities=17% Similarity=0.164 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++.++.|+|+ .|.++.++|..+|+|.+||...+.+....|-.
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 688888888888777 47999999999999999999999888877653
No 49
>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=92.27 E-value=0.39 Score=35.08 Aligned_cols=43 Identities=23% Similarity=0.262 Sum_probs=36.9
Q ss_pred CHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHH
Q psy13113 14 SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEEL 57 (286)
Q Consensus 14 ~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l 57 (286)
.++++.++.++|+ .+.++.+++...++|++|++++-+..+..|
T Consensus 57 d~~~r~iL~~~Yi-~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 57 DPDERLILRMRYI-NKLTWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred ChhHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 4678889999999 578899999999999999999988776544
No 50
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=92.22 E-value=0.42 Score=37.83 Aligned_cols=47 Identities=11% Similarity=-0.003 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|++++-++.|.++. |.++.++|..+|+|.+||...+.+....|-.
T Consensus 109 ~L~~~~r~v~~l~~~~-~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 109 ELPARTRYAFEMYRLH-GETQKDIARELGVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4677777777777665 8899999999999999999998888777765
No 51
>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=92.20 E-value=0.62 Score=41.47 Aligned_cols=52 Identities=12% Similarity=0.128 Sum_probs=42.4
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcccc
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQW 64 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~~ 64 (286)
.||+.++.++.|.++ .|.+++++|..+|+|.+||...+.+....|.+.+...
T Consensus 142 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 193 (324)
T TIGR02960 142 YLPPRQRAVLLLRDV-LGWRAAETAELLGTSTASVNSALQRARATLDEVGPSA 193 (324)
T ss_pred hCCHHHhhHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcccc
Confidence 456666666666665 7789999999999999999999999999998755543
No 52
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=92.16 E-value=0.38 Score=38.98 Aligned_cols=48 Identities=15% Similarity=0.130 Sum_probs=40.7
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|.+++-++.|.|+ .|.++.++|..+|+|.+||...+++....|-..
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 467777777878777 689999999999999999999999888877653
No 53
>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=92.16 E-value=0.53 Score=30.90 Aligned_cols=41 Identities=12% Similarity=0.126 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHhh---cCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 15 PVVKLLAVLRFYA---TGNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 15 ~~~~l~~~L~~L~---~~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
..+.-+-+++.|. ...+-.++|..+|||.+||++.+++..+
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 4567777888888 4458889999999999999999887654
No 54
>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=92.12 E-value=0.42 Score=36.78 Aligned_cols=47 Identities=19% Similarity=0.208 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.+.++ .|.++.++|..+|+|.+||++...++...|-.
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 577777777776665 68999999999999999999999988776643
No 55
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=92.10 E-value=0.2 Score=40.33 Aligned_cols=48 Identities=19% Similarity=0.202 Sum_probs=41.4
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++.++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
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 478888888888877 689999999999999999999998888877653
No 56
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=92.03 E-value=0.47 Score=37.74 Aligned_cols=47 Identities=17% Similarity=0.068 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus 112 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 112 LLSADQREAIILIGA-SGFSYEDAAAICGCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 577788888888877 88999999999999999999999988887765
No 57
>PRK15320 transcriptional activator SprB; Provisional
Probab=92.03 E-value=0.41 Score=39.26 Aligned_cols=46 Identities=17% Similarity=0.136 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.++..+. -.|.+|+.|.+.+++|..+++|.+||+.+..++.+-|..
T Consensus 164 ~LSdREI--EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLgA 209 (251)
T PRK15320 164 GVTQAKY--ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLGM 209 (251)
T ss_pred CCCHHHH--HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHcCC
Confidence 3444443 678889999999999999999999999999998888764
No 58
>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=91.96 E-value=0.46 Score=37.35 Aligned_cols=47 Identities=11% Similarity=0.105 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|-.
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 588888888888776 78999999999999999999999888777754
No 59
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=91.96 E-value=0.47 Score=38.27 Aligned_cols=48 Identities=13% Similarity=0.119 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|++++-.+.|.++ .|.++.++|..+|+|..||...+.+....|-..
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 477888888888876 779999999999999999999999888877653
No 60
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=91.93 E-value=0.44 Score=38.79 Aligned_cols=49 Identities=10% Similarity=-0.009 Sum_probs=42.1
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhc
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCH 61 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~ 61 (286)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-...
T Consensus 111 ~Lp~~~R~v~~L~~~-eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 111 DLPEEQRAALHLVAI-EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 578888888888887 5899999999999999999999988888876543
No 61
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=91.93 E-value=0.3 Score=40.01 Aligned_cols=48 Identities=15% Similarity=0.068 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|++++-++.|+++. |.+++++|..+|+|.+||...+.+....|-..
T Consensus 141 ~L~~~~~~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 141 QLPESQRQVLELAYYE-GLSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred hCCHHHhhhhhhhhhc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3677777777777665 79999999999999999999999888877653
No 62
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=91.92 E-value=0.34 Score=34.83 Aligned_cols=40 Identities=15% Similarity=-0.072 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHH------hhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113 13 HSPVVKLLAVLRF------YATGNFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 13 ~~~~~~l~~~L~~------L~~~~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
++++++-++.++| +..+.+++.++...|||.+||+|+-+.
T Consensus 33 LTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~ 78 (94)
T TIGR01321 33 LTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNN 78 (94)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhh
Confidence 5666666666553 356789999999999999999987653
No 63
>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=91.72 E-value=0.52 Score=30.66 Aligned_cols=26 Identities=27% Similarity=0.353 Sum_probs=22.1
Q ss_pred CChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 30 NFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
.+..+++..++++++|+++++++...
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 58999999999999999999887654
No 64
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=91.71 E-value=0.48 Score=38.91 Aligned_cols=47 Identities=19% Similarity=0.169 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|-.
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~ 182 (196)
T PRK12524 136 ALPERQRQAVVLRHI-EGLSNPEIAEVMEIGVEAVESLTARGKRALAA 182 (196)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 578888888888877 78999999999999999999999998888765
No 65
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=91.70 E-value=0.46 Score=38.86 Aligned_cols=47 Identities=17% Similarity=0.058 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.|+++- |.++.++|..+|+|.+||...+.+....|-.
T Consensus 134 ~Lp~~~R~v~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 134 HLPAQQARVFMMREYL-ELSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred hCCHHHHHHHhHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4677788888888776 8999999999999999999999888887765
No 66
>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=91.66 E-value=0.37 Score=29.78 Aligned_cols=39 Identities=18% Similarity=0.113 Sum_probs=28.1
Q ss_pred HHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 17 VKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 17 ~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
.++-+.........+..+++..+|+|++|+++.++...+
T Consensus 3 ~R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 3 TRLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHH
Confidence 344554444445568999999999999999998876543
No 67
>PF13730 HTH_36: Helix-turn-helix domain
Probab=91.64 E-value=0.51 Score=30.05 Aligned_cols=43 Identities=23% Similarity=0.210 Sum_probs=32.0
Q ss_pred CCH-HHHHHHHHHHhhcC-----CChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 13 HSP-VVKLLAVLRFYATG-----NFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 13 ~~~-~~~l~~~L~~L~~~-----~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
+++ +..|.+.|..+..+ .++..++...|+|+.||.+++++..+
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 455 45566667666632 27789999999999999999987653
No 68
>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=91.61 E-value=0.14 Score=31.68 Aligned_cols=21 Identities=24% Similarity=0.251 Sum_probs=18.8
Q ss_pred ChHhhhhhccccHhHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~ 51 (286)
+.+++|...|||.+||+++++
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHh
Confidence 357899999999999999886
No 69
>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=91.61 E-value=0.52 Score=30.40 Aligned_cols=41 Identities=20% Similarity=0.276 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 15 PVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 15 ~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
..+-.++...+=..+.+..+++..++++++|+++++++...
T Consensus 3 ~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 3 PSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp HHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 33333333333344579999999999999999999886653
No 70
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=91.60 E-value=0.5 Score=38.54 Aligned_cols=47 Identities=19% Similarity=0.195 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|++++-++.|+++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus 131 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 131 KLSPAHREIIDLVYY-HEKSVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 578888888888877 88999999999999999999999988887765
No 71
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=91.56 E-value=0.45 Score=40.38 Aligned_cols=48 Identities=21% Similarity=0.188 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHHh---hcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFY---ATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++.++.|.|+ -.|.+++++|..+|+|.+||.+..++....|..
T Consensus 175 ~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~ 225 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFK 225 (233)
T ss_pred hCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 578889999999886 467899999999999999999988887777765
No 72
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=91.56 E-value=0.48 Score=38.33 Aligned_cols=48 Identities=15% Similarity=0.099 Sum_probs=41.4
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++-++.|.++. |.++.++|..+|+|.+||...+.+....|...
T Consensus 127 ~L~~~~r~v~~l~~~~-g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~ 174 (179)
T PRK09415 127 SLPIKYREVIYLFYYE-ELSIKEIAEVTGVNENTVKTRLKKAKELLKKG 174 (179)
T ss_pred hCCHHHhhHhHhHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5778888888888776 79999999999999999999999888887763
No 73
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=91.56 E-value=0.48 Score=39.82 Aligned_cols=48 Identities=17% Similarity=0.084 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++-++.|+|+ .+.++.++|..+|+|.+||...+++....|...
T Consensus 134 ~Lp~~~R~v~~L~y~-eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~ 181 (216)
T PRK12533 134 KLPVEYREVLVLREL-EDMSYREIAAIADVPVGTVMSRLARARRRLAAL 181 (216)
T ss_pred cCCHHHHhHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467778888888877 689999999999999999999999888877763
No 74
>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=91.52 E-value=0.5 Score=30.08 Aligned_cols=29 Identities=17% Similarity=0.024 Sum_probs=23.6
Q ss_pred CCChHhhhhhccccHhHHHHHHHHHHHHH
Q psy13113 29 GNFQIDSEDYHDISQSTICRLVAKVSEEL 57 (286)
Q Consensus 29 ~~~~~~l~~~Fgvs~stv~~~~~~v~~~l 57 (286)
+.+..++|..+|||+.||.+.++..-+.+
T Consensus 15 ~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 15 PITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp SBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 36889999999999999999998765544
No 75
>PF13551 HTH_29: Winged helix-turn helix
Probab=91.44 E-value=0.34 Score=35.65 Aligned_cols=35 Identities=23% Similarity=0.267 Sum_probs=30.2
Q ss_pred HHHHHhhcCCC-hHhhhhhccccHhHHHHHHHHHHH
Q psy13113 21 AVLRFYATGNF-QIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 21 ~~L~~L~~~~~-~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
.+|..+..|.+ ...+|..+|+|.+||+++++++..
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 35667888995 999999999999999999998753
No 76
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=91.41 E-value=0.6 Score=34.94 Aligned_cols=48 Identities=19% Similarity=0.153 Sum_probs=43.8
Q ss_pred CCCCCHHHHHHHHHHHhhcCCChHhhhhhccc-cHhHHHHHHHHHHHHH
Q psy13113 10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDI-SQSTICRLVAKVSEEL 57 (286)
Q Consensus 10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgv-s~stv~~~~~~v~~~l 57 (286)
+...|.|.++-++-.++..|.+...+|..||| +.+++++|+.+..+.-
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~ 53 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKGG 53 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHcc
Confidence 67899999999999999999999999999996 9999999998877643
No 77
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=91.40 E-value=0.58 Score=37.93 Aligned_cols=47 Identities=11% Similarity=0.111 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++.++.|. .-.|.++.++|..+|+|.+||...+++....|-.
T Consensus 133 ~L~~~~r~i~~l~-~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 133 QLEPARRNCILHA-YVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 4666677666666 4578999999999999999999999998887765
No 78
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=91.31 E-value=0.59 Score=38.35 Aligned_cols=47 Identities=11% Similarity=0.024 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|++++-++.|+++ .|.++.++|..+|+|.+||...+++....|-.
T Consensus 141 ~Lp~~~r~v~~l~~~-eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~ 187 (194)
T PRK12531 141 RLPKAQRDVLQAVYL-EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRH 187 (194)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 466677777777766 78999999999999999999988888877765
No 79
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=91.30 E-value=0.51 Score=42.18 Aligned_cols=69 Identities=12% Similarity=0.093 Sum_probs=50.7
Q ss_pred HHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHH-HHhhcccccCCch-hHHHHHHHhhhhcCCCCceEee
Q psy13113 19 LLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEE-LAKCHQQWIHFPE-DLQTAKNQFSGIAGFPRVVVGC 91 (286)
Q Consensus 19 l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~-l~~~~~~~i~~P~-~~~~~~~~f~~~~~~p~~~~g~ 91 (286)
+-++-+|+-.|.++.++|..+|+|+++|+|++.+.-+. |.+ --|.-|. ....+...+++++++..| +.+
T Consensus 19 ~~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~---I~I~~~~~~~~~Le~~L~~~fgLk~~-iVv 89 (318)
T PRK15418 19 ARIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIR---VQINSRFEGCLELENALRQHFSLQHI-RVL 89 (318)
T ss_pred HHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEE---EEEeCCCccHHHHHHHHHHHhCCCEE-EEE
Confidence 33677888899999999999999999999999876544 332 2233343 445566677888899988 554
No 80
>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=91.30 E-value=0.51 Score=41.06 Aligned_cols=48 Identities=8% Similarity=0.011 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHHHhh-cCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYA-TGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~-~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.||..++..+.|+|+. .+.++.++|..+|||..+|+++.++.+.-|-.
T Consensus 218 ~L~~rer~vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~ 266 (270)
T TIGR02392 218 SLDARSRRIIEARWLDDDKLTLQELAAEYGVSAERIRQIEKNAMKKLKA 266 (270)
T ss_pred cCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5888899999999974 47899999999999999999999888877754
No 81
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=91.23 E-value=0.6 Score=37.83 Aligned_cols=48 Identities=10% Similarity=-0.003 Sum_probs=41.4
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|++++-++.|.|+. |.++.++|..+|+|.+||...+.+....|-..
T Consensus 131 ~L~~~~r~v~~l~~~~-g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12512 131 TLPPRQRDVVQSISVE-GASIKETAAKLSMSEGAVRVALHRGLAALAAK 178 (184)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 5677777788887776 89999999999999999999999988888753
No 82
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=91.18 E-value=0.59 Score=38.20 Aligned_cols=48 Identities=13% Similarity=0.016 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.||+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 116 ~Lp~~~r~i~~L~~~-~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~ 163 (187)
T PRK12516 116 QLPDDQREAIILVGA-SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEI 163 (187)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467788888888777 789999999999999999999999888887763
No 83
>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=91.13 E-value=0.51 Score=38.31 Aligned_cols=50 Identities=16% Similarity=0.060 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcc
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQ 62 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~ 62 (286)
.+|++++-++.|.|+ .|.++.++|..+|+|.+||...+++....|-+.+.
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 456666666666665 78999999999999999999999999888876443
No 84
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=91.07 E-value=0.67 Score=36.50 Aligned_cols=48 Identities=13% Similarity=0.138 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++-++.|.++ .|.+++++|..+|+|.+||...+.+....|...
T Consensus 106 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 106 KLPARQREAFLLRYW-EDMDVAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred hCCHHHHHHHHHHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467777777777765 579999999999999999999999988888753
No 85
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=91.00 E-value=0.56 Score=37.45 Aligned_cols=47 Identities=11% Similarity=0.104 Sum_probs=40.3
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus 125 ~L~~~~r~i~~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 125 ALPVKQREVFLLRYV-EGLSYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred hCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 477787877777777 68999999999999999999999988877765
No 86
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=90.90 E-value=0.59 Score=37.97 Aligned_cols=48 Identities=23% Similarity=0.268 Sum_probs=41.5
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++-++.|.++. |.++.++|..+|+|..||...+++....|...
T Consensus 128 ~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 175 (186)
T PRK05602 128 ALPERQREAIVLQYYQ-GLSNIEAAAVMDISVDALESLLARGRRALRAQ 175 (186)
T ss_pred hCCHHHHHHhhHHHhc-CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 4688888888888775 89999999999999999999999888887763
No 87
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=90.85 E-value=0.7 Score=37.52 Aligned_cols=48 Identities=17% Similarity=0.169 Sum_probs=38.6
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|-..
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 455666666666654 789999999999999999999999888877653
No 88
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=90.85 E-value=0.55 Score=38.02 Aligned_cols=49 Identities=16% Similarity=0.208 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhc
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCH 61 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~ 61 (286)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|....
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 567777777777666 5799999999999999999999999888876543
No 89
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=90.82 E-value=0.63 Score=38.13 Aligned_cols=48 Identities=15% Similarity=0.030 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++.++.|+++ .|.++.++|..+|+|.+||...+.+....|-..
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 478888888877777 779999999999999999998888877777653
No 90
>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=90.75 E-value=0.53 Score=30.45 Aligned_cols=44 Identities=20% Similarity=0.180 Sum_probs=34.4
Q ss_pred CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
++..+.- +|.+++.|.+..++|...|+|.+||......+..-|.
T Consensus 4 LT~~E~~--vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 4 LTERELE--VLRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp S-HHHHH--HHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred cCHHHHH--HHHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 4444433 6777999999999999999999999999988877664
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=90.69 E-value=0.25 Score=38.69 Aligned_cols=47 Identities=13% Similarity=0.117 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-+
T Consensus 105 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 105 RLPENYRTVLILREF-KEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hCCHhheeeeeehhh-ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 356666666666666 68999999999999999999999988877765
No 92
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=90.59 E-value=0.6 Score=38.13 Aligned_cols=51 Identities=16% Similarity=0.102 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhccc
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQ 63 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~ 63 (286)
.+|++++-++.|.++ .|.++.++|..+|+|..||...+.+....|-.....
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 457777777777776 779999999999999999999999988888764433
No 93
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=90.57 E-value=0.58 Score=41.06 Aligned_cols=48 Identities=6% Similarity=-0.005 Sum_probs=42.1
Q ss_pred CCCHHHHHHHHHHHhh-cCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYA-TGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~-~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.++..++..+.++|+. .+.++.++|..+|||+++|+++.++.+.-|-.
T Consensus 230 ~L~~rEr~VL~lry~~~~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~ 278 (284)
T PRK06596 230 GLDERSRDIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAMKKLKA 278 (284)
T ss_pred cCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5888899999999975 57899999999999999999999988877754
No 94
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=90.53 E-value=0.72 Score=39.78 Aligned_cols=48 Identities=21% Similarity=0.150 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+++.++.++.|+|+ .+.++.++|..+|+|.+||++..++....|-..
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 478888888888886 588999999999999999999999988877653
No 95
>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=90.39 E-value=0.78 Score=36.22 Aligned_cols=48 Identities=15% Similarity=0.124 Sum_probs=40.7
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|++++.++.|.+ -.|.++.++|..+|+|.+||...+.+....|-..
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 45778888877777 4589999999999999999999999988887653
No 96
>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=90.35 E-value=0.7 Score=39.60 Aligned_cols=47 Identities=26% Similarity=0.215 Sum_probs=40.3
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|..++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus 161 ~Lp~~~R~v~~L~~~-eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~ 207 (244)
T TIGR03001 161 ALSERERHLLRLHFV-DGLSMDRIGAMYQVHRSTVSRWVAQARERLLE 207 (244)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 467777777777776 78999999999999999999999998888775
No 97
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=90.07 E-value=0.83 Score=37.39 Aligned_cols=49 Identities=10% Similarity=0.010 Sum_probs=43.2
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhc
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCH 61 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~ 61 (286)
.+|+.++-++.|+++ .|.++.++|..+|+|.+||...+.+....|-..+
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 578888888888888 8899999999999999999999999988887643
No 98
>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=90.06 E-value=0.66 Score=30.61 Aligned_cols=40 Identities=18% Similarity=0.246 Sum_probs=30.3
Q ss_pred HHHHHHHHHHhhc----------CCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 16 VVKLLAVLRFYAT----------GNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 16 ~~~l~~~L~~L~~----------~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
+++++-.|..|.. ..+..+++..+|+|++|++++++....
T Consensus 2 ~~ria~~l~~l~~~~~~~~~~~~~~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 2 KERLASFLLNLSLRYGAGDLVQLPLTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred chHHHHHHHHHHHHcCCCccccCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3566666665542 248889999999999999998887654
No 99
>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=90.03 E-value=0.98 Score=36.55 Aligned_cols=47 Identities=15% Similarity=0.106 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.|.++ .|.++.++|...|+|.+||...+++....|-.
T Consensus 140 ~L~~~~r~vi~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 140 KLPEDYREVILLRHL-EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 567777777777776 78999999999999999999999988877754
No 100
>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=90.03 E-value=0.92 Score=38.20 Aligned_cols=47 Identities=21% Similarity=0.324 Sum_probs=40.8
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.|+|+ .|.++.++|..+|+|.+||+...++....|-.
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 578888888888776 57899999999999999999999998887754
No 101
>PRK05572 sporulation sigma factor SigF; Validated
Probab=90.03 E-value=0.88 Score=39.10 Aligned_cols=47 Identities=21% Similarity=0.323 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|..++.++.|+|+ .+.++.++|..+|+|.+||+++.++.+..|-.
T Consensus 202 ~L~~~~~~v~~l~~~-~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~ 248 (252)
T PRK05572 202 ELDERERLIVYLRYF-KDKTQSEVAKRLGISQVQVSRLEKKILKQMKE 248 (252)
T ss_pred cCCHHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 688888888888876 57899999999999999999999999888765
No 102
>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=89.98 E-value=0.32 Score=33.04 Aligned_cols=42 Identities=17% Similarity=0.086 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhcc-ccHhHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHD-ISQSTICRLVAKV 53 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fg-vs~stv~~~~~~v 53 (286)
.+.-..++++.|.+-.++.++.+++..|| .+.|||...++++
T Consensus 28 ~i~~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHstV~~a~~ki 70 (70)
T PF08299_consen 28 KIVEARQVAMYLARELTGLSLSEIGRYFGGRDHSTVIHAIRKI 70 (70)
T ss_dssp HHHHHHHHHHHHHHHHS---HHHHHHHCTSSTHHHHHHHHHHH
T ss_pred hhcchHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHHhC
Confidence 45567888888888888999999999999 9999999888764
No 103
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=89.96 E-value=0.85 Score=37.21 Aligned_cols=48 Identities=13% Similarity=0.117 Sum_probs=41.9
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
..+|++++-++.|+|+ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus 130 ~~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 130 NDLEKLDREIFIRRYL-LGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred HhCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3588888888888886 67999999999999999999999988877764
No 104
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=89.93 E-value=0.88 Score=36.98 Aligned_cols=48 Identities=15% Similarity=-0.005 Sum_probs=41.5
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 111 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~ 158 (182)
T PRK12540 111 KLPQDQREALILVGA-SGFSYEDAAAICGCAVGTIKSRVNRARSKLSAL 158 (182)
T ss_pred hCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 567788888888776 889999999999999999999999888888763
No 105
>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=89.91 E-value=0.93 Score=36.11 Aligned_cols=48 Identities=13% Similarity=0.162 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|..++-++.|.++. |.++.++|..+|+|.+||...+.+....|...
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 5777777777777765 79999999999999999999999888887653
No 106
>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=89.80 E-value=0.75 Score=39.17 Aligned_cols=48 Identities=8% Similarity=0.105 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHHHHh---hcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFY---ATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++..+.|+|. ..+.+++.+|..+|||.++|+++..+.+.-|-.
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 578889999999984 467899999999999999999999988877764
No 107
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=89.79 E-value=0.87 Score=37.29 Aligned_cols=48 Identities=17% Similarity=0.162 Sum_probs=40.3
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 183 (195)
T PRK12532 136 NLPENTARVFTLKEI-LGFSSDEIQQMCGISTSNYHTIMHRARESLRQC 183 (195)
T ss_pred hCCHHHHHHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 466777777777776 688999999999999999999999988888763
No 108
>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=89.73 E-value=1.2 Score=34.39 Aligned_cols=48 Identities=17% Similarity=0.096 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHHhhc-CCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYAT-GNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~-~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.++.+++-++-+.|+.. ..++..+|..+|+|++|+++.-+.++..+..
T Consensus 82 ~Ld~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~ 130 (134)
T TIGR01636 82 EADEQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAE 130 (134)
T ss_pred hCCHHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 37788888999988754 3499999999999999999998888887765
No 109
>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=89.72 E-value=0.91 Score=38.51 Aligned_cols=49 Identities=33% Similarity=0.273 Sum_probs=42.1
Q ss_pred CCCHHHHHHHHHHHh---hcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFY---ATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++.++.|+++ -.|.++.++|...|+|.+||.....+....|-..
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 578888899999885 3688999999999999999999988888777653
No 110
>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=89.71 E-value=0.35 Score=36.53 Aligned_cols=30 Identities=13% Similarity=0.289 Sum_probs=26.5
Q ss_pred HHhhcCCChHhhhhhccccHhHHHHHHHHH
Q psy13113 24 RFYATGNFQIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 24 ~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v 53 (286)
.+...|.+...+|..|+||.+||.+|+.+.
T Consensus 13 ~~~~~g~s~~eaa~~F~VS~~Tv~~W~k~~ 42 (119)
T PF01710_consen 13 AYIEKGKSIREAAKRFGVSRNTVYRWLKRK 42 (119)
T ss_pred HHHHccchHHHHHHHhCcHHHHHHHHHHhc
Confidence 577788899999999999999999998743
No 111
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=89.63 E-value=0.96 Score=35.30 Aligned_cols=46 Identities=11% Similarity=0.151 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
.+|+.++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-
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 578888888888776 4689999999999999999999988777663
No 112
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=89.60 E-value=1.5 Score=37.23 Aligned_cols=68 Identities=10% Similarity=0.068 Sum_probs=50.8
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcccccCCch---hHHHHHHHhhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPE---DLQTAKNQFSG 80 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~~i~~P~---~~~~~~~~f~~ 80 (286)
.+|+.++.++.|.++- |.+++++|...|+|.+||...+.+....|-.....-..-+. +.+.+...|.+
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 5778888877777654 79999999999999999999999999888875544333222 45555555554
No 113
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=89.56 E-value=1 Score=37.46 Aligned_cols=48 Identities=15% Similarity=0.081 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++-++.|.++- |.++.++|..+|+|.+||...+++....|-+.
T Consensus 148 ~L~~~~r~v~~L~~~~-g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~ 195 (206)
T PRK12544 148 GLPAKYARVFMMREFI-ELETNEICHAVDLSVSNLNVLLYRARLRLREC 195 (206)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4666777777776654 89999999999999999999999998888763
No 114
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=89.51 E-value=1 Score=38.81 Aligned_cols=47 Identities=21% Similarity=0.189 Sum_probs=40.0
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.|+|+ .|.++.++|..+|||.+||....++....|-.
T Consensus 205 ~L~~~~r~vl~l~~~-~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~ 251 (257)
T PRK08583 205 VLSDREKSIIQCTFI-ENLSQKETGERLGISQMHVSRLQRQAIKKLRE 251 (257)
T ss_pred hCCHHHHHHHHHHHh-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 467777777777775 68899999999999999999999998888764
No 115
>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=89.40 E-value=1.1 Score=37.82 Aligned_cols=47 Identities=21% Similarity=0.331 Sum_probs=40.0
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|..++.++.|+|+ .+.++.++|..+|+|.++|+++.++...-|-.
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 577888888888765 57899999999999999999999988877754
No 116
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=89.31 E-value=1.1 Score=38.69 Aligned_cols=47 Identities=28% Similarity=0.383 Sum_probs=40.5
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+++.++.++.++|+ .|.++.++|..+|+|.++|+++.++...-|-.
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 678888888888775 57899999999999999999999988877754
No 117
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=89.29 E-value=1.1 Score=35.77 Aligned_cols=47 Identities=11% Similarity=-0.010 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....+..
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 467778888888776 57999999999999999999998887776654
No 118
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=89.27 E-value=0.86 Score=40.10 Aligned_cols=48 Identities=15% Similarity=0.055 Sum_probs=42.8
Q ss_pred CCCHHHHHHHHHHHhh-cCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYA-TGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~-~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++..+.|+|+. .+.++.++|..+|||.++|..+.++.+.-|-.
T Consensus 227 ~L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~ 275 (289)
T PRK07500 227 TLNERELRIIRERRLREDGATLEALGEELGISKERVRQIEARALEKLRR 275 (289)
T ss_pred cCCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5889999999999863 67899999999999999999999998888875
No 119
>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=89.07 E-value=2.1 Score=37.40 Aligned_cols=67 Identities=16% Similarity=0.117 Sum_probs=48.1
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcccccCCchhHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPEDLQTAKNQFS 79 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~~i~~P~~~~~~~~~f~ 79 (286)
.+|+.++-++.|+++ .+.+++++|..+|+|.+||...+++....|-+..+..-.-|.+.+.+...|.
T Consensus 108 ~L~~~~R~v~~L~~~-~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~f~ 174 (281)
T TIGR02957 108 RLSPLERAVFVLREV-FDYPYEEIASIVGKSEANCRQLVSRARRHLDARRPRFEVSREESRQLLERFV 174 (281)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCCCCCChHHHHHHHHHHH
Confidence 466666666666544 5789999999999999999999999999998755543222224445555554
No 120
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=89.04 E-value=1.1 Score=36.27 Aligned_cols=49 Identities=14% Similarity=0.028 Sum_probs=42.4
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
..+|+.++-++.|.++. |.++.++|..+|+|.+||...+++....|-..
T Consensus 130 ~~L~~~~r~v~~l~~~~-g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 130 ARLPEKMRLAIQAVKLE-GLSVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred HhCCHHHHHHHHHHHHc-CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 35788888888888874 89999999999999999999999998888763
No 121
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=89.03 E-value=1.1 Score=35.39 Aligned_cols=46 Identities=22% Similarity=0.062 Sum_probs=37.7
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
.+|++++-++.|.++ .|.++.++|..+|+|.+||...+.+....|.
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 467777777777665 5799999999999999999999988876654
No 122
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=89.00 E-value=1.2 Score=35.49 Aligned_cols=47 Identities=17% Similarity=0.123 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|-.
T Consensus 118 ~L~~~~r~vl~L~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 118 QLSPEHRAVLVRSYY-RGWSTAQIAADLGIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 467777777777665 47999999999999999999988888877765
No 123
>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=88.97 E-value=0.97 Score=32.10 Aligned_cols=37 Identities=14% Similarity=0.118 Sum_probs=29.9
Q ss_pred HHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113 16 VVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 16 ~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
.+++.++=-.|..|.+|++++...|+|-.|++|.-+.
T Consensus 36 ~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr~ 72 (87)
T PF01371_consen 36 AQRWQVAKELLDEGKSYREIAEETGVSIATITRVSRC 72 (87)
T ss_dssp HHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 3455555557889999999999999999999986543
No 124
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=88.91 E-value=1.1 Score=36.49 Aligned_cols=47 Identities=11% Similarity=0.026 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.|.++ .|.+++++|..+|+|.+||...+.+....|..
T Consensus 131 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (191)
T PRK12520 131 RLPPRTGRVFMMREW-LELETEEICQELQITATNAWVLLYRARMRLRE 177 (191)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 467777777777765 46899999999999999999999988888765
No 125
>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=88.80 E-value=1.4 Score=35.60 Aligned_cols=46 Identities=22% Similarity=0.167 Sum_probs=39.3
Q ss_pred CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus 135 Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFF-AGLTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 77787877777766 56899999999999999999999988887764
No 126
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=88.73 E-value=1.6 Score=31.64 Aligned_cols=41 Identities=15% Similarity=0.190 Sum_probs=33.5
Q ss_pred HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+--+-| |+....|...+|..|+||++.|+..|+++...|..
T Consensus 23 ~~Y~~l-yy~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~ 63 (105)
T COG2739 23 KNYLEL-YYLDDLSLSEIAEEFNVSRQAIYDNIKRTEKILED 63 (105)
T ss_pred HHHHHH-HHHhhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 333444 44466899999999999999999999999998874
No 127
>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=88.66 E-value=1.2 Score=36.35 Aligned_cols=48 Identities=17% Similarity=0.068 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++-++.|.|+ .|.+++++|..+|+|.+||...+.+....|-..
T Consensus 131 ~L~~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 131 HLPEQTARVFMMREV-LGFESDEICQELEISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred hCCHHHHHHHHHHHH-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 345555666666655 479999999999999999999999888888764
No 128
>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=88.64 E-value=1.2 Score=38.23 Aligned_cols=48 Identities=23% Similarity=0.346 Sum_probs=41.2
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
..+++.++.++.++|+ .+.++.++|..+|+|.++|+++.++.+.-|..
T Consensus 205 ~~L~~rer~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~ 252 (254)
T TIGR02850 205 KRLNEREKMILNMRFF-EGKTQMEVAEEIGISQAQVSRLEKAALKHMRK 252 (254)
T ss_pred HcCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 3688888888888875 57899999999999999999999988877653
No 129
>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=88.61 E-value=1.2 Score=37.61 Aligned_cols=49 Identities=16% Similarity=0.146 Sum_probs=41.5
Q ss_pred CCCCHHHHHHHHHHHh---hcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 11 VIHSPVVKLLAVLRFY---ATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L---~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
..+|+.++-++.|+|+ ..+.++.++|...|+|.+||....++....|-.
T Consensus 173 ~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 173 SVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred HhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4577888888888876 378899999999999999999998888877754
No 130
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=88.53 E-value=1.2 Score=36.18 Aligned_cols=48 Identities=15% Similarity=-0.058 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|++++.++.|.++ .|.++.++|..+|+|.+||...+.+....|-+.
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 567777777777664 678999999999999999999998888777653
No 131
>PRK06930 positive control sigma-like factor; Validated
Probab=88.37 E-value=1.4 Score=35.50 Aligned_cols=47 Identities=17% Similarity=0.294 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.|. +..|.++.++|..+|+|.+||...+.+....|-.
T Consensus 114 ~L~~rer~V~~L~-~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 114 VLTEREKEVYLMH-RGYGLSYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5667666666665 4688999999999999999999999988887765
No 132
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=88.32 E-value=1.2 Score=35.65 Aligned_cols=52 Identities=12% Similarity=0.148 Sum_probs=39.1
Q ss_pred CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhccccc
Q psy13113 13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWI 65 (286)
Q Consensus 13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~~i 65 (286)
+|+..+-++.| +.-.|.+++++|...|+|.+||...+.+....|...+..+|
T Consensus 120 L~~~~r~i~~l-~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~~ 171 (173)
T PRK12522 120 LNEKYKTVLVL-YYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEGFV 171 (173)
T ss_pred CCHHHHHHHHH-HHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 44444433333 34467999999999999999999999999988887655554
No 133
>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=88.17 E-value=1.1 Score=39.23 Aligned_cols=49 Identities=6% Similarity=0.034 Sum_probs=42.6
Q ss_pred CCCHHHHHHHHHHH-h--hcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRF-Y--ATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~-L--~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.||..++..+.|+| | -.+.+++++|..+|+|.+||....++....|-..
T Consensus 222 ~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~ 273 (285)
T TIGR02394 222 ELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRI 273 (285)
T ss_pred cCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57888888999988 4 4678999999999999999999999988888764
No 134
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=88.15 E-value=1.3 Score=37.57 Aligned_cols=48 Identities=10% Similarity=0.051 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++-++.|.|+ .|.++.++|..+|+|.+||...+++....|-..
T Consensus 184 ~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 184 SLPEREQLVLSLYYQ-EELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred hCCHHHHHHHHhHhc-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467777777777764 678999999999999999999999888887653
No 135
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=88.02 E-value=2.7 Score=36.96 Aligned_cols=67 Identities=12% Similarity=0.028 Sum_probs=47.9
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcccccCCchhHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPEDLQTAKNQFS 79 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~~i~~P~~~~~~~~~f~ 79 (286)
.+|+.++-++.|+++ .+.++.++|..+|+|.+||...+.+....|-+..+..-.-|.+-.++...|.
T Consensus 115 ~L~~~~R~v~~L~~~-~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~~~~~~~~~~~~~v~~f~ 181 (293)
T PRK09636 115 RLSPLERAAFLLHDV-FGVPFDEIASTLGRSPAACRQLASRARKHVRAARPRFPVSDEEGAELVEAFF 181 (293)
T ss_pred hCCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCCCCCCchHHHHHHHHHH
Confidence 466776766666655 4699999999999999999999999999998765543222223334444443
No 136
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=88.00 E-value=1.3 Score=29.37 Aligned_cols=43 Identities=19% Similarity=0.127 Sum_probs=38.5
Q ss_pred HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
++-.+..+|....+..+.|...|++..++.+++..+-..+.++
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 3446788999999999999999999999999999999998875
No 137
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=87.84 E-value=1.8 Score=34.48 Aligned_cols=47 Identities=11% Similarity=-0.003 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++.++.|.+ -.|.++.++|..+|+|.+||...+.+....+..
T Consensus 118 ~L~~~~r~v~~L~~-~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 118 GLSGKARAAFLMSQ-LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 47888888777775 567999999999999999999998888777654
No 138
>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=87.80 E-value=1.2 Score=28.05 Aligned_cols=38 Identities=21% Similarity=0.237 Sum_probs=27.6
Q ss_pred HHHHHHHHhhcC---CChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 18 KLLAVLRFYATG---NFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 18 ~l~~~L~~L~~~---~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
+.+-.|..++.. .+..+++...|++++|+++++.....
T Consensus 4 ral~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 4 RALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp HHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 445555566543 36899999999999999999876553
No 139
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=87.78 E-value=1.3 Score=39.57 Aligned_cols=48 Identities=19% Similarity=0.152 Sum_probs=42.5
Q ss_pred CCCHHHHHHHHHHHh---hcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFY---ATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++..+.|+|. ..+.++.++|..+|||+.+|..+..+...-|-.
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 588999999999986 466899999999999999999999988887765
No 140
>COG3293 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=87.71 E-value=0.33 Score=36.80 Aligned_cols=97 Identities=15% Similarity=0.146 Sum_probs=63.0
Q ss_pred ceeeecCCCccEEEeccCCCCccccccccccchhhhhccccccceEEEccccCCCCCcccccccCCCC---CC--hhhHH
Q psy13113 120 NVQVIGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDRREIRGLLLGDIGYAQNEFTFTPVRNPIT---PT--PSQVA 194 (286)
Q Consensus 120 ~~q~vvd~~g~i~~~~~~~~Gs~~D~~~~~~s~l~~~l~~~~~~~~llgD~gY~~~~~l~~p~~~~~~---l~--~~~~~ 194 (286)
+.+.++|..|+++....+ +|..+ ..... ..+-+ .+ -.-+|+|.+|....+...|-..+.. .. ..+.-
T Consensus 2 ~~~~l~D~~~~~i~~~lp-~~~~~-~~~~~-~~~~~--~~---v~~~i~~~~~~g~~wr~~p~~~~~~~~~~~~~~~~~~ 73 (124)
T COG3293 2 KLHALVDAEWRPVEPLLP-PAKYG-GPPGV-TLLRD--RE---VLNGIADLLYTGCAWRALPADFPPATTVIPYRRFRRW 73 (124)
T ss_pred CcccccccccceeeccCC-CcccC-CCCCC-ccccc--HH---HHHHHHHHhccchHHHHhHHHhCCCceEeCCCcchhh
Confidence 467899999999998886 44433 21111 00100 01 1256789999887776544433211 11 23677
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhhhhhhcccc
Q psy13113 195 YNAAQIRTRNSVERLFGVLKRRFACLRKKLA 225 (286)
Q Consensus 195 ~N~~~~~~R~~vE~~~~~lK~rf~~L~~~~~ 225 (286)
++..+...|..+|+.|+.+|. |+.+...++
T Consensus 74 ~~~g~~~~~~~~~~~f~~~~~-~r~~~~~~~ 103 (124)
T COG3293 74 FKRGLWKRRNLVERTFGRLKQ-FRRTATRYD 103 (124)
T ss_pred HHHHHHHHHHHHHHHHHHHhc-ccceecchh
Confidence 899999999999999999998 888876533
No 141
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=87.47 E-value=1.5 Score=35.56 Aligned_cols=48 Identities=17% Similarity=0.164 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|++++-++.|.++ .|.++.++|...|||.+||...+++....|...
T Consensus 127 ~Lp~~~R~~~~l~~~-~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~ 174 (182)
T COG1595 127 RLPPRQREAFLLRYL-EGLSYEEIAEILGISVGTVKSRLHRARKKLREQ 174 (182)
T ss_pred hCCHHHhHHhhhHhh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467777777777776 568999999999999999999999988888764
No 142
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=87.47 E-value=1.7 Score=37.33 Aligned_cols=47 Identities=19% Similarity=0.111 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.|.|+ .+.+++++|..+|+|.+||...+++....|-.
T Consensus 201 ~L~~~~r~vl~l~~~-~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 201 QLSEKEQLVISLFYK-EELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 467778888888775 78899999999999999999999888877754
No 143
>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=87.33 E-value=2.1 Score=27.83 Aligned_cols=39 Identities=26% Similarity=0.229 Sum_probs=30.3
Q ss_pred HHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 20 LAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 20 ~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
-+++....+ .++...|...++|++++++.++++...+..
T Consensus 5 ~~f~~v~~~-gs~~~AA~~l~is~~~vs~~i~~LE~~lg~ 43 (60)
T PF00126_consen 5 RYFLAVAET-GSISAAAEELGISQSAVSRQIKQLEEELGV 43 (60)
T ss_dssp HHHHHHHHH-SSHHHHHHHCTSSHHHHHHHHHHHHHHHTS
T ss_pred HHHHHHHHh-CCHHHHHHHhhccchHHHHHHHHHHHHhCC
Confidence 333333444 489999999999999999999988877764
No 144
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=87.05 E-value=1.6 Score=37.43 Aligned_cols=47 Identities=30% Similarity=0.294 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.++-.+|+.+.|+| -.+.++..+|...|||++.||++.++.+..|-.
T Consensus 196 ~L~EREk~Vl~l~y-~eelt~kEI~~~LgISes~VSql~kkai~kLr~ 242 (247)
T COG1191 196 PLPEREKLVLVLRY-KEELTQKEIAEVLGISESRVSRLHKKAIKKLRK 242 (247)
T ss_pred ccCHHHHHHHHHHH-HhccCHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 67888999999998 456899999999999999999999998888765
No 145
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=87.01 E-value=2 Score=33.83 Aligned_cols=48 Identities=6% Similarity=-0.042 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 106 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 106 ELPENYRDVVLAHYL-EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred hCCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356666666666554 679999999999999999999888888777653
No 146
>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=87.00 E-value=2 Score=31.39 Aligned_cols=40 Identities=10% Similarity=0.152 Sum_probs=30.7
Q ss_pred HHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 20 LAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 20 ~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
-+.-.|+-.+.|...+|..+|||+.+|+..+++....|..
T Consensus 24 ~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~ 63 (101)
T PF04297_consen 24 EILELYYEEDLSLSEIAEELGISRQAVYDSIKRAEKKLEE 63 (101)
T ss_dssp HHHHHHCTS---HHHHHHHCTS-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3444566778999999999999999999999999988875
No 147
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=86.96 E-value=1.8 Score=35.21 Aligned_cols=47 Identities=9% Similarity=0.054 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.|.|+. |.++.++|..+|+|.+||...+++....|-.
T Consensus 139 ~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 139 TLPEKQREILILRVVV-GLSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5677777777777665 7899999999999999999999888777754
No 148
>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=86.86 E-value=1.8 Score=37.18 Aligned_cols=47 Identities=23% Similarity=0.174 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-.+.|+|+ .|.++.++|..+|+|.+||....++....|-.
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 567888888888775 67899999999999999999999888877754
No 149
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=86.85 E-value=1.8 Score=30.43 Aligned_cols=40 Identities=33% Similarity=0.338 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhhc---CCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 16 VVKLLAVLRFYAT---GNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 16 ~~~l~~~L~~L~~---~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
-++.+-.|.+|.. +.+..+++..+|++++|+++++.....
T Consensus 4 ~~r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 4 LERGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred HHHHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3455556666664 368999999999999999999987754
No 150
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=86.83 E-value=2.1 Score=34.66 Aligned_cols=47 Identities=13% Similarity=0.199 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|..++-++.|+++ .|.++.++|..+|+|.+||...+++....|-.
T Consensus 135 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 135 ALSPEERRVIEVLYY-QGYTHREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 467777777777764 57899999999999999999999988887765
No 151
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=86.78 E-value=1.6 Score=35.47 Aligned_cols=47 Identities=17% Similarity=0.044 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
++|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-+
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 467777777777766 56889999999999999999999988887764
No 152
>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=86.75 E-value=1.5 Score=29.71 Aligned_cols=26 Identities=19% Similarity=0.351 Sum_probs=22.4
Q ss_pred CChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 30 NFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
.+..++|...|+|..|++++++++.+
T Consensus 29 lt~~~iA~~~g~sr~tv~r~l~~l~~ 54 (76)
T PF13545_consen 29 LTQEEIADMLGVSRETVSRILKRLKD 54 (76)
T ss_dssp SSHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 36889999999999999999887654
No 153
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=86.69 E-value=2.1 Score=33.71 Aligned_cols=48 Identities=15% Similarity=0.068 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|++++-++.|.+ -.|.++.++|..+|+|.+||...+.+....|-..
T Consensus 105 ~L~~~~r~v~~l~~-~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 105 ELPPACRDSFLLRK-LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 46677666666654 5779999999999999999999999888887653
No 154
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=86.68 E-value=1.7 Score=35.76 Aligned_cols=47 Identities=17% Similarity=0.189 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++-++.| ++ .|.+++++|..+|+|.+||...+.+....|-..
T Consensus 155 ~L~~~~r~vl~l-~~-e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 155 LLSELEKEVLEL-YL-DGKSYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred hCCHHHHHHHHH-HH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 567777777777 55 789999999999999999999998888777653
No 155
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=86.67 E-value=1.8 Score=37.50 Aligned_cols=47 Identities=28% Similarity=0.316 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.|+|+ .+.++.++|..+|+|.+||.++.++....|-.
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 567777888888875 58899999999999999999999988877754
No 156
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=86.56 E-value=2.1 Score=34.67 Aligned_cols=50 Identities=2% Similarity=0.014 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcc
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQ 62 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~ 62 (286)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-....
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 356666666555544 66999999999999999999999998888876443
No 157
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=86.48 E-value=2 Score=34.65 Aligned_cols=47 Identities=15% Similarity=0.043 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++.++.|.++ .|.+++++|..+|+|.+||...+++....|..
T Consensus 129 ~L~~~~r~v~~l~~~-~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 129 QLPDRQRLPIVHVKL-EGLSVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 466666766666554 67999999999999999999999988887765
No 158
>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=86.47 E-value=1.1 Score=25.36 Aligned_cols=25 Identities=24% Similarity=0.462 Sum_probs=19.6
Q ss_pred CChHhhhhhccccHhHHHHHHHHHH
Q psy13113 30 NFQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
.+.+++|...|++..||+|++..+.
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 4678999999999999999988654
No 159
>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=86.38 E-value=2.2 Score=35.82 Aligned_cols=47 Identities=13% Similarity=0.165 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.|+|+ .+.++.++|..+|+|.+||....++....|-.
T Consensus 175 ~L~~~~r~il~l~y~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 175 SLSEREQLVLSLYYY-EELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred hCCHHHHHHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 467777777888775 67899999999999999999999888777654
No 160
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=86.33 E-value=2.1 Score=31.95 Aligned_cols=48 Identities=21% Similarity=0.095 Sum_probs=38.2
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
..++.+++- ....++.+.++.++++..+|||=+||..-+.+++.+|.-
T Consensus 32 ~~L~~E~~~-Fi~~Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 32 ARLSPEQLE-FIKLFIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred hcCCHHHHH-HHHHHHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 445655554 455566677899999999999999999999999988864
No 161
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=86.23 E-value=3.6 Score=36.20 Aligned_cols=67 Identities=13% Similarity=0.068 Sum_probs=46.7
Q ss_pred CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcccccCCchhHHHHHHHhhh
Q psy13113 13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPEDLQTAKNQFSG 80 (286)
Q Consensus 13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~~i~~P~~~~~~~~~f~~ 80 (286)
+|+.++-++.|+++ .|.++.++|...|+|.+||...+.+....|-...+.+-.-|.+.+.+...|..
T Consensus 119 L~p~~R~vf~L~~~-~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~f~~ 185 (290)
T PRK09635 119 LGPAERVVFVLHEI-FGLPYQQIATTIGSQASTCRQLAHRARRKINESRIAASVEPAQHRVVTRAFIE 185 (290)
T ss_pred CCHHHHHHhhHHHH-hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhCCCCCCChHHHHHHHHHHHH
Confidence 44555555544443 58999999999999999999999999999887554432222244556666643
No 162
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=86.22 E-value=2 Score=28.89 Aligned_cols=41 Identities=12% Similarity=0.137 Sum_probs=31.3
Q ss_pred CHHHHHHHHHHHhhc-CCChHhhhhhccccHhHHHHHHHHHH
Q psy13113 14 SPVVKLLAVLRFYAT-GNFQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 14 ~~~~~l~~~L~~L~~-~~~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
+.+++++.+|..-+. +.+..+||...|++.++|++.+....
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~ 47 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLE 47 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 456777777765544 47899999999999999998776443
No 163
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=86.06 E-value=2 Score=33.88 Aligned_cols=47 Identities=13% Similarity=0.044 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++.++.|.++ .|.++.++|..+|+|.+||...+.+....|-+
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 577888887777766 56899999999999999999999988877754
No 164
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=85.88 E-value=2.1 Score=34.45 Aligned_cols=48 Identities=13% Similarity=0.117 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++-++.|.++ .|.+++++|..+|+|.+||...+++....|-..
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 477878877777655 568999999999999999999888888777653
No 165
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=85.72 E-value=2.2 Score=33.76 Aligned_cols=48 Identities=8% Similarity=-0.083 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 108 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 155 (165)
T PRK09644 108 TLPVIEAQAILLCDV-HELTYEEAASVLDLKLNTYKSHLFRGRKRLKAL 155 (165)
T ss_pred hCCHHHHHHHHhHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467777776666655 568999999999999999999999988887653
No 166
>PF13751 DDE_Tnp_1_6: Transposase DDE domain
Probab=85.67 E-value=0.37 Score=36.54 Aligned_cols=48 Identities=23% Similarity=0.297 Sum_probs=36.4
Q ss_pred HHHHHHHHH-HHHHHHHHHHhhhhhhhccccC-CccchHHHHHHHHHHHhhh
Q psy13113 196 NAAQIRTRN-SVERLFGVLKRRFACLRKKLAN-QPTTCSHIITACAVLHNIA 245 (286)
Q Consensus 196 N~~~~~~R~-~vE~~~~~lK~rf~~L~~~~~~-~~~~~~~ii~a~~~LhN~~ 245 (286)
.+.+.+.|. .||.+||.||. +--+. .+++ ...++..-+...++.|||-
T Consensus 73 ~k~~y~~R~~~VE~~fg~~K~-~~g~~-r~~~rG~~kv~~~~~l~a~a~Nl~ 122 (125)
T PF13751_consen 73 GKELYKQRSIKVEGVFGTIKR-NHGLR-RFRYRGLEKVRIEFLLAAIAYNLK 122 (125)
T ss_pred hhhhhheeecccccccccchh-ccCCc-cccccchhhhHHHHHHHHHHHHHH
Confidence 456778888 99999999999 44444 2343 6677778888888889985
No 167
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=85.45 E-value=1.3 Score=29.21 Aligned_cols=33 Identities=33% Similarity=0.264 Sum_probs=23.5
Q ss_pred HHHHHHHh--hcCCChHhhhhhccccHhHHHHHHH
Q psy13113 19 LLAVLRFY--ATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 19 l~~~L~~L--~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
|+..|..+ +.|.++.++|...|+|.+|++++-+
T Consensus 2 lg~~lr~~R~~~gls~~~lA~~~g~s~s~v~~iE~ 36 (64)
T PF13560_consen 2 LGRRLRRLRERAGLSQAQLADRLGVSQSTVSRIER 36 (64)
T ss_dssp HHHHHHHHHHCHTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 33344444 4678999999999999999998754
No 168
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=85.38 E-value=3.2 Score=37.07 Aligned_cols=69 Identities=25% Similarity=0.269 Sum_probs=47.1
Q ss_pred HHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcccccCCch-hHHHHHHHhhhhcCCCCceEeee
Q psy13113 21 AVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPE-DLQTAKNQFSGIAGFPRVVVGCI 92 (286)
Q Consensus 21 ~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~~i~~P~-~~~~~~~~f~~~~~~p~~~~g~i 92 (286)
++-.|+-.|.++.++|..+|+|+.||+|.+....+. -+..-.|..|. ..-.+....+++++++.| +.+-
T Consensus 18 ~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~--GiV~I~i~~~~~~~~~Le~~L~~~fgL~~a-~VVp 87 (321)
T COG2390 18 AAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREE--GIVKISINSPVEGCLELEQQLKERFGLKEA-IVVP 87 (321)
T ss_pred HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHC--CeEEEEeCCCCcchHHHHHHHHHhcCCCeE-EEEc
Confidence 455677788999999999999999999988765432 02333344333 333455566777888888 5543
No 169
>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=85.32 E-value=2.5 Score=27.44 Aligned_cols=44 Identities=14% Similarity=0.009 Sum_probs=29.7
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCC---ChHhhhhhccccHhHHHHHHH
Q psy13113 8 ARGVIHSPVVKLLAVLRFYATGN---FQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 8 ~~~~~~~~~~~l~~~L~~L~~~~---~~~~l~~~Fgvs~stv~~~~~ 51 (286)
|.+...+++-+|-+.-++..++. .++..|..|||++..|.+|..
T Consensus 1 g~rrsy~~~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 1 GSRRSYTAEFKLKVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -------HHHHHHHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHHT
T ss_pred CCccccChHHHHHHHHHHHHccchhhhHHHHHHHhCccHHHHHHHHH
Confidence 45677889999988888888875 579999999999999988765
No 170
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=85.32 E-value=2.5 Score=34.73 Aligned_cols=52 Identities=17% Similarity=0.133 Sum_probs=42.4
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcccc
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQW 64 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~~ 64 (286)
.+|+.++-++.|.++ .|.+++++|..+|+|.+||...+.+....|-..+.++
T Consensus 133 ~Lp~~~r~v~~l~~~-~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~ 184 (196)
T PRK12535 133 ALPPERREALILTQV-LGYTYEEAAKIADVRVGTIRSRVARARADLIAATATG 184 (196)
T ss_pred cCCHHHHHHhhhHHH-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 466777777777665 4688999999999999999999999999888765554
No 171
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=85.27 E-value=2.4 Score=35.07 Aligned_cols=47 Identities=6% Similarity=-0.045 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|++++.++.|.|+ .|.+++++|..+|+|.+||...+++....|..
T Consensus 153 ~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 153 KLPEAQQTVVKGVYF-QELSQEQLAQQLNVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 466666767666554 57899999999999999999999888877765
No 172
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=85.09 E-value=2.5 Score=39.62 Aligned_cols=51 Identities=16% Similarity=0.079 Sum_probs=46.2
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
+|...+....|++|.|.+=-++.++.+++..||.+.|||...++++-..+.
T Consensus 366 ~R~~~i~~aR~iamyl~r~~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~~ 416 (440)
T PRK14088 366 SRNVKALLARRIGMYVAKNYLGSSLRTIAEKFNRSHPVVVDSVKKVKDSLL 416 (440)
T ss_pred CCCccccHHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 466788899999999999889999999999999999999999999998763
No 173
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=84.92 E-value=1.5 Score=33.99 Aligned_cols=130 Identities=15% Similarity=0.081 Sum_probs=73.9
Q ss_pred eeeeeEEEecCCCCCCccccccCCCccccceeeecCCCccEEEeccCCCCccccccccccchhhhhcccc-ccceEEEcc
Q psy13113 91 CIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDRR-EIRGLLLGD 169 (286)
Q Consensus 91 ~iDgt~i~i~~P~~~~~~~y~~~k~~~s~~~q~vvd~~g~i~~~~~~~~Gs~~D~~~~~~s~l~~~l~~~-~~~~~llgD 169 (286)
.+|-|.|.|.-- . .=+-..+|.+|+++++.+.-.-...++..| +.+.+... ..+..++.|
T Consensus 5 ~~DEt~iki~G~---~------------~yl~~aiD~~~~~l~~~ls~~Rd~~aA~~F----l~~~l~~~~~~p~~ivtD 65 (140)
T PF13610_consen 5 HVDETYIKIKGK---W------------HYLWRAIDAEGNILDFYLSKRRDTAAAKRF----LKRALKRHRGEPRVIVTD 65 (140)
T ss_pred EEeeEEEEECCE---E------------EEEEEeecccccchhhhhhhhcccccceee----ccccceeeccccceeecc
Confidence 689999887721 0 112478999999988888633233333222 22223322 125677878
Q ss_pred cc--CCCC-CcccccccCCCCCChhhHHhHHHHHHHHHHHHHHHHHHHhhhhhhhccccCCccchHHHHHHHHHHHhhhh
Q psy13113 170 IG--YAQN-EFTFTPVRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAVLHNIAI 246 (286)
Q Consensus 170 ~g--Y~~~-~~l~~p~~~~~~l~~~~~~~N~~~~~~R~~vE~~~~~lK~rf~~L~~~~~~~~~~~~~ii~a~~~LhN~~~ 246 (286)
+. |+.- ..+......+..... ....-.++.||+-+..+|.|.+... ++ .+...+..++..-.+.||+..
T Consensus 66 k~~aY~~A~~~l~~~~~~~~~v~~------~~~k~~nN~iE~~h~~~K~r~r~~~-gF-ks~~~A~~~l~~~~~~~n~~r 137 (140)
T PF13610_consen 66 KLPAYPAAIKELNPEGRLHDKVEH------RQRKYLNNRIERDHRTIKRRTRPMN-GF-KSFRSAQRTLSGFEAYHNFRR 137 (140)
T ss_pred cCCccchhhhhcccccccccccce------eechhhhChhhHhhhhhhhhccccc-Cc-CCHHHHHHHHHHHHHHHHHhC
Confidence 75 3221 111111100000000 1111346679999999999886554 34 367888899999999999975
Q ss_pred h
Q psy13113 247 A 247 (286)
Q Consensus 247 ~ 247 (286)
.
T Consensus 138 ~ 138 (140)
T PF13610_consen 138 P 138 (140)
T ss_pred C
Confidence 4
No 174
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=84.86 E-value=2.3 Score=38.11 Aligned_cols=48 Identities=8% Similarity=0.056 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHHH-hh--cCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRF-YA--TGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~-L~--~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.||+.++.++.++| |. .+.++..+|...|||.+||..+.++....|-.
T Consensus 262 ~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~ 312 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLRE 312 (325)
T ss_pred cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 68888888888887 54 56899999999999999999999998888865
No 175
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=84.84 E-value=2.6 Score=34.76 Aligned_cols=48 Identities=10% Similarity=0.061 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 139 ~Lp~~~r~v~~L~~~-eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 186 (201)
T PRK12545 139 HLPEQIGRVFMMREF-LDFEIDDICTELTLTANHCSVLLYRARTRLRTC 186 (201)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456666666666654 678999999999999999999988888877653
No 176
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=84.84 E-value=1.2 Score=37.70 Aligned_cols=49 Identities=10% Similarity=0.064 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhc
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCH 61 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~ 61 (286)
.+|+.++-++.|+++ .|.+++++|..+|+|.+||...+.+....|-...
T Consensus 149 ~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 149 ALPDAFRAVFVLRVV-EELSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred hCCHHHhhhheeehh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 356666666666654 4899999999999999999999988887777643
No 177
>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=84.82 E-value=2.9 Score=33.36 Aligned_cols=48 Identities=15% Similarity=-0.027 Sum_probs=40.3
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++.++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
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 577888777777765 568999999999999999999998888777653
No 178
>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=84.66 E-value=2 Score=34.74 Aligned_cols=45 Identities=13% Similarity=0.117 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHhhc--------------CCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYAT--------------GNFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~--------------~~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
..+++++|+-+|..|+. ..+..++|...|+++.||+|+++++...
T Consensus 112 ~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 112 HRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred hCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 35788999999887742 2478899999999999999999887654
No 179
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=84.57 E-value=2.6 Score=34.33 Aligned_cols=49 Identities=12% Similarity=0.154 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhc
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCH 61 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~ 61 (286)
.+|...+-++.|.++ .|.++.++|...|+|.+||...+.+....|...+
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 456666665555544 5799999999999999999999999888887643
No 180
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=84.30 E-value=2 Score=34.73 Aligned_cols=46 Identities=15% Similarity=0.187 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.|+ =+|.+++.|.+.+++|...++|.+||..++.++..-|..
T Consensus 133 ~LSpREr--EVLrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKLgV 178 (198)
T PRK15201 133 HFSVTER--HLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 3677655 456668999999999999999999999999988877753
No 181
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=84.25 E-value=2.4 Score=38.72 Aligned_cols=48 Identities=17% Similarity=0.153 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHHHHhh---cCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYA---TGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~---~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+++.++..+.|+|.- .+.++..+|..+|||+.+|+.+-.+.+.-|-.
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 5899999999998862 45799999999999999999999988877754
No 182
>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=84.09 E-value=2.2 Score=30.73 Aligned_cols=27 Identities=4% Similarity=0.085 Sum_probs=22.8
Q ss_pred cCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113 28 TGNFQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 28 ~~~~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
...+..++|...|+|+.||++.+++..
T Consensus 46 ~~is~~eLa~~~g~sr~tVsr~L~~Le 72 (95)
T TIGR01610 46 DRVTATVIAELTGLSRTHVSDAIKSLA 72 (95)
T ss_pred CccCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 346889999999999999999887654
No 183
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=83.93 E-value=2.7 Score=32.59 Aligned_cols=43 Identities=14% Similarity=0.101 Sum_probs=30.1
Q ss_pred CCCHHH-HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113 12 IHSPVV-KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 12 ~~~~~~-~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
.+++.+ .++..|.....+.+..+|+..++++++|+++.+++..
T Consensus 28 glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le 71 (144)
T PRK03573 28 ELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLE 71 (144)
T ss_pred CCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHH
Confidence 455554 3344443333456899999999999999999887554
No 184
>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=83.87 E-value=3.1 Score=27.49 Aligned_cols=29 Identities=21% Similarity=0.157 Sum_probs=23.8
Q ss_pred hhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113 26 YATGNFQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 26 L~~~~~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
..++.+..+++..+|++.+|+++.++.+.
T Consensus 17 ~~~~~~~~ei~~~~~i~~~~i~~~l~~L~ 45 (78)
T cd00090 17 LEGPLTVSELAERLGLSQSTVSRHLKKLE 45 (78)
T ss_pred HHCCcCHHHHHHHHCcCHhHHHHHHHHHH
Confidence 33448899999999999999999887653
No 185
>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=83.79 E-value=1.1 Score=28.25 Aligned_cols=28 Identities=29% Similarity=0.196 Sum_probs=22.5
Q ss_pred HhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113 25 FYATGNFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 25 ~L~~~~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
+...|.++.++|...|+|++|++++.+.
T Consensus 5 r~~~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 5 RKEKGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HHHTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHcCCCHHHHHHHhCCCcchhHHHhcC
Confidence 3467899999999999999999998864
No 186
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=83.73 E-value=3 Score=35.34 Aligned_cols=46 Identities=15% Similarity=0.218 Sum_probs=38.6
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
.++..++-.+.|+|. .+.++.++|..+|+|+++|+++.+....-|-
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 567777888888874 6789999999999999999999888777663
No 187
>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=83.73 E-value=2 Score=28.32 Aligned_cols=35 Identities=37% Similarity=0.415 Sum_probs=25.1
Q ss_pred HHHHhh---cCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 22 VLRFYA---TGNFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 22 ~L~~L~---~~~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
+|+++. ...+..+++..++++++++++.+++.++.
T Consensus 8 vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~ 45 (68)
T PF13463_consen 8 VLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEK 45 (68)
T ss_dssp HHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred HHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 455565 34588999999999999999988876543
No 188
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=83.62 E-value=3.3 Score=38.82 Aligned_cols=52 Identities=13% Similarity=-0.004 Sum_probs=46.9
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhc-cccHhHHHHHHHHHHHHHHh
Q psy13113 8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYH-DISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~F-gvs~stv~~~~~~v~~~l~~ 59 (286)
+|...+....|++|.|.+--++.++.++|..| |.+.|||...++++-..+..
T Consensus 381 ~R~~~~~~aR~iamyl~~~~~~~s~~~Ig~~fg~rdhstV~~a~~~i~~~~~~ 433 (450)
T PRK00149 381 SRTRNIARPRQIAMYLAKELTDLSLPEIGRAFGGRDHTTVLHAVRKIEKLLEE 433 (450)
T ss_pred CCCcccChHHHHHHHHHHHhcCCCHHHHHHHcCCCCHhHHHHHHHHHHHHHHh
Confidence 45677888999999999999999999999999 59999999999999987753
No 189
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=83.61 E-value=2.6 Score=39.01 Aligned_cols=48 Identities=13% Similarity=0.095 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHHHh---hcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFY---ATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+++.++-.+.|+|. ..+.++.++|..+|+|.++|..+.++....|-.
T Consensus 350 ~L~~reR~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~KLR~ 400 (415)
T PRK07598 350 DLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQ 400 (415)
T ss_pred hCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 588889989999885 355799999999999999999999988877763
No 190
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=83.52 E-value=3.4 Score=33.80 Aligned_cols=47 Identities=11% Similarity=0.058 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.||..++-++.|.|+ .|.++.++|...|+|.+||...+++....|-.
T Consensus 142 ~L~~~~r~vl~l~~~-~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 142 ALTDTQRESVTLAYY-GGLTYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 577777777777664 56999999999999999999999988887765
No 191
>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=83.49 E-value=3 Score=34.03 Aligned_cols=38 Identities=13% Similarity=0.137 Sum_probs=30.9
Q ss_pred HHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 21 AVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 21 ~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+.+.++ .|.++.++|..+|+|.+||...+++....|-.
T Consensus 158 i~~~~~-~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 158 VLQSYL-DGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred HHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 334454 78999999999999999999888887776654
No 192
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=83.36 E-value=2.4 Score=35.95 Aligned_cols=48 Identities=8% Similarity=0.110 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|..++-++.|+|+ .|.+++++|..+|+|.+||...+.+....|-..
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 456677776666664 679999999999999999999999988888764
No 193
>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=83.20 E-value=2.9 Score=27.21 Aligned_cols=32 Identities=13% Similarity=0.077 Sum_probs=26.2
Q ss_pred HHHHHHHhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113 19 LLAVLRFYATGNFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 19 l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
.+..|++ .|-+..++|...|++.+||+.+..+
T Consensus 5 ~A~~LY~--~G~~~~eIA~~Lg~~~~TV~~W~~r 36 (58)
T PF06056_consen 5 QARSLYL--QGWSIKEIAEELGVPRSTVYSWKDR 36 (58)
T ss_pred HHHHHHH--cCCCHHHHHHHHCCChHHHHHHHHh
Confidence 4455553 5899999999999999999998864
No 194
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=83.20 E-value=3.7 Score=31.85 Aligned_cols=46 Identities=4% Similarity=-0.033 Sum_probs=33.2
Q ss_pred CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
...+++.+-.++...+-..+.+..+|+..++++++|+++.+++...
T Consensus 35 ~~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~ 80 (144)
T PRK11512 35 PLDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVC 80 (144)
T ss_pred ccCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3456666554444334445679999999999999999998876543
No 195
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=83.11 E-value=1.6 Score=27.84 Aligned_cols=25 Identities=8% Similarity=0.159 Sum_probs=21.6
Q ss_pred ChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
+..+++..||+|++|+.+.+.....
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~ 46 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEA 46 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6888999999999999998876554
No 196
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=83.10 E-value=4 Score=33.25 Aligned_cols=46 Identities=22% Similarity=0.289 Sum_probs=35.5
Q ss_pred CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+++++.=.+.|+++ .|.++.++|...|||.+||.+.....-..|..
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 45555555556555 77899999999999999999988877766654
No 197
>PRK13870 transcriptional regulator TraR; Provisional
Probab=83.06 E-value=1.9 Score=36.73 Aligned_cols=47 Identities=13% Similarity=0.171 Sum_probs=39.8
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
..+++.|+ =+|.|.+.|.+..++|...|||++||.-.++++..-|..
T Consensus 172 ~~LT~RE~--E~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga 218 (234)
T PRK13870 172 AWLDPKEA--TYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDV 218 (234)
T ss_pred CCCCHHHH--HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 34666554 467889999999999999999999999999998887764
No 198
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=83.01 E-value=2.7 Score=34.60 Aligned_cols=45 Identities=9% Similarity=0.030 Sum_probs=35.4
Q ss_pred CCCCHHHHHHHHHHHhhc-------------CCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 11 VIHSPVVKLLAVLRFYAT-------------GNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~-------------~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
...++.++++-+|..|+. ..+..++|...|+++.|++|+++++.+
T Consensus 137 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lG~tr~tvsR~l~~l~~ 194 (211)
T PRK11753 137 AFLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKMLED 194 (211)
T ss_pred HhcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 346788999998887763 235688999999999999998876543
No 199
>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=82.81 E-value=2.4 Score=38.89 Aligned_cols=120 Identities=18% Similarity=0.149 Sum_probs=66.5
Q ss_pred hhcCCChHhhhh----hcc---ccHhHHHHHHHHHHHHHHhhcccccCCchhHHHHHHHhhhhcCCCCceEeeeeeeEEE
Q psy13113 26 YATGNFQIDSED----YHD---ISQSTICRLVAKVSEELAKCHQQWIHFPEDLQTAKNQFSGIAGFPRVVVGCIDGTHVP 98 (286)
Q Consensus 26 L~~~~~~~~l~~----~Fg---vs~stv~~~~~~v~~~l~~~~~~~i~~P~~~~~~~~~f~~~~~~p~~~~g~iDgt~i~ 98 (286)
+..|.+.+++.. ..| +|.+||++++..+.+.+.....+- ..+.|-. +..|||+++.
T Consensus 111 y~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~~w~~R~----------------L~~~~y~-~l~iD~~~~k 173 (381)
T PF00872_consen 111 YLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVEAWRNRP----------------LESEPYP-YLWIDGTYFK 173 (381)
T ss_pred hccccccccccchhhhhhcccccCchhhhhhhhhhhhhHHHHhhhc----------------ccccccc-ceeeeeeecc
Confidence 556676666444 446 999999999988877665532111 1122223 5699999998
Q ss_pred ecCCCCCCccccccCCCccccceeeecCCCcc--EEEeccCCCCccccccccccchhhhhcc-cccc-ceEEEccccCCC
Q psy13113 99 IELPSIENGEHYRNRKHFYSINVQVIGGPNLE--IYDVVASWPGSTHDSRIFQNSRVYSRFD-RREI-RGLLLGDIGYAQ 174 (286)
Q Consensus 99 i~~P~~~~~~~y~~~k~~~s~~~q~vvd~~g~--i~~~~~~~~Gs~~D~~~~~~s~l~~~l~-~~~~-~~~llgD~gY~~ 174 (286)
+..- +.-..-++-+-+.+|.+|+ ++.+..+.. -....|.+ +...|. +|.. ...+++|..=.+
T Consensus 174 vr~~---------~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~---Es~~~W~~--~l~~L~~RGl~~~~lvv~Dg~~gl 239 (381)
T PF00872_consen 174 VRED---------GRVVKKAVYVAIGIDEDGRREVLGFWVGDR---ESAASWRE--FLQDLKERGLKDILLVVSDGHKGL 239 (381)
T ss_pred cccc---------cccccchhhhhhhhhcccccceeeeecccC---CccCEeee--cchhhhhccccccceeeccccccc
Confidence 8732 1111224455566677774 677666522 22333332 333332 2222 557778865444
Q ss_pred CC
Q psy13113 175 NE 176 (286)
Q Consensus 175 ~~ 176 (286)
..
T Consensus 240 ~~ 241 (381)
T PF00872_consen 240 KE 241 (381)
T ss_pred cc
Confidence 33
No 200
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=82.78 E-value=2.2 Score=35.49 Aligned_cols=46 Identities=17% Similarity=0.267 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+++.|+ =.|.+++.|.+.+++|...++|.+||..++.++..-|..
T Consensus 137 ~LT~RE~--eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v 182 (207)
T PRK15411 137 SLSRTES--SMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT 182 (207)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 4777665 456679999999999999999999999999988877763
No 201
>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=82.57 E-value=1.5 Score=35.80 Aligned_cols=48 Identities=10% Similarity=-0.030 Sum_probs=37.7
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+..+-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 131 ~Lp~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 178 (193)
T TIGR02947 131 GLPEEFRQAVYLADV-EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQ 178 (193)
T ss_pred hCCHHHhhheeehhh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 355555666666543 568999999999999999999999888888653
No 202
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=82.52 E-value=3.6 Score=40.02 Aligned_cols=52 Identities=12% Similarity=-0.001 Sum_probs=47.0
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.|...+....|++|.|.+=-++.++..++..||.+.+||...++++-..|.+
T Consensus 548 ~R~~~i~~aRqiAMYL~r~lt~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~~ 599 (617)
T PRK14086 548 SRSRVLVTARQIAMYLCRELTDLSLPKIGQQFGRDHTTVMHADRKIRALMAE 599 (617)
T ss_pred CCCcccchHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHh
Confidence 3555788899999999999999999999999999999999999999988764
No 203
>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=82.49 E-value=2.3 Score=28.38 Aligned_cols=38 Identities=24% Similarity=0.264 Sum_probs=28.5
Q ss_pred HHHHHHHHHHhhcC-CChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 16 VVKLLAVLRFYATG-NFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 16 ~~~l~~~L~~L~~~-~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
|.++..+|. .++ .+..+++...|++++||++++++..+
T Consensus 10 E~~vy~~Ll--~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~ 48 (68)
T PF01978_consen 10 EAKVYLALL--KNGPATAEEIAEELGISRSTVYRALKSLEE 48 (68)
T ss_dssp HHHHHHHHH--HHCHEEHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred HHHHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 445555553 444 68999999999999999998876543
No 204
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=82.27 E-value=2.9 Score=38.15 Aligned_cols=48 Identities=15% Similarity=0.099 Sum_probs=40.5
Q ss_pred CCCHHHHHHHHHHHhh---cCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYA---TGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~---~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.|+..++..+.|+|.- .+.++..+|..||||+..|+++-.+.+.-|-.
T Consensus 305 ~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~ 355 (367)
T PRK09210 305 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRH 355 (367)
T ss_pred hCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhC
Confidence 6889999999998853 45799999999999999999998877776653
No 205
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=82.26 E-value=5.1 Score=35.90 Aligned_cols=49 Identities=16% Similarity=0.176 Sum_probs=38.7
Q ss_pred CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcc
Q psy13113 13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQ 62 (286)
Q Consensus 13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~ 62 (286)
||+.++-++.|+++ .|.+++++|..+|+|.+||...+.+....|-...+
T Consensus 154 Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~ 202 (339)
T PRK08241 154 LPPRQRAVLILRDV-LGWSAAEVAELLDTSVAAVNSALQRARATLAERGP 202 (339)
T ss_pred CCHHHhhhhhhHHh-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhcCC
Confidence 45555555555443 67899999999999999999999999999987444
No 206
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=82.24 E-value=3.3 Score=35.92 Aligned_cols=47 Identities=17% Similarity=0.164 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.|+|+ .+.++.++|..+|+|.+||....++....|-.
T Consensus 212 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 258 (268)
T PRK06288 212 TLPEREKKVLILYYY-EDLTLKEIGKVLGVTESRISQLHTKAVLQLRA 258 (268)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 578888888888775 57899999999999999999888877776654
No 207
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=82.14 E-value=1.3 Score=36.13 Aligned_cols=46 Identities=17% Similarity=0.164 Sum_probs=34.5
Q ss_pred CHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 14 SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 14 ~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
|+.++=++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 136 ~~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 136 NPIDREILVLRFV-AELEFQEIADIMHMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred ChhheeeeeeHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3443333344443 678999999999999999999999888887654
No 208
>PRK05949 RNA polymerase sigma factor; Validated
Probab=81.85 E-value=3.3 Score=37.18 Aligned_cols=48 Identities=15% Similarity=0.147 Sum_probs=41.4
Q ss_pred CCCHHHHHHHHHHHh-h--cCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFY-A--TGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L-~--~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+++.++-.+.|+|. . .+.++.++|..+|+|..+|..+..+....|-.
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 588888999999884 3 45799999999999999999999988887765
No 209
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=81.58 E-value=2.1 Score=25.91 Aligned_cols=28 Identities=7% Similarity=0.189 Sum_probs=23.3
Q ss_pred cCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 28 TGNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 28 ~~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
-..+..++|..+|+|.+|+++.++....
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3467889999999999999998876654
No 210
>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=81.53 E-value=2.3 Score=27.89 Aligned_cols=29 Identities=17% Similarity=0.077 Sum_probs=22.8
Q ss_pred HHHhhcC--CChHhhhhhccccHhHHHHHHH
Q psy13113 23 LRFYATG--NFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 23 L~~L~~~--~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
-.|+.++ ....++|..+|||.+||..|-.
T Consensus 14 e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 14 EIYKESNGKIKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred HHHHHhCCCccHHHHHHHHCCCHHHHHHHhh
Confidence 3456554 5899999999999999997643
No 211
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=81.53 E-value=2.5 Score=27.03 Aligned_cols=29 Identities=21% Similarity=0.193 Sum_probs=24.2
Q ss_pred hcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 27 ATGNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 27 ~~~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
....+..+++..+|+|.+|+++.++....
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 44568899999999999999998876554
No 212
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=81.43 E-value=3.3 Score=33.15 Aligned_cols=47 Identities=17% Similarity=0.046 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|++++-++.|.++ .|.++.++|..+|+|.+||...+++....+-.
T Consensus 119 ~L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 119 GLNGKTREAFLLSQL-DGLTYSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred hCCHHHhHHhhhhhc-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 466666655555444 56899999999999999999998888777654
No 213
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=81.24 E-value=1.8 Score=25.85 Aligned_cols=29 Identities=21% Similarity=0.094 Sum_probs=21.7
Q ss_pred hhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113 26 YATGNFQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 26 L~~~~~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
|.++.+..++|..+|+|.+++++.|++..
T Consensus 5 ~~~~~~l~~iA~~~g~S~~~f~r~Fk~~~ 33 (42)
T PF00165_consen 5 LQQKLTLEDIAEQAGFSPSYFSRLFKKET 33 (42)
T ss_dssp T-SS--HHHHHHHHTS-HHHHHHHHHHHT
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45677889999999999999999998753
No 214
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=81.24 E-value=4.2 Score=33.63 Aligned_cols=48 Identities=13% Similarity=0.054 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++-.+.|.+ -.|.++.++|..+|+|.+||...+.+....|-..
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 35555555555554 4679999999999999999999999988887763
No 215
>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=81.16 E-value=3.7 Score=31.50 Aligned_cols=46 Identities=15% Similarity=0.070 Sum_probs=38.1
Q ss_pred CCHHHHHHHHHHHhhc-CCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 13 HSPVVKLLAVLRFYAT-GNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 13 ~~~~~~l~~~L~~L~~-~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
+..+++-.+-|+|.+. +.+|-.+|..+++|++|+.++..+|-+.++
T Consensus 82 l~de~k~Ii~lry~~r~~~TW~~IA~~l~i~erta~r~~~~fK~~i~ 128 (130)
T PF05263_consen 82 LIDEEKRIIKLRYDRRSRRTWYQIAQKLHISERTARRWRDRFKNDIY 128 (130)
T ss_pred hCHHHHHHHHHHHcccccchHHHHHHHhCccHHHHHHHHHHHHHHhc
Confidence 4556777778888877 689999999999999999999988876553
No 216
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=81.11 E-value=3 Score=35.03 Aligned_cols=57 Identities=12% Similarity=0.146 Sum_probs=42.4
Q ss_pred CCCHHHHHHHHHHHhhcC----CChHhhhhhccccHhHHHHHHHHHHHH-HHhhcccccCCc
Q psy13113 12 IHSPVVKLLAVLRFYATG----NFQIDSEDYHDISQSTICRLVAKVSEE-LAKCHQQWIHFP 68 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~----~~~~~l~~~Fgvs~stv~~~~~~v~~~-l~~~~~~~i~~P 68 (286)
..+++++|+.+|..+..+ .+..++|...|+++.|++|.++++.+. +.+.....|..+
T Consensus 148 ~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~~~i~I~ 209 (226)
T PRK10402 148 SFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSKRGYLIK 209 (226)
T ss_pred cChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeCCEEEEe
Confidence 358899999999876532 367899999999999999999988764 444433334333
No 217
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=81.01 E-value=2.6 Score=27.87 Aligned_cols=37 Identities=14% Similarity=0.002 Sum_probs=28.5
Q ss_pred HHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHH
Q psy13113 17 VKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 17 ~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v 53 (286)
++++-+|.....+.+-+++|..+|+|..++..++...
T Consensus 3 e~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~L 39 (62)
T PF04703_consen 3 EKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKL 39 (62)
T ss_dssp HCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4566667777788899999999999999999887643
No 218
>PHA02591 hypothetical protein; Provisional
Probab=80.96 E-value=3.5 Score=28.36 Aligned_cols=38 Identities=8% Similarity=-0.033 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113 15 PVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 15 ~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
-++-+-++=...+.|.+...+|...|+++.+|+++++.
T Consensus 45 ~dd~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 45 EDDLISVTHELARKGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred cchHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 34455556666778999999999999999999999864
No 219
>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=80.84 E-value=2.6 Score=27.44 Aligned_cols=30 Identities=23% Similarity=0.108 Sum_probs=24.5
Q ss_pred hhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 26 YATGNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 26 L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
-..+.+..+++..+|++.+|+++.++...+
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 456679999999999999999998876654
No 220
>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=80.28 E-value=6.8 Score=23.56 Aligned_cols=26 Identities=15% Similarity=0.175 Sum_probs=19.9
Q ss_pred cCCChHhhhhhccccHhHHHHHHHHH
Q psy13113 28 TGNFQIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 28 ~~~~~~~l~~~Fgvs~stv~~~~~~v 53 (286)
.-.++..+|...|+|.+||.+-+++.
T Consensus 16 ~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 16 GRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 33599999999999999999877653
No 221
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=80.23 E-value=5.8 Score=28.04 Aligned_cols=46 Identities=13% Similarity=0.136 Sum_probs=32.9
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
..++..+..++.+.....+.+..+++..+++|++|+++.++...+.
T Consensus 6 ~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~ 51 (101)
T smart00347 6 LGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKK 51 (101)
T ss_pred cCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHC
Confidence 3455544444444444445799999999999999999999877664
No 222
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=79.94 E-value=4.5 Score=33.42 Aligned_cols=46 Identities=24% Similarity=0.205 Sum_probs=39.5
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
..+++.|+ -.|.+++.|.+.+++|...++|.+||..+..++..-|.
T Consensus 149 ~~Lt~rE~--evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~ 194 (216)
T PRK10840 149 KRLSPKES--EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLG 194 (216)
T ss_pred ccCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 35888775 66777899999999999999999999999988877665
No 223
>PRK01381 Trp operon repressor; Provisional
Probab=79.93 E-value=2.3 Score=30.85 Aligned_cols=39 Identities=15% Similarity=-0.012 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHH------hhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 13 HSPVVKLLAVLRF------YATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 13 ~~~~~~l~~~L~~------L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
+++.++=+++.++ ++...+|+.++...|||.+||+|.-+
T Consensus 33 lTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn 77 (99)
T PRK01381 33 LTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITRGSN 77 (99)
T ss_pred CCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHH
Confidence 4455544444432 34458999999999999999997654
No 224
>PF13309 HTH_22: HTH domain
Probab=79.86 E-value=3.2 Score=27.54 Aligned_cols=42 Identities=21% Similarity=0.106 Sum_probs=31.6
Q ss_pred CCCCCHHHHHHHHHHHhhcCC-----ChHhhhhhccccHhHHHHHHH
Q psy13113 10 GVIHSPVVKLLAVLRFYATGN-----FQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 10 ~~~~~~~~~l~~~L~~L~~~~-----~~~~l~~~Fgvs~stv~~~~~ 51 (286)
...++.++++-+.-..-..|- .-..+|..+|||+.||+++++
T Consensus 18 ~~~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YLr 64 (64)
T PF13309_consen 18 PSRLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYLR 64 (64)
T ss_pred hhhCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHcC
Confidence 456777788877666656553 455699999999999999863
No 225
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=79.33 E-value=6.2 Score=28.76 Aligned_cols=39 Identities=21% Similarity=0.126 Sum_probs=28.8
Q ss_pred HHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 16 VVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 16 ~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
+.+++..|.. ....++.+++..+|+|++|+.+.+++...
T Consensus 5 D~~il~~L~~-~~~~~~~~la~~l~~s~~tv~~~l~~L~~ 43 (108)
T smart00344 5 DRKILEELQK-DARISLAELAKKVGLSPSTVHNRVKRLEE 43 (108)
T ss_pred HHHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3444444433 23479999999999999999998887655
No 226
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=79.24 E-value=2.5 Score=34.44 Aligned_cols=47 Identities=9% Similarity=0.007 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|+.++-++.|++ -.|.++.++|...|+|.+||...+.+....|-.
T Consensus 139 ~L~~~~r~i~~l~~-~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 185 (194)
T PRK12513 139 TLPDEQREVFLLRE-HGDLELEEIAELTGVPEETVKSRLRYALQKLRE 185 (194)
T ss_pred hCCHhHhhheeeeh-ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35555555555544 467899999999999999999888887777765
No 227
>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=78.99 E-value=4.1 Score=28.57 Aligned_cols=34 Identities=29% Similarity=0.113 Sum_probs=27.6
Q ss_pred hhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 26 YATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 26 L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
...+.+..++|..+.||++|+.+.++.+-..|..
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 4566799999999999999999999999888874
No 228
>PF13701 DDE_Tnp_1_4: Transposase DDE domain group 1
Probab=78.94 E-value=4.8 Score=37.78 Aligned_cols=152 Identities=21% Similarity=0.135 Sum_probs=83.4
Q ss_pred CCCCCHHHHHHHHHHHhhcC-CChHhhhh---------hcc----------ccHhHHHHHHHHHHHHHH-hhcccccCCc
Q psy13113 10 GVIHSPVVKLLAVLRFYATG-NFQIDSED---------YHD----------ISQSTICRLVAKVSEELA-KCHQQWIHFP 68 (286)
Q Consensus 10 ~~~~~~~~~l~~~L~~L~~~-~~~~~l~~---------~Fg----------vs~stv~~~~~~v~~~l~-~~~~~~i~~P 68 (286)
....+..+.|...++-+..| +...++.. .+| .|++|++|..+.+...-. .+...+
T Consensus 52 ~~~h~~~~ll~q~i~~i~~Gyed~~d~~~LR~Dp~f~~~~g~~~~~~~~~Las~~t~sR~e~~~~~~~~~~~~~~~---- 127 (448)
T PF13701_consen 52 YVRHSLEDLLRQRIFQIAAGYEDDNDADRLRHDPVFKLALGRLPEPGSDRLASQPTLSRLENRPDERDLKRLRRAL---- 127 (448)
T ss_pred cccCcHHHHHHHHHHHHHccCCChHHHHHhccCHHHHHHhccCCCCccccccchhhHHHHHccccHHHHHHHHHHH----
Confidence 45688888888777666554 33333222 122 577888888876644322 222211
Q ss_pred hhHHHHHHHhhhhcCCCCceEeeeeeeEEEecCCCCCCccccccCCCccccceeeecC-CCccEEEeccCCCCccccccc
Q psy13113 69 EDLQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGG-PNLEIYDVVASWPGSTHDSRI 147 (286)
Q Consensus 69 ~~~~~~~~~f~~~~~~p~~~~g~iDgt~i~i~~P~~~~~~~y~~~k~~~s~~~q~vvd-~~g~i~~~~~~~~Gs~~D~~~ 147 (286)
++.....+.+ .-..+ +.=||+|..++.- ..+...|+++++.+++.-.++-+ ..|.++.+.. .||+.|-+.-
T Consensus 128 --~~~~~~~~~~--~~~~i-~LDiD~T~~~~~G--~Qe~~~~n~y~g~~gY~PL~~f~g~~G~~l~a~L-RpGn~~sa~g 199 (448)
T PF13701_consen 128 --VDLFLASYKK--PPKEI-VLDIDSTVDDVHG--EQEGAVFNTYYGEDGYHPLVAFDGQTGYLLAAEL-RPGNVHSAKG 199 (448)
T ss_pred --HHHHHHHhcc--ccceE-EEecccccccchh--hcccccccccCCCcccccceeccCCCCceEEEEc-cCCCCChHHH
Confidence 1111222221 12344 7788999877662 22345577777777777556654 5888888754 5999887644
Q ss_pred cccc--hhhhhcccccc--ceEEEccccCC
Q psy13113 148 FQNS--RVYSRFDRREI--RGLLLGDIGYA 173 (286)
Q Consensus 148 ~~~s--~l~~~l~~~~~--~~~llgD~gY~ 173 (286)
...- .+...+.+... .-.+=||+||.
T Consensus 200 ~~~fL~~~l~~lr~~~~~~~ILvR~DSgF~ 229 (448)
T PF13701_consen 200 AAEFLKRVLRRLRQRWPDTRILVRGDSGFA 229 (448)
T ss_pred HHHHHHHHHHHHhhhCccceEEEEecCccC
Confidence 3320 11222222111 23455999985
No 229
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=78.35 E-value=5.2 Score=33.68 Aligned_cols=45 Identities=16% Similarity=0.225 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHHhhc----------CCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYAT----------GNFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~----------~~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
..+++++|+-+|..+.. ..+.+++|...|+++.|++|+++++.+.
T Consensus 152 ~~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~L~~L~~~ 206 (230)
T PRK09391 152 RKTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLQDR 206 (230)
T ss_pred CCCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 36889999999988754 2367899999999999999998876543
No 230
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=78.30 E-value=7.1 Score=23.88 Aligned_cols=27 Identities=22% Similarity=0.152 Sum_probs=23.1
Q ss_pred CCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 29 GNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 29 ~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
+.+..+++..|++|.+|+++.+..+..
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~~ 40 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLEE 40 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 468889999999999999998876654
No 231
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=78.22 E-value=5.4 Score=35.73 Aligned_cols=48 Identities=13% Similarity=0.078 Sum_probs=40.8
Q ss_pred CCCHHHHHHHHHHHhh---cCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYA---TGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~---~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.++..++..+.++|.- ...++.++|..||||+..|+++-.+.+.-|-.
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 5888899999998852 34799999999999999999999888877754
No 232
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=78.02 E-value=5.1 Score=38.18 Aligned_cols=48 Identities=13% Similarity=0.058 Sum_probs=42.0
Q ss_pred CCCHHHHHHHHHHHh---hcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFY---ATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.|+..++..+.++|. ..+.++..+|..||||+..|+++-.+.+.-|-.
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 588999999999995 456899999999999999999999888877764
No 233
>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=78.01 E-value=5.5 Score=25.64 Aligned_cols=25 Identities=20% Similarity=0.109 Sum_probs=21.0
Q ss_pred CCChHhhhhhccccHhHHHHHHHHH
Q psy13113 29 GNFQIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 29 ~~~~~~l~~~Fgvs~stv~~~~~~v 53 (286)
..+..+++..||||..|+.+-+...
T Consensus 14 ~~s~~ela~~~~VS~~TiRRDl~~L 38 (57)
T PF08220_consen 14 KVSVKELAEEFGVSEMTIRRDLNKL 38 (57)
T ss_pred CEEHHHHHHHHCcCHHHHHHHHHHH
Confidence 3588899999999999999877643
No 234
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=77.96 E-value=4.2 Score=34.06 Aligned_cols=46 Identities=9% Similarity=0.017 Sum_probs=37.8
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
..+++.++= .|..++.|.+.+++|...++|.+||..++.++..-|.
T Consensus 142 ~~LS~RE~e--VL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLg 187 (217)
T PRK13719 142 NKVTKYQND--VFILYSFGFSHEYIAQLLNITVGSSKNKISEILKFFG 187 (217)
T ss_pred CCCCHHHHH--HHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 446665544 4555899999999999999999999999998887775
No 235
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=77.62 E-value=5.3 Score=33.55 Aligned_cols=44 Identities=18% Similarity=0.224 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHhhc--------------CCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYAT--------------GNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~--------------~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
..+++++++.+|..|.. ..+..++|...|+++.|++|+++++..
T Consensus 153 ~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~~ 210 (235)
T PRK11161 153 KKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQK 210 (235)
T ss_pred CCCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 45789999999998763 247789999999999999999876644
No 236
>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=77.49 E-value=2.2 Score=25.78 Aligned_cols=22 Identities=23% Similarity=0.289 Sum_probs=19.1
Q ss_pred ChHhhhhhccccHhHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
+..++|..+|||.+|+.+++.+
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 4578899999999999999875
No 237
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=77.42 E-value=5.2 Score=32.63 Aligned_cols=57 Identities=11% Similarity=0.025 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHHHhhc--------------CCChHhhhhhccccHhHHHHHHHHHHHH-HHhhcccccCCc
Q psy13113 12 IHSPVVKLLAVLRFYAT--------------GNFQIDSEDYHDISQSTICRLVAKVSEE-LAKCHQQWIHFP 68 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~--------------~~~~~~l~~~Fgvs~stv~~~~~~v~~~-l~~~~~~~i~~P 68 (286)
..+++++|+.+|..|+. ..+..++|...|+++.||+|+++++.+. +.+.....|..+
T Consensus 118 ~~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~ 189 (202)
T PRK13918 118 GQRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRETVTKVIGELSREGYIRSGYGKIQLL 189 (202)
T ss_pred hCchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcCCCEEEEE
Confidence 35688999999887763 1268899999999999999999988754 334333334333
No 238
>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=77.01 E-value=6.3 Score=26.28 Aligned_cols=30 Identities=10% Similarity=0.092 Sum_probs=23.6
Q ss_pred hhcC-CChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 26 YATG-NFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 26 L~~~-~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
|+.+ .+..+++..||+|.+||++.+.....
T Consensus 9 L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 9 LADNPFSGEKLGEALGMSRTAVNKHIQTLRE 39 (69)
T ss_pred HHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4443 46889999999999999998876543
No 239
>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=76.80 E-value=6.2 Score=29.40 Aligned_cols=46 Identities=4% Similarity=-0.101 Sum_probs=31.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
..+++.+-.++....-..+.+..+++...|++++|+++.+++....
T Consensus 24 ~~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~ 69 (118)
T TIGR02337 24 HGLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERD 69 (118)
T ss_pred cCCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHC
Confidence 3455555333332233445689999999999999999888766544
No 240
>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=76.73 E-value=8 Score=32.74 Aligned_cols=48 Identities=19% Similarity=0.108 Sum_probs=40.1
Q ss_pred CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
...+++.++=.+.+ .+.|.++.++|..+|+|.+||...+.+...-|..
T Consensus 169 ~~~Lt~re~evl~~--~a~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~ 216 (232)
T TIGR03541 169 AGVLSEREREVLAW--TALGRRQADIAAILGISERTVENHLRSARRKLGV 216 (232)
T ss_pred hccCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence 44688877666665 5899999999999999999999999998877763
No 241
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=76.50 E-value=7.8 Score=36.41 Aligned_cols=52 Identities=13% Similarity=0.033 Sum_probs=46.7
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhcc-ccHhHHHHHHHHHHHHHHh
Q psy13113 8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHD-ISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fg-vs~stv~~~~~~v~~~l~~ 59 (286)
.|...+....|++|.|.+=-++.++..++..|| -+.|||.-.++.+-..+..
T Consensus 380 ~R~~~i~~~RqiamyL~r~~t~~sl~~IG~~FggrdHsTV~~a~~ki~~~~~~ 432 (450)
T PRK14087 380 ARSKSIVTARHIAMYLTKEILNHTLAQIGEEFGGRDHTTVINAERKIEKMLKK 432 (450)
T ss_pred CCCccccHHHHHHHHHHHHHcCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHh
Confidence 356678899999999999999999999999997 9999999999999888764
No 242
>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=76.15 E-value=9.6 Score=29.01 Aligned_cols=45 Identities=16% Similarity=0.194 Sum_probs=31.5
Q ss_pred CCCCCCHHHHHHHH-HHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 9 RGVIHSPVVKLLAV-LRFYATGNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 9 ~~~~~~~~~~l~~~-L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
++..+|.+.+.-+. |. ..|.+-.+++..+.||.++|++++.+.-+
T Consensus 14 nGrPLp~~~R~rIvela--~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~e 59 (125)
T PF00292_consen 14 NGRPLPNELRQRIVELA--KEGVRPCDISRQLRVSHGCVSKILSRYRE 59 (125)
T ss_dssp TTSSS-HHHHHHHHHHH--HTT--HHHHHHHHT--HHHHHHHHHHHHH
T ss_pred CCccCcHHHHHHHHHHh--hhcCCHHHHHHHHccchhHHHHHHHHHHH
Confidence 46677887766655 43 46899999999999999999999998754
No 243
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=75.83 E-value=11 Score=27.82 Aligned_cols=48 Identities=19% Similarity=0.181 Sum_probs=37.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
-.+++++-=++-|..+ .|.++.+.|...|||++|+.+++.+.-.-|..
T Consensus 40 V~L~~dElEAiRL~D~-egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~ 87 (106)
T PF02001_consen 40 VVLTVDELEAIRLVDY-EGLSQEEAAERMGVSRPTFQRILESARKKIAD 87 (106)
T ss_pred EEeeHHHHHHHHHHHH-cCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHH
Confidence 3577777777777666 45899999999999999999999866555543
No 244
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=75.83 E-value=7.1 Score=36.62 Aligned_cols=51 Identities=12% Similarity=0.005 Sum_probs=46.4
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
.|...+....|++|.|.+=-++.++.+++..||-++|||.-.++.+-+.+.
T Consensus 376 ~R~~~i~~~Rqiamyl~r~~t~~s~~~IG~~fgrdHsTV~~a~~ki~~~~~ 426 (445)
T PRK12422 376 SQSREYVLPRQVAMYLCRQKLSLSYVKIGDVFSRDHSTVISSIRAISQKLE 426 (445)
T ss_pred CCCcccccHHHHHHHHHHHhcCCCHHHHHHHhCCChHHHHHHHHHHHHHHH
Confidence 466778889999999999999999999999999999999999999988774
No 245
>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=75.48 E-value=2.9 Score=25.27 Aligned_cols=23 Identities=22% Similarity=0.403 Sum_probs=19.3
Q ss_pred CChHhhhhhccccHhHHHHHHHH
Q psy13113 30 NFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
.+..++|..+|||.+|+.+++++
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHc
Confidence 35678999999999999998753
No 246
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=75.41 E-value=4.9 Score=34.30 Aligned_cols=47 Identities=17% Similarity=0.164 Sum_probs=38.6
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
..+++.++= +|.+++.|.+..++|...+||..||...+.++..-|..
T Consensus 178 ~~LT~rE~e--vl~~~a~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~ 224 (240)
T PRK10188 178 MNFSKREKE--ILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNA 224 (240)
T ss_pred CCCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 456766654 45567999999999999999999999999988877763
No 247
>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=75.37 E-value=2.1 Score=30.74 Aligned_cols=33 Identities=9% Similarity=0.008 Sum_probs=23.1
Q ss_pred hHhhhhhccccHhHHHHHHHHH--HHHHHhhcccc
Q psy13113 32 QIDSEDYHDISQSTICRLVAKV--SEELAKCHQQW 64 (286)
Q Consensus 32 ~~~l~~~Fgvs~stv~~~~~~v--~~~l~~~~~~~ 64 (286)
+.-+|..||+|.+|++|+-..- =.|+.+....+
T Consensus 48 ~~GlAklfgcSv~Ta~RiK~sG~id~AI~Q~Gr~I 82 (96)
T PF12964_consen 48 LKGLAKLFGCSVPTANRIKKSGKIDPAITQIGRKI 82 (96)
T ss_pred HHHHHHHhCCCchhHHHHHhcCCccHHHHHcCCEE
Confidence 4569999999999999998642 24555443333
No 248
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=74.99 E-value=3.7 Score=28.16 Aligned_cols=28 Identities=39% Similarity=0.356 Sum_probs=23.7
Q ss_pred HHhhcCCChHhhhhhcc------ccHhHHHHHHH
Q psy13113 24 RFYATGNFQIDSEDYHD------ISQSTICRLVA 51 (286)
Q Consensus 24 ~~L~~~~~~~~l~~~Fg------vs~stv~~~~~ 51 (286)
.+...|.++.++|...| +|++|++++-+
T Consensus 19 ~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 19 RRIKLGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 44557889999999999 59999999766
No 249
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=74.82 E-value=20 Score=29.99 Aligned_cols=186 Identities=14% Similarity=0.083 Sum_probs=102.4
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhh-----ccccHhHHHHHHHHHHHHHHhhcccccCCchhHHHHHHHhhhhcCCCC
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDY-----HDISQSTICRLVAKVSEELAKCHQQWIHFPEDLQTAKNQFSGIAGFPR 86 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~-----Fgvs~stv~~~~~~v~~~l~~~~~~~i~~P~~~~~~~~~f~~~~~~p~ 86 (286)
..+..-+...+-+||+.+.+++++... ..|+.+|+++++......+....... .. . ++
T Consensus 8 ~f~~~vi~~~V~~yl~~~Ls~r~v~e~l~~rgi~v~h~Ti~rwv~k~~~~~~~~~~~r--------------~~--~-~~ 70 (215)
T COG3316 8 QFPRNIIAVAVWLYLRYGLSLRDVEEMLAERGIEVDHETIHRWVQKYGPLLARRLKRR--------------KR--K-AG 70 (215)
T ss_pred hcchhhHHHHHHHHhhcchhhccHHHHHHHcCcchhHHHHHHHHHHHhHHHHHHhhhh--------------cc--c-cc
Confidence 566667777778888889999987764 35678899999998887776632221 00 0 11
Q ss_pred ceEeeeeeeEEEecCCCCCCccccccCCCccccceeeecCCCccEEEeccCCCCccccccccccchhhhhccccccceEE
Q psy13113 87 VVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDRREIRGLL 166 (286)
Q Consensus 87 ~~~g~iDgt~i~i~~P~~~~~~~y~~~k~~~s~~~q~vvd~~g~i~~~~~~~~Gs~~D~~~~~~s~l~~~l~~~~~~~~l 166 (286)
= .=.||-|.|.+.-- ..- +-..+|.+|..+++...---+...+..|-. ..++....+.-+
T Consensus 71 ~-~w~vDEt~ikv~gk---w~y------------lyrAid~~g~~Ld~~L~~rRn~~aAk~Fl~----kllk~~g~p~v~ 130 (215)
T COG3316 71 D-SWRVDETYIKVNGK---WHY------------LYRAIDADGLTLDVWLSKRRNALAAKAFLK----KLLKKHGEPRVF 130 (215)
T ss_pred c-ceeeeeeEEeeccE---eee------------hhhhhccCCCeEEEEEEcccCcHHHHHHHH----HHHHhcCCCceE
Confidence 1 23789999987621 111 124567778888888763434444444433 223322226688
Q ss_pred EccccCCCCCcccccccCCCCCChhhHHhHHHHHH-HHHHHHHHHHHHHhhhhhhhccccCCccchHHHHHHHHHHHhhh
Q psy13113 167 LGDIGYAQNEFTFTPVRNPITPTPSQVAYNAAQIR-TRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAVLHNIA 245 (286)
Q Consensus 167 lgD~gY~~~~~l~~p~~~~~~l~~~~~~~N~~~~~-~R~~vE~~~~~lK~rf~~L~~~~~~~~~~~~~ii~a~~~LhN~~ 245 (286)
+.|++=.....+- . +.. .+-+.-++ ....+|+-+..+|+|=+-+. .+. +...+...+...-.+|++-
T Consensus 131 vtDka~s~~~A~~----~---l~~---~~ehr~~~ylnN~iE~dh~~iKrr~~~~~-~f~-~~~sa~~~~~gie~i~~~~ 198 (215)
T COG3316 131 VTDKAPSYTAALR----K---LGS---EVEHRTSKYLNNRIEQDHRPIKRRTRPMK-RFK-SLSSAASTISGIESIHMLY 198 (215)
T ss_pred EecCccchHHHHH----h---cCc---chheecccccccchhhcchhHHHHhcccc-cCC-ChHHHHHHHHhHHHHHHHH
Confidence 8887632211110 0 000 00011111 13567888888888655442 121 3444455555555556554
Q ss_pred h
Q psy13113 246 I 246 (286)
Q Consensus 246 ~ 246 (286)
-
T Consensus 199 ~ 199 (215)
T COG3316 199 K 199 (215)
T ss_pred h
Confidence 3
No 250
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=74.70 E-value=5.2 Score=33.32 Aligned_cols=45 Identities=22% Similarity=0.251 Sum_probs=37.6
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
.+++.|+ =.|..++.|.+.+++|...++|..||..+..++..-|.
T Consensus 134 ~LT~RE~--eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KLg 178 (207)
T PRK11475 134 MLSPTER--EILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLG 178 (207)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 4777655 45667899999999999999999999999988877665
No 251
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=74.67 E-value=8.1 Score=24.91 Aligned_cols=37 Identities=22% Similarity=0.312 Sum_probs=31.4
Q ss_pred HHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 22 VLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 22 ~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
.+.+++.|.+..++|...++|..||.....++..-+.
T Consensus 12 v~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~ 48 (65)
T COG2771 12 ILRLVAQGKSNKEIARILGISEETVKTHLRNIYRKLG 48 (65)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 4556788899999999999999999998888766554
No 252
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=74.39 E-value=2.4 Score=28.57 Aligned_cols=21 Identities=19% Similarity=0.289 Sum_probs=18.3
Q ss_pred ChHhhhhhccccHhHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~ 51 (286)
+.+++|..-|||.+||+++++
T Consensus 2 t~~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHC
Confidence 467899999999999999774
No 253
>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=74.21 E-value=4.4 Score=29.00 Aligned_cols=32 Identities=22% Similarity=0.128 Sum_probs=25.1
Q ss_pred CChHhhhhhccccHhHHHHHHHHHHHHHHhhc
Q psy13113 30 NFQIDSEDYHDISQSTICRLVAKVSEELAKCH 61 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~ 61 (286)
.++..+|...||++||++|+-..+..-+..++
T Consensus 24 ~gq~~vA~~~Gv~eStISR~k~~~~~~~a~lL 55 (91)
T PF05269_consen 24 VGQKKVAEAMGVDESTISRWKNDFIEKMAMLL 55 (91)
T ss_dssp HHHHHHHHHHTSSTTTHHHHHHHHHHHHHHHH
T ss_pred HhhHHHHHHhCCCHHHHHHHHhhHHHHHHHHH
Confidence 46788999999999999999877665555443
No 254
>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=74.07 E-value=10 Score=27.93 Aligned_cols=45 Identities=18% Similarity=0.013 Sum_probs=30.9
Q ss_pred CCCHHHH-HHHHHHHhh---cCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 12 IHSPVVK-LLAVLRFYA---TGNFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 12 ~~~~~~~-l~~~L~~L~---~~~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
.+++.+- ++..|..+. .+.+..+++..++++++|+++.++.....
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~k 70 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKK 70 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 4555433 333444222 34799999999999999999998876543
No 255
>PHA01976 helix-turn-helix protein
Probab=73.85 E-value=5 Score=26.42 Aligned_cols=27 Identities=15% Similarity=-0.027 Sum_probs=23.3
Q ss_pred HhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 25 FYATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 25 ~L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
+-..|.+..++|...|+|++|+++|-+
T Consensus 11 R~~~glt~~~lA~~~gvs~~~v~~~e~ 37 (67)
T PHA01976 11 RNARAWSAPELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 445788999999999999999998764
No 256
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=73.73 E-value=3.7 Score=32.76 Aligned_cols=33 Identities=15% Similarity=0.062 Sum_probs=29.3
Q ss_pred cCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 28 TGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 28 ~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.|.++.++|..+|+|.+||...+.+....|...
T Consensus 135 ~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~ 167 (175)
T PRK12518 135 EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKF 167 (175)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999999999888887753
No 257
>PF12728 HTH_17: Helix-turn-helix domain
Probab=73.65 E-value=3 Score=25.94 Aligned_cols=22 Identities=23% Similarity=0.265 Sum_probs=19.1
Q ss_pred CChHhhhhhccccHhHHHHHHH
Q psy13113 30 NFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
.+..++|..+|||.+|+.++++
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 3567899999999999999886
No 258
>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=73.52 E-value=7.1 Score=28.39 Aligned_cols=39 Identities=13% Similarity=0.052 Sum_probs=32.7
Q ss_pred HHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 21 AVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 21 ~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
-+|.-+....++...|...|+|++|+++.+++..+.+..
T Consensus 8 ~~~~av~~~gSis~AA~~L~iS~stvs~~I~~LE~~lg~ 46 (99)
T TIGR00637 8 ALLKAIARMGSISQAAKDAGISYKSAWDYIRAMNNLSGE 46 (99)
T ss_pred HHHHHHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 344455567889999999999999999999999888875
No 259
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=73.35 E-value=12 Score=34.64 Aligned_cols=50 Identities=10% Similarity=0.117 Sum_probs=37.6
Q ss_pred CCCCCHHHHHHHHH-HHhhc--CCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 10 GVIHSPVVKLLAVL-RFYAT--GNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 10 ~~~~~~~~~l~~~L-~~L~~--~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
...++++++....+ ..|-. +.+..+++..++||++|+.+-++.+-..|..
T Consensus 8 ~~~~s~~ER~~~il~~LL~~~~~v~l~~Lae~l~VSrsTi~~DLk~l~~~L~~ 60 (426)
T PRK11564 8 PSVLSAPQRRCQILLMLFQPGLTVTLETFSQLNGVDDDTARQDIAETGREIQR 60 (426)
T ss_pred CcCCCHHHHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 36677777655444 44432 3578899999999999999999999888765
No 260
>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=73.30 E-value=5.7 Score=24.91 Aligned_cols=27 Identities=22% Similarity=0.080 Sum_probs=23.1
Q ss_pred HhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 25 FYATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 25 ~L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
+-..|.++.++|...|+|++|++++.+
T Consensus 11 r~~~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 11 RKALGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 345688999999999999999999864
No 261
>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=73.29 E-value=4.3 Score=26.65 Aligned_cols=24 Identities=8% Similarity=0.178 Sum_probs=18.7
Q ss_pred ChHhhhhhccccHhHHHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
+..+++..||||++|+.+.+....
T Consensus 26 s~~~la~~~~vsr~tvr~al~~L~ 49 (64)
T PF00392_consen 26 SERELAERYGVSRTTVREALRRLE 49 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CHHHHHHHhccCCcHHHHHHHHHH
Confidence 567899999999999998877554
No 262
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=73.05 E-value=6.7 Score=27.14 Aligned_cols=36 Identities=28% Similarity=0.314 Sum_probs=25.7
Q ss_pred HHHHHHHHHHhh--cCCChHhhhhhccccHhHHHHHHH
Q psy13113 16 VVKLLAVLRFYA--TGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 16 ~~~l~~~L~~L~--~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
..+|+..|..+. .+.++.++|...|+++++|+++.+
T Consensus 16 k~~l~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 16 KAQLMAAIRELREERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp HHHHHHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence 345566666555 467999999999999999999874
No 263
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=72.83 E-value=6.5 Score=32.96 Aligned_cols=45 Identities=16% Similarity=0.081 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
.+++.++=. |.+++.|.+.+++|..+++|.+||..++.+...-+.
T Consensus 155 ~Lt~rE~~V--l~l~~~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 155 LLTHREKEI--LNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCHHHHHH--HHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 466655443 444667999999999999999999999998877765
No 264
>PRK09483 response regulator; Provisional
Probab=72.80 E-value=5.8 Score=32.29 Aligned_cols=46 Identities=11% Similarity=0.039 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
..++..+.=.+ .++..|.+.+++|..+++|.+||..+++++..-|.
T Consensus 147 ~~Lt~rE~~vl--~~~~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~ 192 (217)
T PRK09483 147 ASLSERELQIM--LMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLN 192 (217)
T ss_pred cccCHHHHHHH--HHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 35777665554 45789999999999999999999999988877764
No 265
>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=72.78 E-value=8.3 Score=31.48 Aligned_cols=42 Identities=21% Similarity=0.088 Sum_probs=33.4
Q ss_pred CCCCCHHHHHHHHHHHhh-cCCChHhhhhhccccHhHHHHHHH
Q psy13113 10 GVIHSPVVKLLAVLRFYA-TGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 10 ~~~~~~~~~l~~~L~~L~-~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
+..+++.++.......+. .|.+...+|..+|+|+++|++++.
T Consensus 100 r~~lt~~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~ 142 (187)
T TIGR00180 100 REDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLR 142 (187)
T ss_pred ccCCCHHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHH
Confidence 456777777666655554 578999999999999999998875
No 266
>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=72.26 E-value=11 Score=32.46 Aligned_cols=47 Identities=11% Similarity=0.053 Sum_probs=39.3
Q ss_pred CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
...+++.++=.+.| ++.|.+..++|...|||..||...++++..-|.
T Consensus 188 ~~~LT~RE~evl~l--~a~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~ 234 (247)
T TIGR03020 188 AGLITAREAEILAW--VRDGKTNEEIAAILGISSLTVKNHLQHIFKKLD 234 (247)
T ss_pred ccCCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHhC
Confidence 44688877766665 579999999999999999999999998876664
No 267
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=72.16 E-value=5.8 Score=33.10 Aligned_cols=45 Identities=22% Similarity=0.284 Sum_probs=37.3
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
.++.++.- .|..|+.|.+-+++|...++|.+||..++.++..-|.
T Consensus 148 ~LT~RE~e--VL~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~ 192 (211)
T COG2197 148 LLTPRELE--VLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLG 192 (211)
T ss_pred CCCHHHHH--HHHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHcC
Confidence 46666554 4566999999999999999999999999988877665
No 268
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=71.91 E-value=7.2 Score=34.23 Aligned_cols=43 Identities=16% Similarity=0.103 Sum_probs=37.4
Q ss_pred HHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 17 VKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 17 ~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|-.++....++.++...|...+||+++|++.+++....|..
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 4566666677788899999999999999999999999999884
No 269
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=71.84 E-value=5.5 Score=33.32 Aligned_cols=49 Identities=14% Similarity=-0.006 Sum_probs=35.4
Q ss_pred CCCCHHHHHHHHHHH-hhcC-----CChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 11 VIHSPVVKLLAVLRF-YATG-----NFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~-L~~~-----~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
..|+..|.-++.+-| ++.. .+.++||..||||++|+++.+++...-|..
T Consensus 154 ~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~ 208 (215)
T COG3413 154 NDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIE 208 (215)
T ss_pred ccCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 356665554444443 3332 477889999999999999999998877664
No 270
>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=71.44 E-value=2.4 Score=26.35 Aligned_cols=18 Identities=22% Similarity=0.340 Sum_probs=16.1
Q ss_pred hhhhhccccHhHHHHHHH
Q psy13113 34 DSEDYHDISQSTICRLVA 51 (286)
Q Consensus 34 ~l~~~Fgvs~stv~~~~~ 51 (286)
++|...|||.+||+++++
T Consensus 2 ~lA~~~gvs~~tvs~~l~ 19 (52)
T cd01392 2 DIARAAGVSVATVSRVLN 19 (52)
T ss_pred cHHHHHCcCHHHHHHHHc
Confidence 688999999999999876
No 271
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=71.29 E-value=12 Score=25.11 Aligned_cols=39 Identities=18% Similarity=-0.003 Sum_probs=31.9
Q ss_pred HHHHHHHHHHhhcC-CChHhhhhhccc-cHhHHHHHHHHHH
Q psy13113 16 VVKLLAVLRFYATG-NFQIDSEDYHDI-SQSTICRLVAKVS 54 (286)
Q Consensus 16 ~~~l~~~L~~L~~~-~~~~~l~~~Fgv-s~stv~~~~~~v~ 54 (286)
..++.-++.+|..+ .+..++|..+|. |.+++++.|++..
T Consensus 36 ~~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk~~~ 76 (84)
T smart00342 36 DRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLF 76 (84)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 45566677787776 799999999999 9999999998764
No 272
>PRK00215 LexA repressor; Validated
Probab=70.87 E-value=9.2 Score=31.57 Aligned_cols=40 Identities=18% Similarity=0.212 Sum_probs=28.9
Q ss_pred HHHHHHHHH--hhcC--CChHhhhhhccc-cHhHHHHHHHHHHHH
Q psy13113 17 VKLLAVLRF--YATG--NFQIDSEDYHDI-SQSTICRLVAKVSEE 56 (286)
Q Consensus 17 ~~l~~~L~~--L~~~--~~~~~l~~~Fgv-s~stv~~~~~~v~~~ 56 (286)
.+++..|.. ..++ .+..+|+..+|+ +++|+++++......
T Consensus 7 ~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~ 51 (205)
T PRK00215 7 QEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERK 51 (205)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 444444442 3334 488899999999 999999999877654
No 273
>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=70.34 E-value=5.8 Score=25.64 Aligned_cols=25 Identities=8% Similarity=0.143 Sum_probs=21.1
Q ss_pred ChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
+.++++..||+|.+|+++.+....+
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~ 51 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA 51 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4789999999999999988876544
No 274
>PHA00738 putative HTH transcription regulator
Probab=70.00 E-value=12 Score=27.69 Aligned_cols=40 Identities=10% Similarity=-0.087 Sum_probs=28.8
Q ss_pred HHHHHHHHHhhc-CCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 17 VKLLAVLRFYAT-GNFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 17 ~~l~~~L~~L~~-~~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
.++.|..+.... .++-.+++..|++|++|||+.++-..++
T Consensus 13 tRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreA 53 (108)
T PHA00738 13 LRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQ 53 (108)
T ss_pred HHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHC
Confidence 344444433333 3688899999999999999998866655
No 275
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=69.83 E-value=15 Score=28.84 Aligned_cols=46 Identities=11% Similarity=-0.025 Sum_probs=32.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
..++..++-++.+..-..-.++.++|...|+|++||.+-+++..+.
T Consensus 5 ~~lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~ 50 (153)
T PRK11179 5 YQIDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQA 50 (153)
T ss_pred cccCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3455544444444333444799999999999999999888766543
No 276
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=69.72 E-value=11 Score=28.46 Aligned_cols=44 Identities=27% Similarity=0.131 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHHhhc-CCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 13 HSPVVKLLAVLRFYAT-GNFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 13 ~~~~~~l~~~L~~L~~-~~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
++-+.++.+......+ ..+..+++..+|++++|+++.++...++
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 3445556555544443 3578899999999999999999877665
No 277
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=69.46 E-value=11 Score=28.78 Aligned_cols=30 Identities=17% Similarity=0.072 Sum_probs=26.2
Q ss_pred hcCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 27 ATGNFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 27 ~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
..+.+-.++|...+.++|||++.+++.+.+
T Consensus 40 ~~~~tvdelae~lnr~rStv~rsl~~L~~~ 69 (126)
T COG3355 40 NGPLTVDELAEILNRSRSTVYRSLQNLLEA 69 (126)
T ss_pred cCCcCHHHHHHHHCccHHHHHHHHHHHHHc
Confidence 455688999999999999999999887765
No 278
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=69.43 E-value=12 Score=34.62 Aligned_cols=52 Identities=12% Similarity=-0.014 Sum_probs=47.1
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.|...+....|++|.|.+--++.++..++..||-.++||.-.++.+...+.+
T Consensus 344 ~R~~~i~~~RqiamyL~r~lt~~Slp~IG~~FgrdHtTV~~a~~kI~~~~~~ 395 (408)
T COG0593 344 SRTRNIVRPRQIAMYLARELTNLSLPEIGKAFGRDHTTVLHAVRKIEQLIEE 395 (408)
T ss_pred ccccccchHHHHHHHHHHHHccCcHHHHHHHhCCCccHHHHHHHHHHHHHhc
Confidence 4667788899999999999999999999999999999999999998888864
No 279
>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=68.93 E-value=3.1 Score=36.55 Aligned_cols=21 Identities=19% Similarity=0.265 Sum_probs=19.5
Q ss_pred ChHhhhhhccccHhHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~ 51 (286)
+.+++|...|||++|||++++
T Consensus 3 ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 3 TIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred cHHHHHHHhCCCHHHHHHHhC
Confidence 578999999999999999996
No 280
>PRK11050 manganese transport regulator MntR; Provisional
Probab=68.60 E-value=11 Score=29.71 Aligned_cols=28 Identities=18% Similarity=0.321 Sum_probs=24.1
Q ss_pred cCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 28 TGNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 28 ~~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
.+.+..+++..+++|++|+++.+.+...
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~ 77 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLAR 77 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4568999999999999999998876654
No 281
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=67.98 E-value=11 Score=28.43 Aligned_cols=24 Identities=13% Similarity=0.218 Sum_probs=22.4
Q ss_pred cCCChHhhhhhccccHhHHHHHHH
Q psy13113 28 TGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 28 ~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
-|.++..+|...|+|++.|++|++
T Consensus 21 eG~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 21 EGLSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred cCCcHHHHHHHhCCCHHHHHHHHc
Confidence 399999999999999999999986
No 282
>PRK09191 two-component response regulator; Provisional
Probab=67.88 E-value=14 Score=31.28 Aligned_cols=48 Identities=13% Similarity=0.134 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.+|+.++-.+.|.++ .+.++.++|...|+|.+||...+.+....+...
T Consensus 88 ~L~~~~r~v~~l~~~-~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~ 135 (261)
T PRK09191 88 GLTPLPRQAFLLTAL-EGFSVEEAAEILGVDPAEAEALLDDARAEIARQ 135 (261)
T ss_pred hCCHHHhHHHHHHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhcc
Confidence 577777777777766 458899999999999999999999888888753
No 283
>PRK10072 putative transcriptional regulator; Provisional
Probab=67.82 E-value=5.1 Score=29.00 Aligned_cols=26 Identities=15% Similarity=-0.027 Sum_probs=23.1
Q ss_pred hhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 26 YATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 26 L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
-..|.++..+|..+|+|.+||+.|.+
T Consensus 43 ~~~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 43 KGTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 34688999999999999999999875
No 284
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=67.78 E-value=12 Score=32.08 Aligned_cols=40 Identities=20% Similarity=0.083 Sum_probs=32.1
Q ss_pred HHHHHHHHHHhhcC--CChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 16 VVKLLAVLRFYATG--NFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 16 ~~~l~~~L~~L~~~--~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
+++....|.+|... .+..+++..||||++|+.|.++...+
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~ 45 (251)
T PRK13509 4 AQRHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDE 45 (251)
T ss_pred HHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45666667777764 48889999999999999999998754
No 285
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 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 [].; PDB: 2WTE_A 3SQN_A.
Probab=67.55 E-value=16 Score=23.63 Aligned_cols=40 Identities=23% Similarity=0.121 Sum_probs=27.8
Q ss_pred HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
+|+-.|.- ....++.++|...|+|..|+...+.+.-+.+-
T Consensus 9 ~Ll~~L~~-~~~~~~~ela~~l~~S~rti~~~i~~L~~~f~ 48 (59)
T PF08280_consen 9 KLLELLLK-NKWITLKELAKKLNISERTIKNDINELNEFFP 48 (59)
T ss_dssp HHHHHHHH-HTSBBHHHHHHHCTS-HHHHHHHHHHHHTT--
T ss_pred HHHHHHHc-CCCCcHHHHHHHHCCCHHHHHHHHHHHHHHhh
Confidence 34444444 55679999999999999999998876654443
No 286
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=67.12 E-value=11 Score=31.53 Aligned_cols=45 Identities=13% Similarity=0.118 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHhhcC----------CChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATG----------NFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~----------~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
..+++++++-+|..+... .+.+++|...|+++.|++|+++++.+.
T Consensus 146 ~~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~lG~tretvsR~l~~L~~~ 200 (236)
T PRK09392 146 LRSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYLGMTPENLSRAFAALASH 200 (236)
T ss_pred cCCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHhCCChhHHHHHHHHHHhC
Confidence 458899999999877642 235789999999999999999876543
No 287
>PRK09492 treR trehalose repressor; Provisional
Probab=66.81 E-value=3.6 Score=36.09 Aligned_cols=23 Identities=17% Similarity=0.219 Sum_probs=21.0
Q ss_pred CChHhhhhhccccHhHHHHHHHH
Q psy13113 30 NFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
.+.+++|...|||.+|||++++.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCC
Confidence 47899999999999999999974
No 288
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=66.77 E-value=11 Score=33.25 Aligned_cols=43 Identities=14% Similarity=0.090 Sum_probs=37.3
Q ss_pred HHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 17 VKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 17 ~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|-.++....++.++...|...++|++++++.+++..+.+..
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 4566666677788899999999999999999999999998874
No 289
>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=66.59 E-value=4.8 Score=29.80 Aligned_cols=36 Identities=22% Similarity=0.205 Sum_probs=27.4
Q ss_pred HHHhhc-CCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 23 LRFYAT-GNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 23 L~~L~~-~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
+.-|++ |.++..+|..|+||.||+..+..+.-.--+
T Consensus 73 fi~LR~AGlt~~aIAd~F~iS~s~~~nft~~n~~eYy 109 (126)
T PF10654_consen 73 FIELRHAGLTCYAIADYFKISKSTVFNFTQNNKKEYY 109 (126)
T ss_pred HHHHHhcCCChHHHHHHHhHHHHHHHHHHHHhHHHHH
Confidence 334555 679999999999999999988865544433
No 290
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=66.45 E-value=17 Score=22.83 Aligned_cols=42 Identities=14% Similarity=0.020 Sum_probs=25.8
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
|+..|+..||--+-++ ...|.+..+++...|-|+.++.++++
T Consensus 1 RG~~Lt~~Eqaqid~m-~qlG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 1 RGKTLTDAEQAQIDVM-HQLGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp -S----HHHHHHHHHH-HHTT--HHHHHHHHT--HHHHHHHHH
T ss_pred CCCcCCHHHHHHHHHH-HHhchhHHHHHHHhCccHHHHHHHhc
Confidence 3566777777766554 45678999999999999999998875
No 291
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=65.77 E-value=16 Score=31.52 Aligned_cols=46 Identities=15% Similarity=0.065 Sum_probs=36.1
Q ss_pred CCCCCCHHHHHHHHHHHhhcC-CChHhhhhhccccHhHHHHHHHHHH
Q psy13113 9 RGVIHSPVVKLLAVLRFYATG-NFQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 9 ~~~~~~~~~~l~~~L~~L~~~-~~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
....++.+++-.+-+..=+.| ..+.+|....|.|++|++|++++..
T Consensus 189 ~~~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LE 235 (258)
T COG2512 189 NEYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLE 235 (258)
T ss_pred ccCCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHH
Confidence 346677777777766665566 5899999999999999999988654
No 292
>PF09182 PuR_N: Bacterial purine repressor, N-terminal; InterPro: IPR015265 The N-terminal domain of the bacterial purine repressor PuR is a winged-helix domain, a subdivision of the HTH structural family. It consists of a canonical arrangement of secondary structures: a1-b1-a2-T-a3-b2-W-b3, where a2-T-a3 is the HTH motif, a3 is the recognition helix, and W is the wing. The domain allows for recognition of a conserved CGAA sequence in the centre of a DNA PurBox, resulting in binding to the major groove of DNA []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1O57_B 1P4A_D.
Probab=65.34 E-value=27 Score=23.61 Aligned_cols=42 Identities=12% Similarity=0.181 Sum_probs=26.8
Q ss_pred HHHHHHHHHhhcCC----ChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 17 VKLLAVLRFYATGN----FQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 17 ~~l~~~L~~L~~~~----~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
++|.....+|-.+. +....+..|++++||+|+=+.-+-+++.
T Consensus 4 eRlv~it~~L~~~P~~lisL~~Fae~f~~AKSsISEDl~iik~~~~ 49 (70)
T PF09182_consen 4 ERLVAITKYLLENPNKLISLTYFAERFGAAKSSISEDLSIIKETFE 49 (70)
T ss_dssp HHHHHHHHHHHTSTT--EEHHHHHHHHT--HHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHcCCcceEcHHHHHHHhcccccchHHHHHHHHHHHH
Confidence 45555556665543 6677899999999999985554444443
No 293
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=65.08 E-value=18 Score=29.54 Aligned_cols=41 Identities=7% Similarity=-0.031 Sum_probs=29.6
Q ss_pred CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
..+++.+-..+...+-..+.++.++|...+++++|+++++.
T Consensus 41 ~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~ 81 (185)
T PRK13777 41 YDLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSK 81 (185)
T ss_pred CCCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHH
Confidence 45666555444444444578999999999999999988765
No 294
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=64.59 E-value=22 Score=21.15 Aligned_cols=26 Identities=23% Similarity=0.239 Sum_probs=19.8
Q ss_pred hcCCChHhhhhhccccHhHHHHHHHH
Q psy13113 27 ATGNFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 27 ~~~~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
.++......|...|||++|+++-+++
T Consensus 16 ~~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 16 RCGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HTTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HhCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 45668889999999999999986653
No 295
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=64.57 E-value=14 Score=29.40 Aligned_cols=44 Identities=5% Similarity=-0.056 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
++..++-++.+..-..-.++.++|...|+|.+||.+-+++..+.
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~ 55 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQ 55 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 44334444443333334699999999999999999988766543
No 296
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=64.56 E-value=4.2 Score=36.08 Aligned_cols=23 Identities=17% Similarity=0.014 Sum_probs=21.1
Q ss_pred CChHhhhhhccccHhHHHHHHHH
Q psy13113 30 NFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
.+.+++|..+|||.+||+++++.
T Consensus 7 ~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 7 ITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHHCC
Confidence 57899999999999999999875
No 297
>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=64.55 E-value=15 Score=30.42 Aligned_cols=37 Identities=14% Similarity=0.032 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113 15 PVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 15 ~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
...+++..|..- .+.+..+|+..+|++.+||++.+..
T Consensus 2 tr~~IL~~L~~~-~~~t~~eLA~~lgis~~tV~~~L~~ 38 (203)
T TIGR02702 2 TKEDILSYLLKQ-GQATAAALAEALAISPQAVRRHLKD 38 (203)
T ss_pred HHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 345566666543 4479999999999999999987753
No 298
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=64.55 E-value=6.5 Score=25.48 Aligned_cols=26 Identities=31% Similarity=0.325 Sum_probs=19.2
Q ss_pred hcCCChHhhhhhccccHhHHHHHHHH
Q psy13113 27 ATGNFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 27 ~~~~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
..|.+..+||..-|+|++|++++++.
T Consensus 8 ~~~it~~~La~~~gis~~tl~~~~~~ 33 (63)
T PF13443_consen 8 ERGITQKDLARKTGISRSTLSRILNG 33 (63)
T ss_dssp HTT--HHHHHHHHT--HHHHHHHHTT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 46779999999999999999998873
No 299
>PRK10870 transcriptional repressor MprA; Provisional
Probab=64.53 E-value=16 Score=29.54 Aligned_cols=24 Identities=8% Similarity=-0.010 Sum_probs=20.8
Q ss_pred CChHhhhhhccccHhHHHHHHHHH
Q psy13113 30 NFQIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~~v 53 (286)
.+..+|+..++++++|+++++++.
T Consensus 72 it~~eLa~~l~l~~~tvsr~v~rL 95 (176)
T PRK10870 72 IQPSELSCALGSSRTNATRIADEL 95 (176)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHH
Confidence 577999999999999999888644
No 300
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=64.37 E-value=13 Score=36.59 Aligned_cols=48 Identities=19% Similarity=0.203 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHHh---hcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFY---ATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.|+..++..+.++|. ..+.++..+|..||||+..|+++-.+.+.-|-.
T Consensus 556 ~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~ 606 (619)
T PRK05658 556 SLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 606 (619)
T ss_pred cCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhc
Confidence 578889999999885 356799999999999999999988887776654
No 301
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=64.27 E-value=16 Score=23.57 Aligned_cols=36 Identities=14% Similarity=0.125 Sum_probs=30.1
Q ss_pred HHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 23 LRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 23 L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
-.||.++++....|...+|++.|+..-++++.+.+.
T Consensus 6 ~~yl~~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g 41 (59)
T PF13556_consen 6 RAYLENNGNISKTARALHIHRNTLRYRLKKIEELLG 41 (59)
T ss_dssp HHHHHTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 457889999999999999999999999988887765
No 302
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=64.08 E-value=13 Score=29.67 Aligned_cols=45 Identities=18% Similarity=0.058 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
.+++.+. -.|.+|+.|.+.++++..+++|.+|+...+.++..-|.
T Consensus 137 ~Lt~~E~--~il~~l~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRER--QVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3555444 34556888999999999999999999999988877664
No 303
>PRK09526 lacI lac repressor; Reviewed
Probab=64.08 E-value=4.4 Score=35.96 Aligned_cols=23 Identities=22% Similarity=0.332 Sum_probs=20.8
Q ss_pred CChHhhhhhccccHhHHHHHHHH
Q psy13113 30 NFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
.+.+++|...|||.+|||++++.
T Consensus 6 ~ti~dIA~~aGVS~~TVSrvLn~ 28 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRVLNQ 28 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHhcC
Confidence 47889999999999999999973
No 304
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=63.60 E-value=14 Score=32.66 Aligned_cols=43 Identities=16% Similarity=0.109 Sum_probs=36.8
Q ss_pred HHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 17 VKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 17 ~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
++|-.++....++.++...|...++|++||++.+++....|..
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 4565666666677899999999999999999999999999885
No 305
>PRK10651 transcriptional regulator NarL; Provisional
Probab=63.52 E-value=12 Score=30.17 Aligned_cols=45 Identities=20% Similarity=0.208 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
.+++.+. =.|.+|..|.+.++++...++|..||..++.+...-|.
T Consensus 155 ~Lt~rE~--~vl~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 155 QLTPRER--DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 3777654 44556889999999999999999999999998877664
No 306
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=63.33 E-value=16 Score=29.83 Aligned_cols=42 Identities=12% Similarity=-0.016 Sum_probs=32.2
Q ss_pred CHHHHHHHHHHHhhcCC--ChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 14 SPVVKLLAVLRFYATGN--FQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 14 ~~~~~l~~~L~~L~~~~--~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
..+++....|.+|.... +..+|+..||||.+|+.|=+.....
T Consensus 4 ~~~~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~ 47 (185)
T PRK04424 4 SKKERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGI 47 (185)
T ss_pred CHHHHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhc
Confidence 34566666677777654 7889999999999999998876543
No 307
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=63.14 E-value=16 Score=31.53 Aligned_cols=42 Identities=17% Similarity=0.254 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHhhcCC--ChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 15 PVVKLLAVLRFYATGN--FQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 15 ~~~~l~~~L~~L~~~~--~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
.+++....|-+|.... +..+|+..||||..|++|-+....+.
T Consensus 3 ~~eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~ 46 (256)
T PRK10434 3 PRQRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHA 46 (256)
T ss_pred HHHHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 4567777788888654 88899999999999999998876544
No 308
>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=62.98 E-value=21 Score=29.49 Aligned_cols=34 Identities=21% Similarity=0.128 Sum_probs=26.1
Q ss_pred HHHHHhhc--CCChHhhhhhccccHhHHHHHHHHHH
Q psy13113 21 AVLRFYAT--GNFQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 21 ~~L~~L~~--~~~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
..|.+|.. +.+..+++..+|+|++|+++.+....
T Consensus 147 ~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le 182 (203)
T TIGR01884 147 KVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELE 182 (203)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 33455554 45899999999999999999887644
No 309
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=62.34 E-value=9.7 Score=25.62 Aligned_cols=28 Identities=18% Similarity=0.050 Sum_probs=23.0
Q ss_pred HHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 24 RFYATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 24 ~~L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
++-..+.++.+||...|||+.|+..+=+
T Consensus 9 ~R~~~~ltQ~elA~~vgVsRQTi~~iEk 36 (68)
T COG1476 9 LRAELGLTQEELAKLVGVSRQTIIAIEK 36 (68)
T ss_pred HHHHhCcCHHHHHHHcCcCHHHHHHHHc
Confidence 4455789999999999999999886543
No 310
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=62.14 E-value=9.5 Score=32.55 Aligned_cols=40 Identities=15% Similarity=0.107 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
.+-..-++.-.|+.|+..-+|++|+..+|++.+.++||++
T Consensus 6 ~~~~~~~~v~~lr~lk~~~ty~el~~~~g~p~~~l~RYv~ 45 (238)
T PRK08558 6 KVRLQLRAVRVLRSLKKTYTYEELSSITGLPESVLNRYVN 45 (238)
T ss_pred hHHHHHHHHHHHHHHhcccCHHHHHHHHCCCHHHHHHHHc
Confidence 3445566777899999999999999999999999999875
No 311
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=62.02 E-value=8.5 Score=24.06 Aligned_cols=21 Identities=29% Similarity=0.347 Sum_probs=17.0
Q ss_pred ChHhhhhhccccHhHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~ 51 (286)
+..+++...|+|++|+++.++
T Consensus 5 ~~~ev~~~~g~s~~ti~~~~k 25 (51)
T PF05930_consen 5 RIKEVAELLGVSRSTIYRLIK 25 (51)
T ss_dssp -HHHHHHHHSS-HHHHHHHHH
T ss_pred cHHHHHHHHCCCHHHHHHHHh
Confidence 456889999999999999887
No 312
>PRK11569 transcriptional repressor IclR; Provisional
Probab=61.91 E-value=23 Score=30.71 Aligned_cols=46 Identities=15% Similarity=0.179 Sum_probs=37.8
Q ss_pred CCCCHHHHHHHHHHHhhc---CCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 11 VIHSPVVKLLAVLRFYAT---GNFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~---~~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
..++.-++.+-.|.+|+. +.+..+++...|+++||++++++..++.
T Consensus 22 ~~v~sl~ral~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~ 70 (274)
T PRK11569 22 GQVQSLTRGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQ 70 (274)
T ss_pred cCccHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 446677888888888875 3589999999999999999999887654
No 313
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=61.85 E-value=22 Score=30.80 Aligned_cols=45 Identities=18% Similarity=0.175 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHHHHhhc---CCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYAT---GNFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~---~~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
.++.-++.+-.|..++. +.+..+++...|+++||++++++..+..
T Consensus 20 ~~~sl~r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~ 67 (271)
T PRK10163 20 GAQALERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAA 67 (271)
T ss_pred cchHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 46777888888888874 3578999999999999999999887754
No 314
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=61.66 E-value=5.2 Score=35.67 Aligned_cols=21 Identities=19% Similarity=0.210 Sum_probs=19.6
Q ss_pred ChHhhhhhccccHhHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~ 51 (286)
+.+++|...|||.+||+++++
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (346)
T PRK10401 3 TIRDVARQAGVSVATVSRVLN 23 (346)
T ss_pred CHHHHHHHhCCCHHHHHHHHC
Confidence 678999999999999999997
No 315
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=61.32 E-value=4.5 Score=35.82 Aligned_cols=23 Identities=17% Similarity=0.284 Sum_probs=20.4
Q ss_pred CChHhhhhhccccHhHHHHHHHH
Q psy13113 30 NFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
.+.+++|...|||.+|||++++.
T Consensus 6 ~ti~dIA~~agVS~~TVSrvLn~ 28 (331)
T PRK14987 6 PVLQDVADRVGVTKMTVSRFLRN 28 (331)
T ss_pred CcHHHHHHHhCCCHHHhhhhhCC
Confidence 47789999999999999999853
No 316
>PRK10403 transcriptional regulator NarP; Provisional
Probab=61.19 E-value=14 Score=29.63 Aligned_cols=45 Identities=18% Similarity=0.093 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
.++..+.- .|.++..|.+..+++...++|..||..++.++..-|.
T Consensus 153 ~Lt~~e~~--vl~~~~~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 153 VLTERELD--VLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred cCCHHHHH--HHHHHHCCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 35665544 4566789999999999999999999999998877764
No 317
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=61.16 E-value=22 Score=26.61 Aligned_cols=34 Identities=21% Similarity=0.143 Sum_probs=25.4
Q ss_pred HHHHHHhhcCCChHhhhhhccccHhHHHHHHHHH
Q psy13113 20 LAVLRFYATGNFQIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 20 ~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v 53 (286)
+..+.--..+.+..++|..||||.+|+++.+++.
T Consensus 62 L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrl 95 (119)
T PF01710_consen 62 LKALVEENPDATLRELAERLGVSPSTIWRALKRL 95 (119)
T ss_pred HHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHc
Confidence 3444333445688999999999999999887754
No 318
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=61.11 E-value=14 Score=23.98 Aligned_cols=33 Identities=9% Similarity=-0.172 Sum_probs=29.1
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhcc
Q psy13113 8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHD 40 (286)
Q Consensus 8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fg 40 (286)
.|...++...++++.|..--.+.++.+++..||
T Consensus 24 ~R~~~~~~aR~iamyla~~~~~~sl~~Ig~~fg 56 (60)
T smart00760 24 SRKREIVLARQIAMYLARELTDLSLPEIGKIFG 56 (60)
T ss_pred CCCcchhHHHHHHHHHHHHHHCCCHHHHHHHhC
Confidence 345778889999999999989999999999998
No 319
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=61.02 E-value=13 Score=32.83 Aligned_cols=51 Identities=16% Similarity=0.060 Sum_probs=43.1
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+|..+...-+.+-.+.-++...++...|...+||++||++.+++....|..
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 345556666777777888888999999999999999999999999988874
No 320
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=60.92 E-value=5.5 Score=35.34 Aligned_cols=22 Identities=18% Similarity=0.250 Sum_probs=20.2
Q ss_pred ChHhhhhhccccHhHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
+.+++|...|||.+||+++++.
T Consensus 3 Ti~dIA~~agVS~~TVSrvLn~ 24 (341)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINK 24 (341)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 6789999999999999999984
No 321
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=60.88 E-value=16 Score=31.43 Aligned_cols=45 Identities=20% Similarity=0.147 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHhhcC---CChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATG---NFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~---~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
.++.-++.+-.|..|+.. .+..+++..+|++++|++++++.....
T Consensus 6 ~v~sl~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~ 53 (263)
T PRK09834 6 TVRGLSRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEE 53 (263)
T ss_pred hHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 355567777778888642 589999999999999999999887654
No 322
>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=60.84 E-value=18 Score=30.82 Aligned_cols=86 Identities=14% Similarity=0.169 Sum_probs=54.4
Q ss_pred CCCHHHHHHHHHHHhhc---CCChHhhhhhccccHhHHHHHHHHHHHH--HHhhcccccCCch----------------h
Q psy13113 12 IHSPVVKLLAVLRFYAT---GNFQIDSEDYHDISQSTICRLVAKVSEE--LAKCHQQWIHFPE----------------D 70 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~---~~~~~~l~~~Fgvs~stv~~~~~~v~~~--l~~~~~~~i~~P~----------------~ 70 (286)
.++.-++.+-.|..++. +.+..+++...|+++||+++++...... +..-...|.-=|. .
T Consensus 4 ~v~sl~ral~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~~~~~Y~lG~~~~~lg~~~~~~~~l~~~ 83 (248)
T TIGR02431 4 FVASLARGLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTSDGRLFWLTPRVLRLGYAYLSSAPLPKV 83 (248)
T ss_pred hHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCEEEecHHHHHHHHHHHhcCchHHH
Confidence 35556777778888864 3589999999999999999999887654 2111111211111 1
Q ss_pred HHHHHHHhhhhcCCCCceEeeeeeeEEE
Q psy13113 71 LQTAKNQFSGIAGFPRVVVGCIDGTHVP 98 (286)
Q Consensus 71 ~~~~~~~f~~~~~~p~~~~g~iDgt~i~ 98 (286)
....+....+..+..-. +++.|+..+-
T Consensus 84 a~p~l~~L~~~~g~tv~-L~v~~g~~~v 110 (248)
T TIGR02431 84 AQPLLERLSAQTHESCS-VAVLDGDEIV 110 (248)
T ss_pred HHHHHHHHHHHHCCeEE-EEEEeCCEEE
Confidence 22333444555666666 8888887643
No 323
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=60.69 E-value=15 Score=29.51 Aligned_cols=45 Identities=22% Similarity=0.223 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
.++..+. -.|.+|..|.+..+++...++|.+||..++.++..-|.
T Consensus 143 ~lt~~E~--~vl~~l~~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~ 187 (204)
T PRK09958 143 SLSKQEI--SVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLE 187 (204)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 4677654 36677788999999999999999999999988877764
No 324
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=60.64 E-value=5.8 Score=34.98 Aligned_cols=22 Identities=9% Similarity=0.048 Sum_probs=19.8
Q ss_pred ChHhhhhhccccHhHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
+.+++|...|||.+|||++++.
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 5689999999999999999874
No 325
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=60.09 E-value=9.1 Score=28.24 Aligned_cols=30 Identities=17% Similarity=0.203 Sum_probs=21.8
Q ss_pred cCCChHhhhhhccccHhHHHHHHHHHHHHH
Q psy13113 28 TGNFQIDSEDYHDISQSTICRLVAKVSEEL 57 (286)
Q Consensus 28 ~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l 57 (286)
.|.+..+||..||+|..+|.+++++.-...
T Consensus 71 ~G~n~~eLA~kyglS~r~I~~Ii~~~~~~~ 100 (108)
T PF08765_consen 71 NGMNVRELARKYGLSERQIYRIIKRVRRRE 100 (108)
T ss_dssp -SS-HHHHHHHHT--HHHHHHHHHHHHH--
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 478999999999999999999998775543
No 326
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=59.93 E-value=10 Score=26.82 Aligned_cols=25 Identities=12% Similarity=0.344 Sum_probs=21.0
Q ss_pred hHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 32 QIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 32 ~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
..+++..+|++++|+++.+.+....
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~ 26 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKD 26 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHC
Confidence 4689999999999999988876553
No 327
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=59.81 E-value=18 Score=30.84 Aligned_cols=39 Identities=13% Similarity=0.152 Sum_probs=29.5
Q ss_pred HHHHHHHHhhc--CCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 18 KLLAVLRFYAT--GNFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 18 ~l~~~L~~L~~--~~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
+....|.+|.. ..+..+++..||||++|+.|.+......
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~ 45 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQ 45 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 33344455543 4588899999999999999999988663
No 328
>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=59.34 E-value=19 Score=27.27 Aligned_cols=35 Identities=11% Similarity=0.196 Sum_probs=25.8
Q ss_pred HHHHHHHhhcC----CChHhhhhhccccHhHHHHHHHHH
Q psy13113 19 LLAVLRFYATG----NFQIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 19 l~~~L~~L~~~----~~~~~l~~~Fgvs~stv~~~~~~v 53 (286)
-+.+|.+|+.. .+..+++..+|+|.+++++++...
T Consensus 11 al~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L 49 (130)
T TIGR02944 11 ATLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQL 49 (130)
T ss_pred HHHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHH
Confidence 34455566532 488899999999999999887644
No 329
>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=59.30 E-value=13 Score=28.00 Aligned_cols=28 Identities=11% Similarity=-0.050 Sum_probs=24.1
Q ss_pred HHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 24 RFYATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 24 ~~L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
.+-..|.++.++|..+|+|++|+++|-+
T Consensus 73 ~r~~~gltq~~lA~~lg~~~~tis~~e~ 100 (127)
T TIGR03830 73 IRKKLGLSQREAAELLGGGVNAFSRYER 100 (127)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 3455688999999999999999999865
No 330
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=59.07 E-value=16 Score=31.92 Aligned_cols=40 Identities=18% Similarity=0.161 Sum_probs=32.6
Q ss_pred HHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 20 LAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 20 ~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+-++.-++...++...|...|+|++||++.+++....+..
T Consensus 6 L~~F~~v~~~~S~s~AA~~L~isQ~avS~~I~~LE~~lg~ 45 (305)
T PRK11233 6 LKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQ 45 (305)
T ss_pred HHHHHHHHHcCCHHHHHHHhCCCchHHHHHHHHHHHHhCC
Confidence 3344445555699999999999999999999999988874
No 331
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=58.96 E-value=5.3 Score=35.32 Aligned_cols=22 Identities=18% Similarity=0.135 Sum_probs=19.9
Q ss_pred ChHhhhhhccccHhHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
+.+++|...|||.+|||++++.
T Consensus 3 ti~dIA~~agVS~~TVSrvln~ 24 (327)
T PRK10339 3 TLKDIAIEAGVSLATVSRVLND 24 (327)
T ss_pred CHHHHHHHhCCCHHhhhhhhcC
Confidence 5789999999999999999874
No 332
>PF14493 HTH_40: Helix-turn-helix domain
Probab=58.16 E-value=24 Score=24.95 Aligned_cols=37 Identities=16% Similarity=0.197 Sum_probs=32.4
Q ss_pred HHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 20 LAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 20 ~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
..++.++..|.+..++|..-|++.+||...+-+.+..
T Consensus 4 ~~T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~ 40 (91)
T PF14493_consen 4 QITYELFQKGLSIEEIAKIRGLKESTIYGHLAELIES 40 (91)
T ss_pred HHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence 4678888899999999999999999999888776655
No 333
>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=58.15 E-value=12 Score=25.38 Aligned_cols=27 Identities=22% Similarity=0.174 Sum_probs=23.5
Q ss_pred HhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 25 FYATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 25 ~L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
+-..+.+..++|...|+|++|++++.+
T Consensus 14 ~~~~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 14 LEPLGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 355778999999999999999999875
No 334
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=58.05 E-value=21 Score=30.99 Aligned_cols=45 Identities=11% Similarity=0.013 Sum_probs=36.0
Q ss_pred CCCCHHHHHHHHHHHhhcCC--ChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 11 VIHSPVVKLLAVLRFYATGN--FQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~--~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
+.-...++....+.+|.... +..+|+..||||..|+.|-+.....
T Consensus 11 ~~~~~~eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~ 57 (269)
T PRK09802 11 RVTGTSERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEK 57 (269)
T ss_pred hhccHHHHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHh
Confidence 34445678888888887754 8889999999999999999887644
No 335
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=57.85 E-value=5.9 Score=34.83 Aligned_cols=19 Identities=21% Similarity=0.335 Sum_probs=17.7
Q ss_pred HhhhhhccccHhHHHHHHH
Q psy13113 33 IDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 33 ~~l~~~Fgvs~stv~~~~~ 51 (286)
+++|...|||.+|||++++
T Consensus 2 ~dIA~~agVS~~TVSrvLn 20 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVIN 20 (327)
T ss_pred hhHHHHhCCcHHHHHHHhC
Confidence 5899999999999999986
No 336
>PRK14999 histidine utilization repressor; Provisional
Probab=57.83 E-value=35 Score=28.84 Aligned_cols=48 Identities=15% Similarity=0.089 Sum_probs=35.1
Q ss_pred CCCCCCCHHHHHHHHHH-HhhcC-----C---ChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 8 ARGVIHSPVVKLLAVLR-FYATG-----N---FQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 8 ~~~~~~~~~~~l~~~L~-~L~~~-----~---~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
.+....|...|+.-.|. .+..| . +-++|+..||||+.||.+.+.....
T Consensus 6 ~~~~~~ply~qi~~~i~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~ 62 (241)
T PRK14999 6 SRSAPAPFYETVKQDICKKIAGGVWQPHDRIPSEAELVAQYGFSRMTINRALRELTD 62 (241)
T ss_pred cCcCCCcHHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45566788888876664 34443 2 6788999999999999998876543
No 337
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=57.79 E-value=23 Score=30.45 Aligned_cols=41 Identities=15% Similarity=0.152 Sum_probs=31.9
Q ss_pred HHHHHHHHHHhhcCC--ChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 16 VVKLLAVLRFYATGN--FQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 16 ~~~l~~~L~~L~~~~--~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
.++.-..|.+|.... +..+|++.|+||..|++|.+....+.
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~ 46 (252)
T PRK10906 4 TQRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQ 46 (252)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 455556666676654 88899999999999999988877653
No 338
>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=57.79 E-value=9 Score=25.42 Aligned_cols=23 Identities=17% Similarity=0.176 Sum_probs=17.2
Q ss_pred CChHhhhhhccccHhHHH-HHHHH
Q psy13113 30 NFQIDSEDYHDISQSTIC-RLVAK 52 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~-~~~~~ 52 (286)
.+..++|...|||++|++ .+.++
T Consensus 13 ~~~~~lA~~lgis~st~s~~~~~r 36 (66)
T PF07022_consen 13 KSDKELAERLGISKSTLSNNWKKR 36 (66)
T ss_dssp SSCHHHHCCTT--HHHHH-HHHHS
T ss_pred CCHHHHHHHhCcCHHHhhHHHHhC
Confidence 466799999999999999 66653
No 339
>PRK09726 antitoxin HipB; Provisional
Probab=57.65 E-value=11 Score=26.45 Aligned_cols=35 Identities=20% Similarity=0.230 Sum_probs=27.1
Q ss_pred HHHHHHHHHh--hcCCChHhhhhhccccHhHHHHHHH
Q psy13113 17 VKLLAVLRFY--ATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 17 ~~l~~~L~~L--~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
.++...|..+ ..|.++.++|...|||++|++++.+
T Consensus 11 ~~l~~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 11 TQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFEN 47 (88)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 3454445444 4678999999999999999998775
No 340
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=57.58 E-value=16 Score=31.59 Aligned_cols=42 Identities=7% Similarity=0.036 Sum_probs=35.2
Q ss_pred HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+.+-++..++...++...|...++|+++|++.+++..+.+..
T Consensus 4 ~~L~~f~~v~~~gs~s~AA~~L~isQ~avSr~i~~LE~~lg~ 45 (296)
T PRK09906 4 RHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGV 45 (296)
T ss_pred HHHHHHHHHHhhCCHHHHHHHhCCCCcHHHHHHHHHHHHhCC
Confidence 344556666677899999999999999999999999988874
No 341
>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=57.30 E-value=3.5 Score=32.91 Aligned_cols=22 Identities=27% Similarity=0.206 Sum_probs=0.0
Q ss_pred CChHhhhhhccccHhHHHHHHH
Q psy13113 30 NFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
.+.+++|...|++.|||+|+++
T Consensus 50 Lt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 50 LTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp ----------------------
T ss_pred CCHHHHHHHhCCCHhHHHHHHc
Confidence 5788999999999999999775
No 342
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=57.29 E-value=27 Score=29.92 Aligned_cols=40 Identities=23% Similarity=0.282 Sum_probs=30.6
Q ss_pred HHHHHHHHHhhc-CC--ChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 17 VKLLAVLRFYAT-GN--FQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 17 ~~l~~~L~~L~~-~~--~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
++-+-.|.+|+. +. +..+++...|+++||+++++......
T Consensus 4 ~ral~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~ 46 (246)
T COG1414 4 ERALAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVEL 46 (246)
T ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHC
Confidence 445556666663 33 59999999999999999999877654
No 343
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=57.27 E-value=28 Score=26.85 Aligned_cols=39 Identities=10% Similarity=0.083 Sum_probs=26.9
Q ss_pred HHHHHHHHHHhhc--CCChHhhhhhccccHhHHHHHHHHHH
Q psy13113 16 VVKLLAVLRFYAT--GNFQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 16 ~~~l~~~L~~L~~--~~~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
++-|-..+.++.. ..+..+++..+++|.+||++.+++..
T Consensus 7 edyL~~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~ 47 (142)
T PRK03902 7 EDYIEQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLD 47 (142)
T ss_pred HHHHHHHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHH
Confidence 4444444444443 34777899999999999999886543
No 344
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=57.11 E-value=8.2 Score=22.24 Aligned_cols=23 Identities=26% Similarity=0.314 Sum_probs=19.3
Q ss_pred cCCChHhhhhhccccHhHHHHHH
Q psy13113 28 TGNFQIDSEDYHDISQSTICRLV 50 (286)
Q Consensus 28 ~~~~~~~l~~~Fgvs~stv~~~~ 50 (286)
...+.++.+..+|++++|+++++
T Consensus 15 ~F~Si~eAa~~l~i~~~~I~~~l 37 (37)
T PF07453_consen 15 SFDSIREAARYLGISHSTISKYL 37 (37)
T ss_pred EEcCHHHHHHHhCCCHHHHHHhC
Confidence 44688899999999999998763
No 345
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=56.93 E-value=28 Score=25.25 Aligned_cols=28 Identities=11% Similarity=-0.105 Sum_probs=24.3
Q ss_pred hcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113 27 ATGNFQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 27 ~~~~~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
....+..++|..+|+|.+++.+.|++..
T Consensus 19 ~~~~~~~~lA~~~~~S~~~l~r~f~~~~ 46 (107)
T PRK10219 19 DQPLNIDVVAKKSGYSKWYLQRMFRTVT 46 (107)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3456889999999999999999999874
No 346
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=56.87 E-value=10 Score=24.88 Aligned_cols=20 Identities=10% Similarity=0.018 Sum_probs=17.3
Q ss_pred CChHhhhhhccccHhHHHHH
Q psy13113 30 NFQIDSEDYHDISQSTICRL 49 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~ 49 (286)
.+...||..+|||+++|+.|
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 46788999999999999998
No 347
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=56.81 E-value=20 Score=27.76 Aligned_cols=35 Identities=20% Similarity=0.162 Sum_probs=25.7
Q ss_pred CChHhhhhhccccHhHHHHHHH---HHHHHHHhhcccc
Q psy13113 30 NFQIDSEDYHDISQSTICRLVA---KVSEELAKCHQQW 64 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~---~v~~~l~~~~~~~ 64 (286)
.++..+|...||+++|+++|-+ .|+..+..+...+
T Consensus 35 ~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~~~ 72 (142)
T PF13022_consen 35 RTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELADRF 72 (142)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHHHH
T ss_pred chHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence 4788999999999999999985 3666666554444
No 348
>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=56.78 E-value=9.5 Score=23.24 Aligned_cols=29 Identities=14% Similarity=0.099 Sum_probs=23.6
Q ss_pred CCChHhhhhhccccHhHHHHHHHHHHHHH
Q psy13113 29 GNFQIDSEDYHDISQSTICRLVAKVSEEL 57 (286)
Q Consensus 29 ~~~~~~l~~~Fgvs~stv~~~~~~v~~~l 57 (286)
+.+.++++...|+|++++++++..--..+
T Consensus 16 ~~s~~~Ia~~~gvs~~~~y~~f~~k~~l~ 44 (47)
T PF00440_consen 16 AVSIRDIARRAGVSKGSFYRYFPSKDDLL 44 (47)
T ss_dssp TSSHHHHHHHHTSCHHHHHHHCSSHHHHH
T ss_pred hCCHHHHHHHHccchhhHHHHcCCHHHHH
Confidence 46899999999999999999886544443
No 349
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=56.75 E-value=20 Score=28.39 Aligned_cols=45 Identities=18% Similarity=0.226 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
.+++.+.=. |.++..|.+.+++|...++|..||...+.+...-|.
T Consensus 149 ~lt~~e~~v--l~l~~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 149 LLTPRERQI--LKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCCHHHHHH--HHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 355543333 445789999999999999999999999998777665
No 350
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=56.72 E-value=9.7 Score=23.07 Aligned_cols=22 Identities=14% Similarity=-0.053 Sum_probs=18.1
Q ss_pred ChHhhhhhccccHhHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
+-.++|..+||+.+|+..|..+
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHC
Confidence 3467899999999999988653
No 351
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=56.61 E-value=8.7 Score=35.74 Aligned_cols=22 Identities=27% Similarity=0.255 Sum_probs=19.7
Q ss_pred CChHhhhhhccccHhHHHHHHH
Q psy13113 30 NFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
...+++|...|+++|||||++.
T Consensus 331 L~LrdvA~~i~~HESTISRai~ 352 (444)
T COG1508 331 LVLRDVADEIGMHESTISRAIT 352 (444)
T ss_pred ccHHHHHHHhCccHHHHHHHHh
Confidence 4669999999999999999875
No 352
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=56.50 E-value=20 Score=31.47 Aligned_cols=43 Identities=14% Similarity=0.071 Sum_probs=35.7
Q ss_pred HHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 17 VKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 17 ~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|-.++....+|.++...|...++|++||++.+++....|..
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 3555555555666699999999999999999999999999885
No 353
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=56.50 E-value=16 Score=26.02 Aligned_cols=34 Identities=9% Similarity=0.134 Sum_probs=26.7
Q ss_pred HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
.+..+|..++....+.++|..-|||++|++++.+
T Consensus 32 ~~~~~l~~~r~~~glSqLAe~~GIs~stLs~iE~ 65 (89)
T TIGR02684 32 YIAHALGYIARARGMTQLARKTGLSRESLYKALS 65 (89)
T ss_pred HHHHHHHHHHHHCChHHHHHHHCCCHHHHHHHHc
Confidence 4566676777666666799999999999998764
No 354
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=56.31 E-value=15 Score=24.48 Aligned_cols=30 Identities=7% Similarity=0.059 Sum_probs=20.4
Q ss_pred HHHHhhcC--CChHhhhhhccccHhHHHHHHH
Q psy13113 22 VLRFYATG--NFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 22 ~L~~L~~~--~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
.+.+|+.. .+..+||..|++|.++|..++.
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~ 36 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGISPEAVEAMLE 36 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 34455544 4899999999999988776554
No 355
>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=55.94 E-value=19 Score=31.04 Aligned_cols=40 Identities=20% Similarity=0.150 Sum_probs=32.1
Q ss_pred HHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 20 LAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 20 ~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+-.+.-++...++...|...+||++++++.+++..+.+..
T Consensus 6 L~~f~~v~~~gs~s~AA~~L~itqpavS~~Ik~LE~~lg~ 45 (291)
T TIGR03418 6 LRVFESAARLASFTAAARELGSTQPAVSQQVKRLEEELGT 45 (291)
T ss_pred HHHHHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHHHHhCc
Confidence 3344444555699999999999999999999999888763
No 356
>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=55.92 E-value=7.6 Score=34.23 Aligned_cols=22 Identities=14% Similarity=0.137 Sum_probs=19.3
Q ss_pred ChHhhhhhccccHhHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
+.+++|...|||.+|||++++.
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn~ 22 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVING 22 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 3578999999999999999864
No 357
>PF08148 DSHCT: DSHCT (NUC185) domain; InterPro: IPR012961 This C-terminal domain is found in DOB1/SK12/helY-like DEAD box helicases [].; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides; PDB: 4A4Z_A 2XGJ_B 3L9O_A.
Probab=54.94 E-value=22 Score=28.79 Aligned_cols=52 Identities=21% Similarity=0.294 Sum_probs=39.1
Q ss_pred HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhccc--ccCCch
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQ--WIHFPE 69 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~--~i~~P~ 69 (286)
.++-..+.++.|.+|.++-..-++.+..+-|+++++.+.|.++... .+.-|.
T Consensus 103 ~l~~~v~~Wa~G~~~~~i~~~t~l~EGdiVR~~rRl~dlLrql~~aa~~~g~~~ 156 (180)
T PF08148_consen 103 GLMEVVYAWASGASFAEILEMTDLFEGDIVRWIRRLIDLLRQLANAAKIIGDPE 156 (180)
T ss_dssp TTHHHHHHHHCT--HHHHCCT-SS-HHHHHHHHHHHHHHHHHHHHHHHCCT-HH
T ss_pred cHHHHHHHHHCCCCHHHHHhcCCCCchHHHHHHHHHHHHHHHHHHHHHhcCCHH
Confidence 4566788999999999999999999999999999999999976544 444444
No 358
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=54.92 E-value=20 Score=25.77 Aligned_cols=44 Identities=20% Similarity=0.101 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHH
Q psy13113 13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEEL 57 (286)
Q Consensus 13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l 57 (286)
+++++-=++-|.-+ .+.++.+.|...|||++|+.+.++..-.-+
T Consensus 34 lt~eElEAlRLvD~-~~l~QeeAA~rMgISr~Tfwr~l~sAR~Kv 77 (99)
T COG1342 34 LTIEELEALRLVDY-EGLTQEEAALRMGISRQTFWRLLTSARKKV 77 (99)
T ss_pred ecHHHHHHHHHHhH-hhccHHHHHHHhcccHHHHHHHHHHHHHHH
Confidence 44444444433333 457899999999999999998887554433
No 359
>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.
Probab=54.87 E-value=49 Score=23.34 Aligned_cols=43 Identities=9% Similarity=-0.001 Sum_probs=27.3
Q ss_pred CCCHHHHHHHHHHHhhc-CCChHhhhhhc--cccHhHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYAT-GNFQIDSEDYH--DISQSTICRLVAKVSE 55 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~-~~~~~~l~~~F--gvs~stv~~~~~~v~~ 55 (286)
.+|...+-+ +..+|.+ ..+..+|+..+ .||+|++.-.++.+..
T Consensus 37 ~l~~~l~~~-a~lRl~~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl~~ 82 (85)
T PF02650_consen 37 KLPEKLREF-AELRLENPDASLKELGELLEPPISKSGVNHRLRKLKK 82 (85)
T ss_dssp GS-HHHHHH-HHHHHH-TTS-HHHHHHTT--T--HHHHHHHHHHHHH
T ss_pred cCCHHHHHH-HHHHHHCccccHHHHHHHHcCcCcHHHHHHHHHHHHH
Confidence 355555544 4445555 46999999999 9999999988877654
No 360
>PRK06424 transcription factor; Provisional
Probab=54.65 E-value=39 Score=26.43 Aligned_cols=33 Identities=9% Similarity=-0.070 Sum_probs=25.8
Q ss_pred HHHHHHHhh--cCCChHhhhhhccccHhHHHHHHH
Q psy13113 19 LLAVLRFYA--TGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 19 l~~~L~~L~--~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
+.-.|..++ .|.++.+||...|++++++++|-+
T Consensus 85 ~g~~Ir~lRe~~GLSQ~eLA~~iGvs~stIskiE~ 119 (144)
T PRK06424 85 YAELVKNARERLSMSQADLAAKIFERKNVIASIER 119 (144)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 444444444 688999999999999999998765
No 361
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=54.54 E-value=24 Score=31.30 Aligned_cols=43 Identities=16% Similarity=0.083 Sum_probs=35.2
Q ss_pred HHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 17 VKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 17 ~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
++|-.++....+|.++...|...++|++|+++.+++....|..
T Consensus 4 ~~L~~f~avae~g~S~s~AA~~L~iSQpavS~~I~~LE~~lG~ 46 (324)
T PRK12681 4 QQLRYIVEVVNHNLNVSATAEGLYTSQPGISKQVRMLEDELGI 46 (324)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhCC
Confidence 3444555555566799999999999999999999999999884
No 362
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=54.43 E-value=12 Score=27.53 Aligned_cols=24 Identities=25% Similarity=0.112 Sum_probs=18.5
Q ss_pred hhcCCChHhhhhhccccHhHHHHH
Q psy13113 26 YATGNFQIDSEDYHDISQSTICRL 49 (286)
Q Consensus 26 L~~~~~~~~l~~~Fgvs~stv~~~ 49 (286)
=+.+.++...|..+|+|.+||..|
T Consensus 54 e~~~lSQ~vFA~~L~vs~~Tv~~W 77 (104)
T COG2944 54 EKLGLSQPVFARYLGVSVSTVRKW 77 (104)
T ss_pred HHhCCCHHHHHHHHCCCHHHHHHH
Confidence 345678888888888888888865
No 363
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=53.92 E-value=30 Score=27.67 Aligned_cols=40 Identities=10% Similarity=-0.054 Sum_probs=33.6
Q ss_pred CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113 13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
++.+.+-.+==.|.-.+.++...|..+|||.+|+.+|=.+
T Consensus 3 h~~e~R~~~R~~YV~~~~sLe~aA~~~gVs~~TarrWK~~ 42 (165)
T PF08822_consen 3 HPQETRDAVRRAYVFDRLSLEQAAAKCGVSYATARRWKRE 42 (165)
T ss_pred CcHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 4667777777778888899999999999999999998764
No 364
>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=53.70 E-value=47 Score=25.21 Aligned_cols=48 Identities=6% Similarity=0.058 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHHHHhhc-CCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 12 IHSPVVKLLAVLRFYAT-GNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~-~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.++..++-.+...|+.. +.+...++..+|+|+++.++.-++.+..+..
T Consensus 79 ~l~~~~r~Il~~~Yl~~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~ 127 (132)
T TIGR01637 79 QLDEISRQILYDKYLEPDQKYDYQIMMELGYSHRQYYRIKKRALLRFAT 127 (132)
T ss_pred hCCHHHHHHHHHHHcCccccchHHHHHHhCCcHHHHHHHHHHHHHHHHH
Confidence 57888888888888873 4577789999999999999888777766655
No 365
>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=53.64 E-value=8.4 Score=33.94 Aligned_cols=22 Identities=23% Similarity=0.226 Sum_probs=19.7
Q ss_pred ChHhhhhhccccHhHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
+.+++|..-|||.+|||++++.
T Consensus 3 ti~dIA~~agvS~~TVSrvLn~ 24 (329)
T TIGR01481 3 TIYDVAREAGVSMATVSRVVNG 24 (329)
T ss_pred cHHHHHHHhCCCHHHHHHHhCC
Confidence 5789999999999999999864
No 366
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=53.51 E-value=13 Score=27.83 Aligned_cols=21 Identities=24% Similarity=0.203 Sum_probs=18.7
Q ss_pred ChHhhhhhccccHhHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~ 51 (286)
+...||..-|+|+.||++|++
T Consensus 2 T~eELA~~tG~srQTINrWvR 22 (122)
T PF07037_consen 2 TPEELAELTGYSRQTINRWVR 22 (122)
T ss_pred CHHHHHHHhCccHHHHHHHHH
Confidence 456899999999999999986
No 367
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=53.47 E-value=25 Score=30.64 Aligned_cols=41 Identities=20% Similarity=0.186 Sum_probs=34.3
Q ss_pred HHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 19 LLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 19 l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+-++.-+....++...|...++|++++++.+++..+.|..
T Consensus 9 ~L~~f~~v~e~gs~s~AA~~L~isqpavS~~i~~LE~~lg~ 49 (305)
T CHL00180 9 QLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNI 49 (305)
T ss_pred HHHHHHHHHHcCCHHHHHHHhcCCChHHHHHHHHHHHHhCC
Confidence 34455555666799999999999999999999999999884
No 368
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=53.26 E-value=9 Score=34.33 Aligned_cols=22 Identities=18% Similarity=0.271 Sum_probs=19.6
Q ss_pred ChHhhhhhccccHhHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
+.+++|..-|||.+|||++++.
T Consensus 2 TikDVA~~AGVS~sTVSrvln~ 23 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLNG 23 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 5689999999999999998874
No 369
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=53.19 E-value=25 Score=30.89 Aligned_cols=43 Identities=16% Similarity=0.187 Sum_probs=36.3
Q ss_pred HHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 17 VKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 17 ~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
-+.+-++..++...++...|...++|++||++.+++....+..
T Consensus 24 l~~L~~f~avae~gs~s~AA~~L~isQpavS~~I~~LE~~lg~ 66 (314)
T PRK09508 24 LNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFND 66 (314)
T ss_pred hHHHHHHHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhhCC
Confidence 3445666667777889999999999999999999999998874
No 370
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=53.08 E-value=13 Score=29.74 Aligned_cols=27 Identities=22% Similarity=0.320 Sum_probs=23.2
Q ss_pred CChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 30 NFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
+++++++..+|+|.+||++.++...+.
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~ik~L~e~ 102 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRAIKELEEK 102 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHhC
Confidence 388899999999999999999876544
No 371
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=52.91 E-value=8.6 Score=34.21 Aligned_cols=22 Identities=18% Similarity=0.262 Sum_probs=19.8
Q ss_pred ChHhhhhhccccHhHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
+.+++|..-|||.+|||++++.
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn~ 24 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVINN 24 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhCC
Confidence 5789999999999999999863
No 372
>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=52.71 E-value=50 Score=29.63 Aligned_cols=45 Identities=11% Similarity=0.032 Sum_probs=37.3
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHH
Q psy13113 9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v 53 (286)
-|..+|..++.......+..|.+...++..+|+++++|++++.-.
T Consensus 157 ~R~dLS~iE~A~~~~~L~~~G~~~~~ia~~Lg~~ks~vSr~lsl~ 201 (325)
T TIGR03454 157 ARRDLSFIERALFAQRLEDRGFDRDTIMAALSVDKTELSRMISVA 201 (325)
T ss_pred cccCCCHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 467788888877777777888888899999999999999988644
No 373
>PRK09801 transcriptional activator TtdR; Provisional
Probab=52.65 E-value=27 Score=30.75 Aligned_cols=45 Identities=7% Similarity=0.036 Sum_probs=35.1
Q ss_pred CHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 14 SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 14 ~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+.-.+|-.++. ++...++...|...++|++||++.+++..+.|..
T Consensus 6 ~~~~~L~~F~~-v~~~gs~t~AA~~L~iSQpavS~~I~~LE~~LG~ 50 (310)
T PRK09801 6 PLAKDLQVLVE-IVHSGSFSAAAATLGQTPAFVTKRIQILENTLAT 50 (310)
T ss_pred HHHHHHHHHHH-HHHcCCHHHHHHHhCcCHHHHHHHHHHHHHHhCC
Confidence 34455544444 4455789999999999999999999999998874
No 374
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=52.60 E-value=14 Score=24.20 Aligned_cols=22 Identities=9% Similarity=-0.040 Sum_probs=19.0
Q ss_pred ChHhhhhhccccHhHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
+..++|..+|||.+|+..|.++
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 4568999999999999999865
No 375
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=52.40 E-value=27 Score=31.03 Aligned_cols=39 Identities=13% Similarity=0.026 Sum_probs=32.6
Q ss_pred HHHHHhhc-CCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 21 AVLRFYAT-GNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 21 ~~L~~L~~-~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
-.+..++. +.++...|...++|++||++.+++..+.+..
T Consensus 7 ~~F~~vae~~gS~s~AA~~L~isQpavS~~I~~LE~~lG~ 46 (327)
T PRK12680 7 RYLVAIADAELNITLAAARVHATQPGLSKQLKQLEDELGF 46 (327)
T ss_pred HHHHHHHHccCCHHHHHHHhcCCchHHHHHHHHHHHHhCC
Confidence 34444454 5899999999999999999999999999884
No 376
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=52.12 E-value=39 Score=28.96 Aligned_cols=47 Identities=17% Similarity=0.130 Sum_probs=37.1
Q ss_pred CCCCCHHHHHHHHHHHhhcC--CChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 10 GVIHSPVVKLLAVLRFYATG--NFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 10 ~~~~~~~~~l~~~L~~L~~~--~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
...++.-++.+-.|..|+.. .+..+++...|+++||++++++..+..
T Consensus 7 ~~~v~sl~r~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~ 55 (257)
T PRK15090 7 PDSVSSVLKVFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTL 55 (257)
T ss_pred ccccHHHHHHHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 33466777777888877654 478899999999999999999876644
No 377
>COG5421 Transposase [DNA replication, recombination, and repair]
Probab=52.00 E-value=16 Score=34.29 Aligned_cols=54 Identities=20% Similarity=0.241 Sum_probs=38.6
Q ss_pred cccceeeecCCCccEEEeccCCCCccccccccccc--hhhhhccccccceEEEccccCC
Q psy13113 117 YSINVQVIGGPNLEIYDVVASWPGSTHDSRIFQNS--RVYSRFDRREIRGLLLGDIGYA 173 (286)
Q Consensus 117 ~s~~~q~vvd~~g~i~~~~~~~~Gs~~D~~~~~~s--~l~~~l~~~~~~~~llgD~gY~ 173 (286)
.-+++..+++..|..+.+.+ ++|+.+|...+-.. .+.+.+... +.++++|+|+-
T Consensus 155 ~QI~vsMi~~~~gIPl~~~v-~~Gni~D~~~~~~ti~kl~~~l~~~--~~~~V~Dkgf~ 210 (480)
T COG5421 155 PQINVSMIVNQKGIPLFVRV-YSGNISDKNTLIKTIQKLKSVLVKD--EVYLVADKGFN 210 (480)
T ss_pred ceeEEEEEEcCCCCceEEEc-cCCCccchHHHHHHHHHHHHhcccc--eEEEEEccccc
Confidence 56788888888888888877 59999999877653 111222222 36999999995
No 378
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=51.96 E-value=19 Score=27.59 Aligned_cols=27 Identities=11% Similarity=-0.106 Sum_probs=23.1
Q ss_pred HhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 25 FYATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 25 ~L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
+-..|.++.++|...|||.+|+++|.+
T Consensus 14 R~~~gltq~~lA~~~gvs~~~is~~E~ 40 (135)
T PRK09706 14 RKQLKLSQRSLAKAVKVSHVSISQWER 40 (135)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 345678999999999999999998764
No 379
>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent
Probab=51.65 E-value=40 Score=25.54 Aligned_cols=38 Identities=11% Similarity=0.133 Sum_probs=29.9
Q ss_pred HHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 21 AVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 21 ~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
+.+.|+.++.+.+.+|...++|..++.+.+......+.
T Consensus 70 ll~~~Yv~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~ 107 (125)
T PF06530_consen 70 LLILYYVYGWSKRQIARKLKCSEGKIRKRLQRAEGFID 107 (125)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHhhhhHh
Confidence 45555667999999999999999999988776655554
No 380
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=51.38 E-value=23 Score=20.87 Aligned_cols=26 Identities=23% Similarity=0.231 Sum_probs=21.5
Q ss_pred hhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 26 YATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 26 L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
-..+.+..+++...|++.++++.+..
T Consensus 7 ~~~~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 7 EEKGLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 44677999999999999999987653
No 381
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=51.33 E-value=16 Score=30.81 Aligned_cols=23 Identities=13% Similarity=0.081 Sum_probs=19.6
Q ss_pred ChHhhhhhccccHhHHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~v 53 (286)
+-.+|+..||||+.||.+.+...
T Consensus 26 sE~eLa~~~gVSR~TVR~Al~~L 48 (233)
T TIGR02404 26 SEHELMDQYGASRETVRKALNLL 48 (233)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Confidence 66789999999999999877644
No 382
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=51.25 E-value=28 Score=30.44 Aligned_cols=41 Identities=12% Similarity=0.131 Sum_probs=32.7
Q ss_pred HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+|-+++.... ..++...|...++|+++|++.+++..+.+..
T Consensus 8 ~L~~f~av~~-~gS~s~AAe~L~isqsavS~~Ik~LE~~lg~ 48 (309)
T PRK11013 8 HIEIFHAVMT-AGSLTEAARLLHTSQPTVSRELARFEKVIGL 48 (309)
T ss_pred HHHHHHHHHH-hCcHHHHHHHHCCCcHHHHHHHHHHHHHhCc
Confidence 4444444444 4699999999999999999999999988774
No 383
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=51.20 E-value=27 Score=30.58 Aligned_cols=44 Identities=7% Similarity=0.125 Sum_probs=35.4
Q ss_pred HHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 16 VVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 16 ~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
..+.+-++.-++...++...|...++|++++++.+++..+.|..
T Consensus 8 ~~~~L~~F~av~e~gs~s~AA~~L~iSQpavS~~I~~LE~~lg~ 51 (312)
T PRK10341 8 KTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGV 51 (312)
T ss_pred cHHHHHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCC
Confidence 33444445556667899999999999999999999999998874
No 384
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=50.99 E-value=28 Score=30.26 Aligned_cols=42 Identities=14% Similarity=0.147 Sum_probs=34.0
Q ss_pred HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+.+-++.-+....++...|...++|++||++.+++..+.+..
T Consensus 8 ~~L~~f~~v~~~gs~s~AA~~L~isQ~avS~~i~~LE~~lG~ 49 (302)
T PRK09791 8 HQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAA 49 (302)
T ss_pred HHHHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCC
Confidence 344444555555699999999999999999999999998874
No 385
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=50.31 E-value=26 Score=26.85 Aligned_cols=47 Identities=17% Similarity=0.092 Sum_probs=38.5
Q ss_pred CHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 14 SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 14 ~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
+......-+..++..|.+..+.++..||+.+++.++..++...+..+
T Consensus 74 ~~~~~~~~~~~~~~~~~~i~~~a~~l~i~~~~~~r~~~r~~~~~~~~ 120 (129)
T COG3677 74 ALYKIKLQAVTLYMLGLGIRDIARTLGISINTVNRWSKRFGSRVEGL 120 (129)
T ss_pred cchHHHHHHHHHHHcCCCcccHHHHhcccHHHHHHHHHhhcchhhcc
Confidence 44555666666777888999999999999999999999998887653
No 386
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=50.27 E-value=30 Score=30.10 Aligned_cols=41 Identities=20% Similarity=0.229 Sum_probs=32.7
Q ss_pred HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+|-+++....+ .++...|...++|+++|++.+++....+..
T Consensus 5 ~L~~f~~v~~~-gS~s~AA~~L~itQpavS~~i~~LE~~lg~ 45 (305)
T PRK11151 5 DLEYLVALAEH-RHFRRAADSCHVSQPTLSGQIRKLEDELGV 45 (305)
T ss_pred HHHHHHHHHHh-CCHHHHHHHhCCCchHHHHHHHHHHHHhCc
Confidence 34444444455 499999999999999999999999888774
No 387
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=50.22 E-value=28 Score=30.09 Aligned_cols=39 Identities=10% Similarity=0.107 Sum_probs=32.1
Q ss_pred HHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 21 AVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 21 ~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
-++.-+....++...|...++|+++|++.+++..+.+..
T Consensus 8 ~~f~~v~~~gs~t~AA~~L~iSQ~avS~~i~~LE~~lg~ 46 (294)
T PRK13348 8 EALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQ 46 (294)
T ss_pred HHHHHHHHcCCHHHHHHHhCCCchHHHHHHHHHHHHhCc
Confidence 344444555799999999999999999999999988774
No 388
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=50.19 E-value=28 Score=30.16 Aligned_cols=40 Identities=15% Similarity=0.148 Sum_probs=33.0
Q ss_pred HHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 20 LAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 20 ~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+-.+.-+....++...|...++|++++++.+++....+..
T Consensus 8 l~~f~~v~~~gS~s~AA~~L~isq~avS~~I~~LE~~lg~ 47 (300)
T TIGR02424 8 LQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGT 47 (300)
T ss_pred HHHHHHHHHhCCHHHHHHHhCCChHHHHHHHHHHHHHhCC
Confidence 3444445556799999999999999999999999988874
No 389
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=49.92 E-value=39 Score=25.50 Aligned_cols=30 Identities=10% Similarity=-0.031 Sum_probs=25.2
Q ss_pred HhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113 25 FYATGNFQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 25 ~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
.+....+..++|..+|+|.+++.+.|++..
T Consensus 21 ~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~ 50 (127)
T PRK11511 21 NLESPLSLEKVSERSGYSKWHLQRMFKKET 50 (127)
T ss_pred hcCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 334456889999999999999999999874
No 390
>PRK01905 DNA-binding protein Fis; Provisional
Probab=49.67 E-value=45 Score=22.81 Aligned_cols=29 Identities=17% Similarity=0.255 Sum_probs=23.4
Q ss_pred HHhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113 24 RFYATGNFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 24 ~~L~~~~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
.+-.++......|...|+|++|+++.+++
T Consensus 45 aL~~~~gn~s~aAr~LGIsrstL~rklkk 73 (77)
T PRK01905 45 VMEQAGGNQSLAAEYLGINRNTLRKKLQQ 73 (77)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34446677889999999999999987765
No 391
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=49.30 E-value=29 Score=20.65 Aligned_cols=26 Identities=27% Similarity=0.254 Sum_probs=21.9
Q ss_pred hhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 26 YATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 26 L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
-..+.+..+++...|++..+++++.+
T Consensus 9 ~~~~~s~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 9 KEKGLTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 34678999999999999999988654
No 392
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=49.26 E-value=18 Score=22.40 Aligned_cols=25 Identities=20% Similarity=0.246 Sum_probs=20.9
Q ss_pred cCCChHhhhhhccccHhHHHHHHHH
Q psy13113 28 TGNFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 28 ~~~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
...+..+.|..+|++.++++++++.
T Consensus 16 ~f~S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 16 EFSSIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred EecCHHHHHHHhCCCHHHHHHHHhC
Confidence 3467889999999999999988763
No 393
>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=49.09 E-value=58 Score=23.29 Aligned_cols=39 Identities=15% Similarity=0.252 Sum_probs=26.2
Q ss_pred HHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113 16 VVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 16 ~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
+.-++..=.||=.|.+.++++..+||+++-+++.++++-
T Consensus 40 ~kiI~AL~dyLV~G~srkeac~~~gV~~syfs~~L~rL~ 78 (91)
T PF03333_consen 40 EKIIAALRDYLVDGLSRKEACERHGVNQSYFSRALNRLN 78 (91)
T ss_dssp HHHHHHHHHHHTT---HHHHHHHTT--HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 344444446888999999999999999999998887654
No 394
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=49.01 E-value=29 Score=29.86 Aligned_cols=42 Identities=14% Similarity=0.150 Sum_probs=34.6
Q ss_pred HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+.+-++.-+....++...|...++|++++++.+++....+..
T Consensus 6 ~~L~~f~~v~e~~s~t~AA~~L~isqpavS~~I~~LE~~lg~ 47 (290)
T PRK10837 6 RQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGV 47 (290)
T ss_pred HHHHHHHHHHHcCCHHHHHHHhCCCccHHHHHHHHHHHHhCC
Confidence 344555556666799999999999999999999999988874
No 395
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=49.00 E-value=44 Score=24.47 Aligned_cols=35 Identities=20% Similarity=0.064 Sum_probs=21.0
Q ss_pred HHHHHHHHhhcCCChHhhhhhc-----cccHhHHHHHHHH
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYH-----DISQSTICRLVAK 52 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~F-----gvs~stv~~~~~~ 52 (286)
.++-+|.-.....+-.++.... ++|.+||+|.++.
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~ 44 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLEL 44 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence 3344443333334566665554 7999999987753
No 396
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=48.99 E-value=58 Score=25.11 Aligned_cols=26 Identities=19% Similarity=0.239 Sum_probs=22.7
Q ss_pred CChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 30 NFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
.++..+|...|+|.+|+.+.+++..+
T Consensus 23 ~~~~eia~~lglS~~~v~~Ri~~L~~ 48 (154)
T COG1522 23 ISNAELAERVGLSPSTVLRRIKRLEE 48 (154)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 68999999999999999988876544
No 397
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=48.57 E-value=36 Score=27.82 Aligned_cols=40 Identities=10% Similarity=0.013 Sum_probs=28.2
Q ss_pred HHHHHHHHHHh-h-c--CCChHhhhhhcccc-HhHHHHHHHHHHH
Q psy13113 16 VVKLLAVLRFY-A-T--GNFQIDSEDYHDIS-QSTICRLVAKVSE 55 (286)
Q Consensus 16 ~~~l~~~L~~L-~-~--~~~~~~l~~~Fgvs-~stv~~~~~~v~~ 55 (286)
+.+++-+|... . + ..+.+++|..+|++ .+||++.+.....
T Consensus 8 q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~ 52 (199)
T TIGR00498 8 QQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALER 52 (199)
T ss_pred HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 45555555533 2 2 35788999999998 9999988876543
No 398
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=48.47 E-value=32 Score=30.60 Aligned_cols=38 Identities=21% Similarity=0.301 Sum_probs=29.2
Q ss_pred HHHHHHHHhhcC--CChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 18 KLLAVLRFYATG--NFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 18 ~l~~~L~~L~~~--~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
+..-.|..|..+ .+..++|..||+|++||++.++...+
T Consensus 5 r~~~il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~ 44 (319)
T PRK11886 5 VMLQLLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEE 44 (319)
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 344445555554 57788999999999999999988775
No 399
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=48.00 E-value=52 Score=29.66 Aligned_cols=50 Identities=8% Similarity=0.145 Sum_probs=42.9
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.++.+++++|++++|+.+ .|.+-.+++..|=|+++|+..-|.+.-..|.+
T Consensus 117 cHPal~~~~riALtLR~v-~GLs~~eIArAFLv~e~am~QRivRAK~ri~~ 166 (415)
T COG4941 117 CHPALPPEQRIALTLRLV-GGLSTAEIARAFLVPEAAMAQRIVRAKARIRE 166 (415)
T ss_pred cCCCCChhhHHHHHHHHH-cCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHh
Confidence 578899999999999866 56899999999999999998777777766765
No 400
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=47.59 E-value=20 Score=24.49 Aligned_cols=24 Identities=25% Similarity=0.140 Sum_probs=18.3
Q ss_pred CCChHhhhhhccccHhHHHHHHHH
Q psy13113 29 GNFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 29 ~~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
..+-.++|...|||.+||.|.++.
T Consensus 34 ~~si~elA~~~~vS~sti~Rf~kk 57 (77)
T PF01418_consen 34 FMSISELAEKAGVSPSTIVRFCKK 57 (77)
T ss_dssp T--HHHHHHHCTS-HHHHHHHHHH
T ss_pred HccHHHHHHHcCCCHHHHHHHHHH
Confidence 468889999999999999987764
No 401
>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=47.50 E-value=37 Score=32.78 Aligned_cols=43 Identities=19% Similarity=0.068 Sum_probs=35.6
Q ss_pred CCCCCHHHHHHHHHHHhhcCC-ChHhhhhhccccHhHHHHHHHH
Q psy13113 10 GVIHSPVVKLLAVLRFYATGN-FQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 10 ~~~~~~~~~l~~~L~~L~~~~-~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
|..+++-++...+...+..+. +..+++..||+|+++|++.+.-
T Consensus 89 RedLtP~EeA~A~~rLl~~g~~t~eeIA~~lG~S~~~V~rrLkL 132 (554)
T TIGR03734 89 RADMSPAEEAEAAARLLGRCKGDREEAARRLGWSPATLDRRLAL 132 (554)
T ss_pred cCCCCHHHHHHHHHHHhhhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 567888888877777777666 8899999999999999988763
No 402
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=47.42 E-value=37 Score=29.15 Aligned_cols=41 Identities=12% Similarity=0.093 Sum_probs=35.0
Q ss_pred HHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 19 LLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 19 l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+-++..++...++...|...++|++++++.+++....|..
T Consensus 5 ~l~~f~~v~~~gs~s~AA~~L~isqpavS~~I~~LE~~lG~ 45 (275)
T PRK03601 5 LLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGV 45 (275)
T ss_pred HHHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCC
Confidence 34556667777899999999999999999999999998874
No 403
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=47.18 E-value=25 Score=29.86 Aligned_cols=37 Identities=19% Similarity=0.144 Sum_probs=32.0
Q ss_pred HHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 23 LRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 23 L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+.-++...++...|...++|+++|++.+++....+..
T Consensus 5 f~~v~~~gs~~~AA~~L~isqsavS~~i~~LE~~lg~ 41 (279)
T TIGR03339 5 FHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGV 41 (279)
T ss_pred hHHHHhcCCHHHHHHHhcCCchHHHHHHHHHHHHhCC
Confidence 4455666799999999999999999999999988874
No 404
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=46.75 E-value=42 Score=29.63 Aligned_cols=41 Identities=10% Similarity=0.071 Sum_probs=32.9
Q ss_pred HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+|-.++....+ .++...|...++|++||++.+++....+..
T Consensus 6 ~L~~f~av~~~-gs~s~AA~~L~iSqpaVS~~Ik~LE~~lg~ 46 (317)
T PRK15421 6 HLKTLQALRNC-GSLAAAAATLHQTQSALSHQFSDLEQRLGF 46 (317)
T ss_pred HHHHHHHHHHc-CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 44444444444 499999999999999999999999988874
No 405
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=46.59 E-value=43 Score=29.22 Aligned_cols=42 Identities=14% Similarity=0.126 Sum_probs=34.8
Q ss_pred HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+.+-++..++...++...|...++|++|||+.+++....|..
T Consensus 11 ~~L~~F~~va~~gs~s~AA~~L~isQpavS~~I~~LE~~lg~ 52 (302)
T TIGR02036 11 SKMHTFEVAARHQSFSLAAEELSLTPSAISHRINQLEEELGI 52 (302)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 444455556677899999999999999999999999988874
No 406
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=46.53 E-value=45 Score=24.20 Aligned_cols=23 Identities=17% Similarity=0.395 Sum_probs=20.3
Q ss_pred HhhhhhccccHhHHHHHHHHHHH
Q psy13113 33 IDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 33 ~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
.+++...+++++|+++.+++...
T Consensus 40 ~~la~~l~i~~~~vt~~l~~Le~ 62 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRLED 62 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH
Confidence 89999999999999998876554
No 407
>COG5566 Uncharacterized conserved protein [Function unknown]
Probab=46.51 E-value=25 Score=26.68 Aligned_cols=28 Identities=14% Similarity=0.293 Sum_probs=24.6
Q ss_pred cCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 28 TGNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 28 ~~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
.|..+.+|+..+.+|..+|+++++++..
T Consensus 101 dG~n~~eLaKkYrlS~~~Iy~VIrr~~t 128 (137)
T COG5566 101 DGSNYVELAKKYRLSENHIYRVIRRTHT 128 (137)
T ss_pred CCccHHHHHHHhcccHHHHHHHHHHHHH
Confidence 4778999999999999999999996654
No 408
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=46.51 E-value=72 Score=21.10 Aligned_cols=25 Identities=12% Similarity=0.068 Sum_probs=18.8
Q ss_pred CCChHhhhhhcccc-HhHHHHHHHHH
Q psy13113 29 GNFQIDSEDYHDIS-QSTICRLVAKV 53 (286)
Q Consensus 29 ~~~~~~l~~~Fgvs-~stv~~~~~~v 53 (286)
..+.++++..||++ .+||+..+...
T Consensus 25 ~Pt~rEIa~~~g~~S~~tv~~~L~~L 50 (65)
T PF01726_consen 25 PPTVREIAEALGLKSTSTVQRHLKAL 50 (65)
T ss_dssp ---HHHHHHHHTSSSHHHHHHHHHHH
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 35899999999996 88998877644
No 409
>PRK13832 plasmid partitioning protein; Provisional
Probab=46.42 E-value=42 Score=31.95 Aligned_cols=43 Identities=19% Similarity=0.050 Sum_probs=36.9
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
-|..+++-++...+-.....|.+..++|..||+|+++|.+...
T Consensus 98 QRedL~PiEea~AfkrLie~G~T~EeIA~~lG~S~~~V~rlll 140 (520)
T PRK13832 98 AREPLNPVDQWRAIERLVALGWTEEAIAVALALPVRQIRKLRL 140 (520)
T ss_pred CcCCCCHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4677888888888888889999999999999999999998544
No 410
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=46.20 E-value=36 Score=29.84 Aligned_cols=38 Identities=11% Similarity=-0.035 Sum_probs=31.7
Q ss_pred HHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 22 VLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 22 ~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+..+....++...|...++|++++++.+++....+..
T Consensus 9 ~f~~v~e~gs~s~AA~~L~iSQpavS~~I~~LE~~lg~ 46 (308)
T PRK10094 9 TFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGV 46 (308)
T ss_pred HHHHHHHhCCHHHHHHHhcCCHHHHHHHHHHHHHHhCC
Confidence 34444555699999999999999999999999988874
No 411
>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=46.08 E-value=10 Score=35.35 Aligned_cols=22 Identities=18% Similarity=0.155 Sum_probs=19.9
Q ss_pred CChHhhhhhccccHhHHHHHHH
Q psy13113 30 NFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
.+.+++|...|++.|||||+++
T Consensus 319 LtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 319 LTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred CcHHHHHHHhCCCccchhhhhc
Confidence 5889999999999999999774
No 412
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=45.96 E-value=21 Score=29.99 Aligned_cols=44 Identities=11% Similarity=0.147 Sum_probs=31.3
Q ss_pred CCCCHHHHHHHHHHH-hhcC-----C---ChHhhhhhccccHhHHHHHHHHHH
Q psy13113 11 VIHSPVVKLLAVLRF-YATG-----N---FQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~-L~~~-----~---~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
...|...++.-.|.. +.+| . +-.+|+..||||+.||.+.+....
T Consensus 5 ~~~p~y~~i~~~l~~~I~~g~~~~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~ 57 (238)
T TIGR02325 5 SGVALWRQIADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALV 57 (238)
T ss_pred CCCcHHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 346677777766643 3333 2 667899999999999998776544
No 413
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=45.95 E-value=37 Score=29.83 Aligned_cols=42 Identities=14% Similarity=0.225 Sum_probs=34.2
Q ss_pred HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+.+-++.-+....++...|...++|++++|+.+++....+..
T Consensus 11 ~~L~~f~av~e~gs~t~AA~~L~iSQpavS~~I~~LE~~lg~ 52 (319)
T PRK10216 11 NLLLCLQLLMQERSVTKAAKRMNVTPSAVSKSLAKLRAWFDD 52 (319)
T ss_pred HHHHHHHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 344445555566799999999999999999999999998874
No 414
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=45.79 E-value=21 Score=29.91 Aligned_cols=24 Identities=13% Similarity=0.079 Sum_probs=20.3
Q ss_pred ChHhhhhhccccHhHHHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
+-++|+..||||+.||.+.+....
T Consensus 27 sE~eLa~~~~VSR~TVR~Al~~L~ 50 (230)
T TIGR02018 27 SEHELVAQYGCSRMTVNRALRELT 50 (230)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 667899999999999998876544
No 415
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=45.72 E-value=41 Score=29.96 Aligned_cols=44 Identities=18% Similarity=0.261 Sum_probs=35.1
Q ss_pred CCHHHHHHHHHHHhhcCC--ChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 13 HSPVVKLLAVLRFYATGN--FQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 13 ~~~~~~l~~~L~~L~~~~--~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
...-++|+-.+.+|..+. +-+.+|..|+||..|++|-++....+
T Consensus 4 ~~ka~RL~~ii~~L~~~~~vta~~lA~~~~VS~RTi~RDi~~L~~~ 49 (311)
T COG2378 4 MRKAERLLQIIQILRAKETVTAAELADEFEVSVRTIYRDIATLRAA 49 (311)
T ss_pred hhHHHHHHHHHHHHHhCccchHHHHHHhcCCCHHHHHHHHHHHHHC
Confidence 445677888888888765 66789999999999999999866554
No 416
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=45.68 E-value=23 Score=27.93 Aligned_cols=29 Identities=10% Similarity=-0.079 Sum_probs=25.2
Q ss_pred HHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 23 LRFYATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 23 L~~L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
-.+-..|.++.++|...|||++|+++|-+
T Consensus 32 ~~R~~lGmTq~eLAerlGVS~~tIs~iE~ 60 (150)
T TIGR02612 32 AIRKALGMSGAQLAGRLGVTPQRVEALEK 60 (150)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 34566789999999999999999999876
No 417
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=45.59 E-value=57 Score=25.98 Aligned_cols=45 Identities=18% Similarity=0.214 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
.++..+. -.|.+|..|.+.+++|...++|..||...+.+...-|.
T Consensus 149 ~lt~re~--~vl~~l~~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 149 VLSNREV--TILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 3555444 45567989999999999999999999999988877764
No 418
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=45.56 E-value=30 Score=29.80 Aligned_cols=38 Identities=16% Similarity=0.146 Sum_probs=31.6
Q ss_pred HHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 22 VLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 22 ~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
++.-+....++...|...++|+|+|++.+++....+..
T Consensus 8 ~f~~v~~~gs~s~AA~~L~isqsavS~~i~~LE~~lg~ 45 (296)
T PRK11242 8 YFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGV 45 (296)
T ss_pred HHHHHHHhCCHHHHHHHcCCCchHHHHHHHHHHHHhCC
Confidence 34444455799999999999999999999999988874
No 419
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=45.47 E-value=22 Score=30.14 Aligned_cols=45 Identities=13% Similarity=0.199 Sum_probs=30.7
Q ss_pred CCCCCHHHHHHHHHHH-----hhcCC---ChHhhhhhccccHhHHHHHHHHHH
Q psy13113 10 GVIHSPVVKLLAVLRF-----YATGN---FQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 10 ~~~~~~~~~l~~~L~~-----L~~~~---~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
....|..+|+.-.|.. |.-|. +-.+|+..||||+.||.+.+....
T Consensus 8 ~~~~p~Y~qi~~~L~~~I~~~~~~G~~LPsE~eLa~~~~VSR~TVR~Al~~L~ 60 (241)
T PRK10079 8 TSYPTRYQEIAAKLEQELRQHYRCGDYLPAEQQLAARYEVNRHTLRRAIDQLV 60 (241)
T ss_pred CCCCCHHHHHHHHHHHHHhcccCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3344566777665553 23232 667899999999999998776544
No 420
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=45.43 E-value=39 Score=29.84 Aligned_cols=43 Identities=12% Similarity=0.205 Sum_probs=35.2
Q ss_pred HHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 17 VKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 17 ~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
-+.+-++.-+....++...|...++|+++|++.+++....+..
T Consensus 31 l~~L~~f~av~e~gs~s~AA~~L~isQpavS~~I~~LE~~lG~ 73 (317)
T PRK11482 31 LNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPD 73 (317)
T ss_pred hhHHHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCC
Confidence 3344555566667799999999999999999999999988774
No 421
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=45.30 E-value=62 Score=26.16 Aligned_cols=43 Identities=9% Similarity=0.009 Sum_probs=38.3
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
....||-+.+-.|.-.+...|.+.+.++..|||+.+.|.-|++
T Consensus 13 ~~~~lse~~r~~Iy~~~~~~~~sv~~vS~~ygi~~~RV~AIvr 55 (172)
T PF12298_consen 13 SNPVLSEELREQIYEDVMQDGKSVREVSQKYGIKIQRVEAIVR 55 (172)
T ss_pred CCCcCCHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3567888999999999999999999999999999999988776
No 422
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=45.24 E-value=39 Score=29.64 Aligned_cols=42 Identities=17% Similarity=0.152 Sum_probs=35.6
Q ss_pred HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+-+-++..++...++...|...|+|++||++.+++..+.+..
T Consensus 17 ~~L~~f~~va~~gs~s~AA~~L~iSQpavS~~I~~LE~~lG~ 58 (311)
T PRK10086 17 SKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGI 58 (311)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 345566666777899999999999999999999999998864
No 423
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=45.16 E-value=42 Score=28.74 Aligned_cols=40 Identities=18% Similarity=0.119 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHhhcCC--ChHhhhhhccccHhHHHHHHHHHH
Q psy13113 15 PVVKLLAVLRFYATGN--FQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 15 ~~~~l~~~L~~L~~~~--~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
.+++....+.+|.... +-.+|+..||||..|+.|-+....
T Consensus 5 ~~eR~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le 46 (252)
T PRK10681 5 RDERIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHS 46 (252)
T ss_pred HHHHHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhh
Confidence 4566777777787654 888999999999999999998744
No 424
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=44.39 E-value=23 Score=22.83 Aligned_cols=26 Identities=31% Similarity=0.266 Sum_probs=19.7
Q ss_pred hhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 26 YATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 26 L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
-..|.++.++|...|++++++++|.+
T Consensus 9 ~~~~lt~~~~a~~~~i~~~~i~~~e~ 34 (64)
T PF12844_consen 9 EEKGLTQKDLAEKLGISRSTISKIEN 34 (64)
T ss_dssp HHCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 34678999999999999999998875
No 425
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=44.14 E-value=18 Score=23.80 Aligned_cols=23 Identities=13% Similarity=-0.022 Sum_probs=19.8
Q ss_pred hHhhhhhccccHhHHHHHHHHHH
Q psy13113 32 QIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 32 ~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
..++|..+|||.+|+..|.++..
T Consensus 3 i~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHTTS
T ss_pred HHHHHHHHCcCHHHHHHHHHhcC
Confidence 46899999999999999987655
No 426
>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=44.10 E-value=28 Score=26.53 Aligned_cols=22 Identities=18% Similarity=0.226 Sum_probs=19.3
Q ss_pred hhcCCChHhhhhhccccHhHHH
Q psy13113 26 YATGNFQIDSEDYHDISQSTIC 47 (286)
Q Consensus 26 L~~~~~~~~l~~~Fgvs~stv~ 47 (286)
.-.|.++.++|..+|+|.+||.
T Consensus 120 ~~~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 120 FFEDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred HHcCCCHHHHHHHHCcCHHhhc
Confidence 3467899999999999999985
No 427
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=43.66 E-value=21 Score=25.35 Aligned_cols=24 Identities=21% Similarity=0.037 Sum_probs=17.9
Q ss_pred cCCChHhhhhhccccHhHHHHHHH
Q psy13113 28 TGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 28 ~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
.|.++.++|..+|.|++.|++++.
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~l~ 25 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSRSWVSNHLA 25 (93)
T ss_dssp TT--HHHHHHHTT--HHHHHHHHG
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 578899999999999999998775
No 428
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=43.33 E-value=66 Score=22.33 Aligned_cols=39 Identities=15% Similarity=0.122 Sum_probs=27.2
Q ss_pred HHHHHHHHHhhc-CCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 17 VKLLAVLRFYAT-GNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 17 ~~l~~~L~~L~~-~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
+.++..|..+.. ..+-..|+...|+|+.+|.+.+...-+
T Consensus 6 ~~~~~ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~ 45 (79)
T COG1654 6 QMLLLLLLLLTGNFVSGEKLAEELGISRTAVWKHIQQLRE 45 (79)
T ss_pred HHHHHHHHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHH
Confidence 344444433333 268889999999999999988876543
No 429
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 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 is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. 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; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=43.30 E-value=20 Score=21.00 Aligned_cols=19 Identities=11% Similarity=-0.004 Sum_probs=14.6
Q ss_pred HhhhhhccccHhHHHHHHH
Q psy13113 33 IDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 33 ~~l~~~Fgvs~stv~~~~~ 51 (286)
.++|..+|||.+|+..|-.
T Consensus 3 ~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHH
Confidence 5789999999999987654
No 430
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=43.14 E-value=25 Score=29.78 Aligned_cols=42 Identities=12% Similarity=0.142 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHH-hhc-----CC---ChHhhhhhccccHhHHHHHHHHHH
Q psy13113 13 HSPVVKLLAVLRF-YAT-----GN---FQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 13 ~~~~~~l~~~L~~-L~~-----~~---~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
.|...|+.-.|.. +.. |. +-.+|+..||||+.||.+.+....
T Consensus 4 ~ply~qi~~~L~~~I~~g~~~~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~ 54 (240)
T PRK09764 4 KPLYRQIADRIREQIARGELKPGDALPTESALQTEFGVSRVTVRQALRQLV 54 (240)
T ss_pred CcHHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3556666666643 333 22 668899999999999998876544
No 431
>PF13565 HTH_32: Homeodomain-like domain
Probab=43.04 E-value=67 Score=21.48 Aligned_cols=22 Identities=18% Similarity=0.228 Sum_probs=14.0
Q ss_pred CCChHhhhh----hcc--c--cHhHHHHHH
Q psy13113 29 GNFQIDSED----YHD--I--SQSTICRLV 50 (286)
Q Consensus 29 ~~~~~~l~~----~Fg--v--s~stv~~~~ 50 (286)
..+...++. .|| + |.+||++++
T Consensus 48 ~wt~~~i~~~L~~~~g~~~~~S~~tv~R~L 77 (77)
T PF13565_consen 48 RWTPREIAEYLEEEFGISVRVSRSTVYRIL 77 (77)
T ss_pred CCCHHHHHHHHHHHhCCCCCccHhHHHHhC
Confidence 345555444 455 4 999999863
No 432
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=42.88 E-value=35 Score=28.30 Aligned_cols=30 Identities=17% Similarity=0.180 Sum_probs=25.3
Q ss_pred HHHHhhcC---CChHhhhhhccccHhHHHHHHH
Q psy13113 22 VLRFYATG---NFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 22 ~L~~L~~~---~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
.|..++.| .+.+++|...++|..||.+++.
T Consensus 167 Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~ 199 (225)
T PRK10046 167 VRKLFKEPGVQHTAETVAQALTISRTTARRYLE 199 (225)
T ss_pred HHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHH
Confidence 45566664 7999999999999999999885
No 433
>PRK10632 transcriptional regulator; Provisional
Probab=42.55 E-value=44 Score=29.28 Aligned_cols=39 Identities=21% Similarity=0.154 Sum_probs=32.7
Q ss_pred HHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 21 AVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 21 ~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
-++..++...++...|...++|+++|++.+++..+.+..
T Consensus 8 ~~F~~v~e~gS~t~AA~~L~isQpavS~~I~~LE~~lg~ 46 (309)
T PRK10632 8 SVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQV 46 (309)
T ss_pred HHHHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 344455667899999999999999999999999888774
No 434
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=42.55 E-value=46 Score=28.66 Aligned_cols=38 Identities=11% Similarity=0.112 Sum_probs=31.3
Q ss_pred HHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 22 VLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 22 ~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
++.-+....++...|...++|++++++.+++....|..
T Consensus 8 ~f~~v~~~~s~t~AA~~L~isQpavS~~I~~LE~~lg~ 45 (292)
T TIGR03298 8 ALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQ 45 (292)
T ss_pred HHHHHHHcCCHHHHHHHhCCCHHHHHHHHHHHHHHhCc
Confidence 33444445699999999999999999999999988774
No 435
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=42.51 E-value=62 Score=23.26 Aligned_cols=27 Identities=19% Similarity=0.087 Sum_probs=21.9
Q ss_pred hhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113 26 YATGNFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 26 L~~~~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
-.++......|...|+|++|+++.+++
T Consensus 65 ~~~~gn~s~AAr~LGIsRsTL~rKLkr 91 (95)
T PRK00430 65 QYTRGNQTRAALMLGINRGTLRKKLKK 91 (95)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 345677888999999999999887765
No 436
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=42.27 E-value=46 Score=28.95 Aligned_cols=42 Identities=12% Similarity=0.081 Sum_probs=34.7
Q ss_pred HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+.+-++.-++...++...|...++|++++++.+++..+.|..
T Consensus 14 ~~l~~F~av~e~gS~t~AA~~L~iSQpavS~~I~~LE~~lG~ 55 (303)
T PRK10082 14 KWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGV 55 (303)
T ss_pred HHHHHHHHHHhcCCHHHHHHHhCCChHHHHHHHHHHHHHcCC
Confidence 334455556667899999999999999999999999998874
No 437
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=42.17 E-value=45 Score=28.83 Aligned_cols=42 Identities=12% Similarity=-0.019 Sum_probs=33.4
Q ss_pred HHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 17 VKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 17 ~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
.+|-+++ -+....++...|...++|++++++.+++..+.+..
T Consensus 9 ~~l~~f~-~v~~~gs~s~AA~~L~isq~avS~~i~~LE~~lg~ 50 (297)
T PRK11139 9 NALRAFE-AAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGL 50 (297)
T ss_pred HHHHHHH-HHHHhCCHHHHHHHhCCChHHHHHHHHHHHHHhCc
Confidence 3444444 44455889999999999999999999999988874
No 438
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=42.14 E-value=33 Score=22.83 Aligned_cols=25 Identities=20% Similarity=0.101 Sum_probs=21.0
Q ss_pred CChHhhhhhccccHhHHHHHHHHHH
Q psy13113 30 NFQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
.+..++|..+|+|.+++.+.+++..
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 3567899999999999999988664
No 439
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=41.68 E-value=49 Score=28.72 Aligned_cols=39 Identities=18% Similarity=0.027 Sum_probs=32.7
Q ss_pred HHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 21 AVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 21 ~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
-++..+....++...|...++|++++++.+++....+..
T Consensus 8 ~~f~~v~e~~s~s~AA~~L~isQpavS~~I~~LE~~lg~ 46 (300)
T PRK11074 8 EVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAV 46 (300)
T ss_pred HHHHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 444455556799999999999999999999999988875
No 440
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=41.65 E-value=27 Score=29.41 Aligned_cols=23 Identities=4% Similarity=0.254 Sum_probs=19.3
Q ss_pred ChHhhhhhccccHhHHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~v 53 (286)
+-++|+..||||++||.+.+...
T Consensus 33 sE~eLae~~gVSRt~VReAL~~L 55 (239)
T PRK04984 33 AERELSELIGVTRTTLREVLQRL 55 (239)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Confidence 46789999999999999877644
No 441
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=41.19 E-value=49 Score=28.72 Aligned_cols=40 Identities=13% Similarity=0.124 Sum_probs=33.1
Q ss_pred HHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 20 LAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 20 ~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+-++..++...++...|...|+|++++++-+++....+..
T Consensus 9 L~~F~~v~e~gs~s~AA~~L~isqpavS~~I~~LE~~lg~ 48 (296)
T PRK11062 9 LYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQG 48 (296)
T ss_pred HHHHHHHHhcCCHHHHHHHhCCChHHHHHHHHHHHHHcCc
Confidence 3444455667899999999999999999999999888774
No 442
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=41.03 E-value=24 Score=24.14 Aligned_cols=22 Identities=0% Similarity=-0.073 Sum_probs=18.9
Q ss_pred cCCChHhhhhhccccHhHHHHH
Q psy13113 28 TGNFQIDSEDYHDISQSTICRL 49 (286)
Q Consensus 28 ~~~~~~~l~~~Fgvs~stv~~~ 49 (286)
+-.+...+|..+|||.++|+.|
T Consensus 9 yFGs~~kvA~aLGIs~~AVsQW 30 (75)
T PRK09744 9 FFGSKTKLANAAGVRLASVAAW 30 (75)
T ss_pred HhCcHHHHHHHHCCCHHHHHHH
Confidence 3366788999999999999988
No 443
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=40.89 E-value=86 Score=21.17 Aligned_cols=36 Identities=14% Similarity=0.150 Sum_probs=20.1
Q ss_pred HHHHHHHHHhhcC--CChHhhhhh-----ccccHhHHHHHHHH
Q psy13113 17 VKLLAVLRFYATG--NFQIDSEDY-----HDISQSTICRLVAK 52 (286)
Q Consensus 17 ~~l~~~L~~L~~~--~~~~~l~~~-----Fgvs~stv~~~~~~ 52 (286)
.+..+....+... .++.+|... |.++++|+||-+++
T Consensus 5 ~R~~~I~~li~~~~i~sQ~eL~~~L~~~Gi~vTQaTiSRDLke 47 (70)
T PF01316_consen 5 KRQELIKELISEHEISSQEELVELLEEEGIEVTQATISRDLKE 47 (70)
T ss_dssp HHHHHHHHHHHHS---SHHHHHHHHHHTT-T--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHCCcCCHHHHHHHHHHcCCCcchhHHHHHHHH
Confidence 3444444445544 466666553 78899999997764
No 444
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=40.38 E-value=45 Score=28.01 Aligned_cols=27 Identities=15% Similarity=0.191 Sum_probs=24.1
Q ss_pred CChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 30 NFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
.+..+++..+++|++|+++.+.+..+.
T Consensus 22 IS~~eLA~~L~iS~~Tvsr~Lk~LEe~ 48 (217)
T PRK14165 22 ISSSEFANHTGTSSKTAARILKQLEDE 48 (217)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 578999999999999999999988655
No 445
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=40.07 E-value=29 Score=29.38 Aligned_cols=45 Identities=11% Similarity=0.121 Sum_probs=31.4
Q ss_pred CCCCHHHHHHHHHHHhhc------C---CChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 11 VIHSPVVKLLAVLRFYAT------G---NFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~------~---~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
...|..+|+.-.|.-.=. | .+-.+|+..||||+-||.+.+.....
T Consensus 4 ~~~plY~qI~~~i~~~I~~G~~~~G~~LPsE~eLa~~f~VSR~TvRkAL~~L~~ 57 (236)
T COG2188 4 SAMPLYQQIAEDIRQRIESGELPPGDKLPSERELAEQFGVSRMTVRKALDELVE 57 (236)
T ss_pred ccCccHHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 345666666666654332 2 25668999999999999998876554
No 446
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=39.92 E-value=15 Score=34.64 Aligned_cols=22 Identities=23% Similarity=0.175 Sum_probs=19.8
Q ss_pred CChHhhhhhccccHhHHHHHHH
Q psy13113 30 NFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
.+.+++|...|++.|||||+++
T Consensus 344 LtlkdvAe~lglheSTVSRav~ 365 (455)
T PRK05932 344 LVLKDIAEELGMHESTISRATT 365 (455)
T ss_pred ccHHHHHHHhCCCccchhhhhc
Confidence 5789999999999999999774
No 447
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=39.86 E-value=30 Score=29.26 Aligned_cols=44 Identities=14% Similarity=0.015 Sum_probs=31.1
Q ss_pred CCCCHHHHHHHHHHHh-hcC--------CChHhhhhhccccHhHHHHHHHHHH
Q psy13113 11 VIHSPVVKLLAVLRFY-ATG--------NFQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L-~~~--------~~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
...|...|+.-.|..- .+| .+-.+|+..||||+.||.+.+....
T Consensus 6 ~~~p~y~qI~~~i~~~I~~G~~~~g~kLPsE~eLa~~~~VSR~TvR~Al~~L~ 58 (241)
T PRK11402 6 SHQLLYATVRQRLLDDIAQGVYQAGQQIPTENELCTQYNVSRITIRKAISDLV 58 (241)
T ss_pred CCCcHHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3456777776666543 333 2667899999999999998776544
No 448
>PRK06474 hypothetical protein; Provisional
Probab=39.68 E-value=61 Score=26.22 Aligned_cols=39 Identities=13% Similarity=0.147 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHhhcC--CChHhhhhhc-cccHhHHHHHHHHH
Q psy13113 15 PVVKLLAVLRFYATG--NFQIDSEDYH-DISQSTICRLVAKV 53 (286)
Q Consensus 15 ~~~~l~~~L~~L~~~--~~~~~l~~~F-gvs~stv~~~~~~v 53 (286)
-..++.+.-....++ .+-.+++..+ ++|++|+++.++.+
T Consensus 10 ~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L 51 (178)
T PRK06474 10 HPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTM 51 (178)
T ss_pred CHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHH
Confidence 334444443334444 5888888888 79999999987643
No 449
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=39.57 E-value=61 Score=27.12 Aligned_cols=31 Identities=6% Similarity=-0.104 Sum_probs=27.1
Q ss_pred hcCCChHhhhhhccccHhHHHHHHHHHHHHH
Q psy13113 27 ATGNFQIDSEDYHDISQSTICRLVAKVSEEL 57 (286)
Q Consensus 27 ~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l 57 (286)
+.|.+.+++|..+++|..||..++.+.....
T Consensus 176 ~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~ 206 (239)
T PRK10430 176 DYEFSTDELANAVNISRVSCRKYLIWLVNCH 206 (239)
T ss_pred CCCcCHHHHHHHhCchHHHHHHHHHHHHhCC
Confidence 5789999999999999999999998776553
No 450
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=39.55 E-value=56 Score=28.26 Aligned_cols=38 Identities=16% Similarity=0.092 Sum_probs=32.2
Q ss_pred HHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 22 VLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 22 ~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
++.-++...++...|...++|+++|++.+++..+.|..
T Consensus 9 ~f~~va~~gs~s~AA~~L~isQpavS~~I~~LE~~lG~ 46 (301)
T PRK14997 9 WFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGV 46 (301)
T ss_pred HHHHHHHcCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 44445566889999999999999999999999998874
No 451
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=39.42 E-value=54 Score=28.36 Aligned_cols=38 Identities=13% Similarity=0.135 Sum_probs=31.5
Q ss_pred HHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 22 VLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 22 ~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
++.-+....++...|...++|++++++.+++....+..
T Consensus 9 ~f~~v~e~gs~s~AA~~L~isq~avS~~I~~LE~~lg~ 46 (294)
T PRK03635 9 ALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQ 46 (294)
T ss_pred HHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCc
Confidence 33444455699999999999999999999999988874
No 452
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=39.25 E-value=33 Score=27.16 Aligned_cols=33 Identities=15% Similarity=-0.004 Sum_probs=26.1
Q ss_pred HHHHHHHhh--cCCChHhhhhhccccHhHHHHHHH
Q psy13113 19 LLAVLRFYA--TGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 19 l~~~L~~L~--~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
+.-.|..++ .|.++.+||...|++++++++|-+
T Consensus 70 ~g~~Ir~~Re~~glSqeeLA~~lgvs~s~IsriE~ 104 (154)
T TIGR00270 70 YGIIIRREREKRGWSQEQLAKKIQEKESLIKKIEN 104 (154)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 344555555 678999999999999999998764
No 453
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=38.89 E-value=67 Score=25.12 Aligned_cols=34 Identities=21% Similarity=0.034 Sum_probs=29.2
Q ss_pred HhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113 25 FYATGNFQIDSEDYHDISQSTICRLVAKVSEELA 58 (286)
Q Consensus 25 ~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~ 58 (286)
.+..+.+.+.++..+|+|..|+..++.+...-|.
T Consensus 152 ~~~~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~ 185 (202)
T PRK09390 152 GLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQ 185 (202)
T ss_pred HHHccCchHHHHHHcCCCHHHHHHHHHHHHHHHc
Confidence 4667788999999999999999999988877764
No 454
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=38.88 E-value=18 Score=34.24 Aligned_cols=22 Identities=23% Similarity=0.185 Sum_probs=19.8
Q ss_pred CChHhhhhhccccHhHHHHHHH
Q psy13113 30 NFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
.+.+++|...|++.|||||++.
T Consensus 370 LtlkdVAe~lglHeSTVSRa~~ 391 (481)
T PRK12469 370 LVLRDVAEELGLHESTISRATG 391 (481)
T ss_pred CcHHHHHHHhCCCcchhhHHhc
Confidence 4789999999999999999774
No 455
>PRK13698 plasmid-partitioning protein; Provisional
Probab=38.54 E-value=51 Score=29.50 Aligned_cols=40 Identities=18% Similarity=0.086 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHH-Hh-hcCCChHhhhhhccccHhHHHHHHHH
Q psy13113 13 HSPVVKLLAVLR-FY-ATGNFQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 13 ~~~~~~l~~~L~-~L-~~~~~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
+++.+.=..... .. ..+.++..+|..+|+|+++|++.++-
T Consensus 158 ls~iE~A~ay~~~L~~~~~~tQeeLA~~lG~SRs~Vsn~Lrl 199 (323)
T PRK13698 158 TSAYERGLRYASRLQNEFAGNISALADAENISRKIITRCINT 199 (323)
T ss_pred CCHHHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 566555443323 23 45689999999999999999998874
No 456
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=38.28 E-value=32 Score=28.29 Aligned_cols=23 Identities=9% Similarity=0.062 Sum_probs=19.1
Q ss_pred ChHhhhhhccccHhHHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~v 53 (286)
+-.+|+..||||+++|.+.+...
T Consensus 36 ~e~~La~~lgVSRtpVReAL~~L 58 (212)
T TIGR03338 36 NESDIAARLGVSRGPVREAFRAL 58 (212)
T ss_pred cHHHHHHHhCCChHHHHHHHHHH
Confidence 56789999999999999877543
No 457
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=38.19 E-value=1.1e+02 Score=20.88 Aligned_cols=40 Identities=18% Similarity=0.173 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113 13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
++..+.+++.|-.= .++...+-..+|+++.++..++.+..
T Consensus 4 lt~~~~IL~~ls~~--c~TLeeL~ekTgi~k~~LlV~LsrL~ 43 (72)
T PF05584_consen 4 LTVTQKILIILSKR--CCTLEELEEKTGISKNTLLVYLSRLA 43 (72)
T ss_pred hhHHHHHHHHHHhc--cCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 44555555555433 67999999999999999988776543
No 458
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=38.08 E-value=32 Score=27.84 Aligned_cols=26 Identities=15% Similarity=0.201 Sum_probs=22.8
Q ss_pred hhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 26 YATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 26 L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
...|.++.++|...|+|++|+++|-+
T Consensus 17 ~~~glt~~elA~~~gis~~~is~~E~ 42 (185)
T PRK09943 17 QQQGLSQRRAAELSGLTHSAISTIEQ 42 (185)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 34678999999999999999998875
No 459
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=38.00 E-value=29 Score=29.60 Aligned_cols=21 Identities=5% Similarity=0.126 Sum_probs=18.0
Q ss_pred ChHhhhhhccccHhHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~ 51 (286)
+-++|+..||||+++|.+.+.
T Consensus 36 ~EreLae~fgVSR~~vREAl~ 56 (241)
T COG2186 36 SERELAERFGVSRTVVREALK 56 (241)
T ss_pred CHHHHHHHHCCCcHHHHHHHH
Confidence 567899999999999987664
No 460
>PF08769 Spo0A_C: Sporulation initiation factor Spo0A C terminal; InterPro: IPR014879 The response regulator Spo0A is comprised of a phophoacceptor domain and a transcription activation domain. This domain corresponds to the transcription activation domain and forms an alpha helical structure comprising of 6 alpha helices. The structure contains a helix-turn-helix and binds DNA [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005509 calcium ion binding, 0006355 regulation of transcription, DNA-dependent, 0042173 regulation of sporulation resulting in formation of a cellular spore, 0005737 cytoplasm; PDB: 1FC3_C 1LQ1_D.
Probab=37.56 E-value=54 Score=24.15 Aligned_cols=31 Identities=13% Similarity=0.006 Sum_probs=26.8
Q ss_pred CChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113 30 NFQIDSEDYHDISQSTICRLVAKVSEELAKC 60 (286)
Q Consensus 30 ~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~ 60 (286)
.=|..+|..|+.+.+.|.+.++.+++..+..
T Consensus 41 ~LYp~IA~k~~TT~s~VERaIR~aI~~~w~~ 71 (106)
T PF08769_consen 41 ELYPDIAKKYGTTPSRVERAIRHAIEVAWTR 71 (106)
T ss_dssp THHHHHHHHTTS-HHHHHHHHHHHHHHHHHC
T ss_pred hHHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 4577899999999999999999999998864
No 461
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=37.40 E-value=34 Score=29.19 Aligned_cols=23 Identities=4% Similarity=0.159 Sum_probs=19.0
Q ss_pred ChHhhhhhccccHhHHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~v 53 (286)
+-..|+..||||+++|.+.+...
T Consensus 35 sE~eLa~~~gVSRtpVREAL~~L 57 (257)
T PRK10225 35 PEREIAEMLDVTRTVVREALIML 57 (257)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHH
Confidence 46689999999999999877543
No 462
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=37.24 E-value=35 Score=29.02 Aligned_cols=23 Identities=9% Similarity=-0.048 Sum_probs=19.1
Q ss_pred ChHhhhhhccccHhHHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~v 53 (286)
+-++|+..||||+++|.+.+...
T Consensus 33 sE~eLa~~~gVSRtpVREAL~~L 55 (251)
T PRK09990 33 SERRLCEKLGFSRSALREGLTVL 55 (251)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Confidence 46789999999999999877543
No 463
>PF14502 HTH_41: Helix-turn-helix domain
Probab=37.23 E-value=52 Score=20.47 Aligned_cols=23 Identities=13% Similarity=0.089 Sum_probs=18.8
Q ss_pred ChHhhhhhccccHhHHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~v 53 (286)
+..+++..|++|..|+-..++..
T Consensus 8 tI~e~~~~~~vs~GtiQ~Alk~L 30 (48)
T PF14502_consen 8 TISEYSEKFGVSRGTIQNALKFL 30 (48)
T ss_pred CHHHHHHHhCcchhHHHHHHHHH
Confidence 56788999999999998877643
No 464
>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=37.22 E-value=43 Score=26.71 Aligned_cols=37 Identities=8% Similarity=0.095 Sum_probs=29.7
Q ss_pred HHHHHHHHHHhhcCCChHhhhhhcc-ccHhHHHHHHHH
Q psy13113 16 VVKLLAVLRFYATGNFQIDSEDYHD-ISQSTICRLVAK 52 (286)
Q Consensus 16 ~~~l~~~L~~L~~~~~~~~l~~~Fg-vs~stv~~~~~~ 52 (286)
++++...-.+++.|.+..++|..+| ||+..|.-.+++
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 999887765554
No 465
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=36.89 E-value=27 Score=23.64 Aligned_cols=37 Identities=24% Similarity=0.318 Sum_probs=27.2
Q ss_pred ChHhhhhhccccHhHHHHHHHHHHHHHH---hhcccccCCch
Q psy13113 31 FQIDSEDYHDISQSTICRLVAKVSEELA---KCHQQWIHFPE 69 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~v~~~l~---~~~~~~i~~P~ 69 (286)
...+++...|+|++|+++.++.- .+- .+....+.|+.
T Consensus 15 rl~ev~~~~GlSrstiYr~i~~~--~FPkpvklG~r~v~W~~ 54 (70)
T COG3311 15 RLPEVAQLTGLSRSTIYRLIKDG--TFPKPVKLGGRSVAWPE 54 (70)
T ss_pred hHHHHHHHHCccHHHHHHHHccC--CCCCCeecCcccccccH
Confidence 56678889999999999988755 111 24456778887
No 466
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=36.63 E-value=36 Score=29.01 Aligned_cols=23 Identities=13% Similarity=0.111 Sum_probs=19.2
Q ss_pred ChHhhhhhccccHhHHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~v 53 (286)
+-.+|+..||||+++|.+.+...
T Consensus 28 sE~eLae~~gVSRtpVREAL~~L 50 (253)
T PRK10421 28 AERQLAMQLGVSRNSLREALAKL 50 (253)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHH
Confidence 35789999999999999877644
No 467
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=36.46 E-value=31 Score=22.60 Aligned_cols=26 Identities=12% Similarity=0.027 Sum_probs=22.3
Q ss_pred hhcCCChHhhhhhccccHhHHHHHHH
Q psy13113 26 YATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 26 L~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
..++..+..+|...++++.||.++..
T Consensus 13 i~~~GnqtEvaR~l~c~R~TVrKY~~ 38 (64)
T PF06322_consen 13 IETYGNQTEVARRLGCNRATVRKYSR 38 (64)
T ss_pred HHHhCcHHHHHHHhcccHHHHHHHhc
Confidence 34678889999999999999998875
No 468
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=36.34 E-value=82 Score=24.88 Aligned_cols=41 Identities=7% Similarity=0.073 Sum_probs=29.6
Q ss_pred HHHHHHHHHHhhc-C--CChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 16 VVKLLAVLRFYAT-G--NFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 16 ~~~l~~~L~~L~~-~--~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
.+.-+.+++.|.. . ....++|...+||.+||+.++++....
T Consensus 8 ~edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~ 51 (154)
T COG1321 8 EEDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERL 51 (154)
T ss_pred HHHHHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHC
Confidence 4455555554442 2 477789999999999999998876543
No 469
>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth. Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor [] reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change []. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement []. This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 5CRO_A 2ECS_A 2OVG_A 6CRO_A 1D1L_A 2ORC_A 1D1M_B 3ORC_A 1ORC_A 2A63_A ....
Probab=36.31 E-value=36 Score=22.13 Aligned_cols=20 Identities=20% Similarity=0.270 Sum_probs=16.3
Q ss_pred hHhhhhhccccHhHHHHHHH
Q psy13113 32 QIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 32 ~~~l~~~Fgvs~stv~~~~~ 51 (286)
+..+|..+||+++.+++.++
T Consensus 15 Q~kaA~~lGV~Q~AIsKAlr 34 (59)
T PF09048_consen 15 QAKAARALGVTQSAISKALR 34 (59)
T ss_dssp HHHHHHHHTS-HHHHHHHHH
T ss_pred hHHHHHHcCCcHHHHHHHHH
Confidence 67889999999999998664
No 470
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=35.99 E-value=61 Score=24.35 Aligned_cols=27 Identities=11% Similarity=0.119 Sum_probs=22.3
Q ss_pred CCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 29 GNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 29 ~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
..+-.+++..++++.+++.+++.....
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~L~~ 51 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRTLRR 51 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 358889999999999999988875544
No 471
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=35.87 E-value=54 Score=22.62 Aligned_cols=33 Identities=18% Similarity=0.234 Sum_probs=23.5
Q ss_pred HHHHhhcC-----CChHhhhhhccccHhHHHHHHHHHH
Q psy13113 22 VLRFYATG-----NFQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 22 ~L~~L~~~-----~~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
+|.+|+.. .+-+++|...+++.+++.+++....
T Consensus 13 ~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~ 50 (83)
T PF02082_consen 13 ILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLK 50 (83)
T ss_dssp HHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 45555532 3778999999999999998876544
No 472
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=35.84 E-value=38 Score=28.45 Aligned_cols=23 Identities=4% Similarity=0.254 Sum_probs=19.2
Q ss_pred ChHhhhhhccccHhHHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~v 53 (286)
+-.+|+..||||+++|.+.+...
T Consensus 32 sE~~La~~lgVSRtpVREAL~~L 54 (235)
T TIGR02812 32 AERELSELIGVTRTTLREVLQRL 54 (235)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHH
Confidence 46789999999999999877644
No 473
>PRK03837 transcriptional regulator NanR; Provisional
Probab=35.79 E-value=40 Score=28.36 Aligned_cols=22 Identities=0% Similarity=0.111 Sum_probs=18.8
Q ss_pred ChHhhhhhccccHhHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~ 52 (286)
+-.+|+..||||+++|.+.+..
T Consensus 39 ~E~~Lae~~gVSRt~VREAL~~ 60 (241)
T PRK03837 39 SERELMAFFGVGRPAVREALQA 60 (241)
T ss_pred CHHHHHHHhCCCHHHHHHHHHH
Confidence 5678999999999999987753
No 474
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=35.74 E-value=38 Score=28.84 Aligned_cols=23 Identities=9% Similarity=0.225 Sum_probs=19.0
Q ss_pred ChHhhhhhccccHhHHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~v 53 (286)
+-.+|+..||||+++|.+.+...
T Consensus 36 sE~eLa~~lgVSRtpVREAL~~L 58 (254)
T PRK09464 36 PERELAKQFDVSRPSLREAIQRL 58 (254)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHH
Confidence 46789999999999999877543
No 475
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=35.25 E-value=40 Score=25.34 Aligned_cols=25 Identities=12% Similarity=0.077 Sum_probs=22.1
Q ss_pred hcCCChHhhhhhccccHhHHHHHHH
Q psy13113 27 ATGNFQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 27 ~~~~~~~~l~~~Fgvs~stv~~~~~ 51 (286)
..|.++.++|...|||++|++++.+
T Consensus 16 ~~Glsq~eLA~~~Gis~~~is~iE~ 40 (120)
T PRK13890 16 ERHMTKKELSERSGVSISFLSDLTT 40 (120)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence 4678999999999999999998775
No 476
>PRK13558 bacterio-opsin activator; Provisional
Probab=35.14 E-value=95 Score=30.50 Aligned_cols=49 Identities=10% Similarity=-0.084 Sum_probs=38.9
Q ss_pred CCCCHHHHHHHHHHHhhcC------CChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 11 VIHSPVVKLLAVLRFYATG------NFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~------~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
..|+..++=++.+-|...+ .+..+||..+|||++|+++.+++...-|..
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~ 660 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVG 660 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3688877766666666654 488899999999999999999988777664
No 477
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=34.97 E-value=58 Score=27.96 Aligned_cols=41 Identities=17% Similarity=0.109 Sum_probs=32.3
Q ss_pred HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+|-+++. +....++...|...++|+++|++.+++....+..
T Consensus 11 ~l~~f~~-v~~~gs~t~AA~~L~itq~avS~~i~~LE~~lg~ 51 (294)
T PRK09986 11 LLRYFLA-VAEELHFGRAAARLNISQPPLSIHIKELEDQLGT 51 (294)
T ss_pred HHHHHHH-HHHhcCHHHHHHHhCCCCCHHHHHHHHHHHHhCC
Confidence 3333333 4444689999999999999999999999998874
No 478
>PRK15183 Vi polysaccharide biosynthesis protein TviA; Provisional
Probab=34.52 E-value=64 Score=23.62 Aligned_cols=50 Identities=12% Similarity=0.264 Sum_probs=35.2
Q ss_pred HHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcccccCCch
Q psy13113 20 LAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPE 69 (286)
Q Consensus 20 ~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~~i~~P~ 69 (286)
.+-+.|.-+.....++..+|--|.||.++|-++..--....-++|+-.|+
T Consensus 89 i~kmkyflsesgmeelqdrfmns~st~yrwrke~a~kfgvr~prylllpd 138 (143)
T PRK15183 89 IVKMKYFLSESGMEELQDRFMNSSSTMYRWRKELAVKFGVREPRYLLLPD 138 (143)
T ss_pred hhHhhhhhhhccHHHHHHHHccChHHHHHHHHHHHHHhcCCCCceEecCc
Confidence 44555666667788888889889999998888776555555566655553
No 479
>PRK00441 argR arginine repressor; Provisional
Probab=34.52 E-value=78 Score=24.85 Aligned_cols=35 Identities=17% Similarity=0.284 Sum_probs=24.8
Q ss_pred HHHHHHHHhhcC--CChHhhhhh-----ccccHhHHHHHHHH
Q psy13113 18 KLLAVLRFYATG--NFQIDSEDY-----HDISQSTICRLVAK 52 (286)
Q Consensus 18 ~l~~~L~~L~~~--~~~~~l~~~-----Fgvs~stv~~~~~~ 52 (286)
+....+..++.. .++.+|+.. |+||++|++|-+++
T Consensus 5 R~~~I~~ll~~~~~~~q~eL~~~L~~~G~~vSqaTisRDl~~ 46 (149)
T PRK00441 5 RHAKILEIINSKEIETQEELAEELKKMGFDVTQATVSRDIKE 46 (149)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHHhcCCCcCHHHHHHHHHH
Confidence 333444455544 588889998 59999999997763
No 480
>PRK15340 transcriptional regulator InvF; Provisional
Probab=33.92 E-value=55 Score=27.49 Aligned_cols=28 Identities=18% Similarity=0.139 Sum_probs=24.1
Q ss_pred cCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 28 TGNFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 28 ~~~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
...+..++|..+|+|.++++|.|++...
T Consensus 124 ~~~sleeLA~~~gvS~r~f~RlFk~~~G 151 (216)
T PRK15340 124 SGNTMRMLGEDYGVSYTHFRRLCSRALG 151 (216)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHC
Confidence 4468889999999999999999998753
No 481
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=33.42 E-value=44 Score=21.85 Aligned_cols=21 Identities=5% Similarity=0.015 Sum_probs=17.9
Q ss_pred hHhhhhhccccHhHHHHHHHH
Q psy13113 32 QIDSEDYHDISQSTICRLVAK 52 (286)
Q Consensus 32 ~~~l~~~Fgvs~stv~~~~~~ 52 (286)
-.++|..+|||.+|+..|..+
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 467899999999999988764
No 482
>PRK08359 transcription factor; Validated
Probab=33.42 E-value=46 Score=27.00 Aligned_cols=32 Identities=9% Similarity=-0.029 Sum_probs=24.4
Q ss_pred HHHHHHHhh--cCCChHhhhhhccccHhHHHHHH
Q psy13113 19 LLAVLRFYA--TGNFQIDSEDYHDISQSTICRLV 50 (286)
Q Consensus 19 l~~~L~~L~--~~~~~~~l~~~Fgvs~stv~~~~ 50 (286)
+.-.|..++ .|.++.+||...|+|++|+++|=
T Consensus 86 y~~rIkeaRe~kglSQeeLA~~lgvs~stI~~iE 119 (176)
T PRK08359 86 YAERVYEAIQKSGLSYEELSHEVGLSVNDLRRIA 119 (176)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 333455553 68899999999999999998753
No 483
>PRK13503 transcriptional activator RhaS; Provisional
Probab=33.36 E-value=84 Score=26.86 Aligned_cols=26 Identities=15% Similarity=0.037 Sum_probs=22.8
Q ss_pred CCChHhhhhhccccHhHHHHHHHHHH
Q psy13113 29 GNFQIDSEDYHDISQSTICRLVAKVS 54 (286)
Q Consensus 29 ~~~~~~l~~~Fgvs~stv~~~~~~v~ 54 (286)
..+..++|..+|+|++++++.+++..
T Consensus 187 ~~tl~~lA~~~~lS~~~l~r~Fk~~~ 212 (278)
T PRK13503 187 EVNWEALADQFSLSLRTLHRQLKQQT 212 (278)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHh
Confidence 45788999999999999999998774
No 484
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=33.31 E-value=87 Score=27.54 Aligned_cols=41 Identities=15% Similarity=0.197 Sum_probs=32.3
Q ss_pred HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+|-.++. ++...++...|...++|++|+++.+++....|..
T Consensus 8 qL~~F~a-Vae~gSfs~AA~~L~isQpavS~~Ik~LE~eLG~ 48 (297)
T PRK15243 8 KLKIFIT-LMETGSFSIATSVLYITRTPLSRVISDLERELKQ 48 (297)
T ss_pred HHHHHHH-HHHcCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 3434443 3444689999999999999999999999988874
No 485
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=33.30 E-value=86 Score=26.91 Aligned_cols=41 Identities=15% Similarity=0.145 Sum_probs=31.2
Q ss_pred HHHHHHHHHHhhcC--CChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 16 VVKLLAVLRFYATG--NFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 16 ~~~l~~~L~~L~~~--~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
+++.-..|.+|... .+-.+|+..|+||+.|+.|=++...+.
T Consensus 4 ~eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~ 46 (253)
T COG1349 4 EERHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQ 46 (253)
T ss_pred HHHHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHC
Confidence 34555556666654 488899999999999999988776654
No 486
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=32.92 E-value=77 Score=21.86 Aligned_cols=29 Identities=7% Similarity=0.142 Sum_probs=22.0
Q ss_pred cCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113 28 TGNFQIDSEDYHDISQSTICRLVAKVSEE 56 (286)
Q Consensus 28 ~~~~~~~l~~~Fgvs~stv~~~~~~v~~~ 56 (286)
...++.++....|++.+++++.++...++
T Consensus 13 ~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~ 41 (80)
T PF13601_consen 13 EEATFSELKEELGLTDGNLSKHLKKLEEA 41 (80)
T ss_dssp SEEEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHHHHC
Confidence 45799999999999999999887655544
No 487
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=32.89 E-value=44 Score=19.55 Aligned_cols=22 Identities=14% Similarity=0.090 Sum_probs=14.5
Q ss_pred hcCCChHhhhhhccccHhHHHH
Q psy13113 27 ATGNFQIDSEDYHDISQSTICR 48 (286)
Q Consensus 27 ~~~~~~~~l~~~Fgvs~stv~~ 48 (286)
..|.+...+|..||++...+.+
T Consensus 4 ~~gDtl~~IA~~~~~~~~~l~~ 25 (44)
T PF01476_consen 4 QPGDTLWSIAKRYGISVDELME 25 (44)
T ss_dssp -TT--HHHHHHHTTS-HHHHHH
T ss_pred CcCCcHHHHHhhhhhhHhHHHH
Confidence 4678889999999999866654
No 488
>PRK09954 putative kinase; Provisional
Probab=32.85 E-value=97 Score=27.89 Aligned_cols=33 Identities=18% Similarity=0.173 Sum_probs=26.4
Q ss_pred HHHhhcC--CChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 23 LRFYATG--NFQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 23 L~~L~~~--~~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
|..|..+ .++.+++..+|+|++||.+.+++..+
T Consensus 9 l~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~ 43 (362)
T PRK09954 9 LAILRRNPLIQQNEIADILQISRSRVAAHIMDLMR 43 (362)
T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3444443 68999999999999999999987765
No 489
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=32.61 E-value=45 Score=28.37 Aligned_cols=22 Identities=9% Similarity=0.137 Sum_probs=18.3
Q ss_pred hHhhhhhccccHhHHHHHHHHH
Q psy13113 32 QIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 32 ~~~l~~~Fgvs~stv~~~~~~v 53 (286)
-.+|+..||||+++|.+.+...
T Consensus 35 E~eLae~~gVSRtpVREAL~~L 56 (253)
T PRK11523 35 ERFIADEKNVSRTVVREAIIML 56 (253)
T ss_pred HHHHHHHHCCCHHHHHHHHHHH
Confidence 5689999999999999877533
No 490
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=32.45 E-value=92 Score=30.28 Aligned_cols=33 Identities=18% Similarity=0.100 Sum_probs=27.3
Q ss_pred hcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 27 ATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 27 ~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
..+.+..+||..+|||..|+.+.+..+-..|..
T Consensus 15 ~~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~ 47 (584)
T PRK09863 15 QQDRSGGELAQQLGVSRRTIVRDIAYINFTLNG 47 (584)
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 355789999999999999999999877666543
No 491
>PF07180 DUF1401: Protein of unknown function (DUF1401); InterPro: IPR020357 This entry represents CaiF, a specific carnitine-sensitive transcription regulator. CaiF and CRP a cyclic AMP receptor protein, are required to activate the cai and fix operons, which are involved in anaerobic carnitine metabolism [].; GO: 0006351 transcription, DNA-dependent
Probab=32.37 E-value=87 Score=24.45 Aligned_cols=38 Identities=11% Similarity=0.094 Sum_probs=30.3
Q ss_pred HHHHHHHHhhcCC--ChHhhhhhccccHhHHHHHHHHHHH
Q psy13113 18 KLLAVLRFYATGN--FQIDSEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 18 ~l~~~L~~L~~~~--~~~~l~~~Fgvs~stv~~~~~~v~~ 55 (286)
-++++.|-|..+. +-.+++..|.|++..++.++.-+..
T Consensus 25 Yl~VA~Wgl~q~rwitr~dIS~aF~I~~rrA~~ilsYI~s 64 (146)
T PF07180_consen 25 YLIVAWWGLQQNRWITRNDISEAFHITQRRASNILSYILS 64 (146)
T ss_pred ehHHHHHHHHhcCcccHHHHHHhcCCchhhHHHHHHHHHh
Confidence 4788888888875 7789999999999888876655443
No 492
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=32.19 E-value=38 Score=22.15 Aligned_cols=21 Identities=10% Similarity=-0.072 Sum_probs=17.7
Q ss_pred ChHhhhhhccccHhHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVA 51 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~ 51 (286)
+..++|..+|||.+|+..+..
T Consensus 2 s~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 346789999999999998875
No 493
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=32.03 E-value=1.3e+02 Score=22.82 Aligned_cols=39 Identities=21% Similarity=0.199 Sum_probs=26.3
Q ss_pred HHHHHHHHHHhhcCCChHh----hhhhccccHhHHHHHHHHHHH
Q psy13113 16 VVKLLAVLRFYATGNFQID----SEDYHDISQSTICRLVAKVSE 55 (286)
Q Consensus 16 ~~~l~~~L~~L~~~~~~~~----l~~~Fgvs~stv~~~~~~v~~ 55 (286)
|.+++-.||. ....+.++ ++...+++.+|+..++++...
T Consensus 6 E~~VM~vlW~-~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~ 48 (130)
T TIGR02698 6 EWEVMRVVWT-LGETTSRDIIRILAEKKDWSDSTIKTLLGRLVD 48 (130)
T ss_pred HHHHHHHHHc-CCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHH
Confidence 4556666664 33567777 445568999999988876653
No 494
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=31.67 E-value=57 Score=23.58 Aligned_cols=32 Identities=19% Similarity=0.057 Sum_probs=24.9
Q ss_pred HHHHHHHHhhcCCChHhhhhhccccHhHHHHH
Q psy13113 18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRL 49 (286)
Q Consensus 18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~ 49 (286)
++-+.=-.|....+++.++...|+|-.|+.|=
T Consensus 49 Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRG 80 (103)
T COG2973 49 RVRIVEELLRGELSQREIAQKLGVSIATITRG 80 (103)
T ss_pred HHHHHHHHHhccccHHHHHHHhCcchhhhccc
Confidence 33344445788899999999999999988753
No 495
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=31.59 E-value=47 Score=27.59 Aligned_cols=23 Identities=4% Similarity=0.115 Sum_probs=19.0
Q ss_pred ChHhhhhhccccHhHHHHHHHHH
Q psy13113 31 FQIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 31 ~~~~l~~~Fgvs~stv~~~~~~v 53 (286)
+-..|+..||||+++|.+.+...
T Consensus 36 ~e~~La~~lgVSRtpVREAL~~L 58 (221)
T PRK11414 36 ITKNLAEQLGMSITPVREALLRL 58 (221)
T ss_pred CHHHHHHHHCCCchhHHHHHHHH
Confidence 56789999999999999877533
No 496
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=31.30 E-value=45 Score=24.46 Aligned_cols=50 Identities=18% Similarity=0.270 Sum_probs=33.7
Q ss_pred CCChHhhhhhccccHhHHHHHHHHH---HHHHH-hhcccccCCchhHHHHHHHh
Q psy13113 29 GNFQIDSEDYHDISQSTICRLVAKV---SEELA-KCHQQWIHFPEDLQTAKNQF 78 (286)
Q Consensus 29 ~~~~~~l~~~Fgvs~stv~~~~~~v---~~~l~-~~~~~~i~~P~~~~~~~~~f 78 (286)
|.+...+|...||++.|++++++.= ...+. .+.+.|-.-|+-|-++-..|
T Consensus 23 glt~~~lA~~lgV~r~~is~ling~~~iT~dmAlrL~k~fGtspefWlNlQ~~y 76 (104)
T COG3093 23 GLTQTELAEALGVTRNTISELINGRRAITADMALRLAKVFGTSPEFWLNLQNAY 76 (104)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHcCCcCCCHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 7899999999999999999999832 22233 35555555555455444333
No 497
>PRK12423 LexA repressor; Provisional
Probab=31.27 E-value=1.1e+02 Score=25.18 Aligned_cols=26 Identities=15% Similarity=0.075 Sum_probs=21.8
Q ss_pred CChHhhhhhcc-ccHhHHHHHHHHHHH
Q psy13113 30 NFQIDSEDYHD-ISQSTICRLVAKVSE 55 (286)
Q Consensus 30 ~~~~~l~~~Fg-vs~stv~~~~~~v~~ 55 (286)
.+.+++|..|| +|++|+++.+.....
T Consensus 26 Ps~~eia~~~g~~s~~~v~~~l~~L~~ 52 (202)
T PRK12423 26 PSLAEIAQAFGFASRSVARKHVQALAE 52 (202)
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 59999999999 599999987766555
No 498
>PRK03341 arginine repressor; Provisional
Probab=31.25 E-value=97 Score=24.91 Aligned_cols=42 Identities=10% Similarity=0.172 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHHhhcC--CChHhhhhhc-----cccHhHHHHHHHHH
Q psy13113 12 IHSPVVKLLAVLRFYATG--NFQIDSEDYH-----DISQSTICRLVAKV 53 (286)
Q Consensus 12 ~~~~~~~l~~~L~~L~~~--~~~~~l~~~F-----gvs~stv~~~~~~v 53 (286)
.....++....+..+... .++.+|+..+ .+|++|++|-+++.
T Consensus 10 ~m~k~~R~~~I~~li~~~~i~tQ~eL~~~L~~~Gi~vTQaTiSRDl~eL 58 (168)
T PRK03341 10 PATRAARQARIVAILSRQSVRSQAELAALLADEGIEVTQATLSRDLDEL 58 (168)
T ss_pred cCCHHHHHHHHHHHHHHCCCccHHHHHHHHHHcCCcccHHHHHHHHHHh
Confidence 345566666667777765 5888888886 99999999977643
No 499
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=31.13 E-value=64 Score=26.70 Aligned_cols=43 Identities=9% Similarity=-0.043 Sum_probs=35.6
Q ss_pred CCCCHHHHHHHHHHHhhcCC----ChHhhhhhccccHhHHHHHHHHH
Q psy13113 11 VIHSPVVKLLAVLRFYATGN----FQIDSEDYHDISQSTICRLVAKV 53 (286)
Q Consensus 11 ~~~~~~~~l~~~L~~L~~~~----~~~~l~~~Fgvs~stv~~~~~~v 53 (286)
..++.+.-|..++..+.... +.+.++...||++++++.+|..=
T Consensus 2 ~~Lsre~Il~aA~~l~~e~G~~~lsmr~lA~~lgv~~~slY~hf~~K 48 (205)
T PRK13756 2 ARLDKEKVIDSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNK 48 (205)
T ss_pred CccCHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCchHHHHHcCCH
Confidence 35777888888888887644 99999999999999999998643
No 500
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=31.02 E-value=82 Score=26.74 Aligned_cols=40 Identities=23% Similarity=0.253 Sum_probs=33.0
Q ss_pred HHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113 20 LAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK 59 (286)
Q Consensus 20 ~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~ 59 (286)
+-++.-++...++...|...++|+++|++.+++..+.|..
T Consensus 6 L~~F~~v~~~~s~t~AA~~L~isqsavS~~I~~LE~~lg~ 45 (297)
T COG0583 6 LRAFVAVAEEGSFTRAAERLGLSQSAVSRQIKRLEEELGV 45 (297)
T ss_pred HHHHHHHHHcCcHHHHHHHhCCCChHHHHHHHHHHHHhCc
Confidence 3444555557889999999999999999999999998774
Done!