Query 037956
Match_columns 245
No_of_seqs 222 out of 1399
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 06:06:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037956.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037956hhsearch_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 3.3E-37 7.2E-42 271.8 10.0 114 3-116 14-127 (249)
2 PLN03091 hypothetical protein; 100.0 5.7E-37 1.2E-41 287.8 11.3 115 1-115 1-115 (459)
3 KOG0048 Transcription factor, 100.0 8.7E-37 1.9E-41 270.7 11.0 111 9-120 4-114 (238)
4 KOG0049 Transcription factor, 99.8 1.1E-19 2.4E-24 176.9 5.8 106 1-107 347-453 (939)
5 KOG0049 Transcription factor, 99.7 3.5E-18 7.6E-23 166.5 6.9 109 5-113 244-407 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.7 2.1E-17 4.5E-22 116.5 2.9 60 17-78 1-60 (60)
7 COG5147 REB1 Myb superfamily p 99.6 2.7E-16 5.9E-21 152.1 5.6 102 11-113 17-118 (512)
8 KOG0050 mRNA splicing protein 99.6 4.4E-16 9.5E-21 148.8 1.9 101 12-114 5-105 (617)
9 KOG0051 RNA polymerase I termi 99.5 3.8E-14 8.3E-19 138.8 5.5 107 3-114 375-509 (607)
10 PF00249 Myb_DNA-binding: Myb- 99.4 1.6E-13 3.5E-18 92.9 5.4 46 67-112 1-48 (48)
11 PF00249 Myb_DNA-binding: Myb- 99.4 1.7E-14 3.6E-19 97.8 -0.0 48 14-61 1-48 (48)
12 PF13921 Myb_DNA-bind_6: Myb-l 99.3 6.3E-12 1.4E-16 88.4 5.7 44 70-113 1-44 (60)
13 smart00717 SANT SANT SWI3, AD 99.3 1.1E-11 2.3E-16 81.7 6.1 47 67-113 1-48 (49)
14 cd00167 SANT 'SWI3, ADA2, N-Co 99.2 8.1E-11 1.8E-15 76.4 5.9 44 69-112 1-45 (45)
15 smart00717 SANT SANT SWI3, AD 99.1 2.5E-11 5.5E-16 79.9 1.6 48 14-62 1-48 (49)
16 PLN03212 Transcription repress 99.1 1E-11 2.2E-16 110.4 -2.1 60 3-64 67-126 (249)
17 PLN03091 hypothetical protein; 99.0 3.8E-11 8.2E-16 114.1 -0.9 59 3-63 56-114 (459)
18 KOG0048 Transcription factor, 99.0 3.2E-10 7E-15 100.8 4.8 51 63-113 5-57 (238)
19 cd00167 SANT 'SWI3, ADA2, N-Co 99.0 1.9E-10 4.2E-15 74.6 1.3 45 16-61 1-45 (45)
20 KOG0051 RNA polymerase I termi 98.8 2.8E-09 6.1E-14 104.9 5.0 99 14-114 308-430 (607)
21 COG5147 REB1 Myb superfamily p 98.1 1.1E-06 2.3E-11 85.9 2.1 107 3-112 61-167 (512)
22 TIGR01557 myb_SHAQKYF myb-like 98.0 3.2E-06 6.9E-11 59.7 1.7 49 13-61 2-54 (57)
23 KOG0457 Histone acetyltransfer 97.8 5.5E-06 1.2E-10 78.9 1.1 87 13-100 71-179 (438)
24 KOG0457 Histone acetyltransfer 97.7 6.1E-05 1.3E-09 71.9 6.2 52 62-113 67-119 (438)
25 TIGR01557 myb_SHAQKYF myb-like 97.6 0.00016 3.5E-09 51.0 5.9 47 67-113 3-55 (57)
26 PF13325 MCRS_N: N-terminal re 97.3 0.00041 9E-09 60.5 5.5 100 16-118 1-131 (199)
27 KOG0050 mRNA splicing protein 97.2 0.00031 6.6E-09 68.5 3.7 49 65-113 5-54 (617)
28 PF08914 Myb_DNA-bind_2: Rap1 97.1 0.00084 1.8E-08 48.6 4.4 49 67-115 2-60 (65)
29 PF13837 Myb_DNA-bind_4: Myb/S 97.1 0.00054 1.2E-08 51.1 3.5 49 67-115 1-67 (90)
30 COG5259 RSC8 RSC chromatin rem 97.1 0.00017 3.8E-09 69.5 0.8 46 13-60 278-323 (531)
31 KOG1279 Chromatin remodeling f 97.0 0.00098 2.1E-08 65.5 5.5 45 66-110 252-296 (506)
32 COG5259 RSC8 RSC chromatin rem 97.0 0.00093 2E-08 64.6 5.0 43 68-110 280-322 (531)
33 KOG1279 Chromatin remodeling f 96.9 0.00035 7.5E-09 68.6 1.4 47 12-60 251-297 (506)
34 TIGR02894 DNA_bind_RsfA transc 96.8 0.0016 3.4E-08 55.0 4.3 49 66-115 3-58 (161)
35 PF13873 Myb_DNA-bind_5: Myb/S 96.5 0.0097 2.1E-07 43.5 6.0 48 67-114 2-71 (78)
36 PF08914 Myb_DNA-bind_2: Rap1 96.4 0.00067 1.4E-08 49.1 -0.4 52 14-65 2-61 (65)
37 TIGR02894 DNA_bind_RsfA transc 96.2 0.0011 2.3E-08 56.0 -0.5 49 13-63 3-57 (161)
38 PF13837 Myb_DNA-bind_4: Myb/S 96.2 0.00093 2E-08 49.8 -0.8 48 14-61 1-64 (90)
39 PRK13923 putative spore coat p 96.1 0.0072 1.6E-07 51.6 3.9 50 66-116 4-60 (170)
40 COG5114 Histone acetyltransfer 96.0 0.0017 3.6E-08 60.4 -0.3 47 15-62 64-110 (432)
41 COG5114 Histone acetyltransfer 95.7 0.016 3.5E-07 54.0 5.0 49 65-113 61-110 (432)
42 PF13873 Myb_DNA-bind_5: Myb/S 95.4 0.0033 7.2E-08 46.0 -0.6 49 13-61 1-69 (78)
43 PLN03142 Probable chromatin-re 95.1 0.039 8.5E-07 58.8 6.2 98 15-113 825-985 (1033)
44 PRK13923 putative spore coat p 94.4 0.0061 1.3E-07 52.0 -1.6 49 12-62 3-57 (170)
45 KOG2656 DNA methyltransferase 94.0 0.029 6.4E-07 53.4 1.8 47 68-114 131-183 (445)
46 PF09111 SLIDE: SLIDE; InterP 93.6 0.14 3.1E-06 41.2 4.9 50 64-113 46-111 (118)
47 PF12776 Myb_DNA-bind_3: Myb/S 92.7 0.31 6.8E-06 36.5 5.5 46 69-114 1-64 (96)
48 KOG4282 Transcription factor G 91.9 0.24 5.2E-06 46.1 4.8 55 67-121 54-122 (345)
49 PF08281 Sigma70_r4_2: Sigma-7 90.4 0.8 1.7E-05 30.7 5.0 41 72-113 12-52 (54)
50 KOG1194 Predicted DNA-binding 88.8 0.98 2.1E-05 44.1 6.0 49 67-115 187-235 (534)
51 COG5118 BDP1 Transcription ini 87.8 0.97 2.1E-05 43.3 5.2 47 68-114 366-412 (507)
52 PF09111 SLIDE: SLIDE; InterP 85.6 0.51 1.1E-05 38.0 1.8 34 11-44 46-82 (118)
53 COG5118 BDP1 Transcription ini 84.2 0.46 1E-05 45.4 1.1 43 15-59 366-408 (507)
54 smart00595 MADF subfamily of S 80.9 2.7 5.7E-05 31.0 4.0 24 89-113 30-53 (89)
55 PF04545 Sigma70_r4: Sigma-70, 80.2 5.1 0.00011 26.4 4.8 41 73-114 7-47 (50)
56 KOG4282 Transcription factor G 79.7 1.1 2.5E-05 41.6 2.0 47 15-61 55-113 (345)
57 KOG4167 Predicted DNA-binding 78.8 9.1 0.0002 39.7 8.0 47 67-113 619-665 (907)
58 PF11626 Rap1_C: TRF2-interact 77.6 2.4 5.2E-05 31.9 2.8 25 10-34 43-75 (87)
59 KOG4468 Polycomb-group transcr 73.7 5 0.00011 40.7 4.6 47 67-113 88-144 (782)
60 PF13404 HTH_AsnC-type: AsnC-t 72.1 9.3 0.0002 24.9 4.2 38 73-111 3-41 (42)
61 TIGR02985 Sig70_bacteroi1 RNA 69.1 12 0.00026 29.6 5.2 36 77-113 120-155 (161)
62 PF01388 ARID: ARID/BRIGHT DNA 67.2 14 0.0003 27.5 4.9 37 77-113 40-89 (92)
63 PF07750 GcrA: GcrA cell cycle 67.1 7.6 0.00017 32.8 3.8 41 69-110 2-42 (162)
64 cd08319 Death_RAIDD Death doma 66.2 9.5 0.00021 28.7 3.8 30 75-105 2-31 (83)
65 PRK11179 DNA-binding transcrip 64.1 15 0.00032 30.2 4.9 40 73-113 9-49 (153)
66 PF13325 MCRS_N: N-terminal re 62.3 16 0.00036 32.0 5.0 43 69-112 1-46 (199)
67 cd08803 Death_ank3 Death domai 61.2 15 0.00032 27.7 4.0 31 75-106 4-34 (84)
68 smart00501 BRIGHT BRIGHT, ARID 60.6 20 0.00043 26.9 4.7 37 77-113 36-85 (93)
69 PRK11169 leucine-responsive tr 59.5 17 0.00037 30.2 4.6 42 72-114 13-55 (164)
70 TIGR02937 sigma70-ECF RNA poly 58.9 21 0.00046 27.2 4.8 35 78-113 118-152 (158)
71 KOG4167 Predicted DNA-binding 58.9 3.9 8.5E-05 42.3 0.7 42 15-58 620-661 (907)
72 cd08317 Death_ank Death domain 58.3 13 0.00028 27.6 3.3 31 75-106 4-34 (84)
73 PF13404 HTH_AsnC-type: AsnC-t 56.9 3 6.4E-05 27.3 -0.4 37 20-58 3-39 (42)
74 PF11626 Rap1_C: TRF2-interact 54.8 12 0.00027 28.0 2.7 17 63-79 43-59 (87)
75 PRK09652 RNA polymerase sigma 54.2 28 0.00061 28.0 5.0 32 81-113 139-170 (182)
76 cd08318 Death_NMPP84 Death dom 52.7 22 0.00047 26.6 3.7 28 78-106 10-37 (86)
77 KOG4329 DNA-binding protein [G 52.5 28 0.0006 33.5 5.1 45 68-112 278-323 (445)
78 cd08804 Death_ank2 Death domai 52.5 21 0.00046 26.7 3.6 31 75-106 4-34 (84)
79 PRK09643 RNA polymerase sigma 51.5 33 0.00071 28.8 5.1 32 81-113 145-176 (192)
80 PRK11924 RNA polymerase sigma 50.2 34 0.00074 27.4 4.9 29 84-113 139-167 (179)
81 cd06171 Sigma70_r4 Sigma70, re 49.5 50 0.0011 20.5 4.7 38 74-112 14-51 (55)
82 PRK09413 IS2 repressor TnpA; R 48.8 28 0.00061 27.5 4.0 50 7-61 4-53 (121)
83 PRK09641 RNA polymerase sigma 48.6 37 0.00081 27.8 4.9 29 84-113 150-178 (187)
84 cd08777 Death_RIP1 Death Domai 48.4 24 0.00052 26.6 3.3 30 76-106 3-32 (86)
85 PRK09047 RNA polymerase factor 48.3 45 0.00097 26.6 5.2 30 84-114 120-149 (161)
86 TIGR02939 RpoE_Sigma70 RNA pol 47.9 31 0.00066 28.4 4.3 29 85-114 153-181 (190)
87 KOG4468 Polycomb-group transcr 47.8 12 0.00025 38.1 1.9 46 14-61 88-143 (782)
88 PF10545 MADF_DNA_bdg: Alcohol 47.7 17 0.00038 25.8 2.4 26 88-113 28-54 (85)
89 PF11035 SnAPC_2_like: Small n 47.5 63 0.0014 30.5 6.5 85 15-113 22-127 (344)
90 PRK11179 DNA-binding transcrip 47.2 6 0.00013 32.5 -0.1 45 20-66 9-53 (153)
91 KOG2656 DNA methyltransferase 47.0 10 0.00022 36.6 1.4 49 12-61 128-181 (445)
92 cd08311 Death_p75NR Death doma 47.0 25 0.00054 26.0 3.2 34 72-107 2-35 (77)
93 smart00005 DEATH DEATH domain, 46.3 30 0.00065 25.1 3.6 30 75-105 5-35 (88)
94 TIGR02954 Sig70_famx3 RNA poly 46.0 44 0.00096 27.1 4.9 30 84-114 133-162 (169)
95 KOG0384 Chromodomain-helicase 44.6 22 0.00048 39.0 3.5 70 15-93 1134-1206(1373)
96 PRK11169 leucine-responsive tr 44.1 5.6 0.00012 33.1 -0.8 45 19-65 13-57 (164)
97 PRK12523 RNA polymerase sigma 43.9 51 0.0011 26.9 5.0 36 78-114 127-162 (172)
98 KOG2009 Transcription initiati 43.7 26 0.00055 35.6 3.6 48 66-113 408-455 (584)
99 PRK09637 RNA polymerase sigma 43.6 51 0.0011 27.4 5.0 30 83-113 119-148 (181)
100 PRK04217 hypothetical protein; 43.5 60 0.0013 25.8 5.0 44 68-113 41-84 (110)
101 PRK09642 RNA polymerase sigma 43.3 57 0.0012 26.1 5.1 29 84-113 120-148 (160)
102 TIGR02943 Sig70_famx1 RNA poly 43.0 56 0.0012 27.3 5.2 33 81-114 142-174 (188)
103 PRK09648 RNA polymerase sigma 42.9 56 0.0012 27.0 5.2 29 84-113 153-181 (189)
104 PRK11923 algU RNA polymerase s 42.6 50 0.0011 27.4 4.8 29 85-114 153-181 (193)
105 cd08779 Death_PIDD Death Domai 42.6 29 0.00064 26.0 3.0 26 76-102 3-28 (86)
106 PRK12512 RNA polymerase sigma 42.4 58 0.0013 26.8 5.1 30 84-114 145-174 (184)
107 PF11035 SnAPC_2_like: Small n 42.2 87 0.0019 29.6 6.6 44 67-110 21-68 (344)
108 PRK12531 RNA polymerase sigma 41.9 59 0.0013 27.2 5.2 30 84-114 155-184 (194)
109 TIGR02948 SigW_bacill RNA poly 41.8 50 0.0011 27.0 4.7 28 85-113 151-178 (187)
110 PRK12530 RNA polymerase sigma 41.6 59 0.0013 27.2 5.1 28 85-113 149-176 (189)
111 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 41.6 55 0.0012 22.4 4.0 36 73-109 7-42 (50)
112 cd08805 Death_ank1 Death domai 41.1 38 0.00083 25.5 3.5 28 75-103 4-31 (84)
113 PRK09645 RNA polymerase sigma 41.1 63 0.0014 26.2 5.1 30 84-114 132-161 (173)
114 PRK06759 RNA polymerase factor 40.3 69 0.0015 25.3 5.1 28 85-113 121-148 (154)
115 PRK12529 RNA polymerase sigma 40.1 64 0.0014 26.6 5.0 30 83-113 140-169 (178)
116 PF09420 Nop16: Ribosome bioge 39.9 73 0.0016 26.6 5.4 45 67-111 114-162 (164)
117 PF02954 HTH_8: Bacterial regu 39.9 76 0.0016 20.3 4.3 33 74-107 6-38 (42)
118 PRK12524 RNA polymerase sigma 39.8 67 0.0014 26.9 5.2 30 84-114 150-179 (196)
119 KOG1194 Predicted DNA-binding 39.5 23 0.00049 35.0 2.5 41 68-109 471-511 (534)
120 PF04504 DUF573: Protein of un 39.0 54 0.0012 25.2 4.1 46 68-113 5-63 (98)
121 PRK12515 RNA polymerase sigma 38.8 71 0.0015 26.4 5.2 29 84-113 145-173 (189)
122 COG2197 CitB Response regulato 38.0 45 0.00098 28.8 3.9 45 68-115 147-191 (211)
123 TIGR02952 Sig70_famx2 RNA poly 38.0 75 0.0016 25.4 5.1 28 85-113 137-164 (170)
124 KOG3554 Histone deacetylase co 37.6 42 0.00091 33.4 3.9 43 68-110 286-329 (693)
125 PF07638 Sigma70_ECF: ECF sigm 36.9 66 0.0014 27.0 4.7 36 76-112 141-176 (185)
126 PRK12536 RNA polymerase sigma 36.3 82 0.0018 25.9 5.1 30 83-113 142-171 (181)
127 TIGR02999 Sig-70_X6 RNA polyme 35.7 88 0.0019 25.5 5.2 29 84-113 148-176 (183)
128 PRK00118 putative DNA-binding 35.6 96 0.0021 24.3 5.0 41 72-113 19-59 (104)
129 PF13936 HTH_38: Helix-turn-he 35.5 50 0.0011 21.4 3.0 37 69-107 4-40 (44)
130 PRK09649 RNA polymerase sigma 34.8 81 0.0018 26.2 4.9 28 85-113 145-172 (185)
131 PRK12514 RNA polymerase sigma 34.7 88 0.0019 25.5 5.0 28 85-113 144-171 (179)
132 cd01670 Death Death Domain: a 34.6 49 0.0011 23.4 3.1 27 78-105 2-28 (79)
133 cd08306 Death_FADD Fas-associa 34.3 64 0.0014 24.1 3.7 28 78-106 5-32 (86)
134 PRK12532 RNA polymerase sigma 34.1 85 0.0018 26.1 4.9 29 84-113 150-178 (195)
135 smart00344 HTH_ASNC helix_turn 33.6 1.1E+02 0.0024 22.9 5.0 41 73-114 3-44 (108)
136 PRK12528 RNA polymerase sigma 33.5 97 0.0021 24.8 5.0 31 82-113 125-155 (161)
137 PRK12527 RNA polymerase sigma 33.4 1.2E+02 0.0027 24.1 5.6 29 85-114 120-148 (159)
138 PRK09651 RNA polymerase sigma 33.0 84 0.0018 25.7 4.6 28 85-113 134-161 (172)
139 PRK12516 RNA polymerase sigma 32.7 98 0.0021 25.9 5.1 34 79-113 125-158 (187)
140 KOG3841 TEF-1 and related tran 32.7 70 0.0015 31.0 4.5 26 9-34 71-96 (455)
141 TIGR02950 SigM_subfam RNA poly 32.4 35 0.00075 27.0 2.2 27 86-113 121-147 (154)
142 PRK12547 RNA polymerase sigma 32.2 1.1E+02 0.0024 24.7 5.2 29 84-113 126-154 (164)
143 TIGR02984 Sig-70_plancto1 RNA 32.1 1E+02 0.0022 25.1 5.1 29 84-113 154-182 (189)
144 PRK12542 RNA polymerase sigma 32.1 1E+02 0.0022 25.4 5.1 29 84-113 136-164 (185)
145 PRK06811 RNA polymerase factor 32.1 1.3E+02 0.0028 25.0 5.7 27 86-113 147-173 (189)
146 PRK05602 RNA polymerase sigma 31.7 97 0.0021 25.5 4.9 28 85-113 143-170 (186)
147 PRK13919 putative RNA polymera 31.2 1.1E+02 0.0024 25.0 5.1 28 85-113 150-177 (186)
148 PRK11922 RNA polymerase sigma 31.1 54 0.0012 28.4 3.3 29 85-114 164-192 (231)
149 TIGR02983 SigE-fam_strep RNA p 31.1 1.3E+02 0.0027 24.0 5.3 37 76-113 116-152 (162)
150 PRK12545 RNA polymerase sigma 30.9 1.1E+02 0.0023 25.9 5.1 28 85-113 154-181 (201)
151 PRK12520 RNA polymerase sigma 30.8 1.1E+02 0.0024 25.3 5.1 28 85-113 146-173 (191)
152 PRK12546 RNA polymerase sigma 29.9 1E+02 0.0022 25.9 4.8 31 82-113 125-155 (188)
153 KOG2009 Transcription initiati 29.8 36 0.00077 34.6 2.1 48 10-59 405-452 (584)
154 TIGR02960 SigX5 RNA polymerase 29.7 96 0.0021 28.0 4.8 29 85-114 157-185 (324)
155 PRK09646 RNA polymerase sigma 29.6 1.2E+02 0.0026 25.3 5.1 28 85-113 157-184 (194)
156 PF00196 GerE: Bacterial regul 28.4 57 0.0012 22.0 2.4 43 69-114 3-45 (58)
157 PRK12537 RNA polymerase sigma 28.1 1.3E+02 0.0028 24.7 5.0 28 85-113 148-175 (182)
158 PF10440 WIYLD: Ubiquitin-bind 27.1 48 0.001 24.0 1.8 25 70-94 23-48 (65)
159 PRK09638 RNA polymerase sigma 26.8 65 0.0014 26.1 2.9 28 85-113 141-168 (176)
160 PF00046 Homeobox: Homeobox do 26.7 1.9E+02 0.0042 19.0 4.9 44 66-110 3-50 (57)
161 PF00531 Death: Death domain; 26.6 1.2E+02 0.0025 21.4 3.9 23 82-105 8-30 (83)
162 PF09420 Nop16: Ribosome bioge 25.5 48 0.001 27.7 1.9 46 12-58 112-160 (164)
163 PRK06986 fliA flagellar biosyn 25.4 1.4E+02 0.003 25.9 4.9 30 84-114 198-227 (236)
164 PRK09639 RNA polymerase sigma 25.4 1.6E+02 0.0035 23.4 5.0 28 85-113 126-153 (166)
165 PRK12538 RNA polymerase sigma 24.9 1.3E+02 0.0027 26.4 4.5 29 85-114 186-214 (233)
166 PRK12519 RNA polymerase sigma 24.8 1.3E+02 0.0028 24.9 4.4 28 85-113 156-183 (194)
167 PRK01905 DNA-binding protein F 24.7 2E+02 0.0043 20.8 4.9 35 72-107 36-70 (77)
168 PLN03142 Probable chromatin-re 24.6 1.4E+02 0.003 32.6 5.5 46 68-113 825-871 (1033)
169 PF09905 DUF2132: Uncharacteri 24.6 40 0.00086 24.4 1.0 44 22-78 12-62 (64)
170 PRK09647 RNA polymerase sigma 24.4 1.7E+02 0.0037 24.9 5.2 29 85-114 153-181 (203)
171 PRK08241 RNA polymerase factor 23.9 1.3E+02 0.0028 27.5 4.6 28 85-113 168-195 (339)
172 TIGR02989 Sig-70_gvs1 RNA poly 23.8 1.9E+02 0.0041 22.8 5.1 28 85-113 126-153 (159)
173 PF07750 GcrA: GcrA cell cycle 23.8 46 0.001 28.0 1.5 33 16-50 2-35 (162)
174 COG1522 Lrp Transcriptional re 23.6 1.8E+02 0.004 23.0 5.0 40 73-113 8-48 (154)
175 PF09197 Rap1-DNA-bind: Rap1, 23.5 1.4E+02 0.003 23.6 4.1 45 70-114 2-77 (105)
176 PRK10100 DNA-binding transcrip 23.4 1.7E+02 0.0037 25.4 5.1 43 69-114 155-197 (216)
177 PRK09636 RNA polymerase sigma 23.0 1.7E+02 0.0037 26.3 5.1 28 85-113 130-157 (293)
178 PRK07670 RNA polymerase sigma 22.9 1.7E+02 0.0037 25.6 5.0 37 77-114 208-244 (251)
179 PRK12526 RNA polymerase sigma 22.9 1.9E+02 0.0041 24.5 5.2 27 86-113 169-195 (206)
180 PRK09415 RNA polymerase factor 22.8 1.7E+02 0.0036 24.0 4.7 28 85-113 142-169 (179)
181 PRK12511 RNA polymerase sigma 22.8 1.9E+02 0.0041 24.1 5.1 28 85-113 126-153 (182)
182 PRK15411 rcsA colanic acid cap 22.4 1.7E+02 0.0038 24.9 4.9 44 69-115 137-180 (207)
183 PRK12541 RNA polymerase sigma 22.2 1.9E+02 0.0041 23.0 4.8 28 85-113 127-154 (161)
184 PRK12544 RNA polymerase sigma 22.1 2E+02 0.0043 24.5 5.2 28 85-113 163-190 (206)
185 PRK08301 sporulation sigma fac 22.1 1.7E+02 0.0037 25.2 4.8 27 86-113 198-224 (234)
186 COG5352 Uncharacterized protei 22.0 1.2E+02 0.0026 25.5 3.5 40 69-109 2-41 (169)
187 COG2963 Transposase and inacti 21.7 3E+02 0.0065 21.0 5.7 45 67-113 5-50 (116)
188 PRK15201 fimbriae regulatory p 21.6 2.3E+02 0.0051 24.8 5.4 43 69-114 133-175 (198)
189 PRK00430 fis global DNA-bindin 21.4 2.5E+02 0.0053 21.5 5.0 33 73-106 55-87 (95)
190 PRK06930 positive control sigm 21.4 2E+02 0.0042 24.3 4.9 36 77-113 121-156 (170)
191 TIGR02980 SigBFG RNA polymeras 21.3 2E+02 0.0043 24.6 5.0 29 84-113 192-220 (227)
192 TIGR02957 SigX4 RNA polymerase 21.0 1.9E+02 0.0042 25.8 5.1 29 84-113 122-150 (281)
193 PRK08295 RNA polymerase factor 21.0 2E+02 0.0044 23.8 5.0 28 85-113 169-196 (208)
194 PRK10360 DNA-binding transcrip 20.9 2.4E+02 0.0053 22.4 5.3 44 68-114 136-179 (196)
195 KOG0843 Transcription factor E 20.8 2.6E+02 0.0056 24.5 5.4 51 62-113 101-155 (197)
196 TIGR02959 SigZ RNA polymerase 20.7 2.4E+02 0.0052 22.9 5.2 29 84-113 114-142 (170)
197 PRK12513 RNA polymerase sigma 20.7 94 0.002 25.8 2.8 27 86-113 155-181 (194)
198 cd08312 Death_MyD88 Death doma 20.3 96 0.0021 22.8 2.4 22 84-106 14-35 (79)
199 PRK12535 RNA polymerase sigma 20.2 2.1E+02 0.0046 24.1 4.9 28 86-114 149-176 (196)
200 PRK12540 RNA polymerase sigma 20.1 2.3E+02 0.0049 23.5 5.0 28 85-113 126-153 (182)
No 1
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=3.3e-37 Score=271.79 Aligned_cols=114 Identities=55% Similarity=1.075 Sum_probs=109.4
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHHHhCCCCcccccccccCccccccccccccccccCCCCCCCCCHHHHHHHHHHH
Q 037956 3 KAGGSEKPSLRKGSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPDIRRGNFTQEEDETIIKLH 82 (245)
Q Consensus 3 R~~~~~kp~lkkg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~i~k~~WT~EED~~Ll~lv 82 (245)
|++||.|++++|++||+|||++|+.+|++||..+|..||+.++.+|+++|||+||.+||+|.+++++||.|||++|+++|
T Consensus 14 ~~pcc~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~ 93 (249)
T PLN03212 14 TTPCCTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLH 93 (249)
T ss_pred CCCCcccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHH
Confidence 67999999999999999999999999999999899999999964499999999999999999999999999999999999
Q ss_pred HHhCCcHHHHhhhCCCCCHHHHHHHHHHhhhhhh
Q 037956 83 EQLGNRWSAIASRLPGRTDNEIKNHWHSRLSKKR 116 (245)
Q Consensus 83 ~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkkk~ 116 (245)
..||++|..||++|||||+++|||||+.+++++.
T Consensus 94 ~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l 127 (249)
T PLN03212 94 RLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKL 127 (249)
T ss_pred HhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHH
Confidence 9999999999999999999999999999998543
No 2
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=5.7e-37 Score=287.76 Aligned_cols=115 Identities=63% Similarity=1.116 Sum_probs=111.8
Q ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHhCCCCcccccccccCccccccccccccccccCCCCCCCCCHHHHHHHHH
Q 037956 1 MVKAGGSEKPSLRKGSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPDIRRGNFTQEEDETIIK 80 (245)
Q Consensus 1 m~R~~~~~kp~lkkg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~i~k~~WT~EED~~Ll~ 80 (245)
|||++||.|.+++||+||+|||++|+++|.+||..+|..||+.++.+|+++|||+||.+||+|.+++++||+|||++|++
T Consensus 1 mgr~~Cc~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLe 80 (459)
T PLN03091 1 MGRHSCCYKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIE 80 (459)
T ss_pred CCCCccCcCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999755999999999999999999999999999999999
Q ss_pred HHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhhhh
Q 037956 81 LHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLSKK 115 (245)
Q Consensus 81 lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkkk 115 (245)
+|.+||++|..||++|+|||+++|||||+.+|+|+
T Consensus 81 L~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKk 115 (459)
T PLN03091 81 LHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKK 115 (459)
T ss_pred HHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999853
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=8.7e-37 Score=270.72 Aligned_cols=111 Identities=63% Similarity=1.136 Sum_probs=103.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCCcccccccccCccccccccccccccccCCCCCCCCCHHHHHHHHHHHHHhCCc
Q 037956 9 KPSLRKGSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPDIRRGNFTQEEDETIIKLHEQLGNR 88 (245)
Q Consensus 9 kp~lkkg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~i~k~~WT~EED~~Ll~lv~~~G~k 88 (245)
+|.+.||+||+|||++|+++|++||+++|..||+.+|.+|++|+||+||.|||+|++++|.||+|||++|+++|..||++
T Consensus 4 k~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNr 83 (238)
T KOG0048|consen 4 NPELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNR 83 (238)
T ss_pred CccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcH
Confidence 45566899999999999999999999999999999995599999999999999999999999999999999999999999
Q ss_pred HHHHhhhCCCCCHHHHHHHHHHhhhhhhhhhh
Q 037956 89 WSAIASRLPGRTDNEIKNHWHSRLSKKRLTKN 120 (245)
Q Consensus 89 W~~IA~~lpgRT~~~~Knrw~~~lkkk~~~k~ 120 (245)
|+.||++|||||+++|||+|+..||| ++.+.
T Consensus 84 Ws~IA~~LPGRTDNeIKN~Wnt~lkk-kl~~~ 114 (238)
T KOG0048|consen 84 WSLIAGRLPGRTDNEVKNHWNTHLKK-KLLKM 114 (238)
T ss_pred HHHHHhhCCCcCHHHHHHHHHHHHHH-HHHHc
Confidence 99999999999999999999999984 44433
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.78 E-value=1.1e-19 Score=176.90 Aligned_cols=106 Identities=26% Similarity=0.546 Sum_probs=100.9
Q ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHhCCCCcccccccccCccccccccccccccccCCCCCCCCCHHHHHHHHH
Q 037956 1 MVKAGGSEKPSLRKGSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPDIRRGNFTQEEDETIIK 80 (245)
Q Consensus 1 m~R~~~~~kp~lkkg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~i~k~~WT~EED~~Ll~ 80 (245)
++|+..+++|++++|+||++||-+|+.+|.+||..+|-+|-..+|+ |+..|||+||.|.|+...+.+.||-.||+.|+.
T Consensus 347 I~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPn-RSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~ 425 (939)
T KOG0049|consen 347 ITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPN-RSDSQCRERYTNVLNRSAKVERWTLVEDEQLLY 425 (939)
T ss_pred hhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCC-ccHHHHHHHHHHHHHHhhccCceeecchHHHHH
Confidence 4799999999999999999999999999999999999999999999 999999999999999999999999999999999
Q ss_pred HHHHhC-CcHHHHhhhCCCCCHHHHHHH
Q 037956 81 LHEQLG-NRWSAIASRLPGRTDNEIKNH 107 (245)
Q Consensus 81 lv~~~G-~kW~~IA~~lpgRT~~~~Knr 107 (245)
+|..|| ++|.+||..||.||..|...|
T Consensus 426 ~V~~YG~g~WakcA~~Lp~~t~~q~~rr 453 (939)
T KOG0049|consen 426 AVKVYGKGNWAKCAMLLPKKTSRQLRRR 453 (939)
T ss_pred HHHHHccchHHHHHHHccccchhHHHHH
Confidence 999999 789999999999999665443
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.73 E-value=3.5e-18 Score=166.48 Aligned_cols=109 Identities=23% Similarity=0.471 Sum_probs=96.5
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHhCCCCcccccccccCcccccccc------------------------------
Q 037956 5 GGSEKPSLRKGSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCR------------------------------ 54 (245)
Q Consensus 5 ~~~~kp~lkkg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr------------------------------ 54 (245)
+..+.|.++|.-|++|||++|..+...+|..+|..||..+|+.|+.-||.
T Consensus 244 ~n~l~P~~nk~~WS~EE~E~L~AiA~A~~~~~W~~IA~~Lgt~RS~yQC~~kF~t~~~~L~ekeWsEEed~kL~alV~~~ 323 (939)
T KOG0049|consen 244 YNELNPKWNKEHWSNEEVEKLKALAEAPKFVSWPMIALNLGTNRSSYQCMEKFKTEVSQLSEKEWSEEEDTKLIALVKIT 323 (939)
T ss_pred hhhcCCccchhccChHHHHHHHHHHhccccccHHHHHHHhCCCcchHHHHHHHHHHHHHHHhhhcchhhhHHHHHHHHHh
Confidence 45678888888888888888888888888777888887777777777776
Q ss_pred ------------------------ccccccccCCCCCCCCCHHHHHHHHHHHHHhCC-cHHHHhhhCCCCCHHHHHHHHH
Q 037956 55 ------------------------LRWMNYLRPDIRRGNFTQEEDETIIKLHEQLGN-RWSAIASRLPGRTDNEIKNHWH 109 (245)
Q Consensus 55 ------------------------~Rw~n~L~p~i~k~~WT~EED~~Ll~lv~~~G~-kW~~IA~~lpgRT~~~~Knrw~ 109 (245)
.||...|+|.+++|+||.+||.+|+.+|.+||. .|.+|...+|||++.||+.||+
T Consensus 324 ~~nShI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~ 403 (939)
T KOG0049|consen 324 SINSHIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYT 403 (939)
T ss_pred hccCccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHH
Confidence 788888999999999999999999999999996 5999999999999999999999
Q ss_pred Hhhh
Q 037956 110 SRLS 113 (245)
Q Consensus 110 ~~lk 113 (245)
+.|.
T Consensus 404 nvL~ 407 (939)
T KOG0049|consen 404 NVLN 407 (939)
T ss_pred HHHH
Confidence 9987
No 6
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.67 E-value=2.1e-17 Score=116.47 Aligned_cols=60 Identities=45% Similarity=0.932 Sum_probs=55.1
Q ss_pred CCHHHHHHHHHHHHHhCCCCcccccccccCccccccccccccccccCCCCCCCCCHHHHHHH
Q 037956 17 WTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPDIRRGNFTQEEDETI 78 (245)
Q Consensus 17 WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~i~k~~WT~EED~~L 78 (245)
||+|||++|+.+|..||. +|..||++||. |++.||+.||.++|+|.+++++||.+||+.|
T Consensus 1 WT~eEd~~L~~~~~~~g~-~W~~Ia~~l~~-Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN-DWKKIAEHLGN-RTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS--HHHHHHHSTT-S-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc-CHHHHHHHHCc-CCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 999999999999999996 99999999986 9999999999999999999999999999987
No 7
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.62 E-value=2.7e-16 Score=152.13 Aligned_cols=102 Identities=33% Similarity=0.623 Sum_probs=98.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCcccccccccCccccccccccccccccCCCCCCCCCHHHHHHHHHHHHHhCCcHH
Q 037956 11 SLRKGSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPDIRRGNFTQEEDETIIKLHEQLGNRWS 90 (245)
Q Consensus 11 ~lkkg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~i~k~~WT~EED~~Ll~lv~~~G~kW~ 90 (245)
..+.|.|+..||+.|..+|+.||+.+|..||..++. |+++||+.||.++++|.+++.+|+.+||+.|+.+..++|.+|+
T Consensus 17 ~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~-~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~ws 95 (512)
T COG5147 17 KRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLIS-STGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQWS 95 (512)
T ss_pred eecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcc-cccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCchhh
Confidence 456789999999999999999999999999999998 9999999999999999999999999999999999999999999
Q ss_pred HHhhhCCCCCHHHHHHHHHHhhh
Q 037956 91 AIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 91 ~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.||..++||++.+|.+||...+.
T Consensus 96 tia~~~d~rt~~~~~ery~~~~~ 118 (512)
T COG5147 96 TIADYKDRRTAQQCVERYVNTLE 118 (512)
T ss_pred hhccccCccchHHHHHHHHHHhh
Confidence 99999999999999999998776
No 8
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.58 E-value=4.4e-16 Score=148.84 Aligned_cols=101 Identities=28% Similarity=0.645 Sum_probs=96.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCcccccccccCccccccccccccccccCCCCCCCCCHHHHHHHHHHHHHhCCcHHH
Q 037956 12 LRKGSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPDIRRGNFTQEEDETIIKLHEQLGNRWSA 91 (245)
Q Consensus 12 lkkg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~i~k~~WT~EED~~Ll~lv~~~G~kW~~ 91 (245)
++.|.|+.-||+.|..+|.+||.+.|+.|++.+.- .+++||+.||..+|+|.|++..|+.|||+.|+.++..+...|..
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~-kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrt 83 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNR-KTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRT 83 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhh-cchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccch
Confidence 45688999999999999999999999999999998 99999999999999999999999999999999999999999999
Q ss_pred HhhhCCCCCHHHHHHHHHHhhhh
Q 037956 92 IASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 92 IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
||..| ||++++|-.||..+|-.
T Consensus 84 Ia~i~-gr~~~qc~eRy~~ll~~ 105 (617)
T KOG0050|consen 84 IADIM-GRTSQQCLERYNNLLDV 105 (617)
T ss_pred HHHHh-hhhHHHHHHHHHHHHHH
Confidence 99999 99999999999998863
No 9
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.47 E-value=3.8e-14 Score=138.75 Aligned_cols=107 Identities=28% Similarity=0.567 Sum_probs=95.0
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHHHhCCCCcccccccccCccccccccccccccccCC--CCCCCCCHHHHHHHHH
Q 037956 3 KAGGSEKPSLRKGSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPD--IRRGNFTQEEDETIIK 80 (245)
Q Consensus 3 R~~~~~kp~lkkg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~--i~k~~WT~EED~~Ll~ 80 (245)
|++....+ .+|.||+||++.|..+|..+|. .|..|++.|| |.+..||+||.+|..+. .+++.||.||++.|++
T Consensus 375 R~y~~FE~--~rg~wt~ee~eeL~~l~~~~g~-~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk 449 (607)
T KOG0051|consen 375 RAYTPFEN--KRGKWTPEEEEELKKLVVEHGN-DWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLK 449 (607)
T ss_pred hcCCcccc--ccCCCCcchHHHHHHHHHHhcc-cHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHH
Confidence 44444444 8999999999999999999997 9999999999 99999999999999887 4899999999999999
Q ss_pred HHH-------Hh-------------------CCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 81 LHE-------QL-------------------GNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 81 lv~-------~~-------------------G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
+|. .+ +-.|+.|++.+..|+..+|+-+|+.++.+
T Consensus 450 ~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~ 509 (607)
T KOG0051|consen 450 TVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTS 509 (607)
T ss_pred HHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhh
Confidence 995 33 12499999999999999999999999974
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=99.44 E-value=1.6e-13 Score=92.91 Aligned_cols=46 Identities=37% Similarity=0.796 Sum_probs=41.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCc-HHHHhhhCC-CCCHHHHHHHHHHhh
Q 037956 67 RGNFTQEEDETIIKLHEQLGNR-WSAIASRLP-GRTDNEIKNHWHSRL 112 (245)
Q Consensus 67 k~~WT~EED~~Ll~lv~~~G~k-W~~IA~~lp-gRT~~~~Knrw~~~l 112 (245)
+++||+|||++|++++.+||.. |..||..|+ |||..+|++||+.++
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 5789999999999999999988 999999999 999999999999864
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=99.43 E-value=1.7e-14 Score=97.78 Aligned_cols=48 Identities=42% Similarity=0.776 Sum_probs=42.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCcccccccccCccccccccccccccc
Q 037956 14 KGSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYL 61 (245)
Q Consensus 14 kg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L 61 (245)
|++||+|||++|+++|.+||.++|..||..||++|++.||+.||.++|
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 689999999999999999999679999999993399999999999875
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=99.28 E-value=6.3e-12 Score=88.39 Aligned_cols=44 Identities=39% Similarity=0.776 Sum_probs=39.0
Q ss_pred CCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 70 FTQEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 70 WT~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
||+|||++|+++|..||++|..||.+|+.||..+|++||+..|+
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~ 44 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLR 44 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTS
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCc
Confidence 99999999999999999999999999966999999999999775
No 13
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.27 E-value=1.1e-11 Score=81.68 Aligned_cols=47 Identities=43% Similarity=0.890 Sum_probs=44.4
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 67 RGNFTQEEDETIIKLHEQLG-NRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 67 k~~WT~EED~~Ll~lv~~~G-~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
+++||++||.+|+.++..|| .+|..||..|++||+.+|++||+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 46899999999999999999 999999999999999999999998765
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=99.16 E-value=8.1e-11 Score=76.37 Aligned_cols=44 Identities=39% Similarity=0.809 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHHHHHhC-CcHHHHhhhCCCCCHHHHHHHHHHhh
Q 037956 69 NFTQEEDETIIKLHEQLG-NRWSAIASRLPGRTDNEIKNHWHSRL 112 (245)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G-~kW~~IA~~lpgRT~~~~Knrw~~~l 112 (245)
+||.+|+..|+.++..|| .+|..||..|++||..+|++||+.++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 99999999999999999999998753
No 15
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.10 E-value=2.5e-11 Score=79.88 Aligned_cols=48 Identities=44% Similarity=0.859 Sum_probs=44.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCcccccccccCcccccccccccccccc
Q 037956 14 KGSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLR 62 (245)
Q Consensus 14 kg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~ 62 (245)
+++||++||++|..++..||..+|..||..+++ |++.+|+.||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~-rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPG-RTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCC-CCHHHHHHHHHHHcC
Confidence 478999999999999999996699999999998 999999999998764
No 16
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.07 E-value=1e-11 Score=110.36 Aligned_cols=60 Identities=22% Similarity=0.350 Sum_probs=55.1
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHHHhCCCCcccccccccCccccccccccccccccCC
Q 037956 3 KAGGSEKPSLRKGSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPD 64 (245)
Q Consensus 3 R~~~~~kp~lkkg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~ 64 (245)
|+-..++|++++++||+|||++|+.++..||. .|..||++|++ |+..+|+.||...|+..
T Consensus 67 RW~N~L~P~I~kgpWT~EED~lLlel~~~~Gn-KWs~IAk~LpG-RTDnqIKNRWns~LrK~ 126 (249)
T PLN03212 67 RWMNYLRPSVKRGGITSDEEDLILRLHRLLGN-RWSLIAGRIPG-RTDNEIKNYWNTHLRKK 126 (249)
T ss_pred HHHHhhchhcccCCCChHHHHHHHHHHHhccc-cHHHHHhhcCC-CCHHHHHHHHHHHHhHH
Confidence 55667899999999999999999999999997 89999999998 99999999999877754
No 17
>PLN03091 hypothetical protein; Provisional
Probab=99.01 E-value=3.8e-11 Score=114.05 Aligned_cols=59 Identities=19% Similarity=0.383 Sum_probs=54.2
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHHHhCCCCcccccccccCccccccccccccccccC
Q 037956 3 KAGGSEKPSLRKGSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRP 63 (245)
Q Consensus 3 R~~~~~kp~lkkg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p 63 (245)
|+-..++|+++|++||+|||++|++++..||. .|..||++|++ |+..+|+.||...|+.
T Consensus 56 RW~NyLdP~IkKgpWT~EED~lLLeL~k~~Gn-KWskIAk~LPG-RTDnqIKNRWnslLKK 114 (459)
T PLN03091 56 RWINYLRPDLKRGTFSQQEENLIIELHAVLGN-RWSQIAAQLPG-RTDNEIKNLWNSCLKK 114 (459)
T ss_pred HHHhccCCcccCCCCCHHHHHHHHHHHHHhCc-chHHHHHhcCC-CCHHHHHHHHHHHHHH
Confidence 45567899999999999999999999999997 99999999998 9999999999987654
No 18
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.00 E-value=3.2e-10 Score=100.81 Aligned_cols=51 Identities=27% Similarity=0.458 Sum_probs=47.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCC-cHHHHhhhCC-CCCHHHHHHHHHHhhh
Q 037956 63 PDIRRGNFTQEEDETIIKLHEQLGN-RWSAIASRLP-GRTDNEIKNHWHSRLS 113 (245)
Q Consensus 63 p~i~k~~WT~EED~~Ll~lv~~~G~-kW~~IA~~lp-gRT~~~~Knrw~~~lk 113 (245)
+.+.+|+||+|||++|+++|++||. +|..||+.++ ||++.+||-||.++|+
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLr 57 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLR 57 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccC
Confidence 3455899999999999999999995 6999999998 9999999999999997
No 19
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.96 E-value=1.9e-10 Score=74.57 Aligned_cols=45 Identities=42% Similarity=0.804 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHHHHHhCCCCcccccccccCccccccccccccccc
Q 037956 16 SWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYL 61 (245)
Q Consensus 16 ~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L 61 (245)
+||++||+.|+.++..||..+|..||..+++ |++.+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~-rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPG-RTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCC-CCHHHHHHHHHHhC
Confidence 5999999999999999996699999999998 99999999998653
No 20
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.84 E-value=2.8e-09 Score=104.93 Aligned_cols=99 Identities=26% Similarity=0.403 Sum_probs=84.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-----------------------CCcccccccccCccccccccccccccccCCC-CCCC
Q 037956 14 KGSWTPEEDRKLIAYIRRYGI-----------------------WNWSEMPKYAGLLRCGKSCRLRWMNYLRPDI-RRGN 69 (245)
Q Consensus 14 kg~WT~EEDe~L~~~V~~~g~-----------------------~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~i-~k~~ 69 (245)
-+.|+++||..|-..|..|-. +-|..|...+|. |+.+....+-++...|-- .+|.
T Consensus 308 ~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp~-R~~~siy~~~rR~y~~FE~~rg~ 386 (607)
T KOG0051|consen 308 LKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLPY-RDRKSIYHHLRRAYTPFENKRGK 386 (607)
T ss_pred hhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcCc-ccchhHHHHHHhcCCccccccCC
Confidence 378999999999999987721 126778888999 999998774445444433 9999
Q ss_pred CCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 70 FTQEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 70 WT~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
||+||++.|..+|.++|+.|..|+..| ||.+.+|++||..+++-
T Consensus 387 wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~ 430 (607)
T KOG0051|consen 387 WTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKC 430 (607)
T ss_pred CCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhcc
Confidence 999999999999999999999999999 99999999999998864
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=98.12 E-value=1.1e-06 Score=85.93 Aligned_cols=107 Identities=19% Similarity=0.272 Sum_probs=91.6
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHHHhCCCCcccccccccCccccccccccccccccCCCCCCCCCHHHHHHHHHHH
Q 037956 3 KAGGSEKPSLRKGSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPDIRRGNFTQEEDETIIKLH 82 (245)
Q Consensus 3 R~~~~~kp~lkkg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~i~k~~WT~EED~~Ll~lv 82 (245)
|+-..+.|.++++.|+.+||+.|+.+-..+|. .|..||..+++ |++.+|.+||.+.+.+... .+|+.......+..+
T Consensus 61 rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~-~wstia~~~d~-rt~~~~~ery~~~~~~~~s-~~~s~~~~~~~f~k~ 137 (512)
T COG5147 61 RWNNHLNPQLKKKNWSEEEDEQLIDLDKELGT-QWSTIADYKDR-RTAQQCVERYVNTLEDLSS-THDSKLQRRNEFDKI 137 (512)
T ss_pred hhhhhhchhcccccccHHHHHHHHHHHHhcCc-hhhhhccccCc-cchHHHHHHHHHHhhhhhc-cccccccchhhcccc
Confidence 34456789999999999999999999999998 79999999998 9999999999999987666 889999999999999
Q ss_pred HHhCCcHHHHhhhCCCCCHHHHHHHHHHhh
Q 037956 83 EQLGNRWSAIASRLPGRTDNEIKNHWHSRL 112 (245)
Q Consensus 83 ~~~G~kW~~IA~~lpgRT~~~~Knrw~~~l 112 (245)
..|+..|.++....-.+-...|.|++..+.
T Consensus 138 d~f~~~~~~~~~~~~~~~~~~~~N~~~~~~ 167 (512)
T COG5147 138 DPFNENSARRPDIYEDELLEREVNREASYR 167 (512)
T ss_pred CchhhhhhhhhhhhhcccchhhhhHHHHHH
Confidence 999988888877666666667777775443
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=97.98 E-value=3.2e-06 Score=59.71 Aligned_cols=49 Identities=10% Similarity=0.247 Sum_probs=43.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCc---ccccccccCcc-ccccccccccccc
Q 037956 13 RKGSWTPEEDRKLIAYIRRYGIWNW---SEMPKYAGLLR-CGKSCRLRWMNYL 61 (245)
Q Consensus 13 kkg~WT~EEDe~L~~~V~~~g~~nW---~~Ia~~~~~~R-t~kqCr~Rw~n~L 61 (245)
++-.||+||.++++.+|+.+|.++| ..|+..|+..| +..||+.+.+.|.
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 3568999999999999999999899 99999887546 9999999988764
No 23
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.83 E-value=5.5e-06 Score=78.90 Aligned_cols=87 Identities=24% Similarity=0.437 Sum_probs=62.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCcccccccccCccccccccccccccc-cCCCCCCCC-------CHHHHHHHHHH-HH
Q 037956 13 RKGSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYL-RPDIRRGNF-------TQEEDETIIKL-HE 83 (245)
Q Consensus 13 kkg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L-~p~i~k~~W-------T~EED~~Ll~l-v~ 83 (245)
-...||.+|+-+|++++..||-|||..||.++|+ |++.+|+++|.+++ +..+-.-+| ...|+...-.. +.
T Consensus 71 ~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGt-Ktkeeck~hy~k~fv~s~~~~~~~i~~~~~~~q~e~~~~~k~~~~ 149 (438)
T KOG0457|consen 71 LDPSWTADEEILLLEAAETYGFGNWQDIADHIGT-KTKEECKEHYLKHFVNSPIFPLPDISLGIGVNQDEDAAMAKNRAE 149 (438)
T ss_pred CCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcc-cchHHHHHHHHHHHhcCccccccccccccCcchHHHhhhcccccc
Confidence 3567999999999999999999999999999998 99999999999854 333222222 23344433333 22
Q ss_pred HhCC-------------cHHHHhhhCCCCC
Q 037956 84 QLGN-------------RWSAIASRLPGRT 100 (245)
Q Consensus 84 ~~G~-------------kW~~IA~~lpgRT 100 (245)
.++. .=.+|+.+||+|.
T Consensus 150 ~~~~~~~~pr~p~~~~p~~~e~~gyMp~R~ 179 (438)
T KOG0457|consen 150 PFQPTDLVPRKPGVSNPLRREISGYMPGRL 179 (438)
T ss_pred cCCCCCCCCCCCCCCCchHHHHhhhCccch
Confidence 2322 2458888899985
No 24
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.72 E-value=6.1e-05 Score=71.89 Aligned_cols=52 Identities=23% Similarity=0.434 Sum_probs=46.4
Q ss_pred cCCCCCCCCCHHHHHHHHHHHHHhC-CcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 62 RPDIRRGNFTQEEDETIIKLHEQLG-NRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 62 ~p~i~k~~WT~EED~~Ll~lv~~~G-~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
+-.+-...||.+|+-+|++++..|| ++|..||.++..|+..+||.+|.+++-
T Consensus 67 s~~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 67 SFPILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHh
Confidence 3345567899999999999999999 899999999988999999999987664
No 25
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.64 E-value=0.00016 Score=51.04 Aligned_cols=47 Identities=17% Similarity=0.360 Sum_probs=40.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-cH---HHHhhhCC-CC-CHHHHHHHHHHhhh
Q 037956 67 RGNFTQEEDETIIKLHEQLGN-RW---SAIASRLP-GR-TDNEIKNHWHSRLS 113 (245)
Q Consensus 67 k~~WT~EED~~Ll~lv~~~G~-kW---~~IA~~lp-gR-T~~~~Knrw~~~lk 113 (245)
+-.||+||...++++++.||. .| ..|+..|. .| |..+|+.+.+.+.-
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 457999999999999999996 99 99999884 35 99999999886543
No 26
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.31 E-value=0.00041 Score=60.53 Aligned_cols=100 Identities=20% Similarity=0.364 Sum_probs=71.7
Q ss_pred CCCHHHHHHHHHHHHHhCCCCcccccccccCc--cccccccccccccc-cCCC--------------------CCCCCCH
Q 037956 16 SWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLL--RCGKSCRLRWMNYL-RPDI--------------------RRGNFTQ 72 (245)
Q Consensus 16 ~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~--Rt~kqCr~Rw~n~L-~p~i--------------------~k~~WT~ 72 (245)
+|+|++|-.|+.+|..-. +-..|++-+... -|-+.+.+||...| +|.+ .+.+||.
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 599999999999998643 566666654432 34556778998865 4443 2468999
Q ss_pred HHHHHHHHHHHHhCC---cHHHHhh-----hCCCCCHHHHHHHHHHhhhhhhhh
Q 037956 73 EEDETIIKLHEQLGN---RWSAIAS-----RLPGRTDNEIKNHWHSRLSKKRLT 118 (245)
Q Consensus 73 EED~~Ll~lv~~~G~---kW~~IA~-----~lpgRT~~~~Knrw~~~lkkk~~~ 118 (245)
+|+++|........+ .+.+|=. +-++||+.++.++|..+.+ ..+-
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkq-y~LL 131 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQ-YHLL 131 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHH-hchh
Confidence 999999997766543 4777633 2378999999999995443 4443
No 27
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.18 E-value=0.00031 Score=68.54 Aligned_cols=49 Identities=35% Similarity=0.584 Sum_probs=45.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHhC-CcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 65 IRRGNFTQEEDETIIKLHEQLG-NRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 65 i~k~~WT~EED~~Ll~lv~~~G-~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
++.|-|+.-||+.|--++.+|| +.|+.|++.|+-.+..+|++||+..+.
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ld 54 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLD 54 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhC
Confidence 4678899999999999999999 579999999999999999999998775
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=97.10 E-value=0.00084 Score=48.60 Aligned_cols=49 Identities=20% Similarity=0.482 Sum_probs=32.8
Q ss_pred CCCCCHHHHHHHHHHHHHhC--------Cc-HHHHhhhCC-CCCHHHHHHHHHHhhhhh
Q 037956 67 RGNFTQEEDETIIKLHEQLG--------NR-WSAIASRLP-GRTDNEIKNHWHSRLSKK 115 (245)
Q Consensus 67 k~~WT~EED~~Ll~lv~~~G--------~k-W~~IA~~lp-gRT~~~~Knrw~~~lkkk 115 (245)
+.+||.+||..|++.|..+. ++ |.+++..-+ .+|-.+.|+||...|+.+
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~ 60 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGR 60 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT---
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcc
Confidence 45899999999999997653 22 999999877 999999999999888743
No 29
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.09 E-value=0.00054 Score=51.07 Aligned_cols=49 Identities=33% Similarity=0.589 Sum_probs=35.1
Q ss_pred CCCCCHHHHHHHHHHHHH------hC--C------cHHHHhhhC----CCCCHHHHHHHHHHhhhhh
Q 037956 67 RGNFTQEEDETIIKLHEQ------LG--N------RWSAIASRL----PGRTDNEIKNHWHSRLSKK 115 (245)
Q Consensus 67 k~~WT~EED~~Ll~lv~~------~G--~------kW~~IA~~l----pgRT~~~~Knrw~~~lkkk 115 (245)
+..||.+|...|++++.. ++ + -|..||..| ..||+.||+++|.++.++-
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Y 67 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKY 67 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence 357999999999999876 21 1 399999987 3699999999999977643
No 30
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.07 E-value=0.00017 Score=69.46 Aligned_cols=46 Identities=24% Similarity=0.595 Sum_probs=42.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCcccccccccCcccccccccccccc
Q 037956 13 RKGSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNY 60 (245)
Q Consensus 13 kkg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~ 60 (245)
...+||.+|..+|++.|+.||. +|.+||+++|+ |+..||..||.+.
T Consensus 278 ~dk~WS~qE~~LLLEGIe~ygD-dW~kVA~HVgt-Kt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYGD-DWDKVARHVGT-KTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhhh-hHHHHHHHhCC-CCHHHHHHHHHcC
Confidence 4568999999999999999997 99999999998 9999999999863
No 31
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.02 E-value=0.00098 Score=65.50 Aligned_cols=45 Identities=18% Similarity=0.400 Sum_probs=42.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 037956 66 RRGNFTQEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHS 110 (245)
Q Consensus 66 ~k~~WT~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~ 110 (245)
.+..||.+|..+|++++++||..|.+||.++.+||..+|--+|-.
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~ 296 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLR 296 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHh
Confidence 457899999999999999999999999999999999999999865
No 32
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.00 E-value=0.00093 Score=64.57 Aligned_cols=43 Identities=19% Similarity=0.366 Sum_probs=41.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 037956 68 GNFTQEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHS 110 (245)
Q Consensus 68 ~~WT~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~ 110 (245)
.+||.+|..+|++.++.||..|.+||.++..||..||--||-.
T Consensus 280 k~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~ 322 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQ 322 (531)
T ss_pred ccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHc
Confidence 4899999999999999999999999999999999999999865
No 33
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.92 E-value=0.00035 Score=68.62 Aligned_cols=47 Identities=23% Similarity=0.598 Sum_probs=43.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCcccccccccCcccccccccccccc
Q 037956 12 LRKGSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNY 60 (245)
Q Consensus 12 lkkg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~ 60 (245)
.-++.||.+|.-+|+++|+.||. +|.+||.++++ |+..||..++.+.
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~d-dW~kVa~hVg~-ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYGD-DWNKVADHVGT-KSQEQCILKFLRL 297 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhcc-cHHHHHhccCC-CCHHHHHHHHHhc
Confidence 34678999999999999999998 99999999998 9999999999863
No 34
>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=96.81 E-value=0.0016 Score=55.00 Aligned_cols=49 Identities=20% Similarity=0.325 Sum_probs=43.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhC---C----cHHHHhhhCCCCCHHHHHHHHHHhhhhh
Q 037956 66 RRGNFTQEEDETIIKLHEQLG---N----RWSAIASRLPGRTDNEIKNHWHSRLSKK 115 (245)
Q Consensus 66 ~k~~WT~EED~~Ll~lv~~~G---~----kW~~IA~~lpgRT~~~~Knrw~~~lkkk 115 (245)
....||.|||.+|-+.|..|- + ....+|..| +||+.+|.=||+..+|++
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkq 58 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQ 58 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHH
Confidence 457899999999999998873 2 388999999 999999999999999964
No 35
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=96.46 E-value=0.0097 Score=43.51 Aligned_cols=48 Identities=35% Similarity=0.630 Sum_probs=40.1
Q ss_pred CCCCCHHHHHHHHHHHHHhC----C-------------cHHHHhhhC-----CCCCHHHHHHHHHHhhhh
Q 037956 67 RGNFTQEEDETIIKLHEQLG----N-------------RWSAIASRL-----PGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 67 k~~WT~EED~~Ll~lv~~~G----~-------------kW~~IA~~l-----pgRT~~~~Knrw~~~lkk 114 (245)
...||.+|...|++++.+|. + .|..|+..| +.||..+|+.+|..+...
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~ 71 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSK 71 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Confidence 46799999999999998763 1 299999987 359999999999987753
No 36
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=96.42 E-value=0.00067 Score=49.13 Aligned_cols=52 Identities=23% Similarity=0.347 Sum_probs=32.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCC------C--CcccccccccCccccccccccccccccCCC
Q 037956 14 KGSWTPEEDRKLIAYIRRYGI------W--NWSEMPKYAGLLRCGKSCRLRWMNYLRPDI 65 (245)
Q Consensus 14 kg~WT~EEDe~L~~~V~~~g~------~--nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~i 65 (245)
|.+||.+||++|+.+|..+.. | =|.+++..-++.++-.+-|+||...|.+..
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 568999999999999976532 2 299999887754888899999999887643
No 37
>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=96.17 E-value=0.0011 Score=55.99 Aligned_cols=49 Identities=31% Similarity=0.544 Sum_probs=42.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC------CCcccccccccCccccccccccccccccC
Q 037956 13 RKGSWTPEEDRKLIAYIRRYGI------WNWSEMPKYAGLLRCGKSCRLRWMNYLRP 63 (245)
Q Consensus 13 kkg~WT~EEDe~L~~~V~~~g~------~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p 63 (245)
+...||.|||.+|...|.+|-. ....+++..++ ||+--|.-||+.+++.
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~--RTsAACGFRWNs~VRk 57 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN--RTAAACGFRWNAYVRK 57 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc--ccHHHhcchHHHHHHH
Confidence 5678999999999999999832 24788888888 9999999999999874
No 38
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.17 E-value=0.00093 Score=49.79 Aligned_cols=48 Identities=29% Similarity=0.583 Sum_probs=32.6
Q ss_pred CCCCCHHHHHHHHHHHHH--h----C---C----CCcccccccc---cCccccccccccccccc
Q 037956 14 KGSWTPEEDRKLIAYIRR--Y----G---I----WNWSEMPKYA---GLLRCGKSCRLRWMNYL 61 (245)
Q Consensus 14 kg~WT~EEDe~L~~~V~~--~----g---~----~nW~~Ia~~~---~~~Rt~kqCr~Rw~n~L 61 (245)
|..||.+|...|+.++.. + + . .-|..||..| |..|++.||+.||.+..
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 457999999999999876 1 1 1 1499999976 55699999999998743
No 39
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.05 E-value=0.0072 Score=51.60 Aligned_cols=50 Identities=22% Similarity=0.332 Sum_probs=42.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCc-------HHHHhhhCCCCCHHHHHHHHHHhhhhhh
Q 037956 66 RRGNFTQEEDETIIKLHEQLGNR-------WSAIASRLPGRTDNEIKNHWHSRLSKKR 116 (245)
Q Consensus 66 ~k~~WT~EED~~Ll~lv~~~G~k-------W~~IA~~lpgRT~~~~Knrw~~~lkkk~ 116 (245)
+...||.|+|.+|-+.|..|+.. ...++..| +||..+|.-||+..++++.
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 46789999999999998888732 66777888 9999999999999998543
No 40
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.97 E-value=0.0017 Score=60.37 Aligned_cols=47 Identities=21% Similarity=0.578 Sum_probs=44.0
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCcccccccccCcccccccccccccccc
Q 037956 15 GSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLR 62 (245)
Q Consensus 15 g~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~ 62 (245)
--|+..|+-+|++.....|-|||..||.++|. |....|+.+|..++.
T Consensus 64 e~WgadEEllli~~~~TlGlGNW~dIadyiGs-r~kee~k~HylK~y~ 110 (432)
T COG5114 64 EGWGADEELLLIECLDTLGLGNWEDIADYIGS-RAKEEIKSHYLKMYD 110 (432)
T ss_pred CCcCchHHHHHHHHHHhcCCCcHHHHHHHHhh-hhhHHHHHHHHHHHh
Confidence 35999999999999999999999999999997 999999999998765
No 41
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.72 E-value=0.016 Score=53.97 Aligned_cols=49 Identities=27% Similarity=0.512 Sum_probs=43.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHhC-CcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 65 IRRGNFTQEEDETIIKLHEQLG-NRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 65 i~k~~WT~EED~~Ll~lv~~~G-~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
|--..|+..|+.+|++....+| ++|..||.++..|+...||.+|..+.-
T Consensus 61 I~~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 61 IGEEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred ccCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 3446799999999999999999 899999999988999999999986554
No 42
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.37 E-value=0.0033 Score=46.01 Aligned_cols=49 Identities=22% Similarity=0.346 Sum_probs=39.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC----------------CCcccccccc----cCccccccccccccccc
Q 037956 13 RKGSWTPEEDRKLIAYIRRYGI----------------WNWSEMPKYA----GLLRCGKSCRLRWMNYL 61 (245)
Q Consensus 13 kkg~WT~EEDe~L~~~V~~~g~----------------~nW~~Ia~~~----~~~Rt~kqCr~Rw~n~L 61 (245)
++..||++|.+.|+++|..|.. .-|..|+..+ ++.|+..||+.+|.++.
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 3568999999999999998821 2499998865 32499999999998754
No 43
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=95.13 E-value=0.039 Score=58.77 Aligned_cols=98 Identities=13% Similarity=0.289 Sum_probs=74.8
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCcccccccccCcccccccc-------ccccc----------------------------
Q 037956 15 GSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCR-------LRWMN---------------------------- 59 (245)
Q Consensus 15 g~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr-------~Rw~n---------------------------- 59 (245)
+.|+.-+=..++.++.+||..+-..||..|.+ ++...++ .||..
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~-k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~ 903 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEG-KTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAI 903 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcC-CCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45888888888999999998888899998876 6666554 11111
Q ss_pred -------------cc--cCCCCCCCCCHHHHHHHHHHHHHhC-CcHHHHhhh------------CCCCCHHHHHHHHHHh
Q 037956 60 -------------YL--RPDIRRGNFTQEEDETIIKLHEQLG-NRWSAIASR------------LPGRTDNEIKNHWHSR 111 (245)
Q Consensus 60 -------------~L--~p~i~k~~WT~EED~~Ll~lv~~~G-~kW~~IA~~------------lpgRT~~~~Knrw~~~ 111 (245)
.. .+.-++..||.|||..|+-++.+|| ++|..|-.. |..||+..|..|...+
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 00 1223445799999999999999999 789999443 2479999999999998
Q ss_pred hh
Q 037956 112 LS 113 (245)
Q Consensus 112 lk 113 (245)
|+
T Consensus 984 ~~ 985 (1033)
T PLN03142 984 IR 985 (1033)
T ss_pred HH
Confidence 86
No 44
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=94.42 E-value=0.0061 Score=52.02 Aligned_cols=49 Identities=27% Similarity=0.453 Sum_probs=39.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCC------CcccccccccCcccccccccccccccc
Q 037956 12 LRKGSWTPEEDRKLIAYIRRYGIW------NWSEMPKYAGLLRCGKSCRLRWMNYLR 62 (245)
Q Consensus 12 lkkg~WT~EEDe~L~~~V~~~g~~------nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~ 62 (245)
.+...||.|||.+|...|..|+.. ....++..+. |++-.|..||+.+++
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~--rt~aac~fRwNs~vr 57 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALK--RTAAACGFRWNSVVR 57 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHh--hhHHHHHhHHHHHHH
Confidence 466789999999999999988652 2455556666 999999999977766
No 45
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=93.98 E-value=0.029 Score=53.39 Aligned_cols=47 Identities=26% Similarity=0.421 Sum_probs=42.7
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhh-----CCC-CCHHHHHHHHHHhhhh
Q 037956 68 GNFTQEEDETIIKLHEQLGNRWSAIASR-----LPG-RTDNEIKNHWHSRLSK 114 (245)
Q Consensus 68 ~~WT~EED~~Ll~lv~~~G~kW~~IA~~-----lpg-RT~~~~Knrw~~~lkk 114 (245)
..||.+|-+-|+++++.|.-+|..||.. ++. ||-.++|+||+...++
T Consensus 131 n~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~ 183 (445)
T KOG2656|consen 131 NSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYSVCRK 183 (445)
T ss_pred ccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHHHHHH
Confidence 5699999999999999999999999987 555 9999999999988763
No 46
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=93.58 E-value=0.14 Score=41.22 Aligned_cols=50 Identities=18% Similarity=0.448 Sum_probs=40.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC----cHHHHhhhC------------CCCCHHHHHHHHHHhhh
Q 037956 64 DIRRGNFTQEEDETIIKLHEQLGN----RWSAIASRL------------PGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 64 ~i~k~~WT~EED~~Ll~lv~~~G~----kW~~IA~~l------------pgRT~~~~Knrw~~~lk 113 (245)
.-++..||.+||..|+-++.+||- .|..|...+ ..||+..|..|...+|+
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~ 111 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIK 111 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHH
Confidence 445778999999999999999995 798886643 47999999999999886
No 47
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=92.73 E-value=0.31 Score=36.48 Aligned_cols=46 Identities=28% Similarity=0.572 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHHHh---CC----------cHHHHhhhC---CC--CCHHHHHHHHHHhhhh
Q 037956 69 NFTQEEDETIIKLHEQL---GN----------RWSAIASRL---PG--RTDNEIKNHWHSRLSK 114 (245)
Q Consensus 69 ~WT~EED~~Ll~lv~~~---G~----------kW~~IA~~l---pg--RT~~~~Knrw~~~lkk 114 (245)
.||+++++.|++++.+. |+ .|..|+..| +| .+..+|+|||..+-+.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~ 64 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKD 64 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHH
Confidence 49999999999998543 21 299999987 23 5789999999876553
No 48
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=91.92 E-value=0.24 Score=46.13 Aligned_cols=55 Identities=20% Similarity=0.383 Sum_probs=42.5
Q ss_pred CCCCCHHHHHHHHHHHHHh----------CCcHHHHhhhC----CCCCHHHHHHHHHHhhhhhhhhhhc
Q 037956 67 RGNFTQEEDETIIKLHEQL----------GNRWSAIASRL----PGRTDNEIKNHWHSRLSKKRLTKNN 121 (245)
Q Consensus 67 k~~WT~EED~~Ll~lv~~~----------G~kW~~IA~~l----pgRT~~~~Knrw~~~lkkk~~~k~~ 121 (245)
...|+.+|-..||++.... +.-|..||..+ .-||+.+||++|.++.++-+..+..
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k~~ 122 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEKAK 122 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 3689999999999998643 23499999965 2499999999999988754444333
No 49
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=90.43 E-value=0.8 Score=30.73 Aligned_cols=41 Identities=22% Similarity=0.299 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 72 QEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 72 ~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
++++..++.++...|-.|.+||..+ |.+...|+.+.+.-++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARK 52 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHh
Confidence 4677888999999999999999999 9999999998876554
No 50
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=88.83 E-value=0.98 Score=44.12 Aligned_cols=49 Identities=16% Similarity=0.228 Sum_probs=44.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhhhh
Q 037956 67 RGNFTQEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLSKK 115 (245)
Q Consensus 67 k~~WT~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkkk 115 (245)
...||.||--++-+++..||+...+|-+.||.|+-..|...|+..-|.+
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK~~ 235 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKKTR 235 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHHHh
Confidence 4679999999999999999999999999999999999999888765543
No 51
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=87.83 E-value=0.97 Score=43.29 Aligned_cols=47 Identities=23% Similarity=0.310 Sum_probs=43.3
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 68 GNFTQEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 68 ~~WT~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
.+|+.+|-++..++....|..+.-|+..||.|...|||-+|..--|+
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~ 412 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKV 412 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhh
Confidence 47999999999999999999999999999999999999999765543
No 52
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=85.59 E-value=0.51 Score=37.99 Aligned_cols=34 Identities=29% Similarity=0.588 Sum_probs=28.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC---CCcccccccc
Q 037956 11 SLRKGSWTPEEDRKLIAYIRRYGI---WNWSEMPKYA 44 (245)
Q Consensus 11 ~lkkg~WT~EEDe~L~~~V~~~g~---~nW~~Ia~~~ 44 (245)
+.++..||.+||.-|+-.+.+||- +.|..|-..+
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~I 82 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEI 82 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHH
Confidence 566788999999999999999998 8999987755
No 53
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=84.19 E-value=0.46 Score=45.41 Aligned_cols=43 Identities=16% Similarity=0.308 Sum_probs=40.8
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCcccccccccCccccccccccccc
Q 037956 15 GSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMN 59 (245)
Q Consensus 15 g~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n 59 (245)
-+|+.+|-+++.+++..+|. ++..|+.++|+ |..+|++.+|.+
T Consensus 366 ~~Ws~~e~ekFYKALs~wGt-dF~LIs~lfP~-R~RkqIKaKfi~ 408 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGT-DFSLISSLFPN-RERKQIKAKFIK 408 (507)
T ss_pred CcccHHHHHHHHHHHHHhcc-hHHHHHHhcCc-hhHHHHHHHHHH
Confidence 47999999999999999998 99999999999 999999999876
No 54
>smart00595 MADF subfamily of SANT domain.
Probab=80.88 E-value=2.7 Score=31.00 Aligned_cols=24 Identities=33% Similarity=0.670 Sum_probs=21.1
Q ss_pred HHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 89 WSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 89 W~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
|..||..| |-+..+|+.+|+++-.
T Consensus 30 W~~Ia~~l-~~~~~~~~~kw~~LR~ 53 (89)
T smart00595 30 WEEIAEEL-GLSVEECKKRWKNLRD 53 (89)
T ss_pred HHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 99999999 6699999999987643
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=80.21 E-value=5.1 Score=26.45 Aligned_cols=41 Identities=24% Similarity=0.358 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 73 EEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 73 EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
+++..++.++-..|-.+.+||..| |-+...|+.+.+..+++
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 455666666666677899999999 99999999998887764
No 56
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=79.71 E-value=1.1 Score=41.65 Aligned_cols=47 Identities=26% Similarity=0.391 Sum_probs=36.5
Q ss_pred CCCCHHHHHHHHHHHHHh----CC-----CCccccccc---ccCccccccccccccccc
Q 037956 15 GSWTPEEDRKLIAYIRRY----GI-----WNWSEMPKY---AGLLRCGKSCRLRWMNYL 61 (245)
Q Consensus 15 g~WT~EEDe~L~~~V~~~----g~-----~nW~~Ia~~---~~~~Rt~kqCr~Rw~n~L 61 (245)
..|+.+|-..|+.+.... .. .-|..||+. .|..|++.||+.+|.+..
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 679999999999977432 11 259999983 455699999999998744
No 57
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=78.76 E-value=9.1 Score=39.73 Aligned_cols=47 Identities=9% Similarity=0.040 Sum_probs=42.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 67 RGNFTQEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 67 k~~WT~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
...||+.|-.+.-+++-.|.+.+-.|++.++++|-.+|-..||...|
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 35799999999999999999999999999999999999998876443
No 58
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=77.61 E-value=2.4 Score=31.94 Aligned_cols=25 Identities=40% Similarity=0.716 Sum_probs=13.9
Q ss_pred CCCCCCCCCHHHHHHH--------HHHHHHhCC
Q 037956 10 PSLRKGSWTPEEDRKL--------IAYIRRYGI 34 (245)
Q Consensus 10 p~lkkg~WT~EEDe~L--------~~~V~~~g~ 34 (245)
|.-..|-||+++|+.| ..++++||.
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 4455788999999999 345566763
No 59
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=73.75 E-value=5 Score=40.66 Aligned_cols=47 Identities=15% Similarity=0.440 Sum_probs=38.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHhh----------hCCCCCHHHHHHHHHHhhh
Q 037956 67 RGNFTQEEDETIIKLHEQLGNRWSAIAS----------RLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 67 k~~WT~EED~~Ll~lv~~~G~kW~~IA~----------~lpgRT~~~~Knrw~~~lk 113 (245)
+..||-.|++-.+.+++++|+.+.+|-. ...-+|-.+++.+||..++
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~ 144 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVR 144 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHH
Confidence 5689999999999999999999998832 2334677889888888775
No 60
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=72.12 E-value=9.3 Score=24.94 Aligned_cols=38 Identities=21% Similarity=0.450 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHhCC-cHHHHhhhCCCCCHHHHHHHHHHh
Q 037956 73 EEDETIIKLHEQLGN-RWSAIASRLPGRTDNEIKNHWHSR 111 (245)
Q Consensus 73 EED~~Ll~lv~~~G~-kW~~IA~~lpgRT~~~~Knrw~~~ 111 (245)
+=|..|+.+.+.-|. .|.+||+.+ |=|...|..|+..+
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 457889999888885 699999999 99999999998753
No 61
>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=69.10 E-value=12 Score=29.56 Aligned_cols=36 Identities=25% Similarity=0.355 Sum_probs=28.0
Q ss_pred HHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 77 TIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 77 ~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.++.++-..|-.+.+||+.+ |.+...|+++.+..++
T Consensus 120 ~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~ 155 (161)
T TIGR02985 120 KIFILSRFEGKSYKEIAEEL-GISVKTVEYHISKALK 155 (161)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 33444334577899999999 9999999999988665
No 62
>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=67.18 E-value=14 Score=27.47 Aligned_cols=37 Identities=22% Similarity=0.452 Sum_probs=27.6
Q ss_pred HHHHHHHHhC--------CcHHHHhhhCCC---CC--HHHHHHHHHHhhh
Q 037956 77 TIIKLHEQLG--------NRWSAIASRLPG---RT--DNEIKNHWHSRLS 113 (245)
Q Consensus 77 ~Ll~lv~~~G--------~kW~~IA~~lpg---RT--~~~~Knrw~~~lk 113 (245)
.|..+|..+| ++|..||..|.- -+ ..+++..|..+|-
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 5788888888 359999999822 12 3688999988764
No 63
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=67.11 E-value=7.6 Score=32.80 Aligned_cols=41 Identities=32% Similarity=0.380 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 037956 69 NFTQEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHS 110 (245)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~ 110 (245)
.||+|..+.|.+|..+ |-.=++||..|.|.|.|+|.-+-+.
T Consensus 2 ~Wtde~~~~L~~lw~~-G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred CCCHHHHHHHHHHHHc-CCCHHHHHHHhCCcchhhhhhhhhc
Confidence 4999999999999855 8888999999977999999877664
No 64
>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=66.25 E-value=9.5 Score=28.73 Aligned_cols=30 Identities=27% Similarity=0.585 Sum_probs=25.2
Q ss_pred HHHHHHHHHHhCCcHHHHhhhCCCCCHHHHH
Q 037956 75 DETIIKLHEQLGNRWSAIASRLPGRTDNEIK 105 (245)
Q Consensus 75 D~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~K 105 (245)
|+.|..+....|..|..+|.+| |=|..+|.
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I~ 31 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDIY 31 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 5678899999999999999999 77766554
No 65
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=64.11 E-value=15 Score=30.18 Aligned_cols=40 Identities=13% Similarity=0.175 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHhC-CcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 73 EEDETIIKLHEQLG-NRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 73 EED~~Ll~lv~~~G-~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
+-|..|+.+.+.-| -.|+.||+.+ |-+...|..|+..+..
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~ 49 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQ 49 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 56888999988888 4799999999 9999999999988765
No 66
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=62.28 E-value=16 Score=32.01 Aligned_cols=43 Identities=26% Similarity=0.330 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHHhCCcHHHHhhhC---CCCCHHHHHHHHHHhh
Q 037956 69 NFTQEEDETIIKLHEQLGNRWSAIASRL---PGRTDNEIKNHWHSRL 112 (245)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kW~~IA~~l---pgRT~~~~Knrw~~~l 112 (245)
.|++.+|-+|+.+|.. |+.-..|+..+ -.-|-..|..||+.+|
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~ll 46 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALL 46 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHH
Confidence 4999999999998865 66677776643 3468899999999977
No 67
>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=61.20 E-value=15 Score=27.69 Aligned_cols=31 Identities=26% Similarity=0.494 Sum_probs=25.9
Q ss_pred HHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHH
Q 037956 75 DETIIKLHEQLGNRWSAIASRLPGRTDNEIKN 106 (245)
Q Consensus 75 D~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Kn 106 (245)
|..|..+....|..|.++|..| |=+...|.+
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 5678888999999999999999 777766544
No 68
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=60.57 E-value=20 Score=26.92 Aligned_cols=37 Identities=22% Similarity=0.489 Sum_probs=27.8
Q ss_pred HHHHHHHHhCC--------cHHHHhhhCCC-----CCHHHHHHHHHHhhh
Q 037956 77 TIIKLHEQLGN--------RWSAIASRLPG-----RTDNEIKNHWHSRLS 113 (245)
Q Consensus 77 ~Ll~lv~~~G~--------kW~~IA~~lpg-----RT~~~~Knrw~~~lk 113 (245)
.|..+|..+|+ +|..||..|.- .....++..|..+|.
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~ 85 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLL 85 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhH
Confidence 47788888883 69999999832 235778888887764
No 69
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=59.55 E-value=17 Score=30.16 Aligned_cols=42 Identities=12% Similarity=0.133 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHhCC-cHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 72 QEEDETIIKLHEQLGN-RWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 72 ~EED~~Ll~lv~~~G~-kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
.+-|..|+.+.++-|. .|+.||+.+ |-+...|..|++.+.+.
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~ 55 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQ 55 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHC
Confidence 4568889988888884 699999999 99999999999987763
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=58.92 E-value=21 Score=27.21 Aligned_cols=35 Identities=20% Similarity=0.238 Sum_probs=27.1
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 78 IIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 78 Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
++.++...|..+..||+.+ |-+...|+++.+..++
T Consensus 118 ii~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~ 152 (158)
T TIGR02937 118 VLVLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARK 152 (158)
T ss_pred HHhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3344444678899999999 8899999998887665
No 71
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=58.89 E-value=3.9 Score=42.25 Aligned_cols=42 Identities=17% Similarity=0.303 Sum_probs=38.4
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCcccccccccCcccccccccccc
Q 037956 15 GSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWM 58 (245)
Q Consensus 15 g~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~ 58 (245)
..||+.|-.++.+++-.|.. ++..|++++++ ++..||-+-|.
T Consensus 620 d~WTp~E~~lF~kA~y~~~K-DF~~v~km~~~-KtVaqCVeyYY 661 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYSK-DFIFVQKMVKS-KTVAQCVEYYY 661 (907)
T ss_pred ccccHHHHHHHHHHHHHhcc-cHHHHHHHhcc-ccHHHHHHHHH
Confidence 57999999999999999986 99999999999 99999987664
No 72
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=58.33 E-value=13 Score=27.57 Aligned_cols=31 Identities=26% Similarity=0.589 Sum_probs=24.6
Q ss_pred HHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHH
Q 037956 75 DETIIKLHEQLGNRWSAIASRLPGRTDNEIKN 106 (245)
Q Consensus 75 D~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Kn 106 (245)
|..|..+....|..|.++|.+| |=+..+|..
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI~~ 34 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDIDL 34 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHHHH
Confidence 4567788899999999999999 777655543
No 73
>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=56.91 E-value=3 Score=27.33 Aligned_cols=37 Identities=24% Similarity=0.380 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHhCCCCcccccccccCcccccccccccc
Q 037956 20 EEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWM 58 (245)
Q Consensus 20 EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~ 58 (245)
+=|.+|+.+++.-|...|.+||+.+| =+...|+.|+.
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lg--lS~~~v~~Ri~ 39 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELG--LSESTVRRRIR 39 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHT--S-HHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHC--cCHHHHHHHHH
Confidence 34888999999999889999999999 57778888775
No 74
>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=54.80 E-value=12 Score=28.02 Aligned_cols=17 Identities=41% Similarity=0.608 Sum_probs=10.0
Q ss_pred CCCCCCCCCHHHHHHHH
Q 037956 63 PDIRRGNFTQEEDETII 79 (245)
Q Consensus 63 p~i~k~~WT~EED~~Ll 79 (245)
|.-..|-||+++|+.|.
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 55667899999999984
No 75
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=54.21 E-value=28 Score=28.03 Aligned_cols=32 Identities=19% Similarity=0.229 Sum_probs=25.7
Q ss_pred HHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 81 LHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 81 lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
++...|-.+..||..| |.+...|+.+.+..++
T Consensus 139 l~~~~~~s~~eIA~~l-gis~~tV~~~l~ra~~ 170 (182)
T PRK09652 139 LREIEGLSYEEIAEIM-GCPIGTVRSRIFRARE 170 (182)
T ss_pred HHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3334567899999999 9999999998887654
No 76
>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=52.67 E-value=22 Score=26.65 Aligned_cols=28 Identities=32% Similarity=0.652 Sum_probs=21.9
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHH
Q 037956 78 IIKLHEQLGNRWSAIASRLPGRTDNEIKN 106 (245)
Q Consensus 78 Ll~lv~~~G~kW~~IA~~lpgRT~~~~Kn 106 (245)
|..+....|..|..+|.+| |-+..+|..
T Consensus 10 l~~ia~~iG~~Wk~Lar~L-Gls~~dI~~ 37 (86)
T cd08318 10 ITVFANKLGEDWKTLAPHL-EMKDKEIRA 37 (86)
T ss_pred HHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 3446688899999999999 877776643
No 77
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=52.53 E-value=28 Score=33.53 Aligned_cols=45 Identities=16% Similarity=0.203 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhh-hCCCCCHHHHHHHHHHhh
Q 037956 68 GNFTQEEDETIIKLHEQLGNRWSAIAS-RLPGRTDNEIKNHWHSRL 112 (245)
Q Consensus 68 ~~WT~EED~~Ll~lv~~~G~kW~~IA~-~lpgRT~~~~Knrw~~~l 112 (245)
..|+++|=...-+.++.||+.+..|.+ +++.|+--.|-..|+-..
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWK 323 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWK 323 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhh
Confidence 479999999999999999999999954 799999999988777543
No 78
>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=52.47 E-value=21 Score=26.67 Aligned_cols=31 Identities=26% Similarity=0.589 Sum_probs=25.9
Q ss_pred HHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHH
Q 037956 75 DETIIKLHEQLGNRWSAIASRLPGRTDNEIKN 106 (245)
Q Consensus 75 D~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Kn 106 (245)
|..|-.+...+|.+|..+|..| |=+...|.+
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 4567778899999999999999 888777765
No 79
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=51.47 E-value=33 Score=28.78 Aligned_cols=32 Identities=16% Similarity=0.166 Sum_probs=25.8
Q ss_pred HHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 81 LHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 81 lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
+....|-...+||..| |-+...|++|.+..++
T Consensus 145 l~~~~g~s~~EIA~~l-g~s~~tV~~rl~rar~ 176 (192)
T PRK09643 145 AVDMQGYSVADAARML-GVAEGTVKSRCARGRA 176 (192)
T ss_pred HHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 3334567799999999 9999999999976554
No 80
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=50.22 E-value=34 Score=27.44 Aligned_cols=29 Identities=21% Similarity=0.211 Sum_probs=24.5
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
..|-....||..| |-+...|+++.+...+
T Consensus 139 ~~~~~~~eIA~~l-gis~~tv~~~~~ra~~ 167 (179)
T PRK11924 139 VEGLSYREIAEIL-GVPVGTVKSRLRRARQ 167 (179)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 4567799999999 9999999999887654
No 81
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=49.54 E-value=50 Score=20.48 Aligned_cols=38 Identities=24% Similarity=0.378 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhh
Q 037956 74 EDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRL 112 (245)
Q Consensus 74 ED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~l 112 (245)
++..++.++-.-|-.+..||..+ |-+...|+.+.+...
T Consensus 14 ~~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~~ 51 (55)
T cd06171 14 REREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRAL 51 (55)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 34555556556778899999999 888888877666543
No 82
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=48.81 E-value=28 Score=27.45 Aligned_cols=50 Identities=16% Similarity=0.205 Sum_probs=33.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHhCCCCcccccccccCccccccccccccccc
Q 037956 7 SEKPSLRKGSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYL 61 (245)
Q Consensus 7 ~~kp~lkkg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L 61 (245)
|..| .++..||+|+-..++..+...|. .-..||+.++- ..+--.+|.+.+
T Consensus 4 ~~~~-~~rr~ys~EfK~~aV~~~~~~g~-sv~evA~e~gI---s~~tl~~W~r~y 53 (121)
T PRK09413 4 VLGP-EKRRRRTTQEKIAIVQQSFEPGM-TVSLVARQHGV---AASQLFLWRKQY 53 (121)
T ss_pred cCCC-CCCCCCCHHHHHHHHHHHHcCCC-CHHHHHHHHCc---CHHHHHHHHHHH
Confidence 3444 33567999998777776666564 66788888885 444555677654
No 83
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=48.60 E-value=37 Score=27.76 Aligned_cols=29 Identities=14% Similarity=0.029 Sum_probs=24.2
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
..|..+.+||..| |-+...|+++.+...+
T Consensus 150 ~~~~s~~eIA~~l-gis~~~v~~~l~Rar~ 178 (187)
T PRK09641 150 IEDLSLKEISEIL-DLPVGTVKTRIHRGRE 178 (187)
T ss_pred hhCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3467799999999 9999999999887654
No 84
>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=48.39 E-value=24 Score=26.58 Aligned_cols=30 Identities=37% Similarity=0.684 Sum_probs=24.1
Q ss_pred HHHHHHHHHhCCcHHHHhhhCCCCCHHHHHH
Q 037956 76 ETIIKLHEQLGNRWSAIASRLPGRTDNEIKN 106 (245)
Q Consensus 76 ~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Kn 106 (245)
+.|-.+....|..|..+|.+| |=+..+|..
T Consensus 3 ~~l~~l~~~lG~~Wk~lar~L-G~s~~eI~~ 32 (86)
T cd08777 3 KHLDLLRENLGKKWKRCARKL-GFTESEIEE 32 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHc-CCCHHHHHH
Confidence 345556688899999999999 888887765
No 85
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=48.26 E-value=45 Score=26.56 Aligned_cols=30 Identities=13% Similarity=0.155 Sum_probs=24.9
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
..|-.-.+||..| |-+...|+++.+..+++
T Consensus 120 ~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 120 WEDMDVAETAAAM-GCSEGSVKTHCSRATHA 149 (161)
T ss_pred HhcCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466789999999 99999999998876653
No 86
>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=47.91 E-value=31 Score=28.36 Aligned_cols=29 Identities=10% Similarity=0.103 Sum_probs=24.1
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
.|-...+||..| |-+...|+++.+..+++
T Consensus 153 ~~~s~~EIA~~l-gis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 153 EGLSYEDIARIM-DCPVGTVRSRIFRAREA 181 (190)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 456789999999 99999999998876653
No 87
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=47.81 E-value=12 Score=38.14 Aligned_cols=46 Identities=15% Similarity=0.366 Sum_probs=34.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCcccccccc----------cCccccccccccccccc
Q 037956 14 KGSWTPEEDRKLIAYIRRYGIWNWSEMPKYA----------GLLRCGKSCRLRWMNYL 61 (245)
Q Consensus 14 kg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~----------~~~Rt~kqCr~Rw~n~L 61 (245)
|..||..|.+-+..+++.+|. +...|-+.+ .. ++-.|+|.+|.+.+
T Consensus 88 ktaWt~~E~~~Ffdal~~~GK-dFe~VinaklKRrna~s~~~~-Ktkdqvr~~yY~~~ 143 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGK-DFEKVINAKLKRRNATSRVQS-KTKDQVRHYYYRLV 143 (782)
T ss_pred ccccchhhHHHHHHHHHHhcc-cHHHHHHHHHHhcccccchhh-hhhHHHHHHHHHHH
Confidence 668999999999999999997 888883322 22 45567777776544
No 88
>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=47.69 E-value=17 Score=25.76 Aligned_cols=26 Identities=23% Similarity=0.479 Sum_probs=21.1
Q ss_pred cHHHHhhhCCC-CCHHHHHHHHHHhhh
Q 037956 88 RWSAIASRLPG-RTDNEIKNHWHSRLS 113 (245)
Q Consensus 88 kW~~IA~~lpg-RT~~~~Knrw~~~lk 113 (245)
-|..||..|.+ -+...|+.+|..+..
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~ 54 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRD 54 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHH
Confidence 39999999953 678899999988654
No 89
>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=47.50 E-value=63 Score=30.52 Aligned_cols=85 Identities=18% Similarity=0.341 Sum_probs=61.2
Q ss_pred CCCCHHHHHHHHHHHHHhCCCC---cccccccccCccccccccccccccccCCCCCCCCCHHHHHHHHHHHHH-h-----
Q 037956 15 GSWTPEEDRKLIAYIRRYGIWN---WSEMPKYAGLLRCGKSCRLRWMNYLRPDIRRGNFTQEEDETIIKLHEQ-L----- 85 (245)
Q Consensus 15 g~WT~EEDe~L~~~V~~~g~~n---W~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~i~k~~WT~EED~~Ll~lv~~-~----- 85 (245)
..||.-|...|+.+.+...... -.+|++.+.+ |+..++++ |.+.|+ +..+.+++++ |
T Consensus 22 ~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~-Rs~aEI~~-fl~~LK------------~rvareaiqkv~~~g~~ 87 (344)
T PF11035_consen 22 AAWSAREKRQLLRLLQARRGQPEPDAAELAKELPG-RSEAEIRD-FLQQLK------------GRVAREAIQKVHPGGLK 87 (344)
T ss_pred ccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccC-cCHHHHHH-HHHHHH------------HHHHHHHHHHhcccccc
Confidence 4699999999999888653223 3467778887 88887775 444443 3455566655 2
Q ss_pred CCc------------HHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 86 GNR------------WSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 86 G~k------------W~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
|.+ |..+|..+.|.-...+---|...|-
T Consensus 88 ~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~ 127 (344)
T PF11035_consen 88 GPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLT 127 (344)
T ss_pred cccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHH
Confidence 211 9999999999999999988887664
No 90
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=47.25 E-value=6 Score=32.48 Aligned_cols=45 Identities=16% Similarity=0.162 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHhCCCCcccccccccCccccccccccccccccCCCC
Q 037956 20 EEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPDIR 66 (245)
Q Consensus 20 EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~i~ 66 (245)
+-|.+|+.++++.|...|.+||+.+| -+...|+.|+.......+-
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 57899999999999889999999999 7888999999876665433
No 91
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=47.00 E-value=10 Score=36.55 Aligned_cols=49 Identities=18% Similarity=0.324 Sum_probs=41.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccccccc-----ccCccccccccccccccc
Q 037956 12 LRKGSWTPEEDRKLIAYIRRYGIWNWSEMPKY-----AGLLRCGKSCRLRWMNYL 61 (245)
Q Consensus 12 lkkg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~-----~~~~Rt~kqCr~Rw~n~L 61 (245)
+.-..||.+|-+-|++++++|.- .|--||.. .+..|+....++||....
T Consensus 128 l~dn~WskeETD~LF~lck~fDL-Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~ 181 (445)
T KOG2656|consen 128 LNDNSWSKEETDYLFDLCKRFDL-RFFVIADRYDNQQYKKSRTVEDLKERYYSVC 181 (445)
T ss_pred hccccccHHHHHHHHHHHHhcCe-eEEEEeeccchhhccccccHHHHHHHHHHHH
Confidence 44467999999999999999987 89999886 676699999999997543
No 92
>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=46.99 E-value=25 Score=26.03 Aligned_cols=34 Identities=32% Similarity=0.596 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHH
Q 037956 72 QEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNH 107 (245)
Q Consensus 72 ~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knr 107 (245)
.||-++|+.. -..|.+|..+|..| |=+...|++-
T Consensus 2 ~~~v~~ll~~-~nlG~dW~~LA~~L-G~~~~~I~~i 35 (77)
T cd08311 2 QEEVEKLLES-GRPGRDWRSLAGEL-GYEDEAIDTF 35 (77)
T ss_pred hHHHHHHHhC-CCCccCHHHHHHHc-CCCHHHHHHH
Confidence 5777777732 25688999999999 8888887663
No 93
>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=46.27 E-value=30 Score=25.13 Aligned_cols=30 Identities=33% Similarity=0.701 Sum_probs=22.1
Q ss_pred HHHHHHHHHH-hCCcHHHHhhhCCCCCHHHHH
Q 037956 75 DETIIKLHEQ-LGNRWSAIASRLPGRTDNEIK 105 (245)
Q Consensus 75 D~~Ll~lv~~-~G~kW~~IA~~lpgRT~~~~K 105 (245)
.+.|..++.. .|..|..+|.+| |-+..+|.
T Consensus 5 ~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i~ 35 (88)
T smart00005 5 REKLAKLLDHPLGLDWRELARKL-GLSEADID 35 (88)
T ss_pred HHHHHHHHcCccchHHHHHHHHc-CCCHHHHH
Confidence 4556666666 899999999999 55555543
No 94
>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=45.97 E-value=44 Score=27.05 Aligned_cols=30 Identities=20% Similarity=0.242 Sum_probs=24.2
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
..|-....||..| |-|...|+++.+..+++
T Consensus 133 ~~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~ 162 (169)
T TIGR02954 133 YHDLTIKEIAEVM-NKPEGTVKTYLHRALKK 162 (169)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3456789999999 88999999998876653
No 95
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=44.56 E-value=22 Score=39.02 Aligned_cols=70 Identities=17% Similarity=0.285 Sum_probs=44.6
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCccccccc--ccCccccccccccccccccCCCCCCCCCHHHHHHHHHHHHHh-CCcHHH
Q 037956 15 GSWTPEEDRKLIAYIRRYGIWNWSEMPKY--AGLLRCGKSCRLRWMNYLRPDIRRGNFTQEEDETIIKLHEQL-GNRWSA 91 (245)
Q Consensus 15 g~WT~EEDe~L~~~V~~~g~~nW~~Ia~~--~~~~Rt~kqCr~Rw~n~L~p~i~k~~WT~EED~~Ll~lv~~~-G~kW~~ 91 (245)
--|..++|..|+-.|-+||-++|..|-.- ++. ..- ..+.-.+..+.|=...-..|+.+...+ +.+|.+
T Consensus 1134 ~~W~~e~Ds~LLiGI~khGygswe~Ir~Dp~L~l---~dK------i~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~ 1204 (1373)
T KOG0384|consen 1134 CDWGSEDDSMLLIGIFKHGYGSWEAIRLDPDLGL---TDK------IFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPK 1204 (1373)
T ss_pred cCCCchhhhhHhhhhhhcccccHHHhccCccccc---hhh------hcccccCCchHHHHHHHHHHHHHHhhcccCCCch
Confidence 45999999999999999999999988431 111 100 111111344556666677777777766 445554
Q ss_pred Hh
Q 037956 92 IA 93 (245)
Q Consensus 92 IA 93 (245)
..
T Consensus 1205 ~~ 1206 (1373)
T KOG0384|consen 1205 KL 1206 (1373)
T ss_pred hh
Confidence 43
No 96
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=44.06 E-value=5.6 Score=33.12 Aligned_cols=45 Identities=20% Similarity=0.257 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHHhCCCCcccccccccCccccccccccccccccCCC
Q 037956 19 PEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPDI 65 (245)
Q Consensus 19 ~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~i 65 (245)
.+-|.+|+.+.++.|...|.+||+.+| -+...|+.|+.......+
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 556899999999999889999999999 678889999987666544
No 97
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=43.93 E-value=51 Score=26.85 Aligned_cols=36 Identities=19% Similarity=0.232 Sum_probs=28.2
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 78 IIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 78 Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
++.+....|-...+||..| |-+...|+.+.+.-+++
T Consensus 127 v~~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 162 (172)
T PRK12523 127 AFLYNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQ 162 (172)
T ss_pred HHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3333444567899999999 99999999998877764
No 98
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=43.68 E-value=26 Score=35.55 Aligned_cols=48 Identities=21% Similarity=0.334 Sum_probs=43.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 66 RRGNFTQEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 66 ~k~~WT~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
..+.|+.+|-++...+....|.+.+.|+..+|+|...+||-.|..-=+
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~eE~ 455 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKEEK 455 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhhhh
Confidence 346899999999999999999999999999999999999999875444
No 99
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=43.64 E-value=51 Score=27.44 Aligned_cols=30 Identities=23% Similarity=0.151 Sum_probs=24.8
Q ss_pred HHhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 83 EQLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 83 ~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
...|-...+||..| |-+...|+++.+..++
T Consensus 119 ~~~g~~~~EIA~~l-gis~~tV~~~l~Rar~ 148 (181)
T PRK09637 119 ELEGLSQKEIAEKL-GLSLSGAKSRVQRGRV 148 (181)
T ss_pred HhcCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 34567799999999 9999999999886654
No 100
>PRK04217 hypothetical protein; Provisional
Probab=43.50 E-value=60 Score=25.77 Aligned_cols=44 Identities=18% Similarity=0.114 Sum_probs=35.6
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 68 GNFTQEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 68 ~~WT~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
..-+.+| ..++.++...|-...+||+.+ |-+...|+.+++...+
T Consensus 41 ~~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArk 84 (110)
T PRK04217 41 IFMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARK 84 (110)
T ss_pred ccCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 3456666 577777777788999999999 9999999999987654
No 101
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=43.33 E-value=57 Score=26.06 Aligned_cols=29 Identities=7% Similarity=-0.068 Sum_probs=24.0
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
..|-.-.+||..| |-+...|+++.+..++
T Consensus 120 ~~g~s~~EIA~~l-gis~~tV~~~l~Rar~ 148 (160)
T PRK09642 120 LEEKSYQEIALQE-KIEVKTVEMKLYRARK 148 (160)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3456689999999 9999999999887665
No 102
>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=43.03 E-value=56 Score=27.29 Aligned_cols=33 Identities=15% Similarity=0.076 Sum_probs=26.2
Q ss_pred HHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 81 LHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 81 lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
++...|-...+||..| |-+...|+.|.+..+++
T Consensus 142 l~~~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 142 MREVLGFESDEICQEL-EISTSNCHVLLYRARLS 174 (188)
T ss_pred HHHHhCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3334567799999999 99999999998876653
No 103
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=42.90 E-value=56 Score=27.00 Aligned_cols=29 Identities=21% Similarity=0.260 Sum_probs=24.4
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
..|....+||..| |-+...|+.+.+..++
T Consensus 153 ~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~ 181 (189)
T PRK09648 153 VVGLSAEETAEAV-GSTPGAVRVAQHRALA 181 (189)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3467799999999 9999999999887665
No 104
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=42.58 E-value=50 Score=27.38 Aligned_cols=29 Identities=14% Similarity=0.109 Sum_probs=23.7
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
.|-...+||..| |-+...|+++.+..+++
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 455689999999 99999999998876653
No 105
>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=42.58 E-value=29 Score=25.99 Aligned_cols=26 Identities=27% Similarity=0.560 Sum_probs=21.4
Q ss_pred HHHHHHHHHhCCcHHHHhhhCCCCCHH
Q 037956 76 ETIIKLHEQLGNRWSAIASRLPGRTDN 102 (245)
Q Consensus 76 ~~Ll~lv~~~G~kW~~IA~~lpgRT~~ 102 (245)
..|..+....|..|..+|.+| |=+..
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 458888999999999999999 54444
No 106
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=42.38 E-value=58 Score=26.76 Aligned_cols=30 Identities=17% Similarity=0.275 Sum_probs=24.9
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
..|-...+||..| |-+...|+.+.+..+++
T Consensus 145 ~~g~s~~eIA~~l-~is~~tV~~~l~ra~~~ 174 (184)
T PRK12512 145 VEGASIKETAAKL-SMSEGAVRVALHRGLAA 174 (184)
T ss_pred HcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3466789999999 99999999998877653
No 107
>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=42.24 E-value=87 Score=29.61 Aligned_cols=44 Identities=23% Similarity=0.523 Sum_probs=35.3
Q ss_pred CCCCCHHHHHHHHHHHHHh-CC---cHHHHhhhCCCCCHHHHHHHHHH
Q 037956 67 RGNFTQEEDETIIKLHEQL-GN---RWSAIASRLPGRTDNEIKNHWHS 110 (245)
Q Consensus 67 k~~WT~EED~~Ll~lv~~~-G~---kW~~IA~~lpgRT~~~~Knrw~~ 110 (245)
-..||.-|...|+.+.+.. |. .-..|++.++||+..+|++.-..
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~ 68 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQ 68 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHH
Confidence 3579999999988887755 43 36789999999999999985543
No 108
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=41.90 E-value=59 Score=27.16 Aligned_cols=30 Identities=10% Similarity=0.007 Sum_probs=24.3
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
..|-...+||..| |-+...|+.|.+..+++
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 99999999998876653
No 109
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=41.77 E-value=50 Score=26.96 Aligned_cols=28 Identities=14% Similarity=0.052 Sum_probs=23.1
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|..-.+||..| |-+...|+++.+..++
T Consensus 151 ~g~s~~eIA~~l-gis~~~v~~~l~Rar~ 178 (187)
T TIGR02948 151 EDLSLKEISEIL-DLPVGTVKTRIHRGRE 178 (187)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 356689999999 9999999999877654
No 110
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=41.57 E-value=59 Score=27.16 Aligned_cols=28 Identities=7% Similarity=-0.085 Sum_probs=24.0
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-...+||..| |-+...|+.|.+.-++
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~RAr~ 176 (189)
T PRK12530 149 LELSSEQICQEC-DISTSNLHVLLYRARL 176 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 466799999999 9999999999877654
No 111
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=41.55 E-value=55 Score=22.41 Aligned_cols=36 Identities=25% Similarity=0.448 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHH
Q 037956 73 EEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWH 109 (245)
Q Consensus 73 EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~ 109 (245)
+.|+..+.+....|-.-.+||+.+ ||+.+.|++.-.
T Consensus 7 ~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 7 DAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRYLK 42 (50)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHHHH
T ss_pred HHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHHhc
Confidence 455666778888899999999999 999999888644
No 112
>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=41.10 E-value=38 Score=25.52 Aligned_cols=28 Identities=21% Similarity=0.466 Sum_probs=22.2
Q ss_pred HHHHHHHHHHhCCcHHHHhhhCCCCCHHH
Q 037956 75 DETIIKLHEQLGNRWSAIASRLPGRTDNE 103 (245)
Q Consensus 75 D~~Ll~lv~~~G~kW~~IA~~lpgRT~~~ 103 (245)
|..|......+|..|.++|.+| |=+...
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L-~vs~~d 31 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL-QFSVED 31 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc-CCCHHH
Confidence 4567778899999999999998 655543
No 113
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=41.09 E-value=63 Score=26.18 Aligned_cols=30 Identities=27% Similarity=0.322 Sum_probs=24.4
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
..|-.-.+||..| |.+...|+.+.+.-+++
T Consensus 132 ~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 161 (173)
T PRK09645 132 YRGWSTAQIAADL-GIPEGTVKSRLHYALRA 161 (173)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3456689999999 99999999998876653
No 114
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=40.28 E-value=69 Score=25.30 Aligned_cols=28 Identities=18% Similarity=0.214 Sum_probs=22.5
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-...+||..| |-+...|+++-+..++
T Consensus 121 ~~~s~~EIA~~l-~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 121 VGKTMGEIALET-EMTYYQVRWIYRQALE 148 (154)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 345688999999 9999999998877665
No 115
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=40.06 E-value=64 Score=26.61 Aligned_cols=30 Identities=20% Similarity=0.108 Sum_probs=25.4
Q ss_pred HHhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 83 EQLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 83 ~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
...|-...+||..| |-+...|+.|.+.-+.
T Consensus 140 ~~~g~s~~EIA~~l-gis~~tVk~~l~rAl~ 169 (178)
T PRK12529 140 TLDGMKQKDIAQAL-DIALPTVKKYIHQAYV 169 (178)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 34567799999999 9999999999987665
No 116
>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=39.94 E-value=73 Score=26.63 Aligned_cols=45 Identities=20% Similarity=0.236 Sum_probs=37.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHhhhC----CCCCHHHHHHHHHHh
Q 037956 67 RGNFTQEEDETIIKLHEQLGNRWSAIASRL----PGRTDNEIKNHWHSR 111 (245)
Q Consensus 67 k~~WT~EED~~Ll~lv~~~G~kW~~IA~~l----pgRT~~~~Knrw~~~ 111 (245)
...-|..|...|..|+.+||..+..+|.-. --.|..+|+.+...+
T Consensus 114 ~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 114 PRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 456889999999999999999999998753 248999998877654
No 117
>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=39.88 E-value=76 Score=20.25 Aligned_cols=33 Identities=24% Similarity=0.254 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHH
Q 037956 74 EDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNH 107 (245)
Q Consensus 74 ED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knr 107 (245)
|-+.|.++...+|++..+.|+.| |=+...+..+
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 66789999999999999999999 7666655544
No 118
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=39.83 E-value=67 Score=26.88 Aligned_cols=30 Identities=10% Similarity=-0.089 Sum_probs=24.7
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
..|-.+.+||..| |-+...|+++.+..+++
T Consensus 150 ~~g~s~~eIA~~l-gis~~tV~~~l~Ra~~~ 179 (196)
T PRK12524 150 IEGLSNPEIAEVM-EIGVEAVESLTARGKRA 179 (196)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 4566799999999 99999999988876653
No 119
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=39.53 E-value=23 Score=34.96 Aligned_cols=41 Identities=20% Similarity=0.322 Sum_probs=37.2
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHH
Q 037956 68 GNFTQEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWH 109 (245)
Q Consensus 68 ~~WT~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~ 109 (245)
..||++|-. +++....||.....||..+...|..|++.+|-
T Consensus 471 ~~wSp~e~s-~ircf~~y~~~fe~ia~l~~tktp~Q~~~fy~ 511 (534)
T KOG1194|consen 471 YGWSPEEKS-AIRCFHWYKDNFELIAELMATKTPEQIKKFYM 511 (534)
T ss_pred CCCCCcccc-cccCchhhccchHHHHHHhcCCCHHHHHHHhc
Confidence 469999988 88888999999999999999999999999885
No 120
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=38.95 E-value=54 Score=25.24 Aligned_cols=46 Identities=13% Similarity=0.193 Sum_probs=30.3
Q ss_pred CCCCHHHHHHHHHHHHHh----C----CcHHHHhhhCCC-----CCHHHHHHHHHHhhh
Q 037956 68 GNFTQEEDETIIKLHEQL----G----NRWSAIASRLPG-----RTDNEIKNHWHSRLS 113 (245)
Q Consensus 68 ~~WT~EED~~Ll~lv~~~----G----~kW~~IA~~lpg-----RT~~~~Knrw~~~lk 113 (245)
.-||+++|-.|++.+..| | ..|..+-..+.+ =+..|+.++.+.+-+
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~ 63 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKK 63 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHH
Confidence 359999999999998776 5 246555444322 366777776665443
No 121
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=38.79 E-value=71 Score=26.43 Aligned_cols=29 Identities=7% Similarity=0.077 Sum_probs=24.4
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
..|-...+||..| |-+...|+++.+..++
T Consensus 145 ~~~~s~~eIA~~l-gis~~tV~~~l~Rar~ 173 (189)
T PRK12515 145 YHEKSVEEVGEIV-GIPESTVKTRMFYARK 173 (189)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 3566789999999 9999999999987664
No 122
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=38.05 E-value=45 Score=28.81 Aligned_cols=45 Identities=29% Similarity=0.273 Sum_probs=36.8
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhhhh
Q 037956 68 GNFTQEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLSKK 115 (245)
Q Consensus 68 ~~WT~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkkk 115 (245)
...|+.|-+.|.-+.+ |-.=++||..| +.+...||+|..++++|-
T Consensus 147 ~~LT~RE~eVL~lla~--G~snkeIA~~L-~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 147 ELLTPRELEVLRLLAE--GLSNKEIAEEL-NLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCCCHHHHHHHHHHHC--CCCHHHHHHHH-CCCHhHHHHHHHHHHHHc
Confidence 3688888887766554 55556999999 999999999999999854
No 123
>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=37.98 E-value=75 Score=25.42 Aligned_cols=28 Identities=18% Similarity=0.203 Sum_probs=23.0
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-.-.+||+.| |-+...|+.+-+..++
T Consensus 137 ~g~s~~eIA~~l-~is~~tv~~~l~ra~~ 164 (170)
T TIGR02952 137 QNLPIAEVARIL-GKTEGAVKILQFRAIK 164 (170)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 356789999999 9999999998876664
No 124
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=37.60 E-value=42 Score=33.40 Aligned_cols=43 Identities=16% Similarity=0.244 Sum_probs=37.9
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhh-hCCCCCHHHHHHHHHH
Q 037956 68 GNFTQEEDETIIKLHEQLGNRWSAIAS-RLPGRTDNEIKNHWHS 110 (245)
Q Consensus 68 ~~WT~EED~~Ll~lv~~~G~kW~~IA~-~lpgRT~~~~Knrw~~ 110 (245)
..|+..|-.+.-++.++||+.+..|.. +||.++-.+|-..|+-
T Consensus 286 EEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYYm 329 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYYM 329 (693)
T ss_pred hhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHHH
Confidence 369999999999999999999999965 6799999999887763
No 125
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=36.89 E-value=66 Score=26.98 Aligned_cols=36 Identities=19% Similarity=0.292 Sum_probs=28.0
Q ss_pred HHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhh
Q 037956 76 ETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRL 112 (245)
Q Consensus 76 ~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~l 112 (245)
..++.+....|-.+.+||..| |-+...|+.+|...-
T Consensus 141 ~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR 176 (185)
T PF07638_consen 141 RRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 344444445677899999999 999999999998643
No 126
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=36.30 E-value=82 Score=25.93 Aligned_cols=30 Identities=20% Similarity=0.185 Sum_probs=25.2
Q ss_pred HHhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 83 EQLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 83 ~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
...|-...+||..| |.+...|+++-+..++
T Consensus 142 ~~~g~s~~EIA~~l-~is~~tV~~~l~rar~ 171 (181)
T PRK12536 142 KLEGLSVAETAQLT-GLSESAVKVGIHRGLK 171 (181)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 34567799999999 9999999999887665
No 127
>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=35.71 E-value=88 Score=25.52 Aligned_cols=29 Identities=21% Similarity=0.281 Sum_probs=24.0
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
..|-...+||..| |-+...|+.|.+.-++
T Consensus 148 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~ 176 (183)
T TIGR02999 148 FAGLTVEEIAELL-GVSVRTVERDWRFARA 176 (183)
T ss_pred HcCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 3456789999999 9999999999887654
No 128
>PRK00118 putative DNA-binding protein; Validated
Probab=35.62 E-value=96 Score=24.35 Aligned_cols=41 Identities=10% Similarity=0.089 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 72 QEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 72 ~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
++.+..++.++...|-....||..+ |-+...|+.+.+...+
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~RArk 59 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKRTEK 59 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 4556677788888889999999999 9999999998776544
No 129
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=35.47 E-value=50 Score=21.42 Aligned_cols=37 Identities=32% Similarity=0.461 Sum_probs=18.8
Q ss_pred CCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHH
Q 037956 69 NFTQEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNH 107 (245)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knr 107 (245)
.+|.+|=..|..++ .-|..=.+||+.| ||+...|.+.
T Consensus 4 ~Lt~~eR~~I~~l~-~~G~s~~~IA~~l-g~s~sTV~re 40 (44)
T PF13936_consen 4 HLTPEERNQIEALL-EQGMSIREIAKRL-GRSRSTVSRE 40 (44)
T ss_dssp --------HHHHHH-CS---HHHHHHHT-T--HHHHHHH
T ss_pred chhhhHHHHHHHHH-HcCCCHHHHHHHH-CcCcHHHHHH
Confidence 46677766666664 5678889999999 9999888663
No 130
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=34.80 E-value=81 Score=26.19 Aligned_cols=28 Identities=18% Similarity=0.189 Sum_probs=24.0
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-.-.+||..| |-+...|+.+.+..++
T Consensus 145 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~ 172 (185)
T PRK09649 145 LGLSYADAAAVC-GCPVGTIRSRVARARD 172 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 455689999999 9999999999987665
No 131
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=34.73 E-value=88 Score=25.53 Aligned_cols=28 Identities=18% Similarity=0.207 Sum_probs=23.4
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-.-.+||..| |.+...|+.+.+..++
T Consensus 144 ~g~s~~eIA~~l-gis~~tV~~~l~Rar~ 171 (179)
T PRK12514 144 EGLSYKELAERH-DVPLNTMRTWLRRSLL 171 (179)
T ss_pred cCCCHHHHHHHH-CCChHHHHHHHHHHHH
Confidence 356689999999 9999999999887665
No 132
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=34.56 E-value=49 Score=23.37 Aligned_cols=27 Identities=41% Similarity=0.789 Sum_probs=19.8
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHH
Q 037956 78 IIKLHEQLGNRWSAIASRLPGRTDNEIK 105 (245)
Q Consensus 78 Ll~lv~~~G~kW~~IA~~lpgRT~~~~K 105 (245)
+..+....|..|..+|..| |=+..+|.
T Consensus 2 ~~~ia~~lg~~W~~la~~L-gl~~~~I~ 28 (79)
T cd01670 2 LDKLAKKLGKDWKKLARKL-GLSDGEID 28 (79)
T ss_pred HHHHHHHHhhHHHHHHHHh-CCCHHHHH
Confidence 4456778899999999999 54444443
No 133
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=34.28 E-value=64 Score=24.11 Aligned_cols=28 Identities=25% Similarity=0.612 Sum_probs=21.0
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHH
Q 037956 78 IIKLHEQLGNRWSAIASRLPGRTDNEIKN 106 (245)
Q Consensus 78 Ll~lv~~~G~kW~~IA~~lpgRT~~~~Kn 106 (245)
+--+....|..|..+|..| |=|..+|..
T Consensus 5 f~~i~~~lG~~Wk~laR~L-Glse~~Id~ 32 (86)
T cd08306 5 FDVICENVGRDWRKLARKL-GLSETKIES 32 (86)
T ss_pred HHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 3344567799999999999 777776653
No 134
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=34.11 E-value=85 Score=26.12 Aligned_cols=29 Identities=17% Similarity=0.132 Sum_probs=23.9
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
..|-.-.+||..| |-+...|+.+.+..++
T Consensus 150 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~ 178 (195)
T PRK12532 150 ILGFSSDEIQQMC-GISTSNYHTIMHRARE 178 (195)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3466789999999 9999999999887554
No 135
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=33.57 E-value=1.1e+02 Score=22.94 Aligned_cols=41 Identities=15% Similarity=0.227 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHhCC-cHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 73 EEDETIIKLHEQLGN-RWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 73 EED~~Ll~lv~~~G~-kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
+.|..|+.+....|. .+..||+.+ |-+...|..+...+..+
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEE 44 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHC
Confidence 567888888888774 699999999 99999999999887764
No 136
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=33.51 E-value=97 Score=24.78 Aligned_cols=31 Identities=19% Similarity=0.194 Sum_probs=25.0
Q ss_pred HHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 82 HEQLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 82 v~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
..-.|-...+||..| |-+...|+.|.+.-++
T Consensus 125 ~~~~g~s~~EIA~~l-~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 125 AQVDGLGYGEIATEL-GISLATVKRYLNKAAM 155 (161)
T ss_pred HHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 334567789999999 9999999999887654
No 137
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=33.45 E-value=1.2e+02 Score=24.10 Aligned_cols=29 Identities=21% Similarity=0.296 Sum_probs=23.6
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
.|-.=.+||..| |-+...|+.|.+..+++
T Consensus 120 ~~~s~~eIA~~l-gis~~tv~~~l~ra~~~ 148 (159)
T PRK12527 120 EGLSHQQIAEHL-GISRSLVEKHIVNAMKH 148 (159)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 445678999999 99999999998876653
No 138
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=33.02 E-value=84 Score=25.69 Aligned_cols=28 Identities=25% Similarity=0.273 Sum_probs=23.8
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-.-.+||+.| |-+...|+++.+..++
T Consensus 134 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~ 161 (172)
T PRK09651 134 DGLTYSEIAHKL-GVSVSSVKKYVAKATE 161 (172)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 456789999999 9999999999887665
No 139
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=32.74 E-value=98 Score=25.88 Aligned_cols=34 Identities=21% Similarity=0.128 Sum_probs=26.2
Q ss_pred HHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 79 IKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 79 l~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
+.|....|-...+||..| |-+...|+.|-+..++
T Consensus 125 ~~L~~~~g~s~~EIA~~L-gis~~tVk~~l~Rar~ 158 (187)
T PRK12516 125 IILVGASGFAYEEAAEIC-GCAVGTIKSRVNRARQ 158 (187)
T ss_pred HHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 333334567799999999 9999999999877664
No 140
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=32.66 E-value=70 Score=31.00 Aligned_cols=26 Identities=15% Similarity=0.405 Sum_probs=21.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCC
Q 037956 9 KPSLRKGSWTPEEDRKLIAYIRRYGI 34 (245)
Q Consensus 9 kp~lkkg~WT~EEDe~L~~~V~~~g~ 34 (245)
+.+..-|.|+++=|+.+.+++..|..
T Consensus 71 ~~~daegvWSpdIEqsFqEALaiypp 96 (455)
T KOG3841|consen 71 NQRDAEGVWSPDIEQSFQEALAIYPP 96 (455)
T ss_pred cccccccccChhHHHHHHHHHhhcCC
Confidence 33455789999999999999998865
No 141
>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=32.44 E-value=35 Score=26.99 Aligned_cols=27 Identities=15% Similarity=0.123 Sum_probs=23.2
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 86 GNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 86 G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
|-.+.+||..| |-+...|+++.+...+
T Consensus 121 g~s~~eIA~~l-gis~~tv~~~l~Ra~~ 147 (154)
T TIGR02950 121 EFSYKEIAELL-NLSLAKVKSNLFRARK 147 (154)
T ss_pred cCcHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 45699999999 9999999999887664
No 142
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=32.23 E-value=1.1e+02 Score=24.68 Aligned_cols=29 Identities=17% Similarity=0.117 Sum_probs=23.8
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
..|-.-.+||..| |-+...|+++-+..++
T Consensus 126 ~~g~s~~eIA~~l-gis~~tV~~~l~Rar~ 154 (164)
T PRK12547 126 ASGFSYEDAAAIC-GCAVGTIKSRVSRARN 154 (164)
T ss_pred HcCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 3556789999999 9999999998887665
No 143
>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=32.13 E-value=1e+02 Score=25.05 Aligned_cols=29 Identities=21% Similarity=0.478 Sum_probs=23.7
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
..|-.-.+||..| |-+...|+.+.+..++
T Consensus 154 ~~g~s~~eIA~~l-gis~~~v~~~l~Ra~~ 182 (189)
T TIGR02984 154 LEGLSFAEVAERM-DRSEGAVSMLWVRGLA 182 (189)
T ss_pred hcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 3566789999999 9999999998887665
No 144
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=32.10 E-value=1e+02 Score=25.36 Aligned_cols=29 Identities=14% Similarity=0.299 Sum_probs=24.2
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
..|-.-.+||..| |-+...|+++.+..++
T Consensus 136 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~ 164 (185)
T PRK12542 136 FYNLTYQEISSVM-GITEANVRKQFERARK 164 (185)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3566789999999 9999999999877665
No 145
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=32.10 E-value=1.3e+02 Score=24.97 Aligned_cols=27 Identities=30% Similarity=0.421 Sum_probs=21.9
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 86 GNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 86 G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
|-.=.+||..| |.+...|+++-+..++
T Consensus 147 g~s~~EIAe~l-gis~~~V~~~l~Ra~~ 173 (189)
T PRK06811 147 GEKIEEIAKKL-GLTRSAIDNRLSRGRK 173 (189)
T ss_pred cCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 45568999999 9999999998876654
No 146
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=31.70 E-value=97 Score=25.48 Aligned_cols=28 Identities=7% Similarity=-0.041 Sum_probs=22.4
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-.-.+||..| |-+...|+.+.+..++
T Consensus 143 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~ 170 (186)
T PRK05602 143 QGLSNIEAAAVM-DISVDALESLLARGRR 170 (186)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHH
Confidence 456688899988 8999999998877654
No 147
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=31.23 E-value=1.1e+02 Score=25.03 Aligned_cols=28 Identities=25% Similarity=0.196 Sum_probs=23.1
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-.=.+||..| |-+...|+.+.+..++
T Consensus 150 ~~~s~~eIA~~l-gis~~~V~~~l~ra~~ 177 (186)
T PRK13919 150 QGYTHREAAQLL-GLPLGTLKTRARRALS 177 (186)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 345678999999 9999999999887665
No 148
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=31.15 E-value=54 Score=28.41 Aligned_cols=29 Identities=17% Similarity=0.135 Sum_probs=24.0
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
.|-...+||..| |.+...|+++.+..+++
T Consensus 164 ~g~s~~EIAe~l-gis~~tVk~~l~Rar~k 192 (231)
T PRK11922 164 EELSVEETAQAL-GLPEETVKTRLHRARRL 192 (231)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 345689999999 99999999999876653
No 149
>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=31.06 E-value=1.3e+02 Score=24.03 Aligned_cols=37 Identities=16% Similarity=0.180 Sum_probs=27.4
Q ss_pred HHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 76 ETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 76 ~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
..++.+.-..|-.=.+||..| |-+...|+.+.+..++
T Consensus 116 r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~ra~~ 152 (162)
T TIGR02983 116 RAVVVLRYYEDLSEAQVAEAL-GISVGTVKSRLSRALA 152 (162)
T ss_pred HHHhhhHHHhcCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 334444444566778999999 9999999999887665
No 150
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=30.90 E-value=1.1e+02 Score=25.85 Aligned_cols=28 Identities=18% Similarity=0.048 Sum_probs=23.2
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-.-.+||..| |.+...||.|.+..++
T Consensus 154 eg~s~~EIA~~l-gis~~tVk~~l~RAr~ 181 (201)
T PRK12545 154 LDFEIDDICTEL-TLTANHCSVLLYRART 181 (201)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 455689999999 9999999999876554
No 151
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=30.76 E-value=1.1e+02 Score=25.25 Aligned_cols=28 Identities=14% Similarity=-0.105 Sum_probs=23.3
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-.-.+||..| |-+...|++|.+..++
T Consensus 146 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~ 173 (191)
T PRK12520 146 LELETEEICQEL-QITATNAWVLLYRARM 173 (191)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 455678999999 9999999999887665
No 152
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=29.94 E-value=1e+02 Score=25.85 Aligned_cols=31 Identities=13% Similarity=0.080 Sum_probs=25.3
Q ss_pred HHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 82 HEQLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 82 v~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
+...|-...+||..| |-+...|+++.+..++
T Consensus 125 ~~~~g~s~~EIA~~L-giS~~tVk~~l~Rar~ 155 (188)
T PRK12546 125 VGASGFSYEEAAEMC-GVAVGTVKSRANRARA 155 (188)
T ss_pred HHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 334567799999999 9999999999887665
No 153
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=29.84 E-value=36 Score=34.55 Aligned_cols=48 Identities=17% Similarity=0.310 Sum_probs=42.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCcccccccccCccccccccccccc
Q 037956 10 PSLRKGSWTPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMN 59 (245)
Q Consensus 10 p~lkkg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n 59 (245)
+....++|+..|-++...+....|. +...|+..+++ |..+|++..+..
T Consensus 405 k~~~~~~w~~se~e~fyka~~~~gs-~~slis~l~p~-R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 405 KKLETDKWDASETELFYKALSERGS-DFSLISNLFPL-RDRKQIKAKFKK 452 (584)
T ss_pred CccccCcccchhhHHhhhHHhhhcc-ccccccccccc-ccHHHHHHHHhh
Confidence 4556789999999999999999998 99999999999 999999987764
No 154
>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=29.66 E-value=96 Score=27.99 Aligned_cols=29 Identities=21% Similarity=0.272 Sum_probs=24.2
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
+|-.-.+||..| |.+...|++|.+..+++
T Consensus 157 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 185 (324)
T TIGR02960 157 LGWRAAETAELL-GTSTASVNSALQRARAT 185 (324)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456689999999 99999999998876653
No 155
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=29.61 E-value=1.2e+02 Score=25.27 Aligned_cols=28 Identities=21% Similarity=0.251 Sum_probs=22.9
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-.-.+||+.| |-+...|+++-+.-++
T Consensus 157 ~~~s~~EIA~~L-gis~~tVk~~l~ra~~ 184 (194)
T PRK09646 157 GGLTYREVAERL-AVPLGTVKTRMRDGLI 184 (194)
T ss_pred cCCCHHHHHHHh-CCChHhHHHHHHHHHH
Confidence 455689999999 8899999998876664
No 156
>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=28.42 E-value=57 Score=21.96 Aligned_cols=43 Identities=28% Similarity=0.367 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 69 NFTQEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
..|+.|-+.|.-+. -|..=.+||..+ |.+...|+.+...+++|
T Consensus 3 ~LT~~E~~vl~~l~--~G~~~~eIA~~l-~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLA--QGMSNKEIAEEL-GISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHH--TTS-HHHHHHHH-TSHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHH--hcCCcchhHHhc-CcchhhHHHHHHHHHHH
Confidence 35666666555443 366667999999 99999999999888874
No 157
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=28.11 E-value=1.3e+02 Score=24.73 Aligned_cols=28 Identities=29% Similarity=0.315 Sum_probs=23.0
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-.-..||..| |-+...|+++.+..++
T Consensus 148 ~~~s~~eIA~~l-gis~~tV~~~l~ra~~ 175 (182)
T PRK12537 148 DGCSHAEIAQRL-GAPLGTVKAWIKRSLK 175 (182)
T ss_pred cCCCHHHHHHHH-CCChhhHHHHHHHHHH
Confidence 455678999999 9999999999887765
No 158
>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=27.05 E-value=48 Score=24.04 Aligned_cols=25 Identities=16% Similarity=0.425 Sum_probs=18.0
Q ss_pred CCHHHHH-HHHHHHHHhCCcHHHHhh
Q 037956 70 FTQEEDE-TIIKLHEQLGNRWSAIAS 94 (245)
Q Consensus 70 WT~EED~-~Ll~lv~~~G~kW~~IA~ 94 (245)
+.++.-. .|.+|.+.||++|.-|-.
T Consensus 23 ~~~~~v~~vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 23 FSKKQVRPVLKNLLKLYDGNWELIEE 48 (65)
T ss_pred CCHHHHHHHHHHHHHHHcCCchhhhc
Confidence 4444433 588889999999998853
No 159
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=26.82 E-value=65 Score=26.13 Aligned_cols=28 Identities=21% Similarity=0.383 Sum_probs=23.4
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
+|-....||..| |-+...|+.+.+..++
T Consensus 141 ~g~s~~eIA~~l-~is~~~V~~~l~ra~~ 168 (176)
T PRK09638 141 YGYTYEEIAKML-NIPEGTVKSRVHHGIK 168 (176)
T ss_pred cCCCHHHHHHHH-CCChhHHHHHHHHHHH
Confidence 566799999999 8899999998877654
No 160
>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=26.68 E-value=1.9e+02 Score=18.96 Aligned_cols=44 Identities=23% Similarity=0.428 Sum_probs=35.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhC----CcHHHHhhhCCCCCHHHHHHHHHH
Q 037956 66 RRGNFTQEEDETIIKLHEQLG----NRWSAIASRLPGRTDNEIKNHWHS 110 (245)
Q Consensus 66 ~k~~WT~EED~~Ll~lv~~~G----~kW~~IA~~lpgRT~~~~Knrw~~ 110 (245)
.+..+|.+.-..|...+.... ..-..||..+ |-+..+|++-|.+
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 356789999999999998744 2378899999 9999999998875
No 161
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=26.56 E-value=1.2e+02 Score=21.43 Aligned_cols=23 Identities=39% Similarity=0.849 Sum_probs=17.0
Q ss_pred HHHhCCcHHHHhhhCCCCCHHHHH
Q 037956 82 HEQLGNRWSAIASRLPGRTDNEIK 105 (245)
Q Consensus 82 v~~~G~kW~~IA~~lpgRT~~~~K 105 (245)
....|..|..+|..| |=+...|.
T Consensus 8 ~~~~~~~Wk~La~~L-g~~~~~i~ 30 (83)
T PF00531_consen 8 AEDLGSDWKRLARKL-GLSESEIE 30 (83)
T ss_dssp HHSHSTCHHHHHHHT-TS-HHHHH
T ss_pred hhcchhhHHHHHHHh-CcCHHHHH
Confidence 356789999999999 76666554
No 162
>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=25.52 E-value=48 Score=27.71 Aligned_cols=46 Identities=11% Similarity=0.085 Sum_probs=32.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccccccccc---Ccccccccccccc
Q 037956 12 LRKGSWTPEEDRKLIAYIRRYGIWNWSEMPKYAG---LLRCGKSCRLRWM 58 (245)
Q Consensus 12 lkkg~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~---~~Rt~kqCr~Rw~ 58 (245)
.+...-|..|-+-|..+|.+||. ++..++.-.. ...|+.||+.+..
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhGd-Dy~aMarD~KLN~~Q~T~~qlrrki~ 160 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHGD-DYKAMARDRKLNYMQHTPGQLRRKIR 160 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHCc-cHHHHhccCCCCcccCCHHHHHHHHH
Confidence 34556899999999999999997 8888776433 1145555554443
No 163
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=25.39 E-value=1.4e+02 Score=25.88 Aligned_cols=30 Identities=13% Similarity=0.217 Sum_probs=24.7
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
..|-...+||..| |-+...|+.+.+..+++
T Consensus 198 ~~g~s~~EIA~~l-gis~~tV~~~~~ra~~~ 227 (236)
T PRK06986 198 QEELNLKEIGAVL-GVSESRVSQIHSQAIKR 227 (236)
T ss_pred ccCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3456789999999 99999999998877753
No 164
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=25.38 E-value=1.6e+02 Score=23.44 Aligned_cols=28 Identities=18% Similarity=0.277 Sum_probs=22.7
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-.=..||..| |-+...|+++.+..++
T Consensus 126 ~g~s~~eIA~~l-gis~~tV~~~i~ra~~ 153 (166)
T PRK09639 126 SGYSYKEIAEAL-GIKESSVGTTLARAKK 153 (166)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 566678899999 9999999998876654
No 165
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=24.91 E-value=1.3e+02 Score=26.44 Aligned_cols=29 Identities=10% Similarity=0.004 Sum_probs=23.6
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
.|-.-.+||..| |-+...|+.+.+.-+++
T Consensus 186 eg~s~~EIA~~L-gis~~tVk~~l~RAr~k 214 (233)
T PRK12538 186 ENMSNGEIAEVM-DTTVAAVESLLKRGRQQ 214 (233)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 355689999999 99999999998876653
No 166
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=24.84 E-value=1.3e+02 Score=24.87 Aligned_cols=28 Identities=32% Similarity=0.247 Sum_probs=22.2
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-.=.+||..| |-+...|+.+.+..++
T Consensus 156 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~ 183 (194)
T PRK12519 156 EGLSQSEIAKRL-GIPLGTVKARARQGLL 183 (194)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 455678899999 8899999998876665
No 167
>PRK01905 DNA-binding protein Fis; Provisional
Probab=24.72 E-value=2e+02 Score=20.85 Aligned_cols=35 Identities=26% Similarity=0.255 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHH
Q 037956 72 QEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNH 107 (245)
Q Consensus 72 ~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knr 107 (245)
.-|...|.+++..+|+++.+.|..+ |=+...+..+
T Consensus 36 ~~E~~~i~~aL~~~~gn~s~aAr~L-GIsrstL~rk 70 (77)
T PRK01905 36 CVEKPLLEVVMEQAGGNQSLAAEYL-GINRNTLRKK 70 (77)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHH
Confidence 3467788999999999999999998 6565554443
No 168
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=24.63 E-value=1.4e+02 Score=32.56 Aligned_cols=46 Identities=22% Similarity=0.381 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHHHHHhC-CcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 68 GNFTQEEDETIIKLHEQLG-NRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 68 ~~WT~EED~~Ll~lv~~~G-~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
..|+.-+=..++.+..+|| ..-..||..+.|+|..+|+.+......
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~~f~~ 871 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAKVFWE 871 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 3588888888888889999 579999999999999999986554443
No 169
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=24.56 E-value=40 Score=24.39 Aligned_cols=44 Identities=25% Similarity=0.600 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhCCCCcccccccccCccccccccccccccccCCC-------CCCCCCHHHHHHH
Q 037956 22 DRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPDI-------RRGNFTQEEDETI 78 (245)
Q Consensus 22 De~L~~~V~~~g~~nW~~Ia~~~~~~Rt~kqCr~Rw~n~L~p~i-------~k~~WT~EED~~L 78 (245)
+.+|..+|..|| |..++..+.- | |. .-+|.+ ++.+|..+.-+.|
T Consensus 12 e~il~~Lv~~yG---W~~L~~~i~i-~----CF-----~~~PsikSSLkFLRkTpWAR~KVE~l 62 (64)
T PF09905_consen 12 ETILTELVEHYG---WEELGERINI-N----CF-----KNNPSIKSSLKFLRKTPWAREKVENL 62 (64)
T ss_dssp HHHHHHHHHHT----HHHHHHHTTS-S----ST-----TSS--HHHHHHHHHHSHHHHHHHHHH
T ss_pred HHHHHHHHHHhC---HHHHHhhccc-c----cC-----CCCCchHHHHHHHhcCHhHHHHHHHh
Confidence 578899999998 9999987764 3 33 234544 3567877766654
No 170
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=24.38 E-value=1.7e+02 Score=24.90 Aligned_cols=29 Identities=21% Similarity=0.312 Sum_probs=23.4
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
.|-.=.+||..| |-+...|+++.+..+++
T Consensus 153 ~g~s~~EIA~~L-gis~~tV~~~l~RArk~ 181 (203)
T PRK09647 153 EGLSYEEIAATL-GVKLGTVRSRIHRGRQQ 181 (203)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456678999999 99999999998876653
No 171
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=23.85 E-value=1.3e+02 Score=27.51 Aligned_cols=28 Identities=14% Similarity=0.152 Sum_probs=23.6
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-.-.+||..| |.+...||.|.+.-++
T Consensus 168 ~g~s~~EIA~~l-gis~~tVk~~l~RAr~ 195 (339)
T PRK08241 168 LGWSAAEVAELL-DTSVAAVNSALQRARA 195 (339)
T ss_pred hCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 455689999999 9999999999887664
No 172
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=23.83 E-value=1.9e+02 Score=22.75 Aligned_cols=28 Identities=29% Similarity=0.303 Sum_probs=20.5
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-.=..||..| |=+...|+.+.+...+
T Consensus 126 ~g~~~~eIA~~l-~is~~tv~~~l~Rar~ 153 (159)
T TIGR02989 126 RGVSLTALAEQL-GRTVNAVYKALSRLRV 153 (159)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 355678888888 8888888887765543
No 173
>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=23.80 E-value=46 Score=28.04 Aligned_cols=33 Identities=27% Similarity=0.388 Sum_probs=26.4
Q ss_pred CCCHHHHHHHHHHHHHhCCCCcccccccccC-cccc
Q 037956 16 SWTPEEDRKLIAYIRRYGIWNWSEMPKYAGL-LRCG 50 (245)
Q Consensus 16 ~WT~EEDe~L~~~V~~~g~~nW~~Ia~~~~~-~Rt~ 50 (245)
.||+|+.++|.++... |. .=.+||+.||+ .|++
T Consensus 2 ~Wtde~~~~L~~lw~~-G~-SasqIA~~lg~vsRnA 35 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GL-SASQIARQLGGVSRNA 35 (162)
T ss_pred CCCHHHHHHHHHHHHc-CC-CHHHHHHHhCCcchhh
Confidence 5999999999998864 65 67899999993 3544
No 174
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=23.63 E-value=1.8e+02 Score=22.99 Aligned_cols=40 Identities=15% Similarity=0.232 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHhCC-cHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 73 EEDETIIKLHEQLGN-RWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 73 EED~~Ll~lv~~~G~-kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
+-|..|+++.+.-|. .+..||+.+ |-+...|.+|-..+.+
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~ 48 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEE 48 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 557788888888774 699999999 9999999999887665
No 175
>PF09197 Rap1-DNA-bind: Rap1, DNA-binding; InterPro: IPR015280 Members of this entry, which are predominantly found in the yeast protein Rap1, assume a secondary structure consisting of a three-helix bundle and an N-terminal arm. They contain an Arg-Asp-Arg-Lys sequence that interacts with an ACAregion in the 3, region of the DNA-binding site []. ; PDB: 1IGN_A 3UKG_A.
Probab=23.54 E-value=1.4e+02 Score=23.62 Aligned_cols=45 Identities=22% Similarity=0.447 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHHHHHh------------CC-c------------------HHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 70 FTQEEDETIIKLHEQL------------GN-R------------------WSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 70 WT~EED~~Ll~lv~~~------------G~-k------------------W~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
||.+||..|-..|..| |. . ....+...|..|.++=++||+..+..
T Consensus 2 fTA~dDY~Lc~~i~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~fF~~~~~~~p~HT~~sWRDR~RKfv~~ 77 (105)
T PF09197_consen 2 FTADDDYALCKAIKKQFYRDIYQKDPDTGSSLISDGDSKEFIPKRDMRSFFKDLARKNPRHTENSWRDRYRKFVSE 77 (105)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHSB-TTSS-B----------------TTHHHHHHHHTTTS-HHHHHHHHHHTHHH
T ss_pred CChHHHHHHHHHHHHHHHHHHHhhCcccccccccCCCccccccchhhHHHHHHHHHcCCccchhHHHHHHHHHHHH
Confidence 7899999998888543 11 0 56778888999999999999987763
No 176
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=23.42 E-value=1.7e+02 Score=25.35 Aligned_cols=43 Identities=30% Similarity=0.334 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 69 NFTQEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
..|+-|-+.|.-++. |-.-.+||+.| +-+...|+++....++|
T Consensus 155 ~Lt~rE~~Vl~l~~~--G~s~~eIA~~L-~iS~~TVk~~~~~i~~K 197 (216)
T PRK10100 155 LLTHREKEILNKLRI--GASNNEIARSL-FISENTVKTHLYNLFKK 197 (216)
T ss_pred CCCHHHHHHHHHHHc--CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 478766666555554 88899999999 99999999999988874
No 177
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=22.98 E-value=1.7e+02 Score=26.27 Aligned_cols=28 Identities=25% Similarity=0.329 Sum_probs=23.6
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
+|-.-.+||..| |.+...|+.+.+.-.+
T Consensus 130 ~g~s~~EIA~~l-g~s~~tVk~~l~RAr~ 157 (293)
T PRK09636 130 FGVPFDEIASTL-GRSPAACRQLASRARK 157 (293)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 456689999999 9999999999887554
No 178
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=22.91 E-value=1.7e+02 Score=25.64 Aligned_cols=37 Identities=19% Similarity=0.144 Sum_probs=27.1
Q ss_pred HHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 77 TIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 77 ~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
.++.+....|-.-..||..| |-|...|+.+.+..+++
T Consensus 208 ~vl~l~~~~~~s~~EIA~~l-gis~~tV~~~~~ra~~~ 244 (251)
T PRK07670 208 LVISLFYKEELTLTEIGQVL-NLSTSRISQIHSKALFK 244 (251)
T ss_pred HHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 33333334456789999999 99999999988876653
No 179
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=22.89 E-value=1.9e+02 Score=24.46 Aligned_cols=27 Identities=15% Similarity=0.115 Sum_probs=22.5
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 86 GNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 86 G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
|-.=.+||..| |.+...|+.+.+..++
T Consensus 169 g~s~~EIA~~l-gis~~tV~~~l~Ra~~ 195 (206)
T PRK12526 169 ELSQEQLAQQL-NVPLGTVKSRLRLALA 195 (206)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 55678999999 9999999999887665
No 180
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=22.80 E-value=1.7e+02 Score=24.02 Aligned_cols=28 Identities=18% Similarity=0.136 Sum_probs=21.7
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-.=.+||..| |-+...|+.|.+..++
T Consensus 142 ~g~s~~EIA~~l-~is~~tv~~~l~Ra~~ 169 (179)
T PRK09415 142 EELSIKEIAEVT-GVNENTVKTRLKKAKE 169 (179)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 345578888888 7889999998887665
No 181
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=22.78 E-value=1.9e+02 Score=24.07 Aligned_cols=28 Identities=14% Similarity=0.100 Sum_probs=23.0
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-.-.+||..| |-+...|+.+.+..++
T Consensus 126 eg~s~~EIA~~l-gis~~tV~~~l~Rar~ 153 (182)
T PRK12511 126 EGLSYQEAAAVL-GIPIGTLMSRIGRARA 153 (182)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHH
Confidence 456689999999 9999999999876655
No 182
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=22.37 E-value=1.7e+02 Score=24.92 Aligned_cols=44 Identities=11% Similarity=0.140 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhhhh
Q 037956 69 NFTQEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLSKK 115 (245)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkkk 115 (245)
..|+-|-+.|.-+.+ |...++||+.| |-+...|+++-..+++|-
T Consensus 137 ~LT~RE~eVL~lla~--G~snkeIA~~L-~iS~~TVk~h~~~I~~KL 180 (207)
T PRK15411 137 SLSRTESSMLRMWMA--GQGTIQISDQM-NIKAKTVSSHKGNIKRKI 180 (207)
T ss_pred cCCHHHHHHHHHHHc--CCCHHHHHHHc-CCCHHHHHHHHHHHHHHh
Confidence 488888877665544 66678999999 999999999998888743
No 183
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=22.17 E-value=1.9e+02 Score=23.04 Aligned_cols=28 Identities=21% Similarity=0.238 Sum_probs=22.2
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-...+||..| |=+...|+.+.+...+
T Consensus 127 ~~~s~~eIA~~l-gis~~tv~~~l~Rar~ 154 (161)
T PRK12541 127 YGFSYKEIAEMT-GLSLAKVKIELHRGRK 154 (161)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 445678999999 8899999998876554
No 184
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=22.13 E-value=2e+02 Score=24.51 Aligned_cols=28 Identities=4% Similarity=-0.091 Sum_probs=23.4
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-.=.+||..| |-+...|+.|.+..++
T Consensus 163 ~g~s~~EIAe~l-gis~~tV~~~l~RAr~ 190 (206)
T PRK12544 163 IELETNEICHAV-DLSVSNLNVLLYRARL 190 (206)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 455679999999 9999999999887665
No 185
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=22.10 E-value=1.7e+02 Score=25.15 Aligned_cols=27 Identities=15% Similarity=0.118 Sum_probs=23.1
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 86 GNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 86 G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
|-...+||..| |-+...|+++-+..++
T Consensus 198 g~s~~EIA~~l-gis~~tVk~~~~rA~~ 224 (234)
T PRK08301 198 EKTQKEVADML-GISQSYISRLEKRIIK 224 (234)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 66799999999 9999999998777665
No 186
>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.05 E-value=1.2e+02 Score=25.54 Aligned_cols=40 Identities=38% Similarity=0.461 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHH
Q 037956 69 NFTQEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWH 109 (245)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~ 109 (245)
+||+|--++|.+|..+ |-.=++||++|.|=+.+.|--+-+
T Consensus 2 nWtdERve~LkKLWse-GLSASQIAaQLGGVsRnAVIGKVH 41 (169)
T COG5352 2 NWTDERVETLKKLWSE-GLSASQIAAQLGGVSRNAVIGKVH 41 (169)
T ss_pred CchHHHHHHHHHHHHc-ccCHHHHHHHhcCcchhhhheeee
Confidence 5999999999988765 666789999999988887755443
No 187
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.65 E-value=3e+02 Score=20.99 Aligned_cols=45 Identities=20% Similarity=0.370 Sum_probs=35.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCC-CHHHHHHHHHHhhh
Q 037956 67 RGNFTQEEDETIIKLHEQLGNRWSAIASRLPGR-TDNEIKNHWHSRLS 113 (245)
Q Consensus 67 k~~WT~EED~~Ll~lv~~~G~kW~~IA~~lpgR-T~~~~Knrw~~~lk 113 (245)
+..||.|.-..+++++..-|..=+.||..+ |- ..+++.. |...+.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~~-W~~~~~ 50 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLYK-WRIQLQ 50 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHHH-HHHHHH
Confidence 567999999999999999999889999999 76 6665554 544443
No 188
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=21.61 E-value=2.3e+02 Score=24.81 Aligned_cols=43 Identities=21% Similarity=0.269 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 69 NFTQEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
..|+-|-+.|.-+.+ |....+||..| +-+...|+++-..+++|
T Consensus 133 ~LSpRErEVLrLLAq--GkTnKEIAe~L-~IS~rTVkth~srImkK 175 (198)
T PRK15201 133 HFSVTERHLLKLIAS--GYHLSETAALL-SLSEEQTKSLRRSIMRK 175 (198)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 478877776665554 88899999999 99999999998888874
No 189
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=21.44 E-value=2.5e+02 Score=21.46 Aligned_cols=33 Identities=12% Similarity=0.074 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHH
Q 037956 73 EEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKN 106 (245)
Q Consensus 73 EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Kn 106 (245)
-|...|..++..+|+++.+.|+.| |=+...++.
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~L-GIsRsTL~r 87 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALML-GINRGTLRK 87 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHH
Confidence 467788899999999999999999 666655444
No 190
>PRK06930 positive control sigma-like factor; Validated
Probab=21.44 E-value=2e+02 Score=24.27 Aligned_cols=36 Identities=17% Similarity=0.241 Sum_probs=27.8
Q ss_pred HHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 77 TIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 77 ~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.++.++...|..-..||..| |-+...|+.+.+..++
T Consensus 121 ~V~~L~~~eg~s~~EIA~~l-giS~~tVk~~l~Ra~~ 156 (170)
T PRK06930 121 EVYLMHRGYGLSYSEIADYL-NIKKSTVQSMIERAEK 156 (170)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 34444445677899999999 9999999998877665
No 191
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=21.29 E-value=2e+02 Score=24.58 Aligned_cols=29 Identities=24% Similarity=0.228 Sum_probs=23.5
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
..|-.-.+||..+ |-+...|+.+.+..++
T Consensus 192 ~~~~s~~eIA~~l-gis~~~v~~~~~ra~~ 220 (227)
T TIGR02980 192 FEDKTQSEIAERL-GISQMHVSRLLRRALK 220 (227)
T ss_pred hcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 3466789999999 8999999888777665
No 192
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=21.02 E-value=1.9e+02 Score=25.83 Aligned_cols=29 Identities=14% Similarity=0.221 Sum_probs=24.1
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.+|-.-.+||..| |.+...|+.+.+...+
T Consensus 122 ~~g~s~~EIA~~l-g~s~~tVr~~l~RAr~ 150 (281)
T TIGR02957 122 VFDYPYEEIASIV-GKSEANCRQLVSRARR 150 (281)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3566689999999 9999999999887654
No 193
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=21.02 E-value=2e+02 Score=23.82 Aligned_cols=28 Identities=25% Similarity=0.298 Sum_probs=22.8
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-.-.+||..| |-+...|+++.+...+
T Consensus 169 e~~s~~EIA~~l-gis~~tV~~~l~rar~ 196 (208)
T PRK08295 169 DGKSYQEIAEEL-NRHVKSIDNALQRVKR 196 (208)
T ss_pred ccCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 456789999999 9999999998876554
No 194
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=20.94 E-value=2.4e+02 Score=22.35 Aligned_cols=44 Identities=25% Similarity=0.337 Sum_probs=34.5
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 68 GNFTQEEDETIIKLHEQLGNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 68 ~~WT~EED~~Ll~lv~~~G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
...|+.|-+.|.-+.. |-.-.+||..| +-+...++.+.+++++|
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 3688888877766554 55788999999 78999999988887763
No 195
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=20.82 E-value=2.6e+02 Score=24.49 Aligned_cols=51 Identities=24% Similarity=0.328 Sum_probs=39.3
Q ss_pred cCCCCCCCCCHHHHHHHHHHHHHh----CCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 62 RPDIRRGNFTQEEDETIIKLHEQL----GNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 62 ~p~i~k~~WT~EED~~Ll~lv~~~----G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
+|.-.+..||.+.-.+|-.+.+.- |.-=.++|..| +=+..|||-.|.+.-.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L-~LsetQVkvWFQNRRt 155 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSL-SLSETQVKVWFQNRRT 155 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHc-CCChhHhhhhhhhhhH
Confidence 445556789999988888887653 34568899999 9999999998876443
No 196
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=20.69 E-value=2.4e+02 Score=22.92 Aligned_cols=29 Identities=21% Similarity=0.129 Sum_probs=22.5
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
..|-.=.+||..| |-+...|+++.+..++
T Consensus 114 ~~g~s~~eIA~~l-gis~~tV~~~l~Rar~ 142 (170)
T TIGR02959 114 LEGLSQQEIAEKL-GLSLSGAKSRVQRGRK 142 (170)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3455678899999 8899999998876554
No 197
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=20.66 E-value=94 Score=25.76 Aligned_cols=27 Identities=19% Similarity=0.220 Sum_probs=22.5
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 86 GNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 86 G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
|-.-.+||..| |-+...|+++.+..++
T Consensus 155 g~s~~EIA~~l-gis~~tV~~~l~ra~~ 181 (194)
T PRK12513 155 DLELEEIAELT-GVPEETVKSRLRYALQ 181 (194)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 45689999999 8999999998876665
No 198
>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=20.33 E-value=96 Score=22.78 Aligned_cols=22 Identities=32% Similarity=0.584 Sum_probs=17.4
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHH
Q 037956 84 QLGNRWSAIASRLPGRTDNEIKN 106 (245)
Q Consensus 84 ~~G~kW~~IA~~lpgRT~~~~Kn 106 (245)
.+|+.|..+|.+| |-+...|++
T Consensus 14 ~~g~DWr~LA~~L-g~~~~~I~~ 35 (79)
T cd08312 14 VVAADWTALAEEM-GFEYLEIRN 35 (79)
T ss_pred CcccCHHHHHHHc-CCCHHHHHH
Confidence 4789999999999 777666653
No 199
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=20.23 E-value=2.1e+02 Score=24.07 Aligned_cols=28 Identities=11% Similarity=0.075 Sum_probs=23.0
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 037956 86 GNRWSAIASRLPGRTDNEIKNHWHSRLSK 114 (245)
Q Consensus 86 G~kW~~IA~~lpgRT~~~~Knrw~~~lkk 114 (245)
|-.-.+||..| |-+.+.|+.+.+..+++
T Consensus 149 g~s~~EIAe~l-gis~~tV~~~l~Rar~~ 176 (196)
T PRK12535 149 GYTYEEAAKIA-DVRVGTIRSRVARARAD 176 (196)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 45578999999 99999999998876653
No 200
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=20.08 E-value=2.3e+02 Score=23.52 Aligned_cols=28 Identities=21% Similarity=0.156 Sum_probs=22.4
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHhhh
Q 037956 85 LGNRWSAIASRLPGRTDNEIKNHWHSRLS 113 (245)
Q Consensus 85 ~G~kW~~IA~~lpgRT~~~~Knrw~~~lk 113 (245)
.|-.-.+||..| |-+...|+.+-+..++
T Consensus 126 ~g~s~~EIA~~L-gis~~tV~~~l~RAr~ 153 (182)
T PRK12540 126 SGFSYEDAAAIC-GCAVGTIKSRVNRARS 153 (182)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 456688999999 8899999988776554
Done!