Query 009439
Match_columns 535
No_of_seqs 318 out of 1898
Neff 5.4
Searched_HMMs 46136
Date Thu Mar 28 13:07:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009439.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009439hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0048 Transcription factor, 100.0 3.9E-30 8.4E-35 256.1 11.6 110 108-217 5-115 (238)
2 PLN03212 Transcription repress 99.9 4.2E-28 9E-33 239.1 11.4 120 89-215 9-129 (249)
3 PLN03091 hypothetical protein; 99.9 9.2E-27 2E-31 244.3 13.0 109 107-215 9-118 (459)
4 PLN03212 Transcription repress 99.9 4.2E-25 9E-30 217.9 8.4 103 58-161 23-126 (249)
5 KOG0049 Transcription factor, 99.9 4.4E-24 9.6E-29 229.7 11.3 177 33-210 279-459 (939)
6 PLN03091 hypothetical protein; 99.9 2.8E-24 6.1E-29 225.7 8.5 106 56-162 10-116 (459)
7 KOG0048 Transcription factor, 99.9 1.8E-23 3.9E-28 208.4 9.1 98 60-158 9-107 (238)
8 KOG0049 Transcription factor, 99.9 4.4E-22 9.5E-27 214.5 10.8 163 51-214 244-411 (939)
9 KOG0051 RNA polymerase I termi 99.7 9.8E-17 2.1E-21 175.1 11.7 153 60-214 308-512 (607)
10 KOG0051 RNA polymerase I termi 99.6 1.7E-14 3.8E-19 157.7 11.7 151 59-211 383-569 (607)
11 PF13921 Myb_DNA-bind_6: Myb-l 99.5 2.8E-14 6.1E-19 112.7 7.2 60 63-123 1-60 (60)
12 PF13921 Myb_DNA-bind_6: Myb-l 99.5 3.9E-14 8.4E-19 111.9 6.1 60 115-175 1-60 (60)
13 COG5147 REB1 Myb superfamily p 99.4 1.4E-13 3.1E-18 149.4 6.1 154 55-210 15-168 (512)
14 COG5147 REB1 Myb superfamily p 99.4 6.7E-13 1.5E-17 144.1 6.6 106 109-214 17-122 (512)
15 KOG0050 mRNA splicing protein 99.3 7.9E-13 1.7E-17 141.0 5.6 105 110-215 5-109 (617)
16 KOG0050 mRNA splicing protein 99.3 2.5E-13 5.3E-18 144.9 0.6 98 59-158 6-103 (617)
17 PF00249 Myb_DNA-binding: Myb- 99.2 5.8E-12 1.3E-16 95.6 4.0 47 60-106 1-48 (48)
18 PF00249 Myb_DNA-binding: Myb- 99.2 4.1E-11 8.8E-16 91.0 5.1 46 164-209 1-48 (48)
19 smart00717 SANT SANT SWI3, AD 98.9 1.2E-09 2.7E-14 80.5 5.4 47 164-210 1-48 (49)
20 smart00717 SANT SANT SWI3, AD 98.9 2.1E-09 4.6E-14 79.3 5.7 48 60-107 1-48 (49)
21 cd00167 SANT 'SWI3, ADA2, N-Co 98.8 6.8E-09 1.5E-13 75.5 5.5 44 166-209 1-45 (45)
22 cd00167 SANT 'SWI3, ADA2, N-Co 98.8 8.7E-09 1.9E-13 74.9 5.3 45 62-106 1-45 (45)
23 TIGR01557 myb_SHAQKYF myb-like 97.8 3.9E-05 8.5E-10 60.9 5.4 48 60-107 3-55 (57)
24 KOG0457 Histone acetyltransfer 97.5 7.7E-05 1.7E-09 79.8 4.1 49 59-107 71-119 (438)
25 TIGR01557 myb_SHAQKYF myb-like 97.3 0.00062 1.3E-08 54.1 5.7 47 163-209 2-54 (57)
26 TIGR02894 DNA_bind_RsfA transc 97.2 0.00057 1.2E-08 64.7 5.2 54 162-216 2-62 (161)
27 KOG0457 Histone acetyltransfer 97.1 0.00057 1.2E-08 73.3 5.5 48 162-209 70-118 (438)
28 PF13325 MCRS_N: N-terminal re 96.8 0.0068 1.5E-07 59.6 9.4 99 114-214 1-131 (199)
29 COG5259 RSC8 RSC chromatin rem 96.5 0.0023 4.9E-08 69.2 4.2 46 59-105 278-323 (531)
30 COG5259 RSC8 RSC chromatin rem 96.4 0.0033 7.1E-08 68.0 4.3 46 163-208 278-323 (531)
31 PF08914 Myb_DNA-bind_2: Rap1 96.3 0.0027 5.8E-08 51.8 2.6 51 60-110 2-61 (65)
32 KOG1279 Chromatin remodeling f 96.2 0.005 1.1E-07 68.2 5.0 46 164-209 253-298 (506)
33 PF13325 MCRS_N: N-terminal re 96.2 0.013 2.8E-07 57.8 7.2 94 62-157 1-125 (199)
34 PF13837 Myb_DNA-bind_4: Myb/S 96.2 0.0046 1E-07 52.0 3.6 50 164-213 1-68 (90)
35 KOG1279 Chromatin remodeling f 96.2 0.0055 1.2E-07 67.9 5.1 46 59-105 252-297 (506)
36 PF08914 Myb_DNA-bind_2: Rap1 95.8 0.013 2.9E-07 47.8 4.5 51 164-214 2-62 (65)
37 PRK13923 putative spore coat p 95.8 0.012 2.5E-07 56.6 4.8 54 162-216 3-63 (170)
38 COG5114 Histone acetyltransfer 95.6 0.0083 1.8E-07 62.3 3.0 47 61-107 64-110 (432)
39 PLN03142 Probable chromatin-re 95.5 0.042 9.1E-07 65.9 8.8 145 62-214 826-989 (1033)
40 PF13837 Myb_DNA-bind_4: Myb/S 95.2 0.0082 1.8E-07 50.5 1.2 46 61-106 2-64 (90)
41 COG5114 Histone acetyltransfer 94.6 0.035 7.5E-07 57.8 4.1 47 163-209 62-109 (432)
42 PF13873 Myb_DNA-bind_5: Myb/S 94.4 0.095 2.1E-06 43.2 5.5 49 164-212 2-72 (78)
43 TIGR02894 DNA_bind_RsfA transc 94.3 0.025 5.5E-07 53.8 2.1 47 60-107 4-56 (161)
44 PF13873 Myb_DNA-bind_5: Myb/S 93.9 0.049 1.1E-06 45.0 2.9 46 61-106 3-69 (78)
45 KOG2656 DNA methyltransferase 92.6 0.13 2.9E-06 54.9 4.3 61 152-216 122-188 (445)
46 KOG1194 Predicted DNA-binding 91.5 0.52 1.1E-05 51.4 7.3 41 165-206 471-511 (534)
47 COG5118 BDP1 Transcription ini 91.1 0.35 7.7E-06 51.6 5.4 49 163-211 364-412 (507)
48 PRK13923 putative spore coat p 90.6 0.17 3.8E-06 48.7 2.5 47 60-107 5-57 (170)
49 KOG1194 Predicted DNA-binding 89.7 0.88 1.9E-05 49.7 7.1 52 161-212 184-235 (534)
50 KOG4282 Transcription factor G 88.8 0.68 1.5E-05 48.9 5.5 52 164-215 54-119 (345)
51 COG5118 BDP1 Transcription ini 87.8 0.82 1.8E-05 49.0 5.1 46 58-104 363-408 (507)
52 PF12776 Myb_DNA-bind_3: Myb/S 87.5 0.89 1.9E-05 38.6 4.5 49 166-214 1-67 (96)
53 KOG4282 Transcription factor G 86.4 1.5 3.3E-05 46.2 6.4 47 60-106 54-113 (345)
54 PF09111 SLIDE: SLIDE; InterP 86.1 1.3 2.8E-05 40.3 4.9 52 161-212 46-113 (118)
55 KOG2656 DNA methyltransferase 85.7 2.6 5.6E-05 45.5 7.5 44 62-106 132-181 (445)
56 PF09111 SLIDE: SLIDE; InterP 85.0 1 2.3E-05 41.0 3.7 49 58-106 47-110 (118)
57 PF08281 Sigma70_r4_2: Sigma-7 84.3 2.3 5E-05 32.4 4.9 42 169-211 12-53 (54)
58 PF12776 Myb_DNA-bind_3: Myb/S 82.3 1.8 3.9E-05 36.7 4.0 44 62-105 1-61 (96)
59 KOG4167 Predicted DNA-binding 77.6 2.7 5.9E-05 48.5 4.5 42 61-103 620-661 (907)
60 KOG4167 Predicted DNA-binding 74.8 4.7 0.0001 46.6 5.4 47 164-210 619-665 (907)
61 PF04545 Sigma70_r4: Sigma-70, 67.8 12 0.00026 28.1 4.6 42 170-212 7-48 (50)
62 smart00595 MADF subfamily of S 67.2 10 0.00022 31.7 4.6 30 186-216 30-59 (89)
63 PF13404 HTH_AsnC-type: AsnC-t 66.2 8.1 0.00018 28.7 3.3 39 66-105 3-41 (42)
64 PF11035 SnAPC_2_like: Small n 65.7 21 0.00045 37.8 7.3 55 164-218 21-79 (344)
65 KOG4468 Polycomb-group transcr 64.1 20 0.00044 40.8 7.3 47 60-107 88-144 (782)
66 PF04504 DUF573: Protein of un 63.8 18 0.0004 31.7 5.7 51 165-215 5-68 (98)
67 PF07750 GcrA: GcrA cell cycle 61.3 8.1 0.00018 37.0 3.2 42 62-105 2-43 (162)
68 PF13404 HTH_AsnC-type: AsnC-t 60.3 9.1 0.0002 28.5 2.7 38 118-156 3-40 (42)
69 PF11626 Rap1_C: TRF2-interact 59.1 7.1 0.00015 33.3 2.2 24 108-131 43-74 (87)
70 KOG1878 Nuclear receptor coreg 56.7 3.5 7.5E-05 50.8 -0.1 44 59-103 224-267 (1672)
71 PRK11179 DNA-binding transcrip 54.8 15 0.00032 34.3 3.8 47 65-112 8-54 (153)
72 KOG4468 Polycomb-group transcr 54.8 17 0.00037 41.4 4.7 50 164-213 88-147 (782)
73 TIGR02985 Sig70_bacteroi1 RNA 54.0 25 0.00055 31.5 5.1 42 170-212 116-157 (161)
74 PF07750 GcrA: GcrA cell cycle 52.6 15 0.00033 35.2 3.5 42 166-208 2-43 (162)
75 KOG4329 DNA-binding protein [G 52.5 23 0.00049 38.3 5.0 47 56-103 273-320 (445)
76 PRK11169 leucine-responsive tr 52.4 13 0.00029 35.1 3.1 46 65-111 13-58 (164)
77 PRK11179 DNA-binding transcrip 51.6 14 0.0003 34.5 3.0 45 117-162 8-52 (153)
78 PRK11169 leucine-responsive tr 50.5 13 0.00027 35.2 2.6 45 117-162 13-57 (164)
79 PRK09643 RNA polymerase sigma 49.3 38 0.00081 32.4 5.7 42 170-212 137-178 (192)
80 PLN03142 Probable chromatin-re 47.5 24 0.00052 43.1 4.9 48 60-107 926-985 (1033)
81 KOG2009 Transcription initiati 46.1 20 0.00044 40.8 3.7 46 162-207 407-452 (584)
82 KOG4329 DNA-binding protein [G 46.0 91 0.002 33.9 8.2 46 165-210 278-324 (445)
83 PF11626 Rap1_C: TRF2-interact 44.2 11 0.00023 32.3 0.9 17 160-176 43-59 (87)
84 TIGR02937 sigma70-ECF RNA poly 42.7 47 0.001 28.9 4.9 42 170-212 113-154 (158)
85 PF07638 Sigma70_ECF: ECF sigm 42.3 57 0.0012 31.2 5.7 43 169-212 137-179 (185)
86 PRK04217 hypothetical protein; 41.7 76 0.0016 28.7 6.0 48 165-214 41-88 (110)
87 smart00351 PAX Paired Box doma 41.5 94 0.002 28.2 6.7 81 60-142 15-103 (125)
88 PRK09047 RNA polymerase factor 40.9 75 0.0016 28.8 6.1 45 170-215 109-153 (161)
89 PF10545 MADF_DNA_bdg: Alcohol 39.7 37 0.00081 27.4 3.5 32 185-216 28-60 (85)
90 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 38.9 52 0.0011 25.7 3.9 37 167-205 5-41 (50)
91 PRK09652 RNA polymerase sigma 38.3 80 0.0017 28.9 5.9 41 171-212 132-172 (182)
92 KOG2009 Transcription initiati 38.2 36 0.00078 38.9 4.1 47 57-104 406-452 (584)
93 cd06171 Sigma70_r4 Sigma70, re 38.2 77 0.0017 22.5 4.7 42 167-210 11-52 (55)
94 PF11035 SnAPC_2_like: Small n 37.3 87 0.0019 33.4 6.4 44 60-103 21-67 (344)
95 PRK12515 RNA polymerase sigma 37.2 84 0.0018 29.7 6.0 44 170-214 134-177 (189)
96 PRK09645 RNA polymerase sigma 36.1 88 0.0019 28.9 5.8 44 170-214 121-164 (173)
97 KOG3841 TEF-1 and related tran 34.6 72 0.0016 34.7 5.4 59 162-220 74-153 (455)
98 PRK11924 RNA polymerase sigma 33.8 95 0.0021 28.4 5.6 40 172-212 130-169 (179)
99 PRK09642 RNA polymerase sigma 33.4 1.1E+02 0.0025 27.7 6.1 43 170-213 109-151 (160)
100 PF08281 Sigma70_r4_2: Sigma-7 33.0 66 0.0014 24.2 3.7 38 66-105 13-50 (54)
101 PF09197 Rap1-DNA-bind: Rap1, 32.1 73 0.0016 28.7 4.3 46 62-107 1-76 (105)
102 smart00344 HTH_ASNC helix_turn 31.7 68 0.0015 27.5 4.0 45 66-111 3-47 (108)
103 PRK09637 RNA polymerase sigma 31.5 1.1E+02 0.0024 29.0 5.8 43 170-213 109-151 (181)
104 TIGR02939 RpoE_Sigma70 RNA pol 31.0 85 0.0018 29.3 4.9 42 171-213 142-183 (190)
105 PRK09641 RNA polymerase sigma 30.6 1.1E+02 0.0023 28.5 5.5 43 170-213 139-181 (187)
106 smart00595 MADF subfamily of S 30.6 32 0.00069 28.7 1.7 22 83-105 30-51 (89)
107 PF01388 ARID: ARID/BRIGHT DNA 30.4 89 0.0019 26.3 4.5 37 174-210 40-89 (92)
108 TIGR02954 Sig70_famx3 RNA poly 30.3 1.1E+02 0.0023 28.3 5.3 43 170-213 122-164 (169)
109 PRK12547 RNA polymerase sigma 29.5 1.4E+02 0.0029 27.6 5.9 44 170-214 115-158 (164)
110 PRK12529 RNA polymerase sigma 29.5 1.2E+02 0.0026 28.5 5.6 44 170-214 130-173 (178)
111 PRK11923 algU RNA polymerase s 29.1 1.2E+02 0.0026 28.6 5.6 40 173-213 144-183 (193)
112 PRK12516 RNA polymerase sigma 28.3 1.4E+02 0.003 28.5 5.9 46 170-216 119-164 (187)
113 PRK12523 RNA polymerase sigma 27.7 1.4E+02 0.0031 27.7 5.7 43 170-213 122-164 (172)
114 TIGR02943 Sig70_famx1 RNA poly 27.6 1.5E+02 0.0032 28.2 6.0 43 170-213 134-176 (188)
115 PRK00118 putative DNA-binding 27.5 1.8E+02 0.0038 26.1 5.9 45 169-214 19-63 (104)
116 PRK09648 RNA polymerase sigma 27.5 1.4E+02 0.003 28.1 5.7 40 173-213 145-184 (189)
117 COG1522 Lrp Transcriptional re 27.3 68 0.0015 29.2 3.5 47 65-112 7-53 (154)
118 PF09197 Rap1-DNA-bind: Rap1, 26.9 69 0.0015 28.8 3.2 45 114-158 1-75 (105)
119 PRK12524 RNA polymerase sigma 26.3 1.7E+02 0.0036 27.9 6.1 43 171-214 140-182 (196)
120 PRK12530 RNA polymerase sigma 26.3 1.6E+02 0.0034 28.0 5.9 42 170-212 137-178 (189)
121 PRK12512 RNA polymerase sigma 26.2 1.5E+02 0.0033 27.7 5.7 42 171-213 135-176 (184)
122 PRK09413 IS2 repressor TnpA; R 25.9 2.2E+02 0.0047 25.5 6.4 46 59-107 9-54 (121)
123 cd00131 PAX Paired Box domain 25.9 2.6E+02 0.0057 25.5 7.0 83 58-142 13-103 (128)
124 PRK12520 RNA polymerase sigma 25.5 1.9E+02 0.004 27.3 6.2 48 170-218 134-181 (191)
125 PRK12531 RNA polymerase sigma 25.2 1.7E+02 0.0038 27.7 6.0 41 172-213 146-186 (194)
126 smart00344 HTH_ASNC helix_turn 25.2 73 0.0016 27.3 3.1 44 118-162 3-46 (108)
127 PRK05602 RNA polymerase sigma 25.2 1.6E+02 0.0035 27.6 5.7 45 171-216 132-176 (186)
128 TIGR02948 SigW_bacill RNA poly 25.1 1.4E+02 0.003 27.7 5.3 42 171-213 140-181 (187)
129 PRK12545 RNA polymerase sigma 25.0 1.7E+02 0.0036 28.2 5.8 44 170-214 142-185 (201)
130 PF04504 DUF573: Protein of un 24.8 1.9E+02 0.0042 25.3 5.6 20 59-78 3-22 (98)
131 KOG3554 Histone deacetylase co 24.1 1.4E+02 0.0031 33.4 5.5 42 165-206 286-328 (693)
132 KOG3554 Histone deacetylase co 23.9 74 0.0016 35.5 3.4 41 61-102 286-327 (693)
133 PRK12526 RNA polymerase sigma 23.9 1.9E+02 0.0042 27.9 6.1 42 173-215 159-200 (206)
134 PRK06759 RNA polymerase factor 23.7 1.5E+02 0.0033 26.6 5.0 40 171-211 110-149 (154)
135 PF13936 HTH_38: Helix-turn-he 23.5 65 0.0014 23.9 2.1 37 62-101 4-40 (44)
136 PRK09651 RNA polymerase sigma 23.3 1.7E+02 0.0037 27.3 5.4 43 171-214 123-165 (172)
137 PRK09647 RNA polymerase sigma 23.1 2E+02 0.0043 27.9 6.0 45 171-216 142-186 (203)
138 KOG1544 Predicted cysteine pro 22.8 51 0.0011 35.3 1.9 27 480-506 334-360 (470)
139 COG1522 Lrp Transcriptional re 22.5 76 0.0017 28.8 2.8 45 117-162 7-51 (154)
140 PRK12528 RNA polymerase sigma 22.5 1.7E+02 0.0036 26.7 5.1 41 170-211 116-156 (161)
141 PRK12532 RNA polymerase sigma 22.4 1.9E+02 0.0041 27.4 5.6 43 170-213 139-181 (195)
142 cd08319 Death_RAIDD Death doma 22.2 1.1E+02 0.0023 26.2 3.4 29 172-201 2-30 (83)
143 PRK12527 RNA polymerase sigma 22.0 2.5E+02 0.0054 25.5 6.2 44 170-214 108-151 (159)
144 PF04545 Sigma70_r4: Sigma-70, 21.8 1.3E+02 0.0029 22.3 3.6 38 65-105 7-44 (50)
145 PF09420 Nop16: Ribosome bioge 21.7 1.9E+02 0.0041 27.5 5.4 48 162-209 112-163 (164)
146 TIGR02999 Sig-70_X6 RNA polyme 21.6 2.1E+02 0.0046 26.5 5.7 42 170-212 137-178 (183)
147 PRK12536 RNA polymerase sigma 21.6 2.1E+02 0.0046 26.8 5.7 41 172-213 134-174 (181)
148 PRK12514 RNA polymerase sigma 21.5 2.1E+02 0.0045 26.6 5.6 39 173-212 135-173 (179)
149 TIGR02952 Sig70_famx2 RNA poly 21.5 1.7E+02 0.0037 26.6 5.0 42 170-212 125-166 (170)
150 PRK09649 RNA polymerase sigma 21.2 1.8E+02 0.0039 27.5 5.2 38 175-213 138-175 (185)
151 TIGR02983 SigE-fam_strep RNA p 20.9 2.1E+02 0.0047 25.9 5.5 43 170-213 113-155 (162)
152 PF01710 HTH_Tnp_IS630: Transp 20.3 6E+02 0.013 22.6 8.1 98 69-174 9-111 (119)
153 COG2963 Transposase and inacti 20.3 2.4E+02 0.0052 24.7 5.4 46 164-210 5-51 (116)
154 cd08803 Death_ank3 Death domai 20.2 1.4E+02 0.003 25.6 3.7 31 172-203 4-34 (84)
155 smart00501 BRIGHT BRIGHT, ARID 20.1 1.8E+02 0.0039 24.7 4.4 38 174-211 36-86 (93)
156 TIGR02950 SigM_subfam RNA poly 20.0 87 0.0019 28.1 2.6 41 171-212 109-149 (154)
No 1
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.96 E-value=3.9e-30 Score=256.15 Aligned_cols=110 Identities=47% Similarity=0.804 Sum_probs=105.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCchhhhccccc-ccchhhhHhhhhhhcCCCCCCCCCCHHHHHHHHHHHHHhCCch
Q 009439 108 PDLVKGPWTQEEDDKITELVSKYGPTKWSVIAKSLP-GRIGKQCRERWHNHLNPDIKKDAWTLEEELALMNAHRIHGNKW 186 (535)
Q Consensus 108 p~~kKg~WT~EED~~Ll~lV~kyG~~~W~~IAk~Lp-gRt~kqcr~Rw~n~L~p~ik~~~WT~EEd~~Li~lv~~~G~kW 186 (535)
+.+.||+||+|||++|+++|++||+.+|..|++.++ +|++++||.||.|||+|+++++.||+|||++||+||.++|++|
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrW 84 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRW 84 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHH
Confidence 345579999999999999999999999999999999 9999999999999999999999999999999999999999999
Q ss_pred hhHhhhCCCCCHhHHHHHHHHHHHhHHHHHh
Q 009439 187 AEIAKVLPGRTDNSIKNHWNSSLKKKLDFYL 217 (535)
Q Consensus 187 ~~IA~~lpgRT~~qcknRw~~llkkk~~~~~ 217 (535)
+.||++|||||++.|||+|++.++|++....
T Consensus 85 s~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 85 SLIAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred HHHHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 9999999999999999999999999987654
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.95 E-value=4.2e-28 Score=239.09 Aligned_cols=120 Identities=40% Similarity=0.741 Sum_probs=109.8
Q ss_pred cCCCCCHHHHHHHhhhccCCCCCCCCCCHHHHHHHHHHHHHhCCCchhhhcccc-cccchhhhHhhhhhhcCCCCCCCCC
Q 009439 89 FFPDRSEVQCLHRWQKVLNPDLVKGPWTQEEDDKITELVSKYGPTKWSVIAKSL-PGRIGKQCRERWHNHLNPDIKKDAW 167 (535)
Q Consensus 89 ~lp~RT~~qCr~Rw~~~L~p~~kKg~WT~EED~~Ll~lV~kyG~~~W~~IAk~L-pgRt~kqcr~Rw~n~L~p~ik~~~W 167 (535)
-++.|+...|. .+.+++++||+|||++|+++|++||..+|..||+.| ++|+++|||+||.++|+|.+++++|
T Consensus 9 ~~~~~~~pcc~-------K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpW 81 (249)
T PLN03212 9 PVSKKTTPCCT-------KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGI 81 (249)
T ss_pred CCCCCCCCCcc-------cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCC
Confidence 35566665553 346889999999999999999999988999999988 5999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHHHH
Q 009439 168 TLEEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKLDF 215 (535)
Q Consensus 168 T~EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~~~ 215 (535)
|+|||++|++++..||++|..||++|+|||+++|||||+.++++++..
T Consensus 82 T~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r 129 (249)
T PLN03212 82 TSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLR 129 (249)
T ss_pred ChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHh
Confidence 999999999999999999999999999999999999999999988754
No 3
>PLN03091 hypothetical protein; Provisional
Probab=99.94 E-value=9.2e-27 Score=244.28 Aligned_cols=109 Identities=48% Similarity=0.866 Sum_probs=104.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCchhhhccccc-ccchhhhHhhhhhhcCCCCCCCCCCHHHHHHHHHHHHHhCCc
Q 009439 107 NPDLVKGPWTQEEDDKITELVSKYGPTKWSVIAKSLP-GRIGKQCRERWHNHLNPDIKKDAWTLEEELALMNAHRIHGNK 185 (535)
Q Consensus 107 ~p~~kKg~WT~EED~~Ll~lV~kyG~~~W~~IAk~Lp-gRt~kqcr~Rw~n~L~p~ik~~~WT~EEd~~Li~lv~~~G~k 185 (535)
+..+++++||+|||++|+++|++||..+|..||+.|+ +|+++|||+||.++|+|.+++++||+|||++|++++.+||++
T Consensus 9 KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k~~GnK 88 (459)
T PLN03091 9 KQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHAVLGNR 88 (459)
T ss_pred CCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHHHhCcc
Confidence 3578899999999999999999999989999999884 999999999999999999999999999999999999999999
Q ss_pred hhhHhhhCCCCCHhHHHHHHHHHHHhHHHH
Q 009439 186 WAEIAKVLPGRTDNSIKNHWNSSLKKKLDF 215 (535)
Q Consensus 186 W~~IA~~lpgRT~~qcknRw~~llkkk~~~ 215 (535)
|..||++|+|||+++|||||+.+++|+++.
T Consensus 89 WskIAk~LPGRTDnqIKNRWnslLKKklr~ 118 (459)
T PLN03091 89 WSQIAAQLPGRTDNEIKNLWNSCLKKKLRQ 118 (459)
T ss_pred hHHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999998864
No 4
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.91 E-value=4.2e-25 Score=217.93 Aligned_cols=103 Identities=31% Similarity=0.610 Sum_probs=97.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHhcCCChhhhhhcC-CCCCHHHHHHHhhhccCCCCCCCCCCHHHHHHHHHHHHHhCCCchh
Q 009439 58 RAKGGWTPEEDETLRNAVSTFKGKSWKKIAEFF-PDRSEVQCLHRWQKVLNPDLVKGPWTQEEDDKITELVSKYGPTKWS 136 (535)
Q Consensus 58 r~kgkWT~EEDe~L~klV~~yg~~nW~~IAk~l-p~RT~~qCr~Rw~~~L~p~~kKg~WT~EED~~Ll~lV~kyG~~~W~ 136 (535)
..+++||+|||++|+++|.+||..+|..||+.+ ++|+.+||++||.++|+|.+++++||.|||++|++++..|| .+|.
T Consensus 23 lKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~~G-nKWs 101 (249)
T PLN03212 23 MKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLG-NRWS 101 (249)
T ss_pred CcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHhcc-ccHH
Confidence 457889999999999999999999999999998 59999999999999999999999999999999999999999 7899
Q ss_pred hhcccccccchhhhHhhhhhhcCCC
Q 009439 137 VIAKSLPGRIGKQCRERWHNHLNPD 161 (535)
Q Consensus 137 ~IAk~LpgRt~kqcr~Rw~n~L~p~ 161 (535)
.||+.|+||+..+|++||+.+|+..
T Consensus 102 ~IAk~LpGRTDnqIKNRWns~LrK~ 126 (249)
T PLN03212 102 LIAGRIPGRTDNEIKNYWNTHLRKK 126 (249)
T ss_pred HHHhhcCCCCHHHHHHHHHHHHhHH
Confidence 9999999999999999999887644
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.90 E-value=4.4e-24 Score=229.68 Aligned_cols=177 Identities=29% Similarity=0.561 Sum_probs=154.6
Q ss_pred ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHhcC---CChhhhhhcCCCCCHHHHHHHhhhccCCC
Q 009439 33 ILKSPGVSSPATTSPTHRRTTGPIRRAKGGWTPEEDETLRNAVSTFKG---KSWKKIAEFFPDRSEVQCLHRWQKVLNPD 109 (535)
Q Consensus 33 ~~~s~~~~~p~~~~~~~~r~~~~~rr~kgkWT~EEDe~L~klV~~yg~---~nW~~IAk~lp~RT~~qCr~Rw~~~L~p~ 109 (535)
|+.+.+.+++.++|.....+-.. .-....||+|||.+|+.+|++... .+|.+|..+||+|+..|...||.+.|+|.
T Consensus 279 IA~~Lgt~RS~yQC~~kF~t~~~-~L~ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ympgr~~~qLI~R~~~~LdPs 357 (939)
T KOG0049|consen 279 IALNLGTNRSSYQCMEKFKTEVS-QLSEKEWSEEEDTKLIALVKITSINSHIQWDKVVQYMPGRTRQQLITRFSHTLDPS 357 (939)
T ss_pred HHHHhCCCcchHHHHHHHHHHHH-HHHhhhcchhhhHHHHHHHHHhhccCccchHHHHHhcCCcchhhhhhhheeccCcc
Confidence 44556777888887765544321 113367999999999999998743 47999999999999999999999999999
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCchhhhcccccccchhhhHhhhhhhcCCCCCCCCCCHHHHHHHHHHHHHhC-Cchhh
Q 009439 110 LVKGPWTQEEDDKITELVSKYGPTKWSVIAKSLPGRIGKQCRERWHNHLNPDIKKDAWTLEEELALMNAHRIHG-NKWAE 188 (535)
Q Consensus 110 ~kKg~WT~EED~~Ll~lV~kyG~~~W~~IAk~LpgRt~kqcr~Rw~n~L~p~ik~~~WT~EEd~~Li~lv~~~G-~kW~~ 188 (535)
+++|+||.+||.+|+.+|.+||...|-+|-..+|+|+..|||+||.|.|+...+.+.||..||+.||.++.+|| +.|.+
T Consensus 358 ikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~~V~~YG~g~Wak 437 (939)
T KOG0049|consen 358 VKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLYAVKVYGKGNWAK 437 (939)
T ss_pred ccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHHhhccCceeecchHHHHHHHHHHccchHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999 68999
Q ss_pred HhhhCCCCCHhHHHHHHHHHHH
Q 009439 189 IAKVLPGRTDNSIKNHWNSSLK 210 (535)
Q Consensus 189 IA~~lpgRT~~qcknRw~~llk 210 (535)
||..||+||..|...|=..++.
T Consensus 438 cA~~Lp~~t~~q~~rrR~R~~~ 459 (939)
T KOG0049|consen 438 CAMLLPKKTSRQLRRRRLRLIA 459 (939)
T ss_pred HHHHccccchhHHHHHHHHHHH
Confidence 9999999999665555444443
No 6
>PLN03091 hypothetical protein; Provisional
Probab=99.90 E-value=2.8e-24 Score=225.70 Aligned_cols=106 Identities=33% Similarity=0.696 Sum_probs=99.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhcCCChhhhhhcCC-CCCHHHHHHHhhhccCCCCCCCCCCHHHHHHHHHHHHHhCCCc
Q 009439 56 IRRAKGGWTPEEDETLRNAVSTFKGKSWKKIAEFFP-DRSEVQCLHRWQKVLNPDLVKGPWTQEEDDKITELVSKYGPTK 134 (535)
Q Consensus 56 ~rr~kgkWT~EEDe~L~klV~~yg~~nW~~IAk~lp-~RT~~qCr~Rw~~~L~p~~kKg~WT~EED~~Ll~lV~kyG~~~ 134 (535)
.+..+++||+|||++|+++|.+||..+|..||+.++ +|+.+||++||.++|+|.+++++||+|||++|++++++|| .+
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k~~G-nK 88 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHAVLG-NR 88 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHHHhC-cc
Confidence 345678999999999999999999999999999885 9999999999999999999999999999999999999999 78
Q ss_pred hhhhcccccccchhhhHhhhhhhcCCCC
Q 009439 135 WSVIAKSLPGRIGKQCRERWHNHLNPDI 162 (535)
Q Consensus 135 W~~IAk~LpgRt~kqcr~Rw~n~L~p~i 162 (535)
|.+||+.|+||++.+|++||+.+|+..+
T Consensus 89 WskIAk~LPGRTDnqIKNRWnslLKKkl 116 (459)
T PLN03091 89 WSQIAAQLPGRTDNEIKNLWNSCLKKKL 116 (459)
T ss_pred hHHHHHhcCCCCHHHHHHHHHHHHHHHH
Confidence 9999999999999999999998776543
No 7
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.89 E-value=1.8e-23 Score=208.38 Aligned_cols=98 Identities=36% Similarity=0.716 Sum_probs=95.8
Q ss_pred CCCCCHHHHHHHHHHHHHhcCCChhhhhhcCC-CCCHHHHHHHhhhccCCCCCCCCCCHHHHHHHHHHHHHhCCCchhhh
Q 009439 60 KGGWTPEEDETLRNAVSTFKGKSWKKIAEFFP-DRSEVQCLHRWQKVLNPDLVKGPWTQEEDDKITELVSKYGPTKWSVI 138 (535)
Q Consensus 60 kgkWT~EEDe~L~klV~~yg~~nW~~IAk~lp-~RT~~qCr~Rw~~~L~p~~kKg~WT~EED~~Ll~lV~kyG~~~W~~I 138 (535)
+|+||+|||++|+++|.+||.++|..|++.++ +|++++||.||.+||+|++++|.||+|||.+|++++..+| ++|..|
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~G-NrWs~I 87 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLG-NRWSLI 87 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHC-cHHHHH
Confidence 79999999999999999999999999999999 9999999999999999999999999999999999999999 889999
Q ss_pred cccccccchhhhHhhhhhhc
Q 009439 139 AKSLPGRIGKQCRERWHNHL 158 (535)
Q Consensus 139 Ak~LpgRt~kqcr~Rw~n~L 158 (535)
|+.|||||.+.++++|+..|
T Consensus 88 A~~LPGRTDNeIKN~Wnt~l 107 (238)
T KOG0048|consen 88 AGRLPGRTDNEVKNHWNTHL 107 (238)
T ss_pred HhhCCCcCHHHHHHHHHHHH
Confidence 99999999999999998766
No 8
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.86 E-value=4.4e-22 Score=214.45 Aligned_cols=163 Identities=27% Similarity=0.519 Sum_probs=146.0
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHhcCCChhhhhhcCCC-CCHHHHHHHhhhccCCCCCCCCCCHHHHHHHHHHHHH
Q 009439 51 RTTGPIRRAKGGWTPEEDETLRNAVSTFKGKSWKKIAEFFPD-RSEVQCLHRWQKVLNPDLVKGPWTQEEDDKITELVSK 129 (535)
Q Consensus 51 r~~~~~rr~kgkWT~EEDe~L~klV~~yg~~nW~~IAk~lp~-RT~~qCr~Rw~~~L~p~~kKg~WT~EED~~Ll~lV~k 129 (535)
+......-.+..|+.|||++|..+...++..+|..||..|+. |+..||..+|+..+. .+....||+|||.+|+++|+.
T Consensus 244 ~n~l~P~~nk~~WS~EE~E~L~AiA~A~~~~~W~~IA~~Lgt~RS~yQC~~kF~t~~~-~L~ekeWsEEed~kL~alV~~ 322 (939)
T KOG0049|consen 244 YNELNPKWNKEHWSNEEVEKLKALAEAPKFVSWPMIALNLGTNRSSYQCMEKFKTEVS-QLSEKEWSEEEDTKLIALVKI 322 (939)
T ss_pred hhhcCCccchhccChHHHHHHHHHHhccccccHHHHHHHhCCCcchHHHHHHHHHHHH-HHHhhhcchhhhHHHHHHHHH
Confidence 333333456778999999999999999999999999999985 999999999999876 344568999999999999998
Q ss_pred hCC---CchhhhcccccccchhhhHhhhhhhcCCCCCCCCCCHHHHHHHHHHHHHhCC-chhhHhhhCCCCCHhHHHHHH
Q 009439 130 YGP---TKWSVIAKSLPGRIGKQCRERWHNHLNPDIKKDAWTLEEELALMNAHRIHGN-KWAEIAKVLPGRTDNSIKNHW 205 (535)
Q Consensus 130 yG~---~~W~~IAk~LpgRt~kqcr~Rw~n~L~p~ik~~~WT~EEd~~Li~lv~~~G~-kW~~IA~~lpgRT~~qcknRw 205 (535)
... ..|.+|-..||||+..|..-||...|+|.+++|+||.+||.+|+.+|.+||. .|..|-..||||++.||+.||
T Consensus 323 ~~~nShI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY 402 (939)
T KOG0049|consen 323 TSINSHIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERY 402 (939)
T ss_pred hhccCccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHH
Confidence 642 4799999999999999999999999999999999999999999999999996 599999999999999999999
Q ss_pred HHHHHhHHH
Q 009439 206 NSSLKKKLD 214 (535)
Q Consensus 206 ~~llkkk~~ 214 (535)
...|.+.++
T Consensus 403 ~nvL~~s~K 411 (939)
T KOG0049|consen 403 TNVLNRSAK 411 (939)
T ss_pred HHHHHHhhc
Confidence 988876553
No 9
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.69 E-value=9.8e-17 Score=175.14 Aligned_cols=153 Identities=25% Similarity=0.528 Sum_probs=135.6
Q ss_pred CCCCCHHHHHHHHHHHHHhcCC-----------------------ChhhhhhcCCCCCHHHHHHHhhhccCCCC-CCCCC
Q 009439 60 KGGWTPEEDETLRNAVSTFKGK-----------------------SWKKIAEFFPDRSEVQCLHRWQKVLNPDL-VKGPW 115 (535)
Q Consensus 60 kgkWT~EEDe~L~klV~~yg~~-----------------------nW~~IAk~lp~RT~~qCr~Rw~~~L~p~~-kKg~W 115 (535)
.+.|+.|||++|.+.|..|-.. -|+.|...||.|+...++++-++.+++.- .+|.|
T Consensus 308 ~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp~R~~~siy~~~rR~y~~FE~~rg~w 387 (607)
T KOG0051|consen 308 LKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLPYRDRKSIYHHLRRAYTPFENKRGKW 387 (607)
T ss_pred hhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcCcccchhHHHHHHhcCCccccccCCC
Confidence 3679999999999999998211 17888899999999999998777777766 99999
Q ss_pred CHHHHHHHHHHHHHhCCCchhhhcccccccchhhhHhhhhhhcCCCC--CCCCCCHHHHHHHHHHHH-------Hh----
Q 009439 116 TQEEDDKITELVSKYGPTKWSVIAKSLPGRIGKQCRERWHNHLNPDI--KKDAWTLEEELALMNAHR-------IH---- 182 (535)
Q Consensus 116 T~EED~~Ll~lV~kyG~~~W~~IAk~LpgRt~kqcr~Rw~n~L~p~i--k~~~WT~EEd~~Li~lv~-------~~---- 182 (535)
|+||++.|..++.++| ..|..|++.| ||.+..|++||+++...+- +++.||.||++.|+++|+ .+
T Consensus 388 t~ee~eeL~~l~~~~g-~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n 465 (607)
T KOG0051|consen 388 TPEEEEELKKLVVEHG-NDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREALQPQASN 465 (607)
T ss_pred CcchHHHHHHHHHHhc-ccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhhcccccc
Confidence 9999999999999999 8999999999 9999999999999998884 899999999999999995 22
Q ss_pred ---------------CCchhhHhhhCCCCCHhHHHHHHHHHHHhHHH
Q 009439 183 ---------------GNKWAEIAKVLPGRTDNSIKNHWNSSLKKKLD 214 (535)
Q Consensus 183 ---------------G~kW~~IA~~lpgRT~~qcknRw~~llkkk~~ 214 (535)
+-.|..|++.+.+|+..||+.+|+.++.+..-
T Consensus 466 ~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~ 512 (607)
T KOG0051|consen 466 TDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSF 512 (607)
T ss_pred cchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHh
Confidence 11499999999999999999999999987653
No 10
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.55 E-value=1.7e-14 Score=157.71 Aligned_cols=151 Identities=25% Similarity=0.544 Sum_probs=126.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhccCCCC--CCCCCCHHHHHHHHHHHH-------H
Q 009439 59 AKGGWTPEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKVLNPDL--VKGPWTQEEDDKITELVS-------K 129 (535)
Q Consensus 59 ~kgkWT~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~L~p~~--kKg~WT~EED~~Ll~lV~-------k 129 (535)
.+|.||+||++.|.+++.++| ..|.+|++.| +|.+..|+.||+++...+. +++.||-||.+.|+++|+ +
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g-~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~q 460 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHG-NDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREALQ 460 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhc-ccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhhc
Confidence 789999999999999999995 5699999999 9999999999999998875 889999999999999995 2
Q ss_pred h------------------CCCchhhhcccccccchhhhHhhhhhhcCC-CCCCCCCCH-HHHHHHHHHHHHhC------
Q 009439 130 Y------------------GPTKWSVIAKSLPGRIGKQCRERWHNHLNP-DIKKDAWTL-EEELALMNAHRIHG------ 183 (535)
Q Consensus 130 y------------------G~~~W~~IAk~LpgRt~kqcr~Rw~n~L~p-~ik~~~WT~-EEd~~Li~lv~~~G------ 183 (535)
+ ...+|..|++.++.|+..|||.+|..++.. -.....|.. -+...|++-+..++
T Consensus 461 ~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n~~~~~~~~~~v~l~ErL~dl~~~e~~~ 540 (607)
T KOG0051|consen 461 PQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFNKRQESKGSDMVWLLERLSDLDLTEESP 540 (607)
T ss_pred ccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhhcccccccchhHHHHHHHHhcccccCCc
Confidence 3 224799999988999999999999988743 344555554 34445555444444
Q ss_pred CchhhHhhhCCCCC-HhHHHHHHHHHHHh
Q 009439 184 NKWAEIAKVLPGRT-DNSIKNHWNSSLKK 211 (535)
Q Consensus 184 ~kW~~IA~~lpgRT-~~qcknRw~~llkk 211 (535)
-+|..|+.+.||.. ..+|+.+|..+.+.
T Consensus 541 IDW~~l~~~~~g~~~~~e~r~q~~~lk~~ 569 (607)
T KOG0051|consen 541 IDWKSLAEYAPGESTGEELRLQFERLKKK 569 (607)
T ss_pred cCHHHHHHhCCCCCcHHHHHHHHHhHhhc
Confidence 37999999999998 99999999988776
No 11
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.52 E-value=2.8e-14 Score=112.66 Aligned_cols=60 Identities=47% Similarity=0.987 Sum_probs=54.6
Q ss_pred CCHHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhccCCCCCCCCCCHHHHHHH
Q 009439 63 WTPEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKVLNPDLVKGPWTQEEDDKI 123 (535)
Q Consensus 63 WT~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~L~p~~kKg~WT~EED~~L 123 (535)
||+|||++|+.+|..|| .+|..||++|++|+..+|+.||+++|++...+++||++||++|
T Consensus 1 WT~eEd~~L~~~~~~~g-~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYG-NDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHT-S-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC-cCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 99999999999999996 5799999999779999999999999999999999999999987
No 12
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.49 E-value=3.9e-14 Score=111.86 Aligned_cols=60 Identities=53% Similarity=1.029 Sum_probs=54.9
Q ss_pred CCHHHHHHHHHHHHHhCCCchhhhcccccccchhhhHhhhhhhcCCCCCCCCCCHHHHHHH
Q 009439 115 WTQEEDDKITELVSKYGPTKWSVIAKSLPGRIGKQCRERWHNHLNPDIKKDAWTLEEELAL 175 (535)
Q Consensus 115 WT~EED~~Ll~lV~kyG~~~W~~IAk~LpgRt~kqcr~Rw~n~L~p~ik~~~WT~EEd~~L 175 (535)
||+|||++|+.+|.+|| .+|..||+.|+.|++.+|+.||.++|++.+.+++||.+||.+|
T Consensus 1 WT~eEd~~L~~~~~~~g-~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYG-NDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHT-S-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC-cCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 99999999999999999 7899999999779999999999999999999999999999987
No 13
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.42 E-value=1.4e-13 Score=149.36 Aligned_cols=154 Identities=26% Similarity=0.405 Sum_probs=135.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhccCCCCCCCCCCHHHHHHHHHHHHHhCCCc
Q 009439 55 PIRRAKGGWTPEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKVLNPDLVKGPWTQEEDDKITELVSKYGPTK 134 (535)
Q Consensus 55 ~~rr~kgkWT~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~L~p~~kKg~WT~EED~~Ll~lV~kyG~~~ 134 (535)
...+..|.|+..||+.|..+|..||..+|..||..|..|++.||+.||..+++|.+++..|+.|||..|+.+..++| ..
T Consensus 15 ~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~-~~ 93 (512)
T COG5147 15 QTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELG-TQ 93 (512)
T ss_pred cceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcC-ch
Confidence 34567789999999999999999999999999999999999999999999999999999999999999999999999 67
Q ss_pred hhhhcccccccchhhhHhhhhhhcCCCCCCCCCCHHHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHH
Q 009439 135 WSVIAKSLPGRIGKQCRERWHNHLNPDIKKDAWTLEEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLK 210 (535)
Q Consensus 135 W~~IAk~LpgRt~kqcr~Rw~n~L~p~ik~~~WT~EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llk 210 (535)
|..|+..+++|+..+|.+||.+.+..... ..|+..+....+..+..++..|..+....-.+-...+.|++..+..
T Consensus 94 wstia~~~d~rt~~~~~ery~~~~~~~~s-~~~s~~~~~~~f~k~d~f~~~~~~~~~~~~~~~~~~~~N~~~~~~~ 168 (512)
T COG5147 94 WSTIADYKDRRTAQQCVERYVNTLEDLSS-THDSKLQRRNEFDKIDPFNENSARRPDIYEDELLEREVNREASYRL 168 (512)
T ss_pred hhhhccccCccchHHHHHHHHHHhhhhhc-cccccccchhhccccCchhhhhhhhhhhhhcccchhhhhHHHHHHH
Confidence 99999999999999999999999887666 7888888888887888888877777766655666667777654443
No 14
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.36 E-value=6.7e-13 Score=144.15 Aligned_cols=106 Identities=34% Similarity=0.665 Sum_probs=101.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCchhhhcccccccchhhhHhhhhhhcCCCCCCCCCCHHHHHHHHHHHHHhCCchhh
Q 009439 109 DLVKGPWTQEEDDKITELVSKYGPTKWSVIAKSLPGRIGKQCRERWHNHLNPDIKKDAWTLEEELALMNAHRIHGNKWAE 188 (535)
Q Consensus 109 ~~kKg~WT~EED~~Ll~lV~kyG~~~W~~IAk~LpgRt~kqcr~Rw~n~L~p~ik~~~WT~EEd~~Li~lv~~~G~kW~~ 188 (535)
..+.|.|+..||+.|+.+|++||+++|..||..|..+++++|+.||++++++.+++..|+.|||..|+++..++|..|..
T Consensus 17 ~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~wst 96 (512)
T COG5147 17 KRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQWST 96 (512)
T ss_pred eecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCchhhh
Confidence 45678999999999999999999999999999998899999999999999999999999999999999999999999999
Q ss_pred HhhhCCCCCHhHHHHHHHHHHHhHHH
Q 009439 189 IAKVLPGRTDNSIKNHWNSSLKKKLD 214 (535)
Q Consensus 189 IA~~lpgRT~~qcknRw~~llkkk~~ 214 (535)
||..+++|+..+|.+||...+.....
T Consensus 97 ia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 97 IADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hccccCccchHHHHHHHHHHhhhhhc
Confidence 99999999999999999988876654
No 15
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.34 E-value=7.9e-13 Score=141.03 Aligned_cols=105 Identities=32% Similarity=0.714 Sum_probs=99.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCchhhhcccccccchhhhHhhhhhhcCCCCCCCCCCHHHHHHHHHHHHHhCCchhhH
Q 009439 110 LVKGPWTQEEDDKITELVSKYGPTKWSVIAKSLPGRIGKQCRERWHNHLNPDIKKDAWTLEEELALMNAHRIHGNKWAEI 189 (535)
Q Consensus 110 ~kKg~WT~EED~~Ll~lV~kyG~~~W~~IAk~LpgRt~kqcr~Rw~n~L~p~ik~~~WT~EEd~~Li~lv~~~G~kW~~I 189 (535)
++.|.|+..||+.|..+|.+||.+.|..|+..++..+.+||+.||..+++|.+++..|+.|||.+||.+.......|..|
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrtI 84 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRTI 84 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccchH
Confidence 35678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhCCCCCHhHHHHHHHHHHHhHHHH
Q 009439 190 AKVLPGRTDNSIKNHWNSSLKKKLDF 215 (535)
Q Consensus 190 A~~lpgRT~~qcknRw~~llkkk~~~ 215 (535)
+..| ||+.+||-.||+.++-.....
T Consensus 85 a~i~-gr~~~qc~eRy~~ll~~~~s~ 109 (617)
T KOG0050|consen 85 ADIM-GRTSQQCLERYNNLLDVYVSY 109 (617)
T ss_pred HHHh-hhhHHHHHHHHHHHHHHHHhh
Confidence 9998 999999999999999876653
No 16
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.32 E-value=2.5e-13 Score=144.86 Aligned_cols=98 Identities=36% Similarity=0.752 Sum_probs=93.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhccCCCCCCCCCCHHHHHHHHHHHHHhCCCchhhh
Q 009439 59 AKGGWTPEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKVLNPDLVKGPWTQEEDDKITELVSKYGPTKWSVI 138 (535)
Q Consensus 59 ~kgkWT~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~L~p~~kKg~WT~EED~~Ll~lV~kyG~~~W~~I 138 (535)
..|-|+.-||+.|..+|.+||...|.+|++.++..+.+||+.||..+++|.+++..|+.|||++|+-+..... ..|..|
T Consensus 6 kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p-~qwrtI 84 (617)
T KOG0050|consen 6 KGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEP-TQWRTI 84 (617)
T ss_pred ecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcC-CccchH
Confidence 4577999999999999999999999999999999999999999999999999999999999999999998887 789999
Q ss_pred cccccccchhhhHhhhhhhc
Q 009439 139 AKSLPGRIGKQCRERWHNHL 158 (535)
Q Consensus 139 Ak~LpgRt~kqcr~Rw~n~L 158 (535)
+..| +|++.||.+||.+.|
T Consensus 85 a~i~-gr~~~qc~eRy~~ll 103 (617)
T KOG0050|consen 85 ADIM-GRTSQQCLERYNNLL 103 (617)
T ss_pred HHHh-hhhHHHHHHHHHHHH
Confidence 9999 999999999998775
No 17
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.24 E-value=5.8e-12 Score=95.62 Aligned_cols=47 Identities=47% Similarity=0.859 Sum_probs=42.6
Q ss_pred CCCCCHHHHHHHHHHHHHhcCCChhhhhhcCC-CCCHHHHHHHhhhcc
Q 009439 60 KGGWTPEEDETLRNAVSTFKGKSWKKIAEFFP-DRSEVQCLHRWQKVL 106 (535)
Q Consensus 60 kgkWT~EEDe~L~klV~~yg~~nW~~IAk~lp-~RT~~qCr~Rw~~~L 106 (535)
+++||+|||++|+++|.+||..+|..||..|+ +||..||+.||++++
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 57899999999999999998888999999999 999999999999864
No 18
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.16 E-value=4.1e-11 Score=90.99 Aligned_cols=46 Identities=35% Similarity=0.698 Sum_probs=41.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCc-hhhHhhhCC-CCCHhHHHHHHHHHH
Q 009439 164 KDAWTLEEELALMNAHRIHGNK-WAEIAKVLP-GRTDNSIKNHWNSSL 209 (535)
Q Consensus 164 ~~~WT~EEd~~Li~lv~~~G~k-W~~IA~~lp-gRT~~qcknRw~~ll 209 (535)
+++||+||+++|++++.+||.+ |..||.+|+ +||..||++||+.++
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 5789999999999999999988 999999999 999999999999764
No 19
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.95 E-value=1.2e-09 Score=80.52 Aligned_cols=47 Identities=45% Similarity=0.803 Sum_probs=44.3
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CchhhHhhhCCCCCHhHHHHHHHHHHH
Q 009439 164 KDAWTLEEELALMNAHRIHG-NKWAEIAKVLPGRTDNSIKNHWNSSLK 210 (535)
Q Consensus 164 ~~~WT~EEd~~Li~lv~~~G-~kW~~IA~~lpgRT~~qcknRw~~llk 210 (535)
++.||++|+.+|+.++..|| .+|..||..|++||..+|++||+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 36899999999999999999 999999999999999999999998764
No 20
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.92 E-value=2.1e-09 Score=79.28 Aligned_cols=48 Identities=44% Similarity=0.865 Sum_probs=44.2
Q ss_pred CCCCCHHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhccC
Q 009439 60 KGGWTPEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKVLN 107 (535)
Q Consensus 60 kgkWT~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~L~ 107 (535)
++.||++||++|+.++..||..+|..||..|++|+..+|+.||..++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 357999999999999999976889999999999999999999998764
No 21
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.82 E-value=6.8e-09 Score=75.47 Aligned_cols=44 Identities=43% Similarity=0.810 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHHHHHhC-CchhhHhhhCCCCCHhHHHHHHHHHH
Q 009439 166 AWTLEEELALMNAHRIHG-NKWAEIAKVLPGRTDNSIKNHWNSSL 209 (535)
Q Consensus 166 ~WT~EEd~~Li~lv~~~G-~kW~~IA~~lpgRT~~qcknRw~~ll 209 (535)
+||.+|+..|+.++..+| .+|..||..|++|+..+|++||+.++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 89999999999999999999998753
No 22
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.79 E-value=8.7e-09 Score=74.91 Aligned_cols=45 Identities=44% Similarity=0.870 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhcc
Q 009439 62 GWTPEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKVL 106 (535)
Q Consensus 62 kWT~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~L 106 (535)
.||+||++.|++++..||..+|..||+.|++|+..+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 499999999999999998688999999999999999999998753
No 23
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.80 E-value=3.9e-05 Score=60.93 Aligned_cols=48 Identities=27% Similarity=0.424 Sum_probs=42.9
Q ss_pred CCCCCHHHHHHHHHHHHHhcCCCh---hhhhhcCC-CC-CHHHHHHHhhhccC
Q 009439 60 KGGWTPEEDETLRNAVSTFKGKSW---KKIAEFFP-DR-SEVQCLHRWQKVLN 107 (535)
Q Consensus 60 kgkWT~EEDe~L~klV~~yg~~nW---~~IAk~lp-~R-T~~qCr~Rw~~~L~ 107 (535)
+-.||+||.++++++|..+|.++| +.|++.|. .| |..||+.|+++++.
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 457999999999999999998899 99999886 46 99999999998753
No 24
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.51 E-value=7.7e-05 Score=79.75 Aligned_cols=49 Identities=22% Similarity=0.479 Sum_probs=45.5
Q ss_pred CCCCCCHHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhccC
Q 009439 59 AKGGWTPEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKVLN 107 (535)
Q Consensus 59 ~kgkWT~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~L~ 107 (535)
...-||++|+=+|++++..||-+||..||++++.|+..+|++||.+++-
T Consensus 71 ~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 71 LDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHh
Confidence 4456999999999999999999999999999999999999999999763
No 25
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.27 E-value=0.00062 Score=54.13 Aligned_cols=47 Identities=17% Similarity=0.357 Sum_probs=40.6
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC-ch---hhHhhhCC-CC-CHhHHHHHHHHHH
Q 009439 163 KKDAWTLEEELALMNAHRIHGN-KW---AEIAKVLP-GR-TDNSIKNHWNSSL 209 (535)
Q Consensus 163 k~~~WT~EEd~~Li~lv~~~G~-kW---~~IA~~lp-gR-T~~qcknRw~~ll 209 (535)
.+-.||+||...+++++..+|. +| ..|+..|. .| |..||+.++....
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 3568999999999999999996 99 99999874 45 9999999987554
No 26
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=97.16 E-value=0.00057 Score=64.70 Aligned_cols=54 Identities=30% Similarity=0.506 Sum_probs=47.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC-------chhhHhhhCCCCCHhHHHHHHHHHHHhHHHHH
Q 009439 162 IKKDAWTLEEELALMNAHRIHGN-------KWAEIAKVLPGRTDNSIKNHWNSSLKKKLDFY 216 (535)
Q Consensus 162 ik~~~WT~EEd~~Li~lv~~~G~-------kW~~IA~~lpgRT~~qcknRw~~llkkk~~~~ 216 (535)
.+.+.||.|||.+|-+.|-.|-. -+.+++..| +||...|..|||..+||++...
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~~ 62 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEEA 62 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHHH
Confidence 35689999999999999987742 389999999 9999999999999999988754
No 27
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.14 E-value=0.00057 Score=73.25 Aligned_cols=48 Identities=29% Similarity=0.591 Sum_probs=43.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhC-CchhhHhhhCCCCCHhHHHHHHHHHH
Q 009439 162 IKKDAWTLEEELALMNAHRIHG-NKWAEIAKVLPGRTDNSIKNHWNSSL 209 (535)
Q Consensus 162 ik~~~WT~EEd~~Li~lv~~~G-~kW~~IA~~lpgRT~~qcknRw~~ll 209 (535)
+-...||.+||.+||+++..|| ++|..||.++..|+..+|+.+|....
T Consensus 70 i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHH
Confidence 4457899999999999999999 89999999999999999999997544
No 28
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=96.82 E-value=0.0068 Score=59.65 Aligned_cols=99 Identities=23% Similarity=0.370 Sum_probs=74.5
Q ss_pred CCCHHHHHHHHHHHHHhCCCchhhhccccc---ccchhhhHhhhhhhcC----------------CC-----CCCCCCCH
Q 009439 114 PWTQEEDDKITELVSKYGPTKWSVIAKSLP---GRIGKQCRERWHNHLN----------------PD-----IKKDAWTL 169 (535)
Q Consensus 114 ~WT~EED~~Ll~lV~kyG~~~W~~IAk~Lp---gRt~kqcr~Rw~n~L~----------------p~-----ik~~~WT~ 169 (535)
+|++++|-+|+.+|..-. +...|+..+. .-|-..+.+||+.+|- |. ..+.+||.
T Consensus 1 rW~~~DDl~Li~av~~~~--~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~~is~~a~~~m~~l~p~~~~~iq~kalfS~ 78 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTN--DLESVHLGVKFSCKFTLQEIEERWYALLYDPVISRIAVAAMRNLHPELIAAIQSKALFSK 78 (199)
T ss_pred CCCchhhHHHHHHHHHhc--CHHHHHccCCcCCcCcHHHHHHHHHHHHcChhhHHHHHHHHHhCCcchhhcccccCCCCH
Confidence 599999999999997754 6777776653 5677889999987652 22 23578999
Q ss_pred HHHHHHHHHHHHhCC---chhhHhh----hC-CCCCHhHHHHHHHHHHHhHHH
Q 009439 170 EEELALMNAHRIHGN---KWAEIAK----VL-PGRTDNSIKNHWNSSLKKKLD 214 (535)
Q Consensus 170 EEd~~Li~lv~~~G~---kW~~IA~----~l-pgRT~~qcknRw~~llkkk~~ 214 (535)
+|+++|......... .+.+|-. .| ++||+.++.++|..+.+..+-
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~LL 131 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHLL 131 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhchh
Confidence 999999997755543 4666654 23 679999999999976666553
No 29
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.53 E-value=0.0023 Score=69.23 Aligned_cols=46 Identities=17% Similarity=0.499 Sum_probs=41.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhc
Q 009439 59 AKGGWTPEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKV 105 (535)
Q Consensus 59 ~kgkWT~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~ 105 (535)
....|+.+|..+|.++|+.|| .+|.+||.++++|+..||..||.++
T Consensus 278 ~dk~WS~qE~~LLLEGIe~yg-DdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYG-DDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhh-hhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 344799999999999999994 5699999999999999999999875
No 30
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.37 E-value=0.0033 Score=68.03 Aligned_cols=46 Identities=20% Similarity=0.464 Sum_probs=42.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHH
Q 009439 163 KKDAWTLEEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSS 208 (535)
Q Consensus 163 k~~~WT~EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~l 208 (535)
....||.+|..+|+++++.||..|.+||.++.+||..||.-||-++
T Consensus 278 ~dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 3458999999999999999999999999999999999999999754
No 31
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=96.34 E-value=0.0027 Score=51.83 Aligned_cols=51 Identities=24% Similarity=0.322 Sum_probs=33.5
Q ss_pred CCCCCHHHHHHHHHHHHHhc------CC--ChhhhhhcCC-CCCHHHHHHHhhhccCCCC
Q 009439 60 KGGWTPEEDETLRNAVSTFK------GK--SWKKIAEFFP-DRSEVQCLHRWQKVLNPDL 110 (535)
Q Consensus 60 kgkWT~EEDe~L~klV~~yg------~~--nW~~IAk~lp-~RT~~qCr~Rw~~~L~p~~ 110 (535)
+.+||.|||++|++.|..+. .+ =|.++++.-+ ++|..+.++||.+.|.+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~ 61 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRP 61 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccc
Confidence 45799999999999997662 11 2999999888 9999999999999887544
No 32
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.25 E-value=0.005 Score=68.16 Aligned_cols=46 Identities=20% Similarity=0.409 Sum_probs=42.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHH
Q 009439 164 KDAWTLEEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSL 209 (535)
Q Consensus 164 ~~~WT~EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~ll 209 (535)
+..||++|..+|++++..||.+|..||.++.+||..||--||..+=
T Consensus 253 ~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~LP 298 (506)
T KOG1279|consen 253 RPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRLP 298 (506)
T ss_pred CCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhcC
Confidence 5689999999999999999999999999999999999999987543
No 33
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=96.24 E-value=0.013 Score=57.76 Aligned_cols=94 Identities=22% Similarity=0.421 Sum_probs=71.0
Q ss_pred CCCHHHHHHHHHHHHHhcCCChhhhhhcCC---CCCHHHHHHHhhhccC----------------CC-----CCCCCCCH
Q 009439 62 GWTPEEDETLRNAVSTFKGKSWKKIAEFFP---DRSEVQCLHRWQKVLN----------------PD-----LVKGPWTQ 117 (535)
Q Consensus 62 kWT~EEDe~L~klV~~yg~~nW~~IAk~lp---~RT~~qCr~Rw~~~L~----------------p~-----~kKg~WT~ 117 (535)
+|++++|-+|+.+|.. +.+-..|+..+. .-|...+..||+.+|- |. ..+-+||.
T Consensus 1 rW~~~DDl~Li~av~~--~~~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~~is~~a~~~m~~l~p~~~~~iq~kalfS~ 78 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ--TNDLESVHLGVKFSCKFTLQEIEERWYALLYDPVISRIAVAAMRNLHPELIAAIQSKALFSK 78 (199)
T ss_pred CCCchhhHHHHHHHHH--hcCHHHHHccCCcCCcCcHHHHHHHHHHHHcChhhHHHHHHHHHhCCcchhhcccccCCCCH
Confidence 5999999999999988 666788877654 5688899999999762 22 23457999
Q ss_pred HHHHHHHHHHHHhCC--Cchhhhccc----c-cccchhhhHhhhhhh
Q 009439 118 EEDDKITELVSKYGP--TKWSVIAKS----L-PGRIGKQCRERWHNH 157 (535)
Q Consensus 118 EED~~Ll~lV~kyG~--~~W~~IAk~----L-pgRt~kqcr~Rw~n~ 157 (535)
+|+++|........+ ..+.+|-.. + +.||+++...+|..+
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lm 125 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLM 125 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHH
Confidence 999999987655432 245555432 2 589999999999864
No 34
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.22 E-value=0.0046 Score=51.99 Aligned_cols=50 Identities=32% Similarity=0.498 Sum_probs=35.6
Q ss_pred CCCCCHHHHHHHHHHHHH------hC--C------chhhHhhhC----CCCCHhHHHHHHHHHHHhHH
Q 009439 164 KDAWTLEEELALMNAHRI------HG--N------KWAEIAKVL----PGRTDNSIKNHWNSSLKKKL 213 (535)
Q Consensus 164 ~~~WT~EEd~~Li~lv~~------~G--~------kW~~IA~~l----pgRT~~qcknRw~~llkkk~ 213 (535)
+..||.+|...||+++.. ++ . -|..||..| ..||+.||+++|+.|.++..
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk 68 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYK 68 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Confidence 357999999999999876 21 1 399999976 35999999999999777654
No 35
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.21 E-value=0.0055 Score=67.85 Aligned_cols=46 Identities=28% Similarity=0.693 Sum_probs=42.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhc
Q 009439 59 AKGGWTPEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKV 105 (535)
Q Consensus 59 ~kgkWT~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~ 105 (535)
.+..||.+|.-+|+++|+.| +.+|.+||.++..|+..||..|+.++
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y-~ddW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMY-GDDWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred CCCCccHHHHHHHHHHHHHh-cccHHHHHhccCCCCHHHHHHHHHhc
Confidence 45679999999999999999 55699999999999999999999885
No 36
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=95.85 E-value=0.013 Score=47.81 Aligned_cols=51 Identities=24% Similarity=0.421 Sum_probs=32.4
Q ss_pred CCCCCHHHHHHHHHHHHHhC--------Cc-hhhHhhhCC-CCCHhHHHHHHHHHHHhHHH
Q 009439 164 KDAWTLEEELALMNAHRIHG--------NK-WAEIAKVLP-GRTDNSIKNHWNSSLKKKLD 214 (535)
Q Consensus 164 ~~~WT~EEd~~Li~lv~~~G--------~k-W~~IA~~lp-gRT~~qcknRw~~llkkk~~ 214 (535)
+.+||+|||.+|++.+..+. ++ |.+++...+ .+|-.+.++||...|+.+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~~ 62 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRPR 62 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT-----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcccc
Confidence 46899999999999996542 22 999999888 89999999999877766543
No 37
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.83 E-value=0.012 Score=56.62 Aligned_cols=54 Identities=28% Similarity=0.425 Sum_probs=44.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCc-------hhhHhhhCCCCCHhHHHHHHHHHHHhHHHHH
Q 009439 162 IKKDAWTLEEELALMNAHRIHGNK-------WAEIAKVLPGRTDNSIKNHWNSSLKKKLDFY 216 (535)
Q Consensus 162 ik~~~WT~EEd~~Li~lv~~~G~k-------W~~IA~~lpgRT~~qcknRw~~llkkk~~~~ 216 (535)
.+.+.||.|||.+|-+.+..|+.. ...++..| +||..+|..|||..+++++...
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Yee~ 63 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQEQ 63 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHHHH
Confidence 456899999999998888877642 66677777 9999999999999999887643
No 38
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.62 E-value=0.0083 Score=62.31 Aligned_cols=47 Identities=21% Similarity=0.509 Sum_probs=44.6
Q ss_pred CCCCHHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhccC
Q 009439 61 GGWTPEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKVLN 107 (535)
Q Consensus 61 gkWT~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~L~ 107 (535)
..|+..|+-+|++..+..|-+||..||.+++.|+...|+.||.+++.
T Consensus 64 e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 64 EGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 46999999999999999999999999999999999999999999875
No 39
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=95.51 E-value=0.042 Score=65.88 Aligned_cols=145 Identities=13% Similarity=0.228 Sum_probs=94.8
Q ss_pred CCCHHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhccCCCCCCCCCC-HHHHHHHHHHHHHhCCCc---hhh
Q 009439 62 GWTPEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKVLNPDLVKGPWT-QEEDDKITELVSKYGPTK---WSV 137 (535)
Q Consensus 62 kWT~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~L~p~~kKg~WT-~EED~~Ll~lV~kyG~~~---W~~ 137 (535)
.|+.-+=..++++..+||-.+...||..|.+++...++.-.+-... . +. -.+-++++.-|.+-. .+ -..
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~~f~~-~-----~~~~~~~~~~~~~ie~~e-~~~~~~~~ 898 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAKVFWE-R-----YKELNDYDRIIKNIERGE-ARISRKDE 898 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHHHHHH-h-----hhhhccHHHHHHHHHHHH-HHHHHHHH
Confidence 4888888888999999998899999999999999988643222111 0 11 112234444443321 11 111
Q ss_pred hcccccccchhhhHhhhhhhc--CCCCCCCCCCHHHHHHHHHHHHHhC-CchhhHhh------------hCCCCCHhHHH
Q 009439 138 IAKSLPGRIGKQCRERWHNHL--NPDIKKDAWTLEEELALMNAHRIHG-NKWAEIAK------------VLPGRTDNSIK 202 (535)
Q Consensus 138 IAk~LpgRt~kqcr~Rw~n~L--~p~ik~~~WT~EEd~~Li~lv~~~G-~kW~~IA~------------~lpgRT~~qck 202 (535)
+.+.+ .+--.+|+.-|..+- -+..++..||+|||..|+-.+.+|| .+|..|-. .|..||+..|.
T Consensus 899 ~~~~~-~~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~ 977 (1033)
T PLN03142 899 IMKAI-GKKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELA 977 (1033)
T ss_pred HHHHH-HHHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHH
Confidence 11222 334455555554331 1234556799999999999999999 67999954 34689999999
Q ss_pred HHHHHHHHhHHH
Q 009439 203 NHWNSSLKKKLD 214 (535)
Q Consensus 203 nRw~~llkkk~~ 214 (535)
.|-++|++-..+
T Consensus 978 ~r~~~l~~~~~~ 989 (1033)
T PLN03142 978 RRCDTLIRLIEK 989 (1033)
T ss_pred HHHHHHHHHHHH
Confidence 999998876544
No 40
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=95.20 E-value=0.0082 Score=50.47 Aligned_cols=46 Identities=30% Similarity=0.629 Sum_probs=33.1
Q ss_pred CCCCHHHHHHHHHHHHH--h----cC-C------ChhhhhhcCC----CCCHHHHHHHhhhcc
Q 009439 61 GGWTPEEDETLRNAVST--F----KG-K------SWKKIAEFFP----DRSEVQCLHRWQKVL 106 (535)
Q Consensus 61 gkWT~EEDe~L~klV~~--y----g~-~------nW~~IAk~lp----~RT~~qCr~Rw~~~L 106 (535)
..||.+|...|+.++.. + +. . -|..||..|. .|++.||+.+|.++.
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~ 64 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLK 64 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 46999999999999877 2 11 1 3999999874 799999999998853
No 41
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=94.60 E-value=0.035 Score=57.84 Aligned_cols=47 Identities=28% Similarity=0.596 Sum_probs=42.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhC-CchhhHhhhCCCCCHhHHHHHHHHHH
Q 009439 163 KKDAWTLEEELALMNAHRIHG-NKWAEIAKVLPGRTDNSIKNHWNSSL 209 (535)
Q Consensus 163 k~~~WT~EEd~~Li~lv~~~G-~kW~~IA~~lpgRT~~qcknRw~~ll 209 (535)
-...|+.+|+.+||++....| ++|..||.++..|+...||.+|..+.
T Consensus 62 ~~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y 109 (432)
T COG5114 62 GEEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMY 109 (432)
T ss_pred cCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHH
Confidence 346799999999999999999 89999999999999999999987443
No 42
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=94.36 E-value=0.095 Score=43.25 Aligned_cols=49 Identities=29% Similarity=0.453 Sum_probs=40.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-----------------chhhHhhhC-----CCCCHhHHHHHHHHHHHhH
Q 009439 164 KDAWTLEEELALMNAHRIHGN-----------------KWAEIAKVL-----PGRTDNSIKNHWNSSLKKK 212 (535)
Q Consensus 164 ~~~WT~EEd~~Li~lv~~~G~-----------------kW~~IA~~l-----pgRT~~qcknRw~~llkkk 212 (535)
...||.+|...|++++.+|.. -|..|+..| +.|+..+++.+|..+....
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~ 72 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKA 72 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHH
Confidence 457999999999999987731 299999865 3599999999999887654
No 43
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=94.28 E-value=0.025 Score=53.77 Aligned_cols=47 Identities=26% Similarity=0.584 Sum_probs=39.9
Q ss_pred CCCCCHHHHHHHHHHHHHhc--CC----ChhhhhhcCCCCCHHHHHHHhhhccC
Q 009439 60 KGGWTPEEDETLRNAVSTFK--GK----SWKKIAEFFPDRSEVQCLHRWQKVLN 107 (535)
Q Consensus 60 kgkWT~EEDe~L~klV~~yg--~~----nW~~IAk~lp~RT~~qCr~Rw~~~L~ 107 (535)
.-.||.|||.+|...|.+|- |+ -+.+|++.| +||...|--||.-+++
T Consensus 4 QDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VR 56 (161)
T TIGR02894 4 QDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVR 56 (161)
T ss_pred ccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHH
Confidence 34699999999999999981 11 288999999 9999999999988776
No 44
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=93.88 E-value=0.049 Score=44.97 Aligned_cols=46 Identities=33% Similarity=0.514 Sum_probs=38.2
Q ss_pred CCCCHHHHHHHHHHHHHhcC----------------CChhhhhhcCC-----CCCHHHHHHHhhhcc
Q 009439 61 GGWTPEEDETLRNAVSTFKG----------------KSWKKIAEFFP-----DRSEVQCLHRWQKVL 106 (535)
Q Consensus 61 gkWT~EEDe~L~klV~~yg~----------------~nW~~IAk~lp-----~RT~~qCr~Rw~~~L 106 (535)
..||.+|.+.|+++|.+|.. .-|..|+..|. .|+..+++..|.++.
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk 69 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLK 69 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 46999999999999998821 12999998773 699999999999864
No 45
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=92.61 E-value=0.13 Score=54.91 Aligned_cols=61 Identities=26% Similarity=0.366 Sum_probs=52.1
Q ss_pred hhhhhhcCCCCCCCCCCHHHHHHHHHHHHHhCCchhhHhhh-----CCC-CCHhHHHHHHHHHHHhHHHHH
Q 009439 152 ERWHNHLNPDIKKDAWTLEEELALMNAHRIHGNKWAEIAKV-----LPG-RTDNSIKNHWNSSLKKKLDFY 216 (535)
Q Consensus 152 ~Rw~n~L~p~ik~~~WT~EEd~~Li~lv~~~G~kW~~IA~~-----lpg-RT~~qcknRw~~llkkk~~~~ 216 (535)
+-|.++|+. ..||.+|-+-|++|...|.-+|-.|+.. ++. ||-.++|.||+...++.+...
T Consensus 122 eEYe~~l~d----n~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr 188 (445)
T KOG2656|consen 122 EEYEAHLND----NSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKAR 188 (445)
T ss_pred HHHHHhhcc----ccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHHHHHHHHHcc
Confidence 345565553 7899999999999999999999999987 666 999999999999999887643
No 46
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=91.53 E-value=0.52 Score=51.43 Aligned_cols=41 Identities=20% Similarity=0.371 Sum_probs=37.4
Q ss_pred CCCCHHHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHH
Q 009439 165 DAWTLEEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWN 206 (535)
Q Consensus 165 ~~WT~EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~ 206 (535)
-.||++|-. +++....|+.....|+..+...|+.|++.+|.
T Consensus 471 ~~wSp~e~s-~ircf~~y~~~fe~ia~l~~tktp~Q~~~fy~ 511 (534)
T KOG1194|consen 471 YGWSPEEKS-AIRCFHWYKDNFELIAELMATKTPEQIKKFYM 511 (534)
T ss_pred CCCCCcccc-cccCchhhccchHHHHHHhcCCCHHHHHHHhc
Confidence 359998887 88899999999999999999999999999985
No 47
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=91.11 E-value=0.35 Score=51.59 Aligned_cols=49 Identities=22% Similarity=0.352 Sum_probs=43.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHh
Q 009439 163 KKDAWTLEEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKK 211 (535)
Q Consensus 163 k~~~WT~EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkk 211 (535)
...+|+.+|-+++.+++..+|..+..|+.+||.|...|||.+|..--++
T Consensus 364 ~~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~ 412 (507)
T COG5118 364 GALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKV 412 (507)
T ss_pred CCCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhh
Confidence 3468999999999999999999999999999999999999999754443
No 48
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=90.63 E-value=0.17 Score=48.72 Aligned_cols=47 Identities=23% Similarity=0.567 Sum_probs=37.4
Q ss_pred CCCCCHHHHHHHHHHHHHhcCCC------hhhhhhcCCCCCHHHHHHHhhhccC
Q 009439 60 KGGWTPEEDETLRNAVSTFKGKS------WKKIAEFFPDRSEVQCLHRWQKVLN 107 (535)
Q Consensus 60 kgkWT~EEDe~L~klV~~yg~~n------W~~IAk~lp~RT~~qCr~Rw~~~L~ 107 (535)
...||.|||.+|.+.|..|+... ...++..| +|+..+|..||.-+++
T Consensus 5 qdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vr 57 (170)
T PRK13923 5 QDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVR 57 (170)
T ss_pred hhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHH
Confidence 45799999999999999884332 56666777 8999999999966554
No 49
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=89.74 E-value=0.88 Score=49.72 Aligned_cols=52 Identities=25% Similarity=0.383 Sum_probs=46.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhH
Q 009439 161 DIKKDAWTLEEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKK 212 (535)
Q Consensus 161 ~ik~~~WT~EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk 212 (535)
+--...||.||-.++-+++..||.++.+|-+.||.|+-..|..+|....+.+
T Consensus 184 ~~~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK~~ 235 (534)
T KOG1194|consen 184 TEFPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKKTR 235 (534)
T ss_pred CCCcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHHHh
Confidence 3445789999999999999999999999999999999999999988766543
No 50
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=88.76 E-value=0.68 Score=48.86 Aligned_cols=52 Identities=25% Similarity=0.362 Sum_probs=41.6
Q ss_pred CCCCCHHHHHHHHHHHHHh----------CCchhhHhhhC----CCCCHhHHHHHHHHHHHhHHHH
Q 009439 164 KDAWTLEEELALMNAHRIH----------GNKWAEIAKVL----PGRTDNSIKNHWNSSLKKKLDF 215 (535)
Q Consensus 164 ~~~WT~EEd~~Li~lv~~~----------G~kW~~IA~~l----pgRT~~qcknRw~~llkkk~~~ 215 (535)
...|+.+|-..||++.... +.-|..||..+ ..||+.+|+++|.++.++.-+.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~ 119 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKE 119 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHH
Confidence 4789999999999987533 23499999954 3499999999999988876543
No 51
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=87.76 E-value=0.82 Score=48.95 Aligned_cols=46 Identities=24% Similarity=0.447 Sum_probs=40.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhh
Q 009439 58 RAKGGWTPEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQK 104 (535)
Q Consensus 58 r~kgkWT~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~ 104 (535)
...-+|+.+|.+++.+++..+|. ++..|+..||+|.++|++..|.+
T Consensus 363 ~~~~~Ws~~e~ekFYKALs~wGt-dF~LIs~lfP~R~RkqIKaKfi~ 408 (507)
T COG5118 363 KGALRWSKKEIEKFYKALSIWGT-DFSLISSLFPNRERKQIKAKFIK 408 (507)
T ss_pred CCCCcccHHHHHHHHHHHHHhcc-hHHHHHHhcCchhHHHHHHHHHH
Confidence 34457999999999999999954 69999999999999999999875
No 52
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=87.55 E-value=0.89 Score=38.56 Aligned_cols=49 Identities=31% Similarity=0.501 Sum_probs=37.6
Q ss_pred CCCHHHHHHHHHHHHHh---CC----------chhhHhhhC---CC--CCHhHHHHHHHHHHHhHHH
Q 009439 166 AWTLEEELALMNAHRIH---GN----------KWAEIAKVL---PG--RTDNSIKNHWNSSLKKKLD 214 (535)
Q Consensus 166 ~WT~EEd~~Li~lv~~~---G~----------kW~~IA~~l---pg--RT~~qcknRw~~llkkk~~ 214 (535)
.||.++++.|++++.+. |+ .|..|+..| .| .+..||+|||..+.++...
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y~~ 67 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDYRI 67 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHHHH
Confidence 49999999999988544 22 299999876 22 6789999999977766543
No 53
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=86.37 E-value=1.5 Score=46.22 Aligned_cols=47 Identities=28% Similarity=0.490 Sum_probs=37.6
Q ss_pred CCCCCHHHHHHHHHHHHHh---------cCCChhhhhhcCC----CCCHHHHHHHhhhcc
Q 009439 60 KGGWTPEEDETLRNAVSTF---------KGKSWKKIAEFFP----DRSEVQCLHRWQKVL 106 (535)
Q Consensus 60 kgkWT~EEDe~L~klV~~y---------g~~nW~~IAk~lp----~RT~~qCr~Rw~~~L 106 (535)
...|+.+|-..|+.+..+. ....|..||..+. .|+..||+.+|.++.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 4689999999999987543 2335999999653 699999999998754
No 54
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=86.12 E-value=1.3 Score=40.34 Aligned_cols=52 Identities=23% Similarity=0.360 Sum_probs=41.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC----chhhHhh------------hCCCCCHhHHHHHHHHHHHhH
Q 009439 161 DIKKDAWTLEEELALMNAHRIHGN----KWAEIAK------------VLPGRTDNSIKNHWNSSLKKK 212 (535)
Q Consensus 161 ~ik~~~WT~EEd~~Li~lv~~~G~----kW~~IA~------------~lpgRT~~qcknRw~~llkkk 212 (535)
..++..||++||.-|+-.+.+||- .|..|-. .|..||+..|..|=++|++-.
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i 113 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLI 113 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHH
Confidence 456788999999999999999996 7999986 346799999999999888753
No 55
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=85.66 E-value=2.6 Score=45.49 Aligned_cols=44 Identities=23% Similarity=0.370 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHHHHHhcCCChhhhhhc-----CCC-CCHHHHHHHhhhcc
Q 009439 62 GWTPEEDETLRNAVSTFKGKSWKKIAEF-----FPD-RSEVQCLHRWQKVL 106 (535)
Q Consensus 62 kWT~EEDe~L~klV~~yg~~nW~~IAk~-----lp~-RT~~qCr~Rw~~~L 106 (535)
-||.||-+-|.++...| ...|..||+. ++. ||....++||..+.
T Consensus 132 ~WskeETD~LF~lck~f-DLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~ 181 (445)
T KOG2656|consen 132 SWSKEETDYLFDLCKRF-DLRFFVIADRYDNQQYKKSRTVEDLKERYYSVC 181 (445)
T ss_pred cccHHHHHHHHHHHHhc-CeeEEEEeeccchhhccccccHHHHHHHHHHHH
Confidence 49999999999999999 6779999987 664 99999999998754
No 56
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=84.97 E-value=1 Score=40.96 Aligned_cols=49 Identities=20% Similarity=0.317 Sum_probs=37.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHhcC---CChhhhhhcC------------CCCCHHHHHHHhhhcc
Q 009439 58 RAKGGWTPEEDETLRNAVSTFKG---KSWKKIAEFF------------PDRSEVQCLHRWQKVL 106 (535)
Q Consensus 58 r~kgkWT~EEDe~L~klV~~yg~---~nW~~IAk~l------------p~RT~~qCr~Rw~~~L 106 (535)
..+..||.|||.-|+-.+.+||- +.|..|-..+ ..||+..+..|...++
T Consensus 47 ~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi 110 (118)
T PF09111_consen 47 NKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLI 110 (118)
T ss_dssp SS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHH
Confidence 34567999999999999999998 7899996642 3799999988876644
No 57
>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=84.27 E-value=2.3 Score=32.36 Aligned_cols=42 Identities=26% Similarity=0.433 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHh
Q 009439 169 LEEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKK 211 (535)
Q Consensus 169 ~EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkk 211 (535)
.+++..++.++...|-.|.+||..+ |.+...++++....+++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARKK 53 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHhh
Confidence 3677888889999999999999999 99999999998876654
No 58
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=82.32 E-value=1.8 Score=36.66 Aligned_cols=44 Identities=27% Similarity=0.584 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHHh---cCC---------ChhhhhhcCC-----CCCHHHHHHHhhhc
Q 009439 62 GWTPEEDETLRNAVSTF---KGK---------SWKKIAEFFP-----DRSEVQCLHRWQKV 105 (535)
Q Consensus 62 kWT~EEDe~L~klV~~y---g~~---------nW~~IAk~lp-----~RT~~qCr~Rw~~~ 105 (535)
.||+++++.|++++.+. |.. .|..|++.|. ..+..||+.||..+
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~l 61 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTL 61 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHH
Confidence 49999999999988655 222 2999988874 46778999888764
No 59
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=77.62 E-value=2.7 Score=48.46 Aligned_cols=42 Identities=21% Similarity=0.509 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhh
Q 009439 61 GGWTPEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQ 103 (535)
Q Consensus 61 gkWT~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~ 103 (535)
-.||+.|..++.+++..| .+++..|++.++++|..||-+-|.
T Consensus 620 d~WTp~E~~lF~kA~y~~-~KDF~~v~km~~~KtVaqCVeyYY 661 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTY-SKDFIFVQKMVKSKTVAQCVEYYY 661 (907)
T ss_pred ccccHHHHHHHHHHHHHh-cccHHHHHHHhccccHHHHHHHHH
Confidence 369999999999999999 778999999999999999966553
No 60
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=74.78 E-value=4.7 Score=46.62 Aligned_cols=47 Identities=17% Similarity=0.166 Sum_probs=43.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHH
Q 009439 164 KDAWTLEEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLK 210 (535)
Q Consensus 164 ~~~WT~EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llk 210 (535)
...||..|..++-+++..|..++..|++.++++|-.+|-.+|+...|
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtWKK 665 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTWKK 665 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHHHH
Confidence 46899999999999999999999999999999999999999876654
No 61
>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=67.80 E-value=12 Score=28.11 Aligned_cols=42 Identities=24% Similarity=0.336 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKK 212 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk 212 (535)
+++..+|.++-..|..+.+||..+ |-+...|+.+.+..+++.
T Consensus 7 ~~er~vi~~~y~~~~t~~eIa~~l-g~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 7 PREREVIRLRYFEGLTLEEIAERL-GISRSTVRRILKRALKKL 48 (50)
T ss_dssp HHHHHHHHHHHTST-SHHHHHHHH-TSCHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHH-CCcHHHHHHHHHHHHHHh
Confidence 556667777777778999999999 999999999988777653
No 62
>smart00595 MADF subfamily of SANT domain.
Probab=67.17 E-value=10 Score=31.68 Aligned_cols=30 Identities=23% Similarity=0.370 Sum_probs=24.9
Q ss_pred hhhHhhhCCCCCHhHHHHHHHHHHHhHHHHH
Q 009439 186 WAEIAKVLPGRTDNSIKNHWNSSLKKKLDFY 216 (535)
Q Consensus 186 W~~IA~~lpgRT~~qcknRw~~llkkk~~~~ 216 (535)
|..||..|. -+..+|+.+|+.+..+..+..
T Consensus 30 W~~Ia~~l~-~~~~~~~~kw~~LR~~y~~e~ 59 (89)
T smart00595 30 WEEIAEELG-LSVEECKKRWKNLRDRYRREL 59 (89)
T ss_pred HHHHHHHHC-cCHHHHHHHHHHHHHHHHHHH
Confidence 999999994 499999999998876655543
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=66.24 E-value=8.1 Score=28.72 Aligned_cols=39 Identities=21% Similarity=0.238 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhc
Q 009439 66 EEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKV 105 (535)
Q Consensus 66 EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~ 105 (535)
+=|..|++++...+...|.+||+.+ |=+...|..|++++
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l-glS~~~v~~Ri~rL 41 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL-GLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH-TS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH-CcCHHHHHHHHHHh
Confidence 3478889999998888999999999 88999999998764
No 64
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=65.70 E-value=21 Score=37.84 Aligned_cols=55 Identities=25% Similarity=0.410 Sum_probs=44.1
Q ss_pred CCCCCHHHHHHHHHHHHHh-CC---chhhHhhhCCCCCHhHHHHHHHHHHHhHHHHHhh
Q 009439 164 KDAWTLEEELALMNAHRIH-GN---KWAEIAKVLPGRTDNSIKNHWNSSLKKKLDFYLA 218 (535)
Q Consensus 164 ~~~WT~EEd~~Li~lv~~~-G~---kW~~IA~~lpgRT~~qcknRw~~llkkk~~~~~~ 218 (535)
-..||.-|...|+.++... |. +-.+|++.++||+..+|++.-..+..+.+++...
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rvareaiq 79 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRVAREAIQ 79 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 3579999999999988655 43 4668899999999999999888887777765443
No 65
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=64.08 E-value=20 Score=40.84 Aligned_cols=47 Identities=23% Similarity=0.489 Sum_probs=37.0
Q ss_pred CCCCCHHHHHHHHHHHHHhcCCChhhhhhcC----------CCCCHHHHHHHhhhccC
Q 009439 60 KGGWTPEEDETLRNAVSTFKGKSWKKIAEFF----------PDRSEVQCLHRWQKVLN 107 (535)
Q Consensus 60 kgkWT~EEDe~L~klV~~yg~~nW~~IAk~l----------p~RT~~qCr~Rw~~~L~ 107 (535)
+..||-.|.+.+..++.++ ++++..|-+++ .-++..|++++|++.++
T Consensus 88 ktaWt~~E~~~Ffdal~~~-GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~ 144 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQV-GKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVR 144 (782)
T ss_pred ccccchhhHHHHHHHHHHh-cccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHH
Confidence 5579999999999999999 66798883332 24677899999888654
No 66
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=63.76 E-value=18 Score=31.72 Aligned_cols=51 Identities=14% Similarity=0.190 Sum_probs=36.0
Q ss_pred CCCCHHHHHHHHHHHHHh----C----CchhhHhhhC-----CCCCHhHHHHHHHHHHHhHHHH
Q 009439 165 DAWTLEEELALMNAHRIH----G----NKWAEIAKVL-----PGRTDNSIKNHWNSSLKKKLDF 215 (535)
Q Consensus 165 ~~WT~EEd~~Li~lv~~~----G----~kW~~IA~~l-----pgRT~~qcknRw~~llkkk~~~ 215 (535)
.-||+|||..||+++..| | ..|..+-..+ ..=+.+|+..+.+.|.+|....
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~ 68 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNA 68 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHH
Confidence 469999999999998766 5 2455444433 2247889999988777765543
No 67
>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=61.34 E-value=8.1 Score=37.02 Aligned_cols=42 Identities=26% Similarity=0.330 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhc
Q 009439 62 GWTPEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKV 105 (535)
Q Consensus 62 kWT~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~ 105 (535)
.||.|+.++|.++..+ +..=.+||+.|++.|...+.-+.+++
T Consensus 2 ~Wtde~~~~L~~lw~~--G~SasqIA~~lg~vsRnAViGk~hRl 43 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE--GLSASQIARQLGGVSRNAVIGKAHRL 43 (162)
T ss_pred CCCHHHHHHHHHHHHc--CCCHHHHHHHhCCcchhhhhhhhhcc
Confidence 4999999999999877 77889999999878888888777663
No 68
>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=60.32 E-value=9.1 Score=28.46 Aligned_cols=38 Identities=29% Similarity=0.406 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHhCCCchhhhcccccccchhhhHhhhhh
Q 009439 118 EEDDKITELVSKYGPTKWSVIAKSLPGRIGKQCRERWHN 156 (535)
Q Consensus 118 EED~~Ll~lV~kyG~~~W~~IAk~LpgRt~kqcr~Rw~n 156 (535)
+=|.+|+.+++..|...|..||+.+ |=+...|..|+..
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l-glS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL-GLSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH-TS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH-CcCHHHHHHHHHH
Confidence 4588999999999988999999999 8899999999865
No 69
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=59.10 E-value=7.1 Score=33.34 Aligned_cols=24 Identities=42% Similarity=0.847 Sum_probs=13.3
Q ss_pred CCCCCCCCCHHHHHHH--------HHHHHHhC
Q 009439 108 PDLVKGPWTQEEDDKI--------TELVSKYG 131 (535)
Q Consensus 108 p~~kKg~WT~EED~~L--------l~lV~kyG 131 (535)
|....|-||+|+|+.| .+++++||
T Consensus 43 P~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG 74 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLRSGDKDDIERLIKKHG 74 (87)
T ss_dssp -TT-TT---HHHHHHHTS--HHHHHHHHHHH-
T ss_pred CCCCCCCcCHHHHHHHHcCCHHHHHHHHHHhC
Confidence 5567889999999988 34556666
No 70
>KOG1878 consensus Nuclear receptor coregulator SMRT/SMRTER, contains Myb-like domains [Transcription]
Probab=56.73 E-value=3.5 Score=50.83 Aligned_cols=44 Identities=27% Similarity=0.542 Sum_probs=35.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhh
Q 009439 59 AKGGWTPEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQ 103 (535)
Q Consensus 59 ~kgkWT~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~ 103 (535)
....|+++|.+..+.-...| .++...|+.+|-.++..+|..-|+
T Consensus 224 ~~n~Ws~~Ek~~fk~rf~~H-~knf~~~as~~erkSv~d~vlfyy 267 (1672)
T KOG1878|consen 224 RMNEWSPEEKELFKSRFAQH-VKNFGLIASFFERKSVSDCVLFYY 267 (1672)
T ss_pred Hhhhccccccccccchhhhc-Ccchhhhhhhhcccchhhceeeee
Confidence 44579999988888777776 677899999999999999987653
No 71
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=54.82 E-value=15 Score=34.29 Aligned_cols=47 Identities=15% Similarity=0.161 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhccCCCCCC
Q 009439 65 PEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKVLNPDLVK 112 (535)
Q Consensus 65 ~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~L~p~~kK 112 (535)
.+-|..|++++.+.+-..|.+||+.+ |-+...|+.|++++...+.-+
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGIIT 54 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 35788899999998888999999999 899999999999987755443
No 72
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=54.79 E-value=17 Score=41.41 Aligned_cols=50 Identities=20% Similarity=0.445 Sum_probs=40.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCCchhhHhh----------hCCCCCHhHHHHHHHHHHHhHH
Q 009439 164 KDAWTLEEELALMNAHRIHGNKWAEIAK----------VLPGRTDNSIKNHWNSSLKKKL 213 (535)
Q Consensus 164 ~~~WT~EEd~~Li~lv~~~G~kW~~IA~----------~lpgRT~~qcknRw~~llkkk~ 213 (535)
+..||-.|+.-+..+++++|.++..|-. .+.-+|-.|++.+|+.++++.-
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~ 147 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMN 147 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHH
Confidence 6789999999999999999999998832 3344677788888887777644
No 73
>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=53.95 E-value=25 Score=31.51 Aligned_cols=42 Identities=26% Similarity=0.407 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKK 212 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk 212 (535)
+++..++.+....|..+.+||..+ |.+...++++++..+++.
T Consensus 116 ~~~r~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~L 157 (161)
T TIGR02985 116 EQCRKIFILSRFEGKSYKEIAEEL-GISVKTVEYHISKALKEL 157 (161)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 566777777777899999999998 999999999998876654
No 74
>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=52.63 E-value=15 Score=35.17 Aligned_cols=42 Identities=24% Similarity=0.272 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHH
Q 009439 166 AWTLEEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSS 208 (535)
Q Consensus 166 ~WT~EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~l 208 (535)
.||+|+.++|-+|. .-|..=.+||..|.+.|.|.|.-+-+.+
T Consensus 2 ~Wtde~~~~L~~lw-~~G~SasqIA~~lg~vsRnAViGk~hRl 43 (162)
T PF07750_consen 2 SWTDERVERLRKLW-AEGLSASQIARQLGGVSRNAVIGKAHRL 43 (162)
T ss_pred CCCHHHHHHHHHHH-HcCCCHHHHHHHhCCcchhhhhhhhhcc
Confidence 59999999999888 5688899999999889999999887643
No 75
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=52.48 E-value=23 Score=38.29 Aligned_cols=47 Identities=23% Similarity=0.441 Sum_probs=39.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhcCCChhhh-hhcCCCCCHHHHHHHhh
Q 009439 56 IRRAKGGWTPEEDETLRNAVSTFKGKSWKKI-AEFFPDRSEVQCLHRWQ 103 (535)
Q Consensus 56 ~rr~kgkWT~EEDe~L~klV~~yg~~nW~~I-Ak~lp~RT~~qCr~Rw~ 103 (535)
+|-.-..|+.+|-..+...++.| ++++..| +..++.|+...|.+-|.
T Consensus 273 ~rd~l~~wsEeEcr~FEegl~~y-GKDF~lIr~nkvrtRsvgElVeyYY 320 (445)
T KOG4329|consen 273 VRDDLSGWSEEECRNFEEGLELY-GKDFHLIRANKVRTRSVGELVEYYY 320 (445)
T ss_pred cccccccCCHHHHHHHHHHHHHh-cccHHHHHhcccccchHHHHHHHHH
Confidence 34444579999999999999999 6679999 66789999999988775
No 76
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=52.38 E-value=13 Score=35.06 Aligned_cols=46 Identities=15% Similarity=0.193 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhccCCCCC
Q 009439 65 PEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKVLNPDLV 111 (535)
Q Consensus 65 ~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~L~p~~k 111 (535)
.+-|.+|+.++.+.+...|.+||+.+ |-+...|+.|++++...+.-
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~GvI 58 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGFI 58 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 56688899999998888999999999 89999999999998775553
No 77
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=51.60 E-value=14 Score=34.47 Aligned_cols=45 Identities=20% Similarity=0.192 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHhCCCchhhhcccccccchhhhHhhhhhhcCCCC
Q 009439 117 QEEDDKITELVSKYGPTKWSVIAKSLPGRIGKQCRERWHNHLNPDI 162 (535)
Q Consensus 117 ~EED~~Ll~lV~kyG~~~W~~IAk~LpgRt~kqcr~Rw~n~L~p~i 162 (535)
.+-|.+|+.++++.|...|..||+.+ |-+...|+.|+..+...++
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 35789999999999988999999999 9999999999998876554
No 78
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=50.49 E-value=13 Score=35.24 Aligned_cols=45 Identities=20% Similarity=0.207 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHhCCCchhhhcccccccchhhhHhhhhhhcCCCC
Q 009439 117 QEEDDKITELVSKYGPTKWSVIAKSLPGRIGKQCRERWHNHLNPDI 162 (535)
Q Consensus 117 ~EED~~Ll~lV~kyG~~~W~~IAk~LpgRt~kqcr~Rw~n~L~p~i 162 (535)
.+-|.+|+.++++.|...|..||+.+ |-+...|+.|++.+...++
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 46788999999999988999999999 9999999999998876664
No 79
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=49.33 E-value=38 Score=32.39 Aligned_cols=42 Identities=21% Similarity=0.311 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKK 212 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk 212 (535)
+++..++.+....|....+||..+ |-+...+++++...+++.
T Consensus 137 ~~~r~i~~l~~~~g~s~~EIA~~l-g~s~~tV~~rl~rar~~L 178 (192)
T PRK09643 137 VEQRAALVAVDMQGYSVADAARML-GVAEGTVKSRCARGRARL 178 (192)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 455666777777888999999999 999999999996555443
No 80
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=47.51 E-value=24 Score=43.08 Aligned_cols=48 Identities=13% Similarity=0.200 Sum_probs=39.9
Q ss_pred CCCCCHHHHHHHHHHHHHhcCCChhhhhhc------------CCCCCHHHHHHHhhhccC
Q 009439 60 KGGWTPEEDETLRNAVSTFKGKSWKKIAEF------------FPDRSEVQCLHRWQKVLN 107 (535)
Q Consensus 60 kgkWT~EEDe~L~klV~~yg~~nW~~IAk~------------lp~RT~~qCr~Rw~~~L~ 107 (535)
+..||.|||..|+-.+.+||-++|.+|-.. |..||+..+..|...++.
T Consensus 926 ~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~ 985 (1033)
T PLN03142 926 GKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIR 985 (1033)
T ss_pred CCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHH
Confidence 446999999999999999999999999543 347999999988877654
No 81
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=46.13 E-value=20 Score=40.82 Aligned_cols=46 Identities=22% Similarity=0.451 Sum_probs=42.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHH
Q 009439 162 IKKDAWTLEEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNS 207 (535)
Q Consensus 162 ik~~~WT~EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~ 207 (535)
...+.|+.+|-++...+....|.+.+.|+..+|+|...+||.+|..
T Consensus 407 ~~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 407 LETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKK 452 (584)
T ss_pred cccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhh
Confidence 3457899999999999999999999999999999999999999863
No 82
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=45.96 E-value=91 Score=33.89 Aligned_cols=46 Identities=15% Similarity=0.199 Sum_probs=40.7
Q ss_pred CCCCHHHHHHHHHHHHHhCCchhhHhh-hCCCCCHhHHHHHHHHHHH
Q 009439 165 DAWTLEEELALMNAHRIHGNKWAEIAK-VLPGRTDNSIKNHWNSSLK 210 (535)
Q Consensus 165 ~~WT~EEd~~Li~lv~~~G~kW~~IA~-~lpgRT~~qcknRw~~llk 210 (535)
..|+++|=..+-+.+..||.++..|-+ .|+.|+--.|-.+|+...+
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWKk 324 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWKK 324 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhhc
Confidence 479999999999999999999999976 6799999999998875543
No 83
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=44.16 E-value=11 Score=32.30 Aligned_cols=17 Identities=35% Similarity=0.569 Sum_probs=9.8
Q ss_pred CCCCCCCCCHHHHHHHH
Q 009439 160 PDIKKDAWTLEEELALM 176 (535)
Q Consensus 160 p~ik~~~WT~EEd~~Li 176 (535)
|....|-||+|||..|.
T Consensus 43 P~n~~GiWT~eDD~~L~ 59 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLR 59 (87)
T ss_dssp -TT-TT---HHHHHHHT
T ss_pred CCCCCCCcCHHHHHHHH
Confidence 44557899999999984
No 84
>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=42.72 E-value=47 Score=28.87 Aligned_cols=42 Identities=26% Similarity=0.392 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKK 212 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk 212 (535)
+.+..++.++...|..+.+||+.+ |-+...|+++.+..+++.
T Consensus 113 ~~~~~ii~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~kl 154 (158)
T TIGR02937 113 EREREVLVLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKKL 154 (158)
T ss_pred HHHHHHHhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 444455566666789999999999 789999999988766553
No 85
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=42.32 E-value=57 Score=31.22 Aligned_cols=43 Identities=14% Similarity=0.159 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhH
Q 009439 169 LEEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKK 212 (535)
Q Consensus 169 ~EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk 212 (535)
.+++..++.+....|-.|.+||..+ |-+...++.+|..+..+.
T Consensus 137 ~~~~~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR~~l 179 (185)
T PF07638_consen 137 DPRQRRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRARAWL 179 (185)
T ss_pred CHHHHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 3556677777777888999999999 999999999999776443
No 86
>PRK04217 hypothetical protein; Provisional
Probab=41.65 E-value=76 Score=28.66 Aligned_cols=48 Identities=21% Similarity=0.163 Sum_probs=38.8
Q ss_pred CCCCHHHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHHH
Q 009439 165 DAWTLEEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKLD 214 (535)
Q Consensus 165 ~~WT~EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~~ 214 (535)
...+++| ..++.++...|-...+||+.+ |.+...|+++++...++...
T Consensus 41 ~~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 41 IFMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred ccCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHH
Confidence 4466666 577788888889999999999 99999999999976665543
No 87
>smart00351 PAX Paired Box domain.
Probab=41.53 E-value=94 Score=28.18 Aligned_cols=81 Identities=15% Similarity=0.051 Sum_probs=50.1
Q ss_pred CCCCCHHHHHHHHHHHHHhcCCChhhhhhcCC--CCCHHHHHHHhhh--ccCCCC----CCCCCCHHHHHHHHHHHHHhC
Q 009439 60 KGGWTPEEDETLRNAVSTFKGKSWKKIAEFFP--DRSEVQCLHRWQK--VLNPDL----VKGPWTQEEDDKITELVSKYG 131 (535)
Q Consensus 60 kgkWT~EEDe~L~klV~~yg~~nW~~IAk~lp--~RT~~qCr~Rw~~--~L~p~~----kKg~WT~EED~~Ll~lV~kyG 131 (535)
..+++.|+-+.++.++. .+....+||+.|+ ..+...+..||.. .+.|.. ....-+.+++..|++++.+++
T Consensus 15 ~~~~s~~~R~riv~~~~--~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p 92 (125)
T smart00351 15 GRPLPDEERQRIVELAQ--NGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENP 92 (125)
T ss_pred CCCCCHHHHHHHHHHHH--cCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCC
Confidence 34699999999988876 3667899999994 2334445555554 233321 112245566677777888877
Q ss_pred CCchhhhcccc
Q 009439 132 PTKWSVIAKSL 142 (535)
Q Consensus 132 ~~~W~~IAk~L 142 (535)
...-.+|+..|
T Consensus 93 ~~t~~el~~~L 103 (125)
T smart00351 93 GIFAWEIRDRL 103 (125)
T ss_pred CCCHHHHHHHH
Confidence 43334454444
No 88
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=40.87 E-value=75 Score=28.80 Aligned_cols=45 Identities=16% Similarity=0.137 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHHHH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKLDF 215 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~~~ 215 (535)
+++..++.++...|-...+||..| |-+...++++....+++....
T Consensus 109 ~~~r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 109 ARQREAFLLRYWEDMDVAETAAAM-GCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred HHHHHHHHHHHHhcCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHH
Confidence 566778888888899999999999 999999999988777655443
No 89
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=39.70 E-value=37 Score=27.38 Aligned_cols=32 Identities=22% Similarity=0.351 Sum_probs=24.8
Q ss_pred chhhHhhhCCC-CCHhHHHHHHHHHHHhHHHHH
Q 009439 185 KWAEIAKVLPG-RTDNSIKNHWNSSLKKKLDFY 216 (535)
Q Consensus 185 kW~~IA~~lpg-RT~~qcknRw~~llkkk~~~~ 216 (535)
-|..|+..|.. -+..+|+.+|+.+..+..+..
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y~~~~ 60 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRDRYRREL 60 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHHHHHHHH
Confidence 39999999953 678899999998876655443
No 90
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=38.95 E-value=52 Score=25.70 Aligned_cols=37 Identities=24% Similarity=0.303 Sum_probs=24.6
Q ss_pred CCHHHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHH
Q 009439 167 WTLEEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHW 205 (535)
Q Consensus 167 WT~EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw 205 (535)
.|. +|+..|.++...|-+-.+||+.+ ||+.+.|+++-
T Consensus 5 Lt~-~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl 41 (50)
T PF11427_consen 5 LTD-AEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRYL 41 (50)
T ss_dssp --H-HHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHHH
T ss_pred CCH-HHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHHh
Confidence 344 44556678888999999999999 99999888764
No 91
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=38.32 E-value=80 Score=28.94 Aligned_cols=41 Identities=17% Similarity=0.266 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhH
Q 009439 171 EELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKK 212 (535)
Q Consensus 171 Ed~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk 212 (535)
++..++.+....|..+.+||..| |.+...++++....+++.
T Consensus 132 ~~r~vl~l~~~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~L 172 (182)
T PRK09652 132 ELRTAITLREIEGLSYEEIAEIM-GCPIGTVRSRIFRAREAL 172 (182)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 34455556667788999999999 899999999888655544
No 92
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=38.22 E-value=36 Score=38.90 Aligned_cols=47 Identities=23% Similarity=0.410 Sum_probs=41.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhh
Q 009439 57 RRAKGGWTPEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQK 104 (535)
Q Consensus 57 rr~kgkWT~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~ 104 (535)
+....+|+.+|-++..+++..+| -+...|+..+|.|..+|++..|..
T Consensus 406 ~~~~~~w~~se~e~fyka~~~~g-s~~slis~l~p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 406 KLETDKWDASETELFYKALSERG-SDFSLISNLFPLRDRKQIKAKFKK 452 (584)
T ss_pred ccccCcccchhhHHhhhHHhhhc-ccccccccccccccHHHHHHHHhh
Confidence 34567899999999999999994 569999999999999999998764
No 93
>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=38.20 E-value=77 Score=22.46 Aligned_cols=42 Identities=21% Similarity=0.330 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHH
Q 009439 167 WTLEEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLK 210 (535)
Q Consensus 167 WT~EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llk 210 (535)
++.+ +..++.++...|..+..||..+ |-+...|+.+.+...+
T Consensus 11 l~~~-~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 11 LPER-EREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRALK 52 (55)
T ss_pred CCHH-HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 3444 4556666667788999999998 7888888777665443
No 94
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=37.32 E-value=87 Score=33.37 Aligned_cols=44 Identities=23% Similarity=0.383 Sum_probs=34.6
Q ss_pred CCCCCHHHHHHHHHHHHHhcCCC---hhhhhhcCCCCCHHHHHHHhh
Q 009439 60 KGGWTPEEDETLRNAVSTFKGKS---WKKIAEFFPDRSEVQCLHRWQ 103 (535)
Q Consensus 60 kgkWT~EEDe~L~klV~~yg~~n---W~~IAk~lp~RT~~qCr~Rw~ 103 (535)
...||.-|...|++++....+.. -.+|++.+++|+..+++.-.+
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~ 67 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQ 67 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHH
Confidence 45799999999999998775554 457788899999888876543
No 95
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=37.15 E-value=84 Score=29.66 Aligned_cols=44 Identities=14% Similarity=0.243 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHHH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKLD 214 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~~ 214 (535)
+++..++.+....|....+||..| |-+...+++++...+++...
T Consensus 134 ~~~r~vl~l~~~~~~s~~eIA~~l-gis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 134 PAHREIIDLVYYHEKSVEEVGEIV-GIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHH
Confidence 345555666667788999999999 88999999999876655443
No 96
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=36.06 E-value=88 Score=28.92 Aligned_cols=44 Identities=23% Similarity=0.219 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHHH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKLD 214 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~~ 214 (535)
+++..++.+....|..-.+||..| |.+...|+++....+++...
T Consensus 121 ~~~r~vl~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 121 PEHRAVLVRSYYRGWSTAQIAADL-GIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHH
Confidence 445566777777788999999999 99999999999877765443
No 97
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=34.56 E-value=72 Score=34.75 Aligned_cols=59 Identities=20% Similarity=0.211 Sum_probs=47.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC----------------chhhHhhhC-----CCCCHhHHHHHHHHHHHhHHHHHhhcC
Q 009439 162 IKKDAWTLEEELALMNAHRIHGN----------------KWAEIAKVL-----PGRTDNSIKNHWNSSLKKKLDFYLATG 220 (535)
Q Consensus 162 ik~~~WT~EEd~~Li~lv~~~G~----------------kW~~IA~~l-----pgRT~~qcknRw~~llkkk~~~~~~~~ 220 (535)
.-.|.|+++=|+.+.++++.|.. +-..||.++ ..||.+|+..|-..+.|++++..+..-
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~reiq~kl 153 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLREIQAKL 153 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHHhhh
Confidence 45689999999999999998842 467788765 449999999999999999988765433
No 98
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=33.83 E-value=95 Score=28.35 Aligned_cols=40 Identities=18% Similarity=0.282 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhH
Q 009439 172 ELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKK 212 (535)
Q Consensus 172 d~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk 212 (535)
+..++.++...|..+.+||..| |-+...|++++...+++.
T Consensus 130 ~r~i~~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~l 169 (179)
T PRK11924 130 QREVFLLRYVEGLSYREIAEIL-GVPVGTVKSRLRRARQLL 169 (179)
T ss_pred HHHHhhHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3344555556788999999999 999999999988765544
No 99
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=33.40 E-value=1.1e+02 Score=27.73 Aligned_cols=43 Identities=16% Similarity=0.062 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKL 213 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~ 213 (535)
+++..++.+....|-...+||..+ |-+...|+++....+++..
T Consensus 109 ~~~r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr 151 (160)
T PRK09642 109 ENYRDVVLAHYLEEKSYQEIALQE-KIEVKTVEMKLYRARKWIK 151 (160)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 456677888888899999999999 9999999999887666543
No 100
>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=32.96 E-value=66 Score=24.17 Aligned_cols=38 Identities=24% Similarity=0.270 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhc
Q 009439 66 EEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKV 105 (535)
Q Consensus 66 EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~ 105 (535)
+++..+..+... .+..|.+||+.+ +.+...++.+.++-
T Consensus 13 ~~~r~i~~l~~~-~g~s~~eIa~~l-~~s~~~v~~~l~ra 50 (54)
T PF08281_consen 13 ERQREIFLLRYF-QGMSYAEIAEIL-GISESTVKRRLRRA 50 (54)
T ss_dssp HHHHHHHHHHHT-S---HHHHHHHC-TS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHH-HCcCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 444455554433 367899999999 89999998887653
No 101
>PF09197 Rap1-DNA-bind: Rap1, DNA-binding; InterPro: IPR015280 Members of this entry, which are predominantly found in the yeast protein Rap1, assume a secondary structure consisting of a three-helix bundle and an N-terminal arm. They contain an Arg-Asp-Arg-Lys sequence that interacts with an ACAregion in the 3, region of the DNA-binding site []. ; PDB: 1IGN_A 3UKG_A.
Probab=32.12 E-value=73 Score=28.67 Aligned_cols=46 Identities=22% Similarity=0.339 Sum_probs=30.7
Q ss_pred CCCHHHHHHHHHHHHHh------------cC------------------CChhhhhhcCCCCCHHHHHHHhhhccC
Q 009439 62 GWTPEEDETLRNAVSTF------------KG------------------KSWKKIAEFFPDRSEVQCLHRWQKVLN 107 (535)
Q Consensus 62 kWT~EEDe~L~klV~~y------------g~------------------~nW~~IAk~lp~RT~~qCr~Rw~~~L~ 107 (535)
++|++||-.|-..|.+| +. .-....+...|.+|..+=++||++.+.
T Consensus 1 kfTA~dDY~Lc~~i~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~fF~~~~~~~p~HT~~sWRDR~RKfv~ 76 (105)
T PF09197_consen 1 KFTADDDYALCKAIKKQFYRDIYQKDPDTGSSLISDGDSKEFIPKRDMRSFFKDLARKNPRHTENSWRDRYRKFVS 76 (105)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHSB-TTSS-B----------------TTHHHHHHHHTTTS-HHHHHHHHHHTHH
T ss_pred CCChHHHHHHHHHHHHHHHHHHHhhCcccccccccCCCccccccchhhHHHHHHHHHcCCccchhHHHHHHHHHHH
Confidence 48999999999998776 00 014455667788898888999887653
No 102
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=31.74 E-value=68 Score=27.54 Aligned_cols=45 Identities=13% Similarity=0.119 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhccCCCCC
Q 009439 66 EEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKVLNPDLV 111 (535)
Q Consensus 66 EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~L~p~~k 111 (535)
+.|..|+.++...+...|.+||+.+ +-+...|+.+..++...+.-
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~i 47 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGVI 47 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 5678888889888888999999999 88999999999887665443
No 103
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=31.45 E-value=1.1e+02 Score=28.97 Aligned_cols=43 Identities=21% Similarity=0.153 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKL 213 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~ 213 (535)
+++..++.+....|.++.+||..| |.+...++++....+++..
T Consensus 109 ~~~r~i~~l~~~~g~~~~EIA~~l-gis~~tV~~~l~Rar~~Lr 151 (181)
T PRK09637 109 EKYAEALRLTELEGLSQKEIAEKL-GLSLSGAKSRVQRGRVKLK 151 (181)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 457777778888899999999999 9999999999887665543
No 104
>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=30.99 E-value=85 Score=29.29 Aligned_cols=42 Identities=7% Similarity=0.194 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHH
Q 009439 171 EELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKL 213 (535)
Q Consensus 171 Ed~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~ 213 (535)
++..++.+....|..+.+||..+ |-+...|+++....+++..
T Consensus 142 ~~r~v~~l~~~~~~s~~EIA~~l-gis~~tv~~~l~rar~~Lr 183 (190)
T TIGR02939 142 DLRTAITLRELEGLSYEDIARIM-DCPVGTVRSRIFRAREAIA 183 (190)
T ss_pred HHhhhhhhhhhcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 44445555556677899999999 8999999999887666543
No 105
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=30.64 E-value=1.1e+02 Score=28.51 Aligned_cols=43 Identities=14% Similarity=0.126 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKL 213 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~ 213 (535)
+++..++.+....|..+.+||..+ |-+...++++....+++..
T Consensus 139 ~~~r~il~l~~~~~~s~~eIA~~l-gis~~~v~~~l~Rar~~Lr 181 (187)
T PRK09641 139 EKYRTVIVLKYIEDLSLKEISEIL-DLPVGTVKTRIHRGREALR 181 (187)
T ss_pred HHHHHHhhhHHhhCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 344555566667788999999999 9999999999876665543
No 106
>smart00595 MADF subfamily of SANT domain.
Probab=30.62 E-value=32 Score=28.65 Aligned_cols=22 Identities=36% Similarity=0.791 Sum_probs=19.6
Q ss_pred hhhhhhcCCCCCHHHHHHHhhhc
Q 009439 83 WKKIAEFFPDRSEVQCLHRWQKV 105 (535)
Q Consensus 83 W~~IAk~lp~RT~~qCr~Rw~~~ 105 (535)
|..||..|+. +..+|+.+|.++
T Consensus 30 W~~Ia~~l~~-~~~~~~~kw~~L 51 (89)
T smart00595 30 WEEIAEELGL-SVEECKKRWKNL 51 (89)
T ss_pred HHHHHHHHCc-CHHHHHHHHHHH
Confidence 9999999954 999999999875
No 107
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=30.39 E-value=89 Score=26.28 Aligned_cols=37 Identities=30% Similarity=0.469 Sum_probs=26.0
Q ss_pred HHHHHHHHhCC--------chhhHhhhCCC-C--C--HhHHHHHHHHHHH
Q 009439 174 ALMNAHRIHGN--------KWAEIAKVLPG-R--T--DNSIKNHWNSSLK 210 (535)
Q Consensus 174 ~Li~lv~~~G~--------kW~~IA~~lpg-R--T--~~qcknRw~~llk 210 (535)
.|..+|...|+ +|..|+..|.- . + ..++++.|...|.
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhH
Confidence 46667777774 69999999822 1 1 3678888887764
No 108
>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=30.30 E-value=1.1e+02 Score=28.32 Aligned_cols=43 Identities=21% Similarity=0.265 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKL 213 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~ 213 (535)
+++..++.+....|.+..+||..+ |-+...+++++...+++..
T Consensus 122 ~~~r~i~~l~~~~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~Lr 164 (169)
T TIGR02954 122 DKYQTAIILRYYHDLTIKEIAEVM-NKPEGTVKTYLHRALKKLK 164 (169)
T ss_pred HHHhHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 334455556666678899999999 8899999999987776654
No 109
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=29.51 E-value=1.4e+02 Score=27.61 Aligned_cols=44 Identities=11% Similarity=0.159 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHHH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKLD 214 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~~ 214 (535)
+.+..++.++...|-...+||..+ |.+...++++-...+++...
T Consensus 115 ~~~r~v~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 115 ADQREAIILIGASGFSYEDAAAIC-GCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHH
Confidence 556677778778899999999999 99999999998877665443
No 110
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=29.49 E-value=1.2e+02 Score=28.54 Aligned_cols=44 Identities=16% Similarity=0.111 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHHH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKLD 214 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~~ 214 (535)
+++..++.|+...|-...+||..| |-+...++.+....+++-+.
T Consensus 130 ~~~R~v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 130 PRVKQAFLMATLDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 445666777777888999999999 99999999999988777654
No 111
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=29.07 E-value=1.2e+02 Score=28.63 Aligned_cols=40 Identities=10% Similarity=0.140 Sum_probs=29.7
Q ss_pred HHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHH
Q 009439 173 LALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKL 213 (535)
Q Consensus 173 ~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~ 213 (535)
..++.+....|-...+||..+ |-+...|++++...+++..
T Consensus 144 r~v~~l~~~~g~s~~eIA~~l-gis~~tv~~~l~Rar~~Lr 183 (193)
T PRK11923 144 RTALTLREFDGLSYEDIASVM-QCPVGTVRSRIFRAREAID 183 (193)
T ss_pred hHHHhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 334444445567899999999 8999999999887665543
No 112
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=28.25 E-value=1.4e+02 Score=28.50 Aligned_cols=46 Identities=15% Similarity=0.221 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHHHHH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKLDFY 216 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~~~~ 216 (535)
+++..++.|....|....+||..| |-+...++++....+++.....
T Consensus 119 ~~~r~i~~L~~~~g~s~~EIA~~L-gis~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 119 DDQREAIILVGASGFAYEEAAEIC-GCAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHH
Confidence 556777778788899999999999 9999999999887766544433
No 113
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=27.69 E-value=1.4e+02 Score=27.67 Aligned_cols=43 Identities=23% Similarity=0.290 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKL 213 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~ 213 (535)
+++..++.+....|....+||..+ |.+...|+++....+++-.
T Consensus 122 ~~~r~v~~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~~ 164 (172)
T PRK12523 122 SKARAAFLYNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQCY 164 (172)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 356667777777888999999999 9999999999887776654
No 114
>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=27.62 E-value=1.5e+02 Score=28.19 Aligned_cols=43 Identities=12% Similarity=0.039 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKL 213 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~ 213 (535)
+.+..++.+....|....+||..| |-+.+.++.|....+++..
T Consensus 134 ~~~r~v~~l~~~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~Lr 176 (188)
T TIGR02943 134 EQTARVFMMREVLGFESDEICQEL-EISTSNCHVLLYRARLSLR 176 (188)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 456678888888899999999999 9999999999887665543
No 115
>PRK00118 putative DNA-binding protein; Validated
Probab=27.48 E-value=1.8e+02 Score=26.08 Aligned_cols=45 Identities=16% Similarity=0.150 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHHH
Q 009439 169 LEEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKLD 214 (535)
Q Consensus 169 ~EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~~ 214 (535)
.+.+..++.+....|....+||..+ |-+...++.+....+++...
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHH
Confidence 3556677778888899999999999 99999999987766555443
No 116
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=27.45 E-value=1.4e+02 Score=28.14 Aligned_cols=40 Identities=15% Similarity=0.182 Sum_probs=30.0
Q ss_pred HHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHH
Q 009439 173 LALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKL 213 (535)
Q Consensus 173 ~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~ 213 (535)
..++.+....|..+.+||..+ |-+...|+.+....+++..
T Consensus 145 r~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~Lr 184 (189)
T PRK09648 145 REILILRVVVGLSAEETAEAV-GSTPGAVRVAQHRALARLR 184 (189)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 334444455577899999999 9999999999887666543
No 117
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=27.29 E-value=68 Score=29.16 Aligned_cols=47 Identities=17% Similarity=0.150 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhccCCCCCC
Q 009439 65 PEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKVLNPDLVK 112 (535)
Q Consensus 65 ~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~L~p~~kK 112 (535)
.+-|.+|++++.+.+...+.+||+.+ |-+...|..|-+++...++-+
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~GiI~ 53 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGVIK 53 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCcee
Confidence 35578888889888888999999999 899999999998877655443
No 118
>PF09197 Rap1-DNA-bind: Rap1, DNA-binding; InterPro: IPR015280 Members of this entry, which are predominantly found in the yeast protein Rap1, assume a secondary structure consisting of a three-helix bundle and an N-terminal arm. They contain an Arg-Asp-Arg-Lys sequence that interacts with an ACAregion in the 3, region of the DNA-binding site []. ; PDB: 1IGN_A 3UKG_A.
Probab=26.86 E-value=69 Score=28.82 Aligned_cols=45 Identities=18% Similarity=0.377 Sum_probs=27.1
Q ss_pred CCCHHHHHHHHHHHHHhC--------C----C------------------chhhhcccccccchhhhHhhhhhhc
Q 009439 114 PWTQEEDDKITELVSKYG--------P----T------------------KWSVIAKSLPGRIGKQCRERWHNHL 158 (535)
Q Consensus 114 ~WT~EED~~Ll~lV~kyG--------~----~------------------~W~~IAk~LpgRt~kqcr~Rw~n~L 158 (535)
.||++||-.|...|.+|- . . =....+...|..+..+-|+||+..+
T Consensus 1 kfTA~dDY~Lc~~i~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~fF~~~~~~~p~HT~~sWRDR~RKfv 75 (105)
T PF09197_consen 1 KFTADDDYALCKAIKKQFYRDIYQKDPDTGSSLISDGDSKEFIPKRDMRSFFKDLARKNPRHTENSWRDRYRKFV 75 (105)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHSB-TTSS-B----------------TTHHHHHHHHTTTS-HHHHHHHHHHTH
T ss_pred CCChHHHHHHHHHHHHHHHHHHHhhCcccccccccCCCccccccchhhHHHHHHHHHcCCccchhHHHHHHHHHH
Confidence 489999999999887651 0 0 0233445556777777777777655
No 119
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=26.27 E-value=1.7e+02 Score=27.94 Aligned_cols=43 Identities=14% Similarity=0.089 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHHH
Q 009439 171 EELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKLD 214 (535)
Q Consensus 171 Ed~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~~ 214 (535)
++..++.++...|-.+.+||..+ |-+...|+++....+++...
T Consensus 140 ~~r~i~~L~~~~g~s~~eIA~~l-gis~~tV~~~l~Ra~~~Lr~ 182 (196)
T PRK12524 140 RQRQAVVLRHIEGLSNPEIAEVM-EIGVEAVESLTARGKRALAA 182 (196)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHH
Confidence 33445555566778899999999 99999999998876665433
No 120
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=26.27 E-value=1.6e+02 Score=28.05 Aligned_cols=42 Identities=2% Similarity=-0.061 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKK 212 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk 212 (535)
+++..++.+....|-...+||..| |.+...|+.|....+++.
T Consensus 137 ~~~R~v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~RAr~~L 178 (189)
T PRK12530 137 AQQARVFMMREYLELSSEQICQEC-DISTSNLHVLLYRARLQL 178 (189)
T ss_pred HHHHHHHhHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 566777778878899999999999 999999999987666543
No 121
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=26.23 E-value=1.5e+02 Score=27.67 Aligned_cols=42 Identities=12% Similarity=0.202 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHH
Q 009439 171 EELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKL 213 (535)
Q Consensus 171 Ed~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~ 213 (535)
++..++.+....|....+||..| |-+...++.++...+++.-
T Consensus 135 ~~r~v~~l~~~~g~s~~eIA~~l-~is~~tV~~~l~ra~~~Lr 176 (184)
T PRK12512 135 RQRDVVQSISVEGASIKETAAKL-SMSEGAVRVALHRGLAALA 176 (184)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 34455555556688899999999 9999999999887766543
No 122
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=25.93 E-value=2.2e+02 Score=25.51 Aligned_cols=46 Identities=15% Similarity=0.133 Sum_probs=31.6
Q ss_pred CCCCCCHHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhccC
Q 009439 59 AKGGWTPEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKVLN 107 (535)
Q Consensus 59 ~kgkWT~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~L~ 107 (535)
.+..||.|+-..++..+... +..=..||..++= +. +-..+|.+.+.
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~-g~sv~evA~e~gI-s~-~tl~~W~r~y~ 54 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEP-GMTVSLVARQHGV-AA-SQLFLWRKQYQ 54 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcC-CCCHHHHHHHHCc-CH-HHHHHHHHHHh
Confidence 35679999988777766654 4457788888743 43 45567777654
No 123
>cd00131 PAX Paired Box domain
Probab=25.91 E-value=2.6e+02 Score=25.46 Aligned_cols=83 Identities=14% Similarity=0.059 Sum_probs=51.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHhcCCChhhhhhcCC--CCCHHHHHHHhhhc--cCCCCCCC----CCCHHHHHHHHHHHHH
Q 009439 58 RAKGGWTPEEDETLRNAVSTFKGKSWKKIAEFFP--DRSEVQCLHRWQKV--LNPDLVKG----PWTQEEDDKITELVSK 129 (535)
Q Consensus 58 r~kgkWT~EEDe~L~klV~~yg~~nW~~IAk~lp--~RT~~qCr~Rw~~~--L~p~~kKg----~WT~EED~~Ll~lV~k 129 (535)
.-..+.+.++-++++.++.. +.....||+.|. ..+...+..||..- +.|....| .-+++.+..|+.++.+
T Consensus 13 ~m~~~lS~d~R~rIv~~~~~--G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~ 90 (128)
T cd00131 13 VNGRPLPDSIRQRIVELAQS--GIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQE 90 (128)
T ss_pred cCCCcCCHHHHHHHHHHHHc--CCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHH
Confidence 34457899999999988753 667999999984 22334445555542 33332211 2466667777778888
Q ss_pred hCCCchhhhcccc
Q 009439 130 YGPTKWSVIAKSL 142 (535)
Q Consensus 130 yG~~~W~~IAk~L 142 (535)
++...-.+|++.|
T Consensus 91 ~p~~Tl~El~~~L 103 (128)
T cd00131 91 NPGMFAWEIRDRL 103 (128)
T ss_pred CCCCCHHHHHHHH
Confidence 7744444444443
No 124
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=25.47 E-value=1.9e+02 Score=27.34 Aligned_cols=48 Identities=8% Similarity=-0.134 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHHHHHhh
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKLDFYLA 218 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~~~~~~ 218 (535)
+++..++.+....|..-.+||..+ |-+...|+++....+++.......
T Consensus 134 ~~~r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr~~l~~ 181 (191)
T PRK12520 134 PRTGRVFMMREWLELETEEICQEL-QITATNAWVLLYRARMRLRECLDL 181 (191)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHH
Confidence 556777788888899999999999 999999999988777665444333
No 125
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=25.23 E-value=1.7e+02 Score=27.74 Aligned_cols=41 Identities=10% Similarity=0.139 Sum_probs=30.9
Q ss_pred HHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHH
Q 009439 172 ELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKL 213 (535)
Q Consensus 172 d~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~ 213 (535)
+..++.+....|-...+||..| |-+...+++|....+++..
T Consensus 146 ~r~v~~l~~~eg~s~~EIA~~l-gis~~tVk~rl~ra~~~Lr 186 (194)
T PRK12531 146 QRDVLQAVYLEELPHQQVAEMF-DIPLGTVKSRLRLAVEKLR 186 (194)
T ss_pred HHHHHHHHHHcCCCHHHHHHHh-CcCHHHHHHHHHHHHHHHH
Confidence 3345555556677899999999 9999999999876665543
No 126
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=25.20 E-value=73 Score=27.33 Aligned_cols=44 Identities=23% Similarity=0.205 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHhCCCchhhhcccccccchhhhHhhhhhhcCCCC
Q 009439 118 EEDDKITELVSKYGPTKWSVIAKSLPGRIGKQCRERWHNHLNPDI 162 (535)
Q Consensus 118 EED~~Ll~lV~kyG~~~W~~IAk~LpgRt~kqcr~Rw~n~L~p~i 162 (535)
+.|..|+.++++.+...+..|++.+ +-+...|+.|...+...++
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~ 46 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGV 46 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 5688999999999888999999999 8899999999988766554
No 127
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=25.16 E-value=1.6e+02 Score=27.58 Aligned_cols=45 Identities=9% Similarity=0.023 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHHHHH
Q 009439 171 EELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKLDFY 216 (535)
Q Consensus 171 Ed~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~~~~ 216 (535)
++..++.+....|....+||..+ |-+...|+++.+..+++.....
T Consensus 132 ~~r~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 132 RQREAIVLQYYQGLSNIEAAAVM-DISVDALESLLARGRRALRAQL 176 (186)
T ss_pred HHHHHhhHHHhcCCCHHHHHHHh-CcCHHHHHHHHHHHHHHHHHHH
Confidence 34444555556677899999999 9999999999887766544433
No 128
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=25.14 E-value=1.4e+02 Score=27.73 Aligned_cols=42 Identities=10% Similarity=0.078 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHH
Q 009439 171 EELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKL 213 (535)
Q Consensus 171 Ed~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~ 213 (535)
++..++.+....|....+||..+ |.+...++++....+++..
T Consensus 140 ~~r~v~~l~~~~g~s~~eIA~~l-gis~~~v~~~l~Rar~~Lr 181 (187)
T TIGR02948 140 KYRMVIVLKYMEDLSLKEISEIL-DLPVGTVKTRIHRGREALR 181 (187)
T ss_pred HHhHHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 33444455555678899999999 8899999999876665543
No 129
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=24.99 E-value=1.7e+02 Score=28.20 Aligned_cols=44 Identities=11% Similarity=-0.026 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHHH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKLD 214 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~~ 214 (535)
++...++.+....|..-.+||..+ |.+...|+++....+++...
T Consensus 142 ~~~r~v~~L~~~eg~s~~EIA~~l-gis~~tVk~~l~RAr~~Lr~ 185 (201)
T PRK12545 142 EQIGRVFMMREFLDFEIDDICTEL-TLTANHCSVLLYRARTRLRT 185 (201)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHH
Confidence 566777888888899999999999 99999999998866655433
No 130
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=24.77 E-value=1.9e+02 Score=25.30 Aligned_cols=20 Identities=15% Similarity=0.403 Sum_probs=17.2
Q ss_pred CCCCCCHHHHHHHHHHHHHh
Q 009439 59 AKGGWTPEEDETLRNAVSTF 78 (535)
Q Consensus 59 ~kgkWT~EEDe~L~klV~~y 78 (535)
..+.||+|++-.|++++..|
T Consensus 3 ~qR~WS~eDEi~iL~gl~~~ 22 (98)
T PF04504_consen 3 FQRLWSEEDEIVILQGLIDF 22 (98)
T ss_pred CcCCCCchHHHHHHHHHHHH
Confidence 34569999999999999888
No 131
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=24.11 E-value=1.4e+02 Score=33.41 Aligned_cols=42 Identities=21% Similarity=0.354 Sum_probs=37.3
Q ss_pred CCCCHHHHHHHHHHHHHhCCchhhHhhh-CCCCCHhHHHHHHH
Q 009439 165 DAWTLEEELALMNAHRIHGNKWAEIAKV-LPGRTDNSIKNHWN 206 (535)
Q Consensus 165 ~~WT~EEd~~Li~lv~~~G~kW~~IA~~-lpgRT~~qcknRw~ 206 (535)
..|+.-|-.++-+++.+||.++..|-.. ||=++-.+|-.+|+
T Consensus 286 EEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYY 328 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYY 328 (693)
T ss_pred hhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHH
Confidence 4699999999999999999999999875 48899999988876
No 132
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=23.92 E-value=74 Score=35.52 Aligned_cols=41 Identities=22% Similarity=0.563 Sum_probs=33.3
Q ss_pred CCCCHHHHHHHHHHHHHhcCCChhhh-hhcCCCCCHHHHHHHh
Q 009439 61 GGWTPEEDETLRNAVSTFKGKSWKKI-AEFFPDRSEVQCLHRW 102 (535)
Q Consensus 61 gkWT~EEDe~L~klV~~yg~~nW~~I-Ak~lp~RT~~qCr~Rw 102 (535)
..|+.-|-.++.+++++| +++++.| +++||-++..++.+-|
T Consensus 286 EEWSasEanLFEeALeKy-GKDFndIrqdfLPWKSl~sIveyY 327 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKY-GKDFNDIRQDFLPWKSLTSIVEYY 327 (693)
T ss_pred hhccchhhHHHHHHHHHh-cccHHHHHHhhcchHHHHHHHHHH
Confidence 369999999999999999 5679999 6778887777765433
No 133
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=23.89 E-value=1.9e+02 Score=27.87 Aligned_cols=42 Identities=12% Similarity=0.054 Sum_probs=31.0
Q ss_pred HHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHHHH
Q 009439 173 LALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKLDF 215 (535)
Q Consensus 173 ~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~~~ 215 (535)
..++.+....|..-.+||..+ |.+.+.++++.+..+++....
T Consensus 159 r~vl~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 159 QTVVKGVYFQELSQEQLAQQL-NVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHH
Confidence 334444455577899999999 999999999988777665443
No 134
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=23.70 E-value=1.5e+02 Score=26.62 Aligned_cols=40 Identities=20% Similarity=0.176 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHh
Q 009439 171 EELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKK 211 (535)
Q Consensus 171 Ed~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkk 211 (535)
.+..++.+....|....+||..+ |.+...|+++-...+++
T Consensus 110 ~~r~ii~l~~~~~~s~~EIA~~l-~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 110 KEKYIIFERFFVGKTMGEIALET-EMTYYQVRWIYRQALEK 149 (154)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 34555666666788899999999 99999999987766654
No 135
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=23.49 E-value=65 Score=23.91 Aligned_cols=37 Identities=27% Similarity=0.368 Sum_probs=18.9
Q ss_pred CCCHHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHH
Q 009439 62 GWTPEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHR 101 (535)
Q Consensus 62 kWT~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~R 101 (535)
.+|.+|-..|..++.. +..-.+||+.| +|+...+..-
T Consensus 4 ~Lt~~eR~~I~~l~~~--G~s~~~IA~~l-g~s~sTV~re 40 (44)
T PF13936_consen 4 HLTPEERNQIEALLEQ--GMSIREIAKRL-GRSRSTVSRE 40 (44)
T ss_dssp --------HHHHHHCS-----HHHHHHHT-T--HHHHHHH
T ss_pred chhhhHHHHHHHHHHc--CCCHHHHHHHH-CcCcHHHHHH
Confidence 5899999998887654 56789999999 8888777654
No 136
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=23.34 E-value=1.7e+02 Score=27.25 Aligned_cols=43 Identities=21% Similarity=0.224 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHHH
Q 009439 171 EELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKLD 214 (535)
Q Consensus 171 Ed~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~~ 214 (535)
++..++.+....|-...+||..+ |-+...|+++....+++-+.
T Consensus 123 ~~r~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 123 KTREAFLLSQLDGLTYSEIAHKL-GVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred HHhHHhhhhhccCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHH
Confidence 34455556666778899999999 99999999999877766544
No 137
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=23.09 E-value=2e+02 Score=27.91 Aligned_cols=45 Identities=20% Similarity=0.183 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHHHHH
Q 009439 171 EELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKLDFY 216 (535)
Q Consensus 171 Ed~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~~~~ 216 (535)
++..++.+....|.+-.+||..| |-+...|+++....+++..+..
T Consensus 142 ~~r~v~~L~~~~g~s~~EIA~~L-gis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 142 EFRAAVVLCDIEGLSYEEIAATL-GVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHH
Confidence 44455556667788899999999 9999999999987766654433
No 138
>KOG1544 consensus Predicted cysteine proteinase TIN-ag [General function prediction only]
Probab=22.84 E-value=51 Score=35.32 Aligned_cols=27 Identities=22% Similarity=0.555 Sum_probs=23.5
Q ss_pred CCCCCccccCCCccccccchhhhHHhh
Q 009439 480 IEPTGMTFNASPPYRLRSKRTAVFKSV 506 (535)
Q Consensus 480 ~~~~~~~~~~sppyr~r~kr~a~~ksv 506 (535)
..+++..|-.+||||--|.-+.|+|-|
T Consensus 334 ~~~Sn~iyq~tPPYrVSSnE~eImkEl 360 (470)
T KOG1544|consen 334 YVNSNDIYQVTPPYRVSSNEKEIMKEL 360 (470)
T ss_pred ccccCceeeecCCeeccCCHHHHHHHH
Confidence 445778999999999999999999965
No 139
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=22.53 E-value=76 Score=28.84 Aligned_cols=45 Identities=13% Similarity=0.152 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHhCCCchhhhcccccccchhhhHhhhhhhcCCCC
Q 009439 117 QEEDDKITELVSKYGPTKWSVIAKSLPGRIGKQCRERWHNHLNPDI 162 (535)
Q Consensus 117 ~EED~~Ll~lV~kyG~~~W~~IAk~LpgRt~kqcr~Rw~n~L~p~i 162 (535)
.+-|.+|++++++.+...+..||+.+ |-+...|+.|-.++.+.++
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~Gi 51 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGV 51 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCc
Confidence 35688999999999988999999999 8999999999988766553
No 140
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=22.48 E-value=1.7e+02 Score=26.74 Aligned_cols=41 Identities=20% Similarity=0.193 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHh
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKK 211 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkk 211 (535)
+++..++.+....|-...+||..+ |-+...++++....+++
T Consensus 116 ~~~r~v~~L~~~~g~s~~EIA~~l-~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 116 PLVKRAFLLAQVDGLGYGEIATEL-GISLATVKRYLNKAAMR 156 (161)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456667777778889999999999 99999999998876554
No 141
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=22.40 E-value=1.9e+02 Score=27.40 Aligned_cols=43 Identities=14% Similarity=0.149 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKL 213 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~ 213 (535)
+++..++.+....|....+||..| |-+...++++....+++..
T Consensus 139 ~~~r~i~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr 181 (195)
T PRK12532 139 ENTARVFTLKEILGFSSDEIQQMC-GISTSNYHTIMHRARESLR 181 (195)
T ss_pred HHHHHHhhhHHHhCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 456667778888899999999999 9999999999886655433
No 142
>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=22.17 E-value=1.1e+02 Score=26.22 Aligned_cols=29 Identities=21% Similarity=0.389 Sum_probs=22.9
Q ss_pred HHHHHHHHHHhCCchhhHhhhCCCCCHhHH
Q 009439 172 ELALMNAHRIHGNKWAEIAKVLPGRTDNSI 201 (535)
Q Consensus 172 d~~Li~lv~~~G~kW~~IA~~lpgRT~~qc 201 (535)
|+.|..+....|..|..+|.+| |=+..+|
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I 30 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDI 30 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 4568888899999999999988 6555444
No 143
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=22.02 E-value=2.5e+02 Score=25.51 Aligned_cols=44 Identities=16% Similarity=0.167 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHHH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKLD 214 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~~ 214 (535)
+++..++.+....|..-.+||..| |-+...++++....+++...
T Consensus 108 ~~~r~v~~l~~~~~~s~~eIA~~l-gis~~tv~~~l~ra~~~Lr~ 151 (159)
T PRK12527 108 PACRDSFLLRKLEGLSHQQIAEHL-GISRSLVEKHIVNAMKHCRV 151 (159)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHH
Confidence 566778888888888999999999 99999999998876665443
No 144
>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=21.84 E-value=1.3e+02 Score=22.27 Aligned_cols=38 Identities=26% Similarity=0.364 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhc
Q 009439 65 PEEDETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKV 105 (535)
Q Consensus 65 ~EEDe~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~ 105 (535)
++|-+.|...+ +.+..+.+||+.| |-+...++.+..+.
T Consensus 7 ~~er~vi~~~y--~~~~t~~eIa~~l-g~s~~~V~~~~~~a 44 (50)
T PF04545_consen 7 PREREVIRLRY--FEGLTLEEIAERL-GISRSTVRRILKRA 44 (50)
T ss_dssp HHHHHHHHHHH--TST-SHHHHHHHH-TSCHHHHHHHHHHH
T ss_pred HHHHHHHHHHh--cCCCCHHHHHHHH-CCcHHHHHHHHHHH
Confidence 44444444333 5577899999999 77877777765543
No 145
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=21.68 E-value=1.9e+02 Score=27.48 Aligned_cols=48 Identities=13% Similarity=0.074 Sum_probs=38.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCchhhHhhhC----CCCCHhHHHHHHHHHH
Q 009439 162 IKKDAWTLEEELALMNAHRIHGNKWAEIAKVL----PGRTDNSIKNHWNSSL 209 (535)
Q Consensus 162 ik~~~WT~EEd~~Li~lv~~~G~kW~~IA~~l----pgRT~~qcknRw~~ll 209 (535)
......+..|...|..|+.+||.++...+.-. --.|..||+.+.+.+.
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~k 163 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKYK 163 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHhc
Confidence 34567899999999999999999999998643 2489999988876543
No 146
>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=21.62 E-value=2.1e+02 Score=26.54 Aligned_cols=42 Identities=17% Similarity=0.270 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKK 212 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk 212 (535)
+.+..++.+....|-...+||..+ |-+...|+++....+++.
T Consensus 137 ~~~r~v~~l~~~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~L 178 (183)
T TIGR02999 137 PRQAEVVELRFFAGLTVEEIAELL-GVSVRTVERDWRFARAWL 178 (183)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 334455556666778899999999 999999999988766553
No 147
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=21.62 E-value=2.1e+02 Score=26.78 Aligned_cols=41 Identities=20% Similarity=0.219 Sum_probs=32.1
Q ss_pred HHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHH
Q 009439 172 ELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKL 213 (535)
Q Consensus 172 d~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~ 213 (535)
+..++.++...|-+..+||..| |.+...|+++....+++..
T Consensus 134 ~r~v~~l~~~~g~s~~EIA~~l-~is~~tV~~~l~rar~~Lr 174 (181)
T PRK12536 134 QRLPIVHVKLEGLSVAETAQLT-GLSESAVKVGIHRGLKALA 174 (181)
T ss_pred HHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 3445556667788999999999 9999999999887665543
No 148
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=21.53 E-value=2.1e+02 Score=26.60 Aligned_cols=39 Identities=21% Similarity=0.210 Sum_probs=29.7
Q ss_pred HHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhH
Q 009439 173 LALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKK 212 (535)
Q Consensus 173 ~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk 212 (535)
..++.+....|..-.+||..| |.+...++++....+++.
T Consensus 135 r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~Rar~~L 173 (179)
T PRK12514 135 AAAVRRAYLEGLSYKELAERH-DVPLNTMRTWLRRSLLKL 173 (179)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCChHHHHHHHHHHHHHH
Confidence 334444455677899999999 999999999988666554
No 149
>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=21.49 E-value=1.7e+02 Score=26.64 Aligned_cols=42 Identities=21% Similarity=0.264 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKK 212 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk 212 (535)
+.+..++.+....|-+..+||+.| |.+...++++....+++.
T Consensus 125 ~~~r~vl~l~~~~g~s~~eIA~~l-~is~~tv~~~l~ra~~~L 166 (170)
T TIGR02952 125 PKQQHVIALRFGQNLPIAEVARIL-GKTEGAVKILQFRAIKKL 166 (170)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 445566666667788999999999 999999999887665543
No 150
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=21.21 E-value=1.8e+02 Score=27.53 Aligned_cols=38 Identities=18% Similarity=0.221 Sum_probs=28.9
Q ss_pred HHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHH
Q 009439 175 LMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKL 213 (535)
Q Consensus 175 Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~ 213 (535)
++.+....|-...+||..+ |-+...++++....+++..
T Consensus 138 v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr 175 (185)
T PRK09649 138 ALLLTQLLGLSYADAAAVC-GCPVGTIRSRVARARDALL 175 (185)
T ss_pred HhhhHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 3334445566899999999 9999999999887766543
No 151
>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=20.87 E-value=2.1e+02 Score=25.92 Aligned_cols=43 Identities=16% Similarity=0.190 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhHH
Q 009439 170 EEELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKKL 213 (535)
Q Consensus 170 EEd~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk~ 213 (535)
+++..++.+....|-+-.+||..| |-+...++++....+++..
T Consensus 113 ~~~r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~ra~~~Lr 155 (162)
T TIGR02983 113 ARQRAVVVLRYYEDLSEAQVAEAL-GISVGTVKSRLSRALARLR 155 (162)
T ss_pred HHHHHHhhhHHHhcCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 455666667667788999999999 9999999999887776544
No 152
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=20.34 E-value=6e+02 Score=22.60 Aligned_cols=98 Identities=20% Similarity=0.222 Sum_probs=58.6
Q ss_pred HHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHhhhccC-----CCCCCCCCCHHHHHHHHHHHHHhCCCchhhhccccc
Q 009439 69 ETLRNAVSTFKGKSWKKIAEFFPDRSEVQCLHRWQKVLN-----PDLVKGPWTQEEDDKITELVSKYGPTKWSVIAKSLP 143 (535)
Q Consensus 69 e~L~klV~~yg~~nW~~IAk~lp~RT~~qCr~Rw~~~L~-----p~~kKg~WT~EED~~Ll~lV~kyG~~~W~~IAk~Lp 143 (535)
++++..++. +..=.+||..| +=+...| .+|.+... +....+. .=+.+.|.++|+.+....-.+||..|+
T Consensus 9 ~rVl~~~~~--g~s~~eaa~~F-~VS~~Tv-~~W~k~~~~G~~~~k~r~~~--Kid~~~L~~~v~~~pd~tl~Ela~~l~ 82 (119)
T PF01710_consen 9 QRVLAYIEK--GKSIREAAKRF-GVSRNTV-YRWLKRKETGDLEPKPRGRK--KIDRDELKALVEENPDATLRELAERLG 82 (119)
T ss_pred HHHHHHHHc--cchHHHHHHHh-CcHHHHH-HHHHHhcccccccccccccc--cccHHHHHHHHHHCCCcCHHHHHHHcC
Confidence 344444444 44678888888 3333334 46655332 2222222 334567999999998777889998884
Q ss_pred ccchhhhHhhhhhhcCCCCCCCCCCHHHHHH
Q 009439 144 GRIGKQCRERWHNHLNPDIKKDAWTLEEELA 174 (535)
Q Consensus 144 gRt~kqcr~Rw~n~L~p~ik~~~WT~EEd~~ 174 (535)
...+.-.++...|.-..++..|..+++..
T Consensus 83 --Vs~~ti~~~Lkrlg~t~KK~~~~~~~~~~ 111 (119)
T PF01710_consen 83 --VSPSTIWRALKRLGITRKKKTLHSEKDRE 111 (119)
T ss_pred --CCHHHHHHHHHHcCchhccCcccchhHHH
Confidence 24444445556666677777776655544
No 153
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.29 E-value=2.4e+02 Score=24.69 Aligned_cols=46 Identities=15% Similarity=0.169 Sum_probs=37.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCchhhHhhhCCCC-CHhHHHHHHHHHHH
Q 009439 164 KDAWTLEEELALMNAHRIHGNKWAEIAKVLPGR-TDNSIKNHWNSSLK 210 (535)
Q Consensus 164 ~~~WT~EEd~~Li~lv~~~G~kW~~IA~~lpgR-T~~qcknRw~~llk 210 (535)
+..||.|+-..+++++..-|..=..||..+ |. ..+++.+++..+..
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~~W~~~~~~ 51 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLYKWRIQLQK 51 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHHHHHHHHHH
Confidence 568999999999999998888889999999 75 77777765544433
No 154
>cd08803 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) 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-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=20.20 E-value=1.4e+02 Score=25.59 Aligned_cols=31 Identities=19% Similarity=0.377 Sum_probs=23.9
Q ss_pred HHHHHHHHHHhCCchhhHhhhCCCCCHhHHHH
Q 009439 172 ELALMNAHRIHGNKWAEIAKVLPGRTDNSIKN 203 (535)
Q Consensus 172 d~~Li~lv~~~G~kW~~IA~~lpgRT~~qckn 203 (535)
|..|..+....|.+|..+|..| |=+...|.+
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI~~ 34 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEINQ 34 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHHHH
Confidence 5567778889999999999998 666655443
No 155
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=20.13 E-value=1.8e+02 Score=24.71 Aligned_cols=38 Identities=29% Similarity=0.458 Sum_probs=26.6
Q ss_pred HHHHHHHHhCC--------chhhHhhhCCC-----CCHhHHHHHHHHHHHh
Q 009439 174 ALMNAHRIHGN--------KWAEIAKVLPG-----RTDNSIKNHWNSSLKK 211 (535)
Q Consensus 174 ~Li~lv~~~G~--------kW~~IA~~lpg-----RT~~qcknRw~~llkk 211 (535)
.|..+|...|+ .|..|+..|.- .....++..|...|..
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~ 86 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLP 86 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHH
Confidence 46666666664 69999998832 2357788888877654
No 156
>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=20.01 E-value=87 Score=28.14 Aligned_cols=41 Identities=15% Similarity=0.147 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHhCCchhhHhhhCCCCCHhHHHHHHHHHHHhH
Q 009439 171 EELALMNAHRIHGNKWAEIAKVLPGRTDNSIKNHWNSSLKKK 212 (535)
Q Consensus 171 Ed~~Li~lv~~~G~kW~~IA~~lpgRT~~qcknRw~~llkkk 212 (535)
++..++.+....|-.+.+||..| |-+...+++++...+++.
T Consensus 109 ~~r~i~~l~~~~g~s~~eIA~~l-gis~~tv~~~l~Ra~~~L 149 (154)
T TIGR02950 109 NYRTVLILREFKEFSYKEIAELL-NLSLAKVKSNLFRARKEL 149 (154)
T ss_pred hheeeeeehhhccCcHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 34445555666788999999999 999999999988776554
Done!