Query psy3735
Match_columns 91
No_of_seqs 120 out of 1090
Neff 9.2
Searched_HMMs 46136
Date Sat Aug 17 00:12:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3735.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3735hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0484|consensus 99.9 1E-25 2.2E-30 126.7 0.9 63 25-89 13-75 (125)
2 KOG0488|consensus 99.9 1.5E-23 3.3E-28 139.0 4.7 63 26-90 169-231 (309)
3 KOG0850|consensus 99.9 3.8E-23 8.2E-28 130.2 4.7 67 23-91 116-182 (245)
4 KOG0489|consensus 99.9 3.1E-23 6.7E-28 135.2 2.8 62 27-90 157-218 (261)
5 KOG0485|consensus 99.9 6.1E-22 1.3E-26 124.1 4.3 63 25-89 100-162 (268)
6 KOG0842|consensus 99.8 1.3E-21 2.7E-26 128.8 5.5 62 26-89 150-211 (307)
7 KOG0494|consensus 99.8 1.5E-21 3.3E-26 125.1 5.5 61 27-89 138-199 (332)
8 KOG0843|consensus 99.8 1.4E-21 3.1E-26 119.3 3.5 61 27-89 100-160 (197)
9 KOG0487|consensus 99.8 4.6E-21 1E-25 126.2 4.8 63 26-90 232-294 (308)
10 KOG2251|consensus 99.8 8.8E-21 1.9E-25 119.0 3.4 64 24-89 32-95 (228)
11 PF00046 Homeobox: Homeobox do 99.8 2.6E-20 5.6E-25 96.2 3.0 57 30-88 1-57 (57)
12 TIGR01565 homeo_ZF_HD homeobox 99.8 8.8E-20 1.9E-24 93.9 4.0 52 30-83 2-57 (58)
13 KOG0492|consensus 99.8 8.8E-20 1.9E-24 113.7 4.1 59 29-89 144-202 (246)
14 KOG0493|consensus 99.7 1.2E-18 2.7E-23 112.0 3.0 58 30-89 247-304 (342)
15 KOG0848|consensus 99.7 7.1E-19 1.5E-23 113.2 0.9 58 31-90 201-258 (317)
16 KOG3802|consensus 99.7 3.9E-18 8.5E-23 114.7 4.2 61 28-90 293-353 (398)
17 COG5576 Homeodomain-containing 99.7 1.2E-17 2.6E-22 101.5 5.0 61 27-89 49-109 (156)
18 KOG0483|consensus 99.7 4.5E-18 9.7E-23 106.6 2.7 57 31-89 52-108 (198)
19 smart00389 HOX Homeodomain. DN 99.7 2E-17 4.4E-22 84.8 3.7 54 31-86 2-55 (56)
20 cd00086 homeodomain Homeodomai 99.7 3.3E-17 7.2E-22 84.7 4.2 57 31-89 2-58 (59)
21 KOG0486|consensus 99.7 2.9E-17 6.2E-22 107.7 4.3 61 27-89 110-170 (351)
22 KOG0844|consensus 99.7 1.7E-17 3.7E-22 108.7 2.9 62 26-89 178-239 (408)
23 KOG0491|consensus 99.6 1.2E-17 2.5E-22 101.0 -0.8 58 29-88 100-157 (194)
24 KOG4577|consensus 99.6 2.4E-16 5.2E-21 102.7 3.6 61 28-90 166-226 (383)
25 KOG0847|consensus 99.6 1.4E-16 3.1E-21 100.3 2.0 62 26-89 164-225 (288)
26 KOG0490|consensus 99.6 3.3E-16 7.1E-21 100.1 2.9 62 26-89 57-118 (235)
27 KOG0849|consensus 99.5 2.5E-14 5.4E-19 96.9 4.4 63 25-89 172-234 (354)
28 KOG1168|consensus 99.5 9.9E-15 2.1E-19 95.3 2.0 64 26-91 306-369 (385)
29 KOG0775|consensus 98.8 5.4E-09 1.2E-13 68.1 3.6 49 37-87 184-232 (304)
30 KOG2252|consensus 98.8 5.8E-09 1.3E-13 73.3 3.5 56 28-85 419-474 (558)
31 KOG0490|consensus 98.7 9.2E-09 2E-13 65.7 3.4 64 25-90 149-212 (235)
32 PF05920 Homeobox_KN: Homeobox 98.6 9.5E-09 2.1E-13 49.2 0.2 34 50-85 7-40 (40)
33 KOG0774|consensus 98.6 3.9E-08 8.5E-13 63.9 2.5 58 30-89 189-249 (334)
34 KOG1146|consensus 98.3 1.6E-06 3.4E-11 66.3 5.0 60 28-89 902-961 (1406)
35 PF11569 Homez: Homeodomain le 97.2 0.00014 3.1E-09 37.0 0.7 42 41-84 10-51 (56)
36 KOG3623|consensus 96.7 0.0011 2.3E-08 49.2 2.4 44 41-86 568-611 (1007)
37 KOG0773|consensus 96.6 0.0049 1.1E-07 41.9 4.6 55 29-85 239-296 (342)
38 PF04218 CENP-B_N: CENP-B N-te 95.6 0.023 4.9E-07 28.5 3.1 47 30-83 1-47 (53)
39 PF04967 HTH_10: HTH DNA bindi 91.1 0.22 4.7E-06 25.1 2.0 39 36-76 1-41 (53)
40 PF04545 Sigma70_r4: Sigma-70, 82.3 1.1 2.4E-05 21.7 1.6 45 35-86 4-48 (50)
41 COG3413 Predicted DNA binding 81.0 1.7 3.7E-05 27.7 2.5 40 35-76 155-196 (215)
42 KOG1146|consensus 80.0 0.91 2E-05 36.4 1.1 56 30-87 445-500 (1406)
43 PF10668 Phage_terminase: Phag 79.0 0.52 1.1E-05 24.4 -0.3 18 59-78 25-42 (60)
44 PF01527 HTH_Tnp_1: Transposas 77.6 0.63 1.4E-05 24.4 -0.3 42 32-80 3-45 (76)
45 PF09607 BrkDBD: Brinker DNA-b 76.0 3.4 7.4E-05 21.2 2.2 45 33-80 3-47 (58)
46 PF08281 Sigma70_r4_2: Sigma-7 75.8 3 6.5E-05 20.3 2.0 42 36-84 11-52 (54)
47 PF00196 GerE: Bacterial regul 74.9 2.4 5.1E-05 21.1 1.5 44 35-86 3-46 (58)
48 cd06171 Sigma70_r4 Sigma70, re 74.6 3.2 6.9E-05 19.4 1.9 43 36-85 11-53 (55)
49 PRK03975 tfx putative transcri 74.2 3.2 6.9E-05 25.1 2.1 48 33-88 4-51 (141)
50 PRK06759 RNA polymerase factor 71.9 4.2 9.2E-05 23.9 2.3 30 58-89 124-153 (154)
51 PRK09413 IS2 repressor TnpA; R 62.4 13 0.00028 21.5 3.0 42 33-80 10-51 (121)
52 PF08138 Sex_peptide: Sex pept 62.0 2.3 5E-05 21.4 -0.2 17 75-91 31-47 (56)
53 PF12824 MRP-L20: Mitochondria 60.6 14 0.0003 22.9 3.0 43 32-78 82-124 (164)
54 cd00569 HTH_Hin_like Helix-tur 60.4 12 0.00027 15.3 2.5 37 35-78 5-41 (42)
55 COG2944 Predicted transcriptio 59.4 7.5 0.00016 22.3 1.6 41 35-84 43-83 (104)
56 cd04761 HTH_MerR-SF Helix-Turn 59.2 2.1 4.5E-05 20.2 -0.6 17 65-81 7-23 (49)
57 KOG3623|consensus 58.9 9.8 0.00021 29.3 2.5 56 31-88 628-683 (1007)
58 PF13411 MerR_1: MerR HTH fami 58.3 2.7 5.8E-05 21.5 -0.3 15 65-79 7-21 (69)
59 PRK12526 RNA polymerase sigma 56.1 11 0.00025 23.6 2.2 28 58-87 171-198 (206)
60 PF06056 Terminase_5: Putative 56.0 1.6 3.4E-05 22.3 -1.4 19 59-79 16-34 (58)
61 PF08880 QLQ: QLQ; InterPro: 55.6 15 0.00032 17.0 2.0 13 35-47 2-14 (37)
62 PF13936 HTH_38: Helix-turn-he 54.2 5.6 0.00012 18.8 0.4 38 34-78 3-40 (44)
63 PRK12512 RNA polymerase sigma 54.1 13 0.00029 22.6 2.3 28 58-87 149-176 (184)
64 PF00376 MerR: MerR family reg 53.7 2.7 5.9E-05 19.4 -0.7 15 65-79 6-20 (38)
65 PRK09646 RNA polymerase sigma 53.3 16 0.00035 22.5 2.5 28 58-87 160-187 (194)
66 PF13518 HTH_28: Helix-turn-he 52.8 4.7 0.0001 19.2 0.0 22 60-83 16-37 (52)
67 PRK04217 hypothetical protein; 52.5 15 0.00032 21.3 2.1 47 33-86 40-86 (110)
68 TIGR03879 near_KaiC_dom probab 52.4 2.1 4.5E-05 23.0 -1.4 23 57-81 33-55 (73)
69 PRK12541 RNA polymerase sigma 52.3 10 0.00022 22.6 1.4 30 59-90 131-160 (161)
70 COG5484 Uncharacterized conser 52.0 5.1 0.00011 26.7 0.1 25 58-86 21-45 (279)
71 PRK11924 RNA polymerase sigma 51.9 14 0.00031 22.0 2.1 27 59-87 144-170 (179)
72 TIGR02937 sigma70-ECF RNA poly 51.7 15 0.00032 20.9 2.1 28 58-87 128-155 (158)
73 PRK09652 RNA polymerase sigma 51.6 13 0.00029 22.2 1.9 46 35-87 128-173 (182)
74 TIGR02989 Sig-70_gvs1 RNA poly 51.1 17 0.00037 21.4 2.3 28 58-87 129-156 (159)
75 PRK00118 putative DNA-binding 50.9 17 0.00036 20.8 2.1 45 35-86 17-61 (104)
76 cd04764 HTH_MlrA-like_sg1 Heli 50.1 4.1 9E-05 20.8 -0.4 17 65-81 7-23 (67)
77 PRK12514 RNA polymerase sigma 49.2 21 0.00046 21.6 2.6 28 58-87 147-174 (179)
78 PRK10072 putative transcriptio 49.1 3.9 8.3E-05 23.1 -0.7 23 59-83 49-71 (96)
79 PRK12519 RNA polymerase sigma 49.0 13 0.00028 22.9 1.6 28 58-87 159-186 (194)
80 TIGR02985 Sig70_bacteroi1 RNA 49.0 18 0.00039 21.1 2.2 28 58-87 131-158 (161)
81 PF11516 DUF3220: Protein of u 48.2 4.6 0.0001 22.1 -0.4 11 73-83 31-41 (106)
82 smart00421 HTH_LUXR helix_turn 47.6 23 0.00051 16.5 2.2 44 35-86 3-46 (58)
83 PF08280 HTH_Mga: M protein tr 47.4 12 0.00027 18.7 1.1 35 39-79 6-40 (59)
84 cd04763 HTH_MlrA-like Helix-Tu 47.2 4.1 9E-05 20.9 -0.7 16 65-80 7-22 (68)
85 KOG3862|consensus 47.1 6 0.00013 26.7 -0.1 27 32-58 222-248 (327)
86 TIGR02948 SigW_bacill RNA poly 46.3 17 0.00037 22.0 1.8 28 58-87 154-181 (187)
87 PRK12515 RNA polymerase sigma 46.0 21 0.00045 21.9 2.2 27 59-87 150-176 (189)
88 PRK09642 RNA polymerase sigma 45.8 21 0.00047 21.1 2.2 27 59-87 125-151 (160)
89 PRK09648 RNA polymerase sigma 45.2 20 0.00044 21.9 2.1 28 58-87 157-184 (189)
90 TIGR02999 Sig-70_X6 RNA polyme 44.7 21 0.00046 21.6 2.1 28 58-87 152-179 (183)
91 PRK09644 RNA polymerase sigma 44.4 20 0.00042 21.4 1.9 28 58-87 126-153 (165)
92 TIGR02959 SigZ RNA polymerase 44.0 23 0.00049 21.4 2.1 28 58-87 118-145 (170)
93 PRK06811 RNA polymerase factor 43.8 27 0.00058 21.4 2.5 31 58-90 149-179 (189)
94 PF13384 HTH_23: Homeodomain-l 43.4 5.3 0.00012 19.0 -0.6 22 58-81 19-40 (50)
95 PRK05602 RNA polymerase sigma 43.0 21 0.00046 21.8 1.9 27 59-87 147-173 (186)
96 PF13443 HTH_26: Cro/C1-type H 42.5 5.4 0.00012 19.9 -0.7 23 59-83 13-35 (63)
97 PRK12537 RNA polymerase sigma 41.9 33 0.00072 20.8 2.7 27 59-87 152-178 (182)
98 PRK12546 RNA polymerase sigma 41.5 22 0.00048 22.0 1.8 27 59-87 132-158 (188)
99 COG2963 Transposase and inacti 41.0 42 0.00092 18.9 2.8 42 33-80 5-47 (116)
100 PRK09639 RNA polymerase sigma 40.9 33 0.00071 20.3 2.5 44 36-87 113-156 (166)
101 TIGR02983 SigE-fam_strep RNA p 40.6 26 0.00057 20.7 2.0 28 59-88 129-156 (162)
102 TIGR02939 RpoE_Sigma70 RNA pol 40.4 18 0.00039 21.9 1.3 28 58-87 156-183 (190)
103 PRK06930 positive control sigm 40.3 27 0.00057 21.6 2.0 46 35-87 114-159 (170)
104 PRK13558 bacterio-opsin activa 39.9 25 0.00054 25.9 2.1 41 34-76 606-648 (665)
105 PF02796 HTH_7: Helix-turn-hel 39.3 16 0.00035 17.2 0.7 37 35-78 5-41 (45)
106 PRK12530 RNA polymerase sigma 39.2 28 0.00061 21.4 2.0 27 59-87 153-179 (189)
107 PF13551 HTH_29: Winged helix- 38.5 47 0.001 18.1 2.8 20 33-52 55-74 (112)
108 PRK12547 RNA polymerase sigma 38.3 31 0.00068 20.6 2.1 28 58-87 130-157 (164)
109 PRK09637 RNA polymerase sigma 38.1 32 0.0007 21.1 2.2 27 59-87 125-151 (181)
110 cd04762 HTH_MerR-trunc Helix-T 38.0 7.1 0.00015 17.9 -0.6 18 65-82 7-24 (49)
111 PRK10403 transcriptional regul 37.8 28 0.0006 20.9 1.8 45 35-87 153-197 (215)
112 cd01104 HTH_MlrA-CarA Helix-Tu 37.7 8.2 0.00018 19.5 -0.5 16 65-80 7-22 (68)
113 PF08279 HTH_11: HTH domain; 37.5 28 0.0006 16.7 1.5 18 58-77 17-34 (55)
114 PRK09047 RNA polymerase factor 37.1 34 0.00075 20.1 2.1 26 59-86 125-150 (161)
115 cd01392 HTH_LacI Helix-turn-he 36.6 7.6 0.00016 18.5 -0.7 18 65-82 4-21 (52)
116 COG4367 Uncharacterized protei 35.6 34 0.00073 19.2 1.7 36 36-73 3-38 (97)
117 TIGR02954 Sig70_famx3 RNA poly 35.5 41 0.00089 20.1 2.3 28 58-87 137-164 (169)
118 PRK06986 fliA flagellar biosyn 34.6 33 0.00072 21.9 1.9 28 58-87 202-229 (236)
119 PRK11511 DNA-binding transcrip 33.4 18 0.00039 21.0 0.5 23 57-81 26-48 (127)
120 smart00422 HTH_MERR helix_turn 33.3 11 0.00024 19.0 -0.4 15 65-79 7-21 (70)
121 PRK12524 RNA polymerase sigma 33.2 40 0.00087 20.8 2.0 27 59-87 155-181 (196)
122 PF08452 DNAP_B_exo_N: DNA pol 33.1 13 0.00027 15.1 -0.2 9 76-84 6-14 (22)
123 PRK13919 putative RNA polymera 33.0 48 0.001 20.1 2.4 27 59-87 154-180 (186)
124 TIGR02952 Sig70_famx2 RNA poly 32.9 41 0.00089 19.9 2.0 27 59-87 141-167 (170)
125 PF07750 GcrA: GcrA cell cycle 32.7 67 0.0015 19.8 2.9 33 36-75 3-36 (162)
126 TIGR03020 EpsA transcriptional 32.3 47 0.001 21.9 2.3 48 33-88 188-235 (247)
127 TIGR00721 tfx DNA-binding prot 32.2 49 0.0011 19.9 2.2 47 33-87 4-50 (137)
128 PRK12532 RNA polymerase sigma 32.2 42 0.0009 20.6 2.0 27 59-87 155-181 (195)
129 PF09292 Neil1-DNA_bind: Endon 31.9 14 0.00029 17.2 -0.2 7 75-81 26-32 (39)
130 PRK12516 RNA polymerase sigma 31.5 47 0.001 20.5 2.1 27 59-87 135-161 (187)
131 cd01105 HTH_GlnR-like Helix-Tu 31.5 12 0.00026 20.4 -0.5 15 65-79 8-22 (88)
132 PRK12518 RNA polymerase sigma 31.1 18 0.00038 21.8 0.2 28 58-87 138-165 (175)
133 PRK09645 RNA polymerase sigma 30.9 56 0.0012 19.5 2.4 26 59-86 137-162 (173)
134 PRK12536 RNA polymerase sigma 30.8 48 0.001 20.1 2.1 28 58-87 147-174 (181)
135 TIGR02479 FliA_WhiG RNA polyme 30.8 47 0.001 21.0 2.1 46 35-87 175-220 (224)
136 PRK12538 RNA polymerase sigma 30.8 35 0.00076 22.0 1.5 28 58-87 189-216 (233)
137 PRK08583 RNA polymerase sigma 30.6 46 0.001 21.6 2.1 45 36-87 206-250 (257)
138 TIGR03541 reg_near_HchA LuxR f 30.6 53 0.0012 21.1 2.3 47 34-88 170-216 (232)
139 PF07037 DUF1323: Putative tra 30.6 16 0.00034 21.6 -0.1 27 60-90 4-30 (122)
140 PRK10360 DNA-binding transcrip 30.2 47 0.001 19.8 1.9 45 35-87 137-181 (196)
141 PRK09480 slmA division inhibit 30.2 46 0.001 20.1 1.9 35 47-84 22-56 (194)
142 cd04766 HTH_HspR Helix-Turn-He 29.9 13 0.00029 20.2 -0.5 16 65-80 8-23 (91)
143 PRK11923 algU RNA polymerase s 29.9 44 0.00095 20.4 1.8 27 59-87 157-183 (193)
144 PRK15369 two component system 29.8 50 0.0011 19.5 2.0 46 34-87 148-193 (211)
145 cd01106 HTH_TipAL-Mta Helix-Tu 29.3 13 0.00029 20.7 -0.6 17 65-81 7-23 (103)
146 PRK09641 RNA polymerase sigma 29.2 47 0.001 20.0 1.8 27 59-87 155-181 (187)
147 KOG0150|consensus 29.1 19 0.00042 24.7 0.1 13 74-86 15-27 (336)
148 PRK09647 RNA polymerase sigma 28.9 57 0.0012 20.5 2.2 27 59-87 157-183 (203)
149 PRK12543 RNA polymerase sigma 28.7 56 0.0012 19.8 2.1 27 59-87 136-162 (179)
150 PRK12522 RNA polymerase sigma 28.5 62 0.0013 19.4 2.3 27 59-87 138-164 (173)
151 cd06170 LuxR_C_like C-terminal 28.4 46 0.00099 15.5 1.4 26 58-85 17-42 (57)
152 PRK12539 RNA polymerase sigma 28.3 59 0.0013 19.8 2.2 28 58-87 149-176 (184)
153 PRK12545 RNA polymerase sigma 28.2 58 0.0013 20.2 2.2 27 59-87 158-184 (201)
154 TIGR02950 SigM_subfam RNA poly 28.1 18 0.00039 21.1 -0.1 29 57-87 122-150 (154)
155 TIGR02957 SigX4 RNA polymerase 27.8 56 0.0012 21.6 2.1 28 59-88 127-154 (281)
156 PRK12511 RNA polymerase sigma 27.7 62 0.0013 19.9 2.2 27 58-86 129-155 (182)
157 PRK12542 RNA polymerase sigma 27.7 56 0.0012 19.9 2.0 27 59-87 141-167 (185)
158 PRK07037 extracytoplasmic-func 27.6 61 0.0013 19.1 2.1 24 58-83 127-150 (163)
159 KOG3755|consensus 27.6 38 0.00083 25.7 1.4 33 54-88 540-572 (769)
160 PRK09649 RNA polymerase sigma 27.4 55 0.0012 20.0 1.9 27 59-87 149-175 (185)
161 PRK12531 RNA polymerase sigma 27.3 67 0.0014 19.8 2.3 27 59-87 160-186 (194)
162 cd04768 HTH_BmrR-like Helix-Tu 26.4 18 0.00039 20.0 -0.3 17 65-81 7-23 (96)
163 PF07638 Sigma70_ECF: ECF sigm 26.2 59 0.0013 20.0 1.9 27 58-86 153-179 (185)
164 cd04774 HTH_YfmP Helix-Turn-He 26.2 17 0.00037 20.2 -0.4 17 65-81 7-23 (96)
165 cd02413 40S_S3_KH K homology R 26.1 34 0.00073 18.5 0.7 20 59-80 56-75 (81)
166 PRK12535 RNA polymerase sigma 26.1 63 0.0014 20.1 2.0 27 59-87 152-178 (196)
167 PRK12513 RNA polymerase sigma 26.0 22 0.00048 21.8 -0.0 28 58-87 157-184 (194)
168 PRK10651 transcriptional regul 26.0 61 0.0013 19.4 2.0 45 35-87 155-199 (216)
169 TIGR02980 SigBFG RNA polymeras 25.8 65 0.0014 20.4 2.1 45 35-86 178-222 (227)
170 PRK12520 RNA polymerase sigma 25.6 67 0.0014 19.6 2.1 27 59-87 150-176 (191)
171 PRK09935 transcriptional regul 25.5 52 0.0011 19.7 1.6 45 35-87 149-193 (210)
172 TIGR02947 SigH_actino RNA poly 25.4 26 0.00055 21.6 0.2 28 58-87 149-176 (193)
173 PF01726 LexA_DNA_bind: LexA D 25.2 42 0.00091 17.3 0.9 38 35-76 3-44 (65)
174 PF01381 HTH_3: Helix-turn-hel 24.8 14 0.0003 17.7 -0.9 23 59-83 12-34 (55)
175 PF14991 MLANA: Protein melan- 24.7 24 0.00053 20.6 0.0 17 73-89 40-56 (118)
176 TIGR02941 Sigma_B RNA polymera 24.6 61 0.0013 21.0 1.8 47 35-88 205-251 (255)
177 cd04775 HTH_Cfa-like Helix-Tur 24.5 19 0.00042 20.1 -0.4 16 65-80 8-23 (102)
178 PF12244 DUF3606: Protein of u 24.5 32 0.00068 17.3 0.4 18 57-76 21-38 (57)
179 PRK05657 RNA polymerase sigma 24.3 63 0.0014 22.1 1.9 50 35-87 262-311 (325)
180 PRK13870 transcriptional regul 24.2 84 0.0018 20.3 2.4 26 59-86 191-216 (234)
181 PHA02955 hypothetical protein; 24.2 1.3E+02 0.0029 19.6 3.2 47 39-87 61-108 (213)
182 cd04779 HTH_MerR-like_sg4 Heli 24.1 18 0.0004 21.5 -0.6 17 65-81 7-23 (134)
183 PF06971 Put_DNA-bind_N: Putat 24.0 18 0.0004 17.8 -0.5 15 60-76 32-46 (50)
184 cd04789 HTH_Cfa Helix-Turn-Hel 23.9 20 0.00044 20.0 -0.4 16 65-80 8-23 (102)
185 PRK15372 pathogenicity island 23.5 55 0.0012 22.0 1.4 28 35-62 11-38 (292)
186 cd04788 HTH_NolA-AlbR Helix-Tu 23.4 21 0.00046 19.7 -0.4 16 65-80 7-22 (96)
187 TIGR02859 spore_sigH RNA polym 23.4 26 0.00056 21.5 -0.1 28 58-87 167-194 (198)
188 PRK10188 DNA-binding transcrip 23.2 91 0.002 20.3 2.4 45 34-86 178-222 (240)
189 PRK08301 sporulation sigma fac 23.2 67 0.0014 20.4 1.8 27 59-87 201-227 (234)
190 cd04767 HTH_HspR-like_MBC Heli 23.2 19 0.0004 21.2 -0.7 16 65-80 8-23 (120)
191 PRK12533 RNA polymerase sigma 23.0 67 0.0014 20.5 1.8 28 58-87 152-179 (216)
192 PRK12529 RNA polymerase sigma 22.9 85 0.0019 19.0 2.2 25 58-84 145-169 (178)
193 TIGR03001 Sig-70_gmx1 RNA poly 22.8 78 0.0017 20.6 2.0 28 58-87 179-206 (244)
194 PRK07670 RNA polymerase sigma 22.7 77 0.0017 20.5 2.0 28 58-87 219-246 (251)
195 smart00027 EH Eps15 homology d 22.7 1.2E+02 0.0025 16.4 2.5 42 36-79 4-50 (96)
196 PRK08295 RNA polymerase factor 22.6 27 0.00057 21.6 -0.1 28 58-87 172-199 (208)
197 TIGR02943 Sig70_famx1 RNA poly 22.6 85 0.0018 19.3 2.1 27 58-86 149-175 (188)
198 PF01710 HTH_Tnp_IS630: Transp 22.5 82 0.0018 18.1 1.9 20 59-80 21-40 (119)
199 PRK09640 RNA polymerase sigma 22.4 27 0.00059 21.4 -0.1 28 58-87 152-179 (188)
200 COG0789 SoxR Predicted transcr 22.4 24 0.00053 20.0 -0.3 15 65-79 7-21 (124)
201 PF12802 MarR_2: MarR family; 22.3 58 0.0013 15.8 1.2 36 36-75 3-38 (62)
202 TIGR03070 couple_hipB transcri 21.9 24 0.00051 16.8 -0.4 23 59-83 18-40 (58)
203 PRK12544 RNA polymerase sigma 21.8 88 0.0019 19.7 2.1 27 59-87 167-193 (206)
204 PRK12528 RNA polymerase sigma 21.7 98 0.0021 18.2 2.2 23 59-83 132-154 (161)
205 PF11388 DotA: Phagosome traff 21.7 25 0.00053 19.9 -0.4 12 75-86 32-43 (105)
206 PF00325 Crp: Bacterial regula 21.6 22 0.00048 15.8 -0.5 17 58-76 4-20 (32)
207 PLN00131 hypothetical protein; 21.5 26 0.00057 21.8 -0.3 12 73-84 206-217 (218)
208 PRK09636 RNA polymerase sigma 21.3 90 0.0019 20.7 2.2 28 59-88 134-161 (293)
209 cd01109 HTH_YyaN Helix-Turn-He 21.2 26 0.00057 19.9 -0.4 16 65-80 7-22 (113)
210 PRK10100 DNA-binding transcrip 21.1 98 0.0021 19.7 2.2 45 35-87 155-199 (216)
211 cd00592 HTH_MerR-like Helix-Tu 20.7 26 0.00057 19.2 -0.4 17 65-81 7-23 (100)
212 cd04780 HTH_MerR-like_sg5 Heli 20.7 26 0.00056 19.5 -0.4 15 65-79 7-21 (95)
213 cd01111 HTH_MerD Helix-Turn-He 20.7 26 0.00056 19.9 -0.4 16 65-80 7-22 (107)
214 cd04782 HTH_BltR Helix-Turn-He 20.6 26 0.00057 19.4 -0.4 16 65-80 7-22 (97)
215 PF04936 DUF658: Protein of un 20.5 24 0.00052 22.1 -0.6 27 58-86 16-42 (186)
216 cd01107 HTH_BmrR Helix-Turn-He 20.4 28 0.00061 19.6 -0.3 16 65-80 7-22 (108)
217 smart00595 MADF subfamily of S 20.1 31 0.00067 18.4 -0.2 24 65-88 34-57 (89)
218 PRK12534 RNA polymerase sigma 20.1 1.4E+02 0.0031 18.0 2.8 26 59-86 156-181 (187)
219 cd04773 HTH_TioE_rpt2 Second H 20.0 29 0.00062 19.7 -0.4 17 65-81 7-23 (108)
No 1
>KOG0484|consensus
Probab=99.91 E-value=1e-25 Score=126.66 Aligned_cols=63 Identities=44% Similarity=0.679 Sum_probs=59.6
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735 25 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS 89 (91)
Q Consensus 25 ~~~k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~ 89 (91)
..++.+|.||.||..||.+||..|...|||++.+|++| |..+.|++..|||||||||+|++++
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEi--A~kidLTEARVQVWFQNRRAKfRKQ 75 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEI--ALKIDLTEARVQVWFQNRRAKFRKQ 75 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHH--HHhhhhhHHHHHHHHHhhHHHHHHH
Confidence 46678889999999999999999999999999999999 9999999999999999999999875
No 2
>KOG0488|consensus
Probab=99.89 E-value=1.5e-23 Score=138.99 Aligned_cols=63 Identities=25% Similarity=0.394 Sum_probs=59.5
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcCC
Q psy3735 26 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSSK 90 (91)
Q Consensus 26 ~~k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~~ 90 (91)
.+|.++.||.||..|+..||..|+++.|++..+|..| |..|||+..||++||||||+|||+++
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~L--A~~LgLTdaQVKtWfQNRRtKWKrq~ 231 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIEL--AASLGLTDAQVKTWFQNRRTKWKRQT 231 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHH--HHHcCCchhhHHHHHhhhhHHHHHHH
Confidence 4667778999999999999999999999999999999 99999999999999999999999874
No 3
>KOG0850|consensus
Probab=99.88 E-value=3.8e-23 Score=130.21 Aligned_cols=67 Identities=22% Similarity=0.324 Sum_probs=61.8
Q ss_pred CCccCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcCCC
Q psy3735 23 SLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSSKY 91 (91)
Q Consensus 23 ~~~~~k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~~~ 91 (91)
....+|.|+.||.++.-||..|...|+...|+-.++|.+| |..|||+..||+|||||||.|+||+++
T Consensus 116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeL--AAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 116 NGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAEL--AASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred CCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHH--HHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 3456677789999999999999999999999999999999 999999999999999999999999763
No 4
>KOG0489|consensus
Probab=99.87 E-value=3.1e-23 Score=135.16 Aligned_cols=62 Identities=26% Similarity=0.338 Sum_probs=58.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcCC
Q psy3735 27 RKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSSK 90 (91)
Q Consensus 27 ~k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~~ 90 (91)
.+.+|.||.||..|+.+||..|+.+.|++...|.+| |..|.|+++||+|||||||+|||+-+
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEi--A~~L~LtErQIKIWFQNRRMK~Kk~~ 218 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEI--AHALNLTERQIKIWFQNRRMKWKKEN 218 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHH--HhhcchhHHHHHHHHHHHHHHHHHhh
Confidence 456889999999999999999999999999999999 99999999999999999999999753
No 5
>KOG0485|consensus
Probab=99.85 E-value=6.1e-22 Score=124.12 Aligned_cols=63 Identities=16% Similarity=0.259 Sum_probs=59.0
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735 25 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS 89 (91)
Q Consensus 25 ~~~k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~ 89 (91)
...++|+.||+|+..|+..||..|+...|++..+|..| |.+|.|++.||+|||||||.||+|.
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~L--A~sLqLTETQVKIWFQNRRnKwKRq 162 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGL--AASLQLTETQVKIWFQNRRNKWKRQ 162 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHH--HHhhhhhhhhhhhhhhhhhHHHHHH
Confidence 34567789999999999999999999999999999998 9999999999999999999999984
No 6
>KOG0842|consensus
Probab=99.85 E-value=1.3e-21 Score=128.75 Aligned_cols=62 Identities=23% Similarity=0.316 Sum_probs=57.7
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735 26 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS 89 (91)
Q Consensus 26 ~~k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~ 89 (91)
.+++|+.|..||..|..+||+.|..+.|++.++|+.| |..|.|++.||||||||||=|-||.
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~L--A~~LrLT~TQVKIWFQNrRYK~KR~ 211 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHL--ASSLRLTPTQVKIWFQNRRYKTKRQ 211 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHH--HHhcCCCchheeeeeecchhhhhhh
Confidence 4566778899999999999999999999999999999 9999999999999999999998874
No 7
>KOG0494|consensus
Probab=99.85 E-value=1.5e-21 Score=125.08 Aligned_cols=61 Identities=43% Similarity=0.759 Sum_probs=55.9
Q ss_pred CCCCCC-CCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735 27 RKQRRY-RTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS 89 (91)
Q Consensus 27 ~k~~r~-R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~ 89 (91)
++++|. ||.||..|+.+||..|...|||+...|+.| |..+.|.+.+|+|||||||+||++-
T Consensus 138 k~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~l--a~ktelpEDRIqVWfQNRRAKWRk~ 199 (332)
T KOG0494|consen 138 KKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREML--ADKTELPEDRIQVWFQNRRAKWRKT 199 (332)
T ss_pred ccccccccchhhHHHHHHHHHHHhhccCccHHHHHHH--hhhccCchhhhhHHhhhhhHHhhhh
Confidence 334444 999999999999999999999999999999 9999999999999999999999873
No 8
>KOG0843|consensus
Probab=99.84 E-value=1.4e-21 Score=119.27 Aligned_cols=61 Identities=25% Similarity=0.300 Sum_probs=58.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735 27 RKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS 89 (91)
Q Consensus 27 ~k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~ 89 (91)
.+.+|.||.||.+|+..||..|+.++|..-.+|+.| |..|+|++.||+|||||||.|.+|+
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~L--A~~L~LsetQVkvWFQNRRtk~kr~ 160 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQL--AQSLSLSETQVKVWFQNRRTKHKRM 160 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhcCCeeechHHHHH--HHHcCCChhHhhhhhhhhhHHHHHH
Confidence 377889999999999999999999999999999999 9999999999999999999998875
No 9
>KOG0487|consensus
Probab=99.83 E-value=4.6e-21 Score=126.16 Aligned_cols=63 Identities=24% Similarity=0.235 Sum_probs=58.9
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcCC
Q psy3735 26 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSSK 90 (91)
Q Consensus 26 ~~k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~~ 90 (91)
.+..|++|..+|..|+.+||..|..|.|.+...|.+| ++.|+|+++||+|||||||+|-||++
T Consensus 232 ~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~El--Sr~lNLTeRQVKIWFQNRRMK~KK~~ 294 (308)
T KOG0487|consen 232 ARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLEL--SRTLNLTERQVKIWFQNRRMKEKKVN 294 (308)
T ss_pred ccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHH--HHhcccchhheeeeehhhhhHHhhhh
Confidence 3566778899999999999999999999999999999 99999999999999999999999875
No 10
>KOG2251|consensus
Probab=99.81 E-value=8.8e-21 Score=118.99 Aligned_cols=64 Identities=41% Similarity=0.546 Sum_probs=60.2
Q ss_pred CccCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735 24 LPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS 89 (91)
Q Consensus 24 ~~~~k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~ 89 (91)
...++.+|.||.|+-.|+++||.+|.+..||++..|++| |.+|+|.+.+|+|||.|||+|+++.
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEel--AlklnLpeSrVqVWFKNRRAK~r~q 95 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREEL--ALKLNLPESRVQVWFKNRRAKCRRQ 95 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHH--HHHhCCchhhhhhhhccccchhhHh
Confidence 446778899999999999999999999999999999999 9999999999999999999999875
No 11
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.80 E-value=2.6e-20 Score=96.16 Aligned_cols=57 Identities=25% Similarity=0.336 Sum_probs=54.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhc
Q psy3735 30 RRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTS 88 (91)
Q Consensus 30 ~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~ 88 (91)
++.|+.||.+|+..|+..|..++||+..+++.| |..+||+..+|++||+|+|++.++
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~l--a~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREEL--AKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHH--HHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccc--cccccccccccccCHHHhHHHhCc
Confidence 467899999999999999999999999999999 999999999999999999999874
No 12
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.79 E-value=8.8e-20 Score=93.94 Aligned_cols=52 Identities=17% Similarity=0.213 Sum_probs=50.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCC----CCHHHhhhhhhhhhcCCCCCcchhccchhH
Q psy3735 30 RRYRTTFTSFQLEELEKAFSRTHY----PDVFTRQCGRFSRQRSMPGELCVAWTHHLN 83 (91)
Q Consensus 30 ~r~R~~~t~~ql~~Le~~f~~~~~----p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR 83 (91)
+|.||.||.+|+..|+..|+.++| |+...++.| |..+||+..+|+|||||.+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~l--a~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREF--CEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHH--HHHhCCCHHHeeeecccCC
Confidence 678999999999999999999999 999999999 9999999999999999975
No 13
>KOG0492|consensus
Probab=99.79 E-value=8.8e-20 Score=113.72 Aligned_cols=59 Identities=25% Similarity=0.307 Sum_probs=55.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735 29 QRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS 89 (91)
Q Consensus 29 ~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~ 89 (91)
.+..||.||..||..||+.|...+|+++.+|.++ +..|.|++.||+|||||||+|.+|-
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraef--SsSL~LTeTqVKIWFQNRRAKaKRl 202 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEF--SSSLELTETQVKIWFQNRRAKAKRL 202 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhh--hhhhhhhhhheehhhhhhhHHHHHH
Confidence 3557999999999999999999999999999998 9999999999999999999998874
No 14
>KOG0493|consensus
Probab=99.73 E-value=1.2e-18 Score=111.95 Aligned_cols=58 Identities=26% Similarity=0.338 Sum_probs=55.7
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735 30 RRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS 89 (91)
Q Consensus 30 ~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~ 89 (91)
+|.||.||.+||..|...|..+.|+....|.+| |..|+|.+.||+|||||+|+|.+++
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~L--a~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQEL--AQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHH--HHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 678999999999999999999999999999999 9999999999999999999999886
No 15
>KOG0848|consensus
Probab=99.72 E-value=7.1e-19 Score=113.18 Aligned_cols=58 Identities=21% Similarity=0.309 Sum_probs=54.4
Q ss_pred CCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcCC
Q psy3735 31 RYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSSK 90 (91)
Q Consensus 31 r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~~ 90 (91)
+.|.++|..|..+||+.|..++|..+..+.+| |.-|||+++||+|||||||+|=+|.|
T Consensus 201 KYRvVYTDhQRLELEKEfh~SryITirRKSEL--A~~LgLsERQVKIWFQNRRAKERK~n 258 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSEL--AATLGLSERQVKIWFQNRRAKERKDN 258 (317)
T ss_pred ceeEEecchhhhhhhhhhccccceeeehhHHH--HHhhCccHhhhhHhhhhhhHHHHHHH
Confidence 46789999999999999999999999999999 99999999999999999999988764
No 16
>KOG3802|consensus
Probab=99.72 E-value=3.9e-18 Score=114.73 Aligned_cols=61 Identities=16% Similarity=0.162 Sum_probs=58.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcCC
Q psy3735 28 KQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSSK 90 (91)
Q Consensus 28 k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~~ 90 (91)
++|++||.|.......||.+|..|+.|+..+...| |.+|+|..++|+|||||||+|-||++
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~i--A~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHI--AESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHH--HHHhccccceEEEEeeccccccccCC
Confidence 56778999999999999999999999999999999 99999999999999999999999875
No 17
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.71 E-value=1.2e-17 Score=101.48 Aligned_cols=61 Identities=26% Similarity=0.259 Sum_probs=55.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735 27 RKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS 89 (91)
Q Consensus 27 ~k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~ 89 (91)
...+++|++.|.+|+..|+..|..+++|+...|..| +..|+|+++.|||||||+|++.++.
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L--~~~lnm~~ksVqIWFQNkR~~~k~~ 109 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKL--SLLLNMPPKSVQIWFQNKRAKEKKK 109 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHH--HHhcCCChhhhhhhhchHHHHHHHh
Confidence 445667788899999999999999999999999999 9999999999999999999997753
No 18
>KOG0483|consensus
Probab=99.71 E-value=4.5e-18 Score=106.56 Aligned_cols=57 Identities=16% Similarity=0.212 Sum_probs=52.4
Q ss_pred CCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735 31 RYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS 89 (91)
Q Consensus 31 r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~ 89 (91)
.+..+|+.+|...||..|+.+.++....+..| |..|||.++||.||||||||+|+.-
T Consensus 52 ~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~L--Ak~LgL~pRQVavWFQNRRARwK~k 108 (198)
T KOG0483|consen 52 GKKRRLTSEQVKFLEKSFESEKKLEPERKKKL--AKELGLQPRQVAVWFQNRRARWKTK 108 (198)
T ss_pred cccccccHHHHHHhHHhhccccccChHHHHHH--HHhhCCChhHHHHHHhhccccccch
Confidence 34467999999999999999999999999988 9999999999999999999999863
No 19
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.69 E-value=2e-17 Score=84.83 Aligned_cols=54 Identities=33% Similarity=0.483 Sum_probs=50.9
Q ss_pred CCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhh
Q psy3735 31 RYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAF 86 (91)
Q Consensus 31 r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~ 86 (91)
+.|+.|+.+|+..|+..|..++||+..++..| |..+||+..+|++||+|+|++.
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~l--a~~~~l~~~qV~~WF~nrR~~~ 55 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREEL--AAKLGLSERQVKVWFQNRRAKW 55 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHH--HHHHCcCHHHHHHhHHHHhhcc
Confidence 45678999999999999999999999999999 9999999999999999999875
No 20
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.69 E-value=3.3e-17 Score=84.71 Aligned_cols=57 Identities=33% Similarity=0.464 Sum_probs=53.5
Q ss_pred CCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735 31 RYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS 89 (91)
Q Consensus 31 r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~ 89 (91)
+.+..|+.+++..|+..|..++||+..++..| |..+||+..+|++||+|+|++.+++
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~l--a~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREEL--AKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHH--HHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 45788999999999999999999999999999 9999999999999999999998765
No 21
>KOG0486|consensus
Probab=99.68 E-value=2.9e-17 Score=107.74 Aligned_cols=61 Identities=38% Similarity=0.519 Sum_probs=57.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735 27 RKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS 89 (91)
Q Consensus 27 ~k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~ 89 (91)
.|++|.|+.|+..|+.+||..|.++.||+-.+|++| |...++++..|+|||.|||+||++-
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEI--avwtNlTE~rvrvwfknrrakwrkr 170 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEI--AVWTNLTEARVRVWFKNRRAKWRKR 170 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHH--Hhhccccchhhhhhcccchhhhhhh
Confidence 367788999999999999999999999999999999 9999999999999999999999873
No 22
>KOG0844|consensus
Probab=99.68 E-value=1.7e-17 Score=108.72 Aligned_cols=62 Identities=27% Similarity=0.354 Sum_probs=58.4
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735 26 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS 89 (91)
Q Consensus 26 ~~k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~ 89 (91)
..+.+|.||.||-+||..||+.|-+..|-+.+.|.+| |..|+|.+..|+|||||||+|=||+
T Consensus 178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcEL--AAaLNLPEtTIKVWFQNRRMKDKRQ 239 (408)
T KOG0844|consen 178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCEL--AAALNLPETTIKVWFQNRRMKDKRQ 239 (408)
T ss_pred cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhH--HHhhCCCcceeehhhhhchhhhhhh
Confidence 4567889999999999999999999999999999999 9999999999999999999998875
No 23
>KOG0491|consensus
Probab=99.64 E-value=1.2e-17 Score=101.02 Aligned_cols=58 Identities=28% Similarity=0.359 Sum_probs=54.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhc
Q psy3735 29 QRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTS 88 (91)
Q Consensus 29 ~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~ 88 (91)
+++.|++|+..|+..|+..|+.+.|++..++.+| |..|+|++.||+.||||||+|-++
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~EL--an~L~LS~~QVKTWFQNrRMK~Kk 157 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQEL--ANALSLSETQVKTWFQNRRMKHKK 157 (194)
T ss_pred hhhhcccccCccccccHHHHhhhhhcccHHHHHH--HHHhhhhHHHHHHHHHHHHHHHHH
Confidence 3457899999999999999999999999999999 999999999999999999999775
No 24
>KOG4577|consensus
Probab=99.63 E-value=2.4e-16 Score=102.71 Aligned_cols=61 Identities=26% Similarity=0.325 Sum_probs=57.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcCC
Q psy3735 28 KQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSSK 90 (91)
Q Consensus 28 k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~~ 90 (91)
..+|+||.+|..||+.|...|...+.|..+.|+.| +...||..++|||||||||||-+|.|
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQL--sseTGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQL--SSETGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHh--hhccCcceeehhhhhhhhhHHHHhhh
Confidence 45789999999999999999999999999999999 99999999999999999999988765
No 25
>KOG0847|consensus
Probab=99.62 E-value=1.4e-16 Score=100.33 Aligned_cols=62 Identities=21% Similarity=0.354 Sum_probs=57.2
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735 26 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS 89 (91)
Q Consensus 26 ~~k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~ 89 (91)
..+++..|..|+..|+..|+..|+...|+--.++.++ |..+||+..||+|||||||+||++-
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~l--A~~lgmteSqvkVWFQNRRTKWRKk 225 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQL--AQELNMTESQVKVWFQNRRTKWRKK 225 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhhhcccchhHHHh--hccccccHHHHHHHHhcchhhhhhh
Confidence 3556778899999999999999999999999999999 9999999999999999999999873
No 26
>KOG0490|consensus
Probab=99.61 E-value=3.3e-16 Score=100.07 Aligned_cols=62 Identities=29% Similarity=0.335 Sum_probs=58.5
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735 26 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS 89 (91)
Q Consensus 26 ~~k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~ 89 (91)
..++++.|+.|+..|+++|+..|+..|||+...++.+ |..+++++..|+|||||+|++|++.
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~l--a~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECL--ALLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHH--hhcCCCCeeeeehhhhhhcHhhhhh
Confidence 4567889999999999999999999999999999998 9999999999999999999999864
No 27
>KOG0849|consensus
Probab=99.49 E-value=2.5e-14 Score=96.87 Aligned_cols=63 Identities=33% Similarity=0.584 Sum_probs=58.6
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735 25 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS 89 (91)
Q Consensus 25 ~~~k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~ 89 (91)
..++.++.|+.|+..|+..|+..|++++||++..|+.| |.++++++..|+|||+|+|++|++.
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~L--a~~i~l~e~riqvwf~nrra~~rr~ 234 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETL--AKETGLPEPRVQVWFQNRRAKWRRQ 234 (354)
T ss_pred ccccccccccccccchHHHHHHHhcCCCCCchhhHHHH--hhhccCCchHHHHHHhhhhhhhhhc
Confidence 45566778999999999999999999999999999999 9999999999999999999999874
No 28
>KOG1168|consensus
Probab=99.49 E-value=9.9e-15 Score=95.30 Aligned_cols=64 Identities=14% Similarity=0.142 Sum_probs=59.5
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcCCC
Q psy3735 26 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSSKY 91 (91)
Q Consensus 26 ~~k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~~~ 91 (91)
...++|+||.+...+...||.+|..++.|+.....-| |.+|.|...+|+|||||.|+|-+|+||
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaI--AekLDLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAI--AEKLDLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHH--HHhhhhhhceEEEEeeccHHHHHHhhh
Confidence 4457788999999999999999999999999988888 999999999999999999999999987
No 29
>KOG0775|consensus
Probab=98.79 E-value=5.4e-09 Score=68.12 Aligned_cols=49 Identities=8% Similarity=0.065 Sum_probs=43.3
Q ss_pred CHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 37 TSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 37 t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.--...|...|..++||+..++.+| |+..||+..||-.||.|||++=+
T Consensus 184 KekSR~~LrewY~~~~YPsp~eKReL--A~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 184 KEKSRSLLREWYLQNPYPSPREKREL--AEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hHhhHHHHHHHHhcCCCCChHHHHHH--HHHhCCchhhhhhhhhhhhhhhh
Confidence 33446788899999999999999999 99999999999999999999743
No 30
>KOG2252|consensus
Probab=98.78 E-value=5.8e-09 Score=73.31 Aligned_cols=56 Identities=16% Similarity=0.205 Sum_probs=52.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHh
Q psy3735 28 KQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAA 85 (91)
Q Consensus 28 k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k 85 (91)
..++.|.+||+.|...|..+|..+++|+....+.| +.+|+|....|..||.|-|.+
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tI--S~qL~L~~sTV~NfFmNaRRR 474 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETI--SQQLNLELSTVINFFMNARRR 474 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHH--HHHhCCcHHHHHHHHHhhhhh
Confidence 45667999999999999999999999999999999 999999999999999998877
No 31
>KOG0490|consensus
Probab=98.74 E-value=9.2e-09 Score=65.71 Aligned_cols=64 Identities=33% Similarity=0.437 Sum_probs=57.8
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcCC
Q psy3735 25 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSSK 90 (91)
Q Consensus 25 ~~~k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~~ 90 (91)
...+.++.++.+...|+..+...|...++|+...+..| +..+|++...++|||+|+|++.++.+
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l--~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQL--AEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCCCCchhhHHHH--HHhcCCChhhhhhhcccHHHHHHhhc
Confidence 34566778999999999999999999999999999988 99999999999999999999987643
No 32
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.59 E-value=9.5e-09 Score=49.20 Aligned_cols=34 Identities=12% Similarity=0.220 Sum_probs=28.4
Q ss_pred hCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHh
Q psy3735 50 RTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAA 85 (91)
Q Consensus 50 ~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k 85 (91)
.++||+..++..| |...|++..||..||-|.|.+
T Consensus 7 ~nPYPs~~ek~~L--~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEEL--AKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHH--HHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHH--HHHcCCCHHHHHHHHHHhHcc
Confidence 4789999999999 999999999999999999864
No 33
>KOG0774|consensus
Probab=98.56 E-value=3.9e-08 Score=63.95 Aligned_cols=58 Identities=19% Similarity=0.290 Sum_probs=52.8
Q ss_pred CCCCCCCCHHHHHHHHHHHhh---CCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735 30 RRYRTTFTSFQLEELEKAFSR---THYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS 89 (91)
Q Consensus 30 ~r~R~~~t~~ql~~Le~~f~~---~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~ 89 (91)
+|+|..|+..-.+.|...|.. ++||+...+++| |.+++++..||-.||.|.|-++++.
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eL--AkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEEL--AKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHH--HHHcCceehhhccccccceeehhhh
Confidence 567788999999999999865 799999999999 9999999999999999999988864
No 34
>KOG1146|consensus
Probab=98.26 E-value=1.6e-06 Score=66.34 Aligned_cols=60 Identities=17% Similarity=0.309 Sum_probs=54.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735 28 KQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS 89 (91)
Q Consensus 28 k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~ 89 (91)
..++.|+.++..|+..+..+|....+|.-.+.+.| ...+++..++|+|||||-|+|-++-
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l--~~~~~~~~~~i~vw~qna~~~s~k~ 961 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVL--EEPIGLPKRVIQVWFQNARAKSKKA 961 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhh--cccccCCcchhHHhhhhhhhhhhhh
Confidence 45668999999999999999999999988888877 8999999999999999999997764
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.17 E-value=0.00014 Score=36.99 Aligned_cols=42 Identities=10% Similarity=0.040 Sum_probs=29.8
Q ss_pred HHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHH
Q psy3735 41 LEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNA 84 (91)
Q Consensus 41 l~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~ 84 (91)
+..|+..|...+++.......| +.+-+|+..||+.||-.+..
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L--~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDEL--CDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHH--HHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcCCccHhhHHHH--HHHHCCCHHHHHHHHHHhcc
Confidence 4569999999999988888888 99999999999999965543
No 36
>KOG3623|consensus
Probab=96.75 E-value=0.0011 Score=49.21 Aligned_cols=44 Identities=16% Similarity=0.120 Sum_probs=40.4
Q ss_pred HHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhh
Q psy3735 41 LEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAF 86 (91)
Q Consensus 41 l~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~ 86 (91)
...|...|..+..|+..+-..+ |.++|++...|++||+++++.-
T Consensus 568 ~sllkayyaln~~ps~eelski--a~qvglp~~vvk~wfE~~~a~e 611 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKI--AQQVGLPFAVVKAWFEDEEAEE 611 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHH--HHHhcccHHHHHHHHHhhhhhh
Confidence 6788899999999999998888 9999999999999999998863
No 37
>KOG0773|consensus
Probab=96.57 E-value=0.0049 Score=41.88 Aligned_cols=55 Identities=11% Similarity=0.105 Sum_probs=43.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHhh---CCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHh
Q psy3735 29 QRRYRTTFTSFQLEELEKAFSR---THYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAA 85 (91)
Q Consensus 29 ~~r~R~~~t~~ql~~Le~~f~~---~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k 85 (91)
..+....+.......|..-+.. .+||+..+...| |.+.||+..||-.||-|.|-+
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~L--a~~TGLs~~Qv~NWFINaR~R 296 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLML--AKQTGLSRPQVSNWFINARVR 296 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhcccc--chhcCCCcccCCchhhhcccc
Confidence 3445567888877777744222 478998888888 999999999999999998876
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=95.58 E-value=0.023 Score=28.55 Aligned_cols=47 Identities=13% Similarity=0.116 Sum_probs=33.8
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhH
Q psy3735 30 RRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLN 83 (91)
Q Consensus 30 ~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR 83 (91)
+++|..+|.++...+-..++.+. ....+ |..+|++..+|.-|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~i--a~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDI--AREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHH--HHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHH--HHHhCCCHHHHHHHHHhHH
Confidence 35778899988888887787776 34566 9999999999999998754
No 39
>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=91.10 E-value=0.22 Score=25.08 Aligned_cols=39 Identities=18% Similarity=0.150 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHHhhCCC--CCHHHhhhhhhhhhcCCCCCcch
Q psy3735 36 FTSFQLEELEKAFSRTHY--PDVFTRQCGRFSRQRSMPGELCV 76 (91)
Q Consensus 36 ~t~~ql~~Le~~f~~~~~--p~~~~r~~l~~a~~l~l~~~~v~ 76 (91)
+|+.|...|...++...| |-...-.+| |..||++...+.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~el--A~~lgis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEEL--AEELGISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHH--HHHhCCCHHHHH
Confidence 578899999999998876 433445677 999999986543
No 40
>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=82.33 E-value=1.1 Score=21.66 Aligned_cols=45 Identities=4% Similarity=-0.045 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhh
Q psy3735 35 TFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAF 86 (91)
Q Consensus 35 ~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~ 86 (91)
.+++.+...|...|..+ ..-.++ |..+|++...|+.+...-..+.
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eI--a~~lg~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEI--AERLGISRSTVRRILKRALKKL 48 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHH--HHHHTSCHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHH--HHHHCCcHHHHHHHHHHHHHHh
Confidence 46788888888888332 235567 9999999999887765444443
No 41
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=80.97 E-value=1.7 Score=27.66 Aligned_cols=40 Identities=18% Similarity=0.174 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHHhhCCC--CCHHHhhhhhhhhhcCCCCCcch
Q psy3735 35 TFTSFQLEELEKAFSRTHY--PDVFTRQCGRFSRQRSMPGELCV 76 (91)
Q Consensus 35 ~~t~~ql~~Le~~f~~~~~--p~~~~r~~l~~a~~l~l~~~~v~ 76 (91)
.+|+.|+..|...|..+.| |=...-..| |..||+++..+.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dL--A~~lGISkst~~ 196 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDL--AKELGISKSTLS 196 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHH--HHHhCCCHHHHH
Confidence 6999999999999998875 433444567 999999986443
No 42
>KOG1146|consensus
Probab=80.00 E-value=0.91 Score=36.37 Aligned_cols=56 Identities=7% Similarity=-0.199 Sum_probs=46.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 30 RRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 30 ~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
+-.+++++.-|...|...|....+|.--....+ +..|++..+.+..||++++++|.
T Consensus 445 ~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~--a~~L~vhmRskhp~~~~~~c~~g 500 (1406)
T KOG1146|consen 445 LLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKL--AQTLGVHMRSKHPESQSAYCKAG 500 (1406)
T ss_pred hhhhhcccccceeeeecccccccCCccchhhhh--HHHhhhcccccccccchhHhHhc
Confidence 345677888888999999988888877777777 99999999998888888777663
No 43
>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=78.96 E-value=0.52 Score=24.37 Aligned_cols=18 Identities=6% Similarity=0.069 Sum_probs=15.6
Q ss_pred hhhhhhhhhcCCCCCcchhc
Q psy3735 59 RQCGRFSRQRSMPGELCVAW 78 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vW 78 (91)
-..| |..||+++.+|+.|
T Consensus 25 lkdI--A~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 25 LKDI--AEKLGVSESTIRKW 42 (60)
T ss_pred HHHH--HHHHCCCHHHHHHH
Confidence 3456 99999999999999
No 44
>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=77.65 E-value=0.63 Score=24.38 Aligned_cols=42 Identities=7% Similarity=0.086 Sum_probs=26.0
Q ss_pred CCCCCCHHHHHHHHHHH-hhCCCCCHHHhhhhhhhhhcCCCCCcchhccc
Q psy3735 32 YRTTFTSFQLEELEKAF-SRTHYPDVFTRQCGRFSRQRSMPGELCVAWTH 80 (91)
Q Consensus 32 ~R~~~t~~ql~~Le~~f-~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFq 80 (91)
.|..||+++...+-... ..+ .....+ |..+||++.++..|-.
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~g-----~sv~~v--a~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLESG-----ESVSEV--AREYGISPSTLYNWRK 45 (76)
T ss_dssp SS----HHHHHHHHHHHHHHH-----CHHHHH--HHHHTS-HHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHCC-----CceEee--ecccccccccccHHHH
Confidence 46778998877766555 222 245566 9999999999999953
No 45
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=75.99 E-value=3.4 Score=21.18 Aligned_cols=45 Identities=11% Similarity=0.127 Sum_probs=21.4
Q ss_pred CCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccc
Q psy3735 33 RTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTH 80 (91)
Q Consensus 33 R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFq 80 (91)
|..|+.......-..+.....--...|.. |.++|++..+|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RAa---arkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQRAA---ARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HHHH---HHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccchhhhHHHH---HHHhCccHHHHHHHHH
Confidence 34555544333333343332222223432 9999999999999964
No 46
>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=75.79 E-value=3 Score=20.27 Aligned_cols=42 Identities=5% Similarity=-0.102 Sum_probs=25.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHH
Q psy3735 36 FTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNA 84 (91)
Q Consensus 36 ~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~ 84 (91)
+++.+...+...|..+ ..-.++ |..+|++...|+.|.+.-+.
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eI--a~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEI--AEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHH--HHHCTS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHH--HHHHCcCHHHHHHHHHHHHh
Confidence 4455555555444333 345677 99999999999999865544
No 47
>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=74.88 E-value=2.4 Score=21.13 Aligned_cols=44 Identities=9% Similarity=0.066 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhh
Q psy3735 35 TFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAF 86 (91)
Q Consensus 35 ~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~ 86 (91)
.||+.+...|.....-. ...++ |..+++++..|..+..+=+.|+
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eI--A~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEI--AEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHH--HHHHTSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------Ccchh--HHhcCcchhhHHHHHHHHHHHh
Confidence 57888888877654333 35567 9999999999999887776665
No 48
>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=74.63 E-value=3.2 Score=19.36 Aligned_cols=43 Identities=7% Similarity=-0.034 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHh
Q psy3735 36 FTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAA 85 (91)
Q Consensus 36 ~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k 85 (91)
+++.+...+...+..+ .....+ |..+|++...|..|...-+.+
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~i--a~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEI--AEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHH--HHHHCcCHHHHHHHHHHHHHH
Confidence 5666666666655322 234456 889999999999987665544
No 49
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=74.16 E-value=3.2 Score=25.10 Aligned_cols=48 Identities=15% Similarity=0.034 Sum_probs=36.2
Q ss_pred CCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhc
Q psy3735 33 RTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTS 88 (91)
Q Consensus 33 R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~ 88 (91)
...+++.|...|.. +..+ ....++ |..||++...|..|-.+.+.+.++
T Consensus 4 ~~~Lt~rqreVL~l-r~~G-----lTq~EI--Ae~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRL-RERG-----LTQQEI--ADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHH-HHcC-----CCHHHH--HHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35688989999876 3322 245577 999999999999999887777654
No 50
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=71.95 E-value=4.2 Score=23.92 Aligned_cols=30 Identities=10% Similarity=-0.203 Sum_probs=24.1
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS 89 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~ 89 (91)
.-.++ |..+|++...|+.+...-+.+.++.
T Consensus 124 s~~EI--A~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 124 TMGEI--ALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 35577 9999999999999987777776654
No 51
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=62.41 E-value=13 Score=21.54 Aligned_cols=42 Identities=14% Similarity=0.108 Sum_probs=26.5
Q ss_pred CCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccc
Q psy3735 33 RTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTH 80 (91)
Q Consensus 33 R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFq 80 (91)
|..||.++....-.....+.. ....+ |..+|++..+|..|-.
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~----sv~ev--A~e~gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGM----TVSLV--ARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCC----CHHHH--HHHHCcCHHHHHHHHH
Confidence 455777765443332222222 23455 8899999999999953
No 52
>PF08138 Sex_peptide: Sex peptide (SP) family; InterPro: IPR012608 This family consists of Sex Peptides (SP) that are found in Drosophila. On mating, Drosophila females decreases her remating rate and increases her egg-laying rate due, in part, to the transfer of SP from the male to the female. SP are found in seminal fluids transferred from the male to the female during mating. The male seminal fluid proteins are referred to as accessory gland proteins (Acps). The SP is one of the most interesting Acps and plays an important role in reproduction [].; GO: 0005179 hormone activity, 0046008 regulation of female receptivity, post-mating, 0005576 extracellular region; PDB: 2LAQ_A.
Probab=61.97 E-value=2.3 Score=21.39 Aligned_cols=17 Identities=0% Similarity=-0.185 Sum_probs=9.1
Q ss_pred chhccchhHHhhhcCCC
Q psy3735 75 CVAWTHHLNAAFTSSKY 91 (91)
Q Consensus 75 v~vWFqnrR~k~~~~~~ 91 (91)
.-+|=+|-|.||+|.|+
T Consensus 31 ~~i~sp~~r~KWCRLNl 47 (56)
T PF08138_consen 31 FPIPSPNDRDKWCRLNL 47 (56)
T ss_dssp -SSSS-STTSS--SS--
T ss_pred CCCCCCCcHHHhhhhcc
Confidence 34677899999999875
No 53
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=60.56 E-value=14 Score=22.93 Aligned_cols=43 Identities=12% Similarity=0.164 Sum_probs=34.1
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhc
Q psy3735 32 YRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAW 78 (91)
Q Consensus 32 ~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vW 78 (91)
+...+|++++.++...-..+ |..+.+..| |.++||+..-|.+-
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~L--AkkF~~S~~fV~~v 124 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKL--AKKFNCSPLFVSMV 124 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHH--HHHhCCCHHHHHHh
Confidence 34789999999998876555 566889988 99999998766553
No 54
>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=60.43 E-value=12 Score=15.29 Aligned_cols=37 Identities=14% Similarity=0.132 Sum_probs=22.6
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhc
Q psy3735 35 TFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAW 78 (91)
Q Consensus 35 ~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vW 78 (91)
.++..+...+...+.... ....+ |..++++...|..|
T Consensus 5 ~~~~~~~~~i~~~~~~~~-----s~~~i--a~~~~is~~tv~~~ 41 (42)
T cd00569 5 KLTPEQIEEARRLLAAGE-----SVAEI--ARRLGVSRSTLYRY 41 (42)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHH--HHHHCCCHHHHHHh
Confidence 355666666655554322 33455 88889888777665
No 55
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=59.42 E-value=7.5 Score=22.32 Aligned_cols=41 Identities=10% Similarity=0.258 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHH
Q psy3735 35 TFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNA 84 (91)
Q Consensus 35 ~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~ 84 (91)
.+++.++..+...+... .. .+|.-||++...|+-|=|+|+.
T Consensus 43 ~ls~~eIk~iRe~~~lS-------Q~--vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 43 TLSPTEIKAIREKLGLS-------QP--VFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCCHHHHHHHHHHhCCC-------HH--HHHHHHCCCHHHHHHHHcCCcC
Confidence 37888888876654332 22 3389999999999999998763
No 56
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=59.19 E-value=2.1 Score=20.24 Aligned_cols=17 Identities=0% Similarity=-0.029 Sum_probs=14.1
Q ss_pred hhhcCCCCCcchhccch
Q psy3735 65 SRQRSMPGELCVAWTHH 81 (91)
Q Consensus 65 a~~l~l~~~~v~vWFqn 81 (91)
|..+|+++..|+.|.++
T Consensus 7 a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 7 AKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHCcCHHHHHHHHHC
Confidence 88899999999999643
No 57
>KOG3623|consensus
Probab=58.85 E-value=9.8 Score=29.33 Aligned_cols=56 Identities=11% Similarity=0.141 Sum_probs=35.6
Q ss_pred CCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhc
Q psy3735 31 RYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTS 88 (91)
Q Consensus 31 r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~ 88 (91)
+.++..-.++..-|...++.+..+.-.+-..+ +..|...+.+|.|||++|+..-+.
T Consensus 628 kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~--~t~~~n~~pv~ev~dhsrsstpsp 683 (1007)
T KOG3623|consen 628 KVRSPIKEEDQQQLKQAYELQASPSNDEFPLI--ATRLQNDPPVVEVWDHSRSSTPSP 683 (1007)
T ss_pred cccCCCCccchhhhHhhhhcccCccCcccchh--hhhccCCCcchhhcccCCCCCCCC
Confidence 34455555555566777776665544433333 455677788999999999875443
No 58
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=58.34 E-value=2.7 Score=21.47 Aligned_cols=15 Identities=0% Similarity=-0.042 Sum_probs=13.7
Q ss_pred hhhcCCCCCcchhcc
Q psy3735 65 SRQRSMPGELCVAWT 79 (91)
Q Consensus 65 a~~l~l~~~~v~vWF 79 (91)
|..+|++...|+.|=
T Consensus 7 a~~~gvs~~tlr~y~ 21 (69)
T PF13411_consen 7 AKLLGVSPSTLRYYE 21 (69)
T ss_dssp HHHTTTTHHHHHHHH
T ss_pred HHHHCcCHHHHHHHH
Confidence 899999999999994
No 59
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=56.07 E-value=11 Score=23.57 Aligned_cols=28 Identities=11% Similarity=-0.001 Sum_probs=21.8
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|+++...-+.+.+
T Consensus 171 s~~EI--A~~lgis~~tV~~~l~Ra~~~Lr 198 (206)
T PRK12526 171 SQEQL--AQQLNVPLGTVKSRLRLALAKLK 198 (206)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 45567 99999999999998876666554
No 60
>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=55.97 E-value=1.6 Score=22.27 Aligned_cols=19 Identities=11% Similarity=0.254 Sum_probs=16.3
Q ss_pred hhhhhhhhhcCCCCCcchhcc
Q psy3735 59 RQCGRFSRQRSMPGELCVAWT 79 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWF 79 (91)
..++ |..||++...|..|-
T Consensus 16 ~~eI--A~~Lg~~~~TV~~W~ 34 (58)
T PF06056_consen 16 IKEI--AEELGVPRSTVYSWK 34 (58)
T ss_pred HHHH--HHHHCCChHHHHHHH
Confidence 4567 999999999999994
No 61
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=55.63 E-value=15 Score=16.98 Aligned_cols=13 Identities=46% Similarity=0.603 Sum_probs=11.2
Q ss_pred CCCHHHHHHHHHH
Q psy3735 35 TFTSFQLEELEKA 47 (91)
Q Consensus 35 ~~t~~ql~~Le~~ 47 (91)
.||+.|+..|+.-
T Consensus 2 ~FT~~Ql~~L~~Q 14 (37)
T PF08880_consen 2 PFTPAQLQELRAQ 14 (37)
T ss_pred CCCHHHHHHHHHH
Confidence 5899999999864
No 62
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=54.20 E-value=5.6 Score=18.82 Aligned_cols=38 Identities=5% Similarity=-0.004 Sum_probs=17.3
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhc
Q psy3735 34 TTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAW 78 (91)
Q Consensus 34 ~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vW 78 (91)
..+|.++...++..+..+ ....++ |..||++...|..+
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~I--A~~lg~s~sTV~re 40 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREI--AKRLGRSRSTVSRE 40 (44)
T ss_dssp ---------HHHHHHCS--------HHHH--HHHTT--HHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHH--HHHHCcCcHHHHHH
Confidence 457888888888776544 234457 99999988777654
No 63
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=54.15 E-value=13 Score=22.56 Aligned_cols=28 Identities=18% Similarity=0.005 Sum_probs=22.2
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|+.+...-+.+.+
T Consensus 149 s~~eI--A~~l~is~~tV~~~l~ra~~~Lr 176 (184)
T PRK12512 149 SIKET--AAKLSMSEGAVRVALHRGLAALA 176 (184)
T ss_pred CHHHH--HHHhCCCHHHHHHHHHHHHHHHH
Confidence 34566 99999999999998877666654
No 64
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=53.66 E-value=2.7 Score=19.42 Aligned_cols=15 Identities=0% Similarity=-0.037 Sum_probs=12.1
Q ss_pred hhhcCCCCCcchhcc
Q psy3735 65 SRQRSMPGELCVAWT 79 (91)
Q Consensus 65 a~~l~l~~~~v~vWF 79 (91)
|..+|++...++.|=
T Consensus 6 A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 6 AKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHTS-HHHHHHHH
T ss_pred HHHHCCCHHHHHHHH
Confidence 888999999999884
No 65
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=53.30 E-value=16 Score=22.54 Aligned_cols=28 Identities=7% Similarity=-0.102 Sum_probs=22.1
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..||++...|+.+...-|++.+
T Consensus 160 s~~EI--A~~Lgis~~tVk~~l~ra~~~Lr 187 (194)
T PRK09646 160 TYREV--AERLAVPLGTVKTRMRDGLIRLR 187 (194)
T ss_pred CHHHH--HHHhCCChHhHHHHHHHHHHHHH
Confidence 34567 99999999999999877666654
No 66
>PF13518 HTH_28: Helix-turn-helix domain
Probab=52.85 E-value=4.7 Score=19.21 Aligned_cols=22 Identities=9% Similarity=0.197 Sum_probs=17.7
Q ss_pred hhhhhhhhcCCCCCcchhccchhH
Q psy3735 60 QCGRFSRQRSMPGELCVAWTHHLN 83 (91)
Q Consensus 60 ~~l~~a~~l~l~~~~v~vWFqnrR 83 (91)
..+ |..+|++..+|..|.+.-+
T Consensus 16 ~~~--a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 16 REI--AREFGISRSTVYRWIKRYR 37 (52)
T ss_pred HHH--HHHHCCCHhHHHHHHHHHH
Confidence 345 9999999999999975544
No 67
>PRK04217 hypothetical protein; Provisional
Probab=52.46 E-value=15 Score=21.27 Aligned_cols=47 Identities=9% Similarity=-0.065 Sum_probs=33.0
Q ss_pred CCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhh
Q psy3735 33 RTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAF 86 (91)
Q Consensus 33 R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~ 86 (91)
-..++.++...+...+.... ...++ |..+|++...|...+..-+.+.
T Consensus 40 ~~~Lt~eereai~l~~~eGl-----S~~EI--Ak~LGIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL-----TQEEA--GKRMGVSRGTVWRALTSARKKV 86 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC-----CHHHH--HHHHCcCHHHHHHHHHHHHHHH
Confidence 35678888877766554332 35567 9999999999988776655554
No 68
>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=52.42 E-value=2.1 Score=23.00 Aligned_cols=23 Identities=4% Similarity=-0.207 Sum_probs=19.0
Q ss_pred HHhhhhhhhhhcCCCCCcchhccch
Q psy3735 57 FTRQCGRFSRQRSMPGELCVAWTHH 81 (91)
Q Consensus 57 ~~r~~l~~a~~l~l~~~~v~vWFqn 81 (91)
....++ |..+|++...|+.|+.+
T Consensus 33 lS~kEI--Ae~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 33 KTASEI--AEELGRTEQTVRNHLKG 55 (73)
T ss_pred CCHHHH--HHHHCcCHHHHHHHHhc
Confidence 345677 99999999999999854
No 69
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=52.25 E-value=10 Score=22.58 Aligned_cols=30 Identities=10% Similarity=-0.162 Sum_probs=23.3
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhhcCC
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFTSSK 90 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~~ 90 (91)
-.++ |..+|++...|+.+...-|.+.++-|
T Consensus 131 ~~eI--A~~lgis~~tv~~~l~Rar~~L~~~~ 160 (161)
T PRK12541 131 YKEI--AEMTGLSLAKVKIELHRGRKETKSIK 160 (161)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHHHHHHhhc
Confidence 4566 89999999999998877777766543
No 70
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=51.97 E-value=5.1 Score=26.73 Aligned_cols=25 Identities=4% Similarity=0.108 Sum_probs=20.3
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAF 86 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~ 86 (91)
.-..| |..|||++.+|+-| .+|-.|
T Consensus 21 k~~dI--AeklGvspntiksW--Krr~gW 45 (279)
T COG5484 21 KLKDI--AEKLGVSPNTIKSW--KRRDGW 45 (279)
T ss_pred cHHHH--HHHhCCChHHHHHH--HHhcCC
Confidence 34567 99999999999999 566666
No 71
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=51.89 E-value=14 Score=21.96 Aligned_cols=27 Identities=4% Similarity=-0.108 Sum_probs=21.6
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|..|..--+.+.+
T Consensus 144 ~~eI--A~~lgis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 144 YREI--AEILGVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 4567 99999999999999876666654
No 72
>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=51.67 E-value=15 Score=20.90 Aligned_cols=28 Identities=0% Similarity=-0.174 Sum_probs=21.9
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|+++..|..+...-+.+.+
T Consensus 128 s~~eI--A~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 128 SYKEI--AEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 34567 99999999999998877666654
No 73
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=51.62 E-value=13 Score=22.18 Aligned_cols=46 Identities=4% Similarity=-0.109 Sum_probs=28.8
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 35 TFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 35 ~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.+++.+...+...|-.+ ..-.++ |..+|++...|+.|...-+.+.+
T Consensus 128 ~L~~~~r~vl~l~~~~~-----~s~~eI--A~~lgis~~tV~~~l~ra~~~Lr 173 (182)
T PRK09652 128 SLPEELRTAITLREIEG-----LSYEEI--AEIMGCPIGTVRSRIFRAREALR 173 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 35555555554443221 134466 99999999999998865555544
No 74
>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=51.08 E-value=17 Score=21.38 Aligned_cols=28 Identities=7% Similarity=-0.090 Sum_probs=21.0
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|.++...-|.+.+
T Consensus 129 ~~~eI--A~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 129 SLTAL--AEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred CHHHH--HHHhCCCHHHHHHHHHHHHHHHH
Confidence 35567 99999999999988655555543
No 75
>PRK00118 putative DNA-binding protein; Validated
Probab=50.92 E-value=17 Score=20.83 Aligned_cols=45 Identities=7% Similarity=-0.016 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhh
Q psy3735 35 TFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAF 86 (91)
Q Consensus 35 ~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~ 86 (91)
.+++.|...+...|..+ ..-.++ |..+|+++..|..|...-+.+.
T Consensus 17 ~L~ekqRevl~L~y~eg-----~S~~EI--Ae~lGIS~~TV~r~L~RArkkL 61 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD-----YSLGEI--AEEFNVSRQAVYDNIKRTEKLL 61 (104)
T ss_pred cCCHHHHHHHHHHHHcC-----CCHHHH--HHHHCcCHHHHHHHHHHHHHHH
Confidence 34555666665444333 234467 9999999999999886555543
No 76
>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=50.10 E-value=4.1 Score=20.77 Aligned_cols=17 Identities=6% Similarity=-0.066 Sum_probs=14.7
Q ss_pred hhhcCCCCCcchhccch
Q psy3735 65 SRQRSMPGELCVAWTHH 81 (91)
Q Consensus 65 a~~l~l~~~~v~vWFqn 81 (91)
|..+|+++..++.|-++
T Consensus 7 A~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 7 SEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHCcCHHHHHHHHHh
Confidence 88999999999999653
No 77
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=49.25 E-value=21 Score=21.56 Aligned_cols=28 Identities=7% Similarity=0.112 Sum_probs=21.9
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-+++ |..+|++...|+++.+.-|.+.+
T Consensus 147 s~~eI--A~~lgis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 147 SYKEL--AERHDVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred CHHHH--HHHHCCChHHHHHHHHHHHHHHH
Confidence 34567 99999999999998876666554
No 78
>PRK10072 putative transcriptional regulator; Provisional
Probab=49.06 E-value=3.9 Score=23.07 Aligned_cols=23 Identities=9% Similarity=0.039 Sum_probs=19.6
Q ss_pred hhhhhhhhhcCCCCCcchhccchhH
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLN 83 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR 83 (91)
..++ |..+|++...|..|.+.++
T Consensus 49 Q~el--A~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 49 IDDF--ARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred HHHH--HHHhCCCHHHHHHHHcCCC
Confidence 5566 9999999999999997765
No 79
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=49.05 E-value=13 Score=22.86 Aligned_cols=28 Identities=7% Similarity=-0.032 Sum_probs=22.2
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|+.+...-+.+.+
T Consensus 159 s~~EI--A~~lgis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 159 SQSEI--AKRLGIPLGTVKARARQGLLKLR 186 (194)
T ss_pred CHHHH--HHHhCCCHHHHHHHHHHHHHHHH
Confidence 44567 99999999999999876666654
No 80
>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=48.99 E-value=18 Score=21.08 Aligned_cols=28 Identities=0% Similarity=-0.155 Sum_probs=21.4
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
...++ |..+|++...|+.+...-+.+.+
T Consensus 131 ~~~eI--A~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 131 SYKEI--AEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 34566 89999999999988766666654
No 81
>PF11516 DUF3220: Protein of unknown function (DUF3120); InterPro: IPR021597 This family of proteins with unknown function appears to be restricted to Bordetella. ; PDB: 2JPF_A.
Probab=48.18 E-value=4.6 Score=22.08 Aligned_cols=11 Identities=18% Similarity=0.441 Sum_probs=8.7
Q ss_pred CcchhccchhH
Q psy3735 73 ELCVAWTHHLN 83 (91)
Q Consensus 73 ~~v~vWFqnrR 83 (91)
.-|+||.||-.
T Consensus 31 gdvkvwmqnle 41 (106)
T PF11516_consen 31 GDVKVWMQNLE 41 (106)
T ss_dssp HHHHHHHHHHH
T ss_pred ccHHHHHHHHH
Confidence 46899999953
No 82
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=47.56 E-value=23 Score=16.53 Aligned_cols=44 Identities=9% Similarity=0.082 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhh
Q psy3735 35 TFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAF 86 (91)
Q Consensus 35 ~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~ 86 (91)
.+++.+...+.. +..+ ....++ |..+|++...|..|...-+.+.
T Consensus 3 ~l~~~e~~i~~~-~~~g-----~s~~ei--a~~l~is~~tv~~~~~~~~~kl 46 (58)
T smart00421 3 SLTPREREVLRL-LAEG-----LTNKEI--AERLGISEKTVKTHLSNIMRKL 46 (58)
T ss_pred CCCHHHHHHHHH-HHcC-----CCHHHH--HHHHCCCHHHHHHHHHHHHHHH
Confidence 356777776654 3222 134566 8999999999998876555543
No 83
>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=47.41 E-value=12 Score=18.72 Aligned_cols=35 Identities=11% Similarity=-0.014 Sum_probs=23.9
Q ss_pred HHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhcc
Q psy3735 39 FQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWT 79 (91)
Q Consensus 39 ~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWF 79 (91)
.|+..|+-.+. +...+.. +| |..+|++.+.++.-.
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---el--a~~l~~S~rti~~~i 40 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---EL--AKKLNISERTIKNDI 40 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HH--HHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HH--HHHHCCCHHHHHHHH
Confidence 46677777777 5555444 66 999999998887543
No 84
>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=47.21 E-value=4.1 Score=20.87 Aligned_cols=16 Identities=13% Similarity=0.285 Sum_probs=14.3
Q ss_pred hhhcCCCCCcchhccc
Q psy3735 65 SRQRSMPGELCVAWTH 80 (91)
Q Consensus 65 a~~l~l~~~~v~vWFq 80 (91)
|+.+|+++..++.|.+
T Consensus 7 A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 7 ALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHCcCHHHHHHHHH
Confidence 8899999999999964
No 85
>KOG3862|consensus
Probab=47.09 E-value=6 Score=26.71 Aligned_cols=27 Identities=41% Similarity=0.773 Sum_probs=23.0
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCHHH
Q psy3735 32 YRTTFTSFQLEELEKAFSRTHYPDVFT 58 (91)
Q Consensus 32 ~R~~~t~~ql~~Le~~f~~~~~p~~~~ 58 (91)
.-..|+..+++.|+..|++.+|+.+..
T Consensus 222 ~~d~ft~~~~~~ld~~~~r~~y~~~~~ 248 (327)
T KOG3862|consen 222 RADAFTQQHLEPLDRSFERPHYPLVYA 248 (327)
T ss_pred ccccccccccccccceeeccccccccc
Confidence 446899999999999999999987653
No 86
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=46.26 E-value=17 Score=22.00 Aligned_cols=28 Identities=14% Similarity=0.011 Sum_probs=22.0
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|+++.+.-|.+.+
T Consensus 154 s~~eI--A~~lgis~~~v~~~l~Rar~~Lr 181 (187)
T TIGR02948 154 SLKEI--SEILDLPVGTVKTRIHRGREALR 181 (187)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 34566 99999999999999877666654
No 87
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=45.95 E-value=21 Score=21.87 Aligned_cols=27 Identities=4% Similarity=-0.069 Sum_probs=20.6
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|++-...-|.+++
T Consensus 150 ~~eI--A~~lgis~~tV~~~l~Rar~~Lr 176 (189)
T PRK12515 150 VEEV--GEIVGIPESTVKTRMFYARKKLA 176 (189)
T ss_pred HHHH--HHHHCcCHHHHHHHHHHHHHHHH
Confidence 4466 99999999999987766666554
No 88
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=45.83 E-value=21 Score=21.07 Aligned_cols=27 Identities=7% Similarity=-0.227 Sum_probs=20.8
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|++....-|.+.+
T Consensus 125 ~~EI--A~~lgis~~tV~~~l~Rar~~Lr 151 (160)
T PRK09642 125 YQEI--ALQEKIEVKTVEMKLYRARKWIK 151 (160)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 3466 99999999999998766665544
No 89
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=45.18 E-value=20 Score=21.87 Aligned_cols=28 Identities=7% Similarity=-0.071 Sum_probs=21.3
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|+.+...-+.+.+
T Consensus 157 s~~EI--A~~lgis~~tV~~~l~Ra~~~Lr 184 (189)
T PRK09648 157 SAEET--AEAVGSTPGAVRVAQHRALARLR 184 (189)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 35567 99999999999998766555554
No 90
>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=44.69 E-value=21 Score=21.55 Aligned_cols=28 Identities=7% Similarity=-0.230 Sum_probs=21.8
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|++..+.-|.+.+
T Consensus 152 s~~EI--A~~lgis~~tVk~~l~Rar~~Lr 179 (183)
T TIGR02999 152 TVEEI--AELLGVSVRTVERDWRFARAWLA 179 (183)
T ss_pred CHHHH--HHHhCCCHHHHHHHHHHHHHHHH
Confidence 34566 89999999999998876666654
No 91
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=44.44 E-value=20 Score=21.43 Aligned_cols=28 Identities=4% Similarity=-0.124 Sum_probs=21.7
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
...++ |..+|++...|+++.+--|.+.+
T Consensus 126 s~~eI--A~~lgis~~tv~~~l~Rar~~Lr 153 (165)
T PRK09644 126 TYEEA--ASVLDLKLNTYKSHLFRGRKRLK 153 (165)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 34566 89999999999999876666654
No 92
>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=44.02 E-value=23 Score=21.41 Aligned_cols=28 Identities=4% Similarity=-0.101 Sum_probs=20.5
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|+++-+.-|.+++
T Consensus 118 s~~eI--A~~lgis~~tV~~~l~Rar~~Lr 145 (170)
T TIGR02959 118 SQQEI--AEKLGLSLSGAKSRVQRGRKKLK 145 (170)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 34566 99999999999988755555543
No 93
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=43.79 E-value=27 Score=21.44 Aligned_cols=31 Identities=3% Similarity=-0.096 Sum_probs=23.8
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhhcCC
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFTSSK 90 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~~ 90 (91)
...++ |..+|++...|+...+--|.+.++.+
T Consensus 149 s~~EI--Ae~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 149 KIEEI--AKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 34567 99999999999998777676666544
No 94
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=43.37 E-value=5.3 Score=19.00 Aligned_cols=22 Identities=5% Similarity=0.148 Sum_probs=16.0
Q ss_pred HhhhhhhhhhcCCCCCcchhccch
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHH 81 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqn 81 (91)
....+ |..+|++...|..|...
T Consensus 19 s~~~i--a~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 19 SIREI--AKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp -HHHH--HHHHTS-HHHHHHHHT-
T ss_pred CHHHH--HHHHCcCHHHHHHHHHH
Confidence 34566 99999999999999643
No 95
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=42.96 E-value=21 Score=21.76 Aligned_cols=27 Identities=4% Similarity=-0.123 Sum_probs=21.0
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|+.....-|.+.+
T Consensus 147 ~~EI--A~~lgis~~tV~~~l~Rar~~Lr 173 (186)
T PRK05602 147 NIEA--AAVMDISVDALESLLARGRRALR 173 (186)
T ss_pred HHHH--HHHhCcCHHHHHHHHHHHHHHHH
Confidence 4566 99999999999998766665544
No 96
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=42.51 E-value=5.4 Score=19.91 Aligned_cols=23 Identities=4% Similarity=-0.080 Sum_probs=16.3
Q ss_pred hhhhhhhhhcCCCCCcchhccchhH
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLN 83 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR 83 (91)
...| |...|++...|.-|+.++.
T Consensus 13 ~~~L--a~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 13 QKDL--ARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp HHHH--HHHHT--HHHHHHHHTTT-
T ss_pred HHHH--HHHHCcCHHHHHHHHhccc
Confidence 4456 8899999999999997764
No 97
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=41.94 E-value=33 Score=20.84 Aligned_cols=27 Identities=15% Similarity=0.123 Sum_probs=21.1
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|+++-..-+.+.+
T Consensus 152 ~~eI--A~~lgis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 152 HAEI--AQRLGAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred HHHH--HHHHCCChhhHHHHHHHHHHHHH
Confidence 4566 99999999999998766665554
No 98
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=41.52 E-value=22 Score=22.01 Aligned_cols=27 Identities=4% Similarity=-0.043 Sum_probs=21.4
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|+++...-|.+.+
T Consensus 132 ~~EI--A~~LgiS~~tVk~~l~Rar~~Lr 158 (188)
T PRK12546 132 YEEA--AEMCGVAVGTVKSRANRARARLA 158 (188)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 4566 99999999999999876666554
No 99
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=41.04 E-value=42 Score=18.93 Aligned_cols=42 Identities=14% Similarity=0.093 Sum_probs=28.7
Q ss_pred CCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCC-CCCcchhccc
Q psy3735 33 RTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSM-PGELCVAWTH 80 (91)
Q Consensus 33 R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l-~~~~v~vWFq 80 (91)
+..||.+....+-........ ....+ |..+|+ +..++..|-.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~v--Ar~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEV--AREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHH--HHHhCCCChHHHHHHHH
Confidence 677888876665554443332 34566 999996 9999998853
No 100
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=40.93 E-value=33 Score=20.33 Aligned_cols=44 Identities=9% Similarity=-0.017 Sum_probs=27.7
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 36 FTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 36 ~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
+++.+...|...+ .+ ..-.++ |..+|++...|+.+...-+.+.+
T Consensus 113 L~~~~r~il~l~~-~g-----~s~~eI--A~~lgis~~tV~~~i~ra~~~Lr 156 (166)
T PRK09639 113 MTERDRTVLLLRF-SG-----YSYKEI--AEALGIKESSVGTTLARAKKKFR 156 (166)
T ss_pred CCHHHHHHHHHHH-cC-----CCHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 4444544544444 21 234566 99999999999988765555544
No 101
>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=40.64 E-value=26 Score=20.70 Aligned_cols=28 Identities=4% Similarity=-0.140 Sum_probs=21.8
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhhc
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFTS 88 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~ 88 (91)
-.++ |..+|++...|+.+-..-+.+.++
T Consensus 129 ~~eI--A~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 129 EAQV--AEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred HHHH--HHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4566 999999999999987766666543
No 102
>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=40.37 E-value=18 Score=21.94 Aligned_cols=28 Identities=11% Similarity=-0.019 Sum_probs=21.5
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|+++...-|.+.+
T Consensus 156 s~~EI--A~~lgis~~tv~~~l~rar~~Lr 183 (190)
T TIGR02939 156 SYEDI--ARIMDCPVGTVRSRIFRAREAIA 183 (190)
T ss_pred CHHHH--HHHHCcCHHHHHHHHHHHHHHHH
Confidence 34567 99999999999998866665544
No 103
>PRK06930 positive control sigma-like factor; Validated
Probab=40.31 E-value=27 Score=21.64 Aligned_cols=46 Identities=4% Similarity=-0.117 Sum_probs=29.4
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 35 TFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 35 ~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.+++.+...+...|..+ ..-.++ |..+|++...|+.+...-+.+.+
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EI--A~~lgiS~~tVk~~l~Ra~~kLr 159 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEI--ADYLNIKKSTVQSMIERAEKKIA 159 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHH--HHHHCcCHHHHHHHHHHHHHHHH
Confidence 35555555554433222 134466 89999999999999876666644
No 104
>PRK13558 bacterio-opsin activator; Provisional
Probab=39.93 E-value=25 Score=25.93 Aligned_cols=41 Identities=17% Similarity=0.188 Sum_probs=32.7
Q ss_pred CCCCHHHHHHHHHHHhhCCC--CCHHHhhhhhhhhhcCCCCCcch
Q psy3735 34 TTFTSFQLEELEKAFSRTHY--PDVFTRQCGRFSRQRSMPGELCV 76 (91)
Q Consensus 34 ~~~t~~ql~~Le~~f~~~~~--p~~~~r~~l~~a~~l~l~~~~v~ 76 (91)
..+|..|.+.|+..+....| |=...-.+| |..||++...+.
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~--a~~l~is~~t~~ 648 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEEL--AESMGISRSTFH 648 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHH--HHHhCCCHHHHH
Confidence 47999999999999999886 444455677 999999876543
No 105
>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=39.29 E-value=16 Score=17.20 Aligned_cols=37 Identities=11% Similarity=0.175 Sum_probs=22.9
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhc
Q psy3735 35 TFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAW 78 (91)
Q Consensus 35 ~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vW 78 (91)
.++.++++.+...+... + ....+ |..+|++...|.-+
T Consensus 5 ~~~~~~~~~i~~l~~~G-~----si~~I--A~~~gvsr~TvyR~ 41 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-M----SIAEI--AKQFGVSRSTVYRY 41 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHH--HHHTTS-HHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC-C----CHHHH--HHHHCcCHHHHHHH
Confidence 35565666666666666 2 35566 99999998766544
No 106
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=39.22 E-value=28 Score=21.42 Aligned_cols=27 Identities=0% Similarity=-0.146 Sum_probs=20.7
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|+++..|+++...-|.+.+
T Consensus 153 ~~EI--A~~lgis~~tVk~~l~RAr~~Lr 179 (189)
T PRK12530 153 SEQI--CQECDISTSNLHVLLYRARLQLQ 179 (189)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 4567 99999999999998765555543
No 107
>PF13551 HTH_29: Winged helix-turn helix
Probab=38.46 E-value=47 Score=18.14 Aligned_cols=20 Identities=15% Similarity=0.160 Sum_probs=16.2
Q ss_pred CCCCCHHHHHHHHHHHhhCC
Q psy3735 33 RTTFTSFQLEELEKAFSRTH 52 (91)
Q Consensus 33 R~~~t~~ql~~Le~~f~~~~ 52 (91)
+..+++++...|...+..++
T Consensus 55 ~~~l~~~~~~~l~~~~~~~p 74 (112)
T PF13551_consen 55 RKRLSEEQRAQLIELLRENP 74 (112)
T ss_pred CCCCCHHHHHHHHHHHHHCC
Confidence 33489999999999988766
No 108
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=38.27 E-value=31 Score=20.58 Aligned_cols=28 Identities=0% Similarity=-0.154 Sum_probs=21.1
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|+++...-|.+.+
T Consensus 130 s~~eI--A~~lgis~~tV~~~l~Rar~~Lr 157 (164)
T PRK12547 130 SYEDA--AAICGCAVGTIKSRVSRARNRLQ 157 (164)
T ss_pred CHHHH--HHHhCCCHHHHHHHHHHHHHHHH
Confidence 34566 99999999999998766555543
No 109
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=38.14 E-value=32 Score=21.06 Aligned_cols=27 Identities=0% Similarity=-0.132 Sum_probs=20.3
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|+..+..-|.+.+
T Consensus 125 ~~EI--A~~lgis~~tV~~~l~Rar~~Lr 151 (181)
T PRK09637 125 QKEI--AEKLGLSLSGAKSRVQRGRVKLK 151 (181)
T ss_pred HHHH--HHHhCCCHHHHHHHHHHHHHHHH
Confidence 4566 99999999999888765555544
No 110
>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=38.02 E-value=7.1 Score=17.89 Aligned_cols=18 Identities=6% Similarity=0.078 Sum_probs=14.1
Q ss_pred hhhcCCCCCcchhccchh
Q psy3735 65 SRQRSMPGELCVAWTHHL 82 (91)
Q Consensus 65 a~~l~l~~~~v~vWFqnr 82 (91)
|..+|++...|..|..+-
T Consensus 7 a~~lgvs~~tl~~~~~~g 24 (49)
T cd04762 7 AELLGVSPSTLRRWVKEG 24 (49)
T ss_pred HHHHCcCHHHHHHHHHcC
Confidence 788888888888886443
No 111
>PRK10403 transcriptional regulator NarP; Provisional
Probab=37.84 E-value=28 Score=20.88 Aligned_cols=45 Identities=9% Similarity=0.073 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 35 TFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 35 ~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.+|..+...|..... + ....++ |..++++++.|++..+|=+.|..
T Consensus 153 ~Lt~~e~~vl~~~~~-g-----~s~~~i--a~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 153 VLTERELDVLHELAQ-G-----LSNKQI--ASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred cCCHHHHHHHHHHHC-C-----CCHHHH--HHHcCCCHHHHHHHHHHHHHHcC
Confidence 578888888775432 2 345677 89999999999999888777753
No 112
>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=37.69 E-value=8.2 Score=19.51 Aligned_cols=16 Identities=19% Similarity=0.414 Sum_probs=14.0
Q ss_pred hhhcCCCCCcchhccc
Q psy3735 65 SRQRSMPGELCVAWTH 80 (91)
Q Consensus 65 a~~l~l~~~~v~vWFq 80 (91)
|..+|++...++.|-+
T Consensus 7 a~~~gvs~~tlr~w~~ 22 (68)
T cd01104 7 ARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHCcCHHHHHHHHH
Confidence 8899999999999974
No 113
>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=37.46 E-value=28 Score=16.73 Aligned_cols=18 Identities=6% Similarity=-0.112 Sum_probs=12.4
Q ss_pred HhhhhhhhhhcCCCCCcchh
Q psy3735 58 TRQCGRFSRQRSMPGELCVA 77 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~v 77 (91)
...+| |..++++.+.|+-
T Consensus 17 t~~eL--a~~l~vS~rTi~~ 34 (55)
T PF08279_consen 17 TAKEL--AEELGVSRRTIRR 34 (55)
T ss_dssp EHHHH--HHHCTS-HHHHHH
T ss_pred CHHHH--HHHhCCCHHHHHH
Confidence 34566 9999999877653
No 114
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=37.14 E-value=34 Score=20.07 Aligned_cols=26 Identities=4% Similarity=-0.133 Sum_probs=19.4
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAF 86 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~ 86 (91)
-.++ |..||++...|++....-+.+.
T Consensus 125 ~~EI--A~~lgis~~tV~~~l~ra~~~L 150 (161)
T PRK09047 125 VAET--AAAMGCSEGSVKTHCSRATHAL 150 (161)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHHHHH
Confidence 4566 9999999999998765554443
No 115
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=36.63 E-value=7.6 Score=18.49 Aligned_cols=18 Identities=6% Similarity=-0.090 Sum_probs=15.8
Q ss_pred hhhcCCCCCcchhccchh
Q psy3735 65 SRQRSMPGELCVAWTHHL 82 (91)
Q Consensus 65 a~~l~l~~~~v~vWFqnr 82 (91)
|..+|++...|..|+.+.
T Consensus 4 A~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 4 ARAAGVSVATVSRVLNGK 21 (52)
T ss_pred HHHHCcCHHHHHHHHcCC
Confidence 888999999999998776
No 116
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.60 E-value=34 Score=19.18 Aligned_cols=36 Identities=3% Similarity=-0.106 Sum_probs=20.2
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCC
Q psy3735 36 FTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGE 73 (91)
Q Consensus 36 ~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~ 73 (91)
++++|...-...|+.+--.+.-..+++ |..|+.++-
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~i--A~~Ln~t~~ 38 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEI--ATALNWTEV 38 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHH--HHHhCCCHH
Confidence 455565555555544443333445566 778877653
No 117
>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=35.53 E-value=41 Score=20.05 Aligned_cols=28 Identities=11% Similarity=0.026 Sum_probs=20.4
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|++...--|.+.+
T Consensus 137 s~~ei--A~~lgis~~tv~~~l~Ra~~~Lr 164 (169)
T TIGR02954 137 TIKEI--AEVMNKPEGTVKTYLHRALKKLK 164 (169)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 34566 99999999999987655555443
No 118
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=34.62 E-value=33 Score=21.94 Aligned_cols=28 Identities=0% Similarity=-0.205 Sum_probs=22.3
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|+.+...-+.+.+
T Consensus 202 s~~EI--A~~lgis~~tV~~~~~ra~~~Lr 229 (236)
T PRK06986 202 NLKEI--GAVLGVSESRVSQIHSQAIKRLR 229 (236)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 45567 99999999999999877666654
No 119
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=33.39 E-value=18 Score=21.02 Aligned_cols=23 Identities=4% Similarity=-0.163 Sum_probs=18.5
Q ss_pred HHhhhhhhhhhcCCCCCcchhccch
Q psy3735 57 FTRQCGRFSRQRSMPGELCVAWTHH 81 (91)
Q Consensus 57 ~~r~~l~~a~~l~l~~~~v~vWFqn 81 (91)
.....| |..+|+++..+.-+|+.
T Consensus 26 ~sl~~l--A~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 26 LSLEKV--SERSGYSKWHLQRMFKK 48 (127)
T ss_pred CCHHHH--HHHHCcCHHHHHHHHHH
Confidence 455677 99999999999888854
No 120
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=33.28 E-value=11 Score=19.04 Aligned_cols=15 Identities=0% Similarity=-0.039 Sum_probs=12.8
Q ss_pred hhhcCCCCCcchhcc
Q psy3735 65 SRQRSMPGELCVAWT 79 (91)
Q Consensus 65 a~~l~l~~~~v~vWF 79 (91)
|..+|+++..++.|-
T Consensus 7 a~~~gvs~~tlr~~~ 21 (70)
T smart00422 7 AKLAGVSVRTLRYYE 21 (70)
T ss_pred HHHHCcCHHHHHHHH
Confidence 888899999888884
No 121
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=33.25 E-value=40 Score=20.80 Aligned_cols=27 Identities=11% Similarity=-0.087 Sum_probs=20.9
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|+.+..--|.+.+
T Consensus 155 ~~eI--A~~lgis~~tV~~~l~Ra~~~Lr 181 (196)
T PRK12524 155 NPEI--AEVMEIGVEAVESLTARGKRALA 181 (196)
T ss_pred HHHH--HHHHCcCHHHHHHHHHHHHHHHH
Confidence 4566 99999999999998866555544
No 122
>PF08452 DNAP_B_exo_N: DNA polymerase family B exonuclease domain, N-terminal; InterPro: IPR013660 This domain is found in viral DNA polymerases to the N terminus of DNA polymerase family B exonuclease domains (IPR006133 from INTERPRO). ; GO: 0003887 DNA-directed DNA polymerase activity
Probab=33.14 E-value=13 Score=15.09 Aligned_cols=9 Identities=11% Similarity=0.490 Sum_probs=6.4
Q ss_pred hhccchhHH
Q psy3735 76 VAWTHHLNA 84 (91)
Q Consensus 76 ~vWFqnrR~ 84 (91)
-.||.|+.-
T Consensus 6 iNWFE~~ge 14 (22)
T PF08452_consen 6 INWFESRGE 14 (22)
T ss_pred eehhhhCCc
Confidence 479988753
No 123
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=33.00 E-value=48 Score=20.07 Aligned_cols=27 Identities=4% Similarity=-0.013 Sum_probs=20.3
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|+.+...-|.+.+
T Consensus 154 ~~eI--A~~lgis~~~V~~~l~ra~~~Lr 180 (186)
T PRK13919 154 HREA--AQLLGLPLGTLKTRARRALSRLK 180 (186)
T ss_pred HHHH--HHHHCcCHHHHHHHHHHHHHHHH
Confidence 4566 99999999999988765555543
No 124
>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=32.93 E-value=41 Score=19.91 Aligned_cols=27 Identities=4% Similarity=-0.192 Sum_probs=19.0
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..||++...|+....--|.+.+
T Consensus 141 ~~eI--A~~l~is~~tv~~~l~ra~~~Lr 167 (170)
T TIGR02952 141 IAEV--ARILGKTEGAVKILQFRAIKKLA 167 (170)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 4566 88999999988887644444443
No 125
>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=32.68 E-value=67 Score=19.79 Aligned_cols=33 Identities=18% Similarity=0.205 Sum_probs=22.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcC-CCCCcc
Q psy3735 36 FTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRS-MPGELC 75 (91)
Q Consensus 36 ~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~-l~~~~v 75 (91)
.|.+.+..|...+.... .-.+| |.+|| ++...|
T Consensus 3 Wtde~~~~L~~lw~~G~-----SasqI--A~~lg~vsRnAV 36 (162)
T PF07750_consen 3 WTDERVERLRKLWAEGL-----SASQI--ARQLGGVSRNAV 36 (162)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHH--HHHhCCcchhhh
Confidence 57889999998886653 23455 77777 665433
No 126
>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=32.26 E-value=47 Score=21.92 Aligned_cols=48 Identities=10% Similarity=-0.077 Sum_probs=36.0
Q ss_pred CCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhc
Q psy3735 33 RTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTS 88 (91)
Q Consensus 33 R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~ 88 (91)
...+|+.+.+.|.-.. .. ....++ |..|+++...|+....|=+.|..-
T Consensus 188 ~~~LT~RE~evl~l~a-~G-----~s~~eI--A~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 188 AGLITAREAEILAWVR-DG-----KTNEEI--AAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred ccCCCHHHHHHHHHHH-CC-----CCHHHH--HHHHCcCHHHHHHHHHHHHHHhCC
Confidence 3468898888888543 22 245567 899999999999999888777543
No 127
>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=32.23 E-value=49 Score=19.90 Aligned_cols=47 Identities=13% Similarity=0.086 Sum_probs=34.1
Q ss_pred CCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 33 RTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 33 R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.+.++..|...|.-. ..+ ....++ |..+|++...|..+-..-+.+.+
T Consensus 4 ~~~Lte~qr~VL~Lr-~~G-----lTq~EI--Ae~LgiS~stV~~~e~ra~kkLr 50 (137)
T TIGR00721 4 KTFLTERQIKVLELR-EKG-----LSQKEI--AKELKTTRANVSAIEKRAMENIE 50 (137)
T ss_pred cCCCCHHHHHHHHHH-HcC-----CCHHHH--HHHHCcCHHHHHHHHHhHHHHHH
Confidence 357888888888763 222 245677 99999999999988766666654
No 128
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=32.22 E-value=42 Score=20.63 Aligned_cols=27 Identities=4% Similarity=-0.054 Sum_probs=20.3
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|+.....-|.+.+
T Consensus 155 ~~EI--A~~lgis~~tVk~~l~Rar~~Lr 181 (195)
T PRK12532 155 SDEI--QQMCGISTSNYHTIMHRARESLR 181 (195)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 4567 99999999999988765555443
No 129
>PF09292 Neil1-DNA_bind: Endonuclease VIII-like 1, DNA bind; InterPro: IPR015371 This domain is predominantly found in Endonuclease VIII-like 1 proteins and adopts a glucocorticoid receptor-like fold. Structural analysis reveals a zincless finger motif that is required for glycosylase activity []. ; PDB: 1TDH_A.
Probab=31.89 E-value=14 Score=17.24 Aligned_cols=7 Identities=14% Similarity=0.420 Sum_probs=4.5
Q ss_pred chhccch
Q psy3735 75 CVAWTHH 81 (91)
Q Consensus 75 v~vWFqn 81 (91)
=.||||.
T Consensus 26 RTiWFqG 32 (39)
T PF09292_consen 26 RTIWFQG 32 (39)
T ss_dssp -EEEESS
T ss_pred CEEEeeC
Confidence 3589974
No 130
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=31.50 E-value=47 Score=20.46 Aligned_cols=27 Identities=0% Similarity=-0.145 Sum_probs=20.6
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..||++...|++....-|.+.+
T Consensus 135 ~~EI--A~~Lgis~~tVk~~l~Rar~~Lr 161 (187)
T PRK12516 135 YEEA--AEICGCAVGTIKSRVNRARQRLQ 161 (187)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 4466 99999999999998766555543
No 131
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=31.47 E-value=12 Score=20.38 Aligned_cols=15 Identities=13% Similarity=0.248 Sum_probs=13.5
Q ss_pred hhhcCCCCCcchhcc
Q psy3735 65 SRQRSMPGELCVAWT 79 (91)
Q Consensus 65 a~~l~l~~~~v~vWF 79 (91)
|..+|++...++.|-
T Consensus 8 A~~~gvs~~tLR~ye 22 (88)
T cd01105 8 SKLTGVSPRQLRYWE 22 (88)
T ss_pred HHHHCcCHHHHHHHH
Confidence 889999999999994
No 132
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=31.11 E-value=18 Score=21.77 Aligned_cols=28 Identities=4% Similarity=-0.082 Sum_probs=21.9
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|+..+..-|++.+
T Consensus 138 s~~eI--A~~lg~s~~tv~~~l~Rar~~L~ 165 (175)
T PRK12518 138 PQKEI--AEILNIPVGTVKSRLFYARRQLR 165 (175)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 45567 99999999999998876666554
No 133
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=30.95 E-value=56 Score=19.50 Aligned_cols=26 Identities=12% Similarity=-0.005 Sum_probs=19.0
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAF 86 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~ 86 (91)
-.++ |..||++...|+.....-+.+.
T Consensus 137 ~~EI--A~~lgis~~tV~~~l~ra~~~L 162 (173)
T PRK09645 137 TAQI--AADLGIPEGTVKSRLHYALRAL 162 (173)
T ss_pred HHHH--HHHHCcCHHHHHHHHHHHHHHH
Confidence 4566 9999999999988765444443
No 134
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=30.82 E-value=48 Score=20.13 Aligned_cols=28 Identities=7% Similarity=-0.052 Sum_probs=22.0
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|++....-|.+.+
T Consensus 147 s~~EI--A~~l~is~~tV~~~l~rar~~Lr 174 (181)
T PRK12536 147 SVAET--AQLTGLSESAVKVGIHRGLKALA 174 (181)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 34567 99999999999998877666654
No 135
>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=30.79 E-value=47 Score=21.03 Aligned_cols=46 Identities=2% Similarity=-0.090 Sum_probs=29.8
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 35 TFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 35 ~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.+++.+...|...|... ....++ |..+|++...|+.+...-+.+.+
T Consensus 175 ~L~~~~r~il~l~y~~~-----~s~~eI--A~~lgis~~tV~~~~~ra~~~Lr 220 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE-----LNLKEI--GEVLGLTESRVSQIHSQALKKLR 220 (224)
T ss_pred hCCHHHHHHHHHHHhCC-----CCHHHH--HHHhCCCHHHHHHHHHHHHHHHH
Confidence 34555556665554322 234567 99999999999988765555544
No 136
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=30.75 E-value=35 Score=22.00 Aligned_cols=28 Identities=0% Similarity=-0.201 Sum_probs=21.8
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..||++...|++..+.-|.+.+
T Consensus 189 s~~EI--A~~Lgis~~tVk~~l~RAr~kLr 216 (233)
T PRK12538 189 SNGEI--AEVMDTTVAAVESLLKRGRQQLR 216 (233)
T ss_pred CHHHH--HHHHCcCHHHHHHHHHHHHHHHH
Confidence 34567 99999999999998876666654
No 137
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=30.64 E-value=46 Score=21.57 Aligned_cols=45 Identities=2% Similarity=0.030 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 36 FTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 36 ~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
+++.+...|...|-.+ ..-.++ |..+|++...|+.|...-+.+.+
T Consensus 206 L~~~~r~vl~l~~~~g-----~s~~eI--A~~l~is~~tV~~~~~ra~~kLr 250 (257)
T PRK08583 206 LSDREKSIIQCTFIEN-----LSQKET--GERLGISQMHVSRLQRQAIKKLR 250 (257)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 4555555555544222 234567 99999999999998765555543
No 138
>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=30.60 E-value=53 Score=21.11 Aligned_cols=47 Identities=4% Similarity=-0.150 Sum_probs=34.5
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhc
Q psy3735 34 TTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTS 88 (91)
Q Consensus 34 ~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~ 88 (91)
..+|+.+.+.|.-.. .. ..-.++ |..|+++...|+.+..|-+.|..-
T Consensus 170 ~~Lt~re~evl~~~a-~G-----~t~~eI--a~~l~is~~Tv~~~l~~~~~kl~~ 216 (232)
T TIGR03541 170 GVLSEREREVLAWTA-LG-----RRQADI--AAILGISERTVENHLRSARRKLGV 216 (232)
T ss_pred ccCCHHHHHHHHHHH-CC-----CCHHHH--HHHHCcCHHHHHHHHHHHHHHHCC
Confidence 467888888876642 22 244566 889999999999999888877643
No 139
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=30.56 E-value=16 Score=21.62 Aligned_cols=27 Identities=4% Similarity=0.104 Sum_probs=21.0
Q ss_pred hhhhhhhhcCCCCCcchhccchhHHhhhcCC
Q psy3735 60 QCGRFSRQRSMPGELCVAWTHHLNAAFTSSK 90 (91)
Q Consensus 60 ~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~~ 90 (91)
++| |..+|++...|--|- |...|+.++
T Consensus 4 eEL--A~~tG~srQTINrWv--RkegW~T~p 30 (122)
T PF07037_consen 4 EEL--AELTGYSRQTINRWV--RKEGWKTEP 30 (122)
T ss_pred HHH--HHHhCccHHHHHHHH--HhcCceecc
Confidence 567 999999999999994 666676554
No 140
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=30.16 E-value=47 Score=19.78 Aligned_cols=45 Identities=9% Similarity=-0.013 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 35 TFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 35 ~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.+|+.+...|..... + ..+..+ |..++++.+.|++..++=+.|.-
T Consensus 137 ~Lt~~E~~il~~l~~-g-----~~~~~I--a~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRERQVAEKLAQ-G-----MAVKEI--AAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHHHHHHHHHC-C-----CCHHHH--HHHhCCCHHHHHHHHHHHHHHhC
Confidence 577777777765443 2 256677 89999999999998888777753
No 141
>PRK09480 slmA division inhibitor protein; Provisional
Probab=30.16 E-value=46 Score=20.08 Aligned_cols=35 Identities=3% Similarity=-0.161 Sum_probs=26.8
Q ss_pred HHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHH
Q psy3735 47 AFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNA 84 (91)
Q Consensus 47 ~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~ 84 (91)
.|..... ....-..| |...|++...+-.+|.|+-.
T Consensus 22 l~~~~~G-~~~ti~~I--a~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 22 MLESPPG-ERITTAKL--AARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHhcCC-CccCHHHH--HHHhCCCHhHHHHHCCCHHH
Confidence 3444445 55666778 99999999999999998763
No 142
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=29.93 E-value=13 Score=20.22 Aligned_cols=16 Identities=6% Similarity=0.044 Sum_probs=14.3
Q ss_pred hhhcCCCCCcchhccc
Q psy3735 65 SRQRSMPGELCVAWTH 80 (91)
Q Consensus 65 a~~l~l~~~~v~vWFq 80 (91)
|..+|+++..++.|-.
T Consensus 8 A~~~gvs~~tLr~ye~ 23 (91)
T cd04766 8 AELSGMHPQTLRLYER 23 (91)
T ss_pred HHHHCcCHHHHHHHHH
Confidence 8899999999999964
No 143
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=29.86 E-value=44 Score=20.43 Aligned_cols=27 Identities=7% Similarity=-0.104 Sum_probs=21.1
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|++..+.-|.+.+
T Consensus 157 ~~eI--A~~lgis~~tv~~~l~Rar~~Lr 183 (193)
T PRK11923 157 YEDI--ASVMQCPVGTVRSRIFRAREAID 183 (193)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 4567 99999999999988766666554
No 144
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=29.84 E-value=50 Score=19.51 Aligned_cols=46 Identities=11% Similarity=-0.002 Sum_probs=33.3
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 34 TTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 34 ~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
..+|+.+...|.- +..+. ...++ |..++++...|+.+.+|=+.|..
T Consensus 148 ~~lt~~e~~vl~l-~~~g~-----~~~~I--a~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 148 PLLTPRERQILKL-ITEGY-----TNRDI--AEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred cCCCHHHHHHHHH-HHCCC-----CHHHH--HHHhCCCHHHHHHHHHHHHHHhC
Confidence 3478887777765 33332 24567 89999999999999888777653
No 145
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=29.30 E-value=13 Score=20.74 Aligned_cols=17 Identities=0% Similarity=-0.060 Sum_probs=14.0
Q ss_pred hhhcCCCCCcchhccch
Q psy3735 65 SRQRSMPGELCVAWTHH 81 (91)
Q Consensus 65 a~~l~l~~~~v~vWFqn 81 (91)
|..+|++...++.|..+
T Consensus 7 a~~~gvs~~tlR~ye~~ 23 (103)
T cd01106 7 AKLTGVSVRTLHYYDEI 23 (103)
T ss_pred HHHHCcCHHHHHHHHHC
Confidence 88889999999988643
No 146
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=29.21 E-value=47 Score=20.03 Aligned_cols=27 Identities=15% Similarity=-0.007 Sum_probs=20.9
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|......-|.+.+
T Consensus 155 ~~eI--A~~lgis~~~v~~~l~Rar~~Lr 181 (187)
T PRK09641 155 LKEI--SEILDLPVGTVKTRIHRGREALR 181 (187)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 4566 99999999999988766666554
No 147
>KOG0150|consensus
Probab=29.07 E-value=19 Score=24.72 Aligned_cols=13 Identities=23% Similarity=0.598 Sum_probs=10.3
Q ss_pred cchhccchhHHhh
Q psy3735 74 LCVAWTHHLNAAF 86 (91)
Q Consensus 74 ~v~vWFqnrR~k~ 86 (91)
-++|||+|.++..
T Consensus 15 yCKiWi~dN~~Sv 27 (336)
T KOG0150|consen 15 YCKIWIKDNPASV 27 (336)
T ss_pred hhhhhhcCChHHH
Confidence 3689999998753
No 148
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=28.88 E-value=57 Score=20.48 Aligned_cols=27 Identities=4% Similarity=-0.165 Sum_probs=20.5
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..||++...|+++...-|.+.+
T Consensus 157 ~~EI--A~~Lgis~~tV~~~l~RArk~Lr 183 (203)
T PRK09647 157 YEEI--AATLGVKLGTVRSRIHRGRQQLR 183 (203)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 4466 99999999999998765555543
No 149
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=28.75 E-value=56 Score=19.79 Aligned_cols=27 Identities=7% Similarity=-0.029 Sum_probs=20.5
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|++....-+++.+
T Consensus 136 ~~EI--A~~lgis~~tV~~~l~ra~~~Lr 162 (179)
T PRK12543 136 QEEI--AQLLQIPIGTVKSRIHAALKKLR 162 (179)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 4466 89999999999988766666544
No 150
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=28.54 E-value=62 Score=19.40 Aligned_cols=27 Identities=7% Similarity=-0.137 Sum_probs=20.4
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|++....-+.+.+
T Consensus 138 ~~EI--A~~lgis~~tV~~~l~Ra~~~Lr 164 (173)
T PRK12522 138 YKEM--SEILNIPIGTVKYRLNYAKKQMR 164 (173)
T ss_pred HHHH--HHHhCCCHHHHHHHHHHHHHHHH
Confidence 4466 99999999999998765555543
No 151
>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=28.43 E-value=46 Score=15.54 Aligned_cols=26 Identities=4% Similarity=-0.073 Sum_probs=18.7
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAA 85 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k 85 (91)
...++ |..++++...|..|...-+.+
T Consensus 17 s~~ei--a~~l~~s~~tv~~~~~~~~~~ 42 (57)
T cd06170 17 TNKEI--ADILGISEKTVKTHLRNIMRK 42 (57)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHHH
Confidence 34566 889999999999887543333
No 152
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=28.32 E-value=59 Score=19.77 Aligned_cols=28 Identities=11% Similarity=0.017 Sum_probs=20.8
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|+.+...-+.+.+
T Consensus 149 s~~eI--A~~lgis~~tV~~~l~ra~~~Lr 176 (184)
T PRK12539 149 SVAEA--ATRSGMSESAVKVSVHRGLKALA 176 (184)
T ss_pred cHHHH--HHHHCcCHHHHHHHHHHHHHHHH
Confidence 34566 99999999999988765555543
No 153
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=28.18 E-value=58 Score=20.25 Aligned_cols=27 Identities=4% Similarity=0.027 Sum_probs=20.3
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|++....-|.+.+
T Consensus 158 ~~EI--A~~lgis~~tVk~~l~RAr~~Lr 184 (201)
T PRK12545 158 IDDI--CTELTLTANHCSVLLYRARTRLR 184 (201)
T ss_pred HHHH--HHHHCcCHHHHHHHHHHHHHHHH
Confidence 4566 99999999999988765555543
No 154
>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=28.11 E-value=18 Score=21.12 Aligned_cols=29 Identities=3% Similarity=-0.091 Sum_probs=21.9
Q ss_pred HHhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 57 FTRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 57 ~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
..-.++ |..+|++...|+++..--|.+.+
T Consensus 122 ~s~~eI--A~~lgis~~tv~~~l~Ra~~~Lr 150 (154)
T TIGR02950 122 FSYKEI--AELLNLSLAKVKSNLFRARKELK 150 (154)
T ss_pred CcHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 345567 99999999999988766555554
No 155
>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=27.82 E-value=56 Score=21.62 Aligned_cols=28 Identities=4% Similarity=-0.059 Sum_probs=22.1
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhhc
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFTS 88 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~ 88 (91)
-.++ |..+|++...|+..++.-|.+.+.
T Consensus 127 ~~EI--A~~lg~s~~tVr~~l~RAr~~Lr~ 154 (281)
T TIGR02957 127 YEEI--ASIVGKSEANCRQLVSRARRHLDA 154 (281)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHHHHHHh
Confidence 3466 899999999999998777766553
No 156
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=27.70 E-value=62 Score=19.86 Aligned_cols=27 Identities=15% Similarity=0.060 Sum_probs=19.8
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAF 86 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~ 86 (91)
.-.++ |..+|++...|++...--|.+.
T Consensus 129 s~~EI--A~~lgis~~tV~~~l~Rar~~L 155 (182)
T PRK12511 129 SYQEA--AAVLGIPIGTLMSRIGRARAAL 155 (182)
T ss_pred CHHHH--HHHhCcCHHHHHHHHHHHHHHH
Confidence 34566 9999999999998875544443
No 157
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=27.68 E-value=56 Score=19.87 Aligned_cols=27 Identities=7% Similarity=-0.203 Sum_probs=20.3
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|++....-|.+.+
T Consensus 141 ~~EI--A~~lgis~~tVk~~l~Rar~~Lr 167 (185)
T PRK12542 141 YQEI--SSVMGITEANVRKQFERARKRVQ 167 (185)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 4566 99999999999997765555543
No 158
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=27.63 E-value=61 Score=19.09 Aligned_cols=24 Identities=13% Similarity=-0.018 Sum_probs=17.6
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhH
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLN 83 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR 83 (91)
...++ |..+|++...|+....--+
T Consensus 127 s~~EI--A~~lgis~~tV~~~l~ra~ 150 (163)
T PRK07037 127 TQKDI--ARELGVSPTLVNFMIRDAL 150 (163)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHH
Confidence 34566 9999999999998654333
No 159
>KOG3755|consensus
Probab=27.62 E-value=38 Score=25.65 Aligned_cols=33 Identities=9% Similarity=-0.020 Sum_probs=24.0
Q ss_pred CCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhc
Q psy3735 54 PDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTS 88 (91)
Q Consensus 54 p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~ 88 (91)
|+...+... -.-+++..+-+.+||.||++.+.+
T Consensus 540 ~~~~n~~~~--EN~~~~~rh~~~l~q~er~a~~~~ 572 (769)
T KOG3755|consen 540 PSPENRTLW--ENYLHIIRHFLKLPQKERDAIYER 572 (769)
T ss_pred CChhhhhhh--hcchhHHHhhhccchhhhhHHHhh
Confidence 444444443 445788889999999999999864
No 160
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=27.43 E-value=55 Score=20.04 Aligned_cols=27 Identities=7% Similarity=-0.097 Sum_probs=19.9
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|++....-|.+.+
T Consensus 149 ~~EI--A~~lgis~~tVk~~l~Rar~~Lr 175 (185)
T PRK09649 149 YADA--AAVCGCPVGTIRSRVARARDALL 175 (185)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 4566 99999999999988755554443
No 161
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=27.27 E-value=67 Score=19.75 Aligned_cols=27 Identities=7% Similarity=-0.093 Sum_probs=20.0
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|++-...-+.+.+
T Consensus 160 ~~EI--A~~lgis~~tVk~rl~ra~~~Lr 186 (194)
T PRK12531 160 HQQV--AEMFDIPLGTVKSRLRLAVEKLR 186 (194)
T ss_pred HHHH--HHHhCcCHHHHHHHHHHHHHHHH
Confidence 4566 99999999999887655555443
No 162
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=26.43 E-value=18 Score=20.00 Aligned_cols=17 Identities=0% Similarity=-0.064 Sum_probs=14.9
Q ss_pred hhhcCCCCCcchhccch
Q psy3735 65 SRQRSMPGELCVAWTHH 81 (91)
Q Consensus 65 a~~l~l~~~~v~vWFqn 81 (91)
|..+|++...++.|.+.
T Consensus 7 a~~~gvs~~tLRyye~~ 23 (96)
T cd04768 7 AKLAGVSIRTLRHYDDI 23 (96)
T ss_pred HHHHCcCHHHHHHHHHC
Confidence 88999999999999754
No 163
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=26.19 E-value=59 Score=20.03 Aligned_cols=27 Identities=4% Similarity=-0.099 Sum_probs=20.4
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAF 86 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~ 86 (91)
..+++ |..+|++++.|+...+.-|++.
T Consensus 153 s~~EI--A~~lgiS~~tV~r~l~~aR~~l 179 (185)
T PF07638_consen 153 SVEEI--AERLGISERTVRRRLRRARAWL 179 (185)
T ss_pred CHHHH--HHHHCcCHHHHHHHHHHHHHHH
Confidence 45677 9999999999987776666443
No 164
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=26.17 E-value=17 Score=20.17 Aligned_cols=17 Identities=0% Similarity=0.026 Sum_probs=14.6
Q ss_pred hhhcCCCCCcchhccch
Q psy3735 65 SRQRSMPGELCVAWTHH 81 (91)
Q Consensus 65 a~~l~l~~~~v~vWFqn 81 (91)
|..+|++...++.|...
T Consensus 7 a~~~gvs~~tLR~ye~~ 23 (96)
T cd04774 7 AKRLGLTKRTLKYYEEI 23 (96)
T ss_pred HHHHCcCHHHHHHHHHC
Confidence 88899999999999743
No 165
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=26.15 E-value=34 Score=18.51 Aligned_cols=20 Identities=5% Similarity=0.082 Sum_probs=15.7
Q ss_pred hhhhhhhhhcCCCCCcchhccc
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTH 80 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFq 80 (91)
+..| ...++|...++.||+.
T Consensus 56 ~~~L--~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 56 TSLV--QKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHH--HHHhCCCCCeEEEEEE
Confidence 3445 7788999999999984
No 166
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=26.14 E-value=63 Score=20.09 Aligned_cols=27 Identities=4% Similarity=-0.080 Sum_probs=20.4
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|+++...-|.+.+
T Consensus 152 ~~EI--Ae~lgis~~tV~~~l~Rar~~Lr 178 (196)
T PRK12535 152 YEEA--AKIADVRVGTIRSRVARARADLI 178 (196)
T ss_pred HHHH--HHHhCCCHHHHHHHHHHHHHHHH
Confidence 4566 99999999999998765555543
No 167
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=26.02 E-value=22 Score=21.83 Aligned_cols=28 Identities=7% Similarity=-0.061 Sum_probs=21.4
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|+.+...-|.+.+
T Consensus 157 s~~EI--A~~lgis~~tV~~~l~ra~~~Lr 184 (194)
T PRK12513 157 ELEEI--AELTGVPEETVKSRLRYALQKLR 184 (194)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 45567 99999999999988766665544
No 168
>PRK10651 transcriptional regulator NarL; Provisional
Probab=26.00 E-value=61 Score=19.39 Aligned_cols=45 Identities=9% Similarity=0.076 Sum_probs=32.9
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 35 TFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 35 ~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.+|+.+...|..... + .....+ |..++++...|++..+|-+.|..
T Consensus 155 ~Lt~rE~~vl~~l~~-g-----~~~~~i--a~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 155 QLTPRERDILKLIAQ-G-----LPNKMI--ARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred cCCHHHHHHHHHHHc-C-----CCHHHH--HHHcCCCHHHHHHHHHHHHHHcC
Confidence 488888888875442 2 124456 88999999999999888777753
No 169
>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=25.77 E-value=65 Score=20.36 Aligned_cols=45 Identities=7% Similarity=-0.092 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhh
Q psy3735 35 TFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAF 86 (91)
Q Consensus 35 ~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~ 86 (91)
.+++.+...+...|..+ ..-.++ |..+|++...|..|...-+.+.
T Consensus 178 ~L~~~~r~vl~l~y~~~-----~s~~eI--A~~lgis~~~v~~~~~ra~~~L 222 (227)
T TIGR02980 178 ALPERERRILLLRFFED-----KTQSEI--AERLGISQMHVSRLLRRALKKL 222 (227)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHH--HHHHCcCHHHHHHHHHHHHHHH
Confidence 45666666665554322 234567 9999999999998865444443
No 170
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=25.56 E-value=67 Score=19.63 Aligned_cols=27 Identities=0% Similarity=-0.129 Sum_probs=20.4
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|++....-|.+.+
T Consensus 150 ~~EI--A~~lgis~~tV~~~l~Rar~~Lr 176 (191)
T PRK12520 150 TEEI--CQELQITATNAWVLLYRARMRLR 176 (191)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 4566 99999999999988765555543
No 171
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=25.48 E-value=52 Score=19.68 Aligned_cols=45 Identities=7% Similarity=0.050 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 35 TFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 35 ~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.+|..+...|.... .+ ....++ |..++++.+.|+++-.+=|.|..
T Consensus 149 ~lt~re~~vl~~l~-~g-----~s~~eI--a~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 149 VLSNREVTILRYLV-SG-----LSNKEI--ADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred cCCHHHHHHHHHHH-cC-----CCHHHH--HHHhCCCHHHHHHHHHHHHHHcC
Confidence 46777777775432 22 356677 99999999999998888777753
No 172
>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=25.43 E-value=26 Score=21.56 Aligned_cols=28 Identities=7% Similarity=-0.057 Sum_probs=21.7
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|+++...-|.+.+
T Consensus 149 s~~EI--A~~lgis~~tVk~~l~Rar~~Lr 176 (193)
T TIGR02947 149 AYKEI--AEIMGTPIGTVMSRLHRGRKQLR 176 (193)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 34567 99999999999998866666544
No 173
>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=25.22 E-value=42 Score=17.32 Aligned_cols=38 Identities=21% Similarity=0.107 Sum_probs=20.3
Q ss_pred CCCHHHHHHHHHH---HhhCCCCCHHHhhhhhhhhhcCCC-CCcch
Q psy3735 35 TFTSFQLEELEKA---FSRTHYPDVFTRQCGRFSRQRSMP-GELCV 76 (91)
Q Consensus 35 ~~t~~ql~~Le~~---f~~~~~p~~~~r~~l~~a~~l~l~-~~~v~ 76 (91)
.+|.-|...|+-. ...+.|| +...+| |..+|+. ...|+
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~G~~--Pt~rEI--a~~~g~~S~~tv~ 44 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEENGYP--PTVREI--AEALGLKSTSTVQ 44 (65)
T ss_dssp ---HHHHHHHHHHHHHHHHHSS-----HHHH--HHHHTSSSHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHcCCC--CCHHHH--HHHhCCCChHHHH
Confidence 3567777776654 3445565 345567 8899987 44443
No 174
>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=24.79 E-value=14 Score=17.73 Aligned_cols=23 Identities=0% Similarity=-0.127 Sum_probs=16.9
Q ss_pred hhhhhhhhhcCCCCCcchhccchhH
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLN 83 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR 83 (91)
..++ |..+|+++..|.-|..+.+
T Consensus 12 ~~~l--a~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKEL--AEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHH--HHHHTS-HHHHHHHHTTSS
T ss_pred HHHH--HHHhCCCcchhHHHhcCCC
Confidence 3456 8899999999988887643
No 175
>PF14991 MLANA: Protein melan-A; PDB: 2GTZ_F 2GT9_F 3MRO_P 2GUO_C 3MRQ_P 2GTW_C 3L6F_C 3MRP_P.
Probab=24.75 E-value=24 Score=20.63 Aligned_cols=17 Identities=12% Similarity=0.261 Sum_probs=0.0
Q ss_pred CcchhccchhHHhhhcC
Q psy3735 73 ELCVAWTHHLNAAFTSS 89 (91)
Q Consensus 73 ~~v~vWFqnrR~k~~~~ 89 (91)
.-+-.||+.||.-++..
T Consensus 40 LliGCWYckRRSGYk~L 56 (118)
T PF14991_consen 40 LLIGCWYCKRRSGYKTL 56 (118)
T ss_dssp -----------------
T ss_pred HHHhheeeeecchhhhh
Confidence 44678999999988754
No 176
>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=24.55 E-value=61 Score=20.98 Aligned_cols=47 Identities=2% Similarity=0.041 Sum_probs=30.7
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhc
Q psy3735 35 TFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTS 88 (91)
Q Consensus 35 ~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~ 88 (91)
.+++.+...+...|..+ ..-.++ |..+|++...|+.+...-+.+.+.
T Consensus 205 ~L~~~~r~ii~l~~~~g-----~s~~eI--A~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN-----LSQKET--GERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred cCCHHHHHHHHHHHcCC-----CCHHHH--HHHHCcCHHHHHHHHHHHHHHHHH
Confidence 34555555555554322 234567 999999999999987666666553
No 177
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=24.52 E-value=19 Score=20.11 Aligned_cols=16 Identities=13% Similarity=0.156 Sum_probs=13.7
Q ss_pred hhhcCCCCCcchhccc
Q psy3735 65 SRQRSMPGELCVAWTH 80 (91)
Q Consensus 65 a~~l~l~~~~v~vWFq 80 (91)
|..+|++...++.|-+
T Consensus 8 a~~~gvs~~tLR~ye~ 23 (102)
T cd04775 8 SRKFGVSRSTLLYYES 23 (102)
T ss_pred HHHHCcCHHHHHHHHH
Confidence 8889999999998863
No 178
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=24.45 E-value=32 Score=17.33 Aligned_cols=18 Identities=6% Similarity=0.038 Sum_probs=10.6
Q ss_pred HHhhhhhhhhhcCCCCCcch
Q psy3735 57 FTRQCGRFSRQRSMPGELCV 76 (91)
Q Consensus 57 ~~r~~l~~a~~l~l~~~~v~ 76 (91)
.+...+ +..||+++.+++
T Consensus 21 ~ev~yw--a~~~gvt~~~L~ 38 (57)
T PF12244_consen 21 YEVRYW--AKRFGVTEEQLR 38 (57)
T ss_pred HHHHHH--HHHHCcCHHHHH
Confidence 344455 667777766554
No 179
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=24.30 E-value=63 Score=22.08 Aligned_cols=50 Identities=16% Similarity=0.094 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 35 TFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 35 ~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.+++.+...|...|....+ ......++ |..+|++...|+.+...-+.+.+
T Consensus 262 ~L~~~~R~vl~lrygL~~~-e~~s~~EI--A~~Lgis~~tV~~~~~rAl~kLr 311 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGY-EAATLEDV--AREIGLTRERVRQIQVEALRRLR 311 (325)
T ss_pred cCCHHHHHHHHHHhccCCC-CCcCHHHH--HHHHCcCHHHHHHHHHHHHHHHH
Confidence 4566666666655532222 22345677 99999999999998766665554
No 180
>PRK13870 transcriptional regulator TraR; Provisional
Probab=24.23 E-value=84 Score=20.35 Aligned_cols=26 Identities=4% Similarity=-0.185 Sum_probs=21.5
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAF 86 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~ 86 (91)
-.++ |..||++++.|..-..|-+.|.
T Consensus 191 ~~EI--a~ILgISe~TV~~Hl~na~~KL 216 (234)
T PRK13870 191 MEEI--ADVEGVKYNSVRVKLREAMKRF 216 (234)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHHHHc
Confidence 3456 8899999999999888888775
No 181
>PHA02955 hypothetical protein; Provisional
Probab=24.16 E-value=1.3e+02 Score=19.58 Aligned_cols=47 Identities=9% Similarity=-0.183 Sum_probs=33.4
Q ss_pred HHHHHHHHHHhhC-CCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 39 FQLEELEKAFSRT-HYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 39 ~ql~~Le~~f~~~-~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.++..|-..|... ..++..++..+ +..||+....+.-||.+--.+-|
T Consensus 61 ~sf~lli~a~~Et~~~Lp~~qk~~i--a~~lgI~~~~~~~d~~t~~~q~C 108 (213)
T PHA02955 61 KNFQLLIEALIETIENFPEKEQKEI--AADIGINIDDYKAGKKTDLQLHC 108 (213)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHH--HHHhCCChhhccCcccchhhhhc
Confidence 4556665566554 45667778888 99999998778889977654444
No 182
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=24.06 E-value=18 Score=21.52 Aligned_cols=17 Identities=6% Similarity=-0.005 Sum_probs=14.8
Q ss_pred hhhcCCCCCcchhccch
Q psy3735 65 SRQRSMPGELCVAWTHH 81 (91)
Q Consensus 65 a~~l~l~~~~v~vWFqn 81 (91)
|..+|++...++.|.+.
T Consensus 7 a~~~gvs~~TLR~Ye~~ 23 (134)
T cd04779 7 AHLAGVSKRTIDYYTNL 23 (134)
T ss_pred HHHHCcCHHHHHHHHHC
Confidence 88999999999999753
No 183
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=23.97 E-value=18 Score=17.81 Aligned_cols=15 Identities=7% Similarity=-0.170 Sum_probs=11.1
Q ss_pred hhhhhhhhcCCCCCcch
Q psy3735 60 QCGRFSRQRSMPGELCV 76 (91)
Q Consensus 60 ~~l~~a~~l~l~~~~v~ 76 (91)
.+| |..+|+++.||+
T Consensus 32 ~~L--a~~~gi~~~qVR 46 (50)
T PF06971_consen 32 QEL--AEALGITPAQVR 46 (50)
T ss_dssp HHH--HHHHTS-HHHHH
T ss_pred HHH--HHHHCCCHHHhc
Confidence 356 889999998875
No 184
>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=23.93 E-value=20 Score=20.05 Aligned_cols=16 Identities=0% Similarity=0.133 Sum_probs=13.7
Q ss_pred hhhcCCCCCcchhccc
Q psy3735 65 SRQRSMPGELCVAWTH 80 (91)
Q Consensus 65 a~~l~l~~~~v~vWFq 80 (91)
|+.+|+++..++.|-.
T Consensus 8 a~~~gvs~~tlR~ye~ 23 (102)
T cd04789 8 AEKAGISRSTLLYYEK 23 (102)
T ss_pred HHHHCcCHHHHHHHHH
Confidence 8889999999998864
No 185
>PRK15372 pathogenicity island 2 effector protein SseI; Provisional
Probab=23.52 E-value=55 Score=22.01 Aligned_cols=28 Identities=29% Similarity=0.218 Sum_probs=21.1
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHhhhh
Q psy3735 35 TFTSFQLEELEKAFSRTHYPDVFTRQCG 62 (91)
Q Consensus 35 ~~t~~ql~~Le~~f~~~~~p~~~~r~~l 62 (91)
-++..|.++|++.|..+|.|.-..++.+
T Consensus 11 FcsTHq~EAl~CI~~LcHP~~gtTpe~I 38 (292)
T PRK15372 11 FCSTHQTEALECIWTICHPPAGTTREDV 38 (292)
T ss_pred hccccHHHHHHHHHHHhCCCCCCCHHHH
Confidence 3567889999999999998755555544
No 186
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=23.42 E-value=21 Score=19.72 Aligned_cols=16 Identities=13% Similarity=0.258 Sum_probs=14.0
Q ss_pred hhhcCCCCCcchhccc
Q psy3735 65 SRQRSMPGELCVAWTH 80 (91)
Q Consensus 65 a~~l~l~~~~v~vWFq 80 (91)
|..+|++...++.|-.
T Consensus 7 a~~~gvs~~tlR~ye~ 22 (96)
T cd04788 7 ARRTGLSVRTLHHYDH 22 (96)
T ss_pred HHHHCcCHHHHHHHHH
Confidence 8889999999999964
No 187
>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=23.39 E-value=26 Score=21.45 Aligned_cols=28 Identities=4% Similarity=-0.205 Sum_probs=21.6
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|++.+.--|.+.+
T Consensus 167 s~~eI--A~~l~~s~~tV~~~l~r~r~~L~ 194 (198)
T TIGR02859 167 SYQEI--ACDLNRHVKSIDNALQRVKRKLE 194 (198)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 45567 99999999999988866666554
No 188
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=23.21 E-value=91 Score=20.25 Aligned_cols=45 Identities=13% Similarity=0.014 Sum_probs=31.5
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhh
Q psy3735 34 TTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAF 86 (91)
Q Consensus 34 ~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~ 86 (91)
..+|+-++++|.-..+ + ..-.++ |..|+++.+.|+.-..|-+.|+
T Consensus 178 ~~LT~rE~evl~~~a~-G-----~t~~eI--a~~l~is~~TV~~h~~~~~~KL 222 (240)
T PRK10188 178 MNFSKREKEILKWTAE-G-----KTSAEI--AMILSISENTVNFHQKNMQKKF 222 (240)
T ss_pred CCCCHHHHHHHHHHHc-C-----CCHHHH--HHHhCCCHHHHHHHHHHHHHHh
Confidence 4677777777754421 1 234566 8899999999998887777665
No 189
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=23.21 E-value=67 Score=20.45 Aligned_cols=27 Identities=0% Similarity=-0.052 Sum_probs=21.0
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|+.+...-+.+.+
T Consensus 201 ~~EI--A~~lgis~~tVk~~~~rA~~~Lr 227 (234)
T PRK08301 201 QKEV--ADMLGISQSYISRLEKRIIKRLK 227 (234)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 4567 99999999999998766666554
No 190
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=23.18 E-value=19 Score=21.19 Aligned_cols=16 Identities=13% Similarity=0.233 Sum_probs=14.1
Q ss_pred hhhcCCCCCcchhccc
Q psy3735 65 SRQRSMPGELCVAWTH 80 (91)
Q Consensus 65 a~~l~l~~~~v~vWFq 80 (91)
|..+|+++..+++|.+
T Consensus 8 A~~~GVs~~TLR~wE~ 23 (120)
T cd04767 8 AELLNIHPETLRIWER 23 (120)
T ss_pred HHHHCcCHHHHHHHHH
Confidence 8899999999999964
No 191
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=23.03 E-value=67 Score=20.48 Aligned_cols=28 Identities=4% Similarity=-0.044 Sum_probs=20.9
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..||++...|++....-|.+.+
T Consensus 152 s~~EI--Ae~LgiS~~tVk~~L~RAr~~Lr 179 (216)
T PRK12533 152 SYREI--AAIADVPVGTVMSRLARARRRLA 179 (216)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 34567 99999999999988765555543
No 192
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=22.92 E-value=85 Score=19.00 Aligned_cols=25 Identities=4% Similarity=-0.013 Sum_probs=18.4
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHH
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNA 84 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~ 84 (91)
.-.++ |..||++...|+.....-+.
T Consensus 145 s~~EI--A~~lgis~~tVk~~l~rAl~ 169 (178)
T PRK12529 145 KQKDI--AQALDIALPTVKKYIHQAYV 169 (178)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHH
Confidence 34567 99999999999987654433
No 193
>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=22.77 E-value=78 Score=20.65 Aligned_cols=28 Identities=4% Similarity=0.024 Sum_probs=21.6
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|+++...-|.+.+
T Consensus 179 S~~EI--A~~Lgis~~TVk~rl~RAr~~Lr 206 (244)
T TIGR03001 179 SMDRI--GAMYQVHRSTVSRWVAQARERLL 206 (244)
T ss_pred CHHHH--HHHHCcCHHHHHHHHHHHHHHHH
Confidence 34567 99999999999999876665543
No 194
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=22.70 E-value=77 Score=20.51 Aligned_cols=28 Identities=4% Similarity=-0.197 Sum_probs=21.3
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|+..+..-+.+.+
T Consensus 219 s~~EI--A~~lgis~~tV~~~~~ra~~~Lr 246 (251)
T PRK07670 219 TLTEI--GQVLNLSTSRISQIHSKALFKLK 246 (251)
T ss_pred CHHHH--HHHHCcCHHHHHHHHHHHHHHHH
Confidence 34567 99999999999998766555544
No 195
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=22.68 E-value=1.2e+02 Score=16.43 Aligned_cols=42 Identities=10% Similarity=-0.039 Sum_probs=24.2
Q ss_pred CCHHHHHHHHHHHhhC-----CCCCHHHhhhhhhhhhcCCCCCcchhcc
Q psy3735 36 FTSFQLEELEKAFSRT-----HYPDVFTRQCGRFSRQRSMPGELCVAWT 79 (91)
Q Consensus 36 ~t~~ql~~Le~~f~~~-----~~p~~~~r~~l~~a~~l~l~~~~v~vWF 79 (91)
++.+++..+...|..- -+.+..+-..+ ...+|++...|.-+|
T Consensus 4 ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~--l~~~~~~~~ev~~i~ 50 (96)
T smart00027 4 ISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPI--LLKSGLPQTLLAKIW 50 (96)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHH--HHHcCCCHHHHHHHH
Confidence 5677888888777651 23444444443 344677666555544
No 196
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=22.62 E-value=27 Score=21.62 Aligned_cols=28 Identities=4% Similarity=-0.165 Sum_probs=21.5
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|++-...-|.+.+
T Consensus 172 s~~EI--A~~lgis~~tV~~~l~rar~~Lr 199 (208)
T PRK08295 172 SYQEI--AEELNRHVKSIDNALQRVKRKLE 199 (208)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 34566 99999999999988776666654
No 197
>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=22.62 E-value=85 Score=19.27 Aligned_cols=27 Identities=4% Similarity=0.007 Sum_probs=19.5
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAF 86 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~ 86 (91)
.-.++ |..+|++...|+.....-|.+.
T Consensus 149 s~~EI--A~~lgis~~tvk~rl~Rar~~L 175 (188)
T TIGR02943 149 ESDEI--CQELEISTSNCHVLLYRARLSL 175 (188)
T ss_pred CHHHH--HHHhCCCHHHHHHHHHHHHHHH
Confidence 34567 9999999999988765544443
No 198
>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=22.47 E-value=82 Score=18.07 Aligned_cols=20 Identities=5% Similarity=0.194 Sum_probs=16.9
Q ss_pred hhhhhhhhhcCCCCCcchhccc
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTH 80 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFq 80 (91)
..++ |..++++...|..|++
T Consensus 21 ~~ea--a~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 21 IREA--AKRFGVSRNTVYRWLK 40 (119)
T ss_pred HHHH--HHHhCcHHHHHHHHHH
Confidence 3345 8899999999999998
No 199
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=22.42 E-value=27 Score=21.38 Aligned_cols=28 Identities=7% Similarity=-0.260 Sum_probs=21.7
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.-.++ |..+|++...|+++...-+.+.+
T Consensus 152 s~~EI--A~~lgis~~tV~~~l~Ra~~~Lr 179 (188)
T PRK09640 152 EFQEI--ADIMHMGLSATKMRYKRALDKLR 179 (188)
T ss_pred CHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Confidence 44567 99999999999998766555544
No 200
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=22.39 E-value=24 Score=20.00 Aligned_cols=15 Identities=0% Similarity=-0.033 Sum_probs=12.5
Q ss_pred hhhcCCCCCcchhcc
Q psy3735 65 SRQRSMPGELCVAWT 79 (91)
Q Consensus 65 a~~l~l~~~~v~vWF 79 (91)
|..+||+.+.++.|=
T Consensus 7 a~~~gvs~~tLRyYE 21 (124)
T COG0789 7 AKLTGVSVRTLRFYE 21 (124)
T ss_pred HHHhCCCHHHHHHHH
Confidence 888899998888883
No 201
>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=22.30 E-value=58 Score=15.77 Aligned_cols=36 Identities=11% Similarity=-0.010 Sum_probs=22.2
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcc
Q psy3735 36 FTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELC 75 (91)
Q Consensus 36 ~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v 75 (91)
+|..|...|......... .....+| |..+++++..|
T Consensus 3 lt~~q~~vL~~l~~~~~~--~~t~~~l--a~~l~~~~~~v 38 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGE--ELTQSEL--AERLGISKSTV 38 (62)
T ss_dssp STHHHHHHHHHHHHSTTS--GEEHHHH--HHHHTS-HHHH
T ss_pred cCHHHHHHHHHHHHCCCC--CcCHHHH--HHHHCcCHHHH
Confidence 678888888766655542 1134456 88888876544
No 202
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=21.89 E-value=24 Score=16.77 Aligned_cols=23 Identities=0% Similarity=-0.266 Sum_probs=18.0
Q ss_pred hhhhhhhhhcCCCCCcchhccchhH
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLN 83 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR 83 (91)
...+ |..+|++...|.-|...++
T Consensus 18 q~~l--A~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADL--ADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHH--HHHhCCCHHHHHHHHCCCC
Confidence 4456 8999999999999986553
No 203
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=21.78 E-value=88 Score=19.65 Aligned_cols=27 Identities=0% Similarity=-0.231 Sum_probs=20.4
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
-.++ |..+|++...|++..+.-|.+.+
T Consensus 167 ~~EI--Ae~lgis~~tV~~~l~RAr~~Lr 193 (206)
T PRK12544 167 TNEI--CHAVDLSVSNLNVLLYRARLRLR 193 (206)
T ss_pred HHHH--HHHHCcCHHHHHHHHHHHHHHHH
Confidence 4566 99999999999988765555544
No 204
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=21.75 E-value=98 Score=18.22 Aligned_cols=23 Identities=0% Similarity=-0.164 Sum_probs=17.4
Q ss_pred hhhhhhhhhcCCCCCcchhccchhH
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLN 83 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR 83 (91)
-.++ |..+|++...|+++...-+
T Consensus 132 ~~EI--A~~l~is~~tV~~~l~ra~ 154 (161)
T PRK12528 132 YGEI--ATELGISLATVKRYLNKAA 154 (161)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHH
Confidence 4466 8899999999998765443
No 205
>PF11388 DotA: Phagosome trafficking protein DotA; InterPro: IPR021528 DotA is essential for intracellular growth in Legionella []. DotA is thought to play an important role in regulating initial phagosome trafficking decisions either upon or immediately after macrophage uptake [].
Probab=21.71 E-value=25 Score=19.90 Aligned_cols=12 Identities=8% Similarity=0.379 Sum_probs=8.2
Q ss_pred chhccchhHHhh
Q psy3735 75 CVAWTHHLNAAF 86 (91)
Q Consensus 75 v~vWFqnrR~k~ 86 (91)
+=+||||.-.+.
T Consensus 32 LC~WF~~~s~~l 43 (105)
T PF11388_consen 32 LCTWFQNKSDKL 43 (105)
T ss_pred HHHHHccCCchh
Confidence 457999876553
No 206
>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=21.58 E-value=22 Score=15.82 Aligned_cols=17 Identities=24% Similarity=0.055 Sum_probs=10.7
Q ss_pred HhhhhhhhhhcCCCCCcch
Q psy3735 58 TRQCGRFSRQRSMPGELCV 76 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~ 76 (91)
.++++ |.-+|++...|-
T Consensus 4 tr~di--A~~lG~t~ETVS 20 (32)
T PF00325_consen 4 TRQDI--ADYLGLTRETVS 20 (32)
T ss_dssp -HHHH--HHHHTS-HHHHH
T ss_pred CHHHH--HHHhCCcHHHHH
Confidence 35667 888888876553
No 207
>PLN00131 hypothetical protein; Provisional
Probab=21.47 E-value=26 Score=21.80 Aligned_cols=12 Identities=8% Similarity=0.130 Sum_probs=8.9
Q ss_pred CcchhccchhHH
Q psy3735 73 ELCVAWTHHLNA 84 (91)
Q Consensus 73 ~~v~vWFqnrR~ 84 (91)
..++.||-||..
T Consensus 206 kslklwflnrke 217 (218)
T PLN00131 206 KSLKLWFLNRKE 217 (218)
T ss_pred hhhhhhhccccc
Confidence 456789999864
No 208
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=21.25 E-value=90 Score=20.70 Aligned_cols=28 Identities=4% Similarity=-0.072 Sum_probs=21.9
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhhhc
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAFTS 88 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~ 88 (91)
-.++ |..+|++...|+...+.-|.+.+.
T Consensus 134 ~~EI--A~~lg~s~~tVk~~l~RAr~~Lr~ 161 (293)
T PRK09636 134 FDEI--ASTLGRSPAACRQLASRARKHVRA 161 (293)
T ss_pred HHHH--HHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4466 899999999999988776666554
No 209
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.19 E-value=26 Score=19.86 Aligned_cols=16 Identities=0% Similarity=0.152 Sum_probs=13.3
Q ss_pred hhhcCCCCCcchhccc
Q psy3735 65 SRQRSMPGELCVAWTH 80 (91)
Q Consensus 65 a~~l~l~~~~v~vWFq 80 (91)
|..+|++...++.|-+
T Consensus 7 a~~~gvs~~tlr~ye~ 22 (113)
T cd01109 7 AEKTGLSADTLRYYEK 22 (113)
T ss_pred HHHHCcCHHHHHHHHH
Confidence 8888999998888853
No 210
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=21.10 E-value=98 Score=19.75 Aligned_cols=45 Identities=13% Similarity=-0.042 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhh
Q psy3735 35 TFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFT 87 (91)
Q Consensus 35 ~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~ 87 (91)
.+|+-+...|..... . ....++ |..|++++..|+.+..+-..|+.
T Consensus 155 ~Lt~rE~~Vl~l~~~-G-----~s~~eI--A~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 155 LLTHREKEILNKLRI-G-----ASNNEI--ARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCHHHHHHHHHHHc-C-----CCHHHH--HHHhCCCHHHHHHHHHHHHHHhC
Confidence 488888888876554 2 234567 89999999999998877766653
No 211
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.71 E-value=26 Score=19.20 Aligned_cols=17 Identities=0% Similarity=-0.046 Sum_probs=13.8
Q ss_pred hhhcCCCCCcchhccch
Q psy3735 65 SRQRSMPGELCVAWTHH 81 (91)
Q Consensus 65 a~~l~l~~~~v~vWFqn 81 (91)
|..+|+++..|+.|-..
T Consensus 7 a~~~gi~~~tlr~~~~~ 23 (100)
T cd00592 7 AKLLGVSVRTLRYYEEK 23 (100)
T ss_pred HHHHCcCHHHHHHHHHC
Confidence 88889999999988543
No 212
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.71 E-value=26 Score=19.46 Aligned_cols=15 Identities=7% Similarity=0.042 Sum_probs=11.9
Q ss_pred hhhcCCCCCcchhcc
Q psy3735 65 SRQRSMPGELCVAWT 79 (91)
Q Consensus 65 a~~l~l~~~~v~vWF 79 (91)
|..+|++...++.|-
T Consensus 7 a~~~gvs~~tlR~Ye 21 (95)
T cd04780 7 SKRSGVSVATIKYYL 21 (95)
T ss_pred HHHHCcCHHHHHHHH
Confidence 778888888888774
No 213
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=20.65 E-value=26 Score=19.89 Aligned_cols=16 Identities=0% Similarity=0.005 Sum_probs=13.9
Q ss_pred hhhcCCCCCcchhccc
Q psy3735 65 SRQRSMPGELCVAWTH 80 (91)
Q Consensus 65 a~~l~l~~~~v~vWFq 80 (91)
|..+|++...++.|-.
T Consensus 7 A~~~gvs~~tlR~ye~ 22 (107)
T cd01111 7 ALDAGVSVHIVRDYLL 22 (107)
T ss_pred HHHHCcCHHHHHHHHH
Confidence 8899999999999953
No 214
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=20.56 E-value=26 Score=19.38 Aligned_cols=16 Identities=0% Similarity=0.108 Sum_probs=13.7
Q ss_pred hhhcCCCCCcchhccc
Q psy3735 65 SRQRSMPGELCVAWTH 80 (91)
Q Consensus 65 a~~l~l~~~~v~vWFq 80 (91)
|..+|++...++.|.+
T Consensus 7 a~~~gvs~~tlR~ye~ 22 (97)
T cd04782 7 AKLCGISKQTLFHYDK 22 (97)
T ss_pred HHHHCcCHHHHHHHHH
Confidence 8888999999998864
No 215
>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 This entry is represented by Bacteriophage r1t, Orf18. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.
Probab=20.51 E-value=24 Score=22.07 Aligned_cols=27 Identities=7% Similarity=-0.042 Sum_probs=21.6
Q ss_pred HhhhhhhhhhcCCCCCcchhccchhHHhh
Q psy3735 58 TRQCGRFSRQRSMPGELCVAWTHHLNAAF 86 (91)
Q Consensus 58 ~r~~l~~a~~l~l~~~~v~vWFqnrR~k~ 86 (91)
+..+| +.-++++..+|-+|..|=+...
T Consensus 16 t~~e~--~~~~~VS~~sv~~WiKNG~~~~ 42 (186)
T PF04936_consen 16 TIDEL--ADYFDVSRTSVSVWIKNGKDPK 42 (186)
T ss_pred cHHHH--HHHHccCHHHHHHHHHcCCCcc
Confidence 45567 8889999999999998866543
No 216
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=20.42 E-value=28 Score=19.64 Aligned_cols=16 Identities=0% Similarity=0.015 Sum_probs=13.9
Q ss_pred hhhcCCCCCcchhccc
Q psy3735 65 SRQRSMPGELCVAWTH 80 (91)
Q Consensus 65 a~~l~l~~~~v~vWFq 80 (91)
|..+|++...++.|-.
T Consensus 7 a~~~gis~~tlR~ye~ 22 (108)
T cd01107 7 AKLSNLSIKALRYYDK 22 (108)
T ss_pred HHHHCcCHHHHHHHHH
Confidence 8889999999999864
No 217
>smart00595 MADF subfamily of SANT domain.
Probab=20.14 E-value=31 Score=18.38 Aligned_cols=24 Identities=13% Similarity=0.228 Sum_probs=19.5
Q ss_pred hhhcCCCCCcchhccchhHHhhhc
Q psy3735 65 SRQRSMPGELCVAWTHHLNAAFTS 88 (91)
Q Consensus 65 a~~l~l~~~~v~vWFqnrR~k~~~ 88 (91)
|..+|.+...|+.-+.|-|..+.+
T Consensus 34 a~~l~~~~~~~~~kw~~LR~~y~~ 57 (89)
T smart00595 34 AEELGLSVEECKKRWKNLRDRYRR 57 (89)
T ss_pred HHHHCcCHHHHHHHHHHHHHHHHH
Confidence 888898888888888888877654
No 218
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=20.07 E-value=1.4e+02 Score=18.01 Aligned_cols=26 Identities=12% Similarity=0.079 Sum_probs=18.7
Q ss_pred hhhhhhhhhcCCCCCcchhccchhHHhh
Q psy3735 59 RQCGRFSRQRSMPGELCVAWTHHLNAAF 86 (91)
Q Consensus 59 r~~l~~a~~l~l~~~~v~vWFqnrR~k~ 86 (91)
-.++ |..+|++...|++--..-|.+.
T Consensus 156 ~~eI--A~~lgis~~~v~~~l~Rar~~L 181 (187)
T PRK12534 156 YEEL--AARTDTPIGTVKSWIRRGLAKL 181 (187)
T ss_pred HHHH--HHHhCCChhHHHHHHHHHHHHH
Confidence 4466 8999999999887665444443
No 219
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=20.01 E-value=29 Score=19.65 Aligned_cols=17 Identities=12% Similarity=0.307 Sum_probs=14.6
Q ss_pred hhhcCCCCCcchhccch
Q psy3735 65 SRQRSMPGELCVAWTHH 81 (91)
Q Consensus 65 a~~l~l~~~~v~vWFqn 81 (91)
|..+|+++..++.|...
T Consensus 7 a~~~gvs~~tlR~ye~~ 23 (108)
T cd04773 7 AHLLGVPPSTLRHWEKE 23 (108)
T ss_pred HHHHCcCHHHHHHHHHC
Confidence 88899999999999754
Done!