Query 024492
Match_columns 267
No_of_seqs 246 out of 1455
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 05:00:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024492.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024492hhsearch_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 5E-39 1.1E-43 288.8 12.9 119 3-121 14-132 (249)
2 PLN03091 hypothetical protein; 100.0 4.7E-39 1E-43 307.5 11.4 120 1-120 1-120 (459)
3 KOG0048 Transcription factor, 100.0 1.3E-37 2.8E-42 280.5 11.1 112 9-120 4-115 (238)
4 KOG0049 Transcription factor, 99.8 1.7E-19 3.7E-24 178.9 6.6 106 1-107 347-453 (939)
5 KOG0049 Transcription factor, 99.7 1.1E-16 2.4E-21 159.1 7.2 107 12-119 303-413 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.6 8.9E-17 1.9E-21 115.2 3.9 60 17-78 1-60 (60)
7 COG5147 REB1 Myb superfamily p 99.6 5E-16 1.1E-20 153.1 6.5 108 9-117 15-122 (512)
8 KOG0050 mRNA splicing protein 99.6 7.5E-16 1.6E-20 150.1 3.0 106 12-119 5-110 (617)
9 PF00249 Myb_DNA-binding: Myb- 99.4 1.2E-13 2.7E-18 95.2 5.4 46 67-112 1-48 (48)
10 KOG0051 RNA polymerase I termi 99.4 1.1E-13 2.4E-18 138.0 6.5 107 13-122 383-517 (607)
11 PF00249 Myb_DNA-binding: Myb- 99.4 9.5E-14 2.1E-18 95.8 1.1 48 14-61 1-48 (48)
12 PF13921 Myb_DNA-bind_6: Myb-l 99.3 1.3E-12 2.8E-17 93.5 4.4 47 70-116 1-47 (60)
13 PLN03212 Transcription repress 99.3 3.2E-12 6.9E-17 115.8 5.5 68 44-119 10-79 (249)
14 smart00717 SANT SANT SWI3, AD 99.3 7.3E-12 1.6E-16 83.7 5.7 47 67-113 1-48 (49)
15 KOG0048 Transcription factor, 99.2 5E-12 1.1E-16 114.3 3.8 59 63-121 5-65 (238)
16 cd00167 SANT 'SWI3, ADA2, N-Co 99.2 7.1E-11 1.5E-15 77.9 5.7 44 69-112 1-45 (45)
17 PLN03091 hypothetical protein; 99.1 4.9E-11 1.1E-15 115.5 4.7 57 63-119 10-68 (459)
18 smart00717 SANT SANT SWI3, AD 99.0 9.4E-11 2E-15 78.3 2.5 48 14-62 1-48 (49)
19 cd00167 SANT 'SWI3, ADA2, N-Co 98.9 7.3E-10 1.6E-14 72.9 2.1 45 16-61 1-45 (45)
20 KOG0051 RNA polymerase I termi 98.9 2.2E-09 4.7E-14 107.7 5.9 102 13-116 307-432 (607)
21 COG5147 REB1 Myb superfamily p 98.3 6E-08 1.3E-12 96.4 -2.0 97 13-112 290-396 (512)
22 KOG0050 mRNA splicing protein 97.7 2.7E-05 5.9E-10 77.1 4.1 55 65-119 5-60 (617)
23 KOG0457 Histone acetyltransfer 97.7 1.9E-05 4E-10 76.9 2.2 49 12-61 70-118 (438)
24 TIGR01557 myb_SHAQKYF myb-like 97.6 3.6E-05 7.8E-10 55.5 2.6 49 13-61 2-54 (57)
25 KOG0457 Histone acetyltransfer 97.6 0.00011 2.3E-09 71.6 6.0 49 64-112 69-118 (438)
26 PF13325 MCRS_N: N-terminal re 97.6 0.00021 4.5E-09 63.6 7.1 102 16-119 1-133 (199)
27 TIGR01557 myb_SHAQKYF myb-like 97.5 0.00025 5.5E-09 51.1 5.6 46 67-112 3-54 (57)
28 PF13837 Myb_DNA-bind_4: Myb/S 97.3 0.00027 5.8E-09 53.6 3.4 48 68-115 2-67 (90)
29 TIGR02894 DNA_bind_RsfA transc 97.2 0.0005 1.1E-08 59.2 4.6 53 66-119 3-62 (161)
30 PF08914 Myb_DNA-bind_2: Rap1 97.0 0.0011 2.3E-08 49.1 4.6 51 67-117 2-62 (65)
31 KOG1279 Chromatin remodeling f 97.0 0.00097 2.1E-08 66.8 5.3 46 66-111 252-297 (506)
32 COG5259 RSC8 RSC chromatin rem 96.9 0.0012 2.5E-08 65.2 4.5 44 68-111 280-323 (531)
33 PF13873 Myb_DNA-bind_5: Myb/S 96.7 0.0055 1.2E-07 45.7 6.3 49 67-115 2-72 (78)
34 COG5259 RSC8 RSC chromatin rem 96.6 0.00087 1.9E-08 66.0 1.4 46 13-60 278-323 (531)
35 KOG1279 Chromatin remodeling f 96.5 0.0012 2.6E-08 66.2 1.9 46 13-60 252-297 (506)
36 PRK13923 putative spore coat p 96.4 0.0037 7.9E-08 54.5 4.2 52 66-118 4-62 (170)
37 PF08914 Myb_DNA-bind_2: Rap1 96.3 0.0011 2.5E-08 48.9 0.3 52 14-65 2-61 (65)
38 TIGR02894 DNA_bind_RsfA transc 96.1 0.0014 3.1E-08 56.4 -0.2 50 12-63 2-57 (161)
39 PLN03142 Probable chromatin-re 95.9 0.053 1.1E-06 58.8 10.5 103 15-118 825-990 (1033)
40 COG5114 Histone acetyltransfer 95.5 0.016 3.5E-07 55.1 4.3 47 67-113 63-110 (432)
41 COG5114 Histone acetyltransfer 95.2 0.0065 1.4E-07 57.7 0.7 48 14-62 63-110 (432)
42 PF13837 Myb_DNA-bind_4: Myb/S 94.9 0.0047 1E-07 46.8 -1.1 48 14-61 1-64 (90)
43 KOG2656 DNA methyltransferase 94.7 0.027 5.9E-07 54.7 3.3 86 36-122 75-191 (445)
44 PRK13923 putative spore coat p 94.5 0.0096 2.1E-07 51.9 -0.2 50 11-62 2-57 (170)
45 PF13873 Myb_DNA-bind_5: Myb/S 94.0 0.018 3.9E-07 42.9 0.5 49 13-61 1-69 (78)
46 PF12776 Myb_DNA-bind_3: Myb/S 93.8 0.16 3.4E-06 38.8 5.5 46 69-114 1-64 (96)
47 KOG4282 Transcription factor G 93.7 0.15 3.3E-06 48.3 6.2 54 67-120 54-121 (345)
48 PF09111 SLIDE: SLIDE; InterP 93.1 0.24 5.1E-06 40.8 5.6 52 64-115 46-113 (118)
49 COG5118 BDP1 Transcription ini 91.4 0.31 6.6E-06 47.6 4.9 47 68-114 366-412 (507)
50 PF08281 Sigma70_r4_2: Sigma-7 88.3 1.5 3.3E-05 29.9 5.3 41 72-113 12-52 (54)
51 smart00595 MADF subfamily of S 87.1 1.2 2.6E-05 33.5 4.5 25 89-114 30-54 (89)
52 KOG1194 Predicted DNA-binding 83.3 2.9 6.2E-05 41.8 6.2 49 67-115 187-235 (534)
53 PF09111 SLIDE: SLIDE; InterP 82.3 1 2.3E-05 37.0 2.3 34 11-44 46-82 (118)
54 COG5118 BDP1 Transcription ini 80.2 1.2 2.6E-05 43.5 2.4 45 14-60 365-409 (507)
55 KOG4282 Transcription factor G 79.1 0.95 2E-05 42.9 1.3 48 14-61 54-113 (345)
56 PF10545 MADF_DNA_bdg: Alcohol 77.9 3.4 7.5E-05 30.1 3.8 26 89-114 29-55 (85)
57 PF13404 HTH_AsnC-type: AsnC-t 76.4 6 0.00013 26.5 4.2 38 73-111 3-41 (42)
58 PF04545 Sigma70_r4: Sigma-70, 73.9 9.7 0.00021 25.6 4.9 41 73-114 7-47 (50)
59 PRK11179 DNA-binding transcrip 73.3 7.4 0.00016 32.6 5.0 45 72-117 8-53 (153)
60 PF11626 Rap1_C: TRF2-interact 73.0 3.6 7.8E-05 31.6 2.8 23 12-34 45-75 (87)
61 PF07750 GcrA: GcrA cell cycle 71.6 5.5 0.00012 34.3 3.9 41 69-110 2-42 (162)
62 TIGR02985 Sig70_bacteroi1 RNA 68.9 12 0.00026 30.1 5.2 38 76-114 119-156 (161)
63 PRK11169 leucine-responsive tr 68.3 9.7 0.00021 32.3 4.7 45 72-117 13-58 (164)
64 PF11035 SnAPC_2_like: Small n 66.0 24 0.00052 33.9 7.2 49 67-116 21-73 (344)
65 KOG4468 Polycomb-group transcr 65.2 10 0.00022 39.3 4.8 48 67-114 88-145 (782)
66 PF11626 Rap1_C: TRF2-interact 64.0 6.3 0.00014 30.2 2.5 17 63-79 43-59 (87)
67 KOG4167 Predicted DNA-binding 62.6 21 0.00047 37.9 6.7 57 56-112 605-664 (907)
68 KOG4167 Predicted DNA-binding 58.4 5.3 0.00011 42.2 1.5 45 13-59 618-662 (907)
69 PF12776 Myb_DNA-bind_3: Myb/S 58.0 7.6 0.00016 29.3 2.0 43 16-58 1-59 (96)
70 KOG2009 Transcription initiati 57.3 11 0.00024 38.8 3.6 45 66-110 408-452 (584)
71 cd08319 Death_RAIDD Death doma 56.3 16 0.00036 28.1 3.6 29 75-104 2-30 (83)
72 TIGR02937 sigma70-ECF RNA poly 56.0 30 0.00065 26.8 5.3 37 77-114 117-153 (158)
73 KOG2656 DNA methyltransferase 53.5 7.3 0.00016 38.4 1.5 50 11-61 127-181 (445)
74 PF01388 ARID: ARID/BRIGHT DNA 52.7 35 0.00075 25.8 4.9 38 77-114 40-90 (92)
75 cd08803 Death_ank3 Death domai 52.0 24 0.00053 27.1 3.9 31 75-106 4-34 (84)
76 PF13137 DUF3983: Protein of u 50.5 9.1 0.0002 24.9 1.1 11 247-257 23-33 (34)
77 PRK09652 RNA polymerase sigma 50.3 42 0.00092 27.4 5.5 33 81-114 139-171 (182)
78 PF07638 Sigma70_ECF: ECF sigm 50.0 42 0.00092 28.7 5.6 38 74-112 139-176 (185)
79 PF11035 SnAPC_2_like: Small n 50.0 47 0.001 32.0 6.2 86 14-113 21-127 (344)
80 smart00344 HTH_ASNC helix_turn 49.6 31 0.00068 26.5 4.3 44 73-117 3-47 (108)
81 cd06171 Sigma70_r4 Sigma70, re 49.2 53 0.0012 20.7 4.9 37 74-111 14-50 (55)
82 PF06599 DUF1139: Protein of u 49.1 9 0.0002 35.9 1.3 13 244-256 278-290 (309)
83 KOG4329 DNA-binding protein [G 49.0 32 0.00069 33.8 5.0 45 68-112 278-323 (445)
84 PRK11924 RNA polymerase sigma 48.7 37 0.0008 27.7 4.9 30 84-114 139-168 (179)
85 smart00501 BRIGHT BRIGHT, ARID 48.4 45 0.00097 25.5 5.0 38 77-114 36-86 (93)
86 PF13325 MCRS_N: N-terminal re 47.3 39 0.00084 30.3 5.0 44 69-113 1-47 (199)
87 PF13404 HTH_AsnC-type: AsnC-t 46.8 9.3 0.0002 25.5 0.8 38 20-59 3-40 (42)
88 PF02954 HTH_8: Bacterial regu 46.4 46 0.00099 21.8 4.1 34 74-108 6-39 (42)
89 PRK04217 hypothetical protein; 45.7 81 0.0018 25.6 6.2 45 68-114 41-85 (110)
90 PRK09643 RNA polymerase sigma 44.9 47 0.001 28.3 5.1 29 84-113 148-176 (192)
91 cd08317 Death_ank Death domain 44.3 26 0.00057 26.4 3.0 30 75-105 4-33 (84)
92 COG2197 CitB Response regulato 43.2 40 0.00087 29.7 4.5 44 68-114 147-190 (211)
93 PRK09413 IS2 repressor TnpA; R 42.8 46 0.001 26.8 4.4 46 13-62 9-54 (121)
94 PRK09641 RNA polymerase sigma 42.7 51 0.0011 27.4 4.9 29 85-114 151-179 (187)
95 TIGR02939 RpoE_Sigma70 RNA pol 41.2 54 0.0012 27.4 4.8 28 86-114 154-181 (190)
96 cd08804 Death_ank2 Death domai 41.2 36 0.00079 26.0 3.4 31 75-106 4-34 (84)
97 cd08318 Death_NMPP84 Death dom 40.9 38 0.00083 25.8 3.5 27 78-105 10-36 (86)
98 PRK09047 RNA polymerase factor 40.6 66 0.0014 26.0 5.1 29 85-114 121-149 (161)
99 PRK12532 RNA polymerase sigma 40.5 82 0.0018 26.7 5.9 29 84-113 150-178 (195)
100 PRK12529 RNA polymerase sigma 40.4 78 0.0017 26.6 5.7 33 83-116 140-172 (178)
101 PF04504 DUF573: Protein of un 39.9 50 0.0011 26.0 4.1 47 68-114 5-64 (98)
102 TIGR02954 Sig70_famx3 RNA poly 39.8 61 0.0013 26.7 4.9 29 85-114 134-162 (169)
103 KOG0384 Chromodomain-helicase 39.8 28 0.0006 39.1 3.4 73 13-92 1132-1205(1373)
104 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 39.5 67 0.0014 22.6 4.2 35 73-108 7-41 (50)
105 TIGR02948 SigW_bacill RNA poly 39.3 57 0.0012 27.1 4.7 28 86-114 152-179 (187)
106 PRK12523 RNA polymerase sigma 39.0 71 0.0015 26.5 5.2 35 79-114 128-162 (172)
107 cd08311 Death_p75NR Death doma 38.8 39 0.00084 25.6 3.2 33 72-106 2-34 (77)
108 KOG2009 Transcription initiati 38.6 21 0.00046 36.8 2.2 48 10-59 405-452 (584)
109 PRK12515 RNA polymerase sigma 38.4 86 0.0019 26.4 5.7 29 85-114 146-174 (189)
110 PRK09645 RNA polymerase sigma 38.1 74 0.0016 26.2 5.1 29 85-114 133-161 (173)
111 PRK12512 RNA polymerase sigma 37.5 75 0.0016 26.6 5.1 29 85-114 146-174 (184)
112 PRK09637 RNA polymerase sigma 37.2 72 0.0016 27.0 5.0 30 84-114 120-149 (181)
113 KOG4468 Polycomb-group transcr 37.1 35 0.00076 35.6 3.4 47 14-61 88-143 (782)
114 smart00005 DEATH DEATH domain, 37.1 48 0.001 24.5 3.5 29 75-104 5-34 (88)
115 PRK11179 DNA-binding transcrip 37.1 16 0.00036 30.4 1.0 45 20-66 9-53 (153)
116 PRK09642 RNA polymerase sigma 37.0 79 0.0017 25.7 5.1 29 85-114 121-149 (160)
117 TIGR02943 Sig70_famx1 RNA poly 36.8 78 0.0017 26.9 5.2 31 83-114 144-174 (188)
118 PRK11923 algU RNA polymerase s 36.2 71 0.0015 26.9 4.8 28 86-114 154-181 (193)
119 cd08777 Death_RIP1 Death Domai 36.1 44 0.00094 25.7 3.1 30 76-106 3-32 (86)
120 PRK12531 RNA polymerase sigma 35.1 86 0.0019 26.6 5.2 29 85-114 156-184 (194)
121 COG2963 Transposase and inacti 34.7 1.3E+02 0.0028 23.6 5.8 43 67-110 5-48 (116)
122 PRK09648 RNA polymerase sigma 34.5 1.1E+02 0.0024 25.7 5.7 29 85-114 154-182 (189)
123 PF09420 Nop16: Ribosome bioge 34.0 92 0.002 26.5 5.1 46 66-111 113-162 (164)
124 PRK12530 RNA polymerase sigma 33.7 91 0.002 26.5 5.1 28 85-113 149-176 (189)
125 COG1522 Lrp Transcriptional re 33.5 97 0.0021 25.1 5.1 45 72-117 7-52 (154)
126 PRK12524 RNA polymerase sigma 33.1 94 0.002 26.5 5.1 30 84-114 150-179 (196)
127 PF13936 HTH_38: Helix-turn-he 33.1 56 0.0012 21.7 2.9 36 69-106 4-39 (44)
128 PRK11169 leucine-responsive tr 32.6 16 0.00034 31.0 0.2 46 19-66 13-58 (164)
129 cd08805 Death_ank1 Death domai 32.6 58 0.0013 25.1 3.3 27 75-102 4-30 (84)
130 cd08779 Death_PIDD Death Domai 32.3 48 0.0011 25.3 2.8 26 76-102 3-28 (86)
131 PF00046 Homeobox: Homeobox do 32.0 1.6E+02 0.0035 19.8 5.5 44 66-110 3-50 (57)
132 PRK09651 RNA polymerase sigma 31.9 85 0.0018 26.1 4.6 29 85-114 134-162 (172)
133 PRK12514 RNA polymerase sigma 31.3 1.1E+02 0.0023 25.5 5.1 28 86-114 145-172 (179)
134 TIGR02952 Sig70_famx2 RNA poly 31.3 1.1E+02 0.0024 24.9 5.1 28 86-114 138-165 (170)
135 TIGR02999 Sig-70_X6 RNA polyme 30.7 1.2E+02 0.0025 25.2 5.2 29 85-114 149-177 (183)
136 PRK01905 DNA-binding protein F 30.7 1.3E+02 0.0028 22.4 4.9 35 72-107 36-70 (77)
137 PRK12527 RNA polymerase sigma 30.4 1.2E+02 0.0027 24.5 5.3 29 85-114 120-148 (159)
138 PRK13919 putative RNA polymera 30.0 1.2E+02 0.0026 25.3 5.1 28 86-114 151-178 (186)
139 PRK12528 RNA polymerase sigma 29.6 1.3E+02 0.0028 24.5 5.2 30 84-114 127-156 (161)
140 PF00196 GerE: Bacterial regul 29.6 70 0.0015 22.0 3.1 43 69-114 3-45 (58)
141 PRK06759 RNA polymerase factor 29.6 1.4E+02 0.003 23.9 5.4 28 86-114 122-149 (154)
142 TIGR02984 Sig-70_plancto1 RNA 29.6 1.4E+02 0.003 24.7 5.5 29 85-114 155-183 (189)
143 PRK09649 RNA polymerase sigma 29.5 1.3E+02 0.0028 25.5 5.3 29 85-114 145-173 (185)
144 TIGR02950 SigM_subfam RNA poly 29.5 41 0.0009 27.0 2.2 28 86-114 121-148 (154)
145 PF09420 Nop16: Ribosome bioge 29.2 35 0.00075 29.2 1.7 47 12-59 112-161 (164)
146 PRK12536 RNA polymerase sigma 29.2 1.5E+02 0.0032 24.8 5.6 30 84-114 143-172 (181)
147 PRK06811 RNA polymerase factor 28.5 1.5E+02 0.0032 25.1 5.5 28 86-114 147-174 (189)
148 PRK00118 putative DNA-binding 28.5 1.7E+02 0.0037 23.4 5.5 41 72-113 19-59 (104)
149 PRK05602 RNA polymerase sigma 28.4 1.4E+02 0.0031 24.9 5.4 29 85-114 143-171 (186)
150 PRK12516 RNA polymerase sigma 28.2 1.3E+02 0.0028 25.7 5.1 33 81-114 127-159 (187)
151 PRK12520 RNA polymerase sigma 28.1 1.3E+02 0.0028 25.3 5.1 29 85-114 146-174 (191)
152 TIGR02983 SigE-fam_strep RNA p 27.7 1.3E+02 0.0028 24.4 4.9 38 76-114 116-153 (162)
153 PRK12547 RNA polymerase sigma 27.6 1.5E+02 0.0032 24.4 5.2 30 84-114 126-155 (164)
154 PRK09647 RNA polymerase sigma 27.3 1.7E+02 0.0037 25.4 5.8 29 85-114 153-181 (203)
155 PRK12542 RNA polymerase sigma 27.2 1.4E+02 0.003 25.0 5.1 29 85-114 137-165 (185)
156 PRK12545 RNA polymerase sigma 26.9 1.4E+02 0.003 25.7 5.1 28 85-113 154-181 (201)
157 PLN03142 Probable chromatin-re 26.5 1.2E+02 0.0026 33.6 5.6 43 68-110 825-868 (1033)
158 TIGR02960 SigX5 RNA polymerase 26.0 1.4E+02 0.003 27.5 5.2 29 85-114 157-185 (324)
159 PRK00430 fis global DNA-bindin 25.5 1.8E+02 0.0038 22.8 5.0 34 73-107 55-88 (95)
160 PF08870 DUF1832: Domain of un 25.3 2.4E+02 0.0052 22.8 5.9 89 18-117 5-98 (113)
161 PRK12537 RNA polymerase sigma 25.0 1.6E+02 0.0034 24.7 5.1 29 85-114 148-176 (182)
162 PRK11922 RNA polymerase sigma 24.9 97 0.0021 27.3 3.9 28 86-114 165-192 (231)
163 PF10440 WIYLD: Ubiquitin-bind 24.8 49 0.0011 24.6 1.6 18 77-94 31-48 (65)
164 KOG1194 Predicted DNA-binding 24.7 39 0.00084 34.1 1.4 46 12-59 185-230 (534)
165 PRK10100 DNA-binding transcrip 24.6 1.7E+02 0.0038 25.8 5.5 43 69-114 155-197 (216)
166 PRK09646 RNA polymerase sigma 24.1 2.1E+02 0.0045 24.3 5.7 29 85-114 157-185 (194)
167 TIGR02989 Sig-70_gvs1 RNA poly 23.8 1.9E+02 0.0041 23.2 5.2 27 85-112 126-152 (159)
168 PRK09483 response regulator; P 23.2 1.3E+02 0.0027 25.0 4.1 44 68-114 147-190 (217)
169 PRK12546 RNA polymerase sigma 22.9 1.6E+02 0.0035 25.1 4.8 30 84-114 127-156 (188)
170 PRK13858 type IV secretion sys 22.9 1.2E+02 0.0026 26.0 3.8 85 3-101 17-103 (147)
171 PRK09636 RNA polymerase sigma 22.6 1.7E+02 0.0036 26.8 5.1 29 85-114 130-158 (293)
172 cd08306 Death_FADD Fas-associa 22.6 1.2E+02 0.0027 23.0 3.5 28 78-106 5-32 (86)
173 PRK10360 DNA-binding transcrip 22.3 2.3E+02 0.0049 22.9 5.4 44 68-114 136-179 (196)
174 PRK12544 RNA polymerase sigma 22.3 2.3E+02 0.005 24.6 5.7 29 85-114 163-191 (206)
175 cd01670 Death Death Domain: a 22.1 1E+02 0.0022 22.2 2.9 26 78-104 2-27 (79)
176 PRK12519 RNA polymerase sigma 21.9 1.6E+02 0.0034 24.8 4.5 29 85-114 156-184 (194)
177 PRK15201 fimbriae regulatory p 21.5 2.4E+02 0.0052 25.3 5.5 43 69-114 133-175 (198)
178 PRK09638 RNA polymerase sigma 21.5 1E+02 0.0023 25.3 3.2 29 85-114 141-169 (176)
179 TIGR02957 SigX4 RNA polymerase 21.0 1.9E+02 0.0041 26.4 5.1 29 85-114 123-151 (281)
180 PRK09639 RNA polymerase sigma 20.7 2.2E+02 0.0048 23.0 5.0 29 85-114 126-154 (166)
181 PRK09415 RNA polymerase factor 20.6 2E+02 0.0042 24.1 4.7 28 86-114 143-170 (179)
182 PRK12526 RNA polymerase sigma 20.5 2.2E+02 0.0048 24.5 5.2 28 86-114 169-196 (206)
183 PRK06986 fliA flagellar biosyn 20.3 2.4E+02 0.0051 24.9 5.4 30 84-114 198-227 (236)
184 PRK06930 positive control sigm 20.3 2.2E+02 0.0048 24.4 5.1 38 76-114 120-157 (170)
185 PRK12538 RNA polymerase sigma 20.0 1.8E+02 0.0038 26.0 4.6 28 86-114 187-214 (233)
No 1
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=5e-39 Score=288.80 Aligned_cols=119 Identities=66% Similarity=1.303 Sum_probs=113.9
Q ss_pred CccccccCCCCCCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhcccCCCCCCCCCCHHHHHHHHHHH
Q 024492 3 RAPCCEKMGLKKGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFTREEEDTIINLH 82 (267)
Q Consensus 3 R~p~~~K~~lkkG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~L~p~ikkg~WT~EED~~Li~lv 82 (267)
|+|||.|+++++|+||+|||++|+++|++||..+|..||+.++.+|+++|||+||.++|+|.+++++||.|||++|+++|
T Consensus 14 ~~pcc~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~ 93 (249)
T PLN03212 14 TTPCCTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLH 93 (249)
T ss_pred CCCCcccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHH
Confidence 78999999999999999999999999999999999999999975599999999999999999999999999999999999
Q ss_pred HHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhHHHhhhhc
Q 024492 83 EMLGNRWSAIAARLPGRTDNEIKNVWHTHLKKRLKQKQQ 121 (267)
Q Consensus 83 ~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk~~~~~~~ 121 (267)
.+||++|+.||++|||||+++|||||+.++++++.+...
T Consensus 94 ~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i 132 (249)
T PLN03212 94 RLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGI 132 (249)
T ss_pred HhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCC
Confidence 999999999999999999999999999999998776543
No 2
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=4.7e-39 Score=307.50 Aligned_cols=120 Identities=65% Similarity=1.238 Sum_probs=116.1
Q ss_pred CCCccccccCCCCCCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhcccCCCCCCCCCCHHHHHHHHH
Q 024492 1 MVRAPCCEKMGLKKGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFTREEEDTIIN 80 (267)
Q Consensus 1 m~R~p~~~K~~lkkG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~L~p~ikkg~WT~EED~~Li~ 80 (267)
|||++||.|.+++||+||+|||++|+++|.+||..+|..||+.++.+|+++|||+||.+||+|++++++||+|||++|++
T Consensus 1 mgr~~Cc~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLe 80 (459)
T PLN03091 1 MGRHSCCYKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIE 80 (459)
T ss_pred CCCCccCcCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHH
Confidence 99999999999999999999999999999999999999999998756999999999999999999999999999999999
Q ss_pred HHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhHHHhhhh
Q 024492 81 LHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLKKRLKQKQ 120 (267)
Q Consensus 81 lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk~~~~~~ 120 (267)
+|++||++|++||++|||||+++|||||+.++|++++++.
T Consensus 81 L~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~ 120 (459)
T PLN03091 81 LHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRG 120 (459)
T ss_pred HHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcC
Confidence 9999999999999999999999999999999999887553
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=1.3e-37 Score=280.54 Aligned_cols=112 Identities=67% Similarity=1.128 Sum_probs=106.8
Q ss_pred cCCCCCCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhcccCCCCCCCCCCHHHHHHHHHHHHHcCCc
Q 024492 9 KMGLKKGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFTREEEDTIINLHEMLGNR 88 (267)
Q Consensus 9 K~~lkkG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~L~p~ikkg~WT~EED~~Li~lv~~~G~k 88 (267)
|+.+.||+||+|||++|++||++||+++|..||+.+|.+|++|+||+||.|||+|++++|.||+|||++|++||..|||+
T Consensus 4 k~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNr 83 (238)
T KOG0048|consen 4 NPELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNR 83 (238)
T ss_pred CccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcH
Confidence 34456899999999999999999999999999999996699999999999999999999999999999999999999999
Q ss_pred HHHHhhhCCCCCHHHHHHHHHHhhhHHHhhhh
Q 024492 89 WSAIAARLPGRTDNEIKNVWHTHLKKRLKQKQ 120 (267)
Q Consensus 89 Ws~IA~~lpgRT~~q~knRW~~llrk~~~~~~ 120 (267)
|+.||++|||||+++|||+|+.++|+++.+..
T Consensus 84 Ws~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 84 WSLIAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred HHHHHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 99999999999999999999999999988765
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.78 E-value=1.7e-19 Score=178.89 Aligned_cols=106 Identities=25% Similarity=0.499 Sum_probs=100.4
Q ss_pred CCCccccccCCCCCCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhcccCCCCCCCCCCHHHHHHHHH
Q 024492 1 MVRAPCCEKMGLKKGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFTREEEDTIIN 80 (267)
Q Consensus 1 m~R~p~~~K~~lkkG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~L~p~ikkg~WT~EED~~Li~ 80 (267)
++|+-....|++++|+||++||.+|+.+|.+||..+|-+|-..+|+ |+..|||+||.|.|+...|++.||-.||+.|+.
T Consensus 347 I~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPn-RSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~ 425 (939)
T KOG0049|consen 347 ITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPN-RSDSQCRERYTNVLNRSAKVERWTLVEDEQLLY 425 (939)
T ss_pred hhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCC-ccHHHHHHHHHHHHHHhhccCceeecchHHHHH
Confidence 5788899999999999999999999999999999999999999998 999999999999999999999999999999999
Q ss_pred HHHHcC-CcHHHHhhhCCCCCHHHHHHH
Q 024492 81 LHEMLG-NRWSAIAARLPGRTDNEIKNV 107 (267)
Q Consensus 81 lv~~~G-~kWs~IA~~lpgRT~~q~knR 107 (267)
+|++|| ++|.+||..||.||..|...|
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 899999999999999665443
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.66 E-value=1.1e-16 Score=159.11 Aligned_cols=107 Identities=23% Similarity=0.455 Sum_probs=99.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC---CCccccchhhcccccccccccchhcccCCCCCCCCCCHHHHHHHHHHHHHcCCc
Q 024492 12 LKKGPWTPEEDQILINYVKLYGH---GNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFTREEEDTIINLHEMLGNR 88 (267)
Q Consensus 12 lkkG~WT~EEDe~L~~~V~~~G~---~nW~~IA~~l~~~Rt~kqCr~Rw~n~L~p~ikkg~WT~EED~~Li~lv~~~G~k 88 (267)
++...||.|||.+|+++|+.... .+|++|-..|++ |+..|...||...|+|.+++|.||.+||.+|+.+|.+||.+
T Consensus 303 L~ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ympg-r~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~k 381 (939)
T KOG0049|consen 303 LSEKEWSEEEDTKLIALVKITSINSHIQWDKVVQYMPG-RTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAK 381 (939)
T ss_pred HHhhhcchhhhHHHHHHHHHhhccCccchHHHHHhcCC-cchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCcc
Confidence 56789999999999999998743 489999999999 99999999999999999999999999999999999999965
Q ss_pred -HHHHhhhCCCCCHHHHHHHHHHhhhHHHhhh
Q 024492 89 -WSAIAARLPGRTDNEIKNVWHTHLKKRLKQK 119 (267)
Q Consensus 89 -Ws~IA~~lpgRT~~q~knRW~~llrk~~~~~ 119 (267)
|.+|-..+|||++.|||.||++.|..+.|..
T Consensus 382 dw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~ 413 (939)
T KOG0049|consen 382 DWAKVRQAVPNRSDSQCRERYTNVLNRSAKVE 413 (939)
T ss_pred chhhHHHhcCCccHHHHHHHHHHHHHHhhccC
Confidence 9999999999999999999999998876644
No 6
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.65 E-value=8.9e-17 Score=115.16 Aligned_cols=60 Identities=47% Similarity=0.986 Sum_probs=55.0
Q ss_pred CCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhcccCCCCCCCCCCHHHHHHH
Q 024492 17 WTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFTREEEDTI 78 (267)
Q Consensus 17 WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~L~p~ikkg~WT~EED~~L 78 (267)
||+|||++|+.+|..||. +|..||++||. |+..||+.||.++|+|.+++++||.+||++|
T Consensus 1 WT~eEd~~L~~~~~~~g~-~W~~Ia~~l~~-Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN-DWKKIAEHLGN-RTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS--HHHHHHHSTT-S-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc-CHHHHHHHHCc-CCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 999999999999999995 99999999975 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=99.61 E-value=5e-16 Score=153.08 Aligned_cols=108 Identities=31% Similarity=0.515 Sum_probs=102.8
Q ss_pred cCCCCCCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhcccCCCCCCCCCCHHHHHHHHHHHHHcCCc
Q 024492 9 KMGLKKGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFTREEEDTIINLHEMLGNR 88 (267)
Q Consensus 9 K~~lkkG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~L~p~ikkg~WT~EED~~Li~lv~~~G~k 88 (267)
...++.|.|+..||+.|..+|+.||+.+|..||..+.. |+++||+.||+++++|.++++.|+.|||+.|+.+..++|++
T Consensus 15 ~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~-~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~ 93 (512)
T COG5147 15 QTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLIS-STGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQ 93 (512)
T ss_pred cceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcc-cccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCch
Confidence 34567899999999999999999999999999999998 99999999999999999999999999999999999999999
Q ss_pred HHHHhhhCCCCCHHHHHHHHHHhhhHHHh
Q 024492 89 WSAIAARLPGRTDNEIKNVWHTHLKKRLK 117 (267)
Q Consensus 89 Ws~IA~~lpgRT~~q~knRW~~llrk~~~ 117 (267)
|+.||..++|||..+|.+||...+....+
T Consensus 94 wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 94 WSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 99999999999999999999999887665
No 8
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.57 E-value=7.5e-16 Score=150.10 Aligned_cols=106 Identities=26% Similarity=0.619 Sum_probs=100.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhcccCCCCCCCCCCHHHHHHHHHHHHHcCCcHHH
Q 024492 12 LKKGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFTREEEDTIINLHEMLGNRWSA 91 (267)
Q Consensus 12 lkkG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~L~p~ikkg~WT~EED~~Li~lv~~~G~kWs~ 91 (267)
++.|.|+.-||+.|..+|.+||...|.+|++.+.- .+++||+.||..+|+|.|++..|+.|||++|+.+.+.+.+.|..
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~-kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrt 83 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNR-KTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRT 83 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhh-cchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccch
Confidence 57799999999999999999999999999999998 99999999999999999999999999999999999999999999
Q ss_pred HhhhCCCCCHHHHHHHHHHhhhHHHhhh
Q 024492 92 IAARLPGRTDNEIKNVWHTHLKKRLKQK 119 (267)
Q Consensus 92 IA~~lpgRT~~q~knRW~~llrk~~~~~ 119 (267)
||..| ||+.+||-.||..++-.....-
T Consensus 84 Ia~i~-gr~~~qc~eRy~~ll~~~~s~~ 110 (617)
T KOG0050|consen 84 IADIM-GRTSQQCLERYNNLLDVYVSYH 110 (617)
T ss_pred HHHHh-hhhHHHHHHHHHHHHHHHHhhh
Confidence 99999 9999999999999997665443
No 9
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.45 E-value=1.2e-13 Score=95.20 Aligned_cols=46 Identities=33% Similarity=0.719 Sum_probs=42.0
Q ss_pred CCCCCHHHHHHHHHHHHHcCCc-HHHHhhhCC-CCCHHHHHHHHHHhh
Q 024492 67 RGNFTREEEDTIINLHEMLGNR-WSAIAARLP-GRTDNEIKNVWHTHL 112 (267)
Q Consensus 67 kg~WT~EED~~Li~lv~~~G~k-Ws~IA~~lp-gRT~~q~knRW~~ll 112 (267)
|++||.|||++|++++.+||.. |..||..|+ |||..||++||+.++
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 5899999999999999999988 999999999 999999999999874
No 10
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.44 E-value=1.1e-13 Score=138.03 Aligned_cols=107 Identities=28% Similarity=0.561 Sum_probs=95.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhcccCCCC--CCCCCCHHHHHHHHHHHH-------
Q 024492 13 KKGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINYLRPDI--KRGNFTREEEDTIINLHE------- 83 (267)
Q Consensus 13 kkG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~L~p~i--kkg~WT~EED~~Li~lv~------- 83 (267)
.+|.||+||++.|..+|.++|. .|..|++.++ |.+..|++||.+|..++- ++|.||.||+++|+++|.
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~-~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~ 459 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGN-DWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREAL 459 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcc-cHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhh
Confidence 7999999999999999999996 9999999998 999999999999999984 899999999999999995
Q ss_pred Hc-------------------CCcHHHHhhhCCCCCHHHHHHHHHHhhhHHHhhhhcc
Q 024492 84 ML-------------------GNRWSAIAARLPGRTDNEIKNVWHTHLKKRLKQKQQQ 122 (267)
Q Consensus 84 ~~-------------------G~kWs~IA~~lpgRT~~q~knRW~~llrk~~~~~~~~ 122 (267)
++ +-+|..|++.+..|+..|||-+|..++......+.+.
T Consensus 460 q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n~~~~ 517 (607)
T KOG0051|consen 460 QPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFNKRQE 517 (607)
T ss_pred cccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhhcccc
Confidence 33 1259999999999999999999999998766554443
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=99.38 E-value=9.5e-14 Score=95.76 Aligned_cols=48 Identities=46% Similarity=0.858 Sum_probs=42.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhccc
Q 024492 14 KGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINYL 61 (267)
Q Consensus 14 kG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~L 61 (267)
||+||+|||++|+++|.+||..+|..||..+|++|++.||+.||+++|
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 689999999999999999998669999999994499999999999875
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=99.33 E-value=1.3e-12 Score=93.48 Aligned_cols=47 Identities=34% Similarity=0.762 Sum_probs=40.4
Q ss_pred CCHHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhHHH
Q 024492 70 FTREEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLKKRL 116 (267)
Q Consensus 70 WT~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk~~ 116 (267)
||+|||++|+++|++||++|.+||++|+.||..+|++||+.+|++.+
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~ 47 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKI 47 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTS
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccc
Confidence 99999999999999999999999999966999999999999776543
No 13
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.29 E-value=3.2e-12 Score=115.80 Aligned_cols=68 Identities=22% Similarity=0.477 Sum_probs=58.1
Q ss_pred hcccccccccccchhcccCCCCCCCCCCHHHHHHHHHHHHHcC-CcHHHHhhhC-CCCCHHHHHHHHHHhhhHHHhhh
Q 024492 44 AGLLRCGKSCRLRWINYLRPDIKRGNFTREEEDTIINLHEMLG-NRWSAIAARL-PGRTDNEIKNVWHTHLKKRLKQK 119 (267)
Q Consensus 44 l~~~Rt~kqCr~Rw~n~L~p~ikkg~WT~EED~~Li~lv~~~G-~kWs~IA~~l-pgRT~~q~knRW~~llrk~~~~~ 119 (267)
+++ |+.--|. ++.+++++||+|||++|+++|++|| ++|..||+++ +|||.+|||.||.++|++.+++.
T Consensus 10 ~~~-~~~pcc~-------K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kg 79 (249)
T PLN03212 10 VSK-KTTPCCT-------KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRG 79 (249)
T ss_pred CCC-CCCCCcc-------cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccC
Confidence 454 5554443 3588999999999999999999999 6899999998 69999999999999999877654
No 14
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.28 E-value=7.3e-12 Score=83.74 Aligned_cols=47 Identities=40% Similarity=0.837 Sum_probs=44.4
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 024492 67 RGNFTREEEDTIINLHEMLG-NRWSAIAARLPGRTDNEIKNVWHTHLK 113 (267)
Q Consensus 67 kg~WT~EED~~Li~lv~~~G-~kWs~IA~~lpgRT~~q~knRW~~llr 113 (267)
+++||++||.+|+.++.+|| .+|..||..|++||..+|++||+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 46899999999999999999 999999999999999999999998764
No 15
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.23 E-value=5e-12 Score=114.27 Aligned_cols=59 Identities=24% Similarity=0.374 Sum_probs=53.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHcC-CcHHHHhhhCC-CCCHHHHHHHHHHhhhHHHhhhhc
Q 024492 63 PDIKRGNFTREEEDTIINLHEMLG-NRWSAIAARLP-GRTDNEIKNVWHTHLKKRLKQKQQ 121 (267)
Q Consensus 63 p~ikkg~WT~EED~~Li~lv~~~G-~kWs~IA~~lp-gRT~~q~knRW~~llrk~~~~~~~ 121 (267)
|.+.||+||.|||++|+++|++|| .+|..||+.++ ||++++||-||.++|++.+++...
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~f 65 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNF 65 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCC
Confidence 445589999999999999999999 56999999998 999999999999999999887643
No 16
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.16 E-value=7.1e-11 Score=77.86 Aligned_cols=44 Identities=34% Similarity=0.729 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHHHHHcC-CcHHHHhhhCCCCCHHHHHHHHHHhh
Q 024492 69 NFTREEEDTIINLHEMLG-NRWSAIAARLPGRTDNEIKNVWHTHL 112 (267)
Q Consensus 69 ~WT~EED~~Li~lv~~~G-~kWs~IA~~lpgRT~~q~knRW~~ll 112 (267)
+||.||+.+|++++.+|| .+|..||+.|++||..+|++||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 99999999999999999999998753
No 17
>PLN03091 hypothetical protein; Provisional
Probab=99.12 E-value=4.9e-11 Score=115.50 Aligned_cols=57 Identities=19% Similarity=0.453 Sum_probs=51.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHcC-CcHHHHhhhC-CCCCHHHHHHHHHHhhhHHHhhh
Q 024492 63 PDIKRGNFTREEEDTIINLHEMLG-NRWSAIAARL-PGRTDNEIKNVWHTHLKKRLKQK 119 (267)
Q Consensus 63 p~ikkg~WT~EED~~Li~lv~~~G-~kWs~IA~~l-pgRT~~q~knRW~~llrk~~~~~ 119 (267)
+.++++.||+|||++|+++|++|| ++|..||+.+ +||+++|||.||.++|++.+++.
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKg 68 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRG 68 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCC
Confidence 578899999999999999999999 5799999988 59999999999999998876544
No 18
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.05 E-value=9.4e-11 Score=78.31 Aligned_cols=48 Identities=48% Similarity=0.941 Sum_probs=44.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhcccC
Q 024492 14 KGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINYLR 62 (267)
Q Consensus 14 kG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~L~ 62 (267)
+++||++||++|..++..||..+|..||..+++ |++.+|+.||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~-rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPG-RTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCC-CCHHHHHHHHHHHcC
Confidence 478999999999999999996699999999997 999999999998764
No 19
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.89 E-value=7.3e-10 Score=72.94 Aligned_cols=45 Identities=49% Similarity=0.948 Sum_probs=42.0
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhccc
Q 024492 16 PWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINYL 61 (267)
Q Consensus 16 ~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~L 61 (267)
+||++||+.|+.++..||..+|..||+.+++ |++.+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~-rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPG-RTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCC-CCHHHHHHHHHHhC
Confidence 5999999999999999996699999999998 99999999998753
No 20
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.88 E-value=2.2e-09 Score=107.71 Aligned_cols=102 Identities=29% Similarity=0.368 Sum_probs=85.5
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC-----------------------CCccccchhhcccccccccccchhcccCCCC-CCC
Q 024492 13 KKGPWTPEEDQILINYVKLYGH-----------------------GNWRALPKQAGLLRCGKSCRLRWINYLRPDI-KRG 68 (267)
Q Consensus 13 kkG~WT~EEDe~L~~~V~~~G~-----------------------~nW~~IA~~l~~~Rt~kqCr~Rw~n~L~p~i-kkg 68 (267)
+.+.|+++||+.|...|..|-. .-|+.|...+|. |+.+.+..+-++...|.- ++|
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 3489999999999999988711 126788888998 999998774334444433 999
Q ss_pred CCCHHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhHHH
Q 024492 69 NFTREEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLKKRL 116 (267)
Q Consensus 69 ~WT~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk~~ 116 (267)
.||+||++.|..+|.++|+.|..|++.| ||.+..|+.||+.+++..-
T Consensus 386 ~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~ 432 (607)
T KOG0051|consen 386 KWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGS 432 (607)
T ss_pred CCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhcccc
Confidence 9999999999999999999999999999 9999999999999887653
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=98.31 E-value=6e-08 Score=96.36 Aligned_cols=97 Identities=28% Similarity=0.556 Sum_probs=84.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhcccCC--CCCCCCCCHHHHHHHHHHHHHcC----
Q 024492 13 KKGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINYLRP--DIKRGNFTREEEDTIINLHEMLG---- 86 (267)
Q Consensus 13 kkG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~L~p--~ikkg~WT~EED~~Li~lv~~~G---- 86 (267)
.+|.||++|++.|...+..+|. .|..|.+.++ |-...||+||.+|..+ .+++++|+.||+.+|...+...-
T Consensus 290 ~~~~wt~e~~~eL~~~~~~~~~-~w~~ig~~~~--rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e~~~~~~ 366 (512)
T COG5147 290 QRGKWTKEEEQELAKLVVEHGG-SWTEIGKLLG--RMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNEMRLEAQ 366 (512)
T ss_pred hhccCccccccccccccccccc-hhhHhhhhhc--cCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHHHHHHHh
Confidence 4799999999999999999996 9999998777 8899999999999999 68889999999999999887332
Q ss_pred ----CcHHHHhhhCCCCCHHHHHHHHHHhh
Q 024492 87 ----NRWSAIAARLPGRTDNEIKNVWHTHL 112 (267)
Q Consensus 87 ----~kWs~IA~~lpgRT~~q~knRW~~ll 112 (267)
-.|..|+..++.|....|+..+.++.
T Consensus 367 ~~~~~~~~li~~~~~~~~~~~~~~~~~~~~ 396 (512)
T COG5147 367 QSSRILWLLIAQNIRNRLQHHCRDKYGVLI 396 (512)
T ss_pred hhhhhhHHHHHHhhhccccCCCCCcccccc
Confidence 35999999999888888876655433
No 22
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.72 E-value=2.7e-05 Score=77.15 Aligned_cols=55 Identities=29% Similarity=0.506 Sum_probs=50.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHcC-CcHHHHhhhCCCCCHHHHHHHHHHhhhHHHhhh
Q 024492 65 IKRGNFTREEEDTIINLHEMLG-NRWSAIAARLPGRTDNEIKNVWHTHLKKRLKQK 119 (267)
Q Consensus 65 ikkg~WT~EED~~Li~lv~~~G-~kWs~IA~~lpgRT~~q~knRW~~llrk~~~~~ 119 (267)
++.|-|+.-||+.|-.+|.+|| +.|++|++.++-.|..||++||..++.+.+++-
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~t 60 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKT 60 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhh
Confidence 5678999999999999999999 779999999999999999999999998877654
No 23
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.68 E-value=1.9e-05 Score=76.85 Aligned_cols=49 Identities=22% Similarity=0.706 Sum_probs=45.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhccc
Q 024492 12 LKKGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINYL 61 (267)
Q Consensus 12 lkkG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~L 61 (267)
+-...||++|+-+|+++++.||.+||..||.++|. |++.+|+++|.+++
T Consensus 70 i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGt-Ktkeeck~hy~k~f 118 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETYGFGNWQDIADHIGT-KTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcc-cchHHHHHHHHHHH
Confidence 34578999999999999999999999999999998 99999999999876
No 24
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.64 E-value=3.6e-05 Score=55.48 Aligned_cols=49 Identities=12% Similarity=0.233 Sum_probs=43.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCc---cccchhhcccc-cccccccchhccc
Q 024492 13 KKGPWTPEEDQILINYVKLYGHGNW---RALPKQAGLLR-CGKSCRLRWINYL 61 (267)
Q Consensus 13 kkG~WT~EEDe~L~~~V~~~G~~nW---~~IA~~l~~~R-t~kqCr~Rw~n~L 61 (267)
++-.||+||.++++.++..+|.++| ..|+..+...| +..||+.+++.|.
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 3568999999999999999998899 99999887546 9999999988764
No 25
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.60 E-value=0.00011 Score=71.65 Aligned_cols=49 Identities=27% Similarity=0.462 Sum_probs=44.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHcC-CcHHHHhhhCCCCCHHHHHHHHHHhh
Q 024492 64 DIKRGNFTREEEDTIINLHEMLG-NRWSAIAARLPGRTDNEIKNVWHTHL 112 (267)
Q Consensus 64 ~ikkg~WT~EED~~Li~lv~~~G-~kWs~IA~~lpgRT~~q~knRW~~ll 112 (267)
.+-...||.+|+.+|++++..|| ++|..||.++..||..+|+.+|..++
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 34467899999999999999999 99999999998899999999998765
No 26
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.58 E-value=0.00021 Score=63.65 Aligned_cols=102 Identities=22% Similarity=0.388 Sum_probs=72.4
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccchhhcc--cccccccccchhccc-CCCC--------------------CCCCCCH
Q 024492 16 PWTPEEDQILINYVKLYGHGNWRALPKQAGL--LRCGKSCRLRWINYL-RPDI--------------------KRGNFTR 72 (267)
Q Consensus 16 ~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~--~Rt~kqCr~Rw~n~L-~p~i--------------------kkg~WT~ 72 (267)
+|++++|-+|+.+|..-. +-..|+.-+.. .-|-+.+.+||+..| +|.+ .+-+||.
T Consensus 1 rW~~~DDl~Li~av~~~~--~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~~is~~a~~~m~~l~p~~~~~iq~kalfS~ 78 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTN--DLESVHLGVKFSCKFTLQEIEERWYALLYDPVISRIAVAAMRNLHPELIAAIQSKALFSK 78 (199)
T ss_pred CCCchhhHHHHHHHHHhc--CHHHHHccCCcCCcCcHHHHHHHHHHHHcChhhHHHHHHHHHhCCcchhhcccccCCCCH
Confidence 699999999999998854 55555544322 134466778998876 5543 2458999
Q ss_pred HHHHHHHHHHHHcCC---cHHHHhh----hC-CCCCHHHHHHHHHHhhhHHHhhh
Q 024492 73 EEEDTIINLHEMLGN---RWSAIAA----RL-PGRTDNEIKNVWHTHLKKRLKQK 119 (267)
Q Consensus 73 EED~~Li~lv~~~G~---kWs~IA~----~l-pgRT~~q~knRW~~llrk~~~~~ 119 (267)
+|+++|........+ .+.+|-. .| ++||++++.++|..+.+.++-..
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~LL~D 133 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHLLPD 133 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhchhhc
Confidence 999999997766543 4777732 23 78999999999996655555433
No 27
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.52 E-value=0.00025 Score=51.08 Aligned_cols=46 Identities=17% Similarity=0.299 Sum_probs=39.9
Q ss_pred CCCCCHHHHHHHHHHHHHcCC-cH---HHHhhhCC-CC-CHHHHHHHHHHhh
Q 024492 67 RGNFTREEEDTIINLHEMLGN-RW---SAIAARLP-GR-TDNEIKNVWHTHL 112 (267)
Q Consensus 67 kg~WT~EED~~Li~lv~~~G~-kW---s~IA~~lp-gR-T~~q~knRW~~ll 112 (267)
+-.||+||..+++++++.||. .| ..|+..|. .| |..||+.+...+.
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 457999999999999999996 99 99999883 35 9999999887654
No 28
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.25 E-value=0.00027 Score=53.63 Aligned_cols=48 Identities=33% Similarity=0.533 Sum_probs=34.9
Q ss_pred CCCCHHHHHHHHHHHHH------cC--C------cHHHHhhhC----CCCCHHHHHHHHHHhhhHH
Q 024492 68 GNFTREEEDTIINLHEM------LG--N------RWSAIAARL----PGRTDNEIKNVWHTHLKKR 115 (267)
Q Consensus 68 g~WT~EED~~Li~lv~~------~G--~------kWs~IA~~l----pgRT~~q~knRW~~llrk~ 115 (267)
..||.+|...||+++.. ++ + -|..||..| ..||..||+++|.++.+.-
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Y 67 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKY 67 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence 47999999999999877 21 1 399999987 3699999999999866554
No 29
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=97.18 E-value=0.0005 Score=59.17 Aligned_cols=53 Identities=15% Similarity=0.251 Sum_probs=46.2
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-------CcHHHHhhhCCCCCHHHHHHHHHHhhhHHHhhh
Q 024492 66 KRGNFTREEEDTIINLHEMLG-------NRWSAIAARLPGRTDNEIKNVWHTHLKKRLKQK 119 (267)
Q Consensus 66 kkg~WT~EED~~Li~lv~~~G-------~kWs~IA~~lpgRT~~q~knRW~~llrk~~~~~ 119 (267)
....||.|||.+|-+.|..|- .-+..++..| +||.-+|.=||+..+|+++...
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 456899999999999998883 2389999999 9999999999999999987644
No 30
>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=97.05 E-value=0.0011 Score=49.12 Aligned_cols=51 Identities=22% Similarity=0.478 Sum_probs=32.8
Q ss_pred CCCCCHHHHHHHHHHHHHcC--------Cc-HHHHhhhCC-CCCHHHHHHHHHHhhhHHHh
Q 024492 67 RGNFTREEEDTIINLHEMLG--------NR-WSAIAARLP-GRTDNEIKNVWHTHLKKRLK 117 (267)
Q Consensus 67 kg~WT~EED~~Li~lv~~~G--------~k-Ws~IA~~lp-gRT~~q~knRW~~llrk~~~ 117 (267)
+.+||.|||.+|++.|+.+. |+ |.+++..-+ .+|-...|+||...|+.+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~~ 62 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRPR 62 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT-----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcccc
Confidence 45799999999999997652 22 999999776 99999999999998877643
No 31
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.00 E-value=0.00097 Score=66.79 Aligned_cols=46 Identities=20% Similarity=0.374 Sum_probs=42.7
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHh
Q 024492 66 KRGNFTREEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTH 111 (267)
Q Consensus 66 kkg~WT~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~l 111 (267)
.++.||.+|.-+|++.+.+||-.|.+||.++.+||..||--++..+
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 3578999999999999999999999999999999999999888764
No 32
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.86 E-value=0.0012 Score=65.17 Aligned_cols=44 Identities=20% Similarity=0.341 Sum_probs=41.7
Q ss_pred CCCCHHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHh
Q 024492 68 GNFTREEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTH 111 (267)
Q Consensus 68 g~WT~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~l 111 (267)
.+||.+|..+|++.++.||..|.+||.++..||..||--||.++
T Consensus 280 k~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred ccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 48999999999999999999999999999999999999988765
No 33
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=96.73 E-value=0.0055 Score=45.67 Aligned_cols=49 Identities=31% Similarity=0.549 Sum_probs=40.6
Q ss_pred CCCCCHHHHHHHHHHHHHcC----C-------------cHHHHhhhC-----CCCCHHHHHHHHHHhhhHH
Q 024492 67 RGNFTREEEDTIINLHEMLG----N-------------RWSAIAARL-----PGRTDNEIKNVWHTHLKKR 115 (267)
Q Consensus 67 kg~WT~EED~~Li~lv~~~G----~-------------kWs~IA~~l-----pgRT~~q~knRW~~llrk~ 115 (267)
+..||.+|.+.|++++.+|. + -|..|+..| +.||..+|+.+|..+...-
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~ 72 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKA 72 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHH
Confidence 45799999999999998873 1 299999876 3599999999999877553
No 34
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.58 E-value=0.00087 Score=66.04 Aligned_cols=46 Identities=20% Similarity=0.685 Sum_probs=42.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhcc
Q 024492 13 KKGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINY 60 (267)
Q Consensus 13 kkG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~ 60 (267)
....||.+|..+|.+.|+.||. +|.+||+++|+ |+..||..|+.+.
T Consensus 278 ~dk~WS~qE~~LLLEGIe~ygD-dW~kVA~HVgt-Kt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYGD-DWDKVARHVGT-KTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhhh-hHHHHHHHhCC-CCHHHHHHHHHcC
Confidence 5569999999999999999996 99999999998 9999999998764
No 35
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.52 E-value=0.0012 Score=66.16 Aligned_cols=46 Identities=22% Similarity=0.733 Sum_probs=42.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhcc
Q 024492 13 KKGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINY 60 (267)
Q Consensus 13 kkG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~ 60 (267)
-++.||.+|..+|+++|+.||. +|.+||.+++. |+..||..++.+.
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~d-dW~kVa~hVg~-ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGD-DWNKVADHVGT-KSQEQCILKFLRL 297 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcc-cHHHHHhccCC-CCHHHHHHHHHhc
Confidence 4689999999999999999996 99999999998 9999999998764
No 36
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.44 E-value=0.0037 Score=54.47 Aligned_cols=52 Identities=13% Similarity=0.294 Sum_probs=44.3
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCc-------HHHHhhhCCCCCHHHHHHHHHHhhhHHHhh
Q 024492 66 KRGNFTREEEDTIINLHEMLGNR-------WSAIAARLPGRTDNEIKNVWHTHLKKRLKQ 118 (267)
Q Consensus 66 kkg~WT~EED~~Li~lv~~~G~k-------Ws~IA~~lpgRT~~q~knRW~~llrk~~~~ 118 (267)
+...||.|+|.+|-+.|..|+.. ...++..| +||.-+|.-||+..+|+++..
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 46789999999999999888732 67777888 999999999999999987653
No 37
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=96.30 E-value=0.0011 Score=48.93 Aligned_cols=52 Identities=29% Similarity=0.456 Sum_probs=33.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCC--------CCccccchhhcccccccccccchhcccCCCC
Q 024492 14 KGPWTPEEDQILINYVKLYGH--------GNWRALPKQAGLLRCGKSCRLRWINYLRPDI 65 (267)
Q Consensus 14 kG~WT~EEDe~L~~~V~~~G~--------~nW~~IA~~l~~~Rt~kqCr~Rw~n~L~p~i 65 (267)
+-+||+|||+.|+.+|..+.. .=|..+++..++.++-.+-|+||...|.+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~ 61 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRP 61 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccc
Confidence 468999999999999976632 2399999888855888889999999997653
No 38
>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=96.09 E-value=0.0014 Score=56.45 Aligned_cols=50 Identities=26% Similarity=0.538 Sum_probs=41.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC------CCccccchhhcccccccccccchhcccCC
Q 024492 12 LKKGPWTPEEDQILINYVKLYGH------GNWRALPKQAGLLRCGKSCRLRWINYLRP 63 (267)
Q Consensus 12 lkkG~WT~EEDe~L~~~V~~~G~------~nW~~IA~~l~~~Rt~kqCr~Rw~n~L~p 63 (267)
.+...||.|||.+|...|-+|-. .-+..+++.++ ||+--|..||+.+++.
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~--RTsAACGFRWNs~VRk 57 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN--RTAAACGFRWNAYVRK 57 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc--ccHHHhcchHHHHHHH
Confidence 36679999999999999998822 14677888787 9999999999999874
No 39
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=95.90 E-value=0.053 Score=58.84 Aligned_cols=103 Identities=16% Similarity=0.325 Sum_probs=76.4
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccc----------------------------------------
Q 024492 15 GPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCR---------------------------------------- 54 (267)
Q Consensus 15 G~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr---------------------------------------- 54 (267)
+.|+.-+=..++.+..+||-.+-..||..+.+ ++...++
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~-k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~ 903 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEG-KTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAI 903 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcC-CCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46888888889999999998888888888865 5554333
Q ss_pred --------cchhccc--CCCCCCCCCCHHHHHHHHHHHHHcC-CcHHHHhhh------------CCCCCHHHHHHHHHHh
Q 024492 55 --------LRWINYL--RPDIKRGNFTREEEDTIINLHEMLG-NRWSAIAAR------------LPGRTDNEIKNVWHTH 111 (267)
Q Consensus 55 --------~Rw~n~L--~p~ikkg~WT~EED~~Li~lv~~~G-~kWs~IA~~------------lpgRT~~q~knRW~~l 111 (267)
.-|...- -+..++..||.|||..|+-.+.+|| .+|.+|-.. +..||+..|..|-.++
T Consensus 904 ~~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l 983 (1033)
T PLN03142 904 GKKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTL 983 (1033)
T ss_pred HHHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHH
Confidence 2221110 1233445699999999999999999 789999433 2489999999999999
Q ss_pred hhHHHhh
Q 024492 112 LKKRLKQ 118 (267)
Q Consensus 112 lrk~~~~ 118 (267)
++-..+.
T Consensus 984 ~~~~~~e 990 (1033)
T PLN03142 984 IRLIEKE 990 (1033)
T ss_pred HHHHHHH
Confidence 9875444
No 40
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.52 E-value=0.016 Score=55.09 Aligned_cols=47 Identities=26% Similarity=0.442 Sum_probs=42.7
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 024492 67 RGNFTREEEDTIINLHEMLG-NRWSAIAARLPGRTDNEIKNVWHTHLK 113 (267)
Q Consensus 67 kg~WT~EED~~Li~lv~~~G-~kWs~IA~~lpgRT~~q~knRW~~llr 113 (267)
-..|+..|+-+|++....+| ++|.-||.++..|+..+||.+|..+.-
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 34799999999999999999 999999999988999999999876543
No 41
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.23 E-value=0.0065 Score=57.70 Aligned_cols=48 Identities=21% Similarity=0.554 Sum_probs=44.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhcccC
Q 024492 14 KGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINYLR 62 (267)
Q Consensus 14 kG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~L~ 62 (267)
--.|+++|+-+|++...-.|.+||.-||..+|. |....|+.+|..++.
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGs-r~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGS-RAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhh-hhhHHHHHHHHHHHh
Confidence 347999999999999999999999999999997 999999999998775
No 42
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=94.89 E-value=0.0047 Score=46.76 Aligned_cols=48 Identities=29% Similarity=0.620 Sum_probs=32.6
Q ss_pred CCCCCHHHHHHHHHHHHH--h----C--C-----CCccccchhh---cccccccccccchhccc
Q 024492 14 KGPWTPEEDQILINYVKL--Y----G--H-----GNWRALPKQA---GLLRCGKSCRLRWINYL 61 (267)
Q Consensus 14 kG~WT~EEDe~L~~~V~~--~----G--~-----~nW~~IA~~l---~~~Rt~kqCr~Rw~n~L 61 (267)
+-.||.+|...|+.++.. + + . .-|..||..| |..|++.||+.||.+..
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~ 64 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLK 64 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 357999999999999877 2 1 1 1499999885 44599999999998743
No 43
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=94.67 E-value=0.027 Score=54.71 Aligned_cols=86 Identities=21% Similarity=0.383 Sum_probs=64.8
Q ss_pred CccccchhhcccccccccccchhcccCCC-------------------------CCCCCCCHHHHHHHHHHHHHcCCcHH
Q 024492 36 NWRALPKQAGLLRCGKSCRLRWINYLRPD-------------------------IKRGNFTREEEDTIINLHEMLGNRWS 90 (267)
Q Consensus 36 nW~~IA~~l~~~Rt~kqCr~Rw~n~L~p~-------------------------ikkg~WT~EED~~Li~lv~~~G~kWs 90 (267)
.|.-++=..+. |...-...+|....++. ++...||+||-+.|++|.+.|.-+|-
T Consensus 75 ~W~w~pFtn~a-RkD~~~l~HWvr~~d~~~dypfakfNk~vdipsYt~eEYe~~l~dn~WskeETD~LF~lck~fDLRf~ 153 (445)
T KOG2656|consen 75 PWKWVPFTNSA-RKDDATLHHWVRVGDTPKDYPFAKFNKHVDIPSYTDEEYEAHLNDNSWSKEETDYLFDLCKRFDLRFF 153 (445)
T ss_pred CceeeccCCcc-ccCCceEEeeeeccCCCCCCchhhhccccCccccchHHHHHhhccccccHHHHHHHHHHHHhcCeeEE
Confidence 56666544444 66666666676653321 12246999999999999999999999
Q ss_pred HHhhh-----CCC-CCHHHHHHHHHHhhhHHHhhhhcc
Q 024492 91 AIAAR-----LPG-RTDNEIKNVWHTHLKKRLKQKQQQ 122 (267)
Q Consensus 91 ~IA~~-----lpg-RT~~q~knRW~~llrk~~~~~~~~ 122 (267)
.||.. ++. ||-.++|.||+...++-++.+.+.
T Consensus 154 VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~~s 191 (445)
T KOG2656|consen 154 VIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARAPS 191 (445)
T ss_pred EEeeccchhhccccccHHHHHHHHHHHHHHHHHccCCC
Confidence 99987 555 999999999999999887765544
No 44
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=94.50 E-value=0.0096 Score=51.88 Aligned_cols=50 Identities=22% Similarity=0.450 Sum_probs=38.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCC------ccccchhhcccccccccccchhcccC
Q 024492 11 GLKKGPWTPEEDQILINYVKLYGHGN------WRALPKQAGLLRCGKSCRLRWINYLR 62 (267)
Q Consensus 11 ~lkkG~WT~EEDe~L~~~V~~~G~~n------W~~IA~~l~~~Rt~kqCr~Rw~n~L~ 62 (267)
..+...||.|||.+|...|-.|+... ...++..+. |+...|..||+.+++
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 35778999999999999999886532 344445555 999999999977665
No 45
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=94.04 E-value=0.018 Score=42.87 Aligned_cols=49 Identities=22% Similarity=0.400 Sum_probs=39.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC----------------CCccccchhh----cccccccccccchhccc
Q 024492 13 KKGPWTPEEDQILINYVKLYGH----------------GNWRALPKQA----GLLRCGKSCRLRWINYL 61 (267)
Q Consensus 13 kkG~WT~EEDe~L~~~V~~~G~----------------~nW~~IA~~l----~~~Rt~kqCr~Rw~n~L 61 (267)
++..||++|.+.|+.+|.+|.. .-|..|+..+ |+.|+..||+.+|.+..
T Consensus 1 R~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk 69 (78)
T PF13873_consen 1 RKPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLK 69 (78)
T ss_pred CCCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 4678999999999999998822 1499999874 22499999999998854
No 46
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=93.85 E-value=0.16 Score=38.79 Aligned_cols=46 Identities=33% Similarity=0.560 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHHc---CC----------cHHHHhhhC---CC--CCHHHHHHHHHHhhhH
Q 024492 69 NFTREEEDTIINLHEML---GN----------RWSAIAARL---PG--RTDNEIKNVWHTHLKK 114 (267)
Q Consensus 69 ~WT~EED~~Li~lv~~~---G~----------kWs~IA~~l---pg--RT~~q~knRW~~llrk 114 (267)
.||+++++.|++++.+. |+ .|..|+..| +| .|..||++||..+.+.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~ 64 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKD 64 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHH
Confidence 49999999999998543 22 299999877 33 5789999999875554
No 47
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=93.71 E-value=0.15 Score=48.30 Aligned_cols=54 Identities=24% Similarity=0.362 Sum_probs=42.1
Q ss_pred CCCCCHHHHHHHHHHHHHc----------CCcHHHHhhhC----CCCCHHHHHHHHHHhhhHHHhhhh
Q 024492 67 RGNFTREEEDTIINLHEML----------GNRWSAIAARL----PGRTDNEIKNVWHTHLKKRLKQKQ 120 (267)
Q Consensus 67 kg~WT~EED~~Li~lv~~~----------G~kWs~IA~~l----pgRT~~q~knRW~~llrk~~~~~~ 120 (267)
...|+.+|-..||++..+. +.-|..||+.+ .-||+.+||++|.++.++..+.+.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k~ 121 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEKA 121 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHhc
Confidence 3689999999999998653 23499999965 349999999999987776544433
No 48
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=93.12 E-value=0.24 Score=40.76 Aligned_cols=52 Identities=21% Similarity=0.377 Sum_probs=41.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHcCC----cHHHHhhhC------------CCCCHHHHHHHHHHhhhHH
Q 024492 64 DIKRGNFTREEEDTIINLHEMLGN----RWSAIAARL------------PGRTDNEIKNVWHTHLKKR 115 (267)
Q Consensus 64 ~ikkg~WT~EED~~Li~lv~~~G~----kWs~IA~~l------------pgRT~~q~knRW~~llrk~ 115 (267)
..++..||.+||.-|+-++.+||- .|.+|-..+ ..||+..|..|-.++++-.
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i 113 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLI 113 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHH
Confidence 556789999999999999999995 799886542 3799999999999988754
No 49
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=91.42 E-value=0.31 Score=47.55 Aligned_cols=47 Identities=19% Similarity=0.332 Sum_probs=43.3
Q ss_pred CCCCHHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 68 GNFTREEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 68 g~WT~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
-+||.+|-++..++..++|..++.|+..+|.|...|||.+|.+--|+
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 37999999999999999999999999999999999999999875544
No 50
>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=88.32 E-value=1.5 Score=29.92 Aligned_cols=41 Identities=24% Similarity=0.322 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 024492 72 REEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLK 113 (267)
Q Consensus 72 ~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llr 113 (267)
++++..++.++-..|-.|.+||..+ |.|...|+.+.+..++
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 4678889999999999999999999 9999999998776544
No 51
>smart00595 MADF subfamily of SANT domain.
Probab=87.07 E-value=1.2 Score=33.48 Aligned_cols=25 Identities=32% Similarity=0.640 Sum_probs=22.0
Q ss_pred HHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 89 WSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 89 Ws~IA~~lpgRT~~q~knRW~~llrk 114 (267)
|.+||..| |-|..+|+.+|+++...
T Consensus 30 W~~Ia~~l-~~~~~~~~~kw~~LR~~ 54 (89)
T smart00595 30 WEEIAEEL-GLSVEECKKRWKNLRDR 54 (89)
T ss_pred HHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 99999999 55999999999987644
No 52
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=83.32 E-value=2.9 Score=41.82 Aligned_cols=49 Identities=18% Similarity=0.289 Sum_probs=44.0
Q ss_pred CCCCCHHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhHH
Q 024492 67 RGNFTREEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLKKR 115 (267)
Q Consensus 67 kg~WT~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk~ 115 (267)
...||.||-.++.+++..||.++.+|-+.||.|+-..|...|...-+.+
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK~~ 235 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKKTR 235 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHHHh
Confidence 4579999999999999999999999999999999999999888765543
No 53
>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=82.27 E-value=1 Score=36.97 Aligned_cols=34 Identities=32% Similarity=0.630 Sum_probs=28.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC---CCccccchhh
Q 024492 11 GLKKGPWTPEEDQILINYVKLYGH---GNWRALPKQA 44 (267)
Q Consensus 11 ~lkkG~WT~EEDe~L~~~V~~~G~---~nW~~IA~~l 44 (267)
+.++..||.+||.-|+-++.+||. +.|..|-..+
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~I 82 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEI 82 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHH
Confidence 567889999999999999999999 8999997765
No 54
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=80.18 E-value=1.2 Score=43.52 Aligned_cols=45 Identities=13% Similarity=0.276 Sum_probs=41.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhcc
Q 024492 14 KGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINY 60 (267)
Q Consensus 14 kG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~ 60 (267)
--+||.+|-+++..+....|. ++..|+..+|. |..+|+..+|.+-
T Consensus 365 ~~~Ws~~e~ekFYKALs~wGt-dF~LIs~lfP~-R~RkqIKaKfi~E 409 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWGT-DFSLISSLFPN-RERKQIKAKFIKE 409 (507)
T ss_pred CCcccHHHHHHHHHHHHHhcc-hHHHHHHhcCc-hhHHHHHHHHHHH
Confidence 358999999999999999997 99999999999 9999999998874
No 55
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=79.13 E-value=0.95 Score=42.91 Aligned_cols=48 Identities=23% Similarity=0.400 Sum_probs=37.1
Q ss_pred CCCCCHHHHHHHHHHHHHh----C-----CCCccccchh---hcccccccccccchhccc
Q 024492 14 KGPWTPEEDQILINYVKLY----G-----HGNWRALPKQ---AGLLRCGKSCRLRWINYL 61 (267)
Q Consensus 14 kG~WT~EEDe~L~~~V~~~----G-----~~nW~~IA~~---l~~~Rt~kqCr~Rw~n~L 61 (267)
...|+.+|-..|+.+.... . ..-|..||+. .|..|++.||+.||.|..
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 3789999999999987543 1 1259999984 344499999999998744
No 56
>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=77.91 E-value=3.4 Score=30.06 Aligned_cols=26 Identities=23% Similarity=0.482 Sum_probs=21.7
Q ss_pred HHHHhhhCCC-CCHHHHHHHHHHhhhH
Q 024492 89 WSAIAARLPG-RTDNEIKNVWHTHLKK 114 (267)
Q Consensus 89 Ws~IA~~lpg-RT~~q~knRW~~llrk 114 (267)
|..||..|.. -+..+|+.||..+...
T Consensus 29 w~~Ia~~l~~~~~~~~~~~~w~~Lr~~ 55 (85)
T PF10545_consen 29 WQEIARELGKEFSVDDCKKRWKNLRDR 55 (85)
T ss_pred HHHHHHHHccchhHHHHHHHHHHHHHH
Confidence 9999999943 6788999999986654
No 57
>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=76.38 E-value=6 Score=26.46 Aligned_cols=38 Identities=18% Similarity=0.351 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHcC-CcHHHHhhhCCCCCHHHHHHHHHHh
Q 024492 73 EEEDTIINLHEMLG-NRWSAIAARLPGRTDNEIKNVWHTH 111 (267)
Q Consensus 73 EED~~Li~lv~~~G-~kWs~IA~~lpgRT~~q~knRW~~l 111 (267)
+=|.+|+.+...-| -.|.+||+.+ |=|...|..|+..+
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l-glS~~~v~~Ri~rL 41 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL-GLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH-TS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH-CcCHHHHHHHHHHh
Confidence 45888999998888 4599999999 99999999998764
No 58
>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=73.87 E-value=9.7 Score=25.60 Aligned_cols=41 Identities=29% Similarity=0.439 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 73 EEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 73 EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
+++..++.++--.|-.+.+||..| |-|...|+.+-+..+++
T Consensus 7 ~~er~vi~~~y~~~~t~~eIa~~l-g~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 7 PREREVIRLRYFEGLTLEEIAERL-GISRSTVRRILKRALKK 47 (50)
T ss_dssp HHHHHHHHHHHTST-SHHHHHHHH-TSCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHH-CCcHHHHHHHHHHHHHH
Confidence 456666666666677899999999 99999999888777665
No 59
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=73.26 E-value=7.4 Score=32.57 Aligned_cols=45 Identities=9% Similarity=0.089 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHcC-CcHHHHhhhCCCCCHHHHHHHHHHhhhHHHh
Q 024492 72 REEEDTIINLHEMLG-NRWSAIAARLPGRTDNEIKNVWHTHLKKRLK 117 (267)
Q Consensus 72 ~EED~~Li~lv~~~G-~kWs~IA~~lpgRT~~q~knRW~~llrk~~~ 117 (267)
.+-|.+|+++.++-| -.|++||+.+ |-+...|+.|++.+....+-
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 367889999998888 6799999999 99999999999988766543
No 60
>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=73.01 E-value=3.6 Score=31.60 Aligned_cols=23 Identities=39% Similarity=0.716 Sum_probs=13.4
Q ss_pred CCCCCCCHHHHHHHH--------HHHHHhCC
Q 024492 12 LKKGPWTPEEDQILI--------NYVKLYGH 34 (267)
Q Consensus 12 lkkG~WT~EEDe~L~--------~~V~~~G~ 34 (267)
-..|-||+|+|+.|. .++++||.
T Consensus 45 n~~GiWT~eDD~~L~~~~~~~~~~L~~khG~ 75 (87)
T PF11626_consen 45 NMPGIWTPEDDEMLRSGDKDDIERLIKKHGE 75 (87)
T ss_dssp T-TT---HHHHHHHTS--HHHHHHHHHHH-H
T ss_pred CCCCCcCHHHHHHHHcCCHHHHHHHHHHhCH
Confidence 457899999999993 45667664
No 61
>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=71.57 E-value=5.5 Score=34.34 Aligned_cols=41 Identities=27% Similarity=0.288 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHH
Q 024492 69 NFTREEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHT 110 (267)
Q Consensus 69 ~WT~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~ 110 (267)
.||+|..++|.+|. .-|-.=++||+.|.|.|.|+|--+-+.
T Consensus 2 ~Wtde~~~~L~~lw-~~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 2 SWTDERVERLRKLW-AEGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred CCCHHHHHHHHHHH-HcCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 59999999999888 568888999999977999999776664
No 62
>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=68.95 E-value=12 Score=30.06 Aligned_cols=38 Identities=24% Similarity=0.329 Sum_probs=28.4
Q ss_pred HHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 76 DTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 76 ~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
..++.+.-..|-.+.+||+.+ |.+...|+++.+..+++
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 99999999999875444
No 63
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=68.27 E-value=9.7 Score=32.27 Aligned_cols=45 Identities=11% Similarity=0.066 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHcC-CcHHHHhhhCCCCCHHHHHHHHHHhhhHHHh
Q 024492 72 REEEDTIINLHEMLG-NRWSAIAARLPGRTDNEIKNVWHTHLKKRLK 117 (267)
Q Consensus 72 ~EED~~Li~lv~~~G-~kWs~IA~~lpgRT~~q~knRW~~llrk~~~ 117 (267)
.+-|.+|+.+.++-| -.|++||+.+ |-+...|+.|++.+.+..+-
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~GvI 58 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGFI 58 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 567889999888887 5699999999 99999999999998876543
No 64
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=66.00 E-value=24 Score=33.91 Aligned_cols=49 Identities=27% Similarity=0.538 Sum_probs=38.2
Q ss_pred CCCCCHHHHHHHHHHHHHc-CC---cHHHHhhhCCCCCHHHHHHHHHHhhhHHH
Q 024492 67 RGNFTREEEDTIINLHEML-GN---RWSAIAARLPGRTDNEIKNVWHTHLKKRL 116 (267)
Q Consensus 67 kg~WT~EED~~Li~lv~~~-G~---kWs~IA~~lpgRT~~q~knRW~~llrk~~ 116 (267)
-..||.-|...|+.+.+.. |. .-..|++.++||+..+|++--. .||.|+
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~-~LK~rv 73 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQ-QLKGRV 73 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHH-HHHHHH
Confidence 3579999999999998765 43 3678999999999999998544 555544
No 65
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=65.19 E-value=10 Score=39.34 Aligned_cols=48 Identities=13% Similarity=0.463 Sum_probs=38.9
Q ss_pred CCCCCHHHHHHHHHHHHHcCCcHHHHh----------hhCCCCCHHHHHHHHHHhhhH
Q 024492 67 RGNFTREEEDTIINLHEMLGNRWSAIA----------ARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 67 kg~WT~EED~~Li~lv~~~G~kWs~IA----------~~lpgRT~~q~knRW~~llrk 114 (267)
|..||..|+.-...+++++|..+.+|- ..+.-+|..|++.+|+.++++
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 668999999999999999999998882 223346788888888877754
No 66
>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=64.04 E-value=6.3 Score=30.23 Aligned_cols=17 Identities=29% Similarity=0.544 Sum_probs=10.3
Q ss_pred CCCCCCCCCHHHHHHHH
Q 024492 63 PDIKRGNFTREEEDTII 79 (267)
Q Consensus 63 p~ikkg~WT~EED~~Li 79 (267)
|....|-||+|+|+.|.
T Consensus 43 P~n~~GiWT~eDD~~L~ 59 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLR 59 (87)
T ss_dssp -TT-TT---HHHHHHHT
T ss_pred CCCCCCCcCHHHHHHHH
Confidence 66778999999999983
No 67
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=62.57 E-value=21 Score=37.86 Aligned_cols=57 Identities=9% Similarity=0.001 Sum_probs=45.7
Q ss_pred chhcccCCCCC---CCCCCHHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhh
Q 024492 56 RWINYLRPDIK---RGNFTREEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHL 112 (267)
Q Consensus 56 Rw~n~L~p~ik---kg~WT~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~ll 112 (267)
||..|+--+.. ...||..|-.+.-+++-.|...+-.|++.++++|-.+|-..|++..
T Consensus 605 ~~~~h~la~Y~Y~gSd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtWK 664 (907)
T KOG4167|consen 605 RLKCHPLANYHYAGSDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTWK 664 (907)
T ss_pred CccccccceeeecCcccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHHH
Confidence 45554433322 2479999999999999999999999999999999999988766544
No 68
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=58.36 E-value=5.3 Score=42.19 Aligned_cols=45 Identities=16% Similarity=0.312 Sum_probs=40.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhc
Q 024492 13 KKGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWIN 59 (267)
Q Consensus 13 kkG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n 59 (267)
....||+.|-.++.+++..|.. ++..|++++++ ++.+||-+-|+.
T Consensus 618 gSd~WTp~E~~lF~kA~y~~~K-DF~~v~km~~~-KtVaqCVeyYYt 662 (907)
T KOG4167|consen 618 GSDKWTPLERKLFNKALYTYSK-DFIFVQKMVKS-KTVAQCVEYYYT 662 (907)
T ss_pred CcccccHHHHHHHHHHHHHhcc-cHHHHHHHhcc-ccHHHHHHHHHH
Confidence 3568999999999999999985 99999999999 999999887755
No 69
>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=57.95 E-value=7.6 Score=29.35 Aligned_cols=43 Identities=21% Similarity=0.510 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHHHHHh---CCC---------Cccccchhhcc----cccccccccchh
Q 024492 16 PWTPEEDQILINYVKLY---GHG---------NWRALPKQAGL----LRCGKSCRLRWI 58 (267)
Q Consensus 16 ~WT~EEDe~L~~~V~~~---G~~---------nW~~IA~~l~~----~Rt~kqCr~Rw~ 58 (267)
.||+++++.|++++... |.. .|..|+..+.. ..+.+||+.||.
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 59999999999988554 221 37777766443 234455555543
No 70
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=57.28 E-value=11 Score=38.81 Aligned_cols=45 Identities=18% Similarity=0.298 Sum_probs=41.7
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHH
Q 024492 66 KRGNFTREEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHT 110 (267)
Q Consensus 66 kkg~WT~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~ 110 (267)
..+.|+.+|-++......+.|...+.|+..+|+|...|||.++..
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKK 452 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhh
Confidence 346899999999999999999999999999999999999988764
No 71
>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=56.25 E-value=16 Score=28.06 Aligned_cols=29 Identities=24% Similarity=0.563 Sum_probs=24.8
Q ss_pred HHHHHHHHHHcCCcHHHHhhhCCCCCHHHH
Q 024492 75 EDTIINLHEMLGNRWSAIAARLPGRTDNEI 104 (267)
Q Consensus 75 D~~Li~lv~~~G~kWs~IA~~lpgRT~~q~ 104 (267)
|+.|..+...+|..|..+|.+| |=|..+|
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I 30 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDI 30 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 5678999999999999999999 7666655
No 72
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=56.03 E-value=30 Score=26.78 Aligned_cols=37 Identities=24% Similarity=0.289 Sum_probs=27.5
Q ss_pred HHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 77 TIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 77 ~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.++.++-..|-.+..||+.+ |-+...|+++.+..+++
T Consensus 117 ~ii~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 117 EVLVLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred HHHhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 33344444678899999999 78999999988875544
No 73
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=53.48 E-value=7.3 Score=38.36 Aligned_cols=50 Identities=16% Similarity=0.298 Sum_probs=42.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCccccchh-----hcccccccccccchhccc
Q 024492 11 GLKKGPWTPEEDQILINYVKLYGHGNWRALPKQ-----AGLLRCGKSCRLRWINYL 61 (267)
Q Consensus 11 ~lkkG~WT~EEDe~L~~~V~~~G~~nW~~IA~~-----l~~~Rt~kqCr~Rw~n~L 61 (267)
.+.-..||.+|-+.|..++++|.- .|..||.. .+..|+-....+||+...
T Consensus 127 ~l~dn~WskeETD~LF~lck~fDL-Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~ 181 (445)
T KOG2656|consen 127 HLNDNSWSKEETDYLFDLCKRFDL-RFFVIADRYDNQQYKKSRTVEDLKERYYSVC 181 (445)
T ss_pred hhccccccHHHHHHHHHHHHhcCe-eEEEEeeccchhhccccccHHHHHHHHHHHH
Confidence 345578999999999999999997 99999987 566689999999998754
No 74
>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=52.68 E-value=35 Score=25.77 Aligned_cols=38 Identities=16% Similarity=0.312 Sum_probs=27.5
Q ss_pred HHHHHHHHcC--------CcHHHHhhhCCC---CC--HHHHHHHHHHhhhH
Q 024492 77 TIINLHEMLG--------NRWSAIAARLPG---RT--DNEIKNVWHTHLKK 114 (267)
Q Consensus 77 ~Li~lv~~~G--------~kWs~IA~~lpg---RT--~~q~knRW~~llrk 114 (267)
.|..+|.++| ..|..||..|.- -+ ..+++..|..+|-.
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 4777888887 359999998822 22 36788888887753
No 75
>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=51.98 E-value=24 Score=27.11 Aligned_cols=31 Identities=23% Similarity=0.423 Sum_probs=25.6
Q ss_pred HHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHH
Q 024492 75 EDTIINLHEMLGNRWSAIAARLPGRTDNEIKN 106 (267)
Q Consensus 75 D~~Li~lv~~~G~kWs~IA~~lpgRT~~q~kn 106 (267)
|..|..+...+|..|.++|..| |=+...|.+
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI~~ 34 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEINQ 34 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHHHH
Confidence 6778889999999999999999 766665543
No 76
>PF13137 DUF3983: Protein of unknown function (DUF3983)
Probab=50.47 E-value=9.1 Score=24.85 Aligned_cols=11 Identities=45% Similarity=1.008 Sum_probs=9.0
Q ss_pred hHHHHHHhhcC
Q 024492 247 DFWFNLFTKAG 257 (267)
Q Consensus 247 ~fw~~~~~~~~ 257 (267)
.=|.|+|+++|
T Consensus 23 kAWRNiFvqag 33 (34)
T PF13137_consen 23 KAWRNIFVQAG 33 (34)
T ss_pred HHHHHHHHHcc
Confidence 35999999987
No 77
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=50.29 E-value=42 Score=27.43 Aligned_cols=33 Identities=18% Similarity=0.242 Sum_probs=25.1
Q ss_pred HHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 81 LHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 81 lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
+....|-.+..||..| |.+...|+++.+..+++
T Consensus 139 l~~~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 171 (182)
T PRK09652 139 LREIEGLSYEEIAEIM-GCPIGTVRSRIFRAREA 171 (182)
T ss_pred HHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3334567899999999 99999999887764443
No 78
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=50.04 E-value=42 Score=28.71 Aligned_cols=38 Identities=18% Similarity=0.297 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhh
Q 024492 74 EEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHL 112 (267)
Q Consensus 74 ED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~ll 112 (267)
+...++.+..-.|-.+.+||..| |-+...++.+|....
T Consensus 139 ~~~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR 176 (185)
T PF07638_consen 139 RQRRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 33445555555678899999999 999999999999754
No 79
>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=50.03 E-value=47 Score=32.00 Aligned_cols=86 Identities=16% Similarity=0.313 Sum_probs=62.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCC---CccccchhhcccccccccccchhcccCCCCCCCCCCHHHHHHHHHHHHH-c----
Q 024492 14 KGPWTPEEDQILINYVKLYGHG---NWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFTREEEDTIINLHEM-L---- 85 (267)
Q Consensus 14 kG~WT~EEDe~L~~~V~~~G~~---nW~~IA~~l~~~Rt~kqCr~Rw~n~L~p~ikkg~WT~EED~~Li~lv~~-~---- 85 (267)
-..||.-|...|+.+.+..... +-..|++.+++ |...++++ |.+.|+ +..+.+++++ |
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~-Rs~aEI~~-fl~~LK------------~rvareaiqkv~~~g~ 86 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPG-RSEAEIRD-FLQQLK------------GRVAREAIQKVHPGGL 86 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccC-cCHHHHHH-HHHHHH------------HHHHHHHHHHhccccc
Confidence 3589999999999988766322 33467777888 88888775 455553 3445555555 2
Q ss_pred -CCc------------HHHHhhhCCCCCHHHHHHHHHHhhh
Q 024492 86 -GNR------------WSAIAARLPGRTDNEIKNVWHTHLK 113 (267)
Q Consensus 86 -G~k------------Ws~IA~~lpgRT~~q~knRW~~llr 113 (267)
|.+ |..+|..+.|.-...+-.-|.+.|-
T Consensus 87 ~~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~ 127 (344)
T PF11035_consen 87 KGPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLT 127 (344)
T ss_pred ccccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHH
Confidence 211 9999999999999999888887764
No 80
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=49.58 E-value=31 Score=26.51 Aligned_cols=44 Identities=11% Similarity=0.120 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHcC-CcHHHHhhhCCCCCHHHHHHHHHHhhhHHHh
Q 024492 73 EEEDTIINLHEMLG-NRWSAIAARLPGRTDNEIKNVWHTHLKKRLK 117 (267)
Q Consensus 73 EED~~Li~lv~~~G-~kWs~IA~~lpgRT~~q~knRW~~llrk~~~ 117 (267)
+.|..|+.+....| -.+..||+.+ |-+...|+.+...+.+..+-
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~i 47 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGVI 47 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 56888999888887 4699999999 99999999999988776543
No 81
>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=49.22 E-value=53 Score=20.73 Aligned_cols=37 Identities=24% Similarity=0.297 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHh
Q 024492 74 EEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTH 111 (267)
Q Consensus 74 ED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~l 111 (267)
++..++.++-..|-.+..||+.+ |-+...|+.+.+..
T Consensus 14 ~~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~ 50 (55)
T cd06171 14 REREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRA 50 (55)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 34556666656778899999998 78888887765543
No 82
>PF06599 DUF1139: Protein of unknown function (DUF1139); InterPro: IPR009519 This family consists of several hypothetical Fijivirus proteins of unknown function.
Probab=49.07 E-value=9 Score=35.86 Aligned_cols=13 Identities=31% Similarity=1.175 Sum_probs=11.6
Q ss_pred CchhHHHHHHhhc
Q 024492 244 DNTDFWFNLFTKA 256 (267)
Q Consensus 244 ~~m~fw~~~~~~~ 256 (267)
-|.||||+||||+
T Consensus 278 ~dvD~WY~lfmrt 290 (309)
T PF06599_consen 278 TDVDYWYSLFMRT 290 (309)
T ss_pred CCHHHHHHHHHHH
Confidence 4899999999985
No 83
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=49.03 E-value=32 Score=33.85 Aligned_cols=45 Identities=16% Similarity=0.230 Sum_probs=39.7
Q ss_pred CCCCHHHHHHHHHHHHHcCCcHHHHh-hhCCCCCHHHHHHHHHHhh
Q 024492 68 GNFTREEEDTIINLHEMLGNRWSAIA-ARLPGRTDNEIKNVWHTHL 112 (267)
Q Consensus 68 g~WT~EED~~Li~lv~~~G~kWs~IA-~~lpgRT~~q~knRW~~ll 112 (267)
..|+.+|-....+-++.||..+..|- .+++.|+--.|-..|+...
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWK 323 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWK 323 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhh
Confidence 47999999999999999999999995 5899999999988776543
No 84
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=48.70 E-value=37 Score=27.71 Aligned_cols=30 Identities=20% Similarity=0.196 Sum_probs=24.0
Q ss_pred HcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 84 MLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 84 ~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
..|-....||..| |-+...|+++++...++
T Consensus 139 ~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 168 (179)
T PRK11924 139 VEGLSYREIAEIL-GVPVGTVKSRLRRARQL 168 (179)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466799999999 99999999988764433
No 85
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=48.39 E-value=45 Score=25.46 Aligned_cols=38 Identities=18% Similarity=0.341 Sum_probs=27.9
Q ss_pred HHHHHHHHcCC--------cHHHHhhhCCC-----CCHHHHHHHHHHhhhH
Q 024492 77 TIINLHEMLGN--------RWSAIAARLPG-----RTDNEIKNVWHTHLKK 114 (267)
Q Consensus 77 ~Li~lv~~~G~--------kWs~IA~~lpg-----RT~~q~knRW~~llrk 114 (267)
.|..+|.+.|+ .|..||..|.- ....+++..|..+|.+
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 47777888773 69999998832 2356788888887765
No 86
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=47.34 E-value=39 Score=30.33 Aligned_cols=44 Identities=23% Similarity=0.286 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHHHcCCcHHHHhhh--CC-CCCHHHHHHHHHHhhh
Q 024492 69 NFTREEEDTIINLHEMLGNRWSAIAAR--LP-GRTDNEIKNVWHTHLK 113 (267)
Q Consensus 69 ~WT~EED~~Li~lv~~~G~kWs~IA~~--lp-gRT~~q~knRW~~llr 113 (267)
.|++++|-+|+.+|.. |+.-..|+.- |. .-|-..|..||+.+|-
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~lly 47 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALLY 47 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHHc
Confidence 4999999999998854 5556666553 32 4588999999999983
No 87
>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=46.84 E-value=9.3 Score=25.52 Aligned_cols=38 Identities=18% Similarity=0.297 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHhCCCCccccchhhcccccccccccchhc
Q 024492 20 EEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWIN 59 (267)
Q Consensus 20 EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n 59 (267)
+=|.+|+.+.+..+...|..||+.+| =+...|..|+..
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 34788999999999889999999998 477888888653
No 88
>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=46.42 E-value=46 Score=21.82 Aligned_cols=34 Identities=24% Similarity=0.174 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHH
Q 024492 74 EEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVW 108 (267)
Q Consensus 74 ED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW 108 (267)
|-+.|.++.+.++++-.+.|+.| |=+...+..+-
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 67889999999999999999999 76766665543
No 89
>PRK04217 hypothetical protein; Provisional
Probab=45.72 E-value=81 Score=25.57 Aligned_cols=45 Identities=20% Similarity=0.143 Sum_probs=36.6
Q ss_pred CCCCHHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 68 GNFTREEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 68 g~WT~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
..-|.+| ..++.+....|-...+||+.+ |-+...|+++++...++
T Consensus 41 ~~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkk 85 (110)
T PRK04217 41 IFMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKK 85 (110)
T ss_pred ccCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 4566666 677788888888999999999 99999999999875544
No 90
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=44.89 E-value=47 Score=28.34 Aligned_cols=29 Identities=21% Similarity=0.193 Sum_probs=23.6
Q ss_pred HcCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 024492 84 MLGNRWSAIAARLPGRTDNEIKNVWHTHLK 113 (267)
Q Consensus 84 ~~G~kWs~IA~~lpgRT~~q~knRW~~llr 113 (267)
..|-...+||..| |-+...|++|++..++
T Consensus 148 ~~g~s~~EIA~~l-g~s~~tV~~rl~rar~ 176 (192)
T PRK09643 148 MQGYSVADAARML-GVAEGTVKSRCARGRA 176 (192)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 4566799999999 9999999999965443
No 91
>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=44.27 E-value=26 Score=26.41 Aligned_cols=30 Identities=23% Similarity=0.670 Sum_probs=24.1
Q ss_pred HHHHHHHHHHcCCcHHHHhhhCCCCCHHHHH
Q 024492 75 EDTIINLHEMLGNRWSAIAARLPGRTDNEIK 105 (267)
Q Consensus 75 D~~Li~lv~~~G~kWs~IA~~lpgRT~~q~k 105 (267)
|..|..+.+..|..|.++|.+| |=+..+|.
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI~ 33 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDID 33 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHHH
Confidence 4567888899999999999999 66665543
No 92
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=43.24 E-value=40 Score=29.69 Aligned_cols=44 Identities=27% Similarity=0.280 Sum_probs=37.5
Q ss_pred CCCCHHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 68 GNFTREEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 68 g~WT~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
...|+.|-+.|..+.+=+.| .+||..| +.+.+.||++..++++|
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 47899998888777654444 7999999 99999999999999987
No 93
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=42.79 E-value=46 Score=26.76 Aligned_cols=46 Identities=17% Similarity=0.216 Sum_probs=33.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhcccC
Q 024492 13 KKGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINYLR 62 (267)
Q Consensus 13 kkG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~L~ 62 (267)
++..||.|+-..++..+...|. .-..||+.++. ..+-..+|.+.+.
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g~-sv~evA~e~gI---s~~tl~~W~r~y~ 54 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPGM-TVSLVARQHGV---AASQLFLWRKQYQ 54 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCCC-CHHHHHHHHCc---CHHHHHHHHHHHh
Confidence 3578999998888887777664 66788888875 3444567877654
No 94
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=42.65 E-value=51 Score=27.43 Aligned_cols=29 Identities=14% Similarity=0.021 Sum_probs=23.3
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-.+.+||..| |-|...++++.+...++
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456789999999 99999999988765543
No 95
>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=41.23 E-value=54 Score=27.35 Aligned_cols=28 Identities=11% Similarity=0.114 Sum_probs=22.6
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 86 GNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
|-...+||..| |=|...|+++.+..+++
T Consensus 154 ~~s~~EIA~~l-gis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 154 GLSYEDIARIM-DCPVGTVRSRIFRAREA 181 (190)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 45689999999 88999999988765544
No 96
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=41.23 E-value=36 Score=25.96 Aligned_cols=31 Identities=26% Similarity=0.552 Sum_probs=25.9
Q ss_pred HHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHH
Q 024492 75 EDTIINLHEMLGNRWSAIAARLPGRTDNEIKN 106 (267)
Q Consensus 75 D~~Li~lv~~~G~kWs~IA~~lpgRT~~q~kn 106 (267)
|..|-.+...+|..|.++|..| |=+...|.+
T Consensus 4 ~~~l~~ia~~LG~dWk~LAr~L-g~se~dI~~ 34 (84)
T cd08804 4 EERLAVIADHLGFSWTELAREL-DFTEEQIHQ 34 (84)
T ss_pred hhHHHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 5677888899999999999999 777777655
No 97
>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=40.88 E-value=38 Score=25.84 Aligned_cols=27 Identities=33% Similarity=0.636 Sum_probs=21.6
Q ss_pred HHHHHHHcCCcHHHHhhhCCCCCHHHHH
Q 024492 78 IINLHEMLGNRWSAIAARLPGRTDNEIK 105 (267)
Q Consensus 78 Li~lv~~~G~kWs~IA~~lpgRT~~q~k 105 (267)
|..+....|..|.++|.+| |-+..+|.
T Consensus 10 l~~ia~~iG~~Wk~Lar~L-Gls~~dI~ 36 (86)
T cd08318 10 ITVFANKLGEDWKTLAPHL-EMKDKEIR 36 (86)
T ss_pred HHHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 4446788899999999999 77777663
No 98
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=40.56 E-value=66 Score=26.02 Aligned_cols=29 Identities=14% Similarity=0.122 Sum_probs=23.4
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-.-.+||..| |-+...|+++.+..+++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 121 EDMDVAETAAAM-GCSEGSVKTHCSRATHA 149 (161)
T ss_pred hcCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456689999999 99999999988765544
No 99
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=40.52 E-value=82 Score=26.69 Aligned_cols=29 Identities=17% Similarity=0.248 Sum_probs=22.7
Q ss_pred HcCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 024492 84 MLGNRWSAIAARLPGRTDNEIKNVWHTHLK 113 (267)
Q Consensus 84 ~~G~kWs~IA~~lpgRT~~q~knRW~~llr 113 (267)
..|-.-.+||..| |-+...|+.+.+..++
T Consensus 150 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~ 178 (195)
T PRK12532 150 ILGFSSDEIQQMC-GISTSNYHTIMHRARE 178 (195)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3456689999999 9999999988876443
No 100
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=40.43 E-value=78 Score=26.58 Aligned_cols=33 Identities=21% Similarity=0.158 Sum_probs=26.7
Q ss_pred HHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhHHH
Q 024492 83 EMLGNRWSAIAARLPGRTDNEIKNVWHTHLKKRL 116 (267)
Q Consensus 83 ~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk~~ 116 (267)
...|-...+||..| |-+...|+.|.+.-+.+-+
T Consensus 140 ~~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~ 172 (178)
T PRK12529 140 TLDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCL 172 (178)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 34566799999999 9999999999887776543
No 101
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=39.86 E-value=50 Score=26.00 Aligned_cols=47 Identities=19% Similarity=0.167 Sum_probs=31.9
Q ss_pred CCCCHHHHHHHHHHHHHc----C----CcHHHHhh----hCC-CCCHHHHHHHHHHhhhH
Q 024492 68 GNFTREEEDTIINLHEML----G----NRWSAIAA----RLP-GRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 68 g~WT~EED~~Li~lv~~~----G----~kWs~IA~----~lp-gRT~~q~knRW~~llrk 114 (267)
..||+|+|..|++.+..| | ..|..+-. .|. .=+.+|+.++-+.+-++
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~K 64 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKK 64 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHH
Confidence 359999999999998766 5 23544433 332 23778888888765444
No 102
>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=39.84 E-value=61 Score=26.67 Aligned_cols=29 Identities=24% Similarity=0.313 Sum_probs=22.4
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-...+||..| |-|...|+++.+..+++
T Consensus 134 ~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~ 162 (169)
T TIGR02954 134 HDLTIKEIAEVM-NKPEGTVKTYLHRALKK 162 (169)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355688888888 88999999888865554
No 103
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=39.77 E-value=28 Score=39.05 Aligned_cols=73 Identities=15% Similarity=0.178 Sum_probs=44.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhcccCCCCCCCCCCHHHHHHHHHHHHHc-CCcHHH
Q 024492 13 KKGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFTREEEDTIINLHEML-GNRWSA 91 (267)
Q Consensus 13 kkG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~L~p~ikkg~WT~EED~~Li~lv~~~-G~kWs~ 91 (267)
.---|..++|..|+-.|-+||.++|.+|-.- |. =|.. =...+.-.+..+.+=...-..|+.+...+ +.+|.+
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir~D-p~-----L~l~-dKi~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~ 1204 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIRLD-PD-----LGLT-DKIFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPK 1204 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhccC-cc-----ccch-hhhcccccCCchHHHHHHHHHHHHHHhhcccCCCch
Confidence 3467999999999999999999999988422 11 1110 01111112345556666677777777666 344444
Q ss_pred H
Q 024492 92 I 92 (267)
Q Consensus 92 I 92 (267)
.
T Consensus 1205 ~ 1205 (1373)
T KOG0384|consen 1205 K 1205 (1373)
T ss_pred h
Confidence 3
No 104
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=39.53 E-value=67 Score=22.55 Aligned_cols=35 Identities=26% Similarity=0.444 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHH
Q 024492 73 EEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVW 108 (267)
Q Consensus 73 EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW 108 (267)
+.|+..+.+..+.|-.=.+||+.+ ||+.+.|++.-
T Consensus 7 ~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl 41 (50)
T PF11427_consen 7 DAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRYL 41 (50)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHHH
T ss_pred HHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHHh
Confidence 456677888889999999999999 99999888743
No 105
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=39.32 E-value=57 Score=27.12 Aligned_cols=28 Identities=14% Similarity=0.055 Sum_probs=22.1
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 86 GNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
|-...+||..| |-+...|+++.+..+++
T Consensus 152 g~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T TIGR02948 152 DLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 55688999998 88999999988765544
No 106
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=39.00 E-value=71 Score=26.47 Aligned_cols=35 Identities=20% Similarity=0.310 Sum_probs=26.6
Q ss_pred HHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 79 INLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 79 i~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
+.+....|-...+||..| |-+...|+.+-+.-+++
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 333344567799999999 99999999988766554
No 107
>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=38.80 E-value=39 Score=25.59 Aligned_cols=33 Identities=27% Similarity=0.563 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHH
Q 024492 72 REEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKN 106 (267)
Q Consensus 72 ~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~kn 106 (267)
+||-++|+..- ..|..|..+|..| |=+...|++
T Consensus 2 ~~~v~~ll~~~-nlG~dW~~LA~~L-G~~~~~I~~ 34 (77)
T cd08311 2 QEEVEKLLESG-RPGRDWRSLAGEL-GYEDEAIDT 34 (77)
T ss_pred hHHHHHHHhCC-CCccCHHHHHHHc-CCCHHHHHH
Confidence 57777777422 5788999999999 877877765
No 108
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=38.56 E-value=21 Score=36.83 Aligned_cols=48 Identities=15% Similarity=0.313 Sum_probs=42.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhc
Q 024492 10 MGLKKGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWIN 59 (267)
Q Consensus 10 ~~lkkG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n 59 (267)
++...++|+.+|-++...+....|. +...|+..+++ |..+|++.++..
T Consensus 405 k~~~~~~w~~se~e~fyka~~~~gs-~~slis~l~p~-R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 405 KKLETDKWDASETELFYKALSERGS-DFSLISNLFPL-RDRKQIKAKFKK 452 (584)
T ss_pred CccccCcccchhhHHhhhHHhhhcc-ccccccccccc-ccHHHHHHHHhh
Confidence 4556799999999999999999997 99999999998 999999887654
No 109
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=38.44 E-value=86 Score=26.40 Aligned_cols=29 Identities=14% Similarity=0.134 Sum_probs=23.8
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-...+||..| |-+...|+++++..+++
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 456789999999 88999999998875544
No 110
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=38.13 E-value=74 Score=26.25 Aligned_cols=29 Identities=31% Similarity=0.368 Sum_probs=22.9
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-.-.+||..| |.+...|+.+.+.-+++
T Consensus 133 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 161 (173)
T PRK09645 133 RGWSTAQIAADL-GIPEGTVKSRLHYALRA 161 (173)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 455678999999 99999999988765544
No 111
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=37.54 E-value=75 Score=26.56 Aligned_cols=29 Identities=21% Similarity=0.305 Sum_probs=23.3
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-...+||..| |-+...|+.+.+..+++
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 456689999999 99999999988865554
No 112
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=37.18 E-value=72 Score=27.01 Aligned_cols=30 Identities=23% Similarity=0.152 Sum_probs=24.0
Q ss_pred HcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 84 MLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 84 ~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
..|-...+||..| |-+...|+++....+++
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 3466799999999 99999999988765544
No 113
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=37.14 E-value=35 Score=35.58 Aligned_cols=47 Identities=13% Similarity=0.304 Sum_probs=34.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccccchhhccc---------ccccccccchhccc
Q 024492 14 KGPWTPEEDQILINYVKLYGHGNWRALPKQAGLL---------RCGKSCRLRWINYL 61 (267)
Q Consensus 14 kG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~---------Rt~kqCr~Rw~n~L 61 (267)
|..||..|.+.+..++.++|. ++..|-..+-.. ++-.|.|.+|++.+
T Consensus 88 ktaWt~~E~~~Ffdal~~~GK-dFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~ 143 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGK-DFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLV 143 (782)
T ss_pred ccccchhhHHHHHHHHHHhcc-cHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHH
Confidence 668999999999999999995 888883332221 44566777776654
No 114
>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=37.12 E-value=48 Score=24.47 Aligned_cols=29 Identities=28% Similarity=0.657 Sum_probs=21.8
Q ss_pred HHHHHHHHHH-cCCcHHHHhhhCCCCCHHHH
Q 024492 75 EDTIINLHEM-LGNRWSAIAARLPGRTDNEI 104 (267)
Q Consensus 75 D~~Li~lv~~-~G~kWs~IA~~lpgRT~~q~ 104 (267)
.+.|..+... .|..|..+|.+| |=+..+|
T Consensus 5 ~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i 34 (88)
T smart00005 5 REKLAKLLDHPLGLDWRELARKL-GLSEADI 34 (88)
T ss_pred HHHHHHHHcCccchHHHHHHHHc-CCCHHHH
Confidence 4566777777 899999999999 5455554
No 115
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=37.10 E-value=16 Score=30.44 Aligned_cols=45 Identities=16% Similarity=0.130 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHhCCCCccccchhhcccccccccccchhcccCCCCC
Q 024492 20 EEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINYLRPDIK 66 (267)
Q Consensus 20 EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~L~p~ik 66 (267)
+-|.+|+.+.++.|-..|..||+.++ -+...|+.|+.+...-++-
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~lg--lS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQFG--VSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCe
Confidence 57899999999999889999999998 6888999998887665543
No 116
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=36.96 E-value=79 Score=25.68 Aligned_cols=29 Identities=10% Similarity=-0.073 Sum_probs=22.9
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-.-.+||+.| |-+...|+++.+..+++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (160)
T PRK09642 121 EEKSYQEIALQE-KIEVKTVEMKLYRARKW 149 (160)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 455689999999 99999999987765543
No 117
>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=36.81 E-value=78 Score=26.94 Aligned_cols=31 Identities=16% Similarity=0.111 Sum_probs=24.4
Q ss_pred HHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 83 EMLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 83 ~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
-..|-...+||..| |-+...|+.|....+++
T Consensus 144 ~~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 144 EVLGFESDEICQEL-EISTSNCHVLLYRARLS 174 (188)
T ss_pred HHhCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 33466789999999 99999999988765544
No 118
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=36.22 E-value=71 Score=26.93 Aligned_cols=28 Identities=11% Similarity=0.126 Sum_probs=22.0
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 86 GNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
|-...+||..| |-+...|+++.+..+++
T Consensus 154 g~s~~eIA~~l-gis~~tv~~~l~Rar~~ 181 (193)
T PRK11923 154 GLSYEDIASVM-QCPVGTVRSRIFRAREA 181 (193)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 45688999999 88999999988765543
No 119
>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=36.12 E-value=44 Score=25.71 Aligned_cols=30 Identities=37% Similarity=0.629 Sum_probs=24.3
Q ss_pred HHHHHHHHHcCCcHHHHhhhCCCCCHHHHHH
Q 024492 76 DTIINLHEMLGNRWSAIAARLPGRTDNEIKN 106 (267)
Q Consensus 76 ~~Li~lv~~~G~kWs~IA~~lpgRT~~q~kn 106 (267)
+.|-.+....|..|..+|.+| |=+..+|..
T Consensus 3 ~~l~~l~~~lG~~Wk~lar~L-G~s~~eI~~ 32 (86)
T cd08777 3 KHLDLLRENLGKKWKRCARKL-GFTESEIEE 32 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHc-CCCHHHHHH
Confidence 445666788899999999999 888887765
No 120
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=35.09 E-value=86 Score=26.64 Aligned_cols=29 Identities=10% Similarity=0.012 Sum_probs=22.5
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-...+||..| |-+...|+.|.+..+++
T Consensus 156 eg~s~~EIA~~l-gis~~tVk~rl~ra~~~ 184 (194)
T PRK12531 156 EELPHQQVAEMF-DIPLGTVKSRLRLAVEK 184 (194)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 355688999999 99999999887765544
No 121
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=34.72 E-value=1.3e+02 Score=23.57 Aligned_cols=43 Identities=16% Similarity=0.157 Sum_probs=36.0
Q ss_pred CCCCCHHHHHHHHHHHHHcCCcHHHHhhhCCCC-CHHHHHHHHHH
Q 024492 67 RGNFTREEEDTIINLHEMLGNRWSAIAARLPGR-TDNEIKNVWHT 110 (267)
Q Consensus 67 kg~WT~EED~~Li~lv~~~G~kWs~IA~~lpgR-T~~q~knRW~~ 110 (267)
+..||.|.-..+++++..-|..=+.||..+ |- ..++++..++.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~~W~~~ 48 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLYKWRIQ 48 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHHHHHHH
Confidence 567999999999999999999889999999 75 77777665554
No 122
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=34.52 E-value=1.1e+02 Score=25.73 Aligned_cols=29 Identities=21% Similarity=0.297 Sum_probs=23.2
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-...+||..| |-+...|+.+.+..+++
T Consensus 154 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 154 VGLSAEETAEAV-GSTPGAVRVAQHRALAR 182 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466789999999 98999999888765544
No 123
>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=33.99 E-value=92 Score=26.54 Aligned_cols=46 Identities=20% Similarity=0.208 Sum_probs=37.7
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCcHHHHhhhC----CCCCHHHHHHHHHHh
Q 024492 66 KRGNFTREEEDTIINLHEMLGNRWSAIAARL----PGRTDNEIKNVWHTH 111 (267)
Q Consensus 66 kkg~WT~EED~~Li~lv~~~G~kWs~IA~~l----pgRT~~q~knRW~~l 111 (267)
....-|..|..-|..|+++||..+...|.-. --.|..||+.+...+
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 3456889999999999999999999998743 258999998877654
No 124
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=33.70 E-value=91 Score=26.49 Aligned_cols=28 Identities=7% Similarity=-0.049 Sum_probs=23.0
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLK 113 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llr 113 (267)
.|-...+||..| |-+...|+.|.+..++
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~RAr~ 176 (189)
T PRK12530 149 LELSSEQICQEC-DISTSNLHVLLYRARL 176 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 456699999999 9999999998776554
No 125
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=33.45 E-value=97 Score=25.10 Aligned_cols=45 Identities=11% Similarity=0.105 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHcC-CcHHHHhhhCCCCCHHHHHHHHHHhhhHHHh
Q 024492 72 REEEDTIINLHEMLG-NRWSAIAARLPGRTDNEIKNVWHTHLKKRLK 117 (267)
Q Consensus 72 ~EED~~Li~lv~~~G-~kWs~IA~~lpgRT~~q~knRW~~llrk~~~ 117 (267)
.+-|.+|+++.+.-+ -.+..||+.+ |-+...|.+|-+.+.+..+-
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~GiI 52 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGVI 52 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCce
Confidence 356788888888877 5699999999 99999999999888776543
No 126
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=33.15 E-value=94 Score=26.45 Aligned_cols=30 Identities=10% Similarity=0.026 Sum_probs=23.1
Q ss_pred HcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 84 MLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 84 ~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
..|-.+.+||..| |-+...|+++-+..+++
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 3456799999999 88888888877765444
No 127
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=33.12 E-value=56 Score=21.71 Aligned_cols=36 Identities=33% Similarity=0.435 Sum_probs=18.1
Q ss_pred CCCHHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHH
Q 024492 69 NFTREEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKN 106 (267)
Q Consensus 69 ~WT~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~kn 106 (267)
.+|.+|=..|..+ ..-|-.=.+||+.| ||+...|.+
T Consensus 4 ~Lt~~eR~~I~~l-~~~G~s~~~IA~~l-g~s~sTV~r 39 (44)
T PF13936_consen 4 HLTPEERNQIEAL-LEQGMSIREIAKRL-GRSRSTVSR 39 (44)
T ss_dssp --------HHHHH-HCS---HHHHHHHT-T--HHHHHH
T ss_pred chhhhHHHHHHHH-HHcCCCHHHHHHHH-CcCcHHHHH
Confidence 4566666565555 46788889999999 999988865
No 128
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=32.58 E-value=16 Score=30.95 Aligned_cols=46 Identities=20% Similarity=0.171 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhcccCCCCC
Q 024492 19 PEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINYLRPDIK 66 (267)
Q Consensus 19 ~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~L~p~ik 66 (267)
.+-|.+|+.+.++.|...|..||+.++ -+...|+.|+.+...-++-
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lg--lS~~tv~~Ri~rL~~~GvI 58 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVG--LSPTPCLERVRRLERQGFI 58 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCe
Confidence 456899999999999889999999998 5888899998887766543
No 129
>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=32.56 E-value=58 Score=25.08 Aligned_cols=27 Identities=26% Similarity=0.407 Sum_probs=21.8
Q ss_pred HHHHHHHHHHcCCcHHHHhhhCCCCCHH
Q 024492 75 EDTIINLHEMLGNRWSAIAARLPGRTDN 102 (267)
Q Consensus 75 D~~Li~lv~~~G~kWs~IA~~lpgRT~~ 102 (267)
|..|..+...+|..|.++|.+| |=+..
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L-~vs~~ 30 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL-QFSVE 30 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc-CCCHH
Confidence 5678888899999999999998 44443
No 130
>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=32.28 E-value=48 Score=25.34 Aligned_cols=26 Identities=27% Similarity=0.544 Sum_probs=21.4
Q ss_pred HHHHHHHHHcCCcHHHHhhhCCCCCHH
Q 024492 76 DTIINLHEMLGNRWSAIAARLPGRTDN 102 (267)
Q Consensus 76 ~~Li~lv~~~G~kWs~IA~~lpgRT~~ 102 (267)
..|..+....|..|..+|.+| |=+..
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L-Glse~ 28 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL-GLSYR 28 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc-CCCHH
Confidence 568889999999999999999 54443
No 131
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=31.96 E-value=1.6e+02 Score=19.78 Aligned_cols=44 Identities=25% Similarity=0.394 Sum_probs=35.4
Q ss_pred CCCCCCHHHHHHHHHHHHHcC----CcHHHHhhhCCCCCHHHHHHHHHH
Q 024492 66 KRGNFTREEEDTIINLHEMLG----NRWSAIAARLPGRTDNEIKNVWHT 110 (267)
Q Consensus 66 kkg~WT~EED~~Li~lv~~~G----~kWs~IA~~lpgRT~~q~knRW~~ 110 (267)
++..+|.+.-..|...+.... ..-..||..+ |-+..+|++.|.+
T Consensus 3 ~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l-~l~~~~V~~WF~n 50 (57)
T PF00046_consen 3 KRTRFTKEQLKVLEEYFQENPYPSKEEREELAKEL-GLTERQVKNWFQN 50 (57)
T ss_dssp SSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHH-TSSHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHhccccccccccccccc-cccccccccCHHH
Confidence 356789999999999998743 2368889888 9999999997775
No 132
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=31.89 E-value=85 Score=26.12 Aligned_cols=29 Identities=24% Similarity=0.286 Sum_probs=23.7
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-...+||+.| |-+...|+++.+..++.
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 355689999999 99999999988776654
No 133
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=31.32 E-value=1.1e+02 Score=25.47 Aligned_cols=28 Identities=21% Similarity=0.254 Sum_probs=22.5
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 86 GNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
|-.-.+||..| |.+...++++.+..+++
T Consensus 145 g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 172 (179)
T PRK12514 145 GLSYKELAERH-DVPLNTMRTWLRRSLLK 172 (179)
T ss_pred CCCHHHHHHHH-CCChHHHHHHHHHHHHH
Confidence 55688999999 99999999988765544
No 134
>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=31.32 E-value=1.1e+02 Score=24.87 Aligned_cols=28 Identities=25% Similarity=0.334 Sum_probs=21.3
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 86 GNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
|-...+||+.| |-+...|+++-+..+++
T Consensus 138 g~s~~eIA~~l-~is~~tv~~~l~ra~~~ 165 (170)
T TIGR02952 138 NLPIAEVARIL-GKTEGAVKILQFRAIKK 165 (170)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 55678899988 88888888877654443
No 135
>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=30.74 E-value=1.2e+02 Score=25.23 Aligned_cols=29 Identities=21% Similarity=0.218 Sum_probs=22.8
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-...+||..| |-+...|+.|.+..+++
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 177 (183)
T TIGR02999 149 AGLTVEEIAELL-GVSVRTVERDWRFARAW 177 (183)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 345689999999 99999999988765443
No 136
>PRK01905 DNA-binding protein Fis; Provisional
Probab=30.73 E-value=1.3e+02 Score=22.36 Aligned_cols=35 Identities=23% Similarity=0.198 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHH
Q 024492 72 REEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNV 107 (267)
Q Consensus 72 ~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knR 107 (267)
.-|.+.|.+++..+|+++++.|+.+ |=+...++.+
T Consensus 36 ~~E~~~i~~aL~~~~gn~s~aAr~L-GIsrstL~rk 70 (77)
T PRK01905 36 CVEKPLLEVVMEQAGGNQSLAAEYL-GINRNTLRKK 70 (77)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHH
Confidence 3467789999999999999999988 6666655444
No 137
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=30.45 E-value=1.2e+02 Score=24.53 Aligned_cols=29 Identities=21% Similarity=0.231 Sum_probs=22.6
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-.-.+||..| |-+...++.|....++.
T Consensus 120 ~~~s~~eIA~~l-gis~~tv~~~l~ra~~~ 148 (159)
T PRK12527 120 EGLSHQQIAEHL-GISRSLVEKHIVNAMKH 148 (159)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 345678999999 99999999987765544
No 138
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=30.01 E-value=1.2e+02 Score=25.33 Aligned_cols=28 Identities=21% Similarity=0.184 Sum_probs=22.1
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 86 GNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
|-.-.+||..| |-+...|+.+.+..+++
T Consensus 151 ~~s~~eIA~~l-gis~~~V~~~l~ra~~~ 178 (186)
T PRK13919 151 GYTHREAAQLL-GLPLGTLKTRARRALSR 178 (186)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 45578999999 99999999888765544
No 139
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=29.63 E-value=1.3e+02 Score=24.49 Aligned_cols=30 Identities=20% Similarity=0.255 Sum_probs=23.1
Q ss_pred HcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 84 MLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 84 ~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
-.|-...+||..+ |-+...|+.|.+..+++
T Consensus 127 ~~g~s~~EIA~~l-~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 127 VDGLGYGEIATEL-GISLATVKRYLNKAAMR 156 (161)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466789999999 88999998887765443
No 140
>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=29.61 E-value=70 Score=21.99 Aligned_cols=43 Identities=26% Similarity=0.314 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 69 NFTREEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 69 ~WT~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
..|+.|-+.|.-+. -|..=.+||..+ |.+...|+.+...++++
T Consensus 3 ~LT~~E~~vl~~l~--~G~~~~eIA~~l-~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLA--QGMSNKEIAEEL-GISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHH--TTS-HHHHHHHH-TSHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHH--hcCCcchhHHhc-CcchhhHHHHHHHHHHH
Confidence 35666666555544 355568999999 99999999988877665
No 141
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=29.60 E-value=1.4e+02 Score=23.91 Aligned_cols=28 Identities=21% Similarity=0.311 Sum_probs=20.4
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 86 GNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
|-...+||..+ |-+...|+++-+..+++
T Consensus 122 ~~s~~EIA~~l-~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 122 GKTMGEIALET-EMTYYQVRWIYRQALEK 149 (154)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 44578888888 88888888876654443
No 142
>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=29.59 E-value=1.4e+02 Score=24.70 Aligned_cols=29 Identities=21% Similarity=0.546 Sum_probs=22.6
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-...+||..| |-|...|+.+.+..+++
T Consensus 155 ~g~s~~eIA~~l-gis~~~v~~~l~Ra~~~ 183 (189)
T TIGR02984 155 EGLSFAEVAERM-DRSEGAVSMLWVRGLAR 183 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 456688888888 88999998888765544
No 143
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=29.54 E-value=1.3e+02 Score=25.48 Aligned_cols=29 Identities=21% Similarity=0.161 Sum_probs=23.2
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-...+||..| |-+...|+.+.+..+++
T Consensus 145 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 173 (185)
T PRK09649 145 LGLSYADAAAVC-GCPVGTIRSRVARARDA 173 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 345689999999 99999999988765544
No 144
>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=29.49 E-value=41 Score=27.00 Aligned_cols=28 Identities=18% Similarity=0.125 Sum_probs=23.0
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 86 GNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
|-.+.+||..| |=+...|+++.+...++
T Consensus 121 g~s~~eIA~~l-gis~~tv~~~l~Ra~~~ 148 (154)
T TIGR02950 121 EFSYKEIAELL-NLSLAKVKSNLFRARKE 148 (154)
T ss_pred cCcHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 44699999999 99999999998875544
No 145
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=29.22 E-value=35 Score=29.17 Aligned_cols=47 Identities=13% Similarity=0.152 Sum_probs=32.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccccchhhccc---ccccccccchhc
Q 024492 12 LKKGPWTPEEDQILINYVKLYGHGNWRALPKQAGLL---RCGKSCRLRWIN 59 (267)
Q Consensus 12 lkkG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~---Rt~kqCr~Rw~n 59 (267)
-+...=|..|.+-|..+|++||. ++...+.-.-++ .|..||+.+...
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhGd-Dy~aMarD~KLN~~Q~T~~qlrrki~~ 161 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHGD-DYKAMARDRKLNYMQHTPGQLRRKIRK 161 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHCc-cHHHHhccCCCCcccCCHHHHHHHHHH
Confidence 35567789999999999999996 887777543311 455555554433
No 146
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=29.16 E-value=1.5e+02 Score=24.79 Aligned_cols=30 Identities=23% Similarity=0.221 Sum_probs=24.1
Q ss_pred HcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 84 MLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 84 ~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
..|-...+||..| |.+...|+++-+..+++
T Consensus 143 ~~g~s~~EIA~~l-~is~~tV~~~l~rar~~ 172 (181)
T PRK12536 143 LEGLSVAETAQLT-GLSESAVKVGIHRGLKA 172 (181)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3456789999999 99999999988765444
No 147
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=28.52 E-value=1.5e+02 Score=25.09 Aligned_cols=28 Identities=36% Similarity=0.439 Sum_probs=21.0
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 86 GNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
|-.-.+||..| |.|...|+++-+..+++
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 45568888888 88888888887765444
No 148
>PRK00118 putative DNA-binding protein; Validated
Probab=28.47 E-value=1.7e+02 Score=23.44 Aligned_cols=41 Identities=12% Similarity=0.117 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 024492 72 REEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLK 113 (267)
Q Consensus 72 ~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llr 113 (267)
++.+..++.+....|-...+||+.+ |-|...|+.+-+...+
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~RArk 59 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKRTEK 59 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 4567777888888899999999999 9999999887665443
No 149
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=28.35 E-value=1.4e+02 Score=24.92 Aligned_cols=29 Identities=10% Similarity=0.042 Sum_probs=21.2
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-...+||+.| |-+...|+++.+..+++
T Consensus 143 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 171 (186)
T PRK05602 143 QGLSNIEAAAVM-DISVDALESLLARGRRA 171 (186)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 455678888888 88888888887655443
No 150
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=28.23 E-value=1.3e+02 Score=25.67 Aligned_cols=33 Identities=18% Similarity=0.117 Sum_probs=24.6
Q ss_pred HHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 81 LHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 81 lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
|....|-...+||..| |-+...|+.|-+..+++
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 3334466789999999 99999999887755543
No 151
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=28.11 E-value=1.3e+02 Score=25.34 Aligned_cols=29 Identities=14% Similarity=-0.035 Sum_probs=22.7
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-.-.+||..| |-+...|++|.+..+++
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 355678999999 99999999988765543
No 152
>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=27.65 E-value=1.3e+02 Score=24.43 Aligned_cols=38 Identities=16% Similarity=0.163 Sum_probs=26.5
Q ss_pred HHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 76 DTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 76 ~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
..++.+.-..|-.-.+||..| |-+...|+++.+..+++
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 333334334456678889888 88999999988866554
No 153
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=27.60 E-value=1.5e+02 Score=24.42 Aligned_cols=30 Identities=20% Similarity=0.120 Sum_probs=22.7
Q ss_pred HcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 84 MLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 84 ~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
..|-...+||..| |-+...|+++-+..+++
T Consensus 126 ~~g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 155 (164)
T PRK12547 126 ASGFSYEDAAAIC-GCAVGTIKSRVSRARNR 155 (164)
T ss_pred HcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3456689999999 88899998887765443
No 154
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=27.32 E-value=1.7e+02 Score=25.37 Aligned_cols=29 Identities=24% Similarity=0.307 Sum_probs=22.8
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-.-.+||..| |-+...|+++.+..+++
T Consensus 153 ~g~s~~EIA~~L-gis~~tV~~~l~RArk~ 181 (203)
T PRK09647 153 EGLSYEEIAATL-GVKLGTVRSRIHRGRQQ 181 (203)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 455678899999 99999999988766544
No 155
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=27.18 E-value=1.4e+02 Score=25.04 Aligned_cols=29 Identities=14% Similarity=0.350 Sum_probs=22.9
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-.-.+||..| |-+...|+++.+..+++
T Consensus 137 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 165 (185)
T PRK12542 137 YNLTYQEISSVM-GITEANVRKQFERARKR 165 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456689999999 99999999987755543
No 156
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=26.88 E-value=1.4e+02 Score=25.69 Aligned_cols=28 Identities=18% Similarity=0.062 Sum_probs=21.9
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLK 113 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llr 113 (267)
.|-.-.+||..| |.+...|+.|.+..++
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 345689999999 9999999988765443
No 157
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=26.51 E-value=1.2e+02 Score=33.63 Aligned_cols=43 Identities=23% Similarity=0.442 Sum_probs=36.1
Q ss_pred CCCCHHHHHHHHHHHHHcC-CcHHHHhhhCCCCCHHHHHHHHHH
Q 024492 68 GNFTREEEDTIINLHEMLG-NRWSAIAARLPGRTDNEIKNVWHT 110 (267)
Q Consensus 68 g~WT~EED~~Li~lv~~~G-~kWs~IA~~lpgRT~~q~knRW~~ 110 (267)
+.|+.-+=...+.+..+|| ..-..||..|.|+|..+|+.....
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~~ 868 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAKV 868 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHHH
Confidence 3688888888888889999 679999999999999999865443
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=26.00 E-value=1.4e+02 Score=27.47 Aligned_cols=29 Identities=21% Similarity=0.260 Sum_probs=23.2
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
+|-.-.+||..| |.+...|++|.+..+++
T Consensus 157 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 185 (324)
T TIGR02960 157 LGWRAAETAELL-GTSTASVNSALQRARAT 185 (324)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355689999999 99999999988765544
No 159
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=25.45 E-value=1.8e+02 Score=22.77 Aligned_cols=34 Identities=12% Similarity=0.072 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHH
Q 024492 73 EEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNV 107 (267)
Q Consensus 73 EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knR 107 (267)
-|...|..+++.++++..+.|+.| |=+...++.+
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~L-GIsRsTL~rK 88 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALML-GINRGTLRKK 88 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHH
Confidence 477788999999999999999999 6666655443
No 160
>PF08870 DUF1832: Domain of unknown function (DUF1832); InterPro: IPR014969 This entry describes the DndE protein encoded by an operon associated with a sulphur-containing modification to DNA []. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndE is a putative carboxylase homologous to NCAIR synthetases.
Probab=25.30 E-value=2.4e+02 Score=22.82 Aligned_cols=89 Identities=18% Similarity=0.215 Sum_probs=59.7
Q ss_pred CHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhc-ccCC----CCCCCCCCHHHHHHHHHHHHHcCCcHHHH
Q 024492 18 TPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWIN-YLRP----DIKRGNFTREEEDTIINLHEMLGNRWSAI 92 (267)
Q Consensus 18 T~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n-~L~p----~ikkg~WT~EED~~Li~lv~~~G~kWs~I 92 (267)
|++-+++|..+-.+.|..+|..+++.+-. |+-..=. ++.. ...+ .+++--|+-|-++..+.+++++-+
T Consensus 5 S~~~~~~L~~Lk~~tgi~~~Nil~R~A~~-~SL~~~~-~~~~~~~~~d~g~e~~~~t~~Ge~~~~~~~ll~q~~g----- 77 (113)
T PF08870_consen 5 SKKAKEQLKKLKRRTGITPWNILCRIAFC-RSLEEPS-IPSDEDIKDDSGLELNWKTFTGEYDDIYEALLKQRYG----- 77 (113)
T ss_pred CHHHHHHHHHHHHhcCCCcccHHHHHHHH-HHHccCC-CCCCCccCCCCCeEEeeeeecCchHHHHHHHHHHHhC-----
Confidence 67778999999999999999988877443 2221111 1111 1111 234557888888888877766541
Q ss_pred hhhCCCCCHHHHHHHHHHhhhHHHh
Q 024492 93 AARLPGRTDNEIKNVWHTHLKKRLK 117 (267)
Q Consensus 93 A~~lpgRT~~q~knRW~~llrk~~~ 117 (267)
++-++..+...|+.|+.+.+.
T Consensus 78 ----~~~d~~~l~~~~~~Hl~rGi~ 98 (113)
T PF08870_consen 78 ----PELDDEELPKYFKLHLDRGIE 98 (113)
T ss_pred ----CCCCHHHHHHHHHHHHHHhHH
Confidence 355888999999999987664
No 161
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=24.97 E-value=1.6e+02 Score=24.66 Aligned_cols=29 Identities=31% Similarity=0.310 Sum_probs=21.9
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-.-.+||+.| |-+...++++.+..+++
T Consensus 148 ~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 176 (182)
T PRK12537 148 DGCSHAEIAQRL-GAPLGTVKAWIKRSLKA 176 (182)
T ss_pred cCCCHHHHHHHH-CCChhhHHHHHHHHHHH
Confidence 355678888888 88888888888766544
No 162
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=24.87 E-value=97 Score=27.30 Aligned_cols=28 Identities=18% Similarity=0.170 Sum_probs=22.7
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 86 GNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
|-...+||..| |.+...|+++.+..+++
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 45689999999 99999999998765544
No 163
>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=24.82 E-value=49 Score=24.57 Aligned_cols=18 Identities=22% Similarity=0.530 Sum_probs=14.9
Q ss_pred HHHHHHHHcCCcHHHHhh
Q 024492 77 TIINLHEMLGNRWSAIAA 94 (267)
Q Consensus 77 ~Li~lv~~~G~kWs~IA~ 94 (267)
.|.+|++.||++|.-|-.
T Consensus 31 vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 31 VLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHcCCchhhhc
Confidence 477888999999999864
No 164
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=24.67 E-value=39 Score=34.09 Aligned_cols=46 Identities=13% Similarity=0.230 Sum_probs=38.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhc
Q 024492 12 LKKGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWIN 59 (267)
Q Consensus 12 lkkG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n 59 (267)
-....||.||--++-.+.+.||. ++.+|-+.||. |+-.+++.-|+.
T Consensus 185 ~~~d~WT~Ed~vlFe~aF~~~GK-~F~kIrq~LP~-rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 185 EFPDEWTAEDIVLFEQAFQFFGK-DFHKIRQALPH-RSLASLVQYYYS 230 (534)
T ss_pred CCcccchHHHHHHHHHHHHHhcc-cHHHHHHHccC-ccHHHHHHHHHH
Confidence 34578999999999999999996 99999999998 887777765544
No 165
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=24.63 E-value=1.7e+02 Score=25.78 Aligned_cols=43 Identities=26% Similarity=0.268 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 69 NFTREEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 69 ~WT~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
..|+.|-+.|.-+.. |-...+||+.| +-+...++++...+++|
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 478766666555555 88889999999 99999999998887766
No 166
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=24.05 E-value=2.1e+02 Score=24.26 Aligned_cols=29 Identities=21% Similarity=0.227 Sum_probs=21.6
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-...+||+.| |-+...|+++-+..+++
T Consensus 157 ~~~s~~EIA~~L-gis~~tVk~~l~ra~~~ 185 (194)
T PRK09646 157 GGLTYREVAERL-AVPLGTVKTRMRDGLIR 185 (194)
T ss_pred cCCCHHHHHHHh-CCChHhHHHHHHHHHHH
Confidence 345689999999 88999898877654443
No 167
>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=23.79 E-value=1.9e+02 Score=23.20 Aligned_cols=27 Identities=30% Similarity=0.339 Sum_probs=18.4
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhh
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHL 112 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~ll 112 (267)
.|-.-.+||..| |=+...|+.+.+...
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 345567777777 777778877766543
No 168
>PRK09483 response regulator; Provisional
Probab=23.19 E-value=1.3e+02 Score=24.97 Aligned_cols=44 Identities=11% Similarity=0.249 Sum_probs=34.0
Q ss_pred CCCCHHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 68 GNFTREEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 68 g~WT~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
...|+.|-+.|.-+. .|..=.+||..| +-+...++++-+++++|
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 358999988875543 555556999999 77999999988877766
No 169
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=22.93 E-value=1.6e+02 Score=25.12 Aligned_cols=30 Identities=13% Similarity=0.088 Sum_probs=23.6
Q ss_pred HcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 84 MLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 84 ~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
..|-...+||..| |-+...|+++-+..+++
T Consensus 127 ~~g~s~~EIA~~L-giS~~tVk~~l~Rar~~ 156 (188)
T PRK12546 127 ASGFSYEEAAEMC-GVAVGTVKSRANRARAR 156 (188)
T ss_pred hcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3566789999999 89999999887765544
No 170
>PRK13858 type IV secretion system T-DNA border endonuclease VirD1; Provisional
Probab=22.86 E-value=1.2e+02 Score=26.00 Aligned_cols=85 Identities=18% Similarity=0.129 Sum_probs=59.9
Q ss_pred CccccccCCCCCCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccchhcccCCCCCCCCCCHHHHHHHHHHH
Q 024492 3 RAPCCEKMGLKKGPWTPEEDQILINYVKLYGHGNWRALPKQAGLLRCGKSCRLRWINYLRPDIKRGNFTREEEDTIINLH 82 (267)
Q Consensus 3 R~p~~~K~~lkkG~WT~EEDe~L~~~V~~~G~~nW~~IA~~l~~~Rt~kqCr~Rw~n~L~p~ikkg~WT~EED~~Li~lv 82 (267)
|.|+-+.+....-+.|++|-..|..-....|. ...+.-+.+-. +.+ +.+.-..-|.|+-..|+.-+
T Consensus 17 ~~~~~~~~kvVsvRLTe~Ey~~L~~rA~~aGl-S~SEfIRqAi~-~~~------------g~V~v~r~T~e~~~~lir~l 82 (147)
T PRK13858 17 ESAKVEGFKVVSTRLRSAEYESFSAQARLLGL-SDSMAIRVAVR-RIG------------GFLEIDAETREKMEAILQSI 82 (147)
T ss_pred cCccccCCeEEEEecCHHHHHHHHHHHHHcCC-CHHHHHHHHHH-hcC------------CeEeecccCHHHHHHHHHHH
Confidence 34566666777889999999999999999996 44443333321 111 12222557888888899999
Q ss_pred HHcCCcHHHHhhhC--CCCCH
Q 024492 83 EMLGNRWSAIAARL--PGRTD 101 (267)
Q Consensus 83 ~~~G~kWs~IA~~l--pgRT~ 101 (267)
...|++=.+||+++ .|+++
T Consensus 83 ~gianNLNQLAr~aN~~~~~~ 103 (147)
T PRK13858 83 GTLSSNIAALLSAYAENPRPD 103 (147)
T ss_pred HHHHHHHHHHHHHHhcCCCCc
Confidence 99999999999987 44443
No 171
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=22.62 E-value=1.7e+02 Score=26.78 Aligned_cols=29 Identities=24% Similarity=0.387 Sum_probs=23.1
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
+|-.-.+||+.| |.+...|+++.+.-.++
T Consensus 130 ~g~s~~EIA~~l-g~s~~tVk~~l~RAr~~ 158 (293)
T PRK09636 130 FGVPFDEIASTL-GRSPAACRQLASRARKH 158 (293)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355689999999 99999999988764443
No 172
>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=22.57 E-value=1.2e+02 Score=23.04 Aligned_cols=28 Identities=25% Similarity=0.567 Sum_probs=20.9
Q ss_pred HHHHHHHcCCcHHHHhhhCCCCCHHHHHH
Q 024492 78 IINLHEMLGNRWSAIAARLPGRTDNEIKN 106 (267)
Q Consensus 78 Li~lv~~~G~kWs~IA~~lpgRT~~q~kn 106 (267)
+--+.+..|..|..+|.+| |=|..+|..
T Consensus 5 f~~i~~~lG~~Wk~laR~L-Glse~~Id~ 32 (86)
T cd08306 5 FDVICENVGRDWRKLARKL-GLSETKIES 32 (86)
T ss_pred HHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 3445567799999999999 777766643
No 173
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=22.33 E-value=2.3e+02 Score=22.93 Aligned_cols=44 Identities=23% Similarity=0.284 Sum_probs=34.7
Q ss_pred CCCCHHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 68 GNFTREEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 68 g~WT~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
...|+.|-+.|.-+.. |-...+||..+ +-+...++++...+++|
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 4688888877776665 45788999999 78999999888877665
No 174
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=22.29 E-value=2.3e+02 Score=24.59 Aligned_cols=29 Identities=3% Similarity=-0.024 Sum_probs=23.0
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-.-.+||..| |-|...++.|.+..+++
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 99999999987765544
No 175
>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=22.10 E-value=1e+02 Score=22.16 Aligned_cols=26 Identities=38% Similarity=0.740 Sum_probs=19.0
Q ss_pred HHHHHHHcCCcHHHHhhhCCCCCHHHH
Q 024492 78 IINLHEMLGNRWSAIAARLPGRTDNEI 104 (267)
Q Consensus 78 Li~lv~~~G~kWs~IA~~lpgRT~~q~ 104 (267)
+..+....|+.|..+|..| |=+..+|
T Consensus 2 ~~~ia~~lg~~W~~la~~L-gl~~~~I 27 (79)
T cd01670 2 LDKLAKKLGKDWKKLARKL-GLSDGEI 27 (79)
T ss_pred HHHHHHHHhhHHHHHHHHh-CCCHHHH
Confidence 4456778899999999999 4444443
No 176
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=21.89 E-value=1.6e+02 Score=24.78 Aligned_cols=29 Identities=34% Similarity=0.233 Sum_probs=21.0
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-.-.+||..| |-+...|+.+-+..+++
T Consensus 156 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 184 (194)
T PRK12519 156 EGLSQSEIAKRL-GIPLGTVKARARQGLLK 184 (194)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 345578888888 88888888876654443
No 177
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=21.53 E-value=2.4e+02 Score=25.32 Aligned_cols=43 Identities=21% Similarity=0.321 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 69 NFTREEEDTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 69 ~WT~EED~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
..|+.|-+.|.-+.+ |-...+||..| +-+...|+++-..+++|
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 478888777666655 77789999999 99999999988877766
No 178
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=21.51 E-value=1e+02 Score=25.33 Aligned_cols=29 Identities=24% Similarity=0.382 Sum_probs=22.4
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
+|-....||..| |-+...++.+.+..+++
T Consensus 141 ~g~s~~eIA~~l-~is~~~V~~~l~ra~~~ 169 (176)
T PRK09638 141 YGYTYEEIAKML-NIPEGTVKSRVHHGIKQ 169 (176)
T ss_pred cCCCHHHHHHHH-CCChhHHHHHHHHHHHH
Confidence 456789999999 88999888877665443
No 179
>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=21.04 E-value=1.9e+02 Score=26.38 Aligned_cols=29 Identities=10% Similarity=0.306 Sum_probs=23.4
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
+|-.-.+||..| |.|...|+.+.+...++
T Consensus 123 ~g~s~~EIA~~l-g~s~~tVr~~l~RAr~~ 151 (281)
T TIGR02957 123 FDYPYEEIASIV-GKSEANCRQLVSRARRH 151 (281)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456689999999 89999999988765444
No 180
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=20.67 E-value=2.2e+02 Score=23.02 Aligned_cols=29 Identities=24% Similarity=0.338 Sum_probs=21.7
Q ss_pred cCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 85 LGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 85 ~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
.|-.-.+||..| |-+...|+++.+..+++
T Consensus 126 ~g~s~~eIA~~l-gis~~tV~~~i~ra~~~ 154 (166)
T PRK09639 126 SGYSYKEIAEAL-GIKESSVGTTLARAKKK 154 (166)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 555678888888 88888888887655443
No 181
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=20.56 E-value=2e+02 Score=24.07 Aligned_cols=28 Identities=18% Similarity=0.120 Sum_probs=20.2
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 86 GNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
|-.-.+||+.| |-+...|+.|.+..+++
T Consensus 143 g~s~~EIA~~l-~is~~tv~~~l~Ra~~~ 170 (179)
T PRK09415 143 ELSIKEIAEVT-GVNENTVKTRLKKAKEL 170 (179)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 44567888888 77888888877765543
No 182
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=20.49 E-value=2.2e+02 Score=24.48 Aligned_cols=28 Identities=18% Similarity=0.102 Sum_probs=21.7
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 86 GNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
|-.-.+||..| |.+...|+.+.+..+++
T Consensus 169 g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 196 (206)
T PRK12526 169 ELSQEQLAQQL-NVPLGTVKSRLRLALAK 196 (206)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 45578999999 99999998887765543
No 183
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=20.30 E-value=2.4e+02 Score=24.86 Aligned_cols=30 Identities=17% Similarity=0.279 Sum_probs=23.4
Q ss_pred HcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 84 MLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 84 ~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
..|-...+||..| |-+...|+.+.+..+++
T Consensus 198 ~~g~s~~EIA~~l-gis~~tV~~~~~ra~~~ 227 (236)
T PRK06986 198 QEELNLKEIGAVL-GVSESRVSQIHSQAIKR 227 (236)
T ss_pred ccCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3455689999999 99999998887766554
No 184
>PRK06930 positive control sigma-like factor; Validated
Probab=20.27 E-value=2.2e+02 Score=24.42 Aligned_cols=38 Identities=21% Similarity=0.275 Sum_probs=27.2
Q ss_pred HHHHHHHHHcCCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 76 DTIINLHEMLGNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 76 ~~Li~lv~~~G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
..++.++...|-...+||..| |-+...|+.+.+..+++
T Consensus 120 r~V~~L~~~eg~s~~EIA~~l-giS~~tVk~~l~Ra~~k 157 (170)
T PRK06930 120 KEVYLMHRGYGLSYSEIADYL-NIKKSTVQSMIERAEKK 157 (170)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 334444445677789999999 88888888887765544
No 185
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=20.03 E-value=1.8e+02 Score=25.99 Aligned_cols=28 Identities=11% Similarity=0.089 Sum_probs=22.1
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHhhhH
Q 024492 86 GNRWSAIAARLPGRTDNEIKNVWHTHLKK 114 (267)
Q Consensus 86 G~kWs~IA~~lpgRT~~q~knRW~~llrk 114 (267)
|-.-.+||..| |-+...|+++.+..+++
T Consensus 187 g~s~~EIA~~L-gis~~tVk~~l~RAr~k 214 (233)
T PRK12538 187 NMSNGEIAEVM-DTTVAAVESLLKRGRQQ 214 (233)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 45679999999 99999998887765543
Done!