Query psy5541
Match_columns 301
No_of_seqs 332 out of 1895
Neff 7.3
Searched_HMMs 46136
Date Fri Aug 16 20:11:56 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5541.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5541hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0774|consensus 100.0 7.3E-39 1.6E-43 281.6 20.9 170 21-190 101-270 (334)
2 KOG3802|consensus 99.9 8.7E-23 1.9E-27 190.9 3.9 128 39-171 204-354 (398)
3 PF03792 PBC: PBC domain; Int 99.7 1.5E-16 3.2E-21 135.9 11.4 91 16-106 100-190 (191)
4 KOG0842|consensus 99.6 1.4E-15 3E-20 140.1 7.4 66 107-175 152-217 (307)
5 KOG0484|consensus 99.6 1.7E-15 3.6E-20 116.8 6.1 66 105-173 14-79 (125)
6 KOG0489|consensus 99.6 1.1E-15 2.3E-20 140.0 4.3 65 106-173 157-221 (261)
7 KOG0843|consensus 99.6 1.8E-15 3.9E-20 127.7 5.0 62 107-171 101-162 (197)
8 KOG0485|consensus 99.6 3.6E-15 7.8E-20 129.1 6.9 66 107-175 103-168 (268)
9 KOG0488|consensus 99.6 1.4E-15 3E-20 141.9 4.5 67 105-174 169-235 (309)
10 PF00046 Homeobox: Homeobox do 99.6 2.3E-15 4.9E-20 106.1 4.4 57 109-168 1-57 (57)
11 KOG0850|consensus 99.5 5.3E-15 1.1E-19 129.4 4.2 66 103-171 117-182 (245)
12 KOG0492|consensus 99.5 2.9E-14 6.3E-19 122.8 6.4 67 106-175 142-208 (246)
13 KOG0487|consensus 99.5 9.8E-15 2.1E-19 134.5 2.7 62 107-171 234-295 (308)
14 cd00086 homeodomain Homeodomai 99.5 4.8E-14 1E-18 99.4 5.5 57 110-169 2-58 (59)
15 smart00389 HOX Homeodomain. DN 99.5 5E-14 1.1E-18 98.5 5.1 55 110-167 2-56 (56)
16 KOG2251|consensus 99.5 3.5E-14 7.6E-19 123.7 4.2 67 103-172 32-98 (228)
17 KOG1168|consensus 99.4 3.5E-14 7.5E-19 127.7 3.0 122 39-170 218-368 (385)
18 KOG0848|consensus 99.4 1.1E-13 2.3E-18 123.4 4.3 63 109-174 200-262 (317)
19 KOG0494|consensus 99.4 1.7E-13 3.7E-18 121.6 4.4 62 108-172 140-202 (332)
20 KOG0775|consensus 99.4 8.8E-13 1.9E-17 118.0 8.7 63 103-168 171-233 (304)
21 PF05920 Homeobox_KN: Homeobox 99.4 2.2E-13 4.9E-18 89.0 3.1 40 126-165 1-40 (40)
22 TIGR01565 homeo_ZF_HD homeobox 99.3 1.2E-12 2.5E-17 92.3 4.1 52 109-163 2-57 (58)
23 KOG0493|consensus 99.3 1.3E-12 2.8E-17 116.1 4.0 59 109-170 247-305 (342)
24 KOG0491|consensus 99.3 5.8E-13 1.3E-17 110.9 1.3 65 106-173 98-162 (194)
25 KOG0483|consensus 99.3 3.8E-12 8.2E-17 111.1 4.7 61 109-172 51-111 (198)
26 KOG0486|consensus 99.3 2.9E-12 6.3E-17 116.7 3.4 69 103-174 107-175 (351)
27 KOG4577|consensus 99.2 5.5E-11 1.2E-15 107.2 11.1 65 108-175 167-231 (383)
28 KOG0844|consensus 99.2 5.1E-11 1.1E-15 108.1 8.0 65 108-175 181-245 (408)
29 COG5576 Homeodomain-containing 99.2 3.5E-11 7.6E-16 101.6 5.5 64 107-173 50-113 (156)
30 KOG0773|consensus 99.1 7.2E-11 1.6E-15 112.1 5.0 66 108-173 239-304 (342)
31 KOG0847|consensus 99.1 5.8E-11 1.3E-15 103.3 2.5 61 108-171 167-227 (288)
32 KOG2252|consensus 98.9 5.3E-09 1.1E-13 102.1 7.9 124 37-166 336-475 (558)
33 KOG0490|consensus 98.9 1.4E-09 3.1E-14 97.2 3.4 64 105-171 57-120 (235)
34 KOG0849|consensus 98.7 5.1E-08 1.1E-12 93.0 9.6 62 108-172 176-237 (354)
35 KOG0490|consensus 97.5 9.5E-05 2.1E-09 65.9 4.2 62 107-171 152-213 (235)
36 PF11569 Homez: Homeodomain le 96.9 0.0004 8.6E-09 48.4 0.9 42 120-164 10-51 (56)
37 PF03791 KNOX2: KNOX2 domain ; 96.8 0.0028 6.1E-08 43.6 4.5 36 25-60 7-42 (52)
38 KOG1146|consensus 96.7 0.0011 2.5E-08 71.1 3.2 61 108-171 903-963 (1406)
39 PF07526 POX: Associated with 94.9 0.099 2.1E-06 43.6 6.9 65 19-87 69-135 (140)
40 KOG0773|consensus 94.5 0.02 4.4E-07 54.4 2.0 109 34-171 49-157 (342)
41 smart00574 POX domain associat 94.3 0.15 3.2E-06 42.2 6.4 42 19-60 69-110 (140)
42 PF00157 Pou: Pou domain - N-t 92.0 0.047 1E-06 40.4 0.1 56 39-95 5-61 (75)
43 KOG3623|consensus 91.7 0.18 4E-06 51.8 3.9 48 120-170 568-615 (1007)
44 PF04218 CENP-B_N: CENP-B N-te 91.7 0.3 6.5E-06 33.6 3.9 47 109-163 1-47 (53)
45 PF08281 Sigma70_r4_2: Sigma-7 74.0 7.9 0.00017 26.0 4.5 44 114-165 10-53 (54)
46 PF04545 Sigma70_r4: Sigma-70, 73.3 6.1 0.00013 26.2 3.7 47 114-168 4-50 (50)
47 cd06171 Sigma70_r4 Sigma70, re 62.8 7.7 0.00017 24.9 2.5 45 114-166 10-54 (55)
48 PF01527 HTH_Tnp_1: Transposas 57.7 5.8 0.00013 28.5 1.3 46 110-162 2-47 (76)
49 PRK03975 tfx putative transcri 57.4 26 0.00056 29.2 5.2 51 112-171 4-54 (141)
50 PF10668 Phage_terminase: Phag 52.2 8.7 0.00019 27.3 1.3 19 141-159 25-43 (60)
51 PRK06759 RNA polymerase factor 49.2 17 0.00038 29.5 3.0 47 114-168 106-152 (154)
52 PF00196 GerE: Bacterial regul 48.8 35 0.00077 23.2 4.1 48 114-170 3-50 (58)
53 PF03791 KNOX2: KNOX2 domain ; 48.4 88 0.0019 21.5 6.0 44 17-60 6-49 (52)
54 smart00352 POU Found in Pit-Oc 48.3 20 0.00044 26.5 2.8 55 40-95 6-61 (75)
55 PF13551 HTH_29: Winged helix- 46.4 1.3E+02 0.0027 22.7 7.4 50 111-160 54-109 (112)
56 cd00569 HTH_Hin_like Helix-tur 45.3 37 0.0008 19.1 3.4 38 114-159 5-42 (42)
57 PRK11924 RNA polymerase sigma 44.9 22 0.00048 29.3 3.0 49 115-171 126-174 (179)
58 PRK09646 RNA polymerase sigma 44.9 22 0.00047 30.5 3.1 49 114-170 142-190 (194)
59 PRK09652 RNA polymerase sigma 44.6 20 0.00044 29.7 2.8 50 114-171 128-177 (182)
60 PRK00118 putative DNA-binding 43.7 28 0.0006 27.5 3.2 52 114-173 17-68 (104)
61 PRK09642 RNA polymerase sigma 43.3 25 0.00054 28.8 3.1 50 114-171 106-155 (160)
62 TIGR02937 sigma70-ECF RNA poly 41.2 28 0.00061 27.4 3.0 47 114-168 110-156 (158)
63 PRK09644 RNA polymerase sigma 40.8 31 0.00067 28.5 3.3 51 113-171 107-157 (165)
64 PRK12526 RNA polymerase sigma 40.7 27 0.00059 30.3 3.0 49 114-170 153-201 (206)
65 PRK12514 RNA polymerase sigma 40.4 28 0.0006 29.2 3.0 48 115-170 130-177 (179)
66 PF13443 HTH_26: Cro/C1-type H 40.3 17 0.00036 25.0 1.3 27 140-166 12-38 (63)
67 smart00421 HTH_LUXR helix_turn 40.3 61 0.0013 20.9 4.2 45 114-167 3-47 (58)
68 TIGR02939 RpoE_Sigma70 RNA pol 39.4 26 0.00057 29.5 2.7 31 140-170 156-186 (190)
69 PRK12512 RNA polymerase sigma 38.3 30 0.00066 29.1 2.9 50 114-171 131-180 (184)
70 PRK12515 RNA polymerase sigma 37.9 31 0.00068 29.3 2.9 50 114-171 131-180 (189)
71 TIGR02985 Sig70_bacteroi1 RNA 37.0 34 0.00074 27.6 2.9 47 114-168 113-159 (161)
72 TIGR02948 SigW_bacill RNA poly 36.7 33 0.00071 28.8 2.9 49 114-170 136-184 (187)
73 PRK12519 RNA polymerase sigma 36.1 30 0.00066 29.4 2.6 31 140-170 159-189 (194)
74 PRK06811 RNA polymerase factor 35.7 36 0.00077 29.0 2.9 50 114-171 131-180 (189)
75 TIGR02999 Sig-70_X6 RNA polyme 34.7 42 0.0009 28.1 3.2 47 115-169 135-181 (183)
76 PRK09413 IS2 repressor TnpA; R 34.2 76 0.0017 25.2 4.5 45 110-161 8-52 (121)
77 TIGR02989 Sig-70_gvs1 RNA poly 33.9 44 0.00094 27.2 3.1 48 113-168 110-157 (159)
78 KOG1146|consensus 33.8 43 0.00093 37.5 3.6 59 109-170 706-764 (1406)
79 PRK12538 RNA polymerase sigma 33.6 51 0.0011 29.4 3.7 33 141-173 190-222 (233)
80 PRK10072 putative transcriptio 33.2 24 0.00052 27.4 1.3 39 116-164 34-72 (96)
81 PRK05602 RNA polymerase sigma 33.2 43 0.00092 28.3 3.0 31 141-171 147-177 (186)
82 PRK12543 RNA polymerase sigma 32.9 64 0.0014 27.1 4.0 54 114-175 117-170 (179)
83 PRK09648 RNA polymerase sigma 32.8 43 0.00094 28.3 3.0 48 114-169 139-186 (189)
84 PRK12530 RNA polymerase sigma 32.1 50 0.0011 28.2 3.2 49 114-170 134-182 (189)
85 PF06056 Terminase_5: Putative 31.8 28 0.00062 24.3 1.3 26 141-168 16-41 (58)
86 PRK12541 RNA polymerase sigma 31.4 44 0.00095 27.4 2.7 48 114-169 112-159 (161)
87 PF00424 REV: REV protein (ant 31.0 49 0.0011 25.5 2.6 31 131-175 22-52 (91)
88 PRK12546 RNA polymerase sigma 30.8 48 0.001 28.4 2.9 50 114-171 113-162 (188)
89 PRK12518 RNA polymerase sigma 30.5 40 0.00087 28.0 2.4 31 141-171 139-169 (175)
90 PF13518 HTH_28: Helix-turn-he 30.4 40 0.00086 22.0 1.9 22 141-162 15-36 (52)
91 PRK04217 hypothetical protein; 30.2 1.1E+02 0.0023 24.4 4.5 51 112-170 40-90 (110)
92 PRK09639 RNA polymerase sigma 29.7 44 0.00096 27.4 2.5 50 114-172 112-161 (166)
93 TIGR02983 SigE-fam_strep RNA p 29.6 56 0.0012 26.7 3.0 49 114-170 110-158 (162)
94 PRK12547 RNA polymerase sigma 29.2 58 0.0013 26.9 3.1 49 114-170 112-160 (164)
95 PF13384 HTH_23: Homeodomain-l 29.1 33 0.00072 22.4 1.3 21 140-160 19-39 (50)
96 PRK09047 RNA polymerase factor 29.1 57 0.0012 26.5 3.0 49 114-170 106-154 (161)
97 PRK06986 fliA flagellar biosyn 28.8 61 0.0013 28.7 3.3 49 114-170 184-232 (236)
98 TIGR02959 SigZ RNA polymerase 28.8 60 0.0013 27.1 3.1 50 114-171 100-149 (170)
99 PRK09647 RNA polymerase sigma 28.2 80 0.0017 27.4 3.9 32 141-172 157-188 (203)
100 TIGR02954 Sig70_famx3 RNA poly 28.2 61 0.0013 26.8 3.1 48 114-169 119-166 (169)
101 PF13936 HTH_38: Helix-turn-he 28.0 70 0.0015 20.7 2.7 40 113-160 3-42 (44)
102 PRK12537 RNA polymerase sigma 27.9 57 0.0012 27.5 2.9 29 141-169 152-180 (182)
103 PRK06930 positive control sigm 27.9 65 0.0014 27.5 3.2 50 114-171 114-163 (170)
104 PRK09637 RNA polymerase sigma 27.7 59 0.0013 27.5 2.9 49 114-170 106-154 (181)
105 PRK12532 RNA polymerase sigma 27.5 63 0.0014 27.5 3.1 50 114-171 136-185 (195)
106 cd01392 HTH_LacI Helix-turn-he 27.2 25 0.00055 23.0 0.4 21 143-163 2-22 (52)
107 PRK12520 RNA polymerase sigma 27.2 77 0.0017 26.9 3.6 51 114-172 131-181 (191)
108 TIGR02413 Bac_small_yrzI Bacil 27.2 95 0.0021 20.8 3.1 40 8-48 5-44 (46)
109 PF04967 HTH_10: HTH DNA bindi 27.1 1.2E+02 0.0027 20.7 3.9 44 115-159 1-44 (53)
110 TIGR03001 Sig-70_gmx1 RNA poly 27.1 87 0.0019 28.2 4.0 33 141-173 180-212 (244)
111 PRK12533 RNA polymerase sigma 26.9 1.3E+02 0.0029 26.4 5.1 49 114-170 134-182 (216)
112 PRK12524 RNA polymerase sigma 26.7 69 0.0015 27.4 3.2 31 141-171 155-185 (196)
113 PF13411 MerR_1: MerR HTH fami 26.5 44 0.00095 23.3 1.6 18 142-159 4-21 (69)
114 PRK12516 RNA polymerase sigma 26.4 72 0.0016 27.2 3.3 50 114-171 116-165 (187)
115 cd04761 HTH_MerR-SF Helix-Turn 26.3 40 0.00086 21.6 1.3 19 142-160 4-22 (49)
116 PF14555 UBA_4: UBA-like domai 26.2 46 0.001 21.4 1.5 18 282-299 2-19 (43)
117 PF09501 Bac_small_YrzI: Proba 26.0 1.1E+02 0.0023 20.5 3.2 40 8-48 5-44 (46)
118 PRK13919 putative RNA polymera 25.6 73 0.0016 26.7 3.1 49 114-170 135-183 (186)
119 PRK12536 RNA polymerase sigma 25.4 71 0.0015 26.8 3.0 30 141-170 148-177 (181)
120 PRK15369 two component system 25.4 1.2E+02 0.0027 24.6 4.5 48 113-169 148-195 (211)
121 PF01381 HTH_3: Helix-turn-hel 25.3 39 0.00084 22.4 1.1 23 141-163 12-34 (55)
122 PRK12523 RNA polymerase sigma 25.2 74 0.0016 26.5 3.1 48 114-169 119-166 (172)
123 TIGR00721 tfx DNA-binding prot 25.2 1.8E+02 0.0039 24.1 5.2 49 112-169 4-52 (137)
124 PRK09641 RNA polymerase sigma 25.2 70 0.0015 26.7 2.9 31 140-170 154-184 (187)
125 KOG3623|consensus 24.9 83 0.0018 33.2 3.7 99 68-169 582-684 (1007)
126 PRK07670 RNA polymerase sigma 24.8 78 0.0017 28.4 3.3 48 114-169 201-248 (251)
127 PRK11677 hypothetical protein; 24.7 3.1E+02 0.0067 22.6 6.5 48 7-58 15-63 (134)
128 PRK08583 RNA polymerase sigma 24.0 82 0.0018 28.3 3.3 49 114-170 205-253 (257)
129 PRK12513 RNA polymerase sigma 24.0 70 0.0015 27.1 2.7 31 140-170 157-187 (194)
130 TIGR02950 SigM_subfam RNA poly 23.9 64 0.0014 26.0 2.4 31 139-169 122-152 (154)
131 PRK12531 RNA polymerase sigma 23.6 77 0.0017 27.0 2.9 49 114-170 141-189 (194)
132 PF07638 Sigma70_ECF: ECF sigm 23.2 80 0.0017 26.9 2.9 30 140-169 153-182 (185)
133 PRK08295 RNA polymerase factor 23.1 1.7E+02 0.0036 25.0 5.0 48 114-170 155-202 (208)
134 PRK07037 extracytoplasmic-func 22.9 83 0.0018 25.7 2.9 49 114-170 109-157 (163)
135 PRK12545 RNA polymerase sigma 22.5 96 0.0021 26.7 3.3 50 114-171 139-188 (201)
136 PRK12542 RNA polymerase sigma 22.4 81 0.0018 26.5 2.8 49 114-170 122-170 (185)
137 TIGR03070 couple_hipB transcri 22.3 48 0.001 21.8 1.1 23 141-163 18-40 (58)
138 PF13730 HTH_36: Helix-turn-he 22.3 1.4E+02 0.0031 19.6 3.5 24 134-160 24-47 (55)
139 PRK12544 RNA polymerase sigma 22.3 1.2E+02 0.0026 26.3 3.9 50 114-171 148-197 (206)
140 PRK09649 RNA polymerase sigma 22.2 81 0.0018 26.7 2.8 28 141-168 149-176 (185)
141 PRK11923 algU RNA polymerase s 22.1 76 0.0016 26.8 2.6 31 141-171 157-187 (193)
142 TIGR02947 SigH_actino RNA poly 22.0 88 0.0019 26.5 3.0 32 140-171 149-180 (193)
143 PF08452 DNAP_B_exo_N: DNA pol 21.7 28 0.0006 19.4 -0.2 9 156-164 6-14 (22)
144 PRK12535 RNA polymerase sigma 21.5 1.1E+02 0.0024 26.3 3.5 31 141-171 152-182 (196)
145 cd06170 LuxR_C_like C-terminal 21.4 1.8E+02 0.004 18.6 3.9 27 140-166 17-43 (57)
146 PRK05657 RNA polymerase sigma 21.3 2E+02 0.0043 27.1 5.4 54 114-171 262-315 (325)
147 PRK09645 RNA polymerase sigma 21.2 91 0.002 25.8 2.9 49 114-170 118-166 (173)
148 PRK12539 RNA polymerase sigma 21.0 1E+02 0.0022 25.9 3.2 49 114-170 131-179 (184)
149 PRK08301 sporulation sigma fac 20.9 81 0.0018 27.8 2.6 31 141-171 201-231 (234)
150 PRK05803 sporulation sigma fac 20.9 1.1E+02 0.0024 27.0 3.5 54 114-171 175-228 (233)
151 TIGR02943 Sig70_famx1 RNA poly 20.9 1.1E+02 0.0024 26.0 3.3 50 114-171 131-180 (188)
152 PRK12529 RNA polymerase sigma 20.8 93 0.002 26.1 2.8 49 113-169 126-174 (178)
153 TIGR02952 Sig70_famx2 RNA poly 20.4 1.1E+02 0.0024 25.0 3.2 47 114-168 122-168 (170)
No 1
>KOG0774|consensus
Probab=100.00 E-value=7.3e-39 Score=281.65 Aligned_cols=170 Identities=89% Similarity=1.298 Sum_probs=164.2
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhhhhhHHHHHHhhhHHHHHHH
Q psy5541 21 EHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQIIHRKFSSIQMQLKQSTCEAVMI 100 (301)
Q Consensus 21 e~~~~~~kl~qv~~~~~~el~ky~~~~~~f~~~~~~~l~~q~~~~~l~~~~~~~~~~~~~~~f~~~~~~l~~~~~~~~~~ 100 (301)
.+.+|+.||.||+++|+.||+||++.|++||+.++++|+.|++++|++++++++|.+.|+++|+.++.+||+..|+.++.
T Consensus 101 ~hsdYR~kL~qiR~iy~~ElekyeqaCneftthV~nlL~eQsr~RPi~~ke~e~m~~~i~~kF~~iq~~lkqstce~vmi 180 (334)
T KOG0774|consen 101 DHSDYRAKLLQIRQIYHNELEKYEQACNEFTTHVMNLLREQSRTRPIMPKEIERMVQIISKKFSHIQMQLKQSTCEAVMI 180 (334)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 48899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHHHHHHHH
Q psy5541 101 LRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQEEANLY 180 (301)
Q Consensus 101 l~~~~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~~~~~~~ 180 (301)
|+.++.+.||||++|++..+++|..||+.|..||||++++|++||.++|++..||.+||.|.|.|+||...+..++++.+
T Consensus 181 Lr~r~ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~~ee~~l~ 260 (334)
T KOG0774|consen 181 LRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKNQEEANLY 260 (334)
T ss_pred HHHHHHHHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhhhhhhhhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999988888
Q ss_pred HhhhcCCCCC
Q psy5541 181 AAKKAAGASP 190 (301)
Q Consensus 181 ~~~~~~~~~~ 190 (301)
..+.+....+
T Consensus 261 ~~kk~~~~~~ 270 (334)
T KOG0774|consen 261 AAKKAVDATP 270 (334)
T ss_pred hhcccccCCC
Confidence 8877766554
No 2
>KOG3802|consensus
Probab=99.86 E-value=8.7e-23 Score=190.91 Aligned_cols=128 Identities=23% Similarity=0.366 Sum_probs=111.0
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhcCCCCCChHHH-HHHHHHHhhhhhHHHHHHhhhHHHHHHHhhhhhh-----------
Q psy5541 39 ELEKYEQACSEFTTHVMNLLREQSRTRPITPKEI-ERMVQIIHRKFSSIQMQLKQSTCEAVMILRSRFL----------- 106 (301)
Q Consensus 39 el~ky~~~~~~f~~~~~~~l~~q~~~~~l~~~~~-~~~~~~~~~~f~~~~~~l~~~~~~~~~~l~~~~~----------- 106 (301)
.+++++++++.|+.++|.++++|++++....+.+ ..++++.+|+|+.++..+| ++|+ ++.|..+|+
T Consensus 204 ~leELEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALqLSFK-NMCK-LKPLL~KWLeEAes~~~~~~ 281 (398)
T KOG3802|consen 204 DLEELEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEALQLSFK-NMCK-LKPLLEKWLEEAESRESTGS 281 (398)
T ss_pred CHHHHHHHHHHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhhccCHH-HHhh-hHHHHHHHHHHHhcccccCC
Confidence 3555666699999999999999999997666665 5688999999999999998 5674 555555543
Q ss_pred -----------hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 107 -----------DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 107 -----------~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
++|||||.|....+..||..| .+|+.|+.+|+..||++|+|.+++|+|||||||+|.||...
T Consensus 282 ~~~~e~i~a~~RkRKKRTSie~~vr~aLE~~F---~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 282 PNSIEKIGAQSRKRKKRTSIEVNVRGALEKHF---LKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred CCCHHHhhccccccccccceeHHHHHHHHHHH---HhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 368899999999999999999 99999999999999999999999999999999999999653
No 3
>PF03792 PBC: PBC domain; InterPro: IPR005542 Pbx proteins are members of the TALE (three-amino-acid loop extension) family of atypical homeodomain proteins, whose members are characterised by a three-residue insertion in the first helix of the homeodomain involved in their interaction with Hox proteins. Examination of Pbx1 has shown that, in addition to the homeodomain, a short 16-residue C-terminal tail is essential for maximal cooperative interactions with Hox partners as well as for maximal monomeric binding of Pbx1 to DNA. The PBX domain is a bipartite acidic domain [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=99.69 E-value=1.5e-16 Score=135.90 Aligned_cols=91 Identities=82% Similarity=1.192 Sum_probs=88.3
Q ss_pred cCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhhhhhHHHHHHhhhHH
Q psy5541 16 LLHAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQIIHRKFSSIQMQLKQSTC 95 (301)
Q Consensus 16 ~~~~le~~~~~~kl~qv~~~~~~el~ky~~~~~~f~~~~~~~l~~q~~~~~l~~~~~~~~~~~~~~~f~~~~~~l~~~~~ 95 (301)
+++.+++++|..||.+|+.+|+.||++|++.|++|+.++.++|+.|+++||++++++++|...|+++|+.++.+||+++|
T Consensus 100 ~~~~~d~~dYr~kL~~ir~~y~~el~kye~ac~eF~~hV~~lLreQs~~RPIs~keiE~m~~~i~~Kf~~iq~qLKQstC 179 (191)
T PF03792_consen 100 ADNSIDHSDYRAKLSQIRQIYHSELEKYEQACNEFTEHVMNLLREQSEFRPISPKEIERMVNIIHRKFSKIQMQLKQSTC 179 (191)
T ss_pred cccccchHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhhhh
Q psy5541 96 EAVMILRSRFL 106 (301)
Q Consensus 96 ~~~~~l~~~~~ 106 (301)
++++.|+.+++
T Consensus 180 EaVm~LRsRfl 190 (191)
T PF03792_consen 180 EAVMILRSRFL 190 (191)
T ss_pred HHHHHHHHHhc
Confidence 99999988875
No 4
>KOG0842|consensus
Probab=99.60 E-value=1.4e-15 Score=140.05 Aligned_cols=66 Identities=29% Similarity=0.411 Sum_probs=60.6
Q ss_pred hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHHH
Q psy5541 107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQE 175 (301)
Q Consensus 107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~~ 175 (301)
++||.|..|++.|+-+||+.| ....|.+..||+.||..++||++||+|||||||-|.||.......
T Consensus 152 ~kRKrRVLFSqAQV~ELERRF---rqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~ 217 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRF---RQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKAL 217 (307)
T ss_pred cccccccccchhHHHHHHHHH---HhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhh
Confidence 466778899999999999999 999999999999999999999999999999999999998665444
No 5
>KOG0484|consensus
Probab=99.59 E-value=1.7e-15 Score=116.79 Aligned_cols=66 Identities=30% Similarity=0.503 Sum_probs=61.0
Q ss_pred hhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhH
Q psy5541 105 FLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKA 173 (301)
Q Consensus 105 ~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~ 173 (301)
..|+||-|++|+..|+..||+.| ...+||++-.|++||.++.|++..|+|||||||+|.+|+.+..
T Consensus 14 krKQRRIRTTFTS~QLkELErvF---~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a 79 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVF---AETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAA 79 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHH---HhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHH
Confidence 34668899999999999999999 9999999999999999999999999999999999999976543
No 6
>KOG0489|consensus
Probab=99.58 E-value=1.1e-15 Score=139.99 Aligned_cols=65 Identities=28% Similarity=0.458 Sum_probs=60.7
Q ss_pred hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhH
Q psy5541 106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKA 173 (301)
Q Consensus 106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~ 173 (301)
.+.||.|+.|+..|+.+||+.| ..|.|.+...|.+||..|+|+++||+|||||||+||||..+..
T Consensus 157 ~~~kR~RtayT~~QllELEkEF---hfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~ 221 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEF---HFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAK 221 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhh---ccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccc
Confidence 3468899999999999999999 9999999999999999999999999999999999999986543
No 7
>KOG0843|consensus
Probab=99.57 E-value=1.8e-15 Score=127.70 Aligned_cols=62 Identities=26% Similarity=0.429 Sum_probs=59.5
Q ss_pred hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
+.||.||.|+.+|+..||..| ..+.|-...||+.||+.|+|++.||+|||||||.|.||...
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F---~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~ 162 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAF---EGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQ 162 (197)
T ss_pred CCCccccccCHHHHHHHHHHH---hcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHH
Confidence 678999999999999999999 99999999999999999999999999999999999999754
No 8
>KOG0485|consensus
Probab=99.57 E-value=3.6e-15 Score=129.10 Aligned_cols=66 Identities=27% Similarity=0.417 Sum_probs=61.2
Q ss_pred hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHHH
Q psy5541 107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQE 175 (301)
Q Consensus 107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~~ 175 (301)
++||.||+|+..|+..||..| ....|.+..+|..||.++.|+++||++||||||.||||+.....+
T Consensus 103 RKKktRTvFSraQV~qLEs~F---e~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~e 168 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTF---ELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLE 168 (268)
T ss_pred ccccchhhhhHHHHHHHHHHH---HHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhh
Confidence 467889999999999999999 999999999999999999999999999999999999998765444
No 9
>KOG0488|consensus
Probab=99.57 E-value=1.4e-15 Score=141.85 Aligned_cols=67 Identities=28% Similarity=0.420 Sum_probs=62.3
Q ss_pred hhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHH
Q psy5541 105 FLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQ 174 (301)
Q Consensus 105 ~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~ 174 (301)
..|+||.||.|+..|+..||+.| ++..|.+..+|.+||..+||+..||++||||||+||||+.....
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF---~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~ 235 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRF---EKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGG 235 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHH---HHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhh
Confidence 35677889999999999999999 99999999999999999999999999999999999999887633
No 10
>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=99.57 E-value=2.3e-15 Score=106.06 Aligned_cols=57 Identities=51% Similarity=0.896 Sum_probs=54.9
Q ss_pred CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168 (301)
Q Consensus 109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk 168 (301)
||+|+.|+.+++.+|+.+| ..++||+..+++.||..+||+..+|.+||+|+|.++||
T Consensus 1 kr~r~~~t~~q~~~L~~~f---~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYF---QENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHH---HHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHH---HHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 5789999999999999999 88999999999999999999999999999999999986
No 11
>KOG0850|consensus
Probab=99.53 E-value=5.3e-15 Score=129.36 Aligned_cols=66 Identities=29% Similarity=0.416 Sum_probs=61.6
Q ss_pred hhhhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 103 SRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 103 ~~~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
.+..|-||.||.++.-|+..|++.| +++.|.-..||.+||..|||+.+||+|||||||.|.||.++
T Consensus 117 gk~KK~RKPRTIYSS~QLqaL~rRF---QkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 117 GKGKKVRKPRTIYSSLQLQALNRRF---QQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred CCcccccCCcccccHHHHHHHHHHH---hhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 3445668899999999999999999 99999999999999999999999999999999999999876
No 12
>KOG0492|consensus
Probab=99.50 E-value=2.9e-14 Score=122.76 Aligned_cols=67 Identities=27% Similarity=0.377 Sum_probs=61.3
Q ss_pred hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHHH
Q psy5541 106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQE 175 (301)
Q Consensus 106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~~ 175 (301)
...|+.|+-|+..|+..||+-| ....|.++.||.+++..+.|+++||++||||||+|.||..+...+
T Consensus 142 k~nRkPRtPFTtqQLlaLErkf---rekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~E 208 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKF---REKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELE 208 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHH---hHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHH
Confidence 3467889999999999999999 999999999999999999999999999999999999997654444
No 13
>KOG0487|consensus
Probab=99.49 E-value=9.8e-15 Score=134.49 Aligned_cols=62 Identities=37% Similarity=0.533 Sum_probs=59.0
Q ss_pred hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
..||||--+++.|+.+||+.| ..|.|.+.+.|.+|++.|+||++||+|||||||+|.||..+
T Consensus 234 ~~RKKRcPYTK~QtlELEkEF---lfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 234 RGRKKRCPYTKHQTLELEKEF---LFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred ccccccCCchHHHHHHHHHHH---HHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 467889999999999999999 99999999999999999999999999999999999999875
No 14
>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=99.48 E-value=4.8e-14 Score=99.44 Aligned_cols=57 Identities=44% Similarity=0.740 Sum_probs=54.1
Q ss_pred CCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541 110 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN 169 (301)
Q Consensus 110 r~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~ 169 (301)
++|+.|+.+++.+|+.+| ..++||+..++..||..+||+..+|++||+|+|.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f---~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEF---EKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 577899999999999999 889999999999999999999999999999999998864
No 15
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.48 E-value=5e-14 Score=98.54 Aligned_cols=55 Identities=45% Similarity=0.770 Sum_probs=52.1
Q ss_pred CCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhh
Q psy5541 110 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167 (301)
Q Consensus 110 r~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~k 167 (301)
+.|+.|+.+++.+|+.+| ..++||+..++..||..+||+..+|++||+|+|.+.+
T Consensus 2 k~r~~~~~~~~~~L~~~f---~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEF---QKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 567889999999999999 9999999999999999999999999999999999864
No 16
>KOG2251|consensus
Probab=99.46 E-value=3.5e-14 Score=123.69 Aligned_cols=67 Identities=33% Similarity=0.552 Sum_probs=62.4
Q ss_pred hhhhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhh
Q psy5541 103 SRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGK 172 (301)
Q Consensus 103 ~~~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~ 172 (301)
...++.||.||+|+..|+++||..| .+..||+...|++||.+++|.+.+|+|||.|||+|+|++...
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF---~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALF---AKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHH---HhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 3456778999999999999999999 999999999999999999999999999999999999997653
No 17
>KOG1168|consensus
Probab=99.44 E-value=3.5e-14 Score=127.68 Aligned_cols=122 Identities=25% Similarity=0.368 Sum_probs=90.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhcCCCCCChHH----HHHHHHHHhhhhhHH--------------HHHHhhhHHHHHHH
Q psy5541 39 ELEKYEQACSEFTTHVMNLLREQSRTRPITPKE----IERMVQIIHRKFSSI--------------QMQLKQSTCEAVMI 100 (301)
Q Consensus 39 el~ky~~~~~~f~~~~~~~l~~q~~~~~l~~~~----~~~~~~~~~~~f~~~--------------~~~l~~~~~~~~~~ 100 (301)
+||.| +++|++++|.++-+|.+++-..... ...++++.+|+|+.+ +.||.. +...
T Consensus 218 eLEaF---AErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLTLSHNNMiALKPILqaWLEe----AE~a 290 (385)
T KOG1168|consen 218 ELEAF---AERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLTLSHNNMIALKPILQAWLEE----AEAA 290 (385)
T ss_pred HHHHH---HHHHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeeeccccCcchhhhHHHHHHHHH----HHHH
Confidence 45555 8899999999999998876322211 134556667777655 223321 1111
Q ss_pred hhhhh-----------hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541 101 LRSRF-----------LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN 169 (301)
Q Consensus 101 l~~~~-----------~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~ 169 (301)
.+.+. ..+|||||.+-.-..+.||.+| ...|.|+.+.+..||+++.|.+..|+|||||+|+|.||.
T Consensus 291 ~keK~~~pd~~~l~~~~ekKRKRTSIAAPEKRsLEayF---avQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 291 MKEKDTKPDINELLPGGEKKRKRTSIAAPEKRSLEAYF---AVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 367 (385)
T ss_pred HHhhccCCchhhccCccccccccccccCcccccHHHHh---ccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence 22221 2368899999999999999999 999999999999999999999999999999999999984
Q ss_pred h
Q psy5541 170 I 170 (301)
Q Consensus 170 ~ 170 (301)
.
T Consensus 368 ~ 368 (385)
T KOG1168|consen 368 K 368 (385)
T ss_pred h
Confidence 3
No 18
>KOG0848|consensus
Probab=99.42 E-value=1.1e-13 Score=123.43 Aligned_cols=63 Identities=25% Similarity=0.385 Sum_probs=59.0
Q ss_pred CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHH
Q psy5541 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQ 174 (301)
Q Consensus 109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~ 174 (301)
-|-|.+++..|+-+||+.| ..++|.++..|.+||..|||+++||++||||||+|+||.+++..
T Consensus 200 DKYRvVYTDhQRLELEKEf---h~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 200 DKYRVVYTDHQRLELEKEF---HTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred cceeEEecchhhhhhhhhh---ccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 4568899999999999999 99999999999999999999999999999999999999887764
No 19
>KOG0494|consensus
Probab=99.40 E-value=1.7e-13 Score=121.57 Aligned_cols=62 Identities=31% Similarity=0.528 Sum_probs=57.2
Q ss_pred cCCC-CCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhh
Q psy5541 108 ARRK-RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGK 172 (301)
Q Consensus 108 ~rr~-R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~ 172 (301)
+||. ||.|+..|+..||+.| ...+||+...|+.||.+|+|.+..|+|||||||+||||..+.
T Consensus 140 kRRh~RTiFT~~Qle~LEkaF---keaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAF---KEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred ccccccchhhHHHHHHHHHHH---hhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence 3444 8999999999999999 999999999999999999999999999999999999997553
No 20
>KOG0775|consensus
Probab=99.40 E-value=8.8e-13 Score=118.02 Aligned_cols=63 Identities=38% Similarity=0.704 Sum_probs=55.0
Q ss_pred hhhhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541 103 SRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168 (301)
Q Consensus 103 ~~~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk 168 (301)
+.+|+.--+--+|....+..|++|| ..++||++.+|.+||+.|||+..||.|||.|||+|.|-
T Consensus 171 rTIWDGEet~yCFKekSR~~LrewY---~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 171 RTIWDGEETVYCFKEKSRSLLREWY---LQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred CccccCceeeeehhHhhHHHHHHHH---hcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 3444444444578888899999999 99999999999999999999999999999999999984
No 21
>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=99.39 E-value=2.2e-13 Score=88.99 Aligned_cols=40 Identities=53% Similarity=0.932 Sum_probs=35.5
Q ss_pred HhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHH
Q psy5541 126 YFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIR 165 (301)
Q Consensus 126 ~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r 165 (301)
||.+|..+|||+.++|..||..+||+..||.+||.|.|+|
T Consensus 1 Wl~~h~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 1 WLLEHLHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHTTTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 6788999999999999999999999999999999999987
No 22
>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=99.33 E-value=1.2e-12 Score=92.31 Aligned_cols=52 Identities=17% Similarity=0.402 Sum_probs=50.2
Q ss_pred CCCCCCCCHHHHHHHHhHhhcCCCCCC----CCHHHHHHHHHHcCCCchhhhhhhhhhH
Q psy5541 109 RRKRRNFSKQASEILNEYFYSHLSNPY----PSEEAKEELARKCNITLSQVSNWFGNKR 163 (301)
Q Consensus 109 rr~R~~~~~~q~~~L~~~f~~h~~~~y----Ps~~~r~~LA~~~~L~~~qV~~WFqNrR 163 (301)
||.||.|+.+|+..|+..| ..++| |+..++.+||..+||++.+|+|||+|-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~f---e~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFA---EKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHH---HHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 7899999999999999999 99999 9999999999999999999999999964
No 23
>KOG0493|consensus
Probab=99.30 E-value=1.3e-12 Score=116.13 Aligned_cols=59 Identities=34% Similarity=0.575 Sum_probs=56.5
Q ss_pred CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
||.||.|+.+|+..|+..| ..+.|.++..|.+||.+|+|.+.||++||||+|+|.||-.
T Consensus 247 KRPRTAFtaeQL~RLK~EF---~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEF---QENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred cCccccccHHHHHHHHHHH---hhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 5789999999999999999 9999999999999999999999999999999999999954
No 24
>KOG0491|consensus
Probab=99.30 E-value=5.8e-13 Score=110.92 Aligned_cols=65 Identities=29% Similarity=0.450 Sum_probs=60.4
Q ss_pred hhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhH
Q psy5541 106 LDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKA 173 (301)
Q Consensus 106 ~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~ 173 (301)
.+++|.|++|+..|+..|++.| +...|.+..++.+||..++|+++||+.||||||.|.||..++.
T Consensus 98 ~~r~K~Rtvfs~~ql~~l~~rF---e~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~ 162 (194)
T KOG0491|consen 98 CRRRKARTVFSDPQLSGLEKRF---ERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNN 162 (194)
T ss_pred HHhhhhcccccCccccccHHHH---hhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence 4557789999999999999999 9999999999999999999999999999999999999986644
No 25
>KOG0483|consensus
Probab=99.26 E-value=3.8e-12 Score=111.14 Aligned_cols=61 Identities=28% Similarity=0.474 Sum_probs=56.3
Q ss_pred CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhh
Q psy5541 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGK 172 (301)
Q Consensus 109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~ 172 (301)
.+++.+|+.+|+..||..| ..+.|..+..|..||..+||.++||.|||||||+|||.....
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F---~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE 111 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSF---ESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLE 111 (198)
T ss_pred ccccccccHHHHHHhHHhh---ccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence 4566789999999999999 999999999999999999999999999999999999986543
No 26
>KOG0486|consensus
Probab=99.25 E-value=2.9e-12 Score=116.71 Aligned_cols=69 Identities=32% Similarity=0.554 Sum_probs=63.5
Q ss_pred hhhhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHH
Q psy5541 103 SRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQ 174 (301)
Q Consensus 103 ~~~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~ 174 (301)
.++.|+||.|+-|+..|+..||.|| .++.||+...|++||..++|++..|+|||.|||+||||..+...
T Consensus 107 kki~KqrrQrthFtSqqlqele~tF---~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 107 KKISKQRRQRTHFTSQQLQELEATF---QRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred chhhhhhhhhhhhHHHHHHHHHHHH---hhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 4456788899999999999999999 99999999999999999999999999999999999999866544
No 27
>KOG4577|consensus
Probab=99.24 E-value=5.5e-11 Score=107.16 Aligned_cols=65 Identities=23% Similarity=0.471 Sum_probs=60.9
Q ss_pred cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHHH
Q psy5541 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQE 175 (301)
Q Consensus 108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~~ 175 (301)
.||+||+++..|++.|+..| ...|.|-...|++|+..|||+.+.|+|||||||+|+||-++....
T Consensus 167 nKRPRTTItAKqLETLK~AY---n~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T KOG4577|consen 167 NKRPRTTITAKQLETLKQAY---NTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T ss_pred cCCCcceeeHHHHHHHHHHh---cCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcch
Confidence 57899999999999999999 999999999999999999999999999999999999998776554
No 28
>KOG0844|consensus
Probab=99.19 E-value=5.1e-11 Score=108.10 Aligned_cols=65 Identities=26% Similarity=0.404 Sum_probs=60.0
Q ss_pred cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHHH
Q psy5541 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQE 175 (301)
Q Consensus 108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~~ 175 (301)
-||-||.|+.+|+..||+.| .+.-|-+...|.+||..++|.+..|+|||||||.|.||+...+.+
T Consensus 181 mRRYRTAFTReQIaRLEKEF---yrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaW 245 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEF---YRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAW 245 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHH---HHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccC
Confidence 36789999999999999999 788899999999999999999999999999999999998876543
No 29
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.17 E-value=3.5e-11 Score=101.65 Aligned_cols=64 Identities=31% Similarity=0.459 Sum_probs=59.3
Q ss_pred hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhH
Q psy5541 107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKA 173 (301)
Q Consensus 107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~ 173 (301)
..+++|++.+..|+.+|++.| ..+|||+...|..|+..++|+++-|++||||+|++.|+.....
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F---~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~ 113 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREF---EINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGK 113 (156)
T ss_pred cCcccceechHHHHHHHHHHh---ccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccc
Confidence 356788899999999999999 9999999999999999999999999999999999999976543
No 30
>KOG0773|consensus
Probab=99.10 E-value=7.2e-11 Score=112.14 Aligned_cols=66 Identities=38% Similarity=0.662 Sum_probs=61.6
Q ss_pred cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhH
Q psy5541 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKA 173 (301)
Q Consensus 108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~ 173 (301)
++|+++.|++..+.+|+.|+++|..+|||+..+|..||.+|||+..||.|||+|+|.|.|+.....
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~ 304 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIEE 304 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHHH
Confidence 456778999999999999999999999999999999999999999999999999999999987643
No 31
>KOG0847|consensus
Probab=99.06 E-value=5.8e-11 Score=103.27 Aligned_cols=61 Identities=28% Similarity=0.492 Sum_probs=56.8
Q ss_pred cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
++..|.+|+..|+..|+..| ....|+-..++.+||..+|+++.||+|||||||.||||+..
T Consensus 167 rk~srPTf~g~qi~~le~~f---eqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 167 RKQSRPTFTGHQIYQLERKF---EQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred ccccCCCccchhhhhhhhhh---hhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 44568889999999999999 99999999999999999999999999999999999999754
No 32
>KOG2252|consensus
Probab=98.86 E-value=5.3e-09 Score=102.12 Aligned_cols=124 Identities=26% Similarity=0.405 Sum_probs=93.1
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHhhcCCCC--CChHHHHHHHHHHhhhhhHHHHHHhhhHHHH-HHHhhhh---------
Q psy5541 37 QQELEKYEQACSEFTTHVMNLLREQSRTRP--ITPKEIERMVQIIHRKFSSIQMQLKQSTCEA-VMILRSR--------- 104 (301)
Q Consensus 37 ~~el~ky~~~~~~f~~~~~~~l~~q~~~~~--l~~~~~~~~~~~~~~~f~~~~~~l~~~~~~~-~~~l~~~--------- 104 (301)
..||++|.---+-|-+++. +++|+-... ..++.|..+.. -+..|..+..||.+-.... +..|+.+
T Consensus 336 ~~eLk~~sIpQaiFAervL--cRSQGTLSDLLrnPKPW~klKs-GRetFrRM~~WL~eP~~~r~m~~L~~~a~kRke~ep 412 (558)
T KOG2252|consen 336 KAELKRYSIPQAIFAERVL--CRSQGTLSDLLRNPKPWSKLKS-GRETFRRMANWLEEPEFQRLMSALRKKACKRKEQEP 412 (558)
T ss_pred HHHHhhcCCcHHHHHHHHh--hcccchHHHHhhCCCchhhhcc-ccHHHHHHHHHhcCHHHHHHHHHHHHHHhhhcccCC
Confidence 3477777665666777664 667766542 24677776654 5667777777775444444 2223222
Q ss_pred ----hhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHh
Q psy5541 105 ----FLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRY 166 (301)
Q Consensus 105 ----~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~ 166 (301)
....||.|.+|+..|++.|...| ..+++|+.+..+.|+.+|+|....|.|||-|.|+|.
T Consensus 413 ~~d~~~~~KKPRlVfTd~QkrTL~aiF---ke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 413 TDDKMLQTKKPRLVFTDIQKRTLQAIF---KENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred CccccccCCCceeeecHHHHHHHHHHH---hcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 22357889999999999999999 999999999999999999999999999999999996
No 33
>KOG0490|consensus
Probab=98.86 E-value=1.4e-09 Score=97.16 Aligned_cols=64 Identities=23% Similarity=0.250 Sum_probs=59.7
Q ss_pred hhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 105 FLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 105 ~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
..++|+.|+.|+..++.+|++.| ...+||+...++.||..+++++..|+|||||+|++|+++..
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f---~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAF---EKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhh---cCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 34568899999999999999999 89999999999999999999999999999999999999764
No 34
>KOG0849|consensus
Probab=98.73 E-value=5.1e-08 Score=93.01 Aligned_cols=62 Identities=32% Similarity=0.641 Sum_probs=58.3
Q ss_pred cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhh
Q psy5541 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGK 172 (301)
Q Consensus 108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~ 172 (301)
.+|.|++|+..|+..|+++| .+++||....|+.||.++++++..|.+||+|||.|++|....
T Consensus 176 ~rr~rtsft~~Q~~~le~~f---~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 176 GRRNRTSFSPSQLEALEECF---QRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred ccccccccccchHHHHHHHh---cCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 56678999999999999999 999999999999999999999999999999999999998643
No 35
>KOG0490|consensus
Probab=97.51 E-value=9.5e-05 Score=65.87 Aligned_cols=62 Identities=27% Similarity=0.590 Sum_probs=57.4
Q ss_pred hcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 107 ~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
+.++.|+.+...++..+...| ...++|+...+..|+..+|++...|.+||+|+|.+.++...
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~---~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 152 KPRRPRTTFTENQLEVLETVF---RATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccCCCccccccchhHhhhhcc---cCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 456778999999999999999 99999999999999999999999999999999999998654
No 36
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.86 E-value=0.0004 Score=48.40 Aligned_cols=42 Identities=29% Similarity=0.569 Sum_probs=30.5
Q ss_pred HHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHH
Q psy5541 120 SEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRI 164 (301)
Q Consensus 120 ~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~ 164 (301)
+..|+++| ..+.++.+.+-..|..+++|+..||+.||--++.
T Consensus 10 ~~pL~~Yy---~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYY---LKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHH---HHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHH---HHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 45599999 7888999999999999999999999999976543
No 37
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=96.76 E-value=0.0028 Score=43.55 Aligned_cols=36 Identities=25% Similarity=0.295 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHh
Q psy5541 25 YRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLRE 60 (301)
Q Consensus 25 ~~~kl~qv~~~~~~el~ky~~~~~~f~~~~~~~l~~ 60 (301)
-+++||+||+.||.+|.+|++...+...+.+.+++.
T Consensus 7 ~dpELDqFMeaYc~~L~kykeeL~~p~~EA~~f~~~ 42 (52)
T PF03791_consen 7 ADPELDQFMEAYCDMLVKYKEELQRPFQEAMEFCRE 42 (52)
T ss_pred CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 367899999999999999999999988888877743
No 38
>KOG1146|consensus
Probab=96.69 E-value=0.0011 Score=71.14 Aligned_cols=61 Identities=21% Similarity=0.275 Sum_probs=57.6
Q ss_pred cCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 108 ~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
.|+.|+.++..++.++...| ....||...+.+.|-..+++..+.|.+||+|.|.|.||...
T Consensus 903 r~a~~~~~~d~qlk~i~~~~---~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACY---EAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhccchhHHHHHHHHHHH---hhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 57789999999999999999 99999999999999999999999999999999999998754
No 39
>PF07526 POX: Associated with HOX; InterPro: IPR006563 This domain in found exclusively in plant proteins, associated with HOX domains which may suggest these proteins are homeodomain transcription factors.
Probab=94.94 E-value=0.099 Score=43.57 Aligned_cols=65 Identities=15% Similarity=0.294 Sum_probs=47.1
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhh--cCCCCCChHHHHHHHHHHhhhhhHHH
Q psy5541 19 AIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQ--SRTRPITPKEIERMVQIIHRKFSSIQ 87 (301)
Q Consensus 19 ~le~~~~~~kl~qv~~~~~~el~ky~~~~~~f~~~~~~~l~~q--~~~~~l~~~~~~~~~~~~~~~f~~~~ 87 (301)
..+..+++.|..+|+.+..++.++|+++|.++...+.+|-.-- +...+++.-.+.. |.+.|..++
T Consensus 69 ~~~~~e~q~kK~KLl~mL~eVd~RY~qY~~Qmq~VvssFe~vaG~gaA~~YtalAlqa----mSrhFR~LR 135 (140)
T PF07526_consen 69 PAERQELQRKKAKLLSMLDEVDRRYRQYYDQMQAVVSSFEAVAGLGAAAPYTALALQA----MSRHFRCLR 135 (140)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchhhHHHHHHH----HHHHHHHHH
Confidence 3567789999999999999999999999999999999885433 3333444444444 445554443
No 40
>KOG0773|consensus
Probab=94.51 E-value=0.02 Score=54.43 Aligned_cols=109 Identities=28% Similarity=0.382 Sum_probs=76.0
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhhhhhHHHHHHhhhHHHHHHHhhhhhhhcCCCCC
Q psy5541 34 TIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRR 113 (301)
Q Consensus 34 ~~~~~el~ky~~~~~~f~~~~~~~l~~q~~~~~l~~~~~~~~~~~~~~~f~~~~~~l~~~~~~~~~~l~~~~~~~rr~R~ 113 (301)
..+...+...+.+|++||.....++.......++..- . + .........+++.
T Consensus 49 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~--~---------~-----------------~~~~~~~~~~~~~ 100 (342)
T KOG0773|consen 49 LASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRS--P---------A-----------------SLSPPEDKGARRG 100 (342)
T ss_pred cccccccccchhHHhHHhhccccccccccCcCccccc--c---------c-----------------cccCccccccccc
Confidence 3344466666777888888777776555554432110 0 0 0000111224455
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
..+.+. ..|..|...|..++||+..++..++..++|+..+|.+||.|.|++.++...
T Consensus 101 n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~ 157 (342)
T KOG0773|consen 101 NATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELK 157 (342)
T ss_pred cccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccC
Confidence 666666 778889999999999999999999999999999999999999999887543
No 41
>smart00574 POX domain associated with HOX domains.
Probab=94.33 E-value=0.15 Score=42.19 Aligned_cols=42 Identities=14% Similarity=0.255 Sum_probs=36.8
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHh
Q psy5541 19 AIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLRE 60 (301)
Q Consensus 19 ~le~~~~~~kl~qv~~~~~~el~ky~~~~~~f~~~~~~~l~~ 60 (301)
.+|..+++.|..+|+.+..++.++|+++|.++...+.+|-.-
T Consensus 69 ~~~r~e~q~kk~kLl~mL~eVd~RY~qY~~qmq~v~ssFe~v 110 (140)
T smart00574 69 TAERQELQRKKAKLLSMLEEVDRRYKHYYEQMQTVVSSFDQA 110 (140)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 446678999999999999999999999999999998888543
No 42
>PF00157 Pou: Pou domain - N-terminal to homeobox domain; InterPro: IPR000327 POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain. The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [] and the development of an organism []. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [, ], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1). The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327 from INTERPRO), while the C-terminal subunit is a homeobox domain (IPR007103 from INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions []. The subdomains are connected by a flexible linker [, , ]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ]. This entry represents the POU-specific subunit of the POU domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3D1N_O 1AU7_A 3L1P_A 2XSD_C 1O4X_A 1HF0_B 1GT0_C 1POU_A 1CQT_B 1E3O_C ....
Probab=92.04 E-value=0.047 Score=40.45 Aligned_cols=56 Identities=21% Similarity=0.347 Sum_probs=39.0
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhcCCCCCChHHH-HHHHHHHhhhhhHHHHHHhhhHH
Q psy5541 39 ELEKYEQACSEFTTHVMNLLREQSRTRPITPKEI-ERMVQIIHRKFSSIQMQLKQSTC 95 (301)
Q Consensus 39 el~ky~~~~~~f~~~~~~~l~~q~~~~~l~~~~~-~~~~~~~~~~f~~~~~~l~~~~~ 95 (301)
.++..+++++.|+.++|.++.+|.+++..-.... ..++++.+++|+.++..++ ++|
T Consensus 5 ~~~ele~Fa~~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~L~LS~k-n~~ 61 (75)
T PF00157_consen 5 DLKELEQFAKEFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEALQLSFK-NMC 61 (75)
T ss_dssp HHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHTTTSCHH-HHH
T ss_pred CHHHHHHHHHHHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHhcccCHH-HHH
Confidence 3455666699999999999999998764322222 2467888999999988877 444
No 43
>KOG3623|consensus
Probab=91.71 E-value=0.18 Score=51.79 Aligned_cols=48 Identities=23% Similarity=0.477 Sum_probs=44.1
Q ss_pred HHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 120 SEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 120 ~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
+..|..+| ..|+.|+..+-..+|.+.||..+.|+.||.+++.......
T Consensus 568 ~sllkayy---aln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYY---ALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHH---HhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 77889999 9999999999999999999999999999999999876543
No 44
>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=91.70 E-value=0.3 Score=33.63 Aligned_cols=47 Identities=23% Similarity=0.355 Sum_probs=33.2
Q ss_pred CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhH
Q psy5541 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKR 163 (301)
Q Consensus 109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR 163 (301)
||+|..++-++...+-..+ ...+ -...||+.+|++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~---e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRL---EEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHH---HCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHH---HcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 4788899988877776666 4444 477899999999999999998853
No 45
>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=73.99 E-value=7.9 Score=25.96 Aligned_cols=44 Identities=18% Similarity=0.187 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHH
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIR 165 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r 165 (301)
.++..+..++...| -..-.-.++|+.+|++...|++|....|.+
T Consensus 10 ~L~~~~r~i~~l~~--------~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLRY--------FQGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHHH--------TS---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHH--------HHCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 35666677776655 223346789999999999999999877665
No 46
>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=73.31 E-value=6.1 Score=26.22 Aligned_cols=47 Identities=17% Similarity=0.301 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk 168 (301)
.+++.+..+|...|+ .. ..-.++|..+|++...|+.+......|.|+
T Consensus 4 ~L~~~er~vi~~~y~---~~-----~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYF---EG-----LTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHT---ST------SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhc---CC-----CCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 467888888888872 11 235688999999999999998877777654
No 47
>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=62.83 E-value=7.7 Score=24.94 Aligned_cols=45 Identities=18% Similarity=0.175 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRY 166 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~ 166 (301)
.++..+..++...+ ... ..-..+|..+|++...|..|....+.+.
T Consensus 10 ~l~~~~~~~~~~~~---~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 10 KLPEREREVILLRF---GEG-----LSYEEIAEILGISRSTVRQRLHRALKKL 54 (55)
T ss_pred hCCHHHHHHHHHHH---hcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 34566667776665 211 2356789999999999999997666553
No 48
>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=57.71 E-value=5.8 Score=28.50 Aligned_cols=46 Identities=30% Similarity=0.391 Sum_probs=28.0
Q ss_pred CCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhh
Q psy5541 110 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNK 162 (301)
Q Consensus 110 r~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNr 162 (301)
++|+.|+.++...+-... .-.......+|..+|++..+|.+|-.--
T Consensus 2 ~~r~~ys~e~K~~~v~~~-------~~~g~sv~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREY-------LESGESVSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp -SS----HHHHHHHHHHH-------HHHHCHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHH-------HHCCCceEeeecccccccccccHHHHHH
Confidence 456788888876654333 1223456789999999999999997433
No 49
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=57.44 E-value=26 Score=29.23 Aligned_cols=51 Identities=16% Similarity=0.072 Sum_probs=39.5
Q ss_pred CCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 112 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 112 R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
...++..+..+|...+ ... ...++|..+|++...|+.|-.+.+.+.++...
T Consensus 4 ~~~Lt~rqreVL~lr~---~Gl------Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 4 ESFLTERQIEVLRLRE---RGL------TQQEIADILGTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred ccCCCHHHHHHHHHHH---cCC------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4578888999987743 211 24689999999999999999988888777543
No 50
>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=52.25 E-value=8.7 Score=27.25 Aligned_cols=19 Identities=21% Similarity=0.494 Sum_probs=16.7
Q ss_pred HHHHHHHcCCCchhhhhhh
Q psy5541 141 KEELARKCNITLSQVSNWF 159 (301)
Q Consensus 141 r~~LA~~~~L~~~qV~~WF 159 (301)
-..||.++|+++.+|+.|=
T Consensus 25 lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred HHHHHHHHCCCHHHHHHHh
Confidence 3578999999999999995
No 51
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=49.15 E-value=17 Score=29.48 Aligned_cols=47 Identities=17% Similarity=0.265 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk 168 (301)
.+++.+..++...|+ .. -.-.++|..+|++...|++|....|.+.|+
T Consensus 106 ~L~~~~r~ii~l~~~--~~------~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFF--VG------KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHh--cC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 566677777765542 21 225689999999999999999888887765
No 52
>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=48.78 E-value=35 Score=23.18 Aligned_cols=48 Identities=13% Similarity=0.102 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.|+..+..+|.-+. ... ...++|..+|+++..|+.+..+-+.|..-..
T Consensus 3 ~LT~~E~~vl~~l~---~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~ 50 (58)
T PF00196_consen 3 SLTERELEVLRLLA---QGM------SNKEIAEELGISEKTVKSHRRRIMKKLGVKN 50 (58)
T ss_dssp SS-HHHHHHHHHHH---TTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT-SS
T ss_pred ccCHHHHHHHHHHH---hcC------CcchhHHhcCcchhhHHHHHHHHHHHhCCCC
Confidence 57788888887766 222 3568899999999999999998888866543
No 53
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=48.37 E-value=88 Score=21.51 Aligned_cols=44 Identities=18% Similarity=0.228 Sum_probs=38.4
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHh
Q psy5541 17 LHAIEHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLRE 60 (301)
Q Consensus 17 ~~~le~~~~~~kl~qv~~~~~~el~ky~~~~~~f~~~~~~~l~~ 60 (301)
....|.|.+|..=-.++.-|.++|++--+.+..||..+..-|..
T Consensus 6 ~~dpELDqFMeaYc~~L~kykeeL~~p~~EA~~f~~~ie~qL~~ 49 (52)
T PF03791_consen 6 GADPELDQFMEAYCDMLVKYKEELQRPFQEAMEFCREIEQQLSS 49 (52)
T ss_pred CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34568899999999999999999999999999999999877654
No 54
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=48.29 E-value=20 Score=26.55 Aligned_cols=55 Identities=16% Similarity=0.174 Sum_probs=34.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHhhcCCCCCChHH-HHHHHHHHhhhhhHHHHHHhhhHH
Q psy5541 40 LEKYEQACSEFTTHVMNLLREQSRTRPITPKE-IERMVQIIHRKFSSIQMQLKQSTC 95 (301)
Q Consensus 40 l~ky~~~~~~f~~~~~~~l~~q~~~~~l~~~~-~~~~~~~~~~~f~~~~~~l~~~~~ 95 (301)
+++.+.+.+.|...++.+..+|.++....... ..-+.++..++|...+..++ ++|
T Consensus 6 ~~ele~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~ls~~-n~~ 61 (75)
T smart00352 6 PRELEAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQLSFK-NMC 61 (75)
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcCccHH-HHH
Confidence 44555568899999999988887654211100 00245667788887777776 444
No 55
>PF13551 HTH_29: Winged helix-turn helix
Probab=46.36 E-value=1.3e+02 Score=22.75 Aligned_cols=50 Identities=16% Similarity=0.179 Sum_probs=28.9
Q ss_pred CCCCCCHHHHHHHHhHhhcCCCCC--CCCHHHHHH-H-HHHc--CCCchhhhhhhh
Q psy5541 111 KRRNFSKQASEILNEYFYSHLSNP--YPSEEAKEE-L-ARKC--NITLSQVSNWFG 160 (301)
Q Consensus 111 ~R~~~~~~q~~~L~~~f~~h~~~~--yPs~~~r~~-L-A~~~--~L~~~qV~~WFq 160 (301)
++..++.++...|..++.++.... ..+...-.. | .... .++...|..|+.
T Consensus 54 ~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 54 PRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 333389999999999984332111 233333333 4 2232 477778877763
No 56
>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=45.32 E-value=37 Score=19.15 Aligned_cols=38 Identities=13% Similarity=0.225 Sum_probs=24.8
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWF 159 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WF 159 (301)
.++.+....+...+ . +.+ ....+|..+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~---~-~~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLL---A-AGE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHH---H-cCC----CHHHHHHHHCCCHHHHHHhC
Confidence 35555555555555 2 122 34578899999999998884
No 57
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=44.94 E-value=22 Score=29.34 Aligned_cols=49 Identities=10% Similarity=0.156 Sum_probs=34.5
Q ss_pred CCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 115 FSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 115 ~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
++..+..++...+. ....-.++|..+|++...|++|..-.|.|.|+...
T Consensus 126 L~~~~r~i~~l~~~--------~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 126 LPVKQREVFLLRYV--------EGLSYREIAEILGVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred CCHHHHHHhhHHHH--------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45555555554431 11234689999999999999999888888877543
No 58
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=44.92 E-value=22 Score=30.46 Aligned_cols=49 Identities=16% Similarity=0.266 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.|+..+..+|...|+ .. -.-.++|+.+|++...|+++....|.+.|+..
T Consensus 142 ~L~~~~r~vl~l~~~--~~------~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYY--GG------LTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHH--cC------CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 466666777755442 11 23568899999999999999988888887754
No 59
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=44.56 E-value=20 Score=29.67 Aligned_cols=50 Identities=10% Similarity=0.066 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
.+++.+..++...|+ . .+ .-.++|..+|++...|++|....+.+.++...
T Consensus 128 ~L~~~~r~vl~l~~~--~--~~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 128 SLPEELRTAITLREI--E--GL----SYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred hCCHHHHHHHHHHHH--c--CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 466777777766542 1 11 24578999999999999999988888887543
No 60
>PRK00118 putative DNA-binding protein; Validated
Probab=43.72 E-value=28 Score=27.46 Aligned_cols=52 Identities=12% Similarity=0.172 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhH
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKA 173 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~ 173 (301)
.++..+..++..++. . ...-.++|+.+|+++..|..|....|.+.|+...+.
T Consensus 17 ~L~ekqRevl~L~y~---e-----g~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~ 68 (104)
T PRK00118 17 LLTEKQRNYMELYYL---D-----DYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKL 68 (104)
T ss_pred cCCHHHHHHHHHHHH---c-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 456667777766652 1 123457999999999999999998888888765544
No 61
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=43.27 E-value=25 Score=28.85 Aligned_cols=50 Identities=14% Similarity=0.147 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
.++..+..++...++ ... .-.++|..+|++...|+++....|.+.|+...
T Consensus 106 ~Lp~~~r~v~~l~~~--~g~------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (160)
T PRK09642 106 ELPENYRDVVLAHYL--EEK------SYQEIALQEKIEVKTVEMKLYRARKWIKKHWK 155 (160)
T ss_pred hCCHHHHHHHHHHHH--hCC------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 366777777765542 222 24588999999999999999988888887653
No 62
>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=41.16 E-value=28 Score=27.37 Aligned_cols=47 Identities=17% Similarity=0.314 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk 168 (301)
.++..+..++...+ . ..+ ...++|..+|+++..|+.|....+.|.|+
T Consensus 110 ~L~~~~~~ii~~~~---~-~g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRY---L-EGL----SYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHH---h-cCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45666677765554 1 222 34589999999999999999888877765
No 63
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=40.79 E-value=31 Score=28.52 Aligned_cols=51 Identities=14% Similarity=0.040 Sum_probs=37.2
Q ss_pred CCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 113 RNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 113 ~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
..++..+..++...+. .. -..+++|..+|++...|++|..-.|.+.|+...
T Consensus 107 ~~L~~~~r~v~~l~~~--~g------~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 107 HTLPVIEAQAILLCDV--HE------LTYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred HhCCHHHHHHHHhHHH--hc------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3566677777765542 11 235689999999999999999888888877643
No 64
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=40.72 E-value=27 Score=30.31 Aligned_cols=49 Identities=16% Similarity=0.337 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.++..+..++...++ . .-.-.++|+.+|++...|+++....|.+.++..
T Consensus 153 ~L~~~~r~vl~l~~~--~------g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYF--Q------ELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHH--c------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 355555556554331 1 123568899999999999999988888887764
No 65
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=40.44 E-value=28 Score=29.22 Aligned_cols=48 Identities=13% Similarity=0.378 Sum_probs=34.0
Q ss_pred CCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 115 FSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 115 ~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
++..+..++...|+ .. ....++|..+|++...|+++....|.+.|+..
T Consensus 130 L~~~~r~i~~l~~~--~g------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 177 (179)
T PRK12514 130 LEKDRAAAVRRAYL--EG------LSYKELAERHDVPLNTMRTWLRRSLLKLRECL 177 (179)
T ss_pred CCHHHHHHHHHHHH--cC------CCHHHHHHHHCCChHHHHHHHHHHHHHHHHHh
Confidence 55555555554441 11 12568899999999999999998888887753
No 66
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=40.30 E-value=17 Score=25.04 Aligned_cols=27 Identities=30% Similarity=0.356 Sum_probs=18.1
Q ss_pred HHHHHHHHcCCCchhhhhhhhhhHHHh
Q psy5541 140 AKEELARKCNITLSQVSNWFGNKRIRY 166 (301)
Q Consensus 140 ~r~~LA~~~~L~~~qV~~WFqNrR~r~ 166 (301)
....||+.+|++...|..|+.++..+.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~ 38 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNP 38 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT----
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccc
Confidence 356899999999999999998774333
No 67
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=40.28 E-value=61 Score=20.91 Aligned_cols=45 Identities=16% Similarity=0.199 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~k 167 (301)
.++..+..++..++ ... ...++|..+|++...|..|...-+.|..
T Consensus 3 ~l~~~e~~i~~~~~---~g~------s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 3 SLTPREREVLRLLA---EGL------TNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCHHHHHHHHHHH---cCC------CHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 46677777775543 221 3468899999999999999876655544
No 68
>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=39.43 E-value=26 Score=29.48 Aligned_cols=31 Identities=16% Similarity=0.164 Sum_probs=26.4
Q ss_pred HHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 140 AKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 140 ~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.-.++|+.+|++...|+++.-..|.+.|+..
T Consensus 156 s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 156 SYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3568999999999999999988888877754
No 69
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=38.26 E-value=30 Score=29.10 Aligned_cols=50 Identities=8% Similarity=0.040 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
.++..+..++...|. . ...-.++|..+|++...|++++...|.+.|+...
T Consensus 131 ~L~~~~r~v~~l~~~--~------g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 131 TLPPRQRDVVQSISV--E------GASIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred hCCHHHHHHHHHHHH--c------CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 455556666655431 1 1235688999999999999999999998887654
No 70
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=37.88 E-value=31 Score=29.27 Aligned_cols=50 Identities=22% Similarity=0.272 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
.++..+..+|...++ . ...-.++|+.+|++...|++.....|.+.|+...
T Consensus 131 ~L~~~~r~vl~l~~~--~------~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 131 KLSPAHREIIDLVYY--H------EKSVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred hCCHHHHHHHHHHHH--c------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 566667777755441 1 1234678999999999999999988888888644
No 71
>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=37.00 E-value=34 Score=27.58 Aligned_cols=47 Identities=15% Similarity=0.203 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk 168 (301)
.++..+..++...+. ..+ ...++|..+|+++..|+++....|.|.|+
T Consensus 113 ~L~~~~r~il~l~~~----~~~----~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRF----EGK----SYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHH----cCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 455666667665441 122 24578999999999999999877777765
No 72
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=36.69 E-value=33 Score=28.78 Aligned_cols=49 Identities=8% Similarity=0.180 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.++..+..++...++ ....-.++|+.+|++...|++++...|.+.++..
T Consensus 136 ~L~~~~r~v~~l~~~--------~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 136 ALPPKYRMVIVLKYM--------EDLSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHhHHhhhHHh--------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 456666666655331 1223467899999999999999988888877754
No 73
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=36.09 E-value=30 Score=29.39 Aligned_cols=31 Identities=16% Similarity=0.317 Sum_probs=26.1
Q ss_pred HHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 140 AKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 140 ~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.-.++|+.+|++...|++|+...|.+.|+..
T Consensus 159 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 159 SQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 3568899999999999999988888877743
No 74
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=35.67 E-value=36 Score=29.00 Aligned_cols=50 Identities=30% Similarity=0.391 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
.++..+..++.-.|. .. -...++|+.+|++...|++...-.|.+.|++..
T Consensus 131 ~L~~~~r~i~~l~~~--~g------~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 131 DLEKLDREIFIRRYL--LG------EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred hCCHHHHHHHHHHHH--cc------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence 567777777765442 22 235689999999999999999888888887654
No 75
>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=34.74 E-value=42 Score=28.12 Aligned_cols=47 Identities=15% Similarity=0.225 Sum_probs=34.1
Q ss_pred CCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541 115 FSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN 169 (301)
Q Consensus 115 ~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~ 169 (301)
++..+..++...++ .. -.-.++|+.+|++...|++.....|.+.|+.
T Consensus 135 Lp~~~r~v~~l~~~--~g------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 135 VDPRQAEVVELRFF--AG------LTVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCHHHHHHHHHHHH--cC------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 56666666655542 11 1246889999999999999999888887764
No 76
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=34.17 E-value=76 Score=25.24 Aligned_cols=45 Identities=20% Similarity=0.210 Sum_probs=29.5
Q ss_pred CCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhh
Q psy5541 110 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGN 161 (301)
Q Consensus 110 r~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqN 161 (301)
++|+.++.+.....-... ..+.+ ...++|..+|++..+|.+|..-
T Consensus 8 ~~rr~ys~EfK~~aV~~~---~~~g~----sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQS---FEPGM----TVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCCCHHHHHHHHHHH---HcCCC----CHHHHHHHHCcCHHHHHHHHHH
Confidence 345668888765443333 22222 2457899999999999999643
No 77
>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=33.90 E-value=44 Score=27.18 Aligned_cols=48 Identities=17% Similarity=0.242 Sum_probs=34.1
Q ss_pred CCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541 113 RNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168 (301)
Q Consensus 113 ~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk 168 (301)
..++..+..++...|+ . .-.-.++|+.+|++...|.++....|.+.+.
T Consensus 110 ~~L~~~~r~v~~l~~~--~------g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQ--R------GVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHh--c------CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 3567777777776542 1 1235688999999999999998766666554
No 78
>KOG1146|consensus
Probab=33.78 E-value=43 Score=37.46 Aligned_cols=59 Identities=22% Similarity=0.241 Sum_probs=52.5
Q ss_pred CCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 109 rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
+.-+.+.-.++..+|-+|| ..+--|+...+..|......+.+++.+||.|-|.|.+|..
T Consensus 706 ~~~~~~~~~~aa~~l~~a~---~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 706 KLLRLTILPEAAMILGRAY---MQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred ccCcccccHHHHhhhhhcc---cCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 4556667779999999999 8999999999999999999999999999999999998875
No 79
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=33.58 E-value=51 Score=29.44 Aligned_cols=33 Identities=15% Similarity=0.259 Sum_probs=28.0
Q ss_pred HHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhH
Q psy5541 141 KEELARKCNITLSQVSNWFGNKRIRYKKNIGKA 173 (301)
Q Consensus 141 r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~ 173 (301)
-.++|+.+|++...|+++....|.+.|+.....
T Consensus 190 ~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~~~ 222 (233)
T PRK12538 190 NGEIAEVMDTTVAAVESLLKRGRQQLRDLLRRH 222 (233)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 468899999999999999999999888865533
No 80
>PRK10072 putative transcriptional regulator; Provisional
Probab=33.24 E-value=24 Score=27.39 Aligned_cols=39 Identities=18% Similarity=0.175 Sum_probs=29.2
Q ss_pred CHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHH
Q psy5541 116 SKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRI 164 (301)
Q Consensus 116 ~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~ 164 (301)
+...+..|+... .. ...+||+.+|++...|..|...+|.
T Consensus 34 ~~~eik~LR~~~---gl-------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 34 SFTEFEQLRKGT---GL-------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred ChHHHHHHHHHc---CC-------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 555577776654 22 2578999999999999999987753
No 81
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=33.17 E-value=43 Score=28.29 Aligned_cols=31 Identities=13% Similarity=0.232 Sum_probs=26.4
Q ss_pred HHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 141 KEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 141 r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
-.++|+.+|++...|+++....|.+.|+...
T Consensus 147 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 147 NIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4578999999999999999888888887644
No 82
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=32.87 E-value=64 Score=27.06 Aligned_cols=54 Identities=9% Similarity=0.145 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHHH
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQE 175 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~~ 175 (301)
.++..+..++...++++ ..-.++|+.+|++...|++.....|.+.|+.......
T Consensus 117 ~Lp~~~r~i~~l~~~e~--------~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~ 170 (179)
T PRK12543 117 KLPYKLRQVIILRYLHD--------YSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEEI 170 (179)
T ss_pred hCCHHHHHHHHHHHHcc--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666666665544211 1346789999999999999999999999887665544
No 83
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=32.80 E-value=43 Score=28.33 Aligned_cols=48 Identities=19% Similarity=0.091 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN 169 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~ 169 (301)
.++..+..++...|+ . ...-.++|..+|++...|+++....|.+.|+.
T Consensus 139 ~L~~~~r~i~~l~~~--~------g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 139 TLPEKQREILILRVV--V------GLSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred hCCHHHHHHHHHHHH--c------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 455555556655431 1 12356899999999999999998888887764
No 84
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=32.10 E-value=50 Score=28.17 Aligned_cols=49 Identities=18% Similarity=0.382 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.++..+..++.-.++ . .-.-.++|..+|+++..|+++....|.+.|+..
T Consensus 134 ~Lp~~~R~v~~L~~~--~------g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 134 HLPAQQARVFMMREY--L------ELSSEQICQECDISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred hCCHHHHHHHhHHHH--c------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 456666666655542 1 112568899999999999999988888887754
No 85
>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=31.76 E-value=28 Score=24.29 Aligned_cols=26 Identities=23% Similarity=0.482 Sum_probs=20.4
Q ss_pred HHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541 141 KEELARKCNITLSQVSNWFGNKRIRYKK 168 (301)
Q Consensus 141 r~~LA~~~~L~~~qV~~WFqNrR~r~kk 168 (301)
..++|+.+|++...|..|-. |-+|..
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~--r~~W~~ 41 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD--RYKWDE 41 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH--hhCccc
Confidence 46789999999999999973 444444
No 86
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=31.39 E-value=44 Score=27.42 Aligned_cols=48 Identities=17% Similarity=0.119 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN 169 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~ 169 (301)
.++..+..++.-.|. . . -.-.++|..+|++...|+++....|.+.++.
T Consensus 112 ~L~~~~r~v~~l~~~--~--~----~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 112 SLPLERRNVLLLRDY--Y--G----FSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HCCHHHHHHhhhHHh--c--C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 566767777765442 1 1 1246789999999999999998888877764
No 87
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=31.02 E-value=49 Score=25.47 Aligned_cols=31 Identities=39% Similarity=0.656 Sum_probs=16.3
Q ss_pred CCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhHHH
Q psy5541 131 LSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGKAQE 175 (301)
Q Consensus 131 ~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~~~ 175 (301)
..||||+..-... |+ .|||+||++.......
T Consensus 22 qsnPyP~~~GTr~-aR-------------RnRRRRWR~rq~QI~~ 52 (91)
T PF00424_consen 22 QSNPYPSPEGTRQ-AR-------------RNRRRRWRARQRQIRA 52 (91)
T ss_dssp HTS-S--S-S-HH-HH-------------HHHHHHHHHHHHHHHH
T ss_pred ccccCCCCCCccc-cc-------------cchhhhHHHHHHHHHH
Confidence 7789998542222 21 5889999887654433
No 88
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=30.80 E-value=48 Score=28.40 Aligned_cols=50 Identities=18% Similarity=0.170 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
.++..+..++.-.++ .. ..-.++|..+|++...|+++..-.|.+.|+...
T Consensus 113 ~Lp~~~r~v~~L~~~--~g------~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 113 QLPDEQREALILVGA--SG------FSYEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred hCCHHHhHHhhhHHh--cC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 456666666655431 11 224678999999999999999988888887654
No 89
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=30.54 E-value=40 Score=28.00 Aligned_cols=31 Identities=23% Similarity=0.266 Sum_probs=26.9
Q ss_pred HHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 141 KEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 141 r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
-.++|..+|++...|++.+...|.+.|+...
T Consensus 139 ~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 139 QKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5689999999999999999888888887643
No 90
>PF13518 HTH_28: Helix-turn-helix domain
Probab=30.41 E-value=40 Score=21.97 Aligned_cols=22 Identities=32% Similarity=0.495 Sum_probs=18.4
Q ss_pred HHHHHHHcCCCchhhhhhhhhh
Q psy5541 141 KEELARKCNITLSQVSNWFGNK 162 (301)
Q Consensus 141 r~~LA~~~~L~~~qV~~WFqNr 162 (301)
..++|..+|++..+|..|...-
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y 36 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRY 36 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHH
Confidence 4568999999999999998543
No 91
>PRK04217 hypothetical protein; Provisional
Probab=30.15 E-value=1.1e+02 Score=24.44 Aligned_cols=51 Identities=14% Similarity=0.113 Sum_probs=38.2
Q ss_pred CCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 112 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 112 R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
-..++.++..++..++++. - ...+||+.+|++...|.+.+...+.+.+...
T Consensus 40 ~~~Lt~eereai~l~~~eG---l-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEG---L-----TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred cccCCHHHHHHHHHHHHcC---C-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3467888888887776211 1 4567999999999999999988777776643
No 92
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=29.73 E-value=44 Score=27.40 Aligned_cols=50 Identities=16% Similarity=0.238 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGK 172 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~ 172 (301)
.++..+..+|...+ .. -.-.++|..+|++...|+++....|.+.|+....
T Consensus 112 ~L~~~~r~il~l~~-----~g----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~ 161 (166)
T PRK09639 112 KMTERDRTVLLLRF-----SG----YSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQ 161 (166)
T ss_pred cCCHHHHHHHHHHH-----cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 35566666665443 12 2356789999999999999999888888886543
No 93
>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=29.62 E-value=56 Score=26.73 Aligned_cols=49 Identities=10% Similarity=0.252 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.++..+..++...|+ . ...-.++|..+|++...|+++....|.+.|+..
T Consensus 110 ~L~~~~r~i~~l~~~--~------g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 110 RLPARQRAVVVLRYY--E------DLSEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred hCCHHHHHHhhhHHH--h------cCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 345556666655442 1 122467899999999999999988888877743
No 94
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=29.15 E-value=58 Score=26.91 Aligned_cols=49 Identities=14% Similarity=0.110 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.++..+..++.-.++ . .-.-.++|+.+|++...|+++....|.+.|+..
T Consensus 112 ~L~~~~r~v~~l~~~--~------g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 112 LLSADQREAIILIGA--S------GFSYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred hCCHHHHHHHHHHHH--c------CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 456666666655442 1 123568899999999999999988888877643
No 95
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=29.13 E-value=33 Score=22.37 Aligned_cols=21 Identities=24% Similarity=0.525 Sum_probs=16.9
Q ss_pred HHHHHHHHcCCCchhhhhhhh
Q psy5541 140 AKEELARKCNITLSQVSNWFG 160 (301)
Q Consensus 140 ~r~~LA~~~~L~~~qV~~WFq 160 (301)
...++|+.+|++...|..|..
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 356789999999999999974
No 96
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=29.12 E-value=57 Score=26.54 Aligned_cols=49 Identities=10% Similarity=0.072 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.++..+..++.-.++ ... .-.++|+.+|++...|++.....|.+.|+..
T Consensus 106 ~Lp~~~r~v~~l~~~--~g~------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 106 KLPARQREAFLLRYW--EDM------DVAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred hCCHHHHHHHHHHHH--hcC------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 466777777766442 222 2468899999999999999988888777654
No 97
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=28.83 E-value=61 Score=28.74 Aligned_cols=49 Identities=16% Similarity=0.269 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.++..+..++...|+ . .-.-.++|..+|++...|+++....|.+.|+..
T Consensus 184 ~L~~~~r~vl~l~~~---~-----g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 184 SLPEREQLVLSLYYQ---E-----ELNLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred hCCHHHHHHHHhHhc---c-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 456667777766552 1 123568999999999999999999999888754
No 98
>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=28.81 E-value=60 Score=27.08 Aligned_cols=50 Identities=16% Similarity=0.181 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
.++..+..++...|. .. -.-.++|..+|++...|+++..-.|.+.++...
T Consensus 100 ~L~~~~r~v~~l~~~--~g------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTEL--EG------LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHH--cC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 566777777776552 11 135688999999999999999888887777543
No 99
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=28.22 E-value=80 Score=27.41 Aligned_cols=32 Identities=19% Similarity=0.281 Sum_probs=26.9
Q ss_pred HHHHHHHcCCCchhhhhhhhhhHHHhhhhhhh
Q psy5541 141 KEELARKCNITLSQVSNWFGNKRIRYKKNIGK 172 (301)
Q Consensus 141 r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~ 172 (301)
-.++|..+|++...|+++....|.+.++....
T Consensus 157 ~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~ 188 (203)
T PRK09647 157 YEEIAATLGVKLGTVRSRIHRGRQQLRAALAA 188 (203)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 45789999999999999998888888876543
No 100
>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=28.18 E-value=61 Score=26.79 Aligned_cols=48 Identities=15% Similarity=0.182 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN 169 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~ 169 (301)
.++..+..++...|+ .. ..-.++|+.+|++...|+++..-.|.+.++.
T Consensus 119 ~L~~~~r~i~~l~~~--~g------~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 119 TLNDKYQTAIILRYY--HD------LTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred hCCHHHhHHHHHHHH--cC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 355555666654441 11 2346789999999999999998888777764
No 101
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=28.02 E-value=70 Score=20.71 Aligned_cols=40 Identities=13% Similarity=0.193 Sum_probs=20.5
Q ss_pred CCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhh
Q psy5541 113 RNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFG 160 (301)
Q Consensus 113 ~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFq 160 (301)
..|+.++...++.++ ... .-..+||..+|.+...|..|..
T Consensus 3 ~~Lt~~eR~~I~~l~---~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALL---EQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHH---CS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHH---HcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 356777788888776 432 2355799999999999988863
No 102
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=27.93 E-value=57 Score=27.49 Aligned_cols=29 Identities=17% Similarity=0.359 Sum_probs=24.8
Q ss_pred HHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541 141 KEELARKCNITLSQVSNWFGNKRIRYKKN 169 (301)
Q Consensus 141 r~~LA~~~~L~~~qV~~WFqNrR~r~kk~ 169 (301)
-.++|+.+|++...|++|....|.+.|+.
T Consensus 152 ~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 152 HAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred HHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 46789999999999999998888777664
No 103
>PRK06930 positive control sigma-like factor; Validated
Probab=27.86 E-value=65 Score=27.49 Aligned_cols=50 Identities=16% Similarity=0.117 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
.++..+..++...|. ... .-.++|..+|++...|+++....|.+.++...
T Consensus 114 ~L~~rer~V~~L~~~--eg~------s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 114 VLTEREKEVYLMHRG--YGL------SYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred hCCHHHHHHHHHHHH--cCC------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 577777777766441 222 24578999999999999999988888887543
No 104
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=27.70 E-value=59 Score=27.54 Aligned_cols=49 Identities=18% Similarity=0.220 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.++..+..++...++ . . ..-.++|..+|++...|++.+...|.+.++..
T Consensus 106 ~L~~~~r~i~~l~~~--~--g----~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 106 ALPEKYAEALRLTEL--E--G----LSQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred hCCHHHHHHHHHHHh--c--C----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 456666777755431 1 1 23568899999999999999987777777643
No 105
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=27.54 E-value=63 Score=27.51 Aligned_cols=50 Identities=14% Similarity=0.265 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
.++..+..++.-.+. .. -.-.++|+.+|++...|+++....|.+.|+...
T Consensus 136 ~L~~~~r~i~~L~~~--~g------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 136 NLPENTARVFTLKEI--LG------FSSDEIQQMCGISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred hCCHHHHHHhhhHHH--hC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 456666677765431 11 124688999999999999999988888888654
No 106
>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=27.19 E-value=25 Score=23.04 Aligned_cols=21 Identities=24% Similarity=0.461 Sum_probs=19.1
Q ss_pred HHHHHcCCCchhhhhhhhhhH
Q psy5541 143 ELARKCNITLSQVSNWFGNKR 163 (301)
Q Consensus 143 ~LA~~~~L~~~qV~~WFqNrR 163 (301)
+||+.+|++...|..|+.|.+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999998874
No 107
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=27.17 E-value=77 Score=26.86 Aligned_cols=51 Identities=14% Similarity=0.212 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIGK 172 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~ 172 (301)
.++..+..++.-.++ ... .-.++|..+|++...|++.....|.+.|+...+
T Consensus 131 ~Lp~~~r~v~~l~~~--~g~------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 181 (191)
T PRK12520 131 RLPPRTGRVFMMREW--LEL------ETEEICQELQITATNAWVLLYRARMRLRECLDL 181 (191)
T ss_pred hCCHHHHHHHHHHHH--cCC------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 456666676665542 221 246889999999999999999888888876543
No 108
>TIGR02413 Bac_small_yrzI Bacillus tandem small hypothetical proetin. Members of this family are very small proteins, about 47 residues each, in the genus Bacillus. Single members are found in Bacillus subtilis and Bacillus halodurans, but arrays of six in tandem in Bacillus cereus and Bacillus anthracis. An EIxxE motif present in most members of this family resembles cleavage sites by the germination protease GPR in a number small, acid-soluble spore proteins (SASP). A role in sporulation is possible.
Probab=27.16 E-value=95 Score=20.80 Aligned_cols=40 Identities=20% Similarity=0.319 Sum_probs=28.8
Q ss_pred hhhheecccCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5541 8 IYFFTLRILLHAIEHSDYRAKLAQIRTIYQQELEKYEQACS 48 (301)
Q Consensus 8 ~~~~~~~~~~~~le~~~~~~kl~qv~~~~~~el~ky~~~~~ 48 (301)
++|+|+-|.-..+...++.. -.|+.+++.++-++.-.+|.
T Consensus 5 ~fFlTITIqKr~~S~~Ei~~-eqq~k~~~deik~rq~~Yy~ 44 (46)
T TIGR02413 5 LFFLTITIQKRKLSEAEIER-EQQIEKIMDEVKERQSLYYS 44 (46)
T ss_pred EEEEEEEEEeccCCHHHHHH-HHHHHHHHHHHHHHHHHHhc
Confidence 57899999988888877544 35667777777776655554
No 109
>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=27.12 E-value=1.2e+02 Score=20.73 Aligned_cols=44 Identities=27% Similarity=0.271 Sum_probs=30.1
Q ss_pred CCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhh
Q psy5541 115 FSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWF 159 (301)
Q Consensus 115 ~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WF 159 (301)
++..|..+|...+. .-.--+|-...-.+||..+|+++..|..-.
T Consensus 1 LT~~Q~e~L~~A~~-~GYfd~PR~~tl~elA~~lgis~st~~~~L 44 (53)
T PF04967_consen 1 LTDRQREILKAAYE-LGYFDVPRRITLEELAEELGISKSTVSEHL 44 (53)
T ss_pred CCHHHHHHHHHHHH-cCCCCCCCcCCHHHHHHHhCCCHHHHHHHH
Confidence 46778888877751 112234666667899999999998765444
No 110
>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=27.07 E-value=87 Score=28.22 Aligned_cols=33 Identities=18% Similarity=0.341 Sum_probs=28.3
Q ss_pred HHHHHHHcCCCchhhhhhhhhhHHHhhhhhhhH
Q psy5541 141 KEELARKCNITLSQVSNWFGNKRIRYKKNIGKA 173 (301)
Q Consensus 141 r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~~~ 173 (301)
-.++|..+|++...|+++....|.+.|+...+.
T Consensus 180 ~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~ 212 (244)
T TIGR03001 180 MDRIGAMYQVHRSTVSRWVAQARERLLERTRRR 212 (244)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 468899999999999999999999988876433
No 111
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=26.89 E-value=1.3e+02 Score=26.44 Aligned_cols=49 Identities=14% Similarity=0.161 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.++..+..++...|+. .+ .-.++|+.+|++...|+++....|.+.++..
T Consensus 134 ~Lp~~~R~v~~L~y~e----g~----s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 134 KLPVEYREVLVLRELE----DM----SYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCHHHHhHhhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4566666666665421 12 2457899999999999999988888877765
No 112
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=26.69 E-value=69 Score=27.37 Aligned_cols=31 Identities=13% Similarity=0.142 Sum_probs=26.4
Q ss_pred HHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 141 KEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 141 r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
-.++|+.+|++...|+++..-.|.+.|+...
T Consensus 155 ~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 185 (196)
T PRK12524 155 NPEIAEVMEIGVEAVESLTARGKRALAALLA 185 (196)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999888888887543
No 113
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=26.55 E-value=44 Score=23.28 Aligned_cols=18 Identities=17% Similarity=0.250 Sum_probs=16.3
Q ss_pred HHHHHHcCCCchhhhhhh
Q psy5541 142 EELARKCNITLSQVSNWF 159 (301)
Q Consensus 142 ~~LA~~~~L~~~qV~~WF 159 (301)
.++|+.+|++...|+.|=
T Consensus 4 ~eva~~~gvs~~tlr~y~ 21 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYE 21 (69)
T ss_dssp HHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHH
Confidence 578999999999999995
No 114
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=26.37 E-value=72 Score=27.20 Aligned_cols=50 Identities=16% Similarity=0.159 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
.++..+..++.-.++ ..- .-.++|+.+|++...|+++....|.+.++...
T Consensus 116 ~Lp~~~r~i~~L~~~--~g~------s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 116 QLPDDQREAIILVGA--SGF------AYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred hCCHHHHHHHHHHHH--cCC------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 345556666654431 111 24578999999999999999988888887654
No 115
>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=26.33 E-value=40 Score=21.64 Aligned_cols=19 Identities=21% Similarity=0.240 Sum_probs=16.7
Q ss_pred HHHHHHcCCCchhhhhhhh
Q psy5541 142 EELARKCNITLSQVSNWFG 160 (301)
Q Consensus 142 ~~LA~~~~L~~~qV~~WFq 160 (301)
.++|+.+|++...|+.|..
T Consensus 4 ~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 4 GELAKLTGVSPSTLRYYER 22 (49)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999964
No 116
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=26.17 E-value=46 Score=21.44 Aligned_cols=18 Identities=28% Similarity=0.335 Sum_probs=14.3
Q ss_pred HHHHHHhhccccchhHhh
Q psy5541 282 DILQQILNITDQSLDEAQ 299 (301)
Q Consensus 282 ~~l~q~~~~~~~~~~~~~ 299 (301)
+++.|.|.||..+.++|+
T Consensus 2 e~i~~F~~iTg~~~~~A~ 19 (43)
T PF14555_consen 2 EKIAQFMSITGADEDVAI 19 (43)
T ss_dssp HHHHHHHHHH-SSHHHHH
T ss_pred HHHHHHHHHHCcCHHHHH
Confidence 578999999999877775
No 117
>PF09501 Bac_small_YrzI: Probable sporulation protein (Bac_small_yrzI); InterPro: IPR012655 Members of this family are very small proteins, about 47 residues each, in the genus Bacillus. Single members are found in Bacillus subtilis and Bacillus halodurans, while arrays of six members in tandem are found in Bacillus cereus and Bacillus anthracis. An EIxxE motif present in most members of this family resembles cleavage sites by the germination protease GPR in a number of small acid-soluble spore proteins (SASP). A role in sporulation is possible.
Probab=25.97 E-value=1.1e+02 Score=20.54 Aligned_cols=40 Identities=15% Similarity=0.287 Sum_probs=27.4
Q ss_pred hhhheecccCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy5541 8 IYFFTLRILLHAIEHSDYRAKLAQIRTIYQQELEKYEQACS 48 (301)
Q Consensus 8 ~~~~~~~~~~~~le~~~~~~kl~qv~~~~~~el~ky~~~~~ 48 (301)
++|||+-|.-..+...++. .-.++.+++.++.++-..+|.
T Consensus 5 ~fFlTITIqKr~~S~~Ei~-~~qq~~~~~deik~rq~~Y~~ 44 (46)
T PF09501_consen 5 VFFLTITIQKRKYSEEEIL-HEQQIKKIMDEIKDRQSSYYT 44 (46)
T ss_pred EEEEEEEEEeccCCHHHHH-HHHHHHHHHHHHHHHHHHHhc
Confidence 5788998888887777643 335666777777666655553
No 118
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=25.64 E-value=73 Score=26.74 Aligned_cols=49 Identities=14% Similarity=0.226 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.++..+..++...++ . .-.-.++|+.+|++...|+++....|.+.|+..
T Consensus 135 ~L~~~~r~vl~l~~~--~------~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 135 ALSPEERRVIEVLYY--Q------GYTHREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred hCCHHHHHHHHHHHH--c------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 355555666654331 1 112457899999999999999988777777643
No 119
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=25.41 E-value=71 Score=26.84 Aligned_cols=30 Identities=17% Similarity=0.014 Sum_probs=26.2
Q ss_pred HHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 141 KEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 141 r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
-.++|+.+|++...|++..-..|.+.|+..
T Consensus 148 ~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 148 VAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 568899999999999999988888888753
No 120
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=25.38 E-value=1.2e+02 Score=24.61 Aligned_cols=48 Identities=15% Similarity=0.207 Sum_probs=37.1
Q ss_pred CCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541 113 RNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN 169 (301)
Q Consensus 113 ~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~ 169 (301)
..++..+..+|+-+- .+ + ...++|+.++++...|++|.+|-|+|..-.
T Consensus 148 ~~lt~~e~~vl~l~~----~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~ 195 (211)
T PRK15369 148 PLLTPRERQILKLIT----EG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLDVH 195 (211)
T ss_pred cCCCHHHHHHHHHHH----CC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 358888888887643 11 2 256889999999999999999998887643
No 121
>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=25.27 E-value=39 Score=22.35 Aligned_cols=23 Identities=39% Similarity=0.426 Sum_probs=19.0
Q ss_pred HHHHHHHcCCCchhhhhhhhhhH
Q psy5541 141 KEELARKCNITLSQVSNWFGNKR 163 (301)
Q Consensus 141 r~~LA~~~~L~~~qV~~WFqNrR 163 (301)
..+||+.+|++...|..|..+.+
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 36899999999999999998843
No 122
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=25.22 E-value=74 Score=26.46 Aligned_cols=48 Identities=13% Similarity=0.126 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN 169 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~ 169 (301)
.++..+..++.-.++ ... .-.++|+.+|++...|+++....+.+.+..
T Consensus 119 ~Lp~~~r~v~~L~~~--~g~------s~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 119 KLSSKARAAFLYNRL--DGM------GHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred hCCHHHHHHHHHHHH--cCC------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 466666666655432 222 245789999999999999998888887664
No 123
>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=25.21 E-value=1.8e+02 Score=24.09 Aligned_cols=49 Identities=14% Similarity=0.102 Sum_probs=38.1
Q ss_pred CCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541 112 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN 169 (301)
Q Consensus 112 R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~ 169 (301)
.+.++..+..+|.... ... ...++|+.+|++...|+.|-...|.+.++-
T Consensus 4 ~~~Lte~qr~VL~Lr~---~Gl------Tq~EIAe~LgiS~stV~~~e~ra~kkLr~a 52 (137)
T TIGR00721 4 KTFLTERQIKVLELRE---KGL------SQKEIAKELKTTRANVSAIEKRAMENIEKA 52 (137)
T ss_pred cCCCCHHHHHHHHHHH---cCC------CHHHHHHHHCcCHHHHHHHHHhHHHHHHHH
Confidence 4678888888887643 111 356899999999999999998888888763
No 124
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=25.19 E-value=70 Score=26.73 Aligned_cols=31 Identities=13% Similarity=0.258 Sum_probs=26.3
Q ss_pred HHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 140 AKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 140 ~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.-.++|+.+|++...|+++....|.+.|+..
T Consensus 154 s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T PRK09641 154 SLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3568899999999999999988888887753
No 125
>KOG3623|consensus
Probab=24.92 E-value=83 Score=33.24 Aligned_cols=99 Identities=12% Similarity=0.172 Sum_probs=56.8
Q ss_pred ChHHHHHHHHHHhhhhhHHHHHHhhhHHHHHHHhh----hhhhhcCCCCCCCCHHHHHHHHhHhhcCCCCCCCCHHHHHH
Q psy5541 68 TPKEIERMVQIIHRKFSSIQMQLKQSTCEAVMILR----SRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEE 143 (301)
Q Consensus 68 ~~~~~~~~~~~~~~~f~~~~~~l~~~~~~~~~~l~----~~~~~~rr~R~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~ 143 (301)
+..++..+...+.-.|.-.+.|+.+.-.+.+..-+ .....+.|.++....+.-..|...+ ..+--++-.+-..
T Consensus 582 s~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps~psg~~p~kv~sp~k~~dq~ql~~a~---elq~s~~n~~~pl 658 (1007)
T KOG3623|consen 582 SEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPSQPSGERPVKVRSPIKEEDQQQLKQAY---ELQASPSNDEFPL 658 (1007)
T ss_pred CHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCccCCCCCCCccccCCCCccchhhhHhhh---hcccCccCcccch
Confidence 33444455555555555566666544333222211 1111223344455555555666666 5555555555556
Q ss_pred HHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541 144 LARKCNITLSQVSNWFGNKRIRYKKN 169 (301)
Q Consensus 144 LA~~~~L~~~qV~~WFqNrR~r~kk~ 169 (301)
++..+...+..|.+||.+|+.+.++.
T Consensus 659 ~~t~~~n~~pv~ev~dhsrsstpsp~ 684 (1007)
T KOG3623|consen 659 IATRLQNDPPVVEVWDHSRSSTPSPM 684 (1007)
T ss_pred hhhhccCCCcchhhcccCCCCCCCCC
Confidence 66667788889999999999998764
No 126
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=24.85 E-value=78 Score=28.39 Aligned_cols=48 Identities=17% Similarity=0.293 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN 169 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~ 169 (301)
.++..+..++...|+ ..-.-.++|..+|++...|++++...|.+.|+.
T Consensus 201 ~L~~~~r~vl~l~~~--------~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 201 QLSEKEQLVISLFYK--------EELTLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred cCCHHHHHHHHHHHh--------cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 466777777766552 112256899999999999999998888887764
No 127
>PRK11677 hypothetical protein; Provisional
Probab=24.68 E-value=3.1e+02 Score=22.61 Aligned_cols=48 Identities=21% Similarity=0.286 Sum_probs=28.5
Q ss_pred hhhhheecccCCCC-CChHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q psy5541 7 LIYFFTLRILLHAI-EHSDYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLL 58 (301)
Q Consensus 7 ~~~~~~~~~~~~~l-e~~~~~~kl~qv~~~~~~el~ky~~~~~~f~~~~~~~l 58 (301)
+|-||..+.-.... ++..++.+|++.. .+|+.|++...+-+.....++
T Consensus 15 iiG~~~~R~~~~~~~~q~~le~eLe~~k----~ele~YkqeV~~HFa~TA~Ll 63 (134)
T PRK11677 15 IIGAVAMRFGNRKLRQQQALQYELEKNK----AELEEYRQELVSHFARSAELL 63 (134)
T ss_pred HHHHHHHhhccchhhHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHH
Confidence 44455555433333 5566666666554 578888887777666555443
No 128
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=23.99 E-value=82 Score=28.30 Aligned_cols=49 Identities=14% Similarity=0.162 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.++..+..+|...|+ ... .-.++|+.+|++...|+.|....+.|.|+..
T Consensus 205 ~L~~~~r~vl~l~~~--~g~------s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l 253 (257)
T PRK08583 205 VLSDREKSIIQCTFI--ENL------SQKETGERLGISQMHVSRLQRQAIKKLREAA 253 (257)
T ss_pred hCCHHHHHHHHHHHh--CCC------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 467777777776652 111 2468999999999999999988888877653
No 129
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=23.95 E-value=70 Score=27.13 Aligned_cols=31 Identities=13% Similarity=0.146 Sum_probs=26.6
Q ss_pred HHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 140 AKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 140 ~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.-.++|+.+|++...|+++....|.+.|+..
T Consensus 157 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 157 ELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3568899999999999999988888888754
No 130
>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=23.86 E-value=64 Score=26.02 Aligned_cols=31 Identities=26% Similarity=0.222 Sum_probs=25.7
Q ss_pred HHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541 139 EAKEELARKCNITLSQVSNWFGNKRIRYKKN 169 (301)
Q Consensus 139 ~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~ 169 (301)
..-.++|+.+|+++..|+++..-.|.|.++.
T Consensus 122 ~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 122 FSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred CcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999998777777653
No 131
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=23.56 E-value=77 Score=27.01 Aligned_cols=49 Identities=12% Similarity=0.251 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.++..+..++...+. ... .-.++|+.+|++...|++.....|.+.|+..
T Consensus 141 ~Lp~~~r~v~~l~~~--eg~------s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 141 RLPKAQRDVLQAVYL--EEL------PHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred hCCHHHHHHHHHHHH--cCC------CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 345555555554331 222 2457899999999999999888887777654
No 132
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=23.24 E-value=80 Score=26.93 Aligned_cols=30 Identities=20% Similarity=0.309 Sum_probs=25.0
Q ss_pred HHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541 140 AKEELARKCNITLSQVSNWFGNKRIRYKKN 169 (301)
Q Consensus 140 ~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~ 169 (301)
..+++|+.+|+++..|+..+...|.+.++.
T Consensus 153 s~~EIA~~lgiS~~tV~r~l~~aR~~l~~~ 182 (185)
T PF07638_consen 153 SVEEIAERLGISERTVRRRLRRARAWLRRE 182 (185)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999998888776654
No 133
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=23.11 E-value=1.7e+02 Score=24.96 Aligned_cols=48 Identities=19% Similarity=0.294 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.++..+..++..+| .. -.-.++|..+|++...|++.....|.+.|+..
T Consensus 155 ~L~~~~r~vl~l~~---e~------~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 155 LLSELEKEVLELYL---DG------KSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred hCCHHHHHHHHHHH---cc------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34555666665533 21 23467899999999999988887777777643
No 134
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=22.92 E-value=83 Score=25.68 Aligned_cols=49 Identities=10% Similarity=0.235 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.+++.+..++...|+ ..- ...++|+.+|++...|+.+..-.|.+.++..
T Consensus 109 ~L~~~~r~v~~l~~~--~~~------s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 109 ELPARTRYAFEMYRL--HGE------TQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred hCCHHHHHHHHHHHH--cCC------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 456666777765442 211 2568899999999999999877777776643
No 135
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=22.54 E-value=96 Score=26.69 Aligned_cols=50 Identities=12% Similarity=0.216 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
.++..+..++.-.++ ... .-.++|..+|++...|++.....|.+.|+...
T Consensus 139 ~Lp~~~r~v~~L~~~--eg~------s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 139 HLPEQIGRVFMMREF--LDF------EIDDICTELTLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred hCCHHHHHHHHHHHH--cCC------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 466666666655442 111 24578999999999999999988888888653
No 136
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=22.38 E-value=81 Score=26.55 Aligned_cols=49 Identities=16% Similarity=0.269 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.+++.+..++.-.++ .. -.-.++|+.+|++...|++.....|.+.++..
T Consensus 122 ~L~~~~r~i~~l~~~--~g------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 122 ELNESNRQVFKYKVF--YN------LTYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred hCCHHHHHHHHHHHH--cC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 466667777765431 22 12468899999999999999988888887754
No 137
>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=22.30 E-value=48 Score=21.79 Aligned_cols=23 Identities=17% Similarity=0.205 Sum_probs=19.7
Q ss_pred HHHHHHHcCCCchhhhhhhhhhH
Q psy5541 141 KEELARKCNITLSQVSNWFGNKR 163 (301)
Q Consensus 141 r~~LA~~~~L~~~qV~~WFqNrR 163 (301)
..+||..+|++...|..|..+++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 46789999999999999997664
No 138
>PF13730 HTH_36: Helix-turn-helix domain
Probab=22.27 E-value=1.4e+02 Score=19.63 Aligned_cols=24 Identities=25% Similarity=0.386 Sum_probs=19.5
Q ss_pred CCCCHHHHHHHHHHcCCCchhhhhhhh
Q psy5541 134 PYPSEEAKEELARKCNITLSQVSNWFG 160 (301)
Q Consensus 134 ~yPs~~~r~~LA~~~~L~~~qV~~WFq 160 (301)
-||+ ...||..+|++.+.|..+..
T Consensus 24 ~~pS---~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 24 CFPS---QETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CCcC---HHHHHHHHCcCHHHHHHHHH
Confidence 6775 56889999999999988764
No 139
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=22.25 E-value=1.2e+02 Score=26.35 Aligned_cols=50 Identities=8% Similarity=0.218 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
.++..+..++.-.|++. - .-.++|..+|++...|+++....|.+.|+...
T Consensus 148 ~L~~~~r~v~~L~~~~g--~------s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~ 197 (206)
T PRK12544 148 GLPAKYARVFMMREFIE--L------ETNEICHAVDLSVSNLNVLLYRARLRLRECLE 197 (206)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 56666667666554211 1 24688999999999999999988888888654
No 140
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=22.19 E-value=81 Score=26.72 Aligned_cols=28 Identities=11% Similarity=0.158 Sum_probs=24.1
Q ss_pred HHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541 141 KEELARKCNITLSQVSNWFGNKRIRYKK 168 (301)
Q Consensus 141 r~~LA~~~~L~~~qV~~WFqNrR~r~kk 168 (301)
-.++|..+|++...|+++....|.+.|+
T Consensus 149 ~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 149 YADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4688999999999999999877777776
No 141
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=22.05 E-value=76 Score=26.84 Aligned_cols=31 Identities=16% Similarity=0.138 Sum_probs=27.1
Q ss_pred HHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 141 KEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 141 r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
-.++|+.+|++...|++.....|.+.|+...
T Consensus 157 ~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 157 YEDIASVMQCPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999988888888654
No 142
>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=21.97 E-value=88 Score=26.52 Aligned_cols=32 Identities=19% Similarity=0.232 Sum_probs=27.5
Q ss_pred HHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 140 AKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 140 ~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
.-.++|+.+|++...|+++....|.+.|+...
T Consensus 149 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 149 AYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35688999999999999999988888887654
No 143
>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=21.67 E-value=28 Score=19.38 Aligned_cols=9 Identities=33% Similarity=0.826 Sum_probs=6.8
Q ss_pred hhhhhhhHH
Q psy5541 156 SNWFGNKRI 164 (301)
Q Consensus 156 ~~WFqNrR~ 164 (301)
-|||-|+..
T Consensus 6 iNWFE~~ge 14 (22)
T PF08452_consen 6 INWFESRGE 14 (22)
T ss_pred eehhhhCCc
Confidence 489988763
No 144
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=21.51 E-value=1.1e+02 Score=26.31 Aligned_cols=31 Identities=13% Similarity=0.197 Sum_probs=26.3
Q ss_pred HHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 141 KEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 141 r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
-.++|+.+|++...|+++....|.+.|+...
T Consensus 152 ~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 152 YEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 4688999999999999999888888877544
No 145
>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=21.40 E-value=1.8e+02 Score=18.58 Aligned_cols=27 Identities=19% Similarity=0.190 Sum_probs=20.7
Q ss_pred HHHHHHHHcCCCchhhhhhhhhhHHHh
Q psy5541 140 AKEELARKCNITLSQVSNWFGNKRIRY 166 (301)
Q Consensus 140 ~r~~LA~~~~L~~~qV~~WFqNrR~r~ 166 (301)
...++|..++++...|..|....+.+.
T Consensus 17 s~~eia~~l~~s~~tv~~~~~~~~~~l 43 (57)
T cd06170 17 TNKEIADILGISEKTVKTHLRNIMRKL 43 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 346789999999999999986444443
No 146
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=21.26 E-value=2e+02 Score=27.15 Aligned_cols=54 Identities=17% Similarity=0.151 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
.++..+..+|...|. .. |-....-.+||..+|++...|+.+....+.|.|+...
T Consensus 262 ~L~~~~R~vl~lryg---L~-~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~ 315 (325)
T PRK05657 262 ELNDKQREVLARRFG---LL-GYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQ 315 (325)
T ss_pred cCCHHHHHHHHHHhc---cC-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 566777777765541 11 1122345789999999999999999999999887653
No 147
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=21.25 E-value=91 Score=25.77 Aligned_cols=49 Identities=12% Similarity=0.165 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.++..+..+|...++ ... .-.++|+.+|++...|++..-..|.+.|+..
T Consensus 118 ~L~~~~r~vl~L~~~--~g~------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 118 QLSPEHRAVLVRSYY--RGW------STAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred hCCHHHHHHHHHHHH--cCC------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 356666677765542 211 2468899999999999999988887777654
No 148
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=20.97 E-value=1e+02 Score=25.92 Aligned_cols=49 Identities=10% Similarity=-0.010 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNI 170 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~ 170 (301)
.++..+..++.-.|+ ..-.-.++|+.+|++...|+++.-..|.+.|+..
T Consensus 131 ~L~~~~r~v~~l~~~--------~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 131 RLPEKMRLAIQAVKL--------EGLSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred hCCHHHHHHHHHHHH--------cCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 466666666665441 1223568899999999999999987777777643
No 149
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=20.93 E-value=81 Score=27.79 Aligned_cols=31 Identities=29% Similarity=0.239 Sum_probs=26.5
Q ss_pred HHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 141 KEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 141 r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
-.++|..+|++...|+++....|.+.|+...
T Consensus 201 ~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~ 231 (234)
T PRK08301 201 QKEVADMLGISQSYISRLEKRIIKRLKKEIN 231 (234)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5678999999999999999988888887643
No 150
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=20.92 E-value=1.1e+02 Score=27.01 Aligned_cols=54 Identities=17% Similarity=0.151 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
.++..+..++...|+ .+. -....-+++|..+|++...|.+|-...+.+.|+...
T Consensus 175 ~Lp~~~R~i~~l~y~---~~~-~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~ 228 (233)
T PRK05803 175 ILDEREKEVIEMRYG---LGN-GKEKTQREIAKALGISRSYVSRIEKRALKKLFKELY 228 (233)
T ss_pred hCCHHHHHHHHHHhC---CCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 455566666655441 110 111235678999999999999987777777776544
No 151
>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=20.85 E-value=1.1e+02 Score=26.01 Aligned_cols=50 Identities=10% Similarity=0.142 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~~~ 171 (301)
.++..+..++...|+++ -.-.++|+.+|++...|+++....|.+.|+...
T Consensus 131 ~L~~~~r~v~~l~~~~g--------~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~ 180 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG--------FESDEICQELEISTSNCHVLLYRARLSLRACLS 180 (188)
T ss_pred hCCHHHHHHHHHHHHhC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45666777776654211 235689999999999999999888888887654
No 152
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=20.85 E-value=93 Score=26.12 Aligned_cols=49 Identities=8% Similarity=0.109 Sum_probs=36.1
Q ss_pred CCCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhhh
Q psy5541 113 RNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN 169 (301)
Q Consensus 113 ~~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk~ 169 (301)
..++..+..++.-.+. ... .-.++|..+|+++..|++..-..+.+.+..
T Consensus 126 ~~Lp~~~R~v~~L~~~--~g~------s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 126 DTLRPRVKQAFLMATL--DGM------KQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred HhCCHHHHHHHHHHHH--cCC------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 3577777777766542 111 246889999999999999998888777654
No 153
>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=20.41 E-value=1.1e+02 Score=25.00 Aligned_cols=47 Identities=13% Similarity=0.005 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHcCCCchhhhhhhhhhHHHhhh
Q psy5541 114 NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168 (301)
Q Consensus 114 ~~~~~q~~~L~~~f~~h~~~~yPs~~~r~~LA~~~~L~~~qV~~WFqNrR~r~kk 168 (301)
.+++.+..++...|+ .. -.-.++|..+|++...|++...-.|.+.|+
T Consensus 122 ~L~~~~r~vl~l~~~--~g------~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 122 ILTPKQQHVIALRFG--QN------LPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred hCCHHHHHHHHHHHh--cC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 566677777766542 11 224678999999999999988666666655
Done!