Query 044864
Match_columns 214
No_of_seqs 345 out of 1745
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 07:29:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044864.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044864hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03212 Transcription repress 100.0 6E-40 1.3E-44 275.3 12.2 130 2-131 14-143 (249)
2 PLN03091 hypothetical protein; 100.0 1.5E-38 3.3E-43 284.4 11.3 131 2-132 3-133 (459)
3 KOG0048 Transcription factor, 100.0 3.1E-36 6.8E-41 256.6 10.7 114 11-124 7-120 (238)
4 KOG0048 Transcription factor, 99.9 3.4E-25 7.4E-30 188.8 -1.1 97 62-158 5-104 (238)
5 PLN03212 Transcription repress 99.9 2.3E-24 5E-29 181.3 2.7 109 43-159 10-121 (249)
6 KOG0049 Transcription factor, 99.9 1.1E-22 2.3E-27 188.4 3.9 139 11-150 303-447 (939)
7 PLN03091 hypothetical protein; 99.8 1.7E-22 3.7E-27 181.5 -0.8 98 62-159 10-110 (459)
8 KOG0049 Transcription factor, 99.8 1E-20 2.2E-25 175.4 6.0 104 2-106 349-453 (939)
9 PF13921 Myb_DNA-bind_6: Myb-l 99.7 5.1E-18 1.1E-22 114.7 3.5 60 16-77 1-60 (60)
10 COG5147 REB1 Myb superfamily p 99.7 9.4E-17 2E-21 148.3 6.6 115 7-123 14-128 (512)
11 KOG0050 mRNA splicing protein 99.6 8.6E-17 1.9E-21 146.3 2.8 107 11-119 5-111 (617)
12 PF13921 Myb_DNA-bind_6: Myb-l 99.6 4E-16 8.8E-21 105.3 3.3 59 69-127 1-59 (60)
13 KOG0051 RNA polymerase I termi 99.5 6.4E-15 1.4E-19 137.6 5.9 135 12-149 383-554 (607)
14 PF00249 Myb_DNA-binding: Myb- 99.5 3.1E-15 6.7E-20 96.8 1.0 48 13-60 1-48 (48)
15 PF00249 Myb_DNA-binding: Myb- 99.5 3.6E-14 7.9E-19 91.8 4.4 46 66-111 1-48 (48)
16 smart00717 SANT SANT SWI3, AD 99.3 5.9E-12 1.3E-16 80.0 5.0 47 66-112 1-48 (49)
17 KOG0051 RNA polymerase I termi 99.2 7.7E-12 1.7E-16 117.1 3.2 141 12-156 307-502 (607)
18 smart00717 SANT SANT SWI3, AD 99.2 7.2E-12 1.6E-16 79.6 2.1 48 13-61 1-48 (49)
19 cd00167 SANT 'SWI3, ADA2, N-Co 99.2 4.4E-11 9.5E-16 74.8 5.0 44 68-111 1-45 (45)
20 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 5.9E-11 1.3E-15 74.1 1.8 45 15-60 1-45 (45)
21 COG5147 REB1 Myb superfamily p 99.0 4.1E-11 8.9E-16 111.2 -1.7 100 63-162 17-118 (512)
22 KOG0050 mRNA splicing protein 98.7 7.8E-09 1.7E-13 95.0 1.5 93 64-157 5-99 (617)
23 KOG0457 Histone acetyltransfer 98.1 1.5E-06 3.3E-11 78.7 1.7 49 11-60 70-118 (438)
24 TIGR01557 myb_SHAQKYF myb-like 98.0 3.2E-06 6.9E-11 56.6 2.3 48 13-60 3-54 (57)
25 KOG0457 Histone acetyltransfer 97.8 2.2E-05 4.8E-10 71.3 5.0 50 63-112 69-119 (438)
26 PF13325 MCRS_N: N-terminal re 97.8 4.5E-05 9.9E-10 63.3 5.2 99 15-115 1-130 (199)
27 TIGR01557 myb_SHAQKYF myb-like 97.7 6.7E-05 1.5E-09 50.2 5.0 47 66-112 3-55 (57)
28 TIGR02894 DNA_bind_RsfA transc 97.4 0.00015 3.4E-09 57.9 4.0 51 65-116 3-60 (161)
29 COG5259 RSC8 RSC chromatin rem 97.2 0.0001 2.2E-09 67.6 1.2 46 12-59 278-323 (531)
30 COG5259 RSC8 RSC chromatin rem 97.2 0.0003 6.5E-09 64.6 3.7 45 66-110 279-323 (531)
31 KOG1279 Chromatin remodeling f 97.2 0.00016 3.6E-09 67.7 1.8 47 11-59 251-297 (506)
32 PF08914 Myb_DNA-bind_2: Rap1 97.2 0.00056 1.2E-08 47.0 4.0 50 66-115 2-61 (65)
33 KOG1279 Chromatin remodeling f 97.2 0.00053 1.1E-08 64.4 4.8 46 65-110 252-297 (506)
34 PF13837 Myb_DNA-bind_4: Myb/S 97.1 0.0004 8.7E-09 49.7 2.9 49 67-115 2-68 (90)
35 PF08914 Myb_DNA-bind_2: Rap1 97.0 0.00021 4.7E-09 49.0 0.6 51 13-63 2-60 (65)
36 TIGR02894 DNA_bind_RsfA transc 97.0 0.00025 5.4E-09 56.8 0.9 50 11-62 2-57 (161)
37 PRK13923 putative spore coat p 96.4 0.0036 7.9E-08 50.8 3.5 50 65-115 4-60 (170)
38 PF13837 Myb_DNA-bind_4: Myb/S 96.3 0.001 2.2E-08 47.6 0.1 46 14-59 2-63 (90)
39 COG5114 Histone acetyltransfer 96.3 0.0011 2.3E-08 58.5 0.3 48 13-61 63-110 (432)
40 PF13873 Myb_DNA-bind_5: Myb/S 96.2 0.01 2.2E-07 41.6 4.7 49 66-114 2-72 (78)
41 COG5114 Histone acetyltransfer 96.1 0.0054 1.2E-07 54.2 3.4 47 66-112 63-110 (432)
42 PLN03142 Probable chromatin-re 95.9 0.016 3.4E-07 59.0 6.1 100 15-115 826-988 (1033)
43 PRK13923 putative spore coat p 95.7 0.0021 4.7E-08 52.1 -0.6 50 11-62 3-58 (170)
44 PF13873 Myb_DNA-bind_5: Myb/S 95.1 0.0055 1.2E-07 42.9 -0.1 49 12-60 1-69 (78)
45 KOG2656 DNA methyltransferase 94.7 0.069 1.5E-06 48.5 5.7 87 35-122 75-192 (445)
46 COG5118 BDP1 Transcription ini 93.8 0.082 1.8E-06 47.9 4.3 45 68-112 367-411 (507)
47 PF09111 SLIDE: SLIDE; InterP 92.6 0.2 4.3E-06 38.4 4.2 52 63-114 46-113 (118)
48 KOG4282 Transcription factor G 91.7 0.26 5.6E-06 44.1 4.6 51 66-116 54-118 (345)
49 PF09111 SLIDE: SLIDE; InterP 90.3 0.19 4.1E-06 38.5 1.9 34 10-43 46-82 (118)
50 PF12776 Myb_DNA-bind_3: Myb/S 89.3 0.8 1.7E-05 32.8 4.6 47 68-114 1-65 (96)
51 KOG1194 Predicted DNA-binding 88.2 0.85 1.8E-05 42.4 4.9 47 66-112 187-233 (534)
52 COG5118 BDP1 Transcription ini 87.2 0.32 7E-06 44.2 1.5 63 14-78 366-436 (507)
53 PF08281 Sigma70_r4_2: Sigma-7 86.7 1.5 3.4E-05 27.9 4.3 41 71-112 12-52 (54)
54 PF11626 Rap1_C: TRF2-interact 85.4 0.87 1.9E-05 32.7 2.8 28 10-40 44-79 (87)
55 KOG4329 DNA-binding protein [G 78.6 21 0.00046 32.6 9.4 44 67-110 278-322 (445)
56 KOG4282 Transcription factor G 78.3 1.1 2.5E-05 40.0 1.5 47 14-60 55-113 (345)
57 KOG4468 Polycomb-group transcr 77.0 4.8 0.00011 38.8 5.2 57 66-123 88-154 (782)
58 KOG4167 Predicted DNA-binding 76.7 3.9 8.4E-05 40.3 4.6 43 67-109 620-662 (907)
59 PF13404 HTH_AsnC-type: AsnC-t 76.7 4.3 9.4E-05 25.1 3.4 38 72-110 3-41 (42)
60 KOG0384 Chromodomain-helicase 75.0 3 6.4E-05 43.3 3.5 76 12-94 1132-1208(1373)
61 PF12776 Myb_DNA-bind_3: Myb/S 74.9 1.7 3.7E-05 31.0 1.4 44 15-58 1-60 (96)
62 KOG2656 DNA methyltransferase 73.5 2 4.4E-05 39.2 1.7 50 9-59 126-180 (445)
63 PRK11179 DNA-binding transcrip 71.7 5 0.00011 31.6 3.4 46 71-117 8-54 (153)
64 PF04545 Sigma70_r4: Sigma-70, 71.4 8.5 0.00018 24.1 3.9 41 72-113 7-47 (50)
65 PF13325 MCRS_N: N-terminal re 70.1 9.2 0.0002 31.9 4.8 43 68-111 1-46 (199)
66 KOG2009 Transcription initiati 69.7 6.1 0.00013 38.0 4.0 47 65-111 408-454 (584)
67 PF13404 HTH_AsnC-type: AsnC-t 67.7 1.8 4E-05 26.8 0.1 38 19-58 3-40 (42)
68 PRK11169 leucine-responsive tr 65.8 6.3 0.00014 31.4 2.9 45 71-116 13-58 (164)
69 smart00595 MADF subfamily of S 65.5 6.2 0.00013 27.7 2.5 27 87-114 29-55 (89)
70 KOG4167 Predicted DNA-binding 64.4 3.1 6.7E-05 41.0 1.0 44 13-58 619-662 (907)
71 PF11626 Rap1_C: TRF2-interact 64.1 6.9 0.00015 28.0 2.6 17 62-78 43-59 (87)
72 PF01388 ARID: ARID/BRIGHT DNA 63.8 14 0.00029 26.3 4.1 38 76-113 40-90 (92)
73 KOG1194 Predicted DNA-binding 61.0 4.7 0.0001 37.6 1.5 43 13-57 187-229 (534)
74 PRK11179 DNA-binding transcrip 60.4 3.7 8E-05 32.3 0.6 45 18-64 8-52 (153)
75 smart00501 BRIGHT BRIGHT, ARID 59.1 18 0.00038 25.9 4.0 39 76-114 36-87 (93)
76 PF11035 SnAPC_2_like: Small n 58.4 35 0.00075 30.6 6.3 49 66-115 21-73 (344)
77 PLN03142 Probable chromatin-re 58.0 5.1 0.00011 41.3 1.3 33 11-43 924-956 (1033)
78 TIGR02985 Sig70_bacteroi1 RNA 55.9 22 0.00048 27.0 4.4 38 75-113 119-156 (161)
79 PRK11169 leucine-responsive tr 55.4 3.9 8.5E-05 32.6 0.0 45 18-64 13-57 (164)
80 PF07750 GcrA: GcrA cell cycle 52.1 15 0.00032 29.6 2.9 40 68-108 2-41 (162)
81 KOG4468 Polycomb-group transcr 48.5 7.8 0.00017 37.5 0.8 47 13-61 88-144 (782)
82 cd08319 Death_RAIDD Death doma 46.2 23 0.00051 25.2 2.8 29 74-103 2-30 (83)
83 PF09420 Nop16: Ribosome bioge 46.0 48 0.001 26.4 5.0 47 65-111 113-163 (164)
84 PRK09645 RNA polymerase sigma 44.4 50 0.0011 25.7 4.9 37 83-120 132-171 (173)
85 smart00344 HTH_ASNC helix_turn 43.4 40 0.00086 24.3 3.8 45 72-117 3-48 (108)
86 PF10545 MADF_DNA_bdg: Alcohol 42.8 19 0.00041 24.5 1.9 28 87-114 28-56 (85)
87 PF10440 WIYLD: Ubiquitin-bind 42.2 18 0.00039 24.7 1.6 26 68-93 22-48 (65)
88 PF09905 DUF2132: Uncharacteri 40.7 16 0.00034 24.9 1.1 44 21-77 12-62 (64)
89 KOG3554 Histone deacetylase co 39.5 33 0.00072 32.4 3.4 42 67-108 286-328 (693)
90 TIGR02937 sigma70-ECF RNA poly 39.2 50 0.0011 24.2 3.9 34 79-113 120-153 (158)
91 PF11035 SnAPC_2_like: Small n 38.7 78 0.0017 28.4 5.4 87 13-113 21-128 (344)
92 PF02954 HTH_8: Bacterial regu 38.4 51 0.0011 19.9 3.1 34 72-106 5-38 (42)
93 cd06171 Sigma70_r4 Sigma70, re 38.3 71 0.0015 18.8 4.0 37 73-110 14-50 (55)
94 PF07638 Sigma70_ECF: ECF sigm 37.9 48 0.001 26.7 3.8 36 75-111 141-176 (185)
95 cd08803 Death_ank3 Death domai 37.3 44 0.00096 23.8 3.1 29 74-103 4-32 (84)
96 PF04504 DUF573: Protein of un 35.7 62 0.0013 23.7 3.8 48 67-114 5-65 (98)
97 PRK12529 RNA polymerase sigma 35.1 87 0.0019 24.7 4.9 35 82-117 140-174 (178)
98 PRK09652 RNA polymerase sigma 35.0 64 0.0014 24.9 4.1 33 80-113 139-171 (182)
99 KOG2009 Transcription initiati 34.7 30 0.00064 33.5 2.4 48 9-58 405-452 (584)
100 PRK12532 RNA polymerase sigma 33.8 83 0.0018 25.1 4.7 38 83-121 150-190 (195)
101 cd08317 Death_ank Death domain 33.6 38 0.00083 23.8 2.3 29 74-103 4-32 (84)
102 PRK04217 hypothetical protein; 33.6 81 0.0017 23.7 4.2 45 68-114 42-86 (110)
103 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 32.8 61 0.0013 20.9 2.9 34 72-106 7-40 (50)
104 PRK11924 RNA polymerase sigma 32.5 72 0.0016 24.5 4.0 30 83-113 139-168 (179)
105 PRK09643 RNA polymerase sigma 32.2 77 0.0017 25.4 4.2 31 82-113 147-177 (192)
106 COG1522 Lrp Transcriptional re 32.0 64 0.0014 24.6 3.6 44 72-116 8-52 (154)
107 PF13936 HTH_38: Helix-turn-he 31.9 41 0.00088 20.7 1.9 36 68-105 4-39 (44)
108 COG4628 Uncharacterized conser 31.4 41 0.00089 25.7 2.2 45 21-78 21-72 (136)
109 COG2963 Transposase and inacti 29.9 1.3E+02 0.0027 22.1 4.7 45 66-111 5-50 (116)
110 PRK09641 RNA polymerase sigma 29.8 85 0.0018 24.6 4.0 29 84-113 151-179 (187)
111 PRK12523 RNA polymerase sigma 28.8 1.3E+02 0.0028 23.4 5.0 35 79-114 129-163 (172)
112 PRK09047 RNA polymerase factor 28.5 1.1E+02 0.0023 23.3 4.3 30 83-113 120-149 (161)
113 cd08804 Death_ank2 Death domai 28.4 62 0.0013 22.9 2.7 31 74-105 4-34 (84)
114 smart00344 HTH_ASNC helix_turn 28.4 28 0.00061 25.1 0.9 44 19-64 3-46 (108)
115 COG1522 Lrp Transcriptional re 28.4 23 0.0005 27.2 0.4 44 19-64 8-51 (154)
116 TIGR02954 Sig70_famx3 RNA poly 28.2 96 0.0021 24.0 4.0 29 84-113 134-162 (169)
117 PRK09637 RNA polymerase sigma 28.1 98 0.0021 24.6 4.1 30 83-113 120-149 (181)
118 COG2197 CitB Response regulato 27.8 77 0.0017 26.2 3.5 44 68-114 148-191 (211)
119 smart00005 DEATH DEATH domain, 27.5 63 0.0014 22.3 2.6 29 74-103 5-34 (88)
120 TIGR02939 RpoE_Sigma70 RNA pol 27.5 77 0.0017 24.9 3.4 30 84-114 153-182 (190)
121 PF00046 Homeobox: Homeobox do 27.5 1.6E+02 0.0034 18.4 4.3 47 65-112 3-53 (57)
122 cd08318 Death_NMPP84 Death dom 27.3 69 0.0015 22.7 2.8 25 78-103 11-35 (86)
123 PRK12515 RNA polymerase sigma 26.6 1.1E+02 0.0025 24.1 4.3 29 84-113 146-174 (189)
124 PRK12531 RNA polymerase sigma 26.5 1.1E+02 0.0025 24.3 4.3 29 84-113 156-184 (194)
125 PF09420 Nop16: Ribosome bioge 26.0 44 0.00096 26.7 1.7 46 11-57 112-160 (164)
126 PRK05602 RNA polymerase sigma 26.0 1.4E+02 0.0031 23.4 4.8 37 84-121 143-182 (186)
127 PRK09648 RNA polymerase sigma 25.7 1.2E+02 0.0026 24.0 4.3 30 83-113 153-182 (189)
128 PRK12512 RNA polymerase sigma 25.6 1.2E+02 0.0026 23.8 4.3 30 84-114 146-175 (184)
129 PF09197 Rap1-DNA-bind: Rap1, 25.3 64 0.0014 24.2 2.3 26 89-114 53-78 (105)
130 TIGR02948 SigW_bacill RNA poly 25.1 1.1E+02 0.0023 24.0 3.8 28 85-113 152-179 (187)
131 PRK12545 RNA polymerase sigma 24.8 1.4E+02 0.0031 24.1 4.6 37 84-121 154-193 (201)
132 PRK09642 RNA polymerase sigma 24.7 1.3E+02 0.0029 22.9 4.3 29 83-112 120-148 (160)
133 KOG0384 Chromodomain-helicase 24.7 45 0.00098 35.2 1.8 25 68-92 1135-1160(1373)
134 TIGR02943 Sig70_famx1 RNA poly 24.7 1.3E+02 0.0029 23.9 4.3 33 80-113 142-174 (188)
135 PRK01905 DNA-binding protein F 24.2 1.5E+02 0.0032 20.5 3.9 35 71-106 36-70 (77)
136 PRK11923 algU RNA polymerase s 24.1 1.2E+02 0.0026 24.1 3.9 28 85-113 154-181 (193)
137 cd08777 Death_RIP1 Death Domai 24.0 75 0.0016 22.6 2.4 29 76-105 4-32 (86)
138 PRK12530 RNA polymerase sigma 23.2 1.4E+02 0.003 23.8 4.2 28 84-112 149-176 (189)
139 cd08779 Death_PIDD Death Domai 23.0 73 0.0016 22.6 2.2 26 75-101 3-28 (86)
140 cd08311 Death_p75NR Death doma 22.3 79 0.0017 22.1 2.2 33 71-105 2-34 (77)
141 PF07750 GcrA: GcrA cell cycle 22.2 61 0.0013 26.0 1.8 38 15-55 2-39 (162)
142 cd08805 Death_ank1 Death domai 22.2 90 0.002 22.2 2.5 22 74-95 4-25 (84)
143 COG3795 Uncharacterized protei 22.0 83 0.0018 24.3 2.4 59 14-76 15-78 (123)
144 PF00196 GerE: Bacterial regul 21.6 90 0.0019 19.9 2.3 44 68-114 3-46 (58)
145 PRK12514 RNA polymerase sigma 21.5 1.6E+02 0.0034 23.0 4.2 29 84-113 144-172 (179)
146 PRK12527 RNA polymerase sigma 21.2 1.8E+02 0.0039 22.1 4.4 29 84-113 120-148 (159)
147 PRK09651 RNA polymerase sigma 21.0 1.6E+02 0.0035 22.9 4.1 30 84-114 134-163 (172)
148 PRK09649 RNA polymerase sigma 20.9 1.6E+02 0.0034 23.4 4.0 31 84-115 145-175 (185)
149 PRK06759 RNA polymerase factor 20.9 1.8E+02 0.0039 21.9 4.3 29 84-113 121-149 (154)
150 PRK12524 RNA polymerase sigma 20.9 1.7E+02 0.0036 23.4 4.2 30 83-113 150-179 (196)
151 TIGR02999 Sig-70_X6 RNA polyme 20.5 1.8E+02 0.0039 22.6 4.3 29 84-113 149-177 (183)
152 cd01852 AIG1 AIG1 (avrRpt2-ind 20.5 3.8E+02 0.0082 21.2 6.3 70 15-96 95-164 (196)
153 PRK00118 putative DNA-binding 20.4 2E+02 0.0043 21.4 4.2 39 71-110 19-57 (104)
154 PRK00430 fis global DNA-bindin 20.2 1.9E+02 0.0042 20.9 4.0 33 72-105 55-87 (95)
155 PRK12528 RNA polymerase sigma 20.2 1.9E+02 0.0042 22.0 4.3 30 82-112 126-155 (161)
156 PRK12536 RNA polymerase sigma 20.1 1.8E+02 0.0039 22.8 4.2 31 83-114 143-173 (181)
No 1
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=6e-40 Score=275.30 Aligned_cols=130 Identities=61% Similarity=1.250 Sum_probs=123.9
Q ss_pred CCCccCCCCCCcCCCCHHHHHHHHHHHHHhCCCccccccccccccccccccccchhhcccCCCcCCCCChHHHHHHHHHH
Q 044864 2 RKPCCDKQDTNKGAWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYLRPDLKRGNFAEDEEDLIIKLH 81 (214)
Q Consensus 2 r~~~~~k~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~~~~~~Wt~eED~~L~~lv 81 (214)
+.|||+|+++++++||+|||++|+++|++||..+|..||+.++++|+++|||+||.++|+|.+++++||.|||++|++++
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 57999999999999999999999999999999899999999866899999999999999999999999999999999999
Q ss_pred HhhCCchhhhcccCCCCCHHHHHHHHHHHhhhhhhhCCCCccccccccCC
Q 044864 82 ALLGNRWSLIAGRLPGRTANEVKNYWNSHLRRKLINMGIDPKNHRLHHSL 131 (214)
Q Consensus 82 ~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~~~~~~~~~~e~~~~~~~ 131 (214)
..||++|+.||+.|||||+++||+||+.++++++.+.+.++.+..++...
T Consensus 94 ~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~p~~~kp~~~~ 143 (249)
T PLN03212 94 RLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGIDPQTHKPLDAN 143 (249)
T ss_pred HhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCCCCCCCCCCcc
Confidence 99999999999999999999999999999999999999999887765443
No 2
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=1.5e-38 Score=284.37 Aligned_cols=131 Identities=62% Similarity=1.175 Sum_probs=125.1
Q ss_pred CCCccCCCCCCcCCCCHHHHHHHHHHHHHhCCCccccccccccccccccccccchhhcccCCCcCCCCChHHHHHHHHHH
Q 044864 2 RKPCCDKQDTNKGAWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYLRPDLKRGNFAEDEEDLIIKLH 81 (214)
Q Consensus 2 r~~~~~k~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~~~~~~Wt~eED~~L~~lv 81 (214)
|++||+|++++||+||+|||++|+++|.+||.++|..||+.++++|+++|||+||.++|+|.+++++||.|||++|++++
T Consensus 3 r~~Cc~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~ 82 (459)
T PLN03091 3 RHSCCYKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELH 82 (459)
T ss_pred CCccCcCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHH
Confidence 89999999999999999999999999999999999999998876899999999999999999999999999999999999
Q ss_pred HhhCCchhhhcccCCCCCHHHHHHHHHHHhhhhhhhCCCCccccccccCCC
Q 044864 82 ALLGNRWSLIAGRLPGRTANEVKNYWNSHLRRKLINMGIDPKNHRLHHSLP 132 (214)
Q Consensus 82 ~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~~~~~~~~~~e~~~~~~~~ 132 (214)
..||++|..||..|||||+++||+||+.+|+++++..++.+.++.++.+..
T Consensus 83 k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~I~p~t~kpl~e~E 133 (459)
T PLN03091 83 AVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRGIDPNTHKPLSEVE 133 (459)
T ss_pred HHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCCCCCCCCccccc
Confidence 999999999999999999999999999999999998888888877766543
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=3.1e-36 Score=256.58 Aligned_cols=114 Identities=68% Similarity=1.207 Sum_probs=108.9
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCccccccccccccccccccccchhhcccCCCcCCCCChHHHHHHHHHHHhhCCchhh
Q 044864 11 TNKGAWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYLRPDLKRGNFAEDEEDLIIKLHALLGNRWSL 90 (214)
Q Consensus 11 ~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~~~~~~Wt~eED~~L~~lv~~~G~~W~~ 90 (214)
+.||+||+|||++|+++|++||.++|..||+.+|++|++++||.||.|||+|++++|.||+|||++|++++..+|++|+.
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 34899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcccCCCCCHHHHHHHHHHHhhhhhhhCCCCccc
Q 044864 91 IAGRLPGRTANEVKNYWNSHLRRKLINMGIDPKN 124 (214)
Q Consensus 91 Ia~~lpgRt~~q~r~rw~~~l~~~~~~~~~~~~e 124 (214)
||++|||||++.||++|+.+|++++...+..+..
T Consensus 87 IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~~~~~~ 120 (238)
T KOG0048|consen 87 IAGRLPGRTDNEVKNHWNTHLKKKLLKMGIDPST 120 (238)
T ss_pred HHhhCCCcCHHHHHHHHHHHHHHHHHHcCCCCCc
Confidence 9999999999999999999999999988754444
No 4
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.89 E-value=3.4e-25 Score=188.76 Aligned_cols=97 Identities=16% Similarity=0.222 Sum_probs=92.3
Q ss_pred CCCcCCCCChHHHHHHHHHHHhhC-CchhhhcccCC-CCCHHHHHHHHHHHhhhhhhhCCCCccccccccCCCC-CCCCc
Q 044864 62 PDLKRGNFAEDEEDLIIKLHALLG-NRWSLIAGRLP-GRTANEVKNYWNSHLRRKLINMGIDPKNHRLHHSLPH-NSTGA 138 (214)
Q Consensus 62 p~~~~~~Wt~eED~~L~~lv~~~G-~~W~~Ia~~lp-gRt~~q~r~rw~~~l~~~~~~~~~~~~e~~~~~~~~~-~~~~~ 138 (214)
+.+.+|+||.|||++|+++|..|| ++|..|++.++ +|++++||.||.+||+|.|+++.||++|+.+|..++. +|++|
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrW 84 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRW 84 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHH
Confidence 345579999999999999999999 78999999998 9999999999999999999999999999999999998 99999
Q ss_pred cccccccCCCCCCCCCCCCC
Q 044864 139 TSLGQQLVDMNEPAVKPRGD 158 (214)
Q Consensus 139 s~~~~~~~~~~~~~vkn~~~ 158 (214)
+.||..|||||||.|||+++
T Consensus 85 s~IA~~LPGRTDNeIKN~Wn 104 (238)
T KOG0048|consen 85 SLIAGRLPGRTDNEVKNHWN 104 (238)
T ss_pred HHHHhhCCCcCHHHHHHHHH
Confidence 99999999999999999874
No 5
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.89 E-value=2.3e-24 Score=181.30 Aligned_cols=109 Identities=17% Similarity=0.316 Sum_probs=98.5
Q ss_pred ccccccccccccchhhcccCCCcCCCCChHHHHHHHHHHHhhC-CchhhhcccC-CCCCHHHHHHHHHHHhhhhhhhCCC
Q 044864 43 AGLARCGKSCRLRWINYLRPDLKRGNFAEDEEDLIIKLHALLG-NRWSLIAGRL-PGRTANEVKNYWNSHLRRKLINMGI 120 (214)
Q Consensus 43 ~~~~Rs~~qcr~Rw~~~l~p~~~~~~Wt~eED~~L~~lv~~~G-~~W~~Ia~~l-pgRt~~q~r~rw~~~l~~~~~~~~~ 120 (214)
++ .|+..-|. .+.+++++||+|||++|+++|.+|| .+|..||+.| +|||++|||.||.++|+|.+++++|
T Consensus 10 ~~-~~~~pcc~-------K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpW 81 (249)
T PLN03212 10 VS-KKTTPCCT-------KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGI 81 (249)
T ss_pred CC-CCCCCCcc-------cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCC
Confidence 44 56665553 3578899999999999999999999 7899999998 6999999999999999999999999
Q ss_pred CccccccccCCCC-CCCCccccccccCCCCCCCCCCCCCc
Q 044864 121 DPKNHRLHHSLPH-NSTGATSLGQQLVDMNEPAVKPRGDD 159 (214)
Q Consensus 121 ~~~e~~~~~~~~~-~~~~~s~~~~~~~~~~~~~vkn~~~~ 159 (214)
|.+||.+|...+. +|++|+.|+..++||+++.||||++.
T Consensus 82 T~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns 121 (249)
T PLN03212 82 TSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNT 121 (249)
T ss_pred ChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHH
Confidence 9999999888876 89999999999999999999999754
No 6
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.86 E-value=1.1e-22 Score=188.40 Aligned_cols=139 Identities=17% Similarity=0.291 Sum_probs=128.2
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCC---ccccccccccccccccccccchhhcccCCCcCCCCChHHHHHHHHHHHhhC-C
Q 044864 11 TNKGAWSKQEDQKLIDYIRKHGEG---CWRTIPQAAGLARCGKSCRLRWINYLRPDLKRGNFAEDEEDLIIKLHALLG-N 86 (214)
Q Consensus 11 ~~kg~WT~eED~~L~~~v~~~g~~---~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~~~~~~Wt~eED~~L~~lv~~~G-~ 86 (214)
+....||+|||.+|+++|+....+ +|.+|-.+|+ ||+..|...||...|+|++++|+||.+||.+|+.+|.+|| .
T Consensus 303 L~ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ymp-gr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~k 381 (939)
T KOG0049|consen 303 LSEKEWSEEEDTKLIALVKITSINSHIQWDKVVQYMP-GRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAK 381 (939)
T ss_pred HHhhhcchhhhHHHHHHHHHhhccCccchHHHHHhcC-CcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCcc
Confidence 445789999999999999998644 7999999999 9999999999999999999999999999999999999999 6
Q ss_pred chhhhcccCCCCCHHHHHHHHHHHhhhhhhhCCCCccccccccCCCC-CC-CCccccccccCCCCC
Q 044864 87 RWSLIAGRLPGRTANEVKNYWNSHLRRKLINMGIDPKNHRLHHSLPH-NS-TGATSLGQQLVDMNE 150 (214)
Q Consensus 87 ~W~~Ia~~lpgRt~~q~r~rw~~~l~~~~~~~~~~~~e~~~~~~~~~-~~-~~~s~~~~~~~~~~~ 150 (214)
.|.+|-..+|||++.|||.||.+.|...++.+.|+-.||..+..+.. +| ..|..+|..|+.++-
T Consensus 382 dw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~ 447 (939)
T KOG0049|consen 382 DWAKVRQAVPNRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTS 447 (939)
T ss_pred chhhHHHhcCCccHHHHHHHHHHHHHHhhccCceeecchHHHHHHHHHHccchHHHHHHHccccch
Confidence 79999999999999999999999999999999999999887777665 55 559999999998876
No 7
>PLN03091 hypothetical protein; Provisional
Probab=99.84 E-value=1.7e-22 Score=181.46 Aligned_cols=98 Identities=16% Similarity=0.273 Sum_probs=92.4
Q ss_pred CCCcCCCCChHHHHHHHHHHHhhC-CchhhhcccC-CCCCHHHHHHHHHHHhhhhhhhCCCCccccccccCCCC-CCCCc
Q 044864 62 PDLKRGNFAEDEEDLIIKLHALLG-NRWSLIAGRL-PGRTANEVKNYWNSHLRRKLINMGIDPKNHRLHHSLPH-NSTGA 138 (214)
Q Consensus 62 p~~~~~~Wt~eED~~L~~lv~~~G-~~W~~Ia~~l-pgRt~~q~r~rw~~~l~~~~~~~~~~~~e~~~~~~~~~-~~~~~ 138 (214)
+.+++++||+|||++|+++|.+|| .+|..||+.+ +||+++|||.||.++|+|.+++++||++||.+|..++. +|++|
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k~~GnKW 89 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHAVLGNRW 89 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHHHhCcch
Confidence 578899999999999999999999 6899999988 59999999999999999999999999999999988877 99999
Q ss_pred cccccccCCCCCCCCCCCCCc
Q 044864 139 TSLGQQLVDMNEPAVKPRGDD 159 (214)
Q Consensus 139 s~~~~~~~~~~~~~vkn~~~~ 159 (214)
+.|+..++||+++.||||++.
T Consensus 90 skIAk~LPGRTDnqIKNRWns 110 (459)
T PLN03091 90 SQIAAQLPGRTDNEIKNLWNS 110 (459)
T ss_pred HHHHHhcCCCCHHHHHHHHHH
Confidence 999999999999999999753
No 8
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.82 E-value=1e-20 Score=175.42 Aligned_cols=104 Identities=24% Similarity=0.427 Sum_probs=96.7
Q ss_pred CCCccCCCCCCcCCCCHHHHHHHHHHHHHhCCCccccccccccccccccccccchhhcccCCCcCCCCChHHHHHHHHHH
Q 044864 2 RKPCCDKQDTNKGAWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYLRPDLKRGNFAEDEEDLIIKLH 81 (214)
Q Consensus 2 r~~~~~k~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~~~~~~Wt~eED~~L~~lv 81 (214)
|+...-.|++++|.||++||.+|+.+|.+||.++|.+|-+.+| +|+..|||+||.|+|+...+.+.||-.||+.|+.+|
T Consensus 349 R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vP-nRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~~V 427 (939)
T KOG0049|consen 349 RFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVP-NRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLYAV 427 (939)
T ss_pred hheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcC-CccHHHHHHHHHHHHHHhhccCceeecchHHHHHHH
Confidence 4445567999999999999999999999999999999999999 999999999999999999999999999999999999
Q ss_pred HhhC-CchhhhcccCCCCCHHHHHHH
Q 044864 82 ALLG-NRWSLIAGRLPGRTANEVKNY 106 (214)
Q Consensus 82 ~~~G-~~W~~Ia~~lpgRt~~q~r~r 106 (214)
..|| ++|.+||..||+||++|.+.|
T Consensus 428 ~~YG~g~WakcA~~Lp~~t~~q~~rr 453 (939)
T KOG0049|consen 428 KVYGKGNWAKCAMLLPKKTSRQLRRR 453 (939)
T ss_pred HHHccchHHHHHHHccccchhHHHHH
Confidence 9999 899999999999999665433
No 9
>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=99.71 E-value=5.1e-18 Score=114.68 Aligned_cols=60 Identities=38% Similarity=0.887 Sum_probs=55.0
Q ss_pred CCHHHHHHHHHHHHHhCCCccccccccccccccccccccchhhcccCCCcCCCCChHHHHHH
Q 044864 16 WSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYLRPDLKRGNFAEDEEDLI 77 (214)
Q Consensus 16 WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~~~~~~Wt~eED~~L 77 (214)
||+|||++|+.+|..||. +|..||+.|| .|++.||+.||.++|.+.+++++||.+||++|
T Consensus 1 WT~eEd~~L~~~~~~~g~-~W~~Ia~~l~-~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN-DWKKIAEHLG-NRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS--HHHHHHHST-TS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc-CHHHHHHHHC-cCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 999999999999999994 6999999997 89999999999999999999999999999987
No 10
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.66 E-value=9.4e-17 Score=148.32 Aligned_cols=115 Identities=28% Similarity=0.482 Sum_probs=106.8
Q ss_pred CCCCCCcCCCCHHHHHHHHHHHHHhCCCccccccccccccccccccccchhhcccCCCcCCCCChHHHHHHHHHHHhhCC
Q 044864 7 DKQDTNKGAWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYLRPDLKRGNFAEDEEDLIIKLHALLGN 86 (214)
Q Consensus 7 ~k~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~~~~~~Wt~eED~~L~~lv~~~G~ 86 (214)
...+.+.|.|+..||+.|..+|+.||..+|..||..+. .++++||+.||.++++|.+++..|+.+||..|+.+..++|.
T Consensus 14 ~~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~-~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~ 92 (512)
T COG5147 14 MQTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLI-SSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGT 92 (512)
T ss_pred ccceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhc-ccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCc
Confidence 45678899999999999999999999999999999998 79999999999999999999999999999999999999999
Q ss_pred chhhhcccCCCCCHHHHHHHHHHHhhhhhhhCCCCcc
Q 044864 87 RWSLIAGRLPGRTANEVKNYWNSHLRRKLINMGIDPK 123 (214)
Q Consensus 87 ~W~~Ia~~lpgRt~~q~r~rw~~~l~~~~~~~~~~~~ 123 (214)
.|+.||..+++|+..+|.+||...+..... ..++..
T Consensus 93 ~wstia~~~d~rt~~~~~ery~~~~~~~~s-~~~s~~ 128 (512)
T COG5147 93 QWSTIADYKDRRTAQQCVERYVNTLEDLSS-THDSKL 128 (512)
T ss_pred hhhhhccccCccchHHHHHHHHHHhhhhhc-cccccc
Confidence 999999999999999999999999988766 344433
No 11
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.63 E-value=8.6e-17 Score=146.33 Aligned_cols=107 Identities=24% Similarity=0.532 Sum_probs=101.6
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCccccccccccccccccccccchhhcccCCCcCCCCChHHHHHHHHHHHhhCCchhh
Q 044864 11 TNKGAWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYLRPDLKRGNFAEDEEDLIIKLHALLGNRWSL 90 (214)
Q Consensus 11 ~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~~~~~~Wt~eED~~L~~lv~~~G~~W~~ 90 (214)
++.|.|+.-||+.|..+|.+||...|+.|++.+. -.+++||+.||..+|+|.+++..|+.+||++|+.+...+...|..
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 4679999999999999999999999999999998 889999999999999999999999999999999999999999999
Q ss_pred hcccCCCCCHHHHHHHHHHHhhhhhhhCC
Q 044864 91 IAGRLPGRTANEVKNYWNSHLRRKLINMG 119 (214)
Q Consensus 91 Ia~~lpgRt~~q~r~rw~~~l~~~~~~~~ 119 (214)
|+..| ||+++||-.||++.+........
T Consensus 84 Ia~i~-gr~~~qc~eRy~~ll~~~~s~~~ 111 (617)
T KOG0050|consen 84 IADIM-GRTSQQCLERYNNLLDVYVSYHY 111 (617)
T ss_pred HHHHh-hhhHHHHHHHHHHHHHHHHhhhc
Confidence 99999 99999999999999998876543
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=99.60 E-value=4e-16 Score=105.34 Aligned_cols=59 Identities=29% Similarity=0.574 Sum_probs=53.3
Q ss_pred CChHHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHHHHHHHhhhhhhhCCCCcccccc
Q 044864 69 FAEDEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKNYWNSHLRRKLINMGIDPKNHRL 127 (214)
Q Consensus 69 Wt~eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~~~~~~~~~~e~~~ 127 (214)
||++||++|+++|..||.+|..||..|+.||+.+|++||..+|.+.+.+++|+++|+..
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~ 59 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQR 59 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHhc
Confidence 99999999999999999999999999966999999999999999999999999999864
No 13
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.54 E-value=6.4e-15 Score=137.58 Aligned_cols=135 Identities=23% Similarity=0.440 Sum_probs=107.5
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCccccccccccccccccccccchhhcccCCC--cCCCCChHHHHHHHHHHH-------
Q 044864 12 NKGAWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYLRPDL--KRGNFAEDEEDLIIKLHA------- 82 (214)
Q Consensus 12 ~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~~--~~~~Wt~eED~~L~~lv~------- 82 (214)
.+|+||+||++.|..+|.++| ++|..|+..|+ |.+..|++||.+|...+- +++.||.||+++|+++|.
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 799999999999999999999 56999999996 999999999999998884 899999999999999995
Q ss_pred hh-------------------CCchhhhcccCCCCCHHHHHHHHHHHhhhhhhh-CCCCcccc--ccccCCC-----C-C
Q 044864 83 LL-------------------GNRWSLIAGRLPGRTANEVKNYWNSHLRRKLIN-MGIDPKNH--RLHHSLP-----H-N 134 (214)
Q Consensus 83 ~~-------------------G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~~~~-~~~~~~e~--~~~~~~~-----~-~ 134 (214)
.+ +.+|..|+..+..|+..||+-+|+.++...... ..+...-+ .++-.+. . .
T Consensus 460 q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n~~~~~~~~~~v~l~ErL~dl~~~e~~ 539 (607)
T KOG0051|consen 460 QPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFNKRQESKGSDMVWLLERLSDLDLTEES 539 (607)
T ss_pred cccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhhcccccccchhHHHHHHHHhcccccCC
Confidence 33 136999999999999999999999988877554 44443111 1111111 1 2
Q ss_pred CCCccccccccCCCC
Q 044864 135 STGATSLGQQLVDMN 149 (214)
Q Consensus 135 ~~~~s~~~~~~~~~~ 149 (214)
.--|..++...++..
T Consensus 540 ~IDW~~l~~~~~g~~ 554 (607)
T KOG0051|consen 540 PIDWKSLAEYAPGES 554 (607)
T ss_pred ccCHHHHHHhCCCCC
Confidence 344888888877764
No 14
>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=99.51 E-value=3.1e-15 Score=96.85 Aligned_cols=48 Identities=35% Similarity=0.795 Sum_probs=43.6
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCccccccccccccccccccccchhhcc
Q 044864 13 KGAWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYL 60 (214)
Q Consensus 13 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l 60 (214)
||+||+|||++|+++|.+||.++|..||..|+.+||..||+.||.++|
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 689999999999999999998889999999988999999999999875
No 15
>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=99.48 E-value=3.6e-14 Score=91.80 Aligned_cols=46 Identities=33% Similarity=0.702 Sum_probs=41.8
Q ss_pred CCCCChHHHHHHHHHHHhhCCc-hhhhcccCC-CCCHHHHHHHHHHHh
Q 044864 66 RGNFAEDEEDLIIKLHALLGNR-WSLIAGRLP-GRTANEVKNYWNSHL 111 (214)
Q Consensus 66 ~~~Wt~eED~~L~~lv~~~G~~-W~~Ia~~lp-gRt~~q~r~rw~~~l 111 (214)
+++||+|||++|+++|.+||.. |..||..|+ |||..||++||++++
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 5799999999999999999977 999999999 999999999999875
No 16
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.28 E-value=5.9e-12 Score=79.97 Aligned_cols=47 Identities=43% Similarity=0.892 Sum_probs=44.3
Q ss_pred CCCCChHHHHHHHHHHHhhC-CchhhhcccCCCCCHHHHHHHHHHHhh
Q 044864 66 RGNFAEDEEDLIIKLHALLG-NRWSLIAGRLPGRTANEVKNYWNSHLR 112 (214)
Q Consensus 66 ~~~Wt~eED~~L~~lv~~~G-~~W~~Ia~~lpgRt~~q~r~rw~~~l~ 112 (214)
+++||++||.+|+.++..|| .+|..||..|++||+.+|+.||+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 36899999999999999999 999999999999999999999998764
No 17
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.20 E-value=7.7e-12 Score=117.12 Aligned_cols=141 Identities=20% Similarity=0.246 Sum_probs=111.9
Q ss_pred CcCCCCHHHHHHHHHHHHHh----CC-------------------Ccccccccccccccccccccc---chhhcccCCCc
Q 044864 12 NKGAWSKQEDQKLIDYIRKH----GE-------------------GCWRTIPQAAGLARCGKSCRL---RWINYLRPDLK 65 (214)
Q Consensus 12 ~kg~WT~eED~~L~~~v~~~----g~-------------------~~W~~Ia~~~~~~Rs~~qcr~---Rw~~~l~p~~~ 65 (214)
+-+.|+.+||+.|...|..| |- +.|..|...|| .|+....+. |-++.|.+ .
T Consensus 307 ~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp-~R~~~siy~~~rR~y~~FE~--~ 383 (607)
T KOG0051|consen 307 NLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLP-YRDRKSIYHHLRRAYTPFEN--K 383 (607)
T ss_pred hhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcC-cccchhHHHHHHhcCCcccc--c
Confidence 44899999999999999988 10 13778888888 699988877 33334443 8
Q ss_pred CCCCChHHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHHHHHHHhhhh--hhhCCCCccccccccCCC-----------
Q 044864 66 RGNFAEDEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKNYWNSHLRRK--LINMGIDPKNHRLHHSLP----------- 132 (214)
Q Consensus 66 ~~~Wt~eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~--~~~~~~~~~e~~~~~~~~----------- 132 (214)
+|.||++|++.|..+|.++|+.|..|+..| ||.+..|+.||.++.... ..++.|+.+|...+....
T Consensus 384 rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~q~q 462 (607)
T KOG0051|consen 384 RGKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREALQPQ 462 (607)
T ss_pred cCCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhhccc
Confidence 999999999999999999999999999999 999999999999999887 589999988866443221
Q ss_pred --------C--------CCCCccccccccCCCCCCCCCCC
Q 044864 133 --------H--------NSTGATSLGQQLVDMNEPAVKPR 156 (214)
Q Consensus 133 --------~--------~~~~~s~~~~~~~~~~~~~vkn~ 156 (214)
+ .+-.|+.++..+..|+-.++.-.
T Consensus 463 ~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~K 502 (607)
T KOG0051|consen 463 ASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYK 502 (607)
T ss_pred ccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHH
Confidence 1 23458888887777766555443
No 18
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.19 E-value=7.2e-12 Score=79.56 Aligned_cols=48 Identities=38% Similarity=0.864 Sum_probs=44.5
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCccccccccccccccccccccchhhccc
Q 044864 13 KGAWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYLR 61 (214)
Q Consensus 13 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~ 61 (214)
++.||++||++|+.++..||..+|..||..|+ +|++.+|+.||.+++.
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 47899999999999999999767999999999 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=99.17 E-value=4.4e-11 Score=74.75 Aligned_cols=44 Identities=34% Similarity=0.757 Sum_probs=41.7
Q ss_pred CCChHHHHHHHHHHHhhC-CchhhhcccCCCCCHHHHHHHHHHHh
Q 044864 68 NFAEDEEDLIIKLHALLG-NRWSLIAGRLPGRTANEVKNYWNSHL 111 (214)
Q Consensus 68 ~Wt~eED~~L~~lv~~~G-~~W~~Ia~~lpgRt~~q~r~rw~~~l 111 (214)
+||.+|+..|+.++..|| .+|..||..|++||..+|+.||++++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 99999999999999999999998763
No 20
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.06 E-value=5.9e-11 Score=74.14 Aligned_cols=45 Identities=36% Similarity=0.809 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHHHHHHhCCCccccccccccccccccccccchhhcc
Q 044864 15 AWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYL 60 (214)
Q Consensus 15 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l 60 (214)
.||++||+.|+.++..||.++|..||..++ +|+..+|+.||.+++
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 21
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=98.98 E-value=4.1e-11 Score=111.16 Aligned_cols=100 Identities=21% Similarity=0.273 Sum_probs=91.4
Q ss_pred CCcCCCCChHHHHHHHHHHHhhC-CchhhhcccCCCCCHHHHHHHHHHHhhhhhhhCCCCccccccccCCCC-CCCCccc
Q 044864 63 DLKRGNFAEDEEDLIIKLHALLG-NRWSLIAGRLPGRTANEVKNYWNSHLRRKLINMGIDPKNHRLHHSLPH-NSTGATS 140 (214)
Q Consensus 63 ~~~~~~Wt~eED~~L~~lv~~~G-~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~~~~~~~~~~e~~~~~~~~~-~~~~~s~ 140 (214)
..+.|.|+..||+.|..+|..|| ++|+.||..|.-+++++|+.||++++.+.+++.+|+.+|+..+..+.. .|+.|+.
T Consensus 17 ~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~wst 96 (512)
T COG5147 17 KRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQWST 96 (512)
T ss_pred eecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCchhhh
Confidence 45678999999999999999999 789999999988999999999999999999999999999998888776 8999999
Q ss_pred cccccCCCCCCCCCCCCCcccc
Q 044864 141 LGQQLVDMNEPAVKPRGDDIYQ 162 (214)
Q Consensus 141 ~~~~~~~~~~~~vkn~~~~~~~ 162 (214)
|+...++++..++.+++...+.
T Consensus 97 ia~~~d~rt~~~~~ery~~~~~ 118 (512)
T COG5147 97 IADYKDRRTAQQCVERYVNTLE 118 (512)
T ss_pred hccccCccchHHHHHHHHHHhh
Confidence 9999999999999888754444
No 22
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=98.65 E-value=7.8e-09 Score=94.96 Aligned_cols=93 Identities=19% Similarity=0.291 Sum_probs=81.4
Q ss_pred CcCCCCChHHHHHHHHHHHhhC-CchhhhcccCCCCCHHHHHHHHHHHhhhhhhhCCCCccccccccCCCC-CCCCcccc
Q 044864 64 LKRGNFAEDEEDLIIKLHALLG-NRWSLIAGRLPGRTANEVKNYWNSHLRRKLINMGIDPKNHRLHHSLPH-NSTGATSL 141 (214)
Q Consensus 64 ~~~~~Wt~eED~~L~~lv~~~G-~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~~~~~~~~~~e~~~~~~~~~-~~~~~s~~ 141 (214)
++.|.|+.-||+.|-.+|.+|| +.|+.|++.++-.|..||+.||..+++|.|++..|+.+||..++.+.. ..+.|..|
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrtI 84 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRTI 84 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccchH
Confidence 4678999999999999999999 789999999999999999999999999999999999999987666655 78889999
Q ss_pred ccccCCCCCCCCCCCC
Q 044864 142 GQQLVDMNEPAVKPRG 157 (214)
Q Consensus 142 ~~~~~~~~~~~vkn~~ 157 (214)
+..+ ||+.+++-.|+
T Consensus 85 a~i~-gr~~~qc~eRy 99 (617)
T KOG0050|consen 85 ADIM-GRTSQQCLERY 99 (617)
T ss_pred HHHh-hhhHHHHHHHH
Confidence 9876 55666655554
No 23
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.06 E-value=1.5e-06 Score=78.73 Aligned_cols=49 Identities=18% Similarity=0.516 Sum_probs=45.8
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCccccccccccccccccccccchhhcc
Q 044864 11 TNKGAWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYL 60 (214)
Q Consensus 11 ~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l 60 (214)
+-...||.+|+-+|++++..||.|||..||.++| .|+..+|+++|.+++
T Consensus 70 i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIG-tKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETYGFGNWQDIADHIG-TKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHc-ccchHHHHHHHHHHH
Confidence 4567899999999999999999999999999999 999999999999854
No 24
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=98.02 E-value=3.2e-06 Score=56.64 Aligned_cols=48 Identities=13% Similarity=0.315 Sum_probs=42.6
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCcc---ccccccccccc-cccccccchhhcc
Q 044864 13 KGAWSKQEDQKLIDYIRKHGEGCW---RTIPQAAGLAR-CGKSCRLRWINYL 60 (214)
Q Consensus 13 kg~WT~eED~~L~~~v~~~g~~~W---~~Ia~~~~~~R-s~~qcr~Rw~~~l 60 (214)
+-.||+||..+++++|+.+|.++| ..|++.|...+ |..||+.++..|.
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 567999999999999999998899 99999887556 9999999988764
No 25
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.84 E-value=2.2e-05 Score=71.31 Aligned_cols=50 Identities=24% Similarity=0.415 Sum_probs=45.2
Q ss_pred CCcCCCCChHHHHHHHHHHHhhC-CchhhhcccCCCCCHHHHHHHHHHHhh
Q 044864 63 DLKRGNFAEDEEDLIIKLHALLG-NRWSLIAGRLPGRTANEVKNYWNSHLR 112 (214)
Q Consensus 63 ~~~~~~Wt~eED~~L~~lv~~~G-~~W~~Ia~~lpgRt~~q~r~rw~~~l~ 112 (214)
.+-...||.+|+-+|++++..|| ++|..||.++..|+..+|+.+|.+++-
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHh
Confidence 44566899999999999999999 999999999988999999999987654
No 26
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.75 E-value=4.5e-05 Score=63.29 Aligned_cols=99 Identities=18% Similarity=0.375 Sum_probs=72.7
Q ss_pred CCCHHHHHHHHHHHHHhCCCcccccccccccc--ccccccccchhhcc-cCCC--------------------cCCCCCh
Q 044864 15 AWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLA--RCGKSCRLRWINYL-RPDL--------------------KRGNFAE 71 (214)
Q Consensus 15 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~--Rs~~qcr~Rw~~~l-~p~~--------------------~~~~Wt~ 71 (214)
+|++++|-+|+.+|..-. +-..|+..+... -|-..+.+||+..| +|.+ .+.+||.
T Consensus 1 rW~~~DDl~Li~av~~~~--~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~~is~~a~~~m~~l~p~~~~~iq~kalfS~ 78 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTN--DLESVHLGVKFSCKFTLQEIEERWYALLYDPVISRIAVAAMRNLHPELIAAIQSKALFSK 78 (199)
T ss_pred CCCchhhHHHHHHHHHhc--CHHHHHccCCcCCcCcHHHHHHHHHHHHcChhhHHHHHHHHHhCCcchhhcccccCCCCH
Confidence 699999999999998765 366666655432 36678889998765 4332 3668999
Q ss_pred HHHHHHHHHHHhhC---Cchhhh----cccC-CCCCHHHHHHHHHHHhhhhh
Q 044864 72 DEEDLIIKLHALLG---NRWSLI----AGRL-PGRTANEVKNYWNSHLRRKL 115 (214)
Q Consensus 72 eED~~L~~lv~~~G---~~W~~I----a~~l-pgRt~~q~r~rw~~~l~~~~ 115 (214)
+|+++|........ ..+.+| ...| ++||++++.++|..+.+..+
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~L 130 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHL 130 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhch
Confidence 99999999776554 346666 2223 88999999999986655543
No 27
>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=97.74 E-value=6.7e-05 Score=50.22 Aligned_cols=47 Identities=21% Similarity=0.252 Sum_probs=40.5
Q ss_pred CCCCChHHHHHHHHHHHhhCC-ch---hhhcccCC-CC-CHHHHHHHHHHHhh
Q 044864 66 RGNFAEDEEDLIIKLHALLGN-RW---SLIAGRLP-GR-TANEVKNYWNSHLR 112 (214)
Q Consensus 66 ~~~Wt~eED~~L~~lv~~~G~-~W---~~Ia~~lp-gR-t~~q~r~rw~~~l~ 112 (214)
+-.||+||..+.++++..||. +| ..|+..|. .+ |..||+.+...+..
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 457999999999999999995 99 99999873 45 99999998876653
No 28
>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=97.44 E-value=0.00015 Score=57.94 Aligned_cols=51 Identities=20% Similarity=0.359 Sum_probs=44.3
Q ss_pred cCCCCChHHHHHHHHHHHhh---C----CchhhhcccCCCCCHHHHHHHHHHHhhhhhh
Q 044864 65 KRGNFAEDEEDLIIKLHALL---G----NRWSLIAGRLPGRTANEVKNYWNSHLRRKLI 116 (214)
Q Consensus 65 ~~~~Wt~eED~~L~~lv~~~---G----~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~~~ 116 (214)
+...||.|||.+|.+.|-.| | .-+..++..| +||+..|.-||++++++...
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~ 60 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYE 60 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHH
Confidence 45689999999999999887 3 2388999999 99999999999999998754
No 29
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.25 E-value=0.0001 Score=67.60 Aligned_cols=46 Identities=24% Similarity=0.567 Sum_probs=42.3
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCccccccccccccccccccccchhhc
Q 044864 12 NKGAWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINY 59 (214)
Q Consensus 12 ~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~ 59 (214)
....||.+|..+|+++|+.||. +|.+||.+++ +|+.-||..||.++
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 4568999999999999999995 5999999999 99999999999864
No 30
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.21 E-value=0.0003 Score=64.64 Aligned_cols=45 Identities=16% Similarity=0.272 Sum_probs=42.1
Q ss_pred CCCCChHHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHHHHHHH
Q 044864 66 RGNFAEDEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKNYWNSH 110 (214)
Q Consensus 66 ~~~Wt~eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~ 110 (214)
...||.+|..+|++.+..||..|.+||.++.++|..||--+|.++
T Consensus 279 dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred cccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 448999999999999999999999999999999999999999753
No 31
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.19 E-value=0.00016 Score=67.69 Aligned_cols=47 Identities=21% Similarity=0.616 Sum_probs=42.9
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCccccccccccccccccccccchhhc
Q 044864 11 TNKGAWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINY 59 (214)
Q Consensus 11 ~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~ 59 (214)
--++.||.+|+-+|+++|+.||. +|.+||.+++ +|+..||..++.+.
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~d-dW~kVa~hVg-~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYGD-DWNKVADHVG-TKSQEQCILKFLRL 297 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhcc-cHHHHHhccC-CCCHHHHHHHHHhc
Confidence 34789999999999999999995 5999999999 99999999998764
No 32
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=97.18 E-value=0.00056 Score=46.98 Aligned_cols=50 Identities=18% Similarity=0.353 Sum_probs=32.7
Q ss_pred CCCCChHHHHHHHHHHHhhC-------C--chhhhcccCC-CCCHHHHHHHHHHHhhhhh
Q 044864 66 RGNFAEDEEDLIIKLHALLG-------N--RWSLIAGRLP-GRTANEVKNYWNSHLRRKL 115 (214)
Q Consensus 66 ~~~Wt~eED~~L~~lv~~~G-------~--~W~~Ia~~lp-gRt~~q~r~rw~~~l~~~~ 115 (214)
+.+||.+||..|++.|..+. + -|..++..-+ .+|-...|+||...|.++.
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 46899999999999997653 1 2999998877 9999999999999888764
No 33
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.15 E-value=0.00053 Score=64.35 Aligned_cols=46 Identities=17% Similarity=0.361 Sum_probs=42.6
Q ss_pred cCCCCChHHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHHHHHHH
Q 044864 65 KRGNFAEDEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKNYWNSH 110 (214)
Q Consensus 65 ~~~~Wt~eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~ 110 (214)
.+..||.+|..+|++.+..||.+|.+||.++.+||..||-.+|..+
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhc
Confidence 3668999999999999999999999999999999999999988653
No 34
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.11 E-value=0.0004 Score=49.73 Aligned_cols=49 Identities=27% Similarity=0.513 Sum_probs=35.8
Q ss_pred CCCChHHHHHHHHHHHh------hC--C------chhhhcccC----CCCCHHHHHHHHHHHhhhhh
Q 044864 67 GNFAEDEEDLIIKLHAL------LG--N------RWSLIAGRL----PGRTANEVKNYWNSHLRRKL 115 (214)
Q Consensus 67 ~~Wt~eED~~L~~lv~~------~G--~------~W~~Ia~~l----pgRt~~q~r~rw~~~l~~~~ 115 (214)
..||.+|...||.++.. ++ + -|..||..| ..||+.||+++|.++.+...
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk 68 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYK 68 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Confidence 47999999999999877 21 1 399999887 46999999999999777764
No 35
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=97.01 E-value=0.00021 Score=49.05 Aligned_cols=51 Identities=20% Similarity=0.489 Sum_probs=33.1
Q ss_pred cCCCCHHHHHHHHHHHHHhC--------CCccccccccccccccccccccchhhcccCC
Q 044864 13 KGAWSKQEDQKLIDYIRKHG--------EGCWRTIPQAAGLARCGKSCRLRWINYLRPD 63 (214)
Q Consensus 13 kg~WT~eED~~L~~~v~~~g--------~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~ 63 (214)
+.+||.|||+.|+++|..+. ..=|..+++..+..+|-.+-++||...|.+.
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~ 60 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGR 60 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT---
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcc
Confidence 46899999999999997662 2239999887765788899999999988764
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=96.99 E-value=0.00025 Score=56.78 Aligned_cols=50 Identities=32% Similarity=0.701 Sum_probs=42.4
Q ss_pred CCcCCCCHHHHHHHHHHHHHhC-CC-----ccccccccccccccccccccchhhcccC
Q 044864 11 TNKGAWSKQEDQKLIDYIRKHG-EG-----CWRTIPQAAGLARCGKSCRLRWINYLRP 62 (214)
Q Consensus 11 ~~kg~WT~eED~~L~~~v~~~g-~~-----~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p 62 (214)
.++..||.|||.+|.+.|-+|= .| ....|+..++ ||+..|.-||+.+++.
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~--RTsAACGFRWNs~VRk 57 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN--RTAAACGFRWNAYVRK 57 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc--ccHHHhcchHHHHHHH
Confidence 4678999999999999999992 11 4788888885 9999999999998874
No 37
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.36 E-value=0.0036 Score=50.75 Aligned_cols=50 Identities=18% Similarity=0.347 Sum_probs=42.3
Q ss_pred cCCCCChHHHHHHHHHHHhhCC-------chhhhcccCCCCCHHHHHHHHHHHhhhhh
Q 044864 65 KRGNFAEDEEDLIIKLHALLGN-------RWSLIAGRLPGRTANEVKNYWNSHLRRKL 115 (214)
Q Consensus 65 ~~~~Wt~eED~~L~~lv~~~G~-------~W~~Ia~~lpgRt~~q~r~rw~~~l~~~~ 115 (214)
+...||.|+|.+|-+.|..|+. -...++..| +||..+|..||+..+++..
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Y 60 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQY 60 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHH
Confidence 4668999999999999888872 266777888 9999999999999999764
No 38
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.34 E-value=0.001 Score=47.64 Aligned_cols=46 Identities=26% Similarity=0.687 Sum_probs=32.8
Q ss_pred CCCCHHHHHHHHHHHHH--h----CC-------Cccccccccc---cccccccccccchhhc
Q 044864 14 GAWSKQEDQKLIDYIRK--H----GE-------GCWRTIPQAA---GLARCGKSCRLRWINY 59 (214)
Q Consensus 14 g~WT~eED~~L~~~v~~--~----g~-------~~W~~Ia~~~---~~~Rs~~qcr~Rw~~~ 59 (214)
..||.+|...|+.++.. + +. .-|..||..| |..|++.||+.+|.++
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L 63 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL 63 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 57999999999999888 2 11 1399999876 4579999999999875
No 39
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.33 E-value=0.0011 Score=58.49 Aligned_cols=48 Identities=21% Similarity=0.525 Sum_probs=44.5
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCccccccccccccccccccccchhhccc
Q 044864 13 KGAWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYLR 61 (214)
Q Consensus 13 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~ 61 (214)
---|+..|+-+|++.....|.|||..||.++| .|....|+++|..++.
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiG-sr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIG-SRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHh-hhhhHHHHHHHHHHHh
Confidence 34699999999999999999999999999999 9999999999988654
No 40
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=96.21 E-value=0.01 Score=41.56 Aligned_cols=49 Identities=27% Similarity=0.535 Sum_probs=40.3
Q ss_pred CCCCChHHHHHHHHHHHhhC----C-------------chhhhcccC-----CCCCHHHHHHHHHHHhhhh
Q 044864 66 RGNFAEDEEDLIIKLHALLG----N-------------RWSLIAGRL-----PGRTANEVKNYWNSHLRRK 114 (214)
Q Consensus 66 ~~~Wt~eED~~L~~lv~~~G----~-------------~W~~Ia~~l-----pgRt~~q~r~rw~~~l~~~ 114 (214)
...||.+|...|++++.+|. + -|..|+..| +.||..+++.+|.++....
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 399998876 3699999999998876654
No 41
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.08 E-value=0.0054 Score=54.21 Aligned_cols=47 Identities=28% Similarity=0.434 Sum_probs=43.1
Q ss_pred CCCCChHHHHHHHHHHHhhC-CchhhhcccCCCCCHHHHHHHHHHHhh
Q 044864 66 RGNFAEDEEDLIIKLHALLG-NRWSLIAGRLPGRTANEVKNYWNSHLR 112 (214)
Q Consensus 66 ~~~Wt~eED~~L~~lv~~~G-~~W~~Ia~~lpgRt~~q~r~rw~~~l~ 112 (214)
-..|+.+|+.+|++....+| ++|..||.++..|+...|+.+|..+..
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 999999999988999999999976655
No 42
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=95.88 E-value=0.016 Score=59.03 Aligned_cols=100 Identities=16% Similarity=0.305 Sum_probs=77.4
Q ss_pred CCCHHHHHHHHHHHHHhCCCcccccccccccccccccccc-------chhhc----------------------------
Q 044864 15 AWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRL-------RWINY---------------------------- 59 (214)
Q Consensus 15 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~-------Rw~~~---------------------------- 59 (214)
.||..|=..++.+..+||..+-..||..|. +++...++. ||..+
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 599999999999999999989999999997 788776653 22110
Q ss_pred --------------cc-CCCcCCCCChHHHHHHHHHHHhhC-Cchhhhcc------------cCCCCCHHHHHHHHHHHh
Q 044864 60 --------------LR-PDLKRGNFAEDEEDLIIKLHALLG-NRWSLIAG------------RLPGRTANEVKNYWNSHL 111 (214)
Q Consensus 60 --------------l~-p~~~~~~Wt~eED~~L~~lv~~~G-~~W~~Ia~------------~lpgRt~~q~r~rw~~~l 111 (214)
+. +..++..||++||..|+-.+.+|| ++|..|-. ++..||+..+..|...+|
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 00 122344699999999999999999 88998832 235799999999999888
Q ss_pred hhhh
Q 044864 112 RRKL 115 (214)
Q Consensus 112 ~~~~ 115 (214)
.-..
T Consensus 985 ~~~~ 988 (1033)
T PLN03142 985 RLIE 988 (1033)
T ss_pred HHHH
Confidence 7653
No 43
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.72 E-value=0.0021 Score=52.06 Aligned_cols=50 Identities=24% Similarity=0.564 Sum_probs=40.0
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCC------ccccccccccccccccccccchhhcccC
Q 044864 11 TNKGAWSKQEDQKLIDYIRKHGEG------CWRTIPQAAGLARCGKSCRLRWINYLRP 62 (214)
Q Consensus 11 ~~kg~WT~eED~~L~~~v~~~g~~------~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p 62 (214)
.++..||.|||.+|.+.|-.|+.. ....++..+ +|++.+|..||+.+++.
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L--~rt~aac~fRwNs~vrk 58 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL--KRTAAACGFRWNSVVRK 58 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH--hhhHHHHHhHHHHHHHH
Confidence 568899999999999999999633 255566666 59999999999777653
No 44
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.10 E-value=0.0055 Score=42.90 Aligned_cols=49 Identities=24% Similarity=0.478 Sum_probs=39.4
Q ss_pred CcCCCCHHHHHHHHHHHHHhCC----------------Cccccccccc----cccccccccccchhhcc
Q 044864 12 NKGAWSKQEDQKLIDYIRKHGE----------------GCWRTIPQAA----GLARCGKSCRLRWINYL 60 (214)
Q Consensus 12 ~kg~WT~eED~~L~~~v~~~g~----------------~~W~~Ia~~~----~~~Rs~~qcr~Rw~~~l 60 (214)
++..||.+|.+.|+++|.+|.. ..|..|+..| +..|+..|++..|.++.
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 3578999999999999999821 2499999866 12689999999998754
No 45
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=94.72 E-value=0.069 Score=48.46 Aligned_cols=87 Identities=22% Similarity=0.363 Sum_probs=66.5
Q ss_pred ccccccccccccccccccccchhhcccCC-------------------------CcCCCCChHHHHHHHHHHHhhCCchh
Q 044864 35 CWRTIPQAAGLARCGKSCRLRWINYLRPD-------------------------LKRGNFAEDEEDLIIKLHALLGNRWS 89 (214)
Q Consensus 35 ~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~-------------------------~~~~~Wt~eED~~L~~lv~~~G~~W~ 89 (214)
.|.-++=..+ -|...--..+|....++. +....||.+|-+-|.+|...|.-+|-
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 677777777777663321 23457999999999999999999999
Q ss_pred hhccc-----CCC-CCHHHHHHHHHHHhhhhhhhCCCCc
Q 044864 90 LIAGR-----LPG-RTANEVKNYWNSHLRRKLINMGIDP 122 (214)
Q Consensus 90 ~Ia~~-----lpg-Rt~~q~r~rw~~~l~~~~~~~~~~~ 122 (214)
.||.. ++. ||-..+++||+...+..++...-+.
T Consensus 154 VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~~s~ 192 (445)
T KOG2656|consen 154 VIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARAPSN 192 (445)
T ss_pred EEeeccchhhccccccHHHHHHHHHHHHHHHHHccCCCc
Confidence 99988 555 9999999999999888877655543
No 46
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=93.81 E-value=0.082 Score=47.86 Aligned_cols=45 Identities=20% Similarity=0.396 Sum_probs=42.1
Q ss_pred CCChHHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHHHHHHHhh
Q 044864 68 NFAEDEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKNYWNSHLR 112 (214)
Q Consensus 68 ~Wt~eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~ 112 (214)
+||.+|-++..++...+|..++.|+..+|.|..+||+-+|.+--+
T Consensus 367 ~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek 411 (507)
T COG5118 367 RWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEK 411 (507)
T ss_pred cccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhh
Confidence 899999999999999999999999999999999999999976443
No 47
>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=92.57 E-value=0.2 Score=38.39 Aligned_cols=52 Identities=19% Similarity=0.395 Sum_probs=40.1
Q ss_pred CCcCCCCChHHHHHHHHHHHhhCC----chhhhccc------------CCCCCHHHHHHHHHHHhhhh
Q 044864 63 DLKRGNFAEDEEDLIIKLHALLGN----RWSLIAGR------------LPGRTANEVKNYWNSHLRRK 114 (214)
Q Consensus 63 ~~~~~~Wt~eED~~L~~lv~~~G~----~W~~Ia~~------------lpgRt~~q~r~rw~~~l~~~ 114 (214)
..++..||++||.-|+-.+.+||- .|..|-.. +..||+..+..|...++.-.
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 456779999999999999999994 79888542 24699999999998887653
No 48
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=91.73 E-value=0.26 Score=44.11 Aligned_cols=51 Identities=16% Similarity=0.299 Sum_probs=41.1
Q ss_pred CCCCChHHHHHHHHHHHhh----------CCchhhhcccC----CCCCHHHHHHHHHHHhhhhhh
Q 044864 66 RGNFAEDEEDLIIKLHALL----------GNRWSLIAGRL----PGRTANEVKNYWNSHLRRKLI 116 (214)
Q Consensus 66 ~~~Wt~eED~~L~~lv~~~----------G~~W~~Ia~~l----pgRt~~q~r~rw~~~l~~~~~ 116 (214)
...|+.+|-..||++.... +.-|..||..+ .-||+.||+.+|.++.++.-+
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~ 118 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKK 118 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHH
Confidence 3689999999999887643 23499999965 459999999999998887643
No 49
>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=90.25 E-value=0.19 Score=38.50 Aligned_cols=34 Identities=32% Similarity=0.545 Sum_probs=28.9
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCC---Cccccccccc
Q 044864 10 DTNKGAWSKQEDQKLIDYIRKHGE---GCWRTIPQAA 43 (214)
Q Consensus 10 ~~~kg~WT~eED~~L~~~v~~~g~---~~W~~Ia~~~ 43 (214)
+.++..||.+||.-|+-++.+||. +.|..|-..+
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 667889999999999999999998 8899997765
No 50
>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=89.34 E-value=0.8 Score=32.80 Aligned_cols=47 Identities=23% Similarity=0.486 Sum_probs=35.0
Q ss_pred CCChHHHHHHHHHHHhh---CC----------chhhhcccC---CC--CCHHHHHHHHHHHhhhh
Q 044864 68 NFAEDEEDLIIKLHALL---GN----------RWSLIAGRL---PG--RTANEVKNYWNSHLRRK 114 (214)
Q Consensus 68 ~Wt~eED~~L~~lv~~~---G~----------~W~~Ia~~l---pg--Rt~~q~r~rw~~~l~~~ 114 (214)
.||++++..|++++.+. |+ .|..|+..| +| .+..||++||..+.+..
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y 65 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDY 65 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHH
Confidence 49999999999988553 21 389998877 23 47899999997665544
No 51
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=88.22 E-value=0.85 Score=42.37 Aligned_cols=47 Identities=17% Similarity=0.349 Sum_probs=42.4
Q ss_pred CCCCChHHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHHHHHHHhh
Q 044864 66 RGNFAEDEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKNYWNSHLR 112 (214)
Q Consensus 66 ~~~Wt~eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~ 112 (214)
...||.||-.++-++...||.++.+|-+.||.|+-..+..+|+..-+
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK 233 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKK 233 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHH
Confidence 45799999999999999999999999999999999999998875443
No 52
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=87.16 E-value=0.32 Score=44.15 Aligned_cols=63 Identities=21% Similarity=0.318 Sum_probs=49.6
Q ss_pred CCCCHHHHHHHHHHHHHhCCCccccccccccccccccccccchhhc--ccCCC------cCCCCChHHHHHHH
Q 044864 14 GAWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINY--LRPDL------KRGNFAEDEEDLII 78 (214)
Q Consensus 14 g~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~--l~p~~------~~~~Wt~eED~~L~ 78 (214)
-+||.+|-+++.++....|.. +..|+..+| .|..+|+...|.+- .+|.. .+-++..+|-..|.
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtd-F~LIs~lfP-~R~RkqIKaKfi~Eek~nP~rIn~aL~~kkp~d~~eY~k~~ 436 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTD-FSLISSLFP-NRERKQIKAKFIKEEKVNPERINEALNEKKPFDQVEYNKLR 436 (507)
T ss_pred CcccHHHHHHHHHHHHHhcch-HHHHHHhcC-chhHHHHHHHHHHHhhhCHHHHHHHHhccCCCCHHHHhhHH
Confidence 489999999999999999965 999999999 99999999999863 33321 24467766655433
No 53
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=86.69 E-value=1.5 Score=27.91 Aligned_cols=41 Identities=22% Similarity=0.257 Sum_probs=30.7
Q ss_pred hHHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHHHHHHHhh
Q 044864 71 EDEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKNYWNSHLR 112 (214)
Q Consensus 71 ~eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~ 112 (214)
++++..++.++...|-.+.+||..+ |.|...|+.+....++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARK 52 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHh
Confidence 3567788888888999999999999 9999999988776554
No 54
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=85.35 E-value=0.87 Score=32.71 Aligned_cols=28 Identities=36% Similarity=0.662 Sum_probs=16.4
Q ss_pred CCCcCCCCHHHHHHH--------HHHHHHhCCCcccccc
Q 044864 10 DTNKGAWSKQEDQKL--------IDYIRKHGEGCWRTIP 40 (214)
Q Consensus 10 ~~~kg~WT~eED~~L--------~~~v~~~g~~~W~~Ia 40 (214)
.--.|-||+|+|+.| ..++++|| +..|+
T Consensus 44 ~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG---~~~i~ 79 (87)
T PF11626_consen 44 DNMPGIWTPEDDEMLRSGDKDDIERLIKKHG---EERIE 79 (87)
T ss_dssp TT-TT---HHHHHHHTS--HHHHHHHHHHH----HHHHH
T ss_pred CCCCCCcCHHHHHHHHcCCHHHHHHHHHHhC---HHHHH
Confidence 345889999999999 35677887 44554
No 55
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=78.64 E-value=21 Score=32.64 Aligned_cols=44 Identities=23% Similarity=0.373 Sum_probs=39.0
Q ss_pred CCCChHHHHHHHHHHHhhCCchhhh-cccCCCCCHHHHHHHHHHH
Q 044864 67 GNFAEDEEDLIIKLHALLGNRWSLI-AGRLPGRTANEVKNYWNSH 110 (214)
Q Consensus 67 ~~Wt~eED~~L~~lv~~~G~~W~~I-a~~lpgRt~~q~r~rw~~~ 110 (214)
..|+++|=...-+..+.||+++..| +..++.|+-..|-..|+..
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlW 322 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLW 322 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHh
Confidence 4799999999999999999999999 5668999999999887643
No 56
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=78.26 E-value=1.1 Score=39.96 Aligned_cols=47 Identities=23% Similarity=0.474 Sum_probs=36.9
Q ss_pred CCCCHHHHHHHHHHHHHh----CC-----Cccccccccc---cccccccccccchhhcc
Q 044864 14 GAWSKQEDQKLIDYIRKH----GE-----GCWRTIPQAA---GLARCGKSCRLRWINYL 60 (214)
Q Consensus 14 g~WT~eED~~L~~~v~~~----g~-----~~W~~Ia~~~---~~~Rs~~qcr~Rw~~~l 60 (214)
..|+.+|-..|+.+.... .. .-|..||..+ +..|++.||+.+|.++.
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 689999999999987644 11 2499999833 44799999999998753
No 57
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=76.96 E-value=4.8 Score=38.82 Aligned_cols=57 Identities=18% Similarity=0.410 Sum_probs=44.6
Q ss_pred CCCCChHHHHHHHHHHHhhCCchhhhc----------ccCCCCCHHHHHHHHHHHhhhhhhhCCCCcc
Q 044864 66 RGNFAEDEEDLIIKLHALLGNRWSLIA----------GRLPGRTANEVKNYWNSHLRRKLINMGIDPK 123 (214)
Q Consensus 66 ~~~Wt~eED~~L~~lv~~~G~~W~~Ia----------~~lpgRt~~q~r~rw~~~l~~~~~~~~~~~~ 123 (214)
+..||-.|..-...+..++|.++..|- ..+.-+|-.|++.+|+..+.+.-+-. |.++
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k~~-F~~~ 154 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNKLL-FGPD 154 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHhhh-cccc
Confidence 668999999999999999999999882 23344678899999988887664433 5553
No 58
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=76.75 E-value=3.9 Score=40.34 Aligned_cols=43 Identities=12% Similarity=0.220 Sum_probs=40.1
Q ss_pred CCCChHHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHHHHHH
Q 044864 67 GNFAEDEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKNYWNS 109 (214)
Q Consensus 67 ~~Wt~eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~ 109 (214)
..||..|-.+.-++...|..++-.|++.++++|-.||-..|+.
T Consensus 620 d~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYT 662 (907)
T ss_pred ccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHH
Confidence 4799999999999999999999999999999999999998764
No 59
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=76.72 E-value=4.3 Score=25.08 Aligned_cols=38 Identities=18% Similarity=0.268 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHhhC-CchhhhcccCCCCCHHHHHHHHHHH
Q 044864 72 DEEDLIIKLHALLG-NRWSLIAGRLPGRTANEVKNYWNSH 110 (214)
Q Consensus 72 eED~~L~~lv~~~G-~~W~~Ia~~lpgRt~~q~r~rw~~~ 110 (214)
+=|.+|+.+...-| ..|..||..+ |=|...|..|+..+
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 45778888888888 6799999999 99999999998653
No 60
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=74.98 E-value=3 Score=43.35 Aligned_cols=76 Identities=18% Similarity=0.222 Sum_probs=48.5
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCccccccccccccccccccccchhhcccCCCcCCCCChHHHHHHHHHHHhh-CCchhh
Q 044864 12 NKGAWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYLRPDLKRGNFAEDEEDLIIKLHALL-GNRWSL 90 (214)
Q Consensus 12 ~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~~~~~~Wt~eED~~L~~lv~~~-G~~W~~ 90 (214)
.-.-|..+||..|+-.|-+||.++|..|-- .+.-|..- ...+...+-.+.+-..+-+.|+.+...+ +.+|..
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir~------Dp~L~l~d-Ki~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~ 1204 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIRL------DPDLGLTD-KIFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPK 1204 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhcc------Cccccchh-hhcccccCCchHHHHHHHHHHHHHHhhcccCCCch
Confidence 445799999999999999999999999932 11112111 1122222344556666777777777766 556665
Q ss_pred hccc
Q 044864 91 IAGR 94 (214)
Q Consensus 91 Ia~~ 94 (214)
....
T Consensus 1205 ~~~~ 1208 (1373)
T KOG0384|consen 1205 KLKR 1208 (1373)
T ss_pred hhhc
Confidence 5443
No 61
>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=74.93 E-value=1.7 Score=31.01 Aligned_cols=44 Identities=20% Similarity=0.525 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHHHHHh---CCC---------cccccccccc----ccccccccccchhh
Q 044864 15 AWSKQEDQKLIDYIRKH---GEG---------CWRTIPQAAG----LARCGKSCRLRWIN 58 (214)
Q Consensus 15 ~WT~eED~~L~~~v~~~---g~~---------~W~~Ia~~~~----~~Rs~~qcr~Rw~~ 58 (214)
.||+++++.|++++... |.. .|..|+..|. ...+..||+.||..
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~ 60 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKT 60 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHH
Confidence 59999999999988655 211 3888887663 23455677777654
No 62
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=73.48 E-value=2 Score=39.20 Aligned_cols=50 Identities=20% Similarity=0.323 Sum_probs=42.9
Q ss_pred CCCCcCCCCHHHHHHHHHHHHHhCCCcccccccc-----ccccccccccccchhhc
Q 044864 9 QDTNKGAWSKQEDQKLIDYIRKHGEGCWRTIPQA-----AGLARCGKSCRLRWINY 59 (214)
Q Consensus 9 ~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~-----~~~~Rs~~qcr~Rw~~~ 59 (214)
.+++-..||.+|.+-|.++++.|.-. |--||.. ++..||-....+||+.+
T Consensus 126 ~~l~dn~WskeETD~LF~lck~fDLR-f~VIaDRyd~qq~~~sRTvEdLKeRyY~v 180 (445)
T KOG2656|consen 126 AHLNDNSWSKEETDYLFDLCKRFDLR-FFVIADRYDNQQYKKSRTVEDLKERYYSV 180 (445)
T ss_pred HhhccccccHHHHHHHHHHHHhcCee-EEEEeeccchhhccccccHHHHHHHHHHH
Confidence 35666889999999999999999976 9999986 66569999999999865
No 63
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=71.66 E-value=5 Score=31.57 Aligned_cols=46 Identities=9% Similarity=0.126 Sum_probs=39.4
Q ss_pred hHHHHHHHHHHHhhC-CchhhhcccCCCCCHHHHHHHHHHHhhhhhhh
Q 044864 71 EDEEDLIIKLHALLG-NRWSLIAGRLPGRTANEVKNYWNSHLRRKLIN 117 (214)
Q Consensus 71 ~eED~~L~~lv~~~G-~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~~~~ 117 (214)
.+-|.+|+.+...-| ..|+.||+.+ |-|...|+.|+..+....+.+
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 357888888888888 7899999999 999999999998888776543
No 64
>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=71.40 E-value=8.5 Score=24.09 Aligned_cols=41 Identities=27% Similarity=0.376 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 72 DEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 72 eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
+++..++.++-..|-.+.+||..| |-|...|+.+-...+++
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 355566666666667899999999 88999999888776654
No 65
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=70.12 E-value=9.2 Score=31.94 Aligned_cols=43 Identities=16% Similarity=0.234 Sum_probs=32.2
Q ss_pred CCChHHHHHHHHHHHhhCCchhhhcccC---CCCCHHHHHHHHHHHh
Q 044864 68 NFAEDEEDLIIKLHALLGNRWSLIAGRL---PGRTANEVKNYWNSHL 111 (214)
Q Consensus 68 ~Wt~eED~~L~~lv~~~G~~W~~Ia~~l---pgRt~~q~r~rw~~~l 111 (214)
.|++.+|-+|+.+|.. |++-..|+.-+ -.-|-..+..||+.+|
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~ll 46 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALL 46 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHH
Confidence 4999999999988854 55566665544 3458899999998765
No 66
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=69.68 E-value=6.1 Score=38.05 Aligned_cols=47 Identities=21% Similarity=0.360 Sum_probs=42.7
Q ss_pred cCCCCChHHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHHHHHHHh
Q 044864 65 KRGNFAEDEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKNYWNSHL 111 (214)
Q Consensus 65 ~~~~Wt~eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l 111 (214)
..+.|+.+|-++........|.+.+.|+..+|+|+.+|||.+|..-=
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~eE 454 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKEE 454 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhhh
Confidence 45689999999999999999999999999999999999999996433
No 67
>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=67.70 E-value=1.8 Score=26.76 Aligned_cols=38 Identities=16% Similarity=0.363 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHhCCCccccccccccccccccccccchhh
Q 044864 19 QEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWIN 58 (214)
Q Consensus 19 eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~ 58 (214)
+=|.+|+.+....|...|..||+.+| =+...|..|+..
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 45889999999999889999999996 788888888653
No 68
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=65.81 E-value=6.3 Score=31.39 Aligned_cols=45 Identities=13% Similarity=0.064 Sum_probs=38.5
Q ss_pred hHHHHHHHHHHHhhC-CchhhhcccCCCCCHHHHHHHHHHHhhhhhh
Q 044864 71 EDEEDLIIKLHALLG-NRWSLIAGRLPGRTANEVKNYWNSHLRRKLI 116 (214)
Q Consensus 71 ~eED~~L~~lv~~~G-~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~~~ 116 (214)
.+-|.+|+.+.++.| -.|+.||+.+ |=|...|+.|+..+.+..+.
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~GvI 58 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGFI 58 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 456788888888888 7899999999 99999999999888877654
No 69
>smart00595 MADF subfamily of SANT domain.
Probab=65.53 E-value=6.2 Score=27.72 Aligned_cols=27 Identities=33% Similarity=0.591 Sum_probs=22.7
Q ss_pred chhhhcccCCCCCHHHHHHHHHHHhhhh
Q 044864 87 RWSLIAGRLPGRTANEVKNYWNSHLRRK 114 (214)
Q Consensus 87 ~W~~Ia~~lpgRt~~q~r~rw~~~l~~~ 114 (214)
-|..||..| |-+..+|+.+|.++....
T Consensus 29 aW~~Ia~~l-~~~~~~~~~kw~~LR~~y 55 (89)
T smart00595 29 AWEEIAEEL-GLSVEECKKRWKNLRDRY 55 (89)
T ss_pred HHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 499999999 559999999998876554
No 70
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=64.45 E-value=3.1 Score=40.98 Aligned_cols=44 Identities=7% Similarity=0.144 Sum_probs=39.4
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCccccccccccccccccccccchhh
Q 044864 13 KGAWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWIN 58 (214)
Q Consensus 13 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~ 58 (214)
...||+.|-.++.+++..|. +++-.|++.++ +++..||-+-|+.
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~-KDF~~v~km~~-~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYS-KDFIFVQKMVK-SKTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhc-ccHHHHHHHhc-cccHHHHHHHHHH
Confidence 45899999999999999999 56999999999 9999999886653
No 71
>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=64.10 E-value=6.9 Score=27.98 Aligned_cols=17 Identities=18% Similarity=0.559 Sum_probs=10.1
Q ss_pred CCCcCCCCChHHHHHHH
Q 044864 62 PDLKRGNFAEDEEDLII 78 (214)
Q Consensus 62 p~~~~~~Wt~eED~~L~ 78 (214)
|....|-||+++|..|.
T Consensus 43 P~n~~GiWT~eDD~~L~ 59 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLR 59 (87)
T ss_dssp -TT-TT---HHHHHHHT
T ss_pred CCCCCCCcCHHHHHHHH
Confidence 55668899999999984
No 72
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=63.83 E-value=14 Score=26.26 Aligned_cols=38 Identities=21% Similarity=0.301 Sum_probs=28.4
Q ss_pred HHHHHHHhhCC--------chhhhcccCCC---CC--HHHHHHHHHHHhhh
Q 044864 76 LIIKLHALLGN--------RWSLIAGRLPG---RT--ANEVKNYWNSHLRR 113 (214)
Q Consensus 76 ~L~~lv~~~G~--------~W~~Ia~~lpg---Rt--~~q~r~rw~~~l~~ 113 (214)
.|..+|...|+ .|..||..|.- -+ ..+++..|..+|.+
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 47778888774 59999999821 12 36899999988865
No 73
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=61.04 E-value=4.7 Score=37.62 Aligned_cols=43 Identities=16% Similarity=0.148 Sum_probs=38.1
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCccccccccccccccccccccchh
Q 044864 13 KGAWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWI 57 (214)
Q Consensus 13 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~ 57 (214)
...||.||--++-++...|| .++.+|-+.|+ +|+-.++..=|+
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~G-K~F~kIrq~LP-~rsLaSlvqyYy 229 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFG-KDFHKIRQALP-HRSLASLVQYYY 229 (534)
T ss_pred cccchHHHHHHHHHHHHHhc-ccHHHHHHHcc-CccHHHHHHHHH
Confidence 67899999999999999999 55999999999 999988877554
No 74
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=60.40 E-value=3.7 Score=32.29 Aligned_cols=45 Identities=7% Similarity=0.170 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHhCCCccccccccccccccccccccchhhcccCCC
Q 044864 18 KQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYLRPDL 64 (214)
Q Consensus 18 ~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~~ 64 (214)
.+-|.+|+.+.++.|.-.|..||+.++ -+...|+.|+......++
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 357999999999999889999999996 899999999988766554
No 75
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=59.15 E-value=18 Score=25.92 Aligned_cols=39 Identities=23% Similarity=0.378 Sum_probs=29.9
Q ss_pred HHHHHHHhhCC--------chhhhcccC--C---CCCHHHHHHHHHHHhhhh
Q 044864 76 LIIKLHALLGN--------RWSLIAGRL--P---GRTANEVKNYWNSHLRRK 114 (214)
Q Consensus 76 ~L~~lv~~~G~--------~W~~Ia~~l--p---gRt~~q~r~rw~~~l~~~ 114 (214)
.|..+|...|+ .|..||..| + .....+++..|..+|.+.
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~y 87 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLPF 87 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHHH
Confidence 47777877774 699999998 2 224678899999998875
No 76
>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=58.35 E-value=35 Score=30.61 Aligned_cols=49 Identities=20% Similarity=0.486 Sum_probs=36.7
Q ss_pred CCCCChHHHHHHHHHHHhh-CC---chhhhcccCCCCCHHHHHHHHHHHhhhhh
Q 044864 66 RGNFAEDEEDLIIKLHALL-GN---RWSLIAGRLPGRTANEVKNYWNSHLRRKL 115 (214)
Q Consensus 66 ~~~Wt~eED~~L~~lv~~~-G~---~W~~Ia~~lpgRt~~q~r~rw~~~l~~~~ 115 (214)
-..||.-|...|+++.... |. .-.+|++.++||+..+|++.- +.|+.++
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl-~~LK~rv 73 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFL-QQLKGRV 73 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHH-HHHHHHH
Confidence 4589999999888877655 43 456889999999999998744 4455444
No 77
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=57.97 E-value=5.1 Score=41.32 Aligned_cols=33 Identities=18% Similarity=0.380 Sum_probs=28.6
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCccccccccc
Q 044864 11 TNKGAWSKQEDQKLIDYIRKHGEGCWRTIPQAA 43 (214)
Q Consensus 11 ~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~ 43 (214)
.++..||.|||.-|+-++.+||.++|..|-..+
T Consensus 924 ~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i 956 (1033)
T PLN03142 924 NKGKLYNEECDRFMLCMVHKLGYGNWDELKAAF 956 (1033)
T ss_pred CCCCcCCHHHHHHHHHHHHHhccchHHHHHHHH
Confidence 345569999999999999999999999996655
No 78
>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=55.93 E-value=22 Score=26.95 Aligned_cols=38 Identities=24% Similarity=0.304 Sum_probs=28.1
Q ss_pred HHHHHHHHhhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 75 DLIIKLHALLGNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 75 ~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
..++.+.-..|-.+.+||..+ |.+...|+.+....+++
T Consensus 119 r~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 119 RKIFILSRFEGKSYKEIAEEL-GISVKTVEYHISKALKE 156 (161)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 334444344577899999999 99999999998775543
No 79
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=55.36 E-value=3.9 Score=32.58 Aligned_cols=45 Identities=16% Similarity=0.254 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHhCCCccccccccccccccccccccchhhcccCCC
Q 044864 18 KQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYLRPDL 64 (214)
Q Consensus 18 ~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~~ 64 (214)
.+-|.+|+.+.++.|.-.|..||+.++ -+...|+.|+.+....++
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 567999999999999889999999996 888999999988766654
No 80
>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=52.07 E-value=15 Score=29.58 Aligned_cols=40 Identities=28% Similarity=0.269 Sum_probs=33.5
Q ss_pred CCChHHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHHHHH
Q 044864 68 NFAEDEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKNYWN 108 (214)
Q Consensus 68 ~Wt~eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~ 108 (214)
.||+|+.++|.+|.. -|-.=++||..|.|.|.+.|.-+-+
T Consensus 2 ~Wtde~~~~L~~lw~-~G~SasqIA~~lg~vsRnAViGk~h 41 (162)
T PF07750_consen 2 SWTDERVERLRKLWA-EGLSASQIARQLGGVSRNAVIGKAH 41 (162)
T ss_pred CCCHHHHHHHHHHHH-cCCCHHHHHHHhCCcchhhhhhhhh
Confidence 599999999998874 4778899999997699999876654
No 81
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=48.48 E-value=7.8 Score=37.48 Aligned_cols=47 Identities=23% Similarity=0.478 Sum_probs=36.4
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCcccccccc----------ccccccccccccchhhccc
Q 044864 13 KGAWSKQEDQKLIDYIRKHGEGCWRTIPQA----------AGLARCGKSCRLRWINYLR 61 (214)
Q Consensus 13 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~----------~~~~Rs~~qcr~Rw~~~l~ 61 (214)
|..||-.|.+-+..+++.+| +++..|-.+ .. -++..|+|..|++.+.
T Consensus 88 ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~-~Ktkdqvr~~yY~~~~ 144 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQ-SKTKDQVRHYYYRLVR 144 (782)
T ss_pred ccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchh-hhhhHHHHHHHHHHHH
Confidence 66899999999999999999 568888322 22 4566788888887654
No 82
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=46.20 E-value=23 Score=25.22 Aligned_cols=29 Identities=21% Similarity=0.438 Sum_probs=23.8
Q ss_pred HHHHHHHHHhhCCchhhhcccCCCCCHHHH
Q 044864 74 EDLIIKLHALLGNRWSLIAGRLPGRTANEV 103 (214)
Q Consensus 74 D~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~ 103 (214)
|+.|..+....|..|..+|..| |=|..+|
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 4668889999999999999998 6665554
No 83
>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=45.95 E-value=48 Score=26.44 Aligned_cols=47 Identities=17% Similarity=0.148 Sum_probs=38.0
Q ss_pred cCCCCChHHHHHHHHHHHhhCCchhhhcccC----CCCCHHHHHHHHHHHh
Q 044864 65 KRGNFAEDEEDLIIKLHALLGNRWSLIAGRL----PGRTANEVKNYWNSHL 111 (214)
Q Consensus 65 ~~~~Wt~eED~~L~~lv~~~G~~W~~Ia~~l----pgRt~~q~r~rw~~~l 111 (214)
....-|..|..-|..|+.+||.++..++.-. --.|..||+.+...+.
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 3457888999999999999999999888654 2479999998876553
No 84
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=44.44 E-value=50 Score=25.70 Aligned_cols=37 Identities=30% Similarity=0.294 Sum_probs=26.0
Q ss_pred hhCCchhhhcccCCCCCHHHHHHHHHHHh---hhhhhhCCC
Q 044864 83 LLGNRWSLIAGRLPGRTANEVKNYWNSHL---RRKLINMGI 120 (214)
Q Consensus 83 ~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l---~~~~~~~~~ 120 (214)
..|-.-.+||..| |.+...|+.+....+ +..+...++
T Consensus 132 ~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~Lr~~l~~~~~ 171 (173)
T PRK09645 132 YRGWSTAQIAADL-GIPEGTVKSRLHYALRALRLALQERGV 171 (173)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHHHhhcccc
Confidence 3456789999999 899999998876544 444444444
No 85
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=43.44 E-value=40 Score=24.31 Aligned_cols=45 Identities=13% Similarity=0.103 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHhhC-CchhhhcccCCCCCHHHHHHHHHHHhhhhhhh
Q 044864 72 DEEDLIIKLHALLG-NRWSLIAGRLPGRTANEVKNYWNSHLRRKLIN 117 (214)
Q Consensus 72 eED~~L~~lv~~~G-~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~~~~ 117 (214)
+.|..|+.+....| ..+..||+.+ |-+...|+.+...+....+.+
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 46778888888877 6799999999 999999999998888766544
No 86
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=42.75 E-value=19 Score=24.47 Aligned_cols=28 Identities=25% Similarity=0.453 Sum_probs=21.9
Q ss_pred chhhhcccCC-CCCHHHHHHHHHHHhhhh
Q 044864 87 RWSLIAGRLP-GRTANEVKNYWNSHLRRK 114 (214)
Q Consensus 87 ~W~~Ia~~lp-gRt~~q~r~rw~~~l~~~ 114 (214)
-|..||..|. +-+..+|+.+|.++....
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y 56 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRDRY 56 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHHHH
Confidence 4999999984 257889999998876654
No 87
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=42.15 E-value=18 Score=24.74 Aligned_cols=26 Identities=23% Similarity=0.528 Sum_probs=18.7
Q ss_pred CCChHHHH-HHHHHHHhhCCchhhhcc
Q 044864 68 NFAEDEED-LIIKLHALLGNRWSLIAG 93 (214)
Q Consensus 68 ~Wt~eED~-~L~~lv~~~G~~W~~Ia~ 93 (214)
.|+++.-. .|.+|...||++|..|-.
T Consensus 22 G~~~~~v~~vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 22 GFSKKQVRPVLKNLLKLYDGNWELIEE 48 (65)
T ss_pred CCCHHHHHHHHHHHHHHHcCCchhhhc
Confidence 34444444 677888999999999853
No 88
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=40.71 E-value=16 Score=24.89 Aligned_cols=44 Identities=14% Similarity=0.454 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhCCCccccccccccccccccccccchhhcccCCC-------cCCCCChHHHHHH
Q 044864 21 DQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYLRPDL-------KRGNFAEDEEDLI 77 (214)
Q Consensus 21 D~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~~-------~~~~Wt~eED~~L 77 (214)
+.+|.++|..|| |..+++.+. -| |.. -+|++ ++.+|..+.-+.|
T Consensus 12 e~il~~Lv~~yG---W~~L~~~i~-i~----CF~-----~~PsikSSLkFLRkTpWAR~KVE~l 62 (64)
T PF09905_consen 12 ETILTELVEHYG---WEELGERIN-IN----CFK-----NNPSIKSSLKFLRKTPWAREKVENL 62 (64)
T ss_dssp HHHHHHHHHHT----HHHHHHHTT-SS----STT-----SS--HHHHHHHHHHSHHHHHHHHHH
T ss_pred HHHHHHHHHHhC---HHHHHhhcc-cc----cCC-----CCCchHHHHHHHhcCHhHHHHHHHh
Confidence 567889999999 999998776 33 322 24443 4778887766654
No 89
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=39.50 E-value=33 Score=32.40 Aligned_cols=42 Identities=17% Similarity=0.330 Sum_probs=37.3
Q ss_pred CCCChHHHHHHHHHHHhhCCchhhhc-ccCCCCCHHHHHHHHH
Q 044864 67 GNFAEDEEDLIIKLHALLGNRWSLIA-GRLPGRTANEVKNYWN 108 (214)
Q Consensus 67 ~~Wt~eED~~L~~lv~~~G~~W~~Ia-~~lpgRt~~q~r~rw~ 108 (214)
..|+..|-.+.-++..+||.++..|. .+||-++-..|-+.|+
T Consensus 286 EEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYY 328 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYY 328 (693)
T ss_pred hhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHH
Confidence 37999999999999999999999995 5569999999988875
No 90
>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=39.15 E-value=50 Score=24.20 Aligned_cols=34 Identities=26% Similarity=0.270 Sum_probs=25.7
Q ss_pred HHHHhhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 79 KLHALLGNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 79 ~lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
.++-..|..+..||..+ |=+...++.+....+++
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 33334577899999999 77999999888776554
No 91
>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=38.69 E-value=78 Score=28.43 Aligned_cols=87 Identities=15% Similarity=0.258 Sum_probs=61.2
Q ss_pred cCCCCHHHHHHHHHHHHHhCCC---ccccccccccccccccccccchhhcccCCCcCCCCChHHHHHHHHHHHh-h----
Q 044864 13 KGAWSKQEDQKLIDYIRKHGEG---CWRTIPQAAGLARCGKSCRLRWINYLRPDLKRGNFAEDEEDLIIKLHAL-L---- 84 (214)
Q Consensus 13 kg~WT~eED~~L~~~v~~~g~~---~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~~~~~~Wt~eED~~L~~lv~~-~---- 84 (214)
-..||.-|-..|+.+.+..... +-.+|++.++ +|+..++++ |.+.|+ +..+.+++.+ |
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 4589999999999998877423 3457778888 999988876 344433 2233344433 1
Q ss_pred -CC------------chhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 85 -GN------------RWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 85 -G~------------~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
|. -|..+|..+.|.-...+---|-++|.-
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 11 299999999999999888888777653
No 92
>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=38.36 E-value=51 Score=19.94 Aligned_cols=34 Identities=24% Similarity=0.119 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHHH
Q 044864 72 DEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKNY 106 (214)
Q Consensus 72 eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~r 106 (214)
-|...|.++...++++-...|+.| |=+...+..+
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~k 38 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLL-GISRRTLYRK 38 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHH
Confidence 367788999999999999999998 6666666544
No 93
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=38.33 E-value=71 Score=18.83 Aligned_cols=37 Identities=24% Similarity=0.214 Sum_probs=25.6
Q ss_pred HHHHHHHHHHhhCCchhhhcccCCCCCHHHHHHHHHHH
Q 044864 73 EEDLIIKLHALLGNRWSLIAGRLPGRTANEVKNYWNSH 110 (214)
Q Consensus 73 ED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~ 110 (214)
++..++.++-..|..+..||..+ |-+...|+.+....
T Consensus 14 ~~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~ 50 (55)
T cd06171 14 REREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRA 50 (55)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 34455555555678899999998 77777776655443
No 94
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=37.89 E-value=48 Score=26.65 Aligned_cols=36 Identities=22% Similarity=0.241 Sum_probs=28.0
Q ss_pred HHHHHHHHhhCCchhhhcccCCCCCHHHHHHHHHHHh
Q 044864 75 DLIIKLHALLGNRWSLIAGRLPGRTANEVKNYWNSHL 111 (214)
Q Consensus 75 ~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l 111 (214)
..++.+....|-.+.+||..| |-|...++.+|....
T Consensus 141 ~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR 176 (185)
T PF07638_consen 141 RRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 344444445577899999999 999999999997665
No 95
>cd08803 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=37.33 E-value=44 Score=23.79 Aligned_cols=29 Identities=21% Similarity=0.366 Sum_probs=23.5
Q ss_pred HHHHHHHHHhhCCchhhhcccCCCCCHHHH
Q 044864 74 EDLIIKLHALLGNRWSLIAGRLPGRTANEV 103 (214)
Q Consensus 74 D~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~ 103 (214)
|..|..+....|..|..+|..| |=+...+
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI 32 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEI 32 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHH
Confidence 5678888899999999999999 6565544
No 96
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=35.70 E-value=62 Score=23.68 Aligned_cols=48 Identities=13% Similarity=0.111 Sum_probs=30.3
Q ss_pred CCCChHHHHHHHHHHHhh----C----Cchhhhcc----cC-CCCCHHHHHHHHHHHhhhh
Q 044864 67 GNFAEDEEDLIIKLHALL----G----NRWSLIAG----RL-PGRTANEVKNYWNSHLRRK 114 (214)
Q Consensus 67 ~~Wt~eED~~L~~lv~~~----G----~~W~~Ia~----~l-pgRt~~q~r~rw~~~l~~~ 114 (214)
.-||++++..||+.+..| | ..|..+.. .+ ..=+..|+.++-..+-++.
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 469999999999998777 5 24544333 33 1226677766665555444
No 97
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=35.13 E-value=87 Score=24.71 Aligned_cols=35 Identities=26% Similarity=0.137 Sum_probs=28.2
Q ss_pred HhhCCchhhhcccCCCCCHHHHHHHHHHHhhhhhhh
Q 044864 82 ALLGNRWSLIAGRLPGRTANEVKNYWNSHLRRKLIN 117 (214)
Q Consensus 82 ~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~~~~ 117 (214)
...|-...+||..| |-+...|+.|....+..-+..
T Consensus 140 ~~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 140 TLDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHh
Confidence 34467899999999 999999999998877766544
No 98
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=35.02 E-value=64 Score=24.92 Aligned_cols=33 Identities=18% Similarity=0.168 Sum_probs=24.5
Q ss_pred HHHhhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 80 LHALLGNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 80 lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
+....|-.+..||..| |-+...|+.+....+++
T Consensus 139 l~~~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 171 (182)
T PRK09652 139 LREIEGLSYEEIAEIM-GCPIGTVRSRIFRAREA 171 (182)
T ss_pred HHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3334567899999999 88999998877654443
No 99
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=34.72 E-value=30 Score=33.49 Aligned_cols=48 Identities=13% Similarity=0.281 Sum_probs=42.1
Q ss_pred CCCCcCCCCHHHHHHHHHHHHHhCCCccccccccccccccccccccchhh
Q 044864 9 QDTNKGAWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWIN 58 (214)
Q Consensus 9 ~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~ 58 (214)
+....++|+.+|-++...+....|.. ...|+..++ +|..+|++..|..
T Consensus 405 k~~~~~~w~~se~e~fyka~~~~gs~-~slis~l~p-~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 405 KKLETDKWDASETELFYKALSERGSD-FSLISNLFP-LRDRKQIKAKFKK 452 (584)
T ss_pred CccccCcccchhhHHhhhHHhhhccc-ccccccccc-cccHHHHHHHHhh
Confidence 34557899999999999999999965 999999998 9999999988764
No 100
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=33.77 E-value=83 Score=25.09 Aligned_cols=38 Identities=18% Similarity=0.141 Sum_probs=26.8
Q ss_pred hhCCchhhhcccCCCCCHHHHHHHHHH---HhhhhhhhCCCC
Q 044864 83 LLGNRWSLIAGRLPGRTANEVKNYWNS---HLRRKLINMGID 121 (214)
Q Consensus 83 ~~G~~W~~Ia~~lpgRt~~q~r~rw~~---~l~~~~~~~~~~ 121 (214)
..|-.-.+||..| |-+...|+.+... .|+..+.+..+.
T Consensus 150 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr~~l~~~~~~ 190 (195)
T PRK12532 150 ILGFSSDEIQQMC-GISTSNYHTIMHRARESLRQCLQIKWFN 190 (195)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 3466789999999 8899999888765 445555444443
No 101
>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=33.61 E-value=38 Score=23.77 Aligned_cols=29 Identities=24% Similarity=0.583 Sum_probs=22.7
Q ss_pred HHHHHHHHHhhCCchhhhcccCCCCCHHHH
Q 044864 74 EDLIIKLHALLGNRWSLIAGRLPGRTANEV 103 (214)
Q Consensus 74 D~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~ 103 (214)
|..|..+....|..|..+|..| |=+..+|
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI 32 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDI 32 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHH
Confidence 4567788888999999999999 6555444
No 102
>PRK04217 hypothetical protein; Provisional
Probab=33.59 E-value=81 Score=23.74 Aligned_cols=45 Identities=16% Similarity=0.074 Sum_probs=35.0
Q ss_pred CCChHHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHHHHHHHhhhh
Q 044864 68 NFAEDEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKNYWNSHLRRK 114 (214)
Q Consensus 68 ~Wt~eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~ 114 (214)
.-+.+| ..++.+....|-...+||+.+ |-+...|+.++....+.-
T Consensus 42 ~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 42 FMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKKV 86 (110)
T ss_pred cCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 455555 567777777788999999999 999999999987655443
No 103
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=32.76 E-value=61 Score=20.92 Aligned_cols=34 Identities=29% Similarity=0.475 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHHH
Q 044864 72 DEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKNY 106 (214)
Q Consensus 72 eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~r 106 (214)
+.|+..+.+....|-.-.+||+.+ ||+..-|++.
T Consensus 7 ~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~y 40 (50)
T PF11427_consen 7 DAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRY 40 (50)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHH
T ss_pred HHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHH
Confidence 455666777788898999999999 9998888764
No 104
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=32.48 E-value=72 Score=24.54 Aligned_cols=30 Identities=23% Similarity=0.193 Sum_probs=23.2
Q ss_pred hhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 83 LLGNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 83 ~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
..|-....||..| |-+...|+.+....+.+
T Consensus 139 ~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 168 (179)
T PRK11924 139 VEGLSYREIAEIL-GVPVGTVKSRLRRARQL 168 (179)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466799999999 88999998887654443
No 105
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=32.15 E-value=77 Score=25.40 Aligned_cols=31 Identities=23% Similarity=0.147 Sum_probs=24.3
Q ss_pred HhhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 82 ALLGNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 82 ~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
-..|....+||..| |-+...|+.|....++.
T Consensus 147 ~~~g~s~~EIA~~l-g~s~~tV~~rl~rar~~ 177 (192)
T PRK09643 147 DMQGYSVADAARML-GVAEGTVKSRCARGRAR 177 (192)
T ss_pred HHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 34567899999999 89999999998554443
No 106
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=32.01 E-value=64 Score=24.64 Aligned_cols=44 Identities=18% Similarity=0.126 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHhhC-CchhhhcccCCCCCHHHHHHHHHHHhhhhhh
Q 044864 72 DEEDLIIKLHALLG-NRWSLIAGRLPGRTANEVKNYWNSHLRRKLI 116 (214)
Q Consensus 72 eED~~L~~lv~~~G-~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~~~ 116 (214)
+-|.+|+++.+.-+ ..+..||+.+ |-|...|++|-..+.+..+.
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~GiI 52 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGVI 52 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCce
Confidence 45777888877777 6799999999 99999999999877776644
No 107
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=31.87 E-value=41 Score=20.67 Aligned_cols=36 Identities=31% Similarity=0.366 Sum_probs=17.9
Q ss_pred CCChHHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHH
Q 044864 68 NFAEDEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKN 105 (214)
Q Consensus 68 ~Wt~eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~ 105 (214)
.+|.+|-..|..++ .-|..=..||+.| ||+...|..
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 5677789999999 999888754
No 108
>COG4628 Uncharacterized conserved protein [Function unknown]
Probab=31.36 E-value=41 Score=25.69 Aligned_cols=45 Identities=16% Similarity=0.397 Sum_probs=30.6
Q ss_pred HHHHHHHHHHhCCCccccccccccccccccccccchhhcccCC-------CcCCCCChHHHHHHH
Q 044864 21 DQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYLRPD-------LKRGNFAEDEEDLII 78 (214)
Q Consensus 21 D~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~-------~~~~~Wt~eED~~L~ 78 (214)
+.+|.++|..|| |..++..++ ..|.. -+|+ +++.+|..|.-+.|.
T Consensus 21 E~llt~Lvd~YG---Wd~L~~ri~-----inCF~-----ndPSi~SSlKfLrkT~WARekvEa~Y 72 (136)
T COG4628 21 ETLLTELVDFYG---WDGLATRIR-----INCFH-----NDPSIKSSLKFLRKTPWAREKVEALY 72 (136)
T ss_pred HHHHHHHHHHhC---hHHHHhhce-----ecccc-----CCccHHHHHHHHhcCHhHHHHHHHHH
Confidence 567889999999 999986554 44533 1333 357789887766543
No 109
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.87 E-value=1.3e+02 Score=22.11 Aligned_cols=45 Identities=16% Similarity=0.141 Sum_probs=35.4
Q ss_pred CCCCChHHHHHHHHHHHhhCCchhhhcccCCCC-CHHHHHHHHHHHh
Q 044864 66 RGNFAEDEEDLIIKLHALLGNRWSLIAGRLPGR-TANEVKNYWNSHL 111 (214)
Q Consensus 66 ~~~Wt~eED~~L~~lv~~~G~~W~~Ia~~lpgR-t~~q~r~rw~~~l 111 (214)
+..||.|.-..+++++..-|..=+.||+.+ |- +.+++...+..+.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~~W~~~~~ 50 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLYKWRIQLQ 50 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHHHHHHHHH
Confidence 568999999999999999898889999999 75 6666654444333
No 110
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=29.82 E-value=85 Score=24.59 Aligned_cols=29 Identities=14% Similarity=-0.047 Sum_probs=22.8
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 84 LGNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 84 ~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
.|....+||..| |-|...++.+....++.
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 456789999999 88999998887655443
No 111
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=28.83 E-value=1.3e+02 Score=23.38 Aligned_cols=35 Identities=31% Similarity=0.392 Sum_probs=26.9
Q ss_pred HHHHhhCCchhhhcccCCCCCHHHHHHHHHHHhhhh
Q 044864 79 KLHALLGNRWSLIAGRLPGRTANEVKNYWNSHLRRK 114 (214)
Q Consensus 79 ~lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~ 114 (214)
.+....|-...+||..| |-+...|+.+-...++.-
T Consensus 129 ~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 129 LYNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred HHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 33344567899999999 999999999887766654
No 112
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=28.50 E-value=1.1e+02 Score=23.30 Aligned_cols=30 Identities=13% Similarity=0.039 Sum_probs=23.4
Q ss_pred hhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 83 LLGNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 83 ~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
..|-.-.+||..| |-+...|+.+....++.
T Consensus 120 ~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 120 WEDMDVAETAAAM-GCSEGSVKTHCSRATHA 149 (161)
T ss_pred HhcCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3456789999999 88999999887655443
No 113
>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=28.42 E-value=62 Score=22.91 Aligned_cols=31 Identities=23% Similarity=0.425 Sum_probs=24.1
Q ss_pred HHHHHHHHHhhCCchhhhcccCCCCCHHHHHH
Q 044864 74 EDLIIKLHALLGNRWSLIAGRLPGRTANEVKN 105 (214)
Q Consensus 74 D~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~ 105 (214)
|..|..+....|.+|..+|+.| |=+...|..
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 4567778888999999999999 666665543
No 114
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=28.39 E-value=28 Score=25.11 Aligned_cols=44 Identities=11% Similarity=0.174 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHhCCCccccccccccccccccccccchhhcccCCC
Q 044864 19 QEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYLRPDL 64 (214)
Q Consensus 19 eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~~ 64 (214)
+.|.+++.++...+.-.+..||+.++ -+...|+.|.......++
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 56889999999998778999999985 888888888777655443
No 115
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=28.36 E-value=23 Score=27.22 Aligned_cols=44 Identities=7% Similarity=0.116 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHhCCCccccccccccccccccccccchhhcccCCC
Q 044864 19 QEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYLRPDL 64 (214)
Q Consensus 19 eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~~ 64 (214)
+-|.+++++.+..+...+..||+.++ -+...|+.|-.+..+.++
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 56889999999999888999999996 888899998777655553
No 116
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=28.18 E-value=96 Score=24.01 Aligned_cols=29 Identities=21% Similarity=0.280 Sum_probs=22.9
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 84 LGNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 84 ~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
.|-+..+||..| |-|...|+.+....++.
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 456789999999 88999999888766554
No 117
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=28.11 E-value=98 Score=24.60 Aligned_cols=30 Identities=23% Similarity=0.154 Sum_probs=24.0
Q ss_pred hhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 83 LLGNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 83 ~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
..|-...+||..| |-+...|+.+....++.
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 89999999988655544
No 118
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=27.76 E-value=77 Score=26.15 Aligned_cols=44 Identities=23% Similarity=0.186 Sum_probs=35.8
Q ss_pred CCChHHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHHHHHHHhhhh
Q 044864 68 NFAEDEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKNYWNSHLRRK 114 (214)
Q Consensus 68 ~Wt~eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~ 114 (214)
..|+.|-+.|.-+.. |-.=.+||..| +.|.+.|+.+..+++++-
T Consensus 148 ~LT~RE~eVL~lla~--G~snkeIA~~L-~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 148 LLTPRELEVLRLLAE--GLSNKEIAEEL-NLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHH-CCCHhHHHHHHHHHHHHc
Confidence 688888887665543 55568999999 999999999999888775
No 119
>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=27.52 E-value=63 Score=22.28 Aligned_cols=29 Identities=28% Similarity=0.540 Sum_probs=20.7
Q ss_pred HHHHHHHHHh-hCCchhhhcccCCCCCHHHH
Q 044864 74 EDLIIKLHAL-LGNRWSLIAGRLPGRTANEV 103 (214)
Q Consensus 74 D~~L~~lv~~-~G~~W~~Ia~~lpgRt~~q~ 103 (214)
+..|..++.. .|..|..+|+.| |=+..++
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 4556666666 789999999999 4454444
No 120
>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=27.47 E-value=77 Score=24.90 Aligned_cols=30 Identities=13% Similarity=0.001 Sum_probs=23.4
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhhh
Q 044864 84 LGNRWSLIAGRLPGRTANEVKNYWNSHLRRK 114 (214)
Q Consensus 84 ~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~ 114 (214)
.|-...+||..| |-|...|+.+....++.-
T Consensus 153 ~~~s~~EIA~~l-gis~~tv~~~l~rar~~L 182 (190)
T TIGR02939 153 EGLSYEDIARIM-DCPVGTVRSRIFRAREAI 182 (190)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 356789999999 888999998886655543
No 121
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=27.46 E-value=1.6e+02 Score=18.41 Aligned_cols=47 Identities=23% Similarity=0.361 Sum_probs=35.4
Q ss_pred cCCCCChHHHHHHHHHHHhhC----CchhhhcccCCCCCHHHHHHHHHHHhh
Q 044864 65 KRGNFAEDEEDLIIKLHALLG----NRWSLIAGRLPGRTANEVKNYWNSHLR 112 (214)
Q Consensus 65 ~~~~Wt~eED~~L~~lv~~~G----~~W~~Ia~~lpgRt~~q~r~rw~~~l~ 112 (214)
.+..||.++-..|........ ..-..||..+ |=+..+|.+.|.+.-.
T Consensus 3 ~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l-~l~~~~V~~WF~nrR~ 53 (57)
T PF00046_consen 3 KRTRFTKEQLKVLEEYFQENPYPSKEEREELAKEL-GLTERQVKNWFQNRRR 53 (57)
T ss_dssp SSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHH-TSSHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHhccccccccccccccc-cccccccccCHHHhHH
Confidence 356789888888888888744 2357788888 8999999887765443
No 122
>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=27.30 E-value=69 Score=22.69 Aligned_cols=25 Identities=24% Similarity=0.450 Sum_probs=19.5
Q ss_pred HHHHHhhCCchhhhcccCCCCCHHHH
Q 044864 78 IKLHALLGNRWSLIAGRLPGRTANEV 103 (214)
Q Consensus 78 ~~lv~~~G~~W~~Ia~~lpgRt~~q~ 103 (214)
..+....|..|..+|..| |=+..+|
T Consensus 11 ~~ia~~iG~~Wk~Lar~L-Gls~~dI 35 (86)
T cd08318 11 TVFANKLGEDWKTLAPHL-EMKDKEI 35 (86)
T ss_pred HHHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 335577899999999999 7676665
No 123
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=26.60 E-value=1.1e+02 Score=24.14 Aligned_cols=29 Identities=10% Similarity=0.022 Sum_probs=23.4
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 84 LGNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 84 ~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
.|-....||..| |-|...++.+....++.
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 456789999999 88999999998765544
No 124
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=26.53 E-value=1.1e+02 Score=24.34 Aligned_cols=29 Identities=10% Similarity=-0.003 Sum_probs=23.1
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 84 LGNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 84 ~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
.|-...+||..| |-+...|+.|....++.
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 466789999999 99999999887655544
No 125
>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=26.03 E-value=44 Score=26.66 Aligned_cols=46 Identities=17% Similarity=0.218 Sum_probs=30.8
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCccccccccccc---cccccccccchh
Q 044864 11 TNKGAWSKQEDQKLIDYIRKHGEGCWRTIPQAAGL---ARCGKSCRLRWI 57 (214)
Q Consensus 11 ~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~---~Rs~~qcr~Rw~ 57 (214)
.....-|..|.+-|..+|++||. |+..++.-..+ ..|..||+.+..
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhGd-Dy~aMarD~KLN~~Q~T~~qlrrki~ 160 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHGD-DYKAMARDRKLNYMQHTPGQLRRKIR 160 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHCc-cHHHHhccCCCCcccCCHHHHHHHHH
Confidence 34667889999999999999994 57777643221 345555555443
No 126
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=26.03 E-value=1.4e+02 Score=23.42 Aligned_cols=37 Identities=14% Similarity=0.106 Sum_probs=25.2
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHH---hhhhhhhCCCC
Q 044864 84 LGNRWSLIAGRLPGRTANEVKNYWNSH---LRRKLINMGID 121 (214)
Q Consensus 84 ~G~~W~~Ia~~lpgRt~~q~r~rw~~~---l~~~~~~~~~~ 121 (214)
.|-...+||..| |-+...|+.+.... |+..+.+.+.|
T Consensus 143 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr~~l~~~~~~ 182 (186)
T PRK05602 143 QGLSNIEAAAVM-DISVDALESLLARGRRALRAQLADLPGS 182 (186)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 456789999998 88888888886544 44444444433
No 127
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=25.71 E-value=1.2e+02 Score=23.95 Aligned_cols=30 Identities=23% Similarity=0.223 Sum_probs=23.7
Q ss_pred hhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 83 LLGNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 83 ~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
..|....+||..| |-+...|+.+....++.
T Consensus 153 ~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 153 VVGLSAEETAEAV-GSTPGAVRVAQHRALAR 182 (189)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466799999999 88999998887765554
No 128
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=25.56 E-value=1.2e+02 Score=23.76 Aligned_cols=30 Identities=17% Similarity=0.110 Sum_probs=23.9
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhhh
Q 044864 84 LGNRWSLIAGRLPGRTANEVKNYWNSHLRRK 114 (214)
Q Consensus 84 ~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~ 114 (214)
.|-...+||..| |-+...|+.+....++.-
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 466789999999 899999999887655543
No 129
>PF09197 Rap1-DNA-bind: Rap1, DNA-binding; InterPro: IPR015280 Members of this entry, which are predominantly found in the yeast protein Rap1, assume a secondary structure consisting of a three-helix bundle and an N-terminal arm. They contain an Arg-Asp-Arg-Lys sequence that interacts with an ACAregion in the 3, region of the DNA-binding site []. ; PDB: 1IGN_A 3UKG_A.
Probab=25.29 E-value=64 Score=24.19 Aligned_cols=26 Identities=15% Similarity=0.239 Sum_probs=18.4
Q ss_pred hhhcccCCCCCHHHHHHHHHHHhhhh
Q 044864 89 SLIAGRLPGRTANEVKNYWNSHLRRK 114 (214)
Q Consensus 89 ~~Ia~~lpgRt~~q~r~rw~~~l~~~ 114 (214)
...+...|..|.+.=|+||...+...
T Consensus 53 ~~~~~~~p~HT~~sWRDR~RKfv~~~ 78 (105)
T PF09197_consen 53 KDLARKNPRHTENSWRDRYRKFVSEY 78 (105)
T ss_dssp HHHHHHTTTS-HHHHHHHHHHTHHHH
T ss_pred HHHHHcCCccchhHHHHHHHHHHHHc
Confidence 34466778888888888888766654
No 130
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=25.07 E-value=1.1e+02 Score=24.03 Aligned_cols=28 Identities=14% Similarity=-0.015 Sum_probs=22.0
Q ss_pred CCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 85 GNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 85 G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
|..-.+||..| |-+...|+.+....++.
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 56789999999 88999998887655443
No 131
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=24.77 E-value=1.4e+02 Score=24.07 Aligned_cols=37 Identities=27% Similarity=0.206 Sum_probs=26.0
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHH---HhhhhhhhCCCC
Q 044864 84 LGNRWSLIAGRLPGRTANEVKNYWNS---HLRRKLINMGID 121 (214)
Q Consensus 84 ~G~~W~~Ia~~lpgRt~~q~r~rw~~---~l~~~~~~~~~~ 121 (214)
.|..-.+||..| |.+...|+.|... .|+..+...+.+
T Consensus 154 eg~s~~EIA~~l-gis~~tVk~~l~RAr~~Lr~~l~~~~~~ 193 (201)
T PRK12545 154 LDFEIDDICTEL-TLTANHCSVLLYRARTRLRTCLSEKGLT 193 (201)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 356789999999 9999999988754 444445444443
No 132
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=24.72 E-value=1.3e+02 Score=22.87 Aligned_cols=29 Identities=14% Similarity=-0.019 Sum_probs=22.7
Q ss_pred hhCCchhhhcccCCCCCHHHHHHHHHHHhh
Q 044864 83 LLGNRWSLIAGRLPGRTANEVKNYWNSHLR 112 (214)
Q Consensus 83 ~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~ 112 (214)
..|-.-.+||..| |-+...|+.+....+.
T Consensus 120 ~~g~s~~EIA~~l-gis~~tV~~~l~Rar~ 148 (160)
T PRK09642 120 LEEKSYQEIALQE-KIEVKTVEMKLYRARK 148 (160)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3456789999999 9999999988765444
No 133
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=24.70 E-value=45 Score=35.15 Aligned_cols=25 Identities=12% Similarity=0.427 Sum_probs=23.2
Q ss_pred CCChHHHHHHHHHHHhhC-Cchhhhc
Q 044864 68 NFAEDEEDLIIKLHALLG-NRWSLIA 92 (214)
Q Consensus 68 ~Wt~eED~~L~~lv~~~G-~~W~~Ia 92 (214)
.|..++|..|+-.|-+|| ++|..|-
T Consensus 1135 ~W~~e~Ds~LLiGI~khGygswe~Ir 1160 (1373)
T KOG0384|consen 1135 DWGSEDDSMLLIGIFKHGYGSWEAIR 1160 (1373)
T ss_pred CCCchhhhhHhhhhhhcccccHHHhc
Confidence 699999999999999999 9998883
No 134
>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=24.66 E-value=1.3e+02 Score=23.94 Aligned_cols=33 Identities=12% Similarity=0.071 Sum_probs=24.8
Q ss_pred HHHhhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 80 LHALLGNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 80 lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
+....|-...+||..| |-+...|+.|....++.
T Consensus 142 l~~~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 142 MREVLGFESDEICQEL-EISTSNCHVLLYRARLS 174 (188)
T ss_pred HHHHhCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3334467789999999 99999998887655443
No 135
>PRK01905 DNA-binding protein Fis; Provisional
Probab=24.20 E-value=1.5e+02 Score=20.46 Aligned_cols=35 Identities=26% Similarity=0.222 Sum_probs=26.8
Q ss_pred hHHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHHH
Q 044864 71 EDEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKNY 106 (214)
Q Consensus 71 ~eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~r 106 (214)
.-|...+.+++..+|+++...|+.+ |=+...++.+
T Consensus 36 ~~E~~~i~~aL~~~~gn~s~aAr~L-GIsrstL~rk 70 (77)
T PRK01905 36 CVEKPLLEVVMEQAGGNQSLAAEYL-GINRNTLRKK 70 (77)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHH
Confidence 3467788899999999999999988 5555555443
No 136
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=24.07 E-value=1.2e+02 Score=24.07 Aligned_cols=28 Identities=14% Similarity=0.068 Sum_probs=21.8
Q ss_pred CCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 85 GNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 85 G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
|-...+||..| |-+.+.|+.+....++.
T Consensus 154 g~s~~eIA~~l-gis~~tv~~~l~Rar~~ 181 (193)
T PRK11923 154 GLSYEDIASVM-QCPVGTVRSRIFRAREA 181 (193)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 55689999999 88899998887654443
No 137
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=24.00 E-value=75 Score=22.64 Aligned_cols=29 Identities=31% Similarity=0.523 Sum_probs=22.1
Q ss_pred HHHHHHHhhCCchhhhcccCCCCCHHHHHH
Q 044864 76 LIIKLHALLGNRWSLIAGRLPGRTANEVKN 105 (214)
Q Consensus 76 ~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~ 105 (214)
.|-.+....|..|..+|+.| |=+..+|..
T Consensus 4 ~l~~l~~~lG~~Wk~lar~L-G~s~~eI~~ 32 (86)
T cd08777 4 HLDLLRENLGKKWKRCARKL-GFTESEIEE 32 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHc-CCCHHHHHH
Confidence 34555677899999999999 777776654
No 138
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=23.23 E-value=1.4e+02 Score=23.78 Aligned_cols=28 Identities=7% Similarity=-0.092 Sum_probs=22.5
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhh
Q 044864 84 LGNRWSLIAGRLPGRTANEVKNYWNSHLR 112 (214)
Q Consensus 84 ~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~ 112 (214)
.|-...+||..| |-+...|+.|....++
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~RAr~ 176 (189)
T PRK12530 149 LELSSEQICQEC-DISTSNLHVLLYRARL 176 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 466799999999 9999999988764443
No 139
>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=23.01 E-value=73 Score=22.62 Aligned_cols=26 Identities=23% Similarity=0.420 Sum_probs=20.7
Q ss_pred HHHHHHHHhhCCchhhhcccCCCCCHH
Q 044864 75 DLIIKLHALLGNRWSLIAGRLPGRTAN 101 (214)
Q Consensus 75 ~~L~~lv~~~G~~W~~Ia~~lpgRt~~ 101 (214)
..|..+....|..|..+|..| |=+..
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L-Glse~ 28 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL-GLSYR 28 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc-CCCHH
Confidence 457888899999999999998 43333
No 140
>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=22.26 E-value=79 Score=22.12 Aligned_cols=33 Identities=21% Similarity=0.521 Sum_probs=23.7
Q ss_pred hHHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHH
Q 044864 71 EDEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKN 105 (214)
Q Consensus 71 ~eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~ 105 (214)
.||-++|+.. -..|.+|..+|..| |=+...|..
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 5777777732 24578999999999 767766644
No 141
>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=22.20 E-value=61 Score=26.00 Aligned_cols=38 Identities=13% Similarity=0.253 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHHHHHhCCCccccccccccccccccccccc
Q 044864 15 AWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLR 55 (214)
Q Consensus 15 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~R 55 (214)
.||.|+.++|.++... |.. =.+||..|+ +.|...+.-+
T Consensus 2 ~Wtde~~~~L~~lw~~-G~S-asqIA~~lg-~vsRnAViGk 39 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GLS-ASQIARQLG-GVSRNAVIGK 39 (162)
T ss_pred CCCHHHHHHHHHHHHc-CCC-HHHHHHHhC-Ccchhhhhhh
Confidence 5999999999998854 322 679999998 4555444443
No 142
>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=22.17 E-value=90 Score=22.25 Aligned_cols=22 Identities=27% Similarity=0.433 Sum_probs=18.9
Q ss_pred HHHHHHHHHhhCCchhhhcccC
Q 044864 74 EDLIIKLHALLGNRWSLIAGRL 95 (214)
Q Consensus 74 D~~L~~lv~~~G~~W~~Ia~~l 95 (214)
|..|..+....|..|..+|..|
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L 25 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL 25 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc
Confidence 4567778889999999999998
No 143
>COG3795 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.01 E-value=83 Score=24.25 Aligned_cols=59 Identities=27% Similarity=0.380 Sum_probs=39.8
Q ss_pred CCCCHHHHHHHHHHHHHhC-----CCccccccccccccccccccccchhhcccCCCcCCCCChHHHHH
Q 044864 14 GAWSKQEDQKLIDYIRKHG-----EGCWRTIPQAAGLARCGKSCRLRWINYLRPDLKRGNFAEDEEDL 76 (214)
Q Consensus 14 g~WT~eED~~L~~~v~~~g-----~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~~~~~~Wt~eED~~ 76 (214)
-.|+.++|+.|++..-+|. .|-|.-.+...+ ...+...+.+ -=...+..|||.+--|++
T Consensus 15 ~a~~~e~daalm~~~~~y~e~L~~aG~l~~~~~L~p-t~~a~tlr~~---~G~~~viDGPFaEtKEql 78 (123)
T COG3795 15 AAWSVEEDAALMAALGKYNERLAKAGVLGPGARLHP-TTAATTLRFR---GGKRTVIDGPFAETKEQL 78 (123)
T ss_pred hcCCcCccHHHHHHHHHHHHHHHHcCCccccccccC-CccceEEEec---CCcceecCCCchhHHHHh
Confidence 5799999999999988883 334666655555 6666665532 122345678998766655
No 144
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=21.57 E-value=90 Score=19.90 Aligned_cols=44 Identities=23% Similarity=0.259 Sum_probs=30.6
Q ss_pred CCChHHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHHHHHHHhhhh
Q 044864 68 NFAEDEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKNYWNSHLRRK 114 (214)
Q Consensus 68 ~Wt~eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~ 114 (214)
.+|+.|-+.|.-+. -|..=.+||..+ |.+...|+.+...++++-
T Consensus 3 ~LT~~E~~vl~~l~--~G~~~~eIA~~l-~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLA--QGMSNKEIAEEL-GISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHH--TTS-HHHHHHHH-TSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHH--hcCCcchhHHhc-CcchhhHHHHHHHHHHHh
Confidence 45666666555443 356668999999 899999998887777654
No 145
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=21.52 E-value=1.6e+02 Score=22.98 Aligned_cols=29 Identities=17% Similarity=0.260 Sum_probs=22.9
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 84 LGNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 84 ~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
.|-.-.+||..| |.+...|+.+....++.
T Consensus 144 ~g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 172 (179)
T PRK12514 144 EGLSYKELAERH-DVPLNTMRTWLRRSLLK 172 (179)
T ss_pred cCCCHHHHHHHH-CCChHHHHHHHHHHHHH
Confidence 356789999999 99999999887665544
No 146
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=21.25 E-value=1.8e+02 Score=22.15 Aligned_cols=29 Identities=21% Similarity=0.200 Sum_probs=22.4
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 84 LGNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 84 ~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
.|-.-.+||..| |-+...++.|....++.
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 455678999999 89999999887655443
No 147
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=20.97 E-value=1.6e+02 Score=22.94 Aligned_cols=30 Identities=30% Similarity=0.339 Sum_probs=24.2
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhhh
Q 044864 84 LGNRWSLIAGRLPGRTANEVKNYWNSHLRRK 114 (214)
Q Consensus 84 ~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~ 114 (214)
.|-...+||..| |-+...|+.+....+..-
T Consensus 134 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~~ 163 (172)
T PRK09651 134 DGLTYSEIAHKL-GVSVSSVKKYVAKATEHC 163 (172)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 356789999999 999999999887666554
No 148
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=20.89 E-value=1.6e+02 Score=23.42 Aligned_cols=31 Identities=16% Similarity=0.130 Sum_probs=24.8
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhhhh
Q 044864 84 LGNRWSLIAGRLPGRTANEVKNYWNSHLRRKL 115 (214)
Q Consensus 84 ~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~~ 115 (214)
.|-.-.+||..| |-+...|+.+....++.-.
T Consensus 145 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr 175 (185)
T PRK09649 145 LGLSYADAAAVC-GCPVGTIRSRVARARDALL 175 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 356789999999 9999999999876666543
No 149
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=20.89 E-value=1.8e+02 Score=21.87 Aligned_cols=29 Identities=21% Similarity=0.203 Sum_probs=21.9
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 84 LGNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 84 ~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
.|-...+||..| |-+...|+.+-...+++
T Consensus 121 ~~~s~~EIA~~l-~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 121 VGKTMGEIALET-EMTYYQVRWIYRQALEK 149 (154)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 345688999998 88999998877655543
No 150
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=20.89 E-value=1.7e+02 Score=23.41 Aligned_cols=30 Identities=17% Similarity=0.031 Sum_probs=22.5
Q ss_pred hhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 83 LLGNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 83 ~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
..|-.+.+||..| |=+...|+.+-...++.
T Consensus 150 ~~g~s~~eIA~~l-gis~~tV~~~l~Ra~~~ 179 (196)
T PRK12524 150 IEGLSNPEIAEVM-EIGVEAVESLTARGKRA 179 (196)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3456799999999 88888888877654443
No 151
>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=20.51 E-value=1.8e+02 Score=22.64 Aligned_cols=29 Identities=24% Similarity=0.225 Sum_probs=22.9
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 044864 84 LGNRWSLIAGRLPGRTANEVKNYWNSHLRR 113 (214)
Q Consensus 84 ~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~ 113 (214)
.|-...+||..| |-+...|+.+....++.
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 177 (183)
T TIGR02999 149 AGLTVEEIAELL-GVSVRTVERDWRFARAW 177 (183)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 356789999999 89999999988765543
No 152
>cd01852 AIG1 AIG1 (avrRpt2-induced gene 1). This represents Arabidoposis protein AIG1 that appears to be involved in plant resistance to bacteria. The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 exhibits RPS2- and avrRpt1-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2. This subfamily also includes IAN-4 protein, which has GTP-binding activity and shares sequence homology with a novel family of putative GTP-binding proteins: the immuno-associated nucleotide (IAN) family. The evolutionary conservation of the IAN family provides a unique example of a plant pathogen response gene conserved in animals. The IAN/IMAP subfamily has been proposed to regulate apoptosis in vertebrates and angiosperm plants, particularly in relation to cancer, diabetes, and infections. The human IAN genes were renamed GIMAP (GTPase of the immunity associated proteins).
Probab=20.47 E-value=3.8e+02 Score=21.25 Aligned_cols=70 Identities=13% Similarity=0.140 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHHHHHhCCCccccccccccccccccccccchhhcccCCCcCCCCChHHHHHHHHHHHhhCCchhhhccc
Q 044864 15 AWSKQEDQKLIDYIRKHGEGCWRTIPQAAGLARCGKSCRLRWINYLRPDLKRGNFAEDEEDLIIKLHALLGNRWSLIAGR 94 (214)
Q Consensus 15 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rs~~qcr~Rw~~~l~p~~~~~~Wt~eED~~L~~lv~~~G~~W~~Ia~~ 94 (214)
.+|.++.+.|..+.+.+|..-|..+--.+ ++...--...+. .|-.+....|..++.++|+++-.+...
T Consensus 95 ~~t~~d~~~l~~l~~~fg~~~~~~~ivv~--T~~d~l~~~~~~----------~~~~~~~~~l~~l~~~c~~r~~~f~~~ 162 (196)
T cd01852 95 RFTEEEEQAVETLQELFGEKVLDHTIVLF--TRGDDLEGGTLE----------DYLENSCEALKRLLEKCGGRYVAFNNK 162 (196)
T ss_pred CcCHHHHHHHHHHHHHhChHhHhcEEEEE--ECccccCCCcHH----------HHHHhccHHHHHHHHHhCCeEEEEeCC
Confidence 38877777666666667866565443222 232221111111 222334467888999999887665555
Q ss_pred CC
Q 044864 95 LP 96 (214)
Q Consensus 95 lp 96 (214)
.+
T Consensus 163 ~~ 164 (196)
T cd01852 163 AK 164 (196)
T ss_pred CC
Confidence 43
No 153
>PRK00118 putative DNA-binding protein; Validated
Probab=20.41 E-value=2e+02 Score=21.37 Aligned_cols=39 Identities=13% Similarity=0.078 Sum_probs=30.5
Q ss_pred hHHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHHHHHHH
Q 044864 71 EDEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKNYWNSH 110 (214)
Q Consensus 71 ~eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~ 110 (214)
++.+..++.+....|-...+||..+ |-|...++.+-...
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~RA 57 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKRT 57 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 3456667777777788999999999 88998888776543
No 154
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=20.19 E-value=1.9e+02 Score=20.90 Aligned_cols=33 Identities=15% Similarity=0.064 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHhhCCchhhhcccCCCCCHHHHHH
Q 044864 72 DEEDLIIKLHALLGNRWSLIAGRLPGRTANEVKN 105 (214)
Q Consensus 72 eED~~L~~lv~~~G~~W~~Ia~~lpgRt~~q~r~ 105 (214)
-|...|..++..++++....|+.+ |=+...++.
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~L-GIsRsTL~r 87 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALML-GINRGTLRK 87 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHH
Confidence 477788899999999999999998 656555443
No 155
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=20.18 E-value=1.9e+02 Score=22.05 Aligned_cols=30 Identities=30% Similarity=0.334 Sum_probs=23.3
Q ss_pred HhhCCchhhhcccCCCCCHHHHHHHHHHHhh
Q 044864 82 ALLGNRWSLIAGRLPGRTANEVKNYWNSHLR 112 (214)
Q Consensus 82 ~~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~ 112 (214)
-..|-...+||..+ |-+...|+.|....++
T Consensus 126 ~~~g~s~~EIA~~l-~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 126 QVDGLGYGEIATEL-GISLATVKRYLNKAAM 155 (161)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 33466789999999 8899999888766544
No 156
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=20.09 E-value=1.8e+02 Score=22.82 Aligned_cols=31 Identities=23% Similarity=0.073 Sum_probs=24.4
Q ss_pred hhCCchhhhcccCCCCCHHHHHHHHHHHhhhh
Q 044864 83 LLGNRWSLIAGRLPGRTANEVKNYWNSHLRRK 114 (214)
Q Consensus 83 ~~G~~W~~Ia~~lpgRt~~q~r~rw~~~l~~~ 114 (214)
..|-...+||..| |-+...|+.+-...++.-
T Consensus 143 ~~g~s~~EIA~~l-~is~~tV~~~l~rar~~L 173 (181)
T PRK12536 143 LEGLSVAETAQLT-GLSESAVKVGIHRGLKAL 173 (181)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 4466789999999 999999999876655443
Done!