Query 024484
Match_columns 267
No_of_seqs 253 out of 1412
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 04:57:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024484.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024484hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03091 hypothetical protein; 100.0 6.4E-39 1.4E-43 305.5 10.7 118 1-118 1-118 (459)
2 PLN03212 Transcription repress 100.0 6.1E-39 1.3E-43 287.2 9.4 115 3-117 14-128 (249)
3 KOG0048 Transcription factor, 100.0 8.5E-38 1.8E-42 281.4 10.8 109 10-118 5-113 (238)
4 KOG0049 Transcription factor, 99.8 1E-19 2.2E-24 179.8 6.1 108 1-109 347-455 (939)
5 KOG0049 Transcription factor, 99.7 3.5E-18 7.6E-23 169.0 7.5 110 8-117 247-411 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.7 5.8E-17 1.3E-21 115.9 3.2 60 17-78 1-60 (60)
7 COG5147 REB1 Myb superfamily p 99.6 1.6E-16 3.5E-21 156.1 5.8 107 10-117 16-122 (512)
8 KOG0050 mRNA splicing protein 99.6 4.1E-16 8.8E-21 151.3 2.2 104 12-117 5-108 (617)
9 PF00249 Myb_DNA-binding: Myb- 99.5 6.6E-14 1.4E-18 96.3 4.9 46 67-112 1-48 (48)
10 KOG0051 RNA polymerase I termi 99.5 5.1E-14 1.1E-18 140.0 5.8 101 13-116 383-511 (607)
11 PF00249 Myb_DNA-binding: Myb- 99.4 7.8E-14 1.7E-18 95.9 0.3 48 14-61 1-48 (48)
12 PF13921 Myb_DNA-bind_6: Myb-l 99.3 2.9E-12 6.3E-17 91.5 4.6 45 70-114 1-45 (60)
13 smart00717 SANT SANT SWI3, AD 99.3 5E-12 1.1E-16 84.5 5.5 47 67-113 1-48 (49)
14 PLN03212 Transcription repress 99.2 1.4E-11 3E-16 111.3 4.9 55 62-116 20-76 (249)
15 cd00167 SANT 'SWI3, ADA2, N-Co 99.2 4E-11 8.6E-16 79.0 5.5 44 69-112 1-45 (45)
16 KOG0048 Transcription factor, 99.1 7.3E-11 1.6E-15 106.5 3.5 55 63-117 5-61 (238)
17 smart00717 SANT SANT SWI3, AD 99.0 7.8E-11 1.7E-15 78.7 1.9 48 14-62 1-48 (49)
18 PLN03091 hypothetical protein; 99.0 2.1E-10 4.6E-15 110.7 4.0 53 63-115 10-64 (459)
19 cd00167 SANT 'SWI3, ADA2, N-Co 98.9 6.8E-10 1.5E-14 73.0 1.6 45 16-61 1-45 (45)
20 KOG0051 RNA polymerase I termi 98.8 6.4E-09 1.4E-13 104.0 5.4 98 14-115 308-431 (607)
21 COG5147 REB1 Myb superfamily p 98.4 1.8E-08 3.9E-13 99.7 -2.4 98 13-113 290-397 (512)
22 KOG0457 Histone acetyltransfer 97.7 5.9E-05 1.3E-09 73.1 5.9 50 64-113 69-119 (438)
23 TIGR01557 myb_SHAQKYF myb-like 97.7 0.00012 2.5E-09 52.6 5.5 46 67-112 3-54 (57)
24 TIGR01557 myb_SHAQKYF myb-like 97.6 2.8E-05 6.2E-10 55.8 2.1 49 13-61 2-54 (57)
25 KOG0457 Histone acetyltransfer 97.6 1.9E-05 4.1E-10 76.5 1.3 49 12-61 70-118 (438)
26 PF13837 Myb_DNA-bind_4: Myb/S 97.4 0.00017 3.6E-09 54.7 3.4 49 67-115 1-67 (90)
27 KOG0050 mRNA splicing protein 97.4 0.00016 3.5E-09 71.5 4.1 55 65-119 5-60 (617)
28 PF13325 MCRS_N: N-terminal re 97.3 0.00035 7.7E-09 61.9 5.4 98 16-115 1-129 (199)
29 PF08914 Myb_DNA-bind_2: Rap1 97.3 0.0004 8.6E-09 51.1 4.4 50 67-116 2-61 (65)
30 TIGR02894 DNA_bind_RsfA transc 97.2 0.0006 1.3E-08 58.4 5.1 55 66-121 3-64 (161)
31 KOG1279 Chromatin remodeling f 97.0 0.00096 2.1E-08 66.6 5.2 47 66-112 252-298 (506)
32 COG5259 RSC8 RSC chromatin rem 96.9 0.00091 2E-08 65.7 4.2 44 68-111 280-323 (531)
33 COG5259 RSC8 RSC chromatin rem 96.8 0.00041 9E-09 68.0 1.1 46 13-60 278-323 (531)
34 KOG1279 Chromatin remodeling f 96.7 0.0008 1.7E-08 67.2 1.7 47 12-60 251-297 (506)
35 PRK13923 putative spore coat p 96.6 0.0031 6.6E-08 54.7 4.8 55 66-121 4-65 (170)
36 PF13873 Myb_DNA-bind_5: Myb/S 96.6 0.0062 1.3E-07 45.3 5.6 49 67-115 2-72 (78)
37 PF08914 Myb_DNA-bind_2: Rap1 96.1 0.0013 2.9E-08 48.4 -0.1 52 14-65 2-61 (65)
38 COG5114 Histone acetyltransfer 95.9 0.0086 1.9E-07 56.6 4.0 46 67-112 63-109 (432)
39 PLN03142 Probable chromatin-re 95.6 0.06 1.3E-06 58.3 9.6 101 15-116 825-988 (1033)
40 TIGR02894 DNA_bind_RsfA transc 95.5 0.0026 5.7E-08 54.6 -1.0 50 12-63 2-57 (161)
41 PF13837 Myb_DNA-bind_4: Myb/S 95.3 0.0037 8E-08 47.2 -0.5 47 14-60 1-63 (90)
42 COG5114 Histone acetyltransfer 95.1 0.0056 1.2E-07 57.8 -0.2 48 14-62 63-110 (432)
43 KOG2656 DNA methyltransferase 94.9 0.043 9.4E-07 53.1 5.2 84 35-119 74-188 (445)
44 KOG4282 Transcription factor G 94.8 0.063 1.4E-06 50.8 6.1 52 67-118 54-119 (345)
45 PRK13923 putative spore coat p 94.3 0.0094 2E-07 51.7 -0.6 51 11-63 2-58 (170)
46 PF12776 Myb_DNA-bind_3: Myb/S 94.3 0.11 2.5E-06 39.5 5.5 47 69-115 1-65 (96)
47 PF13873 Myb_DNA-bind_5: Myb/S 94.0 0.014 3E-07 43.4 -0.1 49 13-61 1-69 (78)
48 PF09111 SLIDE: SLIDE; InterP 93.7 0.12 2.5E-06 42.4 4.7 52 64-115 46-113 (118)
49 PF08281 Sigma70_r4_2: Sigma-7 91.2 0.57 1.2E-05 32.0 4.9 42 72-114 12-53 (54)
50 COG5118 BDP1 Transcription ini 89.8 0.62 1.4E-05 45.3 5.4 48 68-115 366-413 (507)
51 smart00595 MADF subfamily of S 84.9 2.2 4.8E-05 31.9 5.0 28 89-117 30-57 (89)
52 KOG1194 Predicted DNA-binding 84.5 2.7 5.8E-05 41.8 6.5 50 67-116 187-236 (534)
53 PF11035 SnAPC_2_like: Small n 81.5 7 0.00015 37.3 7.8 56 67-122 21-80 (344)
54 PF04545 Sigma70_r4: Sigma-70, 80.8 4.1 8.8E-05 27.4 4.6 41 73-114 7-47 (50)
55 PF09111 SLIDE: SLIDE; InterP 79.8 1.4 3E-05 36.1 2.3 34 11-44 46-82 (118)
56 KOG4282 Transcription factor G 78.9 0.76 1.6E-05 43.5 0.5 47 15-61 55-113 (345)
57 KOG4167 Predicted DNA-binding 75.4 9 0.0002 40.4 7.0 46 68-113 620-665 (907)
58 PF13404 HTH_AsnC-type: AsnC-t 74.2 6.4 0.00014 26.2 3.9 38 73-111 3-41 (42)
59 TIGR02985 Sig70_bacteroi1 RNA 74.1 6.8 0.00015 31.5 4.9 40 74-114 117-156 (161)
60 KOG4468 Polycomb-group transcr 72.3 5.8 0.00013 40.8 4.8 49 67-115 88-146 (782)
61 PF11626 Rap1_C: TRF2-interact 70.7 4.3 9.2E-05 31.1 2.7 22 12-33 45-74 (87)
62 PF07750 GcrA: GcrA cell cycle 70.4 5.1 0.00011 34.4 3.4 42 69-111 2-43 (162)
63 PRK11179 DNA-binding transcrip 69.7 8.8 0.00019 32.0 4.7 43 72-115 8-51 (153)
64 COG5118 BDP1 Transcription ini 68.2 3.1 6.7E-05 40.6 1.8 44 15-60 366-409 (507)
65 PRK11169 leucine-responsive tr 65.0 11 0.00025 31.8 4.5 43 72-115 13-56 (164)
66 PF01388 ARID: ARID/BRIGHT DNA 64.4 14 0.0003 28.0 4.4 38 77-114 40-90 (92)
67 PF10545 MADF_DNA_bdg: Alcohol 64.4 11 0.00024 27.2 3.9 30 88-117 28-58 (85)
68 KOG4329 DNA-binding protein [G 63.9 60 0.0013 31.9 9.5 46 68-113 278-324 (445)
69 PRK11924 RNA polymerase sigma 63.4 21 0.00045 29.2 5.7 30 84-114 139-168 (179)
70 cd08319 Death_RAIDD Death doma 63.1 9.7 0.00021 29.2 3.4 30 75-105 2-31 (83)
71 PF04504 DUF573: Protein of un 61.7 18 0.00039 28.4 4.8 49 68-116 5-66 (98)
72 TIGR02937 sigma70-ECF RNA poly 61.0 16 0.00035 28.3 4.5 38 76-114 116-153 (158)
73 cd08803 Death_ank3 Death domai 59.4 14 0.0003 28.4 3.6 31 75-106 4-34 (84)
74 PF11626 Rap1_C: TRF2-interact 59.0 9.2 0.0002 29.2 2.6 17 63-79 43-59 (87)
75 smart00501 BRIGHT BRIGHT, ARID 58.7 21 0.00045 27.2 4.6 39 77-115 36-87 (93)
76 PRK09652 RNA polymerase sigma 58.2 19 0.00041 29.5 4.7 35 79-114 137-171 (182)
77 PF11035 SnAPC_2_like: Small n 55.7 27 0.00059 33.4 5.6 86 14-113 21-127 (344)
78 cd08317 Death_ank Death domain 55.6 12 0.00027 28.1 2.8 31 75-106 4-34 (84)
79 PF13325 MCRS_N: N-terminal re 54.1 27 0.00058 31.2 5.1 44 69-113 1-47 (199)
80 PRK09641 RNA polymerase sigma 53.5 24 0.00052 29.4 4.6 29 85-114 151-179 (187)
81 PRK04217 hypothetical protein; 53.3 58 0.0013 26.3 6.5 46 68-115 41-86 (110)
82 PRK09643 RNA polymerase sigma 53.0 44 0.00095 28.5 6.2 35 79-114 143-177 (192)
83 KOG2656 DNA methyltransferase 52.2 7.9 0.00017 37.9 1.5 50 11-61 127-181 (445)
84 COG2197 CitB Response regulato 52.0 22 0.00047 31.3 4.2 45 68-115 147-191 (211)
85 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 52.0 27 0.00058 24.4 3.8 34 73-107 7-40 (50)
86 cd08318 Death_NMPP84 Death dom 51.6 19 0.00041 27.4 3.3 28 78-106 10-37 (86)
87 TIGR02939 RpoE_Sigma70 RNA pol 51.5 22 0.00047 29.7 4.0 29 85-114 153-181 (190)
88 PRK09047 RNA polymerase factor 51.3 32 0.0007 27.9 4.9 29 85-114 121-149 (161)
89 KOG2009 Transcription initiati 51.3 18 0.00039 37.2 4.0 50 66-115 408-457 (584)
90 KOG4167 Predicted DNA-binding 50.9 6.9 0.00015 41.2 0.9 45 13-59 618-662 (907)
91 PF13404 HTH_AsnC-type: AsnC-t 50.1 5 0.00011 26.7 -0.1 37 20-58 3-39 (42)
92 PRK12523 RNA polymerase sigma 49.5 34 0.00075 28.4 4.9 37 78-115 127-163 (172)
93 KOG4468 Polycomb-group transcr 49.5 16 0.00034 37.9 3.2 47 14-61 88-143 (782)
94 cd06171 Sigma70_r4 Sigma70, re 48.2 49 0.0011 20.9 4.5 37 74-111 14-50 (55)
95 PRK12530 RNA polymerase sigma 48.1 55 0.0012 27.8 6.0 29 85-114 149-177 (189)
96 cd08804 Death_ank2 Death domai 48.1 22 0.00049 27.0 3.2 31 75-106 4-34 (84)
97 TIGR02948 SigW_bacill RNA poly 47.7 31 0.00068 28.7 4.4 28 86-114 152-179 (187)
98 PRK12529 RNA polymerase sigma 47.5 38 0.00083 28.4 4.9 34 81-115 138-171 (178)
99 TIGR02954 Sig70_famx3 RNA poly 47.2 36 0.00077 28.1 4.6 29 85-114 134-162 (169)
100 PRK09642 RNA polymerase sigma 47.2 40 0.00086 27.5 4.8 29 85-114 121-149 (160)
101 PRK12532 RNA polymerase sigma 46.6 65 0.0014 27.3 6.2 30 84-114 150-179 (195)
102 TIGR02943 Sig70_famx1 RNA poly 46.2 41 0.00088 28.6 4.9 34 80-114 141-174 (188)
103 PRK12515 RNA polymerase sigma 46.2 63 0.0014 27.2 6.0 30 84-114 145-174 (189)
104 PRK12512 RNA polymerase sigma 46.0 41 0.00088 28.2 4.8 30 85-115 146-175 (184)
105 PRK11923 algU RNA polymerase s 45.9 36 0.00077 28.7 4.5 28 86-114 154-181 (193)
106 PRK09637 RNA polymerase sigma 45.8 39 0.00085 28.6 4.7 31 83-114 119-149 (181)
107 PF13137 DUF3983: Protein of u 45.8 13 0.00027 24.0 1.2 10 250-259 24-33 (34)
108 PRK09645 RNA polymerase sigma 45.7 42 0.0009 27.7 4.8 29 85-114 133-161 (173)
109 PRK09648 RNA polymerase sigma 45.5 42 0.00091 28.2 4.8 31 84-115 153-183 (189)
110 cd08779 Death_PIDD Death Domai 45.4 19 0.00042 27.4 2.5 46 76-122 3-51 (86)
111 PRK12531 RNA polymerase sigma 44.9 43 0.00094 28.5 4.9 29 85-114 156-184 (194)
112 smart00344 HTH_ASNC helix_turn 44.4 50 0.0011 25.3 4.7 42 73-115 3-45 (108)
113 cd08311 Death_p75NR Death doma 44.2 27 0.00058 26.3 3.0 34 72-107 2-35 (77)
114 PF07638 Sigma70_ECF: ECF sigm 42.9 61 0.0013 27.7 5.5 39 73-112 138-176 (185)
115 cd08777 Death_RIP1 Death Domai 42.8 27 0.00059 26.7 2.9 31 76-107 3-33 (86)
116 smart00005 DEATH DEATH domain, 42.8 33 0.00071 25.3 3.3 31 74-105 4-35 (88)
117 PRK12524 RNA polymerase sigma 42.7 48 0.001 28.3 4.8 31 84-115 150-180 (196)
118 PRK09651 RNA polymerase sigma 42.6 62 0.0013 26.9 5.4 30 85-115 134-163 (172)
119 PRK06811 RNA polymerase factor 42.3 49 0.0011 28.0 4.8 29 86-115 147-175 (189)
120 KOG3841 TEF-1 and related tran 42.1 93 0.002 30.7 7.0 75 8-119 70-149 (455)
121 PRK06759 RNA polymerase factor 41.9 55 0.0012 26.3 4.8 29 85-114 121-149 (154)
122 TIGR02952 Sig70_famx2 RNA poly 41.5 53 0.0011 26.8 4.7 28 86-114 138-165 (170)
123 PRK12514 RNA polymerase sigma 40.9 53 0.0012 27.3 4.7 28 86-114 145-172 (179)
124 PRK12536 RNA polymerase sigma 40.1 56 0.0012 27.4 4.8 30 84-114 143-172 (181)
125 PRK12528 RNA polymerase sigma 40.1 61 0.0013 26.4 4.9 32 82-114 125-156 (161)
126 PF00196 GerE: Bacterial regul 39.9 35 0.00076 23.5 2.9 44 69-115 3-46 (58)
127 PF06599 DUF1139: Protein of u 39.5 17 0.00036 34.0 1.5 14 245-258 277-290 (309)
128 TIGR02999 Sig-70_X6 RNA polyme 39.5 61 0.0013 26.9 4.9 29 85-114 149-177 (183)
129 PF09420 Nop16: Ribosome bioge 39.1 65 0.0014 27.4 5.0 46 66-111 113-162 (164)
130 PRK09649 RNA polymerase sigma 38.3 57 0.0012 27.6 4.6 29 85-114 145-173 (185)
131 PRK12547 RNA polymerase sigma 38.0 68 0.0015 26.4 4.9 30 84-114 126-155 (164)
132 PRK12520 RNA polymerase sigma 37.8 1E+02 0.0022 26.0 6.1 30 85-115 146-175 (191)
133 PRK12542 RNA polymerase sigma 37.7 64 0.0014 27.1 4.8 29 85-114 137-165 (185)
134 PRK13919 putative RNA polymera 37.7 65 0.0014 26.9 4.8 28 86-114 151-178 (186)
135 PRK12516 RNA polymerase sigma 37.3 97 0.0021 26.4 5.9 36 78-114 124-159 (187)
136 TIGR02984 Sig-70_plancto1 RNA 37.2 66 0.0014 26.7 4.8 30 84-114 154-183 (189)
137 PRK12527 RNA polymerase sigma 37.2 73 0.0016 25.9 4.9 29 85-114 120-148 (159)
138 TIGR02950 SigM_subfam RNA poly 37.0 23 0.00051 28.5 1.9 28 86-114 121-148 (154)
139 PRK12545 RNA polymerase sigma 37.0 65 0.0014 27.7 4.8 29 85-114 154-182 (201)
140 cd08805 Death_ank1 Death domai 36.7 41 0.00089 25.8 3.1 40 75-115 4-46 (84)
141 TIGR02960 SigX5 RNA polymerase 36.5 56 0.0012 30.0 4.5 29 85-114 157-185 (324)
142 KOG0384 Chromodomain-helicase 36.4 34 0.00073 38.3 3.4 72 14-92 1133-1205(1373)
143 PRK05602 RNA polymerase sigma 35.9 95 0.0021 26.0 5.6 29 85-114 143-171 (186)
144 TIGR02983 SigE-fam_strep RNA p 35.6 70 0.0015 26.0 4.6 41 74-115 114-154 (162)
145 PRK11179 DNA-binding transcrip 35.6 13 0.00029 30.9 0.2 43 20-64 9-51 (153)
146 PRK00118 putative DNA-binding 35.0 85 0.0018 25.1 4.7 41 72-113 19-59 (104)
147 PF02954 HTH_8: Bacterial regu 35.0 74 0.0016 20.7 3.7 34 73-107 5-38 (42)
148 PRK11922 RNA polymerase sigma 34.8 39 0.00085 29.8 3.1 29 86-115 165-193 (231)
149 PRK12537 RNA polymerase sigma 34.8 74 0.0016 26.6 4.7 29 85-114 148-176 (182)
150 PRK12546 RNA polymerase sigma 33.1 74 0.0016 27.2 4.5 34 80-114 123-156 (188)
151 PRK09646 RNA polymerase sigma 32.6 1E+02 0.0022 26.1 5.3 29 85-114 157-185 (194)
152 PRK12544 RNA polymerase sigma 32.5 1.4E+02 0.003 26.0 6.1 30 85-115 163-192 (206)
153 PRK09636 RNA polymerase sigma 32.2 81 0.0017 28.9 4.8 29 85-114 130-158 (293)
154 PRK12519 RNA polymerase sigma 31.9 72 0.0016 26.9 4.2 29 85-114 156-184 (194)
155 PRK09647 RNA polymerase sigma 31.1 1.4E+02 0.0031 25.8 6.0 29 85-114 153-181 (203)
156 PF13936 HTH_38: Helix-turn-he 31.1 53 0.0012 21.7 2.6 36 69-106 4-39 (44)
157 PRK11169 leucine-responsive tr 30.8 13 0.00029 31.3 -0.6 44 19-64 13-56 (164)
158 PRK10100 DNA-binding transcrip 30.8 1.1E+02 0.0024 27.0 5.3 44 69-115 155-198 (216)
159 cd08306 Death_FADD Fas-associa 30.3 67 0.0015 24.4 3.3 31 77-108 4-34 (86)
160 TIGR02957 SigX4 RNA polymerase 30.2 91 0.002 28.5 4.8 29 85-114 123-151 (281)
161 TIGR02989 Sig-70_gvs1 RNA poly 30.0 1.1E+02 0.0024 24.6 4.8 29 85-114 126-154 (159)
162 PRK09415 RNA polymerase factor 29.9 90 0.0019 26.1 4.4 28 86-114 143-170 (179)
163 cd01670 Death Death Domain: a 29.5 55 0.0012 23.5 2.6 26 78-104 2-27 (79)
164 COG1522 Lrp Transcriptional re 28.2 1.1E+02 0.0025 24.6 4.6 43 72-115 7-50 (154)
165 PRK08241 RNA polymerase factor 28.0 85 0.0019 29.1 4.3 29 85-114 168-196 (339)
166 PF09420 Nop16: Ribosome bioge 27.6 45 0.00098 28.4 2.2 47 12-59 112-161 (164)
167 PRK06986 fliA flagellar biosyn 27.3 1.1E+02 0.0023 27.0 4.6 37 78-115 192-228 (236)
168 PRK15201 fimbriae regulatory p 27.3 1.6E+02 0.0034 26.3 5.4 44 69-115 133-176 (198)
169 PRK09639 RNA polymerase sigma 27.2 1.2E+02 0.0027 24.5 4.7 29 85-114 126-154 (166)
170 TIGR03001 Sig-70_gmx1 RNA poly 26.9 1.8E+02 0.0039 26.2 6.0 28 86-114 177-204 (244)
171 PRK12526 RNA polymerase sigma 26.8 1.2E+02 0.0027 26.0 4.8 28 86-114 169-196 (206)
172 COG2963 Transposase and inacti 26.8 1.7E+02 0.0037 22.8 5.3 45 67-113 5-50 (116)
173 PRK09483 response regulator; P 26.8 1E+02 0.0022 25.6 4.1 45 68-115 147-191 (217)
174 TIGR02959 SigZ RNA polymerase 26.4 1.4E+02 0.003 24.8 4.9 29 85-114 115-143 (170)
175 PRK12538 RNA polymerase sigma 26.3 1.5E+02 0.0033 26.3 5.4 28 86-114 187-214 (233)
176 PLN03142 Probable chromatin-re 26.3 1.2E+02 0.0026 33.6 5.5 45 68-112 825-870 (1033)
177 PRK09638 RNA polymerase sigma 26.3 55 0.0012 27.0 2.4 29 85-114 141-169 (176)
178 PRK10360 DNA-binding transcrip 25.9 1.7E+02 0.0037 23.7 5.3 45 68-115 136-180 (196)
179 PRK06930 positive control sigm 25.5 2.1E+02 0.0045 24.5 5.9 38 77-115 121-158 (170)
180 PRK01905 DNA-binding protein F 24.9 1.6E+02 0.0035 21.7 4.5 35 72-107 36-70 (77)
181 PRK12511 RNA polymerase sigma 24.4 1.4E+02 0.0031 25.2 4.7 29 85-114 126-154 (182)
182 PRK15411 rcsA colanic acid cap 24.4 1.2E+02 0.0026 26.4 4.3 44 69-115 137-180 (207)
183 PRK12522 RNA polymerase sigma 24.2 1.5E+02 0.0032 24.5 4.7 28 86-114 135-162 (173)
184 PRK08301 sporulation sigma fac 24.1 1.3E+02 0.0029 26.3 4.6 28 86-114 198-225 (234)
185 PRK15328 invasion protein IagB 24.0 1.8E+02 0.004 24.8 5.2 42 77-118 98-141 (160)
186 KOG2009 Transcription initiati 23.9 54 0.0012 33.8 2.3 48 10-59 405-452 (584)
187 PRK12540 RNA polymerase sigma 23.9 1.5E+02 0.0032 25.1 4.7 29 85-114 126-154 (182)
188 PRK06288 RNA polymerase sigma 23.8 2.3E+02 0.0049 25.6 6.2 29 85-114 227-255 (268)
189 PRK12535 RNA polymerase sigma 23.5 1.4E+02 0.0031 25.6 4.6 28 86-114 149-176 (196)
190 PRK12513 RNA polymerase sigma 23.5 70 0.0015 27.0 2.6 28 86-114 155-182 (194)
191 PRK07670 RNA polymerase sigma 23.4 1.4E+02 0.0031 26.6 4.7 39 75-114 206-244 (251)
192 PRK12543 RNA polymerase sigma 23.0 2.9E+02 0.0063 22.9 6.3 29 85-114 132-160 (179)
193 PF09197 Rap1-DNA-bind: Rap1, 23.0 2.4E+02 0.0052 22.7 5.4 50 69-118 1-81 (105)
194 PRK08295 RNA polymerase factor 22.9 1.5E+02 0.0033 25.0 4.7 29 85-114 169-197 (208)
195 TIGR02947 SigH_actino RNA poly 22.6 78 0.0017 26.7 2.7 28 86-114 147-174 (193)
196 PF09905 DUF2132: Uncharacteri 22.6 47 0.001 24.4 1.1 44 22-78 12-62 (64)
197 PRK09644 RNA polymerase sigma 22.4 1.6E+02 0.0035 24.0 4.5 29 85-114 123-151 (165)
198 TIGR02980 SigBFG RNA polymeras 22.4 1.7E+02 0.0037 25.4 5.0 31 84-115 192-222 (227)
199 PRK12541 RNA polymerase sigma 22.2 1.6E+02 0.0034 23.9 4.4 28 86-114 128-155 (161)
200 PRK00430 fis global DNA-bindin 22.2 1.9E+02 0.0042 22.5 4.6 34 73-107 55-88 (95)
201 PF10440 WIYLD: Ubiquitin-bind 22.1 67 0.0014 23.7 1.8 19 76-94 30-48 (65)
202 KOG1194 Predicted DNA-binding 21.7 41 0.00088 33.8 0.8 44 14-59 187-230 (534)
203 PF00531 Death: Death domain; 21.4 1.4E+02 0.003 21.4 3.5 24 82-106 8-31 (83)
204 PRK12518 RNA polymerase sigma 21.2 1E+02 0.0022 25.3 3.1 29 86-115 136-164 (175)
205 PRK12525 RNA polymerase sigma 20.9 2E+02 0.0044 23.6 4.9 28 86-114 134-161 (168)
206 PRK12534 RNA polymerase sigma 20.2 2E+02 0.0043 24.0 4.7 29 85-114 152-180 (187)
207 TIGR02479 FliA_WhiG RNA polyme 20.1 2E+02 0.0043 25.0 4.8 29 85-114 190-218 (224)
No 1
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=6.4e-39 Score=305.50 Aligned_cols=118 Identities=67% Similarity=1.223 Sum_probs=114.6
Q ss_pred CCCCcccccCCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcccCcccccccccccccCCCCCCCCCHHHHHHHHH
Q 024484 1 MGRAPCCEKMGLKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETIIN 80 (267)
Q Consensus 1 m~R~~~~~k~~lkkg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~ikk~~WT~EED~~Li~ 80 (267)
|||++||+|.+++||+||+|||++|+++|++||..+|..||+.++.+|+++|||+||.+||+|.+++++||+|||++|++
T Consensus 1 mgr~~Cc~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLe 80 (459)
T PLN03091 1 MGRHSCCYKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIE 80 (459)
T ss_pred CCCCccCcCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHH
Confidence 99999999999999999999999999999999999999999998866999999999999999999999999999999999
Q ss_pred HHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHHHHHH
Q 024484 81 LHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAA 118 (267)
Q Consensus 81 l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~~~~ 118 (267)
+|++||++|+.||++|||||+++|||||+.++||+++.
T Consensus 81 L~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~ 118 (459)
T PLN03091 81 LHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQ 118 (459)
T ss_pred HHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999998554
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=6.1e-39 Score=287.15 Aligned_cols=115 Identities=68% Similarity=1.324 Sum_probs=111.1
Q ss_pred CCcccccCCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcccCcccccccccccccCCCCCCCCCHHHHHHHHHHH
Q 024484 3 RAPCCEKMGLKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETIINLH 82 (267)
Q Consensus 3 R~~~~~k~~lkkg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~ikk~~WT~EED~~Li~l~ 82 (267)
|+|||.|++++|++||+|||++|+++|++||..+|..||+.++.+|+++|||+||.+||+|.+++++||+|||++|++++
T Consensus 14 ~~pcc~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~ 93 (249)
T PLN03212 14 TTPCCTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLH 93 (249)
T ss_pred CCCCcccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHH
Confidence 68999999999999999999999999999999999999999975699999999999999999999999999999999999
Q ss_pred HhhCCchhHHhhcCCCCCHHHHHHHHHHHhHHHHH
Q 024484 83 DMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKKAA 117 (267)
Q Consensus 83 ~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~~~ 117 (267)
.+||++|+.||++|||||+++|||||+.++++++.
T Consensus 94 ~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~ 128 (249)
T PLN03212 94 RLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLL 128 (249)
T ss_pred HhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHH
Confidence 99999999999999999999999999999998843
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=8.5e-38 Score=281.40 Aligned_cols=109 Identities=71% Similarity=1.153 Sum_probs=104.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcccCcccccccccccccCCCCCCCCCHHHHHHHHHHHHhhCCch
Q 024484 10 MGLKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETIINLHDMLGNRW 89 (267)
Q Consensus 10 ~~lkkg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~ikk~~WT~EED~~Li~l~~~~G~kW 89 (267)
+.+.||+||+|||++|+++|++||+++|..||+.+|.+||+|+||+||.|||+|++++|.||+|||++|++||..||++|
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrW 84 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRW 84 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHH
Confidence 34558999999999999999999999999999999966999999999999999999999999999999999999999999
Q ss_pred hHHhhcCCCCCHHHHHHHHHHHhHHHHHH
Q 024484 90 SAIAGRLPGRTDNEIKNVWHTHLKKKAAA 118 (267)
Q Consensus 90 s~IA~~lpgRT~~q~KnRw~~~lkk~~~~ 118 (267)
+.||++|||||+|+|||+|+++|||++..
T Consensus 85 s~IA~~LPGRTDNeIKN~Wnt~lkkkl~~ 113 (238)
T KOG0048|consen 85 SLIAGRLPGRTDNEVKNHWNTHLKKKLLK 113 (238)
T ss_pred HHHHhhCCCcCHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999998554
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.78 E-value=1e-19 Score=179.78 Aligned_cols=108 Identities=23% Similarity=0.458 Sum_probs=101.6
Q ss_pred CCCCcccccCCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcccCcccccccccccccCCCCCCCCCHHHHHHHHH
Q 024484 1 MGRAPCCEKMGLKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETIIN 80 (267)
Q Consensus 1 m~R~~~~~k~~lkkg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~ikk~~WT~EED~~Li~ 80 (267)
++|+.+...|++++|+||++||.+|+.+|.+||.+.|.+|-..+++ |+..|||+||.|+|....|++.||-.||+.|+.
T Consensus 347 I~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPn-RSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~ 425 (939)
T KOG0049|consen 347 ITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPN-RSDSQCRERYTNVLNRSAKVERWTLVEDEQLLY 425 (939)
T ss_pred hhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCC-ccHHHHHHHHHHHHHHhhccCceeecchHHHHH
Confidence 4788999999999999999999999999999999999999999998 999999999999999999999999999999999
Q ss_pred HHHhhC-CchhHHhhcCCCCCHHHHHHHHH
Q 024484 81 LHDMLG-NRWSAIAGRLPGRTDNEIKNVWH 109 (267)
Q Consensus 81 l~~~~G-~kWs~IA~~lpgRT~~q~KnRw~ 109 (267)
++++|| ++|.+||..||.||..|...|=.
T Consensus 426 ~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~ 455 (939)
T KOG0049|consen 426 AVKVYGKGNWAKCAMLLPKKTSRQLRRRRL 455 (939)
T ss_pred HHHHHccchHHHHHHHccccchhHHHHHHH
Confidence 999999 78999999999999966654433
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.73 E-value=3.5e-18 Score=168.99 Aligned_cols=110 Identities=20% Similarity=0.424 Sum_probs=102.1
Q ss_pred ccCCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcccCccccc---------------------------------
Q 024484 8 EKMGLKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCR--------------------------------- 54 (267)
Q Consensus 8 ~k~~lkkg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr--------------------------------- 54 (267)
..|.++|..|++|||++|..+...++..+|.+||..+|++|+..||.
T Consensus 247 l~P~~nk~~WS~EE~E~L~AiA~A~~~~~W~~IA~~Lgt~RS~yQC~~kF~t~~~~L~ekeWsEEed~kL~alV~~~~~n 326 (939)
T KOG0049|consen 247 LNPKWNKEHWSNEEVEKLKALAEAPKFVSWPMIALNLGTNRSSYQCMEKFKTEVSQLSEKEWSEEEDTKLIALVKITSIN 326 (939)
T ss_pred cCCccchhccChHHHHHHHHHHhccccccHHHHHHHhCCCcchHHHHHHHHHHHHHHHhhhcchhhhHHHHHHHHHhhcc
Confidence 46889999999999999999999999999999999999999999997
Q ss_pred ---------------------ccccccccCCCCCCCCCHHHHHHHHHHHHhhCCc-hhHHhhcCCCCCHHHHHHHHHHHh
Q 024484 55 ---------------------LRWINYLRPDIKRGNFSKEEEETIINLHDMLGNR-WSAIAGRLPGRTDNEIKNVWHTHL 112 (267)
Q Consensus 55 ---------------------~Rw~n~L~p~ikk~~WT~EED~~Li~l~~~~G~k-Ws~IA~~lpgRT~~q~KnRw~~~l 112 (267)
-||...|+|.+++|+||.+||.+|+.+|.+||.+ |.+|-..+|||++.|||.||++.|
T Consensus 327 ShI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL 406 (939)
T KOG0049|consen 327 SHIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVL 406 (939)
T ss_pred CccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHH
Confidence 5778889999999999999999999999999965 999999999999999999999999
Q ss_pred HHHHH
Q 024484 113 KKKAA 117 (267)
Q Consensus 113 kk~~~ 117 (267)
..+.+
T Consensus 407 ~~s~K 411 (939)
T KOG0049|consen 407 NRSAK 411 (939)
T ss_pred HHhhc
Confidence 77643
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=99.65 E-value=5.8e-17 Score=115.90 Aligned_cols=60 Identities=45% Similarity=0.916 Sum_probs=55.0
Q ss_pred CCHHHHHHHHHHHHHhCCCCccccccccCcccCcccccccccccccCCCCCCCCCHHHHHHH
Q 024484 17 WTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETI 78 (267)
Q Consensus 17 WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~ikk~~WT~EED~~L 78 (267)
||+|||++|+.+|..|| .+|..||+++|. |++.||+.||.++|.|.+++++||++||++|
T Consensus 1 WT~eEd~~L~~~~~~~g-~~W~~Ia~~l~~-Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYG-NDWKKIAEHLGN-RTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHT-S-HHHHHHHSTT-S-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC-cCHHHHHHHHCc-CCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 99999999999999999 799999999975 9999999999999999999999999999987
No 7
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.64 E-value=1.6e-16 Score=156.09 Aligned_cols=107 Identities=33% Similarity=0.532 Sum_probs=101.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcccCcccccccccccccCCCCCCCCCHHHHHHHHHHHHhhCCch
Q 024484 10 MGLKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETIINLHDMLGNRW 89 (267)
Q Consensus 10 ~~lkkg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~ikk~~WT~EED~~Li~l~~~~G~kW 89 (267)
..++.|.|+..||+.|..+|+.||+.+|.+||..+.. |+++||+.||.++++|.+++.+|+.|||..|+.+..++|.+|
T Consensus 16 ~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~-~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~w 94 (512)
T COG5147 16 TKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLIS-STGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQW 94 (512)
T ss_pred ceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcc-cccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCchh
Confidence 3467799999999999999999999999999999997 999999999999999999999999999999999999999999
Q ss_pred hHHhhcCCCCCHHHHHHHHHHHhHHHHH
Q 024484 90 SAIAGRLPGRTDNEIKNVWHTHLKKKAA 117 (267)
Q Consensus 90 s~IA~~lpgRT~~q~KnRw~~~lkk~~~ 117 (267)
+.||..++|||..+|.+||..++....+
T Consensus 95 stia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 95 STIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhccccCccchHHHHHHHHHHhhhhhc
Confidence 9999999999999999999999887643
No 8
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.58 E-value=4.1e-16 Score=151.34 Aligned_cols=104 Identities=27% Similarity=0.610 Sum_probs=99.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcccCcccccccccccccCCCCCCCCCHHHHHHHHHHHHhhCCchhH
Q 024484 12 LKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETIINLHDMLGNRWSA 91 (267)
Q Consensus 12 lkkg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~ikk~~WT~EED~~Li~l~~~~G~kWs~ 91 (267)
++.|.|+.-||+.|..+|.+||.+.|+.|++.+.- .+.+||+.||..+|+|.|++..|+.|||+.|+.+.+.+...|..
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~-kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrt 83 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNR-KTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRT 83 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhh-cchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccch
Confidence 56789999999999999999999999999999987 99999999999999999999999999999999999999999999
Q ss_pred HhhcCCCCCHHHHHHHHHHHhHHHHH
Q 024484 92 IAGRLPGRTDNEIKNVWHTHLKKKAA 117 (267)
Q Consensus 92 IA~~lpgRT~~q~KnRw~~~lkk~~~ 117 (267)
||..| ||+.+||-.||+.+|-....
T Consensus 84 Ia~i~-gr~~~qc~eRy~~ll~~~~s 108 (617)
T KOG0050|consen 84 IADIM-GRTSQQCLERYNNLLDVYVS 108 (617)
T ss_pred HHHHh-hhhHHHHHHHHHHHHHHHHh
Confidence 99999 99999999999999976644
No 9
>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=99.47 E-value=6.6e-14 Score=96.27 Aligned_cols=46 Identities=33% Similarity=0.714 Sum_probs=42.0
Q ss_pred CCCCCHHHHHHHHHHHHhhCCc-hhHHhhcCC-CCCHHHHHHHHHHHh
Q 024484 67 RGNFSKEEEETIINLHDMLGNR-WSAIAGRLP-GRTDNEIKNVWHTHL 112 (267)
Q Consensus 67 k~~WT~EED~~Li~l~~~~G~k-Ws~IA~~lp-gRT~~q~KnRw~~~l 112 (267)
|++||+|||++|++++.+||.. |..||..|| |||..||++||+.++
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 5799999999999999999988 999999999 999999999999875
No 10
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.46 E-value=5.1e-14 Score=140.03 Aligned_cols=101 Identities=30% Similarity=0.605 Sum_probs=92.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccccccCcccCcccccccccccccCCC--CCCCCCHHHHHHHHHHHH-------
Q 024484 13 KKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDI--KRGNFSKEEEETIINLHD------- 83 (267)
Q Consensus 13 kkg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~i--kk~~WT~EED~~Li~l~~------- 83 (267)
.+|.||+||++.|..+|..+| ..|..|++.+| |.+..||+||.+|..+.- +++.||.||++.|+++|.
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g-~~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~ 459 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHG-NDWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREAL 459 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhc-ccHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhh
Confidence 899999999999999999999 89999999998 999999999999998874 899999999999999995
Q ss_pred hh-------------------CCchhHHhhcCCCCCHHHHHHHHHHHhHHHH
Q 024484 84 ML-------------------GNRWSAIAGRLPGRTDNEIKNVWHTHLKKKA 116 (267)
Q Consensus 84 ~~-------------------G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~~ 116 (267)
++ +-.|+.|++.+..|+..|||.+|..++.+..
T Consensus 460 q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s 511 (607)
T KOG0051|consen 460 QPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPS 511 (607)
T ss_pred cccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHH
Confidence 33 1159999999999999999999999998764
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=99.37 E-value=7.8e-14 Score=95.92 Aligned_cols=48 Identities=44% Similarity=0.799 Sum_probs=42.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccccccccCcccCcccccccccccc
Q 024484 14 KGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYL 61 (267)
Q Consensus 14 kg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L 61 (267)
|++||+|||++|+++|.+||..+|..||..++++|++.||+.||.++|
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 689999999999999999997779999999994499999999999875
No 12
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.29 E-value=2.9e-12 Score=91.47 Aligned_cols=45 Identities=38% Similarity=0.747 Sum_probs=39.2
Q ss_pred CCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 70 FSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 70 WT~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
||+|||++|++++.+||++|.+||++|+.||..+|++||+..|++
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 999999999999999999999999999669999999999996653
No 13
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.29 E-value=5e-12 Score=84.51 Aligned_cols=47 Identities=40% Similarity=0.832 Sum_probs=44.4
Q ss_pred CCCCCHHHHHHHHHHHHhhC-CchhHHhhcCCCCCHHHHHHHHHHHhH
Q 024484 67 RGNFSKEEEETIINLHDMLG-NRWSAIAGRLPGRTDNEIKNVWHTHLK 113 (267)
Q Consensus 67 k~~WT~EED~~Li~l~~~~G-~kWs~IA~~lpgRT~~q~KnRw~~~lk 113 (267)
+++||++||.+|+.++.+|| .+|..||..|++||+.+|++||+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 46899999999999999999 999999999999999999999998765
No 14
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.20 E-value=1.4e-11 Score=111.27 Aligned_cols=55 Identities=24% Similarity=0.490 Sum_probs=50.2
Q ss_pred cCCCCCCCCCHHHHHHHHHHHHhhC-CchhHHhhcC-CCCCHHHHHHHHHHHhHHHH
Q 024484 62 RPDIKRGNFSKEEEETIINLHDMLG-NRWSAIAGRL-PGRTDNEIKNVWHTHLKKKA 116 (267)
Q Consensus 62 ~p~ikk~~WT~EED~~Li~l~~~~G-~kWs~IA~~l-pgRT~~q~KnRw~~~lkk~~ 116 (267)
++.+++++||+|||++|+++|++|| ++|..||+++ +|||+.|||.||.++|+..+
T Consensus 20 K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I 76 (249)
T PLN03212 20 KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSV 76 (249)
T ss_pred cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhc
Confidence 3578999999999999999999999 6899999998 69999999999999997654
No 15
>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=99.19 E-value=4e-11 Score=79.00 Aligned_cols=44 Identities=34% Similarity=0.724 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHHHHhhC-CchhHHhhcCCCCCHHHHHHHHHHHh
Q 024484 69 NFSKEEEETIINLHDMLG-NRWSAIAGRLPGRTDNEIKNVWHTHL 112 (267)
Q Consensus 69 ~WT~EED~~Li~l~~~~G-~kWs~IA~~lpgRT~~q~KnRw~~~l 112 (267)
+||.+|+..|+.++.+|| .+|..||..|++||..+|++||..++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 99999999999999999999998763
No 16
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.07 E-value=7.3e-11 Score=106.54 Aligned_cols=55 Identities=20% Similarity=0.355 Sum_probs=50.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhC-CchhHHhhcCC-CCCHHHHHHHHHHHhHHHHH
Q 024484 63 PDIKRGNFSKEEEETIINLHDMLG-NRWSAIAGRLP-GRTDNEIKNVWHTHLKKKAA 117 (267)
Q Consensus 63 p~ikk~~WT~EED~~Li~l~~~~G-~kWs~IA~~lp-gRT~~q~KnRw~~~lkk~~~ 117 (267)
|.+.+|+||.|||++|+++|++|| ++|..||+.++ ||++.+||-||.++|+..++
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ik 61 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLK 61 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCcc
Confidence 445689999999999999999999 56999999999 99999999999999987754
No 17
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.04 E-value=7.8e-11 Score=78.65 Aligned_cols=48 Identities=46% Similarity=0.856 Sum_probs=44.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccccccccCcccCccccccccccccc
Q 024484 14 KGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLR 62 (267)
Q Consensus 14 kg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~ 62 (267)
+++||++||++|+.++..||..+|..||..+++ |++.+|+.||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~-rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPG-RTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCC-CCHHHHHHHHHHHcC
Confidence 478999999999999999998899999999997 999999999998764
No 18
>PLN03091 hypothetical protein; Provisional
Probab=99.00 E-value=2.1e-10 Score=110.71 Aligned_cols=53 Identities=21% Similarity=0.452 Sum_probs=48.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhC-CchhHHhhcC-CCCCHHHHHHHHHHHhHHH
Q 024484 63 PDIKRGNFSKEEEETIINLHDMLG-NRWSAIAGRL-PGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 63 p~ikk~~WT~EED~~Li~l~~~~G-~kWs~IA~~l-pgRT~~q~KnRw~~~lkk~ 115 (267)
+.+++++||+|||++|+++|++|| ++|..||+.+ +||++.|||.||.++|+..
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~ 64 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPD 64 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCc
Confidence 578999999999999999999999 5799999988 5999999999999888644
No 19
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.88 E-value=6.8e-10 Score=73.01 Aligned_cols=45 Identities=47% Similarity=0.882 Sum_probs=42.1
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccCcccCcccccccccccc
Q 024484 16 PWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYL 61 (267)
Q Consensus 16 ~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L 61 (267)
+||++||++|+.++..||..+|..||+.+++ |++.+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~-rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPG-RTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCC-CCHHHHHHHHHHhC
Confidence 5999999999999999998899999999998 99999999998753
No 20
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.78 E-value=6.4e-09 Score=104.03 Aligned_cols=98 Identities=28% Similarity=0.347 Sum_probs=82.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCC---------------CC--------ccccccccCcccCcccccc---cccccccCCCCC
Q 024484 14 KGPWTPEEDRILIVHIKKHGH---------------PN--------WRALPKQAGLLRCGKSCRL---RWINYLRPDIKR 67 (267)
Q Consensus 14 kg~WT~EED~~L~~~V~~~G~---------------~n--------W~~Ia~~~~~~Rt~kqCr~---Rw~n~L~p~ikk 67 (267)
-+.|+++||+.|...|..|-. .. |..|.+.|+. |+.+.+.. |=.+.+.+ ++
T Consensus 308 ~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp~-R~~~siy~~~rR~y~~FE~--~r 384 (607)
T KOG0051|consen 308 LKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLPY-RDRKSIYHHLRRAYTPFEN--KR 384 (607)
T ss_pred hhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcCc-ccchhHHHHHHhcCCcccc--cc
Confidence 388999999999999987711 11 5777788888 99888765 33333443 89
Q ss_pred CCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 68 GNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 68 ~~WT~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
|.||+||++.|..+|.++|+.|..|++.| ||.+..|+.||+.+++..
T Consensus 385 g~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g 431 (607)
T KOG0051|consen 385 GKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCG 431 (607)
T ss_pred CCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccc
Confidence 99999999999999999999999999999 999999999999988755
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=98.43 E-value=1.8e-08 Score=99.73 Aligned_cols=98 Identities=29% Similarity=0.580 Sum_probs=86.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccccccCcccCcccccccccccccC--CCCCCCCCHHHHHHHHHHHHhhC----
Q 024484 13 KKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRP--DIKRGNFSKEEEETIINLHDMLG---- 86 (267)
Q Consensus 13 kkg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p--~ikk~~WT~EED~~Li~l~~~~G---- 86 (267)
.+|.||++|++.|...+..+| ..|..|.+.++ |-+..||+||.+|..+ .+++++|+.||+.+|...+...-
T Consensus 290 ~~~~wt~e~~~eL~~~~~~~~-~~w~~ig~~~~--rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e~~~~~~ 366 (512)
T COG5147 290 QRGKWTKEEEQELAKLVVEHG-GSWTEIGKLLG--RMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNEMRLEAQ 366 (512)
T ss_pred hhccCcccccccccccccccc-chhhHhhhhhc--cCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHHHHHHHh
Confidence 478999999999999999999 89999998887 9999999999999988 78899999999999998887432
Q ss_pred ----CchhHHhhcCCCCCHHHHHHHHHHHhH
Q 024484 87 ----NRWSAIAGRLPGRTDNEIKNVWHTHLK 113 (267)
Q Consensus 87 ----~kWs~IA~~lpgRT~~q~KnRw~~~lk 113 (267)
-.|..|+.+++.|...+|+..+..+..
T Consensus 367 ~~~~~~~~li~~~~~~~~~~~~~~~~~~~~~ 397 (512)
T COG5147 367 QSSRILWLLIAQNIRNRLQHHCRDKYGVLIS 397 (512)
T ss_pred hhhhhhHHHHHHhhhccccCCCCCccccccc
Confidence 259999999999999999888766554
No 22
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.70 E-value=5.9e-05 Score=73.13 Aligned_cols=50 Identities=22% Similarity=0.440 Sum_probs=45.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhC-CchhHHhhcCCCCCHHHHHHHHHHHhH
Q 024484 64 DIKRGNFSKEEEETIINLHDMLG-NRWSAIAGRLPGRTDNEIKNVWHTHLK 113 (267)
Q Consensus 64 ~ikk~~WT~EED~~Li~l~~~~G-~kWs~IA~~lpgRT~~q~KnRw~~~lk 113 (267)
.+-...||.+||.+|++++..|| ++|..||.++..|+..+||.+|.+++-
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHh
Confidence 34557899999999999999999 999999999999999999999987763
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=97.66 E-value=0.00012 Score=52.60 Aligned_cols=46 Identities=13% Similarity=0.272 Sum_probs=40.3
Q ss_pred CCCCCHHHHHHHHHHHHhhCC-ch---hHHhhcCC-CC-CHHHHHHHHHHHh
Q 024484 67 RGNFSKEEEETIINLHDMLGN-RW---SAIAGRLP-GR-TDNEIKNVWHTHL 112 (267)
Q Consensus 67 k~~WT~EED~~Li~l~~~~G~-kW---s~IA~~lp-gR-T~~q~KnRw~~~l 112 (267)
+-.||+||...++++++.||. .| ..|+..|. .| |..||+.+++...
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 557999999999999999996 99 99999874 35 9999999987654
No 24
>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=97.64 E-value=2.8e-05 Score=55.75 Aligned_cols=49 Identities=14% Similarity=0.303 Sum_probs=42.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCc---cccccccCccc-Ccccccccccccc
Q 024484 13 KKGPWTPEEDRILIVHIKKHGHPNW---RALPKQAGLLR-CGKSCRLRWINYL 61 (267)
Q Consensus 13 kkg~WT~EED~~L~~~V~~~G~~nW---~~Ia~~~~~~R-t~kqCr~Rw~n~L 61 (267)
.+-.||+||.++++.+|+.+|.++| ..|++.++..| |..||+.+++.|.
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 3567999999999999999997799 99999887656 9999999887763
No 25
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.62 E-value=1.9e-05 Score=76.53 Aligned_cols=49 Identities=18% Similarity=0.573 Sum_probs=45.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcccCcccccccccccc
Q 024484 12 LKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYL 61 (267)
Q Consensus 12 lkkg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L 61 (267)
+-...||++|+-+|++++..||-+||..||.++|. |++.+|+++|.+++
T Consensus 70 i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGt-Ktkeeck~hy~k~f 118 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETYGFGNWQDIADHIGT-KTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcc-cchHHHHHHHHHHH
Confidence 45678999999999999999999999999999997 99999999998865
No 26
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.37 E-value=0.00017 Score=54.70 Aligned_cols=49 Identities=33% Similarity=0.545 Sum_probs=35.9
Q ss_pred CCCCCHHHHHHHHHHHHh------hC--C------chhHHhhcC----CCCCHHHHHHHHHHHhHHH
Q 024484 67 RGNFSKEEEETIINLHDM------LG--N------RWSAIAGRL----PGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 67 k~~WT~EED~~Li~l~~~------~G--~------kWs~IA~~l----pgRT~~q~KnRw~~~lkk~ 115 (267)
+..||.+|...||+++.. ++ + .|..||..| ..||..||+++|.++.++.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Y 67 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKY 67 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence 357999999999999887 22 1 399999987 4699999999999988776
No 27
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.37 E-value=0.00016 Score=71.51 Aligned_cols=55 Identities=29% Similarity=0.450 Sum_probs=50.1
Q ss_pred CCCCCCCHHHHHHHHHHHHhhC-CchhHHhhcCCCCCHHHHHHHHHHHhHHHHHHH
Q 024484 65 IKRGNFSKEEEETIINLHDMLG-NRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAAV 119 (267)
Q Consensus 65 ikk~~WT~EED~~Li~l~~~~G-~kWs~IA~~lpgRT~~q~KnRw~~~lkk~~~~~ 119 (267)
++-|-|+.-||++|--++.+|| +.|++|+..++-.|..||++||..++...+++.
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~t 60 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKT 60 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhh
Confidence 5678899999999999999999 679999999999999999999999998776554
No 28
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.33 E-value=0.00035 Score=61.92 Aligned_cols=98 Identities=21% Similarity=0.385 Sum_probs=69.8
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccCc--ccCcccccccccccc-cCCC--------------------CCCCCCH
Q 024484 16 PWTPEEDRILIVHIKKHGHPNWRALPKQAGL--LRCGKSCRLRWINYL-RPDI--------------------KRGNFSK 72 (267)
Q Consensus 16 ~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~--~Rt~kqCr~Rw~n~L-~p~i--------------------kk~~WT~ 72 (267)
+|++++|-+|+.+|..-. +-+.|+.-+.- .-|-..+.+||+..| +|.+ .+.+||.
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 599999999999998765 44555443322 245567788998876 4433 3468999
Q ss_pred HHHHHHHHHHHhhCC---chhHHhh-----cCCCCCHHHHHHHHHHHhHHH
Q 024484 73 EEEETIINLHDMLGN---RWSAIAG-----RLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 73 EED~~Li~l~~~~G~---kWs~IA~-----~lpgRT~~q~KnRw~~~lkk~ 115 (267)
+||++|......... .+.+|=. +-++||+.++.++|..+.+.+
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~ 129 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYH 129 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhc
Confidence 999999998766543 4666622 238999999999998554444
No 29
>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=97.29 E-value=0.0004 Score=51.13 Aligned_cols=50 Identities=20% Similarity=0.514 Sum_probs=33.3
Q ss_pred CCCCCHHHHHHHHHHHHhh--------CCc-hhHHhhcCC-CCCHHHHHHHHHHHhHHHH
Q 024484 67 RGNFSKEEEETIINLHDML--------GNR-WSAIAGRLP-GRTDNEIKNVWHTHLKKKA 116 (267)
Q Consensus 67 k~~WT~EED~~Li~l~~~~--------G~k-Ws~IA~~lp-gRT~~q~KnRw~~~lkk~~ 116 (267)
+.+||.|||++|++.++.+ ||+ |.++++.-+ .+|-...|+||...|+.+.
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 4689999999999999664 222 999999877 9999999999998888764
No 30
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=97.19 E-value=0.0006 Score=58.44 Aligned_cols=55 Identities=15% Similarity=0.297 Sum_probs=47.6
Q ss_pred CCCCCCHHHHHHHHHHHHhh---CC----chhHHhhcCCCCCHHHHHHHHHHHhHHHHHHHHH
Q 024484 66 KRGNFSKEEEETIINLHDML---GN----RWSAIAGRLPGRTDNEIKNVWHTHLKKKAAAVLK 121 (267)
Q Consensus 66 kk~~WT~EED~~Li~l~~~~---G~----kWs~IA~~lpgRT~~q~KnRw~~~lkk~~~~~~~ 121 (267)
....||.|||.+|-+.|-.| |+ -..+++..| +||+..|.=||+..+|+++...+.
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~~i~ 64 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEEAIE 64 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHHHHH
Confidence 45789999999999999988 32 388899999 999999999999999998876643
No 31
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.98 E-value=0.00096 Score=66.62 Aligned_cols=47 Identities=15% Similarity=0.353 Sum_probs=43.1
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHh
Q 024484 66 KRGNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHL 112 (267)
Q Consensus 66 kk~~WT~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~l 112 (267)
.+..||.+|..+|++++.+||-.|.+||.++.+||..||--+|.++=
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~LP 298 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRLP 298 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhcC
Confidence 35689999999999999999999999999999999999999986643
No 32
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.92 E-value=0.00091 Score=65.65 Aligned_cols=44 Identities=18% Similarity=0.330 Sum_probs=41.8
Q ss_pred CCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHH
Q 024484 68 GNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTH 111 (267)
Q Consensus 68 ~~WT~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~ 111 (267)
.+||.+|..+|++.++.||..|.+||.++..||..||--||-++
T Consensus 280 k~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred ccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 48999999999999999999999999999999999999999764
No 33
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.82 E-value=0.00041 Score=67.98 Aligned_cols=46 Identities=20% Similarity=0.575 Sum_probs=42.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccccccCcccCccccccccccc
Q 024484 13 KKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINY 60 (267)
Q Consensus 13 kkg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~ 60 (267)
....||.+|..+|++.|+.|| .+|.+||.++|+ |+..||..|+.+.
T Consensus 278 ~dk~WS~qE~~LLLEGIe~yg-DdW~kVA~HVgt-Kt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYG-DDWDKVARHVGT-KTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhh-hhHHHHHHHhCC-CCHHHHHHHHHcC
Confidence 556999999999999999999 899999999998 9999999998764
No 34
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.65 E-value=0.0008 Score=67.16 Aligned_cols=47 Identities=21% Similarity=0.586 Sum_probs=43.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcccCccccccccccc
Q 024484 12 LKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINY 60 (267)
Q Consensus 12 lkkg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~ 60 (267)
..++.||.+|+.+|+++|+.|| .+|.+|+.++|+ |+..||-.++.+.
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~-ddW~kVa~hVg~-ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYG-DDWNKVADHVGT-KSQEQCILKFLRL 297 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhc-ccHHHHHhccCC-CCHHHHHHHHHhc
Confidence 4568899999999999999999 899999999997 9999999998765
No 35
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.62 E-value=0.0031 Score=54.71 Aligned_cols=55 Identities=13% Similarity=0.255 Sum_probs=46.3
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCc-------hhHHhhcCCCCCHHHHHHHHHHHhHHHHHHHHH
Q 024484 66 KRGNFSKEEEETIINLHDMLGNR-------WSAIAGRLPGRTDNEIKNVWHTHLKKKAAAVLK 121 (267)
Q Consensus 66 kk~~WT~EED~~Li~l~~~~G~k-------Ws~IA~~lpgRT~~q~KnRw~~~lkk~~~~~~~ 121 (267)
+...||.|+|.+|-+.+-.|+.. ...++..| +||..+|.-||+..++++....+.
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Yee~I~ 65 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQEQIK 65 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHHHHHH
Confidence 56789999999998888888632 66777888 999999999999999988776654
No 36
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=96.55 E-value=0.0062 Score=45.27 Aligned_cols=49 Identities=33% Similarity=0.555 Sum_probs=40.8
Q ss_pred CCCCCHHHHHHHHHHHHhhC----C-------------chhHHhhcC-----CCCCHHHHHHHHHHHhHHH
Q 024484 67 RGNFSKEEEETIINLHDMLG----N-------------RWSAIAGRL-----PGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 67 k~~WT~EED~~Li~l~~~~G----~-------------kWs~IA~~l-----pgRT~~q~KnRw~~~lkk~ 115 (267)
+..||.+|..+|++++.+|. + -|.+|+..| +.||..+||.+|..+...-
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 46899999999999998862 1 299999976 3699999999999877654
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=96.14 E-value=0.0013 Score=48.35 Aligned_cols=52 Identities=25% Similarity=0.400 Sum_probs=32.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCC--------CCccccccccCcccCcccccccccccccCCC
Q 024484 14 KGPWTPEEDRILIVHIKKHGH--------PNWRALPKQAGLLRCGKSCRLRWINYLRPDI 65 (267)
Q Consensus 14 kg~WT~EED~~L~~~V~~~G~--------~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~i 65 (267)
+.+||.+||++|+..|..+.. .=|..+++..++.++-.+-|+||...|.+..
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 568999999999999976531 1388888887755888888999999887643
No 38
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.89 E-value=0.0086 Score=56.60 Aligned_cols=46 Identities=28% Similarity=0.486 Sum_probs=42.1
Q ss_pred CCCCCHHHHHHHHHHHHhhC-CchhHHhhcCCCCCHHHHHHHHHHHh
Q 024484 67 RGNFSKEEEETIINLHDMLG-NRWSAIAGRLPGRTDNEIKNVWHTHL 112 (267)
Q Consensus 67 k~~WT~EED~~Li~l~~~~G-~kWs~IA~~lpgRT~~q~KnRw~~~l 112 (267)
-..|+..|+.+||+..+.+| ++|..||.++..|+..+||.+|....
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y 109 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMY 109 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHH
Confidence 35799999999999999999 89999999998899999999996554
No 39
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=95.60 E-value=0.06 Score=58.28 Aligned_cols=101 Identities=14% Similarity=0.271 Sum_probs=77.2
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCccccccccCcccCcccccc-------cccc----------------------------
Q 024484 15 GPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRL-------RWIN---------------------------- 59 (267)
Q Consensus 15 g~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~-------Rw~n---------------------------- 59 (267)
+.|+.-+=..++.+..+||..+-..||..+.+ ++...++. ||..
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~-k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~ 903 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEG-KTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAI 903 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcC-CCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35888888899999999998889999998875 76655541 1111
Q ss_pred -------------c--ccCCCCCCCCCHHHHHHHHHHHHhhC-CchhHHhhc------------CCCCCHHHHHHHHHHH
Q 024484 60 -------------Y--LRPDIKRGNFSKEEEETIINLHDMLG-NRWSAIAGR------------LPGRTDNEIKNVWHTH 111 (267)
Q Consensus 60 -------------~--L~p~ikk~~WT~EED~~Li~l~~~~G-~kWs~IA~~------------lpgRT~~q~KnRw~~~ 111 (267)
. -.+..++..+|.|||..|+-++.+|| .+|.+|-.. |..||+..|..|..++
T Consensus 904 ~~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l 983 (1033)
T PLN03142 904 GKKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTL 983 (1033)
T ss_pred HHHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHH
Confidence 0 01233455799999999999999999 789888332 2689999999999999
Q ss_pred hHHHH
Q 024484 112 LKKKA 116 (267)
Q Consensus 112 lkk~~ 116 (267)
++-..
T Consensus 984 ~~~~~ 988 (1033)
T PLN03142 984 IRLIE 988 (1033)
T ss_pred HHHHH
Confidence 98653
No 40
>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=95.47 E-value=0.0026 Score=54.57 Aligned_cols=50 Identities=28% Similarity=0.680 Sum_probs=41.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHh---CC---CCccccccccCcccCcccccccccccccC
Q 024484 12 LKKGPWTPEEDRILIVHIKKH---GH---PNWRALPKQAGLLRCGKSCRLRWINYLRP 63 (267)
Q Consensus 12 lkkg~WT~EED~~L~~~V~~~---G~---~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p 63 (267)
.+...||.|||.+|...|-+| |. .-+..+++.++ ||+..|.=||+.+++.
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~--RTsAACGFRWNs~VRk 57 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN--RTAAACGFRWNAYVRK 57 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc--ccHHHhcchHHHHHHH
Confidence 356789999999999999988 31 13677788787 9999999999999875
No 41
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=95.34 E-value=0.0037 Score=47.24 Aligned_cols=47 Identities=30% Similarity=0.667 Sum_probs=32.0
Q ss_pred CCCCCHHHHHHHHHHHHH--h----C---C----CCcccccccc---CcccCccccccccccc
Q 024484 14 KGPWTPEEDRILIVHIKK--H----G---H----PNWRALPKQA---GLLRCGKSCRLRWINY 60 (267)
Q Consensus 14 kg~WT~EED~~L~~~V~~--~----G---~----~nW~~Ia~~~---~~~Rt~kqCr~Rw~n~ 60 (267)
+..||.+|...|+.++.. + + . .-|..||..| |..|++.||+.||.+.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L 63 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL 63 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 357999999999998877 1 1 1 1499999874 4559999999999875
No 42
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.08 E-value=0.0056 Score=57.82 Aligned_cols=48 Identities=19% Similarity=0.471 Sum_probs=44.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccccccccCcccCccccccccccccc
Q 024484 14 KGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLR 62 (267)
Q Consensus 14 kg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~ 62 (267)
--.|+..|+-+|++.....|.+||.-||..+|. |....|+.+|..++.
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGs-r~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGS-RAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhh-hhhHHHHHHHHHHHh
Confidence 346999999999999999999999999999996 999999999988765
No 43
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=94.88 E-value=0.043 Score=53.09 Aligned_cols=84 Identities=21% Similarity=0.342 Sum_probs=63.5
Q ss_pred CCccccccccCcccCcccccccccccccCC-------------------------CCCCCCCHHHHHHHHHHHHhhCCch
Q 024484 35 PNWRALPKQAGLLRCGKSCRLRWINYLRPD-------------------------IKRGNFSKEEEETIINLHDMLGNRW 89 (267)
Q Consensus 35 ~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~-------------------------ikk~~WT~EED~~Li~l~~~~G~kW 89 (267)
..|..++=.... |...-...+|..+.++. ++...||.+|-+-|++|++.|.-+|
T Consensus 74 ~~W~w~pFtn~a-RkD~~~l~HWvr~~d~~~dypfakfNk~vdipsYt~eEYe~~l~dn~WskeETD~LF~lck~fDLRf 152 (445)
T KOG2656|consen 74 RPWKWVPFTNSA-RKDDATLHHWVRVGDTPKDYPFAKFNKHVDIPSYTDEEYEAHLNDNSWSKEETDYLFDLCKRFDLRF 152 (445)
T ss_pred CCceeeccCCcc-ccCCceEEeeeeccCCCCCCchhhhccccCccccchHHHHHhhccccccHHHHHHHHHHHHhcCeeE
Confidence 357666543443 66666667777764331 1225699999999999999999999
Q ss_pred hHHhhc-----CCC-CCHHHHHHHHHHHhHHHHHHH
Q 024484 90 SAIAGR-----LPG-RTDNEIKNVWHTHLKKKAAAV 119 (267)
Q Consensus 90 s~IA~~-----lpg-RT~~q~KnRw~~~lkk~~~~~ 119 (267)
..||.+ ++. ||-.++|.||..+.++.++.+
T Consensus 153 ~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr 188 (445)
T KOG2656|consen 153 FVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKAR 188 (445)
T ss_pred EEEeeccchhhccccccHHHHHHHHHHHHHHHHHcc
Confidence 999987 666 999999999999888775443
No 44
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=94.78 E-value=0.063 Score=50.84 Aligned_cols=52 Identities=23% Similarity=0.353 Sum_probs=42.9
Q ss_pred CCCCCHHHHHHHHHHHHhh----------CCchhHHhhcC----CCCCHHHHHHHHHHHhHHHHHH
Q 024484 67 RGNFSKEEEETIINLHDML----------GNRWSAIAGRL----PGRTDNEIKNVWHTHLKKKAAA 118 (267)
Q Consensus 67 k~~WT~EED~~Li~l~~~~----------G~kWs~IA~~l----pgRT~~q~KnRw~~~lkk~~~~ 118 (267)
...|+.+|-..||++..+. +..|..||+.+ .-||+.|||++|.++.+++.+.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~ 119 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKE 119 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHH
Confidence 4789999999999998763 23599999965 3499999999999999887543
No 45
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=94.33 E-value=0.0094 Score=51.71 Aligned_cols=51 Identities=22% Similarity=0.498 Sum_probs=39.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCC------ccccccccCcccCcccccccccccccC
Q 024484 11 GLKKGPWTPEEDRILIVHIKKHGHPN------WRALPKQAGLLRCGKSCRLRWINYLRP 63 (267)
Q Consensus 11 ~lkkg~WT~EED~~L~~~V~~~G~~n------W~~Ia~~~~~~Rt~kqCr~Rw~n~L~p 63 (267)
..+...||.|||.+|-..|-+|+... ...++..+. |+..+|.-||+.+++.
T Consensus 2 k~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~--rt~aac~fRwNs~vrk 58 (170)
T PRK13923 2 KTRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALK--RTAAACGFRWNSVVRK 58 (170)
T ss_pred cchhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHh--hhHHHHHhHHHHHHHH
Confidence 45678999999999999999886433 344445565 9999999999877764
No 46
>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=94.31 E-value=0.11 Score=39.54 Aligned_cols=47 Identities=30% Similarity=0.520 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHHhh---CC----------chhHHhhcC---CC--CCHHHHHHHHHHHhHHH
Q 024484 69 NFSKEEEETIINLHDML---GN----------RWSAIAGRL---PG--RTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 69 ~WT~EED~~Li~l~~~~---G~----------kWs~IA~~l---pg--RT~~q~KnRw~~~lkk~ 115 (267)
.||+++++.|++++.+. |+ .|..|+..| +| .+..||+|||..+.+..
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y 65 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDY 65 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHH
Confidence 59999999999998653 22 299999887 33 47899999998776655
No 47
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=94.04 E-value=0.014 Score=43.37 Aligned_cols=49 Identities=24% Similarity=0.453 Sum_probs=38.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC----------------CCcccccccc----CcccCcccccccccccc
Q 024484 13 KKGPWTPEEDRILIVHIKKHGH----------------PNWRALPKQA----GLLRCGKSCRLRWINYL 61 (267)
Q Consensus 13 kkg~WT~EED~~L~~~V~~~G~----------------~nW~~Ia~~~----~~~Rt~kqCr~Rw~n~L 61 (267)
++..||++|.+.|+.+|.+|.. .-|..|+..+ ++.|+..||+.+|.+..
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 3578999999999999999821 1399998763 22599999999998864
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=93.72 E-value=0.12 Score=42.40 Aligned_cols=52 Identities=23% Similarity=0.382 Sum_probs=41.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhCC----chhHHhhc------------CCCCCHHHHHHHHHHHhHHH
Q 024484 64 DIKRGNFSKEEEETIINLHDMLGN----RWSAIAGR------------LPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 64 ~ikk~~WT~EED~~Li~l~~~~G~----kWs~IA~~------------lpgRT~~q~KnRw~~~lkk~ 115 (267)
..++..||++||..|+-++.+||- .|..|-.. |..||+..|..|-+++++-.
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 567789999999999999999995 79887553 26799999999999998743
No 49
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=91.21 E-value=0.57 Score=31.98 Aligned_cols=42 Identities=26% Similarity=0.340 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 72 KEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 72 ~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
++++..++.++...|-.|.+||..+ |.|...|+.+.+..+++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARKK 53 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHhh
Confidence 4678889999999999999999999 99999999988776653
No 50
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=89.80 E-value=0.62 Score=45.26 Aligned_cols=48 Identities=25% Similarity=0.342 Sum_probs=44.0
Q ss_pred CCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 68 GNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 68 ~~WT~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
.+||.+|-++...+..+.|..++.|+..||.|...|||-+|.+--|++
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~n 413 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKVN 413 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhhC
Confidence 479999999999999999999999999999999999999997765544
No 51
>smart00595 MADF subfamily of SANT domain.
Probab=84.92 E-value=2.2 Score=31.93 Aligned_cols=28 Identities=29% Similarity=0.523 Sum_probs=23.5
Q ss_pred hhHHhhcCCCCCHHHHHHHHHHHhHHHHH
Q 024484 89 WSAIAGRLPGRTDNEIKNVWHTHLKKKAA 117 (267)
Q Consensus 89 Ws~IA~~lpgRT~~q~KnRw~~~lkk~~~ 117 (267)
|.+||..| |-|..+|+.+|+++-....+
T Consensus 30 W~~Ia~~l-~~~~~~~~~kw~~LR~~y~~ 57 (89)
T smart00595 30 WEEIAEEL-GLSVEECKKRWKNLRDRYRR 57 (89)
T ss_pred HHHHHHHH-CcCHHHHHHHHHHHHHHHHH
Confidence 99999999 55999999999987665533
No 52
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=84.50 E-value=2.7 Score=41.83 Aligned_cols=50 Identities=14% Similarity=0.260 Sum_probs=44.5
Q ss_pred CCCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHHHH
Q 024484 67 RGNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKKA 116 (267)
Q Consensus 67 k~~WT~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~~ 116 (267)
...||.||--++-++...||....+|-+.||.|+-..|...|....|.+.
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK~~~ 236 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKKTRE 236 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHHHhh
Confidence 45799999999999999999999999999999999999998887766543
No 53
>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=81.45 E-value=7 Score=37.29 Aligned_cols=56 Identities=21% Similarity=0.407 Sum_probs=42.5
Q ss_pred CCCCCHHHHHHHHHHHHhh-CCc---hhHHhhcCCCCCHHHHHHHHHHHhHHHHHHHHHh
Q 024484 67 RGNFSKEEEETIINLHDML-GNR---WSAIAGRLPGRTDNEIKNVWHTHLKKKAAAVLKQ 122 (267)
Q Consensus 67 k~~WT~EED~~Li~l~~~~-G~k---Ws~IA~~lpgRT~~q~KnRw~~~lkk~~~~~~~~ 122 (267)
-..||.-|...|+.+.+-. |.. -.+|++.++||+..+|++.-+.+..+.++..+.+
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rvareaiqk 80 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRVAREAIQK 80 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3579999999999888765 544 5789999999999999996665555555554444
No 54
>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=80.83 E-value=4.1 Score=27.40 Aligned_cols=41 Identities=29% Similarity=0.438 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 73 EEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 73 EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
+++..++.++-..|-.+.+||..| |-|...|+.+.+..+++
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 456667777766677899999999 99999999988887765
No 55
>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=79.82 E-value=1.4 Score=36.10 Aligned_cols=34 Identities=32% Similarity=0.552 Sum_probs=27.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC---CCcccccccc
Q 024484 11 GLKKGPWTPEEDRILIVHIKKHGH---PNWRALPKQA 44 (267)
Q Consensus 11 ~lkkg~WT~EED~~L~~~V~~~G~---~nW~~Ia~~~ 44 (267)
+-++..||.+||.-|+-++.+||. +.|..|-..+
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~I 82 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEI 82 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHH
Confidence 556789999999999999999998 7898886553
No 56
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=78.93 E-value=0.76 Score=43.51 Aligned_cols=47 Identities=26% Similarity=0.448 Sum_probs=36.9
Q ss_pred CCCCHHHHHHHHHHHHHh---------CCCCccccccc---cCcccCcccccccccccc
Q 024484 15 GPWTPEEDRILIVHIKKH---------GHPNWRALPKQ---AGLLRCGKSCRLRWINYL 61 (267)
Q Consensus 15 g~WT~EED~~L~~~V~~~---------G~~nW~~Ia~~---~~~~Rt~kqCr~Rw~n~L 61 (267)
..|+.+|-..|+.+.... ....|..||+. .|..|++.||+.+|.+..
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 789999999999887533 12459999984 455599999999998853
No 57
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=75.37 E-value=9 Score=40.37 Aligned_cols=46 Identities=9% Similarity=0.050 Sum_probs=41.8
Q ss_pred CCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhH
Q 024484 68 GNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLK 113 (267)
Q Consensus 68 ~~WT~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lk 113 (267)
..||..|-.+.-+++-.|-..+-.|++.++++|-.||-..|++..|
T Consensus 620 d~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtWKK 665 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTWKK 665 (907)
T ss_pred ccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHHHH
Confidence 5799999999999999999999999999999999999888776543
No 58
>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=74.23 E-value=6.4 Score=26.18 Aligned_cols=38 Identities=18% Similarity=0.344 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHhhCC-chhHHhhcCCCCCHHHHHHHHHHH
Q 024484 73 EEEETIINLHDMLGN-RWSAIAGRLPGRTDNEIKNVWHTH 111 (267)
Q Consensus 73 EED~~Li~l~~~~G~-kWs~IA~~lpgRT~~q~KnRw~~~ 111 (267)
+=|..|+.+.+.-|. .|.+||+.+ |=|...|..|+..+
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 457889999988884 599999999 99999999998754
No 59
>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=74.06 E-value=6.8 Score=31.49 Aligned_cols=40 Identities=23% Similarity=0.295 Sum_probs=30.0
Q ss_pred HHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 74 EEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 74 ED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
++..++.+.-..|-.+.+||+.+ |.+...|+++.+..+++
T Consensus 117 ~~r~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 117 QCRKIFILSRFEGKSYKEIAEEL-GISVKTVEYHISKALKE 156 (161)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 33444444444577899999999 99999999999886654
No 60
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=72.32 E-value=5.8 Score=40.85 Aligned_cols=49 Identities=12% Similarity=0.443 Sum_probs=39.7
Q ss_pred CCCCCHHHHHHHHHHHHhhCCchhHH----------hhcCCCCCHHHHHHHHHHHhHHH
Q 024484 67 RGNFSKEEEETIINLHDMLGNRWSAI----------AGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 67 k~~WT~EED~~Li~l~~~~G~kWs~I----------A~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
+..||-.|+.-.+.+++++|..+.+| -....-+|-.|++.+|+.++++.
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m 146 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRM 146 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHH
Confidence 56899999999999999999999888 22234467889999988877654
No 61
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=70.66 E-value=4.3 Score=31.08 Aligned_cols=22 Identities=55% Similarity=0.872 Sum_probs=13.0
Q ss_pred CCCCCCCHHHHHHH--------HHHHHHhC
Q 024484 12 LKKGPWTPEEDRIL--------IVHIKKHG 33 (267)
Q Consensus 12 lkkg~WT~EED~~L--------~~~V~~~G 33 (267)
-..|-||+|+|+.| .+++++||
T Consensus 45 n~~GiWT~eDD~~L~~~~~~~~~~L~~khG 74 (87)
T PF11626_consen 45 NMPGIWTPEDDEMLRSGDKDDIERLIKKHG 74 (87)
T ss_dssp T-TT---HHHHHHHTS--HHHHHHHHHHH-
T ss_pred CCCCCcCHHHHHHHHcCCHHHHHHHHHHhC
Confidence 45788999999999 34567776
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=70.38 E-value=5.1 Score=34.44 Aligned_cols=42 Identities=26% Similarity=0.278 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHH
Q 024484 69 NFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTH 111 (267)
Q Consensus 69 ~WT~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~ 111 (267)
.||+|+.+.|.+|..+ |-.=++||+.|.|.|.|.|.-+-|.+
T Consensus 2 ~Wtde~~~~L~~lw~~-G~SasqIA~~lg~vsRnAViGk~hRl 43 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GLSASQIARQLGGVSRNAVIGKAHRL 43 (162)
T ss_pred CCCHHHHHHHHHHHHc-CCCHHHHHHHhCCcchhhhhhhhhcc
Confidence 5999999999999854 77789999999779999998877653
No 63
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=69.67 E-value=8.8 Score=32.04 Aligned_cols=43 Identities=9% Similarity=0.085 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHhhC-CchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 72 KEEEETIINLHDMLG-NRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 72 ~EED~~Li~l~~~~G-~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
.+-|..|+++.++-| ..|++||+.+ |-+...|+.|++.+....
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~G 51 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAG 51 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCC
Confidence 357899999998888 4699999999 999999999998877654
No 64
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=68.16 E-value=3.1 Score=40.61 Aligned_cols=44 Identities=14% Similarity=0.204 Sum_probs=40.5
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCccccccccCcccCccccccccccc
Q 024484 15 GPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINY 60 (267)
Q Consensus 15 g~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~ 60 (267)
-+||.+|-++..++....| .++..|+..++. |..+|+...|.+-
T Consensus 366 ~~Ws~~e~ekFYKALs~wG-tdF~LIs~lfP~-R~RkqIKaKfi~E 409 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWG-TDFSLISSLFPN-RERKQIKAKFIKE 409 (507)
T ss_pred CcccHHHHHHHHHHHHHhc-chHHHHHHhcCc-hhHHHHHHHHHHH
Confidence 4699999999999999999 799999999998 9999999988764
No 65
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=64.97 E-value=11 Score=31.76 Aligned_cols=43 Identities=12% Similarity=0.093 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHhhCC-chhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 72 KEEEETIINLHDMLGN-RWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 72 ~EED~~Li~l~~~~G~-kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
.+-|.+|+.+.++-|. .|++||+.+ |-+...|+.|++.+.+..
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~G 56 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQG 56 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCC
Confidence 5678899998888884 699999999 999999999998887655
No 66
>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=64.41 E-value=14 Score=27.97 Aligned_cols=38 Identities=16% Similarity=0.296 Sum_probs=28.1
Q ss_pred HHHHHHHhhCC--------chhHHhhcCCC---CC--HHHHHHHHHHHhHH
Q 024484 77 TIINLHDMLGN--------RWSAIAGRLPG---RT--DNEIKNVWHTHLKK 114 (267)
Q Consensus 77 ~Li~l~~~~G~--------kWs~IA~~lpg---RT--~~q~KnRw~~~lkk 114 (267)
.|..+|...|+ +|..||+.|.- -+ ..++|..|..+|-.
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 47788888884 59999999822 12 36899999888754
No 67
>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=64.39 E-value=11 Score=27.23 Aligned_cols=30 Identities=20% Similarity=0.370 Sum_probs=23.4
Q ss_pred chhHHhhcCCC-CCHHHHHHHHHHHhHHHHH
Q 024484 88 RWSAIAGRLPG-RTDNEIKNVWHTHLKKKAA 117 (267)
Q Consensus 88 kWs~IA~~lpg-RT~~q~KnRw~~~lkk~~~ 117 (267)
-|..||..|.+ -+..+|+.||.++.....+
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y~~ 58 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRDRYRR 58 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHHHHHH
Confidence 39999999953 5788999999987665533
No 68
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=63.87 E-value=60 Score=31.85 Aligned_cols=46 Identities=17% Similarity=0.263 Sum_probs=40.7
Q ss_pred CCCCHHHHHHHHHHHHhhCCchhHHhh-cCCCCCHHHHHHHHHHHhH
Q 024484 68 GNFSKEEEETIINLHDMLGNRWSAIAG-RLPGRTDNEIKNVWHTHLK 113 (267)
Q Consensus 68 ~~WT~EED~~Li~l~~~~G~kWs~IA~-~lpgRT~~q~KnRw~~~lk 113 (267)
..|+++|-...-+-.+.||..+..|-+ +++.|+--.|-..|+...|
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWKk 324 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWKK 324 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhhc
Confidence 579999999999999999999999955 7999999999888776544
No 69
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=63.37 E-value=21 Score=29.24 Aligned_cols=30 Identities=20% Similarity=0.187 Sum_probs=24.6
Q ss_pred hhCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 84 MLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 84 ~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
..|-.+.+||..| |-+...|+++.+...++
T Consensus 139 ~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 168 (179)
T PRK11924 139 VEGLSYREIAEIL-GVPVGTVKSRLRRARQL 168 (179)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3467799999999 99999999998875544
No 70
>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=63.14 E-value=9.7 Score=29.19 Aligned_cols=30 Identities=23% Similarity=0.484 Sum_probs=25.2
Q ss_pred HHHHHHHHHhhCCchhHHhhcCCCCCHHHHH
Q 024484 75 EETIINLHDMLGNRWSAIAGRLPGRTDNEIK 105 (267)
Q Consensus 75 D~~Li~l~~~~G~kWs~IA~~lpgRT~~q~K 105 (267)
|+.|..+...+|..|..+|.+| |=|..+|.
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I~ 31 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDIY 31 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 5678999999999999999999 76666553
No 71
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=61.75 E-value=18 Score=28.42 Aligned_cols=49 Identities=20% Similarity=0.157 Sum_probs=34.5
Q ss_pred CCCCHHHHHHHHHHHHhh----C----CchhHHhhcCCC-----CCHHHHHHHHHHHhHHHH
Q 024484 68 GNFSKEEEETIINLHDML----G----NRWSAIAGRLPG-----RTDNEIKNVWHTHLKKKA 116 (267)
Q Consensus 68 ~~WT~EED~~Li~l~~~~----G----~kWs~IA~~lpg-----RT~~q~KnRw~~~lkk~~ 116 (267)
.-||+|+|..|++.+..| | ..|..+...+.+ =+.+|+.++.+.+-+|..
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~ 66 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYR 66 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHH
Confidence 359999999999998776 6 245554444322 277899888887766653
No 72
>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=60.95 E-value=16 Score=28.34 Aligned_cols=38 Identities=24% Similarity=0.277 Sum_probs=28.4
Q ss_pred HHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 76 ETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 76 ~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
..++.++-..|-.+.+||+.+ |=+...|+++.+..+++
T Consensus 116 ~~ii~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 116 REVLVLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred HHHHhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 333444444678899999999 77999999988876654
No 73
>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=59.39 E-value=14 Score=28.37 Aligned_cols=31 Identities=26% Similarity=0.452 Sum_probs=25.6
Q ss_pred HHHHHHHHHhhCCchhHHhhcCCCCCHHHHHH
Q 024484 75 EETIINLHDMLGNRWSAIAGRLPGRTDNEIKN 106 (267)
Q Consensus 75 D~~Li~l~~~~G~kWs~IA~~lpgRT~~q~Kn 106 (267)
|..|..+...+|..|.++|..| |=+..+|.+
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI~~ 34 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEINQ 34 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHHHH
Confidence 6778889999999999999999 766665543
No 74
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=59.03 E-value=9.2 Score=29.22 Aligned_cols=17 Identities=29% Similarity=0.548 Sum_probs=10.3
Q ss_pred CCCCCCCCCHHHHHHHH
Q 024484 63 PDIKRGNFSKEEEETII 79 (267)
Q Consensus 63 p~ikk~~WT~EED~~Li 79 (267)
|....|-||+|+|+.|.
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 66778999999999993
No 75
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=58.69 E-value=21 Score=27.22 Aligned_cols=39 Identities=18% Similarity=0.288 Sum_probs=29.3
Q ss_pred HHHHHHHhhCC--------chhHHhhcCCCC-----CHHHHHHHHHHHhHHH
Q 024484 77 TIINLHDMLGN--------RWSAIAGRLPGR-----TDNEIKNVWHTHLKKK 115 (267)
Q Consensus 77 ~Li~l~~~~G~--------kWs~IA~~lpgR-----T~~q~KnRw~~~lkk~ 115 (267)
.|..+|.++|+ +|..||..|.-. ...++|..|...|...
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~y 87 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLPF 87 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHHH
Confidence 47777888775 699999988322 3578899998888654
No 76
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=58.20 E-value=19 Score=29.52 Aligned_cols=35 Identities=17% Similarity=0.255 Sum_probs=26.6
Q ss_pred HHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 79 INLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 79 i~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
+.+....|-.+.+||+.| |.+...|+++.+..+++
T Consensus 137 l~l~~~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 171 (182)
T PRK09652 137 ITLREIEGLSYEEIAEIM-GCPIGTVRSRIFRAREA 171 (182)
T ss_pred HHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 333334577899999999 99999999988765543
No 77
>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=55.75 E-value=27 Score=33.42 Aligned_cols=86 Identities=16% Similarity=0.287 Sum_probs=62.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCC---ccccccccCcccCcccccccccccccCCCCCCCCCHHHHHHHHHHHHh-h----
Q 024484 14 KGPWTPEEDRILIVHIKKHGHPN---WRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETIINLHDM-L---- 85 (267)
Q Consensus 14 kg~WT~EED~~L~~~V~~~G~~n---W~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~ikk~~WT~EED~~Li~l~~~-~---- 85 (267)
-..||.-|...|+.+.+...... -..|++.+.+ |...+++. |.+.|+ +..+.+++++ |
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~-Rs~aEI~~-fl~~LK------------~rvareaiqkv~~~g~ 86 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPG-RSEAEIRD-FLQQLK------------GRVAREAIQKVHPGGL 86 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccC-cCHHHHHH-HHHHHH------------HHHHHHHHHHhccccc
Confidence 35799999999998887763233 3467777887 88888775 455544 4556666666 2
Q ss_pred -CC------------chhHHhhcCCCCCHHHHHHHHHHHhH
Q 024484 86 -GN------------RWSAIAGRLPGRTDNEIKNVWHTHLK 113 (267)
Q Consensus 86 -G~------------kWs~IA~~lpgRT~~q~KnRw~~~lk 113 (267)
|. -|..+|..+.|.-...|---|.+.|-
T Consensus 87 ~~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~ 127 (344)
T PF11035_consen 87 KGPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLT 127 (344)
T ss_pred ccccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHH
Confidence 22 29999999999999998888877764
No 78
>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=55.56 E-value=12 Score=28.12 Aligned_cols=31 Identities=23% Similarity=0.638 Sum_probs=25.0
Q ss_pred HHHHHHHHHhhCCchhHHhhcCCCCCHHHHHH
Q 024484 75 EETIINLHDMLGNRWSAIAGRLPGRTDNEIKN 106 (267)
Q Consensus 75 D~~Li~l~~~~G~kWs~IA~~lpgRT~~q~Kn 106 (267)
|..|..+.+.+|..|.++|.+| |=+..+|..
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI~~ 34 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDIDL 34 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHHHH
Confidence 5567888899999999999999 667665544
No 79
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=54.11 E-value=27 Score=31.22 Aligned_cols=44 Identities=20% Similarity=0.240 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHHhhCCchhHHhhc--C-CCCCHHHHHHHHHHHhH
Q 024484 69 NFSKEEEETIINLHDMLGNRWSAIAGR--L-PGRTDNEIKNVWHTHLK 113 (267)
Q Consensus 69 ~WT~EED~~Li~l~~~~G~kWs~IA~~--l-pgRT~~q~KnRw~~~lk 113 (267)
.|++++|-+||.+|.. |+.-..|+.- | -.-|-..|..||+.+|-
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~lly 47 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALLY 47 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHHc
Confidence 4999999999999865 5555555543 3 33588999999999984
No 80
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=53.54 E-value=24 Score=29.38 Aligned_cols=29 Identities=14% Similarity=0.012 Sum_probs=24.2
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|..+.+||..| |-|...|+++.+...++
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466789999999 99999999998766654
No 81
>PRK04217 hypothetical protein; Provisional
Probab=53.27 E-value=58 Score=26.28 Aligned_cols=46 Identities=20% Similarity=0.132 Sum_probs=37.2
Q ss_pred CCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 68 GNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 68 ~~WT~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
..-|.+| ..++.+....|-...+||+.+ |-+...|+.+++...++-
T Consensus 41 ~~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 41 IFMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKKV 86 (110)
T ss_pred ccCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 3456666 677788888888999999999 999999999998765543
No 82
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=53.04 E-value=44 Score=28.48 Aligned_cols=35 Identities=20% Similarity=0.202 Sum_probs=26.7
Q ss_pred HHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 79 INLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 79 i~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
+.+.-..|-...+||..| |-+...|++|.+..+++
T Consensus 143 ~~l~~~~g~s~~EIA~~l-g~s~~tV~~rl~rar~~ 177 (192)
T PRK09643 143 LVAVDMQGYSVADAARML-GVAEGTVKSRCARGRAR 177 (192)
T ss_pred HHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 333334567799999999 99999999999766544
No 83
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=52.22 E-value=7.9 Score=37.94 Aligned_cols=50 Identities=16% Similarity=0.232 Sum_probs=42.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCccccccc-----cCcccCcccccccccccc
Q 024484 11 GLKKGPWTPEEDRILIVHIKKHGHPNWRALPKQ-----AGLLRCGKSCRLRWINYL 61 (267)
Q Consensus 11 ~lkkg~WT~EED~~L~~~V~~~G~~nW~~Ia~~-----~~~~Rt~kqCr~Rw~n~L 61 (267)
.+.-..||.+|.+-|..++++|. -.|-.|+.. .+..||.....+||..+.
T Consensus 127 ~l~dn~WskeETD~LF~lck~fD-LRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~ 181 (445)
T KOG2656|consen 127 HLNDNSWSKEETDYLFDLCKRFD-LRFFVIADRYDNQQYKKSRTVEDLKERYYSVC 181 (445)
T ss_pred hhccccccHHHHHHHHHHHHhcC-eeEEEEeeccchhhccccccHHHHHHHHHHHH
Confidence 35567899999999999999999 789899877 676799999999997653
No 84
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=52.02 E-value=22 Score=31.30 Aligned_cols=45 Identities=24% Similarity=0.248 Sum_probs=38.4
Q ss_pred CCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 68 GNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 68 ~~WT~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
...|+.|-+.|.-+.+=+.| .+||..| +.+...||++.+++++|-
T Consensus 147 ~~LT~RE~eVL~lla~G~sn--keIA~~L-~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 147 ELLTPRELEVLRLLAEGLSN--KEIAEEL-NLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCCCHHHHHHHHHHHCCCCH--HHHHHHH-CCCHhHHHHHHHHHHHHc
Confidence 36899998888877765555 5999999 999999999999999874
No 85
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=52.01 E-value=27 Score=24.39 Aligned_cols=34 Identities=26% Similarity=0.468 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHH
Q 024484 73 EEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNV 107 (267)
Q Consensus 73 EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnR 107 (267)
.+|+..+.++.+.|-.=.+||+++ ||+.+.|++.
T Consensus 7 ~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~y 40 (50)
T PF11427_consen 7 DAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRY 40 (50)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHH
T ss_pred HHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHH
Confidence 566777888889999999999999 9999988774
No 86
>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=51.60 E-value=19 Score=27.44 Aligned_cols=28 Identities=32% Similarity=0.603 Sum_probs=22.4
Q ss_pred HHHHHHhhCCchhHHhhcCCCCCHHHHHH
Q 024484 78 IINLHDMLGNRWSAIAGRLPGRTDNEIKN 106 (267)
Q Consensus 78 Li~l~~~~G~kWs~IA~~lpgRT~~q~Kn 106 (267)
|..+....|..|.++|.+| |=+..+|..
T Consensus 10 l~~ia~~iG~~Wk~Lar~L-Gls~~dI~~ 37 (86)
T cd08318 10 ITVFANKLGEDWKTLAPHL-EMKDKEIRA 37 (86)
T ss_pred HHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 4447788999999999999 888777743
No 87
>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=51.49 E-value=22 Score=29.73 Aligned_cols=29 Identities=10% Similarity=0.074 Sum_probs=23.8
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-...+||..| |=|...|+++.+..+++
T Consensus 153 ~~~s~~EIA~~l-gis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 153 EGLSYEDIARIM-DCPVGTVRSRIFRAREA 181 (190)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 356789999999 88999999998776654
No 88
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=51.34 E-value=32 Score=27.86 Aligned_cols=29 Identities=10% Similarity=0.100 Sum_probs=24.5
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-.-.+||..| |-+...|++|.+..+++
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 466789999999 99999999999876654
No 89
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=51.30 E-value=18 Score=37.17 Aligned_cols=50 Identities=20% Similarity=0.314 Sum_probs=44.3
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 66 KRGNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 66 kk~~WT~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
..+.|+.+|=++...+..+.|.+.+-|+..+|+|...|||-+|..--+++
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~eE~r~ 457 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKEEKRN 457 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhhhhcc
Confidence 34689999999999999999999999999999999999999886554443
No 90
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=50.95 E-value=6.9 Score=41.19 Aligned_cols=45 Identities=13% Similarity=0.248 Sum_probs=40.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccccccCcccCcccccccccc
Q 024484 13 KKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWIN 59 (267)
Q Consensus 13 kkg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n 59 (267)
....||+.|-.+..+++-.|. +++-.|++.+.+ ++.+||-+-|..
T Consensus 618 gSd~WTp~E~~lF~kA~y~~~-KDF~~v~km~~~-KtVaqCVeyYYt 662 (907)
T KOG4167|consen 618 GSDKWTPLERKLFNKALYTYS-KDFIFVQKMVKS-KTVAQCVEYYYT 662 (907)
T ss_pred CcccccHHHHHHHHHHHHHhc-ccHHHHHHHhcc-ccHHHHHHHHHH
Confidence 356799999999999999999 899999999998 999999987654
No 91
>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=50.13 E-value=5 Score=26.69 Aligned_cols=37 Identities=22% Similarity=0.368 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHhCCCCccccccccCcccCccccccccc
Q 024484 20 EEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWI 58 (267)
Q Consensus 20 EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~ 58 (267)
+=|.+|+.+.+.-|...|..||+.+| =+...|+.|+.
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lg--lS~~~v~~Ri~ 39 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELG--LSESTVRRRIR 39 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHT--S-HHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHC--cCHHHHHHHHH
Confidence 34788999999999889999999998 57777888764
No 92
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=49.55 E-value=34 Score=28.38 Aligned_cols=37 Identities=19% Similarity=0.248 Sum_probs=28.4
Q ss_pred HHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 78 IINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 78 Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
++.+....|-...+||..| |-+...|+.+.+.-+++-
T Consensus 127 v~~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 127 AFLYNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred HHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3344444567899999999 999999999988776654
No 93
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=49.52 E-value=16 Score=37.85 Aligned_cols=47 Identities=13% Similarity=0.283 Sum_probs=34.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccccccccCcc---------cCcccccccccccc
Q 024484 14 KGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLL---------RCGKSCRLRWINYL 61 (267)
Q Consensus 14 kg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~---------Rt~kqCr~Rw~n~L 61 (267)
|..||-.|.+....+++.+| +++.+|-..+... ++-.|+|.+|.+.+
T Consensus 88 ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~ 143 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLV 143 (782)
T ss_pred ccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHH
Confidence 67899999999999999999 8998883332211 44556777665543
No 94
>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=48.19 E-value=49 Score=20.89 Aligned_cols=37 Identities=24% Similarity=0.291 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHH
Q 024484 74 EEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTH 111 (267)
Q Consensus 74 ED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~ 111 (267)
++..++.++-.-|-.+.+||+.+ |=+...|+.+.+..
T Consensus 14 ~~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~ 50 (55)
T cd06171 14 REREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRA 50 (55)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 34555666656777899999998 77888887766544
No 95
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=48.08 E-value=55 Score=27.79 Aligned_cols=29 Identities=7% Similarity=-0.039 Sum_probs=24.4
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-...+||..| |-+...||.|.+..+++
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~RAr~~ 177 (189)
T PRK12530 149 LELSSEQICQEC-DISTSNLHVLLYRARLQ 177 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466799999999 99999999998776644
No 96
>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=48.06 E-value=22 Score=27.01 Aligned_cols=31 Identities=32% Similarity=0.579 Sum_probs=26.1
Q ss_pred HHHHHHHHHhhCCchhHHhhcCCCCCHHHHHH
Q 024484 75 EETIINLHDMLGNRWSAIAGRLPGRTDNEIKN 106 (267)
Q Consensus 75 D~~Li~l~~~~G~kWs~IA~~lpgRT~~q~Kn 106 (267)
|..|-.+...+|..|.++|..| |=+..+|.+
T Consensus 4 ~~~l~~ia~~LG~dWk~LAr~L-g~se~dI~~ 34 (84)
T cd08804 4 EERLAVIADHLGFSWTELAREL-DFTEEQIHQ 34 (84)
T ss_pred hhHHHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 5667788899999999999999 777777765
No 97
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=47.66 E-value=31 Score=28.69 Aligned_cols=28 Identities=14% Similarity=0.045 Sum_probs=23.1
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
|-...+||..| |-+...|+++.+..+++
T Consensus 152 g~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T TIGR02948 152 DLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 56689999999 89999999988766554
No 98
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=47.53 E-value=38 Score=28.43 Aligned_cols=34 Identities=18% Similarity=0.121 Sum_probs=27.4
Q ss_pred HHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 81 LHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 81 l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
|+...|-...+||..| |-+...||.|.+..+++-
T Consensus 138 L~~~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~ 171 (178)
T PRK12529 138 MATLDGMKQKDIAQAL-DIALPTVKKYIHQAYVTC 171 (178)
T ss_pred HHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3334467799999999 999999999998777654
No 99
>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=47.19 E-value=36 Score=28.08 Aligned_cols=29 Identities=24% Similarity=0.304 Sum_probs=23.5
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-...+||..| |-|...|+++.+..+++
T Consensus 134 ~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~ 162 (169)
T TIGR02954 134 HDLTIKEIAEVM-NKPEGTVKTYLHRALKK 162 (169)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 455788999999 88999999998876654
No 100
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=47.15 E-value=40 Score=27.47 Aligned_cols=29 Identities=10% Similarity=-0.110 Sum_probs=24.1
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-.-.+||+.| |-+...|++|.+..+++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (160)
T PRK09642 121 EEKSYQEIALQE-KIEVKTVEMKLYRARKW 149 (160)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456689999999 99999999998876654
No 101
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=46.56 E-value=65 Score=27.27 Aligned_cols=30 Identities=17% Similarity=0.232 Sum_probs=24.5
Q ss_pred hhCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 84 MLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 84 ~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
..|-.-.+||..| |-+...|+.|.+..+++
T Consensus 150 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 179 (195)
T PRK12532 150 ILGFSSDEIQQMC-GISTSNYHTIMHRARES 179 (195)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466789999999 99999999998876654
No 102
>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=46.22 E-value=41 Score=28.64 Aligned_cols=34 Identities=12% Similarity=0.096 Sum_probs=26.4
Q ss_pred HHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 80 NLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 80 ~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.++...|-...+||..| |-+.+.||.|.+..+++
T Consensus 141 ~l~~~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 141 MMREVLGFESDEICQEL-EISTSNCHVLLYRARLS 174 (188)
T ss_pred HHHHHhCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 33334466789999999 99999999998776654
No 103
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=46.16 E-value=63 Score=27.23 Aligned_cols=30 Identities=13% Similarity=0.119 Sum_probs=24.7
Q ss_pred hhCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 84 MLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 84 ~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
..|-...+||..| |-|...|+++.+..+++
T Consensus 145 ~~~~s~~eIA~~l-gis~~tV~~~l~Rar~~ 174 (189)
T PRK12515 145 YHEKSVEEVGEIV-GIPESTVKTRMFYARKK 174 (189)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3466789999999 88999999999876544
No 104
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=46.02 E-value=41 Score=28.15 Aligned_cols=30 Identities=17% Similarity=0.251 Sum_probs=24.7
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
.|-...+||..| |-+...|+.+.+..+++-
T Consensus 146 ~g~s~~eIA~~l-~is~~tV~~~l~ra~~~L 175 (184)
T PRK12512 146 EGASIKETAAKL-SMSEGAVRVALHRGLAAL 175 (184)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 466789999999 999999999988776543
No 105
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=45.93 E-value=36 Score=28.74 Aligned_cols=28 Identities=11% Similarity=0.118 Sum_probs=23.0
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
|-...+||..| |-+...|+++.+..+++
T Consensus 154 g~s~~eIA~~l-gis~~tv~~~l~Rar~~ 181 (193)
T PRK11923 154 GLSYEDIASVM-QCPVGTVRSRIFRAREA 181 (193)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 55689999999 88999999998776654
No 106
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=45.80 E-value=39 Score=28.62 Aligned_cols=31 Identities=23% Similarity=0.168 Sum_probs=25.2
Q ss_pred HhhCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 83 DMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 83 ~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
...|-...+||..| |-+...|+++.+..+++
T Consensus 119 ~~~g~~~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (181)
T PRK09637 119 ELEGLSQKEIAEKL-GLSLSGAKSRVQRGRVK 149 (181)
T ss_pred HhcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 34567799999999 99999999998766544
No 107
>PF13137 DUF3983: Protein of unknown function (DUF3983)
Probab=45.77 E-value=13 Score=24.01 Aligned_cols=10 Identities=50% Similarity=1.032 Sum_probs=7.9
Q ss_pred HHHHHHHhcC
Q 024484 250 FWYNILVTSG 259 (267)
Q Consensus 250 ~~~~~~~~~~ 259 (267)
=|.|+|+++|
T Consensus 24 AWRNiFvqag 33 (34)
T PF13137_consen 24 AWRNIFVQAG 33 (34)
T ss_pred HHHHHHHHcc
Confidence 4888888876
No 108
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=45.71 E-value=42 Score=27.72 Aligned_cols=29 Identities=28% Similarity=0.346 Sum_probs=24.1
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-.-.+||..| |.+...|+.|.+..+++
T Consensus 133 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 161 (173)
T PRK09645 133 RGWSTAQIAADL-GIPEGTVKSRLHYALRA 161 (173)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 455679999999 99999999999877654
No 109
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=45.47 E-value=42 Score=28.25 Aligned_cols=31 Identities=19% Similarity=0.264 Sum_probs=25.0
Q ss_pred hhCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 84 MLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 84 ~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
..|-...+||..| |-+...|+.+.+..+++-
T Consensus 153 ~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~L 183 (189)
T PRK09648 153 VVGLSAEETAEAV-GSTPGAVRVAQHRALARL 183 (189)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3466799999999 999999999987766543
No 110
>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=45.41 E-value=19 Score=27.45 Aligned_cols=46 Identities=24% Similarity=0.346 Sum_probs=31.4
Q ss_pred HHHHHHHHhhCCchhHHhhcCCCCCHH---HHHHHHHHHhHHHHHHHHHh
Q 024484 76 ETIINLHDMLGNRWSAIAGRLPGRTDN---EIKNVWHTHLKKKAAAVLKQ 122 (267)
Q Consensus 76 ~~Li~l~~~~G~kWs~IA~~lpgRT~~---q~KnRw~~~lkk~~~~~~~~ 122 (267)
..|..+...+|..|..+|.+| |=+.. .|+.+|-.-++...-..+..
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L-Glse~~Id~Ie~~~~~dl~eq~~~mL~~ 51 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL-GLSYRELQRIKYNNRDDLDEQIFDMLFS 51 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc-CCCHHHHHHHHHHCccCHHHHHHHHHHH
Confidence 468889999999999999998 44443 45666644455554444443
No 111
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=44.88 E-value=43 Score=28.47 Aligned_cols=29 Identities=10% Similarity=0.003 Sum_probs=23.7
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-...+||..| |-+...|+.|.+..+++
T Consensus 156 eg~s~~EIA~~l-gis~~tVk~rl~ra~~~ 184 (194)
T PRK12531 156 EELPHQQVAEMF-DIPLGTVKSRLRLAVEK 184 (194)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 356789999999 99999999998766654
No 112
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=44.44 E-value=50 Score=25.29 Aligned_cols=42 Identities=12% Similarity=0.121 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHhhC-CchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 73 EEEETIINLHDMLG-NRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 73 EED~~Li~l~~~~G-~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
+.|..|+.+....| -.+++||+.+ |-+...|+.+...+.++.
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 56888888888887 4699999999 999999999998887755
No 113
>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=44.20 E-value=27 Score=26.32 Aligned_cols=34 Identities=32% Similarity=0.631 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHH
Q 024484 72 KEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNV 107 (267)
Q Consensus 72 ~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnR 107 (267)
+||-++|+.. -..|..|..+|..| |=+...|++-
T Consensus 2 ~~~v~~ll~~-~nlG~dW~~LA~~L-G~~~~~I~~i 35 (77)
T cd08311 2 QEEVEKLLES-GRPGRDWRSLAGEL-GYEDEAIDTF 35 (77)
T ss_pred hHHHHHHHhC-CCCccCHHHHHHHc-CCCHHHHHHH
Confidence 5777777732 25788999999999 8888887663
No 114
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=42.94 E-value=61 Score=27.67 Aligned_cols=39 Identities=18% Similarity=0.279 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHh
Q 024484 73 EEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHL 112 (267)
Q Consensus 73 EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~l 112 (267)
++...++++....|-.+.+||..| |-+...|+.+|+.+-
T Consensus 138 ~~~~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR 176 (185)
T PF07638_consen 138 PRQRRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 344455555555677899999999 999999999998765
No 115
>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=42.78 E-value=27 Score=26.74 Aligned_cols=31 Identities=32% Similarity=0.636 Sum_probs=25.0
Q ss_pred HHHHHHHHhhCCchhHHhhcCCCCCHHHHHHH
Q 024484 76 ETIINLHDMLGNRWSAIAGRLPGRTDNEIKNV 107 (267)
Q Consensus 76 ~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnR 107 (267)
+.|-.+....|..|..+|.+| |=++.+|..-
T Consensus 3 ~~l~~l~~~lG~~Wk~lar~L-G~s~~eI~~i 33 (86)
T cd08777 3 KHLDLLRENLGKKWKRCARKL-GFTESEIEEI 33 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHc-CCCHHHHHHH
Confidence 445566688899999999999 8888888663
No 116
>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=42.77 E-value=33 Score=25.35 Aligned_cols=31 Identities=32% Similarity=0.646 Sum_probs=23.3
Q ss_pred HHHHHHHHHHh-hCCchhHHhhcCCCCCHHHHH
Q 024484 74 EEETIINLHDM-LGNRWSAIAGRLPGRTDNEIK 105 (267)
Q Consensus 74 ED~~Li~l~~~-~G~kWs~IA~~lpgRT~~q~K 105 (267)
-.+.|..++.. .|..|..+|..| |=+..+|.
T Consensus 4 ~~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i~ 35 (88)
T smart00005 4 TREKLAKLLDHPLGLDWRELARKL-GLSEADID 35 (88)
T ss_pred HHHHHHHHHcCccchHHHHHHHHc-CCCHHHHH
Confidence 35567777777 899999999999 55555553
No 117
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=42.69 E-value=48 Score=28.26 Aligned_cols=31 Identities=10% Similarity=-0.006 Sum_probs=25.0
Q ss_pred hhCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 84 MLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 84 ~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
..|-.+.+||+.| |=+...|+++.+..+++-
T Consensus 150 ~~g~s~~eIA~~l-gis~~tV~~~l~Ra~~~L 180 (196)
T PRK12524 150 IEGLSNPEIAEVM-EIGVEAVESLTARGKRAL 180 (196)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 3466799999999 999999999887766543
No 118
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=42.57 E-value=62 Score=26.93 Aligned_cols=30 Identities=23% Similarity=0.238 Sum_probs=25.1
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
.|-...+||+.| |-+...|+++.+..+++-
T Consensus 134 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~~ 163 (172)
T PRK09651 134 DGLTYSEIAHKL-GVSVSSVKKYVAKATEHC 163 (172)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 355689999999 999999999998777654
No 119
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=42.31 E-value=49 Score=27.99 Aligned_cols=29 Identities=34% Similarity=0.392 Sum_probs=22.9
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
|-.-.+||+.| |.|...|+++-+..+++-
T Consensus 147 g~s~~EIAe~l-gis~~~V~~~l~Ra~~~L 175 (189)
T PRK06811 147 GEKIEEIAKKL-GLTRSAIDNRLSRGRKKL 175 (189)
T ss_pred cCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 45568999999 999999999887666553
No 120
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=42.10 E-value=93 Score=30.66 Aligned_cols=75 Identities=15% Similarity=0.216 Sum_probs=45.5
Q ss_pred ccCCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcccCcccccccccccccCCCCCCCCCHHHHHHHHHHHHhhCC
Q 024484 8 EKMGLKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETIINLHDMLGN 87 (267)
Q Consensus 8 ~k~~lkkg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~ikk~~WT~EED~~Li~l~~~~G~ 87 (267)
++-+..-|.|++.=|+...++..-|.+-.=++|--. ... +.||.
T Consensus 70 D~~~daegvWSpdIEqsFqEALaiyppcGrrKIils-----deg-------------------------------kmyGR 113 (455)
T KOG3841|consen 70 DNQRDAEGVWSPDIEQSFQEALAIYPPCGRRKIILS-----DEG-------------------------------KMYGR 113 (455)
T ss_pred ccccccccccChhHHHHHHHHHhhcCCCCceeEEEc-----cCc-------------------------------cccch
Confidence 333455688999999999888888874333333211 000 12221
Q ss_pred chhHHhhcC-----CCCCHHHHHHHHHHHhHHHHHHH
Q 024484 88 RWSAIAGRL-----PGRTDNEIKNVWHTHLKKKAAAV 119 (267)
Q Consensus 88 kWs~IA~~l-----pgRT~~q~KnRw~~~lkk~~~~~ 119 (267)
+ ..||+++ ..||..||-.|-+.+-|++.++.
T Consensus 114 N-ELIarYIKlrtgktRTrKQVSSHIQVlarrk~rei 149 (455)
T KOG3841|consen 114 N-ELIARYIKLRTGKTRTRKQVSSHIQVLARRKLREI 149 (455)
T ss_pred H-HHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHH
Confidence 1 2344432 36999999999888888776654
No 121
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=41.86 E-value=55 Score=26.32 Aligned_cols=29 Identities=21% Similarity=0.284 Sum_probs=22.6
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-...+||..+ |-+...|+++-+..+++
T Consensus 121 ~~~s~~EIA~~l-~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 121 VGKTMGEIALET-EMTYYQVRWIYRQALEK 149 (154)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355678999999 99999999987766554
No 122
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=41.54 E-value=53 Score=26.77 Aligned_cols=28 Identities=25% Similarity=0.329 Sum_probs=22.9
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
|-...+||+.| |-+...|+++-+..+++
T Consensus 138 g~s~~eIA~~l-~is~~tv~~~l~ra~~~ 165 (170)
T TIGR02952 138 NLPIAEVARIL-GKTEGAVKILQFRAIKK 165 (170)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 56679999999 99999999988766554
No 123
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=40.90 E-value=53 Score=27.30 Aligned_cols=28 Identities=21% Similarity=0.245 Sum_probs=23.5
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
|-.-.+||..| |.+...|+++.+..+++
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 55689999999 99999999998776654
No 124
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=40.12 E-value=56 Score=27.36 Aligned_cols=30 Identities=23% Similarity=0.212 Sum_probs=25.0
Q ss_pred hhCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 84 MLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 84 ~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
..|-...+||..| |.+...|+++-+..+++
T Consensus 143 ~~g~s~~EIA~~l-~is~~tV~~~l~rar~~ 172 (181)
T PRK12536 143 LEGLSVAETAQLT-GLSESAVKVGIHRGLKA 172 (181)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466789999999 99999999998776654
No 125
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=40.08 E-value=61 Score=26.44 Aligned_cols=32 Identities=19% Similarity=0.223 Sum_probs=25.1
Q ss_pred HHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 82 HDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 82 ~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.-..|-...+||..+ |-+...|+.|.+..+++
T Consensus 125 ~~~~g~s~~EIA~~l-~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 125 AQVDGLGYGEIATEL-GISLATVKRYLNKAAMR 156 (161)
T ss_pred HHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 333466789999999 99999999988776543
No 126
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=39.92 E-value=35 Score=23.47 Aligned_cols=44 Identities=25% Similarity=0.309 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 69 NFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 69 ~WT~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
..|+.|-+.|.-+.. |..=.+||..+ |.+...|+.+...+++|-
T Consensus 3 ~LT~~E~~vl~~l~~--G~~~~eIA~~l-~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ--GMSNKEIAEEL-GISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHT--TS-HHHHHHHH-TSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHh--cCCcchhHHhc-CcchhhHHHHHHHHHHHh
Confidence 356777776666654 44446999999 999999999988887764
No 127
>PF06599 DUF1139: Protein of unknown function (DUF1139); InterPro: IPR009519 This family consists of several hypothetical Fijivirus proteins of unknown function.
Probab=39.52 E-value=17 Score=33.98 Aligned_cols=14 Identities=21% Similarity=0.942 Sum_probs=12.0
Q ss_pred CCchHHHHHHHHhc
Q 024484 245 GGGMDFWYNILVTS 258 (267)
Q Consensus 245 ~~~~~~~~~~~~~~ 258 (267)
+-+.||||+||||+
T Consensus 277 ~~dvD~WY~lfmrt 290 (309)
T PF06599_consen 277 HTDVDYWYSLFMRT 290 (309)
T ss_pred CCCHHHHHHHHHHH
Confidence 44889999999985
No 128
>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=39.47 E-value=61 Score=26.94 Aligned_cols=29 Identities=21% Similarity=0.209 Sum_probs=23.8
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-...+||..| |-+...|+.|.+..+++
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 177 (183)
T TIGR02999 149 AGLTVEEIAELL-GVSVRTVERDWRFARAW 177 (183)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 355689999999 99999999998776554
No 129
>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=39.11 E-value=65 Score=27.39 Aligned_cols=46 Identities=22% Similarity=0.229 Sum_probs=37.6
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCchhHHhhcCC----CCCHHHHHHHHHHH
Q 024484 66 KRGNFSKEEEETIINLHDMLGNRWSAIAGRLP----GRTDNEIKNVWHTH 111 (267)
Q Consensus 66 kk~~WT~EED~~Li~l~~~~G~kWs~IA~~lp----gRT~~q~KnRw~~~ 111 (267)
....-|..|...|..|+++||..+.++|.-.- -.|..||+.+....
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 34568899999999999999999999988542 47999998877654
No 130
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=38.31 E-value=57 Score=27.58 Aligned_cols=29 Identities=17% Similarity=0.139 Sum_probs=23.9
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-...+||..| |-+...|+.|.+..+++
T Consensus 145 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 173 (185)
T PRK09649 145 LGLSYADAAAVC-GCPVGTIRSRVARARDA 173 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355689999999 99999999998766654
No 131
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=38.02 E-value=68 Score=26.41 Aligned_cols=30 Identities=17% Similarity=0.099 Sum_probs=24.2
Q ss_pred hhCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 84 MLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 84 ~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
..|-...+||..| |-+...|+++-+..+++
T Consensus 126 ~~g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 155 (164)
T PRK12547 126 ASGFSYEDAAAIC-GCAVGTIKSRVSRARNR 155 (164)
T ss_pred HcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3466789999999 99999999988776654
No 132
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=37.81 E-value=1e+02 Score=25.97 Aligned_cols=30 Identities=13% Similarity=-0.066 Sum_probs=24.3
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
.|-.-.+||..| |-+...|++|.+..+++-
T Consensus 146 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~L 175 (191)
T PRK12520 146 LELETEEICQEL-QITATNAWVLLYRARMRL 175 (191)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 355679999999 999999999988766543
No 133
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=37.72 E-value=64 Score=27.08 Aligned_cols=29 Identities=14% Similarity=0.342 Sum_probs=24.0
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-...+||..| |-+...|++|.+..+++
T Consensus 137 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 165 (185)
T PRK12542 137 YNLTYQEISSVM-GITEANVRKQFERARKR 165 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456789999999 99999999988766654
No 134
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=37.72 E-value=65 Score=26.89 Aligned_cols=28 Identities=21% Similarity=0.175 Sum_probs=22.9
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
|-.-.+||..+ |-+...|+.+.+..+++
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 45679999999 99999999988776654
No 135
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=37.32 E-value=97 Score=26.36 Aligned_cols=36 Identities=19% Similarity=0.112 Sum_probs=27.1
Q ss_pred HHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 78 IINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 78 Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
++.|....|-...+||+.| |-+...||.|-+..+++
T Consensus 124 i~~L~~~~g~s~~EIA~~L-gis~~tVk~~l~Rar~~ 159 (187)
T PRK12516 124 AIILVGASGFAYEEAAEIC-GCAVGTIKSRVNRARQR 159 (187)
T ss_pred HHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3333344566789999999 99999999998776654
No 136
>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=37.24 E-value=66 Score=26.68 Aligned_cols=30 Identities=20% Similarity=0.550 Sum_probs=24.3
Q ss_pred hhCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 84 MLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 84 ~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
..|-...+||..| |-|...|+.+.+..+++
T Consensus 154 ~~g~s~~eIA~~l-gis~~~v~~~l~Ra~~~ 183 (189)
T TIGR02984 154 LEGLSFAEVAERM-DRSEGAVSMLWVRGLAR 183 (189)
T ss_pred hcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3466789999999 99999999988776654
No 137
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=37.19 E-value=73 Score=25.88 Aligned_cols=29 Identities=21% Similarity=0.221 Sum_probs=23.4
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-.-.+||..| |-+...|+.|....+++
T Consensus 120 ~~~s~~eIA~~l-gis~~tv~~~l~ra~~~ 148 (159)
T PRK12527 120 EGLSHQQIAEHL-GISRSLVEKHIVNAMKH 148 (159)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 355678999999 99999999998766554
No 138
>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=37.02 E-value=23 Score=28.46 Aligned_cols=28 Identities=18% Similarity=0.115 Sum_probs=23.6
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
|-.+.+||..| |=+...|+++.+...++
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 45689999999 99999999999877654
No 139
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=36.98 E-value=65 Score=27.68 Aligned_cols=29 Identities=17% Similarity=0.071 Sum_probs=23.6
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-.-.+||..| |.+...||.|.+..+++
T Consensus 154 eg~s~~EIA~~l-gis~~tVk~~l~RAr~~ 182 (201)
T PRK12545 154 LDFEIDDICTEL-TLTANHCSVLLYRARTR 182 (201)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 355689999999 99999999998765543
No 140
>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=36.68 E-value=41 Score=25.80 Aligned_cols=40 Identities=23% Similarity=0.324 Sum_probs=27.2
Q ss_pred HHHHHHHHHhhCCchhHHhhcCCCCCH---HHHHHHHHHHhHHH
Q 024484 75 EETIINLHDMLGNRWSAIAGRLPGRTD---NEIKNVWHTHLKKK 115 (267)
Q Consensus 75 D~~Li~l~~~~G~kWs~IA~~lpgRT~---~q~KnRw~~~lkk~ 115 (267)
|..|..+.+.+|..|.++|..| |=+. +.|+..+-.-+...
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L-~vs~~dI~~I~~e~p~~l~~Q 46 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL-QFSVEDINRIRVENPNSLLEQ 46 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc-CCCHHHHHHHHHhCCCCHHHH
Confidence 5677888899999999999998 4444 44455444333333
No 141
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 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=36.51 E-value=56 Score=30.03 Aligned_cols=29 Identities=21% Similarity=0.251 Sum_probs=24.0
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-.-.+||..| |.+...||+|.+..+++
T Consensus 157 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 185 (324)
T TIGR02960 157 LGWRAAETAELL-GTSTASVNSALQRARAT 185 (324)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456689999999 99999999998766544
No 142
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=36.40 E-value=34 Score=38.30 Aligned_cols=72 Identities=18% Similarity=0.325 Sum_probs=42.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccccccccCcccCcccccccccccccCCCCCCCCCHHHHHHHHHHHHhh-CCchhHH
Q 024484 14 KGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETIINLHDML-GNRWSAI 92 (267)
Q Consensus 14 kg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~ikk~~WT~EED~~Li~l~~~~-G~kWs~I 92 (267)
---|..++|..|+-.|-+||-++|.+|-.--.. |... ...+.-.+-.+.+=...-..|+.+...+ +.+|.+.
T Consensus 1133 ~~~W~~e~Ds~LLiGI~khGygswe~Ir~Dp~L------~l~d-Ki~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~~ 1205 (1373)
T KOG0384|consen 1133 DCDWGSEDDSMLLIGIFKHGYGSWEAIRLDPDL------GLTD-KIFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPKK 1205 (1373)
T ss_pred ccCCCchhhhhHhhhhhhcccccHHHhccCccc------cchh-hhcccccCCchHHHHHHHHHHHHHHhhcccCCCchh
Confidence 345999999999999999999999988422111 1100 0011111334455555666666666665 4444443
No 143
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=35.93 E-value=95 Score=25.96 Aligned_cols=29 Identities=7% Similarity=0.020 Sum_probs=22.7
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-...+||+.| |-+...|+++.+..+++
T Consensus 143 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 171 (186)
T PRK05602 143 QGLSNIEAAAVM-DISVDALESLLARGRRA 171 (186)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 456678899988 88999999988766644
No 144
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=35.58 E-value=70 Score=25.98 Aligned_cols=41 Identities=15% Similarity=0.149 Sum_probs=29.1
Q ss_pred HHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 74 EEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 74 ED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
++..++.+.-..|-.-.+||..| |-+...|+++.+..+++-
T Consensus 114 ~~r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~ra~~~L 154 (162)
T TIGR02983 114 RQRAVVVLRYYEDLSEAQVAEAL-GISVGTVKSRLSRALARL 154 (162)
T ss_pred HHHHHhhhHHHhcCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 33344444444566778999999 999999999988776653
No 145
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=35.55 E-value=13 Score=30.93 Aligned_cols=43 Identities=16% Similarity=0.203 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHhCCCCccccccccCcccCcccccccccccccCC
Q 024484 20 EEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPD 64 (267)
Q Consensus 20 EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~ 64 (267)
+-|.+|+.+.++.|...|..||+.+| -+...|+.|+.+...-.
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~lg--lS~~tV~~Ri~rL~~~G 51 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQFG--VSPGTIHVRVEKMKQAG 51 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCC
Confidence 57899999999999899999999998 68888999987765443
No 146
>PRK00118 putative DNA-binding protein; Validated
Probab=35.05 E-value=85 Score=25.09 Aligned_cols=41 Identities=12% Similarity=0.118 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhH
Q 024484 72 KEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLK 113 (267)
Q Consensus 72 ~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lk 113 (267)
++.+..++.+....|-...+||+.+ |-|...|+.+.+...+
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~RArk 59 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKRTEK 59 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 4556777788888889999999999 9999999988776544
No 147
>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=34.98 E-value=74 Score=20.69 Aligned_cols=34 Identities=21% Similarity=0.137 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHH
Q 024484 73 EEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNV 107 (267)
Q Consensus 73 EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnR 107 (267)
=|-+.|.++.+.+|++-++.|+.| |=+...+..+
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~k 38 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLL-GISRRTLYRK 38 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHH
Confidence 377889999999999999999998 6666655544
No 148
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=34.77 E-value=39 Score=29.78 Aligned_cols=29 Identities=17% Similarity=0.131 Sum_probs=23.9
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
|-...+||..| |-+...|+++.+..+++-
T Consensus 165 g~s~~EIAe~l-gis~~tVk~~l~Rar~kL 193 (231)
T PRK11922 165 ELSVEETAQAL-GLPEETVKTRLHRARRLL 193 (231)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 45689999999 999999999998766543
No 149
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=34.75 E-value=74 Score=26.64 Aligned_cols=29 Identities=31% Similarity=0.300 Sum_probs=23.7
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-.-.+||+.| |-+...|+++.+..+++
T Consensus 148 ~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 176 (182)
T PRK12537 148 DGCSHAEIAQRL-GAPLGTVKAWIKRSLKA 176 (182)
T ss_pred cCCCHHHHHHHH-CCChhhHHHHHHHHHHH
Confidence 455678999999 99999999998877754
No 150
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=33.06 E-value=74 Score=27.20 Aligned_cols=34 Identities=15% Similarity=0.063 Sum_probs=26.2
Q ss_pred HHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 80 NLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 80 ~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.++...|-...+||..| |-+...|+++.+..+++
T Consensus 123 ~L~~~~g~s~~EIA~~L-giS~~tVk~~l~Rar~~ 156 (188)
T PRK12546 123 ILVGASGFSYEEAAEMC-GVAVGTVKSRANRARAR 156 (188)
T ss_pred hhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 33334566789999999 99999999988776644
No 151
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=32.63 E-value=1e+02 Score=26.11 Aligned_cols=29 Identities=21% Similarity=0.218 Sum_probs=23.0
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-...+||+.| |-+...||++-+..+++
T Consensus 157 ~~~s~~EIA~~L-gis~~tVk~~l~ra~~~ 185 (194)
T PRK09646 157 GGLTYREVAERL-AVPLGTVKTRMRDGLIR 185 (194)
T ss_pred cCCCHHHHHHHh-CCChHhHHHHHHHHHHH
Confidence 355689999999 88999999988766554
No 152
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=32.48 E-value=1.4e+02 Score=25.98 Aligned_cols=30 Identities=3% Similarity=-0.053 Sum_probs=24.4
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
.|-.-.+||..| |-|...+++|.+..+++-
T Consensus 163 ~g~s~~EIAe~l-gis~~tV~~~l~RAr~~L 192 (206)
T PRK12544 163 IELETNEICHAV-DLSVSNLNVLLYRARLRL 192 (206)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 355679999999 999999999988766543
No 153
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=32.19 E-value=81 Score=28.86 Aligned_cols=29 Identities=24% Similarity=0.379 Sum_probs=23.7
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
+|-.-.+||+.| |.+...||++.+...++
T Consensus 130 ~g~s~~EIA~~l-g~s~~tVk~~l~RAr~~ 158 (293)
T PRK09636 130 FGVPFDEIASTL-GRSPAACRQLASRARKH 158 (293)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 455679999999 99999999998765544
No 154
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=31.86 E-value=72 Score=26.88 Aligned_cols=29 Identities=34% Similarity=0.225 Sum_probs=22.6
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-.-.+||..| |-+...|+.+.+..+++
T Consensus 156 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 184 (194)
T PRK12519 156 EGLSQSEIAKRL-GIPLGTVKARARQGLLK 184 (194)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 355678999999 88999999887765554
No 155
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=31.14 E-value=1.4e+02 Score=25.79 Aligned_cols=29 Identities=21% Similarity=0.286 Sum_probs=23.6
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-.-.+||..| |-+...|+++.+..+++
T Consensus 153 ~g~s~~EIA~~L-gis~~tV~~~l~RArk~ 181 (203)
T PRK09647 153 EGLSYEEIAATL-GVKLGTVRSRIHRGRQQ 181 (203)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355678999999 99999999998876554
No 156
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=31.08 E-value=53 Score=21.68 Aligned_cols=36 Identities=31% Similarity=0.419 Sum_probs=18.1
Q ss_pred CCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHH
Q 024484 69 NFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKN 106 (267)
Q Consensus 69 ~WT~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~Kn 106 (267)
.+|.+|=..|..++ .-|-.=.+||+.| ||+...|.+
T Consensus 4 ~Lt~~eR~~I~~l~-~~G~s~~~IA~~l-g~s~sTV~r 39 (44)
T PF13936_consen 4 HLTPEERNQIEALL-EQGMSIREIAKRL-GRSRSTVSR 39 (44)
T ss_dssp --------HHHHHH-CS---HHHHHHHT-T--HHHHHH
T ss_pred chhhhHHHHHHHHH-HcCCCHHHHHHHH-CcCcHHHHH
Confidence 46666666666554 5677789999999 999988866
No 157
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=30.80 E-value=13 Score=31.33 Aligned_cols=44 Identities=23% Similarity=0.275 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHhCCCCccccccccCcccCcccccccccccccCC
Q 024484 19 PEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPD 64 (267)
Q Consensus 19 ~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~ 64 (267)
.+-|.+|+.+.++.|.-.|..||+.+| -+...|+.|+.+..+-.
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lg--lS~~tv~~Ri~rL~~~G 56 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVG--LSPTPCLERVRRLERQG 56 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCC
Confidence 456889999999999889999999998 57778998887765443
No 158
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=30.79 E-value=1.1e+02 Score=26.96 Aligned_cols=44 Identities=25% Similarity=0.234 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 69 NFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 69 ~WT~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
..|+.|-+.|.-+.+ |-...+||+.| +-+...+|++...+++|-
T Consensus 155 ~Lt~rE~~Vl~l~~~--G~s~~eIA~~L-~iS~~TVk~~~~~i~~Kl 198 (216)
T PRK10100 155 LLTHREKEILNKLRI--GASNNEIARSL-FISENTVKTHLYNLFKKI 198 (216)
T ss_pred CCCHHHHHHHHHHHc--CCCHHHHHHHh-CCCHHHHHHHHHHHHHHh
Confidence 478777666665555 88889999999 899999999998888764
No 159
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=30.29 E-value=67 Score=24.41 Aligned_cols=31 Identities=19% Similarity=0.492 Sum_probs=22.8
Q ss_pred HHHHHHHhhCCchhHHhhcCCCCCHHHHHHHH
Q 024484 77 TIINLHDMLGNRWSAIAGRLPGRTDNEIKNVW 108 (267)
Q Consensus 77 ~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw 108 (267)
.+--+.+..|..|..+|+.| |=|..+|..--
T Consensus 4 ~f~~i~~~lG~~Wk~laR~L-Glse~~Id~i~ 34 (86)
T cd08306 4 AFDVICENVGRDWRKLARKL-GLSETKIESIE 34 (86)
T ss_pred HHHHHHHHHhhhHHHHHHHc-CCCHHHHHHHH
Confidence 34445567899999999999 77777765433
No 160
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=30.22 E-value=91 Score=28.46 Aligned_cols=29 Identities=10% Similarity=0.298 Sum_probs=24.0
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
+|-.-.+||+.| |.|...||.+.+...++
T Consensus 123 ~g~s~~EIA~~l-g~s~~tVr~~l~RAr~~ 151 (281)
T TIGR02957 123 FDYPYEEIASIV-GKSEANCRQLVSRARRH 151 (281)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466689999999 89999999988766554
No 161
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=29.98 E-value=1.1e+02 Score=24.59 Aligned_cols=29 Identities=28% Similarity=0.318 Sum_probs=20.7
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-.-.+||..| |=|...|+.+.+...++
T Consensus 126 ~g~~~~eIA~~l-~is~~tv~~~l~Rar~~ 154 (159)
T TIGR02989 126 RGVSLTALAEQL-GRTVNAVYKALSRLRVR 154 (159)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 355668888888 88888888877655443
No 162
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=29.91 E-value=90 Score=26.11 Aligned_cols=28 Identities=18% Similarity=0.111 Sum_probs=22.4
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
|-.-.+||+.| |-+...|+.|.+..+++
T Consensus 143 g~s~~EIA~~l-~is~~tv~~~l~Ra~~~ 170 (179)
T PRK09415 143 ELSIKEIAEVT-GVNENTVKTRLKKAKEL 170 (179)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 45678899988 77999999988877654
No 163
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=29.52 E-value=55 Score=23.51 Aligned_cols=26 Identities=38% Similarity=0.726 Sum_probs=19.5
Q ss_pred HHHHHHhhCCchhHHhhcCCCCCHHHH
Q 024484 78 IINLHDMLGNRWSAIAGRLPGRTDNEI 104 (267)
Q Consensus 78 Li~l~~~~G~kWs~IA~~lpgRT~~q~ 104 (267)
+..+...+|..|..+|..| |=+..+|
T Consensus 2 ~~~ia~~lg~~W~~la~~L-gl~~~~I 27 (79)
T cd01670 2 LDKLAKKLGKDWKKLARKL-GLSDGEI 27 (79)
T ss_pred HHHHHHHHhhHHHHHHHHh-CCCHHHH
Confidence 4567788899999999998 4444444
No 164
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=28.25 E-value=1.1e+02 Score=24.63 Aligned_cols=43 Identities=12% Similarity=0.134 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHhhCC-chhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 72 KEEEETIINLHDMLGN-RWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 72 ~EED~~Li~l~~~~G~-kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
.+-|..|+++.+.-|. .+.+||+.+ |-+...|++|-..+.+..
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~G 50 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEG 50 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCC
Confidence 3567888888888774 599999999 999999999987777654
No 165
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=28.04 E-value=85 Score=29.15 Aligned_cols=29 Identities=14% Similarity=0.127 Sum_probs=23.4
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-.-.+||..| |.+...||.|.+..+++
T Consensus 168 ~g~s~~EIA~~l-gis~~tVk~~l~RAr~~ 196 (339)
T PRK08241 168 LGWSAAEVAELL-DTSVAAVNSALQRARAT 196 (339)
T ss_pred hCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 355679999999 99999999988766554
No 166
>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=27.57 E-value=45 Score=28.36 Aligned_cols=47 Identities=19% Similarity=0.225 Sum_probs=32.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcc---cCcccccccccc
Q 024484 12 LKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLL---RCGKSCRLRWIN 59 (267)
Q Consensus 12 lkkg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~---Rt~kqCr~Rw~n 59 (267)
.....-|..|-+-|..+|.+|| .++.+.+.-...+ .|..||+.+...
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhG-dDy~aMarD~KLN~~Q~T~~qlrrki~~ 161 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHG-DDYKAMARDRKLNYMQHTPGQLRRKIRK 161 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHC-ccHHHHhccCCCCcccCCHHHHHHHHHH
Confidence 3456788999999999999999 7888777543311 555666555443
No 167
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=27.29 E-value=1.1e+02 Score=27.03 Aligned_cols=37 Identities=14% Similarity=0.243 Sum_probs=27.3
Q ss_pred HHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 78 IINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 78 Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
++.++-..|-...+||..| |-+...|+.+.+..+++-
T Consensus 192 vl~l~~~~g~s~~EIA~~l-gis~~tV~~~~~ra~~~L 228 (236)
T PRK06986 192 VLSLYYQEELNLKEIGAVL-GVSESRVSQIHSQAIKRL 228 (236)
T ss_pred HHHhHhccCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3333334456789999999 999999999887776653
No 168
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=27.29 E-value=1.6e+02 Score=26.34 Aligned_cols=44 Identities=20% Similarity=0.293 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 69 NFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 69 ~WT~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
..|+.|-+.|.-+.+ |-...+||..| +-+...|+++-..+++|-
T Consensus 133 ~LSpRErEVLrLLAq--GkTnKEIAe~L-~IS~rTVkth~srImkKL 176 (198)
T PRK15201 133 HFSVTERHLLKLIAS--GYHLSETAALL-SLSEEQTKSLRRSIMRKL 176 (198)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHHh
Confidence 478888877776665 77789999999 999999999888888764
No 169
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=27.17 E-value=1.2e+02 Score=24.53 Aligned_cols=29 Identities=24% Similarity=0.329 Sum_probs=23.2
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-.-.+||..| |-+...|+++.+..+++
T Consensus 126 ~g~s~~eIA~~l-gis~~tV~~~i~ra~~~ 154 (166)
T PRK09639 126 SGYSYKEIAEAL-GIKESSVGTTLARAKKK 154 (166)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 555678999999 99999999988766554
No 170
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=26.86 E-value=1.8e+02 Score=26.20 Aligned_cols=28 Identities=7% Similarity=0.017 Sum_probs=23.6
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
|-...+||..| |=+...||.|.+..+++
T Consensus 177 g~S~~EIA~~L-gis~~TVk~rl~RAr~~ 204 (244)
T TIGR03001 177 GLSMDRIGAMY-QVHRSTVSRWVAQARER 204 (244)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 55789999999 99999999998876654
No 171
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=26.78 E-value=1.2e+02 Score=26.02 Aligned_cols=28 Identities=18% Similarity=0.093 Sum_probs=22.8
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
|-.-.+||..| |.+...|+.+.+..+++
T Consensus 169 g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 196 (206)
T PRK12526 169 ELSQEQLAQQL-NVPLGTVKSRLRLALAK 196 (206)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 45578999999 99999999988766654
No 172
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=26.78 E-value=1.7e+02 Score=22.78 Aligned_cols=45 Identities=22% Similarity=0.356 Sum_probs=35.6
Q ss_pred CCCCCHHHHHHHHHHHHhhCCchhHHhhcCCCC-CHHHHHHHHHHHhH
Q 024484 67 RGNFSKEEEETIINLHDMLGNRWSAIAGRLPGR-TDNEIKNVWHTHLK 113 (267)
Q Consensus 67 k~~WT~EED~~Li~l~~~~G~kWs~IA~~lpgR-T~~q~KnRw~~~lk 113 (267)
+..||.|.-..+++++..-|..=+.||+.+ |- ..++++. |...+.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~~-W~~~~~ 50 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLYK-WRIQLQ 50 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHHH-HHHHHH
Confidence 568999999999999999998889999999 76 5555554 544443
No 173
>PRK09483 response regulator; Provisional
Probab=26.77 E-value=1e+02 Score=25.57 Aligned_cols=45 Identities=13% Similarity=0.239 Sum_probs=34.5
Q ss_pred CCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 68 GNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 68 ~~WT~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
...|+-|-+.|.-++ .|..=.+||..| +-+...|+++-+++++|-
T Consensus 147 ~~Lt~rE~~vl~~~~--~G~~~~~Ia~~l-~is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 147 ASLSERELQIMLMIT--KGQKVNEISEQL-NLSPKTVNSYRYRMFSKL 191 (217)
T ss_pred cccCHHHHHHHHHHH--CCCCHHHHHHHh-CCCHHHHHHHHHHHHHHc
Confidence 358999988886554 444446999999 779999999888888763
No 174
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=26.40 E-value=1.4e+02 Score=24.81 Aligned_cols=29 Identities=28% Similarity=0.173 Sum_probs=22.9
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-.=.+||..| |-+...++++.+..+++
T Consensus 115 ~g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 143 (170)
T TIGR02959 115 EGLSQQEIAEKL-GLSLSGAKSRVQRGRKK 143 (170)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 455678999999 89999999988775543
No 175
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=26.34 E-value=1.5e+02 Score=26.34 Aligned_cols=28 Identities=11% Similarity=0.080 Sum_probs=23.4
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
|-.-.+||..| |-+...|++|.+..+++
T Consensus 187 g~s~~EIA~~L-gis~~tVk~~l~RAr~k 214 (233)
T PRK12538 187 NMSNGEIAEVM-DTTVAAVESLLKRGRQQ 214 (233)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 55679999999 99999999998776654
No 176
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=26.32 E-value=1.2e+02 Score=33.63 Aligned_cols=45 Identities=20% Similarity=0.386 Sum_probs=36.9
Q ss_pred CCCCHHHHHHHHHHHHhhC-CchhHHhhcCCCCCHHHHHHHHHHHh
Q 024484 68 GNFSKEEEETIINLHDMLG-NRWSAIAGRLPGRTDNEIKNVWHTHL 112 (267)
Q Consensus 68 ~~WT~EED~~Li~l~~~~G-~kWs~IA~~lpgRT~~q~KnRw~~~l 112 (267)
..||.-+=...+.+..+|| ..-..||..|.|+|..+|+.......
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~~f~ 870 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAKVFW 870 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHHHHH
Confidence 3588888888888889999 56899999999999999997544433
No 177
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=26.27 E-value=55 Score=27.00 Aligned_cols=29 Identities=24% Similarity=0.374 Sum_probs=23.1
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
+|-...+||..| |-+...|+.+.+..+++
T Consensus 141 ~g~s~~eIA~~l-~is~~~V~~~l~ra~~~ 169 (176)
T PRK09638 141 YGYTYEEIAKML-NIPEGTVKSRVHHGIKQ 169 (176)
T ss_pred cCCCHHHHHHHH-CCChhHHHHHHHHHHHH
Confidence 456789999999 88999998888766544
No 178
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=25.92 E-value=1.7e+02 Score=23.70 Aligned_cols=45 Identities=20% Similarity=0.244 Sum_probs=35.5
Q ss_pred CCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 68 GNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 68 ~~WT~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
...|+.|-++|.-+.+ |-...+||..| +-+...++.+.+++.+|-
T Consensus 136 ~~Lt~~E~~il~~l~~--g~~~~~Ia~~l-~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 136 DPLTKRERQVAEKLAQ--GMAVKEIAAEL-GLSPKTVHVHRANLMEKL 180 (196)
T ss_pred cCCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHHh
Confidence 4688888887777665 44678999999 789999999888877663
No 179
>PRK06930 positive control sigma-like factor; Validated
Probab=25.48 E-value=2.1e+02 Score=24.53 Aligned_cols=38 Identities=21% Similarity=0.250 Sum_probs=28.1
Q ss_pred HHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 77 TIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 77 ~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
.++.++...|-...+||..| |-+...|+.+.+..+++-
T Consensus 121 ~V~~L~~~eg~s~~EIA~~l-giS~~tVk~~l~Ra~~kL 158 (170)
T PRK06930 121 EVYLMHRGYGLSYSEIADYL-NIKKSTVQSMIERAEKKI 158 (170)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 33444445677889999999 899999999887666543
No 180
>PRK01905 DNA-binding protein Fis; Provisional
Probab=24.88 E-value=1.6e+02 Score=21.71 Aligned_cols=35 Identities=20% Similarity=0.178 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHH
Q 024484 72 KEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNV 107 (267)
Q Consensus 72 ~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnR 107 (267)
.-|...|++++...|+.+++.|+.+ |=+...++.+
T Consensus 36 ~~E~~~i~~aL~~~~gn~s~aAr~L-GIsrstL~rk 70 (77)
T PRK01905 36 CVEKPLLEVVMEQAGGNQSLAAEYL-GINRNTLRKK 70 (77)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHH
Confidence 4577789999999999999999988 6565555443
No 181
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=24.44 E-value=1.4e+02 Score=25.20 Aligned_cols=29 Identities=14% Similarity=0.036 Sum_probs=23.4
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-.-.+||..| |-+...|+++.+..+++
T Consensus 126 eg~s~~EIA~~l-gis~~tV~~~l~Rar~~ 154 (182)
T PRK12511 126 EGLSYQEAAAVL-GIPIGTLMSRIGRARAA 154 (182)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 355679999999 99999999998766654
No 182
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=24.42 E-value=1.2e+02 Score=26.39 Aligned_cols=44 Identities=11% Similarity=0.065 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 69 NFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 69 ~WT~EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
..|+-|-+.|.-+++=+. ..+||+.| |-+...++++-..+++|-
T Consensus 137 ~LT~RE~eVL~lla~G~s--nkeIA~~L-~iS~~TVk~h~~~I~~KL 180 (207)
T PRK15411 137 SLSRTESSMLRMWMAGQG--TIQISDQM-NIKAKTVSSHKGNIKRKI 180 (207)
T ss_pred cCCHHHHHHHHHHHcCCC--HHHHHHHc-CCCHHHHHHHHHHHHHHh
Confidence 489999888877776444 47999999 899999999988888764
No 183
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=24.17 E-value=1.5e+02 Score=24.49 Aligned_cols=28 Identities=11% Similarity=0.049 Sum_probs=21.5
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
|-.-.+||..| |-+...|+.|.+..+++
T Consensus 135 ~~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 162 (173)
T PRK12522 135 QYSYKEMSEIL-NIPIGTVKYRLNYAKKQ 162 (173)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 45568899988 88999999887665543
No 184
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=24.08 E-value=1.3e+02 Score=26.30 Aligned_cols=28 Identities=18% Similarity=0.225 Sum_probs=23.0
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
|-...+||..| |-+...|+++-+..+++
T Consensus 198 g~s~~EIA~~l-gis~~tVk~~~~rA~~~ 225 (234)
T PRK08301 198 EKTQKEVADML-GISQSYISRLEKRIIKR 225 (234)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 56789999999 99999999887766554
No 185
>PRK15328 invasion protein IagB; Provisional
Probab=23.97 E-value=1.8e+02 Score=24.84 Aligned_cols=42 Identities=10% Similarity=0.309 Sum_probs=30.8
Q ss_pred HHHHHHHhhCCchhHHhhcC--CCCCHHHHHHHHHHHhHHHHHH
Q 024484 77 TIINLHDMLGNRWSAIAGRL--PGRTDNEIKNVWHTHLKKKAAA 118 (267)
Q Consensus 77 ~Li~l~~~~G~kWs~IA~~l--pgRT~~q~KnRw~~~lkk~~~~ 118 (267)
.|..+++.||+.|..|+.+= +++.....+.+|-..+.+...+
T Consensus 98 ~L~~~~~~~g~~~~alaaYNaG~~~~~~~~~~~Y~~kV~~~y~~ 141 (160)
T PRK15328 98 ILSDMMKIYGYSWEAVGAYNAGTSPKRSDIRKRYAKKIWENYRK 141 (160)
T ss_pred HHHHHHHHcCChHHhhhhccCCCCCCCCHHHHHHHHHHHHHHHH
Confidence 56788899999999999875 3455556677887777666443
No 186
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=23.94 E-value=54 Score=33.83 Aligned_cols=48 Identities=15% Similarity=0.352 Sum_probs=42.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcccCcccccccccc
Q 024484 10 MGLKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWIN 59 (267)
Q Consensus 10 ~~lkkg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n 59 (267)
.+...++|+.+|-++...+....| .+...|+..+++ |..+|++..+..
T Consensus 405 k~~~~~~w~~se~e~fyka~~~~g-s~~slis~l~p~-R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 405 KKLETDKWDASETELFYKALSERG-SDFSLISNLFPL-RDRKQIKAKFKK 452 (584)
T ss_pred CccccCcccchhhHHhhhHHhhhc-cccccccccccc-ccHHHHHHHHhh
Confidence 456678999999999999999999 789999999998 999999987654
No 187
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=23.91 E-value=1.5e+02 Score=25.10 Aligned_cols=29 Identities=21% Similarity=0.124 Sum_probs=22.7
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-.-.+||..| |-+...|+.+-+..+++
T Consensus 126 ~g~s~~EIA~~L-gis~~tV~~~l~RAr~~ 154 (182)
T PRK12540 126 SGFSYEDAAAIC-GCAVGTIKSRVNRARSK 154 (182)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 455678999999 88999999887765544
No 188
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=23.83 E-value=2.3e+02 Score=25.60 Aligned_cols=29 Identities=17% Similarity=0.186 Sum_probs=22.2
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-.-.+||..+ |.+...|+.+.+..+++
T Consensus 227 ~~~s~~eIA~~l-gis~~tV~~~~~ra~~~ 255 (268)
T PRK06288 227 EDLTLKEIGKVL-GVTESRISQLHTKAVLQ 255 (268)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 355678999998 89999998877666554
No 189
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=23.54 E-value=1.4e+02 Score=25.56 Aligned_cols=28 Identities=11% Similarity=0.010 Sum_probs=22.8
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
|-.-.+||..| |-+.+.|++|.+..+++
T Consensus 149 g~s~~EIAe~l-gis~~tV~~~l~Rar~~ 176 (196)
T PRK12535 149 GYTYEEAAKIA-DVRVGTIRSRVARARAD 176 (196)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 44578999999 99999999998766553
No 190
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=23.48 E-value=70 Score=27.01 Aligned_cols=28 Identities=21% Similarity=0.221 Sum_probs=22.6
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
|-...+||..| |-+...|+++.+..+++
T Consensus 155 g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 182 (194)
T PRK12513 155 DLELEEIAELT-GVPEETVKSRLRYALQK 182 (194)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 45689999999 89999999887766644
No 191
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=23.42 E-value=1.4e+02 Score=26.56 Aligned_cols=39 Identities=21% Similarity=0.192 Sum_probs=27.8
Q ss_pred HHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 75 EETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 75 D~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
+..++.+.-..|-...+||..| |-|...|+.+.+..+++
T Consensus 206 ~r~vl~l~~~~~~s~~EIA~~l-gis~~tV~~~~~ra~~~ 244 (251)
T PRK07670 206 EQLVISLFYKEELTLTEIGQVL-NLSTSRISQIHSKALFK 244 (251)
T ss_pred HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3334444444456789999999 99999999988776654
No 192
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=23.04 E-value=2.9e+02 Score=22.92 Aligned_cols=29 Identities=28% Similarity=0.164 Sum_probs=22.6
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-.-.+||..| |-+...++.+.+..+++
T Consensus 132 e~~s~~EIA~~l-gis~~tV~~~l~ra~~~ 160 (179)
T PRK12543 132 HDYSQEEIAQLL-QIPIGTVKSRIHAALKK 160 (179)
T ss_pred ccCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355678999999 88899999988776544
No 193
>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=23.02 E-value=2.4e+02 Score=22.70 Aligned_cols=50 Identities=12% Similarity=0.307 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHhh------------CC-------------------chhHHhhcCCCCCHHHHHHHHHHHhHHHHH
Q 024484 69 NFSKEEEETIINLHDML------------GN-------------------RWSAIAGRLPGRTDNEIKNVWHTHLKKKAA 117 (267)
Q Consensus 69 ~WT~EED~~Li~l~~~~------------G~-------------------kWs~IA~~lpgRT~~q~KnRw~~~lkk~~~ 117 (267)
.||.+||-.|-..+.++ |. -....+...|..|.+.=|+||+..+...-.
T Consensus 1 kfTA~dDY~Lc~~i~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~fF~~~~~~~p~HT~~sWRDR~RKfv~~~gi 80 (105)
T PF09197_consen 1 KFTADDDYALCKAIKKQFYRDIYQKDPDTGSSLISDGDSKEFIPKRDMRSFFKDLARKNPRHTENSWRDRYRKFVSEYGI 80 (105)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHSB-TTSS-B----------------TTHHHHHHHHTTTS-HHHHHHHHHHTHHHH-H
T ss_pred CCChHHHHHHHHHHHHHHHHHHHhhCcccccccccCCCccccccchhhHHHHHHHHHcCCccchhHHHHHHHHHHHHcCh
Confidence 37899999998888654 11 156677888999999999999998876643
Q ss_pred H
Q 024484 118 A 118 (267)
Q Consensus 118 ~ 118 (267)
.
T Consensus 81 ~ 81 (105)
T PF09197_consen 81 Q 81 (105)
T ss_dssp H
T ss_pred H
Confidence 3
No 194
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=22.91 E-value=1.5e+02 Score=24.99 Aligned_cols=29 Identities=28% Similarity=0.357 Sum_probs=23.1
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-...+||..| |-+...|+++.+...++
T Consensus 169 e~~s~~EIA~~l-gis~~tV~~~l~rar~~ 197 (208)
T PRK08295 169 DGKSYQEIAEEL-NRHVKSIDNALQRVKRK 197 (208)
T ss_pred ccCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 356689999999 99999999988765544
No 195
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=22.63 E-value=78 Score=26.73 Aligned_cols=28 Identities=21% Similarity=0.274 Sum_probs=23.1
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
|-.-.+||..| |-+...|+.|.+..+++
T Consensus 147 g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 174 (193)
T TIGR02947 147 GFAYKEIAEIM-GTPIGTVMSRLHRGRKQ 174 (193)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 45679999999 99999999998776654
No 196
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=22.57 E-value=47 Score=24.42 Aligned_cols=44 Identities=23% Similarity=0.561 Sum_probs=27.6
Q ss_pred HHHHHHHHHHhCCCCccccccccCcccCcccccccccccccCCC-------CCCCCCHHHHHHH
Q 024484 22 DRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDI-------KRGNFSKEEEETI 78 (267)
Q Consensus 22 D~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~i-------kk~~WT~EED~~L 78 (267)
+.+|..+|..|| |..+++.+.- | |.. -+|.+ +|.+|-.+.-+.|
T Consensus 12 e~il~~Lv~~yG---W~~L~~~i~i-~----CF~-----~~PsikSSLkFLRkTpWAR~KVE~l 62 (64)
T PF09905_consen 12 ETILTELVEHYG---WEELGERINI-N----CFK-----NNPSIKSSLKFLRKTPWAREKVENL 62 (64)
T ss_dssp HHHHHHHHHHT----HHHHHHHTTS-S----STT-----SS--HHHHHHHHHHSHHHHHHHHHH
T ss_pred HHHHHHHHHHhC---HHHHHhhccc-c----cCC-----CCCchHHHHHHHhcCHhHHHHHHHh
Confidence 468889999999 9999887664 3 432 24554 3467776655544
No 197
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=22.42 E-value=1.6e+02 Score=24.02 Aligned_cols=29 Identities=17% Similarity=0.035 Sum_probs=22.3
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-.-.+||..| |-+...|+.+-+...++
T Consensus 123 ~g~s~~eIA~~l-gis~~tv~~~l~Rar~~ 151 (165)
T PRK09644 123 HELTYEEAASVL-DLKLNTYKSHLFRGRKR 151 (165)
T ss_pred hcCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355678999999 88999999887765544
No 198
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=22.37 E-value=1.7e+02 Score=25.38 Aligned_cols=31 Identities=29% Similarity=0.331 Sum_probs=24.0
Q ss_pred hhCCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 84 MLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 84 ~~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
..|-.-.+||+.+ |-+...|+.+.+..+++-
T Consensus 192 ~~~~s~~eIA~~l-gis~~~v~~~~~ra~~~L 222 (227)
T TIGR02980 192 FEDKTQSEIAERL-GISQMHVSRLLRRALKKL 222 (227)
T ss_pred hcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 3466789999999 889999988877666553
No 199
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=22.22 E-value=1.6e+02 Score=23.91 Aligned_cols=28 Identities=25% Similarity=0.245 Sum_probs=21.8
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
|-...+||..| |=+...|+.+.+...++
T Consensus 128 ~~s~~eIA~~l-gis~~tv~~~l~Rar~~ 155 (161)
T PRK12541 128 GFSYKEIAEMT-GLSLAKVKIELHRGRKE 155 (161)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 44578999999 88888999888766554
No 200
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=22.15 E-value=1.9e+02 Score=22.46 Aligned_cols=34 Identities=12% Similarity=0.035 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHH
Q 024484 73 EEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNV 107 (267)
Q Consensus 73 EED~~Li~l~~~~G~kWs~IA~~lpgRT~~q~KnR 107 (267)
-|...|.++++.+|++.++.|+.| |=+...++.+
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~L-GIsRsTL~rK 88 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALML-GINRGTLRKK 88 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHH
Confidence 477889999999999999999998 6666655443
No 201
>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=22.09 E-value=67 Score=23.72 Aligned_cols=19 Identities=21% Similarity=0.468 Sum_probs=15.4
Q ss_pred HHHHHHHHhhCCchhHHhh
Q 024484 76 ETIINLHDMLGNRWSAIAG 94 (267)
Q Consensus 76 ~~Li~l~~~~G~kWs~IA~ 94 (267)
..|.+|.+.||++|.-|-.
T Consensus 30 ~vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 30 PVLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHHcCCchhhhc
Confidence 3577889999999998864
No 202
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=21.65 E-value=41 Score=33.81 Aligned_cols=44 Identities=14% Similarity=0.195 Sum_probs=37.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccccccccCcccCcccccccccc
Q 024484 14 KGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWIN 59 (267)
Q Consensus 14 kg~WT~EED~~L~~~V~~~G~~nW~~Ia~~~~~~Rt~kqCr~Rw~n 59 (267)
.-.||.||--++-++...|| +++.+|-+.|+. |+-.+++.-|..
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~G-K~F~kIrq~LP~-rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFG-KDFHKIRQALPH-RSLASLVQYYYS 230 (534)
T ss_pred cccchHHHHHHHHHHHHHhc-ccHHHHHHHccC-ccHHHHHHHHHH
Confidence 45699999999999999999 899999999997 888777765543
No 203
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=21.39 E-value=1.4e+02 Score=21.38 Aligned_cols=24 Identities=38% Similarity=0.789 Sum_probs=17.5
Q ss_pred HHhhCCchhHHhhcCCCCCHHHHHH
Q 024484 82 HDMLGNRWSAIAGRLPGRTDNEIKN 106 (267)
Q Consensus 82 ~~~~G~kWs~IA~~lpgRT~~q~Kn 106 (267)
....|+.|..+|..| |=+..+|..
T Consensus 8 ~~~~~~~Wk~La~~L-g~~~~~i~~ 31 (83)
T PF00531_consen 8 AEDLGSDWKRLARKL-GLSESEIEN 31 (83)
T ss_dssp HHSHSTCHHHHHHHT-TS-HHHHHH
T ss_pred hhcchhhHHHHHHHh-CcCHHHHHH
Confidence 456789999999999 766665543
No 204
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=21.24 E-value=1e+02 Score=25.30 Aligned_cols=29 Identities=14% Similarity=-0.021 Sum_probs=23.2
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHHhHHH
Q 024484 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~KnRw~~~lkk~ 115 (267)
|-.-.+||..| |-|...|+++.+..+++-
T Consensus 136 g~s~~eIA~~l-g~s~~tv~~~l~Rar~~L 164 (175)
T PRK12518 136 DLPQKEIAEIL-NIPVGTVKSRLFYARRQL 164 (175)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 44578999999 999999999987766543
No 205
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=20.87 E-value=2e+02 Score=23.57 Aligned_cols=28 Identities=25% Similarity=0.299 Sum_probs=22.1
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
|-...+||..| |-+...|+++....++.
T Consensus 134 g~s~~EIA~~l-~is~~tV~~~l~ra~~~ 161 (168)
T PRK12525 134 GLTYVEIGERL-GVSLSRIHQYMVEAFKC 161 (168)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 55689999999 88899999887665554
No 206
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=20.20 E-value=2e+02 Score=23.99 Aligned_cols=29 Identities=21% Similarity=0.224 Sum_probs=22.4
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-...+||..| |=+...|+++-+..+++
T Consensus 152 ~g~s~~eIA~~l-gis~~~v~~~l~Rar~~ 180 (187)
T PRK12534 152 EGITYEELAART-DTPIGTVKSWIRRGLAK 180 (187)
T ss_pred cCCCHHHHHHHh-CCChhHHHHHHHHHHHH
Confidence 356688999998 88888888887766554
No 207
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=20.09 E-value=2e+02 Score=25.04 Aligned_cols=29 Identities=24% Similarity=0.292 Sum_probs=22.2
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHHhHH
Q 024484 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~KnRw~~~lkk 114 (267)
.|-.-.+||..+ |-+...|+.+.+..+++
T Consensus 190 ~~~s~~eIA~~l-gis~~tV~~~~~ra~~~ 218 (224)
T TIGR02479 190 EELNLKEIGEVL-GLTESRVSQIHSQALKK 218 (224)
T ss_pred CCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 355578888888 88888888888776654
Done!