Query 012200
Match_columns 468
No_of_seqs 213 out of 1678
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 00:06:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012200.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012200hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4585 Predicted transposase 100.0 4.7E-39 1E-43 322.1 14.6 309 139-466 7-324 (326)
2 PF13359 DDE_Tnp_4: DDE superf 100.0 4.6E-37 1E-41 279.0 5.5 154 247-414 1-158 (158)
3 PF04827 Plant_tran: Plant tra 100.0 2.2E-32 4.8E-37 248.1 5.8 194 216-418 2-199 (205)
4 PF13613 HTH_Tnp_4: Helix-turn 98.9 2E-09 4.2E-14 79.7 5.2 51 164-214 2-52 (53)
5 PF13612 DDE_Tnp_1_3: Transpos 98.8 2.3E-09 4.9E-14 97.0 3.9 131 241-393 4-149 (155)
6 PF01609 DDE_Tnp_1: Transposas 97.4 2.5E-06 5.3E-11 79.4 -8.3 150 243-415 5-213 (213)
7 PF13586 DDE_Tnp_1_2: Transpos 97.0 0.00065 1.4E-08 55.4 3.3 52 362-414 34-86 (88)
8 PF04545 Sigma70_r4: Sigma-70, 95.3 0.043 9.4E-07 39.5 5.1 45 164-209 4-48 (50)
9 PF04218 CENP-B_N: CENP-B N-te 95.2 0.031 6.8E-07 41.1 4.1 42 162-204 4-45 (53)
10 PF13936 HTH_38: Helix-turn-he 94.8 0.027 5.9E-07 39.7 2.7 40 164-204 4-43 (44)
11 PF02796 HTH_7: Helix-turn-hel 94.3 0.039 8.5E-07 39.1 2.6 34 170-203 10-43 (45)
12 PF13384 HTH_23: Homeodomain-l 93.1 0.058 1.3E-06 38.7 1.8 37 169-206 6-42 (50)
13 PF13518 HTH_28: Helix-turn-he 92.7 0.15 3.3E-06 36.6 3.6 37 170-207 2-38 (52)
14 PF12116 SpoIIID: Stage III sp 92.6 0.096 2.1E-06 41.5 2.5 46 169-214 7-52 (82)
15 PF08281 Sigma70_r4_2: Sigma-7 92.3 0.3 6.5E-06 35.5 4.8 43 164-207 10-52 (54)
16 PF05225 HTH_psq: helix-turn-h 92.2 0.18 3.9E-06 35.8 3.3 36 168-203 2-38 (45)
17 smart00351 PAX Paired Box doma 91.2 0.37 8.1E-06 42.0 4.9 44 163-207 16-59 (125)
18 cd00131 PAX Paired Box domain 90.3 0.48 1E-05 41.5 4.8 44 163-207 16-59 (128)
19 PF13011 LZ_Tnp_IS481: leucine 90.2 0.49 1.1E-05 38.3 4.4 46 162-207 6-51 (85)
20 PRK09413 IS2 repressor TnpA; R 89.6 0.64 1.4E-05 40.2 5.0 46 162-207 10-55 (121)
21 smart00421 HTH_LUXR helix_turn 89.5 0.83 1.8E-05 32.8 4.9 44 165-210 4-47 (58)
22 cd06171 Sigma70_r4 Sigma70, re 89.2 0.76 1.7E-05 32.3 4.5 42 165-207 11-52 (55)
23 COG3415 Transposase and inacti 89.2 0.43 9.3E-06 42.3 3.6 42 165-206 5-46 (138)
24 PF02209 VHP: Villin headpiece 89.1 0.26 5.7E-06 33.2 1.7 22 131-152 2-23 (36)
25 PF01527 HTH_Tnp_1: Transposas 89.0 0.4 8.7E-06 37.4 3.0 45 162-206 4-48 (76)
26 PRK04217 hypothetical protein; 88.2 0.97 2.1E-05 38.5 5.0 49 164-213 42-90 (110)
27 cd06571 Bac_DnaA_C C-terminal 87.7 1.4 2.9E-05 36.0 5.4 49 163-211 26-75 (90)
28 smart00153 VHP Villin headpiec 87.5 0.43 9.2E-06 32.2 1.9 21 131-151 2-22 (36)
29 PRK15320 transcriptional activ 87.5 1.2 2.5E-05 41.8 5.4 38 173-210 171-208 (251)
30 cd00569 HTH_Hin_like Helix-tur 87.5 0.92 2E-05 28.8 3.7 37 164-201 5-41 (42)
31 TIGR02531 yecD_yerC TrpR-relat 87.1 1.1 2.4E-05 36.6 4.6 31 172-202 41-71 (88)
32 PF13542 HTH_Tnp_ISL3: Helix-t 87.1 0.58 1.3E-05 33.7 2.6 32 174-205 20-51 (52)
33 TIGR03879 near_KaiC_dom probab 87.0 0.94 2E-05 35.6 3.9 41 164-204 15-55 (73)
34 PRK09639 RNA polymerase sigma 86.8 1.2 2.6E-05 40.0 5.2 47 164-212 112-158 (166)
35 PRK00118 putative DNA-binding 86.5 1.6 3.4E-05 36.9 5.3 48 163-211 16-63 (104)
36 PF13340 DUF4096: Putative tra 86.2 1.4 3E-05 34.6 4.6 44 163-207 23-66 (75)
37 PRK12529 RNA polymerase sigma 85.8 1.6 3.5E-05 40.0 5.6 48 164-212 127-174 (178)
38 cd06170 LuxR_C_like C-terminal 85.5 2 4.4E-05 30.8 4.9 33 178-210 12-44 (57)
39 PRK09047 RNA polymerase factor 85.3 1.5 3.3E-05 39.0 5.1 50 164-214 106-155 (161)
40 TIGR02985 Sig70_bacteroi1 RNA 84.9 1.8 3.9E-05 38.2 5.3 46 164-210 113-158 (161)
41 TIGR02937 sigma70-ECF RNA poly 84.3 1.8 4E-05 37.3 5.0 47 164-211 110-156 (158)
42 TIGR02392 rpoH_proteo alternat 83.6 1.9 4.1E-05 42.6 5.3 49 164-212 218-267 (270)
43 TIGR02846 spore_sigmaK RNA pol 83.4 2.1 4.5E-05 41.0 5.3 50 164-213 174-226 (227)
44 PRK07037 extracytoplasmic-func 83.2 2.2 4.7E-05 38.2 5.1 49 164-213 109-157 (163)
45 TIGR02952 Sig70_famx2 RNA poly 83.2 2.2 4.8E-05 38.2 5.2 48 163-211 121-168 (170)
46 PRK09652 RNA polymerase sigma 83.0 2.1 4.6E-05 38.6 5.0 49 164-213 128-176 (182)
47 PRK12547 RNA polymerase sigma 82.9 2.4 5.1E-05 38.2 5.3 49 164-213 112-160 (164)
48 PHA00675 hypothetical protein 82.9 1.5 3.1E-05 34.7 3.2 39 164-202 22-60 (78)
49 PRK08301 sporulation sigma fac 82.6 2.1 4.5E-05 41.1 5.0 50 164-213 178-230 (234)
50 PRK12514 RNA polymerase sigma 82.5 2.5 5.5E-05 38.5 5.3 48 164-212 129-176 (179)
51 PRK12515 RNA polymerase sigma 82.2 2.3 5E-05 39.2 5.0 48 164-212 131-178 (189)
52 smart00342 HTH_ARAC helix_turn 82.2 3.9 8.4E-05 31.5 5.6 73 132-207 3-77 (84)
53 PRK12532 RNA polymerase sigma 82.0 1.9 4E-05 40.1 4.3 50 164-214 136-185 (195)
54 PRK09638 RNA polymerase sigma 81.3 1.5 3.3E-05 39.7 3.4 48 164-212 126-173 (176)
55 PRK07408 RNA polymerase sigma 81.3 2.7 5.8E-05 41.2 5.3 49 164-213 203-251 (256)
56 PRK12512 RNA polymerase sigma 80.8 3 6.6E-05 38.1 5.3 50 164-214 131-180 (184)
57 PRK12516 RNA polymerase sigma 80.8 2.9 6.3E-05 38.8 5.1 49 164-213 116-164 (187)
58 PRK11924 RNA polymerase sigma 80.8 2.8 6.1E-05 37.7 5.0 49 164-213 125-173 (179)
59 PRK05803 sporulation sigma fac 80.8 2.8 6E-05 40.3 5.1 49 164-212 175-226 (233)
60 PRK06596 RNA polymerase factor 80.7 2.8 6.1E-05 41.8 5.3 49 164-212 230-279 (284)
61 PRK12533 RNA polymerase sigma 80.7 2.6 5.7E-05 40.2 4.9 50 164-214 134-183 (216)
62 PRK12530 RNA polymerase sigma 80.5 2.8 6.2E-05 38.8 5.0 49 164-213 134-182 (189)
63 PRK12537 RNA polymerase sigma 80.5 3.1 6.7E-05 38.2 5.2 48 164-212 133-180 (182)
64 PF00356 LacI: Bacterial regul 80.4 0.95 2.1E-05 32.2 1.3 21 183-203 1-21 (46)
65 TIGR02989 Sig-70_gvs1 RNA poly 80.3 3.1 6.7E-05 36.9 5.0 48 163-211 110-157 (159)
66 PRK12531 RNA polymerase sigma 80.2 3.1 6.8E-05 38.6 5.2 50 163-213 140-189 (194)
67 PRK05911 RNA polymerase sigma 80.1 3 6.6E-05 40.8 5.2 49 164-213 205-253 (257)
68 TIGR01321 TrpR trp operon repr 80.0 2.1 4.6E-05 35.4 3.4 38 165-202 33-76 (94)
69 PRK12524 RNA polymerase sigma 79.8 3.2 7E-05 38.6 5.1 49 164-213 136-184 (196)
70 PRK12534 RNA polymerase sigma 79.6 3.7 8.1E-05 37.6 5.5 48 164-212 137-184 (187)
71 PF13730 HTH_36: Helix-turn-he 79.6 3.2 7E-05 30.1 4.0 42 165-206 3-50 (55)
72 PRK15418 transcriptional regul 79.5 1.1 2.3E-05 45.6 1.9 68 173-245 21-88 (318)
73 PRK09641 RNA polymerase sigma 79.3 3.1 6.7E-05 38.0 4.8 48 164-212 136-183 (187)
74 PRK12511 RNA polymerase sigma 79.3 3.4 7.5E-05 38.1 5.1 48 164-212 111-158 (182)
75 PRK12523 RNA polymerase sigma 79.0 3.7 8.1E-05 37.2 5.2 49 164-213 119-167 (172)
76 PRK09645 RNA polymerase sigma 79.0 4.2 9.1E-05 36.7 5.5 50 164-214 118-167 (173)
77 PF13412 HTH_24: Winged helix- 78.8 4.1 8.9E-05 28.7 4.3 37 170-207 7-43 (48)
78 TIGR02885 spore_sigF RNA polym 78.8 3.7 8E-05 39.3 5.3 47 164-211 183-229 (231)
79 PRK09415 RNA polymerase factor 78.7 3.3 7.2E-05 37.9 4.8 49 164-213 127-175 (179)
80 PRK12540 RNA polymerase sigma 78.7 3.5 7.5E-05 38.0 4.9 50 164-214 111-160 (182)
81 TIGR03001 Sig-70_gmx1 RNA poly 78.7 2.3 5.1E-05 41.4 3.9 49 164-213 161-209 (244)
82 TIGR02999 Sig-70_X6 RNA polyme 78.5 4.1 8.8E-05 37.2 5.3 48 164-212 134-181 (183)
83 PRK12519 RNA polymerase sigma 78.5 3.1 6.7E-05 38.5 4.6 48 164-212 141-188 (194)
84 TIGR02393 RpoD_Cterm RNA polym 78.2 2.7 5.9E-05 40.5 4.2 48 164-211 176-226 (238)
85 TIGR03697 NtcA_cyano global ni 78.1 3.2 6.9E-05 38.0 4.5 45 164-208 112-170 (193)
86 PRK05572 sporulation sigma fac 77.9 3.9 8.6E-05 39.8 5.3 48 164-212 202-249 (252)
87 TIGR00721 tfx DNA-binding prot 77.6 4.1 8.9E-05 36.1 4.7 45 164-210 6-50 (137)
88 TIGR02950 SigM_subfam RNA poly 77.4 1.7 3.7E-05 38.4 2.4 47 164-211 105-151 (154)
89 TIGR02844 spore_III_D sporulat 77.2 2.6 5.7E-05 33.8 3.1 36 168-203 5-41 (80)
90 TIGR02980 SigBFG RNA polymeras 77.1 4.4 9.6E-05 38.6 5.3 47 164-211 178-224 (227)
91 PRK07500 rpoH2 RNA polymerase 77.1 4.1 8.9E-05 40.7 5.2 50 164-213 227-277 (289)
92 PRK12546 RNA polymerase sigma 77.0 4.3 9.3E-05 37.7 5.0 49 164-213 113-161 (188)
93 TIGR02984 Sig-70_plancto1 RNA 76.7 4.9 0.00011 36.7 5.3 47 164-211 140-186 (189)
94 PF01371 Trp_repressor: Trp re 76.7 4.1 8.9E-05 33.2 4.1 35 169-203 37-71 (87)
95 PRK08583 RNA polymerase sigma 76.6 4.8 0.0001 39.2 5.5 49 164-213 205-253 (257)
96 TIGR02394 rpoS_proteo RNA poly 76.6 3.8 8.2E-05 40.8 4.8 51 164-214 222-275 (285)
97 PF12802 MarR_2: MarR family; 76.5 5.4 0.00012 29.4 4.5 39 169-207 8-47 (62)
98 PRK05602 RNA polymerase sigma 76.4 4.3 9.3E-05 37.3 4.8 49 164-213 128-176 (186)
99 PRK12539 RNA polymerase sigma 76.4 4.8 0.0001 36.9 5.2 49 164-213 131-179 (184)
100 PRK03975 tfx putative transcri 76.3 5 0.00011 35.8 4.9 46 163-210 5-50 (141)
101 PRK12544 RNA polymerase sigma 76.3 3.4 7.5E-05 39.0 4.2 49 164-213 148-196 (206)
102 TIGR02983 SigE-fam_strep RNA p 76.1 4.5 9.8E-05 36.1 4.8 48 164-212 110-157 (162)
103 PF00196 GerE: Bacterial regul 76.1 2.9 6.3E-05 30.8 2.9 37 174-210 11-47 (58)
104 PRK08215 sporulation sigma fac 75.6 5 0.00011 39.2 5.3 47 164-211 209-255 (258)
105 PRK12520 RNA polymerase sigma 75.4 4.2 9.1E-05 37.5 4.5 50 164-214 131-180 (191)
106 PRK06986 fliA flagellar biosyn 75.2 5 0.00011 38.6 5.1 49 164-213 184-232 (236)
107 TIGR02835 spore_sigmaE RNA pol 75.2 5.2 0.00011 38.4 5.2 49 164-212 178-229 (234)
108 PF01022 HTH_5: Bacterial regu 75.1 5.6 0.00012 28.1 4.1 37 170-206 4-40 (47)
109 TIGR02939 RpoE_Sigma70 RNA pol 75.0 4.4 9.4E-05 37.1 4.5 49 164-213 138-186 (190)
110 PRK09643 RNA polymerase sigma 75.0 5.2 0.00011 37.1 5.0 48 164-212 134-181 (192)
111 PRK09642 RNA polymerase sigma 75.0 5.4 0.00012 35.5 5.0 49 164-213 106-154 (160)
112 PRK06030 hypothetical protein; 74.9 6.2 0.00013 34.4 5.0 47 163-209 51-97 (124)
113 PRK12525 RNA polymerase sigma 74.6 6.1 0.00013 35.7 5.3 48 164-212 118-165 (168)
114 PRK12536 RNA polymerase sigma 74.4 6 0.00013 36.2 5.3 49 164-213 129-177 (181)
115 PRK12528 RNA polymerase sigma 74.4 5.8 0.00013 35.4 5.1 46 164-210 113-158 (161)
116 TIGR02948 SigW_bacill RNA poly 74.3 5.1 0.00011 36.5 4.8 48 164-212 136-183 (187)
117 PF04967 HTH_10: HTH DNA bindi 74.2 3.7 8.1E-05 30.2 3.0 29 181-209 23-51 (53)
118 PF08279 HTH_11: HTH domain; 74.1 6.5 0.00014 28.4 4.4 31 179-209 13-43 (55)
119 TIGR02850 spore_sigG RNA polym 73.8 5.9 0.00013 38.6 5.3 46 164-210 206-251 (254)
120 PRK08295 RNA polymerase factor 73.7 5.5 0.00012 37.1 4.9 48 164-213 155-202 (208)
121 PRK06930 positive control sigm 73.6 5.7 0.00012 36.5 4.8 49 164-213 114-162 (170)
122 COG1191 FliA DNA-directed RNA 73.6 5.8 0.00013 38.8 5.1 49 164-213 196-244 (247)
123 TIGR02997 Sig70-cyanoRpoD RNA 73.2 5 0.00011 40.2 4.7 44 164-207 249-295 (298)
124 PF07374 DUF1492: Protein of u 73.2 6.1 0.00013 32.9 4.5 42 166-208 57-98 (100)
125 PF08299 Bac_DnaA_C: Bacterial 73.2 4.5 9.7E-05 31.4 3.4 41 165-205 29-70 (70)
126 PRK06811 RNA polymerase factor 73.1 6.1 0.00013 36.4 5.0 47 164-211 131-177 (189)
127 TIGR02954 Sig70_famx3 RNA poly 73.1 7.1 0.00015 35.1 5.3 48 164-212 119-166 (169)
128 TIGR02941 Sigma_B RNA polymera 73.0 6.4 0.00014 38.3 5.3 48 164-212 205-252 (255)
129 PRK07670 RNA polymerase sigma 72.8 6.8 0.00015 38.1 5.4 48 164-212 201-248 (251)
130 TIGR02943 Sig70_famx1 RNA poly 72.7 6.5 0.00014 36.4 5.1 49 164-213 131-179 (188)
131 PF13610 DDE_Tnp_IS240: DDE do 72.5 9 0.00019 33.8 5.7 44 374-418 95-138 (140)
132 PRK11753 DNA-binding transcrip 72.4 6.1 0.00013 36.7 4.9 43 164-206 138-193 (211)
133 PF01325 Fe_dep_repress: Iron 72.4 8 0.00017 29.1 4.5 40 167-206 5-47 (60)
134 TIGR02960 SigX5 RNA polymerase 72.4 5.4 0.00012 40.1 4.8 50 164-214 142-191 (324)
135 PRK11923 algU RNA polymerase s 72.3 6.2 0.00013 36.4 4.8 48 164-212 138-185 (193)
136 PF13551 HTH_29: Winged helix- 72.0 4.1 9E-05 33.8 3.3 35 174-208 4-39 (112)
137 PRK06759 RNA polymerase factor 71.8 7.1 0.00015 34.4 4.9 46 164-210 106-151 (154)
138 PRK13919 putative RNA polymera 71.0 8.2 0.00018 35.3 5.3 49 164-213 135-183 (186)
139 PF01710 HTH_Tnp_IS630: Transp 70.8 2.9 6.2E-05 36.0 2.0 29 175-203 12-40 (119)
140 PRK09649 RNA polymerase sigma 70.7 8 0.00017 35.6 5.2 47 164-211 130-176 (185)
141 TIGR02479 FliA_WhiG RNA polyme 70.4 8.5 0.00018 36.6 5.4 47 164-211 175-221 (224)
142 COG2963 Transposase and inacti 70.1 8.9 0.00019 32.5 4.9 46 162-207 5-51 (116)
143 TIGR01636 phage_rinA phage tra 70.0 10 0.00022 33.3 5.4 49 165-213 83-132 (134)
144 PRK07405 RNA polymerase sigma 69.7 7.5 0.00016 39.4 5.1 48 164-211 256-306 (317)
145 PF01047 MarR: MarR family; I 69.7 8.8 0.00019 28.0 4.3 27 180-206 16-42 (59)
146 PRK12545 RNA polymerase sigma 69.6 8.3 0.00018 36.0 5.1 49 164-213 139-187 (201)
147 PRK07122 RNA polymerase sigma 69.5 8.1 0.00018 38.0 5.2 47 164-211 215-261 (264)
148 cd00092 HTH_CRP helix_turn_hel 69.1 5.9 0.00013 29.6 3.3 27 181-207 25-51 (67)
149 PRK09648 RNA polymerase sigma 68.7 9.7 0.00021 35.0 5.3 47 164-211 139-185 (189)
150 PF09339 HTH_IclR: IclR helix- 68.3 5.4 0.00012 28.8 2.8 36 172-207 6-44 (52)
151 PF13751 DDE_Tnp_1_6: Transpos 68.2 2.9 6.3E-05 35.9 1.6 49 368-417 73-123 (125)
152 COG1595 RpoE DNA-directed RNA 68.2 8.5 0.00018 35.2 4.8 49 164-213 127-175 (182)
153 PRK09637 RNA polymerase sigma 67.7 10 0.00022 34.9 5.1 49 164-213 106-154 (181)
154 PF00126 HTH_1: Bacterial regu 67.1 9.5 0.00021 28.3 4.0 41 171-212 4-44 (60)
155 PF07638 Sigma70_ECF: ECF sigm 66.9 11 0.00024 34.8 5.3 47 165-212 136-182 (185)
156 PRK12526 RNA polymerase sigma 66.5 11 0.00023 35.5 5.1 49 164-213 153-201 (206)
157 PHA00542 putative Cro-like pro 66.5 5.3 0.00011 32.0 2.6 29 174-202 24-52 (82)
158 PF13309 HTH_22: HTH domain 66.4 7 0.00015 29.8 3.1 40 163-202 19-63 (64)
159 PRK09391 fixK transcriptional 65.5 13 0.00027 35.6 5.5 44 164-207 152-205 (230)
160 PRK14086 dnaA chromosomal repl 65.3 18 0.00039 40.0 7.2 49 163-211 551-599 (617)
161 PRK09646 RNA polymerase sigma 65.2 12 0.00027 34.5 5.3 49 164-213 142-190 (194)
162 PF01381 HTH_3: Helix-turn-hel 65.1 4 8.7E-05 29.4 1.5 27 177-203 5-31 (55)
163 PRK01381 Trp operon repressor; 65.1 8.9 0.00019 32.0 3.7 25 178-202 52-76 (99)
164 PRK09644 RNA polymerase sigma 65.0 10 0.00023 33.9 4.6 49 164-213 108-156 (165)
165 smart00346 HTH_ICLR helix_turn 64.6 11 0.00024 30.1 4.2 38 170-207 6-46 (91)
166 PRK12527 RNA polymerase sigma 64.5 12 0.00027 33.2 4.9 49 164-213 105-153 (159)
167 COG2390 DeoR Transcriptional r 64.5 4.1 8.9E-05 41.4 2.0 68 173-245 18-85 (321)
168 smart00550 Zalpha Z-DNA-bindin 64.3 13 0.00027 28.6 4.3 40 166-205 6-46 (68)
169 PF01710 HTH_Tnp_IS630: Transp 64.1 23 0.00049 30.4 6.3 72 132-205 20-95 (119)
170 TIGR02959 SigZ RNA polymerase 63.9 14 0.0003 33.5 5.2 49 164-213 100-148 (170)
171 COG2739 Uncharacterized protei 63.8 13 0.00028 31.0 4.4 41 169-210 22-62 (105)
172 PRK11922 RNA polymerase sigma 63.7 7.4 0.00016 37.3 3.6 49 164-213 149-197 (231)
173 PRK12538 RNA polymerase sigma 63.7 10 0.00022 36.5 4.5 49 164-213 171-219 (233)
174 PRK10402 DNA-binding transcrip 63.7 15 0.00034 34.8 5.8 64 164-229 148-216 (226)
175 PRK12542 RNA polymerase sigma 63.6 14 0.00029 33.9 5.2 49 164-213 122-170 (185)
176 PRK06704 RNA polymerase factor 63.5 11 0.00024 36.4 4.6 49 164-213 116-164 (228)
177 TIGR02947 SigH_actino RNA poly 63.5 7.2 0.00016 36.0 3.3 49 164-213 131-179 (193)
178 PRK12427 flagellar biosynthesi 63.4 12 0.00026 36.0 4.9 46 164-210 183-228 (231)
179 PRK06288 RNA polymerase sigma 63.0 12 0.00026 36.7 5.0 48 164-212 212-259 (268)
180 PRK12543 RNA polymerase sigma 62.9 13 0.00028 33.9 4.9 49 164-213 117-165 (179)
181 PRK12541 RNA polymerase sigma 62.6 13 0.00027 33.2 4.7 46 164-210 112-157 (161)
182 PF13560 HTH_31: Helix-turn-he 62.5 6.2 0.00013 29.6 2.2 29 174-202 7-35 (64)
183 TIGR01610 phage_O_Nterm phage 62.4 13 0.00028 30.6 4.3 29 178-206 44-72 (95)
184 PF04297 UPF0122: Putative hel 62.4 15 0.00033 30.8 4.6 41 170-210 22-62 (101)
185 PRK12522 RNA polymerase sigma 62.2 11 0.00024 34.1 4.2 48 164-212 119-166 (173)
186 PRK12535 RNA polymerase sigma 62.0 15 0.00033 34.2 5.2 50 164-214 133-182 (196)
187 PRK07406 RNA polymerase sigma 61.9 13 0.00028 38.7 5.1 47 164-210 311-360 (373)
188 PRK05657 RNA polymerase sigma 61.9 14 0.0003 37.7 5.2 50 164-213 262-314 (325)
189 PF00325 Crp: Bacterial regula 61.8 8.1 0.00018 25.3 2.3 25 182-206 3-27 (32)
190 PRK00149 dnaA chromosomal repl 61.3 25 0.00054 37.4 7.3 48 163-210 384-432 (450)
191 PF13463 HTH_27: Winged helix 61.2 11 0.00024 28.2 3.4 35 174-208 8-45 (68)
192 PRK12513 RNA polymerase sigma 61.0 8.4 0.00018 35.6 3.3 49 164-213 139-187 (194)
193 PRK09210 RNA polymerase sigma 61.0 13 0.00028 38.5 4.9 47 164-210 305-354 (367)
194 TIGR02859 spore_sigH RNA polym 60.7 13 0.00028 34.2 4.5 44 166-211 152-195 (198)
195 PRK12518 RNA polymerase sigma 60.7 7.5 0.00016 35.1 2.8 50 164-214 120-169 (175)
196 PRK03573 transcriptional regul 60.3 13 0.00029 32.6 4.3 43 164-206 28-71 (144)
197 PRK12517 RNA polymerase sigma 60.3 16 0.00034 33.8 5.0 49 164-213 128-176 (188)
198 PRK11161 fumarate/nitrate redu 59.8 16 0.00035 34.6 5.1 43 164-206 153-209 (235)
199 PRK15201 fimbriae regulatory p 59.4 11 0.00023 35.0 3.5 45 163-209 132-176 (198)
200 PRK07598 RNA polymerase sigma 59.2 15 0.00032 38.8 5.0 47 164-210 350-399 (415)
201 PRK15411 rcsA colanic acid cap 58.9 10 0.00023 35.7 3.6 45 164-210 137-181 (207)
202 PF03333 PapB: Adhesin biosynt 58.7 36 0.00079 28.0 6.1 56 142-206 23-78 (91)
203 PRK05949 RNA polymerase sigma 58.6 16 0.00034 37.3 5.0 48 164-211 266-316 (327)
204 PF00872 Transposase_mut: Tran 58.6 12 0.00025 39.0 4.2 63 174-256 107-176 (381)
205 cd07377 WHTH_GntR Winged helix 58.4 20 0.00043 26.3 4.4 24 183-206 27-50 (66)
206 PF13545 HTH_Crp_2: Crp-like h 58.4 13 0.00029 28.5 3.5 28 181-208 28-55 (76)
207 PF02001 DUF134: Protein of un 57.7 12 0.00025 31.7 3.2 48 164-212 41-88 (106)
208 PF09862 DUF2089: Protein of u 57.3 19 0.00042 30.8 4.5 46 164-210 33-78 (113)
209 TIGR02337 HpaR homoprotocatech 56.9 36 0.00077 28.7 6.3 42 164-206 25-67 (118)
210 PF00165 HTH_AraC: Bacterial r 56.8 8.5 0.00018 26.3 1.9 29 178-206 5-33 (42)
211 smart00345 HTH_GNTR helix_turn 56.6 10 0.00022 27.4 2.4 24 183-206 22-45 (60)
212 PRK09392 ftrB transcriptional 56.4 21 0.00046 33.9 5.3 63 164-228 146-218 (236)
213 smart00418 HTH_ARSR helix_turn 56.3 14 0.0003 26.7 3.2 28 179-206 8-35 (66)
214 PRK09640 RNA polymerase sigma 56.0 8.4 0.00018 35.4 2.4 48 164-212 134-181 (188)
215 TIGR03541 reg_near_HchA LuxR f 55.9 31 0.00068 33.1 6.4 46 163-210 170-215 (232)
216 smart00419 HTH_CRP helix_turn_ 55.8 11 0.00025 25.9 2.5 29 179-207 6-34 (48)
217 PRK09651 RNA polymerase sigma 55.2 18 0.00039 32.7 4.4 46 164-210 119-164 (172)
218 PRK14088 dnaA chromosomal repl 55.2 20 0.00043 38.1 5.2 47 163-209 369-415 (440)
219 PRK09647 RNA polymerase sigma 55.0 21 0.00046 33.5 5.0 49 164-213 138-186 (203)
220 cd00090 HTH_ARSR Arsenical Res 54.3 21 0.00046 26.5 4.1 27 179-205 18-44 (78)
221 TIGR02957 SigX4 RNA polymerase 54.0 22 0.00048 35.1 5.1 48 164-212 108-155 (281)
222 PRK07921 RNA polymerase sigma 53.1 22 0.00048 36.1 5.0 48 164-211 262-312 (324)
223 PF04703 FaeA: FaeA-like prote 52.0 18 0.00039 27.5 3.2 36 169-204 3-38 (62)
224 PRK05901 RNA polymerase sigma 51.9 22 0.00049 38.4 5.0 48 164-211 447-497 (509)
225 PRK13870 transcriptional regul 51.6 15 0.00032 35.5 3.4 46 163-210 172-217 (234)
226 PF06056 Terminase_5: Putative 51.3 23 0.00051 26.4 3.6 31 171-203 5-35 (58)
227 COG2522 Predicted transcriptio 51.2 14 0.00031 31.9 2.8 24 180-203 21-44 (119)
228 PF12840 HTH_20: Helix-turn-he 51.0 26 0.00056 26.0 3.9 30 178-207 21-50 (61)
229 PRK13719 conjugal transfer tra 50.9 17 0.00037 34.7 3.5 44 164-209 143-186 (217)
230 TIGR03830 CxxCG_CxxCG_HTH puta 50.8 26 0.00056 29.9 4.5 58 142-202 42-99 (127)
231 PF01978 TrmB: Sugar-specific 50.0 20 0.00044 27.1 3.3 39 168-207 10-48 (68)
232 TIGR03209 P21_Cbot clostridium 50.0 13 0.00029 32.3 2.5 35 164-199 107-141 (142)
233 smart00352 POU Found in Pit-Oc 49.4 12 0.00026 29.6 1.8 30 174-203 17-52 (75)
234 PRK13413 mpi multiple promoter 49.0 14 0.0003 34.6 2.6 29 175-203 166-194 (200)
235 PHA02591 hypothetical protein; 48.9 19 0.00042 28.6 2.9 36 169-204 47-82 (83)
236 PRK14087 dnaA chromosomal repl 48.6 35 0.00076 36.4 5.9 48 163-210 383-431 (450)
237 PRK10840 transcriptional regul 48.2 18 0.0004 33.6 3.4 44 164-209 150-193 (216)
238 PRK09636 RNA polymerase sigma 47.4 31 0.00068 34.2 5.1 48 164-212 115-162 (293)
239 smart00420 HTH_DEOR helix_turn 47.4 38 0.00083 23.4 4.2 27 180-206 13-39 (53)
240 PF05043 Mga: Mga helix-turn-h 47.4 30 0.00065 27.5 4.0 33 178-210 27-59 (87)
241 PRK09191 two-component respons 46.7 34 0.00074 32.6 5.1 53 164-217 88-140 (261)
242 PRK09483 response regulator; P 46.3 20 0.00043 32.8 3.3 44 164-209 148-191 (217)
243 TIGR03070 couple_hipB transcri 46.2 17 0.00037 25.9 2.2 26 177-202 11-36 (58)
244 PRK10188 DNA-binding transcrip 46.1 60 0.0013 31.4 6.6 46 163-210 178-223 (240)
245 COG2771 CsgD DNA-binding HTH d 46.0 29 0.00062 25.4 3.5 36 174-209 12-47 (65)
246 PF13744 HTH_37: Helix-turn-he 45.2 12 0.00026 29.6 1.4 35 169-203 17-53 (80)
247 PRK13918 CRP/FNR family transc 44.9 28 0.0006 32.0 4.0 62 165-228 119-195 (202)
248 PHA01976 helix-turn-helix prot 44.9 19 0.00042 27.0 2.4 27 176-202 10-36 (67)
249 PRK11475 DNA-binding transcrip 44.9 22 0.00048 33.6 3.4 44 164-209 134-177 (207)
250 PHA00738 putative HTH transcri 44.7 20 0.00043 30.4 2.6 27 182-208 27-53 (108)
251 smart00347 HTH_MARR helix_turn 44.6 50 0.0011 26.2 5.0 28 180-207 23-50 (101)
252 PRK08241 RNA polymerase factor 44.6 29 0.00064 35.1 4.4 47 164-211 153-199 (339)
253 PRK11512 DNA-binding transcrip 44.3 44 0.00095 29.3 5.0 42 164-206 37-79 (144)
254 TIGR02405 trehalos_R_Ecol treh 44.0 11 0.00025 37.3 1.3 21 183-203 3-23 (311)
255 COG2197 CitB Response regulato 43.7 24 0.00052 33.4 3.4 44 164-209 148-191 (211)
256 smart00354 HTH_LACI helix_turn 43.6 13 0.00028 28.6 1.3 20 183-202 2-21 (70)
257 PRK09492 treR trehalose repres 43.4 13 0.00028 36.7 1.6 23 182-204 5-27 (315)
258 PRK12682 transcriptional regul 43.3 25 0.00054 34.8 3.6 46 169-214 4-49 (309)
259 PRK12683 transcriptional regul 43.3 27 0.00058 34.7 3.9 46 169-214 4-49 (309)
260 PRK10870 transcriptional repre 42.9 41 0.00089 30.9 4.7 43 164-206 52-96 (176)
261 PRK10100 DNA-binding transcrip 41.4 29 0.00062 33.1 3.5 45 164-210 155-199 (216)
262 PF08765 Mor: Mor transcriptio 41.2 37 0.00081 28.5 3.8 31 180-210 71-101 (108)
263 PF12964 DUF3853: Protein of u 40.7 19 0.00041 29.8 1.8 61 141-210 12-76 (96)
264 cd01392 HTH_LacI Helix-turn-he 40.6 12 0.00026 26.5 0.6 18 186-203 2-19 (52)
265 COG3413 Predicted DNA binding 40.6 27 0.00058 33.1 3.2 32 181-212 178-209 (215)
266 PRK12422 chromosomal replicati 40.4 46 0.00099 35.5 5.2 48 163-210 379-426 (445)
267 cd04762 HTH_MerR-trunc Helix-T 40.1 19 0.00041 24.6 1.6 22 183-204 2-23 (49)
268 PRK00215 LexA repressor; Valid 40.1 42 0.00092 31.3 4.5 27 181-207 23-50 (205)
269 smart00344 HTH_ASNC helix_turn 40.0 54 0.0012 27.0 4.7 39 168-207 5-43 (108)
270 PF05344 DUF746: Domain of Unk 39.7 47 0.001 25.5 3.7 41 171-211 3-43 (65)
271 PRK10014 DNA-binding transcrip 39.4 15 0.00032 36.8 1.3 23 182-204 7-29 (342)
272 PRK09526 lacI lac repressor; R 39.1 15 0.00033 36.7 1.3 22 182-203 6-27 (342)
273 PF00392 GntR: Bacterial regul 38.4 27 0.00058 26.1 2.3 22 184-205 27-48 (64)
274 PF00292 PAX: 'Paired box' dom 38.3 60 0.0013 28.4 4.6 45 162-208 15-60 (125)
275 PRK14987 gluconate operon tran 37.8 15 0.00032 36.7 1.0 22 182-203 6-27 (331)
276 TIGR03020 EpsA transcriptional 37.7 53 0.0011 32.1 4.8 44 164-209 190-233 (247)
277 PF08220 HTH_DeoR: DeoR-like h 37.5 58 0.0013 23.9 3.9 25 181-205 14-38 (57)
278 PF05263 DUF722: Protein of un 37.4 55 0.0012 28.8 4.3 46 165-210 82-128 (130)
279 PRK11233 nitrogen assimilation 37.3 38 0.00082 33.5 3.9 43 170-213 5-47 (305)
280 COG5421 Transposase [DNA repli 37.0 38 0.00082 36.1 3.8 59 273-345 152-210 (480)
281 TIGR01764 excise DNA binding d 36.8 23 0.00051 24.2 1.6 21 183-203 3-23 (49)
282 PF13443 HTH_26: Cro/C1-type H 36.7 19 0.0004 26.7 1.2 25 179-203 8-32 (63)
283 TIGR02404 trehalos_R_Bsub treh 36.7 50 0.0011 31.4 4.4 21 186-206 29-49 (233)
284 PRK05658 RNA polymerase sigma 36.4 50 0.0011 36.7 5.0 47 164-210 556-605 (619)
285 PRK11303 DNA-binding transcrip 36.4 19 0.00041 35.8 1.5 22 183-204 2-23 (328)
286 PF10668 Phage_terminase: Phag 36.1 31 0.00067 26.1 2.2 27 176-202 15-43 (60)
287 TIGR00122 birA_repr_reg BirA b 36.0 54 0.0012 24.8 3.7 29 178-206 9-38 (69)
288 PRK10401 DNA-binding transcrip 36.0 18 0.00039 36.3 1.3 21 183-203 3-23 (346)
289 PRK09635 sigI RNA polymerase s 35.4 54 0.0012 32.7 4.6 47 164-211 118-164 (290)
290 PRK10703 DNA-binding transcrip 34.9 20 0.00043 35.9 1.4 22 183-204 3-24 (341)
291 COG2186 FadR Transcriptional r 34.8 52 0.0011 31.9 4.2 45 142-202 11-55 (241)
292 PF09607 BrkDBD: Brinker DNA-b 34.8 53 0.0012 24.6 3.2 40 163-202 4-46 (58)
293 smart00760 Bac_DnaA_C Bacteria 34.7 50 0.0011 24.5 3.2 30 163-192 27-56 (60)
294 TIGR01889 Staph_reg_Sar staphy 34.7 80 0.0017 26.3 4.9 42 165-206 23-68 (109)
295 PF10654 DUF2481: Protein of u 34.7 22 0.00048 30.3 1.4 32 177-208 75-107 (126)
296 PRK10339 DNA-binding transcrip 34.6 18 0.0004 36.0 1.1 22 183-204 3-24 (327)
297 PRK10651 transcriptional regul 34.5 40 0.00086 30.4 3.3 44 164-209 155-198 (216)
298 PF13551 HTH_29: Winged helix- 34.4 2.1E+02 0.0045 23.2 7.4 73 132-204 14-110 (112)
299 COG0593 DnaA ATPase involved i 34.2 72 0.0016 33.6 5.4 50 162-211 346-395 (408)
300 PRK12679 cbl transcriptional r 33.7 52 0.0011 32.8 4.2 46 169-214 4-49 (316)
301 PRK10360 DNA-binding transcrip 33.6 45 0.00099 29.8 3.5 44 164-209 137-180 (196)
302 PRK10403 transcriptional regul 33.5 43 0.00094 30.1 3.3 44 164-209 153-196 (215)
303 PRK12469 RNA polymerase factor 33.4 30 0.00065 37.2 2.5 32 181-223 369-400 (481)
304 PF06530 Phage_antitermQ: Phag 32.5 68 0.0015 27.8 4.2 41 170-210 67-107 (125)
305 PF05269 Phage_CII: Bacterioph 32.3 52 0.0011 27.1 3.1 28 182-209 24-51 (91)
306 PF14493 HTH_40: Helix-turn-he 32.0 60 0.0013 26.2 3.6 37 172-208 4-40 (91)
307 PRK15215 fimbriae biosynthesis 31.4 2E+02 0.0042 24.1 6.3 55 142-206 31-86 (100)
308 COG1508 RpoN DNA-directed RNA 31.2 30 0.00064 36.7 1.9 31 182-223 331-361 (444)
309 PRK11151 DNA-binding transcrip 31.0 60 0.0013 31.9 4.1 43 170-213 5-47 (305)
310 PRK10141 DNA-binding transcrip 31.0 62 0.0013 27.8 3.6 40 169-208 17-57 (117)
311 PRK12684 transcriptional regul 31.0 54 0.0012 32.6 3.8 47 169-215 4-50 (313)
312 PRK05932 RNA polymerase factor 30.5 35 0.00077 36.4 2.5 32 181-223 343-374 (455)
313 TIGR00637 ModE_repress ModE mo 30.3 57 0.0012 27.0 3.2 40 174-213 9-48 (99)
314 PRK15369 two component system 30.3 56 0.0012 29.0 3.5 45 164-210 149-193 (211)
315 PRK09958 DNA-binding transcrip 30.0 55 0.0012 29.5 3.4 44 164-209 143-186 (204)
316 PF04552 Sigma54_DBD: Sigma-54 29.9 17 0.00038 33.0 0.0 30 181-221 49-78 (160)
317 PRK10163 DNA-binding transcrip 29.8 78 0.0017 31.1 4.6 45 164-208 20-67 (271)
318 TIGR02417 fruct_sucro_rep D-fr 29.6 27 0.00058 34.7 1.3 22 183-204 1-22 (327)
319 PF12728 HTH_17: Helix-turn-he 29.4 35 0.00076 24.1 1.6 21 183-203 3-23 (51)
320 PRK10423 transcriptional repre 29.4 25 0.00053 34.9 1.0 19 185-203 2-20 (327)
321 PRK10072 putative transcriptio 29.3 37 0.00081 28.1 1.9 27 177-203 42-68 (96)
322 COG1342 Predicted DNA-binding 29.3 55 0.0012 27.1 2.8 46 165-211 34-79 (99)
323 TIGR02702 SufR_cyano iron-sulf 29.3 80 0.0017 29.6 4.4 38 168-206 3-40 (203)
324 PRK09834 DNA-binding transcrip 29.2 67 0.0015 31.4 4.0 43 165-207 7-52 (263)
325 PF13404 HTH_AsnC-type: AsnC-t 29.2 1.2E+02 0.0025 21.0 4.1 25 180-204 16-40 (42)
326 PRK15340 transcriptional regul 28.7 1.8E+02 0.004 27.8 6.7 30 179-208 123-152 (216)
327 PRK14999 histidine utilization 28.7 83 0.0018 30.1 4.5 21 185-205 40-60 (241)
328 TIGR02607 antidote_HigA addict 28.6 40 0.00087 26.0 1.9 26 177-202 14-39 (78)
329 PF11198 DUF2857: Protein of u 28.4 2E+02 0.0044 26.6 6.8 75 132-206 89-178 (180)
330 TIGR02325 C_P_lyase_phnF phosp 28.3 87 0.0019 29.7 4.6 22 185-206 36-57 (238)
331 TIGR01481 ccpA catabolite cont 28.2 29 0.00063 34.4 1.3 21 183-203 3-23 (329)
332 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 28.0 86 0.0019 22.8 3.3 39 164-203 4-42 (50)
333 PRK09764 DNA-binding transcrip 28.0 87 0.0019 30.0 4.5 21 185-205 33-53 (240)
334 PRK11050 manganese transport r 27.8 84 0.0018 28.1 4.1 28 180-207 50-77 (152)
335 smart00529 HTH_DTXR Helix-turn 27.8 53 0.0012 26.4 2.6 24 184-207 2-25 (96)
336 TIGR02431 pcaR_pcaU beta-ketoa 27.8 78 0.0017 30.5 4.2 44 165-208 5-51 (248)
337 TIGR00180 parB_part ParB-like 27.8 82 0.0018 29.1 4.2 41 163-203 101-142 (187)
338 cd00131 PAX Paired Box domain 27.6 2.8E+02 0.006 24.0 7.2 75 129-203 32-125 (128)
339 PRK10727 DNA-binding transcrip 27.6 30 0.00065 34.7 1.2 21 183-203 3-23 (343)
340 PRK04140 hypothetical protein; 27.5 70 0.0015 32.5 3.8 72 130-202 83-160 (317)
341 TIGR03418 chol_sulf_TF putativ 27.2 72 0.0016 31.0 3.9 43 170-213 5-47 (291)
342 PRK09726 antitoxin HipB; Provi 27.2 40 0.00087 27.1 1.7 27 177-203 21-47 (88)
343 PRK13348 chromosome replicatio 26.6 81 0.0018 30.7 4.1 38 177-214 12-49 (294)
344 COG1609 PurR Transcriptional r 26.4 34 0.00073 34.8 1.4 21 183-203 2-22 (333)
345 COG4565 CitB Response regulato 26.4 1.2E+02 0.0025 29.1 4.8 65 142-206 130-198 (224)
346 PRK12681 cysB transcriptional 26.2 71 0.0015 32.0 3.7 46 169-214 4-49 (324)
347 PRK11402 DNA-binding transcrip 26.2 98 0.0021 29.6 4.5 44 147-206 11-58 (241)
348 PRK10094 DNA-binding transcrip 26.1 69 0.0015 31.8 3.5 43 170-213 6-48 (308)
349 TIGR02395 rpoN_sigma RNA polym 26.0 36 0.00077 36.1 1.5 31 181-222 318-348 (429)
350 PRK09906 DNA-binding transcrip 25.9 72 0.0016 31.1 3.6 42 173-214 7-48 (296)
351 PRK10219 DNA-binding transcrip 25.9 1.1E+02 0.0024 25.1 4.3 28 179-206 19-46 (107)
352 PF08280 HTH_Mga: M protein tr 25.3 1.2E+02 0.0026 22.3 3.9 39 170-209 9-47 (59)
353 PRK09791 putative DNA-binding 25.2 76 0.0016 31.1 3.6 43 170-213 9-51 (302)
354 COG1846 MarR Transcriptional r 25.2 1E+02 0.0022 25.3 3.9 22 185-206 40-61 (126)
355 PRK11013 DNA-binding transcrip 25.2 82 0.0018 31.1 3.9 43 170-213 8-50 (309)
356 PRK04984 fatty acid metabolism 24.6 99 0.0021 29.4 4.2 20 185-204 35-54 (239)
357 COG0664 Crp cAMP-binding prote 24.5 1.3E+02 0.0028 27.1 4.9 66 140-206 99-196 (214)
358 COG2188 PhnF Transcriptional r 24.3 1.1E+02 0.0025 29.3 4.5 46 146-207 8-57 (236)
359 PF08535 KorB: KorB domain; I 24.1 45 0.00098 27.1 1.5 23 180-202 2-24 (93)
360 PRK11569 transcriptional repre 23.9 1.1E+02 0.0024 30.1 4.5 44 164-207 23-69 (274)
361 TIGR03298 argP transcriptional 23.6 95 0.0021 30.2 4.0 43 171-214 6-48 (292)
362 PRK12680 transcriptional regul 23.5 87 0.0019 31.5 3.8 44 171-214 6-49 (327)
363 PRK08558 adenine phosphoribosy 23.3 80 0.0017 30.6 3.3 39 165-203 7-45 (238)
364 PF00440 TetR_N: Bacterial reg 23.2 46 0.00099 23.2 1.2 26 180-205 15-40 (47)
365 PRK13777 transcriptional regul 23.2 1.5E+02 0.0033 27.5 5.0 41 164-205 42-83 (185)
366 PRK09706 transcriptional repre 23.1 62 0.0014 28.1 2.3 27 176-202 13-39 (135)
367 PRK15090 DNA-binding transcrip 23.0 1.2E+02 0.0027 29.3 4.6 44 164-207 9-54 (257)
368 COG1414 IclR Transcriptional r 22.7 1.2E+02 0.0027 29.3 4.5 38 171-208 6-46 (246)
369 PRK11242 DNA-binding transcrip 22.4 95 0.0021 30.1 3.7 37 177-213 11-47 (296)
370 COG3355 Predicted transcriptio 22.3 1.2E+02 0.0027 26.4 3.9 67 140-228 23-97 (126)
371 TIGR02424 TF_pcaQ pca operon t 22.3 90 0.002 30.5 3.5 42 171-213 8-49 (300)
372 COG2512 Predicted membrane-ass 22.2 1.3E+02 0.0029 29.5 4.6 44 163-206 191-235 (258)
373 PF01418 HTH_6: Helix-turn-hel 22.2 65 0.0014 25.2 2.0 24 181-204 34-57 (77)
374 COG4062 MtrB Tetrahydromethano 22.2 43 0.00093 27.8 0.9 15 14-28 49-63 (108)
375 PF05930 Phage_AlpA: Prophage 22.2 64 0.0014 23.1 1.8 21 183-203 5-25 (51)
376 KOG4425 Uncharacterized conser 22.1 56 0.0012 34.7 2.0 11 20-30 664-674 (900)
377 TIGR02612 mob_myst_A mobile my 21.9 59 0.0013 29.3 1.9 38 164-203 23-60 (150)
378 TIGR01637 phage_arpU phage tra 21.8 2E+02 0.0043 24.8 5.2 50 164-213 79-129 (132)
379 PRK09935 transcriptional regul 21.8 93 0.002 27.9 3.3 44 164-209 149-192 (210)
380 COG1476 Predicted transcriptio 21.8 65 0.0014 25.0 1.8 26 176-201 9-34 (68)
381 TIGR01884 cas_HTH CRISPR locus 21.6 1.6E+02 0.0035 27.5 4.9 33 174-206 148-182 (203)
382 TIGR02944 suf_reg_Xantho FeS a 21.6 1.3E+02 0.0028 25.8 3.9 26 182-207 26-51 (130)
383 PRK15421 DNA-binding transcrip 21.4 98 0.0021 30.9 3.6 44 169-213 5-48 (317)
384 TIGR00498 lexA SOS regulatory 21.2 1.4E+02 0.003 27.7 4.3 38 168-205 8-50 (199)
385 PF01726 LexA_DNA_bind: LexA D 21.2 1.8E+02 0.004 22.1 4.2 24 181-204 25-49 (65)
386 PRK09986 DNA-binding transcrip 21.0 1.2E+02 0.0025 29.5 4.0 43 170-213 11-53 (294)
387 COG3293 Transposase and inacti 20.8 79 0.0017 26.9 2.4 55 338-393 40-99 (124)
388 CHL00180 rbcR LysR transcripti 20.8 1.2E+02 0.0026 29.8 4.1 41 173-213 11-51 (305)
389 PRK10046 dpiA two-component re 20.8 88 0.0019 29.3 3.0 31 174-204 167-200 (225)
390 PF01526 DDE_Tnp_Tn3: Tn3 tran 20.7 4.3E+02 0.0092 27.7 8.2 83 163-258 25-113 (388)
391 PRK10216 DNA-binding transcrip 20.7 1.1E+02 0.0023 30.5 3.7 36 178-213 19-54 (319)
392 smart00530 HTH_XRE Helix-turn- 20.6 84 0.0018 20.9 2.2 25 178-202 7-31 (56)
393 PRK09508 leuO leucine transcri 20.4 97 0.0021 30.7 3.3 43 171-213 26-68 (314)
394 PF12844 HTH_19: Helix-turn-he 20.4 61 0.0013 23.9 1.4 26 177-202 8-33 (64)
395 PF07453 NUMOD1: NUMOD1 domain 20.4 55 0.0012 21.6 1.0 21 181-201 16-36 (37)
396 COG5606 Uncharacterized conser 20.3 63 0.0014 26.3 1.5 60 143-203 2-63 (91)
397 PRK11511 DNA-binding transcrip 20.3 1.6E+02 0.0035 25.3 4.2 30 178-207 22-51 (127)
398 PRK10837 putative DNA-binding 20.0 1.1E+02 0.0024 29.5 3.6 40 174-213 10-49 (290)
399 PRK11074 putative DNA-binding 20.0 1.1E+02 0.0024 30.0 3.6 39 175-213 10-48 (300)
No 1
>KOG4585 consensus Predicted transposase [Replication, recombination and repair]
Probab=100.00 E-value=4.7e-39 Score=322.11 Aligned_cols=309 Identities=31% Similarity=0.437 Sum_probs=250.7
Q ss_pred hcCCCHHHHHHHHHHhccccccCC-----C-CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 139 LYGLSYPVFTTVVEKLKPYIAASN-----L-SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 139 ~fRms~~~F~~L~~~L~p~l~~~~-----~-~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.|++++.+|..++........... . .++...++++.+++++++.+.+.++..||...+|+ ++......
T Consensus 7 ~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~i~~~fg~~~~~~------~~~~~~~~ 80 (326)
T KOG4585|consen 7 EFRKSYTTFDKICSLVQSLNVVKNSGFMLSSLLPADTLVAVALWRLKTGESLRTVEKKFGLGQSTC------KFLEEKED 80 (326)
T ss_pred HHHHHHHHHHHHhhhhhhhhhhcccchhhhccccHHhhhhhhhccccccchHHHHHHHcCCcchhh------hHHHhhhc
Confidence 578899999999988665322111 1 12288999999999999999999999999999998 22333345
Q ss_pred cCCccccCCCchhhhcccccccccccCCCCCccccceeeEEeccCCcccccccccceeeecCceeeEeeeeccccceeee
Q 012200 213 LYPEFIKIPISRRRLIETTQGFEELTSLPNICGAIDGSHIKIGNGKLKHVSLNQNQYRCKYGYNSVLLQVVADHRKIFWD 292 (468)
Q Consensus 213 L~~~~I~~P~~~~~~~~i~~~F~~~~~fP~~vGaIDgT~I~i~~P~~~~~~~~~~~Y~~~k~~~Si~~q~v~D~~g~f~~ 292 (468)
+++.++.|| ....+..+...|+. +|+|+|+||+|||++..|+ .....|.|+ .++.|+|+|||.+++|++
T Consensus 81 ~~~~~~~~p-~~~~~~~i~~~~~~---~~~~~g~~d~~hi~~~~~~-----~~~~~~~n~--~~~~Nvlav~n~d~~f~~ 149 (326)
T KOG4585|consen 81 LAPHFLKWP-SRRILYEIRERFES---LPNCVGAIDTTHIPIRVPP-----KSGSVYFNK--EQSKNLLAVCNFDMRFIY 149 (326)
T ss_pred ccchhhcCc-hhhhhhhhcccccc---ccchhccccccccceecCc-----ccccccccc--ccchhhhheecCCceEEE
Confidence 789999999 56677777777775 9999999999999999998 788888888 788999999999999999
Q ss_pred eccCCCCCCCCccccchhhhhhhhccCCCCCccccccCCccccceeecccCCCCcCCcccCCCCCCCCCCccccchhhhh
Q 012200 293 VCVKASGGADDSAHFRDSLLYNRLISGDIVWDKAINVRGHHVRPYIVGDWCYPLLSFLMTPFSPNGAGTPAQNLFDGMLM 372 (468)
Q Consensus 293 v~~g~pGs~hD~~i~~~S~l~~~l~~~~l~~~~~~~~~G~~~~~~llgD~gYpl~~~lltP~~~~~~lt~~e~~FN~~ls 372 (468)
|++|+||+.||+.|++.+.+......+.-. ...+...|.+.+.|++|+.+||+.+++|+|+.++. .+..++.||++|+
T Consensus 150 v~vg~~Gs~~D~kvl~~~~~~~~~~~~~~~-k~yl~d~~~~~~~~~~g~~~~~~~~~~~~~~~~~~-~~~~~elFN~rh~ 227 (326)
T KOG4585|consen 150 VDVGWPGSAHDTKVLQDSLLYKRNFPHPPL-KYYLVDSGYPLRPGLLGPIGFPLYSLLMFPYGGPQ-PTNSQELFNKRHS 227 (326)
T ss_pred EEccCCCCccHHHHHHhhcccccccccCCc-cccccccCcccccccccccccccchhhhcccCCCC-CCchHHHHhhhhh
Confidence 999999999999999999988776665432 12223356567889999999999999999998875 4788899999999
Q ss_pred cccchHHHHHHHHhhhhhhccc-ccCCCCcHHHHHHHHHHHhhhccccCCC--CCCCCCCCCCCCCCcccccccccccch
Q 012200 373 KGRNVVVEAIGLLKARWKILKD-LNVGINHAPQTIVACCVLHNLCQIAREP--EPEIWKEPDENGTPARVLESEKQFYYF 449 (468)
Q Consensus 373 ~~R~~VE~afG~LK~RfriL~~-l~~~~~~~~~iI~AccvLHN~~~~~~~~--~~~~~~~~~~~~~~~~~~~~e~~~~~~ 449 (468)
.+|.++|++||+||.||+||++ ...+..+.+++|.|||+|||+|++..+. .++.|...++.+++......+.+....
T Consensus 228 ~~r~v~e~~fg~lk~rw~il~~~~~~~~~~~~~iV~a~caLHN~~~~~~~~~~~~~~~e~~~d~~~~~~~~~~~~~~~~~ 307 (326)
T KOG4585|consen 228 SLRSVAERAFGVLKAKWRILQRREKYDLKKLPKIVTACCALHNIIRDSDEEDPDDPKWEKFDDYGENVAHLRYAPQQRDY 307 (326)
T ss_pred hHHHHHHHHHHHhhhhhHHHhhcccccccchHHHHHHHHHHHHHHHhhcccccccccccccccccccchhcccchhHHHH
Confidence 9999999999999999999986 6678899999999999999999988874 445576665544222222333334567
Q ss_pred HHHHHHHHHHHHHHhcc
Q 012200 450 GEGLRQALADDLHQRLS 466 (468)
Q Consensus 450 g~~~R~~l~~~l~~~~~ 466 (468)
++..|+.|+..+.+..+
T Consensus 308 ~~~~r~~l~~~l~~~~~ 324 (326)
T KOG4585|consen 308 MEKIRDNLLSELWNGTR 324 (326)
T ss_pred HHHHHHHHHHHHHhccc
Confidence 89999999999988665
No 2
>PF13359 DDE_Tnp_4: DDE superfamily endonuclease
Probab=100.00 E-value=4.6e-37 Score=279.03 Aligned_cols=154 Identities=36% Similarity=0.545 Sum_probs=138.9
Q ss_pred cceeeEEeccCCcccccccccceeeecCceeeEeeeeccccceeeeeccCCCCCCCCccccchhhhhhhhccCCCCCccc
Q 012200 247 IDGSHIKIGNGKLKHVSLNQNQYRCKYGYNSVLLQVVADHRKIFWDVCVKASGGADDSAHFRDSLLYNRLISGDIVWDKA 326 (468)
Q Consensus 247 IDgT~I~i~~P~~~~~~~~~~~Y~~~k~~~Si~~q~v~D~~g~f~~v~~g~pGs~hD~~i~~~S~l~~~l~~~~l~~~~~ 326 (468)
||||||+|++|.. .+.+...|+++|+.|++|+|+|||++|+|++++.++||++||.++|++|.+...++.. +
T Consensus 1 iDgt~v~i~~P~~--~~~~~~~y~~~k~~~~~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~s~~~~~l~~~-~----- 72 (158)
T PF13359_consen 1 IDGTHVPIQRPSD--KEEQREFYSGKKKNHSLKVQIVCDPDGRIIYVSVGWPGSVHDSTIFRQSGLLDRLEQA-F----- 72 (158)
T ss_pred CccEEEEEEeCCc--cccccccccCCCCcceEeEEEEEeccceeEeeecccccccccccccccccccceeecc-c-----
Confidence 7999999999982 1237789999999999999999999999999999999999999999999988877621 1
Q ss_pred cccCCccccceeecccCCCCcCCcccCCC--CCCCCCCccccchhhhhcccchHHHHHHHHhhhhhhccc-ccCC-CCcH
Q 012200 327 INVRGHHVRPYIVGDWCYPLLSFLMTPFS--PNGAGTPAQNLFDGMLMKGRNVVVEAIGLLKARWKILKD-LNVG-INHA 402 (468)
Q Consensus 327 ~~~~G~~~~~~llgD~gYpl~~~lltP~~--~~~~lt~~e~~FN~~ls~~R~~VE~afG~LK~RfriL~~-l~~~-~~~~ 402 (468)
+.++|++||+|||+.+++|+||+ .+.+++++|+.||++|++.|++||++||+||+||+||++ ++.+ ++.+
T Consensus 73 ------~~~~~~l~D~gy~~~~~~~~P~~~~~~~~l~~~e~~~N~~~s~~R~~vE~~~~~lK~rf~~l~~~~~~~~~~~~ 146 (158)
T PF13359_consen 73 ------PPGEYLLGDSGYPLSPYLLTPYKKPKGRELTPEEKEFNRRHSSARIIVERAFGRLKSRFRILRGRLRLSRPEKA 146 (158)
T ss_pred ------ccCccccccccccccccccccccccccccccccccchhccccceeeeeHHHHHHHHHhcccCCcccCCCcHhHH
Confidence 12369999999999999999997 456789999999999999999999999999999999984 8888 9999
Q ss_pred HHHHHHHHHHhh
Q 012200 403 PQTIVACCVLHN 414 (468)
Q Consensus 403 ~~iI~AccvLHN 414 (468)
.++|.|||+|||
T Consensus 147 ~~ii~~~~~LhN 158 (158)
T PF13359_consen 147 PQIILACCVLHN 158 (158)
T ss_pred HHHHheeEEEEC
Confidence 999999999999
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=99.97 E-value=2.2e-32 Score=248.15 Aligned_cols=194 Identities=25% Similarity=0.381 Sum_probs=169.5
Q ss_pred ccccCCCchhhhcccccccccccCCCCCccccceeeEEeccCCccccccccccee-eecCceeeEeeeeccccceeeeec
Q 012200 216 EFIKIPISRRRLIETTQGFEELTSLPNICGAIDGSHIKIGNGKLKHVSLNQNQYR-CKYGYNSVLLQVVADHRKIFWDVC 294 (468)
Q Consensus 216 ~~I~~P~~~~~~~~i~~~F~~~~~fP~~vGaIDgT~I~i~~P~~~~~~~~~~~Y~-~~k~~~Si~~q~v~D~~g~f~~v~ 294 (468)
+|++-| +.++.+++...++ ..||||.+|.|||+|+....+|. .....|. +++|.+++.+++|++++.+|++..
T Consensus 2 ~YLr~P-~~~d~~rll~~~e-~rGFpGmlGSIDCmHw~WkncP~----aw~g~~~~G~~g~pTiiLEaVAs~dlwIWhaf 75 (205)
T PF04827_consen 2 EYLRRP-TNEDLERLLQIGE-ARGFPGMLGSIDCMHWEWKNCPT----AWKGQYTRGKEGVPTIILEAVASHDLWIWHAF 75 (205)
T ss_pred cccCCC-ChhHHHHHHHhhh-hcCCCccccceeEEEeehhcchH----HhhhcccCCCCCCCeehhhhhhccchhhhhee
Confidence 578889 6778888775444 56999999999999999998874 5666677 999999999999999999999999
Q ss_pred cCCCCCCCCccccchhhhhhhhccCCCCCccccccCCccc-cceeecccCCCCcCCcccCCCCCCCCCCccccchhhhhc
Q 012200 295 VKASGGADDSAHFRDSLLYNRLISGDIVWDKAINVRGHHV-RPYIVGDWCYPLLSFLMTPFSPNGAGTPAQNLFDGMLMK 373 (468)
Q Consensus 295 ~g~pGs~hD~~i~~~S~l~~~l~~~~l~~~~~~~~~G~~~-~~~llgD~gYpl~~~lltP~~~~~~lt~~e~~FN~~ls~ 373 (468)
.|.|||.+|..|+..|+++..+.+|+.. .-.+.++|++- -.|.|+|..||-+..++...+.+ .+++++.|.++..+
T Consensus 76 fG~~GS~NDiNVL~~Splf~~~~~G~ap-~v~f~VNg~~Y~~gYYLaDGiYP~watfvktI~~p--~~~k~k~fa~~QE~ 152 (205)
T PF04827_consen 76 FGMPGSNNDINVLDRSPLFDDLLQGQAP-RVQFTVNGHEYNMGYYLADGIYPEWATFVKTISLP--QGEKRKLFAKHQES 152 (205)
T ss_pred eccCCcccccccccccHHHHHHhcCcCC-ceEEEecCeecccceeeccCcCcchHhHhhhcchh--hchhhHHHHHhCHH
Confidence 9999999999999999999999999742 12345677653 36899999999999999999874 57899999999999
Q ss_pred ccchHHHHHHHHhhhhhhccc--ccCCCCcHHHHHHHHHHHhhhccc
Q 012200 374 GRNVVVEAIGLLKARWKILKD--LNVGINHAPQTIVACCVLHNLCQI 418 (468)
Q Consensus 374 ~R~~VE~afG~LK~RfriL~~--l~~~~~~~~~iI~AccvLHN~~~~ 418 (468)
+|..||||||+|++||+|+++ .-++.+.+..|+.||++||||+..
T Consensus 153 ~RKDVErAFGVLQaRfaIi~~p~r~w~~~~l~~Im~aCiILHNMIvE 199 (205)
T PF04827_consen 153 ARKDVERAFGVLQARFAIIRGPARLWDREDLANIMRACIILHNMIVE 199 (205)
T ss_pred HHHHHHHHHHHHHHHHHHhcCchhccCHHHHHHHHHHHHHhhheeEe
Confidence 999999999999999999996 346888999999999999999963
No 4
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=98.91 E-value=2e-09 Score=79.65 Aligned_cols=51 Identities=24% Similarity=0.249 Sum_probs=48.3
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
+++.++|++++|.||++|.++.++|..||||++||+++++++.++++..+.
T Consensus 2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l~ 52 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVLK 52 (53)
T ss_pred CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhcC
Confidence 589999999999999999999999999999999999999999999997653
No 5
>PF13612 DDE_Tnp_1_3: Transposase DDE domain
Probab=98.83 E-value=2.3e-09 Score=96.95 Aligned_cols=131 Identities=18% Similarity=0.200 Sum_probs=94.0
Q ss_pred CCCccccceeeEEeccCCcc--cccc---cccceeeecCceeeEeeeeccccceeeeeccCCCCCCCCccccchhhhhhh
Q 012200 241 PNICGAIDGSHIKIGNGKLK--HVSL---NQNQYRCKYGYNSVLLQVVADHRKIFWDVCVKASGGADDSAHFRDSLLYNR 315 (468)
Q Consensus 241 P~~vGaIDgT~I~i~~P~~~--~~~~---~~~~Y~~~k~~~Si~~q~v~D~~g~f~~v~~g~pGs~hD~~i~~~S~l~~~ 315 (468)
+..+.+||.+.||++.+... +..- ...-|...+-||++++.++|+..|.++.+... ||++||..++..
T Consensus 4 ~~~i~~iDS~Pi~vC~~~R~~r~k~~~~~a~~G~~a~~~fyGfKlHllv~~~G~i~~~~lT-~an~~D~~~~~~------ 76 (155)
T PF13612_consen 4 CTGIYIIDSFPIPVCHNIRIKRHKVFKGLAYRGYCAMGWFYGFKLHLLVNDSGEIVAFTLT-PANVHDRKVLEE------ 76 (155)
T ss_pred ccEEEEEecCChhHhCccchhhhccccCccccceeccceeEeeeeeeEEccCCcEEEEEEc-cccccccccccc------
Confidence 45677999999999987521 1111 11123334456999999999999999998665 999999998731
Q ss_pred hccCCCCCccccccCCccccceeecccCCCCcC----------CcccCCCCCCCCCCccccchhhhhcccchHHHHHHHH
Q 012200 316 LISGDIVWDKAINVRGHHVRPYIVGDWCYPLLS----------FLMTPFSPNGAGTPAQNLFDGMLMKGRNVVVEAIGLL 385 (468)
Q Consensus 316 l~~~~l~~~~~~~~~G~~~~~~llgD~gYpl~~----------~lltP~~~~~~lt~~e~~FN~~ls~~R~~VE~afG~L 385 (468)
+..+ + ...++||+||-... .++||.+.+- .......+++.+.+.|.+||-+|+.|
T Consensus 77 l~~~---------~-----~g~l~gDkGYis~~L~~~L~~~gI~L~t~~RkNm-k~~~~~~~~~~l~~~R~~IETvfs~L 141 (155)
T PF13612_consen 77 LSEN---------L-----KGKLFGDKGYISKELKDELKEQGIKLITPRRKNM-KNKLMPLFDKLLLRKRRIIETVFSQL 141 (155)
T ss_pred cccc---------c-----ccceecchhhhcchHHhhhhhceEEEeccccccc-cccccchhhhhhhheeeEeehHHHHH
Confidence 1111 1 13699999995433 4889998651 12234567899999999999999999
Q ss_pred hhhhhhcc
Q 012200 386 KARWKILK 393 (468)
Q Consensus 386 K~RfriL~ 393 (468)
|++|.+=+
T Consensus 142 k~~~~ie~ 149 (155)
T PF13612_consen 142 KNQFNIEH 149 (155)
T ss_pred HHhhceEe
Confidence 99988754
No 6
>PF01609 DDE_Tnp_1: Transposase DDE domain; InterPro: IPR002559 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS4 transposase. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 3ECP_A 4DM0_A 1MUS_A 1MUH_A 1MM8_A 1B7E_A.
Probab=97.37 E-value=2.5e-06 Score=79.45 Aligned_cols=150 Identities=19% Similarity=0.166 Sum_probs=81.7
Q ss_pred CccccceeeEEeccCCcccccccccceeeecCceeeEeeeecc-ccceeeeeccCCCCCCCCccccchhhhhhhhccCCC
Q 012200 243 ICGAIDGSHIKIGNGKLKHVSLNQNQYRCKYGYNSVLLQVVAD-HRKIFWDVCVKASGGADDSAHFRDSLLYNRLISGDI 321 (468)
Q Consensus 243 ~vGaIDgT~I~i~~P~~~~~~~~~~~Y~~~k~~~Si~~q~v~D-~~g~f~~v~~g~pGs~hD~~i~~~S~l~~~l~~~~l 321 (468)
.+-+||+|+|+.. +. ......+.+++...+.++++++| ..|.++.+... +|+.+|...+.. +.+. ..+
T Consensus 5 ~~~~iD~T~i~~~-~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~d~~~~~~--ll~~-~~~-- 73 (213)
T PF01609_consen 5 RVVAIDGTTIRTP-HD----KSARRYKKGKKRGFGYKLHLAVDDNSGLPLSVKVT-PGNVHDSKALPE--LLER-KPG-- 73 (213)
T ss_dssp EEEEEETTT--EE-EE----EEE-B-SSGGGHSSHGGHHHHHHHHHGGGGGGEEE-EEEGG-HHHHHH--HHTT------
T ss_pred eEEEEECcEEEee-cc----hhhhcccCCCCcCCCEeEEEEEeecccceeeeecc-ccccceeecccc--cccc-ccc--
Confidence 3458999999998 11 02223344555566678888984 56777777777 999999988876 2222 000
Q ss_pred CCccccccCCccccceeecccCCCCcC----------CcccCCCCCCCCC------------------------------
Q 012200 322 VWDKAINVRGHHVRPYIVGDWCYPLLS----------FLMTPFSPNGAGT------------------------------ 361 (468)
Q Consensus 322 ~~~~~~~~~G~~~~~~llgD~gYpl~~----------~lltP~~~~~~lt------------------------------ 361 (468)
..+.++++|+||...+ ..+.|.+.+....
T Consensus 74 -----------~~~~~vv~D~gy~s~~~~~~l~~~~~~~vi~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 142 (213)
T PF01609_consen 74 -----------RKPDLVVADRGYDSAENLEALKERGIHFVIRLKKNRKKKIQKIENKFWKSFDRRSARKKPKQKSKRVRV 142 (213)
T ss_dssp -------------EEEEEE-S--BBTTHHHHHHTS---EEEEE--EEEE-TTS-EEEE--EEEEEEEEEEETGGGEEEEE
T ss_pred -----------ccccceeecccccceeccccccccccccccccccccccccccchhhccccccccccccccccccccccc
Confidence 1135899999997543 1244444321110
Q ss_pred ---Cccccchhh--------------hhcccchHHHHHHHHhhhhhhccccc-CCCCcHHHHHHHHHHHhhh
Q 012200 362 ---PAQNLFDGM--------------LMKGRNVVVEAIGLLKARWKILKDLN-VGINHAPQTIVACCVLHNL 415 (468)
Q Consensus 362 ---~~e~~FN~~--------------ls~~R~~VE~afG~LK~RfriL~~l~-~~~~~~~~iI~AccvLHN~ 415 (468)
..++..... +.+.|-.||+.|+.||..|. +..++ .+.+.+...+.+|++-.|+
T Consensus 143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Y~~Rw~IE~~f~~lK~~~~-l~~~~~~~~~~~~~~~~~~~la~nl 213 (213)
T PF01609_consen 143 VIRKEQKKKGYFLVTNITTLPRDTAALYRRRWQIERFFRELKQFLG-LERLRVRSPERIEAHLFLTLLAYNL 213 (213)
T ss_dssp EEEEECS--TTS---EEEEEESS--SHHHCGGHHHHHHHHHTTTTT-GGGS--SSHHHHHHHHHHHHHH---
T ss_pred ccccccccccccccccccccccccceeecccchhhHHHHHHHhcCC-CchhcccCHHHHHHHHHHHHhhCcC
Confidence 111111222 88999999999999999655 34433 3455666667777766664
No 7
>PF13586 DDE_Tnp_1_2: Transposase DDE domain
Probab=96.97 E-value=0.00065 Score=55.43 Aligned_cols=52 Identities=21% Similarity=0.179 Sum_probs=39.3
Q ss_pred CccccchhhhhcccchHHHHHHHHhhhhhhcc-cccCCCCcHHHHHHHHHHHhh
Q 012200 362 PAQNLFDGMLMKGRNVVVEAIGLLKARWKILK-DLNVGINHAPQTIVACCVLHN 414 (468)
Q Consensus 362 ~~e~~FN~~ls~~R~~VE~afG~LK~RfriL~-~l~~~~~~~~~iI~AccvLHN 414 (468)
.....+...+.+.|.+||++||.||. |+.|. .+.........+|.-+|++-+
T Consensus 34 ~~~~~~d~~~~~~Rw~VEr~f~wlk~-~Rrl~~ryek~~~s~~~~v~la~~~i~ 86 (88)
T PF13586_consen 34 RRPRKFDFRLYKRRWVVERTFAWLKR-FRRLATRYEKLASSFLAFVHLACIVIW 86 (88)
T ss_pred cccCccchhhhccceehhhhhHHHHH-cCccccccccCHHHHHHHHHHHHHHHH
Confidence 34678899999999999999999997 88776 466666666666655555433
No 8
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=95.27 E-value=0.043 Score=39.53 Aligned_cols=45 Identities=20% Similarity=0.296 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLL 209 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l 209 (468)
.++++++-.+.++| ..|.++.++|..+|+|.++|+++.+....-|
T Consensus 4 ~L~~~er~vi~~~y-~~~~t~~eIa~~lg~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 4 QLPPREREVIRLRY-FEGLTLEEIAERLGISRSTVRRILKRALKKL 48 (50)
T ss_dssp TS-HHHHHHHHHHH-TST-SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh-cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence 57888888888888 7789999999999999999999988776654
No 9
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=95.20 E-value=0.031 Score=41.10 Aligned_cols=42 Identities=21% Similarity=0.333 Sum_probs=31.0
Q ss_pred CCCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHH
Q 012200 162 NLSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNM 204 (468)
Q Consensus 162 ~~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~ 204 (468)
+..+++++++-+ +.++..|.+..++|..|||+++||+.|+..
T Consensus 4 R~~LTl~eK~~i-I~~~e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 4 RKSLTLEEKLEI-IKRLEEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp SSS--HHHHHHH-HHHHHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred CccCCHHHHHHH-HHHHHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 457889998885 556788889999999999999999998753
No 10
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=94.78 E-value=0.027 Score=39.72 Aligned_cols=40 Identities=18% Similarity=0.226 Sum_probs=22.7
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNM 204 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~ 204 (468)
.++.+++..|. .++..|.+.+.||..+|+|++||++.+++
T Consensus 4 ~Lt~~eR~~I~-~l~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 4 HLTPEERNQIE-ALLEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp --------HHH-HHHCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred chhhhHHHHHH-HHHHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 46666766665 34689999999999999999999998764
No 11
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=94.29 E-value=0.039 Score=39.06 Aligned_cols=34 Identities=15% Similarity=0.286 Sum_probs=26.8
Q ss_pred HHHHHHhhhccCccHHHHhhhccCCcchhHHHHH
Q 012200 170 AVAMVLSRLAHGLSAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 170 ~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~ 203 (468)
++.-++..+..|.+..++|..||||++||.|+++
T Consensus 10 ~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 10 QIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp CHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 4556677889999999999999999999999874
No 12
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=93.11 E-value=0.058 Score=38.71 Aligned_cols=37 Identities=14% Similarity=0.183 Sum_probs=22.2
Q ss_pred HHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHH
Q 012200 169 YAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 169 ~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
.++.+.. .+..|.+..++|..+|||++||+++++++.
T Consensus 6 ~R~~ii~-l~~~G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 6 RRAQIIR-LLREGWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp ----HHH-HHHHT--HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHHHHHH-HHHCCCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 3344333 344499999999999999999999987653
No 13
>PF13518 HTH_28: Helix-turn-helix domain
Probab=92.67 E-value=0.15 Score=36.57 Aligned_cols=37 Identities=14% Similarity=0.208 Sum_probs=30.5
Q ss_pred HHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 170 AVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 170 ~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
++.+...++ .|.++..+|..||||.+||.+++...-.
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 455666667 6779999999999999999999877654
No 14
>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=92.60 E-value=0.096 Score=41.52 Aligned_cols=46 Identities=7% Similarity=0.032 Sum_probs=32.5
Q ss_pred HHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 169 YAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 169 ~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
..+-++-|.+.++.+-+..|..||||+|||++=+.+=+.-|...|+
T Consensus 7 R~i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~La 52 (82)
T PF12116_consen 7 RVIEIANYIIETKATVRQAAKVFGVSKSTVHKDVTERLPKINPELA 52 (82)
T ss_dssp HHHHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-HHHH
T ss_pred HHHHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHHH
Confidence 4466788889999999999999999999999877665555554443
No 15
>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=92.34 E-value=0.3 Score=35.52 Aligned_cols=43 Identities=14% Similarity=0.237 Sum_probs=30.1
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
.+|+.++-++.|.|+ .|.++.++|..+|+|.+||...+.+...
T Consensus 10 ~L~~~~r~i~~l~~~-~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 10 QLPERQREIFLLRYF-QGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp CS-HHHHHHHHHHHT-S---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHH-HCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 477888777666555 5899999999999999999888776543
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=92.16 E-value=0.18 Score=35.75 Aligned_cols=36 Identities=11% Similarity=0.274 Sum_probs=28.0
Q ss_pred HHHHHHHHhhhccC-ccHHHHhhhccCCcchhHHHHH
Q 012200 168 DYAVAMVLSRLAHG-LSAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 168 e~~L~i~L~~La~g-~s~~~la~~Fgvs~sTvsri~~ 203 (468)
++.+.-+|..+..| .+++..|..|||+++|+++.++
T Consensus 2 ee~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~ 38 (45)
T PF05225_consen 2 EEDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLR 38 (45)
T ss_dssp HHHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHc
Confidence 56677788888888 9999999999999999987764
No 17
>smart00351 PAX Paired Box domain.
Probab=91.16 E-value=0.37 Score=41.96 Aligned_cols=44 Identities=16% Similarity=0.161 Sum_probs=37.2
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
..++.+.+.-+.+.+. .|.+..++|.+||||++||+++++++-+
T Consensus 16 ~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 16 RPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4588888888777665 8999999999999999999999887643
No 18
>cd00131 PAX Paired Box domain
Probab=90.26 E-value=0.48 Score=41.48 Aligned_cols=44 Identities=18% Similarity=0.190 Sum_probs=37.4
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
..++.+.+.-|.+.+ ..|.+.+.+|.+||||++||.++++++-+
T Consensus 16 ~~lS~d~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e 59 (128)
T cd00131 16 RPLPDSIRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILNRYYE 59 (128)
T ss_pred CcCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 568888877777665 68999999999999999999999877654
No 19
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=90.18 E-value=0.49 Score=38.29 Aligned_cols=46 Identities=13% Similarity=0.096 Sum_probs=41.7
Q ss_pred CCCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 162 NLSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 162 ~~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
+-.+++.-++.++-..+..|.+...++..||||..|+++++.++-.
T Consensus 6 nA~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra 51 (85)
T PF13011_consen 6 NARLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRA 51 (85)
T ss_pred CCCCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3468999999999999999999999999999999999999877654
No 20
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=89.58 E-value=0.64 Score=40.18 Aligned_cols=46 Identities=9% Similarity=0.096 Sum_probs=41.7
Q ss_pred CCCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 162 NLSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 162 ~~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
+...+.+.++-++...+..|.+..++|..|||+.+|++++++....
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 4578999999999999999999999999999999999999887643
No 21
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=89.49 E-value=0.83 Score=32.77 Aligned_cols=44 Identities=23% Similarity=0.297 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 165 LPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 165 l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
++..++-.+ ..+..|.++.++|..+|+|.+||.+++.+...-+.
T Consensus 4 l~~~e~~i~--~~~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 4 LTPREREVL--RLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCHHHHHHH--HHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 566555433 33578999999999999999999999988765553
No 22
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=89.22 E-value=0.76 Score=32.28 Aligned_cols=42 Identities=17% Similarity=0.224 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 165 LPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 165 l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
++.+++-++.+.+ -.|.++.++|..+|++..++.+++.....
T Consensus 11 l~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 11 LPEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred CCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5666665555555 48899999999999999999999877643
No 23
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=89.18 E-value=0.43 Score=42.35 Aligned_cols=42 Identities=17% Similarity=0.246 Sum_probs=36.9
Q ss_pred CCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHH
Q 012200 165 LPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 165 l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
.+.+.+-.++-.++..|.+.+.+|.+||||.+|+.+++++.-
T Consensus 5 ~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 5 FSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred hhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhc
Confidence 455777888999999999999999999999999999987654
No 24
>PF02209 VHP: Villin headpiece domain; InterPro: IPR003128 Villin is an F-actin bundling protein involved in the maintenance of the microvilli of the absorptive epithelia. The villin-type "headpiece" domain is a modular motif found at the extreme C terminus of larger "core" domains in over 25 cytoskeletal proteins in plants and animals, often in assocation with the Gelsolin repeat. Although the headpiece is classified as an F-actin-binding domain, it has been shown that not all headpiece domains are intrinsically F-actin-binding motifs, surface charge distribution may be an important element for F-actin recognition []. An autonomously folding, 35 residue, thermostable subdomain (HP36) of the full-length 76 amino acid residue villin headpiece, is the smallest known example of a cooperatively folded domain of a naturally occurring protein. The structure of HP36, as determined by NMR spectroscopy, consists of three short helices surrounding a tightly packed hydrophobic core []. ; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1ZV6_A 1QZP_A 1UND_A 2PPZ_A 3TJW_B 1YU8_X 2JM0_A 1WY4_A 3MYC_A 1YU5_X ....
Probab=89.15 E-value=0.26 Score=33.19 Aligned_cols=22 Identities=18% Similarity=0.481 Sum_probs=17.3
Q ss_pred CChhhHHHhcCCCHHHHHHHHH
Q 012200 131 LREAHWRSLYGLSYPVFTTVVE 152 (468)
Q Consensus 131 l~d~~fr~~fRms~~~F~~L~~ 152 (468)
|+|++|...|||+++.|..|=.
T Consensus 2 Lsd~dF~~vFgm~~~eF~~lP~ 23 (36)
T PF02209_consen 2 LSDEDFEKVFGMSREEFYKLPK 23 (36)
T ss_dssp S-HHHHHHHHSS-HHHHHHS-H
T ss_pred cCHHHHHHHHCCCHHHHHHChH
Confidence 6899999999999999998743
No 25
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=89.00 E-value=0.4 Score=37.38 Aligned_cols=45 Identities=16% Similarity=0.259 Sum_probs=37.1
Q ss_pred CCCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHH
Q 012200 162 NLSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 162 ~~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
+...+++.+.-++-.++..|.+..+++..+||+.+|+++++....
T Consensus 4 r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 4 RRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp S----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence 356889999999999999999999999999999999999998876
No 26
>PRK04217 hypothetical protein; Provisional
Probab=88.19 E-value=0.97 Score=38.54 Aligned_cols=49 Identities=12% Similarity=0.044 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.++.+++-+ +..+.-.|.++.++|..+|||.+||.++++.....|.+.+
T Consensus 42 ~Lt~eerea-i~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 42 FMTYEEFEA-LRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred cCCHHHHHH-HHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 567777644 3444558899999999999999999999998888877544
No 27
>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=87.67 E-value=1.4 Score=36.04 Aligned_cols=49 Identities=18% Similarity=0.255 Sum_probs=44.1
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhhhcc-CCcchhHHHHHHHHHHHHh
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALASRYS-LEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~~Fg-vs~sTvsri~~~v~~~l~~ 211 (468)
..+..-.+++|.|.+--.|.++.++|..|| .+.|||+..++++-..+.+
T Consensus 26 ~~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 26 KEIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred cCcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 467888899999999999999999999999 9999999999988887753
No 28
>smart00153 VHP Villin headpiece domain.
Probab=87.51 E-value=0.43 Score=32.22 Aligned_cols=21 Identities=14% Similarity=0.475 Sum_probs=19.1
Q ss_pred CChhhHHHhcCCCHHHHHHHH
Q 012200 131 LREAHWRSLYGLSYPVFTTVV 151 (468)
Q Consensus 131 l~d~~fr~~fRms~~~F~~L~ 151 (468)
++|++|...|||+++.|..|=
T Consensus 2 LsdeeF~~vfgmsr~eF~~LP 22 (36)
T smart00153 2 LSDEDFEEVFGMTREEFYKLP 22 (36)
T ss_pred CCHHHHHHHHCCCHHHHHhCc
Confidence 689999999999999998873
No 29
>PRK15320 transcriptional activator SprB; Provisional
Probab=87.45 E-value=1.2 Score=41.83 Aligned_cols=38 Identities=26% Similarity=0.273 Sum_probs=33.9
Q ss_pred HHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 173 MVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 173 i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
-.|..|+.|.+.++||+.+++|.+||+.+.++...-+.
T Consensus 171 EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLg 208 (251)
T PRK15320 171 ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLG 208 (251)
T ss_pred HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence 47889999999999999999999999999888776654
No 30
>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=87.45 E-value=0.92 Score=28.79 Aligned_cols=37 Identities=19% Similarity=0.164 Sum_probs=27.3
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKI 201 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri 201 (468)
.++.+.+..+.. .+..|.+..+++..||++++|++++
T Consensus 5 ~~~~~~~~~i~~-~~~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 5 KLTPEQIEEARR-LLAAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred cCCHHHHHHHHH-HHHcCCCHHHHHHHHCCCHHHHHHh
Confidence 345555444433 4557889999999999999999876
No 31
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=87.15 E-value=1.1 Score=36.60 Aligned_cols=31 Identities=16% Similarity=0.188 Sum_probs=27.1
Q ss_pred HHHHhhhccCccHHHHhhhccCCcchhHHHH
Q 012200 172 AMVLSRLAHGLSAKALASRYSLEPYLISKIT 202 (468)
Q Consensus 172 ~i~L~~La~g~s~~~la~~Fgvs~sTvsri~ 202 (468)
...+.++..|.+..++|..+|||++||+++.
T Consensus 41 ~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 41 LQVAKMLKQGKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 4456678999999999999999999999955
No 32
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=87.08 E-value=0.58 Score=33.69 Aligned_cols=32 Identities=19% Similarity=0.160 Sum_probs=26.2
Q ss_pred HHhhhccCccHHHHhhhccCCcchhHHHHHHH
Q 012200 174 VLSRLAHGLSAKALASRYSLEPYLISKITNMV 205 (468)
Q Consensus 174 ~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v 205 (468)
.+..+..+.++.++|..+|||.+||.+++++.
T Consensus 20 i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 20 ILKLLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 34445555799999999999999999998764
No 33
>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=86.99 E-value=0.94 Score=35.64 Aligned_cols=41 Identities=17% Similarity=0.070 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNM 204 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~ 204 (468)
.+|...+.+..|.+.-.|.++.+||...|+|..||..+++.
T Consensus 15 ~l~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 15 WVDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred cCCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 57888888888888889999999999999999999888753
No 34
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=86.84 E-value=1.2 Score=40.01 Aligned_cols=47 Identities=11% Similarity=0.137 Sum_probs=41.5
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|.+.+-++.|++ .|.++.+||..+|++.+||...+.+....|.+.
T Consensus 112 ~L~~~~r~il~l~~--~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 112 KMTERDRTVLLLRF--SGYSYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred cCCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58899999888877 999999999999999999999888887777654
No 35
>PRK00118 putative DNA-binding protein; Validated
Probab=86.47 E-value=1.6 Score=36.86 Aligned_cols=48 Identities=15% Similarity=0.110 Sum_probs=38.1
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
..++..++-++.++ +-.|.++.++|..+|+|++||.+.+.+....+.+
T Consensus 16 ~~L~ekqRevl~L~-y~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 16 SLLTEKQRNYMELY-YLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred ccCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 34677766666555 5569999999999999999999999887766654
No 36
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)
Probab=86.22 E-value=1.4 Score=34.65 Aligned_cols=44 Identities=11% Similarity=0.067 Sum_probs=38.1
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
...+..+-+-..|+.+.+|+.++.+-..|| +..||++.+++...
T Consensus 23 ~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg-~~~tv~~~f~rW~~ 66 (75)
T PF13340_consen 23 PRIDLREVLNAILYVLRTGCPWRDLPEDFG-PWSTVYRRFRRWSR 66 (75)
T ss_pred CccchHHHHhcccccceecceecccchhcc-CcCcHHHHHHHHHH
Confidence 457788888899999999999999999999 88889888877654
No 37
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=85.82 E-value=1.6 Score=39.98 Aligned_cols=48 Identities=15% Similarity=0.183 Sum_probs=41.4
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|++.+.++.|.++ .|.++.++|..+|+|.+||...+++....+.+.
T Consensus 127 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 127 TLRPRVKQAFLMATL-DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 589999999999888 899999999999999999988877766666544
No 38
>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=85.45 E-value=2 Score=30.76 Aligned_cols=33 Identities=21% Similarity=0.264 Sum_probs=28.5
Q ss_pred hccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 178 LAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 178 La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
+..|.++.++|..+|+|.+|+.+.+++....+.
T Consensus 12 ~~~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~ 44 (57)
T cd06170 12 LAEGKTNKEIADILGISEKTVKTHLRNIMRKLG 44 (57)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 468999999999999999999999887766544
No 39
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=85.32 E-value=1.5 Score=38.99 Aligned_cols=50 Identities=18% Similarity=0.149 Sum_probs=42.6
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
.+|+..+-++.|.++ .|.++.++|...|+|..||...+.+....|.+.+.
T Consensus 106 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 155 (161)
T PRK09047 106 KLPARQREAFLLRYW-EDMDVAETAAAMGCSEGSVKTHCSRATHALAKALE 155 (161)
T ss_pred hCCHHHHHHHHHHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 578888888777765 59999999999999999999999888888876554
No 40
>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=84.85 E-value=1.8 Score=38.19 Aligned_cols=46 Identities=22% Similarity=0.283 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
.++.+++-++.|+++ .|.++.++|..+|+|.+||.....+....|-
T Consensus 113 ~L~~~~r~il~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 113 KLPEQCRKIFILSRF-EGKSYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 478888888888776 6999999999999999999988887766654
No 41
>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=84.27 E-value=1.8 Score=37.32 Aligned_cols=47 Identities=23% Similarity=0.266 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
.+++.++-++.+.++ .|.++.++|..+|+|.++|++...++...|-+
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 467777776666555 69999999999999999999999887766643
No 42
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=83.58 E-value=1.9 Score=42.56 Aligned_cols=49 Identities=20% Similarity=0.224 Sum_probs=42.3
Q ss_pred CCCHHHHHHHHHhhhc-cCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLA-HGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La-~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.++..++..+.|+|+. .|.++.++|..+|||+.+|+++.+....-|...
T Consensus 218 ~L~~rer~vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~ 267 (270)
T TIGR02392 218 SLDARSRRIIEARWLDDDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAA 267 (270)
T ss_pred cCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4888999999999974 489999999999999999999988887776543
No 43
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=83.40 E-value=2.1 Score=41.04 Aligned_cols=50 Identities=12% Similarity=0.088 Sum_probs=43.8
Q ss_pred CCCHHHHHHHHHhhh---ccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRL---AHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|+.++-++.|+|+ ..|.++.++|...|++.+||.+..++....|.+.|
T Consensus 174 ~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~~ 226 (227)
T TIGR02846 174 VLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKEL 226 (227)
T ss_pred hCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 588999999899886 48999999999999999999999888888777654
No 44
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=83.23 E-value=2.2 Score=38.20 Aligned_cols=49 Identities=22% Similarity=0.270 Sum_probs=40.5
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|++++-.+.|.++. |.++.++|..+|+|.+||...+.+...-|-..+
T Consensus 109 ~L~~~~r~v~~l~~~~-~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 109 ELPARTRYAFEMYRLH-GETQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5788888887777665 999999999999999999988877777666443
No 45
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=83.23 E-value=2.2 Score=38.24 Aligned_cols=48 Identities=13% Similarity=0.005 Sum_probs=40.8
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
..+|+.++.++.|+|+ .|.++.++|..+|+|.+||...+.+....|-+
T Consensus 121 ~~L~~~~r~vl~l~~~-~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 121 KILTPKQQHVIALRFG-QNLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred HhCCHHHHHHHHHHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3689999988888776 59999999999999999999888887776653
No 46
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=82.97 E-value=2.1 Score=38.64 Aligned_cols=49 Identities=24% Similarity=0.267 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+++.++.++.|.++ .|.++.++|..+|++.+||...+.+...-|.+.+
T Consensus 128 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREI-EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 488888888878776 7899999999999999999988888777766543
No 47
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=82.95 E-value=2.4 Score=38.23 Aligned_cols=49 Identities=20% Similarity=0.118 Sum_probs=42.4
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|+..+-++.|.++ .|.++.++|..+|+|..||...+.+....|.+.+
T Consensus 112 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 112 LLSADQREAIILIGA-SGFSYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 588888888888877 8999999999999999999988888887776544
No 48
>PHA00675 hypothetical protein
Probab=82.87 E-value=1.5 Score=34.69 Aligned_cols=39 Identities=21% Similarity=0.186 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKIT 202 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~ 202 (468)
.++..+--.|...+-+.|.++..||..||||++||..|.
T Consensus 22 KLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~ 60 (78)
T PHA00675 22 KLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKIC 60 (78)
T ss_pred ccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHH
Confidence 344444344444333788999999999999999999885
No 49
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=82.61 E-value=2.1 Score=41.12 Aligned_cols=50 Identities=16% Similarity=0.176 Sum_probs=43.2
Q ss_pred CCCHHHHHHHHHhhh---ccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRL---AHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|+.++-++.|+|+ -.|.++.++|..+|+|..||....++....|-+.+
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 589999999889874 68999999999999999999999888887776543
No 50
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=82.48 E-value=2.5 Score=38.49 Aligned_cols=48 Identities=27% Similarity=0.170 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|++.+-.+.|.++ .|.++.+||..+|++..||...+.+....|.+.
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 488888888888876 789999999999999999998888877777654
No 51
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=82.23 E-value=2.3 Score=39.20 Aligned_cols=48 Identities=13% Similarity=0.045 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|++.+-++.|+++ .|.++.++|..+|+|..||...+.+....|...
T Consensus 131 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 131 KLSPAHREIIDLVYY-HEKSVEEVGEIVGIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 588998888888887 899999999999999999998888877776654
No 52
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=82.15 E-value=3.9 Score=31.48 Aligned_cols=73 Identities=14% Similarity=0.069 Sum_probs=52.9
Q ss_pred ChhhHHHhcCCCHHHHHHHHHHhccccccCCCCCCHHHHHHHHHhhhccC-ccHHHHhhhccC-CcchhHHHHHHHHH
Q 012200 132 REAHWRSLYGLSYPVFTTVVEKLKPYIAASNLSLPSDYAVAMVLSRLAHG-LSAKALASRYSL-EPYLISKITNMVTR 207 (468)
Q Consensus 132 ~d~~fr~~fRms~~~F~~L~~~L~p~l~~~~~~l~~e~~L~i~L~~La~g-~s~~~la~~Fgv-s~sTvsri~~~v~~ 207 (468)
+-+++-..++++...|..++......-.+ ..-...++.-++.++..+ .+..++|...|. +.+..++.|++...
T Consensus 3 ~~~~la~~~~~s~~~l~~~f~~~~~~s~~---~~~~~~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk~~~g 77 (84)
T smart00342 3 TLEDLAEALGMSPRHLQRLFKKETGTTPK---QYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFG 77 (84)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHhCcCHH---HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHHHHHC
Confidence 44667788999999999888765421111 112234566677777776 799999999999 99999999977653
No 53
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=81.96 E-value=1.9 Score=40.06 Aligned_cols=50 Identities=18% Similarity=0.237 Sum_probs=42.7
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
.+|...+-++.|+++ .|.++.+||..+|++..||...+.+....|.+.+.
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 136 NLPENTARVFTLKEI-LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred hCCHHHHHHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 578888888777776 79999999999999999999998888888876654
No 54
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=81.29 E-value=1.5 Score=39.75 Aligned_cols=48 Identities=10% Similarity=0.206 Sum_probs=41.5
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|+.++.++.|.++ .|.++.++|..+|++.+||...+.+....|.+.
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 588888888888777 699999999999999999998888887777654
No 55
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=81.25 E-value=2.7 Score=41.18 Aligned_cols=49 Identities=22% Similarity=0.242 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.++..++..+.|+|+ .|.++.++|..+|+|.++|+++.++...-|...+
T Consensus 203 ~L~~~~r~vl~l~y~-~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 203 QLEERTREVLEFVFL-HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred cCCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 477888888888876 5999999999999999999999988888776544
No 56
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=80.81 E-value=3 Score=38.14 Aligned_cols=50 Identities=20% Similarity=0.155 Sum_probs=42.6
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
.+|.+.+-.+.|.|+. |.++.+||..+|+|..||...+.+....|.+.+.
T Consensus 131 ~L~~~~r~v~~l~~~~-g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 131 TLPPRQRDVVQSISVE-GASIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 5788888887777666 9999999999999999999999888888876554
No 57
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=80.79 E-value=2.9 Score=38.76 Aligned_cols=49 Identities=22% Similarity=0.200 Sum_probs=42.3
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|+..+-++.|.++ .|.++.+||..+|+|.+||...+.+....|.+.|
T Consensus 116 ~Lp~~~r~i~~L~~~-~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 116 QLPDDQREAIILVGA-SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888888777 8999999999999999999988888888777654
No 58
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=80.79 E-value=2.8 Score=37.71 Aligned_cols=49 Identities=20% Similarity=0.238 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|+..+-.+.|.++ .|.++.+||..+|+|.+||.+.+.+....|.+.+
T Consensus 125 ~L~~~~r~i~~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 125 ALPVKQREVFLLRYV-EGLSYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred hCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888877777776 6999999999999999999999988877776543
No 59
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=80.77 E-value=2.8 Score=40.34 Aligned_cols=49 Identities=10% Similarity=0.100 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHhhh---ccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRL---AHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|+.++..+.|+|+ -.|.+++++|..+|+|.+||.+..++....|...
T Consensus 175 ~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred hCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 689999999999886 5789999999999999999988877776666543
No 60
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=80.68 E-value=2.8 Score=41.76 Aligned_cols=49 Identities=14% Similarity=0.152 Sum_probs=42.4
Q ss_pred CCCHHHHHHHHHhhhc-cCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLA-HGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La-~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.++..++..+.++|+. .+.++.++|..+|||+.+|+++.+....-|-..
T Consensus 230 ~L~~rEr~VL~lry~~~~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~ 279 (284)
T PRK06596 230 GLDERSRDIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAMKKLKAA 279 (284)
T ss_pred cCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4888899999999975 689999999999999999999998887766543
No 61
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=80.66 E-value=2.6 Score=40.18 Aligned_cols=50 Identities=24% Similarity=0.262 Sum_probs=43.5
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
.+|+..+-++.|+|+ .|.++.+||..+|||.+||...+++....|.+.|.
T Consensus 134 ~Lp~~~R~v~~L~y~-eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~ 183 (216)
T PRK12533 134 KLPVEYREVLVLREL-EDMSYREIAAIADVPVGTVMSRLARARRRLAALLG 183 (216)
T ss_pred cCCHHHHhHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHc
Confidence 588888888888877 69999999999999999999999888888876653
No 62
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=80.48 E-value=2.8 Score=38.77 Aligned_cols=49 Identities=14% Similarity=0.191 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|+..+-++.|+++. |.++.++|..+|+|.+||...+.+....|.+.+
T Consensus 134 ~Lp~~~R~v~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 134 HLPAQQARVFMMREYL-ELSSEQICQECDISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred hCCHHHHHHHhHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5888888888888876 999999999999999999888887777776543
No 63
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=80.46 E-value=3.1 Score=38.15 Aligned_cols=48 Identities=13% Similarity=0.073 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|+..+.++.|. +-.|.++.++|..+|+|.+||...+.+....|.+.
T Consensus 133 ~L~~~~r~i~~l~-~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 133 QLEPARRNCILHA-YVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 5888888776666 57899999999999999999999988888777643
No 64
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=80.37 E-value=0.95 Score=32.25 Aligned_cols=21 Identities=19% Similarity=0.303 Sum_probs=18.4
Q ss_pred cHHHHhhhccCCcchhHHHHH
Q 012200 183 SAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 183 s~~~la~~Fgvs~sTvsri~~ 203 (468)
+.+++|...|||.+|||++++
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 357999999999999999874
No 65
>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=80.29 E-value=3.1 Score=36.89 Aligned_cols=48 Identities=21% Similarity=0.153 Sum_probs=40.5
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
..+|+.++-.+.|.++ .|.++.++|..+|+|.+||...+++.-..|.+
T Consensus 110 ~~L~~~~r~v~~l~~~-~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQ-RGVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 3588888888888665 79999999999999999999888887766653
No 66
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=80.19 E-value=3.1 Score=38.58 Aligned_cols=50 Identities=12% Similarity=0.122 Sum_probs=41.7
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
..+|.+.+-++.|+++ .|.++.+||..+|+|.+||...+++....|...+
T Consensus 140 ~~Lp~~~r~v~~l~~~-eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 140 DRLPKAQRDVLQAVYL-EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred HhCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 3588888888888777 7999999999999999999888888777776543
No 67
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=80.10 E-value=3 Score=40.84 Aligned_cols=49 Identities=18% Similarity=0.146 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+++.++..+.|+|+ .|.++.++|..+|+|.++|+++.++...-|.+.+
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 578888888888875 6899999999999999999999988887776543
No 68
>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=80.05 E-value=2.1 Score=35.36 Aligned_cols=38 Identities=16% Similarity=0.123 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHh------hhccCccHHHHhhhccCCcchhHHHH
Q 012200 165 LPSDYAVAMVLS------RLAHGLSAKALASRYSLEPYLISKIT 202 (468)
Q Consensus 165 l~~e~~L~i~L~------~La~g~s~~~la~~Fgvs~sTvsri~ 202 (468)
++++++-++..+ .+..|.+|+.|+...|||.+||+|+=
T Consensus 33 LTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~s 76 (94)
T TIGR01321 33 LTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGS 76 (94)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHH
Confidence 455555444444 34568999999999999999998874
No 69
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=79.77 E-value=3.2 Score=38.58 Aligned_cols=49 Identities=29% Similarity=0.350 Sum_probs=42.5
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|++.+-++.|.++ .|.++.+||..+|++..||...+++....|...+
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 136 ALPERQRQAVVLRHI-EGLSNPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 588989988888877 8999999999999999999999888887776543
No 70
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=79.62 E-value=3.7 Score=37.65 Aligned_cols=48 Identities=13% Similarity=0.028 Sum_probs=40.0
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|...
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 578888777777664 899999999999999999999988887776643
No 71
>PF13730 HTH_36: Helix-turn-helix domain
Probab=79.61 E-value=3.2 Score=30.08 Aligned_cols=42 Identities=19% Similarity=0.226 Sum_probs=31.7
Q ss_pred CCH-HHHHHHHHhhhcc--Cc---cHHHHhhhccCCcchhHHHHHHHH
Q 012200 165 LPS-DYAVAMVLSRLAH--GL---SAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 165 l~~-e~~L~i~L~~La~--g~---s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
+++ +..|.+.|..++. +. ++..+++..|+|+.||.+++++..
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~ 50 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELE 50 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 444 5557777777763 22 679999999999999999987654
No 72
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=79.47 E-value=1.1 Score=45.58 Aligned_cols=68 Identities=15% Similarity=0.158 Sum_probs=47.9
Q ss_pred HHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcCCccccCCCchhhhcccccccccccCCCCCcc
Q 012200 173 MVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLYPEFIKIPISRRRLIETTQGFEELTSLPNICG 245 (468)
Q Consensus 173 i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~~~~I~~P~~~~~~~~i~~~F~~~~~fP~~vG 245 (468)
++=.|+-.|.++.++|+++|+|+++|+|++.+.-+. .+-.--|+-|. ....++.+.+++++|+..|+-
T Consensus 21 vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~---GiV~I~I~~~~--~~~~~Le~~L~~~fgLk~~iV 88 (318)
T PRK15418 21 IAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQS---GIIRVQINSRF--EGCLELENALRQHFSLQHIRV 88 (318)
T ss_pred HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHc---CcEEEEEeCCC--ccHHHHHHHHHHHhCCCEEEE
Confidence 666788889999999999999999999998765433 22222244442 233445667788888888763
No 73
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=79.33 E-value=3.1 Score=38.00 Aligned_cols=48 Identities=21% Similarity=0.270 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|.+++-++.|.++ .|.++.++|..+|+|.+||...+++...-|.+.
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 578888888888777 799999999999999999998888877776643
No 74
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=79.26 E-value=3.4 Score=38.09 Aligned_cols=48 Identities=19% Similarity=0.174 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|+..+-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.
T Consensus 111 ~Lp~~~R~v~~L~~~-eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 158 (182)
T PRK12511 111 DLPEEQRAALHLVAI-EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAF 158 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 588889988888877 599999999999999999998888777776643
No 75
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=79.00 E-value=3.7 Score=37.19 Aligned_cols=49 Identities=20% Similarity=0.236 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|++.+-++.|.++ .|.++.++|..+|+|.+||...+.+...-+...|
T Consensus 119 ~Lp~~~r~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l 167 (172)
T PRK12523 119 KLSSKARAAFLYNRL-DGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIAL 167 (172)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 578888888888776 5999999999999999999988887777766544
No 76
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=78.99 E-value=4.2 Score=36.74 Aligned_cols=50 Identities=18% Similarity=0.189 Sum_probs=41.4
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
.+|+..+-++.|.++ .|.++.++|..+|++.+||...+++....|.+.|.
T Consensus 118 ~L~~~~r~vl~L~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 167 (173)
T PRK09645 118 QLSPEHRAVLVRSYY-RGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQ 167 (173)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 488888887777665 49999999999999999998888888877776543
No 77
>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=78.81 E-value=4.1 Score=28.71 Aligned_cols=37 Identities=11% Similarity=0.201 Sum_probs=25.8
Q ss_pred HHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 170 AVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 170 ~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
+++-.|.- ..+.+..++|..+|+|.+|+++++++..+
T Consensus 7 ~Il~~l~~-~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 7 KILNYLRE-NPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp HHHHHHHH-CTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHH-cCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34333333 34589999999999999999999877653
No 78
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=78.80 E-value=3.7 Score=39.29 Aligned_cols=47 Identities=11% Similarity=0.178 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
.++..++..+.++|+ .|.++.++|..+|+|+.+|+++.++...-|..
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 578888877777664 68999999999999999999999888877654
No 79
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=78.74 E-value=3.3 Score=37.88 Aligned_cols=49 Identities=24% Similarity=0.261 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|...+-++.|.++. |.++.++|..+|+|.+||...+.+....|.+.+
T Consensus 127 ~L~~~~r~v~~l~~~~-g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 127 SLPIKYREVIYLFYYE-ELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred hCCHHHhhHhHhHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5888888888888776 999999999999999999988888777776543
No 80
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=78.72 E-value=3.5 Score=38.04 Aligned_cols=50 Identities=26% Similarity=0.261 Sum_probs=43.2
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
.+|+..+-++.|.++ .|.++.++|..+|+|.+||...+++....|.+.|.
T Consensus 111 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 111 KLPQDQREALILVGA-SGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred hCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 478888888888775 89999999999999999999999888888876654
No 81
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=78.68 E-value=2.3 Score=41.37 Aligned_cols=49 Identities=16% Similarity=0.209 Sum_probs=42.1
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|...+-++.|+++ .|.++.+||..+|||.+||...+.+....|.+.+
T Consensus 161 ~Lp~~~R~v~~L~~~-eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 161 ALSERERHLLRLHFV-DGLSMDRIGAMYQVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 588888888888777 8999999999999999999988888887776544
No 82
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=78.51 E-value=4.1 Score=37.18 Aligned_cols=48 Identities=15% Similarity=0.160 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|+..+-++.|.++ .|.++.++|...|+|.+||...+.+....|.+.
T Consensus 134 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 134 QVDPRQAEVVELRFF-AGLTVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred cCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 488888877666655 589999999999999999999888887777643
No 83
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=78.50 E-value=3.1 Score=38.45 Aligned_cols=48 Identities=19% Similarity=0.164 Sum_probs=40.3
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|++.+-++.|+++. |.++.++|..+|+|.+||...+.+....|.+.
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 4788888887777765 99999999999999999998888877776654
No 84
>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=78.23 E-value=2.7 Score=40.53 Aligned_cols=48 Identities=10% Similarity=0.105 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHhhh---ccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 164 SLPSDYAVAMVLSRL---AHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 164 ~l~~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
.++..++..+.|+|. ..|.++..+|..+|||.++|+++......-|-.
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 588889999999884 578999999999999999999998887777654
No 85
>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=78.07 E-value=3.2 Score=38.02 Aligned_cols=45 Identities=16% Similarity=0.113 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHhhhcc--------------CccHHHHhhhccCCcchhHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAH--------------GLSAKALASRYSLEPYLISKITNMVTRL 208 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~--------------g~s~~~la~~Fgvs~sTvsri~~~v~~~ 208 (468)
..+++++|+-+|.+|+. ..+..++|...|+++.||+|+++++.+-
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 45789999999887642 2478999999999999999999887654
No 86
>PRK05572 sporulation sigma factor SigF; Validated
Probab=77.87 E-value=3.9 Score=39.77 Aligned_cols=48 Identities=13% Similarity=0.235 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|..++.++.++|+ .|.++.++|..+|++.++|+++.+....-|...
T Consensus 202 ~L~~~~~~v~~l~~~-~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~ 249 (252)
T PRK05572 202 ELDERERLIVYLRYF-KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEK 249 (252)
T ss_pred cCCHHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 588888888888775 689999999999999999999999888877654
No 87
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=77.56 E-value=4.1 Score=36.12 Aligned_cols=45 Identities=20% Similarity=0.166 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
.++..++-.+.| +..|.++.++|..+|+|++||+++.++...-|.
T Consensus 6 ~Lte~qr~VL~L--r~~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr 50 (137)
T TIGR00721 6 FLTERQIKVLEL--REKGLSQKEIAKELKTTRANVSAIEKRAMENIE 50 (137)
T ss_pred CCCHHHHHHHHH--HHcCCCHHHHHHHHCcCHHHHHHHHHhHHHHHH
Confidence 467777766666 369999999999999999999988887766665
No 88
>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=77.41 E-value=1.7 Score=38.37 Aligned_cols=47 Identities=19% Similarity=0.270 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
.+|+.++-++.|.++ .|.++.++|..+|++..||...+++....|.+
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 477777777777766 79999999999999999999888887776654
No 89
>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=77.19 E-value=2.6 Score=33.78 Aligned_cols=36 Identities=8% Similarity=0.073 Sum_probs=26.8
Q ss_pred HHHHHHHHhhhccC-ccHHHHhhhccCCcchhHHHHH
Q 012200 168 DYAVAMVLSRLAHG-LSAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 168 e~~L~i~L~~La~g-~s~~~la~~Fgvs~sTvsri~~ 203 (468)
++++...+-+|..| .+..++|..||||.+||++.++
T Consensus 5 ~~R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 5 EERVLEIGKYIVETKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhc
Confidence 34555555555553 4689999999999999999763
No 90
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=77.07 E-value=4.4 Score=38.57 Aligned_cols=47 Identities=15% Similarity=0.253 Sum_probs=40.0
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
.+|+.++-++.++|+ .|.++.++|..+|+|.++|.+..+++...|..
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 578888887777765 68999999999999999999999888877654
No 91
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=77.07 E-value=4.1 Score=40.70 Aligned_cols=50 Identities=18% Similarity=0.181 Sum_probs=43.6
Q ss_pred CCCHHHHHHHHHhhh-ccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRL-AHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~L-a~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+++.++..+.|+|+ ..|.++.++|..+|||..+|+++.++...-|...|
T Consensus 227 ~L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l 277 (289)
T PRK07500 227 TLNERELRIIRERRLREDGATLEALGEELGISKERVRQIEARALEKLRRAL 277 (289)
T ss_pred cCCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 488889999999885 47899999999999999999999998888877554
No 92
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=77.04 E-value=4.3 Score=37.71 Aligned_cols=49 Identities=22% Similarity=0.224 Sum_probs=43.4
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|++++-++.|+++ .|.++.++|..+|+|..||...+.+....|.+.+
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 589999988888888 8999999999999999999999888888887654
No 93
>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=76.70 E-value=4.9 Score=36.67 Aligned_cols=47 Identities=28% Similarity=0.301 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
.+|+.++-++.|.++ .|.++.++|...|+|..||...+++....|.+
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 578888887777776 89999999999999999999988887776654
No 94
>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=76.66 E-value=4.1 Score=33.21 Aligned_cols=35 Identities=14% Similarity=0.165 Sum_probs=28.1
Q ss_pred HHHHHHHhhhccCccHHHHhhhccCCcchhHHHHH
Q 012200 169 YAVAMVLSRLAHGLSAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 169 ~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~ 203 (468)
.++.++=-.|..|.+|++|+...|+|..||+|+-+
T Consensus 37 ~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr 71 (87)
T PF01371_consen 37 QRWQVAKELLDEGKSYREIAEETGVSIATITRVSR 71 (87)
T ss_dssp HHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHH
T ss_pred HHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 34444444788999999999999999999988743
No 95
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=76.62 E-value=4.8 Score=39.25 Aligned_cols=49 Identities=14% Similarity=0.182 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|+.++-++.|+|+ .|.++.++|..+||+..||.+..++....|...+
T Consensus 205 ~L~~~~r~vl~l~~~-~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l 253 (257)
T PRK08583 205 VLSDREKSIIQCTFI-ENLSQKETGERLGISQMHVSRLQRQAIKKLREAA 253 (257)
T ss_pred hCCHHHHHHHHHHHh-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 578888877777765 7999999999999999999999988888776543
No 96
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=76.61 E-value=3.8 Score=40.76 Aligned_cols=51 Identities=14% Similarity=0.044 Sum_probs=44.6
Q ss_pred CCCHHHHHHHHHhh-h--ccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 164 SLPSDYAVAMVLSR-L--AHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 164 ~l~~e~~L~i~L~~-L--a~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
.+|..++..+.|+| | -.|.+++.+|...|+|.+||....++....|.+.|.
T Consensus 222 ~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~ 275 (285)
T TIGR02394 222 ELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILE 275 (285)
T ss_pred cCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 68999999999987 3 578999999999999999999999998888876553
No 97
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=76.52 E-value=5.4 Score=29.44 Aligned_cols=39 Identities=26% Similarity=0.419 Sum_probs=27.6
Q ss_pred HHHHHHHhhhccC-ccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 169 YAVAMVLSRLAHG-LSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 169 ~~L~i~L~~La~g-~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
..++.+|.....+ .+..+|+..+++++++++++++....
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEK 47 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3444444444433 69999999999999999999876543
No 98
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=76.40 E-value=4.3 Score=37.25 Aligned_cols=49 Identities=24% Similarity=0.268 Sum_probs=42.1
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|++++-++.|.++. |.++.++|..+|++..||...+++....|.+.|
T Consensus 128 ~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 128 ALPERQREAIVLQYYQ-GLSNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred hCCHHHHHHhhHHHhc-CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 4788888888888765 999999999999999999999888887777554
No 99
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=76.36 E-value=4.8 Score=36.94 Aligned_cols=49 Identities=22% Similarity=0.291 Sum_probs=42.6
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|+..+-++.|.++. |.++.++|..+|+|..||...+++....|.+.+
T Consensus 131 ~L~~~~r~v~~l~~~~-g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 131 RLPEKMRLAIQAVKLE-GLSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred hCCHHHHHHHHHHHHc-CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5888888888888874 999999999999999999999988888877644
No 100
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=76.33 E-value=5 Score=35.79 Aligned_cols=46 Identities=15% Similarity=0.121 Sum_probs=37.2
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
..+++.++-.+.| ...|.++.++|..+|+|++||+.+.+....-|.
T Consensus 5 ~~Lt~rqreVL~l--r~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr 50 (141)
T PRK03975 5 SFLTERQIEVLRL--RERGLTQQEIADILGTSRANVSSIEKRARENIE 50 (141)
T ss_pred cCCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3577777776666 369999999999999999999999877665544
No 101
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=76.31 E-value=3.4 Score=38.97 Aligned_cols=49 Identities=16% Similarity=0.232 Sum_probs=42.2
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|++.+-++.|.++. |.++.++|..+|++..||...+++....|.+.+
T Consensus 148 ~L~~~~r~v~~L~~~~-g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 148 GLPAKYARVFMMREFI-ELETNEICHAVDLSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5888888888887765 999999999999999999988888888877654
No 102
>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=76.10 E-value=4.5 Score=36.06 Aligned_cols=48 Identities=17% Similarity=0.121 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|++.+.++.|.+ -.|.++.++|..+|+|.+||...+.+....|.+.
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 47888888777776 5699999999999999999999988888777653
No 103
>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=76.08 E-value=2.9 Score=30.85 Aligned_cols=37 Identities=24% Similarity=0.357 Sum_probs=31.1
Q ss_pred HHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 174 VLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 174 ~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
+|..++.|.+..++|...|||..||..+...+..-+-
T Consensus 11 vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 11 VLRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp HHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 6788999999999999999999999988877665543
No 104
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=75.59 E-value=5 Score=39.20 Aligned_cols=47 Identities=11% Similarity=0.188 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
.++..++..+.++|+ .|.++.++|..+|+|.++|+++.++...-|-.
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 477778877777764 68999999999999999999999888777654
No 105
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=75.44 E-value=4.2 Score=37.52 Aligned_cols=50 Identities=10% Similarity=0.066 Sum_probs=41.4
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
.+|+..+-++.|.++ .|.++.+||..+|+|.+||...+.+....|.+.+.
T Consensus 131 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (191)
T PRK12520 131 RLPPRTGRVFMMREW-LELETEEICQELQITATNAWVLLYRARMRLRECLD 180 (191)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 488888888777765 47999999999999999999888888777765543
No 106
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=75.22 E-value=5 Score=38.60 Aligned_cols=49 Identities=20% Similarity=0.290 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|+.++-.+.|+| -.|.++.++|..+|+|.+||...+.+....|.+.|
T Consensus 184 ~L~~~~r~vl~l~~-~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 184 SLPEREQLVLSLYY-QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred hCCHHHHHHHHhHh-ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47787777777766 57899999999999999999999988888776544
No 107
>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=75.18 E-value=5.2 Score=38.45 Aligned_cols=49 Identities=16% Similarity=0.141 Sum_probs=42.6
Q ss_pred CCCHHHHHHHHHhhh---ccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRL---AHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|+.++..+.|+++ -.|.++.++|...|+|.+||.+...+....|-+.
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 589999999999986 4789999999999999999998888777776643
No 108
>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=75.08 E-value=5.6 Score=28.06 Aligned_cols=37 Identities=14% Similarity=0.099 Sum_probs=26.3
Q ss_pred HHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHH
Q 012200 170 AVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 170 ~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
++-|.........+..++++.+|++++|+++.++...
T Consensus 4 R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~ 40 (47)
T PF01022_consen 4 RLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLR 40 (47)
T ss_dssp HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHH
Confidence 3444333334557889999999999999999986654
No 109
>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=75.03 E-value=4.4 Score=37.11 Aligned_cols=49 Identities=24% Similarity=0.283 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|.+.+-++.|.++ .|.++.+||..+|++..||...+++....|.+.+
T Consensus 138 ~L~~~~r~v~~l~~~-~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 138 ALPEDLRTAITLREL-EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCHHHhhhhhhhhh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 477777777767665 8999999999999999999998888888777654
No 110
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=75.03 E-value=5.2 Score=37.09 Aligned_cols=48 Identities=19% Similarity=0.149 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|++.+.++.|+++ .|.++.+||..+|++.+||..-+.+....|.+.
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 478888887777766 789999999999999999988877776666643
No 111
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=75.00 E-value=5.4 Score=35.49 Aligned_cols=49 Identities=12% Similarity=0.135 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|+..+-++.|.+ -.|.++.++|..+|+|.+||...+.+....|.+.|
T Consensus 106 ~Lp~~~r~v~~l~~-~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 106 ELPENYRDVVLAHY-LEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred hCCHHHHHHHHHHH-HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47887777666655 56999999999999999999888888777776654
No 112
>PRK06030 hypothetical protein; Provisional
Probab=74.95 E-value=6.2 Score=34.39 Aligned_cols=47 Identities=13% Similarity=0.182 Sum_probs=41.4
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHH
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLL 209 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l 209 (468)
..+..-.|++|.|.+--+|.++.++|..||.+.|||..-++.+-+.+
T Consensus 51 k~i~~aRqIAMYL~r~~~~~sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 51 REVSRIRQIAMYVAHVSLGWPMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred cccchHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence 45778899999999999999999999999999999988887666554
No 113
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=74.61 E-value=6.1 Score=35.66 Aligned_cols=48 Identities=15% Similarity=0.148 Sum_probs=40.3
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|+..+.++.|++ -.|.++.++|..+|++.+||...+.+....+...
T Consensus 118 ~L~~~~r~v~~L~~-~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 165 (168)
T PRK12525 118 GLSGKARAAFLMSQ-LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQG 165 (168)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 58888888777765 6799999999999999999998888877777654
No 114
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=74.45 E-value=6 Score=36.17 Aligned_cols=49 Identities=22% Similarity=0.228 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|+.++.++.|++ -.|.++.++|..+|+|.+||...+++....|.+.+
T Consensus 129 ~L~~~~r~v~~l~~-~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 129 QLPDRQRLPIVHVK-LEGLSVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred HCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 47787777655554 56999999999999999999999988888777544
No 115
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=74.40 E-value=5.8 Score=35.38 Aligned_cols=46 Identities=17% Similarity=0.229 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
.+|++.+-++.|.++ .|.++.++|..+|+|.+||...+.+....+.
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 578888877666554 6999999999999999999888777766554
No 116
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=74.34 E-value=5.1 Score=36.53 Aligned_cols=48 Identities=21% Similarity=0.288 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|+.++-++.|.++ .|.++.++|..+|++..+|...+.+....|...
T Consensus 136 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLKYM-EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 588888888877766 699999999999999999999988887777654
No 117
>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=74.23 E-value=3.7 Score=30.18 Aligned_cols=29 Identities=17% Similarity=0.210 Sum_probs=24.4
Q ss_pred CccHHHHhhhccCCcchhHHHHHHHHHHH
Q 012200 181 GLSAKALASRYSLEPYLISKITNMVTRLL 209 (468)
Q Consensus 181 g~s~~~la~~Fgvs~sTvsri~~~v~~~l 209 (468)
+.+..++|..+|||++|++..+++...-|
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae~kl 51 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAERKL 51 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 45778999999999999999988776544
No 118
>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=74.11 E-value=6.5 Score=28.44 Aligned_cols=31 Identities=16% Similarity=0.126 Sum_probs=24.1
Q ss_pred ccCccHHHHhhhccCCcchhHHHHHHHHHHH
Q 012200 179 AHGLSAKALASRYSLEPYLISKITNMVTRLL 209 (468)
Q Consensus 179 a~g~s~~~la~~Fgvs~sTvsri~~~v~~~l 209 (468)
..+.+..++|+.+|||+.||.+.++..-...
T Consensus 13 ~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 13 KEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp TTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred CCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 3347899999999999999999987765443
No 119
>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=73.82 E-value=5.9 Score=38.60 Aligned_cols=46 Identities=9% Similarity=0.172 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
.++..++..+.++|+ .|.++.++|..+|+|+.+|+++.++...-|.
T Consensus 206 ~L~~rer~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~ral~kLr 251 (254)
T TIGR02850 206 RLNEREKMILNMRFF-EGKTQMEVAEEIGISQAQVSRLEKAALKHMR 251 (254)
T ss_pred cCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 577778888888764 6899999999999999999999988877665
No 120
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=73.67 E-value=5.5 Score=37.12 Aligned_cols=48 Identities=23% Similarity=0.143 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|+.++-++.| ++ .|.+++++|..+|+|.+||...+.+....|.+.+
T Consensus 155 ~L~~~~r~vl~l-~~-e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 155 LLSELEKEVLEL-YL-DGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred hCCHHHHHHHHH-HH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 477878877777 55 7999999999999999999988888777776544
No 121
>PRK06930 positive control sigma-like factor; Validated
Probab=73.61 E-value=5.7 Score=36.50 Aligned_cols=49 Identities=12% Similarity=0.196 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|+.++-++.|. +..|.++.++|..+|+|.+||...+.+...-|...+
T Consensus 114 ~L~~rer~V~~L~-~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l 162 (170)
T PRK06930 114 VLTEREKEVYLMH-RGYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQI 162 (170)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4677666555544 588999999999999999999999888877776544
No 122
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=73.58 E-value=5.8 Score=38.75 Aligned_cols=49 Identities=20% Similarity=0.325 Sum_probs=42.5
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.++-.+|+.+.|+| -.+.++..+|...|||++.||++..+.+.-|...|
T Consensus 196 ~L~EREk~Vl~l~y-~eelt~kEI~~~LgISes~VSql~kkai~kLr~~l 244 (247)
T COG1191 196 PLPEREKLVLVLRY-KEELTQKEIAEVLGISESRVSRLHKKAIKKLRKEL 244 (247)
T ss_pred ccCHHHHHHHHHHH-HhccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHh
Confidence 56778889999888 56789999999999999999999999888877654
No 123
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=73.19 E-value=5 Score=40.18 Aligned_cols=44 Identities=16% Similarity=0.132 Sum_probs=38.4
Q ss_pred CCCHHHHHHHHHhhh---ccCccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRL---AHGLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 164 ~l~~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
.+|+.++..+.|+|. ..+.++.++|..+|||+.+|..+.++...
T Consensus 249 ~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~ 295 (298)
T TIGR02997 249 ELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALR 295 (298)
T ss_pred cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 588999999999885 68899999999999999999998876554
No 124
>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=73.17 E-value=6.1 Score=32.91 Aligned_cols=42 Identities=10% Similarity=0.138 Sum_probs=35.3
Q ss_pred CHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHH
Q 012200 166 PSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRL 208 (468)
Q Consensus 166 ~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~ 208 (468)
.++++..+.++|+ .+.++.+++...++|++|+.++-+..+.-
T Consensus 57 d~~~r~iL~~~Yi-~~~~~~~I~~~l~~S~~t~yr~~~~Al~~ 98 (100)
T PF07374_consen 57 DPDERLILRMRYI-NKLTWEQIAEELNISRRTYYRIHKKALKE 98 (100)
T ss_pred ChhHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence 4677888888888 68999999999999999999998766543
No 125
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=73.15 E-value=4.5 Score=31.40 Aligned_cols=41 Identities=20% Similarity=0.250 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHhhhccCccHHHHhhhcc-CCcchhHHHHHHH
Q 012200 165 LPSDYAVAMVLSRLAHGLSAKALASRYS-LEPYLISKITNMV 205 (468)
Q Consensus 165 l~~e~~L~i~L~~La~g~s~~~la~~Fg-vs~sTvsri~~~v 205 (468)
+..-.++++.|.+-..|.++.+++..|| ...+||..-+++|
T Consensus 29 i~~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHstV~~a~~ki 70 (70)
T PF08299_consen 29 IVEARQVAMYLARELTGLSLSEIGRYFGGRDHSTVIHAIRKI 70 (70)
T ss_dssp HHHHHHHHHHHHHHHS---HHHHHHHCTSSTHHHHHHHHHHH
T ss_pred hcchHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHHhC
Confidence 4456779999999889999999999999 9999998776653
No 126
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=73.10 E-value=6.1 Score=36.43 Aligned_cols=47 Identities=15% Similarity=0.080 Sum_probs=40.8
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
.+|++++-++.|+++ .|.++.++|..+|+|..||...+.+....|..
T Consensus 131 ~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 131 DLEKLDREIFIRRYL-LGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred hCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 589999988888876 68999999999999999999888887777653
No 127
>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=73.10 E-value=7.1 Score=35.13 Aligned_cols=48 Identities=17% Similarity=0.229 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|...+-++.|.++. |.++.++|..+|++..||...+.+....|.+.
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 4788777766666665 89999999999999999998888877777643
No 128
>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=73.00 E-value=6.4 Score=38.30 Aligned_cols=48 Identities=15% Similarity=0.125 Sum_probs=40.5
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|+.++-.+.|+++ .|.++.++|..+|++.+||+...++....|...
T Consensus 205 ~L~~~~r~ii~l~~~-~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 205 ILSEREKSIIHCTFE-ENLSQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred cCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 578888887777764 699999999999999999999988888777643
No 129
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=72.78 E-value=6.8 Score=38.10 Aligned_cols=48 Identities=17% Similarity=0.111 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|+.++-.+.|+|+ .|.++.++|..+|+|..||...+++....|.+.
T Consensus 201 ~L~~~~r~vl~l~~~-~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 201 QLSEKEQLVISLFYK-EELTLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 578888888887774 899999999999999999999888877776543
No 130
>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=72.72 E-value=6.5 Score=36.36 Aligned_cols=49 Identities=12% Similarity=0.184 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|+..+-++.|.|+- |.++.++|..+|++.+||...+.+....|.+.+
T Consensus 131 ~L~~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l 179 (188)
T TIGR02943 131 HLPEQTARVFMMREVL-GFESDEICQELEISTSNCHVLLYRARLSLRACL 179 (188)
T ss_pred hCCHHHHHHHHHHHHh-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 5788887777776555 999999999999999999888888877776544
No 131
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=72.51 E-value=9 Score=33.79 Aligned_cols=44 Identities=16% Similarity=0.172 Sum_probs=36.1
Q ss_pred ccchHHHHHHHHhhhhhhcccccCCCCcHHHHHHHHHHHhhhccc
Q 012200 374 GRNVVVEAIGLLKARWKILKDLNVGINHAPQTIVACCVLHNLCQI 418 (468)
Q Consensus 374 ~R~~VE~afG~LK~RfriL~~l~~~~~~~~~iI~AccvLHN~~~~ 418 (468)
.++.||+-+..+|.|-+...++. +.+.+..++..-.+.||+.+.
T Consensus 95 ~nN~iE~~h~~~K~r~r~~~gFk-s~~~A~~~l~~~~~~~n~~r~ 138 (140)
T PF13610_consen 95 LNNRIERDHRTIKRRTRPMNGFK-SFRSAQRTLSGFEAYHNFRRP 138 (140)
T ss_pred hhChhhHhhhhhhhhcccccCcC-CHHHHHHHHHHHHHHHHHhCC
Confidence 36789999999999987776653 567788889999999999864
No 132
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=72.43 E-value=6.1 Score=36.74 Aligned_cols=43 Identities=14% Similarity=0.194 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHhhhcc-------------CccHHHHhhhccCCcchhHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAH-------------GLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~-------------g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
..++.++++-+|..++. ..+..++|...|+++.|++|++++..
T Consensus 138 ~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lG~tr~tvsR~l~~l~ 193 (211)
T PRK11753 138 FLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKMLE 193 (211)
T ss_pred hcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 46788999988887753 23468899999999999999987664
No 133
>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=72.43 E-value=8 Score=29.06 Aligned_cols=40 Identities=15% Similarity=0.260 Sum_probs=30.3
Q ss_pred HHHHHHHHHhhhc---cCccHHHHhhhccCCcchhHHHHHHHH
Q 012200 167 SDYAVAMVLSRLA---HGLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 167 ~e~~L~i~L~~La---~g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
..+.-+-+++.|. ...+-.+||..+||+++||+..+++..
T Consensus 5 ~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~ 47 (60)
T PF01325_consen 5 SEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA 47 (60)
T ss_dssp HHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH
Confidence 3455666777777 556789999999999999998877654
No 134
>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=72.40 E-value=5.4 Score=40.10 Aligned_cols=50 Identities=14% Similarity=0.076 Sum_probs=43.4
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
.+|++++.++.|.++ .|.++.+||..+|+|..||...+.+....|.+.+.
T Consensus 142 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 142 YLPPRQRAVLLLRDV-LGWRAAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred hCCHHHhhHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 588888888888776 79999999999999999999999998888876554
No 135
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=72.29 E-value=6.2 Score=36.38 Aligned_cols=48 Identities=21% Similarity=0.225 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|++++-.+.|.++ .|.++.+||..+|++..||...+.+....|...
T Consensus 138 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 185 (193)
T PRK11923 138 QLPEDLRTALTLREF-DGLSYEDIASVMQCPVGTVRSRIFRAREAIDKA 185 (193)
T ss_pred hCCHHHhHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 478888888888776 799999999999999999998888877777654
No 136
>PF13551 HTH_29: Winged helix-turn helix
Probab=72.00 E-value=4.1 Score=33.76 Aligned_cols=35 Identities=20% Similarity=0.218 Sum_probs=30.0
Q ss_pred HHhhhccCcc-HHHHhhhccCCcchhHHHHHHHHHH
Q 012200 174 VLSRLAHGLS-AKALASRYSLEPYLISKITNMVTRL 208 (468)
Q Consensus 174 ~L~~La~g~s-~~~la~~Fgvs~sTvsri~~~v~~~ 208 (468)
+|..+..|.+ ...+|..+|+|..||+++++.+..-
T Consensus 4 ~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~ 39 (112)
T PF13551_consen 4 ILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREG 39 (112)
T ss_pred HHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcc
Confidence 5667889995 9999999999999999999886543
No 137
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=71.78 E-value=7.1 Score=34.38 Aligned_cols=46 Identities=11% Similarity=0.048 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
.+|+.++-++.|.|+ .|.++.++|...|+|.+||.....+....|-
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 578888877777665 5899999999999999999988887766553
No 138
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=71.01 E-value=8.2 Score=35.25 Aligned_cols=49 Identities=12% Similarity=0.059 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|..++-.+.|++ -.|.++.++|..+|++.+||...+++....|.+.|
T Consensus 135 ~L~~~~r~vl~l~~-~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 135 ALSPEERRVIEVLY-YQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 47888888877776 45999999999999999999999888888776544
No 139
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=70.83 E-value=2.9 Score=35.99 Aligned_cols=29 Identities=17% Similarity=0.310 Sum_probs=25.9
Q ss_pred HhhhccCccHHHHhhhccCCcchhHHHHH
Q 012200 175 LSRLAHGLSAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 175 L~~La~g~s~~~la~~Fgvs~sTvsri~~ 203 (468)
|.++..|.+...+|.+|+||..||.+++.
T Consensus 12 l~~~~~g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 12 LAYIEKGKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred HHHHHccchHHHHHHHhCcHHHHHHHHHH
Confidence 45778899999999999999999998875
No 140
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=70.69 E-value=8 Score=35.60 Aligned_cols=47 Identities=23% Similarity=0.179 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
.+|++.+-++.|.++ .|.++.+||..+|+|.+||...+.+....|.+
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 578888877777655 58899999999999999999888887777764
No 141
>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=70.42 E-value=8.5 Score=36.61 Aligned_cols=47 Identities=19% Similarity=0.208 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
.+|+.++-++.|+|+ .|.++.++|..+|+|..||.+..++....|-.
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 477877777777764 78999999999999999999988887776654
No 142
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=70.11 E-value=8.9 Score=32.51 Aligned_cols=46 Identities=11% Similarity=0.181 Sum_probs=39.9
Q ss_pred CCCCCHHHHHHHHHhhhccCccHHHHhhhccC-CcchhHHHHHHHHH
Q 012200 162 NLSLPSDYAVAMVLSRLAHGLSAKALASRYSL-EPYLISKITNMVTR 207 (468)
Q Consensus 162 ~~~l~~e~~L~i~L~~La~g~s~~~la~~Fgv-s~sTvsri~~~v~~ 207 (468)
....+.+.++-++-.++..|.++..+|..||| +.++.++++.....
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~ 51 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQK 51 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 35689999999999999999999999999996 99998887765544
No 143
>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=70.05 E-value=10 Score=33.32 Aligned_cols=49 Identities=14% Similarity=0.129 Sum_probs=40.6
Q ss_pred CCHHHHHHHHHhhhcc-CccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 165 LPSDYAVAMVLSRLAH-GLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 165 l~~e~~L~i~L~~La~-g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
++.+++-.+-+.|+.. ..++..+|..+|+|++|++++-+.++.-++..|
T Consensus 83 Ld~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~l 132 (134)
T TIGR01636 83 ADEQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEEL 132 (134)
T ss_pred CCHHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 6777888888888743 349999999999999999999888888777654
No 144
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=69.74 E-value=7.5 Score=39.41 Aligned_cols=48 Identities=13% Similarity=0.122 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHHhhh---ccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 164 SLPSDYAVAMVLSRL---AHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 164 ~l~~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
.+|+.++..+.|+|. ..+.++.++|..+|||+.+|..+..+...-|..
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 588989999999886 577899999999999999999998887777664
No 145
>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=69.72 E-value=8.8 Score=28.04 Aligned_cols=27 Identities=15% Similarity=0.366 Sum_probs=22.2
Q ss_pred cCccHHHHhhhccCCcchhHHHHHHHH
Q 012200 180 HGLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 180 ~g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
.|.+..+++..+++++++++++++...
T Consensus 16 ~~~~~~~la~~~~~~~~~~t~~i~~L~ 42 (59)
T PF01047_consen 16 GGITQSELAEKLGISRSTVTRIIKRLE 42 (59)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCChhHHHHHHHHHH
Confidence 457999999999999999999876654
No 146
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=69.59 E-value=8.3 Score=36.04 Aligned_cols=49 Identities=14% Similarity=0.166 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|+..+-++.|.+ -.|.++.+||..+|+|.+||...+.+....|.+.|
T Consensus 139 ~Lp~~~r~v~~L~~-~eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 139 HLPEQIGRVFMMRE-FLDFEIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 58888888877775 56899999999999999999988888777776554
No 147
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=69.54 E-value=8.1 Score=38.03 Aligned_cols=47 Identities=17% Similarity=0.287 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
.++..++-.+.|+|+ .|.++.++|..+|+|..+|+++.+....-|..
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 477888888888775 69999999999999999999998887776654
No 148
>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=69.11 E-value=5.9 Score=29.56 Aligned_cols=27 Identities=15% Similarity=0.188 Sum_probs=22.8
Q ss_pred CccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 181 GLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 181 g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
..+..++++.+|++++|++++++....
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 367889999999999999999876654
No 149
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=68.66 E-value=9.7 Score=34.97 Aligned_cols=47 Identities=21% Similarity=0.249 Sum_probs=38.6
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
.+|+.++-++.|.|+. |.++.++|..+|++..||...+++....|-.
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 5788777777776665 8999999999999999998888777766654
No 150
>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=68.32 E-value=5.4 Score=28.76 Aligned_cols=36 Identities=17% Similarity=0.238 Sum_probs=25.6
Q ss_pred HHHHhhhc---cCccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 172 AMVLSRLA---HGLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 172 ~i~L~~La---~g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
+-.|..++ .+.+..+++...|++++|++|++.....
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 33444444 3457899999999999999999876543
No 151
>PF13751 DDE_Tnp_1_6: Transposase DDE domain
Probab=68.23 E-value=2.9 Score=35.88 Aligned_cols=49 Identities=20% Similarity=0.243 Sum_probs=34.8
Q ss_pred hhhhhcccc-hHHHHHHHHhhhhhhccccc-CCCCcHHHHHHHHHHHhhhcc
Q 012200 368 DGMLMKGRN-VVVEAIGLLKARWKILKDLN-VGINHAPQTIVACCVLHNLCQ 417 (468)
Q Consensus 368 N~~ls~~R~-~VE~afG~LK~RfriL~~l~-~~~~~~~~iI~AccvLHN~~~ 417 (468)
.+.+.+.|. .||..||.||. +--|.+++ .+...+..-+.-.|+-|||-+
T Consensus 73 ~k~~y~~R~~~VE~~fg~~K~-~~g~~r~~~rG~~kv~~~~~l~a~a~Nl~r 123 (125)
T PF13751_consen 73 GKELYKQRSIKVEGVFGTIKR-NHGLRRFRYRGLEKVRIEFLLAAIAYNLKR 123 (125)
T ss_pred hhhhhheeecccccccccchh-ccCCccccccchhhhHHHHHHHHHHHHHHH
Confidence 346677788 99999999997 55555432 356666666666677899854
No 152
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=68.20 E-value=8.5 Score=35.23 Aligned_cols=49 Identities=22% Similarity=0.267 Sum_probs=40.5
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|++.+-++.|.++ .|.+|.++|...||+.+||...+++....+.+.+
T Consensus 127 ~Lp~~~R~~~~l~~~-~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l 175 (182)
T COG1595 127 RLPPRQREAFLLRYL-EGLSYEEIAEILGISVGTVKSRLHRARKKLREQL 175 (182)
T ss_pred hCCHHHhHHhhhHhh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888777666665 5999999999999999999998888888777544
No 153
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=67.69 E-value=10 Score=34.87 Aligned_cols=49 Identities=29% Similarity=0.299 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|++++.++.|.+ -.|.++.++|..+|+|.+||...+.+....|.+.+
T Consensus 106 ~L~~~~r~i~~l~~-~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 106 ALPEKYAEALRLTE-LEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred hCCHHHHHHHHHHH-hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 47887777766665 56999999999999999999988888877776543
No 154
>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=67.14 E-value=9.5 Score=28.33 Aligned_cols=41 Identities=17% Similarity=0.194 Sum_probs=31.2
Q ss_pred HHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 171 VAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 171 L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
+-+++....+| ++...|+..|++++++++.+++.-..+-..
T Consensus 4 l~~f~~v~~~g-s~~~AA~~l~is~~~vs~~i~~LE~~lg~~ 44 (60)
T PF00126_consen 4 LRYFLAVAETG-SISAAAEELGISQSAVSRQIKQLEEELGVP 44 (60)
T ss_dssp HHHHHHHHHHS-SHHHHHHHCTSSHHHHHHHHHHHHHHHTS-
T ss_pred HHHHHHHHHhC-CHHHHHHHhhccchHHHHHHHHHHHHhCCe
Confidence 33444444444 899999999999999999999888877643
No 155
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=66.95 E-value=11 Score=34.76 Aligned_cols=47 Identities=17% Similarity=0.210 Sum_probs=36.4
Q ss_pred CCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 165 LPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 165 l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
++++..=.+.|+++ .|.++.+||...|||..||.+-....-..+...
T Consensus 136 l~~~~~~~v~l~~~-~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~~~ 182 (185)
T PF07638_consen 136 LDPRQRRVVELRFF-EGLSVEEIAERLGISERTVRRRLRRARAWLRRE 182 (185)
T ss_pred cCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 56666556666555 799999999999999999999887766555543
No 156
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=66.54 E-value=11 Score=35.48 Aligned_cols=49 Identities=14% Similarity=0.118 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|.+.+.++.|.+ -.|.++.++|..+|+|..||...+++....|.+.+
T Consensus 153 ~L~~~~r~vl~l~~-~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVY-FQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47888888766655 56899999999999999999888887777776543
No 157
>PHA00542 putative Cro-like protein
Probab=66.47 E-value=5.3 Score=32.00 Aligned_cols=29 Identities=21% Similarity=0.244 Sum_probs=25.5
Q ss_pred HHhhhccCccHHHHhhhccCCcchhHHHH
Q 012200 174 VLSRLAHGLSAKALASRYSLEPYLISKIT 202 (468)
Q Consensus 174 ~L~~La~g~s~~~la~~Fgvs~sTvsri~ 202 (468)
...+...|.+..++|...||+++|++++.
T Consensus 24 ~~~l~~~glTq~elA~~lgIs~~tIsr~e 52 (82)
T PHA00542 24 VCALIRAGWSQEQIADATDVSQPTICRIY 52 (82)
T ss_pred HHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 34557889999999999999999999986
No 158
>PF13309 HTH_22: HTH domain
Probab=66.37 E-value=7 Score=29.79 Aligned_cols=40 Identities=10% Similarity=0.169 Sum_probs=31.2
Q ss_pred CCCCHHHHHHHHHhhhccCc-----cHHHHhhhccCCcchhHHHH
Q 012200 163 LSLPSDYAVAMVLSRLAHGL-----SAKALASRYSLEPYLISKIT 202 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~-----s~~~la~~Fgvs~sTvsri~ 202 (468)
..++.++++-+.-.....|. +-..+|+.+|||+.||.+++
T Consensus 19 ~~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 19 SRLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred hhCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHc
Confidence 45777777777766666664 44679999999999999885
No 159
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=65.52 E-value=13 Score=35.59 Aligned_cols=44 Identities=16% Similarity=0.132 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHhhhcc----------CccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAH----------GLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~----------g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
..+++++++-+|..++. ..+..++|...|+++.|++|+++++.+
T Consensus 152 ~~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~L~~L~~ 205 (230)
T PRK09391 152 RKTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLQD 205 (230)
T ss_pred CCCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 46899999999988753 246789999999999999999877654
No 160
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=65.27 E-value=18 Score=40.02 Aligned_cols=49 Identities=18% Similarity=0.233 Sum_probs=44.3
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
..+..-.+++|.|.+--++.++..|+..||.+.+||...++++-+.|.+
T Consensus 551 ~~i~~aRqiAMYL~r~lt~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~~ 599 (617)
T PRK14086 551 RVLVTARQIAMYLCRELTDLSLPKIGQQFGRDHTTVMHADRKIRALMAE 599 (617)
T ss_pred cccchHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHh
Confidence 4677888999999999999999999999999999999999888887764
No 161
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=65.20 E-value=12 Score=34.52 Aligned_cols=49 Identities=16% Similarity=0.093 Sum_probs=40.0
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|..++-++.|+| -.|.++.++|...|++.+||...+++....|...+
T Consensus 142 ~L~~~~r~vl~l~~-~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAY-YGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 57888877666655 56899999999999999999998888887776544
No 162
>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=65.09 E-value=4 Score=29.40 Aligned_cols=27 Identities=41% Similarity=0.546 Sum_probs=21.9
Q ss_pred hhccCccHHHHhhhccCCcchhHHHHH
Q 012200 177 RLAHGLSAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 177 ~La~g~s~~~la~~Fgvs~sTvsri~~ 203 (468)
+-..|.++.++|...|++++|++++.+
T Consensus 5 r~~~gls~~~la~~~gis~~~i~~~~~ 31 (55)
T PF01381_consen 5 RKEKGLSQKELAEKLGISRSTISRIEN 31 (55)
T ss_dssp HHHTTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHcCCCHHHHHHHhCCCcchhHHHhc
Confidence 446899999999999999999999863
No 163
>PRK01381 Trp operon repressor; Provisional
Probab=65.06 E-value=8.9 Score=31.97 Aligned_cols=25 Identities=16% Similarity=0.181 Sum_probs=21.3
Q ss_pred hccCccHHHHhhhccCCcchhHHHH
Q 012200 178 LAHGLSAKALASRYSLEPYLISKIT 202 (468)
Q Consensus 178 La~g~s~~~la~~Fgvs~sTvsri~ 202 (468)
+..+.+|+.|+...|||.+||+|.-
T Consensus 52 ~~g~~sQREIa~~lGvSiaTITRgs 76 (99)
T PRK01381 52 LRGELSQREIKQELGVGIATITRGS 76 (99)
T ss_pred HcCCcCHHHHHHHhCCceeeehhhH
Confidence 3445899999999999999998764
No 164
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=65.03 E-value=10 Score=33.92 Aligned_cols=49 Identities=24% Similarity=0.135 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|++.+-++.|+ +-.|.++.++|..+|+|..||...+.+....|...+
T Consensus 108 ~L~~~~r~v~~l~-~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 108 TLPVIEAQAILLC-DVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred hCCHHHHHHHHhH-HHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5777777765555 556899999999999999999988888888776543
No 165
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=64.64 E-value=11 Score=30.09 Aligned_cols=38 Identities=29% Similarity=0.342 Sum_probs=28.7
Q ss_pred HHHHHHhhhcc---CccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 170 AVAMVLSRLAH---GLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 170 ~L~i~L~~La~---g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
+..-.|.+|+. +.+..+++..+|++++|+++++.....
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34444555543 478999999999999999999876643
No 166
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=64.47 E-value=12 Score=33.15 Aligned_cols=49 Identities=18% Similarity=0.275 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|++.+-++.|. +-.|.++.++|..+|+|.+||...+.+....|.+.+
T Consensus 105 ~L~~~~r~v~~l~-~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 105 ELPPACRDSFLLR-KLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788877766664 567999999999999999999988888777776543
No 167
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=64.45 E-value=4.1 Score=41.40 Aligned_cols=68 Identities=16% Similarity=0.174 Sum_probs=45.5
Q ss_pred HHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcCCccccCCCchhhhcccccccccccCCCCCcc
Q 012200 173 MVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLYPEFIKIPISRRRLIETTQGFEELTSLPNICG 245 (468)
Q Consensus 173 i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~~~~I~~P~~~~~~~~i~~~F~~~~~fP~~vG 245 (468)
++=.||-.|.++.++|+++|||+.+|+|.+...-+ +.+-+-.|.-| .. ..-++.+..++++|++.|+-
T Consensus 18 ~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~---~GiV~I~i~~~-~~-~~~~Le~~L~~~fgL~~a~V 85 (321)
T COG2390 18 AAWLYYVEGLTQSEIAERLGISRATVSRLLAKARE---EGIVKISINSP-VE-GCLELEQQLKERFGLKEAIV 85 (321)
T ss_pred HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH---CCeEEEEeCCC-Cc-chHHHHHHHHHhcCCCeEEE
Confidence 45567788999999999999999999998755432 23333334433 22 22234556777778887763
No 168
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=64.31 E-value=13 Score=28.62 Aligned_cols=40 Identities=13% Similarity=0.105 Sum_probs=31.5
Q ss_pred CHHHHHHHHHhhhcc-CccHHHHhhhccCCcchhHHHHHHH
Q 012200 166 PSDYAVAMVLSRLAH-GLSAKALASRYSLEPYLISKITNMV 205 (468)
Q Consensus 166 ~~e~~L~i~L~~La~-g~s~~~la~~Fgvs~sTvsri~~~v 205 (468)
+.+++++.+|..-+. |.+..+|+...|+++++|++++...
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L 46 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSL 46 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 456777777776655 5899999999999999998886544
No 169
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=64.06 E-value=23 Score=30.37 Aligned_cols=72 Identities=11% Similarity=0.057 Sum_probs=47.0
Q ss_pred ChhhHHHhcCCCHHHHHHHHHHhcccccc-C---CCCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHH
Q 012200 132 REAHWRSLYGLSYPVFTTVVEKLKPYIAA-S---NLSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMV 205 (468)
Q Consensus 132 ~d~~fr~~fRms~~~F~~L~~~L~p~l~~-~---~~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v 205 (468)
+-.+--..|++++.++...+...+..-.. . ...+.. ..+..+.-=-...+..+++..||||.+|+++.++..
T Consensus 20 s~~eaa~~F~VS~~Tv~~W~k~~~~G~~~~k~r~~~Kid~--~~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrl 95 (119)
T PF01710_consen 20 SIREAAKRFGVSRNTVYRWLKRKETGDLEPKPRGRKKIDR--DELKALVEENPDATLRELAERLGVSPSTIWRALKRL 95 (119)
T ss_pred hHHHHHHHhCcHHHHHHHHHHhcccccccccccccccccH--HHHHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHc
Confidence 55667778999999999988844432111 1 113432 223333333455688999999999999998887554
No 170
>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=63.88 E-value=14 Score=33.45 Aligned_cols=49 Identities=24% Similarity=0.308 Sum_probs=40.0
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|++.+.++.|.+ -.|.++.++|..+|++..||...+.+....|...+
T Consensus 100 ~L~~~~r~v~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 100 ELPDEYREAIRLTE-LEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 57888777776665 46899999999999999999988888777776543
No 171
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.79 E-value=13 Score=31.04 Aligned_cols=41 Identities=15% Similarity=0.154 Sum_probs=33.2
Q ss_pred HHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 169 YAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 169 ~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
++--+-| |+....|...+|+.|+||+++|+..++++...+.
T Consensus 22 Q~~Y~~l-yy~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~ 62 (105)
T COG2739 22 QKNYLEL-YYLDDLSLSEIAEEFNVSRQAIYDNIKRTEKILE 62 (105)
T ss_pred HHHHHHH-HHHhhccHHHHHHHhCccHHHHHHHHHHHHHHHH
Confidence 3344444 4556789999999999999999999999998876
No 172
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=63.75 E-value=7.4 Score=37.26 Aligned_cols=49 Identities=24% Similarity=0.329 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|.+.+-++.|+++. |.++++||..+|+|.+||...+.+....|-+.+
T Consensus 149 ~L~~~~r~i~~l~~~~-g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 149 ALPDAFRAVFVLRVVE-ELSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred hCCHHHhhhheeehhc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4788777776666654 999999999999999999988888777776544
No 173
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=63.72 E-value=10 Score=36.52 Aligned_cols=49 Identities=18% Similarity=0.214 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|..++-++.|+| -.|.++.+||..+|+|.+||...+++....|.+.+
T Consensus 171 ~Lp~~~R~v~~L~~-~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 171 RLPEQQRIAVILSY-HENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred hCCHHHHHHhhhHH-hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 46777777666555 56999999999999999999988888888776543
No 174
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=63.71 E-value=15 Score=34.78 Aligned_cols=64 Identities=13% Similarity=0.039 Sum_probs=45.3
Q ss_pred CCCHHHHHHHHHhhhccC----ccHHHHhhhccCCcchhHHHHHHHHHH-HHhhcCCccccCCCchhhhcc
Q 012200 164 SLPSDYAVAMVLSRLAHG----LSAKALASRYSLEPYLISKITNMVTRL-LATKLYPEFIKIPISRRRLIE 229 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g----~s~~~la~~Fgvs~sTvsri~~~v~~~-l~~~L~~~~I~~P~~~~~~~~ 229 (468)
..+++++++-+|..+..+ .+..++|...|+++.|++|.++++.+- +.+ .....|..+ +.+.+..
T Consensus 148 ~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~-~~~~~i~I~-d~~~L~~ 216 (226)
T PRK10402 148 SFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLK-KSKRGYLIK-NRKQLSG 216 (226)
T ss_pred cChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEE-eeCCEEEEe-CHHHHHH
Confidence 458899999999876543 367899999999999999999887764 332 233445555 4444443
No 175
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=63.63 E-value=14 Score=33.89 Aligned_cols=49 Identities=8% Similarity=0.041 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|+..+-++.|.+ -.|.++.++|..+|+|.+||...+.+....|...+
T Consensus 122 ~L~~~~r~i~~l~~-~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 122 ELNESNRQVFKYKV-FYNLTYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 57777776666554 46899999999999999999888888777776543
No 176
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=63.50 E-value=11 Score=36.36 Aligned_cols=49 Identities=16% Similarity=0.049 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|++.+.++.|.++. |.++++||...|+|.+||...+.+....|.+.+
T Consensus 116 ~Lp~~~R~v~lL~~~e-g~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l 164 (228)
T PRK06704 116 SLNVQQSAILLLKDVF-QYSIADIAKVCSVSEGAVKASLFRSRNRLKTVS 164 (228)
T ss_pred hCCHHHhhHhhhHHhh-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5788888877776654 899999999999999999988888888877544
No 177
>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=63.46 E-value=7.2 Score=36.00 Aligned_cols=49 Identities=18% Similarity=0.236 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|+..+-++.|.+ -.|.++.+||...|+|.+||...+.+....|.+.|
T Consensus 131 ~Lp~~~r~i~~L~~-~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 131 GLPEEFRQAVYLAD-VEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred hCCHHHhhheeehh-hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47777777766654 56899999999999999999988888877776543
No 178
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=63.41 E-value=12 Score=36.03 Aligned_cols=46 Identities=17% Similarity=0.212 Sum_probs=38.6
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
.++..++-.+.|+| ..|.++..+|..+|+|+++|+++.+....-|.
T Consensus 183 ~L~~~er~vi~l~~-~~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr 228 (231)
T PRK12427 183 QLDEREQLILHLYY-QHEMSLKEIALVLDLTEARICQLNKKIAQKIK 228 (231)
T ss_pred cCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 47787888888877 46899999999999999999999887776553
No 179
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=62.98 E-value=12 Score=36.75 Aligned_cols=48 Identities=19% Similarity=0.239 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|+.++-++.|+|+ .|.++.++|..+|++.+||.+..++...-|...
T Consensus 212 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 212 TLPEREKKVLILYYY-EDLTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 578887777777764 689999999999999999998887777666543
No 180
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=62.91 E-value=13 Score=33.87 Aligned_cols=49 Identities=16% Similarity=0.190 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|+..+-++.|. +-.|.++.+||..+|+|.+||...+++....|.+.|
T Consensus 117 ~Lp~~~r~i~~l~-~~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 117 KLPYKLRQVIILR-YLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred hCCHHHHHHHHHH-HHccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5888888777775 456889999999999999999888877777766543
No 181
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=62.64 E-value=13 Score=33.17 Aligned_cols=46 Identities=20% Similarity=0.138 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
.+|+..+.++.|.++ .|.++.++|..+|+|..||...+++....|.
T Consensus 112 ~L~~~~r~v~~l~~~-~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~ 157 (161)
T PRK12541 112 SLPLERRNVLLLRDY-YGFSYKEIAEMTGLSLAKVKIELHRGRKETK 157 (161)
T ss_pred HCCHHHHHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 578888887766654 5899999999999999999888877776665
No 182
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=62.46 E-value=6.2 Score=29.62 Aligned_cols=29 Identities=31% Similarity=0.331 Sum_probs=22.6
Q ss_pred HHhhhccCccHHHHhhhccCCcchhHHHH
Q 012200 174 VLSRLAHGLSAKALASRYSLEPYLISKIT 202 (468)
Q Consensus 174 ~L~~La~g~s~~~la~~Fgvs~sTvsri~ 202 (468)
--.+-+.|.++.++|...|+|++++++|-
T Consensus 7 r~~R~~~gls~~~lA~~~g~s~s~v~~iE 35 (64)
T PF13560_consen 7 RRLRERAGLSQAQLADRLGVSQSTVSRIE 35 (64)
T ss_dssp HHHHHCHTS-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 34555679999999999999999999884
No 183
>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=62.38 E-value=13 Score=30.60 Aligned_cols=29 Identities=14% Similarity=0.122 Sum_probs=24.0
Q ss_pred hccCccHHHHhhhccCCcchhHHHHHHHH
Q 012200 178 LAHGLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 178 La~g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
...+.+..++|...|+++.||+|++++..
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le 72 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLA 72 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 34567889999999999999999876654
No 184
>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=62.35 E-value=15 Score=30.79 Aligned_cols=41 Identities=10% Similarity=0.079 Sum_probs=31.0
Q ss_pred HHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 170 AVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 170 ~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
|--++-.|+-...|...||..+|||+.+|+..+++....|.
T Consensus 22 Q~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~ 62 (101)
T PF04297_consen 22 QREILELYYEEDLSLSEIAEELGISRQAVYDSIKRAEKKLE 62 (101)
T ss_dssp HHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 34445567778999999999999999999999999888876
No 185
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=62.22 E-value=11 Score=34.06 Aligned_cols=48 Identities=10% Similarity=0.091 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|++.+- +++.++-.|.++.++|...|+|..||...+.+....|.+.
T Consensus 119 ~L~~~~r~-i~~l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 119 LLNEKYKT-VLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred hCCHHHHH-HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 46666654 4445566799999999999999999999988888887754
No 186
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=61.96 E-value=15 Score=34.18 Aligned_cols=50 Identities=16% Similarity=0.141 Sum_probs=40.8
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
.+|+..+-++.|.++ .|.++.+||..+|+|..||...+.+....|.+.|.
T Consensus 133 ~Lp~~~r~v~~l~~~-~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 133 ALPPERREALILTQV-LGYTYEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred cCCHHHHHHhhhHHH-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 478888777777655 57889999999999999999888888888776543
No 187
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=61.94 E-value=13 Score=38.71 Aligned_cols=47 Identities=13% Similarity=0.077 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHHhhh---ccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRL---AHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 164 ~l~~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
.++..++..+.++|+ ..+.++..||..+|||+.+|+.+-.....-|-
T Consensus 311 ~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR 360 (373)
T PRK07406 311 TLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 360 (373)
T ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHh
Confidence 578888888999886 34689999999999999999999888777665
No 188
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=61.87 E-value=14 Score=37.66 Aligned_cols=50 Identities=16% Similarity=0.090 Sum_probs=42.7
Q ss_pred CCCHHHHHHHHHhh-h--ccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSR-L--AHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~-L--a~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.++..++..+.++| | -.|.++..+|...||+.+||..+.++....|.+.|
T Consensus 262 ~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 68888888888776 3 46899999999999999999999988888877654
No 189
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=61.82 E-value=8.1 Score=25.34 Aligned_cols=25 Identities=16% Similarity=0.268 Sum_probs=19.4
Q ss_pred ccHHHHhhhccCCcchhHHHHHHHH
Q 012200 182 LSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 182 ~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
.+.+++|+..|.+..||+|++..+-
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 4678999999999999999987653
No 190
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=61.27 E-value=25 Score=37.35 Aligned_cols=48 Identities=15% Similarity=0.232 Sum_probs=43.6
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhhhc-cCCcchhHHHHHHHHHHHH
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALASRY-SLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~~F-gvs~sTvsri~~~v~~~l~ 210 (468)
+.+..-.+++|.|.+--+|.++.++|..| |.+.+||...++++-..+.
T Consensus 384 ~~~~~aR~iamyl~~~~~~~s~~~Ig~~fg~rdhstV~~a~~~i~~~~~ 432 (450)
T PRK00149 384 RNIARPRQIAMYLAKELTDLSLPEIGRAFGGRDHTTVLHAVRKIEKLLE 432 (450)
T ss_pred cccChHHHHHHHHHHHhcCCCHHHHHHHcCCCCHhHHHHHHHHHHHHHH
Confidence 56778899999999999999999999999 5999999999999888775
No 191
>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=61.17 E-value=11 Score=28.25 Aligned_cols=35 Identities=26% Similarity=0.340 Sum_probs=24.8
Q ss_pred HHhhhc---cCccHHHHhhhccCCcchhHHHHHHHHHH
Q 012200 174 VLSRLA---HGLSAKALASRYSLEPYLISKITNMVTRL 208 (468)
Q Consensus 174 ~L~~La---~g~s~~~la~~Fgvs~sTvsri~~~v~~~ 208 (468)
+|++++ .+.+..++++.++++++++++.+++..+.
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 455555 45678999999999999999988776543
No 192
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=60.96 E-value=8.4 Score=35.56 Aligned_cols=49 Identities=14% Similarity=0.162 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|+..+-++.|++ -.|.++.++|...|+|.+||...+.+....|.+.+
T Consensus 139 ~L~~~~r~i~~l~~-~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 139 TLPDEQREVFLLRE-HGDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred hCCHhHhhheeeeh-ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47777777666654 67999999999999999999888877777776544
No 193
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=60.95 E-value=13 Score=38.54 Aligned_cols=47 Identities=13% Similarity=0.071 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHhhhc---cCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLA---HGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La---~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
.++..++..+.|+|.- .+.++..||..||||+..|++|-.+.+.-|-
T Consensus 305 ~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr 354 (367)
T PRK09210 305 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 354 (367)
T ss_pred hCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 5788888888888852 5589999999999999999999877666554
No 194
>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=60.70 E-value=13 Score=34.23 Aligned_cols=44 Identities=20% Similarity=0.089 Sum_probs=32.7
Q ss_pred CHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 166 PSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 166 ~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
+...+.++ +.++ .|.++.+||..+|+|.+||...+++....|..
T Consensus 152 ~~~~~~i~-~~~~-~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 152 SDLEWKVL-QSYL-DGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred CHHHHHHH-HHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34444444 4454 89999999999999999998877777666543
No 195
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=60.70 E-value=7.5 Score=35.10 Aligned_cols=50 Identities=18% Similarity=0.143 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
.+|..++-++.|++ -.|.++.++|..+|+|..||...+.+....|.+.+.
T Consensus 120 ~L~~~~r~vl~l~~-~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 120 TLSLEHRAVLVLHD-LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred hCCHHHeeeeeehH-hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46777776655554 458889999999999999999998888888776543
No 196
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=60.30 E-value=13 Score=32.60 Aligned_cols=43 Identities=14% Similarity=0.114 Sum_probs=30.8
Q ss_pred CCCHHH-HHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHH
Q 012200 164 SLPSDY-AVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 164 ~l~~e~-~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
.+++.+ .++..|+....|.+..++++.+|++++|+++++++..
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 355433 4555555444567899999999999999998876654
No 197
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=60.29 E-value=16 Score=33.76 Aligned_cols=49 Identities=18% Similarity=0.254 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|...+-++.|. +-.|.++.+||...|+|.+||...+.+....|.+.+
T Consensus 128 ~Lp~~~r~v~~l~-~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 128 KLDPEYREPLLLQ-VIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred hCCHHHHHHHHHH-HHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4777777765555 455999999999999999999988888877777544
No 198
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=59.80 E-value=16 Score=34.63 Aligned_cols=43 Identities=12% Similarity=0.152 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHhhhcc--------------CccHHHHhhhccCCcchhHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAH--------------GLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~--------------g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
..+++++++-+|..+.. ..+..++|...|+++.|++|++++..
T Consensus 153 ~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~ 209 (235)
T PRK11161 153 KKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQ 209 (235)
T ss_pred CCCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCCcHHHHHHHHHHHH
Confidence 46889999999988763 24778999999999999999986654
No 199
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=59.36 E-value=11 Score=34.99 Aligned_cols=45 Identities=18% Similarity=0.152 Sum_probs=36.2
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHH
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLL 209 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l 209 (468)
..+++.++ =+|..++.|.+.+++|...++|..||..++..+..-+
T Consensus 132 ~~LSpREr--EVLrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKL 176 (198)
T PRK15201 132 RHFSVTER--HLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKL 176 (198)
T ss_pred CCCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 35777554 3577899999999999999999999998877665544
No 200
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=59.22 E-value=15 Score=38.78 Aligned_cols=47 Identities=15% Similarity=0.092 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHhhh---ccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRL---AHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 164 ~l~~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
.+++.++-.+.|+|. ..+.++.+||..+|+|..+|..+.++....|.
T Consensus 350 ~L~~reR~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~KLR 399 (415)
T PRK07598 350 DLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLR 399 (415)
T ss_pred hCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHh
Confidence 578888888888885 35689999999999999999999887766665
No 201
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=58.90 E-value=10 Score=35.72 Aligned_cols=45 Identities=13% Similarity=0.193 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
.+++.++ =.|..++.|.+.+++|.+.++|..||..++..+..-+.
T Consensus 137 ~LT~RE~--eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 137 SLSRTES--SMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 3666554 36788999999999999999999999999877765554
No 202
>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=58.68 E-value=36 Score=27.96 Aligned_cols=56 Identities=25% Similarity=0.265 Sum_probs=35.4
Q ss_pred CCHHHHHHHHHHhccccccCCCCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHH
Q 012200 142 LSYPVFTTVVEKLKPYIAASNLSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 142 ms~~~F~~L~~~L~p~l~~~~~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
++.+.|.-|++.- ++..+.-+...=.+|-.|.+-..++.++||+++..++.+++.-
T Consensus 23 vs~e~F~lLl~ls---------~IrS~kiI~AL~dyLV~G~srkeac~~~gV~~syfs~~L~rL~ 78 (91)
T PF03333_consen 23 VSEEHFWLLLELS---------SIRSEKIIAALRDYLVDGLSRKEACERHGVNQSYFSRALNRLN 78 (91)
T ss_dssp S-HHHHHHHHHHS-------------HHHHHHHHHHHTT---HHHHHHHTT--HHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHC---------CCCcHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 6777787777763 3455555555556889999999999999999999998776543
No 203
>PRK05949 RNA polymerase sigma factor; Validated
Probab=58.61 E-value=16 Score=37.32 Aligned_cols=48 Identities=15% Similarity=0.129 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHhhh---ccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 164 SLPSDYAVAMVLSRL---AHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 164 ~l~~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
.+++.++-.+.|+|. ..+.++.+||..+|+|..+|..+..+...-|..
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 578888888888874 367899999999999999999998887777654
No 204
>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=58.56 E-value=12 Score=39.01 Aligned_cols=63 Identities=24% Similarity=0.339 Sum_probs=39.8
Q ss_pred HHhhhccCccHHHHh----hhcc---CCcchhHHHHHHHHHHHHhhcCCccccCCCchhhhcccccccccccCCCCCccc
Q 012200 174 VLSRLAHGLSAKALA----SRYS---LEPYLISKITNMVTRLLATKLYPEFIKIPISRRRLIETTQGFEELTSLPNICGA 246 (468)
Q Consensus 174 ~L~~La~g~s~~~la----~~Fg---vs~sTvsri~~~v~~~l~~~L~~~~I~~P~~~~~~~~i~~~F~~~~~fP~~vGa 246 (468)
.+..+..|.|.+++. ..+| +|++|||+++..+.+.+.. |- ...+ .+.|-++-.
T Consensus 107 i~~ly~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~~--------w~--~R~L----------~~~~y~~l~ 166 (381)
T PF00872_consen 107 IISLYLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVEA--------WR--NRPL----------ESEPYPYLW 166 (381)
T ss_pred hhhhhccccccccccchhhhhhcccccCchhhhhhhhhhhhhHHH--------Hh--hhcc----------cccccccee
Confidence 334467788777754 4456 8999999998877665542 21 0011 122234558
Q ss_pred cceeeEEecc
Q 012200 247 IDGSHIKIGN 256 (468)
Q Consensus 247 IDgT~I~i~~ 256 (468)
|||+++++..
T Consensus 167 iD~~~~kvr~ 176 (381)
T PF00872_consen 167 IDGTYFKVRE 176 (381)
T ss_pred eeeeeccccc
Confidence 9999999873
No 205
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=58.42 E-value=20 Score=26.32 Aligned_cols=24 Identities=13% Similarity=0.171 Sum_probs=19.8
Q ss_pred cHHHHhhhccCCcchhHHHHHHHH
Q 012200 183 SAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 183 s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
+.++++..||+|++++++.+....
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~ 50 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELE 50 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 477899999999999988776554
No 206
>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=58.37 E-value=13 Score=28.53 Aligned_cols=28 Identities=14% Similarity=0.181 Sum_probs=23.2
Q ss_pred CccHHHHhhhccCCcchhHHHHHHHHHH
Q 012200 181 GLSAKALASRYSLEPYLISKITNMVTRL 208 (468)
Q Consensus 181 g~s~~~la~~Fgvs~sTvsri~~~v~~~ 208 (468)
+.+..++|...|+|+.|++++++++.+-
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~ 55 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKDE 55 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3467899999999999999998776543
No 207
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=57.68 E-value=12 Score=31.73 Aligned_cols=48 Identities=23% Similarity=0.246 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+++++-=++-|..+ .|.++.+.|.+.|||++|++++++..-.-|++.
T Consensus 41 ~L~~dElEAiRL~D~-egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~A 88 (106)
T PF02001_consen 41 VLTVDELEAIRLVDY-EGLSQEEAAERMGVSRPTFQRILESARKKIADA 88 (106)
T ss_pred EeeHHHHHHHHHHHH-cCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHH
Confidence 456666555555555 479999999999999999999997655555443
No 208
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=57.35 E-value=19 Score=30.79 Aligned_cols=46 Identities=7% Similarity=0.019 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
.++.+++-+ ...++.+..+.++++..+|||-+||..-+++++..|-
T Consensus 33 ~L~~E~~~F-i~~Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg 78 (113)
T PF09862_consen 33 RLSPEQLEF-IKLFIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLG 78 (113)
T ss_pred cCCHHHHHH-HHHHHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhC
Confidence 456665544 5556667778999999999999999999998888875
No 209
>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=56.91 E-value=36 Score=28.75 Aligned_cols=42 Identities=12% Similarity=0.143 Sum_probs=29.3
Q ss_pred CCCHHH-HHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHH
Q 012200 164 SLPSDY-AVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 164 ~l~~e~-~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
.++..+ .++..|.. ..+.+..++++..|++++|+++.+++..
T Consensus 25 ~lt~~q~~iL~~l~~-~~~~t~~ela~~~~~~~~tvs~~l~~Le 67 (118)
T TIGR02337 25 GLTEQQWRILRILAE-QGSMEFTQLANQACILRPSLTGILARLE 67 (118)
T ss_pred CCCHHHHHHHHHHHH-cCCcCHHHHHHHhCCCchhHHHHHHHHH
Confidence 355433 34444432 4567899999999999999998876654
No 210
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=56.79 E-value=8.5 Score=26.29 Aligned_cols=29 Identities=21% Similarity=0.330 Sum_probs=21.9
Q ss_pred hccCccHHHHhhhccCCcchhHHHHHHHH
Q 012200 178 LAHGLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 178 La~g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
+.++.+..++|..+|+|.+..+|.|++..
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 56678889999999999999999998764
No 211
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=56.61 E-value=10 Score=27.36 Aligned_cols=24 Identities=13% Similarity=0.212 Sum_probs=20.4
Q ss_pred cHHHHhhhccCCcchhHHHHHHHH
Q 012200 183 SAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 183 s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
+.++++..||+|++|+++.+....
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~ 45 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLE 45 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 678899999999999998876554
No 212
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=56.38 E-value=21 Score=33.90 Aligned_cols=63 Identities=16% Similarity=0.083 Sum_probs=43.9
Q ss_pred CCCHHHHHHHHHhhhccC----------ccHHHHhhhccCCcchhHHHHHHHHHHHHhhcCCccccCCCchhhhc
Q 012200 164 SLPSDYAVAMVLSRLAHG----------LSAKALASRYSLEPYLISKITNMVTRLLATKLYPEFIKIPISRRRLI 228 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g----------~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~~~~I~~P~~~~~~~ 228 (468)
..+++.+++-+|..++.. .+..++|...|+++.|++|++++..+-=. .+....|..+ +.+.++
T Consensus 146 ~~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~lG~tretvsR~l~~L~~~gl-~~~~~~i~I~-d~~~L~ 218 (236)
T PRK09392 146 LRSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYLGMTPENLSRAFAALASHGV-HVDGSAVTIT-DPAGLA 218 (236)
T ss_pred cCCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHhCCChhHHHHHHHHHHhCCe-EeeCCEEEEc-CHHHHH
Confidence 468999999999877642 33578999999999999999987654422 2233455555 444444
No 213
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=56.29 E-value=14 Score=26.68 Aligned_cols=28 Identities=18% Similarity=0.097 Sum_probs=23.6
Q ss_pred ccCccHHHHhhhccCCcchhHHHHHHHH
Q 012200 179 AHGLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 179 a~g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
....+..+++..+|+++++++++++...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~ 35 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLR 35 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4557889999999999999999886654
No 214
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=56.00 E-value=8.4 Score=35.43 Aligned_cols=48 Identities=13% Similarity=-0.031 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|.+++=++.|.+ -.|.++.+||..+|+|.+||...+.+....|-+.
T Consensus 134 ~L~~~~r~v~~l~~-~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 134 HVNPIDREILVLRF-VAELEFQEIADIMHMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred hcChhheeeeeeHH-hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45666555444444 4789999999999999999988888877777654
No 215
>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=55.87 E-value=31 Score=33.09 Aligned_cols=46 Identities=13% Similarity=0.065 Sum_probs=36.6
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
..++..++=.+.+ .+.|.++.++|..+|+|..||...+.....-+.
T Consensus 170 ~~Lt~re~evl~~--~a~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~ 215 (232)
T TIGR03541 170 GVLSEREREVLAW--TALGRRQADIAAILGISERTVENHLRSARRKLG 215 (232)
T ss_pred ccCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence 4677766655444 589999999999999999999988877765554
No 216
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=55.76 E-value=11 Score=25.90 Aligned_cols=29 Identities=14% Similarity=0.169 Sum_probs=23.4
Q ss_pred ccCccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 179 AHGLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 179 a~g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
.-..+..++++.+|++++|++++++...+
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34567889999999999999988866543
No 217
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=55.24 E-value=18 Score=32.70 Aligned_cols=46 Identities=17% Similarity=0.147 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
.+|++.+-++ +.++-.|.++.++|..+|++..||...+++....+-
T Consensus 119 ~L~~~~r~i~-~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 119 GLNGKTREAF-LLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred hCCHHHhHHh-hhhhccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4677666554 455556899999999999999999888777666654
No 218
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=55.19 E-value=20 Score=38.15 Aligned_cols=47 Identities=13% Similarity=0.163 Sum_probs=42.7
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHH
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLL 209 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l 209 (468)
..+..-.+++|.|.+=-+|.++.++|..||.+.+||...++++-..+
T Consensus 369 ~~i~~aR~iamyl~r~~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 369 VKALLARRIGMYVAKNYLGSSLRTIAEKFNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred ccccHHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 46777888999999999999999999999999999999999888865
No 219
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=54.98 E-value=21 Score=33.46 Aligned_cols=49 Identities=24% Similarity=0.338 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+++..+-.+.|.+ -.|.++.++|..+|++..||...+.+....|.+.+
T Consensus 138 ~L~~~~r~v~~L~~-~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 138 SLPPEFRAAVVLCD-IEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47777766665654 67999999999999999999998888877776544
No 220
>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=54.32 E-value=21 Score=26.46 Aligned_cols=27 Identities=22% Similarity=0.260 Sum_probs=22.7
Q ss_pred ccCccHHHHhhhccCCcchhHHHHHHH
Q 012200 179 AHGLSAKALASRYSLEPYLISKITNMV 205 (468)
Q Consensus 179 a~g~s~~~la~~Fgvs~sTvsri~~~v 205 (468)
..+.+..+++..+|++.+++++.++..
T Consensus 18 ~~~~~~~ei~~~~~i~~~~i~~~l~~L 44 (78)
T cd00090 18 EGPLTVSELAERLGLSQSTVSRHLKKL 44 (78)
T ss_pred HCCcCHHHHHHHHCcCHhHHHHHHHHH
Confidence 344889999999999999998887664
No 221
>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=53.99 E-value=22 Score=35.15 Aligned_cols=48 Identities=15% Similarity=0.105 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|+.++-++.|.+ -.|.++.++|..+|+|..||...+++....|.+.
T Consensus 108 ~L~~~~R~v~~L~~-~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 108 RLSPLERAVFVLRE-VFDYPYEEIASIVGKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 57888777766654 4589999999999999999999999888888753
No 222
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=53.06 E-value=22 Score=36.14 Aligned_cols=48 Identities=13% Similarity=0.084 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHhhh---ccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 164 SLPSDYAVAMVLSRL---AHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 164 ~l~~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
.++..++..+.++|. ..+.++.+||..+|||+..|++|-...+.-|..
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 477778888888884 245799999999999999999998877766653
No 223
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=52.02 E-value=18 Score=27.48 Aligned_cols=36 Identities=11% Similarity=0.087 Sum_probs=27.5
Q ss_pred HHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHH
Q 012200 169 YAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNM 204 (468)
Q Consensus 169 ~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~ 204 (468)
++++-+|.....+.+-+++|+.+|+|..++.++...
T Consensus 3 e~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~ 38 (62)
T PF04703_consen 3 EKILEYIKEQNGPLKTREIADALGLSIYQARYYLEK 38 (62)
T ss_dssp HCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 455666667778899999999999999999888643
No 224
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=51.89 E-value=22 Score=38.44 Aligned_cols=48 Identities=15% Similarity=0.108 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHhhh---ccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 164 SLPSDYAVAMVLSRL---AHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 164 ~l~~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
.++..++..+.++|. ..+.++..||..||||+..|++|-...+.-|-.
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 588889999999884 467899999999999999999998887776653
No 225
>PRK13870 transcriptional regulator TraR; Provisional
Probab=51.60 E-value=15 Score=35.49 Aligned_cols=46 Identities=13% Similarity=0.044 Sum_probs=38.1
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
..+++.++= +|.+.+.|.+..+||...|||..||..+++.+.+-|-
T Consensus 172 ~~LT~RE~E--~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~na~~KLg 217 (234)
T PRK13870 172 AWLDPKEAT--YLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFD 217 (234)
T ss_pred CCCCHHHHH--HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 357776543 7899999999999999999999999988887766554
No 226
>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=51.29 E-value=23 Score=26.43 Aligned_cols=31 Identities=19% Similarity=0.163 Sum_probs=25.2
Q ss_pred HHHHHhhhccCccHHHHhhhccCCcchhHHHHH
Q 012200 171 VAMVLSRLAHGLSAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 171 L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~ 203 (468)
.+..||. .|.+..+||...|++.+||+.+..
T Consensus 5 ~A~~LY~--~G~~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 5 QARSLYL--QGWSIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred HHHHHHH--cCCCHHHHHHHHCCChHHHHHHHH
Confidence 4455554 699999999999999999988763
No 227
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=51.23 E-value=14 Score=31.85 Aligned_cols=24 Identities=25% Similarity=0.277 Sum_probs=22.3
Q ss_pred cCccHHHHhhhccCCcchhHHHHH
Q 012200 180 HGLSAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 180 ~g~s~~~la~~Fgvs~sTvsri~~ 203 (468)
.|.++.++|+..|++++.||+|++
T Consensus 21 eG~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 21 EGLSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred cCCcHHHHHHHhCCCHHHHHHHHc
Confidence 399999999999999999999974
No 228
>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=50.96 E-value=26 Score=25.99 Aligned_cols=30 Identities=10% Similarity=0.083 Sum_probs=25.0
Q ss_pred hccCccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 178 LAHGLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 178 La~g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
-..+.+..+++..+|++++|+++.++...+
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 567889999999999999999999876654
No 229
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=50.92 E-value=17 Score=34.73 Aligned_cols=44 Identities=9% Similarity=0.067 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLL 209 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l 209 (468)
.+++.++- +|..++.|.+.+++|...++|..||..++..+..-+
T Consensus 143 ~LS~RE~e--VL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KL 186 (217)
T PRK13719 143 KVTKYQND--VFILYSFGFSHEYIAQLLNITVGSSKNKISEILKFF 186 (217)
T ss_pred CCCHHHHH--HHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 46665543 567789999999999999999999998887765544
No 230
>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=50.80 E-value=26 Score=29.89 Aligned_cols=58 Identities=16% Similarity=0.013 Sum_probs=39.8
Q ss_pred CCHHHHHHHHHHhccccccCCCCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHH
Q 012200 142 LSYPVFTTVVEKLKPYIAASNLSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKIT 202 (468)
Q Consensus 142 ms~~~F~~L~~~L~p~l~~~~~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~ 202 (468)
++.+.-..+...+.....+.+..+.+.+ +--.+-..|.++.++|..+|+++.|++++-
T Consensus 42 ~~~e~~~~~~~~i~~~~~~~~~~~~~~~---i~~~r~~~gltq~~lA~~lg~~~~tis~~e 99 (127)
T TIGR03830 42 LDPEESKRNSAALADFYRKVDGLLTPPE---IRRIRKKLGLSQREAAELLGGGVNAFSRYE 99 (127)
T ss_pred EcHHHHHHHHHHHHHHHHHccCCcCHHH---HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 3566666666666665444433344432 233466679999999999999999999885
No 231
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=50.01 E-value=20 Score=27.10 Aligned_cols=39 Identities=10% Similarity=0.113 Sum_probs=27.9
Q ss_pred HHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 168 DYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 168 e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
|.++...|. -..+.+..+|+...|+++++|+++++...+
T Consensus 10 E~~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~ 48 (68)
T PF01978_consen 10 EAKVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEE 48 (68)
T ss_dssp HHHHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred HHHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 344444443 234468899999999999999998866543
No 232
>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=49.97 E-value=13 Score=32.30 Aligned_cols=35 Identities=9% Similarity=0.132 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLIS 199 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvs 199 (468)
.+|+..+-++.|.+ -.|.++.+||...|+|.+||.
T Consensus 107 ~Lp~~~r~v~~l~~-~~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 107 ILPNKQKKIIYMKF-FEDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHhhc
Confidence 58888887777744 568999999999999999985
No 233
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=49.39 E-value=12 Score=29.61 Aligned_cols=30 Identities=10% Similarity=0.192 Sum_probs=25.0
Q ss_pred HHhhhccCccHHHHhhhcc------CCcchhHHHHH
Q 012200 174 VLSRLAHGLSAKALASRYS------LEPYLISKITN 203 (468)
Q Consensus 174 ~L~~La~g~s~~~la~~Fg------vs~sTvsri~~ 203 (468)
--.+...|.++.++|...| +|++||+|+-+
T Consensus 17 k~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 17 KQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 3456678999999999999 59999999864
No 234
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=48.97 E-value=14 Score=34.59 Aligned_cols=29 Identities=14% Similarity=0.236 Sum_probs=25.7
Q ss_pred HhhhccCccHHHHhhhccCCcchhHHHHH
Q 012200 175 LSRLAHGLSAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 175 L~~La~g~s~~~la~~Fgvs~sTvsri~~ 203 (468)
..++..|.++..+|..+|||++|+.|+.+
T Consensus 166 ~~~~~~g~s~~~iak~lgis~~Tv~r~~k 194 (200)
T PRK13413 166 KKLLDKGTSKSEIARKLGVSRTTLARFLK 194 (200)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34567899999999999999999999975
No 235
>PHA02591 hypothetical protein; Provisional
Probab=48.95 E-value=19 Score=28.57 Aligned_cols=36 Identities=8% Similarity=0.120 Sum_probs=29.2
Q ss_pred HHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHH
Q 012200 169 YAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNM 204 (468)
Q Consensus 169 ~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~ 204 (468)
+-+-++=.....|.+...+|...|+++.+|+++.+.
T Consensus 47 d~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 47 DLISVTHELARKGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred hHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 344555555678999999999999999999998753
No 236
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=48.59 E-value=35 Score=36.38 Aligned_cols=48 Identities=10% Similarity=0.190 Sum_probs=43.3
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhhhcc-CCcchhHHHHHHHHHHHH
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALASRYS-LEPYLISKITNMVTRLLA 210 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~~Fg-vs~sTvsri~~~v~~~l~ 210 (468)
..+..-.|++|.|.+=-++.++.+||..|| .+.+||..-++.+-..+.
T Consensus 383 ~~i~~~RqiamyL~r~~t~~sl~~IG~~FggrdHsTV~~a~~ki~~~~~ 431 (450)
T PRK14087 383 KSIVTARHIAMYLTKEILNHTLAQIGEEFGGRDHTTVINAERKIEKMLK 431 (450)
T ss_pred ccccHHHHHHHHHHHHHcCCCHHHHHHHhCCCChHHHHHHHHHHHHHHH
Confidence 467788999999999999999999999997 999999988888887765
No 237
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=48.24 E-value=18 Score=33.63 Aligned_cols=44 Identities=20% Similarity=0.172 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLL 209 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l 209 (468)
.+++.++ -.|..++.|.+.+++|...++|..||..+...+..-+
T Consensus 150 ~Lt~rE~--evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl 193 (216)
T PRK10840 150 RLSPKES--EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKL 193 (216)
T ss_pred cCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 4777665 4678889999999999999999999998876665444
No 238
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=47.40 E-value=31 Score=34.21 Aligned_cols=48 Identities=15% Similarity=0.211 Sum_probs=40.0
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
.+|++++-++.|+++ .|.++.+||..+|+|.+||...+++....|.+.
T Consensus 115 ~L~~~~R~v~~L~~~-~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~ 162 (293)
T PRK09636 115 RLSPLERAAFLLHDV-FGVPFDEIASTLGRSPAACRQLASRARKHVRAA 162 (293)
T ss_pred hCCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 478888776666554 589999999999999999999998888888764
No 239
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=47.37 E-value=38 Score=23.42 Aligned_cols=27 Identities=19% Similarity=0.164 Sum_probs=22.6
Q ss_pred cCccHHHHhhhccCCcchhHHHHHHHH
Q 012200 180 HGLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 180 ~g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
.+.+..+++..|+++.+|+++.+....
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~ 39 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNKLE 39 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 356888999999999999999886654
No 240
>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=47.36 E-value=30 Score=27.54 Aligned_cols=33 Identities=15% Similarity=0.090 Sum_probs=27.5
Q ss_pred hccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 178 LAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 178 La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
...+.+..++++.++||++|+.+.++.+-+.+.
T Consensus 27 ~~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~ 59 (87)
T PF05043_consen 27 NNEYVSIEDLAEELFISRSTIYRDIKKLNKYLK 59 (87)
T ss_dssp H-SEEEHHHHHHHHT--HHHHHHHHHHHHHHHH
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 567789999999999999999999999988887
No 241
>PRK09191 two-component response regulator; Provisional
Probab=46.75 E-value=34 Score=32.64 Aligned_cols=53 Identities=17% Similarity=0.205 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcCCcc
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLYPEF 217 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~~~~ 217 (468)
.+|+..+-.+.|.++ .|.++.++|...|+|.+||...+.+....+...+..+.
T Consensus 88 ~L~~~~r~v~~l~~~-~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~~~~ 140 (261)
T PRK09191 88 GLTPLPRQAFLLTAL-EGFSVEEAAEILGVDPAEAEALLDDARAEIARQVATRV 140 (261)
T ss_pred hCCHHHhHHHHHHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCCCeE
Confidence 467777666666654 58899999999999999999888888888776554443
No 242
>PRK09483 response regulator; Provisional
Probab=46.30 E-value=20 Score=32.82 Aligned_cols=44 Identities=14% Similarity=0.194 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLL 209 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l 209 (468)
.++..+.-. |..++.|.+.+++|..+++|..||..+++.+..-+
T Consensus 148 ~Lt~rE~~v--l~~~~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 148 SLSERELQI--MLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKL 191 (217)
T ss_pred ccCHHHHHH--HHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 477655543 35678999999999999999999988877665444
No 243
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=46.20 E-value=17 Score=25.92 Aligned_cols=26 Identities=27% Similarity=0.302 Sum_probs=22.8
Q ss_pred hhccCccHHHHhhhccCCcchhHHHH
Q 012200 177 RLAHGLSAKALASRYSLEPYLISKIT 202 (468)
Q Consensus 177 ~La~g~s~~~la~~Fgvs~sTvsri~ 202 (468)
+-..|.++.++|...|+++++++++.
T Consensus 11 r~~~gltq~~lA~~~gvs~~~vs~~e 36 (58)
T TIGR03070 11 RKALGLTQADLADLAGVGLRFIRDVE 36 (58)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 44578999999999999999999885
No 244
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=46.14 E-value=60 Score=31.41 Aligned_cols=46 Identities=11% Similarity=0.141 Sum_probs=37.0
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
..+++.++= +|.+++.|.+..++|...|||..||...+..+.+-+-
T Consensus 178 ~~LT~rE~e--vl~~~a~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~ 223 (240)
T PRK10188 178 MNFSKREKE--ILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFN 223 (240)
T ss_pred CCCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 357776654 5677799999999999999999999988877765543
No 245
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=46.01 E-value=29 Score=25.42 Aligned_cols=36 Identities=22% Similarity=0.251 Sum_probs=30.3
Q ss_pred HHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHH
Q 012200 174 VLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLL 209 (468)
Q Consensus 174 ~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l 209 (468)
.+.+++.|.+..++|...++|..||......+..-+
T Consensus 12 v~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl 47 (65)
T COG2771 12 ILRLVAQGKSNKEIARILGISEETVKTHLRNIYRKL 47 (65)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 567788999999999999999999988877665444
No 246
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=45.16 E-value=12 Score=29.62 Aligned_cols=35 Identities=23% Similarity=0.391 Sum_probs=23.8
Q ss_pred HHHHHHHhhh--ccCccHHHHhhhccCCcchhHHHHH
Q 012200 169 YAVAMVLSRL--AHGLSAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 169 ~~L~i~L~~L--a~g~s~~~la~~Fgvs~sTvsri~~ 203 (468)
.+++..|..+ ..|.++.++|...|+++++|+++.+
T Consensus 17 ~~l~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 17 AQLMAAIRELREERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp HHHHHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence 3344444444 3688999999999999999999863
No 247
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=44.90 E-value=28 Score=32.03 Aligned_cols=62 Identities=15% Similarity=0.039 Sum_probs=42.7
Q ss_pred CCHHHHHHHHHhhhcc--------------CccHHHHhhhccCCcchhHHHHHHHHHH-HHhhcCCccccCCCchhhhc
Q 012200 165 LPSDYAVAMVLSRLAH--------------GLSAKALASRYSLEPYLISKITNMVTRL-LATKLYPEFIKIPISRRRLI 228 (468)
Q Consensus 165 l~~e~~L~i~L~~La~--------------g~s~~~la~~Fgvs~sTvsri~~~v~~~-l~~~L~~~~I~~P~~~~~~~ 228 (468)
.+++++|+-+|..|+. ..++.++|...|+++.|++|++++..+- +.+ .....|..+ +.+.++
T Consensus 119 ~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~-~~~~~i~I~-d~~~L~ 195 (202)
T PRK13918 119 QRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRETVTKVIGELSREGYIR-SGYGKIQLL-DLKGLE 195 (202)
T ss_pred CchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHHHHHHHHHHHHCCCEE-cCCCEEEEE-CHHHHH
Confidence 4678899988876653 2368899999999999999999887653 222 233445555 344443
No 248
>PHA01976 helix-turn-helix protein
Probab=44.86 E-value=19 Score=26.96 Aligned_cols=27 Identities=30% Similarity=0.299 Sum_probs=23.5
Q ss_pred hhhccCccHHHHhhhccCCcchhHHHH
Q 012200 176 SRLAHGLSAKALASRYSLEPYLISKIT 202 (468)
Q Consensus 176 ~~La~g~s~~~la~~Fgvs~sTvsri~ 202 (468)
.+-..|.+..++|...||++++++++-
T Consensus 10 ~R~~~glt~~~lA~~~gvs~~~v~~~e 36 (67)
T PHA01976 10 ARNARAWSAPELSRRAGVRHSLIYDFE 36 (67)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 355688999999999999999999874
No 249
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=44.85 E-value=22 Score=33.58 Aligned_cols=44 Identities=18% Similarity=0.108 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLL 209 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l 209 (468)
.+++.++ =.|..++.|.+.+++|...++|..||..+...+.+-+
T Consensus 134 ~LT~RE~--eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KL 177 (207)
T PRK11475 134 MLSPTER--EILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKL 177 (207)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 4776554 3577889999999999999999999998876665443
No 250
>PHA00738 putative HTH transcription regulator
Probab=44.65 E-value=20 Score=30.41 Aligned_cols=27 Identities=15% Similarity=0.143 Sum_probs=22.9
Q ss_pred ccHHHHhhhccCCcchhHHHHHHHHHH
Q 012200 182 LSAKALASRYSLEPYLISKITNMVTRL 208 (468)
Q Consensus 182 ~s~~~la~~Fgvs~sTvsri~~~v~~~ 208 (468)
.+-.+++..|++|+++||+.++..-++
T Consensus 27 ~~V~eLae~l~lSQptVS~HLKvLreA 53 (108)
T PHA00738 27 LSASLISHTLLLSYTTVLRHLKILNEQ 53 (108)
T ss_pred ccHHHHHHhhCCCHHHHHHHHHHHHHC
Confidence 688899999999999999998655444
No 251
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=44.61 E-value=50 Score=26.24 Aligned_cols=28 Identities=21% Similarity=0.423 Sum_probs=23.9
Q ss_pred cCccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 180 HGLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 180 ~g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
.+.+..+++..++++++++++.++....
T Consensus 23 ~~~~~~~la~~~~~s~~~i~~~l~~L~~ 50 (101)
T smart00347 23 GPLSVSELAKRLGVSPSTVTRVLDRLEK 50 (101)
T ss_pred CCcCHHHHHHHHCCCchhHHHHHHHHHH
Confidence 4578999999999999999998877654
No 252
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=44.58 E-value=29 Score=35.09 Aligned_cols=47 Identities=19% Similarity=0.206 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
.+|++++-++.|++ -.|.++++||..+|+|..||...+.+....|.+
T Consensus 153 ~Lp~~~R~v~~L~~-~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 153 HLPPRQRAVLILRD-VLGWSAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred hCCHHHhhhhhhHH-hhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 47888888777754 568999999999999999999999888888875
No 253
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=44.34 E-value=44 Score=29.34 Aligned_cols=42 Identities=10% Similarity=0.203 Sum_probs=30.6
Q ss_pred CCCH-HHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHH
Q 012200 164 SLPS-DYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 164 ~l~~-e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
.+++ +-.++..|+ -..|.+..+++..++++++|++++++...
T Consensus 37 glt~~q~~vL~~l~-~~~~~t~~eLa~~l~i~~~tvsr~l~~Le 79 (144)
T PRK11512 37 DITAAQFKVLCSIR-CAACITPVELKKVLSVDLGALTRMLDRLV 79 (144)
T ss_pred CCCHHHHHHHHHHH-HcCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4554 334455553 35568999999999999999999886654
No 254
>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=44.04 E-value=11 Score=37.26 Aligned_cols=21 Identities=19% Similarity=0.246 Sum_probs=19.4
Q ss_pred cHHHHhhhccCCcchhHHHHH
Q 012200 183 SAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 183 s~~~la~~Fgvs~sTvsri~~ 203 (468)
+.++||+..|||++||||+++
T Consensus 3 ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 3 TIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred cHHHHHHHhCCCHHHHHHHhC
Confidence 578999999999999999995
No 255
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=43.71 E-value=24 Score=33.38 Aligned_cols=44 Identities=30% Similarity=0.297 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLL 209 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l 209 (468)
.++..+.- .|..++.|.+.++||.+.++|..||..++.....-|
T Consensus 148 ~LT~RE~e--VL~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 148 LLTPRELE--VLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCCHHHHH--HHHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHc
Confidence 35665543 678899999999999999999999998877665544
No 256
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=43.64 E-value=13 Score=28.60 Aligned_cols=20 Identities=15% Similarity=0.190 Sum_probs=17.7
Q ss_pred cHHHHhhhccCCcchhHHHH
Q 012200 183 SAKALASRYSLEPYLISKIT 202 (468)
Q Consensus 183 s~~~la~~Fgvs~sTvsri~ 202 (468)
+.+++|..-|||.+||++++
T Consensus 2 t~~~iA~~~gvS~~TVSr~l 21 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVL 21 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 46789999999999999976
No 257
>PRK09492 treR trehalose repressor; Provisional
Probab=43.44 E-value=13 Score=36.73 Aligned_cols=23 Identities=22% Similarity=0.255 Sum_probs=20.7
Q ss_pred ccHHHHhhhccCCcchhHHHHHH
Q 012200 182 LSAKALASRYSLEPYLISKITNM 204 (468)
Q Consensus 182 ~s~~~la~~Fgvs~sTvsri~~~ 204 (468)
.+.++||+..|||.+||||+++.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCC
Confidence 47899999999999999999973
No 258
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=43.28 E-value=25 Score=34.81 Aligned_cols=46 Identities=13% Similarity=0.104 Sum_probs=38.8
Q ss_pred HHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 169 YAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 169 ~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
.+|-.|+....+|.++...|+..+||+++||+.+++.-..+-..|.
T Consensus 4 ~~L~~F~~v~~~~~s~s~AA~~L~isq~avSr~I~~LE~~lg~~LF 49 (309)
T PRK12682 4 QQLRFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIF 49 (309)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCccHHHHHHHHHHHHHhCCeeE
Confidence 3566677777788899999999999999999999999888865554
No 259
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=43.26 E-value=27 Score=34.75 Aligned_cols=46 Identities=9% Similarity=0.132 Sum_probs=39.1
Q ss_pred HHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 169 YAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 169 ~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
.+|-.|+....+|.++...|++.|++++++|+.+++.-..+-..|.
T Consensus 4 ~~L~~F~~v~~~~~S~s~AA~~L~isQpavS~~I~~LE~~lg~~Lf 49 (309)
T PRK12683 4 QQLRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIF 49 (309)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhCCeeE
Confidence 3566777778888899999999999999999999999888765554
No 260
>PRK10870 transcriptional repressor MprA; Provisional
Probab=42.90 E-value=41 Score=30.89 Aligned_cols=43 Identities=7% Similarity=0.149 Sum_probs=29.6
Q ss_pred CCCH-HHHHHHHHhhhcc-CccHHHHhhhccCCcchhHHHHHHHH
Q 012200 164 SLPS-DYAVAMVLSRLAH-GLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 164 ~l~~-e~~L~i~L~~La~-g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
.++. +-.++..|+.... +.+..++++.++++++|+++++++..
T Consensus 52 gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe 96 (176)
T PRK10870 52 GINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELE 96 (176)
T ss_pred CCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3554 3345555544333 46789999999999999998876553
No 261
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=41.36 E-value=29 Score=33.07 Aligned_cols=45 Identities=16% Similarity=0.149 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
.+++.++= .|..++.|.+++++|...++|..||..++.....-+.
T Consensus 155 ~Lt~rE~~--Vl~l~~~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 155 LLTHREKE--ILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 36664443 4556677999999999999999999998877765543
No 262
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=41.16 E-value=37 Score=28.52 Aligned_cols=31 Identities=29% Similarity=0.445 Sum_probs=22.1
Q ss_pred cCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 180 HGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 180 ~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
.|....++|.+||+|...|.+|++++-....
T Consensus 71 ~G~n~~eLA~kyglS~r~I~~Ii~~~~~~~~ 101 (108)
T PF08765_consen 71 NGMNVRELARKYGLSERQIYRIIKRVRRRER 101 (108)
T ss_dssp -SS-HHHHHHHHT--HHHHHHHHHHHHH---
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4999999999999999999999988765543
No 263
>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=40.71 E-value=19 Score=29.79 Aligned_cols=61 Identities=8% Similarity=0.053 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHhccccccCC--CCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHH--HHHHHH
Q 012200 141 GLSYPVFTTVVEKLKPYIAASN--LSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNM--VTRLLA 210 (468)
Q Consensus 141 Rms~~~F~~L~~~L~p~l~~~~--~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~--v~~~l~ 210 (468)
-|+-+.|-.|.+.....-.... .....+.+.. -.+..+|..||+|.+|++||... .-++|.
T Consensus 12 qmTg~ell~L~~~~~~~~~~~~~~~~~~~~~~yv---------yG~~GlAklfgcSv~Ta~RiK~sG~id~AI~ 76 (96)
T PF12964_consen 12 QMTGEELLFLLKEGKTNSEKQTSQKAKKDEKKYV---------YGLKGLAKLFGCSVPTANRIKKSGKIDPAIT 76 (96)
T ss_pred HhhHHHHHHHHHHHhcCCCccCCccccCccccee---------ehHHHHHHHhCCCchhHHHHHhcCCccHHHH
Confidence 3777888888877744322211 1122222211 23578999999999999999853 334454
No 264
>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=40.63 E-value=12 Score=26.54 Aligned_cols=18 Identities=17% Similarity=0.235 Sum_probs=15.7
Q ss_pred HHhhhccCCcchhHHHHH
Q 012200 186 ALASRYSLEPYLISKITN 203 (468)
Q Consensus 186 ~la~~Fgvs~sTvsri~~ 203 (468)
++|...|||++||+++++
T Consensus 2 ~lA~~~gvs~~tvs~~l~ 19 (52)
T cd01392 2 DIARAAGVSVATVSRVLN 19 (52)
T ss_pred cHHHHHCcCHHHHHHHHc
Confidence 688999999999999863
No 265
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=40.62 E-value=27 Score=33.12 Aligned_cols=32 Identities=22% Similarity=0.187 Sum_probs=26.8
Q ss_pred CccHHHHhhhccCCcchhHHHHHHHHHHHHhh
Q 012200 181 GLSAKALASRYSLEPYLISKITNMVTRLLATK 212 (468)
Q Consensus 181 g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~ 212 (468)
..+.+++|+.||||++|++.++++..+=|.+.
T Consensus 178 ~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~~ 209 (215)
T COG3413 178 RVSLKDLAKELGISKSTLSEHLRRAERKLIEA 209 (215)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 35778999999999999999998877766644
No 266
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=40.38 E-value=46 Score=35.47 Aligned_cols=48 Identities=19% Similarity=0.137 Sum_probs=43.0
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
..+..-.|++|.|.+=-++.++.+|+..||...+||.--++.+-+.+.
T Consensus 379 ~~i~~~Rqiamyl~r~~t~~s~~~IG~~fgrdHsTV~~a~~ki~~~~~ 426 (445)
T PRK12422 379 REYVLPRQVAMYLCRQKLSLSYVKIGDVFSRDHSTVISSIRAISQKLE 426 (445)
T ss_pred cccccHHHHHHHHHHHhcCCCHHHHHHHhCCChHHHHHHHHHHHHHHH
Confidence 467778899999999999999999999999999999888888887773
No 267
>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=40.13 E-value=19 Score=24.56 Aligned_cols=22 Identities=14% Similarity=0.208 Sum_probs=18.4
Q ss_pred cHHHHhhhccCCcchhHHHHHH
Q 012200 183 SAKALASRYSLEPYLISKITNM 204 (468)
Q Consensus 183 s~~~la~~Fgvs~sTvsri~~~ 204 (468)
+..++|..+||+.+|+.+++..
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 4578999999999999888753
No 268
>PRK00215 LexA repressor; Validated
Probab=40.06 E-value=42 Score=31.35 Aligned_cols=27 Identities=19% Similarity=0.270 Sum_probs=22.8
Q ss_pred CccHHHHhhhccC-CcchhHHHHHHHHH
Q 012200 181 GLSAKALASRYSL-EPYLISKITNMVTR 207 (468)
Q Consensus 181 g~s~~~la~~Fgv-s~sTvsri~~~v~~ 207 (468)
+.+..+++..+|+ +++|+++++....+
T Consensus 23 ~~s~~ela~~~~~~~~~tv~~~l~~L~~ 50 (205)
T PRK00215 23 PPSRREIADALGLRSPSAVHEHLKALER 50 (205)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 4488999999999 99999999866553
No 269
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=40.00 E-value=54 Score=27.00 Aligned_cols=39 Identities=18% Similarity=0.212 Sum_probs=28.3
Q ss_pred HHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 168 DYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 168 e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
+.+++..|..- ...++.+++..+|++++|+++.++....
T Consensus 5 D~~il~~L~~~-~~~~~~~la~~l~~s~~tv~~~l~~L~~ 43 (108)
T smart00344 5 DRKILEELQKD-ARISLAELAKKVGLSPSTVHNRVKRLEE 43 (108)
T ss_pred HHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34455444443 3578999999999999999988766543
No 270
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=39.66 E-value=47 Score=25.53 Aligned_cols=41 Identities=17% Similarity=0.258 Sum_probs=36.5
Q ss_pred HHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 171 VAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 171 L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
.-.+..+|+...+..+.|++.|+...+|.+++..+-..+.+
T Consensus 3 ~~~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~ 43 (65)
T PF05344_consen 3 ARAFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQ 43 (65)
T ss_pred HHHHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 44578899999999999999999999999999999888873
No 271
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=39.45 E-value=15 Score=36.80 Aligned_cols=23 Identities=9% Similarity=0.044 Sum_probs=20.8
Q ss_pred ccHHHHhhhccCCcchhHHHHHH
Q 012200 182 LSAKALASRYSLEPYLISKITNM 204 (468)
Q Consensus 182 ~s~~~la~~Fgvs~sTvsri~~~ 204 (468)
.+.++||+..|||.+||||+++.
T Consensus 7 ~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 7 ITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHHCC
Confidence 57899999999999999999864
No 272
>PRK09526 lacI lac repressor; Reviewed
Probab=39.12 E-value=15 Score=36.71 Aligned_cols=22 Identities=14% Similarity=0.147 Sum_probs=20.2
Q ss_pred ccHHHHhhhccCCcchhHHHHH
Q 012200 182 LSAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 182 ~s~~~la~~Fgvs~sTvsri~~ 203 (468)
.+.++||...|||.+||||+++
T Consensus 6 ~ti~dIA~~aGVS~~TVSrvLn 27 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRVLN 27 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHhc
Confidence 4788999999999999999986
No 273
>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=38.41 E-value=27 Score=26.13 Aligned_cols=22 Identities=18% Similarity=0.342 Sum_probs=16.5
Q ss_pred HHHHhhhccCCcchhHHHHHHH
Q 012200 184 AKALASRYSLEPYLISKITNMV 205 (468)
Q Consensus 184 ~~~la~~Fgvs~sTvsri~~~v 205 (468)
..+++.+||||+.|+.+.+...
T Consensus 27 ~~~la~~~~vsr~tvr~al~~L 48 (64)
T PF00392_consen 27 ERELAERYGVSRTTVREALRRL 48 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHhccCCcHHHHHHHHH
Confidence 3578999999999998776544
No 274
>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=38.34 E-value=60 Score=28.35 Aligned_cols=45 Identities=18% Similarity=0.269 Sum_probs=31.0
Q ss_pred CCCCCHHHHHHHH-HhhhccCccHHHHhhhccCCcchhHHHHHHHHHH
Q 012200 162 NLSLPSDYAVAMV-LSRLAHGLSAKALASRYSLEPYLISKITNMVTRL 208 (468)
Q Consensus 162 ~~~l~~e~~L~i~-L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~ 208 (468)
.+.+|.+.+.-|. |. ..|.+-.+++.+++||.++|++|+.+.-+.
T Consensus 15 GrPLp~~~R~rIvela--~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~eT 60 (125)
T PF00292_consen 15 GRPLPNELRQRIVELA--KEGVRPCDISRQLRVSHGCVSKILSRYRET 60 (125)
T ss_dssp TSSS-HHHHHHHHHHH--HTT--HHHHHHHHT--HHHHHHHHHHHHHH
T ss_pred CccCcHHHHHHHHHHh--hhcCCHHHHHHHHccchhHHHHHHHHHHHh
Confidence 3578887776655 43 469999999999999999999999876443
No 275
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=37.76 E-value=15 Score=36.66 Aligned_cols=22 Identities=14% Similarity=0.199 Sum_probs=19.8
Q ss_pred ccHHHHhhhccCCcchhHHHHH
Q 012200 182 LSAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 182 ~s~~~la~~Fgvs~sTvsri~~ 203 (468)
.+.++||+..|||.+||||+++
T Consensus 6 ~ti~dIA~~agVS~~TVSrvLn 27 (331)
T PRK14987 6 PVLQDVADRVGVTKMTVSRFLR 27 (331)
T ss_pred CcHHHHHHHhCCCHHHhhhhhC
Confidence 3678999999999999999985
No 276
>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=37.72 E-value=53 Score=32.10 Aligned_cols=44 Identities=9% Similarity=0.162 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLL 209 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l 209 (468)
.++..++=.+.+ ++.|.++.++|...|||..||...+..+..-+
T Consensus 190 ~LT~RE~evl~l--~a~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL 233 (247)
T TIGR03020 190 LITAREAEILAW--VRDGKTNEEIAAILGISSLTVKNHLQHIFKKL 233 (247)
T ss_pred CCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHh
Confidence 577777665554 57999999999999999999998887765544
No 277
>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=37.53 E-value=58 Score=23.93 Aligned_cols=25 Identities=24% Similarity=0.325 Sum_probs=20.9
Q ss_pred CccHHHHhhhccCCcchhHHHHHHH
Q 012200 181 GLSAKALASRYSLEPYLISKITNMV 205 (468)
Q Consensus 181 g~s~~~la~~Fgvs~sTvsri~~~v 205 (468)
..+..++++.||||..|+.|-+...
T Consensus 14 ~~s~~ela~~~~VS~~TiRRDl~~L 38 (57)
T PF08220_consen 14 KVSVKELAEEFGVSEMTIRRDLNKL 38 (57)
T ss_pred CEEHHHHHHHHCcCHHHHHHHHHHH
Confidence 4577899999999999999887543
No 278
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=37.36 E-value=55 Score=28.75 Aligned_cols=46 Identities=7% Similarity=-0.037 Sum_probs=36.9
Q ss_pred CCHHHHHHHHHhhhcc-CccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 165 LPSDYAVAMVLSRLAH-GLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 165 l~~e~~L~i~L~~La~-g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
+..+++-.+-|+|-.. +.+|..||..++++.+|+.++..++-..|.
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 4555666667777776 799999999999999999999887766543
No 279
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=37.33 E-value=38 Score=33.48 Aligned_cols=43 Identities=12% Similarity=0.036 Sum_probs=33.3
Q ss_pred HHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 170 AVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 170 ~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
+|-.++....+ .++...|+..||++++||+.++..-..+-..|
T Consensus 5 ~L~~F~~v~~~-~S~s~AA~~L~isQ~avS~~I~~LE~~lg~~L 47 (305)
T PRK11233 5 RLKYFVKIVDI-GSLTQAAEVLHIAQPALSQQVATLEGELNQQL 47 (305)
T ss_pred HHHHHHHHHHc-CCHHHHHHHhCCCchHHHHHHHHHHHHhCCce
Confidence 34444444444 49999999999999999999999988876544
No 280
>COG5421 Transposase [DNA replication, recombination, and repair]
Probab=36.99 E-value=38 Score=36.11 Aligned_cols=59 Identities=19% Similarity=0.182 Sum_probs=40.2
Q ss_pred cCceeeEeeeeccccceeeeeccCCCCCCCCccccchhhhhhhhccCCCCCccccccCCccccceeecccCCC
Q 012200 273 YGYNSVLLQVVADHRKIFWDVCVKASGGADDSAHFRDSLLYNRLISGDIVWDKAINVRGHHVRPYIVGDWCYP 345 (468)
Q Consensus 273 k~~~Si~~q~v~D~~g~f~~v~~g~pGs~hD~~i~~~S~l~~~l~~~~l~~~~~~~~~G~~~~~~llgD~gYp 345 (468)
..-+-+++..+++..|.-+.+.+ ++|+.+|...+-. ..+.+.+. +...+.++++|+||-
T Consensus 152 ~dl~QI~vsMi~~~~gIPl~~~v-~~Gni~D~~~~~~--ti~kl~~~-----------l~~~~~~~V~Dkgf~ 210 (480)
T COG5421 152 LDLPQINVSMIVNQKGIPLFVRV-YSGNISDKNTLIK--TIQKLKSV-----------LVKDEVYLVADKGFN 210 (480)
T ss_pred CCcceeEEEEEEcCCCCceEEEc-cCCCccchHHHHH--HHHHHHHh-----------cccceEEEEEccccc
Confidence 34567899888898877776665 6999999987753 34433331 111125899999994
No 281
>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=36.80 E-value=23 Score=24.21 Aligned_cols=21 Identities=5% Similarity=0.120 Sum_probs=17.9
Q ss_pred cHHHHhhhccCCcchhHHHHH
Q 012200 183 SAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 183 s~~~la~~Fgvs~sTvsri~~ 203 (468)
+..+++..+|||.+|+.++++
T Consensus 3 t~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 567899999999999988763
No 282
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=36.74 E-value=19 Score=26.65 Aligned_cols=25 Identities=28% Similarity=0.464 Sum_probs=18.4
Q ss_pred ccCccHHHHhhhccCCcchhHHHHH
Q 012200 179 AHGLSAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 179 a~g~s~~~la~~Fgvs~sTvsri~~ 203 (468)
..|.+..++|..-|++++|++++++
T Consensus 8 ~~~it~~~La~~~gis~~tl~~~~~ 32 (63)
T PF13443_consen 8 ERGITQKDLARKTGISRSTLSRILN 32 (63)
T ss_dssp HTT--HHHHHHHHT--HHHHHHHHT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHh
Confidence 4678999999999999999999874
No 283
>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=36.65 E-value=50 Score=31.44 Aligned_cols=21 Identities=24% Similarity=0.358 Sum_probs=16.8
Q ss_pred HHhhhccCCcchhHHHHHHHH
Q 012200 186 ALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 186 ~la~~Fgvs~sTvsri~~~v~ 206 (468)
+++.+||||+.||.+.+....
T Consensus 29 eLa~~~gVSR~TVR~Al~~L~ 49 (233)
T TIGR02404 29 ELMDQYGASRETVRKALNLLT 49 (233)
T ss_pred HHHHHHCCCHHHHHHHHHHHH
Confidence 567899999999988875543
No 284
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=36.44 E-value=50 Score=36.70 Aligned_cols=47 Identities=15% Similarity=0.123 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHhhh---ccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRL---AHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 164 ~l~~e~~L~i~L~~L---a~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
.++..++..+.++|. ..+.++..+|..||||+..|++|-...+.-|-
T Consensus 556 ~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr 605 (619)
T PRK05658 556 SLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605 (619)
T ss_pred cCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence 478888998999885 46789999999999999999999877766654
No 285
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=36.39 E-value=19 Score=35.78 Aligned_cols=22 Identities=14% Similarity=0.009 Sum_probs=19.5
Q ss_pred cHHHHhhhccCCcchhHHHHHH
Q 012200 183 SAKALASRYSLEPYLISKITNM 204 (468)
Q Consensus 183 s~~~la~~Fgvs~sTvsri~~~ 204 (468)
+.++||+.-|||.+||||+++.
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 5689999999999999999853
No 286
>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=36.06 E-value=31 Score=26.08 Aligned_cols=27 Identities=15% Similarity=0.140 Sum_probs=21.4
Q ss_pred hhhccC--ccHHHHhhhccCCcchhHHHH
Q 012200 176 SRLAHG--LSAKALASRYSLEPYLISKIT 202 (468)
Q Consensus 176 ~~La~g--~s~~~la~~Fgvs~sTvsri~ 202 (468)
.|+.++ ....+||..+||+.+||+++-
T Consensus 15 ~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 15 IYKESNGKIKLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred HHHHhCCCccHHHHHHHHCCCHHHHHHHh
Confidence 345443 678999999999999998764
No 287
>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=35.96 E-value=54 Score=24.85 Aligned_cols=29 Identities=17% Similarity=0.258 Sum_probs=22.8
Q ss_pred hccC-ccHHHHhhhccCCcchhHHHHHHHH
Q 012200 178 LAHG-LSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 178 La~g-~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
|+.+ .+..+++..+|+|.+||++.+...-
T Consensus 9 L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~ 38 (69)
T TIGR00122 9 LADNPFSGEKLGEALGMSRTAVNKHIQTLR 38 (69)
T ss_pred HHcCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4443 4578899999999999999886653
No 288
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=35.96 E-value=18 Score=36.35 Aligned_cols=21 Identities=14% Similarity=0.273 Sum_probs=19.5
Q ss_pred cHHHHhhhccCCcchhHHHHH
Q 012200 183 SAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 183 s~~~la~~Fgvs~sTvsri~~ 203 (468)
+.++||+..|||.+||||+++
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (346)
T PRK10401 3 TIRDVARQAGVSVATVSRVLN 23 (346)
T ss_pred CHHHHHHHhCCCHHHHHHHHC
Confidence 678999999999999999986
No 289
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=35.42 E-value=54 Score=32.69 Aligned_cols=47 Identities=17% Similarity=0.227 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
.+|+.++-++.|++ -.|.++.++|...|+|..||...+++....|.+
T Consensus 118 ~L~p~~R~vf~L~~-~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~ 164 (290)
T PRK09635 118 RLGPAERVVFVLHE-IFGLPYQQIATTIGSQASTCRQLAHRARRKINE 164 (290)
T ss_pred hCCHHHHHHhhHHH-HhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 47777776665554 459999999999999999999999888888775
No 290
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=34.85 E-value=20 Score=35.90 Aligned_cols=22 Identities=23% Similarity=0.312 Sum_probs=20.0
Q ss_pred cHHHHhhhccCCcchhHHHHHH
Q 012200 183 SAKALASRYSLEPYLISKITNM 204 (468)
Q Consensus 183 s~~~la~~Fgvs~sTvsri~~~ 204 (468)
+.++||+..|||++||||+++.
T Consensus 3 Ti~dIA~~agVS~~TVSrvLn~ 24 (341)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINK 24 (341)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 6789999999999999999863
No 291
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=34.79 E-value=52 Score=31.87 Aligned_cols=45 Identities=18% Similarity=0.191 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHhccccccCCCCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHH
Q 012200 142 LSYPVFTTVVEKLKPYIAASNLSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKIT 202 (468)
Q Consensus 142 ms~~~F~~L~~~L~p~l~~~~~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~ 202 (468)
+....+..|.+.|....-+.+..+|.|. +++.+||||+++|...+
T Consensus 11 l~~~v~~~i~~~I~~g~~~~G~~LP~Er----------------eLae~fgVSR~~vREAl 55 (241)
T COG2186 11 LADEVAEQIGALIVSGELPPGDRLPSER----------------ELAERFGVSRTVVREAL 55 (241)
T ss_pred hHHHHHHHHHHHHHcCCCCCCCCCCCHH----------------HHHHHHCCCcHHHHHHH
Confidence 3445555555555543333344677774 67899999999986554
No 292
>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=34.77 E-value=53 Score=24.64 Aligned_cols=40 Identities=13% Similarity=0.182 Sum_probs=28.3
Q ss_pred CCCCHHHHHHHHHhhhccCc---cHHHHhhhccCCcchhHHHH
Q 012200 163 LSLPSDYAVAMVLSRLAHGL---SAKALASRYSLEPYLISKIT 202 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~---s~~~la~~Fgvs~sTvsri~ 202 (468)
.+.+++.+|-+.-++..++. .++..|..|||++..|.++.
T Consensus 4 rsy~~~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~ 46 (58)
T PF09607_consen 4 RSYTAEFKLKVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWR 46 (58)
T ss_dssp ----HHHHHHHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHH
T ss_pred cccChHHHHHHHHHHHHccchhhhHHHHHHHhCccHHHHHHHH
Confidence 46788888888888888887 46999999999998887765
No 293
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=34.72 E-value=50 Score=24.48 Aligned_cols=30 Identities=20% Similarity=0.222 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhhhcc
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALASRYS 192 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~~Fg 192 (468)
..+..-.+++|.|.+--.|.++.++|..||
T Consensus 27 ~~~~~aR~iamyla~~~~~~sl~~Ig~~fg 56 (60)
T smart00760 27 REIVLARQIAMYLARELTDLSLPEIGKIFG 56 (60)
T ss_pred cchhHHHHHHHHHHHHHHCCCHHHHHHHhC
Confidence 567788899999999999999999999998
No 294
>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=34.70 E-value=80 Score=26.34 Aligned_cols=42 Identities=17% Similarity=0.256 Sum_probs=29.4
Q ss_pred CCHH-HHHHHHHhhhc---cCccHHHHhhhccCCcchhHHHHHHHH
Q 012200 165 LPSD-YAVAMVLSRLA---HGLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 165 l~~e-~~L~i~L~~La---~g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
++.. -.++..|+++. .+.+..+++...+++++|++++++...
T Consensus 23 ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le 68 (109)
T TIGR01889 23 LSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLS 68 (109)
T ss_pred CCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4443 33444444322 358899999999999999999886654
No 295
>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=34.65 E-value=22 Score=30.27 Aligned_cols=32 Identities=19% Similarity=0.263 Sum_probs=25.0
Q ss_pred hhc-cCccHHHHhhhccCCcchhHHHHHHHHHH
Q 012200 177 RLA-HGLSAKALASRYSLEPYLISKITNMVTRL 208 (468)
Q Consensus 177 ~La-~g~s~~~la~~Fgvs~sTvsri~~~v~~~ 208 (468)
-|+ -|.+...+|+.|+||+||+..++...-.-
T Consensus 75 ~LR~AGlt~~aIAd~F~iS~s~~~nft~~n~~e 107 (126)
T PF10654_consen 75 ELRHAGLTCYAIADYFKISKSTVFNFTQNNKKE 107 (126)
T ss_pred HHHhcCCChHHHHHHHhHHHHHHHHHHHHhHHH
Confidence 344 38899999999999999998887554433
No 296
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=34.61 E-value=18 Score=35.99 Aligned_cols=22 Identities=18% Similarity=0.184 Sum_probs=19.6
Q ss_pred cHHHHhhhccCCcchhHHHHHH
Q 012200 183 SAKALASRYSLEPYLISKITNM 204 (468)
Q Consensus 183 s~~~la~~Fgvs~sTvsri~~~ 204 (468)
+.++||+..|||++||||+++.
T Consensus 3 ti~dIA~~agVS~~TVSrvln~ 24 (327)
T PRK10339 3 TLKDIAIEAGVSLATVSRVLND 24 (327)
T ss_pred CHHHHHHHhCCCHHhhhhhhcC
Confidence 5789999999999999999853
No 297
>PRK10651 transcriptional regulator NarL; Provisional
Probab=34.50 E-value=40 Score=30.45 Aligned_cols=44 Identities=18% Similarity=0.262 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLL 209 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l 209 (468)
.+++.+. =.|.++..|.+.+.++...++|..||..++.....-+
T Consensus 155 ~Lt~rE~--~vl~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl 198 (216)
T PRK10651 155 QLTPRER--DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKM 198 (216)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 3666554 3456688999999999999999999998887765554
No 298
>PF13551 HTH_29: Winged helix-turn helix
Probab=34.42 E-value=2.1e+02 Score=23.24 Aligned_cols=73 Identities=12% Similarity=0.110 Sum_probs=45.0
Q ss_pred ChhhHHHhcCCCHHHHHHHHHHhcccc----cc-----CC-CC-CCHHHHHHHHHhhhccC------ccHHHHhhh----
Q 012200 132 REAHWRSLYGLSYPVFTTVVEKLKPYI----AA-----SN-LS-LPSDYAVAMVLSRLAHG------LSAKALASR---- 190 (468)
Q Consensus 132 ~d~~fr~~fRms~~~F~~L~~~L~p~l----~~-----~~-~~-l~~e~~L~i~L~~La~g------~s~~~la~~---- 190 (468)
+..+.-..+|+++.++...+....... .. .+ .. ++.+..-.+.=++..+. .+...++..
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~ 93 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEE 93 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHh
Confidence 477888899999999999998876532 11 11 22 56655443332333322 344555542
Q ss_pred -c--cCCcchhHHHHHH
Q 012200 191 -Y--SLEPYLISKITNM 204 (468)
Q Consensus 191 -F--gvs~sTvsri~~~ 204 (468)
+ .+|.+||++++++
T Consensus 94 ~~~~~~s~~ti~r~L~~ 110 (112)
T PF13551_consen 94 EFGIDVSPSTIRRILKR 110 (112)
T ss_pred ccCccCCHHHHHHHHHH
Confidence 3 5789999988764
No 299
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=34.24 E-value=72 Score=33.60 Aligned_cols=50 Identities=14% Similarity=0.213 Sum_probs=44.1
Q ss_pred CCCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 162 NLSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 162 ~~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
++.+..-.|++|.|.+--+..|+..++..||...+||.--++.+...+.+
T Consensus 346 ~~~i~~~RqiamyL~r~lt~~Slp~IG~~FgrdHtTV~~a~~kI~~~~~~ 395 (408)
T COG0593 346 TRNIVRPRQIAMYLARELTNLSLPEIGKAFGRDHTTVLHAVRKIEQLIEE 395 (408)
T ss_pred ccccchHHHHHHHHHHHHccCcHHHHHHHhCCCccHHHHHHHHHHHHHhc
Confidence 35677888999999999999999999999999999998888888877763
No 300
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=33.73 E-value=52 Score=32.77 Aligned_cols=46 Identities=7% Similarity=0.074 Sum_probs=38.7
Q ss_pred HHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 169 YAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 169 ~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
+++-.++....+|.++...|++.++|++++|+.++..-..+-..|.
T Consensus 4 ~~l~~f~~v~~~~~s~s~AA~~L~iSQ~avSr~I~~LE~~lg~~LF 49 (316)
T PRK12679 4 QQLKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIF 49 (316)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhcCCchHHHHHHHHHHHHhCCEEE
Confidence 3566677777788899999999999999999999999888875553
No 301
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=33.63 E-value=45 Score=29.82 Aligned_cols=44 Identities=23% Similarity=0.318 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLL 209 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l 209 (468)
.+++.+. -.|..|+.|.+.++++..+++|..||..++.++.+-+
T Consensus 137 ~Lt~~E~--~il~~l~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 137 PLTKRER--QVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKL 180 (196)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 4555544 3566688899999999999999999988887765544
No 302
>PRK10403 transcriptional regulator NarP; Provisional
Probab=33.52 E-value=43 Score=30.11 Aligned_cols=44 Identities=30% Similarity=0.279 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLL 209 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l 209 (468)
.++..+.- .|.+++.|.+...++...++|..||..++..+..-+
T Consensus 153 ~Lt~~e~~--vl~~~~~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl 196 (215)
T PRK10403 153 VLTERELD--VLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKL 196 (215)
T ss_pred cCCHHHHH--HHHHHHCCCCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 35654443 466788999999999999999999988887776554
No 303
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=33.43 E-value=30 Score=37.24 Aligned_cols=32 Identities=22% Similarity=0.289 Sum_probs=27.1
Q ss_pred CccHHHHhhhccCCcchhHHHHHHHHHHHHhhcCCccccCCCc
Q 012200 181 GLSAKALASRYSLEPYLISKITNMVTRLLATKLYPEFIKIPIS 223 (468)
Q Consensus 181 g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~~~~I~~P~~ 223 (468)
..+.++||...|++.|||||++ ..+|+.-|.+
T Consensus 369 PLtlkdVAe~lglHeSTVSRa~-----------~~KY~~tp~G 400 (481)
T PRK12469 369 PLVLRDVAEELGLHESTISRAT-----------GNKYMATPRG 400 (481)
T ss_pred CCcHHHHHHHhCCCcchhhHHh-----------cCceeecCCc
Confidence 3578999999999999999986 5688988844
No 304
>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=32.47 E-value=68 Score=27.77 Aligned_cols=41 Identities=12% Similarity=0.131 Sum_probs=32.0
Q ss_pred HHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 170 AVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 170 ~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
..-+++.|+.+|.+.+.||...++|..++.+....-...|.
T Consensus 67 ~~~ll~~~Yv~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~ 107 (125)
T PF06530_consen 67 EYDLLILYYVYGWSKRQIARKLKCSEGKIRKRLQRAEGFID 107 (125)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHhhhhHh
Confidence 34556666778999999999999999999888765555444
No 305
>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=32.31 E-value=52 Score=27.09 Aligned_cols=28 Identities=18% Similarity=0.218 Sum_probs=22.0
Q ss_pred ccHHHHhhhccCCcchhHHHHHHHHHHH
Q 012200 182 LSAKALASRYSLEPYLISKITNMVTRLL 209 (468)
Q Consensus 182 ~s~~~la~~Fgvs~sTvsri~~~v~~~l 209 (468)
.++..+|+..||+.|||||+......-+
T Consensus 24 ~gq~~vA~~~Gv~eStISR~k~~~~~~~ 51 (91)
T PF05269_consen 24 VGQKKVAEAMGVDESTISRWKNDFIEKM 51 (91)
T ss_dssp HHHHHHHHHHTSSTTTHHHHHHHHHHHH
T ss_pred HhhHHHHHHhCCCHHHHHHHHhhHHHHH
Confidence 4578899999999999999875544333
No 306
>PF14493 HTH_40: Helix-turn-helix domain
Probab=31.96 E-value=60 Score=26.21 Aligned_cols=37 Identities=16% Similarity=0.125 Sum_probs=30.8
Q ss_pred HHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHH
Q 012200 172 AMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRL 208 (468)
Q Consensus 172 ~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~ 208 (468)
..++..+..|.+..++|..-|++.+||...+-+....
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 4678888899999999999999999998776554433
No 307
>PRK15215 fimbriae biosynthesis regulatory protein; Provisional
Probab=31.37 E-value=2e+02 Score=24.12 Aligned_cols=55 Identities=22% Similarity=0.290 Sum_probs=38.9
Q ss_pred CCHHHHHHHHHHhccccccCCCCCCHHHHHHHHH-hhhccCccHHHHhhhccCCcchhHHHHHHHH
Q 012200 142 LSYPVFTTVVEKLKPYIAASNLSLPSDYAVAMVL-SRLAHGLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 142 ms~~~F~~L~~~L~p~l~~~~~~l~~e~~L~i~L-~~La~g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
|+.+.|.-|++.- ++..+ ++..+| .||-.|.+-++++++++|+++..+-.+++.-
T Consensus 31 v~eehF~LLieIS---------~IrS~-KvI~AL~dyLV~G~trkevCe~~~Vn~gYfS~~L~rL~ 86 (100)
T PRK15215 31 VNEEHFWLLIGIS---------SIHSE-KIIQALRDYLVFGVSRKDVCERYEVNNGYFSTSLNRLS 86 (100)
T ss_pred cCHHHHHHHHHHc---------ccchH-HHHHHHHHHHHcCccHHHHHHccCCCHHHHHHHHHHHH
Confidence 5666666666653 23333 355555 5788999999999999999999887665543
No 308
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=31.22 E-value=30 Score=36.71 Aligned_cols=31 Identities=16% Similarity=0.291 Sum_probs=25.7
Q ss_pred ccHHHHhhhccCCcchhHHHHHHHHHHHHhhcCCccccCCCc
Q 012200 182 LSAKALASRYSLEPYLISKITNMVTRLLATKLYPEFIKIPIS 223 (468)
Q Consensus 182 ~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~~~~I~~P~~ 223 (468)
...+++|+..|++.|||||++ ..+|+.-|.+
T Consensus 331 L~LrdvA~~i~~HESTISRai-----------~nKy~~tprG 361 (444)
T COG1508 331 LVLRDVADEIGMHESTISRAI-----------TNKYLATPRG 361 (444)
T ss_pred ccHHHHHHHhCccHHHHHHHH-----------hcccccCCcc
Confidence 677999999999999999986 4577777743
No 309
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=31.02 E-value=60 Score=31.89 Aligned_cols=43 Identities=12% Similarity=0.091 Sum_probs=34.7
Q ss_pred HHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 170 AVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 170 ~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
++-+++....+| ++...|+..+|++++||+.+++.-..+-..|
T Consensus 5 ~L~~f~~v~~~g-S~s~AA~~L~itQpavS~~i~~LE~~lg~~L 47 (305)
T PRK11151 5 DLEYLVALAEHR-HFRRAADSCHVSQPTLSGQIRKLEDELGVML 47 (305)
T ss_pred HHHHHHHHHHhC-CHHHHHHHhCCCchHHHHHHHHHHHHhCchh
Confidence 455555566666 9999999999999999999999888876544
No 310
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=31.00 E-value=62 Score=27.84 Aligned_cols=40 Identities=15% Similarity=0.087 Sum_probs=28.4
Q ss_pred HHHHHHHhhhcc-CccHHHHhhhccCCcchhHHHHHHHHHH
Q 012200 169 YAVAMVLSRLAH-GLSAKALASRYSLEPYLISKITNMVTRL 208 (468)
Q Consensus 169 ~~L~i~L~~La~-g~s~~~la~~Fgvs~sTvsri~~~v~~~ 208 (468)
.++.|......+ +.+..+++..+|++++||++.++...++
T Consensus 17 tRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~A 57 (117)
T PRK10141 17 TRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRES 57 (117)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 344444333333 4678999999999999999998766554
No 311
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=30.95 E-value=54 Score=32.57 Aligned_cols=47 Identities=11% Similarity=0.076 Sum_probs=38.5
Q ss_pred HHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcCC
Q 012200 169 YAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLYP 215 (468)
Q Consensus 169 ~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~~ 215 (468)
.++-+++....+|.++...|+..++|+++||+.+++.-..+-..|..
T Consensus 4 ~~L~~f~~v~~~g~S~s~AA~~L~isQpavS~~ik~LE~~lg~~Lf~ 50 (313)
T PRK12684 4 HQLRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFT 50 (313)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhcCCChHHHHHHHHHHHHhCCeeEE
Confidence 35666666777777999999999999999999999999888755543
No 312
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=30.53 E-value=35 Score=36.43 Aligned_cols=32 Identities=22% Similarity=0.314 Sum_probs=27.1
Q ss_pred CccHHHHhhhccCCcchhHHHHHHHHHHHHhhcCCccccCCCc
Q 012200 181 GLSAKALASRYSLEPYLISKITNMVTRLLATKLYPEFIKIPIS 223 (468)
Q Consensus 181 g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~~~~I~~P~~ 223 (468)
..+.++||...|++.|||||++ ..+|+..|.+
T Consensus 343 PLtlkdvAe~lglheSTVSRav-----------~~Kyv~tp~G 374 (455)
T PRK05932 343 PLVLKDIAEELGMHESTISRAT-----------TNKYMATPRG 374 (455)
T ss_pred CccHHHHHHHhCCCccchhhhh-----------cCceeecCCc
Confidence 4578999999999999999986 5688888843
No 313
>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=30.30 E-value=57 Score=27.04 Aligned_cols=40 Identities=15% Similarity=0.021 Sum_probs=31.8
Q ss_pred HHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 174 VLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 174 ~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.|.-+....++...|...|+|++++++.++..-..+-..|
T Consensus 9 ~~~av~~~gSis~AA~~L~iS~stvs~~I~~LE~~lg~~L 48 (99)
T TIGR00637 9 LLKAIARMGSISQAAKDAGISYKSAWDYIRAMNNLSGEPL 48 (99)
T ss_pred HHHHHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCCe
Confidence 3444455678899999999999999999998888876443
No 314
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=30.25 E-value=56 Score=29.04 Aligned_cols=45 Identities=16% Similarity=0.162 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLA 210 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~ 210 (468)
.+++.++=. |.++..|.+.+++|...++|..||..++.+..+-+.
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 366544333 445789999999999999999999988877655543
No 315
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=30.04 E-value=55 Score=29.49 Aligned_cols=44 Identities=16% Similarity=0.194 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLL 209 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l 209 (468)
.++..+. -+|..|..|.+..+++...++|..||..++.....-+
T Consensus 143 ~lt~~E~--~vl~~l~~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl 186 (204)
T PRK09958 143 SLSKQEI--SVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKL 186 (204)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 4666544 3677888999999999999999999988877665544
No 316
>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=29.90 E-value=17 Score=33.04 Aligned_cols=30 Identities=23% Similarity=0.404 Sum_probs=0.0
Q ss_pred CccHHHHhhhccCCcchhHHHHHHHHHHHHhhcCCccccCC
Q 012200 181 GLSAKALASRYSLEPYLISKITNMVTRLLATKLYPEFIKIP 221 (468)
Q Consensus 181 g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~~~~I~~P 221 (468)
..+..++|+..|++.|||||++ ..+|+..|
T Consensus 49 PLt~~~iA~~lgl~~STVSRav-----------~~Ky~~t~ 78 (160)
T PF04552_consen 49 PLTMKDIADELGLHESTVSRAV-----------KNKYIQTP 78 (160)
T ss_dssp -----------------------------------------
T ss_pred CCCHHHHHHHhCCCHhHHHHHH-----------cCceeecC
Confidence 4578899999999999999986 34667666
No 317
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=29.80 E-value=78 Score=31.13 Aligned_cols=45 Identities=9% Similarity=0.019 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHhhhcc---CccHHHHhhhccCCcchhHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAH---GLSAKALASRYSLEPYLISKITNMVTRL 208 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~---g~s~~~la~~Fgvs~sTvsri~~~v~~~ 208 (468)
.++.-++.+-.|..++. +.+..+|+...|++++|++|+++..+..
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 46666677777777763 4688999999999999999998776653
No 318
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=29.64 E-value=27 Score=34.68 Aligned_cols=22 Identities=14% Similarity=0.028 Sum_probs=19.0
Q ss_pred cHHHHhhhccCCcchhHHHHHH
Q 012200 183 SAKALASRYSLEPYLISKITNM 204 (468)
Q Consensus 183 s~~~la~~Fgvs~sTvsri~~~ 204 (468)
+.++||+.-|||.+||||+++.
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn~ 22 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVING 22 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 3579999999999999999853
No 319
>PF12728 HTH_17: Helix-turn-helix domain
Probab=29.42 E-value=35 Score=24.10 Aligned_cols=21 Identities=10% Similarity=0.083 Sum_probs=17.9
Q ss_pred cHHHHhhhccCCcchhHHHHH
Q 012200 183 SAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 183 s~~~la~~Fgvs~sTvsri~~ 203 (468)
+..++|..+|||.+|+.++++
T Consensus 3 t~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999988763
No 320
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=29.36 E-value=25 Score=34.87 Aligned_cols=19 Identities=21% Similarity=0.247 Sum_probs=17.6
Q ss_pred HHHhhhccCCcchhHHHHH
Q 012200 185 KALASRYSLEPYLISKITN 203 (468)
Q Consensus 185 ~~la~~Fgvs~sTvsri~~ 203 (468)
++||...|||.+||||+++
T Consensus 2 ~dIA~~agVS~~TVSrvLn 20 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVIN 20 (327)
T ss_pred hhHHHHhCCcHHHHHHHhC
Confidence 5899999999999999986
No 321
>PRK10072 putative transcriptional regulator; Provisional
Probab=29.34 E-value=37 Score=28.14 Aligned_cols=27 Identities=15% Similarity=0.245 Sum_probs=23.4
Q ss_pred hhccCccHHHHhhhccCCcchhHHHHH
Q 012200 177 RLAHGLSAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 177 ~La~g~s~~~la~~Fgvs~sTvsri~~ 203 (468)
+-..|.++..+|..+|+|.+||++|.+
T Consensus 42 R~~~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 42 RKGTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 446699999999999999999998853
No 322
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=29.33 E-value=55 Score=27.13 Aligned_cols=46 Identities=17% Similarity=0.200 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHh
Q 012200 165 LPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLAT 211 (468)
Q Consensus 165 l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~ 211 (468)
+++++-=++-|.-+ .|.++.+.|.+.|||+.|+.+.++..-.-+++
T Consensus 34 lt~eElEAlRLvD~-~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~ 79 (99)
T COG1342 34 LTIEELEALRLVDY-EGLTQEEAALRMGISRQTFWRLLTSARKKVAD 79 (99)
T ss_pred ecHHHHHHHHHHhH-hhccHHHHHHHhcccHHHHHHHHHHHHHHHHH
Confidence 45555444444443 47899999999999999999988654444433
No 323
>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=29.31 E-value=80 Score=29.56 Aligned_cols=38 Identities=16% Similarity=0.165 Sum_probs=28.8
Q ss_pred HHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHH
Q 012200 168 DYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 168 e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
..+++..|..- .+.+..+++..+|++++||++.+....
T Consensus 3 r~~IL~~L~~~-~~~t~~eLA~~lgis~~tV~~~L~~Le 40 (203)
T TIGR02702 3 KEDILSYLLKQ-GQATAAALAEALAISPQAVRRHLKDLE 40 (203)
T ss_pred HHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45566666553 458999999999999999998875543
No 324
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=29.19 E-value=67 Score=31.37 Aligned_cols=43 Identities=19% Similarity=0.180 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHhhhcc---CccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 165 LPSDYAVAMVLSRLAH---GLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 165 l~~e~~L~i~L~~La~---g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
+..-++.+-.|..|+. +.+..+++...|++++|++|+++....
T Consensus 7 v~sl~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~ 52 (263)
T PRK09834 7 VRGLSRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQE 52 (263)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4445566666777753 368999999999999999999876653
No 325
>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=29.17 E-value=1.2e+02 Score=20.99 Aligned_cols=25 Identities=16% Similarity=0.057 Sum_probs=18.5
Q ss_pred cCccHHHHhhhccCCcchhHHHHHH
Q 012200 180 HGLSAKALASRYSLEPYLISKITNM 204 (468)
Q Consensus 180 ~g~s~~~la~~Fgvs~sTvsri~~~ 204 (468)
.-.+|.++|...|+|.+||.+=+.+
T Consensus 16 ~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 16 GRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHH
Confidence 3468999999999999999765543
No 326
>PRK15340 transcriptional regulator InvF; Provisional
Probab=28.72 E-value=1.8e+02 Score=27.82 Aligned_cols=30 Identities=10% Similarity=0.145 Sum_probs=24.5
Q ss_pred ccCccHHHHhhhccCCcchhHHHHHHHHHH
Q 012200 179 AHGLSAKALASRYSLEPYLISKITNMVTRL 208 (468)
Q Consensus 179 a~g~s~~~la~~Fgvs~sTvsri~~~v~~~ 208 (468)
....+..++|..+|+|.++++|.|++.+..
T Consensus 123 ~~~~sleeLA~~~gvS~r~f~RlFk~~~G~ 152 (216)
T PRK15340 123 TSGNTMRMLGEDYGVSYTHFRRLCSRALGG 152 (216)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHCc
Confidence 345678899999999999999999876443
No 327
>PRK14999 histidine utilization repressor; Provisional
Probab=28.67 E-value=83 Score=30.15 Aligned_cols=21 Identities=14% Similarity=0.317 Sum_probs=17.2
Q ss_pred HHHhhhccCCcchhHHHHHHH
Q 012200 185 KALASRYSLEPYLISKITNMV 205 (468)
Q Consensus 185 ~~la~~Fgvs~sTvsri~~~v 205 (468)
++++..||||+.||.+.+...
T Consensus 40 ~eLa~~~gVSR~TVR~Al~~L 60 (241)
T PRK14999 40 AELVAQYGFSRMTINRALREL 60 (241)
T ss_pred HHHHHHHCCCHHHHHHHHHHH
Confidence 467899999999998887554
No 328
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=28.61 E-value=40 Score=25.96 Aligned_cols=26 Identities=31% Similarity=0.340 Sum_probs=23.1
Q ss_pred hhccCccHHHHhhhccCCcchhHHHH
Q 012200 177 RLAHGLSAKALASRYSLEPYLISKIT 202 (468)
Q Consensus 177 ~La~g~s~~~la~~Fgvs~sTvsri~ 202 (468)
+-..|.+..++|...|++++|++++.
T Consensus 14 ~~~~~~t~~~lA~~~gis~~tis~~~ 39 (78)
T TIGR02607 14 LEPLGLSIRALAKALGVSRSTLSRIV 39 (78)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 45678899999999999999999875
No 329
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=28.41 E-value=2e+02 Score=26.58 Aligned_cols=75 Identities=16% Similarity=0.109 Sum_probs=48.2
Q ss_pred ChhhHHHhcCCCHHHHHHHHHHhccccccCCCC-CCHHHHHHHHHhhh----ccCc------cH----HHHhhhccCCcc
Q 012200 132 REAHWRSLYGLSYPVFTTVVEKLKPYIAASNLS-LPSDYAVAMVLSRL----AHGL------SA----KALASRYSLEPY 196 (468)
Q Consensus 132 ~d~~fr~~fRms~~~F~~L~~~L~p~l~~~~~~-l~~e~~L~i~L~~L----a~g~------s~----~~la~~Fgvs~s 196 (468)
+-+-..++||||...+...=..++-...+++++ ++.++...+--.+- ..+. .+ -.+|+..++|-+
T Consensus 89 S~~mm~~~FGls~~ev~~rR~llgi~~~~GR~~~~~ee~~~~iW~~W~~~~~~~~~~~~~~~~~Le~~m~~Ae~~~isL~ 168 (180)
T PF11198_consen 89 SIEMMQRLFGLSSAEVAARRRLLGIPVRKGRPPALSEEEEAAIWRRWQQLMKKRGVDNLDSPDALELMMLLAEETNISLT 168 (180)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHhCCCCCCCCCCCcCHHHHHHHHHHHHHHHhhcCCCCccchHHHHHHHHHHHHhCCCHH
Confidence 566778899999999999888887654444444 44444443333232 1121 12 237888899888
Q ss_pred hhHHHHHHHH
Q 012200 197 LISKITNMVT 206 (468)
Q Consensus 197 Tvsri~~~v~ 206 (468)
+|...+..+.
T Consensus 169 ~iW~~i~~w~ 178 (180)
T PF11198_consen 169 VIWSLIQEWE 178 (180)
T ss_pred HHHHHHHHHH
Confidence 8887776654
No 330
>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=28.25 E-value=87 Score=29.72 Aligned_cols=22 Identities=14% Similarity=0.282 Sum_probs=17.5
Q ss_pred HHHhhhccCCcchhHHHHHHHH
Q 012200 185 KALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 185 ~~la~~Fgvs~sTvsri~~~v~ 206 (468)
++++.+||||+.||.+.+....
T Consensus 36 ~eLa~~~~VSR~TvR~Al~~L~ 57 (238)
T TIGR02325 36 MQLAERFGVNRHTVRRAIAALV 57 (238)
T ss_pred HHHHHHHCCCHHHHHHHHHHHH
Confidence 3668999999999988875543
No 331
>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=28.18 E-value=29 Score=34.40 Aligned_cols=21 Identities=14% Similarity=0.191 Sum_probs=19.2
Q ss_pred cHHHHhhhccCCcchhHHHHH
Q 012200 183 SAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 183 s~~~la~~Fgvs~sTvsri~~ 203 (468)
+.++||+.-|||.+||||+++
T Consensus 3 ti~dIA~~agvS~~TVSrvLn 23 (329)
T TIGR01481 3 TIYDVAREAGVSMATVSRVVN 23 (329)
T ss_pred cHHHHHHHhCCCHHHHHHHhC
Confidence 578999999999999999985
No 332
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=28.00 E-value=86 Score=22.78 Aligned_cols=39 Identities=13% Similarity=0.162 Sum_probs=23.9
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~ 203 (468)
.++..+|-.+-+ +...|.+...++.+.|.|+.+|.++++
T Consensus 4 ~Lt~~Eqaqid~-m~qlG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 4 TLTDAEQAQIDV-MHQLGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp ---HHHHHHHHH-HHHTT--HHHHHHHHT--HHHHHHHHH
T ss_pred cCCHHHHHHHHH-HHHhchhHHHHHHHhCccHHHHHHHhc
Confidence 456666655433 456789999999999999999988864
No 333
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=27.99 E-value=87 Score=30.01 Aligned_cols=21 Identities=10% Similarity=0.252 Sum_probs=17.0
Q ss_pred HHHhhhccCCcchhHHHHHHH
Q 012200 185 KALASRYSLEPYLISKITNMV 205 (468)
Q Consensus 185 ~~la~~Fgvs~sTvsri~~~v 205 (468)
.+++..||||+.||.+.+...
T Consensus 33 ~eL~~~~~VSR~TvR~Al~~L 53 (240)
T PRK09764 33 SALQTEFGVSRVTVRQALRQL 53 (240)
T ss_pred HHHHHHHCCCHHHHHHHHHHH
Confidence 366899999999998877554
No 334
>PRK11050 manganese transport regulator MntR; Provisional
Probab=27.83 E-value=84 Score=28.08 Aligned_cols=28 Identities=14% Similarity=0.214 Sum_probs=23.9
Q ss_pred cCccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 180 HGLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 180 ~g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
.+.+..+++..++++++++++.+.....
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~ 77 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLAR 77 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4678999999999999999998866653
No 335
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=27.77 E-value=53 Score=26.35 Aligned_cols=24 Identities=13% Similarity=0.390 Sum_probs=20.1
Q ss_pred HHHHhhhccCCcchhHHHHHHHHH
Q 012200 184 AKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 184 ~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
..+++..+|++++|+++.+.....
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~ 25 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEK 25 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHH
Confidence 468999999999999999876554
No 336
>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=27.77 E-value=78 Score=30.51 Aligned_cols=44 Identities=14% Similarity=0.069 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHhhhcc---CccHHHHhhhccCCcchhHHHHHHHHHH
Q 012200 165 LPSDYAVAMVLSRLAH---GLSAKALASRYSLEPYLISKITNMVTRL 208 (468)
Q Consensus 165 l~~e~~L~i~L~~La~---g~s~~~la~~Fgvs~sTvsri~~~v~~~ 208 (468)
+..-++.+-.|..++. +.+..+|+...|++++|++|++......
T Consensus 5 v~sl~ral~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~ 51 (248)
T TIGR02431 5 VASLARGLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVEL 51 (248)
T ss_pred HHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3444556666777653 5789999999999999999998776543
No 337
>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=27.76 E-value=82 Score=29.11 Aligned_cols=41 Identities=12% Similarity=0.075 Sum_probs=30.9
Q ss_pred CCCCHHHHHHHHHhhhc-cCccHHHHhhhccCCcchhHHHHH
Q 012200 163 LSLPSDYAVAMVLSRLA-HGLSAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La-~g~s~~~la~~Fgvs~sTvsri~~ 203 (468)
..+++.++...+...+. .|.+...+|..+|+|+++|+++..
T Consensus 101 ~~lt~~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~ 142 (187)
T TIGR00180 101 EDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLR 142 (187)
T ss_pred cCCCHHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHH
Confidence 35777665554444443 688999999999999999998864
No 338
>cd00131 PAX Paired Box domain
Probab=27.60 E-value=2.8e+02 Score=24.03 Aligned_cols=75 Identities=11% Similarity=0.078 Sum_probs=46.5
Q ss_pred CCCChhhHHHhcCCCHHHHHHHHHHhccccc------c-CCCC-CCH-HHHHHHHHhhhccCccHHHHhhhc---cC---
Q 012200 129 APLREAHWRSLYGLSYPVFTTVVEKLKPYIA------A-SNLS-LPS-DYAVAMVLSRLAHGLSAKALASRY---SL--- 193 (468)
Q Consensus 129 ~~l~d~~fr~~fRms~~~F~~L~~~L~p~l~------~-~~~~-l~~-e~~L~i~L~~La~g~s~~~la~~F---gv--- 193 (468)
.-++..+.-..|++++.+...++...+.... . .++. +.. ....++.+..-....+..++++.+ |+
T Consensus 32 ~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~ 111 (128)
T cd00131 32 SGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDK 111 (128)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCccc
Confidence 4567888899999999999999988664211 1 1122 233 233333333333345666666553 55
Q ss_pred ----CcchhHHHHH
Q 012200 194 ----EPYLISKITN 203 (468)
Q Consensus 194 ----s~sTvsri~~ 203 (468)
|.+||+|+++
T Consensus 112 ~~~~s~stI~R~L~ 125 (128)
T cd00131 112 SNVPSVSSINRILR 125 (128)
T ss_pred CCCCCHHHHHHHHH
Confidence 9999998864
No 339
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=27.60 E-value=30 Score=34.71 Aligned_cols=21 Identities=19% Similarity=0.234 Sum_probs=19.3
Q ss_pred cHHHHhhhccCCcchhHHHHH
Q 012200 183 SAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 183 s~~~la~~Fgvs~sTvsri~~ 203 (468)
+.++||+.-|||.+||||+++
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVIN 23 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhC
Confidence 578999999999999999985
No 340
>PRK04140 hypothetical protein; Provisional
Probab=27.48 E-value=70 Score=32.49 Aligned_cols=72 Identities=29% Similarity=0.258 Sum_probs=48.1
Q ss_pred CCChhhHHHhcC---CCHHH-HHHHHHHhccccccC--CCCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHH
Q 012200 130 PLREAHWRSLYG---LSYPV-FTTVVEKLKPYIAAS--NLSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKIT 202 (468)
Q Consensus 130 ~l~d~~fr~~fR---ms~~~-F~~L~~~L~p~l~~~--~~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~ 202 (468)
.+.+.....++| ++.++ |+.+++-..|.+-.. ..-+...-.. +--.+-..|.++.++|...|+|++|+++|-
T Consensus 83 ~le~gvvy~r~gi~~~~~~tl~~~~~~g~~p~v~~~~Gg~~v~i~Ger-Lk~lRe~~GlSq~eLA~~lGVSr~tIskyE 160 (317)
T PRK04140 83 ELEDGVVYERHGIPALSPDTLYDDFVEGEPPLIYAAPGGFYVKIDGDV-LREAREELGLSLGELASELGVSRRTISKYE 160 (317)
T ss_pred ccCCCcEEEecCceeecHHHHHHHHhCCCCceEEEcCCCeeehhhHHH-HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 344444445555 58888 888888887754322 2222222212 233477789999999999999999999885
No 341
>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=27.21 E-value=72 Score=31.01 Aligned_cols=43 Identities=21% Similarity=0.096 Sum_probs=32.9
Q ss_pred HHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 170 AVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 170 ~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
+|-.++....+| ++...|+..+|+++++|+.++..-..+-..|
T Consensus 5 ~L~~f~~v~~~g-s~s~AA~~L~itqpavS~~Ik~LE~~lg~~L 47 (291)
T TIGR03418 5 ALRVFESAARLA-SFTAAARELGSTQPAVSQQVKRLEEELGTPL 47 (291)
T ss_pred HHHHHHHHHHhC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCcHH
Confidence 344444444444 9999999999999999999998888765444
No 342
>PRK09726 antitoxin HipB; Provisional
Probab=27.18 E-value=40 Score=27.08 Aligned_cols=27 Identities=26% Similarity=0.400 Sum_probs=23.1
Q ss_pred hhccCccHHHHhhhccCCcchhHHHHH
Q 012200 177 RLAHGLSAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 177 ~La~g~s~~~la~~Fgvs~sTvsri~~ 203 (468)
+-..|.+..++|...||+++|++++.+
T Consensus 21 R~~~gltq~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 21 RQQNGWTQSELAKKIGIKQATISNFEN 47 (88)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 345789999999999999999998853
No 343
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=26.58 E-value=81 Score=30.72 Aligned_cols=38 Identities=18% Similarity=0.179 Sum_probs=30.5
Q ss_pred hhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 177 RLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 177 ~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
-++...++...|+..++|+++||+.+++.-..+-..|.
T Consensus 12 ~v~~~gs~t~AA~~L~iSQ~avS~~i~~LE~~lg~~Lf 49 (294)
T PRK13348 12 AVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLL 49 (294)
T ss_pred HHHHcCCHHHHHHHhCCCchHHHHHHHHHHHHhCceee
Confidence 33344589999999999999999999998888765443
No 344
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=26.42 E-value=34 Score=34.77 Aligned_cols=21 Identities=19% Similarity=0.246 Sum_probs=19.1
Q ss_pred cHHHHhhhccCCcchhHHHHH
Q 012200 183 SAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 183 s~~~la~~Fgvs~sTvsri~~ 203 (468)
+..++|..-|||++||||+++
T Consensus 2 TikDVA~~AGVS~sTVSrvln 22 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLN 22 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHc
Confidence 568999999999999999985
No 345
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=26.40 E-value=1.2e+02 Score=29.14 Aligned_cols=65 Identities=14% Similarity=0.077 Sum_probs=38.4
Q ss_pred CCHHHHHHHHHHhccccccC--CCCCCH--HHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHH
Q 012200 142 LSYPVFTTVVEKLKPYIAAS--NLSLPS--DYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 142 ms~~~F~~L~~~L~p~l~~~--~~~l~~--e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
++.+..+.|...-...-... .+++.. ..++.-.|.--..+.+-.++|+..|+|+.|++|++....
T Consensus 130 ~sQ~~lD~l~~~~~k~~~~~~LPkGi~~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~ 198 (224)
T COG4565 130 LSQKELDQLFNIQSKEQPPDDLPKGLDELTLQKVREALKEPDQELTAEELAQALGISRVTARRYLEYLV 198 (224)
T ss_pred cCHHHHHHHHhccccccCcccCCCCcCHHHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHH
Confidence 56666666665443211111 122322 333444444344667888999999999999999975543
No 346
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=26.18 E-value=71 Score=32.05 Aligned_cols=46 Identities=20% Similarity=0.228 Sum_probs=37.0
Q ss_pred HHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 169 YAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 169 ~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
.+|-.++....+|.++...|+..++|++++|+.++..-..+-..|.
T Consensus 4 ~~L~~f~avae~g~S~s~AA~~L~iSQpavS~~I~~LE~~lG~~LF 49 (324)
T PRK12681 4 QQLRYIVEVVNHNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIF 49 (324)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhCCEeE
Confidence 3455566666677899999999999999999999999888765443
No 347
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=26.16 E-value=98 Score=29.62 Aligned_cols=44 Identities=23% Similarity=0.399 Sum_probs=28.9
Q ss_pred HHHHHHHhcccccc----CCCCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHH
Q 012200 147 FTTVVEKLKPYIAA----SNLSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 147 F~~L~~~L~p~l~~----~~~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
+..|.+.|+..+.. .+..+|.|. +++..||||+.||.+.+....
T Consensus 11 y~qI~~~i~~~I~~G~~~~g~kLPsE~----------------eLa~~~~VSR~TvR~Al~~L~ 58 (241)
T PRK11402 11 YATVRQRLLDDIAQGVYQAGQQIPTEN----------------ELCTQYNVSRITIRKAISDLV 58 (241)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCcCHH----------------HHHHHHCCCHHHHHHHHHHHH
Confidence 44555555544432 234678776 567899999999988875543
No 348
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=26.08 E-value=69 Score=31.78 Aligned_cols=43 Identities=14% Similarity=0.028 Sum_probs=33.0
Q ss_pred HHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 170 AVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 170 ~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
+|-+++.... ..++...|++.++|++++|+.+++.-..+-..|
T Consensus 6 ~L~~f~~v~e-~gs~s~AA~~L~iSQpavS~~I~~LE~~lg~~L 48 (308)
T PRK10094 6 TLRTFIAVAE-TGSFSKAAERLCKTTATISYRIKLLEENTGVAL 48 (308)
T ss_pred HHHHHHHHHH-hCCHHHHHHHhcCCHHHHHHHHHHHHHHhCCEE
Confidence 3444444444 448999999999999999999999988876544
No 349
>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=26.03 E-value=36 Score=36.14 Aligned_cols=31 Identities=19% Similarity=0.342 Sum_probs=26.5
Q ss_pred CccHHHHhhhccCCcchhHHHHHHHHHHHHhhcCCccccCCC
Q 012200 181 GLSAKALASRYSLEPYLISKITNMVTRLLATKLYPEFIKIPI 222 (468)
Q Consensus 181 g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~~~~I~~P~ 222 (468)
..+.+++|+..|++.|||||++ ..+|+..|.
T Consensus 318 PLtlkdiA~~lglheSTVSRav-----------~~Kyi~tp~ 348 (429)
T TIGR02395 318 PLTLREVAEELGLHESTISRAI-----------NNKYLQTPR 348 (429)
T ss_pred CCcHHHHHHHhCCCccchhhhh-----------cCceEecCC
Confidence 4578999999999999999986 467888884
No 350
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=25.93 E-value=72 Score=31.08 Aligned_cols=42 Identities=12% Similarity=0.073 Sum_probs=33.6
Q ss_pred HHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 173 MVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 173 i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
-++..++...++...|+..++|+++||+.++..-+.+-..|.
T Consensus 7 ~~f~~v~~~gs~s~AA~~L~isQ~avSr~i~~LE~~lg~~Lf 48 (296)
T PRK09906 7 RYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLL 48 (296)
T ss_pred HHHHHHHhhCCHHHHHHHhCCCCcHHHHHHHHHHHHhCCeee
Confidence 344455555699999999999999999999999888765443
No 351
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=25.87 E-value=1.1e+02 Score=25.08 Aligned_cols=28 Identities=14% Similarity=0.297 Sum_probs=22.9
Q ss_pred ccCccHHHHhhhccCCcchhHHHHHHHH
Q 012200 179 AHGLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 179 a~g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
....+..++|..+|+|..+++++|++..
T Consensus 19 ~~~~~~~~lA~~~~~S~~~l~r~f~~~~ 46 (107)
T PRK10219 19 DQPLNIDVVAKKSGYSKWYLQRMFRTVT 46 (107)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3445677899999999999999998764
No 352
>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=25.34 E-value=1.2e+02 Score=22.34 Aligned_cols=39 Identities=15% Similarity=0.221 Sum_probs=28.1
Q ss_pred HHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHH
Q 012200 170 AVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLL 209 (468)
Q Consensus 170 ~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l 209 (468)
+++-.|.- ....++.+++...|+|..|+.+.+.+.-..+
T Consensus 9 ~Ll~~L~~-~~~~~~~ela~~l~~S~rti~~~i~~L~~~f 47 (59)
T PF08280_consen 9 KLLELLLK-NKWITLKELAKKLNISERTIKNDINELNEFF 47 (59)
T ss_dssp HHHHHHHH-HTSBBHHHHHHHCTS-HHHHHHHHHHHHTT-
T ss_pred HHHHHHHc-CCCCcHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 34445555 6667899999999999999988887665443
No 353
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=25.22 E-value=76 Score=31.12 Aligned_cols=43 Identities=14% Similarity=0.186 Sum_probs=33.3
Q ss_pred HHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 170 AVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 170 ~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
+|-.++....+| ++...|+..++|+++||+.++..-..+-..|
T Consensus 9 ~L~~f~~v~~~g-s~s~AA~~L~isQ~avS~~i~~LE~~lG~~L 51 (302)
T PRK09791 9 QIRAFVEVARQG-SIRGASRMLNMSQPALTKSIQELEEGLAAQL 51 (302)
T ss_pred HHHHHHHHHHcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCeE
Confidence 344444444444 9999999999999999999999988876544
No 354
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=25.17 E-value=1e+02 Score=25.30 Aligned_cols=22 Identities=23% Similarity=0.412 Sum_probs=19.5
Q ss_pred HHHhhhccCCcchhHHHHHHHH
Q 012200 185 KALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 185 ~~la~~Fgvs~sTvsri~~~v~ 206 (468)
.+++...++++++++++++...
T Consensus 40 ~~la~~l~i~~~~vt~~l~~Le 61 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRLE 61 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHHH
Confidence 8999999999999999886654
No 355
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=25.17 E-value=82 Score=31.13 Aligned_cols=43 Identities=14% Similarity=0.165 Sum_probs=33.3
Q ss_pred HHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 170 AVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 170 ~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
++-+++....+| ++...|+..++++++||+.+++.-.-+-..|
T Consensus 8 ~L~~f~av~~~g-S~s~AAe~L~isqsavS~~Ik~LE~~lg~~L 50 (309)
T PRK11013 8 HIEIFHAVMTAG-SLTEAARLLHTSQPTVSRELARFEKVIGLKL 50 (309)
T ss_pred HHHHHHHHHHhC-cHHHHHHHHCCCcHHHHHHHHHHHHHhCcee
Confidence 444455445554 9999999999999999999999888876444
No 356
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=24.61 E-value=99 Score=29.42 Aligned_cols=20 Identities=5% Similarity=0.130 Sum_probs=16.2
Q ss_pred HHHhhhccCCcchhHHHHHH
Q 012200 185 KALASRYSLEPYLISKITNM 204 (468)
Q Consensus 185 ~~la~~Fgvs~sTvsri~~~ 204 (468)
++++..||||++||.+.+..
T Consensus 35 ~eLae~~gVSRt~VReAL~~ 54 (239)
T PRK04984 35 RELSELIGVTRTTLREVLQR 54 (239)
T ss_pred HHHHHHHCCCHHHHHHHHHH
Confidence 46789999999999876644
No 357
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=24.50 E-value=1.3e+02 Score=27.13 Aligned_cols=66 Identities=20% Similarity=0.208 Sum_probs=47.1
Q ss_pred cCCCHHHHHHHHHHhccccccC------------------CCCCCHHHHHHHHHhhhcc--------------CccHHHH
Q 012200 140 YGLSYPVFTTVVEKLKPYIAAS------------------NLSLPSDYAVAMVLSRLAH--------------GLSAKAL 187 (468)
Q Consensus 140 fRms~~~F~~L~~~L~p~l~~~------------------~~~l~~e~~L~i~L~~La~--------------g~s~~~l 187 (468)
+.+++..|..++.. .|.+... ....+.+++++.+|..++. ..+...+
T Consensus 99 ~~~~~~~~~~~~~~-~p~l~~~l~~~~~~~l~~~~~~~~~~~~~~~~~r~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~i 177 (214)
T COG0664 99 LEIPRKDFLELLAE-SPKLALALLRLLARRLRQALERLSLLARKDVEERLARFLLNLGRRLGIATEDGILIPLPLTHKDL 177 (214)
T ss_pred EEecHHHHHHHHhh-CcHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHhhccCCCCCCCcEEeccCCHHHH
Confidence 45666677776666 5543210 1246788899999888884 4677889
Q ss_pred hhhccCCcchhHHHHHHHH
Q 012200 188 ASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 188 a~~Fgvs~sTvsri~~~v~ 206 (468)
+...|+++.++++.+.+..
T Consensus 178 a~~~g~~~~~vsr~l~~l~ 196 (214)
T COG0664 178 AEYLGLSRETVSRILKELR 196 (214)
T ss_pred HHHhCCchhhHHHHHHHHH
Confidence 9999999999998876654
No 358
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=24.25 E-value=1.1e+02 Score=29.30 Aligned_cols=46 Identities=17% Similarity=0.393 Sum_probs=31.1
Q ss_pred HHHHHHHHhcccccc----CCCCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 146 VFTTVVEKLKPYIAA----SNLSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 146 ~F~~L~~~L~p~l~~----~~~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
-+..|.+.|+..+.. .+..+|.|. +++..||||+-||.+.+.....
T Consensus 8 lY~qI~~~i~~~I~~G~~~~G~~LPsE~----------------eLa~~f~VSR~TvRkAL~~L~~ 57 (236)
T COG2188 8 LYQQIAEDIRQRIESGELPPGDKLPSER----------------ELAEQFGVSRMTVRKALDELVE 57 (236)
T ss_pred cHHHHHHHHHHHHHhCCCCCCCCCCCHH----------------HHHHHHCCcHHHHHHHHHHHHH
Confidence 445555555555443 235677775 6689999999999988766543
No 359
>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=24.07 E-value=45 Score=27.08 Aligned_cols=23 Identities=17% Similarity=0.232 Sum_probs=17.4
Q ss_pred cCccHHHHhhhccCCcchhHHHH
Q 012200 180 HGLSAKALASRYSLEPYLISKIT 202 (468)
Q Consensus 180 ~g~s~~~la~~Fgvs~sTvsri~ 202 (468)
.|.+..+||.+.|.|++.|++++
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~l 24 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSRSWVSNHL 24 (93)
T ss_dssp TT--HHHHHHHTT--HHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHH
Confidence 58899999999999999999886
No 360
>PRK11569 transcriptional repressor IclR; Provisional
Probab=23.90 E-value=1.1e+02 Score=30.06 Aligned_cols=44 Identities=14% Similarity=0.123 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHhhhcc---CccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAH---GLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~---g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
.+..-++.+-.|.+|+. +.+..+++...|++++|++|+++....
T Consensus 23 ~v~sl~ral~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~ 69 (274)
T PRK11569 23 QVQSLTRGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQ 69 (274)
T ss_pred CccHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 35556666667777764 468999999999999999999876554
No 361
>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=23.64 E-value=95 Score=30.19 Aligned_cols=43 Identities=19% Similarity=0.182 Sum_probs=32.6
Q ss_pred HHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 171 VAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 171 L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
+-.++....+ .++...|+..++|++++|+.+++.-+-+-..|.
T Consensus 6 l~~f~~v~~~-~s~t~AA~~L~isQpavS~~I~~LE~~lg~~Lf 48 (292)
T TIGR03298 6 LAALAAVVEE-GSFERAAAALSVTPSAVSQRIKALEERLGQPLL 48 (292)
T ss_pred HHHHHHHHHc-CCHHHHHHHhCCCHHHHHHHHHHHHHHhCchhe
Confidence 3344444444 499999999999999999999998887764443
No 362
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=23.47 E-value=87 Score=31.47 Aligned_cols=44 Identities=16% Similarity=0.098 Sum_probs=34.2
Q ss_pred HHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhcC
Q 012200 171 VAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKLY 214 (468)
Q Consensus 171 L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L~ 214 (468)
|-+|+....++.++...|+..++++++||+.+++.-+.+-..|.
T Consensus 6 L~~F~~vae~~gS~s~AA~~L~isQpavS~~I~~LE~~lG~~LF 49 (327)
T PRK12680 6 LRYLVAIADAELNITLAAARVHATQPGLSKQLKQLEDELGFLLF 49 (327)
T ss_pred HHHHHHHHHccCCHHHHHHHhcCCchHHHHHHHHHHHHhCCeEE
Confidence 33344334446889999999999999999999999988875554
No 363
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=23.32 E-value=80 Score=30.62 Aligned_cols=39 Identities=18% Similarity=0.207 Sum_probs=33.4
Q ss_pred CCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHH
Q 012200 165 LPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 165 l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~ 203 (468)
+-...++.-.|+.|..-.+|++++..+|++.+.++||++
T Consensus 7 ~~~~~~~v~~lr~lk~~~ty~el~~~~g~p~~~l~RYv~ 45 (238)
T PRK08558 7 VRLQLRAVRVLRSLKKTYTYEELSSITGLPESVLNRYVN 45 (238)
T ss_pred HHHHHHHHHHHHHHhcccCHHHHHHHHCCCHHHHHHHHc
Confidence 344556777899999999999999999999999999974
No 364
>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=23.25 E-value=46 Score=23.22 Aligned_cols=26 Identities=12% Similarity=0.061 Sum_probs=21.5
Q ss_pred cCccHHHHhhhccCCcchhHHHHHHH
Q 012200 180 HGLSAKALASRYSLEPYLISKITNMV 205 (468)
Q Consensus 180 ~g~s~~~la~~Fgvs~sTvsri~~~v 205 (468)
.+.+.++|+.+-|+++++++++|..-
T Consensus 15 ~~~s~~~Ia~~~gvs~~~~y~~f~~k 40 (47)
T PF00440_consen 15 EAVSIRDIARRAGVSKGSFYRYFPSK 40 (47)
T ss_dssp TTSSHHHHHHHHTSCHHHHHHHCSSH
T ss_pred HhCCHHHHHHHHccchhhHHHHcCCH
Confidence 45788999999999999998887443
No 365
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=23.23 E-value=1.5e+02 Score=27.54 Aligned_cols=41 Identities=10% Similarity=0.019 Sum_probs=27.6
Q ss_pred CCCHHHH-HHHHHhhhccCccHHHHhhhccCCcchhHHHHHHH
Q 012200 164 SLPSDYA-VAMVLSRLAHGLSAKALASRYSLEPYLISKITNMV 205 (468)
Q Consensus 164 ~l~~e~~-L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v 205 (468)
.+++.+- ++..|+ -..|.+..++|...++.++|+++++...
T Consensus 42 gLt~~q~~iL~~L~-~~~~itq~eLa~~l~l~~sTvtr~l~rL 83 (185)
T PRK13777 42 DLNINEHHILWIAY-HLKGASISEIAKFGVMHVSTAFNFSKKL 83 (185)
T ss_pred CCCHHHHHHHHHHH-hCCCcCHHHHHHHHCCCHhhHHHHHHHH
Confidence 3554333 333333 3357899999999999999998876543
No 366
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=23.10 E-value=62 Score=28.13 Aligned_cols=27 Identities=26% Similarity=0.217 Sum_probs=23.2
Q ss_pred hhhccCccHHHHhhhccCCcchhHHHH
Q 012200 176 SRLAHGLSAKALASRYSLEPYLISKIT 202 (468)
Q Consensus 176 ~~La~g~s~~~la~~Fgvs~sTvsri~ 202 (468)
.+-..|.++.++|...||+++||++|.
T Consensus 13 ~R~~~gltq~~lA~~~gvs~~~is~~E 39 (135)
T PRK09706 13 RRKQLKLSQRSLAKAVKVSHVSISQWE 39 (135)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 345578899999999999999999874
No 367
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=23.03 E-value=1.2e+02 Score=29.28 Aligned_cols=44 Identities=16% Similarity=0.199 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHhhhccC--ccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHG--LSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g--~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
.++.-++.+-.|..|+.. .+..+++...|++++|++|+++..+.
T Consensus 9 ~v~sl~r~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~ 54 (257)
T PRK15090 9 SVSSVLKVFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKT 54 (257)
T ss_pred ccHHHHHHHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 455666666666666543 57899999999999999999876543
No 368
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=22.75 E-value=1.2e+02 Score=29.33 Aligned_cols=38 Identities=26% Similarity=0.321 Sum_probs=27.8
Q ss_pred HHHHHhhhc-cC--ccHHHHhhhccCCcchhHHHHHHHHHH
Q 012200 171 VAMVLSRLA-HG--LSAKALASRYSLEPYLISKITNMVTRL 208 (468)
Q Consensus 171 L~i~L~~La-~g--~s~~~la~~Fgvs~sTvsri~~~v~~~ 208 (468)
-+-.|..|+ .+ .+..++++..|++++|++|++....+.
T Consensus 6 al~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~ 46 (246)
T COG1414 6 ALAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVEL 46 (246)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHC
Confidence 344455555 23 459999999999999999998765543
No 369
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=22.41 E-value=95 Score=30.12 Aligned_cols=37 Identities=14% Similarity=0.071 Sum_probs=30.3
Q ss_pred hhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 177 RLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 177 ~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+....++...|+..|+++++||+.+++.-+.+-..|
T Consensus 11 ~v~~~gs~s~AA~~L~isqsavS~~i~~LE~~lg~~L 47 (296)
T PRK11242 11 AVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQL 47 (296)
T ss_pred HHHHhCCHHHHHHHcCCCchHHHHHHHHHHHHhCCee
Confidence 3334458999999999999999999999988876544
No 370
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=22.32 E-value=1.2e+02 Score=26.43 Aligned_cols=67 Identities=16% Similarity=0.095 Sum_probs=42.5
Q ss_pred cCCCHHHHHHHHHHhccccccCCCCCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHH-HH-------h
Q 012200 140 YGLSYPVFTTVVEKLKPYIAASNLSLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRL-LA-------T 211 (468)
Q Consensus 140 fRms~~~F~~L~~~L~p~l~~~~~~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~-l~-------~ 211 (468)
||++...++-+...|+. ..+.+-.++|...++++|||+|.++....+ |. +
T Consensus 23 ~GLs~~Dv~v~~~LL~~----------------------~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~ 80 (126)
T COG3355 23 YGLSELDVEVYKALLEE----------------------NGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLK 80 (126)
T ss_pred hCCcHHHHHHHHHHHhh----------------------cCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccC
Confidence 56666666666665532 223455689999999999999999887665 21 1
Q ss_pred hcCCccccCCCchhhhc
Q 012200 212 KLYPEFIKIPISRRRLI 228 (468)
Q Consensus 212 ~L~~~~I~~P~~~~~~~ 228 (468)
.=.+.|+..|.+.++..
T Consensus 81 ~Ggy~yiY~~i~~ee~k 97 (126)
T COG3355 81 GGGYYYLYKPIDPEEIK 97 (126)
T ss_pred CCceeEEEecCCHHHHH
Confidence 11335666565555444
No 371
>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=22.27 E-value=90 Score=30.45 Aligned_cols=42 Identities=19% Similarity=0.150 Sum_probs=32.2
Q ss_pred HHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 171 VAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 171 L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
+-+++... ...++...|+..|+|++++|+.++..-..+-..|
T Consensus 8 l~~f~~v~-~~gS~s~AA~~L~isq~avS~~I~~LE~~lg~~L 49 (300)
T TIGR02424 8 LQCFVEVA-RQGSVKRAAEALHITQPAVSKTLRELEEILGTPL 49 (300)
T ss_pred HHHHHHHH-HhCCHHHHHHHhCCChHHHHHHHHHHHHHhCCeE
Confidence 33344333 4448999999999999999999999988876544
No 372
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=22.24 E-value=1.3e+02 Score=29.53 Aligned_cols=44 Identities=20% Similarity=0.224 Sum_probs=33.9
Q ss_pred CCCCHHHHHHHHHhhhccC-ccHHHHhhhccCCcchhHHHHHHHH
Q 012200 163 LSLPSDYAVAMVLSRLAHG-LSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g-~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
..++.+++-.+-+-+=..| ..+.++.+..|.|++|+||++++..
T Consensus 191 ~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LE 235 (258)
T COG2512 191 YDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLE 235 (258)
T ss_pred CCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHH
Confidence 3567777766655555555 6799999999999999999987654
No 373
>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=22.23 E-value=65 Score=25.18 Aligned_cols=24 Identities=21% Similarity=0.260 Sum_probs=17.8
Q ss_pred CccHHHHhhhccCCcchhHHHHHH
Q 012200 181 GLSAKALASRYSLEPYLISKITNM 204 (468)
Q Consensus 181 g~s~~~la~~Fgvs~sTvsri~~~ 204 (468)
..+..++|...|||++||.|..+.
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 467789999999999999887643
No 374
>COG4062 MtrB Tetrahydromethanopterin S-methyltransferase, subunit B [Coenzyme metabolism]
Probab=22.17 E-value=43 Score=27.84 Aligned_cols=15 Identities=60% Similarity=0.798 Sum_probs=12.0
Q ss_pred hhhccCCcccccccc
Q 012200 14 HLHNSLDPATSLLSS 28 (468)
Q Consensus 14 ~~~~~~~~~~~~~~~ 28 (468)
.|-|+|||+|+.+-|
T Consensus 49 dl~~sldPstp~lnS 63 (108)
T COG4062 49 DLENSLDPSTPPLNS 63 (108)
T ss_pred HHHhccCCCCCCccc
Confidence 467999999888755
No 375
>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=22.15 E-value=64 Score=23.06 Aligned_cols=21 Identities=14% Similarity=0.169 Sum_probs=16.7
Q ss_pred cHHHHhhhccCCcchhHHHHH
Q 012200 183 SAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 183 s~~~la~~Fgvs~sTvsri~~ 203 (468)
+..+++...|+|++|+.+.++
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 457899999999999998876
No 376
>KOG4425 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.09 E-value=56 Score=34.72 Aligned_cols=11 Identities=45% Similarity=0.676 Sum_probs=7.7
Q ss_pred Cccccccccch
Q 012200 20 DPATSLLSSTT 30 (468)
Q Consensus 20 ~~~~~~~~~~~ 30 (468)
||||++.+.|+
T Consensus 664 dpttttttttt 674 (900)
T KOG4425|consen 664 DPTTTTTTTTT 674 (900)
T ss_pred CCccceeeeee
Confidence 68877766665
No 377
>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=21.89 E-value=59 Score=29.28 Aligned_cols=38 Identities=26% Similarity=0.338 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~ 203 (468)
..|+...+ --.+-..|.+..++|.+.|||+++|+++-+
T Consensus 23 ~~p~~~~I--r~~R~~lGmTq~eLAerlGVS~~tIs~iE~ 60 (150)
T TIGR02612 23 QTPKEGWV--RAIRKALGMSGAQLAGRLGVTPQRVEALEK 60 (150)
T ss_pred ccCcHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 44555443 444777899999999999999999998853
No 378
>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family. This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.
Probab=21.84 E-value=2e+02 Score=24.78 Aligned_cols=50 Identities=10% Similarity=-0.080 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHhhhc-cCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 164 SLPSDYAVAMVLSRLA-HGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La-~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.++..++-.+...|+. .+.+...++..+|+|+++..++-+..+.-++..|
T Consensus 79 ~l~~~~r~Il~~~Yl~~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l 129 (132)
T TIGR01637 79 QLDEISRQILYDKYLEPDQKYDYQIMMELGYSHRQYYRIKKRALLRFATLY 129 (132)
T ss_pred hCCHHHHHHHHHHHcCccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHh
Confidence 3667777777888886 3667889999999999999999887777766543
No 379
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=21.83 E-value=93 Score=27.93 Aligned_cols=44 Identities=25% Similarity=0.260 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHH
Q 012200 164 SLPSDYAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLL 209 (468)
Q Consensus 164 ~l~~e~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l 209 (468)
.++..+. -.|.+|..|.+.+.++...++|..||...+.+...-+
T Consensus 149 ~lt~re~--~vl~~l~~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl 192 (210)
T PRK09935 149 VLSNREV--TILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKL 192 (210)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 3555444 3567899999999999999999999988877765554
No 380
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=21.77 E-value=65 Score=25.03 Aligned_cols=26 Identities=27% Similarity=0.259 Sum_probs=22.0
Q ss_pred hhhccCccHHHHhhhccCCcchhHHH
Q 012200 176 SRLAHGLSAKALASRYSLEPYLISKI 201 (468)
Q Consensus 176 ~~La~g~s~~~la~~Fgvs~sTvsri 201 (468)
.|-..|.++.++|...|||+.|+..|
T Consensus 9 ~R~~~~ltQ~elA~~vgVsRQTi~~i 34 (68)
T COG1476 9 LRAELGLTQEELAKLVGVSRQTIIAI 34 (68)
T ss_pred HHHHhCcCHHHHHHHcCcCHHHHHHH
Confidence 34567899999999999999998765
No 381
>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=21.60 E-value=1.6e+02 Score=27.50 Aligned_cols=33 Identities=24% Similarity=0.175 Sum_probs=25.4
Q ss_pred HHhhhcc--CccHHHHhhhccCCcchhHHHHHHHH
Q 012200 174 VLSRLAH--GLSAKALASRYSLEPYLISKITNMVT 206 (468)
Q Consensus 174 ~L~~La~--g~s~~~la~~Fgvs~sTvsri~~~v~ 206 (468)
.|.++.. +.+..++++.+|+|++|+++.+....
T Consensus 148 IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le 182 (203)
T TIGR01884 148 VLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELE 182 (203)
T ss_pred HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3444443 45899999999999999998876643
No 382
>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=21.56 E-value=1.3e+02 Score=25.84 Aligned_cols=26 Identities=27% Similarity=0.290 Sum_probs=21.7
Q ss_pred ccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 182 LSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 182 ~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
.+..+++..+|++++++++++....+
T Consensus 26 ~s~~eia~~l~is~~~v~~~l~~L~~ 51 (130)
T TIGR02944 26 YSAAEIAEQTGLNAPTVSKILKQLSL 51 (130)
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 57899999999999999988765543
No 383
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=21.36 E-value=98 Score=30.89 Aligned_cols=44 Identities=16% Similarity=0.071 Sum_probs=35.0
Q ss_pred HHHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 169 YAVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 169 ~~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+|-.++....+| ++...|+..++|+++||+-++..-..+-..|
T Consensus 5 ~~L~~f~av~~~g-s~s~AA~~L~iSqpaVS~~Ik~LE~~lg~~L 48 (317)
T PRK15421 5 KHLKTLQALRNCG-SLAAAAATLHQTQSALSHQFSDLEQRLGFRL 48 (317)
T ss_pred HHHHHHHHHHHcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCEE
Confidence 3455556666666 9999999999999999999999888876444
No 384
>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=21.21 E-value=1.4e+02 Score=27.71 Aligned_cols=38 Identities=13% Similarity=0.093 Sum_probs=26.5
Q ss_pred HHHHHHHHhhh----ccCccHHHHhhhccCC-cchhHHHHHHH
Q 012200 168 DYAVAMVLSRL----AHGLSAKALASRYSLE-PYLISKITNMV 205 (468)
Q Consensus 168 e~~L~i~L~~L----a~g~s~~~la~~Fgvs-~sTvsri~~~v 205 (468)
+.+++-+|.-. +.+.+.+++|..+|++ ++||++.+...
T Consensus 8 q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L 50 (199)
T TIGR00498 8 QQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKAL 50 (199)
T ss_pred HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHH
Confidence 44455555533 2236788999999998 99998876554
No 385
>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=21.19 E-value=1.8e+02 Score=22.08 Aligned_cols=24 Identities=8% Similarity=0.145 Sum_probs=17.3
Q ss_pred CccHHHHhhhccCC-cchhHHHHHH
Q 012200 181 GLSAKALASRYSLE-PYLISKITNM 204 (468)
Q Consensus 181 g~s~~~la~~Fgvs-~sTvsri~~~ 204 (468)
.-+.++|++.||++ .++|++++..
T Consensus 25 ~Pt~rEIa~~~g~~S~~tv~~~L~~ 49 (65)
T PF01726_consen 25 PPTVREIAEALGLKSTSTVQRHLKA 49 (65)
T ss_dssp ---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHH
Confidence 34789999999996 8888777543
No 386
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=21.02 E-value=1.2e+02 Score=29.48 Aligned_cols=43 Identities=16% Similarity=0.064 Sum_probs=33.5
Q ss_pred HHHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 170 AVAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 170 ~L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
++-+++....+| ++...|+..+|++++||+.+++.-..+-..|
T Consensus 11 ~l~~f~~v~~~g-s~t~AA~~L~itq~avS~~i~~LE~~lg~~L 53 (294)
T PRK09986 11 LLRYFLAVAEEL-HFGRAAARLNISQPPLSIHIKELEDQLGTPL 53 (294)
T ss_pred HHHHHHHHHHhc-CHHHHHHHhCCCCCHHHHHHHHHHHHhCCee
Confidence 344444445554 8999999999999999999999988876544
No 387
>COG3293 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.83 E-value=79 Score=26.93 Aligned_cols=55 Identities=22% Similarity=0.203 Sum_probs=35.9
Q ss_pred eecccCCCCcCCcccCCCCCC-----CCCCccccchhhhhcccchHHHHHHHHhhhhhhcc
Q 012200 338 IVGDWCYPLLSFLMTPFSPNG-----AGTPAQNLFDGMLMKGRNVVVEAIGLLKARWKILK 393 (468)
Q Consensus 338 llgD~gYpl~~~lltP~~~~~-----~lt~~e~~FN~~ls~~R~~VE~afG~LK~RfriL~ 393 (468)
++.|.+|-...|.+-|-..+. .....+.-++..+...|..+|+.|+.+|. |+.+.
T Consensus 40 ~i~~~~~~g~~wr~~p~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~f~~~~~-~r~~~ 99 (124)
T COG3293 40 GIADLLYTGCAWRALPADFPPATTVIPYRRFRRWFKRGLWKRRNLVERTFGRLKQ-FRRTA 99 (124)
T ss_pred HHHHHhccchHHHHhHHHhCCCceEeCCCcchhhHHHHHHHHHHHHHHHHHHHhc-cccee
Confidence 566777766665544432210 01113567788999999999999998886 77664
No 388
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=20.80 E-value=1.2e+02 Score=29.76 Aligned_cols=41 Identities=20% Similarity=0.114 Sum_probs=32.6
Q ss_pred HHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 173 MVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 173 i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
-.+.-++.-.++...|...++|+++||+.+++.-+.+-..|
T Consensus 11 ~~f~~v~e~gs~s~AA~~L~isqpavS~~i~~LE~~lg~~L 51 (305)
T CHL00180 11 RILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPL 51 (305)
T ss_pred HHHHHHHHcCCHHHHHHHhcCCChHHHHHHHHHHHHhCCEE
Confidence 34444444559999999999999999999999998886544
No 389
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=20.76 E-value=88 Score=29.34 Aligned_cols=31 Identities=10% Similarity=0.094 Sum_probs=25.7
Q ss_pred HHhhhcc---CccHHHHhhhccCCcchhHHHHHH
Q 012200 174 VLSRLAH---GLSAKALASRYSLEPYLISKITNM 204 (468)
Q Consensus 174 ~L~~La~---g~s~~~la~~Fgvs~sTvsri~~~ 204 (468)
.|..++. |.+.+++|+..++|..||.+++..
T Consensus 167 Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~ 200 (225)
T PRK10046 167 VRKLFKEPGVQHTAETVAQALTISRTTARRYLEY 200 (225)
T ss_pred HHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHH
Confidence 4566666 479999999999999999998753
No 390
>PF01526 DDE_Tnp_Tn3: Tn3 transposase DDE domain; InterPro: IPR002513 Proteins containing this domain include transposases of Tn3, Tn21, Tn1721, Tn2501, Tn3926 transposons from Escherichia coli. The specific binding of the Tn3 transposase to DNA has been demonstrated. Sequence analysis has suggested that the invariant triad of Asp689, Asp765, Glu895 (numbering as in Tn3) may correspond to the D-D-35-E motif previously implicated in the catalytic performance of numerous transposases [].; GO: 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=20.69 E-value=4.3e+02 Score=27.70 Aligned_cols=83 Identities=12% Similarity=0.121 Sum_probs=51.9
Q ss_pred CCCCHHHHHHHHHhhhccCccHHHHhh-hccCCcchhHHHHHHHHHH-----HHhhcCCccccCCCchhhhccccccccc
Q 012200 163 LSLPSDYAVAMVLSRLAHGLSAKALAS-RYSLEPYLISKITNMVTRL-----LATKLYPEFIKIPISRRRLIETTQGFEE 236 (468)
Q Consensus 163 ~~l~~e~~L~i~L~~La~g~s~~~la~-~Fgvs~sTvsri~~~v~~~-----l~~~L~~~~I~~P~~~~~~~~i~~~F~~ 236 (468)
..-+....|+.+|.-++++.....+|. .-|+|...++.+-++.+.. -...+..-+.+.| +.+
T Consensus 25 k~~~~~~~llA~l~A~GtNlGl~~mA~~~~~is~~~L~~v~~~~i~~etl~~An~~ivna~~~lp------------l~~ 92 (388)
T PF01526_consen 25 KPKDDQRRLLAALFAYGTNLGLKRMARASPGISYDQLSWVNRWYIREETLRAANARIVNAQHKLP------------LAK 92 (388)
T ss_pred CccchHHHHHHHHHHhhhCCChHHHhhcCCCCCHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhCC------------hHH
Confidence 455677889999999999999999998 6677766665544332221 1112222223334 222
Q ss_pred ccCCCCCccccceeeEEeccCC
Q 012200 237 LTSLPNICGAIDGSHIKIGNGK 258 (468)
Q Consensus 237 ~~~fP~~vGaIDgT~I~i~~P~ 258 (468)
.|| -+-..+.||+++++..+.
T Consensus 93 ~wG-~g~~aSsDGq~f~~~~~~ 113 (388)
T PF01526_consen 93 YWG-DGTTASSDGQKFETSDQN 113 (388)
T ss_pred HcC-CCceeccceeEEEeecCc
Confidence 334 244568999999998865
No 391
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=20.66 E-value=1.1e+02 Score=30.49 Aligned_cols=36 Identities=22% Similarity=0.238 Sum_probs=29.9
Q ss_pred hccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 178 LAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 178 La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
++.-.++...|+..++|++++|+.+++.-..+-..|
T Consensus 19 v~e~gs~t~AA~~L~iSQpavS~~I~~LE~~lg~~L 54 (319)
T PRK10216 19 LMQERSVTKAAKRMNVTPSAVSKSLAKLRAWFDDPL 54 (319)
T ss_pred HHHhCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCce
Confidence 334448999999999999999999999988876554
No 392
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=20.64 E-value=84 Score=20.87 Aligned_cols=25 Identities=24% Similarity=0.403 Sum_probs=20.6
Q ss_pred hccCccHHHHhhhccCCcchhHHHH
Q 012200 178 LAHGLSAKALASRYSLEPYLISKIT 202 (468)
Q Consensus 178 La~g~s~~~la~~Fgvs~sTvsri~ 202 (468)
-..+.+..+++...|++..+++++.
T Consensus 7 ~~~~~s~~~la~~~~i~~~~i~~~~ 31 (56)
T smart00530 7 EEKGLTQEELAEKLGVSRSTLSRIE 31 (56)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 3467889999999999999987763
No 393
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=20.42 E-value=97 Score=30.69 Aligned_cols=43 Identities=9% Similarity=0.141 Sum_probs=34.4
Q ss_pred HHHHHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 171 VAMVLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 171 L~i~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+-++..++...++...|+..+|+++|||+.+++.-..+-..|
T Consensus 26 ~L~~f~avae~gs~s~AA~~L~isQpavS~~I~~LE~~lg~~L 68 (314)
T PRK09508 26 LLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDEL 68 (314)
T ss_pred HHHHHHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhhCCCc
Confidence 3445555566667999999999999999999999988876544
No 394
>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=20.36 E-value=61 Score=23.87 Aligned_cols=26 Identities=38% Similarity=0.503 Sum_probs=19.6
Q ss_pred hhccCccHHHHhhhccCCcchhHHHH
Q 012200 177 RLAHGLSAKALASRYSLEPYLISKIT 202 (468)
Q Consensus 177 ~La~g~s~~~la~~Fgvs~sTvsri~ 202 (468)
+-..|.++.++|...|++++++++|.
T Consensus 8 r~~~~lt~~~~a~~~~i~~~~i~~~e 33 (64)
T PF12844_consen 8 REEKGLTQKDLAEKLGISRSTISKIE 33 (64)
T ss_dssp HHHCT--HHHHHHHHTS-HHHHHHHH
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 44568899999999999999999886
No 395
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=20.36 E-value=55 Score=21.63 Aligned_cols=21 Identities=24% Similarity=0.032 Sum_probs=17.7
Q ss_pred CccHHHHhhhccCCcchhHHH
Q 012200 181 GLSAKALASRYSLEPYLISKI 201 (468)
Q Consensus 181 g~s~~~la~~Fgvs~sTvsri 201 (468)
-.+.++.+..+|+++++++++
T Consensus 16 F~Si~eAa~~l~i~~~~I~~~ 36 (37)
T PF07453_consen 16 FDSIREAARYLGISHSTISKY 36 (37)
T ss_pred EcCHHHHHHHhCCCHHHHHHh
Confidence 357788899999999999876
No 396
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=20.33 E-value=63 Score=26.30 Aligned_cols=60 Identities=18% Similarity=0.140 Sum_probs=37.9
Q ss_pred CHHHHHHHHHHhccccccCCCCCCHHHHHH--HHHhhhccCccHHHHhhhccCCcchhHHHHH
Q 012200 143 SYPVFTTVVEKLKPYIAASNLSLPSDYAVA--MVLSRLAHGLSAKALASRYSLEPYLISKITN 203 (468)
Q Consensus 143 s~~~F~~L~~~L~p~l~~~~~~l~~e~~L~--i~L~~La~g~s~~~la~~Fgvs~sTvsri~~ 203 (468)
+-++|..+.+.+.+.-..- ..+-...+|. +.+|.=-.+.++..++..+||+++.+|...+
T Consensus 2 ~~~vF~s~~~~~~D~~e~a-~~m~ir~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~ 63 (91)
T COG5606 2 SNEVFTSVWDAIEDTPEAA-ENMKIRSALMMAIKQWIEQAALSQAQIAELLGVTQPRVSDLAR 63 (91)
T ss_pred CCchhhhHHHHHhccHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHh
Confidence 3456777777766542110 1122333343 4445555678999999999999999987654
No 397
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=20.25 E-value=1.6e+02 Score=25.28 Aligned_cols=30 Identities=17% Similarity=0.236 Sum_probs=23.9
Q ss_pred hccCccHHHHhhhccCCcchhHHHHHHHHH
Q 012200 178 LAHGLSAKALASRYSLEPYLISKITNMVTR 207 (468)
Q Consensus 178 La~g~s~~~la~~Fgvs~sTvsri~~~v~~ 207 (468)
+....+..++|..+|+|+.++.+.|++.+.
T Consensus 22 ~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G 51 (127)
T PRK11511 22 LESPLSLEKVSERSGYSKWHLQRMFKKETG 51 (127)
T ss_pred cCCCCCHHHHHHHHCcCHHHHHHHHHHHHC
Confidence 344567788999999999999999987643
No 398
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=20.02 E-value=1.1e+02 Score=29.51 Aligned_cols=40 Identities=15% Similarity=0.130 Sum_probs=31.9
Q ss_pred HHhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 174 VLSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 174 ~L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
.+.-++...++...|+..++++++||+.++..-..+-..|
T Consensus 10 ~f~~v~e~~s~t~AA~~L~isqpavS~~I~~LE~~lg~~L 49 (290)
T PRK10837 10 VFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQL 49 (290)
T ss_pred HHHHHHHcCCHHHHHHHhCCCccHHHHHHHHHHHHhCCcc
Confidence 3444444569999999999999999999999888876444
No 399
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=20.01 E-value=1.1e+02 Score=30.04 Aligned_cols=39 Identities=23% Similarity=0.160 Sum_probs=31.2
Q ss_pred HhhhccCccHHHHhhhccCCcchhHHHHHHHHHHHHhhc
Q 012200 175 LSRLAHGLSAKALASRYSLEPYLISKITNMVTRLLATKL 213 (468)
Q Consensus 175 L~~La~g~s~~~la~~Fgvs~sTvsri~~~v~~~l~~~L 213 (468)
+.-++.-.++...|+..+++++++|+.+++.-..+-..|
T Consensus 10 f~~v~e~~s~s~AA~~L~isQpavS~~I~~LE~~lg~~L 48 (300)
T PRK11074 10 VDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPL 48 (300)
T ss_pred HHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCee
Confidence 333444458999999999999999999999888876554
Done!