Query 024441
Match_columns 267
No_of_seqs 293 out of 1415
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 04:37:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024441.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024441hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03091 hypothetical protein; 100.0 2.6E-39 5.6E-44 305.8 13.5 138 1-138 1-138 (459)
2 PLN03212 Transcription repress 100.0 1.3E-38 2.8E-43 282.7 11.1 129 3-131 14-142 (249)
3 KOG0048 Transcription factor, 100.0 3.7E-34 8.1E-39 256.8 14.7 119 10-128 5-123 (238)
4 KOG0049 Transcription factor, 99.8 5.5E-21 1.2E-25 187.0 5.8 114 1-115 347-461 (939)
5 KOG0049 Transcription factor, 99.8 2.8E-19 6E-24 175.2 6.7 123 11-134 302-428 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.6 8.1E-17 1.8E-21 114.5 3.4 60 17-78 1-60 (60)
7 KOG0050 mRNA splicing protein 99.6 9.3E-16 2E-20 147.6 4.6 107 11-119 4-110 (617)
8 COG5147 REB1 Myb superfamily p 99.6 2.2E-15 4.8E-20 147.2 6.8 108 9-117 15-122 (512)
9 PLN03212 Transcription repress 99.4 1.2E-13 2.5E-18 123.6 6.7 74 62-135 20-95 (249)
10 KOG0051 RNA polymerase I termi 99.4 1.2E-13 2.5E-18 136.5 6.0 102 13-117 383-512 (607)
11 PF13921 Myb_DNA-bind_6: Myb-l 99.4 4E-14 8.7E-19 100.6 1.4 57 70-126 1-57 (60)
12 PF00249 Myb_DNA-binding: Myb- 99.4 2.2E-13 4.8E-18 93.0 4.8 46 67-112 1-48 (48)
13 PF00249 Myb_DNA-binding: Myb- 99.4 3.8E-14 8.2E-19 96.8 0.8 48 14-61 1-48 (48)
14 KOG0048 Transcription factor, 99.4 2E-13 4.4E-18 122.7 1.9 76 63-138 5-82 (238)
15 PLN03091 hypothetical protein; 99.3 5E-13 1.1E-17 127.6 2.2 72 63-134 10-83 (459)
16 smart00717 SANT SANT SWI3, AD 99.2 2.3E-11 4.9E-16 81.1 5.3 47 67-113 1-48 (49)
17 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 1.6E-10 3.4E-15 75.9 5.3 43 69-111 1-44 (45)
18 smart00717 SANT SANT SWI3, AD 99.0 7.5E-11 1.6E-15 78.5 2.0 48 14-62 1-48 (49)
19 cd00167 SANT 'SWI3, ADA2, N-Co 98.9 5.4E-10 1.2E-14 73.3 1.7 45 16-61 1-45 (45)
20 KOG0051 RNA polymerase I termi 98.9 1.1E-09 2.5E-14 108.6 3.0 118 13-134 307-452 (607)
21 COG5147 REB1 Myb superfamily p 98.3 5.6E-08 1.2E-12 95.6 -2.6 98 13-113 290-397 (512)
22 KOG0050 mRNA splicing protein 98.0 1.9E-06 4E-11 84.1 1.9 73 65-137 5-78 (617)
23 TIGR01557 myb_SHAQKYF myb-like 97.9 8.3E-06 1.8E-10 57.9 2.3 49 13-61 2-54 (57)
24 TIGR01557 myb_SHAQKYF myb-like 97.7 8.9E-05 1.9E-09 52.6 5.5 46 67-112 3-54 (57)
25 KOG0457 Histone acetyltransfer 97.6 8.7E-05 1.9E-09 71.4 5.8 57 65-125 70-127 (438)
26 KOG0457 Histone acetyltransfer 97.6 2.9E-05 6.2E-10 74.7 1.7 50 11-61 69-118 (438)
27 TIGR02894 DNA_bind_RsfA transc 97.4 0.00022 4.7E-09 60.5 4.4 52 66-118 3-61 (161)
28 PF13325 MCRS_N: N-terminal re 97.2 0.00048 1E-08 60.6 4.8 100 16-117 1-131 (199)
29 PF08914 Myb_DNA-bind_2: Rap1 97.0 0.00089 1.9E-08 48.8 4.1 50 67-116 2-61 (65)
30 PF13837 Myb_DNA-bind_4: Myb/S 97.0 0.00063 1.4E-08 51.3 3.0 49 68-116 2-68 (90)
31 COG5259 RSC8 RSC chromatin rem 96.9 0.00088 1.9E-08 65.2 4.0 44 68-111 280-323 (531)
32 COG5259 RSC8 RSC chromatin rem 96.9 0.00034 7.4E-09 68.0 1.2 46 13-60 278-323 (531)
33 KOG1279 Chromatin remodeling f 96.8 0.0015 3.3E-08 64.8 5.1 46 66-111 252-297 (506)
34 KOG1279 Chromatin remodeling f 96.8 0.00051 1.1E-08 68.1 1.5 48 11-60 250-297 (506)
35 PF08914 Myb_DNA-bind_2: Rap1 96.5 0.00075 1.6E-08 49.2 0.1 52 14-65 2-61 (65)
36 PRK13923 putative spore coat p 96.5 0.0034 7.3E-08 54.0 4.0 52 65-117 3-61 (170)
37 PF13837 Myb_DNA-bind_4: Myb/S 96.0 0.0016 3.5E-08 49.1 -0.1 47 14-60 1-63 (90)
38 TIGR02894 DNA_bind_RsfA transc 96.0 0.0026 5.7E-08 54.0 0.9 49 12-62 2-56 (161)
39 COG5114 Histone acetyltransfer 95.9 0.0072 1.6E-07 56.5 3.7 46 68-113 64-110 (432)
40 PF13873 Myb_DNA-bind_5: Myb/S 95.6 0.037 8E-07 40.8 5.8 49 67-115 2-72 (78)
41 PLN03142 Probable chromatin-re 95.3 0.034 7.5E-07 59.8 6.4 101 16-117 826-989 (1033)
42 COG5114 Histone acetyltransfer 94.9 0.0084 1.8E-07 56.1 0.4 49 13-62 62-110 (432)
43 PF13873 Myb_DNA-bind_5: Myb/S 94.2 0.012 2.7E-07 43.4 -0.1 49 13-61 1-69 (78)
44 PRK13923 putative spore coat p 94.2 0.012 2.6E-07 50.6 -0.3 49 12-62 3-57 (170)
45 PF09111 SLIDE: SLIDE; InterP 93.0 0.18 4E-06 40.9 4.8 53 64-116 46-114 (118)
46 KOG2656 DNA methyltransferase 92.6 0.17 3.7E-06 48.6 4.7 53 68-120 131-189 (445)
47 PF12776 Myb_DNA-bind_3: Myb/S 92.6 0.29 6.3E-06 37.1 5.2 46 69-114 1-64 (96)
48 KOG4282 Transcription factor G 91.6 0.33 7.2E-06 45.8 5.3 51 67-117 54-118 (345)
49 COG5118 BDP1 Transcription ini 90.9 0.35 7.5E-06 46.5 4.7 47 68-114 366-412 (507)
50 KOG1194 Predicted DNA-binding 86.4 2.3 5E-05 41.9 7.0 49 66-114 186-234 (534)
51 PF08281 Sigma70_r4_2: Sigma-7 86.1 1.9 4E-05 29.2 4.7 41 72-113 12-52 (54)
52 PF09111 SLIDE: SLIDE; InterP 83.8 0.92 2E-05 36.8 2.6 34 11-44 46-82 (118)
53 KOG4282 Transcription factor G 82.2 0.63 1.4E-05 43.9 1.2 47 15-61 55-113 (345)
54 COG5118 BDP1 Transcription ini 81.5 0.78 1.7E-05 44.2 1.5 45 13-59 364-408 (507)
55 KOG4167 Predicted DNA-binding 76.5 4.7 0.0001 42.0 5.3 45 67-111 619-663 (907)
56 PF11626 Rap1_C: TRF2-interact 76.4 2.2 4.7E-05 32.4 2.3 29 11-42 44-80 (87)
57 KOG4468 Polycomb-group transcr 76.3 4.6 9.9E-05 41.2 5.1 51 67-117 88-148 (782)
58 PF13404 HTH_AsnC-type: AsnC-t 75.2 5.3 0.00011 26.3 3.7 38 73-111 3-41 (42)
59 PF13404 HTH_AsnC-type: AsnC-t 74.3 1.1 2.5E-05 29.5 0.3 38 20-59 3-40 (42)
60 PRK11179 DNA-binding transcrip 70.8 6 0.00013 32.9 3.9 45 73-118 9-54 (153)
61 PF04545 Sigma70_r4: Sigma-70, 69.7 11 0.00024 25.0 4.3 41 73-114 7-47 (50)
62 PF11035 SnAPC_2_like: Small n 66.3 22 0.00048 33.7 6.9 48 67-115 21-72 (344)
63 KOG4167 Predicted DNA-binding 65.6 2.9 6.3E-05 43.5 1.1 44 14-59 619-662 (907)
64 PRK11169 leucine-responsive tr 65.2 7.1 0.00015 32.9 3.3 46 72-118 13-59 (164)
65 smart00595 MADF subfamily of S 64.3 7.9 0.00017 28.7 3.1 26 89-115 30-55 (89)
66 PRK11179 DNA-binding transcrip 63.6 3.1 6.8E-05 34.6 0.8 44 19-64 8-51 (153)
67 PF13325 MCRS_N: N-terminal re 60.4 18 0.0004 32.0 5.0 45 69-114 1-48 (199)
68 PF12776 Myb_DNA-bind_3: Myb/S 59.9 6.9 0.00015 29.4 2.1 44 16-59 1-60 (96)
69 PRK11169 leucine-responsive tr 59.7 3.1 6.8E-05 35.0 0.1 45 19-65 13-57 (164)
70 PF11626 Rap1_C: TRF2-interact 59.2 9.5 0.00021 28.9 2.7 17 63-79 43-59 (87)
71 KOG2009 Transcription initiati 59.2 9.5 0.00021 38.8 3.4 50 65-114 407-456 (584)
72 PF01388 ARID: ARID/BRIGHT DNA 58.6 21 0.00045 26.8 4.5 39 76-114 39-90 (92)
73 KOG4329 DNA-binding protein [G 57.2 81 0.0018 30.7 9.0 43 69-111 279-322 (445)
74 TIGR02985 Sig70_bacteroi1 RNA 56.5 21 0.00046 28.4 4.6 30 84-114 127-156 (161)
75 smart00501 BRIGHT BRIGHT, ARID 55.2 25 0.00053 26.6 4.5 40 76-115 35-87 (93)
76 PF07750 GcrA: GcrA cell cycle 53.2 14 0.00031 31.4 3.1 40 69-109 2-41 (162)
77 cd08319 Death_RAIDD Death doma 51.8 18 0.0004 27.4 3.2 29 75-104 2-30 (83)
78 PF04504 DUF573: Protein of un 46.9 36 0.00078 26.5 4.2 49 68-116 5-66 (98)
79 PF10545 MADF_DNA_bdg: Alcohol 46.0 22 0.00047 25.5 2.8 27 89-115 29-56 (85)
80 PF09420 Nop16: Ribosome bioge 44.6 49 0.0011 28.0 5.1 46 66-111 113-162 (164)
81 smart00344 HTH_ASNC helix_turn 44.3 38 0.00082 25.8 4.0 45 73-118 3-48 (108)
82 PF02954 HTH_8: Bacterial regu 43.5 41 0.00088 21.7 3.5 34 74-108 6-39 (42)
83 TIGR02937 sigma70-ECF RNA poly 41.8 44 0.00096 25.8 4.2 30 84-114 124-153 (158)
84 KOG0384 Chromodomain-helicase 41.7 26 0.00057 38.8 3.6 75 14-95 1133-1208(1373)
85 KOG3841 TEF-1 and related tran 41.6 1.2E+02 0.0026 29.7 7.5 29 7-35 69-97 (455)
86 PRK04217 hypothetical protein; 38.6 1E+02 0.0022 24.6 5.7 46 67-114 40-85 (110)
87 KOG4468 Polycomb-group transcr 38.4 29 0.00062 35.7 3.0 47 14-61 88-143 (782)
88 cd08803 Death_ank3 Death domai 37.9 46 0.001 25.2 3.5 29 75-104 4-32 (84)
89 PRK09652 RNA polymerase sigma 37.9 55 0.0012 26.7 4.3 30 84-114 142-171 (182)
90 PRK09645 RNA polymerase sigma 37.8 77 0.0017 26.0 5.2 29 85-114 133-161 (173)
91 PF07638 Sigma70_ECF: ECF sigm 36.9 80 0.0017 26.8 5.3 36 77-113 142-177 (185)
92 PLN03162 golden-2 like transcr 36.4 2.6E+02 0.0057 27.3 9.0 44 68-111 238-286 (526)
93 PF07750 GcrA: GcrA cell cycle 36.3 26 0.00056 29.8 2.1 33 16-50 2-35 (162)
94 cd08317 Death_ank Death domain 35.6 36 0.00079 25.3 2.6 29 75-104 4-32 (84)
95 cd06171 Sigma70_r4 Sigma70, re 35.2 87 0.0019 19.5 4.2 40 70-111 11-50 (55)
96 PRK12529 RNA polymerase sigma 35.0 89 0.0019 26.1 5.2 33 85-118 142-174 (178)
97 COG1522 Lrp Transcriptional re 34.8 53 0.0011 26.5 3.7 45 73-118 8-53 (154)
98 KOG2656 DNA methyltransferase 34.2 15 0.00033 35.7 0.4 49 11-60 127-180 (445)
99 PRK12523 RNA polymerase sigma 34.2 98 0.0021 25.5 5.3 33 84-117 133-165 (172)
100 PRK11924 RNA polymerase sigma 33.6 68 0.0015 26.0 4.2 29 85-114 140-168 (179)
101 PRK12532 RNA polymerase sigma 33.1 98 0.0021 26.0 5.2 28 85-113 151-178 (195)
102 PRK09643 RNA polymerase sigma 33.0 74 0.0016 26.9 4.4 29 85-114 149-177 (192)
103 cd08318 Death_NMPP84 Death dom 32.5 53 0.0011 24.7 3.1 25 79-104 11-35 (86)
104 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 31.4 74 0.0016 21.9 3.3 36 70-107 5-40 (50)
105 PRK09641 RNA polymerase sigma 30.8 81 0.0018 26.0 4.3 29 85-114 151-179 (187)
106 smart00344 HTH_ASNC helix_turn 30.6 23 0.0005 27.1 0.8 43 20-64 3-45 (108)
107 PRK09047 RNA polymerase factor 30.6 97 0.0021 24.9 4.6 29 85-114 121-149 (161)
108 PF11035 SnAPC_2_like: Small n 29.9 51 0.0011 31.3 3.1 86 14-113 21-127 (344)
109 cd08311 Death_p75NR Death doma 29.7 53 0.0012 24.4 2.6 33 72-106 2-34 (77)
110 COG1522 Lrp Transcriptional re 29.4 20 0.00044 29.0 0.3 42 20-63 8-49 (154)
111 cd08804 Death_ank2 Death domai 29.3 63 0.0014 24.3 3.0 31 75-106 4-34 (84)
112 cd08777 Death_RIP1 Death Domai 28.8 58 0.0012 24.7 2.7 29 77-106 4-32 (86)
113 PRK12512 RNA polymerase sigma 28.8 1.3E+02 0.0029 24.8 5.3 31 85-116 146-176 (184)
114 KOG1194 Predicted DNA-binding 28.3 26 0.00056 34.8 0.9 44 13-58 186-229 (534)
115 TIGR02939 RpoE_Sigma70 RNA pol 28.3 75 0.0016 26.3 3.6 28 86-114 154-181 (190)
116 TIGR02954 Sig70_famx3 RNA poly 28.1 98 0.0021 25.3 4.3 29 85-114 134-162 (169)
117 PRK09637 RNA polymerase sigma 27.8 1E+02 0.0022 25.9 4.4 29 85-114 121-149 (181)
118 PF00196 GerE: Bacterial regul 27.4 66 0.0014 21.8 2.6 44 69-115 3-46 (58)
119 COG2197 CitB Response regulato 27.2 88 0.0019 27.3 4.0 45 68-115 147-191 (211)
120 PRK12515 RNA polymerase sigma 27.1 1.1E+02 0.0024 25.5 4.5 29 85-114 146-174 (189)
121 PRK09642 RNA polymerase sigma 26.8 1.2E+02 0.0026 24.5 4.5 29 85-114 121-149 (160)
122 PRK09648 RNA polymerase sigma 26.5 1.2E+02 0.0025 25.4 4.5 29 85-114 154-182 (189)
123 TIGR02943 Sig70_famx1 RNA poly 26.4 1.2E+02 0.0026 25.6 4.6 29 85-114 146-174 (188)
124 PRK12531 RNA polymerase sigma 26.3 1.2E+02 0.0025 25.6 4.5 28 86-114 157-184 (194)
125 PRK01905 DNA-binding protein F 26.3 1.4E+02 0.003 21.9 4.3 36 71-107 35-70 (77)
126 KOG2009 Transcription initiati 26.2 38 0.00083 34.6 1.6 49 9-59 404-452 (584)
127 smart00005 DEATH DEATH domain, 26.1 73 0.0016 23.3 2.9 29 75-104 5-34 (88)
128 TIGR02948 SigW_bacill RNA poly 26.0 1E+02 0.0022 25.4 4.0 28 86-114 152-179 (187)
129 PRK12530 RNA polymerase sigma 25.4 1.2E+02 0.0026 25.5 4.5 28 85-113 149-176 (189)
130 PRK11923 algU RNA polymerase s 25.0 1.1E+02 0.0024 25.5 4.2 28 86-114 154-181 (193)
131 cd08779 Death_PIDD Death Domai 24.5 78 0.0017 23.9 2.7 21 76-96 3-23 (86)
132 PF09197 Rap1-DNA-bind: Rap1, 24.0 1.9E+02 0.0041 23.0 4.9 47 69-115 1-78 (105)
133 PRK12524 RNA polymerase sigma 23.9 1.3E+02 0.0029 25.3 4.5 29 85-114 151-179 (196)
134 PRK12527 RNA polymerase sigma 23.9 1.5E+02 0.0033 23.9 4.6 28 86-114 121-148 (159)
135 PRK00430 fis global DNA-bindin 23.8 1.6E+02 0.0035 22.7 4.4 34 73-107 55-88 (95)
136 PF13936 HTH_38: Helix-turn-he 23.2 79 0.0017 20.6 2.3 36 69-106 4-39 (44)
137 TIGR02952 Sig70_famx2 RNA poly 22.7 1.5E+02 0.0033 23.9 4.4 28 86-114 138-165 (170)
138 PRK09649 RNA polymerase sigma 22.1 1.4E+02 0.0031 25.0 4.3 30 85-115 145-174 (185)
139 PRK12514 RNA polymerase sigma 21.9 1.5E+02 0.0034 24.3 4.4 28 86-114 145-172 (179)
140 PRK00118 putative DNA-binding 21.7 1.8E+02 0.0039 23.0 4.4 40 73-113 20-59 (104)
141 PRK06759 RNA polymerase factor 21.4 1.8E+02 0.0038 23.2 4.5 28 86-114 122-149 (154)
142 PRK12536 RNA polymerase sigma 21.2 1.7E+02 0.0036 24.3 4.5 30 85-115 144-173 (181)
143 TIGR02999 Sig-70_X6 RNA polyme 21.2 1.7E+02 0.0038 24.0 4.5 28 86-114 150-177 (183)
144 PRK12528 RNA polymerase sigma 20.9 1.8E+02 0.004 23.4 4.6 29 85-114 128-156 (161)
145 cd08805 Death_ank1 Death domai 20.8 1.1E+02 0.0024 23.2 2.9 22 75-96 4-25 (84)
146 PRK12516 RNA polymerase sigma 20.8 1.7E+02 0.0037 24.7 4.5 29 85-114 131-159 (187)
147 COG2963 Transposase and inacti 20.6 2.4E+02 0.0051 21.8 4.9 46 67-114 5-51 (116)
148 PRK09651 RNA polymerase sigma 20.6 1.7E+02 0.0036 24.2 4.3 29 86-115 135-163 (172)
149 PRK12547 RNA polymerase sigma 20.4 1.9E+02 0.0041 23.6 4.6 30 85-115 127-156 (164)
150 PRK12542 RNA polymerase sigma 20.2 1.8E+02 0.0039 24.2 4.5 29 85-114 137-165 (185)
No 1
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=2.6e-39 Score=305.78 Aligned_cols=138 Identities=63% Similarity=1.161 Sum_probs=131.9
Q ss_pred CCCCccccCCCCccCCCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCcccccccccccCCCCCCCCCCHHHHHHHHH
Q 024441 1 MGRQPCCDKLGVKKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNYLRPDLKRGLLTEAEEQLVID 80 (267)
Q Consensus 1 mgr~~~~~k~~ikkg~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L~p~~~~~~WT~eED~~Ll~ 80 (267)
|||++||+|++++|++||+|||++|+++|.+||..+|..||+.++++|+++|||+||.++|+|.+++++||+|||++|++
T Consensus 1 mgr~~Cc~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLe 80 (459)
T PLN03091 1 MGRHSCCYKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIE 80 (459)
T ss_pred CCCCccCcCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHH
Confidence 99999999999999999999999999999999999999999998778999999999999999999999999999999999
Q ss_pred HHHHhCCChhhhhccCCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCCcCcccccccCC
Q 024441 81 LHARLGNRWSKIAARLPGRTDNEIKNHWNTHIKKKLLKMGIDPVTHEPLHKETKAEDN 138 (267)
Q Consensus 81 lv~~~G~~W~~IA~~lpgRT~~q~knRw~~~l~~~~~k~~~~~~~~~~l~~~~~~~~~ 138 (267)
++++||++|.+||++|||||+++||+||+.+++++++..++.+.++.++.+.......
T Consensus 81 L~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~I~p~t~kpl~e~E~~~d~ 138 (459)
T PLN03091 81 LHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRGIDPNTHKPLSEVENGEDK 138 (459)
T ss_pred HHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCCCCCCCCcccccccccc
Confidence 9999999999999999999999999999999999999999999999999876554443
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=1.3e-38 Score=282.71 Aligned_cols=129 Identities=64% Similarity=1.222 Sum_probs=124.0
Q ss_pred CCccccCCCCccCCCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCcccccccccccCCCCCCCCCCHHHHHHHHHHH
Q 024441 3 RQPCCDKLGVKKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNYLRPDLKRGLLTEAEEQLVIDLH 82 (267)
Q Consensus 3 r~~~~~k~~ikkg~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L~p~~~~~~WT~eED~~Ll~lv 82 (267)
|.|||+|++++|++||+|||++|+++|++||..+|..||+.++++|+++|||+||.++|+|.+++++||+|||++|++++
T Consensus 14 ~~pcc~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~ 93 (249)
T PLN03212 14 TTPCCTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLH 93 (249)
T ss_pred CCCCcccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHH
Confidence 67999999999999999999999999999999999999999877899999999999999999999999999999999999
Q ss_pred HHhCCChhhhhccCCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCCcCcc
Q 024441 83 ARLGNRWSKIAARLPGRTDNEIKNHWNTHIKKKLLKMGIDPVTHEPLHK 131 (267)
Q Consensus 83 ~~~G~~W~~IA~~lpgRT~~q~knRw~~~l~~~~~k~~~~~~~~~~l~~ 131 (267)
.+||++|..||+.|||||+++|||||+.++++++.+.++.+.++.++..
T Consensus 94 ~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~p~~~kp~~~ 142 (249)
T PLN03212 94 RLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGIDPQTHKPLDA 142 (249)
T ss_pred HhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCCCCCCCCCCc
Confidence 9999999999999999999999999999999999999999988877643
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=3.7e-34 Score=256.82 Aligned_cols=119 Identities=71% Similarity=1.186 Sum_probs=111.4
Q ss_pred CCCccCCCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCcccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCCCh
Q 024441 10 LGVKKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNYLRPDLKRGLLTEAEEQLVIDLHARLGNRW 89 (267)
Q Consensus 10 ~~ikkg~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L~p~~~~~~WT~eED~~Ll~lv~~~G~~W 89 (267)
+.+.||+||+|||++|+++|.+||..+|..||+.+|++|++++||.||.|||+|+++++.||+|||.+|+++++.+|++|
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrW 84 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRW 84 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHH
Confidence 34558999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhccCCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCCc
Q 024441 90 SKIAARLPGRTDNEIKNHWNTHIKKKLLKMGIDPVTHEP 128 (267)
Q Consensus 90 ~~IA~~lpgRT~~q~knRw~~~l~~~~~k~~~~~~~~~~ 128 (267)
+.||++|||||++.|||+|+..+++++.+....+....+
T Consensus 85 s~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~~~~~~~~~ 123 (238)
T KOG0048|consen 85 SLIAGRLPGRTDNEVKNHWNTHLKKKLLKMGIDPSTHRP 123 (238)
T ss_pred HHHHhhCCCcCHHHHHHHHHHHHHHHHHHcCCCCCcccc
Confidence 999999999999999999999999999988755554333
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.82 E-value=5.5e-21 Score=187.03 Aligned_cols=114 Identities=27% Similarity=0.392 Sum_probs=104.8
Q ss_pred CCCCccccCCCCccCCCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCcccccccccccCCCCCCCCCCHHHHHHHHH
Q 024441 1 MGRQPCCDKLGVKKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNYLRPDLKRGLLTEAEEQLVID 80 (267)
Q Consensus 1 mgr~~~~~k~~ikkg~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L~p~~~~~~WT~eED~~Ll~ 80 (267)
+||..+...|++++|+||.+||.+|+.+|.+||.++|.+|-+.++ +|+..|||+||.|+|+...+.+.||-.||+.|+.
T Consensus 347 I~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vP-nRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~ 425 (939)
T KOG0049|consen 347 ITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVP-NRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLY 425 (939)
T ss_pred hhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcC-CccHHHHHHHHHHHHHHhhccCceeecchHHHHH
Confidence 578899999999999999999999999999999999999999998 9999999999999999999999999999999999
Q ss_pred HHHHhC-CChhhhhccCCCCCHHHHHHHHHHHHHHH
Q 024441 81 LHARLG-NRWSKIAARLPGRTDNEIKNHWNTHIKKK 115 (267)
Q Consensus 81 lv~~~G-~~W~~IA~~lpgRT~~q~knRw~~~l~~~ 115 (267)
+|.+|| ++|.+||.+||+||..|.+.|=...+.-+
T Consensus 426 ~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~~k 461 (939)
T KOG0049|consen 426 AVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIAAK 461 (939)
T ss_pred HHHHHccchHHHHHHHccccchhHHHHHHHHHHHHH
Confidence 999999 89999999999999977655544444433
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.77 E-value=2.8e-19 Score=175.23 Aligned_cols=123 Identities=24% Similarity=0.439 Sum_probs=114.3
Q ss_pred CCccCCCCHHHHHHHHHHHHHhC---CCCCchhchhhcCccCCcccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCC
Q 024441 11 GVKKGPWTAEEDKKLINFILTNG---QCCWRAVPKLAGLRRCGKSCRLRWTNYLRPDLKRGLLTEAEEQLVIDLHARLGN 87 (267)
Q Consensus 11 ~ikkg~WT~eED~~L~~~v~~~g---~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L~p~~~~~~WT~eED~~Ll~lv~~~G~ 87 (267)
.++...||+|||.+|+.+|+... ..+|++|-..|+ +|+..|...||.+.|+|++++|+||.+||.+|+.+|.+||.
T Consensus 302 ~L~ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ymp-gr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~ 380 (939)
T KOG0049|consen 302 QLSEKEWSEEEDTKLIALVKITSINSHIQWDKVVQYMP-GRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGA 380 (939)
T ss_pred HHHhhhcchhhhHHHHHHHHHhhccCccchHHHHHhcC-CcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCc
Confidence 45678999999999999999874 458999999998 99999999999999999999999999999999999999995
Q ss_pred -ChhhhhccCCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCCcCccccc
Q 024441 88 -RWSKIAARLPGRTDNEIKNHWNTHIKKKLLKMGIDPVTHEPLHKETK 134 (267)
Q Consensus 88 -~W~~IA~~lpgRT~~q~knRw~~~l~~~~~k~~~~~~~~~~l~~~~~ 134 (267)
.|.+|...+|||++.|||.||.+.|...++++.|+-.+++-+.....
T Consensus 381 kdw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~~V~ 428 (939)
T KOG0049|consen 381 KDWAKVRQAVPNRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLYAVK 428 (939)
T ss_pred cchhhHHHhcCCccHHHHHHHHHHHHHHhhccCceeecchHHHHHHHH
Confidence 59999999999999999999999999999999999999988776544
No 6
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.65 E-value=8.1e-17 Score=114.55 Aligned_cols=60 Identities=40% Similarity=0.794 Sum_probs=55.0
Q ss_pred CCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCcccccccccccCCCCCCCCCCHHHHHHH
Q 024441 17 WTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNYLRPDLKRGLLTEAEEQLV 78 (267)
Q Consensus 17 WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L~p~~~~~~WT~eED~~L 78 (267)
||+|||++|+.+|..|| .+|..||+.|| .|++.||+.||.++|.|.+++++||++||++|
T Consensus 1 WT~eEd~~L~~~~~~~g-~~W~~Ia~~l~-~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYG-NDWKKIAEHLG-NRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHT-S-HHHHHHHST-TS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC-cCHHHHHHHHC-cCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 99999999999999999 57999999997 89999999999999999999999999999987
No 7
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.58 E-value=9.3e-16 Score=147.60 Aligned_cols=107 Identities=23% Similarity=0.529 Sum_probs=101.6
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCcccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCCChh
Q 024441 11 GVKKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNYLRPDLKRGLLTEAEEQLVIDLHARLGNRWS 90 (267)
Q Consensus 11 ~ikkg~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L~p~~~~~~WT~eED~~Ll~lv~~~G~~W~ 90 (267)
-++.|.|+.-||+.|..+|.+||...|.+|++.+. ..+++||+.||..+|+|.+++..|+.+||++|+.+...+...|.
T Consensus 4 ~~kggvwrntEdeilkaav~kyg~nqws~i~sll~-~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwr 82 (617)
T KOG0050|consen 4 EIKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLN-RKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWR 82 (617)
T ss_pred EEecceecccHHHHHHHHHHHcchHHHHHHHHHHh-hcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccc
Confidence 36789999999999999999999999999999998 89999999999999999999999999999999999999999999
Q ss_pred hhhccCCCCCHHHHHHHHHHHHHHHHhhC
Q 024441 91 KIAARLPGRTDNEIKNHWNTHIKKKLLKM 119 (267)
Q Consensus 91 ~IA~~lpgRT~~q~knRw~~~l~~~~~k~ 119 (267)
.||..| ||+.+||..||+.++-......
T Consensus 83 tIa~i~-gr~~~qc~eRy~~ll~~~~s~~ 110 (617)
T KOG0050|consen 83 TIADIM-GRTSQQCLERYNNLLDVYVSYH 110 (617)
T ss_pred hHHHHh-hhhHHHHHHHHHHHHHHHHhhh
Confidence 999999 9999999999999998876543
No 8
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.58 E-value=2.2e-15 Score=147.17 Aligned_cols=108 Identities=30% Similarity=0.492 Sum_probs=102.4
Q ss_pred CCCCccCCCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCcccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCCC
Q 024441 9 KLGVKKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNYLRPDLKRGLLTEAEEQLVIDLHARLGNR 88 (267)
Q Consensus 9 k~~ikkg~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L~p~~~~~~WT~eED~~Ll~lv~~~G~~ 88 (267)
...++.|.|+..||+.|..+|+.||+.+|.+||..+. .|+++||+.||.++++|.+++..|+.+||..|+.+..++|..
T Consensus 15 ~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~-~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~ 93 (512)
T COG5147 15 QTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLI-SSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQ 93 (512)
T ss_pred cceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhc-ccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCch
Confidence 4467899999999999999999999999999999998 699999999999999999999999999999999999999999
Q ss_pred hhhhhccCCCCCHHHHHHHHHHHHHHHHh
Q 024441 89 WSKIAARLPGRTDNEIKNHWNTHIKKKLL 117 (267)
Q Consensus 89 W~~IA~~lpgRT~~q~knRw~~~l~~~~~ 117 (267)
|+.||..+++|+..+|.+||...+.....
T Consensus 94 wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 94 WSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 99999999999999999999988887655
No 9
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.45 E-value=1.2e-13 Score=123.58 Aligned_cols=74 Identities=18% Similarity=0.387 Sum_probs=67.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhC-CChhhhhccC-CCCCHHHHHHHHHHHHHHHHhhCCCCCCCCCcCcccccc
Q 024441 62 RPDLKRGLLTEAEEQLVIDLHARLG-NRWSKIAARL-PGRTDNEIKNHWNTHIKKKLLKMGIDPVTHEPLHKETKA 135 (267)
Q Consensus 62 ~p~~~~~~WT~eED~~Ll~lv~~~G-~~W~~IA~~l-pgRT~~q~knRw~~~l~~~~~k~~~~~~~~~~l~~~~~~ 135 (267)
++.+++++||+|||++|+++|++|| .+|..||+.+ ++||+.|||.||.++|++.+++++|+.++++.|...+..
T Consensus 20 K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~ 95 (249)
T PLN03212 20 KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRL 95 (249)
T ss_pred cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHh
Confidence 3578999999999999999999999 6899999998 799999999999999999999999999999887765543
No 10
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.43 E-value=1.2e-13 Score=136.54 Aligned_cols=102 Identities=25% Similarity=0.545 Sum_probs=92.3
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCcccccccccccCCCC--CCCCCCHHHHHHHHHHHH-------
Q 024441 13 KKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNYLRPDL--KRGLLTEAEEQLVIDLHA------- 83 (267)
Q Consensus 13 kkg~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L~p~~--~~~~WT~eED~~Ll~lv~------- 83 (267)
++|+||+||++.|..+|..+| .+|..|++.|| |.+..||+||+++..++- +++.||.||+++|+++|.
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g-~~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~ 459 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHG-NDWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREAL 459 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhc-ccHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhh
Confidence 899999999999999999999 66999999998 999999999999999885 899999999999999995
Q ss_pred Hh-------------------CCChhhhhccCCCCCHHHHHHHHHHHHHHHHh
Q 024441 84 RL-------------------GNRWSKIAARLPGRTDNEIKNHWNTHIKKKLL 117 (267)
Q Consensus 84 ~~-------------------G~~W~~IA~~lpgRT~~q~knRw~~~l~~~~~ 117 (267)
.+ +-+|..|++.+..|+..|||.+|+.++.....
T Consensus 460 q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~ 512 (607)
T KOG0051|consen 460 QPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSF 512 (607)
T ss_pred cccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHh
Confidence 23 12599999988999999999999988877644
No 11
>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=99.42 E-value=4e-14 Score=100.60 Aligned_cols=57 Identities=30% Similarity=0.599 Sum_probs=48.9
Q ss_pred CCHHHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHHHHHHHHHHHHhhCCCCCCCC
Q 024441 70 LTEAEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKNHWNTHIKKKLLKMGIDPVTH 126 (267)
Q Consensus 70 WT~eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knRw~~~l~~~~~k~~~~~~~~ 126 (267)
||++||.+|+++|.+||++|..||+.|+.||+.+|++||+..|++.+.+.+|++.++
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd 57 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEED 57 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHH
Confidence 999999999999999999999999999669999999999998888888888776543
No 12
>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=99.42 E-value=2.2e-13 Score=93.00 Aligned_cols=46 Identities=33% Similarity=0.708 Sum_probs=41.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCC-hhhhhccCC-CCCHHHHHHHHHHHH
Q 024441 67 RGLLTEAEEQLVIDLHARLGNR-WSKIAARLP-GRTDNEIKNHWNTHI 112 (267)
Q Consensus 67 ~~~WT~eED~~Ll~lv~~~G~~-W~~IA~~lp-gRT~~q~knRw~~~l 112 (267)
+++||++||++|+++|.+||.+ |..||..|| +||..||++||+.++
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 5789999999999999999988 999999999 999999999998764
No 13
>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=3.8e-14 Score=96.79 Aligned_cols=48 Identities=40% Similarity=0.765 Sum_probs=43.5
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCccccccccccc
Q 024441 14 KGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNYL 61 (267)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L 61 (267)
|++||++||++|+++|.+||..+|..||..|+.+||+.||+.||.++|
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 689999999999999999998889999999988999999999999875
No 14
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.35 E-value=2e-13 Score=122.65 Aligned_cols=76 Identities=16% Similarity=0.229 Sum_probs=70.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhC-CChhhhhccCC-CCCHHHHHHHHHHHHHHHHhhCCCCCCCCCcCcccccccCC
Q 024441 63 PDLKRGLLTEAEEQLVIDLHARLG-NRWSKIAARLP-GRTDNEIKNHWNTHIKKKLLKMGIDPVTHEPLHKETKAEDN 138 (267)
Q Consensus 63 p~~~~~~WT~eED~~Ll~lv~~~G-~~W~~IA~~lp-gRT~~q~knRw~~~l~~~~~k~~~~~~~~~~l~~~~~~~~~ 138 (267)
+.+.+|+||+|||.+|+++|++|| ++|..||+.++ +|++++||-||.++|++.++++.|++++++.+.+.+...++
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GN 82 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGN 82 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCc
Confidence 345579999999999999999999 67999999998 99999999999999999999999999999999998887776
No 15
>PLN03091 hypothetical protein; Provisional
Probab=99.32 E-value=5e-13 Score=127.61 Aligned_cols=72 Identities=14% Similarity=0.316 Sum_probs=66.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhC-CChhhhhccC-CCCCHHHHHHHHHHHHHHHHhhCCCCCCCCCcCccccc
Q 024441 63 PDLKRGLLTEAEEQLVIDLHARLG-NRWSKIAARL-PGRTDNEIKNHWNTHIKKKLLKMGIDPVTHEPLHKETK 134 (267)
Q Consensus 63 p~~~~~~WT~eED~~Ll~lv~~~G-~~W~~IA~~l-pgRT~~q~knRw~~~l~~~~~k~~~~~~~~~~l~~~~~ 134 (267)
+.+++++||+|||++|+++|++|| .+|..||+.+ ++|+++|||.||.++|++.+++++|++++++.|.+.+.
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k 83 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHA 83 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHH
Confidence 578999999999999999999999 5799999988 69999999999999999999999999999987776554
No 16
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.21 E-value=2.3e-11 Score=81.07 Aligned_cols=47 Identities=45% Similarity=0.885 Sum_probs=44.0
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CChhhhhccCCCCCHHHHHHHHHHHHH
Q 024441 67 RGLLTEAEEQLVIDLHARLG-NRWSKIAARLPGRTDNEIKNHWNTHIK 113 (267)
Q Consensus 67 ~~~WT~eED~~Ll~lv~~~G-~~W~~IA~~lpgRT~~q~knRw~~~l~ 113 (267)
+++||++||.+|+.++..|| .+|..||..|++||+.+|++||+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 36899999999999999999 999999999999999999999988764
No 17
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.10 E-value=1.6e-10 Score=75.86 Aligned_cols=43 Identities=37% Similarity=0.772 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHHHHHhC-CChhhhhccCCCCCHHHHHHHHHHH
Q 024441 69 LLTEAEEQLVIDLHARLG-NRWSKIAARLPGRTDNEIKNHWNTH 111 (267)
Q Consensus 69 ~WT~eED~~Ll~lv~~~G-~~W~~IA~~lpgRT~~q~knRw~~~ 111 (267)
+||++|+.+|+.++.+|| .+|..||+.+++||..+|++||..+
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 599999999999999999 8999999999999999999999865
No 18
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.05 E-value=7.5e-11 Score=78.53 Aligned_cols=48 Identities=40% Similarity=0.803 Sum_probs=44.6
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCcccccccccccC
Q 024441 14 KGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNYLR 62 (267)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L~ 62 (267)
+++||++||.+|+.++..||..+|..||..++ +|++.+|+.||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~-~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELP-GRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcC-CCCHHHHHHHHHHHcC
Confidence 47899999999999999999778999999998 9999999999998764
No 19
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.90 E-value=5.4e-10 Score=73.26 Aligned_cols=45 Identities=40% Similarity=0.778 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCccccccccccc
Q 024441 16 PWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNYL 61 (267)
Q Consensus 16 ~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L 61 (267)
+||++||+.|+.++..||..+|..||+.++ +|++.+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~-~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELP-GRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcC-CCCHHHHHHHHHHhC
Confidence 599999999999999999778999999998 899999999998753
No 20
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.85 E-value=1.1e-09 Score=108.56 Aligned_cols=118 Identities=26% Similarity=0.285 Sum_probs=97.6
Q ss_pred ccCCCCHHHHHHHHHHHHHhCC---------------C--------CCchhchhhcCccCCccccc---ccccccCCCCC
Q 024441 13 KKGPWTAEEDKKLINFILTNGQ---------------C--------CWRAVPKLAGLRRCGKSCRL---RWTNYLRPDLK 66 (267)
Q Consensus 13 kkg~WT~eED~~L~~~v~~~g~---------------~--------~W~~IA~~~~~~Rt~~QCr~---Rw~~~L~p~~~ 66 (267)
+-+.|+++||+.|.+.|..|-. . -|..|...++ -|+...+.. |-++.+.+ +
T Consensus 307 ~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp-~R~~~siy~~~rR~y~~FE~--~ 383 (607)
T KOG0051|consen 307 NLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLP-YRDRKSIYHHLRRAYTPFEN--K 383 (607)
T ss_pred hhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcC-cccchhHHHHHHhcCCcccc--c
Confidence 4489999999999999988610 1 2566767777 588887766 44444544 8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHHHHHHHHHHH--HhhCCCCCCCCCcCccccc
Q 024441 67 RGLLTEAEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKNHWNTHIKKK--LLKMGIDPVTHEPLHKETK 134 (267)
Q Consensus 67 ~~~WT~eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knRw~~~l~~~--~~k~~~~~~~~~~l~~~~~ 134 (267)
+|.||++|++.|..+|.++|+.|..|++.| ||.+..|+.||+.+++.. ..++.|+.++.+.|.+...
T Consensus 384 rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~ 452 (607)
T KOG0051|consen 384 RGKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVN 452 (607)
T ss_pred cCCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHH
Confidence 999999999999999999999999999999 999999999999998876 5788899888888877654
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=98.30 E-value=5.6e-08 Score=95.62 Aligned_cols=98 Identities=29% Similarity=0.619 Sum_probs=85.7
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCcccccccccccCC--CCCCCCCCHHHHHHHHHHHHHhC----
Q 024441 13 KKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNYLRP--DLKRGLLTEAEEQLVIDLHARLG---- 86 (267)
Q Consensus 13 kkg~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L~p--~~~~~~WT~eED~~Ll~lv~~~G---- 86 (267)
.+|.||++|++.|...+..+| ..|..|.+.++ |-+..||+||++|..+ .+++++|+.||+.+|...|...-
T Consensus 290 ~~~~wt~e~~~eL~~~~~~~~-~~w~~ig~~~~--rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e~~~~~~ 366 (512)
T COG5147 290 QRGKWTKEEEQELAKLVVEHG-GSWTEIGKLLG--RMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNEMRLEAQ 366 (512)
T ss_pred hhccCcccccccccccccccc-chhhHhhhhhc--cCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHHHHHHHh
Confidence 589999999999999999999 56999999887 8899999999999988 67888999999999998887432
Q ss_pred ----CChhhhhccCCCCCHHHHHHHHHHHHH
Q 024441 87 ----NRWSKIAARLPGRTDNEIKNHWNTHIK 113 (267)
Q Consensus 87 ----~~W~~IA~~lpgRT~~q~knRw~~~l~ 113 (267)
-.|..|+..+++|...+|+.++..+..
T Consensus 367 ~~~~~~~~li~~~~~~~~~~~~~~~~~~~~~ 397 (512)
T COG5147 367 QSSRILWLLIAQNIRNRLQHHCRDKYGVLIS 397 (512)
T ss_pred hhhhhhHHHHHHhhhccccCCCCCccccccc
Confidence 359999999999999999887765544
No 22
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=98.04 E-value=1.9e-06 Score=84.13 Aligned_cols=73 Identities=25% Similarity=0.426 Sum_probs=66.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHhC-CChhhhhccCCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCCcCcccccccC
Q 024441 65 LKRGLLTEAEEQLVIDLHARLG-NRWSKIAARLPGRTDNEIKNHWNTHIKKKLLKMGIDPVTHEPLHKETKAED 137 (267)
Q Consensus 65 ~~~~~WT~eED~~Ll~lv~~~G-~~W~~IA~~lpgRT~~q~knRw~~~l~~~~~k~~~~~~~~~~l~~~~~~~~ 137 (267)
++.+-|+..||++|-.+|.+|| +.|++|+..++-.|+.||++||...+.+.+++..|..++++.+........
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p 78 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEP 78 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcC
Confidence 4667899999999999999999 679999999999999999999999999999999999999988877655443
No 23
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.87 E-value=8.3e-06 Score=57.91 Aligned_cols=49 Identities=12% Similarity=0.273 Sum_probs=43.1
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCC---chhchhhcCcc-CCccccccccccc
Q 024441 13 KKGPWTAEEDKKLINFILTNGQCCW---RAVPKLAGLRR-CGKSCRLRWTNYL 61 (267)
Q Consensus 13 kkg~WT~eED~~L~~~v~~~g~~~W---~~IA~~~~~~R-t~~QCr~Rw~~~L 61 (267)
++-.||+||..+++++|..+|..+| +.|++.|+..| |..||+.+++.|.
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 3568999999999999999998799 99999887666 9999999887764
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=97.71 E-value=8.9e-05 Score=52.64 Aligned_cols=46 Identities=20% Similarity=0.344 Sum_probs=40.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-Ch---hhhhccC-CCC-CHHHHHHHHHHHH
Q 024441 67 RGLLTEAEEQLVIDLHARLGN-RW---SKIAARL-PGR-TDNEIKNHWNTHI 112 (267)
Q Consensus 67 ~~~WT~eED~~Ll~lv~~~G~-~W---~~IA~~l-pgR-T~~q~knRw~~~l 112 (267)
+-.||+||..+.++++..+|. +| ..|+..+ ..| |..||+.|.+.+.
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 457999999999999999995 99 9999988 345 9999999987654
No 25
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.62 E-value=8.7e-05 Score=71.41 Aligned_cols=57 Identities=25% Similarity=0.429 Sum_probs=47.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHhC-CChhhhhccCCCCCHHHHHHHHHHHHHHHHhhCCCCCCC
Q 024441 65 LKRGLLTEAEEQLVIDLHARLG-NRWSKIAARLPGRTDNEIKNHWNTHIKKKLLKMGIDPVT 125 (267)
Q Consensus 65 ~~~~~WT~eED~~Ll~lv~~~G-~~W~~IA~~lpgRT~~q~knRw~~~l~~~~~k~~~~~~~ 125 (267)
+-...||.+|+.+|++++..|| ++|..||.++..|+..+|+.+|.+ .+..+.+.|.+
T Consensus 70 i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k----~fv~s~~~~~~ 127 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLK----HFVNSPIFPLP 127 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHH----HHhcCcccccc
Confidence 3445699999999999999999 999999999999999999999975 44445555544
No 26
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.57 E-value=2.9e-05 Score=74.66 Aligned_cols=50 Identities=20% Similarity=0.445 Sum_probs=46.3
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCccccccccccc
Q 024441 11 GVKKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNYL 61 (267)
Q Consensus 11 ~ikkg~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L 61 (267)
.+-...||++|+-+|++++..||-+||..||.++| +|+..+|+++|.+++
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIG-tKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIG-TKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHc-ccchHHHHHHHHHHH
Confidence 34577899999999999999999999999999999 999999999999865
No 27
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=97.37 E-value=0.00022 Score=60.52 Aligned_cols=52 Identities=21% Similarity=0.398 Sum_probs=45.2
Q ss_pred CCCCCCHHHHHHHHHHHHHh---CC----ChhhhhccCCCCCHHHHHHHHHHHHHHHHhh
Q 024441 66 KRGLLTEAEEQLVIDLHARL---GN----RWSKIAARLPGRTDNEIKNHWNTHIKKKLLK 118 (267)
Q Consensus 66 ~~~~WT~eED~~Ll~lv~~~---G~----~W~~IA~~lpgRT~~q~knRw~~~l~~~~~k 118 (267)
....||.|||.+|.+.|.+| |+ -+..++..| +||+.+|.-||+..+|+.+..
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~ 61 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEE 61 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHH
Confidence 45679999999999999888 32 288999999 999999999999999987654
No 28
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.20 E-value=0.00048 Score=60.56 Aligned_cols=100 Identities=23% Similarity=0.381 Sum_probs=68.9
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCchhchhhc--CccCCccccccccccc-CCC--------------------CCCCCCCH
Q 024441 16 PWTAEEDKKLINFILTNGQCCWRAVPKLAG--LRRCGKSCRLRWTNYL-RPD--------------------LKRGLLTE 72 (267)
Q Consensus 16 ~WT~eED~~L~~~v~~~g~~~W~~IA~~~~--~~Rt~~QCr~Rw~~~L-~p~--------------------~~~~~WT~ 72 (267)
+|++++|-.|+.+|..-. +-..|+..+. ..-|-..+.+||+..| +|. ..+.+||.
T Consensus 1 rW~~~DDl~Li~av~~~~--~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~~is~~a~~~m~~l~p~~~~~iq~kalfS~ 78 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTN--DLESVHLGVKFSCKFTLQEIEERWYALLYDPVISRIAVAAMRNLHPELIAAIQSKALFSK 78 (199)
T ss_pred CCCchhhHHHHHHHHHhc--CHHHHHccCCcCCcCcHHHHHHHHHHHHcChhhHHHHHHHHHhCCcchhhcccccCCCCH
Confidence 699999999999998754 3455554332 1234556677888764 222 24567999
Q ss_pred HHHHHHHHHHHHhCC---Chhhh----hccC-CCCCHHHHHHHHHHHHHHHHh
Q 024441 73 AEEQLVIDLHARLGN---RWSKI----AARL-PGRTDNEIKNHWNTHIKKKLL 117 (267)
Q Consensus 73 eED~~Ll~lv~~~G~---~W~~I----A~~l-pgRT~~q~knRw~~~l~~~~~ 117 (267)
+|+++|......... .+.+| +..| ++||+.++.++|..+.+..+.
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~LL 131 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHLL 131 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhchh
Confidence 999999997766543 46666 2233 899999999999865555443
No 29
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=97.04 E-value=0.00089 Score=48.76 Aligned_cols=50 Identities=16% Similarity=0.387 Sum_probs=32.8
Q ss_pred CCCCCHHHHHHHHHHHHHhC-------CC--hhhhhccCC-CCCHHHHHHHHHHHHHHHH
Q 024441 67 RGLLTEAEEQLVIDLHARLG-------NR--WSKIAARLP-GRTDNEIKNHWNTHIKKKL 116 (267)
Q Consensus 67 ~~~WT~eED~~Ll~lv~~~G-------~~--W~~IA~~lp-gRT~~q~knRw~~~l~~~~ 116 (267)
+.++|.+||++|++.|+++. ++ |.++++.-| .+|-.+.|+||...|+.+.
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~ 61 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRP 61 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccc
Confidence 45799999999999997652 22 999999887 9999999999998887764
No 30
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.97 E-value=0.00063 Score=51.30 Aligned_cols=49 Identities=31% Similarity=0.505 Sum_probs=35.1
Q ss_pred CCCCHHHHHHHHHHHHH------hC--C------ChhhhhccC----CCCCHHHHHHHHHHHHHHHH
Q 024441 68 GLLTEAEEQLVIDLHAR------LG--N------RWSKIAARL----PGRTDNEIKNHWNTHIKKKL 116 (267)
Q Consensus 68 ~~WT~eED~~Ll~lv~~------~G--~------~W~~IA~~l----pgRT~~q~knRw~~~l~~~~ 116 (267)
..||.+|...||+++.. ++ + -|..||..| ..||+.||++||.++.+...
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk 68 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYK 68 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Confidence 47999999999999877 21 1 299999987 46999999999988666543
No 31
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.91 E-value=0.00088 Score=65.16 Aligned_cols=44 Identities=18% Similarity=0.281 Sum_probs=41.5
Q ss_pred CCCCHHHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHHHHHHH
Q 024441 68 GLLTEAEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKNHWNTH 111 (267)
Q Consensus 68 ~~WT~eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knRw~~~ 111 (267)
..||.+|..+|++++..||..|.+||+++..||..||--||..+
T Consensus 280 k~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred ccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 47999999999999999999999999999999999999999754
No 32
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.90 E-value=0.00034 Score=67.96 Aligned_cols=46 Identities=22% Similarity=0.429 Sum_probs=42.4
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCcccccccccc
Q 024441 13 KKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNY 60 (267)
Q Consensus 13 kkg~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~ 60 (267)
....||.+|..+|+++|+.|| .+|.+||.++| +|+.-||..|+.+.
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 566999999999999999999 66999999999 99999999998864
No 33
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.83 E-value=0.0015 Score=64.78 Aligned_cols=46 Identities=20% Similarity=0.330 Sum_probs=42.5
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHHHHHHH
Q 024441 66 KRGLLTEAEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKNHWNTH 111 (267)
Q Consensus 66 ~~~~WT~eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knRw~~~ 111 (267)
.+..||.+|..+|++++..||..|.+||.++.+||..||--||..+
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhc
Confidence 4557999999999999999999999999999999999999998654
No 34
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.79 E-value=0.00051 Score=68.07 Aligned_cols=48 Identities=23% Similarity=0.453 Sum_probs=43.5
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCcccccccccc
Q 024441 11 GVKKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNY 60 (267)
Q Consensus 11 ~ikkg~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~ 60 (267)
.--++.||.+|..+|+++|++|| .+|.+||.++| .|+..||..++.+.
T Consensus 250 ~~~~~~WT~qE~lLLLE~ie~y~-ddW~kVa~hVg-~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 250 ESARPNWTEQETLLLLEAIEMYG-DDWNKVADHVG-TKSQEQCILKFLRL 297 (506)
T ss_pred ccCCCCccHHHHHHHHHHHHHhc-ccHHHHHhccC-CCCHHHHHHHHHhc
Confidence 34578899999999999999999 67999999999 99999999998763
No 35
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=96.46 E-value=0.00075 Score=49.15 Aligned_cols=52 Identities=25% Similarity=0.441 Sum_probs=33.3
Q ss_pred cCCCCHHHHHHHHHHHHHhC--------CCCCchhchhhcCccCCcccccccccccCCCC
Q 024441 14 KGPWTAEEDKKLINFILTNG--------QCCWRAVPKLAGLRRCGKSCRLRWTNYLRPDL 65 (267)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g--------~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L~p~~ 65 (267)
+-+||.+||+.|+..|..+. ..-|+++++..++++|...-|+||.+.|.+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~ 61 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRP 61 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccc
Confidence 45799999999999997653 22399998876668899999999999987643
No 36
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.45 E-value=0.0034 Score=53.95 Aligned_cols=52 Identities=17% Similarity=0.332 Sum_probs=43.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCC-------hhhhhccCCCCCHHHHHHHHHHHHHHHHh
Q 024441 65 LKRGLLTEAEEQLVIDLHARLGNR-------WSKIAARLPGRTDNEIKNHWNTHIKKKLL 117 (267)
Q Consensus 65 ~~~~~WT~eED~~Ll~lv~~~G~~-------W~~IA~~lpgRT~~q~knRw~~~l~~~~~ 117 (267)
.+...||.|+|.+|.+.|..|+.. ...++..| +||..+|.-||+..+++++.
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Ye 61 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQ 61 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHH
Confidence 356789999999999999888732 66667777 99999999999999997643
No 37
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.04 E-value=0.0016 Score=49.07 Aligned_cols=47 Identities=30% Similarity=0.631 Sum_probs=31.8
Q ss_pred cCCCCHHHHHHHHHHHHH--h----C--C-----CCCchhchhh---cCccCCcccccccccc
Q 024441 14 KGPWTAEEDKKLINFILT--N----G--Q-----CCWRAVPKLA---GLRRCGKSCRLRWTNY 60 (267)
Q Consensus 14 kg~WT~eED~~L~~~v~~--~----g--~-----~~W~~IA~~~---~~~Rt~~QCr~Rw~~~ 60 (267)
+-.||.+|...|+.++.. + + . .-|..||..| |..|++.||+.||.+.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L 63 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL 63 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 357999999999998877 2 1 1 1499999755 5679999999999874
No 38
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=95.96 E-value=0.0026 Score=53.99 Aligned_cols=49 Identities=29% Similarity=0.637 Sum_probs=41.1
Q ss_pred CccCCCCHHHHHHHHHHHHHhCC------CCCchhchhhcCccCCcccccccccccC
Q 024441 12 VKKGPWTAEEDKKLINFILTNGQ------CCWRAVPKLAGLRRCGKSCRLRWTNYLR 62 (267)
Q Consensus 12 ikkg~WT~eED~~L~~~v~~~g~------~~W~~IA~~~~~~Rt~~QCr~Rw~~~L~ 62 (267)
.++-.||.|||.+|.+.|.+|-. .....|+..++ ||+..|.-||..++.
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 46789999999999999999821 14777888887 999999999998876
No 39
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.93 E-value=0.0072 Score=56.52 Aligned_cols=46 Identities=30% Similarity=0.458 Sum_probs=42.0
Q ss_pred CCCCHHHHHHHHHHHHHhC-CChhhhhccCCCCCHHHHHHHHHHHHH
Q 024441 68 GLLTEAEEQLVIDLHARLG-NRWSKIAARLPGRTDNEIKNHWNTHIK 113 (267)
Q Consensus 68 ~~WT~eED~~Ll~lv~~~G-~~W~~IA~~lpgRT~~q~knRw~~~l~ 113 (267)
..|+..|+.+|+++....| ++|..||.++..|+...||.||..+..
T Consensus 64 e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 64 EGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 3599999999999999999 899999999999999999999976544
No 40
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.61 E-value=0.037 Score=40.79 Aligned_cols=49 Identities=24% Similarity=0.518 Sum_probs=39.9
Q ss_pred CCCCCHHHHHHHHHHHHHhC----C-------------ChhhhhccC-----CCCCHHHHHHHHHHHHHHH
Q 024441 67 RGLLTEAEEQLVIDLHARLG----N-------------RWSKIAARL-----PGRTDNEIKNHWNTHIKKK 115 (267)
Q Consensus 67 ~~~WT~eED~~Ll~lv~~~G----~-------------~W~~IA~~l-----pgRT~~q~knRw~~~l~~~ 115 (267)
...||.+|..+|++++.+|. + -|..|+..| +.||..+++.+|..+....
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~ 72 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKA 72 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHH
Confidence 34699999999999998872 1 299999876 3699999999998876654
No 41
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=95.28 E-value=0.034 Score=59.79 Aligned_cols=101 Identities=16% Similarity=0.290 Sum_probs=75.9
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCccccc-------ccccc----------------------------
Q 024441 16 PWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRL-------RWTNY---------------------------- 60 (267)
Q Consensus 16 ~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~-------Rw~~~---------------------------- 60 (267)
.||.-+=..++.+..+||..+-..||..|. +++...++. ||...
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 488888888888889999888999998886 677655542 22110
Q ss_pred --------------c-CCCCCCCCCCHHHHHHHHHHHHHhC-CChhhhhccC------------CCCCHHHHHHHHHHHH
Q 024441 61 --------------L-RPDLKRGLLTEAEEQLVIDLHARLG-NRWSKIAARL------------PGRTDNEIKNHWNTHI 112 (267)
Q Consensus 61 --------------L-~p~~~~~~WT~eED~~Ll~lv~~~G-~~W~~IA~~l------------pgRT~~q~knRw~~~l 112 (267)
+ -+..++..+|.+||..|+-++.+|| ++|..|-..+ ..||+..|..|...++
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 0 0233445599999999999999999 7899994322 4799999999999988
Q ss_pred HHHHh
Q 024441 113 KKKLL 117 (267)
Q Consensus 113 ~~~~~ 117 (267)
+-..+
T Consensus 985 ~~~~~ 989 (1033)
T PLN03142 985 RLIEK 989 (1033)
T ss_pred HHHHH
Confidence 87543
No 42
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=94.89 E-value=0.0084 Score=56.09 Aligned_cols=49 Identities=20% Similarity=0.397 Sum_probs=45.1
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCcccccccccccC
Q 024441 13 KKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNYLR 62 (267)
Q Consensus 13 kkg~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L~ 62 (267)
----|+++|+.+|+++....|-+||.-||..+| .|+...|+.+|..++.
T Consensus 62 ~~e~WgadEEllli~~~~TlGlGNW~dIadyiG-sr~kee~k~HylK~y~ 110 (432)
T COG5114 62 GEEGWGADEELLLIECLDTLGLGNWEDIADYIG-SRAKEEIKSHYLKMYD 110 (432)
T ss_pred cCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHh-hhhhHHHHHHHHHHHh
Confidence 345699999999999999999999999999999 9999999999988765
No 43
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=94.20 E-value=0.012 Score=43.36 Aligned_cols=49 Identities=18% Similarity=0.398 Sum_probs=39.0
Q ss_pred ccCCCCHHHHHHHHHHHHHhCC----------------CCCchhchhh----cCccCCccccccccccc
Q 024441 13 KKGPWTAEEDKKLINFILTNGQ----------------CCWRAVPKLA----GLRRCGKSCRLRWTNYL 61 (267)
Q Consensus 13 kkg~WT~eED~~L~~~v~~~g~----------------~~W~~IA~~~----~~~Rt~~QCr~Rw~~~L 61 (267)
++..||.+|.+.|+++|.+|.. ..|..|+..+ +..|+..|++.+|.+..
T Consensus 1 R~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk 69 (78)
T PF13873_consen 1 RKPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLK 69 (78)
T ss_pred CCCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 3578999999999999998721 1499999755 23699999999998754
No 44
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=94.20 E-value=0.012 Score=50.63 Aligned_cols=49 Identities=24% Similarity=0.527 Sum_probs=38.1
Q ss_pred CccCCCCHHHHHHHHHHHHHhCCCC------CchhchhhcCccCCcccccccccccC
Q 024441 12 VKKGPWTAEEDKKLINFILTNGQCC------WRAVPKLAGLRRCGKSCRLRWTNYLR 62 (267)
Q Consensus 12 ikkg~WT~eED~~L~~~v~~~g~~~------W~~IA~~~~~~Rt~~QCr~Rw~~~L~ 62 (267)
.++..||.|+|.+|.+.|..|+... ...++..+. |++.+|..||..++.
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~--rt~aac~fRwNs~vr 57 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALK--RTAAACGFRWNSVVR 57 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHh--hhHHHHHhHHHHHHH
Confidence 4788999999999999999886443 344445555 999999999966554
No 45
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=93.03 E-value=0.18 Score=40.87 Aligned_cols=53 Identities=26% Similarity=0.458 Sum_probs=41.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC----ChhhhhccC------------CCCCHHHHHHHHHHHHHHHH
Q 024441 64 DLKRGLLTEAEEQLVIDLHARLGN----RWSKIAARL------------PGRTDNEIKNHWNTHIKKKL 116 (267)
Q Consensus 64 ~~~~~~WT~eED~~Ll~lv~~~G~----~W~~IA~~l------------pgRT~~q~knRw~~~l~~~~ 116 (267)
..++..+|++||.-|+-++.+||- .|..|...+ ..||+..|..|...+++-..
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 456678999999999999999995 698886533 35999999999999887643
No 46
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=92.64 E-value=0.17 Score=48.63 Aligned_cols=53 Identities=25% Similarity=0.327 Sum_probs=46.4
Q ss_pred CCCCHHHHHHHHHHHHHhCCChhhhhcc-----CCC-CCHHHHHHHHHHHHHHHHhhCC
Q 024441 68 GLLTEAEEQLVIDLHARLGNRWSKIAAR-----LPG-RTDNEIKNHWNTHIKKKLLKMG 120 (267)
Q Consensus 68 ~~WT~eED~~Ll~lv~~~G~~W~~IA~~-----lpg-RT~~q~knRw~~~l~~~~~k~~ 120 (267)
..||.+|-..|.++++.|.-+|..||.. ++. ||-..+|.||+...++.++...
T Consensus 131 n~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~ 189 (445)
T KOG2656|consen 131 NSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARA 189 (445)
T ss_pred ccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHHHHHHHHHccC
Confidence 4699999999999999999999999987 555 9999999999998888765433
No 47
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=92.60 E-value=0.29 Score=37.07 Aligned_cols=46 Identities=33% Similarity=0.596 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHHHh---CC----------ChhhhhccC---CC--CCHHHHHHHHHHHHHH
Q 024441 69 LLTEAEEQLVIDLHARL---GN----------RWSKIAARL---PG--RTDNEIKNHWNTHIKK 114 (267)
Q Consensus 69 ~WT~eED~~Ll~lv~~~---G~----------~W~~IA~~l---pg--RT~~q~knRw~~~l~~ 114 (267)
.||+++++.|++++.+. |+ .|..|+..| +| .+..||++||..+.+.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~ 64 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKD 64 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHH
Confidence 49999999999988553 21 299998877 33 4789999999776655
No 48
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=91.55 E-value=0.33 Score=45.78 Aligned_cols=51 Identities=20% Similarity=0.316 Sum_probs=40.7
Q ss_pred CCCCCHHHHHHHHHHHHHh----------CCChhhhhccC----CCCCHHHHHHHHHHHHHHHHh
Q 024441 67 RGLLTEAEEQLVIDLHARL----------GNRWSKIAARL----PGRTDNEIKNHWNTHIKKKLL 117 (267)
Q Consensus 67 ~~~WT~eED~~Ll~lv~~~----------G~~W~~IA~~l----pgRT~~q~knRw~~~l~~~~~ 117 (267)
...|+.+|-..||++..+. +..|..||+.+ .-||+.|||+||.++.++..+
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~ 118 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKK 118 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHH
Confidence 3679999999999987653 23499999955 459999999999988777543
No 49
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=90.94 E-value=0.35 Score=46.51 Aligned_cols=47 Identities=19% Similarity=0.209 Sum_probs=43.0
Q ss_pred CCCCHHHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 68 GLLTEAEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 68 ~~WT~eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
.+||.+|-++...+....|..+..||..+|.|...|||.+|.+--+.
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~ 412 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKV 412 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhh
Confidence 36999999999999999999999999999999999999999765544
No 50
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=86.39 E-value=2.3 Score=41.86 Aligned_cols=49 Identities=18% Similarity=0.177 Sum_probs=43.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 66 KRGLLTEAEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 66 ~~~~WT~eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
-...||.||-.++-++...||.++.+|.+.||.|+-..+...|+..-+.
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 3457999999999999999999999999999999999999888765443
No 51
>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=86.12 E-value=1.9 Score=29.16 Aligned_cols=41 Identities=20% Similarity=0.265 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHHHHHHHHH
Q 024441 72 EAEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKNHWNTHIK 113 (267)
Q Consensus 72 ~eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knRw~~~l~ 113 (267)
++++..++.++-..|-.+.+||..+ |.|...|+.+....++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARK 52 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHh
Confidence 4567778888888899999999999 9999999998876554
No 52
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=83.76 E-value=0.92 Score=36.79 Aligned_cols=34 Identities=24% Similarity=0.417 Sum_probs=28.5
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCC---CCCchhchhh
Q 024441 11 GVKKGPWTAEEDKKLINFILTNGQ---CCWRAVPKLA 44 (267)
Q Consensus 11 ~ikkg~WT~eED~~L~~~v~~~g~---~~W~~IA~~~ 44 (267)
+-++..||.+||.-|+-.+.+||- +.|..|...+
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~I 82 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEI 82 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHH
Confidence 567889999999999999999998 7899998655
No 53
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=82.23 E-value=0.63 Score=43.88 Aligned_cols=47 Identities=26% Similarity=0.413 Sum_probs=37.2
Q ss_pred CCCCHHHHHHHHHHHHHh---------CCCCCchhchh---hcCccCCccccccccccc
Q 024441 15 GPWTAEEDKKLINFILTN---------GQCCWRAVPKL---AGLRRCGKSCRLRWTNYL 61 (267)
Q Consensus 15 g~WT~eED~~L~~~v~~~---------g~~~W~~IA~~---~~~~Rt~~QCr~Rw~~~L 61 (267)
..|+.+|-..|+++.... ....|..||+. .|..|++.||+.||.+..
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 789999999999887652 22459999973 356799999999998743
No 54
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=81.45 E-value=0.78 Score=44.16 Aligned_cols=45 Identities=16% Similarity=0.226 Sum_probs=40.6
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCccccccccc
Q 024441 13 KKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTN 59 (267)
Q Consensus 13 kkg~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~ 59 (267)
.--+||.+|-+++.+|+...| .+...|+.+++ .|..+|+..+|.+
T Consensus 364 ~~~~Ws~~e~ekFYKALs~wG-tdF~LIs~lfP-~R~RkqIKaKfi~ 408 (507)
T COG5118 364 GALRWSKKEIEKFYKALSIWG-TDFSLISSLFP-NRERKQIKAKFIK 408 (507)
T ss_pred CCCcccHHHHHHHHHHHHHhc-chHHHHHHhcC-chhHHHHHHHHHH
Confidence 345799999999999999999 56999999998 9999999998876
No 55
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=76.50 E-value=4.7 Score=42.00 Aligned_cols=45 Identities=11% Similarity=0.043 Sum_probs=40.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHHHHHHH
Q 024441 67 RGLLTEAEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKNHWNTH 111 (267)
Q Consensus 67 ~~~WT~eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knRw~~~ 111 (267)
...||+.|-.+.-+++..|...+..|++.++++|-.||-..|+..
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtW 663 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTW 663 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHH
Confidence 346999999999999999999999999999999999999887654
No 56
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=76.39 E-value=2.2 Score=32.45 Aligned_cols=29 Identities=28% Similarity=0.483 Sum_probs=16.8
Q ss_pred CCccCCCCHHHHHHH--------HHHHHHhCCCCCchhch
Q 024441 11 GVKKGPWTAEEDKKL--------INFILTNGQCCWRAVPK 42 (267)
Q Consensus 11 ~ikkg~WT~eED~~L--------~~~v~~~g~~~W~~IA~ 42 (267)
.-..|-||+++|+.| .+++++|| +..|+.
T Consensus 44 ~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG---~~~i~~ 80 (87)
T PF11626_consen 44 DNMPGIWTPEDDEMLRSGDKDDIERLIKKHG---EERIER 80 (87)
T ss_dssp TT-TT---HHHHHHHTS--HHHHHHHHHHH----HHHHHH
T ss_pred CCCCCCcCHHHHHHHHcCCHHHHHHHHHHhC---HHHHHH
Confidence 345889999999999 35667777 455553
No 57
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=76.31 E-value=4.6 Score=41.18 Aligned_cols=51 Identities=16% Similarity=0.375 Sum_probs=42.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChhhh----------hccCCCCCHHHHHHHHHHHHHHHHh
Q 024441 67 RGLLTEAEEQLVIDLHARLGNRWSKI----------AARLPGRTDNEIKNHWNTHIKKKLL 117 (267)
Q Consensus 67 ~~~WT~eED~~Ll~lv~~~G~~W~~I----------A~~lpgRT~~q~knRw~~~l~~~~~ 117 (267)
+..||..|+.-...+++++|.++.+| -....-+|..|+|.+|+.++++.-+
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k 148 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNK 148 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHh
Confidence 56799999999999999999999988 2233457889999999988887644
No 58
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=75.16 E-value=5.3 Score=26.27 Aligned_cols=38 Identities=13% Similarity=0.338 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHhC-CChhhhhccCCCCCHHHHHHHHHHH
Q 024441 73 AEEQLVIDLHARLG-NRWSKIAARLPGRTDNEIKNHWNTH 111 (267)
Q Consensus 73 eED~~Ll~lv~~~G-~~W~~IA~~lpgRT~~q~knRw~~~ 111 (267)
+=|..|+.+...-| ..+..||+.+ |=|...|..|+..+
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l-glS~~~v~~Ri~rL 41 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL-GLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH-TS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH-CcCHHHHHHHHHHh
Confidence 34788888888888 4699999999 99999999998654
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=74.26 E-value=1.1 Score=29.48 Aligned_cols=38 Identities=18% Similarity=0.371 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHhCCCCCchhchhhcCccCCccccccccc
Q 024441 20 EEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTN 59 (267)
Q Consensus 20 eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~ 59 (267)
+=|.+|+.++...+...+.+||+.+| =+...|..|+.+
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lg--lS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELG--LSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHT--S-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHC--cCHHHHHHHHHH
Confidence 34889999999999999999999998 667778887653
No 60
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=70.80 E-value=6 Score=32.87 Aligned_cols=45 Identities=7% Similarity=0.173 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHhC-CChhhhhccCCCCCHHHHHHHHHHHHHHHHhh
Q 024441 73 AEEQLVIDLHARLG-NRWSKIAARLPGRTDNEIKNHWNTHIKKKLLK 118 (267)
Q Consensus 73 eED~~Ll~lv~~~G-~~W~~IA~~lpgRT~~q~knRw~~~l~~~~~k 118 (267)
+-|.+|+.+.++-| ..|+.||+.+ |-|...|+.|++.+....+.+
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGIIT 54 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 56888999888888 5799999999 999999999998877776544
No 61
>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=69.65 E-value=11 Score=25.02 Aligned_cols=41 Identities=29% Similarity=0.360 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 73 AEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 73 eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
+++..++.++-..|-.+..||..+ |-|...|+.+....+++
T Consensus 7 ~~er~vi~~~y~~~~t~~eIa~~l-g~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 7 PREREVIRLRYFEGLTLEEIAERL-GISRSTVRRILKRALKK 47 (50)
T ss_dssp HHHHHHHHHHHTST-SHHHHHHHH-TSCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHH-CCcHHHHHHHHHHHHHH
Confidence 344555555555567899999999 99999999988877665
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=66.34 E-value=22 Score=33.66 Aligned_cols=48 Identities=23% Similarity=0.452 Sum_probs=36.4
Q ss_pred CCCCCHHHHHHHHHHHHHh-CCC---hhhhhccCCCCCHHHHHHHHHHHHHHH
Q 024441 67 RGLLTEAEEQLVIDLHARL-GNR---WSKIAARLPGRTDNEIKNHWNTHIKKK 115 (267)
Q Consensus 67 ~~~WT~eED~~Ll~lv~~~-G~~---W~~IA~~lpgRT~~q~knRw~~~l~~~ 115 (267)
...||.-|...|+.+.+.. |.. -..|++.++||+..+|++.-. .||.+
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~-~LK~r 72 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQ-QLKGR 72 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHH-HHHHH
Confidence 4569999999999887765 433 568899999999999988554 44443
No 63
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=65.58 E-value=2.9 Score=43.47 Aligned_cols=44 Identities=18% Similarity=0.209 Sum_probs=39.1
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCccccccccc
Q 024441 14 KGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTN 59 (267)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~ 59 (267)
.-.||+.|-.++.+|+..|. .+.-.|++++. ++|.+||-+-|+.
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~-KDF~~v~km~~-~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYS-KDFIFVQKMVK-SKTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhc-ccHHHHHHHhc-cccHHHHHHHHHH
Confidence 45799999999999999998 67999999998 9999999887653
No 64
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=65.25 E-value=7.1 Score=32.85 Aligned_cols=46 Identities=7% Similarity=0.136 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHhC-CChhhhhccCCCCCHHHHHHHHHHHHHHHHhh
Q 024441 72 EAEEQLVIDLHARLG-NRWSKIAARLPGRTDNEIKNHWNTHIKKKLLK 118 (267)
Q Consensus 72 ~eED~~Ll~lv~~~G-~~W~~IA~~lpgRT~~q~knRw~~~l~~~~~k 118 (267)
.+-|.+|+.+.++-| -.|+.||+.+ |-+...|+.|++.+.+..+.+
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCeE
Confidence 456888888888888 5799999999 999999999998887776543
No 65
>smart00595 MADF subfamily of SANT domain.
Probab=64.30 E-value=7.9 Score=28.72 Aligned_cols=26 Identities=31% Similarity=0.638 Sum_probs=22.1
Q ss_pred hhhhhccCCCCCHHHHHHHHHHHHHHH
Q 024441 89 WSKIAARLPGRTDNEIKNHWNTHIKKK 115 (267)
Q Consensus 89 W~~IA~~lpgRT~~q~knRw~~~l~~~ 115 (267)
|..||..| |-+..+|+.+|+++....
T Consensus 30 W~~Ia~~l-~~~~~~~~~kw~~LR~~y 55 (89)
T smart00595 30 WEEIAEEL-GLSVEECKKRWKNLRDRY 55 (89)
T ss_pred HHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 99999999 559999999998876553
No 66
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=63.57 E-value=3.1 Score=34.57 Aligned_cols=44 Identities=11% Similarity=0.215 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHhCCCCCchhchhhcCccCCcccccccccccCCC
Q 024441 19 AEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNYLRPD 64 (267)
Q Consensus 19 ~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L~p~ 64 (267)
.+-|.+|+.++++.|...|.+||+.+| -+...|+.|+.+....+
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lg--lS~~tV~~Ri~rL~~~G 51 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFG--VSPGTIHVRVEKMKQAG 51 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCC
Confidence 357999999999999999999999998 77888999888765544
No 67
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=60.40 E-value=18 Score=31.96 Aligned_cols=45 Identities=16% Similarity=0.220 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHHhCCChhhhhccC---CCCCHHHHHHHHHHHHHH
Q 024441 69 LLTEAEEQLVIDLHARLGNRWSKIAARL---PGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 69 ~WT~eED~~Ll~lv~~~G~~W~~IA~~l---pgRT~~q~knRw~~~l~~ 114 (267)
.|++.+|-+|+.+|.. |+.-..|++-+ -.-|-..|..||+.+|--
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd 48 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALLYD 48 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHHcC
Confidence 5999999999999865 55566666544 345889999999998865
No 68
>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=59.95 E-value=6.9 Score=29.38 Aligned_cols=44 Identities=23% Similarity=0.601 Sum_probs=29.8
Q ss_pred CCCHHHHHHHHHHHHHh---CC----C-----CCchhchhh----cCccCCccccccccc
Q 024441 16 PWTAEEDKKLINFILTN---GQ----C-----CWRAVPKLA----GLRRCGKSCRLRWTN 59 (267)
Q Consensus 16 ~WT~eED~~L~~~v~~~---g~----~-----~W~~IA~~~----~~~Rt~~QCr~Rw~~ 59 (267)
.||+++++.|++++... |. . .|..|++.+ +...+..||..||..
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 59999999999888653 11 1 377787655 334556777777654
No 69
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=59.67 E-value=3.1 Score=35.01 Aligned_cols=45 Identities=18% Similarity=0.263 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHHhCCCCCchhchhhcCccCCcccccccccccCCCC
Q 024441 19 AEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNYLRPDL 65 (267)
Q Consensus 19 ~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L~p~~ 65 (267)
.+-|.+|+.++++.+...|.+||+.+| -+...|+.|+.+..+.++
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lg--lS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVG--LSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 567999999999999999999999998 777889988887655443
No 70
>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=59.23 E-value=9.5 Score=28.90 Aligned_cols=17 Identities=24% Similarity=0.530 Sum_probs=10.2
Q ss_pred CCCCCCCCCHHHHHHHH
Q 024441 63 PDLKRGLLTEAEEQLVI 79 (267)
Q Consensus 63 p~~~~~~WT~eED~~Ll 79 (267)
|....|-||+++|..|.
T Consensus 43 P~n~~GiWT~eDD~~L~ 59 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLR 59 (87)
T ss_dssp -TT-TT---HHHHHHHT
T ss_pred CCCCCCCcCHHHHHHHH
Confidence 66678889999999984
No 71
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=59.21 E-value=9.5 Score=38.85 Aligned_cols=50 Identities=22% Similarity=0.334 Sum_probs=43.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 65 LKRGLLTEAEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 65 ~~~~~WT~eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
...++|+.+|-++-..+....|.+.+.|+..+|+|...|||.+|..--++
T Consensus 407 ~~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~eE~r 456 (584)
T KOG2009|consen 407 LETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKEEKR 456 (584)
T ss_pred cccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhhhhc
Confidence 34567999999999999999999999999999999999999999754433
No 72
>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=58.62 E-value=21 Score=26.79 Aligned_cols=39 Identities=15% Similarity=0.375 Sum_probs=28.3
Q ss_pred HHHHHHHHHhCC--------ChhhhhccCCC---CC--HHHHHHHHHHHHHH
Q 024441 76 QLVIDLHARLGN--------RWSKIAARLPG---RT--DNEIKNHWNTHIKK 114 (267)
Q Consensus 76 ~~Ll~lv~~~G~--------~W~~IA~~lpg---RT--~~q~knRw~~~l~~ 114 (267)
-.|-.+|.+.|+ +|..||+.|.- -+ ..++|..|..+|.+
T Consensus 39 ~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 39 YKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp HHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred HHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 457777888773 59999999821 22 47899999887754
No 73
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=57.15 E-value=81 Score=30.68 Aligned_cols=43 Identities=16% Similarity=0.119 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHHHHhCCChhhhhc-cCCCCCHHHHHHHHHHH
Q 024441 69 LLTEAEEQLVIDLHARLGNRWSKIAA-RLPGRTDNEIKNHWNTH 111 (267)
Q Consensus 69 ~WT~eED~~Ll~lv~~~G~~W~~IA~-~lpgRT~~q~knRw~~~ 111 (267)
.|+++|=...-+.++.||..+..|.+ .++.|+--.|-..|+..
T Consensus 279 ~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlW 322 (445)
T KOG4329|consen 279 GWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLW 322 (445)
T ss_pred cCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHh
Confidence 59999999999999999999999966 67999999998877543
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=56.46 E-value=21 Score=28.45 Aligned_cols=30 Identities=23% Similarity=0.395 Sum_probs=24.8
Q ss_pred HhCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 84 RLGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 84 ~~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
..|-.+.+||+.+ |.+...|+++....+++
T Consensus 127 ~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 127 FEGKSYKEIAEEL-GISVKTVEYHISKALKE 156 (161)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3467899999999 99999999999775544
No 75
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=55.25 E-value=25 Score=26.64 Aligned_cols=40 Identities=18% Similarity=0.327 Sum_probs=30.0
Q ss_pred HHHHHHHHHhCC--------ChhhhhccCCC-----CCHHHHHHHHHHHHHHH
Q 024441 76 QLVIDLHARLGN--------RWSKIAARLPG-----RTDNEIKNHWNTHIKKK 115 (267)
Q Consensus 76 ~~Ll~lv~~~G~--------~W~~IA~~lpg-----RT~~q~knRw~~~l~~~ 115 (267)
-.|..+|.+.|+ .|..||+.|.- ....+++..|..+|.+-
T Consensus 35 ~~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~y 87 (93)
T smart00501 35 YRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLPF 87 (93)
T ss_pred HHHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHHH
Confidence 457777888774 59999998822 24678899999888764
No 76
>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=53.21 E-value=14 Score=31.40 Aligned_cols=40 Identities=25% Similarity=0.241 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHHHHH
Q 024441 69 LLTEAEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKNHWN 109 (267)
Q Consensus 69 ~WT~eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knRw~ 109 (267)
.||.|..++|.+|-.+ |-.=++||+.|.|.|.++|.-+-+
T Consensus 2 ~Wtde~~~~L~~lw~~-G~SasqIA~~lg~vsRnAViGk~h 41 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GLSASQIARQLGGVSRNAVIGKAH 41 (162)
T ss_pred CCCHHHHHHHHHHHHc-CCCHHHHHHHhCCcchhhhhhhhh
Confidence 4999999999888744 777899999997799999987664
No 77
>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=51.82 E-value=18 Score=27.38 Aligned_cols=29 Identities=28% Similarity=0.614 Sum_probs=23.6
Q ss_pred HHHHHHHHHHhCCChhhhhccCCCCCHHHH
Q 024441 75 EQLVIDLHARLGNRWSKIAARLPGRTDNEI 104 (267)
Q Consensus 75 D~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~ 104 (267)
|+.|..+....|..|..+|++| |=|..+|
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I 30 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDI 30 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 4668889999999999999999 6555544
No 78
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=46.88 E-value=36 Score=26.46 Aligned_cols=49 Identities=16% Similarity=0.194 Sum_probs=33.3
Q ss_pred CCCCHHHHHHHHHHHHHh----CC----Chhhh----hccC-CCCCHHHHHHHHHHHHHHHH
Q 024441 68 GLLTEAEEQLVIDLHARL----GN----RWSKI----AARL-PGRTDNEIKNHWNTHIKKKL 116 (267)
Q Consensus 68 ~~WT~eED~~Ll~lv~~~----G~----~W~~I----A~~l-pgRT~~q~knRw~~~l~~~~ 116 (267)
..||++++..||+++..| |. .|..+ ...+ ..=+..|+.++.+.+.++..
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~ 66 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYR 66 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHH
Confidence 469999999999998776 52 34443 3333 22378898888877666543
No 79
>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=45.99 E-value=22 Score=25.52 Aligned_cols=27 Identities=22% Similarity=0.489 Sum_probs=21.6
Q ss_pred hhhhhccCC-CCCHHHHHHHHHHHHHHH
Q 024441 89 WSKIAARLP-GRTDNEIKNHWNTHIKKK 115 (267)
Q Consensus 89 W~~IA~~lp-gRT~~q~knRw~~~l~~~ 115 (267)
|..||..|. .-+...|+.||..+....
T Consensus 29 w~~Ia~~l~~~~~~~~~~~~w~~Lr~~y 56 (85)
T PF10545_consen 29 WQEIARELGKEFSVDDCKKRWKNLRDRY 56 (85)
T ss_pred HHHHHHHHccchhHHHHHHHHHHHHHHH
Confidence 999999994 357889999998866653
No 80
>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=44.60 E-value=49 Score=27.97 Aligned_cols=46 Identities=17% Similarity=0.221 Sum_probs=38.4
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCChhhhhccCC----CCCHHHHHHHHHHH
Q 024441 66 KRGLLTEAEEQLVIDLHARLGNRWSKIAARLP----GRTDNEIKNHWNTH 111 (267)
Q Consensus 66 ~~~~WT~eED~~Ll~lv~~~G~~W~~IA~~lp----gRT~~q~knRw~~~ 111 (267)
....-|..|..-|..|+.+||.++..+|.-.. -.|..||+.+...+
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 34468999999999999999999999998653 47999999887654
No 81
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=44.32 E-value=38 Score=25.84 Aligned_cols=45 Identities=9% Similarity=0.200 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHhC-CChhhhhccCCCCCHHHHHHHHHHHHHHHHhh
Q 024441 73 AEEQLVIDLHARLG-NRWSKIAARLPGRTDNEIKNHWNTHIKKKLLK 118 (267)
Q Consensus 73 eED~~Ll~lv~~~G-~~W~~IA~~lpgRT~~q~knRw~~~l~~~~~k 118 (267)
+.|..|+.+..+.| -.+..||+.+ |-+...|+.+...+.+..+.+
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 46788888888877 4699999999 999999999998887766543
No 82
>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=43.53 E-value=41 Score=21.70 Aligned_cols=34 Identities=29% Similarity=0.321 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHhCCChhhhhccCCCCCHHHHHHHH
Q 024441 74 EEQLVIDLHARLGNRWSKIAARLPGRTDNEIKNHW 108 (267)
Q Consensus 74 ED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knRw 108 (267)
|-..|.++...++++-.+.|+.| |=+...+..|-
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~kl 39 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLL-GISRRTLYRKL 39 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHH
Confidence 66788899999999999999998 77777665554
No 83
>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=41.84 E-value=44 Score=25.79 Aligned_cols=30 Identities=27% Similarity=0.282 Sum_probs=24.3
Q ss_pred HhCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 84 RLGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 84 ~~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
..|..+..||+.+ |-+...|+++....+++
T Consensus 124 ~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 124 LEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred hcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3577899999999 77999999988775554
No 84
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=41.68 E-value=26 Score=38.77 Aligned_cols=75 Identities=16% Similarity=0.220 Sum_probs=48.6
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCcccccccccccCCCCCCCCCCHHHHHHHHHHHHHh-CCChhhh
Q 024441 14 KGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNYLRPDLKRGLLTEAEEQLVIDLHARL-GNRWSKI 92 (267)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L~p~~~~~~WT~eED~~Ll~lv~~~-G~~W~~I 92 (267)
---|..++|..|+-.|-+||-.+|.+|-.-. .-|..- ...+...+..+.+-...-..|+.+..++ +.+|.+.
T Consensus 1133 ~~~W~~e~Ds~LLiGI~khGygswe~Ir~Dp------~L~l~d-Ki~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~~ 1205 (1373)
T KOG0384|consen 1133 DCDWGSEDDSMLLIGIFKHGYGSWEAIRLDP------DLGLTD-KIFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPKK 1205 (1373)
T ss_pred ccCCCchhhhhHhhhhhhcccccHHHhccCc------cccchh-hhcccccCCchHHHHHHHHHHHHHHhhcccCCCchh
Confidence 4569999999999999999999999995211 111110 1122222445567777777788777776 5566665
Q ss_pred hcc
Q 024441 93 AAR 95 (267)
Q Consensus 93 A~~ 95 (267)
++.
T Consensus 1206 ~~~ 1208 (1373)
T KOG0384|consen 1206 LKR 1208 (1373)
T ss_pred hhc
Confidence 543
No 85
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=41.60 E-value=1.2e+02 Score=29.65 Aligned_cols=29 Identities=14% Similarity=0.385 Sum_probs=24.7
Q ss_pred ccCCCCccCCCCHHHHHHHHHHHHHhCCC
Q 024441 7 CDKLGVKKGPWTAEEDKKLINFILTNGQC 35 (267)
Q Consensus 7 ~~k~~ikkg~WT~eED~~L~~~v~~~g~~ 35 (267)
.|+.+..-|.|+++=++...+|+..|.++
T Consensus 69 ~D~~~daegvWSpdIEqsFqEALaiyppc 97 (455)
T KOG3841|consen 69 TDNQRDAEGVWSPDIEQSFQEALAIYPPC 97 (455)
T ss_pred CccccccccccChhHHHHHHHHHhhcCCC
Confidence 35556678999999999999999999865
No 86
>PRK04217 hypothetical protein; Provisional
Probab=38.59 E-value=1e+02 Score=24.64 Aligned_cols=46 Identities=17% Similarity=0.116 Sum_probs=36.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 67 RGLLTEAEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 67 ~~~WT~eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
-..-|.+| ..++.+....|-...+||+.+ |-+...|+.++....++
T Consensus 40 ~~~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkk 85 (110)
T PRK04217 40 PIFMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKK 85 (110)
T ss_pred cccCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 33467776 567777777788899999999 99999999998765544
No 87
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=38.36 E-value=29 Score=35.69 Aligned_cols=47 Identities=17% Similarity=0.274 Sum_probs=33.9
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCchhchhhcCc---------cCCccccccccccc
Q 024441 14 KGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLR---------RCGKSCRLRWTNYL 61 (267)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~---------Rt~~QCr~Rw~~~L 61 (267)
|..||..|......++..+| .+..+|-..+-.+ ++-.|.|..|++.+
T Consensus 88 ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~ 143 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLV 143 (782)
T ss_pred ccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHH
Confidence 66899999999999999999 6688884333212 34466777666543
No 88
>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=37.91 E-value=46 Score=25.19 Aligned_cols=29 Identities=24% Similarity=0.413 Sum_probs=23.3
Q ss_pred HHHHHHHHHHhCCChhhhhccCCCCCHHHH
Q 024441 75 EQLVIDLHARLGNRWSKIAARLPGRTDNEI 104 (267)
Q Consensus 75 D~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~ 104 (267)
|..|..+....|..|.++|+.| |=+...|
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI 32 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEI 32 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHH
Confidence 5677888889999999999999 6555444
No 89
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=37.89 E-value=55 Score=26.66 Aligned_cols=30 Identities=13% Similarity=0.128 Sum_probs=23.9
Q ss_pred HhCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 84 RLGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 84 ~~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
..|-....||+.+ |.+...|+.+....+++
T Consensus 142 ~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 171 (182)
T PRK09652 142 IEGLSYEEIAEIM-GCPIGTVRSRIFRAREA 171 (182)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3467899999999 99999999887654444
No 90
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=37.78 E-value=77 Score=25.97 Aligned_cols=29 Identities=24% Similarity=0.349 Sum_probs=23.1
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
.|-.-.+||..| |.+...|+.|....+++
T Consensus 133 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 161 (173)
T PRK09645 133 RGWSTAQIAADL-GIPEGTVKSRLHYALRA 161 (173)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 366689999999 99999999998755543
No 91
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=36.86 E-value=80 Score=26.79 Aligned_cols=36 Identities=22% Similarity=0.295 Sum_probs=27.6
Q ss_pred HHHHHHHHhCCChhhhhccCCCCCHHHHHHHHHHHHH
Q 024441 77 LVIDLHARLGNRWSKIAARLPGRTDNEIKNHWNTHIK 113 (267)
Q Consensus 77 ~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knRw~~~l~ 113 (267)
.++.+..-.|-.+.+||..+ |-|...|+.+|.....
T Consensus 142 ~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR~ 177 (185)
T PF07638_consen 142 RVVELRFFEGLSVEEIAERL-GISERTVRRRLRRARA 177 (185)
T ss_pred HHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 33444444577899999999 9999999999976553
No 92
>PLN03162 golden-2 like transcription factor; Provisional
Probab=36.43 E-value=2.6e+02 Score=27.33 Aligned_cols=44 Identities=18% Similarity=0.102 Sum_probs=35.7
Q ss_pred CCCCHHHHHHHHHHHHHhCCC---hhhhhccC--CCCCHHHHHHHHHHH
Q 024441 68 GLLTEAEEQLVIDLHARLGNR---WSKIAARL--PGRTDNEIKNHWNTH 111 (267)
Q Consensus 68 ~~WT~eED~~Ll~lv~~~G~~---W~~IA~~l--pgRT~~q~knRw~~~ 111 (267)
-.||+|=-++.+++|.++|.. =+.|-+.| +|=|..+|+.|.+.+
T Consensus 238 LrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKY 286 (526)
T PLN03162 238 VDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKY 286 (526)
T ss_pred ccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 359999999999999999932 56676665 889999999887544
No 93
>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=36.32 E-value=26 Score=29.84 Aligned_cols=33 Identities=18% Similarity=0.335 Sum_probs=25.1
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCchhchhhc-CccCC
Q 024441 16 PWTAEEDKKLINFILTNGQCCWRAVPKLAG-LRRCG 50 (267)
Q Consensus 16 ~WT~eED~~L~~~v~~~g~~~W~~IA~~~~-~~Rt~ 50 (267)
.||.|+.++|.++...- ..=.+||+.|| ..|++
T Consensus 2 ~Wtde~~~~L~~lw~~G--~SasqIA~~lg~vsRnA 35 (162)
T PF07750_consen 2 SWTDERVERLRKLWAEG--LSASQIARQLGGVSRNA 35 (162)
T ss_pred CCCHHHHHHHHHHHHcC--CCHHHHHHHhCCcchhh
Confidence 59999999999988543 23589999998 44443
No 94
>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=35.60 E-value=36 Score=25.34 Aligned_cols=29 Identities=28% Similarity=0.652 Sum_probs=22.5
Q ss_pred HHHHHHHHHHhCCChhhhhccCCCCCHHHH
Q 024441 75 EQLVIDLHARLGNRWSKIAARLPGRTDNEI 104 (267)
Q Consensus 75 D~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~ 104 (267)
|..|..+....|..|.++|+.| |=+...|
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI 32 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDI 32 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHH
Confidence 4567788888999999999999 5555444
No 95
>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=35.21 E-value=87 Score=19.51 Aligned_cols=40 Identities=28% Similarity=0.343 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHHHHHHH
Q 024441 70 LTEAEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKNHWNTH 111 (267)
Q Consensus 70 WT~eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knRw~~~ 111 (267)
.++++ ..++.++-..|..+..||..+ |-+...|+.+....
T Consensus 11 l~~~~-~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPERE-REVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRA 50 (55)
T ss_pred CCHHH-HHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 34443 445555545677899999998 78888887665443
No 96
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=35.00 E-value=89 Score=26.05 Aligned_cols=33 Identities=18% Similarity=0.024 Sum_probs=27.5
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHHHHHhh
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIKKKLLK 118 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~~~~~k 118 (267)
.|-...+||..+ |-+...|+.|....++.-+..
T Consensus 142 ~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 142 DGMKQKDIAQAL-DIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHh
Confidence 466799999999 999999999998777766544
No 97
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=34.85 E-value=53 Score=26.53 Aligned_cols=45 Identities=11% Similarity=0.165 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHhC-CChhhhhccCCCCCHHHHHHHHHHHHHHHHhh
Q 024441 73 AEEQLVIDLHARLG-NRWSKIAARLPGRTDNEIKNHWNTHIKKKLLK 118 (267)
Q Consensus 73 eED~~Ll~lv~~~G-~~W~~IA~~lpgRT~~q~knRw~~~l~~~~~k 118 (267)
+-|.+|+++.++-+ ..+..||+.+ |-|...|++|-+.+.+..+.+
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~GiI~ 53 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGVIK 53 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCcee
Confidence 45778888888877 4699999999 999999999998877776443
No 98
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=34.22 E-value=15 Score=35.66 Aligned_cols=49 Identities=12% Similarity=0.184 Sum_probs=40.7
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCCCCCchhchh-----hcCccCCcccccccccc
Q 024441 11 GVKKGPWTAEEDKKLINFILTNGQCCWRAVPKL-----AGLRRCGKSCRLRWTNY 60 (267)
Q Consensus 11 ~ikkg~WT~eED~~L~~~v~~~g~~~W~~IA~~-----~~~~Rt~~QCr~Rw~~~ 60 (267)
.+.-..||++|-+.|..+.++|. -.|-.||.. .+..||--...+||+.+
T Consensus 127 ~l~dn~WskeETD~LF~lck~fD-LRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v 180 (445)
T KOG2656|consen 127 HLNDNSWSKEETDYLFDLCKRFD-LRFFVIADRYDNQQYKKSRTVEDLKERYYSV 180 (445)
T ss_pred hhccccccHHHHHHHHHHHHhcC-eeEEEEeeccchhhccccccHHHHHHHHHHH
Confidence 34557899999999999999998 559999964 66569999999999864
No 99
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=34.21 E-value=98 Score=25.46 Aligned_cols=33 Identities=18% Similarity=0.276 Sum_probs=26.7
Q ss_pred HhCCChhhhhccCCCCCHHHHHHHHHHHHHHHHh
Q 024441 84 RLGNRWSKIAARLPGRTDNEIKNHWNTHIKKKLL 117 (267)
Q Consensus 84 ~~G~~W~~IA~~lpgRT~~q~knRw~~~l~~~~~ 117 (267)
..|-...+||..+ |.+...|+.+....+++-..
T Consensus 133 ~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 133 LDGMGHAEIAERL-GVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 3466799999999 99999999998877666543
No 100
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=33.57 E-value=68 Score=26.00 Aligned_cols=29 Identities=21% Similarity=0.223 Sum_probs=23.3
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
.|-....||..+ |-+...|+++....+++
T Consensus 140 ~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 168 (179)
T PRK11924 140 EGLSYREIAEIL-GVPVGTVKSRLRRARQL 168 (179)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466799999999 99999999988764444
No 101
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=33.05 E-value=98 Score=26.05 Aligned_cols=28 Identities=14% Similarity=0.119 Sum_probs=22.4
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIK 113 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~ 113 (267)
.|-.-..||..| |-+...|+.|....++
T Consensus 151 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~ 178 (195)
T PRK12532 151 LGFSSDEIQQMC-GISTSNYHTIMHRARE 178 (195)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 366789999999 9999999998765333
No 102
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=32.96 E-value=74 Score=26.94 Aligned_cols=29 Identities=17% Similarity=0.217 Sum_probs=23.5
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
.|-...+||..+ |-+...|++|....+++
T Consensus 149 ~g~s~~EIA~~l-g~s~~tV~~rl~rar~~ 177 (192)
T PRK09643 149 QGYSVADAARML-GVAEGTVKSRCARGRAR 177 (192)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 466799999999 99999999998554443
No 103
>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=32.50 E-value=53 Score=24.73 Aligned_cols=25 Identities=32% Similarity=0.621 Sum_probs=19.4
Q ss_pred HHHHHHhCCChhhhhccCCCCCHHHH
Q 024441 79 IDLHARLGNRWSKIAARLPGRTDNEI 104 (267)
Q Consensus 79 l~lv~~~G~~W~~IA~~lpgRT~~q~ 104 (267)
..+....|..|.++|+.| |-+..+|
T Consensus 11 ~~ia~~iG~~Wk~Lar~L-Gls~~dI 35 (86)
T cd08318 11 TVFANKLGEDWKTLAPHL-EMKDKEI 35 (86)
T ss_pred HHHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 335577899999999999 7666655
No 104
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=31.40 E-value=74 Score=21.89 Aligned_cols=36 Identities=39% Similarity=0.560 Sum_probs=23.5
Q ss_pred CCHHHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHHH
Q 024441 70 LTEAEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKNH 107 (267)
Q Consensus 70 WT~eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knR 107 (267)
.|.. |+..+.++...|-.=.+||+.+ ||+...|++.
T Consensus 5 Lt~~-Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~y 40 (50)
T PF11427_consen 5 LTDA-EQAQIDVMHQLGMSLREISRRI-GRSRTCIRRY 40 (50)
T ss_dssp --HH-HHHHHHHHHHTT--HHHHHHHH-T--HHHHHHH
T ss_pred CCHH-HHHHHHHHHHhchhHHHHHHHh-CccHHHHHHH
Confidence 3444 4556677888899999999999 9999888663
No 105
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=30.83 E-value=81 Score=26.05 Aligned_cols=29 Identities=10% Similarity=0.007 Sum_probs=23.4
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
.|....+||..+ |-|...|+++....+++
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 366799999999 99999999988655544
No 106
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=30.57 E-value=23 Score=27.06 Aligned_cols=43 Identities=14% Similarity=0.176 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHhCCCCCchhchhhcCccCCcccccccccccCCC
Q 024441 20 EEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNYLRPD 64 (267)
Q Consensus 20 eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L~p~ 64 (267)
+.|.+++.++...+...+..||+.++ -+...|+.|..+..+.+
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~--~s~~tv~~~l~~L~~~g 45 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVG--LSPSTVHNRVKRLEEEG 45 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCC
Confidence 56889999999998889999999987 66777887776655443
No 107
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=30.55 E-value=97 Score=24.88 Aligned_cols=29 Identities=17% Similarity=0.248 Sum_probs=23.6
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
.|-.-.+||..| |-+...|++|....+++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 121 EDMDVAETAAAM-GCSEGSVKTHCSRATHA 149 (161)
T ss_pred hcCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 356789999999 99999999998765544
No 108
>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=29.95 E-value=51 Score=31.31 Aligned_cols=86 Identities=15% Similarity=0.304 Sum_probs=59.0
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCC---chhchhhcCccCCcccccccccccCCCCCCCCCCHHHHHHHHHHHHH-h----
Q 024441 14 KGPWTAEEDKKLINFILTNGQCCW---RAVPKLAGLRRCGKSCRLRWTNYLRPDLKRGLLTEAEEQLVIDLHAR-L---- 85 (267)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g~~~W---~~IA~~~~~~Rt~~QCr~Rw~~~L~p~~~~~~WT~eED~~Ll~lv~~-~---- 85 (267)
-..||.-|...|+++++....... .+|++.+. +|+..++++- .+.|+ +..+.+++++ |
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~-~Rs~aEI~~f-l~~LK------------~rvareaiqkv~~~g~ 86 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELP-GRSEAEIRDF-LQQLK------------GRVAREAIQKVHPGGL 86 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhcc-CcCHHHHHHH-HHHHH------------HHHHHHHHHHhccccc
Confidence 457999999999999887643434 45566676 7888877663 33332 2334445544 2
Q ss_pred -CCC------------hhhhhccCCCCCHHHHHHHHHHHHH
Q 024441 86 -GNR------------WSKIAARLPGRTDNEIKNHWNTHIK 113 (267)
Q Consensus 86 -G~~------------W~~IA~~lpgRT~~q~knRw~~~l~ 113 (267)
|.+ |..+|..+.|.-...+-.-|-..|.
T Consensus 87 ~~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~ 127 (344)
T PF11035_consen 87 KGPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLT 127 (344)
T ss_pred ccccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHH
Confidence 211 9999999999999999888876654
No 109
>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=29.67 E-value=53 Score=24.44 Aligned_cols=33 Identities=27% Similarity=0.559 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHH
Q 024441 72 EAEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKN 106 (267)
Q Consensus 72 ~eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~kn 106 (267)
+||-++|+..- ..|.+|...|+.| |=+...|++
T Consensus 2 ~~~v~~ll~~~-nlG~dW~~LA~~L-G~~~~~I~~ 34 (77)
T cd08311 2 QEEVEKLLESG-RPGRDWRSLAGEL-GYEDEAIDT 34 (77)
T ss_pred hHHHHHHHhCC-CCccCHHHHHHHc-CCCHHHHHH
Confidence 57778887432 4578899999999 766666644
No 110
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=29.44 E-value=20 Score=29.04 Aligned_cols=42 Identities=7% Similarity=0.159 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHhCCCCCchhchhhcCccCCcccccccccccCC
Q 024441 20 EEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTNYLRP 63 (267)
Q Consensus 20 eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~~L~p 63 (267)
+-|.++++++++.+...+..||+.+| -+...|+.|-.+..+.
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~lg--lS~~~v~~Ri~~L~~~ 49 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERVG--LSPSTVLRRIKRLEEE 49 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--CCHHHHHHHHHHHHHC
Confidence 56889999999999999999999998 7777788776655443
No 111
>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=29.27 E-value=63 Score=24.30 Aligned_cols=31 Identities=26% Similarity=0.503 Sum_probs=24.1
Q ss_pred HHHHHHHHHHhCCChhhhhccCCCCCHHHHHH
Q 024441 75 EQLVIDLHARLGNRWSKIAARLPGRTDNEIKN 106 (267)
Q Consensus 75 D~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~kn 106 (267)
|..|..+....|.+|..+|+.| |=+...|.+
T Consensus 4 ~~~l~~ia~~LG~dWk~LAr~L-g~se~dI~~ 34 (84)
T cd08804 4 EERLAVIADHLGFSWTELAREL-DFTEEQIHQ 34 (84)
T ss_pred hhHHHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 4567777788999999999999 666666644
No 112
>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=28.79 E-value=58 Score=24.68 Aligned_cols=29 Identities=34% Similarity=0.629 Sum_probs=22.4
Q ss_pred HHHHHHHHhCCChhhhhccCCCCCHHHHHH
Q 024441 77 LVIDLHARLGNRWSKIAARLPGRTDNEIKN 106 (267)
Q Consensus 77 ~Ll~lv~~~G~~W~~IA~~lpgRT~~q~kn 106 (267)
.|-.+....|..|..+|+.| |=+..+|..
T Consensus 4 ~l~~l~~~lG~~Wk~lar~L-G~s~~eI~~ 32 (86)
T cd08777 4 HLDLLRENLGKKWKRCARKL-GFTESEIEE 32 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHc-CCCHHHHHH
Confidence 34555677899999999999 777777654
No 113
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=28.75 E-value=1.3e+02 Score=24.84 Aligned_cols=31 Identities=13% Similarity=0.189 Sum_probs=24.9
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIKKKL 116 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~~~~ 116 (267)
.|....+||..| |-+...|+.+....+++-.
T Consensus 146 ~g~s~~eIA~~l-~is~~tV~~~l~ra~~~Lr 176 (184)
T PRK12512 146 EGASIKETAAKL-SMSEGAVRVALHRGLAALA 176 (184)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 366789999999 9999999999876665543
No 114
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=28.34 E-value=26 Score=34.80 Aligned_cols=44 Identities=16% Similarity=0.059 Sum_probs=37.0
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCcccccccc
Q 024441 13 KKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWT 58 (267)
Q Consensus 13 kkg~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~ 58 (267)
....||.||--++.++...|| .+..+|-+.++ .|+-..++.-|.
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~G-K~F~kIrq~LP-~rsLaSlvqyYy 229 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFG-KDFHKIRQALP-HRSLASLVQYYY 229 (534)
T ss_pred CcccchHHHHHHHHHHHHHhc-ccHHHHHHHcc-CccHHHHHHHHH
Confidence 467899999999999999999 56999999888 888776666554
No 115
>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=28.25 E-value=75 Score=26.33 Aligned_cols=28 Identities=11% Similarity=0.116 Sum_probs=22.9
Q ss_pred CCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 86 GNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 86 G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
|....+||..+ |-|...|+++....+++
T Consensus 154 ~~s~~EIA~~l-gis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 154 GLSYEDIARIM-DCPVGTVRSRIFRAREA 181 (190)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 56789999999 88999999998765554
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=28.08 E-value=98 Score=25.28 Aligned_cols=29 Identities=17% Similarity=0.245 Sum_probs=23.2
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
.|-....||..+ |-|...|+++....+++
T Consensus 134 ~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~ 162 (169)
T TIGR02954 134 HDLTIKEIAEVM-NKPEGTVKTYLHRALKK 162 (169)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 356789999999 88999999998765554
No 117
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=27.84 E-value=1e+02 Score=25.92 Aligned_cols=29 Identities=24% Similarity=0.161 Sum_probs=23.7
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
.|-....||..| |-+...|+++....+++
T Consensus 121 ~g~~~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (181)
T PRK09637 121 EGLSQKEIAEKL-GLSLSGAKSRVQRGRVK 149 (181)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 467799999999 99999999998755544
No 118
>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=27.43 E-value=66 Score=21.83 Aligned_cols=44 Identities=32% Similarity=0.367 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHHHHHHHHHHH
Q 024441 69 LLTEAEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKNHWNTHIKKK 115 (267)
Q Consensus 69 ~WT~eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knRw~~~l~~~ 115 (267)
..|+.|-+.|.-+.. |..=.+||..+ |.+...|+.+...++++-
T Consensus 3 ~LT~~E~~vl~~l~~--G~~~~eIA~~l-~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ--GMSNKEIAEEL-GISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHT--TS-HHHHHHHH-TSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHh--cCCcchhHHhc-CcchhhHHHHHHHHHHHh
Confidence 356677665554433 55568999999 999999999887777663
No 119
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=27.23 E-value=88 Score=27.28 Aligned_cols=45 Identities=27% Similarity=0.316 Sum_probs=35.7
Q ss_pred CCCCHHHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHHHHHHHHHHH
Q 024441 68 GLLTEAEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKNHWNTHIKKK 115 (267)
Q Consensus 68 ~~WT~eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knRw~~~l~~~ 115 (267)
...|+.|-+.|.-+.+ |-.=++||..| +.+...||+|..++++|-
T Consensus 147 ~~LT~RE~eVL~lla~--G~snkeIA~~L-~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 147 ELLTPRELEVLRLLAE--GLSNKEIAEEL-NLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCCCHHHHHHHHHHHC--CCCHHHHHHHH-CCCHhHHHHHHHHHHHHc
Confidence 3688888876665544 44447999999 999999999999988874
No 120
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=27.06 E-value=1.1e+02 Score=25.54 Aligned_cols=29 Identities=14% Similarity=0.141 Sum_probs=23.4
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
.|-....||..| |-|...|+++....+++
T Consensus 146 ~~~s~~eIA~~l-gis~~tV~~~l~Rar~~ 174 (189)
T PRK12515 146 HEKSVEEVGEIV-GIPESTVKTRMFYARKK 174 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 466789999999 88999999998765443
No 121
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=26.78 E-value=1.2e+02 Score=24.47 Aligned_cols=29 Identities=10% Similarity=-0.026 Sum_probs=23.0
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
.|-.-.+||..+ |-+...|++|....+++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (160)
T PRK09642 121 EEKSYQEIALQE-KIEVKTVEMKLYRARKW 149 (160)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 356689999999 99999999997654443
No 122
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=26.49 E-value=1.2e+02 Score=25.39 Aligned_cols=29 Identities=14% Similarity=0.232 Sum_probs=23.7
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
.|....+||..+ |-+...|+.+....+++
T Consensus 154 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 154 VGLSAEETAEAV-GSTPGAVRVAQHRALAR 182 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 366799999999 99999999998765554
No 123
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=26.45 E-value=1.2e+02 Score=25.60 Aligned_cols=29 Identities=14% Similarity=0.037 Sum_probs=23.6
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
.|.....||..| |-+...|+.|....+++
T Consensus 146 ~g~s~~EIA~~l-gis~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 146 LGFESDEICQEL-EISTSNCHVLLYRARLS 174 (188)
T ss_pred hCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 466789999999 99999999998765544
No 124
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=26.32 E-value=1.2e+02 Score=25.64 Aligned_cols=28 Identities=11% Similarity=0.108 Sum_probs=23.1
Q ss_pred CCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 86 GNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 86 G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
|-...+||..| |-+...|+.|....+++
T Consensus 157 g~s~~EIA~~l-gis~~tVk~rl~ra~~~ 184 (194)
T PRK12531 157 ELPHQQVAEMF-DIPLGTVKSRLRLAVEK 184 (194)
T ss_pred CCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 66789999999 99999999998765554
No 125
>PRK01905 DNA-binding protein Fis; Provisional
Probab=26.25 E-value=1.4e+02 Score=21.88 Aligned_cols=36 Identities=22% Similarity=0.258 Sum_probs=27.6
Q ss_pred CHHHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHHH
Q 024441 71 TEAEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKNH 107 (267)
Q Consensus 71 T~eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knR 107 (267)
..-|...+.+++..+|++..+.|+.+ |=+...++.+
T Consensus 35 ~~~E~~~i~~aL~~~~gn~s~aAr~L-GIsrstL~rk 70 (77)
T PRK01905 35 SCVEKPLLEVVMEQAGGNQSLAAEYL-GINRNTLRKK 70 (77)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHH
Confidence 34467788899999999999999988 6566555444
No 126
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=26.18 E-value=38 Score=34.63 Aligned_cols=49 Identities=14% Similarity=0.268 Sum_probs=42.3
Q ss_pred CCCCccCCCCHHHHHHHHHHHHHhCCCCCchhchhhcCccCCccccccccc
Q 024441 9 KLGVKKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLRRCGKSCRLRWTN 59 (267)
Q Consensus 9 k~~ikkg~WT~eED~~L~~~v~~~g~~~W~~IA~~~~~~Rt~~QCr~Rw~~ 59 (267)
.+....++||.+|-++...++...| .+...|+..++ .|..+|++.+|..
T Consensus 404 sk~~~~~~w~~se~e~fyka~~~~g-s~~slis~l~p-~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 404 SKKLETDKWDASETELFYKALSERG-SDFSLISNLFP-LRDRKQIKAKFKK 452 (584)
T ss_pred cCccccCcccchhhHHhhhHHhhhc-ccccccccccc-cccHHHHHHHHhh
Confidence 3455788999999999999999999 56999999887 9999999887754
No 127
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=26.15 E-value=73 Score=23.25 Aligned_cols=29 Identities=28% Similarity=0.606 Sum_probs=20.3
Q ss_pred HHHHHHHHHH-hCCChhhhhccCCCCCHHHH
Q 024441 75 EQLVIDLHAR-LGNRWSKIAARLPGRTDNEI 104 (267)
Q Consensus 75 D~~Ll~lv~~-~G~~W~~IA~~lpgRT~~q~ 104 (267)
.+.|..++.. .|..|..+|+.| |=+..+|
T Consensus 5 ~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i 34 (88)
T smart00005 5 REKLAKLLDHPLGLDWRELARKL-GLSEADI 34 (88)
T ss_pred HHHHHHHHcCccchHHHHHHHHc-CCCHHHH
Confidence 3456666666 789999999999 4444443
No 128
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=25.97 E-value=1e+02 Score=25.44 Aligned_cols=28 Identities=11% Similarity=0.041 Sum_probs=22.5
Q ss_pred CCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 86 GNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 86 G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
|..-.+||..+ |.+...|+++....+++
T Consensus 152 g~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T TIGR02948 152 DLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 56689999999 88999999988665544
No 129
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=25.42 E-value=1.2e+02 Score=25.51 Aligned_cols=28 Identities=7% Similarity=-0.065 Sum_probs=23.0
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIK 113 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~ 113 (267)
.|-...+||..| |-+...|+.|....++
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~RAr~ 176 (189)
T PRK12530 149 LELSSEQICQEC-DISTSNLHVLLYRARL 176 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 366799999999 9999999999765444
No 130
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=25.00 E-value=1.1e+02 Score=25.53 Aligned_cols=28 Identities=11% Similarity=0.128 Sum_probs=22.4
Q ss_pred CCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 86 GNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 86 G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
|-....||..+ |-+...|++|....+++
T Consensus 154 g~s~~eIA~~l-gis~~tv~~~l~Rar~~ 181 (193)
T PRK11923 154 GLSYEDIASVM-QCPVGTVRSRIFRAREA 181 (193)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 55689999999 88999999998755444
No 131
>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=24.48 E-value=78 Score=23.87 Aligned_cols=21 Identities=29% Similarity=0.615 Sum_probs=18.8
Q ss_pred HHHHHHHHHhCCChhhhhccC
Q 024441 76 QLVIDLHARLGNRWSKIAARL 96 (267)
Q Consensus 76 ~~Ll~lv~~~G~~W~~IA~~l 96 (267)
..|..+....|..|..+|+.|
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L 23 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL 23 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc
Confidence 457888899999999999999
No 132
>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=24.04 E-value=1.9e+02 Score=23.04 Aligned_cols=47 Identities=15% Similarity=0.360 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHHHh------------CC-----------------C--hhhhhccCCCCCHHHHHHHHHHHHHHH
Q 024441 69 LLTEAEEQLVIDLHARL------------GN-----------------R--WSKIAARLPGRTDNEIKNHWNTHIKKK 115 (267)
Q Consensus 69 ~WT~eED~~Ll~lv~~~------------G~-----------------~--W~~IA~~lpgRT~~q~knRw~~~l~~~ 115 (267)
++|.+||..|...|.++ |. . ....++..|..|.++=|.||+..+...
T Consensus 1 kfTA~dDY~Lc~~i~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~fF~~~~~~~p~HT~~sWRDR~RKfv~~~ 78 (105)
T PF09197_consen 1 KFTADDDYALCKAIKKQFYRDIYQKDPDTGSSLISDGDSKEFIPKRDMRSFFKDLARKNPRHTENSWRDRYRKFVSEY 78 (105)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHSB-TTSS-B----------------TTHHHHHHHHTTTS-HHHHHHHHHHTHHHH
T ss_pred CCChHHHHHHHHHHHHHHHHHHHhhCcccccccccCCCccccccchhhHHHHHHHHHcCCccchhHHHHHHHHHHHHc
Confidence 47999999999888664 11 0 456678889999999999999877764
No 133
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=23.94 E-value=1.3e+02 Score=25.32 Aligned_cols=29 Identities=10% Similarity=-0.025 Sum_probs=23.2
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
.|-.+.+||+.+ |-+...|+++....+++
T Consensus 151 ~g~s~~eIA~~l-gis~~tV~~~l~Ra~~~ 179 (196)
T PRK12524 151 EGLSNPEIAEVM-EIGVEAVESLTARGKRA 179 (196)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 466799999999 88999999887655444
No 134
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=23.89 E-value=1.5e+02 Score=23.88 Aligned_cols=28 Identities=25% Similarity=0.381 Sum_probs=22.6
Q ss_pred CCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 86 GNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 86 G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
|-.-..||..| |-+...|+.|....++.
T Consensus 121 ~~s~~eIA~~l-gis~~tv~~~l~ra~~~ 148 (159)
T PRK12527 121 GLSHQQIAEHL-GISRSLVEKHIVNAMKH 148 (159)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 55678999999 99999999998755544
No 135
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=23.80 E-value=1.6e+02 Score=22.68 Aligned_cols=34 Identities=15% Similarity=0.151 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHHH
Q 024441 73 AEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKNH 107 (267)
Q Consensus 73 eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knR 107 (267)
-|...|..++..++++..+.|+.+ |=+...++.+
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~L-GIsRsTL~rK 88 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALML-GINRGTLRKK 88 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHH
Confidence 477788899999999999999998 6666655443
No 136
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=23.15 E-value=79 Score=20.59 Aligned_cols=36 Identities=31% Similarity=0.407 Sum_probs=17.8
Q ss_pred CCCHHHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHH
Q 024441 69 LLTEAEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKN 106 (267)
Q Consensus 69 ~WT~eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~kn 106 (267)
.+|.+|-..|..+ ..-|..=.+||+.| ||+...|.+
T Consensus 4 ~Lt~~eR~~I~~l-~~~G~s~~~IA~~l-g~s~sTV~r 39 (44)
T PF13936_consen 4 HLTPEERNQIEAL-LEQGMSIREIAKRL-GRSRSTVSR 39 (44)
T ss_dssp --------HHHHH-HCS---HHHHHHHT-T--HHHHHH
T ss_pred chhhhHHHHHHHH-HHcCCCHHHHHHHH-CcCcHHHHH
Confidence 4677776666655 45677789999999 999988854
No 137
>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=22.68 E-value=1.5e+02 Score=23.90 Aligned_cols=28 Identities=29% Similarity=0.283 Sum_probs=22.4
Q ss_pred CCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 86 GNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 86 G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
|-.-.+||+.| |-+...|+++-...+++
T Consensus 138 g~s~~eIA~~l-~is~~tv~~~l~ra~~~ 165 (170)
T TIGR02952 138 NLPIAEVARIL-GKTEGAVKILQFRAIKK 165 (170)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 66789999999 99999999987655444
No 138
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=22.11 E-value=1.4e+02 Score=24.97 Aligned_cols=30 Identities=20% Similarity=0.173 Sum_probs=24.3
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIKKK 115 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~~~ 115 (267)
.|-.-.+||..+ |-+...|+.|....+++-
T Consensus 145 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~L 174 (185)
T PRK09649 145 LGLSYADAAAVC-GCPVGTIRSRVARARDAL 174 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 355689999999 999999999987665544
No 139
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=21.93 E-value=1.5e+02 Score=24.33 Aligned_cols=28 Identities=18% Similarity=0.272 Sum_probs=22.9
Q ss_pred CCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 86 GNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 86 G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
|-.-..||..| |.+...|+++....+++
T Consensus 145 g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 172 (179)
T PRK12514 145 GLSYKELAERH-DVPLNTMRTWLRRSLLK 172 (179)
T ss_pred CCCHHHHHHHH-CCChHHHHHHHHHHHHH
Confidence 56689999999 99999999988665544
No 140
>PRK00118 putative DNA-binding protein; Validated
Probab=21.67 E-value=1.8e+02 Score=22.96 Aligned_cols=40 Identities=10% Similarity=0.092 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHhCCChhhhhccCCCCCHHHHHHHHHHHHH
Q 024441 73 AEEQLVIDLHARLGNRWSKIAARLPGRTDNEIKNHWNTHIK 113 (267)
Q Consensus 73 eED~~Ll~lv~~~G~~W~~IA~~lpgRT~~q~knRw~~~l~ 113 (267)
+.+..++.+....|-....||+.+ |-|...|+.+....++
T Consensus 20 ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~RArk 59 (104)
T PRK00118 20 EKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKRTEK 59 (104)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 445666677777788899999999 9999999888765443
No 141
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=21.41 E-value=1.8e+02 Score=23.18 Aligned_cols=28 Identities=18% Similarity=0.245 Sum_probs=22.1
Q ss_pred CCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 86 GNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 86 G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
|-...+||..+ |-+...|+++-...+++
T Consensus 122 ~~s~~EIA~~l-~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 122 GKTMGEIALET-EMTYYQVRWIYRQALEK 149 (154)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 55688999998 99999999987665544
No 142
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=21.24 E-value=1.7e+02 Score=24.32 Aligned_cols=30 Identities=17% Similarity=0.134 Sum_probs=24.5
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIKKK 115 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~~~ 115 (267)
.|-...+||..| |.+...|+++-...+++-
T Consensus 144 ~g~s~~EIA~~l-~is~~tV~~~l~rar~~L 173 (181)
T PRK12536 144 EGLSVAETAQLT-GLSESAVKVGIHRGLKAL 173 (181)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 466789999999 999999999987655543
No 143
>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=21.16 E-value=1.7e+02 Score=24.02 Aligned_cols=28 Identities=21% Similarity=0.287 Sum_probs=23.1
Q ss_pred CCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 86 GNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 86 G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
|-...+||..+ |-+...|+.|....+++
T Consensus 150 g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 177 (183)
T TIGR02999 150 GLTVEEIAELL-GVSVRTVERDWRFARAW 177 (183)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 56789999999 99999999998765544
No 144
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=20.86 E-value=1.8e+02 Score=23.40 Aligned_cols=29 Identities=24% Similarity=0.281 Sum_probs=23.5
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
.|-...+||..+ |-+...|+.|....++.
T Consensus 128 ~g~s~~EIA~~l-~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 128 DGLGYGEIATEL-GISLATVKRYLNKAAMR 156 (161)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466789999999 99999999998765543
No 145
>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=20.81 E-value=1.1e+02 Score=23.19 Aligned_cols=22 Identities=27% Similarity=0.536 Sum_probs=18.7
Q ss_pred HHHHHHHHHHhCCChhhhhccC
Q 024441 75 EQLVIDLHARLGNRWSKIAARL 96 (267)
Q Consensus 75 D~~Ll~lv~~~G~~W~~IA~~l 96 (267)
|..|..+....|..|.++|+.|
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L 25 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL 25 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc
Confidence 4567778888999999999998
No 146
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=20.76 E-value=1.7e+02 Score=24.70 Aligned_cols=29 Identities=21% Similarity=0.198 Sum_probs=23.4
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
.|-...+||..| |-+...|+.|-...+++
T Consensus 131 ~g~s~~EIA~~L-gis~~tVk~~l~Rar~~ 159 (187)
T PRK12516 131 SGFAYEEAAEIC-GCAVGTIKSRVNRARQR 159 (187)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 467799999999 99999999997655443
No 147
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.64 E-value=2.4e+02 Score=21.82 Aligned_cols=46 Identities=20% Similarity=0.345 Sum_probs=35.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChhhhhccCCCC-CHHHHHHHHHHHHHH
Q 024441 67 RGLLTEAEEQLVIDLHARLGNRWSKIAARLPGR-TDNEIKNHWNTHIKK 114 (267)
Q Consensus 67 ~~~WT~eED~~Ll~lv~~~G~~W~~IA~~lpgR-T~~q~knRw~~~l~~ 114 (267)
+..||.|.-..+++++..-|..=+.||+.+ |- ..++++ +|...+..
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~-~W~~~~~~ 51 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLY-KWRIQLQK 51 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHH-HHHHHHHH
Confidence 567999999999999999888889999999 75 665554 46544443
No 148
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=20.63 E-value=1.7e+02 Score=24.16 Aligned_cols=29 Identities=24% Similarity=0.314 Sum_probs=23.9
Q ss_pred CCChhhhhccCCCCCHHHHHHHHHHHHHHH
Q 024441 86 GNRWSKIAARLPGRTDNEIKNHWNTHIKKK 115 (267)
Q Consensus 86 G~~W~~IA~~lpgRT~~q~knRw~~~l~~~ 115 (267)
|-...+||+.+ |-+...|++|....++.-
T Consensus 135 g~s~~EIA~~l-gis~~tV~~~l~Ra~~~~ 163 (172)
T PRK09651 135 GLTYSEIAHKL-GVSVSSVKKYVAKATEHC 163 (172)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 55689999999 999999999987666553
No 149
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=20.45 E-value=1.9e+02 Score=23.57 Aligned_cols=30 Identities=20% Similarity=0.152 Sum_probs=23.8
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIKKK 115 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~~~ 115 (267)
.|-.-..||..+ |-+...|+++-...+++-
T Consensus 127 ~g~s~~eIA~~l-gis~~tV~~~l~Rar~~L 156 (164)
T PRK12547 127 SGFSYEDAAAIC-GCAVGTIKSRVSRARNRL 156 (164)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 356789999999 899999999887655543
No 150
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=20.25 E-value=1.8e+02 Score=24.18 Aligned_cols=29 Identities=14% Similarity=0.398 Sum_probs=23.5
Q ss_pred hCCChhhhhccCCCCCHHHHHHHHHHHHHH
Q 024441 85 LGNRWSKIAARLPGRTDNEIKNHWNTHIKK 114 (267)
Q Consensus 85 ~G~~W~~IA~~lpgRT~~q~knRw~~~l~~ 114 (267)
.|-.-.+||..| |-+...|++|....+++
T Consensus 137 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 165 (185)
T PRK12542 137 YNLTYQEISSVM-GITEANVRKQFERARKR 165 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456789999999 99999999988655544
Done!