Query 028055
Match_columns 214
No_of_seqs 239 out of 1414
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 05:32:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028055.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028055hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03212 Transcription repress 100.0 9.2E-40 2E-44 280.2 11.0 116 3-118 14-129 (249)
2 PLN03091 hypothetical protein; 100.0 2.4E-39 5.2E-44 295.6 12.4 118 1-118 1-118 (459)
3 KOG0048 Transcription factor, 100.0 9.8E-38 2.1E-42 269.6 11.4 109 11-119 6-114 (238)
4 KOG0049 Transcription factor, 99.8 2.4E-20 5.2E-25 176.7 8.0 106 1-107 347-453 (939)
5 KOG0049 Transcription factor, 99.7 2.9E-18 6.4E-23 162.6 7.9 110 7-116 246-410 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.7 7.5E-18 1.6E-22 115.7 4.4 60 17-78 1-60 (60)
7 COG5147 REB1 Myb superfamily p 99.7 1.1E-16 2.4E-21 150.6 6.6 107 10-117 16-122 (512)
8 KOG0050 mRNA splicing protein 99.6 1.9E-16 4.1E-21 147.3 3.8 104 12-117 5-108 (617)
9 KOG0051 RNA polymerase I termi 99.5 1.2E-14 2.5E-19 138.5 7.4 110 3-117 375-512 (607)
10 PF00249 Myb_DNA-binding: Myb- 99.5 5.3E-14 1.2E-18 92.8 5.4 46 67-112 1-48 (48)
11 PF00249 Myb_DNA-binding: Myb- 99.5 1.7E-14 3.7E-19 95.2 2.0 48 14-61 1-48 (48)
12 PF13921 Myb_DNA-bind_6: Myb-l 99.3 2.8E-12 6E-17 87.9 4.7 45 70-114 1-45 (60)
13 smart00717 SANT SANT SWI3, AD 99.3 5.3E-12 1.1E-16 81.2 5.7 47 67-113 1-48 (49)
14 PLN03212 Transcription repress 99.2 1.1E-11 2.3E-16 107.3 5.2 66 44-117 10-77 (249)
15 cd00167 SANT 'SWI3, ADA2, N-Co 99.2 4.6E-11 9.9E-16 75.6 5.8 44 69-112 1-45 (45)
16 smart00717 SANT SANT SWI3, AD 99.2 2.3E-11 4.9E-16 78.2 3.0 48 14-62 1-48 (49)
17 KOG0048 Transcription factor, 99.1 6.2E-11 1.3E-15 102.6 3.3 55 63-117 5-61 (238)
18 PLN03091 hypothetical protein; 99.0 6E-11 1.3E-15 109.7 0.5 59 3-63 56-114 (459)
19 cd00167 SANT 'SWI3, ADA2, N-Co 99.0 2.3E-10 4.9E-15 72.4 2.7 45 16-61 1-45 (45)
20 KOG0051 RNA polymerase I termi 99.0 7.5E-10 1.6E-14 106.0 6.4 101 13-115 307-431 (607)
21 COG5147 REB1 Myb superfamily p 98.5 1.8E-08 3.9E-13 95.5 -1.6 98 13-113 290-397 (512)
22 TIGR01557 myb_SHAQKYF myb-like 97.9 7.8E-06 1.7E-10 56.1 3.2 49 13-61 2-54 (57)
23 KOG0457 Histone acetyltransfer 97.8 1E-05 2.2E-10 75.0 2.7 50 12-62 70-119 (438)
24 KOG0457 Histone acetyltransfer 97.7 5.2E-05 1.1E-09 70.4 5.9 49 64-112 69-118 (438)
25 TIGR01557 myb_SHAQKYF myb-like 97.7 0.0001 2.3E-09 50.5 5.9 46 67-112 3-54 (57)
26 KOG0050 mRNA splicing protein 97.3 0.00019 4.1E-09 68.1 4.1 55 65-119 5-60 (617)
27 PF08914 Myb_DNA-bind_2: Rap1 97.3 0.0005 1.1E-08 48.4 4.6 50 67-116 2-61 (65)
28 PF13325 MCRS_N: N-terminal re 97.2 0.0012 2.6E-08 56.1 7.4 99 16-116 1-130 (199)
29 PF13837 Myb_DNA-bind_4: Myb/S 97.1 0.0005 1.1E-08 49.9 3.4 48 67-114 1-66 (90)
30 KOG1279 Chromatin remodeling f 97.1 0.00075 1.6E-08 64.5 5.2 46 66-111 252-297 (506)
31 COG5259 RSC8 RSC chromatin rem 97.0 0.00077 1.7E-08 63.3 4.5 44 68-111 280-323 (531)
32 COG5259 RSC8 RSC chromatin rem 97.0 0.00034 7.4E-09 65.7 2.0 45 13-59 278-322 (531)
33 TIGR02894 DNA_bind_RsfA transc 96.9 0.0017 3.6E-08 53.3 4.9 53 66-119 3-62 (161)
34 KOG1279 Chromatin remodeling f 96.9 0.00058 1.3E-08 65.2 2.4 48 11-60 250-297 (506)
35 PF08914 Myb_DNA-bind_2: Rap1 96.8 0.00073 1.6E-08 47.5 2.1 52 14-65 2-61 (65)
36 TIGR02894 DNA_bind_RsfA transc 96.4 0.0016 3.6E-08 53.4 1.7 50 12-63 2-57 (161)
37 PF13873 Myb_DNA-bind_5: Myb/S 96.3 0.013 2.8E-07 41.7 5.8 49 67-115 2-72 (78)
38 PRK13923 putative spore coat p 96.2 0.0085 1.8E-07 49.7 4.9 52 66-118 4-62 (170)
39 COG5114 Histone acetyltransfer 96.1 0.0079 1.7E-07 54.5 4.4 46 67-112 63-109 (432)
40 PLN03142 Probable chromatin-re 96.1 0.051 1.1E-06 56.3 10.8 100 16-116 826-988 (1033)
41 PF13837 Myb_DNA-bind_4: Myb/S 96.0 0.003 6.4E-08 45.8 1.3 47 14-60 1-63 (90)
42 COG5114 Histone acetyltransfer 95.9 0.0036 7.9E-08 56.6 1.4 48 14-62 63-110 (432)
43 PRK13923 putative spore coat p 95.8 0.0033 7.1E-08 52.1 0.8 50 11-62 2-57 (170)
44 PF13873 Myb_DNA-bind_5: Myb/S 95.0 0.01 2.2E-07 42.3 1.1 49 13-61 1-69 (78)
45 PF09111 SLIDE: SLIDE; InterP 94.3 0.091 2E-06 41.1 4.9 51 64-114 46-112 (118)
46 KOG2656 DNA methyltransferase 94.1 0.046 9.9E-07 50.7 3.2 51 68-118 131-187 (445)
47 PF12776 Myb_DNA-bind_3: Myb/S 93.2 0.27 5.8E-06 35.9 5.6 45 69-113 1-63 (96)
48 KOG4282 Transcription factor G 92.0 0.34 7.4E-06 43.9 5.8 51 67-117 54-118 (345)
49 PF08281 Sigma70_r4_2: Sigma-7 91.8 0.64 1.4E-05 30.3 5.5 41 72-113 12-52 (54)
50 COG5118 BDP1 Transcription ini 91.8 0.37 8E-06 44.8 5.6 47 68-114 366-412 (507)
51 KOG1194 Predicted DNA-binding 87.4 1.8 3.9E-05 41.2 6.6 50 67-116 187-236 (534)
52 PF09111 SLIDE: SLIDE; InterP 86.1 0.68 1.5E-05 36.2 2.7 34 11-44 46-82 (118)
53 PF04545 Sigma70_r4: Sigma-70, 83.5 4 8.6E-05 26.2 5.1 41 73-114 7-47 (50)
54 COG5118 BDP1 Transcription ini 82.4 0.91 2E-05 42.3 2.2 45 14-60 365-409 (507)
55 KOG4282 Transcription factor G 81.6 0.74 1.6E-05 41.7 1.4 47 15-61 55-113 (345)
56 PF13404 HTH_AsnC-type: AsnC-t 78.6 5.3 0.00011 25.3 4.2 38 73-111 3-41 (42)
57 PF11626 Rap1_C: TRF2-interact 76.9 3.3 7.3E-05 30.2 3.4 17 63-79 43-59 (87)
58 PF11626 Rap1_C: TRF2-interact 76.5 2.6 5.7E-05 30.8 2.7 22 12-33 45-74 (87)
59 PF07750 GcrA: GcrA cell cycle 74.8 4.3 9.3E-05 33.4 3.8 42 69-111 2-43 (162)
60 TIGR02985 Sig70_bacteroi1 RNA 74.7 7.6 0.00016 29.9 5.1 38 76-114 119-156 (161)
61 PRK11179 DNA-binding transcrip 72.9 9.2 0.0002 30.5 5.3 43 73-116 9-52 (153)
62 smart00595 MADF subfamily of S 72.6 4 8.7E-05 29.2 2.8 24 89-113 30-53 (89)
63 PF11035 SnAPC_2_like: Small n 72.0 22 0.00049 32.5 7.9 52 67-118 21-76 (344)
64 KOG4167 Predicted DNA-binding 71.0 15 0.00032 37.2 7.1 45 68-112 620-664 (907)
65 PF13404 HTH_AsnC-type: AsnC-t 70.7 2.8 6.1E-05 26.6 1.5 38 20-59 3-40 (42)
66 cd08319 Death_RAIDD Death doma 69.9 6.9 0.00015 28.6 3.6 31 75-106 2-32 (83)
67 PF12776 Myb_DNA-bind_3: Myb/S 69.6 4.6 9.9E-05 29.2 2.6 43 16-58 1-59 (96)
68 PRK11169 leucine-responsive tr 69.3 11 0.00023 30.5 5.0 44 72-116 13-57 (164)
69 cd08803 Death_ank3 Death domai 66.5 10 0.00023 27.7 3.9 31 75-106 4-34 (84)
70 TIGR02937 sigma70-ECF RNA poly 64.2 19 0.0004 26.8 5.2 36 78-114 118-153 (158)
71 PF01388 ARID: ARID/BRIGHT DNA 63.6 17 0.00037 26.2 4.7 37 77-113 40-89 (92)
72 cd08317 Death_ank Death domain 61.6 9.9 0.00021 27.4 3.0 31 75-106 4-34 (84)
73 PRK09413 IS2 repressor TnpA; R 61.3 21 0.00045 27.4 5.0 46 13-62 9-54 (121)
74 KOG4468 Polycomb-group transcr 60.7 14 0.00031 36.5 4.7 48 67-114 88-145 (782)
75 PRK11924 RNA polymerase sigma 60.5 30 0.00066 27.0 6.0 31 83-114 138-168 (179)
76 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 59.9 17 0.00038 24.1 3.7 35 72-107 6-40 (50)
77 KOG3841 TEF-1 and related tran 59.9 55 0.0012 30.8 8.1 79 7-122 69-152 (455)
78 PRK09652 RNA polymerase sigma 59.9 37 0.0008 26.6 6.4 34 80-114 138-171 (182)
79 KOG4167 Predicted DNA-binding 59.6 5.7 0.00012 40.0 1.9 44 13-58 618-661 (907)
80 PRK04217 hypothetical protein; 59.1 66 0.0014 24.8 7.4 46 68-115 41-86 (110)
81 COG2197 CitB Response regulato 58.9 18 0.00038 30.5 4.6 44 68-114 147-190 (211)
82 cd08804 Death_ank2 Death domai 58.7 14 0.0003 26.9 3.4 31 75-106 4-34 (84)
83 PF10545 MADF_DNA_bdg: Alcohol 58.0 21 0.00046 24.6 4.2 26 88-113 28-54 (85)
84 smart00501 BRIGHT BRIGHT, ARID 57.3 29 0.00063 25.2 5.0 38 77-114 36-86 (93)
85 KOG4329 DNA-binding protein [G 56.6 22 0.00048 33.3 5.0 45 68-112 278-323 (445)
86 PRK11179 DNA-binding transcrip 55.7 7.5 0.00016 31.0 1.7 44 20-65 9-52 (153)
87 KOG2656 DNA methyltransferase 55.5 16 0.00035 34.3 4.0 48 12-60 128-180 (445)
88 TIGR02939 RpoE_Sigma70 RNA pol 55.1 21 0.00045 28.6 4.3 29 85-114 153-181 (190)
89 PRK09643 RNA polymerase sigma 55.1 41 0.00089 27.4 6.1 32 82-114 146-177 (192)
90 cd08318 Death_NMPP84 Death dom 55.0 18 0.00039 26.3 3.5 28 78-106 10-37 (86)
91 KOG2009 Transcription initiati 54.8 15 0.00032 36.2 3.8 49 66-114 408-456 (584)
92 PRK09641 RNA polymerase sigma 54.2 27 0.00059 27.8 4.8 29 85-114 151-179 (187)
93 PF13325 MCRS_N: N-terminal re 52.9 32 0.00069 29.4 5.1 44 69-113 1-47 (199)
94 cd08311 Death_p75NR Death doma 52.7 22 0.00047 25.6 3.6 35 71-107 1-35 (77)
95 PRK12530 RNA polymerase sigma 52.5 51 0.0011 26.8 6.3 29 85-114 149-177 (189)
96 PRK11169 leucine-responsive tr 52.3 6.8 0.00015 31.7 1.0 45 19-65 13-57 (164)
97 PF00196 GerE: Bacterial regul 51.9 21 0.00045 23.5 3.2 43 69-114 3-45 (58)
98 PRK09047 RNA polymerase factor 51.4 57 0.0012 25.2 6.1 29 85-114 121-149 (161)
99 PRK11923 algU RNA polymerase s 51.4 48 0.001 26.7 5.9 29 85-114 153-181 (193)
100 PRK12523 RNA polymerase sigma 51.2 37 0.0008 26.9 5.1 35 79-114 128-162 (172)
101 cd06171 Sigma70_r4 Sigma70, re 51.0 53 0.0012 19.7 5.2 37 74-111 14-50 (55)
102 cd08779 Death_PIDD Death Domai 49.7 18 0.0004 26.3 2.8 28 76-104 3-30 (86)
103 PRK12515 RNA polymerase sigma 49.6 62 0.0013 26.1 6.3 29 85-114 146-174 (189)
104 TIGR02943 Sig70_famx1 RNA poly 49.5 63 0.0014 26.2 6.3 33 81-114 142-174 (188)
105 PF07638 Sigma70_ECF: ECF sigm 49.3 59 0.0013 26.5 6.1 37 75-112 140-176 (185)
106 TIGR02954 Sig70_famx3 RNA poly 49.1 38 0.00081 26.7 4.8 29 85-114 134-162 (169)
107 PRK12529 RNA polymerase sigma 49.0 42 0.0009 27.0 5.1 34 82-116 139-172 (178)
108 TIGR02948 SigW_bacill RNA poly 48.6 35 0.00075 27.2 4.6 29 85-114 151-179 (187)
109 PF04504 DUF573: Protein of un 48.6 46 0.001 24.9 4.9 46 69-114 6-64 (98)
110 cd08805 Death_ank1 Death domai 48.6 25 0.00053 25.8 3.3 29 75-104 4-32 (84)
111 smart00344 HTH_ASNC helix_turn 48.5 47 0.001 24.3 5.0 43 73-116 3-46 (108)
112 PRK12512 RNA polymerase sigma 48.4 42 0.00091 26.8 5.1 29 85-114 146-174 (184)
113 PRK09642 RNA polymerase sigma 48.3 63 0.0014 25.1 6.0 29 85-114 121-149 (160)
114 PRK09648 RNA polymerase sigma 48.2 43 0.00092 27.0 5.1 30 84-114 153-182 (189)
115 PRK09637 RNA polymerase sigma 47.8 41 0.0009 27.2 5.0 30 84-114 120-149 (181)
116 PRK09645 RNA polymerase sigma 47.4 45 0.00098 26.3 5.1 29 85-114 133-161 (173)
117 smart00005 DEATH DEATH domain, 47.1 33 0.00071 24.2 3.8 31 75-106 5-36 (88)
118 cd08777 Death_RIP1 Death Domai 47.0 25 0.00053 25.7 3.1 30 77-107 4-33 (86)
119 PRK12531 RNA polymerase sigma 46.8 65 0.0014 26.1 6.0 29 85-114 156-184 (194)
120 PRK12524 RNA polymerase sigma 45.2 70 0.0015 26.0 6.0 30 84-114 150-179 (196)
121 TIGR02952 Sig70_famx2 RNA poly 45.0 52 0.0011 25.6 5.0 29 85-114 137-165 (170)
122 PRK12532 RNA polymerase sigma 44.9 82 0.0018 25.5 6.4 30 84-114 150-179 (195)
123 KOG1194 Predicted DNA-binding 44.6 28 0.00061 33.4 3.8 40 69-109 472-511 (534)
124 PF02954 HTH_8: Bacterial regu 44.2 56 0.0012 20.2 4.1 34 74-108 6-39 (42)
125 PF11035 SnAPC_2_like: Small n 44.1 90 0.0019 28.7 6.8 85 14-112 21-126 (344)
126 PRK06759 RNA polymerase factor 43.9 58 0.0013 25.0 5.1 29 85-114 121-149 (154)
127 PRK12520 RNA polymerase sigma 43.7 87 0.0019 25.2 6.3 29 85-114 146-174 (191)
128 PF13936 HTH_38: Helix-turn-he 43.3 36 0.00077 21.5 3.1 37 69-107 4-40 (44)
129 KOG4468 Polycomb-group transcr 43.1 32 0.00068 34.2 4.0 47 14-61 88-143 (782)
130 PRK09651 RNA polymerase sigma 42.9 48 0.001 26.4 4.6 29 85-114 134-162 (172)
131 PRK12527 RNA polymerase sigma 42.2 94 0.002 24.1 6.1 29 85-114 120-148 (159)
132 PRK12536 RNA polymerase sigma 42.2 60 0.0013 26.0 5.1 30 84-114 143-172 (181)
133 TIGR02999 Sig-70_X6 RNA polyme 41.8 63 0.0014 25.7 5.1 29 85-114 149-177 (183)
134 PF09420 Nop16: Ribosome bioge 41.6 26 0.00056 28.5 2.8 48 12-60 112-162 (164)
135 PRK12514 RNA polymerase sigma 41.5 61 0.0013 25.7 5.0 29 85-114 144-172 (179)
136 PRK12528 RNA polymerase sigma 41.4 67 0.0015 25.0 5.1 31 82-113 125-155 (161)
137 PRK12547 RNA polymerase sigma 41.3 67 0.0015 25.3 5.2 30 84-114 126-155 (164)
138 PRK00118 putative DNA-binding 41.2 1.1E+02 0.0025 23.2 6.1 41 72-113 19-59 (104)
139 KOG0384 Chromodomain-helicase 41.0 35 0.00077 36.6 4.2 74 13-93 1132-1206(1373)
140 PRK09649 RNA polymerase sigma 40.8 59 0.0013 26.3 4.8 29 85-114 145-173 (185)
141 PF13137 DUF3983: Protein of u 40.6 17 0.00038 22.2 1.2 10 197-206 24-33 (34)
142 PF09420 Nop16: Ribosome bioge 40.6 62 0.0013 26.3 4.9 46 66-111 113-162 (164)
143 PRK12516 RNA polymerase sigma 40.5 96 0.0021 25.2 6.1 33 81-114 127-159 (187)
144 PRK05602 RNA polymerase sigma 40.4 88 0.0019 25.0 5.8 29 85-114 143-171 (186)
145 PRK12542 RNA polymerase sigma 39.9 66 0.0014 25.8 5.0 29 85-114 137-165 (185)
146 TIGR02950 SigM_subfam RNA poly 39.4 23 0.00051 27.2 2.2 28 86-114 121-148 (154)
147 PF06599 DUF1139: Protein of u 39.2 19 0.00041 32.1 1.7 14 192-205 277-290 (309)
148 PRK13919 putative RNA polymera 39.1 71 0.0015 25.5 5.1 28 86-114 151-178 (186)
149 TIGR02984 Sig-70_plancto1 RNA 38.5 73 0.0016 25.2 5.0 30 84-114 154-183 (189)
150 PRK12545 RNA polymerase sigma 38.5 1.1E+02 0.0025 25.0 6.3 28 85-113 154-181 (201)
151 TIGR02983 SigE-fam_strep RNA p 38.4 69 0.0015 24.9 4.8 38 76-114 116-153 (162)
152 PRK11922 RNA polymerase sigma 37.9 60 0.0013 27.3 4.6 28 86-114 165-192 (231)
153 cd08306 Death_FADD Fas-associa 37.3 51 0.0011 23.9 3.5 31 77-108 4-34 (86)
154 PRK09646 RNA polymerase sigma 36.2 1E+02 0.0022 25.0 5.6 29 85-114 157-185 (194)
155 PRK06811 RNA polymerase factor 35.8 85 0.0018 25.3 5.1 28 86-114 147-174 (189)
156 PRK12537 RNA polymerase sigma 35.7 83 0.0018 25.2 5.0 29 85-114 148-176 (182)
157 PRK12544 RNA polymerase sigma 35.7 1.4E+02 0.0029 24.8 6.4 29 85-114 163-191 (206)
158 TIGR02960 SigX5 RNA polymerase 35.2 68 0.0015 28.2 4.7 29 85-114 157-185 (324)
159 PRK12546 RNA polymerase sigma 34.4 81 0.0018 25.8 4.7 32 82-114 125-156 (188)
160 PRK09647 RNA polymerase sigma 34.4 1.4E+02 0.0031 24.6 6.3 29 85-114 153-181 (203)
161 COG1522 Lrp Transcriptional re 33.7 98 0.0021 23.9 4.9 43 73-116 8-51 (154)
162 cd01670 Death Death Domain: a 33.2 50 0.0011 22.6 2.9 27 78-105 2-28 (79)
163 TIGR02989 Sig-70_gvs1 RNA poly 32.8 1.1E+02 0.0024 23.5 5.1 27 85-112 126-152 (159)
164 PRK09639 RNA polymerase sigma 32.7 1.7E+02 0.0037 22.6 6.2 29 85-114 126-154 (166)
165 TIGR03001 Sig-70_gmx1 RNA poly 32.1 1.5E+02 0.0033 25.4 6.3 29 85-114 176-204 (244)
166 PRK12519 RNA polymerase sigma 31.5 1.3E+02 0.0029 24.1 5.6 29 85-114 156-184 (194)
167 PRK10100 DNA-binding transcrip 31.5 1.2E+02 0.0027 25.5 5.5 43 69-114 155-197 (216)
168 PRK12538 RNA polymerase sigma 31.3 1.3E+02 0.0029 25.5 5.7 29 85-114 186-214 (233)
169 PRK09415 RNA polymerase factor 31.1 1.3E+02 0.0029 24.0 5.4 29 85-114 142-170 (179)
170 COG2963 Transposase and inacti 30.2 1.8E+02 0.0039 21.6 5.7 42 67-110 5-47 (116)
171 PRK01905 DNA-binding protein F 30.1 1.5E+02 0.0032 20.9 4.9 35 72-107 36-70 (77)
172 PRK15411 rcsA colanic acid cap 29.9 99 0.0022 25.7 4.6 43 69-114 137-179 (207)
173 PRK09636 RNA polymerase sigma 29.9 1.1E+02 0.0023 26.8 5.0 29 85-114 130-158 (293)
174 PF09905 DUF2132: Uncharacteri 29.1 47 0.001 23.3 2.0 22 22-46 12-33 (64)
175 PRK06930 positive control sigm 29.1 2.3E+02 0.005 23.1 6.6 37 77-114 121-157 (170)
176 PRK12543 RNA polymerase sigma 28.8 2.1E+02 0.0046 22.7 6.3 29 85-114 132-160 (179)
177 PRK12511 RNA polymerase sigma 28.6 1.3E+02 0.0028 24.3 5.0 29 85-114 126-154 (182)
178 PRK15201 fimbriae regulatory p 28.5 1.9E+02 0.004 24.7 5.8 43 69-114 133-175 (198)
179 KOG2009 Transcription initiati 28.3 43 0.00092 33.1 2.3 48 10-59 405-452 (584)
180 PRK12526 RNA polymerase sigma 28.3 1.3E+02 0.0029 24.7 5.1 28 86-114 169-196 (206)
181 PRK09638 RNA polymerase sigma 28.2 76 0.0016 25.0 3.5 29 85-114 141-169 (176)
182 PF01710 HTH_Tnp_IS630: Transp 28.0 1E+02 0.0022 23.5 4.0 55 21-78 58-112 (119)
183 PRK08241 RNA polymerase factor 27.9 98 0.0021 27.5 4.5 29 85-114 168-196 (339)
184 TIGR02957 SigX4 RNA polymerase 27.8 1.2E+02 0.0027 26.3 5.0 29 85-114 123-151 (281)
185 PRK06986 fliA flagellar biosyn 27.8 1.7E+02 0.0036 24.6 5.7 33 81-114 195-227 (236)
186 PRK10360 DNA-binding transcrip 27.7 1.9E+02 0.0041 22.3 5.8 44 68-114 136-179 (196)
187 TIGR02959 SigZ RNA polymerase 27.7 1.5E+02 0.0032 23.5 5.2 29 85-114 115-143 (170)
188 COG5352 Uncharacterized protei 27.7 85 0.0018 25.6 3.6 42 69-111 2-43 (169)
189 PRK08295 RNA polymerase factor 27.6 2E+02 0.0043 23.2 6.0 29 85-114 169-197 (208)
190 PF00531 Death: Death domain; 27.4 1.1E+02 0.0024 20.9 3.9 24 82-106 8-31 (83)
191 PRK08301 sporulation sigma fac 26.9 1.9E+02 0.0042 24.1 6.0 28 86-114 198-225 (234)
192 PRK09483 response regulator; P 26.4 1.2E+02 0.0027 23.9 4.4 44 68-114 147-190 (217)
193 PRK00430 fis global DNA-bindin 26.3 1.8E+02 0.004 21.5 5.0 34 73-107 55-88 (95)
194 PLN03162 golden-2 like transcr 25.7 5.8E+02 0.013 24.2 9.7 43 68-110 238-285 (526)
195 PRK12518 RNA polymerase sigma 25.7 90 0.0019 24.5 3.5 28 86-114 136-163 (175)
196 PRK12522 RNA polymerase sigma 25.7 2.4E+02 0.0052 22.1 6.0 29 85-114 134-162 (173)
197 smart00351 PAX Paired Box doma 25.6 2.7E+02 0.0059 21.3 6.1 73 13-87 14-93 (125)
198 smart00344 HTH_ASNC helix_turn 25.5 53 0.0011 24.0 2.0 43 20-64 3-45 (108)
199 PRK12540 RNA polymerase sigma 25.5 2.3E+02 0.005 22.8 6.0 29 85-114 126-154 (182)
200 PRK12541 RNA polymerase sigma 25.4 1.5E+02 0.0032 23.0 4.7 29 85-114 127-155 (161)
201 PRK07670 RNA polymerase sigma 25.4 1.8E+02 0.0039 24.8 5.5 38 76-114 207-244 (251)
202 PRK09644 RNA polymerase sigma 25.3 2.5E+02 0.0054 21.8 6.0 29 85-114 123-151 (165)
203 PRK12525 RNA polymerase sigma 25.1 1.8E+02 0.0039 22.9 5.1 29 85-114 133-161 (168)
204 PRK12534 RNA polymerase sigma 24.7 1.7E+02 0.0036 23.3 5.0 29 85-114 152-180 (187)
205 PRK12535 RNA polymerase sigma 24.7 1.5E+02 0.0033 24.2 4.8 37 86-124 149-185 (196)
206 PF13384 HTH_23: Homeodomain-l 24.4 95 0.0021 19.3 2.8 29 77-107 9-37 (50)
207 TIGR02980 SigBFG RNA polymeras 24.4 1.6E+02 0.0035 24.4 5.0 30 84-114 192-221 (227)
208 PRK15328 invasion protein IagB 23.9 1.9E+02 0.004 23.7 5.1 43 77-119 98-142 (160)
209 PRK12517 RNA polymerase sigma 23.8 3.3E+02 0.0072 21.9 6.6 28 86-114 144-171 (188)
210 PF10440 WIYLD: Ubiquitin-bind 23.3 58 0.0013 22.9 1.7 18 77-94 31-48 (65)
211 COG1522 Lrp Transcriptional re 23.2 48 0.0011 25.7 1.4 43 20-64 8-50 (154)
212 PRK12513 RNA polymerase sigma 23.0 1.3E+02 0.0028 24.2 4.0 28 86-114 155-182 (194)
213 TIGR02947 SigH_actino RNA poly 23.0 1.4E+02 0.003 24.1 4.1 28 86-114 147-174 (193)
214 PRK12533 RNA polymerase sigma 23.0 1.6E+02 0.0035 24.7 4.7 29 85-114 149-177 (216)
215 PRK06288 RNA polymerase sigma 22.9 2.9E+02 0.0064 23.7 6.4 29 85-114 227-255 (268)
216 PF05263 DUF722: Protein of un 21.8 2.1E+02 0.0045 22.7 4.8 38 74-113 85-124 (130)
217 PRK02866 cyanate hydratase; Va 21.7 1.7E+02 0.0036 23.8 4.3 32 76-108 8-39 (147)
218 PLN03142 Probable chromatin-re 21.7 1.9E+02 0.0041 30.7 5.7 40 69-108 826-866 (1033)
219 TIGR00673 cynS cyanate hydrata 21.3 1.3E+02 0.0028 24.6 3.5 31 76-107 11-41 (150)
220 PF07750 GcrA: GcrA cell cycle 21.3 87 0.0019 25.6 2.6 33 16-50 2-35 (162)
221 PRK10840 transcriptional regul 21.2 1.7E+02 0.0037 23.7 4.4 44 68-114 149-192 (216)
222 TIGR02479 FliA_WhiG RNA polyme 21.1 2.2E+02 0.0047 23.7 5.1 29 85-114 190-218 (224)
223 PRK11475 DNA-binding transcrip 20.5 1.8E+02 0.004 24.3 4.5 44 68-114 133-176 (207)
224 PRK12539 RNA polymerase sigma 20.5 2.9E+02 0.0064 21.9 5.6 28 86-114 147-174 (184)
225 PRK07037 extracytoplasmic-func 20.4 2.6E+02 0.0055 21.6 5.1 27 85-112 124-150 (163)
226 PRK13719 conjugal transfer tra 20.1 3.2E+02 0.0069 23.7 5.9 44 68-114 142-185 (217)
No 1
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=9.2e-40 Score=280.22 Aligned_cols=116 Identities=67% Similarity=1.311 Sum_probs=111.8
Q ss_pred CCcccccCCCCCCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhcccCCCCCCCCCHHHHHHHHHHH
Q 028055 3 RAPCCEKMGLKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETIINLH 82 (214)
Q Consensus 3 r~~~~~k~~l~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p~i~kg~WT~EED~~Ll~l~ 82 (214)
|+|||.|++++|++||+|||++|+++|++||..+|..||+.++.+|+++|||+||.+||+|.+++++||.|||++|++++
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 68999999999999999999999999999999999999999965599999999999999999999999999999999999
Q ss_pred HhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHHHHHH
Q 028055 83 DMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAA 118 (214)
Q Consensus 83 ~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk~~~~ 118 (214)
.+||++|+.||+.|||||+++|||||+.++++++.+
T Consensus 94 ~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r 129 (249)
T PLN03212 94 RLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLR 129 (249)
T ss_pred HhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHh
Confidence 999999999999999999999999999999988754
No 2
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=2.4e-39 Score=295.62 Aligned_cols=118 Identities=67% Similarity=1.223 Sum_probs=114.6
Q ss_pred CCCCcccccCCCCCCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhcccCCCCCCCCCHHHHHHHHH
Q 028055 1 MGRAPCCEKMGLKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETIIN 80 (214)
Q Consensus 1 m~r~~~~~k~~l~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p~i~kg~WT~EED~~Ll~ 80 (214)
|||++||.|.+++||+||+|||++|+++|.+||..+|..||+.++.+|+++|||+||.+||+|.+++++||+|||++|++
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 99999999999999999999999999999999999999999998756999999999999999999999999999999999
Q ss_pred HHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHHHHHH
Q 028055 81 LHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAA 118 (214)
Q Consensus 81 l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk~~~~ 118 (214)
++++||++|+.||++|||||+++|||||+.++||+++.
T Consensus 81 L~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~ 118 (459)
T PLN03091 81 LHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQ 118 (459)
T ss_pred HHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999998753
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=9.8e-38 Score=269.59 Aligned_cols=109 Identities=71% Similarity=1.165 Sum_probs=104.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhcccCCCCCCCCCHHHHHHHHHHHHhcCCcHH
Q 028055 11 GLKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETIINLHDMLGNRWS 90 (214)
Q Consensus 11 ~l~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p~i~kg~WT~EED~~Ll~l~~~~G~kW~ 90 (214)
.+.||+||+|||++|+++|++||+.+|..||+.+|.+|||++||+||.|||+|++++|+||.|||++|+++|..+|++|+
T Consensus 6 ~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrWs 85 (238)
T KOG0048|consen 6 ELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRWS 85 (238)
T ss_pred cccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHHH
Confidence 35589999999999999999999999999999999669999999999999999999999999999999999999999999
Q ss_pred HHHhhCCCCCHHHHHHHHHHHhHHHHHHH
Q 028055 91 AIAGRLPGRTDNEIKNVWHTHLKKKAAAV 119 (214)
Q Consensus 91 ~IA~~lpgRt~~~~knrw~~~lkk~~~~~ 119 (214)
.||++|||||++.|||+|++++||++...
T Consensus 86 ~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~ 114 (238)
T KOG0048|consen 86 LIAGRLPGRTDNEVKNHWNTHLKKKLLKM 114 (238)
T ss_pred HHHhhCCCcCHHHHHHHHHHHHHHHHHHc
Confidence 99999999999999999999999998654
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.81 E-value=2.4e-20 Score=176.66 Aligned_cols=106 Identities=24% Similarity=0.478 Sum_probs=101.4
Q ss_pred CCCCcccccCCCCCCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhcccCCCCCCCCCHHHHHHHHH
Q 028055 1 MGRAPCCEKMGLKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETIIN 80 (214)
Q Consensus 1 m~r~~~~~k~~l~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p~i~kg~WT~EED~~Ll~ 80 (214)
++|+.+...|++++|+||++||.+|..+|.+||..+|-+|-..+|+ |+..|||+||.|.|+...+++.||-.||+.|+.
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 5899999999999999999999999999999999999999999998 999999999999999999999999999999999
Q ss_pred HHHhcC-CcHHHHHhhCCCCCHHHHHHH
Q 028055 81 LHDMLG-NRWSAIAGRLPGRTDNEIKNV 107 (214)
Q Consensus 81 l~~~~G-~kW~~IA~~lpgRt~~~~knr 107 (214)
++++|| ++|.+||..||.||..|...|
T Consensus 426 ~V~~YG~g~WakcA~~Lp~~t~~q~~rr 453 (939)
T KOG0049|consen 426 AVKVYGKGNWAKCAMLLPKKTSRQLRRR 453 (939)
T ss_pred HHHHHccchHHHHHHHccccchhHHHHH
Confidence 999999 789999999999999666544
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.74 E-value=2.9e-18 Score=162.64 Aligned_cols=110 Identities=19% Similarity=0.405 Sum_probs=100.7
Q ss_pred cccCCCCCCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhh-----------------------------
Q 028055 7 CEKMGLKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRW----------------------------- 57 (214)
Q Consensus 7 ~~k~~l~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw----------------------------- 57 (214)
.+.|.++|..|++|||++|.++...+++.+|..||..++++|+..||..|+
T Consensus 246 ~l~P~~nk~~WS~EE~E~L~AiA~A~~~~~W~~IA~~Lgt~RS~yQC~~kF~t~~~~L~ekeWsEEed~kL~alV~~~~~ 325 (939)
T KOG0049|consen 246 ELNPKWNKEHWSNEEVEKLKALAEAPKFVSWPMIALNLGTNRSSYQCMEKFKTEVSQLSEKEWSEEEDTKLIALVKITSI 325 (939)
T ss_pred hcCCccchhccChHHHHHHHHHHhccccccHHHHHHHhCCCcchHHHHHHHHHHHHHHHhhhcchhhhHHHHHHHHHhhc
Confidence 457899999999999999999999999999999999999989999998544
Q ss_pred -------------------------hhcccCCCCCCCCCHHHHHHHHHHHHhcCCc-HHHHHhhCCCCCHHHHHHHHHHH
Q 028055 58 -------------------------INYLRPDIKRGNFSKEEEETIINLHDMLGNR-WSAIAGRLPGRTDNEIKNVWHTH 111 (214)
Q Consensus 58 -------------------------~~~L~p~i~kg~WT~EED~~Ll~l~~~~G~k-W~~IA~~lpgRt~~~~knrw~~~ 111 (214)
...|+|.+++|+||.+||-+|+.+|.+||.+ |..|-..+|||++.|||.||++.
T Consensus 326 nShI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nv 405 (939)
T KOG0049|consen 326 NSHIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNV 405 (939)
T ss_pred cCccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHH
Confidence 6678999999999999999999999999965 99999999999999999999999
Q ss_pred hHHHH
Q 028055 112 LKKKA 116 (214)
Q Consensus 112 lkk~~ 116 (214)
|...+
T Consensus 406 L~~s~ 410 (939)
T KOG0049|consen 406 LNRSA 410 (939)
T ss_pred HHHhh
Confidence 87655
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=99.71 E-value=7.5e-18 Score=115.73 Aligned_cols=60 Identities=45% Similarity=0.916 Sum_probs=55.1
Q ss_pred CCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhcccCCCCCCCCCHHHHHHH
Q 028055 17 WTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETI 78 (214)
Q Consensus 17 WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p~i~kg~WT~EED~~L 78 (214)
||+|||++|+.+|..|| .+|..||+.++. |++.||+.||.++|+|.+++++||.+||++|
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=99.66 E-value=1.1e-16 Score=150.61 Aligned_cols=107 Identities=33% Similarity=0.532 Sum_probs=101.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhcccCCCCCCCCCHHHHHHHHHHHHhcCCcH
Q 028055 10 MGLKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETIINLHDMLGNRW 89 (214)
Q Consensus 10 ~~l~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p~i~kg~WT~EED~~Ll~l~~~~G~kW 89 (214)
..++.|.|+..||+.|..+|+.+|+.+|..||+.+.. |+++||+.||.++++|.+++.+|+.|||..|+.+..++|.+|
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 4578899999999999999999999999999999987 999999999999999999999999999999999999999999
Q ss_pred HHHHhhCCCCCHHHHHHHHHHHhHHHHH
Q 028055 90 SAIAGRLPGRTDNEIKNVWHTHLKKKAA 117 (214)
Q Consensus 90 ~~IA~~lpgRt~~~~knrw~~~lkk~~~ 117 (214)
+.||..++|||..+|.+||...+....+
T Consensus 95 stia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 95 STIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhccccCccchHHHHHHHHHHhhhhhc
Confidence 9999999999999999999988876554
No 8
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.62 E-value=1.9e-16 Score=147.26 Aligned_cols=104 Identities=27% Similarity=0.610 Sum_probs=99.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhcccCCCCCCCCCHHHHHHHHHHHHhcCCcHHH
Q 028055 12 LKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETIINLHDMLGNRWSA 91 (214)
Q Consensus 12 l~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p~i~kg~WT~EED~~Ll~l~~~~G~kW~~ 91 (214)
++.|.|+--||+.|..+|.+||.+.|++|++.+.. .+++||+.||..+|+|.|++..|+.|||++|+.+++.+...|..
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 57899999999999999999999999999999987 99999999999999999999999999999999999999999999
Q ss_pred HHhhCCCCCHHHHHHHHHHHhHHHHH
Q 028055 92 IAGRLPGRTDNEIKNVWHTHLKKKAA 117 (214)
Q Consensus 92 IA~~lpgRt~~~~knrw~~~lkk~~~ 117 (214)
||..| ||+.++|-.||..++-....
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 99999999999999866543
No 9
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.53 E-value=1.2e-14 Score=138.52 Aligned_cols=110 Identities=29% Similarity=0.536 Sum_probs=97.1
Q ss_pred CCcccccCCCCCCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhcccCCC--CCCCCCHHHHHHHHH
Q 028055 3 RAPCCEKMGLKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDI--KRGNFSKEEEETIIN 80 (214)
Q Consensus 3 r~~~~~k~~l~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p~i--~kg~WT~EED~~Ll~ 80 (214)
|++.-..+ .+|.||+||++.|..+|..+| ..|..|++.++ |.+..|++||++|..++- +++.||.||++.|++
T Consensus 375 R~y~~FE~--~rg~wt~ee~eeL~~l~~~~g-~~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk 449 (607)
T KOG0051|consen 375 RAYTPFEN--KRGKWTPEEEEELKKLVVEHG-NDWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLK 449 (607)
T ss_pred hcCCcccc--ccCCCCcchHHHHHHHHHHhc-ccHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHH
Confidence 44444444 899999999999999999999 89999999998 999999999999999984 899999999999999
Q ss_pred HHH-------hc-------------------CCcHHHHHhhCCCCCHHHHHHHHHHHhHHHHH
Q 028055 81 LHD-------ML-------------------GNRWSAIAGRLPGRTDNEIKNVWHTHLKKKAA 117 (214)
Q Consensus 81 l~~-------~~-------------------G~kW~~IA~~lpgRt~~~~knrw~~~lkk~~~ 117 (214)
+|+ ++ +-.|+.|++.+..|+..|||.+|..++.....
T Consensus 450 ~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~ 512 (607)
T KOG0051|consen 450 TVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSF 512 (607)
T ss_pred HHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHh
Confidence 995 33 12599999999999999999999999876553
No 10
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.48 E-value=5.3e-14 Score=92.79 Aligned_cols=46 Identities=33% Similarity=0.714 Sum_probs=41.9
Q ss_pred CCCCCHHHHHHHHHHHHhcCCc-HHHHHhhCC-CCCHHHHHHHHHHHh
Q 028055 67 RGNFSKEEEETIINLHDMLGNR-WSAIAGRLP-GRTDNEIKNVWHTHL 112 (214)
Q Consensus 67 kg~WT~EED~~Ll~l~~~~G~k-W~~IA~~lp-gRt~~~~knrw~~~l 112 (214)
+++||.|||++|++++.+||.. |..||..|| |||..||++||+.++
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 999999999998764
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=99.47 E-value=1.7e-14 Score=95.19 Aligned_cols=48 Identities=44% Similarity=0.799 Sum_probs=42.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhcc
Q 028055 14 KGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYL 61 (214)
Q Consensus 14 kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L 61 (214)
|++||+|||++|+++|.+||..+|..||..++++||+.||+.||.++|
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=99.30 E-value=2.8e-12 Score=87.89 Aligned_cols=45 Identities=38% Similarity=0.747 Sum_probs=39.0
Q ss_pred CCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 70 FSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 70 WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
||+|||++|++++.+||++|..||..|+.||..+|++||+..|++
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 999999999999999999999999999669999999999986643
No 13
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.30 E-value=5.3e-12 Score=81.15 Aligned_cols=47 Identities=40% Similarity=0.832 Sum_probs=44.2
Q ss_pred CCCCCHHHHHHHHHHHHhcC-CcHHHHHhhCCCCCHHHHHHHHHHHhH
Q 028055 67 RGNFSKEEEETIINLHDMLG-NRWSAIAGRLPGRTDNEIKNVWHTHLK 113 (214)
Q Consensus 67 kg~WT~EED~~Ll~l~~~~G-~kW~~IA~~lpgRt~~~~knrw~~~lk 113 (214)
+++||.+||.+|+.++.+|| .+|..||..||+||..+|++||+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 46899999999999999999 999999999999999999999988764
No 14
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.22 E-value=1.1e-11 Score=107.29 Aligned_cols=66 Identities=21% Similarity=0.459 Sum_probs=55.8
Q ss_pred hCCCCCccccchhhhhcccCCCCCCCCCHHHHHHHHHHHHhcC-CcHHHHHhhC-CCCCHHHHHHHHHHHhHHHHH
Q 028055 44 AGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETIINLHDMLG-NRWSAIAGRL-PGRTDNEIKNVWHTHLKKKAA 117 (214)
Q Consensus 44 ~~~~Rt~~qcr~Rw~~~L~p~i~kg~WT~EED~~Ll~l~~~~G-~kW~~IA~~l-pgRt~~~~knrw~~~lkk~~~ 117 (214)
+++ |+..-|. ++.+++++||+|||++|+++|++|| .+|..||+++ +|||..|||.||..+|+..+.
T Consensus 10 ~~~-~~~pcc~-------K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~ 77 (249)
T PLN03212 10 VSK-KTTPCCT-------KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVK 77 (249)
T ss_pred CCC-CCCCCcc-------cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcc
Confidence 444 6655552 3578999999999999999999999 5899999998 699999999999999976543
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=4.6e-11 Score=75.64 Aligned_cols=44 Identities=34% Similarity=0.724 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHHHHHhcC-CcHHHHHhhCCCCCHHHHHHHHHHHh
Q 028055 69 NFSKEEEETIINLHDMLG-NRWSAIAGRLPGRTDNEIKNVWHTHL 112 (214)
Q Consensus 69 ~WT~EED~~Ll~l~~~~G-~kW~~IA~~lpgRt~~~~knrw~~~l 112 (214)
+||.+|+..|+.++.+|| .+|..||..+++||..+|++||..++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 99999999999999999999997653
No 16
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.15 E-value=2.3e-11 Score=78.15 Aligned_cols=48 Identities=46% Similarity=0.856 Sum_probs=44.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhccc
Q 028055 14 KGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLR 62 (214)
Q Consensus 14 kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~ 62 (214)
+++||++||++|+.++..||..+|..||..+++ |++.+|+.||.+++.
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 17
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.08 E-value=6.2e-11 Score=102.60 Aligned_cols=55 Identities=20% Similarity=0.352 Sum_probs=49.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCC-cHHHHHhhCC-CCCHHHHHHHHHHHhHHHHH
Q 028055 63 PDIKRGNFSKEEEETIINLHDMLGN-RWSAIAGRLP-GRTDNEIKNVWHTHLKKKAA 117 (214)
Q Consensus 63 p~i~kg~WT~EED~~Ll~l~~~~G~-kW~~IA~~lp-gRt~~~~knrw~~~lkk~~~ 117 (214)
|.+.+||||.|||++|+++|++||. +|..||+.++ ||+..+||-||.++|+..++
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 4456899999999999999999995 6999999999 99999999999999987553
No 18
>PLN03091 hypothetical protein; Provisional
Probab=99.01 E-value=6e-11 Score=109.67 Aligned_cols=59 Identities=20% Similarity=0.345 Sum_probs=52.8
Q ss_pred CCcccccCCCCCCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhcccC
Q 028055 3 RAPCCEKMGLKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRP 63 (214)
Q Consensus 3 r~~~~~k~~l~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p 63 (214)
|+-....|++++++||+|||++|+++++.|| ..|..||+.+++ |++.+|+.||...|+.
T Consensus 56 RW~NyLdP~IkKgpWT~EED~lLLeL~k~~G-nKWskIAk~LPG-RTDnqIKNRWnslLKK 114 (459)
T PLN03091 56 RWINYLRPDLKRGTFSQQEENLIIELHAVLG-NRWSQIAAQLPG-RTDNEIKNLWNSCLKK 114 (459)
T ss_pred HHHhccCCcccCCCCCHHHHHHHHHHHHHhC-cchHHHHHhcCC-CCHHHHHHHHHHHHHH
Confidence 4445678999999999999999999999999 799999999998 9999999999876543
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=99.00 E-value=2.3e-10 Score=72.40 Aligned_cols=45 Identities=47% Similarity=0.882 Sum_probs=42.1
Q ss_pred CCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhcc
Q 028055 16 PWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYL 61 (214)
Q Consensus 16 ~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L 61 (214)
+||++||+.|+.++..||..+|..||+.+++ |++.+|+.||.+++
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=98.97 E-value=7.5e-10 Score=105.97 Aligned_cols=101 Identities=27% Similarity=0.314 Sum_probs=86.5
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC----C-------------------CcchhchhhCCCCCccccchhhhhcccCCC-CCC
Q 028055 13 KKGPWTPEEDRILIVHIKKHGH----P-------------------NWRALPKQAGLLRCGKSCRLRWINYLRPDI-KRG 68 (214)
Q Consensus 13 ~kg~WT~EED~~L~~~v~~~g~----~-------------------nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p~i-~kg 68 (214)
+-+.|+++||+.|-..|..|-. . -|..|.+.+|. |+.+.+..+-++...|-- .+|
T Consensus 307 ~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp~-R~~~siy~~~rR~y~~FE~~rg 385 (607)
T KOG0051|consen 307 NLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLPY-RDRKSIYHHLRRAYTPFENKRG 385 (607)
T ss_pred hhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcCc-ccchhHHHHHHhcCCccccccC
Confidence 3489999999999999988821 0 16778888998 999998875556666654 899
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHHH
Q 028055 69 NFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (214)
Q Consensus 69 ~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk~ 115 (214)
.||+||++.|..+|.++|+.|..|+..| ||.+..|+.||+.+++..
T Consensus 386 ~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g 431 (607)
T KOG0051|consen 386 KWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCG 431 (607)
T ss_pred CCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccc
Confidence 9999999999999999999999999999 999999999999988654
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=98.46 E-value=1.8e-08 Score=95.53 Aligned_cols=98 Identities=29% Similarity=0.580 Sum_probs=86.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhcccC--CCCCCCCCHHHHHHHHHHHHhcC----
Q 028055 13 KKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRP--DIKRGNFSKEEEETIINLHDMLG---- 86 (214)
Q Consensus 13 ~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p--~i~kg~WT~EED~~Ll~l~~~~G---- 86 (214)
.+|.||++|++.|...+..+| ..|..|.+.++ |-+..||+||.+|..+ .+++++|+.||+.+|...+...-
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 468999999999999999999 89999998776 9999999999999999 68889999999999998886332
Q ss_pred ----CcHHHHHhhCCCCCHHHHHHHHHHHhH
Q 028055 87 ----NRWSAIAGRLPGRTDNEIKNVWHTHLK 113 (214)
Q Consensus 87 ----~kW~~IA~~lpgRt~~~~knrw~~~lk 113 (214)
..|..|+.++++|...+|+..+..+..
T Consensus 367 ~~~~~~~~li~~~~~~~~~~~~~~~~~~~~~ 397 (512)
T COG5147 367 QSSRILWLLIAQNIRNRLQHHCRDKYGVLIS 397 (512)
T ss_pred hhhhhhHHHHHHhhhccccCCCCCccccccc
Confidence 359999999999999999887766554
No 22
>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=97.95 E-value=7.8e-06 Score=56.10 Aligned_cols=49 Identities=14% Similarity=0.303 Sum_probs=43.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCc---chhchhhCCCC-Cccccchhhhhcc
Q 028055 13 KKGPWTPEEDRILIVHIKKHGHPNW---RALPKQAGLLR-CGKSCRLRWINYL 61 (214)
Q Consensus 13 ~kg~WT~EED~~L~~~v~~~g~~nW---~~Ia~~~~~~R-t~~qcr~Rw~~~L 61 (214)
++-.||+||.++++.+|..+|..+| ..|++.+...| |..||+.+.+.|.
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 3568999999999999999997799 99999887556 9999999988774
No 23
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.82 E-value=1e-05 Score=74.98 Aligned_cols=50 Identities=18% Similarity=0.549 Sum_probs=46.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhccc
Q 028055 12 LKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLR 62 (214)
Q Consensus 12 l~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~ 62 (214)
+-...||++|+-+|++++..||-+||..||.++|. |++.+|+++|.+++-
T Consensus 70 i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGt-Ktkeeck~hy~k~fv 119 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETYGFGNWQDIADHIGT-KTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcc-cchHHHHHHHHHHHh
Confidence 55678999999999999999999999999999997 999999999988753
No 24
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.74 E-value=5.2e-05 Score=70.40 Aligned_cols=49 Identities=22% Similarity=0.460 Sum_probs=44.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcC-CcHHHHHhhCCCCCHHHHHHHHHHHh
Q 028055 64 DIKRGNFSKEEEETIINLHDMLG-NRWSAIAGRLPGRTDNEIKNVWHTHL 112 (214)
Q Consensus 64 ~i~kg~WT~EED~~Ll~l~~~~G-~kW~~IA~~lpgRt~~~~knrw~~~l 112 (214)
.+-...||.+||-+|++++..|| ++|..||.++..||..+|+.+|..++
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHH
Confidence 34557899999999999999999 89999999999999999999997664
No 25
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.73 E-value=0.0001 Score=50.51 Aligned_cols=46 Identities=13% Similarity=0.272 Sum_probs=40.0
Q ss_pred CCCCCHHHHHHHHHHHHhcCC-cH---HHHHhhCC-CC-CHHHHHHHHHHHh
Q 028055 67 RGNFSKEEEETIINLHDMLGN-RW---SAIAGRLP-GR-TDNEIKNVWHTHL 112 (214)
Q Consensus 67 kg~WT~EED~~Ll~l~~~~G~-kW---~~IA~~lp-gR-t~~~~knrw~~~l 112 (214)
+-.||+||....+++++.+|. .| ..|+..|. .| |..||+.+.+.+.
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 457999999999999999996 99 99999873 35 9999999987654
No 26
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.35 E-value=0.00019 Score=68.05 Aligned_cols=55 Identities=29% Similarity=0.450 Sum_probs=49.5
Q ss_pred CCCCCCCHHHHHHHHHHHHhcC-CcHHHHHhhCCCCCHHHHHHHHHHHhHHHHHHH
Q 028055 65 IKRGNFSKEEEETIINLHDMLG-NRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAAV 119 (214)
Q Consensus 65 i~kg~WT~EED~~Ll~l~~~~G-~kW~~IA~~lpgRt~~~~knrw~~~lkk~~~~~ 119 (214)
++-|-|+.-||++|-.++.+|| +.|+.|+..++-.|..||++||..++...+++.
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 679999999999999999999999987766543
No 27
>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=97.27 E-value=0.0005 Score=48.37 Aligned_cols=50 Identities=18% Similarity=0.464 Sum_probs=32.6
Q ss_pred CCCCCHHHHHHHHHHHHhcC--------Cc-HHHHHhhCC-CCCHHHHHHHHHHHhHHHH
Q 028055 67 RGNFSKEEEETIINLHDMLG--------NR-WSAIAGRLP-GRTDNEIKNVWHTHLKKKA 116 (214)
Q Consensus 67 kg~WT~EED~~Ll~l~~~~G--------~k-W~~IA~~lp-gRt~~~~knrw~~~lkk~~ 116 (214)
+.+||.|||.+|++.+..+. ++ |.++++.-| .+|-.+.|+||...|+.+.
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 45899999999999996542 22 999999877 9999999999988887654
No 28
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.24 E-value=0.0012 Score=56.08 Aligned_cols=99 Identities=20% Similarity=0.412 Sum_probs=69.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCCcchhchhhCC--CCCccccchhhhhcc----------------cCCC-----CCCCCCH
Q 028055 16 PWTPEEDRILIVHIKKHGHPNWRALPKQAGL--LRCGKSCRLRWINYL----------------RPDI-----KRGNFSK 72 (214)
Q Consensus 16 ~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~--~Rt~~qcr~Rw~~~L----------------~p~i-----~kg~WT~ 72 (214)
+|+|+.|-+|+.+|..-. +-..|+..+.- .-|-..+.+||...| .|.. .+.+||.
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 599999999999998764 55666554332 144556678995443 3332 4468999
Q ss_pred HHHHHHHHHHHhcCC---cHHHHHh----hC-CCCCHHHHHHHHHHHhHHHH
Q 028055 73 EEEETIINLHDMLGN---RWSAIAG----RL-PGRTDNEIKNVWHTHLKKKA 116 (214)
Q Consensus 73 EED~~Ll~l~~~~G~---kW~~IA~----~l-pgRt~~~~knrw~~~lkk~~ 116 (214)
+||++|......... .+.+|-. .| ++||..++.++|+.+.+..+
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~L 130 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHL 130 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhch
Confidence 999999998766543 4666633 23 88999999999986655444
No 29
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.11 E-value=0.0005 Score=49.93 Aligned_cols=48 Identities=33% Similarity=0.571 Sum_probs=33.7
Q ss_pred CCCCCHHHHHHHHHHHHh------cC--C------cHHHHHhhC----CCCCHHHHHHHHHHHhHH
Q 028055 67 RGNFSKEEEETIINLHDM------LG--N------RWSAIAGRL----PGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 67 kg~WT~EED~~Ll~l~~~------~G--~------kW~~IA~~l----pgRt~~~~knrw~~~lkk 114 (214)
+..||.+|...||+++.. ++ + -|..||..| ..||..||+++|.++.++
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~ 66 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKK 66 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Confidence 357999999999999877 21 1 399999987 469999999999886544
No 30
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.09 E-value=0.00075 Score=64.52 Aligned_cols=46 Identities=15% Similarity=0.377 Sum_probs=42.7
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHH
Q 028055 66 KRGNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTH 111 (214)
Q Consensus 66 ~kg~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~ 111 (214)
.+.+||.+|..+|+++++.||..|.+||.++.+||..+|--++..+
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhc
Confidence 3568999999999999999999999999999999999999998654
No 31
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.01 E-value=0.00077 Score=63.35 Aligned_cols=44 Identities=18% Similarity=0.330 Sum_probs=41.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHH
Q 028055 68 GNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTH 111 (214)
Q Consensus 68 g~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~ 111 (214)
.+||.+|..+|++.++.||..|.+||.+++.||..||--||..+
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 48999999999999999999999999999999999999998654
No 32
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.00 E-value=0.00034 Score=65.66 Aligned_cols=45 Identities=20% Similarity=0.588 Sum_probs=42.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhh
Q 028055 13 KKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWIN 59 (214)
Q Consensus 13 ~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~ 59 (214)
....||.+|..+|++.|+.|| .+|.+||+++++ |+..||..|+.+
T Consensus 278 ~dk~WS~qE~~LLLEGIe~yg-DdW~kVA~HVgt-Kt~EqCIl~FL~ 322 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYG-DDWDKVARHVGT-KTKEQCILHFLQ 322 (531)
T ss_pred ccccccHHHHHHHHHHHHHhh-hhHHHHHHHhCC-CCHHHHHHHHHc
Confidence 566999999999999999999 899999999997 999999999954
No 33
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=96.89 E-value=0.0017 Score=53.30 Aligned_cols=53 Identities=15% Similarity=0.283 Sum_probs=45.5
Q ss_pred CCCCCCHHHHHHHHHHHHhc---CC----cHHHHHhhCCCCCHHHHHHHHHHHhHHHHHHH
Q 028055 66 KRGNFSKEEEETIINLHDML---GN----RWSAIAGRLPGRTDNEIKNVWHTHLKKKAAAV 119 (214)
Q Consensus 66 ~kg~WT~EED~~Ll~l~~~~---G~----kW~~IA~~lpgRt~~~~knrw~~~lkk~~~~~ 119 (214)
....||.|||.+|-+.|..| |+ -...++..| +||+-.|.=||+..+|+.+..-
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~~ 62 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEEA 62 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHHH
Confidence 34679999999999999887 32 378889999 9999999999999999988643
No 34
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.86 E-value=0.00058 Score=65.25 Aligned_cols=48 Identities=21% Similarity=0.569 Sum_probs=43.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhc
Q 028055 11 GLKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINY 60 (214)
Q Consensus 11 ~l~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (214)
...++.||.+|.-+|+++|.+|| .+|.+||.++++ |+..||..++.+.
T Consensus 250 ~~~~~~WT~qE~lLLLE~ie~y~-ddW~kVa~hVg~-ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 250 ESARPNWTEQETLLLLEAIEMYG-DDWNKVADHVGT-KSQEQCILKFLRL 297 (506)
T ss_pred ccCCCCccHHHHHHHHHHHHHhc-ccHHHHHhccCC-CCHHHHHHHHHhc
Confidence 34678999999999999999999 899999999997 9999999998653
No 35
>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=96.83 E-value=0.00073 Score=47.53 Aligned_cols=52 Identities=25% Similarity=0.403 Sum_probs=32.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCCC--------CcchhchhhCCCCCccccchhhhhcccCCC
Q 028055 14 KGPWTPEEDRILIVHIKKHGHP--------NWRALPKQAGLLRCGKSCRLRWINYLRPDI 65 (214)
Q Consensus 14 kg~WT~EED~~L~~~v~~~g~~--------nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p~i 65 (214)
+-+||.|||++|+.+|..+... =|..+++..++.+|-.+-|+||.+.|.+..
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 4589999999999999766311 299999888855888888999999998753
No 36
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=96.40 E-value=0.0016 Score=53.36 Aligned_cols=50 Identities=26% Similarity=0.609 Sum_probs=41.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC---C---CcchhchhhCCCCCccccchhhhhcccC
Q 028055 12 LKKGPWTPEEDRILIVHIKKHGH---P---NWRALPKQAGLLRCGKSCRLRWINYLRP 63 (214)
Q Consensus 12 l~kg~WT~EED~~L~~~v~~~g~---~---nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p 63 (214)
.+.-.||.|||.+|...|-+|-. . -+..+++.++ ||+.-|.-||+.+++.
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 46678999999999999999821 1 3778888887 9999999999988874
No 37
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=96.31 E-value=0.013 Score=41.70 Aligned_cols=49 Identities=33% Similarity=0.555 Sum_probs=40.5
Q ss_pred CCCCCHHHHHHHHHHHHhcC----C-------------cHHHHHhhC-----CCCCHHHHHHHHHHHhHHH
Q 028055 67 RGNFSKEEEETIINLHDMLG----N-------------RWSAIAGRL-----PGRTDNEIKNVWHTHLKKK 115 (214)
Q Consensus 67 kg~WT~EED~~Ll~l~~~~G----~-------------kW~~IA~~l-----pgRt~~~~knrw~~~lkk~ 115 (214)
..+||.+|...|++++.+|. + -|..|+..| +.||..+||.+|..+....
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 45899999999999998873 1 299999976 3699999999998886543
No 38
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.20 E-value=0.0085 Score=49.72 Aligned_cols=52 Identities=12% Similarity=0.241 Sum_probs=43.6
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCc-------HHHHHhhCCCCCHHHHHHHHHHHhHHHHHH
Q 028055 66 KRGNFSKEEEETIINLHDMLGNR-------WSAIAGRLPGRTDNEIKNVWHTHLKKKAAA 118 (214)
Q Consensus 66 ~kg~WT~EED~~Ll~l~~~~G~k-------W~~IA~~lpgRt~~~~knrw~~~lkk~~~~ 118 (214)
....||.|+|.+|-+.+..|+.. ...++..| +||..+|.-||+..++++...
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Yee 62 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQE 62 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHHH
Confidence 45689999999998888887632 66777888 999999999999999987754
No 39
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.05 E-value=0.0079 Score=54.46 Aligned_cols=46 Identities=28% Similarity=0.486 Sum_probs=41.8
Q ss_pred CCCCCHHHHHHHHHHHHhcC-CcHHHHHhhCCCCCHHHHHHHHHHHh
Q 028055 67 RGNFSKEEEETIINLHDMLG-NRWSAIAGRLPGRTDNEIKNVWHTHL 112 (214)
Q Consensus 67 kg~WT~EED~~Ll~l~~~~G-~kW~~IA~~lpgRt~~~~knrw~~~l 112 (214)
-..|+..|+.+|++....+| ++|..||.+++.|+...||.+|....
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 89999999998899999999986543
No 40
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=96.05 E-value=0.051 Score=56.31 Aligned_cols=100 Identities=15% Similarity=0.297 Sum_probs=77.2
Q ss_pred CCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccch-------hhh------------------------------
Q 028055 16 PWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRL-------RWI------------------------------ 58 (214)
Q Consensus 16 ~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~-------Rw~------------------------------ 58 (214)
.||.-+=..++.+..+||..+-..||..+.+ ++...++. ||.
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~-k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~~ 904 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEMEG-KTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAIG 904 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhcC-CCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5888888889999999998899999999976 77776652 210
Q ss_pred ----hc---------ccCCCCCCCCCHHHHHHHHHHHHhcC-CcHHHHHhh------------CCCCCHHHHHHHHHHHh
Q 028055 59 ----NY---------LRPDIKRGNFSKEEEETIINLHDMLG-NRWSAIAGR------------LPGRTDNEIKNVWHTHL 112 (214)
Q Consensus 59 ----~~---------L~p~i~kg~WT~EED~~Ll~l~~~~G-~kW~~IA~~------------lpgRt~~~~knrw~~~l 112 (214)
.| -.+..++..+|.|||..|+-++.+|| .+|..|-.. +..||+..|..|..+++
T Consensus 905 ~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~ 984 (1033)
T PLN03142 905 KKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLI 984 (1033)
T ss_pred HHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHH
Confidence 00 01334455799999999999999999 779988432 35899999999999998
Q ss_pred HHHH
Q 028055 113 KKKA 116 (214)
Q Consensus 113 kk~~ 116 (214)
+-..
T Consensus 985 ~~~~ 988 (1033)
T PLN03142 985 RLIE 988 (1033)
T ss_pred HHHH
Confidence 7644
No 41
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.02 E-value=0.003 Score=45.80 Aligned_cols=47 Identities=30% Similarity=0.653 Sum_probs=32.0
Q ss_pred CCCCCHHHHHHHHHHHHH--h----C--CC-----Ccchhchhh---CCCCCccccchhhhhc
Q 028055 14 KGPWTPEEDRILIVHIKK--H----G--HP-----NWRALPKQA---GLLRCGKSCRLRWINY 60 (214)
Q Consensus 14 kg~WT~EED~~L~~~v~~--~----g--~~-----nW~~Ia~~~---~~~Rt~~qcr~Rw~~~ 60 (214)
+..||.+|...|+.++.. + + .. -|..||..| |..|++.||+.+|.+.
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 358999999999998887 2 1 01 399999885 4459999999999763
No 42
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.87 E-value=0.0036 Score=56.58 Aligned_cols=48 Identities=19% Similarity=0.471 Sum_probs=44.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhccc
Q 028055 14 KGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLR 62 (214)
Q Consensus 14 kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~ 62 (214)
---|+..|+-+|++...-.|.+||..||.++|. |+...|+.+|..++.
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 347999999999999999999999999999996 999999999987765
No 43
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.79 E-value=0.0033 Score=52.15 Aligned_cols=50 Identities=22% Similarity=0.512 Sum_probs=40.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCC------cchhchhhCCCCCccccchhhhhccc
Q 028055 11 GLKKGPWTPEEDRILIVHIKKHGHPN------WRALPKQAGLLRCGKSCRLRWINYLR 62 (214)
Q Consensus 11 ~l~kg~WT~EED~~L~~~v~~~g~~n------W~~Ia~~~~~~Rt~~qcr~Rw~~~L~ 62 (214)
..+...||.|||.+|...|-.|+... ...++..+. |++..|..||+-+++
T Consensus 2 k~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~--rt~aac~fRwNs~vr 57 (170)
T PRK13923 2 KTRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALK--RTAAACGFRWNSVVR 57 (170)
T ss_pred cchhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHh--hhHHHHHhHHHHHHH
Confidence 46788999999999999999986433 445556565 999999999977765
No 44
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.05 E-value=0.01 Score=42.27 Aligned_cols=49 Identities=24% Similarity=0.431 Sum_probs=38.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC-----C-----------Ccchhchhh----CCCCCccccchhhhhcc
Q 028055 13 KKGPWTPEEDRILIVHIKKHGH-----P-----------NWRALPKQA----GLLRCGKSCRLRWINYL 61 (214)
Q Consensus 13 ~kg~WT~EED~~L~~~v~~~g~-----~-----------nW~~Ia~~~----~~~Rt~~qcr~Rw~~~L 61 (214)
++..||++|.+.|+++|.+|.. . -|..|+..+ ++.|+..||+.+|.+..
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 3568999999999999999821 1 299998885 22499999999998754
No 45
>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=94.28 E-value=0.091 Score=41.12 Aligned_cols=51 Identities=24% Similarity=0.403 Sum_probs=40.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCC----cHHHHHhh------------CCCCCHHHHHHHHHHHhHH
Q 028055 64 DIKRGNFSKEEEETIINLHDMLGN----RWSAIAGR------------LPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 64 ~i~kg~WT~EED~~Ll~l~~~~G~----kW~~IA~~------------lpgRt~~~~knrw~~~lkk 114 (214)
..++..||++||..|+-++.+||- .|..|-.. +..||+..|..|..++++-
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~ 112 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKL 112 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHH
Confidence 566789999999999999999996 79888553 3579999999999998864
No 46
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=94.08 E-value=0.046 Score=50.69 Aligned_cols=51 Identities=27% Similarity=0.375 Sum_probs=45.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhh-----CCC-CCHHHHHHHHHHHhHHHHHH
Q 028055 68 GNFSKEEEETIINLHDMLGNRWSAIAGR-----LPG-RTDNEIKNVWHTHLKKKAAA 118 (214)
Q Consensus 68 g~WT~EED~~Ll~l~~~~G~kW~~IA~~-----lpg-Rt~~~~knrw~~~lkk~~~~ 118 (214)
..||++|-+-|.++++.|--+|..||.+ ++. ||-.++|.||+...++-+..
T Consensus 131 n~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kA 187 (445)
T KOG2656|consen 131 NSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKA 187 (445)
T ss_pred ccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHHHHHHHHHc
Confidence 5799999999999999999999999987 666 99999999999888776643
No 47
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=93.20 E-value=0.27 Score=35.85 Aligned_cols=45 Identities=31% Similarity=0.555 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHhc---CC----------cHHHHHhhC---CC--CCHHHHHHHHHHHhH
Q 028055 69 NFSKEEEETIINLHDML---GN----------RWSAIAGRL---PG--RTDNEIKNVWHTHLK 113 (214)
Q Consensus 69 ~WT~EED~~Ll~l~~~~---G~----------kW~~IA~~l---pg--Rt~~~~knrw~~~lk 113 (214)
.||.++++.|++++.+. |+ .|..|+..| +| .+..||+|||..+-+
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~ 63 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKK 63 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHH
Confidence 59999999999987543 22 299998876 33 467899999876543
No 48
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=92.01 E-value=0.34 Score=43.90 Aligned_cols=51 Identities=24% Similarity=0.360 Sum_probs=40.9
Q ss_pred CCCCCHHHHHHHHHHHHhc----------CCcHHHHHhhC----CCCCHHHHHHHHHHHhHHHHH
Q 028055 67 RGNFSKEEEETIINLHDML----------GNRWSAIAGRL----PGRTDNEIKNVWHTHLKKKAA 117 (214)
Q Consensus 67 kg~WT~EED~~Ll~l~~~~----------G~kW~~IA~~l----pgRt~~~~knrw~~~lkk~~~ 117 (214)
...|+.+|-..||++..+. +.-|..||+.+ .-||+.+||++|.++.++-..
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~ 118 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKK 118 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHH
Confidence 4689999999999987653 23499999965 349999999999998876443
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=91.80 E-value=0.64 Score=30.34 Aligned_cols=41 Identities=24% Similarity=0.323 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhH
Q 028055 72 KEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLK 113 (214)
Q Consensus 72 ~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lk 113 (214)
++++..++.++...|-.+.+||..+ |.|...|+.+.+.-++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARK 52 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHh
Confidence 3678889999999999999999999 9999999998766544
No 50
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=91.78 E-value=0.37 Score=44.81 Aligned_cols=47 Identities=26% Similarity=0.344 Sum_probs=42.9
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 68 GNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 68 g~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.+||.+|-++..++..++|..++.||..||.|...|||-+|..--|+
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~ 412 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKV 412 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhh
Confidence 37999999999999999999999999999999999999999765444
No 51
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=87.38 E-value=1.8 Score=41.19 Aligned_cols=50 Identities=14% Similarity=0.260 Sum_probs=44.2
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHHHH
Q 028055 67 RGNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKKA 116 (214)
Q Consensus 67 kg~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk~~ 116 (214)
...||.||--++-+++..||....+|-+.||.|+-..|...|....|.+.
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 35799999999999999999999999999999999999998877655443
No 52
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=86.10 E-value=0.68 Score=36.20 Aligned_cols=34 Identities=32% Similarity=0.552 Sum_probs=28.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC---CCcchhchhh
Q 028055 11 GLKKGPWTPEEDRILIVHIKKHGH---PNWRALPKQA 44 (214)
Q Consensus 11 ~l~kg~WT~EED~~L~~~v~~~g~---~nW~~Ia~~~ 44 (214)
.-++..||.+||.-|+-.+.+||. +.|..|-..+
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 567889999999999999999998 7899987764
No 53
>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=83.53 E-value=4 Score=26.21 Aligned_cols=41 Identities=29% Similarity=0.438 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 73 EEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 73 EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
+++..++.+.-..|-.+.+||..+ |-|...|+.+.+..+++
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 456667777777778899999999 99999999988776654
No 54
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=82.37 E-value=0.91 Score=42.29 Aligned_cols=45 Identities=13% Similarity=0.197 Sum_probs=40.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhc
Q 028055 14 KGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINY 60 (214)
Q Consensus 14 kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (214)
.-+||.+|-+++.++....| .++.-|+..+|+ |..+|++..|.+-
T Consensus 365 ~~~Ws~~e~ekFYKALs~wG-tdF~LIs~lfP~-R~RkqIKaKfi~E 409 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWG-TDFSLISSLFPN-RERKQIKAKFIKE 409 (507)
T ss_pred CCcccHHHHHHHHHHHHHhc-chHHHHHHhcCc-hhHHHHHHHHHHH
Confidence 34899999999999999999 799999999998 9999999998653
No 55
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=81.59 E-value=0.74 Score=41.72 Aligned_cols=47 Identities=26% Similarity=0.451 Sum_probs=36.4
Q ss_pred CCCCHHHHHHHHHHHHHh---------CCCCcchhchhh---CCCCCccccchhhhhcc
Q 028055 15 GPWTPEEDRILIVHIKKH---------GHPNWRALPKQA---GLLRCGKSCRLRWINYL 61 (214)
Q Consensus 15 g~WT~EED~~L~~~v~~~---------g~~nW~~Ia~~~---~~~Rt~~qcr~Rw~~~L 61 (214)
..|+.+|-..|+.+.... ....|..||+.+ +..|++.||+.+|.+..
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 789999999999877543 123599999853 44499999999997743
No 56
>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=78.58 E-value=5.3 Score=25.34 Aligned_cols=38 Identities=18% Similarity=0.344 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHhcCC-cHHHHHhhCCCCCHHHHHHHHHHH
Q 028055 73 EEEETIINLHDMLGN-RWSAIAGRLPGRTDNEIKNVWHTH 111 (214)
Q Consensus 73 EED~~Ll~l~~~~G~-kW~~IA~~lpgRt~~~~knrw~~~ 111 (214)
+=|..|+.+...-|. .+.+||+.+ |=|...|..|++.+
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 457888888888884 599999999 99999999998654
No 57
>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=76.89 E-value=3.3 Score=30.24 Aligned_cols=17 Identities=29% Similarity=0.548 Sum_probs=10.5
Q ss_pred CCCCCCCCCHHHHHHHH
Q 028055 63 PDIKRGNFSKEEEETII 79 (214)
Q Consensus 63 p~i~kg~WT~EED~~Ll 79 (214)
|....|-||+|+|+.|.
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 67778999999999994
No 58
>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=76.49 E-value=2.6 Score=30.81 Aligned_cols=22 Identities=55% Similarity=0.872 Sum_probs=13.2
Q ss_pred CCCCCCCHHHHHHH--------HHHHHHhC
Q 028055 12 LKKGPWTPEEDRIL--------IVHIKKHG 33 (214)
Q Consensus 12 l~kg~WT~EED~~L--------~~~v~~~g 33 (214)
-..|-||+|+|+.| .+++++||
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 45789999999999 34667776
No 59
>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=74.77 E-value=4.3 Score=33.35 Aligned_cols=42 Identities=26% Similarity=0.278 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHH
Q 028055 69 NFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTH 111 (214)
Q Consensus 69 ~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~ 111 (214)
.||+|..+.|.+|..+ |-.=++||+.|.|.|.|.|.-+-|.+
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 5999999999999855 77789999999779999998877654
No 60
>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=74.70 E-value=7.6 Score=29.88 Aligned_cols=38 Identities=24% Similarity=0.322 Sum_probs=28.4
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 76 ETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 76 ~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
..++.+.-..|-.+.+||+.+ |.|...|+++.+...++
T Consensus 119 r~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 119 RKIFILSRFEGKSYKEIAEEL-GISVKTVEYHISKALKE 156 (161)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 334444344577899999999 99999999998876543
No 61
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=72.85 E-value=9.2 Score=30.49 Aligned_cols=43 Identities=9% Similarity=0.075 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHhcC-CcHHHHHhhCCCCCHHHHHHHHHHHhHHHH
Q 028055 73 EEEETIINLHDMLG-NRWSAIAGRLPGRTDNEIKNVWHTHLKKKA 116 (214)
Q Consensus 73 EED~~Ll~l~~~~G-~kW~~IA~~lpgRt~~~~knrw~~~lkk~~ 116 (214)
+-|.+|+.+.++-| ..|++||+.+ |-|...|+.|++.+.....
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 57888998888888 4699999999 9999999999987765543
No 62
>smart00595 MADF subfamily of SANT domain.
Probab=72.57 E-value=4 Score=29.18 Aligned_cols=24 Identities=33% Similarity=0.619 Sum_probs=21.1
Q ss_pred HHHHHhhCCCCCHHHHHHHHHHHhH
Q 028055 89 WSAIAGRLPGRTDNEIKNVWHTHLK 113 (214)
Q Consensus 89 W~~IA~~lpgRt~~~~knrw~~~lk 113 (214)
|.+||..| |-|..+|+.+|+++-.
T Consensus 30 W~~Ia~~l-~~~~~~~~~kw~~LR~ 53 (89)
T smart00595 30 WEEIAEEL-GLSVEECKKRWKNLRD 53 (89)
T ss_pred HHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 99999999 6699999999987753
No 63
>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=72.00 E-value=22 Score=32.48 Aligned_cols=52 Identities=23% Similarity=0.401 Sum_probs=38.4
Q ss_pred CCCCCHHHHHHHHHHHHhc-CCc---HHHHHhhCCCCCHHHHHHHHHHHhHHHHHH
Q 028055 67 RGNFSKEEEETIINLHDML-GNR---WSAIAGRLPGRTDNEIKNVWHTHLKKKAAA 118 (214)
Q Consensus 67 kg~WT~EED~~Ll~l~~~~-G~k---W~~IA~~lpgRt~~~~knrw~~~lkk~~~~ 118 (214)
-..||.-|...|+.+.+.. |.. -..|++.++||+..+|++--..+..+.++.
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rvare 76 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRVARE 76 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHHHHH
Confidence 3579999999988887655 543 568899999999999999554444444433
No 64
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=71.00 E-value=15 Score=37.19 Aligned_cols=45 Identities=7% Similarity=0.027 Sum_probs=41.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHh
Q 028055 68 GNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHL 112 (214)
Q Consensus 68 g~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~l 112 (214)
..||..|-.+.-+++..|...+-.|++.++++|-.+|-..|++..
T Consensus 620 d~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtWK 664 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTWK 664 (907)
T ss_pred ccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHHH
Confidence 469999999999999999999999999999999999988877654
No 65
>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=70.73 E-value=2.8 Score=26.62 Aligned_cols=38 Identities=21% Similarity=0.361 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhh
Q 028055 20 EEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWIN 59 (214)
Q Consensus 20 EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~ 59 (214)
+=|.+|+.+.+..|...+.+||+.+| =+...|..|+.+
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lg--lS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELG--LSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHT--S-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHC--cCHHHHHHHHHH
Confidence 34888999999999899999999998 577888888754
No 66
>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=69.94 E-value=6.9 Score=28.63 Aligned_cols=31 Identities=23% Similarity=0.472 Sum_probs=26.2
Q ss_pred HHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHH
Q 028055 75 EETIINLHDMLGNRWSAIAGRLPGRTDNEIKN 106 (214)
Q Consensus 75 D~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~kn 106 (214)
|+.|..+...+|..|..+|.+| |=|..+|..
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I~~ 32 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDIYR 32 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 5678899999999999999999 877776643
No 67
>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=69.55 E-value=4.6 Score=29.20 Aligned_cols=43 Identities=23% Similarity=0.543 Sum_probs=28.4
Q ss_pred CCCHHHHHHHHHHHHHh---CCC---------CcchhchhhCC----CCCccccchhhh
Q 028055 16 PWTPEEDRILIVHIKKH---GHP---------NWRALPKQAGL----LRCGKSCRLRWI 58 (214)
Q Consensus 16 ~WT~EED~~L~~~v~~~---g~~---------nW~~Ia~~~~~----~Rt~~qcr~Rw~ 58 (214)
.||+++++.|++++... |.. .|..|++.+.. ..+..||+.||.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~ 59 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWK 59 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHH
Confidence 59999999999887554 111 27778777533 245556666654
No 68
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=69.26 E-value=11 Score=30.51 Aligned_cols=44 Identities=11% Similarity=0.050 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHhcC-CcHHHHHhhCCCCCHHHHHHHHHHHhHHHH
Q 028055 72 KEEEETIINLHDMLG-NRWSAIAGRLPGRTDNEIKNVWHTHLKKKA 116 (214)
Q Consensus 72 ~EED~~Ll~l~~~~G-~kW~~IA~~lpgRt~~~~knrw~~~lkk~~ 116 (214)
.+-|.+|+.+.++-| -.|++||+.+ |-|...|..|++.+.+...
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 456888888888887 4699999999 9999999999988776544
No 69
>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=66.46 E-value=10 Score=27.70 Aligned_cols=31 Identities=26% Similarity=0.452 Sum_probs=26.2
Q ss_pred HHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHH
Q 028055 75 EETIINLHDMLGNRWSAIAGRLPGRTDNEIKN 106 (214)
Q Consensus 75 D~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~kn 106 (214)
|..|..+...+|..|.++|..| |=+...|.+
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 6678889999999999999999 777766654
No 70
>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=64.19 E-value=19 Score=26.83 Aligned_cols=36 Identities=25% Similarity=0.290 Sum_probs=27.1
Q ss_pred HHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 78 IINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 78 Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
++.++-..|..+.+||+.+ |-|...|+++.+..+++
T Consensus 118 ii~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 118 VLVLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred HHhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3344444678899999999 88999999988775544
No 71
>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=63.61 E-value=17 Score=26.21 Aligned_cols=37 Identities=16% Similarity=0.303 Sum_probs=26.3
Q ss_pred HHHHHHHhcCC--------cHHHHHhhCCCC---C--HHHHHHHHHHHhH
Q 028055 77 TIINLHDMLGN--------RWSAIAGRLPGR---T--DNEIKNVWHTHLK 113 (214)
Q Consensus 77 ~Ll~l~~~~G~--------kW~~IA~~lpgR---t--~~~~knrw~~~lk 113 (214)
.|..+|...|+ +|..||+.|.-- + ..++|..|..+|-
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhH
Confidence 37777777774 699999998221 1 3678898887764
No 72
>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=61.59 E-value=9.9 Score=27.38 Aligned_cols=31 Identities=23% Similarity=0.638 Sum_probs=25.4
Q ss_pred HHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHH
Q 028055 75 EETIINLHDMLGNRWSAIAGRLPGRTDNEIKN 106 (214)
Q Consensus 75 D~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~kn 106 (214)
|..|..+.+..|..|.++|+.| |=+..+|..
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 4567888899999999999999 777766654
No 73
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=61.28 E-value=21 Score=27.42 Aligned_cols=46 Identities=17% Similarity=0.247 Sum_probs=33.6
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhccc
Q 028055 13 KKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLR 62 (214)
Q Consensus 13 ~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~ 62 (214)
++..||+|+-..++..+...| ..=..||+.++. ..+--.+|.+.+.
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g-~sv~evA~e~gI---s~~tl~~W~r~y~ 54 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPG-MTVSLVARQHGV---AASQLFLWRKQYQ 54 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCC-CCHHHHHHHHCc---CHHHHHHHHHHHh
Confidence 457899999887777777767 566788888875 4555667877654
No 74
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=60.74 E-value=14 Score=36.54 Aligned_cols=48 Identities=13% Similarity=0.462 Sum_probs=37.9
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHH----------HhhCCCCCHHHHHHHHHHHhHH
Q 028055 67 RGNFSKEEEETIINLHDMLGNRWSAI----------AGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 67 kg~WT~EED~~Ll~l~~~~G~kW~~I----------A~~lpgRt~~~~knrw~~~lkk 114 (214)
+..||..|+.....+.+++|..+..| -....-+|..|++.+|+.++++
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~ 145 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRR 145 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHH
Confidence 56799999999999999999999888 2223346777888888776654
No 75
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=60.52 E-value=30 Score=27.00 Aligned_cols=31 Identities=19% Similarity=0.152 Sum_probs=24.7
Q ss_pred HhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 83 DMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 83 ~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
...|-...+||..| |-|...|+++.+...++
T Consensus 138 ~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 168 (179)
T PRK11924 138 YVEGLSYREIAEIL-GVPVGTVKSRLRRARQL 168 (179)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 34567799999999 99999999988765433
No 76
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=59.94 E-value=17 Score=24.13 Aligned_cols=35 Identities=26% Similarity=0.455 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHH
Q 028055 72 KEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNV 107 (214)
Q Consensus 72 ~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knr 107 (214)
.+.|+..+.+..+.|-+-.+||+.+ ||+.+.|++.
T Consensus 6 t~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~y 40 (50)
T PF11427_consen 6 TDAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRY 40 (50)
T ss_dssp -HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHH
T ss_pred CHHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHH
Confidence 3567777888899999999999999 9999888764
No 77
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=59.92 E-value=55 Score=30.79 Aligned_cols=79 Identities=14% Similarity=0.189 Sum_probs=49.0
Q ss_pred cccCCCCCCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhcccCCCCCCCCCHHHHHHHHHHHHhcC
Q 028055 7 CEKMGLKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETIINLHDMLG 86 (214)
Q Consensus 7 ~~k~~l~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p~i~kg~WT~EED~~Ll~l~~~~G 86 (214)
.++.+..-|.|++.=|+...++.+.|....=++|- .++ .-+.||
T Consensus 69 ~D~~~daegvWSpdIEqsFqEALaiyppcGrrKIi-----------lsd-------------------------egkmyG 112 (455)
T KOG3841|consen 69 TDNQRDAEGVWSPDIEQSFQEALAIYPPCGRRKII-----------LSD-------------------------EGKMYG 112 (455)
T ss_pred CccccccccccChhHHHHHHHHHhhcCCCCceeEE-----------Ecc-------------------------Cccccc
Confidence 34455667899999999999988888643222221 100 002333
Q ss_pred CcHHHHHhhC-----CCCCHHHHHHHHHHHhHHHHHHHHHh
Q 028055 87 NRWSAIAGRL-----PGRTDNEIKNVWHTHLKKKAAAVLKQ 122 (214)
Q Consensus 87 ~kW~~IA~~l-----pgRt~~~~knrw~~~lkk~~~~~~~~ 122 (214)
.+ ..||+++ ..||..||..+-+.+-|++++....+
T Consensus 113 RN-ELIarYIKlrtgktRTrKQVSSHIQVlarrk~reiq~k 152 (455)
T KOG3841|consen 113 RN-ELIARYIKLRTGKTRTRKQVSSHIQVLARRKLREIQAK 152 (455)
T ss_pred hH-HHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHHhh
Confidence 21 3444432 35999999999988888877665433
No 78
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=59.91 E-value=37 Score=26.57 Aligned_cols=34 Identities=15% Similarity=0.223 Sum_probs=25.9
Q ss_pred HHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 80 NLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 80 ~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.+....|-....||+.| |.+...|+++.+..+++
T Consensus 138 ~l~~~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 171 (182)
T PRK09652 138 TLREIEGLSYEEIAEIM-GCPIGTVRSRIFRAREA 171 (182)
T ss_pred HHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 33334577899999999 99999999987765433
No 79
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=59.60 E-value=5.7 Score=40.00 Aligned_cols=44 Identities=14% Similarity=0.249 Sum_probs=39.4
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhh
Q 028055 13 KKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWI 58 (214)
Q Consensus 13 ~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~ 58 (214)
-.-.||+.|-.++.+++..|. .++..|++.+++ ++.+||-+-|.
T Consensus 618 gSd~WTp~E~~lF~kA~y~~~-KDF~~v~km~~~-KtVaqCVeyYY 661 (907)
T KOG4167|consen 618 GSDKWTPLERKLFNKALYTYS-KDFIFVQKMVKS-KTVAQCVEYYY 661 (907)
T ss_pred CcccccHHHHHHHHHHHHHhc-ccHHHHHHHhcc-ccHHHHHHHHH
Confidence 345899999999999999998 899999999998 99999987764
No 80
>PRK04217 hypothetical protein; Provisional
Probab=59.11 E-value=66 Score=24.78 Aligned_cols=46 Identities=20% Similarity=0.132 Sum_probs=36.9
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHHH
Q 028055 68 GNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKK 115 (214)
Q Consensus 68 g~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk~ 115 (214)
..-|.+| ..++.+....|-...+||+.+ |-+...|+++++...++-
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 3466666 677788877888999999999 999999999998765543
No 81
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=58.88 E-value=18 Score=30.51 Aligned_cols=44 Identities=25% Similarity=0.269 Sum_probs=37.0
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 68 GNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 68 g~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
...|+.|-+.|.-+.+=+.+ .+||..| +.|...||++.+++++|
T Consensus 147 ~~LT~RE~eVL~lla~G~sn--keIA~~L-~iS~~TVk~h~~~i~~K 190 (211)
T COG2197 147 ELLTPRELEVLRLLAEGLSN--KEIAEEL-NLSEKTVKTHVSNILRK 190 (211)
T ss_pred CCCCHHHHHHHHHHHCCCCH--HHHHHHH-CCCHhHHHHHHHHHHHH
Confidence 36899888888777665555 5999999 99999999999998876
No 82
>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=58.72 E-value=14 Score=26.89 Aligned_cols=31 Identities=32% Similarity=0.579 Sum_probs=26.6
Q ss_pred HHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHH
Q 028055 75 EETIINLHDMLGNRWSAIAGRLPGRTDNEIKN 106 (214)
Q Consensus 75 D~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~kn 106 (214)
|..|-.+...+|..|.++|+.| |=+...|.+
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 4567788899999999999999 888888766
No 83
>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=57.98 E-value=21 Score=24.57 Aligned_cols=26 Identities=23% Similarity=0.434 Sum_probs=20.9
Q ss_pred cHHHHHhhCCC-CCHHHHHHHHHHHhH
Q 028055 88 RWSAIAGRLPG-RTDNEIKNVWHTHLK 113 (214)
Q Consensus 88 kW~~IA~~lpg-Rt~~~~knrw~~~lk 113 (214)
-|..||..|.+ -+..+|+.+|..+..
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~ 54 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRD 54 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHH
Confidence 39999999942 678899999988654
No 84
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=57.32 E-value=29 Score=25.22 Aligned_cols=38 Identities=18% Similarity=0.324 Sum_probs=27.2
Q ss_pred HHHHHHHhcCC--------cHHHHHhhCCCC-----CHHHHHHHHHHHhHH
Q 028055 77 TIINLHDMLGN--------RWSAIAGRLPGR-----TDNEIKNVWHTHLKK 114 (214)
Q Consensus 77 ~Ll~l~~~~G~--------kW~~IA~~lpgR-----t~~~~knrw~~~lkk 114 (214)
.|..+|.+.|+ +|..||..|.-. ...++|..|..+|..
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~ 86 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLP 86 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHH
Confidence 36677777774 699999998322 356788888877643
No 85
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=56.55 E-value=22 Score=33.25 Aligned_cols=45 Identities=16% Similarity=0.245 Sum_probs=40.0
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHh-hCCCCCHHHHHHHHHHHh
Q 028055 68 GNFSKEEEETIINLHDMLGNRWSAIAG-RLPGRTDNEIKNVWHTHL 112 (214)
Q Consensus 68 g~WT~EED~~Ll~l~~~~G~kW~~IA~-~lpgRt~~~~knrw~~~l 112 (214)
..|+++|-...-+-.+.||..+..|.+ +++.|+--.|-..|+...
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWK 323 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWK 323 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhh
Confidence 579999999999999999999999966 789999999988776554
No 86
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=55.69 E-value=7.5 Score=31.00 Aligned_cols=44 Identities=18% Similarity=0.229 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhcccCCC
Q 028055 20 EEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDI 65 (214)
Q Consensus 20 EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p~i 65 (214)
+-|.+|+.+.++.|...|.+||+.++ -+...|+.|+.+...-++
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~lg--lS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQFG--VSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 57899999999999899999999998 788889999977655543
No 87
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=55.50 E-value=16 Score=34.33 Aligned_cols=48 Identities=17% Similarity=0.261 Sum_probs=41.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCcchhchh-----hCCCCCccccchhhhhc
Q 028055 12 LKKGPWTPEEDRILIVHIKKHGHPNWRALPKQ-----AGLLRCGKSCRLRWINY 60 (214)
Q Consensus 12 l~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~-----~~~~Rt~~qcr~Rw~~~ 60 (214)
+.-..||++|-+-|..++++|. -.|-.||.. .+..||-...++||...
T Consensus 128 l~dn~WskeETD~LF~lck~fD-LRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v 180 (445)
T KOG2656|consen 128 LNDNSWSKEETDYLFDLCKRFD-LRFFVIADRYDNQQYKKSRTVEDLKERYYSV 180 (445)
T ss_pred hccccccHHHHHHHHHHHHhcC-eeEEEEeeccchhhccccccHHHHHHHHHHH
Confidence 5557899999999999999999 799999987 66669999999999443
No 88
>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=55.13 E-value=21 Score=28.57 Aligned_cols=29 Identities=10% Similarity=0.074 Sum_probs=23.8
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-...+||..+ |-|...|+++.+...++
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 99999999998766544
No 89
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=55.11 E-value=41 Score=27.39 Aligned_cols=32 Identities=22% Similarity=0.227 Sum_probs=25.4
Q ss_pred HHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 82 HDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 82 ~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
....|-...+||..+ |-+...|++|.+...++
T Consensus 146 ~~~~g~s~~EIA~~l-g~s~~tV~~rl~rar~~ 177 (192)
T PRK09643 146 VDMQGYSVADAARML-GVAEGTVKSRCARGRAR 177 (192)
T ss_pred HHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 334567799999999 99999999998665443
No 90
>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=54.97 E-value=18 Score=26.30 Aligned_cols=28 Identities=32% Similarity=0.603 Sum_probs=22.5
Q ss_pred HHHHHHhcCCcHHHHHhhCCCCCHHHHHH
Q 028055 78 IINLHDMLGNRWSAIAGRLPGRTDNEIKN 106 (214)
Q Consensus 78 Ll~l~~~~G~kW~~IA~~lpgRt~~~~kn 106 (214)
|..+....|..|..+|+.| |=+..+|..
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 3346688899999999999 888887744
No 91
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=54.79 E-value=15 Score=36.16 Aligned_cols=49 Identities=20% Similarity=0.315 Sum_probs=43.2
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 66 KRGNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 66 ~kg~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
..+.||.+|-++.-.+..+.|...+.|+..+|+|+..+||-++..--++
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~eE~r 456 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKEEKR 456 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhhhhc
Confidence 4468999999999999999999999999999999999999988654433
No 92
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=54.21 E-value=27 Score=27.82 Aligned_cols=29 Identities=14% Similarity=0.012 Sum_probs=23.8
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|....+||..+ |-|...|+++.+...++
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 466799999999 99999999987665543
No 93
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=52.88 E-value=32 Score=29.38 Aligned_cols=44 Identities=20% Similarity=0.240 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhh--C-CCCCHHHHHHHHHHHhH
Q 028055 69 NFSKEEEETIINLHDMLGNRWSAIAGR--L-PGRTDNEIKNVWHTHLK 113 (214)
Q Consensus 69 ~WT~EED~~Ll~l~~~~G~kW~~IA~~--l-pgRt~~~~knrw~~~lk 113 (214)
.|+.++|-+|+.+|.. |+.-..|+.- | -.-|-..|..||+.+|-
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 5556666553 3 33578999999999984
No 94
>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=52.74 E-value=22 Score=25.57 Aligned_cols=35 Identities=31% Similarity=0.600 Sum_probs=26.8
Q ss_pred CHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHH
Q 028055 71 SKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNV 107 (214)
Q Consensus 71 T~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knr 107 (214)
+.||-++|+..- ..|..|..+|..| |=+...|++-
T Consensus 1 ~~~~v~~ll~~~-nlG~dW~~LA~~L-G~~~~~I~~i 35 (77)
T cd08311 1 KQEEVEKLLESG-RPGRDWRSLAGEL-GYEDEAIDTF 35 (77)
T ss_pred ChHHHHHHHhCC-CCccCHHHHHHHc-CCCHHHHHHH
Confidence 357888887322 5788999999999 8888887763
No 95
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=52.54 E-value=51 Score=26.76 Aligned_cols=29 Identities=7% Similarity=-0.039 Sum_probs=24.1
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-...+||..| |-|...|+.|.+.-.++
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 99999999997765543
No 96
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=52.35 E-value=6.8 Score=31.67 Aligned_cols=45 Identities=22% Similarity=0.276 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhcccCCC
Q 028055 19 PEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDI 65 (214)
Q Consensus 19 ~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p~i 65 (214)
.+-|.+|+.+.++.|...|.+||+.++ -+...|+.|+.+...-++
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lg--lS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVG--LSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 456899999999999899999999998 677889999987765554
No 97
>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=51.94 E-value=21 Score=23.48 Aligned_cols=43 Identities=26% Similarity=0.333 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 69 NFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 69 ~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
..|+.|-+.|.-+.. |..=.+||..+ |.+...|+.+...+.+|
T Consensus 3 ~LT~~E~~vl~~l~~--G~~~~eIA~~l-~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ--GMSNKEIAEEL-GISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHHT--TS-HHHHHHHH-TSHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHh--cCCcchhHHhc-CcchhhHHHHHHHHHHH
Confidence 456677776665554 44446999999 99999999988777655
No 98
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=51.41 E-value=57 Score=25.23 Aligned_cols=29 Identities=10% Similarity=0.100 Sum_probs=24.2
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..| |-+...|+++.+..+++
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 99999999998776544
No 99
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=51.36 E-value=48 Score=26.73 Aligned_cols=29 Identities=10% Similarity=0.068 Sum_probs=23.5
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-...+||..+ |-|...|+++.+...++
T Consensus 153 ~g~s~~eIA~~l-gis~~tv~~~l~Rar~~ 181 (193)
T PRK11923 153 DGLSYEDIASVM-QCPVGTVRSRIFRAREA 181 (193)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355689999999 99999999998766544
No 100
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=51.20 E-value=37 Score=26.94 Aligned_cols=35 Identities=20% Similarity=0.296 Sum_probs=27.1
Q ss_pred HHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 79 INLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 79 l~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
+.+....|-...+||..+ |-+...|+.+.+.-+++
T Consensus 128 ~~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 162 (172)
T PRK12523 128 FLYNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQ 162 (172)
T ss_pred HHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 333444577899999999 99999999998766654
No 101
>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=51.00 E-value=53 Score=19.75 Aligned_cols=37 Identities=24% Similarity=0.291 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHH
Q 028055 74 EEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTH 111 (214)
Q Consensus 74 ED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~ 111 (214)
++..++.++-..|-.+.+||..+ |-+...|+.+.+..
T Consensus 14 ~~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~ 50 (55)
T cd06171 14 REREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRA 50 (55)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 34555566556778899999999 88888887765443
No 102
>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=49.68 E-value=18 Score=26.32 Aligned_cols=28 Identities=29% Similarity=0.551 Sum_probs=22.9
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCCHHHH
Q 028055 76 ETIINLHDMLGNRWSAIAGRLPGRTDNEI 104 (214)
Q Consensus 76 ~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~ 104 (214)
.-|..+....|..|..+|.+| |=+..+|
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L-Glse~~I 30 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL-GLSYREL 30 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc-CCCHHHH
Confidence 457889999999999999999 6555544
No 103
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=49.57 E-value=62 Score=26.07 Aligned_cols=29 Identities=14% Similarity=0.125 Sum_probs=24.1
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-...+||..| |-|...|+++.+...++
T Consensus 146 ~~~s~~eIA~~l-gis~~tV~~~l~Rar~~ 174 (189)
T PRK12515 146 HEKSVEEVGEIV-GIPESTVKTRMFYARKK 174 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 466789999999 99999999998775544
No 104
>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=49.46 E-value=63 Score=26.23 Aligned_cols=33 Identities=12% Similarity=0.121 Sum_probs=25.8
Q ss_pred HHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 81 LHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 81 l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
+....|-...+||..| |-|...|+.|....+++
T Consensus 142 l~~~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 142 MREVLGFESDEICQEL-EISTSNCHVLLYRARLS 174 (188)
T ss_pred HHHHhCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3334467789999999 99999999998766544
No 105
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=49.25 E-value=59 Score=26.51 Aligned_cols=37 Identities=19% Similarity=0.295 Sum_probs=29.0
Q ss_pred HHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHh
Q 028055 75 EETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHL 112 (214)
Q Consensus 75 D~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~l 112 (214)
...++.+....|-.+.+||..+ |-|...|+.+|+..-
T Consensus 140 ~~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR 176 (185)
T PF07638_consen 140 QRRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 3444455555677899999999 999999999997664
No 106
>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=49.15 E-value=38 Score=26.71 Aligned_cols=29 Identities=24% Similarity=0.304 Sum_probs=23.5
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-....||..+ |-|...|+++.+..+++
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 456789999999 88999999998766544
No 107
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=49.04 E-value=42 Score=26.96 Aligned_cols=34 Identities=18% Similarity=0.082 Sum_probs=27.0
Q ss_pred HHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHHHH
Q 028055 82 HDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKKKA 116 (214)
Q Consensus 82 ~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk~~ 116 (214)
+...|-...+||..| |-+...|+.|.+.-+++-.
T Consensus 139 ~~~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~ 172 (178)
T PRK12529 139 ATLDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCL 172 (178)
T ss_pred HHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 334567899999999 9999999999887665543
No 108
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=48.63 E-value=35 Score=27.17 Aligned_cols=29 Identities=14% Similarity=0.012 Sum_probs=23.1
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..| |-+...|+++.+...++
T Consensus 151 ~g~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T TIGR02948 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 356789999999 99999999987665443
No 109
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=48.59 E-value=46 Score=24.87 Aligned_cols=46 Identities=20% Similarity=0.147 Sum_probs=30.4
Q ss_pred CCCHHHHHHHHHHHHhc----C----CcHHHHHhhCC-----CCCHHHHHHHHHHHhHH
Q 028055 69 NFSKEEEETIINLHDML----G----NRWSAIAGRLP-----GRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 69 ~WT~EED~~Ll~l~~~~----G----~kW~~IA~~lp-----gRt~~~~knrw~~~lkk 114 (214)
-||+++|..|++.+-.| | ..|..+...+. .=+.+|+.++-+.+-+|
T Consensus 6 ~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~K 64 (98)
T PF04504_consen 6 LWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKK 64 (98)
T ss_pred CCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHH
Confidence 59999999999988666 6 24554444332 23677888776655433
No 110
>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=48.57 E-value=25 Score=25.78 Aligned_cols=29 Identities=24% Similarity=0.453 Sum_probs=23.2
Q ss_pred HHHHHHHHHhcCCcHHHHHhhCCCCCHHHH
Q 028055 75 EETIINLHDMLGNRWSAIAGRLPGRTDNEI 104 (214)
Q Consensus 75 D~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~ 104 (214)
|..|..+.+.+|..|.++|..| |=+...|
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L-~vs~~dI 32 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL-QFSVEDI 32 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc-CCCHHHH
Confidence 4567788899999999999998 6555444
No 111
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=48.46 E-value=47 Score=24.29 Aligned_cols=43 Identities=12% Similarity=0.119 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHhcC-CcHHHHHhhCCCCCHHHHHHHHHHHhHHHH
Q 028055 73 EEEETIINLHDMLG-NRWSAIAGRLPGRTDNEIKNVWHTHLKKKA 116 (214)
Q Consensus 73 EED~~Ll~l~~~~G-~kW~~IA~~lpgRt~~~~knrw~~~lkk~~ 116 (214)
+.|..|+.+....| -.+++||+.+ |-+...|+.+...+.++..
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~ 46 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGV 46 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 56788888888877 4699999999 9999999999988776544
No 112
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=48.39 E-value=42 Score=26.85 Aligned_cols=29 Identities=17% Similarity=0.283 Sum_probs=24.0
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-...+||..| |-+...|+.+.+..+++
T Consensus 146 ~g~s~~eIA~~l-~is~~tV~~~l~ra~~~ 174 (184)
T PRK12512 146 EGASIKETAAKL-SMSEGAVRVALHRGLAA 174 (184)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 466789999999 99999999998766544
No 113
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=48.25 E-value=63 Score=25.10 Aligned_cols=29 Identities=10% Similarity=-0.110 Sum_probs=23.8
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..+ |-+...|+++.+...++
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 466789999999 99999999998766544
No 114
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=48.21 E-value=43 Score=26.98 Aligned_cols=30 Identities=20% Similarity=0.296 Sum_probs=24.3
Q ss_pred hcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 84 MLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 84 ~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
..|-...+||..| |-+...|+.+.+..+++
T Consensus 153 ~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 153 VVGLSAEETAEAV-GSTPGAVRVAQHRALAR 182 (189)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466799999999 99999999998765544
No 115
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=47.80 E-value=41 Score=27.20 Aligned_cols=30 Identities=23% Similarity=0.143 Sum_probs=24.5
Q ss_pred hcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 84 MLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 84 ~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
..|-...+||..| |-+...|+++.+...++
T Consensus 120 ~~g~~~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (181)
T PRK09637 120 LEGLSQKEIAEKL-GLSLSGAKSRVQRGRVK 149 (181)
T ss_pred hcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3567799999999 99999999998765543
No 116
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=47.38 E-value=45 Score=26.30 Aligned_cols=29 Identities=28% Similarity=0.346 Sum_probs=23.9
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..| |.+...|+.+.+.-+++
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 466689999999 99999999998766644
No 117
>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=47.08 E-value=33 Score=24.19 Aligned_cols=31 Identities=32% Similarity=0.654 Sum_probs=23.1
Q ss_pred HHHHHHHHHh-cCCcHHHHHhhCCCCCHHHHHH
Q 028055 75 EETIINLHDM-LGNRWSAIAGRLPGRTDNEIKN 106 (214)
Q Consensus 75 D~~Ll~l~~~-~G~kW~~IA~~lpgRt~~~~kn 106 (214)
.+.|..++.. .|..|..+|++| |=+..+|..
T Consensus 5 ~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i~~ 36 (88)
T smart00005 5 REKLAKLLDHPLGLDWRELARKL-GLSEADIDQ 36 (88)
T ss_pred HHHHHHHHcCccchHHHHHHHHc-CCCHHHHHH
Confidence 4566677777 899999999999 656665543
No 118
>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=46.95 E-value=25 Score=25.73 Aligned_cols=30 Identities=33% Similarity=0.644 Sum_probs=24.3
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCCHHHHHHH
Q 028055 77 TIINLHDMLGNRWSAIAGRLPGRTDNEIKNV 107 (214)
Q Consensus 77 ~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knr 107 (214)
-|-.+....|..|..+|++| |=+..+|..-
T Consensus 4 ~l~~l~~~lG~~Wk~lar~L-G~s~~eI~~i 33 (86)
T cd08777 4 HLDLLRENLGKKWKRCARKL-GFTESEIEEI 33 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHc-CCCHHHHHHH
Confidence 35556678899999999999 8888888763
No 119
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=46.84 E-value=65 Score=26.14 Aligned_cols=29 Identities=10% Similarity=0.003 Sum_probs=23.8
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-...+||..| |-+...|+.|.+..+++
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 466789999999 99999999998766544
No 120
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=45.16 E-value=70 Score=26.00 Aligned_cols=30 Identities=10% Similarity=0.017 Sum_probs=24.2
Q ss_pred hcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 84 MLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 84 ~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
..|-.+.+||+.| |-+...|+++.+.-+++
T Consensus 150 ~~g~s~~eIA~~l-gis~~tV~~~l~Ra~~~ 179 (196)
T PRK12524 150 IEGLSNPEIAEVM-EIGVEAVESLTARGKRA 179 (196)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3466799999999 99999999987766544
No 121
>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=44.99 E-value=52 Score=25.65 Aligned_cols=29 Identities=24% Similarity=0.299 Sum_probs=23.0
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||+.| |-+...|+++-+...++
T Consensus 137 ~g~s~~eIA~~l-~is~~tv~~~l~ra~~~ 165 (170)
T TIGR02952 137 QNLPIAEVARIL-GKTEGAVKILQFRAIKK 165 (170)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 366789999999 99999999987655543
No 122
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=44.87 E-value=82 Score=25.46 Aligned_cols=30 Identities=17% Similarity=0.232 Sum_probs=24.2
Q ss_pred hcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 84 MLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 84 ~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
..|-.-.+||..| |-+...|+++.+..+++
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 99999999998765543
No 123
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=44.61 E-value=28 Score=33.38 Aligned_cols=40 Identities=23% Similarity=0.359 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHH
Q 028055 69 NFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWH 109 (214)
Q Consensus 69 ~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~ 109 (214)
.||++|-. +++-...||.....||..+...|..|++.+|.
T Consensus 472 ~wSp~e~s-~ircf~~y~~~fe~ia~l~~tktp~Q~~~fy~ 511 (534)
T KOG1194|consen 472 GWSPEEKS-AIRCFHWYKDNFELIAELMATKTPEQIKKFYM 511 (534)
T ss_pred CCCCcccc-cccCchhhccchHHHHHHhcCCCHHHHHHHhc
Confidence 59998887 88888999999999999999999999999984
No 124
>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=44.19 E-value=56 Score=20.25 Aligned_cols=34 Identities=21% Similarity=0.169 Sum_probs=26.1
Q ss_pred HHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHH
Q 028055 74 EEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVW 108 (214)
Q Consensus 74 ED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw 108 (214)
|-..|.++.+.+|++-+..|+.| |=+...+..+-
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~kl 39 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLL-GISRRTLYRKL 39 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHH
Confidence 66788899999999999999999 77776666543
No 125
>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=44.08 E-value=90 Score=28.69 Aligned_cols=85 Identities=18% Similarity=0.328 Sum_probs=58.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCC---CcchhchhhCCCCCccccchhhhhcccCCCCCCCCCHHHHHHHHHHHHh-c----
Q 028055 14 KGPWTPEEDRILIVHIKKHGHP---NWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETIINLHDM-L---- 85 (214)
Q Consensus 14 kg~WT~EED~~L~~~v~~~g~~---nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p~i~kg~WT~EED~~Ll~l~~~-~---- 85 (214)
...||.-|...|+++.+..... +-.+|++.+++ |+..++++ +.+.|+ +..+.+++++ |
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 4589999999998888766323 34567777887 88777765 344443 2344455444 2
Q ss_pred -CCc------------HHHHHhhCCCCCHHHHHHHHHHHh
Q 028055 86 -GNR------------WSAIAGRLPGRTDNEIKNVWHTHL 112 (214)
Q Consensus 86 -G~k------------W~~IA~~lpgRt~~~~knrw~~~l 112 (214)
|.+ |..+|..+.|.-...|-.-|...|
T Consensus 87 ~~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l 126 (344)
T PF11035_consen 87 KGPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVL 126 (344)
T ss_pred ccccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHH
Confidence 221 999999999999988888776655
No 126
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=43.89 E-value=58 Score=24.99 Aligned_cols=29 Identities=21% Similarity=0.284 Sum_probs=22.4
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-...+||..+ |-+...|+++-+..+++
T Consensus 121 ~~~s~~EIA~~l-~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 121 VGKTMGEIALET-EMTYYQVRWIYRQALEK 149 (154)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355689999999 99999999987655443
No 127
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=43.73 E-value=87 Score=25.22 Aligned_cols=29 Identities=14% Similarity=-0.044 Sum_probs=23.9
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..| |-|...|++|.+..+++
T Consensus 146 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 174 (191)
T PRK12520 146 LELETEEICQEL-QITATNAWVLLYRARMR 174 (191)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355679999999 99999999998766544
No 128
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=43.32 E-value=36 Score=21.46 Aligned_cols=37 Identities=30% Similarity=0.372 Sum_probs=18.6
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHH
Q 028055 69 NFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNV 107 (214)
Q Consensus 69 ~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knr 107 (214)
.+|.+|=..|..+ ..-|..=.+||+.| ||+...|.+.
T Consensus 4 ~Lt~~eR~~I~~l-~~~G~s~~~IA~~l-g~s~sTV~re 40 (44)
T PF13936_consen 4 HLTPEERNQIEAL-LEQGMSIREIAKRL-GRSRSTVSRE 40 (44)
T ss_dssp --------HHHHH-HCS---HHHHHHHT-T--HHHHHHH
T ss_pred chhhhHHHHHHHH-HHcCCCHHHHHHHH-CcCcHHHHHH
Confidence 4566666666555 45687889999999 9999888764
No 129
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=43.14 E-value=32 Score=34.22 Aligned_cols=47 Identities=13% Similarity=0.284 Sum_probs=34.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCcchhchhhCC---------CCCccccchhhhhcc
Q 028055 14 KGPWTPEEDRILIVHIKKHGHPNWRALPKQAGL---------LRCGKSCRLRWINYL 61 (214)
Q Consensus 14 kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~---------~Rt~~qcr~Rw~~~L 61 (214)
|..||..|.+....+++.+| .++.+|-..+.. .++-.|+|.+|.+.+
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 66899999999999999999 899888333221 145567777775543
No 130
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=42.93 E-value=48 Score=26.37 Aligned_cols=29 Identities=24% Similarity=0.279 Sum_probs=23.9
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-...+||+.+ |-+...|+++.+.-+++
T Consensus 134 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 162 (172)
T PRK09651 134 DGLTYSEIAHKL-GVSVSSVKKYVAKATEH 162 (172)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 456789999999 99999999998766544
No 131
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=42.22 E-value=94 Score=24.10 Aligned_cols=29 Identities=21% Similarity=0.221 Sum_probs=23.2
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..| |-+...|++|....+++
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 99999999998765544
No 132
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=42.17 E-value=60 Score=26.02 Aligned_cols=30 Identities=23% Similarity=0.212 Sum_probs=24.6
Q ss_pred hcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 84 MLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 84 ~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
..|-...+||..| |.+...|+++-+..+++
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 99999999998765544
No 133
>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=41.79 E-value=63 Score=25.65 Aligned_cols=29 Identities=21% Similarity=0.209 Sum_probs=23.4
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-...+||..+ |-+...|++|.+.-.++
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 99999999998765433
No 134
>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=41.56 E-value=26 Score=28.51 Aligned_cols=48 Identities=21% Similarity=0.275 Sum_probs=34.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCC---CCccccchhhhhc
Q 028055 12 LKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLL---RCGKSCRLRWINY 60 (214)
Q Consensus 12 l~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~---Rt~~qcr~Rw~~~ 60 (214)
-+...-|+.|.+-|..+|.+|| .|....+.-...+ .|..||+.+...|
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhG-dDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHG-DDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHC-ccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 4566788999999999999999 7888777554311 5566666555443
No 135
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=41.50 E-value=61 Score=25.75 Aligned_cols=29 Identities=21% Similarity=0.204 Sum_probs=23.6
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..| |.|...|+++.+..+++
T Consensus 144 ~g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 172 (179)
T PRK12514 144 EGLSYKELAERH-DVPLNTMRTWLRRSLLK 172 (179)
T ss_pred cCCCHHHHHHHH-CCChHHHHHHHHHHHHH
Confidence 356689999999 99999999998766544
No 136
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=41.41 E-value=67 Score=25.02 Aligned_cols=31 Identities=19% Similarity=0.201 Sum_probs=24.4
Q ss_pred HHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhH
Q 028055 82 HDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLK 113 (214)
Q Consensus 82 ~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lk 113 (214)
..-.|-...+||..+ |-+...|++|.+.-++
T Consensus 125 ~~~~g~s~~EIA~~l-~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 125 AQVDGLGYGEIATEL-GISLATVKRYLNKAAM 155 (161)
T ss_pred HHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 334567789999999 9999999998766543
No 137
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=41.28 E-value=67 Score=25.26 Aligned_cols=30 Identities=17% Similarity=0.099 Sum_probs=23.9
Q ss_pred hcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 84 MLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 84 ~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
..|-.-.+||..+ |-+...|+++-+...++
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 99999999987665543
No 138
>PRK00118 putative DNA-binding protein; Validated
Probab=41.21 E-value=1.1e+02 Score=23.19 Aligned_cols=41 Identities=12% Similarity=0.118 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhH
Q 028055 72 KEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLK 113 (214)
Q Consensus 72 ~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lk 113 (214)
.+.+..++.+....|-...+||+.+ |-|...|+.+.+...+
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 3456677788888899999999999 9999999988765443
No 139
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=41.05 E-value=35 Score=36.55 Aligned_cols=74 Identities=16% Similarity=0.261 Sum_probs=44.5
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhcccCCCCCCCCCHHHHHHHHHHHHhc-CCcHHH
Q 028055 13 KKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETIINLHDML-GNRWSA 91 (214)
Q Consensus 13 ~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p~i~kg~WT~EED~~Ll~l~~~~-G~kW~~ 91 (214)
.---|..++|..|+-.|-+||.++|.+|-.- +.-|-.. ...+.-..-.+.+=...-..|+.+...+ +.+|..
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir~D------p~L~l~d-Ki~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~ 1204 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIRLD------PDLGLTD-KIFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPK 1204 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhccC------ccccchh-hhcccccCCchHHHHHHHHHHHHHHhhcccCCCch
Confidence 3457999999999999999999999998321 1111110 0111111334455566666677666665 444544
Q ss_pred HH
Q 028055 92 IA 93 (214)
Q Consensus 92 IA 93 (214)
..
T Consensus 1205 ~~ 1206 (1373)
T KOG0384|consen 1205 KL 1206 (1373)
T ss_pred hh
Confidence 43
No 140
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=40.83 E-value=59 Score=26.30 Aligned_cols=29 Identities=17% Similarity=0.139 Sum_probs=23.6
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..| |-+...|+++.+..+++
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 455689999999 99999999998665544
No 141
>PF13137 DUF3983: Protein of unknown function (DUF3983)
Probab=40.64 E-value=17 Score=22.21 Aligned_cols=10 Identities=50% Similarity=1.032 Sum_probs=7.5
Q ss_pred HHHHHHHhcC
Q 028055 197 FWYNILVTSG 206 (214)
Q Consensus 197 ~~~~~~~~~~ 206 (214)
=|.|+|+++|
T Consensus 24 AWRNiFvqag 33 (34)
T PF13137_consen 24 AWRNIFVQAG 33 (34)
T ss_pred HHHHHHHHcc
Confidence 4788888875
No 142
>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=40.59 E-value=62 Score=26.26 Aligned_cols=46 Identities=22% Similarity=0.216 Sum_probs=37.5
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCcHHHHHhhC----CCCCHHHHHHHHHHH
Q 028055 66 KRGNFSKEEEETIINLHDMLGNRWSAIAGRL----PGRTDNEIKNVWHTH 111 (214)
Q Consensus 66 ~kg~WT~EED~~Ll~l~~~~G~kW~~IA~~l----pgRt~~~~knrw~~~ 111 (214)
....-|..|..-|..|+.+||..+..+|.-. -..|..||+.+...+
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 3456889999999999999999999998853 258999998876544
No 143
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=40.46 E-value=96 Score=25.22 Aligned_cols=33 Identities=18% Similarity=0.118 Sum_probs=25.5
Q ss_pred HHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 81 LHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 81 l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
+....|-...+||+.| |-+...|++|-+..+++
T Consensus 127 L~~~~g~s~~EIA~~L-gis~~tVk~~l~Rar~~ 159 (187)
T PRK12516 127 LVGASGFAYEEAAEIC-GCAVGTIKSRVNRARQR 159 (187)
T ss_pred HHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3334567789999999 99999999997665543
No 144
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=40.44 E-value=88 Score=25.01 Aligned_cols=29 Identities=7% Similarity=0.020 Sum_probs=22.9
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..+ |-+...|+++.+..+++
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 466788999999 99999999987665543
No 145
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=39.87 E-value=66 Score=25.78 Aligned_cols=29 Identities=14% Similarity=0.342 Sum_probs=23.7
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..| |-|...|+++.+...++
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 466789999999 99999999987665543
No 146
>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=39.40 E-value=23 Score=27.23 Aligned_cols=28 Identities=18% Similarity=0.115 Sum_probs=23.2
Q ss_pred CCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 86 G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
|-.+.+||..| |-+...|+++.+...++
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 45699999999 99999999998766543
No 147
>PF06599 DUF1139: Protein of unknown function (DUF1139); InterPro: IPR009519 This family consists of several hypothetical Fijivirus proteins of unknown function.
Probab=39.22 E-value=19 Score=32.12 Aligned_cols=14 Identities=21% Similarity=0.942 Sum_probs=12.1
Q ss_pred CCchHHHHHHHHhc
Q 028055 192 GGGMDFWYNILVTS 205 (214)
Q Consensus 192 ~~~~~~~~~~~~~~ 205 (214)
+.+.||||+|||++
T Consensus 277 ~~dvD~WY~lfmrt 290 (309)
T PF06599_consen 277 HTDVDYWYSLFMRT 290 (309)
T ss_pred CCCHHHHHHHHHHH
Confidence 45899999999985
No 148
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=39.11 E-value=71 Score=25.47 Aligned_cols=28 Identities=21% Similarity=0.175 Sum_probs=22.7
Q ss_pred CCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 86 G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
|-.-.+||..+ |-|...|+++.+..+++
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 55679999999 99999999987765544
No 149
>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=38.52 E-value=73 Score=25.25 Aligned_cols=30 Identities=20% Similarity=0.550 Sum_probs=23.8
Q ss_pred hcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 84 MLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 84 ~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
..|-.-.+||..+ |-|...|+.+.+..+++
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 99999999987766544
No 150
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=38.49 E-value=1.1e+02 Score=24.97 Aligned_cols=28 Identities=18% Similarity=0.042 Sum_probs=23.0
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLK 113 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lk 113 (214)
.|-.-.+||..+ |.+...||+|.+.-.+
T Consensus 154 eg~s~~EIA~~l-gis~~tVk~~l~RAr~ 181 (201)
T PRK12545 154 LDFEIDDICTEL-TLTANHCSVLLYRART 181 (201)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 456789999999 9999999999765544
No 151
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=38.44 E-value=69 Score=24.87 Aligned_cols=38 Identities=16% Similarity=0.161 Sum_probs=27.5
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 76 ETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 76 ~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
..++.+.-..|-.-.+||..| |-+...|+++.+..+++
T Consensus 116 r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~ra~~~ 153 (162)
T TIGR02983 116 RAVVVLRYYEDLSEAQVAEAL-GISVGTVKSRLSRALAR 153 (162)
T ss_pred HHHhhhHHHhcCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 334444444566778999999 99999999998766544
No 152
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=37.89 E-value=60 Score=27.32 Aligned_cols=28 Identities=18% Similarity=0.160 Sum_probs=23.5
Q ss_pred CCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 86 G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
|-...+||..| |.|...|+++.+..+++
T Consensus 165 g~s~~EIAe~l-gis~~tVk~~l~Rar~k 192 (231)
T PRK11922 165 ELSVEETAQAL-GLPEETVKTRLHRARRL 192 (231)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 55689999999 99999999998766544
No 153
>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=37.26 E-value=51 Score=23.91 Aligned_cols=31 Identities=19% Similarity=0.492 Sum_probs=23.4
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHH
Q 028055 77 TIINLHDMLGNRWSAIAGRLPGRTDNEIKNVW 108 (214)
Q Consensus 77 ~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw 108 (214)
.+--+.+..|..|..+|+.| |=|..+|..-=
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 34445677899999999999 88888776543
No 154
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=36.18 E-value=1e+02 Score=25.04 Aligned_cols=29 Identities=21% Similarity=0.218 Sum_probs=22.8
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-...+||+.| |-+...|+++-+.-+++
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 88999999987655544
No 155
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=35.85 E-value=85 Score=25.35 Aligned_cols=28 Identities=36% Similarity=0.431 Sum_probs=22.2
Q ss_pred CCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 86 G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
|-.-.+||+.+ |.|...|+++-+...++
T Consensus 147 g~s~~EIAe~l-gis~~~V~~~l~Ra~~~ 174 (189)
T PRK06811 147 GEKIEEIAKKL-GLTRSAIDNRLSRGRKK 174 (189)
T ss_pred cCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 55678999999 99999999987655444
No 156
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=35.75 E-value=83 Score=25.18 Aligned_cols=29 Identities=31% Similarity=0.300 Sum_probs=23.7
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||+.+ |-|...|+++.+..+++
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 456678999999 99999999998776644
No 157
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=35.70 E-value=1.4e+02 Score=24.85 Aligned_cols=29 Identities=3% Similarity=-0.031 Sum_probs=23.8
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..| |-|...|++|.+..+++
T Consensus 163 ~g~s~~EIAe~l-gis~~tV~~~l~RAr~~ 191 (206)
T PRK12544 163 IELETNEICHAV-DLSVSNLNVLLYRARLR 191 (206)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 455679999999 99999999998766544
No 158
>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=35.16 E-value=68 Score=28.18 Aligned_cols=29 Identities=21% Similarity=0.251 Sum_probs=23.7
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..| |.+...|++|.+...++
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 99999999998765543
No 159
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=34.38 E-value=81 Score=25.75 Aligned_cols=32 Identities=13% Similarity=0.055 Sum_probs=25.1
Q ss_pred HHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 82 HDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 82 ~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
....|-...+||..| |-|...|+++.+..+++
T Consensus 125 ~~~~g~s~~EIA~~L-giS~~tVk~~l~Rar~~ 156 (188)
T PRK12546 125 VGASGFSYEEAAEMC-GVAVGTVKSRANRARAR 156 (188)
T ss_pred HHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 334566789999999 99999999997766543
No 160
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=34.36 E-value=1.4e+02 Score=24.65 Aligned_cols=29 Identities=21% Similarity=0.286 Sum_probs=23.6
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..| |-+...|+++.+...++
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 456679999999 99999999998766544
No 161
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=33.66 E-value=98 Score=23.92 Aligned_cols=43 Identities=12% Similarity=0.107 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHhcC-CcHHHHHhhCCCCCHHHHHHHHHHHhHHHH
Q 028055 73 EEEETIINLHDMLG-NRWSAIAGRLPGRTDNEIKNVWHTHLKKKA 116 (214)
Q Consensus 73 EED~~Ll~l~~~~G-~kW~~IA~~lpgRt~~~~knrw~~~lkk~~ 116 (214)
+-|.+|+++.+.-| ..+..||+.+ |-|...|.+|-..+.+...
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~Gi 51 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGV 51 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCc
Confidence 45778888887777 4699999999 9999999999877765543
No 162
>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=33.18 E-value=50 Score=22.64 Aligned_cols=27 Identities=37% Similarity=0.705 Sum_probs=20.2
Q ss_pred HHHHHHhcCCcHHHHHhhCCCCCHHHHH
Q 028055 78 IINLHDMLGNRWSAIAGRLPGRTDNEIK 105 (214)
Q Consensus 78 Ll~l~~~~G~kW~~IA~~lpgRt~~~~k 105 (214)
+..+....|..|..+|..+ |=+..+|.
T Consensus 2 ~~~ia~~lg~~W~~la~~L-gl~~~~I~ 28 (79)
T cd01670 2 LDKLAKKLGKDWKKLARKL-GLSDGEID 28 (79)
T ss_pred HHHHHHHHhhHHHHHHHHh-CCCHHHHH
Confidence 4456778899999999999 55555554
No 163
>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=32.79 E-value=1.1e+02 Score=23.48 Aligned_cols=27 Identities=30% Similarity=0.329 Sum_probs=20.4
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHh
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHL 112 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~l 112 (214)
.|-.=.+||+.+ |=|...|+.+.+...
T Consensus 126 ~g~~~~eIA~~l-~is~~tv~~~l~Rar 152 (159)
T TIGR02989 126 RGVSLTALAEQL-GRTVNAVYKALSRLR 152 (159)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 455678889988 888888888865543
No 164
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=32.67 E-value=1.7e+02 Score=22.62 Aligned_cols=29 Identities=24% Similarity=0.329 Sum_probs=23.3
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..| |-+...|+++.+..+++
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 566678999999 99999999988665544
No 165
>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=32.12 E-value=1.5e+02 Score=25.44 Aligned_cols=29 Identities=7% Similarity=-0.029 Sum_probs=24.0
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-...+||..+ |-+...|++|.+.-+++
T Consensus 176 eg~S~~EIA~~L-gis~~TVk~rl~RAr~~ 204 (244)
T TIGR03001 176 DGLSMDRIGAMY-QVHRSTVSRWVAQARER 204 (244)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 355799999999 99999999998766544
No 166
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=31.50 E-value=1.3e+02 Score=24.05 Aligned_cols=29 Identities=34% Similarity=0.225 Sum_probs=22.8
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..| |-|...|+.+.+..+++
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 455678999999 89999999887665544
No 167
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=31.47 E-value=1.2e+02 Score=25.47 Aligned_cols=43 Identities=26% Similarity=0.255 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 69 NFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 69 ~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
..|+-|-+.|.-+.. |-.-.+||+.| +-+...++++-..+++|
T Consensus 155 ~Lt~rE~~Vl~l~~~--G~s~~eIA~~L-~iS~~TVk~~~~~i~~K 197 (216)
T PRK10100 155 LLTHREKEILNKLRI--GASNNEIARSL-FISENTVKTHLYNLFKK 197 (216)
T ss_pred CCCHHHHHHHHHHHc--CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 478766665555554 87889999999 99999999998887765
No 168
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=31.28 E-value=1.3e+02 Score=25.51 Aligned_cols=29 Identities=10% Similarity=0.045 Sum_probs=23.6
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..| |-+...|+++.+.-+++
T Consensus 186 eg~s~~EIA~~L-gis~~tVk~~l~RAr~k 214 (233)
T PRK12538 186 ENMSNGEIAEVM-DTTVAAVESLLKRGRQQ 214 (233)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 355689999999 99999999998766544
No 169
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=31.10 E-value=1.3e+02 Score=23.96 Aligned_cols=29 Identities=17% Similarity=0.075 Sum_probs=22.6
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||+.| |-+...|++|.+..+++
T Consensus 142 ~g~s~~EIA~~l-~is~~tv~~~l~Ra~~~ 170 (179)
T PRK09415 142 EELSIKEIAEVT-GVNENTVKTRLKKAKEL 170 (179)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355678999999 88999999988766544
No 170
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=30.16 E-value=1.8e+02 Score=21.63 Aligned_cols=42 Identities=21% Similarity=0.328 Sum_probs=34.3
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhCCCC-CHHHHHHHHHH
Q 028055 67 RGNFSKEEEETIINLHDMLGNRWSAIAGRLPGR-TDNEIKNVWHT 110 (214)
Q Consensus 67 kg~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgR-t~~~~knrw~~ 110 (214)
+-.||.|.-..+++++..-|..=+.||+.+ |- +.++++. |..
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~~-W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLYK-WRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHHH-HHH
Confidence 568999999999999999998889999999 76 6665554 543
No 171
>PRK01905 DNA-binding protein Fis; Provisional
Probab=30.13 E-value=1.5e+02 Score=20.88 Aligned_cols=35 Identities=20% Similarity=0.178 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHH
Q 028055 72 KEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNV 107 (214)
Q Consensus 72 ~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knr 107 (214)
.-|...+.++....|...++.|+.+ |=+...++.+
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 3467788899999999999999988 7676665554
No 172
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=29.92 E-value=99 Score=25.69 Aligned_cols=43 Identities=9% Similarity=0.024 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 69 NFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 69 ~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
..|+-|-+.|.-+++=+ .-.+||+.| |-+...|+++-..+++|
T Consensus 137 ~LT~RE~eVL~lla~G~--snkeIA~~L-~iS~~TVk~h~~~I~~K 179 (207)
T PRK15411 137 SLSRTESSMLRMWMAGQ--GTIQISDQM-NIKAKTVSSHKGNIKRK 179 (207)
T ss_pred cCCHHHHHHHHHHHcCC--CHHHHHHHc-CCCHHHHHHHHHHHHHH
Confidence 48888888777666544 447999999 99999999987777665
No 173
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=29.87 E-value=1.1e+02 Score=26.80 Aligned_cols=29 Identities=24% Similarity=0.379 Sum_probs=23.2
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
+|-.-.+||+.| |.|...|+++.+.-.++
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 455689999999 99999999997655433
No 174
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=29.15 E-value=47 Score=23.26 Aligned_cols=22 Identities=23% Similarity=0.569 Sum_probs=17.9
Q ss_pred HHHHHHHHHHhCCCCcchhchhhCC
Q 028055 22 DRILIVHIKKHGHPNWRALPKQAGL 46 (214)
Q Consensus 22 D~~L~~~v~~~g~~nW~~Ia~~~~~ 46 (214)
+.+|.++|..|| |..+++.+..
T Consensus 12 e~il~~Lv~~yG---W~~L~~~i~i 33 (64)
T PF09905_consen 12 ETILTELVEHYG---WEELGERINI 33 (64)
T ss_dssp HHHHHHHHHHT----HHHHHHHTTS
T ss_pred HHHHHHHHHHhC---HHHHHhhccc
Confidence 578889999998 9999988765
No 175
>PRK06930 positive control sigma-like factor; Validated
Probab=29.11 E-value=2.3e+02 Score=23.11 Aligned_cols=37 Identities=22% Similarity=0.275 Sum_probs=27.5
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 77 TIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 77 ~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.++.++...|-.-.+||..| |-|...|+.+.+..+++
T Consensus 121 ~V~~L~~~eg~s~~EIA~~l-giS~~tVk~~l~Ra~~k 157 (170)
T PRK06930 121 EVYLMHRGYGLSYSEIADYL-NIKKSTVQSMIERAEKK 157 (170)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 33444445677889999999 99999999987666544
No 176
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=28.85 E-value=2.1e+02 Score=22.68 Aligned_cols=29 Identities=28% Similarity=0.164 Sum_probs=22.8
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..+ |-|...++++.+..+++
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 455678999999 99999999987666543
No 177
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=28.59 E-value=1.3e+02 Score=24.34 Aligned_cols=29 Identities=14% Similarity=0.036 Sum_probs=23.4
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..| |-+...|+++.+..+++
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 356689999999 99999999998666544
No 178
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=28.51 E-value=1.9e+02 Score=24.69 Aligned_cols=43 Identities=21% Similarity=0.316 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 69 NFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 69 ~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
..|+-|-+.|.-+.+ |....+||+.| +-+...|+++-..+++|
T Consensus 133 ~LSpRErEVLrLLAq--GkTnKEIAe~L-~IS~rTVkth~srImkK 175 (198)
T PRK15201 133 HFSVTERHLLKLIAS--GYHLSETAALL-SLSEEQTKSLRRSIMRK 175 (198)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 478877777666555 77788999999 99999999988777655
No 179
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=28.34 E-value=43 Score=33.07 Aligned_cols=48 Identities=15% Similarity=0.352 Sum_probs=42.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhh
Q 028055 10 MGLKKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWIN 59 (214)
Q Consensus 10 ~~l~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~ 59 (214)
.....++||.+|-++...+....| .+...|+...++ |..+|++..+..
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 456778999999999999999999 899999999988 999999887744
No 180
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=28.32 E-value=1.3e+02 Score=24.68 Aligned_cols=28 Identities=18% Similarity=0.093 Sum_probs=22.6
Q ss_pred CCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 86 G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
|-.-.+||..+ |.+...|+++.+..+++
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 55678999999 99999999987665544
No 181
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=28.19 E-value=76 Score=25.00 Aligned_cols=29 Identities=24% Similarity=0.374 Sum_probs=23.0
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
+|-...+||..| |-+...|+.+.+..+++
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 466789999999 88999999887655443
No 182
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=28.04 E-value=1e+02 Score=23.50 Aligned_cols=55 Identities=16% Similarity=0.221 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhcccCCCCCCCCCHHHHHHH
Q 028055 21 EDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFSKEEEETI 78 (214)
Q Consensus 21 ED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p~i~kg~WT~EED~~L 78 (214)
+.+.|.++|..++...-.+||+.++- ..+..-+....|.-..++..|..+++..-
T Consensus 58 d~~~L~~~v~~~pd~tl~Ela~~l~V---s~~ti~~~Lkrlg~t~KK~~~~~~~~~~~ 112 (119)
T PF01710_consen 58 DRDELKALVEENPDATLRELAERLGV---SPSTIWRALKRLGITRKKKTLHSEKDREK 112 (119)
T ss_pred cHHHHHHHHHHCCCcCHHHHHHHcCC---CHHHHHHHHHHcCchhccCcccchhHHHH
Confidence 45679999999998888899988864 55666677777777788888877666543
No 183
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=27.92 E-value=98 Score=27.50 Aligned_cols=29 Identities=14% Similarity=0.127 Sum_probs=23.3
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..| |.|...||+|.+.-.++
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 355689999999 99999999997665543
No 184
>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=27.83 E-value=1.2e+02 Score=26.35 Aligned_cols=29 Identities=10% Similarity=0.298 Sum_probs=23.5
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
+|-.-.+||..| |.|...|+.+.+...++
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 89999999987655443
No 185
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=27.78 E-value=1.7e+02 Score=24.63 Aligned_cols=33 Identities=15% Similarity=0.225 Sum_probs=25.4
Q ss_pred HHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 81 LHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 81 l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
++...|-...+||..+ |-|...|+.+.+..+++
T Consensus 195 l~~~~g~s~~EIA~~l-gis~~tV~~~~~ra~~~ 227 (236)
T PRK06986 195 LYYQEELNLKEIGAVL-GVSESRVSQIHSQAIKR 227 (236)
T ss_pred hHhccCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3334466789999999 99999999987766654
No 186
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=27.73 E-value=1.9e+02 Score=22.35 Aligned_cols=44 Identities=20% Similarity=0.265 Sum_probs=33.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 68 GNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 68 g~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
...|..|-+.|.-+.. |-.-.+||..+ +-+...++.+.+++.+|
T Consensus 136 ~~Lt~~E~~il~~l~~--g~~~~~Ia~~l-~~s~~tv~~~~~~l~~K 179 (196)
T PRK10360 136 DPLTKRERQVAEKLAQ--GMAVKEIAAEL-GLSPKTVHVHRANLMEK 179 (196)
T ss_pred cCCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 4688888877766665 45678999999 78999999887776654
No 187
>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=27.71 E-value=1.5e+02 Score=23.47 Aligned_cols=29 Identities=28% Similarity=0.173 Sum_probs=22.8
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.=.+||..| |-|...++++.+..+++
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 99999999987665533
No 188
>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.67 E-value=85 Score=25.59 Aligned_cols=42 Identities=31% Similarity=0.351 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHH
Q 028055 69 NFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTH 111 (214)
Q Consensus 69 ~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~ 111 (214)
+||.|--++|.+|..+ |-.=++||+.|.|=+.+.+--+-|.+
T Consensus 2 nWtdERve~LkKLWse-GLSASQIAaQLGGVsRnAVIGKVHRL 43 (169)
T COG5352 2 NWTDERVETLKKLWSE-GLSASQIAAQLGGVSRNAVIGKVHRL 43 (169)
T ss_pred CchHHHHHHHHHHHHc-ccCHHHHHHHhcCcchhhhheeeeec
Confidence 6999999999988765 55568999999999888876554433
No 189
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=27.55 E-value=2e+02 Score=23.23 Aligned_cols=29 Identities=28% Similarity=0.357 Sum_probs=23.1
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..+ |-+...|+++.+...++
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 456789999999 99999999987665443
No 190
>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=27.35 E-value=1.1e+02 Score=20.88 Aligned_cols=24 Identities=38% Similarity=0.789 Sum_probs=18.2
Q ss_pred HHhcCCcHHHHHhhCCCCCHHHHHH
Q 028055 82 HDMLGNRWSAIAGRLPGRTDNEIKN 106 (214)
Q Consensus 82 ~~~~G~kW~~IA~~lpgRt~~~~kn 106 (214)
....|+.|..+|..| |=+..+|..
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 466789999999999 777776654
No 191
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=26.93 E-value=1.9e+02 Score=24.11 Aligned_cols=28 Identities=18% Similarity=0.225 Sum_probs=22.8
Q ss_pred CCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 86 G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
|-...+||..+ |-+...|+++-+..+++
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 66789999999 99999999887655543
No 192
>PRK09483 response regulator; Provisional
Probab=26.36 E-value=1.2e+02 Score=23.93 Aligned_cols=44 Identities=14% Similarity=0.260 Sum_probs=33.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 68 GNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 68 g~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
...|+-|-+.|.-++ .|..=.+||..+ +-+...|+++-+++++|
T Consensus 147 ~~Lt~rE~~vl~~~~--~G~~~~~Ia~~l-~is~~TV~~~~~~i~~K 190 (217)
T PRK09483 147 ASLSERELQIMLMIT--KGQKVNEISEQL-NLSPKTVNSYRYRMFSK 190 (217)
T ss_pred cccCHHHHHHHHHHH--CCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 358898888875444 455556999999 78999999987777665
No 193
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=26.33 E-value=1.8e+02 Score=21.50 Aligned_cols=34 Identities=12% Similarity=0.035 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHH
Q 028055 73 EEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNV 107 (214)
Q Consensus 73 EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knr 107 (214)
-|...|..+...+|++.++.|+.+ |=+...++.+
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 467788899999999999999999 7776665554
No 194
>PLN03162 golden-2 like transcription factor; Provisional
Probab=25.73 E-value=5.8e+02 Score=24.21 Aligned_cols=43 Identities=16% Similarity=0.154 Sum_probs=34.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCc---HHHHHhhC--CCCCHHHHHHHHHH
Q 028055 68 GNFSKEEEETIINLHDMLGNR---WSAIAGRL--PGRTDNEIKNVWHT 110 (214)
Q Consensus 68 g~WT~EED~~Ll~l~~~~G~k---W~~IA~~l--pgRt~~~~knrw~~ 110 (214)
-.||.|=.++.++++.++|.. =+.|-+.| +|=|..+|+.+.+.
T Consensus 238 LrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQK 285 (526)
T PLN03162 238 VDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQK 285 (526)
T ss_pred ccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHH
Confidence 469999999999999999932 35666654 88999999988543
No 195
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=25.72 E-value=90 Score=24.54 Aligned_cols=28 Identities=14% Similarity=0.003 Sum_probs=22.9
Q ss_pred CCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 86 G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
|-.-.+||..| |-|...|+++.+...++
T Consensus 136 g~s~~eIA~~l-g~s~~tv~~~l~Rar~~ 163 (175)
T PRK12518 136 DLPQKEIAEIL-NIPVGTVKSRLFYARRQ 163 (175)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 44679999999 99999999998766544
No 196
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=25.67 E-value=2.4e+02 Score=22.14 Aligned_cols=29 Identities=10% Similarity=0.015 Sum_probs=22.0
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|..-.+||..| |.+...|+.+.+...++
T Consensus 134 ~~~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 162 (173)
T PRK12522 134 EQYSYKEMSEIL-NIPIGTVKYRLNYAKKQ 162 (173)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 355678999999 99999999887655433
No 197
>smart00351 PAX Paired Box domain.
Probab=25.61 E-value=2.7e+02 Score=21.34 Aligned_cols=73 Identities=15% Similarity=0.173 Sum_probs=43.6
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCcchhchhhCCCC-Cccccchhhhh--cccCCC----CCCCCCHHHHHHHHHHHHhc
Q 028055 13 KKGPWTPEEDRILIVHIKKHGHPNWRALPKQAGLLR-CGKSCRLRWIN--YLRPDI----KRGNFSKEEEETIINLHDML 85 (214)
Q Consensus 13 ~kg~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~~~R-t~~qcr~Rw~~--~L~p~i----~kg~WT~EED~~Ll~l~~~~ 85 (214)
...+.+.++-++++.++. -| ..-.+||+.++..| |...+..||.. .+.|.- ....-+.+.+..|++++.+.
T Consensus 14 ~~~~~s~~~R~riv~~~~-~G-~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~ 91 (125)
T smart00351 14 NGRPLPDEERQRIVELAQ-NG-VRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQEN 91 (125)
T ss_pred CCCCCCHHHHHHHHHHHH-cC-CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHC
Confidence 445688988888888876 45 56789999998632 22223344432 244421 11224556666777777665
Q ss_pred CC
Q 028055 86 GN 87 (214)
Q Consensus 86 G~ 87 (214)
+.
T Consensus 92 p~ 93 (125)
T smart00351 92 PG 93 (125)
T ss_pred CC
Confidence 53
No 198
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=25.48 E-value=53 Score=24.01 Aligned_cols=43 Identities=19% Similarity=0.211 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhcccCC
Q 028055 20 EEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPD 64 (214)
Q Consensus 20 EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p~ 64 (214)
+.|.+++.+++..+...+..||+.++ -+...|+.|..+...-+
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~--~s~~tv~~~l~~L~~~g 45 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVG--LSPSTVHNRVKRLEEEG 45 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCC
Confidence 56888889999998889999999997 67777888776654433
No 199
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=25.47 E-value=2.3e+02 Score=22.78 Aligned_cols=29 Identities=21% Similarity=0.124 Sum_probs=22.5
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..| |-|...|+.+-+...++
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 456689999999 99999999887655433
No 200
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=25.41 E-value=1.5e+02 Score=22.98 Aligned_cols=29 Identities=24% Similarity=0.236 Sum_probs=22.2
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-...+||..| |=|...|+.+.+...++
T Consensus 127 ~~~s~~eIA~~l-gis~~tv~~~l~Rar~~ 155 (161)
T PRK12541 127 YGFSYKEIAEMT-GLSLAKVKIELHRGRKE 155 (161)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 345679999999 99999999887655443
No 201
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=25.38 E-value=1.8e+02 Score=24.76 Aligned_cols=38 Identities=18% Similarity=0.166 Sum_probs=27.2
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 76 ETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 76 ~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
..++.+....|-...+||..+ |-|...|+.+.+..+++
T Consensus 207 r~vl~l~~~~~~s~~EIA~~l-gis~~tV~~~~~ra~~~ 244 (251)
T PRK07670 207 QLVISLFYKEELTLTEIGQVL-NLSTSRISQIHSKALFK 244 (251)
T ss_pred HHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 333344334466789999999 99999999987766544
No 202
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=25.27 E-value=2.5e+02 Score=21.82 Aligned_cols=29 Identities=17% Similarity=0.035 Sum_probs=22.2
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..+ |-+...|+.+-+...++
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 455678999999 88999999887655443
No 203
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=25.13 E-value=1.8e+02 Score=22.87 Aligned_cols=29 Identities=24% Similarity=0.257 Sum_probs=22.6
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-...+||..| |-+...|+++...-++.
T Consensus 133 eg~s~~EIA~~l-~is~~tV~~~l~ra~~~ 161 (168)
T PRK12525 133 EGLTYVEIGERL-GVSLSRIHQYMVEAFKC 161 (168)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355789999999 99999999887655443
No 204
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=24.71 E-value=1.7e+02 Score=23.34 Aligned_cols=29 Identities=21% Similarity=0.224 Sum_probs=22.8
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-...+||..| |=+...|+++-+...++
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 466789999999 88999999887665543
No 205
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=24.68 E-value=1.5e+02 Score=24.23 Aligned_cols=37 Identities=14% Similarity=0.025 Sum_probs=26.3
Q ss_pred CCcHHHHHhhCCCCCHHHHHHHHHHHhHHHHHHHHHhhh
Q 028055 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKKKAAAVLKQNQ 124 (214)
Q Consensus 86 G~kW~~IA~~lpgRt~~~~knrw~~~lkk~~~~~~~~~~ 124 (214)
|-.-.+||..| |.+.+.|+++.+..+++ +++...+.+
T Consensus 149 g~s~~EIAe~l-gis~~tV~~~l~Rar~~-Lr~~l~~~~ 185 (196)
T PRK12535 149 GYTYEEAAKIA-DVRVGTIRSRVARARAD-LIAATATGQ 185 (196)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHH-HHHHhcccc
Confidence 45579999999 99999999998766543 433334433
No 206
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.42 E-value=95 Score=19.34 Aligned_cols=29 Identities=31% Similarity=0.326 Sum_probs=20.0
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCCHHHHHHH
Q 028055 77 TIINLHDMLGNRWSAIAGRLPGRTDNEIKNV 107 (214)
Q Consensus 77 ~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knr 107 (214)
.++.++.. |-...+||+.+ |-+...|.+-
T Consensus 9 ~ii~l~~~-G~s~~~ia~~l-gvs~~Tv~~w 37 (50)
T PF13384_consen 9 QIIRLLRE-GWSIREIAKRL-GVSRSTVYRW 37 (50)
T ss_dssp -HHHHHHH-T--HHHHHHHH-TS-HHHHHHH
T ss_pred HHHHHHHC-CCCHHHHHHHH-CcCHHHHHHH
Confidence 46666666 98999999999 8888877664
No 207
>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=24.36 E-value=1.6e+02 Score=24.40 Aligned_cols=30 Identities=30% Similarity=0.365 Sum_probs=23.3
Q ss_pred hcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 84 MLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 84 ~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
..|..-.+||+.+ |-+...|+.+.+..+++
T Consensus 192 ~~~~s~~eIA~~l-gis~~~v~~~~~ra~~~ 221 (227)
T TIGR02980 192 FEDKTQSEIAERL-GISQMHVSRLLRRALKK 221 (227)
T ss_pred hcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3466789999999 89999998877665544
No 208
>PRK15328 invasion protein IagB; Provisional
Probab=23.93 E-value=1.9e+02 Score=23.66 Aligned_cols=43 Identities=12% Similarity=0.366 Sum_probs=30.5
Q ss_pred HHHHHHHhcCCcHHHHHhhCCC--CCHHHHHHHHHHHhHHHHHHH
Q 028055 77 TIINLHDMLGNRWSAIAGRLPG--RTDNEIKNVWHTHLKKKAAAV 119 (214)
Q Consensus 77 ~Ll~l~~~~G~kW~~IA~~lpg--Rt~~~~knrw~~~lkk~~~~~ 119 (214)
.|..++..||+.|..|+..=.| +.....+.+|-..+.+...+.
T Consensus 98 ~L~~~~~~~g~~~~alaaYNaG~~~~~~~~~~~Y~~kV~~~y~~l 142 (160)
T PRK15328 98 ILSDMMKIYGYSWEAVGAYNAGTSPKRSDIRKRYAKKIWENYRKL 142 (160)
T ss_pred HHHHHHHHcCChHHhhhhccCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 4667888999999999987533 444566777876666665443
No 209
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=23.82 E-value=3.3e+02 Score=21.95 Aligned_cols=28 Identities=18% Similarity=0.095 Sum_probs=22.0
Q ss_pred CCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 86 G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
|-.-.+||..+ |-+...|+.+-+...++
T Consensus 144 g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 171 (188)
T PRK12517 144 GFSGEEIAEIL-DLNKNTVMTRLFRARNQ 171 (188)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 44578999999 99999999987665544
No 210
>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=23.31 E-value=58 Score=22.86 Aligned_cols=18 Identities=22% Similarity=0.503 Sum_probs=15.1
Q ss_pred HHHHHHHhcCCcHHHHHh
Q 028055 77 TIINLHDMLGNRWSAIAG 94 (214)
Q Consensus 77 ~Ll~l~~~~G~kW~~IA~ 94 (214)
.|.+|.+.||++|.-|-.
T Consensus 31 vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 31 VLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHcCCchhhhc
Confidence 577888999999999865
No 211
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=23.21 E-value=48 Score=25.68 Aligned_cols=43 Identities=12% Similarity=0.121 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHhCCCCcchhchhhCCCCCccccchhhhhcccCC
Q 028055 20 EEDRILIVHIKKHGHPNWRALPKQAGLLRCGKSCRLRWINYLRPD 64 (214)
Q Consensus 20 EED~~L~~~v~~~g~~nW~~Ia~~~~~~Rt~~qcr~Rw~~~L~p~ 64 (214)
+-|.+++++.+..+...+..||+.++ -+...|+.|-.+...-+
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~lg--lS~~~v~~Ri~~L~~~G 50 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERVG--LSPSTVLRRIKRLEEEG 50 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCC
Confidence 45888999999999889999999998 67778888876655444
No 212
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=23.04 E-value=1.3e+02 Score=24.18 Aligned_cols=28 Identities=21% Similarity=0.221 Sum_probs=22.4
Q ss_pred CCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 86 G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
|-...+||..| |-+...|+++.+..+++
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 55689999999 89999999887655543
No 213
>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=23.01 E-value=1.4e+02 Score=24.10 Aligned_cols=28 Identities=21% Similarity=0.274 Sum_probs=23.0
Q ss_pred CCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 86 G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
|-.-.+||..| |-|...|++|.+..+++
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 55689999999 99999999997766543
No 214
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=22.95 E-value=1.6e+02 Score=24.72 Aligned_cols=29 Identities=7% Similarity=-0.009 Sum_probs=22.9
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..| |-+...|+.+.+..+++
T Consensus 149 eg~s~~EIAe~L-giS~~tVk~~L~RAr~~ 177 (216)
T PRK12533 149 EDMSYREIAAIA-DVPVGTVMSRLARARRR 177 (216)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355678999999 99999999987765543
No 215
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=22.88 E-value=2.9e+02 Score=23.74 Aligned_cols=29 Identities=17% Similarity=0.186 Sum_probs=22.4
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..+ |.|...|+.+.+..+++
T Consensus 227 ~~~s~~eIA~~l-gis~~tV~~~~~ra~~~ 255 (268)
T PRK06288 227 EDLTLKEIGKVL-GVTESRISQLHTKAVLQ 255 (268)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 355678999999 99999998877655544
No 216
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.75 E-value=2.1e+02 Score=22.70 Aligned_cols=38 Identities=29% Similarity=0.530 Sum_probs=23.8
Q ss_pred HHHHHHHHHHhc--CCcHHHHHhhCCCCCHHHHHHHHHHHhH
Q 028055 74 EEETIINLHDML--GNRWSAIAGRLPGRTDNEIKNVWHTHLK 113 (214)
Q Consensus 74 ED~~Ll~l~~~~--G~kW~~IA~~lpgRt~~~~knrw~~~lk 113 (214)
|++.++++.-.- |..|..||..+ +-+..+|+. |+.-+|
T Consensus 85 e~k~Ii~lry~~r~~~TW~~IA~~l-~i~erta~r-~~~~fK 124 (130)
T PF05263_consen 85 EEKRIIKLRYDRRSRRTWYQIAQKL-HISERTARR-WRDRFK 124 (130)
T ss_pred HHHHHHHHHHcccccchHHHHHHHh-CccHHHHHH-HHHHHH
Confidence 466666665433 36799999998 566666654 333333
No 217
>PRK02866 cyanate hydratase; Validated
Probab=21.70 E-value=1.7e+02 Score=23.83 Aligned_cols=32 Identities=22% Similarity=0.383 Sum_probs=27.0
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHH
Q 028055 76 ETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVW 108 (214)
Q Consensus 76 ~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw 108 (214)
+.|+++-.+-|-.|..||+.+ |++..-+-.-.
T Consensus 8 e~Ll~AK~~kGLTw~~IA~~i-G~S~v~vaaa~ 39 (147)
T PRK02866 8 EKILAAKKEKGLTWADIAEAI-GLSEVWVTAAL 39 (147)
T ss_pred HHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 468888888999999999999 99988776654
No 218
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=21.69 E-value=1.9e+02 Score=30.73 Aligned_cols=40 Identities=23% Similarity=0.432 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHHhcC-CcHHHHHhhCCCCCHHHHHHHH
Q 028055 69 NFSKEEEETIINLHDMLG-NRWSAIAGRLPGRTDNEIKNVW 108 (214)
Q Consensus 69 ~WT~EED~~Ll~l~~~~G-~kW~~IA~~lpgRt~~~~knrw 108 (214)
.||.-+=...+.+..+|| ..-..||..|.|+|..+|+...
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~ 866 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYA 866 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHH
Confidence 577777777888888899 5689999999999999998653
No 219
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=21.34 E-value=1.3e+02 Score=24.60 Aligned_cols=31 Identities=16% Similarity=0.289 Sum_probs=25.4
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHH
Q 028055 76 ETIINLHDMLGNRWSAIAGRLPGRTDNEIKNV 107 (214)
Q Consensus 76 ~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knr 107 (214)
+.|+++-.+-|-.|.+||+.+ |++..-+-.-
T Consensus 11 ~~Ll~AK~~KGLTwe~IAe~i-G~sevwvaaa 41 (150)
T TIGR00673 11 DALLESKKKKGLTFADIADGL-GLAEVFVAAA 41 (150)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHH
Confidence 567888888999999999999 8998755443
No 220
>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=21.27 E-value=87 Score=25.61 Aligned_cols=33 Identities=24% Similarity=0.312 Sum_probs=25.5
Q ss_pred CCCHHHHHHHHHHHHHhCCCCcchhchhhC-CCCCc
Q 028055 16 PWTPEEDRILIVHIKKHGHPNWRALPKQAG-LLRCG 50 (214)
Q Consensus 16 ~WT~EED~~L~~~v~~~g~~nW~~Ia~~~~-~~Rt~ 50 (214)
.||.|+.++|.++... | ..=.+||..++ ..|++
T Consensus 2 ~Wtde~~~~L~~lw~~-G-~SasqIA~~lg~vsRnA 35 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-G-LSASQIARQLGGVSRNA 35 (162)
T ss_pred CCCHHHHHHHHHHHHc-C-CCHHHHHHHhCCcchhh
Confidence 5999999999988743 4 45678999999 34555
No 221
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=21.25 E-value=1.7e+02 Score=23.70 Aligned_cols=44 Identities=23% Similarity=0.262 Sum_probs=33.9
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 68 GNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 68 g~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
...|+-|-+.|.-+.+ |..=.+||+.+ +-|...|+++-.++++|
T Consensus 149 ~~Lt~rE~evl~~~~~--G~s~~eIA~~l-~iS~~TV~~h~~~i~~K 192 (216)
T PRK10840 149 KRLSPKESEVLRLFAE--GFLVTEIAKKL-NRSIKTISSQKKSAMMK 192 (216)
T ss_pred ccCCHHHHHHHHHHHC--CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3588888776665553 55557999999 99999999988777765
No 222
>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=21.15 E-value=2.2e+02 Score=23.66 Aligned_cols=29 Identities=24% Similarity=0.292 Sum_probs=22.2
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.|-.-.+||..+ |-+...|+.+.+..+++
T Consensus 190 ~~~s~~eIA~~l-gis~~tV~~~~~ra~~~ 218 (224)
T TIGR02479 190 EELNLKEIGEVL-GLTESRVSQIHSQALKK 218 (224)
T ss_pred CCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 455678999998 88998898887666544
No 223
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=20.50 E-value=1.8e+02 Score=24.29 Aligned_cols=44 Identities=23% Similarity=0.221 Sum_probs=35.2
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 68 GNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 68 g~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
...|+-|-+.|.-+.+ |..=.+||..| +.|...|+.+-.++++|
T Consensus 133 ~~LT~RE~eVL~ll~~--G~snkeIA~~L-~iS~~TV~~h~~~I~~K 176 (207)
T PRK11475 133 RMLSPTEREILRFMSR--GYSMPQIAEQL-ERNIKTIRAHKFNVMSK 176 (207)
T ss_pred CCCCHHHHHHHHHHHC--CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3588888888777776 44446999999 99999999988777765
No 224
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=20.46 E-value=2.9e+02 Score=21.94 Aligned_cols=28 Identities=29% Similarity=0.319 Sum_probs=20.8
Q ss_pred CCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 86 GNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 86 G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
|-.-.+||..+ |-+...|++|-+..+++
T Consensus 147 g~s~~eIA~~l-gis~~tV~~~l~ra~~~ 174 (184)
T PRK12539 147 GLSVAEAATRS-GMSESAVKVSVHRGLKA 174 (184)
T ss_pred CCcHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 45578888888 77888888887655443
No 225
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=20.45 E-value=2.6e+02 Score=21.57 Aligned_cols=27 Identities=22% Similarity=0.246 Sum_probs=19.3
Q ss_pred cCCcHHHHHhhCCCCCHHHHHHHHHHHh
Q 028055 85 LGNRWSAIAGRLPGRTDNEIKNVWHTHL 112 (214)
Q Consensus 85 ~G~kW~~IA~~lpgRt~~~~knrw~~~l 112 (214)
.|-.=.+||+.+ |-+...|+.+-...+
T Consensus 124 ~~~s~~EIA~~l-gis~~tV~~~l~ra~ 150 (163)
T PRK07037 124 HGETQKDIAREL-GVSPTLVNFMIRDAL 150 (163)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 355678888888 888888887744333
No 226
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=20.10 E-value=3.2e+02 Score=23.65 Aligned_cols=44 Identities=25% Similarity=0.115 Sum_probs=34.7
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhCCCCCHHHHHHHHHHHhHH
Q 028055 68 GNFSKEEEETIINLHDMLGNRWSAIAGRLPGRTDNEIKNVWHTHLKK 114 (214)
Q Consensus 68 g~WT~EED~~Ll~l~~~~G~kW~~IA~~lpgRt~~~~knrw~~~lkk 114 (214)
.+-|+-|-+.|.-+.+ |-.-.+||+.| +-+...|+++-..+++|
T Consensus 142 ~~LS~RE~eVL~Lia~--G~SnkEIA~~L-~IS~~TVk~hvs~I~~K 185 (217)
T PRK13719 142 NKVTKYQNDVFILYSF--GFSHEYIAQLL-NITVGSSKNKISEILKF 185 (217)
T ss_pred CCCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 4678888777766555 77778999999 99999999987666654
Done!