Query 025697
Match_columns 249
No_of_seqs 197 out of 1415
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 08:34:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025697.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025697hhsearch_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 1.4E-34 3.1E-39 256.9 11.9 107 3-109 8-115 (238)
2 PLN03212 Transcription repress 100.0 8.6E-34 1.9E-38 250.1 10.8 107 2-108 23-130 (249)
3 PLN03091 hypothetical protein; 100.0 5.5E-31 1.2E-35 247.5 12.4 106 2-107 12-118 (459)
4 KOG0049 Transcription factor, 99.8 1E-18 2.2E-23 170.1 7.7 92 2-93 358-450 (939)
5 KOG0049 Transcription factor, 99.7 2.8E-17 6.1E-22 160.2 8.1 109 3-111 304-416 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.7 3.9E-17 8.5E-22 115.2 6.3 60 7-67 1-60 (60)
7 KOG0050 mRNA splicing protein 99.6 9.7E-16 2.1E-20 146.5 5.0 109 1-110 4-112 (617)
8 COG5147 REB1 Myb superfamily p 99.6 2.9E-15 6.2E-20 145.2 7.5 105 2-106 18-122 (512)
9 KOG0051 RNA polymerase I termi 99.5 1.9E-14 4.2E-19 140.9 8.7 105 3-109 383-515 (607)
10 PF00249 Myb_DNA-binding: Myb- 99.5 9E-15 2E-19 99.1 3.6 47 4-50 1-48 (48)
11 PF00249 Myb_DNA-binding: Myb- 99.4 4.2E-13 9.1E-18 90.9 4.9 46 56-101 1-48 (48)
12 smart00717 SANT SANT SWI3, AD 99.2 1.1E-11 2.3E-16 81.9 4.9 48 4-51 1-48 (49)
13 PF13921 Myb_DNA-bind_6: Myb-l 99.2 9E-12 1.9E-16 87.7 4.0 45 59-103 1-45 (60)
14 smart00717 SANT SANT SWI3, AD 99.2 2.5E-11 5.3E-16 80.1 5.4 47 56-102 1-48 (49)
15 PLN03212 Transcription repress 99.2 3.8E-11 8.3E-16 106.7 6.2 73 34-113 10-84 (249)
16 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 1.3E-10 2.8E-15 75.5 4.5 45 6-50 1-45 (45)
17 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 2.3E-10 5E-15 74.3 5.5 43 58-100 1-44 (45)
18 KOG0051 RNA polymerase I termi 99.1 3.1E-10 6.6E-15 111.7 7.6 113 3-116 307-443 (607)
19 KOG0048 Transcription factor, 99.0 4.2E-10 9E-15 100.2 3.9 62 52-113 5-68 (238)
20 PLN03091 hypothetical protein; 99.0 5.8E-10 1.3E-14 106.0 4.8 59 51-109 9-69 (459)
21 COG5147 REB1 Myb superfamily p 98.4 3.7E-08 8E-13 96.1 -0.8 98 2-101 289-396 (512)
22 KOG0457 Histone acetyltransfer 98.0 5.5E-06 1.2E-10 78.9 3.9 47 4-50 72-118 (438)
23 TIGR01557 myb_SHAQKYF myb-like 98.0 1.4E-05 3E-10 56.4 4.7 49 2-50 1-54 (57)
24 KOG0457 Histone acetyltransfer 97.8 3.6E-05 7.7E-10 73.5 6.1 49 54-102 70-119 (438)
25 TIGR01557 myb_SHAQKYF myb-like 97.7 8.8E-05 1.9E-09 52.3 5.8 46 56-101 3-54 (57)
26 KOG0050 mRNA splicing protein 97.7 3.3E-05 7.2E-10 75.0 4.0 82 54-135 5-87 (617)
27 PF13325 MCRS_N: N-terminal re 97.5 0.0005 1.1E-08 60.0 8.2 95 6-102 1-127 (199)
28 TIGR02894 DNA_bind_RsfA transc 97.4 0.00038 8.2E-09 58.7 6.2 60 55-115 3-69 (161)
29 COG5259 RSC8 RSC chromatin rem 97.2 0.00032 6.9E-09 67.7 4.2 46 3-49 278-323 (531)
30 KOG1279 Chromatin remodeling f 97.2 0.00032 6.9E-09 68.9 4.1 45 4-49 253-297 (506)
31 COG5259 RSC8 RSC chromatin rem 97.2 0.0004 8.6E-09 67.0 4.3 44 56-99 279-322 (531)
32 KOG1279 Chromatin remodeling f 97.1 0.00063 1.4E-08 66.9 5.2 44 55-98 252-295 (506)
33 PF13837 Myb_DNA-bind_4: Myb/S 96.8 0.0012 2.6E-08 49.3 3.3 50 57-106 2-69 (90)
34 PF13837 Myb_DNA-bind_4: Myb/S 96.7 0.0014 3E-08 48.9 2.7 47 4-50 1-64 (90)
35 PRK13923 putative spore coat p 96.5 0.0057 1.2E-07 52.2 5.9 61 55-116 4-71 (170)
36 TIGR02894 DNA_bind_RsfA transc 96.5 0.0015 3.1E-08 55.2 2.3 48 3-51 3-56 (161)
37 PF08914 Myb_DNA-bind_2: Rap1 96.5 0.0025 5.5E-08 46.1 3.0 50 4-53 2-60 (65)
38 PF08914 Myb_DNA-bind_2: Rap1 96.4 0.0055 1.2E-07 44.3 4.4 50 56-105 2-61 (65)
39 PLN03142 Probable chromatin-re 96.3 0.048 1E-06 58.2 12.7 107 6-112 826-995 (1033)
40 COG5114 Histone acetyltransfer 96.3 0.0026 5.6E-08 59.1 2.7 47 5-51 64-110 (432)
41 PF13873 Myb_DNA-bind_5: Myb/S 96.3 0.0076 1.6E-07 44.1 4.6 48 3-50 1-69 (78)
42 COG5114 Histone acetyltransfer 96.3 0.0047 1E-07 57.4 4.2 47 56-102 63-110 (432)
43 PF13873 Myb_DNA-bind_5: Myb/S 96.0 0.019 4.2E-07 41.9 5.8 49 56-104 2-72 (78)
44 PRK13923 putative spore coat p 95.5 0.0089 1.9E-07 51.0 2.2 49 2-51 3-57 (170)
45 KOG1194 Predicted DNA-binding 93.3 0.78 1.7E-05 44.7 10.1 53 55-107 186-238 (534)
46 KOG4282 Transcription factor G 92.6 0.23 4.9E-06 46.4 5.6 56 56-111 54-123 (345)
47 PF12776 Myb_DNA-bind_3: Myb/S 91.1 0.4 8.6E-06 36.0 4.4 44 58-101 1-62 (96)
48 PF09111 SLIDE: SLIDE; InterP 90.9 0.54 1.2E-05 37.8 5.2 52 53-104 46-113 (118)
49 KOG2656 DNA methyltransferase 90.8 0.23 5E-06 47.4 3.4 84 26-109 75-189 (445)
50 PF09111 SLIDE: SLIDE; InterP 90.7 0.29 6.4E-06 39.4 3.5 46 3-48 48-108 (118)
51 PF11626 Rap1_C: TRF2-interact 89.6 0.44 9.6E-06 36.0 3.5 27 4-33 47-81 (87)
52 COG5118 BDP1 Transcription ini 89.5 0.62 1.3E-05 44.6 5.1 44 57-100 366-409 (507)
53 KOG4167 Predicted DNA-binding 87.0 0.69 1.5E-05 47.5 3.9 43 5-48 620-662 (907)
54 PF12776 Myb_DNA-bind_3: Myb/S 85.6 1.4 3E-05 33.0 4.1 44 6-49 1-61 (96)
55 COG5118 BDP1 Transcription ini 85.5 0.92 2E-05 43.4 3.7 43 5-48 366-408 (507)
56 PF08281 Sigma70_r4_2: Sigma-7 84.7 3.2 7E-05 27.7 5.2 41 61-102 12-52 (54)
57 smart00595 MADF subfamily of S 84.6 3 6.4E-05 30.8 5.5 30 77-107 29-58 (89)
58 KOG4282 Transcription factor G 82.8 1.4 3E-05 41.2 3.7 46 5-50 55-113 (345)
59 PF13404 HTH_AsnC-type: AsnC-t 81.6 2.1 4.6E-05 28.0 3.2 38 10-48 3-40 (42)
60 KOG1194 Predicted DNA-binding 77.2 2.7 5.9E-05 41.1 3.7 44 5-49 188-231 (534)
61 KOG4329 DNA-binding protein [G 76.9 4.6 9.9E-05 38.6 5.0 45 57-101 278-323 (445)
62 PF07750 GcrA: GcrA cell cycle 76.8 3.1 6.8E-05 35.1 3.6 41 58-99 2-42 (162)
63 KOG4468 Polycomb-group transcr 72.7 6.9 0.00015 39.7 5.3 51 56-106 88-148 (782)
64 PF10545 MADF_DNA_bdg: Alcohol 72.6 5.7 0.00012 28.4 3.7 31 77-107 28-59 (85)
65 PRK11179 DNA-binding transcrip 72.5 3.9 8.4E-05 33.7 3.1 45 9-54 8-52 (153)
66 PF13404 HTH_AsnC-type: AsnC-t 72.4 9.2 0.0002 24.9 4.3 38 62-100 3-41 (42)
67 KOG4167 Predicted DNA-binding 72.0 7.5 0.00016 40.3 5.5 45 57-101 620-664 (907)
68 PF11035 SnAPC_2_like: Small n 71.7 21 0.00045 33.6 7.8 55 56-110 21-79 (344)
69 PRK11169 leucine-responsive tr 70.1 4.3 9.3E-05 33.8 2.9 45 9-54 13-57 (164)
70 PRK11179 DNA-binding transcrip 67.9 13 0.00028 30.5 5.3 45 61-106 8-53 (153)
71 KOG4468 Polycomb-group transcr 67.6 9.3 0.0002 38.8 5.0 48 3-51 87-144 (782)
72 PRK11169 leucine-responsive tr 62.9 15 0.00032 30.6 4.7 45 61-106 13-58 (164)
73 PLN03142 Probable chromatin-re 60.2 9.6 0.00021 41.2 3.8 45 3-47 925-981 (1033)
74 PF04545 Sigma70_r4: Sigma-70, 58.3 31 0.00066 22.6 4.8 41 62-103 7-47 (50)
75 PF13325 MCRS_N: N-terminal re 58.2 21 0.00046 31.3 5.0 44 58-102 1-47 (199)
76 TIGR02985 Sig70_bacteroi1 RNA 57.5 30 0.00065 27.3 5.5 30 73-103 127-156 (161)
77 smart00595 MADF subfamily of S 56.6 5.8 0.00013 29.2 1.1 22 27-49 30-51 (89)
78 PF09905 DUF2132: Uncharacteri 56.1 14 0.00029 26.7 2.8 44 12-67 12-62 (64)
79 PF01388 ARID: ARID/BRIGHT DNA 55.8 28 0.0006 25.8 4.8 37 66-102 40-89 (92)
80 PF09197 Rap1-DNA-bind: Rap1, 55.6 16 0.00034 28.9 3.5 45 6-50 1-75 (105)
81 PF07750 GcrA: GcrA cell cycle 54.9 15 0.00033 31.0 3.5 41 6-48 2-42 (162)
82 PF04504 DUF573: Protein of un 54.7 41 0.00088 25.9 5.6 69 4-73 4-94 (98)
83 KOG0384 Chromodomain-helicase 53.2 19 0.00041 39.5 4.6 72 6-83 1135-1207(1373)
84 PF11035 SnAPC_2_like: Small n 53.1 64 0.0014 30.4 7.5 85 5-102 22-127 (344)
85 PF11626 Rap1_C: TRF2-interact 53.1 6.3 0.00014 29.6 0.8 17 52-68 43-59 (87)
86 PF04504 DUF573: Protein of un 51.1 39 0.00084 26.1 5.0 45 57-101 5-62 (98)
87 KOG2656 DNA methyltransferase 50.3 8.6 0.00019 37.1 1.4 46 4-50 130-181 (445)
88 smart00501 BRIGHT BRIGHT, ARID 49.7 42 0.00092 25.1 4.9 38 65-102 35-85 (93)
89 PF08281 Sigma70_r4_2: Sigma-7 48.8 18 0.00038 24.0 2.4 38 9-48 12-49 (54)
90 KOG4329 DNA-binding protein [G 47.8 21 0.00046 34.3 3.6 43 6-49 279-322 (445)
91 smart00344 HTH_ASNC helix_turn 45.7 30 0.00064 26.2 3.6 43 10-53 3-45 (108)
92 cd08319 Death_RAIDD Death doma 45.1 33 0.00073 25.7 3.7 27 64-91 2-28 (83)
93 PRK09413 IS2 repressor TnpA; R 43.9 1E+02 0.0023 24.2 6.6 46 2-50 8-53 (121)
94 PF07638 Sigma70_ECF: ECF sigm 43.8 68 0.0015 26.9 5.9 35 66-101 142-176 (185)
95 KOG2009 Transcription initiati 43.3 26 0.00056 35.5 3.6 44 55-98 408-451 (584)
96 COG1522 Lrp Transcriptional re 43.0 25 0.00055 28.1 3.0 45 9-54 7-51 (154)
97 KOG3554 Histone deacetylase co 41.4 77 0.0017 31.6 6.3 42 57-98 286-328 (693)
98 TIGR02937 sigma70-ECF RNA poly 40.2 73 0.0016 24.2 5.1 30 73-103 124-153 (158)
99 cd08803 Death_ank3 Death domai 40.1 48 0.001 24.9 3.9 28 64-92 4-31 (84)
100 PRK09652 RNA polymerase sigma 40.0 1E+02 0.0022 24.7 6.2 29 74-103 143-171 (182)
101 PRK11924 RNA polymerase sigma 39.5 71 0.0015 25.6 5.2 29 74-103 140-168 (179)
102 smart00344 HTH_ASNC helix_turn 39.5 65 0.0014 24.2 4.7 44 62-106 3-47 (108)
103 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 38.4 63 0.0014 22.1 3.8 35 62-97 7-41 (50)
104 cd06171 Sigma70_r4 Sigma70, re 38.4 96 0.0021 19.1 4.7 36 64-100 15-50 (55)
105 PRK09647 RNA polymerase sigma 38.1 1E+02 0.0022 26.3 6.1 31 74-105 153-183 (203)
106 PRK04217 hypothetical protein; 37.7 95 0.0021 24.6 5.4 44 58-103 42-85 (110)
107 KOG3841 TEF-1 and related tran 37.2 1E+02 0.0022 29.9 6.3 57 55-111 75-152 (455)
108 cd08317 Death_ank Death domain 36.5 44 0.00095 24.7 3.2 27 64-91 4-30 (84)
109 TIGR02954 Sig70_famx3 RNA poly 35.9 88 0.0019 25.3 5.2 30 74-104 134-163 (169)
110 PF13936 HTH_38: Helix-turn-he 35.1 45 0.00099 21.6 2.7 37 58-96 4-40 (44)
111 smart00351 PAX Paired Box doma 35.1 1.6E+02 0.0035 23.3 6.5 73 1-75 12-92 (125)
112 PRK09643 RNA polymerase sigma 33.3 1.1E+02 0.0023 25.7 5.4 27 74-101 149-175 (192)
113 PRK12529 RNA polymerase sigma 32.4 1.2E+02 0.0026 24.9 5.6 32 73-105 141-172 (178)
114 PRK09641 RNA polymerase sigma 32.0 1.1E+02 0.0024 25.0 5.2 28 74-102 151-178 (187)
115 PF01527 HTH_Tnp_1: Transposas 31.1 57 0.0012 22.8 2.9 47 1-50 1-47 (76)
116 cd08318 Death_NMPP84 Death dom 30.1 78 0.0017 23.6 3.6 26 67-93 10-35 (86)
117 PRK12515 RNA polymerase sigma 29.1 1.5E+02 0.0032 24.5 5.6 28 74-102 146-173 (189)
118 cd08805 Death_ank1 Death domai 29.0 52 0.0011 24.8 2.4 23 64-86 4-26 (84)
119 PRK09047 RNA polymerase factor 28.9 1.6E+02 0.0035 23.3 5.6 29 74-103 121-149 (161)
120 cd08804 Death_ank2 Death domai 28.6 83 0.0018 23.4 3.5 30 64-94 4-33 (84)
121 cd08311 Death_p75NR Death doma 28.5 68 0.0015 23.7 3.0 33 61-95 2-34 (77)
122 PF02954 HTH_8: Bacterial regu 28.3 1.1E+02 0.0025 19.4 3.7 33 63-96 6-38 (42)
123 PRK12512 RNA polymerase sigma 28.2 1.6E+02 0.0034 24.2 5.5 29 74-103 146-174 (184)
124 PRK09642 RNA polymerase sigma 27.9 1.7E+02 0.0036 23.3 5.5 28 74-102 121-148 (160)
125 TIGR02948 SigW_bacill RNA poly 27.8 1.1E+02 0.0024 24.9 4.6 27 75-102 152-178 (187)
126 TIGR02939 RpoE_Sigma70 RNA pol 27.7 1.1E+02 0.0024 24.9 4.6 28 75-103 154-181 (190)
127 PRK09645 RNA polymerase sigma 27.6 1.6E+02 0.0034 23.8 5.4 28 74-102 133-160 (173)
128 PRK09637 RNA polymerase sigma 27.6 1.5E+02 0.0032 24.6 5.3 28 74-102 121-148 (181)
129 KOG1878 Nuclear receptor coreg 27.3 29 0.00062 38.8 1.0 42 5-47 226-267 (1672)
130 PRK12523 RNA polymerase sigma 26.7 1.8E+02 0.0039 23.6 5.6 31 73-104 133-163 (172)
131 PF10440 WIYLD: Ubiquitin-bind 26.6 47 0.001 24.1 1.7 17 66-82 31-47 (65)
132 COG1522 Lrp Transcriptional re 26.2 1.5E+02 0.0032 23.6 4.9 47 61-108 7-54 (154)
133 smart00005 DEATH DEATH domain, 26.2 93 0.002 22.5 3.4 28 64-92 5-33 (88)
134 TIGR02943 Sig70_famx1 RNA poly 26.1 1.8E+02 0.0038 24.3 5.5 29 74-103 146-174 (188)
135 PRK12531 RNA polymerase sigma 25.9 1.8E+02 0.0038 24.3 5.5 28 74-102 156-183 (194)
136 PRK09648 RNA polymerase sigma 25.9 1.8E+02 0.0038 24.0 5.5 29 74-103 154-182 (189)
137 PRK11923 algU RNA polymerase s 25.2 1.6E+02 0.0035 24.3 5.1 27 75-102 154-180 (193)
138 PRK12530 RNA polymerase sigma 24.8 1.8E+02 0.004 24.1 5.4 27 74-101 149-175 (189)
139 COG2197 CitB Response regulato 24.6 1.9E+02 0.0042 24.8 5.6 46 57-105 147-192 (211)
140 PRK09651 RNA polymerase sigma 24.6 1.7E+02 0.0036 23.9 5.0 31 75-106 135-165 (172)
141 PRK12524 RNA polymerase sigma 23.5 2E+02 0.0043 24.0 5.4 27 74-101 151-177 (196)
142 TIGR00673 cynS cyanate hydrata 23.3 4.3E+02 0.0093 22.2 7.1 64 13-88 11-76 (150)
143 cd08779 Death_PIDD Death Domai 23.3 95 0.0021 23.2 3.0 22 65-86 3-24 (86)
144 COG4628 Uncharacterized conser 23.1 1.1E+02 0.0023 24.8 3.3 44 12-67 21-71 (136)
145 KOG2009 Transcription initiati 22.9 56 0.0012 33.2 2.1 44 4-48 409-452 (584)
146 PF09420 Nop16: Ribosome bioge 22.9 1.7E+02 0.0037 24.4 4.8 46 55-100 113-162 (164)
147 KOG4128 Bleomycin hydrolases a 22.6 4.1E+02 0.0089 25.6 7.6 56 49-113 138-194 (457)
148 PRK10100 DNA-binding transcrip 22.5 1.9E+02 0.0042 25.0 5.2 45 58-105 155-199 (216)
149 TIGR02999 Sig-70_X6 RNA polyme 22.1 2.4E+02 0.0051 22.9 5.5 27 75-102 150-176 (183)
150 PRK12527 RNA polymerase sigma 21.9 2.7E+02 0.0058 22.1 5.7 27 75-102 121-147 (159)
151 PRK13919 putative RNA polymera 21.6 2.5E+02 0.0054 22.9 5.5 28 75-103 151-178 (186)
152 PRK09649 RNA polymerase sigma 21.5 2.2E+02 0.0047 23.6 5.2 27 75-102 146-172 (185)
153 PRK12532 RNA polymerase sigma 21.5 2.2E+02 0.0047 23.6 5.2 28 74-102 151-178 (195)
154 TIGR02950 SigM_subfam RNA poly 21.4 70 0.0015 25.2 2.1 28 75-103 121-148 (154)
155 PRK06759 RNA polymerase factor 21.1 2.3E+02 0.0049 22.3 5.0 27 75-102 122-148 (154)
156 cd08777 Death_RIP1 Death Domai 21.0 1.3E+02 0.0027 22.6 3.3 29 66-95 4-32 (86)
157 PF01466 Skp1: Skp1 family, di 21.0 1.4E+02 0.003 21.6 3.5 36 27-69 36-71 (78)
158 PRK01905 DNA-binding protein F 20.8 2.5E+02 0.0055 20.3 4.8 34 62-96 37-70 (77)
159 PRK00118 putative DNA-binding 20.8 2.9E+02 0.0063 21.6 5.4 40 61-101 19-58 (104)
160 PF07555 NAGidase: beta-N-acet 20.8 1.6E+02 0.0035 27.4 4.6 21 5-25 10-30 (306)
161 PRK12514 RNA polymerase sigma 20.8 2.5E+02 0.0055 22.8 5.4 28 75-103 145-172 (179)
162 PRK12536 RNA polymerase sigma 20.7 2.6E+02 0.0055 22.9 5.4 28 74-102 144-171 (181)
163 PRK15201 fimbriae regulatory p 20.7 2.9E+02 0.0063 24.2 5.7 45 58-105 133-177 (198)
164 TIGR02984 Sig-70_plancto1 RNA 20.5 2.5E+02 0.0055 22.7 5.4 29 74-103 155-183 (189)
No 1
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=1.4e-34 Score=256.90 Aligned_cols=107 Identities=40% Similarity=0.786 Sum_probs=103.7
Q ss_pred CCCCCCHHHHHHHHHHHHHHCCCChhHhhHHhc-CCChhhhhhhhhcccCCCCCCCCCCHHHHHHHHHHHHHhCCchHHH
Q 025697 3 TRGHWRPAEDEKLRELVERYGPHNWNAIAEKLQ-GRSGKSCRLRWFNQLDPRINRSPFTEEEEERLLASHRIHGNRWAVI 81 (249)
Q Consensus 3 ~Kg~WT~EED~~L~~~V~~~G~~~W~~IA~~l~-~Rt~~qcr~Rw~~~L~p~lkkg~WT~EED~~Llelv~~~G~~Ws~I 81 (249)
.||+||+|||.+|+.+|.+||+++|..||+.++ +|++++||.||.|||+|.+++|.||+|||.+|+++|..+|++|+.|
T Consensus 8 ~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrWs~I 87 (238)
T KOG0048|consen 8 VKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRWSLI 87 (238)
T ss_pred cCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHHHHH
Confidence 359999999999999999999999999999998 9999999999999999999999999999999999999999999999
Q ss_pred hhhCCCCCHHHHHHHHHHHHHHHHhhhh
Q 025697 82 ARLFPGRTDNAVKNHWHVIMARRCRERS 109 (249)
Q Consensus 82 A~~lpgRT~~~cknrW~~~lkr~~~~~~ 109 (249)
|++|||||+++|||+|++.++|++....
T Consensus 88 A~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 88 AGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred HhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 9999999999999999999999987654
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=8.6e-34 Score=250.13 Aligned_cols=107 Identities=40% Similarity=0.814 Sum_probs=102.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCChhHhhHHh-cCCChhhhhhhhhcccCCCCCCCCCCHHHHHHHHHHHHHhCCchHH
Q 025697 2 CTRGHWRPAEDEKLRELVERYGPHNWNAIAEKL-QGRSGKSCRLRWFNQLDPRINRSPFTEEEEERLLASHRIHGNRWAV 80 (249)
Q Consensus 2 ~~Kg~WT~EED~~L~~~V~~~G~~~W~~IA~~l-~~Rt~~qcr~Rw~~~L~p~lkkg~WT~EED~~Llelv~~~G~~Ws~ 80 (249)
++||+||+|||++|+++|++||..+|..||+.+ ++|+++|||+||.++|+|.+++++||.|||++|++++..||++|+.
T Consensus 23 lKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~~GnKWs~ 102 (249)
T PLN03212 23 MKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLGNRWSL 102 (249)
T ss_pred CcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHhccccHHH
Confidence 689999999999999999999998999999998 5999999999999999999999999999999999999999999999
Q ss_pred HhhhCCCCCHHHHHHHHHHHHHHHHhhh
Q 025697 81 IARLFPGRTDNAVKNHWHVIMARRCRER 108 (249)
Q Consensus 81 IA~~lpgRT~~~cknrW~~~lkr~~~~~ 108 (249)
||+.|||||+++|||||+.++++++...
T Consensus 103 IAk~LpGRTDnqIKNRWns~LrK~l~r~ 130 (249)
T PLN03212 103 IAGRIPGRTDNEIKNYWNTHLRKKLLRQ 130 (249)
T ss_pred HHhhcCCCCHHHHHHHHHHHHhHHHHhc
Confidence 9999999999999999999999887653
No 3
>PLN03091 hypothetical protein; Provisional
Probab=99.97 E-value=5.5e-31 Score=247.51 Aligned_cols=106 Identities=42% Similarity=0.889 Sum_probs=102.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCChhHhhHHh-cCCChhhhhhhhhcccCCCCCCCCCCHHHHHHHHHHHHHhCCchHH
Q 025697 2 CTRGHWRPAEDEKLRELVERYGPHNWNAIAEKL-QGRSGKSCRLRWFNQLDPRINRSPFTEEEEERLLASHRIHGNRWAV 80 (249)
Q Consensus 2 ~~Kg~WT~EED~~L~~~V~~~G~~~W~~IA~~l-~~Rt~~qcr~Rw~~~L~p~lkkg~WT~EED~~Llelv~~~G~~Ws~ 80 (249)
++||+||+|||++|+++|.+||..+|..||+.+ ++|+++|||+||.++|+|.+++++||.|||++|++++.+||++|+.
T Consensus 12 lrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k~~GnKWsk 91 (459)
T PLN03091 12 LRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHAVLGNRWSQ 91 (459)
T ss_pred CcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHHHhCcchHH
Confidence 579999999999999999999999999999988 4999999999999999999999999999999999999999999999
Q ss_pred HhhhCCCCCHHHHHHHHHHHHHHHHhh
Q 025697 81 IARLFPGRTDNAVKNHWHVIMARRCRE 107 (249)
Q Consensus 81 IA~~lpgRT~~~cknrW~~~lkr~~~~ 107 (249)
||+.|||||+++||+||+.+++++++.
T Consensus 92 IAk~LPGRTDnqIKNRWnslLKKklr~ 118 (459)
T PLN03091 92 IAAQLPGRTDNEIKNLWNSCLKKKLRQ 118 (459)
T ss_pred HHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999998774
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.76 E-value=1e-18 Score=170.12 Aligned_cols=92 Identities=32% Similarity=0.593 Sum_probs=88.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhcccCCCCCCCCCCHHHHHHHHHHHHHhC-CchHH
Q 025697 2 CTRGHWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQLDPRINRSPFTEEEEERLLASHRIHG-NRWAV 80 (249)
Q Consensus 2 ~~Kg~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~L~p~lkkg~WT~EED~~Llelv~~~G-~~Ws~ 80 (249)
+++|+||++||-+|+.+|++||..+|.+|-..+|+|+..|||+||.|.|+...|++.||-.||+.|+.+|.+|| ++|.+
T Consensus 358 ikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~~V~~YG~g~Wak 437 (939)
T KOG0049|consen 358 VKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLYAVKVYGKGNWAK 437 (939)
T ss_pred ccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHHhhccCceeecchHHHHHHHHHHccchHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999 89999
Q ss_pred HhhhCCCCCHHHH
Q 025697 81 IARLFPGRTDNAV 93 (249)
Q Consensus 81 IA~~lpgRT~~~c 93 (249)
||..||.||..|.
T Consensus 438 cA~~Lp~~t~~q~ 450 (939)
T KOG0049|consen 438 CAMLLPKKTSRQL 450 (939)
T ss_pred HHHHccccchhHH
Confidence 9999999999443
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.70 E-value=2.8e-17 Score=160.19 Aligned_cols=109 Identities=22% Similarity=0.481 Sum_probs=100.6
Q ss_pred CCCCCCHHHHHHHHHHHHHHCC---CChhHhhHHhcCCChhhhhhhhhcccCCCCCCCCCCHHHHHHHHHHHHHhC-Cch
Q 025697 3 TRGHWRPAEDEKLRELVERYGP---HNWNAIAEKLQGRSGKSCRLRWFNQLDPRINRSPFTEEEEERLLASHRIHG-NRW 78 (249)
Q Consensus 3 ~Kg~WT~EED~~L~~~V~~~G~---~~W~~IA~~l~~Rt~~qcr~Rw~~~L~p~lkkg~WT~EED~~Llelv~~~G-~~W 78 (249)
++..||+|||.+|+.+|..... .+|.+|-.+||||+..|..-||...|+|.+++|+||.+||.+|+.+|.+|| ..|
T Consensus 304 ~ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw 383 (939)
T KOG0049|consen 304 SEKEWSEEEDTKLIALVKITSINSHIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDW 383 (939)
T ss_pred HhhhcchhhhHHHHHHHHHhhccCccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccch
Confidence 4678999999999999998743 479999999999999999999999999999999999999999999999999 569
Q ss_pred HHHhhhCCCCCHHHHHHHHHHHHHHHHhhhhhH
Q 025697 79 AVIARLFPGRTDNAVKNHWHVIMARRCRERSRL 111 (249)
Q Consensus 79 s~IA~~lpgRT~~~cknrW~~~lkr~~~~~~~~ 111 (249)
.+|-..+|||++.||+.||...|.++.+...+.
T Consensus 384 ~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~rW~ 416 (939)
T KOG0049|consen 384 AKVRQAVPNRSDSQCRERYTNVLNRSAKVERWT 416 (939)
T ss_pred hhHHHhcCCccHHHHHHHHHHHHHHhhccCcee
Confidence 999999999999999999999999888765444
No 6
>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=99.69 E-value=3.9e-17 Score=115.17 Aligned_cols=60 Identities=53% Similarity=1.040 Sum_probs=54.9
Q ss_pred CCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhcccCCCCCCCCCCHHHHHHH
Q 025697 7 WRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQLDPRINRSPFTEEEEERL 67 (249)
Q Consensus 7 WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~L~p~lkkg~WT~EED~~L 67 (249)
||+|||++|+.+|..|| .+|..||+.|+.||+.+|+.||.++|.|.+++++||.+||.+|
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 5799999999779999999999999999999999999999987
No 7
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.58 E-value=9.7e-16 Score=146.46 Aligned_cols=109 Identities=30% Similarity=0.640 Sum_probs=103.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhcccCCCCCCCCCCHHHHHHHHHHHHHhCCchHH
Q 025697 1 MCTRGHWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQLDPRINRSPFTEEEEERLLASHRIHGNRWAV 80 (249)
Q Consensus 1 ~~~Kg~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~L~p~lkkg~WT~EED~~Llelv~~~G~~Ws~ 80 (249)
+|+.|.|+.-||+.|..+|.+||.+.|.+|+..++..+++||+.||..+|+|.+++..|+.|||++|+.+...+...|..
T Consensus 4 ~~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrt 83 (617)
T KOG0050|consen 4 EIKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRT 83 (617)
T ss_pred EEecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccch
Confidence 47889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhCCCCCHHHHHHHHHHHHHHHHhhhhh
Q 025697 81 IARLFPGRTDNAVKNHWHVIMARRCRERSR 110 (249)
Q Consensus 81 IA~~lpgRT~~~cknrW~~~lkr~~~~~~~ 110 (249)
||..| ||+.+||-.||..++-........
T Consensus 84 Ia~i~-gr~~~qc~eRy~~ll~~~~s~~~~ 112 (617)
T KOG0050|consen 84 IADIM-GRTSQQCLERYNNLLDVYVSYHYH 112 (617)
T ss_pred HHHHh-hhhHHHHHHHHHHHHHHHHhhhcc
Confidence 99999 999999999999998877765544
No 8
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.58 E-value=2.9e-15 Score=145.15 Aligned_cols=105 Identities=30% Similarity=0.630 Sum_probs=100.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhcccCCCCCCCCCCHHHHHHHHHHHHHhCCchHHH
Q 025697 2 CTRGHWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQLDPRINRSPFTEEEEERLLASHRIHGNRWAVI 81 (249)
Q Consensus 2 ~~Kg~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~L~p~lkkg~WT~EED~~Llelv~~~G~~Ws~I 81 (249)
.+.|.|+..||+.|..+|+.+|+.+|.+||..+..|++++|+.||+++++|.+++..|+.|||..|+.+..++|..|+.|
T Consensus 18 ~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~wsti 97 (512)
T COG5147 18 RKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQWSTI 97 (512)
T ss_pred ecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCchhhhh
Confidence 46799999999999999999999999999999988999999999999999999999999999999999999999999999
Q ss_pred hhhCCCCCHHHHHHHHHHHHHHHHh
Q 025697 82 ARLFPGRTDNAVKNHWHVIMARRCR 106 (249)
Q Consensus 82 A~~lpgRT~~~cknrW~~~lkr~~~ 106 (249)
|..+++|+..+|.++|...+.....
T Consensus 98 a~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 98 ADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred ccccCccchHHHHHHHHHHhhhhhc
Confidence 9999999999999999887766554
No 9
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.53 E-value=1.9e-14 Score=140.87 Aligned_cols=105 Identities=29% Similarity=0.609 Sum_probs=94.2
Q ss_pred CCCCCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhcccCCC--CCCCCCCHHHHHHHHHHHH-------H
Q 025697 3 TRGHWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQLDPR--INRSPFTEEEEERLLASHR-------I 73 (249)
Q Consensus 3 ~Kg~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~L~p~--lkkg~WT~EED~~Llelv~-------~ 73 (249)
.||.||+||++.|..++.++| ..|..|++.| ||.+..|++||+++...+ .+++.||.||++.|+.+|. +
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g-~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~q 460 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHG-NDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREALQ 460 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhc-ccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhhc
Confidence 799999999999999999999 5799999988 899999999999999887 4899999999999999995 3
Q ss_pred h-------------------CCchHHHhhhCCCCCHHHHHHHHHHHHHHHHhhhh
Q 025697 74 H-------------------GNRWAVIARLFPGRTDNAVKNHWHVIMARRCRERS 109 (249)
Q Consensus 74 ~-------------------G~~Ws~IA~~lpgRT~~~cknrW~~~lkr~~~~~~ 109 (249)
+ +.+|+.|++.+++|+..+|+.+|+.++.+..-...
T Consensus 461 ~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n~~ 515 (607)
T KOG0051|consen 461 PQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFNKR 515 (607)
T ss_pred ccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhhcc
Confidence 3 23699999999999999999999999887765443
No 10
>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=99.51 E-value=9e-15 Score=99.11 Aligned_cols=47 Identities=51% Similarity=0.985 Sum_probs=42.8
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCChhHhhHHhc-CCChhhhhhhhhccc
Q 025697 4 RGHWRPAEDEKLRELVERYGPHNWNAIAEKLQ-GRSGKSCRLRWFNQL 50 (249)
Q Consensus 4 Kg~WT~EED~~L~~~V~~~G~~~W~~IA~~l~-~Rt~~qcr~Rw~~~L 50 (249)
||+||+|||++|+++|.+||..+|..||..|| +||+.||+.||.++|
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 78999999999999999999877999999999 999999999999875
No 11
>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=4.2e-13 Score=90.89 Aligned_cols=46 Identities=37% Similarity=0.771 Sum_probs=41.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCCc-hHHHhhhCC-CCCHHHHHHHHHHHH
Q 025697 56 RSPFTEEEEERLLASHRIHGNR-WAVIARLFP-GRTDNAVKNHWHVIM 101 (249)
Q Consensus 56 kg~WT~EED~~Llelv~~~G~~-Ws~IA~~lp-gRT~~~cknrW~~~l 101 (249)
+++||+|||++|+++|.+||.. |..||..|| |||..||++||+.++
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 5799999999999999999977 999999999 999999999998763
No 12
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.24 E-value=1.1e-11 Score=81.87 Aligned_cols=48 Identities=50% Similarity=1.014 Sum_probs=44.9
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhcccC
Q 025697 4 RGHWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQLD 51 (249)
Q Consensus 4 Kg~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~L~ 51 (249)
++.||++||.+|+.++..||..+|..||..|++||+.+|+.||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 579999999999999999997789999999999999999999998764
No 13
>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=9e-12 Score=87.68 Aligned_cols=45 Identities=33% Similarity=0.554 Sum_probs=38.8
Q ss_pred CCHHHHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHHHHHHHHH
Q 025697 59 FTEEEEERLLASHRIHGNRWAVIARLFPGRTDNAVKNHWHVIMAR 103 (249)
Q Consensus 59 WT~EED~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr 103 (249)
||.|||++|+++|.+||.+|..||+.|+.||+.+|++||...++.
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~ 45 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRP 45 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTST
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcc
Confidence 999999999999999999999999999779999999999885543
No 14
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.21 E-value=2.5e-11 Score=80.08 Aligned_cols=47 Identities=34% Similarity=0.714 Sum_probs=43.9
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CchHHHhhhCCCCCHHHHHHHHHHHHH
Q 025697 56 RSPFTEEEEERLLASHRIHG-NRWAVIARLFPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 56 kg~WT~EED~~Llelv~~~G-~~Ws~IA~~lpgRT~~~cknrW~~~lk 102 (249)
+++||.+|+.+|+.++..|| .+|..||..||+||+.+|+.+|+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 46899999999999999999 999999999999999999999987653
No 15
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.17 E-value=3.8e-11 Score=106.71 Aligned_cols=73 Identities=18% Similarity=0.351 Sum_probs=61.9
Q ss_pred hcCCChhhhhhhhhcccCCCCCCCCCCHHHHHHHHHHHHHhC-CchHHHhhhC-CCCCHHHHHHHHHHHHHHHHhhhhhH
Q 025697 34 LQGRSGKSCRLRWFNQLDPRINRSPFTEEEEERLLASHRIHG-NRWAVIARLF-PGRTDNAVKNHWHVIMARRCRERSRL 111 (249)
Q Consensus 34 l~~Rt~~qcr~Rw~~~L~p~lkkg~WT~EED~~Llelv~~~G-~~Ws~IA~~l-pgRT~~~cknrW~~~lkr~~~~~~~~ 111 (249)
++.|+..-|.. +.+++++||+|||++|+++|.+|| .+|..||+.+ ++||..||+.||..+|+..+.+....
T Consensus 10 ~~~~~~pcc~K-------~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT 82 (249)
T PLN03212 10 VSKKTTPCCTK-------MGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGIT 82 (249)
T ss_pred CCCCCCCCccc-------CCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCC
Confidence 56677665533 578999999999999999999999 6899999988 59999999999999998888776554
Q ss_pred HH
Q 025697 112 YA 113 (249)
Q Consensus 112 ~~ 113 (249)
..
T Consensus 83 ~E 84 (249)
T PLN03212 83 SD 84 (249)
T ss_pred hH
Confidence 44
No 16
>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=99.09 E-value=1.3e-10 Score=75.50 Aligned_cols=45 Identities=51% Similarity=0.960 Sum_probs=42.1
Q ss_pred CCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhccc
Q 025697 6 HWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQL 50 (249)
Q Consensus 6 ~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~L 50 (249)
+||++||+.|+.++..||..+|..||..+++|++.+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999778999999999999999999998753
No 17
>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=99.08 E-value=2.3e-10 Score=74.31 Aligned_cols=43 Identities=42% Similarity=0.825 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHHHHHhC-CchHHHhhhCCCCCHHHHHHHHHHH
Q 025697 58 PFTEEEEERLLASHRIHG-NRWAVIARLFPGRTDNAVKNHWHVI 100 (249)
Q Consensus 58 ~WT~EED~~Llelv~~~G-~~Ws~IA~~lpgRT~~~cknrW~~~ 100 (249)
+||.+|+..|+.++.++| .+|..||..+++||..+|+++|..+
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 599999999999999999 9999999999999999999999765
No 18
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.06 E-value=3.1e-10 Score=111.65 Aligned_cols=113 Identities=23% Similarity=0.322 Sum_probs=92.9
Q ss_pred CCCCCCHHHHHHHHHHHHHHC----CC-------------------ChhHhhHHhcCCChhhhhhhhhcccCCCC-CCCC
Q 025697 3 TRGHWRPAEDEKLRELVERYG----PH-------------------NWNAIAEKLQGRSGKSCRLRWFNQLDPRI-NRSP 58 (249)
Q Consensus 3 ~Kg~WT~EED~~L~~~V~~~G----~~-------------------~W~~IA~~l~~Rt~~qcr~Rw~~~L~p~l-kkg~ 58 (249)
+-+.|+.+||..|...|..|- -. =|+.|...||.|+..+++.+-++...|.- ++|.
T Consensus 307 ~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp~R~~~siy~~~rR~y~~FE~~rg~ 386 (607)
T KOG0051|consen 307 NLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLPYRDRKSIYHHLRRAYTPFENKRGK 386 (607)
T ss_pred hhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcCcccchhHHHHHHhcCCccccccCC
Confidence 448899999999999999771 00 17888888999999999885555555544 9999
Q ss_pred CCHHHHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHHHHHHHHHHHhhhhhHHHHHH
Q 025697 59 FTEEEEERLLASHRIHGNRWAVIARLFPGRTDNAVKNHWHVIMARRCRERSRLYAKRA 116 (249)
Q Consensus 59 WT~EED~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr~~~~~~~~~~~~~ 116 (249)
||+||++.|..+|.++|+.|..|++.| ||.+.+|+.+|..+++..-......|+..+
T Consensus 387 wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eE 443 (607)
T KOG0051|consen 387 WTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEE 443 (607)
T ss_pred CCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHH
Confidence 999999999999999999999999999 999999999999998877543444444433
No 19
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.96 E-value=4.2e-10 Score=100.24 Aligned_cols=62 Identities=16% Similarity=0.308 Sum_probs=54.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhC-CchHHHhhhCC-CCCHHHHHHHHHHHHHHHHhhhhhHHH
Q 025697 52 PRINRSPFTEEEEERLLASHRIHG-NRWAVIARLFP-GRTDNAVKNHWHVIMARRCRERSRLYA 113 (249)
Q Consensus 52 p~lkkg~WT~EED~~Llelv~~~G-~~Ws~IA~~lp-gRT~~~cknrW~~~lkr~~~~~~~~~~ 113 (249)
+.+.+|+||.|||++|+++|.+|| ++|..||+.++ +|+..+||-||..+|+..++++.....
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~e 68 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDE 68 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHH
Confidence 344579999999999999999999 67999999999 999999999999999999886554443
No 20
>PLN03091 hypothetical protein; Provisional
Probab=98.96 E-value=5.8e-10 Score=106.04 Aligned_cols=59 Identities=15% Similarity=0.372 Sum_probs=52.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhC-CchHHHhhhCC-CCCHHHHHHHHHHHHHHHHhhhh
Q 025697 51 DPRINRSPFTEEEEERLLASHRIHG-NRWAVIARLFP-GRTDNAVKNHWHVIMARRCRERS 109 (249)
Q Consensus 51 ~p~lkkg~WT~EED~~Llelv~~~G-~~Ws~IA~~lp-gRT~~~cknrW~~~lkr~~~~~~ 109 (249)
++.+++++||.|||++|+++|.+|| ++|..||+.++ ||+..||+.||..+|...+.+..
T Consensus 9 KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgp 69 (459)
T PLN03091 9 KQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGT 69 (459)
T ss_pred CCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCC
Confidence 3578999999999999999999999 67999999885 99999999999988877766543
No 21
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=98.41 E-value=3.7e-08 Score=96.07 Aligned_cols=98 Identities=29% Similarity=0.533 Sum_probs=85.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhcccCC--CCCCCCCCHHHHHHHHHHHHHhC----
Q 025697 2 CTRGHWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQLDP--RINRSPFTEEEEERLLASHRIHG---- 75 (249)
Q Consensus 2 ~~Kg~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~L~p--~lkkg~WT~EED~~Llelv~~~G---- 75 (249)
-.+|.||.+|+..|...+..+|+ .|..|...+ +|-+..|++||.++... .+++++|+.||+.+|...+...-
T Consensus 289 ~~~~~wt~e~~~eL~~~~~~~~~-~w~~ig~~~-~rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e~~~~~~ 366 (512)
T COG5147 289 EQRGKWTKEEEQELAKLVVEHGG-SWTEIGKLL-GRMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNEMRLEAQ 366 (512)
T ss_pred hhhccCccccccccccccccccc-hhhHhhhhh-ccCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHHHHHHHh
Confidence 35899999999999999999995 599999877 89999999999999888 67888999999999998876432
Q ss_pred ----CchHHHhhhCCCCCHHHHHHHHHHHH
Q 025697 76 ----NRWAVIARLFPGRTDNAVKNHWHVIM 101 (249)
Q Consensus 76 ----~~Ws~IA~~lpgRT~~~cknrW~~~l 101 (249)
..|..|+..+++|....|+.++.++.
T Consensus 367 ~~~~~~~~li~~~~~~~~~~~~~~~~~~~~ 396 (512)
T COG5147 367 QSSRILWLLIAQNIRNRLQHHCRDKYGVLI 396 (512)
T ss_pred hhhhhhHHHHHHhhhccccCCCCCcccccc
Confidence 36999999999999999988775543
No 22
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.98 E-value=5.5e-06 Score=78.92 Aligned_cols=47 Identities=26% Similarity=0.608 Sum_probs=44.5
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhccc
Q 025697 4 RGHWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQL 50 (249)
Q Consensus 4 Kg~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~L 50 (249)
.+.||.+|+-+|+++++.||.+||..||.+++.|+...|+++|.+++
T Consensus 72 ~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 72 DPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHH
Confidence 46799999999999999999999999999999999999999998864
No 23
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.96 E-value=1.4e-05 Score=56.39 Aligned_cols=49 Identities=14% Similarity=0.266 Sum_probs=42.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCh---hHhhHHhc-CC-Chhhhhhhhhccc
Q 025697 2 CTRGHWRPAEDEKLRELVERYGPHNW---NAIAEKLQ-GR-SGKSCRLRWFNQL 50 (249)
Q Consensus 2 ~~Kg~WT~EED~~L~~~V~~~G~~~W---~~IA~~l~-~R-t~~qcr~Rw~~~L 50 (249)
++|-.||+||..+++++|+.+|.++| ..|++.|. .| |..||+.++..|.
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 35778999999999999999998799 99999884 46 9999999987764
No 24
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.80 E-value=3.6e-05 Score=73.48 Aligned_cols=49 Identities=27% Similarity=0.383 Sum_probs=44.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHhC-CchHHHhhhCCCCCHHHHHHHHHHHHH
Q 025697 54 INRSPFTEEEEERLLASHRIHG-NRWAVIARLFPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 54 lkkg~WT~EED~~Llelv~~~G-~~Ws~IA~~lpgRT~~~cknrW~~~lk 102 (249)
+-...||.+|+.+|++++..|| |+|..||.+++.||..+|+.||..+.-
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 3456899999999999999999 999999999999999999999976653
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=97.74 E-value=8.8e-05 Score=52.31 Aligned_cols=46 Identities=26% Similarity=0.413 Sum_probs=40.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-ch---HHHhhhCC-CC-CHHHHHHHHHHHH
Q 025697 56 RSPFTEEEEERLLASHRIHGN-RW---AVIARLFP-GR-TDNAVKNHWHVIM 101 (249)
Q Consensus 56 kg~WT~EED~~Llelv~~~G~-~W---s~IA~~lp-gR-T~~~cknrW~~~l 101 (249)
+-.||+||..++++++..+|. +| ..|++.+. .| |..+|+.|.+.+.
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 458999999999999999995 99 99999875 45 9999999987654
No 26
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.69 E-value=3.3e-05 Score=75.04 Aligned_cols=82 Identities=18% Similarity=0.245 Sum_probs=64.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHhC-CchHHHhhhCCCCCHHHHHHHHHHHHHHHHhhhhhHHHHHHHhhhhcCCCCCCCCCC
Q 025697 54 INRSPFTEEEEERLLASHRIHG-NRWAVIARLFPGRTDNAVKNHWHVIMARRCRERSRLYAKRAAQTFLNDQKSSSSSRP 132 (249)
Q Consensus 54 lkkg~WT~EED~~Llelv~~~G-~~Ws~IA~~lpgRT~~~cknrW~~~lkr~~~~~~~~~~~~~~~~~~~~~~sS~ss~p 132 (249)
++.|-|+.-||+.|-.+|.+|| +.|++|++.++-.|..||++||..++...++...+............-.-+..+..+
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 5678999999999999999999 789999999999999999999999999998877666655554443333444444444
Q ss_pred CCC
Q 025697 133 NHH 135 (249)
Q Consensus 133 ~~~ 135 (249)
.+.
T Consensus 85 a~i 87 (617)
T KOG0050|consen 85 ADI 87 (617)
T ss_pred HHH
Confidence 443
No 27
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.49 E-value=0.0005 Score=60.02 Aligned_cols=95 Identities=21% Similarity=0.463 Sum_probs=72.0
Q ss_pred CCCHHHHHHHHHHHHHHCCCChhHhhHHhc---CCChhhhhhhhhccc----------------CCC-----CCCCCCCH
Q 025697 6 HWRPAEDEKLRELVERYGPHNWNAIAEKLQ---GRSGKSCRLRWFNQL----------------DPR-----INRSPFTE 61 (249)
Q Consensus 6 ~WT~EED~~L~~~V~~~G~~~W~~IA~~l~---~Rt~~qcr~Rw~~~L----------------~p~-----lkkg~WT~ 61 (249)
+|++++|-.|+.+|..-. +-..|+..++ .-|...+..||+.+| .|. ..+.+||.
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 699999999999999766 6777877653 467788899998865 221 14668999
Q ss_pred HHHHHHHHHHHHhCC---chHHHhh-----hCCCCCHHHHHHHHHHHHH
Q 025697 62 EEEERLLASHRIHGN---RWAVIAR-----LFPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 62 EED~~Llelv~~~G~---~Ws~IA~-----~lpgRT~~~cknrW~~~lk 102 (249)
+|+++|......... .+.+|-. .-++||+.++.++|..+.+
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkq 127 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQ 127 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHH
Confidence 999999997765542 4666632 3468999999999975543
No 28
>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=97.41 E-value=0.00038 Score=58.66 Aligned_cols=60 Identities=22% Similarity=0.322 Sum_probs=50.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhC---C----chHHHhhhCCCCCHHHHHHHHHHHHHHHHhhhhhHHHHH
Q 025697 55 NRSPFTEEEEERLLASHRIHG---N----RWAVIARLFPGRTDNAVKNHWHVIMARRCRERSRLYAKR 115 (249)
Q Consensus 55 kkg~WT~EED~~Llelv~~~G---~----~Ws~IA~~lpgRT~~~cknrW~~~lkr~~~~~~~~~~~~ 115 (249)
....||.|||.+|.+.|..|- + -...++..| +||+.+|.=||+..++++.........+.
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~~i~~AKkq 69 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEEAIELAKKQ 69 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHHHHHHHHHH
Confidence 345899999999999998873 2 278888899 99999999999999999988776655543
No 29
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.22 E-value=0.00032 Score=67.69 Aligned_cols=46 Identities=24% Similarity=0.546 Sum_probs=42.3
Q ss_pred CCCCCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhcc
Q 025697 3 TRGHWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQ 49 (249)
Q Consensus 3 ~Kg~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~ 49 (249)
....||.+|.-+|+++|+.|| .+|.+||.++++|+..||..|+.++
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 456899999999999999999 5799999999999999999999764
No 30
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.21 E-value=0.00032 Score=68.93 Aligned_cols=45 Identities=31% Similarity=0.696 Sum_probs=42.1
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhcc
Q 025697 4 RGHWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQ 49 (249)
Q Consensus 4 Kg~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~ 49 (249)
++.||.+|+-+|+++|+.|| .+|.+||.++++||..||..++.++
T Consensus 253 ~~~WT~qE~lLLLE~ie~y~-ddW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 253 RPNWTEQETLLLLEAIEMYG-DDWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred CCCccHHHHHHHHHHHHHhc-ccHHHHHhccCCCCHHHHHHHHHhc
Confidence 68899999999999999999 5799999999999999999998763
No 31
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.18 E-value=0.0004 Score=67.03 Aligned_cols=44 Identities=20% Similarity=0.325 Sum_probs=41.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHHHHH
Q 025697 56 RSPFTEEEEERLLASHRIHGNRWAVIARLFPGRTDNAVKNHWHV 99 (249)
Q Consensus 56 kg~WT~EED~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknrW~~ 99 (249)
..+||.+|..+|++.+..||-.|.+||.++++||..||.-||..
T Consensus 279 dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~ 322 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQ 322 (531)
T ss_pred cccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHc
Confidence 34899999999999999999999999999999999999999943
No 32
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.12 E-value=0.00063 Score=66.86 Aligned_cols=44 Identities=20% Similarity=0.348 Sum_probs=41.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHHHH
Q 025697 55 NRSPFTEEEEERLLASHRIHGNRWAVIARLFPGRTDNAVKNHWH 98 (249)
Q Consensus 55 kkg~WT~EED~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknrW~ 98 (249)
-+..||.+|..+|++++..||-.|.+||.++++||..+|--++.
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL 295 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFL 295 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHH
Confidence 34689999999999999999999999999999999999999984
No 33
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.81 E-value=0.0012 Score=49.29 Aligned_cols=50 Identities=22% Similarity=0.424 Sum_probs=35.6
Q ss_pred CCCCHHHHHHHHHHHHH------hC--C------chHHHhhhCC----CCCHHHHHHHHHHHHHHHHh
Q 025697 57 SPFTEEEEERLLASHRI------HG--N------RWAVIARLFP----GRTDNAVKNHWHVIMARRCR 106 (249)
Q Consensus 57 g~WT~EED~~Llelv~~------~G--~------~Ws~IA~~lp----gRT~~~cknrW~~~lkr~~~ 106 (249)
..||.+|...|++++.. ++ + -|..||..|. .||+.||+++|..+.++...
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~ 69 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKK 69 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHC
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence 47999999999998876 21 1 3999998653 69999999999887665544
No 34
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.67 E-value=0.0014 Score=48.95 Aligned_cols=47 Identities=34% Similarity=0.632 Sum_probs=33.7
Q ss_pred CCCCCHHHHHHHHHHHHH--H----C--CC-----ChhHhhHHhc----CCChhhhhhhhhccc
Q 025697 4 RGHWRPAEDEKLRELVER--Y----G--PH-----NWNAIAEKLQ----GRSGKSCRLRWFNQL 50 (249)
Q Consensus 4 Kg~WT~EED~~L~~~V~~--~----G--~~-----~W~~IA~~l~----~Rt~~qcr~Rw~~~L 50 (249)
|..||.+|...|+.++.. + + .. -|..||..|. .||+.||+.+|.++.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~ 64 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLK 64 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 568999999999999987 2 1 11 3999999984 699999999998754
No 35
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.55 E-value=0.0057 Score=52.19 Aligned_cols=61 Identities=18% Similarity=0.306 Sum_probs=49.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCc-------hHHHhhhCCCCCHHHHHHHHHHHHHHHHhhhhhHHHHHH
Q 025697 55 NRSPFTEEEEERLLASHRIHGNR-------WAVIARLFPGRTDNAVKNHWHVIMARRCRERSRLYAKRA 116 (249)
Q Consensus 55 kkg~WT~EED~~Llelv~~~G~~-------Ws~IA~~lpgRT~~~cknrW~~~lkr~~~~~~~~~~~~~ 116 (249)
+...||.|+|.+|.+.|..|+.. ...++..| +||..+|.-||+.+++++.........+.-
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Yee~I~~AKK~R 71 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQEQIKLAKKER 71 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHHHHHHHHHHhh
Confidence 45689999999999999888732 55566777 899999999999999998887666555433
No 36
>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=96.54 E-value=0.0015 Score=55.18 Aligned_cols=48 Identities=25% Similarity=0.474 Sum_probs=40.6
Q ss_pred CCCCCCHHHHHHHHHHHHHHCCC------ChhHhhHHhcCCChhhhhhhhhcccC
Q 025697 3 TRGHWRPAEDEKLRELVERYGPH------NWNAIAEKLQGRSGKSCRLRWFNQLD 51 (249)
Q Consensus 3 ~Kg~WT~EED~~L~~~V~~~G~~------~W~~IA~~l~~Rt~~qcr~Rw~~~L~ 51 (249)
+.-.||.|||.+|.+.|-+|-.. .+..++..| +||+..|.-||+.+++
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VR 56 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVR 56 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHH
Confidence 56789999999999999999311 377888877 8999999999998875
No 37
>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=96.49 E-value=0.0025 Score=46.08 Aligned_cols=50 Identities=26% Similarity=0.426 Sum_probs=32.7
Q ss_pred CCCCCHHHHHHHHHHHHHHCC------CC--hhHhhHHhc-CCChhhhhhhhhcccCCC
Q 025697 4 RGHWRPAEDEKLRELVERYGP------HN--WNAIAEKLQ-GRSGKSCRLRWFNQLDPR 53 (249)
Q Consensus 4 Kg~WT~EED~~L~~~V~~~G~------~~--W~~IA~~l~-~Rt~~qcr~Rw~~~L~p~ 53 (249)
|-++|.+||..|+.+|..+.. +| |..+++.-+ .+|-.+-++||...|.+.
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 568999999999999976531 12 999999888 888889999999988764
No 38
>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=96.42 E-value=0.0055 Score=44.31 Aligned_cols=50 Identities=24% Similarity=0.406 Sum_probs=31.7
Q ss_pred CCCCCHHHHHHHHHHHHHhC-------C--chHHHhhhCC-CCCHHHHHHHHHHHHHHHH
Q 025697 56 RSPFTEEEEERLLASHRIHG-------N--RWAVIARLFP-GRTDNAVKNHWHVIMARRC 105 (249)
Q Consensus 56 kg~WT~EED~~Llelv~~~G-------~--~Ws~IA~~lp-gRT~~~cknrW~~~lkr~~ 105 (249)
+.++|.+||..|++.|..+. + -|..+++.-| .+|-.+.++||...++.+.
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 45899999999999996652 1 2999999877 8999999999976665543
No 39
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=96.35 E-value=0.048 Score=58.15 Aligned_cols=107 Identities=14% Similarity=0.277 Sum_probs=82.9
Q ss_pred CCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhh-------hhcc------c----------------------
Q 025697 6 HWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLR-------WFNQ------L---------------------- 50 (249)
Q Consensus 6 ~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~R-------w~~~------L---------------------- 50 (249)
.||.-+=..++.+..+||..+-..||..|.++|...++.. |..+ +
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~~~ 905 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAIGK 905 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5999999999999999998899999999988888776532 1111 0
Q ss_pred ---------------CCCCCCCCCCHHHHHHHHHHHHHhC-CchHHHhhh------------CCCCCHHHHHHHHHHHHH
Q 025697 51 ---------------DPRINRSPFTEEEEERLLASHRIHG-NRWAVIARL------------FPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 51 ---------------~p~lkkg~WT~EED~~Llelv~~~G-~~Ws~IA~~------------lpgRT~~~cknrW~~~lk 102 (249)
-+..++..+|+|||..|+-++.+|| ++|..|-.. +..||+..+..|..++++
T Consensus 906 k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~ 985 (1033)
T PLN03142 906 KLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIR 985 (1033)
T ss_pred HHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHH
Confidence 1222344699999999999999999 789999432 357999999999999988
Q ss_pred HHHhhhhhHH
Q 025697 103 RRCRERSRLY 112 (249)
Q Consensus 103 r~~~~~~~~~ 112 (249)
-..+......
T Consensus 986 ~~~~e~~~~~ 995 (1033)
T PLN03142 986 LIEKENQEYD 995 (1033)
T ss_pred HHHHHHhhhh
Confidence 7766544433
No 40
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.31 E-value=0.0026 Score=59.06 Aligned_cols=47 Identities=23% Similarity=0.483 Sum_probs=43.6
Q ss_pred CCCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhcccC
Q 025697 5 GHWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQLD 51 (249)
Q Consensus 5 g~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~L~ 51 (249)
-.|+.+|+-+|++.....|-+||..||.+++.|+...|+.+|..++.
T Consensus 64 e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 64 EGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 36999999999999999999999999999999999999999987653
No 41
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=96.29 E-value=0.0076 Score=44.13 Aligned_cols=48 Identities=35% Similarity=0.529 Sum_probs=39.8
Q ss_pred CCCCCCHHHHHHHHHHHHHH-----CCC-----------ChhHhhHHhc-----CCChhhhhhhhhccc
Q 025697 3 TRGHWRPAEDEKLRELVERY-----GPH-----------NWNAIAEKLQ-----GRSGKSCRLRWFNQL 50 (249)
Q Consensus 3 ~Kg~WT~EED~~L~~~V~~~-----G~~-----------~W~~IA~~l~-----~Rt~~qcr~Rw~~~L 50 (249)
.+..||++|...|+++|.+| |.. -|..|+..|. .|+..+|+..|.++.
T Consensus 1 R~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk 69 (78)
T PF13873_consen 1 RKPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLK 69 (78)
T ss_pred CCCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 35789999999999999988 211 2999999982 599999999998864
No 42
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.28 E-value=0.0047 Score=57.41 Aligned_cols=47 Identities=21% Similarity=0.395 Sum_probs=42.7
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CchHHHhhhCCCCCHHHHHHHHHHHHH
Q 025697 56 RSPFTEEEEERLLASHRIHG-NRWAVIARLFPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 56 kg~WT~EED~~Llelv~~~G-~~Ws~IA~~lpgRT~~~cknrW~~~lk 102 (249)
-..|+.+|+.+|++.....| ++|..||.+++.|+...||.||..+.-
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 34699999999999999999 999999999999999999999976554
No 43
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=96.04 E-value=0.019 Score=41.94 Aligned_cols=49 Identities=27% Similarity=0.485 Sum_probs=39.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-----------------chHHHhhhC-----CCCCHHHHHHHHHHHHHHH
Q 025697 56 RSPFTEEEEERLLASHRIHGN-----------------RWAVIARLF-----PGRTDNAVKNHWHVIMARR 104 (249)
Q Consensus 56 kg~WT~EED~~Llelv~~~G~-----------------~Ws~IA~~l-----pgRT~~~cknrW~~~lkr~ 104 (249)
...||.+|...|++++.+|.. -|..|+..| +.||..+++.+|..+...-
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~ 72 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKA 72 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHH
Confidence 457999999999999988731 399998754 2699999999998775443
No 44
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.47 E-value=0.0089 Score=51.02 Aligned_cols=49 Identities=22% Similarity=0.500 Sum_probs=38.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCC------hhHhhHHhcCCChhhhhhhhhcccC
Q 025697 2 CTRGHWRPAEDEKLRELVERYGPHN------WNAIAEKLQGRSGKSCRLRWFNQLD 51 (249)
Q Consensus 2 ~~Kg~WT~EED~~L~~~V~~~G~~~------W~~IA~~l~~Rt~~qcr~Rw~~~L~ 51 (249)
.+...||.|||.+|.+.|..|+... ...++..| +|+..+|..||+.+++
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vr 57 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVR 57 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHH
Confidence 3567899999999999999997543 44444445 7999999999977665
No 45
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=93.27 E-value=0.78 Score=44.73 Aligned_cols=53 Identities=13% Similarity=0.162 Sum_probs=46.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHHHHHHHHHHHhh
Q 025697 55 NRSPFTEEEEERLLASHRIHGNRWAVIARLFPGRTDNAVKNHWHVIMARRCRE 107 (249)
Q Consensus 55 kkg~WT~EED~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr~~~~ 107 (249)
-...||.||--++-.+...||.+..+|.+.||.|+-..+..+|+...+.+-..
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK~~~~~ 238 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKKTREYD 238 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHHHhhHH
Confidence 45689999999999999999999999999999999999999998886665543
No 46
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=92.65 E-value=0.23 Score=46.38 Aligned_cols=56 Identities=20% Similarity=0.319 Sum_probs=43.8
Q ss_pred CCCCCHHHHHHHHHHHHHh----------CCchHHHhhhCC----CCCHHHHHHHHHHHHHHHHhhhhhH
Q 025697 56 RSPFTEEEEERLLASHRIH----------GNRWAVIARLFP----GRTDNAVKNHWHVIMARRCRERSRL 111 (249)
Q Consensus 56 kg~WT~EED~~Llelv~~~----------G~~Ws~IA~~lp----gRT~~~cknrW~~~lkr~~~~~~~~ 111 (249)
...|+.+|-..||++..+. +.-|..||+.+. -||+.+|+.+|..+.++..+.+...
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k~~~ 123 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEKAKK 123 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 3689999999999987653 235999998442 5999999999999988777654443
No 47
>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=91.06 E-value=0.4 Score=35.96 Aligned_cols=44 Identities=32% Similarity=0.482 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHHHh---CC----------chHHHhhhCC-----CCCHHHHHHHHHHHH
Q 025697 58 PFTEEEEERLLASHRIH---GN----------RWAVIARLFP-----GRTDNAVKNHWHVIM 101 (249)
Q Consensus 58 ~WT~EED~~Llelv~~~---G~----------~Ws~IA~~lp-----gRT~~~cknrW~~~l 101 (249)
.||++++..|++++.+. |+ .|..|+..|. ..+..+|++||..+.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk 62 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLK 62 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHH
Confidence 59999999999987543 21 3999987653 247899999996654
No 48
>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=90.94 E-value=0.54 Score=37.84 Aligned_cols=52 Identities=21% Similarity=0.352 Sum_probs=40.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC----chHHHhhh------------CCCCCHHHHHHHHHHHHHHH
Q 025697 53 RINRSPFTEEEEERLLASHRIHGN----RWAVIARL------------FPGRTDNAVKNHWHVIMARR 104 (249)
Q Consensus 53 ~lkkg~WT~EED~~Llelv~~~G~----~Ws~IA~~------------lpgRT~~~cknrW~~~lkr~ 104 (249)
..++..+|++||.-|+-++.+||- .|..|-.. +..||+..+..|-.++++-.
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 556779999999999999999995 79888653 24699999999998887644
No 49
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=90.80 E-value=0.23 Score=47.42 Aligned_cols=84 Identities=19% Similarity=0.329 Sum_probs=63.5
Q ss_pred ChhHhhHHhcCCChhhhhhhhhcccCCC-------------------------CCCCCCCHHHHHHHHHHHHHhCCchHH
Q 025697 26 NWNAIAEKLQGRSGKSCRLRWFNQLDPR-------------------------INRSPFTEEEEERLLASHRIHGNRWAV 80 (249)
Q Consensus 26 ~W~~IA~~l~~Rt~~qcr~Rw~~~L~p~-------------------------lkkg~WT~EED~~Llelv~~~G~~Ws~ 80 (249)
.|.-+.-..+.|...-...+|....++. +....||.+|-+-|+++++.|.-+|-.
T Consensus 75 ~W~w~pFtn~aRkD~~~l~HWvr~~d~~~dypfakfNk~vdipsYt~eEYe~~l~dn~WskeETD~LF~lck~fDLRf~V 154 (445)
T KOG2656|consen 75 PWKWVPFTNSARKDDATLHHWVRVGDTPKDYPFAKFNKHVDIPSYTDEEYEAHLNDNSWSKEETDYLFDLCKRFDLRFFV 154 (445)
T ss_pred CceeeccCCccccCCceEEeeeeccCCCCCCchhhhccccCccccchHHHHHhhccccccHHHHHHHHHHHHhcCeeEEE
Confidence 4666655556676666666776653221 123469999999999999999999999
Q ss_pred Hhhh-----CCC-CCHHHHHHHHHHHHHHHHhhhh
Q 025697 81 IARL-----FPG-RTDNAVKNHWHVIMARRCRERS 109 (249)
Q Consensus 81 IA~~-----lpg-RT~~~cknrW~~~lkr~~~~~~ 109 (249)
||.. ++. ||-..+|.||+.+.++.++-+.
T Consensus 155 IaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~ 189 (445)
T KOG2656|consen 155 IADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARA 189 (445)
T ss_pred EeeccchhhccccccHHHHHHHHHHHHHHHHHccC
Confidence 9875 665 9999999999998888776443
No 50
>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=90.67 E-value=0.29 Score=39.37 Aligned_cols=46 Identities=22% Similarity=0.412 Sum_probs=35.8
Q ss_pred CCCCCCHHHHHHHHHHHHHHCC---CChhHhhHHh------------cCCChhhhhhhhhc
Q 025697 3 TRGHWRPAEDEKLRELVERYGP---HNWNAIAEKL------------QGRSGKSCRLRWFN 48 (249)
Q Consensus 3 ~Kg~WT~EED~~L~~~V~~~G~---~~W~~IA~~l------------~~Rt~~qcr~Rw~~ 48 (249)
++..||.+||.-|+-++.+||- +.|..|...+ ..||+..+..|-..
T Consensus 48 ~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~t 108 (118)
T PF09111_consen 48 KKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNT 108 (118)
T ss_dssp S-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHH
T ss_pred CCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHH
Confidence 5678999999999999999998 7899998875 25888877777544
No 51
>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=89.60 E-value=0.44 Score=35.98 Aligned_cols=27 Identities=33% Similarity=0.716 Sum_probs=17.6
Q ss_pred CCCCCHHHHHHH--------HHHHHHHCCCChhHhhHH
Q 025697 4 RGHWRPAEDEKL--------RELVERYGPHNWNAIAEK 33 (249)
Q Consensus 4 Kg~WT~EED~~L--------~~~V~~~G~~~W~~IA~~ 33 (249)
.|-||+++|+.| ..++++|| +..|+..
T Consensus 47 ~GiWT~eDD~~L~~~~~~~~~~L~~khG---~~~i~~R 81 (87)
T PF11626_consen 47 PGIWTPEDDEMLRSGDKDDIERLIKKHG---EERIERR 81 (87)
T ss_dssp TT---HHHHHHHTS--HHHHHHHHHHH----HHHHHHH
T ss_pred CCCcCHHHHHHHHcCCHHHHHHHHHHhC---HHHHHHH
Confidence 688999999999 56667887 6777654
No 52
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=89.53 E-value=0.62 Score=44.56 Aligned_cols=44 Identities=23% Similarity=0.465 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHHHHHH
Q 025697 57 SPFTEEEEERLLASHRIHGNRWAVIARLFPGRTDNAVKNHWHVI 100 (249)
Q Consensus 57 g~WT~EED~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknrW~~~ 100 (249)
.+||.+|-+++..+...+|...+.|+..+|.|...|||.+|..-
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~E 409 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKE 409 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHH
Confidence 48999999999999999999999999999999999999998543
No 53
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=86.95 E-value=0.69 Score=47.52 Aligned_cols=43 Identities=12% Similarity=0.434 Sum_probs=39.7
Q ss_pred CCCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhc
Q 025697 5 GHWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFN 48 (249)
Q Consensus 5 g~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~ 48 (249)
-.||+.|..++.+++..|. .++..|++.++++|..+|-+.|+.
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 3699999999999999999 679999999999999999988765
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=85.59 E-value=1.4 Score=32.97 Aligned_cols=44 Identities=27% Similarity=0.554 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHHHH---CCC---------ChhHhhHHhcC-----CChhhhhhhhhcc
Q 025697 6 HWRPAEDEKLRELVERY---GPH---------NWNAIAEKLQG-----RSGKSCRLRWFNQ 49 (249)
Q Consensus 6 ~WT~EED~~L~~~V~~~---G~~---------~W~~IA~~l~~-----Rt~~qcr~Rw~~~ 49 (249)
+||+++++.|++++... |.. .|..|+..|.. .+..||+.||..+
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 59999999999998755 222 39999999842 4567888887654
No 55
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=85.47 E-value=0.92 Score=43.42 Aligned_cols=43 Identities=19% Similarity=0.413 Sum_probs=40.0
Q ss_pred CCCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhc
Q 025697 5 GHWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFN 48 (249)
Q Consensus 5 g~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~ 48 (249)
-+||.+|.+++..++...|. ++..|+..+|.|..+|++..|.+
T Consensus 366 ~~Ws~~e~ekFYKALs~wGt-dF~LIs~lfP~R~RkqIKaKfi~ 408 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGT-DFSLISSLFPNRERKQIKAKFIK 408 (507)
T ss_pred CcccHHHHHHHHHHHHHhcc-hHHHHHHhcCchhHHHHHHHHHH
Confidence 36999999999999999995 69999999999999999999876
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=84.67 E-value=3.2 Score=27.71 Aligned_cols=41 Identities=20% Similarity=0.337 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 025697 61 EEEEERLLASHRIHGNRWAVIARLFPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 61 ~EED~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknrW~~~lk 102 (249)
++++..++.++-..|-.|.+||..+ |.|...|+.+....++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARK 52 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHh
Confidence 4677888888888999999999999 8999999998766544
No 57
>smart00595 MADF subfamily of SANT domain.
Probab=84.65 E-value=3 Score=30.78 Aligned_cols=30 Identities=27% Similarity=0.426 Sum_probs=23.8
Q ss_pred chHHHhhhCCCCCHHHHHHHHHHHHHHHHhh
Q 025697 77 RWAVIARLFPGRTDNAVKNHWHVIMARRCRE 107 (249)
Q Consensus 77 ~Ws~IA~~lpgRT~~~cknrW~~~lkr~~~~ 107 (249)
-|..||..|+. |...|+.+|+.+-.+-.+.
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~LR~~y~~e 58 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKNLRDRYRRE 58 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHHHHHHHHHH
Confidence 39999999955 9999999998876554443
No 58
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=82.82 E-value=1.4 Score=41.16 Aligned_cols=46 Identities=28% Similarity=0.463 Sum_probs=37.1
Q ss_pred CCCCHHHHHHHHHHHHHH------C---CCChhHhhHHhc----CCChhhhhhhhhccc
Q 025697 5 GHWRPAEDEKLRELVERY------G---PHNWNAIAEKLQ----GRSGKSCRLRWFNQL 50 (249)
Q Consensus 5 g~WT~EED~~L~~~V~~~------G---~~~W~~IA~~l~----~Rt~~qcr~Rw~~~L 50 (249)
..|+.+|-..|+.+.... | ..-|..||..+. -|++.+|+.+|.++.
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 579999999999998743 1 124999999763 499999999998864
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=81.58 E-value=2.1 Score=27.98 Aligned_cols=38 Identities=29% Similarity=0.409 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhc
Q 025697 10 AEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFN 48 (249)
Q Consensus 10 EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~ 48 (249)
+=|.+|+.++...|...|..||+.+ |=+...|..|+..
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 4588899999999988999999988 8999999998764
No 60
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=77.18 E-value=2.7 Score=41.10 Aligned_cols=44 Identities=16% Similarity=0.320 Sum_probs=40.0
Q ss_pred CCCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhcc
Q 025697 5 GHWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQ 49 (249)
Q Consensus 5 g~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~ 49 (249)
-.||.||--++-++...|| .++.+|-+.||.|+-.++...|+..
T Consensus 188 d~WT~Ed~vlFe~aF~~~G-K~F~kIrq~LP~rsLaSlvqyYy~~ 231 (534)
T KOG1194|consen 188 DEWTAEDIVLFEQAFQFFG-KDFHKIRQALPHRSLASLVQYYYSW 231 (534)
T ss_pred ccchHHHHHHHHHHHHHhc-ccHHHHHHHccCccHHHHHHHHHHH
Confidence 4699999999999999999 5799999999999999999888654
No 61
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=76.93 E-value=4.6 Score=38.65 Aligned_cols=45 Identities=16% Similarity=0.197 Sum_probs=40.4
Q ss_pred CCCCHHHHHHHHHHHHHhCCchHHHhh-hCCCCCHHHHHHHHHHHH
Q 025697 57 SPFTEEEEERLLASHRIHGNRWAVIAR-LFPGRTDNAVKNHWHVIM 101 (249)
Q Consensus 57 g~WT~EED~~Llelv~~~G~~Ws~IA~-~lpgRT~~~cknrW~~~l 101 (249)
..|+++|...+-+.++.||+....|.. .+++|+--.|-.+|+...
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWK 323 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWK 323 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhh
Confidence 479999999999999999999999965 899999999998876653
No 62
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=76.77 E-value=3.1 Score=35.14 Aligned_cols=41 Identities=34% Similarity=0.340 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHHHHH
Q 025697 58 PFTEEEEERLLASHRIHGNRWAVIARLFPGRTDNAVKNHWHV 99 (249)
Q Consensus 58 ~WT~EED~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknrW~~ 99 (249)
.||+|..++|.+|. .-|..=++||..|+|.|.++|..+-+.
T Consensus 2 ~Wtde~~~~L~~lw-~~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 2 SWTDERVERLRKLW-AEGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred CCCHHHHHHHHHHH-HcCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 59999999999988 668889999999988999999988754
No 63
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=72.74 E-value=6.9 Score=39.70 Aligned_cols=51 Identities=18% Similarity=0.380 Sum_probs=42.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCCchHHH----------hhhCCCCCHHHHHHHHHHHHHHHHh
Q 025697 56 RSPFTEEEEERLLASHRIHGNRWAVI----------ARLFPGRTDNAVKNHWHVIMARRCR 106 (249)
Q Consensus 56 kg~WT~EED~~Llelv~~~G~~Ws~I----------A~~lpgRT~~~cknrW~~~lkr~~~ 106 (249)
+..||-.|+.-+..++.++|.+...| -..+.-+|..|++.+|+..+++...
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k 148 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNK 148 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHh
Confidence 55799999999999999999999888 2344557899999999888877654
No 64
>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=72.60 E-value=5.7 Score=28.38 Aligned_cols=31 Identities=29% Similarity=0.468 Sum_probs=23.6
Q ss_pred chHHHhhhCCC-CCHHHHHHHHHHHHHHHHhh
Q 025697 77 RWAVIARLFPG-RTDNAVKNHWHVIMARRCRE 107 (249)
Q Consensus 77 ~Ws~IA~~lpg-RT~~~cknrW~~~lkr~~~~ 107 (249)
-|..||..|+. -+...|+.+|..+...-.+.
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y~~~ 59 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRDRYRRE 59 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHHHHHHH
Confidence 39999999963 57889999998876544443
No 65
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=72.55 E-value=3.9 Score=33.66 Aligned_cols=45 Identities=16% Similarity=0.158 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhcccCCCC
Q 025697 9 PAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQLDPRI 54 (249)
Q Consensus 9 ~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~L~p~l 54 (249)
.+-|.+|+.+.+..|...|..||+.+ |-+...|+.|+.+....++
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 35789999999999988999999998 8999999999988765543
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=72.41 E-value=9.2 Score=24.94 Aligned_cols=38 Identities=18% Similarity=0.359 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHhC-CchHHHhhhCCCCCHHHHHHHHHHH
Q 025697 62 EEEERLLASHRIHG-NRWAVIARLFPGRTDNAVKNHWHVI 100 (249)
Q Consensus 62 EED~~Llelv~~~G-~~Ws~IA~~lpgRT~~~cknrW~~~ 100 (249)
+=|..|+.+...-| -.|..||+.+ |=|...|..|+..+
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 45778888888888 5699999999 77999999998654
No 67
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=72.02 E-value=7.5 Score=40.27 Aligned_cols=45 Identities=7% Similarity=0.065 Sum_probs=41.2
Q ss_pred CCCCHHHHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHHHHHHH
Q 025697 57 SPFTEEEEERLLASHRIHGNRWAVIARLFPGRTDNAVKNHWHVIM 101 (249)
Q Consensus 57 g~WT~EED~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknrW~~~l 101 (249)
..||..|-.++-+++-.|.+..-.|++.++++|-.+|-.+|+...
T Consensus 620 d~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtWK 664 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTWK 664 (907)
T ss_pred ccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHHH
Confidence 479999999999999999999999999999999999998876553
No 68
>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=71.74 E-value=21 Score=33.65 Aligned_cols=55 Identities=22% Similarity=0.429 Sum_probs=42.2
Q ss_pred CCCCCHHHHHHHHHHHHHh-CC---chHHHhhhCCCCCHHHHHHHHHHHHHHHHhhhhh
Q 025697 56 RSPFTEEEEERLLASHRIH-GN---RWAVIARLFPGRTDNAVKNHWHVIMARRCRERSR 110 (249)
Q Consensus 56 kg~WT~EED~~Llelv~~~-G~---~Ws~IA~~lpgRT~~~cknrW~~~lkr~~~~~~~ 110 (249)
-..||.-|...|+.+..-. |. .-+.|++.++||+..+|++.-..+..|..+...+
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rvareaiq 79 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRVAREAIQ 79 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 4579999999888876554 43 3578899999999999999887776666654433
No 69
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=70.10 E-value=4.3 Score=33.85 Aligned_cols=45 Identities=13% Similarity=0.139 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhcccCCCC
Q 025697 9 PAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQLDPRI 54 (249)
Q Consensus 9 ~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~L~p~l 54 (249)
.+-|.+|+.+.+..|...|..||+.+ |-+...|+.|+.++...++
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 45689999999999988999999999 8999999999988766544
No 70
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=67.86 E-value=13 Score=30.51 Aligned_cols=45 Identities=11% Similarity=0.180 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHhC-CchHHHhhhCCCCCHHHHHHHHHHHHHHHHh
Q 025697 61 EEEEERLLASHRIHG-NRWAVIARLFPGRTDNAVKNHWHVIMARRCR 106 (249)
Q Consensus 61 ~EED~~Llelv~~~G-~~Ws~IA~~lpgRT~~~cknrW~~~lkr~~~ 106 (249)
.+-|..|+.+..+-| ..|+.||+.+ |-|...|..|++.+.....-
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 357888888888888 6799999999 88999999999777665543
No 71
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=67.57 E-value=9.3 Score=38.79 Aligned_cols=48 Identities=10% Similarity=0.399 Sum_probs=36.6
Q ss_pred CCCCCCHHHHHHHHHHHHHHCCCChhHhhHHh-c---------CCChhhhhhhhhcccC
Q 025697 3 TRGHWRPAEDEKLRELVERYGPHNWNAIAEKL-Q---------GRSGKSCRLRWFNQLD 51 (249)
Q Consensus 3 ~Kg~WT~EED~~L~~~V~~~G~~~W~~IA~~l-~---------~Rt~~qcr~Rw~~~L~ 51 (249)
+|..||-.|...+..++..+| .++.+|-..+ . -++-.|+|.+|++.+.
T Consensus 87 ~ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~ 144 (782)
T KOG4468|consen 87 AKTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVR 144 (782)
T ss_pred cccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHH
Confidence 367899999999999999999 5798883332 2 2555788888876543
No 72
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=62.88 E-value=15 Score=30.62 Aligned_cols=45 Identities=7% Similarity=0.076 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHhC-CchHHHhhhCCCCCHHHHHHHHHHHHHHHHh
Q 025697 61 EEEEERLLASHRIHG-NRWAVIARLFPGRTDNAVKNHWHVIMARRCR 106 (249)
Q Consensus 61 ~EED~~Llelv~~~G-~~Ws~IA~~lpgRT~~~cknrW~~~lkr~~~ 106 (249)
.+-|.+|+.+..+-| -.|+.||+.+ |=|...|..|++.+.+...-
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 567888888888888 5799999999 88999999999887766653
No 73
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=60.15 E-value=9.6 Score=41.15 Aligned_cols=45 Identities=16% Similarity=0.262 Sum_probs=35.4
Q ss_pred CCCCCCHHHHHHHHHHHHHHCCCChhHhhHHhc------------CCChhhhhhhhh
Q 025697 3 TRGHWRPAEDEKLRELVERYGPHNWNAIAEKLQ------------GRSGKSCRLRWF 47 (249)
Q Consensus 3 ~Kg~WT~EED~~L~~~V~~~G~~~W~~IA~~l~------------~Rt~~qcr~Rw~ 47 (249)
++..+|.|||.-|+-++.+||-++|..|...+. .||+..+..|-.
T Consensus 925 ~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~ 981 (1033)
T PLN03142 925 KGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCD 981 (1033)
T ss_pred CCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHH
Confidence 345699999999999999999999999977651 466666665543
No 74
>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=58.30 E-value=31 Score=22.58 Aligned_cols=41 Identities=15% Similarity=0.222 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHHHHHHHHH
Q 025697 62 EEEERLLASHRIHGNRWAVIARLFPGRTDNAVKNHWHVIMAR 103 (249)
Q Consensus 62 EED~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr 103 (249)
+++..++.++=-.|..+..||..+ |-|...|+.+-...+++
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 455566666555667899999999 77999999887666654
No 75
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=58.16 E-value=21 Score=31.30 Aligned_cols=44 Identities=14% Similarity=0.249 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHHHhCCchHHHhhh--CCC-CCHHHHHHHHHHHHH
Q 025697 58 PFTEEEEERLLASHRIHGNRWAVIARL--FPG-RTDNAVKNHWHVIMA 102 (249)
Q Consensus 58 ~WT~EED~~Llelv~~~G~~Ws~IA~~--lpg-RT~~~cknrW~~~lk 102 (249)
.|+.++|-.|+.+|. .|+.-..|+.. |.. -|-..+..||+.+|=
T Consensus 1 rW~~~DDl~Li~av~-~~~~L~~v~~gvkFS~~fT~~Ei~~RW~~lly 47 (199)
T PF13325_consen 1 RWKPEDDLLLINAVE-QTNDLESVHLGVKFSCKFTLQEIEERWYALLY 47 (199)
T ss_pred CCCchhhHHHHHHHH-HhcCHHHHHccCCcCCcCcHHHHHHHHHHHHc
Confidence 499999999999885 45555555543 332 388999999998874
No 76
>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=57.47 E-value=30 Score=27.26 Aligned_cols=30 Identities=20% Similarity=0.314 Sum_probs=24.3
Q ss_pred HhCCchHHHhhhCCCCCHHHHHHHHHHHHHH
Q 025697 73 IHGNRWAVIARLFPGRTDNAVKNHWHVIMAR 103 (249)
Q Consensus 73 ~~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr 103 (249)
..|-.+..||..+ |.|..+|+++.....++
T Consensus 127 ~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 127 FEGKSYKEIAEEL-GISVKTVEYHISKALKE 156 (161)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3467899999999 88999999998776443
No 77
>smart00595 MADF subfamily of SANT domain.
Probab=56.64 E-value=5.8 Score=29.15 Aligned_cols=22 Identities=45% Similarity=0.835 Sum_probs=19.6
Q ss_pred hhHhhHHhcCCChhhhhhhhhcc
Q 025697 27 WNAIAEKLQGRSGKSCRLRWFNQ 49 (249)
Q Consensus 27 W~~IA~~l~~Rt~~qcr~Rw~~~ 49 (249)
|..||..|+. ++..|+.+|.++
T Consensus 30 W~~Ia~~l~~-~~~~~~~kw~~L 51 (89)
T smart00595 30 WEEIAEELGL-SVEECKKRWKNL 51 (89)
T ss_pred HHHHHHHHCc-CHHHHHHHHHHH
Confidence 9999999954 999999999875
No 78
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=56.12 E-value=14 Score=26.70 Aligned_cols=44 Identities=34% Similarity=0.704 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhcccCCC-------CCCCCCCHHHHHHH
Q 025697 12 DEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQLDPR-------INRSPFTEEEEERL 67 (249)
Q Consensus 12 D~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~L~p~-------lkkg~WT~EED~~L 67 (249)
+.+|.++|+.|| |..+++.++-|+-. -+|. +++.||-.+..+.|
T Consensus 12 e~il~~Lv~~yG---W~~L~~~i~i~CF~---------~~PsikSSLkFLRkTpWAR~KVE~l 62 (64)
T PF09905_consen 12 ETILTELVEHYG---WEELGERININCFK---------NNPSIKSSLKFLRKTPWAREKVENL 62 (64)
T ss_dssp HHHHHHHHHHT----HHHHHHHTTSSSTT---------SS--HHHHHHHHHHSHHHHHHHHHH
T ss_pred HHHHHHHHHHhC---HHHHHhhcccccCC---------CCCchHHHHHHHhcCHhHHHHHHHh
Confidence 568899999999 99999998765531 2232 34567777665544
No 79
>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=55.83 E-value=28 Score=25.80 Aligned_cols=37 Identities=19% Similarity=0.394 Sum_probs=26.2
Q ss_pred HHHHHHHHhCC--------chHHHhhhCCCC---C--HHHHHHHHHHHHH
Q 025697 66 RLLASHRIHGN--------RWAVIARLFPGR---T--DNAVKNHWHVIMA 102 (249)
Q Consensus 66 ~Llelv~~~G~--------~Ws~IA~~lpgR---T--~~~cknrW~~~lk 102 (249)
.|..+|...|+ .|..||+.|+-- + ..+++..|..+|.
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhH
Confidence 57788888885 599999988422 1 3567888876653
No 80
>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=55.63 E-value=16 Score=28.93 Aligned_cols=45 Identities=18% Similarity=0.284 Sum_probs=29.6
Q ss_pred CCCHHHHHHHHHHHHHH--------CC----C------------------ChhHhhHHhcCCChhhhhhhhhccc
Q 025697 6 HWRPAEDEKLRELVERY--------GP----H------------------NWNAIAEKLQGRSGKSCRLRWFNQL 50 (249)
Q Consensus 6 ~WT~EED~~L~~~V~~~--------G~----~------------------~W~~IA~~l~~Rt~~qcr~Rw~~~L 50 (249)
++|++||-.|...|.+| +. . =....+...|..|..+-|+||+..+
T Consensus 1 kfTA~dDY~Lc~~i~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~fF~~~~~~~p~HT~~sWRDR~RKfv 75 (105)
T PF09197_consen 1 KFTADDDYALCKAIKKQFYRDIYQKDPDTGSSLISDGDSKEFIPKRDMRSFFKDLARKNPRHTENSWRDRYRKFV 75 (105)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHSB-TTSS-B----------------TTHHHHHHHHTTTS-HHHHHHHHHHTH
T ss_pred CCChHHHHHHHHHHHHHHHHHHHhhCcccccccccCCCccccccchhhHHHHHHHHHcCCccchhHHHHHHHHHH
Confidence 58999999999999877 11 0 0455566667788888888887764
No 81
>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=54.87 E-value=15 Score=30.97 Aligned_cols=41 Identities=27% Similarity=0.349 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhc
Q 025697 6 HWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFN 48 (249)
Q Consensus 6 ~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~ 48 (249)
.||+|+.++|.++... | ..=..||..|++.|...+.-+-++
T Consensus 2 ~Wtde~~~~L~~lw~~-G-~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-G-LSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred CCCHHHHHHHHHHHHc-C-CCHHHHHHHhCCcchhhhhhhhhc
Confidence 5999999999999965 4 468999999987777777655444
No 82
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=54.67 E-value=41 Score=25.95 Aligned_cols=69 Identities=14% Similarity=0.332 Sum_probs=42.3
Q ss_pred CCCCCHHHHHHHHHHHHHH----CC---CChhHhhHHhcCC-----Ch-------hhhhhhhhcccCCCCCCC---CCCH
Q 025697 4 RGHWRPAEDEKLRELVERY----GP---HNWNAIAEKLQGR-----SG-------KSCRLRWFNQLDPRINRS---PFTE 61 (249)
Q Consensus 4 Kg~WT~EED~~L~~~V~~~----G~---~~W~~IA~~l~~R-----t~-------~qcr~Rw~~~L~p~lkkg---~WT~ 61 (249)
...||++++-.|++++..| |. .+|..+...+.+. +. ...+.||.+.... .+.| .++.
T Consensus 4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~~~k-~~~g~~~~~~~ 82 (98)
T PF04504_consen 4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNAVKK-SKNGKDPSFSK 82 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHhhh-cccCcCCCCCC
Confidence 4579999999999999877 52 2566666555321 22 2344555554443 2222 5677
Q ss_pred HHHHHHHHHHHH
Q 025697 62 EEEERLLASHRI 73 (249)
Q Consensus 62 EED~~Llelv~~ 73 (249)
.-|..+.+|..+
T Consensus 83 ~hd~~~f~Lsk~ 94 (98)
T PF04504_consen 83 PHDRRLFELSKK 94 (98)
T ss_pred HhHHHHHHHHHH
Confidence 777777776654
No 83
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=53.22 E-value=19 Score=39.51 Aligned_cols=72 Identities=17% Similarity=0.154 Sum_probs=48.0
Q ss_pred CCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhcccCCCCCCCCCCHHHHHHHHHHHHHh-CCchHHHhh
Q 025697 6 HWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQLDPRINRSPFTEEEEERLLASHRIH-GNRWAVIAR 83 (249)
Q Consensus 6 ~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~L~p~lkkg~WT~EED~~Llelv~~~-G~~Ws~IA~ 83 (249)
-|..++|.+|+-.|-+||-++|.+|-.- +.-|..- ...+....-.+.|-...-..|+.+.... +.+|....+
T Consensus 1135 ~W~~e~Ds~LLiGI~khGygswe~Ir~D-----p~L~l~d-Ki~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~~~~ 1207 (1373)
T KOG0384|consen 1135 DWGSEDDSMLLIGIFKHGYGSWEAIRLD-----PDLGLTD-KIFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPKKLK 1207 (1373)
T ss_pred CCCchhhhhHhhhhhhcccccHHHhccC-----ccccchh-hhcccccCCchHHHHHHHHHHHHHHhhcccCCCchhhh
Confidence 5999999999999999999999999531 1111111 1112222445567777778888887777 566766543
No 84
>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=53.15 E-value=64 Score=30.45 Aligned_cols=85 Identities=21% Similarity=0.343 Sum_probs=61.0
Q ss_pred CCCCHHHHHHHHHHHHHHCCC---ChhHhhHHhcCCChhhhhhhhhcccCCCCCCCCCCHHHHHHHHHHHHH-h-----C
Q 025697 5 GHWRPAEDEKLRELVERYGPH---NWNAIAEKLQGRSGKSCRLRWFNQLDPRINRSPFTEEEEERLLASHRI-H-----G 75 (249)
Q Consensus 5 g~WT~EED~~L~~~V~~~G~~---~W~~IA~~l~~Rt~~qcr~Rw~~~L~p~lkkg~WT~EED~~Llelv~~-~-----G 75 (249)
..||.-|...|+.+.+..... +-..|++.+++|+...++.-- +.|+ +..+.+++.+ | |
T Consensus 22 ~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl-~~LK------------~rvareaiqkv~~~g~~~ 88 (344)
T PF11035_consen 22 AAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFL-QQLK------------GRVAREAIQKVHPGGLKG 88 (344)
T ss_pred ccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHH-HHHH------------HHHHHHHHHHhccccccc
Confidence 369999999999998866322 466888889999999887643 3332 2344455544 2 1
Q ss_pred C------------chHHHhhhCCCCCHHHHHHHHHHHHH
Q 025697 76 N------------RWAVIARLFPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 76 ~------------~Ws~IA~~lpgRT~~~cknrW~~~lk 102 (249)
. -|..+|+.+.|.-...+-.-|-.+|-
T Consensus 89 ~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~ 127 (344)
T PF11035_consen 89 PRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLT 127 (344)
T ss_pred ccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHH
Confidence 1 29999999999988888888876664
No 85
>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=53.14 E-value=6.3 Score=29.63 Aligned_cols=17 Identities=29% Similarity=0.345 Sum_probs=10.0
Q ss_pred CCCCCCCCCHHHHHHHH
Q 025697 52 PRINRSPFTEEEEERLL 68 (249)
Q Consensus 52 p~lkkg~WT~EED~~Ll 68 (249)
|....|-||+++|..|.
T Consensus 43 P~n~~GiWT~eDD~~L~ 59 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLR 59 (87)
T ss_dssp -TT-TT---HHHHHHHT
T ss_pred CCCCCCCcCHHHHHHHH
Confidence 55667899999999984
No 86
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=51.12 E-value=39 Score=26.07 Aligned_cols=45 Identities=13% Similarity=0.093 Sum_probs=28.9
Q ss_pred CCCCHHHHHHHHHHHHHh----C----CchHHHhh----hCCC-CCHHHHHHHHHHHH
Q 025697 57 SPFTEEEEERLLASHRIH----G----NRWAVIAR----LFPG-RTDNAVKNHWHVIM 101 (249)
Q Consensus 57 g~WT~EED~~Llelv~~~----G----~~Ws~IA~----~lpg-RT~~~cknrW~~~l 101 (249)
.-||+++|..||+.+..| | ..|..+.. .|.. =+..|+..+-+.+.
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK 62 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLK 62 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHH
Confidence 369999999999988776 5 24544433 3322 26677777764443
No 87
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=50.30 E-value=8.6 Score=37.08 Aligned_cols=46 Identities=20% Similarity=0.451 Sum_probs=39.3
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCChhHhhHH-----hcC-CChhhhhhhhhccc
Q 025697 4 RGHWRPAEDEKLRELVERYGPHNWNAIAEK-----LQG-RSGKSCRLRWFNQL 50 (249)
Q Consensus 4 Kg~WT~EED~~L~~~V~~~G~~~W~~IA~~-----l~~-Rt~~qcr~Rw~~~L 50 (249)
-..||.+|.+-|..+...|. ..|.-||.. ++. ||....++||+...
T Consensus 130 dn~WskeETD~LF~lck~fD-LRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~ 181 (445)
T KOG2656|consen 130 DNSWSKEETDYLFDLCKRFD-LRFFVIADRYDNQQYKKSRTVEDLKERYYSVC 181 (445)
T ss_pred cccccHHHHHHHHHHHHhcC-eeEEEEeeccchhhccccccHHHHHHHHHHHH
Confidence 35799999999999999998 569999987 454 99999999997643
No 88
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=49.66 E-value=42 Score=25.07 Aligned_cols=38 Identities=21% Similarity=0.375 Sum_probs=26.9
Q ss_pred HHHHHHHHHhCC--------chHHHhhhCCCC-----CHHHHHHHHHHHHH
Q 025697 65 ERLLASHRIHGN--------RWAVIARLFPGR-----TDNAVKNHWHVIMA 102 (249)
Q Consensus 65 ~~Llelv~~~G~--------~Ws~IA~~lpgR-----T~~~cknrW~~~lk 102 (249)
-.|..+|.+.|| .|..||+.|.-. ...+++..|..+|.
T Consensus 35 ~~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~ 85 (93)
T smart00501 35 YRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLL 85 (93)
T ss_pred HHHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhH
Confidence 357778888885 699999987533 24567777766654
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=48.79 E-value=18 Score=24.00 Aligned_cols=38 Identities=26% Similarity=0.286 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhc
Q 025697 9 PAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFN 48 (249)
Q Consensus 9 ~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~ 48 (249)
++++..++.+....| ..|..||..+ |.+...++.+..+
T Consensus 12 ~~~~r~i~~l~~~~g-~s~~eIa~~l-~~s~~~v~~~l~r 49 (54)
T PF08281_consen 12 PERQREIFLLRYFQG-MSYAEIAEIL-GISESTVKRRLRR 49 (54)
T ss_dssp -HHHHHHHHHHHTS----HHHHHHHC-TS-HHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHC-cCHHHHHHHH-CcCHHHHHHHHHH
Confidence 456677777777777 5799999988 7999888877654
No 90
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=47.80 E-value=21 Score=34.27 Aligned_cols=43 Identities=23% Similarity=0.359 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHHHHHHCCCChhHhhH-HhcCCChhhhhhhhhcc
Q 025697 6 HWRPAEDEKLRELVERYGPHNWNAIAE-KLQGRSGKSCRLRWFNQ 49 (249)
Q Consensus 6 ~WT~EED~~L~~~V~~~G~~~W~~IA~-~l~~Rt~~qcr~Rw~~~ 49 (249)
.|+.+|-..+.+.++.|| .++..|-. ++++|+..-|-..|+..
T Consensus 279 ~wsEeEcr~FEegl~~yG-KDF~lIr~nkvrtRsvgElVeyYYlW 322 (445)
T KOG4329|consen 279 GWSEEECRNFEEGLELYG-KDFHLIRANKVRTRSVGELVEYYYLW 322 (445)
T ss_pred cCCHHHHHHHHHHHHHhc-ccHHHHHhcccccchHHHHHHHHHHh
Confidence 599999999999999999 57988865 46899999998887654
No 91
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=45.65 E-value=30 Score=26.15 Aligned_cols=43 Identities=19% Similarity=0.151 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhcccCCC
Q 025697 10 AEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQLDPR 53 (249)
Q Consensus 10 EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~L~p~ 53 (249)
+.|.+|+.++...|...+..||+.+ +-+...|+.+.......+
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 5688999999999888999999988 889999999887765543
No 92
>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=45.13 E-value=33 Score=25.74 Aligned_cols=27 Identities=15% Similarity=0.278 Sum_probs=21.7
Q ss_pred HHHHHHHHHHhCCchHHHhhhCCCCCHH
Q 025697 64 EERLLASHRIHGNRWAVIARLFPGRTDN 91 (249)
Q Consensus 64 D~~Llelv~~~G~~Ws~IA~~lpgRT~~ 91 (249)
|+.|..+....|..|..+|.+| |=|..
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~ 28 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQT 28 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHH
Confidence 4568889999999999999998 43443
No 93
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=43.88 E-value=1e+02 Score=24.18 Aligned_cols=46 Identities=13% Similarity=0.094 Sum_probs=32.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhccc
Q 025697 2 CTRGHWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQL 50 (249)
Q Consensus 2 ~~Kg~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~L 50 (249)
.++..||+|+-..++..+...| ..=..||..++- +...+ .+|.+.+
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g-~sv~evA~e~gI-s~~tl-~~W~r~y 53 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPG-MTVSLVARQHGV-AASQL-FLWRKQY 53 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCC-CCHHHHHHHHCc-CHHHH-HHHHHHH
Confidence 3578899999888888777767 467889988844 54444 4576644
No 94
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=43.76 E-value=68 Score=26.93 Aligned_cols=35 Identities=17% Similarity=0.213 Sum_probs=26.9
Q ss_pred HHHHHHHHhCCchHHHhhhCCCCCHHHHHHHHHHHH
Q 025697 66 RLLASHRIHGNRWAVIARLFPGRTDNAVKNHWHVIM 101 (249)
Q Consensus 66 ~Llelv~~~G~~Ws~IA~~lpgRT~~~cknrW~~~l 101 (249)
.++++..-.|-.+.+||..+ |-|...|+.+|..+-
T Consensus 142 ~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR 176 (185)
T PF07638_consen 142 RVVELRFFEGLSVEEIAERL-GISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 33344444577899999999 889999999997764
No 95
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=43.34 E-value=26 Score=35.55 Aligned_cols=44 Identities=20% Similarity=0.432 Sum_probs=40.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHHHH
Q 025697 55 NRSPFTEEEEERLLASHRIHGNRWAVIARLFPGRTDNAVKNHWH 98 (249)
Q Consensus 55 kkg~WT~EED~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknrW~ 98 (249)
..++|+.+|-++........|...+.|+..+|+|...++|.++.
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~ 451 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFK 451 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHh
Confidence 45689999999999999999999999999999999999999873
No 96
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=43.05 E-value=25 Score=28.14 Aligned_cols=45 Identities=16% Similarity=0.150 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhcccCCCC
Q 025697 9 PAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQLDPRI 54 (249)
Q Consensus 9 ~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~L~p~l 54 (249)
.+-|.+++++.+..|...+..||+.+ |-+...|+.|-.++.+.++
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 7999999999887765543
No 97
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=41.39 E-value=77 Score=31.58 Aligned_cols=42 Identities=10% Similarity=0.205 Sum_probs=36.6
Q ss_pred CCCCHHHHHHHHHHHHHhCCchHHHhh-hCCCCCHHHHHHHHH
Q 025697 57 SPFTEEEEERLLASHRIHGNRWAVIAR-LFPGRTDNAVKNHWH 98 (249)
Q Consensus 57 g~WT~EED~~Llelv~~~G~~Ws~IA~-~lpgRT~~~cknrW~ 98 (249)
..|+..|-.++-++..+||.....|.. .||=++-..|-.+|+
T Consensus 286 EEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYY 328 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYY 328 (693)
T ss_pred hhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHH
Confidence 479999999999999999999999964 888888888877764
No 98
>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=40.16 E-value=73 Score=24.21 Aligned_cols=30 Identities=20% Similarity=0.324 Sum_probs=23.2
Q ss_pred HhCCchHHHhhhCCCCCHHHHHHHHHHHHHH
Q 025697 73 IHGNRWAVIARLFPGRTDNAVKNHWHVIMAR 103 (249)
Q Consensus 73 ~~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr 103 (249)
..|..+..||+.+ |=+...|+++....+++
T Consensus 124 ~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 124 LEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred hcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3577899999999 55899998888765443
No 99
>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=40.11 E-value=48 Score=24.88 Aligned_cols=28 Identities=18% Similarity=0.272 Sum_probs=22.2
Q ss_pred HHHHHHHHHHhCCchHHHhhhCCCCCHHH
Q 025697 64 EERLLASHRIHGNRWAVIARLFPGRTDNA 92 (249)
Q Consensus 64 D~~Llelv~~~G~~Ws~IA~~lpgRT~~~ 92 (249)
|..|..+....|..|..+|+.| |=+...
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~d 31 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDE 31 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHH
Confidence 5678888999999999999988 434433
No 100
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=40.05 E-value=1e+02 Score=24.74 Aligned_cols=29 Identities=17% Similarity=0.226 Sum_probs=23.1
Q ss_pred hCCchHHHhhhCCCCCHHHHHHHHHHHHHH
Q 025697 74 HGNRWAVIARLFPGRTDNAVKNHWHVIMAR 103 (249)
Q Consensus 74 ~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr 103 (249)
.|-.+..||..+ |-+...|+++....+++
T Consensus 143 ~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 171 (182)
T PRK09652 143 EGLSYEEIAEIM-GCPIGTVRSRIFRAREA 171 (182)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466899999999 88999999888654433
No 101
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=39.53 E-value=71 Score=25.59 Aligned_cols=29 Identities=21% Similarity=0.242 Sum_probs=23.2
Q ss_pred hCCchHHHhhhCCCCCHHHHHHHHHHHHHH
Q 025697 74 HGNRWAVIARLFPGRTDNAVKNHWHVIMAR 103 (249)
Q Consensus 74 ~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr 103 (249)
.|-.+..||..+ |-|...|++++...+++
T Consensus 140 ~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 168 (179)
T PRK11924 140 EGLSYREIAEIL-GVPVGTVKSRLRRARQL 168 (179)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466799999999 88999999988665443
No 102
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=39.50 E-value=65 Score=24.23 Aligned_cols=44 Identities=16% Similarity=0.182 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHhC-CchHHHhhhCCCCCHHHHHHHHHHHHHHHHh
Q 025697 62 EEEERLLASHRIHG-NRWAVIARLFPGRTDNAVKNHWHVIMARRCR 106 (249)
Q Consensus 62 EED~~Llelv~~~G-~~Ws~IA~~lpgRT~~~cknrW~~~lkr~~~ 106 (249)
+.|..|+.+....| ..++.||+.+ |-+...|..+...+.+..+-
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~i 47 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGVI 47 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 56778888888877 5799999999 88999999999888776543
No 103
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=38.39 E-value=63 Score=22.10 Aligned_cols=35 Identities=17% Similarity=0.279 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHHH
Q 025697 62 EEEERLLASHRIHGNRWAVIARLFPGRTDNAVKNHW 97 (249)
Q Consensus 62 EED~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknrW 97 (249)
+.|+-.+.+..+.|-.-..||+.+ ||+.+.|+++-
T Consensus 7 ~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl 41 (50)
T PF11427_consen 7 DAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRYL 41 (50)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHHH
T ss_pred HHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHHh
Confidence 455666777888999999999999 99999888763
No 104
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=38.38 E-value=96 Score=19.11 Aligned_cols=36 Identities=19% Similarity=0.307 Sum_probs=25.3
Q ss_pred HHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHHHHHH
Q 025697 64 EERLLASHRIHGNRWAVIARLFPGRTDNAVKNHWHVI 100 (249)
Q Consensus 64 D~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknrW~~~ 100 (249)
+..++.++-..|-.+..||..+ |=+...|+.+....
T Consensus 15 ~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~ 50 (55)
T cd06171 15 EREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRA 50 (55)
T ss_pred HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 4455555555677899999998 66777777766544
No 105
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=38.10 E-value=1e+02 Score=26.34 Aligned_cols=31 Identities=19% Similarity=0.160 Sum_probs=23.9
Q ss_pred hCCchHHHhhhCCCCCHHHHHHHHHHHHHHHH
Q 025697 74 HGNRWAVIARLFPGRTDNAVKNHWHVIMARRC 105 (249)
Q Consensus 74 ~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr~~ 105 (249)
.|..-..||..| |-+...|+++....+++..
T Consensus 153 ~g~s~~EIA~~L-gis~~tV~~~l~RArk~Lr 183 (203)
T PRK09647 153 EGLSYEEIAATL-GVKLGTVRSRIHRGRQQLR 183 (203)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 355678899999 8899999999877654444
No 106
>PRK04217 hypothetical protein; Provisional
Probab=37.69 E-value=95 Score=24.60 Aligned_cols=44 Identities=16% Similarity=0.028 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHHHHHHHHH
Q 025697 58 PFTEEEEERLLASHRIHGNRWAVIARLFPGRTDNAVKNHWHVIMAR 103 (249)
Q Consensus 58 ~WT~EED~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr 103 (249)
.-|.+| ..++.+....|-....||+.+ |-+...|+.+++...++
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 355555 677777777888999999999 88999999999765433
No 107
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=37.20 E-value=1e+02 Score=29.93 Aligned_cols=57 Identities=25% Similarity=0.303 Sum_probs=44.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC----------------chHHHhhhC-----CCCCHHHHHHHHHHHHHHHHhhhhhH
Q 025697 55 NRSPFTEEEEERLLASHRIHGN----------------RWAVIARLF-----PGRTDNAVKNHWHVIMARRCRERSRL 111 (249)
Q Consensus 55 kkg~WT~EED~~Llelv~~~G~----------------~Ws~IA~~l-----pgRT~~~cknrW~~~lkr~~~~~~~~ 111 (249)
.-|.|+++=|+...++.+.|.. +-..||+.+ ..||..||-.|-+.+.|++.+.-...
T Consensus 75 aegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~reiq~k 152 (455)
T KOG3841|consen 75 AEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLREIQAK 152 (455)
T ss_pred cccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHHhh
Confidence 4578999999999999998852 467788755 25899999999988888887764443
No 108
>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=36.55 E-value=44 Score=24.65 Aligned_cols=27 Identities=26% Similarity=0.556 Sum_probs=21.3
Q ss_pred HHHHHHHHHHhCCchHHHhhhCCCCCHH
Q 025697 64 EERLLASHRIHGNRWAVIARLFPGRTDN 91 (249)
Q Consensus 64 D~~Llelv~~~G~~Ws~IA~~lpgRT~~ 91 (249)
|..|..+....|..|..+|+.| |=+..
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~ 30 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSET 30 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHH
Confidence 4567788889999999999998 44443
No 109
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=35.94 E-value=88 Score=25.29 Aligned_cols=30 Identities=20% Similarity=0.293 Sum_probs=22.9
Q ss_pred hCCchHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 025697 74 HGNRWAVIARLFPGRTDNAVKNHWHVIMARR 104 (249)
Q Consensus 74 ~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr~ 104 (249)
.|-....||..+ |-|...|++++...+++.
T Consensus 134 ~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~L 163 (169)
T TIGR02954 134 HDLTIKEIAEVM-NKPEGTVKTYLHRALKKL 163 (169)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 355788999988 779999999987665443
No 110
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=35.10 E-value=45 Score=21.62 Aligned_cols=37 Identities=27% Similarity=0.333 Sum_probs=18.4
Q ss_pred CCCHHHHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHH
Q 025697 58 PFTEEEEERLLASHRIHGNRWAVIARLFPGRTDNAVKNH 96 (249)
Q Consensus 58 ~WT~EED~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknr 96 (249)
.+|.+|=..|..++ .-|..=..||+.| ||+...|.+-
T Consensus 4 ~Lt~~eR~~I~~l~-~~G~s~~~IA~~l-g~s~sTV~re 40 (44)
T PF13936_consen 4 HLTPEERNQIEALL-EQGMSIREIAKRL-GRSRSTVSRE 40 (44)
T ss_dssp --------HHHHHH-CS---HHHHHHHT-T--HHHHHHH
T ss_pred chhhhHHHHHHHHH-HcCCCHHHHHHHH-CcCcHHHHHH
Confidence 46666666666554 5777889999999 9999888653
No 111
>smart00351 PAX Paired Box domain.
Probab=35.08 E-value=1.6e+02 Score=23.30 Aligned_cols=73 Identities=12% Similarity=0.127 Sum_probs=46.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHCCCChhHhhHHhc--CCChhhhhhhhhc--ccCCCC----CCCCCCHHHHHHHHHHHH
Q 025697 1 MCTRGHWRPAEDEKLRELVERYGPHNWNAIAEKLQ--GRSGKSCRLRWFN--QLDPRI----NRSPFTEEEEERLLASHR 72 (249)
Q Consensus 1 ~~~Kg~WT~EED~~L~~~V~~~G~~~W~~IA~~l~--~Rt~~qcr~Rw~~--~L~p~l----kkg~WT~EED~~Llelv~ 72 (249)
|+...+.+.++-.+++.++. -| ..-..||+.++ ..|...+..||.. .+.|.. ....-+.+++..|++++.
T Consensus 12 ~~~~~~~s~~~R~riv~~~~-~G-~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~ 89 (125)
T smart00351 12 FVNGRPLPDEERQRIVELAQ-NG-VRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQ 89 (125)
T ss_pred ecCCCCCCHHHHHHHHHHHH-cC-CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHH
Confidence 34556789999999988886 45 46899999983 3455666667654 344421 122345566666676666
Q ss_pred HhC
Q 025697 73 IHG 75 (249)
Q Consensus 73 ~~G 75 (249)
..+
T Consensus 90 ~~p 92 (125)
T smart00351 90 ENP 92 (125)
T ss_pred HCC
Confidence 554
No 112
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=33.35 E-value=1.1e+02 Score=25.71 Aligned_cols=27 Identities=26% Similarity=0.263 Sum_probs=22.0
Q ss_pred hCCchHHHhhhCCCCCHHHHHHHHHHHH
Q 025697 74 HGNRWAVIARLFPGRTDNAVKNHWHVIM 101 (249)
Q Consensus 74 ~G~~Ws~IA~~lpgRT~~~cknrW~~~l 101 (249)
.|....+||..+ |-+..+|++++....
T Consensus 149 ~g~s~~EIA~~l-g~s~~tV~~rl~rar 175 (192)
T PRK09643 149 QGYSVADAARML-GVAEGTVKSRCARGR 175 (192)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 466799999999 889999999985543
No 113
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=32.41 E-value=1.2e+02 Score=24.92 Aligned_cols=32 Identities=19% Similarity=0.107 Sum_probs=25.7
Q ss_pred HhCCchHHHhhhCCCCCHHHHHHHHHHHHHHHH
Q 025697 73 IHGNRWAVIARLFPGRTDNAVKNHWHVIMARRC 105 (249)
Q Consensus 73 ~~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr~~ 105 (249)
..|-...+||..| |-+...|+.+...-+.+..
T Consensus 141 ~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~ 172 (178)
T PRK12529 141 LDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCL 172 (178)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 3466899999999 8899999999876665554
No 114
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=31.98 E-value=1.1e+02 Score=24.97 Aligned_cols=28 Identities=14% Similarity=0.055 Sum_probs=22.1
Q ss_pred hCCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 025697 74 HGNRWAVIARLFPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 74 ~G~~Ws~IA~~lpgRT~~~cknrW~~~lk 102 (249)
.|..+..||..+ |-|...|+++.....+
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar~ 178 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGRE 178 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 356789999999 8899999988765543
No 115
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=31.08 E-value=57 Score=22.83 Aligned_cols=47 Identities=17% Similarity=0.174 Sum_probs=30.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhccc
Q 025697 1 MCTRGHWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQL 50 (249)
Q Consensus 1 ~~~Kg~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~L 50 (249)
|.++..||+|+-..++..+...| .....||..++- ..+...+|...+
T Consensus 1 m~~r~~ys~e~K~~~v~~~~~~g-~sv~~va~~~gi--~~~~l~~W~~~~ 47 (76)
T PF01527_consen 1 MRKRRRYSPEFKLQAVREYLESG-ESVSEVAREYGI--SPSTLYNWRKQY 47 (76)
T ss_dssp --SS----HHHHHHHHHHHHHHH-CHHHHHHHHHTS---HHHHHHHHHHH
T ss_pred CCCCCCCCHHHHHHHHHHHHHCC-CceEeeeccccc--ccccccHHHHHH
Confidence 56789999999999999996666 568889988844 344455676654
No 116
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=30.14 E-value=78 Score=23.60 Aligned_cols=26 Identities=15% Similarity=0.334 Sum_probs=19.2
Q ss_pred HHHHHHHhCCchHHHhhhCCCCCHHHH
Q 025697 67 LLASHRIHGNRWAVIARLFPGRTDNAV 93 (249)
Q Consensus 67 Llelv~~~G~~Ws~IA~~lpgRT~~~c 93 (249)
|..+....|..|..+|+.| |=+..+|
T Consensus 10 l~~ia~~iG~~Wk~Lar~L-Gls~~dI 35 (86)
T cd08318 10 ITVFANKLGEDWKTLAPHL-EMKDKEI 35 (86)
T ss_pred HHHHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 3335677899999999999 5565555
No 117
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=29.13 E-value=1.5e+02 Score=24.51 Aligned_cols=28 Identities=14% Similarity=0.232 Sum_probs=22.5
Q ss_pred hCCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 025697 74 HGNRWAVIARLFPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 74 ~G~~Ws~IA~~lpgRT~~~cknrW~~~lk 102 (249)
.|-....||..| |-|..+|++++...++
T Consensus 146 ~~~s~~eIA~~l-gis~~tV~~~l~Rar~ 173 (189)
T PRK12515 146 HEKSVEEVGEIV-GIPESTVKTRMFYARK 173 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 456789999999 7799999999866543
No 118
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) 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-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=29.03 E-value=52 Score=24.80 Aligned_cols=23 Identities=26% Similarity=0.409 Sum_probs=19.5
Q ss_pred HHHHHHHHHHhCCchHHHhhhCC
Q 025697 64 EERLLASHRIHGNRWAVIARLFP 86 (249)
Q Consensus 64 D~~Llelv~~~G~~Ws~IA~~lp 86 (249)
|..|..+....|..|..+|+.|.
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L~ 26 (84)
T cd08805 4 EMKMAVIREHLGLSWAELARELQ 26 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHcC
Confidence 45677888999999999999873
No 119
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=28.89 E-value=1.6e+02 Score=23.25 Aligned_cols=29 Identities=21% Similarity=0.171 Sum_probs=22.7
Q ss_pred hCCchHHHhhhCCCCCHHHHHHHHHHHHHH
Q 025697 74 HGNRWAVIARLFPGRTDNAVKNHWHVIMAR 103 (249)
Q Consensus 74 ~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr 103 (249)
.|-.-..||..| |-+...|+++....+++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 121 EDMDVAETAAAM-GCSEGSVKTHCSRATHA 149 (161)
T ss_pred hcCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355789999999 78999999988665443
No 120
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=28.58 E-value=83 Score=23.43 Aligned_cols=30 Identities=30% Similarity=0.441 Sum_probs=22.7
Q ss_pred HHHHHHHHHHhCCchHHHhhhCCCCCHHHHH
Q 025697 64 EERLLASHRIHGNRWAVIARLFPGRTDNAVK 94 (249)
Q Consensus 64 D~~Llelv~~~G~~Ws~IA~~lpgRT~~~ck 94 (249)
|..|..+....|.+|..+|+.| |=+...|.
T Consensus 4 ~~~l~~ia~~LG~dWk~LAr~L-g~se~dI~ 33 (84)
T cd08804 4 EERLAVIADHLGFSWTELAREL-DFTEEQIH 33 (84)
T ss_pred hhHHHHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 4567788889999999999998 44554443
No 121
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptor
Probab=28.50 E-value=68 Score=23.70 Aligned_cols=33 Identities=36% Similarity=0.591 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHH
Q 025697 61 EEEEERLLASHRIHGNRWAVIARLFPGRTDNAVKN 95 (249)
Q Consensus 61 ~EED~~Llelv~~~G~~Ws~IA~~lpgRT~~~ckn 95 (249)
.||.++|+.. ...|.+|..+|+.| |=+...|.+
T Consensus 2 ~~~v~~ll~~-~nlG~dW~~LA~~L-G~~~~~I~~ 34 (77)
T cd08311 2 QEEVEKLLES-GRPGRDWRSLAGEL-GYEDEAIDT 34 (77)
T ss_pred hHHHHHHHhC-CCCccCHHHHHHHc-CCCHHHHHH
Confidence 5788888742 25678999999999 556665554
No 122
>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=28.29 E-value=1.1e+02 Score=19.39 Aligned_cols=33 Identities=18% Similarity=0.243 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHH
Q 025697 63 EEERLLASHRIHGNRWAVIARLFPGRTDNAVKNH 96 (249)
Q Consensus 63 ED~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknr 96 (249)
|-..|.++...+|++.+..|+.| |=+...+..+
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~k 38 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLL-GISRRTLYRK 38 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHH
Confidence 56678889999999999999988 4455554443
No 123
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=28.21 E-value=1.6e+02 Score=24.15 Aligned_cols=29 Identities=21% Similarity=0.182 Sum_probs=22.3
Q ss_pred hCCchHHHhhhCCCCCHHHHHHHHHHHHHH
Q 025697 74 HGNRWAVIARLFPGRTDNAVKNHWHVIMAR 103 (249)
Q Consensus 74 ~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr 103 (249)
.|.....||..| |-+...|+.+....+++
T Consensus 146 ~g~s~~eIA~~l-~is~~tV~~~l~ra~~~ 174 (184)
T PRK12512 146 EGASIKETAAKL-SMSEGAVRVALHRGLAA 174 (184)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 356788999998 88999999988665443
No 124
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=27.94 E-value=1.7e+02 Score=23.32 Aligned_cols=28 Identities=11% Similarity=-0.104 Sum_probs=22.1
Q ss_pred hCCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 025697 74 HGNRWAVIARLFPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 74 ~G~~Ws~IA~~lpgRT~~~cknrW~~~lk 102 (249)
.|-.-..||..+ |-+...|+++.....+
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~ 148 (160)
T PRK09642 121 EEKSYQEIALQE-KIEVKTVEMKLYRARK 148 (160)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 355789999999 8899999998765543
No 125
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=27.77 E-value=1.1e+02 Score=24.88 Aligned_cols=27 Identities=15% Similarity=0.052 Sum_probs=21.1
Q ss_pred CCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 025697 75 GNRWAVIARLFPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 75 G~~Ws~IA~~lpgRT~~~cknrW~~~lk 102 (249)
|.....||..+ |-+...|+++.....+
T Consensus 152 g~s~~eIA~~l-gis~~~v~~~l~Rar~ 178 (187)
T TIGR02948 152 DLSLKEISEIL-DLPVGTVKTRIHRGRE 178 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 55688999998 7799999998865543
No 126
>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=27.67 E-value=1.1e+02 Score=24.95 Aligned_cols=28 Identities=18% Similarity=0.202 Sum_probs=22.0
Q ss_pred CCchHHHhhhCCCCCHHHHHHHHHHHHHH
Q 025697 75 GNRWAVIARLFPGRTDNAVKNHWHVIMAR 103 (249)
Q Consensus 75 G~~Ws~IA~~lpgRT~~~cknrW~~~lkr 103 (249)
|-....||..+ |=|...|+++.+..+++
T Consensus 154 ~~s~~EIA~~l-gis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 154 GLSYEDIARIM-DCPVGTVRSRIFRAREA 181 (190)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 45789999999 77899999988665443
No 127
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=27.63 E-value=1.6e+02 Score=23.79 Aligned_cols=28 Identities=29% Similarity=0.315 Sum_probs=21.9
Q ss_pred hCCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 025697 74 HGNRWAVIARLFPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 74 ~G~~Ws~IA~~lpgRT~~~cknrW~~~lk 102 (249)
.|-.-..||..| |.+...|+.+.+..++
T Consensus 133 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~ 160 (173)
T PRK09645 133 RGWSTAQIAADL-GIPEGTVKSRLHYALR 160 (173)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 355678999999 8899999998865543
No 128
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=27.61 E-value=1.5e+02 Score=24.62 Aligned_cols=28 Identities=18% Similarity=0.051 Sum_probs=22.1
Q ss_pred hCCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 025697 74 HGNRWAVIARLFPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 74 ~G~~Ws~IA~~lpgRT~~~cknrW~~~lk 102 (249)
.|-....||..| |-+...|+++.....+
T Consensus 121 ~g~~~~EIA~~l-gis~~tV~~~l~Rar~ 148 (181)
T PRK09637 121 EGLSQKEIAEKL-GLSLSGAKSRVQRGRV 148 (181)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 456789999999 8899999998865543
No 129
>KOG1878 consensus Nuclear receptor coregulator SMRT/SMRTER, contains Myb-like domains [Transcription]
Probab=27.29 E-value=29 Score=38.80 Aligned_cols=42 Identities=24% Similarity=0.491 Sum_probs=34.2
Q ss_pred CCCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhh
Q 025697 5 GHWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWF 47 (249)
Q Consensus 5 g~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~ 47 (249)
..|+++|-+....=...|- ++...|+..+..++..+|...|+
T Consensus 226 n~Ws~~Ek~~fk~rf~~H~-knf~~~as~~erkSv~d~vlfyy 267 (1672)
T KOG1878|consen 226 NEWSPEEKELFKSRFAQHV-KNFGLIASFFERKSVSDCVLFYY 267 (1672)
T ss_pred hhccccccccccchhhhcC-cchhhhhhhhcccchhhceeeee
Confidence 4699999877777777776 56888999998889988887773
No 130
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=26.74 E-value=1.8e+02 Score=23.60 Aligned_cols=31 Identities=19% Similarity=0.163 Sum_probs=24.0
Q ss_pred HhCCchHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 025697 73 IHGNRWAVIARLFPGRTDNAVKNHWHVIMARR 104 (249)
Q Consensus 73 ~~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr~ 104 (249)
..|-....||..+ |-+...|+.+-..-+++.
T Consensus 133 ~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 133 LDGMGHAEIAERL-GVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3466789999999 889999999876655443
No 131
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=26.59 E-value=47 Score=24.07 Aligned_cols=17 Identities=18% Similarity=0.388 Sum_probs=14.3
Q ss_pred HHHHHHHHhCCchHHHh
Q 025697 66 RLLASHRIHGNRWAVIA 82 (249)
Q Consensus 66 ~Llelv~~~G~~Ws~IA 82 (249)
.|.+|...||++|.-|-
T Consensus 31 vl~~LL~lY~~nW~lIE 47 (65)
T PF10440_consen 31 VLKNLLKLYDGNWELIE 47 (65)
T ss_pred HHHHHHHHHcCCchhhh
Confidence 56688899999999985
No 132
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=26.22 E-value=1.5e+02 Score=23.60 Aligned_cols=47 Identities=13% Similarity=0.098 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHhC-CchHHHhhhCCCCCHHHHHHHHHHHHHHHHhhh
Q 025697 61 EEEEERLLASHRIHG-NRWAVIARLFPGRTDNAVKNHWHVIMARRCRER 108 (249)
Q Consensus 61 ~EED~~Llelv~~~G-~~Ws~IA~~lpgRT~~~cknrW~~~lkr~~~~~ 108 (249)
.+-|.+|+++...-| ..++.||+.+ |-|...|..|-+.+.+..+-++
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~GiI~~ 54 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGVIKG 54 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCceee
Confidence 356778888887777 5799999999 8899999999977776665443
No 133
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=26.17 E-value=93 Score=22.45 Aligned_cols=28 Identities=21% Similarity=0.277 Sum_probs=20.0
Q ss_pred HHHHHHHHHH-hCCchHHHhhhCCCCCHHH
Q 025697 64 EERLLASHRI-HGNRWAVIARLFPGRTDNA 92 (249)
Q Consensus 64 D~~Llelv~~-~G~~Ws~IA~~lpgRT~~~ 92 (249)
...|..++.. .|..|..+|+.|+- +...
T Consensus 5 ~~~~~~l~~~~~g~~W~~la~~Lg~-~~~~ 33 (88)
T smart00005 5 REKLAKLLDHPLGLDWRELARKLGL-SEAD 33 (88)
T ss_pred HHHHHHHHcCccchHHHHHHHHcCC-CHHH
Confidence 4556666666 89999999999953 4433
No 134
>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=26.09 E-value=1.8e+02 Score=24.28 Aligned_cols=29 Identities=7% Similarity=-0.132 Sum_probs=22.6
Q ss_pred hCCchHHHhhhCCCCCHHHHHHHHHHHHHH
Q 025697 74 HGNRWAVIARLFPGRTDNAVKNHWHVIMAR 103 (249)
Q Consensus 74 ~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr 103 (249)
.|-....||..+ |-|...|+.+....+++
T Consensus 146 ~g~s~~EIA~~l-gis~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 146 LGFESDEICQEL-EISTSNCHVLLYRARLS 174 (188)
T ss_pred hCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 456789999999 88999999987665443
No 135
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=25.94 E-value=1.8e+02 Score=24.29 Aligned_cols=28 Identities=14% Similarity=0.172 Sum_probs=21.3
Q ss_pred hCCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 025697 74 HGNRWAVIARLFPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 74 ~G~~Ws~IA~~lpgRT~~~cknrW~~~lk 102 (249)
.|-...+||..+ |-+...|+.+.+..++
T Consensus 156 eg~s~~EIA~~l-gis~~tVk~rl~ra~~ 183 (194)
T PRK12531 156 EELPHQQVAEMF-DIPLGTVKSRLRLAVE 183 (194)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHH
Confidence 355788899988 8899999888755543
No 136
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=25.89 E-value=1.8e+02 Score=24.00 Aligned_cols=29 Identities=31% Similarity=0.249 Sum_probs=22.4
Q ss_pred hCCchHHHhhhCCCCCHHHHHHHHHHHHHH
Q 025697 74 HGNRWAVIARLFPGRTDNAVKNHWHVIMAR 103 (249)
Q Consensus 74 ~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr 103 (249)
.|.....||..+ |-+...|+.+.+..+++
T Consensus 154 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 154 VGLSAEETAEAV-GSTPGAVRVAQHRALAR 182 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 356789999999 77899999887655443
No 137
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=25.15 E-value=1.6e+02 Score=24.30 Aligned_cols=27 Identities=15% Similarity=0.130 Sum_probs=20.9
Q ss_pred CCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 025697 75 GNRWAVIARLFPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 75 G~~Ws~IA~~lpgRT~~~cknrW~~~lk 102 (249)
|-....||..+ |-|...|+++....++
T Consensus 154 g~s~~eIA~~l-gis~~tv~~~l~Rar~ 180 (193)
T PRK11923 154 GLSYEDIASVM-QCPVGTVRSRIFRARE 180 (193)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 45678899988 7789999998866543
No 138
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=24.75 E-value=1.8e+02 Score=24.13 Aligned_cols=27 Identities=4% Similarity=-0.214 Sum_probs=22.1
Q ss_pred hCCchHHHhhhCCCCCHHHHHHHHHHHH
Q 025697 74 HGNRWAVIARLFPGRTDNAVKNHWHVIM 101 (249)
Q Consensus 74 ~G~~Ws~IA~~lpgRT~~~cknrW~~~l 101 (249)
.|-....||..| |-+...|+.+.....
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~RAr 175 (189)
T PRK12530 149 LELSSEQICQEC-DISTSNLHVLLYRAR 175 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 356799999999 889999999975554
No 139
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=24.58 E-value=1.9e+02 Score=24.84 Aligned_cols=46 Identities=24% Similarity=0.168 Sum_probs=37.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHHHHHHHHHHH
Q 025697 57 SPFTEEEEERLLASHRIHGNRWAVIARLFPGRTDNAVKNHWHVIMARRC 105 (249)
Q Consensus 57 g~WT~EED~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr~~ 105 (249)
...|+.|-+.|.-+. .|-.=..||..| +.|...||+|...+++|.-
T Consensus 147 ~~LT~RE~eVL~lla--~G~snkeIA~~L-~iS~~TVk~h~~~i~~KL~ 192 (211)
T COG2197 147 ELLTPRELEVLRLLA--EGLSNKEIAEEL-NLSEKTVKTHVSNILRKLG 192 (211)
T ss_pred CCCCHHHHHHHHHHH--CCCCHHHHHHHH-CCCHhHHHHHHHHHHHHcC
Confidence 368888887766554 466679999999 9999999999999987653
No 140
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=24.56 E-value=1.7e+02 Score=23.90 Aligned_cols=31 Identities=19% Similarity=0.133 Sum_probs=24.6
Q ss_pred CCchHHHhhhCCCCCHHHHHHHHHHHHHHHHh
Q 025697 75 GNRWAVIARLFPGRTDNAVKNHWHVIMARRCR 106 (249)
Q Consensus 75 G~~Ws~IA~~lpgRT~~~cknrW~~~lkr~~~ 106 (249)
|-...+||+.+ |-+...|+++....+++...
T Consensus 135 g~s~~EIA~~l-gis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 135 GLTYSEIAHKL-GVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHH
Confidence 45789999999 88999999998766655443
No 141
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=23.54 E-value=2e+02 Score=23.97 Aligned_cols=27 Identities=19% Similarity=-0.043 Sum_probs=21.2
Q ss_pred hCCchHHHhhhCCCCCHHHHHHHHHHHH
Q 025697 74 HGNRWAVIARLFPGRTDNAVKNHWHVIM 101 (249)
Q Consensus 74 ~G~~Ws~IA~~lpgRT~~~cknrW~~~l 101 (249)
.|-.+..||+.+ |=+...|+++-...+
T Consensus 151 ~g~s~~eIA~~l-gis~~tV~~~l~Ra~ 177 (196)
T PRK12524 151 EGLSNPEIAEVM-EIGVEAVESLTARGK 177 (196)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 456799999999 778899988875543
No 142
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=23.27 E-value=4.3e+02 Score=22.18 Aligned_cols=64 Identities=20% Similarity=0.186 Sum_probs=0.0
Q ss_pred HHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhcccCCCCCCCCCCHHHHHHHHHHHHHhCCchHHHhh--hCCCC
Q 025697 13 EKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQLDPRINRSPFTEEEEERLLASHRIHGNRWAVIAR--LFPGR 88 (249)
Q Consensus 13 ~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~L~p~lkkg~WT~EED~~Llelv~~~G~~Ws~IA~--~lpgR 88 (249)
+.|+++-..-| ..|..||+.+ |++.--|..-....-.+ +.|+=++|.++. |-.|..+.. .+|.|
T Consensus 11 ~~Ll~AK~~KG-LTwe~IAe~i-G~sevwvaaa~lGQ~~l-------s~e~A~kla~lL---gL~~e~~~~l~~~P~r 76 (150)
T TIGR00673 11 DALLESKKKKG-LTFADIADGL-GLAEVFVAAALYGQAAA-------PADEARLVGAKL---DLDEDSILELQMAPLR 76 (150)
T ss_pred HHHHHHHHHcC-CCHHHHHHHH-CCCHHHHHHHHhCCCCC-------CHHHHHHHHHHh---CcCHHHHHHHhcCCCC
No 143
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=23.27 E-value=95 Score=23.19 Aligned_cols=22 Identities=23% Similarity=0.303 Sum_probs=19.1
Q ss_pred HHHHHHHHHhCCchHHHhhhCC
Q 025697 65 ERLLASHRIHGNRWAVIARLFP 86 (249)
Q Consensus 65 ~~Llelv~~~G~~Ws~IA~~lp 86 (249)
..|..+..+.|..|..+|++|+
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~LG 24 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHLG 24 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHcC
Confidence 4578889999999999999884
No 144
>COG4628 Uncharacterized conserved protein [Function unknown]
Probab=23.08 E-value=1.1e+02 Score=24.85 Aligned_cols=44 Identities=34% Similarity=0.772 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhcccCCC-------CCCCCCCHHHHHHH
Q 025697 12 DEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFNQLDPR-------INRSPFTEEEEERL 67 (249)
Q Consensus 12 D~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~~L~p~-------lkkg~WT~EED~~L 67 (249)
+.+|.++|..|| |..++..++ .-|.. -+|. +.+.+|-.|..+.|
T Consensus 21 E~llt~Lvd~YG---Wd~L~~ri~----inCF~-----ndPSi~SSlKfLrkT~WARekvEa~ 71 (136)
T COG4628 21 ETLLTELVDFYG---WDGLATRIR----INCFH-----NDPSIKSSLKFLRKTPWAREKVEAL 71 (136)
T ss_pred HHHHHHHHHHhC---hHHHHhhce----ecccc-----CCccHHHHHHHHhcCHhHHHHHHHH
Confidence 568889999999 999997664 23321 1222 45778888766654
No 145
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=22.85 E-value=56 Score=33.20 Aligned_cols=44 Identities=16% Similarity=0.360 Sum_probs=40.0
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCChhHhhHHhcCCChhhhhhhhhc
Q 025697 4 RGHWRPAEDEKLRELVERYGPHNWNAIAEKLQGRSGKSCRLRWFN 48 (249)
Q Consensus 4 Kg~WT~EED~~L~~~V~~~G~~~W~~IA~~l~~Rt~~qcr~Rw~~ 48 (249)
.++||..|-++...+....|. +...|+..+|+|..+|++..+..
T Consensus 409 ~~~w~~se~e~fyka~~~~gs-~~slis~l~p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 409 TDKWDASETELFYKALSERGS-DFSLISNLFPLRDRKQIKAKFKK 452 (584)
T ss_pred cCcccchhhHHhhhHHhhhcc-cccccccccccccHHHHHHHHhh
Confidence 578999999999999999995 69999999999999999998754
No 146
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=22.85 E-value=1.7e+02 Score=24.38 Aligned_cols=46 Identities=17% Similarity=0.176 Sum_probs=36.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCchHHHhhhC--C--CCCHHHHHHHHHHH
Q 025697 55 NRSPFTEEEEERLLASHRIHGNRWAVIARLF--P--GRTDNAVKNHWHVI 100 (249)
Q Consensus 55 kkg~WT~EED~~Llelv~~~G~~Ws~IA~~l--p--gRT~~~cknrW~~~ 100 (249)
....-|..|..-|..|+.+||.++..++.-. . -.|..+|+.+...+
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 3446788999999999999999999998632 1 47999998876543
No 147
>KOG4128 consensus Bleomycin hydrolases and aminopeptidases of cysteine protease family [Amino acid transport and metabolism]
Probab=22.64 E-value=4.1e+02 Score=25.63 Aligned_cols=56 Identities=11% Similarity=0.188 Sum_probs=40.4
Q ss_pred ccCCCCCCCCCCHHHHHHHHHHHHHhCCchHHHhh-hCCCCCHHHHHHHHHHHHHHHHhhhhhHHH
Q 025697 49 QLDPRINRSPFTEEEEERLLASHRIHGNRWAVIAR-LFPGRTDNAVKNHWHVIMARRCRERSRLYA 113 (249)
Q Consensus 49 ~L~p~lkkg~WT~EED~~Llelv~~~G~~Ws~IA~-~lpgRT~~~cknrW~~~lkr~~~~~~~~~~ 113 (249)
+.+|.-..|.|. +++.+|++||- |.+ .++.-...+--.+|+.+|+.++|.-..+..
T Consensus 138 l~nP~~DGGqw~-----MfvNlVkKYGv----iPKkcy~~sysT~atrkmN~iL~~KlREfa~~Lr 194 (457)
T KOG4128|consen 138 LKNPVPDGGQWQ-----MFVNLVKKYGV----IPKKCYLHSYSTQATRKMNLILKSKLREFASMLR 194 (457)
T ss_pred HhCCCCCCchHH-----HHHHHHHHhCC----CcHHhccccchhhHHHHHHHHHHHHHHHHHHHHH
Confidence 346777788884 78999999995 343 444445667778999999999887554443
No 148
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=22.48 E-value=1.9e+02 Score=25.01 Aligned_cols=45 Identities=31% Similarity=0.371 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHHHHHHHHHHH
Q 025697 58 PFTEEEEERLLASHRIHGNRWAVIARLFPGRTDNAVKNHWHVIMARRC 105 (249)
Q Consensus 58 ~WT~EED~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr~~ 105 (249)
..|+-|-+ ++.++.. |....+||+.| +-+...++++...++++--
T Consensus 155 ~Lt~rE~~-Vl~l~~~-G~s~~eIA~~L-~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 155 LLTHREKE-ILNKLRI-GASNNEIARSL-FISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCHHHHH-HHHHHHc-CCCHHHHHHHh-CCCHHHHHHHHHHHHHHhC
Confidence 46765554 4555555 98899999999 7899999999988876543
No 149
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=22.09 E-value=2.4e+02 Score=22.93 Aligned_cols=27 Identities=30% Similarity=0.444 Sum_probs=21.7
Q ss_pred CCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 025697 75 GNRWAVIARLFPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 75 G~~Ws~IA~~lpgRT~~~cknrW~~~lk 102 (249)
|-....||..+ |-+...|+.+....++
T Consensus 150 g~s~~EIA~~l-gis~~tVk~~l~Rar~ 176 (183)
T TIGR02999 150 GLTVEEIAELL-GVSVRTVERDWRFARA 176 (183)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 55789999999 8899999998865543
No 150
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=21.92 E-value=2.7e+02 Score=22.14 Aligned_cols=27 Identities=26% Similarity=0.266 Sum_probs=20.8
Q ss_pred CCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 025697 75 GNRWAVIARLFPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 75 G~~Ws~IA~~lpgRT~~~cknrW~~~lk 102 (249)
|..-..||..| |-+...|+.+....++
T Consensus 121 ~~s~~eIA~~l-gis~~tv~~~l~ra~~ 147 (159)
T PRK12527 121 GLSHQQIAEHL-GISRSLVEKHIVNAMK 147 (159)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 45678999999 8899999998765443
No 151
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=21.57 E-value=2.5e+02 Score=22.93 Aligned_cols=28 Identities=21% Similarity=0.254 Sum_probs=21.5
Q ss_pred CCchHHHhhhCCCCCHHHHHHHHHHHHHH
Q 025697 75 GNRWAVIARLFPGRTDNAVKNHWHVIMAR 103 (249)
Q Consensus 75 G~~Ws~IA~~lpgRT~~~cknrW~~~lkr 103 (249)
|-.-..||..+ |-|...|+.+.+..+++
T Consensus 151 ~~s~~eIA~~l-gis~~~V~~~l~ra~~~ 178 (186)
T PRK13919 151 GYTHREAAQLL-GLPLGTLKTRARRALSR 178 (186)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 45678999998 78899999887665443
No 152
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=21.51 E-value=2.2e+02 Score=23.62 Aligned_cols=27 Identities=15% Similarity=0.134 Sum_probs=21.8
Q ss_pred CCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 025697 75 GNRWAVIARLFPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 75 G~~Ws~IA~~lpgRT~~~cknrW~~~lk 102 (249)
|-.-..||..+ |-+...|+.+....++
T Consensus 146 g~s~~EIA~~l-gis~~tVk~~l~Rar~ 172 (185)
T PRK09649 146 GLSYADAAAVC-GCPVGTIRSRVARARD 172 (185)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 45689999999 8899999999865544
No 153
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=21.46 E-value=2.2e+02 Score=23.61 Aligned_cols=28 Identities=14% Similarity=0.095 Sum_probs=21.9
Q ss_pred hCCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 025697 74 HGNRWAVIARLFPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 74 ~G~~Ws~IA~~lpgRT~~~cknrW~~~lk 102 (249)
.|-.-..||..+ |-+...|+.+....++
T Consensus 151 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~ 178 (195)
T PRK12532 151 LGFSSDEIQQMC-GISTSNYHTIMHRARE 178 (195)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 356789999999 8899999998865543
No 154
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=21.41 E-value=70 Score=25.22 Aligned_cols=28 Identities=18% Similarity=0.108 Sum_probs=22.3
Q ss_pred CCchHHHhhhCCCCCHHHHHHHHHHHHHH
Q 025697 75 GNRWAVIARLFPGRTDNAVKNHWHVIMAR 103 (249)
Q Consensus 75 G~~Ws~IA~~lpgRT~~~cknrW~~~lkr 103 (249)
|-.+..||..+ |=+..+|++++....++
T Consensus 121 g~s~~eIA~~l-gis~~tv~~~l~Ra~~~ 148 (154)
T TIGR02950 121 EFSYKEIAELL-NLSLAKVKSNLFRARKE 148 (154)
T ss_pred cCcHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 34699999999 77999999998666443
No 155
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=21.12 E-value=2.3e+02 Score=22.26 Aligned_cols=27 Identities=19% Similarity=0.065 Sum_probs=20.0
Q ss_pred CCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 025697 75 GNRWAVIARLFPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 75 G~~Ws~IA~~lpgRT~~~cknrW~~~lk 102 (249)
|.....||..+ |-+..+|+++-...++
T Consensus 122 ~~s~~EIA~~l-~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 122 GKTMGEIALET-EMTYYQVRWIYRQALE 148 (154)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 45678888888 7788888887655443
No 156
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=21.04 E-value=1.3e+02 Score=22.61 Aligned_cols=29 Identities=24% Similarity=0.416 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCchHHHhhhCCCCCHHHHHH
Q 025697 66 RLLASHRIHGNRWAVIARLFPGRTDNAVKN 95 (249)
Q Consensus 66 ~Llelv~~~G~~Ws~IA~~lpgRT~~~ckn 95 (249)
-|-.+....|..|..+|+.| |=+...|..
T Consensus 4 ~l~~l~~~lG~~Wk~lar~L-G~s~~eI~~ 32 (86)
T cd08777 4 HLDLLRENLGKKWKRCARKL-GFTESEIEE 32 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHc-CCCHHHHHH
Confidence 34455677899999999999 556666554
No 157
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=21.00 E-value=1.4e+02 Score=21.64 Aligned_cols=36 Identities=31% Similarity=0.379 Sum_probs=25.7
Q ss_pred hhHhhHHhcCCChhhhhhhhhcccCCCCCCCCCCHHHHHHHHH
Q 025697 27 WNAIAEKLQGRSGKSCRLRWFNQLDPRINRSPFTEEEEERLLA 69 (249)
Q Consensus 27 W~~IA~~l~~Rt~~qcr~Rw~~~L~p~lkkg~WT~EED~~Lle 69 (249)
...||..+.|+|+.++|..+. + ...+|+||+..|.+
T Consensus 36 ~~~iA~~i~gks~eeir~~fg------i-~~d~t~eee~~i~~ 71 (78)
T PF01466_consen 36 CKYIANMIKGKSPEEIRKYFG------I-ENDLTPEEEEEIRK 71 (78)
T ss_dssp HHHHHHHHTTS-HHHHHHHHT----------TSSHHHHHHHHH
T ss_pred HHHHHHHhcCCCHHHHHHHcC------C-CCCCCHHHHHHHHH
Confidence 677899999999999998761 2 23688888877554
No 158
>PRK01905 DNA-binding protein Fis; Provisional
Probab=20.81 E-value=2.5e+02 Score=20.27 Aligned_cols=34 Identities=18% Similarity=0.228 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHH
Q 025697 62 EEEERLLASHRIHGNRWAVIARLFPGRTDNAVKNH 96 (249)
Q Consensus 62 EED~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknr 96 (249)
-|...+.+++...|++++..|+.+ |=+...++.+
T Consensus 37 ~E~~~i~~aL~~~~gn~s~aAr~L-GIsrstL~rk 70 (77)
T PRK01905 37 VEKPLLEVVMEQAGGNQSLAAEYL-GINRNTLRKK 70 (77)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHH
Confidence 466678899999999999999988 4455544443
No 159
>PRK00118 putative DNA-binding protein; Validated
Probab=20.78 E-value=2.9e+02 Score=21.62 Aligned_cols=40 Identities=15% Similarity=0.135 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHHHHHHH
Q 025697 61 EEEEERLLASHRIHGNRWAVIARLFPGRTDNAVKNHWHVIM 101 (249)
Q Consensus 61 ~EED~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknrW~~~l 101 (249)
++.+..++.+.-..|-..+.||+.+ |-|...|+.+-....
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~RAr 58 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKRTE 58 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 3556667777777888999999999 889999988765543
No 160
>PF07555 NAGidase: beta-N-acetylglucosaminidase ; InterPro: IPR011496 This family consists of both eukaryotic and prokaryotic hyaluronidases. Human Q9HAR0 from SWISSPROT is expressed during meningioma []. Clostridium perfringens, P26831 from SWISSPROT, is involved in pathogenesis and is likely to act on connectivity tissue during gas gangrene []. It catalyses the random hydrolysis of 1->4-linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate.; PDB: 2WB5_B 2V5C_B 2VUR_A 2V5D_A 2YDS_A 2CBI_A 2XPK_A 2CBJ_B 2J62_A 2X0Y_A ....
Probab=20.76 E-value=1.6e+02 Score=27.39 Aligned_cols=21 Identities=19% Similarity=0.415 Sum_probs=14.8
Q ss_pred CCCCHHHHHHHHHHHHHHCCC
Q 025697 5 GHWRPAEDEKLRELVERYGPH 25 (249)
Q Consensus 5 g~WT~EED~~L~~~V~~~G~~ 25 (249)
.+||.|+-..|++....+|.+
T Consensus 10 ~PWs~e~R~~l~~f~~~~kmN 30 (306)
T PF07555_consen 10 RPWSHEDRLDLIRFLGRYKMN 30 (306)
T ss_dssp S---HHHHHHHHHHHHHTT--
T ss_pred CCCCHHHHHHHHHHHHHcCCc
Confidence 389999999999999999743
No 161
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=20.75 E-value=2.5e+02 Score=22.77 Aligned_cols=28 Identities=11% Similarity=0.139 Sum_probs=22.0
Q ss_pred CCchHHHhhhCCCCCHHHHHHHHHHHHHH
Q 025697 75 GNRWAVIARLFPGRTDNAVKNHWHVIMAR 103 (249)
Q Consensus 75 G~~Ws~IA~~lpgRT~~~cknrW~~~lkr 103 (249)
|-.-..||..| |.+..+|+++....+++
T Consensus 145 g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 172 (179)
T PRK12514 145 GLSYKELAERH-DVPLNTMRTWLRRSLLK 172 (179)
T ss_pred CCCHHHHHHHH-CCChHHHHHHHHHHHHH
Confidence 55688999999 88999999988665443
No 162
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=20.69 E-value=2.6e+02 Score=22.94 Aligned_cols=28 Identities=32% Similarity=0.261 Sum_probs=22.3
Q ss_pred hCCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 025697 74 HGNRWAVIARLFPGRTDNAVKNHWHVIMA 102 (249)
Q Consensus 74 ~G~~Ws~IA~~lpgRT~~~cknrW~~~lk 102 (249)
.|-....||..| |-+...|+++-...++
T Consensus 144 ~g~s~~EIA~~l-~is~~tV~~~l~rar~ 171 (181)
T PRK12536 144 EGLSVAETAQLT-GLSESAVKVGIHRGLK 171 (181)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 456789999999 8899999998765443
No 163
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=20.66 E-value=2.9e+02 Score=24.24 Aligned_cols=45 Identities=20% Similarity=0.203 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHHHhCCchHHHhhhCCCCCHHHHHHHHHHHHHHHH
Q 025697 58 PFTEEEEERLLASHRIHGNRWAVIARLFPGRTDNAVKNHWHVIMARRC 105 (249)
Q Consensus 58 ~WT~EED~~Llelv~~~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr~~ 105 (249)
..|+-|-+.|.-+.. |....+||..| +-+...|+++...++++.-
T Consensus 133 ~LSpRErEVLrLLAq--GkTnKEIAe~L-~IS~rTVkth~srImkKLg 177 (198)
T PRK15201 133 HFSVTERHLLKLIAS--GYHLSETAALL-SLSEEQTKSLRRSIMRKLH 177 (198)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHHhC
Confidence 477777666555443 88899999999 8899999999988876653
No 164
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=20.52 E-value=2.5e+02 Score=22.72 Aligned_cols=29 Identities=31% Similarity=0.461 Sum_probs=22.0
Q ss_pred hCCchHHHhhhCCCCCHHHHHHHHHHHHHH
Q 025697 74 HGNRWAVIARLFPGRTDNAVKNHWHVIMAR 103 (249)
Q Consensus 74 ~G~~Ws~IA~~lpgRT~~~cknrW~~~lkr 103 (249)
.|-....||..+ |-|...|+.+....+++
T Consensus 155 ~g~s~~eIA~~l-gis~~~v~~~l~Ra~~~ 183 (189)
T TIGR02984 155 EGLSFAEVAERM-DRSEGAVSMLWVRGLAR 183 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 456788888888 77899998887665543
Done!