Query 044490
Match_columns 430
No_of_seqs 195 out of 1512
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 03:43:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044490.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044490hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK11057 ATP-dependent DNA hel 99.9 4.5E-25 9.7E-30 239.1 17.2 161 1-182 444-604 (607)
2 PLN03137 ATP-dependent DNA hel 99.9 1.7E-23 3.6E-28 233.6 18.5 185 1-188 908-1108(1195)
3 TIGR01389 recQ ATP-dependent D 99.9 2.4E-21 5.2E-26 209.4 16.0 159 1-180 433-591 (591)
4 COG4955 Uncharacterized protei 99.9 3.2E-22 6.9E-27 192.3 6.2 274 4-322 37-340 (343)
5 PF14493 HTH_40: Helix-turn-he 99.8 4.8E-20 1E-24 152.5 10.2 91 214-315 1-91 (91)
6 COG0514 RecQ Superfamily II DN 99.8 5.5E-20 1.2E-24 195.3 10.0 150 1-181 439-588 (590)
7 PF00570 HRDC: HRDC domain Blo 99.6 1.8E-15 3.9E-20 117.9 6.4 68 110-177 1-68 (68)
8 smart00341 HRDC Helicase and R 99.5 8.4E-14 1.8E-18 111.9 10.8 77 109-185 3-79 (81)
9 PF09382 RQC: RQC domain; Int 99.3 6.7E-12 1.5E-16 106.1 6.5 65 1-66 34-100 (106)
10 PRK10829 ribonuclease D; Provi 98.5 6.7E-07 1.5E-11 92.0 9.8 76 106-182 209-284 (373)
11 TIGR01388 rnd ribonuclease D. 98.4 8.3E-07 1.8E-11 91.3 9.8 77 105-182 204-280 (367)
12 PF11408 Helicase_Sgs1: Sgs1 R 98.1 8.1E-06 1.8E-10 65.7 6.6 73 110-183 5-77 (80)
13 COG0349 Rnd Ribonuclease D [Tr 97.6 0.00023 5E-09 72.4 8.4 77 105-182 204-280 (361)
14 KOG2206 Exosome 3'-5' exoribon 95.4 0.07 1.5E-06 57.3 9.0 76 106-182 402-478 (687)
15 PF00196 GerE: Bacterial regul 94.1 0.052 1.1E-06 40.6 3.2 43 211-258 3-45 (58)
16 PF02796 HTH_7: Helix-turn-hel 94.0 0.079 1.7E-06 37.9 3.7 34 215-253 10-43 (45)
17 smart00421 HTH_LUXR helix_turn 92.6 0.22 4.8E-06 35.8 4.4 41 212-257 4-44 (58)
18 PF08281 Sigma70_r4_2: Sigma-7 92.4 0.21 4.5E-06 36.6 4.0 43 211-257 10-52 (54)
19 PF13551 HTH_29: Winged helix- 92.0 1.2 2.7E-05 36.8 8.9 88 219-315 4-109 (112)
20 PF13936 HTH_38: Helix-turn-he 91.1 0.17 3.7E-06 36.0 2.2 30 220-253 13-42 (44)
21 cd06170 LuxR_C_like C-terminal 91.1 0.37 8E-06 34.8 4.2 38 215-257 4-41 (57)
22 PRK15411 rcsA colanic acid cap 90.8 0.32 7E-06 45.9 4.5 44 211-259 137-180 (207)
23 TIGR03879 near_KaiC_dom probab 90.8 0.23 4.9E-06 39.6 2.8 45 212-260 16-61 (73)
24 KOG0351 ATP-dependent DNA heli 90.6 0.032 6.9E-07 63.9 -3.0 175 2-181 707-902 (941)
25 PRK00118 putative DNA-binding 90.6 0.52 1.1E-05 40.1 5.1 43 212-258 18-60 (104)
26 PF06056 Terminase_5: Putative 90.3 0.37 8E-06 36.6 3.5 34 217-255 4-37 (58)
27 COG2771 CsgD DNA-binding HTH d 90.1 0.48 1E-05 35.4 4.1 43 212-259 5-47 (65)
28 PRK10840 transcriptional regul 90.1 0.36 7.9E-06 45.0 4.2 44 211-259 150-193 (216)
29 PRK15201 fimbriae regulatory p 89.9 0.47 1E-05 44.2 4.5 45 210-259 132-176 (198)
30 COG2197 CitB Response regulato 88.8 0.51 1.1E-05 44.8 4.1 44 211-259 148-191 (211)
31 PRK11475 DNA-binding transcrip 88.6 0.57 1.2E-05 44.4 4.3 44 211-259 134-177 (207)
32 PF00633 HHH: Helix-hairpin-he 88.5 0.52 1.1E-05 30.9 2.8 23 146-168 4-26 (30)
33 PRK04217 hypothetical protein; 88.5 0.71 1.5E-05 39.7 4.4 44 209-256 40-83 (110)
34 PF13412 HTH_24: Winged helix- 88.4 0.73 1.6E-05 32.9 3.8 41 216-260 5-46 (48)
35 PF12840 HTH_20: Helix-turn-he 88.1 0.52 1.1E-05 35.6 3.0 43 214-260 10-53 (61)
36 PRK13719 conjugal transfer tra 88.0 0.72 1.6E-05 44.2 4.5 46 209-259 141-186 (217)
37 PF14947 HTH_45: Winged helix- 87.5 1 2.2E-05 35.9 4.4 39 20-62 30-68 (77)
38 PF01022 HTH_5: Bacterial regu 87.0 0.53 1.2E-05 33.7 2.3 42 215-260 3-44 (47)
39 PF04297 UPF0122: Putative hel 86.8 0.69 1.5E-05 39.1 3.3 43 212-258 18-60 (101)
40 PF13384 HTH_23: Homeodomain-l 86.3 0.38 8.3E-06 34.5 1.3 39 217-260 8-46 (50)
41 PRK09483 response regulator; P 86.2 0.97 2.1E-05 41.3 4.3 45 210-259 147-191 (217)
42 PF04545 Sigma70_r4: Sigma-70, 85.6 1.2 2.6E-05 32.0 3.7 42 212-257 5-46 (50)
43 PRK09642 RNA polymerase sigma 85.1 1.2 2.6E-05 39.5 4.2 42 212-257 107-148 (160)
44 PF01726 LexA_DNA_bind: LexA D 85.1 1.6 3.5E-05 33.8 4.3 30 230-264 28-58 (65)
45 cd06171 Sigma70_r4 Sigma70, re 83.8 1.9 4.2E-05 30.0 4.1 42 212-257 11-52 (55)
46 TIGR02999 Sig-70_X6 RNA polyme 83.6 1.6 3.6E-05 39.5 4.5 42 212-257 135-176 (183)
47 PRK10188 DNA-binding transcrip 83.5 1.5 3.2E-05 42.5 4.4 44 211-259 179-222 (240)
48 PRK12547 RNA polymerase sigma 83.0 1.7 3.6E-05 39.0 4.3 43 211-257 112-154 (164)
49 PRK09047 RNA polymerase factor 82.9 1.6 3.5E-05 38.6 4.1 43 211-257 106-148 (161)
50 PRK12525 RNA polymerase sigma 82.2 2 4.2E-05 38.8 4.4 43 211-257 118-160 (168)
51 PRK12529 RNA polymerase sigma 82.0 2 4.2E-05 39.3 4.4 44 211-258 127-170 (178)
52 PRK10100 DNA-binding transcrip 82.0 1.8 3.9E-05 41.3 4.2 44 211-259 155-198 (216)
53 PF13518 HTH_28: Helix-turn-he 81.7 2.7 5.8E-05 30.0 4.2 38 218-260 4-41 (52)
54 PRK15369 two component system 81.5 2 4.3E-05 38.3 4.2 45 211-260 149-193 (211)
55 TIGR02989 Sig-70_gvs1 RNA poly 81.5 1.8 3.8E-05 38.3 3.8 43 210-257 110-153 (159)
56 PRK12528 RNA polymerase sigma 81.5 2.1 4.5E-05 38.1 4.3 43 211-257 113-155 (161)
57 PRK12536 RNA polymerase sigma 80.7 2.1 4.6E-05 39.0 4.1 42 212-257 130-171 (181)
58 TIGR03541 reg_near_HchA LuxR f 80.7 2.1 4.5E-05 41.2 4.2 44 211-259 171-214 (232)
59 PRK12542 RNA polymerase sigma 80.5 2.2 4.8E-05 39.0 4.2 44 211-258 122-165 (185)
60 TIGR02983 SigE-fam_strep RNA p 80.1 2.2 4.7E-05 37.9 3.9 43 211-257 110-152 (162)
61 PRK13870 transcriptional regul 79.9 2.3 4.9E-05 41.1 4.2 44 211-259 173-216 (234)
62 PRK12530 RNA polymerase sigma 79.8 2.4 5.1E-05 39.2 4.2 44 210-257 133-176 (189)
63 PRK12520 RNA polymerase sigma 79.7 2.4 5.2E-05 39.0 4.1 43 211-257 131-173 (191)
64 PRK15320 transcriptional activ 79.6 2.7 5.9E-05 39.9 4.4 48 207-259 160-207 (251)
65 PRK12516 RNA polymerase sigma 79.6 2.4 5.3E-05 39.1 4.2 43 211-257 116-158 (187)
66 PRK08241 RNA polymerase factor 79.6 4.3 9.2E-05 41.0 6.3 92 211-308 153-246 (339)
67 PRK06759 RNA polymerase factor 79.2 2.9 6.2E-05 36.7 4.4 43 211-257 106-148 (154)
68 PRK12523 RNA polymerase sigma 79.1 2.8 6.1E-05 37.8 4.4 44 211-258 119-162 (172)
69 PF13463 HTH_27: Winged helix 79.1 3.6 7.9E-05 31.0 4.3 37 20-56 29-68 (68)
70 TIGR00721 tfx DNA-binding prot 79.0 2.7 5.8E-05 37.6 4.0 43 211-258 6-48 (137)
71 COG3432 Predicted transcriptio 78.9 3.2 7E-05 34.7 4.2 43 20-63 42-85 (95)
72 PRK09649 RNA polymerase sigma 78.7 2.6 5.7E-05 38.7 4.0 44 211-258 130-173 (185)
73 PRK10651 transcriptional regul 78.6 3.2 6.8E-05 37.4 4.5 44 211-259 155-198 (216)
74 PRK12511 RNA polymerase sigma 78.4 2.7 5.9E-05 38.7 4.1 43 211-257 111-153 (182)
75 TIGR03020 EpsA transcriptional 78.3 2.7 5.9E-05 41.1 4.2 45 210-259 189-233 (247)
76 PRK12532 RNA polymerase sigma 78.2 2.6 5.6E-05 38.9 3.9 44 211-258 136-179 (195)
77 TIGR02952 Sig70_famx2 RNA poly 78.2 2.9 6.3E-05 37.2 4.1 43 211-257 122-164 (170)
78 TIGR02960 SigX5 RNA polymerase 78.1 4.5 9.8E-05 40.4 5.9 93 211-308 142-236 (324)
79 PRK12527 RNA polymerase sigma 77.8 3.4 7.4E-05 36.6 4.4 42 212-257 106-147 (159)
80 PRK12540 RNA polymerase sigma 77.8 2.9 6.2E-05 38.5 4.0 43 211-257 111-153 (182)
81 PRK06930 positive control sigm 77.5 3 6.4E-05 38.5 4.0 44 210-257 113-156 (170)
82 smart00351 PAX Paired Box doma 77.2 12 0.00026 32.5 7.6 40 216-260 23-62 (125)
83 PRK12522 RNA polymerase sigma 77.1 3.2 6.8E-05 37.5 4.1 43 212-258 120-162 (173)
84 PRK09645 RNA polymerase sigma 77.0 3.5 7.7E-05 37.0 4.3 43 211-257 118-160 (173)
85 PRK12545 RNA polymerase sigma 77.0 3.3 7.3E-05 38.6 4.3 43 211-257 139-181 (201)
86 PRK09639 RNA polymerase sigma 76.9 3.3 7.1E-05 36.8 4.1 43 211-258 112-154 (166)
87 PRK10046 dpiA two-component re 76.8 3.2 7E-05 39.1 4.2 41 215-260 163-206 (225)
88 TIGR02941 Sigma_B RNA polymera 76.4 31 0.00068 33.3 11.1 44 210-257 204-247 (255)
89 PRK07037 extracytoplasmic-func 76.3 3.9 8.5E-05 36.3 4.4 43 211-257 109-151 (163)
90 PF01978 TrmB: Sugar-specific 76.1 1.6 3.4E-05 33.5 1.5 44 213-260 7-51 (68)
91 PF00356 LacI: Bacterial regul 76.1 2.5 5.3E-05 30.5 2.4 43 229-290 1-43 (46)
92 PRK12537 RNA polymerase sigma 75.9 3.9 8.5E-05 37.3 4.4 43 211-257 133-175 (182)
93 cd00569 HTH_Hin_like Helix-tur 75.8 3.7 8E-05 25.7 3.1 30 218-252 13-42 (42)
94 TIGR02959 SigZ RNA polymerase 75.1 4.1 8.9E-05 36.8 4.3 42 211-256 100-141 (170)
95 COG3415 Transposase and inacti 75.1 17 0.00036 32.6 7.9 93 226-324 20-115 (138)
96 PRK03975 tfx putative transcri 75.0 4.6 0.0001 36.2 4.4 43 210-257 5-47 (141)
97 COG2739 Uncharacterized protei 74.9 3.8 8.3E-05 34.6 3.5 41 213-257 19-59 (105)
98 TIGR02985 Sig70_bacteroi1 RNA 74.8 4 8.7E-05 35.6 4.0 41 212-257 114-155 (161)
99 PRK12533 RNA polymerase sigma 74.7 3.7 8.1E-05 39.1 4.0 43 211-257 134-176 (216)
100 PHA02591 hypothetical protein; 74.1 2.3 5E-05 34.2 2.0 33 217-254 50-82 (83)
101 PRK13919 putative RNA polymera 74.1 4.4 9.5E-05 36.9 4.2 44 210-257 134-177 (186)
102 PRK12543 RNA polymerase sigma 73.9 4.4 9.6E-05 36.8 4.2 42 212-257 118-159 (179)
103 PRK09636 RNA polymerase sigma 73.8 7 0.00015 38.7 5.9 89 211-308 115-203 (293)
104 TIGR02948 SigW_bacill RNA poly 73.5 3.8 8.2E-05 37.1 3.6 42 211-257 136-178 (187)
105 TIGR02531 yecD_yerC TrpR-relat 73.5 2.7 5.8E-05 34.7 2.3 36 211-252 36-71 (88)
106 TIGR03001 Sig-70_gmx1 RNA poly 73.4 4.4 9.5E-05 39.4 4.2 46 210-259 160-205 (244)
107 PRK09651 RNA polymerase sigma 73.3 4.1 8.8E-05 36.9 3.7 45 211-259 119-163 (172)
108 cd00131 PAX Paired Box domain 73.1 51 0.0011 28.8 10.5 79 216-301 23-103 (128)
109 PRK10430 DNA-binding transcrip 72.8 5.4 0.00012 37.8 4.6 31 226-260 177-207 (239)
110 TIGR02943 Sig70_famx1 RNA poly 72.4 4.9 0.00011 37.0 4.1 43 211-257 131-173 (188)
111 PRK09652 RNA polymerase sigma 72.2 5.2 0.00011 35.8 4.2 43 211-257 128-170 (182)
112 smart00550 Zalpha Z-DNA-bindin 71.9 7.2 0.00016 30.2 4.3 42 215-260 7-51 (68)
113 TIGR02947 SigH_actino RNA poly 71.6 2.6 5.7E-05 38.8 2.1 43 211-257 131-173 (193)
114 PF04967 HTH_10: HTH DNA bindi 71.6 8.4 0.00018 28.7 4.4 28 226-257 22-49 (53)
115 PRK10403 transcriptional regul 71.5 6 0.00013 35.4 4.5 44 211-259 153-196 (215)
116 PRK10360 DNA-binding transcrip 71.4 5.7 0.00012 35.5 4.3 43 211-258 137-179 (196)
117 PRK06811 RNA polymerase factor 71.3 5.5 0.00012 36.6 4.2 43 211-257 131-173 (189)
118 PRK12514 RNA polymerase sigma 71.3 5.7 0.00012 35.9 4.3 43 211-257 129-171 (179)
119 PRK11923 algU RNA polymerase s 70.9 5.1 0.00011 36.7 3.9 41 212-257 139-180 (193)
120 PRK12539 RNA polymerase sigma 70.8 5.7 0.00012 36.3 4.1 43 211-257 131-173 (184)
121 PRK12541 RNA polymerase sigma 70.3 5.5 0.00012 35.4 3.8 42 212-257 113-154 (161)
122 PRK09415 RNA polymerase factor 70.3 5.5 0.00012 36.2 3.9 44 211-258 127-170 (179)
123 PRK11924 RNA polymerase sigma 70.2 6 0.00013 35.2 4.1 43 211-257 125-167 (179)
124 PRK08301 sporulation sigma fac 70.1 5.3 0.00011 38.1 3.9 44 210-257 177-224 (234)
125 COG1595 RpoE DNA-directed RNA 70.0 5.2 0.00011 36.5 3.7 45 210-258 126-170 (182)
126 PRK12535 RNA polymerase sigma 69.9 5.9 0.00013 36.9 4.1 44 210-257 132-175 (196)
127 PF13601 HTH_34: Winged helix 69.9 9.4 0.0002 30.6 4.7 43 20-62 25-71 (80)
128 PRK12524 RNA polymerase sigma 69.8 5.9 0.00013 36.6 4.1 44 211-258 136-179 (196)
129 PRK09648 RNA polymerase sigma 69.8 6.6 0.00014 35.9 4.4 44 210-257 138-181 (189)
130 PRK12531 RNA polymerase sigma 69.8 6.7 0.00014 36.2 4.4 43 211-257 141-183 (194)
131 PRK09647 RNA polymerase sigma 69.6 6.3 0.00014 37.0 4.2 43 211-257 138-180 (203)
132 PF09339 HTH_IclR: IclR helix- 69.5 2.7 5.9E-05 30.6 1.4 31 226-260 17-47 (52)
133 PRK09643 RNA polymerase sigma 69.4 6.3 0.00014 36.4 4.1 42 211-256 134-175 (192)
134 PRK12512 RNA polymerase sigma 69.3 6.2 0.00014 35.8 4.1 44 210-257 130-173 (184)
135 COG4189 Predicted transcriptio 69.3 5.7 0.00012 38.6 3.8 42 215-260 24-66 (308)
136 TIGR02954 Sig70_famx3 RNA poly 69.2 6.6 0.00014 35.1 4.2 42 212-257 120-161 (169)
137 PRK12546 RNA polymerase sigma 69.2 5.9 0.00013 36.7 3.9 44 211-258 113-156 (188)
138 PRK12544 RNA polymerase sigma 68.9 6.5 0.00014 37.0 4.2 46 209-258 146-191 (206)
139 PRK05602 RNA polymerase sigma 68.7 6.2 0.00013 36.0 3.9 43 211-257 128-170 (186)
140 PRK09646 RNA polymerase sigma 68.6 6.8 0.00015 36.1 4.2 44 210-257 141-184 (194)
141 PRK12538 RNA polymerase sigma 68.6 5.4 0.00012 38.4 3.6 45 210-258 170-214 (233)
142 PRK09958 DNA-binding transcrip 68.4 7.3 0.00016 35.1 4.3 44 211-259 143-186 (204)
143 PRK09191 two-component respons 68.0 6.3 0.00014 37.4 3.9 75 209-289 86-161 (261)
144 PRK09935 transcriptional regul 67.9 7.6 0.00016 34.9 4.3 43 212-259 150-192 (210)
145 PRK12526 RNA polymerase sigma 67.5 7.4 0.00016 36.4 4.3 44 210-257 152-195 (206)
146 PF01710 HTH_Tnp_IS630: Transp 67.5 28 0.00061 29.9 7.5 92 218-325 10-101 (119)
147 COG3355 Predicted transcriptio 67.4 8.6 0.00019 33.9 4.3 46 211-260 24-71 (126)
148 PF08279 HTH_11: HTH domain; 67.4 8.1 0.00017 28.1 3.6 30 227-260 15-44 (55)
149 PRK09637 RNA polymerase sigma 67.3 7.3 0.00016 35.7 4.1 42 212-257 107-148 (181)
150 PRK12519 RNA polymerase sigma 67.3 5.6 0.00012 36.5 3.3 43 211-257 141-183 (194)
151 PF13730 HTH_36: Helix-turn-he 67.3 10 0.00022 27.6 4.1 28 229-260 27-54 (55)
152 PRK12517 RNA polymerase sigma 67.1 7.8 0.00017 35.7 4.3 44 211-258 128-171 (188)
153 PRK12513 RNA polymerase sigma 67.0 3.5 7.6E-05 37.9 1.9 44 211-258 139-182 (194)
154 PRK12534 RNA polymerase sigma 66.9 7.9 0.00017 35.2 4.2 42 212-257 138-179 (187)
155 PF13932 GIDA_assoc_3: GidA as 66.7 7 0.00015 30.9 3.3 32 136-167 37-68 (72)
156 PRK10141 DNA-binding transcrip 66.3 9.6 0.00021 33.1 4.3 43 214-260 16-59 (117)
157 PF01638 HxlR: HxlR-like helix 66.1 12 0.00027 30.3 4.8 44 18-61 28-74 (90)
158 PRK03902 manganese transport t 65.9 10 0.00022 33.4 4.6 39 20-61 33-71 (142)
159 TIGR02984 Sig-70_plancto1 RNA 65.7 8 0.00017 35.0 4.0 42 212-257 141-182 (189)
160 PRK04841 transcriptional regul 65.6 6.9 0.00015 44.5 4.3 44 211-259 838-881 (903)
161 PF06969 HemN_C: HemN C-termin 65.2 11 0.00023 28.6 4.0 31 23-57 35-65 (66)
162 smart00347 HTH_MARR helix_turn 64.8 11 0.00023 30.2 4.2 43 20-63 35-81 (101)
163 PRK05803 sporulation sigma fac 64.2 7.8 0.00017 37.0 3.8 44 210-257 174-221 (233)
164 PF07900 DUF1670: Protein of u 64.2 37 0.0008 32.7 8.2 99 150-281 106-206 (220)
165 PRK12515 RNA polymerase sigma 64.1 9.6 0.00021 34.9 4.2 42 211-256 131-172 (189)
166 TIGR03209 P21_Cbot clostridium 64.0 5.8 0.00013 34.5 2.6 35 211-249 107-141 (142)
167 PF08461 HTH_12: Ribonuclease 63.8 7.1 0.00015 30.2 2.8 40 18-60 27-66 (66)
168 PHA00738 putative HTH transcri 63.5 13 0.00028 31.9 4.4 44 213-260 11-55 (108)
169 PRK09644 RNA polymerase sigma 63.3 9 0.00019 34.2 3.8 43 211-257 108-150 (165)
170 PRK08295 RNA polymerase factor 63.2 9.5 0.00021 35.2 4.1 41 212-257 156-196 (208)
171 PRK06704 RNA polymerase factor 63.0 8.4 0.00018 37.2 3.7 43 212-258 117-159 (228)
172 COG1846 MarR Transcriptional r 62.5 13 0.00028 30.7 4.4 45 20-64 47-94 (126)
173 PRK03573 transcriptional regul 62.5 12 0.00025 32.9 4.3 43 21-63 58-103 (144)
174 TIGR02937 sigma70-ECF RNA poly 62.3 10 0.00022 32.1 3.9 42 211-257 110-152 (158)
175 COG1318 Predicted transcriptio 61.8 4.5 9.8E-05 37.4 1.5 33 224-260 58-90 (182)
176 PRK09638 RNA polymerase sigma 61.7 5.3 0.00012 35.9 2.0 42 212-258 127-169 (176)
177 PRK06986 fliA flagellar biosyn 61.2 10 0.00022 36.3 3.9 44 210-257 183-226 (236)
178 PRK11512 DNA-binding transcrip 60.8 14 0.0003 32.5 4.5 43 20-62 65-110 (144)
179 TIGR02835 spore_sigmaE RNA pol 60.7 11 0.00023 36.1 4.0 44 210-257 177-224 (234)
180 PF10668 Phage_terminase: Phag 60.5 12 0.00025 28.8 3.3 37 212-252 5-43 (60)
181 TIGR00122 birA_repr_reg BirA b 60.4 14 0.00031 28.2 4.0 40 219-262 5-44 (69)
182 PF07638 Sigma70_ECF: ECF sigm 59.4 12 0.00026 34.5 4.0 41 212-256 136-176 (185)
183 PRK08583 RNA polymerase sigma 59.3 12 0.00027 36.2 4.2 44 210-257 204-247 (257)
184 TIGR02846 spore_sigmaK RNA pol 59.1 11 0.00024 35.9 3.8 44 210-257 173-220 (227)
185 TIGR00498 lexA SOS regulatory 58.3 13 0.00029 34.5 4.2 45 212-260 4-55 (199)
186 smart00420 HTH_DEOR helix_turn 57.8 13 0.00027 26.1 3.0 32 225-260 12-43 (53)
187 smart00529 HTH_DTXR Helix-turn 57.5 18 0.00038 29.2 4.3 40 20-62 10-49 (96)
188 PRK09641 RNA polymerase sigma 57.2 14 0.00029 33.5 3.9 43 211-257 136-178 (187)
189 TIGR02957 SigX4 RNA polymerase 57.1 26 0.00056 34.5 6.2 88 211-308 108-196 (281)
190 PRK07670 RNA polymerase sigma 57.1 15 0.00032 35.6 4.3 44 210-257 200-243 (251)
191 PF12802 MarR_2: MarR family; 56.4 15 0.00032 27.0 3.4 29 228-260 22-50 (62)
192 PF10007 DUF2250: Uncharacteri 56.2 22 0.00048 29.5 4.6 24 19-42 31-54 (92)
193 PRK09640 RNA polymerase sigma 55.8 6.9 0.00015 35.9 1.7 40 214-257 137-176 (188)
194 PRK12518 RNA polymerase sigma 55.7 7.1 0.00015 35.1 1.7 42 212-257 121-162 (175)
195 PRK14165 winged helix-turn-hel 55.5 21 0.00045 34.3 5.0 44 20-63 32-75 (217)
196 TIGR02980 SigBFG RNA polymeras 55.2 16 0.00034 34.6 4.2 44 210-257 177-220 (227)
197 smart00346 HTH_ICLR helix_turn 55.2 22 0.00048 28.2 4.4 38 219-260 10-49 (91)
198 TIGR02337 HpaR homoprotocatech 55.1 18 0.00039 30.6 4.1 44 20-63 53-99 (118)
199 TIGR02939 RpoE_Sigma70 RNA pol 55.0 13 0.00028 33.7 3.4 43 211-257 138-180 (190)
200 TIGR02479 FliA_WhiG RNA polyme 54.6 17 0.00037 34.4 4.2 44 210-257 174-217 (224)
201 PRK06474 hypothetical protein; 54.2 20 0.00044 33.2 4.6 43 214-260 11-56 (178)
202 TIGR01889 Staph_reg_Sar staphy 54.0 21 0.00045 30.0 4.3 43 20-62 54-99 (109)
203 PRK12423 LexA repressor; Provi 53.5 22 0.00048 33.4 4.8 48 212-264 4-58 (202)
204 PF03551 PadR: Transcriptional 53.0 23 0.0005 27.6 4.1 42 20-61 28-74 (75)
205 COG1796 POL4 DNA polymerase IV 52.8 33 0.00071 34.9 6.0 46 140-185 80-129 (326)
206 PF11313 DUF3116: Protein of u 52.4 22 0.00048 29.2 3.9 58 4-62 23-80 (85)
207 TIGR02859 spore_sigH RNA polym 52.4 19 0.00041 32.9 4.1 33 220-257 159-191 (198)
208 TIGR02950 SigM_subfam RNA poly 52.3 7.5 0.00016 34.0 1.3 28 226-257 120-147 (154)
209 PF14520 HHH_5: Helix-hairpin- 52.2 19 0.00042 26.9 3.4 27 140-169 28-54 (60)
210 PRK11922 RNA polymerase sigma 52.2 11 0.00025 35.8 2.7 43 210-256 148-190 (231)
211 PRK00135 scpB segregation and 51.8 62 0.0013 30.4 7.4 107 144-260 14-130 (188)
212 cd00090 HTH_ARSR Arsenical Res 51.4 33 0.00071 25.3 4.7 41 20-61 31-71 (78)
213 smart00419 HTH_CRP helix_turn_ 50.8 15 0.00033 25.3 2.5 30 227-260 8-37 (48)
214 COG5045 Ribosomal protein S10E 50.7 20 0.00042 29.8 3.3 53 12-64 24-80 (105)
215 PF03501 S10_plectin: Plectin/ 50.4 26 0.00056 29.4 4.1 45 20-64 34-78 (95)
216 smart00344 HTH_ASNC helix_turn 49.8 29 0.00063 28.6 4.5 39 218-260 7-46 (108)
217 PRK10870 transcriptional repre 49.5 26 0.00056 32.2 4.5 43 21-63 83-128 (176)
218 COG3413 Predicted DNA binding 48.5 25 0.00055 33.2 4.4 44 211-258 155-205 (215)
219 TIGR01884 cas_HTH CRISPR locus 48.3 30 0.00064 32.4 4.8 46 211-260 140-186 (203)
220 smart00418 HTH_ARSR helix_turn 48.3 42 0.0009 23.9 4.7 41 21-61 22-63 (66)
221 cd00092 HTH_CRP helix_turn_hel 48.1 19 0.00041 26.8 2.8 33 226-263 24-56 (67)
222 PRK15418 transcriptional regul 48.0 24 0.00052 35.8 4.3 39 217-260 20-58 (318)
223 PRK05572 sporulation sigma fac 47.8 25 0.00053 34.0 4.2 44 210-257 201-244 (252)
224 TIGR01388 rnd ribonuclease D. 47.6 34 0.00074 35.4 5.5 67 109-178 298-365 (367)
225 TIGR02394 rpoS_proteo RNA poly 46.5 20 0.00044 35.4 3.5 46 209-258 220-269 (285)
226 PRK09635 sigI RNA polymerase s 46.2 23 0.00049 35.3 3.8 85 211-305 118-203 (290)
227 smart00418 HTH_ARSR helix_turn 46.1 26 0.00057 25.0 3.3 32 225-260 8-39 (66)
228 PRK06288 RNA polymerase sigma 46.0 28 0.00061 34.0 4.4 44 210-257 211-254 (268)
229 smart00354 HTH_LACI helix_turn 45.6 45 0.00097 25.7 4.6 43 229-290 2-44 (70)
230 PF01047 MarR: MarR family; I 45.1 19 0.00041 26.3 2.3 36 221-260 11-46 (59)
231 PRK11303 DNA-binding transcrip 44.9 26 0.00057 34.4 4.0 48 228-291 1-48 (328)
232 COG1339 Transcriptional regula 44.8 27 0.00058 33.2 3.7 44 20-63 30-73 (214)
233 smart00347 HTH_MARR helix_turn 44.7 41 0.00089 26.6 4.5 47 212-263 8-55 (101)
234 PRK07408 RNA polymerase sigma 44.7 28 0.00062 33.8 4.1 44 210-257 202-245 (256)
235 COG1497 Predicted transcriptio 43.6 34 0.00073 33.5 4.3 41 20-63 36-76 (260)
236 PRK09390 fixJ response regulat 43.6 31 0.00067 30.2 3.9 45 211-260 141-185 (202)
237 COG1321 TroR Mn-dependent tran 43.0 35 0.00077 30.9 4.2 40 20-62 35-74 (154)
238 PF09639 YjcQ: YjcQ protein; 42.9 31 0.00067 28.2 3.5 43 21-63 22-70 (88)
239 PRK05911 RNA polymerase sigma 42.4 32 0.0007 33.5 4.2 44 210-257 204-247 (257)
240 TIGR01481 ccpA catabolite cont 42.3 37 0.0008 33.3 4.6 45 228-291 2-46 (329)
241 PRK10727 DNA-binding transcrip 42.0 41 0.00088 33.4 4.9 44 229-291 3-46 (343)
242 cd00090 HTH_ARSR Arsenical Res 41.6 56 0.0012 24.0 4.6 39 218-260 11-49 (78)
243 smart00345 HTH_GNTR helix_turn 41.4 24 0.00053 25.3 2.4 28 229-260 22-49 (60)
244 PRK10829 ribonuclease D; Provi 41.0 42 0.00091 34.9 4.9 65 109-179 302-372 (373)
245 smart00278 HhH1 Helix-hairpin- 40.7 21 0.00046 22.2 1.7 16 154-169 2-17 (26)
246 PF01476 LysM: LysM domain; I 40.7 30 0.00065 23.6 2.7 31 133-163 1-32 (44)
247 PRK07598 RNA polymerase sigma 40.7 4.6E+02 0.01 27.8 12.5 45 210-258 349-397 (415)
248 cd01104 HTH_MlrA-CarA Helix-Tu 40.6 54 0.0012 24.5 4.4 62 228-301 1-67 (68)
249 COG2390 DeoR Transcriptional r 40.4 39 0.00084 34.5 4.4 40 216-260 16-55 (321)
250 PRK10703 DNA-binding transcrip 40.4 47 0.001 32.8 5.1 46 228-292 2-47 (341)
251 TIGR02885 spore_sigF RNA polym 40.4 36 0.00077 32.3 4.0 44 210-257 182-225 (231)
252 PRK15183 Vi polysaccharide bio 40.2 27 0.00059 29.8 2.7 26 115-140 113-140 (143)
253 COG1555 ComEA DNA uptake prote 39.9 80 0.0017 28.5 6.0 41 137-185 81-121 (149)
254 PTZ00034 40S ribosomal protein 39.9 22 0.00049 31.1 2.3 44 21-64 38-81 (124)
255 TIGR02417 fruct_sucro_rep D-fr 39.5 39 0.00085 33.2 4.3 47 229-291 1-47 (327)
256 PRK10339 DNA-binding transcrip 38.8 37 0.0008 33.5 4.0 47 228-291 2-48 (327)
257 PF14338 Mrr_N: Mrr N-terminal 38.5 28 0.0006 28.4 2.5 31 29-62 60-90 (92)
258 COG2345 Predicted transcriptio 37.7 51 0.0011 31.8 4.6 42 215-260 12-54 (218)
259 PF08784 RPA_C: Replication pr 37.7 23 0.0005 29.3 2.0 45 212-260 45-94 (102)
260 PRK13413 mpi multiple promoter 37.1 36 0.00079 31.6 3.5 33 217-254 163-195 (200)
261 PRK13777 transcriptional regul 36.7 52 0.0011 30.8 4.4 42 21-62 71-115 (185)
262 PRK10014 DNA-binding transcrip 36.4 43 0.00093 33.1 4.0 46 226-290 5-50 (342)
263 PRK09526 lacI lac repressor; R 36.2 52 0.0011 32.5 4.6 45 227-290 5-49 (342)
264 PF07750 GcrA: GcrA cell cycle 36.0 20 0.00043 32.8 1.5 33 218-255 10-43 (162)
265 PF08220 HTH_DeoR: DeoR-like h 36.0 34 0.00074 25.4 2.5 32 225-260 12-43 (57)
266 PRK07122 RNA polymerase sigma 36.0 43 0.00093 32.8 3.9 44 210-257 214-257 (264)
267 cd04764 HTH_MlrA-like_sg1 Heli 36.0 74 0.0016 23.9 4.4 62 228-301 1-66 (67)
268 PF09862 DUF2089: Protein of u 35.9 66 0.0014 27.8 4.5 49 262-318 26-74 (113)
269 PRK09413 IS2 repressor TnpA; R 35.6 50 0.0011 28.4 3.8 38 218-259 20-57 (121)
270 PRK11050 manganese transport r 35.4 63 0.0014 28.9 4.6 39 20-61 62-100 (152)
271 TIGR02405 trehalos_R_Ecol treh 35.2 56 0.0012 32.0 4.6 45 228-291 2-46 (311)
272 TIGR02702 SufR_cyano iron-sulf 34.4 56 0.0012 30.6 4.2 34 223-260 11-44 (203)
273 PRK10344 DNA-binding transcrip 34.2 24 0.00051 29.3 1.4 33 223-259 17-49 (92)
274 PRK09975 DNA-binding transcrip 34.2 41 0.00089 31.0 3.3 31 218-252 19-52 (213)
275 PRK08609 hypothetical protein; 34.1 62 0.0013 35.6 5.1 46 139-184 74-123 (570)
276 COG1733 Predicted transcriptio 33.9 77 0.0017 27.5 4.7 42 20-61 48-92 (120)
277 PRK09492 treR trehalose repres 33.9 46 0.00099 32.4 3.8 46 226-290 3-48 (315)
278 COG5625 Predicted transcriptio 33.8 44 0.00096 28.4 3.0 34 223-260 32-65 (113)
279 PF12826 HHH_2: Helix-hairpin- 33.7 62 0.0013 24.7 3.6 24 148-171 30-53 (64)
280 PRK04172 pheS phenylalanyl-tRN 33.4 53 0.0011 35.3 4.4 44 20-64 31-74 (489)
281 PF09012 FeoC: FeoC like trans 33.4 26 0.00057 26.9 1.6 31 226-260 13-43 (69)
282 PF13693 HTH_35: Winged helix- 33.3 7.7 0.00017 31.3 -1.5 26 223-252 11-36 (78)
283 COG2238 RPS19A Ribosomal prote 33.3 50 0.0011 29.6 3.4 37 22-62 94-130 (147)
284 PRK14987 gluconate operon tran 33.2 55 0.0012 32.2 4.2 46 227-291 5-50 (331)
285 PRK13558 bacterio-opsin activa 32.8 54 0.0012 36.0 4.5 44 211-258 607-657 (665)
286 PF00325 Crp: Bacterial regula 32.7 34 0.00075 22.8 1.8 28 228-259 3-30 (32)
287 COG2909 MalT ATP-dependent tra 32.6 33 0.00071 39.3 2.7 44 211-259 831-874 (894)
288 TIGR02850 spore_sigG RNA polym 32.6 58 0.0013 31.5 4.2 44 210-257 205-248 (254)
289 cd07377 WHTH_GntR Winged helix 32.5 40 0.00087 24.6 2.4 28 229-260 27-54 (66)
290 PRK00215 LexA repressor; Valid 32.4 76 0.0016 29.5 4.8 30 227-260 23-53 (205)
291 PRK05657 RNA polymerase sigma 32.4 34 0.00074 34.7 2.6 45 210-258 261-309 (325)
292 PRK10401 DNA-binding transcrip 32.3 65 0.0014 32.0 4.6 45 228-291 2-46 (346)
293 PRK08215 sporulation sigma fac 32.3 61 0.0013 31.4 4.3 43 211-257 209-251 (258)
294 COG1191 FliA DNA-directed RNA 32.2 1.7E+02 0.0036 28.8 7.2 43 211-257 196-238 (247)
295 PRK10668 DNA-binding transcrip 32.1 42 0.0009 31.0 3.0 31 218-252 19-52 (215)
296 TIGR02698 CopY_TcrY copper tra 32.1 3.1E+02 0.0068 23.8 8.4 96 222-322 13-119 (130)
297 TIGR02393 RpoD_Cterm RNA polym 32.0 55 0.0012 31.3 3.9 46 210-259 175-224 (238)
298 PRK09416 lstR lineage-specific 31.9 57 0.0012 29.1 3.6 45 20-64 74-119 (135)
299 COG1522 Lrp Transcriptional re 31.9 76 0.0016 27.7 4.5 45 212-260 6-51 (154)
300 PF05225 HTH_psq: helix-turn-h 31.9 45 0.00098 23.7 2.4 32 217-253 6-38 (45)
301 TIGR02997 Sig70-cyanoRpoD RNA 31.8 56 0.0012 32.6 4.0 44 210-257 248-295 (298)
302 TIGR02431 pcaR_pcaU beta-ketoa 31.8 37 0.00081 32.6 2.7 39 218-260 13-53 (248)
303 PRK11552 putative DNA-binding 31.7 40 0.00086 32.0 2.8 31 218-252 21-53 (225)
304 PF01527 HTH_Tnp_1: Transposas 31.5 31 0.00067 26.5 1.7 34 219-256 15-48 (76)
305 TIGR02337 HpaR homoprotocatech 31.3 2.4E+02 0.0052 23.6 7.4 35 222-260 37-71 (118)
306 PF13309 HTH_22: HTH domain 31.3 20 0.00043 27.5 0.5 22 227-252 42-63 (64)
307 COG0349 Rnd Ribonuclease D [Tr 31.3 75 0.0016 33.0 4.8 64 108-178 297-360 (361)
308 PF08535 KorB: KorB domain; I 31.1 30 0.00066 28.2 1.6 25 225-253 1-25 (93)
309 PF13601 HTH_34: Winged helix 30.9 37 0.00081 27.1 2.1 36 224-264 11-46 (80)
310 PHA00542 putative Cro-like pro 30.9 70 0.0015 25.6 3.7 54 219-290 23-76 (82)
311 TIGR02607 antidote_HigA addict 30.8 92 0.002 23.9 4.3 26 223-252 14-39 (78)
312 PRK05949 RNA polymerase sigma 30.7 5.8E+02 0.013 25.8 13.2 44 210-257 265-312 (327)
313 PF12728 HTH_17: Helix-turn-he 30.6 32 0.00068 24.5 1.5 21 228-252 2-22 (51)
314 PF07848 PaaX: PaaX-like prote 30.6 88 0.0019 24.5 4.1 36 21-56 35-70 (70)
315 PF01381 HTH_3: Helix-turn-hel 30.3 38 0.00081 24.2 1.9 27 224-254 6-32 (55)
316 KOG2841 Structure-specific end 30.2 52 0.0011 32.1 3.2 30 144-173 218-247 (254)
317 PF04218 CENP-B_N: CENP-B N-te 29.3 46 0.001 24.4 2.2 32 216-252 12-43 (53)
318 PF09202 Rio2_N: Rio2, N-termi 29.3 1.2E+02 0.0025 24.7 4.7 41 20-61 35-75 (82)
319 COG1654 BirA Biotin operon rep 29.2 98 0.0021 25.0 4.2 33 228-264 20-52 (79)
320 TIGR03433 padR_acidobact trans 28.3 70 0.0015 26.5 3.4 44 20-63 36-84 (100)
321 PF13613 HTH_Tnp_4: Helix-turn 28.3 1.1E+02 0.0025 22.1 4.2 37 215-256 8-44 (53)
322 COG4565 CitB Response regulato 28.0 2.9E+02 0.0062 26.8 7.8 47 210-260 153-202 (224)
323 TIGR02392 rpoH_proteo alternat 27.9 71 0.0015 31.3 3.9 43 211-257 218-262 (270)
324 PF02082 Rrf2: Transcriptional 27.8 1.1E+02 0.0024 24.2 4.4 36 20-56 36-71 (83)
325 PF00440 TetR_N: Bacterial reg 27.5 33 0.00071 24.2 1.1 23 226-252 15-37 (47)
326 PF05155 Phage_X: Phage X fami 27.2 1.1E+02 0.0024 25.3 4.4 41 215-267 16-56 (92)
327 cd00092 HTH_CRP helix_turn_hel 27.2 1.2E+02 0.0026 22.2 4.3 32 20-54 36-67 (67)
328 PF07381 DUF1495: Winged helix 27.1 60 0.0013 26.9 2.7 40 16-61 48-88 (90)
329 PF14277 DUF4364: Domain of un 26.8 96 0.0021 28.4 4.3 39 25-63 35-74 (163)
330 COG2906 Bfd Bacterioferritin-a 26.6 70 0.0015 24.8 2.8 28 137-164 10-37 (63)
331 PF10711 DUF2513: Hypothetical 26.5 93 0.002 26.0 3.8 50 14-64 25-81 (102)
332 PHA02510 X gene X product; Rev 26.3 1.4E+02 0.0029 26.1 4.8 50 210-268 24-76 (116)
333 PF02787 CPSase_L_D3: Carbamoy 25.9 3.1E+02 0.0067 23.8 7.1 73 146-251 20-92 (123)
334 PF09012 FeoC: FeoC like trans 25.7 72 0.0016 24.4 2.8 23 20-42 25-47 (69)
335 smart00342 HTH_ARAC helix_turn 25.6 1.6E+02 0.0035 21.9 4.9 61 228-303 2-62 (84)
336 PF13542 HTH_Tnp_ISL3: Helix-t 25.5 88 0.0019 22.1 3.1 32 219-255 20-51 (52)
337 PRK07500 rpoH2 RNA polymerase 25.5 82 0.0018 31.3 3.9 44 211-258 227-272 (289)
338 PRK10163 DNA-binding transcrip 25.4 59 0.0013 31.9 2.8 40 217-260 28-69 (271)
339 TIGR01764 excise DNA binding d 25.3 45 0.00097 22.8 1.5 21 228-252 2-22 (49)
340 PRK09954 putative kinase; Prov 25.3 96 0.0021 31.5 4.5 40 217-260 6-46 (362)
341 PF13443 HTH_26: Cro/C1-type H 25.2 46 0.001 24.5 1.6 28 222-253 5-32 (63)
342 PRK11569 transcriptional repre 25.2 56 0.0012 32.1 2.6 39 218-260 32-72 (274)
343 PF04255 DUF433: Protein of un 25.1 1.1E+02 0.0023 22.7 3.5 33 215-252 20-53 (56)
344 cd07153 Fur_like Ferric uptake 24.8 1.1E+02 0.0024 25.4 4.1 34 227-260 16-50 (116)
345 PF08822 DUF1804: Protein of u 24.4 1.4E+02 0.0031 27.5 4.8 43 220-268 12-54 (165)
346 TIGR02944 suf_reg_Xantho FeS a 24.2 64 0.0014 27.7 2.5 31 226-260 24-54 (130)
347 COG1386 scpB Chromosome segreg 24.0 1.6E+02 0.0036 27.5 5.3 100 144-253 18-128 (184)
348 smart00346 HTH_ICLR helix_turn 23.6 1.3E+02 0.0029 23.6 4.2 38 20-59 31-68 (91)
349 PF08280 HTH_Mga: M protein tr 23.3 80 0.0017 23.5 2.6 30 223-256 15-44 (59)
350 PRK11169 leucine-responsive tr 23.2 84 0.0018 28.4 3.2 45 212-260 12-57 (164)
351 TIGR02702 SufR_cyano iron-sulf 23.1 1.4E+02 0.0031 27.8 4.9 43 20-62 26-73 (203)
352 PRK09480 slmA division inhibit 22.9 75 0.0016 28.5 2.9 32 219-254 19-53 (194)
353 COG1695 Predicted transcriptio 22.8 1.1E+02 0.0023 26.6 3.7 44 20-63 41-89 (138)
354 COG1609 PurR Transcriptional r 22.7 1.1E+02 0.0025 30.7 4.4 44 229-291 2-45 (333)
355 cd04763 HTH_MlrA-like Helix-Tu 22.7 1.7E+02 0.0037 22.0 4.4 59 228-301 1-67 (68)
356 COG1460 Uncharacterized protei 22.5 2.7E+02 0.0059 24.1 5.9 47 136-182 66-113 (114)
357 PF09114 MotA_activ: Transcrip 22.4 1.7E+02 0.0036 24.4 4.4 40 19-62 42-81 (96)
358 TIGR02277 PaaX_trns_reg phenyl 22.4 1.2E+02 0.0025 30.2 4.3 44 20-63 31-74 (280)
359 PRK11512 DNA-binding transcrip 22.4 1E+02 0.0022 26.9 3.6 85 223-317 50-139 (144)
360 PRK10423 transcriptional repre 22.3 1.2E+02 0.0025 29.7 4.3 43 230-291 1-43 (327)
361 TIGR03734 PRTRC_parB PRTRC sys 22.2 2.9E+02 0.0063 30.4 7.5 57 226-287 107-173 (554)
362 PRK03573 transcriptional regul 22.2 5E+02 0.011 22.4 7.9 31 226-260 45-75 (144)
363 PRK11179 DNA-binding transcrip 22.0 1.3E+02 0.0029 26.7 4.2 45 212-260 7-52 (153)
364 PRK10072 putative transcriptio 22.0 3.7E+02 0.008 22.4 6.5 54 112-169 9-66 (96)
365 PF05559 DUF763: Protein of un 22.0 95 0.0021 31.6 3.5 31 138-168 254-284 (319)
366 PRK07758 hypothetical protein; 21.7 44 0.00096 28.0 0.9 25 144-168 58-82 (95)
367 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 21.7 90 0.0019 23.0 2.5 39 212-254 5-43 (50)
368 COG1414 IclR Transcriptional r 21.6 1.4E+02 0.003 29.0 4.6 38 219-260 9-48 (246)
369 cd00141 NT_POLXc Nucleotidyltr 21.5 65 0.0014 32.4 2.3 32 139-170 71-102 (307)
370 cd04762 HTH_MerR-trunc Helix-T 21.5 58 0.0013 22.0 1.4 23 228-254 1-23 (49)
371 PRK15090 DNA-binding transcrip 21.2 80 0.0017 30.5 2.8 31 226-260 27-57 (257)
372 PHA02535 P terminase ATPase su 21.0 1.9E+02 0.0042 32.0 5.9 41 216-268 8-48 (581)
373 PF13411 MerR_1: MerR HTH fami 20.8 44 0.00095 25.1 0.7 62 228-302 1-67 (69)
374 COG1710 Uncharacterized protei 20.6 1.5E+02 0.0033 26.0 4.0 38 215-257 98-135 (139)
375 COG0640 ArsR Predicted transcr 20.6 1.8E+02 0.0038 22.3 4.3 43 214-260 25-68 (110)
376 cd04789 HTH_Cfa Helix-Turn-Hel 20.5 2.2E+02 0.0049 23.5 5.1 67 228-307 2-73 (102)
377 PTZ00095 40S ribosomal protein 20.1 1.3E+02 0.0029 27.8 3.8 40 21-62 117-156 (169)
No 1
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=99.93 E-value=4.5e-25 Score=239.05 Aligned_cols=161 Identities=22% Similarity=0.332 Sum_probs=136.4
Q ss_pred ChhhhhhcccccCcccCCCCCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhcCCCCCCCCCeeeecccccc
Q 044490 1 SKKVVDAQFDKLLLHGLGKDHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLGSARPDHQPPLLLTFNGEMV 80 (430)
Q Consensus 1 ~kkI~~~~~d~l~~fG~Gk~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~g~~kv~~~~l~l~~~~~~~ 80 (430)
+++|.++||+++++||+|+++++.||++++++|+.+|||.+. .+.|++++||++|+.+|+|..++ .+.... .
T Consensus 444 ~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~~~~l~~~~~~~~~l~~~~~~-----~~~~~~--~ 515 (607)
T PRK11057 444 NQRIRDYGHDKLKVYGIGRDKSHEHWVSVIRQLIHLGLVTQN-IAQHSALQLTEAARPVLRGEVSL-----QLAVPR--I 515 (607)
T ss_pred cchhhhcccccCCccCcCCcCCHHHHHHHHHHHHHcCCceec-cCccceEEECHHHHHHhcCCceE-----EEeccc--c
Confidence 589999999999999999999999999999999999999998 68899999999999999998653 222110 0
Q ss_pred cchhhhhcccCcCCCCccccccccCCChHHHHHHHHHHHHHHHHHHHhCCCCeeecchHHHHHHHHhCCCCHHHHhccCC
Q 044490 81 DAEEHETISSNVGDLKSSATLENEGFSEADMQLYHMLLEERKKLARVTGTAPYALCGDQTIKKIALARPSTKARLANIDG 160 (430)
Q Consensus 81 ~~~~~~s~~~~~~~~~pk~~~~~~~~~e~~~~L~~~L~~~R~~lA~e~~vppy~Ifsd~tL~emA~~~P~T~~eL~~I~G 160 (430)
.+.. . .+ +. .......+..||++|++||.++|.+.++|||+||+|.||.+||..+|.|.++|.+|+|
T Consensus 516 ~~~~---~-~~-----~~----~~~~~~~~~~l~~~Lr~~R~~~a~~~~~~~~~if~d~tL~~ia~~~P~t~~~l~~i~G 582 (607)
T PRK11057 516 VALK---P-RA-----MQ----KSFGGNYDRKLFAKLRKLRKSIADEENIPPYVVFNDATLIEMAEQMPITASEMLSVNG 582 (607)
T ss_pred cccc---c-cc-----cc----ccccccchHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHcCCCC
Confidence 0000 0 00 00 0111234689999999999999999999999999999999999999999999999999
Q ss_pred CCHHHHHHHHHHHHHHHHHHHH
Q 044490 161 VNQHLVITHGDHLLQTIRHLSQ 182 (430)
Q Consensus 161 vg~~k~~kyG~~fL~~I~~~~~ 182 (430)
||+.|+++||..|+++|+.++.
T Consensus 583 vg~~K~~~yg~~~l~~i~~~~~ 604 (607)
T PRK11057 583 VGQRKLERFGKPFMALIRAHVD 604 (607)
T ss_pred CCHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999875
No 2
>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional
Probab=99.91 E-value=1.7e-23 Score=233.60 Aligned_cols=185 Identities=22% Similarity=0.292 Sum_probs=139.3
Q ss_pred ChhhhhhcccccCcccCCCCCCHHHHHHHHHHHHHcCCceeeec--Cccc----eEEeCc-chHhhhcCCCCCCCCCeee
Q 044490 1 SKKVVDAQFDKLLLHGLGKDHSSNWWKTLAYQLISYGYLTETIK--DVYR----TVSVSQ-QGKQYLGSARPDHQPPLLL 73 (430)
Q Consensus 1 ~kkI~~~~~d~l~~fG~Gk~ls~~~wk~li~qLi~~GyL~e~~~--~~y~----~l~LT~-kg~~~L~g~~kv~~~~l~l 73 (430)
+++|.++||+++++||+|+++++.+|++++++|+.+|||.++.. +.|+ +|+||+ +|+.+|+|..++. +.+
T Consensus 908 ~~~i~~~~~d~l~~~G~gk~~s~~~~~~li~~Li~~g~L~~~~~~~~~y~~~~~~L~l~~~ka~~vL~g~~~v~---l~~ 984 (1195)
T PLN03137 908 NQYVKKHRHETLSLHGAGKHLSKGEASRILHYLVTEDILAEDVKKSDLYGSVSSLLKVNESKAYKLFSGGQTII---MRF 984 (1195)
T ss_pred cHHHHHhCcccccccCccccCCHHHHHHHHHHHHHcCCceeeccccccCCccceEEEeChHHHHHHhCCCceEE---Eec
Confidence 57899999999999999999999999999999999999998731 4686 799999 5999999997642 111
Q ss_pred ecccccccchhhhhcccCc--CCCC-ccccc----cccCCChHHHHHHHHHHHHHHHHHHH--hCCCCeeecchHHHHHH
Q 044490 74 TFNGEMVDAEEHETISSNV--GDLK-SSATL----ENEGFSEADMQLYHMLLEERKKLARV--TGTAPYALCGDQTIKKI 144 (430)
Q Consensus 74 ~~~~~~~~~~~~~s~~~~~--~~~~-pk~~~----~~~~~~e~~~~L~~~L~~~R~~lA~e--~~vppy~Ifsd~tL~em 144 (430)
+......+.....+...+. .... ..... ......+.+..||++|++||.++|.+ .++|||+||+|.||++|
T Consensus 985 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~Lfe~Lr~lR~elA~e~~~~vppyvIFsD~TL~eI 1064 (1195)
T PLN03137 985 PSSVKASKPSKFEATPAKGPLTSGKQSTLPMATPAQPPVDLNLSAILYTALRKLRTALVKEAGDGVMAYHIFGNATLQQI 1064 (1195)
T ss_pred ccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHhhhcCCCCeEEECHHHHHHH
Confidence 1100000000000000000 0000 00000 00001124678999999999999999 59999999999999999
Q ss_pred HHhCCCCHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHhhccCC
Q 044490 145 ALARPSTKARLANIDGVNQHLVITHGDHLLQTIRHLSQKLNLSL 188 (430)
Q Consensus 145 A~~~P~T~~eL~~I~Gvg~~k~~kyG~~fL~~I~~~~~e~~~~~ 188 (430)
|..+|.|.++|.+|+|||+.|+++||..||++|+.|+.+++.+.
T Consensus 1065 A~~~P~T~~eLl~I~GVG~~KlekYG~~fL~vI~~~~~ey~~~~ 1108 (1195)
T PLN03137 1065 SKRIPRTKEELLEINGLGKAKVSKYGDRLLETIESTINEYYKTD 1108 (1195)
T ss_pred HHHCCCCHHHHhcCCCccHHHHHHHHHHHHHHHHHHHHHhcCCc
Confidence 99999999999999999999999999999999999999998654
No 3
>TIGR01389 recQ ATP-dependent DNA helicase RecQ. The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.
Probab=99.86 E-value=2.4e-21 Score=209.40 Aligned_cols=159 Identities=28% Similarity=0.432 Sum_probs=131.7
Q ss_pred ChhhhhhcccccCcccCCCCCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhcCCCCCCCCCeeeecccccc
Q 044490 1 SKKVVDAQFDKLLLHGLGKDHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLGSARPDHQPPLLLTFNGEMV 80 (430)
Q Consensus 1 ~kkI~~~~~d~l~~fG~Gk~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~g~~kv~~~~l~l~~~~~~~ 80 (430)
+++|.+.+|+++++||+|++++..+|+.++++|+..|||.+. .++|+.+++|++++.+|.++..+ .+.......
T Consensus 433 ~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~l~~~~~l~~~-~~~~~~~~~~~~~~~~l~~e~~~-----~~~~~~~~~ 506 (591)
T TIGR01389 433 NDKILQKGHDQLSTYGIGKDYTQKEWRSLIDQLIAEGLLTEN-DEIYIGLQLTEAARKVLKNEVEV-----LLRPFKVVA 506 (591)
T ss_pred chhHHhcCcccCCccCcCCCCCHHHHHHHHHHHHHcCCceec-cCcCceEEeccchhhhccCccee-----eeccccccc
Confidence 478889999999999999999999999999999999999998 67899999999999999998653 122110000
Q ss_pred cchhhhhcccCcCCCCccccccccCCChHHHHHHHHHHHHHHHHHHHhCCCCeeecchHHHHHHHHhCCCCHHHHhccCC
Q 044490 81 DAEEHETISSNVGDLKSSATLENEGFSEADMQLYHMLLEERKKLARVTGTAPYALCGDQTIKKIALARPSTKARLANIDG 160 (430)
Q Consensus 81 ~~~~~~s~~~~~~~~~pk~~~~~~~~~e~~~~L~~~L~~~R~~lA~e~~vppy~Ifsd~tL~emA~~~P~T~~eL~~I~G 160 (430)
.... . .........+..||++|++||.++|++.++|||+||+|.+|.+||+.+|.|.++|.+|+|
T Consensus 507 ~~~~------~---------~~~~~~~~~~~~l~~~L~~wR~~~A~~~~~p~~~If~d~~L~~ia~~~P~~~~~l~~i~g 571 (591)
T TIGR01389 507 KEKT------R---------VQKNLSVGVDNALFEALRELRKEQADEQNVPPYVIFSDSTLREMAEKRPATLNALLKIKG 571 (591)
T ss_pred chhh------h---------hccccccccHHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHhCCCC
Confidence 0000 0 000001122448999999999999999999999999999999999999999999999999
Q ss_pred CCHHHHHHHHHHHHHHHHHH
Q 044490 161 VNQHLVITHGDHLLQTIRHL 180 (430)
Q Consensus 161 vg~~k~~kyG~~fL~~I~~~ 180 (430)
||+.|+++||..||++|+.|
T Consensus 572 v~~~k~~~~G~~~l~~i~~~ 591 (591)
T TIGR01389 572 VGQNKLDRYGEAFLEVIREY 591 (591)
T ss_pred CCHHHHHHHHHHHHHHHHhC
Confidence 99999999999999999864
No 4
>COG4955 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.86 E-value=3.2e-22 Score=192.28 Aligned_cols=274 Identities=21% Similarity=0.208 Sum_probs=196.6
Q ss_pred hhhhc-ccccCcccCCCCCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhcCCCCCCCCCeeeeccc-----
Q 044490 4 VVDAQ-FDKLLLHGLGKDHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLGSARPDHQPPLLLTFNG----- 77 (430)
Q Consensus 4 I~~~~-~d~l~~fG~Gk~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~g~~kv~~~~l~l~~~~----- 77 (430)
|.+.+ |+.+++||+.+.+++.+++..+..|-.+|||..+ ++ .+++|.+|+..|.-... + ++++.
T Consensus 37 iqDahlfq~~~~fgllp~lkr~~fe~~LekL~k~~~ltv~-~~---~y~Vtakgnaele~~l~----~--fhG~~~qq~~ 106 (343)
T COG4955 37 IQDAHLFQQLSLFGLLPLLKRPSFELFLEKLNKQGILTVT-EN---GYTVTAKGNAELEIMLH----P--FHGRYTQQSM 106 (343)
T ss_pred HhhhHHHHHHHHhccchhcCchhHHHHHHHHhhcCceeec-cC---ceEEeecchHHHHhhhc----c--cchHHHHHHH
Confidence 44444 7889999999999999999999999999999987 44 37999999999986543 2 34442
Q ss_pred -ccccc----hhhhhcc-cCcCCCCcc-----------ccccccCCChHHHHHHHHHHHHHHHHHHHhCCCCeeecc---
Q 044490 78 -EMVDA----EEHETIS-SNVGDLKSS-----------ATLENEGFSEADMQLYHMLLEERKKLARVTGTAPYALCG--- 137 (430)
Q Consensus 78 -~~~~~----~~~~s~~-~~~~~~~pk-----------~~~~~~~~~e~~~~L~~~L~~~R~~lA~e~~vppy~Ifs--- 137 (430)
.+|.+ .|+.|+. .....+.|. .++......+....||.+|.+|.+.++..... |+|.+
T Consensus 107 ~~~~~~LqLlvQvlSnk~qg~~~f~PVt~n~kvqqwVK~~l~~q~~iqla~rl~~eL~~~fkkie~k~~e--~lv~~lsg 184 (343)
T COG4955 107 GQTFQALQLLVQVLSNKKQGVFHFVPVTQNNKVQQWVKIVLNYQKEIQLAIRLENELHNLFKKIELKGPE--YLVYYLSG 184 (343)
T ss_pred HHHHHHHHHHHHHHhhhccceEEEEeeeccHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHhhcCCe--EEEEeccC
Confidence 12322 3344442 111122331 11111112234578999999999999876544 78765
Q ss_pred ----hHHHHHHHHhCCCCHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHhhccCCCCCcCcccccccccceecccccCCC
Q 044490 138 ----DQTIKKIALARPSTKARLANIDGVNQHLVITHGDHLLQTIRHLSQKLNLSLDGKVGEHTAFTRKLHVVVNTRTKLT 213 (430)
Q Consensus 138 ----d~tL~emA~~~P~T~~eL~~I~Gvg~~k~~kyG~~fL~~I~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 213 (430)
+.|.+++|.....+... ....|+.-++.+......-.+.-+.+. +.+.+.+..++
T Consensus 185 ~~~igyT~eQiA~~lkld~w~--------------vy~~~l~e~h~lv~~~~Ece~~~~~ll-------ss~~~~~n~Lt 243 (343)
T COG4955 185 YDEIGYTREQIALILKLDKWS--------------VYQLFLYEMHNLVTMMFECESGEYTLL-------SSIIMKPNTLT 243 (343)
T ss_pred CCccchhHHHHHHHHhhhHHH--------------HHHHHHHHHHHHHHHhhhhhhhHHHHH-------HhccCccchhh
Confidence 77888887765553333 357788888887665432111111000 11124455688
Q ss_pred chHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCCCCC
Q 044490 214 PAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGCKDK 293 (430)
Q Consensus 214 ~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~~~~ 293 (430)
.+..+||.||. +|++++.||.+ |+|+.+||+||++++...|+-+++++++ +.+...+|...+.... +.+
T Consensus 244 nst~kT~tm~~-qgf~le~Ia~i----r~LKtsTIeDHfVEI~lh~~af~~~dyV-----p~e~q~qiiqfa~~~r-t~k 312 (343)
T COG4955 244 NSTYKTYTMLL-QGFTLEDIAAI----RQLKTSTIEDHFVEILLHGYAFNYDDYV-----PLEDQLQIIQFAQQHR-TEK 312 (343)
T ss_pred HHHHHHHHHHH-hcCCHHHHHHH----Hhhhhhhhhhhheeeeecccccchhhcc-----CcccHHHHHHHHHHhh-hhh
Confidence 89999999999 99999999999 9999999999999999999999999998 5556666666666655 589
Q ss_pred hHHHHHhCCCCCCHHHHHHHHHHHHhCCC
Q 044490 294 LKPIKNELPDDITYAHIKACLVMENCGIS 322 (430)
Q Consensus 294 LkpIke~l~~~isY~~Irl~la~~~~~~~ 322 (430)
||+||+.|+ ..||++||+++..++.+-.
T Consensus 313 Lk~ikdqf~-~lsYfQIRLalvk~e~~~~ 340 (343)
T COG4955 313 LKFIKDQFD-TLSYFQIRLALVKFERGDL 340 (343)
T ss_pred hhHHHhhCC-CcCeeeEeeeeeehhhhhc
Confidence 999999999 7999999999988776643
No 5
>PF14493 HTH_40: Helix-turn-helix domain
Probab=99.82 E-value=4.8e-20 Score=152.51 Aligned_cols=91 Identities=34% Similarity=0.573 Sum_probs=86.4
Q ss_pred chHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCCCCC
Q 044490 214 PAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGCKDK 293 (430)
Q Consensus 214 ~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~~~~ 293 (430)
+|...||+||+ +|+|++|||++ |+|+++||++||.+++..|+++++.+|+ +++.++.|..++.+.+. .+
T Consensus 1 ~t~~~T~~l~~-~G~si~eIA~~----R~L~~sTI~~HL~~~~~~g~~~~~~~~l-----~~e~~~~I~~~~~~~~~-~~ 69 (91)
T PF14493_consen 1 DTAQITYELFQ-KGLSIEEIAKI----RGLKESTIYGHLAELIESGEPLDIEELL-----SEEEIKQIEDAIEKLGS-EK 69 (91)
T ss_pred CHHHHHHHHHH-cCCCHHHHHHH----cCCCHHHHHHHHHHHHHhCCCCCHHHhC-----CHHHHHHHHHHHHHcCc-cc
Confidence 36789999999 99999999999 9999999999999999999999999997 89999999999999885 89
Q ss_pred hHHHHHhCCCCCCHHHHHHHHH
Q 044490 294 LKPIKNELPDDITYAHIKACLV 315 (430)
Q Consensus 294 LkpIke~l~~~isY~~Irl~la 315 (430)
|+|||++||+.+||++||+++|
T Consensus 70 lk~i~e~l~~~~sy~~iRl~~A 91 (91)
T PF14493_consen 70 LKPIKEALPGDYSYFEIRLVLA 91 (91)
T ss_pred HHHHHHHCCCCCCHHHHHHHhC
Confidence 9999999999999999999985
No 6
>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]
Probab=99.81 E-value=5.5e-20 Score=195.30 Aligned_cols=150 Identities=25% Similarity=0.366 Sum_probs=130.8
Q ss_pred ChhhhhhcccccCcccCCCCCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhcCCCCCCCCCeeeecccccc
Q 044490 1 SKKVVDAQFDKLLLHGLGKDHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLGSARPDHQPPLLLTFNGEMV 80 (430)
Q Consensus 1 ~kkI~~~~~d~l~~fG~Gk~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~g~~kv~~~~l~l~~~~~~~ 80 (430)
++||..++|+.+++||+|++.+..+|..++++|+..|||.+. .+. +.++++++++.+|+|+.++. +...
T Consensus 439 ~~~~~~~~~~~l~~~G~~k~~~~~~~~~~~~~l~~~~~~~~~-~~~-~~l~l~~~~~~vl~ge~~~~-----l~~~---- 507 (590)
T COG0514 439 NLKIRLLGHEKLSTYGIGKDLSKKTWGSLIRQLIALGLLRQS-LGT-PGLKLTEKARNVLRGELSVE-----LAVP---- 507 (590)
T ss_pred chhhhhcccccccccCCCcccCccchhhhHHHHHhcCceeec-CCc-ccccccHhhhHhhccceeee-----eccc----
Confidence 578999999999999999999999999999999999999998 444 89999999999999997642 2210
Q ss_pred cchhhhhcccCcCCCCccccccccCCChHHHHHHHHHHHHHHHHHHHhCCCCeeecchHHHHHHHHhCCCCHHHHhccCC
Q 044490 81 DAEEHETISSNVGDLKSSATLENEGFSEADMQLYHMLLEERKKLARVTGTAPYALCGDQTIKKIALARPSTKARLANIDG 160 (430)
Q Consensus 81 ~~~~~~s~~~~~~~~~pk~~~~~~~~~e~~~~L~~~L~~~R~~lA~e~~vppy~Ifsd~tL~emA~~~P~T~~eL~~I~G 160 (430)
+.... . . ..+..||++|+.||.++|+++++|||+||+|.||.+||+.+|.+..+|.+|.|
T Consensus 508 -~~~~~----~------------~---~~~~~lf~~lr~~r~~~a~~~~vp~~vif~d~tl~~ma~~~p~~~~~~~~i~g 567 (590)
T COG0514 508 -RLRAL----S------------I---GEDRDLFERLRALRKEIADEENVPPYVVFSDATLKEMAEKQPQSADELLSING 567 (590)
T ss_pred -ccccc----c------------c---cccHHHHHHHHHHHHHhhhhhcCCceEEecchHHHHHHHHcCCCHHHHHHhcC
Confidence 00000 0 0 01567999999999999999999999999999999999999999999999999
Q ss_pred CCHHHHHHHHHHHHHHHHHHH
Q 044490 161 VNQHLVITHGDHLLQTIRHLS 181 (430)
Q Consensus 161 vg~~k~~kyG~~fL~~I~~~~ 181 (430)
||..|+.+||..|+++|+++.
T Consensus 568 vg~~k~~~yg~~fl~~i~~~~ 588 (590)
T COG0514 568 VGEAKLERYGQAFLAVIQAHA 588 (590)
T ss_pred CcccchhhccHHHHHHHHHhc
Confidence 999999999999999999875
No 7
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=99.59 E-value=1.8e-15 Score=117.88 Aligned_cols=68 Identities=31% Similarity=0.486 Sum_probs=62.0
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCeeecchHHHHHHHHhCCCCHHHHhccCCCCHHHHHHHHHHHHHHH
Q 044490 110 DMQLYHMLLEERKKLARVTGTAPYALCGDQTIKKIALARPSTKARLANIDGVNQHLVITHGDHLLQTI 177 (430)
Q Consensus 110 ~~~L~~~L~~~R~~lA~e~~vppy~Ifsd~tL~emA~~~P~T~~eL~~I~Gvg~~k~~kyG~~fL~~I 177 (430)
+.++|++|.+||.++|++.|+|||+||+|.+|.+||..+|.|.++|.+|+||+..++++||..|+++|
T Consensus 1 q~~~~~~L~~~R~~~A~~~~~~~~~Il~~~~L~~ia~~~P~s~~~L~~i~g~~~~~~~~~g~~il~~I 68 (68)
T PF00570_consen 1 QLALLKALKEWREELAREEDVPPYRILSDEALLEIAKRLPTSIEELLQIPGMGKRKVRKYGDEILEII 68 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHHTS-HHHHS-HHHHHHHHHH--SSHHHHHTSTTCGHHHHHHCHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHcCcCcccccCHHHHHHHHHhCCCCHHHHHHccCCCHHHHHHHHHHHHhhC
Confidence 46899999999999999999999999999999999999999999999999999999999999999986
No 8
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=99.53 E-value=8.4e-14 Score=111.89 Aligned_cols=77 Identities=30% Similarity=0.425 Sum_probs=73.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCCCeeecchHHHHHHHHhCCCCHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHhhc
Q 044490 109 ADMQLYHMLLEERKKLARVTGTAPYALCGDQTIKKIALARPSTKARLANIDGVNQHLVITHGDHLLQTIRHLSQKLN 185 (430)
Q Consensus 109 ~~~~L~~~L~~~R~~lA~e~~vppy~Ifsd~tL~emA~~~P~T~~eL~~I~Gvg~~k~~kyG~~fL~~I~~~~~e~~ 185 (430)
.+..+|+.|..||.++|++.++||++||+|.+|.+||..+|.|..+|.+|.|++..++++||..|+++|+.+++..+
T Consensus 3 ~~~~~~~~L~~wR~~~A~~~~~~~~~I~~~~~L~~ia~~~P~~~~~L~~i~g~~~~~~~~~g~~~~~~i~~~~~~~~ 79 (81)
T smart00341 3 RQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRYGKDLLAVIQEASDSPS 79 (81)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHhccc
Confidence 36789999999999999999999999999999999999999999999999999999999999999999999877543
No 9
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=99.27 E-value=6.7e-12 Score=106.07 Aligned_cols=65 Identities=35% Similarity=0.563 Sum_probs=57.3
Q ss_pred ChhhhhhcccccCcccCCCCCCHHHHHHHHHHHHHcCCceeeecC--ccceEEeCcchHhhhcCCCCC
Q 044490 1 SKKVVDAQFDKLLLHGLGKDHSSNWWKTLAYQLISYGYLTETIKD--VYRTVSVSQQGKQYLGSARPD 66 (430)
Q Consensus 1 ~kkI~~~~~d~l~~fG~Gk~ls~~~wk~li~qLi~~GyL~e~~~~--~y~~l~LT~kg~~~L~g~~kv 66 (430)
|++|.+.+|+++++||+|+++++++|++++++|+.+|||.+. .+ .|++|++|++|+++|+|..++
T Consensus 34 ~~~i~~~~~~~l~~yG~gk~~~~~~~~~li~~Li~~g~L~~~-~~~~~~~~l~~~~~~~~~l~g~~~v 100 (106)
T PF09382_consen 34 SKKIREKGHDQLPTYGIGKDMSKDDWERLIRQLILEGYLSED-NGGFAYPYLKLTPKGKELLNGKQKV 100 (106)
T ss_dssp -CCCHHTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEE-ECCCCTEEEEE-GGGHHHHCTTS--
T ss_pred chhhhhcCCCcCcccCCcccCCHHHHHHHHHHHHHcCCceec-CCcccccEEEECHHHHHHHCCCceE
Confidence 578999999999999999999999999999999999999888 67 889999999999999998764
No 10
>PRK10829 ribonuclease D; Provisional
Probab=98.46 E-value=6.7e-07 Score=92.01 Aligned_cols=76 Identities=17% Similarity=0.256 Sum_probs=71.3
Q ss_pred CChHHHHHHHHHHHHHHHHHHHhCCCCeeecchHHHHHHHHhCCCCHHHHhccCCCCHHHHHHHHHHHHHHHHHHHH
Q 044490 106 FSEADMQLYHMLLEERKKLARVTGTAPYALCGDQTIKKIALARPSTKARLANIDGVNQHLVITHGDHLLQTIRHLSQ 182 (430)
Q Consensus 106 ~~e~~~~L~~~L~~~R~~lA~e~~vppy~Ifsd~tL~emA~~~P~T~~eL~~I~Gvg~~k~~kyG~~fL~~I~~~~~ 182 (430)
+...+..++++|..||.++|++.|+||.+|++|.+|.+||+..|.|..+|.++ |+....+++||..++++|....+
T Consensus 209 L~~~~lavl~~L~~WRe~~Ar~~d~p~~~Vl~d~~L~~lA~~~P~~~~~L~~~-~~~~~~~r~~g~~ll~~i~~a~~ 284 (373)
T PRK10829 209 LRTRQLACLQLLADWRLRKARERDLAVNFVVREEHLWQVARYMPGSLGELDSL-GLSGSEIRFHGKTLLALVAKAQA 284 (373)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhCCCcceecChHHHHHHHHhCCCCHHHHHhc-cCChHhHHhhHHHHHHHHHHHhc
Confidence 45667899999999999999999999999999999999999999999999999 99999999999999999998744
No 11
>TIGR01388 rnd ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown.
Probab=98.44 E-value=8.3e-07 Score=91.29 Aligned_cols=77 Identities=18% Similarity=0.270 Sum_probs=72.0
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHhCCCCeeecchHHHHHHHHhCCCCHHHHhccCCCCHHHHHHHHHHHHHHHHHHHH
Q 044490 105 GFSEADMQLYHMLLEERKKLARVTGTAPYALCGDQTIKKIALARPSTKARLANIDGVNQHLVITHGDHLLQTIRHLSQ 182 (430)
Q Consensus 105 ~~~e~~~~L~~~L~~~R~~lA~e~~vppy~Ifsd~tL~emA~~~P~T~~eL~~I~Gvg~~k~~kyG~~fL~~I~~~~~ 182 (430)
.++..+..++++|..||.++|++.|+||.+|++|..|.+||+..|.|..+|.++ |+....+++||..++++|....+
T Consensus 204 ~l~~~~l~~l~~L~~wRe~~A~~~d~p~~~il~d~~l~~lA~~~P~~~~~l~~~-~~~~~~~r~~~~~l~~~i~~a~~ 280 (367)
T TIGR01388 204 QLRPQQLAVLQALAAWREREARERDLPRNFVLKEEALWELARQAPGNLTELASL-GPKGSEIRKHGDTLLALVKTALA 280 (367)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHcCCCcceeeCHHHHHHHHHhCCCCHHHHHhc-cCChHHHHhhHHHHHHHHHHHhh
Confidence 345667899999999999999999999999999999999999999999999999 99999999999999999998744
No 12
>PF11408 Helicase_Sgs1: Sgs1 RecQ helicase; InterPro: IPR022758 RecQ helicases unwind DNA in an ATP-dependent manner. Sgs1 has a HRDC (helicase and RNaseD C-terminal) domain which modulates the helicase function via auxiliary contacts to DNA []. The proteins matching this entry are restricted to fungi (Saccharomycetaceae). ; PDB: 1D8B_A.
Probab=98.11 E-value=8.1e-06 Score=65.74 Aligned_cols=73 Identities=19% Similarity=0.255 Sum_probs=55.6
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCeeecchHHHHHHHHhCCCCHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHh
Q 044490 110 DMQLYHMLLEERKKLARVTGTAPYALCGDQTIKKIALARPSTKARLANIDGVNQHLVITHGDHLLQTIRHLSQK 183 (430)
Q Consensus 110 ~~~L~~~L~~~R~~lA~e~~vppy~Ifsd~tL~emA~~~P~T~~eL~~I~Gvg~~k~~kyG~~fL~~I~~~~~e 183 (430)
....|++|++.|..++.+.|.|--..++|.+|++||...|.|..++.++.|+++...++| ..|-.+|....++
T Consensus 5 i~~aY~~Lr~~~~~~~~~~n~p~~~f~sd~~LKk~A~~LP~te~eF~~l~g~~~~~~~kF-kyFK~tl~~Lrre 77 (80)
T PF11408_consen 5 ITSAYEKLREISINLSNRMNPPNDNFMSDTILKKMATKLPTTEEEFSKLVGINEQQRKKF-KYFKDTLMRLRRE 77 (80)
T ss_dssp HHHHHHHHHHHHHHHHHSSSS--S-SS-HHHHHHHHHH---SHHHHGGGS---HHHHHHG-GGTHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhhccCCCccccCCHHHHHHHHHHCCCCHHHHHHhcCCcHHHHHHH-HHHHHHHHHHHHh
Confidence 467899999999999999999877788999999999999999999999999999987776 7787777766554
No 13
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=97.58 E-value=0.00023 Score=72.44 Aligned_cols=77 Identities=17% Similarity=0.186 Sum_probs=70.8
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHhCCCCeeecchHHHHHHHHhCCCCHHHHhccCCCCHHHHHHHHHHHHHHHHHHHH
Q 044490 105 GFSEADMQLYHMLLEERKKLARVTGTAPYALCGDQTIKKIALARPSTKARLANIDGVNQHLVITHGDHLLQTIRHLSQ 182 (430)
Q Consensus 105 ~~~e~~~~L~~~L~~~R~~lA~e~~vppy~Ifsd~tL~emA~~~P~T~~eL~~I~Gvg~~k~~kyG~~fL~~I~~~~~ 182 (430)
........+.++|..||.+.|+..++|+.+|+.|..|.++|...|.+..+|..+.+++. ..+++|..++.+|.+...
T Consensus 204 ~~~p~~la~l~~La~wRe~~Ar~rd~~~~~vl~de~i~~~a~~~P~~~~~l~~l~~~~~-~~~~~~~~l~~~~~~a~~ 280 (361)
T COG0349 204 SLDPRELAVLRELAAWREREARERDLARNFVLKDEALWELARYTPKNLKELDALGLIPK-ERRRHGKLLLALLANALA 280 (361)
T ss_pred cCChHHHHHHHHHHHHHHHHHHHhccccccccchhHHHHHHHhCCCCHHHHHhccCCcc-cchhhhHHHHHHHHHHHh
Confidence 34456789999999999999999999999999999999999999999999999999998 788899999999988755
No 14
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=95.40 E-value=0.07 Score=57.32 Aligned_cols=76 Identities=18% Similarity=0.244 Sum_probs=64.1
Q ss_pred CChHHHHHHHHHHHHHHHHHHHhCCCCeeecchHHHHHHHHhCCCCHHHHhc-cCCCCHHHHHHHHHHHHHHHHHHHH
Q 044490 106 FSEADMQLYHMLLEERKKLARVTGTAPYALCGDQTIKKIALARPSTKARLAN-IDGVNQHLVITHGDHLLQTIRHLSQ 182 (430)
Q Consensus 106 ~~e~~~~L~~~L~~~R~~lA~e~~vppy~Ifsd~tL~emA~~~P~T~~eL~~-I~Gvg~~k~~kyG~~fL~~I~~~~~ 182 (430)
+...+..+++.|.+||.-+|+..+-.+.+|++|.+|..||+.+|.++..|.. +.++.+.--++ -..|+.+|++..+
T Consensus 402 ln~~q~~~l~~L~~wRd~iARaeDES~~yVlpN~~ll~l~e~~P~~v~gl~~~ln~~~p~vkq~-~~~~~~ii~~a~~ 478 (687)
T KOG2206|consen 402 LNSSQLDVLRALLRWRDFIARAEDESVHYVLPNDQLLKLAEERPDTVDGLLGGLNRLSPLVKQN-VMDFLYIIRSAGR 478 (687)
T ss_pred cchhHHHHHHHHHHHHHHHHhhccCCCceecccHHHHHHHHHCCccHHHHHHhccCCCHHHHHH-HHHHHHHHHHHhh
Confidence 4456789999999999999999999999999999999999999999999875 56777764444 4678888877644
No 15
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=94.13 E-value=0.052 Score=40.64 Aligned_cols=43 Identities=26% Similarity=0.294 Sum_probs=36.3
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
.+|+...+.+.++. .|++..+||.. .++++.||..|+..+...
T Consensus 3 ~LT~~E~~vl~~l~-~G~~~~eIA~~----l~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLA-QGMSNKEIAEE----LGISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHH-TTS-HHHHHHH----HTSHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHH-hcCCcchhHHh----cCcchhhHHHHHHHHHHH
Confidence 36677778888888 99999999999 999999999999988764
No 16
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=93.97 E-value=0.079 Score=37.86 Aligned_cols=34 Identities=29% Similarity=0.389 Sum_probs=27.0
Q ss_pred hHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHH
Q 044490 215 AKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLL 253 (430)
Q Consensus 215 t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~ 253 (430)
......+|+. +|+|+.+||.. -+++.+||+.+|.
T Consensus 10 ~~~~i~~l~~-~G~si~~IA~~----~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 10 QIEEIKELYA-EGMSIAEIAKQ----FGVSRSTVYRYLN 43 (45)
T ss_dssp CHHHHHHHHH-TT--HHHHHHH----TTS-HHHHHHHHC
T ss_pred HHHHHHHHHH-CCCCHHHHHHH----HCcCHHHHHHHHh
Confidence 3567788888 99999999999 9999999998874
No 17
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=92.61 E-value=0.22 Score=35.83 Aligned_cols=41 Identities=32% Similarity=0.423 Sum_probs=34.0
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
+++.....+.++. .|+|..+||+. -+++.+||..|+..+..
T Consensus 4 l~~~e~~i~~~~~-~g~s~~eia~~----l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 4 LTPREREVLRLLA-EGLTNKEIAER----LGISEKTVKTHLSNIMR 44 (58)
T ss_pred CCHHHHHHHHHHH-cCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 4455556777776 99999999999 99999999999988744
No 18
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=92.36 E-value=0.21 Score=36.55 Aligned_cols=43 Identities=28% Similarity=0.257 Sum_probs=32.4
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..++.+.+..-+|+|..|||+. -+++.+||..|+..+.+
T Consensus 10 ~L~~~~r~i~~l~~~~g~s~~eIa~~----l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQGMSYAEIAEI----LGISESTVKRRLRRARK 52 (54)
T ss_dssp CS-HHHHHHHHHHHTS---HHHHHHH----CTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHCcCHHHHHHH----HCcCHHHHHHHHHHHHh
Confidence 46677778888866699999999999 99999999999988754
No 19
>PF13551 HTH_29: Winged helix-turn helix
Probab=92.04 E-value=1.2 Score=36.82 Aligned_cols=88 Identities=22% Similarity=0.246 Sum_probs=62.5
Q ss_pred HHHHHHhcCCC-HHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhh-------ccC-CCHHHHHHHHHHHHHhC
Q 044490 219 AWKMWHEDGLS-IQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCD-------EVG-LTDEIFSAIQEAISKVG 289 (430)
Q Consensus 219 T~~l~~~~G~s-i~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~-------~~~-l~~e~~~~I~~a~~~~g 289 (430)
...++. +|.+ +.+||.. -+++..||+.++..+-..|. +.+.+ .-. ++++....|.+.+.+..
T Consensus 4 ~l~l~~-~g~~~~~~ia~~----lg~s~~Tv~r~~~~~~~~G~----~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p 74 (112)
T PF13551_consen 4 ILLLLA-EGVSTIAEIARR----LGISRRTVYRWLKRYREGGI----EGLLPRKPRGGRPRKRLSEEQRAQLIELLRENP 74 (112)
T ss_pred HHHHHH-cCCCcHHHHHHH----HCcCHHHHHHHHHHHHcccH----HHHHhccccCCCCCCCCCHHHHHHHHHHHHHCC
Confidence 345666 9995 9999999 99999999999999998883 12222 112 68999999998888742
Q ss_pred C----CCChHHH-----HHhCCCCCCHHHHHHHHH
Q 044490 290 C----KDKLKPI-----KNELPDDITYAHIKACLV 315 (430)
Q Consensus 290 ~----~~~LkpI-----ke~l~~~isY~~Irl~la 315 (430)
. .-.+..| .+.++-.+++..|+-+|.
T Consensus 75 ~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 75 PEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 1 1123344 444577888888886654
No 20
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=91.12 E-value=0.17 Score=36.03 Aligned_cols=30 Identities=30% Similarity=0.264 Sum_probs=20.0
Q ss_pred HHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHH
Q 044490 220 WKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLL 253 (430)
Q Consensus 220 ~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~ 253 (430)
.+.+.++|+|+.+||.. -+.+.+||...|-
T Consensus 13 I~~l~~~G~s~~~IA~~----lg~s~sTV~relk 42 (44)
T PF13936_consen 13 IEALLEQGMSIREIAKR----LGRSRSTVSRELK 42 (44)
T ss_dssp HHHHHCS---HHHHHHH----TT--HHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHH----HCcCcHHHHHHHh
Confidence 33344599999999999 9999999998874
No 21
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=91.11 E-value=0.37 Score=34.76 Aligned_cols=38 Identities=24% Similarity=0.300 Sum_probs=31.7
Q ss_pred hHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 215 AKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 215 t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.....+.++. .|+|..+||+. -+++.+||..|+..+..
T Consensus 4 ~e~~i~~~~~-~~~s~~eia~~----l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 4 REREVLRLLA-EGKTNKEIADI----LGISEKTVKTHLRNIMR 41 (57)
T ss_pred HHHHHHHHHH-cCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 3445666776 99999999999 99999999999988654
No 22
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=90.82 E-value=0.32 Score=45.92 Aligned_cols=44 Identities=20% Similarity=0.242 Sum_probs=40.6
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
.+|+...+.+.|+. +|+|..|||++ -++++.||..|+..+..+=
T Consensus 137 ~LT~RE~eVL~lla-~G~snkeIA~~----L~iS~~TVk~h~~~I~~KL 180 (207)
T PRK15411 137 SLSRTESSMLRMWM-AGQGTIQISDQ----MNIKAKTVSSHKGNIKRKI 180 (207)
T ss_pred cCCHHHHHHHHHHH-cCCCHHHHHHH----cCCCHHHHHHHHHHHHHHh
Confidence 48899999999999 99999999999 9999999999999987754
No 23
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=90.79 E-value=0.23 Score=39.58 Aligned_cols=45 Identities=24% Similarity=0.138 Sum_probs=37.3
Q ss_pred CCchHHHHHHHHH-hcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 212 LTPAKYEAWKMWH-EDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 212 l~~t~~~T~~l~~-~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
+.+..+..|.|.+ .+|+|..|||++ -+++++||..|+......|-
T Consensus 16 l~~~~r~af~L~R~~eGlS~kEIAe~----LGIS~~TVk~~l~~~~~~~~ 61 (73)
T TIGR03879 16 VDSLAEAAAALAREEAGKTASEIAEE----LGRTEQTVRNHLKGETKAGG 61 (73)
T ss_pred CCHHHHHHHHHHHHHcCCCHHHHHHH----HCcCHHHHHHHHhcCcccch
Confidence 4455677888864 389999999999 99999999999998777774
No 24
>KOG0351 consensus ATP-dependent DNA helicase [Replication, recombination and repair]
Probab=90.60 E-value=0.032 Score=63.86 Aligned_cols=175 Identities=14% Similarity=0.082 Sum_probs=97.6
Q ss_pred hhhhhhc--ccccCcccCCCCCCHHHHHHHHHHHHHcCCceeee-cCccc---e-EEeCcchH--hhhcCCCCCCCCCee
Q 044490 2 KKVVDAQ--FDKLLLHGLGKDHSSNWWKTLAYQLISYGYLTETI-KDVYR---T-VSVSQQGK--QYLGSARPDHQPPLL 72 (430)
Q Consensus 2 kkI~~~~--~d~l~~fG~Gk~ls~~~wk~li~qLi~~GyL~e~~-~~~y~---~-l~LT~kg~--~~L~g~~kv~~~~l~ 72 (430)
+++..++ ++.++.||.|+.++..||++++++|+.+||+++.. .+.+. . ..+...+. .++.+.....
T Consensus 707 ~~~~~~~~~~~~~~~~g~~~~~~~~~~~r~~~~Lv~~~~~~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~----- 781 (941)
T KOG0351|consen 707 QKAAKAEPLHDGLPAHGKGKGQSTSDAERLLRKLVAEGFIEEYDSANSSYQLKSYKNLGNLALRCKVLTLRFSLK----- 781 (941)
T ss_pred HHHHHhcCccccccccCcccccccchHHHHHHHHHhhhhHHHhhhhhhhhhHhHhhhhcccccchhhhhcccccc-----
Confidence 3455555 48999999999999999999999999999999973 11111 1 12222222 4555544321
Q ss_pred eecccccccchhhhhcccCcCC-CCccccccccCCChHHHHHHHHHHHHHHHHHHHhCCCCeeecc----------hHHH
Q 044490 73 LTFNGEMVDAEEHETISSNVGD-LKSSATLENEGFSEADMQLYHMLLEERKKLARVTGTAPYALCG----------DQTI 141 (430)
Q Consensus 73 l~~~~~~~~~~~~~s~~~~~~~-~~pk~~~~~~~~~e~~~~L~~~L~~~R~~lA~e~~vppy~Ifs----------d~tL 141 (430)
+.+................... ...................|-.+.+.+...+.+.......... +.+|
T Consensus 782 ~~~~~~a~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 861 (941)
T KOG0351|consen 782 VVGEESASETKVAVKSLSGTSASCSGSISPQSRSSSSTAEVSLGELTEICLRPGSRSSTCVKSFSNANGLLEYGLERMTL 861 (941)
T ss_pred ccccccchhhhcccccccchhhhhccccCccccccccceeeecccchhhhhccccccchhHHhhhccchhhhccccccch
Confidence 1111100000000000000000 0000000000000112334555555555555555544333333 5667
Q ss_pred HHHHHh-CCCCHHHHhccCCCCHHHHHHHHHHHHHHHHHHH
Q 044490 142 KKIALA-RPSTKARLANIDGVNQHLVITHGDHLLQTIRHLS 181 (430)
Q Consensus 142 ~emA~~-~P~T~~eL~~I~Gvg~~k~~kyG~~fL~~I~~~~ 181 (430)
..++.. .|.+...+..|+++...++..||..++.+.+.+.
T Consensus 862 ~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~i~~~~~ 902 (941)
T KOG0351|consen 862 EHIRESKLSDGVRGVVRIGIVTRDKDKFGGRAIRRIFQVIY 902 (941)
T ss_pred hhhcccccCCCceecccCCCcccccccccchhheeechhcc
Confidence 777776 8999999999999999999999999988877764
No 25
>PRK00118 putative DNA-binding protein; Validated
Probab=90.55 E-value=0.52 Score=40.08 Aligned_cols=43 Identities=21% Similarity=0.212 Sum_probs=35.1
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
+++...+.+.++..+|+|+.|||+. -|++++||..++..+...
T Consensus 18 L~ekqRevl~L~y~eg~S~~EIAe~----lGIS~~TV~r~L~RArkk 60 (104)
T PRK00118 18 LTEKQRNYMELYYLDDYSLGEIAEE----FNVSRQAVYDNIKRTEKL 60 (104)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHH----HCcCHHHHHHHHHHHHHH
Confidence 4455567777766699999999999 999999999999876543
No 26
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=90.28 E-value=0.37 Score=36.58 Aligned_cols=34 Identities=24% Similarity=0.266 Sum_probs=29.7
Q ss_pred HHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHH
Q 044490 217 YEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEA 255 (430)
Q Consensus 217 ~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~ 255 (430)
.....||. +|+++.+||++ -+++.+||+++....
T Consensus 4 ~~A~~LY~-~G~~~~eIA~~----Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 4 EQARSLYL-QGWSIKEIAEE----LGVPRSTVYSWKDRY 37 (58)
T ss_pred HHHHHHHH-cCCCHHHHHHH----HCCChHHHHHHHHhh
Confidence 45667888 99999999999 999999999987765
No 27
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=90.14 E-value=0.48 Score=35.37 Aligned_cols=43 Identities=30% Similarity=0.285 Sum_probs=37.2
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
+++...+.+.++. +|++..|||.. -+++..||..|+..+...-
T Consensus 5 Lt~rE~~v~~l~~-~G~s~~eia~~----l~is~~tV~~h~~~i~~Kl 47 (65)
T COG2771 5 LTPREREILRLVA-QGKSNKEIARI----LGISEETVKTHLRNIYRKL 47 (65)
T ss_pred CCHHHHHHHHHHH-CCCCHHHHHHH----HCCCHHHHHHHHHHHHHHH
Confidence 5666677777887 99999999999 9999999999999996655
No 28
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=90.07 E-value=0.36 Score=44.99 Aligned_cols=44 Identities=18% Similarity=0.288 Sum_probs=40.2
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
.+|+...+.+.++. +|+|..|||+. .+++..||..|+..+...=
T Consensus 150 ~Lt~rE~evl~~~~-~G~s~~eIA~~----l~iS~~TV~~h~~~i~~Kl 193 (216)
T PRK10840 150 RLSPKESEVLRLFA-EGFLVTEIAKK----LNRSIKTISSQKKSAMMKL 193 (216)
T ss_pred cCCHHHHHHHHHHH-CCCCHHHHHHH----HCCCHHHHHHHHHHHHHHc
Confidence 47888889999998 99999999999 9999999999999987754
No 29
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=89.92 E-value=0.47 Score=44.16 Aligned_cols=45 Identities=9% Similarity=0.121 Sum_probs=40.9
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
..+|+...+.+.+.. +|+|..|||+. -+++.+||..|+..+...-
T Consensus 132 ~~LSpRErEVLrLLA-qGkTnKEIAe~----L~IS~rTVkth~srImkKL 176 (198)
T PRK15201 132 RHFSVTERHLLKLIA-SGYHLSETAAL----LSLSEEQTKSLRRSIMRKL 176 (198)
T ss_pred CCCCHHHHHHHHHHH-CCCCHHHHHHH----hCCCHHHHHHHHHHHHHHh
Confidence 347888899999998 99999999999 9999999999999987765
No 30
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=88.75 E-value=0.51 Score=44.80 Aligned_cols=44 Identities=27% Similarity=0.348 Sum_probs=39.9
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
.+|+...+.+.|+. +|+|..|||.. -+++++||..|+..+..+=
T Consensus 148 ~LT~RE~eVL~lla-~G~snkeIA~~----L~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 148 LLTPRELEVLRLLA-EGLSNKEIAEE----LNLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCCHHHHHHHHHHH-CCCCHHHHHHH----HCCCHhHHHHHHHHHHHHc
Confidence 47888889999998 99999999999 9999999999999987654
No 31
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=88.55 E-value=0.57 Score=44.44 Aligned_cols=44 Identities=20% Similarity=0.251 Sum_probs=40.7
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
.+|+...+.+.++. +|+|..|||+. .++++.||..|+..+.++=
T Consensus 134 ~LT~RE~eVL~ll~-~G~snkeIA~~----L~iS~~TV~~h~~~I~~KL 177 (207)
T PRK11475 134 MLSPTEREILRFMS-RGYSMPQIAEQ----LERNIKTIRAHKFNVMSKL 177 (207)
T ss_pred CCCHHHHHHHHHHH-CCCCHHHHHHH----HCCCHHHHHHHHHHHHHHc
Confidence 58889999999999 99999999999 9999999999999997754
No 32
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=88.50 E-value=0.52 Score=30.94 Aligned_cols=23 Identities=13% Similarity=0.202 Sum_probs=19.0
Q ss_pred HhCCCCHHHHhccCCCCHHHHHH
Q 044490 146 LARPSTKARLANIDGVNQHLVIT 168 (430)
Q Consensus 146 ~~~P~T~~eL~~I~Gvg~~k~~k 168 (430)
...|.|.++|.+|+|||+..++.
T Consensus 4 g~~pas~eeL~~lpGIG~~tA~~ 26 (30)
T PF00633_consen 4 GLIPASIEELMKLPGIGPKTANA 26 (30)
T ss_dssp HHHTSSHHHHHTSTT-SHHHHHH
T ss_pred CcCCCCHHHHHhCCCcCHHHHHH
Confidence 45799999999999999997754
No 33
>PRK04217 hypothetical protein; Provisional
Probab=88.45 E-value=0.71 Score=39.68 Aligned_cols=44 Identities=20% Similarity=0.218 Sum_probs=37.0
Q ss_pred ccCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHH
Q 044490 209 RTKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAV 256 (430)
Q Consensus 209 ~~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i 256 (430)
...+++...+.+.++..+|+|+.|||+. -+++.+||+.++..+.
T Consensus 40 ~~~Lt~eereai~l~~~eGlS~~EIAk~----LGIS~sTV~r~L~RAr 83 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGLTQEEAGKR----MGVSRGTVWRALTSAR 83 (110)
T ss_pred cccCCHHHHHHHHHHHHcCCCHHHHHHH----HCcCHHHHHHHHHHHH
Confidence 4456777778888777699999999999 9999999999988753
No 34
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=88.42 E-value=0.73 Score=32.86 Aligned_cols=41 Identities=17% Similarity=0.255 Sum_probs=31.3
Q ss_pred HHHHHHHH-HhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 216 KYEAWKMW-HEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 216 ~~~T~~l~-~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
..+-+..+ .+.+.|..+||+. -+++.+||..||-++...|.
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~----~~is~~tv~~~l~~L~~~g~ 46 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEK----LGISRSTVNRYLKKLEEKGL 46 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHH----HTS-HHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHcCCCCHHHHHHH----hCCCHHHHHHHHHHHHHCcC
Confidence 33444444 4357999999999 99999999999999999984
No 35
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=88.06 E-value=0.52 Score=35.58 Aligned_cols=43 Identities=16% Similarity=0.295 Sum_probs=36.8
Q ss_pred chHHHHHHHH-HhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 214 PAKYEAWKMW-HEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 214 ~t~~~T~~l~-~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
++...-+.++ ...++|+.+||+. -+++.+|++-||..+...|.
T Consensus 10 p~R~~Il~~L~~~~~~t~~ela~~----l~~~~~t~s~hL~~L~~aGl 53 (61)
T PF12840_consen 10 PTRLRILRLLASNGPMTVSELAEE----LGISQSTVSYHLKKLEEAGL 53 (61)
T ss_dssp HHHHHHHHHHHHCSTBEHHHHHHH----HTS-HHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHH----HCCCHHHHHHHHHHHHHCCC
Confidence 4566777777 6689999999999 99999999999999999995
No 36
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=88.02 E-value=0.72 Score=44.23 Aligned_cols=46 Identities=17% Similarity=0.177 Sum_probs=41.2
Q ss_pred ccCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 209 RTKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 209 ~~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
...+|+...+.+.|+. +|+|-.|||+. .+++++||..|+..+...=
T Consensus 141 ~~~LS~RE~eVL~Lia-~G~SnkEIA~~----L~IS~~TVk~hvs~I~~KL 186 (217)
T PRK13719 141 KNKVTKYQNDVFILYS-FGFSHEYIAQL----LNITVGSSKNKISEILKFF 186 (217)
T ss_pred cCCCCHHHHHHHHHHH-CCCCHHHHHHH----hCCCHHHHHHHHHHHHHHh
Confidence 3457888899999998 99999999999 9999999999999987654
No 37
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=87.50 E-value=1 Score=35.92 Aligned_cols=39 Identities=15% Similarity=0.253 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhcC
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLGS 62 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~g 62 (430)
+++...+..++..|+..|++... ...+.+|++|.++|..
T Consensus 30 ~L~~~~~~~yL~~L~~~gLI~~~----~~~Y~lTekG~~~l~~ 68 (77)
T PF14947_consen 30 NLNYSTLKKYLKELEEKGLIKKK----DGKYRLTEKGKEFLEE 68 (77)
T ss_dssp T--HHHHHHHHHHHHHTTSEEEE----TTEEEE-HHHHHHHHH
T ss_pred CcCHHHHHHHHHHHHHCcCeeCC----CCEEEECccHHHHHHH
Confidence 58999999999999999999653 2678999999999874
No 38
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=86.98 E-value=0.53 Score=33.71 Aligned_cols=42 Identities=19% Similarity=0.292 Sum_probs=34.2
Q ss_pred hHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 215 AKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 215 t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
+..+...++.+..+++.|||+. -+++.+||..||..+...|.
T Consensus 3 ~R~~Il~~L~~~~~~~~el~~~----l~~s~~~vs~hL~~L~~~gl 44 (47)
T PF01022_consen 3 TRLRILKLLSEGPLTVSELAEE----LGLSQSTVSHHLKKLREAGL 44 (47)
T ss_dssp HHHHHHHHHTTSSEEHHHHHHH----HTS-HHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHhCCCchhhHHHh----ccccchHHHHHHHHHHHCcC
Confidence 4445555565588999999999 99999999999999999984
No 39
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=86.82 E-value=0.69 Score=39.14 Aligned_cols=43 Identities=30% Similarity=0.371 Sum_probs=33.7
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
+|+...+.++++..+.+|+.|||+. -+++.+.|++++-.+...
T Consensus 18 LT~kQ~~~l~lyy~eDlSlsEIAe~----~~iSRqaV~d~ikr~~~~ 60 (101)
T PF04297_consen 18 LTEKQREILELYYEEDLSLSEIAEE----LGISRQAVYDSIKRAEKK 60 (101)
T ss_dssp S-HHHHHHHHHHCTS---HHHHHHH----CTS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHccCCCHHHHHHH----HCCCHHHHHHHHHHHHHH
Confidence 5777888999998899999999999 999999999999987643
No 40
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=86.34 E-value=0.38 Score=34.53 Aligned_cols=39 Identities=23% Similarity=0.378 Sum_probs=24.6
Q ss_pred HHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 217 YEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 217 ~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
...+.++. +|+|..+||+. -+++.+||+..+-.+...|.
T Consensus 8 ~~ii~l~~-~G~s~~~ia~~----lgvs~~Tv~~w~kr~~~~G~ 46 (50)
T PF13384_consen 8 AQIIRLLR-EGWSIREIAKR----LGVSRSTVYRWIKRYREEGL 46 (50)
T ss_dssp --HHHHHH-HT--HHHHHHH----HTS-HHHHHHHHT-------
T ss_pred HHHHHHHH-CCCCHHHHHHH----HCcCHHHHHHHHHHcccccc
Confidence 35667777 79999999999 99999999999999888774
No 41
>PRK09483 response regulator; Provisional
Probab=86.20 E-value=0.97 Score=41.30 Aligned_cols=45 Identities=18% Similarity=0.236 Sum_probs=40.1
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
..+|+...+.+.++. +|++..+||+. .+++.+||..|+..+..+=
T Consensus 147 ~~Lt~rE~~vl~~~~-~G~~~~~Ia~~----l~is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 147 ASLSERELQIMLMIT-KGQKVNEISEQ----LNLSPKTVNSYRYRMFSKL 191 (217)
T ss_pred cccCHHHHHHHHHHH-CCCCHHHHHHH----hCCCHHHHHHHHHHHHHHc
Confidence 347888889999988 99999999998 9999999999999987764
No 42
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=85.56 E-value=1.2 Score=32.04 Aligned_cols=42 Identities=29% Similarity=0.379 Sum_probs=32.2
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
+++.....+.+..-+|+|..|||+. -|++.+||..+...++.
T Consensus 5 L~~~er~vi~~~y~~~~t~~eIa~~----lg~s~~~V~~~~~~al~ 46 (50)
T PF04545_consen 5 LPPREREVIRLRYFEGLTLEEIAER----LGISRSTVRRILKRALK 46 (50)
T ss_dssp S-HHHHHHHHHHHTST-SHHHHHHH----HTSCHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhcCCCCHHHHHHH----HCCcHHHHHHHHHHHHH
Confidence 4555555666555599999999999 99999999998888764
No 43
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=85.07 E-value=1.2 Score=39.54 Aligned_cols=42 Identities=24% Similarity=0.049 Sum_probs=34.6
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
+++..+..+.|..-+|+|..|||++ -|++++||..||..+..
T Consensus 107 Lp~~~r~v~~l~~~~g~s~~EIA~~----lgis~~tV~~~l~Rar~ 148 (160)
T PRK09642 107 LPENYRDVVLAHYLEEKSYQEIALQ----EKIEVKTVEMKLYRARK 148 (160)
T ss_pred CCHHHHHHHHHHHHhCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 4455667777755599999999999 99999999999988754
No 44
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=85.07 E-value=1.6 Score=33.80 Aligned_cols=30 Identities=27% Similarity=0.338 Sum_probs=24.7
Q ss_pred HHHHhcCCCCCCCCC-hhhHHHHHHHHHHcCCCcch
Q 044490 230 IQKIANYPGRSAPIK-EQTVVDYLLEAVSEGFDINW 264 (430)
Q Consensus 230 i~eIA~~~~r~R~L~-~sTI~~HL~~~i~~G~~l~~ 264 (430)
+.|||+. -+++ .+||..||..+...|+ |..
T Consensus 28 ~rEIa~~----~g~~S~~tv~~~L~~Le~kG~-I~r 58 (65)
T PF01726_consen 28 VREIAEA----LGLKSTSTVQRHLKALERKGY-IRR 58 (65)
T ss_dssp HHHHHHH----HTSSSHHHHHHHHHHHHHTTS-EEE
T ss_pred HHHHHHH----hCCCChHHHHHHHHHHHHCcC-ccC
Confidence 3468887 8887 9999999999999996 543
No 45
>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=83.79 E-value=1.9 Score=30.04 Aligned_cols=42 Identities=29% Similarity=0.307 Sum_probs=32.6
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
+++.....+.++..+|++..+||.. -+++.+||..++..+..
T Consensus 11 l~~~~~~~~~~~~~~~~~~~~ia~~----~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 11 LPEREREVILLRFGEGLSYEEIAEI----LGISRSTVRQRLHRALK 52 (55)
T ss_pred CCHHHHHHHHHHHhcCCCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 3444455555554499999999999 99999999999887643
No 46
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=83.55 E-value=1.6 Score=39.55 Aligned_cols=42 Identities=21% Similarity=0.226 Sum_probs=36.4
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
+++..++.+.|..-+|+|..|||++ -+++++||..+|..+..
T Consensus 135 Lp~~~r~v~~l~~~~g~s~~EIA~~----lgis~~tVk~~l~Rar~ 176 (183)
T TIGR02999 135 VDPRQAEVVELRFFAGLTVEEIAEL----LGVSVRTVERDWRFARA 176 (183)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHH----hCCCHHHHHHHHHHHHH
Confidence 5667778888875599999999999 99999999999988754
No 47
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=83.51 E-value=1.5 Score=42.52 Aligned_cols=44 Identities=20% Similarity=0.073 Sum_probs=39.6
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
.+|+...+.+.+.. +|+|-.|||.+ .++++.||..|+..+.++=
T Consensus 179 ~LT~rE~evl~~~a-~G~t~~eIa~~----l~is~~TV~~h~~~~~~KL 222 (240)
T PRK10188 179 NFSKREKEILKWTA-EGKTSAEIAMI----LSISENTVNFHQKNMQKKF 222 (240)
T ss_pred CCCHHHHHHHHHHH-cCCCHHHHHHH----hCCCHHHHHHHHHHHHHHh
Confidence 47888888888887 99999999999 9999999999999987654
No 48
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=82.99 E-value=1.7 Score=39.03 Aligned_cols=43 Identities=19% Similarity=0.132 Sum_probs=36.5
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..++.+.|..-+|+|.+|||++ -+++++||..+|..+..
T Consensus 112 ~L~~~~r~v~~l~~~~g~s~~eIA~~----lgis~~tV~~~l~Rar~ 154 (164)
T PRK12547 112 LLSADQREAIILIGASGFSYEDAAAI----CGCAVGTIKSRVSRARN 154 (164)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----hCCCHHHHHHHHHHHHH
Confidence 45667778888864499999999999 99999999999988754
No 49
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=82.90 E-value=1.6 Score=38.59 Aligned_cols=43 Identities=19% Similarity=0.139 Sum_probs=36.0
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.|++..+..+.|..-+|+|..|||+. -|++.+||..|+..+..
T Consensus 106 ~Lp~~~r~v~~l~~~~g~s~~EIA~~----lgis~~tV~~~l~ra~~ 148 (161)
T PRK09047 106 KLPARQREAFLLRYWEDMDVAETAAA----MGCSEGSVKTHCSRATH 148 (161)
T ss_pred hCCHHHHHHHHHHHHhcCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 45667778888854499999999999 99999999999988754
No 50
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=82.22 E-value=2 Score=38.76 Aligned_cols=43 Identities=21% Similarity=0.305 Sum_probs=36.4
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..++.+.|..-+|+|.+|||++ -+++++||..||..+..
T Consensus 118 ~L~~~~r~v~~L~~~eg~s~~EIA~~----l~is~~tV~~~l~ra~~ 160 (168)
T PRK12525 118 GLSGKARAAFLMSQLEGLTYVEIGER----LGVSLSRIHQYMVEAFK 160 (168)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 45667778888854499999999999 99999999999987754
No 51
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=82.00 E-value=2 Score=39.26 Aligned_cols=44 Identities=30% Similarity=0.331 Sum_probs=36.5
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
.|++..+..+.|..-+|+|.+|||++ -|++++||..|+..+...
T Consensus 127 ~Lp~~~R~v~~L~~~~g~s~~EIA~~----lgis~~tVk~~l~rAl~~ 170 (178)
T PRK12529 127 TLRPRVKQAFLMATLDGMKQKDIAQA----LDIALPTVKKYIHQAYVT 170 (178)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----HCCCHHHHHHHHHHHHHH
Confidence 45566777888854499999999999 999999999999877653
No 52
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=81.97 E-value=1.8 Score=41.28 Aligned_cols=44 Identities=27% Similarity=0.130 Sum_probs=40.1
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
.+++...+.+.++. +|+|-.|||+. -++++.||..|+..+...-
T Consensus 155 ~Lt~rE~~Vl~l~~-~G~s~~eIA~~----L~iS~~TVk~~~~~i~~Kl 198 (216)
T PRK10100 155 LLTHREKEILNKLR-IGASNNEIARS----LFISENTVKTHLYNLFKKI 198 (216)
T ss_pred CCCHHHHHHHHHHH-cCCCHHHHHHH----hCCCHHHHHHHHHHHHHHh
Confidence 47888899999998 89999999999 9999999999999997765
No 53
>PF13518 HTH_28: Helix-turn-helix domain
Probab=81.70 E-value=2.7 Score=30.01 Aligned_cols=38 Identities=21% Similarity=0.320 Sum_probs=33.1
Q ss_pred HHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 218 EAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 218 ~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
....++. +|.|+.+||.. -+++.+||...+..+-..|.
T Consensus 4 ~iv~~~~-~g~s~~~~a~~----~gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 4 QIVELYL-EGESVREIARE----FGISRSTVYRWIKRYREGGI 41 (52)
T ss_pred HHHHHHH-cCCCHHHHHHH----HCCCHhHHHHHHHHHHhcCH
Confidence 4456677 89999999999 99999999999999988884
No 54
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=81.54 E-value=2 Score=38.26 Aligned_cols=45 Identities=24% Similarity=0.225 Sum_probs=39.8
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
.+++...+-+.++. +|++..+||+. -+++..||..|+..+.+.-.
T Consensus 149 ~lt~~e~~vl~l~~-~g~~~~~Ia~~----l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 149 LLTPRERQILKLIT-EGYTNRDIAEQ----LSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCCHHHHHHHHHHH-CCCCHHHHHHH----hCCCHHHHHHHHHHHHHHhC
Confidence 46777788888988 99999999998 99999999999999988764
No 55
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=81.54 E-value=1.8 Score=38.27 Aligned_cols=43 Identities=19% Similarity=0.213 Sum_probs=35.6
Q ss_pred cCCCchHHHHHHH-HHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKM-WHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l-~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++.....+.| +. .|+|..|||+. -+++.+||..|+..+-.
T Consensus 110 ~~L~~~~r~v~~l~~~-~g~~~~eIA~~----l~is~~tv~~~l~Rar~ 153 (159)
T TIGR02989 110 EKLPERQRELLQLRYQ-RGVSLTALAEQ----LGRTVNAVYKALSRLRV 153 (159)
T ss_pred HHCCHHHHHHHHHHHh-cCCCHHHHHHH----hCCCHHHHHHHHHHHHH
Confidence 3466667778888 55 99999999999 99999999999887643
No 56
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=81.53 E-value=2.1 Score=38.14 Aligned_cols=43 Identities=33% Similarity=0.320 Sum_probs=36.0
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..++.+.|..-+|+|..|||++ -+++.+||..||..+.+
T Consensus 113 ~L~~~~r~v~~L~~~~g~s~~EIA~~----l~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 113 GLPPLVKRAFLLAQVDGLGYGEIATE----LGISLATVKRYLNKAAM 155 (161)
T ss_pred HCCHHHHHHHHHHHHcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 35566777887764499999999999 99999999999988854
No 57
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=80.70 E-value=2.1 Score=39.00 Aligned_cols=42 Identities=17% Similarity=0.139 Sum_probs=34.8
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
+++.....+.|..-+|+|.+|||+. -+++++||..||..+.+
T Consensus 130 L~~~~r~v~~l~~~~g~s~~EIA~~----l~is~~tV~~~l~rar~ 171 (181)
T PRK12536 130 LPDRQRLPIVHVKLEGLSVAETAQL----TGLSESAVKVGIHRGLK 171 (181)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 4555666777765599999999999 99999999999988754
No 58
>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=80.67 E-value=2.1 Score=41.18 Aligned_cols=44 Identities=25% Similarity=0.099 Sum_probs=39.2
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
.+++...+.+.+.. +|+|..|||.+ -++++.||..|+..+.+.=
T Consensus 171 ~Lt~re~evl~~~a-~G~t~~eIa~~----l~is~~Tv~~~l~~~~~kl 214 (232)
T TIGR03541 171 VLSEREREVLAWTA-LGRRQADIAAI----LGISERTVENHLRSARRKL 214 (232)
T ss_pred cCCHHHHHHHHHHH-CCCCHHHHHHH----HCcCHHHHHHHHHHHHHHH
Confidence 57888888998887 99999999999 9999999999999986544
No 59
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=80.48 E-value=2.2 Score=39.00 Aligned_cols=44 Identities=20% Similarity=0.168 Sum_probs=36.1
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
.+++..++.+.|..-+|+|.+|||+. -+++.+||..|+..+...
T Consensus 122 ~L~~~~r~i~~l~~~~g~s~~EIA~~----lgis~~tVk~~l~Rar~~ 165 (185)
T PRK12542 122 ELNESNRQVFKYKVFYNLTYQEISSV----MGITEANVRKQFERARKR 165 (185)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----HCCCHHHHHHHHHHHHHH
Confidence 45566778888843399999999999 999999999999877543
No 60
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=80.06 E-value=2.2 Score=37.93 Aligned_cols=43 Identities=21% Similarity=0.149 Sum_probs=35.9
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..++.+.|..-+|+|..|||+. -+++.+||..|+..+..
T Consensus 110 ~L~~~~r~i~~l~~~~g~s~~eIA~~----lgis~~tV~~~l~ra~~ 152 (162)
T TIGR02983 110 RLPARQRAVVVLRYYEDLSEAQVAEA----LGISVGTVKSRLSRALA 152 (162)
T ss_pred hCCHHHHHHhhhHHHhcCCHHHHHHH----hCCCHHHHHHHHHHHHH
Confidence 45566677777754499999999999 99999999999988765
No 61
>PRK13870 transcriptional regulator TraR; Provisional
Probab=79.95 E-value=2.3 Score=41.12 Aligned_cols=44 Identities=23% Similarity=0.185 Sum_probs=39.0
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
.+|+...+.+.+.. +|+|-.|||.+ -++++.||.-||..+.++=
T Consensus 173 ~LT~RE~E~L~W~A-~GKT~~EIa~I----LgISe~TV~~Hl~na~~KL 216 (234)
T PRK13870 173 WLDPKEATYLRWIA-VGKTMEEIADV----EGVKYNSVRVKLREAMKRF 216 (234)
T ss_pred CCCHHHHHHHHHHH-cCCCHHHHHHH----HCCCHHHHHHHHHHHHHHc
Confidence 47788888888877 99999999999 9999999999999987653
No 62
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=79.85 E-value=2.4 Score=39.15 Aligned_cols=44 Identities=18% Similarity=0.132 Sum_probs=36.6
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..|++..++.+.|..-+|+|..|||++ -+++++||..||..+..
T Consensus 133 ~~Lp~~~R~v~~L~~~~g~s~~EIA~~----lgis~~tVk~~l~RAr~ 176 (189)
T PRK12530 133 NHLPAQQARVFMMREYLELSSEQICQE----CDISTSNLHVLLYRARL 176 (189)
T ss_pred HhCCHHHHHHHhHHHHcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 345666778888865589999999999 99999999999988754
No 63
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=79.73 E-value=2.4 Score=38.98 Aligned_cols=43 Identities=19% Similarity=0.132 Sum_probs=36.1
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..++.+.|..-+|+|..|||+. -|++++||..||..+..
T Consensus 131 ~Lp~~~r~v~~l~~~~g~s~~EIA~~----lgis~~tV~~~l~Rar~ 173 (191)
T PRK12520 131 RLPPRTGRVFMMREWLELETEEICQE----LQITATNAWVLLYRARM 173 (191)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 45666777788865599999999999 99999999999987744
No 64
>PRK15320 transcriptional activator SprB; Provisional
Probab=79.64 E-value=2.7 Score=39.93 Aligned_cols=48 Identities=21% Similarity=0.174 Sum_probs=40.8
Q ss_pred ccccCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 207 NTRTKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 207 ~~~~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
|.+-.+++...+-+.++. +|+|-.|||+. -+++.+||..|+..+...=
T Consensus 160 ~~~~~LSdREIEVL~LLA-kG~SNKEIAek----L~LS~KTVSTYKnRLLeKL 207 (251)
T PRK15320 160 NLPPGVTQAKYALLILLS-SGHPAIELAKK----FGLGTKTVSIYRKKVMYRL 207 (251)
T ss_pred cCCCCCCHHHHHHHHHHH-cCCCHHHHHHH----hccchhhHHHHHHHHHHHc
Confidence 334567777788888988 99999999999 9999999999999987654
No 65
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=79.61 E-value=2.4 Score=39.14 Aligned_cols=43 Identities=16% Similarity=0.128 Sum_probs=36.3
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.|++..++.+.|..-+|+|..|||++ -+++++||..||..+..
T Consensus 116 ~Lp~~~r~i~~L~~~~g~s~~EIA~~----Lgis~~tVk~~l~Rar~ 158 (187)
T PRK12516 116 QLPDDQREAIILVGASGFAYEEAAEI----CGCAVGTIKSRVNRARQ 158 (187)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 45667778888854499999999999 99999999999988753
No 66
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=79.57 E-value=4.3 Score=40.98 Aligned_cols=92 Identities=14% Similarity=0.081 Sum_probs=61.4
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchh--hhhhccCCCHHHHHHHHHHHHHh
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWT--RLCDEVGLTDEIFSAIQEAISKV 288 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~--~~i~~~~l~~e~~~~I~~a~~~~ 288 (430)
.|++..++.+.|..-+|+|..|||++ -+++++||..||..+.+.=..--.. ...+.. .++...+.+...+..+
T Consensus 153 ~Lp~~~R~v~~L~~~~g~s~~EIA~~----lgis~~tVk~~l~RAr~~Lr~~~~~~~~~~~~~-~~~~~~~~v~~~~~A~ 227 (339)
T PRK08241 153 HLPPRQRAVLILRDVLGWSAAEVAEL----LDTSVAAVNSALQRARATLAERGPSAADTLREP-DDPEERALLARYVAAF 227 (339)
T ss_pred hCCHHHhhhhhhHHhhCCCHHHHHHH----hCCCHHHHHHHHHHHHHHHhhcCCCcccccCCC-CChHHHHHHHHHHHHH
Confidence 45566667777765599999999999 9999999999998876544321100 000111 2455555666666665
Q ss_pred CCCCChHHHHHhCCCCCCHH
Q 044490 289 GCKDKLKPIKNELPDDITYA 308 (430)
Q Consensus 289 g~~~~LkpIke~l~~~isY~ 308 (430)
.. .-+..+.+.|.+++.|.
T Consensus 228 ~~-gD~~~l~~lla~Dv~~~ 246 (339)
T PRK08241 228 EA-YDVDALVALLTEDATWS 246 (339)
T ss_pred hc-CCHHHHHHHhcCCEEEE
Confidence 42 45788889999988766
No 67
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=79.23 E-value=2.9 Score=36.73 Aligned_cols=43 Identities=14% Similarity=-0.086 Sum_probs=34.3
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..+..+.+..-+|+|..|||+. -+++.+||..++..+..
T Consensus 106 ~L~~~~r~ii~l~~~~~~s~~EIA~~----l~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 106 VLDEKEKYIIFERFFVGKTMGEIALE----TEMTYYQVRWIYRQALE 148 (154)
T ss_pred hCCHHHHHHHHHHHhcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 35555666666543399999999999 99999999999988754
No 68
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=79.15 E-value=2.8 Score=37.80 Aligned_cols=44 Identities=23% Similarity=0.305 Sum_probs=36.9
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
.+++..++.+.|..-+|+|..|||+. -+++++||..||..+.+.
T Consensus 119 ~Lp~~~r~v~~L~~~~g~s~~EIA~~----lgis~~tV~~~l~ra~~~ 162 (172)
T PRK12523 119 KLSSKARAAFLYNRLDGMGHAEIAER----LGVSVSRVRQYLAQGLRQ 162 (172)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----HCCCHHHHHHHHHHHHHH
Confidence 45666778888865599999999999 999999999999887654
No 69
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=79.09 E-value=3.6 Score=31.00 Aligned_cols=37 Identities=11% Similarity=0.097 Sum_probs=26.7
Q ss_pred CCCHHHHHHHHHHHHHcCCceeee---cCccceEEeCcch
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETI---KDVYRTVSVSQQG 56 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~---~~~y~~l~LT~kg 56 (430)
++++..+.+.++.|+..|||...- +.....|.||++|
T Consensus 29 ~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G 68 (68)
T PF13463_consen 29 GISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG 68 (68)
T ss_dssp T--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred CcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence 468889999999999999997762 1222468999987
No 70
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=78.97 E-value=2.7 Score=37.57 Aligned_cols=43 Identities=21% Similarity=0.198 Sum_probs=37.0
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
-+++...+.+.|+. +|+|.+|||+. -+++.+||..|+..+...
T Consensus 6 ~Lte~qr~VL~Lr~-~GlTq~EIAe~----LgiS~stV~~~e~ra~kk 48 (137)
T TIGR00721 6 FLTERQIKVLELRE-KGLSQKEIAKE----LKTTRANVSAIEKRAMEN 48 (137)
T ss_pred CCCHHHHHHHHHHH-cCCCHHHHHHH----HCcCHHHHHHHHHhHHHH
Confidence 46777788888876 99999999999 999999999998887554
No 71
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=78.90 E-value=3.2 Score=34.71 Aligned_cols=43 Identities=12% Similarity=0.239 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHHcCCceeeecCc-cceEEeCcchHhhhcCC
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETIKDV-YRTVSVSQQGKQYLGSA 63 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~~~~-y~~l~LT~kg~~~L~g~ 63 (430)
.++..-.+.++..|+..|++... .++ -..+.+|+||..+|..-
T Consensus 42 Nlny~~~~~yi~~L~~~Gli~~~-~~~~~~~y~lT~KG~~fle~y 85 (95)
T COG3432 42 NLNYKRAQKYIEMLVEKGLIIKQ-DNGRRKVYELTEKGKRFLEKY 85 (95)
T ss_pred CcCHHHHHHHHHHHHhCCCEEec-cCCccceEEEChhHHHHHHHH
Confidence 57888999999999999955544 332 23899999999998754
No 72
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=78.65 E-value=2.6 Score=38.72 Aligned_cols=44 Identities=23% Similarity=0.112 Sum_probs=37.0
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
.+++..++.+.|..-+|+|..|||+. -+++++||..||..+...
T Consensus 130 ~Lp~~~r~v~~L~~~~g~s~~EIA~~----lgis~~tVk~~l~Rar~~ 173 (185)
T PRK09649 130 DLTTDQREALLLTQLLGLSYADAAAV----CGCPVGTIRSRVARARDA 173 (185)
T ss_pred hCCHHHhHHhhhHHHcCCCHHHHHHH----HCCCHHHHHHHHHHHHHH
Confidence 45667778888865599999999999 999999999999877543
No 73
>PRK10651 transcriptional regulator NarL; Provisional
Probab=78.56 E-value=3.2 Score=37.42 Aligned_cols=44 Identities=27% Similarity=0.283 Sum_probs=39.7
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
.+++...+.+.++. +|++..+||.. -+++..||..|+..+..+=
T Consensus 155 ~Lt~rE~~vl~~l~-~g~~~~~ia~~----l~is~~tV~~~~~~l~~Kl 198 (216)
T PRK10651 155 QLTPRERDILKLIA-QGLPNKMIARR----LDITESTVKVHVKHMLKKM 198 (216)
T ss_pred cCCHHHHHHHHHHH-cCCCHHHHHHH----cCCCHHHHHHHHHHHHHHc
Confidence 47888889999988 99999999998 9999999999999997765
No 74
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=78.41 E-value=2.7 Score=38.70 Aligned_cols=43 Identities=23% Similarity=0.184 Sum_probs=36.2
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..++.+.|..-+|+|..|||+. -+++++||..|+..+..
T Consensus 111 ~Lp~~~R~v~~L~~~eg~s~~EIA~~----lgis~~tV~~~l~Rar~ 153 (182)
T PRK12511 111 DLPEEQRAALHLVAIEGLSYQEAAAV----LGIPIGTLMSRIGRARA 153 (182)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----hCcCHHHHHHHHHHHHH
Confidence 46677788888854499999999999 99999999999877644
No 75
>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=78.26 E-value=2.7 Score=41.11 Aligned_cols=45 Identities=22% Similarity=0.141 Sum_probs=39.9
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
..+++...+.+.+.. +|+|-.|||++ -++++.||..|+..+...-
T Consensus 189 ~~LT~RE~evl~l~a-~G~s~~eIA~~----L~IS~~TVk~hl~~i~~KL 233 (247)
T TIGR03020 189 GLITAREAEILAWVR-DGKTNEEIAAI----LGISSLTVKNHLQHIFKKL 233 (247)
T ss_pred cCCCHHHHHHHHHHH-CCCCHHHHHHH----HCcCHHHHHHHHHHHHHHh
Confidence 357888888888887 99999999999 9999999999999997654
No 76
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=78.18 E-value=2.6 Score=38.88 Aligned_cols=44 Identities=14% Similarity=0.127 Sum_probs=35.7
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
.+++..++.+.|..-+|+|.+|||+. -|++.+||..|+..+...
T Consensus 136 ~L~~~~r~i~~L~~~~g~s~~EIA~~----lgis~~tVk~~l~Rar~~ 179 (195)
T PRK12532 136 NLPENTARVFTLKEILGFSSDEIQQM----CGISTSNYHTIMHRARES 179 (195)
T ss_pred hCCHHHHHHhhhHHHhCCCHHHHHHH----HCCCHHHHHHHHHHHHHH
Confidence 35566677787744499999999999 999999999999887543
No 77
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=78.18 E-value=2.9 Score=37.22 Aligned_cols=43 Identities=21% Similarity=0.223 Sum_probs=36.3
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..++.+.|..-+|+|..|||+. -+++.+||..++..+..
T Consensus 122 ~L~~~~r~vl~l~~~~g~s~~eIA~~----l~is~~tv~~~l~ra~~ 164 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQNLPIAEVARI----LGKTEGAVKILQFRAIK 164 (170)
T ss_pred hCCHHHHHHHHHHHhcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 46677778888843399999999999 99999999999988764
No 78
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=78.06 E-value=4.5 Score=40.37 Aligned_cols=93 Identities=13% Similarity=0.010 Sum_probs=60.2
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCC-cchh-hhhhccCCCHHHHHHHHHHHHHh
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFD-INWT-RLCDEVGLTDEIFSAIQEAISKV 288 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~-l~~~-~~i~~~~l~~e~~~~I~~a~~~~ 288 (430)
.|++..+..+.|..-+|+|..|||++ -+++++||..||..+.+.=.. +.-. ...+..-.+++..+.+...+..+
T Consensus 142 ~Lp~~~R~v~~L~~~~g~s~~EIA~~----lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~~~~~~~~~~~~~v~~~~~a~ 217 (324)
T TIGR02960 142 YLPPRQRAVLLLRDVLGWRAAETAEL----LGTSTASVNSALQRARATLDEVGPSARDDQLAQPPSPEEQDLLERYIAAF 217 (324)
T ss_pred hCCHHHhhHhhhHHHhCCCHHHHHHH----HCCCHHHHHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHH
Confidence 45566677888865599999999999 999999999999877654321 1100 00000002455555555555555
Q ss_pred CCCCChHHHHHhCCCCCCHH
Q 044490 289 GCKDKLKPIKNELPDDITYA 308 (430)
Q Consensus 289 g~~~~LkpIke~l~~~isY~ 308 (430)
.. ..+..+.+.|.+++.|.
T Consensus 218 ~~-gD~~~l~~Lla~Dv~~~ 236 (324)
T TIGR02960 218 ES-YDLDALTALLHEDAIWE 236 (324)
T ss_pred Hc-CCHHHHHHHhcCCeEEE
Confidence 42 45777888888887665
No 79
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=77.77 E-value=3.4 Score=36.65 Aligned_cols=42 Identities=29% Similarity=0.370 Sum_probs=34.8
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
+++...+.+.|..-+|+|.+|||+. -+++.+||..|+..+..
T Consensus 106 L~~~~r~v~~l~~~~~~s~~eIA~~----lgis~~tv~~~l~ra~~ 147 (159)
T PRK12527 106 LPPACRDSFLLRKLEGLSHQQIAEH----LGISRSLVEKHIVNAMK 147 (159)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHH----hCCCHHHHHHHHHHHHH
Confidence 4556667777764499999999999 99999999999987744
No 80
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=77.77 E-value=2.9 Score=38.49 Aligned_cols=43 Identities=23% Similarity=0.163 Sum_probs=36.0
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..++.+.|..-+|+|.+|||+. -+++.+||..||..+..
T Consensus 111 ~Lp~~~R~v~~L~~~~g~s~~EIA~~----Lgis~~tV~~~l~RAr~ 153 (182)
T PRK12540 111 KLPQDQREALILVGASGFSYEDAAAI----CGCAVGTIKSRVNRARS 153 (182)
T ss_pred hCCHHHHHHhhHHHHcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 45667778888854499999999999 99999999999887744
No 81
>PRK06930 positive control sigma-like factor; Validated
Probab=77.45 E-value=3 Score=38.48 Aligned_cols=44 Identities=34% Similarity=0.400 Sum_probs=37.0
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++..+..+.|..-+|+|..|||.. -+++.+||..|+..+..
T Consensus 113 ~~L~~rer~V~~L~~~eg~s~~EIA~~----lgiS~~tVk~~l~Ra~~ 156 (170)
T PRK06930 113 SVLTEREKEVYLMHRGYGLSYSEIADY----LNIKKSTVQSMIERAEK 156 (170)
T ss_pred HhCCHHHHHHHHHHHHcCCCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 356777888888843499999999999 99999999999987754
No 82
>smart00351 PAX Paired Box domain.
Probab=77.15 E-value=12 Score=32.51 Aligned_cols=40 Identities=13% Similarity=0.084 Sum_probs=34.8
Q ss_pred HHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 216 KYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 216 ~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
......++. +|.|..+||.. -+++.+||+..+..+...|.
T Consensus 23 R~riv~~~~-~G~s~~~iA~~----~gvs~~tV~kwi~r~~~~G~ 62 (125)
T smart00351 23 RQRIVELAQ-NGVRPCDISRQ----LCVSHGCVSKILGRYYETGS 62 (125)
T ss_pred HHHHHHHHH-cCCCHHHHHHH----HCcCHHHHHHHHHHHHHcCC
Confidence 345566676 99999999998 99999999999999999985
No 83
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=77.07 E-value=3.2 Score=37.47 Aligned_cols=43 Identities=16% Similarity=0.054 Sum_probs=34.6
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
+++.....+.|..-+|+|.+|||+. -|++.+||..||..+.+.
T Consensus 120 L~~~~r~i~~l~~~~~~s~~EIA~~----lgis~~tV~~~l~Ra~~~ 162 (173)
T PRK12522 120 LNEKYKTVLVLYYYEQYSYKEMSEI----LNIPIGTVKYRLNYAKKQ 162 (173)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHH----hCCCHHHHHHHHHHHHHH
Confidence 4445556676654499999999999 999999999999887554
No 84
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=76.99 E-value=3.5 Score=37.02 Aligned_cols=43 Identities=28% Similarity=0.176 Sum_probs=35.7
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..++.+.|..-+|+|.+|||+. -|++++||..|+..+..
T Consensus 118 ~L~~~~r~vl~L~~~~g~s~~EIA~~----lgis~~tV~~~l~ra~~ 160 (173)
T PRK09645 118 QLSPEHRAVLVRSYYRGWSTAQIAAD----LGIPEGTVKSRLHYALR 160 (173)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 45666777888754499999999999 99999999999988754
No 85
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=76.95 E-value=3.3 Score=38.58 Aligned_cols=43 Identities=14% Similarity=0.083 Sum_probs=36.2
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..++.+.|..-+|+|..|||++ -|++++||..+|..+..
T Consensus 139 ~Lp~~~r~v~~L~~~eg~s~~EIA~~----lgis~~tVk~~l~RAr~ 181 (201)
T PRK12545 139 HLPEQIGRVFMMREFLDFEIDDICTE----LTLTANHCSVLLYRART 181 (201)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 46667778888865599999999999 99999999999887643
No 86
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=76.93 E-value=3.3 Score=36.83 Aligned_cols=43 Identities=28% Similarity=0.264 Sum_probs=36.8
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
.+++..+..+.|.. +|+|..|||+. -|++.+||..++..+...
T Consensus 112 ~L~~~~r~il~l~~-~g~s~~eIA~~----lgis~~tV~~~i~ra~~~ 154 (166)
T PRK09639 112 KMTERDRTVLLLRF-SGYSYKEIAEA----LGIKESSVGTTLARAKKK 154 (166)
T ss_pred cCCHHHHHHHHHHH-cCCCHHHHHHH----HCCCHHHHHHHHHHHHHH
Confidence 45666778888889 99999999999 999999999999877543
No 87
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=76.75 E-value=3.2 Score=39.06 Aligned_cols=41 Identities=17% Similarity=0.212 Sum_probs=35.6
Q ss_pred hHHHHHHHHHhc---CCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 215 AKYEAWKMWHED---GLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 215 t~~~T~~l~~~~---G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
|.++.+.++. + |+|..|||+. .++++.||..|+..+...|.
T Consensus 163 t~r~Vl~~~~-~g~~g~s~~eIa~~----l~iS~~Tv~~~~~~~~~~~~ 206 (225)
T PRK10046 163 TLNAVRKLFK-EPGVQHTAETVAQA----LTISRTTARRYLEYCASRHL 206 (225)
T ss_pred HHHHHHHHHH-cCCCCcCHHHHHHH----hCccHHHHHHHHHHHHhCCe
Confidence 3346777877 7 5899999999 99999999999999999995
No 88
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=76.36 E-value=31 Score=33.28 Aligned_cols=44 Identities=18% Similarity=0.133 Sum_probs=37.0
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++..+..+.+..-+|+|..|||+. -+++.+||..++..+..
T Consensus 204 ~~L~~~~r~ii~l~~~~g~s~~eIA~~----lgis~~~V~~~~~ra~~ 247 (255)
T TIGR02941 204 PILSEREKSIIHCTFEENLSQKETGER----LGISQMHVSRLQRQAIS 247 (255)
T ss_pred HcCCHHHHHHHHHHHcCCCCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 457777778887775599999999999 99999999999877654
No 89
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=76.32 E-value=3.9 Score=36.29 Aligned_cols=43 Identities=19% Similarity=0.199 Sum_probs=34.3
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..+..+.|..-+|+|.+|||++ -+++.+||..++..+..
T Consensus 109 ~L~~~~r~v~~l~~~~~~s~~EIA~~----lgis~~tV~~~l~ra~~ 151 (163)
T PRK07037 109 ELPARTRYAFEMYRLHGETQKDIARE----LGVSPTLVNFMIRDALV 151 (163)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 34556667777643499999999999 99999999999877643
No 90
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=76.14 E-value=1.6 Score=33.54 Aligned_cols=44 Identities=16% Similarity=0.167 Sum_probs=36.1
Q ss_pred CchHHHHHHHH-HhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 213 TPAKYEAWKMW-HEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 213 ~~t~~~T~~l~-~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
+.+..+.|..+ ...+.|+.+||+. -+++.+||+.+|..+...|.
T Consensus 7 s~~E~~vy~~Ll~~~~~t~~eIa~~----l~i~~~~v~~~L~~L~~~Gl 51 (68)
T PF01978_consen 7 SENEAKVYLALLKNGPATAEEIAEE----LGISRSTVYRALKSLEEKGL 51 (68)
T ss_dssp HHHHHHHHHHHHHHCHEEHHHHHHH----HTSSHHHHHHHHHHHHHTTS
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHH----HCcCHHHHHHHHHHHHHCCC
Confidence 34445555443 5589999999999 99999999999999999995
No 91
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=76.11 E-value=2.5 Score=30.53 Aligned_cols=43 Identities=30% Similarity=0.377 Sum_probs=34.3
Q ss_pred CHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCC
Q 044490 229 SIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGC 290 (430)
Q Consensus 229 si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~ 290 (430)
|+.+||.. -|++.+||...| .|+ . +++++..+.|.++++++|+
T Consensus 1 Ti~dIA~~----agvS~~TVSr~l-----n~~-----~-----~vs~~tr~rI~~~a~~lgY 43 (46)
T PF00356_consen 1 TIKDIARE----AGVSKSTVSRVL-----NGP-----P-----RVSEETRERILEAAEELGY 43 (46)
T ss_dssp CHHHHHHH----HTSSHHHHHHHH-----TTC-----S-----SSTHHHHHHHHHHHHHHTB
T ss_pred CHHHHHHH----HCcCHHHHHHHH-----hCC-----C-----CCCHHHHHHHHHHHHHHCC
Confidence 68899999 999999996543 332 1 2489999999999999885
No 92
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=75.93 E-value=3.9 Score=37.30 Aligned_cols=43 Identities=23% Similarity=0.196 Sum_probs=34.9
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..++.+.|..-+|+|.+|||+. -|++++||..|+..+.+
T Consensus 133 ~L~~~~r~i~~l~~~~~~s~~eIA~~----lgis~~tV~~~l~ra~~ 175 (182)
T PRK12537 133 QLEPARRNCILHAYVDGCSHAEIAQR----LGAPLGTVKAWIKRSLK 175 (182)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----HCCChhhHHHHHHHHHH
Confidence 35556666677644499999999999 99999999999988764
No 93
>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=75.84 E-value=3.7 Score=25.65 Aligned_cols=30 Identities=30% Similarity=0.432 Sum_probs=24.3
Q ss_pred HHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHH
Q 044490 218 EAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYL 252 (430)
Q Consensus 218 ~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL 252 (430)
....++. .|.++.+||.. -+++.+||+.|+
T Consensus 13 ~i~~~~~-~~~s~~~ia~~----~~is~~tv~~~~ 42 (42)
T cd00569 13 EARRLLA-AGESVAEIARR----LGVSRSTLYRYL 42 (42)
T ss_pred HHHHHHH-cCCCHHHHHHH----HCCCHHHHHHhC
Confidence 3444555 89999999998 899999998774
No 94
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=75.11 E-value=4.1 Score=36.81 Aligned_cols=42 Identities=21% Similarity=0.159 Sum_probs=34.9
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAV 256 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i 256 (430)
.+++..+..+.|..-+|+|..|||++ -+++++||..+|..+.
T Consensus 100 ~L~~~~r~v~~l~~~~g~s~~eIA~~----lgis~~tV~~~l~Rar 141 (170)
T TIGR02959 100 ELPDEYREAIRLTELEGLSQQEIAEK----LGLSLSGAKSRVQRGR 141 (170)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----HCCCHHHHHHHHHHHH
Confidence 35566677888854499999999999 9999999999987764
No 95
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=75.09 E-value=17 Score=32.59 Aligned_cols=93 Identities=19% Similarity=0.207 Sum_probs=61.5
Q ss_pred cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhh-hhccCCCHHHHHHHHHHHHHhCCCCChHHHHHhCCC-
Q 044490 226 DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRL-CDEVGLTDEIFSAIQEAISKVGCKDKLKPIKNELPD- 303 (430)
Q Consensus 226 ~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~-i~~~~l~~e~~~~I~~a~~~~g~~~~LkpIke~l~~- 303 (430)
+|+|..|||++ -+++.+||+..+..+-..|..+-.... -..--++++.++.+...+++-. -.|+.+.+.+..
T Consensus 20 ~G~S~re~Ak~----~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~--wTl~~~~~~l~~e 93 (138)
T COG3415 20 EGLSCREAAKR----FGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKD--WTLKELVEELGLE 93 (138)
T ss_pred cCccHHHHHHH----hCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhccc--chHHHHHHHHhhh
Confidence 99999999999 999999999999999999964221100 0001247888888877777633 456666555442
Q ss_pred -CCCHHHHHHHHHHHHhCCCCC
Q 044490 304 -DITYAHIKACLVMENCGISPE 324 (430)
Q Consensus 304 -~isY~~Irl~la~~~~~~~~~ 324 (430)
.+.|..=.+-....+.|++-.
T Consensus 94 ~gv~y~~~~v~~~l~~~Glsyk 115 (138)
T COG3415 94 FGVWYHASAVRRLLHELGLSYK 115 (138)
T ss_pred cCeEEeHHHHHHHHHHcCCCcC
Confidence 244443344455566677544
No 96
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=74.95 E-value=4.6 Score=36.21 Aligned_cols=43 Identities=23% Similarity=0.227 Sum_probs=36.3
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..|++...+-+.++. +|+|..|||+. -+++.+||..|...+.+
T Consensus 5 ~~Lt~rqreVL~lr~-~GlTq~EIAe~----LGiS~~tVs~ie~ra~k 47 (141)
T PRK03975 5 SFLTERQIEVLRLRE-RGLTQQEIADI----LGTSRANVSSIEKRARE 47 (141)
T ss_pred cCCCHHHHHHHHHHH-cCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 346788888888876 99999999999 99999999988876544
No 97
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=74.88 E-value=3.8 Score=34.61 Aligned_cols=41 Identities=20% Similarity=0.251 Sum_probs=33.9
Q ss_pred CchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 213 TPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 213 ~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
|......++++...-+|+.|||+. -+++.+.|++|+-....
T Consensus 19 T~KQ~~Y~~lyy~dDlSl~EIAee----~~VSRqAIyDnIKr~~~ 59 (105)
T COG2739 19 TKKQKNYLELYYLDDLSLSEIAEE----FNVSRQAIYDNIKRTEK 59 (105)
T ss_pred hHHHHHHHHHHHHhhccHHHHHHH----hCccHHHHHHHHHHHHH
Confidence 344556677777799999999999 99999999999987744
No 98
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=74.83 E-value=4 Score=35.60 Aligned_cols=41 Identities=22% Similarity=0.196 Sum_probs=33.3
Q ss_pred CCchHHHHHHH-HHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 212 LTPAKYEAWKM-WHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 212 l~~t~~~T~~l-~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
+++...+.+.| +. +|+|+.|||+. -|++++||..++..+..
T Consensus 114 L~~~~r~il~l~~~-~~~~~~eIA~~----lgis~~tv~~~~~ra~~ 155 (161)
T TIGR02985 114 LPEQCRKIFILSRF-EGKSYKEIAEE----LGISVKTVEYHISKALK 155 (161)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 44555666666 55 99999999999 99999999999988754
No 99
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=74.68 E-value=3.7 Score=39.07 Aligned_cols=43 Identities=26% Similarity=0.217 Sum_probs=35.8
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.|++..++.+.|+.-+|+|..|||+. -+++++||..||..+..
T Consensus 134 ~Lp~~~R~v~~L~y~eg~s~~EIAe~----LgiS~~tVk~~L~RAr~ 176 (216)
T PRK12533 134 KLPVEYREVLVLRELEDMSYREIAAI----ADVPVGTVMSRLARARR 176 (216)
T ss_pred cCCHHHHhHhhhHHhcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 45666778888854499999999999 99999999999987643
No 100
>PHA02591 hypothetical protein; Provisional
Probab=74.14 E-value=2.3 Score=34.22 Aligned_cols=33 Identities=21% Similarity=0.338 Sum_probs=27.8
Q ss_pred HHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHH
Q 044490 217 YEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLE 254 (430)
Q Consensus 217 ~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~ 254 (430)
-.+-+|.. +|+|+++||.. -+++..||..++..
T Consensus 50 ~vA~eL~e-qGlSqeqIA~~----LGVsqetVrKYL~~ 82 (83)
T PHA02591 50 SVTHELAR-KGFTVEKIASL----LGVSVRKVRRYLES 82 (83)
T ss_pred HHHHHHHH-cCCCHHHHHHH----hCCCHHHHHHHHhc
Confidence 34556766 99999999999 99999999988764
No 101
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=74.11 E-value=4.4 Score=36.88 Aligned_cols=44 Identities=16% Similarity=0.151 Sum_probs=36.6
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++...+.+.|..-+|+|..|||+. -|++.+||..++..+..
T Consensus 134 ~~L~~~~r~vl~l~~~~~~s~~eIA~~----lgis~~~V~~~l~ra~~ 177 (186)
T PRK13919 134 KALSPEERRVIEVLYYQGYTHREAAQL----LGLPLGTLKTRARRALS 177 (186)
T ss_pred HhCCHHHHHHHHHHHHcCCCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 346677778888754499999999999 99999999999988754
No 102
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=73.94 E-value=4.4 Score=36.81 Aligned_cols=42 Identities=19% Similarity=0.066 Sum_probs=34.4
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
+++..++.+.|..-+|+|..|||+. -|++.+||..|+..+..
T Consensus 118 Lp~~~r~i~~l~~~e~~s~~EIA~~----lgis~~tV~~~l~ra~~ 159 (179)
T PRK12543 118 LPYKLRQVIILRYLHDYSQEEIAQL----LQIPIGTVKSRIHAALK 159 (179)
T ss_pred CCHHHHHHHHHHHHccCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 4556667777743399999999999 99999999999988844
No 103
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=73.81 E-value=7 Score=38.73 Aligned_cols=89 Identities=13% Similarity=0.119 Sum_probs=55.9
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCC
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGC 290 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~ 290 (430)
.+++..+..+.|..-+|+|.+|||++ -+++++||..+|..+-..=... ...+- ..+++..+.+...+..++.
T Consensus 115 ~L~~~~R~v~~L~~~~g~s~~EIA~~----lg~s~~tVk~~l~RAr~~Lr~~-~~~~~---~~~~~~~~~v~~f~~A~~~ 186 (293)
T PRK09636 115 RLSPLERAAFLLHDVFGVPFDEIAST----LGRSPAACRQLASRARKHVRAA-RPRFP---VSDEEGAELVEAFFAALAS 186 (293)
T ss_pred hCCHHHHHHHHHHHHhCCCHHHHHHH----HCCCHHHHHHHHHHHHHHHHhh-CCCCC---CCchHHHHHHHHHHHHHHh
Confidence 46667778888865599999999999 9999999999998775543211 11110 0123333334333333331
Q ss_pred CCChHHHHHhCCCCCCHH
Q 044490 291 KDKLKPIKNELPDDITYA 308 (430)
Q Consensus 291 ~~~LkpIke~l~~~isY~ 308 (430)
..+..+-+.|.+++.|.
T Consensus 187 -gD~~~l~~Lla~Dv~~~ 203 (293)
T PRK09636 187 -GDLDALVALLAPDVVLH 203 (293)
T ss_pred -CCHHHHHHHHhhCeEEE
Confidence 34666677777766553
No 104
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=73.50 E-value=3.8 Score=37.15 Aligned_cols=42 Identities=17% Similarity=0.214 Sum_probs=35.0
Q ss_pred CCCchHHHHHHH-HHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKM-WHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l-~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..+..+.| +. +|+|.+|||+. -|++.+||..++..+..
T Consensus 136 ~L~~~~r~v~~l~~~-~g~s~~eIA~~----lgis~~~v~~~l~Rar~ 178 (187)
T TIGR02948 136 ALPPKYRMVIVLKYM-EDLSLKEISEI----LDLPVGTVKTRIHRGRE 178 (187)
T ss_pred hCCHHHhHHhhhHHh-cCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 456667777777 45 99999999999 99999999999987654
No 105
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=73.48 E-value=2.7 Score=34.69 Aligned_cols=36 Identities=17% Similarity=0.155 Sum_probs=28.4
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYL 252 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL 252 (430)
.+++. ...+.+.. +|+|..+||.. -+++.+||+.+.
T Consensus 36 ~Ls~R-~~I~~ll~-~G~S~~eIA~~----LgISrsTIyRi~ 71 (88)
T TIGR02531 36 SLAQR-LQVAKMLK-QGKTYSDIEAE----TGASTATISRVK 71 (88)
T ss_pred hhhHH-HHHHHHHH-CCCCHHHHHHH----HCcCHHHHHHHH
Confidence 35555 45555655 99999999999 999999999854
No 106
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=73.39 E-value=4.4 Score=39.40 Aligned_cols=46 Identities=20% Similarity=0.308 Sum_probs=38.2
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
..+++..++.+.|..-+|+|..|||++ -+++++||..||..+...=
T Consensus 160 ~~Lp~~~R~v~~L~~~eg~S~~EIA~~----Lgis~~TVk~rl~RAr~~L 205 (244)
T TIGR03001 160 AALSERERHLLRLHFVDGLSMDRIGAM----YQVHRSTVSRWVAQARERL 205 (244)
T ss_pred HhCCHHHHHHHHHHHHcCCCHHHHHHH----HCcCHHHHHHHHHHHHHHH
Confidence 345666778888876699999999999 9999999999999886543
No 107
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=73.29 E-value=4.1 Score=36.87 Aligned_cols=45 Identities=24% Similarity=0.306 Sum_probs=36.1
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
.+++..++.+.|..-+|+|.+|||++ -|++.+||..|+..+...-
T Consensus 119 ~L~~~~r~i~~l~~~~g~s~~EIA~~----lgis~~tV~~~l~Ra~~~~ 163 (172)
T PRK09651 119 GLNGKTREAFLLSQLDGLTYSEIAHK----LGVSVSSVKKYVAKATEHC 163 (172)
T ss_pred hCCHHHhHHhhhhhccCCCHHHHHHH----hCCCHHHHHHHHHHHHHHH
Confidence 34555667777754499999999999 9999999999998886543
No 108
>cd00131 PAX Paired Box domain
Probab=73.10 E-value=51 Score=28.78 Aligned_cols=79 Identities=14% Similarity=0.040 Sum_probs=53.8
Q ss_pred HHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhh-hh-ccCCCHHHHHHHHHHHHHhCCCCC
Q 044490 216 KYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRL-CD-EVGLTDEIFSAIQEAISKVGCKDK 293 (430)
Q Consensus 216 ~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~-i~-~~~l~~e~~~~I~~a~~~~g~~~~ 293 (430)
......++. +|+|..+||.. -+++.+||...+..+.+.|. +....- -. .--++++....|...+.+.++ ..
T Consensus 23 R~rIv~~~~-~G~s~~~iA~~----~~Vs~~tV~r~i~r~~e~G~-v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~-~T 95 (128)
T cd00131 23 RQRIVELAQ-SGIRPCDISRQ----LRVSHGCVSKILNRYYETGS-IRPGAIGGSKPRVATPEVVKKIEIYKQENPG-MF 95 (128)
T ss_pred HHHHHHHHH-cCCCHHHHHHH----HCcCHHHHHHHHHHHHHcCC-cCCCCCCCCCCCcCCHHHHHHHHHHHHHCCC-CC
Confidence 345566666 99999999998 99999999999999999994 443211 00 001245555666655666553 56
Q ss_pred hHHHHHhC
Q 044490 294 LKPIKNEL 301 (430)
Q Consensus 294 LkpIke~l 301 (430)
+..|.+.|
T Consensus 96 l~El~~~L 103 (128)
T cd00131 96 AWEIRDRL 103 (128)
T ss_pred HHHHHHHH
Confidence 77777775
No 109
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=72.78 E-value=5.4 Score=37.84 Aligned_cols=31 Identities=23% Similarity=0.229 Sum_probs=29.6
Q ss_pred cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 226 DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 226 ~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
+|+|..+||.. .++++.||..|+..++..|-
T Consensus 177 ~g~s~~eIA~~----l~iS~~Tv~~~~~~~~~~~~ 207 (239)
T PRK10430 177 YEFSTDELANA----VNISRVSCRKYLIWLVNCHI 207 (239)
T ss_pred CCcCHHHHHHH----hCchHHHHHHHHHHHHhCCE
Confidence 89999999999 99999999999999999885
No 110
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=72.40 E-value=4.9 Score=37.04 Aligned_cols=43 Identities=16% Similarity=0.112 Sum_probs=35.3
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..++.+.|..-+|+|..|||++ -+++.+||..||..+..
T Consensus 131 ~L~~~~r~v~~l~~~~g~s~~EIA~~----lgis~~tvk~rl~Rar~ 173 (188)
T TIGR02943 131 HLPEQTARVFMMREVLGFESDEICQE----LEISTSNCHVLLYRARL 173 (188)
T ss_pred hCCHHHHHHHHHHHHhCCCHHHHHHH----hCCCHHHHHHHHHHHHH
Confidence 45566677787754499999999999 99999999999988744
No 111
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=72.24 E-value=5.2 Score=35.75 Aligned_cols=43 Identities=23% Similarity=0.190 Sum_probs=35.3
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..+..+.+..-.|+|..+||+. -+++++||..++..+.+
T Consensus 128 ~L~~~~r~vl~l~~~~~~s~~eIA~~----lgis~~tV~~~l~ra~~ 170 (182)
T PRK09652 128 SLPEELRTAITLREIEGLSYEEIAEI----MGCPIGTVRSRIFRARE 170 (182)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 46667777777754499999999999 99999999999887644
No 112
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=71.92 E-value=7.2 Score=30.21 Aligned_cols=42 Identities=10% Similarity=0.094 Sum_probs=35.1
Q ss_pred hHHHHHHHHHhc-C--CCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 215 AKYEAWKMWHED-G--LSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 215 t~~~T~~l~~~~-G--~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
+....+.++.+. + ++..+||.. -+++.+||..||..+...|.
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~----lgl~~~~v~r~L~~L~~~G~ 51 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKN----LGLPKKEVNRVLYSLEKKGK 51 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHH----HCCCHHHHHHHHHHHHHCCC
Confidence 345566666543 4 899999999 99999999999999999996
No 113
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=71.61 E-value=2.6 Score=38.79 Aligned_cols=43 Identities=19% Similarity=0.123 Sum_probs=34.1
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..++.+.|..-+|+|..|||+. -|++++||..||..+..
T Consensus 131 ~Lp~~~r~i~~L~~~~g~s~~EIA~~----lgis~~tVk~~l~Rar~ 173 (193)
T TIGR02947 131 GLPEEFRQAVYLADVEGFAYKEIAEI----MGTPIGTVMSRLHRGRK 173 (193)
T ss_pred hCCHHHhhheeehhhcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 34455556666644499999999999 99999999999988754
No 114
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=71.60 E-value=8.4 Score=28.71 Aligned_cols=28 Identities=21% Similarity=0.272 Sum_probs=24.7
Q ss_pred cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 226 DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 226 ~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+-|+.+||++ -+++.+|+..||-.+..
T Consensus 22 R~~tl~elA~~----lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 22 RRITLEELAEE----LGISKSTVSEHLRRAER 49 (53)
T ss_pred CcCCHHHHHHH----hCCCHHHHHHHHHHHHH
Confidence 46799999999 99999999999988754
No 115
>PRK10403 transcriptional regulator NarP; Provisional
Probab=71.54 E-value=6 Score=35.43 Aligned_cols=44 Identities=27% Similarity=0.231 Sum_probs=38.3
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
.+++...+-+.++. +|+|-.+||+. -+++..||..|+..+...=
T Consensus 153 ~Lt~~e~~vl~~~~-~g~s~~~ia~~----l~~s~~tv~~~~~~i~~kl 196 (215)
T PRK10403 153 VLTERELDVLHELA-QGLSNKQIASV----LNISEQTVKVHIRNLLRKL 196 (215)
T ss_pred cCCHHHHHHHHHHH-CCCCHHHHHHH----cCCCHHHHHHHHHHHHHHc
Confidence 46777778888888 99999999998 8999999999999997664
No 116
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=71.41 E-value=5.7 Score=35.50 Aligned_cols=43 Identities=16% Similarity=0.160 Sum_probs=38.2
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
.+++...+.+.++. +|++..+||+. .+++.+||..|+..+.+.
T Consensus 137 ~Lt~~E~~il~~l~-~g~~~~~Ia~~----l~~s~~tv~~~~~~l~~K 179 (196)
T PRK10360 137 PLTKRERQVAEKLA-QGMAVKEIAAE----LGLSPKTVHVHRANLMEK 179 (196)
T ss_pred CCCHHHHHHHHHHH-CCCCHHHHHHH----hCCCHHHHHHHHHHHHHH
Confidence 47777888888988 99999999998 899999999999998765
No 117
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=71.30 E-value=5.5 Score=36.58 Aligned_cols=43 Identities=16% Similarity=0.095 Sum_probs=35.3
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++...+.+.|..-+|+|..|||++ -+++.+||..++..+..
T Consensus 131 ~L~~~~r~i~~l~~~~g~s~~EIAe~----lgis~~~V~~~l~Ra~~ 173 (189)
T PRK06811 131 DLEKLDREIFIRRYLLGEKIEEIAKK----LGLTRSAIDNRLSRGRK 173 (189)
T ss_pred hCCHHHHHHHHHHHHccCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 46667777777743399999999999 99999999999887743
No 118
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=71.30 E-value=5.7 Score=35.91 Aligned_cols=43 Identities=19% Similarity=0.210 Sum_probs=33.7
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++...+.+.+..-+|+|.+|||+. -|++++||..||..+..
T Consensus 129 ~L~~~~r~i~~l~~~~g~s~~eIA~~----lgis~~tV~~~l~Rar~ 171 (179)
T PRK12514 129 ELEKDRAAAVRRAYLEGLSYKELAER----HDVPLNTMRTWLRRSLL 171 (179)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----HCCChHHHHHHHHHHHH
Confidence 35555555565554499999999999 99999999999987643
No 119
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=70.92 E-value=5.1 Score=36.74 Aligned_cols=41 Identities=27% Similarity=0.226 Sum_probs=33.3
Q ss_pred CCchHHHHHHH-HHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 212 LTPAKYEAWKM-WHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 212 l~~t~~~T~~l-~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
+++..+..+.| +. +|+|..|||+. -|+++.||..|+..+-.
T Consensus 139 L~~~~r~v~~l~~~-~g~s~~eIA~~----lgis~~tv~~~l~Rar~ 180 (193)
T PRK11923 139 LPEDLRTALTLREF-DGLSYEDIASV----MQCPVGTVRSRIFRARE 180 (193)
T ss_pred CCHHHhHHHhhHHh-cCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 44555666777 45 99999999999 99999999999888743
No 120
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=70.76 E-value=5.7 Score=36.27 Aligned_cols=43 Identities=19% Similarity=0.176 Sum_probs=35.8
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..++.+.|..-+|+|..|||+. -|++.+||..|+..+.+
T Consensus 131 ~L~~~~r~v~~l~~~~g~s~~eIA~~----lgis~~tV~~~l~ra~~ 173 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEGLSVAEAATR----SGMSESAVKVSVHRGLK 173 (184)
T ss_pred hCCHHHHHHHHHHHHcCCcHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 45666777888744499999999999 99999999999988754
No 121
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=70.31 E-value=5.5 Score=35.39 Aligned_cols=42 Identities=17% Similarity=0.099 Sum_probs=34.9
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
+++..+..+.|..-+|+|.+|||.. -|++.+||..|+..+..
T Consensus 113 L~~~~r~v~~l~~~~~~s~~eIA~~----lgis~~tv~~~l~Rar~ 154 (161)
T PRK12541 113 LPLERRNVLLLRDYYGFSYKEIAEM----TGLSLAKVKIELHRGRK 154 (161)
T ss_pred CCHHHHHHhhhHHhcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 4556667777754499999999999 99999999999988754
No 122
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=70.31 E-value=5.5 Score=36.23 Aligned_cols=44 Identities=27% Similarity=0.232 Sum_probs=35.7
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
.+++..++.+.|..-+|+|..|||+. -+++.+||..|+..+...
T Consensus 127 ~L~~~~r~v~~l~~~~g~s~~EIA~~----l~is~~tv~~~l~Ra~~~ 170 (179)
T PRK09415 127 SLPIKYREVIYLFYYEELSIKEIAEV----TGVNENTVKTRLKKAKEL 170 (179)
T ss_pred hCCHHHhhHhHhHHhcCCCHHHHHHH----HCCCHHHHHHHHHHHHHH
Confidence 45566667777743399999999999 999999999999888643
No 123
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=70.17 E-value=6 Score=35.19 Aligned_cols=43 Identities=26% Similarity=0.235 Sum_probs=34.9
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++.....+.+..-+|++.+|||+. -+++.+||..++..+..
T Consensus 125 ~L~~~~r~i~~l~~~~~~~~~eIA~~----lgis~~tv~~~~~ra~~ 167 (179)
T PRK11924 125 ALPVKQREVFLLRYVEGLSYREIAEI----LGVPVGTVKSRLRRARQ 167 (179)
T ss_pred hCCHHHHHHhhHHHHcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 45566666776754499999999999 99999999999988754
No 124
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=70.11 E-value=5.3 Score=38.09 Aligned_cols=44 Identities=9% Similarity=0.143 Sum_probs=36.0
Q ss_pred cCCCchHHHHHHHHH----hcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWH----EDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~----~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++..++.+.|.. -+|+|..|||+. -|++.+||..++..+..
T Consensus 177 ~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~----lgis~~tVk~~~~rA~~ 224 (234)
T PRK08301 177 KKLSDREKQIMELRFGLNGGEEKTQKEVADM----LGISQSYISRLEKRIIK 224 (234)
T ss_pred HhCCHHHHHHHHHHhccCCCCCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 356677777777753 389999999999 99999999999888754
No 125
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=69.97 E-value=5.2 Score=36.54 Aligned_cols=45 Identities=31% Similarity=0.354 Sum_probs=37.5
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
..+++..++.+.|..-+|+|..|||+. -+++.+||..|+..+...
T Consensus 126 ~~Lp~~~R~~~~l~~~~gls~~EIA~~----l~i~~~tVks~l~ra~~~ 170 (182)
T COG1595 126 ARLPPRQREAFLLRYLEGLSYEEIAEI----LGISVGTVKSRLHRARKK 170 (182)
T ss_pred HhCCHHHhHHhhhHhhcCCCHHHHHHH----HCCCHHHHHHHHHHHHHH
Confidence 356667777777776689999999999 999999999999887654
No 126
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=69.93 E-value=5.9 Score=36.88 Aligned_cols=44 Identities=20% Similarity=0.240 Sum_probs=36.5
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++..++.+.|..-+|+|..|||+. -+++++||..||..+..
T Consensus 132 ~~Lp~~~r~v~~l~~~~g~s~~EIAe~----lgis~~tV~~~l~Rar~ 175 (196)
T PRK12535 132 DALPPERREALILTQVLGYTYEEAAKI----ADVRVGTIRSRVARARA 175 (196)
T ss_pred HcCCHHHHHHhhhHHHhCCCHHHHHHH----hCCCHHHHHHHHHHHHH
Confidence 356677777787765599999999999 99999999999987644
No 127
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=69.92 E-value=9.4 Score=30.63 Aligned_cols=43 Identities=12% Similarity=0.109 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHHHcCCceeee--cCccc--eEEeCcchHhhhcC
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETI--KDVYR--TVSVSQQGKQYLGS 62 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~--~~~y~--~l~LT~kg~~~L~g 62 (430)
+++.......+..|...||+...- .+..| .+.||++|++.+..
T Consensus 25 ~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~ 71 (80)
T PF13601_consen 25 GLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFER 71 (80)
T ss_dssp T--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHH
T ss_pred CcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHH
Confidence 478888999999999999999862 22223 58999999998764
No 128
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=69.84 E-value=5.9 Score=36.60 Aligned_cols=44 Identities=23% Similarity=0.207 Sum_probs=36.7
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
.+++..+..+.|..-+|+|.+|||+. -+++.+||..+|..+...
T Consensus 136 ~L~~~~r~i~~L~~~~g~s~~eIA~~----lgis~~tV~~~l~Ra~~~ 179 (196)
T PRK12524 136 ALPERQRQAVVLRHIEGLSNPEIAEV----MEIGVEAVESLTARGKRA 179 (196)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----HCcCHHHHHHHHHHHHHH
Confidence 46677777888854499999999999 999999999999887543
No 129
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=69.81 E-value=6.6 Score=35.89 Aligned_cols=44 Identities=18% Similarity=0.057 Sum_probs=35.8
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++..++.+.+..-+|+|..|||++ -|++.+||..++..+..
T Consensus 138 ~~L~~~~r~i~~l~~~~g~s~~EIA~~----lgis~~tV~~~l~Ra~~ 181 (189)
T PRK09648 138 DTLPEKQREILILRVVVGLSAEETAEA----VGSTPGAVRVAQHRALA 181 (189)
T ss_pred HhCCHHHHHHHHHHHHcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 356666777888743399999999999 99999999999887643
No 130
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=69.78 E-value=6.7 Score=36.19 Aligned_cols=43 Identities=26% Similarity=0.177 Sum_probs=35.0
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..+..+.|..-+|+|.+|||+. -|++.+||..+|..+.+
T Consensus 141 ~Lp~~~r~v~~l~~~eg~s~~EIA~~----lgis~~tVk~rl~ra~~ 183 (194)
T PRK12531 141 RLPKAQRDVLQAVYLEELPHQQVAEM----FDIPLGTVKSRLRLAVE 183 (194)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----hCcCHHHHHHHHHHHHH
Confidence 45566677777744499999999999 99999999999887754
No 131
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=69.56 E-value=6.3 Score=37.00 Aligned_cols=43 Identities=26% Similarity=0.223 Sum_probs=35.0
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.|++..+..+.|..-+|++..|||+. -|++.+||..||..+..
T Consensus 138 ~L~~~~r~v~~L~~~~g~s~~EIA~~----Lgis~~tV~~~l~RArk 180 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEGLSYEEIAAT----LGVKLGTVRSRIHRGRQ 180 (203)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 45566666666654499999999999 99999999999988843
No 132
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=69.50 E-value=2.7 Score=30.56 Aligned_cols=31 Identities=29% Similarity=0.400 Sum_probs=27.6
Q ss_pred cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 226 DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 226 ~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
.++++.|||+. -++..+|++.+|..+...|+
T Consensus 17 ~~~t~~eia~~----~gl~~stv~r~L~tL~~~g~ 47 (52)
T PF09339_consen 17 GPLTLSEIARA----LGLPKSTVHRLLQTLVEEGY 47 (52)
T ss_dssp SCEEHHHHHHH----HTS-HHHHHHHHHHHHHTTS
T ss_pred CCCCHHHHHHH----HCcCHHHHHHHHHHHHHCcC
Confidence 46789999998 99999999999999999995
No 133
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=69.38 E-value=6.3 Score=36.41 Aligned_cols=42 Identities=19% Similarity=0.131 Sum_probs=34.0
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAV 256 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i 256 (430)
.+++..++.+.|..-+|+|..|||++ -+++.+||..+|..+.
T Consensus 134 ~Lp~~~r~i~~l~~~~g~s~~EIA~~----lg~s~~tV~~rl~rar 175 (192)
T PRK09643 134 RLPVEQRAALVAVDMQGYSVADAARM----LGVAEGTVKSRCARGR 175 (192)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----HCcCHHHHHHHHHHHH
Confidence 35566677777744499999999999 9999999999987663
No 134
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=69.33 E-value=6.2 Score=35.84 Aligned_cols=44 Identities=20% Similarity=0.235 Sum_probs=36.6
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++..++.+.+..-+|+|.+|||+. -+++.+||..++..+..
T Consensus 130 ~~L~~~~r~v~~l~~~~g~s~~eIA~~----l~is~~tV~~~l~ra~~ 173 (184)
T PRK12512 130 ETLPPRQRDVVQSISVEGASIKETAAK----LSMSEGAVRVALHRGLA 173 (184)
T ss_pred HhCCHHHHHHHHHHHHcCCCHHHHHHH----hCCCHHHHHHHHHHHHH
Confidence 346667778888864499999999999 99999999999987754
No 135
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=69.29 E-value=5.7 Score=38.61 Aligned_cols=42 Identities=17% Similarity=0.314 Sum_probs=37.0
Q ss_pred hHHHHHHHHHhcC-CCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 215 AKYEAWKMWHEDG-LSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 215 t~~~T~~l~~~~G-~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
...+.+++++++| +.+.|||+. -+|..+|+..|+..+.+.|.
T Consensus 24 vRv~Il~lL~~k~plNvneiAe~----lgLpqst~s~~ik~Le~aGl 66 (308)
T COG4189 24 VRVAILQLLHRKGPLNVNEIAEA----LGLPQSTMSANIKVLEKAGL 66 (308)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHH----hCCchhhhhhhHHHHHhcCc
Confidence 4456778887777 999999999 99999999999999999995
No 136
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=69.22 E-value=6.6 Score=35.14 Aligned_cols=42 Identities=29% Similarity=0.242 Sum_probs=34.2
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
+++...+.+.+..-+|+|..|||+. -|++++||..++..+..
T Consensus 120 L~~~~r~i~~l~~~~g~s~~eiA~~----lgis~~tv~~~l~Ra~~ 161 (169)
T TIGR02954 120 LNDKYQTAIILRYYHDLTIKEIAEV----MNKPEGTVKTYLHRALK 161 (169)
T ss_pred CCHHHhHHHHHHHHcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 4555566776654499999999999 99999999999988754
No 137
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=69.17 E-value=5.9 Score=36.69 Aligned_cols=44 Identities=20% Similarity=0.169 Sum_probs=36.7
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
.|++..+..+.|..-+|+|.+|||+. -|++.+||..||..+...
T Consensus 113 ~Lp~~~r~v~~L~~~~g~s~~EIA~~----LgiS~~tVk~~l~Rar~~ 156 (188)
T PRK12546 113 QLPDEQREALILVGASGFSYEEAAEM----CGVAVGTVKSRANRARAR 156 (188)
T ss_pred hCCHHHhHHhhhHHhcCCCHHHHHHH----HCCCHHHHHHHHHHHHHH
Confidence 45666777888864499999999999 999999999999888544
No 138
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=68.90 E-value=6.5 Score=36.99 Aligned_cols=46 Identities=13% Similarity=0.029 Sum_probs=38.1
Q ss_pred ccCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 209 RTKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 209 ~~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
...+++..++.+.|..-+|+|..|||+. -+++.+||..||..+.+.
T Consensus 146 L~~L~~~~r~v~~L~~~~g~s~~EIAe~----lgis~~tV~~~l~RAr~~ 191 (206)
T PRK12544 146 LDGLPAKYARVFMMREFIELETNEICHA----VDLSVSNLNVLLYRARLR 191 (206)
T ss_pred HHhCCHHHHHHHHHHHHcCCCHHHHHHH----HCcCHHHHHHHHHHHHHH
Confidence 3457777788888865599999999999 999999999999877543
No 139
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=68.74 E-value=6.2 Score=36.00 Aligned_cols=43 Identities=21% Similarity=0.115 Sum_probs=34.2
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..++.+.|..-+|+|.+|||+. -+++.+||..++..+..
T Consensus 128 ~L~~~~r~i~~l~~~~g~s~~EIA~~----lgis~~tV~~~l~Rar~ 170 (186)
T PRK05602 128 ALPERQREAIVLQYYQGLSNIEAAAV----MDISVDALESLLARGRR 170 (186)
T ss_pred hCCHHHHHHhhHHHhcCCCHHHHHHH----hCcCHHHHHHHHHHHHH
Confidence 45566666676643399999999999 99999999999887753
No 140
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=68.59 E-value=6.8 Score=36.13 Aligned_cols=44 Identities=18% Similarity=0.191 Sum_probs=36.4
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..|++..++.+.|..-+|+|.+|||+. -+++.+||..++..+.+
T Consensus 141 ~~L~~~~r~vl~l~~~~~~s~~EIA~~----Lgis~~tVk~~l~ra~~ 184 (194)
T PRK09646 141 DALTDTQRESVTLAYYGGLTYREVAER----LAVPLGTVKTRMRDGLI 184 (194)
T ss_pred HhCCHHHHHHHHHHHHcCCCHHHHHHH----hCCChHhHHHHHHHHHH
Confidence 356677778887754499999999999 99999999999987754
No 141
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=68.57 E-value=5.4 Score=38.41 Aligned_cols=45 Identities=16% Similarity=0.087 Sum_probs=37.1
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
..|++..++.+.|..-+|+|..|||++ -+++.+||..+|..+...
T Consensus 170 ~~Lp~~~R~v~~L~~~eg~s~~EIA~~----Lgis~~tVk~~l~RAr~k 214 (233)
T PRK12538 170 QRLPEQQRIAVILSYHENMSNGEIAEV----MDTTVAAVESLLKRGRQQ 214 (233)
T ss_pred HhCCHHHHHHhhhHHhcCCCHHHHHHH----HCcCHHHHHHHHHHHHHH
Confidence 456677777777765599999999999 999999999999887543
No 142
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=68.43 E-value=7.3 Score=35.05 Aligned_cols=44 Identities=20% Similarity=0.191 Sum_probs=39.3
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
.+++...+.+.++. +|.+.++||+. .+++..||..|+..+.++-
T Consensus 143 ~lt~~E~~vl~~l~-~g~~~~~I~~~----l~~s~~tv~~~~~~l~~Kl 186 (204)
T PRK09958 143 SLSKQEISVMRYIL-DGKDNNDIAEK----MFISNKTVSTYKSRLMEKL 186 (204)
T ss_pred cCCHHHHHHHHHHH-cCCCHHHHHHH----hCCCHHHHHHHHHHHHHHc
Confidence 47777788889998 99999999998 9999999999999998765
No 143
>PRK09191 two-component response regulator; Provisional
Probab=67.96 E-value=6.3 Score=37.43 Aligned_cols=75 Identities=17% Similarity=0.188 Sum_probs=49.6
Q ss_pred ccCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC-CcchhhhhhccCCCHHHHHHHHHHHHH
Q 044490 209 RTKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF-DINWTRLCDEVGLTDEIFSAIQEAISK 287 (430)
Q Consensus 209 ~~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~-~l~~~~~i~~~~l~~e~~~~I~~a~~~ 287 (430)
...+++..++.+.|..-+|+|..|||+. -+++++||..++..+.+.-. .+...-++ +.=+......+...++.
T Consensus 86 l~~L~~~~r~v~~l~~~~~~s~~eIA~~----l~~s~~tV~~~l~ra~~~l~~~~~~~~li--idd~~~~~~~l~~~L~~ 159 (261)
T PRK09191 86 LAGLTPLPRQAFLLTALEGFSVEEAAEI----LGVDPAEAEALLDDARAEIARQVATRVLI--IEDEPIIAMDLEQLVES 159 (261)
T ss_pred HHhCCHHHhHHHHHHHHhcCCHHHHHHH----HCCCHHHHHHHHHHHHHHHhccCCCeEEE--EcCcHHHHHHHHHHHhc
Confidence 3456677788888865599999999999 99999999999988876543 12212122 11134445555555554
Q ss_pred hC
Q 044490 288 VG 289 (430)
Q Consensus 288 ~g 289 (430)
.|
T Consensus 160 ~~ 161 (261)
T PRK09191 160 LG 161 (261)
T ss_pred CC
Confidence 33
No 144
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=67.94 E-value=7.6 Score=34.87 Aligned_cols=43 Identities=19% Similarity=0.146 Sum_probs=36.7
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
++.....-+.++. +|+|.++||.. -+++..||..|+..+...=
T Consensus 150 lt~re~~vl~~l~-~g~s~~eIa~~----l~~s~~tv~~~~~~~~~kl 192 (210)
T PRK09935 150 LSNREVTILRYLV-SGLSNKEIADQ----LLLSNKTVSAHKSNIYGKL 192 (210)
T ss_pred CCHHHHHHHHHHH-cCCCHHHHHHH----hCCCHHHHHHHHHHHHHHc
Confidence 5666667777777 99999999999 9999999999999997654
No 145
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=67.53 E-value=7.4 Score=36.37 Aligned_cols=44 Identities=25% Similarity=0.100 Sum_probs=35.9
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++..++.+.|..-+|+|.+|||++ -+++.+||..++..+..
T Consensus 152 ~~L~~~~r~vl~l~~~~g~s~~EIA~~----lgis~~tV~~~l~Ra~~ 195 (206)
T PRK12526 152 EKLPEAQQTVVKGVYFQELSQEQLAQQ----LNVPLGTVKSRLRLALA 195 (206)
T ss_pred HhCCHHHHHHHHHHHHcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 346667777788744499999999999 99999999999877654
No 146
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=67.49 E-value=28 Score=29.90 Aligned_cols=92 Identities=15% Similarity=0.172 Sum_probs=61.2
Q ss_pred HHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCCCCChHHH
Q 044490 218 EAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGCKDKLKPI 297 (430)
Q Consensus 218 ~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~~~~LkpI 297 (430)
..+..+. +|.|+.++|.. -+++.+||+..+. -...|. +....--.. -++ .+.+...+....+ ..|..+
T Consensus 10 rVl~~~~-~g~s~~eaa~~----F~VS~~Tv~~W~k-~~~~G~-~~~k~r~~~-Kid---~~~L~~~v~~~pd-~tl~El 77 (119)
T PF01710_consen 10 RVLAYIE-KGKSIREAAKR----FGVSRNTVYRWLK-RKETGD-LEPKPRGRK-KID---RDELKALVEENPD-ATLREL 77 (119)
T ss_pred HHHHHHH-ccchHHHHHHH----hCcHHHHHHHHHH-hccccc-ccccccccc-ccc---HHHHHHHHHHCCC-cCHHHH
Confidence 4445555 99999999998 9999999999998 667774 332211000 122 2345566666554 788999
Q ss_pred HHhCCCCCCHHHHHHHHHHHHhCCCCCC
Q 044490 298 KNELPDDITYAHIKACLVMENCGISPEV 325 (430)
Q Consensus 298 ke~l~~~isY~~Irl~la~~~~~~~~~~ 325 (430)
.+.|+ |++..|--+| .+.|+...+
T Consensus 78 a~~l~--Vs~~ti~~~L--krlg~t~KK 101 (119)
T PF01710_consen 78 AERLG--VSPSTIWRAL--KRLGITRKK 101 (119)
T ss_pred HHHcC--CCHHHHHHHH--HHcCchhcc
Confidence 99995 8888887554 445554443
No 147
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=67.44 E-value=8.6 Score=33.87 Aligned_cols=46 Identities=20% Similarity=0.268 Sum_probs=38.4
Q ss_pred CCCchHHHHHHHHH--hcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 211 KLTPAKYEAWKMWH--EDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 211 ~l~~t~~~T~~l~~--~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
+++++..+.|..+- +.++|+++||++ -+++.|||+.-|..++..|.
T Consensus 24 GLs~~Dv~v~~~LL~~~~~~tvdelae~----lnr~rStv~rsl~~L~~~Gl 71 (126)
T COG3355 24 GLSELDVEVYKALLEENGPLTVDELAEI----LNRSRSTVYRSLQNLLEAGL 71 (126)
T ss_pred CCcHHHHHHHHHHHhhcCCcCHHHHHHH----HCccHHHHHHHHHHHHHcCC
Confidence 35566666666554 579999999999 99999999999999999995
No 148
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=67.41 E-value=8.1 Score=28.07 Aligned_cols=30 Identities=13% Similarity=0.173 Sum_probs=26.3
Q ss_pred CCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 227 GLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 227 G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
..|..+||+. -+++..||..||..+-..|.
T Consensus 15 ~it~~eLa~~----l~vS~rTi~~~i~~L~~~~~ 44 (55)
T PF08279_consen 15 PITAKELAEE----LGVSRRTIRRDIKELREWGI 44 (55)
T ss_dssp SBEHHHHHHH----CTS-HHHHHHHHHHHHHTT-
T ss_pred CcCHHHHHHH----hCCCHHHHHHHHHHHHHCCC
Confidence 3899999999 99999999999999988883
No 149
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=67.29 E-value=7.3 Score=35.70 Aligned_cols=42 Identities=19% Similarity=0.136 Sum_probs=33.5
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
+++..+..+.|..-+|++++|||.+ -|++.+||..++..+..
T Consensus 107 L~~~~r~i~~l~~~~g~~~~EIA~~----lgis~~tV~~~l~Rar~ 148 (181)
T PRK09637 107 LPEKYAEALRLTELEGLSQKEIAEK----LGLSLSGAKSRVQRGRV 148 (181)
T ss_pred CCHHHHHHHHHHHhcCCCHHHHHHH----hCCCHHHHHHHHHHHHH
Confidence 4455566776653399999999999 99999999999877743
No 150
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=67.28 E-value=5.6 Score=36.48 Aligned_cols=43 Identities=21% Similarity=0.159 Sum_probs=34.7
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++...+.+.|..-+|+|..|||+. -+++.+||..|+..+..
T Consensus 141 ~L~~~~~~v~~l~~~~g~s~~EIA~~----lgis~~tV~~~l~Ra~~ 183 (194)
T PRK12519 141 QLPESQRQVLELAYYEGLSQSEIAKR----LGIPLGTVKARARQGLL 183 (194)
T ss_pred hCCHHHhhhhhhhhhcCCCHHHHHHH----hCCCHHHHHHHHHHHHH
Confidence 45566667776643399999999999 99999999999988754
No 151
>PF13730 HTH_36: Helix-turn-helix domain
Probab=67.25 E-value=10 Score=27.55 Aligned_cols=28 Identities=21% Similarity=0.248 Sum_probs=26.1
Q ss_pred CHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 229 SIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 229 si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
|.+.||+. -+++..||..++.++...|.
T Consensus 27 S~~~la~~----~g~s~~Tv~~~i~~L~~~G~ 54 (55)
T PF13730_consen 27 SQETLAKD----LGVSRRTVQRAIKELEEKGL 54 (55)
T ss_pred CHHHHHHH----HCcCHHHHHHHHHHHHHCcC
Confidence 78999998 99999999999999999984
No 152
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=67.11 E-value=7.8 Score=35.73 Aligned_cols=44 Identities=27% Similarity=0.320 Sum_probs=35.7
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
.|++..+..+.|..-+|++..|||+. -+++.+||..||..+...
T Consensus 128 ~Lp~~~r~v~~l~~~~g~s~~EIA~~----lgis~~tV~~~l~Rar~~ 171 (188)
T PRK12517 128 KLDPEYREPLLLQVIGGFSGEEIAEI----LDLNKNTVMTRLFRARNQ 171 (188)
T ss_pred hCCHHHHHHHHHHHHhCCCHHHHHHH----HCCCHHHHHHHHHHHHHH
Confidence 45566666776764499999999999 999999999999887543
No 153
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=66.98 E-value=3.5 Score=37.91 Aligned_cols=44 Identities=23% Similarity=0.321 Sum_probs=35.3
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
.+++..++.+.|..-+|+|..|||++ -|++.+||..++..+...
T Consensus 139 ~L~~~~r~i~~l~~~~g~s~~EIA~~----lgis~~tV~~~l~ra~~~ 182 (194)
T PRK12513 139 TLPDEQREVFLLREHGDLELEEIAEL----TGVPEETVKSRLRYALQK 182 (194)
T ss_pred hCCHhHhhheeeehccCCCHHHHHHH----HCCCHHHHHHHHHHHHHH
Confidence 45666667777743399999999999 999999999998877543
No 154
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=66.87 E-value=7.9 Score=35.24 Aligned_cols=42 Identities=17% Similarity=0.278 Sum_probs=32.3
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
+++.....+.+..-+|+|.+|||.. -|++.+||..+|..+..
T Consensus 138 L~~~~r~i~~l~~~~g~s~~eIA~~----lgis~~~v~~~l~Rar~ 179 (187)
T PRK12534 138 LEPPRSELIRTAFFEGITYEELAAR----TDTPIGTVKSWIRRGLA 179 (187)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHH----hCCChhHHHHHHHHHHH
Confidence 3344444555543399999999999 99999999999988754
No 155
>PF13932 GIDA_assoc_3: GidA associated domain 3; PDB: 3CES_C 3CP2_A 3G05_A 3CP8_A 2ZXI_B 2ZXH_A.
Probab=66.68 E-value=7 Score=30.90 Aligned_cols=32 Identities=22% Similarity=0.344 Sum_probs=24.0
Q ss_pred cchHHHHHHHHhCCCCHHHHhccCCCCHHHHH
Q 044490 136 CGDQTIKKIALARPSTKARLANIDGVNQHLVI 167 (430)
Q Consensus 136 fsd~tL~emA~~~P~T~~eL~~I~Gvg~~k~~ 167 (430)
++......+...+|.|..+..+|+||++.-+.
T Consensus 37 LS~E~~ekL~~~rP~Ti~~A~rI~GvtPa~i~ 68 (72)
T PF13932_consen 37 LSNEAREKLEKIRPRTIGQASRIPGVTPAAIS 68 (72)
T ss_dssp --CHHHHHHHHH--SCHHHHTTSTTS-HHHHH
T ss_pred cHHHHHHHHHhcCCCCHHHHHhCCCCCHHHHH
Confidence 45777888999999999999999999998653
No 156
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=66.33 E-value=9.6 Score=33.06 Aligned_cols=43 Identities=9% Similarity=0.098 Sum_probs=36.1
Q ss_pred chHHHHHHHHHh-cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 214 PAKYEAWKMWHE-DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 214 ~t~~~T~~l~~~-~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
++....+.++.. .++++.+||+. -+++.+||..||..+...|.
T Consensus 16 ptRl~IL~~L~~~~~~~v~ela~~----l~lsqstvS~HL~~L~~AGL 59 (117)
T PRK10141 16 ETRLGIVLLLRESGELCVCDLCTA----LDQSQPKISRHLALLRESGL 59 (117)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHH----HCcCHHHHHHHHHHHHHCCc
Confidence 455566776653 46899999998 99999999999999999995
No 157
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=66.07 E-value=12 Score=30.34 Aligned_cols=44 Identities=16% Similarity=0.115 Sum_probs=33.3
Q ss_pred CCCCCHHHHHHHHHHHHHcCCceeeecCccc---eEEeCcchHhhhc
Q 044490 18 GKDHSSNWWKTLAYQLISYGYLTETIKDVYR---TVSVSQQGKQYLG 61 (430)
Q Consensus 18 Gk~ls~~~wk~li~qLi~~GyL~e~~~~~y~---~l~LT~kg~~~L~ 61 (430)
.++.|...+.+-++.|...|++........+ .+.||++|.+++.
T Consensus 28 l~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~~ 74 (90)
T PF01638_consen 28 LPGISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELLP 74 (90)
T ss_dssp STTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHHH
T ss_pred cchhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHHH
Confidence 3468999999999999999999886322223 4899999999874
No 158
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=65.94 E-value=10 Score=33.42 Aligned_cols=39 Identities=18% Similarity=0.189 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhc
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLG 61 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~ 61 (430)
+++...+...++.|...|||... .++.+.||++|+.+..
T Consensus 33 ~vs~~svs~~l~~L~~~Gli~~~---~~~~i~LT~~G~~~a~ 71 (142)
T PRK03902 33 SVHPSSVTKMVQKLDKDEYLIYE---KYRGLVLTPKGKKIGK 71 (142)
T ss_pred CCChhHHHHHHHHHHHCCCEEEe---cCceEEECHHHHHHHH
Confidence 46889999999999999999854 3468999999998754
No 159
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=65.67 E-value=8 Score=35.00 Aligned_cols=42 Identities=21% Similarity=0.236 Sum_probs=34.0
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
+++..+..+.+..-.|+|..|||.+ -+++.+||..++..+..
T Consensus 141 L~~~~r~vi~l~~~~g~s~~eIA~~----lgis~~~v~~~l~Ra~~ 182 (189)
T TIGR02984 141 LPEDYREVILLRHLEGLSFAEVAER----MDRSEGAVSMLWVRGLA 182 (189)
T ss_pred CCHHHHHHHHHHHhcCCCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 4556667777733399999999999 99999999999887754
No 160
>PRK04841 transcriptional regulator MalT; Provisional
Probab=65.58 E-value=6.9 Score=44.49 Aligned_cols=44 Identities=16% Similarity=0.166 Sum_probs=39.6
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
.+|+...+...++. +|+|-.|||.. .+++.+||..|+..++.+=
T Consensus 838 ~lt~~e~~v~~~~~-~g~~~~~ia~~----l~~s~~tv~~h~~~~~~kl 881 (903)
T PRK04841 838 PLTQREWQVLGLIY-SGYSNEQIAGE----LDVAATTIKTHIRNLYQKL 881 (903)
T ss_pred CCCHHHHHHHHHHH-cCCCHHHHHHH----hCCCHHHHHHHHHHHHHHh
Confidence 47888888999988 99999999999 9999999999999987654
No 161
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=65.22 E-value=11 Score=28.57 Aligned_cols=31 Identities=13% Similarity=0.220 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHcCCceeeecCccceEEeCcchH
Q 044490 23 SNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGK 57 (430)
Q Consensus 23 ~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~ 57 (430)
.+.|...+..|+..|+|..+ + ..+.||++|+
T Consensus 35 ~~~~~~~l~~l~~~Gll~~~-~---~~l~lT~~G~ 65 (66)
T PF06969_consen 35 AEEFQKELEELQEDGLLEID-G---GRLRLTEKGR 65 (66)
T ss_dssp HHH-HHHHHHHHHTTSEEE--S---SEEEE-TTTG
T ss_pred HHHHHHHHHHHHHCCCEEEe-C---CEEEECcccC
Confidence 45568889999999999876 3 6899999996
No 162
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=64.81 E-value=11 Score=30.17 Aligned_cols=43 Identities=14% Similarity=0.152 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHHcCCceeeecC----ccceEEeCcchHhhhcCC
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETIKD----VYRTVSVSQQGKQYLGSA 63 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~~~----~y~~l~LT~kg~~~L~g~ 63 (430)
+++...+...++.|...|||... .+ ....+.||++|+.++...
T Consensus 35 ~~s~~~i~~~l~~L~~~g~v~~~-~~~~~~r~~~~~lT~~g~~~~~~~ 81 (101)
T smart00347 35 GVSPSTVTRVLDRLEKKGLIRRL-PSPEDRRSVLVSLTEEGRELIEEL 81 (101)
T ss_pred CCCchhHHHHHHHHHHCCCeEec-CCCCCCCeEEEEECHhHHHHHHHH
Confidence 46788899999999999999876 22 223689999999988753
No 163
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=64.20 E-value=7.8 Score=37.02 Aligned_cols=44 Identities=18% Similarity=0.069 Sum_probs=35.9
Q ss_pred cCCCchHHHHHHHHH----hcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWH----EDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~----~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++..++.+.+.. -+|+|.+|||++ -|++.+||..|+..+..
T Consensus 174 ~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~----lgis~~tV~~~~~rA~~ 221 (233)
T PRK05803 174 DILDEREKEVIEMRYGLGNGKEKTQREIAKA----LGISRSYVSRIEKRALK 221 (233)
T ss_pred HhCCHHHHHHHHHHhCCCCCCCcCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 356677778888744 389999999999 99999999999877653
No 164
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=64.16 E-value=37 Score=32.71 Aligned_cols=99 Identities=17% Similarity=0.226 Sum_probs=61.9
Q ss_pred CCHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHhhccCC--CCCcCcccccccccceecccccCCCchHHHHHHHHHhcC
Q 044490 150 STKARLANIDGVNQHLVITHGDHLLQTIRHLSQKLNLSL--DGKVGEHTAFTRKLHVVVNTRTKLTPAKYEAWKMWHEDG 227 (430)
Q Consensus 150 ~T~~eL~~I~Gvg~~k~~kyG~~fL~~I~~~~~e~~~~~--~~~~~~~~~~~~~~~~~~~~~~~l~~t~~~T~~l~~~~G 227 (430)
.|.+||..|-|++..-+.++ |..|.++++.-. -.... .....++. +.....+|. +|
T Consensus 106 LT~~Dla~LL~~S~~TI~~~-------i~~yq~e~g~vvPtrG~i~-------------DiGp~~tH-K~~ii~~~l-~g 163 (220)
T PF07900_consen 106 LTQEDLAMLLGISPRTISKD-------IKEYQKEHGVVVPTRGTIH-------------DIGPGVTH-KKIIIRLYL-KG 163 (220)
T ss_pred ccHHHHHHHHCCCHHHHHHH-------HHHHHHHcCceeccCCccc-------------ccCCcchH-HHHHHHHHH-cC
Confidence 46677777788888777664 677777777322 11110 00111222 246688898 99
Q ss_pred CCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHH
Q 044490 228 LSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAI 281 (430)
Q Consensus 228 ~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I 281 (430)
++..|||.. -.-++..|..|+..+-+--. |-.-|++.+++..+
T Consensus 164 ~~~~eiar~----t~HS~~av~rYi~~F~rV~~-------l~~~~~~~~eia~~ 206 (220)
T PF07900_consen 164 KPTPEIARR----TNHSPEAVDRYIKDFKRVLM-------LYEKGMSPEEIAFI 206 (220)
T ss_pred CCHHHHHHH----hccCHHHHHHHHHhhHHhHH-------HHHcCCCHHHHHHH
Confidence 999999987 88899999888876654332 22234466665555
No 165
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=64.07 E-value=9.6 Score=34.85 Aligned_cols=42 Identities=26% Similarity=0.275 Sum_probs=35.2
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAV 256 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i 256 (430)
.+++..++.+.|..-+|+|..|||+. -+++++||..+|..+.
T Consensus 131 ~L~~~~r~vl~l~~~~~~s~~eIA~~----lgis~~tV~~~l~Rar 172 (189)
T PRK12515 131 KLSPAHREIIDLVYYHEKSVEEVGEI----VGIPESTVKTRMFYAR 172 (189)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----HCcCHHHHHHHHHHHH
Confidence 46667778887754499999999999 9999999999987764
No 166
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=64.03 E-value=5.8 Score=34.48 Aligned_cols=35 Identities=20% Similarity=0.086 Sum_probs=29.2
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVV 249 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~ 249 (430)
.|++..++.+.|..-+|+|.+|||++ -+++++||.
T Consensus 107 ~Lp~~~r~v~~l~~~~~~s~~EIA~~----l~is~~tV~ 141 (142)
T TIGR03209 107 ILPNKQKKIIYMKFFEDMKEIDIAKK----LHISRQSVY 141 (142)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----HCcCHHhhc
Confidence 35566778888865599999999999 999999984
No 167
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=63.83 E-value=7.1 Score=30.24 Aligned_cols=40 Identities=13% Similarity=0.104 Sum_probs=33.7
Q ss_pred CCCCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhh
Q 044490 18 GKDHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYL 60 (430)
Q Consensus 18 Gk~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L 60 (430)
|-++|+..+.+.++.|-.+||+... .|..-.+|++|.+.|
T Consensus 27 g~~~se~avRrrLr~me~~Glt~~~---g~~G~~iT~~G~~~L 66 (66)
T PF08461_consen 27 GEELSEEAVRRRLRAMERDGLTRKV---GRQGRIITEKGLDEL 66 (66)
T ss_pred ChhhhHHHHHHHHHHHHHCCCcccc---CCcccccCHHHHhhC
Confidence 6678999999999999999977743 466679999998875
No 168
>PHA00738 putative HTH transcription regulator
Probab=63.52 E-value=13 Score=31.90 Aligned_cols=44 Identities=18% Similarity=0.144 Sum_probs=36.8
Q ss_pred CchHHHHHHHHHhc-CCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 213 TPAKYEAWKMWHED-GLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 213 ~~t~~~T~~l~~~~-G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
.++.+..+.++... ++++.+||+. -+++.+||..||..+-..|.
T Consensus 11 dptRr~IL~lL~~~e~~~V~eLae~----l~lSQptVS~HLKvLreAGL 55 (108)
T PHA00738 11 KILRRKILELIAENYILSASLISHT----LLLSYTTVLRHLKILNEQGY 55 (108)
T ss_pred CHHHHHHHHHHHHcCCccHHHHHHh----hCCCHHHHHHHHHHHHHCCc
Confidence 35666777777633 4999999998 89999999999999999995
No 169
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=63.31 E-value=9 Score=34.17 Aligned_cols=43 Identities=16% Similarity=0.117 Sum_probs=34.8
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..++.+.|..-+|+|.+|||.+ -+++.+||..+|..+-.
T Consensus 108 ~L~~~~r~v~~l~~~~g~s~~eIA~~----lgis~~tv~~~l~Rar~ 150 (165)
T PRK09644 108 TLPVIEAQAILLCDVHELTYEEAASV----LDLKLNTYKSHLFRGRK 150 (165)
T ss_pred hCCHHHHHHHHhHHHhcCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 35566677787754499999999999 99999999998887643
No 170
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=63.21 E-value=9.5 Score=35.25 Aligned_cols=41 Identities=22% Similarity=0.243 Sum_probs=33.2
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
+++..+..+.++. +|+|..|||+. -|++.+||..++..+..
T Consensus 156 L~~~~r~vl~l~~-e~~s~~EIA~~----lgis~~tV~~~l~rar~ 196 (208)
T PRK08295 156 LSELEKEVLELYL-DGKSYQEIAEE----LNRHVKSIDNALQRVKR 196 (208)
T ss_pred CCHHHHHHHHHHH-ccCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 4455566777766 99999999999 99999999988877643
No 171
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=63.03 E-value=8.4 Score=37.19 Aligned_cols=43 Identities=19% Similarity=0.134 Sum_probs=34.2
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
+++..+..+.|..-+|+|..|||+. -|++++||..||..+.+.
T Consensus 117 Lp~~~R~v~lL~~~eg~S~~EIAe~----LgiS~~tVksrL~Rark~ 159 (228)
T PRK06704 117 LNVQQSAILLLKDVFQYSIADIAKV----CSVSEGAVKASLFRSRNR 159 (228)
T ss_pred CCHHHhhHhhhHHhhCCCHHHHHHH----HCcCHHHHHHHHHHHHHH
Confidence 4455566777754489999999999 999999999998777553
No 172
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=62.54 E-value=13 Score=30.66 Aligned_cols=45 Identities=16% Similarity=0.152 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHHcCCceeee--cCc-cceEEeCcchHhhhcCCC
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETI--KDV-YRTVSVSQQGKQYLGSAR 64 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~--~~~-y~~l~LT~kg~~~L~g~~ 64 (430)
.+++..+.++++.|...||+.... .+. -..+.||++|++++..-.
T Consensus 47 ~i~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~ 94 (126)
T COG1846 47 GLDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQLL 94 (126)
T ss_pred CCCHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHhc
Confidence 478899999999999999999873 111 236899999999998653
No 173
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=62.50 E-value=12 Score=32.85 Aligned_cols=43 Identities=7% Similarity=0.091 Sum_probs=34.3
Q ss_pred CCHHHHHHHHHHHHHcCCceeee-cCcc--ceEEeCcchHhhhcCC
Q 044490 21 HSSNWWKTLAYQLISYGYLTETI-KDVY--RTVSVSQQGKQYLGSA 63 (430)
Q Consensus 21 ls~~~wk~li~qLi~~GyL~e~~-~~~y--~~l~LT~kg~~~L~g~ 63 (430)
+++.-+.++++.|...|||.... ..+- ..|.||++|++++..-
T Consensus 58 ~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~ 103 (144)
T PRK03573 58 IEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEV 103 (144)
T ss_pred CChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHHH
Confidence 67888999999999999999862 1111 3689999999998853
No 174
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=62.32 E-value=10 Score=32.08 Aligned_cols=42 Identities=31% Similarity=0.268 Sum_probs=32.7
Q ss_pred CCCchHHHHHHHH-HhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMW-HEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~-~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++.....+.+. . .|+|..+||+. -+++++||..++..+..
T Consensus 110 ~L~~~~~~ii~~~~~-~g~s~~eIA~~----l~~s~~~v~~~~~~~~~ 152 (158)
T TIGR02937 110 KLPEREREVLVLRYL-EGLSYKEIAEI----LGISVGTVKRRLKRARK 152 (158)
T ss_pred hCCHHHHHHHhhHHh-cCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 3444555555554 5 89999999999 99999999999988753
No 175
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=61.83 E-value=4.5 Score=37.38 Aligned_cols=33 Identities=30% Similarity=0.330 Sum_probs=29.5
Q ss_pred HhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 224 HEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 224 ~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
.+.|+|+.+||.. -|.+++||..||..--.+|.
T Consensus 58 ekag~Ti~EIAee----lG~TeqTir~hlkgetkAG~ 90 (182)
T COG1318 58 EKAGMTISEIAEE----LGRTEQTVRNHLKGETKAGQ 90 (182)
T ss_pred HHccCcHHHHHHH----hCCCHHHHHHHHhcchhhhh
Confidence 3479999999999 99999999999998888775
No 176
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=61.71 E-value=5.3 Score=35.89 Aligned_cols=42 Identities=21% Similarity=0.231 Sum_probs=33.3
Q ss_pred CCchHHHHHHH-HHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 212 LTPAKYEAWKM-WHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 212 l~~t~~~T~~l-~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
+++.....+.| +. .|+|.++||+. -+++.+||..++..+...
T Consensus 127 L~~~~r~v~~l~~~-~g~s~~eIA~~----l~is~~~V~~~l~ra~~~ 169 (176)
T PRK09638 127 LDPEFRAPVILKHY-YGYTYEEIAKM----LNIPEGTVKSRVHHGIKQ 169 (176)
T ss_pred CCHHHhheeeehhh-cCCCHHHHHHH----HCCChhHHHHHHHHHHHH
Confidence 44555555555 44 89999999999 999999999999887653
No 177
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=61.17 E-value=10 Score=36.30 Aligned_cols=44 Identities=14% Similarity=0.236 Sum_probs=37.0
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++..+..+.+..-+|+|..|||.. -|++.+||..++..+..
T Consensus 183 ~~L~~~~r~vl~l~~~~g~s~~EIA~~----lgis~~tV~~~~~ra~~ 226 (236)
T PRK06986 183 ESLPEREQLVLSLYYQEELNLKEIGAV----LGVSESRVSQIHSQAIK 226 (236)
T ss_pred HhCCHHHHHHHHhHhccCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 456777778887755599999999999 99999999999887754
No 178
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=60.81 E-value=14 Score=32.54 Aligned_cols=43 Identities=9% Similarity=0.071 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHHcCCceeee-cCc--cceEEeCcchHhhhcC
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETI-KDV--YRTVSVSQQGKQYLGS 62 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~-~~~--y~~l~LT~kg~~~L~g 62 (430)
.+++..+-++++.|...|||.... .++ -..|.||++|++++..
T Consensus 65 ~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~ 110 (144)
T PRK11512 65 SVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQ 110 (144)
T ss_pred CCCHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHH
Confidence 368888999999999999999762 111 2358999999998864
No 179
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=60.72 E-value=11 Score=36.13 Aligned_cols=44 Identities=9% Similarity=0.105 Sum_probs=35.6
Q ss_pred cCCCchHHHHHHHHH----hcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWH----EDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~----~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++..+..+.|.. .+|+|..|||+. -|++++||..|+..+..
T Consensus 177 ~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~----Lgis~~tV~~~l~ra~~ 224 (234)
T TIGR02835 177 AKLNDREKKIMELRFGLVGGTEKTQKEVADM----LGISQSYISRLEKRILK 224 (234)
T ss_pred HhCCHHHHHHHHHHHccCCCCCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 456777777777754 279999999999 99999999999877643
No 180
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=60.48 E-value=12 Score=28.78 Aligned_cols=37 Identities=19% Similarity=0.436 Sum_probs=29.7
Q ss_pred CCchHHHHHHHHHhc--CCCHHHHhcCCCCCCCCChhhHHHHH
Q 044490 212 LTPAKYEAWKMWHED--GLSIQKIANYPGRSAPIKEQTVVDYL 252 (430)
Q Consensus 212 l~~t~~~T~~l~~~~--G~si~eIA~~~~r~R~L~~sTI~~HL 252 (430)
-+|.....+++|.+. ++++.+||++ -+++.+||...-
T Consensus 5 Rsp~rdkA~e~y~~~~g~i~lkdIA~~----Lgvs~~tIr~WK 43 (60)
T PF10668_consen 5 RSPNRDKAFEIYKESNGKIKLKDIAEK----LGVSESTIRKWK 43 (60)
T ss_pred CCcCHHHHHHHHHHhCCCccHHHHHHH----HCCCHHHHHHHh
Confidence 356677888888743 6899999999 999999997554
No 181
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=60.43 E-value=14 Score=28.25 Aligned_cols=40 Identities=13% Similarity=0.148 Sum_probs=32.7
Q ss_pred HHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCc
Q 044490 219 AWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDI 262 (430)
Q Consensus 219 T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l 262 (430)
.+.++.+...+..+||+. -+++.+||..|+..+...|..+
T Consensus 5 il~~L~~~~~~~~eLa~~----l~vS~~tv~~~l~~L~~~g~~i 44 (69)
T TIGR00122 5 LLALLADNPFSGEKLGEA----LGMSRTAVNKHIQTLREWGVDV 44 (69)
T ss_pred HHHHHHcCCcCHHHHHHH----HCCCHHHHHHHHHHHHHCCCeE
Confidence 344455456789999998 9999999999999999988644
No 182
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=59.35 E-value=12 Score=34.49 Aligned_cols=41 Identities=32% Similarity=0.366 Sum_probs=32.5
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHH
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAV 256 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i 256 (430)
+.+...+.+.+..-.|+|.+|||+. -|+++.||...+..+-
T Consensus 136 l~~~~~~~v~l~~~~Gls~~EIA~~----lgiS~~tV~r~l~~aR 176 (185)
T PF07638_consen 136 LDPRQRRVVELRFFEGLSVEEIAER----LGISERTVRRRLRRAR 176 (185)
T ss_pred cCHHHHHHHHHHHHCCCCHHHHHHH----HCcCHHHHHHHHHHHH
Confidence 5556666666643399999999999 9999999998877653
No 183
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=59.26 E-value=12 Score=36.16 Aligned_cols=44 Identities=14% Similarity=0.078 Sum_probs=36.4
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++..+..+.|..-+|+|..|||+. -+++++||..++..+..
T Consensus 204 ~~L~~~~r~vl~l~~~~g~s~~eIA~~----l~is~~tV~~~~~ra~~ 247 (257)
T PRK08583 204 PVLSDREKSIIQCTFIENLSQKETGER----LGISQMHVSRLQRQAIK 247 (257)
T ss_pred HhCCHHHHHHHHHHHhCCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 356777778888854599999999999 99999999998876654
No 184
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=59.09 E-value=11 Score=35.85 Aligned_cols=44 Identities=18% Similarity=0.070 Sum_probs=34.4
Q ss_pred cCCCchHHHHHHHHH----hcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWH----EDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~----~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++..++.+.|.. .+|+|.+|||++ -+++++||..|+..+.+
T Consensus 173 ~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~----lgis~~tV~~~~~rAl~ 220 (227)
T TIGR02846 173 SVLDGREREVIEMRYGLGDGRRKTQREIAKI----LGISRSYVSRIEKRALM 220 (227)
T ss_pred HhCCHHHHHHHHHHHcCCCCCCcCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 345666666777653 289999999999 99999999999877643
No 185
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=58.27 E-value=13 Score=34.46 Aligned_cols=45 Identities=20% Similarity=0.262 Sum_probs=33.9
Q ss_pred CCchHHHHHHHHHh----c--CCCHHHHhcCCCCCCCCC-hhhHHHHHHHHHHcCC
Q 044490 212 LTPAKYEAWKMWHE----D--GLSIQKIANYPGRSAPIK-EQTVVDYLLEAVSEGF 260 (430)
Q Consensus 212 l~~t~~~T~~l~~~----~--G~si~eIA~~~~r~R~L~-~sTI~~HL~~~i~~G~ 260 (430)
+++...+.+..++. . ..|+.|||+. -+++ .+||..||..+.+.|.
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~----~~~~s~~tv~~~l~~L~~~g~ 55 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPSIREIARA----VGLRSPSAAEEHLKALERKGY 55 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHH----hCCCChHHHHHHHHHHHHCCC
Confidence 44454455554441 2 2677799998 9998 9999999999999996
No 186
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=57.81 E-value=13 Score=26.08 Aligned_cols=32 Identities=19% Similarity=0.313 Sum_probs=29.1
Q ss_pred hcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 225 EDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 225 ~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
+.+.++.+||+. -+++.+||..+|..+...|.
T Consensus 12 ~~~~s~~~l~~~----l~~s~~tv~~~l~~L~~~g~ 43 (53)
T smart00420 12 QGKVSVEELAEL----LGVSEMTIRRDLNKLEEQGL 43 (53)
T ss_pred cCCcCHHHHHHH----HCCCHHHHHHHHHHHHHCCC
Confidence 367999999998 89999999999999999985
No 187
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=57.51 E-value=18 Score=29.24 Aligned_cols=40 Identities=13% Similarity=0.175 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhcC
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLGS 62 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~g 62 (430)
++++.-+.++++.|...|||... .+ ..+.||++|..+...
T Consensus 10 ~is~stvs~~l~~L~~~glI~r~-~~--~~~~lT~~g~~~~~~ 49 (96)
T smart00529 10 NVSPPTVTQMLKKLEKDGLVEYE-PY--RGITLTEKGRRLARR 49 (96)
T ss_pred CCChHHHHHHHHHHHHCCCEEEc-CC--CceEechhHHHHHHH
Confidence 47889999999999999999986 43 579999999998754
No 188
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=57.19 E-value=14 Score=33.47 Aligned_cols=43 Identities=14% Similarity=0.090 Sum_probs=34.2
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++...+.+.|..-.|+|.+|||+. -|++.+||..++..+..
T Consensus 136 ~L~~~~r~il~l~~~~~~s~~eIA~~----lgis~~~v~~~l~Rar~ 178 (187)
T PRK09641 136 QLPEKYRTVIVLKYIEDLSLKEISEI----LDLPVGTVKTRIHRGRE 178 (187)
T ss_pred hCCHHHHHHhhhHHhhCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 34555667776654499999999999 99999999999887644
No 189
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=57.12 E-value=26 Score=34.52 Aligned_cols=88 Identities=14% Similarity=0.119 Sum_probs=54.4
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHH-HHhC
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAI-SKVG 289 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~-~~~g 289 (430)
.|++..+..+.|..-.|+|..|||++ -+++++||..++..+...=... ..++- .+++....+..++ ....
T Consensus 108 ~L~~~~R~v~~L~~~~g~s~~EIA~~----lg~s~~tVr~~l~RAr~~Lr~~-~~~~~----~~~~~~~~~~~~f~~a~~ 178 (281)
T TIGR02957 108 RLSPLERAVFVLREVFDYPYEEIASI----VGKSEANCRQLVSRARRHLDAR-RPRFE----VSREESRQLLERFVEAAQ 178 (281)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHH----HCCCHHHHHHHHHHHHHHHHhh-CCCCC----CChHHHHHHHHHHHHHHH
Confidence 35667777888865599999999999 9999999999998876543211 11111 1333333333322 2222
Q ss_pred CCCChHHHHHhCCCCCCHH
Q 044490 290 CKDKLKPIKNELPDDITYA 308 (430)
Q Consensus 290 ~~~~LkpIke~l~~~isY~ 308 (430)
...+..+...|.+++.+.
T Consensus 179 -~gD~~~l~~lL~~dv~~~ 196 (281)
T TIGR02957 179 -TGDLDGLLELLAEDVVLY 196 (281)
T ss_pred -hCCHHHHHHHHhhceEEE
Confidence 134666777777766443
No 190
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=57.10 E-value=15 Score=35.59 Aligned_cols=44 Identities=9% Similarity=0.182 Sum_probs=37.0
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++..++.+.|..-+|+|..|||.+ -+++.+||..++..+..
T Consensus 200 ~~L~~~~r~vl~l~~~~~~s~~EIA~~----lgis~~tV~~~~~ra~~ 243 (251)
T PRK07670 200 KQLSEKEQLVISLFYKEELTLTEIGQV----LNLSTSRISQIHSKALF 243 (251)
T ss_pred hcCCHHHHHHHHHHHhcCCCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 456777788888865599999999999 99999999999877654
No 191
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=56.42 E-value=15 Score=27.04 Aligned_cols=29 Identities=21% Similarity=0.264 Sum_probs=26.8
Q ss_pred CCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 228 LSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 228 ~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
+++.+||+. -+++.+||...+..+...|.
T Consensus 22 ~t~~~la~~----l~~~~~~vs~~v~~L~~~Gl 50 (62)
T PF12802_consen 22 LTQSELAER----LGISKSTVSRIVKRLEKKGL 50 (62)
T ss_dssp EEHHHHHHH----HTS-HHHHHHHHHHHHHTTS
T ss_pred cCHHHHHHH----HCcCHHHHHHHHHHHHHCCC
Confidence 799999999 99999999999999999995
No 192
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=56.18 E-value=22 Score=29.55 Aligned_cols=24 Identities=13% Similarity=-0.001 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHHHHHHHcCCceee
Q 044490 19 KDHSSNWWKTLAYQLISYGYLTET 42 (430)
Q Consensus 19 k~ls~~~wk~li~qLi~~GyL~e~ 42 (430)
-.++.+++..+++.|...|+|+..
T Consensus 31 l~~~~~~v~~~l~~Le~~GLler~ 54 (92)
T PF10007_consen 31 LKIPLEEVREALEKLEEMGLLERV 54 (92)
T ss_pred HCCCHHHHHHHHHHHHHCCCeEEe
Confidence 368899999999999999999987
No 193
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=55.76 E-value=6.9 Score=35.86 Aligned_cols=40 Identities=18% Similarity=0.128 Sum_probs=30.9
Q ss_pred chHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 214 PAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 214 ~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
+..+..+.|..-+|+|.+|||+. -+++.+||..++..+..
T Consensus 137 ~~~r~v~~l~~~~g~s~~EIA~~----lgis~~tV~~~l~Ra~~ 176 (188)
T PRK09640 137 PIDREILVLRFVAELEFQEIADI----MHMGLSATKMRYKRALD 176 (188)
T ss_pred hhheeeeeeHHhcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 33344555543399999999999 99999999999988753
No 194
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=55.67 E-value=7.1 Score=35.06 Aligned_cols=42 Identities=21% Similarity=0.150 Sum_probs=32.6
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
+++..+..+.|..-+|+|.+|||+. -|++.+||..++..+..
T Consensus 121 L~~~~r~vl~l~~~~g~s~~eIA~~----lg~s~~tv~~~l~Rar~ 162 (175)
T PRK12518 121 LSLEHRAVLVLHDLEDLPQKEIAEI----LNIPVGTVKSRLFYARR 162 (175)
T ss_pred CCHHHeeeeeehHhcCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 4445556666633399999999999 99999999999877643
No 195
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=55.54 E-value=21 Score=34.35 Aligned_cols=44 Identities=25% Similarity=0.264 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhcCC
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLGSA 63 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~g~ 63 (430)
++|.....+.++.|...|||..........+.||++|+++|...
T Consensus 32 ~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~~ 75 (217)
T PRK14165 32 GTSSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYNE 75 (217)
T ss_pred CcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHHH
Confidence 47899999999999999999876323346799999999998654
No 196
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=55.21 E-value=16 Score=34.56 Aligned_cols=44 Identities=16% Similarity=0.109 Sum_probs=36.5
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++.....+.+..-+|+|+.|||+. -+++.+||..++..+..
T Consensus 177 ~~L~~~~r~vl~l~y~~~~s~~eIA~~----lgis~~~v~~~~~ra~~ 220 (227)
T TIGR02980 177 AALPERERRILLLRFFEDKTQSEIAER----LGISQMHVSRLLRRALK 220 (227)
T ss_pred HcCCHHHHHHHHHHHhcCCCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 457777777777764489999999999 99999999999887654
No 197
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=55.18 E-value=22 Score=28.24 Aligned_cols=38 Identities=18% Similarity=0.290 Sum_probs=31.8
Q ss_pred HHHHHHh--cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 219 AWKMWHE--DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 219 T~~l~~~--~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
.++++.+ .++++.+||+. -+++.+||..+|..+...|.
T Consensus 10 Il~~l~~~~~~~t~~~ia~~----l~i~~~tv~r~l~~L~~~g~ 49 (91)
T smart00346 10 VLRALAEEPGGLTLAELAER----LGLSKSTAHRLLNTLQELGY 49 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHH----hCCCHHHHHHHHHHHHHCCC
Confidence 3444432 36999999999 99999999999999999996
No 198
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=55.11 E-value=18 Score=30.58 Aligned_cols=44 Identities=14% Similarity=0.052 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHHHcCCceeee-cCc--cceEEeCcchHhhhcCC
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETI-KDV--YRTVSVSQQGKQYLGSA 63 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~-~~~--y~~l~LT~kg~~~L~g~ 63 (430)
.+++..+-.+++.|...|||.... ..+ -..+.||++|++++..-
T Consensus 53 ~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~ 99 (118)
T TIGR02337 53 CILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYASL 99 (118)
T ss_pred CCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHh
Confidence 367778899999999999999862 111 13689999999999854
No 199
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=54.97 E-value=13 Score=33.69 Aligned_cols=43 Identities=23% Similarity=0.186 Sum_probs=33.3
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++..+..+.|..-+|+|..|||+. -|++.+||..++..+-.
T Consensus 138 ~L~~~~r~v~~l~~~~~~s~~EIA~~----lgis~~tv~~~l~rar~ 180 (190)
T TIGR02939 138 ALPEDLRTAITLRELEGLSYEDIARI----MDCPVGTVRSRIFRARE 180 (190)
T ss_pred cCCHHHhhhhhhhhhcCCCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 34455556666643399999999999 99999999999877643
No 200
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=54.62 E-value=17 Score=34.39 Aligned_cols=44 Identities=14% Similarity=0.210 Sum_probs=36.8
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++..++.+.+..-+|+|..|||.. -+++.+||..++..+..
T Consensus 174 ~~L~~~~r~il~l~y~~~~s~~eIA~~----lgis~~tV~~~~~ra~~ 217 (224)
T TIGR02479 174 ESLSEREQLVLSLYYYEELNLKEIGEV----LGLTESRVSQIHSQALK 217 (224)
T ss_pred HhCCHHHHHHHHHHHhCCCCHHHHHHH----hCCCHHHHHHHHHHHHH
Confidence 457777788888855599999999999 99999999998877654
No 201
>PRK06474 hypothetical protein; Provisional
Probab=54.24 E-value=20 Score=33.16 Aligned_cols=43 Identities=14% Similarity=0.264 Sum_probs=33.8
Q ss_pred chHHHHHHHHHhcC--CCHHHHhcCCCCCC-CCChhhHHHHHHHHHHcCC
Q 044490 214 PAKYEAWKMWHEDG--LSIQKIANYPGRSA-PIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 214 ~t~~~T~~l~~~~G--~si~eIA~~~~r~R-~L~~sTI~~HL~~~i~~G~ 260 (430)
+.....+..+.+.+ +|+.+|+.. - +++.+||+.||..+...|.
T Consensus 11 p~R~~Il~~L~~~~~~~ta~el~~~----l~~is~aTvYrhL~~L~e~GL 56 (178)
T PRK06474 11 PVRMKICQVLMRNKEGLTPLELVKI----LKDVPQATLYRHLQTMVDSGI 56 (178)
T ss_pred HHHHHHHHHHHhCCCCCCHHHHHHH----hcCCCHHHHHHHHHHHHHCCC
Confidence 34455666665344 899999986 4 6899999999999999995
No 202
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=54.03 E-value=21 Score=29.99 Aligned_cols=43 Identities=16% Similarity=0.196 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHHHcCCceeee-c-Cc-cceEEeCcchHhhhcC
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETI-K-DV-YRTVSVSQQGKQYLGS 62 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~-~-~~-y~~l~LT~kg~~~L~g 62 (430)
.+++..+-.+++.|...|||.... . +. --.+.||++|.+++..
T Consensus 54 ~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~ 99 (109)
T TIGR01889 54 LIKQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIES 99 (109)
T ss_pred CCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHH
Confidence 478899999999999999999752 1 21 2358999999998763
No 203
>PRK12423 LexA repressor; Provisional
Probab=53.46 E-value=22 Score=33.37 Aligned_cols=48 Identities=21% Similarity=0.254 Sum_probs=36.9
Q ss_pred CCchHHHHHHHHHh----cCC--CHHHHhcCCCCCCCC-ChhhHHHHHHHHHHcCCCcch
Q 044490 212 LTPAKYEAWKMWHE----DGL--SIQKIANYPGRSAPI-KEQTVVDYLLEAVSEGFDINW 264 (430)
Q Consensus 212 l~~t~~~T~~l~~~----~G~--si~eIA~~~~r~R~L-~~sTI~~HL~~~i~~G~~l~~ 264 (430)
+|++.++-+..+.+ .|+ |+.|||+. -++ +.+||..||..+.+.|. +..
T Consensus 4 lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~----~g~~s~~~v~~~l~~L~~~G~-l~~ 58 (202)
T PRK12423 4 LTPKRAAILAFIRERIAQAGQPPSLAEIAQA----FGFASRSVARKHVQALAEAGL-IEV 58 (202)
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCCHHHHHHH----hCCCChHHHHHHHHHHHHCCC-EEe
Confidence 45666666665442 455 99999998 895 89999999999999996 543
No 204
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=52.96 E-value=23 Score=27.55 Aligned_cols=42 Identities=12% Similarity=0.138 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHHcCCceeeecC--c---cceEEeCcchHhhhc
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETIKD--V---YRTVSVSQQGKQYLG 61 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~~~--~---y~~l~LT~kg~~~L~ 61 (430)
..+...+=..++.|..+|+|...... . -..+.+|++|++.|+
T Consensus 28 ~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~ 74 (75)
T PF03551_consen 28 KISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREELR 74 (75)
T ss_dssp ETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHHHH
T ss_pred ccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHHhc
Confidence 57899999999999999999986311 1 136899999999875
No 205
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=52.75 E-value=33 Score=34.90 Aligned_cols=46 Identities=11% Similarity=0.229 Sum_probs=37.8
Q ss_pred HHHHHHHhCCCCHHHHhccCCCCHHHHHHHHHHH----HHHHHHHHHhhc
Q 044490 140 TIKKIALARPSTKARLANIDGVNQHLVITHGDHL----LQTIRHLSQKLN 185 (430)
Q Consensus 140 tL~emA~~~P~T~~eL~~I~Gvg~~k~~kyG~~f----L~~I~~~~~e~~ 185 (430)
.|.++...+|....+|+.++|+|+.|+.+-...+ ++-++..+..+.
T Consensus 80 ~le~lk~~~P~gl~~Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~~~~ 129 (326)
T COG1796 80 KLEALKKEVPEGLEPLLKVPGLGPKKIVSLYKELGIKDLEELQEALENGK 129 (326)
T ss_pred HHHHHHHhCCcchHHHhhCCCCCcHHHHHHHHHHCcccHHHHHHHHHhCC
Confidence 7889999999999999999999999999877776 455555565444
No 206
>PF11313 DUF3116: Protein of unknown function (DUF3116); InterPro: IPR021464 This family of proteins with unknown function appears to be restricted to Bacillales.
Probab=52.45 E-value=22 Score=29.19 Aligned_cols=58 Identities=21% Similarity=0.287 Sum_probs=41.9
Q ss_pred hhhhcccccCcccCCCCCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhcC
Q 044490 4 VVDAQFDKLLLHGLGKDHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLGS 62 (430)
Q Consensus 4 I~~~~~d~l~~fG~Gk~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~g 62 (430)
|...-++-..+.|.+ ++++++.---+-.|-..|||...-.+.-..+.+|++|..+|..
T Consensus 23 i~~L~~e~~~~~~~~-~~TKNelL~~vYWLE~ngyI~R~~~~~~~rY~~T~kG~~ll~~ 80 (85)
T PF11313_consen 23 INHLTFEFIDFPGAY-DFTKNELLYTVYWLEENGYIFRDNNNNEKRYSLTEKGKELLAE 80 (85)
T ss_pred HHHHHHHHHhccccc-cccHHHHHHHHHHHhhcCeeEeecCCCcceeEEeccHHHHHHH
Confidence 334444444444444 6999999999999999999998721112358999999999864
No 207
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=52.42 E-value=19 Score=32.91 Aligned_cols=33 Identities=21% Similarity=0.168 Sum_probs=27.7
Q ss_pred HHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 220 WKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 220 ~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
+..+. +|+|..|||+. -+++.+||..++..+.+
T Consensus 159 ~~~~~-~~~s~~eIA~~----l~~s~~tV~~~l~r~r~ 191 (198)
T TIGR02859 159 LQSYL-DGKSYQEIACD----LNRHVKSIDNALQRVKR 191 (198)
T ss_pred HHHHH-cCCCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 34456 99999999999 99999999988877654
No 208
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=52.34 E-value=7.5 Score=33.98 Aligned_cols=28 Identities=21% Similarity=0.226 Sum_probs=25.6
Q ss_pred cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 226 DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 226 ~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
+|+|.+|||+. -|++++||..++..+..
T Consensus 120 ~g~s~~eIA~~----lgis~~tv~~~l~Ra~~ 147 (154)
T TIGR02950 120 KEFSYKEIAEL----LNLSLAKVKSNLFRARK 147 (154)
T ss_pred ccCcHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 89999999999 99999999999987743
No 209
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=52.21 E-value=19 Score=26.86 Aligned_cols=27 Identities=26% Similarity=0.352 Sum_probs=22.2
Q ss_pred HHHHHHHhCCCCHHHHhccCCCCHHHHHHH
Q 044490 140 TIKKIALARPSTKARLANIDGVNQHLVITH 169 (430)
Q Consensus 140 tL~emA~~~P~T~~eL~~I~Gvg~~k~~ky 169 (430)
|+.+++.. +.++|.+|+|||+.++++.
T Consensus 28 t~~~l~~a---~~~~L~~i~Gig~~~a~~i 54 (60)
T PF14520_consen 28 TLEDLANA---DPEELAEIPGIGEKTAEKI 54 (60)
T ss_dssp SHHHHHTS---HHHHHHTSTTSSHHHHHHH
T ss_pred cHHHHHcC---CHHHHhcCCCCCHHHHHHH
Confidence 56777764 7789999999999988775
No 210
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=52.19 E-value=11 Score=35.82 Aligned_cols=43 Identities=23% Similarity=0.188 Sum_probs=34.1
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAV 256 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i 256 (430)
..+++..++.+.|..-+|+|.+|||+. -+++.+||..++..+.
T Consensus 148 ~~L~~~~r~i~~l~~~~g~s~~EIAe~----lgis~~tVk~~l~Rar 190 (231)
T PRK11922 148 DALPDAFRAVFVLRVVEELSVEETAQA----LGLPEETVKTRLHRAR 190 (231)
T ss_pred HhCCHHHhhhheeehhcCCCHHHHHHH----HCcCHHHHHHHHHHHH
Confidence 345666667777733399999999999 9999999998887664
No 211
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=51.82 E-value=62 Score=30.39 Aligned_cols=107 Identities=13% Similarity=0.055 Sum_probs=61.7
Q ss_pred HHHhCC-CCHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHhh-ccCCC----CCc-Ccccccc-cccceec-ccccCCCc
Q 044490 144 IALARP-STKARLANIDGVNQHLVITHGDHLLQTIRHLSQKL-NLSLD----GKV-GEHTAFT-RKLHVVV-NTRTKLTP 214 (430)
Q Consensus 144 mA~~~P-~T~~eL~~I~Gvg~~k~~kyG~~fL~~I~~~~~e~-~~~~~----~~~-~~~~~~~-~~~~~~~-~~~~~l~~ 214 (430)
++...| .|..+|+++-|+....++. .+-++...|.... ++..- .+. ..++... .-..+.. .....++.
T Consensus 14 F~sg~pgls~~~La~~l~~~~~~v~~---~l~~L~~~y~~~~~gi~i~~~~~~y~l~tk~e~~~~v~~~~~~~~~~~LS~ 90 (188)
T PRK00135 14 FVSGEEGLSLEQLAEILELEPTEVQQ---LLEELQEKYEGDDRGLKLIEFNDVYKLVTKEENADYLQKLVKTPIKQSLSQ 90 (188)
T ss_pred HHcCCCCCCHHHHHHHHCCCHHHHHH---HHHHHHHHHhhCCCCEEEEEECCEEEEEEcHHHHHHHHHHhcccccCCCCH
Confidence 455676 9999999998888654322 2333333343221 11110 000 0010000 0000111 12346889
Q ss_pred hHHHHHHHH-HhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 215 AKYEAWKMW-HEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 215 t~~~T~~l~-~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
+..+|+... .++..|..+|+++ ||++. .+|+.++...|.
T Consensus 91 aaLEtLaiIay~qPiTr~eI~~i----rGv~~---~~ii~~L~~~gL 130 (188)
T PRK00135 91 AALEVLAIIAYKQPITRIEIDEI----RGVNS---DGALQTLLAKGL 130 (188)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHH----HCCCH---HHHHHHHHHCCC
Confidence 999988865 4489999999999 99984 678888888884
No 212
>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=51.45 E-value=33 Score=25.26 Aligned_cols=41 Identities=12% Similarity=0.030 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhc
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLG 61 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~ 61 (430)
+.+...+...++.|...|+|...-......+.+|+ |.+++.
T Consensus 31 ~i~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~-g~~~~~ 71 (78)
T cd00090 31 GLSQSTVSRHLKKLEEAGLVESRREGRRVYYSLTD-AERLLA 71 (78)
T ss_pred CcCHhHHHHHHHHHHHCCCeEEEEeccEEEEEeCC-chHHHH
Confidence 46889999999999999999976222235689997 776654
No 213
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=50.83 E-value=15 Score=25.30 Aligned_cols=30 Identities=30% Similarity=0.325 Sum_probs=27.4
Q ss_pred CCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 227 GLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 227 G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
..+..+||+. -+++.+||..+|..+...|.
T Consensus 8 ~~s~~~la~~----l~~s~~tv~~~l~~L~~~g~ 37 (48)
T smart00419 8 PLTRQEIAEL----LGLTRETVSRTLKRLEKEGL 37 (48)
T ss_pred ccCHHHHHHH----HCCCHHHHHHHHHHHHHCCC
Confidence 4678899998 99999999999999999995
No 214
>COG5045 Ribosomal protein S10E [Translation, ribosomal structure and biogenesis]
Probab=50.74 E-value=20 Score=29.84 Aligned_cols=53 Identities=23% Similarity=0.192 Sum_probs=40.0
Q ss_pred cCcccCCCC----CCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhcCCC
Q 044490 12 LLLHGLGKD----HSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLGSAR 64 (430)
Q Consensus 12 l~~fG~Gk~----ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~g~~ 64 (430)
..-|..|+. ..-=.+......|+..||++....-+|.++.||+.|.+.|+...
T Consensus 24 kkDfnl~kH~el~ipNL~vika~qsl~S~GYvkt~~~W~~~YytLT~eGveyLREyL 80 (105)
T COG5045 24 KKDFNLGKHRELEIPNLHVIKAMQSLISYGYVKTIHVWRHSYYTLTPEGVEYLREYL 80 (105)
T ss_pred hhhccccCCcccCCCchHHHHHHHHHhhcceeEEEeeeeeeEEEecHHHHHHHHHHh
Confidence 344555553 34446777888999999999764566778999999999999763
No 215
>PF03501 S10_plectin: Plectin/S10 domain; InterPro: IPR005326 This presumed domain is found at the N terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein. This domain may be involved in RNA binding.; PDB: 2XZM_7 2XZN_7 3U5C_K 3U5G_K.
Probab=50.35 E-value=26 Score=29.37 Aligned_cols=45 Identities=18% Similarity=0.101 Sum_probs=37.9
Q ss_pred CCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhcCCC
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLGSAR 64 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~g~~ 64 (430)
+.+-=.+..+.+.|...||+.+.+.-+|-+..||++|-+.|+...
T Consensus 34 ~vpNL~V~k~mqSL~SrgyVke~faWrh~Yw~LT~eGIeyLR~yL 78 (95)
T PF03501_consen 34 NVPNLHVIKAMQSLKSRGYVKEQFAWRHYYWYLTNEGIEYLREYL 78 (95)
T ss_dssp SSBHHHHHHHHHHHHHCTSEEEEECTTEEEEEE-HHHHHHHHHHC
T ss_pred CCCcHHHHHHHhcccchhhhcCeecceEEEEEEcchhHHHHHHHh
Confidence 667778889999999999999986666678899999999999863
No 216
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=49.82 E-value=29 Score=28.64 Aligned_cols=39 Identities=15% Similarity=0.215 Sum_probs=32.2
Q ss_pred HHHHHHHh-cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 218 EAWKMWHE-DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 218 ~T~~l~~~-~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
.-+..+++ ...|..+||+. -+++++||..++..+...|.
T Consensus 7 ~il~~L~~~~~~~~~~la~~----l~~s~~tv~~~l~~L~~~g~ 46 (108)
T smart00344 7 KILEELQKDARISLAELAKK----VGLSPSTVHNRVKRLEEEGV 46 (108)
T ss_pred HHHHHHHHhCCCCHHHHHHH----HCcCHHHHHHHHHHHHHCCC
Confidence 34444443 46899999998 99999999999999999995
No 217
>PRK10870 transcriptional repressor MprA; Provisional
Probab=49.45 E-value=26 Score=32.24 Aligned_cols=43 Identities=14% Similarity=0.251 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHHHcCCceeee-cCc--cceEEeCcchHhhhcCC
Q 044490 21 HSSNWWKTLAYQLISYGYLTETI-KDV--YRTVSVSQQGKQYLGSA 63 (430)
Q Consensus 21 ls~~~wk~li~qLi~~GyL~e~~-~~~--y~~l~LT~kg~~~L~g~ 63 (430)
+++.-+-++++.|...|||.... .++ -..|.||++|++++..-
T Consensus 83 l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~i 128 (176)
T PRK10870 83 SSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREV 128 (176)
T ss_pred CCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHH
Confidence 68888999999999999999862 111 13689999999999863
No 218
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=48.51 E-value=25 Score=33.22 Aligned_cols=44 Identities=23% Similarity=0.282 Sum_probs=36.6
Q ss_pred CCCchHHHHHHHHHhcC-------CCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 211 KLTPAKYEAWKMWHEDG-------LSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G-------~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
.||+...+.+......| -++.+||++ -|++.+|+..||-.+.+.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~----lGISkst~~ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKE----LGISKSTLSEHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHH----hCCCHHHHHHHHHHHHHH
Confidence 57888877777665555 599999999 999999999999988653
No 219
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=48.27 E-value=30 Score=32.45 Aligned_cols=46 Identities=17% Similarity=0.182 Sum_probs=38.0
Q ss_pred CCCchHHHHHHHHHh-cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 211 KLTPAKYEAWKMWHE-DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~-~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
.+++.....+..+.+ .+.++.+||+. -+++.+|+..||..+.+.|.
T Consensus 140 ~ls~~~~~IL~~l~~~g~~s~~eia~~----l~is~stv~r~L~~Le~~Gl 186 (203)
T TIGR01884 140 GLSREELKVLEVLKAEGEKSVKNIAKK----LGKSLSTISRHLRELEKKGL 186 (203)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHH----HCcCHHHHHHHHHHHHHCCC
Confidence 456666667777764 35699999999 99999999999999999995
No 220
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=48.27 E-value=42 Score=23.94 Aligned_cols=41 Identities=12% Similarity=-0.014 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHHHcCCceeeecCccceEEeCc-chHhhhc
Q 044490 21 HSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQ-QGKQYLG 61 (430)
Q Consensus 21 ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~-kg~~~L~ 61 (430)
.+...+...++.|...|++.....+....+.+|. .+.+++.
T Consensus 22 is~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~~~~~~~~~~ 63 (66)
T smart00418 22 LSQSTVSHHLKKLREAGLVESRREGKRVYYSLTDEKVADLLE 63 (66)
T ss_pred CCHHHHHHHHHHHHHCCCeeeeecCCEEEEEEchHHHHHHHH
Confidence 7889999999999999999976223334678888 7777664
No 221
>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=48.08 E-value=19 Score=26.77 Aligned_cols=33 Identities=36% Similarity=0.429 Sum_probs=29.5
Q ss_pred cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcc
Q 044490 226 DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDIN 263 (430)
Q Consensus 226 ~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~ 263 (430)
..+|..+||+. -+++.+||..+|..+...|. +.
T Consensus 24 ~~~s~~ela~~----~g~s~~tv~r~l~~L~~~g~-i~ 56 (67)
T cd00092 24 LPLTRQEIADY----LGLTRETVSRTLKELEEEGL-IS 56 (67)
T ss_pred CCcCHHHHHHH----HCCCHHHHHHHHHHHHHCCC-EE
Confidence 56889999999 99999999999999999995 44
No 222
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=47.97 E-value=24 Score=35.75 Aligned_cols=39 Identities=26% Similarity=0.417 Sum_probs=34.3
Q ss_pred HHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 217 YEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 217 ~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
+..|..|. +|+|-.|||++ -+++..||...|.++-..|.
T Consensus 20 ~vA~lYY~-~g~tQ~eIA~~----lgiSR~~VsRlL~~Ar~~Gi 58 (318)
T PRK15418 20 RIAWFYYH-DGLTQSEIGER----LGLTRLKVSRLLEKGRQSGI 58 (318)
T ss_pred HHHHHHHh-cCCCHHHHHHH----hCCCHHHHHHHHHHHHHcCc
Confidence 34555555 99999999999 99999999999999999996
No 223
>PRK05572 sporulation sigma factor SigF; Validated
Probab=47.81 E-value=25 Score=34.03 Aligned_cols=44 Identities=9% Similarity=-0.034 Sum_probs=36.5
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++.....+.+..-+|+|+.+||.. -|++.+||..+...+..
T Consensus 201 ~~L~~~~~~v~~l~~~~~~s~~eIA~~----lgis~~~V~~~~~ral~ 244 (252)
T PRK05572 201 RELDERERLIVYLRYFKDKTQSEVAKR----LGISQVQVSRLEKKILK 244 (252)
T ss_pred HcCCHHHHHHHHHHHhCCCCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 467777777777765589999999999 99999999988877654
No 224
>TIGR01388 rnd ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown.
Probab=47.65 E-value=34 Score=35.35 Aligned_cols=67 Identities=13% Similarity=0.083 Sum_probs=50.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCCCeeecchHHHHHHHHhC-CCCHHHHhccCCCCHHHHHHHHHHHHHHHH
Q 044490 109 ADMQLYHMLLEERKKLARVTGTAPYALCGDQTIKKIALAR-PSTKARLANIDGVNQHLVITHGDHLLQTIR 178 (430)
Q Consensus 109 ~~~~L~~~L~~~R~~lA~e~~vppy~Ifsd~tL~emA~~~-P~T~~eL~~I~Gvg~~k~~kyG~~fL~~I~ 178 (430)
....+++.|+.+...+|.+.|+||-+|.+.+.|.+++... +.... ...+.+..|+.+ +|..++..+.
T Consensus 298 ~~~~~~~~l~~~~~~~a~~~~i~~~~l~~~~~l~~l~~~~~~~~~~--~~~~~~~gWR~~-~~~~~~~~~~ 365 (367)
T TIGR01388 298 GYKALFKLLKVLVKDVSETLGLASELLASRRQLEQLLAWGWKLKPN--ALPPLLQGWRRE-LGEEALKNLL 365 (367)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCCHHHcCCHHHHHHHHHhhcccccc--cccHHHHhhHHH-HHHHHHHHhc
Confidence 4578999999999999999999999999999999998642 21111 112245667766 7777776553
No 225
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=46.49 E-value=20 Score=35.36 Aligned_cols=46 Identities=13% Similarity=0.169 Sum_probs=37.4
Q ss_pred ccCCCchHHHHHHHHH----hcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 209 RTKLTPAKYEAWKMWH----EDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 209 ~~~l~~t~~~T~~l~~----~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
...|++..+..+.|.. -+|+|..|||+. -+++.+||..++..+...
T Consensus 220 l~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~----Lgis~~tVk~~l~rAlkk 269 (285)
T TIGR02394 220 LAELNERQREVLARRFGLLGYEPATLEEVAAE----VGLTRERVRQIQVEALKK 269 (285)
T ss_pred HHcCCHHHHHHHHHHhCCCCCCCccHHHHHHH----HCCCHHHHHHHHHHHHHH
Confidence 4567777777777652 399999999999 999999999998887543
No 226
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=46.24 E-value=23 Score=35.34 Aligned_cols=85 Identities=15% Similarity=0.119 Sum_probs=53.2
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCC-HHHHHHHHHHHHHhC
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLT-DEIFSAIQEAISKVG 289 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~-~e~~~~I~~a~~~~g 289 (430)
.|++..+..+.|..-.|+|..|||+. -+++++||..++..+...=.... .++- .+ ++....+...+....
T Consensus 118 ~L~p~~R~vf~L~~~~g~s~~EIA~~----Lgis~~tVr~~l~RAr~~Lr~~~-~~~~----~~~~~~~~~~~~f~~a~~ 188 (290)
T PRK09635 118 RLGPAERVVFVLHEIFGLPYQQIATT----IGSQASTCRQLAHRARRKINESR-IAAS----VEPAQHRVVTRAFIEACS 188 (290)
T ss_pred hCCHHHHHHhhHHHHhCCCHHHHHHH----HCcCHHHHHHHHHHHHHHHHhhC-CCCC----CChHHHHHHHHHHHHHHH
Confidence 46677778888865599999999999 99999999999987755432111 1111 13 333333333333332
Q ss_pred CCCChHHHHHhCCCCC
Q 044490 290 CKDKLKPIKNELPDDI 305 (430)
Q Consensus 290 ~~~~LkpIke~l~~~i 305 (430)
...+..+.+.|.+++
T Consensus 189 -~gd~~~l~~ll~~d~ 203 (290)
T PRK09635 189 -NGDLDTLLEVLDPGV 203 (290)
T ss_pred -hCCHHHHHHHhhhhh
Confidence 134666777776655
No 227
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=46.07 E-value=26 Score=25.03 Aligned_cols=32 Identities=22% Similarity=0.294 Sum_probs=29.4
Q ss_pred hcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 225 EDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 225 ~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
....++.+||.. -+++.+||..+|..+...|.
T Consensus 8 ~~~~~~~~i~~~----l~is~~~v~~~l~~L~~~g~ 39 (66)
T smart00418 8 EGELCVCELAEI----LGLSQSTVSHHLKKLREAGL 39 (66)
T ss_pred cCCccHHHHHHH----HCCCHHHHHHHHHHHHHCCC
Confidence 478899999998 89999999999999999995
No 228
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=45.99 E-value=28 Score=33.97 Aligned_cols=44 Identities=14% Similarity=0.225 Sum_probs=35.3
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++..+..+.+..-+|+|..|||+. -+++.+||..++..+..
T Consensus 211 ~~L~~~~r~vl~l~~~~~~s~~eIA~~----lgis~~tV~~~~~ra~~ 254 (268)
T PRK06288 211 KTLPEREKKVLILYYYEDLTLKEIGKV----LGVTESRISQLHTKAVL 254 (268)
T ss_pred HhCCHHHHHHHHHHHHcCCCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 356777777777755599999999999 99999999887766543
No 229
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=45.62 E-value=45 Score=25.70 Aligned_cols=43 Identities=23% Similarity=0.385 Sum_probs=33.7
Q ss_pred CHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCC
Q 044490 229 SIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGC 290 (430)
Q Consensus 229 si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~ 290 (430)
++.+||.. .|++.+||...| .|. . +++++..+.|.++++++|+
T Consensus 2 t~~~iA~~----~gvS~~TVSr~l-----n~~-----~-----~v~~~t~~~i~~~~~~~gy 44 (70)
T smart00354 2 TIKDVARL----AGVSKATVSRVL-----NGN-----G-----RVSEETREKVLAAMEELGY 44 (70)
T ss_pred CHHHHHHH----HCCCHHHHHHHH-----CCC-----C-----CCCHHHHHHHHHHHHHhCC
Confidence 67889988 899999995533 342 2 2478899999999999986
No 230
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=45.08 E-value=19 Score=26.33 Aligned_cols=36 Identities=17% Similarity=0.328 Sum_probs=31.2
Q ss_pred HHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 221 KMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 221 ~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
.++...|.++.+||+. -+++.+|+...+..+...|.
T Consensus 11 ~l~~~~~~~~~~la~~----~~~~~~~~t~~i~~L~~~g~ 46 (59)
T PF01047_consen 11 ILYENGGITQSELAEK----LGISRSTVTRIIKRLEKKGL 46 (59)
T ss_dssp HHHHHSSEEHHHHHHH----HTS-HHHHHHHHHHHHHTTS
T ss_pred HHHHcCCCCHHHHHHH----HCCChhHHHHHHHHHHHCCC
Confidence 3456579999999999 99999999999999999995
No 231
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=44.92 E-value=26 Score=34.39 Aligned_cols=48 Identities=13% Similarity=0.222 Sum_probs=36.7
Q ss_pred CCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCCC
Q 044490 228 LSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGCK 291 (430)
Q Consensus 228 ~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~~ 291 (430)
+|+.+||+. -|++.+||..-| .|..- +. +++++..+.|.++++++|+.
T Consensus 1 ~ti~dIA~~----aGVS~~TVSrvL-----n~~~~--~~-----~Vs~~tr~rV~~~a~elgY~ 48 (328)
T PRK11303 1 MKLDEIARL----AGVSRTTASYVI-----NGKAK--QY-----RVSDKTVEKVMAVVREHNYH 48 (328)
T ss_pred CCHHHHHHH----hCCCHHHHHHHH-----cCCCC--CC-----CcCHHHHHHHHHHHHHhCCC
Confidence 488999999 999999997665 34310 00 24899999999999999863
No 232
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=44.79 E-value=27 Score=33.17 Aligned_cols=44 Identities=23% Similarity=0.231 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhcCC
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLGSA 63 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~g~ 63 (430)
+.|..-.-+++.+|...||+..++....+.+.+|++|+++|...
T Consensus 30 ~~S~qta~R~l~~le~~~~I~R~~~~~Gq~i~iTekG~~~L~~~ 73 (214)
T COG1339 30 GVSSQTAARKLKELEDEGYITRTISKRGQLITITEKGIDLLYKE 73 (214)
T ss_pred CcCcHHHHHHHHhhccCCcEEEEecCCCcEEEehHhHHHHHHHH
Confidence 46777888899999999999987533447899999999999865
No 233
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=44.72 E-value=41 Score=26.61 Aligned_cols=47 Identities=26% Similarity=0.379 Sum_probs=36.8
Q ss_pred CCchHHHHHHHHH-hcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcc
Q 044490 212 LTPAKYEAWKMWH-EDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDIN 263 (430)
Q Consensus 212 l~~t~~~T~~l~~-~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~ 263 (430)
++.+....+.++. ..+.++.+||+. -+++.+||..+|-.+...|. +.
T Consensus 8 l~~~~~~il~~l~~~~~~~~~~la~~----~~~s~~~i~~~l~~L~~~g~-v~ 55 (101)
T smart00347 8 LTPTQFLVLRILYEEGPLSVSELAKR----LGVSPSTVTRVLDRLEKKGL-IR 55 (101)
T ss_pred CCHHHHHHHHHHHHcCCcCHHHHHHH----HCCCchhHHHHHHHHHHCCC-eE
Confidence 4455555555554 346899999998 89999999999999999995 53
No 234
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=44.66 E-value=28 Score=33.83 Aligned_cols=44 Identities=16% Similarity=0.129 Sum_probs=35.6
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++..+..+.+..-+|+|..|||.. -|++.+||..++..+..
T Consensus 202 ~~L~~~~r~vl~l~y~~~~s~~eIA~~----lgvs~~~V~~~~~ra~~ 245 (256)
T PRK07408 202 AQLEERTREVLEFVFLHDLTQKEAAER----LGISPVTVSRRVKKGLD 245 (256)
T ss_pred HcCCHHHHHHHHHHHHCCCCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 356666667766665599999999999 99999999998887754
No 235
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=43.59 E-value=34 Score=33.53 Aligned_cols=41 Identities=10% Similarity=0.160 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhcCC
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLGSA 63 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~g~ 63 (430)
+.|-.-+-..++.|+.+||+... +. ..+.+|.+|-+||..+
T Consensus 36 giT~QaVsehiK~Lv~eG~i~~~-gR--~~Y~iTkkG~e~l~~~ 76 (260)
T COG1497 36 GITLQAVSEHIKELVKEGLIEKE-GR--GEYEITKKGAEWLLEQ 76 (260)
T ss_pred CCCHHHHHHHHHHHHhccceeec-CC--eeEEEehhHHHHHHHH
Confidence 46788899999999999999975 33 5799999999999865
No 236
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=43.55 E-value=31 Score=30.24 Aligned_cols=45 Identities=22% Similarity=0.152 Sum_probs=37.5
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
.+++...+.+.++. .|++..+||+. -+++..||..|+..+...-.
T Consensus 141 ~l~~~e~~vl~~~~-~~~~~~~ia~~----l~~s~~tv~~~~~~~~~kl~ 185 (202)
T PRK09390 141 SLSERERQVMDGLV-AGLSNKVIARD----LDISPRTVEVYRANVMTKMQ 185 (202)
T ss_pred hhhhhHHHHHHHHH-ccCchHHHHHH----cCCCHHHHHHHHHHHHHHHc
Confidence 35566667777776 89999999998 89999999999999987754
No 237
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=43.02 E-value=35 Score=30.91 Aligned_cols=40 Identities=15% Similarity=0.202 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhcC
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLGS 62 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~g 62 (430)
+.+..-+...++.|...||+.-. .|+.+.||++|++....
T Consensus 35 ~Vsp~sVt~ml~rL~~~GlV~~~---~y~gi~LT~~G~~~a~~ 74 (154)
T COG1321 35 KVSPPSVTEMLKRLERLGLVEYE---PYGGVTLTEKGREKAKE 74 (154)
T ss_pred CCCcHHHHHHHHHHHHCCCeEEe---cCCCeEEChhhHHHHHH
Confidence 35677788899999999999865 67899999999977653
No 238
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=42.85 E-value=31 Score=28.16 Aligned_cols=43 Identities=16% Similarity=0.441 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHHHHcCCceee-e-c----CccceEEeCcchHhhhcCC
Q 044490 21 HSSNWWKTLAYQLISYGYLTET-I-K----DVYRTVSVSQQGKQYLGSA 63 (430)
Q Consensus 21 ls~~~wk~li~qLi~~GyL~e~-~-~----~~y~~l~LT~kg~~~L~g~ 63 (430)
.....|..+++.|..+||+.=. + . .......+|.+|-+.|...
T Consensus 22 ~~~~~~~~il~~L~d~GyI~G~~~~~~~~~~~~~~~~IT~~Gi~YL~EN 70 (88)
T PF09639_consen 22 ITDSYWSDILRMLQDEGYIKGVSVVRYSPYVALSDPRITLKGIEYLEEN 70 (88)
T ss_dssp S-HHHHHHHHHHHHHHTSEE--EESSSSEE--SS--EE-HHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHCCCccceEEEeccceeecCCceEcHHHHHHHHHH
Confidence 4559999999999999999521 1 0 1123468899999999854
No 239
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=42.45 E-value=32 Score=33.50 Aligned_cols=44 Identities=14% Similarity=0.180 Sum_probs=36.2
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++..+..+.|..-+|+|..|||+. -|++.+||..++..+..
T Consensus 204 ~~L~~~er~vi~l~y~e~~t~~EIA~~----lgis~~~V~~~~~ral~ 247 (257)
T PRK05911 204 LALEEKERKVMALYYYEELVLKEIGKI----LGVSESRVSQIHSKALL 247 (257)
T ss_pred HcCCHHHHHHHHHHHhcCCCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 356677777777765599999999999 99999999999887754
No 240
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=42.31 E-value=37 Score=33.34 Aligned_cols=45 Identities=18% Similarity=0.249 Sum_probs=36.5
Q ss_pred CCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCCC
Q 044490 228 LSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGCK 291 (430)
Q Consensus 228 ~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~~ 291 (430)
.|+.+||+. -|++.+||..-| .|. . +++++..+.|.++++++|+.
T Consensus 2 ~ti~dIA~~----agvS~~TVSrvL-----n~~-----~-----~vs~~tr~rV~~~a~~lgY~ 46 (329)
T TIGR01481 2 VTIYDVARE----AGVSMATVSRVV-----NGN-----P-----NVKPATRKKVLEVIKRLDYR 46 (329)
T ss_pred CcHHHHHHH----hCCCHHHHHHHh-----CCC-----C-----CCCHHHHHHHHHHHHHHCCC
Confidence 478999999 999999997765 342 1 24899999999999999863
No 241
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=41.97 E-value=41 Score=33.41 Aligned_cols=44 Identities=16% Similarity=0.224 Sum_probs=36.1
Q ss_pred CHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCCC
Q 044490 229 SIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGCK 291 (430)
Q Consensus 229 si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~~ 291 (430)
||.+||+. -|++.+||..-| .|. . +++++..+.|.++++++|+.
T Consensus 3 ti~dIA~~----aGVS~~TVSrvL-----n~~----~------~Vs~~tr~rV~~~a~elgY~ 46 (343)
T PRK10727 3 TIKDVARL----AGVSVATVSRVI-----NNS----P------KASEASRLAVHSAMESLSYH 46 (343)
T ss_pred CHHHHHHH----hCCCHHHHHHHh-----CCC----C------CCCHHHHHHHHHHHHHHCCC
Confidence 78999999 999999997666 343 1 24899999999999999863
No 242
>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=41.60 E-value=56 Score=23.95 Aligned_cols=39 Identities=18% Similarity=0.270 Sum_probs=31.5
Q ss_pred HHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 218 EAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 218 ~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
..+..+...+.+..+||+. .+++.+||..+|..+...|.
T Consensus 11 ~il~~l~~~~~~~~ei~~~----~~i~~~~i~~~l~~L~~~g~ 49 (78)
T cd00090 11 RILRLLLEGPLTVSELAER----LGLSQSTVSRHLKKLEEAGL 49 (78)
T ss_pred HHHHHHHHCCcCHHHHHHH----HCcCHhHHHHHHHHHHHCCC
Confidence 3344333255999999998 89999999999999999985
No 243
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=41.43 E-value=24 Score=25.25 Aligned_cols=28 Identities=25% Similarity=0.277 Sum_probs=26.0
Q ss_pred CHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 229 SIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 229 si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
|..+||+. -+++.+||..++..+...|.
T Consensus 22 s~~~la~~----~~vs~~tv~~~l~~L~~~g~ 49 (60)
T smart00345 22 SERELAAQ----LGVSRTTVREALSRLEAEGL 49 (60)
T ss_pred CHHHHHHH----HCCCHHHHHHHHHHHHHCCC
Confidence 78889998 99999999999999999995
No 244
>PRK10829 ribonuclease D; Provisional
Probab=41.02 E-value=42 Score=34.89 Aligned_cols=65 Identities=6% Similarity=0.063 Sum_probs=51.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCCCeeecchHHHHHHHHh------CCCCHHHHhccCCCCHHHHHHHHHHHHHHHHH
Q 044490 109 ADMQLYHMLLEERKKLARVTGTAPYALCGDQTIKKIALA------RPSTKARLANIDGVNQHLVITHGDHLLQTIRH 179 (430)
Q Consensus 109 ~~~~L~~~L~~~R~~lA~e~~vppy~Ifsd~tL~emA~~------~P~T~~eL~~I~Gvg~~k~~kyG~~fL~~I~~ 179 (430)
....+++.|+......|++.|+||-++.+-+.|.+++.. .+..+ ..+.-|+.+-+|..+.+++..
T Consensus 302 ~~~~~~~~l~~~v~~~a~~~~i~~ellas~~~l~~l~~~~~~~~~~~~~p------~~l~GWR~e~~g~~l~~~l~~ 372 (373)
T PRK10829 302 GYRKAFKAIKALIQEVSETHGLSAELLASRRQINQLLNWHWKLKPQNGLP------ELISGWRGELLAEALTEILQE 372 (373)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCCHHHhCCHHHHHHHHHhhcccCCccCCc------hHhhhhhHHHHHHHHHHHHhc
Confidence 346899999999999999999999999999999999851 11111 245678888889998887754
No 245
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=40.73 E-value=21 Score=22.17 Aligned_cols=16 Identities=13% Similarity=0.229 Sum_probs=13.4
Q ss_pred HHhccCCCCHHHHHHH
Q 044490 154 RLANIDGVNQHLVITH 169 (430)
Q Consensus 154 eL~~I~Gvg~~k~~ky 169 (430)
+|.+|+|||+..+++.
T Consensus 2 ~L~~i~GiG~k~A~~i 17 (26)
T smart00278 2 ELLKVPGIGPKTAEKI 17 (26)
T ss_pred hhhhCCCCCHHHHHHH
Confidence 5789999999877764
No 246
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=40.69 E-value=30 Score=23.59 Aligned_cols=31 Identities=16% Similarity=0.245 Sum_probs=22.9
Q ss_pred eeecchHHHHHHHHhCCCCHHHHhccC-CCCH
Q 044490 133 YALCGDQTIKKIALARPSTKARLANID-GVNQ 163 (430)
Q Consensus 133 y~Ifsd~tL~emA~~~P~T~~eL~~I~-Gvg~ 163 (430)
|.|=++.|+..||.++-.+.++|.+.+ ++..
T Consensus 1 y~V~~gDtl~~IA~~~~~~~~~l~~~N~~~~~ 32 (44)
T PF01476_consen 1 YTVQPGDTLWSIAKRYGISVDELMELNPNIDS 32 (44)
T ss_dssp EEE-TT--HHHHHHHTTS-HHHHHHHCCTTHG
T ss_pred CEECcCCcHHHHHhhhhhhHhHHHHhcCCCCc
Confidence 567789999999999999999998888 6644
No 247
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=40.66 E-value=4.6e+02 Score=27.78 Aligned_cols=45 Identities=16% Similarity=0.199 Sum_probs=35.6
Q ss_pred cCCCchHHHHHHHHHh----cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 210 TKLTPAKYEAWKMWHE----DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~----~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
..|++..+..+.|..- +++|++|||.. -+++..||..++..+...
T Consensus 349 ~~L~~reR~VI~LRygl~d~~~~Tl~EIA~~----LGvS~erVRqie~rAl~K 397 (415)
T PRK07598 349 ADLTSRERDVIRMRFGLADGHTYSLAEIGRA----LDLSRERVRQIESKALQK 397 (415)
T ss_pred HhCCHHHHHHHHHHHhcCCCCCCCHHHHHHH----HCcCHHHHHHHHHHHHHH
Confidence 4577777777777543 57999999999 999999998888777554
No 248
>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=40.55 E-value=54 Score=24.53 Aligned_cols=62 Identities=8% Similarity=0.016 Sum_probs=36.7
Q ss_pred CCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCc---chhhhhhccCCCHHHHHHHHHHHHH--hCCCCChHHHHHhC
Q 044490 228 LSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDI---NWTRLCDEVGLTDEIFSAIQEAISK--VGCKDKLKPIKNEL 301 (430)
Q Consensus 228 ~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l---~~~~~i~~~~l~~e~~~~I~~a~~~--~g~~~~LkpIke~l 301 (430)
+|+.|+|+. -+++.+|+..+..+. |... +-... --++++++..++....- .| -.|+.|++.+
T Consensus 1 ~s~~eva~~----~gvs~~tlr~w~~~~---g~~~~~r~~~~~---r~yt~~~v~~l~~i~~l~~~g--~~l~~i~~~~ 67 (68)
T cd01104 1 YTIGAVARL----TGVSPDTLRAWERRY---GLPAPQRTDGGH---RLYSEADVARLRLIRRLTSEG--VRISQAAALA 67 (68)
T ss_pred CCHHHHHHH----HCcCHHHHHHHHHhC---CCCCCCcCCCCC---eecCHHHHHHHHHHHHHHHCC--CCHHHHHHHh
Confidence 578899998 999999998765432 3211 11010 01477777776544333 34 5677777654
No 249
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=40.43 E-value=39 Score=34.46 Aligned_cols=40 Identities=33% Similarity=0.467 Sum_probs=35.3
Q ss_pred HHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 216 KYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 216 ~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
....|..|. +|+|-.|||+. -+++..||...|..+...|.
T Consensus 16 ~~~A~lYY~-~gltQ~eIA~~----LgiSR~~v~rlL~~Ar~~Gi 55 (321)
T COG2390 16 ARAAWLYYV-EGLTQSEIAER----LGISRATVSRLLAKAREEGI 55 (321)
T ss_pred HHHHHHHHh-cCCCHHHHHHH----hCCCHHHHHHHHHHHHHCCe
Confidence 345566666 99999999999 99999999999999999995
No 250
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=40.39 E-value=47 Score=32.82 Aligned_cols=46 Identities=22% Similarity=0.251 Sum_probs=36.8
Q ss_pred CCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCCCC
Q 044490 228 LSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGCKD 292 (430)
Q Consensus 228 ~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~~~ 292 (430)
.|+.+||+. -|++.+||...| .|. . +++++..+.|.++++++|+..
T Consensus 2 ~Ti~dIA~~----agVS~~TVSrvL-----n~~-----~-----~vs~~tr~~V~~~a~elgY~p 47 (341)
T PRK10703 2 ATIKDVAKR----AGVSTTTVSHVI-----NKT-----R-----FVAEETRNAVWAAIKELHYSP 47 (341)
T ss_pred CCHHHHHHH----hCCCHHHHHHHH-----cCC-----C-----CCCHHHHHHHHHHHHHHCCCc
Confidence 489999999 999999998777 232 1 248899999999999988633
No 251
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=40.36 E-value=36 Score=32.28 Aligned_cols=44 Identities=14% Similarity=0.079 Sum_probs=34.9
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++.....+.+..-+|+|+.|||+. -|++.+||..+...+..
T Consensus 182 ~~L~~~e~~i~~~~~~~~~t~~eIA~~----lgis~~~V~~~~~~al~ 225 (231)
T TIGR02885 182 SKLDERERQIIMLRYFKDKTQTEVANM----LGISQVQVSRLEKKVLK 225 (231)
T ss_pred HcCCHHHHHHHHHHHHcCCCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 456677777776654489999999999 99999999888776654
No 252
>PRK15183 Vi polysaccharide biosynthesis protein TviA; Provisional
Probab=40.16 E-value=27 Score=29.85 Aligned_cols=26 Identities=31% Similarity=0.336 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHhCC--CCeeecchHH
Q 044490 115 HMLLEERKKLARVTGT--APYALCGDQT 140 (430)
Q Consensus 115 ~~L~~~R~~lA~e~~v--ppy~Ifsd~t 140 (430)
..|..||+++|-+.|+ |.|+.++|..
T Consensus 113 st~yrwrke~a~kfgvr~prylllpdsv 140 (143)
T PRK15183 113 STMYRWRKELAVKFGVREPRYLLLPDSV 140 (143)
T ss_pred HHHHHHHHHHHHHhcCCCCceEecCccc
Confidence 4589999999999997 8999988764
No 253
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=39.91 E-value=80 Score=28.45 Aligned_cols=41 Identities=10% Similarity=0.119 Sum_probs=29.0
Q ss_pred chHHHHHHHHhCCCCHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHhhc
Q 044490 137 GDQTIKKIALARPSTKARLANIDGVNQHLVITHGDHLLQTIRHLSQKLN 185 (430)
Q Consensus 137 sd~tL~emA~~~P~T~~eL~~I~Gvg~~k~~kyG~~fL~~I~~~~~e~~ 185 (430)
+..+..++....=-|.++|..++|||+.++++ |.+|.++++
T Consensus 81 ~~~~~~~~vNiNtAs~eeL~~lpgIG~~kA~a--------Ii~yRe~~G 121 (149)
T COG1555 81 SSAEEEKKVNINTASAEELQALPGIGPKKAQA--------IIDYREENG 121 (149)
T ss_pred cccCccccccccccCHHHHHHCCCCCHHHHHH--------HHHHHHHcC
Confidence 33444455566777899999999999998755 455655554
No 254
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=39.88 E-value=22 Score=31.11 Aligned_cols=44 Identities=18% Similarity=0.093 Sum_probs=37.8
Q ss_pred CCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhcCCC
Q 044490 21 HSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLGSAR 64 (430)
Q Consensus 21 ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~g~~ 64 (430)
..-=++-.+.+.|...||+.+.+.-+|-+..||+.|-+.|+...
T Consensus 38 vpNL~Vik~mqSL~Srg~Vke~f~WrhyYw~LT~eGieyLR~yL 81 (124)
T PTZ00034 38 VPNLHVMMLMRSLKSRGLVKEQFAWQHYYYYLTDEGIEYLRTYL 81 (124)
T ss_pred CccHHHHHHHHccccCCceEEEEeeEEEEEEEchHHHHHHHHHh
Confidence 56667888899999999999986666778999999999999874
No 255
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=39.49 E-value=39 Score=33.15 Aligned_cols=47 Identities=15% Similarity=0.270 Sum_probs=35.9
Q ss_pred CHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCCC
Q 044490 229 SIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGCK 291 (430)
Q Consensus 229 si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~~ 291 (430)
|+.+||+. -|++.+||..-| .|..- . .+++++..+.|.++++++|+.
T Consensus 1 ti~dIA~~----aGVS~~TVSrvL-----n~~~~--~-----~~vs~~tr~rV~~~a~~lgY~ 47 (327)
T TIGR02417 1 TLSDIAKL----AGVSKTTASYVI-----NGKAK--E-----YRISQETVERVMAVVREQGYQ 47 (327)
T ss_pred CHHHHHHH----hCCCHHHHHHHH-----cCCCC--C-----CccCHHHHHHHHHHHHHhCCC
Confidence 67899999 999999997766 34310 0 024899999999999998863
No 256
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=38.77 E-value=37 Score=33.47 Aligned_cols=47 Identities=23% Similarity=0.196 Sum_probs=35.9
Q ss_pred CCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCCC
Q 044490 228 LSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGCK 291 (430)
Q Consensus 228 ~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~~ 291 (430)
.|+.+||+. -|++.+||..-| .|.+ . ..++++..+.|.++++++|+.
T Consensus 2 ~ti~dIA~~----agVS~~TVSrvl-----n~~~----~----~~vs~~tr~rV~~~a~~lgY~ 48 (327)
T PRK10339 2 ATLKDIAIE----AGVSLATVSRVL-----NDDP----T----LNVKEETKHRILEIAEKLEYK 48 (327)
T ss_pred CCHHHHHHH----hCCCHHhhhhhh-----cCCC----C----CCcCHHHHHHHHHHHHHhCCC
Confidence 488999999 999999996655 3421 0 014899999999999998863
No 257
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=38.48 E-value=28 Score=28.41 Aligned_cols=31 Identities=13% Similarity=0.189 Sum_probs=25.2
Q ss_pred HHHHHHHcCCceeeecCccceEEeCcchHhhhcC
Q 044490 29 LAYQLISYGYLTETIKDVYRTVSVSQQGKQYLGS 62 (430)
Q Consensus 29 li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~g 62 (430)
-...|...|+|... ..+.+.||++|+++|..
T Consensus 60 a~~~L~~aGli~~~---~rG~~~iT~~G~~~l~~ 90 (92)
T PF14338_consen 60 ARSYLKKAGLIERP---KRGIWRITEKGRKALAE 90 (92)
T ss_pred HHHHHHHCCCccCC---CCCceEECHhHHHHHhh
Confidence 45679999999754 34799999999999975
No 258
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=37.72 E-value=51 Score=31.77 Aligned_cols=42 Identities=17% Similarity=0.185 Sum_probs=34.4
Q ss_pred hHHHHHHHHH-hcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 215 AKYEAWKMWH-EDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 215 t~~~T~~l~~-~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
|...-+.++. ..+.|..|||++ -+++..+|-.||..+...|.
T Consensus 12 tr~~il~lL~~~g~~sa~elA~~----Lgis~~avR~HL~~Le~~Gl 54 (218)
T COG2345 12 TRERILELLKKSGPVSADELAEE----LGISPMAVRRHLDDLEAEGL 54 (218)
T ss_pred HHHHHHHHHhccCCccHHHHHHH----hCCCHHHHHHHHHHHHhCcc
Confidence 4444444443 369999999999 99999999999999999994
No 259
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein 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. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=37.67 E-value=23 Score=29.30 Aligned_cols=45 Identities=24% Similarity=0.343 Sum_probs=34.0
Q ss_pred CCchHHHHHHHHH-----hcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 212 LTPAKYEAWKMWH-----EDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 212 l~~t~~~T~~l~~-----~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
+++-..+.|..++ ++|.++.+||+. .++....|...|..++..|+
T Consensus 45 ~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~----l~~~~~~v~~al~~L~~eG~ 94 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQQPNSEEGVHVDEIAQQ----LGMSENEVRKALDFLSNEGH 94 (102)
T ss_dssp S-HHHHHHHHHHHC----TTTEEHHHHHHH----STS-HHHHHHHHHHHHHTTS
T ss_pred CCHHHHHHHHHHHhcCCCCCcccHHHHHHH----hCcCHHHHHHHHHHHHhCCe
Confidence 3444445555554 269999999998 79999999999999999996
No 260
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=37.14 E-value=36 Score=31.64 Aligned_cols=33 Identities=21% Similarity=0.240 Sum_probs=27.7
Q ss_pred HHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHH
Q 044490 217 YEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLE 254 (430)
Q Consensus 217 ~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~ 254 (430)
...+.++. +|+|+.+||.. -+++.+||+.++..
T Consensus 163 ~~i~~~~~-~g~s~~~iak~----lgis~~Tv~r~~k~ 195 (200)
T PRK13413 163 EKIKKLLD-KGTSKSEIARK----LGVSRTTLARFLKT 195 (200)
T ss_pred HHHHHHHH-CCCCHHHHHHH----HCCCHHHHHHHHHh
Confidence 34566666 99999999998 89999999999863
No 261
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=36.72 E-value=52 Score=30.80 Aligned_cols=42 Identities=19% Similarity=0.206 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHHHHcCCceeee-cCc--cceEEeCcchHhhhcC
Q 044490 21 HSSNWWKTLAYQLISYGYLTETI-KDV--YRTVSVSQQGKQYLGS 62 (430)
Q Consensus 21 ls~~~wk~li~qLi~~GyL~e~~-~~~--y~~l~LT~kg~~~L~g 62 (430)
++..-+-.+++.|...|||.... .++ ...|.||++|++++..
T Consensus 71 l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~ 115 (185)
T PRK13777 71 MHVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLE 115 (185)
T ss_pred CCHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence 46677888999999999999752 122 2358999999999874
No 262
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=36.37 E-value=43 Score=33.07 Aligned_cols=46 Identities=22% Similarity=0.248 Sum_probs=37.7
Q ss_pred cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCC
Q 044490 226 DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGC 290 (430)
Q Consensus 226 ~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~ 290 (430)
+..|+.+||+. -|++.+||..-|- |. . +++++..+.|.++++++|+
T Consensus 5 ~~~Ti~dIA~~----agVS~~TVSr~Ln-----~~-----~-----~vs~~tr~~V~~~a~elgY 50 (342)
T PRK10014 5 KKITIHDVALA----AGVSVSTVSLVLS-----GK-----G-----RISTATGERVNQAIEELGF 50 (342)
T ss_pred CCCcHHHHHHH----hCCCHHHHHHHHC-----CC-----C-----CCCHHHHHHHHHHHHHhCC
Confidence 45799999999 9999999977763 32 1 2489999999999999886
No 263
>PRK09526 lacI lac repressor; Reviewed
Probab=36.18 E-value=52 Score=32.46 Aligned_cols=45 Identities=18% Similarity=0.298 Sum_probs=36.5
Q ss_pred CCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCC
Q 044490 227 GLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGC 290 (430)
Q Consensus 227 G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~ 290 (430)
..|+.+||+. -|++.+||..-| .|. . +++++..+.|.++++++|+
T Consensus 5 ~~ti~dIA~~----aGVS~~TVSrvL-----n~~----~------~vs~~tr~rV~~~a~elgY 49 (342)
T PRK09526 5 PVTLYDVARY----AGVSYQTVSRVL-----NQA----S------HVSAKTREKVEAAMAELNY 49 (342)
T ss_pred CCcHHHHHHH----hCCCHHHHHHHh-----cCC----C------CCCHHHHHHHHHHHHHHCC
Confidence 3589999999 999999997766 332 1 2489999999999999886
No 264
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=36.02 E-value=20 Score=32.85 Aligned_cols=33 Identities=24% Similarity=0.416 Sum_probs=26.2
Q ss_pred HHHHHHHhcCCCHHHHhcCCCCCCC-CChhhHHHHHHHH
Q 044490 218 EAWKMWHEDGLSIQKIANYPGRSAP-IKEQTVVDYLLEA 255 (430)
Q Consensus 218 ~T~~l~~~~G~si~eIA~~~~r~R~-L~~sTI~~HL~~~ 255 (430)
.--+||. +|+|..|||.. -| ++.+.|++.+-.+
T Consensus 10 ~L~~lw~-~G~SasqIA~~----lg~vsRnAViGk~hRl 43 (162)
T PF07750_consen 10 RLRKLWA-EGLSASQIARQ----LGGVSRNAVIGKAHRL 43 (162)
T ss_pred HHHHHHH-cCCCHHHHHHH----hCCcchhhhhhhhhcc
Confidence 3445676 99999999998 77 8999997766654
No 265
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=36.01 E-value=34 Score=25.40 Aligned_cols=32 Identities=19% Similarity=0.265 Sum_probs=29.0
Q ss_pred hcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 225 EDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 225 ~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
+.-.++.++|+. -+++..||...|..+...|.
T Consensus 12 ~~~~s~~ela~~----~~VS~~TiRRDl~~L~~~g~ 43 (57)
T PF08220_consen 12 KGKVSVKELAEE----FGVSEMTIRRDLNKLEKQGL 43 (57)
T ss_pred cCCEEHHHHHHH----HCcCHHHHHHHHHHHHHCCC
Confidence 357899999999 99999999999999999995
No 266
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=36.01 E-value=43 Score=32.83 Aligned_cols=44 Identities=14% Similarity=0.172 Sum_probs=36.2
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++..+..+.+..-+|+|..|||+. -+++.+||..++..+..
T Consensus 214 ~~L~~rer~vl~l~y~~~~t~~EIA~~----lgis~~~V~~~~~ral~ 257 (264)
T PRK07122 214 AALPERERTVLVLRFFESMTQTQIAER----VGISQMHVSRLLAKTLA 257 (264)
T ss_pred HcCCHHHHHHHHHHhcCCCCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 456777777777755489999999999 99999999998877754
No 267
>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=35.97 E-value=74 Score=23.94 Aligned_cols=62 Identities=21% Similarity=0.162 Sum_probs=35.2
Q ss_pred CCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCc--chhhhhhccCCCHHHHHHHHHHHH--HhCCCCChHHHHHhC
Q 044490 228 LSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDI--NWTRLCDEVGLTDEIFSAIQEAIS--KVGCKDKLKPIKNEL 301 (430)
Q Consensus 228 ~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l--~~~~~i~~~~l~~e~~~~I~~a~~--~~g~~~~LkpIke~l 301 (430)
+++.|+|+. -+++.+||--+-.+.....+.- .... ++.+.+..+..... ..| -.|+.|++.+
T Consensus 1 ~~i~evA~~----~gvs~~tlR~~~~~g~l~~~~~~~g~R~------y~~~~l~~l~~i~~l~~~g--~~l~~i~~~l 66 (67)
T cd04764 1 YTIKEVSEI----IGVKPHTLRYYEKEFNLYIPRTENGRRY------YTDEDIELLKKIKTLLEKG--LSIKEIKEIL 66 (67)
T ss_pred CCHHHHHHH----HCcCHHHHHHHHHhcCCCCCCCCCCcee------eCHHHHHHHHHHHHHHHCC--CCHHHHHHHh
Confidence 578899998 9999999875543311111100 1111 36666666654332 234 5777777654
No 268
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=35.94 E-value=66 Score=27.85 Aligned_cols=49 Identities=24% Similarity=0.316 Sum_probs=37.6
Q ss_pred cchhhhhhccCCCHHHHHHHHHHHHHhCCCCChHHHHHhCCCCCCHHHHHHHHHHHH
Q 044490 262 INWTRLCDEVGLTDEIFSAIQEAISKVGCKDKLKPIKNELPDDITYAHIKACLVMEN 318 (430)
Q Consensus 262 l~~~~~i~~~~l~~e~~~~I~~a~~~~g~~~~LkpIke~l~~~isY~~Irl~la~~~ 318 (430)
|.+.+|. .|++|.+..|+..+...| +||.+-..++ +||..+|.-+-.+-
T Consensus 26 F~l~~~~---~L~~E~~~Fi~~Fi~~rG---nlKe~e~~lg--iSYPTvR~rLd~ii 74 (113)
T PF09862_consen 26 FELPWFA---RLSPEQLEFIKLFIKNRG---NLKEMEKELG--ISYPTVRNRLDKII 74 (113)
T ss_pred eccchhh---cCCHHHHHHHHHHHHhcC---CHHHHHHHHC--CCcHHHHHHHHHHH
Confidence 5555554 469999999998888866 6999988886 78999887665433
No 269
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=35.63 E-value=50 Score=28.39 Aligned_cols=38 Identities=8% Similarity=0.079 Sum_probs=31.3
Q ss_pred HHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 218 EAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 218 ~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
....+..+.|.|+.+||.. -+++.+||+.++.++-..|
T Consensus 20 ~aV~~~~~~g~sv~evA~e----~gIs~~tl~~W~r~y~~~~ 57 (121)
T PRK09413 20 AIVQQSFEPGMTVSLVARQ----HGVAASQLFLWRKQYQEGS 57 (121)
T ss_pred HHHHHHHcCCCCHHHHHHH----HCcCHHHHHHHHHHHhhcc
Confidence 3444444489999999999 9999999999999987655
No 270
>PRK11050 manganese transport regulator MntR; Provisional
Probab=35.45 E-value=63 Score=28.93 Aligned_cols=39 Identities=18% Similarity=0.205 Sum_probs=32.9
Q ss_pred CCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhc
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLG 61 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~ 61 (430)
++++.-+.+.++.|...|||... . +..+.||++|+.++.
T Consensus 62 ~is~stVsr~l~~Le~~GlI~r~-~--~~~v~LT~~G~~l~~ 100 (152)
T PRK11050 62 GVSQPTVAKMLKRLARDGLVEMR-P--YRGVFLTPEGEKLAQ 100 (152)
T ss_pred CCCHHHHHHHHHHHHHCCCEEEe-c--CCceEECchHHHHHH
Confidence 47889999999999999999865 2 357899999998865
No 271
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=35.23 E-value=56 Score=31.96 Aligned_cols=45 Identities=24% Similarity=0.302 Sum_probs=36.2
Q ss_pred CCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCCC
Q 044490 228 LSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGCK 291 (430)
Q Consensus 228 ~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~~ 291 (430)
.|+.+||+. -|++.+||...| .|. . +++++..+.|.++++++|+.
T Consensus 2 ~ti~dIA~~----agVS~sTVSr~L-----n~~----~------~vs~~tr~rV~~~a~~lgY~ 46 (311)
T TIGR02405 2 LTIKDIARL----AGVGKSTVSRVL-----NNE----P------KVSIETRERVEQVIQQSGFV 46 (311)
T ss_pred CcHHHHHHH----hCCCHHHHHHHh-----CCC----C------CCCHHHHHHHHHHHHHHCCC
Confidence 478999999 999999998777 332 1 13889999999999998863
No 272
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=34.35 E-value=56 Score=30.60 Aligned_cols=34 Identities=21% Similarity=0.233 Sum_probs=30.6
Q ss_pred HHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 223 WHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 223 ~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
+...+.|+.+||+. -+++.+||..||..+...|.
T Consensus 11 ~~~~~~t~~eLA~~----lgis~~tV~~~L~~Le~~Gl 44 (203)
T TIGR02702 11 LKQGQATAAALAEA----LAISPQAVRRHLKDLETEGL 44 (203)
T ss_pred HHcCCCCHHHHHHH----HCcCHHHHHHHHHHHHHCCC
Confidence 34468999999999 99999999999999999995
No 273
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=34.25 E-value=24 Score=29.32 Aligned_cols=33 Identities=15% Similarity=0.223 Sum_probs=26.2
Q ss_pred HHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 223 WHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 223 ~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
++..|.|+.+|+.. -||+.+|..+-|..-...|
T Consensus 17 L~KrG~sLa~lsr~----~Gls~~TL~nAL~rp~PKg 49 (92)
T PRK10344 17 LRKKGTSMAAESRR----NGLSSSTLANALSRPWPKG 49 (92)
T ss_pred HHHcCCcHHHHHHH----cCCChHHHHHHHcCCCchH
Confidence 34499999999988 9999999877766555444
No 274
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=34.20 E-value=41 Score=30.97 Aligned_cols=31 Identities=13% Similarity=0.122 Sum_probs=25.3
Q ss_pred HHHHHHHhc---CCCHHHHhcCCCCCCCCChhhHHHHH
Q 044490 218 EAWKMWHED---GLSIQKIANYPGRSAPIKEQTVVDYL 252 (430)
Q Consensus 218 ~T~~l~~~~---G~si~eIA~~~~r~R~L~~sTI~~HL 252 (430)
.++++|.++ +.|+.+||+. -|++.+|+|.|.
T Consensus 19 aa~~lf~~~G~~~~ti~~Ia~~----agvsk~t~Y~~F 52 (213)
T PRK09975 19 TAIAQFALRGVSNTTLNDIADA----ANVTRGAIYWHF 52 (213)
T ss_pred HHHHHHHHcCcccCCHHHHHHH----cCCCHHHHHHHc
Confidence 455667655 4799999999 999999999885
No 275
>PRK08609 hypothetical protein; Provisional
Probab=34.11 E-value=62 Score=35.56 Aligned_cols=46 Identities=9% Similarity=0.175 Sum_probs=33.0
Q ss_pred HHHHHHHHhCCCCHHHHhccCCCCHHHHHHHHHHH----HHHHHHHHHhh
Q 044490 139 QTIKKIALARPSTKARLANIDGVNQHLVITHGDHL----LQTIRHLSQKL 184 (430)
Q Consensus 139 ~tL~emA~~~P~T~~eL~~I~Gvg~~k~~kyG~~f----L~~I~~~~~e~ 184 (430)
.-|.++....|...-+|.+|+|||+.++++....+ ++-+...+++.
T Consensus 74 ~~le~l~~~~p~~~~~l~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~~~ 123 (570)
T PRK08609 74 SVLQELKKEVPEGLLPLLKLPGLGGKKIAKLYKELGVVDKESLKEACENG 123 (570)
T ss_pred HHHHHHHhhCcHHHHHHhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHHhC
Confidence 34566666789899999999999999998865433 45555555543
No 276
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=33.92 E-value=77 Score=27.47 Aligned_cols=42 Identities=12% Similarity=0.126 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHHHcCCceeeecCccc---eEEeCcchHhhhc
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETIKDVYR---TVSVSQQGKQYLG 61 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~~~~y~---~l~LT~kg~~~L~ 61 (430)
++|.....+-++.|...|++........| -+.||++|+.++.
T Consensus 48 ~Is~k~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~LT~~G~~L~~ 92 (120)
T COG1733 48 GISPKMLSRRLKELEEDGLVERVVYPEEPPRVEYRLTEKGRDLLP 92 (120)
T ss_pred ccCHHHHHHHHHHHHHCCCEEeeecCCCCceeEEEEhhhHHHHHH
Confidence 38899999999999999999987311112 3899999999875
No 277
>PRK09492 treR trehalose repressor; Provisional
Probab=33.91 E-value=46 Score=32.42 Aligned_cols=46 Identities=24% Similarity=0.377 Sum_probs=36.8
Q ss_pred cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCC
Q 044490 226 DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGC 290 (430)
Q Consensus 226 ~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~ 290 (430)
+..|+.+||+. -|++.+||..-|- +. . +++++..+.|.++++++|+
T Consensus 3 ~~~ti~dIA~~----agVS~~TVSrvLn-----~~----~------~vs~~tr~rV~~~a~elgY 48 (315)
T PRK09492 3 NKLTIKDIARL----SGVGKSTVSRVLN-----NE----S------GVSEETRERVEAVINQHGF 48 (315)
T ss_pred CCCcHHHHHHH----hCCCHHHHhHHhC-----CC----C------CCCHHHHHHHHHHHHHHCC
Confidence 34699999999 9999999976663 32 1 2488999999999999886
No 278
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=33.82 E-value=44 Score=28.36 Aligned_cols=34 Identities=24% Similarity=0.280 Sum_probs=29.7
Q ss_pred HHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 223 WHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 223 ~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
+...|+-+.||+.+ -+++.-|+.+|+..+.+.|.
T Consensus 32 e~~~~mri~ei~rE----l~is~rtvr~~v~~l~rrGl 65 (113)
T COG5625 32 EKGRGMRIREIQRE----LGISERTVRAAVAVLLRRGL 65 (113)
T ss_pred HhcCCchHHHHHHH----HhHHHHHHHHHHHHHHHhhH
Confidence 34467999999988 99999999999999998884
No 279
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=33.71 E-value=62 Score=24.66 Aligned_cols=24 Identities=13% Similarity=0.228 Sum_probs=15.4
Q ss_pred CCCCHHHHhccCCCCHHHHHHHHH
Q 044490 148 RPSTKARLANIDGVNQHLVITHGD 171 (430)
Q Consensus 148 ~P~T~~eL~~I~Gvg~~k~~kyG~ 171 (430)
.-.|.++|.+|+|||+...+..-.
T Consensus 30 ~~a~~e~L~~i~gIG~~~A~si~~ 53 (64)
T PF12826_consen 30 MNASVEELSAIPGIGPKIAQSIYE 53 (64)
T ss_dssp CC--HHHHCTSTT--HHHHHHHHH
T ss_pred HHcCHHHHhccCCcCHHHHHHHHH
Confidence 345889999999999987766533
No 280
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=33.43 E-value=53 Score=35.32 Aligned_cols=44 Identities=16% Similarity=0.123 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhcCCC
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLGSAR 64 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~g~~ 64 (430)
+++...+.+.++.|...||+... ......+.||+.|++++..-.
T Consensus 31 ~l~~~tVt~~i~~Le~kGlV~~~-~~~~~~i~LTeeG~~~~~~g~ 74 (489)
T PRK04172 31 GLPPEAVMRAAEWLEEKGLVKVE-ERVEEVYVLTEEGKKYAEEGL 74 (489)
T ss_pred CcCHHHHHHHHHHHHhCCCEEEE-eeeEEEEEECHHHHHHHHhcC
Confidence 46789999999999999999987 444568999999999998543
No 281
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=33.37 E-value=26 Score=26.92 Aligned_cols=31 Identities=19% Similarity=0.326 Sum_probs=26.5
Q ss_pred cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 226 DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 226 ~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
...|+.+||.. -++++.+|..-|..+++.|+
T Consensus 13 ~~~S~~eLa~~----~~~s~~~ve~mL~~l~~kG~ 43 (69)
T PF09012_consen 13 GRVSLAELARE----FGISPEAVEAMLEQLIRKGY 43 (69)
T ss_dssp -SEEHHHHHHH----TT--HHHHHHHHHHHHCCTS
T ss_pred CCcCHHHHHHH----HCcCHHHHHHHHHHHHHCCc
Confidence 56799999999 99999999999999999997
No 282
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=33.28 E-value=7.7 Score=31.30 Aligned_cols=26 Identities=19% Similarity=0.289 Sum_probs=18.8
Q ss_pred HHhcCCCHHHHhcCCCCCCCCChhhHHHHH
Q 044490 223 WHEDGLSIQKIANYPGRSAPIKEQTVVDYL 252 (430)
Q Consensus 223 ~~~~G~si~eIA~~~~r~R~L~~sTI~~HL 252 (430)
++..|.|+.+||.+ -||+.+|+.+-|
T Consensus 11 L~krG~sL~~lsr~----~Gl~~~tl~nal 36 (78)
T PF13693_consen 11 LRKRGTSLAALSRE----AGLSSSTLRNAL 36 (78)
T ss_dssp HCTTS--HHHHHHH----HSS-HHHHHHTT
T ss_pred HHHcCCCHHHHHHH----cCCCHHHHHHHH
Confidence 44589999999999 999999986544
No 283
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=33.26 E-value=50 Score=29.65 Aligned_cols=37 Identities=19% Similarity=0.266 Sum_probs=30.9
Q ss_pred CHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhcC
Q 044490 22 SSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLGS 62 (430)
Q Consensus 22 s~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~g 62 (430)
+.+-.+.++.||-..||++.+ .. -=.||++|+.+|+.
T Consensus 94 sgsI~RkilqqLE~~G~V~k~-~~---GR~ltp~GrsllD~ 130 (147)
T COG2238 94 SGSIIRKVLQQLEKAGLVEKT-PK---GRVLTPKGRSLLDR 130 (147)
T ss_pred CchHHHHHHHHHHHCCceeec-CC---CceeCccchhHHHH
Confidence 567788999999999999987 42 33799999999985
No 284
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=33.19 E-value=55 Score=32.21 Aligned_cols=46 Identities=17% Similarity=0.260 Sum_probs=37.0
Q ss_pred CCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCCC
Q 044490 227 GLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGCK 291 (430)
Q Consensus 227 G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~~ 291 (430)
..|+.+||+. -|++.+||..-| .|. . +++++..+.|.++++++|+.
T Consensus 5 ~~ti~dIA~~----agVS~~TVSrvL-----n~~----~------~vs~~tr~rV~~~a~elgY~ 50 (331)
T PRK14987 5 RPVLQDVADR----VGVTKMTVSRFL-----RNP----E------QVSVALRGKIAAALDELGYI 50 (331)
T ss_pred CCcHHHHHHH----hCCCHHHhhhhh-----CCC----C------CCCHHHHHHHHHHHHHhCCC
Confidence 3589999999 999999997766 332 1 24889999999999999863
No 285
>PRK13558 bacterio-opsin activator; Provisional
Probab=32.79 E-value=54 Score=36.01 Aligned_cols=44 Identities=20% Similarity=0.124 Sum_probs=39.4
Q ss_pred CCCchHHHHHHHHHhcCC-------CHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 211 KLTPAKYEAWKMWHEDGL-------SIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~-------si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
.||+...+.++...+.|+ |.+|||.. -+++.+|+..||-.+..+
T Consensus 607 ~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~----l~is~~t~~~~lr~a~~~ 657 (665)
T PRK13558 607 DLTDRQLTALQKAYVSGYFEWPRRVEGEELAES----MGISRSTFHQHLRAAERK 657 (665)
T ss_pred hCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHH----hCCCHHHHHHHHHHHHHH
Confidence 588888999998888999 99999999 999999999999887543
No 286
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=32.71 E-value=34 Score=22.81 Aligned_cols=28 Identities=29% Similarity=0.426 Sum_probs=21.9
Q ss_pred CCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 228 LSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 228 ~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
+|-+|||.. -|++..||..-|.++.+.|
T Consensus 3 mtr~diA~~----lG~t~ETVSR~l~~l~~~g 30 (32)
T PF00325_consen 3 MTRQDIADY----LGLTRETVSRILKKLERQG 30 (32)
T ss_dssp --HHHHHHH----HTS-HHHHHHHHHHHHHTT
T ss_pred cCHHHHHHH----hCCcHHHHHHHHHHHHHcC
Confidence 567889998 9999999999998888877
No 287
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=32.64 E-value=33 Score=39.29 Aligned_cols=44 Identities=23% Similarity=0.157 Sum_probs=39.1
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
.+|....+.+.+.. +|+|-+|||++ -.++.+||-.|+-.++.+=
T Consensus 831 ~Ls~RE~eVL~Lia-~G~SN~eIa~~----L~isl~TVKtH~rniy~KL 874 (894)
T COG2909 831 PLSQRELEVLGLIA-QGLSNEEIAQE----LFISLTTVKTHIRNIYQKL 874 (894)
T ss_pred CccHHHHHHHHHHH-ccCCHHHHHHH----HHHHHHHHHHHHHHHHHHh
Confidence 46777788899998 99999999999 9999999999999987654
No 288
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=32.57 E-value=58 Score=31.49 Aligned_cols=44 Identities=16% Similarity=0.129 Sum_probs=35.2
Q ss_pred cCCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++..+..+.+..-+|+|+.+||.. -|++.++|..+...+..
T Consensus 205 ~~L~~rer~vi~~~~~~~~t~~eIA~~----lgis~~~V~~~~~ral~ 248 (254)
T TIGR02850 205 KRLNEREKMILNMRFFEGKTQMEVAEE----IGISQAQVSRLEKAALK 248 (254)
T ss_pred HcCCHHHHHHHHHHHcCCCCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 356666677777765589999999999 99999999988777654
No 289
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=32.54 E-value=40 Score=24.59 Aligned_cols=28 Identities=29% Similarity=0.316 Sum_probs=25.4
Q ss_pred CHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 229 SIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 229 si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
+..+||.. -+++..||..+|..+...|.
T Consensus 27 ~~~~la~~----~~is~~~v~~~l~~L~~~G~ 54 (66)
T cd07377 27 SERELAEE----LGVSRTTVREALRELEAEGL 54 (66)
T ss_pred CHHHHHHH----HCCCHHHHHHHHHHHHHCCC
Confidence 47789988 89999999999999999995
No 290
>PRK00215 LexA repressor; Validated
Probab=32.43 E-value=76 Score=29.54 Aligned_cols=30 Identities=23% Similarity=0.232 Sum_probs=27.5
Q ss_pred CCCHHHHhcCCCCCCCC-ChhhHHHHHHHHHHcCC
Q 044490 227 GLSIQKIANYPGRSAPI-KEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 227 G~si~eIA~~~~r~R~L-~~sTI~~HL~~~i~~G~ 260 (430)
+.|+.|||.. -++ +.+|+..+|..+...|.
T Consensus 23 ~~s~~ela~~----~~~~~~~tv~~~l~~L~~~g~ 53 (205)
T PRK00215 23 PPSRREIADA----LGLRSPSAVHEHLKALERKGF 53 (205)
T ss_pred CCCHHHHHHH----hCCCChHHHHHHHHHHHHCCC
Confidence 4489999998 999 89999999999999996
No 291
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=32.43 E-value=34 Score=34.73 Aligned_cols=45 Identities=13% Similarity=0.165 Sum_probs=35.4
Q ss_pred cCCCchHHHHHHH----HHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 210 TKLTPAKYEAWKM----WHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 210 ~~l~~t~~~T~~l----~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
..|++..+..+.+ ..-+|+|.+|||.. -+++.+||..++..+...
T Consensus 261 ~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~----Lgis~~tV~~~~~rAl~k 309 (325)
T PRK05657 261 FELNDKQREVLARRFGLLGYEAATLEDVARE----IGLTRERVRQIQVEALRR 309 (325)
T ss_pred HcCCHHHHHHHHHHhccCCCCCcCHHHHHHH----HCcCHHHHHHHHHHHHHH
Confidence 4677777777763 22389999999999 999999999998887543
No 292
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=32.30 E-value=65 Score=31.96 Aligned_cols=45 Identities=22% Similarity=0.341 Sum_probs=36.3
Q ss_pred CCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCCC
Q 044490 228 LSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGCK 291 (430)
Q Consensus 228 ~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~~ 291 (430)
.|+.+||+. -|++.+||..-| .|. . +++++..+.|.++++++|+.
T Consensus 2 ~ti~dIA~~----aGVS~~TVSrvL-----n~~----~------~Vs~~tr~kV~~~a~elgY~ 46 (346)
T PRK10401 2 ITIRDVARQ----AGVSVATVSRVL-----NNS----A------LVSADTREAVMKAVSELGYR 46 (346)
T ss_pred CCHHHHHHH----hCCCHHHHHHHH-----CCC----C------CCCHHHHHHHHHHHHHHCCC
Confidence 478999999 999999997666 332 1 24899999999999998863
No 293
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=32.26 E-value=61 Score=31.40 Aligned_cols=43 Identities=16% Similarity=0.102 Sum_probs=33.5
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.+++.....+.+..-+|+|+.|||+. -|++.+||..+...+..
T Consensus 209 ~L~~~er~vi~~~~~~~~t~~eIA~~----lgis~~~V~~~~~~al~ 251 (258)
T PRK08215 209 KLNDREKLILNLRFFQGKTQMEVAEE----IGISQAQVSRLEKAALK 251 (258)
T ss_pred cCCHHHHHHHHHHHhcCCCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 56666666666654489999999999 99999999888776543
No 294
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=32.19 E-value=1.7e+02 Score=28.80 Aligned_cols=43 Identities=19% Similarity=0.163 Sum_probs=33.0
Q ss_pred CCCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.++...+..+.|+.-+++|..|||+. -|+++++|..-..+++.
T Consensus 196 ~L~EREk~Vl~l~y~eelt~kEI~~~----LgISes~VSql~kkai~ 238 (247)
T COG1191 196 PLPEREKLVLVLRYKEELTQKEIAEV----LGISESRVSRLHKKAIK 238 (247)
T ss_pred ccCHHHHHHHHHHHHhccCHHHHHHH----hCccHHHHHHHHHHHHH
Confidence 56666667777776699999999999 99999888665555543
No 295
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=32.11 E-value=42 Score=31.02 Aligned_cols=31 Identities=19% Similarity=0.351 Sum_probs=25.4
Q ss_pred HHHHHHHhcCC---CHHHHhcCCCCCCCCChhhHHHHH
Q 044490 218 EAWKMWHEDGL---SIQKIANYPGRSAPIKEQTVVDYL 252 (430)
Q Consensus 218 ~T~~l~~~~G~---si~eIA~~~~r~R~L~~sTI~~HL 252 (430)
..+.+|.++|+ |+.+||.. -|++.+|+|.|.
T Consensus 19 AA~~lf~e~G~~~~t~~~Ia~~----agvs~~tlY~~F 52 (215)
T PRK10668 19 AALRLFSQQGVSATSLADIAKA----AGVTRGAIYWHF 52 (215)
T ss_pred HHHHHHHHcCcccCCHHHHHHH----hCCChHHHHHHC
Confidence 45567766765 79999999 999999999875
No 296
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=32.06 E-value=3.1e+02 Score=23.83 Aligned_cols=96 Identities=14% Similarity=0.167 Sum_probs=62.9
Q ss_pred HHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchh------hhhhccCCCHHHHHH--HHHHHHHh-CCCC
Q 044490 222 MWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWT------RLCDEVGLTDEIFSA--IQEAISKV-GCKD 292 (430)
Q Consensus 222 l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~------~~i~~~~l~~e~~~~--I~~a~~~~-g~~~ 292 (430)
+|...+.|+.+|.+.-...++++.+||..-|..+...|. +.-. .|-+. +++++... +...+.++ + .
T Consensus 13 lW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~-v~~~k~gr~~~Y~p~--vs~ee~~~~~~~~~~~~~f~--g 87 (130)
T TIGR02698 13 VWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGC-LTTEKEGRKFIYTAL--VSEDEAVENAAQELFSRICS--R 87 (130)
T ss_pred HHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCc-eeeecCCCcEEEEec--CCHHHHHHHHHHHHHHHHHC--C
Confidence 566678899996553223378999999999999999995 5421 11111 36555432 34455553 3 4
Q ss_pred ChHHHHHhC--CCCCCHHHHHHHHHHHHhCCC
Q 044490 293 KLKPIKNEL--PDDITYAHIKACLVMENCGIS 322 (430)
Q Consensus 293 ~LkpIke~l--~~~isY~~Irl~la~~~~~~~ 322 (430)
.++++..+| ...+|=.+|.-....++....
T Consensus 88 s~~~ll~~l~~~~~ls~eele~L~~li~~~~~ 119 (130)
T TIGR02698 88 KVGAVIADLIEESPLSQTDIEKLEKLLSEKKS 119 (130)
T ss_pred CHHHHHHHHHhcCCCCHHHHHHHHHHHHhccc
Confidence 677776666 557898998888777765543
No 297
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=32.00 E-value=55 Score=31.31 Aligned_cols=46 Identities=9% Similarity=0.098 Sum_probs=36.0
Q ss_pred cCCCchHHHHHHHHH----hcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcC
Q 044490 210 TKLTPAKYEAWKMWH----EDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEG 259 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~----~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G 259 (430)
..+++..+..+.+.. .+|+|..|||+. -|++.++|......+...=
T Consensus 175 ~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~----lgis~~~V~q~~~~al~kL 224 (238)
T TIGR02393 175 ETLTERERKVLRMRYGLLDGRPHTLEEVGKE----FNVTRERIRQIESKALRKL 224 (238)
T ss_pred HhCCHHHHHHHHHHhCCCCCCCccHHHHHHH----HCCCHHHHHHHHHHHHHHH
Confidence 356777777777755 489999999999 9999999988877775543
No 298
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=31.94 E-value=57 Score=29.10 Aligned_cols=45 Identities=13% Similarity=0.196 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHHcCCceeee-cCccceEEeCcchHhhhcCCC
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETI-KDVYRTVSVSQQGKQYLGSAR 64 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~-~~~y~~l~LT~kg~~~L~g~~ 64 (430)
..+...+=.+++.|..+|+|.... +..-..+.||++|++.|..+.
T Consensus 74 ~~s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~L~e~~ 119 (135)
T PRK09416 74 EGNEGSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKMLRKAE 119 (135)
T ss_pred cCCCccHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHHHHHHH
Confidence 457888889999999999998752 222357999999999998763
No 299
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=31.89 E-value=76 Score=27.74 Aligned_cols=45 Identities=20% Similarity=0.269 Sum_probs=37.9
Q ss_pred CCchHHHHHHHHHhc-CCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 212 LTPAKYEAWKMWHED-GLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 212 l~~t~~~T~~l~~~~-G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
+.+...+.+.+++.. ..|..+||+. -+++.+||...+.++...|-
T Consensus 6 lD~~D~~IL~~L~~d~r~~~~eia~~----lglS~~~v~~Ri~~L~~~Gi 51 (154)
T COG1522 6 LDDIDRRILRLLQEDARISNAELAER----VGLSPSTVLRRIKRLEEEGV 51 (154)
T ss_pred ccHHHHHHHHHHHHhCCCCHHHHHHH----HCCCHHHHHHHHHHHHHCCc
Confidence 455666777777643 6789999999 99999999999999999995
No 300
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=31.88 E-value=45 Score=23.72 Aligned_cols=32 Identities=25% Similarity=0.238 Sum_probs=22.7
Q ss_pred HHHHHHHHhcC-CCHHHHhcCCCCCCCCChhhHHHHHH
Q 044490 217 YEAWKMWHEDG-LSIQKIANYPGRSAPIKEQTVVDYLL 253 (430)
Q Consensus 217 ~~T~~l~~~~G-~si~eIA~~~~r~R~L~~sTI~~HL~ 253 (430)
...+.-+. .| +|+.+.|.. -++..+|+.+++-
T Consensus 6 ~~Ai~~v~-~g~~S~r~AA~~----ygVp~sTL~~r~~ 38 (45)
T PF05225_consen 6 QKAIEAVK-NGKMSIRKAAKK----YGVPRSTLRRRLR 38 (45)
T ss_dssp HHHHHHHH-TTSS-HHHHHHH----HT--HHHHHHHHH
T ss_pred HHHHHHHH-hCCCCHHHHHHH----HCcCHHHHHHHHc
Confidence 34555566 66 999999999 9999999987764
No 301
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=31.83 E-value=56 Score=32.55 Aligned_cols=44 Identities=16% Similarity=0.287 Sum_probs=36.2
Q ss_pred cCCCchHHHHHHHHH----hcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWH----EDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~----~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..|++..+..+.+.. .+++|++|||+. -|++..||..++..+..
T Consensus 248 ~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~----lgiS~erVrq~~~rAl~ 295 (298)
T TIGR02997 248 AELTPRERQVLRLRFGLDGGEPLTLAEIGRR----LNLSRERVRQIEAKALR 295 (298)
T ss_pred HcCCHHHHHHHHHHhccCCCCCcCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 457777777777754 489999999999 99999999998887764
No 302
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=31.81 E-value=37 Score=32.63 Aligned_cols=39 Identities=15% Similarity=0.322 Sum_probs=32.7
Q ss_pred HHHHHHH--hcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 218 EAWKMWH--EDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 218 ~T~~l~~--~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
..+++|. ..++++.|||+. -++..+|++.+|..+...|+
T Consensus 13 ~IL~~l~~~~~~~~l~eia~~----lglpksT~~RlL~tL~~~G~ 53 (248)
T TIGR02431 13 AVIEAFGAERPRLTLTDVAEA----TGLTRAAARRFLLTLVELGY 53 (248)
T ss_pred HHHHHHhcCCCCCCHHHHHHH----HCcCHHHHHHHHHHHHHCCC
Confidence 3444453 257999999998 99999999999999999996
No 303
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=31.67 E-value=40 Score=31.98 Aligned_cols=31 Identities=26% Similarity=0.310 Sum_probs=25.9
Q ss_pred HHHHHHHhcCC--CHHHHhcCCCCCCCCChhhHHHHH
Q 044490 218 EAWKMWHEDGL--SIQKIANYPGRSAPIKEQTVVDYL 252 (430)
Q Consensus 218 ~T~~l~~~~G~--si~eIA~~~~r~R~L~~sTI~~HL 252 (430)
...++|.+.|+ |+.+||+. -|++.+||+.|.
T Consensus 21 aA~~lF~~~Gy~~s~~~IA~~----AGvsk~tiy~~F 53 (225)
T PRK11552 21 AALAQFGEYGLHATTRDIAAQ----AGQNIAAITYYF 53 (225)
T ss_pred HHHHHHHHhCccCCHHHHHHH----hCCCHHHHHHHc
Confidence 45667877785 89999988 899999999885
No 304
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=31.48 E-value=31 Score=26.48 Aligned_cols=34 Identities=21% Similarity=0.228 Sum_probs=27.8
Q ss_pred HHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHH
Q 044490 219 AWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAV 256 (430)
Q Consensus 219 T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i 256 (430)
...++...|.|+.+||.. -|+..+|++..+.++.
T Consensus 15 ~v~~~~~~g~sv~~va~~----~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 15 AVREYLESGESVSEVARE----YGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHHHHHHHHCHHHHHHHH----HTS-HHHHHHHHHHHH
T ss_pred HHHHHHHCCCceEeeecc----cccccccccHHHHHHh
Confidence 333443399999999999 9999999999999997
No 305
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=31.33 E-value=2.4e+02 Score=23.56 Aligned_cols=35 Identities=17% Similarity=0.286 Sum_probs=31.2
Q ss_pred HHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 222 MWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 222 l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
++.+.+.++.+||.. -+++.+||...+..+...|.
T Consensus 37 l~~~~~~t~~ela~~----~~~~~~tvs~~l~~Le~~Gl 71 (118)
T TIGR02337 37 LAEQGSMEFTQLANQ----ACILRPSLTGILARLERDGL 71 (118)
T ss_pred HHHcCCcCHHHHHHH----hCCCchhHHHHHHHHHHCCC
Confidence 344478999999998 99999999999999999995
No 306
>PF13309 HTH_22: HTH domain
Probab=31.31 E-value=20 Score=27.51 Aligned_cols=22 Identities=27% Similarity=0.311 Sum_probs=19.8
Q ss_pred CCCHHHHhcCCCCCCCCChhhHHHHH
Q 044490 227 GLSIQKIANYPGRSAPIKEQTVVDYL 252 (430)
Q Consensus 227 G~si~eIA~~~~r~R~L~~sTI~~HL 252 (430)
.-+++.+|+. -+++..|||.||
T Consensus 42 Kgav~~vA~~----L~iS~~TVY~YL 63 (64)
T PF13309_consen 42 KGAVEYVAEK----LGISRATVYRYL 63 (64)
T ss_pred CcHHHHHHHH----HCCCHHHHHHHc
Confidence 3588999999 999999999997
No 307
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=31.29 E-value=75 Score=32.96 Aligned_cols=64 Identities=13% Similarity=0.095 Sum_probs=54.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHhCCCCeeecchHHHHHHHHhCCCCHHHHhccCCCCHHHHHHHHHHHHHHHH
Q 044490 108 EADMQLYHMLLEERKKLARVTGTAPYALCGDQTIKKIALARPSTKARLANIDGVNQHLVITHGDHLLQTIR 178 (430)
Q Consensus 108 e~~~~L~~~L~~~R~~lA~e~~vppy~Ifsd~tL~emA~~~P~T~~eL~~I~Gvg~~k~~kyG~~fL~~I~ 178 (430)
+...++++.|+.+.+.++.+.|+|+-++.|- .|.+++.-.+. .++.+..+..+-+|..++.++.
T Consensus 297 p~~~~~~~~lk~l~~~~s~~~gv~~e~las~-~l~~l~~~~~~------~~~~l~gWr~e~~~~~l~~ll~ 360 (361)
T COG0349 297 PGYKAALKALKALLKSVSEKHGVAAELLASR-DLERLLAWGDD------RPEALRGWRRELFGEILLALLE 360 (361)
T ss_pred hhHHHHHHHHHHHHHHhhhhcCCcHHHhccH-HHHHHHHccCC------ChHHHHHHHHHHhHHHHHHHhc
Confidence 4568999999999999999999999999999 99988887633 6667788888888888877663
No 308
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=31.05 E-value=30 Score=28.22 Aligned_cols=25 Identities=24% Similarity=0.141 Sum_probs=18.3
Q ss_pred hcCCCHHHHhcCCCCCCCCChhhHHHHHH
Q 044490 225 EDGLSIQKIANYPGRSAPIKEQTVVDYLL 253 (430)
Q Consensus 225 ~~G~si~eIA~~~~r~R~L~~sTI~~HL~ 253 (430)
+.|+|..|||.. -|.+.+.|..||.
T Consensus 1 ~~G~tq~eIA~~----lGks~s~Vs~~l~ 25 (93)
T PF08535_consen 1 EFGWTQEEIAKR----LGKSRSWVSNHLA 25 (93)
T ss_dssp HTT--HHHHHHH----TT--HHHHHHHHG
T ss_pred CCCCCHHHHHHH----HCCCHHHHHHHHH
Confidence 379999999998 9999999988876
No 309
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=30.89 E-value=37 Score=27.14 Aligned_cols=36 Identities=6% Similarity=0.187 Sum_probs=30.3
Q ss_pred HhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcch
Q 044490 224 HEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINW 264 (430)
Q Consensus 224 ~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~ 264 (430)
..+..+..+|.+. -+++.+++..||..+...|+ +..
T Consensus 11 ~~~~~~f~~L~~~----l~lt~g~Ls~hL~~Le~~Gy-V~~ 46 (80)
T PF13601_consen 11 ANEEATFSELKEE----LGLTDGNLSKHLKKLEEAGY-VEV 46 (80)
T ss_dssp HHSEEEHHHHHHH----TT--HHHHHHHHHHHHHTTS-EEE
T ss_pred hcCCCCHHHHHHH----hCcCHHHHHHHHHHHHHCCC-EEE
Confidence 3488999999998 99999999999999999997 554
No 310
>PHA00542 putative Cro-like protein
Probab=30.86 E-value=70 Score=25.61 Aligned_cols=54 Identities=11% Similarity=0.107 Sum_probs=37.6
Q ss_pred HHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCC
Q 044490 219 AWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGC 290 (430)
Q Consensus 219 T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~ 290 (430)
...++...|+|..++|+. -+++.+||..++ .|. . .. .+.+.+..|.+++.++++
T Consensus 23 l~~~l~~~glTq~elA~~----lgIs~~tIsr~e-----~g~-~---~~-----p~~~~l~ki~~~~~~~~~ 76 (82)
T PHA00542 23 LVCALIRAGWSQEQIADA----TDVSQPTICRIY-----SGR-H---KD-----PRYSVVEKLRHLVLNLDD 76 (82)
T ss_pred HHHHHHHCCCCHHHHHHH----HCcCHHHHHHHH-----cCC-C---CC-----CCHHHHHHHHHHHHHhch
Confidence 344455589999999999 999999996553 332 0 00 145678888888888653
No 311
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=30.83 E-value=92 Score=23.89 Aligned_cols=26 Identities=23% Similarity=0.284 Sum_probs=21.6
Q ss_pred HHhcCCCHHHHhcCCCCCCCCChhhHHHHH
Q 044490 223 WHEDGLSIQKIANYPGRSAPIKEQTVVDYL 252 (430)
Q Consensus 223 ~~~~G~si~eIA~~~~r~R~L~~sTI~~HL 252 (430)
..+.|+|..++|.. .+++.+||...+
T Consensus 14 ~~~~~~t~~~lA~~----~gis~~tis~~~ 39 (78)
T TIGR02607 14 LEPLGLSIRALAKA----LGVSRSTLSRIV 39 (78)
T ss_pred HHHcCCCHHHHHHH----hCCCHHHHHHHH
Confidence 34589999999999 999999997643
No 312
>PRK05949 RNA polymerase sigma factor; Validated
Probab=30.73 E-value=5.8e+02 Score=25.85 Aligned_cols=44 Identities=20% Similarity=0.308 Sum_probs=33.4
Q ss_pred cCCCchHHHHHHHHHh----cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 210 TKLTPAKYEAWKMWHE----DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~----~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
..+++..+..+.|..- +++|++|||+. -|++..||..++..+..
T Consensus 265 ~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~----lgiS~erVrq~~~rAl~ 312 (327)
T PRK05949 265 AELTPQQREVLTLRFGLEDGKELSLAKVGER----LNLSRERVRQLEHQALA 312 (327)
T ss_pred HhCCHHHHHHHHHHhccCCCCCCCHHHHHHH----HCcCHHHHHHHHHHHHH
Confidence 3567777777776432 67999999998 99999999888777654
No 313
>PF12728 HTH_17: Helix-turn-helix domain
Probab=30.62 E-value=32 Score=24.51 Aligned_cols=21 Identities=24% Similarity=0.431 Sum_probs=18.0
Q ss_pred CCHHHHhcCCCCCCCCChhhHHHHH
Q 044490 228 LSIQKIANYPGRSAPIKEQTVVDYL 252 (430)
Q Consensus 228 ~si~eIA~~~~r~R~L~~sTI~~HL 252 (430)
+|+.|+|+. -+++.+||+..+
T Consensus 2 lt~~e~a~~----l~is~~tv~~~~ 22 (51)
T PF12728_consen 2 LTVKEAAEL----LGISRSTVYRWI 22 (51)
T ss_pred CCHHHHHHH----HCcCHHHHHHHH
Confidence 689999999 999999987655
No 314
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=30.60 E-value=88 Score=24.54 Aligned_cols=36 Identities=17% Similarity=0.220 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHHHHHcCCceeeecCccceEEeCcch
Q 044490 21 HSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQG 56 (430)
Q Consensus 21 ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg 56 (430)
+++.-.+.-+..|..+|+|...-.+....+.||++|
T Consensus 35 v~e~avR~alsRl~~~G~L~~~r~Gr~~~Y~Lt~~g 70 (70)
T PF07848_consen 35 VSESAVRTALSRLVRRGWLESERRGRRSYYRLTERG 70 (70)
T ss_dssp --HHHHHHHHHHHHHTTSEEEECCCTEEEEEE-HHH
T ss_pred CChHHHHHHHHHHHHcCceeeeecCccceEeeCCCC
Confidence 678999999999999999998722334578999876
No 315
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=30.28 E-value=38 Score=24.24 Aligned_cols=27 Identities=26% Similarity=0.263 Sum_probs=20.4
Q ss_pred HhcCCCHHHHhcCCCCCCCCChhhHHHHHHH
Q 044490 224 HEDGLSIQKIANYPGRSAPIKEQTVVDYLLE 254 (430)
Q Consensus 224 ~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~ 254 (430)
.+.|+|..++|.. -+++.+||..++..
T Consensus 6 ~~~gls~~~la~~----~gis~~~i~~~~~g 32 (55)
T PF01381_consen 6 KEKGLSQKELAEK----LGISRSTISRIENG 32 (55)
T ss_dssp HHTTS-HHHHHHH----HTS-HHHHHHHHTT
T ss_pred HHcCCCHHHHHHH----hCCCcchhHHHhcC
Confidence 3489999999998 99999999766543
No 316
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=30.15 E-value=52 Score=32.13 Aligned_cols=30 Identities=10% Similarity=0.128 Sum_probs=24.0
Q ss_pred HHHhCCCCHHHHhccCCCCHHHHHHHHHHH
Q 044490 144 IALARPSTKARLANIDGVNQHLVITHGDHL 173 (430)
Q Consensus 144 mA~~~P~T~~eL~~I~Gvg~~k~~kyG~~f 173 (430)
+.+.--.+.++|.+++|+|+.|+++..+.|
T Consensus 218 Lq~~~~AS~~ele~~~G~G~~kak~l~~~l 247 (254)
T KOG2841|consen 218 LQQISNASEGELEQCPGLGPAKAKRLHKFL 247 (254)
T ss_pred HHHHHhcCHhHHHhCcCcCHHHHHHHHHHH
Confidence 445556789999999999999999875544
No 317
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=29.35 E-value=46 Score=24.45 Aligned_cols=32 Identities=31% Similarity=0.274 Sum_probs=23.5
Q ss_pred HHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHH
Q 044490 216 KYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYL 252 (430)
Q Consensus 216 ~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL 252 (430)
..+...++. .|.+..+||.. -|+..+||.+-+
T Consensus 12 K~~iI~~~e-~g~s~~~ia~~----fgv~~sTv~~I~ 43 (53)
T PF04218_consen 12 KLEIIKRLE-EGESKRDIARE----FGVSRSTVSTIL 43 (53)
T ss_dssp HHHHHHHHH-CTT-HHHHHHH----HT--CCHHHHHH
T ss_pred HHHHHHHHH-cCCCHHHHHHH----hCCCHHHHHHHH
Confidence 356667777 99999999999 999999997644
No 318
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=29.27 E-value=1.2e+02 Score=24.66 Aligned_cols=41 Identities=15% Similarity=0.184 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhc
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLG 61 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~ 61 (430)
.++.......+..|+..+++.-. ...|..++||-.|-++|.
T Consensus 35 ~l~~~~~~~~L~~L~~~kLv~~~-~~~Y~GYrLT~~GYD~LA 75 (82)
T PF09202_consen 35 GLSEGEVEKRLKRLVKLKLVSRR-NKPYDGYRLTFLGYDYLA 75 (82)
T ss_dssp T--HHHHHHHHHHHHHTTSEEEE--SSS-EEEE-HHHHHHHH
T ss_pred CcCHHHHHHHHHHHHhcCCcccc-CCCcceEEEeecchhHHH
Confidence 46788999999999999999987 677888999999998874
No 319
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=29.23 E-value=98 Score=24.98 Aligned_cols=33 Identities=27% Similarity=0.261 Sum_probs=30.0
Q ss_pred CCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcch
Q 044490 228 LSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINW 264 (430)
Q Consensus 228 ~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~ 264 (430)
.|=++||++ -++++.+|.-|+..+-..|.+|+-
T Consensus 20 ~SGe~La~~----LgiSRtaVwK~Iq~Lr~~G~~I~s 52 (79)
T COG1654 20 VSGEKLAEE----LGISRTAVWKHIQQLREEGVDIES 52 (79)
T ss_pred ccHHHHHHH----HCccHHHHHHHHHHHHHhCCceEe
Confidence 788999999 999999999999999999986663
No 320
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=28.31 E-value=70 Score=26.45 Aligned_cols=44 Identities=9% Similarity=0.133 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHHcCCceeee--cC-c--cceEEeCcchHhhhcCC
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETI--KD-V--YRTVSVSQQGKQYLGSA 63 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~--~~-~--y~~l~LT~kg~~~L~g~ 63 (430)
..+...+=.+++.|..+|+|.... .+ + -..+.+|++|++.|...
T Consensus 36 ~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~~ 84 (100)
T TIGR03433 36 QVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAAE 84 (100)
T ss_pred ccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHHH
Confidence 466777888999999999999741 11 1 13699999999999864
No 321
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=28.25 E-value=1.1e+02 Score=22.13 Aligned_cols=37 Identities=19% Similarity=0.096 Sum_probs=30.5
Q ss_pred hHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHH
Q 044490 215 AKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAV 256 (430)
Q Consensus 215 t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i 256 (430)
....++..++ .|.+.+++|.. -+++.+||...+..++
T Consensus 8 ~lll~L~~LR-~~~~~~~La~~----FgIs~stvsri~~~~~ 44 (53)
T PF13613_consen 8 QLLLTLMYLR-LNLTFQDLAYR----FGISQSTVSRIFHEWI 44 (53)
T ss_pred HHHHHHHHHH-cCCcHhHHhhh----eeecHHHHHHHHHHHH
Confidence 3456777777 99999999998 9999999988776654
No 322
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=27.96 E-value=2.9e+02 Score=26.78 Aligned_cols=47 Identities=21% Similarity=0.225 Sum_probs=36.4
Q ss_pred cCCCch-HHHHHHHHH--hcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 210 TKLTPA-KYEAWKMWH--EDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 210 ~~l~~t-~~~T~~l~~--~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
++++.. ...-++.++ .+++|.+|+|+. -+++..|+..||.-++..|.
T Consensus 153 kGi~~~Tl~~i~~~~~~~~~~~Taeela~~----~giSRvTaRRYLeyl~~~~~ 202 (224)
T COG4565 153 KGLDELTLQKVREALKEPDQELTAEELAQA----LGISRVTARRYLEYLVSNGI 202 (224)
T ss_pred CCcCHHHHHHHHHHHhCcCCccCHHHHHHH----hCccHHHHHHHHHHHHhcCe
Confidence 445443 334444444 479999999999 99999999999999999985
No 323
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=27.92 E-value=71 Score=31.28 Aligned_cols=43 Identities=14% Similarity=0.165 Sum_probs=32.4
Q ss_pred CCCchHHHHHHHHH--hcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 211 KLTPAKYEAWKMWH--EDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 211 ~l~~t~~~T~~l~~--~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
.|++..+..+.+.. .+|+|..|||+. -+++..||..+...++.
T Consensus 218 ~L~~rer~vl~l~y~~~~~~t~~eIA~~----lgvS~~~V~q~~~~Al~ 262 (270)
T TIGR02392 218 SLDARSRRIIEARWLDDDKLTLQELAAE----YGVSAERIRQIEKNAMK 262 (270)
T ss_pred cCCHHHHHHHHHHhcCCCCcCHHHHHHH----HCCCHHHHHHHHHHHHH
Confidence 46666666666643 358999999998 99999999888777754
No 324
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=27.82 E-value=1.1e+02 Score=24.16 Aligned_cols=36 Identities=8% Similarity=0.148 Sum_probs=27.1
Q ss_pred CCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcch
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQG 56 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg 56 (430)
+.+......++..|...|||.-. .+..+.+.|+...
T Consensus 36 ~i~~~~l~kil~~L~~~Gli~s~-~G~~GGy~L~~~~ 71 (83)
T PF02082_consen 36 GISPSYLRKILQKLKKAGLIESS-RGRGGGYRLARPP 71 (83)
T ss_dssp TS-HHHHHHHHHHHHHTTSEEEE-TSTTSEEEESS-C
T ss_pred CcCHHHHHHHHHHHhhCCeeEec-CCCCCceeecCCH
Confidence 47889999999999999999876 5555666666533
No 325
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=27.50 E-value=33 Score=24.19 Aligned_cols=23 Identities=26% Similarity=0.469 Sum_probs=20.7
Q ss_pred cCCCHHHHhcCCCCCCCCChhhHHHHH
Q 044490 226 DGLSIQKIANYPGRSAPIKEQTVVDYL 252 (430)
Q Consensus 226 ~G~si~eIA~~~~r~R~L~~sTI~~HL 252 (430)
.+.|+.+||+. -+++.++++.|.
T Consensus 15 ~~~s~~~Ia~~----~gvs~~~~y~~f 37 (47)
T PF00440_consen 15 EAVSIRDIARR----AGVSKGSFYRYF 37 (47)
T ss_dssp TTSSHHHHHHH----HTSCHHHHHHHC
T ss_pred HhCCHHHHHHH----HccchhhHHHHc
Confidence 67899999998 999999999885
No 326
>PF05155 Phage_X: Phage X family ; InterPro: IPR022688 The sequences matched by this entry represent a family of phage and plasmid replication proteins. In bacteriophage IKe and related phage, the full-length protein is designated gene II protein. A much shorter protein of unknown function, translated from a conserved in-frame alternative initiator, is designated gene X protein. Members of this family also include plasmid replication proteins. ; GO: 0006260 DNA replication
Probab=27.22 E-value=1.1e+02 Score=25.25 Aligned_cols=41 Identities=17% Similarity=0.216 Sum_probs=31.7
Q ss_pred hHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhh
Q 044490 215 AKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRL 267 (430)
Q Consensus 215 t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~ 267 (430)
+..-.+.+|. .|-.+.+. ++.+|.+.|..++..-| ||+...
T Consensus 16 ~~~~y~~lw~-~G~~lk~~---------~~kstfyrhr~~L~~~G--Idia~~ 56 (92)
T PF05155_consen 16 AFRFYALLWQ-HGDDLKST---------LSKSTFYRHRARLLKIG--IDIAQL 56 (92)
T ss_pred HHHHHHHHHH-CChHHhhh---------ccHHHHHHHHHHHHHcC--CCHHHh
Confidence 4556777888 99555443 88899999999999999 676655
No 327
>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=27.16 E-value=1.2e+02 Score=22.25 Aligned_cols=32 Identities=9% Similarity=0.005 Sum_probs=25.3
Q ss_pred CCCHHHHHHHHHHHHHcCCceeeecCccceEEeCc
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQ 54 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~ 54 (430)
++++..+.++++.|...|+|... . .+.+.+++
T Consensus 36 g~s~~tv~r~l~~L~~~g~i~~~-~--~~~~~l~~ 67 (67)
T cd00092 36 GLTRETVSRTLKELEEEGLISRR-G--RGKYRVNP 67 (67)
T ss_pred CCCHHHHHHHHHHHHHCCCEEec-C--CCeEEeCC
Confidence 37889999999999999999976 3 34566653
No 328
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=27.07 E-value=60 Score=26.90 Aligned_cols=40 Identities=23% Similarity=0.380 Sum_probs=27.6
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCCce-eeecCccceEEeCcchHhhhc
Q 044490 16 GLGKDHSSNWWKTLAYQLISYGYLT-ETIKDVYRTVSVSQQGKQYLG 61 (430)
Q Consensus 16 G~Gk~ls~~~wk~li~qLi~~GyL~-e~~~~~y~~l~LT~kg~~~L~ 61 (430)
|.|+.++.+ ..|+..|++. +....++..+++|++|+.+..
T Consensus 48 G~g~rY~~e------~SLv~lGLV~~~~~~~g~k~Y~lT~~G~~~~~ 88 (90)
T PF07381_consen 48 GDGKRYNKE------DSLVGLGLVEEEEEKGGFKYYRLTEKGKRIAE 88 (90)
T ss_pred cCCCCcCcc------hhHHHcCCeeEeeecCCeeEEEeChhhhhHHh
Confidence 555555554 3699999993 322355678999999998753
No 329
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=26.83 E-value=96 Score=28.41 Aligned_cols=39 Identities=21% Similarity=0.217 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHcCCceeee-cCccceEEeCcchHhhhcCC
Q 044490 25 WWKTLAYQLISYGYLTETI-KDVYRTVSVSQQGKQYLGSA 63 (430)
Q Consensus 25 ~wk~li~qLi~~GyL~e~~-~~~y~~l~LT~kg~~~L~g~ 63 (430)
...+.+..|+..|+|.... .++-..+.+|++|++.|.-.
T Consensus 35 ~lqq~l~eL~es~~i~~~~~~~~~~~y~iTe~G~~tl~~F 74 (163)
T PF14277_consen 35 TLQQALSELVESGLITLETDSDNKTRYSITEKGKETLEFF 74 (163)
T ss_pred HHHHHHHHHHHCCCEEEeeccCCCcEEEECHhhHHHHHHH
Confidence 4678889999999999641 22335799999999999743
No 330
>COG2906 Bfd Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]
Probab=26.64 E-value=70 Score=24.81 Aligned_cols=28 Identities=21% Similarity=0.342 Sum_probs=26.3
Q ss_pred chHHHHHHHHhCCCCHHHHhccCCCCHH
Q 044490 137 GDQTIKKIALARPSTKARLANIDGVNQH 164 (430)
Q Consensus 137 sd~tL~emA~~~P~T~~eL~~I~Gvg~~ 164 (430)
+|+.+++.+..-|.|+.+|.+..|+|..
T Consensus 10 tD~~Ir~av~~g~tt~~el~~~~gvGs~ 37 (63)
T COG2906 10 TDKQIREAVAQGATTLKELRRFTGVGSQ 37 (63)
T ss_pred cHHHHHHHHHHcCCCHHHHHHHcCcccc
Confidence 7999999999999999999999999976
No 331
>PF10711 DUF2513: Hypothetical protein (DUF2513); InterPro: IPR019650 The function of this family is not known.
Probab=26.48 E-value=93 Score=25.96 Aligned_cols=50 Identities=12% Similarity=0.013 Sum_probs=39.7
Q ss_pred cccCCCCCCHHHHHHHHHHHHHcCCceeeecCcc-------ceEEeCcchHhhhcCCC
Q 044490 14 LHGLGKDHSSNWWKTLAYQLISYGYLTETIKDVY-------RTVSVSQQGKQYLGSAR 64 (430)
Q Consensus 14 ~fG~Gk~ls~~~wk~li~qLi~~GyL~e~~~~~y-------~~l~LT~kg~~~L~g~~ 64 (430)
..-...+++.+.+.--+.+|...|||.-.. ..+ ....||..|.++|..-+
T Consensus 25 ~~~~~~~y~~~~i~YHl~lL~eagli~~~~-~~~~~~~~~~~i~~LT~~GHdFLd~IR 81 (102)
T PF10711_consen 25 EEDEIDGYSKEEIAYHLKLLDEAGLIEGSV-SGTMNGPYSFIIKRLTWSGHDFLDAIR 81 (102)
T ss_pred chhcccCCCHHHHHHHHHHHHHCCCeeecc-ccccCCccchhhcccChhHHHHHHHhc
Confidence 455667899999999999999999999762 211 23589999999999754
No 332
>PHA02510 X gene X product; Reviewed
Probab=26.28 E-value=1.4e+02 Score=26.06 Aligned_cols=50 Identities=18% Similarity=0.106 Sum_probs=38.8
Q ss_pred cCCCchHHHHHHHHHhcCCC---HHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhh
Q 044490 210 TKLTPAKYEAWKMWHEDGLS---IQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLC 268 (430)
Q Consensus 210 ~~l~~t~~~T~~l~~~~G~s---i~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i 268 (430)
+.++.+...+|..|. .|+. -+++.+. +..+|.+.|..++..-| ||+....
T Consensus 24 G~~s~aka~~~f~~y-~~l~~~g~~~vk~~------l~k~tFyrhr~~L~~iG--Idia~l~ 76 (116)
T PHA02510 24 GNLSSAKAMRYFGFY-RRLVNEGYDNVADT------MSRATFWRHRKVLKEFG--IDKAQLM 76 (116)
T ss_pred CCcCHHHHHHHHHHH-HhhhhhhHHHHHHH------ccHHHHHHHHHHHHHcC--CChhhcc
Confidence 456778888999998 8888 3444443 88899999999999999 6766654
No 333
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 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 the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=25.92 E-value=3.1e+02 Score=23.82 Aligned_cols=73 Identities=14% Similarity=0.171 Sum_probs=39.0
Q ss_pred HhCCCCHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHhhccCCCCCcCcccccccccceecccccCCCchHHHHHHHHHh
Q 044490 146 LARPSTKARLANIDGVNQHLVITHGDHLLQTIRHLSQKLNLSLDGKVGEHTAFTRKLHVVVNTRTKLTPAKYEAWKMWHE 225 (430)
Q Consensus 146 ~~~P~T~~eL~~I~Gvg~~k~~kyG~~fL~~I~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~t~~~T~~l~~~ 225 (430)
-++..|++++.++.+|.++.+.+. ..++++-... .+...+ -....+...++
T Consensus 20 lrrG~sveeI~e~T~ID~wFL~~i-~~Iv~~e~~L-~~~~~~---------------------------~~~~~L~~aK~ 70 (123)
T PF02787_consen 20 LRRGYSVEEIHELTKIDPWFLEQI-KNIVDMEKEL-KEYLNE---------------------------LDPELLRKAKR 70 (123)
T ss_dssp HHTTB-HHHHHHHH---HHHHHHH-HHHHHHHHHH-HHHGGG-----------------------------HHHHHHHHH
T ss_pred HHcCCCHHHHHHHHCccHHHHHHH-HHHHHHHHHH-HHhhcc---------------------------chHHHHHHHHH
Confidence 467889999999999999988776 3333333332 221100 01124444566
Q ss_pred cCCCHHHHhcCCCCCCCCChhhHHHH
Q 044490 226 DGLSIQKIANYPGRSAPIKEQTVVDY 251 (430)
Q Consensus 226 ~G~si~eIA~~~~r~R~L~~sTI~~H 251 (430)
.|+|=.+||.. .+.++..|...
T Consensus 71 ~GFsD~~IA~l----~~~~e~~vr~~ 92 (123)
T PF02787_consen 71 LGFSDRQIARL----WGVSEEEVREL 92 (123)
T ss_dssp TT--HHHHHHH----HTS-HHHHHHH
T ss_pred cCCCHHHHHhc----cCCCHHHHHHH
Confidence 89999999987 66665555443
No 334
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=25.71 E-value=72 Score=24.45 Aligned_cols=23 Identities=26% Similarity=0.328 Sum_probs=19.6
Q ss_pred CCCHHHHHHHHHHHHHcCCceee
Q 044490 20 DHSSNWWKTLAYQLISYGYLTET 42 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~ 42 (430)
+.+...++.++.+|+..|||...
T Consensus 25 ~~s~~~ve~mL~~l~~kG~I~~~ 47 (69)
T PF09012_consen 25 GISPEAVEAMLEQLIRKGYIRKV 47 (69)
T ss_dssp T--HHHHHHHHHHHHCCTSCEEE
T ss_pred CcCHHHHHHHHHHHHHCCcEEEe
Confidence 47899999999999999999986
No 335
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=25.58 E-value=1.6e+02 Score=21.93 Aligned_cols=61 Identities=7% Similarity=0.068 Sum_probs=40.4
Q ss_pred CCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCCCCChHHHHHhCCC
Q 044490 228 LSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGCKDKLKPIKNELPD 303 (430)
Q Consensus 228 ~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~~~~LkpIke~l~~ 303 (430)
.|+++||+. -+++.+++...+.+..... ...++ ....+..+...+... ...+..|-+.++=
T Consensus 2 ~~~~~la~~----~~~s~~~l~~~f~~~~~~s----~~~~~-----~~~r~~~a~~~l~~~--~~~~~~ia~~~g~ 62 (84)
T smart00342 2 LTLEDLAEA----LGMSPRHLQRLFKKETGTT----PKQYL-----RDRRLERARRLLRDT--DLSVTEIALRVGF 62 (84)
T ss_pred CCHHHHHHH----hCCCHHHHHHHHHHHhCcC----HHHHH-----HHHHHHHHHHHHHcC--CCCHHHHHHHhCC
Confidence 688999998 9999988877777664333 34444 333455555555442 3678888888776
No 336
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=25.51 E-value=88 Score=22.14 Aligned_cols=32 Identities=16% Similarity=0.096 Sum_probs=24.7
Q ss_pred HHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHH
Q 044490 219 AWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEA 255 (430)
Q Consensus 219 T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~ 255 (430)
.+.+.. +..|+.+||.. -+++.+||..-+.++
T Consensus 20 i~~~~~-~~~s~~~vA~~----~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 20 ILKLLR-ESRSFKDVARE----LGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHh-hcCCHHHHHHH----HCCCHHHHHHHHHhh
Confidence 334444 55799999999 999999998877654
No 337
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=25.50 E-value=82 Score=31.32 Aligned_cols=44 Identities=16% Similarity=0.234 Sum_probs=32.2
Q ss_pred CCCchHHHHHHHHH--hcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHc
Q 044490 211 KLTPAKYEAWKMWH--EDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSE 258 (430)
Q Consensus 211 ~l~~t~~~T~~l~~--~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~ 258 (430)
.+++..+..+.+.. .+|+|..|||+. -+++..||..++..+...
T Consensus 227 ~L~~rer~vl~lr~~~~~~~t~~EIa~~----lgvs~~~V~q~~~~Al~k 272 (289)
T PRK07500 227 TLNERELRIIRERRLREDGATLEALGEE----LGISKERVRQIEARALEK 272 (289)
T ss_pred cCCHHHHHHHHHHhcCCCCCCHHHHHHH----HCCCHHHHHHHHHHHHHH
Confidence 46666666666632 278999999998 889998888777776543
No 338
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=25.45 E-value=59 Score=31.91 Aligned_cols=40 Identities=13% Similarity=0.091 Sum_probs=33.7
Q ss_pred HHHHHHHHh--cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 217 YEAWKMWHE--DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 217 ~~T~~l~~~--~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
...+++|.. .++++.|||+. -++..+|++..|..+...|+
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~----lglpkStv~RlL~tL~~~G~ 69 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLN----LDLPLSTTFRLLKVLQAADF 69 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHH----HCcCHHHHHHHHHHHHHCCC
Confidence 345555643 46899999999 99999999999999999997
No 339
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=25.30 E-value=45 Score=22.79 Aligned_cols=21 Identities=24% Similarity=0.502 Sum_probs=18.2
Q ss_pred CCHHHHhcCCCCCCCCChhhHHHHH
Q 044490 228 LSIQKIANYPGRSAPIKEQTVVDYL 252 (430)
Q Consensus 228 ~si~eIA~~~~r~R~L~~sTI~~HL 252 (430)
+|+.|+|+. -+++.+||...+
T Consensus 2 lt~~e~a~~----lgis~~ti~~~~ 22 (49)
T TIGR01764 2 LTVEEAAEY----LGVSKDTVYRLI 22 (49)
T ss_pred CCHHHHHHH----HCCCHHHHHHHH
Confidence 588999998 999999998765
No 340
>PRK09954 putative kinase; Provisional
Probab=25.27 E-value=96 Score=31.46 Aligned_cols=40 Identities=15% Similarity=0.213 Sum_probs=33.0
Q ss_pred HHHHHHHHh-cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 217 YEAWKMWHE-DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 217 ~~T~~l~~~-~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
.+-+.++++ .-.|..+||+. -+++.+||..||.++.+.|.
T Consensus 6 ~~il~~l~~~~~~s~~~la~~----l~~s~~~v~~~i~~L~~~g~ 46 (362)
T PRK09954 6 KEILAILRRNPLIQQNEIADI----LQISRSRVAAHIMDLMRKGR 46 (362)
T ss_pred HHHHHHHHHCCCCCHHHHHHH----HCCCHHHHHHHHHHHHHCCC
Confidence 345555552 36899999998 99999999999999999886
No 341
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=25.21 E-value=46 Score=24.54 Aligned_cols=28 Identities=21% Similarity=0.307 Sum_probs=19.6
Q ss_pred HHHhcCCCHHHHhcCCCCCCCCChhhHHHHHH
Q 044490 222 MWHEDGLSIQKIANYPGRSAPIKEQTVVDYLL 253 (430)
Q Consensus 222 l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~ 253 (430)
+..+.|+|..++|+. -|++.+|+...+.
T Consensus 5 ~m~~~~it~~~La~~----~gis~~tl~~~~~ 32 (63)
T PF13443_consen 5 LMAERGITQKDLARK----TGISRSTLSRILN 32 (63)
T ss_dssp HHHHTT--HHHHHHH----HT--HHHHHHHHT
T ss_pred HHHHcCCCHHHHHHH----HCcCHHHHHHHHh
Confidence 445689999999998 9999999977655
No 342
>PRK11569 transcriptional repressor IclR; Provisional
Probab=25.16 E-value=56 Score=32.08 Aligned_cols=39 Identities=18% Similarity=0.278 Sum_probs=32.8
Q ss_pred HHHHHHHh--cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 218 EAWKMWHE--DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 218 ~T~~l~~~--~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
..+++|.+ .++++.|||+. -++..+|++.+|..+...|+
T Consensus 32 ~IL~~l~~~~~~~~lseia~~----lglpksTv~RlL~tL~~~G~ 72 (274)
T PRK11569 32 KLLEWIAESNGSVALTELAQQ----AGLPNSTTHRLLTTMQQQGF 72 (274)
T ss_pred HHHHHHHhCCCCcCHHHHHHH----HCcCHHHHHHHHHHHHHCCC
Confidence 34444542 46899999998 99999999999999999997
No 343
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=25.12 E-value=1.1e+02 Score=22.72 Aligned_cols=33 Identities=18% Similarity=0.205 Sum_probs=21.4
Q ss_pred hHHHHHHHHHhcCCCHHHHhcCCCCCCC-CChhhHHHHH
Q 044490 215 AKYEAWKMWHEDGLSIQKIANYPGRSAP-IKEQTVVDYL 252 (430)
Q Consensus 215 t~~~T~~l~~~~G~si~eIA~~~~r~R~-L~~sTI~~HL 252 (430)
+...-+.++. .|.|++||++. -+ |+...|..-|
T Consensus 20 ~v~~i~~~~~-~G~s~eeI~~~----yp~Lt~~~i~aAl 53 (56)
T PF04255_consen 20 PVRDILDLLA-AGESPEEIAED----YPSLTLEDIRAAL 53 (56)
T ss_dssp BHHHHHHHHH-TT--HHHHHHH----STT--HHHHHHHH
T ss_pred cHHHHHHHHH-cCCCHHHHHHH----CCCCCHHHHHHHH
Confidence 4456677776 99999999987 65 7777776554
No 344
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=24.78 E-value=1.1e+02 Score=25.43 Aligned_cols=34 Identities=21% Similarity=0.150 Sum_probs=25.6
Q ss_pred CCCHHHHhcCCCCC-CCCChhhHHHHHHHHHHcCC
Q 044490 227 GLSIQKIANYPGRS-APIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 227 G~si~eIA~~~~r~-R~L~~sTI~~HL~~~i~~G~ 260 (430)
-+|+++|.+..++. .+++.+|||..|..+...|.
T Consensus 16 ~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gl 50 (116)
T cd07153 16 HLTAEEIYERLRKKGPSISLATVYRTLELLEEAGL 50 (116)
T ss_pred CCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCC
Confidence 47788877652111 25899999999999999995
No 345
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=24.39 E-value=1.4e+02 Score=27.54 Aligned_cols=43 Identities=21% Similarity=0.292 Sum_probs=36.0
Q ss_pred HHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhh
Q 044490 220 WKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLC 268 (430)
Q Consensus 220 ~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i 268 (430)
..+|--+++|++.+|.. -|++.+|+..+-.++-..|. ||+...
T Consensus 12 R~~YV~~~~sLe~aA~~----~gVs~~TarrWK~~Ak~~GD--DWDk~R 54 (165)
T PF08822_consen 12 RRAYVFDRLSLEQAAAK----CGVSYATARRWKREAKAKGD--DWDKAR 54 (165)
T ss_pred HHHHHhCCCCHHHHHHH----hCCCHHHHHHHHHHHHHcCC--cHHHHH
Confidence 33444489999999999 99999999999999999995 676543
No 346
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=24.15 E-value=64 Score=27.74 Aligned_cols=31 Identities=23% Similarity=0.231 Sum_probs=28.3
Q ss_pred cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 226 DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 226 ~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
...|+.+||+. -+++.+++..+|..+.+.|.
T Consensus 24 ~~~s~~eia~~----l~is~~~v~~~l~~L~~~Gl 54 (130)
T TIGR02944 24 QPYSAAEIAEQ----TGLNAPTVSKILKQLSLAGI 54 (130)
T ss_pred CCccHHHHHHH----HCcCHHHHHHHHHHHHHCCc
Confidence 34799999998 99999999999999999995
No 347
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=23.99 E-value=1.6e+02 Score=27.52 Aligned_cols=100 Identities=17% Similarity=0.226 Sum_probs=55.1
Q ss_pred HHHhCCCCHHHHhccCCCCHHHHHHHHHHHHHHHHHHH---HhhccCCCCCcC-----ccccc-ccccceec-ccccCCC
Q 044490 144 IALARPSTKARLANIDGVNQHLVITHGDHLLQTIRHLS---QKLNLSLDGKVG-----EHTAF-TRKLHVVV-NTRTKLT 213 (430)
Q Consensus 144 mA~~~P~T~~eL~~I~Gvg~~k~~kyG~~fL~~I~~~~---~e~~~~~~~~~~-----~~~~~-~~~~~~~~-~~~~~l~ 213 (430)
+|...|.|..+|.+|-|+. + ...+...|.+.. ...++....+.. ..+.. .--..+.. ....++|
T Consensus 18 ~a~~~pls~~~L~~il~~~--~----~~~~~~~l~~l~~~y~~rg~~L~~~~~~~r~~t~~~~~~~~~~l~~~~~~~~LS 91 (184)
T COG1386 18 FAGGEPLSLKELAEILGIV--S----ADAIIDALAELKEEYEDRGLELVEVAEGWRLQTKQEYAEYLEKLQEQRPKRELS 91 (184)
T ss_pred HhcCCCCCHHHHHHHhCCC--c----hHHHHHHHHHHHHhhcCCCeeEEEEcCceeEEehHHHHHHHHHHhccccccccc
Confidence 5778999999999998885 1 122333333322 333322211110 00000 00000111 1124688
Q ss_pred chHHHHHHHH-HhcCCCHHHHhcCCCCCCCCChhhHHHHHH
Q 044490 214 PAKYEAWKMW-HEDGLSIQKIANYPGRSAPIKEQTVVDYLL 253 (430)
Q Consensus 214 ~t~~~T~~l~-~~~G~si~eIA~~~~r~R~L~~sTI~~HL~ 253 (430)
.+..+|+... .++-.|-.+|-++ ||...+++.++|.
T Consensus 92 raalEtLAiIAY~QPiTR~eI~~i----RGv~~~~~i~~L~ 128 (184)
T COG1386 92 RAALETLAIIAYKQPVTRSEIEEI----RGVAVSQVISTLL 128 (184)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHH----hCccHHHHHHHHH
Confidence 8888888754 2389999999999 9998877655544
No 348
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=23.56 E-value=1.3e+02 Score=23.56 Aligned_cols=38 Identities=13% Similarity=0.086 Sum_probs=28.5
Q ss_pred CCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhh
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQY 59 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~ 59 (430)
++++..+.+++..|...|||... . ..+.+.+++....+
T Consensus 31 ~i~~~tv~r~l~~L~~~g~l~~~-~-~~~~y~l~~~~~~~ 68 (91)
T smart00346 31 GLSKSTAHRLLNTLQELGYVEQD-G-QNGRYRLGPKVLEL 68 (91)
T ss_pred CCCHHHHHHHHHHHHHCCCeeec-C-CCCceeecHHHHHH
Confidence 47899999999999999999875 2 23456776654433
No 349
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=23.28 E-value=80 Score=23.52 Aligned_cols=30 Identities=17% Similarity=0.240 Sum_probs=25.0
Q ss_pred HHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHH
Q 044490 223 WHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAV 256 (430)
Q Consensus 223 ~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i 256 (430)
+.+...++.+||+. -+++..||..++.++-
T Consensus 15 ~~~~~~~~~ela~~----l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 15 LKNKWITLKELAKK----LNISERTIKNDINELN 44 (59)
T ss_dssp HHHTSBBHHHHHHH----CTS-HHHHHHHHHHHH
T ss_pred HcCCCCcHHHHHHH----HCCCHHHHHHHHHHHH
Confidence 34578999999999 9999999999988875
No 350
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=23.20 E-value=84 Score=28.39 Aligned_cols=45 Identities=11% Similarity=0.188 Sum_probs=37.5
Q ss_pred CCchHHHHHHHHHhc-CCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 212 LTPAKYEAWKMWHED-GLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 212 l~~t~~~T~~l~~~~-G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
+.....+-+..+++. ..|..+||+. -|++.+||...+.++...|-
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~----lglS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKR----VGLSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHH----HCcCHHHHHHHHHHHHHCCC
Confidence 445556667677544 7899999999 99999999999999999995
No 351
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=23.10 E-value=1.4e+02 Score=27.78 Aligned_cols=43 Identities=14% Similarity=0.044 Sum_probs=32.9
Q ss_pred CCCHHHHHHHHHHHHHcCCceeee---cCccc--eEEeCcchHhhhcC
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETI---KDVYR--TVSVSQQGKQYLGS 62 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~---~~~y~--~l~LT~kg~~~L~g 62 (430)
+++..-+...++.|...|+|.... +.+.+ .+.||++|+..+..
T Consensus 26 gis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~~~~ 73 (203)
T TIGR02702 26 AISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQFPQ 73 (203)
T ss_pred CcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhhccc
Confidence 478999999999999999998651 12222 46999999987653
No 352
>PRK09480 slmA division inhibitor protein; Provisional
Probab=22.94 E-value=75 Score=28.54 Aligned_cols=32 Identities=13% Similarity=0.171 Sum_probs=25.1
Q ss_pred HHHHHHh---cCCCHHHHhcCCCCCCCCChhhHHHHHHH
Q 044490 219 AWKMWHE---DGLSIQKIANYPGRSAPIKEQTVVDYLLE 254 (430)
Q Consensus 219 T~~l~~~---~G~si~eIA~~~~r~R~L~~sTI~~HL~~ 254 (430)
+..+|.+ .+-|+.+||+. -|++.+|+|.|...
T Consensus 19 a~~l~~~~~G~~~ti~~Ia~~----agvs~gt~Y~~F~~ 53 (194)
T PRK09480 19 LAQMLESPPGERITTAKLAAR----VGVSEAALYRHFPS 53 (194)
T ss_pred HHHHHHhcCCCccCHHHHHHH----hCCCHhHHHHHCCC
Confidence 3455543 38899999999 99999999988644
No 353
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=22.75 E-value=1.1e+02 Score=26.64 Aligned_cols=44 Identities=16% Similarity=0.147 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHHcCCceeee--cCc---cceEEeCcchHhhhcCC
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETI--KDV---YRTVSVSQQGKQYLGSA 63 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~--~~~---y~~l~LT~kg~~~L~g~ 63 (430)
..+...+=-+++.|..+||+.... .++ -.++.+|++|++.|...
T Consensus 41 ~~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~~ 89 (138)
T COG1695 41 EPSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAEL 89 (138)
T ss_pred cCCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHHH
Confidence 356777788999999999999763 111 24789999999999864
No 354
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=22.67 E-value=1.1e+02 Score=30.75 Aligned_cols=44 Identities=25% Similarity=0.423 Sum_probs=35.0
Q ss_pred CHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCCC
Q 044490 229 SIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGCK 291 (430)
Q Consensus 229 si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~~ 291 (430)
|+.+||.. -|++.+||..-| .|.+ . +++|..+.|.++++++|+.
T Consensus 2 TikDVA~~----AGVS~sTVSrvl-----n~~~-----~-----Vs~eTr~kV~~a~~elgY~ 45 (333)
T COG1609 2 TIKDVAKL----AGVSKATVSRVL-----NGSP-----Y-----VSEETREKVLAAIKELGYR 45 (333)
T ss_pred CHHHHHHH----hCCCHHHHHHHH-----cCCC-----C-----CCHHHHHHHHHHHHHHCCC
Confidence 78999999 999999995433 3431 2 4899999999999999863
No 355
>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=22.66 E-value=1.7e+02 Score=22.02 Aligned_cols=59 Identities=24% Similarity=0.282 Sum_probs=34.8
Q ss_pred CCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcch------hhhhhccCCCHHHHHHHHHH--HHHhCCCCChHHHHH
Q 044490 228 LSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINW------TRLCDEVGLTDEIFSAIQEA--ISKVGCKDKLKPIKN 299 (430)
Q Consensus 228 ~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~------~~~i~~~~l~~e~~~~I~~a--~~~~g~~~~LkpIke 299 (430)
+++.|+|+. -+++.+||..+-.+. |. +.. .++ ++.+.+..+... +.+.| ..|..|++
T Consensus 1 ~~i~e~A~~----~gVs~~tlr~ye~~~---gl-~~~~r~~~g~R~-----yt~~di~~l~~i~~l~~~g--~~l~~i~~ 65 (68)
T cd04763 1 YTIGEVALL----TGIKPHVLRAWEREF---GL-LKPQRSDGGHRL-----FNDADIDRILEIKRWIDNG--VQVSKVKK 65 (68)
T ss_pred CCHHHHHHH----HCcCHHHHHHHHHhc---CC-CCCCcCCCCCcc-----cCHHHHHHHHHHHHHHHcC--CCHHHHHH
Confidence 478899998 999999997553221 32 211 111 466666666432 22344 57777776
Q ss_pred hC
Q 044490 300 EL 301 (430)
Q Consensus 300 ~l 301 (430)
.+
T Consensus 66 ~l 67 (68)
T cd04763 66 LL 67 (68)
T ss_pred Hh
Confidence 54
No 356
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.47 E-value=2.7e+02 Score=24.13 Aligned_cols=47 Identities=19% Similarity=0.219 Sum_probs=30.9
Q ss_pred cchHHHHHHHHhCCCCHHHHhccCCCCHHHH-HHHHHHHHHHHHHHHH
Q 044490 136 CGDQTIKKIALARPSTKARLANIDGVNQHLV-ITHGDHLLQTIRHLSQ 182 (430)
Q Consensus 136 fsd~tL~emA~~~P~T~~eL~~I~Gvg~~k~-~kyG~~fL~~I~~~~~ 182 (430)
++....-.||..+|.|..+|..|--.-...+ ..-=..|++++.+|+.
T Consensus 66 ~~e~~avkIadI~P~t~~ElRsIla~e~~~~s~E~l~~Ildiv~Ky~~ 113 (114)
T COG1460 66 MSEKIAVKIADIMPRTPDELRSILAKERVMLSDEELDKILDIVDKYRE 113 (114)
T ss_pred ccHHHHHHHHHhCCCCHHHHHHHHHHccCCCCHHHHHHHHHHHHHHhc
Confidence 4788889999999999999998832211111 0012556777776653
No 357
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=22.45 E-value=1.7e+02 Score=24.43 Aligned_cols=40 Identities=13% Similarity=0.171 Sum_probs=32.0
Q ss_pred CCCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhcC
Q 044490 19 KDHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLGS 62 (430)
Q Consensus 19 k~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~g 62 (430)
.+++...+.+=|..|+..||++.. +++ +.+|..|..+|..
T Consensus 42 ~~~~~~~V~SNIGvLIKkglIEKS-GDG---lv~T~~g~~Ii~~ 81 (96)
T PF09114_consen 42 TEMNKASVNSNIGVLIKKGLIEKS-GDG---LVITEEGMDIIIQ 81 (96)
T ss_dssp TTS-HHHHHHHHHHHHHTTSEEEE-TTE---EEE-HHHHHHHHH
T ss_pred HHhhhhHHHHhHHHHHHcCccccc-CCc---eEEechHHHHHHH
Confidence 357888888889999999999987 553 7999999999864
No 358
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.
Probab=22.38 E-value=1.2e+02 Score=30.23 Aligned_cols=44 Identities=18% Similarity=0.286 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhcCC
Q 044490 20 DHSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLGSA 63 (430)
Q Consensus 20 ~ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~g~ 63 (430)
++++.-+...+..|+.+|+|...-.+.-.++.||++|++.+...
T Consensus 31 gi~~~~vr~al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~~ 74 (280)
T TIGR02277 31 GINERLVRTAVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAAA 74 (280)
T ss_pred CCCcchHHHHHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHHH
Confidence 46788899999999999999876212235789999999998754
No 359
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=22.36 E-value=1e+02 Score=26.90 Aligned_cols=85 Identities=13% Similarity=0.140 Sum_probs=51.6
Q ss_pred HHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcch-----hhhhhccCCCHHHHHHHHHHHHHhCCCCChHHH
Q 044490 223 WHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINW-----TRLCDEVGLTDEIFSAIQEAISKVGCKDKLKPI 297 (430)
Q Consensus 223 ~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~-----~~~i~~~~l~~e~~~~I~~a~~~~g~~~~LkpI 297 (430)
+.+.|.+..+||+. -+++.+||..-+..+.+.|. +.- ++=...+.+|++=.+.+..+..... ..+
T Consensus 50 ~~~~~~t~~eLa~~----l~i~~~tvsr~l~~Le~~Gl-I~R~~~~~DrR~~~l~LT~~G~~~~~~~~~~~~-----~~~ 119 (144)
T PRK11512 50 RCAACITPVELKKV----LSVDLGALTRMLDRLVCKGW-VERLPNPNDKRGVLVKLTTSGAAICEQCHQLVG-----QDL 119 (144)
T ss_pred HHcCCCCHHHHHHH----HCCCHHHHHHHHHHHHHCCC-EEeccCcccCCeeEeEEChhHHHHHHHHHHHHH-----HHH
Confidence 44468999999999 99999999999999999996 321 1111113356544444433333221 012
Q ss_pred HHhCCCCCCHHHHHHHHHHH
Q 044490 298 KNELPDDITYAHIKACLVME 317 (430)
Q Consensus 298 ke~l~~~isY~~Irl~la~~ 317 (430)
.+.+-..++-.++..+...+
T Consensus 120 ~~~l~~~ls~ee~~~l~~~L 139 (144)
T PRK11512 120 HQELTKNLTADEVATLEHLL 139 (144)
T ss_pred HHHHHccCCHHHHHHHHHHH
Confidence 33344456667776655544
No 360
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=22.28 E-value=1.2e+02 Score=29.68 Aligned_cols=43 Identities=19% Similarity=0.300 Sum_probs=34.2
Q ss_pred HHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHHhCCC
Q 044490 230 IQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISKVGCK 291 (430)
Q Consensus 230 i~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~~g~~ 291 (430)
+.+||+. -|++.+||..-| .|. . +++++..+.|.++++++|+.
T Consensus 1 i~dIA~~----agVS~~TVSrvL-----n~~-----~-----~vs~~tr~rV~~~a~~lgY~ 43 (327)
T PRK10423 1 MKDVARL----AGVSTSTVSHVI-----NKD-----R-----FVSEAITAKVEAAIKELNYA 43 (327)
T ss_pred ChhHHHH----hCCcHHHHHHHh-----CCC-----C-----CCCHHHHHHHHHHHHHHCCC
Confidence 4689998 999999997776 332 1 24899999999999998863
No 361
>TIGR03734 PRTRC_parB PRTRC system ParB family protein. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family the member related to ParB, and is designated PRTRC system ParB family protein.
Probab=22.22 E-value=2.9e+02 Score=30.44 Aligned_cols=57 Identities=16% Similarity=0.017 Sum_probs=37.1
Q ss_pred cCC-CHHHHhcCCCCCCCCChhhHHHHH---------HHHHHcCCCcchhhhhhccCCCHHHHHHHHHHHHH
Q 044490 226 DGL-SIQKIANYPGRSAPIKEQTVVDYL---------LEAVSEGFDINWTRLCDEVGLTDEIFSAIQEAISK 287 (430)
Q Consensus 226 ~G~-si~eIA~~~~r~R~L~~sTI~~HL---------~~~i~~G~~l~~~~~i~~~~l~~e~~~~I~~a~~~ 287 (430)
+|. +.++||.. -++++++|..+| .+++..| .+.+.....-..++++.++.+...+..
T Consensus 107 ~g~~t~eeIA~~----lG~S~~~V~rrLkL~~L~p~ll~al~~g-~Itl~~A~aLA~l~~e~Q~~vl~~~~~ 173 (554)
T TIGR03734 107 RCKGDREEAARR----LGWSPATLDRRLALMNCTDEVRQALIDR-KILLGHAELLAGLPKDKQDNVLTAILA 173 (554)
T ss_pred hcCCCHHHHHHH----HCCCHHHHHHHHHHcCCCHHHHHHHHcC-CCChHHHHHHhcCCHHHHHHHHHHHHH
Confidence 666 99999988 899999988776 4455555 355543322223566666666665543
No 362
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=22.16 E-value=5e+02 Score=22.36 Aligned_cols=31 Identities=19% Similarity=0.195 Sum_probs=28.9
Q ss_pred cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 226 DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 226 ~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
.|.+..+||+. .+++.+||..-+..+.+.|.
T Consensus 45 ~~~t~~eLa~~----l~~~~~tvt~~v~~Le~~Gl 75 (144)
T PRK03573 45 PEQSQIQLAKA----IGIEQPSLVRTLDQLEEKGL 75 (144)
T ss_pred CCCCHHHHHHH----hCCChhhHHHHHHHHHHCCC
Confidence 36899999999 99999999999999999996
No 363
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=22.05 E-value=1.3e+02 Score=26.72 Aligned_cols=45 Identities=9% Similarity=0.050 Sum_probs=36.9
Q ss_pred CCchHHHHHHHHHhc-CCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 212 LTPAKYEAWKMWHED-GLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 212 l~~t~~~T~~l~~~~-G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
+.+....-+..++.. ..|..+||+. -|++++||..-+..+...|.
T Consensus 7 lD~~D~~Il~~Lq~d~R~s~~eiA~~----lglS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 7 IDNLDRGILEALMENARTPYAELAKQ----FGVSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHH----HCcCHHHHHHHHHHHHHCCC
Confidence 344555666667633 6899999999 99999999999999999995
No 364
>PRK10072 putative transcriptional regulator; Provisional
Probab=21.99 E-value=3.7e+02 Score=22.40 Aligned_cols=54 Identities=15% Similarity=0.075 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHHHHhCCCCeeec----chHHHHHHHHhCCCCHHHHhccCCCCHHHHHHH
Q 044490 112 QLYHMLLEERKKLARVTGTAPYALC----GDQTIKKIALARPSTKARLANIDGVNQHLVITH 169 (430)
Q Consensus 112 ~L~~~L~~~R~~lA~e~~vppy~If----sd~tL~emA~~~P~T~~eL~~I~Gvg~~k~~ky 169 (430)
.|.+.|.++- + ..|..+..++ +..-|+++....-.|-.+|+..-||+..-+.+|
T Consensus 9 ~l~~~~~~~~---~-~~~~~~~~~~~~~~~~~eik~LR~~~glTQ~elA~~lGvS~~TVs~W 66 (96)
T PRK10072 9 ELLSSLEQIV---F-KDETQKITLTQKTTSFTEFEQLRKGTGLKIDDFARVLGVSVAMVKEW 66 (96)
T ss_pred HHHHHHHHHH---H-hcCCccceeecccCChHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Confidence 4444444444 4 4453555655 677799999999999999999999997766665
No 365
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=21.97 E-value=95 Score=31.61 Aligned_cols=31 Identities=23% Similarity=0.201 Sum_probs=27.5
Q ss_pred hHHHHHHHHhCCCCHHHHhccCCCCHHHHHH
Q 044490 138 DQTIKKIALARPSTKARLANIDGVNQHLVIT 168 (430)
Q Consensus 138 d~tL~emA~~~P~T~~eL~~I~Gvg~~k~~k 168 (430)
.+.|..+.+..|.+.++|+.++|||+..++-
T Consensus 254 ~~~l~~~~e~~p~~feeLL~~~GvGp~TlRA 284 (319)
T PF05559_consen 254 WKVLEKAYERQPSDFEELLLIKGVGPSTLRA 284 (319)
T ss_pred HHHHHHHhhCCccCHHHHHhcCCCCHHHHHH
Confidence 4577888899999999999999999998876
No 366
>PRK07758 hypothetical protein; Provisional
Probab=21.69 E-value=44 Score=27.99 Aligned_cols=25 Identities=4% Similarity=0.129 Sum_probs=19.1
Q ss_pred HHHhCCCCHHHHhccCCCCHHHHHH
Q 044490 144 IALARPSTKARLANIDGVNQHLVIT 168 (430)
Q Consensus 144 mA~~~P~T~~eL~~I~Gvg~~k~~k 168 (430)
+......|.++|++|.|||+.-++.
T Consensus 58 L~dLv~~te~ELl~iknlGkKSL~E 82 (95)
T PRK07758 58 VEELSKYSEKEILKLHGMGPASLPK 82 (95)
T ss_pred HHHHHcCCHHHHHHccCCCHHHHHH
Confidence 4444557999999999999886654
No 367
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=21.67 E-value=90 Score=23.02 Aligned_cols=39 Identities=23% Similarity=0.340 Sum_probs=21.5
Q ss_pred CCchHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHH
Q 044490 212 LTPAKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLE 254 (430)
Q Consensus 212 l~~t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~ 254 (430)
|++..+--.......|+|+.+||.. .+-+...|-.||.+
T Consensus 5 Lt~~Eqaqid~m~qlG~s~~~isr~----i~RSr~~Ir~yl~d 43 (50)
T PF11427_consen 5 LTDAEQAQIDVMHQLGMSLREISRR----IGRSRTCIRRYLKD 43 (50)
T ss_dssp --HHHHHHHHHHHHTT--HHHHHHH----HT--HHHHHHHHHS
T ss_pred CCHHHHHHHHHHHHhchhHHHHHHH----hCccHHHHHHHhcC
Confidence 3444433344444499999999988 66666777777643
No 368
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=21.58 E-value=1.4e+02 Score=28.96 Aligned_cols=38 Identities=26% Similarity=0.378 Sum_probs=31.4
Q ss_pred HHHHHHhc--CCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 219 AWKMWHED--GLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 219 T~~l~~~~--G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
-+++|.+. ++++.|||+. -++..+|+..+|..++..|+
T Consensus 9 iL~~l~~~~~~l~l~ela~~----~glpksT~~RlL~tL~~~G~ 48 (246)
T COG1414 9 ILDLLAEGPGGLSLAELAER----LGLPKSTVHRLLQTLVELGY 48 (246)
T ss_pred HHHHHHhCCCCCCHHHHHHH----hCcCHHHHHHHHHHHHHCCC
Confidence 34445433 4569999999 99999999999999999996
No 369
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=21.55 E-value=65 Score=32.45 Aligned_cols=32 Identities=13% Similarity=0.129 Sum_probs=27.0
Q ss_pred HHHHHHHHhCCCCHHHHhccCCCCHHHHHHHH
Q 044490 139 QTIKKIALARPSTKARLANIDGVNQHLVITHG 170 (430)
Q Consensus 139 ~tL~emA~~~P~T~~eL~~I~Gvg~~k~~kyG 170 (430)
.-|.++-...|..+.+|.+|+|||+.+++++.
T Consensus 71 ~~le~l~~~~~~~l~~l~~i~GiGpk~a~~l~ 102 (307)
T cd00141 71 RKLEELREDVPPGLLLLLRVPGVGPKTARKLY 102 (307)
T ss_pred HHHHHHhccchHHHHHHHcCCCCCHHHHHHHH
Confidence 35566666689999999999999999999975
No 370
>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=21.50 E-value=58 Score=22.01 Aligned_cols=23 Identities=17% Similarity=0.286 Sum_probs=18.3
Q ss_pred CCHHHHhcCCCCCCCCChhhHHHHHHH
Q 044490 228 LSIQKIANYPGRSAPIKEQTVVDYLLE 254 (430)
Q Consensus 228 ~si~eIA~~~~r~R~L~~sTI~~HL~~ 254 (430)
+|+.|+|+. -+++.+||..++.+
T Consensus 1 ~s~~e~a~~----lgvs~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAEL----LGVSPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHH----HCcCHHHHHHHHHc
Confidence 578899998 88999998766543
No 371
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=21.17 E-value=80 Score=30.53 Aligned_cols=31 Identities=16% Similarity=0.342 Sum_probs=29.2
Q ss_pred cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 226 DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 226 ~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
.++++.|||+. -++..+|+...|..+...|+
T Consensus 27 ~~l~l~eia~~----lgl~kstv~Rll~tL~~~G~ 57 (257)
T PRK15090 27 REIGITELSQR----VMMSKSTVYRFLQTMKTLGY 57 (257)
T ss_pred CCCCHHHHHHH----HCcCHHHHHHHHHHHHHCCC
Confidence 46899999998 99999999999999999997
No 372
>PHA02535 P terminase ATPase subunit; Provisional
Probab=21.01 E-value=1.9e+02 Score=31.97 Aligned_cols=41 Identities=20% Similarity=0.342 Sum_probs=31.1
Q ss_pred HHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhh
Q 044490 216 KYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLC 268 (430)
Q Consensus 216 ~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i 268 (430)
..+...|+. +|+|+.+||++ -+++.+||+....+ ..|+...
T Consensus 8 K~~Av~Ly~-~G~sv~eIA~~----LGv~~~Tl~~W~kr-------~~w~~~~ 48 (581)
T PHA02535 8 RRAAKFLYW-QGWTVAEIAEE----LGLKSRTIYSWKER-------DGWRDLL 48 (581)
T ss_pred HHHHHHHHH-cCCCHHHHHHH----hCCChhHHHHHhcc-------ccccccC
Confidence 345557787 79999999999 99999999877432 3566655
No 373
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=20.84 E-value=44 Score=25.13 Aligned_cols=62 Identities=27% Similarity=0.363 Sum_probs=35.8
Q ss_pred CCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhc---cCCCHHHHHHHHHH--HHHhCCCCChHHHHHhCC
Q 044490 228 LSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDE---VGLTDEIFSAIQEA--ISKVGCKDKLKPIKNELP 302 (430)
Q Consensus 228 ~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~---~~l~~e~~~~I~~a--~~~~g~~~~LkpIke~l~ 302 (430)
+|+.|+|+. -+++.+||--+. ..|. +...+ .. --++++.+..+... +.+.| -.|..|++.+.
T Consensus 1 yti~eva~~----~gvs~~tlr~y~----~~gl-l~~~~--~~~g~r~y~~~dv~~l~~i~~l~~~G--~sl~~I~~~l~ 67 (69)
T PF13411_consen 1 YTIKEVAKL----LGVSPSTLRYYE----REGL-LPPPR--DENGYRYYSEEDVERLREIKELRKQG--MSLEEIKKLLK 67 (69)
T ss_dssp EEHHHHHHH----TTTTHHHHHHHH----HTTS-STTBE--STTSSEEE-HHHHHHHHHHHHHHHTT--THHHHHHHHH-
T ss_pred CcHHHHHHH----HCcCHHHHHHHH----HhcC-ccccc--ccCceeeccHHHHHHHHHHHHHHHCc--CCHHHHHHHHc
Confidence 478899998 999999986654 4443 33222 00 01366676666432 23345 56777776654
No 374
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.58 E-value=1.5e+02 Score=25.97 Aligned_cols=38 Identities=18% Similarity=0.134 Sum_probs=31.6
Q ss_pred hHHHHHHHHHhcCCCHHHHhcCCCCCCCCChhhHHHHHHHHHH
Q 044490 215 AKYEAWKMWHEDGLSIQKIANYPGRSAPIKEQTVVDYLLEAVS 257 (430)
Q Consensus 215 t~~~T~~l~~~~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~ 257 (430)
|....-+|++ .|+++.|||.. -|+...|++=|+..+-.
T Consensus 98 t~~~i~emlr-~gk~preIsk~----lGIpirTvyY~l~k~k~ 135 (139)
T COG1710 98 TLLRIREMLR-NGKTPREISKD----LGIPIRTVYYLLKKLKK 135 (139)
T ss_pred HHHHHHHHHH-cCCCHHHHHHh----hCCchhhhHHHHHHHhh
Confidence 4445566777 99999999999 99999999999987654
No 375
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=20.57 E-value=1.8e+02 Score=22.34 Aligned_cols=43 Identities=21% Similarity=0.317 Sum_probs=34.6
Q ss_pred chHHHHHHHHHh-cCCCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCC
Q 044490 214 PAKYEAWKMWHE-DGLSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGF 260 (430)
Q Consensus 214 ~t~~~T~~l~~~-~G~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~ 260 (430)
++....+.++.. ...++.+|+.. -+++.+||..||..+...|.
T Consensus 25 ~~r~~il~~l~~~~~~~~~~l~~~----~~~~~~~v~~hL~~L~~~gl 68 (110)
T COG0640 25 PTRLEILSLLAEGGELTVGELAEA----LGLSQSTVSHHLKVLREAGL 68 (110)
T ss_pred HHHHHHHHHHHhcCCccHHHHHHH----HCCChhHHHHHHHHHHHCCC
Confidence 345566666663 26889999987 68999999999999999995
No 376
>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=20.55 E-value=2.2e+02 Score=23.54 Aligned_cols=67 Identities=22% Similarity=0.181 Sum_probs=42.2
Q ss_pred CCHHHHhcCCCCCCCCChhhHHHHHHHHHHcCCCcchhhhhhcc---CCCHHHHHHHHH--HHHHhCCCCChHHHHHhCC
Q 044490 228 LSIQKIANYPGRSAPIKEQTVVDYLLEAVSEGFDINWTRLCDEV---GLTDEIFSAIQE--AISKVGCKDKLKPIKNELP 302 (430)
Q Consensus 228 ~si~eIA~~~~r~R~L~~sTI~~HL~~~i~~G~~l~~~~~i~~~---~l~~e~~~~I~~--a~~~~g~~~~LkpIke~l~ 302 (430)
+++.|+|+. -|++.+||- .+...|. +...+ .+. -++++.+..+.. ..+..| -.|+.|++.+.
T Consensus 2 ~~i~eva~~----~gvs~~tlR----~ye~~Gl-l~~~r--~~~g~R~Y~~~~l~~l~~I~~l~~~G--~~l~ei~~~l~ 68 (102)
T cd04789 2 YTISELAEK----AGISRSTLL----YYEKLGL-ITGTR--NANGYRLYPDSDLQRLLLIQQLQAGG--LSLKECLACLQ 68 (102)
T ss_pred CCHHHHHHH----HCcCHHHHH----HHHHCCC-CCCCc--CCCCCeeCCHHHHHHHHHHHHHHHCC--CCHHHHHHHHc
Confidence 688999998 999999986 3334453 32111 000 147777777653 333445 68899999888
Q ss_pred CCCCH
Q 044490 303 DDITY 307 (430)
Q Consensus 303 ~~isY 307 (430)
+....
T Consensus 69 ~~~~~ 73 (102)
T cd04789 69 GKLTR 73 (102)
T ss_pred CCcHH
Confidence 76543
No 377
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=20.11 E-value=1.3e+02 Score=27.80 Aligned_cols=40 Identities=13% Similarity=0.233 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHHHHcCCceeeecCccceEEeCcchHhhhcC
Q 044490 21 HSSNWWKTLAYQLISYGYLTETIKDVYRTVSVSQQGKQYLGS 62 (430)
Q Consensus 21 ls~~~wk~li~qLi~~GyL~e~~~~~y~~l~LT~kg~~~L~g 62 (430)
-|..-++.++.||-..||++.+ .+. .-=.||++|+..|+.
T Consensus 117 aSg~iiR~~LQqLE~~glVek~-~~~-~GR~lT~~Gr~~LD~ 156 (169)
T PTZ00095 117 ASGKILRWICQQLEKLGLVEQG-PKK-KGRRLTRKGCNFANA 156 (169)
T ss_pred CchHHHHHHHHHHHHCCCEEec-CCC-CCCEECHhHHHHHHH
Confidence 4678899999999999999976 321 223899999999985
Done!