Query 046581
Match_columns 470
No_of_seqs 319 out of 2087
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 13:36:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046581.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046581hhsearch_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 5.8E-31 1.3E-35 257.3 11.7 110 169-278 5-115 (238)
2 PLN03212 Transcription repress 100.0 2E-30 4.4E-35 251.9 13.0 110 168-277 20-130 (249)
3 PLN03091 hypothetical protein; 100.0 7.4E-29 1.6E-33 256.4 12.8 107 169-275 10-117 (459)
4 KOG0049 Transcription factor, 99.9 2E-25 4.2E-30 237.1 9.4 185 79-272 224-463 (939)
5 PLN03212 Transcription repress 99.9 8.1E-24 1.8E-28 206.0 6.6 102 105-222 23-126 (249)
6 PLN03091 hypothetical protein; 99.9 7E-23 1.5E-27 212.3 7.0 105 103-223 10-116 (459)
7 KOG0048 Transcription factor, 99.9 1.1E-22 2.3E-27 199.2 7.2 101 105-221 7-109 (238)
8 KOG0049 Transcription factor, 99.8 1.2E-18 2.6E-23 185.9 10.0 144 133-285 219-421 (939)
9 PF13921 Myb_DNA-bind_6: Myb-l 99.6 9.5E-16 2.1E-20 119.0 6.9 60 176-236 1-60 (60)
10 KOG0051 RNA polymerase I termi 99.6 5.9E-15 1.3E-19 159.0 9.8 158 99-272 375-569 (607)
11 KOG0051 RNA polymerase I termi 99.5 1.3E-14 2.7E-19 156.5 9.2 167 100-275 301-512 (607)
12 KOG0050 mRNA splicing protein 99.5 3.5E-14 7.6E-19 149.3 6.5 105 171-276 5-109 (617)
13 COG5147 REB1 Myb superfamily p 99.5 4.7E-14 1E-18 150.7 7.5 108 168-275 15-122 (512)
14 PF00249 Myb_DNA-binding: Myb- 99.4 4.4E-13 9.5E-18 100.2 5.1 47 173-219 1-48 (48)
15 COG5147 REB1 Myb superfamily p 99.4 4.6E-13 1E-17 143.2 6.8 152 104-272 17-169 (512)
16 PF13921 Myb_DNA-bind_6: Myb-l 99.2 1.6E-11 3.4E-16 95.3 5.6 58 228-285 1-58 (60)
17 PF00249 Myb_DNA-binding: Myb- 99.2 1.5E-11 3.3E-16 91.9 5.3 46 225-270 1-48 (48)
18 KOG0050 mRNA splicing protein 99.2 1.5E-12 3.1E-17 137.3 -2.0 98 105-219 5-103 (617)
19 smart00717 SANT SANT SWI3, AD 99.1 1.8E-10 4E-15 83.4 5.4 48 173-220 1-48 (49)
20 smart00717 SANT SANT SWI3, AD 99.0 3.6E-10 7.8E-15 81.9 5.6 47 225-271 1-48 (49)
21 cd00167 SANT 'SWI3, ADA2, N-Co 98.9 1.2E-09 2.6E-14 78.1 5.0 45 175-219 1-45 (45)
22 cd00167 SANT 'SWI3, ADA2, N-Co 98.9 3E-09 6.5E-14 76.0 5.7 43 227-269 1-44 (45)
23 PF13325 MCRS_N: N-terminal re 97.6 0.00021 4.6E-09 69.0 8.8 98 175-274 1-130 (199)
24 KOG0457 Histone acetyltransfer 97.5 0.00012 2.6E-09 77.2 5.7 59 162-220 61-119 (438)
25 TIGR01557 myb_SHAQKYF myb-like 97.4 0.00026 5.7E-09 55.5 5.0 47 173-219 3-54 (57)
26 TIGR02894 DNA_bind_RsfA transc 97.4 0.00031 6.6E-09 65.6 5.7 52 224-276 3-61 (161)
27 TIGR01557 myb_SHAQKYF myb-like 97.2 0.00093 2E-08 52.4 5.8 46 225-270 3-54 (57)
28 KOG0457 Histone acetyltransfer 97.1 0.00063 1.4E-08 71.9 5.7 49 223-271 70-119 (438)
29 PF13837 Myb_DNA-bind_4: Myb/S 96.9 0.0015 3.2E-08 54.0 4.5 53 225-277 1-71 (90)
30 TIGR02894 DNA_bind_RsfA transc 96.8 0.00097 2.1E-08 62.3 3.0 50 171-221 2-57 (161)
31 COG5259 RSC8 RSC chromatin rem 96.7 0.0016 3.5E-08 69.4 4.8 46 172-218 278-323 (531)
32 PF08914 Myb_DNA-bind_2: Rap1 96.4 0.0034 7.3E-08 50.5 3.7 51 173-223 2-61 (65)
33 KOG1279 Chromatin remodeling f 96.4 0.0034 7.4E-08 68.3 4.5 49 169-218 249-297 (506)
34 PF13837 Myb_DNA-bind_4: Myb/S 96.3 0.0049 1.1E-07 50.9 4.2 46 174-219 2-64 (90)
35 COG5259 RSC8 RSC chromatin rem 96.3 0.0051 1.1E-07 65.8 4.9 46 224-269 278-323 (531)
36 KOG1279 Chromatin remodeling f 96.0 0.0083 1.8E-07 65.4 5.3 48 224-271 252-299 (506)
37 PRK13923 putative spore coat p 95.8 0.011 2.3E-07 56.1 4.3 52 223-275 3-61 (170)
38 PF13873 Myb_DNA-bind_5: Myb/S 95.8 0.022 4.8E-07 46.2 5.6 51 225-275 2-74 (78)
39 PLN03142 Probable chromatin-re 95.5 0.079 1.7E-06 62.5 10.6 98 176-273 827-987 (1033)
40 PRK13923 putative spore coat p 95.4 0.013 2.8E-07 55.5 3.1 50 171-221 3-58 (170)
41 PF08914 Myb_DNA-bind_2: Rap1 95.3 0.029 6.3E-07 45.2 4.5 49 225-273 2-60 (65)
42 COG5114 Histone acetyltransfer 95.0 0.026 5.7E-07 58.0 4.3 46 225-270 63-109 (432)
43 PF13873 Myb_DNA-bind_5: Myb/S 94.8 0.04 8.7E-07 44.7 4.1 47 173-219 2-69 (78)
44 COG5114 Histone acetyltransfer 94.8 0.025 5.3E-07 58.2 3.4 50 171-220 61-110 (432)
45 PF12776 Myb_DNA-bind_3: Myb/S 91.9 0.33 7.2E-06 40.4 5.1 48 227-274 1-66 (96)
46 KOG4282 Transcription factor G 91.3 0.26 5.6E-06 51.0 4.7 53 225-277 54-120 (345)
47 PF09111 SLIDE: SLIDE; InterP 90.5 0.51 1.1E-05 42.3 5.2 52 222-273 46-113 (118)
48 KOG2656 DNA methyltransferase 90.3 0.24 5.1E-06 52.4 3.3 50 226-275 131-186 (445)
49 PF09111 SLIDE: SLIDE; InterP 89.9 0.56 1.2E-05 42.1 4.9 50 170-219 46-110 (118)
50 COG5118 BDP1 Transcription ini 88.5 0.72 1.6E-05 48.7 5.3 46 226-271 366-411 (507)
51 COG5118 BDP1 Transcription ini 86.1 0.93 2E-05 48.0 4.4 44 173-217 365-408 (507)
52 KOG1194 Predicted DNA-binding 85.7 3.2 7E-05 45.0 8.2 51 224-274 186-236 (534)
53 KOG4282 Transcription factor G 83.9 1.3 2.8E-05 45.9 4.4 48 173-220 54-114 (345)
54 PF12776 Myb_DNA-bind_3: Myb/S 83.7 2 4.3E-05 35.7 4.7 44 175-218 1-61 (96)
55 PF13325 MCRS_N: N-terminal re 82.8 2.6 5.6E-05 41.2 5.6 48 171-218 71-125 (199)
56 PF08281 Sigma70_r4_2: Sigma-7 81.6 3.6 7.8E-05 30.7 4.9 42 230-272 12-53 (54)
57 PLN03138 Protein TOC75; Provis 80.6 0.92 2E-05 52.3 2.0 20 107-126 179-198 (796)
58 PF11705 RNA_pol_3_Rpc31: DNA- 79.3 2.4 5.3E-05 41.8 4.2 6 361-366 210-215 (233)
59 PF13404 HTH_AsnC-type: AsnC-t 75.2 5.5 0.00012 29.2 4.1 38 179-217 3-40 (42)
60 smart00595 MADF subfamily of S 75.2 4.5 9.7E-05 33.2 4.1 29 246-275 29-57 (89)
61 PF11626 Rap1_C: TRF2-interact 75.1 4.2 9.1E-05 34.2 3.9 16 169-184 43-58 (87)
62 KOG4167 Predicted DNA-binding 74.1 3.9 8.5E-05 46.7 4.4 43 174-217 620-662 (907)
63 KOG4167 Predicted DNA-binding 74.0 16 0.00034 42.1 9.0 45 225-269 619-663 (907)
64 KOG2656 DNA methyltransferase 72.7 2.3 4.9E-05 45.3 2.1 47 173-220 130-182 (445)
65 PLN03138 Protein TOC75; Provis 72.2 2.4 5.1E-05 49.1 2.3 12 114-125 166-177 (796)
66 PF13404 HTH_AsnC-type: AsnC-t 68.9 13 0.00028 27.2 4.8 38 231-269 3-41 (42)
67 PRK11179 DNA-binding transcrip 66.1 8 0.00017 35.4 4.0 44 178-222 8-51 (153)
68 PRK11179 DNA-binding transcrip 66.0 12 0.00025 34.4 5.1 45 230-275 8-53 (153)
69 KOG1456 Heterogeneous nuclear 65.3 5.3 0.00011 42.5 2.9 14 142-155 100-113 (494)
70 PF04545 Sigma70_r4: Sigma-70, 62.7 19 0.00041 26.5 4.8 41 231-272 7-47 (50)
71 PRK11169 leucine-responsive tr 62.4 9.1 0.0002 35.5 3.7 45 178-223 13-57 (164)
72 KOG1194 Predicted DNA-binding 62.1 11 0.00024 41.0 4.7 45 172-217 186-230 (534)
73 KOG0037 Ca2+-binding protein, 59.7 9.8 0.00021 37.7 3.5 41 171-216 106-147 (221)
74 PF11035 SnAPC_2_like: Small n 59.0 27 0.00059 36.5 6.7 51 225-275 21-75 (344)
75 PRK11169 leucine-responsive tr 58.8 15 0.00033 34.0 4.6 45 230-275 13-58 (164)
76 PF11035 SnAPC_2_like: Small n 58.6 70 0.0015 33.6 9.5 91 168-271 16-127 (344)
77 KOG4468 Polycomb-group transcr 57.4 15 0.00033 41.2 4.8 48 225-272 88-145 (782)
78 PF11626 Rap1_C: TRF2-interact 56.6 5.3 0.00012 33.5 1.0 18 221-238 43-60 (87)
79 TIGR02985 Sig70_bacteroi1 RNA 54.8 28 0.00062 30.5 5.5 42 231-273 116-157 (161)
80 PF04504 DUF573: Protein of un 54.5 22 0.00048 30.7 4.5 51 226-276 5-68 (98)
81 KOG3074 Transcriptional regula 51.8 9.5 0.00021 38.2 2.0 14 181-194 158-171 (263)
82 KOG3915 Transcription regulato 50.5 17 0.00038 39.7 3.9 9 38-46 116-124 (641)
83 PF07750 GcrA: GcrA cell cycle 50.2 19 0.00041 33.9 3.7 42 227-269 2-43 (162)
84 PF05268 GP38: Phage tail fibr 49.8 9.6 0.00021 37.9 1.7 12 18-29 174-185 (260)
85 KOG4468 Polycomb-group transcr 48.4 32 0.0007 38.8 5.5 47 173-220 88-144 (782)
86 PF10545 MADF_DNA_bdg: Alcohol 48.3 16 0.00036 28.9 2.6 31 246-276 28-59 (85)
87 PLN03142 Probable chromatin-re 48.2 24 0.00053 42.3 5.0 49 169-217 922-982 (1033)
88 KOG4329 DNA-binding protein [G 45.6 78 0.0017 33.9 7.6 45 226-270 278-323 (445)
89 PF08281 Sigma70_r4_2: Sigma-7 45.4 32 0.00069 25.5 3.6 39 178-218 12-50 (54)
90 PF06682 DUF1183: Protein of u 45.1 22 0.00047 37.2 3.5 8 35-42 213-220 (318)
91 KOG2009 Transcription initiati 43.4 23 0.00049 39.8 3.5 48 224-271 408-455 (584)
92 smart00595 MADF subfamily of S 41.0 20 0.00043 29.4 2.1 23 195-218 29-51 (89)
93 PF07750 GcrA: GcrA cell cycle 40.9 34 0.00074 32.2 3.9 41 175-217 2-42 (162)
94 PF09197 Rap1-DNA-bind: Rap1, 40.3 51 0.0011 29.2 4.6 46 175-220 1-76 (105)
95 TIGR02937 sigma70-ECF RNA poly 40.2 59 0.0013 27.6 5.0 43 228-272 111-153 (158)
96 smart00344 HTH_ASNC helix_turn 38.2 47 0.001 28.0 4.0 43 179-222 3-45 (108)
97 PRK06341 single-stranded DNA-b 36.9 38 0.00083 32.1 3.5 17 10-26 120-136 (166)
98 cd06171 Sigma70_r4 Sigma70, re 36.2 96 0.0021 21.5 4.9 42 228-271 11-52 (55)
99 smart00344 HTH_ASNC helix_turn 36.0 73 0.0016 26.8 4.9 45 231-276 3-48 (108)
100 TIGR02877 spore_yhbH sporulati 36.0 24 0.00052 37.6 2.2 11 223-233 299-309 (371)
101 KOG0037 Ca2+-binding protein, 35.1 46 0.001 33.1 3.8 26 23-49 13-38 (221)
102 KOG3074 Transcriptional regula 34.5 24 0.00052 35.5 1.8 10 235-244 160-169 (263)
103 PF07638 Sigma70_ECF: ECF sigm 34.2 80 0.0017 29.6 5.3 41 231-272 138-178 (185)
104 PRK09652 RNA polymerase sigma 33.4 86 0.0019 28.1 5.2 39 234-273 134-172 (182)
105 KOG4006 Anti-proliferation fac 33.2 42 0.00092 34.9 3.4 45 11-59 262-306 (311)
106 PF01388 ARID: ARID/BRIGHT DNA 32.7 90 0.0019 25.8 4.8 38 234-271 39-89 (92)
107 PLN02705 beta-amylase 31.7 28 0.00061 39.4 2.0 20 38-57 139-158 (681)
108 PF04504 DUF573: Protein of un 31.3 1.4E+02 0.0031 25.7 5.9 68 174-242 5-94 (98)
109 PRK11924 RNA polymerase sigma 30.9 99 0.0021 27.6 5.1 37 236-273 133-169 (179)
110 PRK04217 hypothetical protein; 30.7 1.1E+02 0.0023 27.3 5.1 44 227-272 42-85 (110)
111 COG1522 Lrp Transcriptional re 29.3 74 0.0016 28.3 4.0 45 178-223 7-51 (154)
112 PRK09643 RNA polymerase sigma 28.8 1.1E+02 0.0025 28.5 5.3 41 231-272 137-177 (192)
113 smart00501 BRIGHT BRIGHT, ARID 28.6 1.2E+02 0.0026 25.3 4.9 39 234-272 35-86 (93)
114 PRK09641 RNA polymerase sigma 28.1 1.2E+02 0.0025 27.7 5.2 41 232-273 140-180 (187)
115 PF01388 ARID: ARID/BRIGHT DNA 27.6 70 0.0015 26.4 3.3 41 181-221 38-90 (92)
116 PF02954 HTH_8: Bacterial regu 27.1 1.3E+02 0.0029 21.6 4.2 35 232-267 6-40 (42)
117 cd08319 Death_RAIDD Death doma 26.7 92 0.002 26.2 3.8 29 233-262 2-30 (83)
118 PF00740 Parvo_coat: Parvoviru 26.5 19 0.00042 40.0 -0.4 13 59-71 81-93 (529)
119 COG1522 Lrp Transcriptional re 26.2 1.2E+02 0.0027 26.9 4.9 45 230-275 7-52 (154)
120 KOG3554 Histone deacetylase co 25.9 1.2E+02 0.0026 33.6 5.3 61 197-267 267-328 (693)
121 KOG3841 TEF-1 and related tran 25.5 98 0.0021 33.3 4.5 58 223-280 74-152 (455)
122 KOG2009 Transcription initiati 25.5 46 0.001 37.5 2.3 48 169-217 405-452 (584)
123 KOG4817 Unnamed protein [Funct 25.4 66 0.0014 34.5 3.2 24 42-65 224-247 (468)
124 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 25.3 1.4E+02 0.0031 23.0 4.3 36 231-267 7-42 (50)
125 PRK09637 RNA polymerase sigma 25.3 1.4E+02 0.0031 27.7 5.3 40 232-272 110-149 (181)
126 TIGR02954 Sig70_famx3 RNA poly 25.2 1.4E+02 0.0031 26.8 5.2 41 232-273 123-163 (169)
127 PRK09047 RNA polymerase factor 24.5 1.7E+02 0.0038 25.8 5.5 41 232-273 110-150 (161)
128 KOG0921 Dosage compensation co 24.1 76 0.0016 37.9 3.7 20 11-30 1192-1211(1282)
129 TIGR02939 RpoE_Sigma70 RNA pol 23.9 1.2E+02 0.0026 27.7 4.5 39 234-273 144-182 (190)
130 PF08949 DUF1860: Domain of un 23.9 26 0.00056 33.1 -0.0 11 14-24 71-81 (220)
131 TIGR02948 SigW_bacill RNA poly 23.8 1.3E+02 0.0029 27.3 4.7 39 234-273 142-180 (187)
132 KOG4329 DNA-binding protein [G 23.5 1.1E+02 0.0024 32.9 4.4 44 173-217 277-321 (445)
133 TIGR02943 Sig70_famx1 RNA poly 23.2 1.8E+02 0.0038 27.2 5.5 41 232-273 135-175 (188)
134 cd08803 Death_ank3 Death domai 23.1 1.2E+02 0.0026 25.5 3.9 29 233-262 4-32 (84)
135 PRK12512 RNA polymerase sigma 23.1 1.7E+02 0.0038 26.7 5.4 41 232-273 135-175 (184)
136 PRK06759 RNA polymerase factor 23.0 1.9E+02 0.0041 25.5 5.4 38 234-272 112-149 (154)
137 PRK09645 RNA polymerase sigma 22.6 1.8E+02 0.004 26.2 5.4 41 232-273 122-162 (173)
138 PRK09648 RNA polymerase sigma 22.5 1.8E+02 0.0039 26.8 5.4 37 235-272 146-182 (189)
139 PRK09642 RNA polymerase sigma 22.3 1.9E+02 0.0041 25.7 5.3 41 231-272 109-149 (160)
140 PRK12530 RNA polymerase sigma 22.1 1.8E+02 0.004 27.0 5.4 40 232-272 138-177 (189)
141 PRK11923 algU RNA polymerase s 22.1 1.7E+02 0.0036 27.0 5.1 32 241-273 151-182 (193)
142 PF00740 Parvo_coat: Parvoviru 22.0 27 0.00059 38.8 -0.3 14 108-121 80-93 (529)
143 PRK06958 single-stranded DNA-b 21.9 1.1E+02 0.0025 29.5 3.9 9 40-48 162-170 (182)
144 PF04545 Sigma70_r4: Sigma-70, 21.5 1.3E+02 0.0028 22.0 3.4 39 179-219 7-45 (50)
145 PRK12523 RNA polymerase sigma 21.2 2E+02 0.0042 26.2 5.3 41 232-273 123-163 (172)
146 cd08317 Death_ank Death domain 21.0 1.2E+02 0.0025 25.1 3.3 29 233-262 4-32 (84)
147 PRK12531 RNA polymerase sigma 20.6 2.1E+02 0.0046 26.6 5.5 40 233-273 146-185 (194)
148 PF11705 RNA_pol_3_Rpc31: DNA- 20.5 94 0.002 30.6 3.1 6 36-41 31-36 (233)
149 TIGR02952 Sig70_famx2 RNA poly 20.0 2.2E+02 0.0048 25.3 5.3 40 232-272 126-165 (170)
No 1
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.97 E-value=5.8e-31 Score=257.32 Aligned_cols=110 Identities=42% Similarity=0.834 Sum_probs=104.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCchHHHHHHHhc-CCChhhhhhhhhhccccccccCCCCHHHHHHHHHHHHHhCChH
Q 046581 169 VALIKGQWTDEEDRKLIKLVKQYGVRKWAQISERMA-GRAGKQCRERWHNHLRPDIKKDSWSEEEERILVEAHARIGNRW 247 (470)
Q Consensus 169 p~lkKG~WT~EED~~Ll~lV~~yG~~~Ws~IA~~lp-gRT~~Qcr~Rw~~~L~p~ikk~~WT~EED~~Ll~lv~~~G~kW 247 (470)
+.+.||+||+|||.+|+++|++||.++|..||+.++ +|++++||.||.+||+|+++++.||+|||.+|+++|..+|++|
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 335689999999999999999999999999999999 9999999999999999999999999999999999999999999
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhHHhhhhccc
Q 046581 248 AEIAKHIPGRTENSIKNHWNATKRRQNSRRK 278 (470)
Q Consensus 248 s~IAk~LpgRT~~q~KnRw~~llrr~~~k~k 278 (470)
++||++|||||+++|||+|+..+||+..+..
T Consensus 85 s~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 85 SLIAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred HHHHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 9999999999999999999999888766543
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.97 E-value=2e-30 Score=251.91 Aligned_cols=110 Identities=41% Similarity=0.818 Sum_probs=104.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCchHHHHHHHh-cCCChhhhhhhhhhccccccccCCCCHHHHHHHHHHHHHhCCh
Q 046581 168 SVALIKGQWTDEEDRKLIKLVKQYGVRKWAQISERM-AGRAGKQCRERWHNHLRPDIKKDSWSEEEERILVEAHARIGNR 246 (470)
Q Consensus 168 ~p~lkKG~WT~EED~~Ll~lV~~yG~~~Ws~IA~~l-pgRT~~Qcr~Rw~~~L~p~ikk~~WT~EED~~Ll~lv~~~G~k 246 (470)
.+.+++++||+|||++|+++|++||..+|..||+.+ ++|+++|||+||.++|+|.+++++||.|||++|++++.+||++
T Consensus 20 K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~~GnK 99 (249)
T PLN03212 20 KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLGNR 99 (249)
T ss_pred cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHhcccc
Confidence 578899999999999999999999988999999998 5999999999999999999999999999999999999999999
Q ss_pred HHHHhhhCCCCCHHHHHHHHHHhHHhhhhcc
Q 046581 247 WAEIAKHIPGRTENSIKNHWNATKRRQNSRR 277 (470)
Q Consensus 247 Ws~IAk~LpgRT~~q~KnRw~~llrr~~~k~ 277 (470)
|+.||++|||||+++|||||+.++|++..+.
T Consensus 100 Ws~IAk~LpGRTDnqIKNRWns~LrK~l~r~ 130 (249)
T PLN03212 100 WSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQ 130 (249)
T ss_pred HHHHHhhcCCCCHHHHHHHHHHHHhHHHHhc
Confidence 9999999999999999999999998775543
No 3
>PLN03091 hypothetical protein; Provisional
Probab=99.96 E-value=7.4e-29 Score=256.45 Aligned_cols=107 Identities=44% Similarity=0.917 Sum_probs=102.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCchHHHHHHHhc-CCChhhhhhhhhhccccccccCCCCHHHHHHHHHHHHHhCChH
Q 046581 169 VALIKGQWTDEEDRKLIKLVKQYGVRKWAQISERMA-GRAGKQCRERWHNHLRPDIKKDSWSEEEERILVEAHARIGNRW 247 (470)
Q Consensus 169 p~lkKG~WT~EED~~Ll~lV~~yG~~~Ws~IA~~lp-gRT~~Qcr~Rw~~~L~p~ikk~~WT~EED~~Ll~lv~~~G~kW 247 (470)
..++|++||+|||++|+++|.+||..+|..||+.++ +|+++|||+||.++|+|.+++++||+|||++|++++.++|++|
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k~~GnKW 89 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHAVLGNRW 89 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHHHhCcch
Confidence 568899999999999999999999989999999985 9999999999999999999999999999999999999999999
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhHHhhhh
Q 046581 248 AEIAKHIPGRTENSIKNHWNATKRRQNS 275 (470)
Q Consensus 248 s~IAk~LpgRT~~q~KnRw~~llrr~~~ 275 (470)
++||++|||||+++|||||+.++||+.+
T Consensus 90 skIAk~LPGRTDnqIKNRWnslLKKklr 117 (459)
T PLN03091 90 SQIAAQLPGRTDNEIKNLWNSCLKKKLR 117 (459)
T ss_pred HHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999988765
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.92 E-value=2e-25 Score=237.14 Aligned_cols=185 Identities=23% Similarity=0.362 Sum_probs=159.5
Q ss_pred eeeeeeccCCCCCccccccCCCc-cCCCCCCCCCchHHHHHHHHHHHcCCCCcccccChhhcccccCC--Cccccc----
Q 046581 79 VISLCAFSSTSGASTAAAYGGQH-EALRTSTTTTTLEPTSFVDGFFADGTANDQSLINWSYDIIYKEG--SKSACN---- 151 (470)
Q Consensus 79 ~~S~~~~s~~s~~~~~~~~g~~~-~~~~k~g~WT~EED~~Ll~~V~~~G~~~~~~~~nW~~IA~~~gr--s~~~cR---- 151 (470)
.||..+|++..++-...++|++. .+...+-.|++|||++|+.+..++| ..+|..||.-+|+ +.-||.
T Consensus 224 ~ISn~dfEgsrS~~~~~~~W~n~l~P~~nk~~WS~EE~E~L~AiA~A~~------~~~W~~IA~~Lgt~RS~yQC~~kF~ 297 (939)
T KOG0049|consen 224 AISNFDFEGSRSEWAVKSKWYNELNPKWNKEHWSNEEVEKLKALAEAPK------FVSWPMIALNLGTNRSSYQCMEKFK 297 (939)
T ss_pred HhccccccccCCHHHHHHHHhhhcCCccchhccChHHHHHHHHHHhccc------cccHHHHHHHhCCCcchHHHHHHHH
Confidence 36788999999999888888885 4555668999999999999988887 3569999987765 446665
Q ss_pred --------------------------------------------CccccccccccccccCCCCCCCCCCCHHHHHHHHHH
Q 046581 152 --------------------------------------------NNKGMIGHKRSNKKGASVALIKGQWTDEEDRKLIKL 187 (470)
Q Consensus 152 --------------------------------------------~~~q~~~~~rRw~~~l~p~lkKG~WT~EED~~Ll~l 187 (470)
+..|+. .||.+.|.|.+++|+||++||.+|+.+
T Consensus 298 t~~~~L~ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ympgr~~~qLI---~R~~~~LdPsikhg~wt~~ED~~L~~A 374 (939)
T KOG0049|consen 298 TEVSQLSEKEWSEEEDTKLIALVKITSINSHIQWDKVVQYMPGRTRQQLI---TRFSHTLDPSVKHGRWTDQEDVLLVCA 374 (939)
T ss_pred HHHHHHHhhhcchhhhHHHHHHHHHhhccCccchHHHHHhcCCcchhhhh---hhheeccCccccCCCCCCHHHHHHHHH
Confidence 333333 399999999999999999999999999
Q ss_pred HHHhCCchHHHHHHHhcCCChhhhhhhhhhccccccccCCCCHHHHHHHHHHHHHhC-ChHHHHhhhCCCCCH---HHHH
Q 046581 188 VKQYGVRKWAQISERMAGRAGKQCRERWHNHLRPDIKKDSWSEEEERILVEAHARIG-NRWAEIAKHIPGRTE---NSIK 263 (470)
Q Consensus 188 V~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L~p~ikk~~WT~EED~~Ll~lv~~~G-~kWs~IAk~LpgRT~---~q~K 263 (470)
|.+||...|.+|-+.+|||+..|||+||.+.|....+++.||..||+.|+.+|.+|| ++|.+||.+||.||. ..||
T Consensus 375 V~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR 454 (939)
T KOG0049|consen 375 VSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRR 454 (939)
T ss_pred HHHhCccchhhHHHhcCCccHHHHHHHHHHHHHHhhccCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999 689999999999999 4555
Q ss_pred HHHHHhHHh
Q 046581 264 NHWNATKRR 272 (470)
Q Consensus 264 nRw~~llrr 272 (470)
.|+-.++++
T Consensus 455 ~R~~~~k~r 463 (939)
T KOG0049|consen 455 LRLIAAKLR 463 (939)
T ss_pred HHHHHHHHH
Confidence 555554443
No 5
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.89 E-value=8.1e-24 Score=205.99 Aligned_cols=102 Identities=20% Similarity=0.351 Sum_probs=93.3
Q ss_pred CCCCCCCchHHHHHHHHHHHcCCCCcccccChhhccccc--CCCcccccCccccccccccccccCCCCCCCCCCCHHHHH
Q 046581 105 RTSTTTTTLEPTSFVDGFFADGTANDQSLINWSYDIIYK--EGSKSACNNNKGMIGHKRSNKKGASVALIKGQWTDEEDR 182 (470)
Q Consensus 105 ~k~g~WT~EED~~Ll~~V~~~G~~~~~~~~nW~~IA~~~--grs~~~cR~~~q~~~~~rRw~~~l~p~lkKG~WT~EED~ 182 (470)
.++++||+|||++|+++|.+||.. +|..||..+ +|+..+|| .||.++|+|.+++++||+|||+
T Consensus 23 lKRg~WT~EEDe~L~~lV~kyG~~------nW~~IAk~~g~gRT~KQCR---------eRW~N~L~P~I~kgpWT~EED~ 87 (249)
T PLN03212 23 MKRGPWTVEEDEILVSFIKKEGEG------RWRSLPKRAGLLRCGKSCR---------LRWMNYLRPSVKRGGITSDEED 87 (249)
T ss_pred CcCCCCCHHHHHHHHHHHHHhCcc------cHHHHHHhhhcCCCcchHH---------HHHHHhhchhcccCCCChHHHH
Confidence 567899999999999999999965 499999854 67888887 6999999999999999999999
Q ss_pred HHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhccccc
Q 046581 183 KLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNHLRPD 222 (470)
Q Consensus 183 ~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L~p~ 222 (470)
+|++++..|| ++|+.||+.|||||+.+|++||+.+|++.
T Consensus 88 lLlel~~~~G-nKWs~IAk~LpGRTDnqIKNRWns~LrK~ 126 (249)
T PLN03212 88 LILRLHRLLG-NRWSLIAGRIPGRTDNEIKNYWNTHLRKK 126 (249)
T ss_pred HHHHHHHhcc-ccHHHHHhhcCCCCHHHHHHHHHHHHhHH
Confidence 9999999999 69999999999999999999999987744
No 6
>PLN03091 hypothetical protein; Provisional
Probab=99.87 E-value=7e-23 Score=212.30 Aligned_cols=105 Identities=17% Similarity=0.334 Sum_probs=94.6
Q ss_pred CCCCCCCCCchHHHHHHHHHHHcCCCCcccccChhhccccc--CCCcccccCccccccccccccccCCCCCCCCCCCHHH
Q 046581 103 ALRTSTTTTTLEPTSFVDGFFADGTANDQSLINWSYDIIYK--EGSKSACNNNKGMIGHKRSNKKGASVALIKGQWTDEE 180 (470)
Q Consensus 103 ~~~k~g~WT~EED~~Ll~~V~~~G~~~~~~~~nW~~IA~~~--grs~~~cR~~~q~~~~~rRw~~~l~p~lkKG~WT~EE 180 (470)
...++++||+|||++|+++|.+||.. +|..||..+ +|+.++|| .||.++|+|.++|++||+||
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~------nWs~IAk~~g~gRT~KQCR---------ERW~NyLdP~IkKgpWT~EE 74 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHG------CWSSVPKQAGLQRCGKSCR---------LRWINYLRPDLKRGTFSQQE 74 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcC------CHHHHhhhhccCcCcchHh---------HHHHhccCCcccCCCCCHHH
Confidence 34567899999999999999999965 499999854 57778887 69999999999999999999
Q ss_pred HHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhcccccc
Q 046581 181 DRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNHLRPDI 223 (470)
Q Consensus 181 D~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L~p~i 223 (470)
|++|++++.+|| .+|.+||+.|||||+.+||+||+.+|++.+
T Consensus 75 D~lLLeL~k~~G-nKWskIAk~LPGRTDnqIKNRWnslLKKkl 116 (459)
T PLN03091 75 ENLIIELHAVLG-NRWSQIAAQLPGRTDNEIKNLWNSCLKKKL 116 (459)
T ss_pred HHHHHHHHHHhC-cchHHHHHhcCCCCHHHHHHHHHHHHHHHH
Confidence 999999999999 699999999999999999999998887644
No 7
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.87 E-value=1.1e-22 Score=199.18 Aligned_cols=101 Identities=22% Similarity=0.355 Sum_probs=92.5
Q ss_pred CCCCCCCchHHHHHHHHHHHcCCCCcccccChhhccccc--CCCcccccCccccccccccccccCCCCCCCCCCCHHHHH
Q 046581 105 RTSTTTTTLEPTSFVDGFFADGTANDQSLINWSYDIIYK--EGSKSACNNNKGMIGHKRSNKKGASVALIKGQWTDEEDR 182 (470)
Q Consensus 105 ~k~g~WT~EED~~Ll~~V~~~G~~~~~~~~nW~~IA~~~--grs~~~cR~~~q~~~~~rRw~~~l~p~lkKG~WT~EED~ 182 (470)
+.+|+||+|||++|+++|.+||..+ |..|+... +|..++|| .||.+||+|.++||.||+|||+
T Consensus 7 ~~kGpWt~EED~~L~~~V~~~G~~~------W~~i~k~~gl~R~GKSCR---------lRW~NyLrP~ikrg~fT~eEe~ 71 (238)
T KOG0048|consen 7 LVKGPWTQEEDLTQIRSIKSFGKHN------GTALPKLAGLRRCGKSCR---------LRWTNYLRPDLKRGNFSDEEED 71 (238)
T ss_pred ccCCCCChHHHHHHHHHHHHhCCCC------cchhhhhcCCCccchHHH---------HHhhcccCCCccCCCCCHHHHH
Confidence 3469999999999999999999764 99999843 67888888 7999999999999999999999
Q ss_pred HHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhcccc
Q 046581 183 KLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNHLRP 221 (470)
Q Consensus 183 ~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L~p 221 (470)
+|++++..+| ++|+.||++|||||++.++++|+.+|+.
T Consensus 72 ~Ii~lH~~~G-NrWs~IA~~LPGRTDNeIKN~Wnt~lkk 109 (238)
T KOG0048|consen 72 LIIKLHALLG-NRWSLIAGRLPGRTDNEVKNHWNTHLKK 109 (238)
T ss_pred HHHHHHHHHC-cHHHHHHhhCCCcCHHHHHHHHHHHHHH
Confidence 9999999999 7999999999999999999999887753
No 8
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.76 E-value=1.2e-18 Score=185.93 Aligned_cols=144 Identities=22% Similarity=0.456 Sum_probs=120.1
Q ss_pred ccChhhccc--ccCC-CcccccCccccccccccccccCCCCCCCCCCCHHHHHHHHHHHHHhCCch--------------
Q 046581 133 LINWSYDII--YKEG-SKSACNNNKGMIGHKRSNKKGASVALIKGQWTDEEDRKLIKLVKQYGVRK-------------- 195 (470)
Q Consensus 133 ~~nW~~IA~--~~gr-s~~~cR~~~q~~~~~rRw~~~l~p~lkKG~WT~EED~~Ll~lV~~yG~~~-------------- 195 (470)
..+|..|.. |-|+ +.-.|+ ..|.+++.|.++|..|++|||++|+.+...++.-+
T Consensus 219 ~~DW~~ISn~dfEgsrS~~~~~---------~~W~n~l~P~~nk~~WS~EE~E~L~AiA~A~~~~~W~~IA~~Lgt~RS~ 289 (939)
T KOG0049|consen 219 YVDWTAISNFDFEGSRSEWAVK---------SKWYNELNPKWNKEHWSNEEVEKLKALAEAPKFVSWPMIALNLGTNRSS 289 (939)
T ss_pred ccCHHHhccccccccCCHHHHH---------HHHhhhcCCccchhccChHHHHHHHHHHhccccccHHHHHHHhCCCcch
Confidence 378999987 4453 445565 59999999999999999999999988876553333
Q ss_pred -----------------------------------------HHHHHHHhcCCChhhhhhhhhhccccccccCCCCHHHHH
Q 046581 196 -----------------------------------------WAQISERMAGRAGKQCRERWHNHLRPDIKKDSWSEEEER 234 (470)
Q Consensus 196 -----------------------------------------Ws~IA~~lpgRT~~Qcr~Rw~~~L~p~ikk~~WT~EED~ 234 (470)
|.+|-.+||||+..|..-||...|+|.+++++||.+||.
T Consensus 290 yQC~~kF~t~~~~L~ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~ 369 (939)
T KOG0049|consen 290 YQCMEKFKTEVSQLSEKEWSEEEDTKLIALVKITSINSHIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDV 369 (939)
T ss_pred HHHHHHHHHHHHHHHhhhcchhhhHHHHHHHHHhhccCccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHH
Confidence 666666666666666677778889999999999999999
Q ss_pred HHHHHHHHhCCh-HHHHhhhCCCCCHHHHHHHHHHhHHhhhhccccchhhhh
Q 046581 235 ILVEAHARIGNR-WAEIAKHIPGRTENSIKNHWNATKRRQNSRRKNKQNEKQ 285 (470)
Q Consensus 235 ~Ll~lv~~~G~k-Ws~IAk~LpgRT~~q~KnRw~~llrr~~~k~k~~~~e~~ 285 (470)
+|+.+|.+||.+ |.+|-..+|||++.|||.||...+.+.+++..|.-.+++
T Consensus 370 ~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~rW~l~ede 421 (939)
T KOG0049|consen 370 LLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNRSAKVERWTLVEDE 421 (939)
T ss_pred HHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHHhhccCceeecchH
Confidence 999999999965 999999999999999999999999988888888776654
No 9
>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=99.62 E-value=9.5e-16 Score=119.02 Aligned_cols=60 Identities=52% Similarity=1.116 Sum_probs=54.9
Q ss_pred CCHHHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhccccccccCCCCHHHHHHH
Q 046581 176 WTDEEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNHLRPDIKKDSWSEEEERIL 236 (470)
Q Consensus 176 WT~EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L~p~ikk~~WT~EED~~L 236 (470)
||+|||++|+++|..|| .+|..||+.|+.||+.+|+.||.++|.+.+++++||.+||.+|
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 6999999999669999999999999999999999999999987
No 10
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.57 E-value=5.9e-15 Score=159.03 Aligned_cols=158 Identities=20% Similarity=0.340 Sum_probs=131.7
Q ss_pred CCccCCC-CCCCCCchHHHHHHHHHHHcCCCCcccccChhhcccccCCCcccccCccccccccccccccCCCC--CCCCC
Q 046581 99 GQHEALR-TSTTTTTLEPTSFVDGFFADGTANDQSLINWSYDIIYKEGSKSACNNNKGMIGHKRSNKKGASVA--LIKGQ 175 (470)
Q Consensus 99 ~~~~~~~-k~g~WT~EED~~Ll~~V~~~G~~~~~~~~nW~~IA~~~grs~~~cR~~~q~~~~~rRw~~~l~p~--lkKG~ 175 (470)
+...+.. ++|.||++|++.|..+++.+|++ |.+|+..+||++++||+ +|..+.... .++|+
T Consensus 375 R~y~~FE~~rg~wt~ee~eeL~~l~~~~g~~-------W~~Ig~~lgr~P~~crd---------~wr~~~~~g~~~~r~~ 438 (607)
T KOG0051|consen 375 RAYTPFENKRGKWTPEEEEELKKLVVEHGND-------WKEIGKALGRMPMDCRD---------RWRQYVKCGSKRNRGA 438 (607)
T ss_pred hcCCccccccCCCCcchHHHHHHHHHHhccc-------HHHHHHHHccCcHHHHH---------HHHHhhccccccccCc
Confidence 5666777 88999999999999999999987 99999999999999995 666655555 69999
Q ss_pred CCHHHHHHHHHHHH-------Hh------------------CCchHHHHHHHhcCCChhhhhhhhhhcc-ccccccCCCC
Q 046581 176 WTDEEDRKLIKLVK-------QY------------------GVRKWAQISERMAGRAGKQCRERWHNHL-RPDIKKDSWS 229 (470)
Q Consensus 176 WT~EED~~Ll~lV~-------~y------------------G~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L-~p~ikk~~WT 229 (470)
||.||.++|+++|+ ++ ...+|..|++.++.|+..|||.+|..++ .|..+...|.
T Consensus 439 Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n~~~~~ 518 (607)
T KOG0051|consen 439 WSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFNKRQES 518 (607)
T ss_pred chHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhhccccc
Confidence 99999999999996 33 2247999999999999999999999987 4455666777
Q ss_pred H-HHHHHHHHHHHHhC------ChHHHHhhhCCCCC-HHHHHHHHHHhHHh
Q 046581 230 E-EEERILVEAHARIG------NRWAEIAKHIPGRT-ENSIKNHWNATKRR 272 (470)
Q Consensus 230 ~-EED~~Ll~lv~~~G------~kWs~IAk~LpgRT-~~q~KnRw~~llrr 272 (470)
. .+...|++-+..++ -.|..|+...||.. +.+|+.+|..+++.
T Consensus 519 ~~~~~v~l~ErL~dl~~~e~~~IDW~~l~~~~~g~~~~~e~r~q~~~lk~~ 569 (607)
T KOG0051|consen 519 KGSDMVWLLERLSDLDLTEESPIDWKSLAEYAPGESTGEELRLQFERLKKK 569 (607)
T ss_pred ccchhHHHHHHHHhcccccCCccCHHHHHHhCCCCCcHHHHHHHHHhHhhc
Confidence 5 34455666655554 26999999999998 99999999998765
No 11
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.54 E-value=1.3e-14 Score=156.47 Aligned_cols=167 Identities=20% Similarity=0.366 Sum_probs=126.5
Q ss_pred CccCCCCCCCCCchHHHHHHHHHHHcCCCCcccccChhhccc---------------ccCC--CcccccCcccccccccc
Q 046581 100 QHEALRTSTTTTTLEPTSFVDGFFADGTANDQSLINWSYDII---------------YKEG--SKSACNNNKGMIGHKRS 162 (470)
Q Consensus 100 ~~~~~~k~g~WT~EED~~Ll~~V~~~G~~~~~~~~nW~~IA~---------------~~gr--s~~~cR~~~q~~~~~rR 162 (470)
+.+.....+.|+++||..|-..|..|-.. ..|..... +... ....-|+...++.+-+|
T Consensus 301 ~~~~e~~~~~F~~eed~ale~~V~~y~~~-----eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp~R~~~siy~~~rR 375 (607)
T KOG0051|consen 301 TKEDEINLKKFSKEEDAALENFVNEYLAN-----EGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLPYRDRKSIYHHLRR 375 (607)
T ss_pred chhhhhhhhhccHHHHHHHHHHHHHHHHh-----hCcchhhhhhheeccCcchHHHHHHHhhhhhcCcccchhHHHHHHh
Confidence 33455666899999999998888766211 11332211 1110 01112555555554445
Q ss_pred ccccCCCCCCCCCCCHHHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhcccccc--ccCCCCHHHHHHHHHHH
Q 046581 163 NKKGASVALIKGQWTDEEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNHLRPDI--KKDSWSEEEERILVEAH 240 (470)
Q Consensus 163 w~~~l~p~lkKG~WT~EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L~p~i--kk~~WT~EED~~Ll~lv 240 (470)
-++.+.+ .+|.||+||++.|..+|.++| +.|..|++.| ||.+..|++||+++....- +++.||.||++.|+.+|
T Consensus 376 ~y~~FE~--~rg~wt~ee~eeL~~l~~~~g-~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V 451 (607)
T KOG0051|consen 376 AYTPFEN--KRGKWTPEEEEELKKLVVEHG-NDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTV 451 (607)
T ss_pred cCCcccc--ccCCCCcchHHHHHHHHHHhc-ccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHH
Confidence 5555554 999999999999999999999 7999999999 9999999999999998874 88999999999999999
Q ss_pred H-------Hh-------------------CChHHHHhhhCCCCCHHHHHHHHHHhHHhhhh
Q 046581 241 A-------RI-------------------GNRWAEIAKHIPGRTENSIKNHWNATKRRQNS 275 (470)
Q Consensus 241 ~-------~~-------------------G~kWs~IAk~LpgRT~~q~KnRw~~llrr~~~ 275 (470)
. ++ +-.|+.|+..+..|+..+|+.+|..++.+...
T Consensus 452 ~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~ 512 (607)
T KOG0051|consen 452 NEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSF 512 (607)
T ss_pred HHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHh
Confidence 5 23 11599999999999999999999999876543
No 12
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.48 E-value=3.5e-14 Score=149.32 Aligned_cols=105 Identities=30% Similarity=0.598 Sum_probs=99.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhccccccccCCCCHHHHHHHHHHHHHhCChHHHH
Q 046581 171 LIKGQWTDEEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNHLRPDIKKDSWSEEEERILVEAHARIGNRWAEI 250 (470)
Q Consensus 171 lkKG~WT~EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L~p~ikk~~WT~EED~~Ll~lv~~~G~kWs~I 250 (470)
++.|-|+..||+.|..+|.+||.+.|++|++.++-.+++||+.||..+|+|.|++..|+.|||+.||.+...+...|..|
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 56789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhCCCCCHHHHHHHHHHhHHhhhhc
Q 046581 251 AKHIPGRTENSIKNHWNATKRRQNSR 276 (470)
Q Consensus 251 Ak~LpgRT~~q~KnRw~~llrr~~~k 276 (470)
|..+ ||+.+||-.||+.++--...+
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 9999 999999999999887654443
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=99.48 E-value=4.7e-14 Score=150.69 Aligned_cols=108 Identities=32% Similarity=0.641 Sum_probs=101.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhccccccccCCCCHHHHHHHHHHHHHhCChH
Q 046581 168 SVALIKGQWTDEEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNHLRPDIKKDSWSEEEERILVEAHARIGNRW 247 (470)
Q Consensus 168 ~p~lkKG~WT~EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L~p~ikk~~WT~EED~~Ll~lv~~~G~kW 247 (470)
...++.|.|+..||+.|..+|+.||.++|++||..+.-|+++||+.||+++++|.+++..|+.+||..|+.+..++|..|
T Consensus 15 ~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~w 94 (512)
T COG5147 15 QTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQW 94 (512)
T ss_pred cceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCchh
Confidence 44567899999999999999999999999999999988999999999999999999999999999999999999999999
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhHHhhhh
Q 046581 248 AEIAKHIPGRTENSIKNHWNATKRRQNS 275 (470)
Q Consensus 248 s~IAk~LpgRT~~q~KnRw~~llrr~~~ 275 (470)
+.||..+++|+..+|.+||..++....+
T Consensus 95 stia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 95 STIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhccccCccchHHHHHHHHHHhhhhhc
Confidence 9999999999999999999987765444
No 14
>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=99.39 E-value=4.4e-13 Score=100.21 Aligned_cols=47 Identities=53% Similarity=1.088 Sum_probs=42.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCCchHHHHHHHhc-CCChhhhhhhhhhcc
Q 046581 173 KGQWTDEEDRKLIKLVKQYGVRKWAQISERMA-GRAGKQCRERWHNHL 219 (470)
Q Consensus 173 KG~WT~EED~~Ll~lV~~yG~~~Ws~IA~~lp-gRT~~Qcr~Rw~~~L 219 (470)
|++||+|||++|+++|.+||..+|..||..|| +||..||+.||+++|
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 68999999999999999999767999999999 999999999999875
No 15
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.38 E-value=4.6e-13 Score=143.17 Aligned_cols=152 Identities=20% Similarity=0.219 Sum_probs=132.1
Q ss_pred CCCCCCCCchHHHHHHHHHHHcCCCCcccccChhhcccccCC-CcccccCccccccccccccccCCCCCCCCCCCHHHHH
Q 046581 104 LRTSTTTTTLEPTSFVDGFFADGTANDQSLINWSYDIIYKEG-SKSACNNNKGMIGHKRSNKKGASVALIKGQWTDEEDR 182 (470)
Q Consensus 104 ~~k~g~WT~EED~~Ll~~V~~~G~~~~~~~~nW~~IA~~~gr-s~~~cR~~~q~~~~~rRw~~~l~p~lkKG~WT~EED~ 182 (470)
.++.|.|+..||+.|+.+|..+|..+ |..||..+.. ...+|+ .||..+++|.++++.|+.|||.
T Consensus 17 ~~k~gsw~~~EDe~l~~~vk~l~~nn------ws~vas~~~~~~~kq~~---------~rw~~~lnp~lk~~~~~~eed~ 81 (512)
T COG5147 17 KRKGGSWKRTEDEDLKALVKKLGPNN------WSKVASLLISSTGKQSS---------NRWNNHLNPQLKKKNWSEEEDE 81 (512)
T ss_pred eecCCCCCCcchhHHHHHHhhccccc------HHHHHHHhccccccccc---------chhhhhhchhcccccccHHHHH
Confidence 35668999999999999999998764 9999986654 556666 5999999999999999999999
Q ss_pred HHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhccccccccCCCCHHHHHHHHHHHHHhCChHHHHhhhCCCCCHHHH
Q 046581 183 KLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNHLRPDIKKDSWSEEEERILVEAHARIGNRWAEIAKHIPGRTENSI 262 (470)
Q Consensus 183 ~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L~p~ikk~~WT~EED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~ 262 (470)
.|+.+..++|. .|+.||..+++|+..+|.+||.+.|.+... ..|+..++...+..+..|...|..+....-.+-...|
T Consensus 82 ~li~l~~~~~~-~wstia~~~d~rt~~~~~ery~~~~~~~~s-~~~s~~~~~~~f~k~d~f~~~~~~~~~~~~~~~~~~~ 159 (512)
T COG5147 82 QLIDLDKELGT-QWSTIADYKDRRTAQQCVERYVNTLEDLSS-THDSKLQRRNEFDKIDPFNENSARRPDIYEDELLERE 159 (512)
T ss_pred HHHHHHHhcCc-hhhhhccccCccchHHHHHHHHHHhhhhhc-cccccccchhhccccCchhhhhhhhhhhhhcccchhh
Confidence 99999999995 899999999999999999999999987666 8899999988888888899999888877667778888
Q ss_pred HHHHHHhHHh
Q 046581 263 KNHWNATKRR 272 (470)
Q Consensus 263 KnRw~~llrr 272 (470)
.|++..+..+
T Consensus 160 ~N~~~~~~~~ 169 (512)
T COG5147 160 VNREASYRLR 169 (512)
T ss_pred hhHHHHHHHH
Confidence 8888665544
No 16
>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=99.22 E-value=1.6e-11 Score=95.31 Aligned_cols=58 Identities=34% Similarity=0.673 Sum_probs=48.3
Q ss_pred CCHHHHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHhhhhccccchhhhh
Q 046581 228 WSEEEERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRRQNSRRKNKQNEKQ 285 (470)
Q Consensus 228 WT~EED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr~~~k~k~~~~e~~ 285 (470)
||+|||++|+++|.+||++|.+||+.|+.||+.+|++||...++...++.++..+++.
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~ 58 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQ 58 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHh
Confidence 9999999999999999999999999996699999999999977776677777666543
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=99.22 E-value=1.5e-11 Score=91.85 Aligned_cols=46 Identities=35% Similarity=0.750 Sum_probs=41.7
Q ss_pred cCCCCHHHHHHHHHHHHHhCCh-HHHHhhhCC-CCCHHHHHHHHHHhH
Q 046581 225 KDSWSEEEERILVEAHARIGNR-WAEIAKHIP-GRTENSIKNHWNATK 270 (470)
Q Consensus 225 k~~WT~EED~~Ll~lv~~~G~k-Ws~IAk~Lp-gRT~~q~KnRw~~ll 270 (470)
+++||+|||++|+++|.+||.+ |..||..|| +||..||++||+.++
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 18
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.19 E-value=1.5e-12 Score=137.30 Aligned_cols=98 Identities=26% Similarity=0.433 Sum_probs=89.3
Q ss_pred CCCCCCCchHHHHHHHHHHHcCCCCcccccChhhcccccCC-CcccccCccccccccccccccCCCCCCCCCCCHHHHHH
Q 046581 105 RTSTTTTTLEPTSFVDGFFADGTANDQSLINWSYDIIYKEG-SKSACNNNKGMIGHKRSNKKGASVALIKGQWTDEEDRK 183 (470)
Q Consensus 105 ~k~g~WT~EED~~Ll~~V~~~G~~~~~~~~nW~~IA~~~gr-s~~~cR~~~q~~~~~rRw~~~l~p~lkKG~WT~EED~~ 183 (470)
++.|.|+..||++|...|.+||... |.+|+.++.+ +..+|+ .||..+++|.+++--|+.|||.+
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nq------ws~i~sll~~kt~rqC~---------~rw~e~ldp~i~~tews~eeder 69 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQ------WSRIASLLNRKTARQCK---------ARWEEWLDPAIKKTEWSREEDER 69 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHH------HHHHHHHHhhcchhHHH---------HHHHHHhCHHHhhhhhhhhHHHH
Confidence 5678999999999999999999776 9999997765 567776 59999999999999999999999
Q ss_pred HHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhcc
Q 046581 184 LIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNHL 219 (470)
Q Consensus 184 Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L 219 (470)
|+-+..... ..|..|+..| ||++.||-+||.++|
T Consensus 70 lLhlakl~p-~qwrtIa~i~-gr~~~qc~eRy~~ll 103 (617)
T KOG0050|consen 70 LLHLAKLEP-TQWRTIADIM-GRTSQQCLERYNNLL 103 (617)
T ss_pred HHHHHHhcC-CccchHHHHh-hhhHHHHHHHHHHHH
Confidence 999999998 5999999999 999999999998766
No 19
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.08 E-value=1.8e-10 Score=83.41 Aligned_cols=48 Identities=54% Similarity=1.155 Sum_probs=44.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhccc
Q 046581 173 KGQWTDEEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNHLR 220 (470)
Q Consensus 173 KG~WT~EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L~ 220 (470)
+++||++||.+|+.++..||..+|..||..|++||+.+|+.||..++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 468999999999999999997799999999999999999999998764
No 20
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.04 E-value=3.6e-10 Score=81.86 Aligned_cols=47 Identities=40% Similarity=0.897 Sum_probs=44.2
Q ss_pred cCCCCHHHHHHHHHHHHHhC-ChHHHHhhhCCCCCHHHHHHHHHHhHH
Q 046581 225 KDSWSEEEERILVEAHARIG-NRWAEIAKHIPGRTENSIKNHWNATKR 271 (470)
Q Consensus 225 k~~WT~EED~~Ll~lv~~~G-~kWs~IAk~LpgRT~~q~KnRw~~llr 271 (470)
+.+||++||.+|+.++..+| .+|..||..|++||+.+|++||+.+++
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 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=98.94 E-value=1.2e-09 Score=78.06 Aligned_cols=45 Identities=51% Similarity=1.073 Sum_probs=42.2
Q ss_pred CCCHHHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhcc
Q 046581 175 QWTDEEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNHL 219 (470)
Q Consensus 175 ~WT~EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L 219 (470)
+||+|||.+|+.++..||..+|..||..|++|+..+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999779999999999999999999998753
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=98.90 E-value=3e-09 Score=75.97 Aligned_cols=43 Identities=42% Similarity=0.937 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHHHHhC-ChHHHHhhhCCCCCHHHHHHHHHHh
Q 046581 227 SWSEEEERILVEAHARIG-NRWAEIAKHIPGRTENSIKNHWNAT 269 (470)
Q Consensus 227 ~WT~EED~~Ll~lv~~~G-~kWs~IAk~LpgRT~~q~KnRw~~l 269 (470)
+||++||.+|+.++.++| .+|..||+.+++||..+|++||+.+
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 599999999999999999 8999999999999999999999875
No 23
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.65 E-value=0.00021 Score=68.98 Aligned_cols=98 Identities=28% Similarity=0.453 Sum_probs=75.8
Q ss_pred CCCHHHHHHHHHHHHHhCCchHHHHHHHhc---CCChhhhhhhhhhcc-cccc--------------------ccCCCCH
Q 046581 175 QWTDEEDRKLIKLVKQYGVRKWAQISERMA---GRAGKQCRERWHNHL-RPDI--------------------KKDSWSE 230 (470)
Q Consensus 175 ~WT~EED~~Ll~lV~~yG~~~Ws~IA~~lp---gRT~~Qcr~Rw~~~L-~p~i--------------------kk~~WT~ 230 (470)
+|++++|-+|+.+|..-. +-..|+.-++ ..|-..+.+||+.+| +|.+ .+.+||.
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 599999999999997544 7888877665 678899999998876 3322 4578999
Q ss_pred HHHHHHHHHHHHhCC---hHHHHhh----hC-CCCCHHHHHHHHHHhHHhhh
Q 046581 231 EEERILVEAHARIGN---RWAEIAK----HI-PGRTENSIKNHWNATKRRQN 274 (470)
Q Consensus 231 EED~~Ll~lv~~~G~---kWs~IAk----~L-pgRT~~q~KnRw~~llrr~~ 274 (470)
+||++|......... .+.+|-. .| ++||+.++.++|..|++...
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~L 130 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHL 130 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhch
Confidence 999999987655443 5777732 23 78999999999998876543
No 24
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.52 E-value=0.00012 Score=77.18 Aligned_cols=59 Identities=20% Similarity=0.583 Sum_probs=51.7
Q ss_pred cccccCCCCCCCCCCCHHHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhccc
Q 046581 162 SNKKGASVALIKGQWTDEEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNHLR 220 (470)
Q Consensus 162 Rw~~~l~p~lkKG~WT~EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L~ 220 (470)
|....+.-.+-...||.+|+-+|++++..||.+||..||.+++.|+...|+++|.+++-
T Consensus 61 rim~~~s~~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 61 RIMDTNSFPILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFV 119 (438)
T ss_pred eeecCCCCCCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHh
Confidence 33344456677889999999999999999999999999999999999999999988763
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=97.41 E-value=0.00026 Score=55.47 Aligned_cols=47 Identities=19% Similarity=0.401 Sum_probs=41.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCchH---HHHHHHhc-CC-Chhhhhhhhhhcc
Q 046581 173 KGQWTDEEDRKLIKLVKQYGVRKW---AQISERMA-GR-AGKQCRERWHNHL 219 (470)
Q Consensus 173 KG~WT~EED~~Ll~lV~~yG~~~W---s~IA~~lp-gR-T~~Qcr~Rw~~~L 219 (470)
+-.||+||..+++++++.+|.++| +.|++.|. .| |..||+.+++.+.
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 456999999999999999997799 99999985 45 9999999998764
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=97.37 E-value=0.00031 Score=65.63 Aligned_cols=52 Identities=31% Similarity=0.619 Sum_probs=45.2
Q ss_pred ccCCCCHHHHHHHHHHHHHh---CC----hHHHHhhhCCCCCHHHHHHHHHHhHHhhhhc
Q 046581 224 KKDSWSEEEERILVEAHARI---GN----RWAEIAKHIPGRTENSIKNHWNATKRRQNSR 276 (470)
Q Consensus 224 kk~~WT~EED~~Ll~lv~~~---G~----kWs~IAk~LpgRT~~q~KnRw~~llrr~~~k 276 (470)
+...||.|||.+|-+.|..| |+ -..++++.| +||..+|.-|||+.+|++...
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~ 61 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEE 61 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHH
Confidence 55789999999999998876 32 389999999 999999999999999987754
No 27
>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=97.19 E-value=0.00093 Score=52.40 Aligned_cols=46 Identities=17% Similarity=0.472 Sum_probs=40.5
Q ss_pred cCCCCHHHHHHHHHHHHHhCC-hH---HHHhhhCC-CC-CHHHHHHHHHHhH
Q 046581 225 KDSWSEEEERILVEAHARIGN-RW---AEIAKHIP-GR-TENSIKNHWNATK 270 (470)
Q Consensus 225 k~~WT~EED~~Ll~lv~~~G~-kW---s~IAk~Lp-gR-T~~q~KnRw~~ll 270 (470)
+-.||+||...+++++..+|. +| ..|+..+. .| |..||+.|+....
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 457999999999999999996 99 99999874 45 9999999998754
No 28
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.13 E-value=0.00063 Score=71.91 Aligned_cols=49 Identities=35% Similarity=0.611 Sum_probs=44.6
Q ss_pred cccCCCCHHHHHHHHHHHHHhC-ChHHHHhhhCCCCCHHHHHHHHHHhHH
Q 046581 223 IKKDSWSEEEERILVEAHARIG-NRWAEIAKHIPGRTENSIKNHWNATKR 271 (470)
Q Consensus 223 ikk~~WT~EED~~Ll~lv~~~G-~kWs~IAk~LpgRT~~q~KnRw~~llr 271 (470)
+-...||.+||.+||+++..|| ++|..||.++..|+..+||.+|..+.-
T Consensus 70 i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHh
Confidence 4457899999999999999999 899999999999999999999987643
No 29
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.86 E-value=0.0015 Score=54.00 Aligned_cols=53 Identities=26% Similarity=0.671 Sum_probs=38.2
Q ss_pred cCCCCHHHHHHHHHHHHH------hC--C------hHHHHhhhCC----CCCHHHHHHHHHHhHHhhhhcc
Q 046581 225 KDSWSEEEERILVEAHAR------IG--N------RWAEIAKHIP----GRTENSIKNHWNATKRRQNSRR 277 (470)
Q Consensus 225 k~~WT~EED~~Ll~lv~~------~G--~------kWs~IAk~Lp----gRT~~q~KnRw~~llrr~~~k~ 277 (470)
+..||.+|...||+++.. ++ + -|..||..|. .||+.||++||+.|.++.+..+
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~~k 71 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKKIK 71 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHCSS
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 357999999999999877 21 1 3999999873 6999999999999988765443
No 30
>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=96.77 E-value=0.00097 Score=62.35 Aligned_cols=50 Identities=26% Similarity=0.522 Sum_probs=42.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHh---CC---chHHHHHHHhcCCChhhhhhhhhhcccc
Q 046581 171 LIKGQWTDEEDRKLIKLVKQY---GV---RKWAQISERMAGRAGKQCRERWHNHLRP 221 (470)
Q Consensus 171 lkKG~WT~EED~~Ll~lV~~y---G~---~~Ws~IA~~lpgRT~~Qcr~Rw~~~L~p 221 (470)
.+...||.|||.+|.+.|-+| |. .-...|++.| +||+..|.-||+.+++.
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRk 57 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRK 57 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHH
Confidence 356789999999999999998 31 1478889998 99999999999998874
No 31
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.74 E-value=0.0016 Score=69.38 Aligned_cols=46 Identities=17% Similarity=0.484 Sum_probs=42.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhc
Q 046581 172 IKGQWTDEEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNH 218 (470)
Q Consensus 172 kKG~WT~EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~ 218 (470)
....||.+|..+|++.|+.|| ..|.+||.+++.||..||..||.++
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 566999999999999999999 5999999999999999999999763
No 32
>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=96.44 E-value=0.0034 Score=50.54 Aligned_cols=51 Identities=27% Similarity=0.559 Sum_probs=34.2
Q ss_pred CCCCCHHHHHHHHHHHHHh--------CCchHHHHHHHhc-CCChhhhhhhhhhcccccc
Q 046581 173 KGQWTDEEDRKLIKLVKQY--------GVRKWAQISERMA-GRAGKQCRERWHNHLRPDI 223 (470)
Q Consensus 173 KG~WT~EED~~Ll~lV~~y--------G~~~Ws~IA~~lp-gRT~~Qcr~Rw~~~L~p~i 223 (470)
+-+||+|||+.|++.|..+ |..-|..+++.-+ .+|-.+-|+||.+.|.+..
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 3479999999999999766 3224999999988 9999999999999887643
No 33
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.38 E-value=0.0034 Score=68.34 Aligned_cols=49 Identities=18% Similarity=0.548 Sum_probs=44.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhc
Q 046581 169 VALIKGQWTDEEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNH 218 (470)
Q Consensus 169 p~lkKG~WT~EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~ 218 (470)
..-.++.||.+|..+|++.|..|| .+|.+||.+++.||..||..++.++
T Consensus 249 ~~~~~~~WT~qE~lLLLE~ie~y~-ddW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 249 GESARPNWTEQETLLLLEAIEMYG-DDWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred cccCCCCccHHHHHHHHHHHHHhc-ccHHHHHhccCCCCHHHHHHHHHhc
Confidence 445678899999999999999999 5999999999999999999999763
No 34
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.32 E-value=0.0049 Score=50.85 Aligned_cols=46 Identities=41% Similarity=0.827 Sum_probs=33.8
Q ss_pred CCCCHHHHHHHHHHHHH--h----C--C-----chHHHHHHHhc----CCChhhhhhhhhhcc
Q 046581 174 GQWTDEEDRKLIKLVKQ--Y----G--V-----RKWAQISERMA----GRAGKQCRERWHNHL 219 (470)
Q Consensus 174 G~WT~EED~~Ll~lV~~--y----G--~-----~~Ws~IA~~lp----gRT~~Qcr~Rw~~~L 219 (470)
-.||.+|...|++++.. + + . .-|..||..|. .||+.||+.+|.++.
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 46999999999999987 2 1 0 14999999985 699999999998754
No 35
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.27 E-value=0.0051 Score=65.76 Aligned_cols=46 Identities=24% Similarity=0.540 Sum_probs=43.0
Q ss_pred ccCCCCHHHHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHh
Q 046581 224 KKDSWSEEEERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNAT 269 (470)
Q Consensus 224 kk~~WT~EED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~l 269 (470)
....||.+|..+|++.+..||-.|.+||+++..||..||--||..+
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 3458999999999999999999999999999999999999999765
No 36
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.04 E-value=0.0083 Score=65.41 Aligned_cols=48 Identities=21% Similarity=0.473 Sum_probs=44.2
Q ss_pred ccCCCCHHHHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHH
Q 046581 224 KKDSWSEEEERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKR 271 (470)
Q Consensus 224 kk~~WT~EED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llr 271 (470)
.+..||++|..+|++++..||-.|.+||.++.+||..+|--||..+-.
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~LPi 299 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRLPI 299 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhcCc
Confidence 356899999999999999999999999999999999999999987633
No 37
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.80 E-value=0.011 Score=56.10 Aligned_cols=52 Identities=25% Similarity=0.510 Sum_probs=43.6
Q ss_pred cccCCCCHHHHHHHHHHHHHhCC-------hHHHHhhhCCCCCHHHHHHHHHHhHHhhhh
Q 046581 223 IKKDSWSEEEERILVEAHARIGN-------RWAEIAKHIPGRTENSIKNHWNATKRRQNS 275 (470)
Q Consensus 223 ikk~~WT~EED~~Ll~lv~~~G~-------kWs~IAk~LpgRT~~q~KnRw~~llrr~~~ 275 (470)
.+...||.|||.+|-+.|..++. -...++..| +||..+|..|||..+|++..
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Ye 61 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQ 61 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHH
Confidence 45678999999999888887763 267778888 99999999999999997654
No 38
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.79 E-value=0.022 Score=46.20 Aligned_cols=51 Identities=33% Similarity=0.592 Sum_probs=41.6
Q ss_pred cCCCCHHHHHHHHHHHHHhCC-----------------hHHHHhhhC-----CCCCHHHHHHHHHHhHHhhhh
Q 046581 225 KDSWSEEEERILVEAHARIGN-----------------RWAEIAKHI-----PGRTENSIKNHWNATKRRQNS 275 (470)
Q Consensus 225 k~~WT~EED~~Ll~lv~~~G~-----------------kWs~IAk~L-----pgRT~~q~KnRw~~llrr~~~ 275 (470)
+..||.+|..+|++++.++.. -|.+|+..| +.||..+||.+|..++..-++
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk 74 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKK 74 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 457999999999999987631 399999876 269999999999998776443
No 39
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=95.45 E-value=0.079 Score=62.53 Aligned_cols=98 Identities=17% Similarity=0.375 Sum_probs=74.8
Q ss_pred CCHHHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhh-------hh------cc-----------------------
Q 046581 176 WTDEEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERW-------HN------HL----------------------- 219 (470)
Q Consensus 176 WT~EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw-------~~------~L----------------------- 219 (470)
|+.-+=..++.+..+||..+-..||..|.|+|...++... .. ++
T Consensus 827 w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~~~k 906 (1033)
T PLN03142 827 WSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAIGKK 906 (1033)
T ss_pred ccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6666666677888899988899999999999998876322 11 00
Q ss_pred --------------ccccccCCCCHHHHHHHHHHHHHhC-ChHHHHhhh------------CCCCCHHHHHHHHHHhHHh
Q 046581 220 --------------RPDIKKDSWSEEEERILVEAHARIG-NRWAEIAKH------------IPGRTENSIKNHWNATKRR 272 (470)
Q Consensus 220 --------------~p~ikk~~WT~EED~~Ll~lv~~~G-~kWs~IAk~------------LpgRT~~q~KnRw~~llrr 272 (470)
-+..++..||+|||..|+-.+.+|| .+|.+|-.. |..||+..|..|.+.|++.
T Consensus 907 ~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~~ 986 (1033)
T PLN03142 907 LDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIRL 986 (1033)
T ss_pred HHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHHH
Confidence 0112345699999999999999999 789999443 3489999999999998876
Q ss_pred h
Q 046581 273 Q 273 (470)
Q Consensus 273 ~ 273 (470)
.
T Consensus 987 ~ 987 (1033)
T PLN03142 987 I 987 (1033)
T ss_pred H
Confidence 4
No 40
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.36 E-value=0.013 Score=55.52 Aligned_cols=50 Identities=22% Similarity=0.471 Sum_probs=40.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCc------hHHHHHHHhcCCChhhhhhhhhhcccc
Q 046581 171 LIKGQWTDEEDRKLIKLVKQYGVR------KWAQISERMAGRAGKQCRERWHNHLRP 221 (470)
Q Consensus 171 lkKG~WT~EED~~Ll~lV~~yG~~------~Ws~IA~~lpgRT~~Qcr~Rw~~~L~p 221 (470)
.++..||.|||.+|.+.|-+|+.. -...++..| +||..+|..||+.+++.
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk 58 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRK 58 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHH
Confidence 467889999999999999988532 255666777 89999999999887763
No 41
>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=95.28 E-value=0.029 Score=45.17 Aligned_cols=49 Identities=20% Similarity=0.422 Sum_probs=32.0
Q ss_pred cCCCCHHHHHHHHHHHHHhC--------Ch-HHHHhhhCC-CCCHHHHHHHHHHhHHhh
Q 046581 225 KDSWSEEEERILVEAHARIG--------NR-WAEIAKHIP-GRTENSIKNHWNATKRRQ 273 (470)
Q Consensus 225 k~~WT~EED~~Ll~lv~~~G--------~k-Ws~IAk~Lp-gRT~~q~KnRw~~llrr~ 273 (470)
+.+||.+||.+|+..|.++. ++ |.+++..-| .+|-.+.|+||...++.+
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~ 60 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGR 60 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT---
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcc
Confidence 45899999999999996542 22 999998877 899999999998766543
No 42
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=94.99 E-value=0.026 Score=57.98 Aligned_cols=46 Identities=30% Similarity=0.670 Sum_probs=42.7
Q ss_pred cCCCCHHHHHHHHHHHHHhC-ChHHHHhhhCCCCCHHHHHHHHHHhH
Q 046581 225 KDSWSEEEERILVEAHARIG-NRWAEIAKHIPGRTENSIKNHWNATK 270 (470)
Q Consensus 225 k~~WT~EED~~Ll~lv~~~G-~kWs~IAk~LpgRT~~q~KnRw~~ll 270 (470)
-..|+..|+.+|+++....| ++|..||.++..|+...||.+|..+.
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y 109 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMY 109 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHH
Confidence 45799999999999999999 89999999999999999999998764
No 43
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=94.79 E-value=0.04 Score=44.70 Aligned_cols=47 Identities=30% Similarity=0.599 Sum_probs=39.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCC----------------chHHHHHHHhc-----CCChhhhhhhhhhcc
Q 046581 173 KGQWTDEEDRKLIKLVKQYGV----------------RKWAQISERMA-----GRAGKQCRERWHNHL 219 (470)
Q Consensus 173 KG~WT~EED~~Ll~lV~~yG~----------------~~Ws~IA~~lp-----gRT~~Qcr~Rw~~~L 219 (470)
+..||++|...|+++|.+|.. ..|..|+..|. .|+..||+.+|.++.
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk 69 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLK 69 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 467999999999999998811 13999999883 699999999998854
No 44
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=94.76 E-value=0.025 Score=58.20 Aligned_cols=50 Identities=18% Similarity=0.472 Sum_probs=45.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhccc
Q 046581 171 LIKGQWTDEEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNHLR 220 (470)
Q Consensus 171 lkKG~WT~EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L~ 220 (470)
+-.-.|+..|+-+|++...-.|.++|..||.+++.|+...|+++|.+++.
T Consensus 61 I~~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 61 IGEEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred ccCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 44456999999999999999999999999999999999999999988765
No 45
>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=91.89 E-value=0.33 Score=40.44 Aligned_cols=48 Identities=31% Similarity=0.641 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHHHHHHh---CC----------hHHHHhhhCC-----CCCHHHHHHHHHHhHHhhh
Q 046581 227 SWSEEEERILVEAHARI---GN----------RWAEIAKHIP-----GRTENSIKNHWNATKRRQN 274 (470)
Q Consensus 227 ~WT~EED~~Ll~lv~~~---G~----------kWs~IAk~Lp-----gRT~~q~KnRw~~llrr~~ 274 (470)
.||+++++.|++++.+. |+ .|..|+..|. ..+..+|++||..+++.-.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y~ 66 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDYR 66 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHHH
Confidence 49999999999998653 21 3999988763 3678999999999887643
No 46
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=91.27 E-value=0.26 Score=51.04 Aligned_cols=53 Identities=26% Similarity=0.528 Sum_probs=42.4
Q ss_pred cCCCCHHHHHHHHHHHHHh----------CChHHHHhhhC----CCCCHHHHHHHHHHhHHhhhhcc
Q 046581 225 KDSWSEEEERILVEAHARI----------GNRWAEIAKHI----PGRTENSIKNHWNATKRRQNSRR 277 (470)
Q Consensus 225 k~~WT~EED~~Ll~lv~~~----------G~kWs~IAk~L----pgRT~~q~KnRw~~llrr~~~k~ 277 (470)
...|+.+|-..||++..+. +.-|..||+.+ --||+.+||+||..++++.++.+
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k 120 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEK 120 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 3689999999999987543 22499999854 25999999999999998866543
No 47
>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=90.55 E-value=0.51 Score=42.31 Aligned_cols=52 Identities=27% Similarity=0.446 Sum_probs=41.5
Q ss_pred ccccCCCCHHHHHHHHHHHHHhCC----hHHHHhhh------------CCCCCHHHHHHHHHHhHHhh
Q 046581 222 DIKKDSWSEEEERILVEAHARIGN----RWAEIAKH------------IPGRTENSIKNHWNATKRRQ 273 (470)
Q Consensus 222 ~ikk~~WT~EED~~Ll~lv~~~G~----kWs~IAk~------------LpgRT~~q~KnRw~~llrr~ 273 (470)
..++..||++||.-|+-.+.++|- .|..|-.. |..||+..|..|-+.|++-.
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 456779999999999999999996 79988654 23799999999999998753
No 48
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=90.26 E-value=0.24 Score=52.38 Aligned_cols=50 Identities=28% Similarity=0.415 Sum_probs=44.3
Q ss_pred CCCCHHHHHHHHHHHHHhCChHHHHhhh-----CCC-CCHHHHHHHHHHhHHhhhh
Q 046581 226 DSWSEEEERILVEAHARIGNRWAEIAKH-----IPG-RTENSIKNHWNATKRRQNS 275 (470)
Q Consensus 226 ~~WT~EED~~Ll~lv~~~G~kWs~IAk~-----Lpg-RT~~q~KnRw~~llrr~~~ 275 (470)
..||.+|-+-|+++.+.|.-+|-.||.. ++. ||-.++|.||..+.++-.+
T Consensus 131 n~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~k 186 (445)
T KOG2656|consen 131 NSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLK 186 (445)
T ss_pred ccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHHHHHHHHH
Confidence 6799999999999999999999999987 555 9999999999987776443
No 49
>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=89.93 E-value=0.56 Score=42.06 Aligned_cols=50 Identities=24% Similarity=0.507 Sum_probs=38.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC---chHHHHHHHh------------cCCChhhhhhhhhhcc
Q 046581 170 ALIKGQWTDEEDRKLIKLVKQYGV---RKWAQISERM------------AGRAGKQCRERWHNHL 219 (470)
Q Consensus 170 ~lkKG~WT~EED~~Ll~lV~~yG~---~~Ws~IA~~l------------pgRT~~Qcr~Rw~~~L 219 (470)
..++..||++||.-|+-++.+||. +.|..|-..+ ..||+..+..|-..+|
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi 110 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLI 110 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHH
Confidence 567888999999999999999998 8999997755 2688888887776544
No 50
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=88.55 E-value=0.72 Score=48.73 Aligned_cols=46 Identities=22% Similarity=0.378 Sum_probs=42.7
Q ss_pred CCCCHHHHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHH
Q 046581 226 DSWSEEEERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKR 271 (470)
Q Consensus 226 ~~WT~EED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llr 271 (470)
.+|+.+|-++...++..+|..++.|+..+|.|...|||.+|..--|
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek 411 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEK 411 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhh
Confidence 5799999999999999999999999999999999999999976544
No 51
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=86.10 E-value=0.93 Score=47.95 Aligned_cols=44 Identities=23% Similarity=0.437 Sum_probs=41.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhh
Q 046581 173 KGQWTDEEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHN 217 (470)
Q Consensus 173 KG~WT~EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~ 217 (470)
--+||.+|-.+..++...+| ..++.|+..+|.|..+|++.+|.+
T Consensus 365 ~~~Ws~~e~ekFYKALs~wG-tdF~LIs~lfP~R~RkqIKaKfi~ 408 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWG-TDFSLISSLFPNRERKQIKAKFIK 408 (507)
T ss_pred CCcccHHHHHHHHHHHHHhc-chHHHHHHhcCchhHHHHHHHHHH
Confidence 35899999999999999999 599999999999999999999976
No 52
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=85.71 E-value=3.2 Score=44.95 Aligned_cols=51 Identities=20% Similarity=0.395 Sum_probs=45.7
Q ss_pred ccCCCCHHHHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHhhh
Q 046581 224 KKDSWSEEEERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRRQN 274 (470)
Q Consensus 224 kk~~WT~EED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr~~ 274 (470)
-...||.||-.++-++...||.+..+|-+.||.|+-..+...|...+|...
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK~~~ 236 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKKTRE 236 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHHHhh
Confidence 446899999999999999999999999999999999999999987776543
No 53
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=83.87 E-value=1.3 Score=45.85 Aligned_cols=48 Identities=27% Similarity=0.585 Sum_probs=38.1
Q ss_pred CCCCCHHHHHHHHHHHHHh----C-----CchHHHHHHHhc----CCChhhhhhhhhhccc
Q 046581 173 KGQWTDEEDRKLIKLVKQY----G-----VRKWAQISERMA----GRAGKQCRERWHNHLR 220 (470)
Q Consensus 173 KG~WT~EED~~Ll~lV~~y----G-----~~~Ws~IA~~lp----gRT~~Qcr~Rw~~~L~ 220 (470)
...|+.+|-..|+++..+. . ..-|..||..|. -||+.||+.+|.++..
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k 114 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKK 114 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 3569999999999998754 1 124999999774 5999999999988543
No 54
>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=83.72 E-value=2 Score=35.71 Aligned_cols=44 Identities=32% Similarity=0.647 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHHh---CCc---------hHHHHHHHhc-----CCChhhhhhhhhhc
Q 046581 175 QWTDEEDRKLIKLVKQY---GVR---------KWAQISERMA-----GRAGKQCRERWHNH 218 (470)
Q Consensus 175 ~WT~EED~~Ll~lV~~y---G~~---------~Ws~IA~~lp-----gRT~~Qcr~Rw~~~ 218 (470)
.||+++++.|++++.+. |.. .|..|+..|. ..+..||++||..+
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 49999999999998655 211 3999999884 35679999998653
No 55
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=82.77 E-value=2.6 Score=41.16 Aligned_cols=48 Identities=15% Similarity=0.313 Sum_probs=35.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC--chHHHHHHH-----hcCCChhhhhhhhhhc
Q 046581 171 LIKGQWTDEEDRKLIKLVKQYGV--RKWAQISER-----MAGRAGKQCRERWHNH 218 (470)
Q Consensus 171 lkKG~WT~EED~~Ll~lV~~yG~--~~Ws~IA~~-----lpgRT~~Qcr~Rw~~~ 218 (470)
-.+-+||.+|+++|......... ..+.+|-.. -++||+++...+|...
T Consensus 71 q~kalfS~~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lm 125 (199)
T PF13325_consen 71 QSKALFSKEEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLM 125 (199)
T ss_pred cccCCCCHHHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHH
Confidence 35578999999999998765532 256666432 2489999999999863
No 56
>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=81.60 E-value=3.6 Score=30.72 Aligned_cols=42 Identities=24% Similarity=0.386 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHh
Q 046581 230 EEEERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRR 272 (470)
Q Consensus 230 ~EED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr 272 (470)
++++..++.++...|-.|.+||..+ |.|...|+.+....+++
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 4567788888888899999999999 99999999998876543
No 57
>PLN03138 Protein TOC75; Provisional
Probab=80.60 E-value=0.92 Score=52.35 Aligned_cols=20 Identities=10% Similarity=0.036 Sum_probs=10.5
Q ss_pred CCCCCchHHHHHHHHHHHcC
Q 046581 107 STTTTTLEPTSFVDGFFADG 126 (470)
Q Consensus 107 ~g~WT~EED~~Ll~~V~~~G 126 (470)
....|..+=+.-++.|...|
T Consensus 179 G~v~trsqLq~dv~~I~~tG 198 (796)
T PLN03138 179 GGVYTKAQLQKELETLASCG 198 (796)
T ss_pred CCccCHHHHHHHHHHHHhcC
Confidence 45666655555555554443
No 58
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=79.27 E-value=2.4 Score=41.77 Aligned_cols=6 Identities=50% Similarity=1.049 Sum_probs=3.0
Q ss_pred HHhhcC
Q 046581 361 MQNYFP 366 (470)
Q Consensus 361 ~q~~~~ 366 (470)
+.+||-
T Consensus 210 a~~YFD 215 (233)
T PF11705_consen 210 AENYFD 215 (233)
T ss_pred hhccCC
Confidence 445554
No 59
>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=75.24 E-value=5.5 Score=29.22 Aligned_cols=38 Identities=32% Similarity=0.614 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhh
Q 046581 179 EEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHN 217 (470)
Q Consensus 179 EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~ 217 (470)
+=|.+|+.+...-+...|..||+.+ |=+...|..|+..
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 8999999999865
No 60
>smart00595 MADF subfamily of SANT domain.
Probab=75.19 E-value=4.5 Score=33.21 Aligned_cols=29 Identities=28% Similarity=0.638 Sum_probs=24.2
Q ss_pred hHHHHhhhCCCCCHHHHHHHHHHhHHhhhh
Q 046581 246 RWAEIAKHIPGRTENSIKNHWNATKRRQNS 275 (470)
Q Consensus 246 kWs~IAk~LpgRT~~q~KnRw~~llrr~~~ 275 (470)
-|.+||..| +-+..+|+.+|+.|..+-.+
T Consensus 29 aW~~Ia~~l-~~~~~~~~~kw~~LR~~y~~ 57 (89)
T smart00595 29 AWEEIAEEL-GLSVEECKKRWKNLRDRYRR 57 (89)
T ss_pred HHHHHHHHH-CcCHHHHHHHHHHHHHHHHH
Confidence 499999999 55999999999998765443
No 61
>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=75.10 E-value=4.2 Score=34.18 Aligned_cols=16 Identities=38% Similarity=0.657 Sum_probs=9.9
Q ss_pred CCCCCCCCCHHHHHHH
Q 046581 169 VALIKGQWTDEEDRKL 184 (470)
Q Consensus 169 p~lkKG~WT~EED~~L 184 (470)
|....|-||+|+|+.|
T Consensus 43 P~n~~GiWT~eDD~~L 58 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEML 58 (87)
T ss_dssp -TT-TT---HHHHHHH
T ss_pred CCCCCCCcCHHHHHHH
Confidence 6678899999999998
No 62
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=74.10 E-value=3.9 Score=46.65 Aligned_cols=43 Identities=19% Similarity=0.401 Sum_probs=40.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhh
Q 046581 174 GQWTDEEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHN 217 (470)
Q Consensus 174 G~WT~EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~ 217 (470)
..||+.|-.++.+++-.|. +++-.|++.++++|.+||-+.|+.
T Consensus 620 d~WTp~E~~lF~kA~y~~~-KDF~~v~km~~~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYS-KDFIFVQKMVKSKTVAQCVEYYYT 662 (907)
T ss_pred ccccHHHHHHHHHHHHHhc-ccHHHHHHHhccccHHHHHHHHHH
Confidence 5799999999999999999 799999999999999999998865
No 63
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=74.05 E-value=16 Score=42.08 Aligned_cols=45 Identities=13% Similarity=0.236 Sum_probs=40.7
Q ss_pred cCCCCHHHHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHh
Q 046581 225 KDSWSEEEERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNAT 269 (470)
Q Consensus 225 k~~WT~EED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~l 269 (470)
...||+.|-.++-.++..|...+..|++.++++|-.+|-..|..-
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtW 663 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTW 663 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHH
Confidence 357999999999999999999999999999999999998776543
No 64
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=72.71 E-value=2.3 Score=45.28 Aligned_cols=47 Identities=26% Similarity=0.527 Sum_probs=40.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCchHHHHHHH-----hcC-CChhhhhhhhhhccc
Q 046581 173 KGQWTDEEDRKLIKLVKQYGVRKWAQISER-----MAG-RAGKQCRERWHNHLR 220 (470)
Q Consensus 173 KG~WT~EED~~Ll~lV~~yG~~~Ws~IA~~-----lpg-RT~~Qcr~Rw~~~L~ 220 (470)
...||.||-+-|.+++++|.. .|-.||.. .+. ||....++||+.+..
T Consensus 130 dn~WskeETD~LF~lck~fDL-Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r 182 (445)
T KOG2656|consen 130 DNSWSKEETDYLFDLCKRFDL-RFFVIADRYDNQQYKKSRTVEDLKERYYSVCR 182 (445)
T ss_pred cccccHHHHHHHHHHHHhcCe-eEEEEeeccchhhccccccHHHHHHHHHHHHH
Confidence 367999999999999999995 89999887 555 999999999987653
No 65
>PLN03138 Protein TOC75; Provisional
Probab=72.15 E-value=2.4 Score=49.09 Aligned_cols=12 Identities=17% Similarity=0.121 Sum_probs=6.2
Q ss_pred HHHHHHHHHHHc
Q 046581 114 EPTSFVDGFFAD 125 (470)
Q Consensus 114 ED~~Ll~~V~~~ 125 (470)
.++.|.+.+...
T Consensus 166 ~e~~l~~~i~~k 177 (796)
T PLN03138 166 TEDSFFEMVTLR 177 (796)
T ss_pred hHHHHHHHHhcC
Confidence 445555655433
No 66
>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=68.87 E-value=13 Score=27.23 Aligned_cols=38 Identities=21% Similarity=0.405 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHhCC-hHHHHhhhCCCCCHHHHHHHHHHh
Q 046581 231 EEERILVEAHARIGN-RWAEIAKHIPGRTENSIKNHWNAT 269 (470)
Q Consensus 231 EED~~Ll~lv~~~G~-kWs~IAk~LpgRT~~q~KnRw~~l 269 (470)
+=|..|+.+.+.-+. .|.+||+.+ |=|...|..|++.|
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 457788888888874 599999999 99999999999876
No 67
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=66.06 E-value=8 Score=35.42 Aligned_cols=44 Identities=14% Similarity=0.259 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhccccc
Q 046581 178 DEEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNHLRPD 222 (470)
Q Consensus 178 ~EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L~p~ 222 (470)
.+-|.+|+.+.++-|...|+.||+.+ |-+...|+.|+.++....
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~G 51 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAG 51 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCC
Confidence 45799999999999988999999999 999999999998876554
No 68
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=65.97 E-value=12 Score=34.37 Aligned_cols=45 Identities=22% Similarity=0.271 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHhC-ChHHHHhhhCCCCCHHHHHHHHHHhHHhhhh
Q 046581 230 EEEERILVEAHARIG-NRWAEIAKHIPGRTENSIKNHWNATKRRQNS 275 (470)
Q Consensus 230 ~EED~~Ll~lv~~~G-~kWs~IAk~LpgRT~~q~KnRw~~llrr~~~ 275 (470)
++-|..|+.+.++-| ..|++||+.+ |-|...|+.|++.|.....-
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 356888888888887 4699999999 99999999999999876543
No 69
>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]
Probab=65.30 E-value=5.3 Score=42.52 Aligned_cols=14 Identities=29% Similarity=0.330 Sum_probs=7.3
Q ss_pred ccCCCcccccCccc
Q 046581 142 YKEGSKSACNNNKG 155 (470)
Q Consensus 142 ~~grs~~~cR~~~q 155 (470)
+++-+..+|-.+..
T Consensus 100 l~NyStsq~i~R~g 113 (494)
T KOG1456|consen 100 LFNYSTSQCIERPG 113 (494)
T ss_pred hcccchhhhhccCC
Confidence 55555556654433
No 70
>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=62.73 E-value=19 Score=26.53 Aligned_cols=41 Identities=17% Similarity=0.288 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHh
Q 046581 231 EEERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRR 272 (470)
Q Consensus 231 EED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr 272 (470)
+++..++.++-..+-.+.+||..+ |-|...|+.+.+..+++
T Consensus 7 ~~er~vi~~~y~~~~t~~eIa~~l-g~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 7 PREREVIRLRYFEGLTLEEIAERL-GISRSTVRRILKRALKK 47 (50)
T ss_dssp HHHHHHHHHHHTST-SHHHHHHHH-TSCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHH-CCcHHHHHHHHHHHHHH
Confidence 455566666665567899999999 89999999998877765
No 71
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=62.36 E-value=9.1 Score=35.52 Aligned_cols=45 Identities=24% Similarity=0.385 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhcccccc
Q 046581 178 DEEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNHLRPDI 223 (470)
Q Consensus 178 ~EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L~p~i 223 (470)
.+-|.+|+.+.++-|...|+.||+.+ |-+...|+.|+.++.+..+
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 56799999999999988999999999 9999999999998766554
No 72
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=62.11 E-value=11 Score=40.98 Aligned_cols=45 Identities=13% Similarity=0.311 Sum_probs=40.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhh
Q 046581 172 IKGQWTDEEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHN 217 (470)
Q Consensus 172 kKG~WT~EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~ 217 (470)
....||.||--++-++...|| .+..+|-+.||.|+-..+...|+.
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~G-K~F~kIrq~LP~rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFG-KDFHKIRQALPHRSLASLVQYYYS 230 (534)
T ss_pred CcccchHHHHHHHHHHHHHhc-ccHHHHHHHccCccHHHHHHHHHH
Confidence 456799999999999999999 699999999999999999887754
No 73
>KOG0037 consensus Ca2+-binding protein, EF-Hand protein superfamily [Signal transduction mechanisms]
Probab=59.73 E-value=9.8 Score=37.73 Aligned_cols=41 Identities=17% Similarity=0.225 Sum_probs=26.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCchHHHHHHHhc-CCChhhhhhhhh
Q 046581 171 LIKGQWTDEEDRKLIKLVKQYGVRKWAQISERMA-GRAGKQCRERWH 216 (470)
Q Consensus 171 lkKG~WT~EED~~Ll~lV~~yG~~~Ws~IA~~lp-gRT~~Qcr~Rw~ 216 (470)
-+.|.--.+|=..|.+.+ ++|..|-+..- .|++.-+..-.+
T Consensus 106 ~~~G~i~f~EF~~Lw~~i-----~~Wr~vF~~~D~D~SG~I~~sEL~ 147 (221)
T KOG0037|consen 106 DNSGTIGFKEFKALWKYI-----NQWRNVFRTYDRDRSGTIDSSELR 147 (221)
T ss_pred CCCCccCHHHHHHHHHHH-----HHHHHHHHhcccCCCCcccHHHHH
Confidence 355666777777777777 47888877663 566655544333
No 74
>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=58.98 E-value=27 Score=36.53 Aligned_cols=51 Identities=33% Similarity=0.534 Sum_probs=41.8
Q ss_pred cCCCCHHHHHHHHHHHHHh-CC---hHHHHhhhCCCCCHHHHHHHHHHhHHhhhh
Q 046581 225 KDSWSEEEERILVEAHARI-GN---RWAEIAKHIPGRTENSIKNHWNATKRRQNS 275 (470)
Q Consensus 225 k~~WT~EED~~Ll~lv~~~-G~---kWs~IAk~LpgRT~~q~KnRw~~llrr~~~ 275 (470)
-..||.-|...|+.+.+.. |. .-++|++.++||+..+|++--..++.|..+
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rvar 75 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRVAR 75 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHHHH
Confidence 3579999999999988765 33 367899999999999999988888776543
No 75
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=58.83 E-value=15 Score=33.99 Aligned_cols=45 Identities=13% Similarity=0.201 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHhCC-hHHHHhhhCCCCCHHHHHHHHHHhHHhhhh
Q 046581 230 EEEERILVEAHARIGN-RWAEIAKHIPGRTENSIKNHWNATKRRQNS 275 (470)
Q Consensus 230 ~EED~~Ll~lv~~~G~-kWs~IAk~LpgRT~~q~KnRw~~llrr~~~ 275 (470)
++-|..|+.+.++-|. .|++||+.+ |-+...|+.|++.|.+...-
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 5568888888888874 699999999 99999999999999887553
No 76
>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=58.61 E-value=70 Score=33.58 Aligned_cols=91 Identities=21% Similarity=0.472 Sum_probs=67.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHh-CC--chHHHHHHHhcCCChhhhhhhhhhccccccccCCCCHHHHHHHHHHHHHh-
Q 046581 168 SVALIKGQWTDEEDRKLIKLVKQY-GV--RKWAQISERMAGRAGKQCRERWHNHLRPDIKKDSWSEEEERILVEAHARI- 243 (470)
Q Consensus 168 ~p~lkKG~WT~EED~~Ll~lV~~y-G~--~~Ws~IA~~lpgRT~~Qcr~Rw~~~L~p~ikk~~WT~EED~~Ll~lv~~~- 243 (470)
.....--.||.-|...|+++.+.. |. -+-..|++.++||+..+|++.-. .|+ +..+.+++++.
T Consensus 16 g~~~gp~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~-~LK------------~rvareaiqkv~ 82 (344)
T PF11035_consen 16 GEVTGPAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQ-QLK------------GRVAREAIQKVH 82 (344)
T ss_pred CCCCCcccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHH-HHH------------HHHHHHHHHHhc
Confidence 333345689999999999998765 31 24678999999999999988544 343 24555666552
Q ss_pred -----CC------------hHHHHhhhCCCCCHHHHHHHHHHhHH
Q 046581 244 -----GN------------RWAEIAKHIPGRTENSIKNHWNATKR 271 (470)
Q Consensus 244 -----G~------------kWs~IAk~LpgRT~~q~KnRw~~llr 271 (470)
|. -|..+|..+.|.-...+-.-|-.++-
T Consensus 83 ~~g~~~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~ 127 (344)
T PF11035_consen 83 PGGLKGPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLT 127 (344)
T ss_pred ccccccccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHH
Confidence 11 39999999999999999999987664
No 77
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=57.35 E-value=15 Score=41.24 Aligned_cols=48 Identities=19% Similarity=0.544 Sum_probs=39.3
Q ss_pred cCCCCHHHHHHHHHHHHHhCChHHHHhh----------hCCCCCHHHHHHHHHHhHHh
Q 046581 225 KDSWSEEEERILVEAHARIGNRWAEIAK----------HIPGRTENSIKNHWNATKRR 272 (470)
Q Consensus 225 k~~WT~EED~~Ll~lv~~~G~kWs~IAk----------~LpgRT~~q~KnRw~~llrr 272 (470)
+..||-.|+.-...+++++|.++..|-+ ...-+|..|++.+|+.++++
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~ 145 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRR 145 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHH
Confidence 6789999999999999999999998822 23347888999988876655
No 78
>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=56.58 E-value=5.3 Score=33.54 Aligned_cols=18 Identities=28% Similarity=0.650 Sum_probs=10.4
Q ss_pred cccccCCCCHHHHHHHHH
Q 046581 221 PDIKKDSWSEEEERILVE 238 (470)
Q Consensus 221 p~ikk~~WT~EED~~Ll~ 238 (470)
|....+-||+++|..|..
T Consensus 43 P~n~~GiWT~eDD~~L~~ 60 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLRS 60 (87)
T ss_dssp -TT-TT---HHHHHHHTS
T ss_pred CCCCCCCcCHHHHHHHHc
Confidence 556678999999999853
No 79
>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=54.77 E-value=28 Score=30.52 Aligned_cols=42 Identities=19% Similarity=0.289 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHhh
Q 046581 231 EEERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRRQ 273 (470)
Q Consensus 231 EED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr~ 273 (470)
+++..++.+.-..|-.+.+||+.+ |.+...|+++....+++-
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 355666666566788999999999 999999999999876653
No 80
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=54.53 E-value=22 Score=30.73 Aligned_cols=51 Identities=16% Similarity=0.325 Sum_probs=36.5
Q ss_pred CCCCHHHHHHHHHHHHHh----CC----hHHHH----hhhC-CCCCHHHHHHHHHHhHHhhhhc
Q 046581 226 DSWSEEEERILVEAHARI----GN----RWAEI----AKHI-PGRTENSIKNHWNATKRRQNSR 276 (470)
Q Consensus 226 ~~WT~EED~~Ll~lv~~~----G~----kWs~I----Ak~L-pgRT~~q~KnRw~~llrr~~~k 276 (470)
..||+++|..||+.+..| |. .|..+ ...| ..=+..|+..+-+.|++|....
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 469999999999998877 52 35444 3334 2347889999999888875543
No 81
>KOG3074 consensus Transcriptional regulator of the PUR family, single-stranded-DNA-binding [Transcription]
Probab=51.84 E-value=9.5 Score=38.23 Aligned_cols=14 Identities=21% Similarity=0.480 Sum_probs=10.4
Q ss_pred HHHHHHHHHHhCCc
Q 046581 181 DRKLIKLVKQYGVR 194 (470)
Q Consensus 181 D~~Ll~lV~~yG~~ 194 (470)
-+.|.+++..||..
T Consensus 158 rdaLaelle~~G~~ 171 (263)
T KOG3074|consen 158 RDALAELLEDFGEG 171 (263)
T ss_pred HHHHHHHHHHhCCc
Confidence 45788888888854
No 82
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=50.54 E-value=17 Score=39.69 Aligned_cols=9 Identities=11% Similarity=0.416 Sum_probs=5.1
Q ss_pred CCCCCCCCC
Q 046581 38 HQVYRPSPP 46 (470)
Q Consensus 38 ~~~~~~~p~ 46 (470)
.+.|+.+|+
T Consensus 116 ~gl~~s~p~ 124 (641)
T KOG3915|consen 116 GGLFSSTPI 124 (641)
T ss_pred CCccCCCCC
Confidence 556655554
No 83
>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=50.23 E-value=19 Score=33.92 Aligned_cols=42 Identities=21% Similarity=0.333 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHh
Q 046581 227 SWSEEEERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNAT 269 (470)
Q Consensus 227 ~WT~EED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~l 269 (470)
.||+|+.+.|.++. .-|-.=++||..|.+.|.++|.-+-+.+
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 59999999998887 6677889999999779999998776654
No 84
>PF05268 GP38: Phage tail fibre adhesin Gp38; InterPro: IPR007932 This entry is represented by Bacteriophage T2, Gp38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family contains several Gp38 proteins from T-even-like phages. Gp38, together with a second phage protein, Gp57, catalyses the organisation of Gp37 but is absent from the phage particle. Gp37 is responsible for receptor recognition [].
Probab=49.77 E-value=9.6 Score=37.93 Aligned_cols=12 Identities=33% Similarity=0.667 Sum_probs=10.2
Q ss_pred CCCCCCCCcccc
Q 046581 18 GGSGNTSFRYQN 29 (470)
Q Consensus 18 g~~~~~~~~~~~ 29 (470)
||+|++||+..-
T Consensus 174 GGGGGRPfG~gG 185 (260)
T PF05268_consen 174 GGGGGRPFGAGG 185 (260)
T ss_pred cCCCCCccCCCC
Confidence 578899999887
No 85
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=48.39 E-value=32 Score=38.81 Aligned_cols=47 Identities=19% Similarity=0.474 Sum_probs=37.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCCchHHHHHHHh----------cCCChhhhhhhhhhccc
Q 046581 173 KGQWTDEEDRKLIKLVKQYGVRKWAQISERM----------AGRAGKQCRERWHNHLR 220 (470)
Q Consensus 173 KG~WT~EED~~Ll~lV~~yG~~~Ws~IA~~l----------pgRT~~Qcr~Rw~~~L~ 220 (470)
|..||-.|..-...+++++| +++.+|-..+ .-+|..|+|.+|++.+.
T Consensus 88 ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~ 144 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVR 144 (782)
T ss_pred ccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHH
Confidence 77899999999999999999 6887772222 23566889998887665
No 86
>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=48.29 E-value=16 Score=28.94 Aligned_cols=31 Identities=23% Similarity=0.526 Sum_probs=24.5
Q ss_pred hHHHHhhhCC-CCCHHHHHHHHHHhHHhhhhc
Q 046581 246 RWAEIAKHIP-GRTENSIKNHWNATKRRQNSR 276 (470)
Q Consensus 246 kWs~IAk~Lp-gRT~~q~KnRw~~llrr~~~k 276 (470)
-|.+||..|. .-+...|+.||+.+...-.+.
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y~~~ 59 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRDRYRRE 59 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHHHHHHH
Confidence 4999999995 367889999999987654443
No 87
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=48.24 E-value=24 Score=42.32 Aligned_cols=49 Identities=16% Similarity=0.323 Sum_probs=37.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCchHHHHHHHh------------cCCChhhhhhhhhh
Q 046581 169 VALIKGQWTDEEDRKLIKLVKQYGVRKWAQISERM------------AGRAGKQCRERWHN 217 (470)
Q Consensus 169 p~lkKG~WT~EED~~Ll~lV~~yG~~~Ws~IA~~l------------pgRT~~Qcr~Rw~~ 217 (470)
+..++..||.|||..|+-++.+||..+|.+|-..+ ..||+..+..|...
T Consensus 922 ~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~ 982 (1033)
T PLN03142 922 GQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDT 982 (1033)
T ss_pred CCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHH
Confidence 34455679999999999999999999999996654 14666666665544
No 88
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=45.56 E-value=78 Score=33.95 Aligned_cols=45 Identities=24% Similarity=0.337 Sum_probs=39.7
Q ss_pred CCCCHHHHHHHHHHHHHhCChHHHHh-hhCCCCCHHHHHHHHHHhH
Q 046581 226 DSWSEEEERILVEAHARIGNRWAEIA-KHIPGRTENSIKNHWNATK 270 (470)
Q Consensus 226 ~~WT~EED~~Ll~lv~~~G~kWs~IA-k~LpgRT~~q~KnRw~~ll 270 (470)
..|+++|-..+-+-++.||+.+..|. ..++.|+--.|-..|..-+
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWK 323 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWK 323 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhh
Confidence 47999999999999999999999995 5789999999988777543
No 89
>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=45.39 E-value=32 Score=25.51 Aligned_cols=39 Identities=23% Similarity=0.356 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhc
Q 046581 178 DEEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNH 218 (470)
Q Consensus 178 ~EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~ 218 (470)
++++..++.++-..| -.|.+||..+ |.+...++.+...-
T Consensus 12 ~~~~r~i~~l~~~~g-~s~~eIa~~l-~~s~~~v~~~l~ra 50 (54)
T PF08281_consen 12 PERQREIFLLRYFQG-MSYAEIAEIL-GISESTVKRRLRRA 50 (54)
T ss_dssp -HHHHHHHHHHHTS----HHHHHHHC-TS-HHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHC-cCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 466778888887778 5999999999 89999998877653
No 90
>PF06682 DUF1183: Protein of unknown function (DUF1183); InterPro: IPR009567 This family consists of several eukaryotic proteins of around 360 residues in length. The function of this family is unknown.
Probab=45.14 E-value=22 Score=37.22 Aligned_cols=8 Identities=13% Similarity=0.517 Sum_probs=3.6
Q ss_pred CCCCCCCC
Q 046581 35 KPHHQVYR 42 (470)
Q Consensus 35 ~~~~~~~~ 42 (470)
.|+|..|+
T Consensus 213 ~PPPPyfk 220 (318)
T PF06682_consen 213 DPPPPYFK 220 (318)
T ss_pred CCCCCCCc
Confidence 34455443
No 91
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=43.41 E-value=23 Score=39.84 Aligned_cols=48 Identities=21% Similarity=0.474 Sum_probs=43.2
Q ss_pred ccCCCCHHHHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHH
Q 046581 224 KKDSWSEEEERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKR 271 (470)
Q Consensus 224 kk~~WT~EED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llr 271 (470)
...+|+.+|-++.-.+....|.+.+.|+..+|+|+..+||.+|..--+
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~eE~ 455 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKEEK 455 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhhhh
Confidence 346899999999999999999999999999999999999999975433
No 92
>smart00595 MADF subfamily of SANT domain.
Probab=41.03 E-value=20 Score=29.36 Aligned_cols=23 Identities=35% Similarity=1.004 Sum_probs=20.0
Q ss_pred hHHHHHHHhcCCChhhhhhhhhhc
Q 046581 195 KWAQISERMAGRAGKQCRERWHNH 218 (470)
Q Consensus 195 ~Ws~IA~~lpgRT~~Qcr~Rw~~~ 218 (470)
-|..||..| |-+...|+.+|.++
T Consensus 29 aW~~Ia~~l-~~~~~~~~~kw~~L 51 (89)
T smart00595 29 AWEEIAEEL-GLSVEECKKRWKNL 51 (89)
T ss_pred HHHHHHHHH-CcCHHHHHHHHHHH
Confidence 499999999 55999999999874
No 93
>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=40.91 E-value=34 Score=32.22 Aligned_cols=41 Identities=29% Similarity=0.419 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhh
Q 046581 175 QWTDEEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHN 217 (470)
Q Consensus 175 ~WT~EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~ 217 (470)
.||+|+.++|.+|.. -| -.=++||..|++.|.+.+.-+.+.
T Consensus 2 ~Wtde~~~~L~~lw~-~G-~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 2 SWTDERVERLRKLWA-EG-LSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred CCCHHHHHHHHHHHH-cC-CCHHHHHHHhCCcchhhhhhhhhc
Confidence 499999999999985 45 368999999987888877766554
No 94
>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=40.25 E-value=51 Score=29.20 Aligned_cols=46 Identities=17% Similarity=0.400 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHHHh------------C------------------CchHHHHHHHhcCCChhhhhhhhhhccc
Q 046581 175 QWTDEEDRKLIKLVKQY------------G------------------VRKWAQISERMAGRAGKQCRERWHNHLR 220 (470)
Q Consensus 175 ~WT~EED~~Ll~lV~~y------------G------------------~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L~ 220 (470)
+||++||-.|...|.+| | ..-....+...|..|..+=|+||++.+.
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 48999999999999776 1 1125666777788888888888887654
No 95
>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=40.25 E-value=59 Score=27.57 Aligned_cols=43 Identities=19% Similarity=0.304 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHh
Q 046581 228 WSEEEERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRR 272 (470)
Q Consensus 228 WT~EED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr 272 (470)
.++.|- .++.++...|-.+.+||+.+ |=+...|+++.+..+++
T Consensus 111 L~~~~~-~ii~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 111 LPERER-EVLVLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred CCHHHH-HHHhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 333333 44455545688999999999 77999999999887665
No 96
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=38.23 E-value=47 Score=27.99 Aligned_cols=43 Identities=16% Similarity=0.252 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhccccc
Q 046581 179 EEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNHLRPD 222 (470)
Q Consensus 179 EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L~p~ 222 (470)
+.|.+|+.+..+.+...++.||+.+ |-+...|+.|...+....
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g 45 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEG 45 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCC
Confidence 5688999999998877999999999 899999999998766544
No 97
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=36.88 E-value=38 Score=32.15 Aligned_cols=17 Identities=59% Similarity=1.289 Sum_probs=7.6
Q ss_pred CCCCCCCCCCCCCCCCc
Q 046581 10 GGGGGGGGGGSGNTSFR 26 (470)
Q Consensus 10 ~~g~g~~gg~~~~~~~~ 26 (470)
|||||+||+-.|+.+|+
T Consensus 120 ~~~~~~~~~~~~~~~~~ 136 (166)
T PRK06341 120 GGGGGGGGDDGGGGDFG 136 (166)
T ss_pred CCCCCCCCCccCCCccc
Confidence 33334444444444565
No 98
>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=36.19 E-value=96 Score=21.49 Aligned_cols=42 Identities=19% Similarity=0.325 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHH
Q 046581 228 WSEEEERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKR 271 (470)
Q Consensus 228 WT~EED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llr 271 (470)
++++ +..++.++-..|-.+.+||..+ |-+...|+.+....++
T Consensus 11 l~~~-~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 11 LPER-EREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRALK 52 (55)
T ss_pred CCHH-HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 4444 4455555556777899999998 7888888777666543
No 99
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=36.02 E-value=73 Score=26.82 Aligned_cols=45 Identities=20% Similarity=0.283 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHhC-ChHHHHhhhCCCCCHHHHHHHHHHhHHhhhhc
Q 046581 231 EEERILVEAHARIG-NRWAEIAKHIPGRTENSIKNHWNATKRRQNSR 276 (470)
Q Consensus 231 EED~~Ll~lv~~~G-~kWs~IAk~LpgRT~~q~KnRw~~llrr~~~k 276 (470)
+.|..|+.++...+ -.+++||+.+ |-+...|..|.+.+.+...-+
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 56788888888877 4699999999 999999999999998765443
No 100
>TIGR02877 spore_yhbH sporulation protein YhbH. This protein family, typified by YhbH in Bacillus subtilis, is found in nearly every endospore-forming bacterium and in no other genome (but note that the trusted cutoff score is set high to exclude a single high-scoring sequence from Nitrosococcus oceani ATCC 19707, which is classified in the Gammaproteobacteria). The gene in Bacillus subtilis was shown to be in the regulon of the sporulation sigma factor, sigma-E, and its mutation was shown to create a sporulation defect.
Probab=35.99 E-value=24 Score=37.65 Aligned_cols=11 Identities=18% Similarity=0.347 Sum_probs=5.8
Q ss_pred cccCCCCHHHH
Q 046581 223 IKKDSWSEEEE 233 (470)
Q Consensus 223 ikk~~WT~EED 233 (470)
-....|+.+-.
T Consensus 299 SDGDNw~~D~~ 309 (371)
T TIGR02877 299 SDGDNLTSDNE 309 (371)
T ss_pred ccCCCccCCcH
Confidence 34556774433
No 101
>KOG0037 consensus Ca2+-binding protein, EF-Hand protein superfamily [Signal transduction mechanisms]
Probab=35.12 E-value=46 Score=33.12 Aligned_cols=26 Identities=8% Similarity=-0.075 Sum_probs=12.0
Q ss_pred CCCcccccccCCCCCCCCCCCCCCcch
Q 046581 23 TSFRYQNLQQNNKPHHQVYRPSPPLTA 49 (470)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~p~~~~ 49 (470)
.++++.+-+.-.+ +++.+.++||+++
T Consensus 13 ~~gg~~g~p~~~~-a~~~~~~~p~~~~ 38 (221)
T KOG0037|consen 13 MPGGQGGAPYQAA-APGGPGAPPPQAS 38 (221)
T ss_pred cCCCcCCCccccc-CCCCCCCCCChhh
Confidence 5555555444432 3333445555544
No 102
>KOG3074 consensus Transcriptional regulator of the PUR family, single-stranded-DNA-binding [Transcription]
Probab=34.46 E-value=24 Score=35.49 Aligned_cols=10 Identities=30% Similarity=0.371 Sum_probs=5.4
Q ss_pred HHHHHHHHhC
Q 046581 235 ILVEAHARIG 244 (470)
Q Consensus 235 ~Ll~lv~~~G 244 (470)
.|.+++..||
T Consensus 160 aLaelle~~G 169 (263)
T KOG3074|consen 160 ALAELLEDFG 169 (263)
T ss_pred HHHHHHHHhC
Confidence 4555555555
No 103
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=34.23 E-value=80 Score=29.61 Aligned_cols=41 Identities=22% Similarity=0.304 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHh
Q 046581 231 EEERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRR 272 (470)
Q Consensus 231 EED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr 272 (470)
++...++++....|-.+.+||..| |-+...|+.+|.....+
T Consensus 138 ~~~~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR~~ 178 (185)
T PF07638_consen 138 PRQRRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRARAW 178 (185)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 344556666666777899999999 99999999999987643
No 104
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=33.37 E-value=86 Score=28.12 Aligned_cols=39 Identities=15% Similarity=0.226 Sum_probs=29.8
Q ss_pred HHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHhh
Q 046581 234 RILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRRQ 273 (470)
Q Consensus 234 ~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr~ 273 (470)
..++.+....|-.+.+||..| |.+...|+.+....+++-
T Consensus 134 r~vl~l~~~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~L 172 (182)
T PRK09652 134 RTAITLREIEGLSYEEIAEIM-GCPIGTVRSRIFRAREAL 172 (182)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 345555556678999999999 899999999887665543
No 105
>KOG4006 consensus Anti-proliferation factor BTG1/TOB [Signal transduction mechanisms; General function prediction only]
Probab=33.23 E-value=42 Score=34.88 Aligned_cols=45 Identities=27% Similarity=0.355 Sum_probs=28.5
Q ss_pred CCCCCCCCCCCCCCCcccccccCCCCCCCCCCCCCCcchhhhhcccCCc
Q 046581 11 GGGGGGGGGSGNTSFRYQNLQQNNKPHHQVYRPSPPLTAIDRFLWGQNN 59 (470)
Q Consensus 11 ~g~g~~gg~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~d~f~~g~~~ 59 (470)
|++|.-+|-.++.+|+|.+...+ ...|+|-++..++|||.|--+|
T Consensus 262 gq~s~~~~~~p~~~~~ys~s~~~----~~~y~~~~~~~~~d~~~~~~~~ 306 (311)
T KOG4006|consen 262 GQVSYTPGFFPGVPFGYSNSGDK----AKPYRPINEPMHVDRLSWILNH 306 (311)
T ss_pred cccCCCCCCCCCCCcCccccccc----cccccCCCCCcccccceeeccc
Confidence 34444445555568888877766 4555554444779999876554
No 106
>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=32.67 E-value=90 Score=25.79 Aligned_cols=38 Identities=21% Similarity=0.402 Sum_probs=27.2
Q ss_pred HHHHHHHHHhCC--------hHHHHhhhCCC---CC--HHHHHHHHHHhHH
Q 046581 234 RILVEAHARIGN--------RWAEIAKHIPG---RT--ENSIKNHWNATKR 271 (470)
Q Consensus 234 ~~Ll~lv~~~G~--------kWs~IAk~Lpg---RT--~~q~KnRw~~llr 271 (470)
-.|..+|...|+ .|..||..|.- -+ ..++|..|...+.
T Consensus 39 ~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 39 YKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhH
Confidence 357788888875 59999998821 12 3678888887654
No 107
>PLN02705 beta-amylase
Probab=31.72 E-value=28 Score=39.42 Aligned_cols=20 Identities=25% Similarity=0.388 Sum_probs=14.8
Q ss_pred CCCCCCCCCcchhhhhcccC
Q 046581 38 HQVYRPSPPLTAIDRFLWGQ 57 (470)
Q Consensus 38 ~~~~~~~p~~~~~d~f~~g~ 57 (470)
+-.|+..|+++++--|.|-.
T Consensus 139 g~~yr~~~~~~~~~~~~~~~ 158 (681)
T PLN02705 139 GTTYRQSPQPSHVGSFPVRS 158 (681)
T ss_pred CCcccCCCCCcccccccccC
Confidence 67788888888877776643
No 108
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=31.31 E-value=1.4e+02 Score=25.71 Aligned_cols=68 Identities=18% Similarity=0.398 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHHHHHHHh----CC---chHHHHHHHhcC-----CChhhh-------hhhhhhcccccccc---CCCCHH
Q 046581 174 GQWTDEEDRKLIKLVKQY----GV---RKWAQISERMAG-----RAGKQC-------RERWHNHLRPDIKK---DSWSEE 231 (470)
Q Consensus 174 G~WT~EED~~Ll~lV~~y----G~---~~Ws~IA~~lpg-----RT~~Qc-------r~Rw~~~L~p~ikk---~~WT~E 231 (470)
..||+|++-.|++.+..| |. .+|..+...+.+ =+..|+ +.||.+.+.. .+. ..++..
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~~~k-~~~g~~~~~~~~ 83 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNAVKK-SKNGKDPSFSKP 83 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHhhh-cccCcCCCCCCH
Confidence 459999999999999888 42 246555544432 233444 4444444433 222 257777
Q ss_pred HHHHHHHHHHH
Q 046581 232 EERILVEAHAR 242 (470)
Q Consensus 232 ED~~Ll~lv~~ 242 (470)
-|..+.++-.+
T Consensus 84 hd~~~f~Lsk~ 94 (98)
T PF04504_consen 84 HDRRLFELSKK 94 (98)
T ss_pred hHHHHHHHHHH
Confidence 77777777553
No 109
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=30.85 E-value=99 Score=27.62 Aligned_cols=37 Identities=16% Similarity=0.207 Sum_probs=29.0
Q ss_pred HHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHhh
Q 046581 236 LVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRRQ 273 (470)
Q Consensus 236 Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr~ 273 (470)
++.+....|-.+.+||..| |-+...|+++....+++-
T Consensus 133 i~~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~l 169 (179)
T PRK11924 133 VFLLRYVEGLSYREIAEIL-GVPVGTVKSRLRRARQLL 169 (179)
T ss_pred HhhHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 4445555678899999999 999999999988765543
No 110
>PRK04217 hypothetical protein; Provisional
Probab=30.71 E-value=1.1e+02 Score=27.26 Aligned_cols=44 Identities=14% Similarity=0.129 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHh
Q 046581 227 SWSEEEERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRR 272 (470)
Q Consensus 227 ~WT~EED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr 272 (470)
.-|++| ..++.++...|-...+||+.+ |-+...|+.+++...++
T Consensus 42 ~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkk 85 (110)
T PRK04217 42 FMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKK 85 (110)
T ss_pred cCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 455555 577777777888999999999 99999999999876554
No 111
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=29.31 E-value=74 Score=28.34 Aligned_cols=45 Identities=20% Similarity=0.344 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhcccccc
Q 046581 178 DEEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNHLRPDI 223 (470)
Q Consensus 178 ~EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L~p~i 223 (470)
.+-|.+|+++.++-+...+..||+.+ |-+...|+.|-.++.+..+
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 112
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=28.82 E-value=1.1e+02 Score=28.47 Aligned_cols=41 Identities=24% Similarity=0.311 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHh
Q 046581 231 EEERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRR 272 (470)
Q Consensus 231 EED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr 272 (470)
+++..++.+....|-...+||..| |-+...|++|+...+++
T Consensus 137 ~~~r~i~~l~~~~g~s~~EIA~~l-g~s~~tV~~rl~rar~~ 177 (192)
T PRK09643 137 VEQRAALVAVDMQGYSVADAARML-GVAEGTVKSRCARGRAR 177 (192)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 445566666667788899999999 99999999999765554
No 113
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=28.56 E-value=1.2e+02 Score=25.35 Aligned_cols=39 Identities=21% Similarity=0.344 Sum_probs=28.5
Q ss_pred HHHHHHHHHhCC--------hHHHHhhhCCC-----CCHHHHHHHHHHhHHh
Q 046581 234 RILVEAHARIGN--------RWAEIAKHIPG-----RTENSIKNHWNATKRR 272 (470)
Q Consensus 234 ~~Ll~lv~~~G~--------kWs~IAk~Lpg-----RT~~q~KnRw~~llrr 272 (470)
..|..+|.+.|+ .|.+||..|.- ....++|..|...+..
T Consensus 35 ~~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~ 86 (93)
T smart00501 35 YRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLP 86 (93)
T ss_pred HHHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHH
Confidence 357778888775 69999998832 2357788888877654
No 114
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=28.15 E-value=1.2e+02 Score=27.73 Aligned_cols=41 Identities=10% Similarity=0.067 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHhh
Q 046581 232 EERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRRQ 273 (470)
Q Consensus 232 ED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr~ 273 (470)
++..++.+....|..+.+||..| |-|...|+++....+++-
T Consensus 140 ~~r~il~l~~~~~~s~~eIA~~l-gis~~~v~~~l~Rar~~L 180 (187)
T PRK09641 140 KYRTVIVLKYIEDLSLKEISEIL-DLPVGTVKTRIHRGREAL 180 (187)
T ss_pred HHHHHhhhHHhhCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 34445555556778899999999 999999999987766543
No 115
>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=27.62 E-value=70 Score=26.43 Aligned_cols=41 Identities=27% Similarity=0.462 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhCC-------chHHHHHHHhcCC---C--hhhhhhhhhhcccc
Q 046581 181 DRKLIKLVKQYGV-------RKWAQISERMAGR---A--GKQCRERWHNHLRP 221 (470)
Q Consensus 181 D~~Ll~lV~~yG~-------~~Ws~IA~~lpgR---T--~~Qcr~Rw~~~L~p 221 (470)
--+|..+|.+.|- +.|..||..|+-- + ..+++..|.++|-|
T Consensus 38 L~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 38 LYKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp HHHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred HHHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 3478888888762 2599999999521 1 36788888877753
No 116
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=27.13 E-value=1.3e+02 Score=21.57 Aligned_cols=35 Identities=17% Similarity=0.359 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHH
Q 046581 232 EERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWN 267 (470)
Q Consensus 232 ED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~ 267 (470)
|...|.+++..++++.++.|+.| |=+...+..|-+
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~klk 40 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLL-GISRRTLYRKLK 40 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHHH
Confidence 66789999999999999999998 666666655543
No 117
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=26.67 E-value=92 Score=26.22 Aligned_cols=29 Identities=24% Similarity=0.588 Sum_probs=23.0
Q ss_pred HHHHHHHHHHhCChHHHHhhhCCCCCHHHH
Q 046581 233 ERILVEAHARIGNRWAEIAKHIPGRTENSI 262 (470)
Q Consensus 233 D~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~ 262 (470)
|+.|..+....|..|..+|.+| |=|..+|
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 4568888899999999999998 5555444
No 118
>PF00740 Parvo_coat: Parvovirus coat protein VP2 This family is a subset of the SCOP family; InterPro: IPR001403 Parvoviruses are some of the smallest viruses containing linear, non-segmented single-stranded DNA genomes, with an average genome size of 5000 nucleotides. Parvoviruses have been described that infect a wide range of invertebrates and vertebrates and are well known for causing enteric disease in mammals. Genomes contains two large ORFs: NS1 and VP1; other ORFs are found in some sub-types and different gene products can arise from splice variants and the use of different start codons []. The Parvovirus coat protein VP1 together with VP2 forms a capsomer. Both of these proteins are formed from the same transcript using alternative translation start codons. As a result, VP1 and VP2 differ only in the N terminus region. VP2 is involved in packaging the viral DNA []. The mature viron contains three capsid proteins VP1, VP2, and VP3 and a noncapsid protein NS1. VP3 may arise from a third start codon with a favorable translation initiation context which is present at position 3067 in the ChPV genome and which has been described in the goose and Muscovy duck parvoviruses [].; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 1C8G_A 1C8F_A 1C8E_A 1FPV_A 3KIC_L 3KIE_Q 3UX1_A 2G8G_A 1VU0_U 3SHM_L ....
Probab=26.53 E-value=19 Score=39.98 Aligned_cols=13 Identities=23% Similarity=0.107 Sum_probs=4.9
Q ss_pred ccchHHHHHHhhh
Q 046581 59 NCSQQQQQQTQNI 71 (470)
Q Consensus 59 ~~~~~~q~~~~~~ 71 (470)
|++|.-=|.+.|+
T Consensus 81 hfsP~dwQ~l~n~ 93 (529)
T PF00740_consen 81 HFSPRDWQRLINN 93 (529)
T ss_dssp TS-HHHHHHHHHH
T ss_pred ccCHHHHHHHHHh
Confidence 5555433333333
No 119
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=26.24 E-value=1.2e+02 Score=26.90 Aligned_cols=45 Identities=11% Similarity=0.172 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHHhCC-hHHHHhhhCCCCCHHHHHHHHHHhHHhhhh
Q 046581 230 EEEERILVEAHARIGN-RWAEIAKHIPGRTENSIKNHWNATKRRQNS 275 (470)
Q Consensus 230 ~EED~~Ll~lv~~~G~-kWs~IAk~LpgRT~~q~KnRw~~llrr~~~ 275 (470)
++-|..|+++.+.-+. .+.+||+.+ |-+...|.+|-+.|.+...-
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~GiI 52 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGVI 52 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCce
Confidence 3557778888877774 699999999 89999999999999887543
No 120
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=25.94 E-value=1.2e+02 Score=33.59 Aligned_cols=61 Identities=23% Similarity=0.409 Sum_probs=47.1
Q ss_pred HHHHHHhcCCChhhhhhhhhhccccccccCCCCHHHHHHHHHHHHHhCChHHHHh-hhCCCCCHHHHHHHHH
Q 046581 197 AQISERMAGRAGKQCRERWHNHLRPDIKKDSWSEEEERILVEAHARIGNRWAEIA-KHIPGRTENSIKNHWN 267 (470)
Q Consensus 197 s~IA~~lpgRT~~Qcr~Rw~~~L~p~ikk~~WT~EED~~Ll~lv~~~G~kWs~IA-k~LpgRT~~q~KnRw~ 267 (470)
+.|+..+|-=-+.-||+.. ..|+..|-.++-+++.+||..+..|- .+||-++-.+|-..|.
T Consensus 267 ~Ais~LVPlGGPvLCRDem----------EEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYY 328 (693)
T KOG3554|consen 267 KAISYLVPLGGPVLCRDEM----------EEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYY 328 (693)
T ss_pred HHHHHhhcCCCceeehhhh----------hhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHH
Confidence 4566666644455565533 46999999999999999999999995 5679999888877664
No 121
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=25.51 E-value=98 Score=33.32 Aligned_cols=58 Identities=28% Similarity=0.291 Sum_probs=45.3
Q ss_pred cccCCCCHHHHHHHHHHHHHhCC----------------hHHHHhhhCC-----CCCHHHHHHHHHHhHHhhhhccccc
Q 046581 223 IKKDSWSEEEERILVEAHARIGN----------------RWAEIAKHIP-----GRTENSIKNHWNATKRRQNSRRKNK 280 (470)
Q Consensus 223 ikk~~WT~EED~~Ll~lv~~~G~----------------kWs~IAk~Lp-----gRT~~q~KnRw~~llrr~~~k~k~~ 280 (470)
.-.+.|+++=|+-..++...|.. +=..||+++. .||..||-.|-.-+.||+.++.+.+
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~reiq~k 152 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLREIQAK 152 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHHhh
Confidence 34578999999999999987753 4578888763 5999999999999988877654443
No 122
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=25.46 E-value=46 Score=37.47 Aligned_cols=48 Identities=21% Similarity=0.369 Sum_probs=43.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhh
Q 046581 169 VALIKGQWTDEEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHN 217 (470)
Q Consensus 169 p~lkKG~WT~EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~ 217 (470)
+....++|+.+|-.+........| .+.+.|+..+|+|..+|+|..+..
T Consensus 405 k~~~~~~w~~se~e~fyka~~~~g-s~~slis~l~p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 405 KKLETDKWDASETELFYKALSERG-SDFSLISNLFPLRDRKQIKAKFKK 452 (584)
T ss_pred CccccCcccchhhHHhhhHHhhhc-ccccccccccccccHHHHHHHHhh
Confidence 345668999999999999999999 599999999999999999998864
No 123
>KOG4817 consensus Unnamed protein [Function unknown]
Probab=25.43 E-value=66 Score=34.49 Aligned_cols=24 Identities=46% Similarity=0.281 Sum_probs=13.7
Q ss_pred CCCCCcchhhhhcccCCccchHHH
Q 046581 42 RPSPPLTAIDRFLWGQNNCSQQQQ 65 (470)
Q Consensus 42 ~~~p~~~~~d~f~~g~~~~~~~~q 65 (470)
++.||.||--+==-+++...++||
T Consensus 224 ~~~apTTa~~s~~~~~~s~r~~q~ 247 (468)
T KOG4817|consen 224 TWSAPTTAHESGSGGQNSGRQQQQ 247 (468)
T ss_pred CCCCCccccccCccCCccCccccc
Confidence 478898885553334444444444
No 124
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=25.33 E-value=1.4e+02 Score=22.97 Aligned_cols=36 Identities=22% Similarity=0.474 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHH
Q 046581 231 EEERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWN 267 (470)
Q Consensus 231 EED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~ 267 (470)
+.|+-.+.++.+.|-.-.+||+.+ +|+.+.|++.-+
T Consensus 7 ~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 7 DAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRYLK 42 (50)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHHHH
T ss_pred HHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHHhc
Confidence 345566777788999999999999 999998876543
No 125
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=25.26 E-value=1.4e+02 Score=27.65 Aligned_cols=40 Identities=15% Similarity=0.109 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHh
Q 046581 232 EERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRR 272 (470)
Q Consensus 232 ED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr 272 (470)
++..++.+....|-...+||..| |-+...|++|....+++
T Consensus 110 ~~r~i~~l~~~~g~~~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (181)
T PRK09637 110 KYAEALRLTELEGLSQKEIAEKL-GLSLSGAKSRVQRGRVK 149 (181)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 45667777777888999999999 99999999998876554
No 126
>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=25.15 E-value=1.4e+02 Score=26.84 Aligned_cols=41 Identities=12% Similarity=0.114 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHhh
Q 046581 232 EERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRRQ 273 (470)
Q Consensus 232 ED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr~ 273 (470)
++..++.+....|-...+||..| |-|...|+++....+++-
T Consensus 123 ~~r~i~~l~~~~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~L 163 (169)
T TIGR02954 123 KYQTAIILRYYHDLTIKEIAEVM-NKPEGTVKTYLHRALKKL 163 (169)
T ss_pred HHhHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 34455666666677899999999 889999999998766553
No 127
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=24.47 E-value=1.7e+02 Score=25.84 Aligned_cols=41 Identities=22% Similarity=0.169 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHhh
Q 046581 232 EERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRRQ 273 (470)
Q Consensus 232 ED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr~ 273 (470)
+...++.++...|-...+||..| |-+...|++|....+++-
T Consensus 110 ~~r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~L 150 (161)
T PRK09047 110 RQREAFLLRYWEDMDVAETAAAM-GCSEGSVKTHCSRATHAL 150 (161)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 44567777777788899999999 999999999988765543
No 128
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=24.12 E-value=76 Score=37.92 Aligned_cols=20 Identities=45% Similarity=0.627 Sum_probs=8.4
Q ss_pred CCCCCCCCCCCCCCCccccc
Q 046581 11 GGGGGGGGGSGNTSFRYQNL 30 (470)
Q Consensus 11 ~g~g~~gg~~~~~~~~~~~~ 30 (470)
||=|||++|||+++-||++.
T Consensus 1192 GGYGggys~gGygsGGYGgs 1211 (1282)
T KOG0921|consen 1192 GGYGGGYSGGGYGSGGYGGS 1211 (1282)
T ss_pred CCcCCCCCCCCcCCCCCCCC
Confidence 33333344444444444443
No 129
>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=23.90 E-value=1.2e+02 Score=27.66 Aligned_cols=39 Identities=10% Similarity=0.181 Sum_probs=28.7
Q ss_pred HHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHhh
Q 046581 234 RILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRRQ 273 (470)
Q Consensus 234 ~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr~ 273 (470)
..++.+....|-...+||..+ |=|...|+++....+++-
T Consensus 144 r~v~~l~~~~~~s~~EIA~~l-gis~~tv~~~l~rar~~L 182 (190)
T TIGR02939 144 RTAITLRELEGLSYEDIARIM-DCPVGTVRSRIFRAREAI 182 (190)
T ss_pred hhhhhhhhhcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 334444444566799999999 889999999988776653
No 130
>PF08949 DUF1860: Domain of unknown function (DUF1860); InterPro: IPR015044 This entry is represented by Bacteriophage PRD1, P5. This protein has no known function though it is sometimes found in the C terminus of bacteriophage spike proteins []. ; PDB: 1YQ8_A 1YQ5_A 1YQ6_B.
Probab=23.85 E-value=26 Score=33.08 Aligned_cols=11 Identities=73% Similarity=1.434 Sum_probs=0.8
Q ss_pred CCCCCCCCCCC
Q 046581 14 GGGGGGSGNTS 24 (470)
Q Consensus 14 g~~gg~~~~~~ 24 (470)
||||||||.++
T Consensus 71 ggggggggvtd 81 (220)
T PF08949_consen 71 GGGGGGGGVTD 81 (220)
T ss_dssp ---------SE
T ss_pred CCCCCccchhh
Confidence 33444444443
No 131
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=23.77 E-value=1.3e+02 Score=27.30 Aligned_cols=39 Identities=10% Similarity=0.116 Sum_probs=28.9
Q ss_pred HHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHhh
Q 046581 234 RILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRRQ 273 (470)
Q Consensus 234 ~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr~ 273 (470)
..++.+....|-...+||..| |-+...|+++....+++-
T Consensus 142 r~v~~l~~~~g~s~~eIA~~l-gis~~~v~~~l~Rar~~L 180 (187)
T TIGR02948 142 RMVIVLKYMEDLSLKEISEIL-DLPVGTVKTRIHRGREAL 180 (187)
T ss_pred hHHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 334444444567899999999 899999999988766543
No 132
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=23.48 E-value=1.1e+02 Score=32.91 Aligned_cols=44 Identities=20% Similarity=0.373 Sum_probs=37.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCchHHHHH-HHhcCCChhhhhhhhhh
Q 046581 173 KGQWTDEEDRKLIKLVKQYGVRKWAQIS-ERMAGRAGKQCRERWHN 217 (470)
Q Consensus 173 KG~WT~EED~~Ll~lV~~yG~~~Ws~IA-~~lpgRT~~Qcr~Rw~~ 217 (470)
-..|+++|-..+-+.++.|| +++..|. -+|+.|+...|-..|+-
T Consensus 277 l~~wsEeEcr~FEegl~~yG-KDF~lIr~nkvrtRsvgElVeyYYl 321 (445)
T KOG4329|consen 277 LSGWSEEECRNFEEGLELYG-KDFHLIRANKVRTRSVGELVEYYYL 321 (445)
T ss_pred cccCCHHHHHHHHHHHHHhc-ccHHHHHhcccccchHHHHHHHHHH
Confidence 35799999999999999999 6888885 47789999999888753
No 133
>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=23.22 E-value=1.8e+02 Score=27.16 Aligned_cols=41 Identities=7% Similarity=0.037 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHhh
Q 046581 232 EERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRRQ 273 (470)
Q Consensus 232 ED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr~ 273 (470)
.+..++.+....|-...+||..| |-+...|+.|....+++-
T Consensus 135 ~~r~v~~l~~~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~L 175 (188)
T TIGR02943 135 QTARVFMMREVLGFESDEICQEL-EISTSNCHVLLYRARLSL 175 (188)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 45567777777788999999999 999999999988776654
No 134
>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=23.15 E-value=1.2e+02 Score=25.48 Aligned_cols=29 Identities=17% Similarity=0.422 Sum_probs=23.0
Q ss_pred HHHHHHHHHHhCChHHHHhhhCCCCCHHHH
Q 046581 233 ERILVEAHARIGNRWAEIAKHIPGRTENSI 262 (470)
Q Consensus 233 D~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~ 262 (470)
|..|..+....|..|.++|..| |=+...|
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI 32 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEI 32 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHH
Confidence 5667788889999999999998 5555444
No 135
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=23.14 E-value=1.7e+02 Score=26.72 Aligned_cols=41 Identities=15% Similarity=0.161 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHhh
Q 046581 232 EERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRRQ 273 (470)
Q Consensus 232 ED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr~ 273 (470)
++..++.+....|-...+||..| |-+...|+.+....+++-
T Consensus 135 ~~r~v~~l~~~~g~s~~eIA~~l-~is~~tV~~~l~ra~~~L 175 (184)
T PRK12512 135 RQRDVVQSISVEGASIKETAAKL-SMSEGAVRVALHRGLAAL 175 (184)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 34455555556677899999999 999999999988766554
No 136
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=23.02 E-value=1.9e+02 Score=25.46 Aligned_cols=38 Identities=13% Similarity=0.164 Sum_probs=28.3
Q ss_pred HHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHh
Q 046581 234 RILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRR 272 (470)
Q Consensus 234 ~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr 272 (470)
..++.+.-..|-...+||..+ |-+...|+++-...+++
T Consensus 112 r~ii~l~~~~~~s~~EIA~~l-~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 112 KYIIFERFFVGKTMGEIALET-EMTYYQVRWIYRQALEK 149 (154)
T ss_pred HHHHHHHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 344444455567789999999 99999999988766554
No 137
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=22.62 E-value=1.8e+02 Score=26.19 Aligned_cols=41 Identities=24% Similarity=0.261 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHhh
Q 046581 232 EERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRRQ 273 (470)
Q Consensus 232 ED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr~ 273 (470)
++..++.+....|-.-.+||..| |.+...|+.|....+++-
T Consensus 122 ~~r~vl~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~L 162 (173)
T PRK09645 122 EHRAVLVRSYYRGWSTAQIAADL-GIPEGTVKSRLHYALRAL 162 (173)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 44556666666677899999999 999999999987665543
No 138
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=22.52 E-value=1.8e+02 Score=26.78 Aligned_cols=37 Identities=16% Similarity=0.197 Sum_probs=27.4
Q ss_pred HHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHh
Q 046581 235 ILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRR 272 (470)
Q Consensus 235 ~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr 272 (470)
.++.++...|-...+||..| |-+...|+.+....+++
T Consensus 146 ~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 146 EILILRVVVGLSAEETAEAV-GSTPGAVRVAQHRALAR 182 (189)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 34444444566899999999 89999999988766554
No 139
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=22.34 E-value=1.9e+02 Score=25.73 Aligned_cols=41 Identities=20% Similarity=0.146 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHh
Q 046581 231 EEERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRR 272 (470)
Q Consensus 231 EED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr 272 (470)
++...++.+....|-.-.+||..| |-+...|++|....+++
T Consensus 109 ~~~r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (160)
T PRK09642 109 ENYRDVVLAHYLEEKSYQEIALQE-KIEVKTVEMKLYRARKW 149 (160)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 344567777777888999999999 99999999998766554
No 140
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=22.09 E-value=1.8e+02 Score=27.00 Aligned_cols=40 Identities=3% Similarity=0.011 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHh
Q 046581 232 EERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRR 272 (470)
Q Consensus 232 ED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr 272 (470)
+...++.+....|-...+||..| |-+...||.|....+++
T Consensus 138 ~~R~v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~RAr~~ 177 (189)
T PRK12530 138 QQARVFMMREYLELSSEQICQEC-DISTSNLHVLLYRARLQ 177 (189)
T ss_pred HHHHHHhHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 44556666666688899999999 99999999998765544
No 141
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=22.05 E-value=1.7e+02 Score=27.04 Aligned_cols=32 Identities=9% Similarity=0.107 Sum_probs=24.7
Q ss_pred HHhCChHHHHhhhCCCCCHHHHHHHHHHhHHhh
Q 046581 241 ARIGNRWAEIAKHIPGRTENSIKNHWNATKRRQ 273 (470)
Q Consensus 241 ~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr~ 273 (470)
...|-...+||..| |-+...|++|....+++-
T Consensus 151 ~~~g~s~~eIA~~l-gis~~tv~~~l~Rar~~L 182 (193)
T PRK11923 151 EFDGLSYEDIASVM-QCPVGTVRSRIFRAREAI 182 (193)
T ss_pred HhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 34455689999999 889999999988766543
No 142
>PF00740 Parvo_coat: Parvovirus coat protein VP2 This family is a subset of the SCOP family; InterPro: IPR001403 Parvoviruses are some of the smallest viruses containing linear, non-segmented single-stranded DNA genomes, with an average genome size of 5000 nucleotides. Parvoviruses have been described that infect a wide range of invertebrates and vertebrates and are well known for causing enteric disease in mammals. Genomes contains two large ORFs: NS1 and VP1; other ORFs are found in some sub-types and different gene products can arise from splice variants and the use of different start codons []. The Parvovirus coat protein VP1 together with VP2 forms a capsomer. Both of these proteins are formed from the same transcript using alternative translation start codons. As a result, VP1 and VP2 differ only in the N terminus region. VP2 is involved in packaging the viral DNA []. The mature viron contains three capsid proteins VP1, VP2, and VP3 and a noncapsid protein NS1. VP3 may arise from a third start codon with a favorable translation initiation context which is present at position 3067 in the ChPV genome and which has been described in the goose and Muscovy duck parvoviruses [].; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 1C8G_A 1C8F_A 1C8E_A 1FPV_A 3KIC_L 3KIE_Q 3UX1_A 2G8G_A 1VU0_U 3SHM_L ....
Probab=21.96 E-value=27 Score=38.82 Aligned_cols=14 Identities=0% Similarity=0.040 Sum_probs=8.2
Q ss_pred CCCCchHHHHHHHH
Q 046581 108 TTTTTLEPTSFVDG 121 (470)
Q Consensus 108 g~WT~EED~~Ll~~ 121 (470)
..+++.|=+.|+..
T Consensus 80 ~hfsP~dwQ~l~n~ 93 (529)
T PF00740_consen 80 CHFSPRDWQRLINN 93 (529)
T ss_dssp GTS-HHHHHHHHHH
T ss_pred eccCHHHHHHHHHh
Confidence 34777776666655
No 143
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=21.86 E-value=1.1e+02 Score=29.49 Aligned_cols=9 Identities=44% Similarity=0.678 Sum_probs=4.9
Q ss_pred CCCCCCCcc
Q 046581 40 VYRPSPPLT 48 (470)
Q Consensus 40 ~~~~~p~~~ 48 (470)
--+|+||++
T Consensus 162 ~~~~~~~~~ 170 (182)
T PRK06958 162 ASRPSAPAG 170 (182)
T ss_pred ccCcCCCCC
Confidence 345666654
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=21.54 E-value=1.3e+02 Score=21.99 Aligned_cols=39 Identities=26% Similarity=0.376 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHhCCchHHHHHHHhcCCChhhhhhhhhhcc
Q 046581 179 EEDRKLIKLVKQYGVRKWAQISERMAGRAGKQCRERWHNHL 219 (470)
Q Consensus 179 EED~~Ll~lV~~yG~~~Ws~IA~~lpgRT~~Qcr~Rw~~~L 219 (470)
+++..++.+.-..+ ..+..||..| |-+...++.+....+
T Consensus 7 ~~er~vi~~~y~~~-~t~~eIa~~l-g~s~~~V~~~~~~al 45 (50)
T PF04545_consen 7 PREREVIRLRYFEG-LTLEEIAERL-GISRSTVRRILKRAL 45 (50)
T ss_dssp HHHHHHHHHHHTST--SHHHHHHHH-TSCHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCC-CCHHHHHHHH-CCcHHHHHHHHHHHH
Confidence 34555555554334 5899999999 788888877765543
No 145
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=21.19 E-value=2e+02 Score=26.16 Aligned_cols=41 Identities=20% Similarity=0.179 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHhh
Q 046581 232 EERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRRQ 273 (470)
Q Consensus 232 ED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr~ 273 (470)
++..++.+....|-...+||..+ |-+...|+.+...-+++-
T Consensus 123 ~~r~v~~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 123 KARAAFLYNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 45556666667788899999999 999999999987665543
No 146
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. 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. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. 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-associati
Probab=20.98 E-value=1.2e+02 Score=25.12 Aligned_cols=29 Identities=24% Similarity=0.612 Sum_probs=22.1
Q ss_pred HHHHHHHHHHhCChHHHHhhhCCCCCHHHH
Q 046581 233 ERILVEAHARIGNRWAEIAKHIPGRTENSI 262 (470)
Q Consensus 233 D~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~ 262 (470)
|..|..+....|..|.++|+.| |=+..+|
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI 32 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDI 32 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHH
Confidence 4457777888999999999999 5555444
No 147
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=20.62 E-value=2.1e+02 Score=26.61 Aligned_cols=40 Identities=10% Similarity=0.062 Sum_probs=30.4
Q ss_pred HHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHhh
Q 046581 233 ERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRRQ 273 (470)
Q Consensus 233 D~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr~ 273 (470)
+..++.+....|-...+||..| |-+...|+.|....+++-
T Consensus 146 ~r~v~~l~~~eg~s~~EIA~~l-gis~~tVk~rl~ra~~~L 185 (194)
T PRK12531 146 QRDVLQAVYLEELPHQQVAEMF-DIPLGTVKSRLRLAVEKL 185 (194)
T ss_pred HHHHHHHHHHcCCCHHHHHHHh-CcCHHHHHHHHHHHHHHH
Confidence 4445555556677899999999 999999999987665543
No 148
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=20.54 E-value=94 Score=30.62 Aligned_cols=6 Identities=0% Similarity=0.241 Sum_probs=2.4
Q ss_pred CCCCCC
Q 046581 36 PHHQVY 41 (470)
Q Consensus 36 ~~~~~~ 41 (470)
.|+..|
T Consensus 31 ~P~~lf 36 (233)
T PF11705_consen 31 QPPPLF 36 (233)
T ss_pred CCCCCC
Confidence 334444
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=20.04 E-value=2.2e+02 Score=25.33 Aligned_cols=40 Identities=18% Similarity=0.225 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHhCChHHHHhhhCCCCCHHHHHHHHHHhHHh
Q 046581 232 EERILVEAHARIGNRWAEIAKHIPGRTENSIKNHWNATKRR 272 (470)
Q Consensus 232 ED~~Ll~lv~~~G~kWs~IAk~LpgRT~~q~KnRw~~llrr 272 (470)
.+..++.+.-..|-...+||+.| |-+...|+.+-...+++
T Consensus 126 ~~r~vl~l~~~~g~s~~eIA~~l-~is~~tv~~~l~ra~~~ 165 (170)
T TIGR02952 126 KQQHVIALRFGQNLPIAEVARIL-GKTEGAVKILQFRAIKK 165 (170)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 34556666556678899999999 99999999988776554
Done!