Query psy14727
Match_columns 67
No_of_seqs 143 out of 1073
Neff 9.2
Searched_HMMs 46136
Date Fri Aug 16 19:06:52 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14727.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14727hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2251|consensus 99.5 1.9E-14 4E-19 84.2 5.4 51 17-67 32-82 (228)
2 TIGR01565 homeo_ZF_HD homeobox 99.5 3.6E-14 7.9E-19 68.3 5.1 45 23-67 2-50 (58)
3 KOG0488|consensus 99.5 3.1E-14 6.7E-19 87.4 5.3 49 19-67 169-217 (309)
4 KOG0484|consensus 99.5 5E-15 1.1E-19 78.1 1.2 49 19-67 14-62 (125)
5 KOG0850|consensus 99.5 9E-14 1.9E-18 81.8 4.2 50 18-67 118-167 (245)
6 KOG0842|consensus 99.5 1.6E-13 3.5E-18 83.8 5.4 49 19-67 150-198 (307)
7 KOG0843|consensus 99.4 2.1E-13 4.5E-18 77.9 4.0 48 20-67 100-147 (197)
8 KOG0489|consensus 99.4 2E-13 4.3E-18 82.2 2.7 48 20-67 157-204 (261)
9 PF00046 Homeobox: Homeobox do 99.3 1.6E-12 3.6E-17 62.0 3.2 45 23-67 1-45 (57)
10 KOG0485|consensus 99.3 3.3E-12 7.1E-17 75.0 3.5 49 19-67 101-149 (268)
11 KOG0487|consensus 99.3 8.8E-12 1.9E-16 76.3 5.0 50 18-67 231-280 (308)
12 KOG0492|consensus 99.2 1.5E-11 3.3E-16 71.8 4.3 49 19-67 141-189 (246)
13 KOG0494|consensus 99.2 2.2E-11 4.9E-16 73.1 4.5 47 21-67 140-186 (332)
14 smart00389 HOX Homeodomain. DN 99.2 7E-11 1.5E-15 55.9 4.4 44 24-67 2-45 (56)
15 KOG0486|consensus 99.1 5.4E-11 1.2E-15 72.8 4.0 48 20-67 110-157 (351)
16 KOG0493|consensus 99.1 9.4E-11 2E-15 70.6 4.7 45 23-67 247-291 (342)
17 cd00086 homeodomain Homeodomai 99.1 2.1E-10 4.6E-15 54.6 4.2 44 24-67 2-45 (59)
18 KOG0848|consensus 99.0 1.5E-10 3.3E-15 69.7 1.3 45 23-67 200-244 (317)
19 KOG0849|consensus 98.9 1.6E-09 3.5E-14 67.8 4.4 51 17-67 171-221 (354)
20 KOG0491|consensus 98.9 1.4E-10 3.1E-15 65.7 -0.6 47 21-67 99-145 (194)
21 KOG0844|consensus 98.8 2.3E-09 5E-14 65.9 1.7 47 21-67 180-226 (408)
22 COG5576 Homeodomain-containing 98.8 1.5E-08 3.3E-13 57.2 4.8 48 20-67 49-96 (156)
23 KOG0490|consensus 98.8 6.1E-09 1.3E-13 61.1 2.8 49 19-67 57-105 (235)
24 KOG3802|consensus 98.5 1.6E-07 3.5E-12 59.2 4.6 47 21-67 293-339 (398)
25 KOG4577|consensus 98.3 1E-06 2.3E-11 54.1 3.6 46 22-67 167-212 (383)
26 KOG0483|consensus 98.1 3.2E-06 6.9E-11 49.5 3.6 44 24-67 52-95 (198)
27 KOG0847|consensus 98.1 2.1E-06 4.5E-11 51.0 1.8 49 19-67 164-212 (288)
28 KOG2252|consensus 98.0 1.4E-05 3E-10 52.5 4.6 47 20-66 418-464 (558)
29 KOG0774|consensus 97.5 0.00013 2.9E-09 44.5 3.4 44 23-66 189-235 (334)
30 PF05920 Homeobox_KN: Homeobox 97.3 0.00011 2.4E-09 32.8 0.9 24 43-66 7-30 (40)
31 KOG0775|consensus 97.2 0.00038 8.2E-09 42.7 3.1 45 22-66 167-220 (304)
32 KOG1168|consensus 97.2 0.00021 4.5E-09 44.3 1.8 48 19-66 306-353 (385)
33 KOG0490|consensus 97.2 0.0005 1.1E-08 40.3 3.3 50 18-67 149-198 (235)
34 PF04967 HTH_10: HTH DNA bindi 95.3 0.022 4.8E-07 26.8 2.4 37 29-65 1-39 (53)
35 PF04218 CENP-B_N: CENP-B N-te 94.0 0.19 4.2E-06 23.4 3.8 39 23-66 1-39 (53)
36 KOG1146|consensus 92.7 0.23 5E-06 36.5 4.0 47 21-67 902-948 (1406)
37 COG3413 Predicted DNA binding 92.3 0.2 4.2E-06 29.5 2.9 37 28-64 155-193 (215)
38 PF11569 Homez: Homeodomain le 89.0 0.2 4.4E-06 23.9 0.8 34 34-67 10-43 (56)
39 PF04545 Sigma70_r4: Sigma-70, 80.0 1.6 3.5E-05 19.6 1.6 34 28-66 4-37 (50)
40 COG4367 Uncharacterized protei 79.3 2 4.4E-05 22.4 1.9 37 28-64 2-38 (97)
41 PF13936 HTH_38: Helix-turn-he 79.3 1.5 3.3E-05 19.4 1.3 34 28-66 4-37 (44)
42 PF08280 HTH_Mga: M protein tr 78.4 1.7 3.7E-05 20.4 1.4 31 32-66 6-36 (59)
43 PRK13558 bacterio-opsin activa 76.1 2.9 6.3E-05 28.2 2.5 38 27-64 606-645 (665)
44 KOG0773|consensus 73.7 8.6 0.00019 24.2 4.0 44 23-66 240-286 (342)
45 PF08880 QLQ: QLQ; InterPro: 71.3 5.5 0.00012 17.3 2.0 15 28-42 2-16 (37)
46 PF01527 HTH_Tnp_1: Transposas 71.1 7.2 0.00016 18.7 2.7 36 25-65 3-39 (76)
47 PF12824 MRP-L20: Mitochondria 70.5 11 0.00024 21.7 3.7 38 25-64 82-119 (164)
48 COG1905 NuoE NADH:ubiquinone o 65.0 14 0.00031 21.2 3.4 36 31-66 25-60 (160)
49 PF08281 Sigma70_r4_2: Sigma-7 64.2 8.9 0.00019 17.2 2.1 32 30-66 12-43 (54)
50 PF02796 HTH_7: Helix-turn-hel 62.1 9.4 0.0002 16.8 1.9 33 29-66 6-38 (45)
51 PRK05988 formate dehydrogenase 61.7 16 0.00035 20.7 3.2 33 34-66 26-58 (156)
52 TIGR01958 nuoE_fam NADH-quinon 60.1 17 0.00038 20.2 3.1 33 34-66 19-51 (148)
53 PRK07539 NADH dehydrogenase su 60.0 17 0.00037 20.4 3.1 33 34-66 25-57 (154)
54 PF10668 Phage_terminase: Phag 59.8 3.1 6.7E-05 20.0 0.1 16 51-66 24-39 (60)
55 cd06171 Sigma70_r4 Sigma70, re 59.3 12 0.00026 15.9 2.0 33 29-66 11-43 (55)
56 PF06971 Put_DNA-bind_N: Putat 58.9 2.4 5.3E-05 19.6 -0.4 16 52-67 31-46 (50)
57 PRK03975 tfx putative transcri 56.7 13 0.00028 20.9 2.2 34 27-66 5-38 (141)
58 PRK07571 bidirectional hydroge 56.4 22 0.00048 20.5 3.2 31 36-66 41-71 (169)
59 PF01257 2Fe-2S_thioredx: Thio 55.5 15 0.00033 20.4 2.4 33 34-66 16-48 (145)
60 PF08279 HTH_11: HTH domain; 54.3 11 0.00024 16.9 1.5 16 51-66 17-32 (55)
61 TIGR03879 near_KaiC_dom probab 54.2 1.7 3.7E-05 21.8 -1.4 28 39-66 22-49 (73)
62 PF07750 GcrA: GcrA cell cycle 52.7 32 0.0007 19.7 3.4 32 28-64 2-34 (162)
63 PF13404 HTH_AsnC-type: AsnC-t 52.6 5.3 0.00012 17.6 0.2 15 52-66 20-34 (42)
64 TIGR03209 P21_Cbot clostridium 50.7 30 0.00066 18.5 3.1 17 51-67 125-141 (142)
65 PF10078 DUF2316: Uncharacteri 49.7 6 0.00013 20.6 0.2 27 36-66 14-40 (89)
66 PRK06759 RNA polymerase factor 49.2 20 0.00042 19.4 2.2 16 51-66 124-139 (154)
67 TIGR02959 SigZ RNA polymerase 49.1 20 0.00043 20.0 2.2 16 51-66 118-133 (170)
68 PRK12529 RNA polymerase sigma 48.0 21 0.00046 20.0 2.3 17 51-67 145-161 (178)
69 PF00196 GerE: Bacterial regul 47.7 24 0.00051 16.1 2.1 33 28-66 3-35 (58)
70 PRK07037 extracytoplasmic-func 46.5 24 0.00051 19.3 2.2 16 51-66 127-142 (163)
71 TIGR00721 tfx DNA-binding prot 45.6 25 0.00054 19.7 2.2 35 26-66 4-38 (137)
72 PRK09648 RNA polymerase sigma 45.3 24 0.00051 19.9 2.2 33 29-66 140-172 (189)
73 TIGR02989 Sig-70_gvs1 RNA poly 44.9 26 0.00057 19.0 2.3 16 51-66 129-144 (159)
74 PRK09642 RNA polymerase sigma 44.2 27 0.00058 19.1 2.2 16 51-66 124-139 (160)
75 PRK09047 RNA polymerase factor 44.0 27 0.00058 19.0 2.2 17 51-67 124-140 (161)
76 PRK09646 RNA polymerase sigma 43.7 31 0.00067 19.6 2.5 17 51-67 160-176 (194)
77 PF09607 BrkDBD: Brinker DNA-b 43.6 33 0.00071 16.4 2.2 40 27-67 4-43 (58)
78 TIGR02999 Sig-70_X6 RNA polyme 43.5 27 0.00058 19.5 2.2 17 51-67 152-168 (183)
79 PRK04217 hypothetical protein; 43.4 29 0.00063 18.7 2.2 35 27-66 41-75 (110)
80 KOG3623|consensus 42.9 29 0.00064 25.1 2.6 34 34-67 568-601 (1007)
81 PRK09645 RNA polymerase sigma 42.8 31 0.00067 19.1 2.4 16 51-66 136-151 (173)
82 PF05848 CtsR: Firmicute trans 42.7 14 0.0003 21.2 0.9 16 51-66 27-42 (152)
83 PRK12526 RNA polymerase sigma 41.5 30 0.00065 20.0 2.2 16 51-66 171-186 (206)
84 PRK12541 RNA polymerase sigma 41.0 25 0.00055 19.2 1.8 16 51-66 130-145 (161)
85 PRK12537 RNA polymerase sigma 40.2 41 0.00089 18.9 2.6 17 51-67 151-167 (182)
86 PF06056 Terminase_5: Putative 40.1 4.5 9.7E-05 19.2 -1.1 16 51-66 15-30 (58)
87 PRK12530 RNA polymerase sigma 39.7 31 0.00068 19.6 2.1 17 51-67 152-168 (189)
88 PRK09652 RNA polymerase sigma 39.4 31 0.00067 18.9 2.0 33 29-66 129-161 (182)
89 KOG0041|consensus 39.2 63 0.0014 19.7 3.3 37 28-64 92-133 (244)
90 PRK12512 RNA polymerase sigma 38.7 36 0.00079 19.0 2.3 16 51-66 149-164 (184)
91 PRK12515 RNA polymerase sigma 38.5 36 0.00079 19.2 2.3 16 51-66 149-164 (189)
92 cd08313 Death_TNFR1 Death doma 37.5 18 0.00038 18.3 0.8 15 52-66 14-28 (80)
93 TIGR02985 Sig70_bacteroi1 RNA 37.5 38 0.00083 18.1 2.2 16 51-66 131-146 (161)
94 PF00325 Crp: Bacterial regula 37.4 15 0.00032 15.4 0.4 14 51-64 4-17 (32)
95 TIGR02952 Sig70_famx2 RNA poly 37.0 38 0.00082 18.5 2.1 16 51-66 140-155 (170)
96 PRK12514 RNA polymerase sigma 36.7 48 0.001 18.4 2.5 17 51-67 147-163 (179)
97 PF13730 HTH_36: Helix-turn-he 36.7 17 0.00037 16.3 0.6 19 48-66 24-42 (55)
98 TIGR02954 Sig70_famx3 RNA poly 36.6 42 0.0009 18.5 2.3 16 51-66 137-152 (169)
99 PF04539 Sigma70_r3: Sigma-70 36.4 22 0.00047 17.2 1.0 16 51-66 22-37 (78)
100 TIGR02983 SigE-fam_strep RNA p 36.2 38 0.00082 18.4 2.0 17 51-67 128-144 (162)
101 PRK09639 RNA polymerase sigma 36.1 39 0.00085 18.4 2.1 16 51-66 129-144 (166)
102 PF13412 HTH_24: Winged helix- 35.9 44 0.00095 14.5 2.0 32 31-66 3-34 (48)
103 PRK05602 RNA polymerase sigma 35.5 36 0.00078 19.1 1.9 16 51-66 146-161 (186)
104 PRK12547 RNA polymerase sigma 35.1 43 0.00094 18.4 2.2 16 51-66 130-145 (164)
105 PRK15411 rcsA colanic acid cap 34.8 9.1 0.0002 22.3 -0.6 34 28-67 137-170 (207)
106 PRK09649 RNA polymerase sigma 34.8 39 0.00084 19.1 2.0 16 51-66 148-163 (185)
107 PF11212 DUF2999: Protein of u 34.0 69 0.0015 16.2 2.7 33 28-64 12-44 (82)
108 PRK12528 RNA polymerase sigma 33.7 48 0.001 18.1 2.2 16 51-66 131-146 (161)
109 cd00569 HTH_Hin_like Helix-tur 33.5 35 0.00076 12.6 3.2 32 29-65 6-37 (42)
110 PF07638 Sigma70_ECF: ECF sigm 33.4 43 0.00094 19.1 2.0 16 51-66 153-168 (185)
111 PRK09651 RNA polymerase sigma 33.2 34 0.00074 19.0 1.6 17 50-66 136-152 (172)
112 PRK12534 RNA polymerase sigma 33.1 63 0.0014 18.1 2.7 16 51-66 155-170 (187)
113 PF12802 MarR_2: MarR family; 33.1 29 0.00063 15.7 1.1 35 29-65 3-37 (62)
114 PRK12511 RNA polymerase sigma 32.9 49 0.0011 18.8 2.2 16 51-66 129-144 (182)
115 PRK12516 RNA polymerase sigma 32.2 51 0.0011 18.8 2.2 17 51-67 134-150 (187)
116 PRK12543 RNA polymerase sigma 31.9 52 0.0011 18.4 2.2 16 51-66 135-150 (179)
117 PRK11924 RNA polymerase sigma 31.8 52 0.0011 18.0 2.1 16 51-66 143-158 (179)
118 PF12793 SgrR_N: Sugar transpo 31.8 35 0.00077 18.3 1.4 33 33-67 5-37 (115)
119 PRK09643 RNA polymerase sigma 31.7 53 0.0012 18.7 2.2 16 51-66 152-167 (192)
120 cd08306 Death_FADD Fas-associa 31.6 22 0.00049 18.0 0.6 14 53-66 17-30 (86)
121 TIGR02937 sigma70-ECF RNA poly 31.1 67 0.0015 16.6 2.5 33 29-66 111-143 (158)
122 PRK15183 Vi polysaccharide bio 30.9 63 0.0014 17.6 2.2 37 28-64 95-131 (143)
123 PRK12545 RNA polymerase sigma 30.7 57 0.0012 18.8 2.2 17 51-67 157-173 (201)
124 PRK12523 RNA polymerase sigma 30.6 59 0.0013 18.0 2.2 16 51-66 137-152 (172)
125 PRK12524 RNA polymerase sigma 30.6 54 0.0012 18.7 2.1 16 51-66 154-169 (196)
126 PRK12539 RNA polymerase sigma 30.5 59 0.0013 18.3 2.3 16 51-66 149-164 (184)
127 PF01726 LexA_DNA_bind: LexA D 30.3 73 0.0016 15.3 2.8 32 29-62 4-38 (65)
128 PRK12527 RNA polymerase sigma 30.2 60 0.0013 17.6 2.2 16 51-66 123-138 (159)
129 PRK00118 putative DNA-binding 30.2 65 0.0014 17.1 2.2 33 29-66 18-50 (104)
130 TIGR00498 lexA SOS regulatory 30.2 1.1E+02 0.0025 17.5 3.4 34 29-64 4-41 (199)
131 PRK12542 RNA polymerase sigma 30.2 54 0.0012 18.4 2.1 16 51-66 140-155 (185)
132 PRK12532 RNA polymerase sigma 30.1 54 0.0012 18.6 2.1 16 51-66 154-169 (195)
133 PRK12536 RNA polymerase sigma 30.0 58 0.0013 18.2 2.2 16 51-66 147-162 (181)
134 PRK10430 DNA-binding transcrip 29.9 51 0.0011 19.2 2.0 39 28-67 158-196 (239)
135 PRK12531 RNA polymerase sigma 29.7 64 0.0014 18.3 2.3 16 51-66 159-174 (194)
136 PF12200 DUF3597: Domain of un 29.7 51 0.0011 18.4 1.8 17 47-63 83-99 (127)
137 TIGR02943 Sig70_famx1 RNA poly 29.6 60 0.0013 18.4 2.2 16 51-66 149-164 (188)
138 PF14174 YycC: YycC-like prote 29.5 45 0.00097 15.6 1.3 18 48-65 7-24 (53)
139 PF07954 DUF1689: Protein of u 29.5 98 0.0021 17.7 3.0 23 37-59 4-26 (152)
140 COG5126 FRQ1 Ca2+-binding prot 29.2 68 0.0015 18.5 2.3 38 25-62 10-52 (160)
141 PRK06811 RNA polymerase factor 29.0 68 0.0015 18.1 2.3 16 51-66 149-164 (189)
142 PRK09637 RNA polymerase sigma 28.8 63 0.0014 18.3 2.2 16 51-66 124-139 (181)
143 TIGR02885 spore_sigF RNA polym 28.7 74 0.0016 18.7 2.5 33 29-66 184-216 (231)
144 PRK12373 NADH dehydrogenase su 28.6 1E+02 0.0022 20.6 3.2 33 34-66 40-72 (400)
145 TIGR02939 RpoE_Sigma70 RNA pol 28.5 41 0.00089 18.8 1.4 17 50-66 155-171 (190)
146 PRK12525 RNA polymerase sigma 28.4 67 0.0014 17.7 2.2 16 51-66 136-151 (168)
147 PF08765 Mor: Mor transcriptio 28.3 21 0.00045 18.8 0.1 16 51-66 74-89 (108)
148 PRK12520 RNA polymerase sigma 27.8 66 0.0014 18.1 2.2 16 51-66 149-164 (191)
149 PRK12546 RNA polymerase sigma 27.6 57 0.0012 18.6 1.9 16 51-66 131-146 (188)
150 PF13443 HTH_26: Cro/C1-type H 27.6 73 0.0016 14.4 2.4 27 39-65 29-56 (63)
151 PRK09413 IS2 repressor TnpA; R 27.5 1.1E+02 0.0023 16.3 4.0 37 26-66 10-46 (121)
152 PRK09644 RNA polymerase sigma 27.5 62 0.0013 17.7 2.0 16 51-66 126-141 (165)
153 PRK12538 RNA polymerase sigma 27.5 49 0.0011 19.7 1.6 16 51-66 189-204 (233)
154 PRK08583 RNA polymerase sigma 27.5 66 0.0014 19.3 2.2 33 29-66 206-238 (257)
155 PF13384 HTH_23: Homeodomain-l 27.4 23 0.00051 15.4 0.2 17 50-66 18-34 (50)
156 cd08315 Death_TRAILR_DR4_DR5 D 27.3 82 0.0018 16.3 2.3 16 51-66 21-36 (96)
157 PRK13919 putative RNA polymera 27.2 79 0.0017 17.6 2.4 16 51-66 153-168 (186)
158 TIGR02948 SigW_bacill RNA poly 27.0 59 0.0013 18.1 1.8 17 50-66 153-169 (187)
159 PRK08215 sporulation sigma fac 26.8 66 0.0014 19.3 2.1 34 28-66 209-242 (258)
160 PF13309 HTH_22: HTH domain 26.7 85 0.0018 14.9 2.6 37 29-65 21-58 (64)
161 PRK12540 RNA polymerase sigma 26.5 70 0.0015 18.1 2.1 16 51-66 129-144 (182)
162 cd08319 Death_RAIDD Death doma 26.2 32 0.00069 17.5 0.6 14 53-66 17-30 (83)
163 PRK12519 RNA polymerase sigma 26.1 54 0.0012 18.5 1.6 17 50-66 158-174 (194)
164 cd08318 Death_NMPP84 Death dom 26.1 32 0.0007 17.4 0.6 32 28-66 4-35 (86)
165 PRK10840 transcriptional regul 25.8 91 0.002 17.8 2.5 34 28-67 150-183 (216)
166 PF02042 RWP-RK: RWP-RK domain 25.5 64 0.0014 15.0 1.5 11 54-64 20-30 (52)
167 PRK12533 RNA polymerase sigma 25.4 62 0.0013 19.1 1.8 16 51-66 152-167 (216)
168 PRK15372 pathogenicity island 25.4 59 0.0013 20.4 1.7 30 29-58 12-41 (292)
169 smart00421 HTH_LUXR helix_turn 25.2 72 0.0016 13.6 2.9 32 29-66 4-35 (58)
170 TIGR01321 TrpR trp operon repr 25.2 1E+02 0.0022 16.2 2.4 39 28-66 32-72 (94)
171 TIGR02980 SigBFG RNA polymeras 25.2 77 0.0017 18.5 2.2 34 28-66 178-211 (227)
172 cd04761 HTH_MerR-SF Helix-Turn 25.1 24 0.00052 15.2 -0.0 13 53-65 4-16 (49)
173 PRK12535 RNA polymerase sigma 24.9 77 0.0017 18.2 2.1 16 51-66 151-166 (196)
174 COG2197 CitB Response regulato 24.5 31 0.00068 20.2 0.4 34 28-67 148-181 (211)
175 PF05269 Phage_CII: Bacterioph 24.4 53 0.0012 17.1 1.2 16 51-66 25-40 (91)
176 PRK12522 RNA polymerase sigma 24.3 92 0.002 17.2 2.3 16 51-66 137-152 (173)
177 PF13518 HTH_28: Helix-turn-he 24.2 39 0.00086 14.6 0.7 16 51-66 14-29 (52)
178 PRK05657 RNA polymerase sigma 24.1 66 0.0014 20.3 1.8 39 28-67 262-300 (325)
179 TIGR02479 FliA_WhiG RNA polyme 23.9 84 0.0018 18.4 2.1 33 29-66 176-208 (224)
180 PRK06930 positive control sigm 23.9 85 0.0018 18.0 2.1 34 28-66 114-147 (170)
181 TIGR02984 Sig-70_plancto1 RNA 23.6 88 0.0019 17.4 2.1 17 50-66 157-173 (189)
182 PRK11475 DNA-binding transcrip 23.6 1E+02 0.0022 18.1 2.5 33 28-66 134-166 (207)
183 TIGR01889 Staph_reg_Sar staphy 23.1 1.2E+02 0.0025 15.7 2.4 38 28-65 22-59 (109)
184 PTZ00183 centrin; Provisional 23.1 1.3E+02 0.0029 15.9 5.5 41 21-61 3-48 (158)
185 PF04760 IF2_N: Translation in 22.9 30 0.00065 15.7 0.1 13 53-65 7-19 (54)
186 cd08779 Death_PIDD Death Domai 22.9 42 0.0009 17.0 0.6 14 53-66 17-30 (86)
187 TIGR02393 RpoD_Cterm RNA polym 22.8 89 0.0019 18.5 2.1 38 28-66 176-213 (238)
188 PF01325 Fe_dep_repress: Iron 22.8 22 0.00048 16.7 -0.4 31 35-65 8-38 (60)
189 PRK09647 RNA polymerase sigma 22.6 99 0.0021 17.9 2.3 16 51-66 156-171 (203)
190 cd01670 Death Death Domain: a 22.4 32 0.00069 16.5 0.2 14 53-66 14-27 (79)
191 PRK00215 LexA repressor; Valid 22.3 77 0.0017 18.3 1.8 34 29-64 2-39 (205)
192 PF12898 Stc1: Stc1 domain; I 22.1 92 0.002 15.7 1.8 23 22-44 7-29 (84)
193 PF10410 DnaB_bind: DnaB-helic 22.1 81 0.0017 14.1 1.5 13 53-65 46-58 (59)
194 PRK09415 RNA polymerase factor 22.0 79 0.0017 17.7 1.7 16 51-66 145-160 (179)
195 TIGR02950 SigM_subfam RNA poly 21.9 21 0.00045 19.2 -0.6 20 47-66 119-138 (154)
196 PRK06288 RNA polymerase sigma 21.8 97 0.0021 18.8 2.2 33 29-66 213-245 (268)
197 PRK06986 fliA flagellar biosyn 21.8 88 0.0019 18.5 2.0 16 51-66 202-217 (236)
198 PF06154 YagB_YeeU_YfjZ: YagB/ 21.7 98 0.0021 16.5 1.9 17 26-42 36-52 (103)
199 PRK10100 DNA-binding transcrip 21.5 1.2E+02 0.0026 17.9 2.5 34 28-67 155-188 (216)
200 PF13413 HTH_25: Helix-turn-he 21.4 47 0.001 15.7 0.6 38 26-65 19-61 (62)
201 cd08784 Death_DRs Death Domain 21.4 47 0.001 16.4 0.7 16 51-66 13-28 (79)
202 PF12518 DUF3721: Protein of u 21.3 90 0.0019 13.3 2.3 18 46-63 1-18 (34)
203 PRK12544 RNA polymerase sigma 21.1 1.1E+02 0.0023 17.8 2.2 16 51-66 166-181 (206)
204 smart00550 Zalpha Z-DNA-bindin 21.1 47 0.001 15.9 0.6 17 50-66 23-39 (68)
205 cd08804 Death_ank2 Death domai 21.0 48 0.001 16.7 0.6 14 53-66 19-32 (84)
206 PF01047 MarR: MarR family; I 20.9 75 0.0016 14.2 1.3 31 30-64 2-32 (59)
207 KOG0031|consensus 20.8 95 0.0021 18.1 1.8 33 28-60 25-62 (171)
208 cd08777 Death_RIP1 Death Domai 20.6 48 0.001 16.8 0.6 14 53-66 17-30 (86)
209 PRK07670 RNA polymerase sigma 20.5 1E+02 0.0022 18.4 2.1 16 51-66 219-234 (251)
210 TIGR02941 Sigma_B RNA polymera 20.4 1E+02 0.0022 18.5 2.0 33 29-66 206-238 (255)
211 TIGR03792 uncharacterized cyan 20.3 1.5E+02 0.0032 15.4 2.7 20 28-47 64-87 (90)
212 PRK12518 RNA polymerase sigma 20.3 40 0.00086 18.6 0.3 20 47-66 134-153 (175)
213 TIGR03001 Sig-70_gmx1 RNA poly 20.1 1.1E+02 0.0024 18.5 2.1 17 51-67 179-195 (244)
No 1
>KOG2251|consensus
Probab=99.53 E-value=1.9e-14 Score=84.16 Aligned_cols=51 Identities=67% Similarity=0.927 Sum_probs=48.4
Q ss_pred ccccccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 17 FVRRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 17 ~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
..+++.||.||.|+..|+.+||..|.+..||+...|++||.+|+|++.+||
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVq 82 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQ 82 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhh
Confidence 457889999999999999999999999999999999999999999999886
No 2
>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=99.52 E-value=3.6e-14 Score=68.25 Aligned_cols=45 Identities=20% Similarity=0.269 Sum_probs=43.4
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCC----CCHHHHHHHHHHcCCCccccC
Q psy14727 23 RRNRTTFTLQQLEELETAFAQTHY----PDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 23 rr~Rt~~s~~q~~~Le~~F~~~~y----p~~~~r~~La~~l~l~~~qVk 67 (67)
+|.||.||.+|+..|+..|..+.| |+...+.+||..|||++.+||
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvK 50 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFK 50 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHee
Confidence 678999999999999999999999 999999999999999999886
No 3
>KOG0488|consensus
Probab=99.51 E-value=3.1e-14 Score=87.37 Aligned_cols=49 Identities=41% Similarity=0.611 Sum_probs=47.0
Q ss_pred ccccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 19 RRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 19 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
++|+|+.||.||..|+.+||+.|++.+|++..+|.+||..|||+.+|||
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVK 217 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVK 217 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHH
Confidence 5778889999999999999999999999999999999999999999996
No 4
>KOG0484|consensus
Probab=99.50 E-value=5e-15 Score=78.14 Aligned_cols=49 Identities=71% Similarity=1.073 Sum_probs=46.4
Q ss_pred ccccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 19 RRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 19 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
.++.||-||.||..|+.+||+.|...+||++-.|++||.++.|++..||
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQ 62 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQ 62 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHH
Confidence 5678899999999999999999999999999999999999999998875
No 5
>KOG0850|consensus
Probab=99.45 E-value=9e-14 Score=81.77 Aligned_cols=50 Identities=34% Similarity=0.521 Sum_probs=47.4
Q ss_pred cccccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 18 VRRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 18 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
+.+|.|+.||.|+..||..|.+.|++++|+..++|.+||..|||+..|||
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVK 167 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVK 167 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhh
Confidence 46677889999999999999999999999999999999999999999997
No 6
>KOG0842|consensus
Probab=99.45 E-value=1.6e-13 Score=83.81 Aligned_cols=49 Identities=39% Similarity=0.571 Sum_probs=46.3
Q ss_pred ccccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 19 RRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 19 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
.+++|+.|..||..|..+||+.|...+|++..+|++||..|+|++.|||
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVK 198 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVK 198 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchhee
Confidence 5567778999999999999999999999999999999999999999997
No 7
>KOG0843|consensus
Probab=99.42 E-value=2.1e-13 Score=77.86 Aligned_cols=48 Identities=38% Similarity=0.515 Sum_probs=46.0
Q ss_pred cccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 20 ~~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
.+.+|.||.||.+|+..||..|..++|....+|++||..|+|++.|||
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVk 147 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVK 147 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhh
Confidence 378889999999999999999999999999999999999999999997
No 8
>KOG0489|consensus
Probab=99.39 E-value=2e-13 Score=82.24 Aligned_cols=48 Identities=40% Similarity=0.517 Sum_probs=45.8
Q ss_pred cccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 20 ~~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
.+.||.||.||..|+.+||+.|+.|+|+++..|.+||..|+|+|+|||
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIK 204 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIK 204 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHH
Confidence 457889999999999999999999999999999999999999999997
No 9
>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=99.32 E-value=1.6e-12 Score=62.00 Aligned_cols=45 Identities=44% Similarity=0.667 Sum_probs=42.3
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 23 RRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 23 rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
|+.|+.||.+|+..|+..|..++||+..++..||..+||+..+|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~ 45 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVK 45 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccc
Confidence 468999999999999999999999999999999999999998873
No 10
>KOG0485|consensus
Probab=99.28 E-value=3.3e-12 Score=75.00 Aligned_cols=49 Identities=31% Similarity=0.509 Sum_probs=46.3
Q ss_pred ccccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 19 RRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 19 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
..++++.||+|+..|+..||..|+..+|++..+|..||.+|.|+|.|||
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVK 149 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVK 149 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhh
Confidence 4567789999999999999999999999999999999999999999997
No 11
>KOG0487|consensus
Probab=99.27 E-value=8.8e-12 Score=76.33 Aligned_cols=50 Identities=34% Similarity=0.445 Sum_probs=47.0
Q ss_pred cccccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 18 VRRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 18 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
..++.|++|..||..|+.+||+.|..|.|++...|.+|+..|+|+++|||
T Consensus 231 ~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVK 280 (308)
T KOG0487|consen 231 SARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVK 280 (308)
T ss_pred cccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhhee
Confidence 34667889999999999999999999999999999999999999999997
No 12
>KOG0492|consensus
Probab=99.23 E-value=1.5e-11 Score=71.78 Aligned_cols=49 Identities=35% Similarity=0.579 Sum_probs=45.7
Q ss_pred ccccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 19 RRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 19 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
.+..|+.||.||..|+..||+.|...+|+++.+|.+++..|.|++.|||
T Consensus 141 hk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVK 189 (246)
T KOG0492|consen 141 HKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVK 189 (246)
T ss_pred cCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhhee
Confidence 3455778999999999999999999999999999999999999999997
No 13
>KOG0494|consensus
Probab=99.21 E-value=2.2e-11 Score=73.13 Aligned_cols=47 Identities=60% Similarity=0.832 Sum_probs=42.9
Q ss_pred ccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 21 KQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 21 ~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
++|+-||.||..|+.+||..|...+||+...|+-||.++.|++.+||
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIq 186 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQ 186 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhh
Confidence 34445999999999999999999999999999999999999998875
No 14
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.17 E-value=7e-11 Score=55.94 Aligned_cols=44 Identities=50% Similarity=0.760 Sum_probs=41.2
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 24 RNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 24 r~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
+.|+.|+..|+..|+..|..++||+..++..||..+||+..+|+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~ 45 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVK 45 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHH
Confidence 46788999999999999999999999999999999999998874
No 15
>KOG0486|consensus
Probab=99.14 E-value=5.4e-11 Score=72.84 Aligned_cols=48 Identities=60% Similarity=0.861 Sum_probs=45.2
Q ss_pred cccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 20 ~~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
+|+||.||.|+..|+++||..|++|.||+...|++||.-++|++.+|+
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvr 157 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVR 157 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhh
Confidence 378899999999999999999999999999999999999999998774
No 16
>KOG0493|consensus
Probab=99.13 E-value=9.4e-11 Score=70.57 Aligned_cols=45 Identities=33% Similarity=0.619 Sum_probs=43.3
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 23 RRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 23 rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
+|.||.||.+|+..|...|+.|+|+....|.+||..|+|.+.|||
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIK 291 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIK 291 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhh
Confidence 578999999999999999999999999999999999999999986
No 17
>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=99.09 E-value=2.1e-10 Score=54.64 Aligned_cols=44 Identities=50% Similarity=0.736 Sum_probs=41.2
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 24 RNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 24 r~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
+.|+.|+..|+..|+..|..++||+..++..||..+||+..+|+
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~ 45 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVK 45 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHH
Confidence 46788999999999999999999999999999999999998874
No 18
>KOG0848|consensus
Probab=98.98 E-value=1.5e-10 Score=69.73 Aligned_cols=45 Identities=29% Similarity=0.462 Sum_probs=42.4
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 23 RRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 23 rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
-+.|.+||+.|+.+||+.|..++|+++..+.+||..|+|+|+|||
T Consensus 200 DKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVK 244 (317)
T KOG0848|consen 200 DKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVK 244 (317)
T ss_pred cceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhh
Confidence 346889999999999999999999999999999999999999997
No 19
>KOG0849|consensus
Probab=98.93 E-value=1.6e-09 Score=67.81 Aligned_cols=51 Identities=51% Similarity=0.753 Sum_probs=46.1
Q ss_pred ccccccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 17 FVRRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 17 ~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
...++.+|.||.|+..|+..|++.|++++||+...|++||..+++++..|+
T Consensus 171 ~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riq 221 (354)
T KOG0849|consen 171 ALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQ 221 (354)
T ss_pred cccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHH
Confidence 345667788999999999999999999999999999999999999997764
No 20
>KOG0491|consensus
Probab=98.91 E-value=1.4e-10 Score=65.68 Aligned_cols=47 Identities=34% Similarity=0.567 Sum_probs=44.2
Q ss_pred ccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 21 KQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 21 ~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
++++.||+|+..|+..|++.|+..+|++..++.+||..|+|++.|||
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVK 145 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVK 145 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHH
Confidence 45668999999999999999999999999999999999999999986
No 21
>KOG0844|consensus
Probab=98.79 E-value=2.3e-09 Score=65.88 Aligned_cols=47 Identities=36% Similarity=0.538 Sum_probs=44.3
Q ss_pred ccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 21 KQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 21 ~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
.-||.||.||.+|+..||+.|-+..|.+++.|.+||..|+|++..||
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIK 226 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIK 226 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceee
Confidence 35789999999999999999999999999999999999999998886
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.79 E-value=1.5e-08 Score=57.23 Aligned_cols=48 Identities=31% Similarity=0.421 Sum_probs=43.3
Q ss_pred cccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 20 ~~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
+..++.|+.-|.+|+..|++.|..++||+...|..|+..|+|++..||
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVq 96 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQ 96 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhh
Confidence 445666777899999999999999999999999999999999998876
No 23
>KOG0490|consensus
Probab=98.76 E-value=6.1e-09 Score=61.06 Aligned_cols=49 Identities=43% Similarity=0.560 Sum_probs=45.7
Q ss_pred ccccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 19 RRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 19 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
..+.|+.||.|+.+|+..|++.|+..+||+...++.||..+++++..||
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVq 105 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQ 105 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeee
Confidence 4567889999999999999999999999999999999999999998875
No 24
>KOG3802|consensus
Probab=98.54 E-value=1.6e-07 Score=59.25 Aligned_cols=47 Identities=21% Similarity=0.343 Sum_probs=44.2
Q ss_pred ccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 21 KQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 21 ~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
++|++||.|.......||..|.+|+.|+..+...||.+|+|...+|+
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVR 339 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVR 339 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEE
Confidence 57788999999999999999999999999999999999999998774
No 25
>KOG4577|consensus
Probab=98.28 E-value=1e-06 Score=54.09 Aligned_cols=46 Identities=37% Similarity=0.481 Sum_probs=43.8
Q ss_pred cCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 22 QRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 22 ~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
.+|+||.+|..|++.|..+|...+-|.+..|++|+..+||..++||
T Consensus 167 nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQ 212 (383)
T KOG4577|consen 167 NKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQ 212 (383)
T ss_pred cCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehh
Confidence 5789999999999999999999999999999999999999999886
No 26
>KOG0483|consensus
Probab=98.14 E-value=3.2e-06 Score=49.50 Aligned_cols=44 Identities=20% Similarity=0.292 Sum_probs=40.0
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 24 RNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 24 r~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
++...|+.+|...||..|+.+.++....+..||..|||.++||.
T Consensus 52 ~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVa 95 (198)
T KOG0483|consen 52 GKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVA 95 (198)
T ss_pred cccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHH
Confidence 34446999999999999999999999999999999999999983
No 27
>KOG0847|consensus
Probab=98.07 E-value=2.1e-06 Score=51.03 Aligned_cols=49 Identities=37% Similarity=0.546 Sum_probs=44.3
Q ss_pred ccccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 19 RRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 19 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
..+++-.|..|+..|+..|+..|+..+|+-..+|.+||..+|+++.||+
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvk 212 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVK 212 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHH
Confidence 3455667889999999999999999999999999999999999999875
No 28
>KOG2252|consensus
Probab=97.99 E-value=1.4e-05 Score=52.50 Aligned_cols=47 Identities=23% Similarity=0.341 Sum_probs=42.6
Q ss_pred cccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 20 ~~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
-..++.|.+||..|...|...|+.+++|+......|+.+|+|....|
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV 464 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTV 464 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHH
Confidence 34567799999999999999999999999999999999999987655
No 29
>KOG0774|consensus
Probab=97.52 E-value=0.00013 Score=44.47 Aligned_cols=44 Identities=36% Similarity=0.523 Sum_probs=39.5
Q ss_pred CCCCCCCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 23 RRNRTTFTLQQLEELETAFA---QTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 23 rr~Rt~~s~~q~~~Le~~F~---~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
+|+|..|+..-...|...|. .|+||+...+++||.+.+++-.||
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQv 235 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQV 235 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhh
Confidence 56778899999999999986 678999999999999999998876
No 30
>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=97.29 E-value=0.00011 Score=32.78 Aligned_cols=24 Identities=25% Similarity=0.504 Sum_probs=19.2
Q ss_pred hcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 43 QTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 43 ~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
.++||+..++..||..+||+..||
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi 30 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQI 30 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHH
Confidence 478999999999999999999886
No 31
>KOG0775|consensus
Probab=97.24 E-value=0.00038 Score=42.67 Aligned_cols=45 Identities=24% Similarity=0.255 Sum_probs=37.2
Q ss_pred cCCCCCCCCHHH---------HHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 22 QRRNRTTFTLQQ---------LEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 22 ~rr~Rt~~s~~q---------~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
---+||.+..++ ...|...|..++||+-.++.+||+.+||+..||
T Consensus 167 fPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQV 220 (304)
T KOG0775|consen 167 FPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQV 220 (304)
T ss_pred CCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhh
Confidence 334577655444 568889999999999999999999999999887
No 32
>KOG1168|consensus
Probab=97.22 E-value=0.00021 Score=44.28 Aligned_cols=48 Identities=25% Similarity=0.315 Sum_probs=43.2
Q ss_pred ccccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 19 RRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 19 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
...++|+||.+..-....||..|...+-|+.+....||++|+|...+|
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVV 353 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVV 353 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceE
Confidence 345678899999999999999999999999999999999999988766
No 33
>KOG0490|consensus
Probab=97.20 E-value=0.0005 Score=40.29 Aligned_cols=50 Identities=50% Similarity=0.597 Sum_probs=44.9
Q ss_pred cccccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 18 VRRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 18 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
...+.++.|+.+...|+..+...|..+++|+...+..|+..+|+++..|+
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q 198 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQ 198 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhh
Confidence 34567788999999999999999999999999999999999999987653
No 34
>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=95.33 E-value=0.022 Score=26.83 Aligned_cols=37 Identities=27% Similarity=0.407 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHcCCCccc
Q psy14727 29 FTLQQLEELETAFAQTHY--PDVFTREDLAMKINLTEAR 65 (67)
Q Consensus 29 ~s~~q~~~Le~~F~~~~y--p~~~~r~~La~~l~l~~~q 65 (67)
+|+.|...|..++....| |-...-.+||..+|++...
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st 39 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKST 39 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHH
Confidence 478899999999998876 6666778999999998753
No 35
>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=93.96 E-value=0.19 Score=23.38 Aligned_cols=39 Identities=21% Similarity=0.438 Sum_probs=28.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 23 RRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 23 rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
++.|..+|-++-..+-..++.+. ....||..+|++..+|
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv 39 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTV 39 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHH
Confidence 46788899999998888888776 5678999999998775
No 36
>KOG1146|consensus
Probab=92.68 E-value=0.23 Score=36.54 Aligned_cols=47 Identities=23% Similarity=0.253 Sum_probs=42.4
Q ss_pred ccCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 21 KQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 21 ~~rr~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
.+|+.||.++..|+..+...|....||...+-+.|...++++.+.|+
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~ 948 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQ 948 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhH
Confidence 35678999999999999999999999999999999999999988763
No 37
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=92.29 E-value=0.2 Score=29.52 Aligned_cols=37 Identities=27% Similarity=0.433 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHcCCCcc
Q psy14727 28 TFTLQQLEELETAFAQTHY--PDVFTREDLAMKINLTEA 64 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~y--p~~~~r~~La~~l~l~~~ 64 (67)
.+|+.|+..|..+|....| |-...-.+||..+|++..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISks 193 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKS 193 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHH
Confidence 6999999999999998875 766777899999999874
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=88.97 E-value=0.2 Score=23.87 Aligned_cols=34 Identities=15% Similarity=0.202 Sum_probs=23.7
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 34 LEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 34 ~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
+..|+..|...+++....-..|..+.+|+..||+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr 43 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVR 43 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHH
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHH
Confidence 4569999999999999999999999999988874
No 39
>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=79.99 E-value=1.6 Score=19.56 Aligned_cols=34 Identities=15% Similarity=0.334 Sum_probs=23.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 28 TFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
.+++.+...+...|..+ ..-.++|..+|++...|
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V 37 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTV 37 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHH
Confidence 35777888888887333 24568999999998655
No 40
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.30 E-value=2 Score=22.41 Aligned_cols=37 Identities=16% Similarity=0.216 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcc
Q psy14727 28 TFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEA 64 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~ 64 (67)
+++++|...-...|+.|--.+.-..+++|..|+.++-
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~ 38 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEV 38 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHH
Confidence 3567777776677776666666677789999998874
No 41
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=79.30 E-value=1.5 Score=19.44 Aligned_cols=34 Identities=15% Similarity=0.321 Sum_probs=15.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 28 TFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
.+|.++...++.....+ ....+||..+|.+...|
T Consensus 4 ~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV 37 (44)
T PF13936_consen 4 HLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTV 37 (44)
T ss_dssp --------HHHHHHCS--------HHHHHHHTT--HHHH
T ss_pred chhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHH
Confidence 46777888877665533 35668999999887654
No 42
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=78.40 E-value=1.7 Score=20.45 Aligned_cols=31 Identities=29% Similarity=0.454 Sum_probs=21.7
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 32 QQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 32 ~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
-|+..|+-.+. +.+.+.. +||..+|++++.|
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti 36 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTI 36 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHH
Confidence 35666777777 6666554 7899999998765
No 43
>PRK13558 bacterio-opsin activator; Provisional
Probab=76.14 E-value=2.9 Score=28.22 Aligned_cols=38 Identities=24% Similarity=0.425 Sum_probs=33.4
Q ss_pred CCCCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHcCCCcc
Q psy14727 27 TTFTLQQLEELETAFAQTHY--PDVFTREDLAMKINLTEA 64 (67)
Q Consensus 27 t~~s~~q~~~Le~~F~~~~y--p~~~~r~~La~~l~l~~~ 64 (67)
..+|..|...|+.++....| |-...-.+||..||++..
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~ 645 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRS 645 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHH
Confidence 36999999999999999987 777778899999999874
No 44
>KOG0773|consensus
Probab=73.69 E-value=8.6 Score=24.19 Aligned_cols=44 Identities=20% Similarity=0.239 Sum_probs=33.4
Q ss_pred CCCCCCCCHHHHHHHHHH-Hh--hcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 23 RRNRTTFTLQQLEELETA-FA--QTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 23 rr~Rt~~s~~q~~~Le~~-F~--~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
.+.+..+.......|+.- |+ ..+||+..++..||..+||+..||
T Consensus 240 ~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv 286 (342)
T KOG0773|consen 240 WRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQV 286 (342)
T ss_pred CCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccC
Confidence 344446777777777744 33 357999999999999999999886
No 45
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=71.26 E-value=5.5 Score=17.26 Aligned_cols=15 Identities=40% Similarity=0.527 Sum_probs=12.2
Q ss_pred CCCHHHHHHHHHHHh
Q psy14727 28 TFTLQQLEELETAFA 42 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~ 42 (67)
.||..|+..|+.-..
T Consensus 2 ~FT~~Ql~~L~~Qi~ 16 (37)
T PF08880_consen 2 PFTPAQLQELRAQIL 16 (37)
T ss_pred CCCHHHHHHHHHHHH
Confidence 699999999987543
No 46
>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=71.08 E-value=7.2 Score=18.69 Aligned_cols=36 Identities=6% Similarity=0.121 Sum_probs=21.1
Q ss_pred CCCCCCHHHHHHHHHHH-hhcCCCCHHHHHHHHHHcCCCccc
Q psy14727 25 NRTTFTLQQLEELETAF-AQTHYPDVFTREDLAMKINLTEAR 65 (67)
Q Consensus 25 ~Rt~~s~~q~~~Le~~F-~~~~yp~~~~r~~La~~l~l~~~q 65 (67)
.|..||+++...+-... ... .....+|..+|+++..
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~ 39 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPST 39 (76)
T ss_dssp SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHH
T ss_pred CCCCCCHHHHHHHHHHHHHCC-----CceEeeeccccccccc
Confidence 46678998887776555 322 3567889999987654
No 47
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=70.48 E-value=11 Score=21.66 Aligned_cols=38 Identities=26% Similarity=0.434 Sum_probs=30.9
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcc
Q psy14727 25 NRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEA 64 (67)
Q Consensus 25 ~Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~ 64 (67)
....+|++++.++...-..+ |....+..||.++|++..
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~ 119 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPL 119 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHH
Confidence 45689999999988765555 677889999999999864
No 48
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=64.97 E-value=14 Score=21.22 Aligned_cols=36 Identities=22% Similarity=0.150 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 31 LQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 31 ~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
..-+..|.......-|.+......+|..||++...|
T Consensus 25 sAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v 60 (160)
T COG1905 25 SALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARV 60 (160)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHh
Confidence 455677888888888999999999999999998654
No 49
>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=64.18 E-value=8.9 Score=17.19 Aligned_cols=32 Identities=19% Similarity=0.206 Sum_probs=17.6
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 30 TLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 30 s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
++.+...+... |.....-.++|..+|+++..|
T Consensus 12 ~~~~r~i~~l~-----~~~g~s~~eIa~~l~~s~~~v 43 (54)
T PF08281_consen 12 PERQREIFLLR-----YFQGMSYAEIAEILGISESTV 43 (54)
T ss_dssp -HHHHHHHHHH-----HTS---HHHHHHHCTS-HHHH
T ss_pred CHHHHHHHHHH-----HHHCcCHHHHHHHHCcCHHHH
Confidence 44454555433 333446778999999998655
No 50
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=62.12 E-value=9.4 Score=16.80 Aligned_cols=33 Identities=18% Similarity=0.453 Sum_probs=20.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 29 FTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 29 ~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
++.++...+...+... ....++|..+|++...|
T Consensus 6 ~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~Tv 38 (45)
T PF02796_consen 6 LSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTV 38 (45)
T ss_dssp SSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHH
T ss_pred CCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHH
Confidence 5665556555556555 24668999999987644
No 51
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=61.74 E-value=16 Score=20.72 Aligned_cols=33 Identities=24% Similarity=0.162 Sum_probs=25.2
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 34 LEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 34 ~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
+..|...=+...|.+...-..+|..+|++..+|
T Consensus 26 i~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V 58 (156)
T PRK05988 26 LPILHAIQDEFGYVPEDAVPVIAEALNLSRAEV 58 (156)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHH
Confidence 444544445567999999999999999998765
No 52
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=60.13 E-value=17 Score=20.22 Aligned_cols=33 Identities=15% Similarity=0.080 Sum_probs=24.3
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 34 LEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 34 ~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
+..|...=....|.+...-..+|..+|++...|
T Consensus 19 i~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v 51 (148)
T TIGR01958 19 MPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWV 51 (148)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHH
Confidence 334444434556899999999999999998765
No 53
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=60.04 E-value=17 Score=20.40 Aligned_cols=33 Identities=15% Similarity=0.096 Sum_probs=24.6
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 34 LEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 34 ~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
+..|...=....|.+......+|..++++..+|
T Consensus 25 l~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v 57 (154)
T PRK07539 25 IPALKIVQEQRGWVPDEAIEAVADYLGMPAIDV 57 (154)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHH
Confidence 334444444567899999999999999998765
No 54
>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=59.83 E-value=3.1 Score=20.05 Aligned_cols=16 Identities=25% Similarity=0.507 Sum_probs=13.1
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.+||..||+++.+|
T Consensus 24 ~lkdIA~~Lgvs~~tI 39 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTI 39 (60)
T ss_pred cHHHHHHHHCCCHHHH
Confidence 3457999999999876
No 55
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=59.27 E-value=12 Score=15.93 Aligned_cols=33 Identities=15% Similarity=0.299 Sum_probs=20.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 29 FTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 29 ~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
+++.+...+...+..+ ..-.++|..+|++...|
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i 43 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTV 43 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHH
Confidence 4566666666554322 24567899999887654
No 56
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=58.87 E-value=2.4 Score=19.59 Aligned_cols=16 Identities=31% Similarity=0.522 Sum_probs=11.9
Q ss_pred HHHHHHHcCCCccccC
Q psy14727 52 REDLAMKINLTEARVQ 67 (67)
Q Consensus 52 r~~La~~l~l~~~qVk 67 (67)
-.+||..+|+++.||+
T Consensus 31 S~~La~~~gi~~~qVR 46 (50)
T PF06971_consen 31 SQELAEALGITPAQVR 46 (50)
T ss_dssp HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHCCCHHHhc
Confidence 3478999999998873
No 57
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=56.73 E-value=13 Score=20.89 Aligned_cols=34 Identities=24% Similarity=0.325 Sum_probs=24.6
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 27 TTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 27 t~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
..+++.|...|... ..+ ....++|..+|++...|
T Consensus 5 ~~Lt~rqreVL~lr-~~G-----lTq~EIAe~LGiS~~tV 38 (141)
T PRK03975 5 SFLTERQIEVLRLR-ERG-----LTQQEIADILGTSRANV 38 (141)
T ss_pred cCCCHHHHHHHHHH-HcC-----CCHHHHHHHHCCCHHHH
Confidence 46788888888773 222 25678999999988654
No 58
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=56.43 E-value=22 Score=20.54 Aligned_cols=31 Identities=23% Similarity=0.087 Sum_probs=23.3
Q ss_pred HHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 36 ELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 36 ~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
.|...=....|.+......+|..||++...|
T Consensus 41 ~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V 71 (169)
T PRK07571 41 VLHKAQELFGYLERDLLLYVARQLKLPLSRV 71 (169)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHhCcCHHHH
Confidence 3443334556899999999999999998665
No 59
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=55.47 E-value=15 Score=20.38 Aligned_cols=33 Identities=21% Similarity=0.194 Sum_probs=22.1
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 34 LEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 34 ~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
+..|...=....|.+...-..+|..++++..+|
T Consensus 16 l~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v 48 (145)
T PF01257_consen 16 LPILHEVQEEYGYIPEEALEEIAEALGIPPAEV 48 (145)
T ss_dssp HHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHH
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHH
Confidence 344544445566999999999999999998765
No 60
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=54.35 E-value=11 Score=16.91 Aligned_cols=16 Identities=19% Similarity=0.430 Sum_probs=11.3
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
...+||..++++.+.|
T Consensus 17 t~~eLa~~l~vS~rTi 32 (55)
T PF08279_consen 17 TAKELAEELGVSRRTI 32 (55)
T ss_dssp EHHHHHHHCTS-HHHH
T ss_pred CHHHHHHHhCCCHHHH
Confidence 3458899999988654
No 61
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=54.22 E-value=1.7 Score=21.77 Aligned_cols=28 Identities=25% Similarity=0.144 Sum_probs=18.9
Q ss_pred HHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 39 TAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 39 ~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
..|....|.......+||..+|+++..|
T Consensus 22 ~af~L~R~~eGlS~kEIAe~LGIS~~TV 49 (73)
T TIGR03879 22 AAAALAREEAGKTASEIAEELGRTEQTV 49 (73)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHH
Confidence 3444444444456778999999998665
No 62
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=52.74 E-value=32 Score=19.67 Aligned_cols=32 Identities=16% Similarity=0.358 Sum_probs=23.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcC-CCcc
Q psy14727 28 TFTLQQLEELETAFAQTHYPDVFTREDLAMKIN-LTEA 64 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~-l~~~ 64 (67)
.+|.+.+..|.+.+.... ...+||..|| ++..
T Consensus 2 ~Wtde~~~~L~~lw~~G~-----SasqIA~~lg~vsRn 34 (162)
T PF07750_consen 2 SWTDERVERLRKLWAEGL-----SASQIARQLGGVSRN 34 (162)
T ss_pred CCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCcchh
Confidence 478888998888776654 5667888888 6654
No 63
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=52.55 E-value=5.3 Score=17.57 Aligned_cols=15 Identities=33% Similarity=0.514 Sum_probs=11.0
Q ss_pred HHHHHHHcCCCcccc
Q psy14727 52 REDLAMKINLTEARV 66 (67)
Q Consensus 52 r~~La~~l~l~~~qV 66 (67)
-.+||..+|+++..|
T Consensus 20 ~~~la~~lglS~~~v 34 (42)
T PF13404_consen 20 YAELAEELGLSESTV 34 (42)
T ss_dssp HHHHHHHHTS-HHHH
T ss_pred HHHHHHHHCcCHHHH
Confidence 457899999998654
No 64
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=50.69 E-value=30 Score=18.49 Aligned_cols=17 Identities=24% Similarity=0.384 Sum_probs=12.7
Q ss_pred HHHHHHHHcCCCccccC
Q psy14727 51 TREDLAMKINLTEARVQ 67 (67)
Q Consensus 51 ~r~~La~~l~l~~~qVk 67 (67)
.-.++|..+|++...|+
T Consensus 125 s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 125 KEIDIAKKLHISRQSVY 141 (142)
T ss_pred CHHHHHHHHCcCHHhhc
Confidence 35578888888887664
No 65
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=49.69 E-value=6 Score=20.58 Aligned_cols=27 Identities=19% Similarity=0.348 Sum_probs=17.7
Q ss_pred HHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 36 ELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 36 ~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
+|...|....+. .+.+|..|+++...|
T Consensus 14 ELq~nf~~~~ls----~~~ia~dL~~s~~~l 40 (89)
T PF10078_consen 14 ELQANFELSGLS----LEQIAADLGTSPEHL 40 (89)
T ss_pred HHHHHHHHcCCC----HHHHHHHhCCCHHHH
Confidence 566666665544 567788888877543
No 66
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=49.15 E-value=20 Score=19.40 Aligned_cols=16 Identities=25% Similarity=0.366 Sum_probs=12.7
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 124 s~~EIA~~l~is~~tV 139 (154)
T PRK06759 124 TMGEIALETEMTYYQV 139 (154)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 5668899999988765
No 67
>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=49.06 E-value=20 Score=20.02 Aligned_cols=16 Identities=19% Similarity=0.416 Sum_probs=11.9
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|+++..|
T Consensus 118 s~~eIA~~lgis~~tV 133 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGA 133 (170)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4567888888887655
No 68
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=47.95 E-value=21 Score=20.04 Aligned_cols=17 Identities=18% Similarity=0.430 Sum_probs=12.7
Q ss_pred HHHHHHHHcCCCccccC
Q psy14727 51 TREDLAMKINLTEARVQ 67 (67)
Q Consensus 51 ~r~~La~~l~l~~~qVk 67 (67)
.-.++|..+|+++..|+
T Consensus 145 s~~EIA~~lgis~~tVk 161 (178)
T PRK12529 145 KQKDIAQALDIALPTVK 161 (178)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45688999999886653
No 69
>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=47.73 E-value=24 Score=16.11 Aligned_cols=33 Identities=21% Similarity=0.344 Sum_probs=20.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 28 TFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
.+|+.++..|.....-. ...++|..+++++..|
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV 35 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTV 35 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhH
Confidence 46777777776554433 4567888888776544
No 70
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=46.45 E-value=24 Score=19.30 Aligned_cols=16 Identities=25% Similarity=0.468 Sum_probs=12.2
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
...++|..+|++...|
T Consensus 127 s~~EIA~~lgis~~tV 142 (163)
T PRK07037 127 TQKDIARELGVSPTLV 142 (163)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4568888999887665
No 71
>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=45.64 E-value=25 Score=19.66 Aligned_cols=35 Identities=26% Similarity=0.404 Sum_probs=25.0
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 26 RTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 26 Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
.+.++..|...+... ..+ ....++|..+|++...|
T Consensus 4 ~~~Lte~qr~VL~Lr-~~G-----lTq~EIAe~LgiS~stV 38 (137)
T TIGR00721 4 KTFLTERQIKVLELR-EKG-----LSQKEIAKELKTTRANV 38 (137)
T ss_pred cCCCCHHHHHHHHHH-HcC-----CCHHHHHHHHCcCHHHH
Confidence 356788888888763 222 25678999999987654
No 72
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=45.27 E-value=24 Score=19.93 Aligned_cols=33 Identities=21% Similarity=0.119 Sum_probs=19.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 29 FTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 29 ~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
+++.|...+...|-. ...-.++|..+|++...|
T Consensus 140 L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV 172 (189)
T PRK09648 140 LPEKQREILILRVVV-----GLSAEETAEAVGSTPGAV 172 (189)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHH
Confidence 444444444443322 234668899999987655
No 73
>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=44.90 E-value=26 Score=18.96 Aligned_cols=16 Identities=25% Similarity=0.187 Sum_probs=11.8
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 129 ~~~eIA~~l~is~~tv 144 (159)
T TIGR02989 129 SLTALAEQLGRTVNAV 144 (159)
T ss_pred CHHHHHHHhCCCHHHH
Confidence 4567888888887655
No 74
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=44.21 E-value=27 Score=19.06 Aligned_cols=16 Identities=13% Similarity=0.320 Sum_probs=11.7
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 124 s~~EIA~~lgis~~tV 139 (160)
T PRK09642 124 SYQEIALQEKIEVKTV 139 (160)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 3457888888887665
No 75
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=44.03 E-value=27 Score=18.96 Aligned_cols=17 Identities=18% Similarity=0.245 Sum_probs=12.6
Q ss_pred HHHHHHHHcCCCccccC
Q psy14727 51 TREDLAMKINLTEARVQ 67 (67)
Q Consensus 51 ~r~~La~~l~l~~~qVk 67 (67)
.-.++|..+|++...|+
T Consensus 124 s~~EIA~~lgis~~tV~ 140 (161)
T PRK09047 124 DVAETAAAMGCSEGSVK 140 (161)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 35688999999886653
No 76
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=43.69 E-value=31 Score=19.65 Aligned_cols=17 Identities=18% Similarity=0.305 Sum_probs=12.5
Q ss_pred HHHHHHHHcCCCccccC
Q psy14727 51 TREDLAMKINLTEARVQ 67 (67)
Q Consensus 51 ~r~~La~~l~l~~~qVk 67 (67)
.-.++|..+|++...|+
T Consensus 160 s~~EIA~~Lgis~~tVk 176 (194)
T PRK09646 160 TYREVAERLAVPLGTVK 176 (194)
T ss_pred CHHHHHHHhCCChHhHH
Confidence 45678888888876653
No 77
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=43.56 E-value=33 Score=16.44 Aligned_cols=40 Identities=15% Similarity=0.103 Sum_probs=16.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 27 TTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 27 t~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
..|+...-...-..+....---...| ..|.+.|+++.+|+
T Consensus 4 rsy~~~FKL~Vv~~a~~~~nc~~~~R-Aaarkf~V~r~~Vr 43 (58)
T PF09607_consen 4 RSYTAEFKLKVVEYAEKDNNCKGNQR-AAARKFNVSRRQVR 43 (58)
T ss_dssp ----HHHHHHHHHHHHH-TTTTT-HH-HHHHHTTS-HHHHH
T ss_pred cccChHHHHHHHHHHHHccchhhhHH-HHHHHhCccHHHHH
Confidence 34555443333333333322222334 34888888887763
No 78
>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=43.52 E-value=27 Score=19.48 Aligned_cols=17 Identities=24% Similarity=0.331 Sum_probs=12.4
Q ss_pred HHHHHHHHcCCCccccC
Q psy14727 51 TREDLAMKINLTEARVQ 67 (67)
Q Consensus 51 ~r~~La~~l~l~~~qVk 67 (67)
.-.++|..+|+++..|+
T Consensus 152 s~~EIA~~lgis~~tVk 168 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVE 168 (183)
T ss_pred CHHHHHHHhCCCHHHHH
Confidence 45678888888876653
No 79
>PRK04217 hypothetical protein; Provisional
Probab=43.40 E-value=29 Score=18.67 Aligned_cols=35 Identities=17% Similarity=0.256 Sum_probs=24.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 27 TTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 27 t~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
..++..+...+...+.... ...++|..+|++...|
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV 75 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTV 75 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHH
Confidence 3577888777766654333 4668999999987654
No 80
>KOG3623|consensus
Probab=42.85 E-value=29 Score=25.08 Aligned_cols=34 Identities=21% Similarity=0.199 Sum_probs=30.0
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 34 LEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 34 ~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
...|...|..|..|+..+-..+|.+.|++.+.||
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk 601 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVK 601 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHH
Confidence 5678888999999999999999999999987664
No 81
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=42.81 E-value=31 Score=19.06 Aligned_cols=16 Identities=19% Similarity=0.430 Sum_probs=12.0
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|+++..|
T Consensus 136 s~~EIA~~lgis~~tV 151 (173)
T PRK09645 136 STAQIAADLGIPEGTV 151 (173)
T ss_pred CHHHHHHHHCcCHHHH
Confidence 4567888888887665
No 82
>PF05848 CtsR: Firmicute transcriptional repressor of class III stress genes (CtsR); InterPro: IPR008463 This family consists of several Firmicute transcriptional repressor of class III stress gene (CtsR) proteins. CtsR of Listeria monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon [].; PDB: 3H0D_A.
Probab=42.67 E-value=14 Score=21.16 Aligned_cols=16 Identities=25% Similarity=0.499 Sum_probs=12.7
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.|.+||..++|-++||
T Consensus 27 qR~eLA~~F~CvPSQI 42 (152)
T PF05848_consen 27 QRNELAERFNCVPSQI 42 (152)
T ss_dssp -HHHHHHHTTS-THHH
T ss_pred eHHHHHHHhCCchhhh
Confidence 6889999999999886
No 83
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=41.53 E-value=30 Score=20.00 Aligned_cols=16 Identities=31% Similarity=0.497 Sum_probs=12.1
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 171 s~~EIA~~lgis~~tV 186 (206)
T PRK12526 171 SQEQLAQQLNVPLGTV 186 (206)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4567888888887665
No 84
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=41.01 E-value=25 Score=19.21 Aligned_cols=16 Identities=25% Similarity=0.343 Sum_probs=11.1
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 130 s~~eIA~~lgis~~tv 145 (161)
T PRK12541 130 SYKEIAEMTGLSLAKV 145 (161)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 3457788888877654
No 85
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=40.18 E-value=41 Score=18.87 Aligned_cols=17 Identities=12% Similarity=0.319 Sum_probs=12.6
Q ss_pred HHHHHHHHcCCCccccC
Q psy14727 51 TREDLAMKINLTEARVQ 67 (67)
Q Consensus 51 ~r~~La~~l~l~~~qVk 67 (67)
.-.++|..+|++...|+
T Consensus 151 s~~eIA~~lgis~~tV~ 167 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVK 167 (182)
T ss_pred CHHHHHHHHCCChhhHH
Confidence 45678888898887653
No 86
>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=40.09 E-value=4.5 Score=19.17 Aligned_cols=16 Identities=13% Similarity=0.360 Sum_probs=12.4
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..||++...|
T Consensus 15 ~~~eIA~~Lg~~~~TV 30 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTV 30 (58)
T ss_pred CHHHHHHHHCCChHHH
Confidence 4568899999987655
No 87
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=39.73 E-value=31 Score=19.59 Aligned_cols=17 Identities=6% Similarity=0.374 Sum_probs=13.0
Q ss_pred HHHHHHHHcCCCccccC
Q psy14727 51 TREDLAMKINLTEARVQ 67 (67)
Q Consensus 51 ~r~~La~~l~l~~~qVk 67 (67)
.-.++|..+|+++..|+
T Consensus 152 s~~EIA~~lgis~~tVk 168 (189)
T PRK12530 152 SSEQICQECDISTSNLH 168 (189)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45688999999987663
No 88
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=39.39 E-value=31 Score=18.93 Aligned_cols=33 Identities=9% Similarity=0.035 Sum_probs=19.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 29 FTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 29 ~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
+++.+...+...|-. ...-.++|..+|++...|
T Consensus 129 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV 161 (182)
T PRK09652 129 LPEELRTAITLREIE-----GLSYEEIAEIMGCPIGTV 161 (182)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHH
Confidence 455555555444322 223557899999988665
No 89
>KOG0041|consensus
Probab=39.23 E-value=63 Score=19.72 Aligned_cols=37 Identities=16% Similarity=0.397 Sum_probs=30.7
Q ss_pred CCCHHHHHHHHHHHh-----hcCCCCHHHHHHHHHHcCCCcc
Q psy14727 28 TFTLQQLEELETAFA-----QTHYPDVFTREDLAMKINLTEA 64 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~-----~~~yp~~~~r~~La~~l~l~~~ 64 (67)
-|+..|+..++..|. ++-|++..+-...-.+||.+..
T Consensus 92 eFsrkqIk~~~~~Fk~yDe~rDgfIdl~ELK~mmEKLgapQT 133 (244)
T KOG0041|consen 92 EFSRKQIKDAESMFKQYDEDRDGFIDLMELKRMMEKLGAPQT 133 (244)
T ss_pred HHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHhCCchh
Confidence 478889999999985 5668999888888999998764
No 90
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=38.70 E-value=36 Score=19.03 Aligned_cols=16 Identities=25% Similarity=0.449 Sum_probs=12.0
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 149 s~~eIA~~l~is~~tV 164 (184)
T PRK12512 149 SIKETAAKLSMSEGAV 164 (184)
T ss_pred CHHHHHHHhCCCHHHH
Confidence 4567888888887655
No 91
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=38.49 E-value=36 Score=19.19 Aligned_cols=16 Identities=19% Similarity=0.383 Sum_probs=11.6
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 149 s~~eIA~~lgis~~tV 164 (189)
T PRK12515 149 SVEEVGEIVGIPESTV 164 (189)
T ss_pred CHHHHHHHHCcCHHHH
Confidence 4557888888887655
No 92
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation a
Probab=37.55 E-value=18 Score=18.33 Aligned_cols=15 Identities=7% Similarity=0.446 Sum_probs=11.9
Q ss_pred HHHHHHHcCCCcccc
Q psy14727 52 REDLAMKINLTEARV 66 (67)
Q Consensus 52 r~~La~~l~l~~~qV 66 (67)
=.+++..+||++.+|
T Consensus 14 wk~~~R~LGlse~~I 28 (80)
T cd08313 14 WKEFVRRLGLSDNEI 28 (80)
T ss_pred HHHHHHHcCCCHHHH
Confidence 346899999998765
No 93
>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=37.52 E-value=38 Score=18.09 Aligned_cols=16 Identities=13% Similarity=0.343 Sum_probs=12.1
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
...++|..+|+++..|
T Consensus 131 ~~~eIA~~lgis~~tv 146 (161)
T TIGR02985 131 SYKEIAEELGISVKTV 146 (161)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4567888899888665
No 94
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=37.36 E-value=15 Score=15.38 Aligned_cols=14 Identities=43% Similarity=0.567 Sum_probs=9.3
Q ss_pred HHHHHHHHcCCCcc
Q psy14727 51 TREDLAMKINLTEA 64 (67)
Q Consensus 51 ~r~~La~~l~l~~~ 64 (67)
.+.+||..+|++..
T Consensus 4 tr~diA~~lG~t~E 17 (32)
T PF00325_consen 4 TRQDIADYLGLTRE 17 (32)
T ss_dssp -HHHHHHHHTS-HH
T ss_pred CHHHHHHHhCCcHH
Confidence 46788888888764
No 95
>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=37.03 E-value=38 Score=18.50 Aligned_cols=16 Identities=25% Similarity=0.237 Sum_probs=11.5
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 140 s~~eIA~~l~is~~tv 155 (170)
T TIGR02952 140 PIAEVARILGKTEGAV 155 (170)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4567888888887655
No 96
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=36.71 E-value=48 Score=18.44 Aligned_cols=17 Identities=12% Similarity=0.245 Sum_probs=12.9
Q ss_pred HHHHHHHHcCCCccccC
Q psy14727 51 TREDLAMKINLTEARVQ 67 (67)
Q Consensus 51 ~r~~La~~l~l~~~qVk 67 (67)
.-.++|..+|+++..|+
T Consensus 147 s~~eIA~~lgis~~tV~ 163 (179)
T PRK12514 147 SYKELAERHDVPLNTMR 163 (179)
T ss_pred CHHHHHHHHCCChHHHH
Confidence 45688999999887653
No 97
>PF13730 HTH_36: Helix-turn-helix domain
Probab=36.67 E-value=17 Score=16.28 Aligned_cols=19 Identities=21% Similarity=0.259 Sum_probs=13.6
Q ss_pred CHHHHHHHHHHcCCCcccc
Q psy14727 48 DVFTREDLAMKINLTEARV 66 (67)
Q Consensus 48 ~~~~r~~La~~l~l~~~qV 66 (67)
..+....||..+|++...|
T Consensus 24 ~~pS~~~la~~~g~s~~Tv 42 (55)
T PF13730_consen 24 CFPSQETLAKDLGVSRRTV 42 (55)
T ss_pred CCcCHHHHHHHHCcCHHHH
Confidence 3335668899999987655
No 98
>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=36.56 E-value=42 Score=18.49 Aligned_cols=16 Identities=31% Similarity=0.358 Sum_probs=12.1
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 137 s~~eiA~~lgis~~tv 152 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTV 152 (169)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4567888899887665
No 99
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; 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: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=36.40 E-value=22 Score=17.16 Aligned_cols=16 Identities=25% Similarity=0.466 Sum_probs=11.4
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
...+||..+|++...|
T Consensus 22 t~eEiA~~lgis~~~v 37 (78)
T PF04539_consen 22 TDEEIAEELGISVEEV 37 (78)
T ss_dssp BHHHHHHHHTS-HHHH
T ss_pred CHHHHHHHHcccHHHH
Confidence 5568999999987654
No 100
>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=36.21 E-value=38 Score=18.45 Aligned_cols=17 Identities=12% Similarity=0.304 Sum_probs=12.7
Q ss_pred HHHHHHHHcCCCccccC
Q psy14727 51 TREDLAMKINLTEARVQ 67 (67)
Q Consensus 51 ~r~~La~~l~l~~~qVk 67 (67)
.-.++|..+|++...|+
T Consensus 128 s~~eIA~~lgis~~tV~ 144 (162)
T TIGR02983 128 SEAQVAEALGISVGTVK 144 (162)
T ss_pred CHHHHHHHhCCCHHHHH
Confidence 45678899999887653
No 101
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=36.12 E-value=39 Score=18.44 Aligned_cols=16 Identities=19% Similarity=0.426 Sum_probs=11.5
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 129 s~~eIA~~lgis~~tV 144 (166)
T PRK09639 129 SYKEIAEALGIKESSV 144 (166)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4557888888887655
No 102
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=35.87 E-value=44 Score=14.45 Aligned_cols=32 Identities=22% Similarity=0.184 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 31 LQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 31 ~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
..+...|..... ++.. ...+||..+|++...|
T Consensus 3 ~~~~~Il~~l~~-~~~~---t~~ela~~~~is~~tv 34 (48)
T PF13412_consen 3 ETQRKILNYLRE-NPRI---TQKELAEKLGISRSTV 34 (48)
T ss_dssp HHHHHHHHHHHH-CTTS----HHHHHHHHTS-HHHH
T ss_pred HHHHHHHHHHHH-cCCC---CHHHHHHHhCCCHHHH
Confidence 344555544444 4333 5668999999987543
No 103
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=35.53 E-value=36 Score=19.11 Aligned_cols=16 Identities=6% Similarity=0.181 Sum_probs=12.1
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 146 s~~EIA~~lgis~~tV 161 (186)
T PRK05602 146 SNIEAAAVMDISVDAL 161 (186)
T ss_pred CHHHHHHHhCcCHHHH
Confidence 4567888899887665
No 104
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=35.10 E-value=43 Score=18.43 Aligned_cols=16 Identities=19% Similarity=0.133 Sum_probs=12.0
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|+++..|
T Consensus 130 s~~eIA~~lgis~~tV 145 (164)
T PRK12547 130 SYEDAAAICGCAVGTI 145 (164)
T ss_pred CHHHHHHHhCCCHHHH
Confidence 4567888888887655
No 105
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=34.80 E-value=9.1 Score=22.34 Aligned_cols=34 Identities=12% Similarity=0.104 Sum_probs=24.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 28 TFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
.+|+.+++.|...-+ +....++|..|++++..|+
T Consensus 137 ~LT~RE~eVL~lla~------G~snkeIA~~L~iS~~TVk 170 (207)
T PRK15411 137 SLSRTESSMLRMWMA------GQGTIQISDQMNIKAKTVS 170 (207)
T ss_pred cCCHHHHHHHHHHHc------CCCHHHHHHHcCCCHHHHH
Confidence 388888888754333 2246689999999987663
No 106
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=34.79 E-value=39 Score=19.14 Aligned_cols=16 Identities=13% Similarity=0.057 Sum_probs=11.6
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|+++..|
T Consensus 148 s~~EIA~~lgis~~tV 163 (185)
T PRK09649 148 SYADAAAVCGCPVGTI 163 (185)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 3467888888887655
No 107
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=34.03 E-value=69 Score=16.15 Aligned_cols=33 Identities=15% Similarity=0.213 Sum_probs=21.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcc
Q psy14727 28 TFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEA 64 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~ 64 (67)
..|.+|+.+|-..+..|+. ....+-.+||++..
T Consensus 12 nvsd~qi~elFq~lT~NPl----~AMa~i~qLGip~e 44 (82)
T PF11212_consen 12 NVSDEQINELFQALTQNPL----AAMATIQQLGIPQE 44 (82)
T ss_pred CCCHHHHHHHHHHHhhCHH----HHHHHHHHcCCCHH
Confidence 4688888888877777763 23344566676654
No 108
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=33.70 E-value=48 Score=18.07 Aligned_cols=16 Identities=19% Similarity=0.316 Sum_probs=11.4
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 131 s~~EIA~~l~is~~tV 146 (161)
T PRK12528 131 GYGEIATELGISLATV 146 (161)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4557788888887655
No 109
>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=33.50 E-value=35 Score=12.61 Aligned_cols=32 Identities=19% Similarity=0.324 Sum_probs=19.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccc
Q psy14727 29 FTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEAR 65 (67)
Q Consensus 29 ~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~q 65 (67)
++..+...+...+... + ....+|..++++...
T Consensus 6 ~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~t 37 (42)
T cd00569 6 LTPEQIEEARRLLAAG-E----SVAEIARRLGVSRST 37 (42)
T ss_pred CCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHH
Confidence 5566666665555432 2 345778888887643
No 110
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=33.43 E-value=43 Score=19.09 Aligned_cols=16 Identities=25% Similarity=0.530 Sum_probs=12.6
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
..+++|..+|+++..|
T Consensus 153 s~~EIA~~lgiS~~tV 168 (185)
T PF07638_consen 153 SVEEIAERLGISERTV 168 (185)
T ss_pred CHHHHHHHHCcCHHHH
Confidence 5668889999988765
No 111
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=33.19 E-value=34 Score=19.05 Aligned_cols=17 Identities=24% Similarity=0.425 Sum_probs=12.7
Q ss_pred HHHHHHHHHcCCCcccc
Q psy14727 50 FTREDLAMKINLTEARV 66 (67)
Q Consensus 50 ~~r~~La~~l~l~~~qV 66 (67)
..-.++|..+|++...|
T Consensus 136 ~s~~EIA~~lgis~~tV 152 (172)
T PRK09651 136 LTYSEIAHKLGVSVSSV 152 (172)
T ss_pred CCHHHHHHHhCCCHHHH
Confidence 35668899999887655
No 112
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=33.11 E-value=63 Score=18.10 Aligned_cols=16 Identities=31% Similarity=0.351 Sum_probs=12.2
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 155 s~~eIA~~lgis~~~v 170 (187)
T PRK12534 155 TYEELAARTDTPIGTV 170 (187)
T ss_pred CHHHHHHHhCCChhHH
Confidence 4567888999888665
No 113
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=33.09 E-value=29 Score=15.69 Aligned_cols=35 Identities=17% Similarity=0.240 Sum_probs=21.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccc
Q psy14727 29 FTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEAR 65 (67)
Q Consensus 29 ~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~q 65 (67)
++..|...|........- .....+||..++++...
T Consensus 3 lt~~q~~vL~~l~~~~~~--~~t~~~la~~l~~~~~~ 37 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGE--ELTQSELAERLGISKST 37 (62)
T ss_dssp STHHHHHHHHHHHHSTTS--GEEHHHHHHHHTS-HHH
T ss_pred cCHHHHHHHHHHHHCCCC--CcCHHHHHHHHCcCHHH
Confidence 567777777665554432 12455788888887643
No 114
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=32.86 E-value=49 Score=18.77 Aligned_cols=16 Identities=6% Similarity=0.177 Sum_probs=11.9
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 129 s~~EIA~~lgis~~tV 144 (182)
T PRK12511 129 SYQEAAAVLGIPIGTL 144 (182)
T ss_pred CHHHHHHHhCcCHHHH
Confidence 4567888888887655
No 115
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=32.23 E-value=51 Score=18.78 Aligned_cols=17 Identities=12% Similarity=0.073 Sum_probs=12.0
Q ss_pred HHHHHHHHcCCCccccC
Q psy14727 51 TREDLAMKINLTEARVQ 67 (67)
Q Consensus 51 ~r~~La~~l~l~~~qVk 67 (67)
.-.++|..||+++..|+
T Consensus 134 s~~EIA~~Lgis~~tVk 150 (187)
T PRK12516 134 AYEEAAEICGCAVGTIK 150 (187)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 34578888888876553
No 116
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=31.91 E-value=52 Score=18.39 Aligned_cols=16 Identities=19% Similarity=0.393 Sum_probs=11.6
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 135 s~~EIA~~lgis~~tV 150 (179)
T PRK12543 135 SQEEIAQLLQIPIGTV 150 (179)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4557888888887655
No 117
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=31.85 E-value=52 Score=17.97 Aligned_cols=16 Identities=13% Similarity=0.227 Sum_probs=12.3
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 143 ~~~eIA~~lgis~~tv 158 (179)
T PRK11924 143 SYREIAEILGVPVGTV 158 (179)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4568899999988665
No 118
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=31.83 E-value=35 Score=18.34 Aligned_cols=33 Identities=18% Similarity=0.210 Sum_probs=20.4
Q ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 33 QLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 33 q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
+-..|...|... +....-.+||..+.++++.++
T Consensus 5 ~y~~L~~~~~~~--~~~vtl~elA~~l~cS~Rn~r 37 (115)
T PF12793_consen 5 QYQRLWQHYGGQ--PVEVTLDELAELLFCSRRNAR 37 (115)
T ss_pred HHHHHHHHcCCC--CcceeHHHHHHHhCCCHHHHH
Confidence 344555555522 333455689999999987653
No 119
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=31.65 E-value=53 Score=18.68 Aligned_cols=16 Identities=25% Similarity=0.318 Sum_probs=11.6
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 152 s~~EIA~~lg~s~~tV 167 (192)
T PRK09643 152 SVADAARMLGVAEGTV 167 (192)
T ss_pred CHHHHHHHHCcCHHHH
Confidence 4557888888887655
No 120
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=31.63 E-value=22 Score=17.98 Aligned_cols=14 Identities=36% Similarity=0.655 Sum_probs=11.1
Q ss_pred HHHHHHcCCCcccc
Q psy14727 53 EDLAMKINLTEARV 66 (67)
Q Consensus 53 ~~La~~l~l~~~qV 66 (67)
..||..||+++..|
T Consensus 17 k~laR~LGlse~~I 30 (86)
T cd08306 17 RKLARKLGLSETKI 30 (86)
T ss_pred HHHHHHcCCCHHHH
Confidence 46899999998654
No 121
>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=31.13 E-value=67 Score=16.62 Aligned_cols=33 Identities=12% Similarity=0.219 Sum_probs=19.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 29 FTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 29 ~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
+++.+...+...+- ....-.++|..+|+++..|
T Consensus 111 L~~~~~~ii~~~~~-----~g~s~~eIA~~l~~s~~~v 143 (158)
T TIGR02937 111 LPEREREVLVLRYL-----EGLSYKEIAEILGISVGTV 143 (158)
T ss_pred CCHHHHHHHhhHHh-----cCCCHHHHHHHHCCCHHHH
Confidence 34555555443322 2224558899999987654
No 122
>PRK15183 Vi polysaccharide biosynthesis protein TviA; Provisional
Probab=30.93 E-value=63 Score=17.60 Aligned_cols=37 Identities=24% Similarity=0.319 Sum_probs=25.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcc
Q psy14727 28 TFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEA 64 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~ 64 (67)
.++..-..+|...|-..+---..-|.+||.+.|+.+.
T Consensus 95 flsesgmeelqdrfmns~st~yrwrke~a~kfgvr~p 131 (143)
T PRK15183 95 FLSESGMEELQDRFMNSSSTMYRWRKELAVKFGVREP 131 (143)
T ss_pred hhhhccHHHHHHHHccChHHHHHHHHHHHHHhcCCCC
Confidence 3556666778888876654444457899999998653
No 123
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=30.72 E-value=57 Score=18.75 Aligned_cols=17 Identities=18% Similarity=0.376 Sum_probs=12.7
Q ss_pred HHHHHHHHcCCCccccC
Q psy14727 51 TREDLAMKINLTEARVQ 67 (67)
Q Consensus 51 ~r~~La~~l~l~~~qVk 67 (67)
.-.++|..+|++...|+
T Consensus 157 s~~EIA~~lgis~~tVk 173 (201)
T PRK12545 157 EIDDICTELTLTANHCS 173 (201)
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 45688999999886653
No 124
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=30.64 E-value=59 Score=18.02 Aligned_cols=16 Identities=19% Similarity=0.457 Sum_probs=11.8
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 137 s~~EIA~~lgis~~tV 152 (172)
T PRK12523 137 GHAEIAERLGVSVSRV 152 (172)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4567888888887655
No 125
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=30.57 E-value=54 Score=18.66 Aligned_cols=16 Identities=13% Similarity=0.241 Sum_probs=11.7
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 154 s~~eIA~~lgis~~tV 169 (196)
T PRK12524 154 SNPEIAEVMEIGVEAV 169 (196)
T ss_pred CHHHHHHHHCcCHHHH
Confidence 3557888888887655
No 126
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=30.51 E-value=59 Score=18.25 Aligned_cols=16 Identities=19% Similarity=0.333 Sum_probs=11.9
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 149 s~~eIA~~lgis~~tV 164 (184)
T PRK12539 149 SVAEAATRSGMSESAV 164 (184)
T ss_pred cHHHHHHHHCcCHHHH
Confidence 4567888888887655
No 127
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=30.29 E-value=73 Score=15.27 Aligned_cols=32 Identities=31% Similarity=0.406 Sum_probs=19.1
Q ss_pred CCHHHHHHHHH---HHhhcCCCCHHHHHHHHHHcCCC
Q psy14727 29 FTLQQLEELET---AFAQTHYPDVFTREDLAMKINLT 62 (67)
Q Consensus 29 ~s~~q~~~Le~---~F~~~~yp~~~~r~~La~~l~l~ 62 (67)
+|..|...|+- ....+.||. ...+||..+|+.
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~P--t~rEIa~~~g~~ 38 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPP--TVREIAEALGLK 38 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSS
T ss_pred CCHHHHHHHHHHHHHHHHcCCCC--CHHHHHHHhCCC
Confidence 45666665554 355677874 455899999987
No 128
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=30.25 E-value=60 Score=17.64 Aligned_cols=16 Identities=13% Similarity=0.391 Sum_probs=11.1
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
...++|..+|++...|
T Consensus 123 s~~eIA~~lgis~~tv 138 (159)
T PRK12527 123 SHQQIAEHLGISRSLV 138 (159)
T ss_pred CHHHHHHHhCCCHHHH
Confidence 4567788888877544
No 129
>PRK00118 putative DNA-binding protein; Validated
Probab=30.22 E-value=65 Score=17.13 Aligned_cols=33 Identities=18% Similarity=0.245 Sum_probs=20.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 29 FTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 29 ~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
.+..|...+...|.... .-.++|..+|++...|
T Consensus 18 L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV 50 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAV 50 (104)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHH
Confidence 35556666655444332 4567899999987654
No 130
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=30.19 E-value=1.1e+02 Score=17.49 Aligned_cols=34 Identities=26% Similarity=0.351 Sum_probs=23.0
Q ss_pred CCHHHHHHHHHHH---hhcCCCCHHHHHHHHHHcCCC-cc
Q psy14727 29 FTLQQLEELETAF---AQTHYPDVFTREDLAMKINLT-EA 64 (67)
Q Consensus 29 ~s~~q~~~Le~~F---~~~~yp~~~~r~~La~~l~l~-~~ 64 (67)
.|..|...|+... ..+.++.. -.+||..+|++ ..
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~--~~ela~~~~~~s~~ 41 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPS--IREIARAVGLRSPS 41 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCc--HHHHHHHhCCCChH
Confidence 4677777776665 44566533 45899999998 43
No 131
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=30.17 E-value=54 Score=18.40 Aligned_cols=16 Identities=31% Similarity=0.497 Sum_probs=11.7
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 140 s~~EIA~~lgis~~tV 155 (185)
T PRK12542 140 TYQEISSVMGITEANV 155 (185)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 3457888888887655
No 132
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=30.08 E-value=54 Score=18.57 Aligned_cols=16 Identities=0% Similarity=0.225 Sum_probs=12.4
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 154 s~~EIA~~lgis~~tV 169 (195)
T PRK12532 154 SSDEIQQMCGISTSNY 169 (195)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4568899999988665
No 133
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=30.05 E-value=58 Score=18.23 Aligned_cols=16 Identities=25% Similarity=0.272 Sum_probs=12.0
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 147 s~~EIA~~l~is~~tV 162 (181)
T PRK12536 147 SVAETAQLTGLSESAV 162 (181)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4567888888887655
No 134
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=29.94 E-value=51 Score=19.23 Aligned_cols=39 Identities=21% Similarity=0.250 Sum_probs=24.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 28 TFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
.+|+.++..+......+ +-....-.++|..+++++..|+
T Consensus 158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~ 196 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCR 196 (239)
T ss_pred CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHH
Confidence 36666666554444322 3334456789999999987764
No 135
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=29.74 E-value=64 Score=18.34 Aligned_cols=16 Identities=13% Similarity=0.233 Sum_probs=11.9
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 159 s~~EIA~~lgis~~tV 174 (194)
T PRK12531 159 PHQQVAEMFDIPLGTV 174 (194)
T ss_pred CHHHHHHHhCcCHHHH
Confidence 4567888888887655
No 136
>PF12200 DUF3597: Domain of unknown function (DUF3597); InterPro: IPR022016 This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 126 and 281 amino acids in length. The function of this domain is unknown. The structure of this domain has been found to contain five helices with a long flexible loop between helices one and two. ; PDB: 2GQB_A.
Probab=29.70 E-value=51 Score=18.35 Aligned_cols=17 Identities=24% Similarity=0.407 Sum_probs=11.7
Q ss_pred CCHHHHHHHHHHcCCCc
Q psy14727 47 PDVFTREDLAMKINLTE 63 (67)
Q Consensus 47 p~~~~r~~La~~l~l~~ 63 (67)
.+...|.+||..||++.
T Consensus 83 SSl~aRkeLA~eL~~~~ 99 (127)
T PF12200_consen 83 SSLAARKELAKELGYTG 99 (127)
T ss_dssp -SHHHHHHHHHHHT---
T ss_pred CCHHHHHHHHHHhCCCC
Confidence 56789999999999864
No 137
>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=29.58 E-value=60 Score=18.42 Aligned_cols=16 Identities=0% Similarity=0.374 Sum_probs=12.1
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 149 s~~EIA~~lgis~~tv 164 (188)
T TIGR02943 149 ESDEICQELEISTSNC 164 (188)
T ss_pred CHHHHHHHhCCCHHHH
Confidence 4568899999887654
No 138
>PF14174 YycC: YycC-like protein
Probab=29.54 E-value=45 Score=15.56 Aligned_cols=18 Identities=17% Similarity=0.113 Sum_probs=12.7
Q ss_pred CHHHHHHHHHHcCCCccc
Q psy14727 48 DVFTREDLAMKINLTEAR 65 (67)
Q Consensus 48 ~~~~r~~La~~l~l~~~q 65 (67)
+..+...||..||++-.+
T Consensus 7 S~eTA~kLs~~L~vPlE~ 24 (53)
T PF14174_consen 7 SPETAVKLSKKLGVPLEQ 24 (53)
T ss_pred CHHHHHHHHHHHCCcHHH
Confidence 445666789999887644
No 139
>PF07954 DUF1689: Protein of unknown function (DUF1689) ; InterPro: IPR012470 Family of fungal proteins with unknown function. A member of this family has been found to localise in the mitochondria [].
Probab=29.53 E-value=98 Score=17.71 Aligned_cols=23 Identities=17% Similarity=0.117 Sum_probs=19.0
Q ss_pred HHHHHhhcCCCCHHHHHHHHHHc
Q psy14727 37 LETAFAQTHYPDVFTREDLAMKI 59 (67)
Q Consensus 37 Le~~F~~~~yp~~~~r~~La~~l 59 (67)
.-+.++.++.++..+|.+|+..+
T Consensus 4 av~FYEaD~~L~~~DR~eL~~~~ 26 (152)
T PF07954_consen 4 AVEFYEADQKLDHEDRLELAKDL 26 (152)
T ss_pred HHHHHHhhccCCHHHHHHHHHHH
Confidence 34567889999999999999876
No 140
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=29.17 E-value=68 Score=18.46 Aligned_cols=38 Identities=21% Similarity=0.225 Sum_probs=25.4
Q ss_pred CCCCCCHHHHHHHHHHHhh-----cCCCCHHHHHHHHHHcCCC
Q psy14727 25 NRTTFTLQQLEELETAFAQ-----THYPDVFTREDLAMKINLT 62 (67)
Q Consensus 25 ~Rt~~s~~q~~~Le~~F~~-----~~yp~~~~r~~La~~l~l~ 62 (67)
..+.|+..|++.|..+|.. .-+.+..+-..+-+.+|..
T Consensus 10 ~~~~~t~~qi~~lkeaF~l~D~d~~G~I~~~el~~ilr~lg~~ 52 (160)
T COG5126 10 TFTQLTEEQIQELKEAFQLFDRDSDGLIDRNELGKILRSLGFN 52 (160)
T ss_pred hcccCCHHHHHHHHHHHHHhCcCCCCCCcHHHHHHHHHHcCCC
Confidence 5678999999999999863 3345555544444455543
No 141
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=28.97 E-value=68 Score=18.12 Aligned_cols=16 Identities=31% Similarity=0.515 Sum_probs=11.7
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
...++|..+|++...|
T Consensus 149 s~~EIAe~lgis~~~V 164 (189)
T PRK06811 149 KIEEIAKKLGLTRSAI 164 (189)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4567888888887655
No 142
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=28.79 E-value=63 Score=18.26 Aligned_cols=16 Identities=19% Similarity=0.405 Sum_probs=11.4
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 124 ~~~EIA~~lgis~~tV 139 (181)
T PRK09637 124 SQKEIAEKLGLSLSGA 139 (181)
T ss_pred CHHHHHHHhCCCHHHH
Confidence 4557888888887655
No 143
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=28.75 E-value=74 Score=18.65 Aligned_cols=33 Identities=9% Similarity=0.180 Sum_probs=20.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 29 FTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 29 ~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
++..+...+...|.. ...-.++|..+|++...|
T Consensus 184 L~~~e~~i~~~~~~~-----~~t~~eIA~~lgis~~~V 216 (231)
T TIGR02885 184 LDERERQIIMLRYFK-----DKTQTEVANMLGISQVQV 216 (231)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHH
Confidence 455555555544432 235678899999988655
No 144
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=28.57 E-value=1e+02 Score=20.55 Aligned_cols=33 Identities=21% Similarity=0.158 Sum_probs=24.3
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 34 LEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 34 ~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
+..|...=....|++......+|..|+|+..+|
T Consensus 40 IplL~~~Qe~~GyIp~~ai~~VAe~Lgvp~~~V 72 (400)
T PRK12373 40 IPLLMRAQEQEGWVTRAAIEKVADMLDMAYIRV 72 (400)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHH
Confidence 344444444556899999999999999997655
No 145
>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=28.47 E-value=41 Score=18.77 Aligned_cols=17 Identities=24% Similarity=0.325 Sum_probs=12.7
Q ss_pred HHHHHHHHHcCCCcccc
Q psy14727 50 FTREDLAMKINLTEARV 66 (67)
Q Consensus 50 ~~r~~La~~l~l~~~qV 66 (67)
..-.++|..+|++...|
T Consensus 155 ~s~~EIA~~lgis~~tv 171 (190)
T TIGR02939 155 LSYEDIARIMDCPVGTV 171 (190)
T ss_pred CCHHHHHHHHCcCHHHH
Confidence 34568899999987665
No 146
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=28.43 E-value=67 Score=17.75 Aligned_cols=16 Identities=13% Similarity=0.378 Sum_probs=11.8
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 136 s~~EIA~~l~is~~tV 151 (168)
T PRK12525 136 TYVEIGERLGVSLSRI 151 (168)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4567888888887655
No 147
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=28.25 E-value=21 Score=18.81 Aligned_cols=16 Identities=31% Similarity=0.466 Sum_probs=10.8
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
...+||.+.||++.+|
T Consensus 74 n~~eLA~kyglS~r~I 89 (108)
T PF08765_consen 74 NVRELARKYGLSERQI 89 (108)
T ss_dssp -HHHHHHHHT--HHHH
T ss_pred CHHHHHHHHCcCHHHH
Confidence 4568999999998765
No 148
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=27.76 E-value=66 Score=18.14 Aligned_cols=16 Identities=13% Similarity=0.403 Sum_probs=12.2
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 149 s~~EIA~~lgis~~tV 164 (191)
T PRK12520 149 ETEEICQELQITATNA 164 (191)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4568899999988665
No 149
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=27.60 E-value=57 Score=18.63 Aligned_cols=16 Identities=19% Similarity=0.154 Sum_probs=12.1
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 131 s~~EIA~~LgiS~~tV 146 (188)
T PRK12546 131 SYEEAAEMCGVAVGTV 146 (188)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4567888899887655
No 150
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=27.56 E-value=73 Score=14.43 Aligned_cols=27 Identities=19% Similarity=0.223 Sum_probs=14.2
Q ss_pred HHHhhc-CCCCHHHHHHHHHHcCCCccc
Q psy14727 39 TAFAQT-HYPDVFTREDLAMKINLTEAR 65 (67)
Q Consensus 39 ~~F~~~-~yp~~~~r~~La~~l~l~~~q 65 (67)
+.+... ..++...-..||..|+++...
T Consensus 29 ~~~~~~~~~~~~~~l~~ia~~l~~~~~e 56 (63)
T PF13443_consen 29 RILNGKPSNPSLDTLEKIAKALNCSPEE 56 (63)
T ss_dssp HHHTTT-----HHHHHHHHHHHT--HHH
T ss_pred HHHhcccccccHHHHHHHHHHcCCCHHH
Confidence 334433 467777888889988887643
No 151
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=27.54 E-value=1.1e+02 Score=16.32 Aligned_cols=37 Identities=14% Similarity=0.033 Sum_probs=20.6
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 26 RTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 26 Rt~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
|..||.+.....-.....+.+ ...++|..+|++...|
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl 46 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQL 46 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHH
Confidence 445777765543332222322 3457788898876543
No 152
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=27.50 E-value=62 Score=17.74 Aligned_cols=16 Identities=25% Similarity=0.206 Sum_probs=10.5
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
...++|..+|++...|
T Consensus 126 s~~eIA~~lgis~~tv 141 (165)
T PRK09644 126 TYEEAASVLDLKLNTY 141 (165)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4557777777776544
No 153
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=27.46 E-value=49 Score=19.73 Aligned_cols=16 Identities=25% Similarity=0.302 Sum_probs=11.9
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 189 s~~EIA~~Lgis~~tV 204 (233)
T PRK12538 189 SNGEIAEVMDTTVAAV 204 (233)
T ss_pred CHHHHHHHHCcCHHHH
Confidence 4567888888887655
No 154
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=27.45 E-value=66 Score=19.26 Aligned_cols=33 Identities=6% Similarity=0.302 Sum_probs=20.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 29 FTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 29 ~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
+++.+...+...|-. ...-.++|..+|++...|
T Consensus 206 L~~~~r~vl~l~~~~-----g~s~~eIA~~l~is~~tV 238 (257)
T PRK08583 206 LSDREKSIIQCTFIE-----NLSQKETGERLGISQMHV 238 (257)
T ss_pred CCHHHHHHHHHHHhC-----CCCHHHHHHHHCCCHHHH
Confidence 455555555544422 224568899999988765
No 155
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=27.41 E-value=23 Score=15.44 Aligned_cols=17 Identities=12% Similarity=0.462 Sum_probs=11.0
Q ss_pred HHHHHHHHHcCCCcccc
Q psy14727 50 FTREDLAMKINLTEARV 66 (67)
Q Consensus 50 ~~r~~La~~l~l~~~qV 66 (67)
....++|..+|++...|
T Consensus 18 ~s~~~ia~~lgvs~~Tv 34 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTV 34 (50)
T ss_dssp --HHHHHHHHTS-HHHH
T ss_pred CCHHHHHHHHCcCHHHH
Confidence 35668899999987654
No 156
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=27.29 E-value=82 Score=16.33 Aligned_cols=16 Identities=19% Similarity=0.399 Sum_probs=11.7
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.=..||..|||++..|
T Consensus 21 ~Wk~laR~LGLse~~I 36 (96)
T cd08315 21 SWNRLMRQLGLSENEI 36 (96)
T ss_pred HHHHHHHHcCCCHHHH
Confidence 3456899999988654
No 157
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=27.24 E-value=79 Score=17.64 Aligned_cols=16 Identities=19% Similarity=0.229 Sum_probs=11.7
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 153 s~~eIA~~lgis~~~V 168 (186)
T PRK13919 153 THREAAQLLGLPLGTL 168 (186)
T ss_pred CHHHHHHHHCcCHHHH
Confidence 4457888888887665
No 158
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=26.99 E-value=59 Score=18.07 Aligned_cols=17 Identities=12% Similarity=0.313 Sum_probs=12.6
Q ss_pred HHHHHHHHHcCCCcccc
Q psy14727 50 FTREDLAMKINLTEARV 66 (67)
Q Consensus 50 ~~r~~La~~l~l~~~qV 66 (67)
..-.++|..+|+++..|
T Consensus 153 ~s~~eIA~~lgis~~~v 169 (187)
T TIGR02948 153 LSLKEISEILDLPVGTV 169 (187)
T ss_pred CCHHHHHHHHCCCHHHH
Confidence 34568899999987655
No 159
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=26.78 E-value=66 Score=19.33 Aligned_cols=34 Identities=24% Similarity=0.257 Sum_probs=22.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 28 TFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
.++..+...+...|..+ ..-.++|..+|++...|
T Consensus 209 ~L~~~er~vi~~~~~~~-----~t~~eIA~~lgis~~~V 242 (258)
T PRK08215 209 KLNDREKLILNLRFFQG-----KTQMEVAEEIGISQAQV 242 (258)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHH
Confidence 45666666666665322 24568999999988665
No 160
>PF13309 HTH_22: HTH domain
Probab=26.68 E-value=85 Score=14.89 Aligned_cols=37 Identities=14% Similarity=0.170 Sum_probs=22.3
Q ss_pred CCHHHHHH-HHHHHhhcCCCCHHHHHHHHHHcCCCccc
Q psy14727 29 FTLQQLEE-LETAFAQTHYPDVFTREDLAMKINLTEAR 65 (67)
Q Consensus 29 ~s~~q~~~-Le~~F~~~~yp~~~~r~~La~~l~l~~~q 65 (67)
.+..+... ....++..-|.-...-..+|..||++...
T Consensus 21 l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~T 58 (64)
T PF13309_consen 21 LSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRAT 58 (64)
T ss_pred CCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHH
Confidence 34444433 34445555555555667889999998754
No 161
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=26.55 E-value=70 Score=18.11 Aligned_cols=16 Identities=19% Similarity=0.133 Sum_probs=11.7
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 129 s~~EIA~~Lgis~~tV 144 (182)
T PRK12540 129 SYEDAAAICGCAVGTI 144 (182)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4567888888887655
No 162
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=26.16 E-value=32 Score=17.47 Aligned_cols=14 Identities=14% Similarity=0.529 Sum_probs=11.1
Q ss_pred HHHHHHcCCCcccc
Q psy14727 53 EDLAMKINLTEARV 66 (67)
Q Consensus 53 ~~La~~l~l~~~qV 66 (67)
+.||..||+++..|
T Consensus 17 ~~Lar~Lgls~~~I 30 (83)
T cd08319 17 EQVLLDLGLSQTDI 30 (83)
T ss_pred HHHHHHcCCCHHHH
Confidence 46899999998654
No 163
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=26.11 E-value=54 Score=18.48 Aligned_cols=17 Identities=12% Similarity=0.421 Sum_probs=12.3
Q ss_pred HHHHHHHHHcCCCcccc
Q psy14727 50 FTREDLAMKINLTEARV 66 (67)
Q Consensus 50 ~~r~~La~~l~l~~~qV 66 (67)
..-.++|..+|++...|
T Consensus 158 ~s~~EIA~~lgis~~tV 174 (194)
T PRK12519 158 LSQSEIAKRLGIPLGTV 174 (194)
T ss_pred CCHHHHHHHhCCCHHHH
Confidence 34567888888887655
No 164
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=26.08 E-value=32 Score=17.37 Aligned_cols=32 Identities=13% Similarity=0.277 Sum_probs=20.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 28 TFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
+.|.+|+..+-..... .=..||..||+++..|
T Consensus 4 ~~t~~~l~~ia~~iG~-------~Wk~Lar~LGls~~dI 35 (86)
T cd08318 4 PVTGEQITVFANKLGE-------DWKTLAPHLEMKDKEI 35 (86)
T ss_pred CCCHHHHHHHHHHHhh-------hHHHHHHHcCCCHHHH
Confidence 3577777776532221 2246999999997654
No 165
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=25.80 E-value=91 Score=17.75 Aligned_cols=34 Identities=18% Similarity=0.203 Sum_probs=23.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 28 TFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
.+|+-+.+.|.....- ..-.++|..+++++..|+
T Consensus 150 ~Lt~rE~evl~~~~~G------~s~~eIA~~l~iS~~TV~ 183 (216)
T PRK10840 150 RLSPKESEVLRLFAEG------FLVTEIAKKLNRSIKTIS 183 (216)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHHCCCHHHHH
Confidence 4788888887665432 245688899988887653
No 166
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=25.45 E-value=64 Score=15.00 Aligned_cols=11 Identities=9% Similarity=0.271 Sum_probs=6.6
Q ss_pred HHHHHcCCCcc
Q psy14727 54 DLAMKINLTEA 64 (67)
Q Consensus 54 ~La~~l~l~~~ 64 (67)
+.|..||+...
T Consensus 20 eAA~~Lgv~~T 30 (52)
T PF02042_consen 20 EAAKELGVSVT 30 (52)
T ss_pred HHHHHhCCCHH
Confidence 44667776653
No 167
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=25.38 E-value=62 Score=19.08 Aligned_cols=16 Identities=13% Similarity=0.216 Sum_probs=12.3
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|+++..|
T Consensus 152 s~~EIAe~LgiS~~tV 167 (216)
T PRK12533 152 SYREIAAIADVPVGTV 167 (216)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4568899999988665
No 168
>PRK15372 pathogenicity island 2 effector protein SseI; Provisional
Probab=25.35 E-value=59 Score=20.40 Aligned_cols=30 Identities=33% Similarity=0.413 Sum_probs=23.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHH
Q psy14727 29 FTLQQLEELETAFAQTHYPDVFTREDLAMK 58 (67)
Q Consensus 29 ~s~~q~~~Le~~F~~~~yp~~~~r~~La~~ 58 (67)
++..|-.+|+..|..++.|....+++++..
T Consensus 12 csTHq~EAl~CI~~LcHP~~gtTpe~I~s~ 41 (292)
T PRK15372 12 CSTHQTEALECIWTICHPPAGTTREDVVSR 41 (292)
T ss_pred ccccHHHHHHHHHHHhCCCCCCCHHHHHHH
Confidence 567788999999999999877777766544
No 169
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=25.25 E-value=72 Score=13.57 Aligned_cols=32 Identities=22% Similarity=0.334 Sum_probs=19.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 29 FTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 29 ~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
++..+...+...+. . ....++|..+|++...|
T Consensus 4 l~~~e~~i~~~~~~-g-----~s~~eia~~l~is~~tv 35 (58)
T smart00421 4 LTPREREVLRLLAE-G-----LTNKEIAERLGISEKTV 35 (58)
T ss_pred CCHHHHHHHHHHHc-C-----CCHHHHHHHHCCCHHHH
Confidence 56667666654322 2 14467889999887654
No 170
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=25.22 E-value=1e+02 Score=16.17 Aligned_cols=39 Identities=15% Similarity=0.230 Sum_probs=22.2
Q ss_pred CCCHHHHHHHHHHHhhcCCC--CHHHHHHHHHHcCCCcccc
Q psy14727 28 TFTLQQLEELETAFAQTHYP--DVFTREDLAMKINLTEARV 66 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp--~~~~r~~La~~l~l~~~qV 66 (67)
.+|+..+..+...+..-.-+ ......++|..+|++.+.|
T Consensus 32 lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atI 72 (94)
T TIGR01321 32 ILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATI 72 (94)
T ss_pred hCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhh
Confidence 35666666666665543311 1123457888888876544
No 171
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=25.19 E-value=77 Score=18.48 Aligned_cols=34 Identities=15% Similarity=0.231 Sum_probs=21.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 28 TFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
.+++.+...+...|.. ...-.++|..+|++...|
T Consensus 178 ~L~~~~r~vl~l~y~~-----~~s~~eIA~~lgis~~~v 211 (227)
T TIGR02980 178 ALPERERRILLLRFFE-----DKTQSEIAERLGISQMHV 211 (227)
T ss_pred cCCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHH
Confidence 3555555555554432 224568899999987655
No 172
>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=25.07 E-value=24 Score=15.15 Aligned_cols=13 Identities=15% Similarity=0.215 Sum_probs=7.9
Q ss_pred HHHHHHcCCCccc
Q psy14727 53 EDLAMKINLTEAR 65 (67)
Q Consensus 53 ~~La~~l~l~~~q 65 (67)
.++|..+|++...
T Consensus 4 ~e~a~~~gv~~~t 16 (49)
T cd04761 4 GELAKLTGVSPST 16 (49)
T ss_pred HHHHHHHCcCHHH
Confidence 3566677766544
No 173
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=24.91 E-value=77 Score=18.20 Aligned_cols=16 Identities=19% Similarity=0.193 Sum_probs=11.3
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 151 s~~EIAe~lgis~~tV 166 (196)
T PRK12535 151 TYEEAAKIADVRVGTI 166 (196)
T ss_pred CHHHHHHHhCCCHHHH
Confidence 4557888888887655
No 174
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=24.48 E-value=31 Score=20.22 Aligned_cols=34 Identities=26% Similarity=0.376 Sum_probs=23.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 28 TFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
.+|+.+...|...-+ +..-.++|.+|++++..||
T Consensus 148 ~LT~RE~eVL~lla~------G~snkeIA~~L~iS~~TVk 181 (211)
T COG2197 148 LLTPRELEVLRLLAE------GLSNKEIAEELNLSEKTVK 181 (211)
T ss_pred CCCHHHHHHHHHHHC------CCCHHHHHHHHCCCHhHHH
Confidence 578888887754322 1245689999999998774
No 175
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=24.39 E-value=53 Score=17.13 Aligned_cols=16 Identities=13% Similarity=0.339 Sum_probs=13.0
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
....+|..+|+++.+|
T Consensus 25 gq~~vA~~~Gv~eStI 40 (91)
T PF05269_consen 25 GQKKVAEAMGVDESTI 40 (91)
T ss_dssp HHHHHHHHHTSSTTTH
T ss_pred hhHHHHHHhCCCHHHH
Confidence 4457899999999876
No 176
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=24.27 E-value=92 Score=17.21 Aligned_cols=16 Identities=13% Similarity=0.291 Sum_probs=12.0
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 137 s~~EIA~~lgis~~tV 152 (173)
T PRK12522 137 SYKEMSEILNIPIGTV 152 (173)
T ss_pred CHHHHHHHhCCCHHHH
Confidence 4567888899887655
No 177
>PF13518 HTH_28: Helix-turn-helix domain
Probab=24.22 E-value=39 Score=14.62 Aligned_cols=16 Identities=13% Similarity=0.370 Sum_probs=11.6
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
...++|..+|++..+|
T Consensus 14 s~~~~a~~~gis~~tv 29 (52)
T PF13518_consen 14 SVREIAREFGISRSTV 29 (52)
T ss_pred CHHHHHHHHCCCHhHH
Confidence 3456899999887654
No 178
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=24.08 E-value=66 Score=20.35 Aligned_cols=39 Identities=33% Similarity=0.313 Sum_probs=25.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 28 TFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
.+++.+...+...|... |.....-.+||..+|++...|+
T Consensus 262 ~L~~~~R~vl~lrygL~-~~e~~s~~EIA~~Lgis~~tV~ 300 (325)
T PRK05657 262 ELNDKQREVLARRFGLL-GYEAATLEDVAREIGLTRERVR 300 (325)
T ss_pred cCCHHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHH
Confidence 46667777777666322 2233455789999999987653
No 179
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=23.93 E-value=84 Score=18.36 Aligned_cols=33 Identities=18% Similarity=0.296 Sum_probs=20.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 29 FTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 29 ~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
+++.+...+...|... ..-.++|..+|++...|
T Consensus 176 L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV 208 (224)
T TIGR02479 176 LSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRV 208 (224)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHH
Confidence 4555555555544322 24568899999887655
No 180
>PRK06930 positive control sigma-like factor; Validated
Probab=23.87 E-value=85 Score=17.98 Aligned_cols=34 Identities=15% Similarity=0.144 Sum_probs=19.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 28 TFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
.+++.+...+...|..+ ..-.++|..+|++...|
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tV 147 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTV 147 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHH
Confidence 34555555555433222 24567888888887655
No 181
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=23.64 E-value=88 Score=17.36 Aligned_cols=17 Identities=18% Similarity=0.370 Sum_probs=12.2
Q ss_pred HHHHHHHHHcCCCcccc
Q psy14727 50 FTREDLAMKINLTEARV 66 (67)
Q Consensus 50 ~~r~~La~~l~l~~~qV 66 (67)
..-.++|..+|++...|
T Consensus 157 ~s~~eIA~~lgis~~~v 173 (189)
T TIGR02984 157 LSFAEVAERMDRSEGAV 173 (189)
T ss_pred CCHHHHHHHHCcCHHHH
Confidence 34567888888887655
No 182
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=23.60 E-value=1e+02 Score=18.09 Aligned_cols=33 Identities=9% Similarity=0.032 Sum_probs=23.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 28 TFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
.+|+-+.+.|+..-+-. .-.++|..|++++..|
T Consensus 134 ~LT~RE~eVL~ll~~G~------snkeIA~~L~iS~~TV 166 (207)
T PRK11475 134 MLSPTEREILRFMSRGY------SMPQIAEQLERNIKTI 166 (207)
T ss_pred CCCHHHHHHHHHHHCCC------CHHHHHHHHCCCHHHH
Confidence 47888888776554422 4567888888888665
No 183
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=23.14 E-value=1.2e+02 Score=15.73 Aligned_cols=38 Identities=13% Similarity=0.113 Sum_probs=23.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccc
Q psy14727 28 TFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEAR 65 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~q 65 (67)
-++..|...|................+||..++++...
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~st 59 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSA 59 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHH
Confidence 46788888886655211112233456788888887643
No 184
>PTZ00183 centrin; Provisional
Probab=23.07 E-value=1.3e+02 Score=15.92 Aligned_cols=41 Identities=22% Similarity=0.208 Sum_probs=27.2
Q ss_pred ccCCCCCCCCHHHHHHHHHHHhh-----cCCCCHHHHHHHHHHcCC
Q psy14727 21 KQRRNRTTFTLQQLEELETAFAQ-----THYPDVFTREDLAMKINL 61 (67)
Q Consensus 21 ~~rr~Rt~~s~~q~~~Le~~F~~-----~~yp~~~~r~~La~~l~l 61 (67)
+++-.+..++..+...++..|.. +.+.+..+-..+...+|+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~g~ 48 (158)
T PTZ00183 3 KRRSERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGF 48 (158)
T ss_pred ccccccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHhCC
Confidence 44556788999999999998864 334555555554555553
No 185
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=22.91 E-value=30 Score=15.65 Aligned_cols=13 Identities=15% Similarity=0.371 Sum_probs=8.8
Q ss_pred HHHHHHcCCCccc
Q psy14727 53 EDLAMKINLTEAR 65 (67)
Q Consensus 53 ~~La~~l~l~~~q 65 (67)
.+||..+|++...
T Consensus 7 ~elAk~l~v~~~~ 19 (54)
T PF04760_consen 7 SELAKELGVPSKE 19 (54)
T ss_dssp THHHHHHSSSHHH
T ss_pred HHHHHHHCcCHHH
Confidence 3678888877643
No 186
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=22.89 E-value=42 Score=17.00 Aligned_cols=14 Identities=7% Similarity=0.375 Sum_probs=11.1
Q ss_pred HHHHHHcCCCcccc
Q psy14727 53 EDLAMKINLTEARV 66 (67)
Q Consensus 53 ~~La~~l~l~~~qV 66 (67)
..||..||+++..|
T Consensus 17 k~lar~LGlse~~I 30 (86)
T cd08779 17 QAIGLHLGLSYREL 30 (86)
T ss_pred HHHHHHcCCCHHHH
Confidence 47899999988654
No 187
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=22.84 E-value=89 Score=18.53 Aligned_cols=38 Identities=21% Similarity=0.270 Sum_probs=22.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 28 TFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
.+++.+...|...|....+ ....-.++|..+|++...|
T Consensus 176 ~L~~~er~vl~l~ygl~~~-~~~t~~EIA~~lgis~~~V 213 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDG-RPHTLEEVGKEFNVTRERI 213 (238)
T ss_pred hCCHHHHHHHHHHhCCCCC-CCccHHHHHHHHCCCHHHH
Confidence 3455566666665532221 2224568899999988665
No 188
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=22.75 E-value=22 Score=16.74 Aligned_cols=31 Identities=10% Similarity=0.238 Sum_probs=15.6
Q ss_pred HHHHHHHhhcCCCCHHHHHHHHHHcCCCccc
Q psy14727 35 EELETAFAQTHYPDVFTREDLAMKINLTEAR 65 (67)
Q Consensus 35 ~~Le~~F~~~~yp~~~~r~~La~~l~l~~~q 65 (67)
..|+..|....--.......||..|++++..
T Consensus 8 ~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~t 38 (60)
T PF01325_consen 8 DYLKAIYELSEEGGPVRTKDIAERLGVSPPT 38 (60)
T ss_dssp HHHHHHHHHHHCTSSBBHHHHHHHHTS-HHH
T ss_pred HHHHHHHHHHcCCCCccHHHHHHHHCCChHH
Confidence 3455555443211112345789998887653
No 189
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=22.62 E-value=99 Score=17.93 Aligned_cols=16 Identities=19% Similarity=0.347 Sum_probs=11.6
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 156 s~~EIA~~Lgis~~tV 171 (203)
T PRK09647 156 SYEEIAATLGVKLGTV 171 (203)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 3557888888887655
No 190
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=22.37 E-value=32 Score=16.46 Aligned_cols=14 Identities=29% Similarity=0.596 Sum_probs=10.1
Q ss_pred HHHHHHcCCCcccc
Q psy14727 53 EDLAMKINLTEARV 66 (67)
Q Consensus 53 ~~La~~l~l~~~qV 66 (67)
..||..||+++..|
T Consensus 14 ~~la~~Lgl~~~~I 27 (79)
T cd01670 14 KKLARKLGLSDGEI 27 (79)
T ss_pred HHHHHHhCCCHHHH
Confidence 36888888887554
No 191
>PRK00215 LexA repressor; Validated
Probab=22.32 E-value=77 Score=18.28 Aligned_cols=34 Identities=29% Similarity=0.432 Sum_probs=21.6
Q ss_pred CCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHcCC-Ccc
Q psy14727 29 FTLQQLEELETAFA---QTHYPDVFTREDLAMKINL-TEA 64 (67)
Q Consensus 29 ~s~~q~~~Le~~F~---~~~yp~~~~r~~La~~l~l-~~~ 64 (67)
.|..|...|+...+ .+.++. ...+||..+|+ +..
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~--s~~ela~~~~~~~~~ 39 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPP--SRREIADALGLRSPS 39 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCC--CHHHHHHHhCCCChH
Confidence 46778887776643 334332 34588999998 654
No 192
>PF12898 Stc1: Stc1 domain; InterPro: IPR024630 The domain contains 8 conserved cysteines that may bind to zinc. In S. pombe, proteins containing the domain act as protein linkers, which link the chromatin modifying CLRC complex to RNAi by tethering it to the RITS complex. This domain has a slightly different arrangement of its CxxC pairs from the LIM domain, hence it is not part of that family []. The tandem zinc-finger structure could mediate protein-protein interactions.
Probab=22.13 E-value=92 Score=15.72 Aligned_cols=23 Identities=22% Similarity=0.367 Sum_probs=17.1
Q ss_pred cCCCCCCCCHHHHHHHHHHHhhc
Q psy14727 22 QRRNRTTFTLQQLEELETAFAQT 44 (67)
Q Consensus 22 ~rr~Rt~~s~~q~~~Le~~F~~~ 44 (67)
..+.+..||..|+..+.......
T Consensus 7 ~~k~~~~FS~~Ql~~~~~~~~~~ 29 (84)
T PF12898_consen 7 KWKPLSAFSKNQLEKLRKQIRAN 29 (84)
T ss_pred eECChHHcCHHHHHHHHHHHhhc
Confidence 34577889999999987655444
No 193
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=22.09 E-value=81 Score=14.13 Aligned_cols=13 Identities=23% Similarity=0.524 Sum_probs=8.9
Q ss_pred HHHHHHcCCCccc
Q psy14727 53 EDLAMKINLTEAR 65 (67)
Q Consensus 53 ~~La~~l~l~~~q 65 (67)
..||..+|+++.+
T Consensus 46 ~~la~~~~i~~~~ 58 (59)
T PF10410_consen 46 RELAERLGISEDA 58 (59)
T ss_dssp HHHHHHCT-SSTT
T ss_pred HHHHHHhCcCccc
Confidence 4688888888764
No 194
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=21.98 E-value=79 Score=17.68 Aligned_cols=16 Identities=19% Similarity=0.275 Sum_probs=11.2
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 145 s~~EIA~~l~is~~tv 160 (179)
T PRK09415 145 SIKEIAEVTGVNENTV 160 (179)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 3457888888877554
No 195
>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=21.89 E-value=21 Score=19.25 Aligned_cols=20 Identities=30% Similarity=0.406 Sum_probs=13.8
Q ss_pred CCHHHHHHHHHHcCCCcccc
Q psy14727 47 PDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 47 p~~~~r~~La~~l~l~~~qV 66 (67)
.....-.++|..+|+++..|
T Consensus 119 ~~g~s~~eIA~~lgis~~tv 138 (154)
T TIGR02950 119 FKEFSYKEIAELLNLSLAKV 138 (154)
T ss_pred hccCcHHHHHHHHCCCHHHH
Confidence 34445668888888887655
No 196
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=21.84 E-value=97 Score=18.76 Aligned_cols=33 Identities=15% Similarity=0.289 Sum_probs=19.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 29 FTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 29 ~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
+++.+...+...|... ..-.++|..+|++...|
T Consensus 213 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV 245 (268)
T PRK06288 213 LPEREKKVLILYYYED-----LTLKEIGKVLGVTESRI 245 (268)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHH
Confidence 4455555555444322 24568899999887655
No 197
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=21.79 E-value=88 Score=18.46 Aligned_cols=16 Identities=19% Similarity=0.468 Sum_probs=12.5
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 202 s~~EIA~~lgis~~tV 217 (236)
T PRK06986 202 NLKEIGAVLGVSESRV 217 (236)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 5568899999988655
No 198
>PF06154 YagB_YeeU_YfjZ: YagB/YeeU/YfjZ family; InterPro: IPR009320 This family of proteins includes three proteins from Escherichia coli proteins YagB, YeeU and YfjZ. The function of these proteins is unknown. They are about 120 amino acids in length.; PDB: 2H28_A 2INW_B 2JN7_A 2EA9_A.
Probab=21.73 E-value=98 Score=16.55 Aligned_cols=17 Identities=29% Similarity=0.542 Sum_probs=11.6
Q ss_pred CCCCCHHHHHHHHHHHh
Q psy14727 26 RTTFTLQQLEELETAFA 42 (67)
Q Consensus 26 Rt~~s~~q~~~Le~~F~ 42 (67)
+-.|++.+...|+.+|-
T Consensus 36 ~G~Fs~~~~~~Ld~aFP 52 (103)
T PF06154_consen 36 TGTFSEEEAQHLDQAFP 52 (103)
T ss_dssp ES---HHHHHHHHHHHH
T ss_pred EEEcCHHHHHHHHhHhH
Confidence 34699999999998885
No 199
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=21.55 E-value=1.2e+02 Score=17.91 Aligned_cols=34 Identities=18% Similarity=0.206 Sum_probs=24.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccC
Q psy14727 28 TFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qVk 67 (67)
.+|+.+.+.|....+- ....++|..|++++..|+
T Consensus 155 ~Lt~rE~~Vl~l~~~G------~s~~eIA~~L~iS~~TVk 188 (216)
T PRK10100 155 LLTHREKEILNKLRIG------ASNNEIARSLFISENTVK 188 (216)
T ss_pred CCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHH
Confidence 4788888888765552 235688999999887653
No 200
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=21.38 E-value=47 Score=15.71 Aligned_cols=38 Identities=21% Similarity=0.309 Sum_probs=20.8
Q ss_pred CCCCCHHHHHHHHHH-HhhcCCCCHH----HHHHHHHHcCCCccc
Q psy14727 26 RTTFTLQQLEELETA-FAQTHYPDVF----TREDLAMKINLTEAR 65 (67)
Q Consensus 26 Rt~~s~~q~~~Le~~-F~~~~yp~~~----~r~~La~~l~l~~~q 65 (67)
.|.++..++..||.. |.. +|... .-...|..||++...
T Consensus 19 ~t~I~~~~l~aiE~~~~~~--lp~~~y~rg~lr~Ya~~Lgld~~~ 61 (62)
T PF13413_consen 19 ETKISVSYLEAIENGDFDS--LPSPVYARGYLRKYARFLGLDPDE 61 (62)
T ss_dssp HCS--HHHHHHHHCT-GCC--SSSHHHHHHHHHHHHHHTT--HHH
T ss_pred HhCCCHHHHHHHHCcChhh--CCcHHHHHHHHHHHHHHhCcCccc
Confidence 456788888888865 433 33332 224578888887654
No 201
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=21.37 E-value=47 Score=16.45 Aligned_cols=16 Identities=13% Similarity=0.362 Sum_probs=11.9
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.=..||..||+++..|
T Consensus 13 ~Wk~laR~LGls~~~I 28 (79)
T cd08784 13 QHKRFFRKLGLSDNEI 28 (79)
T ss_pred HHHHHHHHcCCCHHHH
Confidence 3357899999988654
No 202
>PF12518 DUF3721: Protein of unknown function; InterPro: IPR022196 This domain family is found in bacteria and eukaryotes, and is approximately 30 amino acids in length. There is a conserved WMPC sequence motif. There are two completely conserved residues (A and C) that may be functionally important.
Probab=21.34 E-value=90 Score=13.26 Aligned_cols=18 Identities=22% Similarity=0.294 Sum_probs=12.3
Q ss_pred CCCHHHHHHHHHHcCCCc
Q psy14727 46 YPDVFTREDLAMKINLTE 63 (67)
Q Consensus 46 yp~~~~r~~La~~l~l~~ 63 (67)
|++..+-+.-|..+|+.-
T Consensus 1 y~tk~eAe~~A~~~GC~G 18 (34)
T PF12518_consen 1 YPTKAEAEKRAKELGCKG 18 (34)
T ss_pred CCcHHHHHHHHHHcCCcc
Confidence 566666667788887653
No 203
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=21.10 E-value=1.1e+02 Score=17.82 Aligned_cols=16 Identities=6% Similarity=0.355 Sum_probs=12.0
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 166 s~~EIAe~lgis~~tV 181 (206)
T PRK12544 166 ETNEICHAVDLSVSNL 181 (206)
T ss_pred CHHHHHHHHCcCHHHH
Confidence 3468899999887655
No 204
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=21.09 E-value=47 Score=15.89 Aligned_cols=17 Identities=29% Similarity=0.294 Sum_probs=12.6
Q ss_pred HHHHHHHHHcCCCcccc
Q psy14727 50 FTREDLAMKINLTEARV 66 (67)
Q Consensus 50 ~~r~~La~~l~l~~~qV 66 (67)
..-.+||..+|++...|
T Consensus 23 ~ta~eLa~~lgl~~~~v 39 (68)
T smart00550 23 STALQLAKNLGLPKKEV 39 (68)
T ss_pred cCHHHHHHHHCCCHHHH
Confidence 34568999999987543
No 205
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=20.95 E-value=48 Score=16.73 Aligned_cols=14 Identities=29% Similarity=0.624 Sum_probs=10.7
Q ss_pred HHHHHHcCCCcccc
Q psy14727 53 EDLAMKINLTEARV 66 (67)
Q Consensus 53 ~~La~~l~l~~~qV 66 (67)
.+||..||+++..|
T Consensus 19 k~LAr~Lg~se~dI 32 (84)
T cd08804 19 TELARELDFTEEQI 32 (84)
T ss_pred HHHHHHcCCCHHHH
Confidence 47899999987543
No 206
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=20.90 E-value=75 Score=14.16 Aligned_cols=31 Identities=23% Similarity=0.320 Sum_probs=18.7
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcc
Q psy14727 30 TLQQLEELETAFAQTHYPDVFTREDLAMKINLTEA 64 (67)
Q Consensus 30 s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~ 64 (67)
|..|...|........ . .-.+||..++++..
T Consensus 2 t~~q~~iL~~l~~~~~-~---~~~~la~~~~~~~~ 32 (59)
T PF01047_consen 2 TPSQFRILRILYENGG-I---TQSELAEKLGISRS 32 (59)
T ss_dssp THHHHHHHHHHHHHSS-E---EHHHHHHHHTS-HH
T ss_pred CHHHHHHHHHHHHcCC-C---CHHHHHHHHCCChh
Confidence 5667777776665444 2 23378888887653
No 207
>KOG0031|consensus
Probab=20.80 E-value=95 Score=18.11 Aligned_cols=33 Identities=21% Similarity=0.373 Sum_probs=22.7
Q ss_pred CCCHHHHHHHHHHHh-----hcCCCCHHHHHHHHHHcC
Q psy14727 28 TFTLQQLEELETAFA-----QTHYPDVFTREDLAMKIN 60 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~-----~~~yp~~~~r~~La~~l~ 60 (67)
.|+..|++++..+|. +.-+.+...-...-.++|
T Consensus 25 mf~q~QIqEfKEAF~~mDqnrDG~IdkeDL~d~~aSlG 62 (171)
T KOG0031|consen 25 MFDQSQIQEFKEAFNLMDQNRDGFIDKEDLRDMLASLG 62 (171)
T ss_pred HhhHHHHHHHHHHHHHHhccCCCcccHHHHHHHHHHcC
Confidence 589999999999995 233566555555555554
No 208
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=20.58 E-value=48 Score=16.83 Aligned_cols=14 Identities=29% Similarity=0.458 Sum_probs=11.0
Q ss_pred HHHHHHcCCCcccc
Q psy14727 53 EDLAMKINLTEARV 66 (67)
Q Consensus 53 ~~La~~l~l~~~qV 66 (67)
..||..||+++..|
T Consensus 17 k~lar~LG~s~~eI 30 (86)
T cd08777 17 KRCARKLGFTESEI 30 (86)
T ss_pred HHHHHHcCCCHHHH
Confidence 47899999987654
No 209
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=20.50 E-value=1e+02 Score=18.42 Aligned_cols=16 Identities=25% Similarity=0.509 Sum_probs=12.6
Q ss_pred HHHHHHHHcCCCcccc
Q psy14727 51 TREDLAMKINLTEARV 66 (67)
Q Consensus 51 ~r~~La~~l~l~~~qV 66 (67)
.-.++|..+|++...|
T Consensus 219 s~~EIA~~lgis~~tV 234 (251)
T PRK07670 219 TLTEIGQVLNLSTSRI 234 (251)
T ss_pred CHHHHHHHHCcCHHHH
Confidence 4568899999988765
No 210
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=20.37 E-value=1e+02 Score=18.45 Aligned_cols=33 Identities=6% Similarity=0.336 Sum_probs=20.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccc
Q psy14727 29 FTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 29 ~s~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV 66 (67)
+++.+...+...|..+ ..-.++|..+|++...|
T Consensus 206 L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V 238 (255)
T TIGR02941 206 LSEREKSIIHCTFEEN-----LSQKETGERLGISQMHV 238 (255)
T ss_pred CCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHH
Confidence 4555555555544322 24468899999988655
No 211
>TIGR03792 uncharacterized cyanobacterial protein, TIGR03792 family. Members of this family are found, no more than one to a genome, exclusively in (but not universal to) the Cyanobacteria. These proteins are small, 100-150 amino acids. The function is unknown.
Probab=20.35 E-value=1.5e+02 Score=15.39 Aligned_cols=20 Identities=35% Similarity=0.674 Sum_probs=16.7
Q ss_pred CCCHHHHHHHHHHHhh----cCCC
Q psy14727 28 TFTLQQLEELETAFAQ----THYP 47 (67)
Q Consensus 28 ~~s~~q~~~Le~~F~~----~~yp 47 (67)
.+..+.+..++..|.. ++||
T Consensus 64 ~i~~~~~~~~~~~f~~~~~~~~~~ 87 (90)
T TIGR03792 64 AIPQEELEAVEQRFEQEMGGNPYP 87 (90)
T ss_pred cCCHHHHHHHHHHHHHhhcCCCCc
Confidence 5788999999999997 6666
No 212
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=20.28 E-value=40 Score=18.63 Aligned_cols=20 Identities=15% Similarity=0.292 Sum_probs=13.9
Q ss_pred CCHHHHHHHHHHcCCCcccc
Q psy14727 47 PDVFTREDLAMKINLTEARV 66 (67)
Q Consensus 47 p~~~~r~~La~~l~l~~~qV 66 (67)
.....-.++|..+|++...|
T Consensus 134 ~~g~s~~eIA~~lg~s~~tv 153 (175)
T PRK12518 134 LEDLPQKEIAEILNIPVGTV 153 (175)
T ss_pred hcCCCHHHHHHHHCCCHHHH
Confidence 33345668888899887665
No 213
>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=20.13 E-value=1.1e+02 Score=18.47 Aligned_cols=17 Identities=6% Similarity=0.194 Sum_probs=12.5
Q ss_pred HHHHHHHHcCCCccccC
Q psy14727 51 TREDLAMKINLTEARVQ 67 (67)
Q Consensus 51 ~r~~La~~l~l~~~qVk 67 (67)
.-.++|..+|++...|+
T Consensus 179 S~~EIA~~Lgis~~TVk 195 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVS 195 (244)
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 45678888988876653
Done!