Query 041991
Match_columns 325
No_of_seqs 231 out of 1275
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 12:53:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041991.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041991hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03212 Transcription repress 100.0 7.5E-40 1.6E-44 303.5 13.1 132 1-132 10-141 (249)
2 PLN03091 hypothetical protein; 100.0 1.5E-39 3.2E-44 320.7 14.5 161 4-166 2-162 (459)
3 KOG0048 Transcription factor, 100.0 3.8E-39 8.2E-44 299.2 12.5 114 14-127 7-120 (238)
4 KOG0049 Transcription factor, 99.7 6.4E-18 1.4E-22 173.0 9.9 105 7-112 351-456 (939)
5 KOG0049 Transcription factor, 99.6 1.3E-16 2.9E-21 163.5 6.2 119 1-120 283-412 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.6 2.1E-16 4.6E-21 116.7 4.7 60 19-80 1-60 (60)
7 COG5147 REB1 Myb superfamily p 99.6 2.4E-15 5.1E-20 153.1 5.7 108 11-119 15-122 (512)
8 KOG0050 mRNA splicing protein 99.5 1.7E-14 3.7E-19 145.2 6.6 152 13-166 4-160 (617)
9 KOG0051 RNA polymerase I termi 99.4 2.2E-13 4.7E-18 140.3 7.2 102 15-119 383-512 (607)
10 PF00249 Myb_DNA-binding: Myb- 99.4 7.2E-14 1.6E-18 99.4 2.1 48 16-63 1-48 (48)
11 PF00249 Myb_DNA-binding: Myb- 99.4 1.1E-12 2.3E-17 93.4 5.3 46 69-114 1-48 (48)
12 PF13921 Myb_DNA-bind_6: Myb-l 99.2 1.1E-11 2.4E-16 91.4 4.5 46 72-117 1-46 (60)
13 smart00717 SANT SANT SWI3, AD 99.2 2.7E-11 5.9E-16 83.3 5.7 47 69-115 1-48 (49)
14 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 2.2E-10 4.7E-15 77.7 5.8 44 71-114 1-45 (45)
15 PLN03212 Transcription repress 99.1 1.1E-10 2.3E-15 109.5 5.7 57 64-120 20-78 (249)
16 smart00717 SANT SANT SWI3, AD 99.0 1.5E-10 3.2E-15 79.6 3.5 48 16-64 1-48 (49)
17 KOG0048 Transcription factor, 99.0 4.7E-10 1E-14 104.6 4.0 60 64-123 4-65 (238)
18 cd00167 SANT 'SWI3, ADA2, N-Co 98.9 1E-09 2.2E-14 74.4 3.1 45 18-63 1-45 (45)
19 PLN03091 hypothetical protein; 98.9 8.3E-10 1.8E-14 110.5 2.2 54 11-66 62-115 (459)
20 KOG0051 RNA polymerase I termi 98.8 1.1E-08 2.3E-13 106.1 7.0 103 13-117 305-431 (607)
21 COG5147 REB1 Myb superfamily p 98.4 4.9E-08 1.1E-12 100.1 -0.9 94 14-110 289-392 (512)
22 TIGR01557 myb_SHAQKYF myb-like 98.0 8.4E-06 1.8E-10 60.8 3.7 49 15-63 2-54 (57)
23 TIGR01557 myb_SHAQKYF myb-like 97.6 0.00018 3.9E-09 53.7 5.7 47 69-115 3-55 (57)
24 KOG0457 Histone acetyltransfer 97.6 4.4E-05 9.4E-10 76.8 3.0 50 13-63 69-118 (438)
25 PF13325 MCRS_N: N-terminal re 97.6 0.00028 6E-09 65.0 7.8 100 18-119 1-131 (199)
26 KOG0457 Histone acetyltransfer 97.4 0.00027 5.9E-09 71.2 5.9 50 66-115 69-119 (438)
27 KOG0050 mRNA splicing protein 97.3 0.00022 4.8E-09 73.2 4.0 55 66-120 4-59 (617)
28 PF08914 Myb_DNA-bind_2: Rap1 97.1 0.00069 1.5E-08 51.9 4.3 51 69-119 2-62 (65)
29 PF13837 Myb_DNA-bind_4: Myb/S 97.1 0.00051 1.1E-08 53.7 3.3 51 69-119 1-69 (90)
30 TIGR02894 DNA_bind_RsfA transc 97.0 0.0012 2.5E-08 59.0 4.9 52 68-120 3-61 (161)
31 COG5259 RSC8 RSC chromatin rem 96.7 0.00087 1.9E-08 68.2 2.0 46 15-62 278-323 (531)
32 TIGR02894 DNA_bind_RsfA transc 96.6 0.00068 1.5E-08 60.4 1.1 50 14-65 2-57 (161)
33 KOG1279 Chromatin remodeling f 96.6 0.0029 6.2E-08 65.6 5.3 47 68-114 252-298 (506)
34 COG5259 RSC8 RSC chromatin rem 96.6 0.0023 4.9E-08 65.3 4.4 45 69-113 279-323 (531)
35 KOG1279 Chromatin remodeling f 96.6 0.0014 3.1E-08 67.8 2.9 49 12-62 249-297 (506)
36 PF13837 Myb_DNA-bind_4: Myb/S 96.1 0.0023 5.1E-08 50.0 1.3 48 16-63 1-64 (90)
37 PF08914 Myb_DNA-bind_2: Rap1 96.1 0.0026 5.7E-08 48.7 1.4 52 16-67 2-61 (65)
38 PRK13923 putative spore coat p 95.9 0.011 2.3E-07 53.4 4.4 50 68-118 4-60 (170)
39 PF13873 Myb_DNA-bind_5: Myb/S 95.7 0.026 5.6E-07 43.4 5.5 51 69-119 2-74 (78)
40 COG5114 Histone acetyltransfer 95.2 0.0086 1.9E-07 58.8 1.6 50 14-64 61-110 (432)
41 PLN03142 Probable chromatin-re 95.2 0.063 1.4E-06 60.2 8.2 103 17-120 825-990 (1033)
42 COG5114 Histone acetyltransfer 95.2 0.024 5.2E-07 55.8 4.4 47 69-115 63-110 (432)
43 PRK13923 putative spore coat p 94.9 0.0083 1.8E-07 54.1 0.4 51 13-65 2-58 (170)
44 PF13873 Myb_DNA-bind_5: Myb/S 94.8 0.012 2.5E-07 45.4 1.0 49 15-63 1-69 (78)
45 PF09111 SLIDE: SLIDE; InterP 94.3 0.076 1.7E-06 45.2 4.9 53 66-118 46-114 (118)
46 KOG4282 Transcription factor G 94.3 0.12 2.6E-06 50.6 7.0 54 69-122 54-121 (345)
47 PF12776 Myb_DNA-bind_3: Myb/S 93.8 0.16 3.5E-06 40.1 5.6 46 71-116 1-64 (96)
48 KOG2656 DNA methyltransferase 92.4 0.1 2.2E-06 52.6 3.0 54 69-122 130-189 (445)
49 COG5118 BDP1 Transcription ini 91.5 0.26 5.7E-06 49.6 4.7 48 70-117 366-413 (507)
50 KOG1194 Predicted DNA-binding 90.9 0.83 1.8E-05 47.0 7.6 48 68-115 186-233 (534)
51 PF08281 Sigma70_r4_2: Sigma-7 88.7 1.4 3E-05 31.2 5.4 42 74-116 12-53 (54)
52 KOG4282 Transcription factor G 85.0 0.57 1.2E-05 45.9 2.2 48 16-63 54-113 (345)
53 COG5118 BDP1 Transcription ini 84.7 0.66 1.4E-05 46.9 2.5 49 12-62 361-409 (507)
54 PF09111 SLIDE: SLIDE; InterP 83.5 0.84 1.8E-05 38.9 2.3 37 10-46 43-82 (118)
55 PF04545 Sigma70_r4: Sigma-70, 74.9 9.1 0.0002 26.7 5.1 41 75-116 7-47 (50)
56 PF11035 SnAPC_2_like: Small n 71.2 15 0.00033 36.5 7.2 51 69-119 21-75 (344)
57 PF13404 HTH_AsnC-type: AsnC-t 69.4 12 0.00025 26.0 4.5 38 75-113 3-41 (42)
58 TIGR02985 Sig70_bacteroi1 RNA 68.7 15 0.00032 30.5 5.9 40 76-116 117-156 (161)
59 KOG4468 Polycomb-group transcr 68.4 8.7 0.00019 41.2 5.2 49 69-117 88-146 (782)
60 PF11626 Rap1_C: TRF2-interact 66.3 5.7 0.00012 31.6 2.7 25 12-36 43-75 (87)
61 KOG4167 Predicted DNA-binding 66.3 11 0.00023 41.3 5.5 47 69-115 619-665 (907)
62 PF07750 GcrA: GcrA cell cycle 66.2 7.9 0.00017 34.6 3.9 40 71-111 2-41 (162)
63 smart00595 MADF subfamily of S 64.1 10 0.00022 29.4 3.7 25 91-116 30-54 (89)
64 PF12776 Myb_DNA-bind_3: Myb/S 63.5 8.9 0.00019 30.0 3.4 45 18-62 1-61 (96)
65 PF13404 HTH_AsnC-type: AsnC-t 61.2 5.4 0.00012 27.7 1.5 38 22-61 3-40 (42)
66 KOG4329 DNA-binding protein [G 60.6 15 0.00032 37.4 5.0 46 70-115 278-324 (445)
67 PF04504 DUF573: Protein of un 60.2 28 0.00061 28.5 5.8 51 70-120 5-68 (98)
68 PRK11179 DNA-binding transcrip 59.8 17 0.00036 31.5 4.7 46 74-120 8-54 (153)
69 PRK11179 DNA-binding transcrip 58.5 6.4 0.00014 34.1 1.8 45 22-68 9-53 (153)
70 TIGR02937 sigma70-ECF RNA poly 58.4 27 0.00059 27.9 5.5 38 78-116 116-153 (158)
71 PF07638 Sigma70_ECF: ECF sigm 56.5 29 0.00064 30.8 5.8 41 76-117 139-179 (185)
72 PF11035 SnAPC_2_like: Small n 54.4 2.4E+02 0.0052 28.3 12.0 86 16-115 21-127 (344)
73 KOG2009 Transcription initiati 54.3 12 0.00027 39.8 3.5 45 68-112 408-452 (584)
74 KOG4468 Polycomb-group transcr 54.3 16 0.00034 39.3 4.2 48 15-64 87-144 (782)
75 cd06171 Sigma70_r4 Sigma70, re 54.2 43 0.00092 22.0 5.1 38 76-114 14-51 (55)
76 PRK09652 RNA polymerase sigma 52.8 34 0.00074 29.0 5.4 37 80-117 136-172 (182)
77 PRK11169 leucine-responsive tr 52.6 6.6 0.00014 34.4 1.0 45 21-67 13-57 (164)
78 KOG1194 Predicted DNA-binding 52.1 21 0.00046 37.1 4.6 40 71-111 472-511 (534)
79 KOG3841 TEF-1 and related tran 51.4 69 0.0015 32.8 7.9 55 67-121 74-149 (455)
80 PRK11169 leucine-responsive tr 51.3 24 0.00052 30.9 4.3 45 74-119 13-58 (164)
81 PRK12532 RNA polymerase sigma 50.4 48 0.001 29.1 6.2 41 83-124 147-190 (195)
82 PRK11924 RNA polymerase sigma 50.2 36 0.00078 28.7 5.1 33 83-116 136-168 (179)
83 KOG0384 Chromodomain-helicase 49.3 16 0.00035 42.2 3.5 74 15-95 1132-1206(1373)
84 PRK12512 RNA polymerase sigma 49.1 54 0.0012 28.4 6.2 38 83-121 142-179 (184)
85 KOG4167 Predicted DNA-binding 48.2 12 0.00025 41.1 2.1 44 16-61 619-662 (907)
86 PF10545 MADF_DNA_bdg: Alcohol 47.4 25 0.00054 26.3 3.4 27 91-117 29-56 (85)
87 smart00351 PAX Paired Box doma 47.2 1.3E+02 0.0029 25.2 8.1 84 14-110 13-103 (125)
88 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 47.1 41 0.0009 24.6 4.3 36 74-110 6-41 (50)
89 PRK04217 hypothetical protein; 46.8 50 0.0011 27.8 5.3 45 71-117 42-86 (110)
90 PRK12529 RNA polymerase sigma 46.1 64 0.0014 28.1 6.2 40 81-121 136-175 (178)
91 PF13325 MCRS_N: N-terminal re 45.7 45 0.00097 31.0 5.3 44 71-115 1-47 (199)
92 PF01388 ARID: ARID/BRIGHT DNA 45.4 8.6 0.00019 30.2 0.5 40 26-65 40-90 (92)
93 KOG2009 Transcription initiati 44.9 25 0.00054 37.6 4.0 51 9-61 402-452 (584)
94 PRK09641 RNA polymerase sigma 44.5 55 0.0012 28.1 5.5 30 87-117 151-180 (187)
95 PRK09643 RNA polymerase sigma 44.2 59 0.0013 28.7 5.7 36 80-116 142-177 (192)
96 cd08319 Death_RAIDD Death doma 43.8 35 0.00075 27.3 3.7 29 77-106 2-30 (83)
97 PRK12530 RNA polymerase sigma 43.6 61 0.0013 28.6 5.7 29 86-115 148-176 (189)
98 PRK12523 RNA polymerase sigma 42.7 80 0.0017 27.1 6.2 42 79-121 126-167 (172)
99 cd08803 Death_ank3 Death domai 42.7 41 0.00089 26.8 4.0 31 77-108 4-34 (84)
100 TIGR02939 RpoE_Sigma70 RNA pol 42.1 51 0.0011 28.4 4.9 31 87-118 153-183 (190)
101 PRK09047 RNA polymerase factor 41.9 79 0.0017 26.4 6.0 33 83-116 117-149 (161)
102 smart00344 HTH_ASNC helix_turn 41.9 54 0.0012 26.1 4.7 45 75-120 3-48 (108)
103 PF09420 Nop16: Ribosome bioge 41.6 33 0.00073 30.3 3.7 49 14-63 112-163 (164)
104 PRK13858 type IV secretion sys 40.9 37 0.0008 30.2 3.8 84 1-98 13-96 (147)
105 PRK09413 IS2 repressor TnpA; R 39.9 64 0.0014 26.9 5.0 46 15-64 9-54 (121)
106 COG2197 CitB Response regulato 39.8 58 0.0013 29.7 5.1 44 70-116 147-190 (211)
107 TIGR02954 Sig70_famx3 RNA poly 39.4 78 0.0017 27.0 5.6 32 86-118 133-164 (169)
108 KOG2656 DNA methyltransferase 39.0 24 0.00052 36.1 2.6 50 12-62 126-180 (445)
109 PRK09645 RNA polymerase sigma 38.7 98 0.0021 26.4 6.2 33 83-116 129-161 (173)
110 TIGR02948 SigW_bacill RNA poly 38.7 74 0.0016 27.3 5.4 30 87-117 151-180 (187)
111 PF01388 ARID: ARID/BRIGHT DNA 38.5 73 0.0016 24.9 4.9 37 79-115 40-89 (92)
112 PRK12515 RNA polymerase sigma 38.3 75 0.0016 27.7 5.5 31 85-116 144-174 (189)
113 PF11626 Rap1_C: TRF2-interact 38.0 17 0.00036 28.9 1.1 17 65-81 43-59 (87)
114 cd08317 Death_ank Death domain 37.9 38 0.00083 26.5 3.2 30 77-107 4-33 (84)
115 PRK11923 algU RNA polymerase s 37.6 79 0.0017 27.6 5.5 29 87-116 153-181 (193)
116 PRK09648 RNA polymerase sigma 37.1 95 0.0021 27.0 5.9 33 84-117 151-183 (189)
117 smart00501 BRIGHT BRIGHT, ARID 36.9 17 0.00038 28.8 1.1 41 25-65 35-86 (93)
118 PRK09637 RNA polymerase sigma 35.7 82 0.0018 27.6 5.3 34 82-116 116-149 (181)
119 PRK09649 RNA polymerase sigma 34.7 1.2E+02 0.0025 26.6 6.1 32 87-119 145-176 (185)
120 PF09420 Nop16: Ribosome bioge 33.9 82 0.0018 27.8 5.0 46 68-113 113-162 (164)
121 PRK05602 RNA polymerase sigma 33.5 1.1E+02 0.0024 26.6 5.7 32 86-118 142-173 (186)
122 PRK12545 RNA polymerase sigma 33.0 1.2E+02 0.0025 27.1 5.9 36 87-123 154-192 (201)
123 TIGR02999 Sig-70_X6 RNA polyme 32.9 1.3E+02 0.0028 25.9 6.0 29 87-116 149-177 (183)
124 cd08318 Death_NMPP84 Death dom 32.6 63 0.0014 25.6 3.6 26 81-107 11-36 (86)
125 PRK09642 RNA polymerase sigma 32.2 1.3E+02 0.0028 25.3 5.8 33 83-116 117-149 (160)
126 smart00005 DEATH DEATH domain, 32.2 65 0.0014 24.6 3.6 30 76-106 4-34 (88)
127 TIGR02943 Sig70_famx1 RNA poly 32.1 1.2E+02 0.0025 26.7 5.7 36 80-116 139-174 (188)
128 PF02954 HTH_8: Bacterial regu 31.8 97 0.0021 21.1 4.0 33 76-109 6-38 (42)
129 PRK12547 RNA polymerase sigma 31.6 1.4E+02 0.0031 25.3 6.0 37 82-119 122-158 (164)
130 PF05263 DUF722: Protein of un 31.4 1E+02 0.0023 26.7 5.0 57 51-119 70-128 (130)
131 PF13936 HTH_38: Helix-turn-he 31.3 62 0.0013 22.4 3.0 36 71-108 4-39 (44)
132 PRK12531 RNA polymerase sigma 31.2 1.3E+02 0.0028 26.4 5.8 30 86-116 155-184 (194)
133 cd08804 Death_ank2 Death domai 31.1 67 0.0014 25.4 3.5 31 77-108 4-34 (84)
134 smart00501 BRIGHT BRIGHT, ARID 30.3 1.1E+02 0.0025 24.0 4.8 38 79-116 36-86 (93)
135 cd00131 PAX Paired Box domain 29.9 2.7E+02 0.0059 23.5 7.4 74 13-88 12-92 (128)
136 cd08311 Death_p75NR Death doma 29.6 66 0.0014 25.3 3.2 33 74-108 2-34 (77)
137 PLN03162 golden-2 like transcr 29.2 3.3E+02 0.0072 28.1 8.8 45 70-114 238-287 (526)
138 COG2963 Transposase and inacti 29.2 1.7E+02 0.0036 23.8 5.8 45 69-115 5-50 (116)
139 TIGR02950 SigM_subfam RNA poly 28.9 47 0.001 27.6 2.5 28 88-116 121-148 (154)
140 PRK12524 RNA polymerase sigma 28.6 1.3E+02 0.0028 26.5 5.4 33 83-116 147-179 (196)
141 PRK12514 RNA polymerase sigma 28.3 1.6E+02 0.0035 25.2 5.8 29 87-116 144-172 (179)
142 PRK13919 putative RNA polymera 28.3 1.8E+02 0.0038 25.1 6.1 30 87-117 150-179 (186)
143 PRK10100 DNA-binding transcrip 28.0 1.4E+02 0.0031 27.3 5.7 43 71-116 155-197 (216)
144 TIGR02984 Sig-70_plancto1 RNA 27.5 1.4E+02 0.0031 25.5 5.4 34 82-116 150-183 (189)
145 smart00344 HTH_ASNC helix_turn 27.5 47 0.001 26.4 2.1 44 22-67 3-46 (108)
146 PRK09651 RNA polymerase sigma 27.4 1.2E+02 0.0026 26.1 4.9 29 87-116 134-162 (172)
147 PRK12536 RNA polymerase sigma 27.4 1.7E+02 0.0037 25.3 5.9 34 83-117 140-173 (181)
148 TIGR02983 SigE-fam_strep RNA p 27.4 1.9E+02 0.0041 24.3 6.0 42 76-118 114-155 (162)
149 PRK12516 RNA polymerase sigma 26.9 1.6E+02 0.0035 25.9 5.7 36 80-116 124-159 (187)
150 PRK12537 RNA polymerase sigma 26.7 1.8E+02 0.0038 25.2 5.8 31 86-117 147-177 (182)
151 PRK09638 RNA polymerase sigma 26.6 77 0.0017 27.0 3.5 31 87-118 141-171 (176)
152 cd08779 Death_PIDD Death Domai 26.2 46 0.001 26.4 1.8 26 78-104 3-28 (86)
153 PRK15201 fimbriae regulatory p 26.1 1.8E+02 0.0039 27.1 5.8 43 71-116 133-175 (198)
154 PRK06759 RNA polymerase factor 26.0 1.7E+02 0.0037 24.2 5.4 29 87-116 121-149 (154)
155 PRK15411 rcsA colanic acid cap 26.0 1.4E+02 0.0031 26.9 5.2 43 71-116 137-179 (207)
156 PRK10360 DNA-binding transcrip 25.6 1.9E+02 0.0041 24.2 5.7 44 70-116 136-179 (196)
157 PRK12528 RNA polymerase sigma 25.3 1.8E+02 0.0039 24.5 5.5 33 82-115 123-155 (161)
158 PRK09647 RNA polymerase sigma 25.3 1.8E+02 0.0039 26.2 5.7 33 87-120 153-185 (203)
159 PRK12527 RNA polymerase sigma 25.1 2.1E+02 0.0045 24.0 5.8 30 87-117 120-149 (159)
160 TIGR02952 Sig70_famx2 RNA poly 24.9 2.1E+02 0.0044 24.1 5.8 29 87-116 137-165 (170)
161 COG5352 Uncharacterized protei 24.9 91 0.002 27.9 3.5 37 71-108 2-38 (169)
162 PRK09646 RNA polymerase sigma 24.9 2.2E+02 0.0047 25.0 6.1 31 87-118 157-187 (194)
163 PRK12542 RNA polymerase sigma 24.8 1.8E+02 0.0038 25.3 5.4 30 86-116 136-165 (185)
164 PRK00118 putative DNA-binding 24.8 1.9E+02 0.0042 24.1 5.3 40 74-114 19-58 (104)
165 PRK09483 response regulator; P 24.8 1.1E+02 0.0024 26.2 4.1 44 70-116 147-190 (217)
166 cd08777 Death_RIP1 Death Domai 24.7 90 0.002 24.9 3.3 29 79-108 4-32 (86)
167 PF00046 Homeobox: Homeobox do 24.6 2.5E+02 0.0054 19.6 6.3 44 68-112 3-50 (57)
168 PRK12520 RNA polymerase sigma 24.4 1.8E+02 0.0039 25.4 5.4 29 87-116 146-174 (191)
169 cd08805 Death_ank1 Death domai 24.3 1E+02 0.0022 24.7 3.4 27 77-104 4-30 (84)
170 COG1522 Lrp Transcriptional re 24.2 46 0.00099 28.0 1.6 44 22-67 8-51 (154)
171 TIGR02960 SigX5 RNA polymerase 24.1 1.7E+02 0.0037 27.8 5.6 31 86-117 156-186 (324)
172 PF07750 GcrA: GcrA cell cycle 24.1 46 0.00099 29.7 1.6 34 18-53 2-36 (162)
173 PF01527 HTH_Tnp_1: Transposas 23.7 1.4E+02 0.003 22.0 4.0 46 68-115 3-48 (76)
174 PRK12546 RNA polymerase sigma 23.4 1.9E+02 0.0041 25.6 5.5 38 81-119 122-159 (188)
175 PRK11922 RNA polymerase sigma 23.3 97 0.0021 28.3 3.6 29 88-117 165-193 (231)
176 cd08312 Death_MyD88 Death doma 23.2 87 0.0019 24.4 2.9 22 85-107 13-34 (79)
177 PF10440 WIYLD: Ubiquitin-bind 21.8 63 0.0014 25.0 1.7 18 79-96 31-48 (65)
178 PF00196 GerE: Bacterial regul 21.6 2.2E+02 0.0048 20.2 4.6 42 72-116 4-45 (58)
179 TIGR02989 Sig-70_gvs1 RNA poly 21.5 2.3E+02 0.0051 23.5 5.4 29 86-115 125-153 (159)
180 PRK01905 DNA-binding protein F 20.6 2.5E+02 0.0054 21.6 5.0 33 74-107 36-68 (77)
181 PRK06811 RNA polymerase factor 20.3 2.8E+02 0.006 24.2 5.8 29 87-116 146-174 (189)
No 1
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=7.5e-40 Score=303.53 Aligned_cols=132 Identities=52% Similarity=0.994 Sum_probs=127.0
Q ss_pred CCCCCCcccccCCCCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhcCCCCCCCCCChHHHHHH
Q 041991 1 MGKRKTPFCDMEKMKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPDIKRGPFAPEEVATI 80 (325)
Q Consensus 1 lG~~R~~~cdk~~lkKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkrg~WT~EED~~L 80 (325)
|++++.|||+|.+++|++||+|||++|+++|++||..+|..||+.++.+|+++|||+||.|||+|.+++++||+|||++|
T Consensus 10 ~~~~~~pcc~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lL 89 (249)
T PLN03212 10 VSKKTTPCCTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLI 89 (249)
T ss_pred CCCCCCCCcccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHH
Confidence 57899999999999999999999999999999999999999999997789999999999999999999999999999999
Q ss_pred HHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHHHHhhcccCcCCCCCCC
Q 041991 81 IQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKHLQSMNHNLLTYQSPS 132 (325)
Q Consensus 81 l~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkkl~~~~~~~~~~~~~s 132 (325)
++++.+||++|+.||++|||||+++|||||+.++++++.+.++++.++++..
T Consensus 90 lel~~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~p~~~kp~~ 141 (249)
T PLN03212 90 LRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGIDPQTHKPLD 141 (249)
T ss_pred HHHHHhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCCCCCCCCCC
Confidence 9999999999999999999999999999999999999999999988877643
No 2
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=1.5e-39 Score=320.73 Aligned_cols=161 Identities=47% Similarity=0.842 Sum_probs=145.4
Q ss_pred CCCcccccCCCCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhcCCCCCCCCCChHHHHHHHHH
Q 041991 4 RKTPFCDMEKMKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPDIKRGPFAPEEVATIIQL 83 (325)
Q Consensus 4 ~R~~~cdk~~lkKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkrg~WT~EED~~Ll~l 83 (325)
+|++||||.+++||+||+|||++|+++|++||..+|..||+.++++|+++|||+||.|||+|++++++||+|||++|+++
T Consensus 2 gr~~Cc~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL 81 (459)
T PLN03091 2 GRHSCCYKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIEL 81 (459)
T ss_pred CCCccCcCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHH
Confidence 68999999999999999999999999999999999999999998789999999999999999999999999999999999
Q ss_pred HHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHHHHhhcccCcCCCCCCCCCCCCCCCCCCCCCccccchhhhhhhhhhcC
Q 041991 84 HGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKHLQSMNHNLLTYQSPSSSGPSTVKSDFPSTRQMVKCASARVEAEAGL 163 (325)
Q Consensus 84 ~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkkl~~~~~~~~~~~~~sss~~~~~~s~~ps~~h~~q~esarlEaearl 163 (325)
|++||++|+.||++|||||+++|||||+.++||++++.++++.++++..... ......|....+++..++++++|..+
T Consensus 82 ~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~I~p~t~kpl~e~E--~~~d~~p~~~~~~~~~s~~~~~el~~ 159 (459)
T PLN03091 82 HAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRGIDPNTHKPLSEVE--NGEDKNPPTDDKSDKASSVVSNELNL 159 (459)
T ss_pred HHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCCCCCCCCccccc--cccccCCccccccccchhhhhhhhhh
Confidence 9999999999999999999999999999999999999999999988865432 12234567778888888888777654
Q ss_pred CCc
Q 041991 164 PIE 166 (325)
Q Consensus 164 ~~~ 166 (325)
...
T Consensus 160 ~~~ 162 (459)
T PLN03091 160 LKA 162 (459)
T ss_pred hhh
Confidence 433
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=3.8e-39 Score=299.18 Aligned_cols=114 Identities=55% Similarity=0.954 Sum_probs=109.4
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhcCCCCCCCCCChHHHHHHHHHHHhhCCCHHH
Q 041991 14 MKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPDIKRGPFAPEEVATIIQLHGLFGNKWAA 93 (325)
Q Consensus 14 lkKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkrg~WT~EED~~Ll~l~~~~G~kWs~ 93 (325)
+.||+||+|||++|++||++||+++|..||+.+|++||+|+||+||+|||+|++++|.||+|||++|+++|..|||+|+.
T Consensus 7 ~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrWs~ 86 (238)
T KOG0048|consen 7 LVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRWSL 86 (238)
T ss_pred ccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHHHH
Confidence 45899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhCCCCCHHHHHHHHHHHHHHHHhhcccCcCC
Q 041991 94 IASHLPGRTDNDIKNLWNTRLKKHLQSMNHNLLT 127 (325)
Q Consensus 94 IA~~LpGRT~nq~KnRW~t~lkkkl~~~~~~~~~ 127 (325)
||++|||||+|+|||||++.+||++..+++++..
T Consensus 87 IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~~~~~~ 120 (238)
T KOG0048|consen 87 IAGRLPGRTDNEVKNHWNTHLKKKLLKMGIDPST 120 (238)
T ss_pred HHhhCCCcCHHHHHHHHHHHHHHHHHHcCCCCCc
Confidence 9999999999999999999999999998855443
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.73 E-value=6.4e-18 Score=173.01 Aligned_cols=105 Identities=23% Similarity=0.400 Sum_probs=96.4
Q ss_pred cccccCCCCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhcCCCCCCCCCChHHHHHHHHHHHh
Q 041991 7 PFCDMEKMKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPDIKRGPFAPEEVATIIQLHGL 86 (325)
Q Consensus 7 ~~cdk~~lkKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkrg~WT~EED~~Ll~l~~~ 86 (325)
...-.|++++|+||.+||-+|+.+|.+||..+|..|-..++ +|+..|||+||+|.|....|.+.||-.||+.|+.++.+
T Consensus 351 ~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vP-nRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~~V~~ 429 (939)
T KOG0049|consen 351 SHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVP-NRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLYAVKV 429 (939)
T ss_pred eeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcC-CccHHHHHHHHHHHHHHhhccCceeecchHHHHHHHHH
Confidence 34446999999999999999999999999999999999998 89999999999999999999999999999999999999
Q ss_pred hC-CCHHHHHhhCCCCCHHHHHHHHHH
Q 041991 87 FG-NKWAAIASHLPGRTDNDIKNLWNT 112 (325)
Q Consensus 87 ~G-~kWs~IA~~LpGRT~nq~KnRW~t 112 (325)
|| ++|.+||..||+||..|...|=..
T Consensus 430 YG~g~WakcA~~Lp~~t~~q~~rrR~R 456 (939)
T KOG0049|consen 430 YGKGNWAKCAMLLPKKTSRQLRRRRLR 456 (939)
T ss_pred HccchHHHHHHHccccchhHHHHHHHH
Confidence 99 679999999999999766554333
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.64 E-value=1.3e-16 Score=163.51 Aligned_cols=119 Identities=22% Similarity=0.473 Sum_probs=106.0
Q ss_pred CCCCCCc--ccc-----cCCCCcCCCCHHHHHHHHHHHHHhCCC---CcccccccccccccchhhhhhhhhhcCCCCCCC
Q 041991 1 MGKRKTP--FCD-----MEKMKRGVWSPEEDAKLIQYIKEHGHG---TWRHLPKQAGILRSGKSCRLRWMNYLRPDIKRG 70 (325)
Q Consensus 1 lG~~R~~--~cd-----k~~lkKG~WT~EEDe~L~~lV~k~G~~---nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkrg 70 (325)
||+.|+. |.. ..-++...||.|||.+|..+|+....+ +|++|-..|+ +|+..|...||.+.|+|.+++|
T Consensus 283 Lgt~RS~yQC~~kF~t~~~~L~ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ymp-gr~~~qLI~R~~~~LdPsikhg 361 (939)
T KOG0049|consen 283 LGTNRSSYQCMEKFKTEVSQLSEKEWSEEEDTKLIALVKITSINSHIQWDKVVQYMP-GRTRQQLITRFSHTLDPSVKHG 361 (939)
T ss_pred hCCCcchHHHHHHHHHHHHHHHhhhcchhhhHHHHHHHHHhhccCccchHHHHHhcC-CcchhhhhhhheeccCccccCC
Confidence 6787775 432 234778999999999999999988544 8999999998 8999999999999999999999
Q ss_pred CCChHHHHHHHHHHHhhCCC-HHHHHhhCCCCCHHHHHHHHHHHHHHHHhh
Q 041991 71 PFAPEEVATIIQLHGLFGNK-WAAIASHLPGRTDNDIKNLWNTRLKKHLQS 120 (325)
Q Consensus 71 ~WT~EED~~Ll~l~~~~G~k-Ws~IA~~LpGRT~nq~KnRW~t~lkkkl~~ 120 (325)
+||.+||.+|+.++.+||.+ |.+|-..+|||++.||+.||.+.|....+.
T Consensus 362 ~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~ 412 (939)
T KOG0049|consen 362 RWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNRSAKV 412 (939)
T ss_pred CCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHHhhcc
Confidence 99999999999999999976 999999999999999999999988765543
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=99.63 E-value=2.1e-16 Score=116.67 Aligned_cols=60 Identities=42% Similarity=0.899 Sum_probs=55.0
Q ss_pred CCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhcCCCCCCCCCChHHHHHH
Q 041991 19 WSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPDIKRGPFAPEEVATI 80 (325)
Q Consensus 19 WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkrg~WT~EED~~L 80 (325)
||+|||++|+.+|.+||. +|..||+.++ .|++.+|+.||.++|+|.+++++||.+||++|
T Consensus 1 WT~eEd~~L~~~~~~~g~-~W~~Ia~~l~-~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN-DWKKIAEHLG-NRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS--HHHHHHHST-TS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc-CHHHHHHHHC-cCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 999999999999999996 9999999997 79999999999999999999999999999987
No 7
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.56 E-value=2.4e-15 Score=153.07 Aligned_cols=108 Identities=27% Similarity=0.464 Sum_probs=103.0
Q ss_pred cCCCCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhcCCCCCCCCCChHHHHHHHHHHHhhCCC
Q 041991 11 MEKMKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPDIKRGPFAPEEVATIIQLHGLFGNK 90 (325)
Q Consensus 11 k~~lkKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkrg~WT~EED~~Ll~l~~~~G~k 90 (325)
..+++.|.|+..||+.|..+|+++|..+|..||..+. .|+++||+.||.++++|.+++..|+.+||+.|+.+..++|++
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 5678899999999999999999999999999999998 499999999999999999999999999999999999999999
Q ss_pred HHHHHhhCCCCCHHHHHHHHHHHHHHHHh
Q 041991 91 WAAIASHLPGRTDNDIKNLWNTRLKKHLQ 119 (325)
Q Consensus 91 Ws~IA~~LpGRT~nq~KnRW~t~lkkkl~ 119 (325)
|+.||..++|||..+|.+||...+.....
T Consensus 94 wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 94 WSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 99999999999999999999988876655
No 8
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.51 E-value=1.7e-14 Score=145.18 Aligned_cols=152 Identities=23% Similarity=0.406 Sum_probs=121.8
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhcCCCCCCCCCChHHHHHHHHHHHhhCCCHH
Q 041991 13 KMKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPDIKRGPFAPEEVATIIQLHGLFGNKWA 92 (325)
Q Consensus 13 ~lkKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkrg~WT~EED~~Ll~l~~~~G~kWs 92 (325)
-++.|-|+.-||+.|...|.+||...|..|++.+. ..+.+||+.||..+|+|.|++..|+.|||++||.+.+.+...|.
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 36789999999999999999999999999999997 68999999999999999999999999999999999999999999
Q ss_pred HHHhhCCCCCHHHHHHHHHHHHHHHHhhccc-CcCC---CCCCCCCCCCCCCCCCCCCccccchhhhhh-hhhhcCCCc
Q 041991 93 AIASHLPGRTDNDIKNLWNTRLKKHLQSMNH-NLLT---YQSPSSSGPSTVKSDFPSTRQMVKCASARV-EAEAGLPIE 166 (325)
Q Consensus 93 ~IA~~LpGRT~nq~KnRW~t~lkkkl~~~~~-~~~~---~~~~sss~~~~~~s~~ps~~h~~q~esarl-Eaearl~~~ 166 (325)
.|+..| ||+.++|-.||+.++-........ .+.+ ..+.-..|-.-....-|-.-.|-..+..++ ||.|||++-
T Consensus 83 tIa~i~-gr~~~qc~eRy~~ll~~~~s~~~~~~~~~D~rLk~gE~ePn~e~~~aRpd~~dmdEde~eMl~eaRarlaNt 160 (617)
T KOG0050|consen 83 TIADIM-GRTSQQCLERYNNLLDVYVSYHYHSEPYIDAKLKEGEIEPNQETNPARPDGFDMDEDEGEMLSEARARLANT 160 (617)
T ss_pred hHHHHh-hhhHHHHHHHHHHHHHHHHhhhcccccccccccCCCcCCCccccccccCCcccchHHHHHHHHHHHHHHhcc
Confidence 999999 999999999999999776554333 1111 222222211111223344446777777777 888888775
No 9
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.42 E-value=2.2e-13 Score=140.35 Aligned_cols=102 Identities=27% Similarity=0.572 Sum_probs=92.9
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhcCCC--CCCCCCChHHHHHHHHHHH-------
Q 041991 15 KRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPD--IKRGPFAPEEVATIIQLHG------- 85 (325)
Q Consensus 15 kKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~--lkrg~WT~EED~~Ll~l~~------- 85 (325)
.+|.||+||++.|..+|.++|. .|..|++.++ |.+..||+||.+|..+. .+++.||.||++.|++++.
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~-~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~ 459 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGN-DWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREAL 459 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcc-cHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhh
Confidence 8999999999999999999997 9999999987 99999999999999997 4899999999999999995
Q ss_pred hh-------------------CCCHHHHHhhCCCCCHHHHHHHHHHHHHHHHh
Q 041991 86 LF-------------------GNKWAAIASHLPGRTDNDIKNLWNTRLKKHLQ 119 (325)
Q Consensus 86 ~~-------------------G~kWs~IA~~LpGRT~nq~KnRW~t~lkkkl~ 119 (325)
++ +..|..|++.+..|+..+|+.+|+.++.+...
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 34 13599999988899999999999999886543
No 10
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.41 E-value=7.2e-14 Score=99.45 Aligned_cols=48 Identities=40% Similarity=0.785 Sum_probs=43.6
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhc
Q 041991 16 RGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYL 63 (325)
Q Consensus 16 KG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L 63 (325)
|++||+|||++|+++|.+||.++|..|++.++.+|+..||+.||.++|
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 689999999999999999999779999999987899999999999986
No 11
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.35 E-value=1.1e-12 Score=93.37 Aligned_cols=46 Identities=30% Similarity=0.684 Sum_probs=42.0
Q ss_pred CCCCChHHHHHHHHHHHhhCCC-HHHHHhhCC-CCCHHHHHHHHHHHH
Q 041991 69 RGPFAPEEVATIIQLHGLFGNK-WAAIASHLP-GRTDNDIKNLWNTRL 114 (325)
Q Consensus 69 rg~WT~EED~~Ll~l~~~~G~k-Ws~IA~~Lp-GRT~nq~KnRW~t~l 114 (325)
+++||+|||++|++++.+||.+ |..||..|| |||..||++||+.++
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 5799999999999999999998 999999999 999999999999874
No 12
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.22 E-value=1.1e-11 Score=91.41 Aligned_cols=46 Identities=33% Similarity=0.661 Sum_probs=39.8
Q ss_pred CChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 041991 72 FAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKH 117 (325)
Q Consensus 72 WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkk 117 (325)
||+|||++|++++.+||++|..||++|+.||..+|++||+..|++.
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~ 46 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPK 46 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTT
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCccc
Confidence 9999999999999999999999999996699999999999977543
No 13
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.21 E-value=2.7e-11 Score=83.31 Aligned_cols=47 Identities=40% Similarity=0.784 Sum_probs=44.4
Q ss_pred CCCCChHHHHHHHHHHHhhC-CCHHHHHhhCCCCCHHHHHHHHHHHHH
Q 041991 69 RGPFAPEEVATIIQLHGLFG-NKWAAIASHLPGRTDNDIKNLWNTRLK 115 (325)
Q Consensus 69 rg~WT~EED~~Ll~l~~~~G-~kWs~IA~~LpGRT~nq~KnRW~t~lk 115 (325)
+++||++||.+|+.++.+|| .+|..||..|++||..+|++||+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 46899999999999999999 999999999999999999999998764
No 14
>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=99.09 E-value=2.2e-10 Score=77.73 Aligned_cols=44 Identities=34% Similarity=0.725 Sum_probs=41.8
Q ss_pred CCChHHHHHHHHHHHhhC-CCHHHHHhhCCCCCHHHHHHHHHHHH
Q 041991 71 PFAPEEVATIIQLHGLFG-NKWAAIASHLPGRTDNDIKNLWNTRL 114 (325)
Q Consensus 71 ~WT~EED~~Ll~l~~~~G-~kWs~IA~~LpGRT~nq~KnRW~t~l 114 (325)
+||.+|++.|++++.+|| .+|..||..+++||..+|++||++++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 89999999999999999999998763
No 15
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.09 E-value=1.1e-10 Score=109.47 Aligned_cols=57 Identities=19% Similarity=0.422 Sum_probs=52.3
Q ss_pred CCCCCCCCCChHHHHHHHHHHHhhC-CCHHHHHhhC-CCCCHHHHHHHHHHHHHHHHhh
Q 041991 64 RPDIKRGPFAPEEVATIIQLHGLFG-NKWAAIASHL-PGRTDNDIKNLWNTRLKKHLQS 120 (325)
Q Consensus 64 ~P~lkrg~WT~EED~~Ll~l~~~~G-~kWs~IA~~L-pGRT~nq~KnRW~t~lkkkl~~ 120 (325)
++.+++++||+|||++|++++++|| ++|..||+++ +|||..||+.||.++|+..+++
T Consensus 20 K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~k 78 (249)
T PLN03212 20 KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKR 78 (249)
T ss_pred cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhccc
Confidence 3678999999999999999999999 5799999998 6999999999999999987665
No 16
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.05 E-value=1.5e-10 Score=79.63 Aligned_cols=48 Identities=38% Similarity=0.834 Sum_probs=44.7
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhcC
Q 041991 16 RGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLR 64 (325)
Q Consensus 16 KG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~ 64 (325)
+++||++||++|+.++.+||..+|..|++.++ +|++.+|+.||.++++
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 57899999999999999999669999999998 8999999999998875
No 17
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.95 E-value=4.7e-10 Score=104.61 Aligned_cols=60 Identities=25% Similarity=0.408 Sum_probs=53.6
Q ss_pred CCCCCCCCCChHHHHHHHHHHHhhCCC-HHHHHhhCC-CCCHHHHHHHHHHHHHHHHhhccc
Q 041991 64 RPDIKRGPFAPEEVATIIQLHGLFGNK-WAAIASHLP-GRTDNDIKNLWNTRLKKHLQSMNH 123 (325)
Q Consensus 64 ~P~lkrg~WT~EED~~Ll~l~~~~G~k-Ws~IA~~Lp-GRT~nq~KnRW~t~lkkkl~~~~~ 123 (325)
++.+.+|+||.|||++|+++|++||.+ |..|++.++ ||+..+|+-||.++|+..+++..+
T Consensus 4 k~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~f 65 (238)
T KOG0048|consen 4 NPELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNF 65 (238)
T ss_pred CccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCC
Confidence 344567999999999999999999955 999999998 999999999999999998886444
No 18
>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=1e-09 Score=74.38 Aligned_cols=45 Identities=38% Similarity=0.780 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhc
Q 041991 18 VWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYL 63 (325)
Q Consensus 18 ~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L 63 (325)
+||++||++|+.++.+||..+|..|++.++ +|+..+|+.||.+++
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 599999999999999999669999999998 799999999998764
No 19
>PLN03091 hypothetical protein; Provisional
Probab=98.86 E-value=8.3e-10 Score=110.51 Aligned_cols=54 Identities=22% Similarity=0.449 Sum_probs=50.5
Q ss_pred cCCCCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhcCCC
Q 041991 11 MEKMKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPD 66 (325)
Q Consensus 11 k~~lkKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~ 66 (325)
.+.++||+||+|||++|++++++||. .|..||+.++ +|++.+|+.||...|+..
T Consensus 62 dP~IkKgpWT~EED~lLLeL~k~~Gn-KWskIAk~LP-GRTDnqIKNRWnslLKKk 115 (459)
T PLN03091 62 RPDLKRGTFSQQEENLIIELHAVLGN-RWSQIAAQLP-GRTDNEIKNLWNSCLKKK 115 (459)
T ss_pred CCcccCCCCCHHHHHHHHHHHHHhCc-chHHHHHhcC-CCCHHHHHHHHHHHHHHH
Confidence 68999999999999999999999998 9999999997 899999999999887653
No 20
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.77 E-value=1.1e-08 Score=106.14 Aligned_cols=103 Identities=30% Similarity=0.424 Sum_probs=83.9
Q ss_pred CCCcCCCCHHHHHHHHHHHHHh----CC-------------------CCcccccccccccccchhhhhhhhhhcCCCC-C
Q 041991 13 KMKRGVWSPEEDAKLIQYIKEH----GH-------------------GTWRHLPKQAGILRSGKSCRLRWMNYLRPDI-K 68 (325)
Q Consensus 13 ~lkKG~WT~EEDe~L~~lV~k~----G~-------------------~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~l-k 68 (325)
.++.+.|+.+||..|-..|..| |- +.|..|.+.++. |+.+.+..+-++.-.|-- +
T Consensus 305 e~~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp~-R~~~siy~~~rR~y~~FE~~ 383 (607)
T KOG0051|consen 305 EINLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLPY-RDRKSIYHHLRRAYTPFENK 383 (607)
T ss_pred hhhhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcCc-ccchhHHHHHHhcCCccccc
Confidence 3555899999999999999888 11 135778888885 999888663223323322 8
Q ss_pred CCCCChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 041991 69 RGPFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKH 117 (325)
Q Consensus 69 rg~WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkk 117 (325)
+|.||+||++.|..+|.++|+.|..|++.| ||.+..|+.+|+.+.+..
T Consensus 384 rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g 431 (607)
T KOG0051|consen 384 RGKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCG 431 (607)
T ss_pred cCCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccc
Confidence 999999999999999999999999999999 999999999999887643
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=98.38 E-value=4.9e-08 Score=100.14 Aligned_cols=94 Identities=28% Similarity=0.594 Sum_probs=81.8
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhcCC--CCCCCCCChHHHHHHHHHHHhhC---
Q 041991 14 MKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRP--DIKRGPFAPEEVATIIQLHGLFG--- 88 (325)
Q Consensus 14 lkKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P--~lkrg~WT~EED~~Ll~l~~~~G--- 88 (325)
-.+|.||+||++.|...+.++|. .|..|.+.++ |-+..||+||.+|..+ .+++++|+.||+.+|...+...-
T Consensus 289 ~~~~~wt~e~~~eL~~~~~~~~~-~w~~ig~~~~--rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e~~~~~ 365 (512)
T COG5147 289 EQRGKWTKEEEQELAKLVVEHGG-SWTEIGKLLG--RMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNEMRLEA 365 (512)
T ss_pred hhhccCccccccccccccccccc-hhhHhhhhhc--cCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHHHHHHH
Confidence 45699999999999999999997 9999998775 9999999999999999 68899999999999998887322
Q ss_pred -----CCHHHHHhhCCCCCHHHHHHHH
Q 041991 89 -----NKWAAIASHLPGRTDNDIKNLW 110 (325)
Q Consensus 89 -----~kWs~IA~~LpGRT~nq~KnRW 110 (325)
..|..|+.++++|....|+.++
T Consensus 366 ~~~~~~~~~li~~~~~~~~~~~~~~~~ 392 (512)
T COG5147 366 QQSSRILWLLIAQNIRNRLQHHCRDKY 392 (512)
T ss_pred hhhhhhhHHHHHHhhhccccCCCCCcc
Confidence 3499999999888887776644
No 22
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.95 E-value=8.4e-06 Score=60.85 Aligned_cols=49 Identities=14% Similarity=0.344 Sum_probs=44.1
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCc---ccccccccccc-cchhhhhhhhhhc
Q 041991 15 KRGVWSPEEDAKLIQYIKEHGHGTW---RHLPKQAGILR-SGKSCRLRWMNYL 63 (325)
Q Consensus 15 kKG~WT~EEDe~L~~lV~k~G~~nW---~~IAk~lg~~R-t~kQCR~RW~n~L 63 (325)
++-.||+||.++++++|+.+|.++| ..|++.++..| +..||+.+++.|.
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 4568999999999999999999999 99999887667 9999999998874
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=97.58 E-value=0.00018 Score=53.71 Aligned_cols=47 Identities=13% Similarity=0.185 Sum_probs=40.9
Q ss_pred CCCCChHHHHHHHHHHHhhCC-CH---HHHHhhCC-CC-CHHHHHHHHHHHHH
Q 041991 69 RGPFAPEEVATIIQLHGLFGN-KW---AAIASHLP-GR-TDNDIKNLWNTRLK 115 (325)
Q Consensus 69 rg~WT~EED~~Ll~l~~~~G~-kW---s~IA~~Lp-GR-T~nq~KnRW~t~lk 115 (325)
+-.||+||..++++++..||. +| ..|++.|. .| |..+|+.|.+.+.-
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 558999999999999999996 89 99999984 35 99999999876653
No 24
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.56 E-value=4.4e-05 Score=76.79 Aligned_cols=50 Identities=16% Similarity=0.577 Sum_probs=46.6
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhc
Q 041991 13 KMKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYL 63 (325)
Q Consensus 13 ~lkKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L 63 (325)
.+-..-||.+|+-+|++++..||-|||..||+++| .|+..+|+++|.+++
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 45568899999999999999999999999999999 899999999999875
No 25
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.55 E-value=0.00028 Score=64.97 Aligned_cols=100 Identities=20% Similarity=0.346 Sum_probs=74.2
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccccc--ccchhhhhhhhhhcC-CCC--------------------CCCCCCh
Q 041991 18 VWSPEEDAKLIQYIKEHGHGTWRHLPKQAGIL--RSGKSCRLRWMNYLR-PDI--------------------KRGPFAP 74 (325)
Q Consensus 18 ~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~--Rt~kQCR~RW~n~L~-P~l--------------------krg~WT~ 74 (325)
+|++++|-+|+.+|..-. +-..|.+-+.+. -|-+.+..||+..|. |.+ .+-+||.
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 699999999999998765 556666544432 366778899999874 332 3558999
Q ss_pred HHHHHHHHHHHhhCC---CHHHHHh-----hCCCCCHHHHHHHHHHHHHHHHh
Q 041991 75 EEVATIIQLHGLFGN---KWAAIAS-----HLPGRTDNDIKNLWNTRLKKHLQ 119 (325)
Q Consensus 75 EED~~Ll~l~~~~G~---kWs~IA~-----~LpGRT~nq~KnRW~t~lkkkl~ 119 (325)
+||++|......... .+.+|=. +.++||+.++.++|+.+.+.++-
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 3777732 23789999999999976665553
No 26
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.38 E-value=0.00027 Score=71.21 Aligned_cols=50 Identities=18% Similarity=0.413 Sum_probs=44.7
Q ss_pred CCCCCCCChHHHHHHHHHHHhhC-CCHHHHHhhCCCCCHHHHHHHHHHHHH
Q 041991 66 DIKRGPFAPEEVATIIQLHGLFG-NKWAAIASHLPGRTDNDIKNLWNTRLK 115 (325)
Q Consensus 66 ~lkrg~WT~EED~~Ll~l~~~~G-~kWs~IA~~LpGRT~nq~KnRW~t~lk 115 (325)
.+-...||.+||.+||+++..|| ++|..||.++..||..+||.||..++-
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHh
Confidence 34556899999999999999999 889999999988999999999986653
No 27
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.28 E-value=0.00022 Score=73.19 Aligned_cols=55 Identities=27% Similarity=0.457 Sum_probs=49.9
Q ss_pred CCCCCCCChHHHHHHHHHHHhhC-CCHHHHHhhCCCCCHHHHHHHHHHHHHHHHhh
Q 041991 66 DIKRGPFAPEEVATIIQLHGLFG-NKWAAIASHLPGRTDNDIKNLWNTRLKKHLQS 120 (325)
Q Consensus 66 ~lkrg~WT~EED~~Ll~l~~~~G-~kWs~IA~~LpGRT~nq~KnRW~t~lkkkl~~ 120 (325)
.++.|-|+.-||++|-..+.+|| +.|+.|++.++-.|..||++||...+...+++
T Consensus 4 ~~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~ 59 (617)
T KOG0050|consen 4 EIKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKK 59 (617)
T ss_pred EEecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhh
Confidence 35789999999999999999999 55999999999999999999999988877655
No 28
>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=97.11 E-value=0.00069 Score=51.87 Aligned_cols=51 Identities=24% Similarity=0.427 Sum_probs=33.2
Q ss_pred CCCCChHHHHHHHHHHHhh--------CCC-HHHHHhhCC-CCCHHHHHHHHHHHHHHHHh
Q 041991 69 RGPFAPEEVATIIQLHGLF--------GNK-WAAIASHLP-GRTDNDIKNLWNTRLKKHLQ 119 (325)
Q Consensus 69 rg~WT~EED~~Ll~l~~~~--------G~k-Ws~IA~~Lp-GRT~nq~KnRW~t~lkkkl~ 119 (325)
|-+||.|||.+|++.++++ ||+ |.++++..+ .+|-...++||...|+.+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~~ 62 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRPR 62 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT-----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcccc
Confidence 4589999999999999664 233 999999987 89999999999888876543
No 29
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.07 E-value=0.00051 Score=53.74 Aligned_cols=51 Identities=31% Similarity=0.484 Sum_probs=36.1
Q ss_pred CCCCChHHHHHHHHHHHh------hC--C------CHHHHHhhC----CCCCHHHHHHHHHHHHHHHHh
Q 041991 69 RGPFAPEEVATIIQLHGL------FG--N------KWAAIASHL----PGRTDNDIKNLWNTRLKKHLQ 119 (325)
Q Consensus 69 rg~WT~EED~~Ll~l~~~------~G--~------kWs~IA~~L----pGRT~nq~KnRW~t~lkkkl~ 119 (325)
|..||.+|...||+++.. ++ . .|..||..| ..||..||+++|+++.++..+
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~ 69 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKK 69 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHC
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence 357999999999999877 32 1 399999987 359999999999997765443
No 30
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=96.96 E-value=0.0012 Score=58.96 Aligned_cols=52 Identities=17% Similarity=0.308 Sum_probs=45.3
Q ss_pred CCCCCChHHHHHHHHHHHhh---CCC----HHHHHhhCCCCCHHHHHHHHHHHHHHHHhh
Q 041991 68 KRGPFAPEEVATIIQLHGLF---GNK----WAAIASHLPGRTDNDIKNLWNTRLKKHLQS 120 (325)
Q Consensus 68 krg~WT~EED~~Ll~l~~~~---G~k----Ws~IA~~LpGRT~nq~KnRW~t~lkkkl~~ 120 (325)
+...||.|||.+|.+.+-.| |.. +..++..| +||.-.|.=|||..+||++..
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 45689999999999999887 432 88999999 999999999999999988754
No 31
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.65 E-value=0.00087 Score=68.24 Aligned_cols=46 Identities=22% Similarity=0.554 Sum_probs=43.4
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhh
Q 041991 15 KRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNY 62 (325)
Q Consensus 15 kKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~ 62 (325)
....||.+|..+|++.|+.||. +|..||+++| +|+.-||.+||.+.
T Consensus 278 ~dk~WS~qE~~LLLEGIe~ygD-dW~kVA~HVg-tKt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYGD-DWDKVARHVG-TKTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhhh-hHHHHHHHhC-CCCHHHHHHHHHcC
Confidence 6679999999999999999998 9999999999 89999999999875
No 32
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=96.65 E-value=0.00068 Score=60.40 Aligned_cols=50 Identities=26% Similarity=0.646 Sum_probs=42.4
Q ss_pred CCcCCCCHHHHHHHHHHHHHhC-CC-----CcccccccccccccchhhhhhhhhhcCC
Q 041991 14 MKRGVWSPEEDAKLIQYIKEHG-HG-----TWRHLPKQAGILRSGKSCRLRWMNYLRP 65 (325)
Q Consensus 14 lkKG~WT~EEDe~L~~lV~k~G-~~-----nW~~IAk~lg~~Rt~kQCR~RW~n~L~P 65 (325)
.++-.||.|||.+|.+.|-+|- .| -+..|++.++ ||.--|.-||..+++.
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~--RTsAACGFRWNs~VRk 57 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN--RTAAACGFRWNAYVRK 57 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc--ccHHHhcchHHHHHHH
Confidence 4678999999999999999992 22 3678888775 9999999999999884
No 33
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.59 E-value=0.0029 Score=65.57 Aligned_cols=47 Identities=13% Similarity=0.340 Sum_probs=43.4
Q ss_pred CCCCCChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHH
Q 041991 68 KRGPFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRL 114 (325)
Q Consensus 68 krg~WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~l 114 (325)
-++.||++|..+|++.+..||..|.+||.++.+||..+|--|+..+=
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~LP 298 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRLP 298 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhcC
Confidence 46789999999999999999999999999999999999999987654
No 34
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.59 E-value=0.0023 Score=65.31 Aligned_cols=45 Identities=13% Similarity=0.334 Sum_probs=42.0
Q ss_pred CCCCChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHH
Q 041991 69 RGPFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTR 113 (325)
Q Consensus 69 rg~WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~ 113 (325)
...||.+|..+|++.+..||..|.+||+|+..||..||--||-++
T Consensus 279 dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred cccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 348999999999999999999999999999999999999999754
No 35
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.57 E-value=0.0014 Score=67.79 Aligned_cols=49 Identities=22% Similarity=0.566 Sum_probs=44.5
Q ss_pred CCCCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhh
Q 041991 12 EKMKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNY 62 (325)
Q Consensus 12 ~~lkKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~ 62 (325)
...-++.||.+|+.+|++.|+.||. +|..|+.+++ .|+..||-+++.+.
T Consensus 249 ~~~~~~~WT~qE~lLLLE~ie~y~d-dW~kVa~hVg-~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 249 GESARPNWTEQETLLLLEAIEMYGD-DWNKVADHVG-TKSQEQCILKFLRL 297 (506)
T ss_pred cccCCCCccHHHHHHHHHHHHHhcc-cHHHHHhccC-CCCHHHHHHHHHhc
Confidence 3445789999999999999999998 9999999999 89999999998765
No 36
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.13 E-value=0.0023 Score=49.97 Aligned_cols=48 Identities=33% Similarity=0.722 Sum_probs=33.1
Q ss_pred cCCCCHHHHHHHHHHHHH--h----CC-C------Ccccccccc---cccccchhhhhhhhhhc
Q 041991 16 RGVWSPEEDAKLIQYIKE--H----GH-G------TWRHLPKQA---GILRSGKSCRLRWMNYL 63 (325)
Q Consensus 16 KG~WT~EEDe~L~~lV~k--~----G~-~------nW~~IAk~l---g~~Rt~kQCR~RW~n~L 63 (325)
+-.||.+|...|++++.. + +. + -|..|+..| |..|++.||+.||.+..
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~ 64 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLK 64 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 357999999999999988 2 11 1 499999875 45699999999998864
No 37
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=96.10 E-value=0.0026 Score=48.68 Aligned_cols=52 Identities=31% Similarity=0.552 Sum_probs=32.9
Q ss_pred cCCCCHHHHHHHHHHHHHhCC------C--CcccccccccccccchhhhhhhhhhcCCCC
Q 041991 16 RGVWSPEEDAKLIQYIKEHGH------G--TWRHLPKQAGILRSGKSCRLRWMNYLRPDI 67 (325)
Q Consensus 16 KG~WT~EEDe~L~~lV~k~G~------~--nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~l 67 (325)
+-+||.|||+.|+++|.++.. | -|..+++..+..++-.+-|+||...|.+..
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 458999999999999976621 2 399998887656888889999999997643
No 38
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.87 E-value=0.011 Score=53.38 Aligned_cols=50 Identities=14% Similarity=0.253 Sum_probs=42.1
Q ss_pred CCCCCChHHHHHHHHHHHhhCCC-------HHHHHhhCCCCCHHHHHHHHHHHHHHHH
Q 041991 68 KRGPFAPEEVATIIQLHGLFGNK-------WAAIASHLPGRTDNDIKNLWNTRLKKHL 118 (325)
Q Consensus 68 krg~WT~EED~~Ll~l~~~~G~k-------Ws~IA~~LpGRT~nq~KnRW~t~lkkkl 118 (325)
+.+.||.|||.+|.+.+-.|+.. ...++..| +||.-+|.-|||.++++++
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Y 60 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQY 60 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHH
Confidence 46789999999998888887632 66667788 9999999999999998765
No 39
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.74 E-value=0.026 Score=43.42 Aligned_cols=51 Identities=25% Similarity=0.423 Sum_probs=41.1
Q ss_pred CCCCChHHHHHHHHHHHhhC----C-------------CHHHHHhhC-----CCCCHHHHHHHHHHHHHHHHh
Q 041991 69 RGPFAPEEVATIIQLHGLFG----N-------------KWAAIASHL-----PGRTDNDIKNLWNTRLKKHLQ 119 (325)
Q Consensus 69 rg~WT~EED~~Ll~l~~~~G----~-------------kWs~IA~~L-----pGRT~nq~KnRW~t~lkkkl~ 119 (325)
...||.+|.+.|++++.+|- + -|..|+..| +.||..+|+.+|..+....-+
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk 74 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKK 74 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 45799999999999998872 1 299999886 249999999999988765433
No 40
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.24 E-value=0.0086 Score=58.80 Aligned_cols=50 Identities=18% Similarity=0.498 Sum_probs=45.7
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhcC
Q 041991 14 MKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLR 64 (325)
Q Consensus 14 lkKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~ 64 (325)
+----|+.+|+.+|++.....|-|||..||..+| .|....|+++|..++.
T Consensus 61 I~~e~WgadEEllli~~~~TlGlGNW~dIadyiG-sr~kee~k~HylK~y~ 110 (432)
T COG5114 61 IGEEGWGADEELLLIECLDTLGLGNWEDIADYIG-SRAKEEIKSHYLKMYD 110 (432)
T ss_pred ccCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHh-hhhhHHHHHHHHHHHh
Confidence 3345799999999999999999999999999999 8999999999998865
No 41
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=95.17 E-value=0.063 Score=60.19 Aligned_cols=103 Identities=12% Similarity=0.234 Sum_probs=76.7
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhh-------hhhh---------h------------------
Q 041991 17 GVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRL-------RWMN---------Y------------------ 62 (325)
Q Consensus 17 G~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~-------RW~n---------~------------------ 62 (325)
+.|+.-+=..++.+..+||..+...||..+. +++...++. ||.. .
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~-~k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~ 903 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEME-GKTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAI 903 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhc-CCCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3488888888888999999888888988886 566666552 1111 0
Q ss_pred ---------------c-CCCCCCCCCChHHHHHHHHHHHhhC-CCHHHHHh------------hCCCCCHHHHHHHHHHH
Q 041991 63 ---------------L-RPDIKRGPFAPEEVATIIQLHGLFG-NKWAAIAS------------HLPGRTDNDIKNLWNTR 113 (325)
Q Consensus 63 ---------------L-~P~lkrg~WT~EED~~Ll~l~~~~G-~kWs~IA~------------~LpGRT~nq~KnRW~t~ 113 (325)
+ .+.-++..||+|||..|+-++.+|| .+|..|-. ++..||+.+|..|.+++
T Consensus 904 ~~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l 983 (1033)
T PLN03142 904 GKKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTL 983 (1033)
T ss_pred HHHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHH
Confidence 0 1223445799999999999999999 67999944 24689999999999999
Q ss_pred HHHHHhh
Q 041991 114 LKKHLQS 120 (325)
Q Consensus 114 lkkkl~~ 120 (325)
++-..+.
T Consensus 984 ~~~~~~e 990 (1033)
T PLN03142 984 IRLIEKE 990 (1033)
T ss_pred HHHHHHH
Confidence 8765443
No 42
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.16 E-value=0.024 Score=55.78 Aligned_cols=47 Identities=19% Similarity=0.383 Sum_probs=42.2
Q ss_pred CCCCChHHHHHHHHHHHhhC-CCHHHHHhhCCCCCHHHHHHHHHHHHH
Q 041991 69 RGPFAPEEVATIIQLHGLFG-NKWAAIASHLPGRTDNDIKNLWNTRLK 115 (325)
Q Consensus 69 rg~WT~EED~~Ll~l~~~~G-~kWs~IA~~LpGRT~nq~KnRW~t~lk 115 (325)
...|+.+||.+|++....+| ++|..||.++..|+..+||.||..+.-
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 34799999999999999999 789999999988999999999875543
No 43
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=94.88 E-value=0.0083 Score=54.09 Aligned_cols=51 Identities=22% Similarity=0.528 Sum_probs=40.0
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCC------CcccccccccccccchhhhhhhhhhcCC
Q 041991 13 KMKRGVWSPEEDAKLIQYIKEHGHG------TWRHLPKQAGILRSGKSCRLRWMNYLRP 65 (325)
Q Consensus 13 ~lkKG~WT~EEDe~L~~lV~k~G~~------nW~~IAk~lg~~Rt~kQCR~RW~n~L~P 65 (325)
+.++..||.|||.+|.+.|.+|+.. -...++..+ +|+...|..||..+++.
T Consensus 2 k~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L--~rt~aac~fRwNs~vrk 58 (170)
T PRK13923 2 KTRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL--KRTAAACGFRWNSVVRK 58 (170)
T ss_pred cchhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH--hhhHHHHHhHHHHHHHH
Confidence 4578899999999999999998542 234555555 49999999999877763
No 44
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=94.84 E-value=0.012 Score=45.36 Aligned_cols=49 Identities=22% Similarity=0.449 Sum_probs=39.6
Q ss_pred CcCCCCHHHHHHHHHHHHHhCC----------------CCcccccccc----cccccchhhhhhhhhhc
Q 041991 15 KRGVWSPEEDAKLIQYIKEHGH----------------GTWRHLPKQA----GILRSGKSCRLRWMNYL 63 (325)
Q Consensus 15 kKG~WT~EEDe~L~~lV~k~G~----------------~nW~~IAk~l----g~~Rt~kQCR~RW~n~L 63 (325)
++..||.+|.+.|+++|.+|.. .-|..|+..+ +..|+..||+.+|.|+.
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 4678999999999999999822 1599888765 22599999999998864
No 45
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=94.31 E-value=0.076 Score=45.19 Aligned_cols=53 Identities=21% Similarity=0.333 Sum_probs=42.3
Q ss_pred CCCCCCCChHHHHHHHHHHHhhCC----CHHHHHhh------------CCCCCHHHHHHHHHHHHHHHH
Q 041991 66 DIKRGPFAPEEVATIIQLHGLFGN----KWAAIASH------------LPGRTDNDIKNLWNTRLKKHL 118 (325)
Q Consensus 66 ~lkrg~WT~EED~~Ll~l~~~~G~----kWs~IA~~------------LpGRT~nq~KnRW~t~lkkkl 118 (325)
.-++..||++||.-|+-++.+||- .|..|-.. +..||+.+|..|.+++++-..
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 556789999999999999999997 69998652 367999999999999987543
No 46
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=94.29 E-value=0.12 Score=50.55 Aligned_cols=54 Identities=22% Similarity=0.335 Sum_probs=43.2
Q ss_pred CCCCChHHHHHHHHHHHhh----------CCCHHHHHhhC----CCCCHHHHHHHHHHHHHHHHhhcc
Q 041991 69 RGPFAPEEVATIIQLHGLF----------GNKWAAIASHL----PGRTDNDIKNLWNTRLKKHLQSMN 122 (325)
Q Consensus 69 rg~WT~EED~~Ll~l~~~~----------G~kWs~IA~~L----pGRT~nq~KnRW~t~lkkkl~~~~ 122 (325)
...|+.+|-..||++..+. +..|..||+.+ --||+.+||++|.++.++..+...
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k~ 121 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEKA 121 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHhc
Confidence 3689999999999988653 23499999965 239999999999999887665533
No 47
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=93.80 E-value=0.16 Score=40.08 Aligned_cols=46 Identities=33% Similarity=0.550 Sum_probs=36.4
Q ss_pred CCChHHHHHHHHHHHhh---CC----------CHHHHHhhC---CC--CCHHHHHHHHHHHHHH
Q 041991 71 PFAPEEVATIIQLHGLF---GN----------KWAAIASHL---PG--RTDNDIKNLWNTRLKK 116 (325)
Q Consensus 71 ~WT~EED~~Ll~l~~~~---G~----------kWs~IA~~L---pG--RT~nq~KnRW~t~lkk 116 (325)
.||+++++.|++++.+. |+ .|..|+..| +| .|..+|+|||..+.+.
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 59999999999998653 22 299999887 33 5789999999877765
No 48
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=92.41 E-value=0.1 Score=52.59 Aligned_cols=54 Identities=22% Similarity=0.320 Sum_probs=47.8
Q ss_pred CCCCChHHHHHHHHHHHhhCCCHHHHHhh-----CCC-CCHHHHHHHHHHHHHHHHhhcc
Q 041991 69 RGPFAPEEVATIIQLHGLFGNKWAAIASH-----LPG-RTDNDIKNLWNTRLKKHLQSMN 122 (325)
Q Consensus 69 rg~WT~EED~~Ll~l~~~~G~kWs~IA~~-----LpG-RT~nq~KnRW~t~lkkkl~~~~ 122 (325)
...||.+|-.-|.++++.|.-+|-.||.. ++. ||-.++|.||+.+.++.++-.+
T Consensus 130 dn~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~ 189 (445)
T KOG2656|consen 130 DNSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARA 189 (445)
T ss_pred cccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHHHHHHHHHccC
Confidence 35799999999999999999999999987 555 9999999999999998876543
No 49
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=91.47 E-value=0.26 Score=49.64 Aligned_cols=48 Identities=19% Similarity=0.354 Sum_probs=44.0
Q ss_pred CCCChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 041991 70 GPFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKH 117 (325)
Q Consensus 70 g~WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkk 117 (325)
.+|+.+|-++.+++..++|..++.|+..||.|...|||-+|..--|+.
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~n 413 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKVN 413 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhhC
Confidence 389999999999999999999999999999999999999998665543
No 50
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=90.85 E-value=0.83 Score=47.05 Aligned_cols=48 Identities=19% Similarity=0.328 Sum_probs=43.4
Q ss_pred CCCCCChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHH
Q 041991 68 KRGPFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLK 115 (325)
Q Consensus 68 krg~WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lk 115 (325)
-...||.||-.++-+++..||.++.+|-+.||.|+-..|..+|....|
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK 233 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKK 233 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHH
Confidence 345899999999999999999999999999999999999998876554
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=88.70 E-value=1.4 Score=31.24 Aligned_cols=42 Identities=31% Similarity=0.389 Sum_probs=31.9
Q ss_pred hHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 74 PEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 74 ~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
++++..++.++...|-.|.+||..+ |.+...|+++....+++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARKK 53 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHhh
Confidence 4678889999999999999999999 99999999987665553
No 52
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=84.98 E-value=0.57 Score=45.87 Aligned_cols=48 Identities=31% Similarity=0.542 Sum_probs=37.8
Q ss_pred cCCCCHHHHHHHHHHHHHh----CCC-----Ccccccccc---cccccchhhhhhhhhhc
Q 041991 16 RGVWSPEEDAKLIQYIKEH----GHG-----TWRHLPKQA---GILRSGKSCRLRWMNYL 63 (325)
Q Consensus 16 KG~WT~EEDe~L~~lV~k~----G~~-----nW~~IAk~l---g~~Rt~kQCR~RW~n~L 63 (325)
-..|+.+|-..|+++..+. ..+ .|..|++.+ |..|++.||+.||.|..
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 3789999999999988644 222 599999843 44599999999998854
No 53
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=84.67 E-value=0.66 Score=46.87 Aligned_cols=49 Identities=16% Similarity=0.220 Sum_probs=43.6
Q ss_pred CCCCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhh
Q 041991 12 EKMKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNY 62 (325)
Q Consensus 12 ~~lkKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~ 62 (325)
.+..--+||.+|-+++.+++...|. ++..|+..+| +|..+|+..+|.+-
T Consensus 361 ~~~~~~~Ws~~e~ekFYKALs~wGt-dF~LIs~lfP-~R~RkqIKaKfi~E 409 (507)
T COG5118 361 KKKGALRWSKKEIEKFYKALSIWGT-DFSLISSLFP-NRERKQIKAKFIKE 409 (507)
T ss_pred CCCCCCcccHHHHHHHHHHHHHhcc-hHHHHHHhcC-chhHHHHHHHHHHH
Confidence 3444568999999999999999998 9999999998 89999999999875
No 54
>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=83.48 E-value=0.84 Score=38.88 Aligned_cols=37 Identities=27% Similarity=0.452 Sum_probs=30.3
Q ss_pred ccCCCCcCCCCHHHHHHHHHHHHHhCC---CCcccccccc
Q 041991 10 DMEKMKRGVWSPEEDAKLIQYIKEHGH---GTWRHLPKQA 46 (325)
Q Consensus 10 dk~~lkKG~WT~EEDe~L~~lV~k~G~---~nW~~IAk~l 46 (325)
+.+..++..||.+||.-|+-.+.+||. +.|..|-..+
T Consensus 43 y~~~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~I 82 (118)
T PF09111_consen 43 YPPNNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEI 82 (118)
T ss_dssp STSTSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHH
T ss_pred cCCCCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHH
Confidence 345778999999999999999999999 8998887655
No 55
>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=74.88 E-value=9.1 Score=26.73 Aligned_cols=41 Identities=24% Similarity=0.357 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 75 EEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 75 EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
+++..++.++-..|-.+.+||..| |-+...|+++-+..+++
T Consensus 7 ~~er~vi~~~y~~~~t~~eIa~~l-g~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 7 PREREVIRLRYFEGLTLEEIAERL-GISRSTVRRILKRALKK 47 (50)
T ss_dssp HHHHHHHHHHHTST-SHHHHHHHH-TSCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHH-CCcHHHHHHHHHHHHHH
Confidence 456666666666677899999999 99999999988777664
No 56
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=71.20 E-value=15 Score=36.49 Aligned_cols=51 Identities=20% Similarity=0.378 Sum_probs=39.8
Q ss_pred CCCCChHHHHHHHHHHHhh-CCC---HHHHHhhCCCCCHHHHHHHHHHHHHHHHh
Q 041991 69 RGPFAPEEVATIIQLHGLF-GNK---WAAIASHLPGRTDNDIKNLWNTRLKKHLQ 119 (325)
Q Consensus 69 rg~WT~EED~~Ll~l~~~~-G~k---Ws~IA~~LpGRT~nq~KnRW~t~lkkkl~ 119 (325)
-..||.-|...|+.+.+.. |.. -..|++.++||+..+|++.-+.+..+.++
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rvar 75 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRVAR 75 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHHHH
Confidence 3589999999999888765 433 67899999999999999976665554443
No 57
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=69.37 E-value=12 Score=26.04 Aligned_cols=38 Identities=21% Similarity=0.308 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHhhCCC-HHHHHhhCCCCCHHHHHHHHHHH
Q 041991 75 EEVATIIQLHGLFGNK-WAAIASHLPGRTDNDIKNLWNTR 113 (325)
Q Consensus 75 EED~~Ll~l~~~~G~k-Ws~IA~~LpGRT~nq~KnRW~t~ 113 (325)
+=|..|+.+...-|.. |..||+.+ |=+...|..|++.+
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 4578889888888855 99999999 99999999998654
No 58
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=68.72 E-value=15 Score=30.47 Aligned_cols=40 Identities=23% Similarity=0.326 Sum_probs=30.3
Q ss_pred HHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 76 EVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 76 ED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
++..++.++...|-.+.+||+.+ |.+...|++++...+++
T Consensus 117 ~~r~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 117 QCRKIFILSRFEGKSYKEIAEEL-GISVKTVEYHISKALKE 156 (161)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 33444455445578899999999 99999999999876554
No 59
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=68.37 E-value=8.7 Score=41.16 Aligned_cols=49 Identities=8% Similarity=0.324 Sum_probs=39.3
Q ss_pred CCCCChHHHHHHHHHHHhhCCCHHHHH----------hhCCCCCHHHHHHHHHHHHHHH
Q 041991 69 RGPFAPEEVATIIQLHGLFGNKWAAIA----------SHLPGRTDNDIKNLWNTRLKKH 117 (325)
Q Consensus 69 rg~WT~EED~~Ll~l~~~~G~kWs~IA----------~~LpGRT~nq~KnRW~t~lkkk 117 (325)
+..||.+|++-...+++++|.++..|- ....-+|..|++.||+..+++.
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m 146 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRM 146 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHH
Confidence 668999999999999999999998882 2233467788888888766643
No 60
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=66.34 E-value=5.7 Score=31.62 Aligned_cols=25 Identities=40% Similarity=0.830 Sum_probs=14.1
Q ss_pred CCCCcCCCCHHHHHHH--------HHHHHHhCC
Q 041991 12 EKMKRGVWSPEEDAKL--------IQYIKEHGH 36 (325)
Q Consensus 12 ~~lkKG~WT~EEDe~L--------~~lV~k~G~ 36 (325)
|.-..|-||+|+|+.| ..++++||.
T Consensus 43 P~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG~ 75 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLRSGDKDDIERLIKKHGE 75 (87)
T ss_dssp -TT-TT---HHHHHHHTS--HHHHHHHHHHH-H
T ss_pred CCCCCCCcCHHHHHHHHcCCHHHHHHHHHHhCH
Confidence 3455789999999999 446667764
No 61
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=66.30 E-value=11 Score=41.34 Aligned_cols=47 Identities=11% Similarity=0.114 Sum_probs=42.4
Q ss_pred CCCCChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHH
Q 041991 69 RGPFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLK 115 (325)
Q Consensus 69 rg~WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lk 115 (325)
...||..|-.++-+++..|-..+-.|++.++++|-.+|-.+|++..|
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtWKK 665 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTWKK 665 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHHHH
Confidence 35899999999999999999999999999999999999998776543
No 62
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=66.21 E-value=7.9 Score=34.58 Aligned_cols=40 Identities=23% Similarity=0.259 Sum_probs=34.4
Q ss_pred CCChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHH
Q 041991 71 PFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWN 111 (325)
Q Consensus 71 ~WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~ 111 (325)
.||+|+.++|.+|..+ |..=++||..|.|.|.|.|.-+-+
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 5999999999999855 888899999997799999976543
No 63
>smart00595 MADF subfamily of SANT domain.
Probab=64.08 E-value=10 Score=29.41 Aligned_cols=25 Identities=28% Similarity=0.625 Sum_probs=21.7
Q ss_pred HHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 91 WAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 91 Ws~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
|..||..| |-+..+|+.+|+++...
T Consensus 30 W~~Ia~~l-~~~~~~~~~kw~~LR~~ 54 (89)
T smart00595 30 WEEIAEEL-GLSVEECKKRWKNLRDR 54 (89)
T ss_pred HHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 99999999 55999999999987654
No 64
>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=63.50 E-value=8.9 Score=30.00 Aligned_cols=45 Identities=24% Similarity=0.656 Sum_probs=29.8
Q ss_pred CCCHHHHHHHHHHHHHh---CC----C-----Ccccccccc----cccccchhhhhhhhhh
Q 041991 18 VWSPEEDAKLIQYIKEH---GH----G-----TWRHLPKQA----GILRSGKSCRLRWMNY 62 (325)
Q Consensus 18 ~WT~EEDe~L~~lV~k~---G~----~-----nW~~IAk~l----g~~Rt~kQCR~RW~n~ 62 (325)
.||+++++.|++++.+. |. + .|..|++.+ +...+.+||+.||...
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~l 61 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTL 61 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHH
Confidence 59999999999998655 21 1 266666544 2335667777776543
No 65
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=61.22 E-value=5.4 Score=27.73 Aligned_cols=38 Identities=26% Similarity=0.462 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhh
Q 041991 22 EEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMN 61 (325)
Q Consensus 22 EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n 61 (325)
+=|.+|+.++++.+.-.|..|++.+| =+...|+.|+..
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 577778887754
No 66
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=60.62 E-value=15 Score=37.35 Aligned_cols=46 Identities=15% Similarity=0.260 Sum_probs=40.3
Q ss_pred CCCChHHHHHHHHHHHhhCCCHHHHH-hhCCCCCHHHHHHHHHHHHH
Q 041991 70 GPFAPEEVATIIQLHGLFGNKWAAIA-SHLPGRTDNDIKNLWNTRLK 115 (325)
Q Consensus 70 g~WT~EED~~Ll~l~~~~G~kWs~IA-~~LpGRT~nq~KnRW~t~lk 115 (325)
..|+++|-+..-+.++.||..+..|- -+++.|+--+|-.+|+...|
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWKk 324 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWKK 324 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhhc
Confidence 37999999999999999999999995 45899999999988765554
No 67
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=60.16 E-value=28 Score=28.48 Aligned_cols=51 Identities=20% Similarity=0.158 Sum_probs=36.1
Q ss_pred CCCChHHHHHHHHHHHhh----C----CCHHHHHhhCCC-----CCHHHHHHHHHHHHHHHHhh
Q 041991 70 GPFAPEEVATIIQLHGLF----G----NKWAAIASHLPG-----RTDNDIKNLWNTRLKKHLQS 120 (325)
Q Consensus 70 g~WT~EED~~Ll~l~~~~----G----~kWs~IA~~LpG-----RT~nq~KnRW~t~lkkkl~~ 120 (325)
.-||+++|..||+.+..| | ..|..+-..+.+ =+.+|+.++-+.+.+|....
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~ 68 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNA 68 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHH
Confidence 469999999999999877 6 246555444322 37789988887777665443
No 68
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=59.82 E-value=17 Score=31.46 Aligned_cols=46 Identities=11% Similarity=0.051 Sum_probs=38.2
Q ss_pred hHHHHHHHHHHHhhCC-CHHHHHhhCCCCCHHHHHHHHHHHHHHHHhh
Q 041991 74 PEEVATIIQLHGLFGN-KWAAIASHLPGRTDNDIKNLWNTRLKKHLQS 120 (325)
Q Consensus 74 ~EED~~Ll~l~~~~G~-kWs~IA~~LpGRT~nq~KnRW~t~lkkkl~~ 120 (325)
.+-|..|+++.++-|. .|+.||+.+ |-+...|++|++.+....+.+
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGIIT 54 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 3578888888888774 499999999 999999999998887766543
No 69
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=58.52 E-value=6.4 Score=34.11 Aligned_cols=45 Identities=20% Similarity=0.251 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhcCCCCC
Q 041991 22 EEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPDIK 68 (325)
Q Consensus 22 EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lk 68 (325)
+-|.+|+.++++.|.-.|..||+.++ -+...|+.|+.+...-++-
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~lg--lS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQFG--VSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCe
Confidence 57999999999999999999999997 7889999999887665543
No 70
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=58.38 E-value=27 Score=27.91 Aligned_cols=38 Identities=26% Similarity=0.276 Sum_probs=28.6
Q ss_pred HHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 78 ATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 78 ~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
..++.++...|..+..||+.+ |-+...|+++.+..+++
T Consensus 116 ~~ii~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 116 REVLVLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred HHHHhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 334444445688899999999 77999999988876554
No 71
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=56.50 E-value=29 Score=30.76 Aligned_cols=41 Identities=15% Similarity=0.158 Sum_probs=31.9
Q ss_pred HHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 041991 76 EVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKH 117 (325)
Q Consensus 76 ED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkk 117 (325)
+...++++..-.|-.+.+||..| |-+...|+.+|.....+-
T Consensus 139 ~~~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR~~l 179 (185)
T PF07638_consen 139 RQRRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRARAWL 179 (185)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 34455555555688999999999 999999999998776443
No 72
>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=54.36 E-value=2.4e+02 Score=28.32 Aligned_cols=86 Identities=17% Similarity=0.295 Sum_probs=62.4
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCc---ccccccccccccchhhhhhhhhhcCCCCCCCCCChHHHHHHHHHHHh-h----
Q 041991 16 RGVWSPEEDAKLIQYIKEHGHGTW---RHLPKQAGILRSGKSCRLRWMNYLRPDIKRGPFAPEEVATIIQLHGL-F---- 87 (325)
Q Consensus 16 KG~WT~EEDe~L~~lV~k~G~~nW---~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkrg~WT~EED~~Ll~l~~~-~---- 87 (325)
-..||.-|...|+.+.+......+ ..|++.+. +|+..++++ |.+.|+ +..+.+++++ |
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~-~Rs~aEI~~-fl~~LK------------~rvareaiqkv~~~g~ 86 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELP-GRSEAEIRD-FLQQLK------------GRVAREAIQKVHPGGL 86 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhcc-CcCHHHHHH-HHHHHH------------HHHHHHHHHHhccccc
Confidence 468999999999999987643333 46777787 799988876 445554 3344455544 1
Q ss_pred -CC------------CHHHHHhhCCCCCHHHHHHHHHHHHH
Q 041991 88 -GN------------KWAAIASHLPGRTDNDIKNLWNTRLK 115 (325)
Q Consensus 88 -G~------------kWs~IA~~LpGRT~nq~KnRW~t~lk 115 (325)
|. -|..+|+.+.|.-...|---|-++|.
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 21 29999999999999999888877765
No 73
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=54.28 E-value=12 Score=39.79 Aligned_cols=45 Identities=16% Similarity=0.268 Sum_probs=41.9
Q ss_pred CCCCCChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHH
Q 041991 68 KRGPFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNT 112 (325)
Q Consensus 68 krg~WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t 112 (325)
..++|+.+|-++......++|.+.+.|+..+|+|...+||.++..
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKK 452 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhh
Confidence 456899999999999999999999999999999999999998854
No 74
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=54.28 E-value=16 Score=39.27 Aligned_cols=48 Identities=10% Similarity=0.383 Sum_probs=35.8
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCccccccc----------ccccccchhhhhhhhhhcC
Q 041991 15 KRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQ----------AGILRSGKSCRLRWMNYLR 64 (325)
Q Consensus 15 kKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~----------lg~~Rt~kQCR~RW~n~L~ 64 (325)
+|..||..|.+-+..+++++|. ++..|-+. .. .++-.|+|.+|.+.+.
T Consensus 87 ~ktaWt~~E~~~Ffdal~~~GK-dFe~VinaklKRrna~s~~~-~Ktkdqvr~~yY~~~~ 144 (782)
T KOG4468|consen 87 AKTAWTHQEEESFFDALRQVGK-DFEKVINAKLKRRNATSRVQ-SKTKDQVRHYYYRLVR 144 (782)
T ss_pred cccccchhhHHHHHHHHHHhcc-cHHHHHHHHHHhcccccchh-hhhhHHHHHHHHHHHH
Confidence 3668999999999999999998 88877221 21 2566778887766543
No 75
>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=54.21 E-value=43 Score=22.01 Aligned_cols=38 Identities=21% Similarity=0.220 Sum_probs=27.8
Q ss_pred HHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHH
Q 041991 76 EVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRL 114 (325)
Q Consensus 76 ED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~l 114 (325)
++..++.++...|-.+..||+.+ |-+...|+.+.+...
T Consensus 14 ~~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~~ 51 (55)
T cd06171 14 REREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRAL 51 (55)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 34556666656778899999999 788888877665543
No 76
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=52.83 E-value=34 Score=28.96 Aligned_cols=37 Identities=16% Similarity=0.160 Sum_probs=27.6
Q ss_pred HHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 041991 80 IIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKH 117 (325)
Q Consensus 80 Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkk 117 (325)
++.++...|-.+..||..| |.+...|+++....+++-
T Consensus 136 vl~l~~~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~L 172 (182)
T PRK09652 136 AITLREIEGLSYEEIAEIM-GCPIGTVRSRIFRAREAL 172 (182)
T ss_pred HHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3334444577899999999 999999999887655443
No 77
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=52.64 E-value=6.6 Score=34.44 Aligned_cols=45 Identities=20% Similarity=0.262 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhcCCCC
Q 041991 21 PEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPDI 67 (325)
Q Consensus 21 ~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~l 67 (325)
-+-|.+|+.++++.|.-.|..||+.++ -+...|+.|+....+-++
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 457999999999999999999999997 688889999988766554
No 78
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=52.07 E-value=21 Score=37.15 Aligned_cols=40 Identities=23% Similarity=0.439 Sum_probs=36.6
Q ss_pred CCChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHH
Q 041991 71 PFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWN 111 (325)
Q Consensus 71 ~WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~ 111 (325)
.||++|-. +++....||.+...||..+...|+.|++.+|.
T Consensus 472 ~wSp~e~s-~ircf~~y~~~fe~ia~l~~tktp~Q~~~fy~ 511 (534)
T KOG1194|consen 472 GWSPEEKS-AIRCFHWYKDNFELIAELMATKTPEQIKKFYM 511 (534)
T ss_pred CCCCcccc-cccCchhhccchHHHHHHhcCCCHHHHHHHhc
Confidence 69998887 88888899999999999999999999999884
No 79
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=51.38 E-value=69 Score=32.80 Aligned_cols=55 Identities=13% Similarity=0.251 Sum_probs=43.6
Q ss_pred CCCCCCChHHHHHHHHHHHhhC----------------CCHHHHHhhC-----CCCCHHHHHHHHHHHHHHHHhhc
Q 041991 67 IKRGPFAPEEVATIIQLHGLFG----------------NKWAAIASHL-----PGRTDNDIKNLWNTRLKKHLQSM 121 (325)
Q Consensus 67 lkrg~WT~EED~~Ll~l~~~~G----------------~kWs~IA~~L-----pGRT~nq~KnRW~t~lkkkl~~~ 121 (325)
.-.|.|+++=|+-..++..+|- +|=..||+++ ..||..||-.|-+-+-|+++++.
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~rei 149 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLREI 149 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHH
Confidence 4568999999999999999873 2468888875 34899999999887777776653
No 80
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=51.33 E-value=24 Score=30.90 Aligned_cols=45 Identities=7% Similarity=-0.034 Sum_probs=37.8
Q ss_pred hHHHHHHHHHHHhhCC-CHHHHHhhCCCCCHHHHHHHHHHHHHHHHh
Q 041991 74 PEEVATIIQLHGLFGN-KWAAIASHLPGRTDNDIKNLWNTRLKKHLQ 119 (325)
Q Consensus 74 ~EED~~Ll~l~~~~G~-kWs~IA~~LpGRT~nq~KnRW~t~lkkkl~ 119 (325)
.+-|.+|+.+.++-|. .|+.||+.+ |-+...|..|++.+.+..+.
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~GvI 58 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGFI 58 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 4568888888877774 599999999 99999999999888877654
No 81
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=50.37 E-value=48 Score=29.10 Aligned_cols=41 Identities=20% Similarity=0.263 Sum_probs=29.4
Q ss_pred HHHhhCCCHHHHHhhCCCCCHHHHHHHHHH---HHHHHHhhcccC
Q 041991 83 LHGLFGNKWAAIASHLPGRTDNDIKNLWNT---RLKKHLQSMNHN 124 (325)
Q Consensus 83 l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t---~lkkkl~~~~~~ 124 (325)
++...|-.-.+||..| |-+...|+++... .|++.+.+.++.
T Consensus 147 L~~~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr~~l~~~~~~ 190 (195)
T PRK12532 147 LKEILGFSSDEIQQMC-GISTSNYHTIMHRARESLRQCLQIKWFN 190 (195)
T ss_pred hHHHhCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 3334567789999999 9999999998875 445555554444
No 82
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=50.15 E-value=36 Score=28.74 Aligned_cols=33 Identities=21% Similarity=0.177 Sum_probs=25.6
Q ss_pred HHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 83 LHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 83 l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
++...|-.+..||..| |-+...|++++...+++
T Consensus 136 l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 168 (179)
T PRK11924 136 LRYVEGLSYREIAEIL-GVPVGTVKSRLRRARQL 168 (179)
T ss_pred HHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3334577899999999 99999999988765543
No 83
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=49.28 E-value=16 Score=42.16 Aligned_cols=74 Identities=15% Similarity=0.238 Sum_probs=45.3
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhcCCCCCCCCCChHHHHHHHHHHHhh-CCCHHH
Q 041991 15 KRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPDIKRGPFAPEEVATIIQLHGLF-GNKWAA 93 (325)
Q Consensus 15 kKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkrg~WT~EED~~Ll~l~~~~-G~kWs~ 93 (325)
.---|..+||.+|+-.|-+||.|+|..|----.++=+. ...+...+-.+.|=..+-..|+.+.... +.+|..
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir~Dp~L~l~d-------Ki~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~ 1204 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIRLDPDLGLTD-------KIFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPK 1204 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhccCccccchh-------hhcccccCCchHHHHHHHHHHHHHHhhcccCCCch
Confidence 34579999999999999999999999885321111111 1112222334556666666777776665 444444
Q ss_pred HH
Q 041991 94 IA 95 (325)
Q Consensus 94 IA 95 (325)
..
T Consensus 1205 ~~ 1206 (1373)
T KOG0384|consen 1205 KL 1206 (1373)
T ss_pred hh
Confidence 43
No 84
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=49.12 E-value=54 Score=28.39 Aligned_cols=38 Identities=11% Similarity=0.108 Sum_probs=28.4
Q ss_pred HHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHHHHhhc
Q 041991 83 LHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKHLQSM 121 (325)
Q Consensus 83 l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkkl~~~ 121 (325)
++...|-...+||..| |-+...|+.++...+++-....
T Consensus 142 l~~~~g~s~~eIA~~l-~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 142 SISVEGASIKETAAKL-SMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred HHHHcCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHHHh
Confidence 3333467799999999 9999999999887766544443
No 85
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=48.18 E-value=12 Score=41.09 Aligned_cols=44 Identities=11% Similarity=0.223 Sum_probs=39.1
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhh
Q 041991 16 RGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMN 61 (325)
Q Consensus 16 KG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n 61 (325)
--.||+.|-.++.+++..|.. ++..|++.+. +++-+||-+-|..
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~K-DF~~v~km~~-~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSK-DFIFVQKMVK-SKTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhcc-cHHHHHHHhc-cccHHHHHHHHHH
Confidence 468999999999999999987 8999999998 8999999876644
No 86
>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=47.43 E-value=25 Score=26.30 Aligned_cols=27 Identities=26% Similarity=0.458 Sum_probs=22.0
Q ss_pred HHHHHhhCCC-CCHHHHHHHHHHHHHHH
Q 041991 91 WAAIASHLPG-RTDNDIKNLWNTRLKKH 117 (325)
Q Consensus 91 Ws~IA~~LpG-RT~nq~KnRW~t~lkkk 117 (325)
|..||..|.. -+.++|+.+|+++...-
T Consensus 29 w~~Ia~~l~~~~~~~~~~~~w~~Lr~~y 56 (85)
T PF10545_consen 29 WQEIARELGKEFSVDDCKKRWKNLRDRY 56 (85)
T ss_pred HHHHHHHHccchhHHHHHHHHHHHHHHH
Confidence 9999999953 57889999999876543
No 87
>smart00351 PAX Paired Box domain.
Probab=47.18 E-value=1.3e+02 Score=25.23 Aligned_cols=84 Identities=17% Similarity=0.209 Sum_probs=52.6
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccc-cchhhhhhhhh--hcCCCC----CCCCCChHHHHHHHHHHHh
Q 041991 14 MKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILR-SGKSCRLRWMN--YLRPDI----KRGPFAPEEVATIIQLHGL 86 (325)
Q Consensus 14 lkKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~R-t~kQCR~RW~n--~L~P~l----krg~WT~EED~~Ll~l~~~ 86 (325)
.+..+++.++-++++.++. -|. .-..||+.++..| +...+..||.. .+.|.- ....-+.+++..|++++.+
T Consensus 13 ~~~~~~s~~~R~riv~~~~-~G~-s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~ 90 (125)
T smart00351 13 VNGRPLPDEERQRIVELAQ-NGV-RPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQE 90 (125)
T ss_pred cCCCCCCHHHHHHHHHHHH-cCC-CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHH
Confidence 4556799999999998886 454 7799999998654 34445555543 244432 2223555666667766655
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHH
Q 041991 87 FGNKWAAIASHLPGRTDNDIKNLW 110 (325)
Q Consensus 87 ~G~kWs~IA~~LpGRT~nq~KnRW 110 (325)
. |..|..+++..|
T Consensus 91 ~-----------p~~t~~el~~~L 103 (125)
T smart00351 91 N-----------PGIFAWEIRDRL 103 (125)
T ss_pred C-----------CCCCHHHHHHHH
Confidence 3 455565555544
No 88
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=47.13 E-value=41 Score=24.56 Aligned_cols=36 Identities=17% Similarity=0.292 Sum_probs=26.3
Q ss_pred hHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHH
Q 041991 74 PEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLW 110 (325)
Q Consensus 74 ~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW 110 (325)
.+.|+-.+.++.+.|-.-.+||+++ ||+.+.|+++-
T Consensus 6 t~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl 41 (50)
T PF11427_consen 6 TDAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRYL 41 (50)
T ss_dssp -HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHHH
T ss_pred CHHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHHh
Confidence 4566777888889999999999999 99999988754
No 89
>PRK04217 hypothetical protein; Provisional
Probab=46.77 E-value=50 Score=27.82 Aligned_cols=45 Identities=16% Similarity=0.104 Sum_probs=36.4
Q ss_pred CCChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 041991 71 PFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKH 117 (325)
Q Consensus 71 ~WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkk 117 (325)
.-|.+| ..++.++...|-...+||+.+ |-+...|+++|+...++-
T Consensus 42 ~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 42 FMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKKV 86 (110)
T ss_pred cCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 455555 677777777888999999999 999999999998765543
No 90
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=46.15 E-value=64 Score=28.07 Aligned_cols=40 Identities=23% Similarity=0.140 Sum_probs=31.3
Q ss_pred HHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHHHHhhc
Q 041991 81 IQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKHLQSM 121 (325)
Q Consensus 81 l~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkkl~~~ 121 (325)
+.++...|-...+||..| |-+.+.|+.+....+++-+.++
T Consensus 136 ~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~~~~ 175 (178)
T PRK12529 136 FLMATLDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCLSLM 175 (178)
T ss_pred HHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHhC
Confidence 334444577899999999 9999999999988877766553
No 91
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=45.69 E-value=45 Score=31.04 Aligned_cols=44 Identities=18% Similarity=0.243 Sum_probs=34.8
Q ss_pred CCChHHHHHHHHHHHhhCCCHHHHHhhC--C-CCCHHHHHHHHHHHHH
Q 041991 71 PFAPEEVATIIQLHGLFGNKWAAIASHL--P-GRTDNDIKNLWNTRLK 115 (325)
Q Consensus 71 ~WT~EED~~Ll~l~~~~G~kWs~IA~~L--p-GRT~nq~KnRW~t~lk 115 (325)
.|+.++|-+|+..+.. |+.-..|+..+ . .-|-.+|..||+.+|-
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~lly 47 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALLY 47 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHHc
Confidence 4999999999988855 67777776654 2 3588999999998874
No 92
>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=45.40 E-value=8.6 Score=30.21 Aligned_cols=40 Identities=28% Similarity=0.576 Sum_probs=28.1
Q ss_pred HHHHHHHHhCC-------CCccccccccccccc----chhhhhhhhhhcCC
Q 041991 26 KLIQYIKEHGH-------GTWRHLPKQAGILRS----GKSCRLRWMNYLRP 65 (325)
Q Consensus 26 ~L~~lV~k~G~-------~nW~~IAk~lg~~Rt----~kQCR~RW~n~L~P 65 (325)
+|..+|.++|. +.|..|++.+++... ..+++..|.+||.|
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 57777777763 369999999986542 35678888887753
No 93
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=44.92 E-value=25 Score=37.58 Aligned_cols=51 Identities=16% Similarity=0.331 Sum_probs=45.2
Q ss_pred cccCCCCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhh
Q 041991 9 CDMEKMKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMN 61 (325)
Q Consensus 9 cdk~~lkKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n 61 (325)
.+.++...++|+.+|-++........|. +...|+..++ .|..+|++.+|.+
T Consensus 402 t~sk~~~~~~w~~se~e~fyka~~~~gs-~~slis~l~p-~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 402 TYSKKLETDKWDASETELFYKALSERGS-DFSLISNLFP-LRDRKQIKAKFKK 452 (584)
T ss_pred hccCccccCcccchhhHHhhhHHhhhcc-cccccccccc-cccHHHHHHHHhh
Confidence 3456777899999999999999999998 9999999888 7999999998765
No 94
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=44.52 E-value=55 Score=28.13 Aligned_cols=30 Identities=10% Similarity=-0.061 Sum_probs=24.5
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 041991 87 FGNKWAAIASHLPGRTDNDIKNLWNTRLKKH 117 (325)
Q Consensus 87 ~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkk 117 (325)
.|..+.+||..| |-+...|+++.....++-
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar~~L 180 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREAL 180 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 467799999999 999999999887665543
No 95
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=44.18 E-value=59 Score=28.72 Aligned_cols=36 Identities=17% Similarity=0.163 Sum_probs=27.0
Q ss_pred HHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 80 IIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 80 Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
++.++...|-...+||..| |-+...|++++...+++
T Consensus 142 i~~l~~~~g~s~~EIA~~l-g~s~~tV~~rl~rar~~ 177 (192)
T PRK09643 142 ALVAVDMQGYSVADAARML-GVAEGTVKSRCARGRAR 177 (192)
T ss_pred HHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3334444577899999999 99999999999654443
No 96
>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=43.78 E-value=35 Score=27.27 Aligned_cols=29 Identities=28% Similarity=0.486 Sum_probs=23.8
Q ss_pred HHHHHHHHHhhCCCHHHHHhhCCCCCHHHH
Q 041991 77 VATIIQLHGLFGNKWAAIASHLPGRTDNDI 106 (325)
Q Consensus 77 D~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~ 106 (325)
|+.|..+...+|..|..+|.+| |=|..+|
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 5668888999999999999999 6666555
No 97
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=43.61 E-value=61 Score=28.55 Aligned_cols=29 Identities=7% Similarity=-0.012 Sum_probs=23.7
Q ss_pred hhCCCHHHHHhhCCCCCHHHHHHHHHHHHH
Q 041991 86 LFGNKWAAIASHLPGRTDNDIKNLWNTRLK 115 (325)
Q Consensus 86 ~~G~kWs~IA~~LpGRT~nq~KnRW~t~lk 115 (325)
..|-...+||..| |-+...||.|....++
T Consensus 148 ~~g~s~~EIA~~l-gis~~tVk~~l~RAr~ 176 (189)
T PRK12530 148 YLELSSEQICQEC-DISTSNLHVLLYRARL 176 (189)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3467799999999 9999999998775443
No 98
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=42.70 E-value=80 Score=27.12 Aligned_cols=42 Identities=19% Similarity=0.257 Sum_probs=30.9
Q ss_pred HHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHHHHhhc
Q 041991 79 TIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKHLQSM 121 (325)
Q Consensus 79 ~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkkl~~~ 121 (325)
.++.++...|-...+||+.| |-+...|+++-..-+++-....
T Consensus 126 ~v~~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~~~~l 167 (172)
T PRK12523 126 AAFLYNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQCYIAL 167 (172)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHh
Confidence 34444444577899999999 9999999998877666544433
No 99
>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=42.66 E-value=41 Score=26.85 Aligned_cols=31 Identities=16% Similarity=0.337 Sum_probs=25.2
Q ss_pred HHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHH
Q 041991 77 VATIIQLHGLFGNKWAAIASHLPGRTDNDIKN 108 (325)
Q Consensus 77 D~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~Kn 108 (325)
|..|..+...+|..|.++|..| |=+..+|.+
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI~~ 34 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEINQ 34 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHHHH
Confidence 6678888899999999999999 666665543
No 100
>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=42.05 E-value=51 Score=28.44 Aligned_cols=31 Identities=10% Similarity=0.002 Sum_probs=24.7
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHHHHHH
Q 041991 87 FGNKWAAIASHLPGRTDNDIKNLWNTRLKKHL 118 (325)
Q Consensus 87 ~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkkl 118 (325)
.|-...+||..| |-+.+.|+++....+++-.
T Consensus 153 ~~~s~~EIA~~l-gis~~tv~~~l~rar~~Lr 183 (190)
T TIGR02939 153 EGLSYEDIARIM-DCPVGTVRSRIFRAREAIA 183 (190)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 356799999999 8899999999876665433
No 101
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=41.91 E-value=79 Score=26.42 Aligned_cols=33 Identities=15% Similarity=0.118 Sum_probs=25.7
Q ss_pred HHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 83 LHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 83 l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
++...|-.-.+||..| |-+.+.|+++....+++
T Consensus 117 l~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 117 LRYWEDMDVAETAAAM-GCSEGSVKTHCSRATHA 149 (161)
T ss_pred HHHHhcCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3334467799999999 99999999998765544
No 102
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=41.87 E-value=54 Score=26.06 Aligned_cols=45 Identities=13% Similarity=0.072 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHhhCC-CHHHHHhhCCCCCHHHHHHHHHHHHHHHHhh
Q 041991 75 EEVATIIQLHGLFGN-KWAAIASHLPGRTDNDIKNLWNTRLKKHLQS 120 (325)
Q Consensus 75 EED~~Ll~l~~~~G~-kWs~IA~~LpGRT~nq~KnRW~t~lkkkl~~ 120 (325)
+.|..|+.+..+.|. .+..||+.+ |-+...|..+.+.+.++.+-+
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 568888888888774 599999999 999999999998888765433
No 103
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=41.60 E-value=33 Score=30.31 Aligned_cols=49 Identities=16% Similarity=0.228 Sum_probs=36.8
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCcccccccccc---cccchhhhhhhhhhc
Q 041991 14 MKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGI---LRSGKSCRLRWMNYL 63 (325)
Q Consensus 14 lkKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~---~Rt~kQCR~RW~n~L 63 (325)
.+..+-+..|.+-|..+|.+||. ++...+.-.-+ ..|.+||+.+...|.
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhGd-Dy~aMarD~KLN~~Q~T~~qlrrki~~~k 163 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHGD-DYKAMARDRKLNYMQHTPGQLRRKIRKYK 163 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHCc-cHHHHhccCCCCcccCCHHHHHHHHHHhc
Confidence 45677889999999999999997 88877754332 377777777665553
No 104
>PRK13858 type IV secretion system T-DNA border endonuclease VirD1; Provisional
Probab=40.94 E-value=37 Score=30.23 Aligned_cols=84 Identities=17% Similarity=0.091 Sum_probs=64.7
Q ss_pred CCCCCCcccccCCCCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhcCCCCCCCCCChHHHHHH
Q 041991 1 MGKRKTPFCDMEKMKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPDIKRGPFAPEEVATI 80 (325)
Q Consensus 1 lG~~R~~~cdk~~lkKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkrg~WT~EED~~L 80 (325)
+|+.|.|+-+-+++..-+.|++|=..|..-....|. +..++-+.+- .|.+ +.++-..-|.|+-..|
T Consensus 13 ~~~~~~~~~~~~kvVsvRLTe~Ey~~L~~rA~~aGl-S~SEfIRqAi-~~~~------------g~V~v~r~T~e~~~~l 78 (147)
T PRK13858 13 VDRRESAKVEGFKVVSTRLRSAEYESFSAQARLLGL-SDSMAIRVAV-RRIG------------GFLEIDAETREKMEAI 78 (147)
T ss_pred cccccCccccCCeEEEEecCHHHHHHHHHHHHHcCC-CHHHHHHHHH-HhcC------------CeEeecccCHHHHHHH
Confidence 477888888888999999999999999999999997 5554444332 1111 2232356788888889
Q ss_pred HHHHHhhCCCHHHHHhhC
Q 041991 81 IQLHGLFGNKWAAIASHL 98 (325)
Q Consensus 81 l~l~~~~G~kWs~IA~~L 98 (325)
+.-+...|++-.+||+++
T Consensus 79 ir~l~gianNLNQLAr~a 96 (147)
T PRK13858 79 LQSIGTLSSNIAALLSAY 96 (147)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 999999999999999987
No 105
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=39.94 E-value=64 Score=26.87 Aligned_cols=46 Identities=24% Similarity=0.320 Sum_probs=33.8
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhcC
Q 041991 15 KRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLR 64 (325)
Q Consensus 15 kKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~ 64 (325)
++..||.|+-..++..+...|. +-..|++.+++ ..+--.+|.+.+.
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g~-sv~evA~e~gI---s~~tl~~W~r~y~ 54 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPGM-TVSLVARQHGV---AASQLFLWRKQYQ 54 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCCC-CHHHHHHHHCc---CHHHHHHHHHHHh
Confidence 4578999998888888877776 67789998885 3334456777654
No 106
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=39.83 E-value=58 Score=29.66 Aligned_cols=44 Identities=23% Similarity=0.299 Sum_probs=35.7
Q ss_pred CCCChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 70 GPFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 70 g~WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
...|+.|-+.|.-+.+ |-.=.+||..| +.+...||+|..++++|
T Consensus 147 ~~LT~RE~eVL~lla~--G~snkeIA~~L-~iS~~TVk~h~~~i~~K 190 (211)
T COG2197 147 ELLTPRELEVLRLLAE--GLSNKEIAEEL-NLSEKTVKTHVSNILRK 190 (211)
T ss_pred CCCCHHHHHHHHHHHC--CCCHHHHHHHH-CCCHhHHHHHHHHHHHH
Confidence 3688888777665543 55568999999 99999999999999986
No 107
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=39.42 E-value=78 Score=26.97 Aligned_cols=32 Identities=19% Similarity=0.226 Sum_probs=25.3
Q ss_pred hhCCCHHHHHhhCCCCCHHHHHHHHHHHHHHHH
Q 041991 86 LFGNKWAAIASHLPGRTDNDIKNLWNTRLKKHL 118 (325)
Q Consensus 86 ~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkkl 118 (325)
..|-....||..| |-|...|++++...+++-.
T Consensus 133 ~~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~Lr 164 (169)
T TIGR02954 133 YHDLTIKEIAEVM-NKPEGTVKTYLHRALKKLK 164 (169)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 3466789999999 8899999999887666533
No 108
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=38.99 E-value=24 Score=36.12 Aligned_cols=50 Identities=16% Similarity=0.252 Sum_probs=42.1
Q ss_pred CCCCcCCCCHHHHHHHHHHHHHhCCCCccccccc-----ccccccchhhhhhhhhh
Q 041991 12 EKMKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQ-----AGILRSGKSCRLRWMNY 62 (325)
Q Consensus 12 ~~lkKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~-----lg~~Rt~kQCR~RW~n~ 62 (325)
..++-.-||.||-+-|++++++|.- .|-.|+.+ .+..|+--...+||...
T Consensus 126 ~~l~dn~WskeETD~LF~lck~fDL-Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v 180 (445)
T KOG2656|consen 126 AHLNDNSWSKEETDYLFDLCKRFDL-RFFVIADRYDNQQYKKSRTVEDLKERYYSV 180 (445)
T ss_pred HhhccccccHHHHHHHHHHHHhcCe-eEEEEeeccchhhccccccHHHHHHHHHHH
Confidence 4456678999999999999999997 89999987 55449999999998765
No 109
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=38.70 E-value=98 Score=26.38 Aligned_cols=33 Identities=24% Similarity=0.212 Sum_probs=25.6
Q ss_pred HHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 83 LHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 83 l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
++...|-.-.+||..| |.+...|+.+....+++
T Consensus 129 L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 161 (173)
T PRK09645 129 RSYYRGWSTAQIAADL-GIPEGTVKSRLHYALRA 161 (173)
T ss_pred HHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3334467789999999 99999999998866554
No 110
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=38.69 E-value=74 Score=27.32 Aligned_cols=30 Identities=10% Similarity=-0.061 Sum_probs=24.1
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 041991 87 FGNKWAAIASHLPGRTDNDIKNLWNTRLKKH 117 (325)
Q Consensus 87 ~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkk 117 (325)
.|....+||..| |-+.+.|+++....+++-
T Consensus 151 ~g~s~~eIA~~l-gis~~~v~~~l~Rar~~L 180 (187)
T TIGR02948 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREAL 180 (187)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 356789999999 889999999887665543
No 111
>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=38.47 E-value=73 Score=24.86 Aligned_cols=37 Identities=19% Similarity=0.291 Sum_probs=25.7
Q ss_pred HHHHHHHhhC--------CCHHHHHhhCCC---CC--HHHHHHHHHHHHH
Q 041991 79 TIIQLHGLFG--------NKWAAIASHLPG---RT--DNDIKNLWNTRLK 115 (325)
Q Consensus 79 ~Ll~l~~~~G--------~kWs~IA~~LpG---RT--~nq~KnRW~t~lk 115 (325)
.|..+|.+.| .+|..||+.|.- -+ ..+++..|..+|-
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhH
Confidence 4666677777 369999999822 12 3678888877764
No 112
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=38.34 E-value=75 Score=27.73 Aligned_cols=31 Identities=13% Similarity=0.077 Sum_probs=24.9
Q ss_pred HhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 85 GLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 85 ~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
...|-...+||..| |-+...|++++...+++
T Consensus 144 ~~~~~s~~eIA~~l-gis~~tV~~~l~Rar~~ 174 (189)
T PRK12515 144 YYHEKSVEEVGEIV-GIPESTVKTRMFYARKK 174 (189)
T ss_pred HHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 33567799999999 88999999998865543
No 113
>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=38.01 E-value=17 Score=28.91 Aligned_cols=17 Identities=29% Similarity=0.514 Sum_probs=10.1
Q ss_pred CCCCCCCCChHHHHHHH
Q 041991 65 PDIKRGPFAPEEVATII 81 (325)
Q Consensus 65 P~lkrg~WT~EED~~Ll 81 (325)
|.-..|-||+++|+.|.
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 55668899999999984
No 114
>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=37.92 E-value=38 Score=26.48 Aligned_cols=30 Identities=27% Similarity=0.647 Sum_probs=23.7
Q ss_pred HHHHHHHHHhhCCCHHHHHhhCCCCCHHHHH
Q 041991 77 VATIIQLHGLFGNKWAAIASHLPGRTDNDIK 107 (325)
Q Consensus 77 D~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~K 107 (325)
|..|..+...+|..|.++|.+| |=+..+|.
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI~ 33 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDID 33 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHHH
Confidence 4567788889999999999999 66655553
No 115
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=37.56 E-value=79 Score=27.58 Aligned_cols=29 Identities=14% Similarity=0.051 Sum_probs=23.5
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 87 FGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 87 ~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
.|-...+||..| |-+.+.|++++...+++
T Consensus 153 ~g~s~~eIA~~l-gis~~tv~~~l~Rar~~ 181 (193)
T PRK11923 153 DGLSYEDIASVM-QCPVGTVRSRIFRAREA 181 (193)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466789999999 88999999998765543
No 116
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=37.15 E-value=95 Score=27.01 Aligned_cols=33 Identities=15% Similarity=0.155 Sum_probs=25.6
Q ss_pred HHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 041991 84 HGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKH 117 (325)
Q Consensus 84 ~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkk 117 (325)
+...|....+||..| |-+...|+.+....+++-
T Consensus 151 ~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~L 183 (189)
T PRK09648 151 RVVVGLSAEETAEAV-GSTPGAVRVAQHRALARL 183 (189)
T ss_pred HHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 333467899999999 999999999887666543
No 117
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=36.91 E-value=17 Score=28.77 Aligned_cols=41 Identities=27% Similarity=0.611 Sum_probs=29.1
Q ss_pred HHHHHHHHHhCC-------CCcccccccccccc----cchhhhhhhhhhcCC
Q 041991 25 AKLIQYIKEHGH-------GTWRHLPKQAGILR----SGKSCRLRWMNYLRP 65 (325)
Q Consensus 25 e~L~~lV~k~G~-------~nW~~IAk~lg~~R----t~kQCR~RW~n~L~P 65 (325)
-+|..+|.+.|. ..|..|+..+++.- ...+.+..|.+||.|
T Consensus 35 ~~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~ 86 (93)
T smart00501 35 YRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLP 86 (93)
T ss_pred HHHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHH
Confidence 357777877754 37999999998643 245667778777765
No 118
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=35.74 E-value=82 Score=27.61 Aligned_cols=34 Identities=26% Similarity=0.164 Sum_probs=26.3
Q ss_pred HHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 82 QLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 82 ~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
.+....|-...+||..| |-+...|+++....+++
T Consensus 116 ~l~~~~g~~~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (181)
T PRK09637 116 RLTELEGLSQKEIAEKL-GLSLSGAKSRVQRGRVK 149 (181)
T ss_pred HHHHhcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 33334577899999999 99999999998765544
No 119
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=34.66 E-value=1.2e+02 Score=26.65 Aligned_cols=32 Identities=19% Similarity=0.154 Sum_probs=26.0
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHHHHHHh
Q 041991 87 FGNKWAAIASHLPGRTDNDIKNLWNTRLKKHLQ 119 (325)
Q Consensus 87 ~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkkl~ 119 (325)
.|-.-.+||..| |-+...|+++....+++-.+
T Consensus 145 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 145 LGLSYADAAAVC-GCPVGTIRSRVARARDALLA 176 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHh
Confidence 456789999999 99999999998777665444
No 120
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=33.93 E-value=82 Score=27.83 Aligned_cols=46 Identities=17% Similarity=0.201 Sum_probs=37.8
Q ss_pred CCCCCChHHHHHHHHHHHhhCCCHHHHHhhCC----CCCHHHHHHHHHHH
Q 041991 68 KRGPFAPEEVATIIQLHGLFGNKWAAIASHLP----GRTDNDIKNLWNTR 113 (325)
Q Consensus 68 krg~WT~EED~~Ll~l~~~~G~kWs~IA~~Lp----GRT~nq~KnRW~t~ 113 (325)
....-+..|...|..|+.+||.++...+.-.. -.|..||+.+.+.+
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 44578899999999999999999999987643 38999998877654
No 121
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=33.46 E-value=1.1e+02 Score=26.56 Aligned_cols=32 Identities=9% Similarity=0.014 Sum_probs=24.3
Q ss_pred hhCCCHHHHHhhCCCCCHHHHHHHHHHHHHHHH
Q 041991 86 LFGNKWAAIASHLPGRTDNDIKNLWNTRLKKHL 118 (325)
Q Consensus 86 ~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkkl 118 (325)
..|-...+||+.| |-+.+.|+++....+++-.
T Consensus 142 ~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr 173 (186)
T PRK05602 142 YQGLSNIEAAAVM-DISVDALESLLARGRRALR 173 (186)
T ss_pred hcCCCHHHHHHHh-CcCHHHHHHHHHHHHHHHH
Confidence 3466789999999 9999999998776554433
No 122
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=33.04 E-value=1.2e+02 Score=27.07 Aligned_cols=36 Identities=19% Similarity=0.152 Sum_probs=26.0
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHH---HHHHHhhccc
Q 041991 87 FGNKWAAIASHLPGRTDNDIKNLWNTR---LKKHLQSMNH 123 (325)
Q Consensus 87 ~G~kWs~IA~~LpGRT~nq~KnRW~t~---lkkkl~~~~~ 123 (325)
.|-.-.+||..| |.+...||++.... |++.+...+.
T Consensus 154 eg~s~~EIA~~l-gis~~tVk~~l~RAr~~Lr~~l~~~~~ 192 (201)
T PRK12545 154 LDFEIDDICTEL-TLTANHCSVLLYRARTRLRTCLSEKGL 192 (201)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 456789999999 99999999987644 4444544333
No 123
>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=32.92 E-value=1.3e+02 Score=25.86 Aligned_cols=29 Identities=21% Similarity=0.200 Sum_probs=23.9
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 87 FGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 87 ~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
.|-...+||..| |-+...|+++....+++
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 177 (183)
T TIGR02999 149 AGLTVEEIAELL-GVSVRTVERDWRFARAW 177 (183)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 466799999999 99999999988766554
No 124
>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=32.55 E-value=63 Score=25.58 Aligned_cols=26 Identities=27% Similarity=0.640 Sum_probs=20.4
Q ss_pred HHHHHhhCCCHHHHHhhCCCCCHHHHH
Q 041991 81 IQLHGLFGNKWAAIASHLPGRTDNDIK 107 (325)
Q Consensus 81 l~l~~~~G~kWs~IA~~LpGRT~nq~K 107 (325)
..+....|..|..+|.+| |=+..+|.
T Consensus 11 ~~ia~~iG~~Wk~Lar~L-Gls~~dI~ 36 (86)
T cd08318 11 TVFANKLGEDWKTLAPHL-EMKDKEIR 36 (86)
T ss_pred HHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 335577899999999999 77777663
No 125
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=32.16 E-value=1.3e+02 Score=25.25 Aligned_cols=33 Identities=15% Similarity=-0.033 Sum_probs=25.2
Q ss_pred HHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 83 LHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 83 l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
++...|-.-.+||..| |-+...|+++....+++
T Consensus 117 l~~~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (160)
T PRK09642 117 AHYLEEKSYQEIALQE-KIEVKTVEMKLYRARKW 149 (160)
T ss_pred HHHHhCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3334467789999999 99999999987755543
No 126
>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=32.16 E-value=65 Score=24.65 Aligned_cols=30 Identities=27% Similarity=0.535 Sum_probs=22.0
Q ss_pred HHHHHHHHHHh-hCCCHHHHHhhCCCCCHHHH
Q 041991 76 EVATIIQLHGL-FGNKWAAIASHLPGRTDNDI 106 (325)
Q Consensus 76 ED~~Ll~l~~~-~G~kWs~IA~~LpGRT~nq~ 106 (325)
-++.|..+... .|..|..+|++| |=+..+|
T Consensus 4 ~~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i 34 (88)
T smart00005 4 TREKLAKLLDHPLGLDWRELARKL-GLSEADI 34 (88)
T ss_pred HHHHHHHHHcCccchHHHHHHHHc-CCCHHHH
Confidence 34566677777 899999999999 4455554
No 127
>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=32.07 E-value=1.2e+02 Score=26.75 Aligned_cols=36 Identities=11% Similarity=0.144 Sum_probs=27.3
Q ss_pred HHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 80 IIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 80 Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
++.++...|....+||..| |-+.+.|+.|....+++
T Consensus 139 v~~l~~~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 139 VFMMREVLGFESDEICQEL-EISTSNCHVLLYRARLS 174 (188)
T ss_pred HHHHHHHhCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3344444577899999999 99999999988766554
No 128
>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=31.84 E-value=97 Score=21.06 Aligned_cols=33 Identities=21% Similarity=0.121 Sum_probs=25.1
Q ss_pred HHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHH
Q 041991 76 EVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNL 109 (325)
Q Consensus 76 ED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnR 109 (325)
|...|.++...+|++....|+.| |=+...+..+
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~k 38 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLL-GISRRTLYRK 38 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHH
Confidence 67788899999999999999999 6666655443
No 129
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=31.60 E-value=1.4e+02 Score=25.34 Aligned_cols=37 Identities=19% Similarity=0.131 Sum_probs=27.0
Q ss_pred HHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHHHHh
Q 041991 82 QLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKHLQ 119 (325)
Q Consensus 82 ~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkkl~ 119 (325)
.++...|-...+||..| |-+...|+++-...+++-..
T Consensus 122 ~l~~~~g~s~~eIA~~l-gis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 122 ILIGASGFSYEDAAAIC-GCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred HHHHHcCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHH
Confidence 33334567799999999 88999999987766655433
No 130
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=31.39 E-value=1e+02 Score=26.71 Aligned_cols=57 Identities=26% Similarity=0.438 Sum_probs=33.0
Q ss_pred cchhhhhhhhhhcCCCCCCCCCChHHHHHHHHHHHhh--CCCHHHHHhhCCCCCHHHHHHHHHHHHHHHHh
Q 041991 51 SGKSCRLRWMNYLRPDIKRGPFAPEEVATIIQLHGLF--GNKWAAIASHLPGRTDNDIKNLWNTRLKKHLQ 119 (325)
Q Consensus 51 t~kQCR~RW~n~L~P~lkrg~WT~EED~~Ll~l~~~~--G~kWs~IA~~LpGRT~nq~KnRW~t~lkkkl~ 119 (325)
-.+.+-++|...|. +|++.+++++-.- |..|-.||..| +-+..+|+ +|+.-+|..+.
T Consensus 70 ~~k~~id~~~~~l~----------de~k~Ii~lry~~r~~~TW~~IA~~l-~i~erta~-r~~~~fK~~i~ 128 (130)
T PF05263_consen 70 RQKEAIDRWLETLI----------DEEKRIIKLRYDRRSRRTWYQIAQKL-HISERTAR-RWRDRFKNDIY 128 (130)
T ss_pred HHHHHHHHHHHhhC----------HHHHHHHHHHHcccccchHHHHHHHh-CccHHHHH-HHHHHHHHHhc
Confidence 34445555555443 3456666665433 36699999998 45555554 46666665443
No 131
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=31.27 E-value=62 Score=22.36 Aligned_cols=36 Identities=31% Similarity=0.389 Sum_probs=18.4
Q ss_pred CCChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHH
Q 041991 71 PFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKN 108 (325)
Q Consensus 71 ~WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~Kn 108 (325)
.+|.+|-..|..++ .-|..=.+||+.| ||+...|.+
T Consensus 4 ~Lt~~eR~~I~~l~-~~G~s~~~IA~~l-g~s~sTV~r 39 (44)
T PF13936_consen 4 HLTPEERNQIEALL-EQGMSIREIAKRL-GRSRSTVSR 39 (44)
T ss_dssp --------HHHHHH-CS---HHHHHHHT-T--HHHHHH
T ss_pred chhhhHHHHHHHHH-HcCCCHHHHHHHH-CcCcHHHHH
Confidence 46777777766665 5678889999999 999988865
No 132
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=31.17 E-value=1.3e+02 Score=26.43 Aligned_cols=30 Identities=13% Similarity=0.047 Sum_probs=24.1
Q ss_pred hhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 86 LFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 86 ~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
..|-...+||..| |-+...|+.|....+++
T Consensus 155 ~eg~s~~EIA~~l-gis~~tVk~rl~ra~~~ 184 (194)
T PRK12531 155 LEELPHQQVAEMF-DIPLGTVKSRLRLAVEK 184 (194)
T ss_pred HcCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 3466789999999 99999999988765554
No 133
>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=31.08 E-value=67 Score=25.44 Aligned_cols=31 Identities=19% Similarity=0.406 Sum_probs=25.1
Q ss_pred HHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHH
Q 041991 77 VATIIQLHGLFGNKWAAIASHLPGRTDNDIKN 108 (325)
Q Consensus 77 D~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~Kn 108 (325)
|..|-.+...+|.+|..+|+.| |=+..+|.+
T Consensus 4 ~~~l~~ia~~LG~dWk~LAr~L-g~se~dI~~ 34 (84)
T cd08804 4 EERLAVIADHLGFSWTELAREL-DFTEEQIHQ 34 (84)
T ss_pred hhHHHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 4567777888999999999999 777776655
No 134
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=30.33 E-value=1.1e+02 Score=24.04 Aligned_cols=38 Identities=21% Similarity=0.330 Sum_probs=26.3
Q ss_pred HHHHHHHhhC--------CCHHHHHhhCCC-----CCHHHHHHHHHHHHHH
Q 041991 79 TIIQLHGLFG--------NKWAAIASHLPG-----RTDNDIKNLWNTRLKK 116 (325)
Q Consensus 79 ~Ll~l~~~~G--------~kWs~IA~~LpG-----RT~nq~KnRW~t~lkk 116 (325)
.|..++.+.| +.|..|+..|.- ....+++..|..+|..
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~ 86 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLP 86 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHH
Confidence 3556666666 369999999832 2356788888877754
No 135
>cd00131 PAX Paired Box domain
Probab=29.95 E-value=2.7e+02 Score=23.55 Aligned_cols=74 Identities=14% Similarity=0.111 Sum_probs=46.2
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccc-cchhhhhhhhhh--cCCCCCCC----CCChHHHHHHHHHHH
Q 041991 13 KMKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILR-SGKSCRLRWMNY--LRPDIKRG----PFAPEEVATIIQLHG 85 (325)
Q Consensus 13 ~lkKG~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~R-t~kQCR~RW~n~--L~P~lkrg----~WT~EED~~Ll~l~~ 85 (325)
.....+.+.++-++++.++. .|. ....||+.++..+ +-..+..||... +.|....| .-+.+.+..|+.++.
T Consensus 12 ~~m~~~lS~d~R~rIv~~~~-~G~-s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~ 89 (128)
T cd00131 12 FVNGRPLPDSIRQRIVELAQ-SGI-RPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQ 89 (128)
T ss_pred ccCCCcCCHHHHHHHHHHHH-cCC-CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHH
Confidence 34567889999999998885 565 8899999887543 233334444432 44533222 246666676776665
Q ss_pred hhC
Q 041991 86 LFG 88 (325)
Q Consensus 86 ~~G 88 (325)
+.+
T Consensus 90 ~~p 92 (128)
T cd00131 90 ENP 92 (128)
T ss_pred HCC
Confidence 543
No 136
>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=29.57 E-value=66 Score=25.25 Aligned_cols=33 Identities=30% Similarity=0.560 Sum_probs=25.3
Q ss_pred hHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHH
Q 041991 74 PEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKN 108 (325)
Q Consensus 74 ~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~Kn 108 (325)
.||.++|+..- ..|.+|..+|.+| |=+...|.+
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 46777777422 5688999999999 777877765
No 137
>PLN03162 golden-2 like transcription factor; Provisional
Probab=29.24 E-value=3.3e+02 Score=28.07 Aligned_cols=45 Identities=13% Similarity=0.094 Sum_probs=36.7
Q ss_pred CCCChHHHHHHHHHHHhhCCC---HHHHHhhC--CCCCHHHHHHHHHHHH
Q 041991 70 GPFAPEEVATIIQLHGLFGNK---WAAIASHL--PGRTDNDIKNLWNTRL 114 (325)
Q Consensus 70 g~WT~EED~~Ll~l~~~~G~k---Ws~IA~~L--pGRT~nq~KnRW~t~l 114 (325)
=.||.|-.++.++++.++|.. =..|=+.| +|=|..+|+.|.+.+.
T Consensus 238 LrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYR 287 (526)
T PLN03162 238 VDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYR 287 (526)
T ss_pred ccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHH
Confidence 479999999999999999943 56676665 8899999998876543
No 138
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.24 E-value=1.7e+02 Score=23.77 Aligned_cols=45 Identities=20% Similarity=0.349 Sum_probs=36.0
Q ss_pred CCCCChHHHHHHHHHHHhhCCCHHHHHhhCCCC-CHHHHHHHHHHHHH
Q 041991 69 RGPFAPEEVATIIQLHGLFGNKWAAIASHLPGR-TDNDIKNLWNTRLK 115 (325)
Q Consensus 69 rg~WT~EED~~Ll~l~~~~G~kWs~IA~~LpGR-T~nq~KnRW~t~lk 115 (325)
+..||.|.-..+++++.+-|..=+.||+.+ |- ..+++. +|...+.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~-~W~~~~~ 50 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLY-KWRIQLQ 50 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHH-HHHHHHH
Confidence 568999999999999999998889999999 75 565554 4654444
No 139
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=28.85 E-value=47 Score=27.63 Aligned_cols=28 Identities=18% Similarity=0.077 Sum_probs=23.5
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 88 GNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 88 G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
|-.+.+||..| |-+...|++++...+++
T Consensus 121 g~s~~eIA~~l-gis~~tv~~~l~Ra~~~ 148 (154)
T TIGR02950 121 EFSYKEIAELL-NLSLAKVKSNLFRARKE 148 (154)
T ss_pred cCcHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 45799999999 99999999998766554
No 140
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=28.64 E-value=1.3e+02 Score=26.48 Aligned_cols=33 Identities=15% Similarity=0.080 Sum_probs=24.7
Q ss_pred HHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 83 LHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 83 l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
++...|-.+.+||+.| |-+.+.|+++-...+++
T Consensus 147 L~~~~g~s~~eIA~~l-gis~~tV~~~l~Ra~~~ 179 (196)
T PRK12524 147 LRHIEGLSNPEIAEVM-EIGVEAVESLTARGKRA 179 (196)
T ss_pred HHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3333467899999999 88899998887655443
No 141
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=28.32 E-value=1.6e+02 Score=25.25 Aligned_cols=29 Identities=17% Similarity=0.173 Sum_probs=23.6
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 87 FGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 87 ~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
.|-.-..||..| |.+...|+++....+++
T Consensus 144 ~g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 172 (179)
T PRK12514 144 EGLSYKELAERH-DVPLNTMRTWLRRSLLK 172 (179)
T ss_pred cCCCHHHHHHHH-CCChHHHHHHHHHHHHH
Confidence 366789999999 99999999988765554
No 142
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=28.30 E-value=1.8e+02 Score=25.12 Aligned_cols=30 Identities=20% Similarity=0.127 Sum_probs=23.8
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 041991 87 FGNKWAAIASHLPGRTDNDIKNLWNTRLKKH 117 (325)
Q Consensus 87 ~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkk 117 (325)
.|-.-.+||..+ |-+...|+++.+..+++-
T Consensus 150 ~~~s~~eIA~~l-gis~~~V~~~l~ra~~~L 179 (186)
T PRK13919 150 QGYTHREAAQLL-GLPLGTLKTRARRALSRL 179 (186)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 355689999999 999999999887666543
No 143
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=28.00 E-value=1.4e+02 Score=27.29 Aligned_cols=43 Identities=21% Similarity=0.193 Sum_probs=33.8
Q ss_pred CCChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 71 PFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 71 ~WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
..|+.|-+.| +++.+ |....+||+.| +-+...|++|...+++|
T Consensus 155 ~Lt~rE~~Vl-~l~~~-G~s~~eIA~~L-~iS~~TVk~~~~~i~~K 197 (216)
T PRK10100 155 LLTHREKEIL-NKLRI-GASNNEIARSL-FISENTVKTHLYNLFKK 197 (216)
T ss_pred CCCHHHHHHH-HHHHc-CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 4777665555 45544 88899999999 89999999988888765
No 144
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=27.50 E-value=1.4e+02 Score=25.51 Aligned_cols=34 Identities=26% Similarity=0.508 Sum_probs=25.7
Q ss_pred HHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 82 QLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 82 ~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
.++...|-...+||..| |-+...|+++....+++
T Consensus 150 ~l~~~~g~s~~eIA~~l-gis~~~v~~~l~Ra~~~ 183 (189)
T TIGR02984 150 LLRHLEGLSFAEVAERM-DRSEGAVSMLWVRGLAR 183 (189)
T ss_pred HHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 33334567789999999 99999999988766654
No 145
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=27.49 E-value=47 Score=26.41 Aligned_cols=44 Identities=18% Similarity=0.233 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhcCCCC
Q 041991 22 EEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPDI 67 (325)
Q Consensus 22 EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~l 67 (325)
+.|.+++.++.+.+.-.+..|++.++ -+...|+.|.......++
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~--~s~~tv~~~l~~L~~~g~ 46 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVG--LSPSTVHNRVKRLEEEGV 46 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 57889999999998889999999987 678888888777665443
No 146
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=27.39 E-value=1.2e+02 Score=26.10 Aligned_cols=29 Identities=21% Similarity=0.277 Sum_probs=23.7
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 87 FGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 87 ~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
.|-...+||+.| |-+.+.|+++....+++
T Consensus 134 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 162 (172)
T PRK09651 134 DGLTYSEIAHKL-GVSVSSVKKYVAKATEH 162 (172)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 456799999999 99999999988765543
No 147
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=27.37 E-value=1.7e+02 Score=25.29 Aligned_cols=34 Identities=24% Similarity=0.094 Sum_probs=26.3
Q ss_pred HHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 041991 83 LHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKH 117 (325)
Q Consensus 83 l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkk 117 (325)
++...|-...+||+.| |.+...|+++-...+++-
T Consensus 140 l~~~~g~s~~EIA~~l-~is~~tV~~~l~rar~~L 173 (181)
T PRK12536 140 HVKLEGLSVAETAQLT-GLSESAVKVGIHRGLKAL 173 (181)
T ss_pred HHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3334567899999999 999999999887655543
No 148
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=27.35 E-value=1.9e+02 Score=24.27 Aligned_cols=42 Identities=17% Similarity=0.114 Sum_probs=30.4
Q ss_pred HHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHHHH
Q 041991 76 EVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKHL 118 (325)
Q Consensus 76 ED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkkl 118 (325)
++..++.+....|-.=.+||..| |-+...|+++....+++-.
T Consensus 114 ~~r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~ra~~~Lr 155 (162)
T TIGR02983 114 RQRAVVVLRYYEDLSEAQVAEAL-GISVGTVKSRLSRALARLR 155 (162)
T ss_pred HHHHHhhhHHHhcCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 33444444445577789999999 9999999999887666543
No 149
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=26.87 E-value=1.6e+02 Score=25.92 Aligned_cols=36 Identities=25% Similarity=0.206 Sum_probs=26.7
Q ss_pred HHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 80 IIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 80 Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
++.+....|-...+||+.| |-+...|+++-...+++
T Consensus 124 i~~L~~~~g~s~~EIA~~L-gis~~tVk~~l~Rar~~ 159 (187)
T PRK12516 124 AIILVGASGFAYEEAAEIC-GCAVGTIKSRVNRARQR 159 (187)
T ss_pred HHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3444444577899999999 99999999987655443
No 150
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=26.73 E-value=1.8e+02 Score=25.23 Aligned_cols=31 Identities=29% Similarity=0.284 Sum_probs=24.5
Q ss_pred hhCCCHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 041991 86 LFGNKWAAIASHLPGRTDNDIKNLWNTRLKKH 117 (325)
Q Consensus 86 ~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkk 117 (325)
..|-.-..||+.| |-+...|+++....+++-
T Consensus 147 ~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~L 177 (182)
T PRK12537 147 VDGCSHAEIAQRL-GAPLGTVKAWIKRSLKAL 177 (182)
T ss_pred HcCCCHHHHHHHH-CCChhhHHHHHHHHHHHH
Confidence 3466788999999 899999999888776543
No 151
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=26.59 E-value=77 Score=27.05 Aligned_cols=31 Identities=19% Similarity=0.330 Sum_probs=24.1
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHHHHHH
Q 041991 87 FGNKWAAIASHLPGRTDNDIKNLWNTRLKKHL 118 (325)
Q Consensus 87 ~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkkl 118 (325)
+|-....||..| |-+...|+++....+++-.
T Consensus 141 ~g~s~~eIA~~l-~is~~~V~~~l~ra~~~l~ 171 (176)
T PRK09638 141 YGYTYEEIAKML-NIPEGTVKSRVHHGIKQLR 171 (176)
T ss_pred cCCCHHHHHHHH-CCChhHHHHHHHHHHHHHH
Confidence 466799999999 8899999888776555433
No 152
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=26.21 E-value=46 Score=26.44 Aligned_cols=26 Identities=31% Similarity=0.668 Sum_probs=20.8
Q ss_pred HHHHHHHHhhCCCHHHHHhhCCCCCHH
Q 041991 78 ATIIQLHGLFGNKWAAIASHLPGRTDN 104 (325)
Q Consensus 78 ~~Ll~l~~~~G~kWs~IA~~LpGRT~n 104 (325)
..|..+...+|..|..+|.+| |=+..
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L-Glse~ 28 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL-GLSYR 28 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc-CCCHH
Confidence 457888899999999999998 54433
No 153
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=26.07 E-value=1.8e+02 Score=27.11 Aligned_cols=43 Identities=19% Similarity=0.258 Sum_probs=34.4
Q ss_pred CCChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 71 PFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 71 ~WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
..|+.|-+.|.-+. + |....+||..| +-+...|+++...+++|
T Consensus 133 ~LSpRErEVLrLLA-q-GkTnKEIAe~L-~IS~rTVkth~srImkK 175 (198)
T PRK15201 133 HFSVTERHLLKLIA-S-GYHLSETAALL-SLSEEQTKSLRRSIMRK 175 (198)
T ss_pred CCCHHHHHHHHHHH-C-CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 57887776655444 3 88899999999 99999999988877775
No 154
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=25.97 E-value=1.7e+02 Score=24.22 Aligned_cols=29 Identities=21% Similarity=0.282 Sum_probs=21.8
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 87 FGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 87 ~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
.|-...+||..+ |-+...|+++-...+++
T Consensus 121 ~~~s~~EIA~~l-~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 121 VGKTMGEIALET-EMTYYQVRWIYRQALEK 149 (154)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 356688899998 88888998876655443
No 155
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=25.96 E-value=1.4e+02 Score=26.88 Aligned_cols=43 Identities=9% Similarity=0.114 Sum_probs=33.9
Q ss_pred CCChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 71 PFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 71 ~WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
..|+.|-+.|..+.. |....+||+.| +-+...|++|-+.+++|
T Consensus 137 ~LT~RE~eVL~lla~--G~snkeIA~~L-~iS~~TVk~h~~~I~~K 179 (207)
T PRK15411 137 SLSRTESSMLRMWMA--GQGTIQISDQM-NIKAKTVSSHKGNIKRK 179 (207)
T ss_pred cCCHHHHHHHHHHHc--CCCHHHHHHHc-CCCHHHHHHHHHHHHHH
Confidence 488888776655443 66679999999 89999999988777765
No 156
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=25.62 E-value=1.9e+02 Score=24.23 Aligned_cols=44 Identities=20% Similarity=0.258 Sum_probs=34.4
Q ss_pred CCCChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 70 GPFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 70 g~WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
...|+.|-+.|.-+.. |-...+||..+ +-+...|++|.+++++|
T Consensus 136 ~~Lt~~E~~il~~l~~--g~~~~~Ia~~l-~~s~~tv~~~~~~l~~K 179 (196)
T PRK10360 136 DPLTKRERQVAEKLAQ--GMAVKEIAAEL-GLSPKTVHVHRANLMEK 179 (196)
T ss_pred cCCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 4688887776665554 56789999999 77999999988877765
No 157
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=25.30 E-value=1.8e+02 Score=24.48 Aligned_cols=33 Identities=24% Similarity=0.257 Sum_probs=25.0
Q ss_pred HHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHH
Q 041991 82 QLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLK 115 (325)
Q Consensus 82 ~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lk 115 (325)
.++...|-...+||..+ |-+.+.|+++....++
T Consensus 123 ~L~~~~g~s~~EIA~~l-~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 123 LLAQVDGLGYGEIATEL-GISLATVKRYLNKAAM 155 (161)
T ss_pred HHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 33334567799999999 8999999998776654
No 158
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=25.30 E-value=1.8e+02 Score=26.15 Aligned_cols=33 Identities=15% Similarity=0.169 Sum_probs=25.8
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHHHHHHhh
Q 041991 87 FGNKWAAIASHLPGRTDNDIKNLWNTRLKKHLQS 120 (325)
Q Consensus 87 ~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkkl~~ 120 (325)
.|..-.+||+.| |-+...|++++...+++-.+.
T Consensus 153 ~g~s~~EIA~~L-gis~~tV~~~l~RArk~Lr~~ 185 (203)
T PRK09647 153 EGLSYEEIAATL-GVKLGTVRSRIHRGRQQLRAA 185 (203)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHH
Confidence 466788999999 999999999988766654443
No 159
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=25.14 E-value=2.1e+02 Score=24.04 Aligned_cols=30 Identities=23% Similarity=0.245 Sum_probs=23.7
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 041991 87 FGNKWAAIASHLPGRTDNDIKNLWNTRLKKH 117 (325)
Q Consensus 87 ~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkk 117 (325)
.|-.-.+||..| |-+...|+++....+++-
T Consensus 120 ~~~s~~eIA~~l-gis~~tv~~~l~ra~~~L 149 (159)
T PRK12527 120 EGLSHQQIAEHL-GISRSLVEKHIVNAMKHC 149 (159)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 355678999999 999999999987655543
No 160
>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=24.94 E-value=2.1e+02 Score=24.05 Aligned_cols=29 Identities=31% Similarity=0.307 Sum_probs=22.3
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 87 FGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 87 ~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
.|-...+||+.| |-+...|+++-...+++
T Consensus 137 ~g~s~~eIA~~l-~is~~tv~~~l~ra~~~ 165 (170)
T TIGR02952 137 QNLPIAEVARIL-GKTEGAVKILQFRAIKK 165 (170)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 366789999999 88899998877655443
No 161
>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.93 E-value=91 Score=27.86 Aligned_cols=37 Identities=27% Similarity=0.346 Sum_probs=31.3
Q ss_pred CCChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHH
Q 041991 71 PFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKN 108 (325)
Q Consensus 71 ~WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~Kn 108 (325)
.||+|..++|.+|..+ |-.=++||.+|.|=+.|.|--
T Consensus 2 nWtdERve~LkKLWse-GLSASQIAaQLGGVsRnAVIG 38 (169)
T COG5352 2 NWTDERVETLKKLWSE-GLSASQIAAQLGGVSRNAVIG 38 (169)
T ss_pred CchHHHHHHHHHHHHc-ccCHHHHHHHhcCcchhhhhe
Confidence 5999999999888765 667799999999988887754
No 162
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=24.93 E-value=2.2e+02 Score=24.99 Aligned_cols=31 Identities=16% Similarity=0.117 Sum_probs=23.5
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHHHHHH
Q 041991 87 FGNKWAAIASHLPGRTDNDIKNLWNTRLKKHL 118 (325)
Q Consensus 87 ~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkkl 118 (325)
.|-...+||+.| |-+...|+++-...+++-.
T Consensus 157 ~~~s~~EIA~~L-gis~~tVk~~l~ra~~~Lr 187 (194)
T PRK09646 157 GGLTYREVAERL-AVPLGTVKTRMRDGLIRLR 187 (194)
T ss_pred cCCCHHHHHHHh-CCChHhHHHHHHHHHHHHH
Confidence 456789999999 8899999988765555433
No 163
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=24.77 E-value=1.8e+02 Score=25.28 Aligned_cols=30 Identities=17% Similarity=0.449 Sum_probs=24.2
Q ss_pred hhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 86 LFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 86 ~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
..|-.-.+||..| |-+...|+++....+++
T Consensus 136 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 165 (185)
T PRK12542 136 FYNLTYQEISSVM-GITEANVRKQFERARKR 165 (185)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3567789999999 99999999987755544
No 164
>PRK00118 putative DNA-binding protein; Validated
Probab=24.76 E-value=1.9e+02 Score=24.07 Aligned_cols=40 Identities=13% Similarity=0.067 Sum_probs=32.0
Q ss_pred hHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHH
Q 041991 74 PEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRL 114 (325)
Q Consensus 74 ~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~l 114 (325)
++.+..++.++...|-....||+.+ |-+.+.|+++-....
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~RAr 58 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKRTE 58 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 3456677778778889999999999 999999988766433
No 165
>PRK09483 response regulator; Provisional
Probab=24.76 E-value=1.1e+02 Score=26.22 Aligned_cols=44 Identities=14% Similarity=0.260 Sum_probs=34.0
Q ss_pred CCCChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 70 GPFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 70 g~WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
...|+.|-+.|.-+ ..|..=.+||..| +-+...|++|-+++++|
T Consensus 147 ~~Lt~rE~~vl~~~--~~G~~~~~Ia~~l-~is~~TV~~~~~~i~~K 190 (217)
T PRK09483 147 ASLSERELQIMLMI--TKGQKVNEISEQL-NLSPKTVNSYRYRMFSK 190 (217)
T ss_pred cccCHHHHHHHHHH--HCCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 35888888887543 3566667999999 77999999988887776
No 166
>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=24.69 E-value=90 Score=24.88 Aligned_cols=29 Identities=31% Similarity=0.549 Sum_probs=23.1
Q ss_pred HHHHHHHhhCCCHHHHHhhCCCCCHHHHHH
Q 041991 79 TIIQLHGLFGNKWAAIASHLPGRTDNDIKN 108 (325)
Q Consensus 79 ~Ll~l~~~~G~kWs~IA~~LpGRT~nq~Kn 108 (325)
-|-.+....|.+|..+|++| |=++.+|.+
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 34455677899999999999 888887766
No 167
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=24.56 E-value=2.5e+02 Score=19.56 Aligned_cols=44 Identities=23% Similarity=0.348 Sum_probs=33.7
Q ss_pred CCCCCChHHHHHHHHHHHhhCC----CHHHHHhhCCCCCHHHHHHHHHH
Q 041991 68 KRGPFAPEEVATIIQLHGLFGN----KWAAIASHLPGRTDNDIKNLWNT 112 (325)
Q Consensus 68 krg~WT~EED~~Ll~l~~~~G~----kWs~IA~~LpGRT~nq~KnRW~t 112 (325)
++..||.++-..|.+.+..... .-..||..+ |-+..+|++-|.+
T Consensus 3 ~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l-~l~~~~V~~WF~n 50 (57)
T PF00046_consen 3 KRTRFTKEQLKVLEEYFQENPYPSKEEREELAKEL-GLTERQVKNWFQN 50 (57)
T ss_dssp SSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHH-TSSHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHhccccccccccccccc-cccccccccCHHH
Confidence 3567899999999988887332 267888888 9999999885543
No 168
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=24.38 E-value=1.8e+02 Score=25.38 Aligned_cols=29 Identities=14% Similarity=0.005 Sum_probs=23.5
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 87 FGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 87 ~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
.|-.-.+||..| |-+.+.|+++....+++
T Consensus 146 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 174 (191)
T PRK12520 146 LELETEEICQEL-QITATNAWVLLYRARMR 174 (191)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466789999999 99999999998755443
No 169
>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=24.33 E-value=1e+02 Score=24.72 Aligned_cols=27 Identities=19% Similarity=0.315 Sum_probs=21.3
Q ss_pred HHHHHHHHHhhCCCHHHHHhhCCCCCHH
Q 041991 77 VATIIQLHGLFGNKWAAIASHLPGRTDN 104 (325)
Q Consensus 77 D~~Ll~l~~~~G~kWs~IA~~LpGRT~n 104 (325)
|..|..+...+|..|.++|.+| |=+..
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L-~vs~~ 30 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL-QFSVE 30 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc-CCCHH
Confidence 5567788889999999999998 44443
No 170
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=24.24 E-value=46 Score=28.03 Aligned_cols=44 Identities=14% Similarity=0.213 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHhCCCCcccccccccccccchhhhhhhhhhcCCCC
Q 041991 22 EEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPDI 67 (325)
Q Consensus 22 EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~l 67 (325)
+-|.++++++++.+...+..||+.++ -+..-|+.|-.+..+-.+
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~lg--lS~~~v~~Ri~~L~~~Gi 51 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERVG--LSPSTVLRRIKRLEEEGV 51 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCCc
Confidence 56889999999999999999999997 788888888777666554
No 171
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=24.14 E-value=1.7e+02 Score=27.79 Aligned_cols=31 Identities=16% Similarity=0.205 Sum_probs=24.9
Q ss_pred hhCCCHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 041991 86 LFGNKWAAIASHLPGRTDNDIKNLWNTRLKKH 117 (325)
Q Consensus 86 ~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkk 117 (325)
..|-.-.+||..| |.+.+.|+++....+++-
T Consensus 156 ~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~L 186 (324)
T TIGR02960 156 VLGWRAAETAELL-GTSTASVNSALQRARATL 186 (324)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3467789999999 999999999887655543
No 172
>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=24.08 E-value=46 Score=29.73 Aligned_cols=34 Identities=24% Similarity=0.444 Sum_probs=26.5
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccc-ccccch
Q 041991 18 VWSPEEDAKLIQYIKEHGHGTWRHLPKQAG-ILRSGK 53 (325)
Q Consensus 18 ~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg-~~Rt~k 53 (325)
.||.|+.++|.++..+ |. .=.+|++.|| ..|+..
T Consensus 2 ~Wtde~~~~L~~lw~~-G~-SasqIA~~lg~vsRnAV 36 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GL-SASQIARQLGGVSRNAV 36 (162)
T ss_pred CCCHHHHHHHHHHHHc-CC-CHHHHHHHhCCcchhhh
Confidence 5999999999999854 43 6689999998 445543
No 173
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=23.70 E-value=1.4e+02 Score=22.02 Aligned_cols=46 Identities=20% Similarity=0.338 Sum_probs=32.4
Q ss_pred CCCCCChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHH
Q 041991 68 KRGPFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLK 115 (325)
Q Consensus 68 krg~WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lk 115 (325)
++..||+|+-..++..+..-|..-..||..+ |=+...+.+ |....+
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~g~sv~~va~~~-gi~~~~l~~-W~~~~~ 48 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLESGESVSEVAREY-GISPSTLYN-WRKQYR 48 (76)
T ss_dssp SS----HHHHHHHHHHHHHHHCHHHHHHHHH-TS-HHHHHH-HHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHCCCceEeeeccc-ccccccccH-HHHHHh
Confidence 3568999999999999988888899999998 546666655 765554
No 174
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=23.37 E-value=1.9e+02 Score=25.60 Aligned_cols=38 Identities=18% Similarity=0.160 Sum_probs=27.8
Q ss_pred HHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHHHHh
Q 041991 81 IQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKHLQ 119 (325)
Q Consensus 81 l~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkkkl~ 119 (325)
+.++...|-...+||..| |-+...|+++-...+++-.+
T Consensus 122 ~~L~~~~g~s~~EIA~~L-giS~~tVk~~l~Rar~~Lr~ 159 (188)
T PRK12546 122 LILVGASGFSYEEAAEMC-GVAVGTVKSRANRARARLAE 159 (188)
T ss_pred hhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 334444577899999999 89999999988766654333
No 175
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=23.29 E-value=97 Score=28.29 Aligned_cols=29 Identities=14% Similarity=0.092 Sum_probs=23.7
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 041991 88 GNKWAAIASHLPGRTDNDIKNLWNTRLKKH 117 (325)
Q Consensus 88 G~kWs~IA~~LpGRT~nq~KnRW~t~lkkk 117 (325)
|-...+||..| |.+...|+++....+++-
T Consensus 165 g~s~~EIAe~l-gis~~tVk~~l~Rar~kL 193 (231)
T PRK11922 165 ELSVEETAQAL-GLPEETVKTRLHRARRLL 193 (231)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 56789999999 999999999987655543
No 176
>cd08312 Death_MyD88 Death domain of Myeloid Differentation primary response protein MyD88. Death Domain (DD) of Myeloid Differentiation primary response protein 88 (MyD88). MyD88 is an adaptor protein involved in interleukin-1 receptor (IL-1R)- and Toll-like receptor (TLR)-induced activation of nuclear factor-kappaB (NF-kB) and mitogen activated protein kinase pathways that lead to the induction of proinflammatory cytokines. It is a key component in the signaling pathway of pathogen recognition in the innate immune system. MyD88 contains an N-terminal DD and a C-terminal Toll/IL-1 Receptor (TIR) homology domain that mediates interaction with TLRs and IL-1R. 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
Probab=23.18 E-value=87 Score=24.44 Aligned_cols=22 Identities=23% Similarity=0.521 Sum_probs=16.9
Q ss_pred HhhCCCHHHHHhhCCCCCHHHHH
Q 041991 85 GLFGNKWAAIASHLPGRTDNDIK 107 (325)
Q Consensus 85 ~~~G~kWs~IA~~LpGRT~nq~K 107 (325)
..+|++|..+|.+| |=+...|+
T Consensus 13 ~~~g~DWr~LA~~L-g~~~~~I~ 34 (79)
T cd08312 13 RVVAADWTALAEEM-GFEYLEIR 34 (79)
T ss_pred CCcccCHHHHHHHc-CCCHHHHH
Confidence 34789999999999 65555554
No 177
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=21.84 E-value=63 Score=24.98 Aligned_cols=18 Identities=22% Similarity=0.556 Sum_probs=14.7
Q ss_pred HHHHHHHhhCCCHHHHHh
Q 041991 79 TIIQLHGLFGNKWAAIAS 96 (325)
Q Consensus 79 ~Ll~l~~~~G~kWs~IA~ 96 (325)
.|.+|.+.||++|.-|-.
T Consensus 31 vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 31 VLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHcCCchhhhc
Confidence 466888899999999964
No 178
>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=21.61 E-value=2.2e+02 Score=20.19 Aligned_cols=42 Identities=24% Similarity=0.308 Sum_probs=29.9
Q ss_pred CChHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 72 FAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 72 WT~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
+|+.|-+.|.-+. -|..=.+||..+ |.+...|+.+...+++|
T Consensus 4 LT~~E~~vl~~l~--~G~~~~eIA~~l-~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 4 LTERELEVLRLLA--QGMSNKEIAEEL-GISEKTVKSHRRRIMKK 45 (58)
T ss_dssp S-HHHHHHHHHHH--TTS-HHHHHHHH-TSHHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHH--hcCCcchhHHhc-CcchhhHHHHHHHHHHH
Confidence 4566665544333 366678999999 99999999988877775
No 179
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=21.55 E-value=2.3e+02 Score=23.47 Aligned_cols=29 Identities=28% Similarity=0.249 Sum_probs=21.0
Q ss_pred hhCCCHHHHHhhCCCCCHHHHHHHHHHHHH
Q 041991 86 LFGNKWAAIASHLPGRTDNDIKNLWNTRLK 115 (325)
Q Consensus 86 ~~G~kWs~IA~~LpGRT~nq~KnRW~t~lk 115 (325)
..|-.=..||..| |=+...|+.+.....+
T Consensus 125 ~~g~~~~eIA~~l-~is~~tv~~~l~Rar~ 153 (159)
T TIGR02989 125 QRGVSLTALAEQL-GRTVNAVYKALSRLRV 153 (159)
T ss_pred hcCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 3466678888888 8888888887655444
No 180
>PRK01905 DNA-binding protein Fis; Provisional
Probab=20.61 E-value=2.5e+02 Score=21.60 Aligned_cols=33 Identities=18% Similarity=0.129 Sum_probs=25.5
Q ss_pred hHHHHHHHHHHHhhCCCHHHHHhhCCCCCHHHHH
Q 041991 74 PEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIK 107 (325)
Q Consensus 74 ~EED~~Ll~l~~~~G~kWs~IA~~LpGRT~nq~K 107 (325)
.-|...|.+++..+|.++.+.|+.+ |=+...++
T Consensus 36 ~~E~~~i~~aL~~~~gn~s~aAr~L-GIsrstL~ 68 (77)
T PRK01905 36 CVEKPLLEVVMEQAGGNQSLAAEYL-GINRNTLR 68 (77)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHH
Confidence 3467788899999999999999998 54554443
No 181
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=20.27 E-value=2.8e+02 Score=24.23 Aligned_cols=29 Identities=38% Similarity=0.444 Sum_probs=22.6
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 041991 87 FGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116 (325)
Q Consensus 87 ~G~kWs~IA~~LpGRT~nq~KnRW~t~lkk 116 (325)
-|-.=.+||+.| |.+...|+++-...+++
T Consensus 146 ~g~s~~EIAe~l-gis~~~V~~~l~Ra~~~ 174 (189)
T PRK06811 146 LGEKIEEIAKKL-GLTRSAIDNRLSRGRKK 174 (189)
T ss_pred ccCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 356678999999 99999999987665544
Done!