Query 020613
Match_columns 323
No_of_seqs 281 out of 1375
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 03:47:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020613.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020613hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03091 hypothetical protein; 100.0 1.6E-37 3.5E-42 306.3 12.3 121 1-121 1-121 (459)
2 PLN03212 Transcription repress 100.0 9.3E-37 2E-41 282.9 11.2 121 3-123 14-134 (249)
3 KOG0048 Transcription factor, 100.0 3.1E-34 6.7E-39 266.0 10.0 109 12-120 7-115 (238)
4 KOG0049 Transcription factor, 99.8 1.4E-19 3.1E-24 185.0 7.1 112 1-113 347-459 (939)
5 KOG0049 Transcription factor, 99.7 8E-18 1.7E-22 172.3 7.2 108 11-119 302-413 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.6 1.4E-16 3E-21 117.5 3.9 60 17-78 1-60 (60)
7 COG5147 REB1 Myb superfamily p 99.6 1.5E-15 3.2E-20 154.5 6.1 108 9-117 15-122 (512)
8 KOG0050 mRNA splicing protein 99.6 1.2E-15 2.5E-20 153.5 2.7 108 12-121 5-112 (617)
9 KOG0051 RNA polymerase I termi 99.4 8.9E-14 1.9E-18 143.1 6.0 105 13-120 383-515 (607)
10 PF00249 Myb_DNA-binding: Myb- 99.4 2.8E-13 6.1E-18 96.4 5.0 46 67-112 1-48 (48)
11 PF00249 Myb_DNA-binding: Myb- 99.4 1.4E-13 3.1E-18 97.9 1.1 48 14-61 1-48 (48)
12 PF13921 Myb_DNA-bind_6: Myb-l 99.3 3.3E-12 7.2E-17 94.1 5.4 49 70-118 1-49 (60)
13 smart00717 SANT SANT SWI3, AD 99.2 1.7E-11 3.7E-16 84.2 5.9 47 67-113 1-48 (49)
14 PLN03212 Transcription repress 99.2 1.1E-11 2.4E-16 116.0 6.0 59 62-120 20-80 (249)
15 KOG0048 Transcription factor, 99.2 2.9E-11 6.3E-16 112.6 5.2 60 63-122 5-66 (238)
16 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 1.5E-10 3.2E-15 78.5 5.7 44 69-112 1-45 (45)
17 PLN03091 hypothetical protein; 99.1 7.3E-11 1.6E-15 118.0 5.7 59 62-120 9-69 (459)
18 smart00717 SANT SANT SWI3, AD 99.0 1.5E-10 3.2E-15 79.5 2.6 48 14-62 1-48 (49)
19 cd00167 SANT 'SWI3, ADA2, N-Co 98.9 1E-09 2.2E-14 74.3 2.2 45 16-61 1-45 (45)
20 KOG0051 RNA polymerase I termi 98.8 3.4E-09 7.3E-14 109.7 5.2 103 12-116 306-432 (607)
21 COG5147 REB1 Myb superfamily p 98.4 3.2E-08 6.9E-13 101.4 -2.2 97 13-112 290-396 (512)
22 TIGR01557 myb_SHAQKYF myb-like 97.7 2.5E-05 5.5E-10 58.3 2.8 49 13-61 2-54 (57)
23 TIGR01557 myb_SHAQKYF myb-like 97.7 0.00012 2.7E-09 54.6 6.0 47 67-113 3-55 (57)
24 KOG0050 mRNA splicing protein 97.6 4.5E-05 9.8E-10 78.1 3.0 56 65-120 5-61 (617)
25 KOG0457 Histone acetyltransfer 97.5 4.1E-05 9E-10 76.9 1.9 50 11-61 69-118 (438)
26 TIGR02894 DNA_bind_RsfA transc 97.3 0.00019 4.2E-09 63.9 3.9 50 66-116 3-59 (161)
27 KOG0457 Histone acetyltransfer 97.3 0.00032 7E-09 70.7 5.7 49 64-112 69-118 (438)
28 PF13837 Myb_DNA-bind_4: Myb/S 97.0 0.00058 1.2E-08 53.4 2.8 48 68-115 2-67 (90)
29 PF08914 Myb_DNA-bind_2: Rap1 96.9 0.0013 2.9E-08 50.3 4.5 51 67-117 2-62 (65)
30 PF13325 MCRS_N: N-terminal re 96.9 0.0038 8.3E-08 57.5 7.9 100 16-117 1-131 (199)
31 COG5259 RSC8 RSC chromatin rem 96.8 0.0012 2.6E-08 67.3 4.4 46 66-111 278-323 (531)
32 KOG1279 Chromatin remodeling f 96.8 0.0015 3.4E-08 67.5 5.2 47 66-112 252-298 (506)
33 COG5259 RSC8 RSC chromatin rem 96.6 0.00088 1.9E-08 68.2 1.5 46 13-60 278-323 (531)
34 PRK13923 putative spore coat p 96.5 0.0024 5.2E-08 57.5 3.6 51 65-116 3-60 (170)
35 KOG1279 Chromatin remodeling f 96.4 0.0022 4.8E-08 66.4 3.3 49 10-60 249-297 (506)
36 TIGR02894 DNA_bind_RsfA transc 96.4 0.00097 2.1E-08 59.5 0.3 51 11-63 1-57 (161)
37 PF08914 Myb_DNA-bind_2: Rap1 96.1 0.0018 3.8E-08 49.7 0.5 52 14-65 2-61 (65)
38 PF13837 Myb_DNA-bind_4: Myb/S 95.8 0.0025 5.4E-08 49.7 0.1 48 14-61 1-64 (90)
39 PF13873 Myb_DNA-bind_5: Myb/S 95.8 0.013 2.8E-07 45.1 4.0 49 67-115 2-72 (78)
40 COG5114 Histone acetyltransfer 94.9 0.027 5.9E-07 55.5 4.0 47 67-113 63-110 (432)
41 PRK13923 putative spore coat p 94.8 0.0073 1.6E-07 54.4 -0.2 50 11-62 2-57 (170)
42 COG5114 Histone acetyltransfer 94.7 0.01 2.2E-07 58.4 0.5 50 12-62 61-110 (432)
43 PLN03142 Probable chromatin-re 94.0 0.11 2.3E-06 58.3 6.5 98 16-114 826-986 (1033)
44 PF13873 Myb_DNA-bind_5: Myb/S 93.9 0.015 3.3E-07 44.6 -0.2 49 13-61 1-69 (78)
45 KOG2656 DNA methyltransferase 93.8 0.064 1.4E-06 54.0 3.9 83 36-119 75-188 (445)
46 KOG4282 Transcription factor G 92.7 0.21 4.6E-06 48.8 5.6 50 67-116 54-117 (345)
47 PF12776 Myb_DNA-bind_3: Myb/S 92.1 0.35 7.6E-06 38.1 5.3 46 69-114 1-64 (96)
48 PF09111 SLIDE: SLIDE; InterP 91.7 0.21 4.4E-06 42.6 3.7 52 64-115 46-113 (118)
49 COG5118 BDP1 Transcription ini 90.8 0.38 8.2E-06 48.6 5.0 46 68-113 366-411 (507)
50 PF08281 Sigma70_r4_2: Sigma-7 87.8 1.3 2.7E-05 31.4 4.7 42 72-114 12-53 (54)
51 KOG1194 Predicted DNA-binding 86.9 1.7 3.7E-05 44.9 6.7 49 66-114 186-234 (534)
52 PF09111 SLIDE: SLIDE; InterP 81.6 1.1 2.4E-05 38.1 2.4 34 11-44 46-82 (118)
53 PF11626 Rap1_C: TRF2-interact 80.9 0.89 1.9E-05 36.3 1.5 29 11-42 44-80 (87)
54 KOG4167 Predicted DNA-binding 78.2 3.4 7.5E-05 45.0 5.1 47 67-113 619-665 (907)
55 KOG4282 Transcription factor G 77.6 1 2.2E-05 44.1 1.0 47 15-61 55-113 (345)
56 KOG4468 Polycomb-group transcr 74.5 4.4 9.5E-05 43.3 4.6 49 67-115 88-146 (782)
57 PF13404 HTH_AsnC-type: AsnC-t 71.9 7.9 0.00017 26.9 4.1 38 73-111 3-41 (42)
58 PF04545 Sigma70_r4: Sigma-70, 71.3 9.3 0.0002 26.7 4.4 41 73-114 7-47 (50)
59 PRK11179 DNA-binding transcrip 68.4 10 0.00022 32.8 4.9 46 72-118 8-54 (153)
60 COG5118 BDP1 Transcription ini 68.0 3.8 8.2E-05 41.6 2.4 109 11-121 362-484 (507)
61 smart00595 MADF subfamily of S 64.2 6.5 0.00014 30.5 2.6 26 88-114 29-54 (89)
62 PRK11169 leucine-responsive tr 63.1 12 0.00026 32.8 4.4 46 72-118 13-59 (164)
63 KOG4329 DNA-binding protein [G 62.7 13 0.00029 37.7 5.1 47 68-114 278-325 (445)
64 PF12776 Myb_DNA-bind_3: Myb/S 62.5 4.8 0.0001 31.5 1.6 45 16-60 1-61 (96)
65 TIGR02985 Sig70_bacteroi1 RNA 60.1 17 0.00037 30.1 4.7 36 78-114 121-156 (161)
66 KOG2009 Transcription initiati 58.2 11 0.00025 40.0 3.9 47 65-111 407-453 (584)
67 PF07750 GcrA: GcrA cell cycle 57.7 11 0.00025 33.6 3.3 42 69-111 2-43 (162)
68 PF11626 Rap1_C: TRF2-interact 56.5 5.1 0.00011 31.9 0.8 17 63-79 43-59 (87)
69 PF13325 MCRS_N: N-terminal re 55.0 25 0.00054 32.7 5.2 44 69-113 1-47 (199)
70 cd08319 Death_RAIDD Death doma 53.9 17 0.00036 29.1 3.4 29 75-104 2-30 (83)
71 PF01388 ARID: ARID/BRIGHT DNA 53.7 28 0.00061 27.2 4.7 38 77-114 40-90 (92)
72 KOG0384 Chromodomain-helicase 53.4 15 0.00033 42.3 4.1 74 13-93 1132-1206(1373)
73 PF13404 HTH_AsnC-type: AsnC-t 52.9 5.7 0.00012 27.7 0.5 38 20-59 3-40 (42)
74 KOG4167 Predicted DNA-binding 52.3 7.5 0.00016 42.5 1.5 45 13-59 618-662 (907)
75 smart00501 BRIGHT BRIGHT, ARID 50.3 32 0.00069 27.3 4.5 38 77-114 36-86 (93)
76 PRK11179 DNA-binding transcrip 49.9 8 0.00017 33.4 1.1 45 19-65 8-52 (153)
77 cd08803 Death_ank3 Death domai 49.2 24 0.00053 28.1 3.7 31 75-106 4-34 (84)
78 PF11035 SnAPC_2_like: Small n 48.2 49 0.0011 33.0 6.2 48 67-114 21-72 (344)
79 TIGR02937 sigma70-ECF RNA poly 47.0 33 0.00071 27.4 4.2 34 80-114 120-153 (158)
80 smart00344 HTH_ASNC helix_turn 45.0 49 0.0011 26.3 4.9 45 73-118 3-48 (108)
81 PF10545 MADF_DNA_bdg: Alcohol 44.4 19 0.00042 26.9 2.4 27 88-114 28-55 (85)
82 PRK11169 leucine-responsive tr 43.8 7.5 0.00016 34.1 -0.0 45 19-65 13-57 (164)
83 cd08317 Death_ank Death domain 43.5 24 0.00052 27.6 2.8 29 75-104 4-32 (84)
84 PRK09652 RNA polymerase sigma 41.7 51 0.0011 27.8 4.8 31 83-114 141-171 (182)
85 PF11035 SnAPC_2_like: Small n 41.5 60 0.0013 32.5 5.7 87 14-114 21-128 (344)
86 PF04504 DUF573: Protein of un 40.2 43 0.00092 27.4 3.9 48 68-115 5-65 (98)
87 KOG3841 TEF-1 and related tran 40.0 49 0.0011 33.9 4.9 75 10-121 72-151 (455)
88 PRK11924 RNA polymerase sigma 39.3 49 0.0011 27.9 4.3 30 84-114 139-168 (179)
89 PF07638 Sigma70_ECF: ECF sigm 39.1 58 0.0013 28.8 4.9 37 76-113 141-177 (185)
90 PF02757 YLP: YLP motif; Inte 38.4 12 0.00027 18.4 0.3 6 237-242 3-8 (9)
91 cd08318 Death_NMPP84 Death dom 37.9 39 0.00085 26.8 3.2 26 78-104 10-35 (86)
92 cd06171 Sigma70_r4 Sigma70, re 37.9 75 0.0016 20.7 4.3 40 70-111 11-50 (55)
93 PRK09643 RNA polymerase sigma 36.3 60 0.0013 28.7 4.5 29 84-113 148-176 (192)
94 cd08804 Death_ank2 Death domai 36.0 43 0.00092 26.6 3.2 31 75-106 4-34 (84)
95 PF09420 Nop16: Ribosome bioge 35.3 84 0.0018 27.7 5.3 47 66-112 113-163 (164)
96 PRK04217 hypothetical protein; 33.7 90 0.0019 26.3 4.9 44 69-114 42-85 (110)
97 PRK09641 RNA polymerase sigma 33.6 67 0.0015 27.6 4.3 29 85-114 151-179 (187)
98 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 33.5 76 0.0017 23.2 3.9 35 72-107 6-40 (50)
99 TIGR02939 RpoE_Sigma70 RNA pol 32.3 58 0.0013 28.1 3.7 28 86-114 154-181 (190)
100 cd08777 Death_RIP1 Death Domai 32.0 48 0.001 26.5 2.9 30 76-106 3-32 (86)
101 COG1522 Lrp Transcriptional re 31.9 84 0.0018 26.4 4.5 47 72-119 7-54 (154)
102 TIGR02954 Sig70_famx3 RNA poly 31.9 76 0.0016 27.0 4.3 29 85-114 134-162 (169)
103 smart00005 DEATH DEATH domain, 31.8 54 0.0012 25.1 3.1 29 75-104 5-34 (88)
104 cd08311 Death_p75NR Death doma 31.7 49 0.0011 26.0 2.8 33 72-106 2-34 (77)
105 KOG2656 DNA methyltransferase 31.2 33 0.00071 35.2 2.2 48 12-60 128-180 (445)
106 PRK12523 RNA polymerase sigma 30.8 89 0.0019 26.8 4.6 32 83-115 132-163 (172)
107 PRK09637 RNA polymerase sigma 30.8 82 0.0018 27.6 4.4 30 84-114 120-149 (181)
108 PRK09047 RNA polymerase factor 30.6 95 0.0021 25.9 4.6 29 85-114 121-149 (161)
109 PRK12512 RNA polymerase sigma 30.5 83 0.0018 27.2 4.4 30 85-115 146-175 (184)
110 cd08805 Death_ank1 Death domai 30.2 58 0.0013 26.1 3.1 27 75-102 4-30 (84)
111 TIGR02943 Sig70_famx1 RNA poly 30.0 92 0.002 27.4 4.7 31 83-114 144-174 (188)
112 KOG1194 Predicted DNA-binding 29.4 34 0.00075 35.7 2.0 46 12-59 185-230 (534)
113 PRK12531 RNA polymerase sigma 29.4 94 0.002 27.3 4.6 29 85-114 156-184 (194)
114 PRK09648 RNA polymerase sigma 28.9 98 0.0021 26.9 4.6 29 85-114 154-182 (189)
115 cd08779 Death_PIDD Death Domai 28.5 61 0.0013 25.8 2.9 25 76-101 3-27 (86)
116 TIGR02948 SigW_bacill RNA poly 28.3 86 0.0019 26.9 4.1 28 86-114 152-179 (187)
117 PRK11923 algU RNA polymerase s 28.2 89 0.0019 27.2 4.2 28 86-114 154-181 (193)
118 PF02954 HTH_8: Bacterial regu 28.0 1E+02 0.0022 20.9 3.6 35 73-108 5-39 (42)
119 PRK09645 RNA polymerase sigma 27.8 1.1E+02 0.0023 26.2 4.5 29 85-114 133-161 (173)
120 PRK09642 RNA polymerase sigma 27.8 1.1E+02 0.0024 25.7 4.6 29 85-114 121-149 (160)
121 PRK12515 RNA polymerase sigma 27.6 1.1E+02 0.0023 26.7 4.6 29 85-114 146-174 (189)
122 COG2197 CitB Response regulato 27.4 86 0.0019 28.5 4.1 45 68-115 147-191 (211)
123 PRK12530 RNA polymerase sigma 27.4 1E+02 0.0023 27.0 4.5 28 85-113 149-176 (189)
124 PRK12529 RNA polymerase sigma 27.2 1.1E+02 0.0024 26.5 4.6 33 84-117 141-173 (178)
125 PRK09413 IS2 repressor TnpA; R 27.0 1.2E+02 0.0026 25.3 4.5 46 13-62 9-54 (121)
126 KOG4468 Polycomb-group transcr 26.9 52 0.0011 35.6 2.8 49 13-62 87-144 (782)
127 PRK12524 RNA polymerase sigma 26.0 1.1E+02 0.0025 26.8 4.5 29 85-114 151-179 (196)
128 PF04504 DUF573: Protein of un 24.5 80 0.0017 25.8 3.0 71 13-84 3-94 (98)
129 PF00196 GerE: Bacterial regul 24.5 76 0.0017 22.6 2.6 43 69-114 3-45 (58)
130 PRK06759 RNA polymerase factor 24.4 1.4E+02 0.003 24.8 4.6 28 86-114 122-149 (154)
131 KOG2009 Transcription initiati 24.0 61 0.0013 34.8 2.7 50 8-59 403-452 (584)
132 TIGR02952 Sig70_famx2 RNA poly 23.8 1.4E+02 0.003 25.1 4.5 28 86-114 138-165 (170)
133 PF13936 HTH_38: Helix-turn-he 23.5 82 0.0018 21.7 2.5 36 69-106 4-39 (44)
134 PF09420 Nop16: Ribosome bioge 23.4 80 0.0017 27.9 3.0 48 12-60 112-162 (164)
135 PRK09651 RNA polymerase sigma 23.2 1.2E+02 0.0025 26.2 4.0 28 86-114 135-162 (172)
136 TIGR02999 Sig-70_X6 RNA polyme 23.1 1.5E+02 0.0032 25.4 4.6 29 85-114 149-177 (183)
137 PRK12527 RNA polymerase sigma 22.8 1.6E+02 0.0035 24.7 4.7 29 85-114 120-148 (159)
138 PRK12528 RNA polymerase sigma 22.5 1.6E+02 0.0035 24.8 4.6 30 84-114 127-156 (161)
139 PRK12532 RNA polymerase sigma 22.5 1.4E+02 0.003 26.2 4.3 29 84-113 150-178 (195)
140 PRK09649 RNA polymerase sigma 22.4 1.4E+02 0.003 26.1 4.3 29 85-114 145-173 (185)
141 PRK12536 RNA polymerase sigma 22.1 1.5E+02 0.0034 25.6 4.5 30 84-114 143-172 (181)
142 smart00344 HTH_ASNC helix_turn 22.1 47 0.001 26.4 1.1 44 20-65 3-46 (108)
143 cd08306 Death_FADD Fas-associa 21.9 1.1E+02 0.0025 24.1 3.3 29 76-105 3-31 (86)
144 PRK05602 RNA polymerase sigma 21.9 1.4E+02 0.0031 25.8 4.3 29 85-114 143-171 (186)
145 PRK12542 RNA polymerase sigma 21.8 1.6E+02 0.0034 25.6 4.5 30 84-114 136-165 (185)
146 PRK12514 RNA polymerase sigma 21.6 1.6E+02 0.0034 25.3 4.5 28 86-114 145-172 (179)
147 COG1522 Lrp Transcriptional re 21.5 38 0.00083 28.5 0.6 44 20-65 8-51 (154)
148 PRK00118 putative DNA-binding 21.5 1.8E+02 0.0038 24.3 4.5 41 72-113 19-59 (104)
149 TIGR02950 SigM_subfam RNA poly 21.4 56 0.0012 27.1 1.6 28 86-114 121-148 (154)
150 PRK12516 RNA polymerase sigma 21.2 1.6E+02 0.0035 25.9 4.5 30 83-113 129-158 (187)
151 cd01670 Death Death Domain: a 21.1 92 0.002 23.2 2.6 26 78-104 2-27 (79)
152 PRK12547 RNA polymerase sigma 20.9 1.8E+02 0.0039 24.7 4.6 29 85-114 127-155 (164)
153 KOG3554 Histone deacetylase co 20.8 1.1E+02 0.0024 32.4 3.7 43 69-111 287-330 (693)
154 TIGR02983 SigE-fam_strep RNA p 20.5 1.7E+02 0.0036 24.6 4.3 38 76-114 116-153 (162)
155 COG2963 Transposase and inacti 20.1 4.6E+02 0.01 21.1 6.7 46 67-114 5-51 (116)
No 1
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=1.6e-37 Score=306.28 Aligned_cols=121 Identities=70% Similarity=1.339 Sum_probs=116.8
Q ss_pred CCCCCccccCCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhccCCCCCCCCCCHHHHHHHHH
Q 020613 1 MGHHSCCNQQKVKRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYLRPDIRRGRFTPEEEKLIIS 80 (323)
Q Consensus 1 mgr~~c~~~~kvkKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p~ikkg~WT~EED~~Ll~ 80 (323)
|||++||++++++||+||+|||++|+++|++||.++|..||+.++.+|+++|||+||.+||+|.+++++||+|||++|++
T Consensus 1 mgr~~Cc~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLe 80 (459)
T PLN03091 1 MGRHSCCYKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIE 80 (459)
T ss_pred CCCCccCcCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHH
Confidence 99999999999999999999999999999999999999999998778999999999999999999999999999999999
Q ss_pred HHHHhCCChHHHhccCCCCCHHHHHHHHHHHhhhhccCCCC
Q 020613 81 LHSVVGNRWAHIASHLPGRTDNEIKNYWNSWIKKKIRKPST 121 (323)
Q Consensus 81 lv~~~G~kWskIAk~LpgRT~~qcKnRW~~lLkkk~kK~~~ 121 (323)
++++||++|++||++|+|||+++|||||+.+++++++..+.
T Consensus 81 L~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~I 121 (459)
T PLN03091 81 LHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRGI 121 (459)
T ss_pred HHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCC
Confidence 99999999999999999999999999999999998775443
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=9.3e-37 Score=282.92 Aligned_cols=121 Identities=54% Similarity=1.127 Sum_probs=115.5
Q ss_pred CCCccccCCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhccCCCCCCCCCCHHHHHHHHHHH
Q 020613 3 HHSCCNQQKVKRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYLRPDIRRGRFTPEEEKLIISLH 82 (323)
Q Consensus 3 r~~c~~~~kvkKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p~ikkg~WT~EED~~Ll~lv 82 (323)
|+|||.++.++|++||+|||++|+++|++||..+|..||+.++.+|+++|||+||.+||+|.+++++||+|||++|++++
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 68999999999999999999999999999999999999999966899999999999999999999999999999999999
Q ss_pred HHhCCChHHHhccCCCCCHHHHHHHHHHHhhhhccCCCCCC
Q 020613 83 SVVGNRWAHIASHLPGRTDNEIKNYWNSWIKKKIRKPSTVP 123 (323)
Q Consensus 83 ~~~G~kWskIAk~LpgRT~~qcKnRW~~lLkkk~kK~~~~~ 123 (323)
.+||++|+.||+.|||||+++|||||+.++++++++....+
T Consensus 94 ~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~p 134 (249)
T PLN03212 94 RLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGIDP 134 (249)
T ss_pred HhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCCC
Confidence 99999999999999999999999999999999887765443
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=3.1e-34 Score=266.01 Aligned_cols=109 Identities=57% Similarity=1.041 Sum_probs=106.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhccCCCCCCCCCCHHHHHHHHHHHHHhCCChHH
Q 020613 12 VKRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYLRPDIRRGRFTPEEEKLIISLHSVVGNRWAH 91 (323)
Q Consensus 12 vkKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p~ikkg~WT~EED~~Ll~lv~~~G~kWsk 91 (323)
+.||+||+|||++|+++|++||.++|..||+.+|++|++++||.||.|||+|++++|.||+|||++|++++..+|++|+.
T Consensus 7 ~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrWs~ 86 (238)
T KOG0048|consen 7 LVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRWSL 86 (238)
T ss_pred ccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHHHH
Confidence 34799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhccCCCCCHHHHHHHHHHHhhhhccCCC
Q 020613 92 IASHLPGRTDNEIKNYWNSWIKKKIRKPS 120 (323)
Q Consensus 92 IAk~LpgRT~~qcKnRW~~lLkkk~kK~~ 120 (323)
||++|||||++.|||+|+..+++++.+..
T Consensus 87 IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 87 IAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred HHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 99999999999999999999999998776
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.78 E-value=1.4e-19 Score=185.04 Aligned_cols=112 Identities=26% Similarity=0.441 Sum_probs=103.1
Q ss_pred CCCCCccccCCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhccCCCCCCCCCCHHHHHHHHH
Q 020613 1 MGHHSCCNQQKVKRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYLRPDIRRGRFTPEEEKLIIS 80 (323)
Q Consensus 1 mgr~~c~~~~kvkKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p~ikkg~WT~EED~~Ll~ 80 (323)
+||++-...|.+++|+||.+||.+|..+|.+||.++|.+|-+.++ ||+..|||+||.|+|+...|++.||-.||+.|+.
T Consensus 347 I~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vP-nRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~ 425 (939)
T KOG0049|consen 347 ITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVP-NRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLY 425 (939)
T ss_pred hhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcC-CccHHHHHHHHHHHHHHhhccCceeecchHHHHH
Confidence 589999999999999999999999999999999999999999999 9999999999999999999999999999999999
Q ss_pred HHHHhC-CChHHHhccCCCCCHHHHHHHHHHHhh
Q 020613 81 LHSVVG-NRWAHIASHLPGRTDNEIKNYWNSWIK 113 (323)
Q Consensus 81 lv~~~G-~kWskIAk~LpgRT~~qcKnRW~~lLk 113 (323)
+|++|| .+|.+||.+||.||..|.+.|=...+.
T Consensus 426 ~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~ 459 (939)
T KOG0049|consen 426 AVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIA 459 (939)
T ss_pred HHHHHccchHHHHHHHccccchhHHHHHHHHHHH
Confidence 999999 579999999999999665444333333
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.71 E-value=8e-18 Score=172.35 Aligned_cols=108 Identities=24% Similarity=0.503 Sum_probs=100.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCC---CccccccccCcCcCcccccchhhhccCCCCCCCCCCHHHHHHHHHHHHHhCC
Q 020613 11 KVKRGLWSPEEDEKLIRYITTHGYG---CWSEVPEKAGLQRCGKSCRLRWINYLRPDIRRGRFTPEEEKLIISLHSVVGN 87 (323)
Q Consensus 11 kvkKG~WT~EEDe~L~~lV~kyG~~---nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p~ikkg~WT~EED~~Ll~lv~~~G~ 87 (323)
-+++..||+|||.+|+.+|+....+ +|++|...|+ ||+..|...||...|+|.+++|+||.+||.+|+.+|.+||.
T Consensus 302 ~L~ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ymp-gr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~ 380 (939)
T KOG0049|consen 302 QLSEKEWSEEEDTKLIALVKITSINSHIQWDKVVQYMP-GRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGA 380 (939)
T ss_pred HHHhhhcchhhhHHHHHHHHHhhccCccchHHHHHhcC-CcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCc
Confidence 3567899999999999999998655 7999999999 99999999999999999999999999999999999999996
Q ss_pred -ChHHHhccCCCCCHHHHHHHHHHHhhhhccCC
Q 020613 88 -RWAHIASHLPGRTDNEIKNYWNSWIKKKIRKP 119 (323)
Q Consensus 88 -kWskIAk~LpgRT~~qcKnRW~~lLkkk~kK~ 119 (323)
.|.+|-..+|||++.|||.||.+.|....++.
T Consensus 381 kdw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~ 413 (939)
T KOG0049|consen 381 KDWAKVRQAVPNRSDSQCRERYTNVLNRSAKVE 413 (939)
T ss_pred cchhhHHHhcCCccHHHHHHHHHHHHHHhhccC
Confidence 49999999999999999999999998766554
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=99.64 E-value=1.4e-16 Score=117.53 Aligned_cols=60 Identities=43% Similarity=0.864 Sum_probs=55.2
Q ss_pred CCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhccCCCCCCCCCCHHHHHHH
Q 020613 17 WSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYLRPDIRRGRFTPEEEKLI 78 (323)
Q Consensus 17 WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p~ikkg~WT~EED~~L 78 (323)
||+|||++|+.+|..|| .+|..||..|+ .|++.+|+.||.++|++.+++++||.+||++|
T Consensus 1 WT~eEd~~L~~~~~~~g-~~W~~Ia~~l~-~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYG-NDWKKIAEHLG-NRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHT-S-HHHHHHHST-TS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC-cCHHHHHHHHC-cCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 99999999999999999 57999999997 89999999999999999999999999999987
No 7
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.58 E-value=1.5e-15 Score=154.46 Aligned_cols=108 Identities=28% Similarity=0.478 Sum_probs=103.2
Q ss_pred cCCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhccCCCCCCCCCCHHHHHHHHHHHHHhCCC
Q 020613 9 QQKVKRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYLRPDIRRGRFTPEEEKLIISLHSVVGNR 88 (323)
Q Consensus 9 ~~kvkKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p~ikkg~WT~EED~~Ll~lv~~~G~k 88 (323)
+.+++.|.|+..||+.|..+|+++|+.+|..||..+. .|+++||+.||.++++|.++++.|+.|||+.|+.+..++|.+
T Consensus 15 ~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~-~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~ 93 (512)
T COG5147 15 QTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLI-SSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQ 93 (512)
T ss_pred cceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhc-ccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCch
Confidence 4578899999999999999999999999999999999 699999999999999999999999999999999999999999
Q ss_pred hHHHhccCCCCCHHHHHHHHHHHhhhhcc
Q 020613 89 WAHIASHLPGRTDNEIKNYWNSWIKKKIR 117 (323)
Q Consensus 89 WskIAk~LpgRT~~qcKnRW~~lLkkk~k 117 (323)
|+.||..+++||..+|.+||...+.....
T Consensus 94 wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 94 WSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 99999999999999999999998877655
No 8
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.55 E-value=1.2e-15 Score=153.50 Aligned_cols=108 Identities=24% Similarity=0.550 Sum_probs=102.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhccCCCCCCCCCCHHHHHHHHHHHHHhCCChHH
Q 020613 12 VKRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYLRPDIRRGRFTPEEEKLIISLHSVVGNRWAH 91 (323)
Q Consensus 12 vkKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p~ikkg~WT~EED~~Ll~lv~~~G~kWsk 91 (323)
++.|.|+.-||+.|..+|.+||.+.|++|+..+. .++++||+.||..+|+|.|++..|+.|||++|+.+++.+...|..
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~-~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrt 83 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLN-RKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRT 83 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHh-hcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccch
Confidence 5789999999999999999999999999999998 889999999999999999999999999999999999999999999
Q ss_pred HhccCCCCCHHHHHHHHHHHhhhhccCCCC
Q 020613 92 IASHLPGRTDNEIKNYWNSWIKKKIRKPST 121 (323)
Q Consensus 92 IAk~LpgRT~~qcKnRW~~lLkkk~kK~~~ 121 (323)
||..| ||+.+||-.||+.++.....+...
T Consensus 84 Ia~i~-gr~~~qc~eRy~~ll~~~~s~~~~ 112 (617)
T KOG0050|consen 84 IADIM-GRTSQQCLERYNNLLDVYVSYHYH 112 (617)
T ss_pred HHHHh-hhhHHHHHHHHHHHHHHHHhhhcc
Confidence 99999 999999999999999877665544
No 9
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.44 E-value=8.9e-14 Score=143.11 Aligned_cols=105 Identities=29% Similarity=0.588 Sum_probs=94.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhccCCC--CCCCCCCHHHHHHHHHHHH-------
Q 020613 13 KRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYLRPD--IRRGRFTPEEEKLIISLHS------- 83 (323)
Q Consensus 13 kKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p~--ikkg~WT~EED~~Ll~lv~------- 83 (323)
++|+||+||++.|..+|..+| +.|..|+..|+ |.+..||+||.+|...+ .+++.||.||+++|+++|.
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g-~~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~ 459 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHG-NDWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREAL 459 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhc-ccHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhh
Confidence 899999999999999999999 66999999998 99999999999999987 4899999999999999995
Q ss_pred Hh-------C------------CChHHHhccCCCCCHHHHHHHHHHHhhhhccCCC
Q 020613 84 VV-------G------------NRWAHIASHLPGRTDNEIKNYWNSWIKKKIRKPS 120 (323)
Q Consensus 84 ~~-------G------------~kWskIAk~LpgRT~~qcKnRW~~lLkkk~kK~~ 120 (323)
++ | -.|+.|++.+..|+..|||.+|+.++........
T Consensus 460 q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n~~ 515 (607)
T KOG0051|consen 460 QPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFNKR 515 (607)
T ss_pred cccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhhcc
Confidence 33 1 2499999999999999999999999987654433
No 10
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.41 E-value=2.8e-13 Score=96.37 Aligned_cols=46 Identities=28% Similarity=0.641 Sum_probs=42.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCC-hHHHhccCC-CCCHHHHHHHHHHHh
Q 020613 67 RGRFTPEEEKLIISLHSVVGNR-WAHIASHLP-GRTDNEIKNYWNSWI 112 (323)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~G~k-WskIAk~Lp-gRT~~qcKnRW~~lL 112 (323)
|++||+|||++|++++.+||.+ |..||..|+ |||..||++||+.++
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 5799999999999999999998 999999999 999999999999875
No 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=99.36 E-value=1.4e-13 Score=97.90 Aligned_cols=48 Identities=38% Similarity=0.721 Sum_probs=43.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhcc
Q 020613 14 RGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYL 61 (323)
Q Consensus 14 KG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L 61 (323)
|++||+|||++|+++|.+||.++|..||..|+.+||+.||+.||.++|
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 689999999999999999998889999999998999999999999875
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=99.30 E-value=3.3e-12 Score=94.13 Aligned_cols=49 Identities=37% Similarity=0.731 Sum_probs=41.6
Q ss_pred CCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHHhhhhccC
Q 020613 70 FTPEEEKLIISLHSVVGNRWAHIASHLPGRTDNEIKNYWNSWIKKKIRK 118 (323)
Q Consensus 70 WT~EED~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKnRW~~lLkkk~kK 118 (323)
||+|||++|+++|.+||++|..||+.|+.||..+|++||+..|++++++
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~ 49 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKISR 49 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTS
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccccC
Confidence 9999999999999999999999999996699999999999977655443
No 13
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.24 E-value=1.7e-11 Score=84.20 Aligned_cols=47 Identities=43% Similarity=0.863 Sum_probs=44.5
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CChHHHhccCCCCCHHHHHHHHHHHhh
Q 020613 67 RGRFTPEEEKLIISLHSVVG-NRWAHIASHLPGRTDNEIKNYWNSWIK 113 (323)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~G-~kWskIAk~LpgRT~~qcKnRW~~lLk 113 (323)
+++||++||.+|+.++..|| .+|..||..|++||..+|++||+.+++
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
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.23 E-value=1.1e-11 Score=116.04 Aligned_cols=59 Identities=19% Similarity=0.515 Sum_probs=54.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhC-CChHHHhccC-CCCCHHHHHHHHHHHhhhhccCCC
Q 020613 62 RPDIRRGRFTPEEEKLIISLHSVVG-NRWAHIASHL-PGRTDNEIKNYWNSWIKKKIRKPS 120 (323)
Q Consensus 62 ~p~ikkg~WT~EED~~Ll~lv~~~G-~kWskIAk~L-pgRT~~qcKnRW~~lLkkk~kK~~ 120 (323)
++++++++||+|||++|+++|++|| .+|..||+.+ ++||+.|||.||.++|++.+++..
T Consensus 20 K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgp 80 (249)
T PLN03212 20 KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGG 80 (249)
T ss_pred cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCC
Confidence 3678999999999999999999999 5799999998 699999999999999999988754
No 15
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.16 E-value=2.9e-11 Score=112.56 Aligned_cols=60 Identities=15% Similarity=0.341 Sum_probs=54.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCC-ChHHHhccCC-CCCHHHHHHHHHHHhhhhccCCCCC
Q 020613 63 PDIRRGRFTPEEEKLIISLHSVVGN-RWAHIASHLP-GRTDNEIKNYWNSWIKKKIRKPSTV 122 (323)
Q Consensus 63 p~ikkg~WT~EED~~Ll~lv~~~G~-kWskIAk~Lp-gRT~~qcKnRW~~lLkkk~kK~~~~ 122 (323)
+.+.+|+||+|||++|+++|++||. +|..||+.++ +|++++||-||.++|++.+++...+
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT 66 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFS 66 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCC
Confidence 3455799999999999999999995 5999999998 9999999999999999999987653
No 16
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.11 E-value=1.5e-10 Score=78.50 Aligned_cols=44 Identities=34% Similarity=0.739 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHHHHHhC-CChHHHhccCCCCCHHHHHHHHHHHh
Q 020613 69 RFTPEEEKLIISLHSVVG-NRWAHIASHLPGRTDNEIKNYWNSWI 112 (323)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G-~kWskIAk~LpgRT~~qcKnRW~~lL 112 (323)
+||.+||++|+.++.+|| .+|..||+.|++||..+|++||+.++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 89999999999999999999998763
No 17
>PLN03091 hypothetical protein; Provisional
Probab=99.11 E-value=7.3e-11 Score=117.97 Aligned_cols=59 Identities=15% Similarity=0.522 Sum_probs=53.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCC-ChHHHhccC-CCCCHHHHHHHHHHHhhhhccCCC
Q 020613 62 RPDIRRGRFTPEEEKLIISLHSVVGN-RWAHIASHL-PGRTDNEIKNYWNSWIKKKIRKPS 120 (323)
Q Consensus 62 ~p~ikkg~WT~EED~~Ll~lv~~~G~-kWskIAk~L-pgRT~~qcKnRW~~lLkkk~kK~~ 120 (323)
+..+++++||+|||++|+++|++||. +|..||+.+ +||+++|||.||.++|++.++|..
T Consensus 9 KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgp 69 (459)
T PLN03091 9 KQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGT 69 (459)
T ss_pred CCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCC
Confidence 46789999999999999999999995 699999988 599999999999999999887654
No 18
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.02 E-value=1.5e-10 Score=79.49 Aligned_cols=48 Identities=35% Similarity=0.774 Sum_probs=44.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhccC
Q 020613 14 RGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYLR 62 (323)
Q Consensus 14 KG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L~ 62 (323)
++.||++||++|..++..||..+|..||..++ +|++.+|+.||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~-~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELP-GRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcC-CCCHHHHHHHHHHHcC
Confidence 47899999999999999999777999999999 9999999999998764
No 19
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.87 E-value=1e-09 Score=74.35 Aligned_cols=45 Identities=36% Similarity=0.717 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhcc
Q 020613 16 LWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYL 61 (323)
Q Consensus 16 ~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L 61 (323)
.||++||+.|..++.+||..+|..||..++ +|++.+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~-~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELP-GRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcC-CCCHHHHHHHHHHhC
Confidence 599999999999999999778999999999 899999999998753
No 20
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.82 E-value=3.4e-09 Score=109.73 Aligned_cols=103 Identities=26% Similarity=0.423 Sum_probs=85.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHh----CC-------------------CCccccccccCcCcCcccccchhhhccCCCC-CC
Q 020613 12 VKRGLWSPEEDEKLIRYITTH----GY-------------------GCWSEVPEKAGLQRCGKSCRLRWINYLRPDI-RR 67 (323)
Q Consensus 12 vkKG~WT~EEDe~L~~lV~ky----G~-------------------~nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p~i-kk 67 (323)
++-+.|+.+||++|...|..| |- +-|..|...++ -|+.+.++..-++...|-- ++
T Consensus 306 ~~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp-~R~~~siy~~~rR~y~~FE~~r 384 (607)
T KOG0051|consen 306 INLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLP-YRDRKSIYHHLRRAYTPFENKR 384 (607)
T ss_pred hhhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcC-cccchhHHHHHHhcCCcccccc
Confidence 455899999999999999887 11 12677888888 5999998773334334433 99
Q ss_pred CCCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHHhhhhc
Q 020613 68 GRFTPEEEKLIISLHSVVGNRWAHIASHLPGRTDNEIKNYWNSWIKKKI 116 (323)
Q Consensus 68 g~WT~EED~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKnRW~~lLkkk~ 116 (323)
|.||+||++.|..+|.++|+.|..|++.| ||.+.+|+.||+.+++..-
T Consensus 385 g~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~ 432 (607)
T KOG0051|consen 385 GKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGS 432 (607)
T ss_pred CCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhcccc
Confidence 99999999999999999999999999999 9999999999999987653
No 21
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=98.38 E-value=3.2e-08 Score=101.44 Aligned_cols=97 Identities=30% Similarity=0.683 Sum_probs=84.4
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhccCC--CCCCCCCCHHHHHHHHHHHHHhC----
Q 020613 13 KRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYLRP--DIRRGRFTPEEEKLIISLHSVVG---- 86 (323)
Q Consensus 13 kKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p--~ikkg~WT~EED~~Ll~lv~~~G---- 86 (323)
.+|.||++|+..|...+..+| +.|..|...++ |-+..||+||.+|... .+++++|+.||+.+|...+...-
T Consensus 290 ~~~~wt~e~~~eL~~~~~~~~-~~w~~ig~~~~--rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e~~~~~~ 366 (512)
T COG5147 290 QRGKWTKEEEQELAKLVVEHG-GSWTEIGKLLG--RMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNEMRLEAQ 366 (512)
T ss_pred hhccCcccccccccccccccc-chhhHhhhhhc--cCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHHHHHHHh
Confidence 578999999999999999999 56999998887 9999999999999988 68889999999999999887432
Q ss_pred ----CChHHHhccCCCCCHHHHHHHHHHHh
Q 020613 87 ----NRWAHIASHLPGRTDNEIKNYWNSWI 112 (323)
Q Consensus 87 ----~kWskIAk~LpgRT~~qcKnRW~~lL 112 (323)
-.|..|+..++.|...+|+..+..+.
T Consensus 367 ~~~~~~~~li~~~~~~~~~~~~~~~~~~~~ 396 (512)
T COG5147 367 QSSRILWLLIAQNIRNRLQHHCRDKYGVLI 396 (512)
T ss_pred hhhhhhHHHHHHhhhccccCCCCCcccccc
Confidence 24999999999888888887665443
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=97.71 E-value=2.5e-05 Score=58.29 Aligned_cols=49 Identities=12% Similarity=0.289 Sum_probs=43.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCc---cccccccCcCc-Ccccccchhhhcc
Q 020613 13 KRGLWSPEEDEKLIRYITTHGYGCW---SEVPEKAGLQR-CGKSCRLRWINYL 61 (323)
Q Consensus 13 kKG~WT~EEDe~L~~lV~kyG~~nW---~~IA~~l~~~R-t~kQCR~Rw~n~L 61 (323)
++-.||+||..+++++|+.+|.++| +.|++.|...| |..||+.++..|.
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 4568999999999999999998899 99999987566 9999999988764
No 23
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.67 E-value=0.00012 Score=54.60 Aligned_cols=47 Identities=13% Similarity=0.244 Sum_probs=41.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-Ch---HHHhccCC-CC-CHHHHHHHHHHHhh
Q 020613 67 RGRFTPEEEKLIISLHSVVGN-RW---AHIASHLP-GR-TDNEIKNYWNSWIK 113 (323)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~G~-kW---skIAk~Lp-gR-T~~qcKnRW~~lLk 113 (323)
+-.||+||..++++++..+|. +| ..|++.|. .| |..||+.+++.+.-
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 457999999999999999997 99 99999883 45 99999999987653
No 24
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.56 E-value=4.5e-05 Score=78.13 Aligned_cols=56 Identities=29% Similarity=0.607 Sum_probs=51.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHhC-CChHHHhccCCCCCHHHHHHHHHHHhhhhccCCC
Q 020613 65 IRRGRFTPEEEKLIISLHSVVG-NRWAHIASHLPGRTDNEIKNYWNSWIKKKIRKPS 120 (323)
Q Consensus 65 ikkg~WT~EED~~Ll~lv~~~G-~kWskIAk~LpgRT~~qcKnRW~~lLkkk~kK~~ 120 (323)
++-|.|+.-||+.|..+|.+|| +.|++|++.++-.|..||++||..++.+.+++..
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~te 61 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTE 61 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhh
Confidence 5678999999999999999999 5699999999999999999999999999887753
No 25
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.51 E-value=4.1e-05 Score=76.94 Aligned_cols=50 Identities=18% Similarity=0.595 Sum_probs=46.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhcc
Q 020613 11 KVKRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYL 61 (323)
Q Consensus 11 kvkKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L 61 (323)
.+-..-||.+|+-+|++++..||-|||..||.++| .|++.+|+++|.+++
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIG-tKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIG-TKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHc-ccchHHHHHHHHHHH
Confidence 35567899999999999999999999999999999 999999999999965
No 26
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=97.34 E-value=0.00019 Score=63.87 Aligned_cols=50 Identities=22% Similarity=0.365 Sum_probs=44.6
Q ss_pred CCCCCCHHHHHHHHHHHHHhC---C----ChHHHhccCCCCCHHHHHHHHHHHhhhhc
Q 020613 66 RRGRFTPEEEKLIISLHSVVG---N----RWAHIASHLPGRTDNEIKNYWNSWIKKKI 116 (323)
Q Consensus 66 kkg~WT~EED~~Ll~lv~~~G---~----kWskIAk~LpgRT~~qcKnRW~~lLkkk~ 116 (323)
+...||.|||.+|.+.|..|= . -...+++.| +||+..|.-|||..+|+.+
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY 59 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQY 59 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHH
Confidence 567899999999999999883 2 389999999 9999999999999999865
No 27
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.33 E-value=0.00032 Score=70.67 Aligned_cols=49 Identities=27% Similarity=0.458 Sum_probs=44.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhC-CChHHHhccCCCCCHHHHHHHHHHHh
Q 020613 64 DIRRGRFTPEEEKLIISLHSVVG-NRWAHIASHLPGRTDNEIKNYWNSWI 112 (323)
Q Consensus 64 ~ikkg~WT~EED~~Ll~lv~~~G-~kWskIAk~LpgRT~~qcKnRW~~lL 112 (323)
.+-...||.+|+-+|++++..|| ++|..||.++..||..+||.+|.++.
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHH
Confidence 34566899999999999999999 78999999999999999999998775
No 28
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.97 E-value=0.00058 Score=53.38 Aligned_cols=48 Identities=35% Similarity=0.545 Sum_probs=34.9
Q ss_pred CCCCHHHHHHHHHHHHH------hC--C------ChHHHhccC----CCCCHHHHHHHHHHHhhhh
Q 020613 68 GRFTPEEEKLIISLHSV------VG--N------RWAHIASHL----PGRTDNEIKNYWNSWIKKK 115 (323)
Q Consensus 68 g~WT~EED~~Ll~lv~~------~G--~------kWskIAk~L----pgRT~~qcKnRW~~lLkkk 115 (323)
..||.+|...|++++.. ++ . -|..||..| -.||..||++||.++.+.-
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Y 67 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKY 67 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence 47999999999999877 22 1 399999987 3699999999999976553
No 29
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=96.95 E-value=0.0013 Score=50.35 Aligned_cols=51 Identities=18% Similarity=0.375 Sum_probs=33.1
Q ss_pred CCCCCHHHHHHHHHHHHHhC--------CC-hHHHhccCC-CCCHHHHHHHHHHHhhhhcc
Q 020613 67 RGRFTPEEEKLIISLHSVVG--------NR-WAHIASHLP-GRTDNEIKNYWNSWIKKKIR 117 (323)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~G--------~k-WskIAk~Lp-gRT~~qcKnRW~~lLkkk~k 117 (323)
+.+||.|||+.|++.|+++. ++ |..+++.-+ .+|-...|+||...|+.+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~~ 62 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRPR 62 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT-----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcccc
Confidence 45899999999999997653 22 999999877 99999999999988877644
No 30
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=96.89 E-value=0.0038 Score=57.54 Aligned_cols=100 Identities=22% Similarity=0.365 Sum_probs=72.2
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccCc--CcCcccccchhhhccC-CCC--------------------CCCCCCH
Q 020613 16 LWSPEEDEKLIRYITTHGYGCWSEVPEKAGL--QRCGKSCRLRWINYLR-PDI--------------------RRGRFTP 72 (323)
Q Consensus 16 ~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~--~Rt~kQCR~Rw~n~L~-p~i--------------------kkg~WT~ 72 (323)
+|++++|-+|+.+|..-. +-..|+..+.. .-|-..+.+||+..|- |.+ .+.+||.
T Consensus 1 rW~~~DDl~Li~av~~~~--~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~~is~~a~~~m~~l~p~~~~~iq~kalfS~ 78 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTN--DLESVHLGVKFSCKFTLQEIEERWYALLYDPVISRIAVAAMRNLHPELIAAIQSKALFSK 78 (199)
T ss_pred CCCchhhHHHHHHHHHhc--CHHHHHccCCcCCcCcHHHHHHHHHHHHcChhhHHHHHHHHHhCCcchhhcccccCCCCH
Confidence 699999999999998754 35555554432 2366778899998752 222 4568999
Q ss_pred HHHHHHHHHHHHhCC---ChHHHhc-----cCCCCCHHHHHHHHHHHhhhhcc
Q 020613 73 EEEKLIISLHSVVGN---RWAHIAS-----HLPGRTDNEIKNYWNSWIKKKIR 117 (323)
Q Consensus 73 EED~~Ll~lv~~~G~---kWskIAk-----~LpgRT~~qcKnRW~~lLkkk~k 117 (323)
+|+++|......... .+.+|=. +-++||+.++.++|..+.+..+-
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~LL 131 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHLL 131 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhchh
Confidence 999999997765543 3655543 23889999999999977666554
No 31
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.83 E-value=0.0012 Score=67.27 Aligned_cols=46 Identities=17% Similarity=0.331 Sum_probs=43.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHH
Q 020613 66 RRGRFTPEEEKLIISLHSVVGNRWAHIASHLPGRTDNEIKNYWNSW 111 (323)
Q Consensus 66 kkg~WT~EED~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKnRW~~l 111 (323)
....||.+|..+|++.+..||..|.+||+++..||..||--||-++
T Consensus 278 ~dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 3448999999999999999999999999999999999999999865
No 32
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.82 E-value=0.0015 Score=67.49 Aligned_cols=47 Identities=17% Similarity=0.350 Sum_probs=43.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHHh
Q 020613 66 RRGRFTPEEEKLIISLHSVVGNRWAHIASHLPGRTDNEIKNYWNSWI 112 (323)
Q Consensus 66 kkg~WT~EED~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKnRW~~lL 112 (323)
-++.||.+|..+|++++..||.+|.+||.++.+||..||-.+|..+=
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~LP 298 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRLP 298 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhcC
Confidence 45689999999999999999999999999999999999999998763
No 33
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.58 E-value=0.00088 Score=68.20 Aligned_cols=46 Identities=24% Similarity=0.477 Sum_probs=42.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhc
Q 020613 13 KRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINY 60 (323)
Q Consensus 13 kKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~ 60 (323)
....||.+|..+|++.|+.||+ +|.+||.+++ +|+..||..|+.+.
T Consensus 278 ~dk~WS~qE~~LLLEGIe~ygD-dW~kVA~HVg-tKt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYGD-DWDKVARHVG-TKTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhhh-hHHHHHHHhC-CCCHHHHHHHHHcC
Confidence 6679999999999999999995 5999999999 99999999999874
No 34
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.50 E-value=0.0024 Score=57.51 Aligned_cols=51 Identities=22% Similarity=0.327 Sum_probs=43.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCC-------hHHHhccCCCCCHHHHHHHHHHHhhhhc
Q 020613 65 IRRGRFTPEEEKLIISLHSVVGNR-------WAHIASHLPGRTDNEIKNYWNSWIKKKI 116 (323)
Q Consensus 65 ikkg~WT~EED~~Ll~lv~~~G~k-------WskIAk~LpgRT~~qcKnRW~~lLkkk~ 116 (323)
.+.+.||.|||.+|-+.|..|+.. ...++..| +||..+|..||+.++++++
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Y 60 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQY 60 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHH
Confidence 356789999999999999888743 77777888 9999999999999998754
No 35
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.42 E-value=0.0022 Score=66.37 Aligned_cols=49 Identities=22% Similarity=0.524 Sum_probs=44.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhc
Q 020613 10 QKVKRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINY 60 (323)
Q Consensus 10 ~kvkKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~ 60 (323)
...-++.||.+|+-+|+++|++||+ +|.+||.+++ .|+..||..++.+.
T Consensus 249 ~~~~~~~WT~qE~lLLLE~ie~y~d-dW~kVa~hVg-~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 249 GESARPNWTEQETLLLLEAIEMYGD-DWNKVADHVG-TKSQEQCILKFLRL 297 (506)
T ss_pred cccCCCCccHHHHHHHHHHHHHhcc-cHHHHHhccC-CCCHHHHHHHHHhc
Confidence 3456789999999999999999995 5999999999 99999999998774
No 36
>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=96.38 E-value=0.00097 Score=59.45 Aligned_cols=51 Identities=31% Similarity=0.635 Sum_probs=43.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHh---CCC---CccccccccCcCcCcccccchhhhccCC
Q 020613 11 KVKRGLWSPEEDEKLIRYITTH---GYG---CWSEVPEKAGLQRCGKSCRLRWINYLRP 63 (323)
Q Consensus 11 kvkKG~WT~EEDe~L~~lV~ky---G~~---nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p 63 (323)
+.++..||.|||.+|.+.|-+| |.. ...+|+..++ ||+..|.-||..+++.
T Consensus 1 ~~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~--RTsAACGFRWNs~VRk 57 (161)
T TIGR02894 1 KTRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN--RTAAACGFRWNAYVRK 57 (161)
T ss_pred CccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc--ccHHHhcchHHHHHHH
Confidence 3678899999999999999998 211 3778888887 9999999999998863
No 37
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=96.12 E-value=0.0018 Score=49.65 Aligned_cols=52 Identities=29% Similarity=0.486 Sum_probs=33.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCC------C--CccccccccCcCcCcccccchhhhccCCCC
Q 020613 14 RGLWSPEEDEKLIRYITTHGY------G--CWSEVPEKAGLQRCGKSCRLRWINYLRPDI 65 (323)
Q Consensus 14 KG~WT~EEDe~L~~lV~kyG~------~--nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p~i 65 (323)
|-+||.+||+.|.+.|..+.. | -|.++++.-+..++..+-|+||.+.|.+..
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 457999999999999976521 2 299998887667899999999999987643
No 38
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=95.80 E-value=0.0025 Score=49.74 Aligned_cols=48 Identities=31% Similarity=0.613 Sum_probs=33.2
Q ss_pred CCCCCHHHHHHHHHHHHH--h----C--CC-----Ccccccccc---CcCcCcccccchhhhcc
Q 020613 14 RGLWSPEEDEKLIRYITT--H----G--YG-----CWSEVPEKA---GLQRCGKSCRLRWINYL 61 (323)
Q Consensus 14 KG~WT~EEDe~L~~lV~k--y----G--~~-----nW~~IA~~l---~~~Rt~kQCR~Rw~n~L 61 (323)
|..||.+|...|+.++.. + + .. -|..||..| |..|++.||+.||.+..
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 457999999999999987 2 1 11 399999987 45799999999998853
No 39
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.77 E-value=0.013 Score=45.06 Aligned_cols=49 Identities=27% Similarity=0.515 Sum_probs=40.7
Q ss_pred CCCCCHHHHHHHHHHHHHhC----C-------------ChHHHhccC-----CCCCHHHHHHHHHHHhhhh
Q 020613 67 RGRFTPEEEKLIISLHSVVG----N-------------RWAHIASHL-----PGRTDNEIKNYWNSWIKKK 115 (323)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~G----~-------------kWskIAk~L-----pgRT~~qcKnRW~~lLkkk 115 (323)
...||.+|.+.|++++.+|. + -|..|+..| +.||..++|.+|.++...-
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~ 72 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKA 72 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHH
Confidence 45799999999999998873 1 299999976 3699999999999987553
No 40
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=94.93 E-value=0.027 Score=55.45 Aligned_cols=47 Identities=26% Similarity=0.451 Sum_probs=42.9
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CChHHHhccCCCCCHHHHHHHHHHHhh
Q 020613 67 RGRFTPEEEKLIISLHSVVG-NRWAHIASHLPGRTDNEIKNYWNSWIK 113 (323)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~G-~kWskIAk~LpgRT~~qcKnRW~~lLk 113 (323)
-..|+.+|+.+|++.+...| .+|..||.+++.|+...||.+|..+..
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 44799999999999999999 789999999999999999999987654
No 41
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=94.81 E-value=0.0073 Score=54.44 Aligned_cols=50 Identities=26% Similarity=0.521 Sum_probs=39.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCC------ccccccccCcCcCcccccchhhhccC
Q 020613 11 KVKRGLWSPEEDEKLIRYITTHGYGC------WSEVPEKAGLQRCGKSCRLRWINYLR 62 (323)
Q Consensus 11 kvkKG~WT~EEDe~L~~lV~kyG~~n------W~~IA~~l~~~Rt~kQCR~Rw~n~L~ 62 (323)
+.++..||.|||.+|.+.|-+|+... ...++..+. |++..|..||..+++
T Consensus 2 k~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~--rt~aac~fRwNs~vr 57 (170)
T PRK13923 2 KTRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALK--RTAAACGFRWNSVVR 57 (170)
T ss_pred cchhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHh--hhHHHHHhHHHHHHH
Confidence 46889999999999999999986442 445555565 999999999976665
No 42
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=94.71 E-value=0.01 Score=58.40 Aligned_cols=50 Identities=20% Similarity=0.526 Sum_probs=45.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhccC
Q 020613 12 VKRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYLR 62 (323)
Q Consensus 12 vkKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L~ 62 (323)
+---.|+..|+-+|+++....|.|||..||..+| .|+...|+++|..++.
T Consensus 61 I~~e~WgadEEllli~~~~TlGlGNW~dIadyiG-sr~kee~k~HylK~y~ 110 (432)
T COG5114 61 IGEEGWGADEELLLIECLDTLGLGNWEDIADYIG-SRAKEEIKSHYLKMYD 110 (432)
T ss_pred ccCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHh-hhhhHHHHHHHHHHHh
Confidence 3445799999999999999999999999999999 9999999999998765
No 43
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=93.96 E-value=0.11 Score=58.35 Aligned_cols=98 Identities=13% Similarity=0.305 Sum_probs=75.4
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccc-------hhhhc----------------------------
Q 020613 16 LWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRL-------RWINY---------------------------- 60 (323)
Q Consensus 16 ~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~-------Rw~n~---------------------------- 60 (323)
.|+.-+=..++.+..+||..+...||..+. +++...++. ||...
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~-~k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~~ 904 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEME-GKTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAIG 904 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhc-CCCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 488888888888899999889999999997 777776652 22111
Q ss_pred --------------c-CCCCCCCCCCHHHHHHHHHHHHHhC-CChHHHhcc------------CCCCCHHHHHHHHHHHh
Q 020613 61 --------------L-RPDIRRGRFTPEEEKLIISLHSVVG-NRWAHIASH------------LPGRTDNEIKNYWNSWI 112 (323)
Q Consensus 61 --------------L-~p~ikkg~WT~EED~~Ll~lv~~~G-~kWskIAk~------------LpgRT~~qcKnRW~~lL 112 (323)
+ .+..++..||.|||..|+-.+.+|| .+|.+|-.. +..||+..+..|...++
T Consensus 905 ~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~ 984 (1033)
T PLN03142 905 KKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLI 984 (1033)
T ss_pred HHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHH
Confidence 0 1223345699999999999999999 679999432 35799999999999988
Q ss_pred hh
Q 020613 113 KK 114 (323)
Q Consensus 113 kk 114 (323)
+-
T Consensus 985 ~~ 986 (1033)
T PLN03142 985 RL 986 (1033)
T ss_pred HH
Confidence 64
No 44
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=93.86 E-value=0.015 Score=44.65 Aligned_cols=49 Identities=27% Similarity=0.490 Sum_probs=39.5
Q ss_pred CCCCCCHHHHHHHHHHHHHh-----CC-----------CCccccccccC----cCcCcccccchhhhcc
Q 020613 13 KRGLWSPEEDEKLIRYITTH-----GY-----------GCWSEVPEKAG----LQRCGKSCRLRWINYL 61 (323)
Q Consensus 13 kKG~WT~EEDe~L~~lV~ky-----G~-----------~nW~~IA~~l~----~~Rt~kQCR~Rw~n~L 61 (323)
++..||.+|.+.|+++|.+| +. .-|..|+..+. ..|+..+++.+|.++.
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 46789999999999999988 21 13999988772 2699999999998864
No 45
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=93.76 E-value=0.064 Score=53.98 Aligned_cols=83 Identities=19% Similarity=0.300 Sum_probs=61.9
Q ss_pred CccccccccCcCcCcccccchhhhccCCC-------------------------CCCCCCCHHHHHHHHHHHHHhCCChH
Q 020613 36 CWSEVPEKAGLQRCGKSCRLRWINYLRPD-------------------------IRRGRFTPEEEKLIISLHSVVGNRWA 90 (323)
Q Consensus 36 nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p~-------------------------ikkg~WT~EED~~Ll~lv~~~G~kWs 90 (323)
.|..++-..+ .|...--..+|....++. ++...||.+|-+-|+++++.|.-+|-
T Consensus 75 ~W~w~pFtn~-aRkD~~~l~HWvr~~d~~~dypfakfNk~vdipsYt~eEYe~~l~dn~WskeETD~LF~lck~fDLRf~ 153 (445)
T KOG2656|consen 75 PWKWVPFTNS-ARKDDATLHHWVRVGDTPKDYPFAKFNKHVDIPSYTDEEYEAHLNDNSWSKEETDYLFDLCKRFDLRFF 153 (445)
T ss_pred CceeeccCCc-cccCCceEEeeeeccCCCCCCchhhhccccCccccchHHHHHhhccccccHHHHHHHHHHHHhcCeeEE
Confidence 4766654444 565555555666552211 12346999999999999999999999
Q ss_pred HHhcc-----CCC-CCHHHHHHHHHHHhhhhccCC
Q 020613 91 HIASH-----LPG-RTDNEIKNYWNSWIKKKIRKP 119 (323)
Q Consensus 91 kIAk~-----Lpg-RT~~qcKnRW~~lLkkk~kK~ 119 (323)
.||.. ++. ||-.++|.||+...++-++-.
T Consensus 154 VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr 188 (445)
T KOG2656|consen 154 VIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKAR 188 (445)
T ss_pred EEeeccchhhccccccHHHHHHHHHHHHHHHHHcc
Confidence 99987 655 999999999999988766543
No 46
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=92.67 E-value=0.21 Score=48.79 Aligned_cols=50 Identities=22% Similarity=0.345 Sum_probs=40.5
Q ss_pred CCCCCHHHHHHHHHHHHHh----------CCChHHHhccC----CCCCHHHHHHHHHHHhhhhc
Q 020613 67 RGRFTPEEEKLIISLHSVV----------GNRWAHIASHL----PGRTDNEIKNYWNSWIKKKI 116 (323)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~----------G~kWskIAk~L----pgRT~~qcKnRW~~lLkkk~ 116 (323)
...|+.+|-..||++..+. +..|..||+.+ --||+.+||+||.++.++..
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk 117 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYK 117 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHH
Confidence 3689999999999987653 23499999965 35999999999999876643
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=92.11 E-value=0.35 Score=38.06 Aligned_cols=46 Identities=30% Similarity=0.620 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHHh---CC----------ChHHHhccC---C--CCCHHHHHHHHHHHhhh
Q 020613 69 RFTPEEEKLIISLHSVV---GN----------RWAHIASHL---P--GRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 69 ~WT~EED~~Ll~lv~~~---G~----------kWskIAk~L---p--gRT~~qcKnRW~~lLkk 114 (323)
.||+++++.|++++.+. |+ .|..|++.| . ..+..||++||..+.+.
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 49999999999998553 21 299999977 2 34789999999887665
No 48
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=91.72 E-value=0.21 Score=42.58 Aligned_cols=52 Identities=21% Similarity=0.460 Sum_probs=41.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC----ChHHHhccC------------CCCCHHHHHHHHHHHhhhh
Q 020613 64 DIRRGRFTPEEEKLIISLHSVVGN----RWAHIASHL------------PGRTDNEIKNYWNSWIKKK 115 (323)
Q Consensus 64 ~ikkg~WT~EED~~Ll~lv~~~G~----kWskIAk~L------------pgRT~~qcKnRW~~lLkkk 115 (323)
..++..||++||.-|+-++.+||- .|..|...+ ..||+..+..|-..+++--
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i 113 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLI 113 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHH
Confidence 556779999999999999999996 698887632 4699999999999998753
No 49
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=90.76 E-value=0.38 Score=48.56 Aligned_cols=46 Identities=24% Similarity=0.289 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHHhh
Q 020613 68 GRFTPEEEKLIISLHSVVGNRWAHIASHLPGRTDNEIKNYWNSWIK 113 (323)
Q Consensus 68 g~WT~EED~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKnRW~~lLk 113 (323)
.+||.+|-++..++...+|..++.||..+|.|...|||.+|.+--+
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek 411 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEK 411 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhh
Confidence 4799999999999999999999999999999999999999976443
No 50
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=87.84 E-value=1.3 Score=31.42 Aligned_cols=42 Identities=31% Similarity=0.404 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 72 PEEEKLIISLHSVVGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 72 ~EED~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
++++..++.++...|-.|.+||+.+ |.|...|+.+....+++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARKK 53 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHhh
Confidence 4678888899999999999999999 99999999998876653
No 51
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=86.94 E-value=1.7 Score=44.89 Aligned_cols=49 Identities=24% Similarity=0.421 Sum_probs=44.5
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 66 RRGRFTPEEEKLIISLHSVVGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 66 kkg~WT~EED~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
-...||.||--++-++...||++..+|-+.||.|+-..+...|+...+.
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK~ 234 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKKT 234 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHHH
Confidence 4567999999999999999999999999999999999999999877654
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=81.57 E-value=1.1 Score=38.10 Aligned_cols=34 Identities=29% Similarity=0.614 Sum_probs=28.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC---CCcccccccc
Q 020613 11 KVKRGLWSPEEDEKLIRYITTHGY---GCWSEVPEKA 44 (323)
Q Consensus 11 kvkKG~WT~EEDe~L~~lV~kyG~---~nW~~IA~~l 44 (323)
.-+++.||.+||..|+-.+.+||. +.|..|-..+
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 557889999999999999999999 7898886654
No 53
>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=80.92 E-value=0.89 Score=36.26 Aligned_cols=29 Identities=38% Similarity=0.736 Sum_probs=17.4
Q ss_pred CCCCCCCCHHHHHHH--------HHHHHHhCCCCcccccc
Q 020613 11 KVKRGLWSPEEDEKL--------IRYITTHGYGCWSEVPE 42 (323)
Q Consensus 11 kvkKG~WT~EEDe~L--------~~lV~kyG~~nW~~IA~ 42 (323)
.-..|-||+++|+.| .+++++|| +..|+.
T Consensus 44 ~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG---~~~i~~ 80 (87)
T PF11626_consen 44 DNMPGIWTPEDDEMLRSGDKDDIERLIKKHG---EERIER 80 (87)
T ss_dssp TT-TT---HHHHHHHTS--HHHHHHHHHHH----HHHHHH
T ss_pred CCCCCCcCHHHHHHHHcCCHHHHHHHHHHhC---HHHHHH
Confidence 345789999999999 55777888 556654
No 54
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=78.18 E-value=3.4 Score=44.97 Aligned_cols=47 Identities=19% Similarity=0.376 Sum_probs=43.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHHhh
Q 020613 67 RGRFTPEEEKLIISLHSVVGNRWAHIASHLPGRTDNEIKNYWNSWIK 113 (323)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKnRW~~lLk 113 (323)
...||+.|-.+.-+++-.|.+++-.|++.++++|-.||-..|+.+.|
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 34799999999999999999999999999999999999998887654
No 55
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=77.56 E-value=1 Score=44.10 Aligned_cols=47 Identities=32% Similarity=0.455 Sum_probs=37.4
Q ss_pred CCCCHHHHHHHHHHHHHh----CC-----CCcccccccc---CcCcCcccccchhhhcc
Q 020613 15 GLWSPEEDEKLIRYITTH----GY-----GCWSEVPEKA---GLQRCGKSCRLRWINYL 61 (323)
Q Consensus 15 G~WT~EEDe~L~~lV~ky----G~-----~nW~~IA~~l---~~~Rt~kQCR~Rw~n~L 61 (323)
..|+.+|-..|+++..+. .. .-|..||..+ +..|++.||+.||.+..
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 789999999999988643 11 2499999854 44699999999998864
No 56
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=74.47 E-value=4.4 Score=43.33 Aligned_cols=49 Identities=16% Similarity=0.455 Sum_probs=40.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChHHHh----------ccCCCCCHHHHHHHHHHHhhhh
Q 020613 67 RGRFTPEEEKLIISLHSVVGNRWAHIA----------SHLPGRTDNEIKNYWNSWIKKK 115 (323)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~G~kWskIA----------k~LpgRT~~qcKnRW~~lLkkk 115 (323)
+..||-.|+.-...+.+++|++..+|- ....-+|..|++.+|+..+++.
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m 146 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRM 146 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHH
Confidence 668999999999999999999999992 2334468889999999887663
No 57
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=71.88 E-value=7.9 Score=26.92 Aligned_cols=38 Identities=21% Similarity=0.378 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHhCC-ChHHHhccCCCCCHHHHHHHHHHH
Q 020613 73 EEEKLIISLHSVVGN-RWAHIASHLPGRTDNEIKNYWNSW 111 (323)
Q Consensus 73 EED~~Ll~lv~~~G~-kWskIAk~LpgRT~~qcKnRW~~l 111 (323)
+=|..|+.+...-|. .|..||+.+ |=|...|..|+..+
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 457888888888775 599999999 99999999998764
No 58
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=71.28 E-value=9.3 Score=26.68 Aligned_cols=41 Identities=24% Similarity=0.348 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 73 EEEKLIISLHSVVGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 73 EED~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
+++..++.+.-..|..+..||+.| |-|...|+.+....+++
T Consensus 7 ~~er~vi~~~y~~~~t~~eIa~~l-g~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 7 PREREVIRLRYFEGLTLEEIAERL-GISRSTVRRILKRALKK 47 (50)
T ss_dssp HHHHHHHHHHHTST-SHHHHHHHH-TSCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHH-CCcHHHHHHHHHHHHHH
Confidence 456666666666677899999999 99999999998887765
No 59
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=68.37 E-value=10 Score=32.85 Aligned_cols=46 Identities=13% Similarity=0.114 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHHHhCC-ChHHHhccCCCCCHHHHHHHHHHHhhhhccC
Q 020613 72 PEEEKLIISLHSVVGN-RWAHIASHLPGRTDNEIKNYWNSWIKKKIRK 118 (323)
Q Consensus 72 ~EED~~Ll~lv~~~G~-kWskIAk~LpgRT~~qcKnRW~~lLkkk~kK 118 (323)
.+-|.+|+.+..+-|. .|+.||+.+ |-|...|+.|++.+....+-+
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGIIT 54 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 3578888888888775 699999999 999999999999998887654
No 60
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=67.95 E-value=3.8 Score=41.63 Aligned_cols=109 Identities=18% Similarity=0.216 Sum_probs=69.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhc--cCCC-----C-CCCCCCHHHHHHHHHH-
Q 020613 11 KVKRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINY--LRPD-----I-RRGRFTPEEEKLIISL- 81 (323)
Q Consensus 11 kvkKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~--L~p~-----i-kkg~WT~EED~~Ll~l- 81 (323)
+..--+||.+|-+++.+++...|. +..-|+..+| +|..+|+..+|.+- .+|. + .+.|+..+|--.+...
T Consensus 362 ~~~~~~Ws~~e~ekFYKALs~wGt-dF~LIs~lfP-~R~RkqIKaKfi~Eek~nP~rIn~aL~~kkp~d~~eY~k~~~~~ 439 (507)
T COG5118 362 KKGALRWSKKEIEKFYKALSIWGT-DFSLISSLFP-NRERKQIKAKFIKEEKVNPERINEALNEKKPFDQVEYNKLRSYL 439 (507)
T ss_pred CCCCCcccHHHHHHHHHHHHHhcc-hHHHHHHhcC-chhHHHHHHHHHHHhhhCHHHHHHHHhccCCCCHHHHhhHHHHH
Confidence 344558999999999999999995 4999999999 99999999998874 2221 1 2457777776443322
Q ss_pred ---HHHhCCChHHHhccC--CCCCHHHHHHHHHHHhhhhccCCCC
Q 020613 82 ---HSVVGNRWAHIASHL--PGRTDNEIKNYWNSWIKKKIRKPST 121 (323)
Q Consensus 82 ---v~~~G~kWskIAk~L--pgRT~~qcKnRW~~lLkkk~kK~~~ 121 (323)
+.++.+--..|-+.+ ..|+...+-.--+.+....+.+.+.
T Consensus 440 ~e~l~Elq~E~k~~~~~~EE~k~~A~E~~q~~Q~l~~~~L~k~~~ 484 (507)
T COG5118 440 LEKLIELQNEHKHHMKEIEEAKNTAKEEDQTAQRLNDANLNKKGS 484 (507)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhhhhhhccCC
Confidence 122222223333333 2456665555555555555555443
No 61
>smart00595 MADF subfamily of SANT domain.
Probab=64.17 E-value=6.5 Score=30.46 Aligned_cols=26 Identities=31% Similarity=0.636 Sum_probs=22.3
Q ss_pred ChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 88 RWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 88 kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
-|..||..| |-|..+|+.+|+++...
T Consensus 29 aW~~Ia~~l-~~~~~~~~~kw~~LR~~ 54 (89)
T smart00595 29 AWEEIAEEL-GLSVEECKKRWKNLRDR 54 (89)
T ss_pred HHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 399999999 55999999999988543
No 62
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=63.10 E-value=12 Score=32.84 Aligned_cols=46 Identities=7% Similarity=0.049 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHHHhCC-ChHHHhccCCCCCHHHHHHHHHHHhhhhccC
Q 020613 72 PEEEKLIISLHSVVGN-RWAHIASHLPGRTDNEIKNYWNSWIKKKIRK 118 (323)
Q Consensus 72 ~EED~~Ll~lv~~~G~-kWskIAk~LpgRT~~qcKnRW~~lLkkk~kK 118 (323)
.+-|.+|+.+..+-|+ .|+.||+.+ |-|...|+.|++.+.+..+-+
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCeE
Confidence 5678888888877775 699999999 999999999999999887654
No 63
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=62.65 E-value=13 Score=37.66 Aligned_cols=47 Identities=19% Similarity=0.335 Sum_probs=42.4
Q ss_pred CCCCHHHHHHHHHHHHHhCCChHHHhc-cCCCCCHHHHHHHHHHHhhh
Q 020613 68 GRFTPEEEKLIISLHSVVGNRWAHIAS-HLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 68 g~WT~EED~~Ll~lv~~~G~kWskIAk-~LpgRT~~qcKnRW~~lLkk 114 (323)
..|+++|-+..-+..+.||+....|.+ +++.|+--.|-..|+.+.+.
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWKkS 325 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWKKS 325 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhhcC
Confidence 379999999999999999999999987 68999999999998877654
No 64
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=62.50 E-value=4.8 Score=31.51 Aligned_cols=45 Identities=24% Similarity=0.593 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHHHHHh---CC----C-----CccccccccC----cCcCcccccchhhhc
Q 020613 16 LWSPEEDEKLIRYITTH---GY----G-----CWSEVPEKAG----LQRCGKSCRLRWINY 60 (323)
Q Consensus 16 ~WT~EEDe~L~~lV~ky---G~----~-----nW~~IA~~l~----~~Rt~kQCR~Rw~n~ 60 (323)
.||+++++.|++++... |. + .|..|+..|. ...+..||+.||...
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~l 61 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTL 61 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHH
Confidence 59999999999988654 21 1 2777777663 245667777776543
No 65
>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=60.06 E-value=17 Score=30.06 Aligned_cols=36 Identities=22% Similarity=0.319 Sum_probs=27.6
Q ss_pred HHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 78 IISLHSVVGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 78 Ll~lv~~~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
++.+.-..|-.+..||+.+ |.|...|+.+....+++
T Consensus 121 il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 121 IFILSRFEGKSYKEIAEEL-GISVKTVEYHISKALKE 156 (161)
T ss_pred HHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3333334477899999999 99999999999886544
No 66
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=58.18 E-value=11 Score=40.05 Aligned_cols=47 Identities=19% Similarity=0.324 Sum_probs=42.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHH
Q 020613 65 IRRGRFTPEEEKLIISLHSVVGNRWAHIASHLPGRTDNEIKNYWNSW 111 (323)
Q Consensus 65 ikkg~WT~EED~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKnRW~~l 111 (323)
...++|+.+|-++...+....|.+.+.|+..+|+|+..|||.+|..-
T Consensus 407 ~~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~e 453 (584)
T KOG2009|consen 407 LETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKE 453 (584)
T ss_pred cccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhh
Confidence 34568999999999999999999999999999999999999988653
No 67
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=57.70 E-value=11 Score=33.56 Aligned_cols=42 Identities=21% Similarity=0.214 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHH
Q 020613 69 RFTPEEEKLIISLHSVVGNRWAHIASHLPGRTDNEIKNYWNSW 111 (323)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKnRW~~l 111 (323)
.||+|+.++|.+|..+ |-.=++||+.|.|.|.+.|.-+-+.+
T Consensus 2 ~Wtde~~~~L~~lw~~-G~SasqIA~~lg~vsRnAViGk~hRl 43 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GLSASQIARQLGGVSRNAVIGKAHRL 43 (162)
T ss_pred CCCHHHHHHHHHHHHc-CCCHHHHHHHhCCcchhhhhhhhhcc
Confidence 5999999999988755 77889999999779999998876654
No 68
>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=56.50 E-value=5.1 Score=31.88 Aligned_cols=17 Identities=35% Similarity=0.749 Sum_probs=10.2
Q ss_pred CCCCCCCCCHHHHHHHH
Q 020613 63 PDIRRGRFTPEEEKLII 79 (323)
Q Consensus 63 p~ikkg~WT~EED~~Ll 79 (323)
|....|-||+|+|+.|.
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 55678899999999994
No 69
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=55.01 E-value=25 Score=32.72 Aligned_cols=44 Identities=23% Similarity=0.348 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhccC---CCCCHHHHHHHHHHHhh
Q 020613 69 RFTPEEEKLIISLHSVVGNRWAHIASHL---PGRTDNEIKNYWNSWIK 113 (323)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kWskIAk~L---pgRT~~qcKnRW~~lLk 113 (323)
.|++++|-+|+.+|.. |+.-..|++-+ -.-|-..|..||+.+|-
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~lly 47 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALLY 47 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHHc
Confidence 5999999999998865 55566666533 44588999999999984
No 70
>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=53.88 E-value=17 Score=29.12 Aligned_cols=29 Identities=21% Similarity=0.526 Sum_probs=24.2
Q ss_pred HHHHHHHHHHhCCChHHHhccCCCCCHHHH
Q 020613 75 EKLIISLHSVVGNRWAHIASHLPGRTDNEI 104 (323)
Q Consensus 75 D~~Ll~lv~~~G~kWskIAk~LpgRT~~qc 104 (323)
|+.|..++...|..|..+|..| |=|..+|
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I 30 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDI 30 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 5678899999999999999999 6666554
No 71
>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=53.67 E-value=28 Score=27.24 Aligned_cols=38 Identities=13% Similarity=0.323 Sum_probs=27.1
Q ss_pred HHHHHHHHhC--------CChHHHhccCCC---CC--HHHHHHHHHHHhhh
Q 020613 77 LIISLHSVVG--------NRWAHIASHLPG---RT--DNEIKNYWNSWIKK 114 (323)
Q Consensus 77 ~Ll~lv~~~G--------~kWskIAk~Lpg---RT--~~qcKnRW~~lLkk 114 (323)
.|..+|.+.| ++|..||+.|.- -+ ..++|..|..+|..
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 4667777776 369999999822 12 36799999888753
No 72
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=53.42 E-value=15 Score=42.34 Aligned_cols=74 Identities=19% Similarity=0.282 Sum_probs=46.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhccCCCCCCCCCCHHHHHHHHHHHHHh-CCChHH
Q 020613 13 KRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYLRPDIRRGRFTPEEEKLIISLHSVV-GNRWAH 91 (323)
Q Consensus 13 kKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p~ikkg~WT~EED~~Ll~lv~~~-G~kWsk 91 (323)
.---|..++|..|+-.|-+||.++|..|-. ......-=...+...+-.+.|=..+-..|+.+...+ +.+|.+
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir~-------Dp~L~l~dKi~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~ 1204 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIRL-------DPDLGLTDKIFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPK 1204 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhcc-------CccccchhhhcccccCCchHHHHHHHHHHHHHHhhcccCCCch
Confidence 345799999999999999999999998832 111111001122222445566667777777777666 444544
Q ss_pred Hh
Q 020613 92 IA 93 (323)
Q Consensus 92 IA 93 (323)
.+
T Consensus 1205 ~~ 1206 (1373)
T KOG0384|consen 1205 KL 1206 (1373)
T ss_pred hh
Confidence 43
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=52.92 E-value=5.7 Score=27.65 Aligned_cols=38 Identities=26% Similarity=0.435 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhh
Q 020613 20 EEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWIN 59 (323)
Q Consensus 20 EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n 59 (323)
+=|.+|+.+++..+...|.+||+.+| =+...|+.|+..
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lg--lS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELG--LSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHT--S-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHC--cCHHHHHHHHHH
Confidence 45889999999999889999999998 778888888754
No 74
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=52.31 E-value=7.5 Score=42.51 Aligned_cols=45 Identities=13% Similarity=0.181 Sum_probs=39.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhh
Q 020613 13 KRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWIN 59 (323)
Q Consensus 13 kKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n 59 (323)
-...||+.|-.++.+++-.|. ++...|++.+. +++.+||-+-|+.
T Consensus 618 gSd~WTp~E~~lF~kA~y~~~-KDF~~v~km~~-~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 618 GSDKWTPLERKLFNKALYTYS-KDFIFVQKMVK-SKTVAQCVEYYYT 662 (907)
T ss_pred CcccccHHHHHHHHHHHHHhc-ccHHHHHHHhc-cccHHHHHHHHHH
Confidence 345899999999999999998 66999999998 9999999987754
No 75
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=50.28 E-value=32 Score=27.25 Aligned_cols=38 Identities=16% Similarity=0.362 Sum_probs=27.7
Q ss_pred HHHHHHHHhC--------CChHHHhccCCC-----CCHHHHHHHHHHHhhh
Q 020613 77 LIISLHSVVG--------NRWAHIASHLPG-----RTDNEIKNYWNSWIKK 114 (323)
Q Consensus 77 ~Ll~lv~~~G--------~kWskIAk~Lpg-----RT~~qcKnRW~~lLkk 114 (323)
.|..+|.+.| +.|..||+.|.- ....++|..|..+|.+
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~ 86 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLP 86 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHH
Confidence 3666677766 369999998822 2357889999888765
No 76
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=49.93 E-value=8 Score=33.45 Aligned_cols=45 Identities=11% Similarity=0.172 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhccCCCC
Q 020613 19 PEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYLRPDI 65 (323)
Q Consensus 19 ~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p~i 65 (323)
.+-|.+|+.++++.|...|.+||+.++ -+...|+.|+.+..+.++
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lg--lS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFG--VSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 357999999999999889999999998 889999999988766554
No 77
>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=49.20 E-value=24 Score=28.15 Aligned_cols=31 Identities=19% Similarity=0.374 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhCCChHHHhccCCCCCHHHHHH
Q 020613 75 EKLIISLHSVVGNRWAHIASHLPGRTDNEIKN 106 (323)
Q Consensus 75 D~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKn 106 (323)
|..|..+....|..|..+|+.| |=+..+|..
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 6678888999999999999999 766665543
No 78
>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=48.17 E-value=49 Score=33.05 Aligned_cols=48 Identities=23% Similarity=0.495 Sum_probs=37.1
Q ss_pred CCCCCHHHHHHHHHHHHHh-CCC---hHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 67 RGRFTPEEEKLIISLHSVV-GNR---WAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~-G~k---WskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
-..||.-|...|+++.... |.. -..|++.++||+..+|++.-+.+..+
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~r 72 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGR 72 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHH
Confidence 3479999999888887654 433 57889999999999999966655433
No 79
>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=47.02 E-value=33 Score=27.40 Aligned_cols=34 Identities=26% Similarity=0.254 Sum_probs=26.5
Q ss_pred HHHHHhCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 80 SLHSVVGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 80 ~lv~~~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
.++-..|..+..||+.+ |-|...|+++....+++
T Consensus 120 ~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 120 VLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred hhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 33334578899999999 78999999988886554
No 80
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=45.00 E-value=49 Score=26.27 Aligned_cols=45 Identities=16% Similarity=0.180 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHhCC-ChHHHhccCCCCCHHHHHHHHHHHhhhhccC
Q 020613 73 EEEKLIISLHSVVGN-RWAHIASHLPGRTDNEIKNYWNSWIKKKIRK 118 (323)
Q Consensus 73 EED~~Ll~lv~~~G~-kWskIAk~LpgRT~~qcKnRW~~lLkkk~kK 118 (323)
+.|..|+.+..+.|. .++.||+.+ |-+...|+.|.+.+.+..+-+
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 568888888888774 699999999 999999999999998877544
No 81
>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=44.43 E-value=19 Score=26.87 Aligned_cols=27 Identities=22% Similarity=0.484 Sum_probs=21.9
Q ss_pred ChHHHhccCCC-CCHHHHHHHHHHHhhh
Q 020613 88 RWAHIASHLPG-RTDNEIKNYWNSWIKK 114 (323)
Q Consensus 88 kWskIAk~Lpg-RT~~qcKnRW~~lLkk 114 (323)
-|..||..|.+ -+..+|+.||.++...
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~ 55 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRDR 55 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHHH
Confidence 49999999943 5788999999987653
No 82
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=43.85 E-value=7.5 Score=34.08 Aligned_cols=45 Identities=16% Similarity=0.207 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhccCCCC
Q 020613 19 PEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYLRPDI 65 (323)
Q Consensus 19 ~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p~i 65 (323)
.+-|.+|+.+.++.|.-.|.+||+.++ -+...|+.|+.+..+.++
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 567899999999999889999999998 788889999988766654
No 83
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=43.46 E-value=24 Score=27.65 Aligned_cols=29 Identities=21% Similarity=0.647 Sum_probs=23.5
Q ss_pred HHHHHHHHHHhCCChHHHhccCCCCCHHHH
Q 020613 75 EKLIISLHSVVGNRWAHIASHLPGRTDNEI 104 (323)
Q Consensus 75 D~~Ll~lv~~~G~kWskIAk~LpgRT~~qc 104 (323)
|..|..+++..|..|.++|+.| |=+..+|
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI 32 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDI 32 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHH
Confidence 4567888899999999999999 6665544
No 84
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=41.74 E-value=51 Score=27.83 Aligned_cols=31 Identities=13% Similarity=0.132 Sum_probs=24.6
Q ss_pred HHhCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 83 SVVGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 83 ~~~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
...|-.+..||+.| |.+...|+.+....+++
T Consensus 141 ~~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 171 (182)
T PRK09652 141 EIEGLSYEEIAEIM-GCPIGTVRSRIFRAREA 171 (182)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 34467899999999 99999999887765443
No 85
>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=41.47 E-value=60 Score=32.45 Aligned_cols=87 Identities=16% Similarity=0.317 Sum_probs=63.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCCC---CccccccccCcCcCcccccchhhhccCCCCCCCCCCHHHHHHHHHHHHH-h----
Q 020613 14 RGLWSPEEDEKLIRYITTHGYG---CWSEVPEKAGLQRCGKSCRLRWINYLRPDIRRGRFTPEEEKLIISLHSV-V---- 85 (323)
Q Consensus 14 KG~WT~EEDe~L~~lV~kyG~~---nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p~ikkg~WT~EED~~Ll~lv~~-~---- 85 (323)
-..||..|...|+++.+..... +-.+|++.+. +|+..++++ |.+.|+ +..+.+++.+ |
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~-~Rs~aEI~~-fl~~LK------------~rvareaiqkv~~~g~ 86 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELP-GRSEAEIRD-FLQQLK------------GRVAREAIQKVHPGGL 86 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhcc-CcCHHHHHH-HHHHHH------------HHHHHHHHHHhccccc
Confidence 4589999999999998876433 3457788888 899998876 344443 2334444444 2
Q ss_pred -CCC------------hHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 86 -GNR------------WAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 86 -G~k------------WskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
|.+ |..+|+.+.|.-...+-.-|.++|.-
T Consensus 87 ~~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~i 128 (344)
T PF11035_consen 87 KGPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLTI 128 (344)
T ss_pred ccccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHHH
Confidence 211 99999999999999999999988754
No 86
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=40.20 E-value=43 Score=27.42 Aligned_cols=48 Identities=15% Similarity=0.120 Sum_probs=33.2
Q ss_pred CCCCHHHHHHHHHHHHHh----C----CChHHHhccCC-----CCCHHHHHHHHHHHhhhh
Q 020613 68 GRFTPEEEKLIISLHSVV----G----NRWAHIASHLP-----GRTDNEIKNYWNSWIKKK 115 (323)
Q Consensus 68 g~WT~EED~~Ll~lv~~~----G----~kWskIAk~Lp-----gRT~~qcKnRW~~lLkkk 115 (323)
..||+|+|-.|++.+..| | ..|...-..+. .=+.+|+.++-+.+.++.
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky 65 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKY 65 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHH
Confidence 359999999999998776 5 24554444332 237788888887766553
No 87
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=40.00 E-value=49 Score=33.86 Aligned_cols=75 Identities=17% Similarity=0.220 Sum_probs=46.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhccCCCCCCCCCCHHHHHHHHHHHHHhCCCh
Q 020613 10 QKVKRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYLRPDIRRGRFTPEEEKLIISLHSVVGNRW 89 (323)
Q Consensus 10 ~kvkKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p~ikkg~WT~EED~~Ll~lv~~~G~kW 89 (323)
.+..-|.|+++=|+...+++..|.+. ||...-+++-= +.||+ =
T Consensus 72 ~~daegvWSpdIEqsFqEALaiyppc-----------GrrKIilsdeg-------------------------kmyGR-N 114 (455)
T KOG3841|consen 72 QRDAEGVWSPDIEQSFQEALAIYPPC-----------GRRKIILSDEG-------------------------KMYGR-N 114 (455)
T ss_pred ccccccccChhHHHHHHHHHhhcCCC-----------CceeEEEccCc-------------------------cccch-H
Confidence 34566888888888888888888754 33333222210 12222 2
Q ss_pred HHHhccC-----CCCCHHHHHHHHHHHhhhhccCCCC
Q 020613 90 AHIASHL-----PGRTDNEIKNYWNSWIKKKIRKPST 121 (323)
Q Consensus 90 skIAk~L-----pgRT~~qcKnRW~~lLkkk~kK~~~ 121 (323)
..||+++ ..||.+||-.+-+-+-|++.++...
T Consensus 115 ELIarYIKlrtgktRTrKQVSSHIQVlarrk~reiq~ 151 (455)
T KOG3841|consen 115 ELIARYIKLRTGKTRTRKQVSSHIQVLARRKLREIQA 151 (455)
T ss_pred HHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHHh
Confidence 4444433 4699999999998888887765443
No 88
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=39.26 E-value=49 Score=27.87 Aligned_cols=30 Identities=23% Similarity=0.196 Sum_probs=24.2
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 84 VVGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 84 ~~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
..|..+..||+.| |-|...|+++.....++
T Consensus 139 ~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 168 (179)
T PRK11924 139 VEGLSYREIAEIL-GVPVGTVKSRLRRARQL 168 (179)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3467899999999 99999999988765443
No 89
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=39.06 E-value=58 Score=28.84 Aligned_cols=37 Identities=16% Similarity=0.229 Sum_probs=28.7
Q ss_pred HHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHHhh
Q 020613 76 KLIISLHSVVGNRWAHIASHLPGRTDNEIKNYWNSWIK 113 (323)
Q Consensus 76 ~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKnRW~~lLk 113 (323)
..++.+....|-.+.+||+.| |-|...|+.+|.....
T Consensus 141 ~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR~ 177 (185)
T PF07638_consen 141 RRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRARA 177 (185)
T ss_pred HHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 333444444577899999999 9999999999987753
No 90
>PF02757 YLP: YLP motif; InterPro: IPR004019 The YLP motif is found in one or several copies in various Drosophila proteins. Its function is unknown, however the presence of completely conserved tyrosine residues and its presence in the human Erbb-2 and ErbB-4 receptor protein-tyrosine kinases (2.7.10.1 from EC) may suggest it could be a substrate for tyrosine kinases. ErbBs (1-4) are single-pass transmembrane proteins that activate a wide variety of signalling pathways, including those involved in proliferation, migration, differentiation, survival, and apoptosis; they are frequently misregulated in cancer []. ErbB-2 is an essential component of a neuregulin-receptor complex, although neuregulins do not interact with it alone. ErbB-4 specifically binds and is activated by neuregulins, NRG-2, NRG-3, heparin-binding EGF-like growth factor, betacellulin and NTAK [].
Probab=38.44 E-value=12 Score=18.44 Aligned_cols=6 Identities=67% Similarity=1.619 Sum_probs=5.0
Q ss_pred CCCchh
Q 020613 237 HYLPPL 242 (323)
Q Consensus 237 ~~~~~~ 242 (323)
.||||.
T Consensus 3 eYLpP~ 8 (9)
T PF02757_consen 3 EYLPPV 8 (9)
T ss_pred cccCCC
Confidence 699985
No 91
>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=37.94 E-value=39 Score=26.76 Aligned_cols=26 Identities=35% Similarity=0.662 Sum_probs=20.7
Q ss_pred HHHHHHHhCCChHHHhccCCCCCHHHH
Q 020613 78 IISLHSVVGNRWAHIASHLPGRTDNEI 104 (323)
Q Consensus 78 Ll~lv~~~G~kWskIAk~LpgRT~~qc 104 (323)
|..+....|..|.++|+.| |-+..+|
T Consensus 10 l~~ia~~iG~~Wk~Lar~L-Gls~~dI 35 (86)
T cd08318 10 ITVFANKLGEDWKTLAPHL-EMKDKEI 35 (86)
T ss_pred HHHHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 3346688899999999999 7777766
No 92
>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=37.88 E-value=75 Score=20.74 Aligned_cols=40 Identities=20% Similarity=0.260 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHH
Q 020613 70 FTPEEEKLIISLHSVVGNRWAHIASHLPGRTDNEIKNYWNSW 111 (323)
Q Consensus 70 WT~EED~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKnRW~~l 111 (323)
.+++ +..++.+.-.-|..+..||+.+ |-+...|+.+....
T Consensus 11 l~~~-~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPER-EREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRA 50 (55)
T ss_pred CCHH-HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 4444 4555555556678899999998 88888887766554
No 93
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=36.30 E-value=60 Score=28.66 Aligned_cols=29 Identities=21% Similarity=0.171 Sum_probs=24.0
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHHhh
Q 020613 84 VVGNRWAHIASHLPGRTDNEIKNYWNSWIK 113 (323)
Q Consensus 84 ~~G~kWskIAk~LpgRT~~qcKnRW~~lLk 113 (323)
..|....+||..| |-+...|++|....++
T Consensus 148 ~~g~s~~EIA~~l-g~s~~tV~~rl~rar~ 176 (192)
T PRK09643 148 MQGYSVADAARML-GVAEGTVKSRCARGRA 176 (192)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 3467899999999 9999999999965443
No 94
>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=36.04 E-value=43 Score=26.57 Aligned_cols=31 Identities=23% Similarity=0.472 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhCCChHHHhccCCCCCHHHHHH
Q 020613 75 EKLIISLHSVVGNRWAHIASHLPGRTDNEIKN 106 (323)
Q Consensus 75 D~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKn 106 (323)
|..|-.+....|.+|..+|+.| |=+..+|.+
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 4567788899999999999999 777776655
No 95
>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=35.27 E-value=84 Score=27.74 Aligned_cols=47 Identities=15% Similarity=0.203 Sum_probs=39.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCChHHHhccC----CCCCHHHHHHHHHHHh
Q 020613 66 RRGRFTPEEEKLIISLHSVVGNRWAHIASHL----PGRTDNEIKNYWNSWI 112 (323)
Q Consensus 66 kkg~WT~EED~~Ll~lv~~~G~kWskIAk~L----pgRT~~qcKnRW~~lL 112 (323)
....-|..|..-|..|+.+||.++...|.-. --.|..||+.+...+.
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~k 163 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKYK 163 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHhc
Confidence 4457889999999999999999999999854 2489999999887654
No 96
>PRK04217 hypothetical protein; Provisional
Probab=33.70 E-value=90 Score=26.30 Aligned_cols=44 Identities=20% Similarity=0.083 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 69 RFTPEEEKLIISLHSVVGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
.-|.+| ..++.+....|-....||+.+ |.+...|+.+++...++
T Consensus 42 ~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkk 85 (110)
T PRK04217 42 FMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKK 85 (110)
T ss_pred cCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 456666 677777777788999999999 99999999999876543
No 97
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=33.64 E-value=67 Score=27.56 Aligned_cols=29 Identities=10% Similarity=-0.050 Sum_probs=23.9
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 85 VGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 85 ~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
.|..+..||+.| |-|...|+++.....++
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 467799999999 99999999988765543
No 98
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=33.54 E-value=76 Score=23.19 Aligned_cols=35 Identities=23% Similarity=0.442 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHH
Q 020613 72 PEEEKLIISLHSVVGNRWAHIASHLPGRTDNEIKNY 107 (323)
Q Consensus 72 ~EED~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKnR 107 (323)
.++|+-.+.+..+.|-.=..||+.+ ||+.+.|++.
T Consensus 6 t~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~y 40 (50)
T PF11427_consen 6 TDAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRY 40 (50)
T ss_dssp -HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHH
T ss_pred CHHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHH
Confidence 3556667788899999999999999 9999988775
No 99
>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=32.32 E-value=58 Score=28.05 Aligned_cols=28 Identities=11% Similarity=0.058 Sum_probs=23.6
Q ss_pred CCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 86 GNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 86 G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
|.....||+.| |-|...|+++....+++
T Consensus 154 ~~s~~EIA~~l-gis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 154 GLSYEDIARIM-DCPVGTVRSRIFRAREA 181 (190)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 56799999999 89999999998776554
No 100
>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=32.04 E-value=48 Score=26.46 Aligned_cols=30 Identities=33% Similarity=0.578 Sum_probs=23.5
Q ss_pred HHHHHHHHHhCCChHHHhccCCCCCHHHHHH
Q 020613 76 KLIISLHSVVGNRWAHIASHLPGRTDNEIKN 106 (323)
Q Consensus 76 ~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKn 106 (323)
+.|-.+....|.+|..+|+.| |=+..+|..
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 345566688899999999999 777777654
No 101
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=31.92 E-value=84 Score=26.37 Aligned_cols=47 Identities=13% Similarity=0.135 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHhCC-ChHHHhccCCCCCHHHHHHHHHHHhhhhccCC
Q 020613 72 PEEEKLIISLHSVVGN-RWAHIASHLPGRTDNEIKNYWNSWIKKKIRKP 119 (323)
Q Consensus 72 ~EED~~Ll~lv~~~G~-kWskIAk~LpgRT~~qcKnRW~~lLkkk~kK~ 119 (323)
.+-|.+|+++..+-|. .+..||+.+ |-|...|++|-+.+.+..+-+.
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~GiI~~ 54 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGVIKG 54 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCceee
Confidence 3557777777777664 599999999 9999999999999998876543
No 102
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=31.88 E-value=76 Score=27.01 Aligned_cols=29 Identities=21% Similarity=0.314 Sum_probs=24.2
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 85 VGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 85 ~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
.|-+...||+.| |-|...|+++....+++
T Consensus 134 ~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~ 162 (169)
T TIGR02954 134 HDLTIKEIAEVM-NKPEGTVKTYLHRALKK 162 (169)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466799999999 88999999998876654
No 103
>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=31.75 E-value=54 Score=25.09 Aligned_cols=29 Identities=24% Similarity=0.528 Sum_probs=21.6
Q ss_pred HHHHHHHHHH-hCCChHHHhccCCCCCHHHH
Q 020613 75 EKLIISLHSV-VGNRWAHIASHLPGRTDNEI 104 (323)
Q Consensus 75 D~~Ll~lv~~-~G~kWskIAk~LpgRT~~qc 104 (323)
++.|..+++. .|.+|..+|+.| |=+..+|
T Consensus 5 ~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i 34 (88)
T smart00005 5 REKLAKLLDHPLGLDWRELARKL-GLSEADI 34 (88)
T ss_pred HHHHHHHHcCccchHHHHHHHHc-CCCHHHH
Confidence 4566677777 899999999999 5455443
No 104
>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=31.70 E-value=49 Score=25.99 Aligned_cols=33 Identities=27% Similarity=0.504 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHH
Q 020613 72 PEEEKLIISLHSVVGNRWAHIASHLPGRTDNEIKN 106 (323)
Q Consensus 72 ~EED~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKn 106 (323)
.||-++|+.. ...|.+|...|+.| |=+...|++
T Consensus 2 ~~~v~~ll~~-~nlG~dW~~LA~~L-G~~~~~I~~ 34 (77)
T cd08311 2 QEEVEKLLES-GRPGRDWRSLAGEL-GYEDEAIDT 34 (77)
T ss_pred hHHHHHHHhC-CCCccCHHHHHHHc-CCCHHHHHH
Confidence 5788888732 25688999999999 877877765
No 105
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=31.22 E-value=33 Score=35.16 Aligned_cols=48 Identities=15% Similarity=0.266 Sum_probs=40.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccccccc-----cCcCcCcccccchhhhc
Q 020613 12 VKRGLWSPEEDEKLIRYITTHGYGCWSEVPEK-----AGLQRCGKSCRLRWINY 60 (323)
Q Consensus 12 vkKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~-----l~~~Rt~kQCR~Rw~n~ 60 (323)
++-..||.+|.+.|.++.++|--. |--||.. ++..||-....+||..+
T Consensus 128 l~dn~WskeETD~LF~lck~fDLR-f~VIaDRyd~qq~~~sRTvEdLKeRyY~v 180 (445)
T KOG2656|consen 128 LNDNSWSKEETDYLFDLCKRFDLR-FFVIADRYDNQQYKKSRTVEDLKERYYSV 180 (445)
T ss_pred hccccccHHHHHHHHHHHHhcCee-EEEEeeccchhhccccccHHHHHHHHHHH
Confidence 445679999999999999999855 9999987 56569999999999765
No 106
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=30.82 E-value=89 Score=26.78 Aligned_cols=32 Identities=22% Similarity=0.350 Sum_probs=26.4
Q ss_pred HHhCCChHHHhccCCCCCHHHHHHHHHHHhhhh
Q 020613 83 SVVGNRWAHIASHLPGRTDNEIKNYWNSWIKKK 115 (323)
Q Consensus 83 ~~~G~kWskIAk~LpgRT~~qcKnRW~~lLkkk 115 (323)
...|-....||+.| |.+...|+.|...-+++-
T Consensus 132 ~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 132 RLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 34467899999999 999999999988776653
No 107
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=30.80 E-value=82 Score=27.61 Aligned_cols=30 Identities=23% Similarity=0.094 Sum_probs=24.7
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 84 VVGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 84 ~~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
..|-....||..| |-|...|++|....+++
T Consensus 120 ~~g~~~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (181)
T PRK09637 120 LEGLSQKEIAEKL-GLSLSGAKSRVQRGRVK 149 (181)
T ss_pred hcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3467899999999 99999999998766543
No 108
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=30.56 E-value=95 Score=25.92 Aligned_cols=29 Identities=14% Similarity=0.121 Sum_probs=24.1
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 85 VGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 85 ~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
.|-.-..||..| |-+...|+.|....+++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 121 EDMDVAETAAAM-GCSEGSVKTHCSRATHA 149 (161)
T ss_pred hcCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466799999999 99999999998766543
No 109
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=30.47 E-value=83 Score=27.19 Aligned_cols=30 Identities=10% Similarity=0.122 Sum_probs=25.2
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHHhhhh
Q 020613 85 VGNRWAHIASHLPGRTDNEIKNYWNSWIKKK 115 (323)
Q Consensus 85 ~G~kWskIAk~LpgRT~~qcKnRW~~lLkkk 115 (323)
.|.....||..| |-+...|+.+....+++-
T Consensus 146 ~g~s~~eIA~~l-~is~~tV~~~l~ra~~~L 175 (184)
T PRK12512 146 EGASIKETAAKL-SMSEGAVRVALHRGLAAL 175 (184)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 367799999999 999999999988776553
No 110
>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=30.19 E-value=58 Score=26.06 Aligned_cols=27 Identities=22% Similarity=0.363 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhCCChHHHhccCCCCCHH
Q 020613 75 EKLIISLHSVVGNRWAHIASHLPGRTDN 102 (323)
Q Consensus 75 D~~Ll~lv~~~G~kWskIAk~LpgRT~~ 102 (323)
|..|..+++..|..|.++|+.| |=+..
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L-~vs~~ 30 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL-QFSVE 30 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc-CCCHH
Confidence 4567788899999999999998 54443
No 111
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=30.02 E-value=92 Score=27.40 Aligned_cols=31 Identities=13% Similarity=0.027 Sum_probs=25.1
Q ss_pred HHhCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 83 SVVGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 83 ~~~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
...|.....||+.| |-|...|+.|....+++
T Consensus 144 ~~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 144 EVLGFESDEICQEL-EISTSNCHVLLYRARLS 174 (188)
T ss_pred HHhCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 33467899999999 99999999998776543
No 112
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=29.37 E-value=34 Score=35.68 Aligned_cols=46 Identities=11% Similarity=0.085 Sum_probs=39.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhh
Q 020613 12 VKRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWIN 59 (323)
Q Consensus 12 vkKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n 59 (323)
-....||.||--++.++...|| ++..+|-+.|+ .|+-.+++.-|..
T Consensus 185 ~~~d~WT~Ed~vlFe~aF~~~G-K~F~kIrq~LP-~rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 185 EFPDEWTAEDIVLFEQAFQFFG-KDFHKIRQALP-HRSLASLVQYYYS 230 (534)
T ss_pred CCcccchHHHHHHHHHHHHHhc-ccHHHHHHHcc-CccHHHHHHHHHH
Confidence 3566899999999999999999 56999999999 9999888876654
No 113
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=29.36 E-value=94 Score=27.30 Aligned_cols=29 Identities=10% Similarity=0.013 Sum_probs=24.3
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 85 VGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 85 ~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
.|-....||+.| |-+...|+.|....+++
T Consensus 156 eg~s~~EIA~~l-gis~~tVk~rl~ra~~~ 184 (194)
T PRK12531 156 EELPHQQVAEMF-DIPLGTVKSRLRLAVEK 184 (194)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 467799999999 99999999998766554
No 114
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=28.93 E-value=98 Score=26.91 Aligned_cols=29 Identities=17% Similarity=0.190 Sum_probs=24.2
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 85 VGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 85 ~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
.|.....||..| |-+...|+.|....+++
T Consensus 154 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 154 VGLSAEETAEAV-GSTPGAVRVAQHRALAR 182 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 467899999999 99999999998766554
No 115
>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=28.53 E-value=61 Score=25.76 Aligned_cols=25 Identities=28% Similarity=0.522 Sum_probs=20.6
Q ss_pred HHHHHHHHHhCCChHHHhccCCCCCH
Q 020613 76 KLIISLHSVVGNRWAHIASHLPGRTD 101 (323)
Q Consensus 76 ~~Ll~lv~~~G~kWskIAk~LpgRT~ 101 (323)
+.|..+....|..|..+|+.| |=+.
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L-Glse 27 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL-GLSY 27 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc-CCCH
Confidence 457889999999999999998 4333
No 116
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=28.31 E-value=86 Score=26.89 Aligned_cols=28 Identities=11% Similarity=-0.029 Sum_probs=23.3
Q ss_pred CCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 86 GNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 86 G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
|..-..||+.| |.|...|+++....+++
T Consensus 152 g~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T TIGR02948 152 DLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 56799999999 99999999988765544
No 117
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=28.19 E-value=89 Score=27.19 Aligned_cols=28 Identities=14% Similarity=0.076 Sum_probs=23.2
Q ss_pred CCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 86 GNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 86 G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
|-....||+.| |-|...|++|....+++
T Consensus 154 g~s~~eIA~~l-gis~~tv~~~l~Rar~~ 181 (193)
T PRK11923 154 GLSYEDIASVM-QCPVGTVRSRIFRAREA 181 (193)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 56799999999 99999999998766543
No 118
>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=27.99 E-value=1e+02 Score=20.94 Aligned_cols=35 Identities=20% Similarity=0.164 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHH
Q 020613 73 EEEKLIISLHSVVGNRWAHIASHLPGRTDNEIKNYW 108 (323)
Q Consensus 73 EED~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKnRW 108 (323)
=|...|.++...++.+.++.|+.| |=+...+..|-
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~kl 39 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLL-GISRRTLYRKL 39 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHH
Confidence 367888899999999999999998 77776666554
No 119
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=27.83 E-value=1.1e+02 Score=26.16 Aligned_cols=29 Identities=24% Similarity=0.296 Sum_probs=24.0
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 85 VGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 85 ~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
.|-.-..||+.| |.+...|+.|....+++
T Consensus 133 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 161 (173)
T PRK09645 133 RGWSTAQIAADL-GIPEGTVKSRLHYALRA 161 (173)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 466789999999 99999999998866543
No 120
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=27.81 E-value=1.1e+02 Score=25.71 Aligned_cols=29 Identities=10% Similarity=-0.106 Sum_probs=23.8
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 85 VGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 85 ~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
.|-.-..||+.| |-+...|++|....+++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (160)
T PRK09642 121 EEKSYQEIALQE-KIEVKTVEMKLYRARKW 149 (160)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466799999999 99999999987765543
No 121
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=27.62 E-value=1.1e+02 Score=26.73 Aligned_cols=29 Identities=14% Similarity=0.074 Sum_probs=24.2
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 85 VGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 85 ~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
.|-....||..| |-|...|++|....+++
T Consensus 146 ~~~s~~eIA~~l-gis~~tV~~~l~Rar~~ 174 (189)
T PRK12515 146 HEKSVEEVGEIV-GIPESTVKTRMFYARKK 174 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 466799999999 88999999998876543
No 122
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=27.42 E-value=86 Score=28.54 Aligned_cols=45 Identities=22% Similarity=0.279 Sum_probs=36.9
Q ss_pred CCCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHHhhhh
Q 020613 68 GRFTPEEEKLIISLHSVVGNRWAHIASHLPGRTDNEIKNYWNSWIKKK 115 (323)
Q Consensus 68 g~WT~EED~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKnRW~~lLkkk 115 (323)
...|+.|-+.|.-+.+ |..=..||..| +.|..-||++..++++|-
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 3689888887766654 44458999999 999999999999999874
No 123
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=27.41 E-value=1e+02 Score=27.02 Aligned_cols=28 Identities=4% Similarity=-0.103 Sum_probs=23.7
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHHhh
Q 020613 85 VGNRWAHIASHLPGRTDNEIKNYWNSWIK 113 (323)
Q Consensus 85 ~G~kWskIAk~LpgRT~~qcKnRW~~lLk 113 (323)
.|-....||..| |-|...||.|....++
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 367799999999 9999999999776554
No 124
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=27.16 E-value=1.1e+02 Score=26.49 Aligned_cols=33 Identities=18% Similarity=0.152 Sum_probs=27.2
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHHhhhhcc
Q 020613 84 VVGNRWAHIASHLPGRTDNEIKNYWNSWIKKKIR 117 (323)
Q Consensus 84 ~~G~kWskIAk~LpgRT~~qcKnRW~~lLkkk~k 117 (323)
..|-....||+.| |-+...||.|....+++-+.
T Consensus 141 ~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 141 LDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 3467899999999 99999999999877765443
No 125
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=26.96 E-value=1.2e+02 Score=25.25 Aligned_cols=46 Identities=17% Similarity=0.213 Sum_probs=31.4
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhccC
Q 020613 13 KRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYLR 62 (323)
Q Consensus 13 kKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L~ 62 (323)
++..||.|+-...+..+...| ..-..||..++. +.. -..+|.+.+.
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g-~sv~evA~e~gI--s~~-tl~~W~r~y~ 54 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPG-MTVSLVARQHGV--AAS-QLFLWRKQYQ 54 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCC-CCHHHHHHHHCc--CHH-HHHHHHHHHh
Confidence 467899999877777776666 346789988883 333 3446776543
No 126
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=26.92 E-value=52 Score=35.61 Aligned_cols=49 Identities=14% Similarity=0.289 Sum_probs=35.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccccccCc---------CcCcccccchhhhccC
Q 020613 13 KRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGL---------QRCGKSCRLRWINYLR 62 (323)
Q Consensus 13 kKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~---------~Rt~kQCR~Rw~n~L~ 62 (323)
+|..||-.|.+-...+++.+| ++..+|-..+-. -++..|.|..|++.+.
T Consensus 87 ~ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~ 144 (782)
T KOG4468|consen 87 AKTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVR 144 (782)
T ss_pred cccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHH
Confidence 366899999999999999999 568887332211 3566678887776543
No 127
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=26.00 E-value=1.1e+02 Score=26.82 Aligned_cols=29 Identities=10% Similarity=-0.031 Sum_probs=23.5
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 85 VGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 85 ~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
.|-.+..||+.| |-+...|+++....+++
T Consensus 151 ~g~s~~eIA~~l-gis~~tV~~~l~Ra~~~ 179 (196)
T PRK12524 151 EGLSNPEIAEVM-EIGVEAVESLTARGKRA 179 (196)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 466799999999 89999999887765543
No 128
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=24.51 E-value=80 Score=25.79 Aligned_cols=71 Identities=13% Similarity=0.284 Sum_probs=39.5
Q ss_pred CCCCCCHHHHHHHHHHHHHh----CCC---Ccccccccc----CcCcCccc-------ccchhhhccCCCCCCC---CCC
Q 020613 13 KRGLWSPEEDEKLIRYITTH----GYG---CWSEVPEKA----GLQRCGKS-------CRLRWINYLRPDIRRG---RFT 71 (323)
Q Consensus 13 kKG~WT~EEDe~L~~lV~ky----G~~---nW~~IA~~l----~~~Rt~kQ-------CR~Rw~n~L~p~ikkg---~WT 71 (323)
-...||++++-.|++.+..| |.. +|..+...+ ...=+..| .+.||.+.... .+.| .++
T Consensus 3 ~qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~~~k-~~~g~~~~~~ 81 (98)
T PF04504_consen 3 FQRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNAVKK-SKNGKDPSFS 81 (98)
T ss_pred CcCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHhhh-cccCcCCCCC
Confidence 34579999999999988776 532 333322222 21112223 33455554443 2233 577
Q ss_pred HHHHHHHHHHHHH
Q 020613 72 PEEEKLIISLHSV 84 (323)
Q Consensus 72 ~EED~~Ll~lv~~ 84 (323)
..-|..+.+|.++
T Consensus 82 ~~hd~~~f~Lsk~ 94 (98)
T PF04504_consen 82 KPHDRRLFELSKK 94 (98)
T ss_pred CHhHHHHHHHHHH
Confidence 7777777777654
No 129
>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=24.50 E-value=76 Score=22.65 Aligned_cols=43 Identities=26% Similarity=0.319 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 69 RFTPEEEKLIISLHSVVGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
..|+.|-+.|.-+.. |..=..||+.+ |.+...|+.+...++++
T Consensus 3 ~LT~~E~~vl~~l~~--G~~~~eIA~~l-~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ--GMSNKEIAEEL-GISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHHT--TS-HHHHHHHH-TSHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHh--cCCcchhHHhc-CcchhhHHHHHHHHHHH
Confidence 356666665554443 55568999999 99999999998888776
No 130
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=24.44 E-value=1.4e+02 Score=24.76 Aligned_cols=28 Identities=18% Similarity=0.213 Sum_probs=23.2
Q ss_pred CCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 86 GNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 86 G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
|.....||+.+ |.+...|+.+-...+++
T Consensus 122 ~~s~~EIA~~l-~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 122 GKTMGEIALET-EMTYYQVRWIYRQALEK 149 (154)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 56789999999 99999999987765544
No 131
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=23.95 E-value=61 Score=34.77 Aligned_cols=50 Identities=16% Similarity=0.302 Sum_probs=43.8
Q ss_pred ccCCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhh
Q 020613 8 NQQKVKRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWIN 59 (323)
Q Consensus 8 ~~~kvkKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n 59 (323)
..++...++|+.+|-++........|.. .+.|+..++ .|+.+|++..|..
T Consensus 403 ~sk~~~~~~w~~se~e~fyka~~~~gs~-~slis~l~p-~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 403 YSKKLETDKWDASETELFYKALSERGSD-FSLISNLFP-LRDRKQIKAKFKK 452 (584)
T ss_pred ccCccccCcccchhhHHhhhHHhhhccc-ccccccccc-cccHHHHHHHHhh
Confidence 4566778899999999999999999954 999999999 9999999987754
No 132
>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=23.76 E-value=1.4e+02 Score=25.09 Aligned_cols=28 Identities=32% Similarity=0.285 Sum_probs=23.1
Q ss_pred CCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 86 GNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 86 G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
|-+-..||+.| |.+...|+.+-...+++
T Consensus 138 g~s~~eIA~~l-~is~~tv~~~l~ra~~~ 165 (170)
T TIGR02952 138 NLPIAEVARIL-GKTEGAVKILQFRAIKK 165 (170)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 66789999999 99999999987765543
No 133
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=23.47 E-value=82 Score=21.74 Aligned_cols=36 Identities=33% Similarity=0.470 Sum_probs=18.2
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHH
Q 020613 69 RFTPEEEKLIISLHSVVGNRWAHIASHLPGRTDNEIKN 106 (323)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKn 106 (323)
.+|.+|-..|..++ .-|..=.+||+.| ||+...|.+
T Consensus 4 ~Lt~~eR~~I~~l~-~~G~s~~~IA~~l-g~s~sTV~r 39 (44)
T PF13936_consen 4 HLTPEERNQIEALL-EQGMSIREIAKRL-GRSRSTVSR 39 (44)
T ss_dssp --------HHHHHH-CS---HHHHHHHT-T--HHHHHH
T ss_pred chhhhHHHHHHHHH-HcCCCHHHHHHHH-CcCcHHHHH
Confidence 46777777766664 5677889999999 999988765
No 134
>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=23.41 E-value=80 Score=27.91 Aligned_cols=48 Identities=23% Similarity=0.207 Sum_probs=33.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccccccccCc---CcCcccccchhhhc
Q 020613 12 VKRGLWSPEEDEKLIRYITTHGYGCWSEVPEKAGL---QRCGKSCRLRWINY 60 (323)
Q Consensus 12 vkKG~WT~EEDe~L~~lV~kyG~~nW~~IA~~l~~---~Rt~kQCR~Rw~n~ 60 (323)
.+...=|..|.+-+..+|++|| .++...+.-..+ ..|..||+.+...|
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhG-dDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHG-DDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHC-ccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 5667789999999999999999 457776653321 35666666554443
No 135
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=23.21 E-value=1.2e+02 Score=26.15 Aligned_cols=28 Identities=25% Similarity=0.404 Sum_probs=23.9
Q ss_pred CCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 86 GNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 86 G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
|-...+||+.| |-+...|++|....++.
T Consensus 135 g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 162 (172)
T PRK09651 135 GLTYSEIAHKL-GVSVSSVKKYVAKATEH 162 (172)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 56799999999 99999999998876654
No 136
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=23.06 E-value=1.5e+02 Score=25.42 Aligned_cols=29 Identities=21% Similarity=0.197 Sum_probs=24.0
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 85 VGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 85 ~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
.|-....||+.| |-+...|+.|....+++
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 177 (183)
T TIGR02999 149 AGLTVEEIAELL-GVSVRTVERDWRFARAW 177 (183)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 356799999999 99999999998866543
No 137
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=22.75 E-value=1.6e+02 Score=24.70 Aligned_cols=29 Identities=24% Similarity=0.281 Sum_probs=23.5
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 85 VGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 85 ~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
.|-.-..||..| |-+...|+.|....++.
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 355689999999 99999999998765543
No 138
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=22.52 E-value=1.6e+02 Score=24.77 Aligned_cols=30 Identities=30% Similarity=0.403 Sum_probs=24.6
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 84 VVGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 84 ~~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
..|-...+||+.+ |-+...|+.|....+++
T Consensus 127 ~~g~s~~EIA~~l-~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 127 VDGLGYGEIATEL-GISLATVKRYLNKAAMR 156 (161)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3467899999999 99999999998776543
No 139
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=22.48 E-value=1.4e+02 Score=26.16 Aligned_cols=29 Identities=10% Similarity=0.101 Sum_probs=23.6
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHHhh
Q 020613 84 VVGNRWAHIASHLPGRTDNEIKNYWNSWIK 113 (323)
Q Consensus 84 ~~G~kWskIAk~LpgRT~~qcKnRW~~lLk 113 (323)
..|-.-..||+.| |-+...|+.|....++
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 3467799999999 9999999998876543
No 140
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=22.38 E-value=1.4e+02 Score=26.14 Aligned_cols=29 Identities=17% Similarity=0.117 Sum_probs=24.3
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 85 VGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 85 ~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
.|-.-..||+.| |-|...|+.|....+++
T Consensus 145 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 173 (185)
T PRK09649 145 LGLSYADAAAVC-GCPVGTIRSRVARARDA 173 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 356789999999 99999999998776654
No 141
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=22.08 E-value=1.5e+02 Score=25.56 Aligned_cols=30 Identities=20% Similarity=0.143 Sum_probs=24.9
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 84 VVGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 84 ~~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
..|-....||+.| |.+...|+++-...+++
T Consensus 143 ~~g~s~~EIA~~l-~is~~tV~~~l~rar~~ 172 (181)
T PRK12536 143 LEGLSVAETAQLT-GLSESAVKVGIHRGLKA 172 (181)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3467899999999 99999999998766544
No 142
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=22.06 E-value=47 Score=26.42 Aligned_cols=44 Identities=16% Similarity=0.179 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhccCCCC
Q 020613 20 EEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYLRPDI 65 (323)
Q Consensus 20 EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p~i 65 (323)
+.|.+++.++...+...+.+||+.++ -+...|+.|..+..+.++
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~--~s~~tv~~~l~~L~~~g~ 46 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVG--LSPSTVHNRVKRLEEEGV 46 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 56889999999988888999999997 788888888777655443
No 143
>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=21.86 E-value=1.1e+02 Score=24.13 Aligned_cols=29 Identities=24% Similarity=0.500 Sum_probs=21.3
Q ss_pred HHHHHHHHHhCCChHHHhccCCCCCHHHHH
Q 020613 76 KLIISLHSVVGNRWAHIASHLPGRTDNEIK 105 (323)
Q Consensus 76 ~~Ll~lv~~~G~kWskIAk~LpgRT~~qcK 105 (323)
..+--+++..|..|..+|+.| |=|..+|.
T Consensus 3 ~~f~~i~~~lG~~Wk~laR~L-Glse~~Id 31 (86)
T cd08306 3 AAFDVICENVGRDWRKLARKL-GLSETKIE 31 (86)
T ss_pred HHHHHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 334455677899999999999 66666554
No 144
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=21.86 E-value=1.4e+02 Score=25.79 Aligned_cols=29 Identities=7% Similarity=-0.003 Sum_probs=23.4
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 85 VGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 85 ~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
.|.....||+.| |-+...|+.+....+++
T Consensus 143 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 171 (186)
T PRK05602 143 QGLSNIEAAAVM-DISVDALESLLARGRRA 171 (186)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 467799999999 99999999987765543
No 145
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=21.76 E-value=1.6e+02 Score=25.57 Aligned_cols=30 Identities=17% Similarity=0.309 Sum_probs=24.4
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 84 VVGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 84 ~~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
..|-.-..||..| |-|...|+.|....+++
T Consensus 136 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 165 (185)
T PRK12542 136 FYNLTYQEISSVM-GITEANVRKQFERARKR 165 (185)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466799999999 99999999988765543
No 146
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=21.58 E-value=1.6e+02 Score=25.27 Aligned_cols=28 Identities=14% Similarity=0.231 Sum_probs=23.5
Q ss_pred CCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 86 GNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 86 G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
|-.-..||+.| |.|...|+.+....+++
T Consensus 145 g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 172 (179)
T PRK12514 145 GLSYKELAERH-DVPLNTMRTWLRRSLLK 172 (179)
T ss_pred CCCHHHHHHHH-CCChHHHHHHHHHHHHH
Confidence 66789999999 99999999988766543
No 147
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=21.48 E-value=38 Score=28.46 Aligned_cols=44 Identities=14% Similarity=0.203 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHhCCCCccccccccCcCcCcccccchhhhccCCCC
Q 020613 20 EEDEKLIRYITTHGYGCWSEVPEKAGLQRCGKSCRLRWINYLRPDI 65 (323)
Q Consensus 20 EEDe~L~~lV~kyG~~nW~~IA~~l~~~Rt~kQCR~Rw~n~L~p~i 65 (323)
+-|.++++++++.+...+.+||+.++ -+...|+.|-.+..+.++
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~lg--lS~~~v~~Ri~~L~~~Gi 51 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERVG--LSPSTVLRRIKRLEEEGV 51 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCCc
Confidence 56889999999999889999999998 788888888777655543
No 148
>PRK00118 putative DNA-binding protein; Validated
Probab=21.46 E-value=1.8e+02 Score=24.31 Aligned_cols=41 Identities=12% Similarity=0.105 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHHhh
Q 020613 72 PEEEKLIISLHSVVGNRWAHIASHLPGRTDNEIKNYWNSWIK 113 (323)
Q Consensus 72 ~EED~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKnRW~~lLk 113 (323)
++.+..++.+....|-....||+.+ |-|...|+.+.....+
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 4556667777778889999999999 9999999888765443
No 149
>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=21.44 E-value=56 Score=27.10 Aligned_cols=28 Identities=18% Similarity=0.068 Sum_probs=23.5
Q ss_pred CCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 86 GNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 86 G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
|-.+..||..| |-+...|+++.....++
T Consensus 121 g~s~~eIA~~l-gis~~tv~~~l~Ra~~~ 148 (154)
T TIGR02950 121 EFSYKEIAELL-NLSLAKVKSNLFRARKE 148 (154)
T ss_pred cCcHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 45799999999 99999999998876544
No 150
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=21.22 E-value=1.6e+02 Score=25.93 Aligned_cols=30 Identities=20% Similarity=0.116 Sum_probs=24.2
Q ss_pred HHhCCChHHHhccCCCCCHHHHHHHHHHHhh
Q 020613 83 SVVGNRWAHIASHLPGRTDNEIKNYWNSWIK 113 (323)
Q Consensus 83 ~~~G~kWskIAk~LpgRT~~qcKnRW~~lLk 113 (323)
...|-...+||+.| |-+...|+.|-...++
T Consensus 129 ~~~g~s~~EIA~~L-gis~~tVk~~l~Rar~ 158 (187)
T PRK12516 129 GASGFAYEEAAEIC-GCAVGTIKSRVNRARQ 158 (187)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 34467899999999 9999999998776544
No 151
>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=21.10 E-value=92 Score=23.19 Aligned_cols=26 Identities=35% Similarity=0.670 Sum_probs=18.9
Q ss_pred HHHHHHHhCCChHHHhccCCCCCHHHH
Q 020613 78 IISLHSVVGNRWAHIASHLPGRTDNEI 104 (323)
Q Consensus 78 Ll~lv~~~G~kWskIAk~LpgRT~~qc 104 (323)
+..++...|+.|..+|+.| |=+..+|
T Consensus 2 ~~~ia~~lg~~W~~la~~L-gl~~~~I 27 (79)
T cd01670 2 LDKLAKKLGKDWKKLARKL-GLSDGEI 27 (79)
T ss_pred HHHHHHHHhhHHHHHHHHh-CCCHHHH
Confidence 4466788899999999998 4444433
No 152
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=20.92 E-value=1.8e+02 Score=24.73 Aligned_cols=29 Identities=17% Similarity=0.118 Sum_probs=24.0
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 85 VGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 85 ~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
.|-....||+.| |-+...|++|-...+++
T Consensus 127 ~g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 155 (164)
T PRK12547 127 SGFSYEDAAAIC-GCAVGTIKSRVSRARNR 155 (164)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 466799999999 99999999988766554
No 153
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=20.79 E-value=1.1e+02 Score=32.38 Aligned_cols=43 Identities=21% Similarity=0.439 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhc-cCCCCCHHHHHHHHHHH
Q 020613 69 RFTPEEEKLIISLHSVVGNRWAHIAS-HLPGRTDNEIKNYWNSW 111 (323)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kWskIAk-~LpgRT~~qcKnRW~~l 111 (323)
.|+..|-.+..++..+||+....|-. +||-++-..|-..|+-+
T Consensus 287 EWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYYmw 330 (693)
T KOG3554|consen 287 EWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYYMW 330 (693)
T ss_pred hccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHHHH
Confidence 69999999999999999999999987 56999999998887644
No 154
>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=20.49 E-value=1.7e+02 Score=24.56 Aligned_cols=38 Identities=16% Similarity=0.191 Sum_probs=28.1
Q ss_pred HHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHHhhh
Q 020613 76 KLIISLHSVVGNRWAHIASHLPGRTDNEIKNYWNSWIKK 114 (323)
Q Consensus 76 ~~Ll~lv~~~G~kWskIAk~LpgRT~~qcKnRW~~lLkk 114 (323)
..++.+.-..|-+=..||..| |-+...|+.+....+++
T Consensus 116 r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~ra~~~ 153 (162)
T TIGR02983 116 RAVVVLRYYEDLSEAQVAEAL-GISVGTVKSRLSRALAR 153 (162)
T ss_pred HHHhhhHHHhcCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 333444444567789999999 99999999998876654
No 155
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.11 E-value=4.6e+02 Score=21.11 Aligned_cols=46 Identities=20% Similarity=0.408 Sum_probs=35.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChHHHhccCCCC-CHHHHHHHHHHHhhh
Q 020613 67 RGRFTPEEEKLIISLHSVVGNRWAHIASHLPGR-TDNEIKNYWNSWIKK 114 (323)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~G~kWskIAk~LpgR-T~~qcKnRW~~lLkk 114 (323)
+..||.|.-..+++++..-|..=+.||+.+ |- +.++++. |...+..
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~~-W~~~~~~ 51 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLYK-WRIQLQK 51 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHHH-HHHHHHH
Confidence 557999999999999999998889999999 76 5555554 5444433
Done!