Query gi|254780694|ref|YP_003065107.1| probable transcriptional regulator protein, LuxR family [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 246
No_of_seqs 114 out of 7661
Neff 9.8
Searched_HMMs 39220
Date Sun May 29 23:12:31 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780694.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10188 DNA-binding transcrip 100.0 3.8E-36 9.7E-41 250.9 16.4 218 29-246 10-240 (240)
2 PRK13870 transcriptional regul 100.0 4.2E-34 1.1E-38 237.8 17.0 202 39-246 15-234 (234)
3 TIGR03541 reg_near_HchA LuxR f 100.0 2.8E-33 7E-38 232.5 18.9 214 31-246 6-232 (232)
4 PRK09935 transcriptional regul 99.9 2.3E-24 5.9E-29 175.2 15.0 210 5-246 1-210 (210)
5 PRK09483 response regulator; P 99.9 6.4E-24 1.6E-28 172.4 15.6 207 9-246 3-209 (216)
6 PRK10840 transcriptional regul 99.9 2.7E-23 6.9E-28 168.4 15.6 208 5-246 1-211 (216)
7 PRK10100 DNA-binding transcrip 99.9 1.7E-23 4.3E-28 169.7 14.3 123 115-244 92-214 (216)
8 PRK10651 transcriptional regul 99.9 2.5E-23 6.4E-28 168.6 12.9 211 5-245 4-215 (216)
9 COG2197 CitB Response regulato 99.9 2.1E-22 5.2E-27 162.7 14.9 157 74-246 52-209 (211)
10 PRK09390 fixJ response regulat 99.9 1.2E-22 3E-27 164.3 12.7 201 6-246 2-202 (202)
11 PRK09958 DNA-binding transcrip 99.9 3.2E-22 8E-27 161.6 14.7 202 9-245 2-203 (204)
12 PRK10403 transcriptional regul 99.9 6.8E-22 1.7E-26 159.4 14.5 207 6-243 5-211 (215)
13 PRK10360 DNA-binding transcrip 99.9 1.5E-21 3.9E-26 157.1 15.1 195 8-245 2-196 (196)
14 PRK04841 transcriptional regul 99.9 5.1E-22 1.3E-26 160.2 11.3 60 184-243 837-896 (903)
15 TIGR03020 EpsA transcriptional 99.8 1.1E-20 2.9E-25 151.6 8.5 94 149-242 143-247 (247)
16 COG2909 MalT ATP-dependent tra 99.8 9.6E-20 2.5E-24 145.6 6.1 62 185-246 831-892 (894)
17 COG4566 TtrR Response regulato 99.7 1.2E-16 3E-21 125.8 12.9 185 38-245 9-202 (202)
18 PRK11475 DNA-binding transcrip 99.7 1.6E-17 4.1E-22 131.3 8.3 104 122-241 87-190 (205)
19 pfam00196 GerE Bacterial regul 99.7 3.6E-17 9.3E-22 129.1 7.4 57 184-240 2-58 (58)
20 cd06170 LuxR_C_like C-terminal 99.7 7.5E-17 1.9E-21 127.0 7.9 57 186-242 1-57 (57)
21 smart00421 HTH_LUXR helix_turn 99.7 2.4E-16 6.2E-21 123.8 7.5 57 184-240 2-58 (58)
22 COG2771 CsgD DNA-binding HTH d 99.5 3.9E-14 1E-18 109.6 8.6 63 184-246 3-65 (65)
23 pfam03472 Autoind_bind Autoind 98.8 2.3E-08 6E-13 72.5 6.5 129 42-171 2-144 (146)
24 TIGR02985 Sig70_bacteroi1 RNA 98.7 5.5E-08 1.4E-12 70.1 6.0 46 184-229 118-164 (167)
25 PRK06930 positive control sigm 98.5 2.7E-07 6.9E-12 65.7 5.8 47 184-230 113-160 (170)
26 pfam07638 Sigma70_ECF ECF sigm 98.4 6.5E-07 1.6E-11 63.3 6.3 46 184-229 134-180 (185)
27 PRK12523 RNA polymerase sigma 98.4 9.4E-07 2.4E-11 62.2 6.4 46 184-229 118-164 (172)
28 TIGR02937 sigma70-ECF RNA poly 98.3 1.3E-06 3.3E-11 61.3 6.1 46 184-229 113-159 (162)
29 PRK07037 extracytoplasmic-func 98.3 1.7E-06 4.2E-11 60.6 6.3 45 184-228 122-167 (183)
30 PRK12525 RNA polymerase sigma 98.3 2E-06 5E-11 60.2 6.2 44 184-227 117-161 (168)
31 PRK12527 RNA polymerase sigma 98.3 1.9E-06 4.9E-11 60.2 6.2 46 185-230 105-151 (159)
32 PRK09646 RNA polymerase sigma 98.3 1.8E-06 4.5E-11 60.5 5.9 45 184-228 141-186 (194)
33 PRK09637 RNA polymerase sigma 98.2 3.1E-06 7.9E-11 58.9 6.3 46 184-229 105-151 (181)
34 PRK12519 RNA polymerase sigma 98.2 2.9E-06 7.3E-11 59.1 6.1 46 184-229 140-186 (194)
35 PRK11922 RNA polymerase sigma 98.2 3.3E-06 8.4E-11 58.7 6.3 46 184-229 148-194 (231)
36 PRK13919 putative RNA polymera 98.2 3.5E-06 8.9E-11 58.6 6.4 45 185-229 136-181 (187)
37 PRK12529 RNA polymerase sigma 98.2 3.4E-06 8.6E-11 58.6 6.3 44 184-227 126-170 (178)
38 PRK09645 RNA polymerase sigma 98.2 3.8E-06 9.7E-11 58.3 6.3 46 184-229 115-161 (171)
39 PRK09652 RNA polymerase sigma 98.2 4.3E-06 1.1E-10 58.0 6.2 46 184-229 136-182 (192)
40 PRK09638 RNA polymerase sigma 98.2 4.9E-06 1.2E-10 57.6 6.3 46 184-229 126-172 (177)
41 PRK09047 RNA polymerase factor 98.2 4.3E-06 1.1E-10 58.0 6.1 46 184-229 105-151 (161)
42 PRK05602 RNA polymerase sigma 98.2 4.8E-06 1.2E-10 57.7 6.3 46 184-229 127-173 (186)
43 PRK09651 RNA polymerase sigma 98.2 5E-06 1.3E-10 57.6 6.3 45 184-228 118-163 (172)
44 PRK12526 RNA polymerase sigma 98.2 5.3E-06 1.4E-10 57.4 6.3 46 184-229 152-198 (206)
45 PRK12534 RNA polymerase sigma 98.2 5.4E-06 1.4E-10 57.4 6.3 46 184-229 136-182 (187)
46 PRK12537 RNA polymerase sigma 98.2 5.3E-06 1.3E-10 57.4 6.2 45 185-229 135-180 (184)
47 PRK12543 RNA polymerase sigma 98.2 6E-06 1.5E-10 57.1 6.4 45 185-229 129-174 (190)
48 PRK12514 RNA polymerase sigma 98.2 5.4E-06 1.4E-10 57.3 6.1 45 185-229 129-174 (179)
49 PRK12512 RNA polymerase sigma 98.1 6.4E-06 1.6E-10 56.9 6.3 47 184-230 130-177 (184)
50 PRK12524 RNA polymerase sigma 98.1 6.3E-06 1.6E-10 56.9 6.3 46 184-229 135-181 (196)
51 PRK09639 RNA polymerase sigma 98.1 5.9E-06 1.5E-10 57.1 6.2 46 184-229 111-156 (166)
52 PRK12541 RNA polymerase sigma 98.1 6.2E-06 1.6E-10 56.9 6.3 46 184-229 111-157 (161)
53 PRK12516 RNA polymerase sigma 98.1 6.4E-06 1.6E-10 56.9 6.3 45 185-229 119-164 (190)
54 PRK08295 RNA polymerase factor 98.1 6.3E-06 1.6E-10 56.9 6.2 45 185-229 155-199 (209)
55 cd06171 Sigma70_r4 Sigma70, re 98.1 7.7E-06 2E-10 56.4 6.3 45 184-228 9-54 (55)
56 pfam08281 Sigma70_r4_2 Sigma-7 98.1 6.2E-06 1.6E-10 56.9 5.8 45 184-228 9-54 (54)
57 PRK09641 RNA polymerase sigma 98.1 7.6E-06 1.9E-10 56.4 6.2 46 184-229 135-181 (187)
58 PRK12528 RNA polymerase sigma 98.1 7.9E-06 2E-10 56.3 6.1 44 184-227 118-162 (167)
59 PRK09643 RNA polymerase sigma 98.1 8.8E-06 2.2E-10 56.0 6.3 46 184-229 130-176 (197)
60 PRK12547 RNA polymerase sigma 98.1 9.2E-06 2.3E-10 55.9 6.3 45 185-229 112-157 (164)
61 PRK12538 RNA polymerase sigma 98.1 1E-05 2.5E-10 55.6 6.4 47 184-230 170-217 (233)
62 PRK09647 RNA polymerase sigma 98.1 9.9E-06 2.5E-10 55.6 6.2 46 184-229 156-202 (222)
63 PRK12533 RNA polymerase sigma 98.1 1.1E-05 2.7E-10 55.5 6.2 46 184-229 136-182 (217)
64 PRK12515 RNA polymerase sigma 98.1 1.2E-05 3E-10 55.2 6.4 58 184-245 130-188 (189)
65 PRK12517 RNA polymerase sigma 98.1 1.2E-05 3E-10 55.1 6.4 45 185-229 128-173 (188)
66 PRK11923 algU RNA polymerase s 98.1 1.2E-05 2.9E-10 55.2 6.3 46 184-229 137-183 (193)
67 PRK09648 RNA polymerase sigma 98.1 1.2E-05 3E-10 55.2 6.3 46 184-229 136-182 (187)
68 PRK12513 RNA polymerase sigma 98.1 1.2E-05 3.1E-10 55.1 6.4 46 184-229 138-184 (194)
69 PRK12531 RNA polymerase sigma 98.1 1.3E-05 3.3E-10 54.9 6.4 45 185-229 141-186 (194)
70 PRK12542 RNA polymerase sigma 98.1 1.2E-05 3E-10 55.2 6.1 45 185-229 122-167 (185)
71 PRK12522 RNA polymerase sigma 98.0 1.4E-05 3.6E-10 54.7 6.3 46 184-229 118-164 (173)
72 PRK11924 RNA polymerase sigma 98.0 1.2E-05 3.2E-10 55.0 6.1 46 184-229 124-170 (180)
73 PRK12511 RNA polymerase sigma 98.0 5.1E-06 1.3E-10 57.5 4.1 45 185-229 111-156 (182)
74 PRK06811 RNA polymerase factor 98.0 1.6E-05 4E-10 54.4 6.4 46 184-229 127-173 (185)
75 PRK12546 RNA polymerase sigma 98.0 1.5E-05 3.8E-10 54.5 6.2 45 185-229 113-158 (188)
76 PRK12540 RNA polymerase sigma 98.0 1.6E-05 4.2E-10 54.2 6.2 47 184-230 110-157 (181)
77 PRK09644 RNA polymerase sigma 98.0 1.7E-05 4.2E-10 54.2 6.1 46 184-229 107-153 (165)
78 PRK10336 DNA-binding transcrip 98.0 1.3E-05 3.4E-10 54.8 5.6 112 115-230 83-203 (219)
79 PRK12539 RNA polymerase sigma 98.0 2E-05 5E-10 53.8 6.4 46 184-229 130-176 (184)
80 PRK09640 RNA polymerase sigma 98.0 2.1E-05 5.4E-10 53.5 6.3 45 185-229 134-179 (188)
81 PRK12518 RNA polymerase sigma 98.0 2.2E-05 5.6E-10 53.4 6.4 45 185-229 120-165 (175)
82 PRK12536 RNA polymerase sigma 98.0 2.4E-05 6.2E-10 53.1 6.3 45 185-229 126-171 (178)
83 PRK09415 RNA polymerase factor 97.9 2.7E-05 6.8E-10 52.9 6.3 45 185-229 127-172 (177)
84 PRK06759 RNA polymerase factor 97.9 2.9E-05 7.5E-10 52.6 6.4 45 185-229 106-151 (154)
85 PRK12535 RNA polymerase sigma 97.9 3.1E-05 7.8E-10 52.5 6.3 45 185-229 132-177 (195)
86 PRK09649 RNA polymerase sigma 97.9 3.2E-05 8.2E-10 52.4 6.4 47 184-230 129-176 (185)
87 PRK09642 RNA polymerase sigma 97.9 3.1E-05 7.8E-10 52.5 6.2 45 185-229 106-151 (160)
88 PRK12520 RNA polymerase sigma 97.9 3.2E-05 8.2E-10 52.4 6.2 46 184-229 130-176 (191)
89 PRK12544 RNA polymerase sigma 97.9 4.7E-05 1.2E-09 51.3 6.3 45 185-229 149-194 (207)
90 PRK12532 RNA polymerase sigma 97.8 4.8E-05 1.2E-09 51.3 6.2 46 184-229 135-181 (195)
91 PRK12530 RNA polymerase sigma 97.8 6.8E-05 1.7E-09 50.3 6.3 45 185-229 136-181 (191)
92 COG1595 RpoE DNA-directed RNA 97.8 7.3E-05 1.8E-09 50.1 6.2 47 184-230 126-173 (182)
93 pfam04545 Sigma70_r4 Sigma-70, 97.7 8.5E-05 2.2E-09 49.7 5.7 46 184-229 3-49 (50)
94 pfam04967 HTH_10 HTH DNA bindi 97.6 0.00024 6.2E-09 46.7 6.3 43 186-228 1-51 (53)
95 TIGR02983 SigE-fam_strep RNA p 97.6 8E-05 2E-09 49.8 3.7 46 185-230 113-159 (165)
96 COG3413 Predicted DNA binding 97.5 0.00025 6.4E-09 46.7 6.0 46 183-228 153-206 (215)
97 PRK10046 dpiA two-component re 97.4 0.001 2.7E-08 42.7 7.4 189 7-225 4-202 (225)
98 PRK08583 RNA polymerase sigma 97.4 0.00059 1.5E-08 44.2 6.1 46 184-229 204-250 (257)
99 TIGR01884 cas_HTH CRISPR locus 97.3 0.00058 1.5E-08 44.3 5.9 48 180-227 161-211 (231)
100 PRK07408 RNA polymerase sigma 97.3 0.00068 1.7E-08 43.9 6.2 46 184-229 202-248 (256)
101 PRK10710 DNA-binding transcrip 97.3 0.00048 1.2E-08 44.9 5.2 113 117-231 94-215 (240)
102 PRK12427 flagellar biosynthesi 97.3 0.00067 1.7E-08 43.9 5.8 47 184-230 180-227 (229)
103 PRK07122 RNA polymerase sigma 97.2 0.00093 2.4E-08 43.0 6.1 46 184-229 213-259 (263)
104 PRK12545 RNA polymerase sigma 97.2 0.00093 2.4E-08 43.0 6.1 45 185-229 139-184 (201)
105 PRK09636 RNA polymerase sigma 97.2 0.00085 2.2E-08 43.2 5.7 49 184-232 110-159 (289)
106 PRK10161 transcriptional regul 97.2 0.00092 2.3E-08 43.0 5.7 184 39-231 8-209 (229)
107 PRK11517 transcriptional regul 97.2 0.0025 6.3E-08 40.3 7.8 112 115-231 82-202 (223)
108 PRK06288 RNA polymerase sigma 97.2 0.0011 2.7E-08 42.6 5.8 46 184-229 207-253 (261)
109 PRK05572 sporulation sigma fac 97.1 0.0013 3.4E-08 42.0 6.0 46 184-229 200-246 (251)
110 PRK10430 DNA-binding transcrip 97.1 0.0036 9.1E-08 39.2 8.0 140 72-225 53-203 (239)
111 COG0745 OmpR Response regulato 97.1 0.00078 2E-08 43.5 4.3 186 39-232 6-209 (229)
112 PRK08301 sporulation sigma fac 97.1 0.0016 4E-08 41.5 5.8 46 184-229 182-232 (239)
113 PRK10643 DNA-binding transcrip 97.1 0.0015 3.7E-08 41.7 5.7 110 117-230 85-203 (222)
114 PRK06986 fliA flagellar biosyn 97.1 0.0015 3.7E-08 41.7 5.6 45 185-229 183-228 (234)
115 PRK08215 sporulation sigma fac 97.0 0.0018 4.7E-08 41.1 6.0 45 185-229 209-254 (257)
116 TIGR02999 Sig-70_X6 RNA polyme 97.0 0.0015 3.9E-08 41.6 5.5 48 183-230 143-191 (194)
117 PRK13558 bacterio-opsin activa 97.0 0.0014 3.6E-08 41.8 5.2 44 185-228 616-667 (674)
118 PRK07670 RNA polymerase sigma 97.0 0.0017 4.5E-08 41.2 5.7 46 184-229 196-242 (250)
119 PRK05803 sporulation sigma fac 97.0 0.002 5E-08 40.9 5.8 46 184-229 173-223 (228)
120 PRK09836 DNA-binding transcrip 96.9 0.00096 2.4E-08 42.9 3.8 112 116-231 84-205 (226)
121 PRK09468 ompR osmolarity respo 96.9 0.00054 1.4E-08 44.5 2.4 201 6-231 4-216 (239)
122 PRK05911 RNA polymerase sigma 96.9 0.0023 6E-08 40.4 5.7 46 184-229 204-250 (257)
123 PRK07500 rpoH2 RNA polymerase 96.9 0.0025 6.4E-08 40.2 5.5 47 184-230 226-275 (289)
124 PRK03975 tfx putative transcri 96.8 0.0034 8.7E-08 39.4 5.5 45 185-229 4-48 (139)
125 PRK12423 LexA repressor; Provi 96.8 0.0024 6.2E-08 40.3 4.6 44 185-228 3-54 (202)
126 pfam01726 LexA_DNA_bind LexA D 96.7 0.0036 9.2E-08 39.2 5.5 43 185-227 3-53 (65)
127 PRK00215 LexA repressor; Valid 96.7 0.0035 9E-08 39.3 5.3 42 186-227 2-51 (204)
128 PRK11083 DNA-binding response 96.7 0.0019 4.9E-08 41.0 3.9 199 5-231 1-210 (229)
129 PRK06596 RNA polymerase factor 96.7 0.005 1.3E-07 38.3 6.0 46 184-229 229-277 (284)
130 PRK10766 DNA-binding transcrip 96.7 0.0017 4.2E-08 41.4 3.3 113 118-230 87-216 (224)
131 PRK10701 DNA-binding transcrip 96.6 0.0015 3.9E-08 41.6 2.8 115 117-231 85-216 (240)
132 PRK05901 RNA polymerase sigma 96.6 0.008 2.1E-07 37.0 6.4 53 185-237 335-392 (398)
133 PRK10816 DNA-binding transcrip 96.6 0.0017 4.4E-08 41.3 2.9 111 117-231 85-204 (223)
134 PRK07598 RNA polymerase sigma 96.6 0.011 2.8E-07 36.1 7.0 54 185-238 345-403 (410)
135 PRK13413 mpi multiple promoter 96.5 0.0057 1.5E-07 37.9 5.3 43 184-226 156-198 (200)
136 PRK09635 sigI RNA polymerase s 96.5 0.0072 1.8E-07 37.3 5.8 49 184-232 117-166 (290)
137 TIGR02952 Sig70_famx2 RNA poly 96.5 0.0036 9.2E-08 39.2 4.0 46 184-229 122-168 (171)
138 PRK05949 RNA polymerase sigma 96.5 0.0091 2.3E-07 36.6 6.0 48 184-231 265-317 (327)
139 PRK05657 RNA polymerase sigma 96.4 0.0093 2.4E-07 36.6 5.9 50 184-233 264-318 (328)
140 CHL00148 orf27 Ycf27; Reviewed 96.4 0.0016 4.1E-08 41.5 1.9 117 115-231 88-218 (240)
141 PRK07406 RNA polymerase sigma 96.4 0.016 4.1E-07 35.0 6.9 54 185-238 323-381 (385)
142 PRK07921 RNA polymerase sigma 96.4 0.013 3.2E-07 35.7 6.3 52 185-236 258-314 (320)
143 PRK08241 RNA polymerase factor 96.3 0.0057 1.4E-07 37.9 4.3 46 185-230 156-202 (341)
144 PRK07405 RNA polymerase sigma 96.3 0.012 2.9E-07 36.0 5.8 47 184-230 256-307 (318)
145 PRK09210 RNA polymerase sigma 96.2 0.017 4.4E-07 34.8 6.4 53 184-236 305-362 (368)
146 COG4565 CitB Response regulato 96.2 0.077 2E-06 30.7 9.6 102 121-224 91-197 (224)
147 PRK10955 DNA-binding transcrip 96.1 0.005 1.3E-07 38.3 3.2 115 117-231 84-211 (232)
148 pfam08279 HTH_11 HTH domain. T 96.1 0.014 3.6E-07 35.4 5.4 41 189-230 1-44 (55)
149 PRK13719 conjugal transfer tra 96.1 0.0073 1.9E-07 37.2 3.9 60 187-246 147-206 (220)
150 PRK10529 DNA-binding transcrip 96.1 0.0043 1.1E-07 38.7 2.7 112 117-231 85-206 (225)
151 cd00569 HTH_Hin_like Helix-tur 96.1 0.014 3.5E-07 35.4 5.2 40 182-221 2-42 (42)
152 cd00090 HTH_ARSR Arsenical Res 96.0 0.018 4.6E-07 34.7 5.6 41 186-226 4-46 (78)
153 COG1191 FliA DNA-directed RNA 96.0 0.021 5.2E-07 34.4 5.8 45 185-229 196-241 (247)
154 COG0856 Orotate phosphoribosyl 95.9 0.013 3.3E-07 35.6 4.4 42 191-232 9-50 (203)
155 PRK13856 two-component respons 95.8 0.011 2.8E-07 36.1 3.7 114 118-231 87-210 (241)
156 pfam02001 DUF134 Protein of un 95.7 0.033 8.3E-07 33.1 5.8 46 183-228 34-80 (100)
157 TIGR02997 Sig70-cyanoRpoD RNA 95.7 0.021 5.2E-07 34.4 4.7 44 185-228 287-335 (336)
158 COG3355 Predicted transcriptio 95.6 0.037 9.4E-07 32.7 5.8 44 184-227 23-69 (126)
159 PRK11173 two-component respons 95.6 0.053 1.3E-06 31.7 6.5 112 118-232 88-216 (237)
160 COG0568 RpoD DNA-directed RNA 95.5 0.038 9.6E-07 32.7 5.5 51 186-236 280-336 (342)
161 TIGR02984 Sig-70_plancto1 RNA 95.4 0.042 1.1E-06 32.4 5.4 46 184-229 140-186 (190)
162 pfam01371 Trp_repressor Trp re 95.3 0.026 6.5E-07 33.8 4.2 40 185-224 26-73 (88)
163 pfam00486 Trans_reg_C Transcri 95.3 0.043 1.1E-06 32.3 5.2 49 183-231 3-60 (77)
164 COG2345 Predicted transcriptio 95.2 0.052 1.3E-06 31.8 5.4 40 188-227 11-52 (218)
165 pfam01022 HTH_5 Bacterial regu 95.2 0.059 1.5E-06 31.4 5.7 39 188-226 2-41 (47)
166 cd00383 trans_reg_C Effector d 95.1 0.05 1.3E-06 31.9 5.1 52 181-232 19-79 (95)
167 pfam09862 DUF2089 Protein of u 95.1 0.18 4.6E-06 28.3 7.9 66 181-246 29-103 (113)
168 COG1318 Predicted transcriptio 95.1 0.013 3.4E-07 35.6 2.1 32 197-228 58-89 (182)
169 PRK04217 hypothetical protein; 95.0 0.079 2E-06 30.6 5.8 45 184-228 41-86 (110)
170 pfam03444 DUF293 Domain of unk 94.9 0.063 1.6E-06 31.2 5.3 45 185-230 1-52 (79)
171 TIGR02846 spore_sigmaK RNA pol 94.9 0.042 1.1E-06 32.4 4.2 45 185-229 175-224 (228)
172 COG5625 Predicted transcriptio 94.8 0.034 8.6E-07 33.0 3.6 44 184-227 17-63 (113)
173 TIGR02479 FliA_WhiG RNA polyme 94.7 0.089 2.3E-06 30.3 5.5 47 184-230 177-224 (227)
174 smart00862 Trans_reg_C Transcr 94.7 0.075 1.9E-06 30.7 5.1 49 183-231 3-61 (78)
175 TIGR03001 Sig-70_gmx1 RNA poly 94.7 0.062 1.6E-06 31.3 4.7 56 184-239 165-221 (249)
176 PRK05658 RNA polymerase sigma 94.7 0.32 8.3E-06 26.7 9.4 53 185-237 557-614 (620)
177 PRK00118 putative DNA-binding 94.6 0.11 2.9E-06 29.6 6.0 44 185-228 17-61 (105)
178 TIGR02989 Sig-70_gvs1 RNA poly 94.6 0.09 2.3E-06 30.3 5.4 47 184-230 114-161 (163)
179 COG3415 Transposase and inacti 94.6 0.077 2E-06 30.7 5.0 40 186-225 7-46 (138)
180 PRK02277 orotate phosphoribosy 94.6 0.041 1E-06 32.4 3.6 37 192-228 10-46 (201)
181 pfam01978 TrmB Sugar-specific 94.5 0.12 3E-06 29.5 5.8 45 183-227 3-49 (68)
182 pfam04297 UPF0122 Putative hel 94.4 0.13 3.4E-06 29.1 6.0 44 185-228 17-61 (101)
183 smart00418 HTH_ARSR helix_turn 94.4 0.065 1.7E-06 31.1 4.4 34 193-226 2-36 (66)
184 TIGR02859 spore_sigH RNA polym 94.4 0.063 1.6E-06 31.2 4.2 45 185-229 150-194 (198)
185 PRK11179 DNA-binding transcrip 94.4 0.15 3.8E-06 28.8 6.2 45 182-226 3-49 (153)
186 pfam02796 HTH_7 Helix-turn-hel 94.4 0.078 2E-06 30.6 4.6 39 184-222 4-43 (45)
187 COG1522 Lrp Transcriptional re 94.3 0.16 4.1E-06 28.7 6.0 44 183-226 3-48 (154)
188 TIGR02954 Sig70_famx3 RNA poly 94.3 0.033 8.4E-07 33.1 2.5 45 186-230 123-168 (173)
189 pfam03811 Ins_element1 Inserti 94.1 0.068 1.7E-06 31.0 3.9 39 186-224 49-87 (88)
190 smart00344 HTH_ASNC helix_turn 94.1 0.14 3.5E-06 29.1 5.4 39 188-226 3-43 (108)
191 PRK11557 putative DNA-binding 94.0 0.21 5.3E-06 27.9 6.2 14 49-62 51-64 (282)
192 TIGR02154 PhoB phosphate regul 93.9 0.0018 4.7E-08 41.1 -4.5 154 75-237 53-215 (226)
193 smart00347 HTH_MARR helix_turn 93.8 0.18 4.6E-06 28.3 5.6 46 182-227 4-51 (101)
194 PRK11337 DNA-binding transcrip 93.3 0.35 8.8E-06 26.5 6.3 14 49-62 64-77 (293)
195 TIGR02233 Myxo_sigma_rel Myxoc 93.3 0.16 4.1E-06 28.6 4.6 56 184-239 23-79 (106)
196 COG3398 Uncharacterized protei 93.3 0.16 4.1E-06 28.6 4.6 35 191-225 177-213 (240)
197 TIGR02959 SigZ RNA polymerase 93.2 0.078 2E-06 30.6 2.9 44 185-228 100-144 (170)
198 pfam03965 Pencillinase_R Penic 93.2 0.22 5.7E-06 27.7 5.2 45 186-230 1-51 (115)
199 COG2865 Predicted transcriptio 92.8 0.21 5.3E-06 27.9 4.6 42 185-226 399-442 (467)
200 PRK11886 biotin--protein ligas 92.8 0.29 7.3E-06 27.0 5.3 16 43-59 33-48 (319)
201 PRK03573 transcriptional regul 92.8 0.35 8.8E-06 26.5 5.7 45 183-227 26-73 (144)
202 pfam01047 MarR MarR family. Th 92.7 0.34 8.7E-06 26.5 5.6 42 186-227 1-44 (59)
203 PRK11302 DNA-binding transcrip 92.6 0.47 1.2E-05 25.7 6.2 14 49-62 51-64 (284)
204 PRK06704 RNA polymerase factor 92.5 0.56 1.4E-05 25.1 6.5 59 185-243 116-186 (228)
205 pfam03428 RP-C Replication pro 92.5 0.37 9.5E-06 26.3 5.6 43 184-226 39-97 (177)
206 COG1737 RpiR Transcriptional r 92.5 0.55 1.4E-05 25.2 6.4 14 49-62 53-66 (281)
207 TIGR02980 SigBFG RNA polymeras 92.4 0.094 2.4E-06 30.1 2.4 45 184-228 179-224 (229)
208 COG1710 Uncharacterized protei 92.4 0.23 6E-06 27.6 4.5 42 186-227 94-136 (139)
209 TIGR02950 SigM_subfam RNA poly 92.4 0.13 3.2E-06 29.3 3.0 45 186-230 114-159 (162)
210 PRK09191 two-component respons 92.3 0.39 1E-05 26.1 5.5 47 184-230 87-134 (261)
211 COG1342 Predicted DNA-binding 92.3 0.38 9.6E-06 26.3 5.4 47 182-228 30-77 (99)
212 COG2390 DeoR Transcriptional r 92.3 0.19 4.9E-06 28.1 3.9 16 231-246 288-303 (321)
213 COG1356 tfx Transcriptional re 92.2 0.09 2.3E-06 30.2 2.1 46 184-229 7-52 (143)
214 PRK11512 DNA-binding transcrip 92.2 0.7 1.8E-05 24.5 6.6 46 182-227 34-81 (144)
215 TIGR02702 SufR_cyano iron-sulf 92.1 0.12 3E-06 29.5 2.6 31 194-224 8-39 (215)
216 TIGR02941 Sigma_B RNA polymera 92.0 0.21 5.4E-06 27.9 3.8 46 184-229 205-251 (256)
217 COG5484 Uncharacterized conser 91.7 0.31 7.8E-06 26.8 4.4 17 185-201 153-169 (279)
218 TIGR00721 tfx DNA-binding prot 91.4 0.39 1E-05 26.1 4.6 46 184-229 5-50 (142)
219 pfam09339 HTH_IclR IclR helix- 91.0 0.69 1.8E-05 24.6 5.6 39 188-226 3-44 (52)
220 PRK11169 leucine-responsive tr 90.9 0.9 2.3E-05 23.8 6.1 43 184-226 10-54 (164)
221 pfam04218 CENP-B_N CENP-B N-te 90.9 0.61 1.6E-05 24.9 5.2 41 184-224 5-46 (53)
222 pfam01418 HTH_6 Helix-turn-hel 90.9 0.67 1.7E-05 24.7 5.4 49 184-236 12-66 (106)
223 pfam00126 HTH_1 Bacterial regu 90.4 0.87 2.2E-05 23.9 5.7 43 189-231 2-44 (60)
224 PRK09801 transcriptional activ 90.2 1 2.6E-05 23.4 5.9 14 185-198 280-293 (310)
225 PRK11074 putative DNA-binding 90.2 1.2 3E-05 23.1 6.1 16 185-200 276-291 (300)
226 TIGR02960 SigX5 RNA polymerase 90.2 0.67 1.7E-05 24.6 4.9 47 185-231 143-190 (329)
227 COG3877 Uncharacterized protei 90.1 0.93 2.4E-05 23.7 5.6 53 180-232 36-89 (122)
228 pfam08461 HTH_12 Ribonuclease 90.1 0.56 1.4E-05 25.1 4.5 33 192-224 2-42 (66)
229 TIGR02957 SigX4 RNA polymerase 89.9 0.99 2.5E-05 23.6 5.6 48 184-231 108-157 (287)
230 PRK01381 Trp operon repressor; 89.8 0.35 8.8E-06 26.5 3.2 36 185-220 32-75 (99)
231 PRK11242 DNA-binding transcrip 89.7 1.1 2.8E-05 23.3 5.7 11 186-196 276-286 (292)
232 COG1846 MarR Transcriptional r 89.3 1 2.6E-05 23.5 5.3 44 184-227 18-63 (126)
233 TIGR02393 RpoD_Cterm RNA polym 89.2 0.78 2E-05 24.2 4.6 53 185-237 177-235 (240)
234 COG2522 Predicted transcriptio 89.2 0.81 2.1E-05 24.1 4.7 35 189-223 11-45 (119)
235 pfam01527 Transposase_8 Transp 89.0 0.9 2.3E-05 23.8 4.8 36 191-226 13-49 (75)
236 PRK11139 DNA-binding transcrip 89.0 1.5 3.9E-05 22.4 6.0 12 186-197 277-288 (295)
237 pfam07900 DUF1670 Protein of u 89.0 0.59 1.5E-05 25.0 3.9 46 178-224 142-187 (220)
238 cd04762 HTH_MerR-trunc Helix-T 88.8 0.41 1E-05 26.0 3.0 23 201-223 1-23 (49)
239 PRK12683 transcriptional regul 88.3 1.8 4.5E-05 21.9 6.0 30 182-211 276-305 (308)
240 smart00420 HTH_DEOR helix_turn 88.3 0.83 2.1E-05 24.1 4.3 39 189-227 1-41 (53)
241 COG3682 Predicted transcriptio 88.3 1.3 3.3E-05 22.8 5.3 47 184-230 2-54 (123)
242 COG1654 BirA Biotin operon rep 88.2 1.1 2.9E-05 23.2 4.9 44 186-230 4-48 (79)
243 COG1321 TroR Mn-dependent tran 88.2 1.3 3.3E-05 22.8 5.2 42 185-226 3-50 (154)
244 smart00346 HTH_ICLR helix_turn 88.0 1.7 4.4E-05 22.0 5.7 39 188-226 5-46 (91)
245 PRK10086 DNA-binding transcrip 87.8 1.9 4.8E-05 21.8 5.8 13 186-198 292-304 (311)
246 PRK10341 DNA-binding transcrip 87.6 1.9 4.7E-05 21.8 5.7 16 184-199 281-296 (312)
247 smart00419 HTH_CRP helix_turn_ 87.3 0.81 2.1E-05 24.1 3.7 26 201-226 9-34 (48)
248 PRK09834 DNA-binding transcrip 86.7 1.9 5E-05 21.7 5.4 26 184-211 229-256 (264)
249 PRK10632 putative DNA-binding 86.6 2.2 5.7E-05 21.3 5.9 15 185-199 276-290 (309)
250 PRK10141 DNA-binding transcrip 86.5 2.2 5.7E-05 21.3 5.6 39 188-226 14-54 (106)
251 PRK12679 cbl transcriptional r 86.5 2.2 5.7E-05 21.3 6.2 28 184-211 278-305 (316)
252 PRK12684 transcriptional regul 86.3 2.3 5.9E-05 21.2 6.0 32 183-214 277-308 (313)
253 COG2964 Uncharacterized protei 86.3 2.3 5.9E-05 21.2 6.6 38 188-225 174-216 (220)
254 PRK11151 DNA-binding transcrip 86.2 2.3 5.9E-05 21.2 6.0 15 184-198 276-290 (305)
255 pfam06056 Terminase_5 Putative 85.9 1.2 3.1E-05 23.0 4.0 30 194-223 7-36 (58)
256 PRK10163 DNA-binding transcrip 85.8 2.4 6.2E-05 21.1 5.8 27 184-212 240-267 (271)
257 pfam10668 Phage_terminase Phag 85.7 0.95 2.4E-05 23.7 3.4 21 200-220 22-42 (60)
258 PRK11013 DNA-binding transcrip 85.3 2.6 6.6E-05 20.9 6.1 12 186-197 279-290 (309)
259 pfam07750 GcrA GcrA cell cycle 84.9 0.99 2.5E-05 23.6 3.2 42 188-233 5-48 (162)
260 pfam08220 HTH_DeoR DeoR-like h 84.6 1.7 4.3E-05 22.1 4.2 38 189-226 1-40 (57)
261 smart00354 HTH_LACI helix_turn 84.4 0.63 1.6E-05 24.8 2.0 42 202-244 2-43 (70)
262 PRK00423 tfb transcription ini 84.2 2.6 6.7E-05 20.8 5.1 38 194-231 270-307 (310)
263 pfam11268 DUF3071 Protein of u 84.2 2.9 7.4E-05 20.6 5.5 41 183-225 53-93 (169)
264 pfam08280 HTH_Mga M protein tr 83.9 2.5 6.3E-05 21.0 4.9 40 188-227 5-46 (59)
265 PRK04172 pheS phenylalanyl-tRN 83.9 3 7.5E-05 20.5 5.7 18 204-221 335-352 (501)
266 PRK10082 putative DNA-binding 83.9 3 7.6E-05 20.5 5.6 11 186-196 284-294 (303)
267 PRK13824 replication initiatio 83.7 3 7.7E-05 20.5 5.6 33 204-240 325-357 (404)
268 CHL00180 rbcR LysR transcripti 83.7 3 7.7E-05 20.4 6.3 17 42-58 33-49 (307)
269 TIGR02939 RpoE_Sigma70 RNA pol 83.5 0.56 1.4E-05 25.1 1.4 34 186-226 149-182 (192)
270 pfam04645 DUF603 Protein of un 83.4 1.4 3.7E-05 22.5 3.5 22 196-217 14-36 (181)
271 PRK09791 putative DNA-binding 83.3 3.1 8E-05 20.3 6.4 15 184-198 280-294 (302)
272 PRK12680 transcriptional regul 82.9 3.2 8.2E-05 20.3 5.9 17 215-231 202-218 (327)
273 PRK00876 nadE NAD synthetase; 82.8 3.3 8.3E-05 20.2 5.3 47 185-231 262-309 (325)
274 pfam00325 Crp Bacterial regula 82.8 1.5 3.9E-05 22.4 3.4 27 201-227 3-29 (32)
275 pfam00376 MerR MerR family reg 82.5 1.4 3.6E-05 22.6 3.2 22 202-223 1-22 (38)
276 pfam01710 Transposase_14 Trans 82.5 2.4 6.2E-05 21.1 4.3 39 188-231 58-98 (120)
277 COG3711 BglG Transcriptional a 82.1 1.8 4.6E-05 21.9 3.6 28 201-228 101-128 (491)
278 COG0583 LysR Transcriptional r 81.9 3.5 9E-05 20.0 5.9 11 190-200 222-232 (297)
279 cd00092 HTH_CRP helix_turn_hel 81.8 1.9 4.8E-05 21.7 3.6 28 199-226 24-51 (67)
280 PRK11233 nitrogen assimilation 81.4 3.7 9.4E-05 19.9 5.7 18 183-200 273-290 (305)
281 PRK03887 methylated-DNA--prote 81.4 3.2 8.3E-05 20.2 4.7 40 182-221 86-131 (172)
282 pfam00356 LacI Bacterial regul 81.2 1.1 2.9E-05 23.2 2.3 42 202-244 1-42 (46)
283 COG1414 IclR Transcriptional r 81.2 3.8 9.6E-05 19.8 5.7 10 188-197 224-233 (246)
284 smart00351 PAX Paired Box doma 81.1 3.6 9.2E-05 20.0 4.8 46 186-231 18-64 (125)
285 PRK04140 hypothetical protein; 80.9 1.7 4.2E-05 22.1 3.0 25 198-222 136-160 (319)
286 pfam08784 RPA_C Replication pr 80.6 3.9 1E-04 19.7 5.9 40 185-224 44-90 (103)
287 PRK11477 carbohydrate diacid t 80.5 3.9 0.0001 19.7 5.1 40 193-232 327-366 (385)
288 TIGR01764 excise DNA binding d 80.1 1.6 4E-05 22.3 2.7 23 201-223 2-24 (49)
289 pfam05043 Mga Mga helix-turn-h 79.8 3.4 8.8E-05 20.1 4.4 37 192-228 20-58 (87)
290 cd00131 PAX Paired Box domain 79.0 4.4 0.00011 19.4 4.7 39 190-229 23-61 (128)
291 TIGR02835 spore_sigmaE RNA pol 79.0 2.8 7.2E-05 20.6 3.7 46 184-229 177-227 (234)
292 pfam04552 Sigma54_DBD Sigma-54 78.9 2.3 5.8E-05 21.3 3.2 29 201-233 122-155 (160)
293 pfam01325 Fe_dep_repress Iron 78.9 2.1 5.4E-05 21.4 3.0 26 201-226 21-46 (58)
294 COG2973 TrpR Trp operon repres 78.9 3.3 8.3E-05 20.2 4.0 38 186-223 38-83 (103)
295 PRK12682 transcriptional regul 78.8 4.5 0.00011 19.4 6.0 23 183-205 277-299 (309)
296 COG1675 TFA1 Transcription ini 78.8 4.4 0.00011 19.4 4.6 36 191-226 21-58 (176)
297 PRK06266 transcription initiat 78.7 2.7 6.9E-05 20.7 3.6 37 191-227 25-63 (178)
298 PRK10820 DNA-binding transcrip 78.7 4.5 0.00011 19.3 5.0 40 190-233 469-509 (513)
299 COG4496 Uncharacterized protei 78.6 2.8 7.3E-05 20.6 3.6 30 191-220 47-76 (100)
300 PRK10870 transcriptional repre 78.4 4.6 0.00012 19.3 5.6 42 183-224 50-95 (176)
301 pfam00440 TetR_N Bacterial reg 78.4 2.2 5.5E-05 21.4 3.0 26 198-223 14-39 (47)
302 pfam05263 DUF722 Protein of un 78.3 4.6 0.00012 19.3 5.6 44 185-228 81-127 (130)
303 PRK11050 manganese transport r 77.9 2.2 5.7E-05 21.3 2.9 22 203-224 57-78 (155)
304 KOG0709 consensus 77.6 4.8 0.00012 19.1 4.7 56 174-232 230-285 (472)
305 PRK09906 DNA-binding transcrip 77.5 4.9 0.00012 19.1 5.6 11 186-196 276-286 (296)
306 cd01392 HTH_LacI Helix-turn-he 77.2 1.1 2.9E-05 23.2 1.2 21 204-224 1-21 (52)
307 cd04768 HTH_BmrR-like Helix-Tu 77.0 2.5 6.3E-05 21.0 2.9 38 185-222 38-79 (96)
308 COG2524 Predicted transcriptio 76.1 5.3 0.00014 18.9 5.1 28 191-218 221-248 (294)
309 COG0640 ArsR Predicted transcr 76.1 5.3 0.00014 18.9 5.0 39 189-227 26-66 (110)
310 pfam07374 DUF1492 Protein of u 76.0 4.6 0.00012 19.3 4.1 42 188-229 58-100 (100)
311 PRK12681 cysB transcriptional 75.8 5.4 0.00014 18.8 5.9 45 184-231 278-322 (324)
312 smart00550 Zalpha Z-DNA-bindin 75.8 5.4 0.00014 18.8 5.0 45 188-232 6-54 (68)
313 pfam02787 CPSase_L_D3 Carbamoy 75.6 3.6 9.3E-05 19.9 3.5 41 185-231 58-98 (122)
314 pfam01381 HTH_3 Helix-turn-hel 75.3 5.6 0.00014 18.7 5.0 42 198-243 7-48 (55)
315 TIGR00331 hrcA heat-inducible 75.1 3 7.7E-05 20.4 3.0 11 198-208 185-195 (343)
316 cd04769 HTH_MerR2 Helix-Turn-H 75.1 3 7.6E-05 20.5 2.9 26 186-211 38-67 (116)
317 cd04781 HTH_MerR-like_sg6 Heli 75.0 2.9 7.4E-05 20.6 2.9 43 186-228 38-90 (120)
318 PRK03902 manganese transport t 74.4 3.4 8.7E-05 20.1 3.1 21 202-222 24-44 (142)
319 COG1497 Predicted transcriptio 74.4 3.9 9.9E-05 19.8 3.4 12 78-89 64-75 (260)
320 COG2512 Predicted membrane-ass 74.1 6 0.00015 18.6 5.0 45 182-226 189-236 (258)
321 pfam05331 DUF742 Protein of un 73.7 3.2 8.1E-05 20.3 2.8 44 183-226 38-81 (114)
322 PRK11161 fumarate/nitrate redu 73.2 4.9 0.00012 19.1 3.7 27 201-227 185-211 (235)
323 cd01107 HTH_BmrR Helix-Turn-He 73.2 3.5 9E-05 20.0 2.9 28 185-212 39-70 (108)
324 cd04772 HTH_TioE_rpt1 First He 73.0 4.2 0.00011 19.5 3.3 12 206-217 6-17 (99)
325 cd04761 HTH_MerR-SF Helix-Turn 72.9 3.5 9E-05 20.0 2.9 23 201-223 1-23 (49)
326 cd04773 HTH_TioE_rpt2 Second H 72.8 3.7 9.4E-05 19.9 2.9 28 185-212 38-69 (108)
327 TIGR02607 antidote_HigA addict 72.7 3 7.8E-05 20.4 2.5 25 198-222 18-42 (81)
328 smart00530 HTH_XRE Helix-turn- 72.6 3.4 8.6E-05 20.1 2.7 28 197-224 7-34 (56)
329 cd04787 HTH_HMRTR_unk Helix-Tu 72.4 4.4 0.00011 19.4 3.3 27 186-212 39-69 (133)
330 TIGR00738 rrf2_super rrf2 fami 72.3 4.4 0.00011 19.4 3.2 27 201-231 26-52 (133)
331 COG0789 SoxR Predicted transcr 72.1 3.9 9.9E-05 19.8 2.9 16 198-213 55-70 (124)
332 cd04770 HTH_HMRTR Helix-Turn-H 72.1 3.9 9.9E-05 19.8 2.9 44 185-228 38-95 (123)
333 TIGR03418 chol_sulf_TF putativ 71.8 6.8 0.00017 18.2 5.9 11 186-196 277-287 (291)
334 cd04783 HTH_MerR1 Helix-Turn-H 71.7 3.9 0.0001 19.7 2.9 27 186-212 39-69 (126)
335 cd04789 HTH_Cfa Helix-Turn-Hel 71.3 4 0.0001 19.6 2.9 43 185-227 38-86 (102)
336 pfam11662 DUF3263 Protein of u 71.3 6.6 0.00017 18.2 4.0 42 185-226 2-48 (77)
337 smart00422 HTH_MERR helix_turn 70.9 4.9 0.00013 19.1 3.2 26 186-211 39-68 (70)
338 PRK09430 djlA Dna-J like membr 70.8 7.1 0.00018 18.1 4.6 16 184-199 143-158 (269)
339 pfam08535 KorB KorB domain. Th 70.7 4.9 0.00013 19.1 3.2 24 199-222 2-25 (93)
340 cd04776 HTH_GnyR Helix-Turn-He 70.1 4.5 0.00012 19.3 2.9 45 184-228 35-89 (118)
341 PRK13752 putative transcriptio 70.1 4.2 0.00011 19.5 2.7 13 200-212 64-76 (144)
342 COG1405 SUA7 Transcription ini 70.1 4.5 0.00011 19.4 2.9 34 199-232 250-283 (285)
343 PHA01976 helix-turn-helix prot 70.0 5.5 0.00014 18.8 3.3 27 196-222 11-37 (67)
344 TIGR00373 TIGR00373 conserved 69.9 6.5 0.00017 18.3 3.7 36 191-226 19-56 (168)
345 cd04780 HTH_MerR-like_sg5 Heli 69.9 5.5 0.00014 18.8 3.3 47 184-230 37-90 (95)
346 smart00529 HTH_DTXR Helix-turn 69.8 5 0.00013 19.0 3.1 21 204-224 3-23 (96)
347 COG2739 Uncharacterized protei 69.6 7.5 0.00019 17.9 5.3 42 185-226 17-59 (105)
348 cd01108 HTH_CueR Helix-Turn-He 69.5 4.8 0.00012 19.2 2.9 28 185-212 38-69 (127)
349 cd04785 HTH_CadR-PbrR-like Hel 69.4 4.8 0.00012 19.2 2.9 28 185-212 38-69 (126)
350 cd04774 HTH_YfmP Helix-Turn-He 69.3 4.8 0.00012 19.2 2.9 44 185-228 37-85 (96)
351 cd04782 HTH_BltR Helix-Turn-He 69.3 4.9 0.00012 19.1 2.9 26 186-211 39-68 (97)
352 TIGR03384 betaine_BetI transcr 69.2 5.2 0.00013 18.9 3.1 13 192-204 152-164 (189)
353 cd04777 HTH_MerR-like_sg1 Heli 69.1 4.9 0.00012 19.1 2.9 30 184-213 35-68 (107)
354 TIGR02947 SigH_actino RNA poly 68.7 7.9 0.0002 17.8 5.5 50 192-245 139-188 (193)
355 PRK09940 transcriptional regul 68.6 5.6 0.00014 18.7 3.1 26 198-223 148-173 (253)
356 cd01110 HTH_SoxR Helix-Turn-He 68.6 5.1 0.00013 19.0 2.9 11 200-210 57-67 (139)
357 cd04766 HTH_HspR Helix-Turn-He 68.0 5.2 0.00013 18.9 2.8 46 183-228 36-88 (91)
358 PRK00767 transcriptional regul 67.8 5.8 0.00015 18.6 3.1 40 191-230 153-196 (197)
359 cd01111 HTH_MerD Helix-Turn-He 67.8 6 0.00015 18.5 3.1 30 185-214 38-71 (107)
360 cd04786 HTH_MerR-like_sg7 Heli 67.4 5.6 0.00014 18.7 2.9 44 185-228 38-94 (131)
361 cd01109 HTH_YyaN Helix-Turn-He 67.1 5.7 0.00015 18.7 2.9 29 184-212 37-69 (113)
362 cd04764 HTH_MlrA-like_sg1 Heli 66.9 5.7 0.00015 18.7 2.9 27 185-211 37-67 (67)
363 PRK13756 tetracycline represso 66.9 3.2 8.2E-05 20.3 1.6 17 49-65 27-43 (205)
364 cd01106 HTH_TipAL-Mta Helix-Tu 66.6 6 0.00015 18.6 2.9 44 185-228 38-85 (103)
365 cd06571 Bac_DnaA_C C-terminal 66.3 8.8 0.00022 17.5 6.4 52 191-242 32-87 (90)
366 cd00093 HTH_XRE Helix-turn-hel 66.2 8.8 0.00022 17.5 3.9 42 198-243 10-51 (58)
367 PRK10227 DNA-binding transcrip 65.2 6.6 0.00017 18.3 2.9 11 200-210 57-67 (135)
368 cd00592 HTH_MerR-like Helix-Tu 65.1 6.6 0.00017 18.3 2.9 33 183-215 35-71 (100)
369 COG4189 Predicted transcriptio 65.0 9.3 0.00024 17.3 4.6 23 201-223 38-60 (308)
370 PRK10072 putative transcriptio 64.8 6.7 0.00017 18.2 2.9 32 190-222 37-68 (96)
371 pfam00292 PAX 'Paired box' dom 64.6 9.4 0.00024 17.3 4.5 38 190-227 23-60 (125)
372 cd01282 HTH_MerR-like_sg3 Heli 64.6 6.9 0.00018 18.1 2.9 27 185-211 37-67 (112)
373 TIGR02948 SigW_bacill RNA poly 64.4 1.8 4.6E-05 21.9 -0.1 35 190-225 143-177 (187)
374 cd04763 HTH_MlrA-like Helix-Tu 64.4 6.2 0.00016 18.4 2.7 26 185-210 38-67 (68)
375 PRK09392 ftrB transcriptional 64.2 9.6 0.00025 17.2 3.6 29 201-230 174-202 (236)
376 cd04775 HTH_Cfa-like Helix-Tur 64.0 7.1 0.00018 18.1 2.9 44 185-228 38-87 (102)
377 PHA00675 hypothetical protein 63.2 10 0.00026 17.1 5.3 41 182-222 19-61 (78)
378 pfam08765 Mor Mor transcriptio 62.6 10 0.00026 17.0 4.2 46 181-227 53-98 (107)
379 smart00345 HTH_GNTR helix_turn 62.5 10 0.00026 17.1 3.5 25 202-226 22-46 (60)
380 pfam10078 DUF2316 Uncharacteri 62.4 9.7 0.00025 17.2 3.4 27 195-221 18-44 (89)
381 cd04784 HTH_CadR-PbrR Helix-Tu 62.4 7.9 0.0002 17.8 2.9 44 185-228 38-95 (127)
382 PRK05932 RNA polymerase factor 61.8 5.1 0.00013 19.0 1.9 22 201-222 422-448 (461)
383 pfam04233 Phage_Mu_F Phage Mu 61.6 8 0.0002 17.7 2.8 21 190-210 4-24 (110)
384 cd01105 HTH_GlnR-like Helix-Tu 61.1 9.1 0.00023 17.4 3.0 27 185-211 39-69 (88)
385 pfam07508 Recombinase Recombin 61.1 8.1 0.00021 17.7 2.8 33 191-223 8-51 (101)
386 cd04779 HTH_MerR-like_sg4 Heli 60.9 8.6 0.00022 17.5 2.9 14 198-211 54-67 (134)
387 PRK09508 leuO leucine transcri 60.7 11 0.00028 16.8 5.4 12 47-58 55-66 (314)
388 PRK09514 zntR zinc-responsive 60.5 9 0.00023 17.4 2.9 11 200-210 58-68 (140)
389 PRK09975 DNA-binding transcrip 60.4 5.6 0.00014 18.7 1.9 16 185-200 185-200 (213)
390 PRK09706 transcriptional repre 60.1 10 0.00026 17.0 3.2 27 183-210 82-108 (135)
391 PRK11753 cAMP-regulatory prote 59.8 11 0.00029 16.7 3.7 26 201-226 169-194 (211)
392 PRK09480 slmA nucleoid occlusi 59.4 9.4 0.00024 17.3 2.9 14 51-64 35-48 (194)
393 COG3093 VapI Plasmid maintenan 59.4 9 0.00023 17.4 2.8 37 187-223 9-46 (104)
394 KOG0723 consensus 59.3 6.5 0.00017 18.3 2.0 36 199-234 51-86 (112)
395 COG1395 Predicted transcriptio 59.3 8.9 0.00023 17.4 2.7 27 197-223 135-161 (313)
396 cd04788 HTH_NolA-AlbR Helix-Tu 58.5 9.5 0.00024 17.3 2.8 43 185-227 38-88 (96)
397 pfam00392 GntR Bacterial regul 58.2 12 0.00031 16.6 3.3 24 202-225 26-49 (64)
398 pfam01498 Transposase_5 Transp 58.1 9.8 0.00025 17.2 2.8 23 201-223 14-41 (72)
399 PRK10402 DNA-binding transcrip 58.0 12 0.00031 16.5 3.6 26 201-226 157-182 (213)
400 COG3177 Fic family protein [Fu 57.9 12 0.00031 16.5 3.7 28 199-226 303-330 (348)
401 TIGR01321 TrpR trp operon repr 57.9 12 0.00032 16.5 3.7 33 187-219 43-75 (95)
402 cd01104 HTH_MlrA-CarA Helix-Tu 56.7 11 0.00028 16.8 2.9 26 184-209 37-66 (68)
403 TIGR02612 mob_myst_A mobile my 56.7 8.9 0.00023 17.4 2.4 18 200-217 38-55 (150)
404 pfam06322 Phage_NinH Phage Nin 55.8 7.5 0.00019 17.9 1.9 24 203-226 19-42 (64)
405 PRK12469 RNA polymerase factor 55.7 6.2 0.00016 18.5 1.4 27 199-225 362-388 (475)
406 PRK06474 hypothetical protein; 55.3 14 0.00035 16.2 5.5 13 42-54 42-54 (180)
407 smart00342 HTH_ARAC helix_turn 55.1 14 0.00035 16.2 3.7 34 191-227 40-74 (84)
408 pfam09999 DUF2240 Uncharacteri 54.6 14 0.00036 16.2 5.4 42 204-245 92-135 (144)
409 PHA00542 putative Cro-like pro 54.0 14 0.00036 16.1 3.6 38 184-222 16-53 (82)
410 cd07377 WHTH_GntR Winged helix 53.8 14 0.00037 16.1 3.6 24 202-225 27-50 (66)
411 pfam07022 Phage_CI_repr Bacter 53.2 14 0.00037 16.1 3.0 42 198-244 9-51 (65)
412 COG2469 Uncharacterized conser 52.7 8.4 0.00021 17.6 1.7 47 181-227 209-255 (284)
413 cd04767 HTH_HspR-like_MBC Heli 52.1 14 0.00036 16.1 2.8 28 186-213 38-70 (120)
414 pfam06970 RepA_N Replication i 51.6 15 0.00039 15.9 2.9 22 201-222 53-74 (76)
415 COG3677 Transposase and inacti 51.5 16 0.0004 15.9 3.4 44 186-229 75-118 (129)
416 COG2508 Regulator of polyketid 51.3 16 0.0004 15.8 5.2 41 191-231 357-397 (421)
417 PRK11608 pspF phage shock prot 51.0 16 0.00041 15.8 4.5 36 188-223 285-322 (325)
418 COG2944 Predicted transcriptio 50.8 16 0.00041 15.8 5.2 38 183-221 41-78 (104)
419 TIGR01369 CPSaseII_lrg carbamo 50.7 16 0.00041 15.8 3.2 46 185-230 483-534 (1089)
420 PRK13918 CRP/FNR family transc 49.8 17 0.00042 15.7 3.6 44 201-244 146-198 (201)
421 TIGR02850 spore_sigG RNA polym 49.8 17 0.00042 15.7 4.1 46 184-229 205-251 (254)
422 COG1725 Predicted transcriptio 49.3 15 0.00038 16.0 2.6 14 204-217 39-52 (125)
423 pfam04492 Phage_rep_O Bacterio 49.2 17 0.00043 15.6 5.0 42 184-225 28-79 (100)
424 pfam04703 FaeA FaeA-like prote 48.6 17 0.00044 15.6 4.2 41 192-233 4-47 (61)
425 pfam04539 Sigma70_r3 Sigma-70 48.5 17 0.00044 15.6 4.1 37 188-224 8-44 (78)
426 cd01279 HTH_HspR-like Helix-Tu 47.9 18 0.00045 15.5 2.9 39 182-220 35-78 (98)
427 cd04765 HTH_MlrA-like_sg2 Heli 47.9 18 0.00045 15.5 2.9 32 181-212 34-70 (99)
428 PRK09391 fixK transcriptional 47.8 18 0.00045 15.5 3.7 28 200-227 173-200 (224)
429 smart00531 TFIIE Transcription 47.0 18 0.00047 15.4 3.8 29 201-229 16-45 (147)
430 pfam06971 Put_DNA-bind_N Putat 47.0 15 0.00038 16.0 2.3 25 196-220 20-47 (49)
431 TIGR03286 methan_mark_15 putat 46.3 19 0.00048 15.3 3.2 47 184-232 306-357 (404)
432 pfam11994 DUF3489 Protein of u 45.9 19 0.00049 15.3 3.8 45 191-235 13-60 (72)
433 pfam08069 Ribosomal_S13_N Ribo 45.8 19 0.00049 15.3 2.9 30 182-211 24-55 (60)
434 pfam07453 NUMOD1 NUMOD1 domain 45.3 10 0.00026 17.0 1.2 21 201-221 17-37 (37)
435 KOG0489 consensus 45.1 19 0.00049 15.3 2.6 40 193-232 171-218 (261)
436 pfam11740 KfrA_N Plasmid repli 44.5 20 0.00051 15.2 4.8 37 195-231 12-51 (120)
437 pfam05732 RepL Firmicute plasm 44.4 20 0.00051 15.2 2.9 39 188-226 55-101 (165)
438 pfam00872 Transposase_mut Tran 44.4 20 0.00051 15.2 5.6 17 191-207 105-121 (381)
439 COG3655 Predicted transcriptio 43.7 20 0.00051 15.2 2.5 25 195-219 10-34 (73)
440 pfam02042 RWP-RK RWP-RK domain 42.6 21 0.00055 15.0 3.8 28 201-232 16-43 (52)
441 KOG1597 consensus 42.4 22 0.00055 15.0 3.4 37 192-228 252-288 (308)
442 COG1373 Predicted ATPase (AAA+ 42.1 22 0.00055 14.9 3.2 37 188-224 220-261 (398)
443 TIGR03613 RutR pyrimidine util 41.8 22 0.00056 14.9 3.0 16 187-202 185-200 (202)
444 TIGR02395 rpoN_sigma RNA polym 40.3 11 0.00029 16.7 0.8 22 201-222 366-387 (477)
445 PRK12815 carB carbamoyl phosph 40.2 23 0.00059 14.7 3.5 35 193-231 484-518 (1068)
446 COG1961 PinR Site-specific rec 39.8 16 0.0004 15.8 1.5 43 186-228 162-205 (222)
447 COG4367 Uncharacterized protei 38.4 25 0.00063 14.6 3.1 24 198-221 21-44 (97)
448 PTZ00100 DnaJ chaperone protei 37.5 24 0.00062 14.6 2.1 33 199-231 58-90 (114)
449 PRK11388 DNA-binding transcrip 37.4 26 0.00066 14.5 5.3 39 185-223 587-627 (639)
450 cd06445 ATase The DNA repair p 37.2 26 0.00066 14.5 3.2 32 192-223 7-42 (79)
451 COG3088 CcmH Uncharacterized p 36.8 26 0.00067 14.4 2.3 19 181-199 133-151 (153)
452 TIGR00498 lexA LexA repressor; 36.6 26 0.00068 14.4 3.8 42 186-227 4-53 (227)
453 pfam09012 FeoC FeoC like trans 36.5 27 0.00068 14.4 3.6 30 200-229 14-43 (68)
454 pfam04936 DUF658 Protein of un 36.3 27 0.00068 14.4 2.2 43 196-240 84-126 (134)
455 pfam04182 B-block_TFIIIC B-blo 35.6 27 0.0007 14.3 4.1 41 187-227 1-45 (73)
456 pfam05344 DUF746 Domain of Unk 35.6 27 0.0007 14.3 4.9 48 189-236 2-52 (65)
457 pfam12116 SpoIIID Stage III sp 35.2 28 0.00071 14.3 5.2 42 188-229 6-48 (82)
458 COG1974 LexA SOS-response tran 35.2 28 0.00071 14.2 4.5 10 40-49 38-47 (201)
459 pfam00382 TFIIB Transcription 34.9 20 0.0005 15.2 1.3 25 193-217 47-71 (71)
460 COG1476 Predicted transcriptio 34.8 28 0.00072 14.2 2.7 27 197-223 11-37 (68)
461 cd00086 homeodomain Homeodomai 34.1 29 0.00074 14.1 3.7 28 203-230 30-57 (59)
462 COG1444 Predicted P-loop ATPas 34.0 29 0.00074 14.1 6.1 48 182-229 701-749 (758)
463 pfam03918 CcmH Cytochrome C bi 33.9 29 0.00074 14.1 2.4 15 183-197 129-143 (145)
464 PRK13832 plasmid partitioning 33.8 29 0.00075 14.1 4.1 31 1-31 157-187 (518)
465 pfam07506 RepB RepB plasmid pa 32.9 30 0.00077 14.0 6.7 59 188-246 9-92 (185)
466 PRK01905 DNA-binding protein F 32.7 31 0.00078 14.0 2.8 19 205-223 55-73 (77)
467 pfam02082 Rrf2 Transcriptional 32.7 31 0.00078 14.0 4.7 36 191-226 10-50 (82)
468 pfam05066 RNA_pol_delta DNA-di 32.2 31 0.00079 13.9 3.5 31 204-234 38-68 (94)
469 COG4941 Predicted RNA polymera 32.2 31 0.00079 13.9 4.2 32 197-228 133-164 (415)
470 PRK09258 3-oxoacyl-(acyl carri 32.0 17 0.00043 15.7 0.6 32 202-233 16-47 (339)
471 TIGR02047 CadR-PbrR Cd(II)/Pb( 31.9 22 0.00055 15.0 1.1 17 204-220 4-20 (127)
472 pfam02954 HTH_8 Bacterial regu 31.9 31 0.0008 13.9 5.2 36 188-223 6-41 (42)
473 pfam00046 Homeobox Homeobox do 31.5 32 0.00081 13.9 5.2 42 186-227 7-54 (57)
474 PRK02363 DNA-directed RNA poly 31.5 32 0.00081 13.9 3.5 31 204-234 38-68 (185)
475 smart00497 IENR1 Intron encode 30.7 23 0.00058 14.8 1.1 22 202-223 19-40 (53)
476 TIGR02531 yecD_yerC TrpR homol 30.6 33 0.00084 13.8 4.2 34 191-224 41-74 (88)
477 PRK06816 3-oxoacyl-(acyl carri 30.4 33 0.00085 13.8 1.9 43 201-243 17-73 (378)
478 TIGR00014 arsC arsenate reduct 30.4 31 0.00079 14.0 1.7 41 191-233 13-54 (114)
479 PRK11014 transcriptional repre 30.1 34 0.00086 13.7 3.5 26 202-227 27-52 (141)
480 COG2411 Uncharacterized conser 29.6 34 0.00088 13.7 5.6 43 186-228 138-182 (188)
481 pfam01388 ARID ARID/BRIGHT DNA 29.5 35 0.00088 13.6 2.7 25 204-228 61-86 (91)
482 pfam10826 DUF2551 Protein of u 29.3 35 0.00089 13.6 4.9 40 191-230 14-59 (83)
483 PHA00738 putative HTH transcri 29.2 33 0.00084 13.8 1.7 32 191-222 16-49 (112)
484 PRK05294 carB carbamoyl phosph 28.8 36 0.00091 13.6 3.5 24 200-223 491-514 (1063)
485 COG1777 Predicted transcriptio 28.6 36 0.00091 13.6 3.7 32 191-222 18-50 (217)
486 PRK05782 precorrin-8X methylmu 28.5 36 0.00091 13.5 2.2 63 182-244 159-221 (332)
487 PTZ00037 DnaJ_C chaperone prot 28.5 27 0.00068 14.4 1.1 21 208-228 30-50 (422)
488 PRK13626 transcriptional regul 28.4 36 0.00092 13.5 3.4 26 202-227 25-50 (551)
489 COG5407 SEC63 Preprotein trans 28.4 29 0.00075 14.1 1.3 39 193-231 74-125 (610)
490 PRK00430 fis DNA-binding prote 28.3 36 0.00092 13.5 2.5 17 207-223 78-94 (98)
491 COG3311 AlpA Predicted transcr 28.1 36 0.00093 13.5 2.7 22 201-222 14-35 (70)
492 TIGR03070 couple_hipB transcri 28.1 37 0.00093 13.5 3.1 22 198-219 13-34 (58)
493 TIGR02392 rpoH_proteo alternat 28.0 37 0.00093 13.5 4.4 44 185-228 226-273 (279)
494 pfam10654 DUF2481 Protein of u 27.9 37 0.00094 13.5 3.9 33 191-223 71-103 (126)
495 pfam08004 DUF1699 Protein of u 27.7 37 0.00095 13.4 3.9 32 192-223 96-131 (131)
496 pfam07037 DUF1323 Putative tra 27.7 37 0.00095 13.4 3.1 23 201-223 1-23 (122)
497 TIGR01610 phage_O_Nterm phage 27.4 37 0.00096 13.4 4.7 46 182-227 19-81 (104)
498 pfam04695 Pex14_N Peroxisomal 27.4 38 0.00096 13.4 2.0 30 187-216 21-50 (79)
499 TIGR03192 benz_CoA_bzdQ benzoy 27.3 38 0.00096 13.4 3.5 40 190-232 202-241 (293)
500 PRK04984 fatty acid metabolism 27.3 38 0.00096 13.4 5.4 38 190-227 13-58 (239)
No 1
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=100.00 E-value=3.8e-36 Score=250.90 Aligned_cols=218 Identities=19% Similarity=0.156 Sum_probs=176.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEECCCCCHHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf 21379999732799999999999998719302300026663111232100068958999999966984517389999852
Q gi|254780694|r 29 RSDLLARMIPLDCTVSWTMRMYALTEYVGASHFLLVRWDLFQEQKLDSIVSSDWPFDLVRCMALSEKDKYYNVLQRPTEL 108 (246)
Q Consensus 29 ~~d~~~~l~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~ 108 (246)
+.|++.++..+.+..++...+...++.+||++|.|....+.+...+...+.++||.+|...|...++...||++..+..+
T Consensus 10 ~~~~l~~~~~a~~~~~~~~~l~~~~~~lGFey~~~~~~~p~p~~~p~~~l~snYP~~W~~~Y~~~~y~~iDPvv~~~~~s 89 (240)
T PRK10188 10 RRTMLLRFQEMAAAEEVYHELQLQTQQLEYDYYSLCVRHPVPFTRPKVAFYTTYPEAWVSHYQAENYLAIDPVLKPENFS 89 (240)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCEEEECCCCHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf 99999999847999999999999999759825898874268888876688728999999999987791449510244468
Q ss_pred HHHHHCCCH--------HHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCC--CCC-HHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 324430325--------43333214457147503373689999999717875--469-8999999999999997542014
Q gi|254780694|r 109 FCPVFHTLP--------ENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGR--IIL-RDRLWEIGLLAAYQANMFKSYD 177 (246)
Q Consensus 109 ~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~-~~~~~~~~~~~~~~~~~~~~~~ 177 (246)
..|+.|... ...+..+|+..|+..+...+.+..+.+.+...... ... ......+.++.......+....
T Consensus 90 ~~P~~W~~~l~~~~~~~~~eA~~~Gl~~G~t~p~~~~~g~~g~lSla~~~~~~~~~~~~~~~l~l~~l~~~~~~~~~~~~ 169 (240)
T PRK10188 90 QGHLMWNDDLFSEAQALWDAARAHGLRRGVTQCLMLPNRALGFLSFSRSSLREIPILSDELELRLQLLVRESLMALMRLE 169 (240)
T ss_pred CCCEECCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 98730784012420999999998298676178887279983899985478877754355999999999999999998640
Q ss_pred --CCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC
Q ss_conf --677988888977999999998599979999994999889999999999980799889999999975898
Q gi|254780694|r 178 --VHWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNIV 246 (246)
Q Consensus 178 --~~~~~~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~Gli 246 (246)
....+...||+||+|||+|+|+|||+.|||.+|+||++||++|++|+++|||+.||+|||++|+..|||
T Consensus 170 ~~~~~~~~~~LT~RE~E~L~W~A~GKTs~EIa~IL~ISe~TV~fHl~na~~KL~a~Nr~qAva~A~~~GLI 240 (240)
T PRK10188 170 DEMVMTPEMNFSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240 (240)
T ss_pred CCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC
T ss_conf 44457987889989999999997799999999883999999999999999995899899999999985899
No 2
>PRK13870 transcriptional regulator TraR; Provisional
Probab=100.00 E-value=4.2e-34 Score=237.78 Aligned_cols=202 Identities=14% Similarity=0.083 Sum_probs=158.6
Q ss_pred CCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEECCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCC--
Q ss_conf 279999999999999871930230002666311123210006895899999996698451738999985232443032--
Q gi|254780694|r 39 LDCTVSWTMRMYALTEYVGASHFLLVRWDLFQEQKLDSIVSSDWPFDLVRCMALSEKDKYYNVLQRPTELFCPVFHTL-- 116 (246)
Q Consensus 39 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~-- 116 (246)
..+...+...+..+++.+||+.|+|... ..++..+.++||.+|...|...++..+||++..+..+..|+.|..
T Consensus 15 ~~de~~~~~~l~~~a~~~gf~~~ayl~~-----~~~~~~~isnYP~eW~~~Y~~~~Y~~iDPVv~~a~~~~~Pf~Ws~~~ 89 (234)
T PRK13870 15 EGDECILKTGLADIAEHFGFTGYAYLHI-----QHRHITAVTNYHREWQSTYFDKKFDALDPVVKRARSRKHIFTWSGEQ 89 (234)
T ss_pred HCCHHHHHHHHHHHHHHCCCCCEEEEEE-----CCCCEEEEECCCHHHHHHHHHCCCEEECHHHHHHHCCCCCEEECCCC
T ss_conf 3539999999999999839985798750-----79975787279999999999888903087999883489897608765
Q ss_pred -----------HHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHH-HHHHH--HHHHHHHHHHHHH--CCCCC
Q ss_conf -----------54333321445714750337368999999971787546989-99999--9999999975420--14677
Q gi|254780694|r 117 -----------PENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRD-RLWEI--GLLAAYQANMFKS--YDVHW 180 (246)
Q Consensus 117 -----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~--~~~~~~~~~~~~~--~~~~~ 180 (246)
+...+..+++..|+..|.+++.+..+.+.+.... ...... ..... .......+.+... .....
T Consensus 90 ~~~~~~~~~r~f~~eA~~~Gl~~G~tiPi~~~~G~~~~lSlas~~-~~~~~~~~~~~~~~~~~~~~~h~~~~~l~~~~~~ 168 (234)
T PRK13870 90 ERPSLSKDERAFYAHAADFGIRSGITIPIKTANGSMSMFTLASEK-PVIDLDREIDAVAAAATIGQIHARISFLRTTPTA 168 (234)
T ss_pred CCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCCEEEEEEECCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 544348689999999998599966999888799998999981399-8421678899999999999999999862048888
Q ss_pred CCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC
Q ss_conf 988888977999999998599979999994999889999999999980799889999999975898
Q gi|254780694|r 181 GKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNIV 246 (246)
Q Consensus 181 ~~~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~Gli 246 (246)
.+...||+||+|||+|+|+|||+.|||.+|+||++||++|++|+++|||+.||+|||++|+++|||
T Consensus 169 ~~~~~LT~RE~E~L~W~A~GKT~~EIA~ILgISe~TV~fHl~na~~KL~a~nr~qAVa~Ai~~gLI 234 (234)
T PRK13870 169 EDAAWLDPKEATYLRWIAVGMTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234 (234)
T ss_pred CCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC
T ss_conf 776679979999999997899899999997988999999999999995899899999999985899
No 3
>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=100.00 E-value=2.8e-33 Score=232.54 Aligned_cols=214 Identities=20% Similarity=0.139 Sum_probs=169.3
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEE-ECCCCCHHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf 37999973279999999999999871930230002666311123210-00689589999999669845173899998523
Q gi|254780694|r 31 DLLARMIPLDCTVSWTMRMYALTEYVGASHFLLVRWDLFQEQKLDSI-VSSDWPFDLVRCMALSEKDKYYNVLQRPTELF 109 (246)
Q Consensus 31 d~~~~l~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~-l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~ 109 (246)
|++..+..+.+.+++...+..+.+.+||++|.|....+......... +....+.++...|+..++...||++..+....
T Consensus 6 ~~l~~l~~a~t~~~l~~~l~~~~~~~Gfd~~~y~~~~~~~~~~~~~~~~~~~~w~~~~~~y~~~~Y~~~DPvv~~~~~~~ 85 (232)
T TIGR03541 6 QAVRQIEQASTLEAIQDAVREFAQNLGYDRFVLFSAHSAKDELIERIFWVEGDWFDDGNAVDAQTYLRHCPVTRHILEAD 85 (232)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCEECCCCCHHHHHHHHHHCCCCCCCCHHHHHHHCC
T ss_conf 99999984899999999999999984998899963477766556400037874577899998839910698999998579
Q ss_pred HHHHCCCHH----------HHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCC-
Q ss_conf 244303254----------333321445714750337368999999971787546989999999999999975420146-
Q gi|254780694|r 110 CPVFHTLPE----------NITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAYQANMFKSYDV- 178 (246)
Q Consensus 110 ~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 178 (246)
.|+.|.... ......+ ..|+..|.+.+.+..+.+.+.+ .....+......+.++..+.+........
T Consensus 86 ~Pf~Ws~~~~~~~~~~~~~~~a~~~G-~~G~tvPi~~~~G~~g~~s~a~-~~~d~~~~~~~~l~l~~~~a~~~~~~l~~~ 163 (232)
T TIGR03541 86 EPFFWSKTPNENGERYRVVRNPSGRG-VHGLQVPVFGRTGLEGAVSLGG-KLIDLSARFRLALQLLCVTAFFAARRLLEA 163 (232)
T ss_pred CCEECCCCCCCCHHHHHHHHHHHHCC-CCEEEEEEECCCCCEEEEEECC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 99623888766877899999998639-9589998888999868998416-877789999999999999999999997358
Q ss_pred -CCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC
Q ss_conf -77988888977999999998599979999994999889999999999980799889999999975898
Q gi|254780694|r 179 -HWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNIV 246 (246)
Q Consensus 179 -~~~~~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~Gli 246 (246)
...+...||+||+|||+|+|+|||+.|||.+|+||++||++|++|+++|||+.||+|||++|+++|||
T Consensus 164 ~~~~~~~~LT~RE~E~L~w~A~Gkt~~eIa~iL~iSe~TV~~hl~~a~~KLga~nr~qAVa~Ai~~GlI 232 (232)
T TIGR03541 164 PLLREAGVLSEREREVLAWTALGRRQADIAAILGISERTVENHLRSARRKLGVATTAQAIAIALRKGDI 232 (232)
T ss_pred CCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC
T ss_conf 998889998989999999998799999999996989999999999999984899999999999987999
No 4
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=99.93 E-value=2.3e-24 Score=175.23 Aligned_cols=210 Identities=16% Similarity=0.140 Sum_probs=140.5
Q ss_pred HHHEEEEECCCCHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEECCCCCH
Q ss_conf 01100022144588887655302321379999732799999999999998719302300026663111232100068958
Q gi|254780694|r 5 IQQVNIVLNREDEQRTSFVSHLPTRSDLLARMIPLDCTVSWTMRMYALTEYVGASHFLLVRWDLFQEQKLDSIVSSDWPF 84 (246)
Q Consensus 5 ~~~~~~~l~r~d~~r~~~v~~l~~~~d~~~~l~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~ 84 (246)
|.+++|++..+++.-...+..+......+.-+..+.+..+....+.. .. ++....+..+.+..+.
T Consensus 1 M~p~~VlIvDDh~l~r~gl~~~l~~~~~~~vv~~a~~~~~~~~~l~~----~~-----------~DvvllD~~lp~~~g~ 65 (210)
T PRK09935 1 MKPASVIIMDEHPIVRMSIEVLLQKNSNIQVVLKTDDSRITIDYLRT----YP-----------VDLVILDIELPGTDGF 65 (210)
T ss_pred CCCCEEEEECCCHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHH----CC-----------CCEEEECCCCCCCCCC
T ss_conf 99788999859699999999999629892899998999999999974----79-----------9999988999998864
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf 99999996698451738999985232443032543333214457147503373689999999717875469899999999
Q gi|254780694|r 85 DLVRCMALSEKDKYYNVLQRPTELFCPVFHTLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGL 164 (246)
Q Consensus 85 ~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 164 (246)
+..+...... |.... -.................++.||+.+....+....++..+..+..+.........
T Consensus 66 ~~i~~i~~~~-----p~~~i---lvls~~~~~~~~~~a~~~Ga~g~l~K~~~~~~l~~ai~~v~~G~~~~~~~~~~~~-- 135 (210)
T PRK09935 66 TLLKRIKQIQ-----ETVKV---LFLSSKSECFYAGRAIRAGANGFVSKRKDLNDIYNAVQMILSGYSFFPSETLNFI-- 135 (210)
T ss_pred CHHHHHHHHC-----CCCCE---EEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCCCCCCCHHHHHHH--
T ss_conf 0567898738-----99708---9971767299999999668776886789999999999999859953698999998--
Q ss_pred HHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCC
Q ss_conf 99999975420146779888889779999999985999799999949998899999999999807998899999999758
Q gi|254780694|r 165 LAAYQANMFKSYDVHWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNN 244 (246)
Q Consensus 165 ~~~~~~~~~~~~~~~~~~~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~G 244 (246)
... ...........||+||.|||+++++|+||+|||+.|+||++||++|++|||+|||++||+|+|.+|+++|
T Consensus 136 -----~~~--~~~~~~~~~~~Lt~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KL~v~nr~elv~~A~~~~ 208 (210)
T PRK09935 136 -----KSN--KCSKGSSTDMPLSNREVTVLRYLANGLSNKEIAEQLLLSNKTISAHKSNIYGKLGLHSIVELIDYAKSHE 208 (210)
T ss_pred -----HHC--CCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCC
T ss_conf -----734--3666655678999899999999986999999998949889999999999999819999999999999859
Q ss_pred CC
Q ss_conf 98
Q gi|254780694|r 245 IV 246 (246)
Q Consensus 245 li 246 (246)
||
T Consensus 209 Li 210 (210)
T PRK09935 209 LL 210 (210)
T ss_pred CC
T ss_conf 99
No 5
>PRK09483 response regulator; Provisional
Probab=99.92 E-value=6.4e-24 Score=172.40 Aligned_cols=207 Identities=15% Similarity=0.127 Sum_probs=130.2
Q ss_pred EEEECCCCHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEECCCCCHHHHH
Q ss_conf 00221445888876553023213799997327999999999999987193023000266631112321000689589999
Q gi|254780694|r 9 NIVLNREDEQRTSFVSHLPTRSDLLARMIPLDCTVSWTMRMYALTEYVGASHFLLVRWDLFQEQKLDSIVSSDWPFDLVR 88 (246)
Q Consensus 9 ~~~l~r~d~~r~~~v~~l~~~~d~~~~l~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~ 88 (246)
+|++..+++.-...+..+....+-+.-+..+.+..+....+.. ... +....+..+.+..+.+..+
T Consensus 3 ~VlIvDDh~l~r~gl~~~L~~~~~~~vv~~a~~~~~~l~~~~~----~~p-----------DvvllDl~lp~~~Gl~~~~ 67 (216)
T PRK09483 3 NVLLVDDHELVRAGIRRILEDIKGIKVVGEASCGEDAVKWCRT----NAV-----------DVVLMDMNMPGIGGLEATR 67 (216)
T ss_pred EEEEECCCHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHH----CCC-----------CEEEECCCCCCCCCHHHHH
T ss_conf 8999849999999999999748995899998999999999985----599-----------9999868898987523778
Q ss_pred HHHHCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
Q ss_conf 99966984517389999852324430325433332144571475033736899999997178754698999999999999
Q gi|254780694|r 89 CMALSEKDKYYNVLQRPTELFCPVFHTLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAY 168 (246)
Q Consensus 89 ~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 168 (246)
..... .|.... ..................++.||+.+....+....++..+..+....++........
T Consensus 68 ~i~~~-----~p~~~v---ivls~~~~~~~~~~al~~Ga~gyl~K~~~~~~l~~ai~~v~~G~~~~~~~~~~~~~~---- 135 (216)
T PRK09483 68 KILRS-----TPDVKI---IMLTVHTENPLPAKVMQAGAAGYLSKGAAPQEVVSAIRSVHSGQRYIASDIAQQMAL---- 135 (216)
T ss_pred HHHHH-----CCCCCE---EEECCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHH----
T ss_conf 88740-----899857---863056632889999974887899479999999999999985997069899999987----
Q ss_pred HHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC
Q ss_conf 997542014677988888977999999998599979999994999889999999999980799889999999975898
Q gi|254780694|r 169 QANMFKSYDVHWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNIV 246 (246)
Q Consensus 169 ~~~~~~~~~~~~~~~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~Gli 246 (246)
.... .....+...||+||+||++|+++|+||+|||..|+||++||++|++|||+|||++||+|++.+|+++|||
T Consensus 136 --~~~~--~~~~~~~~~LT~RE~eVl~ll~~G~snkeIA~~L~iS~~TV~~h~~~i~~KL~v~~r~el~~~A~~~gli 209 (216)
T PRK09483 136 --SQFE--PATENPFASLSERELQIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAIRHGLL 209 (216)
T ss_pred --HCCC--CCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC
T ss_conf --3237--6545654568999999999998799999999996989999999999999980999999999999995991
No 6
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=99.91 E-value=2.7e-23 Score=168.41 Aligned_cols=208 Identities=12% Similarity=0.026 Sum_probs=134.4
Q ss_pred HHHEEEEECCCCHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEECCC---
Q ss_conf 01100022144588887655302321379999732799999999999998719302300026663111232100068---
Q gi|254780694|r 5 IQQVNIVLNREDEQRTSFVSHLPTRSDLLARMIPLDCTVSWTMRMYALTEYVGASHFLLVRWDLFQEQKLDSIVSSD--- 81 (246)
Q Consensus 5 ~~~~~~~l~r~d~~r~~~v~~l~~~~d~~~~l~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~--- 81 (246)
|.+.+|++..+++.-...+..++...+...-+..+.+..++...+.. .. ++-...+..+.+.
T Consensus 1 M~~irIlIvDDh~lvr~Gl~~~L~~~~~~~vvg~a~~~~~~~~~~~~----~~-----------pDvvllDl~mpg~~~~ 65 (216)
T PRK10840 1 MNNMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPK----LD-----------AHVLITDLSMPGDKYG 65 (216)
T ss_pred CCCCEEEEECCHHHHHHHHHHHHCCCCCCEEEEEECCHHHHHHHHHH----CC-----------CCEEEEECCCCCCCCC
T ss_conf 99888999889799999999998159996899987999999999862----39-----------8989982677999887
Q ss_pred CCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHH
Q ss_conf 95899999996698451738999985232443032543333214457147503373689999999717875469899999
Q gi|254780694|r 82 WPFDLVRCMALSEKDKYYNVLQRPTELFCPVFHTLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWE 161 (246)
Q Consensus 82 ~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 161 (246)
.+.++.+..... .|... ...................++.||+.+.........++..+..+....+......
T Consensus 66 dGl~~~~~i~~~-----~p~~~---vivls~~~~~~~v~~al~~Ga~Gyl~K~~~~~~L~~AI~~v~~G~~~~~~~~~~~ 137 (216)
T PRK10840 66 DGITLIKYIKRH-----FPSLS---IIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRL 137 (216)
T ss_pred CHHHHHHHHHHH-----CCCCE---EEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCCCCCCCHHHHHH
T ss_conf 899999999985-----89980---8998477878999999858974899878999999999999987994396999999
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf 99999999975420146779888889779999999985999799999949998899999999999807998899999999
Q gi|254780694|r 162 IGLLAAYQANMFKSYDVHWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAV 241 (246)
Q Consensus 162 ~~~~~~~~~~~~~~~~~~~~~~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~ 241 (246)
+. ...........||+||+|||+|+++|+||+|||+.|+||++||++|++|||+|||++||+|+|.||.
T Consensus 138 l~-----------~~~~~~~~~~~LT~RE~eVL~lla~G~snkeIA~~L~iS~~TV~~h~~~i~~KLgv~n~~eLv~ya~ 206 (216)
T PRK10840 138 LE-----------KISAGGYGDKRLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYLS 206 (216)
T ss_pred HH-----------HHCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHH
T ss_conf 99-----------7205888778999899999999986999999998969899999999999999829998999999999
Q ss_pred HCCCC
Q ss_conf 75898
Q gi|254780694|r 242 RNNIV 246 (246)
Q Consensus 242 ~~Gli 246 (246)
+.||+
T Consensus 207 ~~gl~ 211 (216)
T PRK10840 207 SVTLS 211 (216)
T ss_pred HCCCC
T ss_conf 86999
No 7
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=99.91 E-value=1.7e-23 Score=169.70 Aligned_cols=123 Identities=24% Similarity=0.159 Sum_probs=99.9
Q ss_pred CCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHH
Q ss_conf 32543333214457147503373689999999717875469899999999999999754201467798888897799999
Q gi|254780694|r 115 TLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAYQANMFKSYDVHWGKDFELTGREVECL 194 (246)
Q Consensus 115 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LT~RE~eVl 194 (246)
..........+++.||+.+..+++....++..+..++.++++.....+.. ..............||+||+|||
T Consensus 92 d~e~v~~al~aGa~GyllK~~~~~~Li~aIr~v~~G~~~l~~~~~~~l~~-------~~~~~~~~~~~~~~LT~RE~eIL 164 (216)
T PRK10100 92 DYPYREIENWPHINGVFYAMEDQERVVNGLQGVLRGECYFTQKLASYLIT-------HSGNYRYNSTESALLTHREKEIL 164 (216)
T ss_pred CHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHH-------HHCCCCCCCCCCCCCCHHHHHHH
T ss_conf 48999999765876676689999999999999987997239999999997-------10225678877789998999999
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCC
Q ss_conf 99985999799999949998899999999999807998899999999758
Q gi|254780694|r 195 TWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNN 244 (246)
Q Consensus 195 ~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~G 244 (246)
+++++|+||+|||+.|+||++|||+|++|||+|||++||+|||.||.++.
T Consensus 165 ~lla~G~sNkEIA~~L~iSe~TVk~H~~~I~~KL~v~~R~qav~~A~~nl 214 (216)
T PRK10100 165 NKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWANDNL 214 (216)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHC
T ss_conf 99987999999998949889899999999999809999999999999866
No 8
>PRK10651 transcriptional regulator NarL; Provisional
Probab=99.91 E-value=2.5e-23 Score=168.60 Aligned_cols=211 Identities=14% Similarity=0.066 Sum_probs=131.8
Q ss_pred HHHEEEEECCCCHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEECCCCCH
Q ss_conf 01100022144588887655302321379999732799999999999998719302300026663111232100068958
Q gi|254780694|r 5 IQQVNIVLNREDEQRTSFVSHLPTRSDLLARMIPLDCTVSWTMRMYALTEYVGASHFLLVRWDLFQEQKLDSIVSSDWPF 84 (246)
Q Consensus 5 ~~~~~~~l~r~d~~r~~~v~~l~~~~d~~~~l~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~ 84 (246)
.++++|++..+++.-...+..+....+.+.-+..+.+..+....+. ....+-..+ +..+.+..+.
T Consensus 4 ~~pirVlIvDDh~l~r~gl~~~L~~~~~~~vv~~a~~~~ea~~~~~----~~~pDlvll-----------Dl~lp~~~G~ 68 (216)
T PRK10651 4 QEPATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAE----SLDPDLILL-----------DLNMPGMNGL 68 (216)
T ss_pred CCCCEEEEECCCHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHH----HCCCCEEEE-----------ECCCCCCCCC
T ss_conf 9997899983999999999999975899389999899999999987----079999999-----------5999998887
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf 99999996698451738999985232443032543333214457147503373689999999717875469899999999
Q gi|254780694|r 85 DLVRCMALSEKDKYYNVLQRPTELFCPVFHTLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGL 164 (246)
Q Consensus 85 ~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 164 (246)
+..+..... .|.... ..................++.||+.+.........++..+..+....++.....+.
T Consensus 69 ~~~~~l~~~-----~~~~~i---ivlt~~~~~~~~~~al~~Ga~gyl~K~~~~~~L~~ai~~v~~g~~~~~~~~~~~l~- 139 (216)
T PRK10651 69 ETLDKLREK-----SLSGRI---VVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAAAGEMVLSEALTPVLA- 139 (216)
T ss_pred CCCCCCCCC-----CCCCCE---EEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCCCCCCCHHHHHHHH-
T ss_conf 642323345-----788746---76305541889999996698789837899999999999998599716988999999-
Q ss_pred HHHHHHHHHHH-CCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHC
Q ss_conf 99999975420-14677988888977999999998599979999994999889999999999980799889999999975
Q gi|254780694|r 165 LAAYQANMFKS-YDVHWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRN 243 (246)
Q Consensus 165 ~~~~~~~~~~~-~~~~~~~~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~ 243 (246)
. .... ..........||+||.|||+++++|+||+|||..|+||++||++|+++||+|||++||+||+.||+++
T Consensus 140 --~----~~~~~~~~~~~~~~~LT~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~i~~KLgv~nr~ea~~~a~~~ 213 (216)
T PRK10651 140 --A----SLRANRATTERDVNQLTPRERDILKLIAQGLSNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQE 213 (216)
T ss_pred --H----HHHCCCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHC
T ss_conf --8----7522666544442348989999999998599999999996978999999999999984899999999999983
Q ss_pred CC
Q ss_conf 89
Q gi|254780694|r 244 NI 245 (246)
Q Consensus 244 Gl 245 (246)
+|
T Consensus 214 ~l 215 (216)
T PRK10651 214 RI 215 (216)
T ss_pred CC
T ss_conf 69
No 9
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=99.90 E-value=2.1e-22 Score=162.74 Aligned_cols=157 Identities=20% Similarity=0.175 Sum_probs=112.2
Q ss_pred CCEEECCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCC
Q ss_conf 32100068958999999966984517389999852324430325433332144571475033736899999997178754
Q gi|254780694|r 74 LDSIVSSDWPFDLVRCMALSEKDKYYNVLQRPTELFCPVFHTLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRI 153 (246)
Q Consensus 74 ~~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 153 (246)
.+..+++..+.+..+.+....... ....................++.||+.+..+.+....++..+..+...
T Consensus 52 ~Dl~mP~~~G~e~~~~l~~~~p~~--------~vvvlt~~~~~~~v~~~l~~Ga~gyl~K~~~~~~l~~ai~~v~~G~~~ 123 (211)
T COG2197 52 LDLSMPGMDGLEALKQLRARGPDI--------KVVVLTAHDDPAYVIRALRAGADGYLLKDASPEELVEAIRAVAAGGTY 123 (211)
T ss_pred EECCCCCCCHHHHHHHHHHHCCCC--------EEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCCCCE
T ss_conf 837889987599999999868997--------299996778989999999779969986799999999999999758858
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCCCCC-CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 698999999999999997542014677988-8889779999999985999799999949998899999999999807998
Q gi|254780694|r 154 ILRDRLWEIGLLAAYQANMFKSYDVHWGKD-FELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKT 232 (246)
Q Consensus 154 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~ 232 (246)
+.+.....+..... ... ..... ..||+||.|||+++++|+||+|||+.|+||++||++|++|||+|||++|
T Consensus 124 ~~~~~~~~~~~~~~-------~~~-~~~~~~~~LT~RE~eVl~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v~~ 195 (211)
T COG2197 124 LPPDIARKLAGLLP-------SSS-AEAPLAELLTPRELEVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLGVRN 195 (211)
T ss_pred ECHHHHHHHHHCCC-------CCC-CCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC
T ss_conf 78899999975035-------655-4433357899899999999987998899999978789899999999999839998
Q ss_pred HHHHHHHHHHCCCC
Q ss_conf 89999999975898
Q gi|254780694|r 233 RSGAIAYAVRNNIV 246 (246)
Q Consensus 233 R~eav~~A~~~Gli 246 (246)
|+||+.+|.++|++
T Consensus 196 Rtea~~~a~~~g~~ 209 (211)
T COG2197 196 RTEAAIRALRLGLI 209 (211)
T ss_pred HHHHHHHHHHCCCC
T ss_conf 99999999982675
No 10
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=99.89 E-value=1.2e-22 Score=164.28 Aligned_cols=201 Identities=15% Similarity=0.106 Sum_probs=128.0
Q ss_pred HHEEEEECCCCHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEECCCCCHH
Q ss_conf 11000221445888876553023213799997327999999999999987193023000266631112321000689589
Q gi|254780694|r 6 QQVNIVLNREDEQRTSFVSHLPTRSDLLARMIPLDCTVSWTMRMYALTEYVGASHFLLVRWDLFQEQKLDSIVSSDWPFD 85 (246)
Q Consensus 6 ~~~~~~l~r~d~~r~~~v~~l~~~~d~~~~l~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 85 (246)
.|.+|++..+++.-...+..++...++. +....+..+....+ + ...+.....|..+++..+.+
T Consensus 2 ~k~tIliVDDh~~vr~gl~~lL~~~~~~--v~~~~~~~~~l~~~----~-----------~~~pdlvllDi~mP~~~G~e 64 (202)
T PRK09390 2 TKGVVHVVDDDEAMRDSLAFLLDSAGFE--VRLFESAQAFLDAL----P-----------GLRFGCVVTDVRMPGIDGIE 64 (202)
T ss_pred CCCEEEEECCCHHHHHHHHHHHHHCCCE--EEEECCHHHHHHHH----H-----------CCCCCEEEECCCCCCCCCHH
T ss_conf 9997999849999999999999988998--99989999999997----6-----------57979998779999989607
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf 99999966984517389999852324430325433332144571475033736899999997178754698999999999
Q gi|254780694|r 86 LVRCMALSEKDKYYNVLQRPTELFCPVFHTLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLL 165 (246)
Q Consensus 86 ~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 165 (246)
..+........ .|+ ..................++.||+.++...+....++..+.............
T Consensus 65 ~l~~l~~~~p~--~~v------ivlT~~~~~~~~~~al~~GA~gyl~K~~~~~~L~~aI~~~l~~~~~~~~~~~~----- 131 (202)
T PRK09390 65 LLRRLKARGSP--LPV------IVMTGHGDVPLAVEAMKLGAIDFIEKPFEDERLIGAIERALAQAPAAAKSEAV----- 131 (202)
T ss_pred HHHHHHHCCCC--CCE------EEEEECCCHHHHHHHHHCCCHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCHHH-----
T ss_conf 99998722899--867------99974574888899998294644559999999999999999715232421466-----
Q ss_pred HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCC
Q ss_conf 99999754201467798888897799999999859997999999499988999999999998079988999999997589
Q gi|254780694|r 166 AAYQANMFKSYDVHWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245 (246)
Q Consensus 166 ~~~~~~~~~~~~~~~~~~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~Gl 245 (246)
. .....+...||+||+|||+++++|+||+|||+.|+||++||++|++|||+|||++||+|+|.+|++.||
T Consensus 132 ~----------~~~~~~~~~LT~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KL~v~~~~elv~~A~~~Gl 201 (202)
T PRK09390 132 A----------ADIRARIASLSERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSLSELVRMALRAGA 201 (202)
T ss_pred H----------HHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCC
T ss_conf 7----------888740066998999999999838968999999798788999999999999688988999999998599
Q ss_pred C
Q ss_conf 8
Q gi|254780694|r 246 V 246 (246)
Q Consensus 246 i 246 (246)
|
T Consensus 202 l 202 (202)
T PRK09390 202 L 202 (202)
T ss_pred C
T ss_conf 9
No 11
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=99.89 E-value=3.2e-22 Score=161.55 Aligned_cols=202 Identities=15% Similarity=0.074 Sum_probs=129.5
Q ss_pred EEEECCCCHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEECCCCCHHHHH
Q ss_conf 00221445888876553023213799997327999999999999987193023000266631112321000689589999
Q gi|254780694|r 9 NIVLNREDEQRTSFVSHLPTRSDLLARMIPLDCTVSWTMRMYALTEYVGASHFLLVRWDLFQEQKLDSIVSSDWPFDLVR 88 (246)
Q Consensus 9 ~~~l~r~d~~r~~~v~~l~~~~d~~~~l~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~ 88 (246)
+|++..+++.-...+..+....+ +.-+..+.+..+..+.+. . ..|+....+..+.+..+.+..+
T Consensus 2 ~vlivDDh~lvr~gl~~ll~~~~-~~vv~~~~~~~~~l~~~~----~-----------~~pDvvllDl~lp~~~G~~~~~ 65 (204)
T PRK09958 2 NAIIIDDHPLAIAAIRNLLIKND-IEILAELTEGGSAVQRVE----T-----------LKPDIVIIDVDIPGVNGIQVLE 65 (204)
T ss_pred EEEEECCCHHHHHHHHHHHHHCC-CEEEEEECCHHHHHHHHH----H-----------CCCCEEEEECCCCCCCCHHHHH
T ss_conf 89998698999999999998689-989999799999999987----4-----------3979999958999998416788
Q ss_pred HHHHCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
Q ss_conf 99966984517389999852324430325433332144571475033736899999997178754698999999999999
Q gi|254780694|r 89 CMALSEKDKYYNVLQRPTELFCPVFHTLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAY 168 (246)
Q Consensus 89 ~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 168 (246)
........ .. ...................++.||+.+.........++..+..+....+.......
T Consensus 66 ~ir~~~~~-----~~---viv~s~~~~~~~~~~a~~~Ga~g~l~K~~~~~~l~~aI~~v~~G~~~~~~~~~~~~------ 131 (204)
T PRK09958 66 TLRKRQYS-----GI---IIIVSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGYCYFPFSLNRFV------ 131 (204)
T ss_pred HHHHHCCC-----EE---EEEEECCCCCHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCCCCCCCHHHHHHH------
T ss_conf 89872798-----05---99997246521144335268637997899999999999999779970889999998------
Q ss_pred HHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCC
Q ss_conf 99754201467798888897799999999859997999999499988999999999998079988999999997589
Q gi|254780694|r 169 QANMFKSYDVHWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245 (246)
Q Consensus 169 ~~~~~~~~~~~~~~~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~Gl 245 (246)
........+...||+||+|||+++++|+||+|||++|+||++||++|+++||+|||++||+|++.+|.++||
T Consensus 132 -----~~~~~~~~~~~~Lt~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~i~~KL~v~~r~el~~~A~~~~l 203 (204)
T PRK09958 132 -----GSLTSDQQKLDSLSKQEISVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLYTFAQRNKI 203 (204)
T ss_pred -----HHCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCC
T ss_conf -----631356311256899999999999869999999989788999999999999998489999999999998289
No 12
>PRK10403 transcriptional regulator NarP; Provisional
Probab=99.89 E-value=6.8e-22 Score=159.42 Aligned_cols=207 Identities=14% Similarity=0.068 Sum_probs=126.1
Q ss_pred HHEEEEECCCCHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEECCCCCHH
Q ss_conf 11000221445888876553023213799997327999999999999987193023000266631112321000689589
Q gi|254780694|r 6 QQVNIVLNREDEQRTSFVSHLPTRSDLLARMIPLDCTVSWTMRMYALTEYVGASHFLLVRWDLFQEQKLDSIVSSDWPFD 85 (246)
Q Consensus 6 ~~~~~~l~r~d~~r~~~v~~l~~~~d~~~~l~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 85 (246)
...+|++-.+++.-...+..++....-+.-+..+.+..+..+.+.. .. ++....+..+.+..+.+
T Consensus 5 ~pirIlIvDD~~l~r~gl~~~L~~~~~~~vv~~a~~~~~~~~~~~~----~~-----------pDlvllD~~lp~~~G~~ 69 (215)
T PRK10403 5 TPFQVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLANR----LD-----------IDVILLDLNMKGMSGLD 69 (215)
T ss_pred CCCEEEEECCCHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHH----CC-----------CCEEEECCCCCCCCCCC
T ss_conf 9757999839899999999999758992899998999999999864----49-----------98999808998998741
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf 99999966984517389999852324430325433332144571475033736899999997178754698999999999
Q gi|254780694|r 86 LVRCMALSEKDKYYNVLQRPTELFCPVFHTLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLL 165 (246)
Q Consensus 86 ~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 165 (246)
..+...... |.... -.................++.||+.+....+....++.....+...........+.
T Consensus 70 ~~~~l~~~~-----p~~~i---ivlt~~~~~~~~~~al~~Ga~gyl~K~~~~~~l~~ai~~v~~G~~~~~~~~~~~l~-- 139 (215)
T PRK10403 70 TLNALRRDG-----VTAQI---IILTVSDASSDIFALIDAGADGYLLKDSDPEVLLEAIRAGAKGSKVFSERVNQYLR-- 139 (215)
T ss_pred HHHHHHHCC-----CCCCE---EEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCCCCCCCHHHHHHHH--
T ss_conf 233565418-----87736---88632432367899874687668848999999999999998499847989999998--
Q ss_pred HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHC
Q ss_conf 999997542014677988888977999999998599979999994999889999999999980799889999999975
Q gi|254780694|r 166 AAYQANMFKSYDVHWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRN 243 (246)
Q Consensus 166 ~~~~~~~~~~~~~~~~~~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~ 243 (246)
.. ........+...||+||.|||+++++|+||+|||..|+||++||++|++|||+|||++||+|||.+|.++
T Consensus 140 -----~~-~~~~~~~~~~~~LT~RE~eVL~lla~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv~nR~ea~~~~~~~ 211 (215)
T PRK10403 140 -----ER-EMFGAEEDPFSVLTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATILFLQQ 211 (215)
T ss_pred -----HH-HCCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf -----74-2124667744568999999999998699999999997982999999999999986899899999999998
No 13
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=99.88 E-value=1.5e-21 Score=157.13 Aligned_cols=195 Identities=14% Similarity=0.075 Sum_probs=126.2
Q ss_pred EEEEECCCCHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEECCCCCHHHH
Q ss_conf 00022144588887655302321379999732799999999999998719302300026663111232100068958999
Q gi|254780694|r 8 VNIVLNREDEQRTSFVSHLPTRSDLLARMIPLDCTVSWTMRMYALTEYVGASHFLLVRWDLFQEQKLDSIVSSDWPFDLV 87 (246)
Q Consensus 8 ~~~~l~r~d~~r~~~v~~l~~~~d~~~~l~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 87 (246)
.+|++..+++.-...+..+......+.-+..+.+..+....+.. ...+. ...+..+.+..+.+..
T Consensus 2 i~I~IvDDh~l~r~gl~~~l~~~~~~~vv~~~~~~~~~l~~~~~----~~~dv-----------vllD~~mp~~~g~~~~ 66 (196)
T PRK10360 2 ITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPG----RGVQV-----------CICDISMPDISGLELL 66 (196)
T ss_pred EEEEEECCCHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHH----CCCCE-----------EEECCCCCCCCCHHHH
T ss_conf 19999879799999999998129995999998999999998874----49999-----------9987887886207799
Q ss_pred HHHHHCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH
Q ss_conf 99996698451738999985232443032543333214457147503373689999999717875469899999999999
Q gi|254780694|r 88 RCMALSEKDKYYNVLQRPTELFCPVFHTLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAA 167 (246)
Q Consensus 88 ~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 167 (246)
+.+... .++ -.................++.||+.+....+....++..+..+....++.....+.
T Consensus 67 ~~l~~~-----~~v------ivls~~~~~~~~~~a~~~Ga~g~l~K~~~~~el~~aI~~v~~G~~~~~~~~~~~l~---- 131 (196)
T PRK10360 67 SQLPKG-----MAT------IMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLA---- 131 (196)
T ss_pred HHHHCC-----CCE------EEEEECCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCCCCCCCHHHHHHHH----
T ss_conf 998438-----748------99973075999999997599889977899999999999998699567999999987----
Q ss_pred HHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCC
Q ss_conf 999754201467798888897799999999859997999999499988999999999998079988999999997589
Q gi|254780694|r 168 YQANMFKSYDVHWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245 (246)
Q Consensus 168 ~~~~~~~~~~~~~~~~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~Gl 245 (246)
..+...||+||+|||+++++|+||+|||..|+||++||++|++|||+|||++||+|++.+|.+ ||
T Consensus 132 ------------~~~~~~LT~RE~eVL~lia~G~snkeIA~~L~IS~~TVk~h~~~i~~KL~v~~r~el~r~a~~-~~ 196 (196)
T PRK10360 132 ------------SGRQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARRMFD-GW 196 (196)
T ss_pred ------------CCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHC-CC
T ss_conf ------------167689997999999999879999999999699999999999999998199999999999970-69
No 14
>PRK04841 transcriptional regulator MalT; Provisional
Probab=99.88 E-value=5.1e-22 Score=160.19 Aligned_cols=60 Identities=27% Similarity=0.318 Sum_probs=58.0
Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHC
Q ss_conf 888977999999998599979999994999889999999999980799889999999975
Q gi|254780694|r 184 FELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRN 243 (246)
Q Consensus 184 ~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~ 243 (246)
..||+||.|||+++++|+||+|||+.|+||++|||+|++|||+||||+||+|||++|+++
T Consensus 837 ~~LT~RE~eVL~lLa~GlSNkeIA~~L~IS~~TVK~HlrnIy~KLgV~sR~~AV~~AreL 896 (903)
T PRK04841 837 SPLTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQLAQQL 896 (903)
T ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf 897999999999997689999999881998769999999998565999899999999999
No 15
>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=99.83 E-value=1.1e-20 Score=151.55 Aligned_cols=94 Identities=31% Similarity=0.408 Sum_probs=73.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC-------C----CCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHH
Q ss_conf 7875469899999999999999754201467-------7----9888889779999999985999799999949998899
Q gi|254780694|r 149 PKGRIILRDRLWEIGLLAAYQANMFKSYDVH-------W----GKDFELTGREVECLTWISEGKTSDEIAVILGISRNTV 217 (246)
Q Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~----~~~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV 217 (246)
......++....-+.++..+.+..+.+.... + .....||+||+|||+|+++|+||+|||.+|+||++||
T Consensus 143 ~~~~~~~~~~~~~LelL~P~Lh~AL~rv~~l~~q~~~~~~~~~~~~glLT~RE~EVL~~va~G~sn~eIA~~L~iS~~TV 222 (247)
T TIGR03020 143 RSSVPLDARHAYFLELLLPYLDSALRRVLFLPNQHRTRPLGERHSAGLITAREAEILAWVRDGKTNEEIAAILGISSLTV 222 (247)
T ss_pred ECCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHH
T ss_conf 15889987799999976889999999863164335455555677678999899999999987999999999949799999
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 9999999998079988999999997
Q gi|254780694|r 218 NNYIASIMRKTATKTRSGAIAYAVR 242 (246)
Q Consensus 218 ~~hl~~i~~KLgv~~R~eav~~A~~ 242 (246)
|+|++|||+||||+||+|||++|+.
T Consensus 223 k~H~~~i~~KL~v~nR~qAV~kAla 247 (247)
T TIGR03020 223 KNHLQHIFKKLDVRNRAQAVAKAIA 247 (247)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHC
T ss_conf 9999999998099989999999859
No 16
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=99.79 E-value=9.6e-20 Score=145.59 Aligned_cols=62 Identities=34% Similarity=0.401 Sum_probs=60.4
Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC
Q ss_conf 88977999999998599979999994999889999999999980799889999999975898
Q gi|254780694|r 185 ELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNIV 246 (246)
Q Consensus 185 ~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~Gli 246 (246)
.||.||.|||.+|++|.||+|||++|+||.+|||+|++|||.||||.||+|||.+|.+.|++
T Consensus 831 ~Ls~RE~eVL~Lia~G~SN~eIa~~L~isl~TVKtH~rniy~KLgV~~RtqAV~rAk~L~lL 892 (894)
T COG2909 831 PLSQRELEVLGLIAQGLSNEEIAQELFISLTTVKTHIRNIYQKLGVANRTQAVQRAKELGLL 892 (894)
T ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 76388999999998257778999998898988999999999884821589999999998754
No 17
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=99.73 E-value=1.2e-16 Score=125.78 Aligned_cols=185 Identities=17% Similarity=0.094 Sum_probs=120.4
Q ss_pred HCCCHHHHHHHHHHHHHHHCCCEEEEECCC---------CCCCCCCCEEECCCCCHHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf 327999999999999987193023000266---------63111232100068958999999966984517389999852
Q gi|254780694|r 38 PLDCTVSWTMRMYALTEYVGASHFLLVRWD---------LFQEQKLDSIVSSDWPFDLVRCMALSEKDKYYNVLQRPTEL 108 (246)
Q Consensus 38 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---------~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~ 108 (246)
.+++.......+.-+.+..||....+.... .++....+.-+++..+.++.......+. ..|+ .
T Consensus 9 vVDDD~~vr~al~~Ll~s~G~~v~~~~s~~~fL~~~~~~~pGclllDvrMPg~sGlelq~~L~~~~~--~~PV------I 80 (202)
T COG4566 9 VVDDDESVRDALAFLLESAGFQVKCFASAEEFLAAAPLDRPGCLLLDVRMPGMSGLELQDRLAERGI--RLPV------I 80 (202)
T ss_pred EECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCC--CCCE------E
T ss_conf 9768488999999999838953665047999983066788976998557888850899999995399--9887------9
Q ss_pred HHHHHCCCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCH
Q ss_conf 32443032543333214457147503373689999999717875469899999999999999754201467798888897
Q gi|254780694|r 109 FCPVFHTLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAYQANMFKSYDVHWGKDFELTG 188 (246)
Q Consensus 109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LT~ 188 (246)
........+....+...++..|+.++++......++..+.............. ... ......|||
T Consensus 81 fiTGhgDIpmaV~AmK~GAvDFLeKP~~~q~Lldav~~Al~~~~~~~~~~~~~-----~~~----------~~~l~tLT~ 145 (202)
T COG4566 81 FLTGHGDIPMAVQAMKAGAVDFLEKPFSEQDLLDAVERALARDASRRAEADRQ-----AAI----------RARLATLTP 145 (202)
T ss_pred EEECCCCHHHHHHHHHCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH-----HHH----------HHHHHHCCH
T ss_conf 98278872899999974215677478854899999999999888888767789-----999----------999986698
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCC
Q ss_conf 799999999859997999999499988999999999998079988999999997589
Q gi|254780694|r 189 REVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245 (246)
Q Consensus 189 RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~Gl 245 (246)
||+|||..+.+|+.||+||..|+||++||+.|..|+|+|+++.|-+++|..|...|.
T Consensus 146 RERqVl~~vV~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr~a~~~~~ 202 (202)
T COG4566 146 RERQVLDLVVRGLMNKQIAFDLGISERTVELHRANVMEKMQARSLAELVRMALSLGL 202 (202)
T ss_pred HHHHHHHHHHCCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCC
T ss_conf 899999999837630899998398664599999999999733319999999985459
No 18
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=99.73 E-value=1.6e-17 Score=131.35 Aligned_cols=104 Identities=17% Similarity=0.094 Sum_probs=79.1
Q ss_pred HHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 32144571475033736899999997178754698999999999999997542014677988888977999999998599
Q gi|254780694|r 122 PPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAYQANMFKSYDVHWGKDFELTGREVECLTWISEGK 201 (246)
Q Consensus 122 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LT~RE~eVl~lia~G~ 201 (246)
...++..||+.+....+....++.....+...... ...... ..+....|||||+|||+++++|+
T Consensus 87 L~~aga~Gyl~K~~~~~eL~~Ai~~~~~g~~~~~~---------------~~~~~~-~~~~~~~Lt~rE~eVl~l~a~G~ 150 (205)
T PRK11475 87 LSPSPLDGVLSKASTLEILQQELFLSLNGVRQATD---------------RLNNQW-YINQSRMLSPTEREILRFMSRGY 150 (205)
T ss_pred HHHHHCCEEEECCCCHHHHHHHHHHHHCCCHHHCH---------------HHHCCC-CCCCCCCCCHHHHHHHHHHHCCC
T ss_conf 99841668885678899999999998706113134---------------665345-67767889858999999997699
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf 9799999949998899999999999807998899999999
Q gi|254780694|r 202 TSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAV 241 (246)
Q Consensus 202 t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~ 241 (246)
||+|||..|++|.+||++|.+|+|+|||++|.++++-.|-
T Consensus 151 s~~eIA~~L~~S~kTv~thr~~~m~KLgv~s~a~Li~~a~ 190 (205)
T PRK11475 151 SMPQIAEQLERNIKTIRAHKFNVMSKLGVSSDAGLLDAAD 190 (205)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHH
T ss_conf 9999999978888899999999999829998799999999
No 19
>pfam00196 GerE Bacterial regulatory proteins, luxR family.
Probab=99.70 E-value=3.6e-17 Score=129.06 Aligned_cols=57 Identities=42% Similarity=0.494 Sum_probs=55.3
Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 888977999999998599979999994999889999999999980799889999999
Q gi|254780694|r 184 FELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYA 240 (246)
Q Consensus 184 ~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A 240 (246)
..|||||.+||.|+++|+|++|||..|+||++||++|+++||+|||++||+|+|.+|
T Consensus 2 ~~LT~RE~~il~~l~~G~s~~eIA~~L~is~~TV~~h~~~i~~Kl~v~nr~elv~~A 58 (58)
T pfam00196 2 DSLSPREREVLRLLAAGKSNKEIADILGISEKTVKVHRSNIMRKLNVHSRVELIRLA 58 (58)
T ss_pred CCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHC
T ss_conf 977999999999998079999999997888999999999999980999999999559
No 20
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=99.69 E-value=7.5e-17 Score=127.02 Aligned_cols=57 Identities=53% Similarity=0.725 Sum_probs=55.9
Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 897799999999859997999999499988999999999998079988999999997
Q gi|254780694|r 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVR 242 (246)
Q Consensus 186 LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~ 242 (246)
|||||.+||.|+++|+|++|||+.|+||++||++|+++||.|||++||+|+|++|++
T Consensus 1 LT~rE~~il~~~~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~~~~r~elv~~A~r 57 (57)
T cd06170 1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57 (57)
T ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHC
T ss_conf 988999999999807999999999897899999999999998689999999998729
No 21
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=99.66 E-value=2.4e-16 Score=123.76 Aligned_cols=57 Identities=44% Similarity=0.570 Sum_probs=55.2
Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 888977999999998599979999994999889999999999980799889999999
Q gi|254780694|r 184 FELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYA 240 (246)
Q Consensus 184 ~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A 240 (246)
..||+||.+|+.|+++|+|++|||+.|+||++||++|+++||+|||++||+|+|++|
T Consensus 2 ~~LT~rE~~il~~l~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~v~~r~elv~~A 58 (58)
T smart00421 2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58 (58)
T ss_pred CCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHC
T ss_conf 761899999999998179999999898978989999999999984899999999549
No 22
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=99.53 E-value=3.9e-14 Score=109.58 Aligned_cols=63 Identities=41% Similarity=0.572 Sum_probs=60.8
Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC
Q ss_conf 888977999999998599979999994999889999999999980799889999999975898
Q gi|254780694|r 184 FELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNIV 246 (246)
Q Consensus 184 ~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~Gli 246 (246)
..||+||.+|+.|+++|+|++|||..|++|++||++|+++||+|+|+.||++++.++...|.+
T Consensus 3 ~~Lt~rE~~~~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~~r~~~~~~~~~~~~~ 65 (65)
T COG2771 3 ADLTPREREILRLVAQGKSNKEIARILGISEETVKTHLRNIYRKLGVKNRVELVALALRLGLI 65 (65)
T ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCC
T ss_conf 113888999999998699899999998779999999999999997758699999999985449
No 23
>pfam03472 Autoind_bind Autoinducer binding domain. This domain is found a a large family of transcriptional regulators. This domain specifically binds to autoinducer molecules.
Probab=98.75 E-value=2.3e-08 Score=72.52 Aligned_cols=129 Identities=13% Similarity=-0.024 Sum_probs=101.6
Q ss_pred HHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEECCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCH----
Q ss_conf 9999999999998719302300026663111232100068958999999966984517389999852324430325----
Q gi|254780694|r 42 TVSWTMRMYALTEYVGASHFLLVRWDLFQEQKLDSIVSSDWPFDLVRCMALSEKDKYYNVLQRPTELFCPVFHTLP---- 117 (246)
Q Consensus 42 ~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~---- 117 (246)
..++.+.+..+.+.+||++|.+...++.........+.+++|.+|...|...++...||++..+.....|+.|...
T Consensus 2 ~~~l~~~l~~~~~~lGf~~~~y~~~~~~~~~~~~~~~~~~yP~~W~~~Y~~~~y~~~DPv~~~~~~~~~p~~W~~~~~~~ 81 (146)
T pfam03472 2 EEELWDLLERLAAALGFDYFAYGLLPPSPGSRPDVLLLSNYPAEWVERYVEEGYYRIDPVVRHALRSSTPFSWSDLDLAS 81 (146)
T ss_pred HHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCEEEEECCCHHHHHHHHHCCCEECCHHHHHHHCCCCCEECCCCCCCC
T ss_conf 79999999999997699879997435898998767997089999999999779555087999986289998877686679
Q ss_pred ------HHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHH----HHHHHHHHHHHHHH
Q ss_conf ------4333321445714750337368999999971787546989----99999999999997
Q gi|254780694|r 118 ------ENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRD----RLWEIGLLAAYQAN 171 (246)
Q Consensus 118 ------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~ 171 (246)
......+++..|+..+.+.+.+..+.+........ .... ....+.+++.+.+.
T Consensus 82 ~~~~~~~~~a~~~Gl~~G~~~pv~~~~g~~g~~s~a~~~~~-~~~~~~~~~~~~l~~la~~~h~ 144 (146)
T pfam03472 82 PRARRVFDEARDFGLRAGYTVPVHGPNGRLGALSLAGDGRD-LDAVELIRARAELQLLAIHAHL 144 (146)
T ss_pred HHHHHHHHHHHHCCCCCEEEEEEECCCCCEEEEEEECCCCC-CCHHHHHHHHHHHHHHHHHHHH
T ss_conf 77999999999859962589998879998899998569999-8989999989999999999996
No 24
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; InterPro: IPR014327 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 recognized by the major sigma factors , . This group of sigma factors are members of the sigma-70 family and are found primarily in the genus Bacteroides. This appears to have resulted from a lineage-specific expansion as Bacteroides thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037 (Tannerella forsythensis ATCC 43037), Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currently only two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=98.66 E-value=5.5e-08 Score=70.12 Aligned_cols=46 Identities=30% Similarity=0.252 Sum_probs=43.1
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8889779999999-985999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|+++=++|..+ --+|+||+|||+.||||++||+.|+..++++|-
T Consensus 118 ~~LPe~~R~iF~lsr~eg~s~~EIA~~L~iS~~TVe~hi~~ALk~LR 164 (167)
T TIGR02985 118 EKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLR 164 (167)
T ss_pred HHCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 75689899999998861798678998848988899999999999998
No 25
>PRK06930 positive control sigma-like factor; Validated
Probab=98.49 E-value=2.7e-07 Score=65.69 Aligned_cols=47 Identities=34% Similarity=0.337 Sum_probs=42.1
Q ss_pred CCCCHHHHHHH-HHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 88897799999-999859997999999499988999999999998079
Q gi|254780694|r 184 FELTGREVECL-TWISEGKTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 184 ~~LT~RE~eVl-~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
..||+||+||. -.-.+|+|+.|||..|+||.+||++|++++..|+.-
T Consensus 113 s~Lt~rErevfll~~~~glsy~EIA~~L~Is~~tV~~~l~RA~~Ki~~ 160 (170)
T PRK06930 113 SVLTEREKEVYLMHRGYGLSYSEIAAYLNIKKSTVQSMIERAEKKIAK 160 (170)
T ss_pred HHCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 856988889998897618889999999798899999999999999999
No 26
>pfam07638 Sigma70_ECF ECF sigma factor. These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545.
Probab=98.42 E-value=6.5e-07 Score=63.26 Aligned_cols=46 Identities=30% Similarity=0.304 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 888977999999998-5999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWIS-EGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~lia-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|.|.+++|+.|-- +|+|++|||+.||||++||+++++.+..||-
T Consensus 134 ~~Lpp~~r~v~~L~~~eglS~~EIAe~Lgis~~TVk~rl~~Ar~~Lr 180 (185)
T pfam07638 134 FSLSPRQARLVELRFFAGLSNDEIAERLGVSERTVERNWALARAWLH 180 (185)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 64899888898889975999999999979699899999999999999
No 27
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=98.38 E-value=9.4e-07 Score=62.22 Aligned_cols=46 Identities=26% Similarity=0.359 Sum_probs=42.1
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8889779999999-985999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++++++|+.| --+|+|++|||+.||||++||+.|+.+.++++-
T Consensus 118 ~~Lp~~~R~v~~L~~~eGls~~EIA~~LgiS~~tVk~~l~rAl~~~~ 164 (172)
T PRK12523 118 GKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQCY 164 (172)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 64999999999999993999999999989399999999999999999
No 28
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family; InterPro: IPR014284 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 recognized by the major sigma factors , . This entry is found in all varieties of the sigma-70 type sigma factors, including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (IPR000394 from INTERPRO) are included within this entry. ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=98.33 E-value=1.3e-06 Score=61.29 Aligned_cols=46 Identities=39% Similarity=0.412 Sum_probs=43.0
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|+++|++|+.|- -+|+|.+|||+.||||++||+.+++++.+||-
T Consensus 113 ~~Lp~~~r~~~~l~~~~~~s~~eIA~~lg~s~~~v~~~~~ra~~~L~ 159 (162)
T TIGR02937 113 EKLPEREREVLVLRYLEGLSYKEIAEILGISEGTVKSRLKRARKKLR 159 (162)
T ss_pred HHCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 74799899999999971899889999868999999999999999998
No 29
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=98.31 E-value=1.7e-06 Score=60.63 Aligned_cols=45 Identities=29% Similarity=0.354 Sum_probs=41.3
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 88897799999999-8599979999994999889999999999980
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
..|.++.++|+.+. -+|+|++|||+.||||++||+.|+++.+++|
T Consensus 122 ~~LP~~~R~v~~L~~~eg~s~~EIAe~LgiS~~tVk~~l~rAl~~L 167 (183)
T PRK07037 122 DELPARTRAAFEMVRLRGETLQDIARELNVSQTLVNFMIRDALRHC 167 (183)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 8199999999898987398999999998929999999999999999
No 30
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=98.29 E-value=2e-06 Score=60.17 Aligned_cols=44 Identities=25% Similarity=0.335 Sum_probs=40.3
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 88897799999999-859997999999499988999999999998
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
..|+|+.++|+-|- -+|+|++|||+.||||++||+.|+.++++-
T Consensus 117 ~~LP~~~R~vflL~~~eGlsy~EIAe~LgIS~~tV~~~l~rAl~~ 161 (168)
T PRK12525 117 DGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFKC 161 (168)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 639999999999999929999999999897999999999999999
No 31
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=98.29 E-value=1.9e-06 Score=60.20 Aligned_cols=46 Identities=33% Similarity=0.341 Sum_probs=42.6
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 8897799999999-859997999999499988999999999998079
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
.|+|+.++|+.+- -+|+|++|||+.|+||++||++|+.+++++|-.
T Consensus 105 ~Lp~~~R~v~~L~~~egls~~EIA~~lgis~~tVk~~l~rA~k~Lr~ 151 (159)
T PRK12527 105 ELPPICRESFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRV 151 (159)
T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 69999989998898739799999999891999999999999999999
No 32
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=98.29 E-value=1.8e-06 Score=60.46 Aligned_cols=45 Identities=27% Similarity=0.259 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 88897799999999-8599979999994999889999999999980
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
..|++++++|+.|. -+|+|++|||+.|+||++||++|+.+..+||
T Consensus 141 ~~Lp~~~R~vi~L~~~~g~s~~EIA~~Lgis~~TVk~rl~rA~~~L 186 (194)
T PRK09646 141 DALTDTQREAITLAYYGGLTYREVAERLAVPLGTVKTRMRDGLRRL 186 (194)
T ss_pred HHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 8678157899999999399999999998919999999999999999
No 33
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=98.24 E-value=3.1e-06 Score=58.89 Aligned_cols=46 Identities=26% Similarity=0.211 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++..++|+.+. -+|+|++|||+.|+||++||++++.+++.||-
T Consensus 105 ~~Lp~~~R~v~~L~~~eg~s~~EIA~~L~is~~tVksrl~RAr~~Lr 151 (181)
T PRK09637 105 DALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLK 151 (181)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 76999998997999885999999999989499999999999999999
No 34
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=98.24 E-value=2.9e-06 Score=59.10 Aligned_cols=46 Identities=28% Similarity=0.253 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8889779999999-985999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++++++|+.| .-+|+|++|||+.|+||++||++++.++..||-
T Consensus 140 ~~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tVk~rl~rA~~~Lr 186 (194)
T PRK12519 140 AQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKLR 186 (194)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 81998875688999981999999999989499999999999999999
No 35
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=98.23 E-value=3.3e-06 Score=58.72 Aligned_cols=46 Identities=20% Similarity=0.137 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++.+++|+.|- -+|+|++|||++|+||++||++++.+.++||-
T Consensus 148 ~~Lp~~~R~v~~L~~~eglS~~EIA~~Lgis~~TVKsrL~RArk~LR 194 (231)
T PRK11922 148 DALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRLLR 194 (231)
T ss_pred HHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 80999999999999993999999999989399999999999999999
No 36
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=98.23 E-value=3.5e-06 Score=58.56 Aligned_cols=45 Identities=22% Similarity=0.308 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 889779999999-985999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|+|.+++|+.+ .-+|+|++|||+.|+||++||++|+.+...||-
T Consensus 136 ~L~~~~r~vi~L~~~~g~s~~EIA~~L~is~~TVk~~l~rA~k~Lr 181 (187)
T PRK13919 136 ALSPEERRVIEVLYYQGYTHREAARLLGLPLGTLKTWARRALSKLK 181 (187)
T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 4999999999999985999999999989399999999999999999
No 37
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=98.22 E-value=3.4e-06 Score=58.65 Aligned_cols=44 Identities=25% Similarity=0.268 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 88897799999999-859997999999499988999999999998
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
..|+|+.++|+.+- .+|+|++|||+.||||++||+.|+.+++..
T Consensus 126 ~~Lp~r~R~vF~L~r~eGls~~EIAe~LgiS~~tV~~~l~rAl~~ 170 (178)
T PRK12529 126 DTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYVT 170 (178)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 569978889987998829999999999895999999999999999
No 38
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=98.21 E-value=3.8e-06 Score=58.31 Aligned_cols=46 Identities=24% Similarity=0.265 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++++++|+.+. -+|+|++|||..|+||++||++|+.+..+||-
T Consensus 115 ~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tVk~~l~ra~~~Lr 161 (171)
T PRK09645 115 AQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYAVRALR 161 (171)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 75999988798999986999999999989299999999999999999
No 39
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=98.19 E-value=4.3e-06 Score=58.00 Aligned_cols=46 Identities=26% Similarity=0.202 Sum_probs=42.8
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++++++|+.+. -+|+|.+|||..|++|++||++|+.++..||-
T Consensus 136 ~~L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tVk~~l~Ra~~~Lr 182 (192)
T PRK09652 136 ESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALR 182 (192)
T ss_pred HHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 83999999888899972999999999989399999999999999999
No 40
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=98.18 E-value=4.9e-06 Score=57.64 Aligned_cols=46 Identities=26% Similarity=0.270 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++.+++|+.+- -+|+|++|||+.|+||++||++++.++.+||-
T Consensus 126 ~~Lp~~~r~v~~L~~~eg~s~~EIA~~l~is~~tVk~~l~rA~~~Lr 172 (177)
T PRK09638 126 MKLPPELRAPFILKHYYGYTYEEIAKMLGIPEGTVKSRVHHGLKKIR 172 (177)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 75999898999999991999999999989399999999999999999
No 41
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=98.18 E-value=4.3e-06 Score=57.97 Aligned_cols=46 Identities=22% Similarity=0.199 Sum_probs=42.4
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++++++|+.|- -+|+|++|||+.|+||++||++|+.+++.||-
T Consensus 105 ~~Lp~~qR~vl~L~~~egls~~EIA~~l~is~~tVk~~l~RAr~~Lr 151 (161)
T PRK09047 105 QKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHTLA 151 (161)
T ss_pred HHCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 81999999998999998779999999989699999999999999999
No 42
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=98.18 E-value=4.8e-06 Score=57.69 Aligned_cols=46 Identities=22% Similarity=0.319 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8889779999999-985999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++++++|+.| .-+|+|++|||..|+||++||++++.++..||-
T Consensus 127 ~~Lp~~~R~v~~L~~~~g~s~~EIA~~l~is~~tVk~~l~RAr~~Lr 173 (186)
T PRK05602 127 AALPERQREAIVLQYYQGLSNIEAARVMGLSVDALESLLARARRALR 173 (186)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 75998788999999863899999999989399999999999999999
No 43
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=98.18 E-value=5e-06 Score=57.58 Aligned_cols=45 Identities=31% Similarity=0.418 Sum_probs=40.6
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 8889779999999-98599979999994999889999999999980
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
..|+++.++|+.| --+|+|++|||..||||++||++|+.+..+.+
T Consensus 118 ~~Lp~~~R~v~~L~~~egls~~EIA~~lgiS~~tVk~~l~rAlk~c 163 (172)
T PRK09651 118 DGLNGKTREAFLLSQLDGLTYSEIAHKLGVSISSVKKYVAKAVEHC 163 (172)
T ss_pred HHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 7099999999999988399999999998939999999999999999
No 44
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=98.17 E-value=5.3e-06 Score=57.37 Aligned_cols=46 Identities=13% Similarity=0.153 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 888977999999998-5999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWIS-EGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~lia-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|.+..++|+.+.- +|+|++|||..|+||++||++|+.+.+.||-
T Consensus 152 ~~LP~~~R~vi~L~~~egls~~EIA~~l~is~~TVksrl~rAlk~LR 198 (206)
T PRK12526 152 EKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALAKLK 198 (206)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 86899988898999985999999999989399999999999999999
No 45
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=98.17 E-value=5.4e-06 Score=57.37 Aligned_cols=46 Identities=26% Similarity=0.207 Sum_probs=42.2
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|+|..++|+.+. -+|+|++|||+.|++|++||++++.+..+||-
T Consensus 136 ~~L~~~~r~vi~l~~~eg~s~~EIA~~l~i~~gTVksrl~ra~~~Lr 182 (187)
T PRK12534 136 AELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLAKLK 182 (187)
T ss_pred HHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 86899899999999984999999999989199999999999999999
No 46
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=98.16 E-value=5.3e-06 Score=57.41 Aligned_cols=45 Identities=24% Similarity=0.375 Sum_probs=40.8
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8897799999999-85999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|+|..++|+.+. -+|+|++|||+.|+||++||++|+.+.+.||-
T Consensus 135 ~L~~~~r~~i~l~~~eg~s~~EIA~~l~is~~TVk~rl~rA~~~LR 180 (184)
T PRK12537 135 QLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALR 180 (184)
T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 0999899999998843999999999989299999999999999999
No 47
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=98.16 E-value=6e-06 Score=57.06 Aligned_cols=45 Identities=22% Similarity=0.251 Sum_probs=42.0
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8897799999999-85999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|++.+++|+.|- -+|+|.+|||..|+||++||++++.++.+||-
T Consensus 129 ~Lp~~~R~vi~L~~~~g~s~~EIA~~l~is~~tVk~rl~rA~k~LR 174 (190)
T PRK12543 129 KLPYKLKQVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLR 174 (190)
T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 4999999999999985999999999989399999999999999999
No 48
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=98.15 E-value=5.4e-06 Score=57.34 Aligned_cols=45 Identities=20% Similarity=0.234 Sum_probs=41.4
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8897799999999-85999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|++..++|+.+. -+|+|++|||+.|+||++||++++.+++.||-
T Consensus 129 ~Lp~~~r~~~~l~~~eg~s~~EIA~~l~is~~tVk~~l~rA~~~Lr 174 (179)
T PRK12514 129 ELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 7559999999999606998999999889099999999999999999
No 49
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=98.15 E-value=6.4e-06 Score=56.89 Aligned_cols=47 Identities=21% Similarity=0.188 Sum_probs=42.9
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 8889779999999-9859997999999499988999999999998079
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
..|++++++|+.+ .-+|+|++|||+.|++|++||++++.+..+||.-
T Consensus 130 ~~Lp~~~R~vi~L~~~~g~s~~EIA~~lgis~~tVk~~l~RA~~~Lr~ 177 (184)
T PRK12512 130 ETLPPRQRDVVQSIAVEGASIKETAAKLSMSEGAVRVALHRGLAALAA 177 (184)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 689999999999998559799999999891999999999999999999
No 50
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=98.15 E-value=6.3e-06 Score=56.90 Aligned_cols=46 Identities=26% Similarity=0.273 Sum_probs=42.6
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++++++|+.|- -+|+|++|||+.|+||++||++++.+.++||-
T Consensus 135 ~~Lp~~~R~vi~L~~~eg~s~~EIA~~lgis~~tVk~~l~Rark~Lr 181 (196)
T PRK12524 135 AALPERQRQAVVLRHIEGLSNPEIAEVMQIGVEAVESLTARGKRALA 181 (196)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 85999999998999980899999999989299999999999999999
No 51
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=98.15 E-value=5.9e-06 Score=57.08 Aligned_cols=46 Identities=26% Similarity=0.299 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8889779999999985999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++++++|+.+--+|+|++|||..|+||++||++++.++..||-
T Consensus 111 ~~Lp~~~r~v~~l~~~g~s~~EIA~~l~is~~tVk~~l~RA~~~Lr 156 (166)
T PRK09639 111 AKMTERDRTVLLLRFSGYSYKEIAQALGIDESSVGTTLHRAKKKFR 156 (166)
T ss_pred HHCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 8399999999999993899999999989199999999999999999
No 52
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=98.15 E-value=6.2e-06 Score=56.94 Aligned_cols=46 Identities=22% Similarity=0.104 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++.+++|+.|- -+|+|++|||+.||||++||++++.++..||-
T Consensus 111 ~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~RArk~Lr 157 (161)
T PRK12541 111 SSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETK 157 (161)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 81999999999989974999999999989399999999999999998
No 53
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=98.14 E-value=6.4e-06 Score=56.85 Aligned_cols=45 Identities=18% Similarity=0.230 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 889779999999-985999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|++..++|+.| .-+|+|++|||+.|+||++||++++.+.++||-
T Consensus 119 ~Lp~~~R~vl~L~~~egls~~EIAe~Lgis~~TVksrl~RAr~~Lr 164 (190)
T PRK12516 119 QLPDDQREAIILIGASGFAYEEAAEICGCAVGTIKSRVSRARARLQ 164 (190)
T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 1999998999989982999999999989499999999999999999
No 54
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=98.14 E-value=6.3e-06 Score=56.91 Aligned_cols=45 Identities=29% Similarity=0.332 Sum_probs=43.0
Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 889779999999985999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|+++|++|+.+.-+|+|.+|||..|++|++||++-+.++.+||-
T Consensus 155 ~l~~~e~~V~~~~~eg~s~~EIA~~l~is~~tV~~~l~RarkkLr 199 (209)
T PRK08295 155 LLSDLEKEVLELYLDGKSYQEIAEELNRHVKSIDNALQRVKRKLE 199 (209)
T ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 691899999999986999999999989299999999999999999
No 55
>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=98.12 E-value=7.7e-06 Score=56.35 Aligned_cols=45 Identities=40% Similarity=0.474 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 888977999999998-599979999994999889999999999980
Q gi|254780694|r 184 FELTGREVECLTWIS-EGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 184 ~~LT~RE~eVl~lia-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
..|++++++|+.|-- +|+|.+|||..|++|++||++++.++..||
T Consensus 9 ~~L~~~~r~vl~l~y~~~~s~~EIa~~lgis~~tVk~~l~rA~~~L 54 (55)
T cd06171 9 DKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54 (55)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
T ss_conf 8399999898999998099999999998959999999999999875
No 56
>pfam08281 Sigma70_r4_2 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.
Probab=98.12 E-value=6.2e-06 Score=56.94 Aligned_cols=45 Identities=36% Similarity=0.395 Sum_probs=42.1
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 88897799999999-8599979999994999889999999999980
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
..|++++++++.+. -+|+|++|||+.|++|++||++++.+...||
T Consensus 9 ~~Lp~~~r~~~~l~~~~~~s~~eIA~~lg~s~~tVk~~l~RA~~~L 54 (54)
T pfam08281 9 EELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54 (54)
T ss_pred HCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
T ss_conf 8599999989687998785999999998949999999999999719
No 57
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=98.11 E-value=7.6e-06 Score=56.38 Aligned_cols=46 Identities=20% Similarity=0.157 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++++++|+.|. -+|+|.+|||+.|+||++||++++.++..||-
T Consensus 135 ~~Lp~~~r~v~~L~~~~~~s~~EIA~~l~is~~tVk~~l~RAr~~Lr 181 (187)
T PRK09641 135 LQLPDKYRTVIVLKYIEELSLKEISEILDLPVGTVKTRIHRGREALR 181 (187)
T ss_pred HHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 82898888999999982998999999989399999999999999999
No 58
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=98.10 E-value=7.9e-06 Score=56.28 Aligned_cols=44 Identities=27% Similarity=0.246 Sum_probs=39.7
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 8889779999999-9859997999999499988999999999998
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
..|.++.++|+.+ --+|+|++|||+.||||++||++|+.+.+..
T Consensus 118 ~~LP~~~R~vf~L~r~~gls~~EIA~~LgiS~~tVk~~l~rA~~~ 162 (167)
T PRK12528 118 DGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMR 162 (167)
T ss_pred HCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 709999999999999829899999999797999999999999999
No 59
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=98.10 E-value=8.8e-06 Score=55.98 Aligned_cols=46 Identities=22% Similarity=0.216 Sum_probs=42.4
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8889779999999-985999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++.+++|+.| .-+|+|.+|||+.|+||++||++++.++..||-
T Consensus 130 ~~Lp~~~R~vl~L~~~eg~s~~EIA~~lgis~~tVKsrl~RAr~~Lr 176 (197)
T PRK09643 130 MRLPVEQRAALVAVDMQGYSVADTARMLGVAEGTVKSRCARGRARLA 176 (197)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 76999887999999981999999999989399999999999999999
No 60
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=98.09 E-value=9.2e-06 Score=55.86 Aligned_cols=45 Identities=20% Similarity=0.276 Sum_probs=42.2
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8897799999999-85999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|++.+++|+.+. -+|+|.+|||..|++|++||++++.++..||-
T Consensus 112 ~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tVksrl~rAr~~Lr 157 (164)
T PRK12547 112 LLPADQREAIILIGASGFSYEEAAEICGCAVGTIKSRVSRARNRLQ 157 (164)
T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 5899999999989984999999999989399999999999999999
No 61
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=98.09 E-value=1e-05 Score=55.62 Aligned_cols=47 Identities=13% Similarity=0.127 Sum_probs=42.7
Q ss_pred CCCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 888977999999998-59997999999499988999999999998079
Q gi|254780694|r 184 FELTGREVECLTWIS-EGKTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 184 ~~LT~RE~eVl~lia-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
..|+++.++|+.|.- +|+|++|||..|++|++|||+++.+.++||--
T Consensus 170 ~~Lp~~~R~vl~L~~~egls~~EIA~~Lgis~~TVKsrL~RAr~~LR~ 217 (233)
T PRK12538 170 QRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRD 217 (233)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 759999999999999849999999999892999999999999999999
No 62
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=98.08 E-value=9.9e-06 Score=55.65 Aligned_cols=46 Identities=24% Similarity=0.180 Sum_probs=42.7
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++.+++|+.|. -+|+|.+|||+.|++|++||++++.+...||-
T Consensus 156 ~~Lp~~qR~vl~Lr~~eglS~~EIAe~Lgis~gTVKsrl~RAr~~LR 202 (222)
T PRK09647 156 DSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQALR 202 (222)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 82999998899879963999999999989399999999999999999
No 63
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=98.07 E-value=1.1e-05 Score=55.46 Aligned_cols=46 Identities=28% Similarity=0.205 Sum_probs=42.4
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++.+++|+-|. -+|+|++|||+.|+||++|||+++.+..+||-
T Consensus 136 ~~Lp~~~R~vl~Lr~~eglS~~EIAeiLgip~gTVKSRL~RAR~~Lr 182 (217)
T PRK12533 136 AKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRRLA 182 (217)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 80999886899999980999999999989499999999999999999
No 64
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=98.07 E-value=1.2e-05 Score=55.17 Aligned_cols=58 Identities=21% Similarity=0.192 Sum_probs=48.9
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCC
Q ss_conf 8889779999999-9859997999999499988999999999998079988999999997589
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~Gl 245 (246)
..|++++++|+.+ .-+|+|.+|||+.|+||++||++++.++.+|| |-.+-+..+..|+
T Consensus 130 ~~L~~~~R~vi~l~~~e~~s~~EIA~~lgis~~tV~~~l~RAr~~L----r~~L~~~g~~~g~ 188 (189)
T PRK12515 130 AKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKL----AELLKAAGVERGW 188 (189)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH----HHHHHHHCCCCCC
T ss_conf 7599999999999998499999999998929999999999999999----9999972833589
No 65
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=98.07 E-value=1.2e-05 Score=55.15 Aligned_cols=45 Identities=27% Similarity=0.238 Sum_probs=42.1
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8897799999999-85999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|++.+++|+.|- -+|+|++|||..|+||++||++++.++..||-
T Consensus 128 ~Lp~~~R~vi~L~~~eg~s~~EIA~~Lgis~~tVksrl~RAr~~Lr 173 (188)
T PRK12517 128 KLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLK 173 (188)
T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 6999999999999983999999999989399999999999999999
No 66
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=98.06 E-value=1.2e-05 Score=55.23 Aligned_cols=46 Identities=20% Similarity=0.161 Sum_probs=42.7
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++.+++|+.|- -+|+|++|||..|+||++||++++.++..||-
T Consensus 137 ~~Lp~~~R~v~~L~~~egls~~EIA~~l~is~~tVk~rl~RAr~~Lr 183 (193)
T PRK11923 137 QQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRAREAID 183 (193)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 81789899999999994999999999989299999999999999999
No 67
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=98.06 E-value=1.2e-05 Score=55.16 Aligned_cols=46 Identities=17% Similarity=0.138 Sum_probs=42.7
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++++++|+.|- -+|+|++|||+.|++|++||+.++.++..||-
T Consensus 136 ~~Lp~~~R~vl~L~~~~g~s~~EIA~~lg~s~~tVk~~l~RA~~~Lr 182 (187)
T PRK09648 136 EILPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALSRLR 182 (187)
T ss_pred HHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 83999999999999984999999999989399999999999999999
No 68
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=98.06 E-value=1.2e-05 Score=55.06 Aligned_cols=46 Identities=20% Similarity=0.219 Sum_probs=42.6
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8889779999999-985999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++++++|+.+ .-+|+|++|||+.|++|++||++++.++.+||-
T Consensus 138 ~~Lp~~~r~il~L~~~~g~s~~EIA~~l~is~~tVk~~l~rA~~~Lr 184 (194)
T PRK12513 138 ETLPDEQREVFLLREHGDLSLEEIAQLTGVPLETVKSRLRYALQKLR 184 (194)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 72998999999999984999999999989499999999999999999
No 69
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=98.05 E-value=1.3e-05 Score=54.93 Aligned_cols=45 Identities=18% Similarity=0.196 Sum_probs=41.2
Q ss_pred CCCHHHHHHHH-HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88977999999-9985999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLT-WISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~-lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|++.+++|+. ..-+|+|++|||+.|+||++||++|+.+.++||-
T Consensus 141 ~Lp~~~R~vi~L~~~e~~s~~EIAe~l~is~~TVKsrl~rA~k~LR 186 (194)
T PRK12531 141 RLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEKLR 186 (194)
T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 6999999999999886999999999989299999999999999999
No 70
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=98.05 E-value=1.2e-05 Score=55.18 Aligned_cols=45 Identities=18% Similarity=0.302 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88977999999998-5999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWIS-EGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~lia-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|++.+++|+.|-- +|+|++|||..|+||++||++++.++..||-
T Consensus 122 ~Lp~~~R~v~~L~~~~gls~~EIA~~L~is~~tVk~rl~RArk~Lr 167 (185)
T PRK12542 122 ELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRVQ 167 (185)
T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 2999888997679983999999999989299999999999999999
No 71
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=98.04 E-value=1.4e-05 Score=54.67 Aligned_cols=46 Identities=20% Similarity=0.138 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 888977999999998-5999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWIS-EGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~lia-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++.+++|+.|.- +|+|.+|||..|+||++||++++.++..||-
T Consensus 118 ~~L~~~~R~vi~L~~~~~~s~~EIA~~l~is~~tVksrl~rAr~~Lr 164 (173)
T PRK12522 118 QLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMR 164 (173)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 81999999999999983999999999989399999999999999999
No 72
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=98.04 E-value=1.2e-05 Score=55.03 Aligned_cols=46 Identities=26% Similarity=0.260 Sum_probs=42.6
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|+|++++|+.+. .+|+|.+|||+.||||++||++|+.++..||-
T Consensus 124 ~~L~~~~r~il~l~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr 170 (180)
T PRK11924 124 DALPEKQREVFLLRYVEGLSYQEIADQLGVPLGTVKSRLRRARQKLR 170 (180)
T ss_pred HHCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 85999999999999996859999999989499999999999999999
No 73
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=98.04 E-value=5.1e-06 Score=57.50 Aligned_cols=45 Identities=24% Similarity=0.288 Sum_probs=42.0
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8897799999999-85999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|++.+++|+.|. -+|+|++|||+.|+||++||++++.+...+|-
T Consensus 111 ~Lp~~~R~vl~L~~~egls~~EIAe~Lgis~gTVKsrl~RAr~~LR 156 (182)
T PRK12511 111 DLPEEQRAALHLVAIEGLSYQEAANVLGIPIGTLMSRIGRARAALR 156 (182)
T ss_pred CCCHHHHHHEEEEEECCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 6999895011241007999999999989399999999999999999
No 74
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=98.03 E-value=1.6e-05 Score=54.40 Aligned_cols=46 Identities=24% Similarity=0.297 Sum_probs=42.0
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|+|.+++|+.+- -+|+|++|||+.|++|++||++++.++..||-
T Consensus 127 ~~L~~~~r~v~~l~~~~~~s~~EIA~~l~is~~tVk~rl~Rar~~Lr 173 (185)
T PRK06811 127 NDLKKLDREIFIKRYLLGESIEEIAKKLGLTRSAIDNRLSRGRKKLK 173 (185)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 48999999999999994999999999989299999999999999999
No 75
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=98.02 E-value=1.5e-05 Score=54.51 Aligned_cols=45 Identities=22% Similarity=0.309 Sum_probs=42.3
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8897799999999-85999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|.+.+++|+.|. -+|+|++|||++|+||++||++++.+..+||-
T Consensus 113 ~LP~~~R~vl~L~~~egls~~EIAe~Lgis~gTVKsRL~RAR~~Lr 158 (188)
T PRK12546 113 QLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLA 158 (188)
T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 6999998895879982989999999989399999999999999999
No 76
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=98.01 E-value=1.6e-05 Score=54.24 Aligned_cols=47 Identities=19% Similarity=0.268 Sum_probs=43.4
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 88897799999999-859997999999499988999999999998079
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
..|++.+++|+.|. -+|+|.+|||+.|++|.+||++.+.+++.||-.
T Consensus 110 ~~Lp~~~R~vl~L~~~egls~~EIA~iL~is~gTVKsRL~RAr~kLr~ 157 (181)
T PRK12540 110 EKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSA 157 (181)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 819999989988799809999999999894999999999999999999
No 77
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=98.00 E-value=1.7e-05 Score=54.21 Aligned_cols=46 Identities=17% Similarity=0.153 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++.+++|+.|. -+|+|.+|||+.|++|++||++++.++..||-
T Consensus 107 ~~Lp~~~r~v~~L~~~~~~s~~EIA~~l~is~~tVk~rl~RAr~~Lr 153 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHELTYEEAASVLDLKENTYKSHLFRGRKRLK 153 (165)
T ss_pred HCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 72999999999999998889999999989399999999999999999
No 78
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=98.00 E-value=1.3e-05 Score=54.85 Aligned_cols=112 Identities=17% Similarity=0.154 Sum_probs=74.4
Q ss_pred CCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHH
Q ss_conf 32543333214457147503373689999999717875469899999999999999754201467798888897799999
Q gi|254780694|r 115 TLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAYQANMFKSYDVHWGKDFELTGREVECL 194 (246)
Q Consensus 115 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LT~RE~eVl 194 (246)
...+.......++..|+.++++.......+................. . ..........-...+....||++|.++|
T Consensus 83 ~~~d~i~~l~~GAdDYl~KPf~~~eL~ari~allrr~~~~~~~~~~~-g---~~~ld~~~~~~~~~g~~i~LT~~E~~lL 158 (219)
T PRK10336 83 ALAERVEGLRLGADDYLCKPFALIEVAARLEALMRRTNGQASNELRH-G---NVMLDPGKRIATLAGEPLTLKPKEFALL 158 (219)
T ss_pred CHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCCC-C---CEEECHHHEEEECCCEEEEECHHHHHHH
T ss_conf 99999999976998886889767999999999961154666643102-7---7898313629964997998378999999
Q ss_pred HHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHHCC
Q ss_conf 999859----99799999949-----9988999999999998079
Q gi|254780694|r 195 TWISEG----KTSDEIAVILG-----ISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 195 ~lia~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLgv 230 (246)
.++++. .|..+|...+. ++.+||+.|++++++||+-
T Consensus 159 ~~L~~~~g~vvsre~l~~~vw~~~~~~~~~~vdv~I~rLRkKl~~ 203 (219)
T PRK10336 159 ELLMRNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLGS 203 (219)
T ss_pred HHHHHCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf 999968996397999999962889888858199999999976798
No 79
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=97.99 E-value=2e-05 Score=53.75 Aligned_cols=46 Identities=17% Similarity=0.133 Sum_probs=42.6
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8889779999999-985999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|.++.++|+.| -.+|+|++|||..|++|++||++++.+.++||-
T Consensus 130 ~~Lp~~~r~v~~L~~~eg~s~~EIA~~lgis~~tVks~l~Rark~Lr 176 (184)
T PRK12539 130 ARLPEKMRLAIQAVKLDGLSVAEAATRSGMSESAVKVSVHRGLKALA 176 (184)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 84999999999999994999999999989199999999999999999
No 80
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=97.97 E-value=2.1e-05 Score=53.52 Aligned_cols=45 Identities=16% Similarity=0.102 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 889779999999-985999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|+|.+++|+.| .-+|+|.+|||.+|++|++||++++.++..||-
T Consensus 134 ~L~~~~R~vl~L~~~~~ls~~EIA~~l~is~~tVksrl~RAr~~Lr 179 (188)
T PRK09640 134 HVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLR 179 (188)
T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 4899999999999992999999999989299999999999999999
No 81
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=97.97 E-value=2.2e-05 Score=53.42 Aligned_cols=45 Identities=27% Similarity=0.188 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 889779999999-985999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|++.+++|+.+ .-+|+|++|||..|++|++||++++.++..||-
T Consensus 120 ~Lp~~~r~vi~l~~~~~~s~~EIA~~l~is~~tVk~~l~Ra~k~Lr 165 (175)
T PRK12518 120 TLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLR 165 (175)
T ss_pred CCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 6999999999999992999999999989599999999999999999
No 82
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=97.96 E-value=2.4e-05 Score=53.15 Aligned_cols=45 Identities=24% Similarity=0.300 Sum_probs=41.5
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8897799999999-85999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|++.+++|+.+. -+|+|.+|||++|++|++||++++.+..++|-
T Consensus 126 ~Lp~~~R~~~~l~~~eg~s~~EIA~~lgis~~tVk~rl~Ra~k~Lr 171 (178)
T PRK12536 126 QLPDRQRLPIVHVKLEGLSVEETAQLTGLSESAVKVGIHRGLKALA 171 (178)
T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 6999899999999885999999999989299999999999999999
No 83
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=97.94 E-value=2.7e-05 Score=52.87 Aligned_cols=45 Identities=20% Similarity=0.213 Sum_probs=42.4
Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 889779999999-985999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|++++++|+.+ .-+|+|++|||..|++|++||++++.++.+||.
T Consensus 127 ~L~~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~rl~Rark~Lr 172 (177)
T PRK09415 127 SLPIKYREVIYLFYYEELSIKEIATVTGVNENTIKTRLKKAKELLK 172 (177)
T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 6999999999999980998999999889299999999999999999
No 84
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=97.93 E-value=2.9e-05 Score=52.63 Aligned_cols=45 Identities=22% Similarity=0.097 Sum_probs=42.7
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8897799999999-85999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|++||+.|+.+. -+|+|-+|||.+++||..||+...+++..||-
T Consensus 106 ~L~~re~~ii~~~~~~g~t~~EIA~~~gis~~~Vk~~~r~Al~KLR 151 (154)
T PRK06759 106 VLDEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 4999999999999996998999999989899999999999999987
No 85
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=97.92 E-value=3.1e-05 Score=52.50 Aligned_cols=45 Identities=22% Similarity=0.192 Sum_probs=42.3
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8897799999999-85999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|.+.+++|+.|. -+|+|.+|||.+|+||++|||+++.+...||-
T Consensus 132 ~Lp~~~R~~l~L~~~~g~s~~EIA~ilgi~~gTVKsRl~RAr~~Lr 177 (195)
T PRK12535 132 ALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARARADLV 177 (195)
T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 4999887999999982998999999989399999999999999999
No 86
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=97.92 E-value=3.2e-05 Score=52.36 Aligned_cols=47 Identities=19% Similarity=0.180 Sum_probs=43.0
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 88897799999999-859997999999499988999999999998079
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
..|++.+++|+-|. -+|+|++|||+.|++|++|||+++.+...||-.
T Consensus 129 ~~Lp~~~R~vl~L~~~egls~~EIA~~lg~~~gTVKsRl~RAR~~L~a 176 (185)
T PRK09649 129 ADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 849999999999899729999999999893999999999999999997
No 87
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=97.92 E-value=3.1e-05 Score=52.50 Aligned_cols=45 Identities=22% Similarity=0.102 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8897799999999-85999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|++..++|+.|- -+|+|.+|||..|++|++||++|+.++..+|-
T Consensus 106 ~Lp~~~R~v~~L~~~e~~s~~EIA~~l~is~~tVk~~l~RArk~Lk 151 (160)
T PRK09642 106 ELPENYRDVVLAHYLEEKSYQEIALQENIEVKTVEMKLYRARKWIK 151 (160)
T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 7999999997999982999999999989199999999999999999
No 88
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=97.90 E-value=3.2e-05 Score=52.37 Aligned_cols=46 Identities=13% Similarity=0.034 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 888977999999998-5999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWIS-EGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~lia-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++++++|+.+-- +|+|++|||..|++|++||+.++.++..||-
T Consensus 130 ~~Lp~~~R~v~~Lr~~~~ls~~EIA~~l~~s~~tVk~~l~RAR~~Lr 176 (191)
T PRK12520 130 ERLPARTGRVFMMREWLELETEEICKELQITATNLWVMLYRARLRLR 176 (191)
T ss_pred HHCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 87749999999999993899999999989499999999999999999
No 89
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=97.85 E-value=4.7e-05 Score=51.33 Aligned_cols=45 Identities=9% Similarity=-0.009 Sum_probs=42.2
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8897799999999-85999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|++..++|+.|- -+|+|++|||+.|+||++||+..+.++..||-
T Consensus 149 ~Lp~~~R~vl~Lr~~eglS~~EIAe~Lgis~~tVks~L~RAR~~Lr 194 (207)
T PRK12544 149 ALPAKYARVFMMREFIELETPEICHNEDLTVSNLNVMLYRSRLRLR 194 (207)
T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 3999999999999981999999999979799999999999999999
No 90
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=97.84 E-value=4.8e-05 Score=51.25 Aligned_cols=46 Identities=22% Similarity=0.271 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|.++.++|+.|- -+|+|++|||+.|++|++||++++.++..||-
T Consensus 135 ~~Lp~~~R~vl~L~~~egls~~EIA~~lgis~~tVks~l~RAR~~Lr 181 (195)
T PRK12532 135 YNLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRARESLR 181 (195)
T ss_pred HHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 85999998999999981999999999989599999999999999999
No 91
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=97.79 E-value=6.8e-05 Score=50.27 Aligned_cols=45 Identities=9% Similarity=0.059 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8897799999999-85999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|+++.++|+.+- -+|+|++|||+.|++|++||+.++.++..||-
T Consensus 136 ~LP~~~R~v~~Lr~~~~ls~~EIA~~l~is~~tVksrL~RAR~~Lr 181 (191)
T PRK12530 136 KLPAQQARVFMMREFLELSSEQICQECHITTSNLHVLLYRARLQLQ 181 (191)
T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 6999999999999992999999999989699999999999999999
No 92
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=97.77 E-value=7.3e-05 Score=50.10 Aligned_cols=47 Identities=34% Similarity=0.367 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 888977999999998-59997999999499988999999999998079
Q gi|254780694|r 184 FELTGREVECLTWIS-EGKTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 184 ~~LT~RE~eVl~lia-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
..|++++++|+-+.- +|+|++|||+.|+||.+||++++.+...||.-
T Consensus 126 ~~Lp~~~R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~ 173 (182)
T COG1595 126 ARLPPRQREAFLLRYLEGLSYEEIAEILGISVGTVKSRLHRARKKLRE 173 (182)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 839999999999999859999999989599999999999999999999
No 93
>pfam04545 Sigma70_r4 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are 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.
Probab=97.71 E-value=8.5e-05 Score=49.66 Aligned_cols=46 Identities=39% Similarity=0.416 Sum_probs=42.0
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|+|+|++|+.+. -+|+|..|||+.|++|..||+..+++++.||-
T Consensus 3 ~~L~~~~r~ii~l~y~~~~t~~EIA~~lgis~~~V~~~~~ral~~LR 49 (50)
T pfam04545 3 ASLPPREREVLVLRFGEGLTLEEIGERLGISRERVRQIEKRALRKLR 49 (50)
T ss_pred HHCCHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHC
T ss_conf 66899999999987068824999999989799999999999999862
No 94
>pfam04967 HTH_10 HTH DNA binding domain.
Probab=97.56 E-value=0.00024 Score=46.73 Aligned_cols=43 Identities=30% Similarity=0.321 Sum_probs=40.2
Q ss_pred CCHHHHHHHHHHH--------CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 8977999999998--------599979999994999889999999999980
Q gi|254780694|r 186 LTGREVECLTWIS--------EGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 186 LT~RE~eVl~lia--------~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
||+||+||+...- ++.|-+|||..|+||..|+..|++++-+|+
T Consensus 1 LT~rQ~evl~~A~~~GYfd~PR~~~l~elA~~lgis~sT~~~hLr~ae~ki 51 (53)
T pfam04967 1 LTDRQREILRLAYKMGYFDYPRRVTLKDLAKELGISKSTLSEHLRRAESKL 51 (53)
T ss_pred CCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 988999999999986897788768899999996989999999999999987
No 95
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family; InterPro: IPR014325 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 recognized by the major sigma factors , . This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor . The protein appears to include a paralogous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives..
Probab=97.55 E-value=8e-05 Score=49.84 Aligned_cols=46 Identities=24% Similarity=0.349 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 889779999999-9859997999999499988999999999998079
Q gi|254780694|r 185 ELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 185 ~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
.|.+|+++|+=| --+++|.+|||..||||.+|||+|+++...||.-
T Consensus 113 ~LP~rQR~vvVLRY~eDlSe~~~A~~LG~SvGTVKS~~sRal~~LR~ 159 (165)
T TIGR02983 113 RLPARQRAVVVLRYYEDLSEAEVAEVLGISVGTVKSRLSRALARLRE 159 (165)
T ss_pred HCCHHCCEEEEEECCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf 35641236723204578986899988199932289989999999887
No 96
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=97.53 E-value=0.00025 Score=46.65 Aligned_cols=46 Identities=28% Similarity=0.364 Sum_probs=41.9
Q ss_pred CCCCCHHHHHHHHHHH--------CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 8888977999999998--------599979999994999889999999999980
Q gi|254780694|r 183 DFELTGREVECLTWIS--------EGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 183 ~~~LT~RE~eVl~lia--------~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
...||+||+++|+..- +.-+-+|||..||||..|+..||+++-+||
T Consensus 153 ~~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl 206 (215)
T COG3413 153 KNDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKL 206 (215)
T ss_pred CCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 446999999999999985898887658999999995998889999999999999
No 97
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=97.35 E-value=0.001 Score=42.65 Aligned_cols=189 Identities=10% Similarity=0.032 Sum_probs=93.7
Q ss_pred HEEEEECCCCHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEECCCCCHHH
Q ss_conf 10002214458888765530232137999973279999999999999871930230002666311123210006895899
Q gi|254780694|r 7 QVNIVLNREDEQRTSFVSHLPTRSDLLARMIPLDCTVSWTMRMYALTEYVGASHFLLVRWDLFQEQKLDSIVSSDWPFDL 86 (246)
Q Consensus 7 ~~~~~l~r~d~~r~~~v~~l~~~~d~~~~l~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ 86 (246)
..+|++-.+|+.-...........+-+..+..+.+..+....+. ...+.....++.+++..+.++
T Consensus 4 ~i~VLIVEDd~~v~~~l~~~L~~~~gf~~V~~A~~~~eA~~~l~---------------~~~pDLvLLDi~LPd~~Glel 68 (225)
T PRK10046 4 PLTLLIVEDETPLAEMHAEYIRHIPGFSQILLAGNLAQARMMIE---------------RFKPGLILLDNYLPDGRGINL 68 (225)
T ss_pred CCEEEEEECCHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHH---------------HCCCCEEEEECCCCCCCHHHH
T ss_conf 88699995989999999999972899549999899999999997---------------359999998289899979999
Q ss_pred HHHHHHCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCC------CCCCHHHHH
Q ss_conf 99999669845173899998523244303254333321445714750337368999999971787------546989999
Q gi|254780694|r 87 VRCMALSEKDKYYNVLQRPTELFCPVFHTLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKG------RIILRDRLW 160 (246)
Q Consensus 87 ~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~ 160 (246)
++.....+... ++ ..............+...++.+|+.+++..++...++....... ...++..+.
T Consensus 69 l~~lr~~~~~~--~V------I~iTA~~d~~~~~~Al~~Ga~DYLvKPf~~erl~~~L~~y~~~~~~l~~~~~~~Q~~iD 140 (225)
T PRK10046 69 LHELVQAHYPG--DV------VFTTAASDMETVSEAVRCGVFDYLIKPIAYERLGQTLTRFRQRKHMLESIDSASQKQID 140 (225)
T ss_pred HHHHHHHCCCC--CE------EEEECCCCHHHHHHHHHCCCCCCEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHHH
T ss_conf 99999648799--88------99968999999999997499831028999999999999999999986357768999999
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCH----HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 9999999999754201467798888897----7999999998599979999994999889999999999
Q gi|254780694|r 161 EIGLLAAYQANMFKSYDVHWGKDFELTG----REVECLTWISEGKTSDEIAVILGISRNTVNNYIASIM 225 (246)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~~LT~----RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~ 225 (246)
.+. ...........-+-+|++ +=+++++-...+.|..|||+.+|+|.-|++.|+.-.-
T Consensus 141 ~~~-------~~~~~~~~~~~lpKGl~~~Tl~~v~~~l~~~~~~~ta~eva~~~giSrvTaRRYLe~L~ 202 (225)
T PRK10046 141 EMF-------NAYARGEPKDELPTGIDPLTLNAVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCA 202 (225)
T ss_pred HHH-------CCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 996-------23356888565899999899999999997179986899999985851999999999998
No 98
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=97.35 E-value=0.00059 Score=44.25 Aligned_cols=46 Identities=24% Similarity=0.234 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++||++|+.+. .+|+|-+|||..||||...|+..-++++.||-
T Consensus 204 ~~L~erEr~Ii~lry~~~~t~~eIa~~lGiS~eRVrQi~~~Al~kLR 250 (257)
T PRK08583 204 PVLSDREKSIIQCTFIENLSQKETGERLGISQMHVSRLQRQAIKKLR 250 (257)
T ss_pred HCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 54999999999999579999999999989699999999999999987
No 99
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein; InterPro: IPR010163 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=97.33 E-value=0.00058 Score=44.31 Aligned_cols=48 Identities=27% Similarity=0.291 Sum_probs=42.6
Q ss_pred CCCCCCCCHHHHHHHHHHHC--C-CCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 79888889779999999985--9-997999999499988999999999998
Q gi|254780694|r 180 WGKDFELTGREVECLTWISE--G-KTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 180 ~~~~~~LT~RE~eVl~lia~--G-~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
....+++|.+|.+||..+.. | ++.+.||..|++|+.|+.+|++.+-.|
T Consensus 161 ~~~~~~~s~~~~~vL~~L~~~~Ge~~v~~iA~~lg~s~~T~~~~~~~Lek~ 211 (231)
T TIGR01884 161 VPLLAGLSREELKVLEALKAEKGEKSVKNIAKKLGKSLSTISRHLAELEKK 211 (231)
T ss_pred CCCCCCCCHHHHHHHHHHHCCCCEECHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 244678889999999998507880528779988578887999999988744
No 100
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=97.33 E-value=0.00068 Score=43.86 Aligned_cols=46 Identities=28% Similarity=0.299 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++||+.|+.+- .+++|-+|||..||||...|+...+++..||-
T Consensus 202 ~~L~eREr~Il~~ry~~~~tl~EIa~~lgvS~~rVsqi~~~AL~kLR 248 (256)
T PRK07408 202 AQLEERTREVLEFVFLHDLTQKEAAERLGISPVTVSRRVKKGLQQLK 248 (256)
T ss_pred HCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 56999999999999637998999998979899999999999999999
No 101
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=97.30 E-value=0.00048 Score=44.85 Aligned_cols=113 Identities=12% Similarity=0.084 Sum_probs=69.7
Q ss_pred HHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 54333321445714750337368999999971787546989999999999999975420146779888889779999999
Q gi|254780694|r 117 PENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAYQANMFKSYDVHWGKDFELTGREVECLTW 196 (246)
Q Consensus 117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LT~RE~eVl~l 196 (246)
.....+...++.+|+.+++........+................. .............-...+....||++|.++|.+
T Consensus 94 ~~~~~al~~GAddYl~KPf~~~eLlari~~~lrr~~~~~~~~~~~--~~~~l~ld~~~~~~~~~~~~i~LT~~E~~lL~~ 171 (240)
T PRK10710 94 IDRLLGLEIGADDYICKPYSPREVVARVKTILRRCKPQRELQQQD--AESPLIIDESRFQASWRGKMLDLTPAEFRLLKT 171 (240)
T ss_pred HHHHHHHHCCCCEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCE--EECCEEEECCCEEEEECCEEEECCHHHHHHHHH
T ss_conf 999999986998760077653899999999984523555644300--004789985631999899998558999999999
Q ss_pred HHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHHCCC
Q ss_conf 9859----99799999949-----99889999999999980799
Q gi|254780694|r 197 ISEG----KTSDEIAVILG-----ISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 197 ia~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLgv~ 231 (246)
+++. .|..+|...+. .+.+||+.|++++++||...
T Consensus 172 L~~~~g~vvSre~L~~~vw~~~~~~~~rsid~~I~rLRkKl~~~ 215 (240)
T PRK10710 172 LSHEPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLESL 215 (240)
T ss_pred HHHCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCC
T ss_conf 99779973989999999628888888465999999999960106
No 102
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=97.29 E-value=0.00067 Score=43.89 Aligned_cols=47 Identities=19% Similarity=0.258 Sum_probs=43.3
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 8889779999999-9859997999999499988999999999998079
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
..|++||+.|+.+ .-+|+|-+|||..||||+..|..-.+++..||-.
T Consensus 180 ~~L~erEr~Vi~l~y~e~ltlkEIa~~LgvS~~RVsQi~~kal~kLR~ 227 (229)
T PRK12427 180 SQLDEREQMILHLYYQQELSMKEIAQVLDLTEARICQLNKKLVQKIKS 227 (229)
T ss_pred HHCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 719999999999980589989999999798899999999999999884
No 103
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=97.25 E-value=0.00093 Score=42.99 Aligned_cols=46 Identities=28% Similarity=0.285 Sum_probs=42.7
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++||++|+.+- .+++|-+|||..|+||...|+.-.+++..||-
T Consensus 213 ~~L~eREr~Vi~lry~e~~Tl~EIa~~lGiSreRVrQIe~~AL~KLR 259 (263)
T PRK07122 213 AALPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAKSLARLR 259 (263)
T ss_pred HCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 75999999999999569998999999989799999999999999999
No 104
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=97.24 E-value=0.00093 Score=42.97 Aligned_cols=45 Identities=11% Similarity=0.028 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8897799999999-85999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|++..++|+.|- -+|+|++|||..|+||++||+..+.+...||-
T Consensus 139 ~LP~~~R~v~~Lr~~egls~~EIA~~L~is~~tVksrL~RAR~~LR 184 (201)
T PRK12545 139 HLPEQIGRVFMMREFLDFEIDDICTELTLTANHCSVLLYRARTRLR 184 (201)
T ss_pred HCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 5999998898999992898999999989699999999999999999
No 105
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=97.22 E-value=0.00085 Score=43.23 Aligned_cols=49 Identities=20% Similarity=0.144 Sum_probs=43.7
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 88897799999999-85999799999949998899999999999807998
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTATKT 232 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~ 232 (246)
..|+|.|+.|+-|- ..|+++.|||+.|++|+.|||..+.+..+||....
T Consensus 110 ~~L~p~qRav~vLrdv~g~s~~EIA~iLg~s~~avR~~l~RAR~~l~~~~ 159 (289)
T PRK09636 110 ERLSPLERAAFLLHDVFGVPFDEIASTLGRSEAACRQLASRARKHVRAAR 159 (289)
T ss_pred HHCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHCCC
T ss_conf 73999896254049860999999999981799999999999999873448
No 106
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=97.20 E-value=0.00092 Score=43.01 Aligned_cols=184 Identities=8% Similarity=0.042 Sum_probs=94.9
Q ss_pred CCCHHHHHHHHHHHHHHHCCCEEEEECC---------CCCCCCCCCEEECCCCCHHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf 2799999999999998719302300026---------6631112321000689589999999669845173899998523
Q gi|254780694|r 39 LDCTVSWTMRMYALTEYVGASHFLLVRW---------DLFQEQKLDSIVSSDWPFDLVRCMALSEKDKYYNVLQRPTELF 109 (246)
Q Consensus 39 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~---------~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~ 109 (246)
+++...+...+....+..|+........ ..+.....+..+++..+.++++..........-|++ .
T Consensus 8 VEDd~~l~~~l~~~L~~~g~~v~~a~~g~~a~~~l~~~~~DliilDi~lP~~dG~~~~~~ir~~~~~~~~PII------~ 81 (229)
T PRK10161 8 VEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVV------M 81 (229)
T ss_pred EECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHCCCCCCCCEE------E
T ss_conf 9599999999999999779999998999999999852899899997899887633587887750246897589------9
Q ss_pred HHHHCCCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHH
Q ss_conf 24430325433332144571475033736899999997178754698999999999999997542014677988888977
Q gi|254780694|r 110 CPVFHTLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAYQANMFKSYDVHWGKDFELTGR 189 (246)
Q Consensus 110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LT~R 189 (246)
........+.......++..|+.+++.......-+...................-+ ........-...+....||++
T Consensus 82 lta~~~~~d~v~gl~~GADDYl~KPf~~~EL~aRi~a~lrR~~~~~~~~~~~~~~l---~~d~~~~~v~~~~~~i~LT~~ 158 (229)
T PRK10161 82 LTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRRISPMAVEEVIEMQGL---SLDPTSHRVMAGEEPLEMGPT 158 (229)
T ss_pred EECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCEEECCE---EEEEEEEEEEECCEEEECCHH
T ss_conf 95566657799998769876520899989999999999712377776543267778---986101599999999870689
Q ss_pred HHHHHHHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHHCCC
Q ss_conf 99999999859----99799999949-----99889999999999980799
Q gi|254780694|r 190 EVECLTWISEG----KTSDEIAVILG-----ISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 190 E~eVl~lia~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLgv~ 231 (246)
|.++|.++++- .|-.+|-..+. .+.+||+.|++++++||.-.
T Consensus 159 E~~LL~~L~~~~g~vvsr~~L~~~vwg~~~~~~~rtldv~I~rLRkKl~~~ 209 (229)
T PRK10161 159 EFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPG 209 (229)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf 999999999779987979999998639998988473999999999974567
No 107
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=97.18 E-value=0.0025 Score=40.26 Aligned_cols=112 Identities=15% Similarity=0.126 Sum_probs=72.0
Q ss_pred CCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHH
Q ss_conf 32543333214457147503373689999999717875469899999999999999754201467798888897799999
Q gi|254780694|r 115 TLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAYQANMFKSYDVHWGKDFELTGREVECL 194 (246)
Q Consensus 115 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LT~RE~eVl 194 (246)
...+.......++..|+.++++......-+............. . ... ..........-...+....||++|.++|
T Consensus 82 ~~~d~i~~l~~GADDYl~KPf~~~EL~aRi~a~lrr~~~~~~~-~-~~~---~l~ld~~~~~v~~~~~~i~LT~~E~~LL 156 (223)
T PRK11517 82 SVDDRVRGLDSGANDYLVKPFSFSELLARVRAQLRQHHALNST-L-EIS---GLRMDSVSQSVSRDNISITLTRKEFQLL 156 (223)
T ss_pred CHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCCCCCCCCC-E-EEC---CEEEEHHHEEEEECCEEECCCHHHHHHH
T ss_conf 6578999998398776208977899999999996414577871-7-988---7898001318962998982999999999
Q ss_pred HHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHHCCC
Q ss_conf 999859----99799999949-----99889999999999980799
Q gi|254780694|r 195 TWISEG----KTSDEIAVILG-----ISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 195 ~lia~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLgv~ 231 (246)
.++++- .|-.+|.+.+. .+.+||+.|++++++||+-.
T Consensus 157 ~~L~~~~g~vvsre~l~~~vwg~~~~~~~~~idv~I~rLRkKl~~~ 202 (223)
T PRK11517 157 WLLASRAGEIIPRTVIASEIWGINFDSDTNTVDVAIRRLRAKVDDP 202 (223)
T ss_pred HHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf 9998689985989999999629887888587999999999985788
No 108
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=97.17 E-value=0.0011 Score=42.60 Aligned_cols=46 Identities=22% Similarity=0.282 Sum_probs=42.6
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8889779999999-985999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++||++|+.+ ..+|+|-+|||..||||...|+.--+++..||-
T Consensus 207 ~~L~erEr~Il~lry~e~~Tl~eIa~~lgiS~eRVrQie~~AL~kLR 253 (261)
T PRK06288 207 NTLPEREKKVITLYYYEDLTLKEIGEVLGVTESRISQIHTKAVLQLR 253 (261)
T ss_pred HCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 70899999999998079988999999979789999999999999999
No 109
>PRK05572 sporulation sigma factor SigF; Validated
Probab=97.14 E-value=0.0013 Score=42.00 Aligned_cols=46 Identities=30% Similarity=0.302 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++||++|+.+- .+++|-+|||..||||...|+..-++++.||-
T Consensus 200 ~~L~~rEr~Vi~~ry~~~~tl~EIa~~lgiS~eRVrQI~~~Al~kLR 246 (251)
T PRK05572 200 RELDERERLIIYLRYFKDKTQSEVAKRLGISQVQVSRLEKKILKQMK 246 (251)
T ss_pred HCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 72899999999998178988999999979799999999999999999
No 110
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=97.10 E-value=0.0036 Score=39.23 Aligned_cols=140 Identities=15% Similarity=0.083 Sum_probs=73.7
Q ss_pred CCCCEEECCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHC--
Q ss_conf 123210006895899999996698451738999985232443032543333214457147503373689999999717--
Q gi|254780694|r 72 QKLDSIVSSDWPFDLVRCMALSEKDKYYNVLQRPTELFCPVFHTLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFP-- 149 (246)
Q Consensus 72 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-- 149 (246)
...++.+++..+.+.+......+.. .+ ...............+...++.+|+.+++..++...++.....
T Consensus 53 ILLDi~mPd~~Glell~~lR~~~~~--~~------VI~ITa~~d~~~v~~Al~~Ga~DYLiKPf~~~rl~~~L~~y~~~~ 124 (239)
T PRK10430 53 ILLDIYMQQENGLDLLPVLHEAGCK--SD------VIVISSAADAATIKDSLHYGVVDYLIKPFQASRFEEALTGWRQKK 124 (239)
T ss_pred EEECCCCCCCCHHHHHHHHHHHCCC--CE------EEEEEECCCHHHHHHHHHCCCHHHEECCCCHHHHHHHHHHHHHHH
T ss_conf 9978999999789999999985899--81------999972688999999998395030489999999999999999999
Q ss_pred ----CCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHH-HHHHHH---HC-CCCHHHHHHHHCCCHHHHHHH
Q ss_conf ----875469899999999999999754201467798888897799-999999---85-999799999949998899999
Q gi|254780694|r 150 ----KGRIILRDRLWEIGLLAAYQANMFKSYDVHWGKDFELTGREV-ECLTWI---SE-GKTSDEIAVILGISRNTVNNY 220 (246)
Q Consensus 150 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LT~RE~-eVl~li---a~-G~t~~eIA~~L~iS~~TV~~h 220 (246)
.....++..+..+. +...........-+-+|++--. .|...+ .. ++|..|||+.+|+|.-|++.|
T Consensus 125 ~~l~~~~~~~Q~~iD~l~------~~~~~~~~~~~~lPKGl~~~TL~~i~~~l~~~~~~~~sa~eva~~~giSRvTaRRY 198 (239)
T PRK10430 125 MALEKRQYYDQAELDQLI------HGSSSNEQDPRRLPKGLTPQTLRTLCQWIDAHQDYEFSTDELANEVNISRVSCRKY 198 (239)
T ss_pred HHHCCCCCCCHHHHHHHH------HCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 985457878999999998------50578888766699999999999999999827999846999998858529889999
Q ss_pred HHHHH
Q ss_conf 99999
Q gi|254780694|r 221 IASIM 225 (246)
Q Consensus 221 l~~i~ 225 (246)
+.-.-
T Consensus 199 Le~L~ 203 (239)
T PRK10430 199 LIWLV 203 (239)
T ss_pred HHHHH
T ss_conf 99998
No 111
>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=97.07 E-value=0.00078 Score=43.48 Aligned_cols=186 Identities=13% Similarity=0.094 Sum_probs=98.7
Q ss_pred CCCHHHHHHHHHHHHHHHCCCEEEEECCC----CCCCCCCCEEECCC-----CCHHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf 27999999999999987193023000266----63111232100068-----9589999999669845173899998523
Q gi|254780694|r 39 LDCTVSWTMRMYALTEYVGASHFLLVRWD----LFQEQKLDSIVSSD-----WPFDLVRCMALSEKDKYYNVLQRPTELF 109 (246)
Q Consensus 39 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~~----~~~~~~~~~~l~~~-----~~~~~~~~~~~~~~~~~~p~~~~~~~~~ 109 (246)
+++..++...+....+..||......... ..... ++.++.+. .+.++++.+... .....|++ .
T Consensus 6 veDd~~i~~~l~~~L~~~G~~v~~~~~~~~a~~~~~~~-~dlviLD~~lP~~dG~~~~~~iR~~-~~~~~PIi------~ 77 (229)
T COG0745 6 VEDDPELAELLKEYLEEEGYEVDVAADGEEALEAAREQ-PDLVLLDLMLPDLDGLELCRRLRAK-KGSGPPII------V 77 (229)
T ss_pred EECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCC-CCEEEEECCCCCCCHHHHHHHHHHC-CCCCCCEE------E
T ss_conf 91888999999999987597899978989999997269-9999998899985689999999851-68999889------9
Q ss_pred HHHHCCCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHH
Q ss_conf 24430325433332144571475033736899999997178754698999999999999997542014677988888977
Q gi|254780694|r 110 CPVFHTLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAYQANMFKSYDVHWGKDFELTGR 189 (246)
Q Consensus 110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LT~R 189 (246)
........+.......+++.|+.+++.+.+...-+...-............................-........||++
T Consensus 78 Lta~~~~~d~v~gl~~GADDYl~KPf~~~EL~ARi~a~lRR~~~~~~~~~~~~~~~g~l~~d~~~~~v~~~~~~l~Lt~~ 157 (229)
T COG0745 78 LTARDDEEDRVLGLEAGADDYLTKPFSPRELLARLRALLRRNAGASRAEASEVLVFGDLTLDPDTRTVTLNGRELTLTPK 157 (229)
T ss_pred EECCCCHHHHHHHHHCCCHHHCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCEEEECCEEEECCCCEEEECCEEECCCHH
T ss_conf 96687288899999756342334889989999999999673656655454650798899998021989989987317889
Q ss_pred HHHHHHHHHCC----CCHHHHHHHH-----CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 99999999859----9979999994-----9998899999999999807998
Q gi|254780694|r 190 EVECLTWISEG----KTSDEIAVIL-----GISRNTVNNYIASIMRKTATKT 232 (246)
Q Consensus 190 E~eVl~lia~G----~t~~eIA~~L-----~iS~~TV~~hl~~i~~KLgv~~ 232 (246)
|.++|..+++- .|-.+|-..+ ..+.+||+.|++++.+||+-..
T Consensus 158 Ef~lL~~L~~~~g~v~sR~~L~~~vw~~~~~~~~rtvdvhI~rLR~Kl~~~~ 209 (229)
T COG0745 158 EFELLELLARHPGRVLSREQLLEAVWGYDFEVDSRTVDVHISRLRKKLEKDP 209 (229)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCEEHHHHHHHHHHHCCCC
T ss_conf 9999999996699526899999986086668764330599889999733567
No 112
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=97.07 E-value=0.0016 Score=41.52 Aligned_cols=46 Identities=28% Similarity=0.408 Sum_probs=42.2
Q ss_pred CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-----85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-----SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++||++|+.+- .+.+|-+|||..|+||...|+.--+++.+||-
T Consensus 182 ~~L~eREr~Ii~lRfGL~~~~~~Tl~EIa~~lgISrerVrQIe~~AL~KLR 232 (239)
T PRK08301 182 KKLNDREKQIMELRFGLAGGEEKTQKEVADMLGISQSYISRLEKRIIKRLK 232 (239)
T ss_pred HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 648999999999995788998406999999989789999999999999999
No 113
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=97.07 E-value=0.0015 Score=41.72 Aligned_cols=110 Identities=15% Similarity=0.092 Sum_probs=68.0
Q ss_pred HHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 54333321445714750337368999999971787546989999999999999975420146779888889779999999
Q gi|254780694|r 117 PENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAYQANMFKSYDVHWGKDFELTGREVECLTW 196 (246)
Q Consensus 117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LT~RE~eVl~l 196 (246)
.........++.+|..++++.......+..+............. ............-...+....||++|.++|.+
T Consensus 85 ~~~~~~l~~GAddyi~KP~~~~eL~ari~~~lrr~~~~~~~~~~----~~~~~~d~~~~~~~~~~~~i~LT~~E~~lL~~ 160 (222)
T PRK10643 85 EDRIAGLDVGADDYLVKPFALEELHARIRALLRRHNNQGESELQ----VGNLTLNLGRQQVWLDGQELILTPKEYALLSR 160 (222)
T ss_pred HHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCEE----ECCEEECCCCCEEEECCEEEEECHHHHHHHHH
T ss_conf 88999997599776438876899999999997032366777326----77689810006898899888708799999999
Q ss_pred HHCC----CCHHHHHHHH-----CCCHHHHHHHHHHHHHHHCC
Q ss_conf 9859----9979999994-----99988999999999998079
Q gi|254780694|r 197 ISEG----KTSDEIAVIL-----GISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 197 ia~G----~t~~eIA~~L-----~iS~~TV~~hl~~i~~KLgv 230 (246)
+.+- .|-.+|...+ ..+.+||+.|++++++||+=
T Consensus 161 L~~~~g~vvsre~L~~~v~~~~~~~~~~~ld~~I~rLRkKl~~ 203 (222)
T PRK10643 161 LMLKAGSPVHREILYNDIYNWDNEPSTNTLEVHIHNLRDKVGK 203 (222)
T ss_pred HHHCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCC
T ss_conf 9967999868999999960878888867699999999976699
No 114
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=97.06 E-value=0.0015 Score=41.74 Aligned_cols=45 Identities=24% Similarity=0.369 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8897799999999-85999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|++||+.|+.+. -+++|-+|||..|+||...|+.-.++++.||-
T Consensus 183 ~L~~rEr~Ii~l~y~~~~tl~eIa~~lgiS~eRVrQie~~AL~kLR 228 (234)
T PRK06986 183 KLPEREQLVLSLYYDEELNLKEIGAVLGVSESRVSQIHSQAIKRLR 228 (234)
T ss_pred HCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 0999999999987389989999999979789999999999999999
No 115
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=97.04 E-value=0.0018 Score=41.07 Aligned_cols=45 Identities=29% Similarity=0.337 Sum_probs=42.1
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8897799999999-85999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|++||++|+.+- .+|+|-.|||..||||...|+.--++++.||-
T Consensus 209 ~L~~REr~Ii~~ry~~~~Tl~eIa~~lGvSreRVrQie~~AL~kLR 254 (257)
T PRK08215 209 RLNDREKMILNLRFFQGKTQMEVADEIGISQAQVSRLEKAALKHMR 254 (257)
T ss_pred CCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 4999999999999479998999999989699999999999999998
No 116
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family; InterPro: IPR011517 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 recognized by the major sigma factors , . This entry represents a group of sigma factors that are able to regulate extra cellular function (ECF) . Eubacteria display considerable genetic diversity between ECF-sigma factors, but all retain two features: the ability to respond to extra-cytoplasmic functions; and regulation by anti-sigma and anti-anti-sigma factors . This family show sequence similarity to IPR007627 from INTERPRO and IPR007630 from INTERPRO.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=97.03 E-value=0.0015 Score=41.60 Aligned_cols=48 Identities=25% Similarity=0.178 Sum_probs=41.6
Q ss_pred CCCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 888897799999999-859997999999499988999999999998079
Q gi|254780694|r 183 DFELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 183 ~~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
.....||-.+|++|= =-|+|++|||+.|+||++||+.+.+-+...|..
T Consensus 143 L~~~~Pr~a~~veLr~F~Gl~~~E~A~~L~~S~~Tv~Rdw~~ARaWL~~ 191 (194)
T TIGR02999 143 LAQVDPRQAEVVELRFFAGLTVEEIAELLGVSVRTVERDWRFARAWLLD 191 (194)
T ss_pred HHHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 7400678899885311048898999998688887899879999999987
No 117
>PRK13558 bacterio-opsin activator; Provisional
Probab=97.02 E-value=0.0014 Score=41.79 Aligned_cols=44 Identities=18% Similarity=0.234 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHH--------CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 88977999999998--------599979999994999889999999999980
Q gi|254780694|r 185 ELTGREVECLTWIS--------EGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 185 ~LT~RE~eVl~lia--------~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
.||+|++++|+..= +.-|-+|||..|+||+.|...||+...+||
T Consensus 616 ~LTDRQ~eaLqtAY~sGyFEwPR~sTGeElAesLgIS~pTfhqHLRaaerKL 667 (674)
T PRK13558 616 DLTDRQLTALQKAYVSGYFEWPRRAEGKQLAESMDIVPSTYHQHLQAAKQKL 667 (674)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf 6049899999999864757788778789999870988388999999999999
No 118
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=97.01 E-value=0.0017 Score=41.22 Aligned_cols=46 Identities=22% Similarity=0.253 Sum_probs=41.8
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++||+.|+.+. .+++|-+|||..||||...|+..-+++..||-
T Consensus 196 ~~L~~rEr~Vl~l~y~e~~Tl~eIa~~lgvS~erVrQi~~~AL~kLr 242 (250)
T PRK07670 196 KELNEKEQLVISLFYKEELTLTEIGQVLNLSTSRISQIHSKALFKLK 242 (250)
T ss_pred HCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 55899999999997489868999999989799999999999999999
No 119
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=97.00 E-value=0.002 Score=40.92 Aligned_cols=46 Identities=35% Similarity=0.322 Sum_probs=42.4
Q ss_pred CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-----85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-----SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++||++|+.+- .+.+|-.|||..|+||...|+..-++++.||.
T Consensus 173 ~~L~~REr~II~~RfGL~~~~~~Tl~eIg~~lgiSrERVRQIe~~Al~KLr 223 (228)
T PRK05803 173 DILDPREKEVIEMRYGLGDGKEKTQREIAKALGISRSYVSRIEKKALKKLF 223 (228)
T ss_pred HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 518988999999986478999715999999989799999999999999999
No 120
>PRK09836 DNA-binding transcriptional activator CusR; Provisional
Probab=96.93 E-value=0.00096 Score=42.90 Aligned_cols=112 Identities=13% Similarity=0.174 Sum_probs=71.2
Q ss_pred CHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHH
Q ss_conf 254333321445714750337368999999971787546-9899999999999999754201467798888897799999
Q gi|254780694|r 116 LPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRII-LRDRLWEIGLLAAYQANMFKSYDVHWGKDFELTGREVECL 194 (246)
Q Consensus 116 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LT~RE~eVl 194 (246)
..+.......++..|+.+++.......-+.......... ...... .. ..........-...+....||++|.++|
T Consensus 84 ~~d~i~~l~~GADDYl~KPf~~~EL~aRi~allrr~~~~~~~~~~~-~~---~l~~d~~~~~v~~~g~~v~LT~~E~~lL 159 (226)
T PRK09836 84 IEHRVKGLELGADDYLVKPFAFAELLARVRTLLRRGAAVIIESQFQ-VA---DLMVDLVSRKVTRSGTRITLTSKEFTLL 159 (226)
T ss_pred HHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCCCCCCCCCCEEE-EC---CEEEECCCEEEEECCEEEECCHHHHHHH
T ss_conf 8899999976996886368767999999999966266667765079-87---7998514118988999985688999999
Q ss_pred HHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHHCCC
Q ss_conf 999859----99799999949-----99889999999999980799
Q gi|254780694|r 195 TWISEG----KTSDEIAVILG-----ISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 195 ~lia~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLgv~ 231 (246)
.++++- .|-.+|...+. .+.+||+.|++++++||+-.
T Consensus 160 ~~L~~~~g~vvsre~l~~~vw~~~~~~~~~~vdv~I~rLR~Kl~~~ 205 (226)
T PRK09836 160 EFFLRHQGEVLPRSLIASQVWDMNFDSDTNAIDVAVKRLRGKIDND 205 (226)
T ss_pred HHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf 9998689964879999999628887888588999999999985788
No 121
>PRK09468 ompR osmolarity response regulator; Provisional
Probab=96.92 E-value=0.00054 Score=44.51 Aligned_cols=201 Identities=9% Similarity=0.074 Sum_probs=98.2
Q ss_pred HHEEEEECCCCHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEECCCCCHH
Q ss_conf 11000221445888876553023213799997327999999999999987193023000266631112321000689589
Q gi|254780694|r 6 QQVNIVLNREDEQRTSFVSHLPTRSDLLARMIPLDCTVSWTMRMYALTEYVGASHFLLVRWDLFQEQKLDSIVSSDWPFD 85 (246)
Q Consensus 6 ~~~~~~l~r~d~~r~~~v~~l~~~~d~~~~l~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 85 (246)
.+.+|++-.+|+.-...+...+...++ .+..+.+..+....+ ... .+.....+..+.+..+.+
T Consensus 4 ~~~kILiVEDd~~~~~~l~~~L~~~g~--~v~~a~~~~~a~~~~----~~~-----------~~DlvilDi~lp~~dG~~ 66 (239)
T PRK09468 4 ENYKILVVDDDMRLRALLERYLTEQGF--QVRSAANAEQMDRLL----TRE-----------SFHLMVLDLMLPGEDGLS 66 (239)
T ss_pred CCCEEEEEECCHHHHHHHHHHHHHCCC--EEEEECCHHHHHHHH----HHC-----------CCCEEEECCCCCCCCCCH
T ss_conf 897899990999999999999998899--999989999999999----758-----------998999878998888734
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCC--CH-HHHHHH
Q ss_conf 999999669845173899998523244303254333321445714750337368999999971787546--98-999999
Q gi|254780694|r 86 LVRCMALSEKDKYYNVLQRPTELFCPVFHTLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRII--LR-DRLWEI 162 (246)
Q Consensus 86 ~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~-~~~~~~ 162 (246)
+++.....+. ..|++ .........+.......++..|+.++++......-+.......... +. ......
T Consensus 67 l~~~iR~~~~--~~pII------~LTa~~~~~d~i~~l~~GADDYi~KPf~~~EL~aRI~allrR~~~~~~~~~~~~~~~ 138 (239)
T PRK09468 67 ICRRLRSQNN--PTPII------MLTAKGEEVDRIVGLEMGADDYLPKPFNPRELLARIRAVLRRQAPELPGAPSQEEEV 138 (239)
T ss_pred HHHHHHHHCC--CCCEE------EEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCE
T ss_conf 6777875057--87789------994667878999999769868855899989999999999863234456776677876
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCC----CCHHHHHHHH-----CCCHHHHHHHHHHHHHHHCCC
Q ss_conf 99999999754201467798888897799999999859----9979999994-----999889999999999980799
Q gi|254780694|r 163 GLLAAYQANMFKSYDVHWGKDFELTGREVECLTWISEG----KTSDEIAVIL-----GISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~LT~RE~eVl~lia~G----~t~~eIA~~L-----~iS~~TV~~hl~~i~~KLgv~ 231 (246)
..+...........-...+....||++|.++|.++++- .|-.+|-+.+ ..+.+||+.|++++++||...
T Consensus 139 ~~~g~l~ld~~~~~v~~~~~~i~LT~~E~~LL~~L~~~~g~vvsre~Ll~~vwg~~~~~~~rtidv~I~rLRkKl~~~ 216 (239)
T PRK09468 139 IAFGEFSLNLGTRELFRGDEPIPLTTGEFAVLKALVRHPREPLSRDKLMNLARGREYSAMERSIDVQISRLRRLIEPD 216 (239)
T ss_pred EEECCEEEECCCCEEEECCEEEECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCC
T ss_conf 999999999777999989998876789999999999779966769999999629887888483999999999975207
No 122
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=96.92 E-value=0.0023 Score=40.40 Aligned_cols=46 Identities=24% Similarity=0.303 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8889779999999-985999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++||+.|+.+ ..+++|-+|||..||||...|+.-.+.+..||-
T Consensus 204 ~~L~erEr~Ii~lry~e~~Tl~EIg~~lgvS~eRVrQi~~~AL~kLR 250 (257)
T PRK05911 204 LALEEKERKVMALYYYEELVLKEIGKILGVSESRVSQIHSKALLKLR 250 (257)
T ss_pred HCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 65899999999987489878999998979889999999999999999
No 123
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=96.87 E-value=0.0025 Score=40.20 Aligned_cols=47 Identities=26% Similarity=0.284 Sum_probs=41.3
Q ss_pred CCCCHHHHHHHHH---HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 8889779999999---9859997999999499988999999999998079
Q gi|254780694|r 184 FELTGREVECLTW---ISEGKTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 184 ~~LT~RE~eVl~l---ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
..|++||+.|+.+ --+|+|-+|||..||||...|+.--+++..||--
T Consensus 226 ~~L~eREr~Ii~~r~~~~e~~TL~EIg~~lgvSreRVRQIe~kAL~KLR~ 275 (289)
T PRK07500 226 QTLNERELFIIRERRLREDGATLEALGEELGISKERVRQIEARALEKLRR 275 (289)
T ss_pred HCCCHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 54999999999997668998589999999797999999999999999999
No 124
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=96.77 E-value=0.0034 Score=39.37 Aligned_cols=45 Identities=33% Similarity=0.355 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 889779999999985999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
-||+|+.+||++=.+|+|-.|||..|+.|...|..--++++.+..
T Consensus 4 ~Lt~~q~~vL~lR~~G~tQ~eIA~~lgTSraNvs~iEk~A~eNIe 48 (139)
T PRK03975 4 FLTERQIEVLRLRKRGLTQQEIADILGTSRANISIIEKRARENIE 48 (139)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 568999999999982897999999977328899999999999999
No 125
>PRK12423 LexA repressor; Provisional
Probab=96.75 E-value=0.0024 Score=40.32 Aligned_cols=44 Identities=27% Similarity=0.431 Sum_probs=38.6
Q ss_pred CCCHHHHHHHHHHHC-----C--CCHHHHHHHHCC-CHHHHHHHHHHHHHHH
Q ss_conf 889779999999985-----9--997999999499-9889999999999980
Q gi|254780694|r 185 ELTGREVECLTWISE-----G--KTSDEIAVILGI-SRNTVNNYIASIMRKT 228 (246)
Q Consensus 185 ~LT~RE~eVl~lia~-----G--~t~~eIA~~L~i-S~~TV~~hl~~i~~KL 228 (246)
.||+|+++||.++.+ | =|.+|||+.+++ |++||..|++.+-+|=
T Consensus 3 ~LT~kQ~~iL~fI~~~~~~~G~~Pt~rEI~~~~g~~S~~~v~~hl~~L~~kG 54 (202)
T PRK12423 3 TLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAG 54 (202)
T ss_pred CCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHCC
T ss_conf 2089999999999999996298988999999829998678999999999887
No 126
>pfam01726 LexA_DNA_bind LexA DNA binding domain. This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins. The aligned region contains a variant form of the helix-turn-helix DNA binding motif. This domain is found associated with pfam00717 the auto-proteolytic domain of LexA EC:3.4.21.88.
Probab=96.74 E-value=0.0036 Score=39.20 Aligned_cols=43 Identities=37% Similarity=0.548 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHHC-----C--CCHHHHHHHHCC-CHHHHHHHHHHHHHH
Q ss_conf 889779999999985-----9--997999999499-988999999999998
Q gi|254780694|r 185 ELTGREVECLTWISE-----G--KTSDEIAVILGI-SRNTVNNYIASIMRK 227 (246)
Q Consensus 185 ~LT~RE~eVl~lia~-----G--~t~~eIA~~L~i-S~~TV~~hl~~i~~K 227 (246)
.||+|+.+||.+|.+ | =|.+||+..+++ |++||..|++.+-+|
T Consensus 3 ~LT~rQ~~il~~I~~~~~~~G~~Pt~rEI~~~~g~~S~s~v~~~l~~Le~k 53 (65)
T pfam01726 3 PLTERQREVLDFIKASIEETGYPPSRREIAQALGLRSPNAAEEHLKALERK 53 (65)
T ss_pred CCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHC
T ss_conf 337999999999999999828898799999993899809999999999998
No 127
>PRK00215 LexA repressor; Validated
Probab=96.72 E-value=0.0035 Score=39.28 Aligned_cols=42 Identities=36% Similarity=0.521 Sum_probs=37.6
Q ss_pred CCHHHHHHHHHHHC-------CCCHHHHHHHHCC-CHHHHHHHHHHHHHH
Q ss_conf 89779999999985-------9997999999499-988999999999998
Q gi|254780694|r 186 LTGREVECLTWISE-------GKTSDEIAVILGI-SRNTVNNYIASIMRK 227 (246)
Q Consensus 186 LT~RE~eVl~lia~-------G~t~~eIA~~L~i-S~~TV~~hl~~i~~K 227 (246)
||+|+.+||+++.+ .=|.+|||+.+++ |++||..|++.+-+|
T Consensus 2 LT~kQ~~il~fI~~~~~~~g~~Ps~rEI~~~~g~~S~~tV~~~l~~Le~k 51 (204)
T PRK00215 2 LTARQQEILDFIKDRIEETGYPPSRREIADALGLRSPSAVHEHLKALERK 51 (204)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHC
T ss_conf 89899999999999999748899899999980999818999999999879
No 128
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=96.71 E-value=0.0019 Score=40.95 Aligned_cols=199 Identities=12% Similarity=0.059 Sum_probs=97.5
Q ss_pred HHHEEEEECCCCHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEECCCCCH
Q ss_conf 01100022144588887655302321379999732799999999999998719302300026663111232100068958
Q gi|254780694|r 5 IQQVNIVLNREDEQRTSFVSHLPTRSDLLARMIPLDCTVSWTMRMYALTEYVGASHFLLVRWDLFQEQKLDSIVSSDWPF 84 (246)
Q Consensus 5 ~~~~~~~l~r~d~~r~~~v~~l~~~~d~~~~l~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~ 84 (246)
|+|-+|++-.+|+.-...+...+..... .+..+.+..+....+. .. .+.....+..+.+..+.
T Consensus 1 M~~~kILiVEDd~~l~~~l~~~L~~~g~--~v~~~~~~~~al~~~~----~~-----------~~DlvilDi~LP~~~G~ 63 (229)
T PRK11083 1 MQQPTILLVEDEQAIADTLVYALQSEGF--TVEWFERGLPALDKLR----QQ-----------PPDLVILDVGLPDISGF 63 (229)
T ss_pred CCCCEEEEEECCHHHHHHHHHHHHHCCC--EEEEECCHHHHHHHHH----HC-----------CCCEEEECCCCCCCCHH
T ss_conf 9999999996999999999999998899--9999899999999997----18-----------99899973889998768
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCC--HHHHHHH
Q ss_conf 99999996698451738999985232443032543333214457147503373689999999717875469--8999999
Q gi|254780694|r 85 DLVRCMALSEKDKYYNVLQRPTELFCPVFHTLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIIL--RDRLWEI 162 (246)
Q Consensus 85 ~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~ 162 (246)
++++...... ..-|++ .........+.......++..|+.++++......-+........... .......
T Consensus 64 ~l~~~iR~~~--~~~pII------~lta~~~~~d~i~~l~~GADDYl~KPf~~~EL~aRi~a~lrR~~~~~~~~~~~~~~ 135 (229)
T PRK11083 64 ELCRQLRAFH--PALPVI------FLTARSDEVDRLVGLEIGADDYVAKPFSPREVAARVRTILRRVKKFAAPSPVIRIA 135 (229)
T ss_pred HHHHHHHHHC--CCCEEE------EEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEE
T ss_conf 8999999708--997299------98367898999999975998773087428999999999997643567777632564
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHHCCC
Q ss_conf 99999999754201467798888897799999999859----99799999949-----99889999999999980799
Q gi|254780694|r 163 GLLAAYQANMFKSYDVHWGKDFELTGREVECLTWISEG----KTSDEIAVILG-----ISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~LT~RE~eVl~lia~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLgv~ 231 (246)
. ..........-...+....||++|.++|.++++- .|-.+|-..+. .+.+||+.|++++++||...
T Consensus 136 ~---~~~ld~~~~~v~~~g~~i~LT~~E~~LL~~L~~~~g~vvsr~~L~~~vw~~~~~~~~rtidv~I~rLR~KL~~~ 210 (229)
T PRK11083 136 G---HFELDEPGARISYFGTPLSLTRYEFLLLKTLLLSPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRAI 210 (229)
T ss_pred C---CEEEECCCCEEEECCEECCCCHHHHHHHHHHHHCCCCEECHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf 7---88998786199999995459999999999998679940969999998559988888466999999999987526
No 129
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=96.71 E-value=0.005 Score=38.33 Aligned_cols=46 Identities=20% Similarity=0.226 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHHHH---HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999---85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI---SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li---a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|++||++|+.+- -+++|-+|||..||||...|+.--+++++||-
T Consensus 229 ~~L~~REr~Il~~Ry~~d~~~TL~EIg~~lgiSrERVRQIe~kAL~KLR 277 (284)
T PRK06596 229 ETLDERSRDIIEARWLDDDKSTLQELAAEYGVSAERIRQIEKNAMKKLK 277 (284)
T ss_pred HHCCHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 6099999999999767999948999999979799999999999999999
No 130
>PRK10766 DNA-binding transcriptional regulator TorR; Provisional
Probab=96.66 E-value=0.0017 Score=41.38 Aligned_cols=113 Identities=15% Similarity=0.136 Sum_probs=65.0
Q ss_pred HHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCH------HHHH--HHHHHHHHHHHHHHHCCCCCCCCCCCCHH
Q ss_conf 433332144571475033736899999997178754698------9999--99999999997542014677988888977
Q gi|254780694|r 118 ENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILR------DRLW--EIGLLAAYQANMFKSYDVHWGKDFELTGR 189 (246)
Q Consensus 118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~LT~R 189 (246)
+...+...++.+|+.++++......-+...-........ .... ....+...........-...+....||++
T Consensus 87 ~~i~al~~GaddYl~KPf~~~eL~ari~allrR~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~l~~~~~~i~LT~~ 166 (224)
T PRK10766 87 DRIVGLEMGADDYVTKPFELRELLVRVKNLLWRISLARQAQAVAEQPETQDNCYRFAGYCLNVNRRTLERNGEPIKLTKA 166 (224)
T ss_pred HHHHHHHCCCHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEECCEEEECCCCEEEECCEEEECCHH
T ss_conf 99999984941451399988999999999972524421121123466777876999999998888899989999867899
Q ss_pred HHHHHHHHHCC----CCHHHHHHHH-----CCCHHHHHHHHHHHHHHHCC
Q ss_conf 99999999859----9979999994-----99988999999999998079
Q gi|254780694|r 190 EVECLTWISEG----KTSDEIAVIL-----GISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 190 E~eVl~lia~G----~t~~eIA~~L-----~iS~~TV~~hl~~i~~KLgv 230 (246)
|.++|.++++- .|-.+|-..+ ..+.+||+.|++++++||+-
T Consensus 167 E~~lL~~L~~~~g~vvsre~L~~~vw~~~~~~~~~sid~~I~rLRkKl~~ 216 (224)
T PRK10766 167 EYELLVAFVTNPGQVLSRERLLRMLSHRVEDPNDRTIDVLIRRLRHKLNP 216 (224)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf 99999999967997396999999964888788847299999999976798
No 131
>PRK10701 DNA-binding transcriptional regulator RstA; Provisional
Probab=96.61 E-value=0.0015 Score=41.61 Aligned_cols=115 Identities=16% Similarity=0.058 Sum_probs=68.1
Q ss_pred HHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHH-HHHHHHHHHHH--HHHHH-----HHCCCCCCCCCCCCH
Q ss_conf 54333321445714750337368999999971787546989-99999999999--99754-----201467798888897
Q gi|254780694|r 117 PENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRD-RLWEIGLLAAY--QANMF-----KSYDVHWGKDFELTG 188 (246)
Q Consensus 117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~--~~~~~-----~~~~~~~~~~~~LT~ 188 (246)
.+.......++..|+.++++......-+...-......... ........... ....+ ...-...+....||+
T Consensus 85 ~d~v~gl~~GADDYl~KPf~~~eL~aRi~a~lrr~~~~~~~~~~~~~~~~~~~~~~~g~l~ld~~~~~v~~~g~~i~LT~ 164 (240)
T PRK10701 85 MNHILALEMGACDYILKTTPPAVLLARLRLHLRQNEQATQAKGLQETSLTPYKALHFGTLTIDPINRVVTLAGEEISLST 164 (240)
T ss_pred HHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEECCEEEECCCCEEEECCEEEECCH
T ss_conf 88999997688776417998799999999999653254443222345557664389877999888899999999987678
Q ss_pred HHHHHHHHHHCC----CCHHHHHHHH-----CCCHHHHHHHHHHHHHHHCCC
Q ss_conf 799999999859----9979999994-----999889999999999980799
Q gi|254780694|r 189 REVECLTWISEG----KTSDEIAVIL-----GISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 189 RE~eVl~lia~G----~t~~eIA~~L-----~iS~~TV~~hl~~i~~KLgv~ 231 (246)
+|.++|..+++- .|-.+|-+.+ ..+.+||+.|++++++||+-.
T Consensus 165 ~E~~lL~~L~~~~g~vvsre~L~~~vwg~~~~~~~rtvdv~I~rLRkKl~~~ 216 (240)
T PRK10701 165 ADFELLWELATHAGQIMDRDALLKNLRGVSYDGLDRSVDVAISRLRKKLLDN 216 (240)
T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf 9999999999779987389999998539887888678999999999987528
No 132
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=96.59 E-value=0.008 Score=36.97 Aligned_cols=53 Identities=28% Similarity=0.426 Sum_probs=47.6
Q ss_pred CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHH
Q ss_conf 8897799999999-----8599979999994999889999999999980799889999
Q gi|254780694|r 185 ELTGREVECLTWI-----SEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAI 237 (246)
Q Consensus 185 ~LT~RE~eVl~li-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav 237 (246)
.|++||++|+.+- .+-+|-.|||..|+||..-|+..-+++++||--++|.+-.
T Consensus 335 ~L~~REr~Ii~~RyGL~~~~~~TL~eIg~~lgvSrERVRQIE~kAL~KLR~~~~~~~l 392 (398)
T PRK05901 335 TLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTMRKLRHPSRSQVL 392 (398)
T ss_pred CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHH
T ss_conf 8999999999997589998960399999897969999999999999996783788799
No 133
>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional
Probab=96.58 E-value=0.0017 Score=41.29 Aligned_cols=111 Identities=11% Similarity=0.170 Sum_probs=71.9
Q ss_pred HHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 54333321445714750337368999999971787546989999999999999975420146779888889779999999
Q gi|254780694|r 117 PENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAYQANMFKSYDVHWGKDFELTGREVECLTW 196 (246)
Q Consensus 117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LT~RE~eVl~l 196 (246)
.....+...++..|+.++++.......+................ ............-...+....||++|.++|.+
T Consensus 85 ~~~~~al~~Gaddyl~KP~~~~eL~arv~~~lrr~~~~~~~~~~----~~~~~~d~~~~~~~~~g~~i~LT~~E~~LL~~ 160 (223)
T PRK10816 85 QDKVEVLSAGADDYVTKPFHIEEVMARMQALMRRNSGLASQVIS----LPPFQVDLSRRELSINDEVIKLTAFEYTIMET 160 (223)
T ss_pred HHHHHHHHCCCCEEECCCCCHHHHHHHHHHHHCCCCCCCCCEEE----ECCEEEEHHHCEEEECCEEEEECHHHHHHHHH
T ss_conf 78999998699886418977789999999996655578776188----78868711005898799899706899999999
Q ss_pred HHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHHCCC
Q ss_conf 9859----99799999949-----99889999999999980799
Q gi|254780694|r 197 ISEG----KTSDEIAVILG-----ISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 197 ia~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLgv~ 231 (246)
+.+- .|-.+|-+.+. .+.+||+.|++++.+||...
T Consensus 161 L~~~~~~vvsre~l~~~vw~~~~~~~~~sld~~I~rLRkKl~~~ 204 (223)
T PRK10816 161 LIRNNGKVVSKDSLMLQLYPDAELRESHTIDVLMGRLRKKIQAQ 204 (223)
T ss_pred HHHCCCEEECHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf 99879923839999998549987888677999999999974335
No 134
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=96.58 E-value=0.011 Score=36.10 Aligned_cols=54 Identities=26% Similarity=0.309 Sum_probs=47.4
Q ss_pred CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHH
Q ss_conf 8897799999999-----85999799999949998899999999999807998899999
Q gi|254780694|r 185 ELTGREVECLTWI-----SEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIA 238 (246)
Q Consensus 185 ~LT~RE~eVl~li-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~ 238 (246)
.|++||++|+.+- .+-+|-+||+..++||...|+.--+++++||--+.|.+-+.
T Consensus 345 ~L~~REr~IL~lRfGL~dg~~~TL~EIG~~lgISRERVRQIE~kAL~KLR~p~r~~~Lr 403 (410)
T PRK07598 345 DLTSRERDVIRMRFGLADGRTYSLAEIGRALDLSRERVRQIEAKALQKLRQPKRRNRIR 403 (410)
T ss_pred CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf 69999999999964899979668999998979699999999999999967737789999
No 135
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=96.53 E-value=0.0057 Score=37.94 Aligned_cols=43 Identities=28% Similarity=0.482 Sum_probs=37.8
Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 8889779999999985999799999949998899999999999
Q gi|254780694|r 184 FELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 184 ~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
..+...+..+..|...|+|..+||..++||..||..|++..+.
T Consensus 156 ~~~~~~~~~i~~~~~~g~s~~~iak~~gvsrsTvyR~lK~~~e 198 (200)
T PRK13413 156 YKLHGKEEVITKELKKGTTKSEIAKKLKVSRTTLARFLKTMYE 198 (200)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHC
T ss_conf 1247999999999988899999999989299999999974410
No 136
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=96.53 E-value=0.0072 Score=37.30 Aligned_cols=49 Identities=18% Similarity=0.108 Sum_probs=43.1
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 88897799999999-85999799999949998899999999999807998
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTATKT 232 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~ 232 (246)
..|||.|+.|+-|= ..|.++.|||+.|++|+.+|+..+.+..+||....
T Consensus 117 e~L~P~eRaa~vLrdvfg~~~~EIA~~Lg~s~~a~Rqll~RAR~~l~~~~ 166 (290)
T PRK09635 117 ERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKINESR 166 (290)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHCCC
T ss_conf 62998685455269860898899999968998999999999999873238
No 137
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family; InterPro: IPR014298 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 recognized by the major sigma factors , . This group of sigma factors 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.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=96.47 E-value=0.0036 Score=39.20 Aligned_cols=46 Identities=24% Similarity=0.305 Sum_probs=42.4
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8889779999999-985999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|||.|++|+.| .++|++++|||+.||+.++.|+.-..+.-+||-
T Consensus 122 ~~L~p~qq~viaLrF~~~L~~~EvA~ilGk~~gavk~Lq~rAv~~L~ 168 (171)
T TIGR02952 122 KKLTPKQQEVIALRFAQNLPIAEVARILGKTEGAVKALQFRAVKKLA 168 (171)
T ss_pred HHCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf 61083231203332116883878998726897468999999999987
No 138
>PRK05949 RNA polymerase sigma factor; Validated
Probab=96.47 E-value=0.0091 Score=36.63 Aligned_cols=48 Identities=21% Similarity=0.199 Sum_probs=42.1
Q ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Q ss_conf 888977999999998-----599979999994999889999999999980799
Q gi|254780694|r 184 FELTGREVECLTWIS-----EGKTSDEIAVILGISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 184 ~~LT~RE~eVl~lia-----~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~ 231 (246)
..|++||++|+.+-= +-+|-+|||..+|||..-|+.--+++++||-=+
T Consensus 265 ~~L~~REr~Ii~~RfGl~~~~~~TL~EIg~~lgiSrERVRQIE~rAL~KLR~~ 317 (327)
T PRK05949 265 AELTPQQREVLTLRFGLEDGKELSLAKVGQRLNLSRERVRQLEHQALAHLRRR 317 (327)
T ss_pred HCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHC
T ss_conf 56999999999997189996985799999998959999999999999998625
No 139
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=96.43 E-value=0.0093 Score=36.58 Aligned_cols=50 Identities=24% Similarity=0.374 Sum_probs=43.2
Q ss_pred CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCH
Q ss_conf 88897799999999-----859997999999499988999999999998079988
Q gi|254780694|r 184 FELTGREVECLTWI-----SEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTR 233 (246)
Q Consensus 184 ~~LT~RE~eVl~li-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R 233 (246)
..|++||++|+.+- .+.+|-+|||..+|||..-|+..-++++.||--.-+
T Consensus 264 ~~L~~REr~II~~RfGL~~~e~~TL~EIg~~lgvSRERVRQIE~~AL~KLR~~l~ 318 (328)
T PRK05657 264 FELNDKQREVIERRFGLNGYEAATLEEVAREIGLTRERVRQIQVEALRRLREILQ 318 (328)
T ss_pred HCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 0699999999999808899896059999989697999999999999999879999
No 140
>CHL00148 orf27 Ycf27; Reviewed
Probab=96.41 E-value=0.0016 Score=41.48 Aligned_cols=117 Identities=15% Similarity=0.113 Sum_probs=68.3
Q ss_pred CCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCH-HHHHHHHH--HHHHHHHHHHHCCCCCCCCCCCCHHHH
Q ss_conf 325433332144571475033736899999997178754698-99999999--999999754201467798888897799
Q gi|254780694|r 115 TLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILR-DRLWEIGL--LAAYQANMFKSYDVHWGKDFELTGREV 191 (246)
Q Consensus 115 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~LT~RE~ 191 (246)
...+.......++..|+.+++.......-+............ ........ ............-...+....||++|.
T Consensus 88 ~~~d~v~gl~~GADDYi~KPf~~~EL~aRi~allrr~~~~~~~~~~~~~~~l~~g~l~~d~~~~~v~~~g~~i~LT~~E~ 167 (240)
T CHL00148 88 DVSDRITGLELGADDYVVKPFSPKELEARIRSVLRRVNKISATSGPKNSGIIRIGFLEIDTNKKQVYKNNERIRLTGMEF 167 (240)
T ss_pred CHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEECCEEEECCCCEEEECCEEEECCHHHH
T ss_conf 98999999976997895278447999999999986630344556677786599878999878899998999986589999
Q ss_pred HHHHHHHCC----CCHHHHHHHHC-------CCHHHHHHHHHHHHHHHCCC
Q ss_conf 999999859----99799999949-------99889999999999980799
Q gi|254780694|r 192 ECLTWISEG----KTSDEIAVILG-------ISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 192 eVl~lia~G----~t~~eIA~~L~-------iS~~TV~~hl~~i~~KLgv~ 231 (246)
++|.++++- .|-.+|-+.+. .+.+||+.|++++++||+..
T Consensus 168 ~lL~~L~~~~g~vvsre~L~~~vWg~~~~~~~~~r~vdv~I~rLRkKl~~~ 218 (240)
T CHL00148 168 SLLELLISESGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLEDD 218 (240)
T ss_pred HHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf 999999967997496999999972888766787557999999999974107
No 141
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=96.39 E-value=0.016 Score=35.04 Aligned_cols=54 Identities=28% Similarity=0.430 Sum_probs=47.6
Q ss_pred CCCHHHHHHHHHHH---CC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHH
Q ss_conf 88977999999998---59--99799999949998899999999999807998899999
Q gi|254780694|r 185 ELTGREVECLTWIS---EG--KTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIA 238 (246)
Q Consensus 185 ~LT~RE~eVl~lia---~G--~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~ 238 (246)
.|++||++|+.+-= .| +|-+|||..|+||...|+..-+.+++||--.+|.+-..
T Consensus 323 ~L~eREr~II~lRfGL~dg~~~TL~EIg~~lgISRERVRQIE~rAL~KLR~p~r~~~L~ 381 (385)
T PRK07406 323 TLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLK 381 (385)
T ss_pred CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf 49999999999975899999646999998979599999999999999967717789999
No 142
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=96.37 E-value=0.013 Score=35.72 Aligned_cols=52 Identities=25% Similarity=0.357 Sum_probs=45.5
Q ss_pred CCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHH
Q ss_conf 88977999999998-----59997999999499988999999999998079988999
Q gi|254780694|r 185 ELTGREVECLTWIS-----EGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGA 236 (246)
Q Consensus 185 ~LT~RE~eVl~lia-----~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~ea 236 (246)
.|++||++|+.+-= +-+|-+|||..+|||..-|+.--+++++||--+.|.+-
T Consensus 258 ~L~eREr~IL~~RfGl~~~~~~TL~EIg~~lgvSrERVRQIE~~AL~KLR~~~~~~~ 314 (320)
T PRK07921 258 TLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRHGERADR 314 (320)
T ss_pred CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHH
T ss_conf 599999999999748999897479999989796999999999999999707288888
No 143
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=96.33 E-value=0.0057 Score=37.94 Aligned_cols=46 Identities=26% Similarity=0.245 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 8897799999999-859997999999499988999999999998079
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
.|+|+|+.|+-|- ..|.+++|||+.|++|+.+||+.+.+....|..
T Consensus 156 ~Lpp~QRavlvLRdV~g~s~~EiAe~Lg~S~aAVks~L~RARa~L~~ 202 (341)
T PRK08241 156 HLPPRQRAVLLLRDVLGWSAAEVAEALGTSTAAVNSALQRARATLAE 202 (341)
T ss_pred HCCHHHHEEEEHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 39997902001297529988999999789999999999999999986
No 144
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=96.32 E-value=0.012 Score=35.97 Aligned_cols=47 Identities=23% Similarity=0.195 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 888977999999998-----59997999999499988999999999998079
Q gi|254780694|r 184 FELTGREVECLTWIS-----EGKTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 184 ~~LT~RE~eVl~lia-----~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
..|++||++|+.+-= +-+|-+|||..++||...|+..-++++.||-=
T Consensus 256 ~~L~eREr~II~lRfGl~~~~~~TL~EIg~~lgvSrERVRQIE~~AL~KLR~ 307 (318)
T PRK07405 256 ADLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK 307 (318)
T ss_pred HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 6299989999999807789897479999989795999999999999999987
No 145
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=96.25 E-value=0.017 Score=34.84 Aligned_cols=53 Identities=26% Similarity=0.379 Sum_probs=46.4
Q ss_pred CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHH
Q ss_conf 88897799999999-----859997999999499988999999999998079988999
Q gi|254780694|r 184 FELTGREVECLTWI-----SEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGA 236 (246)
Q Consensus 184 ~~LT~RE~eVl~li-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~ea 236 (246)
..|++||++|+.+- .+-+|-.|||..++||..-|+.--+++++||-=++|..-
T Consensus 305 ~~L~~REr~Il~~RfGL~~~~~~TLeEIg~~lgvSRERVRQIE~kAL~KLR~~~~~~~ 362 (368)
T PRK09210 305 DTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQ 362 (368)
T ss_pred HCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHH
T ss_conf 1799999999999759996896149999989697989999999999999767368789
No 146
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=96.22 E-value=0.077 Score=30.67 Aligned_cols=102 Identities=18% Similarity=0.087 Sum_probs=61.2
Q ss_pred HHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCC-CCCCCH-HHHHHHHHHH
Q ss_conf 33214457147503373689999999717875469899999999999999754201467798-888897-7999999998
Q gi|254780694|r 121 TPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAYQANMFKSYDVHWGK-DFELTG-REVECLTWIS 198 (246)
Q Consensus 121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~LT~-RE~eVl~lia 198 (246)
.+.+.+.-+|+.+++...+...++.........+....-.....+-........ .....+ +-+|++ ....|.+++.
T Consensus 91 ~alr~Gv~DYLiKPf~~eRl~~aL~~y~~~r~~l~~~~~~sQ~~lD~l~~~~~k--~~~~~~LPkGi~~~Tl~~i~~~~~ 168 (224)
T COG4565 91 EALRYGVVDYLIKPFTFERLQQALTRYRQKRHALESHQQLSQKELDQLFNIQSK--EQPPDDLPKGLDELTLQKVREALK 168 (224)
T ss_pred HHHHCCCHHHEECCEEHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCC--CCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 999658232205634099999999999999999862010279999999832254--567554787767999999999986
Q ss_pred ---CCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf ---59997999999499988999999999
Q gi|254780694|r 199 ---EGKTSDEIAVILGISRNTVNNYIASI 224 (246)
Q Consensus 199 ---~G~t~~eIA~~L~iS~~TV~~hl~~i 224 (246)
+++|..|.|+.++||.-|++.|+.-.
T Consensus 169 ~~~~~~Taeela~~~giSRvTaRRYLeyl 197 (224)
T COG4565 169 EPDQELTAEELAQALGISRVTARRYLEYL 197 (224)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 75776479999988372199999999999
No 147
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=96.14 E-value=0.005 Score=38.30 Aligned_cols=115 Identities=11% Similarity=0.135 Sum_probs=68.8
Q ss_pred HHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH-H---HHCCCCCCCCCCCCHHHHH
Q ss_conf 54333321445714750337368999999971787546989999999999999975-4---2014677988888977999
Q gi|254780694|r 117 PENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAYQANM-F---KSYDVHWGKDFELTGREVE 192 (246)
Q Consensus 117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~---~~~~~~~~~~~~LT~RE~e 192 (246)
.+.......++.+|+.+++.......-+...-........................ + ...-...+....||++|.+
T Consensus 84 ~d~i~~l~~GADDYl~KPf~~~eL~ari~allrR~~~~~~~~~~~~~~~~~~~~~l~ld~~~~~~~~~~~~i~LT~~E~~ 163 (232)
T PRK10955 84 LDRVLGLELGADDYLPKPFNDRELVARIRAILRRSHWSEQQQNNDNGSPTLEVDALSLNPGRQEASFDGQTLELTGTEFT 163 (232)
T ss_pred HHHHHHHHCCCCEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEECCEEEECCCCEEEECCEEEECCHHHHH
T ss_conf 88999997697576338999899999999997615431001235678856998989998787799999999966899999
Q ss_pred HHHHHHCC----CCHHHHHHHH-----CCCHHHHHHHHHHHHHHHCCC
Q ss_conf 99999859----9979999994-----999889999999999980799
Q gi|254780694|r 193 CLTWISEG----KTSDEIAVIL-----GISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 193 Vl~lia~G----~t~~eIA~~L-----~iS~~TV~~hl~~i~~KLgv~ 231 (246)
+|.++++- .|-.+|-+.+ ..+.+||+.|++++++||+-.
T Consensus 164 lL~~L~~~~g~vvsre~L~~~vwg~~~~~~~rtidv~I~rLRkKL~~~ 211 (232)
T PRK10955 164 LLYLLAQHLGQVVSREHLSQEVLGKRLTPFDRAIDMHISNLRRKLPDR 211 (232)
T ss_pred HHHHHHHCCCCEECHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCC
T ss_conf 999999789950979999999718898888582999999999954116
No 148
>pfam08279 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins.
Probab=96.11 E-value=0.014 Score=35.40 Aligned_cols=41 Identities=24% Similarity=0.342 Sum_probs=32.7
Q ss_pred HHHHHHHHHH--CC-CCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 7999999998--59-997999999499988999999999998079
Q gi|254780694|r 189 REVECLTWIS--EG-KTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 189 RE~eVl~lia--~G-~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
|..+++.++- ++ .|..+||+.|+||.+||..+++.+- +.|+
T Consensus 1 R~~~il~~L~~~~~~vt~~~La~~l~VSr~TV~rdi~~L~-~~G~ 44 (55)
T pfam08279 1 RLLQILELLLQAREPISGQELAEKLGVSRRTIRRDIKALE-ALGV 44 (55)
T ss_pred CHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHH-HCCC
T ss_conf 9899999999769991899999996988999999999999-8899
No 149
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=96.09 E-value=0.0073 Score=37.23 Aligned_cols=60 Identities=18% Similarity=0.280 Sum_probs=55.2
Q ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC
Q ss_conf 977999999998599979999994999889999999999980799889999999975898
Q gi|254780694|r 187 TGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNIV 246 (246)
Q Consensus 187 T~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~Gli 246 (246)
|+=|.+|..+-+-|.|-..||+.|+|+.+|=|.++.+|++++|++||-++.......|++
T Consensus 147 ~~~~~~vf~~Ys~G~SH~~ia~~L~It~~sSkn~~s~i~k~~gissrde~l~~l~~s~~~ 206 (220)
T PRK13719 147 TSIQYDVFILYSFGFSHNSIASLLNITNGSSKNKISEILKFFGISSRDELLIILHTSEMI 206 (220)
T ss_pred EEEEEEEEEEEECCCCHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf 200466898875242468899884741354077999999972988599999999997689
No 150
>PRK10529 DNA-binding transcriptional activator KdpE; Provisional
Probab=96.09 E-value=0.0043 Score=38.70 Aligned_cols=112 Identities=13% Similarity=0.135 Sum_probs=68.2
Q ss_pred HHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHH
Q ss_conf 543333214457147503373689999999717875-4698999999999999997542014677988888977999999
Q gi|254780694|r 117 PENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGR-IILRDRLWEIGLLAAYQANMFKSYDVHWGKDFELTGREVECLT 195 (246)
Q Consensus 117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LT~RE~eVl~ 195 (246)
.+.......++..|+.++++......-+...-.... .......... ...........-...+....||++|.++|.
T Consensus 85 ~d~i~~l~~GADDYl~KPf~~~eL~aRi~a~lrr~~~~~~~~~~~~~---~~l~~d~~~~~v~~~g~~i~LT~~E~~lL~ 161 (225)
T PRK10529 85 SDKIAALDAGADDYLSKPFGIGELQARLRVALRRHSATPAPDPLVKF---SDVTVDLAARVIHRGEEEVHLTPIEFRLLA 161 (225)
T ss_pred HHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCEEEE---CCEEEECCCCEEEECCCCCCCCHHHHHHHH
T ss_conf 99999997698765407854599999999997140378887864999---999999033999999961313668999999
Q ss_pred HHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHHCCC
Q ss_conf 99859----99799999949-----99889999999999980799
Q gi|254780694|r 196 WISEG----KTSDEIAVILG-----ISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 196 lia~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLgv~ 231 (246)
++.+- .|-.+|-..+. .+.+||+.|++++++||+..
T Consensus 162 ~L~~~~g~vvsre~L~~~vw~~~~~~~~~~idv~I~rLRkKl~~~ 206 (225)
T PRK10529 162 VLLNNAGKVLTQRQLLNQVWGPNAVEHSHYLRIYMGHLRQKLEQD 206 (225)
T ss_pred HHHHCCCCEECHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf 999779961969999999649998988687999999999972007
No 151
>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=96.06 E-value=0.014 Score=35.45 Aligned_cols=40 Identities=33% Similarity=0.487 Sum_probs=33.8
Q ss_pred CCCCCCHHH-HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 888889779-9999999859997999999499988999999
Q gi|254780694|r 182 KDFELTGRE-VECLTWISEGKTSDEIAVILGISRNTVNNYI 221 (246)
Q Consensus 182 ~~~~LT~RE-~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl 221 (246)
+...||+-+ .++.++++.|.|..+||..++||..|+..|+
T Consensus 2 R~~~lt~~q~~~ar~l~~~G~~~~~iA~~~GVsr~Tiyr~l 42 (42)
T cd00569 2 RPPKLTPEQIEEARRLLAAGESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHC
T ss_conf 89869999999999999978989999999797999998659
No 152
>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=96.03 E-value=0.018 Score=34.74 Aligned_cols=41 Identities=29% Similarity=0.409 Sum_probs=36.8
Q ss_pred CC-HHHHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 89-7799999999859-99799999949998899999999999
Q gi|254780694|r 186 LT-GREVECLTWISEG-KTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 186 LT-~RE~eVl~lia~G-~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
|+ +.-.+|+..+.+| +|..|||+.+++|..||..|++.+.+
T Consensus 4 l~~~~r~~Il~~L~~~~~~~~eia~~l~is~~~vs~hL~~L~~ 46 (78)
T cd00090 4 LSDPTRLRILRLLLEGPLTVSELAERLGLSQSTVSRHLKKLEE 46 (78)
T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 2799999999999848906999987778487899999999998
No 153
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=96.00 E-value=0.021 Score=34.36 Aligned_cols=45 Identities=33% Similarity=0.360 Sum_probs=40.8
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8897799999999-85999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.|.+||+.|+.+. -+++|-+|||..|+||+.+|..-.+.+..||-
T Consensus 196 ~L~EREk~Vl~l~y~eelt~kEI~~~LgISes~VSql~kkai~kLr 241 (247)
T COG1191 196 PLPEREKLVLVLRYKEELTQKEIAEVLGISESRVSRLHKKAIKKLR 241 (247)
T ss_pred CCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 6689999999999970157999999949149899999999999999
No 154
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=95.88 E-value=0.013 Score=35.61 Aligned_cols=42 Identities=26% Similarity=0.295 Sum_probs=36.7
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 999999985999799999949998899999999999807998
Q gi|254780694|r 191 VECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKT 232 (246)
Q Consensus 191 ~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~ 232 (246)
....+|-..|+|..|||.+|++|..|+.+-+.+.+.+..+..
T Consensus 9 ~kA~eLk~~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~~~ 50 (203)
T COG0856 9 KKARELKSKGLTTGEIADELNVSRETATWLLTRAFKKESVPA 50 (203)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCCC
T ss_conf 999999877985777676641048778888754431147888
No 155
>PRK13856 two-component response regulator VirG; Provisional
Probab=95.79 E-value=0.011 Score=36.14 Aligned_cols=114 Identities=11% Similarity=0.123 Sum_probs=65.4
Q ss_pred HHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH-HHHHCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 433332144571475033736899999997178754698999999999999997-5420146779888889779999999
Q gi|254780694|r 118 ENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAYQAN-MFKSYDVHWGKDFELTGREVECLTW 196 (246)
Q Consensus 118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~LT~RE~eVl~l 196 (246)
+.......++..|+.++++......-+...-....................... ...+.-...+....||++|.++|.+
T Consensus 87 d~i~~l~~GADDYl~KPf~~~EL~aRi~~~lrr~~~~~~~~~~~~~~~~~~~ld~~~~~l~~~~~~~v~LT~~E~~lL~~ 166 (241)
T PRK13856 87 DKVVALELGATDFIAKPFGTREFLARIRVALRVRPNVVRTKDRRSFCFADWTLNLRQRRLISEAGGEVKLTAGEFNLLVA 166 (241)
T ss_pred HHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEECCEEEECCCCEEEEECCEEEECCHHHHHHHHH
T ss_conf 99999876998899777677799999999987454656777674499899999757878999799698678899999999
Q ss_pred HHCC----CCHHHHHHHH-----CCCHHHHHHHHHHHHHHHCCC
Q ss_conf 9859----9979999994-----999889999999999980799
Q gi|254780694|r 197 ISEG----KTSDEIAVIL-----GISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 197 ia~G----~t~~eIA~~L-----~iS~~TV~~hl~~i~~KLgv~ 231 (246)
+++- .|-.+|-..+ ..+.+|++.|++++++||.-.
T Consensus 167 L~~~~~~vvsRe~L~~~~~~~~~~~~~r~id~~I~rLRkKL~~~ 210 (241)
T PRK13856 167 FLEKPRDVLSREQLLIASRVREEEVYDRSIDVLILRLRRKLEQD 210 (241)
T ss_pred HHHCCCCEEEHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf 98769943819999998445677888686999999999973138
No 156
>pfam02001 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function.
Probab=95.70 E-value=0.033 Score=33.07 Aligned_cols=46 Identities=33% Similarity=0.395 Sum_probs=43.3
Q ss_pred CCCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 888897799999999-8599979999994999889999999999980
Q gi|254780694|r 183 DFELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 183 ~~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
...||.-|.|.++|+ -+|++-.|-|..++||..|+..-+.++.+|+
T Consensus 34 ~v~L~~dE~EAiRL~D~egl~QeeaA~~MgVSR~Tf~ril~~ARkKv 80 (100)
T pfam02001 34 KVIITLDEFEAIRLVDYEDYTQEEAAKLMGISRRTVWRLLTSARKKI 80 (100)
T ss_pred EEEECHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf 38734999999998736079899999884976999999999999999
No 157
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family.
Probab=95.68 E-value=0.021 Score=34.36 Aligned_cols=44 Identities=39% Similarity=0.407 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHH---H--HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 889779999999---9--8599979999994999889999999999980
Q gi|254780694|r 185 ELTGREVECLTW---I--SEGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 185 ~LT~RE~eVl~l---i--a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
.|||+|++||.| + .+.+|-+||++.|+||..=|+.-=+.+++||
T Consensus 287 ~L~p~e~~VL~LRfGL~~~~~~TL~eiG~~l~lSRERVRQiE~~AL~kL 335 (336)
T TIGR02997 287 ELTPRERQVLRLRFGLDDGEPLTLAEIGERLNLSRERVRQIEAKALRKL 335 (336)
T ss_pred HCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
T ss_conf 3798899999985789989753278999883883688889999997534
No 158
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=95.62 E-value=0.037 Score=32.73 Aligned_cols=44 Identities=30% Similarity=0.366 Sum_probs=39.8
Q ss_pred CCCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 888977999999998---59997999999499988999999999998
Q gi|254780694|r 184 FELTGREVECLTWIS---EGKTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 184 ~~LT~RE~eVl~lia---~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
++||+.+.+|+.-+. .++|..+||..|++|..||..-++|+..+
T Consensus 23 ~GLs~~Dv~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~ 69 (126)
T COG3355 23 YGLSELDVEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEA 69 (126)
T ss_pred HCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 38968899999999864699579999999783199999999999985
No 159
>PRK11173 two-component response regulator; Provisional
Probab=95.57 E-value=0.053 Score=31.74 Aligned_cols=112 Identities=15% Similarity=0.188 Sum_probs=64.2
Q ss_pred HHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCC--CCCCCHHHHHHHHHHHHHHHH----HH--HHCCCCCCCCCCCCHH
Q ss_conf 433332144571475033736899999997178--754698999999999999997----54--2014677988888977
Q gi|254780694|r 118 ENITPPAGMDNRYCSLTFDVARIRIGLMLLFPK--GRIILRDRLWEIGLLAAYQAN----MF--KSYDVHWGKDFELTGR 189 (246)
Q Consensus 118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~----~~--~~~~~~~~~~~~LT~R 189 (246)
+...+...++..|..++++......-+...-.. ............ ...... .. +..-...+....||++
T Consensus 88 ~~i~~l~~GaddYi~KPf~~~EL~arv~~~l~r~~~~~~~~~~~~~~---~~~~~~~~~ld~~~~~l~~~~g~~i~Lt~~ 164 (237)
T PRK11173 88 DKILGLEIGADDYITKPFNPRELTIRARNLLSRTMNLGTVSEERRSV---ESYKFNGWELDINSRSLISPDGEQYKLPRS 164 (237)
T ss_pred HHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCC---CEEEECCEEEECCCCEEEECCCEEEECCHH
T ss_conf 89999976976788789887999999999986641356653334665---438988899972684799719979976999
Q ss_pred HHHHHHHHHCC----CCHHHHHHHH-----CCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 99999999859----9979999994-----9998899999999999807998
Q gi|254780694|r 190 EVECLTWISEG----KTSDEIAVIL-----GISRNTVNNYIASIMRKTATKT 232 (246)
Q Consensus 190 E~eVl~lia~G----~t~~eIA~~L-----~iS~~TV~~hl~~i~~KLgv~~ 232 (246)
|.++|.++++- .|-.+|-..+ ..+.+||+.|++++++||+...
T Consensus 165 E~~lL~~L~~~~~~vvsR~~L~~~vwg~~~~~~~r~ld~~I~rLRkKl~~~~ 216 (237)
T PRK11173 165 EFRAMLHFCENPGKIQSRAELLKKMTGRELKPHDRTVDVTIRRIRKHFESTP 216 (237)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf 9999999986799876899999996198878885869999999999765279
No 160
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=95.49 E-value=0.038 Score=32.67 Aligned_cols=51 Identities=35% Similarity=0.426 Sum_probs=43.6
Q ss_pred CCHHHHHHHHH---H--HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC-CCCHHHH
Q ss_conf 89779999999---9--85999799999949998899999999999807-9988999
Q gi|254780694|r 186 LTGREVECLTW---I--SEGKTSDEIAVILGISRNTVNNYIASIMRKTA-TKTRSGA 236 (246)
Q Consensus 186 LT~RE~eVl~l---i--a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg-v~~R~ea 236 (246)
|||||+.|+.+ + -+++|-.+|+..++||..-|+...+++++||- ..++..-
T Consensus 280 Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~vsrERvRQIE~kAl~KLr~~~~~~~~ 336 (342)
T COG0568 280 LTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRKLRRHPERSAL 336 (342)
T ss_pred CCHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999999556799955199999895986999999999999999870632227
No 161
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1; InterPro: IPR014326 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 recognized by the major sigma factors , . This group of sigma factors are members of the sigma-70 family (IPR014284 from INTERPRO) and are apparently found only in the Planctomycetaceae family including the genus s Gemmata and Pirellula, in which seven sequences are found.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=95.38 E-value=0.042 Score=32.37 Aligned_cols=46 Identities=17% Similarity=0.112 Sum_probs=39.0
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8889779999999-985999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|.+-.+||+.| ..+|+|+.|||..++.|+.+|.--.-+..+||-
T Consensus 140 ~~L~e~~REvi~LR~~EGLS~~EvA~~Md~~~~av~~l~~Ral~~Lr 186 (190)
T TIGR02984 140 AKLPEDYREVILLRHLEGLSFAEVAERMDRSEGAVSMLWVRALARLR 186 (190)
T ss_pred HHCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 64792258999998760355589998707975898758999999998
No 162
>pfam01371 Trp_repressor Trp repressor protein. This protein binds to tryptophan and represses transcription of the Trp operon.
Probab=95.32 E-value=0.026 Score=33.75 Aligned_cols=40 Identities=25% Similarity=0.165 Sum_probs=32.2
Q ss_pred CCCHHHH-------HHHH-HHHCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 8897799-------9999-99859997999999499988999999999
Q gi|254780694|r 185 ELTGREV-------ECLT-WISEGKTSDEIAVILGISRNTVNNYIASI 224 (246)
Q Consensus 185 ~LT~RE~-------eVl~-lia~G~t~~eIA~~L~iS~~TV~~hl~~i 224 (246)
-+||.|+ +|++ ++..|+|+++|+..+++|..||-.-=+.+
T Consensus 26 l~T~~E~~ala~R~~va~~LL~~~~syreI~~~~g~S~aTItRvsr~L 73 (88)
T pfam01371 26 LLTPDEREALAQRLRIAKELLRGELSQREIAQELGASIATITRGSNCL 73 (88)
T ss_pred HCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 399999999999999999999789989999998598523147889998
No 163
>pfam00486 Trans_reg_C Transcriptional regulatory protein, C terminal.
Probab=95.26 E-value=0.043 Score=32.29 Aligned_cols=49 Identities=22% Similarity=0.365 Sum_probs=42.9
Q ss_pred CCCCCHHHHHHHHHHHCC----CCHHHHHHHH-----CCCHHHHHHHHHHHHHHHCCC
Q ss_conf 888897799999999859----9979999994-----999889999999999980799
Q gi|254780694|r 183 DFELTGREVECLTWISEG----KTSDEIAVIL-----GISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 183 ~~~LT~RE~eVl~lia~G----~t~~eIA~~L-----~iS~~TV~~hl~~i~~KLgv~ 231 (246)
...||++|.++|..+.+- .|..+|.+.+ ..|.++|+.|+.++.+||+..
T Consensus 3 ~i~Lt~~E~~lL~~L~~~~~~~vsr~~l~~~iw~~~~~~~~~sl~~~I~rLR~kl~~~ 60 (77)
T pfam00486 3 EVELTPKEFDLLELLARNPGRVVSREELLEEVWGEDFDVDDNTVDVHISRLRKKLEDD 60 (77)
T ss_pred EEECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf 7233899999999999679971979999999638766655330999999999987544
No 164
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=95.18 E-value=0.052 Score=31.76 Aligned_cols=40 Identities=23% Similarity=0.268 Sum_probs=22.3
Q ss_pred HHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 77999999998--59997999999499988999999999998
Q gi|254780694|r 188 GREVECLTWIS--EGKTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 188 ~RE~eVl~lia--~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
+++..|+.++. .+.|-.|||.+|+||+.+|+.|+.++-.+
T Consensus 11 ~tr~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~ 52 (218)
T COG2345 11 STRERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAE 52 (218)
T ss_pred CHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 589999999831698249999988599989999999999868
No 165
>pfam01022 HTH_5 Bacterial regulatory protein, arsR family. Members of this family contains a DNA binding 'helix-turn-helix' motif. This family includes other proteins which are not included in the Prosite definition.
Probab=95.18 E-value=0.059 Score=31.42 Aligned_cols=39 Identities=31% Similarity=0.420 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 7799999999859-99799999949998899999999999
Q gi|254780694|r 188 GREVECLTWISEG-KTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 188 ~RE~eVl~lia~G-~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
|.=.+|+.++++| ++..||+..+++|..||..|++.++.
T Consensus 2 p~Rl~Il~~L~~~~~~v~el~~~l~~sq~~vS~HL~~L~~ 41 (47)
T pfam01022 2 PTRLKILYLLSEGELCVCELAEILGLSQSTVSHHLKKLRE 41 (47)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 5899999999808996999999989588699999999989
No 166
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=95.08 E-value=0.05 Score=31.89 Aligned_cols=52 Identities=21% Similarity=0.328 Sum_probs=44.0
Q ss_pred CCCCCCCHHHHHHHHHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHHCCCC
Q ss_conf 98888897799999999859----99799999949-----998899999999999807998
Q gi|254780694|r 181 GKDFELTGREVECLTWISEG----KTSDEIAVILG-----ISRNTVNNYIASIMRKTATKT 232 (246)
Q Consensus 181 ~~~~~LT~RE~eVl~lia~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLgv~~ 232 (246)
+....||++|.++|.++.+- .|-.+|.+.+. .+.++|+.|++++.+||+-..
T Consensus 19 ~~~i~Lt~~E~~lL~~L~~~~~~vvsr~~l~~~vw~~~~~~~~~~l~~~I~rLRkkl~~~~ 79 (95)
T cd00383 19 GEPVELTPKEFELLELLARNPGRVLSREQLLEAVWGDDYDVDDRTVDVHISRLRKKLEDDP 79 (95)
T ss_pred CEEEECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf 9998779999999999987799745699999985397645574549999999999975268
No 167
>pfam09862 DUF2089 Protein of unknown function(DUF2089). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=95.06 E-value=0.18 Score=28.30 Aligned_cols=66 Identities=21% Similarity=0.182 Sum_probs=50.6
Q ss_pred CCCCCCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC--------CHHHHHHHHHHCCCC
Q ss_conf 988888977999999998-599979999994999889999999999980799--------889999999975898
Q gi|254780694|r 181 GKDFELTGREVECLTWIS-EGKTSDEIAVILGISRNTVNNYIASIMRKTATK--------TRSGAIAYAVRNNIV 246 (246)
Q Consensus 181 ~~~~~LT~RE~eVl~lia-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~--------~R~eav~~A~~~Gli 246 (246)
+....||+-+.+-+.... ..-+-+++|..|+||-.||++.+..|..|||-. ...+-|--+.+.|-|
T Consensus 29 ~~f~~L~~E~l~Fi~~fi~~~Gnlke~~~~lgiSYpTvR~rLd~ii~~lGy~~~~~~~~~~~~~eIL~~Le~GEI 103 (113)
T pfam09862 29 CKFCRLTPEQLEFVELFIKCRGNIKEVEKELGISYPTVRNRLDEIIAALGYEEEPEPEKRVDKKEILDKLEKGEI 103 (113)
T ss_pred CHHHCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCC
T ss_conf 065238999999999999916889999999788818899999999998089877777776229999999984997
No 168
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=95.06 E-value=0.013 Score=35.58 Aligned_cols=32 Identities=31% Similarity=0.298 Sum_probs=27.1
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 98599979999994999889999999999980
Q gi|254780694|r 197 ISEGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 197 ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
---|+|..+||..||+++.||++|++.--.+.
T Consensus 58 ekag~Ti~EIAeelG~TeqTir~hlkgetkAG 89 (182)
T COG1318 58 EKAGMTISEIAEELGRTEQTVRNHLKGETKAG 89 (182)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHCCHHHH
T ss_conf 87037499999996877999999975140331
No 169
>PRK04217 hypothetical protein; Provisional
Probab=94.95 E-value=0.079 Score=30.61 Aligned_cols=45 Identities=33% Similarity=0.401 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 88897799999999-8599979999994999889999999999980
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
..||.-|.|.++|+ -+|++-.|.|...+||..|+..-+.++.+|+
T Consensus 41 V~LtvdE~EaiRL~D~egl~qeeaA~~M~VSR~Tf~ril~~AR~Kv 86 (110)
T PRK04217 41 IIMTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKV 86 (110)
T ss_pred EEECHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf 5611999999998736079899999884976999999999999999
No 170
>pfam03444 DUF293 Domain of unknown function. This domain is always found with a pair of CBS domains pfam00571. this region may be distantly related to the HrcA proteins of prokaryotes (Bateman A pers. obs.).
Probab=94.94 E-value=0.063 Score=31.22 Aligned_cols=45 Identities=33% Similarity=0.399 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHC-----C--CCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 889779999999985-----9--997999999499988999999999998079
Q gi|254780694|r 185 ELTGREVECLTWISE-----G--KTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 185 ~LT~RE~eVl~lia~-----G--~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
.||+++++||.-+-+ | -.+++||+.+++|+.||++.+..+ +.||.
T Consensus 1 ~LT~~Qr~IL~aLI~lY~~~~~pVks~~IAe~l~~spgTIRN~M~~L-~~LGL 52 (79)
T pfam03444 1 ELTPVQKEILQALINLYRKKGRAVKGEEIADIIGRNPGTVRNQMQSL-KALGL 52 (79)
T ss_pred CCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHH-HHCCC
T ss_conf 97789999999999999972998667999999878908899999999-98588
No 171
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor; InterPro: IPR014209 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 recognized by the major sigma factors , . 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 homologue sigma-E (sigma-29, see IPR014200 from INTERPRO), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note: that in Bacillus subtilis (and apparently also in 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 .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=94.87 E-value=0.042 Score=32.38 Aligned_cols=45 Identities=42% Similarity=0.566 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHH---HHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 889779999999---9859--99799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTW---ISEG--KTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~l---ia~G--~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
-|++||++|+.. +.+| +|=+|||..||||..=|-.-=+++..||-
T Consensus 175 ~L~~rE~~vi~~RyGL~~~~~~tQREIA~~LgISRSYVSRIEK~Al~Kl~ 224 (228)
T TIGR02846 175 VLKGREREVIEMRYGLKDGREKTQREIAKILGISRSYVSRIEKKALKKLY 224 (228)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf 74088899998743668889541789987708650045488899999998
No 172
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=94.82 E-value=0.034 Score=32.99 Aligned_cols=44 Identities=30% Similarity=0.431 Sum_probs=37.2
Q ss_pred CCCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 888977999999998---59997999999499988999999999998
Q gi|254780694|r 184 FELTGREVECLTWIS---EGKTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 184 ~~LT~RE~eVl~lia---~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
.+|-+-|..|-.|+. .|+..+||+.+|+||.+||+.|+.+.|+|
T Consensus 17 ~glk~~eI~IY~lLve~~~~mri~ei~rEl~is~rtvr~~v~~l~rr 63 (113)
T COG5625 17 IGLKKNEIRIYSLLVEKGRGMRIREIQRELGISERTVRAAVAVLLRR 63 (113)
T ss_pred CCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 17783300155689884677417899999829999999999999985
No 173
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family; InterPro: IPR012845 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 recognized by the major sigma factors , . 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.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0045449 regulation of transcription.
Probab=94.68 E-value=0.089 Score=30.27 Aligned_cols=47 Identities=26% Similarity=0.311 Sum_probs=41.5
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 88897799999999-859997999999499988999999999998079
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
..||+||+=|+.|. -+|+|-||||..|++|+.=|.---+.+..||..
T Consensus 177 ~~L~eRE~LVl~LYY~eELnLKEIg~VL~lsESRvSQiHs~A~~~Lr~ 224 (227)
T TIGR02479 177 EKLSEREKLVLSLYYYEELNLKEIGEVLGLSESRVSQIHSQALKKLRA 224 (227)
T ss_pred HHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 406855788888864127668899988378705799999999999987
No 174
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.
Probab=94.67 E-value=0.075 Score=30.74 Aligned_cols=49 Identities=18% Similarity=0.269 Sum_probs=41.1
Q ss_pred CCCCCHHHHHHHHHHHCC----CCHHHHHHHHC------CCHHHHHHHHHHHHHHHCCC
Q ss_conf 888897799999999859----99799999949------99889999999999980799
Q gi|254780694|r 183 DFELTGREVECLTWISEG----KTSDEIAVILG------ISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 183 ~~~LT~RE~eVl~lia~G----~t~~eIA~~L~------iS~~TV~~hl~~i~~KLgv~ 231 (246)
...||++|.++|.++++- .|..+|.+.+. .+.++++.|+.++.+||+-.
T Consensus 3 ~v~Lt~~e~~lL~~L~~~~~~~vs~~~l~~~lw~~~~~~~~~~~l~~~I~~LR~kl~~~ 61 (78)
T smart00862 3 PIKLTPKEFRLLELLLRNPGRVVSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLEDD 61 (78)
T ss_pred EEECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf 73248999999999984799629699999876288878888602789999999997645
No 175
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1; InterPro: IPR011745 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 recognized by the major sigma factors , . This entry describes sigma-70 factors in Myxococcus xanthus DK 1622 and in other members of the Mycococcales. Each of the six members in M. xanthusis is encoded near a gene for a predicted serine/threonine kinase. Members of this family show sequence similarity to members of Pfam family IPR007630 from INTERPRO (region 4 of sigma-70 like sigma-factors), a helix-turn-helix family in which trusted and noise cutoffs deliberately are set artificially high and which therefore has many false negatives.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=94.66 E-value=0.062 Score=31.28 Aligned_cols=56 Identities=23% Similarity=0.339 Sum_probs=50.5
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf 8889779999999-9859997999999499988999999999998079988999999
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAY 239 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~ 239 (246)
..||+||+..|+| ..+|+|..+||..=+.|..||-.+++.+...+=-.+|.++..+
T Consensus 165 ~~L~~rER~LLRLHfv~~Ls~~r~g~my~~~~STvsR~~~~ARe~lle~Tr~~La~R 221 (249)
T TIGR03001 165 AALSERERTLLRLHFVEGLSMDRLGAMYQVHRSTVSRWVAQARERLLERTRRRLAER 221 (249)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 328986876555688203329999877457750789999999999999999999997
No 176
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=94.66 E-value=0.32 Score=26.67 Aligned_cols=53 Identities=26% Similarity=0.391 Sum_probs=47.1
Q ss_pred CCCHHHHHHHHH---H--HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHH
Q ss_conf 889779999999---9--8599979999994999889999999999980799889999
Q gi|254780694|r 185 ELTGREVECLTW---I--SEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAI 237 (246)
Q Consensus 185 ~LT~RE~eVl~l---i--a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav 237 (246)
.|||||.+||++ + ...+|-.||++..+|+.-=|+.-=+.+.+||--++|+.-.
T Consensus 557 ~Lt~rE~~vl~~RfGi~~~~~~TLeevg~~f~vtRERiRQIEakalrklrhp~r~~~l 614 (620)
T PRK05658 557 SLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKL 614 (620)
T ss_pred CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHH
T ss_conf 7999999999995799999967899999882976898999999999985687257888
No 177
>PRK00118 putative DNA-binding protein; Validated
Probab=94.64 E-value=0.11 Score=29.59 Aligned_cols=44 Identities=20% Similarity=0.207 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 8897799999999-8599979999994999889999999999980
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
-||+++++++.+- -+-+|-.|||..++||...|.-++++.-.+|
T Consensus 17 LLT~kQ~~~~~lyy~~DlSl~EIAe~~~iSRQaV~D~ikr~~~~L 61 (105)
T PRK00118 17 LLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLL 61 (105)
T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 755999999999988549999998996985999999999999999
No 178
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; InterPro: IPR014331 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 recognized by the major sigma factors , . This entry of sigma factors are members of the sigma-70 family and are abundantly found in the species Rhodopirellula baltica, and Verrucomicrobium spinosum and to a lesser extent in Gemmata obscuriglobus.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=94.63 E-value=0.09 Score=30.25 Aligned_cols=47 Identities=21% Similarity=0.249 Sum_probs=44.0
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 8889779999999-9859997999999499988999999999998079
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
..|.+++++++.+ --+|.+..+||..+|.|++.|..-|.+|..+|.-
T Consensus 114 ~~L~~~~R~Ll~~rY~~G~~~~~~A~~~g~~~~A~~~~L~R~R~~L~~ 161 (163)
T TIGR02989 114 EKLPERQRELLQLRYQRGVSLEALAEQLGRTVNAVYKALSRLRVRLRE 161 (163)
T ss_pred HHCCHHHHHHHHHHHCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHH
T ss_conf 635978899999982279787899988471389999999999999750
No 179
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=94.59 E-value=0.077 Score=30.68 Aligned_cols=40 Identities=25% Similarity=0.220 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 8977999999998599979999994999889999999999
Q gi|254780694|r 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIM 225 (246)
Q Consensus 186 LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~ 225 (246)
.=-|++-+-....+|+|.++||.++++|.+||...+++--
T Consensus 7 ~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 7 NDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHC
T ss_conf 8999999999997685499999996922999999998733
No 180
>PRK02277 orotate phosphoribosyltransferase-like protein; Provisional
Probab=94.57 E-value=0.041 Score=32.44 Aligned_cols=37 Identities=30% Similarity=0.322 Sum_probs=29.8
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 9999998599979999994999889999999999980
Q gi|254780694|r 192 ECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 192 eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
...+|-.+|++..|||++|++|..||.+-+.+-....
T Consensus 10 kA~eL~~~Gls~geIAdELnvS~eT~~WLl~~~~~~~ 46 (201)
T PRK02277 10 KALELRSEGLSTGEIADELNVSRETATWLLTRSKKLE 46 (201)
T ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 9999998699766635554026999999983476766
No 181
>pfam01978 TrmB Sugar-specific transcriptional regulator TrmB. One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis.
Probab=94.54 E-value=0.12 Score=29.53 Aligned_cols=45 Identities=29% Similarity=0.364 Sum_probs=39.4
Q ss_pred CCCCCHHHHHHHHHHH-CC-CCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 8888977999999998-59-997999999499988999999999998
Q gi|254780694|r 183 DFELTGREVECLTWIS-EG-KTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 183 ~~~LT~RE~eVl~lia-~G-~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
.++||+.|.+|-..+. .| .|..|||..++|+..||...+.++..|
T Consensus 3 ~~Gls~~E~~vY~~Ll~~g~~t~~eia~~~~i~r~~vY~~L~~L~~k 49 (68)
T pfam01978 3 KLGLSEYEAKVYLALLKLGPATADEIAEESGVPRSKVYEVLRSLEKK 49 (68)
T ss_pred CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 23989999999999998199889999999598898999999999988
No 182
>pfam04297 UPF0122 Putative helix-turn-helix protein, YlxM / p13 like. Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13. 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.
Probab=94.45 E-value=0.13 Score=29.14 Aligned_cols=44 Identities=20% Similarity=0.219 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 8897799999999-8599979999994999889999999999980
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
-||+++++++.+- -+-+|-.|||..++||...|.-++++.-.+|
T Consensus 17 LLT~KQ~~~~~lyy~eDlSL~EIAe~~~iSRQaV~D~ikR~~~~L 61 (101)
T pfam04297 17 LLTDKQKNYFELYYLDDLSLSEIAEEFNVSRQAVYDNIKRTEKML 61 (101)
T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 765999999999987639899999881985999999999999999
No 183
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=94.44 E-value=0.065 Score=31.14 Aligned_cols=34 Identities=32% Similarity=0.474 Sum_probs=28.7
Q ss_pred HHHHHHCC-CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 99999859-99799999949998899999999999
Q gi|254780694|r 193 CLTWISEG-KTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 193 Vl~lia~G-~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
|+.++.+| ++..|||+.+++|+.||..|++.+.+
T Consensus 2 Il~~L~~~~~~~~ela~~l~is~~tvs~HL~~L~~ 36 (66)
T smart00418 2 ILKLLAEGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 58897739966999999988298888799999998
No 184
>TIGR02859 spore_sigH RNA polymerase sigma-H factor; InterPro: IPR014218 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 recognized by the major sigma factors , . Members of this entry represent the RNA polymerase sigma-H factor required for sporulation in endospore-forming bacteria. These proteins are also called Sigma-30 and SigH. Related sequences exist in Listeria, but as Listeria does not form spores the role of these related sigma factors in that genus is in doubt.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=94.41 E-value=0.063 Score=31.23 Aligned_cols=45 Identities=27% Similarity=0.333 Sum_probs=43.3
Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 889779999999985999799999949998899999999999807
Q gi|254780694|r 185 ELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 185 ~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
-||.-|.+||....+|+|+.|||..|+...+.+.+-+.++.+||.
T Consensus 150 ~ls~le~~vl~~yl~G~~yqei~~~l~r~~ksidnalqrvkrkle 194 (198)
T TIGR02859 150 LLSDLELKVLVLYLDGKSYQEIAEDLNRHVKSIDNALQRVKRKLE 194 (198)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999999845740788998864566789999999999997
No 185
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=94.41 E-value=0.15 Score=28.80 Aligned_cols=45 Identities=16% Similarity=0.304 Sum_probs=37.6
Q ss_pred CCCCCCHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 8888897799999999859--99799999949998899999999999
Q gi|254780694|r 182 KDFELTGREVECLTWISEG--KTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 182 ~~~~LT~RE~eVl~lia~G--~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
....|-+--++||+++.+- .|++|||+.+|+|+.||...++++-.
T Consensus 3 ~~~klD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~stv~~Ri~rLe~ 49 (153)
T PRK11179 3 ENYQIDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQ 49 (153)
T ss_pred CCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 65767899999999999848999999999989299999999999997
No 186
>pfam02796 HTH_7 Helix-turn-helix domain of resolvase.
Probab=94.35 E-value=0.078 Score=30.62 Aligned_cols=39 Identities=41% Similarity=0.554 Sum_probs=32.9
Q ss_pred CCCCHH-HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 888977-999999998599979999994999889999999
Q gi|254780694|r 184 FELTGR-EVECLTWISEGKTSDEIAVILGISRNTVNNYIA 222 (246)
Q Consensus 184 ~~LT~R-E~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~ 222 (246)
..|++- --+|..|+.+|.+-++||.+.+||..||..|+.
T Consensus 4 ~kl~~~~~~~v~~L~~~G~~i~~IA~~~~vsrsTvYRyl~ 43 (45)
T pfam02796 4 PKLNEEDINEVITLLEEGISIKQIAKIFGISRSTVYRYLA 43 (45)
T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHCCHHHHHHHHCC
T ss_conf 1038999999999998799499999998600888876445
No 187
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=94.26 E-value=0.16 Score=28.65 Aligned_cols=44 Identities=23% Similarity=0.268 Sum_probs=38.4
Q ss_pred CCCCCHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 888897799999999859--99799999949998899999999999
Q gi|254780694|r 183 DFELTGREVECLTWISEG--KTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 183 ~~~LT~RE~eVl~lia~G--~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
...|.+-++++|+.+.++ .|.++||+.+++|+.||...++++-.
T Consensus 3 ~~~lD~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~ 48 (154)
T COG1522 3 MMKLDDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEE 48 (154)
T ss_pred CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 4553799999999999727657999999979798999999999998
No 188
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family; InterPro: IPR014300 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 recognized by the major sigma factors , . This group of sigma factors appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This entry is found in certain Bacillus and Clostridium species.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=94.26 E-value=0.033 Score=33.05 Aligned_cols=45 Identities=18% Similarity=0.239 Sum_probs=33.1
Q ss_pred CCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 89779999999-9859997999999499988999999999998079
Q gi|254780694|r 186 LTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 186 LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
|-+-++-++=| -=.-++-.|||+...++++||++||++...+|+.
T Consensus 123 L~~~~~t~IIL~Yy~DL~I~eIa~vM~~P~gTvKtyl~Ra~~~lk~ 168 (173)
T TIGR02954 123 LNDKYKTAIILRYYHDLKIKEIAEVMNKPEGTVKTYLRRAKKKLKK 168 (173)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHH
T ss_conf 1145440264332179984259985168985178999999999888
No 189
>pfam03811 Ins_element1 Insertion element protein.
Probab=94.12 E-value=0.068 Score=31.03 Aligned_cols=39 Identities=21% Similarity=0.151 Sum_probs=34.8
Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 897799999999859997999999499988999999999
Q gi|254780694|r 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASI 224 (246)
Q Consensus 186 LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i 224 (246)
-..-..+|+++...|..-++||+.|+||.+||=.+|+|-
T Consensus 49 ~p~vkeqiv~m~~nG~GiRdtaRvl~Is~nTVlrtLK~s 87 (88)
T pfam03811 49 QPGTKEQIVDMAMNGAGCRYTARTLKIGINTVIRTLKNS 87 (88)
T ss_pred CCCHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCC
T ss_conf 814789999997679854044787375689999987535
No 190
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=94.11 E-value=0.14 Score=29.10 Aligned_cols=39 Identities=21% Similarity=0.256 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 7799999999859--99799999949998899999999999
Q gi|254780694|r 188 GREVECLTWISEG--KTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 188 ~RE~eVl~lia~G--~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
+-.++|++.+.+- .|+.+||+.+++|+.||+..++++..
T Consensus 3 ~~D~~Il~~L~~n~R~s~~~iA~~lg~S~~tv~~Ri~~L~~ 43 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEE 43 (108)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 89999999999828999999999989399999999999960
No 191
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=94.02 E-value=0.21 Score=27.90 Aligned_cols=14 Identities=14% Similarity=0.285 Sum_probs=7.5
Q ss_pred HHHHHHHHCCCEEE
Q ss_conf 99999871930230
Q gi|254780694|r 49 MYALTEYVGASHFL 62 (246)
Q Consensus 49 ~~~~~~~~g~~~~~ 62 (246)
+.++...+||..|.
T Consensus 51 VvRf~kkLGf~Gf~ 64 (282)
T PRK11557 51 VVKFAQKLGYKGFP 64 (282)
T ss_pred HHHHHHHHCCCCHH
T ss_conf 99999993899899
No 192
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB; InterPro: IPR011879 PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself . It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006817 phosphate transport.
Probab=93.88 E-value=0.0018 Score=41.07 Aligned_cols=154 Identities=12% Similarity=0.089 Sum_probs=87.6
Q ss_pred CEEECCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCC
Q ss_conf 21000689589999999669845173899998523244303254333321445714750337368999999971787546
Q gi|254780694|r 75 DSIVSSDWPFDLVRCMALSEKDKYYNVLQRPTELFCPVFHTLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRII 154 (246)
Q Consensus 75 ~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 154 (246)
|.-|++..+.+.++........+.=| -.++..-....+-......+++.|.+|+|++.++.+-+..+-..-.-.
T Consensus 53 DWMLPG~SGIel~R~Lr~~~~Tr~iP------IIMLTARGeE~Drv~GLetGADDYvtKPFSp~EL~ARikAVLRR~~P~ 126 (226)
T TIGR02154 53 DWMLPGTSGIELARRLRREPETRAIP------IIMLTARGEEEDRVRGLETGADDYVTKPFSPRELLARIKAVLRRIRPE 126 (226)
T ss_pred CCCCCCCCHHHHHHHHCCCCCCCCCC------EEEEECCCCCCCCCCCCCCCCCCEEECCCCHHHHHHHHHHHHHCCCHH
T ss_conf 14789975699998734763314888------177405556000113113688750367886588999999998316712
Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHC---------CCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 989999999999999975420146779888889779999999985---------99979999994999889999999999
Q gi|254780694|r 155 LRDRLWEIGLLAAYQANMFKSYDVHWGKDFELTGREVECLTWISE---------GKTSDEIAVILGISRNTVNNYIASIM 225 (246)
Q Consensus 155 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LT~RE~eVl~lia~---------G~t~~eIA~~L~iS~~TV~~hl~~i~ 225 (246)
..+..-...-+... ...+.=...+....|+|.|-.-|+.+=+ =+=|.-=+...+|-.+||.-||+++.
T Consensus 127 ~~~~~i~~~~l~lD---~~~HRV~~~~~~~~lGPTEfRLL~FFM~HPeRV~SReQLLD~VWG~dvyVE~RTVDVHIRRLR 203 (226)
T TIGR02154 127 LSDEVIEVGDLELD---PVAHRVKRGGQPLELGPTEFRLLHFFMTHPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLR 203 (226)
T ss_pred HHCCEEEECCEEEC---CCCCEEEECCEECCCCCHHHHHHHHHHHCCCCEEEHHHHHHHHCCCCEEEECCCEEEEECCHH
T ss_conf 42020110347775---102404313602146870478899986237734404232011058943251350003220005
Q ss_pred HHHCCCCHHHHH
Q ss_conf 980799889999
Q gi|254780694|r 226 RKTATKTRSGAI 237 (246)
Q Consensus 226 ~KLgv~~R~eav 237 (246)
+.|+...-...|
T Consensus 204 KaL~~~g~~~~v 215 (226)
T TIGR02154 204 KALEPGGLEDLV 215 (226)
T ss_pred HHCCCCCCCCCE
T ss_conf 423878888715
No 193
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=93.82 E-value=0.18 Score=28.33 Aligned_cols=46 Identities=26% Similarity=0.306 Sum_probs=40.0
Q ss_pred CCCCCCHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 88888977999999998--59997999999499988999999999998
Q gi|254780694|r 182 KDFELTGREVECLTWIS--EGKTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 182 ~~~~LT~RE~eVl~lia--~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
..++||+.+..||..+. .|.|-.+||..++++..||...+++.-.|
T Consensus 4 ~~~glt~~q~~vL~~l~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~ 51 (101)
T smart00347 4 KPLGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKK 51 (101)
T ss_pred HHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCC
T ss_conf 113949999999999997699799999999896887999999999458
No 194
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=93.27 E-value=0.35 Score=26.49 Aligned_cols=14 Identities=21% Similarity=0.389 Sum_probs=6.8
Q ss_pred HHHHHHHHCCCEEE
Q ss_conf 99999871930230
Q gi|254780694|r 49 MYALTEYVGASHFL 62 (246)
Q Consensus 49 ~~~~~~~~g~~~~~ 62 (246)
+.++...+||..|.
T Consensus 64 VvRf~kkLGf~Gf~ 77 (293)
T PRK11337 64 IVKVAKLLGFSGFR 77 (293)
T ss_pred HHHHHHHHCCCCHH
T ss_conf 99999995789789
No 195
>TIGR02233 Myxo_sigma_rel Myxococcus probable DNA-binding regulatory protein.
Probab=93.26 E-value=0.16 Score=28.63 Aligned_cols=56 Identities=25% Similarity=0.331 Sum_probs=50.7
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf 8889779999999-9859997999999499988999999999998079988999999
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAY 239 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~ 239 (246)
..|+++|+++|+| .-+|+|-..||..=+.+..||-.++..+...|=-.+|-++..+
T Consensus 23 a~L~~~eR~lLRLH~~~gLsldR~~~lY~~hrStvaR~v~~are~Ll~~Tr~~LaeR 79 (106)
T TIGR02233 23 AALSERERTLLRLHHVEGLSLDRLGTLYGVHRSTVARWVAGARELLLERTRQELAER 79 (106)
T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 528963335666776236558999988478861699999999999999989987674
No 196
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=93.26 E-value=0.16 Score=28.60 Aligned_cols=35 Identities=26% Similarity=0.139 Sum_probs=29.0
Q ss_pred HHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 9999999859--9979999994999889999999999
Q gi|254780694|r 191 VECLTWISEG--KTSDEIAVILGISRNTVNNYIASIM 225 (246)
Q Consensus 191 ~eVl~lia~G--~t~~eIA~~L~iS~~TV~~hl~~i~ 225 (246)
+.|...+-++ .||.+||..+++|..||..|++++-
T Consensus 177 k~I~~eiq~~~~~t~~~ia~~l~ls~aTV~~~lk~l~ 213 (240)
T COG3398 177 KAIIYEIQENKCNTNLLIAYELNLSVATVAYHLKKLE 213 (240)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 8999998628741599998870865999999999898
No 197
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family; InterPro: IPR014304 This entry is a group of RNA polymerase sigma factors where one of the members is designated as SigZ in Bacillus subtilis . This group has a very sporadic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member Dechloromonas aromatica (strain RCB), that appears to have two of these sigma factors. A member of which appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri (strain ATCC 700601 / ES114), where a second one is chromosomally encoded..
Probab=93.22 E-value=0.078 Score=30.64 Aligned_cols=44 Identities=27% Similarity=0.285 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 8897799999999-8599979999994999889999999999980
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
.|.+--+|-+.|+ -+|.|=+|||+.||+|..++|+-+.+-+.||
T Consensus 100 ~LP~~~r~a~~L~el~G~sQ~e~A~kLGlSlSGaKSRVQRGR~~L 144 (170)
T TIGR02959 100 ELPDEYREAIRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRKKL 144 (170)
T ss_pred HCCHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf 569867889888750799827998761753351567889999999
No 198
>pfam03965 Pencillinase_R Penicillinase repressor. The penicillinase repressor negatively regulates expression of the penicillinase gene. The N-terminal region of this protein is involved in operator recognition, while the C-terminal is responsible for dimerization of the protein.
Probab=93.16 E-value=0.22 Score=27.70 Aligned_cols=45 Identities=20% Similarity=0.303 Sum_probs=35.5
Q ss_pred CCHHHHHHHH--HHHCCCCHHHHHHHH----CCCHHHHHHHHHHHHHHHCC
Q ss_conf 8977999999--998599979999994----99988999999999998079
Q gi|254780694|r 186 LTGREVECLT--WISEGKTSDEIAVIL----GISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 186 LT~RE~eVl~--lia~G~t~~eIA~~L----~iS~~TV~~hl~~i~~KLgv 230 (246)
||+.|.+|++ |-..+.|.+||-+.| +.+..||.+.++++..|==+
T Consensus 1 Ls~~E~~IM~~lW~~~~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~KG~l 51 (115)
T pfam03965 1 IGDAEWEVMRILWALGPATVKEVVEELPEPRDWAYSTVKTLLTRLVKKGLL 51 (115)
T ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCE
T ss_conf 988999999999807997799999985145688572899999999977862
No 199
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=92.81 E-value=0.21 Score=27.89 Aligned_cols=42 Identities=36% Similarity=0.517 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 889779999999985--999799999949998899999999999
Q gi|254780694|r 185 ELTGREVECLTWISE--GKTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 185 ~LT~RE~eVl~lia~--G~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
.++.++..|++|+.+ -.|+++++..|++|..|+..++.++..
T Consensus 399 ~~~~~~~~il~~~~en~~~T~~~L~~~l~is~~~i~r~i~~Lv~ 442 (467)
T COG2865 399 SLSERQEKILELIKENGKVTARELREILGISSETIRRRIANLVK 442 (467)
T ss_pred CHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHC
T ss_conf 76677899999975266558899998857564569999999844
No 200
>PRK11886 biotin--protein ligase; Provisional
Probab=92.80 E-value=0.29 Score=26.99 Aligned_cols=16 Identities=13% Similarity=0.023 Sum_probs=6.0
Q ss_pred HHHHHHHHHHHHHHCCC
Q ss_conf 99999999999871930
Q gi|254780694|r 43 VSWTMRMYALTEYVGAS 59 (246)
Q Consensus 43 ~~~~~~~~~~~~~~g~~ 59 (246)
..+...+..+- ..|+.
T Consensus 33 ~aVwK~i~~L~-~~G~~ 48 (319)
T PRK11886 33 AAIWKHIQTLE-EWGLD 48 (319)
T ss_pred HHHHHHHHHHH-HCCCE
T ss_conf 99999999999-77973
No 201
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=92.79 E-value=0.35 Score=26.49 Aligned_cols=45 Identities=20% Similarity=0.268 Sum_probs=39.4
Q ss_pred CCCCCHHHHHHHHHHHC---CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 88889779999999985---9997999999499988999999999998
Q gi|254780694|r 183 DFELTGREVECLTWISE---GKTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 183 ~~~LT~RE~eVl~lia~---G~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
.++||+-+.-||..+.+ |.|-+++|+.++|++.||-..+.+.-+|
T Consensus 26 ~~gLt~~q~~~L~~L~~~~~g~tq~eLa~~l~v~~~t~tr~ld~LE~~ 73 (144)
T PRK03573 26 PLELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEEK 73 (144)
T ss_pred HCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 669982599999999973989899999999798783699999999988
No 202
>pfam01047 MarR MarR family. The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.
Probab=92.74 E-value=0.34 Score=26.52 Aligned_cols=42 Identities=29% Similarity=0.339 Sum_probs=36.8
Q ss_pred CCHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 8977999999998--59997999999499988999999999998
Q gi|254780694|r 186 LTGREVECLTWIS--EGKTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 186 LT~RE~eVl~lia--~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
||.-|..||..+. .|.|.++||..+++++.||-.-++++-+|
T Consensus 1 lT~~Q~~vL~~l~~~~~~s~~~la~~~~~~~~~vs~~i~~Le~~ 44 (59)
T pfam01047 1 LTLTQFHILRILYEHGPLTVSELAEKLGVDRSTVTRVLDRLEKK 44 (59)
T ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 98999999999994699299999999885865499999999889
No 203
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=92.59 E-value=0.47 Score=25.65 Aligned_cols=14 Identities=7% Similarity=0.133 Sum_probs=7.4
Q ss_pred HHHHHHHHCCCEEE
Q ss_conf 99999871930230
Q gi|254780694|r 49 MYALTEYVGASHFL 62 (246)
Q Consensus 49 ~~~~~~~~g~~~~~ 62 (246)
+.++...+||..|.
T Consensus 51 V~Rf~kkLGf~Gf~ 64 (284)
T PRK11302 51 VNRFCRSLDTKGFP 64 (284)
T ss_pred HHHHHHHHCCCCHH
T ss_conf 99999995789789
No 204
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=92.54 E-value=0.56 Score=25.12 Aligned_cols=59 Identities=14% Similarity=0.123 Sum_probs=47.7
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC-----------CCHHHHHHHHHHC
Q ss_conf 8897799999999-859997999999499988999999999998079-----------9889999999975
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTAT-----------KTRSGAIAYAVRN 243 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv-----------~~R~eav~~A~~~ 243 (246)
.|||++.-|+-|- .-+.|-.|||..+++|+++|+.-+.+.+.+|.. ..-.++++.|+++
T Consensus 116 ~L~p~Q~vIfLLkDVF~ys~~eiAe~~s~sEGaVKasLfRsR~RLK~~~ee~~~~~~~~~D~e~~V~air~ 186 (228)
T PRK06704 116 SLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEEGIEIVEFTDDMEVVVTSIRE 186 (228)
T ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCHHHHHHHHHH
T ss_conf 25888899999999987559999999556634999999999999873385312456667762799999986
No 205
>pfam03428 RP-C Replication protein C N-terminal domain. Replication protein C is involved in the early stages of viral DNA replication.
Probab=92.50 E-value=0.37 Score=26.28 Aligned_cols=43 Identities=14% Similarity=0.309 Sum_probs=29.1
Q ss_pred CCCCHHHHHHHHHHHC---------------CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Q ss_conf 8889779999999985---------------99979999994-9998899999999999
Q gi|254780694|r 184 FELTGREVECLTWISE---------------GKTSDEIAVIL-GISRNTVNNYIASIMR 226 (246)
Q Consensus 184 ~~LT~RE~eVl~lia~---------------G~t~~eIA~~L-~iS~~TV~~hl~~i~~ 226 (246)
.+||++...||.++-. -.||.+++..+ |+|+.|++.|++.+..
T Consensus 39 lgl~~r~l~vL~aLlsf~~~~d~~~~~~~iVfpSN~~La~r~~G~s~~tlrrhla~Lve 97 (177)
T pfam03428 39 LGISDRALAVLNALLSFYPEDELTGEGRLIVFPSNAQLSLRAHGMSESTLRRHLAALVD 97 (177)
T ss_pred CCCCHHHHHHHHHHHHHCCHHHCCCCCCCEEECCHHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf 59987699999999963988444889887350289999999849988999999999998
No 206
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=92.47 E-value=0.55 Score=25.18 Aligned_cols=14 Identities=14% Similarity=0.254 Sum_probs=7.5
Q ss_pred HHHHHHHHCCCEEE
Q ss_conf 99999871930230
Q gi|254780694|r 49 MYALTEYVGASHFL 62 (246)
Q Consensus 49 ~~~~~~~~g~~~~~ 62 (246)
+.++.+.+||+.|.
T Consensus 53 v~Rf~~kLGf~Gf~ 66 (281)
T COG1737 53 VVRFARKLGFEGFS 66 (281)
T ss_pred HHHHHHHCCCCCHH
T ss_conf 99999985999889
No 207
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; InterPro: IPR014322 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 recognized by the major sigma factors , . This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:IPR014236 from INTERPRO and SigG:IPR014212 from INTERPRO as well as SigB:IPR014288 from INTERPRO), and the high GC Gram-positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=92.43 E-value=0.094 Score=30.11 Aligned_cols=45 Identities=33% Similarity=0.380 Sum_probs=39.0
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 8889779999999-98599979999994999889999999999980
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
..|.+||+.||.| .-++||=+|||++||||-==|-.-++++..||
T Consensus 179 ~~LpeRER~il~lRFf~~~TQ~eiA~~lGiSQMhVSRl~~~~L~~L 224 (229)
T TIGR02980 179 AALPERERRILLLRFFEDKTQSEIAERLGISQMHVSRLLRRALKRL 224 (229)
T ss_pred HHCCHHHCEEEEEEEECCCCHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf 5079027076100010697789999781843678899999999999
No 208
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=92.43 E-value=0.23 Score=27.57 Aligned_cols=42 Identities=26% Similarity=0.309 Sum_probs=33.1
Q ss_pred CCHHHHH-HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 8977999-99999859997999999499988999999999998
Q gi|254780694|r 186 LTGREVE-CLTWISEGKTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 186 LT~RE~e-Vl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
-+.+-+. |=.++-.|++.+||+..|||-.+||..|+++.-.|
T Consensus 94 yd~~t~~~i~emlr~gk~preIsk~lGIpirTvyY~l~k~k~~ 136 (139)
T COG1710 94 YDRNTLLRIREMLRNGKTPREISKDLGIPIRTVYYLLKKLKKK 136 (139)
T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 3454899999999849987788886098622069999987665
No 209
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family; InterPro: IPR014296 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 recognized by the major sigma factors , . This family of RNA polymerase sigma factors is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors, as two proteins from this family are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these do not apparently represent the same two sigma factors in each species). One of these proteins is designated as SigM in B. subtilis (SP: SIGM_BACSU) and is activated by various stressors , .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=92.36 E-value=0.13 Score=29.30 Aligned_cols=45 Identities=18% Similarity=0.100 Sum_probs=36.6
Q ss_pred CCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 897799999999-859997999999499988999999999998079
Q gi|254780694|r 186 LTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 186 LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
|-+--++|+-|. =+|.|++|||..+++|..-||.-+-+.++.|..
T Consensus 114 Lpe~yr~vl~Lr~~~efSYkEia~~~n~sl~~vK~~LfRaR~eLk~ 159 (162)
T TIGR02950 114 LPENYRTVLLLREFKEFSYKEIAELLNLSLAKVKSELFRARKELKK 159 (162)
T ss_pred CHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 7087656567543126688899998456022100444487799987
No 210
>PRK09191 two-component response regulator; Provisional
Probab=92.34 E-value=0.39 Score=26.12 Aligned_cols=47 Identities=23% Similarity=0.296 Sum_probs=40.8
Q ss_pred CCCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 888977999999998-59997999999499988999999999998079
Q gi|254780694|r 184 FELTGREVECLTWIS-EGKTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 184 ~~LT~RE~eVl~lia-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
..|||..++.+-|.+ +|.|..|+|++|++|+..|+.-+...+..+.-
T Consensus 87 ~~ltp~~RqAlLL~alEgFs~~eaA~Il~v~~~e~~~l~~~A~~ei~~ 134 (261)
T PRK09191 87 SAITPLPRQAFLLTALEGFSEEEAAEILGVDPAEVAALLDDASREIAR 134 (261)
T ss_pred HHCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 748930349999898828988999999789999999999999999973
No 211
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=92.29 E-value=0.38 Score=26.25 Aligned_cols=47 Identities=36% Similarity=0.454 Sum_probs=43.0
Q ss_pred CCCCCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 88888977999999998-599979999994999889999999999980
Q gi|254780694|r 182 KDFELTGREVECLTWIS-EGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 182 ~~~~LT~RE~eVl~lia-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
....||.-|.|.++|+- +|++-.|-|.+.+||..|+-+-++++..|.
T Consensus 30 ~~V~lt~eElEAlRLvD~~~l~QeeAA~rMgISr~Tfwr~l~sAR~Kv 77 (99)
T COG1342 30 EPVILTIEELEALRLVDYEGLTQEEAALRMGISRQTFWRLLTSARKKV 77 (99)
T ss_pred CCEEECHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 643522999889998868610578999984642999999999999999
No 212
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=92.28 E-value=0.19 Score=28.13 Aligned_cols=16 Identities=25% Similarity=0.434 Sum_probs=9.8
Q ss_pred CCHHHHHHHHHHCCCC
Q ss_conf 9889999999975898
Q gi|254780694|r 231 KTRSGAIAYAVRNNIV 246 (246)
Q Consensus 231 ~~R~eav~~A~~~Gli 246 (246)
.++++|+.=|.+-|++
T Consensus 288 ~~K~~AI~aaL~gg~~ 303 (321)
T COG2390 288 ESKAEAILAALRGGYI 303 (321)
T ss_pred CCCHHHHHHHHHCCCC
T ss_conf 6028999999847998
No 213
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=92.19 E-value=0.09 Score=30.24 Aligned_cols=46 Identities=26% Similarity=0.294 Sum_probs=39.1
Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8889779999999985999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.-||+++.+||.+=.+|.|-+|||.+|+-|...|..--++++.+..
T Consensus 7 tflte~qikvl~lRekG~tQ~eIA~~L~TTraNvSaIEkrA~enIe 52 (143)
T COG1356 7 TFLTEQQIKVLVLREKGLTQSEIARILKTTRANVSAIEKRALENIE 52 (143)
T ss_pred CEEEHHHEEEEEHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf 1100230235652640564899999975451017999999999899
No 214
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=92.16 E-value=0.7 Score=24.51 Aligned_cols=46 Identities=15% Similarity=0.266 Sum_probs=38.8
Q ss_pred CCCCCCHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 88888977999999998--59997999999499988999999999998
Q gi|254780694|r 182 KDFELTGREVECLTWIS--EGKTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 182 ~~~~LT~RE~eVl~lia--~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
..++||+.+..||..+. .|.|-.|||+.++++..||-..+.+.-+|
T Consensus 34 ~~~gLt~~Q~~vL~~L~~~~~~t~~eLa~~l~id~~tvt~~ldrLe~~ 81 (144)
T PRK11512 34 SPLDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCK 81 (144)
T ss_pred HHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 545999999999999998699799999999788887899999999978
No 215
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR; InterPro: IPR014075 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry represents members of the SufR cyanobacterial protein family of transcriptional regulators that control the SUF system. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to 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=92.09 E-value=0.12 Score=29.50 Aligned_cols=31 Identities=23% Similarity=0.272 Sum_probs=23.1
Q ss_pred HHHHHCC-CCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 9999859-997999999499988999999999
Q gi|254780694|r 194 LTWISEG-KTSDEIAVILGISRNTVNNYIASI 224 (246)
Q Consensus 194 l~lia~G-~t~~eIA~~L~iS~~TV~~hl~~i 224 (246)
--|+-+| .|..+||..|+|||-.||.|||-+
T Consensus 8 ~~LL~~Gq~sA~~lA~~L~iSpQAvRrHLKDL 39 (215)
T TIGR02702 8 EYLLKEGQASALALAEELAISPQAVRRHLKDL 39 (215)
T ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 99886004889999997278867887654332
No 216
>TIGR02941 Sigma_B RNA polymerase sigma-B factor; InterPro: IPR014288 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 recognized by the major sigma factors , . This entry represents the sigma factor, sigmaB. It is restricted to certain species within the order Bacillales including Staphylococcus aureus , Listeria monocytogenes and Bacillus cereus (strain ATCC 14579 / DSM 31) ..
Probab=91.98 E-value=0.21 Score=27.87 Aligned_cols=46 Identities=26% Similarity=0.244 Sum_probs=39.9
Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999-85999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.-||+||++|++++ -+|++=||.++.||||-==|-.--+...+||.
T Consensus 205 piLserE~~ii~c~f~enlsQKeTGErlGiSQMHVSRl~R~ai~KL~ 251 (256)
T TIGR02941 205 PILSEREKEIIECTFIENLSQKETGERLGISQMHVSRLQRRAIKKLK 251 (256)
T ss_pred HHCCHHHHHHHHHHHHCCCCCCHHHHHCCHHHHHHHHHHHHHHHHHH
T ss_conf 00054456766655314787300232224035567788899999999
No 217
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=91.71 E-value=0.31 Score=26.82 Aligned_cols=17 Identities=12% Similarity=-0.021 Sum_probs=10.9
Q ss_pred CCCHHHHHHHHHHHCCC
Q ss_conf 88977999999998599
Q gi|254780694|r 185 ELTGREVECLTWISEGK 201 (246)
Q Consensus 185 ~LT~RE~eVl~lia~G~ 201 (246)
-+|.||..|..+.-.+-
T Consensus 153 ~~s~~E~~i~k~~~~~e 169 (279)
T COG5484 153 WYSAREAFIDKLTTKQE 169 (279)
T ss_pred HHHHHHHHHHHHHHHHH
T ss_conf 24678888887652135
No 218
>TIGR00721 tfx DNA-binding protein, Tfx family; InterPro: IPR004645 This is a family of Tfx DNA-binding proteins, which is restricted to the archaea. Homology among the members is strongest in the helix-turn-helix-containing N-terminal region. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.; GO: 0003677 DNA binding.
Probab=91.41 E-value=0.39 Score=26.15 Aligned_cols=46 Identities=26% Similarity=0.283 Sum_probs=40.8
Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8889779999999985999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
.=||+++..||.|=.+|++=++||..|+-|..-|-.-=++++.|..
T Consensus 5 tFLTe~Q~kVL~lR~kGl~Q~eIAk~LkTtRaNvS~iEkrA~EnIe 50 (142)
T TIGR00721 5 TFLTERQIKVLELREKGLKQKEIAKILKTTRANVSIIEKRALENIE 50 (142)
T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf 4340656899998633888788987726720137898887443237
No 219
>pfam09339 HTH_IclR IclR helix-turn-helix domain.
Probab=91.03 E-value=0.69 Score=24.57 Aligned_cols=39 Identities=23% Similarity=0.411 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHC---CCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 779999999985---999799999949998899999999999
Q gi|254780694|r 188 GREVECLTWISE---GKTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 188 ~RE~eVl~lia~---G~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
.|=.+||++++. +++.+|||+.++++..||..++..+-+
T Consensus 3 ~r~l~iL~~~~~~~~~~~l~eia~~~gl~kstv~RlL~tL~~ 44 (52)
T pfam09339 3 DRALAILEALAEAPGGLSLTEIARRTGLPKSTAHRLLQTLVE 44 (52)
T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 999999999862899989999999989199999999999998
No 220
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=90.94 E-value=0.9 Score=23.82 Aligned_cols=43 Identities=16% Similarity=0.229 Sum_probs=34.9
Q ss_pred CCCCHHHHHHHHHHHC-C-CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 8889779999999985-9-99799999949998899999999999
Q gi|254780694|r 184 FELTGREVECLTWISE-G-KTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 184 ~~LT~RE~eVl~lia~-G-~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
-.|=+--++||..+-+ | .|+.|||..+++|+.||...++++-.
T Consensus 10 ~~LD~~D~~IL~~Lq~daR~s~~eLA~~vglS~stv~~RikrLe~ 54 (164)
T PRK11169 10 KDLDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLER 54 (164)
T ss_pred CCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 455199999999999848999999999989299999999999997
No 221
>pfam04218 CENP-B_N CENP-B N-terminal DNA-binding domain. 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.
Probab=90.89 E-value=0.61 Score=24.90 Aligned_cols=41 Identities=24% Similarity=0.385 Sum_probs=36.3
Q ss_pred CCCCHHH-HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 8889779-9999999859997999999499988999999999
Q gi|254780694|r 184 FELTGRE-VECLTWISEGKTSDEIAVILGISRNTVNNYIASI 224 (246)
Q Consensus 184 ~~LT~RE-~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i 224 (246)
..||-.| .+|++-+-+|.|..++|...+|.+.||+.-++|=
T Consensus 5 ~~LTl~eKi~iI~~~e~G~s~~~lar~~gi~~STl~~I~Knk 46 (53)
T pfam04218 5 TSLTLREKIEVIQRSEEGESKASLARRFNVPRSTLRDILKNK 46 (53)
T ss_pred EEECHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 141699999999999858968899999698797999999809
No 222
>pfam01418 HTH_6 Helix-turn-helix domain, rpiR family. This domain contains a helix-turn-helix motif. The best characterized member of this family is RpiR, a regulator of the expression of rpiB gene.
Probab=90.88 E-value=0.67 Score=24.66 Aligned_cols=49 Identities=24% Similarity=0.203 Sum_probs=41.2
Q ss_pred CCCCHHHHHHHHHHHCC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHH
Q ss_conf 88897799999999859------997999999499988999999999998079988999
Q gi|254780694|r 184 FELTGREVECLTWISEG------KTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGA 236 (246)
Q Consensus 184 ~~LT~RE~eVl~lia~G------~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~ea 236 (246)
..||+.|+.|.+++-+- +|-++||+..++|+.||- +..+|||-.+=.+.
T Consensus 12 ~~lt~~e~~ia~yil~~~~~~~~~si~~lA~~~~vS~atv~----Rf~kklG~~Gf~ef 66 (106)
T pfam01418 12 SKLTKSEKKIADYILASPDNAIHLSIAELAKAAGVSEASVV----RFCRKLGFSGFSDL 66 (106)
T ss_pred HHCCHHHHHHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHH----HHHHHHCCCCHHHH
T ss_conf 76499999999999929999988339999989699899999----99999589989999
No 223
>pfam00126 HTH_1 Bacterial regulatory helix-turn-helix protein, lysR family.
Probab=90.43 E-value=0.87 Score=23.91 Aligned_cols=43 Identities=19% Similarity=0.257 Sum_probs=39.5
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Q ss_conf 7999999998599979999994999889999999999980799
Q gi|254780694|r 189 REVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 189 RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~ 231 (246)
+..+++..+++=.|-...|+.|+||..||..+++++=..+|+.
T Consensus 2 ~~l~~f~~v~~~gs~~~AA~~l~isqs~vs~~i~~LE~~lg~~ 44 (60)
T pfam00126 2 RQLRVFVAVAEEGSFTAAAERLGLSQPAVSRQIKRLEEELGVP 44 (60)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCE
T ss_conf 7799999999809999999997989889999999999995997
No 224
>PRK09801 transcriptional activator TtdR; Provisional
Probab=90.19 E-value=1 Score=23.43 Aligned_cols=14 Identities=7% Similarity=0.235 Sum_probs=7.2
Q ss_pred CCCHHHHHHHHHHH
Q ss_conf 88977999999998
Q gi|254780694|r 185 ELTGREVECLTWIS 198 (246)
Q Consensus 185 ~LT~RE~eVl~lia 198 (246)
.+++|=+-.+.++.
T Consensus 280 ~~~~rvr~fidfl~ 293 (310)
T PRK09801 280 YRSMKLRVCVEFLA 293 (310)
T ss_pred CCCHHHHHHHHHHH
T ss_conf 77879999999999
No 225
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=90.15 E-value=1.2 Score=23.09 Aligned_cols=16 Identities=6% Similarity=0.225 Sum_probs=8.7
Q ss_pred CCCHHHHHHHHHHHCC
Q ss_conf 8897799999999859
Q gi|254780694|r 185 ELTGREVECLTWISEG 200 (246)
Q Consensus 185 ~LT~RE~eVl~lia~G 200 (246)
.+||.=+-.+.++++-
T Consensus 276 ~~sPa~r~fld~L~d~ 291 (300)
T PRK11074 276 DMSPALAWLLDYLGDS 291 (300)
T ss_pred CCCHHHHHHHHHHHCC
T ss_conf 9998999999998371
No 226
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family; InterPro: IPR014305 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 recognized by the major sigma factors , . This group of sigma factors appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution and represent a conserved family.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=90.15 E-value=0.67 Score=24.64 Aligned_cols=47 Identities=26% Similarity=0.227 Sum_probs=43.5
Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Q ss_conf 8897799999999-8599979999994999889999999999980799
Q gi|254780694|r 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 185 ~LT~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~ 231 (246)
.|+||++.||-|- +-|.+-.|+|+.|+.|...||+-|-+++..|+-+
T Consensus 143 ~LpPrQRAvL~LRdvlGw~A~E~A~~L~~s~ASVnSaLQRARAtL~~~ 190 (329)
T TIGR02960 143 LLPPRQRAVLLLRDVLGWKAAEVAELLGTSVASVNSALQRARATLAES 190 (329)
T ss_pred CCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHC
T ss_conf 488145789998988355556899874383267865888878866531
No 227
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.12 E-value=0.93 Score=23.74 Aligned_cols=53 Identities=23% Similarity=0.209 Sum_probs=44.2
Q ss_pred CCCCCCCCHHHHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 798888897799999999859-99799999949998899999999999807998
Q gi|254780694|r 180 WGKDFELTGREVECLTWISEG-KTSDEIAVILGISRNTVNNYIASIMRKTATKT 232 (246)
Q Consensus 180 ~~~~~~LT~RE~eVl~lia~G-~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~ 232 (246)
..+-..||+-|.|-+.+.-+- -+-+||-+.|++|--||++.+..+.+|+|-..
T Consensus 36 ~s~F~~Lt~d~LeFv~lf~r~RGnlKEvEr~lg~sYptvR~kld~vlramgy~p 89 (122)
T COG3877 36 MSKFEYLTSDQLEFVELFLRCRGNLKEVERELGISYPTVRTKLDEVLRAMGYNP 89 (122)
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCCCC
T ss_conf 263323587576899999997257999999977761789989999999808998
No 228
>pfam08461 HTH_12 Ribonuclease R winged-helix domain. This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaebacteria.
Probab=90.10 E-value=0.56 Score=25.14 Aligned_cols=33 Identities=24% Similarity=0.234 Sum_probs=27.7
Q ss_pred HHHHHHHCC---CCHHHHHHHH-----CCCHHHHHHHHHHH
Q ss_conf 999999859---9979999994-----99988999999999
Q gi|254780694|r 192 ECLTWISEG---KTSDEIAVIL-----GISRNTVNNYIASI 224 (246)
Q Consensus 192 eVl~lia~G---~t~~eIA~~L-----~iS~~TV~~hl~~i 224 (246)
|||+-+++- .+.++||+.| +||++||+.|++.+
T Consensus 2 eILriL~~~~~Pigak~ia~~L~~rG~~i~eRaVRYhL~~L 42 (66)
T pfam08461 2 EILRILAESDKPIGAKIIAEELNLRGYDIGERAVRYHLRIL 42 (66)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf 78999998599864999999999828584089999999999
No 229
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family; InterPro: IPR014303 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 recognized by the major sigma factors , . This group of sigma factors appear by homology, tree building and bidirectional best hits, to represent a conserved family. This entry is found in a limited number of bacterial lineages and ncludes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis str. MC2 155, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM 10152.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=89.94 E-value=0.99 Score=23.56 Aligned_cols=48 Identities=21% Similarity=0.178 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH-CCC
Q ss_conf 8889779999999-98599979999994999889999999999980-799
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKT-ATK 231 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL-gv~ 231 (246)
..|||-|+.|.=| =+=+..++|||...+.|+..++.-.+++.+|| ...
T Consensus 108 ErL~P~ERAVF~LREVF~y~Y~EIA~~v~kS~ancRQl~~RAr~~lr~~~ 157 (287)
T TIGR02957 108 ERLSPLERAVFLLREVFDYDYEEIASIVGKSEANCRQLVSRARRHLRAAR 157 (287)
T ss_pred HHCCHHHHHHHHHHHHHCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf 30797899999999874588267897606895799999999999997528
No 230
>PRK01381 Trp operon repressor; Provisional
Probab=89.83 E-value=0.35 Score=26.48 Aligned_cols=36 Identities=28% Similarity=0.253 Sum_probs=29.3
Q ss_pred CCCHHHHH-------HHHHHHCC-CCHHHHHHHHCCCHHHHHHH
Q ss_conf 88977999-------99999859-99799999949998899999
Q gi|254780694|r 185 ELTGREVE-------CLTWISEG-KTSDEIAVILGISRNTVNNY 220 (246)
Q Consensus 185 ~LT~RE~e-------Vl~lia~G-~t~~eIA~~L~iS~~TV~~h 220 (246)
-|||.|++ |.+.+.+| +|-+|||..|++|..||..-
T Consensus 32 lLTp~Er~al~~R~~I~~~Ll~ge~sQReIa~~lgvsiAtITRG 75 (99)
T PRK01381 32 LLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITRG 75 (99)
T ss_pred HCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCEECCCC
T ss_conf 78999999999999999999948764999999849740200002
No 231
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=89.69 E-value=1.1 Score=23.27 Aligned_cols=11 Identities=0% Similarity=-0.046 Sum_probs=3.7
Q ss_pred CCHHHHHHHHH
Q ss_conf 89779999999
Q gi|254780694|r 186 LTGREVECLTW 196 (246)
Q Consensus 186 LT~RE~eVl~l 196 (246)
+|+..+.-++.
T Consensus 276 ~s~~~~~Fid~ 286 (292)
T PRK11242 276 RSAAARAFIEL 286 (292)
T ss_pred CCHHHHHHHHH
T ss_conf 89999999999
No 232
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=89.30 E-value=1 Score=23.49 Aligned_cols=44 Identities=27% Similarity=0.365 Sum_probs=37.3
Q ss_pred CCCCHHHHHHHHHHHCCCC-H-HHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 8889779999999985999-7-999999499988999999999998
Q gi|254780694|r 184 FELTGREVECLTWISEGKT-S-DEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 184 ~~LT~RE~eVl~lia~G~t-~-~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
.+||+.|..|+..+..... + .+||..++++..||..+++++-.|
T Consensus 18 ~~l~~~q~~~L~~l~~~~~~~~~~la~~l~~~~~~vt~~l~~Le~~ 63 (126)
T COG1846 18 LGLTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDK 63 (126)
T ss_pred CCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 4999899999999998489999999999787888899999999988
No 233
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD; InterPro: IPR012760 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 recognized by the major sigma factors , . This entry represents the C-terminal region of sigma 70 (RpoD) which contains the well-conserved regions 2, 3 and 4. Region 2 of sigma-70 is the most conserved region of the entire protein. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime , . The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation , . Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme .Region 4 is involved in binding to the -35 promoter element via a helix-turn-helix motif .; GO: 0003677 DNA binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=89.23 E-value=0.78 Score=24.23 Aligned_cols=53 Identities=26% Similarity=0.417 Sum_probs=47.4
Q ss_pred CCCHHHHHHHHH---HHCC---CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHH
Q ss_conf 889779999999---9859---9979999994999889999999999980799889999
Q gi|254780694|r 185 ELTGREVECLTW---ISEG---KTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAI 237 (246)
Q Consensus 185 ~LT~RE~eVl~l---ia~G---~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav 237 (246)
.||+||..|+++ +.+| +|-.||+...+|+.-=|+--=..+.+||--.+|..-.
T Consensus 177 ~L~~rE~~Vl~~RyGL~d~~~~~TLEEVG~~f~VTRERIRQIE~KALRKLrhp~r~~~L 235 (240)
T TIGR02393 177 TLTERERKVLRMRYGLLDGEKPKTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKL 235 (240)
T ss_pred CCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf 17888999998743899887653378887651787114568889998850284366777
No 234
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=89.21 E-value=0.81 Score=24.13 Aligned_cols=35 Identities=29% Similarity=0.517 Sum_probs=29.6
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 79999999985999799999949998899999999
Q gi|254780694|r 189 REVECLTWISEGKTSDEIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 189 RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~ 223 (246)
|=.-...|+-+|+|-.+||..||+|+..|..|++.
T Consensus 11 Ra~lA~~L~eeG~Sq~~iA~LLGltqaAVS~Yls~ 45 (119)
T COG2522 11 RALLAKELIEEGLSQYRIAKLLGLTQAAVSQYLSG 45 (119)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
T ss_conf 99999999995886999999968889999999736
No 235
>pfam01527 Transposase_8 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family.
Probab=88.98 E-value=0.9 Score=23.83 Aligned_cols=36 Identities=17% Similarity=0.172 Sum_probs=29.7
Q ss_pred HHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 9999999-85999799999949998899999999999
Q gi|254780694|r 191 VECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 191 ~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
.+++.++ ..|.|..+||..+|||+.|+..-++....
T Consensus 13 ~~~V~~~~~~g~sv~~var~~gi~~~~l~~W~k~~~~ 49 (75)
T pfam01527 13 ARAVKESLEPGASVSELAREHGVSPATLYKWRKKYRG 49 (75)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHC
T ss_conf 9999999809984999999989599999999999846
No 236
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=88.97 E-value=1.5 Score=22.36 Aligned_cols=12 Identities=8% Similarity=0.257 Sum_probs=4.4
Q ss_pred CCHHHHHHHHHH
Q ss_conf 897799999999
Q gi|254780694|r 186 LTGREVECLTWI 197 (246)
Q Consensus 186 LT~RE~eVl~li 197 (246)
++|+-+....|+
T Consensus 277 ~~p~v~~F~~~L 288 (295)
T PRK11139 277 ELPKVAAFRQWL 288 (295)
T ss_pred CCHHHHHHHHHH
T ss_conf 898999999999
No 237
>pfam07900 DUF1670 Protein of unknown function (DUF1670). The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=88.95 E-value=0.59 Score=24.98 Aligned_cols=46 Identities=17% Similarity=0.214 Sum_probs=33.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 67798888897799999999859997999999499988999999999
Q gi|254780694|r 178 VHWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASI 224 (246)
Q Consensus 178 ~~~~~~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i 224 (246)
...+=..++|-+..- +++.-+|++..|||+...=|+..|+.|++.-
T Consensus 142 ~i~DiGp~vTHK~ii-v~~~lkg~~t~eiaR~t~HS~~AvdRYi~df 187 (220)
T pfam07900 142 IIKDIGPSVTHKRKI-VELYLKGYQTSEIARLTNHSPESIDRYIKDF 187 (220)
T ss_pred CCCCCCCCCCHHHHH-HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 203458762068999-9999826888899998537989999999876
No 238
>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=88.85 E-value=0.41 Score=26.03 Aligned_cols=23 Identities=30% Similarity=0.527 Sum_probs=20.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 99799999949998899999999
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~~ 223 (246)
+|.+|.|+.|+||+.|++...++
T Consensus 1 lt~~e~A~~lgVs~~TlrrW~~~ 23 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 98899999979899999999987
No 239
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=88.34 E-value=1.8 Score=21.94 Aligned_cols=30 Identities=20% Similarity=0.169 Sum_probs=24.7
Q ss_pred CCCCCCHHHHHHHHHHHCCCCHHHHHHHHC
Q ss_conf 888889779999999985999799999949
Q gi|254780694|r 182 KDFELTGREVECLTWISEGKTSDEIAVILG 211 (246)
Q Consensus 182 ~~~~LT~RE~eVl~lia~G~t~~eIA~~L~ 211 (246)
+...||+.-++-+.++.+-++-.+|+..|-
T Consensus 276 k~~~Ls~~a~~Fie~l~~~l~~~~~~~~~~ 305 (308)
T PRK12683 276 RGAYLRGYAYRFIEMFAPHLSEAEIAGALR 305 (308)
T ss_pred CCCCCCHHHHHHHHHHHHHHCHHHHHHHHH
T ss_conf 968579999999999888629899999875
No 240
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=88.30 E-value=0.83 Score=24.06 Aligned_cols=39 Identities=21% Similarity=0.406 Sum_probs=31.5
Q ss_pred HHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 799999999859--997999999499988999999999998
Q gi|254780694|r 189 REVECLTWISEG--KTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 189 RE~eVl~lia~G--~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
|..+|+.++-+- .|..++|+.+++|+.||+.-+..+-.+
T Consensus 1 R~~~Il~~l~~~~~~~i~~La~~~~VS~~TiRRDl~~L~~~ 41 (53)
T smart00420 1 RQQQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQ 41 (53)
T ss_pred CHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 98999999998697979999999897999999969999988
No 241
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=88.28 E-value=1.3 Score=22.79 Aligned_cols=47 Identities=21% Similarity=0.240 Sum_probs=35.3
Q ss_pred CCCCHHHHHHHHHH--HCCCCHHHHHHHH----CCCHHHHHHHHHHHHHHHCC
Q ss_conf 88897799999999--8599979999994----99988999999999998079
Q gi|254780694|r 184 FELTGREVECLTWI--SEGKTSDEIAVIL----GISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 184 ~~LT~RE~eVl~li--a~G~t~~eIA~~L----~iS~~TV~~hl~~i~~KLgv 230 (246)
..+|+-|.||++-+ -.-.|.+||=+.| ..|..||++-++++++|=-+
T Consensus 2 ~~Is~aE~eVM~ilW~~~~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l 54 (123)
T COG3682 2 MSISAAEWEVMEILWSRGPATVREIIEELPADREWSYSTVKTLLNRLVKKGLL 54 (123)
T ss_pred CCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCH
T ss_conf 85658999999999972886699999998632360087899999999864304
No 242
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=88.17 E-value=1.1 Score=23.18 Aligned_cols=44 Identities=20% Similarity=0.233 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 897799999999859-997999999499988999999999998079
Q gi|254780694|r 186 LTGREVECLTWISEG-KTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 186 LT~RE~eVl~lia~G-~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
.+.+...++.+.... .|-.+||+.|++|+.+|..|+..+. +-|+
T Consensus 4 ~~~~~~~ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr-~~G~ 48 (79)
T COG1654 4 TSQMLLLLLLLLTGNFVSGEKLAEELGISRTAVWKHIQQLR-EEGV 48 (79)
T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH-HHCC
T ss_conf 38999999997379966689999997865999999999999-8097
No 243
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=88.15 E-value=1.3 Score=22.80 Aligned_cols=42 Identities=26% Similarity=0.344 Sum_probs=27.6
Q ss_pred CCCHHHHHHHHHHH-----CC-CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 88977999999998-----59-99799999949998899999999999
Q gi|254780694|r 185 ELTGREVECLTWIS-----EG-KTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 185 ~LT~RE~eVl~lia-----~G-~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
.+|+++.+.|.-|- .| ..+++||..|+||+.||..-++++.+
T Consensus 3 ~~s~~~edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~ 50 (154)
T COG1321 3 MLSETEEDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLER 50 (154)
T ss_pred CCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 542168999999999984368751999999858992789999999987
No 244
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=87.97 E-value=1.7 Score=22.00 Aligned_cols=39 Identities=28% Similarity=0.439 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHC---CCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 779999999985---999799999949998899999999999
Q gi|254780694|r 188 GREVECLTWISE---GKTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 188 ~RE~eVl~lia~---G~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
+|=.+||+++++ +.|..|||..++++..||..+++..-.
T Consensus 5 ~ral~IL~~l~~~~~~~sl~eia~~~~l~ksT~~RlL~tL~~ 46 (91)
T smart00346 5 ERGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 999999999972899989999999989099999999999998
No 245
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=87.80 E-value=1.9 Score=21.75 Aligned_cols=13 Identities=8% Similarity=0.271 Sum_probs=5.0
Q ss_pred CCHHHHHHHHHHH
Q ss_conf 8977999999998
Q gi|254780694|r 186 LTGREVECLTWIS 198 (246)
Q Consensus 186 LT~RE~eVl~lia 198 (246)
.+|+=+..+.|+.
T Consensus 292 ~~p~vr~Fid~L~ 304 (311)
T PRK10086 292 QWPKIEAFIDWLK 304 (311)
T ss_pred CCHHHHHHHHHHH
T ss_conf 8989999999999
No 246
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=87.64 E-value=1.9 Score=21.80 Aligned_cols=16 Identities=6% Similarity=0.131 Sum_probs=8.6
Q ss_pred CCCCHHHHHHHHHHHC
Q ss_conf 8889779999999985
Q gi|254780694|r 184 FELTGREVECLTWISE 199 (246)
Q Consensus 184 ~~LT~RE~eVl~lia~ 199 (246)
..||+....-++++-+
T Consensus 281 ~~ls~a~~~fie~~ke 296 (312)
T PRK10341 281 YRIKKAASVLVELAKE 296 (312)
T ss_pred CCCCHHHHHHHHHHHH
T ss_conf 9889999999999998
No 247
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=87.30 E-value=0.81 Score=24.12 Aligned_cols=26 Identities=35% Similarity=0.557 Sum_probs=23.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 99799999949998899999999999
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
+|.+|||..||.|+.||...++...+
T Consensus 9 lt~~~iA~~lG~tretvsR~l~~l~~ 34 (48)
T smart00419 9 LTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 79999999979979999999999998
No 248
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=86.68 E-value=1.9 Score=21.67 Aligned_cols=26 Identities=15% Similarity=0.089 Sum_probs=11.0
Q ss_pred CCCCHHH--HHHHHHHHCCCCHHHHHHHHC
Q ss_conf 8889779--999999985999799999949
Q gi|254780694|r 184 FELTGRE--VECLTWISEGKTSDEIAVILG 211 (246)
Q Consensus 184 ~~LT~RE--~eVl~lia~G~t~~eIA~~L~ 211 (246)
..+|+.| .+++..+.+ +-++|.+.|+
T Consensus 229 ~r~~~~~~~~~~~~~l~~--aA~~Is~~Lg 256 (264)
T PRK09834 229 SAMSIEEAVSRYLPALQR--AAKAIEEGLE 256 (264)
T ss_pred CCCCHHHHHHHHHHHHHH--HHHHHHHHHC
T ss_conf 229999999999999999--9999999875
No 249
>PRK10632 putative DNA-binding transcriptional regulator; Provisional
Probab=86.60 E-value=2.2 Score=21.30 Aligned_cols=15 Identities=7% Similarity=0.284 Sum_probs=7.6
Q ss_pred CCCHHHHHHHHHHHC
Q ss_conf 889779999999985
Q gi|254780694|r 185 ELTGREVECLTWISE 199 (246)
Q Consensus 185 ~LT~RE~eVl~lia~ 199 (246)
.+++|=+-.+.++.+
T Consensus 276 ~~~~rvr~fidfl~e 290 (309)
T PRK10632 276 KLPLKVQVVINYLTD 290 (309)
T ss_pred CCCHHHHHHHHHHHH
T ss_conf 648999999999999
No 250
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=86.51 E-value=2.2 Score=21.30 Aligned_cols=39 Identities=13% Similarity=0.191 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHC-C-CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 779999999985-9-99799999949998899999999999
Q gi|254780694|r 188 GREVECLTWISE-G-KTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 188 ~RE~eVl~lia~-G-~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
|.=.+|+.++.+ | ++.-||+..|++|..||..|++-+..
T Consensus 14 ~tRl~Il~lL~~~gelcV~eL~~~l~~sQs~vS~HL~~L~~ 54 (106)
T PRK10141 14 ETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRE 54 (106)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 99999999998749956999998869988899999999998
No 251
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=86.49 E-value=2.2 Score=21.27 Aligned_cols=28 Identities=11% Similarity=-0.022 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHC
Q ss_conf 8889779999999985999799999949
Q gi|254780694|r 184 FELTGREVECLTWISEGKTSDEIAVILG 211 (246)
Q Consensus 184 ~~LT~RE~eVl~lia~G~t~~eIA~~L~ 211 (246)
..|++-=.+-+++++..+|.++|.+.+-
T Consensus 278 ~~l~~~~~~Fi~~~~~~l~~~~~~~~~~ 305 (316)
T PRK12679 278 QLQRNYVWRFLELCNAGLSVEDIKRQVM 305 (316)
T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 7556999999997520289999999987
No 252
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=86.31 E-value=2.3 Score=21.21 Aligned_cols=32 Identities=13% Similarity=-0.017 Sum_probs=22.8
Q ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCH
Q ss_conf 88889779999999985999799999949998
Q gi|254780694|r 183 DFELTGREVECLTWISEGKTSDEIAVILGISR 214 (246)
Q Consensus 183 ~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~ 214 (246)
.-.||+.-+.-+.++.+-++-+-+-+.|.=-.
T Consensus 277 ~~~ls~~~r~FIe~l~e~l~r~~~~~~~~~~~ 308 (313)
T PRK12684 277 GAYLRGYVYTFIELFSPTLNRKLVEQALKGEA 308 (313)
T ss_pred CCCCCHHHHHHHHHHHHHCCHHHHHHHHHCCC
T ss_conf 88668999999999874659899999983777
No 253
>COG2964 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=86.27 E-value=2.3 Score=21.19 Aligned_cols=38 Identities=26% Similarity=0.297 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHCCC-----CHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 77999999998599-----979999994999889999999999
Q gi|254780694|r 188 GREVECLTWISEGK-----TSDEIAVILGISRNTVNNYIASIM 225 (246)
Q Consensus 188 ~RE~eVl~lia~G~-----t~~eIA~~L~iS~~TV~~hl~~i~ 225 (246)
.+-.=|..|-.+|. ....+|..|+||+.||..|++.+-
T Consensus 174 ~~reiV~~L~EkGiF~lK~Ai~~VA~~L~iSr~TVY~YL~~~k 216 (220)
T COG2964 174 KNREIVKALYEKGIFNLKDAINIVADRLGISRHTVYRYLRKFK 216 (220)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 7899999998667641144899999996887589999999865
No 254
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=86.25 E-value=2.3 Score=21.19 Aligned_cols=15 Identities=20% Similarity=0.005 Sum_probs=8.9
Q ss_pred CCCCHHHHHHHHHHH
Q ss_conf 888977999999998
Q gi|254780694|r 184 FELTGREVECLTWIS 198 (246)
Q Consensus 184 ~~LT~RE~eVl~lia 198 (246)
..||++-.+.++++.
T Consensus 276 ~~ls~~~~~~~e~ir 290 (305)
T PRK11151 276 SPLRSRYEQLAEAIR 290 (305)
T ss_pred CCCCHHHHHHHHHHH
T ss_conf 987899999999999
No 255
>pfam06056 Terminase_5 Putative ATPase subunit of terminase (gpP-like). 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.
Probab=85.94 E-value=1.2 Score=23.02 Aligned_cols=30 Identities=30% Similarity=0.308 Sum_probs=25.3
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 999985999799999949998899999999
Q gi|254780694|r 194 LTWISEGKTSDEIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 194 l~lia~G~t~~eIA~~L~iS~~TV~~hl~~ 223 (246)
-.|--+|.+.+|||+.|+++++||.+--.+
T Consensus 7 r~LY~qg~~~~eIA~~Lg~~~~tVysWk~r 36 (58)
T pfam06056 7 RTLYWQGYRPAEIAQELGLKARTVYSWKDR 36 (58)
T ss_pred HHHHHCCCCHHHHHHHHCCCCCHHHHHHHH
T ss_conf 999996898999999978993145658652
No 256
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=85.82 E-value=2.4 Score=21.05 Aligned_cols=27 Identities=30% Similarity=0.364 Sum_probs=12.2
Q ss_pred CCCCH-HHHHHHHHHHCCCCHHHHHHHHCC
Q ss_conf 88897-799999999859997999999499
Q gi|254780694|r 184 FELTG-REVECLTWISEGKTSDEIAVILGI 212 (246)
Q Consensus 184 ~~LT~-RE~eVl~lia~G~t~~eIA~~L~i 212 (246)
..+|+ +..++..++.+ +.++|...||-
T Consensus 240 ~r~~~~~~~~~~~~l~~--~A~~IS~~LG~ 267 (271)
T PRK10163 240 SRLTEDRFVSQGELVRD--TARDISTALGL 267 (271)
T ss_pred HHCCHHHHHHHHHHHHH--HHHHHHHHHCC
T ss_conf 65799899999999999--99999998688
No 257
>pfam10668 Phage_terminase Phage terminase small subunit. This family of small highly conserved proteins come from a subset of Firmicute species. Its putative function is as a phage terminase small subunit.
Probab=85.66 E-value=0.95 Score=23.67 Aligned_cols=21 Identities=19% Similarity=0.320 Sum_probs=18.9
Q ss_pred CCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999799999949998899999
Q gi|254780694|r 200 GKTSDEIAVILGISRNTVNNY 220 (246)
Q Consensus 200 G~t~~eIA~~L~iS~~TV~~h 220 (246)
.+++++||..|++|+.||+.-
T Consensus 22 ~~~l~~IA~~L~vs~~~IrkW 42 (60)
T pfam10668 22 TMKLKDIANKLNVSESQIRKW 42 (60)
T ss_pred CEEHHHHHHHHCCCHHHHHHC
T ss_conf 644999999968798887603
No 258
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=85.27 E-value=2.6 Score=20.88 Aligned_cols=12 Identities=0% Similarity=-0.222 Sum_probs=4.9
Q ss_pred CCHHHHHHHHHH
Q ss_conf 897799999999
Q gi|254780694|r 186 LTGREVECLTWI 197 (246)
Q Consensus 186 LT~RE~eVl~li 197 (246)
+|+.=..-++|+
T Consensus 279 ~s~~~~aF~~~L 290 (309)
T PRK11013 279 SSALVDAFSEHL 290 (309)
T ss_pred CCHHHHHHHHHH
T ss_conf 799999999999
No 259
>pfam07750 GcrA GcrA cell cycle regulator. GcrA is a master cell cycle regulator that, together with CtrA (see pfam00072 and pfam00486), is involved in controlling cell cycle progression and asymmetric polar morphogenesis. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery.
Probab=84.90 E-value=0.99 Score=23.57 Aligned_cols=42 Identities=33% Similarity=0.440 Sum_probs=22.8
Q ss_pred HHHHHHH-HHHHCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHCCCCH
Q ss_conf 7799999-99985999799999949-9988999999999998079988
Q gi|254780694|r 188 GREVECL-TWISEGKTSDEIAVILG-ISRNTVNNYIASIMRKTATKTR 233 (246)
Q Consensus 188 ~RE~eVl-~lia~G~t~~eIA~~L~-iS~~TV~~hl~~i~~KLgv~~R 233 (246)
+--.|.| +|=.+|+|..|||.+|| +|.|-|=--. +.||...|
T Consensus 5 dErve~LkkLW~eGlSaSqIA~~LGgvTRNAVIGKa----HRLgLs~R 48 (162)
T pfam07750 5 DERVELLKKLWLEGLSASQIAAQLGGVSRNAVIGKV----HRLGLSGR 48 (162)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCEEEHH----HHCCCCCC
T ss_conf 899999999998536599999997655400000022----42255656
No 260
>pfam08220 HTH_DeoR DeoR-like helix-turn-helix domain.
Probab=84.61 E-value=1.7 Score=22.07 Aligned_cols=38 Identities=21% Similarity=0.353 Sum_probs=30.5
Q ss_pred HHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 799999999859--99799999949998899999999999
Q gi|254780694|r 189 REVECLTWISEG--KTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 189 RE~eVl~lia~G--~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
|-.+|+.++.+= .+.+|+++.+++|+.||+.-+..+-.
T Consensus 1 R~~~Il~~l~~~~~v~i~~La~~f~VS~~TiRRDl~~L~~ 40 (57)
T pfam08220 1 RIQQILELLKQQGTLSVEELAELLGVSEMTIRRDLNELEE 40 (57)
T ss_pred CHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 9899999999869797999999989599999996999998
No 261
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=84.42 E-value=0.63 Score=24.79 Aligned_cols=42 Identities=21% Similarity=0.302 Sum_probs=27.2
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCC
Q ss_conf 9799999949998899999999999807998899999999758
Q gi|254780694|r 202 TSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNN 244 (246)
Q Consensus 202 t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~G 244 (246)
|-+|||+..|+|..||-..+++= .+..-.+|...-..|.++|
T Consensus 2 Ti~dvA~~aGVS~sTVSr~ln~~-~~Vs~~tr~rV~~~a~~lg 43 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLNGN-GRVSEETREKVLAAMEELG 43 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHHHHC
T ss_conf 89999999895999999997799-9899999999999999978
No 262
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=84.18 E-value=2.6 Score=20.85 Aligned_cols=38 Identities=26% Similarity=0.298 Sum_probs=33.6
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Q ss_conf 99998599979999994999889999999999980799
Q gi|254780694|r 194 LTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 194 l~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~ 231 (246)
..+.....|-++||...+||+.|++.-.+.+..+|+..
T Consensus 270 ~~~~~~~~t~~~Ia~v~~vsevTIr~~ykel~~~l~~~ 307 (310)
T PRK00423 270 SLLEGERRTQREVAEVAGVTEVTVRNRYKELAEKLDIK 307 (310)
T ss_pred HHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
T ss_conf 99948898999999896988999999999999984872
No 263
>pfam11268 DUF3071 Protein of unknown function (DUF3071). Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=84.16 E-value=2.9 Score=20.57 Aligned_cols=41 Identities=24% Similarity=0.507 Sum_probs=33.5
Q ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 8888977999999998599979999994999889999999999
Q gi|254780694|r 183 DFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIM 225 (246)
Q Consensus 183 ~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~ 225 (246)
...|||||++ ..|-.|.|..|||+..+++..-|+.|=.-|+
T Consensus 53 ~~~lspreIQ--arIRaGas~eevA~~~g~~~~rVerfa~PVl 93 (169)
T pfam11268 53 DPTLSPREIQ--ARIRAGASAEEVAEAAGVPEERVERFEGPVL 93 (169)
T ss_pred CCCCCHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHCCCHHH
T ss_conf 7888989999--9988799999999995999999874223388
No 264
>pfam08280 HTH_Mga M protein trans-acting positive regulator (MGA) HTH domain. 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.
Probab=83.94 E-value=2.5 Score=21.01 Aligned_cols=40 Identities=33% Similarity=0.460 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 779999999985--9997999999499988999999999998
Q gi|254780694|r 188 GREVECLTWISE--GKTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 188 ~RE~eVl~lia~--G~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
.|+.+++.++-+ -.+..|+|..|+.|+.|++.++.++-.-
T Consensus 5 ~rk~~Ll~lL~~~~~~~l~el~~~l~ls~~tl~~~i~~L~~~ 46 (59)
T pfam08280 5 KRKLKLLELLTENKSITLDELAKQLGLSELTLKSYIHELNEL 46 (59)
T ss_pred HHHHHHHHHHHCCCCEEHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf 899999999980883649999988099799999999999987
No 265
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=83.94 E-value=3 Score=20.51 Aligned_cols=18 Identities=22% Similarity=0.159 Sum_probs=6.4
Q ss_pred HHHHHHHCCCHHHHHHHH
Q ss_conf 999999499988999999
Q gi|254780694|r 204 DEIAVILGISRNTVNNYI 221 (246)
Q Consensus 204 ~eIA~~L~iS~~TV~~hl 221 (246)
.++|..+-+=.+|--..+
T Consensus 335 ~~~~~~~~lRthtt~~~~ 352 (501)
T PRK04172 335 EDIAKRLVLRTHTTALSA 352 (501)
T ss_pred HHHHHHHCCCCCCCHHHH
T ss_conf 556643010436746679
No 266
>PRK10082 putative DNA-binding transcriptional regulator; Provisional
Probab=83.86 E-value=3 Score=20.49 Aligned_cols=11 Identities=0% Similarity=-0.233 Sum_probs=4.0
Q ss_pred CCHHHHHHHHH
Q ss_conf 89779999999
Q gi|254780694|r 186 LTGREVECLTW 196 (246)
Q Consensus 186 LT~RE~eVl~l 196 (246)
|||.-....++
T Consensus 284 lsP~a~~F~~~ 294 (303)
T PRK10082 284 MNPVAERFWRE 294 (303)
T ss_pred CCHHHHHHHHH
T ss_conf 89899999999
No 267
>PRK13824 replication initiation protein RepC; Provisional
Probab=83.72 E-value=3 Score=20.45 Aligned_cols=33 Identities=15% Similarity=0.158 Sum_probs=20.2
Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 9999994999889999999999980799889999999
Q gi|254780694|r 204 DEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYA 240 (246)
Q Consensus 204 ~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A 240 (246)
..+...||||+.+.. .....+|-.+-+-+++.-
T Consensus 325 ~~lr~mlGIS~saw~----eA~~~mG~~~AAvaiA~i 357 (404)
T PRK13824 325 VVVRSMLGVSPSAYQ----EACEVMGPENAAIVIACI 357 (404)
T ss_pred HHHHHHHCCCHHHHH----HHHHHHCHHHHHHHHHHH
T ss_conf 999987098999999----999986968899999999
No 268
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=83.67 E-value=3 Score=20.44 Aligned_cols=17 Identities=6% Similarity=0.155 Sum_probs=6.8
Q ss_pred HHHHHHHHHHHHHHHCC
Q ss_conf 99999999999987193
Q gi|254780694|r 42 TVSWTMRMYALTEYVGA 58 (246)
Q Consensus 42 ~~~~~~~~~~~~~~~g~ 58 (246)
...+-+.+..+-+.+|.
T Consensus 33 QpavS~~I~~LE~~lg~ 49 (307)
T CHL00180 33 QPAVSLQIQNLEKQLNI 49 (307)
T ss_pred HHHHHHHHHHHHHHHCC
T ss_conf 78999999999998699
No 269
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE; InterPro: IPR014286 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 recognized by the major sigma factors , . This entry represents the clade of sigma factors called RpoE. These proteins are variously annotated as sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=83.53 E-value=0.56 Score=25.12 Aligned_cols=34 Identities=32% Similarity=0.373 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 89779999999985999799999949998899999999999
Q gi|254780694|r 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 186 LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
.|=||. +|+|+.|||++.+.-.+||++-|=++..
T Consensus 149 i~LREl-------eGLSYe~IA~~MdCPvGTVRSRIFRARE 182 (192)
T TIGR02939 149 ITLREL-------EGLSYEDIAEIMDCPVGTVRSRIFRARE 182 (192)
T ss_pred HHHHHC-------CCCCHHHHHHHCCCCCCCCCCHHHHHHH
T ss_conf 446512-------6878788873306998862114677589
No 270
>pfam04645 DUF603 Protein of unknown function, DUF603. This family includes several uncharacterized proteins from Borrelia species.
Probab=83.37 E-value=1.4 Score=22.51 Aligned_cols=22 Identities=45% Similarity=0.650 Sum_probs=10.0
Q ss_pred HHHCC-CCHHHHHHHHCCCHHHH
Q ss_conf 99859-99799999949998899
Q gi|254780694|r 196 WISEG-KTSDEIAVILGISRNTV 217 (246)
Q Consensus 196 lia~G-~t~~eIA~~L~iS~~TV 217 (246)
+.-+| +++.|||.+||+|...|
T Consensus 14 yF~eG~L~D~eIA~~LGVsr~nV 36 (181)
T pfam04645 14 YFKEGSLSDAEIAKELGVSRVNV 36 (181)
T ss_pred HHHCCCCCHHHHHHHHCCHHHHH
T ss_conf 99617875799999978309999
No 271
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=83.30 E-value=3.1 Score=20.35 Aligned_cols=15 Identities=13% Similarity=-0.068 Sum_probs=8.1
Q ss_pred CCCCHHHHHHHHHHH
Q ss_conf 888977999999998
Q gi|254780694|r 184 FELTGREVECLTWIS 198 (246)
Q Consensus 184 ~~LT~RE~eVl~lia 198 (246)
..+||.....++++.
T Consensus 280 ~~~spa~~~fi~~lr 294 (302)
T PRK09791 280 SRQTPLTASLITQFR 294 (302)
T ss_pred CCCCHHHHHHHHHHH
T ss_conf 988999999999999
No 272
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=82.95 E-value=3.2 Score=20.26 Aligned_cols=17 Identities=0% Similarity=0.049 Sum_probs=8.7
Q ss_pred HHHHHHHHHHHHHHCCC
Q ss_conf 89999999999980799
Q gi|254780694|r 215 NTVNNYIASIMRKTATK 231 (246)
Q Consensus 215 ~TV~~hl~~i~~KLgv~ 231 (246)
.|.+.++.+++++-|+.
T Consensus 202 ~~~r~~id~af~~~Gl~ 218 (327)
T PRK12680 202 TRPGSSLQRAFAQVGLE 218 (327)
T ss_pred CCHHHHHHHHHHHCCCC
T ss_conf 86799999999977997
No 273
>PRK00876 nadE NAD synthetase; Reviewed
Probab=82.85 E-value=3.3 Score=20.23 Aligned_cols=47 Identities=23% Similarity=0.287 Sum_probs=37.7
Q ss_pred CCCHHHH-HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Q ss_conf 8897799-9999998599979999994999889999999999980799
Q gi|254780694|r 185 ELTGREV-ECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 185 ~LT~RE~-eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~ 231 (246)
+++=.+. .||...-.|++..+||..|+++..+|+.-.+.|-+|=.+.
T Consensus 262 g~~Y~~lD~~L~~~~~~~~~~~~~~~~g~~~e~v~~v~~~i~~kr~~t 309 (325)
T PRK00876 262 RLPYDIMDLCLYAQNHGVPAEVVAAALGLTPEQVERVWRDIEAKRRTT 309 (325)
T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHC
T ss_conf 998899999999876499999999883989999999999999875302
No 274
>pfam00325 Crp Bacterial regulatory proteins, crp family.
Probab=82.77 E-value=1.5 Score=22.37 Aligned_cols=27 Identities=33% Similarity=0.516 Sum_probs=23.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 997999999499988999999999998
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
+|..+||..|+.|..||..-++...+|
T Consensus 3 msrqdIadylGlt~ETVsR~l~~L~~~ 29 (32)
T pfam00325 3 MSRQEIADYLGLTRETVSRLLKRLREK 29 (32)
T ss_pred CCHHHHHHHHCCHHHHHHHHHHHHHHC
T ss_conf 658899998472599999999999985
No 275
>pfam00376 MerR MerR family regulatory protein.
Probab=82.53 E-value=1.4 Score=22.57 Aligned_cols=22 Identities=36% Similarity=0.492 Sum_probs=19.5
Q ss_pred CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 9799999949998899999999
Q gi|254780694|r 202 TSDEIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 202 t~~eIA~~L~iS~~TV~~hl~~ 223 (246)
|-+|+|+.++||++|++.|-+.
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~ 22 (38)
T pfam00376 1 TIGEVAKLLGVSPRTLRYYEKI 22 (38)
T ss_pred CHHHHHHHHCCCHHHHHHHHHC
T ss_conf 9899999988799999999986
No 276
>pfam01710 Transposase_14 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes insertion sequences from Synechocystis PCC 6803 three of which are characterized as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily.
Probab=82.47 E-value=2.4 Score=21.07 Aligned_cols=39 Identities=13% Similarity=0.204 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Q ss_conf 779999999985--99979999994999889999999999980799
Q gi|254780694|r 188 GREVECLTWISE--GKTSDEIAVILGISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 188 ~RE~eVl~lia~--G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~ 231 (246)
+.| +...++-+ .++-.|+|..+++|+.||..-+ .|+|..
T Consensus 58 d~~-~L~~~V~~~pD~tl~E~A~~~gVs~~tI~~aL----krlgiT 98 (120)
T pfam01710 58 DRD-ALKNDVKDNPDAYLKERAKKFGVTPSSIHYAL----KKMKIT 98 (120)
T ss_pred CHH-HHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHH----HHHCCC
T ss_conf 899-99999998867209999998398799999999----990873
No 277
>COG3711 BglG Transcriptional antiterminator [Transcription]
Probab=82.13 E-value=1.8 Score=21.91 Aligned_cols=28 Identities=25% Similarity=0.197 Sum_probs=17.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 9979999994999889999999999980
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
.+..+.|+.|++|..||.++++++..++
T Consensus 101 ~~l~~La~~l~vs~~ti~~dl~~v~~~l 128 (491)
T COG3711 101 LSLHELADELFVSKSTIINDLKDVRLKL 128 (491)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 5799999998466999999999899999
No 278
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=81.87 E-value=3.5 Score=20.00 Aligned_cols=11 Identities=18% Similarity=0.238 Sum_probs=5.9
Q ss_pred HHHHHHHHHCC
Q ss_conf 99999999859
Q gi|254780694|r 190 EVECLTWISEG 200 (246)
Q Consensus 190 E~eVl~lia~G 200 (246)
-..++.++..|
T Consensus 222 ~~~~~~~v~~g 232 (297)
T COG0583 222 AEALLQAVAAG 232 (297)
T ss_pred HHHHHHHHHHC
T ss_conf 99999999969
No 279
>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=81.83 E-value=1.9 Score=21.74 Aligned_cols=28 Identities=32% Similarity=0.389 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 5999799999949998899999999999
Q gi|254780694|r 199 EGKTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 199 ~G~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
--+|-+|||..||+|+.||...++...+
T Consensus 24 l~ltr~eiA~~lG~t~eTVsR~l~~l~~ 51 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 1779999999978909999999999998
No 280
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=81.42 E-value=3.7 Score=19.90 Aligned_cols=18 Identities=6% Similarity=-0.095 Sum_probs=11.9
Q ss_pred CCCCCHHHHHHHHHHHCC
Q ss_conf 888897799999999859
Q gi|254780694|r 183 DFELTGREVECLTWISEG 200 (246)
Q Consensus 183 ~~~LT~RE~eVl~lia~G 200 (246)
...|||..+....++.+=
T Consensus 273 ~r~lspaa~af~d~L~~~ 290 (305)
T PRK11233 273 RANLSPQAQAVKEILLSL 290 (305)
T ss_pred CCCCCHHHHHHHHHHHHH
T ss_conf 098899999999999997
No 281
>PRK03887 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=81.39 E-value=3.2 Score=20.25 Aligned_cols=40 Identities=28% Similarity=0.293 Sum_probs=32.7
Q ss_pred CCCCCCHHHHHHHHHHHC----C--CCHHHHHHHHCCCHHHHHHHH
Q ss_conf 888889779999999985----9--997999999499988999999
Q gi|254780694|r 182 KDFELTGREVECLTWISE----G--KTSDEIAVILGISRNTVNNYI 221 (246)
Q Consensus 182 ~~~~LT~RE~eVl~lia~----G--~t~~eIA~~L~iS~~TV~~hl 221 (246)
...++||-|+.|-+++.+ | .|+.+||..|+.|++.|-.-+
T Consensus 86 ~~~g~T~FqrkVy~~L~k~IP~G~t~TYgeiAk~lgts~RAVG~A~ 131 (172)
T PRK03887 86 SFEGLTKFERKVYEWLVKNVKRGEVITYGELAKALNTSPRAVGGAM 131 (172)
T ss_pred CCCCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 4257997999999999710899874949999999788778999997
No 282
>pfam00356 LacI Bacterial regulatory proteins, lacI family.
Probab=81.25 E-value=1.1 Score=23.16 Aligned_cols=42 Identities=21% Similarity=0.275 Sum_probs=27.5
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCC
Q ss_conf 9799999949998899999999999807998899999999758
Q gi|254780694|r 202 TSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNN 244 (246)
Q Consensus 202 t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~G 244 (246)
|-++||...|+|..||...+++= .+..-.+|.-.-..|.++|
T Consensus 1 Ti~DIA~~agVS~~TVSr~ln~~-~~vs~~tr~rI~~~a~~lg 42 (46)
T pfam00356 1 TIKDVARLAGVSKATVSRVLNNP-ERVSEETREKVEAAMEELG 42 (46)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHHHHC
T ss_conf 99999999897999999998797-9899999999999999978
No 283
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=81.15 E-value=3.8 Score=19.84 Aligned_cols=10 Identities=20% Similarity=-0.027 Sum_probs=3.5
Q ss_pred HHHHHHHHHH
Q ss_conf 7799999999
Q gi|254780694|r 188 GREVECLTWI 197 (246)
Q Consensus 188 ~RE~eVl~li 197 (246)
++..++..++
T Consensus 224 ~~~~~~~~~l 233 (246)
T COG1414 224 ERLEELGPLL 233 (246)
T ss_pred HHHHHHHHHH
T ss_conf 8899999999
No 284
>smart00351 PAX Paired Box domain.
Probab=81.12 E-value=3.6 Score=19.96 Aligned_cols=46 Identities=15% Similarity=0.220 Sum_probs=37.8
Q ss_pred CCHHH-HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Q ss_conf 89779-99999998599979999994999889999999999980799
Q gi|254780694|r 186 LTGRE-VECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 186 LT~RE-~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~ 231 (246)
|+.-. .+|++|...|..--+|++.|.+|...|..-+.+.++.-.+.
T Consensus 18 Lp~~~R~kIveLa~~G~rpcdISr~L~VShGCVSKIL~Ry~etGsi~ 64 (125)
T smart00351 18 LPDEERQRIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYETGSIR 64 (125)
T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCCCHHHHHHHHHHHCCCCC
T ss_conf 97899999999998599899987564577106999999997138878
No 285
>PRK04140 hypothetical protein; Provisional
Probab=80.87 E-value=1.7 Score=22.11 Aligned_cols=25 Identities=36% Similarity=0.526 Sum_probs=21.4
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 8599979999994999889999999
Q gi|254780694|r 198 SEGKTSDEIAVILGISRNTVNNYIA 222 (246)
Q Consensus 198 a~G~t~~eIA~~L~iS~~TV~~hl~ 222 (246)
-.|+|-.+.|..||+|.+||..|-+
T Consensus 136 ~~g~SlG~LA~~LGVSRrtv~~YE~ 160 (319)
T PRK04140 136 KLGLSLGELASELGVSRRTISKYEN 160 (319)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 8198888999984986999999970
No 286
>pfam08784 RPA_C Replication protein A C terminal. This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints.
Probab=80.61 E-value=3.9 Score=19.72 Aligned_cols=40 Identities=30% Similarity=0.414 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHH------CCCCHHHHHHHH-CCCHHHHHHHHHHH
Q ss_conf 88977999999998------599979999994-99988999999999
Q gi|254780694|r 185 ELTGREVECLTWIS------EGKTSDEIAVIL-GISRNTVNNYIASI 224 (246)
Q Consensus 185 ~LT~RE~eVl~lia------~G~t~~eIA~~L-~iS~~TV~~hl~~i 224 (246)
.|||-.++|+.++. +|....||+++| +++...|+.-+..+
T Consensus 44 ~ls~~~~~V~~~i~~~~~~~eG~h~~~l~~~l~~~~~~~i~~a~d~L 90 (103)
T pfam08784 44 GLTPLQDQVLNLIKQSCPGEEGVHVDELAAQLNGLPVNDIRQAVDFL 90 (103)
T ss_pred CCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 87899999999999548898872799999998299999999999999
No 287
>PRK11477 carbohydrate diacid transcriptional activator CdaR; Provisional
Probab=80.50 E-value=3.9 Score=19.70 Aligned_cols=40 Identities=20% Similarity=0.199 Sum_probs=36.9
Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 9999985999799999949998899999999999807998
Q gi|254780694|r 193 CLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKT 232 (246)
Q Consensus 193 Vl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~ 232 (246)
+-.|+..+.+..+.|+.|+|=.+|+...+++|...+|..=
T Consensus 327 L~~yfe~n~si~~tA~~L~IHRNTL~YRL~KI~~lTGldp 366 (385)
T PRK11477 327 LAAWFRHNVQPLATSKALFIHRNTLEYRLNRISELTGLDL 366 (385)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
T ss_conf 9999980999999999848645069999999999978197
No 288
>TIGR01764 excise DNA binding domain, excisionase family; InterPro: IPR010093 An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This entry 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 entry 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 (IPR000551 from INTERPRO).; GO: 0003677 DNA binding.
Probab=80.14 E-value=1.6 Score=22.26 Aligned_cols=23 Identities=39% Similarity=0.482 Sum_probs=20.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 99799999949998899999999
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~~ 223 (246)
+|.+|+|..|+||..||..=+.+
T Consensus 2 lTv~EaA~yLgv~~~t~~~l~~~ 24 (49)
T TIGR01764 2 LTVEEAAEYLGVSKSTVYRLIEE 24 (49)
T ss_pred CCHHHHHHHCCCCHHHHHHHHHC
T ss_conf 87788997719990578999971
No 289
>pfam05043 Mga Mga helix-turn-helix domain. M regulator protein trans-acting positive regulator (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. This domain is found in the centre of the Mga proteins. This family also contains a number of bacterial RofA transcriptional regulators that seem to be largely restricted to streptococci. These proteins have been shown to regulate the expression of important bacterial adhesins. This is presumably a DNA-binding domain.
Probab=79.79 E-value=3.4 Score=20.07 Aligned_cols=37 Identities=22% Similarity=0.181 Sum_probs=28.8
Q ss_pred HHHHHH--HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 999999--8599979999994999889999999999980
Q gi|254780694|r 192 ECLTWI--SEGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 192 eVl~li--a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
.++..+ .+..|..+.|+.++||..|+..+++.+-.-|
T Consensus 20 ~il~~lf~~~~~s~~~~a~~l~iS~sTl~R~ik~l~~~L 58 (87)
T pfam05043 20 QLLKFLFFHEFFSLTSLAQKLFISESTLYRLIKKLNKLL 58 (87)
T ss_pred HHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 999999818999899999997889999999999999999
No 290
>cd00131 PAX Paired Box domain
Probab=79.05 E-value=4.4 Score=19.41 Aligned_cols=39 Identities=15% Similarity=0.189 Sum_probs=33.4
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 9999999985999799999949998899999999999807
Q gi|254780694|r 190 EVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 190 E~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
-.+|++|..+|..--+|+++|.+|..-|..-+.+ |.+.|
T Consensus 23 R~kIVeLa~~G~RpcdISR~L~VShGCVSKIL~R-y~eTG 61 (128)
T cd00131 23 RQRIVELAQSGIRPCDISRQLRVSHGCVSKILNR-YYETG 61 (128)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHH-HHHCC
T ss_conf 9999999985997888887637772168999998-87027
No 291
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor; InterPro: IPR014200 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 recognized by the major sigma factors , . Members of this entry represent the endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. In Bacillus subtilis, sigma-29 is synthesized as a precursor (P31), specifically in the mother cell compartment, and is activated by a cleavage that removes the N-terminal 29 amino acids .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=79.04 E-value=2.8 Score=20.65 Aligned_cols=46 Identities=26% Similarity=0.382 Sum_probs=37.7
Q ss_pred CCCCHHHHHHHHHH---HC--CCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 88897799999999---85--999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTWI---SE--GKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~li---a~--G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|+.||..|+.+= .. -+|.+++|+.||||..-+..--++|+++|.
T Consensus 177 ~~l~~re~~i~~lrfGl~~~~e~tqk~vad~lGisqsyisrlek~i~krl~ 227 (234)
T TIGR02835 177 KKLNDREKKIMELRFGLAGGTEKTQKEVADLLGISQSYISRLEKRILKRLK 227 (234)
T ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 987676787667630436772146788898862468999999999999999
No 292
>pfam04552 Sigma54_DBD Sigma-54, DNA binding domain. 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.
Probab=78.88 E-value=2.3 Score=21.25 Aligned_cols=29 Identities=28% Similarity=0.389 Sum_probs=21.3
Q ss_pred CCHHHHHHHHC-----CCHHHHHHHHHHHHHHHCCCCH
Q ss_conf 99799999949-----9988999999999998079988
Q gi|254780694|r 201 KTSDEIAVILG-----ISRNTVNNYIASIMRKTATKTR 233 (246)
Q Consensus 201 ~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLgv~~R 233 (246)
+|+.+|+..|. ||.+||..|.. +||..+-
T Consensus 122 lSD~~I~~~L~~~Gi~IaRRTVaKYR~----~L~Ip~s 155 (160)
T pfam04552 122 LSDDKIVELLKEQGIDIARRTVAKYRE----ALNIPSS 155 (160)
T ss_pred CCHHHHHHHHHHCCCCEEHHHHHHHHH----HCCCCCH
T ss_conf 999999999997799521461999998----8399966
No 293
>pfam01325 Fe_dep_repress Iron dependent repressor, N-terminal DNA binding domain. This family includes the Diphtheria toxin repressor. DNA binding is through a helix-turn-helix motif.
Probab=78.87 E-value=2.1 Score=21.44 Aligned_cols=26 Identities=19% Similarity=0.350 Sum_probs=22.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 99799999949998899999999999
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
-++.+||+.|++|+.||..-++++-.
T Consensus 21 v~~~~iA~~L~Vs~~SVt~mlkkL~~ 46 (58)
T pfam01325 21 VKTKDLAERLNVSPSTVSEMLKKLEK 46 (58)
T ss_pred EEHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 12999999959992529999999998
No 294
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=78.87 E-value=3.3 Score=20.24 Aligned_cols=38 Identities=32% Similarity=0.253 Sum_probs=28.0
Q ss_pred CCHHHHH--------HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 8977999--------9999985999799999949998899999999
Q gi|254780694|r 186 LTGREVE--------CLTWISEGKTSDEIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 186 LT~RE~e--------Vl~lia~G~t~~eIA~~L~iS~~TV~~hl~~ 223 (246)
|||-|+| |-+|+-.-+|-+||++.||+|..|+..-=++
T Consensus 38 LTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGSN~ 83 (103)
T COG2973 38 LTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATITRGSNS 83 (103)
T ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHCCCHHH
T ss_conf 6876899999999999999956353999999858625655044444
No 295
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=78.80 E-value=4.5 Score=19.36 Aligned_cols=23 Identities=4% Similarity=-0.005 Sum_probs=14.5
Q ss_pred CCCCCHHHHHHHHHHHCCCCHHH
Q ss_conf 88889779999999985999799
Q gi|254780694|r 183 DFELTGREVECLTWISEGKTSDE 205 (246)
Q Consensus 183 ~~~LT~RE~eVl~lia~G~t~~e 205 (246)
...||+.-+.-..++.+-++-.-
T Consensus 277 ~~~l~~~~~~FId~l~e~l~~~~ 299 (309)
T PRK12682 277 GAYLRNYVYDFIELLAPHLSREL 299 (309)
T ss_pred CCCCCHHHHHHHHHHHHHCCHHH
T ss_conf 66118999999999998729899
No 296
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=78.76 E-value=4.4 Score=19.39 Aligned_cols=36 Identities=31% Similarity=0.483 Sum_probs=22.1
Q ss_pred HHHHHHHHC-C-CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 999999985-9-99799999949998899999999999
Q gi|254780694|r 191 VECLTWISE-G-KTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 191 ~eVl~lia~-G-~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
..|+..+-+ | .|+.+||..|+|..++|+.-+..+|.
T Consensus 21 ~~v~~~l~~kge~tDeela~~l~i~~~~vrriL~~L~e 58 (176)
T COG1675 21 VLVVDALLEKGELTDEELAELLGIKKNEVRRILYALYE 58 (176)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 57999887527767489988867639999999999985
No 297
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=78.67 E-value=2.7 Score=20.73 Aligned_cols=37 Identities=32% Similarity=0.390 Sum_probs=28.8
Q ss_pred HHHHHHHHC-C-CCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 999999985-9-997999999499988999999999998
Q gi|254780694|r 191 VECLTWISE-G-KTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 191 ~eVl~lia~-G-~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
.+|+.-+-. | .|+.+||..|+|..++||.-|-.+|.+
T Consensus 25 ~~v~~~l~~~~evTDEeiAe~~gi~lN~VRk~LY~Lye~ 63 (178)
T PRK06266 25 FEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDA 63 (178)
T ss_pred HHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 699997265465789999999699789999999999857
No 298
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=78.66 E-value=4.5 Score=19.33 Aligned_cols=40 Identities=23% Similarity=0.326 Sum_probs=29.9
Q ss_pred HHHHHH-HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCH
Q ss_conf 999999-99859997999999499988999999999998079988
Q gi|254780694|r 190 EVECLT-WISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTR 233 (246)
Q Consensus 190 E~eVl~-lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R 233 (246)
|+++++ +.....++++.|..||||..|+.+.+ +|+|...+
T Consensus 469 Er~~l~~l~~~~~~~~kaAk~LGISrttL~~Kl----kkyGI~~k 509 (513)
T PRK10820 469 ERSVLTQLYRNYPSTRKLAKRLGVSHTAIANKL----REYGLSQK 509 (513)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH----HHCCCCCC
T ss_conf 999999999878899999999799899999999----98089987
No 299
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=78.62 E-value=2.8 Score=20.61 Aligned_cols=30 Identities=23% Similarity=0.340 Sum_probs=27.1
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999999985999799999949998899999
Q gi|254780694|r 191 VECLTWISEGKTSDEIAVILGISRNTVNNY 220 (246)
Q Consensus 191 ~eVl~lia~G~t~~eIA~~L~iS~~TV~~h 220 (246)
.+|.+++-+|.|+..|-...|+|..|+..-
T Consensus 47 lqVa~mL~eg~tY~~I~~eTGaStaTIsRV 76 (100)
T COG4496 47 LQVAKMLKEGRTYRDIEDETGASTATISRV 76 (100)
T ss_pred HHHHHHHHCCCCCCHHHHCCCCCHHHHHHH
T ss_conf 999999976897224664148405559999
No 300
>PRK10870 transcriptional repressor MprA; Provisional
Probab=78.39 E-value=4.6 Score=19.28 Aligned_cols=42 Identities=14% Similarity=0.178 Sum_probs=20.8
Q ss_pred CCCCCHHHHHHHHHHHC----CCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 88889779999999985----9997999999499988999999999
Q gi|254780694|r 183 DFELTGREVECLTWISE----GKTSDEIAVILGISRNTVNNYIASI 224 (246)
Q Consensus 183 ~~~LT~RE~eVl~lia~----G~t~~eIA~~L~iS~~TV~~hl~~i 224 (246)
.++||+.|-.||-.+.. +++..|||+.+++|..++-.-+.++
T Consensus 50 ~~GLs~~~f~vL~~L~~~~~~~l~PseLa~~l~~s~a~iTr~vD~L 95 (176)
T PRK10870 50 AQGINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADEL 95 (176)
T ss_pred HCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 8299888999999997189998598999999778710199999999
No 301
>pfam00440 TetR_N Bacterial regulatory proteins, tetR family.
Probab=78.37 E-value=2.2 Score=21.39 Aligned_cols=26 Identities=27% Similarity=0.317 Sum_probs=22.7
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 85999799999949998899999999
Q gi|254780694|r 198 SEGKTSDEIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 198 a~G~t~~eIA~~L~iS~~TV~~hl~~ 223 (246)
-+|.|.++||+..++|..|+.+|-++
T Consensus 14 ~~~~s~~~Ia~~agvs~~~iy~~F~~ 39 (47)
T pfam00440 14 YDATTVREIAKEAGVSKGALYRHFPS 39 (47)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHCCC
T ss_conf 15077999999979698899988769
No 302
>pfam05263 DUF722 Protein of unknown function (DUF722). This family contains several bacteriophage proteins of unknown function.
Probab=78.34 E-value=4.6 Score=19.27 Aligned_cols=44 Identities=23% Similarity=0.185 Sum_probs=37.3
Q ss_pred CCCHHHHHHHHHHHCCC---CHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 88977999999998599---979999994999889999999999980
Q gi|254780694|r 185 ELTGREVECLTWISEGK---TSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 185 ~LT~RE~eVl~lia~G~---t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
.|++-|++|+++=-.|. |=-.||..+++|++|++....+....+
T Consensus 81 ~~~~~~k~ii~lrY~~r~~~sW~~Va~~l~i~er~~~~~~~~FK~~i 127 (130)
T pfam05263 81 VLTEEEKRIIELRYKGRNGMTWYQVAQELDISEKKAKRIYYSFKNDI 127 (130)
T ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 85189999999986764675499999996511999999999998876
No 303
>PRK11050 manganese transport regulator MntR; Provisional
Probab=77.91 E-value=2.2 Score=21.28 Aligned_cols=22 Identities=32% Similarity=0.483 Sum_probs=9.5
Q ss_pred HHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 7999999499988999999999
Q gi|254780694|r 203 SDEIAVILGISRNTVNNYIASI 224 (246)
Q Consensus 203 ~~eIA~~L~iS~~TV~~hl~~i 224 (246)
+.+||..|++|+.||..-++++
T Consensus 57 ~~DIA~~LgVs~pSVt~mlkrL 78 (155)
T PRK11050 57 QVDIAARLGVSQPTVAKMLKRL 78 (155)
T ss_pred HHHHHHHHCCCCHHHHHHHHHH
T ss_conf 9999989099933199999999
No 304
>KOG0709 consensus
Probab=77.57 E-value=4.8 Score=19.13 Aligned_cols=56 Identities=18% Similarity=0.156 Sum_probs=46.9
Q ss_pred HHCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 20146779888889779999999985999799999949998899999999999807998
Q gi|254780694|r 174 KSYDVHWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKT 232 (246)
Q Consensus 174 ~~~~~~~~~~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~ 232 (246)
...+...+....||.+|.+||+-+.+=.-||++|++ |.++=+-|+...=.++++.+
T Consensus 230 ~kEG~slPs~lPLTKaEEriLKrvRRKIrNK~SAQE---SRrkKkeYid~LE~rv~~~t 285 (472)
T KOG0709 230 TKEGYSLPSKLPLTKAEERILKRVRRKIRNKRSAQE---SRRKKKEYIDGLESRVSAFT 285 (472)
T ss_pred HHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHCC
T ss_conf 861676722377508899999999999876566677---77767667888764221024
No 305
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=77.49 E-value=4.9 Score=19.11 Aligned_cols=11 Identities=0% Similarity=-0.016 Sum_probs=3.7
Q ss_pred CCHHHHHHHHH
Q ss_conf 89779999999
Q gi|254780694|r 186 LTGREVECLTW 196 (246)
Q Consensus 186 LT~RE~eVl~l 196 (246)
+||.-+.-+.+
T Consensus 276 ~spa~~~Fi~~ 286 (296)
T PRK09906 276 MKPALRDFIAI 286 (296)
T ss_pred CCHHHHHHHHH
T ss_conf 99999999999
No 306
>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=77.24 E-value=1.1 Score=23.20 Aligned_cols=21 Identities=29% Similarity=0.351 Sum_probs=17.7
Q ss_pred HHHHHHHCCCHHHHHHHHHHH
Q ss_conf 999999499988999999999
Q gi|254780694|r 204 DEIAVILGISRNTVNNYIASI 224 (246)
Q Consensus 204 ~eIA~~L~iS~~TV~~hl~~i 224 (246)
++||+.+++|+.||...+++=
T Consensus 1 ~diA~~~gvS~~TVSr~ln~~ 21 (52)
T cd01392 1 KDIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred CHHHHHHCCCHHHHHHHHCCC
T ss_conf 928888785999999998798
No 307
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=76.96 E-value=2.5 Score=21.00 Aligned_cols=38 Identities=13% Similarity=0.050 Sum_probs=23.2
Q ss_pred CCCHHHHHH----HHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 889779999----99998599979999994999889999999
Q gi|254780694|r 185 ELTGREVEC----LTWISEGKTSDEIAVILGISRNTVNNYIA 222 (246)
Q Consensus 185 ~LT~RE~eV----l~lia~G~t~~eIA~~L~iS~~TV~~hl~ 222 (246)
.-|+..... ..+=.-|.|-+||...|..+...+..-+.
T Consensus 38 ~Y~~~~~~~l~~I~~lr~~G~~L~eIk~~l~~~~~~~~~~l~ 79 (96)
T cd04768 38 YYSYAQLYQLQFILFLRELGFSLAEIKELLDTEMEELTAMLL 79 (96)
T ss_pred ECCHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHH
T ss_conf 179999999999999999799999999999399699999999
No 308
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=76.09 E-value=5.3 Score=18.87 Aligned_cols=28 Identities=14% Similarity=0.183 Sum_probs=17.2
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHH
Q ss_conf 9999999859997999999499988999
Q gi|254780694|r 191 VECLTWISEGKTSDEIAVILGISRNTVN 218 (246)
Q Consensus 191 ~eVl~lia~G~t~~eIA~~L~iS~~TV~ 218 (246)
-+|...+++|.-+.......--..=||+
T Consensus 221 ~dI~~aia~g~~~~kV~~~M~k~vitI~ 248 (294)
T COG2524 221 SDIAKAIANGNLDAKVSDYMRKNVITIN 248 (294)
T ss_pred HHHHHHHHCCCCCCCHHHHHCCCCCEEC
T ss_conf 9999999768965438887505770475
No 309
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=76.05 E-value=5.3 Score=18.86 Aligned_cols=39 Identities=28% Similarity=0.411 Sum_probs=31.7
Q ss_pred HHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 79999999985--9997999999499988999999999998
Q gi|254780694|r 189 REVECLTWISE--GKTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 189 RE~eVl~lia~--G~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
.=.+++..+.+ ..+..+|+..+++|..||..|++.....
T Consensus 26 ~r~~il~~l~~~~~~~~~~l~~~~~~~~~~v~~hL~~L~~~ 66 (110)
T COG0640 26 TRLEILSLLAEGGELTVGELAEALGLSQSTVSHHLKVLREA 66 (110)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 89999999987351379999988576788999999999878
No 310
>pfam07374 DUF1492 Protein of unknown function (DUF1492). This family consists of several hypothetical, highly conserved Streptococcal and related phage proteins of around 100 residues in length. The function of this family is unknown. It appears to be distantly related to pfam08281.
Probab=75.97 E-value=4.6 Score=19.30 Aligned_cols=42 Identities=14% Similarity=0.083 Sum_probs=34.3
Q ss_pred HHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 7799999999-85999799999949998899999999999807
Q gi|254780694|r 188 GREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 188 ~RE~eVl~li-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
|-++-||++. -..++..+|++.|++|..|+-..++.+.+-||
T Consensus 58 p~~RtvL~m~Yid~~~~~~v~e~l~~Sr~Tyyr~~r~Ai~~L~ 100 (100)
T pfam07374 58 PDSRTILRMVYIDKMTVWQVCDKLNCSRTTYYRKLRVAIKELN 100 (100)
T ss_pred HHHHHHHEEEEECCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC
T ss_conf 0221311143443474999999976666789999999998529
No 311
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=75.79 E-value=5.4 Score=18.82 Aligned_cols=45 Identities=11% Similarity=0.127 Sum_probs=26.0
Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Q ss_conf 888977999999998599979999994999889999999999980799
Q gi|254780694|r 184 FELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 184 ~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~ 231 (246)
..|++-=.+-.++++..+|-+.|-+.+....+ .-+.++|.++...
T Consensus 278 ~~l~~~~~~Fi~~~~p~l~~~~~~~~~~~~~~---~~~~~~~~~~~~~ 322 (324)
T PRK12681 278 TFLRSYMYDFIERFAPHLTRDVVEKAVALRSN---EEIEALFKDIELP 322 (324)
T ss_pred CCHHHHHHHHHHHHHCCCCHHHHHHHHHCCCH---HHHHHHHHHCCCC
T ss_conf 71579999999986120489999999834788---9999997307888
No 312
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=75.76 E-value=5.4 Score=18.82 Aligned_cols=45 Identities=22% Similarity=0.310 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHC---C-CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 779999999985---9-99799999949998899999999999807998
Q gi|254780694|r 188 GREVECLTWISE---G-KTSDEIAVILGISRNTVNNYIASIMRKTATKT 232 (246)
Q Consensus 188 ~RE~eVl~lia~---G-~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~ 232 (246)
+-|..||.++.. + -|...||..|+|+-+.|+.++-++.+|=.|+.
T Consensus 6 ~~eqkil~~L~~~g~~~~tA~~lak~lg~~Kk~vN~~LY~L~k~g~v~~ 54 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHCCCEEC
T ss_conf 7999999999974886403999999949989999999999997488310
No 313
>pfam02787 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerisation domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain.
Probab=75.64 E-value=3.6 Score=19.92 Aligned_cols=41 Identities=20% Similarity=0.254 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Q ss_conf 88977999999998599979999994999889999999999980799
Q gi|254780694|r 185 ELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 185 ~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~ 231 (246)
.+++- ...+.=..|.|+++||..++.|+..|+...+ ++|+.
T Consensus 58 ~~~~~--~l~~aK~~GFSD~~IA~l~~~~e~~Ir~~R~----~~~i~ 98 (122)
T pfam02787 58 PLSDD--LLLKAKKLGFSDAQIAKLLGVTEEEVRKLRK----ELGIR 98 (122)
T ss_pred CCCHH--HHHHHHHHCCCHHHHHHHHCCCHHHHHHHHH----HCCCC
T ss_conf 99999--9999999499989999883986999999999----87991
No 314
>pfam01381 HTH_3 Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI.
Probab=75.34 E-value=5.6 Score=18.75 Aligned_cols=42 Identities=21% Similarity=0.199 Sum_probs=29.4
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHC
Q ss_conf 8599979999994999889999999999980799889999999975
Q gi|254780694|r 198 SEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRN 243 (246)
Q Consensus 198 a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~ 243 (246)
..|+|-+++|+.+++|+.||..+-+.. ...+-..+...|...
T Consensus 7 ~~g~tq~~lA~~~gis~~~is~~E~g~----~~p~~~~l~~ia~~l 48 (55)
T pfam01381 7 ELGLSQEELAEKLGVSRSTISKIENGK----REPSLETLKKLAEAL 48 (55)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHCCC----CCCCHHHHHHHHHHH
T ss_conf 829989999999896999999998799----999999999999997
No 315
>TIGR00331 hrcA heat-inducible transcription repressor HrcA; InterPro: IPR002571 In response to elevated temperature, both prokaryotic and eukaryotic cells increase expression of a small family of chaperones. The regulatory network that functions to control the transcription of the heat shock genes in bacteria includes unique structural motifs in the promoter region of these genes and the expression of alternate sigma factors. One of the conserved structural motifs, the inverted repeat CIRCE element, is found in the 5' region of many heat shock operons . For Bacillus subtilis three classes of heat shock genes regulated by different mechanisms have been described. Regulation of class I heat shock genes (dnaK and groE operons) involves an inverted repeat (CIRCE element) which most probably serves as an operator for a repressor .; GO: 0006355 regulation of transcription DNA-dependent.
Probab=75.14 E-value=3 Score=20.43 Aligned_cols=11 Identities=36% Similarity=0.413 Sum_probs=3.6
Q ss_pred HCCCCHHHHHH
Q ss_conf 85999799999
Q gi|254780694|r 198 SEGKTSDEIAV 208 (246)
Q Consensus 198 a~G~t~~eIA~ 208 (246)
-.|.+-.+|..
T Consensus 185 L~g~~~~~~~~ 195 (343)
T TIGR00331 185 LRGRTLSEIRE 195 (343)
T ss_pred CCCCCHHHHHH
T ss_conf 07872778899
No 316
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=75.08 E-value=3 Score=20.48 Aligned_cols=26 Identities=31% Similarity=0.413 Sum_probs=12.2
Q ss_pred CCHHHHHHHH----HHHCCCCHHHHHHHHC
Q ss_conf 8977999999----9985999799999949
Q gi|254780694|r 186 LTGREVECLT----WISEGKTSDEIAVILG 211 (246)
Q Consensus 186 LT~RE~eVl~----lia~G~t~~eIA~~L~ 211 (246)
-++...+.+. +-.-|.|-+||...|.
T Consensus 38 Y~~~~l~~l~~I~~~r~~GfsL~eI~~ll~ 67 (116)
T cd04769 38 YDAQHVECLRFIKEARQLGFTLAELKAIFA 67 (116)
T ss_pred CCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 289999999999999997999999999996
No 317
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=75.01 E-value=2.9 Score=20.55 Aligned_cols=43 Identities=21% Similarity=0.294 Sum_probs=20.5
Q ss_pred CCHHHHHHHHHH----HCCCCHHHHHHHHCCC------HHHHHHHHHHHHHHH
Q ss_conf 897799999999----8599979999994999------889999999999980
Q gi|254780694|r 186 LTGREVECLTWI----SEGKTSDEIAVILGIS------RNTVNNYIASIMRKT 228 (246)
Q Consensus 186 LT~RE~eVl~li----a~G~t~~eIA~~L~iS------~~TV~~hl~~i~~KL 228 (246)
-++...+-+.+| .-|+|-+||...|... ...++.|+..|-.|.
T Consensus 38 Y~~~~l~rl~~I~~~r~lGfsL~EI~~ll~~~~~~~~~~~~l~~~~~~i~~~I 90 (120)
T cd04781 38 YDPQVLDRLALIALGRAAGFSLDEIQAMLSHDGKPPIDRQLLKAKAAELDQQI 90 (120)
T ss_pred CCHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 88999999999999999599999999988426898379999999999999999
No 318
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=74.40 E-value=3.4 Score=20.11 Aligned_cols=21 Identities=19% Similarity=0.349 Sum_probs=8.1
Q ss_pred CHHHHHHHHCCCHHHHHHHHH
Q ss_conf 979999994999889999999
Q gi|254780694|r 202 TSDEIAVILGISRNTVNNYIA 222 (246)
Q Consensus 202 t~~eIA~~L~iS~~TV~~hl~ 222 (246)
++.+||+.|++|+.||..-++
T Consensus 24 r~~dIA~~L~Vs~~SVs~mik 44 (142)
T PRK03902 24 RVSDIAEALSVHPSSVTKMVQ 44 (142)
T ss_pred CHHHHHHHHCCCCHHHHHHHH
T ss_conf 299999997899533999999
No 319
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=74.38 E-value=3.9 Score=19.75 Aligned_cols=12 Identities=0% Similarity=-0.288 Sum_probs=5.2
Q ss_pred ECCCCCHHHHHH
Q ss_conf 006895899999
Q gi|254780694|r 78 VSSDWPFDLVRC 89 (246)
Q Consensus 78 l~~~~~~~~~~~ 89 (246)
..+.-..+|+..
T Consensus 64 ~iTkkG~e~l~~ 75 (260)
T COG1497 64 EITKKGAEWLLE 75 (260)
T ss_pred EEEHHHHHHHHH
T ss_conf 972668999999
No 320
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=74.13 E-value=6 Score=18.55 Aligned_cols=45 Identities=31% Similarity=0.522 Sum_probs=38.3
Q ss_pred CCCCCCHHHHHHHHHHHC--C-CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 888889779999999985--9-99799999949998899999999999
Q gi|254780694|r 182 KDFELTGREVECLTWISE--G-KTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 182 ~~~~LT~RE~eVl~lia~--G-~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
....|.+-|++|+..+.+ | .+=+|+-..|++|..||-.+++++=+
T Consensus 189 ~~~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk 236 (258)
T COG2512 189 NEYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEK 236 (258)
T ss_pred CCCCCCHHHHHHHHHHHHHCCEEEHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 357899789999999998589786999888609976779999999986
No 321
>pfam05331 DUF742 Protein of unknown function (DUF742). This family consists of several uncharacterized Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=73.68 E-value=3.2 Score=20.31 Aligned_cols=44 Identities=16% Similarity=0.145 Sum_probs=38.1
Q ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 88889779999999985999799999949998899999999999
Q gi|254780694|r 183 DFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 183 ~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
..+|++-.+.|++++..-.|..|||..|++-...|+--+..+..
T Consensus 38 ~~~l~pE~~~Il~lC~~p~SVAEiAA~L~LPl~VvrVLl~DL~~ 81 (114)
T pfam05331 38 PPTLQPEHRRILRLCRAPLSVAEIAARLDLPVGVVRVLLSDLLD 81 (114)
T ss_pred CCCCCHHHHHHHHHHCCCCCHHHHHHHHCCCCEEEEEEHHHHHH
T ss_conf 88889799999999558520999997318984023015876875
No 322
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=73.23 E-value=4.9 Score=19.10 Aligned_cols=27 Identities=19% Similarity=0.394 Sum_probs=24.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 997999999499988999999999998
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
+|..|||..+|+|+.||...++...++
T Consensus 185 lt~~dLA~~lG~trEtVsR~L~~L~~~ 211 (235)
T PRK11161 185 MTRGDIGNYLGLTVETISRLLGRFQKS 211 (235)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 789999988789899999999999978
No 323
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=73.21 E-value=3.5 Score=20.01 Aligned_cols=28 Identities=25% Similarity=0.233 Sum_probs=17.6
Q ss_pred CCCHHHHHHHHH----HHCCCCHHHHHHHHCC
Q ss_conf 889779999999----9859997999999499
Q gi|254780694|r 185 ELTGREVECLTW----ISEGKTSDEIAVILGI 212 (246)
Q Consensus 185 ~LT~RE~eVl~l----ia~G~t~~eIA~~L~i 212 (246)
.-|+...+.+.+ =.-|+|-+||...+.-
T Consensus 39 ~Y~~~~i~~l~~I~~lr~~G~sL~eI~~~l~~ 70 (108)
T cd01107 39 YYSAEQLERLNRIKYLRDLGFPLEEIKEILDA 70 (108)
T ss_pred EECHHHHHHHHHHHHHHHCCCCHHHHHHHHHC
T ss_conf 37788989999999999979999999999816
No 324
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=73.03 E-value=4.2 Score=19.53 Aligned_cols=12 Identities=42% Similarity=0.625 Sum_probs=3.7
Q ss_pred HHHHHCCCHHHH
Q ss_conf 999949998899
Q gi|254780694|r 206 IAVILGISRNTV 217 (246)
Q Consensus 206 IA~~L~iS~~TV 217 (246)
+|...|||+.||
T Consensus 6 lA~~~Gvs~~ti 17 (99)
T cd04772 6 LARAIGLSPQTV 17 (99)
T ss_pred HHHHHCCCHHHH
T ss_conf 999989699999
No 325
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=72.90 E-value=3.5 Score=20.01 Aligned_cols=23 Identities=30% Similarity=0.365 Sum_probs=19.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 99799999949998899999999
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~~ 223 (246)
.|-.|+|+.+++|++|+++|-+.
T Consensus 1 ytI~eva~~~gvs~~tlR~ye~~ 23 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 95889999989399999999997
No 326
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=72.83 E-value=3.7 Score=19.90 Aligned_cols=28 Identities=14% Similarity=0.103 Sum_probs=17.2
Q ss_pred CCCHHHHH----HHHHHHCCCCHHHHHHHHCC
Q ss_conf 88977999----99999859997999999499
Q gi|254780694|r 185 ELTGREVE----CLTWISEGKTSDEIAVILGI 212 (246)
Q Consensus 185 ~LT~RE~e----Vl~lia~G~t~~eIA~~L~i 212 (246)
..++.... |..+-..|.|.++|.+.|..
T Consensus 38 ~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~~ 69 (108)
T cd04773 38 VYDPSDVRDARLIHLLRRGGYLLEQIATVVEQ 69 (108)
T ss_pred ECCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 67999999999999999969999999999987
No 327
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family; InterPro: IPR013430 Proteins in this entry form a distinct group of helix-turn-helix proteins, which are strictly bacterial and nearly always shorter than 110 amino acids. They include the characterised 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 encoded by the upstream member of the gene pair.; GO: 0003677 DNA binding.
Probab=72.69 E-value=3 Score=20.42 Aligned_cols=25 Identities=28% Similarity=0.456 Sum_probs=21.6
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 8599979999994999889999999
Q gi|254780694|r 198 SEGKTSDEIAVILGISRNTVNNYIA 222 (246)
Q Consensus 198 a~G~t~~eIA~~L~iS~~TV~~hl~ 222 (246)
--|.|..+.|+.|+||+.|+..-++
T Consensus 18 PLg~s~~~LA~~LgVsr~~~sriv~ 42 (81)
T TIGR02607 18 PLGLSVRALAKALGVSRSTLSRIVN 42 (81)
T ss_pred CCCHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 0470689999870999788888874
No 328
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=72.63 E-value=3.4 Score=20.13 Aligned_cols=28 Identities=32% Similarity=0.418 Sum_probs=23.8
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 9859997999999499988999999999
Q gi|254780694|r 197 ISEGKTSDEIAVILGISRNTVNNYIASI 224 (246)
Q Consensus 197 ia~G~t~~eIA~~L~iS~~TV~~hl~~i 224 (246)
-..|+|-+++|+.+++|+.||..+.+.-
T Consensus 7 ~~~glsq~~lA~~~gis~~~is~~E~g~ 34 (56)
T smart00530 7 EEKGLTQEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHCCC
T ss_conf 7729999999999895999999999799
No 329
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=72.45 E-value=4.4 Score=19.42 Aligned_cols=27 Identities=22% Similarity=0.353 Sum_probs=12.9
Q ss_pred CCHHHHHHHHHH----HCCCCHHHHHHHHCC
Q ss_conf 897799999999----859997999999499
Q gi|254780694|r 186 LTGREVECLTWI----SEGKTSDEIAVILGI 212 (246)
Q Consensus 186 LT~RE~eVl~li----a~G~t~~eIA~~L~i 212 (246)
.|+...+.+.+| .-|+|-+||.+.|.+
T Consensus 39 Y~~~~~~~l~~I~~~r~~G~sL~eIr~ll~l 69 (133)
T cd04787 39 YSEKDLSRLRFILSARQLGFSLKDIKEILSH 69 (133)
T ss_pred CHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 3299999999999999869999999999988
No 330
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator); InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulphovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis strain PCC 6803 hypothetical protein slr0846. These are small proteins of 12 to 18 kD which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators..
Probab=72.31 E-value=4.4 Score=19.41 Aligned_cols=27 Identities=33% Similarity=0.507 Sum_probs=20.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Q ss_conf 9979999994999889999999999980799
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~ 231 (246)
.+.+|||+..+||++ |+..|+.+|.-.
T Consensus 26 v~~~~ia~~~~Is~~----yL~K~l~~L~~~ 52 (133)
T TIGR00738 26 VSVKEIAERQGISRS----YLEKVLRTLRKA 52 (133)
T ss_pred CCHHHHHHHHCCCHH----HHHHHHHHHHHC
T ss_conf 078999988489987----999999988770
No 331
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=72.13 E-value=3.9 Score=19.75 Aligned_cols=16 Identities=25% Similarity=0.266 Sum_probs=10.2
Q ss_pred HCCCCHHHHHHHHCCC
Q ss_conf 8599979999994999
Q gi|254780694|r 198 SEGKTSDEIAVILGIS 213 (246)
Q Consensus 198 a~G~t~~eIA~~L~iS 213 (246)
..|.+-++|...|..-
T Consensus 55 ~~G~sL~eI~~~l~~~ 70 (124)
T COG0789 55 ELGFSLAEIKELLDLL 70 (124)
T ss_pred HCCCCHHHHHHHHHHC
T ss_conf 8699899999999852
No 332
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=72.11 E-value=3.9 Score=19.76 Aligned_cols=44 Identities=14% Similarity=0.099 Sum_probs=23.7
Q ss_pred CCCHHHHHH----HHHHHCCCCHHHHHHHHCCCH----------HHHHHHHHHHHHHH
Q ss_conf 889779999----999985999799999949998----------89999999999980
Q gi|254780694|r 185 ELTGREVEC----LTWISEGKTSDEIAVILGISR----------NTVNNYIASIMRKT 228 (246)
Q Consensus 185 ~LT~RE~eV----l~lia~G~t~~eIA~~L~iS~----------~TV~~hl~~i~~KL 228 (246)
..|+...+- ..+-.-|+|-+||...|.... ..++.|+..|-.|.
T Consensus 38 ~Y~~~~l~~l~~I~~lr~~G~sL~eI~~ll~~~~~~~~~~~~~~~~l~~~~~~i~~~i 95 (123)
T cd04770 38 LYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGAAPCAEVRALLEEKLAEVEAKI 95 (123)
T ss_pred EEHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 2137787889999999986999999999985250699988999999999999999999
No 333
>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=71.77 E-value=6.8 Score=18.20 Aligned_cols=11 Identities=9% Similarity=0.069 Sum_probs=3.9
Q ss_pred CCHHHHHHHHH
Q ss_conf 89779999999
Q gi|254780694|r 186 LTGREVECLTW 196 (246)
Q Consensus 186 LT~RE~eVl~l 196 (246)
+||.-+.-..+
T Consensus 277 ~~~~~r~Fid~ 287 (291)
T TIGR03418 277 RGPAVRRFRDW 287 (291)
T ss_pred CCHHHHHHHHH
T ss_conf 89999999999
No 334
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=71.73 E-value=3.9 Score=19.70 Aligned_cols=27 Identities=33% Similarity=0.270 Sum_probs=14.2
Q ss_pred CCHHHHHHH----HHHHCCCCHHHHHHHHCC
Q ss_conf 897799999----999859997999999499
Q gi|254780694|r 186 LTGREVECL----TWISEGKTSDEIAVILGI 212 (246)
Q Consensus 186 LT~RE~eVl----~lia~G~t~~eIA~~L~i 212 (246)
-++...+-| .+-.-|+|-+||.+.|.+
T Consensus 39 Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~~ 69 (126)
T cd04783 39 YPEETVTRLRFIKRAQELGFTLDEIAELLEL 69 (126)
T ss_pred CCHHHHHHHHHHHHHHHCCCCHHHHHHHHCC
T ss_conf 7799999999999999879989999999742
No 335
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=71.34 E-value=4 Score=19.64 Aligned_cols=43 Identities=12% Similarity=0.113 Sum_probs=23.1
Q ss_pred CCCHHHHHH----HHHHHCCCCHHHHHHHHCC--CHHHHHHHHHHHHHH
Q ss_conf 889779999----9999859997999999499--988999999999998
Q gi|254780694|r 185 ELTGREVEC----LTWISEGKTSDEIAVILGI--SRNTVNNYIASIMRK 227 (246)
Q Consensus 185 ~LT~RE~eV----l~lia~G~t~~eIA~~L~i--S~~TV~~hl~~i~~K 227 (246)
.-|+...+- ..+-.-|.|-+||...|.- +......++..+-+|
T Consensus 38 ~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~l~~~~~~l~~~ 86 (102)
T cd04789 38 LYPDSDLQRLLLIQQLQAGGLSLKECLACLQGKLTRSLLLERLSSLAEQ 86 (102)
T ss_pred CCCHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf 0699999999999999997998999999985985569999999999999
No 336
>pfam11662 DUF3263 Protein of unknown function (DUF3263). This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=71.29 E-value=6.6 Score=18.25 Aligned_cols=42 Identities=24% Similarity=0.491 Sum_probs=33.6
Q ss_pred CCCHHHHHHHH-----HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 88977999999-----9985999799999949998899999999999
Q gi|254780694|r 185 ELTGREVECLT-----WISEGKTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 185 ~LT~RE~eVl~-----lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
.||++|+.||. |-..|-....|-+.+++|+--...-++.+..
T Consensus 2 ~Ls~rd~~IL~fEr~ww~~~GaKe~AIRe~fglS~~rYYQ~LN~LiD 48 (77)
T pfam11662 2 ELTERDRAILDFERQWWKHAGAKEQAIRELFGLSSTRYYQLLNALID 48 (77)
T ss_pred CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHC
T ss_conf 88899999999998733687818999999978888999999999868
No 337
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=70.95 E-value=4.9 Score=19.08 Aligned_cols=26 Identities=23% Similarity=0.296 Sum_probs=12.1
Q ss_pred CCHHHHHHHH----HHHCCCCHHHHHHHHC
Q ss_conf 8977999999----9985999799999949
Q gi|254780694|r 186 LTGREVECLT----WISEGKTSDEIAVILG 211 (246)
Q Consensus 186 LT~RE~eVl~----lia~G~t~~eIA~~L~ 211 (246)
-|+...+.+. +-..|+|.++|.+.|.
T Consensus 39 Y~~~di~~l~~I~~lr~~G~~l~~Ik~~l~ 68 (70)
T smart00422 39 YSDEDLERLRFIKRLKELGFSLEEIKELLE 68 (70)
T ss_pred CCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 399999999999999997899999999996
No 338
>PRK09430 djlA Dna-J like membrane chaperone protein; Provisional
Probab=70.77 E-value=7.1 Score=18.06 Aligned_cols=16 Identities=31% Similarity=0.187 Sum_probs=12.0
Q ss_pred CCCCHHHHHHHHHHHC
Q ss_conf 8889779999999985
Q gi|254780694|r 184 FELTGREVECLTWISE 199 (246)
Q Consensus 184 ~~LT~RE~eVl~lia~ 199 (246)
..+++.|.++|+-+++
T Consensus 143 G~l~~~E~~~L~~Ia~ 158 (269)
T PRK09430 143 GSLHPNERQVLYVIAE 158 (269)
T ss_pred CCCCHHHHHHHHHHHH
T ss_conf 8999999999999999
No 339
>pfam08535 KorB KorB domain. This family consists of 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.
Probab=70.69 E-value=4.9 Score=19.09 Aligned_cols=24 Identities=38% Similarity=0.451 Sum_probs=14.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 599979999994999889999999
Q gi|254780694|r 199 EGKTSDEIAVILGISRNTVNNYIA 222 (246)
Q Consensus 199 ~G~t~~eIA~~L~iS~~TV~~hl~ 222 (246)
.|++-.+||..||-|..=|..|++
T Consensus 2 ~G~kk~~IAk~LGks~s~VS~hla 25 (93)
T pfam08535 2 KGVKQAEIAKKLGKSKSFVSQHLA 25 (93)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 987799999997889889999999
No 340
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=70.14 E-value=4.5 Score=19.31 Aligned_cols=45 Identities=20% Similarity=0.320 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHHHH----HCCCCHHHHHHHHCC------CHHHHHHHHHHHHHHH
Q ss_conf 88897799999999----859997999999499------9889999999999980
Q gi|254780694|r 184 FELTGREVECLTWI----SEGKTSDEIAVILGI------SRNTVNNYIASIMRKT 228 (246)
Q Consensus 184 ~~LT~RE~eVl~li----a~G~t~~eIA~~L~i------S~~TV~~hl~~i~~KL 228 (246)
-..++...+-+.+| .-|+|-+||...|.+ +...++..+..+-.|.
T Consensus 35 R~Y~~~~~~~l~~I~~~r~~G~sL~eI~~~L~l~~~~~~~~~~l~~~l~~l~~~i 89 (118)
T cd04776 35 RVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDPPGGNRKQLEKMLEKIEKRR 89 (118)
T ss_pred CCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
T ss_conf 8608999999999999998299899999999644699972999999999999999
No 341
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=70.10 E-value=4.2 Score=19.54 Aligned_cols=13 Identities=46% Similarity=0.618 Sum_probs=5.0
Q ss_pred CCCHHHHHHHHCC
Q ss_conf 9997999999499
Q gi|254780694|r 200 GKTSDEIAVILGI 212 (246)
Q Consensus 200 G~t~~eIA~~L~i 212 (246)
|.|-+||.+.|.+
T Consensus 64 GfsL~eI~~LL~l 76 (144)
T PRK13752 64 GFSLDEIAELLRL 76 (144)
T ss_pred CCCHHHHHHHHCC
T ss_conf 9989999999777
No 342
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=70.08 E-value=4.5 Score=19.35 Aligned_cols=34 Identities=21% Similarity=0.341 Sum_probs=30.7
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 5999799999949998899999999999807998
Q gi|254780694|r 199 EGKTSDEIAVILGISRNTVNNYIASIMRKTATKT 232 (246)
Q Consensus 199 ~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~ 232 (246)
.=+|-+|||...++++-|++++.+.+..+++..+
T Consensus 250 ~~~tq~eva~v~~vtevTIrnrykel~~~~~i~~ 283 (285)
T COG1405 250 ERRTQKEVAKVAGVTEVTIRNRYKELADALDIEV 283 (285)
T ss_pred CCHHHHHHHHHHCCEEEHHHHHHHHHHHHHCCCC
T ss_conf 7027999998838722079988999877322556
No 343
>PHA01976 helix-turn-helix protein
Probab=69.99 E-value=5.5 Score=18.79 Aligned_cols=27 Identities=11% Similarity=0.203 Sum_probs=23.2
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 998599979999994999889999999
Q gi|254780694|r 196 WISEGKTSDEIAVILGISRNTVNNYIA 222 (246)
Q Consensus 196 lia~G~t~~eIA~~L~iS~~TV~~hl~ 222 (246)
--+.|+|-.|.|..++||..||..+-+
T Consensus 11 R~~~g~sQ~eLA~~lGVs~~~is~wE~ 37 (67)
T PHA01976 11 RNARAWSAPELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHC
T ss_conf 998699999999994998999999987
No 344
>TIGR00373 TIGR00373 conserved hypothetical protein TIGR00373; InterPro: IPR005241 This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain. .
Probab=69.94 E-value=6.5 Score=18.31 Aligned_cols=36 Identities=31% Similarity=0.445 Sum_probs=30.8
Q ss_pred HHHHHHHH-CC-CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 99999998-59-99799999949998899999999999
Q gi|254780694|r 191 VECLTWIS-EG-KTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 191 ~eVl~lia-~G-~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
..||..+. +| .|+.|||..|+|..+-||.-|=.+|.
T Consensus 19 ~~vl~~L~~kGe~Tdeeis~elg~klN~vRk~Ly~LYd 56 (168)
T TIGR00373 19 IEVLESLLIKGEVTDEEISKELGIKLNVVRKLLYKLYD 56 (168)
T ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHC
T ss_conf 34442220268747788888838405578899998730
No 345
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=69.86 E-value=5.5 Score=18.80 Aligned_cols=47 Identities=19% Similarity=0.215 Sum_probs=29.1
Q ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCC--CHHHHHHHHHHHHHHHCC
Q ss_conf 888977999999998-----59997999999499--988999999999998079
Q gi|254780694|r 184 FELTGREVECLTWIS-----EGKTSDEIAVILGI--SRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 184 ~~LT~RE~eVl~lia-----~G~t~~eIA~~L~i--S~~TV~~hl~~i~~KLgv 230 (246)
..-++...+-|++|. -|+|-+||.+.|.. -.++-++-+.-+..+++.
T Consensus 37 r~Y~~~~v~rL~~Ir~l~~~lG~sL~eIr~lL~~~~d~~~p~~l~~~~~~~~~~ 90 (95)
T cd04780 37 AEYSEAHVERLRLIRALQQEGGLPISQIKEVLDAIADASLPSTLLALAVQRFGL 90 (95)
T ss_pred EECCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHCC
T ss_conf 154999999999999999936999999999984368899951799999999557
No 346
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=69.79 E-value=5 Score=19.01 Aligned_cols=21 Identities=33% Similarity=0.419 Sum_probs=9.7
Q ss_pred HHHHHHHCCCHHHHHHHHHHH
Q ss_conf 999999499988999999999
Q gi|254780694|r 204 DEIAVILGISRNTVNNYIASI 224 (246)
Q Consensus 204 ~eIA~~L~iS~~TV~~hl~~i 224 (246)
.+||..|++|+.||..-++++
T Consensus 3 ~diA~~L~vs~~sVs~~l~~L 23 (96)
T smart00529 3 SEIAERLNVSPPTVTQMLKKL 23 (96)
T ss_pred HHHHHHHCCCCHHHHHHHHHH
T ss_conf 889988499916799999999
No 347
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=69.63 E-value=7.5 Score=17.90 Aligned_cols=42 Identities=21% Similarity=0.254 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 889779999999-985999799999949998899999999999
Q gi|254780694|r 185 ELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 185 ~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
-||.++...+.+ ..+-+|-.|||...+||...|--++++--.
T Consensus 17 LLT~KQ~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIKr~~~ 59 (105)
T COG2739 17 LLTKKQKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIKRTEK 59 (105)
T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 9868899999999981166999999957509999999999999
No 348
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=69.52 E-value=4.8 Score=19.16 Aligned_cols=28 Identities=29% Similarity=0.458 Sum_probs=15.2
Q ss_pred CCCHHHHHHHHHH----HCCCCHHHHHHHHCC
Q ss_conf 8897799999999----859997999999499
Q gi|254780694|r 185 ELTGREVECLTWI----SEGKTSDEIAVILGI 212 (246)
Q Consensus 185 ~LT~RE~eVl~li----a~G~t~~eIA~~L~i 212 (246)
..++...+-+.+| .-|+|-+||...|.+
T Consensus 38 ~Y~~~~~~~l~~I~~~r~~G~sL~eI~~ll~~ 69 (127)
T cd01108 38 VYNQRDIEELRFIRRARDLGFSLEEIRELLAL 69 (127)
T ss_pred CCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 25199999999999999879989999999853
No 349
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=69.42 E-value=4.8 Score=19.16 Aligned_cols=28 Identities=25% Similarity=0.231 Sum_probs=16.3
Q ss_pred CCCHHHHHHH----HHHHCCCCHHHHHHHHCC
Q ss_conf 8897799999----999859997999999499
Q gi|254780694|r 185 ELTGREVECL----TWISEGKTSDEIAVILGI 212 (246)
Q Consensus 185 ~LT~RE~eVl----~lia~G~t~~eIA~~L~i 212 (246)
.-++...+-+ .+-.-|+|-+||.+.|.+
T Consensus 38 ~Y~~~~l~~l~~I~~~r~~GfsL~eI~~ll~l 69 (126)
T cd04785 38 LYGAAHVERLRFIRRARDLGFSLEEIRALLAL 69 (126)
T ss_pred CCCHHHHHHHHHHHHHHHCCCCHHHHHHHHCC
T ss_conf 27899999999999999879989999999713
No 350
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=69.34 E-value=4.8 Score=19.15 Aligned_cols=44 Identities=11% Similarity=0.040 Sum_probs=29.6
Q ss_pred CCCHHHHH----HHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 88977999----999998-599979999994999889999999999980
Q gi|254780694|r 185 ELTGREVE----CLTWIS-EGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 185 ~LT~RE~e----Vl~lia-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
.-|+...+ |..+-. .|+|-+||...|..-..-++........||
T Consensus 37 ~Y~~~dl~rL~~I~~l~~~lGfsL~eIk~lL~~~~~p~~~~~~~~~e~L 85 (96)
T cd04774 37 LYSEEDLKRLERILRLREVLGFSLQEVTHFLERPLEPVDGGHRYSAESL 85 (96)
T ss_pred CCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
T ss_conf 3599999999999999995799899999998198883045999999999
No 351
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=69.31 E-value=4.9 Score=19.10 Aligned_cols=26 Identities=31% Similarity=0.222 Sum_probs=16.0
Q ss_pred CCHHHHHHHHHH----HCCCCHHHHHHHHC
Q ss_conf 897799999999----85999799999949
Q gi|254780694|r 186 LTGREVECLTWI----SEGKTSDEIAVILG 211 (246)
Q Consensus 186 LT~RE~eVl~li----a~G~t~~eIA~~L~ 211 (246)
-|......+..| .-|.|-+||...+.
T Consensus 39 Y~~~~~~~l~~I~~~r~lG~sL~eI~~~~~ 68 (97)
T cd04782 39 YTLEQFEQLDIILLLKELGISLKEIKDYLD 68 (97)
T ss_pred CCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 799999999999999996999999999982
No 352
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=69.17 E-value=5.2 Score=18.91 Aligned_cols=13 Identities=23% Similarity=0.128 Sum_probs=4.9
Q ss_pred HHHHHHHCCCCHH
Q ss_conf 9999998599979
Q gi|254780694|r 192 ECLTWISEGKTSD 204 (246)
Q Consensus 192 eVl~lia~G~t~~ 204 (246)
..+.-+.+|++..
T Consensus 152 ~~l~AliDGl~l~ 164 (189)
T TIGR03384 152 EGLAALIDGLWLR 164 (189)
T ss_pred HHHHHHHHHHHHH
T ss_conf 9999999899999
No 353
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=69.10 E-value=4.9 Score=19.11 Aligned_cols=30 Identities=17% Similarity=0.104 Sum_probs=19.7
Q ss_pred CCCCHHHHHHH----HHHHCCCCHHHHHHHHCCC
Q ss_conf 88897799999----9998599979999994999
Q gi|254780694|r 184 FELTGREVECL----TWISEGKTSDEIAVILGIS 213 (246)
Q Consensus 184 ~~LT~RE~eVl----~lia~G~t~~eIA~~L~iS 213 (246)
...++...+-| .+=.-|.|-.||.+.|.+.
T Consensus 35 r~Y~~~d~~~L~~I~~~k~lgfsL~eIk~ll~l~ 68 (107)
T cd04777 35 YFFDEKCQDDLEFILELKGLGFSLIEIQKIFSYK 68 (107)
T ss_pred CCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 6619999999999999988899899999999624
No 354
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family; InterPro: IPR014293 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 recognized by the major sigma factors , . This group of sigma factors are members of the sigma-70 family (IPR014284 from INTERPRO). They and appear by homology, tree building, bidirectional best hits and (with one exception, a paralog in Thermobifida fusca strain YX) their 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 (see IPR014295 from INTERPRO) in an apparent operon.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=68.69 E-value=7.9 Score=17.78 Aligned_cols=50 Identities=22% Similarity=0.123 Sum_probs=39.9
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCC
Q ss_conf 999999859997999999499988999999999998079988999999997589
Q gi|254780694|r 192 ECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245 (246)
Q Consensus 192 eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~Gl 245 (246)
-|+--=.+|..++||+.+++...+||-+.+.+..+.| |..++-.|..+|+
T Consensus 139 ~v~~adveGf~ykei~~im~tP~Gtvmsrl~r~rk~l----~~~l~d~a~~rG~ 188 (193)
T TIGR02947 139 AVYFADVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQL----RDLLADVAAERGF 188 (193)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH----HHHHHHHHHHCCC
T ss_conf 8887620353157799885474779999989999999----9999988874054
No 355
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=68.60 E-value=5.6 Score=18.73 Aligned_cols=26 Identities=15% Similarity=0.107 Sum_probs=18.9
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 85999799999949998899999999
Q gi|254780694|r 198 SEGKTSDEIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 198 a~G~t~~eIA~~L~iS~~TV~~hl~~ 223 (246)
++-=+-++||..|++|+.|.|.++++
T Consensus 148 s~~W~L~dIA~~L~mSEStLkRkLk~ 173 (253)
T PRK09940 148 AHPWKLKDICDCLYISESLLKKKLKQ 173 (253)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 00460999998874589999999998
No 356
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=68.58 E-value=5.1 Score=18.97 Aligned_cols=11 Identities=45% Similarity=0.453 Sum_probs=4.5
Q ss_pred CCCHHHHHHHH
Q ss_conf 99979999994
Q gi|254780694|r 200 GKTSDEIAVIL 210 (246)
Q Consensus 200 G~t~~eIA~~L 210 (246)
|.|-+||.+.|
T Consensus 57 GfsL~eI~~lL 67 (139)
T cd01110 57 GLSLAEIAEAL 67 (139)
T ss_pred CCCHHHHHHHH
T ss_conf 99899999999
No 357
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=68.04 E-value=5.2 Score=18.95 Aligned_cols=46 Identities=15% Similarity=0.229 Sum_probs=33.6
Q ss_pred CCCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHH--HHHHHHHHHHHHH
Q ss_conf 8888977999999998-----59997999999499988--9999999999980
Q gi|254780694|r 183 DFELTGREVECLTWIS-----EGKTSDEIAVILGISRN--TVNNYIASIMRKT 228 (246)
Q Consensus 183 ~~~LT~RE~eVl~lia-----~G~t~~eIA~~L~iS~~--TV~~hl~~i~~KL 228 (246)
.-.-|+.+.+-++.|. .|+|-++|...|..... ..+.+++.+..|+
T Consensus 36 ~R~Ys~~di~~l~~I~~L~~~~G~sl~~I~~~L~l~~~~~~l~a~~~~l~~r~ 88 (91)
T cd04766 36 TRRYSERDIERLRRIQRLTQELGVNLAGVKRILELEEELAELRAELDELRARL 88 (91)
T ss_pred CEECCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 97447999999999999999869989999999980844999999999999998
No 358
>PRK00767 transcriptional regulator BetI; Validated
Probab=67.84 E-value=5.8 Score=18.63 Aligned_cols=40 Identities=15% Similarity=0.075 Sum_probs=16.4
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCC----HHHHHHHHHHHHHHHCC
Q ss_conf 99999998599979999994999----88999999999998079
Q gi|254780694|r 191 VECLTWISEGKTSDEIAVILGIS----RNTVNNYIASIMRKTAT 230 (246)
Q Consensus 191 ~eVl~lia~G~t~~eIA~~L~iS----~~TV~~hl~~i~~KLgv 230 (246)
.+.+.-+.+|++-...-.-=..+ ...|..|+...+.+.|.
T Consensus 153 A~~L~AliDGL~l~~~l~p~~~~~e~~~~~~~~~l~~~l~~~~~ 196 (197)
T PRK00767 153 AEGLAALIDGLWLRGALSGDPEDTEAARALAKDYIDQQLAQYGS 196 (197)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCC
T ss_conf 99999999899999986689999999999999999999886379
No 359
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=67.75 E-value=6 Score=18.53 Aligned_cols=30 Identities=17% Similarity=0.208 Sum_probs=18.5
Q ss_pred CCCHHHHHHHHHHH----CCCCHHHHHHHHCCCH
Q ss_conf 88977999999998----5999799999949998
Q gi|254780694|r 185 ELTGREVECLTWIS----EGKTSDEIAVILGISR 214 (246)
Q Consensus 185 ~LT~RE~eVl~lia----~G~t~~eIA~~L~iS~ 214 (246)
..++...+-|.+|. -|+|-+||.+.|....
T Consensus 38 ~Y~~~~l~rL~fI~~~r~~G~sl~eI~~lL~~~d 71 (107)
T cd01111 38 LFDDCALQRLRFVRAAFEAGIGLDELARLCRALD 71 (107)
T ss_pred CCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHC
T ss_conf 3599999999999999987999999999996053
No 360
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=67.35 E-value=5.6 Score=18.72 Aligned_cols=44 Identities=23% Similarity=0.233 Sum_probs=22.2
Q ss_pred CCCHHHHHHHHHH----HCCCCHHHHHHHHCCCH---------HHHHHHHHHHHHHH
Q ss_conf 8897799999999----85999799999949998---------89999999999980
Q gi|254780694|r 185 ELTGREVECLTWI----SEGKTSDEIAVILGISR---------NTVNNYIASIMRKT 228 (246)
Q Consensus 185 ~LT~RE~eVl~li----a~G~t~~eIA~~L~iS~---------~TV~~hl~~i~~KL 228 (246)
.-|+...+.+.+| .-|.|-+||.+.|.+.. ...+.++..|-.|+
T Consensus 38 ~Y~~~~i~~l~~I~~~r~lGfsL~eI~~ll~~~~~~~~~~~~~~~L~~kl~~I~~~i 94 (131)
T cd04786 38 DYPPETVWVLEIISSAQQAGFSLDEIRQLLPADASNWQHDELLAALERKVADIEALE 94 (131)
T ss_pred EECHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 349999999999999999699999999986845789888999999999999999999
No 361
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=67.07 E-value=5.7 Score=18.66 Aligned_cols=29 Identities=21% Similarity=0.379 Sum_probs=17.4
Q ss_pred CCCCHHHHHHHHHH----HCCCCHHHHHHHHCC
Q ss_conf 88897799999999----859997999999499
Q gi|254780694|r 184 FELTGREVECLTWI----SEGKTSDEIAVILGI 212 (246)
Q Consensus 184 ~~LT~RE~eVl~li----a~G~t~~eIA~~L~i 212 (246)
-.-|+...+.++.| .-|.|-+||...|..
T Consensus 37 R~Y~~~~v~rl~~I~~lr~lG~sL~eI~~~l~~ 69 (113)
T cd01109 37 RDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAEL 69 (113)
T ss_pred EECCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 623498989999797599879989999999988
No 362
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=66.92 E-value=5.7 Score=18.68 Aligned_cols=27 Identities=30% Similarity=0.423 Sum_probs=15.3
Q ss_pred CCCHHHHHHHH----HHHCCCCHHHHHHHHC
Q ss_conf 88977999999----9985999799999949
Q gi|254780694|r 185 ELTGREVECLT----WISEGKTSDEIAVILG 211 (246)
Q Consensus 185 ~LT~RE~eVl~----lia~G~t~~eIA~~L~ 211 (246)
.-|+...+-|+ |...|+|-++|.+.|+
T Consensus 37 ~Ys~~di~~l~~I~~l~~~G~sl~~Ik~~LN 67 (67)
T cd04764 37 YYTDEDIELLKKIKTLLEKGLSIKEIKEILN 67 (67)
T ss_pred CCCHHHHHHHHHHHHHHHCCCCHHHHHHHHC
T ss_conf 2399999999999999996998999999859
No 363
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=66.86 E-value=3.2 Score=20.26 Aligned_cols=17 Identities=18% Similarity=0.149 Sum_probs=6.9
Q ss_pred HHHHHHHHCCCEEEEEC
Q ss_conf 99999871930230002
Q gi|254780694|r 49 MYALTEYVGASHFLLVR 65 (246)
Q Consensus 49 ~~~~~~~~g~~~~~~~~ 65 (246)
++++++.+|...-.+++
T Consensus 27 MRrLA~~LgV~~~sLY~ 43 (205)
T PRK13756 27 TRKLAQKLGVEQPTLYW 43 (205)
T ss_pred HHHHHHHHCCCCHHHHH
T ss_conf 99999994899317898
No 364
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=66.60 E-value=6 Score=18.55 Aligned_cols=44 Identities=16% Similarity=0.061 Sum_probs=26.8
Q ss_pred CCCHHHHH----HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 88977999----999998599979999994999889999999999980
Q gi|254780694|r 185 ELTGREVE----CLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 185 ~LT~RE~e----Vl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
.-|+...+ |..+-..|.|-++|...|.-+.......+..-...|
T Consensus 38 ~Y~~~~i~~l~~I~~lr~~G~~l~eI~~~l~~~~~~~~~~L~~~~~~l 85 (103)
T cd01106 38 LYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALREQKELL 85 (103)
T ss_pred ECCHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHHHH
T ss_conf 568999999999999999799999999998089711999999999999
No 365
>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=66.30 E-value=8.8 Score=17.47 Aligned_cols=52 Identities=13% Similarity=0.123 Sum_probs=39.3
Q ss_pred HHHHHHHHC---CCCHHHHHHHHC-CCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 999999985---999799999949-9988999999999998079988999999997
Q gi|254780694|r 191 VECLTWISE---GKTSDEIAVILG-ISRNTVNNYIASIMRKTATKTRSGAIAYAVR 242 (246)
Q Consensus 191 ~eVl~lia~---G~t~~eIA~~L~-iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~ 242 (246)
+.|+-+++. |+|..+||..++ .+..||-+-++++-.++........-...++
T Consensus 32 R~ia~yL~r~~~~~s~~~Ig~~fg~rdHsTV~~a~~kv~~~~~~d~~~~~~v~~i~ 87 (90)
T cd06571 32 RQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEEDPELKEDVEELE 87 (90)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHH
T ss_conf 99999999999788999999995899714999999999999983999999999999
No 366
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=66.22 E-value=8.8 Score=17.46 Aligned_cols=42 Identities=24% Similarity=0.227 Sum_probs=29.2
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHC
Q ss_conf 8599979999994999889999999999980799889999999975
Q gi|254780694|r 198 SEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRN 243 (246)
Q Consensus 198 a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~ 243 (246)
..|+|-.++|..++||+.+|..+.++-. ..+-..+...|...
T Consensus 10 ~~~ls~~~lA~~~gis~~~l~~~e~g~~----~p~~~~l~~la~~~ 51 (58)
T cd00093 10 EKGLTQEELAEKLGVSRSTISRIENGKR----NPSLETLEKLAKAL 51 (58)
T ss_pred HCCCCHHHHHHHCCCCHHHHHHHHCCCC----CCCHHHHHHHHHHH
T ss_conf 7599999995714999999999987998----99999999999993
No 367
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=65.19 E-value=6.6 Score=18.26 Aligned_cols=11 Identities=18% Similarity=0.286 Sum_probs=3.8
Q ss_pred CCCHHHHHHHH
Q ss_conf 99979999994
Q gi|254780694|r 200 GKTSDEIAVIL 210 (246)
Q Consensus 200 G~t~~eIA~~L 210 (246)
|.|-+||.+.|
T Consensus 57 GfsL~EI~~LL 67 (135)
T PRK10227 57 GFNLEESGELV 67 (135)
T ss_pred CCCHHHHHHHH
T ss_conf 99999999997
No 368
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=65.11 E-value=6.6 Score=18.27 Aligned_cols=33 Identities=18% Similarity=0.126 Sum_probs=21.5
Q ss_pred CCCCCHHHHHHH----HHHHCCCCHHHHHHHHCCCHH
Q ss_conf 888897799999----999859997999999499988
Q gi|254780694|r 183 DFELTGREVECL----TWISEGKTSDEIAVILGISRN 215 (246)
Q Consensus 183 ~~~LT~RE~eVl----~lia~G~t~~eIA~~L~iS~~ 215 (246)
.-.-|+...+-+ .+-..|+|-++|.+.|.....
T Consensus 35 ~R~Y~~~~i~~l~~I~~lr~~G~sl~~I~~~l~~~~~ 71 (100)
T cd00592 35 YRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDE 71 (100)
T ss_pred CCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCC
T ss_conf 7425699999999999999979999999999835577
No 369
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=65.04 E-value=9.3 Score=17.32 Aligned_cols=23 Identities=30% Similarity=0.421 Sum_probs=9.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 99799999949998899999999
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~~ 223 (246)
+-..|||+.|+++..|+..|++.
T Consensus 38 lNvneiAe~lgLpqst~s~~ik~ 60 (308)
T COG4189 38 LNVNEIAEALGLPQSTMSANIKV 60 (308)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 87899998858865666655788
No 370
>PRK10072 putative transcriptional regulator; Provisional
Probab=64.84 E-value=6.7 Score=18.24 Aligned_cols=32 Identities=31% Similarity=0.441 Sum_probs=24.5
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 999999998599979999994999889999999
Q gi|254780694|r 190 EVECLTWISEGKTSDEIAVILGISRNTVNNYIA 222 (246)
Q Consensus 190 E~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~ 222 (246)
|.+-++ -.-|++-.|-|+.+|+|..||++-=.
T Consensus 37 dvkaIR-~~tgl~q~eFA~~lGvSv~tvksWEq 68 (96)
T PRK10072 37 EFEQLR-KGTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred CHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 399999-88099999999997777999999996
No 371
>pfam00292 PAX 'Paired box' domain.
Probab=64.62 E-value=9.4 Score=17.27 Aligned_cols=38 Identities=13% Similarity=0.178 Sum_probs=32.8
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 99999999859997999999499988999999999998
Q gi|254780694|r 190 EVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 190 E~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
-.+|++|...|..--+|++.|.+|..-|..-+.+.++.
T Consensus 23 R~kIVeLa~~G~RpCdISR~L~VShGCVSKIL~Ry~et 60 (125)
T pfam00292 23 RQKIVELAHSGVRPCDISRQLRVSHGCVSKILGRYQET 60 (125)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHC
T ss_conf 99999999849978888776267621689999988722
No 372
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=64.62 E-value=6.9 Score=18.14 Aligned_cols=27 Identities=22% Similarity=0.324 Sum_probs=17.5
Q ss_pred CCCHHHHHHHH----HHHCCCCHHHHHHHHC
Q ss_conf 88977999999----9985999799999949
Q gi|254780694|r 185 ELTGREVECLT----WISEGKTSDEIAVILG 211 (246)
Q Consensus 185 ~LT~RE~eVl~----lia~G~t~~eIA~~L~ 211 (246)
..|+...+-+. +-.-|+|-+||.+.|.
T Consensus 37 ~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~l~ 67 (112)
T cd01282 37 DYDEAAVDRVRQIRRLLAAGLTLEEIREFLP 67 (112)
T ss_pred ECCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 0599999999999999996999999999998
No 373
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor; InterPro: IPR014294 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 recognized by the major sigma factors , . This entry represents sigmaW, which is restricted to certain lineages of the order Bacillales..
Probab=64.40 E-value=1.8 Score=21.90 Aligned_cols=35 Identities=29% Similarity=0.304 Sum_probs=27.2
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 999999998599979999994999889999999999
Q gi|254780694|r 190 EVECLTWISEGKTSDEIAVILGISRNTVNNYIASIM 225 (246)
Q Consensus 190 E~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~ 225 (246)
-.=||+.+ +-+|-+||+++|++-..||++-+.+=.
T Consensus 143 ~~ivLKY~-edLSL~EIS~IL~lPVgTVKTRiHRGR 177 (187)
T TIGR02948 143 SVIVLKYM-EDLSLKEISEILDLPVGTVKTRIHRGR 177 (187)
T ss_pred EEHHHHHH-HHHHHHHHHHHHCCCCCCEECCCCCCH
T ss_conf 22245444-442188899985789431002430245
No 374
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=64.36 E-value=6.2 Score=18.43 Aligned_cols=26 Identities=15% Similarity=0.479 Sum_probs=15.9
Q ss_pred CCCHHHHH----HHHHHHCCCCHHHHHHHH
Q ss_conf 88977999----999998599979999994
Q gi|254780694|r 185 ELTGREVE----CLTWISEGKTSDEIAVIL 210 (246)
Q Consensus 185 ~LT~RE~e----Vl~lia~G~t~~eIA~~L 210 (246)
.-|+.+.+ |..|...|+|-++|+..|
T Consensus 38 ~Ys~~di~~l~~I~~l~~~G~~i~~i~~lL 67 (68)
T cd04763 38 LFNDADIDRILEIKRWIDNGVQVSKVKKLL 67 (68)
T ss_pred CCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 549999999999999999799899999972
No 375
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=64.16 E-value=9.6 Score=17.22 Aligned_cols=29 Identities=14% Similarity=0.282 Sum_probs=24.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 997999999499988999999999998079
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
+|-.+||..||+|+.||...++..-++ |+
T Consensus 174 ~t~~~lA~~lG~tretvsR~L~~L~~~-GI 202 (236)
T PRK09392 174 YEKRTLASYLGMTPENLSRAFAALASH-GV 202 (236)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHC-CC
T ss_conf 789999998789899999999999979-96
No 376
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=63.96 E-value=7.1 Score=18.05 Aligned_cols=44 Identities=16% Similarity=0.192 Sum_probs=25.0
Q ss_pred CCCHHHHH----HHHHHHCCCCHHHHHHHHCCC--HHHHHHHHHHHHHHH
Q ss_conf 88977999----999998599979999994999--889999999999980
Q gi|254780694|r 185 ELTGREVE----CLTWISEGKTSDEIAVILGIS--RNTVNNYIASIMRKT 228 (246)
Q Consensus 185 ~LT~RE~e----Vl~lia~G~t~~eIA~~L~iS--~~TV~~hl~~i~~KL 228 (246)
.-|+...+ |..+=.-|.|-+||...|.-. ....+.++..|-++.
T Consensus 38 ~Y~~~~i~~l~~I~~lr~~G~sL~eIk~lL~~~~~~~~l~~~~~~i~~~I 87 (102)
T cd04775 38 LYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQPHVQAILEERLQSLNREI 87 (102)
T ss_pred ECCHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf 37899999999999999969999999999859957999999999999999
No 377
>PHA00675 hypothetical protein
Probab=63.17 E-value=10 Score=17.10 Aligned_cols=41 Identities=22% Similarity=0.242 Sum_probs=35.3
Q ss_pred CCCCCCHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 888889779999999985--99979999994999889999999
Q gi|254780694|r 182 KDFELTGREVECLTWISE--GKTSDEIAVILGISRNTVNNYIA 222 (246)
Q Consensus 182 ~~~~LT~RE~eVl~lia~--G~t~~eIA~~L~iS~~TV~~hl~ 222 (246)
....||+-+.|..+-+-+ |+++..+|....+|..||-...+
T Consensus 19 hna~ltd~~Vd~IR~LrE~~gl~Yg~La~~f~~pkgtIAkICq 61 (78)
T PHA00675 19 PNAKLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred CCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 5565778999999999987284389999997275689999988
No 378
>pfam08765 Mor Mor transcription activator family. 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 dimerization region, and the C terminal contains a helix-turn-helix motif which binds DNA.
Probab=62.64 E-value=10 Score=17.04 Aligned_cols=46 Identities=22% Similarity=0.362 Sum_probs=39.8
Q ss_pred CCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 98888897799999999859997999999499988999999999998
Q gi|254780694|r 181 GKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 181 ~~~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
+.....+.|..+|..-. .|....|+|.+=++|+.+|..-+++..+-
T Consensus 53 ~~~~~~~~Rd~~I~~eF-nG~N~~eLArkY~ls~~~i~~ii~~~rk~ 98 (107)
T pfam08765 53 GQSLRLALRDLEIYNEF-NGNNHAELARKYGVSEQWIYKIIKRVRKL 98 (107)
T ss_pred CHHHHHHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 54888999999999980-79879999999698899999999999999
No 379
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=62.49 E-value=10 Score=17.06 Aligned_cols=25 Identities=32% Similarity=0.512 Sum_probs=20.0
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 9799999949998899999999999
Q gi|254780694|r 202 TSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 202 t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
|-+++|+.+++|..||+.=++.+..
T Consensus 22 s~~~la~~~~vSr~tvr~A~~~L~~ 46 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEA 46 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 0999999989499999999999998
No 380
>pfam10078 DUF2316 Uncharacterized protein conserved in bacteria (DUF2316). Members of this family of hypothetical bacterial proteins have no known function.
Probab=62.44 E-value=9.7 Score=17.19 Aligned_cols=27 Identities=19% Similarity=0.265 Sum_probs=21.3
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 999859997999999499988999999
Q gi|254780694|r 195 TWISEGKTSDEIAVILGISRNTVNNYI 221 (246)
Q Consensus 195 ~lia~G~t~~eIA~~L~iS~~TV~~hl 221 (246)
..--.|+|-.+||..|++|+.-|+.-+
T Consensus 18 Nf~~~~ls~~~iA~dL~~s~~~ve~vL 44 (89)
T pfam10078 18 NFELSGLTIEQVAKDLNTTPEKVEALL 44 (89)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 998838989999989499999999999
No 381
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=62.42 E-value=7.9 Score=17.76 Aligned_cols=44 Identities=23% Similarity=0.295 Sum_probs=22.1
Q ss_pred CCCHHHHHHHHHH----HCCCCHHHHHHHHCC------CH----HHHHHHHHHHHHHH
Q ss_conf 8897799999999----859997999999499------98----89999999999980
Q gi|254780694|r 185 ELTGREVECLTWI----SEGKTSDEIAVILGI------SR----NTVNNYIASIMRKT 228 (246)
Q Consensus 185 ~LT~RE~eVl~li----a~G~t~~eIA~~L~i------S~----~TV~~hl~~i~~KL 228 (246)
.-++...+-+.+| .-|.|-+||...|.+ +. ..++.|+..|-.|.
T Consensus 38 ~Y~~~~l~~l~~I~~lr~~GfsL~eI~~ll~l~~~~~~~~~~~~~ll~~kl~~i~~~I 95 (127)
T cd04784 38 LYDEEHLERLLFIRRCRSLDMSLDEIRTLLQLQDDPEASCAEVNALIDEHLAHVRARI 95 (127)
T ss_pred ECCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 3639999999999999864987999999997772899989999999999999999999
No 382
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=61.82 E-value=5.1 Score=18.96 Aligned_cols=22 Identities=32% Similarity=0.498 Sum_probs=13.2
Q ss_pred CCHHHHHHHHC-----CCHHHHHHHHH
Q ss_conf 99799999949-----99889999999
Q gi|254780694|r 201 KTSDEIAVILG-----ISRNTVNNYIA 222 (246)
Q Consensus 201 ~t~~eIA~~L~-----iS~~TV~~hl~ 222 (246)
+|+.+|+..|. ||.|||-.|..
T Consensus 422 lSD~~i~~~L~~~Gi~iaRRTVaKYRe 448 (461)
T PRK05932 422 LSDSKIAELLKEQGIDVARRTVAKYRE 448 (461)
T ss_pred CCHHHHHHHHHHCCCCEEECCHHHHHH
T ss_conf 999999999996799764214799998
No 383
>pfam04233 Phage_Mu_F Phage Mu protein F like protein. Members of this family are found in double-stranded DNA bacteriophages, and in some bacteria. A member of this family is required for viral head morphogenesis in bacteriophage SPP1. This family is possibly a minor head protein. This family may be related to the family TT_ORF1 (pfam02956).
Probab=61.55 E-value=8 Score=17.72 Aligned_cols=21 Identities=24% Similarity=0.165 Sum_probs=11.3
Q ss_pred HHHHHHHHHCCCCHHHHHHHH
Q ss_conf 999999998599979999994
Q gi|254780694|r 190 EVECLTWISEGKTSDEIAVIL 210 (246)
Q Consensus 190 E~eVl~lia~G~t~~eIA~~L 210 (246)
+.++.+-+.+|++..+||..|
T Consensus 4 ~~~l~~gi~~G~~~~~ia~~i 24 (110)
T pfam04233 4 RDALTQAIMRGEGYEELAKRL 24 (110)
T ss_pred HHHHHHHHHCCCCHHHHHHHH
T ss_conf 999999999399999999999
No 384
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=61.09 E-value=9.1 Score=17.37 Aligned_cols=27 Identities=19% Similarity=0.139 Sum_probs=19.7
Q ss_pred CCCHHHHH----HHHHHHCCCCHHHHHHHHC
Q ss_conf 88977999----9999985999799999949
Q gi|254780694|r 185 ELTGREVE----CLTWISEGKTSDEIAVILG 211 (246)
Q Consensus 185 ~LT~RE~e----Vl~lia~G~t~~eIA~~L~ 211 (246)
.-|+...+ |..|...|.|-++|++.|.
T Consensus 39 ~Ys~~dl~~l~~I~~l~~~G~sl~~i~~~L~ 69 (88)
T cd01105 39 KYSLADVDRLLVIKELLDEGFTLAAAVEKLR 69 (88)
T ss_pred ECCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 4799999999999999997998999999999
No 385
>pfam07508 Recombinase Recombinase. This domain is usually found associated with pfam00239 in putative integrases/recombinases of mobile genetic elements of diverse bacteria and phages.
Probab=61.08 E-value=8.1 Score=17.70 Aligned_cols=33 Identities=27% Similarity=0.306 Sum_probs=21.1
Q ss_pred HHHHHHHHCCCCHHHHHHHHC-----------CCHHHHHHHHHH
Q ss_conf 999999985999799999949-----------998899999999
Q gi|254780694|r 191 VECLTWISEGKTSDEIAVILG-----------ISRNTVNNYIAS 223 (246)
Q Consensus 191 ~eVl~lia~G~t~~eIA~~L~-----------iS~~TV~~hl~~ 223 (246)
++|..+.++|+|..+||..|+ -|..||..-|+|
T Consensus 8 r~if~~~~~g~s~~~Ia~~Ln~~g~~~~~~~~w~~~~I~~iL~N 51 (101)
T pfam07508 8 RLIFELYLEGKSLREIARYLNERGIPTPRGKKWTKSTVRRILTN 51 (101)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHCC
T ss_conf 99999998389999999999874996778982464435566208
No 386
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=60.91 E-value=8.6 Score=17.54 Aligned_cols=14 Identities=21% Similarity=0.090 Sum_probs=6.6
Q ss_pred HCCCCHHHHHHHHC
Q ss_conf 85999799999949
Q gi|254780694|r 198 SEGKTSDEIAVILG 211 (246)
Q Consensus 198 a~G~t~~eIA~~L~ 211 (246)
.-|+|-+||-+.|.
T Consensus 54 ~lg~sL~eIk~lL~ 67 (134)
T cd04779 54 GQRLSLAEIKDQLE 67 (134)
T ss_pred HCCCCHHHHHHHHH
T ss_conf 97998999999984
No 387
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=60.70 E-value=11 Score=16.82 Aligned_cols=12 Identities=8% Similarity=-0.047 Sum_probs=4.2
Q ss_pred HHHHHHHHHHCC
Q ss_conf 999999987193
Q gi|254780694|r 47 MRMYALTEYVGA 58 (246)
Q Consensus 47 ~~~~~~~~~~g~ 58 (246)
..+.++-+.+|.
T Consensus 55 ~aL~rLr~~~gd 66 (314)
T PRK09508 55 NAVARLKVMFND 66 (314)
T ss_pred HHHHHHHHHHCC
T ss_conf 999999998199
No 388
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=60.49 E-value=9 Score=17.40 Aligned_cols=11 Identities=45% Similarity=0.555 Sum_probs=3.9
Q ss_pred CCCHHHHHHHH
Q ss_conf 99979999994
Q gi|254780694|r 200 GKTSDEIAVIL 210 (246)
Q Consensus 200 G~t~~eIA~~L 210 (246)
|+|-+||.+.|
T Consensus 58 GfsL~eI~~ll 68 (140)
T PRK09514 58 GFTLEEIRELL 68 (140)
T ss_pred CCCHHHHHHHH
T ss_conf 99999999998
No 389
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=60.41 E-value=5.6 Score=18.73 Aligned_cols=16 Identities=6% Similarity=-0.039 Sum_probs=5.0
Q ss_pred CCCHHHHHHHHHHHCC
Q ss_conf 8897799999999859
Q gi|254780694|r 185 ELTGREVECLTWISEG 200 (246)
Q Consensus 185 ~LT~RE~eVl~lia~G 200 (246)
+|.+.=...+..+-+|
T Consensus 185 dL~~~~~~lvd~~l~~ 200 (213)
T PRK09975 185 DLYKQAPALVDNVLRM 200 (213)
T ss_pred CHHHHHHHHHHHHHHH
T ss_conf 9899999999999987
No 390
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=60.08 E-value=10 Score=17.02 Aligned_cols=27 Identities=22% Similarity=0.209 Sum_probs=17.5
Q ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 8888977999999998599979999994
Q gi|254780694|r 183 DFELTGREVECLTWISEGKTSDEIAVIL 210 (246)
Q Consensus 183 ~~~LT~RE~eVl~lia~G~t~~eIA~~L 210 (246)
...||+.|.+.|.++-+ +...|-=..|
T Consensus 82 ~~~L~~~q~~LLeLf~~-LP~sEq~~~l 108 (135)
T PRK09706 82 PVELSEDQKELLELFDA-LPESEQEAQL 108 (135)
T ss_pred CCCCCHHHHHHHHHHHH-CCHHHHHHHH
T ss_conf 55589999999999997-8899999999
No 391
>PRK11753 cAMP-regulatory protein; Provisional
Probab=59.81 E-value=11 Score=16.72 Aligned_cols=26 Identities=31% Similarity=0.388 Sum_probs=22.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 99799999949998899999999999
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
.|-.|||..+|+|+.||..-++..-+
T Consensus 169 lt~~eLA~~lG~sretvsR~L~~L~~ 194 (211)
T PRK11753 169 ITRQEIGRIVGCSREMVGRVLKMLED 194 (211)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 69999998869989999999999998
No 392
>PRK09480 slmA nucleoid occlusion protein; Provisional
Probab=59.43 E-value=9.4 Score=17.29 Aligned_cols=14 Identities=36% Similarity=0.346 Sum_probs=5.1
Q ss_pred HHHHHHCCCEEEEE
Q ss_conf 99987193023000
Q gi|254780694|r 51 ALTEYVGASHFLLV 64 (246)
Q Consensus 51 ~~~~~~g~~~~~~~ 64 (246)
.++..+|...-+++
T Consensus 35 ~iA~~~gvs~aalY 48 (194)
T PRK09480 35 KLAARVGVSEAALY 48 (194)
T ss_pred HHHHHHCCCHHHHH
T ss_conf 99989099789999
No 393
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=59.37 E-value=9 Score=17.41 Aligned_cols=37 Identities=30% Similarity=0.456 Sum_probs=23.8
Q ss_pred CHHHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 9779999999985-999799999949998899999999
Q gi|254780694|r 187 TGREVECLTWISE-GKTSDEIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 187 T~RE~eVl~lia~-G~t~~eIA~~L~iS~~TV~~hl~~ 223 (246)
+|-|.=-=+++-. |+|-.+.|+.|+|+++||..-+++
T Consensus 9 ~PGEiL~eeflep~glt~~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 9 HPGEILREEFLEPLGLTQTELAEALGVTRNTISELING 46 (104)
T ss_pred CCHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHCC
T ss_conf 94188999984521698999999939989999999837
No 394
>KOG0723 consensus
Probab=59.28 E-value=6.5 Score=18.29 Aligned_cols=36 Identities=19% Similarity=0.266 Sum_probs=30.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHH
Q ss_conf 599979999994999889999999999980799889
Q gi|254780694|r 199 EGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRS 234 (246)
Q Consensus 199 ~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~ 234 (246)
.-+|-+|-+.+|++|+.+.+..++...+|.=+.|-.
T Consensus 51 ~kMsr~EA~lIL~v~~s~~k~KikeaHrriM~~NHP 86 (112)
T KOG0723 51 PKMSRREAALILGVTPSLDKDKIKEAHRRIMLANHP 86 (112)
T ss_pred CCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCC
T ss_conf 321568899882787545688999999999980798
No 395
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=59.26 E-value=8.9 Score=17.44 Aligned_cols=27 Identities=33% Similarity=0.516 Sum_probs=21.5
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 985999799999949998899999999
Q gi|254780694|r 197 ISEGKTSDEIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 197 ia~G~t~~eIA~~L~iS~~TV~~hl~~ 223 (246)
--.|+|-.+.|..|++|.+||..|=+.
T Consensus 135 ee~glSlG~lA~~lgVSRktV~~YE~G 161 (313)
T COG1395 135 EEMGLSLGDLATMLGVSRKTVYKYEKG 161 (313)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHCCC
T ss_conf 980867878898838468889876247
No 396
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=58.50 E-value=9.5 Score=17.25 Aligned_cols=43 Identities=12% Similarity=0.077 Sum_probs=26.1
Q ss_pred CCCHHHHHH----HHHHHCCCCHHHHHHHHCCCHHH----HHHHHHHHHHH
Q ss_conf 889779999----99998599979999994999889----99999999998
Q gi|254780694|r 185 ELTGREVEC----LTWISEGKTSDEIAVILGISRNT----VNNYIASIMRK 227 (246)
Q Consensus 185 ~LT~RE~eV----l~lia~G~t~~eIA~~L~iS~~T----V~~hl~~i~~K 227 (246)
.-|+.+.+. ..+-.-|+|-+||...|+-+... .+.|+..+-.+
T Consensus 38 ~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~~~~~~~~e~l~~~~~~le~q 88 (96)
T cd04788 38 LYDRADIRRLHQIIALRRLGFSLREIGRALDGPDFDPLELLRRQLARLEEQ 88 (96)
T ss_pred ECCHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
T ss_conf 189999999999999999799999999998089813999999999999999
No 397
>pfam00392 GntR Bacterial regulatory proteins, gntR family. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor.
Probab=58.21 E-value=12 Score=16.55 Aligned_cols=24 Identities=29% Similarity=0.479 Sum_probs=19.2
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 979999994999889999999999
Q gi|254780694|r 202 TSDEIAVILGISRNTVNNYIASIM 225 (246)
Q Consensus 202 t~~eIA~~L~iS~~TV~~hl~~i~ 225 (246)
|-+++|+.+++|..||+.=++.+-
T Consensus 26 s~~~La~~~~vSr~tvr~Al~~L~ 49 (64)
T pfam00392 26 SERELAAEFGVSRTTVREALRRLE 49 (64)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 799999997969999999999999
No 398
>pfam01498 Transposase_5 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of C.elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in. Tc3 is a member of the Tc1/mariner family of transposable elements.
Probab=58.11 E-value=9.8 Score=17.16 Aligned_cols=23 Identities=26% Similarity=0.332 Sum_probs=18.0
Q ss_pred CCHHHHHHHH-----CCCHHHHHHHHHH
Q ss_conf 9979999994-----9998899999999
Q gi|254780694|r 201 KTSDEIAVIL-----GISRNTVNNYIAS 223 (246)
Q Consensus 201 ~t~~eIA~~L-----~iS~~TV~~hl~~ 223 (246)
.|..+|+.+| .||+.||+..|.+
T Consensus 14 ~T~~~i~~~l~~~g~~vS~~Tvrr~L~~ 41 (72)
T pfam01498 14 ITLRDLANELQEIGKSVSRSTIRRRLHK 41 (72)
T ss_pred CCHHHHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf 4699999999985997279999999998
No 399
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=58.05 E-value=12 Score=16.53 Aligned_cols=26 Identities=19% Similarity=0.248 Sum_probs=22.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 99799999949998899999999999
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
.+..|||..+|+|..||...++....
T Consensus 157 ~~~~elA~~lG~Sretl~R~L~~f~~ 182 (213)
T PRK10402 157 EKHTQAAEYLGVSYRHLLYVLAQFCQ 182 (213)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 67999999979889999999999998
No 400
>COG3177 Fic family protein [Function unknown]
Probab=57.94 E-value=12 Score=16.52 Aligned_cols=28 Identities=29% Similarity=0.425 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 5999799999949998899999999999
Q gi|254780694|r 199 EGKTSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 199 ~G~t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
.+.|..++...+++|..|++.+++.+-.
T Consensus 303 ~~~t~~~~~~~~~~s~~Ta~r~l~~l~~ 330 (348)
T COG3177 303 GYLTAAEIEAILGVSKATATRDLKELLE 330 (348)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 7645999999828988889999999974
No 401
>TIGR01321 TrpR trp operon repressor; InterPro: IPR013335 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. This entry represents Trp repressors found in proteobacterial and chlamydial species.; GO: 0016564 transcription repressor activity, 0006355 regulation of transcription DNA-dependent.
Probab=57.89 E-value=12 Score=16.52 Aligned_cols=33 Identities=24% Similarity=0.212 Sum_probs=24.9
Q ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 977999999998599979999994999889999
Q gi|254780694|r 187 TGREVECLTWISEGKTSDEIAVILGISRNTVNN 219 (246)
Q Consensus 187 T~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~ 219 (246)
..|=+=|-.|+-.-+|=+||+..||+|..|+-.
T Consensus 43 ~~R~~I~~~LL~~~~~QREi~~~lG~SiA~ITR 75 (95)
T TIGR01321 43 GSRVRIVEELLEGEMSQREIAEKLGVSIATITR 75 (95)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 879999999961489747888863761667878
No 402
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=56.73 E-value=11 Score=16.80 Aligned_cols=26 Identities=23% Similarity=0.206 Sum_probs=13.8
Q ss_pred CCCCHHHHHHHHH----HHCCCCHHHHHHH
Q ss_conf 8889779999999----9859997999999
Q gi|254780694|r 184 FELTGREVECLTW----ISEGKTSDEIAVI 209 (246)
Q Consensus 184 ~~LT~RE~eVl~l----ia~G~t~~eIA~~ 209 (246)
-.-|+...+.+.+ ...|.+-++|++.
T Consensus 37 R~Ys~~dv~~l~~I~~l~~~G~~l~~I~~l 66 (68)
T cd01104 37 RLYSEADVARLRLIRRLTSEGVRISQAAAL 66 (68)
T ss_pred EECCHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 504999999999999999978999999987
No 403
>TIGR02612 mob_myst_A mobile mystery protein A; InterPro: IPR013435 Proteins in this entry are more often encoded within mobilisation-related contexts than not. This includes a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and plasmids in Agrobacterium tumefaciens and Coxiella burnetii. They are found together with mobile mystery protein B, a member of the Fic protein family (IPR003812 from INTERPRO). Mobile mystery protein A is encoded by the upstream member of the gene pair and contains a helix-turn-helix domain..
Probab=56.72 E-value=8.9 Score=17.44 Aligned_cols=18 Identities=28% Similarity=0.549 Sum_probs=5.9
Q ss_pred CCCHHHHHHHHCCCHHHH
Q ss_conf 999799999949998899
Q gi|254780694|r 200 GKTSDEIAVILGISRNTV 217 (246)
Q Consensus 200 G~t~~eIA~~L~iS~~TV 217 (246)
|+|-.+.|.+|||.+.+|
T Consensus 38 Gms~~QLA~RlGV~p~Rv 55 (150)
T TIGR02612 38 GMSGAQLAARLGVTPQRV 55 (150)
T ss_pred CCCHHHHHHHCCCCHHHH
T ss_conf 515788766528973779
No 404
>pfam06322 Phage_NinH Phage NinH protein. This family consists of several phage NinH proteins. The function of this family is unknown.
Probab=55.80 E-value=7.5 Score=17.91 Aligned_cols=24 Identities=38% Similarity=0.394 Sum_probs=19.3
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 799999949998899999999999
Q gi|254780694|r 203 SDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 203 ~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
-.|+|+.|+.|.+||+.|....-.
T Consensus 19 ~teVaR~L~c~R~TVrkY~~D~~~ 42 (64)
T pfam06322 19 QTEVARRLNCSRNTVRKYAEDKEG 42 (64)
T ss_pred HHHHHHHHCCHHHHHHHHHCCCCC
T ss_conf 999978851108889987235556
No 405
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=55.68 E-value=6.2 Score=18.45 Aligned_cols=27 Identities=19% Similarity=0.207 Sum_probs=18.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 599979999994999889999999999
Q gi|254780694|r 199 EGKTSDEIAVILGISRNTVNNYIASIM 225 (246)
Q Consensus 199 ~G~t~~eIA~~L~iS~~TV~~hl~~i~ 225 (246)
.-++.++||..|++++.||-.-+++=|
T Consensus 362 kPL~lkdiA~~lglheSTVSRav~~Ky 388 (475)
T PRK12469 362 KPLVLRDVAEELGLHESTVSRATGNKY 388 (475)
T ss_pred CCCCHHHHHHHHCCCCCHHHHHHCCCE
T ss_conf 673499999981998203768862750
No 406
>PRK06474 hypothetical protein; Provisional
Probab=55.28 E-value=14 Score=16.24 Aligned_cols=13 Identities=0% Similarity=0.148 Sum_probs=5.1
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 9999999999998
Q gi|254780694|r 42 TVSWTMRMYALTE 54 (246)
Q Consensus 42 ~~~~~~~~~~~~~ 54 (246)
...+.+.+..+.+
T Consensus 42 qATLYRHv~~L~e 54 (180)
T PRK06474 42 QATLYRQIQTMVD 54 (180)
T ss_pred HHHHHHHHHHHHH
T ss_conf 7999999999975
No 407
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=55.06 E-value=14 Score=16.22 Aligned_cols=34 Identities=21% Similarity=0.367 Sum_probs=19.9
Q ss_pred HHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 9999999859-997999999499988999999999998
Q gi|254780694|r 191 VECLTWISEG-KTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 191 ~eVl~lia~G-~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
..+..++..+ .+..+||..+|.+-. .|..+.|+|
T Consensus 40 ~~a~~~L~~~~~~i~~ia~~~Gy~~~---s~f~r~Fk~ 74 (84)
T smart00342 40 ERARRLLRDTDLSVTEIALRVGFSSQ---SYFSRAFKK 74 (84)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCCCH---HHHHHHHHH
T ss_conf 99999998576349999888199999---999999999
No 408
>pfam09999 DUF2240 Uncharacterized protein conserved in archaea (DUF2240). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=54.57 E-value=14 Score=16.17 Aligned_cols=42 Identities=24% Similarity=0.305 Sum_probs=36.0
Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHC--CCCHHHHHHHHHHCCC
Q ss_conf 99999949998899999999999807--9988999999997589
Q gi|254780694|r 204 DEIAVILGISRNTVNNYIASIMRKTA--TKTRSGAIAYAVRNNI 245 (246)
Q Consensus 204 ~eIA~~L~iS~~TV~~hl~~i~~KLg--v~~R~eav~~A~~~Gl 245 (246)
..|+...+++.+.|-.-++.+.+-|| +.=.+.++.+|.+.|+
T Consensus 92 d~i~a~~g~~k~Evv~~in~~q~~l~~lvt~e~A~llvAre~Gl 135 (144)
T pfam09999 92 DRIAASAGIEKQEVVAEINELQETLGGLVDPEAAALLVAKKYGI 135 (144)
T ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCC
T ss_conf 99999649988999999999999855668799999999999499
No 409
>PHA00542 putative Cro-like protein
Probab=53.98 E-value=14 Score=16.11 Aligned_cols=38 Identities=18% Similarity=0.259 Sum_probs=29.9
Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 888977999999998599979999994999889999999
Q gi|254780694|r 184 FELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIA 222 (246)
Q Consensus 184 ~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~ 222 (246)
+.-+|-|. |..|++.|.|-.+|+..-+|+..++..-+.
T Consensus 16 y~k~P~E~-V~aLi~~G~tQ~qI~~~tgv~QpsisRils 53 (82)
T PHA00542 16 YTQRPDEL-VCALIRAGWSQEQIADATDVSQPTICRIYS 53 (82)
T ss_pred HHCCHHHH-HHHHHHCCCCHHHHHHHHCCCCHHHHHHHC
T ss_conf 53298999-999998225699999860877036899980
No 410
>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=53.84 E-value=14 Score=16.10 Aligned_cols=24 Identities=33% Similarity=0.484 Sum_probs=19.6
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 979999994999889999999999
Q gi|254780694|r 202 TSDEIAVILGISRNTVNNYIASIM 225 (246)
Q Consensus 202 t~~eIA~~L~iS~~TV~~hl~~i~ 225 (246)
|-+++|+.+++|..||+.=++.+-
T Consensus 27 s~~~La~~~~vSr~tvr~Al~~L~ 50 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELE 50 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 799999997988899999999999
No 411
>pfam07022 Phage_CI_repr Bacteriophage CI repressor helix-turn-helix domain. This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic.
Probab=53.20 E-value=14 Score=16.10 Aligned_cols=42 Identities=24% Similarity=0.349 Sum_probs=26.5
Q ss_pred HCC-CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCC
Q ss_conf 859-99799999949998899999999999807998899999999758
Q gi|254780694|r 198 SEG-KTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNN 244 (246)
Q Consensus 198 a~G-~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~G 244 (246)
+-| +|..|.|+.|+||..||.+-.+ =|.-.---.|..|.+.|
T Consensus 9 a~G~~t~~eLA~~LgI~~stis~w~~-----R~~~P~e~iv~~~~~tG 51 (65)
T pfam07022 9 AYGFKSRSELADHLGVSKSTLSTWYK-----RDSFPAEWVIRCALETG 51 (65)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHH-----CCCCCHHHHHHHHHHHC
T ss_conf 96888699999996988888999998-----69998999999999988
No 412
>COG2469 Uncharacterized conserved protein [Function unknown]
Probab=52.68 E-value=8.4 Score=17.60 Aligned_cols=47 Identities=17% Similarity=0.279 Sum_probs=42.1
Q ss_pred CCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 98888897799999999859997999999499988999999999998
Q gi|254780694|r 181 GKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 181 ~~~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
.+...||+-|.++|-++-.|-.+.++...|+++..-++....++..|
T Consensus 209 k~~~~LsE~E~qiLvalYSg~~~~sl~~~lG~~~~el~~l~drlI~~ 255 (284)
T COG2469 209 KEKETLSEIEKQILVALYSGGDSASLELFLGVDTDELEILYDRLIDK 255 (284)
T ss_pred CCCCCCCHHHHEEEEEEECCCCCHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 32223330312113667528982303567487699999999999873
No 413
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=52.06 E-value=14 Score=16.13 Aligned_cols=28 Identities=14% Similarity=0.156 Sum_probs=17.9
Q ss_pred CCHHH----HHHHHHH-HCCCCHHHHHHHHCCC
Q ss_conf 89779----9999999-8599979999994999
Q gi|254780694|r 186 LTGRE----VECLTWI-SEGKTSDEIAVILGIS 213 (246)
Q Consensus 186 LT~RE----~eVl~li-a~G~t~~eIA~~L~iS 213 (246)
-|+.. +.|.+|+ ..|.+-.+|.+.|.+-
T Consensus 38 Ys~~Di~rLrfIkrL~~e~G~nlagI~~iLsl~ 70 (120)
T cd04767 38 YSNNDLKRLRFIKKLINEKGLNIAGVKQILSMY 70 (120)
T ss_pred CCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCC
T ss_conf 799999999999999997596899999998063
No 414
>pfam06970 RepA_N Replication initiator protein A (RepA) N-terminus. This of family of predicted proteins represents the N-terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids. Most proteins in this family are bacterial, but archaeal and eukaryotic members are also included.
Probab=51.64 E-value=15 Score=15.92 Aligned_cols=22 Identities=23% Similarity=0.253 Sum_probs=18.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 9979999994999889999999
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIA 222 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~ 222 (246)
.|+.|++..|++|..||-.-.+
T Consensus 53 ft~~el~~~L~~s~~~v~k~~k 74 (76)
T pfam06970 53 FTNEELMELLNCSKQKVIKIKK 74 (76)
T ss_pred EEHHHHHHHHCCCHHHHHHHHH
T ss_conf 6499999997878889999996
No 415
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=51.46 E-value=16 Score=15.86 Aligned_cols=44 Identities=30% Similarity=0.306 Sum_probs=36.1
Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 89779999999985999799999949998899999999999807
Q gi|254780694|r 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 186 LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
|=+.-..+..++-.|.+-..||+.++|+..||...+++...+..
T Consensus 75 ~~~~~~~~~~~~~~~~~i~~~a~~l~i~~~~v~r~~~r~~~~~~ 118 (129)
T COG3677 75 LYKIKLQAVTLYMLGLGIRDIARTLGISINTVNRWSKRFGSRVE 118 (129)
T ss_pred CHHHHHHHHHHHHCCCCCCCHHHHHCCCHHHHHHHHHHCCCHHC
T ss_conf 27799999999864999666999955469999999996031000
No 416
>COG2508 Regulator of polyketide synthase expression [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=51.34 E-value=16 Score=15.84 Aligned_cols=41 Identities=17% Similarity=0.135 Sum_probs=36.2
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Q ss_conf 99999998599979999994999889999999999980799
Q gi|254780694|r 191 VECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 191 ~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~ 231 (246)
.-+-..+-.+....+.|+.|+|=++|++.-+++|...+|..
T Consensus 357 ~TL~~yl~~~~ni~~tAk~L~iHRNTL~YRi~kieEltg~d 397 (421)
T COG2508 357 ETLRAYLKNNGNISATAKRLFVHRNTLRYRLKKIEELTGID 397 (421)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
T ss_conf 99999998489799999983745423999999999994879
No 417
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=50.97 E-value=16 Score=15.81 Aligned_cols=36 Identities=17% Similarity=0.212 Sum_probs=26.5
Q ss_pred HHHHHHHH--HHHCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 77999999--9985999799999949998899999999
Q gi|254780694|r 188 GREVECLT--WISEGKTSDEIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 188 ~RE~eVl~--lia~G~t~~eIA~~L~iS~~TV~~hl~~ 223 (246)
.-|++++. |-..|-.-...|+.||||.+|....+++
T Consensus 285 ~~Ek~~I~~aL~~~~gn~~~aA~~LGIsR~tL~~klkk 322 (325)
T PRK11608 285 QQEKELLQRSLQQAKFNQKRAAELLGLTYHQFRALLKK 322 (325)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 99999999999993998999999988899999999997
No 418
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=50.76 E-value=16 Score=15.79 Aligned_cols=38 Identities=24% Similarity=0.255 Sum_probs=32.5
Q ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 888897799999999859997999999499988999999
Q gi|254780694|r 183 DFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYI 221 (246)
Q Consensus 183 ~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl 221 (246)
...||+-|.+.++- ..|+|-.+-|..|++|..||+.-=
T Consensus 41 ~~~ls~~eIk~iRe-~~~lSq~vFA~~L~vs~~Tv~~WE 78 (104)
T COG2944 41 VKTLSPTEIKAIRE-KLGLSQPVFARYLGVSVSTVRKWE 78 (104)
T ss_pred CCCCCHHHHHHHHH-HHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 78998899999999-828889999999888799999998
No 419
>TIGR01369 CPSaseII_lrg carbamoyl-phosphate synthase, large subunit; InterPro: IPR006275 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates , . CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate . The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain . CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites . The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein . The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP . There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia . CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains . This entry represents glutamine-dependent CPSase (6.3.5.5 from EC) from prokaryotes and eukaryotes (CPSase II). ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process.
Probab=50.72 E-value=16 Score=15.78 Aligned_cols=46 Identities=15% Similarity=0.182 Sum_probs=30.7
Q ss_pred CCC---HHHHHHHHHH-HCCCCHHHHHHHHCCCHHH--HHHHHHHHHHHHCC
Q ss_conf 889---7799999999-8599979999994999889--99999999998079
Q gi|254780694|r 185 ELT---GREVECLTWI-SEGKTSDEIAVILGISRNT--VNNYIASIMRKTAT 230 (246)
Q Consensus 185 ~LT---~RE~eVl~li-a~G~t~~eIA~~L~iS~~T--V~~hl~~i~~KLgv 230 (246)
.|+ +--.|.|+-+ ..|.|+++||..++.++.+ =...+++++.++|+
T Consensus 483 ~~~~I~~~~~e~L~~aK~lGFSD~~iA~~~~~~~~~~~~~~~vR~~R~~~gi 534 (1089)
T TIGR01369 483 KLTGIEELDKELLRKAKKLGFSDAQIARLVNVTEAESIEELEVRKLRKELGI 534 (1089)
T ss_pred CCCCCCCCCHHHHHHHHHCCCCHHHHHHHHCCCHHHCCCHHHHHHHHHHCCC
T ss_conf 2445334898899998641888789999868974442006899999984697
No 420
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=49.82 E-value=17 Score=15.69 Aligned_cols=44 Identities=25% Similarity=0.282 Sum_probs=31.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH---------HHCCCCHHHHHHHHHHCC
Q ss_conf 99799999949998899999999999---------807998899999999758
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIASIMR---------KTATKTRSGAIAYAVRNN 244 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~~i~~---------KLgv~~R~eav~~A~~~G 244 (246)
.|-.|||..+|.|+.||...++..-+ |.-+.|+..+-..|-..|
T Consensus 146 lT~~eLA~~iGttREtVsR~L~~l~~~GlI~~~~~~I~I~D~~~L~~lAe~~g 198 (201)
T PRK13918 146 ATHDELAAAVGSVRETVTKVVGELSREGVIRSGYGKIQLLDLKALKELAESRG 198 (201)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCEEEEECHHHHHHHHHHCC
T ss_conf 79999998859868999999999998898896799899928999999987447
No 421
>TIGR02850 spore_sigG RNA polymerase sigma-G factor; InterPro: IPR014212 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 recognized by the major sigma factors , . Members of this entry comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also designated stage III sporulation protein G (SpoIIIG). Members of this entry are closely related to sigma-F (SpoIIAC), another sporulation sigma factor.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=49.75 E-value=17 Score=15.69 Aligned_cols=46 Identities=30% Similarity=0.336 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8889779999999-985999799999949998899999999999807
Q gi|254780694|r 184 FELTGREVECLTW-ISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 184 ~~LT~RE~eVl~l-ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
..|.+||+-|+.. .-+|+|--|+|.+.|||..-|..--+.+..++.
T Consensus 205 ~~l~~re~~il~~rff~G~tqmeva~eiGisqaqvsrlek~a~~~~~ 251 (254)
T TIGR02850 205 KRLNEREKLILKLRFFEGKTQMEVAEEIGISQAQVSRLEKAALKHMR 251 (254)
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHH
T ss_conf 98766788777755314631334565403016888888899999975
No 422
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=49.31 E-value=15 Score=15.96 Aligned_cols=14 Identities=50% Similarity=0.629 Sum_probs=4.9
Q ss_pred HHHHHHHCCCHHHH
Q ss_conf 99999949998899
Q gi|254780694|r 204 DEIAVILGISRNTV 217 (246)
Q Consensus 204 ~eIA~~L~iS~~TV 217 (246)
+|-|..++|+++||
T Consensus 39 RelA~~~~VNpnTv 52 (125)
T COG1725 39 RELAKDLGVNPNTV 52 (125)
T ss_pred HHHHHHHCCCHHHH
T ss_conf 99999819898899
No 423
>pfam04492 Phage_rep_O Bacteriophage replication protein O. Replication protein O is necessary for the initiation of bacteriophage DNA replication. Protein O interacts with the lambda replication origin, and also with replication protein P to form an oligomer. It is speculated that the N-terminal half interacts with the replication origin while the C terminal half mediates protein-protein interaction.
Probab=49.25 E-value=17 Score=15.64 Aligned_cols=42 Identities=29% Similarity=0.457 Sum_probs=34.0
Q ss_pred CCCCHHHHHHHHHHHC----------CCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 8889779999999985----------99979999994999889999999999
Q gi|254780694|r 184 FELTGREVECLTWISE----------GKTSDEIAVILGISRNTVNNYIASIM 225 (246)
Q Consensus 184 ~~LT~RE~eVl~lia~----------G~t~~eIA~~L~iS~~TV~~hl~~i~ 225 (246)
..||.||..|+-.+.+ -.|+.+||...++++.+|..-++.+-
T Consensus 28 ~~lt~rq~kv~~aV~RkTyG~nK~~d~I~~sqi~~mtgi~~~~Vs~a~~~Li 79 (100)
T pfam04492 28 ADLSGRQLKVLLAVIRKTYGWNKPMDRVTNEQIAELTGLSRTHVSEAKKSLV 79 (100)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 8887889999999999860778503362299999997888545999999999
No 424
>pfam04703 FaeA FaeA-like protein. This family represents a number of fimbrial protein transcription regulators found in Gram-negative bacteria. These proteins are thought to facilitate binding of the leucine-rich regulatory protein to regulatory elements, possibly by inhibiting deoxyadenosine methylation of these elements by deoxyadenosine methylase.
Probab=48.63 E-value=17 Score=15.58 Aligned_cols=41 Identities=29% Similarity=0.410 Sum_probs=29.3
Q ss_pred HHHHHHHC---CCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCH
Q ss_conf 99999985---9997999999499988999999999998079988
Q gi|254780694|r 192 ECLTWISE---GKTSDEIAVILGISRNTVNNYIASIMRKTATKTR 233 (246)
Q Consensus 192 eVl~lia~---G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R 233 (246)
+||..+-+ +...+|||+.+++|.--++.|+-.+ .|-|.-.|
T Consensus 4 ~Il~~i~~i~~p~~T~eIAda~gls~YQaR~YL~~L-ek~g~i~r 47 (61)
T pfam04703 4 SILTFINSIGAPCKTREIADALGLSAYQARYYLEQL-EKEGKIER 47 (61)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHHHH-HHCCCEEC
T ss_conf 899999874898418899998550799999999999-87075230
No 425
>pfam04539 Sigma70_r3 Sigma-70 region 3. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.
Probab=48.48 E-value=17 Score=15.56 Aligned_cols=37 Identities=27% Similarity=0.282 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 7799999999859997999999499988999999999
Q gi|254780694|r 188 GREVECLTWISEGKTSDEIAVILGISRNTVNNYIASI 224 (246)
Q Consensus 188 ~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i 224 (246)
....+..+-+.+-=|..|||..|++|+..|+..+...
T Consensus 8 ka~~~L~q~lgR~Pt~eEiA~~l~~s~~~v~~~~~~~ 44 (78)
T pfam04539 8 RAQRELEQELGREPTPEEIAEELGISEEKVREVLEAA 44 (78)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHC
T ss_conf 9999999998889999999999694999999999875
No 426
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=47.94 E-value=18 Score=15.51 Aligned_cols=39 Identities=15% Similarity=0.117 Sum_probs=25.8
Q ss_pred CCCCCCHHHHHHHH----HH-HCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 88888977999999----99-85999799999949998899999
Q gi|254780694|r 182 KDFELTGREVECLT----WI-SEGKTSDEIAVILGISRNTVNNY 220 (246)
Q Consensus 182 ~~~~LT~RE~eVl~----li-a~G~t~~eIA~~L~iS~~TV~~h 220 (246)
..-.-|+...+-|+ |+ ..|.|-.+|-..|.+....-.-+
T Consensus 35 G~R~Ys~~Dl~~L~~I~~L~~~~G~~l~gik~iL~l~~q~~~l~ 78 (98)
T cd01279 35 GGRRYSNNDLELLRQVQRLSQDEGFNLAGIKRIIELYPQVLLLQ 78 (98)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 99434999999999999999958988999999999899999999
No 427
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=47.91 E-value=18 Score=15.50 Aligned_cols=32 Identities=25% Similarity=0.206 Sum_probs=23.7
Q ss_pred CCCCCCCHHHHHHHHHH-----HCCCCHHHHHHHHCC
Q ss_conf 98888897799999999-----859997999999499
Q gi|254780694|r 181 GKDFELTGREVECLTWI-----SEGKTSDEIAVILGI 212 (246)
Q Consensus 181 ~~~~~LT~RE~eVl~li-----a~G~t~~eIA~~L~i 212 (246)
+..-.-|+...+.+.+| -+|+|-+.|-..|.-
T Consensus 34 ~g~R~Ys~~di~~l~~Ik~Ll~~~G~ti~~~k~~L~~ 70 (99)
T cd04765 34 GGRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKE 70 (99)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 9885068999999999999999879879999999983
No 428
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=47.79 E-value=18 Score=15.49 Aligned_cols=28 Identities=21% Similarity=0.355 Sum_probs=23.8
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 9997999999499988999999999998
Q gi|254780694|r 200 GKTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 200 G~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
.+|-.|||..+|+|+.||...++...++
T Consensus 173 ~lT~~dLA~~lG~trETVsR~L~~L~~e 200 (224)
T PRK09391 173 PMSRRDIADYLGLTIETVSRALSQLKDR 200 (224)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 5799999988799799999999999988
No 429
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=47.03 E-value=18 Score=15.42 Aligned_cols=29 Identities=21% Similarity=0.387 Sum_probs=19.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH-HHC
Q ss_conf 99799999949998899999999999-807
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIASIMR-KTA 229 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~~i~~-KLg 229 (246)
.|..+||..|+++.++|+.-+..++. ||.
T Consensus 16 v~dedLa~~l~~~~n~vRkiL~~L~e~~lv 45 (147)
T smart00531 16 VTEEDLAELLGIKQKQLRKILYLLYDEKLI 45 (147)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
T ss_conf 079999999799999999999999977964
No 430
>pfam06971 Put_DNA-bind_N Putative DNA-binding protein N-terminus. This family represents the N-terminus (approximately 50 residues) of a number of putative bacterial DNA-binding proteins.
Probab=46.99 E-value=15 Score=15.96 Aligned_cols=25 Identities=24% Similarity=0.457 Sum_probs=19.5
Q ss_pred HHHCC---CCHHHHHHHHCCCHHHHHHH
Q ss_conf 99859---99799999949998899999
Q gi|254780694|r 196 WISEG---KTSDEIAVILGISRNTVNNY 220 (246)
Q Consensus 196 lia~G---~t~~eIA~~L~iS~~TV~~h 220 (246)
+..+| -|++|+|+.++|++.+|+.-
T Consensus 20 L~~~g~~~vSS~eLa~~~gv~~aqiRKD 47 (49)
T pfam06971 20 LLEEGVERVSSKELSEAIGIDAAQIRKD 47 (49)
T ss_pred HHHCCCCEECHHHHHHHHCCCHHHHHCC
T ss_conf 9985990497999999979399996142
No 431
>TIGR03286 methan_mark_15 putative methanogenesis marker protein 15. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. Related proteins include the BadF/BadG/BcrA/BcrD ATPase family (pfam01869), which includes an activator for (R)-2-hydroxyglutaryl-CoA dehydratase.
Probab=46.31 E-value=19 Score=15.35 Aligned_cols=47 Identities=11% Similarity=0.187 Sum_probs=36.7
Q ss_pred CCCCHH-----HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 888977-----9999999985999799999949998899999999999807998
Q gi|254780694|r 184 FELTGR-----EVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKT 232 (246)
Q Consensus 184 ~~LT~R-----E~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~ 232 (246)
..++.+ |.||..++++|.+..+|+.-++-|. +++++.+..++.++..
T Consensus 306 V~IsS~CTVFAESEvIslla~G~~~EDIaAGlc~SV--A~rvl~~l~k~v~i~~ 357 (404)
T TIGR03286 306 VRMNSYCIVFGIQDLVTALAEGASPEDVAAAACHSV--AEQVYEQQLQEIDVRE 357 (404)
T ss_pred CCCCCEEEEEEEHHHHHHHHCCCCHHHHHHHHHHHH--HHHHHHHHHCCCCCCC
T ss_conf 753576489851899999977999899999999999--9999999844368899
No 432
>pfam11994 DUF3489 Protein of unknown function (DUF3489). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=45.91 E-value=19 Score=15.31 Aligned_cols=45 Identities=22% Similarity=0.314 Sum_probs=35.1
Q ss_pred HHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHHHHH-HHHCCCCHHH
Q ss_conf 99999998--599979999994999889999999999-9807998899
Q gi|254780694|r 191 VECLTWIS--EGKTSDEIAVILGISRNTVNNYIASIM-RKTATKTRSG 235 (246)
Q Consensus 191 ~eVl~lia--~G~t~~eIA~~L~iS~~TV~~hl~~i~-~KLgv~~R~e 235 (246)
..++.++. +|-|-.+|...++=-+|||+--+..++ +|||...-++
T Consensus 13 a~li~mL~~p~Gati~~i~~atGWq~HTvRgalaG~lkKklgl~i~se 60 (72)
T pfam11994 13 ARVIAMLRRPEGATIAAISEATGWQPHTVRGALAGLLKKKLGLTITSE 60 (72)
T ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf 999999648889879999998687403589999888886338567875
No 433
>pfam08069 Ribosomal_S13_N Ribosomal S13/S15 N-terminal domain. This domain is found at the N-terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021.
Probab=45.79 E-value=19 Score=15.30 Aligned_cols=30 Identities=23% Similarity=0.263 Sum_probs=23.4
Q ss_pred CCCCCCHHH--HHHHHHHHCCCCHHHHHHHHC
Q ss_conf 888889779--999999985999799999949
Q gi|254780694|r 182 KDFELTGRE--VECLTWISEGKTSDEIAVILG 211 (246)
Q Consensus 182 ~~~~LT~RE--~eVl~lia~G~t~~eIA~~L~ 211 (246)
.....|+-| ..|++|.-+|+|..+|...|-
T Consensus 24 ~W~~~~~~eve~~I~klakkG~~pSqIG~iLR 55 (60)
T pfam08069 24 EWLKYSPEEVEELIVKLAKKGLTPSQIGVILR 55 (60)
T ss_pred CCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 65568999999999999987998889735653
No 434
>pfam07453 NUMOD1 NUMOD1 domain. This domain probably represents a DNA-binding helix-turn-helix based on its similarity to other families (Bateman A pers obs).
Probab=45.32 E-value=10 Score=17.00 Aligned_cols=21 Identities=43% Similarity=0.651 Sum_probs=17.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHH
Q ss_conf 997999999499988999999
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYI 221 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl 221 (246)
.|-.|.|+.|++|.+|++.|+
T Consensus 17 ~Si~~aa~~L~i~~~tI~~~~ 37 (37)
T pfam07453 17 SSIREAARALGISHSTINKYL 37 (37)
T ss_pred HHHHHHHHHHCCCHHHHHCCC
T ss_conf 679999998476465665029
No 435
>KOG0489 consensus
Probab=45.05 E-value=19 Score=15.30 Aligned_cols=40 Identities=18% Similarity=0.101 Sum_probs=29.3
Q ss_pred HHHHHHCCCCH--------HHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 99999859997--------99999949998899999999999807998
Q gi|254780694|r 193 CLTWISEGKTS--------DEIAVILGISRNTVNNYIASIMRKTATKT 232 (246)
Q Consensus 193 Vl~lia~G~t~--------~eIA~~L~iS~~TV~~hl~~i~~KLgv~~ 232 (246)
+|+|=.+.+.| -|||..|+++++=||..--|.+.|---.+
T Consensus 171 llELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~ 218 (261)
T KOG0489 171 LLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKEN 218 (261)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 766444320112323168899874010068899999988899998763
No 436
>pfam11740 KfrA_N Plasmid replication region DNA-binding N-term. The broad host-range plasmid RK2 is able to replicate in and be inherited in a stable manner in diverse Gram-negative bacterial species. It encodes a number of co-ordinately regulated operons including a central control korF1 operon that represses the kfrA operon. The KfrA polypeptide is a site-specific DNA-binding protein whose operator overlaps the kfrA promoter. The N-terminus, containing an helix-turn-helix motif, is essential for function. Downstream from this family is an extended coiled-coil domain containing a heptad repeat segment which is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning.
Probab=44.52 E-value=20 Score=15.17 Aligned_cols=37 Identities=22% Similarity=0.353 Sum_probs=18.2
Q ss_pred HHHHCCC--CHHHHHHHHC-CCHHHHHHHHHHHHHHHCCC
Q ss_conf 9998599--9799999949-99889999999999980799
Q gi|254780694|r 195 TWISEGK--TSDEIAVILG-ISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 195 ~lia~G~--t~~eIA~~L~-iS~~TV~~hl~~i~~KLgv~ 231 (246)
.|++.|. |...|=..|| =|.+||..|++......+..
T Consensus 12 ~L~~~G~~PTv~~VR~~lG~GS~stI~~~L~~w~~~~~~~ 51 (120)
T pfam11740 12 ALLAAGERPTVDAVREELGTGSPTTISKYLKEWREEQRAA 51 (120)
T ss_pred HHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHC
T ss_conf 9987489995999999977978888999999999986501
No 437
>pfam05732 RepL Firmicute plasmid replication protein (RepL). This family consists of Firmicute RepL proteins which are involved in plasmid replication.
Probab=44.42 E-value=20 Score=15.16 Aligned_cols=39 Identities=26% Similarity=0.388 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHCCC--------CHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 77999999998599--------9799999949998899999999999
Q gi|254780694|r 188 GREVECLTWISEGK--------TSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 188 ~RE~eVl~lia~G~--------t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
-...+|+.|+.+-+ |+++||...++|..||..-++-+..
T Consensus 55 nkk~~Vv~yileN~nsnNtlI~T~R~lae~~gvs~~TV~~tmK~L~e 101 (165)
T pfam05732 55 NQKTRLVFWLIDNLNSNNTLIMTQREIAEETGISLETVRQTMKALEE 101 (165)
T ss_pred CCCHHHHHHHHHCCCCCCEEEEEHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 63012256676536888649987899999839529999999999975
No 438
>pfam00872 Transposase_mut Transposase, Mutator family.
Probab=44.39 E-value=20 Score=15.16 Aligned_cols=17 Identities=12% Similarity=0.214 Sum_probs=6.0
Q ss_pred HHHHHHHHCCCCHHHHH
Q ss_conf 99999998599979999
Q gi|254780694|r 191 VECLTWISEGKTSDEIA 207 (246)
Q Consensus 191 ~eVl~lia~G~t~~eIA 207 (246)
.-|+.+.+.|+|.++|.
T Consensus 105 ~~i~~lY~~G~Str~i~ 121 (381)
T pfam00872 105 AVVAEMYVKGVSTREVS 121 (381)
T ss_pred HHHHHHHHCCCCHHHHH
T ss_conf 99999996588777899
No 439
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=43.70 E-value=20 Score=15.20 Aligned_cols=25 Identities=20% Similarity=0.286 Sum_probs=21.4
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 9998599979999994999889999
Q gi|254780694|r 195 TWISEGKTSDEIAVILGISRNTVNN 219 (246)
Q Consensus 195 ~lia~G~t~~eIA~~L~iS~~TV~~ 219 (246)
-|+.++.+.++-|+..+||+.|+..
T Consensus 10 ~l~~r~~~~~eLa~~igis~~~ls~ 34 (73)
T COG3655 10 MLADRKISLKELAEAIGISEANLSK 34 (73)
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHH
T ss_conf 9999750177899998436989999
No 440
>pfam02042 RWP-RK RWP-RK domain. This domain is named RWP-RK after a conserved motif at the C terminus of the presumed domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development.
Probab=42.57 E-value=21 Score=14.98 Aligned_cols=28 Identities=21% Similarity=0.230 Sum_probs=23.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 99799999949998899999999999807998
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIASIMRKTATKT 232 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~ 232 (246)
++-+|.|..|||+..+ ++++.+++|+..
T Consensus 16 lpi~~AA~~Lgv~~T~----LKk~CR~~gI~R 43 (52)
T pfam02042 16 LPIKEAAKELGVCLTV----LKKICRQLGIPR 43 (52)
T ss_pred CCHHHHHHHHCCCHHH----HHHHHHHCCCCC
T ss_conf 7599999996877999----999999879987
No 441
>KOG1597 consensus
Probab=42.42 E-value=22 Score=14.97 Aligned_cols=37 Identities=22% Similarity=0.261 Sum_probs=28.5
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 9999998599979999994999889999999999980
Q gi|254780694|r 192 ECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 192 eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
-+.++..+-+|-+||....++++.|+|.--+-+|..+
T Consensus 252 misqls~~kkt~keI~~vtgVaE~TIr~sYK~Lyp~~ 288 (308)
T KOG1597 252 MISQLSDEKKTQKEIGEVTGVAEVTIRNSYKDLYPHA 288 (308)
T ss_pred HHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCH
T ss_conf 9998504765488898885344888998899873046
No 442
>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=42.13 E-value=22 Score=14.94 Aligned_cols=37 Identities=22% Similarity=0.389 Sum_probs=27.9
Q ss_pred HHHHHHHHHHH----CCCCHHHHHHHH-CCCHHHHHHHHHHH
Q ss_conf 77999999998----599979999994-99988999999999
Q gi|254780694|r 188 GREVECLTWIS----EGKTSDEIAVIL-GISRNTVNNYIASI 224 (246)
Q Consensus 188 ~RE~eVl~lia----~G~t~~eIA~~L-~iS~~TV~~hl~~i 224 (246)
.-..+++..++ .-.|...||..+ ++|.+||.+|+.-.
T Consensus 220 ~~~k~i~~~l~~~~g~~~s~~~l~~~l~~is~~Tv~~yl~~l 261 (398)
T COG1373 220 DLMKRILRFLASNIGSPISYSSLARELKGISKDTIRKYLSYL 261 (398)
T ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 999999999875036645699999997234466899999998
No 443
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=41.82 E-value=22 Score=14.91 Aligned_cols=16 Identities=13% Similarity=0.061 Sum_probs=8.2
Q ss_pred CHHHHHHHHHHHCCCC
Q ss_conf 9779999999985999
Q gi|254780694|r 187 TGREVECLTWISEGKT 202 (246)
Q Consensus 187 T~RE~eVl~lia~G~t 202 (246)
..+-..|.+++..|..
T Consensus 185 ~~~~~~v~~lvL~Gl~ 200 (202)
T TIGR03613 185 NETVANVQRIVLEGIL 200 (202)
T ss_pred HHHHHHHHHHHHHHCC
T ss_conf 9999999999983025
No 444
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor; InterPro: IPR000394 Sigma factors are bacterial transcription initiation factors that promote the attachment of the core RNA polymerase to specific initiation sites and are then released. They alter the specificity of promoter recognition. 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. The sigma-70 family has many different sigma factors (see the relevant entry IPR000943 from INTERPRO). The sigma-54 family consists exclusively of sigma-54 factor , required for the transcription of promoters that have a characteristic -24 and -12 consensus recognition element but which are devoid of the typical -10, -35 sequences recognized by the major sigma factors. The sigma-54 factor is also characterised by its interaction with ATP-dependent positive regulatory proteins that bind to upstream activating sequences. Structurally sigma-54 factors consist of three distinct regions: A relatively well conserved N-terminal glutamine-rich region of about 50 residues that contains a potential leucine zipper motif. A region of variable length which is not well conserved. A well conserved C-terminal region of about 350 residues that contains a second potential leucine zipper, a potential DNA-binding 'helix-turn-helix' motif and a perfectly conserved octapeptide whose function is not known. ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=40.35 E-value=11 Score=16.74 Aligned_cols=22 Identities=32% Similarity=0.385 Sum_probs=14.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 9979999994999889999999
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIA 222 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~ 222 (246)
+|-++||..|++++.||-.=++
T Consensus 366 L~L~~vA~el~~heSTiSRai~ 387 (477)
T TIGR02395 366 LTLREVAEELGLHESTISRAIN 387 (477)
T ss_pred CCHHHHHHHHCCCCCCEEEEEC
T ss_conf 6389999885889872463317
No 445
>PRK12815 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=40.15 E-value=23 Score=14.74 Aligned_cols=35 Identities=17% Similarity=0.213 Sum_probs=27.7
Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Q ss_conf 999998599979999994999889999999999980799
Q gi|254780694|r 193 CLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 193 Vl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~ 231 (246)
..++=..|.|+++||..+++|+..|+.+. .|+|+.
T Consensus 484 l~~aK~~GFSD~~Ia~l~~~~e~~vr~~R----~~~~i~ 518 (1068)
T PRK12815 484 LRKAKEKGFSDRLIAELTGVTEEDVRELR----KKLGIR 518 (1068)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHH----HHCCCC
T ss_conf 99999849999999977099999999999----976995
No 446
>COG1961 PinR Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]
Probab=39.78 E-value=16 Score=15.84 Aligned_cols=43 Identities=26% Similarity=0.393 Sum_probs=35.0
Q ss_pred CCHHHHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 897799999999859-9979999994999889999999999980
Q gi|254780694|r 186 LTGREVECLTWISEG-KTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 186 LT~RE~eVl~lia~G-~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
-......|..++..| .+..+||..+++|..||..++++...+-
T Consensus 162 ~~~~~~~v~~l~~~~~~~~~~~a~~~~i~~~t~~r~~~~~~~~~ 205 (222)
T COG1961 162 AEEQAAAVRRLLADGLGSYSEIARALGISRSTVYRILNKLKKRG 205 (222)
T ss_pred CHHHHHHHHHHHHHCCCCHHHHHHHHCCCCEEEEECCCCCCCCC
T ss_conf 36779999999983463499999981777414440012222221
No 447
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.38 E-value=25 Score=14.57 Aligned_cols=24 Identities=17% Similarity=0.184 Sum_probs=17.4
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 859997999999499988999999
Q gi|254780694|r 198 SEGKTSDEIAVILGISRNTVNNYI 221 (246)
Q Consensus 198 a~G~t~~eIA~~L~iS~~TV~~hl 221 (246)
-.-+|..+||..|++|+.-++.-+
T Consensus 21 l~~LS~~~iA~~Ln~t~~~lekil 44 (97)
T COG4367 21 LCPLSDEEIATALNWTEVKLEKIL 44 (97)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 064529999999588799999999
No 448
>PTZ00100 DnaJ chaperone protein; Provisional
Probab=37.53 E-value=24 Score=14.65 Aligned_cols=33 Identities=15% Similarity=0.217 Sum_probs=23.8
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Q ss_conf 599979999994999889999999999980799
Q gi|254780694|r 199 EGKTSDEIAVILGISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 199 ~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~ 231 (246)
.-+|-+|...+|++++..-+.-++..++||=..
T Consensus 58 ~~Mt~~EA~~ILGl~~~as~~~I~~ahrkLM~k 90 (114)
T PTZ00100 58 HKMSKSEACKILNIPPTANKERIREVHKQLMLR 90 (114)
T ss_pred CCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
T ss_conf 985999999981999999999999999999997
No 449
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=37.41 E-value=26 Score=14.47 Aligned_cols=39 Identities=26% Similarity=0.318 Sum_probs=27.0
Q ss_pred CCCHHHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 8897799999--99985999799999949998899999999
Q gi|254780694|r 185 ELTGREVECL--TWISEGKTSDEIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 185 ~LT~RE~eVl--~lia~G~t~~eIA~~L~iS~~TV~~hl~~ 223 (246)
.|.+-|++.+ .|-..|-.-.+.|+.||||..|...+++.
T Consensus 587 ~l~~~Er~~I~~aL~~~~gN~s~aA~~LGIsR~TLYRKlk~ 627 (639)
T PRK11388 587 SLAELEKQAIINAAQVCGGRIQEMAALLGIGRTTLWRKMKQ 627 (639)
T ss_pred CHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 79999999999999994997999999989899999999999
No 450
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=37.20 E-value=26 Score=14.45 Aligned_cols=32 Identities=31% Similarity=0.389 Sum_probs=19.6
Q ss_pred HHHHHHHCC--CCHHHHHHHHCC--CHHHHHHHHHH
Q ss_conf 999999859--997999999499--98899999999
Q gi|254780694|r 192 ECLTWISEG--KTSDEIAVILGI--SRNTVNNYIAS 223 (246)
Q Consensus 192 eVl~lia~G--~t~~eIA~~L~i--S~~TV~~hl~~ 223 (246)
+++..|-.| .|+.+||+.++. +.+.|-+.+++
T Consensus 7 ~~l~~IP~G~v~TYg~iA~~~G~p~~~RaVg~al~~ 42 (79)
T cd06445 7 EALRQIPYGEVTTYGQIAKLAGTPKAARAVGSALAR 42 (79)
T ss_pred HHHHCCCCCCCCCHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf 999468998769799999995899853999999996
No 451
>COG3088 CcmH Uncharacterized protein involved in biosynthesis of c-type cytochromes [Posttranslational modification, protein turnover, chaperones]
Probab=36.82 E-value=26 Score=14.41 Aligned_cols=19 Identities=16% Similarity=0.094 Sum_probs=9.6
Q ss_pred CCCCCCCHHHHHHHHHHHC
Q ss_conf 9888889779999999985
Q gi|254780694|r 181 GKDFELTGREVECLTWISE 199 (246)
Q Consensus 181 ~~~~~LT~RE~eVl~lia~ 199 (246)
.+...||+-|.+-+.-+-+
T Consensus 133 ~~~~~Ls~ee~~rl~~ll~ 151 (153)
T COG3088 133 EPPQTLSAEEEARLARLLR 151 (153)
T ss_pred CCCCCCCHHHHHHHHHHHC
T ss_conf 6889998667999998754
No 452
>TIGR00498 lexA LexA repressor; InterPro: IPR006200 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This group of proteins are serine peptidases belong to MEROPS peptidase S24 (LexA family, clan SF). The family contains the LexA proteins. LexA represses around 20 genes of the cellular SOS response to DNA damage in Escherichia coli . Damage to cellular DNA results in inactivation of LexA, allowing transcription of the genes involved in DNA repair. In E. coli, this derepression of the DNA repair system is mediated by RecA, which binds to LexA upon interaction with single-stranded DNA. This results in inactivation of LexA by proteolytic self cleavage, disrupting the DNA-binding capabilities of LexA. LexA consists of around 200 amino acids, of which the first 90 form the DNA-binding domain. The remaining residues form the protease domain, Ser-119 and Lys-156 being the active residues. The crystal structures of the wild type and several mutant forms of LexA reveal two distinct conformations: one compatible with cleavage, and the other in which the cleavage site is approximately 20 A from the catalytic centre. It is suggested that recA activates the self-cleavage of LexA and related proteins through selective stabilisation of the cleavable conformation .; GO: 0008992 repressor LexA activity, 0006508 proteolysis.
Probab=36.58 E-value=26 Score=14.39 Aligned_cols=42 Identities=29% Similarity=0.419 Sum_probs=17.2
Q ss_pred CCHHHHHHHHHHHCC-------CCHHHHHHHHCCC-HHHHHHHHHHHHHH
Q ss_conf 897799999999859-------9979999994999-88999999999998
Q gi|254780694|r 186 LTGREVECLTWISEG-------KTSDEIAVILGIS-RNTVNNYIASIMRK 227 (246)
Q Consensus 186 LT~RE~eVl~lia~G-------~t~~eIA~~L~iS-~~TV~~hl~~i~~K 227 (246)
||.++.+++.|+..- -+.++|++.+++. +.++..|+..+.+|
T Consensus 4 l~~~~~~~~~~~~~~~~~~g~pp~~~~~~~~~~~~~~~~~~~~l~~l~~~ 53 (227)
T TIGR00498 4 LTERQREVLDLLKAHIESTGYPPSVREIARALGLTSPSAAEEHLKALERK 53 (227)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHC
T ss_conf 24788999999998765148870178898873355730478898887644
No 453
>pfam09012 FeoC FeoC like transcriptional regulator. This family contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependant transcriptional repressor.
Probab=36.46 E-value=27 Score=14.38 Aligned_cols=30 Identities=20% Similarity=0.252 Sum_probs=25.0
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 999799999949998899999999999807
Q gi|254780694|r 200 GKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 200 G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
-.|-.|||..+.+|+.+|+.-+....+|=-
T Consensus 14 ~~s~~~Ls~~f~~~~~~v~~ML~~wi~kGk 43 (68)
T pfam09012 14 RASLAELARHFKMSPDAVEAMLEVWIRKGK 43 (68)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCC
T ss_conf 847999998979399999999999998797
No 454
>pfam04936 DUF658 Protein of unknown function (DUF658). Protein of unknown function found in Lactococcus lactis bacteriophages.
Probab=36.33 E-value=27 Score=14.36 Aligned_cols=43 Identities=14% Similarity=0.033 Sum_probs=17.3
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 998599979999994999889999999999980799889999999
Q gi|254780694|r 196 WISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYA 240 (246)
Q Consensus 196 lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A 240 (246)
|.-.|-|.++|.+.+. .+--+.|-..=-+.|--.=|+|....+
T Consensus 84 ~fim~GtareIS~e~k--~k~rrkhetkeerrlrrniraqmaie~ 126 (134)
T pfam04936 84 EFIMGGSAREISDEIK--DKDRRKHETKEERRLRRNIRAQMAIEA 126 (134)
T ss_pred CCCCCCCHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 4134662666658888--888751203889999998899998885
No 455
>pfam04182 B-block_TFIIIC B-block binding subunit of TFIIIC. Yeast transcription factor IIIC (TFIIIC) is a multi-subunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding.
Probab=35.62 E-value=27 Score=14.29 Aligned_cols=41 Identities=22% Similarity=0.264 Sum_probs=34.4
Q ss_pred CHHHHHHHHHHHC----CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 9779999999985----9997999999499988999999999998
Q gi|254780694|r 187 TGREVECLTWISE----GKTSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 187 T~RE~eVl~lia~----G~t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
++-|.++|.+||. |.+..+.+..+++-+++|-.|++.+..+
T Consensus 1 ~~~~~~lL~~Ia~~r~~Gi~q~dL~k~~~~D~rs~~~~~k~L~~~ 45 (73)
T pfam04182 1 PALQFELLEEIARSRYNGITQSDLAKLTGQDPRSVFYRLKKLEDK 45 (73)
T ss_pred CCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHC
T ss_conf 924899999999517688018999999689964317989999878
No 456
>pfam05344 DUF746 Domain of Unknown Function (DUF746). This is a short conserved region found in some transposons.
Probab=35.57 E-value=27 Score=14.29 Aligned_cols=48 Identities=13% Similarity=0.155 Sum_probs=36.1
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH---HHCCCCHHHH
Q ss_conf 79999999985999799999949998899999999999---8079988999
Q gi|254780694|r 189 REVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMR---KTATKTRSGA 236 (246)
Q Consensus 189 RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~---KLgv~~R~ea 236 (246)
+-.+..++++.=+|-.|.|+.|+.++.+|..-++.-.+ .|+-+.+-++
T Consensus 2 r~~~~IrlLs~p~s~~qaa~~lg~~~~~i~~wv~~fr~~ll~LDPSG~~e~ 52 (65)
T pfam05344 2 RMRLFIRLLSQPISCAQAADQLGTDEGIIRKWVRMFRRWLLQLDPSGHLER 52 (65)
T ss_pred CHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCHHH
T ss_conf 387999982666659999999787888999999999999986198877188
No 457
>pfam12116 SpoIIID Stage III sporulation protein D. This stage III sporulation protein is a small DNA-binding family that is essential for gene expression of the mother-cell compartment during sporulation. The domain is found in bacteria and viruses, and is about 40 amino acids in length. It has a conserved RGG sequence motif.
Probab=35.22 E-value=28 Score=14.25 Aligned_cols=42 Identities=26% Similarity=0.396 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 7799999999859-99799999949998899999999999807
Q gi|254780694|r 188 GREVECLTWISEG-KTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 188 ~RE~eVl~lia~G-~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
+|-.+|...|.+- .|.++.|...|||-.||-.-+..-..+++
T Consensus 6 eR~~~i~~YIi~~~aTVR~tAk~FGvSKSTVHkDvTeRL~~in 48 (82)
T pfam12116 6 ERVLEIANYIIENKATVRQAAKVFGVSKSTVHKDVTERLPKIN 48 (82)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHCC
T ss_conf 9999999999962628999999969609889887999998739
No 458
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=35.17 E-value=28 Score=14.25 Aligned_cols=10 Identities=0% Similarity=-0.001 Sum_probs=3.4
Q ss_pred CCHHHHHHHH
Q ss_conf 7999999999
Q gi|254780694|r 40 DCTVSWTMRM 49 (246)
Q Consensus 40 ~~~~~~~~~~ 49 (246)
.+...+...+
T Consensus 38 ~s~~~~~~~l 47 (201)
T COG1974 38 ASPSAIHSHL 47 (201)
T ss_pred CCHHHHHHHH
T ss_conf 9848999999
No 459
>pfam00382 TFIIB Transcription factor TFIIB repeat.
Probab=34.92 E-value=20 Score=15.22 Aligned_cols=25 Identities=20% Similarity=0.227 Sum_probs=18.7
Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHH
Q ss_conf 9999985999799999949998899
Q gi|254780694|r 193 CLTWISEGKTSDEIAVILGISRNTV 217 (246)
Q Consensus 193 Vl~lia~G~t~~eIA~~L~iS~~TV 217 (246)
..++.....|-+||+...++|+.|+
T Consensus 47 Acr~~~~~rt~~eia~v~~vs~~tI 71 (71)
T pfam00382 47 ACRLEEVKRTLKEISSVAQVSEKTI 71 (71)
T ss_pred HHHHCCCCCCHHHHHHHHCCCCCCC
T ss_conf 9998089989999999968987869
No 460
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=34.82 E-value=28 Score=14.21 Aligned_cols=27 Identities=30% Similarity=0.428 Sum_probs=21.5
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 985999799999949998899999999
Q gi|254780694|r 197 ISEGKTSDEIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 197 ia~G~t~~eIA~~L~iS~~TV~~hl~~ 223 (246)
.-.|+|-.+.|..+++|..|+..-=+.
T Consensus 11 ~~~~ltQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 11 AELGLTQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred HHHCCCHHHHHHHCCCCHHHHHHHHCC
T ss_conf 982858999999919579999999917
No 461
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=34.07 E-value=29 Score=14.13 Aligned_cols=28 Identities=21% Similarity=0.315 Sum_probs=23.7
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 7999999499988999999999998079
Q gi|254780694|r 203 SDEIAVILGISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 203 ~~eIA~~L~iS~~TV~~hl~~i~~KLgv 230 (246)
-.+||..+++|+..|+..-.|-..|..-
T Consensus 30 ~~~La~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 30 REELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 9999999792999999999989988873
No 462
>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]
Probab=34.04 E-value=29 Score=14.13 Aligned_cols=48 Identities=25% Similarity=0.249 Sum_probs=40.7
Q ss_pred CCCCCCHHHHHHH-HHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 8888897799999-99985999799999949998899999999999807
Q gi|254780694|r 182 KDFELTGREVECL-TWISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229 (246)
Q Consensus 182 ~~~~LT~RE~eVl-~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 229 (246)
....|++.|..+| .-+.++++-++.|..|+.+.++|..-+...+.|+-
T Consensus 701 ~~~~L~~~~~~~Li~~~lQ~k~w~~~a~~l~~~~~~~~~~l~~~~~~~~ 749 (758)
T COG1444 701 DSPDLSEVEELVLIGRVLQAKPWREVAKELGLASNDVMTILLKDLRKLL 749 (758)
T ss_pred CCCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 7643316789999999974175889998846670799999999999999
No 463
>pfam03918 CcmH Cytochrome C biogenesis protein. Members of this family include NrfF, CcmH, CycL, Ccl2.
Probab=33.90 E-value=29 Score=14.12 Aligned_cols=15 Identities=20% Similarity=0.140 Sum_probs=9.7
Q ss_pred CCCCCHHHHHHHHHH
Q ss_conf 888897799999999
Q gi|254780694|r 183 DFELTGREVECLTWI 197 (246)
Q Consensus 183 ~~~LT~RE~eVl~li 197 (246)
...||+-|+.-++-+
T Consensus 129 ~~~ls~~e~~~l~~l 143 (145)
T pfam03918 129 EPPLSEEERARLKAL 143 (145)
T ss_pred CCCCCHHHHHHHHHH
T ss_conf 999899999999998
No 464
>PRK13832 plasmid partitioning protein; Provisional
Probab=33.76 E-value=29 Score=14.10 Aligned_cols=31 Identities=32% Similarity=0.391 Sum_probs=19.4
Q ss_pred CCCCHHHEEEEECCCCHHHHHHHHHHCCCCH
Q ss_conf 9721011000221445888876553023213
Q gi|254780694|r 1 MNFEIQQVNIVLNREDEQRTSFVSHLPTRSD 31 (246)
Q Consensus 1 ~~~~~~~~~~~l~r~d~~r~~~v~~l~~~~d 31 (246)
|-.|.+.-+|.....|++...+-.+-+...|
T Consensus 157 mP~e~qlrtiA~asldeQ~eVWk~~kp~k~d 187 (518)
T PRK13832 157 MPNEQQLRTIAAASLDEQKEVWKAHKPKKGD 187 (518)
T ss_pred CCCHHHHHHHHHCCHHHHHHHHHHCCCCCCC
T ss_conf 8759999998716878899999850877788
No 465
>pfam07506 RepB RepB plasmid partitioning protein. This family includes proteins with sequence similarity to the RepB partitioning protein of the large Ti (tumour-inducing) plasmids of Agrobacterium tumefaciens.
Probab=32.91 E-value=30 Score=14.01 Aligned_cols=59 Identities=22% Similarity=0.254 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH-------------------------HHHHHHCCCCHHHHHHHHHH
Q ss_conf 77999999998599979999994999889999999-------------------------99998079988999999997
Q gi|254780694|r 188 GREVECLTWISEGKTSDEIAVILGISRNTVNNYIA-------------------------SIMRKTATKTRSGAIAYAVR 242 (246)
Q Consensus 188 ~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~-------------------------~i~~KLgv~~R~eav~~A~~ 242 (246)
++=..+.+++..|.+-..|+..|++...+|...+. .+.+|.|-....|++..-..
T Consensus 9 e~~~~a~rl~~~G~~~~~I~~aL~vd~~~is~~~~~~~~~~i~~e~~~lL~d~~~~~~~ig~a~kigr~Rw~e~aelm~a 88 (185)
T pfam07506 9 ERARFAARLLERGVPRAEIAAALGLDPQTVSKMVARAIPEGICPEEEALLKDVETGIAAFGLARKIGRDRWVELAELLAA 88 (185)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCHHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf 99999999998699999999998679999999999987511688999986034564988765100582789999999987
Q ss_pred CCCC
Q ss_conf 5898
Q gi|254780694|r 243 NNIV 246 (246)
Q Consensus 243 ~Gli 246 (246)
.+.+
T Consensus 89 ~~~~ 92 (185)
T pfam07506 89 AKNV 92 (185)
T ss_pred HHHC
T ss_conf 5301
No 466
>PRK01905 DNA-binding protein Fis; Provisional
Probab=32.71 E-value=31 Score=13.99 Aligned_cols=19 Identities=37% Similarity=0.462 Sum_probs=0.0
Q ss_pred HHHHHHCCCHHHHHHHHHH
Q ss_conf 9999949998899999999
Q gi|254780694|r 205 EIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 205 eIA~~L~iS~~TV~~hl~~ 223 (246)
..|+.|||+.+|.+.-++.
T Consensus 55 kAA~~LGinR~TLRkKlk~ 73 (77)
T PRK01905 55 LAAEYLGINRNTLRKKLQQ 73 (77)
T ss_pred HHHHHHCCCHHHHHHHHHH
T ss_conf 9999978658889999998
No 467
>pfam02082 Rrf2 Transcriptional regulator. This family is related to pfam001022 and other transcription regulation families (personal obs: Yeats C).
Probab=32.65 E-value=31 Score=13.99 Aligned_cols=36 Identities=25% Similarity=0.326 Sum_probs=0.0
Q ss_pred HHHHHHHH---CCC--CHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 99999998---599--9799999949998899999999999
Q gi|254780694|r 191 VECLTWIS---EGK--TSDEIAVILGISRNTVNNYIASIMR 226 (246)
Q Consensus 191 ~eVl~lia---~G~--t~~eIA~~L~iS~~TV~~hl~~i~~ 226 (246)
..+|-.++ ++. |.++||+.+++++..++.-+..+.+
T Consensus 10 l~~l~~La~~~~~~~~s~~~iA~~~~i~~~~l~kil~~L~~ 50 (82)
T pfam02082 10 LHALLYLALHPGEGPVTSEEIAERQNISPVYLRKILAKLRK 50 (82)
T ss_pred HHHHHHHHHCCCCCEECHHHHHHHHCCCHHHHHHHHHHHHC
T ss_conf 99999998189998495999998789099999999998102
No 468
>pfam05066 RNA_pol_delta DNA-directed RNA polymerase delta subunit. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich carboxyl-terminal region.
Probab=32.24 E-value=31 Score=13.94 Aligned_cols=31 Identities=26% Similarity=0.389 Sum_probs=0.0
Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHCCCCHH
Q ss_conf 9999994999889999999999980799889
Q gi|254780694|r 204 DEIAVILGISRNTVNNYIASIMRKTATKTRS 234 (246)
Q Consensus 204 ~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~ 234 (246)
+||+..+++|..-++.-+...|.-|+..+|.
T Consensus 38 ~ev~~~~g~s~ee~~~~iaqfYTdln~DgRF 68 (94)
T pfam05066 38 NEIQKLLGISDEEIRERLAQFYTDLNIDGRF 68 (94)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHCCCCE
T ss_conf 9999995989889999999999998514520
No 469
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=32.22 E-value=31 Score=13.94 Aligned_cols=32 Identities=16% Similarity=0.216 Sum_probs=0.0
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 98599979999994999889999999999980
Q gi|254780694|r 197 ISEGKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 197 ia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
+..|+|.+|||..--+|+.|....|.+..+|+
T Consensus 133 ~v~GLs~~eIArAFLv~e~am~QRivRAK~ri 164 (415)
T COG4941 133 LVGGLSTAEIARAFLVPEAAMAQRIVRAKARI 164 (415)
T ss_pred HHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf 98287599999998078078999999999999
No 470
>PRK09258 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed
Probab=32.00 E-value=17 Score=15.68 Aligned_cols=32 Identities=22% Similarity=0.159 Sum_probs=0.0
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCH
Q ss_conf 97999999499988999999999998079988
Q gi|254780694|r 202 TSDEIAVILGISRNTVNNYIASIMRKTATKTR 233 (246)
Q Consensus 202 t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R 233 (246)
||+||+.+|+-+..+.+.--.-|.+|.|++.|
T Consensus 16 tn~el~~~~~~~~~~~~~~~~~i~~~tGI~~R 47 (339)
T PRK09258 16 TSSEIESRLAPLYQRLRIPMGQLEALTGIRER 47 (339)
T ss_pred CHHHHHHHHCCCHHHHCCCCCHHHHCCCCEEE
T ss_conf 48999977533045425871132334673035
No 471
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator; InterPro: IPR011791 This entry represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system , . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix ..
Probab=31.92 E-value=22 Score=14.96 Aligned_cols=17 Identities=35% Similarity=0.495 Sum_probs=0.0
Q ss_pred HHHHHHHCCCHHHHHHH
Q ss_conf 99999949998899999
Q gi|254780694|r 204 DEIAVILGISRNTVNNY 220 (246)
Q Consensus 204 ~eIA~~L~iS~~TV~~h 220 (246)
.|.|+..++|..|+++|
T Consensus 4 GeLA~~t~v~v~TIRFY 20 (127)
T TIGR02047 4 GELAKKTGVSVETIRFY 20 (127)
T ss_pred HHHHHHHCCCCCHHHHH
T ss_conf 34545533440022464
No 472
>pfam02954 HTH_8 Bacterial regulatory protein, Fis family.
Probab=31.91 E-value=31 Score=13.91 Aligned_cols=36 Identities=25% Similarity=0.306 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 779999999985999799999949998899999999
Q gi|254780694|r 188 GREVECLTWISEGKTSDEIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 188 ~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~ 223 (246)
+|+.=.-.|-..|-.-.+.|+.||||+.|...-++.
T Consensus 6 Er~~I~~aL~~~~gn~~~aA~~LGisr~tL~~kmkk 41 (42)
T pfam02954 6 EKELIEAALERTGGNKSKAARLLGISRRTLYRKLKK 41 (42)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999999999994997999999979699999999973
No 473
>pfam00046 Homeobox Homeobox domain.
Probab=31.54 E-value=32 Score=13.87 Aligned_cols=42 Identities=24% Similarity=0.264 Sum_probs=0.0
Q ss_pred CCHHHHHHHHHHHCCCCH------HHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 897799999999859997------999999499988999999999998
Q gi|254780694|r 186 LTGREVECLTWISEGKTS------DEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 186 LT~RE~eVl~lia~G~t~------~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
+|+.+.++|+-+=+--.+ .+||..|++|+..|+.--.|=..|
T Consensus 7 ft~~Q~~~Le~~F~~~~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR~k 54 (57)
T pfam00046 7 FTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAK 54 (57)
T ss_pred CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 999999999999985799998999999998399989978976875863
No 474
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=31.52 E-value=32 Score=13.87 Aligned_cols=31 Identities=23% Similarity=0.335 Sum_probs=0.0
Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHCCCCHH
Q ss_conf 9999994999889999999999980799889
Q gi|254780694|r 204 DEIAVILGISRNTVNNYIASIMRKTATKTRS 234 (246)
Q Consensus 204 ~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~ 234 (246)
++|+..+++|..-++.-+...|.-|++-+|.
T Consensus 38 ~ei~~~~g~s~eei~~ri~qfYTDLN~DGrF 68 (185)
T PRK02363 38 NEIQKLLGKSDEEIRERLPQFYTDLNTDGRF 68 (185)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHCCCCCE
T ss_conf 9999995899999999999987741036743
No 475
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=30.66 E-value=23 Score=14.80 Aligned_cols=22 Identities=32% Similarity=0.585 Sum_probs=0.0
Q ss_pred CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 9799999949998899999999
Q gi|254780694|r 202 TSDEIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 202 t~~eIA~~L~iS~~TV~~hl~~ 223 (246)
|-.|.|+.|++|..|+..|+++
T Consensus 19 Si~~aak~l~~~~~~I~~~l~~ 40 (53)
T smart00497 19 SIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred HHHHHHHHHCCCCCCHHHHHCC
T ss_conf 7999999858883238887067
No 476
>TIGR02531 yecD_yerC TrpR homolog YerC/YecD; InterPro: IPR013368 These proteins are found mostly in the Firmicutes (Bacillus and other related Gram-positive bacteria). They are similar in sequence to the trp operon repressor TrpR IPR013335 from INTERPRO, but represents a distinct clade. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and IPR013335 from INTERPRO. 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=30.60 E-value=33 Score=13.77 Aligned_cols=34 Identities=29% Similarity=0.352 Sum_probs=0.0
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 9999999859997999999499988999999999
Q gi|254780694|r 191 VECLTWISEGKTSDEIAVILGISRNTVNNYIASI 224 (246)
Q Consensus 191 ~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i 224 (246)
.+|.+++.+|.|+..|...-+-|..|+..--+.+
T Consensus 41 l~va~ml~~~~ty~~i~~~~~astatisrv~~~l 74 (88)
T TIGR02531 41 LEVAKMLKEGKTYSEIEEETGASTATISRVKRCL 74 (88)
T ss_pred HHHHHHHHHCHHHHHHHHHHCCHHHHHHHHHHHH
T ss_conf 9999998604179999875243189999999999
No 477
>PRK06816 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed
Probab=30.43 E-value=33 Score=13.75 Aligned_cols=43 Identities=28% Similarity=0.392 Sum_probs=0.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCH--------------HHHHHHHHHC
Q ss_conf 997999999499988999999999998079988--------------9999999975
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIASIMRKTATKTR--------------SGAIAYAVRN 243 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R--------------~eav~~A~~~ 243 (246)
.||.|+.+.++....--.+--..|.+|.|++.| +++.+.|.+.
T Consensus 17 vtN~el~~~~~~~~~~~~~~~~~I~~rtGI~~Rr~a~~~~~~~~et~sdma~~Aa~~ 73 (378)
T PRK06816 17 VDNDEMEAYLGLINGRPSRLRRIILRNNGIKTRHYAIDPTGETTHSNAQMAAHAIRD 73 (378)
T ss_pred CCHHHHHHHHCCCCCCCCCHHHHHHHCCCCEEEEEECCCCCCCCCCHHHHHHHHHHH
T ss_conf 558999998641578877488897754582137874078888766789999999999
No 478
>TIGR00014 arsC arsenate reductase; InterPro: IPR006659 This entry describes a distinct clade, including ArsC itself, of the broader family of ArsC and related proteins. This clade is almost completely restricted to the proteobacteria. An anion-translocating ATPase has been identified as the product of the arsenical resistance operon of resistance plasmid R773 . When expressed in Escherichia coli this ATP-driven oxyanion pump catalyses extrusion of the oxyanions arsenite, antimonite and arsenate. The pump is composed of two polypeptides, the products of the arsA and arsB genes. The pump alone produces resistance to arsenite and antimonite. This protein, ArsC, catalyzes the reduction of arsenate to arsenite, and thus extends resistance to include arsenate. ; GO: 0008794 arsenate reductase (glutaredoxin) activity, 0006118 electron transport.
Probab=30.37 E-value=31 Score=13.97 Aligned_cols=41 Identities=12% Similarity=0.210 Sum_probs=0.0
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC-H
Q ss_conf 999999985999799999949998899999999999807998-8
Q gi|254780694|r 191 VECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKT-R 233 (246)
Q Consensus 191 ~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~-R 233 (246)
|+-|.++-+=--+.+|=+.|.-.+. ++-|++|+.|||++. |
T Consensus 13 R~tLalL~dkgi~P~vV~YL~~pp~--~seL~~~~~~LG~~~ar 54 (114)
T TIGR00014 13 RQTLALLEDKGIEPEVVKYLKNPPT--KSELKALLAKLGISSAR 54 (114)
T ss_pred HHHHHHHHHCCCCCEEEECCCCCCC--HHHHHHHHHHCCCCHHH
T ss_conf 8999999856999547414589748--68899999870897036
No 479
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=30.05 E-value=34 Score=13.71 Aligned_cols=26 Identities=27% Similarity=0.487 Sum_probs=0.0
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 97999999499988999999999998
Q gi|254780694|r 202 TSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 202 t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
|.++||+..+||.+.+...++..-++
T Consensus 27 ~~~eIae~~~Ip~~~L~KIl~~L~~a 52 (141)
T PRK11014 27 SISEVTEVYGVSRNHMVKIINQLSRA 52 (141)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 49999998794999999999999887
No 480
>COG2411 Uncharacterized conserved protein [Function unknown]
Probab=29.61 E-value=34 Score=13.66 Aligned_cols=43 Identities=19% Similarity=0.220 Sum_probs=0.0
Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCC--CHHHHHHHHHHHHHHH
Q ss_conf 897799999999859997999999499--9889999999999980
Q gi|254780694|r 186 LTGREVECLTWISEGKTSDEIAVILGI--SRNTVNNYIASIMRKT 228 (246)
Q Consensus 186 LT~RE~eVl~lia~G~t~~eIA~~L~i--S~~TV~~hl~~i~~KL 228 (246)
||++|+.||.++.+--|-+..|..|+= ...-|+.-++.+|+-|
T Consensus 138 Ls~~~~~iL~~~~~~gslRkaA~klgg~~kr~~ir~vLrKay~~L 182 (188)
T COG2411 138 LSERDKRILELFVEEGSLRKAAKKLGGLEKRGRIRRVLRKAYHEL 182 (188)
T ss_pred CCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf 898899999999975929999999558412038999999999999
No 481
>pfam01388 ARID ARID/BRIGHT DNA binding domain. This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain.
Probab=29.47 E-value=35 Score=13.65 Aligned_cols=25 Identities=36% Similarity=0.341 Sum_probs=0.0
Q ss_pred HHHHHHHCCC-HHHHHHHHHHHHHHH
Q ss_conf 9999994999-889999999999980
Q gi|254780694|r 204 DEIAVILGIS-RNTVNNYIASIMRKT 228 (246)
Q Consensus 204 ~eIA~~L~iS-~~TV~~hl~~i~~KL 228 (246)
++||+.|+++ ..|+-..++++|.|.
T Consensus 61 ~~ia~~lg~~~~~~~~~~Lk~~Y~k~ 86 (91)
T pfam01388 61 REVAQKLGIPPGITSAQELRSIYEKY 86 (91)
T ss_pred HHHHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf 99999868797565799999999998
No 482
>pfam10826 DUF2551 Protein of unknown function (DUF2551). This Archaeal family of proteins has no known function.
Probab=29.34 E-value=35 Score=13.63 Aligned_cols=40 Identities=20% Similarity=0.145 Sum_probs=0.0
Q ss_pred HHHHHHHHCC--CCHHHHHHHH----CCCHHHHHHHHHHHHHHHCC
Q ss_conf 9999999859--9979999994----99988999999999998079
Q gi|254780694|r 191 VECLTWISEG--KTSDEIAVIL----GISRNTVNNYIASIMRKTAT 230 (246)
Q Consensus 191 ~eVl~lia~G--~t~~eIA~~L----~iS~~TV~~hl~~i~~KLgv 230 (246)
++||+++-+| .|..||-+.| .||.++|-.-+.=|-.|||+
T Consensus 14 r~vL~lFl~~k~~T~~~i~e~L~~~f~Vs~~gV~aMVGli~SrlGI 59 (83)
T pfam10826 14 RAVLRLFLKVKKFTIDDIHERLAKKFDVSYHGVAAMVGLIHSRLGI 59 (83)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHEE
T ss_conf 9999999947776389999999962886442079999999873212
No 483
>PHA00738 putative HTH transcription regulator
Probab=29.17 E-value=33 Score=13.79 Aligned_cols=32 Identities=25% Similarity=0.180 Sum_probs=0.0
Q ss_pred HHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 9999999859--9979999994999889999999
Q gi|254780694|r 191 VECLTWISEG--KTSDEIAVILGISRNTVNNYIA 222 (246)
Q Consensus 191 ~eVl~lia~G--~t~~eIA~~L~iS~~TV~~hl~ 222 (246)
+.|++++|+- +|..-|.-.|-+|-.||-.|++
T Consensus 16 rKIl~LiaENY~LSaslISHtlLLSYatvlrHLr 49 (112)
T PHA00738 16 KKILELIAENYILSASLISHTLLLSYATVLRHLR 49 (112)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999998898999999999999999999999
No 484
>PRK05294 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=28.78 E-value=36 Score=13.57 Aligned_cols=24 Identities=25% Similarity=0.452 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 999799999949998899999999
Q gi|254780694|r 200 GKTSDEIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 200 G~t~~eIA~~L~iS~~TV~~hl~~ 223 (246)
|.|+++||..+++|+..|+...+.
T Consensus 491 GFSD~~IA~l~~~~~~~Vr~~R~~ 514 (1063)
T PRK05294 491 GFSDARIAKLLGVTEDEVRKLRKE 514 (1063)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 998599998849999999999998
No 485
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=28.62 E-value=36 Score=13.56 Aligned_cols=32 Identities=22% Similarity=0.242 Sum_probs=0.0
Q ss_pred HHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 9999999859-9979999994999889999999
Q gi|254780694|r 191 VECLTWISEG-KTSDEIAVILGISRNTVNNYIA 222 (246)
Q Consensus 191 ~eVl~lia~G-~t~~eIA~~L~iS~~TV~~hl~ 222 (246)
++|++++++- .=.-||.+.||+|+..|=.|++
T Consensus 18 R~Il~lLt~~p~yvsEiS~~lgvsqkAVl~HL~ 50 (217)
T COG1777 18 RRILQLLTRRPCYVSEISRELGVSQKAVLKHLR 50 (217)
T ss_pred HHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 999999854713999877660867899999999
No 486
>PRK05782 precorrin-8X methylmutase; Validated
Probab=28.54 E-value=36 Score=13.55 Aligned_cols=63 Identities=16% Similarity=0.086 Sum_probs=0.0
Q ss_pred CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCC
Q ss_conf 888889779999999985999799999949998899999999999807998899999999758
Q gi|254780694|r 182 KDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNN 244 (246)
Q Consensus 182 ~~~~LT~RE~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~R~eav~~A~~~G 244 (246)
......++|++|++-+-.---+-|++..|..|+.-|+.=++.+..+-.+-.-++.|.-.++.+
T Consensus 159 ~~~~~~~~e~~Vv~R~IHaTgDfe~a~~l~fs~~Av~aGi~AL~~G~~IvtDv~Mv~aGI~~~ 221 (332)
T PRK05782 159 DLSNWRDREKEIIARAVYASGNLELAKYVYISNDLLDAGIEALKAGIPIVADVKMVAAGIRWR 221 (332)
T ss_pred CCCCCCHHHHHHHHHHEECCCCCCHHHHEEECHHHHHHHHHHHHCCCCEEECHHHHHHHCCCC
T ss_conf 434799455003776412266721285367890599999999986999998258998537704
No 487
>PTZ00037 DnaJ_C chaperone protein; Provisional
Probab=28.46 E-value=27 Score=14.36 Aligned_cols=21 Identities=24% Similarity=0.373 Sum_probs=0.0
Q ss_pred HHHCCCHHHHHHHHHHHHHHH
Q ss_conf 994999889999999999980
Q gi|254780694|r 208 VILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 208 ~~L~iS~~TV~~hl~~i~~KL 228 (246)
..|+||+..=..-|+.+|+||
T Consensus 30 ~iLGV~~~As~~EIKKAYRKL 50 (422)
T PTZ00037 30 EVLNLSKDCTESEIKKAYRKL 50 (422)
T ss_pred HHHCCCCCCCHHHHHHHHHHH
T ss_conf 865989998999999999999
No 488
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=28.38 E-value=36 Score=13.53 Aligned_cols=26 Identities=23% Similarity=0.422 Sum_probs=0.0
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 97999999499988999999999998
Q gi|254780694|r 202 TSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 202 t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
|-.|||..|+.|++-+++.+++.-.+
T Consensus 25 tl~elA~~l~cS~Rn~r~lL~~m~~~ 50 (551)
T PRK13626 25 TLNELAELLNCSRRHMRTLLNTMQDR 50 (551)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 39999998688857899999999988
No 489
>COG5407 SEC63 Preprotein translocase subunit Sec63 [Intracellular trafficking and secretion]
Probab=28.37 E-value=29 Score=14.10 Aligned_cols=39 Identities=26% Similarity=0.364 Sum_probs=0.0
Q ss_pred HHHHHHCCCCHHHHHH-------------HHCCCHHHHHHHHHHHHHHHCCC
Q ss_conf 9999985999799999-------------94999889999999999980799
Q gi|254780694|r 193 CLTWISEGKTSDEIAV-------------ILGISRNTVNNYIASIMRKTATK 231 (246)
Q Consensus 193 Vl~lia~G~t~~eIA~-------------~L~iS~~TV~~hl~~i~~KLgv~ 231 (246)
|+.|++-|.-..-|+. +|||+..|-..-+++.|+||.++
T Consensus 74 ivgWl~i~~L~~~I~~~k~~~~~~fDPyEILGI~~~ts~rdik~~yr~Ls~K 125 (610)
T COG5407 74 IVGWLVISYLISNIRTLKIEYRRGFDPYEILGIDQDTSERDIKKRYRMLSMK 125 (610)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCCCCCHHHHHHHHHHHEEE
T ss_conf 8999999999998777789987088818861246787577899999866240
No 490
>PRK00430 fis DNA-binding protein Fis; Provisional
Probab=28.29 E-value=36 Score=13.52 Aligned_cols=17 Identities=35% Similarity=0.649 Sum_probs=0.0
Q ss_pred HHHHCCCHHHHHHHHHH
Q ss_conf 99949998899999999
Q gi|254780694|r 207 AVILGISRNTVNNYIAS 223 (246)
Q Consensus 207 A~~L~iS~~TV~~hl~~ 223 (246)
|+.|||+.+|.+..++.
T Consensus 78 A~~LGInR~TLRkKlk~ 94 (98)
T PRK00430 78 ALMLGINRGTLRKKLKK 94 (98)
T ss_pred HHHHCCCHHHHHHHHHH
T ss_conf 99978778899999998
No 491
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=28.14 E-value=36 Score=13.50 Aligned_cols=22 Identities=32% Similarity=0.445 Sum_probs=0.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 9979999994999889999999
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIA 222 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~ 222 (246)
+.-+|+++.+++|..|+..+++
T Consensus 14 lrl~ev~~~~GlSrstiYr~i~ 35 (70)
T COG3311 14 LRLPEVAQLTGLSRSTIYRLIK 35 (70)
T ss_pred HHHHHHHHHHCCCHHHHHHHHC
T ss_conf 2089999997766899999980
No 492
>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=28.07 E-value=37 Score=13.49 Aligned_cols=22 Identities=18% Similarity=0.356 Sum_probs=0.0
Q ss_pred HCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 8599979999994999889999
Q gi|254780694|r 198 SEGKTSDEIAVILGISRNTVNN 219 (246)
Q Consensus 198 a~G~t~~eIA~~L~iS~~TV~~ 219 (246)
+.|+|-.+.|...++|.+|+..
T Consensus 13 ~~glTQ~~LA~~aGvs~~~Is~ 34 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRD 34 (58)
T ss_pred HCCCCHHHHHHHHCCCHHHHHH
T ss_conf 9499899999881998999999
No 493
>TIGR02392 rpoH_proteo alternative sigma factor RpoH; InterPro: IPR012759 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 recognized by the major sigma factors , . This entry represents the proteobacterial clade of sigma factors called RpoH. 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.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0008270 zinc ion binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent, 0009408 response to heat.
Probab=28.01 E-value=37 Score=13.49 Aligned_cols=44 Identities=20% Similarity=0.255 Sum_probs=0.0
Q ss_pred CCCHHHHHHHH---HHHC-CCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 88977999999---9985-99979999994999889999999999980
Q gi|254780694|r 185 ELTGREVECLT---WISE-GKTSDEIAVILGISRNTVNNYIASIMRKT 228 (246)
Q Consensus 185 ~LT~RE~eVl~---lia~-G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 228 (246)
.|=.||+.|+. |-=+ +.|-.++|.+.+||.-=||--=+++|.|+
T Consensus 226 ~Ld~RsR~I~~~RwL~d~~~~TL~~LA~eygvSaERiRQiE~~Am~K~ 273 (279)
T TIGR02392 226 SLDARSRRIIEARWLDDDGKLTLHELAAEYGVSAERIRQIEKNAMKKL 273 (279)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 522887999987302788996478999884874667999999999999
No 494
>pfam10654 DUF2481 Protein of unknown function (DUF2481). This is a hypothetical protein family homologous to Lmo2305 in Bacteriophage A118 systems.
Probab=27.93 E-value=37 Score=13.48 Aligned_cols=33 Identities=24% Similarity=0.282 Sum_probs=0.0
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 999999985999799999949998899999999
Q gi|254780694|r 191 VECLTWISEGKTSDEIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 191 ~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~ 223 (246)
.|-..|=-.|+|--+||+.-.||..||-++..+
T Consensus 71 ~Efv~LRhAGlt~~aIAD~F~iS~s~~~nft~~ 103 (126)
T pfam10654 71 IEFVELRHAGLTGYAIADHFKVSKSVVFNFTRR 103 (126)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999998855886079999974779999999996
No 495
>pfam08004 DUF1699 Protein of unknown function (DUF1699). This family contains many archaeal proteins which have very conserved sequences.
Probab=27.68 E-value=37 Score=13.45 Aligned_cols=32 Identities=22% Similarity=0.262 Sum_probs=0.0
Q ss_pred HHHHHHHCCCCHHHHHHHH----CCCHHHHHHHHHH
Q ss_conf 9999998599979999994----9998899999999
Q gi|254780694|r 192 ECLTWISEGKTSDEIAVIL----GISRNTVNNYIAS 223 (246)
Q Consensus 192 eVl~lia~G~t~~eIA~~L----~iS~~TV~~hl~~ 223 (246)
.|-.+-++|+|+.+|+..+ .+|+.-|..-+++
T Consensus 96 kI~el~~eG~s~E~i~~k~~re~kl~p~mi~yil~~ 131 (131)
T pfam08004 96 RIRELKAEGISNEEIAEKLSRESKLSPDMILYILKT 131 (131)
T ss_pred HHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHCC
T ss_conf 999999769988999999876424899999998509
No 496
>pfam07037 DUF1323 Putative transcription regulator (DUF1323). This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. This family appears to have an HTH domain and is therefore likely to act as a transcriptional regulator.
Probab=27.66 E-value=37 Score=13.45 Aligned_cols=23 Identities=35% Similarity=0.616 Sum_probs=0.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 99799999949998899999999
Q gi|254780694|r 201 KTSDEIAVILGISRNTVNNYIAS 223 (246)
Q Consensus 201 ~t~~eIA~~L~iS~~TV~~hl~~ 223 (246)
+|..|.|..+|.|.-||+.-.+.
T Consensus 1 mT~eELa~~~G~srQtINkwaRk 23 (122)
T pfam07037 1 MTPEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred CCHHHHHHHHCCHHHHHHHHHHH
T ss_conf 98789988747129999999997
No 497
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain; InterPro: IPR006497 This set of protein sequences, defined by an N-terminal domain, represent phage lambda replication protein O and other homologous phage and prophage proteins. ; GO: 0006260 DNA replication.
Probab=27.43 E-value=37 Score=13.42 Aligned_cols=46 Identities=33% Similarity=0.461 Sum_probs=0.0
Q ss_pred CCCCCCHHHHHHHHHHH----------CCCCHHHHHHHHC-------CCHHHHHHHHHHHHHH
Q ss_conf 88888977999999998----------5999799999949-------9988999999999998
Q gi|254780694|r 182 KDFELTGREVECLTWIS----------EGKTSDEIAVILG-------ISRNTVNNYIASIMRK 227 (246)
Q Consensus 182 ~~~~LT~RE~eVl~lia----------~G~t~~eIA~~L~-------iS~~TV~~hl~~i~~K 227 (246)
....||.||..|+.-|. +=.|+.+||...+ ++...|..=++++.++
T Consensus 19 ~~~~L~~Ref~v~~Ai~R~T~Gyn~~~~rvt~~~ia~lt~Pdeakaal~~~~vs~A~~~L~~~ 81 (104)
T TIGR01610 19 AGADLSGREFRVLLAILRLTYGYNKEADRVTASEIAELTKPDEAKAALERKRVSEAIKSLVRR 81 (104)
T ss_pred HCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHHHHHH
T ss_conf 148784357999999998741566603566688888532831355521344788999998875
No 498
>pfam04695 Pex14_N Peroxisomal membrane anchor protein (Pex14p) conserved region. Family of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N-terminus of the protein.
Probab=27.39 E-value=38 Score=13.42 Aligned_cols=30 Identities=27% Similarity=0.154 Sum_probs=0.0
Q ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCHHH
Q ss_conf 977999999998599979999994999889
Q gi|254780694|r 187 TGREVECLTWISEGKTSDEIAVILGISRNT 216 (246)
Q Consensus 187 T~RE~eVl~lia~G~t~~eIA~~L~iS~~T 216 (246)
+|-+..+-=|-.+|+|..||-..|+.+..+
T Consensus 21 sp~~~k~~FL~sKgLt~~eI~~a~~~~~~~ 50 (79)
T pfam04695 21 SPLEKKIEFLESKGLTEEEIDEALKRAGNP 50 (79)
T ss_pred CCHHHHHHHHHHCCCCHHHHHHHHHHCCCC
T ss_conf 858999999997599999999999863999
No 499
>TIGR03192 benz_CoA_bzdQ benzoyl-CoA reductase, bzd-type, Q subunit. Members of this family are the Q subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Probab=27.34 E-value=38 Score=13.41 Aligned_cols=40 Identities=13% Similarity=0.224 Sum_probs=0.0
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 9999999985999799999949998899999999999807998
Q gi|254780694|r 190 EVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKT 232 (246)
Q Consensus 190 E~eVl~lia~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLgv~~ 232 (246)
|.||..++++|.+..+|+.-++.|... .+.++.+|++...
T Consensus 202 ESevis~l~~G~~~edI~aGl~~sia~---rv~~l~~r~~~~~ 241 (293)
T TIGR03192 202 KSEALGLLKAGYTKNMVIAAYCQAMAE---RVVSLLERIGVEE 241 (293)
T ss_pred EHHHHHHHHCCCCHHHHHHHHHHHHHH---HHHHHHHHCCCCC
T ss_conf 176999998699899999999999999---9999976338899
No 500
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=27.31 E-value=38 Score=13.41 Aligned_cols=38 Identities=18% Similarity=0.389 Sum_probs=0.0
Q ss_pred HHHHHHHHHCCC--------CHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 999999998599--------97999999499988999999999998
Q gi|254780694|r 190 EVECLTWISEGK--------TSDEIAVILGISRNTVNNYIASIMRK 227 (246)
Q Consensus 190 E~eVl~lia~G~--------t~~eIA~~L~iS~~TV~~hl~~i~~K 227 (246)
|..|.+.|..|. +-+|.|..++||..||+--++.+-.+
T Consensus 13 e~~i~~~I~~g~~~~G~~LP~EreLa~~~gVsR~tvReal~~L~~~ 58 (239)
T PRK04984 13 EEYIIESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARD 58 (239)
T ss_pred HHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 9999999986999999989889999999798889999999999988
Done!