Query 025221
Match_columns 256
No_of_seqs 229 out of 1425
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 03:44:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025221.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025221hhsearch_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 7.3E-35 1.6E-39 256.9 12.6 113 5-117 20-132 (249)
2 KOG0048 Transcription factor, 100.0 4.8E-35 1.1E-39 260.6 10.3 113 4-116 3-115 (238)
3 PLN03091 hypothetical protein; 100.0 9.4E-33 2E-37 259.4 12.6 113 5-117 9-121 (459)
4 KOG0049 Transcription factor, 99.8 4.5E-20 9.7E-25 179.5 7.3 113 2-115 352-465 (939)
5 KOG0049 Transcription factor, 99.8 1.2E-18 2.7E-23 169.5 7.6 112 3-114 246-412 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.7 6.5E-17 1.4E-21 114.2 5.0 60 13-74 1-60 (60)
7 COG5147 REB1 Myb superfamily p 99.6 2.3E-15 5.1E-20 145.9 7.1 109 4-113 14-122 (512)
8 KOG0050 mRNA splicing protein 99.5 1.2E-14 2.5E-19 139.1 6.3 109 7-117 4-112 (617)
9 KOG0051 RNA polymerase I termi 99.5 8.9E-14 1.9E-18 136.3 6.6 100 9-111 383-510 (607)
10 PF00249 Myb_DNA-binding: Myb- 99.4 6.3E-14 1.4E-18 95.0 2.0 48 10-57 1-48 (48)
11 PF00249 Myb_DNA-binding: Myb- 99.4 1.5E-13 3.4E-18 93.1 3.9 46 63-108 1-48 (48)
12 PF13921 Myb_DNA-bind_6: Myb-l 99.2 2.1E-12 4.5E-17 91.1 1.7 45 66-110 1-45 (60)
13 smart00717 SANT SANT SWI3, AD 99.2 1.1E-11 2.3E-16 82.1 3.9 47 63-109 1-48 (49)
14 PLN03212 Transcription repress 99.1 1.3E-11 2.7E-16 109.8 0.6 55 3-59 71-125 (249)
15 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 9.6E-11 2.1E-15 76.3 4.2 44 65-108 1-45 (45)
16 smart00717 SANT SANT SWI3, AD 99.1 7.9E-11 1.7E-15 77.9 3.5 48 10-58 1-48 (49)
17 PLN03091 hypothetical protein; 99.0 5.6E-11 1.2E-15 112.9 1.7 56 3-60 60-115 (459)
18 KOG0048 Transcription factor, 99.0 1.1E-10 2.4E-15 104.2 2.8 58 60-117 6-65 (238)
19 KOG0051 RNA polymerase I termi 99.0 2.1E-10 4.6E-15 112.8 4.6 103 8-112 306-432 (607)
20 cd00167 SANT 'SWI3, ADA2, N-Co 99.0 5.1E-10 1.1E-14 72.8 3.1 45 12-57 1-45 (45)
21 COG5147 REB1 Myb superfamily p 98.2 9E-07 1.9E-11 86.6 2.6 105 3-110 65-169 (512)
22 TIGR01557 myb_SHAQKYF myb-like 98.0 8E-06 1.7E-10 57.6 3.5 49 9-57 2-54 (57)
23 KOG0457 Histone acetyltransfer 97.8 1.4E-05 3E-10 76.3 3.4 50 8-58 70-119 (438)
24 TIGR01557 myb_SHAQKYF myb-like 97.6 0.00012 2.7E-09 51.5 4.6 47 63-109 3-55 (57)
25 PF13325 MCRS_N: N-terminal re 97.4 0.00073 1.6E-08 59.0 7.6 99 12-112 1-130 (199)
26 KOG0457 Histone acetyltransfer 97.2 0.00036 7.8E-09 66.7 4.4 51 60-110 69-120 (438)
27 PF13837 Myb_DNA-bind_4: Myb/S 97.1 0.00026 5.6E-09 53.0 2.2 54 63-116 1-72 (90)
28 KOG0050 mRNA splicing protein 97.1 0.00015 3.2E-09 70.6 0.3 53 3-58 52-104 (617)
29 COG5259 RSC8 RSC chromatin rem 97.0 0.00041 9E-09 66.9 2.3 46 9-56 278-323 (531)
30 TIGR02894 DNA_bind_RsfA transc 96.9 0.00084 1.8E-08 56.5 3.5 50 62-112 3-59 (161)
31 KOG1279 Chromatin remodeling f 96.9 0.00085 1.8E-08 66.0 4.1 50 61-110 251-300 (506)
32 COG5259 RSC8 RSC chromatin rem 96.9 0.00068 1.5E-08 65.4 3.0 45 64-108 280-324 (531)
33 KOG1279 Chromatin remodeling f 96.8 0.0008 1.7E-08 66.2 2.8 49 6-56 249-297 (506)
34 PF08914 Myb_DNA-bind_2: Rap1 96.8 0.0014 3E-08 47.4 3.3 50 63-112 2-61 (65)
35 TIGR02894 DNA_bind_RsfA transc 96.3 0.0017 3.6E-08 54.8 1.4 49 8-58 2-56 (161)
36 PF08914 Myb_DNA-bind_2: Rap1 96.2 0.0022 4.8E-08 46.3 1.2 52 10-61 2-61 (65)
37 PF13837 Myb_DNA-bind_4: Myb/S 96.1 0.0023 5.1E-08 47.8 1.2 47 11-57 2-64 (90)
38 PF13873 Myb_DNA-bind_5: Myb/S 95.9 0.012 2.6E-07 43.1 4.2 51 63-113 2-74 (78)
39 COG5114 Histone acetyltransfer 95.8 0.0043 9.3E-08 57.6 1.5 47 11-58 64-110 (432)
40 PRK13923 putative spore coat p 95.8 0.0085 1.8E-07 51.1 3.1 49 62-111 4-59 (170)
41 PLN03142 Probable chromatin-re 95.7 0.076 1.6E-06 56.8 10.4 101 12-113 826-989 (1033)
42 PF13873 Myb_DNA-bind_5: Myb/S 95.6 0.0058 1.3E-07 44.8 1.3 49 9-57 1-69 (78)
43 PRK13923 putative spore coat p 95.1 0.0091 2E-07 50.9 1.2 49 8-58 3-57 (170)
44 PF09111 SLIDE: SLIDE; InterP 95.0 0.028 6.1E-07 45.3 3.6 53 60-112 46-114 (118)
45 KOG4282 Transcription factor G 94.9 0.049 1.1E-06 51.0 5.5 56 63-118 54-123 (345)
46 KOG2656 DNA methyltransferase 94.0 0.1 2.2E-06 49.7 5.5 83 32-115 75-188 (445)
47 COG5114 Histone acetyltransfer 94.0 0.041 8.9E-07 51.2 2.8 46 64-109 64-110 (432)
48 PF12776 Myb_DNA-bind_3: Myb/S 92.2 0.21 4.5E-06 37.6 3.9 48 65-112 1-66 (96)
49 COG5118 BDP1 Transcription ini 90.5 0.27 5.8E-06 46.9 3.5 47 64-110 366-412 (507)
50 PF09111 SLIDE: SLIDE; InterP 89.9 0.34 7.4E-06 39.0 3.2 34 7-40 46-82 (118)
51 KOG4167 Predicted DNA-binding 88.2 1.1 2.3E-05 46.2 6.0 44 10-55 619-662 (907)
52 KOG1194 Predicted DNA-binding 87.2 1.9 4.2E-05 42.1 6.9 49 62-110 186-234 (534)
53 PF08281 Sigma70_r4_2: Sigma-7 87.2 1 2.2E-05 30.2 3.8 42 68-110 12-53 (54)
54 PF11626 Rap1_C: TRF2-interact 86.2 0.75 1.6E-05 34.7 2.9 30 6-38 43-80 (87)
55 COG5118 BDP1 Transcription ini 85.1 0.68 1.5E-05 44.2 2.6 63 9-73 364-434 (507)
56 KOG4282 Transcription factor G 81.5 1.1 2.4E-05 41.9 2.5 47 11-57 55-113 (345)
57 smart00595 MADF subfamily of S 81.0 1.7 3.6E-05 32.2 2.9 30 84-114 29-58 (89)
58 PF12776 Myb_DNA-bind_3: Myb/S 78.1 2.2 4.7E-05 31.9 2.8 44 12-55 1-60 (96)
59 PF13404 HTH_AsnC-type: AsnC-t 77.2 1.6 3.6E-05 28.5 1.6 38 16-55 3-40 (42)
60 PF13404 HTH_AsnC-type: AsnC-t 72.8 4.9 0.00011 26.2 3.0 38 69-107 3-41 (42)
61 PRK11179 DNA-binding transcrip 72.6 4.8 0.0001 33.1 3.7 43 69-112 9-52 (153)
62 PF11035 SnAPC_2_like: Small n 71.8 34 0.00074 32.2 9.3 89 10-112 21-130 (344)
63 KOG4468 Polycomb-group transcr 71.4 5.7 0.00012 40.2 4.4 49 63-111 88-146 (782)
64 PRK11169 leucine-responsive tr 71.0 4.9 0.00011 33.5 3.4 44 68-112 13-57 (164)
65 PF04545 Sigma70_r4: Sigma-70, 70.8 8.9 0.00019 25.3 4.0 42 69-111 7-48 (50)
66 PRK11179 DNA-binding transcrip 70.3 2.9 6.3E-05 34.5 1.9 45 16-62 9-53 (153)
67 PF07750 GcrA: GcrA cell cycle 67.6 4.1 8.8E-05 34.5 2.2 41 65-106 2-42 (162)
68 PRK11169 leucine-responsive tr 65.7 3 6.5E-05 34.9 1.1 46 15-62 13-58 (164)
69 PLN03142 Probable chromatin-re 65.4 4.9 0.00011 43.4 2.8 35 6-40 922-956 (1033)
70 KOG2009 Transcription initiati 65.3 8.1 0.00018 39.0 4.1 47 62-108 408-454 (584)
71 PF11035 SnAPC_2_like: Small n 65.3 18 0.00038 34.1 6.0 49 63-111 21-73 (344)
72 PF13325 MCRS_N: N-terminal re 64.4 11 0.00024 33.1 4.4 41 65-109 1-47 (199)
73 PF10545 MADF_DNA_bdg: Alcohol 62.2 6.5 0.00014 28.2 2.2 34 84-117 28-62 (85)
74 TIGR02985 Sig70_bacteroi1 RNA 61.8 13 0.00028 29.5 4.1 39 72-111 119-157 (161)
75 PF11626 Rap1_C: TRF2-interact 59.0 8.8 0.00019 28.8 2.5 17 59-75 43-59 (87)
76 COG2197 CitB Response regulato 56.9 13 0.00028 32.3 3.5 45 64-111 147-191 (211)
77 smart00501 BRIGHT BRIGHT, ARID 55.8 5.6 0.00012 30.0 1.0 39 20-58 36-85 (93)
78 PF04504 DUF573: Protein of un 54.5 27 0.00059 26.9 4.6 51 64-114 5-68 (98)
79 PF01388 ARID: ARID/BRIGHT DNA 54.2 5.8 0.00012 29.6 0.8 39 20-58 40-89 (92)
80 KOG4167 Predicted DNA-binding 54.0 16 0.00034 38.0 4.0 43 63-105 619-661 (907)
81 KOG1194 Predicted DNA-binding 53.2 12 0.00025 36.9 2.8 47 7-55 184-230 (534)
82 cd08319 Death_RAIDD Death doma 51.8 11 0.00025 28.3 2.0 30 71-101 2-31 (83)
83 KOG4329 DNA-binding protein [G 50.0 76 0.0016 30.6 7.5 43 64-106 278-321 (445)
84 KOG4468 Polycomb-group transcr 49.9 24 0.00051 36.0 4.4 49 9-58 87-144 (782)
85 PF00196 GerE: Bacterial regul 47.1 18 0.0004 24.5 2.4 44 65-111 3-46 (58)
86 cd08803 Death_ank3 Death domai 46.5 18 0.00039 27.2 2.4 31 71-102 4-34 (84)
87 PF08281 Sigma70_r4_2: Sigma-7 46.5 11 0.00024 25.0 1.1 38 15-55 12-49 (54)
88 TIGR02937 sigma70-ECF RNA poly 46.3 29 0.00063 26.6 3.7 35 76-111 120-154 (158)
89 smart00344 HTH_ASNC helix_turn 45.5 27 0.00058 26.5 3.3 43 69-112 3-46 (108)
90 PF02954 HTH_8: Bacterial regu 45.3 18 0.00039 23.2 1.9 29 16-45 5-33 (42)
91 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 44.6 25 0.00055 24.0 2.7 36 69-105 7-42 (50)
92 PRK09652 RNA polymerase sigma 43.7 35 0.00075 27.7 3.9 33 77-110 139-171 (182)
93 cd08317 Death_ank Death domain 43.0 15 0.00033 27.2 1.5 31 71-102 4-34 (84)
94 PRK04217 hypothetical protein; 41.2 53 0.0011 26.1 4.4 45 65-111 42-86 (110)
95 PF07638 Sigma70_ECF: ECF sigm 40.9 41 0.00088 28.4 4.0 38 72-110 141-178 (185)
96 COG1522 Lrp Transcriptional re 40.6 18 0.00038 29.2 1.7 44 16-61 8-51 (154)
97 KOG2656 DNA methyltransferase 40.2 15 0.00032 35.5 1.3 48 8-56 128-180 (445)
98 PF09420 Nop16: Ribosome bioge 40.1 44 0.00096 28.0 4.1 46 62-107 113-162 (164)
99 cd08318 Death_NMPP84 Death dom 39.9 22 0.00048 26.6 2.0 27 75-102 11-37 (86)
100 PRK09643 RNA polymerase sigma 39.7 62 0.0014 27.2 5.0 34 76-110 144-177 (192)
101 cd06171 Sigma70_r4 Sigma70, re 39.0 46 0.00099 20.7 3.2 41 66-108 11-51 (55)
102 smart00344 HTH_ASNC helix_turn 38.7 25 0.00054 26.7 2.2 45 16-62 3-47 (108)
103 PRK09641 RNA polymerase sigma 38.5 44 0.00095 27.5 3.8 30 81-111 151-180 (187)
104 PRK11924 RNA polymerase sigma 38.4 43 0.00093 27.0 3.7 31 80-111 139-169 (179)
105 cd08311 Death_p75NR Death doma 38.0 26 0.00057 25.9 2.1 33 68-102 2-34 (77)
106 KOG3841 TEF-1 and related tran 37.6 45 0.00097 32.2 4.0 54 61-114 74-148 (455)
107 KOG4329 DNA-binding protein [G 37.4 25 0.00055 33.7 2.4 41 12-54 279-320 (445)
108 PRK09413 IS2 repressor TnpA; R 36.8 95 0.0021 24.4 5.4 46 8-57 8-53 (121)
109 smart00005 DEATH DEATH domain, 36.3 31 0.00066 25.1 2.3 32 70-102 4-36 (88)
110 TIGR02948 SigW_bacill RNA poly 34.2 53 0.0011 27.0 3.6 29 82-111 152-180 (187)
111 TIGR02939 RpoE_Sigma70 RNA pol 34.1 47 0.001 27.4 3.3 29 82-111 154-182 (190)
112 PF07750 GcrA: GcrA cell cycle 33.4 43 0.00093 28.3 2.9 33 12-46 2-35 (162)
113 PRK09047 RNA polymerase factor 32.7 71 0.0015 25.5 4.1 30 81-111 121-150 (161)
114 cd08804 Death_ank2 Death domai 32.2 33 0.00072 25.6 1.9 31 71-102 4-34 (84)
115 cd08777 Death_RIP1 Death Domai 31.6 31 0.00068 25.9 1.7 30 72-102 3-32 (86)
116 TIGR02954 Sig70_famx3 RNA poly 31.5 68 0.0015 26.0 3.9 30 81-111 134-163 (169)
117 PF01710 HTH_Tnp_IS630: Transp 31.0 85 0.0018 24.7 4.2 55 17-74 58-112 (119)
118 PRK09637 RNA polymerase sigma 30.9 70 0.0015 26.7 3.9 30 80-110 120-149 (181)
119 PRK09645 RNA polymerase sigma 30.5 78 0.0017 25.7 4.1 30 81-111 133-162 (173)
120 KOG2009 Transcription initiati 30.3 34 0.00075 34.7 2.1 47 7-55 406-452 (584)
121 TIGR02943 Sig70_famx1 RNA poly 30.0 77 0.0017 26.6 4.0 32 79-111 144-175 (188)
122 PRK09648 RNA polymerase sigma 30.0 80 0.0017 26.2 4.1 31 80-111 153-183 (189)
123 PRK09642 RNA polymerase sigma 29.6 84 0.0018 25.2 4.1 30 80-110 120-149 (160)
124 PRK12512 RNA polymerase sigma 29.6 82 0.0018 26.0 4.1 30 81-111 146-175 (184)
125 PRK12515 RNA polymerase sigma 29.6 83 0.0018 26.2 4.1 30 81-111 146-175 (189)
126 COG1522 Lrp Transcriptional re 29.4 70 0.0015 25.6 3.5 45 68-113 7-52 (154)
127 COG4628 Uncharacterized conser 29.3 59 0.0013 26.3 2.9 44 18-74 21-71 (136)
128 PRK12530 RNA polymerase sigma 28.9 80 0.0017 26.4 3.9 29 81-110 149-177 (189)
129 PRK12529 RNA polymerase sigma 28.9 86 0.0019 25.9 4.1 33 79-112 140-172 (178)
130 KOG0384 Chromodomain-helicase 28.8 76 0.0016 35.2 4.4 70 11-89 1134-1206(1373)
131 PRK12531 RNA polymerase sigma 28.7 87 0.0019 26.2 4.1 30 81-111 156-185 (194)
132 PRK12523 RNA polymerase sigma 28.5 73 0.0016 26.0 3.5 36 75-111 128-163 (172)
133 PRK15411 rcsA colanic acid cap 28.3 74 0.0016 27.3 3.7 44 65-111 137-180 (207)
134 PRK11923 algU RNA polymerase s 27.8 79 0.0017 26.3 3.7 29 82-111 154-182 (193)
135 PF09905 DUF2132: Uncharacteri 27.1 51 0.0011 23.7 2.0 44 18-74 12-62 (64)
136 TIGR02952 Sig70_famx2 RNA poly 27.1 96 0.0021 24.9 4.0 28 82-110 138-165 (170)
137 cd08779 Death_PIDD Death Domai 26.8 43 0.00094 25.1 1.7 26 72-98 3-28 (86)
138 PRK12527 RNA polymerase sigma 26.6 1.3E+02 0.0028 24.1 4.7 30 81-111 120-149 (159)
139 PF13936 HTH_38: Helix-turn-he 26.3 60 0.0013 21.0 2.1 37 65-103 4-40 (44)
140 PRK00118 putative DNA-binding 26.2 1.1E+02 0.0023 24.0 3.9 42 68-110 19-60 (104)
141 PRK12514 RNA polymerase sigma 26.2 96 0.0021 25.4 3.9 28 82-110 145-172 (179)
142 cd08319 Death_RAIDD Death doma 26.2 51 0.0011 24.7 2.0 24 18-42 2-25 (83)
143 cd08805 Death_ank1 Death domai 26.1 48 0.001 25.0 1.8 27 71-98 4-30 (84)
144 COG2963 Transposase and inacti 25.6 1.2E+02 0.0026 23.3 4.1 46 63-110 5-51 (116)
145 PRK09649 RNA polymerase sigma 25.4 93 0.002 25.9 3.7 31 81-112 145-175 (185)
146 PRK15201 fimbriae regulatory p 25.4 1.2E+02 0.0026 26.5 4.3 44 65-111 133-176 (198)
147 PRK12536 RNA polymerase sigma 25.3 1.1E+02 0.0023 25.3 4.1 31 80-111 143-173 (181)
148 PF10440 WIYLD: Ubiquitin-bind 25.0 41 0.00089 24.3 1.2 18 73-90 31-48 (65)
149 PRK05602 RNA polymerase sigma 24.7 1E+02 0.0022 25.4 3.8 30 81-111 143-172 (186)
150 PRK09483 response regulator; P 24.4 89 0.0019 25.6 3.4 45 64-111 147-191 (217)
151 PRK13919 putative RNA polymera 24.2 1.2E+02 0.0025 25.0 4.1 29 82-111 151-179 (186)
152 smart00351 PAX Paired Box doma 24.1 3E+02 0.0064 21.8 6.2 73 8-82 13-92 (125)
153 PRK09651 RNA polymerase sigma 24.0 1.1E+02 0.0023 25.2 3.7 31 81-112 134-164 (172)
154 PF00046 Homeobox: Homeobox do 23.7 2.2E+02 0.0048 18.7 4.8 44 62-106 3-50 (57)
155 TIGR02999 Sig-70_X6 RNA polyme 23.6 1.3E+02 0.0027 24.7 4.1 29 81-110 149-177 (183)
156 PRK12524 RNA polymerase sigma 23.6 1.2E+02 0.0026 25.4 4.1 30 81-111 151-180 (196)
157 PRK12532 RNA polymerase sigma 23.5 1.1E+02 0.0023 25.6 3.7 30 80-110 150-179 (195)
158 PRK12528 RNA polymerase sigma 23.4 1E+02 0.0023 24.7 3.5 31 79-110 126-156 (161)
159 cd08306 Death_FADD Fas-associa 23.4 64 0.0014 24.1 2.1 29 73-102 4-32 (86)
160 PRK06759 RNA polymerase factor 23.3 1.1E+02 0.0023 24.3 3.5 29 81-110 121-149 (154)
161 TIGR02950 SigM_subfam RNA poly 23.2 43 0.00092 26.6 1.1 29 82-111 121-149 (154)
162 TIGR02983 SigE-fam_strep RNA p 23.1 1.1E+02 0.0025 24.4 3.7 40 71-111 115-154 (162)
163 PRK10100 DNA-binding transcrip 22.8 1.2E+02 0.0026 26.4 4.0 44 65-111 155-198 (216)
164 PRK12547 RNA polymerase sigma 22.8 1.4E+02 0.003 24.2 4.2 30 80-110 126-155 (164)
165 TIGR02984 Sig-70_plancto1 RNA 22.2 1.3E+02 0.0028 24.6 3.9 30 81-111 155-184 (189)
166 PRK10360 DNA-binding transcrip 21.9 1.5E+02 0.0032 23.8 4.2 45 64-111 136-180 (196)
167 PRK12516 RNA polymerase sigma 21.7 1.4E+02 0.003 25.0 4.1 35 75-110 125-159 (187)
168 PRK12520 RNA polymerase sigma 21.4 1.4E+02 0.003 24.8 4.0 28 82-110 147-174 (191)
169 TIGR02960 SigX5 RNA polymerase 21.3 1.1E+02 0.0025 27.6 3.7 30 81-111 157-186 (324)
170 PRK09647 RNA polymerase sigma 20.6 1.7E+02 0.0037 24.9 4.5 32 81-113 153-184 (203)
171 PRK11922 RNA polymerase sigma 20.3 84 0.0018 27.3 2.5 30 82-112 165-194 (231)
172 PF09197 Rap1-DNA-bind: Rap1, 20.1 90 0.002 24.7 2.3 24 88-111 55-78 (105)
No 1
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=7.3e-35 Score=256.86 Aligned_cols=113 Identities=55% Similarity=1.027 Sum_probs=107.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccCCCCcCCCCCHHHHHHHHHHHhhcCCc
Q 025221 5 QEEVRKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLHPGLKRGKMTPQEERLVLELHAKWGNR 84 (256)
Q Consensus 5 ~~~~kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~l~k~~WT~EED~~Ll~lv~~~G~~ 84 (256)
++++++++||+|||++|+++|++||..+|..||+.++++|+++|||+||.++|+|.+++++||+|||++|++++.+||++
T Consensus 20 K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~~GnK 99 (249)
T PLN03212 20 KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLGNR 99 (249)
T ss_pred cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHhcccc
Confidence 46799999999999999999999998899999999877999999999999999999999999999999999999999999
Q ss_pred cccccccCCCCCHHHHHHHHHHHhHHHHHhhhh
Q 025221 85 WSRIARKLPGRTDNEIKNYWRTHMRKKAQERKR 117 (256)
Q Consensus 85 W~~Ia~~l~gRt~~~~knrw~~~lrk~~~~~~~ 117 (256)
|+.||++|+|||+++|||||+.+++++..+...
T Consensus 100 Ws~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i 132 (249)
T PLN03212 100 WSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGI 132 (249)
T ss_pred HHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCC
Confidence 999999999999999999999999998766544
No 2
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=4.8e-35 Score=260.58 Aligned_cols=113 Identities=51% Similarity=0.962 Sum_probs=107.5
Q ss_pred cCCCCCCCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccCCCCcCCCCCHHHHHHHHHHHhhcCC
Q 025221 4 QQEEVRKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLHPGLKRGKMTPQEERLVLELHAKWGN 83 (256)
Q Consensus 4 l~~~~kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~l~k~~WT~EED~~Ll~lv~~~G~ 83 (256)
.++.+.||+||+|||++|+++|++||.++|..||+.+|++|++++||.||.|||+|++++|.||+|||++|++++..+|+
T Consensus 3 kk~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GN 82 (238)
T KOG0048|consen 3 RNPELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGN 82 (238)
T ss_pred CCccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCc
Confidence 34556789999999999999999999999999999998899999999999999999999999999999999999999999
Q ss_pred ccccccccCCCCCHHHHHHHHHHHhHHHHHhhh
Q 025221 84 RWSRIARKLPGRTDNEIKNYWRTHMRKKAQERK 116 (256)
Q Consensus 84 ~W~~Ia~~l~gRt~~~~knrw~~~lrk~~~~~~ 116 (256)
+|+.||++|||||+|+|||+|+.+++|+.....
T Consensus 83 rWs~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 83 RWSLIAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred HHHHHHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 999999999999999999999999999877654
No 3
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=9.4e-33 Score=259.40 Aligned_cols=113 Identities=52% Similarity=1.003 Sum_probs=107.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccCCCCcCCCCCHHHHHHHHHHHhhcCCc
Q 025221 5 QEEVRKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLHPGLKRGKMTPQEERLVLELHAKWGNR 84 (256)
Q Consensus 5 ~~~~kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~l~k~~WT~EED~~Ll~lv~~~G~~ 84 (256)
++.++||+||+|||++|+++|.+||..+|..||+.++++|+++|||+||.++|+|.+++++||+|||++|++++++||++
T Consensus 9 KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k~~GnK 88 (459)
T PLN03091 9 KQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHAVLGNR 88 (459)
T ss_pred CCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHHHhCcc
Confidence 46799999999999999999999999999999999878999999999999999999999999999999999999999999
Q ss_pred cccccccCCCCCHHHHHHHHHHHhHHHHHhhhh
Q 025221 85 WSRIARKLPGRTDNEIKNYWRTHMRKKAQERKR 117 (256)
Q Consensus 85 W~~Ia~~l~gRt~~~~knrw~~~lrk~~~~~~~ 117 (256)
|++||++|+|||+++|||||+.++||+.+.+..
T Consensus 89 WskIAk~LPGRTDnqIKNRWnslLKKklr~~~I 121 (459)
T PLN03091 89 WSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRGI 121 (459)
T ss_pred hHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCC
Confidence 999999999999999999999999998775443
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.80 E-value=4.5e-20 Score=179.45 Aligned_cols=113 Identities=27% Similarity=0.486 Sum_probs=102.8
Q ss_pred cccCCCCCCCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccCCCCcCCCCCHHHHHHHHHHHhhc
Q 025221 2 VVQQEEVRKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLHPGLKRGKMTPQEERLVLELHAKW 81 (256)
Q Consensus 2 ~~l~~~~kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~l~k~~WT~EED~~Ll~lv~~~ 81 (256)
+.|+|.+++|+||++||.+|+.+|.+||.+.|-+|-+.+ |||+..|||+||.|.|+..++++.||-.||+.|+.+|++|
T Consensus 352 ~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~v-PnRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~~V~~Y 430 (939)
T KOG0049|consen 352 HTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAV-PNRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLYAVKVY 430 (939)
T ss_pred eccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhc-CCccHHHHHHHHHHHHHHhhccCceeecchHHHHHHHHHH
Confidence 468999999999999999999999999999999999999 8999999999999999999999999999999999999999
Q ss_pred CC-ccccccccCCCCCHHHHHHHHHHHhHHHHHhh
Q 025221 82 GN-RWSRIARKLPGRTDNEIKNYWRTHMRKKAQER 115 (256)
Q Consensus 82 G~-~W~~Ia~~l~gRt~~~~knrw~~~lrk~~~~~ 115 (256)
|. +|.+||..||+||..|.+.|=..+++.+..-.
T Consensus 431 G~g~WakcA~~Lp~~t~~q~~rrR~R~~~~k~rl~ 465 (939)
T KOG0049|consen 431 GKGNWAKCAMLLPKKTSRQLRRRRLRLIAAKLRLA 465 (939)
T ss_pred ccchHHHHHHHccccchhHHHHHHHHHHHHHHHHh
Confidence 96 89999999999999777666555555544433
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.75 E-value=1.2e-18 Score=169.49 Aligned_cols=112 Identities=23% Similarity=0.458 Sum_probs=102.7
Q ss_pred ccCCCCCCCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccc---------------------------------
Q 025221 3 VQQEEVRKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSC--------------------------------- 49 (256)
Q Consensus 3 ~l~~~~kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qc--------------------------------- 49 (256)
.++|.++|..|++|||++|+.+...++..+|..||..+|.+|+..||
T Consensus 246 ~l~P~~nk~~WS~EE~E~L~AiA~A~~~~~W~~IA~~Lgt~RS~yQC~~kF~t~~~~L~ekeWsEEed~kL~alV~~~~~ 325 (939)
T KOG0049|consen 246 ELNPKWNKEHWSNEEVEKLKALAEAPKFVSWPMIALNLGTNRSSYQCMEKFKTEVSQLSEKEWSEEEDTKLIALVKITSI 325 (939)
T ss_pred hcCCccchhccChHHHHHHHHHHhccccccHHHHHHHhCCCcchHHHHHHHHHHHHHHHhhhcchhhhHHHHHHHHHhhc
Confidence 47899999999999999999999999988999999999866888888
Q ss_pred ---------------------cchhhhccCCCCcCCCCCHHHHHHHHHHHhhcCC-ccccccccCCCCCHHHHHHHHHHH
Q 025221 50 ---------------------RLRWVNYLHPGLKRGKMTPQEERLVLELHAKWGN-RWSRIARKLPGRTDNEIKNYWRTH 107 (256)
Q Consensus 50 ---------------------r~Rw~~~L~p~l~k~~WT~EED~~Ll~lv~~~G~-~W~~Ia~~l~gRt~~~~knrw~~~ 107 (256)
..||...|+|++++|+||.+||.+|+.+|.+||. .|-+|-..+|||++.|||.||.+.
T Consensus 326 nShI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nv 405 (939)
T KOG0049|consen 326 NSHIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNV 405 (939)
T ss_pred cCccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHH
Confidence 5688888999999999999999999999999997 799999999999999999999999
Q ss_pred hHHHHHh
Q 025221 108 MRKKAQE 114 (256)
Q Consensus 108 lrk~~~~ 114 (256)
|.+..+.
T Consensus 406 L~~s~K~ 412 (939)
T KOG0049|consen 406 LNRSAKV 412 (939)
T ss_pred HHHhhcc
Confidence 9877543
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=99.67 E-value=6.5e-17 Score=114.20 Aligned_cols=60 Identities=45% Similarity=0.850 Sum_probs=54.9
Q ss_pred CCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccCCCCcCCCCCHHHHHHH
Q 025221 13 WTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLHPGLKRGKMTPQEERLV 74 (256)
Q Consensus 13 WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~l~k~~WT~EED~~L 74 (256)
||+|||++|+.+|..|| .+|..||+.|| +|+..+|+.||.++|.+.+++++||++||+.|
T Consensus 1 WT~eEd~~L~~~~~~~g-~~W~~Ia~~l~-~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYG-NDWKKIAEHLG-NRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHT-S-HHHHHHHST-TS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC-cCHHHHHHHHC-cCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 99999999999999999 68999999995 89999999999999999999999999999987
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=99.58 E-value=2.3e-15 Score=145.90 Aligned_cols=109 Identities=27% Similarity=0.482 Sum_probs=103.1
Q ss_pred cCCCCCCCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccCCCCcCCCCCHHHHHHHHHHHhhcCC
Q 025221 4 QQEEVRKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLHPGLKRGKMTPQEERLVLELHAKWGN 83 (256)
Q Consensus 4 l~~~~kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~l~k~~WT~EED~~Ll~lv~~~G~ 83 (256)
+.-.++.|.|+..||+.|..+|+.+|+.+|..||..+. .|+++||+.||.++++|.+++..|+.+||+.|+.+..++|.
T Consensus 14 ~~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~-~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~ 92 (512)
T COG5147 14 MQTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLI-SSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGT 92 (512)
T ss_pred ccceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhc-ccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCc
Confidence 44567899999999999999999999999999999995 69999999999999999999999999999999999999999
Q ss_pred ccccccccCCCCCHHHHHHHHHHHhHHHHH
Q 025221 84 RWSRIARKLPGRTDNEIKNYWRTHMRKKAQ 113 (256)
Q Consensus 84 ~W~~Ia~~l~gRt~~~~knrw~~~lrk~~~ 113 (256)
+|+.||..++||+..+|.+||...+.....
T Consensus 93 ~wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 93 QWSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 999999999999999999999999987644
No 8
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.52 E-value=1.2e-14 Score=139.07 Aligned_cols=109 Identities=25% Similarity=0.520 Sum_probs=102.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccCCCCcCCCCCHHHHHHHHHHHhhcCCccc
Q 025221 7 EVRKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLHPGLKRGKMTPQEERLVLELHAKWGNRWS 86 (256)
Q Consensus 7 ~~kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~l~k~~WT~EED~~Ll~lv~~~G~~W~ 86 (256)
.++.|.|+--||+.|..+|.+||.+.|.+||+.+ ...+++||+.||..+|+|.+++..|+.|||+.||.++......|.
T Consensus 4 ~~kggvwrntEdeilkaav~kyg~nqws~i~sll-~~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwr 82 (617)
T KOG0050|consen 4 EIKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLL-NRKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWR 82 (617)
T ss_pred EEecceecccHHHHHHHHHHHcchHHHHHHHHHH-hhcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccc
Confidence 4678999999999999999999999999999999 589999999999999999999999999999999999999999999
Q ss_pred cccccCCCCCHHHHHHHHHHHhHHHHHhhhh
Q 025221 87 RIARKLPGRTDNEIKNYWRTHMRKKAQERKR 117 (256)
Q Consensus 87 ~Ia~~l~gRt~~~~knrw~~~lrk~~~~~~~ 117 (256)
.|+..| ||+.++|-.||.+++-........
T Consensus 83 tIa~i~-gr~~~qc~eRy~~ll~~~~s~~~~ 112 (617)
T KOG0050|consen 83 TIADIM-GRTSQQCLERYNNLLDVYVSYHYH 112 (617)
T ss_pred hHHHHh-hhhHHHHHHHHHHHHHHHHhhhcc
Confidence 999999 999999999999999887665444
No 9
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.45 E-value=8.9e-14 Score=136.31 Aligned_cols=100 Identities=27% Similarity=0.506 Sum_probs=91.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccCCCC--cCCCCCHHHHHHHHHHHh-------
Q 025221 9 RKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLHPGL--KRGKMTPQEERLVLELHA------- 79 (256)
Q Consensus 9 kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~l--~k~~WT~EED~~Ll~lv~------- 79 (256)
.+|+||+||++.|..+|..+| ..|..|++.|| |.+..|++||+++...+- +++.||.||+++|+++|+
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g-~~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~ 459 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHG-NDWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREAL 459 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhc-ccHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhh
Confidence 899999999999999999999 68999999996 999999999999999884 899999999999999995
Q ss_pred hc-------------------CCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 80 KW-------------------GNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 80 ~~-------------------G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
++ +-.|+.|+..+..|+..+||.+|..++...
T Consensus 460 q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~ 510 (607)
T KOG0051|consen 460 QPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSP 510 (607)
T ss_pred cccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhH
Confidence 33 126999999888899999999999999864
No 10
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.41 E-value=6.3e-14 Score=95.00 Aligned_cols=48 Identities=46% Similarity=0.792 Sum_probs=42.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhcc
Q 025221 10 KGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYL 57 (256)
Q Consensus 10 kg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L 57 (256)
||+||+|||++|+++|.+||..+|..||+.++++||+.||+.||.++|
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 689999999999999999997669999999944999999999999875
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=99.41 E-value=1.5e-13 Score=93.07 Aligned_cols=46 Identities=33% Similarity=0.733 Sum_probs=42.1
Q ss_pred CCCCCHHHHHHHHHHHhhcCCc-cccccccCC-CCCHHHHHHHHHHHh
Q 025221 63 RGKMTPQEERLVLELHAKWGNR-WSRIARKLP-GRTDNEIKNYWRTHM 108 (256)
Q Consensus 63 k~~WT~EED~~Ll~lv~~~G~~-W~~Ia~~l~-gRt~~~~knrw~~~l 108 (256)
|++||+|||++|++++.+||.+ |..||..|+ |||..||++||++++
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 5799999999999999999998 999999999 999999999999875
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=99.25 E-value=2.1e-12 Score=91.05 Aligned_cols=45 Identities=44% Similarity=0.843 Sum_probs=39.2
Q ss_pred CCHHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 66 MTPQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 66 WT~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
||+|||++|+++|.+||++|..||..|+.||..+|++||+.+|+.
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~ 45 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRP 45 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTST
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcc
Confidence 999999999999999999999999999669999999999996653
No 13
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.22 E-value=1.1e-11 Score=82.10 Aligned_cols=47 Identities=38% Similarity=0.894 Sum_probs=44.4
Q ss_pred CCCCCHHHHHHHHHHHhhcC-CccccccccCCCCCHHHHHHHHHHHhH
Q 025221 63 RGKMTPQEERLVLELHAKWG-NRWSRIARKLPGRTDNEIKNYWRTHMR 109 (256)
Q Consensus 63 k~~WT~EED~~Ll~lv~~~G-~~W~~Ia~~l~gRt~~~~knrw~~~lr 109 (256)
+++||++||.+|+.++..|| .+|..||..|++||..+|++||+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 46899999999999999999 899999999999999999999998764
No 14
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.11 E-value=1.3e-11 Score=109.77 Aligned_cols=55 Identities=27% Similarity=0.488 Sum_probs=51.7
Q ss_pred ccCCCCCCCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccCC
Q 025221 3 VQQEEVRKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLHP 59 (256)
Q Consensus 3 ~l~~~~kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p 59 (256)
+|+|.+++|+||+|||++|++++..|| .+|..||+.| |+||..+|+.||..+|..
T Consensus 71 ~L~P~I~kgpWT~EED~lLlel~~~~G-nKWs~IAk~L-pGRTDnqIKNRWns~LrK 125 (249)
T PLN03212 71 YLRPSVKRGGITSDEEDLILRLHRLLG-NRWSLIAGRI-PGRTDNEIKNYWNTHLRK 125 (249)
T ss_pred hhchhcccCCCChHHHHHHHHHHHhcc-ccHHHHHhhc-CCCCHHHHHHHHHHHHhH
Confidence 589999999999999999999999999 6899999999 799999999999988864
No 15
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.10 E-value=9.6e-11 Score=76.32 Aligned_cols=44 Identities=41% Similarity=0.850 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHHHhhcC-CccccccccCCCCCHHHHHHHHHHHh
Q 025221 65 KMTPQEERLVLELHAKWG-NRWSRIARKLPGRTDNEIKNYWRTHM 108 (256)
Q Consensus 65 ~WT~EED~~Ll~lv~~~G-~~W~~Ia~~l~gRt~~~~knrw~~~l 108 (256)
+||++|+++|+.++.+|| .+|..||..|++||..+|++||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 89999999999999999999998763
No 16
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.09 E-value=7.9e-11 Score=77.85 Aligned_cols=48 Identities=48% Similarity=0.912 Sum_probs=44.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccC
Q 025221 10 KGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLH 58 (256)
Q Consensus 10 kg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~ 58 (256)
++.||++||++|+.++..||..+|..||+.+ ++|++.+|+.||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~-~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKEL-PGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHc-CCCCHHHHHHHHHHHcC
Confidence 4789999999999999999977899999999 59999999999998764
No 17
>PLN03091 hypothetical protein; Provisional
Probab=99.04 E-value=5.6e-11 Score=112.91 Aligned_cols=56 Identities=23% Similarity=0.516 Sum_probs=52.0
Q ss_pred ccCCCCCCCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccCCC
Q 025221 3 VQQEEVRKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLHPG 60 (256)
Q Consensus 3 ~l~~~~kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~ 60 (256)
+|+|.++||+||+|||++|++++++|| .+|..||+.| ++|++.+|+.||...|...
T Consensus 60 yLdP~IkKgpWT~EED~lLLeL~k~~G-nKWskIAk~L-PGRTDnqIKNRWnslLKKk 115 (459)
T PLN03091 60 YLRPDLKRGTFSQQEENLIIELHAVLG-NRWSQIAAQL-PGRTDNEIKNLWNSCLKKK 115 (459)
T ss_pred ccCCcccCCCCCHHHHHHHHHHHHHhC-cchHHHHHhc-CCCCHHHHHHHHHHHHHHH
Confidence 589999999999999999999999999 5899999999 7999999999999877543
No 18
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.02 E-value=1.1e-10 Score=104.16 Aligned_cols=58 Identities=14% Similarity=0.233 Sum_probs=52.3
Q ss_pred CCcCCCCCHHHHHHHHHHHhhcCC-ccccccccCC-CCCHHHHHHHHHHHhHHHHHhhhh
Q 025221 60 GLKRGKMTPQEERLVLELHAKWGN-RWSRIARKLP-GRTDNEIKNYWRTHMRKKAQERKR 117 (256)
Q Consensus 60 ~l~k~~WT~EED~~Ll~lv~~~G~-~W~~Ia~~l~-gRt~~~~knrw~~~lrk~~~~~~~ 117 (256)
.+.+|+||+|||++|+++|++||. +|..|++.++ ||++.+||-||.++||..++++..
T Consensus 6 ~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~f 65 (238)
T KOG0048|consen 6 ELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNF 65 (238)
T ss_pred cccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCC
Confidence 455899999999999999999998 6999999998 999999999999999988765443
No 19
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.02 E-value=2.1e-10 Score=112.80 Aligned_cols=103 Identities=28% Similarity=0.429 Sum_probs=87.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC-----------------------CCchhhhhhcccccccccccchhhhccCCCC-cC
Q 025221 8 VRKGPWTEQEDILLVNFVQLFGD-----------------------RRWDFIAKVSGLNRTGKSCRLRWVNYLHPGL-KR 63 (256)
Q Consensus 8 ~kkg~WT~EED~~L~~lv~~~g~-----------------------~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~l-~k 63 (256)
++-+.|+++||+.|...|..|-. +-|..|.+.| |-|+...+..+-++..+|-- ++
T Consensus 306 ~~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~L-p~R~~~siy~~~rR~y~~FE~~r 384 (607)
T KOG0051|consen 306 INLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLL-PYRDRKSIYHHLRRAYTPFENKR 384 (607)
T ss_pred hhhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhc-CcccchhHHHHHHhcCCcccccc
Confidence 45589999999999999988820 0167888888 68999999885445444433 99
Q ss_pred CCCCHHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHHHH
Q 025221 64 GKMTPQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRKKA 112 (256)
Q Consensus 64 ~~WT~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~~ 112 (256)
|.||+||++.|..+|.++|+.|..|++.| ||.+.+|++||+++++...
T Consensus 385 g~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~ 432 (607)
T KOG0051|consen 385 GKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGS 432 (607)
T ss_pred CCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhcccc
Confidence 99999999999999999999999999999 9999999999999998764
No 20
>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=98.95 E-value=5.1e-10 Score=72.84 Aligned_cols=45 Identities=51% Similarity=0.915 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhcc
Q 025221 12 PWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYL 57 (256)
Q Consensus 12 ~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L 57 (256)
+||++||+.|+.++..+|..+|..||+.+ ++|++.+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~-~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKEL-PGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHc-CCCCHHHHHHHHHHhC
Confidence 59999999999999999977999999999 5899999999998753
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=98.16 E-value=9e-07 Score=86.60 Aligned_cols=105 Identities=19% Similarity=0.242 Sum_probs=91.5
Q ss_pred ccCCCCCCCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccCCCCcCCCCCHHHHHHHHHHHhhcC
Q 025221 3 VQQEEVRKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLHPGLKRGKMTPQEERLVLELHAKWG 82 (256)
Q Consensus 3 ~l~~~~kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~l~k~~WT~EED~~Ll~lv~~~G 82 (256)
.++|.++++.|+.|||++|+.+-..+|+ .|..||..+ ++|++.+|.+||.+.|.+... ..|+..+.......+..|+
T Consensus 65 ~lnp~lk~~~~~~eed~~li~l~~~~~~-~wstia~~~-d~rt~~~~~ery~~~~~~~~s-~~~s~~~~~~~f~k~d~f~ 141 (512)
T COG5147 65 HLNPQLKKKNWSEEEDEQLIDLDKELGT-QWSTIADYK-DRRTAQQCVERYVNTLEDLSS-THDSKLQRRNEFDKIDPFN 141 (512)
T ss_pred hhchhcccccccHHHHHHHHHHHHhcCc-hhhhhcccc-CccchHHHHHHHHHHhhhhhc-cccccccchhhccccCchh
Confidence 3678899999999999999999999996 599999999 599999999999999987666 8899999999888899999
Q ss_pred CccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 83 NRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 83 ~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
..|.++......+-...+.|++.++...
T Consensus 142 ~~~~~~~~~~~~~~~~~~~N~~~~~~~~ 169 (512)
T COG5147 142 ENSARRPDIYEDELLEREVNREASYRLR 169 (512)
T ss_pred hhhhhhhhhhhcccchhhhhHHHHHHHH
Confidence 9888888776667777788888666544
No 22
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.96 E-value=8e-06 Score=57.56 Aligned_cols=49 Identities=20% Similarity=0.295 Sum_probs=43.5
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCc---hhhhhhccccc-ccccccchhhhcc
Q 025221 9 RKGPWTEQEDILLVNFVQLFGDRRW---DFIAKVSGLNR-TGKSCRLRWVNYL 57 (256)
Q Consensus 9 kkg~WT~EED~~L~~lv~~~g~~~W---~~IA~~lgp~R-t~~qcr~Rw~~~L 57 (256)
.+-.||+||..+++.+++.+|.++| ..|++.++..| |..||+.+.+.|.
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 3567999999999999999997799 99999887667 9999999988775
No 23
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.81 E-value=1.4e-05 Score=76.26 Aligned_cols=50 Identities=26% Similarity=0.576 Sum_probs=46.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccC
Q 025221 8 VRKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLH 58 (256)
Q Consensus 8 ~kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~ 58 (256)
+-.+-||++|+-+|++++..||.+||..||.++| +|+...|+++|.+++-
T Consensus 70 i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIG-tKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETYGFGNWQDIADHIG-TKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHc-ccchHHHHHHHHHHHh
Confidence 4567899999999999999999999999999998 9999999999999863
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=97.58 E-value=0.00012 Score=51.51 Aligned_cols=47 Identities=19% Similarity=0.220 Sum_probs=40.7
Q ss_pred CCCCCHHHHHHHHHHHhhcCC-cc---ccccccCC-CC-CHHHHHHHHHHHhH
Q 025221 63 RGKMTPQEERLVLELHAKWGN-RW---SRIARKLP-GR-TDNEIKNYWRTHMR 109 (256)
Q Consensus 63 k~~WT~EED~~Ll~lv~~~G~-~W---~~Ia~~l~-gR-t~~~~knrw~~~lr 109 (256)
+-.||+||...++++++.+|. +| ..|+..+. .| |..+|+.+...+.-
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 457999999999999999997 99 99999884 35 99999998876643
No 25
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.35 E-value=0.00073 Score=58.98 Aligned_cols=99 Identities=19% Similarity=0.340 Sum_probs=72.0
Q ss_pred CCCHHHHHHHHHHHHHhCCCCchhhhhhcc--cccccccccchhhhcc-CCCC--------------------cCCCCCH
Q 025221 12 PWTEQEDILLVNFVQLFGDRRWDFIAKVSG--LNRTGKSCRLRWVNYL-HPGL--------------------KRGKMTP 68 (256)
Q Consensus 12 ~WT~EED~~L~~lv~~~g~~~W~~IA~~lg--p~Rt~~qcr~Rw~~~L-~p~l--------------------~k~~WT~ 68 (256)
+|+++.|-+|+.+|.... +-..|++.+. ..-|-.-+.+||...| +|.+ .+.+||.
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 699999999999999865 5677776442 2445566788999886 3332 3567999
Q ss_pred HHHHHHHHHHhhcCC---ccccccc-----cCCCCCHHHHHHHHHHHhHHHH
Q 025221 69 QEERLVLELHAKWGN---RWSRIAR-----KLPGRTDNEIKNYWRTHMRKKA 112 (256)
Q Consensus 69 EED~~Ll~lv~~~G~---~W~~Ia~-----~l~gRt~~~~knrw~~~lrk~~ 112 (256)
+|+++|......... .+.+|=. +-++||+.++.++|+.+.+...
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~L 130 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHL 130 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhch
Confidence 999999998766543 3555522 2378999999999996555443
No 26
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.20 E-value=0.00036 Score=66.73 Aligned_cols=51 Identities=27% Similarity=0.446 Sum_probs=45.3
Q ss_pred CCcCCCCCHHHHHHHHHHHhhcC-CccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 60 GLKRGKMTPQEERLVLELHAKWG-NRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 60 ~l~k~~WT~EED~~Ll~lv~~~G-~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
.+-...||.+|+-+||+++..|| .+|..||.++..|+..+|+.+|.+++-.
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv~ 120 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFVN 120 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHhc
Confidence 34556799999999999999999 5999999999889999999999877654
No 27
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.14 E-value=0.00026 Score=53.04 Aligned_cols=54 Identities=28% Similarity=0.540 Sum_probs=38.6
Q ss_pred CCCCCHHHHHHHHHHHhh------cC--C------ccccccccC----CCCCHHHHHHHHHHHhHHHHHhhh
Q 025221 63 RGKMTPQEERLVLELHAK------WG--N------RWSRIARKL----PGRTDNEIKNYWRTHMRKKAQERK 116 (256)
Q Consensus 63 k~~WT~EED~~Ll~lv~~------~G--~------~W~~Ia~~l----~gRt~~~~knrw~~~lrk~~~~~~ 116 (256)
+..||.+|...|++++.+ ++ . -|..||..| ..||..||+++|+++.+.-.....
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~~k~ 72 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKKIKD 72 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHCSSS
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 357999999999999877 22 1 499999987 259999999999998887655443
No 28
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.07 E-value=0.00015 Score=70.63 Aligned_cols=53 Identities=30% Similarity=0.585 Sum_probs=48.3
Q ss_pred ccCCCCCCCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccC
Q 025221 3 VQQEEVRKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLH 58 (256)
Q Consensus 3 ~l~~~~kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~ 58 (256)
.++|.+++-.|+.|||++|+.+.....+ .|..||..|| |++.||.+||.+.|.
T Consensus 52 ~ldp~i~~tews~eederlLhlakl~p~-qwrtIa~i~g--r~~~qc~eRy~~ll~ 104 (617)
T KOG0050|consen 52 WLDPAIKKTEWSREEDERLLHLAKLEPT-QWRTIADIMG--RTSQQCLERYNNLLD 104 (617)
T ss_pred HhCHHHhhhhhhhhHHHHHHHHHHhcCC-ccchHHHHhh--hhHHHHHHHHHHHHH
Confidence 4688999999999999999999999984 7999999996 999999999998763
No 29
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.96 E-value=0.00041 Score=66.88 Aligned_cols=46 Identities=30% Similarity=0.738 Sum_probs=43.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhc
Q 025221 9 RKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNY 56 (256)
Q Consensus 9 kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~ 56 (256)
+...||.+|-.+|++.|+.|| ..|..||.++| +|+..||..||.+.
T Consensus 278 ~dk~WS~qE~~LLLEGIe~yg-DdW~kVA~HVg-tKt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYG-DDWDKVARHVG-TKTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhh-hhHHHHHHHhC-CCCHHHHHHHHHcC
Confidence 567899999999999999999 58999999998 99999999999875
No 30
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=96.92 E-value=0.00084 Score=56.54 Aligned_cols=50 Identities=24% Similarity=0.403 Sum_probs=43.4
Q ss_pred cCCCCCHHHHHHHHHHHhhc---CC----ccccccccCCCCCHHHHHHHHHHHhHHHH
Q 025221 62 KRGKMTPQEERLVLELHAKW---GN----RWSRIARKLPGRTDNEIKNYWRTHMRKKA 112 (256)
Q Consensus 62 ~k~~WT~EED~~Ll~lv~~~---G~----~W~~Ia~~l~gRt~~~~knrw~~~lrk~~ 112 (256)
....||.|||.+|-+.|-.| |. -...++..| +||+.+|.-||+..+|+..
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY 59 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQY 59 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHH
Confidence 34679999999999999887 43 478889999 9999999999999999864
No 31
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.92 E-value=0.00085 Score=66.04 Aligned_cols=50 Identities=20% Similarity=0.304 Sum_probs=44.9
Q ss_pred CcCCCCCHHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 61 LKRGKMTPQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 61 l~k~~WT~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
..+..||.+|.-+|++.++.||-+|.+||.++.+||..+|--++.++=..
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~LPie 300 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRLPIE 300 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhcCcc
Confidence 34568999999999999999999999999999999999999998766544
No 32
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.88 E-value=0.00068 Score=65.42 Aligned_cols=45 Identities=22% Similarity=0.319 Sum_probs=42.2
Q ss_pred CCCCHHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHh
Q 025221 64 GKMTPQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHM 108 (256)
Q Consensus 64 ~~WT~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l 108 (256)
..||.+|..+|++.++.||-.|.+||+++..||..||--|+.++=
T Consensus 280 k~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~LP 324 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQLP 324 (531)
T ss_pred ccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcCC
Confidence 479999999999999999999999999999999999999997653
No 33
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.79 E-value=0.0008 Score=66.20 Aligned_cols=49 Identities=29% Similarity=0.729 Sum_probs=44.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhc
Q 025221 6 EEVRKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNY 56 (256)
Q Consensus 6 ~~~kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~ 56 (256)
....++.||.+|..+|+++|+.|| .+|..||.++| +|+..||..++.+.
T Consensus 249 ~~~~~~~WT~qE~lLLLE~ie~y~-ddW~kVa~hVg-~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 249 GESARPNWTEQETLLLLEAIEMYG-DDWNKVADHVG-TKSQEQCILKFLRL 297 (506)
T ss_pred cccCCCCccHHHHHHHHHHHHHhc-ccHHHHHhccC-CCCHHHHHHHHHhc
Confidence 345678899999999999999999 58999999998 99999999999875
No 34
>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=96.78 E-value=0.0014 Score=47.38 Aligned_cols=50 Identities=20% Similarity=0.398 Sum_probs=32.7
Q ss_pred CCCCCHHHHHHHHHHHhhcC--------C-ccccccccCC-CCCHHHHHHHHHHHhHHHH
Q 025221 63 RGKMTPQEERLVLELHAKWG--------N-RWSRIARKLP-GRTDNEIKNYWRTHMRKKA 112 (256)
Q Consensus 63 k~~WT~EED~~Ll~lv~~~G--------~-~W~~Ia~~l~-gRt~~~~knrw~~~lrk~~ 112 (256)
+.++|.|||++|++.|.++. + =|.+++..-+ .+|-.+.|+||...|+.+.
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 45799999999999996542 2 2999999876 8999999999998888754
No 35
>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=96.32 E-value=0.0017 Score=54.76 Aligned_cols=49 Identities=29% Similarity=0.625 Sum_probs=42.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC------CCchhhhhhcccccccccccchhhhccC
Q 025221 8 VRKGPWTEQEDILLVNFVQLFGD------RRWDFIAKVSGLNRTGKSCRLRWVNYLH 58 (256)
Q Consensus 8 ~kkg~WT~EED~~L~~lv~~~g~------~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~ 58 (256)
.|...||.|||.+|.+.|-+|-. ...++|++.++ ||+.-|.=||+.++.
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~--RTsAACGFRWNs~VR 56 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN--RTAAACGFRWNAYVR 56 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc--ccHHHhcchHHHHHH
Confidence 46788999999999999999821 14889999995 999999999999875
No 36
>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=96.16 E-value=0.0022 Score=46.35 Aligned_cols=52 Identities=23% Similarity=0.356 Sum_probs=32.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCC------C--CchhhhhhcccccccccccchhhhccCCCC
Q 025221 10 KGPWTEQEDILLVNFVQLFGD------R--RWDFIAKVSGLNRTGKSCRLRWVNYLHPGL 61 (256)
Q Consensus 10 kg~WT~EED~~L~~lv~~~g~------~--~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~l 61 (256)
+-+||+|||+.|+..|..+.. + =|..+++.-...+|-.+-|+||.+.|.+..
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 357999999999999976631 1 299998776238999999999999987643
No 37
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.12 E-value=0.0023 Score=47.78 Aligned_cols=47 Identities=34% Similarity=0.690 Sum_probs=32.7
Q ss_pred CCCCHHHHHHHHHHHHH--h----CC--C-----Cchhhhhhc---ccccccccccchhhhcc
Q 025221 11 GPWTEQEDILLVNFVQL--F----GD--R-----RWDFIAKVS---GLNRTGKSCRLRWVNYL 57 (256)
Q Consensus 11 g~WT~EED~~L~~lv~~--~----g~--~-----~W~~IA~~l---gp~Rt~~qcr~Rw~~~L 57 (256)
-.||.+|...|+.++.. + +. . -|..||..| |..|++.||+.+|.+..
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~ 64 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLK 64 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 47999999999999877 2 10 1 399999765 56899999999998753
No 38
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.92 E-value=0.012 Score=43.12 Aligned_cols=51 Identities=24% Similarity=0.491 Sum_probs=41.6
Q ss_pred CCCCCHHHHHHHHHHHhhcC-----------------CccccccccC-----CCCCHHHHHHHHHHHhHHHHH
Q 025221 63 RGKMTPQEERLVLELHAKWG-----------------NRWSRIARKL-----PGRTDNEIKNYWRTHMRKKAQ 113 (256)
Q Consensus 63 k~~WT~EED~~Ll~lv~~~G-----------------~~W~~Ia~~l-----~gRt~~~~knrw~~~lrk~~~ 113 (256)
...||.+|.+.|++++.+|- .-|..|+..| +.||..++|.+|.++...-.+
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk 74 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKK 74 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 35799999999999998873 1399999876 249999999999998876443
No 39
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.77 E-value=0.0043 Score=57.58 Aligned_cols=47 Identities=21% Similarity=0.524 Sum_probs=44.4
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccC
Q 025221 11 GPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLH 58 (256)
Q Consensus 11 g~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~ 58 (256)
.-|+.+|+.+|++..+..|-+||..||..+| .|+...|+.+|..++.
T Consensus 64 e~WgadEEllli~~~~TlGlGNW~dIadyiG-sr~kee~k~HylK~y~ 110 (432)
T COG5114 64 EGWGADEELLLIECLDTLGLGNWEDIADYIG-SRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCcCchHHHHHHHHHHhcCCCcHHHHHHHHh-hhhhHHHHHHHHHHHh
Confidence 4599999999999999999999999999998 9999999999999875
No 40
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.75 E-value=0.0085 Score=51.12 Aligned_cols=49 Identities=18% Similarity=0.331 Sum_probs=41.2
Q ss_pred cCCCCCHHHHHHHHHHHhhcCCc-------cccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 62 KRGKMTPQEERLVLELHAKWGNR-------WSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 62 ~k~~WT~EED~~Ll~lv~~~G~~-------W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
....||.|+|.+|-+.|-.|+.. ...++..| +||..+|..||+..+|++
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~ 59 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQ 59 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHH
Confidence 45689999999999999888742 55666778 999999999999999875
No 41
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=95.66 E-value=0.076 Score=56.80 Aligned_cols=101 Identities=17% Similarity=0.307 Sum_probs=76.1
Q ss_pred CCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccc----------------------------------------
Q 025221 12 PWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRL---------------------------------------- 51 (256)
Q Consensus 12 ~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~---------------------------------------- 51 (256)
-||.-+=..++.+..+||..+-..||..++ +++...++.
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~-~k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~~ 904 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEME-GKTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAIG 904 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhc-CCCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 488888888899999999888999999884 677765531
Q ss_pred --------hhhhc-c-CCCCcCCCCCHHHHHHHHHHHhhcC-Ccccccccc------------CCCCCHHHHHHHHHHHh
Q 025221 52 --------RWVNY-L-HPGLKRGKMTPQEERLVLELHAKWG-NRWSRIARK------------LPGRTDNEIKNYWRTHM 108 (256)
Q Consensus 52 --------Rw~~~-L-~p~l~k~~WT~EED~~Ll~lv~~~G-~~W~~Ia~~------------l~gRt~~~~knrw~~~l 108 (256)
-|... + .+..++..+|.|||+.|+-.+.+|| .+|.+|-.. |..||+..|..|..+++
T Consensus 905 ~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~ 984 (1033)
T PLN03142 905 KKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLI 984 (1033)
T ss_pred HHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHH
Confidence 11111 0 1223445699999999999999999 479888322 47899999999999999
Q ss_pred HHHHH
Q 025221 109 RKKAQ 113 (256)
Q Consensus 109 rk~~~ 113 (256)
+-..+
T Consensus 985 ~~~~~ 989 (1033)
T PLN03142 985 RLIEK 989 (1033)
T ss_pred HHHHH
Confidence 86543
No 42
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.57 E-value=0.0058 Score=44.81 Aligned_cols=49 Identities=29% Similarity=0.456 Sum_probs=39.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhC----------------CCCchhhhhhc----ccccccccccchhhhcc
Q 025221 9 RKGPWTEQEDILLVNFVQLFG----------------DRRWDFIAKVS----GLNRTGKSCRLRWVNYL 57 (256)
Q Consensus 9 kkg~WT~EED~~L~~lv~~~g----------------~~~W~~IA~~l----gp~Rt~~qcr~Rw~~~L 57 (256)
++..||++|.+.|+++|.+|. ..-|..|+..+ ++.|+..|++.+|.+..
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 467899999999999999982 11399999765 23799999999998865
No 43
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.12 E-value=0.0091 Score=50.95 Aligned_cols=49 Identities=24% Similarity=0.518 Sum_probs=39.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCC------CchhhhhhcccccccccccchhhhccC
Q 025221 8 VRKGPWTEQEDILLVNFVQLFGDR------RWDFIAKVSGLNRTGKSCRLRWVNYLH 58 (256)
Q Consensus 8 ~kkg~WT~EED~~L~~lv~~~g~~------~W~~IA~~lgp~Rt~~qcr~Rw~~~L~ 58 (256)
.++..||.|||.+|.+.|-.|+.. -...++..| +|+...|..||+.++.
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L--~rt~aac~fRwNs~vr 57 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL--KRTAAACGFRWNSVVR 57 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH--hhhHHHHHhHHHHHHH
Confidence 578899999999999999998632 266677777 5999999999966553
No 44
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=94.96 E-value=0.028 Score=45.26 Aligned_cols=53 Identities=23% Similarity=0.441 Sum_probs=42.5
Q ss_pred CCcCCCCCHHHHHHHHHHHhhcCC----cccccccc------------CCCCCHHHHHHHHHHHhHHHH
Q 025221 60 GLKRGKMTPQEERLVLELHAKWGN----RWSRIARK------------LPGRTDNEIKNYWRTHMRKKA 112 (256)
Q Consensus 60 ~l~k~~WT~EED~~Ll~lv~~~G~----~W~~Ia~~------------l~gRt~~~~knrw~~~lrk~~ 112 (256)
..++..+|++||..|+-.+.+||- .|..|... |..||+..|..|..++++--.
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i~ 114 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLIE 114 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHHH
Confidence 556778999999999999999996 78888543 478999999999999998643
No 45
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=94.86 E-value=0.049 Score=50.98 Aligned_cols=56 Identities=21% Similarity=0.423 Sum_probs=45.0
Q ss_pred CCCCCHHHHHHHHHHHhhc----------CCccccccccC--CC--CCHHHHHHHHHHHhHHHHHhhhhc
Q 025221 63 RGKMTPQEERLVLELHAKW----------GNRWSRIARKL--PG--RTDNEIKNYWRTHMRKKAQERKRA 118 (256)
Q Consensus 63 k~~WT~EED~~Ll~lv~~~----------G~~W~~Ia~~l--~g--Rt~~~~knrw~~~lrk~~~~~~~~ 118 (256)
...|+.+|-..||++..+. +..|..||+.+ .| ||+.+||++|.++.++..+.+...
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k~~~ 123 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEKAKK 123 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 3689999999999997653 34699999965 23 999999999999999876655554
No 46
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=94.03 E-value=0.1 Score=49.75 Aligned_cols=83 Identities=19% Similarity=0.351 Sum_probs=61.8
Q ss_pred CchhhhhhcccccccccccchhhhccCCC-------------------------CcCCCCCHHHHHHHHHHHhhcCCccc
Q 025221 32 RWDFIAKVSGLNRTGKSCRLRWVNYLHPG-------------------------LKRGKMTPQEERLVLELHAKWGNRWS 86 (256)
Q Consensus 32 ~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~-------------------------l~k~~WT~EED~~Ll~lv~~~G~~W~ 86 (256)
.|..+.=.. +-|...-...+|.+..++. ++...||.+|-.-|.+|.+.|.-+|-
T Consensus 75 ~W~w~pFtn-~aRkD~~~l~HWvr~~d~~~dypfakfNk~vdipsYt~eEYe~~l~dn~WskeETD~LF~lck~fDLRf~ 153 (445)
T KOG2656|consen 75 PWKWVPFTN-SARKDDATLHHWVRVGDTPKDYPFAKFNKHVDIPSYTDEEYEAHLNDNSWSKEETDYLFDLCKRFDLRFF 153 (445)
T ss_pred CceeeccCC-ccccCCceEEeeeeccCCCCCCchhhhccccCccccchHHHHHhhccccccHHHHHHHHHHHHhcCeeEE
Confidence 466655333 4566666666666552221 22346999999999999999999999
Q ss_pred ccccc-----CCC-CCHHHHHHHHHHHhHHHHHhh
Q 025221 87 RIARK-----LPG-RTDNEIKNYWRTHMRKKAQER 115 (256)
Q Consensus 87 ~Ia~~-----l~g-Rt~~~~knrw~~~lrk~~~~~ 115 (256)
.||.. ++. ||-.++|.||..+.|+-.+.+
T Consensus 154 VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr 188 (445)
T KOG2656|consen 154 VIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKAR 188 (445)
T ss_pred EEeeccchhhccccccHHHHHHHHHHHHHHHHHcc
Confidence 99998 655 999999999999988876544
No 47
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=93.99 E-value=0.041 Score=51.24 Aligned_cols=46 Identities=26% Similarity=0.364 Sum_probs=41.7
Q ss_pred CCCCHHHHHHHHHHHhhcCC-ccccccccCCCCCHHHHHHHHHHHhH
Q 025221 64 GKMTPQEERLVLELHAKWGN-RWSRIARKLPGRTDNEIKNYWRTHMR 109 (256)
Q Consensus 64 ~~WT~EED~~Ll~lv~~~G~-~W~~Ia~~l~gRt~~~~knrw~~~lr 109 (256)
..|+.+|+-+|++.....|- +|..||.+++.|+...||.+|....-
T Consensus 64 e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 64 EGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 36999999999999999995 99999999988999999999876654
No 48
>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=92.16 E-value=0.21 Score=37.59 Aligned_cols=48 Identities=33% Similarity=0.648 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHHHhhc---CC----------ccccccccC---CC--CCHHHHHHHHHHHhHHHH
Q 025221 65 KMTPQEERLVLELHAKW---GN----------RWSRIARKL---PG--RTDNEIKNYWRTHMRKKA 112 (256)
Q Consensus 65 ~WT~EED~~Ll~lv~~~---G~----------~W~~Ia~~l---~g--Rt~~~~knrw~~~lrk~~ 112 (256)
.||+++++.|++++.+. |+ .|..|+..| .| .+..+|+|||..+.+.-.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y~ 66 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDYR 66 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHHH
Confidence 49999999999998543 21 389998876 33 577999999998877653
No 49
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=90.47 E-value=0.27 Score=46.91 Aligned_cols=47 Identities=19% Similarity=0.326 Sum_probs=43.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 64 GKMTPQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 64 ~~WT~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
.+|+.+|-+++..+...+|...+.|+..||.|...|||-+|.+--|+
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 37999999999999999999999999999999999999988765554
No 50
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=89.90 E-value=0.34 Score=38.99 Aligned_cols=34 Identities=24% Similarity=0.465 Sum_probs=29.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC---CCchhhhhhc
Q 025221 7 EVRKGPWTEQEDILLVNFVQLFGD---RRWDFIAKVS 40 (256)
Q Consensus 7 ~~kkg~WT~EED~~L~~lv~~~g~---~~W~~IA~~l 40 (256)
..++..||.+||.-|+.++.+||. +.|+.|-+.+
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 778889999999999999999998 7899998766
No 51
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=88.24 E-value=1.1 Score=46.20 Aligned_cols=44 Identities=18% Similarity=0.356 Sum_probs=39.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhh
Q 025221 10 KGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVN 55 (256)
Q Consensus 10 kg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~ 55 (256)
.-+||+.|-.++.+++..|. +++.+|++++ +++|.+||-+.|..
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~-KDF~~v~km~-~~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYS-KDFIFVQKMV-KSKTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhc-ccHHHHHHHh-ccccHHHHHHHHHH
Confidence 35799999999999999998 6899999999 69999999887753
No 52
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=87.22 E-value=1.9 Score=42.07 Aligned_cols=49 Identities=16% Similarity=0.304 Sum_probs=43.1
Q ss_pred cCCCCCHHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 62 KRGKMTPQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 62 ~k~~WT~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
-...||.||--++-+++..||.+..+|-+.||.|+-..|..+|....+.
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK~ 234 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKKT 234 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHHH
Confidence 3457999999999999999999999999999999999999887655443
No 53
>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=87.21 E-value=1 Score=30.21 Aligned_cols=42 Identities=26% Similarity=0.411 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 68 PQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 68 ~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
+++++.++.++-..|-.+.+||..+ |.|.+.|+.+...-+++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARKK 53 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHhh
Confidence 4678888999999999999999999 99999999987665543
No 54
>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=86.21 E-value=0.75 Score=34.72 Aligned_cols=30 Identities=23% Similarity=0.472 Sum_probs=17.9
Q ss_pred CCCCCCCCCHHHHHHH--------HHHHHHhCCCCchhhhh
Q 025221 6 EEVRKGPWTEQEDILL--------VNFVQLFGDRRWDFIAK 38 (256)
Q Consensus 6 ~~~kkg~WT~EED~~L--------~~lv~~~g~~~W~~IA~ 38 (256)
|....|-||+|+|+.| .+++++|| +..|++
T Consensus 43 P~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG---~~~i~~ 80 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLRSGDKDDIERLIKKHG---EERIER 80 (87)
T ss_dssp -TT-TT---HHHHHHHTS--HHHHHHHHHHH----HHHHHH
T ss_pred CCCCCCCcCHHHHHHHHcCCHHHHHHHHHHhC---HHHHHH
Confidence 4566889999999999 45677777 556654
No 55
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=85.11 E-value=0.68 Score=44.24 Aligned_cols=63 Identities=16% Similarity=0.308 Sum_probs=49.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhcc--CCC-----C-cCCCCCHHHHHH
Q 025221 9 RKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYL--HPG-----L-KRGKMTPQEERL 73 (256)
Q Consensus 9 kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L--~p~-----l-~k~~WT~EED~~ 73 (256)
.--+||.+|-+++.+++...|+ .+..|+.++ |+|..+|++.+|.+-- +|. | .+.|+..+|-..
T Consensus 364 ~~~~Ws~~e~ekFYKALs~wGt-dF~LIs~lf-P~R~RkqIKaKfi~Eek~nP~rIn~aL~~kkp~d~~eY~k 434 (507)
T COG5118 364 GALRWSKKEIEKFYKALSIWGT-DFSLISSLF-PNRERKQIKAKFIKEEKVNPERINEALNEKKPFDQVEYNK 434 (507)
T ss_pred CCCcccHHHHHHHHHHHHHhcc-hHHHHHHhc-CchhHHHHHHHHHHHhhhCHHHHHHHHhccCCCCHHHHhh
Confidence 3446999999999999999996 799999999 8999999999887642 221 1 345666666543
No 56
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=81.48 E-value=1.1 Score=41.91 Aligned_cols=47 Identities=23% Similarity=0.492 Sum_probs=37.4
Q ss_pred CCCCHHHHHHHHHHHHHh----C-----CCCchhhhhh---cccccccccccchhhhcc
Q 025221 11 GPWTEQEDILLVNFVQLF----G-----DRRWDFIAKV---SGLNRTGKSCRLRWVNYL 57 (256)
Q Consensus 11 g~WT~EED~~L~~lv~~~----g-----~~~W~~IA~~---lgp~Rt~~qcr~Rw~~~L 57 (256)
..|+.+|-..|+.+.... . ..-|..||+. .|..|++.||+.+|.+..
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 679999999999987654 1 1249999973 456899999999998754
No 57
>smart00595 MADF subfamily of SANT domain.
Probab=81.02 E-value=1.7 Score=32.18 Aligned_cols=30 Identities=30% Similarity=0.594 Sum_probs=25.0
Q ss_pred ccccccccCCCCCHHHHHHHHHHHhHHHHHh
Q 025221 84 RWSRIARKLPGRTDNEIKNYWRTHMRKKAQE 114 (256)
Q Consensus 84 ~W~~Ia~~l~gRt~~~~knrw~~~lrk~~~~ 114 (256)
-|.+||..| |-+..+|+.+|+++...-.+.
T Consensus 29 aW~~Ia~~l-~~~~~~~~~kw~~LR~~y~~e 58 (89)
T smart00595 29 AWEEIAEEL-GLSVEECKKRWKNLRDRYRRE 58 (89)
T ss_pred HHHHHHHHH-CcCHHHHHHHHHHHHHHHHHH
Confidence 499999999 559999999999987765444
No 58
>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=78.14 E-value=2.2 Score=31.93 Aligned_cols=44 Identities=30% Similarity=0.563 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHHHHh---CCC---------Cchhhhhhcc----cccccccccchhhh
Q 025221 12 PWTEQEDILLVNFVQLF---GDR---------RWDFIAKVSG----LNRTGKSCRLRWVN 55 (256)
Q Consensus 12 ~WT~EED~~L~~lv~~~---g~~---------~W~~IA~~lg----p~Rt~~qcr~Rw~~ 55 (256)
.||+++++.|++++... |.. .|..|++.|. ...+..||+.||..
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~ 60 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKT 60 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHH
Confidence 59999999999988554 211 3888887663 34556677777654
No 59
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=77.24 E-value=1.6 Score=28.49 Aligned_cols=38 Identities=21% Similarity=0.236 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhh
Q 025221 16 QEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVN 55 (256)
Q Consensus 16 EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~ 55 (256)
+=|.+|+.+++.-+...+..||+.+| =+...|..|..+
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 44889999999999889999999996 788888888754
No 60
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=72.83 E-value=4.9 Score=26.24 Aligned_cols=38 Identities=21% Similarity=0.415 Sum_probs=30.6
Q ss_pred HHHHHHHHHHhhcCC-ccccccccCCCCCHHHHHHHHHHH
Q 025221 69 QEERLVLELHAKWGN-RWSRIARKLPGRTDNEIKNYWRTH 107 (256)
Q Consensus 69 EED~~Ll~lv~~~G~-~W~~Ia~~l~gRt~~~~knrw~~~ 107 (256)
+=|..|+.+..+-|. .+..||..+ |=|...|..|++.+
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 458889999988887 799999999 99999999998765
No 61
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=72.57 E-value=4.8 Score=33.15 Aligned_cols=43 Identities=14% Similarity=0.180 Sum_probs=38.1
Q ss_pred HHHHHHHHHHhhcCC-ccccccccCCCCCHHHHHHHHHHHhHHHH
Q 025221 69 QEERLVLELHAKWGN-RWSRIARKLPGRTDNEIKNYWRTHMRKKA 112 (256)
Q Consensus 69 EED~~Ll~lv~~~G~-~W~~Ia~~l~gRt~~~~knrw~~~lrk~~ 112 (256)
+-|..|+++.++-|. .|++||+.+ |-|...|++|++.+.....
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 578899999988886 899999999 9999999999998887653
No 62
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=71.83 E-value=34 Score=32.21 Aligned_cols=89 Identities=20% Similarity=0.300 Sum_probs=64.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCC---CchhhhhhcccccccccccchhhhccCCCCcCCCCCHHHHHHHHHHHhh-c----
Q 025221 10 KGPWTEQEDILLVNFVQLFGDR---RWDFIAKVSGLNRTGKSCRLRWVNYLHPGLKRGKMTPQEERLVLELHAK-W---- 81 (256)
Q Consensus 10 kg~WT~EED~~L~~lv~~~g~~---~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~l~k~~WT~EED~~Ll~lv~~-~---- 81 (256)
--.||.-|...|+++++..... +-.+|++.+ ++|+...+++ |.+.|+ ++.+.+++++ |
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l-~~Rs~aEI~~-fl~~LK------------~rvareaiqkv~~~g~ 86 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKEL-PGRSEAEIRD-FLQQLK------------GRVAREAIQKVHPGGL 86 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhc-cCcCHHHHHH-HHHHHH------------HHHHHHHHHHhccccc
Confidence 3469999999999999886323 345778888 6999888765 344443 3455555554 2
Q ss_pred -CC------------ccccccccCCCCCHHHHHHHHHHHhHHHH
Q 025221 82 -GN------------RWSRIARKLPGRTDNEIKNYWRTHMRKKA 112 (256)
Q Consensus 82 -G~------------~W~~Ia~~l~gRt~~~~knrw~~~lrk~~ 112 (256)
|. -|..+|..+.|.-...+---|.++|---.
T Consensus 87 ~~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~iaa 130 (344)
T PF11035_consen 87 KGPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLTIAA 130 (344)
T ss_pred ccccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHHHhh
Confidence 22 29999999999999999998888876543
No 63
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=71.44 E-value=5.7 Score=40.24 Aligned_cols=49 Identities=16% Similarity=0.435 Sum_probs=38.9
Q ss_pred CCCCCHHHHHHHHHHHhhcCCccccc----------cccCCCCCHHHHHHHHHHHhHHH
Q 025221 63 RGKMTPQEERLVLELHAKWGNRWSRI----------ARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 63 k~~WT~EED~~Ll~lv~~~G~~W~~I----------a~~l~gRt~~~~knrw~~~lrk~ 111 (256)
+..||.+|+..+..+++++|.+...| -....-+|..|+|.+|++++++-
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m 146 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRM 146 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHH
Confidence 56799999999999999999998888 22334467778888887776654
No 64
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=70.96 E-value=4.9 Score=33.54 Aligned_cols=44 Identities=16% Similarity=0.147 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHhhcCC-ccccccccCCCCCHHHHHHHHHHHhHHHH
Q 025221 68 PQEERLVLELHAKWGN-RWSRIARKLPGRTDNEIKNYWRTHMRKKA 112 (256)
Q Consensus 68 ~EED~~Ll~lv~~~G~-~W~~Ia~~l~gRt~~~~knrw~~~lrk~~ 112 (256)
.+-|..|+.+.++-|. .|++||+.+ |=+...|++|++.+.+...
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 5678899999988887 899999999 9999999999999988764
No 65
>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=70.78 E-value=8.9 Score=25.26 Aligned_cols=42 Identities=24% Similarity=0.344 Sum_probs=32.2
Q ss_pred HHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 69 QEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 69 EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
++++.++.++-..|-.+.+||..| |-|...|+.+-+..+++-
T Consensus 7 ~~er~vi~~~y~~~~t~~eIa~~l-g~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 7 PREREVIRLRYFEGLTLEEIAERL-GISRSTVRRILKRALKKL 48 (50)
T ss_dssp HHHHHHHHHHHTST-SHHHHHHHH-TSCHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHH-CCcHHHHHHHHHHHHHHh
Confidence 455666666666677899999999 999999999887777653
No 66
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=70.27 E-value=2.9 Score=34.48 Aligned_cols=45 Identities=13% Similarity=0.082 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccCCCCc
Q 025221 16 QEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLHPGLK 62 (256)
Q Consensus 16 EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~l~ 62 (256)
+-|.+|+.++++.|...|.+||+.+| -+...|+.|+.+....++-
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 57999999999999889999999996 8999999999887766554
No 67
>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=67.56 E-value=4.1 Score=34.48 Aligned_cols=41 Identities=24% Similarity=0.187 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHH
Q 025221 65 KMTPQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRT 106 (256)
Q Consensus 65 ~WT~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~ 106 (256)
.||+|+.+.|.+|. .-|..=++||..|.|.|.|.|.-+-+.
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 59999999999987 557778899999977999999886654
No 68
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=65.69 E-value=3 Score=34.87 Aligned_cols=46 Identities=20% Similarity=0.121 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccCCCCc
Q 025221 15 EQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLHPGLK 62 (256)
Q Consensus 15 ~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~l~ 62 (256)
.+-|.+|+.++++-|.-.|..||+.+| -+...|+.|+.+..+.++-
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 456999999999999889999999996 8888999999887766553
No 69
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=65.44 E-value=4.9 Score=43.41 Aligned_cols=35 Identities=17% Similarity=0.329 Sum_probs=30.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCchhhhhhc
Q 025221 6 EEVRKGPWTEQEDILLVNFVQLFGDRRWDFIAKVS 40 (256)
Q Consensus 6 ~~~kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~l 40 (256)
+..++..||.|||..|+..+.+||.++|++|-..+
T Consensus 922 ~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i 956 (1033)
T PLN03142 922 GQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAF 956 (1033)
T ss_pred CCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHH
Confidence 45556669999999999999999999999997766
No 70
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=65.33 E-value=8.1 Score=39.03 Aligned_cols=47 Identities=21% Similarity=0.331 Sum_probs=42.1
Q ss_pred cCCCCCHHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHh
Q 025221 62 KRGKMTPQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHM 108 (256)
Q Consensus 62 ~k~~WT~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l 108 (256)
..++|+.+|-++.......+|.+-+.|+..+++|...+||.++..--
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~eE 454 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKEE 454 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhhh
Confidence 45679999999999999999999999999999999999999765433
No 71
>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=65.33 E-value=18 Score=34.05 Aligned_cols=49 Identities=24% Similarity=0.487 Sum_probs=37.8
Q ss_pred CCCCCHHHHHHHHHHHhhc-CC---ccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 63 RGKMTPQEERLVLELHAKW-GN---RWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 63 k~~WT~EED~~Ll~lv~~~-G~---~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
-..||.-|.+.|+.+.+.. |. .-..|++.++||+..+|++.-..+..+.
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rv 73 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRV 73 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHH
Confidence 3469999999999888654 54 4568899999999999998766555443
No 72
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=64.38 E-value=11 Score=33.06 Aligned_cols=41 Identities=17% Similarity=0.359 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHHhhcCCcc------ccccccCCCCCHHHHHHHHHHHhH
Q 025221 65 KMTPQEERLVLELHAKWGNRW------SRIARKLPGRTDNEIKNYWRTHMR 109 (256)
Q Consensus 65 ~WT~EED~~Ll~lv~~~G~~W------~~Ia~~l~gRt~~~~knrw~~~lr 109 (256)
+|++.+|-+|+.+|..-. .- .+.+..| |-..|..||..+|-
T Consensus 1 rW~~~DDl~Li~av~~~~-~L~~v~~gvkFS~~f---T~~Ei~~RW~~lly 47 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTN-DLESVHLGVKFSCKF---TLQEIEERWYALLY 47 (199)
T ss_pred CCCchhhHHHHHHHHHhc-CHHHHHccCCcCCcC---cHHHHHHHHHHHHc
Confidence 599999999999986533 22 3444445 88999999999884
No 73
>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=62.17 E-value=6.5 Score=28.15 Aligned_cols=34 Identities=26% Similarity=0.506 Sum_probs=25.7
Q ss_pred ccccccccCCC-CCHHHHHHHHHHHhHHHHHhhhh
Q 025221 84 RWSRIARKLPG-RTDNEIKNYWRTHMRKKAQERKR 117 (256)
Q Consensus 84 ~W~~Ia~~l~g-Rt~~~~knrw~~~lrk~~~~~~~ 117 (256)
-|..||..|.. -+.++|+.+|+++...-....+.
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y~~~~~~ 62 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRDRYRRELKK 62 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHHHHHHHHHH
Confidence 48999999943 57889999999988765444443
No 74
>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=61.81 E-value=13 Score=29.54 Aligned_cols=39 Identities=18% Similarity=0.262 Sum_probs=29.0
Q ss_pred HHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 72 RLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 72 ~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
..++.+.-..|-.+.+||..+ |.+...|+++....+++-
T Consensus 119 r~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~L 157 (161)
T TIGR02985 119 RKIFILSRFEGKSYKEIAEEL-GISVKTVEYHISKALKEL 157 (161)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 333444334467899999999 999999999988866553
No 75
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=59.00 E-value=8.8 Score=28.84 Aligned_cols=17 Identities=24% Similarity=0.509 Sum_probs=10.3
Q ss_pred CCCcCCCCCHHHHHHHH
Q 025221 59 PGLKRGKMTPQEERLVL 75 (256)
Q Consensus 59 p~l~k~~WT~EED~~Ll 75 (256)
|....|-||+|+|+.|.
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 56678889999999994
No 76
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=56.94 E-value=13 Score=32.31 Aligned_cols=45 Identities=24% Similarity=0.307 Sum_probs=38.9
Q ss_pred CCCCHHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 64 GKMTPQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 64 ~~WT~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
...|+.|-+.|.-+.+-+.+ .+||..| +.+...||++..++++|-
T Consensus 147 ~~LT~RE~eVL~lla~G~sn--keIA~~L-~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 147 ELLTPRELEVLRLLAEGLSN--KEIAEEL-NLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCCCHHHHHHHHHHHCCCCH--HHHHHHH-CCCHhHHHHHHHHHHHHc
Confidence 36899999988887765655 4999999 999999999999999984
No 77
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=55.82 E-value=5.6 Score=29.97 Aligned_cols=39 Identities=33% Similarity=0.526 Sum_probs=26.3
Q ss_pred HHHHHHHHhC-------CCCchhhhhhccccc----ccccccchhhhccC
Q 025221 20 LLVNFVQLFG-------DRRWDFIAKVSGLNR----TGKSCRLRWVNYLH 58 (256)
Q Consensus 20 ~L~~lv~~~g-------~~~W~~IA~~lgp~R----t~~qcr~Rw~~~L~ 58 (256)
+|..+|.+.| ...|..||..+|..- .+.+.+..|.++|.
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~ 85 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLL 85 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhH
Confidence 5777787776 247999999997432 23455666776664
No 78
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=54.50 E-value=27 Score=26.95 Aligned_cols=51 Identities=14% Similarity=0.200 Sum_probs=34.4
Q ss_pred CCCCHHHHHHHHHHHhhc----CC----ccccc----cccCC-CCCHHHHHHHHHHHhHHHHHh
Q 025221 64 GKMTPQEERLVLELHAKW----GN----RWSRI----ARKLP-GRTDNEIKNYWRTHMRKKAQE 114 (256)
Q Consensus 64 ~~WT~EED~~Ll~lv~~~----G~----~W~~I----a~~l~-gRt~~~~knrw~~~lrk~~~~ 114 (256)
.-||++++-.||+.+..| |. .+..+ ...|. .=+.+|+.++-+.+-+|-...
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~ 68 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNA 68 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHH
Confidence 359999999999998776 62 34333 23331 137789988888877775443
No 79
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=54.16 E-value=5.8 Score=29.63 Aligned_cols=39 Identities=23% Similarity=0.433 Sum_probs=25.9
Q ss_pred HHHHHHHHhC-------CCCchhhhhhcccccc----cccccchhhhccC
Q 025221 20 LLVNFVQLFG-------DRRWDFIAKVSGLNRT----GKSCRLRWVNYLH 58 (256)
Q Consensus 20 ~L~~lv~~~g-------~~~W~~IA~~lgp~Rt----~~qcr~Rw~~~L~ 58 (256)
+|..+|.+.| .+.|..||+.+|.... +.+++..|.++|.
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhH
Confidence 5677777776 2369999999974332 3456677777664
No 80
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=54.01 E-value=16 Score=38.04 Aligned_cols=43 Identities=16% Similarity=0.278 Sum_probs=39.0
Q ss_pred CCCCCHHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHH
Q 025221 63 RGKMTPQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWR 105 (256)
Q Consensus 63 k~~WT~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~ 105 (256)
...||+.|-+++-+++-.|-.+.-.|++.++++|-.+|-.+|.
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYY 661 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYY 661 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHH
Confidence 3469999999999999999999999999999999999987643
No 81
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=53.16 E-value=12 Score=36.88 Aligned_cols=47 Identities=19% Similarity=0.289 Sum_probs=40.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhh
Q 025221 7 EVRKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVN 55 (256)
Q Consensus 7 ~~kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~ 55 (256)
.-.+..||.||--+|-++...|| .++.+|-++| |.|+-.+++..|..
T Consensus 184 ~~~~d~WT~Ed~vlFe~aF~~~G-K~F~kIrq~L-P~rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 184 TEFPDEWTAEDIVLFEQAFQFFG-KDFHKIRQAL-PHRSLASLVQYYYS 230 (534)
T ss_pred CCCcccchHHHHHHHHHHHHHhc-ccHHHHHHHc-cCccHHHHHHHHHH
Confidence 34567799999999999999999 6899999999 89999888776654
No 82
>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=51.81 E-value=11 Score=28.26 Aligned_cols=30 Identities=23% Similarity=0.536 Sum_probs=24.4
Q ss_pred HHHHHHHHhhcCCccccccccCCCCCHHHHH
Q 025221 71 ERLVLELHAKWGNRWSRIARKLPGRTDNEIK 101 (256)
Q Consensus 71 D~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~k 101 (256)
|+.|..+....|..|..+|++| |=|..+|.
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I~ 31 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDIY 31 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 5678889999999999999998 76665543
No 83
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=49.96 E-value=76 Score=30.64 Aligned_cols=43 Identities=21% Similarity=0.251 Sum_probs=37.5
Q ss_pred CCCCHHHHHHHHHHHhhcCCccccccc-cCCCCCHHHHHHHHHH
Q 025221 64 GKMTPQEERLVLELHAKWGNRWSRIAR-KLPGRTDNEIKNYWRT 106 (256)
Q Consensus 64 ~~WT~EED~~Ll~lv~~~G~~W~~Ia~-~l~gRt~~~~knrw~~ 106 (256)
..|+++|-+.+-+.++.||++...|.+ .++.|+--.|-.+|..
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYl 321 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYL 321 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHH
Confidence 469999999999999999999999955 6899999999876543
No 84
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=49.88 E-value=24 Score=36.00 Aligned_cols=49 Identities=16% Similarity=0.329 Sum_probs=35.6
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCchhhhhhccc---------ccccccccchhhhccC
Q 025221 9 RKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGL---------NRTGKSCRLRWVNYLH 58 (256)
Q Consensus 9 kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp---------~Rt~~qcr~Rw~~~L~ 58 (256)
.|..||-.|.+-+..+++.+| .+++.|-+.+-- -+|-.|+|.+|++.++
T Consensus 87 ~ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~ 144 (782)
T KOG4468|consen 87 AKTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVR 144 (782)
T ss_pred cccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHH
Confidence 366799999999999999999 689888332211 2444577887776653
No 85
>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=47.09 E-value=18 Score=24.49 Aligned_cols=44 Identities=27% Similarity=0.355 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 65 KMTPQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 65 ~WT~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
..|+.|-+.|.-+..-+.. .+||..+ |.+...|+.+-..+++|-
T Consensus 3 ~LT~~E~~vl~~l~~G~~~--~eIA~~l-~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGMSN--KEIAEEL-GISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-H--HHHHHHH-TSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcCCc--chhHHhc-CcchhhHHHHHHHHHHHh
Confidence 4577777777666654444 5999999 999999999998888874
No 86
>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=46.51 E-value=18 Score=27.21 Aligned_cols=31 Identities=23% Similarity=0.411 Sum_probs=25.4
Q ss_pred HHHHHHHHhhcCCccccccccCCCCCHHHHHH
Q 025221 71 ERLVLELHAKWGNRWSRIARKLPGRTDNEIKN 102 (256)
Q Consensus 71 D~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~kn 102 (256)
|..|..+....|..|.++|+.| |=+..+|.+
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 6678888899999999999998 767665544
No 87
>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=46.46 E-value=11 Score=25.02 Aligned_cols=38 Identities=13% Similarity=0.155 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhh
Q 025221 15 EQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVN 55 (256)
Q Consensus 15 ~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~ 55 (256)
++++..++.+....| ..+.+||+.+| .+...++.+..+
T Consensus 12 ~~~~r~i~~l~~~~g-~s~~eIa~~l~--~s~~~v~~~l~r 49 (54)
T PF08281_consen 12 PERQREIFLLRYFQG-MSYAEIAEILG--ISESTVKRRLRR 49 (54)
T ss_dssp -HHHHHHHHHHHTS----HHHHHHHCT--S-HHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHC-cCHHHHHHHHC--cCHHHHHHHHHH
Confidence 456677777777777 58999999996 888887776554
No 88
>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=46.30 E-value=29 Score=26.65 Aligned_cols=35 Identities=23% Similarity=0.210 Sum_probs=26.8
Q ss_pred HHHhhcCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 76 ELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 76 ~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
.++-..|-.+.+||+.+ |-+...|+++.+..+++-
T Consensus 120 ~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~kl 154 (158)
T TIGR02937 120 VLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKKL 154 (158)
T ss_pred hhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 33334577899999999 789999999888766553
No 89
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=45.49 E-value=27 Score=26.48 Aligned_cols=43 Identities=19% Similarity=0.240 Sum_probs=36.9
Q ss_pred HHHHHHHHHHhhcCC-ccccccccCCCCCHHHHHHHHHHHhHHHH
Q 025221 69 QEERLVLELHAKWGN-RWSRIARKLPGRTDNEIKNYWRTHMRKKA 112 (256)
Q Consensus 69 EED~~Ll~lv~~~G~-~W~~Ia~~l~gRt~~~~knrw~~~lrk~~ 112 (256)
+.|..|+.+..+.|. .+++||+.+ |-+...|+.+.+.+..+..
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~ 46 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGV 46 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 568888888888875 799999999 9999999999998887653
No 90
>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=45.31 E-value=18 Score=23.24 Aligned_cols=29 Identities=21% Similarity=0.261 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHhCCCCchhhhhhcccccc
Q 025221 16 QEDILLVNFVQLFGDRRWDFIAKVSGLNRT 45 (256)
Q Consensus 16 EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt 45 (256)
-|.+.|.+++..++ ++....|+.+|-+|+
T Consensus 5 ~E~~~i~~aL~~~~-gn~~~aA~~Lgisr~ 33 (42)
T PF02954_consen 5 FEKQLIRQALERCG-GNVSKAARLLGISRR 33 (42)
T ss_dssp HHHHHHHHHHHHTT-T-HHHHHHHHTS-HH
T ss_pred HHHHHHHHHHHHhC-CCHHHHHHHHCCCHH
Confidence 37788889999998 789999999985554
No 91
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=44.58 E-value=25 Score=24.00 Aligned_cols=36 Identities=22% Similarity=0.511 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHH
Q 025221 69 QEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWR 105 (256)
Q Consensus 69 EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~ 105 (256)
++|+..+.+..+.|-.=.+||+.+ ||+.+.|+++-+
T Consensus 7 ~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 7 DAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRYLK 42 (50)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHHHH
T ss_pred HHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHHhc
Confidence 456777888889999999999999 999999988643
No 92
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=43.68 E-value=35 Score=27.66 Aligned_cols=33 Identities=15% Similarity=0.123 Sum_probs=25.4
Q ss_pred HHhhcCCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 77 LHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 77 lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
++-..|-....||..| |.+...|+++....+++
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 99999999887765554
No 93
>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=43.04 E-value=15 Score=27.22 Aligned_cols=31 Identities=23% Similarity=0.568 Sum_probs=24.3
Q ss_pred HHHHHHHHhhcCCccccccccCCCCCHHHHHH
Q 025221 71 ERLVLELHAKWGNRWSRIARKLPGRTDNEIKN 102 (256)
Q Consensus 71 D~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~kn 102 (256)
|..|..+.+..|.+|.++|+.| |=+..+|..
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI~~ 34 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDIDL 34 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHHHH
Confidence 4567788889999999999999 666655543
No 94
>PRK04217 hypothetical protein; Provisional
Probab=41.24 E-value=53 Score=26.06 Aligned_cols=45 Identities=18% Similarity=0.112 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 65 KMTPQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 65 ~WT~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
..|++| ..++.++...|-.-.+||+.+ |-+...|+++++...++-
T Consensus 42 ~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 42 FMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKKV 86 (110)
T ss_pred cCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 466666 677777777788899999999 999999999998766554
No 95
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=40.92 E-value=41 Score=28.38 Aligned_cols=38 Identities=26% Similarity=0.274 Sum_probs=29.3
Q ss_pred HHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 72 RLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 72 ~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
..++++..-.|-.+.+||..| |-+...|+.+|.....+
T Consensus 141 ~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR~~ 178 (185)
T PF07638_consen 141 RRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRARAW 178 (185)
T ss_pred HHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 334444444577899999999 99999999999887644
No 96
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=40.56 E-value=18 Score=29.17 Aligned_cols=44 Identities=14% Similarity=0.034 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccCCCC
Q 025221 16 QEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLHPGL 61 (256)
Q Consensus 16 EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~l 61 (256)
+-|.+++++++..+...+..||+.+| -+...|+.|-.+..+.++
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~lg--lS~~~v~~Ri~~L~~~Gi 51 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERVG--LSPSTVLRRIKRLEEEGV 51 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCCc
Confidence 55889999999999889999999996 888889888777665554
No 97
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=40.17 E-value=15 Score=35.48 Aligned_cols=48 Identities=21% Similarity=0.351 Sum_probs=40.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCchhhhhh-----cccccccccccchhhhc
Q 025221 8 VRKGPWTEQEDILLVNFVQLFGDRRWDFIAKV-----SGLNRTGKSCRLRWVNY 56 (256)
Q Consensus 8 ~kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~-----lgp~Rt~~qcr~Rw~~~ 56 (256)
++...||.+|-.-|..+.+.|. -+|-.||.. .+..||....++||...
T Consensus 128 l~dn~WskeETD~LF~lck~fD-LRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v 180 (445)
T KOG2656|consen 128 LNDNSWSKEETDYLFDLCKRFD-LRFFVIADRYDNQQYKKSRTVEDLKERYYSV 180 (445)
T ss_pred hccccccHHHHHHHHHHHHhcC-eeEEEEeeccchhhccccccHHHHHHHHHHH
Confidence 3456799999999999999998 689999965 65459999999998765
No 98
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=40.09 E-value=44 Score=28.00 Aligned_cols=46 Identities=20% Similarity=0.290 Sum_probs=37.9
Q ss_pred cCCCCCHHHHHHHHHHHhhcCCccccccccCC----CCCHHHHHHHHHHH
Q 025221 62 KRGKMTPQEERLVLELHAKWGNRWSRIARKLP----GRTDNEIKNYWRTH 107 (256)
Q Consensus 62 ~k~~WT~EED~~Ll~lv~~~G~~W~~Ia~~l~----gRt~~~~knrw~~~ 107 (256)
....-|..|...|..|+++||.+...++.-.. -.|..||+.+....
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 34568999999999999999999999988643 38999999876654
No 99
>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=39.87 E-value=22 Score=26.63 Aligned_cols=27 Identities=30% Similarity=0.538 Sum_probs=21.1
Q ss_pred HHHHhhcCCccccccccCCCCCHHHHHH
Q 025221 75 LELHAKWGNRWSRIARKLPGRTDNEIKN 102 (256)
Q Consensus 75 l~lv~~~G~~W~~Ia~~l~gRt~~~~kn 102 (256)
..+....|.+|.++|+.| |=+..+|..
T Consensus 11 ~~ia~~iG~~Wk~Lar~L-Gls~~dI~~ 37 (86)
T cd08318 11 TVFANKLGEDWKTLAPHL-EMKDKEIRA 37 (86)
T ss_pred HHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 335677899999999999 877777643
No 100
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=39.69 E-value=62 Score=27.18 Aligned_cols=34 Identities=18% Similarity=0.133 Sum_probs=25.9
Q ss_pred HHHhhcCCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 76 ELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 76 ~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
.+.-..|-...+||..| |-+...|++|...-+++
T Consensus 144 ~l~~~~g~s~~EIA~~l-g~s~~tV~~rl~rar~~ 177 (192)
T PRK09643 144 VAVDMQGYSVADAARML-GVAEGTVKSRCARGRAR 177 (192)
T ss_pred HHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 33334567899999999 99999999998655544
No 101
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=38.97 E-value=46 Score=20.73 Aligned_cols=41 Identities=22% Similarity=0.319 Sum_probs=27.7
Q ss_pred CCHHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHh
Q 025221 66 MTPQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHM 108 (256)
Q Consensus 66 WT~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l 108 (256)
.+++ +..++.++-.-|-.+..||..+ |-+...|+.+.....
T Consensus 11 l~~~-~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~~ 51 (55)
T cd06171 11 LPER-EREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRAL 51 (55)
T ss_pred CCHH-HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 3444 4455555555677889999998 788888877665543
No 102
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=38.68 E-value=25 Score=26.65 Aligned_cols=45 Identities=16% Similarity=0.037 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccCCCCc
Q 025221 16 QEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLHPGLK 62 (256)
Q Consensus 16 EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~l~ 62 (256)
+.|.+|+.++...+...+..||+.+| -+...|+.|..+..+.++-
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~--~s~~tv~~~l~~L~~~g~i 47 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVG--LSPSTVHNRVKRLEEEGVI 47 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCe
Confidence 56889999999988778999999996 7888888887776655443
No 103
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=38.48 E-value=44 Score=27.46 Aligned_cols=30 Identities=10% Similarity=-0.068 Sum_probs=24.3
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 81 WGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 81 ~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
.|....+||..| |-|...|+++.....++-
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar~~L 180 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREAL 180 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 456789999999 999999999877666553
No 104
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=38.40 E-value=43 Score=27.01 Aligned_cols=31 Identities=23% Similarity=0.179 Sum_probs=24.5
Q ss_pred hcCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 80 KWGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 80 ~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
..|-....||..| |-+...|+++....+++-
T Consensus 139 ~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~l 169 (179)
T PRK11924 139 VEGLSYREIAEIL-GVPVGTVKSRLRRARQLL 169 (179)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3466789999999 999999999877655543
No 105
>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=38.04 E-value=26 Score=25.91 Aligned_cols=33 Identities=30% Similarity=0.527 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHhhcCCccccccccCCCCCHHHHHH
Q 025221 68 PQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKN 102 (256)
Q Consensus 68 ~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~kn 102 (256)
.||.++|+.. -..|.+|...|..| |=+...|++
T Consensus 2 ~~~v~~ll~~-~nlG~dW~~LA~~L-G~~~~~I~~ 34 (77)
T cd08311 2 QEEVEKLLES-GRPGRDWRSLAGEL-GYEDEAIDT 34 (77)
T ss_pred hHHHHHHHhC-CCCccCHHHHHHHc-CCCHHHHHH
Confidence 5777887742 25788999999999 888888776
No 106
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=37.57 E-value=45 Score=32.21 Aligned_cols=54 Identities=28% Similarity=0.328 Sum_probs=40.9
Q ss_pred CcCCCCCHHHHHHHHHHHhhcC----------------CccccccccC---CC--CCHHHHHHHHHHHhHHHHHh
Q 025221 61 LKRGKMTPQEERLVLELHAKWG----------------NRWSRIARKL---PG--RTDNEIKNYWRTHMRKKAQE 114 (256)
Q Consensus 61 l~k~~WT~EED~~Ll~lv~~~G----------------~~W~~Ia~~l---~g--Rt~~~~knrw~~~lrk~~~~ 114 (256)
..-|-|+++=|+.+.++...|- .+-..||+++ .| ||..||-.+=..+-|++.++
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~re 148 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLRE 148 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHH
Confidence 3457899999999999998873 2457888876 33 88899988877777766544
No 107
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=37.36 E-value=25 Score=33.73 Aligned_cols=41 Identities=17% Similarity=0.282 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHHHhCCCCchhhh-hhcccccccccccchhh
Q 025221 12 PWTEQEDILLVNFVQLFGDRRWDFIA-KVSGLNRTGKSCRLRWV 54 (256)
Q Consensus 12 ~WT~EED~~L~~lv~~~g~~~W~~IA-~~lgp~Rt~~qcr~Rw~ 54 (256)
.|+.+|-..+-+.++.|| +++..|- ..+ ++|+..-|-..|.
T Consensus 279 ~wsEeEcr~FEegl~~yG-KDF~lIr~nkv-rtRsvgElVeyYY 320 (445)
T KOG4329|consen 279 GWSEEECRNFEEGLELYG-KDFHLIRANKV-RTRSVGELVEYYY 320 (445)
T ss_pred cCCHHHHHHHHHHHHHhc-ccHHHHHhccc-ccchHHHHHHHHH
Confidence 499999999999999999 6888885 567 6899998877664
No 108
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=36.78 E-value=95 Score=24.43 Aligned_cols=46 Identities=22% Similarity=0.258 Sum_probs=32.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhcc
Q 025221 8 VRKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYL 57 (256)
Q Consensus 8 ~kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L 57 (256)
.++..||.|+-..++..+...| ..=..||+.+|. +. +-..+|.+.+
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g-~sv~evA~e~gI--s~-~tl~~W~r~y 53 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPG-MTVSLVARQHGV--AA-SQLFLWRKQY 53 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCC-CCHHHHHHHHCc--CH-HHHHHHHHHH
Confidence 4457899999888888877777 467899999873 33 3345666655
No 109
>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=36.32 E-value=31 Score=25.13 Aligned_cols=32 Identities=28% Similarity=0.554 Sum_probs=23.2
Q ss_pred HHHHHHHHHhh-cCCccccccccCCCCCHHHHHH
Q 025221 70 EERLVLELHAK-WGNRWSRIARKLPGRTDNEIKN 102 (256)
Q Consensus 70 ED~~Ll~lv~~-~G~~W~~Ia~~l~gRt~~~~kn 102 (256)
-.+.|..++.. .|..|..+|+.| |=+..+|..
T Consensus 4 ~~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i~~ 36 (88)
T smart00005 4 TREKLAKLLDHPLGLDWRELARKL-GLSEADIDQ 36 (88)
T ss_pred HHHHHHHHHcCccchHHHHHHHHc-CCCHHHHHH
Confidence 34566677777 899999999999 555555533
No 110
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=34.17 E-value=53 Score=26.97 Aligned_cols=29 Identities=10% Similarity=-0.021 Sum_probs=23.4
Q ss_pred CCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 82 GNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 82 G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
|..-.+||..| |.+.+.|+++....+++-
T Consensus 152 g~s~~eIA~~l-gis~~~v~~~l~Rar~~L 180 (187)
T TIGR02948 152 DLSLKEISEIL-DLPVGTVKTRIHRGREAL 180 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 56788999999 999999999887666553
No 111
>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=34.15 E-value=47 Score=27.39 Aligned_cols=29 Identities=14% Similarity=0.114 Sum_probs=23.5
Q ss_pred CCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 82 GNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 82 G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
|-...+||..| |-|.+.|+++....+++-
T Consensus 154 ~~s~~EIA~~l-gis~~tv~~~l~rar~~L 182 (190)
T TIGR02939 154 GLSYEDIARIM-DCPVGTVRSRIFRAREAI 182 (190)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 55789999999 889999999887666553
No 112
>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=33.39 E-value=43 Score=28.28 Aligned_cols=33 Identities=21% Similarity=0.187 Sum_probs=26.1
Q ss_pred CCCHHHHHHHHHHHHHhCCCCchhhhhhcc-ccccc
Q 025221 12 PWTEQEDILLVNFVQLFGDRRWDFIAKVSG-LNRTG 46 (256)
Q Consensus 12 ~WT~EED~~L~~lv~~~g~~~W~~IA~~lg-p~Rt~ 46 (256)
.||+|+.++|.+|...-- .=.+||+.|| ..|+.
T Consensus 2 ~Wtde~~~~L~~lw~~G~--SasqIA~~lg~vsRnA 35 (162)
T PF07750_consen 2 SWTDERVERLRKLWAEGL--SASQIARQLGGVSRNA 35 (162)
T ss_pred CCCHHHHHHHHHHHHcCC--CHHHHHHHhCCcchhh
Confidence 599999999999996632 4689999998 44544
No 113
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=32.74 E-value=71 Score=25.49 Aligned_cols=30 Identities=10% Similarity=0.057 Sum_probs=24.1
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 81 WGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 81 ~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
.|-.-.+||..| |-+.+.|+++....+++-
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~L 150 (161)
T PRK09047 121 EDMDVAETAAAM-GCSEGSVKTHCSRATHAL 150 (161)
T ss_pred hcCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 356789999999 999999999877665543
No 114
>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=32.24 E-value=33 Score=25.62 Aligned_cols=31 Identities=26% Similarity=0.502 Sum_probs=25.1
Q ss_pred HHHHHHHHhhcCCccccccccCCCCCHHHHHH
Q 025221 71 ERLVLELHAKWGNRWSRIARKLPGRTDNEIKN 102 (256)
Q Consensus 71 D~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~kn 102 (256)
|..|..+....|.+|..+|+.| |=+..+|.+
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 4567777888999999999999 777777655
No 115
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=31.65 E-value=31 Score=25.93 Aligned_cols=30 Identities=40% Similarity=0.689 Sum_probs=23.5
Q ss_pred HHHHHHHhhcCCccccccccCCCCCHHHHHH
Q 025221 72 RLVLELHAKWGNRWSRIARKLPGRTDNEIKN 102 (256)
Q Consensus 72 ~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~kn 102 (256)
+-|-.+....|.+|..+|+.| |=+..+|.+
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 344555677899999999999 878887765
No 116
>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=31.49 E-value=68 Score=26.03 Aligned_cols=30 Identities=17% Similarity=0.324 Sum_probs=23.8
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 81 WGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 81 ~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
.|-...+||..| |-|...|+++....+++-
T Consensus 134 ~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~L 163 (169)
T TIGR02954 134 HDLTIKEIAEVM-NKPEGTVKTYLHRALKKL 163 (169)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 356788999998 889999999887766553
No 117
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=31.03 E-value=85 Score=24.69 Aligned_cols=55 Identities=18% Similarity=0.099 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccCCCCcCCCCCHHHHHHH
Q 025221 17 EDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLHPGLKRGKMTPQEERLV 74 (256)
Q Consensus 17 ED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~l~k~~WT~EED~~L 74 (256)
+.+.|..+|+.+....-.+||+.+| ...+..-+..+.|.-..++..|..+++..-
T Consensus 58 d~~~L~~~v~~~pd~tl~Ela~~l~---Vs~~ti~~~Lkrlg~t~KK~~~~~~~~~~~ 112 (119)
T PF01710_consen 58 DRDELKALVEENPDATLRELAERLG---VSPSTIWRALKRLGITRKKKTLHSEKDREK 112 (119)
T ss_pred cHHHHHHHHHHCCCcCHHHHHHHcC---CCHHHHHHHHHHcCchhccCcccchhHHHH
Confidence 4667999999998777789999996 355556677888888888888877666554
No 118
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=30.88 E-value=70 Score=26.69 Aligned_cols=30 Identities=27% Similarity=0.103 Sum_probs=24.3
Q ss_pred hcCCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 80 KWGNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 80 ~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
-.|-...+||..| |-+...|+++....+++
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 3466889999999 99999999987766554
No 119
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=30.46 E-value=78 Score=25.74 Aligned_cols=30 Identities=23% Similarity=0.285 Sum_probs=24.0
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 81 WGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 81 ~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
.|-.-.+||..| |.+...|+.+...-+++-
T Consensus 133 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~L 162 (173)
T PRK09645 133 RGWSTAQIAADL-GIPEGTVKSRLHYALRAL 162 (173)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 456778999999 999999999877666543
No 120
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=30.35 E-value=34 Score=34.67 Aligned_cols=47 Identities=15% Similarity=0.307 Sum_probs=41.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCchhhhhhcccccccccccchhhh
Q 025221 7 EVRKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVN 55 (256)
Q Consensus 7 ~~kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~ 55 (256)
....++|+.+|-++........|. +...|+..+ |.|..+|++..+..
T Consensus 406 ~~~~~~w~~se~e~fyka~~~~gs-~~slis~l~-p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 406 KLETDKWDASETELFYKALSERGS-DFSLISNLF-PLRDRKQIKAKFKK 452 (584)
T ss_pred ccccCcccchhhHHhhhHHhhhcc-ccccccccc-ccccHHHHHHHHhh
Confidence 456788999999999999999994 799999999 79999999887654
No 121
>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=30.02 E-value=77 Score=26.55 Aligned_cols=32 Identities=9% Similarity=-0.015 Sum_probs=25.1
Q ss_pred hhcCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 79 AKWGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 79 ~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
-..|-.-.+||..| |-+.+.|+.|....+++-
T Consensus 144 ~~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~L 175 (188)
T TIGR02943 144 EVLGFESDEICQEL-EISTSNCHVLLYRARLSL 175 (188)
T ss_pred HHhCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 33466789999999 999999999877665543
No 122
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=29.95 E-value=80 Score=26.17 Aligned_cols=31 Identities=13% Similarity=0.103 Sum_probs=24.6
Q ss_pred hcCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 80 KWGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 80 ~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
..|....+||..| |-+...|+.+...-+++-
T Consensus 153 ~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~L 183 (189)
T PRK09648 153 VVGLSAEETAEAV-GSTPGAVRVAQHRALARL 183 (189)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3466899999999 999999999877665543
No 123
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=29.64 E-value=84 Score=25.18 Aligned_cols=30 Identities=7% Similarity=-0.117 Sum_probs=23.4
Q ss_pred hcCCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 80 KWGNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 80 ~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
..|-.-.+||..| |-+...|+++-...+++
T Consensus 120 ~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (160)
T PRK09642 120 LEEKSYQEIALQE-KIEVKTVEMKLYRARKW 149 (160)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3456788999999 99999999987655544
No 124
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=29.61 E-value=82 Score=25.95 Aligned_cols=30 Identities=13% Similarity=0.131 Sum_probs=24.5
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 81 WGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 81 ~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
.|-...+||..| |-+...|+.+....+++-
T Consensus 146 ~g~s~~eIA~~l-~is~~tV~~~l~ra~~~L 175 (184)
T PRK12512 146 EGASIKETAAKL-SMSEGAVRVALHRGLAAL 175 (184)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 356789999999 999999999887766654
No 125
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=29.56 E-value=83 Score=26.15 Aligned_cols=30 Identities=10% Similarity=0.099 Sum_probs=24.3
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 81 WGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 81 ~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
.|-...+||..| |-+...|+++....+++-
T Consensus 146 ~~~s~~eIA~~l-gis~~tV~~~l~Rar~~L 175 (189)
T PRK12515 146 HEKSVEEVGEIV-GIPESTVKTRMFYARKKL 175 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 456789999999 889999999987766553
No 126
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=29.40 E-value=70 Score=25.58 Aligned_cols=45 Identities=11% Similarity=0.133 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHhhcCC-ccccccccCCCCCHHHHHHHHHHHhHHHHH
Q 025221 68 PQEERLVLELHAKWGN-RWSRIARKLPGRTDNEIKNYWRTHMRKKAQ 113 (256)
Q Consensus 68 ~EED~~Ll~lv~~~G~-~W~~Ia~~l~gRt~~~~knrw~~~lrk~~~ 113 (256)
.+-|..|+++.++-|. .+..||+.+ |-+...|++|-+++.+...-
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 3567888888888886 799999999 99999999998888877543
No 127
>COG4628 Uncharacterized conserved protein [Function unknown]
Probab=29.29 E-value=59 Score=26.25 Aligned_cols=44 Identities=23% Similarity=0.512 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccCCC-------CcCCCCCHHHHHHH
Q 025221 18 DILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLHPG-------LKRGKMTPQEERLV 74 (256)
Q Consensus 18 D~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~-------l~k~~WT~EED~~L 74 (256)
+.+|.++|..|| |+.+|..+. ..|..- +|+ +.+.+|..|..+.|
T Consensus 21 E~llt~Lvd~YG---Wd~L~~ri~-----inCF~n-----dPSi~SSlKfLrkT~WARekvEa~ 71 (136)
T COG4628 21 ETLLTELVDFYG---WDGLATRIR-----INCFHN-----DPSIKSSLKFLRKTPWAREKVEAL 71 (136)
T ss_pred HHHHHHHHHHhC---hHHHHhhce-----eccccC-----CccHHHHHHHHhcCHhHHHHHHHH
Confidence 568889999999 999987662 344321 333 34667777665554
No 128
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=28.93 E-value=80 Score=26.44 Aligned_cols=29 Identities=3% Similarity=-0.047 Sum_probs=23.5
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 81 WGNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 81 ~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
.|-...+||..| |-+...|+.|...-+++
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~RAr~~ 177 (189)
T PRK12530 149 LELSSEQICQEC-DISTSNLHVLLYRARLQ 177 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 366789999999 99999999986655543
No 129
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=28.88 E-value=86 Score=25.91 Aligned_cols=33 Identities=18% Similarity=0.094 Sum_probs=26.8
Q ss_pred hhcCCccccccccCCCCCHHHHHHHHHHHhHHHH
Q 025221 79 AKWGNRWSRIARKLPGRTDNEIKNYWRTHMRKKA 112 (256)
Q Consensus 79 ~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~~ 112 (256)
...|-...+||..| |-+.+.|+.|...-+++-.
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 34467889999999 9999999999887776653
No 130
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=28.80 E-value=76 Score=35.17 Aligned_cols=70 Identities=20% Similarity=0.260 Sum_probs=45.7
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCchhhhh--hcccccccccccchhhhccCCCCcCCCCCHHHHHHHHHHHhhc-CCcccc
Q 025221 11 GPWTEQEDILLVNFVQLFGDRRWDFIAK--VSGLNRTGKSCRLRWVNYLHPGLKRGKMTPQEERLVLELHAKW-GNRWSR 87 (256)
Q Consensus 11 g~WT~EED~~L~~lv~~~g~~~W~~IA~--~lgp~Rt~~qcr~Rw~~~L~p~l~k~~WT~EED~~Ll~lv~~~-G~~W~~ 87 (256)
--|..++|..|+-.|-+||.++|..|-. .|+ =+.+ ..+...+..+.+=...-..|+.+.... +.+|..
T Consensus 1134 ~~W~~e~Ds~LLiGI~khGygswe~Ir~Dp~L~--l~dK-------i~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~ 1204 (1373)
T KOG0384|consen 1134 CDWGSEDDSMLLIGIFKHGYGSWEAIRLDPDLG--LTDK-------IFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPK 1204 (1373)
T ss_pred cCCCchhhhhHhhhhhhcccccHHHhccCcccc--chhh-------hcccccCCchHHHHHHHHHHHHHHhhcccCCCch
Confidence 4599999999999999999999999852 222 1111 111222445556667777777777666 445544
Q ss_pred cc
Q 025221 88 IA 89 (256)
Q Consensus 88 Ia 89 (256)
..
T Consensus 1205 ~~ 1206 (1373)
T KOG0384|consen 1205 KL 1206 (1373)
T ss_pred hh
Confidence 43
No 131
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=28.71 E-value=87 Score=26.24 Aligned_cols=30 Identities=13% Similarity=0.035 Sum_probs=23.8
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 81 WGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 81 ~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
.|-...+||..| |-+.+.|+.|....+++-
T Consensus 156 eg~s~~EIA~~l-gis~~tVk~rl~ra~~~L 185 (194)
T PRK12531 156 EELPHQQVAEMF-DIPLGTVKSRLRLAVEKL 185 (194)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHHH
Confidence 356788999999 999999999876665543
No 132
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=28.45 E-value=73 Score=26.05 Aligned_cols=36 Identities=19% Similarity=0.302 Sum_probs=27.1
Q ss_pred HHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 75 LELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 75 l~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
+.+....|-...+||..| |-+.+.|+.+-..-+++-
T Consensus 128 ~~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 128 FLYNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred HHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 333334566889999999 999999999877666554
No 133
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=28.27 E-value=74 Score=27.34 Aligned_cols=44 Identities=14% Similarity=0.143 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 65 KMTPQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 65 ~WT~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
..|+-|-+.|.-+.+-+.+ .+||+.| |-+...|+++-+++++|-
T Consensus 137 ~LT~RE~eVL~lla~G~sn--keIA~~L-~iS~~TVk~h~~~I~~KL 180 (207)
T PRK15411 137 SLSRTESSMLRMWMAGQGT--IQISDQM-NIKAKTVSSHKGNIKRKI 180 (207)
T ss_pred cCCHHHHHHHHHHHcCCCH--HHHHHHc-CCCHHHHHHHHHHHHHHh
Confidence 4899999888877765555 6999999 999999999998888875
No 134
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=27.78 E-value=79 Score=26.27 Aligned_cols=29 Identities=10% Similarity=0.049 Sum_probs=23.1
Q ss_pred CCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 82 GNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 82 G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
|-...+||..| |-+...|+++....+++-
T Consensus 154 g~s~~eIA~~l-gis~~tv~~~l~Rar~~L 182 (193)
T PRK11923 154 GLSYEDIASVM-QCPVGTVRSRIFRAREAI 182 (193)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 45688999999 889999999877666553
No 135
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=27.11 E-value=51 Score=23.71 Aligned_cols=44 Identities=14% Similarity=0.431 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhCCCCchhhhhhcccccccccccchhhhccCCCC-------cCCCCCHHHHHHH
Q 025221 18 DILLVNFVQLFGDRRWDFIAKVSGLNRTGKSCRLRWVNYLHPGL-------KRGKMTPQEERLV 74 (256)
Q Consensus 18 D~~L~~lv~~~g~~~W~~IA~~lgp~Rt~~qcr~Rw~~~L~p~l-------~k~~WT~EED~~L 74 (256)
+..|.++|+.|| |+.+++.+. = .|.. -+|++ .+.+|..+..+.|
T Consensus 12 e~il~~Lv~~yG---W~~L~~~i~-i----~CF~-----~~PsikSSLkFLRkTpWAR~KVE~l 62 (64)
T PF09905_consen 12 ETILTELVEHYG---WEELGERIN-I----NCFK-----NNPSIKSSLKFLRKTPWAREKVENL 62 (64)
T ss_dssp HHHHHHHHHHT----HHHHHHHTT-S----SSTT-----SS--HHHHHHHHHHSHHHHHHHHHH
T ss_pred HHHHHHHHHHhC---HHHHHhhcc-c----ccCC-----CCCchHHHHHHHhcCHhHHHHHHHh
Confidence 568899999998 999998773 2 2322 24443 4567777665554
No 136
>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=27.05 E-value=96 Score=24.90 Aligned_cols=28 Identities=25% Similarity=0.337 Sum_probs=22.5
Q ss_pred CCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 82 GNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 82 G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
|-.-.+||..| |-+...|+++-...+++
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 56788999999 99999999987665554
No 137
>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=26.84 E-value=43 Score=25.07 Aligned_cols=26 Identities=23% Similarity=0.446 Sum_probs=21.1
Q ss_pred HHHHHHHhhcCCccccccccCCCCCHH
Q 025221 72 RLVLELHAKWGNRWSRIARKLPGRTDN 98 (256)
Q Consensus 72 ~~Ll~lv~~~G~~W~~Ia~~l~gRt~~ 98 (256)
..|..+....|.+|..+|++| |=+..
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 457888899999999999998 54443
No 138
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=26.59 E-value=1.3e+02 Score=24.08 Aligned_cols=30 Identities=20% Similarity=0.208 Sum_probs=23.3
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 81 WGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 81 ~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
.|-.-.+||..| |-+...|++|...-+++-
T Consensus 120 ~~~s~~eIA~~l-gis~~tv~~~l~ra~~~L 149 (159)
T PRK12527 120 EGLSHQQIAEHL-GISRSLVEKHIVNAMKHC 149 (159)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 345678999999 999999999877655543
No 139
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=26.26 E-value=60 Score=21.00 Aligned_cols=37 Identities=27% Similarity=0.463 Sum_probs=18.9
Q ss_pred CCCHHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHH
Q 025221 65 KMTPQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNY 103 (256)
Q Consensus 65 ~WT~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knr 103 (256)
.+|.+|=..|..++ +-|..=.+||+.| ||+...|.+.
T Consensus 4 ~Lt~~eR~~I~~l~-~~G~s~~~IA~~l-g~s~sTV~re 40 (44)
T PF13936_consen 4 HLTPEERNQIEALL-EQGMSIREIAKRL-GRSRSTVSRE 40 (44)
T ss_dssp --------HHHHHH-CS---HHHHHHHT-T--HHHHHHH
T ss_pred chhhhHHHHHHHHH-HcCCCHHHHHHHH-CcCcHHHHHH
Confidence 46666666666664 5777788999999 9999988763
No 140
>PRK00118 putative DNA-binding protein; Validated
Probab=26.23 E-value=1.1e+02 Score=24.04 Aligned_cols=42 Identities=12% Similarity=0.111 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 68 PQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 68 ~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
++.++.++.++-..|-...+||..+ |-|.+.|+.+-....++
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~RArkk 60 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKRTEKL 60 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3456666777777788999999999 99999998876655544
No 141
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=26.18 E-value=96 Score=25.40 Aligned_cols=28 Identities=18% Similarity=0.353 Sum_probs=23.1
Q ss_pred CCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 82 GNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 82 G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
|-.-.+||..| |.+...|+++....+++
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 56788999999 99999999987765554
No 142
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=26.17 E-value=51 Score=24.74 Aligned_cols=24 Identities=29% Similarity=0.451 Sum_probs=20.6
Q ss_pred HHHHHHHHHHhCCCCchhhhhhccc
Q 025221 18 DILLVNFVQLFGDRRWDFIAKVSGL 42 (256)
Q Consensus 18 D~~L~~lv~~~g~~~W~~IA~~lgp 42 (256)
|+.|..+....| ..|+.+|..+|.
T Consensus 2 ~~~L~~la~~LG-~~W~~Lar~Lgl 25 (83)
T cd08319 2 DRELNQLAQRLG-PEWEQVLLDLGL 25 (83)
T ss_pred HHHHHHHHHHHh-hhHHHHHHHcCC
Confidence 567888999999 689999999983
No 143
>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=26.13 E-value=48 Score=24.97 Aligned_cols=27 Identities=22% Similarity=0.385 Sum_probs=21.2
Q ss_pred HHHHHHHHhhcCCccccccccCCCCCHH
Q 025221 71 ERLVLELHAKWGNRWSRIARKLPGRTDN 98 (256)
Q Consensus 71 D~~Ll~lv~~~G~~W~~Ia~~l~gRt~~ 98 (256)
|-.|..+.+..|..|.++|+.| |=+..
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 4567778889999999999998 54443
No 144
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.56 E-value=1.2e+02 Score=23.34 Aligned_cols=46 Identities=26% Similarity=0.485 Sum_probs=36.3
Q ss_pred CCCCCHHHHHHHHHHHhhcCCccccccccCCCC-CHHHHHHHHHHHhHH
Q 025221 63 RGKMTPQEERLVLELHAKWGNRWSRIARKLPGR-TDNEIKNYWRTHMRK 110 (256)
Q Consensus 63 k~~WT~EED~~Ll~lv~~~G~~W~~Ia~~l~gR-t~~~~knrw~~~lrk 110 (256)
+..||+|.-..+++++.+-|..=+.||+.+ |- +.+++ .+|...++.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l-~~W~~~~~~ 51 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQL-YKWRIQLQK 51 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHH-HHHHHHHHH
Confidence 567999999999999999999889999999 76 55554 456555544
No 145
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=25.40 E-value=93 Score=25.93 Aligned_cols=31 Identities=13% Similarity=0.037 Sum_probs=24.7
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHHhHHHH
Q 025221 81 WGNRWSRIARKLPGRTDNEIKNYWRTHMRKKA 112 (256)
Q Consensus 81 ~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~~ 112 (256)
.|-.-.+||..| |-+...|+.+...-+++-.
T Consensus 145 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr 175 (185)
T PRK09649 145 LGLSYADAAAVC-GCPVGTIRSRVARARDALL 175 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 355788999999 9999999998876666543
No 146
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=25.36 E-value=1.2e+02 Score=26.49 Aligned_cols=44 Identities=25% Similarity=0.322 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 65 KMTPQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 65 ~WT~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
..|+.|-+.|.-+.+ |....+||..| +-+...|+++-..+++|-
T Consensus 133 ~LSpRErEVLrLLAq--GkTnKEIAe~L-~IS~rTVkth~srImkKL 176 (198)
T PRK15201 133 HFSVTERHLLKLIAS--GYHLSETAALL-SLSEEQTKSLRRSIMRKL 176 (198)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHHh
Confidence 488888887776665 66778999999 999999999999988875
No 147
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=25.34 E-value=1.1e+02 Score=25.29 Aligned_cols=31 Identities=13% Similarity=0.063 Sum_probs=24.8
Q ss_pred hcCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 80 KWGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 80 ~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
..|-...+||..| |.+...|+++-...+++-
T Consensus 143 ~~g~s~~EIA~~l-~is~~tV~~~l~rar~~L 173 (181)
T PRK12536 143 LEGLSVAETAQLT-GLSESAVKVGIHRGLKAL 173 (181)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 4466889999999 999999999876655543
No 148
>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=24.96 E-value=41 Score=24.32 Aligned_cols=18 Identities=17% Similarity=0.436 Sum_probs=14.3
Q ss_pred HHHHHHhhcCCccccccc
Q 025221 73 LVLELHAKWGNRWSRIAR 90 (256)
Q Consensus 73 ~Ll~lv~~~G~~W~~Ia~ 90 (256)
.|.+|++.||++|..|-.
T Consensus 31 vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 31 VLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHcCCchhhhc
Confidence 466788889999999853
No 149
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=24.69 E-value=1e+02 Score=25.44 Aligned_cols=30 Identities=10% Similarity=-0.011 Sum_probs=22.9
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 81 WGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 81 ~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
.|..-.+||..| |-+.+.|+++....+++-
T Consensus 143 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~L 172 (186)
T PRK05602 143 QGLSNIEAAAVM-DISVDALESLLARGRRAL 172 (186)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHHH
Confidence 456788899998 889999998876555543
No 150
>PRK09483 response regulator; Provisional
Probab=24.36 E-value=89 Score=25.61 Aligned_cols=45 Identities=16% Similarity=0.322 Sum_probs=35.2
Q ss_pred CCCCHHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 64 GKMTPQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 64 ~~WT~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
...|+-|-+.|.-+. .|..=.+||..| +-+...|+++-+++++|-
T Consensus 147 ~~Lt~rE~~vl~~~~--~G~~~~~Ia~~l-~is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 147 ASLSERELQIMLMIT--KGQKVNEISEQL-NLSPKTVNSYRYRMFSKL 191 (217)
T ss_pred cccCHHHHHHHHHHH--CCCCHHHHHHHh-CCCHHHHHHHHHHHHHHc
Confidence 358999988886554 444445999999 779999999988888874
No 151
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=24.19 E-value=1.2e+02 Score=25.00 Aligned_cols=29 Identities=21% Similarity=0.211 Sum_probs=23.0
Q ss_pred CCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 82 GNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 82 G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
|-.-.+||..+ |-+...|+.+.+..+++-
T Consensus 151 ~~s~~eIA~~l-gis~~~V~~~l~ra~~~L 179 (186)
T PRK13919 151 GYTHREAAQLL-GLPLGTLKTRARRALSRL 179 (186)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 45678999999 999999999877665543
No 152
>smart00351 PAX Paired Box domain.
Probab=24.05 E-value=3e+02 Score=21.80 Aligned_cols=73 Identities=19% Similarity=0.199 Sum_probs=44.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCchhhhhhccccc-ccccccchhhhc--cCCCC----cCCCCCHHHHHHHHHHHhh
Q 025221 8 VRKGPWTEQEDILLVNFVQLFGDRRWDFIAKVSGLNR-TGKSCRLRWVNY--LHPGL----KRGKMTPQEERLVLELHAK 80 (256)
Q Consensus 8 ~kkg~WT~EED~~L~~lv~~~g~~~W~~IA~~lgp~R-t~~qcr~Rw~~~--L~p~l----~k~~WT~EED~~Ll~lv~~ 80 (256)
....+.+.++-++++.++. -| ..-..||+.+|-.| +...+..||... +.|.- ....-+++++..|++++.+
T Consensus 13 ~~~~~~s~~~R~riv~~~~-~G-~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~ 90 (125)
T smart00351 13 VNGRPLPDEERQRIVELAQ-NG-VRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQE 90 (125)
T ss_pred cCCCCCCHHHHHHHHHHHH-cC-CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHH
Confidence 3456699999999998886 45 46789999997433 244444555432 33321 1223566666777776655
Q ss_pred cC
Q 025221 81 WG 82 (256)
Q Consensus 81 ~G 82 (256)
.+
T Consensus 91 ~p 92 (125)
T smart00351 91 NP 92 (125)
T ss_pred CC
Confidence 44
No 153
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=23.98 E-value=1.1e+02 Score=25.15 Aligned_cols=31 Identities=29% Similarity=0.333 Sum_probs=24.8
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHHhHHHH
Q 025221 81 WGNRWSRIARKLPGRTDNEIKNYWRTHMRKKA 112 (256)
Q Consensus 81 ~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~~ 112 (256)
.|-.-.+||..+ |-+.+.|+++...-+++-.
T Consensus 134 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 134 DGLTYSEIAHKL-GVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 355789999999 9999999998877666543
No 154
>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=23.70 E-value=2.2e+02 Score=18.66 Aligned_cols=44 Identities=23% Similarity=0.447 Sum_probs=33.9
Q ss_pred cCCCCCHHHHHHHHHHHhhcCC----ccccccccCCCCCHHHHHHHHHH
Q 025221 62 KRGKMTPQEERLVLELHAKWGN----RWSRIARKLPGRTDNEIKNYWRT 106 (256)
Q Consensus 62 ~k~~WT~EED~~Ll~lv~~~G~----~W~~Ia~~l~gRt~~~~knrw~~ 106 (256)
.+..+|+++-..|.+.+..... .-..||..+ |=+..+|++-|.+
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 3567899999999999987432 357788888 8899999875543
No 155
>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=23.62 E-value=1.3e+02 Score=24.68 Aligned_cols=29 Identities=24% Similarity=0.252 Sum_probs=23.5
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 81 WGNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 81 ~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
.|-...+||..| |-+...|+.|...-+++
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 356789999999 99999999987765554
No 156
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=23.60 E-value=1.2e+02 Score=25.41 Aligned_cols=30 Identities=13% Similarity=-0.017 Sum_probs=23.5
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 81 WGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 81 ~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
.|-...+||..| |-+.+.|+++-..-+++-
T Consensus 151 ~g~s~~eIA~~l-gis~~tV~~~l~Ra~~~L 180 (196)
T PRK12524 151 EGLSNPEIAEVM-EIGVEAVESLTARGKRAL 180 (196)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 456799999999 989999999776655543
No 157
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=23.49 E-value=1.1e+02 Score=25.60 Aligned_cols=30 Identities=10% Similarity=0.059 Sum_probs=23.2
Q ss_pred hcCCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 80 KWGNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 80 ~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
..|-.-.+||..| |-+...|+.+....+++
T Consensus 150 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 179 (195)
T PRK12532 150 ILGFSSDEIQQMC-GISTSNYHTIMHRARES 179 (195)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466788999999 99999999987664443
No 158
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=23.44 E-value=1e+02 Score=24.69 Aligned_cols=31 Identities=23% Similarity=0.289 Sum_probs=24.6
Q ss_pred hhcCCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 79 AKWGNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 79 ~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
--.|-.-.+||..+ |-+.+.|+.|...-+++
T Consensus 126 ~~~g~s~~EIA~~l-~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 126 QVDGLGYGEIATEL-GISLATVKRYLNKAAMR 156 (161)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 33466789999999 99999999987766554
No 159
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=23.35 E-value=64 Score=24.10 Aligned_cols=29 Identities=28% Similarity=0.570 Sum_probs=21.2
Q ss_pred HHHHHHhhcCCccccccccCCCCCHHHHHH
Q 025221 73 LVLELHAKWGNRWSRIARKLPGRTDNEIKN 102 (256)
Q Consensus 73 ~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~kn 102 (256)
.+--+.+..|.+|..+|+.| |=|..+|..
T Consensus 4 ~f~~i~~~lG~~Wk~laR~L-Glse~~Id~ 32 (86)
T cd08306 4 AFDVICENVGRDWRKLARKL-GLSETKIES 32 (86)
T ss_pred HHHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 34445567899999999998 767666543
No 160
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=23.31 E-value=1.1e+02 Score=24.30 Aligned_cols=29 Identities=21% Similarity=0.254 Sum_probs=22.5
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 81 WGNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 81 ~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
.|-.-.+||..+ |-+...|+++-...+++
T Consensus 121 ~~~s~~EIA~~l-~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 121 VGKTMGEIALET-EMTYYQVRWIYRQALEK 149 (154)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355678999998 99999999976665554
No 161
>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=23.25 E-value=43 Score=26.59 Aligned_cols=29 Identities=14% Similarity=0.081 Sum_probs=23.4
Q ss_pred CCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 82 GNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 82 G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
|-.+.+||..| |-+...|+++.....++-
T Consensus 121 g~s~~eIA~~l-gis~~tv~~~l~Ra~~~L 149 (154)
T TIGR02950 121 EFSYKEIAELL-NLSLAKVKSNLFRARKEL 149 (154)
T ss_pred cCcHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 45789999998 889999999887766553
No 162
>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=23.13 E-value=1.1e+02 Score=24.39 Aligned_cols=40 Identities=18% Similarity=0.157 Sum_probs=28.1
Q ss_pred HHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 71 ERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 71 D~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
++.++.+.-..|-.-.+||..| |-+...|+++....+++-
T Consensus 115 ~r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~ra~~~L 154 (162)
T TIGR02983 115 QRAVVVLRYYEDLSEAQVAEAL-GISVGTVKSRLSRALARL 154 (162)
T ss_pred HHHHhhhHHHhcCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 3334444334456778999999 999999999887766654
No 163
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=22.80 E-value=1.2e+02 Score=26.37 Aligned_cols=44 Identities=25% Similarity=0.311 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 65 KMTPQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 65 ~WT~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
..|+.|-+.|.-+.. |....+||+.| +-+...|+++-.++++|-
T Consensus 155 ~Lt~rE~~Vl~l~~~--G~s~~eIA~~L-~iS~~TVk~~~~~i~~Kl 198 (216)
T PRK10100 155 LLTHREKEILNKLRI--GASNNEIARSL-FISENTVKTHLYNLFKKI 198 (216)
T ss_pred CCCHHHHHHHHHHHc--CCCHHHHHHHh-CCCHHHHHHHHHHHHHHh
Confidence 478766666555554 87888999999 999999999999888874
No 164
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=22.77 E-value=1.4e+02 Score=24.21 Aligned_cols=30 Identities=17% Similarity=0.082 Sum_probs=23.6
Q ss_pred hcCCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 80 KWGNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 80 ~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
..|-.-.+||..| |-+...|+++-...+++
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 3456789999999 99999999987665554
No 165
>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=22.21 E-value=1.3e+02 Score=24.61 Aligned_cols=30 Identities=13% Similarity=0.439 Sum_probs=24.0
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 81 WGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 81 ~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
.|-.-.+||..| |-|...|+.+....+++-
T Consensus 155 ~g~s~~eIA~~l-gis~~~v~~~l~Ra~~~L 184 (189)
T TIGR02984 155 EGLSFAEVAERM-DRSEGAVSMLWVRGLARL 184 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 456788999998 999999999877666553
No 166
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=21.92 E-value=1.5e+02 Score=23.78 Aligned_cols=45 Identities=22% Similarity=0.258 Sum_probs=35.5
Q ss_pred CCCCHHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 64 GKMTPQEERLVLELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 64 ~~WT~EED~~Ll~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
...|+.|-+.|.-+.. |-.-.+||..+ +-+...|+.+-+++++|-
T Consensus 136 ~~Lt~~E~~il~~l~~--g~~~~~Ia~~l-~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 136 DPLTKRERQVAEKLAQ--GMAVKEIAAEL-GLSPKTVHVHRANLMEKL 180 (196)
T ss_pred cCCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHHh
Confidence 4688888877776665 44667999999 789999999888887763
No 167
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=21.72 E-value=1.4e+02 Score=25.05 Aligned_cols=35 Identities=17% Similarity=0.124 Sum_probs=25.7
Q ss_pred HHHHhhcCCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 75 LELHAKWGNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 75 l~lv~~~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
+.|....|-...+||..| |-+...|+.|-..-+++
T Consensus 125 ~~L~~~~g~s~~EIA~~L-gis~~tVk~~l~Rar~~ 159 (187)
T PRK12516 125 IILVGASGFAYEEAAEIC-GCAVGTIKSRVNRARQR 159 (187)
T ss_pred HHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 333334466889999999 99999999986655544
No 168
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=21.38 E-value=1.4e+02 Score=24.83 Aligned_cols=28 Identities=11% Similarity=-0.064 Sum_probs=22.9
Q ss_pred CCccccccccCCCCCHHHHHHHHHHHhHH
Q 025221 82 GNRWSRIARKLPGRTDNEIKNYWRTHMRK 110 (256)
Q Consensus 82 G~~W~~Ia~~l~gRt~~~~knrw~~~lrk 110 (256)
|-.-.+||..| |-+.+.|++|....+++
T Consensus 147 g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 174 (191)
T PRK12520 147 ELETEEICQEL-QITATNAWVLLYRARMR 174 (191)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 55678999999 99999999987766554
No 169
>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=21.29 E-value=1.1e+02 Score=27.63 Aligned_cols=30 Identities=17% Similarity=0.168 Sum_probs=24.0
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHHhHHH
Q 025221 81 WGNRWSRIARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 81 ~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
.|-.-.+||..| |.+.+.|++|-..-+++-
T Consensus 157 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~L 186 (324)
T TIGR02960 157 LGWRAAETAELL-GTSTASVNSALQRARATL 186 (324)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 356788999999 999999999876665544
No 170
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=20.64 E-value=1.7e+02 Score=24.94 Aligned_cols=32 Identities=16% Similarity=0.160 Sum_probs=25.0
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHHhHHHHH
Q 025221 81 WGNRWSRIARKLPGRTDNEIKNYWRTHMRKKAQ 113 (256)
Q Consensus 81 ~G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~~~ 113 (256)
.|..-.+||..| |-+...|+++....+++-.+
T Consensus 153 ~g~s~~EIA~~L-gis~~tV~~~l~RArk~Lr~ 184 (203)
T PRK09647 153 EGLSYEEIAATL-GVKLGTVRSRIHRGRQQLRA 184 (203)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 355678999999 99999999988777665443
No 171
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=20.28 E-value=84 Score=27.31 Aligned_cols=30 Identities=17% Similarity=0.124 Sum_probs=23.8
Q ss_pred CCccccccccCCCCCHHHHHHHHHHHhHHHH
Q 025221 82 GNRWSRIARKLPGRTDNEIKNYWRTHMRKKA 112 (256)
Q Consensus 82 G~~W~~Ia~~l~gRt~~~~knrw~~~lrk~~ 112 (256)
|-.-.+||..| |.+...|+++....+++-.
T Consensus 165 g~s~~EIAe~l-gis~~tVk~~l~Rar~kLr 194 (231)
T PRK11922 165 ELSVEETAQAL-GLPEETVKTRLHRARRLLR 194 (231)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 45688999999 9999999998876665543
No 172
>PF09197 Rap1-DNA-bind: Rap1, DNA-binding; InterPro: IPR015280 Members of this entry, which are predominantly found in the yeast protein Rap1, assume a secondary structure consisting of a three-helix bundle and an N-terminal arm. They contain an Arg-Asp-Arg-Lys sequence that interacts with an ACAregion in the 3, region of the DNA-binding site []. ; PDB: 1IGN_A 3UKG_A.
Probab=20.12 E-value=90 Score=24.65 Aligned_cols=24 Identities=29% Similarity=0.516 Sum_probs=18.4
Q ss_pred ccccCCCCCHHHHHHHHHHHhHHH
Q 025221 88 IARKLPGRTDNEIKNYWRTHMRKK 111 (256)
Q Consensus 88 Ia~~l~gRt~~~~knrw~~~lrk~ 111 (256)
.+...|..|.++=|+|++..+...
T Consensus 55 ~~~~~p~HT~~sWRDR~RKfv~~~ 78 (105)
T PF09197_consen 55 LARKNPRHTENSWRDRYRKFVSEY 78 (105)
T ss_dssp HHHHTTTS-HHHHHHHHHHTHHHH
T ss_pred HHHcCCccchhHHHHHHHHHHHHc
Confidence 466778899999999998877654
Done!