Query 045583
Match_columns 319
No_of_seqs 217 out of 1415
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 03:32:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045583.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045583hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03091 hypothetical protein; 100.0 5.4E-38 1.2E-42 308.2 12.5 128 1-129 1-128 (459)
2 PLN03212 Transcription repress 100.0 1.1E-37 2.5E-42 287.5 12.2 123 3-126 14-136 (249)
3 KOG0048 Transcription factor, 100.0 6.4E-36 1.4E-40 277.0 10.5 112 9-121 4-115 (238)
4 KOG0049 Transcription factor, 99.7 3.4E-18 7.5E-23 174.0 7.4 120 8-128 247-421 (939)
5 KOG0049 Transcription factor, 99.7 1.5E-17 3.2E-22 169.5 5.2 117 1-120 347-467 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.6 2.7E-16 5.8E-21 115.7 3.1 60 17-79 1-60 (60)
7 COG5147 REB1 Myb superfamily p 99.5 4.9E-15 1.1E-19 150.1 5.9 108 9-118 15-122 (512)
8 KOG0050 mRNA splicing protein 99.5 6E-15 1.3E-19 147.6 1.8 109 11-122 4-112 (617)
9 KOG0051 RNA polymerase I termi 99.5 5.8E-14 1.3E-18 143.9 5.7 104 13-120 383-514 (607)
10 PF00249 Myb_DNA-binding: Myb- 99.3 8.4E-13 1.8E-17 93.5 4.2 46 68-113 1-48 (48)
11 PF00249 Myb_DNA-binding: Myb- 99.3 3.4E-13 7.4E-18 95.5 0.3 48 14-62 1-48 (48)
12 PF13921 Myb_DNA-bind_6: Myb-l 99.3 2.2E-12 4.7E-17 94.9 4.1 54 71-124 1-54 (60)
13 PLN03212 Transcription repress 99.2 6.7E-12 1.5E-16 116.8 5.2 66 63-128 20-87 (249)
14 smart00717 SANT SANT SWI3, AD 99.2 3.8E-11 8.2E-16 82.4 5.0 47 68-114 1-48 (49)
15 KOG0048 Transcription factor, 99.1 6.6E-11 1.4E-15 110.0 4.4 64 63-126 4-69 (238)
16 PLN03091 hypothetical protein; 99.1 1.2E-10 2.5E-15 115.9 4.7 65 63-127 9-75 (459)
17 cd00167 SANT 'SWI3, ADA2, N-Co 99.0 3.3E-10 7E-15 76.7 4.9 43 70-112 1-44 (45)
18 smart00717 SANT SANT SWI3, AD 98.9 4.1E-10 8.9E-15 77.2 1.8 48 14-63 1-48 (49)
19 cd00167 SANT 'SWI3, ADA2, N-Co 98.8 2.3E-09 5E-14 72.5 1.6 45 16-62 1-45 (45)
20 KOG0051 RNA polymerase I termi 98.7 9.8E-09 2.1E-13 105.9 5.0 113 13-129 307-446 (607)
21 COG5147 REB1 Myb superfamily p 98.3 4E-08 8.7E-13 100.3 -2.6 97 13-113 290-396 (512)
22 TIGR01557 myb_SHAQKYF myb-like 97.6 3.2E-05 6.9E-10 57.4 2.0 49 13-62 2-54 (57)
23 TIGR01557 myb_SHAQKYF myb-like 97.5 0.00016 3.4E-09 53.6 5.0 47 68-114 3-55 (57)
24 PF13325 MCRS_N: N-terminal re 97.4 0.00047 1E-08 63.1 7.1 101 16-119 1-132 (199)
25 TIGR02894 DNA_bind_RsfA transc 97.4 0.00017 3.7E-09 63.8 3.6 52 67-119 3-61 (161)
26 KOG0457 Histone acetyltransfer 97.2 0.00013 2.7E-09 73.1 1.4 51 10-62 68-118 (438)
27 KOG0050 mRNA splicing protein 97.1 0.00033 7.1E-09 71.6 3.0 64 65-128 4-68 (617)
28 KOG0457 Histone acetyltransfer 96.9 0.0011 2.4E-08 66.5 5.2 49 65-113 69-118 (438)
29 PF13837 Myb_DNA-bind_4: Myb/S 96.9 0.00059 1.3E-08 53.2 2.4 49 68-116 1-67 (90)
30 TIGR02894 DNA_bind_RsfA transc 96.8 0.0004 8.7E-09 61.5 0.4 51 12-64 2-57 (161)
31 COG5259 RSC8 RSC chromatin rem 96.6 0.00066 1.4E-08 68.7 1.0 46 13-61 278-323 (531)
32 KOG1279 Chromatin remodeling f 96.6 0.0022 4.8E-08 66.1 4.8 47 66-112 251-297 (506)
33 COG5259 RSC8 RSC chromatin rem 96.6 0.0018 3.8E-08 65.7 3.9 45 68-112 279-323 (531)
34 PRK13923 putative spore coat p 96.4 0.0024 5.2E-08 57.2 3.1 51 67-118 4-61 (170)
35 PF08914 Myb_DNA-bind_2: Rap1 96.4 0.0037 7.9E-08 47.6 3.7 50 68-117 2-61 (65)
36 KOG1279 Chromatin remodeling f 96.4 0.0014 3.1E-08 67.4 1.7 48 11-61 250-297 (506)
37 PF08914 Myb_DNA-bind_2: Rap1 96.2 0.002 4.3E-08 49.0 1.2 52 14-65 2-60 (65)
38 PRK13923 putative spore coat p 95.4 0.0033 7.3E-08 56.3 -0.6 51 11-63 2-57 (170)
39 PF13873 Myb_DNA-bind_5: Myb/S 95.2 0.026 5.6E-07 43.2 4.0 48 68-115 2-71 (78)
40 PF13837 Myb_DNA-bind_4: Myb/S 95.1 0.0031 6.8E-08 49.1 -1.6 49 14-62 1-64 (90)
41 PLN03142 Probable chromatin-re 94.6 0.069 1.5E-06 59.7 6.7 99 16-116 826-987 (1033)
42 COG5114 Histone acetyltransfer 94.0 0.015 3.3E-07 56.8 0.0 50 12-63 61-110 (432)
43 PF09111 SLIDE: SLIDE; InterP 93.5 0.097 2.1E-06 44.3 4.0 51 65-115 46-112 (118)
44 COG5114 Histone acetyltransfer 93.5 0.066 1.4E-06 52.4 3.3 48 66-113 61-109 (432)
45 PF13873 Myb_DNA-bind_5: Myb/S 93.4 0.036 7.7E-07 42.5 1.1 50 13-62 1-69 (78)
46 KOG2656 DNA methyltransferase 93.1 0.13 2.7E-06 51.6 4.7 55 68-122 130-190 (445)
47 KOG4282 Transcription factor G 92.6 0.15 3.2E-06 49.8 4.4 49 68-116 54-116 (345)
48 KOG1194 Predicted DNA-binding 91.8 0.33 7.1E-06 49.6 5.8 49 67-115 186-234 (534)
49 PF12776 Myb_DNA-bind_3: Myb/S 91.6 0.32 7E-06 38.2 4.5 46 70-115 1-64 (96)
50 COG5118 BDP1 Transcription ini 89.0 0.5 1.1E-05 47.4 4.3 47 69-115 366-412 (507)
51 PF08281 Sigma70_r4_2: Sigma-7 87.2 1.2 2.5E-05 31.4 4.2 42 73-115 12-53 (54)
52 KOG4282 Transcription factor G 84.9 0.4 8.6E-06 46.8 1.0 48 15-62 55-113 (345)
53 PF11626 Rap1_C: TRF2-interact 78.8 2 4.2E-05 34.1 2.8 25 10-34 43-75 (87)
54 COG5118 BDP1 Transcription ini 75.7 1.4 3.1E-05 44.3 1.4 64 14-80 365-436 (507)
55 PRK11179 DNA-binding transcrip 74.0 3.5 7.7E-05 35.6 3.3 46 73-119 8-54 (153)
56 PF09111 SLIDE: SLIDE; InterP 72.6 2.9 6.3E-05 35.4 2.4 35 11-45 46-82 (118)
57 PRK11169 leucine-responsive tr 71.0 4.1 8.9E-05 35.6 3.1 47 73-120 13-60 (164)
58 PF04545 Sigma70_r4: Sigma-70, 70.3 7.8 0.00017 26.9 3.8 41 74-115 7-47 (50)
59 KOG4329 DNA-binding protein [G 70.1 34 0.00073 34.6 9.4 43 69-111 278-321 (445)
60 KOG4167 Predicted DNA-binding 68.6 6.7 0.00015 42.6 4.5 45 68-112 619-663 (907)
61 PF13404 HTH_AsnC-type: AsnC-t 66.5 9.2 0.0002 26.3 3.5 38 74-112 3-41 (42)
62 PF11035 SnAPC_2_like: Small n 65.9 15 0.00033 36.2 6.0 49 68-117 21-73 (344)
63 PF07750 GcrA: GcrA cell cycle 65.5 5.4 0.00012 35.4 2.7 41 70-111 2-42 (162)
64 smart00595 MADF subfamily of S 62.4 6 0.00013 30.5 2.2 25 89-114 29-53 (89)
65 TIGR02985 Sig70_bacteroi1 RNA 61.4 13 0.00029 30.7 4.2 36 79-115 121-156 (161)
66 KOG4468 Polycomb-group transcr 61.1 12 0.00026 39.9 4.6 48 68-115 88-145 (782)
67 PF13325 MCRS_N: N-terminal re 59.3 17 0.00037 33.6 4.8 46 70-116 1-49 (199)
68 PF12776 Myb_DNA-bind_3: Myb/S 57.1 6.3 0.00014 30.8 1.4 46 16-61 1-61 (96)
69 PRK09413 IS2 repressor TnpA; R 56.8 20 0.00043 29.8 4.5 47 12-63 8-54 (121)
70 KOG1194 Predicted DNA-binding 54.3 9.2 0.0002 39.5 2.4 41 70-111 472-512 (534)
71 cd08319 Death_RAIDD Death doma 53.2 13 0.00028 29.5 2.7 30 76-106 2-31 (83)
72 KOG2009 Transcription initiati 52.3 17 0.00037 38.6 4.1 46 66-111 407-452 (584)
73 smart00344 HTH_ASNC helix_turn 51.7 20 0.00042 28.5 3.5 45 74-119 3-48 (108)
74 PF13404 HTH_AsnC-type: AsnC-t 49.3 4.8 0.0001 27.8 -0.3 38 20-60 3-40 (42)
75 PF07638 Sigma70_ECF: ECF sigm 48.1 26 0.00056 31.0 4.1 39 75-114 139-177 (185)
76 KOG2656 DNA methyltransferase 46.8 10 0.00023 38.3 1.4 50 11-62 127-181 (445)
77 cd08803 Death_ank3 Death domai 46.4 22 0.00048 28.2 3.0 31 76-107 4-34 (84)
78 KOG0384 Chromodomain-helicase 46.3 21 0.00046 41.0 3.8 72 13-92 1132-1204(1373)
79 PRK11179 DNA-binding transcrip 46.2 7.2 0.00016 33.6 0.2 46 19-67 8-53 (153)
80 TIGR02937 sigma70-ECF RNA poly 45.8 30 0.00065 27.6 3.9 34 81-115 120-153 (158)
81 PF10545 MADF_DNA_bdg: Alcohol 44.7 16 0.00034 27.3 1.8 26 89-114 28-54 (85)
82 PRK09652 RNA polymerase sigma 44.6 32 0.00069 29.1 4.0 31 84-115 141-171 (182)
83 PRK11169 leucine-responsive tr 44.4 6.1 0.00013 34.5 -0.5 46 19-67 13-58 (164)
84 PRK11924 RNA polymerase sigma 43.3 33 0.00071 28.9 3.9 30 85-115 139-168 (179)
85 cd06171 Sigma70_r4 Sigma70, re 42.9 47 0.001 21.7 3.9 40 71-112 11-50 (55)
86 KOG4167 Predicted DNA-binding 42.3 9.5 0.00021 41.5 0.4 44 14-60 619-662 (907)
87 cd08317 Death_ank Death domain 42.0 20 0.00044 27.9 2.1 30 76-106 4-33 (84)
88 PF07750 GcrA: GcrA cell cycle 41.7 17 0.00036 32.3 1.8 33 16-51 2-35 (162)
89 COG2197 CitB Response regulato 41.7 41 0.00089 30.5 4.4 45 69-116 147-191 (211)
90 cd08318 Death_NMPP84 Death dom 41.3 25 0.00054 27.7 2.6 25 81-106 12-36 (86)
91 PRK09643 RNA polymerase sigma 41.3 38 0.00083 29.8 4.1 30 85-115 148-177 (192)
92 KOG2782 Putative SAM dependent 41.3 21 0.00045 34.1 2.4 28 254-281 119-149 (303)
93 cd08311 Death_p75NR Death doma 40.5 27 0.00058 27.3 2.6 34 73-108 2-35 (77)
94 smart00351 PAX Paired Box doma 40.5 42 0.00091 28.1 4.0 84 12-109 13-103 (125)
95 PRK04217 hypothetical protein; 38.9 73 0.0016 26.6 5.1 45 69-115 41-85 (110)
96 PRK09641 RNA polymerase sigma 38.3 44 0.00095 28.7 3.9 29 86-115 151-179 (187)
97 PF04504 DUF573: Protein of un 38.1 38 0.00083 27.5 3.3 48 69-116 5-65 (98)
98 PF11626 Rap1_C: TRF2-interact 37.8 30 0.00064 27.3 2.5 17 64-80 43-59 (87)
99 cd00131 PAX Paired Box domain 37.3 52 0.0011 27.8 4.1 71 14-87 15-92 (128)
100 cd08804 Death_ank2 Death domai 37.3 31 0.00066 27.2 2.5 31 76-107 4-34 (84)
101 TIGR02939 RpoE_Sigma70 RNA pol 36.6 39 0.00085 29.1 3.3 28 87-115 154-181 (190)
102 cd08777 Death_RIP1 Death Domai 35.6 30 0.00066 27.4 2.3 30 77-107 3-32 (86)
103 PF14722 KRAP_IP3R_bind: Ki-ra 35.3 7.8 0.00017 34.6 -1.3 49 218-270 3-51 (160)
104 PRK09047 RNA polymerase factor 34.5 63 0.0014 27.0 4.2 29 86-115 121-149 (161)
105 TIGR02954 Sig70_famx3 RNA poly 34.4 56 0.0012 27.8 3.9 29 86-115 134-162 (169)
106 smart00005 DEATH DEATH domain, 34.1 41 0.00089 25.6 2.8 30 75-105 4-34 (88)
107 PF13936 HTH_38: Helix-turn-he 33.9 31 0.00067 23.7 1.8 37 70-108 4-40 (44)
108 PRK12529 RNA polymerase sigma 33.8 72 0.0016 27.6 4.6 33 85-118 141-173 (178)
109 COG1522 Lrp Transcriptional re 33.0 53 0.0012 27.5 3.5 47 73-120 7-54 (154)
110 PF01388 ARID: ARID/BRIGHT DNA 32.4 72 0.0016 24.7 4.0 38 77-114 39-89 (92)
111 PRK11923 algU RNA polymerase s 32.3 60 0.0013 28.3 3.8 28 87-115 154-181 (193)
112 TIGR02948 SigW_bacill RNA poly 31.7 60 0.0013 27.8 3.7 28 87-115 152-179 (187)
113 PRK09637 RNA polymerase sigma 31.3 68 0.0015 28.0 4.0 30 85-115 120-149 (181)
114 PRK12530 RNA polymerase sigma 31.0 71 0.0015 28.0 4.1 28 86-114 149-176 (189)
115 PRK12515 RNA polymerase sigma 30.9 74 0.0016 27.7 4.2 29 86-115 146-174 (189)
116 PF00196 GerE: Bacterial regul 30.7 68 0.0015 22.8 3.3 44 70-116 3-46 (58)
117 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 30.6 56 0.0012 23.6 2.7 37 71-109 5-41 (50)
118 PRK09648 RNA polymerase sigma 30.6 75 0.0016 27.6 4.2 29 86-115 154-182 (189)
119 PRK09645 RNA polymerase sigma 30.4 76 0.0016 27.0 4.1 29 86-115 133-161 (173)
120 PRK12512 RNA polymerase sigma 30.4 75 0.0016 27.4 4.1 29 86-115 146-174 (184)
121 PRK12523 RNA polymerase sigma 30.3 79 0.0017 27.1 4.2 33 83-116 131-163 (172)
122 TIGR02943 Sig70_famx1 RNA poly 29.6 81 0.0018 27.7 4.2 30 85-115 145-174 (188)
123 cd08779 Death_PIDD Death Domai 29.5 40 0.00087 26.6 2.0 26 77-103 3-28 (86)
124 KOG4468 Polycomb-group transcr 29.4 43 0.00093 35.9 2.7 48 14-63 88-144 (782)
125 PRK09642 RNA polymerase sigma 29.4 83 0.0018 26.4 4.1 28 86-114 121-148 (160)
126 PF09420 Nop16: Ribosome bioge 29.3 1.3E+02 0.0028 26.4 5.4 46 67-112 113-162 (164)
127 PRK12531 RNA polymerase sigma 29.3 81 0.0018 27.7 4.2 29 86-115 156-184 (194)
128 PLN03162 golden-2 like transcr 27.9 3.5E+02 0.0075 27.7 8.6 45 68-112 237-286 (526)
129 PRK15411 rcsA colanic acid cap 27.7 1E+02 0.0023 27.6 4.7 44 70-116 137-180 (207)
130 cd08805 Death_ank1 Death domai 27.6 53 0.0012 26.1 2.4 27 76-103 4-30 (84)
131 smart00501 BRIGHT BRIGHT, ARID 27.6 96 0.0021 24.3 3.9 39 77-115 35-86 (93)
132 PRK15201 fimbriae regulatory p 27.3 1.1E+02 0.0025 28.1 4.7 44 70-116 133-176 (198)
133 PRK12524 RNA polymerase sigma 26.8 93 0.002 27.3 4.1 29 86-115 151-179 (196)
134 PRK09651 RNA polymerase sigma 26.6 81 0.0018 27.1 3.6 31 87-118 135-165 (172)
135 PF09420 Nop16: Ribosome bioge 26.5 48 0.001 29.2 2.2 46 12-59 112-160 (164)
136 TIGR02999 Sig-70_X6 RNA polyme 26.0 1E+02 0.0022 26.3 4.2 29 86-115 149-177 (183)
137 PRK06759 RNA polymerase factor 25.9 1.1E+02 0.0023 25.4 4.2 29 86-115 121-149 (154)
138 TIGR02950 SigM_subfam RNA poly 25.6 38 0.00082 28.1 1.3 28 87-115 121-148 (154)
139 PRK12514 RNA polymerase sigma 24.7 1.1E+02 0.0023 26.3 4.0 28 87-115 145-172 (179)
140 PRK12532 RNA polymerase sigma 24.4 1E+02 0.0022 26.9 3.9 26 86-112 151-176 (195)
141 TIGR02952 Sig70_famx2 RNA poly 24.0 1.2E+02 0.0025 25.5 4.1 28 87-115 138-165 (170)
142 PRK09649 RNA polymerase sigma 23.9 1.1E+02 0.0023 26.8 3.9 30 86-116 145-174 (185)
143 PRK05602 RNA polymerase sigma 23.5 1.1E+02 0.0024 26.5 3.9 28 86-114 143-170 (186)
144 PRK12528 RNA polymerase sigma 23.3 1.3E+02 0.0028 25.3 4.2 30 85-115 127-156 (161)
145 cd08306 Death_FADD Fas-associa 23.3 81 0.0018 24.8 2.7 28 78-106 4-31 (86)
146 TIGR02984 Sig-70_plancto1 RNA 23.2 1.2E+02 0.0026 25.9 4.1 29 86-115 155-183 (189)
147 PRK12542 RNA polymerase sigma 23.1 1.2E+02 0.0026 26.2 4.1 29 86-115 137-165 (185)
148 PRK12536 RNA polymerase sigma 22.8 1.2E+02 0.0027 26.1 4.1 30 85-115 143-172 (181)
149 PRK10100 DNA-binding transcrip 22.8 1.4E+02 0.0031 27.2 4.6 44 70-116 155-198 (216)
150 TIGR02983 SigE-fam_strep RNA p 22.7 1.2E+02 0.0026 25.4 3.9 38 77-115 116-153 (162)
151 PRK12516 RNA polymerase sigma 22.5 1.3E+02 0.0027 26.5 4.1 30 84-114 129-158 (187)
152 cd00569 HTH_Hin_like Helix-tur 22.3 1.7E+02 0.0036 16.7 4.0 36 70-107 5-40 (42)
153 PRK12547 RNA polymerase sigma 22.2 1.4E+02 0.003 25.3 4.2 29 86-115 127-155 (164)
154 COG2963 Transposase and inacti 22.1 1.6E+02 0.0035 23.8 4.4 46 68-115 5-51 (116)
155 PF05263 DUF722: Protein of un 21.6 1.4E+02 0.0031 25.7 4.1 41 75-117 85-127 (130)
156 PRK13919 putative RNA polymera 21.5 1.4E+02 0.003 25.7 4.1 28 87-115 151-178 (186)
157 PRK10360 DNA-binding transcrip 21.2 1.7E+02 0.0038 24.4 4.6 45 69-116 136-180 (196)
158 cd01670 Death Death Domain: a 20.7 74 0.0016 23.6 2.0 26 79-105 2-27 (79)
159 COG5352 Uncharacterized protei 20.7 79 0.0017 28.0 2.3 37 70-107 2-38 (169)
160 PRK12527 RNA polymerase sigma 20.7 1.6E+02 0.0034 24.7 4.2 28 87-115 121-148 (159)
161 PRK12545 RNA polymerase sigma 20.6 1.4E+02 0.0031 26.4 4.1 32 87-119 155-189 (201)
162 PRK00118 putative DNA-binding 20.6 1.6E+02 0.0035 24.4 4.0 39 74-113 20-58 (104)
163 PF11035 SnAPC_2_like: Small n 20.2 1.9E+02 0.0042 28.8 5.1 87 14-114 21-127 (344)
No 1
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=5.4e-38 Score=308.19 Aligned_cols=128 Identities=52% Similarity=1.041 Sum_probs=121.6
Q ss_pred CCCCCCCCCCCCCcCCCCHHHHHHHHHHHHHhCCCCCcccccccccCcccccccccccccccCCCCCCCCCCHHHHHHHH
Q 045583 1 MGRAPCCDKANVKRGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNYLRPDIKHGNFTEDEDHVIC 80 (319)
Q Consensus 1 MGr~~cc~Kp~lkkg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~L~p~lkrg~WT~EED~~Ll 80 (319)
|||++||.|++++|++||+|||++|+++|++||. .+|..||+.++++|+++|||+||.++|+|.+++++||+|||++|+
T Consensus 1 mgr~~Cc~KqklrKg~WTpEEDe~L~~~V~kyG~-~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLL 79 (459)
T PLN03091 1 MGRHSCCYKQKLRKGLWSPEEDEKLLRHITKYGH-GCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLII 79 (459)
T ss_pred CCCCccCcCCCCcCCCCCHHHHHHHHHHHHHhCc-CCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHH
Confidence 9999999999999999999999999999999998 699999999888999999999999999999999999999999999
Q ss_pred HHHhhhCCchhhhcccCCCCCHHHHHHHHHHHhhhHHhcCCCcccccCC
Q 045583 81 TLYSQIGSRWSIIASRLPGRTDNDVKNYWNTKLKKKLLAGKVSLLTSNN 129 (319)
Q Consensus 81 ~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkkkl~~~k~s~~~~~~ 129 (319)
+++++||++|++||+.|||||+++|||||+.++||++.+.++...++..
T Consensus 80 eL~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~I~p~t~kp 128 (459)
T PLN03091 80 ELHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRGIDPNTHKP 128 (459)
T ss_pred HHHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCCCCCCCC
Confidence 9999999999999999999999999999999999999887776654443
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=1.1e-37 Score=287.52 Aligned_cols=123 Identities=55% Similarity=1.137 Sum_probs=117.3
Q ss_pred CCCCCCCCCCCcCCCCHHHHHHHHHHHHHhCCCCCcccccccccCcccccccccccccccCCCCCCCCCCHHHHHHHHHH
Q 045583 3 RAPCCDKANVKRGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNYLRPDIKHGNFTEDEDHVICTL 82 (319)
Q Consensus 3 r~~cc~Kp~lkkg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~L~p~lkrg~WT~EED~~Ll~l 82 (319)
++|||.|++++|++||+|||++|+++|++||. .+|..||++++.+|+++|||+||.++|+|.+++++||+|||++|+++
T Consensus 14 ~~pcc~K~glKRg~WT~EEDe~L~~lV~kyG~-~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel 92 (249)
T PLN03212 14 TTPCCTKMGMKRGPWTVEEDEILVSFIKKEGE-GRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRL 92 (249)
T ss_pred CCCCcccCCCcCCCCCHHHHHHHHHHHHHhCc-ccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHH
Confidence 67999999999999999999999999999997 59999999997799999999999999999999999999999999999
Q ss_pred HhhhCCchhhhcccCCCCCHHHHHHHHHHHhhhHHhcCCCcccc
Q 045583 83 YSQIGSRWSIIASRLPGRTDNDVKNYWNTKLKKKLLAGKVSLLT 126 (319)
Q Consensus 83 v~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkkkl~~~k~s~~~ 126 (319)
+.+||++|+.||+.|||||+++|||||+.++++++.+.+....+
T Consensus 93 ~~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~p~~ 136 (249)
T PLN03212 93 HRLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGIDPQT 136 (249)
T ss_pred HHhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCCCCC
Confidence 99999999999999999999999999999999999987766544
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=6.4e-36 Score=276.99 Aligned_cols=112 Identities=58% Similarity=1.060 Sum_probs=107.2
Q ss_pred CCCCCcCCCCHHHHHHHHHHHHHhCCCCCcccccccccCcccccccccccccccCCCCCCCCCCHHHHHHHHHHHhhhCC
Q 045583 9 KANVKRGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNYLRPDIKHGNFTEDEDHVICTLYSQIGS 88 (319)
Q Consensus 9 Kp~lkkg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~L~p~lkrg~WT~EED~~Ll~lv~~~G~ 88 (319)
|+.+.||+||+|||++|+++|++||. ++|..||+.+|++|++++||+||.|||+|++++|.||+|||++|++++..+|+
T Consensus 4 k~~~~kGpWt~EED~~L~~~V~~~G~-~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GN 82 (238)
T KOG0048|consen 4 NPELVKGPWTQEEDLTQIRSIKSFGK-HNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGN 82 (238)
T ss_pred CccccCCCCChHHHHHHHHHHHHhCC-CCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCc
Confidence 44456899999999999999999999 69999999999999999999999999999999999999999999999999999
Q ss_pred chhhhcccCCCCCHHHHHHHHHHHhhhHHhcCC
Q 045583 89 RWSIIASRLPGRTDNDVKNYWNTKLKKKLLAGK 121 (319)
Q Consensus 89 kWs~IA~~lpgRT~~qcKnRW~~~lkkkl~~~k 121 (319)
+|+.||++|||||+++|||+|++.+||++....
T Consensus 83 rWs~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 83 RWSLIAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred HHHHHHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 999999999999999999999999999998765
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.73 E-value=3.4e-18 Score=174.03 Aligned_cols=120 Identities=23% Similarity=0.471 Sum_probs=111.8
Q ss_pred CCCCCCcCCCCHHHHHHHHHHHHHhCCCCCcccccccccCccccccccc-------------------------------
Q 045583 8 DKANVKRGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRL------------------------------- 56 (319)
Q Consensus 8 ~Kp~lkkg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~------------------------------- 56 (319)
..|.++|-.|++|||++|+++...+|. .+|..||..+|.+|+..||..
T Consensus 247 l~P~~nk~~WS~EE~E~L~AiA~A~~~-~~W~~IA~~Lgt~RS~yQC~~kF~t~~~~L~ekeWsEEed~kL~alV~~~~~ 325 (939)
T KOG0049|consen 247 LNPKWNKEHWSNEEVEKLKALAEAPKF-VSWPMIALNLGTNRSSYQCMEKFKTEVSQLSEKEWSEEEDTKLIALVKITSI 325 (939)
T ss_pred cCCccchhccChHHHHHHHHHHhcccc-ccHHHHHHHhCCCcchHHHHHHHHHHHHHHHhhhcchhhhHHHHHHHHHhhc
Confidence 468899999999999999999999998 699999999998899999865
Q ss_pred -----------------------ccccccCCCCCCCCCCHHHHHHHHHHHhhhCC-chhhhcccCCCCCHHHHHHHHHHH
Q 045583 57 -----------------------RWLNYLRPDIKHGNFTEDEDHVICTLYSQIGS-RWSIIASRLPGRTDNDVKNYWNTK 112 (319)
Q Consensus 57 -----------------------Rw~n~L~p~lkrg~WT~EED~~Ll~lv~~~G~-kWs~IA~~lpgRT~~qcKnRW~~~ 112 (319)
||...|+|++++|+||.+||.+|+.+|.+||. .|.+|...+|||++.|||.||.+.
T Consensus 326 nShI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nv 405 (939)
T KOG0049|consen 326 NSHIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNV 405 (939)
T ss_pred cCccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHH
Confidence 99999999999999999999999999999997 599999999999999999999999
Q ss_pred hhhHHhcCCCcccccC
Q 045583 113 LKKKLLAGKVSLLTSN 128 (319)
Q Consensus 113 lkkkl~~~k~s~~~~~ 128 (319)
|....+.+.|++....
T Consensus 406 L~~s~K~~rW~l~ede 421 (939)
T KOG0049|consen 406 LNRSAKVERWTLVEDE 421 (939)
T ss_pred HHHhhccCceeecchH
Confidence 9999999999987543
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.69 E-value=1.5e-17 Score=169.46 Aligned_cols=117 Identities=27% Similarity=0.387 Sum_probs=103.3
Q ss_pred CCCCCCCCCCCCCcCCCCHHHHHHHHHHHHHhCCCCCcccccccccCcccccccccccccccCCCCCCCCCCHHHHHHHH
Q 045583 1 MGRAPCCDKANVKRGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNYLRPDIKHGNFTEDEDHVIC 80 (319)
Q Consensus 1 MGr~~cc~Kp~lkkg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~L~p~lkrg~WT~EED~~Ll 80 (319)
+||......|++++|+||++||.+|+.+|.+||. .+|-+|-..++ +|+..|||+||.|.|....|.+.||-.||+.|+
T Consensus 347 I~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~-kdw~k~R~~vP-nRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~ 424 (939)
T KOG0049|consen 347 ITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGA-KDWAKVRQAVP-NRSDSQCRERYTNVLNRSAKVERWTLVEDEQLL 424 (939)
T ss_pred hhhheeccCccccCCCCCCHHHHHHHHHHHHhCc-cchhhHHHhcC-CccHHHHHHHHHHHHHHhhccCceeecchHHHH
Confidence 4777888899999999999999999999999998 59999988888 999999999999999999999999999999999
Q ss_pred HHHhhhCC-chhhhcccCCCCCH---HHHHHHHHHHhhhHHhcC
Q 045583 81 TLYSQIGS-RWSIIASRLPGRTD---NDVKNYWNTKLKKKLLAG 120 (319)
Q Consensus 81 ~lv~~~G~-kWs~IA~~lpgRT~---~qcKnRW~~~lkkkl~~~ 120 (319)
.+|++||. .|.+||..||.||. ..||.|+. ..++++..+
T Consensus 425 ~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~-~~k~rl~~~ 467 (939)
T KOG0049|consen 425 YAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLI-AAKLRLAAG 467 (939)
T ss_pred HHHHHHccchHHHHHHHccccchhHHHHHHHHHH-HHHHHHhcC
Confidence 99999997 89999999999999 44555552 234444443
No 6
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.61 E-value=2.7e-16 Score=115.75 Aligned_cols=60 Identities=40% Similarity=0.823 Sum_probs=55.2
Q ss_pred CCHHHHHHHHHHHHHhCCCCCcccccccccCcccccccccccccccCCCCCCCCCCHHHHHHH
Q 045583 17 WSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNYLRPDIKHGNFTEDEDHVI 79 (319)
Q Consensus 17 WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~L~p~lkrg~WT~EED~~L 79 (319)
||+|||++|+++|.+||. +|..||+.++ .|++.||+.||.++|++.+++++||.+||.+|
T Consensus 1 WT~eEd~~L~~~~~~~g~--~W~~Ia~~l~-~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN--DWKKIAEHLG-NRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS---HHHHHHHST-TS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc--CHHHHHHHHC-cCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 999999999999999996 8999999997 89999999999999999999999999999987
No 7
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.54 E-value=4.9e-15 Score=150.14 Aligned_cols=108 Identities=30% Similarity=0.510 Sum_probs=101.4
Q ss_pred CCCCCcCCCCHHHHHHHHHHHHHhCCCCCcccccccccCcccccccccccccccCCCCCCCCCCHHHHHHHHHHHhhhCC
Q 045583 9 KANVKRGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNYLRPDIKHGNFTEDEDHVICTLYSQIGS 88 (319)
Q Consensus 9 Kp~lkkg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~L~p~lkrg~WT~EED~~Ll~lv~~~G~ 88 (319)
...++.|.|+..||+.|..+|+++|. .+|..||..+. .|+++||+.||.++++|.+++..|+.|||+.|+.+..++|.
T Consensus 15 ~~~~k~gsw~~~EDe~l~~~vk~l~~-nnws~vas~~~-~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~ 92 (512)
T COG5147 15 QTKRKGGSWKRTEDEDLKALVKKLGP-NNWSKVASLLI-SSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGT 92 (512)
T ss_pred cceecCCCCCCcchhHHHHHHhhccc-ccHHHHHHHhc-ccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCc
Confidence 35678899999999999999999999 58999999998 68999999999999999999999999999999999999999
Q ss_pred chhhhcccCCCCCHHHHHHHHHHHhhhHHh
Q 045583 89 RWSIIASRLPGRTDNDVKNYWNTKLKKKLL 118 (319)
Q Consensus 89 kWs~IA~~lpgRT~~qcKnRW~~~lkkkl~ 118 (319)
+|+.||..+++||+.+|.+||...+.....
T Consensus 93 ~wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 93 QWSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 999999999999999999999988776544
No 8
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.49 E-value=6e-15 Score=147.64 Aligned_cols=109 Identities=26% Similarity=0.504 Sum_probs=101.3
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCCCcccccccccCcccccccccccccccCCCCCCCCCCHHHHHHHHHHHhhhCCch
Q 045583 11 NVKRGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNYLRPDIKHGNFTEDEDHVICTLYSQIGSRW 90 (319)
Q Consensus 11 ~lkkg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~L~p~lkrg~WT~EED~~Ll~lv~~~G~kW 90 (319)
-++.|-|+.-||+.|..+|.+||. ..|+.|++.+. ..+++||+.||..+|+|.|++..|+.|||++|+.+++.+...|
T Consensus 4 ~~kggvwrntEdeilkaav~kyg~-nqws~i~sll~-~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qw 81 (617)
T KOG0050|consen 4 EIKGGVWRNTEDEVLKAAVMKYGK-NQWSRIASLLN-RKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQW 81 (617)
T ss_pred EEecceecccHHHHHHHHHHHcch-HHHHHHHHHHh-hcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCcc
Confidence 357889999999999999999999 58999999987 7799999999999999999999999999999999999999999
Q ss_pred hhhcccCCCCCHHHHHHHHHHHhhhHHhcCCC
Q 045583 91 SIIASRLPGRTDNDVKNYWNTKLKKKLLAGKV 122 (319)
Q Consensus 91 s~IA~~lpgRT~~qcKnRW~~~lkkkl~~~k~ 122 (319)
..||..| |||.+||-.||+.++-..+....-
T Consensus 82 rtIa~i~-gr~~~qc~eRy~~ll~~~~s~~~~ 112 (617)
T KOG0050|consen 82 RTIADIM-GRTSQQCLERYNNLLDVYVSYHYH 112 (617)
T ss_pred chHHHHh-hhhHHHHHHHHHHHHHHHHhhhcc
Confidence 9999999 999999999999998877665443
No 9
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.45 E-value=5.8e-14 Score=143.87 Aligned_cols=104 Identities=26% Similarity=0.582 Sum_probs=94.5
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCCcccccccccCcccccccccccccccCCCC--CCCCCCHHHHHHHHHHHh------
Q 045583 13 KRGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNYLRPDI--KHGNFTEDEDHVICTLYS------ 84 (319)
Q Consensus 13 kkg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~L~p~l--krg~WT~EED~~Ll~lv~------ 84 (319)
.||.||+||++.|..+|.++|. .|..|++.+| |.+..||+||+++...+- +++.||.||++.|+++|.
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~--~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~ 458 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGN--DWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREA 458 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcc--cHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHh
Confidence 8999999999999999999997 8999999987 999999999999999874 899999999999999995
Q ss_pred -hh-------------------CCchhhhcccCCCCCHHHHHHHHHHHhhhHHhcC
Q 045583 85 -QI-------------------GSRWSIIASRLPGRTDNDVKNYWNTKLKKKLLAG 120 (319)
Q Consensus 85 -~~-------------------G~kWs~IA~~lpgRT~~qcKnRW~~~lkkkl~~~ 120 (319)
++ +..|+.|++.+.+|+..|||.+|..++......+
T Consensus 459 ~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n~ 514 (607)
T KOG0051|consen 459 LQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFNK 514 (607)
T ss_pred hcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhhc
Confidence 23 2369999999999999999999999988776543
No 10
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.34 E-value=8.4e-13 Score=93.51 Aligned_cols=46 Identities=33% Similarity=0.652 Sum_probs=41.7
Q ss_pred CCCCCHHHHHHHHHHHhhhCCc-hhhhcccCC-CCCHHHHHHHHHHHh
Q 045583 68 HGNFTEDEDHVICTLYSQIGSR-WSIIASRLP-GRTDNDVKNYWNTKL 113 (319)
Q Consensus 68 rg~WT~EED~~Ll~lv~~~G~k-Ws~IA~~lp-gRT~~qcKnRW~~~l 113 (319)
+++||+|||++|++++.+||.+ |..||..|+ +||..||++||+.++
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 5799999999999999999998 999999999 999999999998764
No 11
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.30 E-value=3.4e-13 Score=95.55 Aligned_cols=48 Identities=40% Similarity=0.748 Sum_probs=42.9
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCcccccccccCccccccccccccccc
Q 045583 14 RGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNYL 62 (319)
Q Consensus 14 kg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~L 62 (319)
|++||+|||++|+++|.+||. ++|..||..++.+||+.||+.||.++|
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~-~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGK-DNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTT-THHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCC-cHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 689999999999999999998 359999999988999999999999875
No 12
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.30 E-value=2.2e-12 Score=94.89 Aligned_cols=54 Identities=30% Similarity=0.591 Sum_probs=46.8
Q ss_pred CCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHHhhhHHhcCCCcc
Q 045583 71 FTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTKLKKKLLAGKVSL 124 (319)
Q Consensus 71 WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkkkl~~~k~s~ 124 (319)
||+|||++|++++.+||.+|..||++|+.||..+|++||...|++.+.+++|+.
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~ 54 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTK 54 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCH
Confidence 999999999999999999999999999669999999999998887777777764
No 13
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.24 E-value=6.7e-12 Score=116.82 Aligned_cols=66 Identities=20% Similarity=0.429 Sum_probs=60.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhhCC-chhhhcccC-CCCCHHHHHHHHHHHhhhHHhcCCCcccccC
Q 045583 63 RPDIKHGNFTEDEDHVICTLYSQIGS-RWSIIASRL-PGRTDNDVKNYWNTKLKKKLLAGKVSLLTSN 128 (319)
Q Consensus 63 ~p~lkrg~WT~EED~~Ll~lv~~~G~-kWs~IA~~l-pgRT~~qcKnRW~~~lkkkl~~~k~s~~~~~ 128 (319)
++.+++++||+|||++|+++|++||. +|..||+++ ++||..|||.||..+|+..+.++.|+.....
T Consensus 20 K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~ 87 (249)
T PLN03212 20 KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEED 87 (249)
T ss_pred cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHH
Confidence 36889999999999999999999995 899999998 6999999999999999999999999876544
No 14
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.17 E-value=3.8e-11 Score=82.43 Aligned_cols=47 Identities=40% Similarity=0.820 Sum_probs=44.0
Q ss_pred CCCCCHHHHHHHHHHHhhhC-CchhhhcccCCCCCHHHHHHHHHHHhh
Q 045583 68 HGNFTEDEDHVICTLYSQIG-SRWSIIASRLPGRTDNDVKNYWNTKLK 114 (319)
Q Consensus 68 rg~WT~EED~~Ll~lv~~~G-~kWs~IA~~lpgRT~~qcKnRW~~~lk 114 (319)
+++||++||.+|+.++.++| .+|..||..|++||..+|++||..+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 46899999999999999999 899999999999999999999987664
No 15
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.09 E-value=6.6e-11 Score=110.04 Aligned_cols=64 Identities=19% Similarity=0.306 Sum_probs=58.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhhCC-chhhhcccCC-CCCHHHHHHHHHHHhhhHHhcCCCcccc
Q 045583 63 RPDIKHGNFTEDEDHVICTLYSQIGS-RWSIIASRLP-GRTDNDVKNYWNTKLKKKLLAGKVSLLT 126 (319)
Q Consensus 63 ~p~lkrg~WT~EED~~Ll~lv~~~G~-kWs~IA~~lp-gRT~~qcKnRW~~~lkkkl~~~k~s~~~ 126 (319)
++.+.+|+||.|||++|+++|++||. +|..||+.++ +|+..+||-||.++|+..+++|.|+...
T Consensus 4 k~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eE 69 (238)
T KOG0048|consen 4 NPELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEE 69 (238)
T ss_pred CccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHH
Confidence 34566899999999999999999998 6999999998 9999999999999999999999988754
No 16
>PLN03091 hypothetical protein; Provisional
Probab=99.06 E-value=1.2e-10 Score=115.94 Aligned_cols=65 Identities=18% Similarity=0.382 Sum_probs=59.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhhCC-chhhhcccC-CCCCHHHHHHHHHHHhhhHHhcCCCccccc
Q 045583 63 RPDIKHGNFTEDEDHVICTLYSQIGS-RWSIIASRL-PGRTDNDVKNYWNTKLKKKLLAGKVSLLTS 127 (319)
Q Consensus 63 ~p~lkrg~WT~EED~~Ll~lv~~~G~-kWs~IA~~l-pgRT~~qcKnRW~~~lkkkl~~~k~s~~~~ 127 (319)
+..+++++||+|||++|+++|.+||. +|..||+.+ ++||..|||.||..+|+..++++.|+....
T Consensus 9 KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED 75 (459)
T PLN03091 9 KQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEE 75 (459)
T ss_pred CCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHH
Confidence 35789999999999999999999996 799999988 599999999999999999999999886543
No 17
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.04 E-value=3.3e-10 Score=76.70 Aligned_cols=43 Identities=33% Similarity=0.697 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHHHhhhC-CchhhhcccCCCCCHHHHHHHHHHH
Q 045583 70 NFTEDEDHVICTLYSQIG-SRWSIIASRLPGRTDNDVKNYWNTK 112 (319)
Q Consensus 70 ~WT~EED~~Ll~lv~~~G-~kWs~IA~~lpgRT~~qcKnRW~~~ 112 (319)
+||+||+.+|+.++.++| .+|..||+.+++||..+|++||..+
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 599999999999999999 8999999999999999999999765
No 18
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.92 E-value=4.1e-10 Score=77.22 Aligned_cols=48 Identities=35% Similarity=0.758 Sum_probs=44.1
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCcccccccccCcccccccccccccccC
Q 045583 14 RGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNYLR 63 (319)
Q Consensus 14 kg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~L~ 63 (319)
++.||+|||++|+.++.+||. .+|..||..++ +|++.+|+.||.++++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~-~~w~~Ia~~~~-~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGK-NNWEKIAKELP-GRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCc-CCHHHHHHHcC-CCCHHHHHHHHHHHcC
Confidence 478999999999999999995 38999999998 9999999999998764
No 19
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.78 E-value=2.3e-09 Score=72.47 Aligned_cols=45 Identities=40% Similarity=0.769 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCcccccccccCccccccccccccccc
Q 045583 16 PWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNYL 62 (319)
Q Consensus 16 ~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~L 62 (319)
+||+|||++|+.++.+||. .+|..||+.++ +|++.+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~-~~w~~Ia~~~~-~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGK-NNWEKIAKELP-GRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCc-CCHHHHHhHcC-CCCHHHHHHHHHHhC
Confidence 5999999999999999995 48999999998 899999999998753
No 20
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.73 E-value=9.8e-09 Score=105.90 Aligned_cols=113 Identities=26% Similarity=0.330 Sum_probs=90.2
Q ss_pred CcCCCCHHHHHHHHHHHHHh----CCC------------------CCcccccccccCccccccccc---ccccccCCCCC
Q 045583 13 KRGPWSPEEDATLKRYVETH----GTG------------------GNWIALPQKAGLKRCGKSCRL---RWLNYLRPDIK 67 (319)
Q Consensus 13 kkg~WT~EEDe~L~~lV~k~----G~~------------------~~W~~IA~~lg~~Rt~kQCr~---Rw~n~L~p~lk 67 (319)
+-+.|++|||+.|.+.|..| |.. +-|..|-..++ -|+.+.+.. |-.+.|.+ +
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 34899999999999999877 221 12566666776 488888766 33344443 9
Q ss_pred CCCCCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHHhhhH--HhcCCCcccccCC
Q 045583 68 HGNFTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTKLKKK--LLAGKVSLLTSNN 129 (319)
Q Consensus 68 rg~WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkkk--l~~~k~s~~~~~~ 129 (319)
+|.||+||++.|..+|.++|+.|..|++.| ||.+..|+.||+.+++-. ..++.|+......
T Consensus 384 rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~ 446 (607)
T KOG0051|consen 384 RGKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEK 446 (607)
T ss_pred cCCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHH
Confidence 999999999999999999999999999999 999999999999988765 4778888755443
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=98.34 E-value=4e-08 Score=100.31 Aligned_cols=97 Identities=24% Similarity=0.618 Sum_probs=85.0
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCCcccccccccCcccccccccccccccCC--CCCCCCCCHHHHHHHHHHHhhhC---
Q 045583 13 KRGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNYLRP--DIKHGNFTEDEDHVICTLYSQIG--- 87 (319)
Q Consensus 13 kkg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~L~p--~lkrg~WT~EED~~Ll~lv~~~G--- 87 (319)
.+|.||+||++.|...+.++|. .|..|.+.++ |-+..||+||.+|... .+++++|+.||+.+|...+.+.-
T Consensus 290 ~~~~wt~e~~~eL~~~~~~~~~--~w~~ig~~~~--rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e~~~~~ 365 (512)
T COG5147 290 QRGKWTKEEEQELAKLVVEHGG--SWTEIGKLLG--RMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNEMRLEA 365 (512)
T ss_pred hhccCccccccccccccccccc--hhhHhhhhhc--cCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHHHHHHH
Confidence 4789999999999999999997 8999988765 9999999999999998 68889999999999999887432
Q ss_pred -----CchhhhcccCCCCCHHHHHHHHHHHh
Q 045583 88 -----SRWSIIASRLPGRTDNDVKNYWNTKL 113 (319)
Q Consensus 88 -----~kWs~IA~~lpgRT~~qcKnRW~~~l 113 (319)
..|..|+..+++|....|+.++....
T Consensus 366 ~~~~~~~~~li~~~~~~~~~~~~~~~~~~~~ 396 (512)
T COG5147 366 QQSSRILWLLIAQNIRNRLQHHCRDKYGVLI 396 (512)
T ss_pred hhhhhhhHHHHHHhhhccccCCCCCcccccc
Confidence 36999999999999988888775443
No 22
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.60 E-value=3.2e-05 Score=57.35 Aligned_cols=49 Identities=12% Similarity=0.224 Sum_probs=43.1
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCCc---ccccccccCcc-ccccccccccccc
Q 045583 13 KRGPWSPEEDATLKRYVETHGTGGNW---IALPQKAGLKR-CGKSCRLRWLNYL 62 (319)
Q Consensus 13 kkg~WT~EEDe~L~~lV~k~G~~~~W---~~IA~~lg~~R-t~kQCr~Rw~n~L 62 (319)
++-.||+||.++++++|+.+|. ++| ..|++.++..| |..||+.+...|.
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~-g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGG-PDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCC-CcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 4678999999999999999997 699 99999887667 9999999887764
No 23
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.54 E-value=0.00016 Score=53.63 Aligned_cols=47 Identities=17% Similarity=0.196 Sum_probs=40.9
Q ss_pred CCCCCHHHHHHHHHHHhhhCC-ch---hhhcccCC-CC-CHHHHHHHHHHHhh
Q 045583 68 HGNFTEDEDHVICTLYSQIGS-RW---SIIASRLP-GR-TDNDVKNYWNTKLK 114 (319)
Q Consensus 68 rg~WT~EED~~Ll~lv~~~G~-kW---s~IA~~lp-gR-T~~qcKnRW~~~lk 114 (319)
+-.||+||..+++++++.+|. +| ..|++.+. .| |..||+.|...+.-
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 557999999999999999998 99 99999873 45 99999999876643
No 24
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.39 E-value=0.00047 Score=63.13 Aligned_cols=101 Identities=23% Similarity=0.403 Sum_probs=73.0
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCcccccccccC--cccccccccccccccC-CCC--------------------CCCCCC
Q 045583 16 PWSPEEDATLKRYVETHGTGGNWIALPQKAGL--KRCGKSCRLRWLNYLR-PDI--------------------KHGNFT 72 (319)
Q Consensus 16 ~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~--~Rt~kQCr~Rw~n~L~-p~l--------------------krg~WT 72 (319)
+|++++|-+|+.+|..-. +-..|+.-+.. .-|-..+.+||...|. |.+ .+.+||
T Consensus 1 rW~~~DDl~Li~av~~~~---~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~~is~~a~~~m~~l~p~~~~~iq~kalfS 77 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTN---DLESVHLGVKFSCKFTLQEIEERWYALLYDPVISRIAVAAMRNLHPELIAAIQSKALFS 77 (199)
T ss_pred CCCchhhHHHHHHHHHhc---CHHHHHccCCcCCcCcHHHHHHHHHHHHcChhhHHHHHHHHHhCCcchhhcccccCCCC
Confidence 699999999999998654 46666554432 3366777889988764 322 355899
Q ss_pred HHHHHHHHHHHhhhCC---chhhhcc----cC-CCCCHHHHHHHHHHHhhhHHhc
Q 045583 73 EDEDHVICTLYSQIGS---RWSIIAS----RL-PGRTDNDVKNYWNTKLKKKLLA 119 (319)
Q Consensus 73 ~EED~~Ll~lv~~~G~---kWs~IA~----~l-pgRT~~qcKnRW~~~lkkkl~~ 119 (319)
.+|+++|......... .+.+|=. .| ++||+.++.++|..+.+..+..
T Consensus 78 ~~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~LL~ 132 (199)
T PF13325_consen 78 KEEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHLLP 132 (199)
T ss_pred HHHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhchhh
Confidence 9999999998765433 4666622 23 7899999999998766666554
No 25
>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=97.35 E-value=0.00017 Score=63.77 Aligned_cols=52 Identities=21% Similarity=0.378 Sum_probs=45.2
Q ss_pred CCCCCCHHHHHHHHHHHhhh---CC----chhhhcccCCCCCHHHHHHHHHHHhhhHHhc
Q 045583 67 KHGNFTEDEDHVICTLYSQI---GS----RWSIIASRLPGRTDNDVKNYWNTKLKKKLLA 119 (319)
Q Consensus 67 krg~WT~EED~~Ll~lv~~~---G~----kWs~IA~~lpgRT~~qcKnRW~~~lkkkl~~ 119 (319)
+...||.|||.+|.+.|.+| |. -...++..| +||+..|.-|||+.+|++...
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~ 61 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEE 61 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHH
Confidence 45789999999999999887 33 278899999 999999999999999987654
No 26
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.21 E-value=0.00013 Score=73.13 Aligned_cols=51 Identities=24% Similarity=0.548 Sum_probs=46.5
Q ss_pred CCCCcCCCCHHHHHHHHHHHHHhCCCCCcccccccccCccccccccccccccc
Q 045583 10 ANVKRGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNYL 62 (319)
Q Consensus 10 p~lkkg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~L 62 (319)
..+-...||.+|+-+|+++++.||- |||..||..+| .|+..+|+++|.+++
T Consensus 68 ~~i~~~~WtadEEilLLea~~t~G~-GNW~dIA~hIG-tKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 68 FPILDPSWTADEEILLLEAAETYGF-GNWQDIADHIG-TKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCCCChHHHHHHHHHHHHhCC-CcHHHHHHHHc-ccchHHHHHHHHHHH
Confidence 3455778999999999999999999 79999999999 999999999998864
No 27
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.09 E-value=0.00033 Score=71.57 Aligned_cols=64 Identities=28% Similarity=0.398 Sum_probs=56.6
Q ss_pred CCCCCCCCHHHHHHHHHHHhhhCC-chhhhcccCCCCCHHHHHHHHHHHhhhHHhcCCCcccccC
Q 045583 65 DIKHGNFTEDEDHVICTLYSQIGS-RWSIIASRLPGRTDNDVKNYWNTKLKKKLLAGKVSLLTSN 128 (319)
Q Consensus 65 ~lkrg~WT~EED~~Ll~lv~~~G~-kWs~IA~~lpgRT~~qcKnRW~~~lkkkl~~~k~s~~~~~ 128 (319)
.++.|-|+.-||+.|..+|.+||. .|++|+..++-.|+.||++||...+...+++-.|+.....
T Consensus 4 ~~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~eede 68 (617)
T KOG0050|consen 4 EIKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREEDE 68 (617)
T ss_pred EEecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhHHH
Confidence 356788999999999999999997 7999999999999999999999999998888777765433
No 28
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.95 E-value=0.0011 Score=66.51 Aligned_cols=49 Identities=20% Similarity=0.356 Sum_probs=44.4
Q ss_pred CCCCCCCCHHHHHHHHHHHhhhCC-chhhhcccCCCCCHHHHHHHHHHHh
Q 045583 65 DIKHGNFTEDEDHVICTLYSQIGS-RWSIIASRLPGRTDNDVKNYWNTKL 113 (319)
Q Consensus 65 ~lkrg~WT~EED~~Ll~lv~~~G~-kWs~IA~~lpgRT~~qcKnRW~~~l 113 (319)
.+-...||.+|+-+|++++..||- +|..||.++..||..+||.+|.+++
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHH
Confidence 455678999999999999999995 9999999999999999999997665
No 29
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.91 E-value=0.00059 Score=53.22 Aligned_cols=49 Identities=29% Similarity=0.546 Sum_probs=34.5
Q ss_pred CCCCCHHHHHHHHHHHhh------hC--C------chhhhcccC----CCCCHHHHHHHHHHHhhhH
Q 045583 68 HGNFTEDEDHVICTLYSQ------IG--S------RWSIIASRL----PGRTDNDVKNYWNTKLKKK 116 (319)
Q Consensus 68 rg~WT~EED~~Ll~lv~~------~G--~------kWs~IA~~l----pgRT~~qcKnRW~~~lkkk 116 (319)
|..||.+|...||+++.+ ++ . -|..||..| ..||..||+++|.++.++-
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Y 67 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKY 67 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence 357999999999999876 22 1 399999987 3699999999998766554
No 30
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=96.77 E-value=0.0004 Score=61.46 Aligned_cols=51 Identities=27% Similarity=0.566 Sum_probs=42.8
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCC-----CcccccccccCcccccccccccccccCC
Q 045583 12 VKRGPWSPEEDATLKRYVETHGTGG-----NWIALPQKAGLKRCGKSCRLRWLNYLRP 64 (319)
Q Consensus 12 lkkg~WT~EEDe~L~~lV~k~G~~~-----~W~~IA~~lg~~Rt~kQCr~Rw~n~L~p 64 (319)
.+.-.||.|||.+|.+.|.+|-..| .+..|+..++ ||+..|..||+.+++.
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 4677899999999999999994433 3778888875 9999999999999874
No 31
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.63 E-value=0.00066 Score=68.66 Aligned_cols=46 Identities=24% Similarity=0.517 Sum_probs=43.0
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCCcccccccccCcccccccccccccc
Q 045583 13 KRGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNY 61 (319)
Q Consensus 13 kkg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~ 61 (319)
....||.+|-.+|++.|+.||. +|.+||+++| +|+..||-.|+.+.
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 5669999999999999999997 8999999999 99999999999864
No 32
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.63 E-value=0.0022 Score=66.07 Aligned_cols=47 Identities=15% Similarity=0.257 Sum_probs=43.1
Q ss_pred CCCCCCCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHH
Q 045583 66 IKHGNFTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTK 112 (319)
Q Consensus 66 lkrg~WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~ 112 (319)
..+..||++|..+|++++..||..|.+||.++.+||..||--|+..+
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhc
Confidence 34678999999999999999999999999999999999999998553
No 33
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.62 E-value=0.0018 Score=65.66 Aligned_cols=45 Identities=13% Similarity=0.200 Sum_probs=42.0
Q ss_pred CCCCCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHH
Q 045583 68 HGNFTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTK 112 (319)
Q Consensus 68 rg~WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~ 112 (319)
...||.+|..+|++.+..||..|.+||.|+.+||..||--||-.+
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 348999999999999999999999999999999999999999654
No 34
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.43 E-value=0.0024 Score=57.16 Aligned_cols=51 Identities=16% Similarity=0.326 Sum_probs=42.5
Q ss_pred CCCCCCHHHHHHHHHHHhhhCCc-------hhhhcccCCCCCHHHHHHHHHHHhhhHHh
Q 045583 67 KHGNFTEDEDHVICTLYSQIGSR-------WSIIASRLPGRTDNDVKNYWNTKLKKKLL 118 (319)
Q Consensus 67 krg~WT~EED~~Ll~lv~~~G~k-------Ws~IA~~lpgRT~~qcKnRW~~~lkkkl~ 118 (319)
+...||.|||.+|.+.|..|+.. ...++..| +||..+|..|||.+++++..
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Ye 61 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQ 61 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHH
Confidence 46789999999999998888642 56667778 99999999999999987643
No 35
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=96.43 E-value=0.0037 Score=47.58 Aligned_cols=50 Identities=18% Similarity=0.401 Sum_probs=32.8
Q ss_pred CCCCCHHHHHHHHHHHhhh--------CCc-hhhhcccCC-CCCHHHHHHHHHHHhhhHH
Q 045583 68 HGNFTEDEDHVICTLYSQI--------GSR-WSIIASRLP-GRTDNDVKNYWNTKLKKKL 117 (319)
Q Consensus 68 rg~WT~EED~~Ll~lv~~~--------G~k-Ws~IA~~lp-gRT~~qcKnRW~~~lkkkl 117 (319)
+.+||.|||.+|++.|+++ |++ |..+++.-+ .+|-...|+||...|+.+.
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 4589999999999999654 232 999998877 9999999999988887654
No 36
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.40 E-value=0.0014 Score=67.42 Aligned_cols=48 Identities=23% Similarity=0.562 Sum_probs=44.1
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCCCcccccccccCcccccccccccccc
Q 045583 11 NVKRGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNY 61 (319)
Q Consensus 11 ~lkkg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~ 61 (319)
.-.++.||.+|+-+|+++|++||. +|.+||..+| +|+..||-.++.+.
T Consensus 250 ~~~~~~WT~qE~lLLLE~ie~y~d--dW~kVa~hVg-~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 250 ESARPNWTEQETLLLLEAIEMYGD--DWNKVADHVG-TKSQEQCILKFLRL 297 (506)
T ss_pred ccCCCCccHHHHHHHHHHHHHhcc--cHHHHHhccC-CCCHHHHHHHHHhc
Confidence 345789999999999999999997 8999999999 99999999998764
No 37
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=96.21 E-value=0.002 Score=49.01 Aligned_cols=52 Identities=35% Similarity=0.538 Sum_probs=33.3
Q ss_pred cCCCCHHHHHHHHHHHHHhCCC-----C--CcccccccccCcccccccccccccccCCC
Q 045583 14 RGPWSPEEDATLKRYVETHGTG-----G--NWIALPQKAGLKRCGKSCRLRWLNYLRPD 65 (319)
Q Consensus 14 kg~WT~EEDe~L~~lV~k~G~~-----~--~W~~IA~~lg~~Rt~kQCr~Rw~n~L~p~ 65 (319)
|.+||.|||+.|+.+|..+... | -|.++++.....++..+-|+||.+.|.+.
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 5689999999999999766321 2 39999887766789999999999988764
No 38
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.40 E-value=0.0033 Score=56.26 Aligned_cols=51 Identities=25% Similarity=0.545 Sum_probs=40.3
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCCC-----cccccccccCcccccccccccccccC
Q 045583 11 NVKRGPWSPEEDATLKRYVETHGTGGN-----WIALPQKAGLKRCGKSCRLRWLNYLR 63 (319)
Q Consensus 11 ~lkkg~WT~EEDe~L~~lV~k~G~~~~-----W~~IA~~lg~~Rt~kQCr~Rw~n~L~ 63 (319)
..++..||.|||.+|.+.|.+|+..+. ...++..+ +|+..+|..||+-+++
T Consensus 2 k~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L--~rt~aac~fRwNs~vr 57 (170)
T PRK13923 2 KTRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL--KRTAAACGFRWNSVVR 57 (170)
T ss_pred cchhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH--hhhHHHHHhHHHHHHH
Confidence 356788999999999999999976432 44555555 5999999999977765
No 39
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.25 E-value=0.026 Score=43.22 Aligned_cols=48 Identities=27% Similarity=0.495 Sum_probs=39.0
Q ss_pred CCCCCHHHHHHHHHHHhhh-----C------------CchhhhcccC-----CCCCHHHHHHHHHHHhhh
Q 045583 68 HGNFTEDEDHVICTLYSQI-----G------------SRWSIIASRL-----PGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 68 rg~WT~EED~~Ll~lv~~~-----G------------~kWs~IA~~l-----pgRT~~qcKnRW~~~lkk 115 (319)
...||.+|.+.|++++.++ | .-|..|+..| +.||..++|.+|..+...
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~ 71 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSK 71 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Confidence 4579999999999999876 2 1299999886 369999999999776543
No 40
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=95.08 E-value=0.0031 Score=49.09 Aligned_cols=49 Identities=24% Similarity=0.533 Sum_probs=32.8
Q ss_pred cCCCCHHHHHHHHHHHHH--h----C---C-CC--Ccccccccc---cCccccccccccccccc
Q 045583 14 RGPWSPEEDATLKRYVET--H----G---T-GG--NWIALPQKA---GLKRCGKSCRLRWLNYL 62 (319)
Q Consensus 14 kg~WT~EEDe~L~~lV~k--~----G---~-~~--~W~~IA~~l---g~~Rt~kQCr~Rw~n~L 62 (319)
|..||.+|...|++++.. + + . .. -|..||..| |..|++.||+.||.+..
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~ 64 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLK 64 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 457999999999999987 1 1 1 01 499999765 56899999999998854
No 41
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=94.60 E-value=0.069 Score=59.65 Aligned_cols=99 Identities=15% Similarity=0.305 Sum_probs=73.1
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCcccccccccCcccccccc----------------------------------------
Q 045583 16 PWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCR---------------------------------------- 55 (319)
Q Consensus 16 ~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr---------------------------------------- 55 (319)
.|+.-+=..++.++.+||. .+-..||..+. +++...++
T Consensus 826 ~w~~~~f~~f~~~~~~~gr-~~~~~i~~~~~-~k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~ 903 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGR-NDIKSIASEME-GKTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAI 903 (1033)
T ss_pred cccHHHHHHHHHHHHHhCH-hHHHHHHHHhc-CCCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4888888888889999997 68888988886 56654433
Q ss_pred --------ccccccc--CCCCCCCCCCHHHHHHHHHHHhhhCC-chhhhccc------------CCCCCHHHHHHHHHHH
Q 045583 56 --------LRWLNYL--RPDIKHGNFTEDEDHVICTLYSQIGS-RWSIIASR------------LPGRTDNDVKNYWNTK 112 (319)
Q Consensus 56 --------~Rw~n~L--~p~lkrg~WT~EED~~Ll~lv~~~G~-kWs~IA~~------------lpgRT~~qcKnRW~~~ 112 (319)
..|.... .+..++..||+|||..|+..+.+||- +|..|-.. |..||+.+|..|.+++
T Consensus 904 ~~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l 983 (1033)
T PLN03142 904 GKKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTL 983 (1033)
T ss_pred HHHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHH
Confidence 2332211 12334556999999999999999994 79988332 2589999999999888
Q ss_pred hhhH
Q 045583 113 LKKK 116 (319)
Q Consensus 113 lkkk 116 (319)
++--
T Consensus 984 ~~~~ 987 (1033)
T PLN03142 984 IRLI 987 (1033)
T ss_pred HHHH
Confidence 7553
No 42
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=94.02 E-value=0.015 Score=56.77 Aligned_cols=50 Identities=22% Similarity=0.514 Sum_probs=45.6
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCCcccccccccCcccccccccccccccC
Q 045583 12 VKRGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNYLR 63 (319)
Q Consensus 12 lkkg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~L~ 63 (319)
+----|+..|+-+|+++....|- |+|..||..+| .|+...|+++|..++.
T Consensus 61 I~~e~WgadEEllli~~~~TlGl-GNW~dIadyiG-sr~kee~k~HylK~y~ 110 (432)
T COG5114 61 IGEEGWGADEELLLIECLDTLGL-GNWEDIADYIG-SRAKEEIKSHYLKMYD 110 (432)
T ss_pred ccCCCcCchHHHHHHHHHHhcCC-CcHHHHHHHHh-hhhhHHHHHHHHHHHh
Confidence 33456999999999999999999 79999999999 9999999999998775
No 43
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=93.49 E-value=0.097 Score=44.28 Aligned_cols=51 Identities=24% Similarity=0.440 Sum_probs=40.4
Q ss_pred CCCCCCCCHHHHHHHHHHHhhhCC----chhhhcccC------------CCCCHHHHHHHHHHHhhh
Q 045583 65 DIKHGNFTEDEDHVICTLYSQIGS----RWSIIASRL------------PGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 65 ~lkrg~WT~EED~~Ll~lv~~~G~----kWs~IA~~l------------pgRT~~qcKnRW~~~lkk 115 (319)
.-++..||++||..|+-.+.+||- .|..|-..+ ..||+.+|..|-+++++-
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~ 112 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKL 112 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHH
Confidence 556778999999999999999997 798886542 479999999999888764
No 44
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=93.46 E-value=0.066 Score=52.44 Aligned_cols=48 Identities=19% Similarity=0.390 Sum_probs=42.3
Q ss_pred CCCCCCCHHHHHHHHHHHhhhCC-chhhhcccCCCCCHHHHHHHHHHHh
Q 045583 66 IKHGNFTEDEDHVICTLYSQIGS-RWSIIASRLPGRTDNDVKNYWNTKL 113 (319)
Q Consensus 66 lkrg~WT~EED~~Ll~lv~~~G~-kWs~IA~~lpgRT~~qcKnRW~~~l 113 (319)
|-...|+.+|+.+|++.....|- +|..||.++..|+..+||.+|..+.
T Consensus 61 I~~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y 109 (432)
T COG5114 61 IGEEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMY 109 (432)
T ss_pred ccCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHH
Confidence 33457999999999999999996 8999999998899999999996554
No 45
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=93.38 E-value=0.036 Score=42.46 Aligned_cols=50 Identities=26% Similarity=0.418 Sum_probs=39.4
Q ss_pred CcCCCCHHHHHHHHHHHHHh-----CC----------CCCcccccccc----cCccccccccccccccc
Q 045583 13 KRGPWSPEEDATLKRYVETH-----GT----------GGNWIALPQKA----GLKRCGKSCRLRWLNYL 62 (319)
Q Consensus 13 kkg~WT~EEDe~L~~lV~k~-----G~----------~~~W~~IA~~l----g~~Rt~kQCr~Rw~n~L 62 (319)
++..||++|.+.|+++|.+| |. ...|..|+..+ +..|+..||+.+|.++.
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 35689999999999999987 31 12499998765 23689999999998864
No 46
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=93.12 E-value=0.13 Score=51.60 Aligned_cols=55 Identities=24% Similarity=0.353 Sum_probs=47.8
Q ss_pred CCCCCHHHHHHHHHHHhhhCCchhhhccc-----CCC-CCHHHHHHHHHHHhhhHHhcCCC
Q 045583 68 HGNFTEDEDHVICTLYSQIGSRWSIIASR-----LPG-RTDNDVKNYWNTKLKKKLLAGKV 122 (319)
Q Consensus 68 rg~WT~EED~~Ll~lv~~~G~kWs~IA~~-----lpg-RT~~qcKnRW~~~lkkkl~~~k~ 122 (319)
...||.||-+.|.++++.|.-+|-.||-+ ++. ||-.++|.||...-++-++.+..
T Consensus 130 dn~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~~ 190 (445)
T KOG2656|consen 130 DNSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARAP 190 (445)
T ss_pred cccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHHHHHHHHHccCC
Confidence 34699999999999999999999999988 555 99999999999888887765543
No 47
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=92.59 E-value=0.15 Score=49.84 Aligned_cols=49 Identities=18% Similarity=0.340 Sum_probs=39.7
Q ss_pred CCCCCHHHHHHHHHHHhhh----------CCchhhhcccC----CCCCHHHHHHHHHHHhhhH
Q 045583 68 HGNFTEDEDHVICTLYSQI----------GSRWSIIASRL----PGRTDNDVKNYWNTKLKKK 116 (319)
Q Consensus 68 rg~WT~EED~~Ll~lv~~~----------G~kWs~IA~~l----pgRT~~qcKnRW~~~lkkk 116 (319)
...|+.+|-..||++..+. +.-|..||+.+ --||+.+||++|.++.++.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Y 116 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKY 116 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHH
Confidence 4689999999999997653 34599999965 3499999999998776654
No 48
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=91.82 E-value=0.33 Score=49.57 Aligned_cols=49 Identities=16% Similarity=0.263 Sum_probs=43.1
Q ss_pred CCCCCCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 67 KHGNFTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 67 krg~WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
-...||.||..++-+++..||.++.+|...||.|+-..+..+|....|.
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK~ 234 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKKT 234 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHHH
Confidence 3467999999999999999999999999999999999999888665443
No 49
>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=91.60 E-value=0.32 Score=38.16 Aligned_cols=46 Identities=26% Similarity=0.480 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHhhh---CC----------chhhhcccC---C--CCCHHHHHHHHHHHhhh
Q 045583 70 NFTEDEDHVICTLYSQI---GS----------RWSIIASRL---P--GRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 70 ~WT~EED~~Ll~lv~~~---G~----------kWs~IA~~l---p--gRT~~qcKnRW~~~lkk 115 (319)
.||+++++.|++++.+. |+ .|..|++.| + ..|..||++||..+.+.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~ 64 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKD 64 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHH
Confidence 49999999999997543 22 299998887 2 35789999999665544
No 50
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=88.99 E-value=0.5 Score=47.36 Aligned_cols=47 Identities=21% Similarity=0.294 Sum_probs=42.6
Q ss_pred CCCCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 69 GNFTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 69 g~WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
.+||.+|-++..++...+|..++.|+..||.|...|||.+|..--|+
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~ 412 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKV 412 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhh
Confidence 37999999999999999999999999999999999999999654333
No 51
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=87.16 E-value=1.2 Score=31.44 Aligned_cols=42 Identities=26% Similarity=0.265 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 73 EDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 73 ~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
++++..++.++...|-.|.+||+.+ |.|...|+.+....+++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARKK 53 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHhh
Confidence 3578888888888999999999999 99999999988766553
No 52
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=84.85 E-value=0.4 Score=46.82 Aligned_cols=48 Identities=29% Similarity=0.436 Sum_probs=37.7
Q ss_pred CCCCHHHHHHHHHHHHHh----CC----CCCccccccc---ccCccccccccccccccc
Q 045583 15 GPWSPEEDATLKRYVETH----GT----GGNWIALPQK---AGLKRCGKSCRLRWLNYL 62 (319)
Q Consensus 15 g~WT~EEDe~L~~lV~k~----G~----~~~W~~IA~~---lg~~Rt~kQCr~Rw~n~L 62 (319)
..|+.+|-..|+.+..+. .. ..-|..||++ .|.-|++.||+.+|.+..
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 789999999999988643 11 1259999974 356799999999998864
No 53
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=78.80 E-value=2 Score=34.09 Aligned_cols=25 Identities=36% Similarity=0.833 Sum_probs=14.4
Q ss_pred CCCCcCCCCHHHHHHH--------HHHHHHhCC
Q 045583 10 ANVKRGPWSPEEDATL--------KRYVETHGT 34 (319)
Q Consensus 10 p~lkkg~WT~EEDe~L--------~~lV~k~G~ 34 (319)
|.-..|-||+|+|+.| .+++++||.
T Consensus 43 P~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG~ 75 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLRSGDKDDIERLIKKHGE 75 (87)
T ss_dssp -TT-TT---HHHHHHHTS--HHHHHHHHHHH-H
T ss_pred CCCCCCCcCHHHHHHHHcCCHHHHHHHHHHhCH
Confidence 3445788999999999 456678874
No 54
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=75.70 E-value=1.4 Score=44.28 Aligned_cols=64 Identities=16% Similarity=0.264 Sum_probs=50.8
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCcccccccccCcccccccccccccc--cCCCC------CCCCCCHHHHHHHH
Q 045583 14 RGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNY--LRPDI------KHGNFTEDEDHVIC 80 (319)
Q Consensus 14 kg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~--L~p~l------krg~WT~EED~~Ll 80 (319)
--+||.+|-++..++....|+ ++..|+..++ +|..+|++..|.+- .+|.. .+.++..+|...+.
T Consensus 365 ~~~Ws~~e~ekFYKALs~wGt--dF~LIs~lfP-~R~RkqIKaKfi~Eek~nP~rIn~aL~~kkp~d~~eY~k~~ 436 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWGT--DFSLISSLFP-NRERKQIKAKFIKEEKVNPERINEALNEKKPFDQVEYNKLR 436 (507)
T ss_pred CCcccHHHHHHHHHHHHHhcc--hHHHHHHhcC-chhHHHHHHHHHHHhhhCHHHHHHHHhccCCCCHHHHhhHH
Confidence 357999999999999999999 8999999998 99999999988763 23311 34577777765543
No 55
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=73.96 E-value=3.5 Score=35.56 Aligned_cols=46 Identities=9% Similarity=0.148 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHhhhCC-chhhhcccCCCCCHHHHHHHHHHHhhhHHhc
Q 045583 73 EDEDHVICTLYSQIGS-RWSIIASRLPGRTDNDVKNYWNTKLKKKLLA 119 (319)
Q Consensus 73 ~EED~~Ll~lv~~~G~-kWs~IA~~lpgRT~~qcKnRW~~~lkkkl~~ 119 (319)
++-|..|+++..+-|. .|+.||+.+ |-+...|+.|+..+...-+.+
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 3578889988888876 799999999 999999999998877666554
No 56
>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=72.65 E-value=2.9 Score=35.36 Aligned_cols=35 Identities=34% Similarity=0.446 Sum_probs=28.0
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCC--CCCcccccccc
Q 045583 11 NVKRGPWSPEEDATLKRYVETHGT--GGNWIALPQKA 45 (319)
Q Consensus 11 ~lkkg~WT~EEDe~L~~lV~k~G~--~~~W~~IA~~l 45 (319)
+-++..||.|||.-|+-++.+||. .+.|..|-..+
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 677899999999999999999997 24798887654
No 57
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=70.99 E-value=4.1 Score=35.63 Aligned_cols=47 Identities=13% Similarity=0.138 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHhhhCC-chhhhcccCCCCCHHHHHHHHHHHhhhHHhcC
Q 045583 73 EDEDHVICTLYSQIGS-RWSIIASRLPGRTDNDVKNYWNTKLKKKLLAG 120 (319)
Q Consensus 73 ~EED~~Ll~lv~~~G~-kWs~IA~~lpgRT~~qcKnRW~~~lkkkl~~~ 120 (319)
++-|.+|+.+..+-|. .|+.||+.+ |-+...|+.|++.+.+..+.++
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCeEE
Confidence 5678888888888776 799999999 9999999999988877766543
No 58
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=70.32 E-value=7.8 Score=26.91 Aligned_cols=41 Identities=27% Similarity=0.296 Sum_probs=32.2
Q ss_pred HHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 74 DEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 74 EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
+++..++.+.-..|..+..||+.+ |-|...|+.+-...+++
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 456666666666677999999999 99999999988777765
No 59
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=70.14 E-value=34 Score=34.64 Aligned_cols=43 Identities=16% Similarity=0.322 Sum_probs=38.9
Q ss_pred CCCCHHHHHHHHHHHhhhCCchhhh-cccCCCCCHHHHHHHHHH
Q 045583 69 GNFTEDEDHVICTLYSQIGSRWSII-ASRLPGRTDNDVKNYWNT 111 (319)
Q Consensus 69 g~WT~EED~~Ll~lv~~~G~kWs~I-A~~lpgRT~~qcKnRW~~ 111 (319)
..|+++|-+.+-+.++.||..+..| +.+++.|+--+|-.+|..
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYl 321 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYL 321 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHH
Confidence 4799999999999999999999999 668999999999887744
No 60
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=68.61 E-value=6.7 Score=42.58 Aligned_cols=45 Identities=11% Similarity=0.158 Sum_probs=40.7
Q ss_pred CCCCCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHH
Q 045583 68 HGNFTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTK 112 (319)
Q Consensus 68 rg~WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~ 112 (319)
...||+.|..++-+++..|-..+-.|++.++++|-.+|-.+|.+.
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtW 663 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTW 663 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHH
Confidence 357999999999999999999999999999999999998876543
No 61
>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=66.50 E-value=9.2 Score=26.34 Aligned_cols=38 Identities=21% Similarity=0.323 Sum_probs=30.1
Q ss_pred HHHHHHHHHHhhhCC-chhhhcccCCCCCHHHHHHHHHHH
Q 045583 74 DEDHVICTLYSQIGS-RWSIIASRLPGRTDNDVKNYWNTK 112 (319)
Q Consensus 74 EED~~Ll~lv~~~G~-kWs~IA~~lpgRT~~qcKnRW~~~ 112 (319)
+=|..|+.+..+-|. .|..||+.+ |=|...|..|+..+
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 457888888888776 699999999 99999999998653
No 62
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=65.87 E-value=15 Score=36.23 Aligned_cols=49 Identities=20% Similarity=0.478 Sum_probs=37.1
Q ss_pred CCCCCHHHHHHHHHHHhhh-CCc---hhhhcccCCCCCHHHHHHHHHHHhhhHH
Q 045583 68 HGNFTEDEDHVICTLYSQI-GSR---WSIIASRLPGRTDNDVKNYWNTKLKKKL 117 (319)
Q Consensus 68 rg~WT~EED~~Ll~lv~~~-G~k---Ws~IA~~lpgRT~~qcKnRW~~~lkkkl 117 (319)
-..||.-|...|+++.... |.. -..|++.++||+..+|++.- ..||.++
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 4579999999999887644 544 45788999999999999865 4444443
No 63
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=65.50 E-value=5.4 Score=35.44 Aligned_cols=41 Identities=24% Similarity=0.305 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHH
Q 045583 70 NFTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNT 111 (319)
Q Consensus 70 ~WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~ 111 (319)
.||+|+.+.|.+|..+ |..=++||+.|.|.|.|.|.-+-+.
T Consensus 2 ~Wtde~~~~L~~lw~~-G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred CCCHHHHHHHHHHHHc-CCCHHHHHHHhCCcchhhhhhhhhc
Confidence 5999999999999865 8888999999977999988776543
No 64
>smart00595 MADF subfamily of SANT domain.
Probab=62.42 E-value=6 Score=30.53 Aligned_cols=25 Identities=28% Similarity=0.569 Sum_probs=21.1
Q ss_pred chhhhcccCCCCCHHHHHHHHHHHhh
Q 045583 89 RWSIIASRLPGRTDNDVKNYWNTKLK 114 (319)
Q Consensus 89 kWs~IA~~lpgRT~~qcKnRW~~~lk 114 (319)
-|..||..| |.|..+|+.+|+++..
T Consensus 29 aW~~Ia~~l-~~~~~~~~~kw~~LR~ 53 (89)
T smart00595 29 AWEEIAEEL-GLSVEECKKRWKNLRD 53 (89)
T ss_pred HHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 499999999 5599999999987643
No 65
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=61.41 E-value=13 Score=30.70 Aligned_cols=36 Identities=28% Similarity=0.279 Sum_probs=27.6
Q ss_pred HHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 79 ICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 79 Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
++.+....|-.+..||+.+ |.+...|+++++..+++
T Consensus 121 il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 121 IFILSRFEGKSYKEIAEEL-GISVKTVEYHISKALKE 156 (161)
T ss_pred HHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3334334477899999999 99999999999776544
No 66
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=61.06 E-value=12 Score=39.89 Aligned_cols=48 Identities=19% Similarity=0.481 Sum_probs=39.2
Q ss_pred CCCCCHHHHHHHHHHHhhhCCchhhh----------cccCCCCCHHHHHHHHHHHhhh
Q 045583 68 HGNFTEDEDHVICTLYSQIGSRWSII----------ASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 68 rg~WT~EED~~Ll~lv~~~G~kWs~I----------A~~lpgRT~~qcKnRW~~~lkk 115 (319)
+..||-+|++-...+.+++|..+..| -.+..-+|..|++.+|+..+++
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~ 145 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRR 145 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHH
Confidence 66899999999999999999999888 2334457888999988776554
No 67
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=59.26 E-value=17 Score=33.58 Aligned_cols=46 Identities=11% Similarity=0.187 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHhhhCCchhhhcccC---CCCCHHHHHHHHHHHhhhH
Q 045583 70 NFTEDEDHVICTLYSQIGSRWSIIASRL---PGRTDNDVKNYWNTKLKKK 116 (319)
Q Consensus 70 ~WT~EED~~Ll~lv~~~G~kWs~IA~~l---pgRT~~qcKnRW~~~lkkk 116 (319)
.|++++|.+|+.+|.. |+.-..|+.-+ -.-|-.+|..||+.++--.
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~ 49 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALLYDP 49 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHHcCh
Confidence 4999999999999875 55566665543 3468999999999987544
No 68
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=57.09 E-value=6.3 Score=30.75 Aligned_cols=46 Identities=22% Similarity=0.515 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHHHHh---CCC---C-----Cccccccccc----Ccccccccccccccc
Q 045583 16 PWSPEEDATLKRYVETH---GTG---G-----NWIALPQKAG----LKRCGKSCRLRWLNY 61 (319)
Q Consensus 16 ~WT~EEDe~L~~lV~k~---G~~---~-----~W~~IA~~lg----~~Rt~kQCr~Rw~n~ 61 (319)
.||+++++.|++++... |.. + .|..|++.+. ...+..||+.||...
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~l 61 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTL 61 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHH
Confidence 59999999999998655 221 1 3777775543 344667777776554
No 69
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=56.78 E-value=20 Score=29.83 Aligned_cols=47 Identities=15% Similarity=0.202 Sum_probs=34.1
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCCcccccccccCcccccccccccccccC
Q 045583 12 VKRGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNYLR 63 (319)
Q Consensus 12 lkkg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~L~ 63 (319)
.++..||.|+-..++..+...|. .-..||+.+|. ..+--.+|.+.+.
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g~--sv~evA~e~gI---s~~tl~~W~r~y~ 54 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPGM--TVSLVARQHGV---AASQLFLWRKQYQ 54 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCCC--CHHHHHHHHCc---CHHHHHHHHHHHh
Confidence 44688999998888888877776 68899998884 3334456766543
No 70
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=54.34 E-value=9.2 Score=39.46 Aligned_cols=41 Identities=12% Similarity=0.348 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHH
Q 045583 70 NFTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNT 111 (319)
Q Consensus 70 ~WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~ 111 (319)
.||++|-. +++...-|+.....||..+...|..|++.+|..
T Consensus 472 ~wSp~e~s-~ircf~~y~~~fe~ia~l~~tktp~Q~~~fy~~ 512 (534)
T KOG1194|consen 472 GWSPEEKS-AIRCFHWYKDNFELIAELMATKTPEQIKKFYMD 512 (534)
T ss_pred CCCCcccc-cccCchhhccchHHHHHHhcCCCHHHHHHHhcC
Confidence 59998888 788888899999999999999999999999843
No 71
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=53.23 E-value=13 Score=29.48 Aligned_cols=30 Identities=23% Similarity=0.524 Sum_probs=24.5
Q ss_pred HHHHHHHHhhhCCchhhhcccCCCCCHHHHH
Q 045583 76 DHVICTLYSQIGSRWSIIASRLPGRTDNDVK 106 (319)
Q Consensus 76 D~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcK 106 (319)
|+.|..++..+|..|..+|.+| |=|..+|.
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I~ 31 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDIY 31 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 5678889999999999999999 76666553
No 72
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=52.33 E-value=17 Score=38.56 Aligned_cols=46 Identities=20% Similarity=0.407 Sum_probs=42.1
Q ss_pred CCCCCCCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHH
Q 045583 66 IKHGNFTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNT 111 (319)
Q Consensus 66 lkrg~WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~ 111 (319)
...++|+.+|-++.-.+..+.|...+.|+..+|+|+..+||.++..
T Consensus 407 ~~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 407 LETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKK 452 (584)
T ss_pred cccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhh
Confidence 3456899999999999999999999999999999999999998844
No 73
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=51.66 E-value=20 Score=28.54 Aligned_cols=45 Identities=13% Similarity=0.146 Sum_probs=38.3
Q ss_pred HHHHHHHHHHhhhCC-chhhhcccCCCCCHHHHHHHHHHHhhhHHhc
Q 045583 74 DEDHVICTLYSQIGS-RWSIIASRLPGRTDNDVKNYWNTKLKKKLLA 119 (319)
Q Consensus 74 EED~~Ll~lv~~~G~-kWs~IA~~lpgRT~~qcKnRW~~~lkkkl~~ 119 (319)
+.|..|+.+..+.|. .++.||+.+ |-+...|+.+...+.+..+.+
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 578888888888775 799999999 999999999998888776655
No 74
>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=49.34 E-value=4.8 Score=27.77 Aligned_cols=38 Identities=21% Similarity=0.340 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHhCCCCCcccccccccCccccccccccccc
Q 045583 20 EEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLN 60 (319)
Q Consensus 20 EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n 60 (319)
+=|.+|+.+.+.-|. ..|.+||+.+| -+...|+.|+.+
T Consensus 3 ~~D~~Il~~Lq~d~r-~s~~~la~~lg--lS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGR-RSYAELAEELG--LSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TT-S-HHHHHHHHT--S-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCC-ccHHHHHHHHC--cCHHHHHHHHHH
Confidence 458899999999987 68999999998 677778887654
No 75
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=48.13 E-value=26 Score=31.01 Aligned_cols=39 Identities=21% Similarity=0.183 Sum_probs=29.9
Q ss_pred HHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHHhh
Q 045583 75 EDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTKLK 114 (319)
Q Consensus 75 ED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lk 114 (319)
+...++++....|-.+.+||+.| |-+...|+.+|.....
T Consensus 139 ~~~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR~ 177 (185)
T PF07638_consen 139 RQRRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRARA 177 (185)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 33444445445588999999999 9999999999977653
No 76
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=46.76 E-value=10 Score=38.33 Aligned_cols=50 Identities=14% Similarity=0.266 Sum_probs=42.2
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCCCccccccc-----ccCccccccccccccccc
Q 045583 11 NVKRGPWSPEEDATLKRYVETHGTGGNWIALPQK-----AGLKRCGKSCRLRWLNYL 62 (319)
Q Consensus 11 ~lkkg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~-----lg~~Rt~kQCr~Rw~n~L 62 (319)
.+.-..||.||-+-|.+++++|.- .|-.||.+ .+..||....++||..+.
T Consensus 127 ~l~dn~WskeETD~LF~lck~fDL--Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~ 181 (445)
T KOG2656|consen 127 HLNDNSWSKEETDYLFDLCKRFDL--RFFVIADRYDNQQYKKSRTVEDLKERYYSVC 181 (445)
T ss_pred hhccccccHHHHHHHHHHHHhcCe--eEEEEeeccchhhccccccHHHHHHHHHHHH
Confidence 345577999999999999999987 89999987 565699999999997553
No 77
>cd08803 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=46.40 E-value=22 Score=28.16 Aligned_cols=31 Identities=16% Similarity=0.421 Sum_probs=25.6
Q ss_pred HHHHHHHHhhhCCchhhhcccCCCCCHHHHHH
Q 045583 76 DHVICTLYSQIGSRWSIIASRLPGRTDNDVKN 107 (319)
Q Consensus 76 D~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKn 107 (319)
|..|..+....|..|..+|+.| |=+..+|..
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI~~ 34 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEINQ 34 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHHHH
Confidence 5678888899999999999999 777766544
No 78
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=46.32 E-value=21 Score=41.03 Aligned_cols=72 Identities=17% Similarity=0.255 Sum_probs=42.9
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCCcccccccccCcccccccccccccccCCCCCCCCCCHHHHHHHHHHHhhh-CCchh
Q 045583 13 KRGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNYLRPDIKHGNFTEDEDHVICTLYSQI-GSRWS 91 (319)
Q Consensus 13 kkg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~L~p~lkrg~WT~EED~~Ll~lv~~~-G~kWs 91 (319)
.---|..+||..|+-.|-+||. ++|.+|-.---++-+. ...+....-.+.|=..+-..|+.+.... +.+|.
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGy-gswe~Ir~Dp~L~l~d-------Ki~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~ 1203 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGY-GSWEAIRLDPDLGLTD-------KIFLVETVPQAKHLQRRADYLLSLLRKHDKGNTP 1203 (1373)
T ss_pred cccCCCchhhhhHhhhhhhccc-ccHHHhccCccccchh-------hhcccccCCchHHHHHHHHHHHHHHhhcccCCCc
Confidence 4567999999999999999999 7999983211111111 1111112334455556666666666555 33443
Q ss_pred h
Q 045583 92 I 92 (319)
Q Consensus 92 ~ 92 (319)
.
T Consensus 1204 ~ 1204 (1373)
T KOG0384|consen 1204 K 1204 (1373)
T ss_pred h
Confidence 3
No 79
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=46.15 E-value=7.2 Score=33.63 Aligned_cols=46 Identities=11% Similarity=0.098 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHhCCCCCcccccccccCcccccccccccccccCCCCC
Q 045583 19 PEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNYLRPDIK 67 (319)
Q Consensus 19 ~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~L~p~lk 67 (319)
.+-|.+|+++.++-|. ..|.+||+.+| -+...|+.|+.+....++-
T Consensus 8 D~~D~~Il~~Lq~d~R-~s~~eiA~~lg--lS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 8 DNLDRGILEALMENAR-TPYAELAKQFG--VSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred CHHHHHHHHHHHHcCC-CCHHHHHHHHC--cCHHHHHHHHHHHHHCCCe
Confidence 4679999999999987 69999999987 8888999999888665543
No 80
>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=45.83 E-value=30 Score=27.63 Aligned_cols=34 Identities=29% Similarity=0.217 Sum_probs=26.2
Q ss_pred HHHhhhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 81 TLYSQIGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 81 ~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
.++...|..+..||+.+ |-+...|+++....+++
T Consensus 120 ~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 120 VLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred hhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 33334578899999999 88999999988776544
No 81
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=44.70 E-value=16 Score=27.33 Aligned_cols=26 Identities=27% Similarity=0.452 Sum_probs=20.5
Q ss_pred chhhhcccCCC-CCHHHHHHHHHHHhh
Q 045583 89 RWSIIASRLPG-RTDNDVKNYWNTKLK 114 (319)
Q Consensus 89 kWs~IA~~lpg-RT~~qcKnRW~~~lk 114 (319)
-|..||..|.. -+..+|+.+|..+..
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~ 54 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRD 54 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHH
Confidence 49999999942 678899999977654
No 82
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=44.62 E-value=32 Score=29.09 Aligned_cols=31 Identities=16% Similarity=0.087 Sum_probs=24.5
Q ss_pred hhhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 84 SQIGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 84 ~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
...|-.+..||+.| |.+...|+++....+++
T Consensus 141 ~~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 171 (182)
T PRK09652 141 EIEGLSYEEIAEIM-GCPIGTVRSRIFRAREA 171 (182)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 34477899999999 99999999987654443
No 83
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=44.43 E-value=6.1 Score=34.52 Aligned_cols=46 Identities=15% Similarity=0.188 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHhCCCCCcccccccccCcccccccccccccccCCCCC
Q 045583 19 PEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLNYLRPDIK 67 (319)
Q Consensus 19 ~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n~L~p~lk 67 (319)
.+-|.+|+.+.++-|. -.|.+||+.+| -+...|+.|+.+..+.++-
T Consensus 13 D~~D~~IL~~Lq~d~R-~s~~eiA~~lg--lS~~tv~~Ri~rL~~~GvI 58 (164)
T PRK11169 13 DRIDRNILNELQKDGR-ISNVELSKRVG--LSPTPCLERVRRLERQGFI 58 (164)
T ss_pred HHHHHHHHHHhccCCC-CCHHHHHHHHC--cCHHHHHHHHHHHHHCCCe
Confidence 6679999999999997 69999999998 7778899999888766543
No 84
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=43.29 E-value=33 Score=28.90 Aligned_cols=30 Identities=23% Similarity=0.153 Sum_probs=24.2
Q ss_pred hhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 85 QIGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 85 ~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
..|..+..||+.| |-|...|++++...+++
T Consensus 139 ~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 168 (179)
T PRK11924 139 VEGLSYREIAEIL-GVPVGTVKSRLRRARQL 168 (179)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3467899999999 99999999998765443
No 85
>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=42.85 E-value=47 Score=21.70 Aligned_cols=40 Identities=20% Similarity=0.239 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHH
Q 045583 71 FTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTK 112 (319)
Q Consensus 71 WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~ 112 (319)
++++ +..++.++..-|..+..||+.+ |-+...|+.+....
T Consensus 11 l~~~-~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPER-EREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRA 50 (55)
T ss_pred CCHH-HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 3444 4555555555677899999998 88888887776554
No 86
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=42.33 E-value=9.5 Score=41.47 Aligned_cols=44 Identities=14% Similarity=0.313 Sum_probs=38.6
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCcccccccccCccccccccccccc
Q 045583 14 RGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKRCGKSCRLRWLN 60 (319)
Q Consensus 14 kg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~Rt~kQCr~Rw~n 60 (319)
...||+.|..+..+++-.|.. ++..|++++. +++.+||-+-|..
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~K--DF~~v~km~~-~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSK--DFIFVQKMVK-SKTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhcc--cHHHHHHHhc-cccHHHHHHHHHH
Confidence 457999999999999999987 8999999998 9999999775543
No 87
>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=42.04 E-value=20 Score=27.91 Aligned_cols=30 Identities=27% Similarity=0.612 Sum_probs=24.0
Q ss_pred HHHHHHHHhhhCCchhhhcccCCCCCHHHHH
Q 045583 76 DHVICTLYSQIGSRWSIIASRLPGRTDNDVK 106 (319)
Q Consensus 76 D~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcK 106 (319)
|..|..+++.+|..|.++|.+| |=+..+|.
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI~ 33 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDID 33 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHHH
Confidence 4567788899999999999999 66665543
No 88
>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=41.68 E-value=17 Score=32.31 Aligned_cols=33 Identities=18% Similarity=0.414 Sum_probs=26.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCccccccccc-Ccccc
Q 045583 16 PWSPEEDATLKRYVETHGTGGNWIALPQKAG-LKRCG 51 (319)
Q Consensus 16 ~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg-~~Rt~ 51 (319)
.||+|+.++|.++.. -|. .-.+||+.|| ..|++
T Consensus 2 ~Wtde~~~~L~~lw~-~G~--SasqIA~~lg~vsRnA 35 (162)
T PF07750_consen 2 SWTDERVERLRKLWA-EGL--SASQIARQLGGVSRNA 35 (162)
T ss_pred CCCHHHHHHHHHHHH-cCC--CHHHHHHHhCCcchhh
Confidence 599999999999995 444 6889999999 45554
No 89
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=41.65 E-value=41 Score=30.54 Aligned_cols=45 Identities=27% Similarity=0.197 Sum_probs=38.0
Q ss_pred CCCCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHHhhhH
Q 045583 69 GNFTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTKLKKK 116 (319)
Q Consensus 69 g~WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkkk 116 (319)
...|+.|-+.|.-+.+ |..=.+||..| +.+...||+|..++++|-
T Consensus 147 ~~LT~RE~eVL~lla~--G~snkeIA~~L-~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 147 ELLTPRELEVLRLLAE--GLSNKEIAEEL-NLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCCCHHHHHHHHHHHC--CCCHHHHHHHH-CCCHhHHHHHHHHHHHHc
Confidence 3689999888877776 55556999999 999999999999998874
No 90
>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=41.35 E-value=25 Score=27.71 Aligned_cols=25 Identities=20% Similarity=0.627 Sum_probs=20.2
Q ss_pred HHHhhhCCchhhhcccCCCCCHHHHH
Q 045583 81 TLYSQIGSRWSIIASRLPGRTDNDVK 106 (319)
Q Consensus 81 ~lv~~~G~kWs~IA~~lpgRT~~qcK 106 (319)
.+....|..|..+|.+| |-++.+|.
T Consensus 12 ~ia~~iG~~Wk~Lar~L-Gls~~dI~ 36 (86)
T cd08318 12 VFANKLGEDWKTLAPHL-EMKDKEIR 36 (86)
T ss_pred HHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 35678899999999999 87777663
No 91
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=41.30 E-value=38 Score=29.81 Aligned_cols=30 Identities=20% Similarity=0.130 Sum_probs=24.3
Q ss_pred hhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 85 QIGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 85 ~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
..|....+||..| |-+...|++|+...+++
T Consensus 148 ~~g~s~~EIA~~l-g~s~~tV~~rl~rar~~ 177 (192)
T PRK09643 148 MQGYSVADAARML-GVAEGTVKSRCARGRAR 177 (192)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3467899999999 99999999999654433
No 92
>KOG2782 consensus Putative SAM dependent methyltransferases [General function prediction only]
Probab=41.26 E-value=21 Score=34.09 Aligned_cols=28 Identities=36% Similarity=0.592 Sum_probs=18.7
Q ss_pred cceeeeecCCC---CCCCccceeeccCceee
Q 045583 254 ADQILMDFGFG---IGDPCDQYYVNNNGTLW 281 (319)
Q Consensus 254 ~~~~~~d~~~~---~~~~~~~~~~~~~~~~~ 281 (319)
+||||||+|.. +.+|---|-|.-+|-|=
T Consensus 119 vDGiLmDlGcSSMQ~d~peRGFSv~~dGpLD 149 (303)
T KOG2782|consen 119 VDGILMDLGCSSMQVDNPERGFSVLQDGPLD 149 (303)
T ss_pred cceEEeecCccccccCCccccceeeccCCcc
Confidence 59999999943 34466666666666543
No 93
>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=40.47 E-value=27 Score=27.30 Aligned_cols=34 Identities=21% Similarity=0.488 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHH
Q 045583 73 EDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNY 108 (319)
Q Consensus 73 ~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnR 108 (319)
.||.++|+.. -..|.+|..+|..| |=++.+|++.
T Consensus 2 ~~~v~~ll~~-~nlG~dW~~LA~~L-G~~~~~I~~i 35 (77)
T cd08311 2 QEEVEKLLES-GRPGRDWRSLAGEL-GYEDEAIDTF 35 (77)
T ss_pred hHHHHHHHhC-CCCccCHHHHHHHc-CCCHHHHHHH
Confidence 5788888742 25788999999999 8888877653
No 94
>smart00351 PAX Paired Box domain.
Probab=40.47 E-value=42 Score=28.14 Aligned_cols=84 Identities=15% Similarity=0.192 Sum_probs=53.6
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCCcccccccccCcc-ccccccccccc--ccCCCC----CCCCCCHHHHHHHHHHHh
Q 045583 12 VKRGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKR-CGKSCRLRWLN--YLRPDI----KHGNFTEDEDHVICTLYS 84 (319)
Q Consensus 12 lkkg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~R-t~kQCr~Rw~n--~L~p~l----krg~WT~EED~~Ll~lv~ 84 (319)
+...+++.++-++++.++. -|. .-.+||+.++..| +...+..||.. .+.|.- ....-+++++..|++++.
T Consensus 13 ~~~~~~s~~~R~riv~~~~-~G~--s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~ 89 (125)
T smart00351 13 VNGRPLPDEERQRIVELAQ-NGV--RPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQ 89 (125)
T ss_pred cCCCCCCHHHHHHHHHHHH-cCC--CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHH
Confidence 4456699999999998886 454 7899999999666 45555666643 344421 222355666667776666
Q ss_pred hhCCchhhhcccCCCCCHHHHHHHH
Q 045583 85 QIGSRWSIIASRLPGRTDNDVKNYW 109 (319)
Q Consensus 85 ~~G~kWs~IA~~lpgRT~~qcKnRW 109 (319)
+.+ ..|..+++..|
T Consensus 90 ~~p-----------~~t~~el~~~L 103 (125)
T smart00351 90 ENP-----------GIFAWEIRDRL 103 (125)
T ss_pred HCC-----------CCCHHHHHHHH
Confidence 543 44555555554
No 95
>PRK04217 hypothetical protein; Provisional
Probab=38.86 E-value=73 Score=26.65 Aligned_cols=45 Identities=20% Similarity=0.079 Sum_probs=35.6
Q ss_pred CCCCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 69 GNFTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 69 g~WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
...|++| ..++.+....|-....||+.+ |.+...|+.+++...++
T Consensus 41 ~~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkk 85 (110)
T PRK04217 41 IFMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKK 85 (110)
T ss_pred ccCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3466666 567777777788999999999 99999999999765433
No 96
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=38.34 E-value=44 Score=28.70 Aligned_cols=29 Identities=14% Similarity=-0.041 Sum_probs=23.9
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 86 IGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 86 ~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
.|..+..||..| |-|...|+++....+++
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 367899999999 99999999998665544
No 97
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=38.14 E-value=38 Score=27.51 Aligned_cols=48 Identities=17% Similarity=0.153 Sum_probs=32.1
Q ss_pred CCCCHHHHHHHHHHHhhh----CC----chhhh----cccC-CCCCHHHHHHHHHHHhhhH
Q 045583 69 GNFTEDEDHVICTLYSQI----GS----RWSII----ASRL-PGRTDNDVKNYWNTKLKKK 116 (319)
Q Consensus 69 g~WT~EED~~Ll~lv~~~----G~----kWs~I----A~~l-pgRT~~qcKnRW~~~lkkk 116 (319)
.-||+|+|-.|++.+..| |. .|..+ ...| ..=+.+|+..+-+.+.+|-
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 359999999999998766 52 34333 3333 2247788888876655553
No 98
>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=37.83 E-value=30 Score=27.31 Aligned_cols=17 Identities=29% Similarity=0.571 Sum_probs=10.1
Q ss_pred CCCCCCCCCHHHHHHHH
Q 045583 64 PDIKHGNFTEDEDHVIC 80 (319)
Q Consensus 64 p~lkrg~WT~EED~~Ll 80 (319)
|.-..|-||+|+|+.|.
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 55668889999999994
No 99
>cd00131 PAX Paired Box domain
Probab=37.29 E-value=52 Score=27.81 Aligned_cols=71 Identities=13% Similarity=0.135 Sum_probs=45.2
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCcccccccccCcc-ccccccccccc--ccCCCCCCC----CCCHHHHHHHHHHHhhh
Q 045583 14 RGPWSPEEDATLKRYVETHGTGGNWIALPQKAGLKR-CGKSCRLRWLN--YLRPDIKHG----NFTEDEDHVICTLYSQI 86 (319)
Q Consensus 14 kg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~~R-t~kQCr~Rw~n--~L~p~lkrg----~WT~EED~~Ll~lv~~~ 86 (319)
..+.|.++-++++.+++ -|. ....||+.++..+ +...+..||.. .+.|.-..| .-+++.+..|+.++.+.
T Consensus 15 ~~~lS~d~R~rIv~~~~-~G~--s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~ 91 (128)
T cd00131 15 GRPLPDSIRQRIVELAQ-SGI--RPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQEN 91 (128)
T ss_pred CCcCCHHHHHHHHHHHH-cCC--CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHC
Confidence 35688999999998886 565 7999999998555 34445555543 244432212 24666667777666654
Q ss_pred C
Q 045583 87 G 87 (319)
Q Consensus 87 G 87 (319)
+
T Consensus 92 p 92 (128)
T cd00131 92 P 92 (128)
T ss_pred C
Confidence 3
No 100
>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=37.25 E-value=31 Score=27.20 Aligned_cols=31 Identities=16% Similarity=0.472 Sum_probs=25.8
Q ss_pred HHHHHHHHhhhCCchhhhcccCCCCCHHHHHH
Q 045583 76 DHVICTLYSQIGSRWSIIASRLPGRTDNDVKN 107 (319)
Q Consensus 76 D~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKn 107 (319)
|..|-.+...+|.+|..+|+.| |=+..+|.+
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 5567778899999999999999 777777755
No 101
>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=36.56 E-value=39 Score=29.07 Aligned_cols=28 Identities=14% Similarity=0.064 Sum_probs=23.3
Q ss_pred CCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 87 GSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 87 G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
|-....||+.| |-|...|+++.+..+++
T Consensus 154 ~~s~~EIA~~l-gis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 154 GLSYEDIARIM-DCPVGTVRSRIFRAREA 181 (190)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 56789999999 89999999998766544
No 102
>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=35.64 E-value=30 Score=27.42 Aligned_cols=30 Identities=23% Similarity=0.548 Sum_probs=23.7
Q ss_pred HHHHHHHhhhCCchhhhcccCCCCCHHHHHH
Q 045583 77 HVICTLYSQIGSRWSIIASRLPGRTDNDVKN 107 (319)
Q Consensus 77 ~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKn 107 (319)
+.|-.+....|..|..+|++| |=++.+|..
T Consensus 3 ~~l~~l~~~lG~~Wk~lar~L-G~s~~eI~~ 32 (86)
T cd08777 3 KHLDLLRENLGKKWKRCARKL-GFTESEIEE 32 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHc-CCCHHHHHH
Confidence 345556678899999999999 888887765
No 103
>PF14722 KRAP_IP3R_bind: Ki-ras-induced actin-interacting protein-IP3R-interacting domain
Probab=35.27 E-value=7.8 Score=34.56 Aligned_cols=49 Identities=33% Similarity=0.379 Sum_probs=29.9
Q ss_pred cccccCCCCCCccccccCCCceeecCCCCCCCCccCcceeeeecCCCCCCCcc
Q 045583 218 HQLGTSLKNSPVLTSSQEGSSVTLPAGNNVNGGVEDADQILMDFGFGIGDPCD 270 (319)
Q Consensus 218 ~~~~~s~~~~~~~~~s~~~ss~s~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~ 270 (319)
...|+|||.++.-+.++-.|||+-=+..+. ||+..||.|.|||-.+|-.
T Consensus 3 ~~~g~S~nS~~s~sssst~SSv~e~L~~~~----~DpeeiLl~LGFG~de~~~ 51 (160)
T PF14722_consen 3 LSRGRSMNSSGSGSSSSTPSSVSELLEFRE----EDPEEILLNLGFGRDEPDI 51 (160)
T ss_pred cccccccccCCCCCCCCccchHHHHHHHhc----cCHHHHHHhccCCCCCccc
Confidence 356889988873333333444442233322 6766899999999866543
No 104
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=34.53 E-value=63 Score=26.98 Aligned_cols=29 Identities=14% Similarity=0.108 Sum_probs=23.5
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 86 IGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 86 ~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
.|-.-..||..| |-+...|+++....+++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 121 EDMDVAETAAAM-GCSEGSVKTHCSRATHA 149 (161)
T ss_pred hcCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 366789999999 99999999998665443
No 105
>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=34.42 E-value=56 Score=27.79 Aligned_cols=29 Identities=28% Similarity=0.347 Sum_probs=23.8
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 86 IGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 86 ~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
.|-....||..| |-|...|++++...+++
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 366789999999 88999999998776654
No 106
>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=34.12 E-value=41 Score=25.64 Aligned_cols=30 Identities=23% Similarity=0.595 Sum_probs=22.3
Q ss_pred HHHHHHHHHhh-hCCchhhhcccCCCCCHHHH
Q 045583 75 EDHVICTLYSQ-IGSRWSIIASRLPGRTDNDV 105 (319)
Q Consensus 75 ED~~Ll~lv~~-~G~kWs~IA~~lpgRT~~qc 105 (319)
-.+.|..++.. .|..|..+|++| |=+..+|
T Consensus 4 ~~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i 34 (88)
T smart00005 4 TREKLAKLLDHPLGLDWRELARKL-GLSEADI 34 (88)
T ss_pred HHHHHHHHHcCccchHHHHHHHHc-CCCHHHH
Confidence 34566777777 899999999999 5555544
No 107
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=33.91 E-value=31 Score=23.70 Aligned_cols=37 Identities=32% Similarity=0.418 Sum_probs=18.2
Q ss_pred CCCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHH
Q 045583 70 NFTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNY 108 (319)
Q Consensus 70 ~WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnR 108 (319)
.+|.+|-..|..++ .-|..=..||+.| ||+...|.+.
T Consensus 4 ~Lt~~eR~~I~~l~-~~G~s~~~IA~~l-g~s~sTV~re 40 (44)
T PF13936_consen 4 HLTPEERNQIEALL-EQGMSIREIAKRL-GRSRSTVSRE 40 (44)
T ss_dssp --------HHHHHH-CS---HHHHHHHT-T--HHHHHHH
T ss_pred chhhhHHHHHHHHH-HcCCCHHHHHHHH-CcCcHHHHHH
Confidence 46776666666554 5677888999999 9999887653
No 108
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=33.78 E-value=72 Score=27.64 Aligned_cols=33 Identities=24% Similarity=0.115 Sum_probs=27.6
Q ss_pred hhCCchhhhcccCCCCCHHHHHHHHHHHhhhHHh
Q 045583 85 QIGSRWSIIASRLPGRTDNDVKNYWNTKLKKKLL 118 (319)
Q Consensus 85 ~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkkkl~ 118 (319)
..|-...+||+.| |-+...||.|....+++-..
T Consensus 141 ~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 141 LDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 3467899999999 99999999999887776544
No 109
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=33.05 E-value=53 Score=27.51 Aligned_cols=47 Identities=19% Similarity=0.222 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHhhhCC-chhhhcccCCCCCHHHHHHHHHHHhhhHHhcC
Q 045583 73 EDEDHVICTLYSQIGS-RWSIIASRLPGRTDNDVKNYWNTKLKKKLLAG 120 (319)
Q Consensus 73 ~EED~~Ll~lv~~~G~-kWs~IA~~lpgRT~~qcKnRW~~~lkkkl~~~ 120 (319)
++-|.+|+++.++-+. .+..||+.+ |-+...|++|-..+.+.-+.++
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~GiI~~ 54 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGVIKG 54 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCceee
Confidence 3567778888777665 799999999 9999999999877776665544
No 110
>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=32.41 E-value=72 Score=24.74 Aligned_cols=38 Identities=16% Similarity=0.325 Sum_probs=26.8
Q ss_pred HHHHHHHhhhC--------CchhhhcccCC---CCC--HHHHHHHHHHHhh
Q 045583 77 HVICTLYSQIG--------SRWSIIASRLP---GRT--DNDVKNYWNTKLK 114 (319)
Q Consensus 77 ~~Ll~lv~~~G--------~kWs~IA~~lp---gRT--~~qcKnRW~~~lk 114 (319)
-.|..+|.+.| .+|..||+.|. .-+ ..++|..|..+|.
T Consensus 39 ~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 39 YKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhH
Confidence 45667777776 46999999982 122 3678998887764
No 111
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=32.32 E-value=60 Score=28.25 Aligned_cols=28 Identities=18% Similarity=0.084 Sum_probs=22.7
Q ss_pred CCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 87 GSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 87 G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
|-....||+.| |-|...|++++...+++
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 56789999999 99999999998665443
No 112
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=31.73 E-value=60 Score=27.84 Aligned_cols=28 Identities=14% Similarity=-0.010 Sum_probs=22.9
Q ss_pred CCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 87 GSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 87 G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
|.....||+.| |.+...|+++....+++
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 99999999998665544
No 113
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=31.32 E-value=68 Score=28.02 Aligned_cols=30 Identities=23% Similarity=0.107 Sum_probs=24.1
Q ss_pred hhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 85 QIGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 85 ~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
..|-....||..| |-+...|+++....+++
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 99999999998655433
No 114
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=30.96 E-value=71 Score=28.01 Aligned_cols=28 Identities=4% Similarity=-0.071 Sum_probs=23.3
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhh
Q 045583 86 IGSRWSIIASRLPGRTDNDVKNYWNTKLK 114 (319)
Q Consensus 86 ~G~kWs~IA~~lpgRT~~qcKnRW~~~lk 114 (319)
.|-....||..| |.+...||.|....++
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 367899999999 9999999999765543
No 115
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=30.85 E-value=74 Score=27.68 Aligned_cols=29 Identities=17% Similarity=0.071 Sum_probs=23.6
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 86 IGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 86 ~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
.|-....||..| |-|...|++++...+++
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 366789999999 99999999998665443
No 116
>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=30.74 E-value=68 Score=22.77 Aligned_cols=44 Identities=32% Similarity=0.314 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHHhhhH
Q 045583 70 NFTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTKLKKK 116 (319)
Q Consensus 70 ~WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkkk 116 (319)
.+|+.|-+.|.-++. |..=..||..+ +.+...|+.+...+++|-
T Consensus 3 ~LT~~E~~vl~~l~~--G~~~~eIA~~l-~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ--GMSNKEIAEEL-GISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHT--TS-HHHHHHHH-TSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHh--cCCcchhHHhc-CcchhhHHHHHHHHHHHh
Confidence 457777776666655 55667999999 999999999998777663
No 117
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=30.65 E-value=56 Score=23.64 Aligned_cols=37 Identities=22% Similarity=0.469 Sum_probs=24.4
Q ss_pred CCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHH
Q 045583 71 FTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYW 109 (319)
Q Consensus 71 WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW 109 (319)
.|. +|+..+.++.+.|-.-.+||+++ ||+.+.|+++-
T Consensus 5 Lt~-~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl 41 (50)
T PF11427_consen 5 LTD-AEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRYL 41 (50)
T ss_dssp --H-HHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHHH
T ss_pred CCH-HHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHHh
Confidence 344 45556677788899999999999 99998888753
No 118
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=30.57 E-value=75 Score=27.57 Aligned_cols=29 Identities=21% Similarity=0.217 Sum_probs=23.9
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 86 IGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 86 ~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
.|.....||..| |-+...|+.+....+++
T Consensus 154 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 154 VGLSAEETAEAV-GSTPGAVRVAQHRALAR 182 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 467899999999 99999999998665544
No 119
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=30.44 E-value=76 Score=27.00 Aligned_cols=29 Identities=28% Similarity=0.291 Sum_probs=23.2
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 86 IGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 86 ~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
.|-.-..||+.| |.+...|+.+.+..+++
T Consensus 133 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 161 (173)
T PRK09645 133 RGWSTAQIAADL-GIPEGTVKSRLHYALRA 161 (173)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 366778999999 99999999998665433
No 120
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=30.43 E-value=75 Score=27.37 Aligned_cols=29 Identities=17% Similarity=0.199 Sum_probs=23.9
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 86 IGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 86 ~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
.|.....||..| |-+...|+.+....+++
T Consensus 146 ~g~s~~eIA~~l-~is~~tV~~~l~ra~~~ 174 (184)
T PRK12512 146 EGASIKETAAKL-SMSEGAVRVALHRGLAA 174 (184)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 367789999999 99999999998765544
No 121
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=30.25 E-value=79 Score=27.05 Aligned_cols=33 Identities=27% Similarity=0.323 Sum_probs=26.4
Q ss_pred HhhhCCchhhhcccCCCCCHHHHHHHHHHHhhhH
Q 045583 83 YSQIGSRWSIIASRLPGRTDNDVKNYWNTKLKKK 116 (319)
Q Consensus 83 v~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkkk 116 (319)
....|-...+||+.+ |.+...|+.+-...+++-
T Consensus 131 ~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 131 NRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred HHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 334477899999999 999999999987766553
No 122
>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=29.56 E-value=81 Score=27.67 Aligned_cols=30 Identities=10% Similarity=0.025 Sum_probs=24.1
Q ss_pred hhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 85 QIGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 85 ~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
..|.....||+.| |-|...||.|....+++
T Consensus 145 ~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 145 VLGFESDEICQEL-EISTSNCHVLLYRARLS 174 (188)
T ss_pred HhCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3467889999999 99999999998665443
No 123
>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=29.53 E-value=40 Score=26.61 Aligned_cols=26 Identities=19% Similarity=0.436 Sum_probs=21.0
Q ss_pred HHHHHHHhhhCCchhhhcccCCCCCHH
Q 045583 77 HVICTLYSQIGSRWSIIASRLPGRTDN 103 (319)
Q Consensus 77 ~~Ll~lv~~~G~kWs~IA~~lpgRT~~ 103 (319)
..|..+..++|..|..+|.+| |=++.
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 457888999999999999998 54443
No 124
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=29.42 E-value=43 Score=35.94 Aligned_cols=48 Identities=10% Similarity=0.267 Sum_probs=34.8
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCcccccccccC---------cccccccccccccccC
Q 045583 14 RGPWSPEEDATLKRYVETHGTGGNWIALPQKAGL---------KRCGKSCRLRWLNYLR 63 (319)
Q Consensus 14 kg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~---------~Rt~kQCr~Rw~n~L~ 63 (319)
|..||-.|.+-...+++++|. ++..|-..... -++-.|.|..|.+.+.
T Consensus 88 ktaWt~~E~~~Ffdal~~~GK--dFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~ 144 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGK--DFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVR 144 (782)
T ss_pred ccccchhhHHHHHHHHHHhcc--cHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHH
Confidence 678999999999999999998 88888322211 2344677777766543
No 125
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=29.41 E-value=83 Score=26.37 Aligned_cols=28 Identities=14% Similarity=-0.070 Sum_probs=22.8
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhh
Q 045583 86 IGSRWSIIASRLPGRTDNDVKNYWNTKLK 114 (319)
Q Consensus 86 ~G~kWs~IA~~lpgRT~~qcKnRW~~~lk 114 (319)
.|-.-..||+.| |-+...|+++....++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~ 148 (160)
T PRK09642 121 EEKSYQEIALQE-KIEVKTVEMKLYRARK 148 (160)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 366789999999 9999999999765543
No 126
>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=29.30 E-value=1.3e+02 Score=26.42 Aligned_cols=46 Identities=17% Similarity=0.168 Sum_probs=38.2
Q ss_pred CCCCCCHHHHHHHHHHHhhhCCchhhhcccCC----CCCHHHHHHHHHHH
Q 045583 67 KHGNFTEDEDHVICTLYSQIGSRWSIIASRLP----GRTDNDVKNYWNTK 112 (319)
Q Consensus 67 krg~WT~EED~~Ll~lv~~~G~kWs~IA~~lp----gRT~~qcKnRW~~~ 112 (319)
....-|+.|...|..|+.+||..+...|...- -.|..||+.+....
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 44578999999999999999999999988653 37999999887554
No 127
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=29.27 E-value=81 Score=27.65 Aligned_cols=29 Identities=14% Similarity=0.014 Sum_probs=23.5
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 86 IGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 86 ~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
.|-...+||+.| |-+...|+.|....+++
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 366789999999 99999999998665544
No 128
>PLN03162 golden-2 like transcription factor; Provisional
Probab=27.93 E-value=3.5e+02 Score=27.74 Aligned_cols=45 Identities=13% Similarity=0.099 Sum_probs=35.5
Q ss_pred CCCCCHHHHHHHHHHHhhhCCc---hhhhcccC--CCCCHHHHHHHHHHH
Q 045583 68 HGNFTEDEDHVICTLYSQIGSR---WSIIASRL--PGRTDNDVKNYWNTK 112 (319)
Q Consensus 68 rg~WT~EED~~Ll~lv~~~G~k---Ws~IA~~l--pgRT~~qcKnRW~~~ 112 (319)
|-.||+|=.++++++|.++|.. =+.|-+.| +|=|..+|+.|..++
T Consensus 237 RLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKY 286 (526)
T PLN03162 237 KVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKY 286 (526)
T ss_pred cccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 3479999999999999999942 34565554 889999999887544
No 129
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=27.69 E-value=1e+02 Score=27.64 Aligned_cols=44 Identities=11% Similarity=0.129 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHHhhhH
Q 045583 70 NFTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTKLKKK 116 (319)
Q Consensus 70 ~WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkkk 116 (319)
..|+-|-+.|..+++ |....+||+.| +-+...|++|-..+++|-
T Consensus 137 ~LT~RE~eVL~lla~--G~snkeIA~~L-~iS~~TVk~h~~~I~~KL 180 (207)
T PRK15411 137 SLSRTESSMLRMWMA--GQGTIQISDQM-NIKAKTVSSHKGNIKRKI 180 (207)
T ss_pred cCCHHHHHHHHHHHc--CCCHHHHHHHc-CCCHHHHHHHHHHHHHHh
Confidence 489989888877776 66778999999 999999999987777664
No 130
>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=27.64 E-value=53 Score=26.08 Aligned_cols=27 Identities=15% Similarity=0.365 Sum_probs=21.5
Q ss_pred HHHHHHHHhhhCCchhhhcccCCCCCHH
Q 045583 76 DHVICTLYSQIGSRWSIIASRLPGRTDN 103 (319)
Q Consensus 76 D~~Ll~lv~~~G~kWs~IA~~lpgRT~~ 103 (319)
|-.|..++..+|..|.++|..| |=+..
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L-~vs~~ 30 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL-QFSVE 30 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc-CCCHH
Confidence 4567778889999999999998 54443
No 131
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=27.64 E-value=96 Score=24.33 Aligned_cols=39 Identities=18% Similarity=0.295 Sum_probs=27.1
Q ss_pred HHHHHHHhhhC--------CchhhhcccCCC-----CCHHHHHHHHHHHhhh
Q 045583 77 HVICTLYSQIG--------SRWSIIASRLPG-----RTDNDVKNYWNTKLKK 115 (319)
Q Consensus 77 ~~Ll~lv~~~G--------~kWs~IA~~lpg-----RT~~qcKnRW~~~lkk 115 (319)
-.|..+|.+.| .+|..||..|.- ....++|..|...|..
T Consensus 35 ~~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~ 86 (93)
T smart00501 35 YRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLP 86 (93)
T ss_pred HHHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHH
Confidence 34666677666 369999998822 2356788888877654
No 132
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=27.31 E-value=1.1e+02 Score=28.12 Aligned_cols=44 Identities=23% Similarity=0.321 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHHhhhH
Q 045583 70 NFTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTKLKKK 116 (319)
Q Consensus 70 ~WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkkk 116 (319)
..|+.|-+.|.-+++ |....+||+.| +-+...|+++...+++|-
T Consensus 133 ~LSpRErEVLrLLAq--GkTnKEIAe~L-~IS~rTVkth~srImkKL 176 (198)
T PRK15201 133 HFSVTERHLLKLIAS--GYHLSETAALL-SLSEEQTKSLRRSIMRKL 176 (198)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHHh
Confidence 488888887776666 88899999999 999999999988887764
No 133
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=26.80 E-value=93 Score=27.32 Aligned_cols=29 Identities=14% Similarity=-0.031 Sum_probs=23.1
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 86 IGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 86 ~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
.|-.+..||+.| |-+...|+++-...+++
T Consensus 151 ~g~s~~eIA~~l-gis~~tV~~~l~Ra~~~ 179 (196)
T PRK12524 151 EGLSNPEIAEVM-EIGVEAVESLTARGKRA 179 (196)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 467899999999 99999999887654433
No 134
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=26.58 E-value=81 Score=27.08 Aligned_cols=31 Identities=35% Similarity=0.464 Sum_probs=25.4
Q ss_pred CCchhhhcccCCCCCHHHHHHHHHHHhhhHHh
Q 045583 87 GSRWSIIASRLPGRTDNDVKNYWNTKLKKKLL 118 (319)
Q Consensus 87 G~kWs~IA~~lpgRT~~qcKnRW~~~lkkkl~ 118 (319)
|-...+||+.+ |-+...|+++....++.-.+
T Consensus 135 g~s~~EIA~~l-gis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 135 GLTYSEIAHKL-GVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHH
Confidence 56789999999 99999999999777665433
No 135
>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=26.50 E-value=48 Score=29.17 Aligned_cols=46 Identities=20% Similarity=0.237 Sum_probs=32.1
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCCcccccccccC---cccccccccccc
Q 045583 12 VKRGPWSPEEDATLKRYVETHGTGGNWIALPQKAGL---KRCGKSCRLRWL 59 (319)
Q Consensus 12 lkkg~WT~EEDe~L~~lV~k~G~~~~W~~IA~~lg~---~Rt~kQCr~Rw~ 59 (319)
.+..+-|..|.+-|..+|++||. ++...+.-..+ ..|..||+.+..
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 55677899999999999999997 78887653321 234445544433
No 136
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=25.97 E-value=1e+02 Score=26.35 Aligned_cols=29 Identities=24% Similarity=0.211 Sum_probs=23.8
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 86 IGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 86 ~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
.|-....||+.| |-+...|+.+.+..+++
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 366789999999 99999999998765544
No 137
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=25.90 E-value=1.1e+02 Score=25.39 Aligned_cols=29 Identities=24% Similarity=0.239 Sum_probs=22.9
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 86 IGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 86 ~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
.|-....||+.+ |.+...|+++-...+++
T Consensus 121 ~~~s~~EIA~~l-~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 121 VGKTMGEIALET-EMTYYQVRWIYRQALEK 149 (154)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 356788999999 99999999987665544
No 138
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=25.61 E-value=38 Score=28.12 Aligned_cols=28 Identities=21% Similarity=0.073 Sum_probs=23.3
Q ss_pred CCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 87 GSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 87 G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
|-.+..||+.| |-+...|++++...+++
T Consensus 121 g~s~~eIA~~l-gis~~tv~~~l~Ra~~~ 148 (154)
T TIGR02950 121 EFSYKEIAELL-NLSLAKVKSNLFRARKE 148 (154)
T ss_pred cCcHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 55789999999 99999999998766544
No 139
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=24.74 E-value=1.1e+02 Score=26.30 Aligned_cols=28 Identities=21% Similarity=0.305 Sum_probs=23.0
Q ss_pred CCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 87 GSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 87 G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
|-.-..||+.| |.+...|+++....+++
T Consensus 145 g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 172 (179)
T PRK12514 145 GLSYKELAERH-DVPLNTMRTWLRRSLLK 172 (179)
T ss_pred CCCHHHHHHHH-CCChHHHHHHHHHHHHH
Confidence 56788999999 99999999998665543
No 140
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=24.38 E-value=1e+02 Score=26.90 Aligned_cols=26 Identities=12% Similarity=0.123 Sum_probs=21.8
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHH
Q 045583 86 IGSRWSIIASRLPGRTDNDVKNYWNTK 112 (319)
Q Consensus 86 ~G~kWs~IA~~lpgRT~~qcKnRW~~~ 112 (319)
.|-.-..||+.| |-+...|+.+....
T Consensus 151 ~g~s~~EIA~~l-gis~~tVk~~l~Ra 176 (195)
T PRK12532 151 LGFSSDEIQQMC-GISTSNYHTIMHRA 176 (195)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 366789999999 99999999988654
No 141
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=24.04 E-value=1.2e+02 Score=25.51 Aligned_cols=28 Identities=29% Similarity=0.265 Sum_probs=22.4
Q ss_pred CCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 87 GSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 87 G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
|-+...||+.| |-+...|+++-...+++
T Consensus 138 g~s~~eIA~~l-~is~~tv~~~l~ra~~~ 165 (170)
T TIGR02952 138 NLPIAEVARIL-GKTEGAVKILQFRAIKK 165 (170)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 66788999999 99999999987655544
No 142
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=23.90 E-value=1.1e+02 Score=26.78 Aligned_cols=30 Identities=10% Similarity=0.079 Sum_probs=24.4
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhhH
Q 045583 86 IGSRWSIIASRLPGRTDNDVKNYWNTKLKKK 116 (319)
Q Consensus 86 ~G~kWs~IA~~lpgRT~~qcKnRW~~~lkkk 116 (319)
.|-.-.+||+.| |-+...|+.+....+++-
T Consensus 145 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~L 174 (185)
T PRK09649 145 LGLSYADAAAVC-GCPVGTIRSRVARARDAL 174 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 356789999999 999999999987666543
No 143
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=23.48 E-value=1.1e+02 Score=26.47 Aligned_cols=28 Identities=7% Similarity=-0.020 Sum_probs=22.1
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhh
Q 045583 86 IGSRWSIIASRLPGRTDNDVKNYWNTKLK 114 (319)
Q Consensus 86 ~G~kWs~IA~~lpgRT~~qcKnRW~~~lk 114 (319)
.|.....||+.| |-+...|+++.+..++
T Consensus 143 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~ 170 (186)
T PRK05602 143 QGLSNIEAAAVM-DISVDALESLLARGRR 170 (186)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHH
Confidence 466788999999 9999999988765543
No 144
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=23.34 E-value=1.3e+02 Score=25.30 Aligned_cols=30 Identities=30% Similarity=0.349 Sum_probs=24.2
Q ss_pred hhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 85 QIGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 85 ~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
..|-...+||+.+ |-+...|+.|....+++
T Consensus 127 ~~g~s~~EIA~~l-~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 127 VDGLGYGEIATEL-GISLATVKRYLNKAAMR 156 (161)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3467889999999 99999999998766544
No 145
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=23.33 E-value=81 Score=24.82 Aligned_cols=28 Identities=18% Similarity=0.570 Sum_probs=21.1
Q ss_pred HHHHHHhhhCCchhhhcccCCCCCHHHHH
Q 045583 78 VICTLYSQIGSRWSIIASRLPGRTDNDVK 106 (319)
Q Consensus 78 ~Ll~lv~~~G~kWs~IA~~lpgRT~~qcK 106 (319)
.+--++...|..|..+|++| |=|+.+|.
T Consensus 4 ~f~~i~~~lG~~Wk~laR~L-Glse~~Id 31 (86)
T cd08306 4 AFDVICENVGRDWRKLARKL-GLSETKIE 31 (86)
T ss_pred HHHHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 34455677899999999999 77766654
No 146
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=23.18 E-value=1.2e+02 Score=25.89 Aligned_cols=29 Identities=24% Similarity=0.509 Sum_probs=23.7
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 86 IGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 86 ~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
.|-....||..| |-|...|+.+....+++
T Consensus 155 ~g~s~~eIA~~l-gis~~~v~~~l~Ra~~~ 183 (189)
T TIGR02984 155 EGLSFAEVAERM-DRSEGAVSMLWVRGLAR 183 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 466789999999 99999999998766554
No 147
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=23.14 E-value=1.2e+02 Score=26.18 Aligned_cols=29 Identities=21% Similarity=0.360 Sum_probs=23.6
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 86 IGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 86 ~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
.|-.-..||..| |-+...|+++....+++
T Consensus 137 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 165 (185)
T PRK12542 137 YNLTYQEISSVM-GITEANVRKQFERARKR 165 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466789999999 99999999988655443
No 148
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=22.82 E-value=1.2e+02 Score=26.08 Aligned_cols=30 Identities=23% Similarity=0.100 Sum_probs=24.5
Q ss_pred hhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 85 QIGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 85 ~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
..|-....||+.| |.+...|+++-+..+++
T Consensus 143 ~~g~s~~EIA~~l-~is~~tV~~~l~rar~~ 172 (181)
T PRK12536 143 LEGLSVAETAQLT-GLSESAVKVGIHRGLKA 172 (181)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3467899999999 99999999998665544
No 149
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=22.75 E-value=1.4e+02 Score=27.17 Aligned_cols=44 Identities=27% Similarity=0.234 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHHhhhH
Q 045583 70 NFTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTKLKKK 116 (319)
Q Consensus 70 ~WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkkk 116 (319)
..|+.|-+.|.-++. |....+||+.| +-+...+|++...+++|-
T Consensus 155 ~Lt~rE~~Vl~l~~~--G~s~~eIA~~L-~iS~~TVk~~~~~i~~Kl 198 (216)
T PRK10100 155 LLTHREKEILNKLRI--GASNNEIARSL-FISENTVKTHLYNLFKKI 198 (216)
T ss_pred CCCHHHHHHHHHHHc--CCCHHHHHHHh-CCCHHHHHHHHHHHHHHh
Confidence 478877666655555 88889999999 999999999998887764
No 150
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=22.68 E-value=1.2e+02 Score=25.37 Aligned_cols=38 Identities=18% Similarity=0.145 Sum_probs=27.3
Q ss_pred HHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 77 HVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 77 ~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
..++.+....|-.=..||..| |-+...|+++....+++
T Consensus 116 r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~ra~~~ 153 (162)
T TIGR02983 116 RAVVVLRYYEDLSEAQVAEAL-GISVGTVKSRLSRALAR 153 (162)
T ss_pred HHHhhhHHHhcCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 333434344466778999999 99999999998766554
No 151
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=22.49 E-value=1.3e+02 Score=26.53 Aligned_cols=30 Identities=17% Similarity=0.101 Sum_probs=23.7
Q ss_pred hhhCCchhhhcccCCCCCHHHHHHHHHHHhh
Q 045583 84 SQIGSRWSIIASRLPGRTDNDVKNYWNTKLK 114 (319)
Q Consensus 84 ~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lk 114 (319)
...|-...+||+.| |-+...||.+-...++
T Consensus 129 ~~~g~s~~EIA~~L-gis~~tVk~~l~Rar~ 158 (187)
T PRK12516 129 GASGFAYEEAAEIC-GCAVGTIKSRVNRARQ 158 (187)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 33477899999999 9999999998765443
No 152
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=22.28 E-value=1.7e+02 Score=16.68 Aligned_cols=36 Identities=22% Similarity=0.258 Sum_probs=21.9
Q ss_pred CCCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHH
Q 045583 70 NFTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKN 107 (319)
Q Consensus 70 ~WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKn 107 (319)
.++.++-..+++++ .-|..+..||+.+ |.+...+.+
T Consensus 5 ~~~~~~~~~i~~~~-~~~~s~~~ia~~~-~is~~tv~~ 40 (42)
T cd00569 5 KLTPEQIEEARRLL-AAGESVAEIARRL-GVSRSTLYR 40 (42)
T ss_pred cCCHHHHHHHHHHH-HcCCCHHHHHHHH-CCCHHHHHH
Confidence 35555544555544 3456788888888 666665544
No 153
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=22.19 E-value=1.4e+02 Score=25.34 Aligned_cols=29 Identities=14% Similarity=0.094 Sum_probs=23.4
Q ss_pred hCCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 86 IGSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 86 ~G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
.|-....||+.+ |-+...|+++-...+++
T Consensus 127 ~g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 155 (164)
T PRK12547 127 SGFSYEDAAAIC-GCAVGTIKSRVSRARNR 155 (164)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 466789999999 99999999988665544
No 154
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.13 E-value=1.6e+02 Score=23.75 Aligned_cols=46 Identities=20% Similarity=0.352 Sum_probs=35.6
Q ss_pred CCCCCHHHHHHHHHHHhhhCCchhhhcccCCCC-CHHHHHHHHHHHhhh
Q 045583 68 HGNFTEDEDHVICTLYSQIGSRWSIIASRLPGR-TDNDVKNYWNTKLKK 115 (319)
Q Consensus 68 rg~WT~EED~~Ll~lv~~~G~kWs~IA~~lpgR-T~~qcKnRW~~~lkk 115 (319)
+..||.|.-..+++++.+-|..=+.||+.+ |- ..++++ +|...+..
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~-~W~~~~~~ 51 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLY-KWRIQLQK 51 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHH-HHHHHHHH
Confidence 567999999999999999888888999999 76 555554 45444433
No 155
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.61 E-value=1.4e+02 Score=25.70 Aligned_cols=41 Identities=22% Similarity=0.483 Sum_probs=25.3
Q ss_pred HHHHHHHHHhhh--CCchhhhcccCCCCCHHHHHHHHHHHhhhHH
Q 045583 75 EDHVICTLYSQI--GSRWSIIASRLPGRTDNDVKNYWNTKLKKKL 117 (319)
Q Consensus 75 ED~~Ll~lv~~~--G~kWs~IA~~lpgRT~~qcKnRW~~~lkkkl 117 (319)
|++.++++.-.- |..|..||..+ +-+..+|+. |+.-+|..+
T Consensus 85 e~k~Ii~lry~~r~~~TW~~IA~~l-~i~erta~r-~~~~fK~~i 127 (130)
T PF05263_consen 85 EEKRIIKLRYDRRSRRTWYQIAQKL-HISERTARR-WRDRFKNDI 127 (130)
T ss_pred HHHHHHHHHHcccccchHHHHHHHh-CccHHHHHH-HHHHHHHHh
Confidence 456666654332 36799999988 555656654 545555543
No 156
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=21.53 E-value=1.4e+02 Score=25.71 Aligned_cols=28 Identities=21% Similarity=0.144 Sum_probs=22.8
Q ss_pred CCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 87 GSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 87 G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
|-.-..||+.+ |-|...|+.+.+..+++
T Consensus 151 ~~s~~eIA~~l-gis~~~V~~~l~ra~~~ 178 (186)
T PRK13919 151 GYTHREAAQLL-GLPLGTLKTRARRALSR 178 (186)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 45678999999 99999999998766554
No 157
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=21.24 E-value=1.7e+02 Score=24.40 Aligned_cols=45 Identities=24% Similarity=0.219 Sum_probs=35.5
Q ss_pred CCCCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHHhhhH
Q 045583 69 GNFTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTKLKKK 116 (319)
Q Consensus 69 g~WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~lkkk 116 (319)
...|+.|-+.|.-+.. |-....||..+ +-+...++.+...+++|-
T Consensus 136 ~~Lt~~E~~il~~l~~--g~~~~~Ia~~l-~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 136 DPLTKRERQVAEKLAQ--GMAVKEIAAEL-GLSPKTVHVHRANLMEKL 180 (196)
T ss_pred cCCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHHh
Confidence 4688888877766665 55778999999 789999999987777663
No 158
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=20.73 E-value=74 Score=23.60 Aligned_cols=26 Identities=27% Similarity=0.680 Sum_probs=19.1
Q ss_pred HHHHHhhhCCchhhhcccCCCCCHHHH
Q 045583 79 ICTLYSQIGSRWSIIASRLPGRTDNDV 105 (319)
Q Consensus 79 Ll~lv~~~G~kWs~IA~~lpgRT~~qc 105 (319)
+..++..+|..|..+|..| |=+..+|
T Consensus 2 ~~~ia~~lg~~W~~la~~L-gl~~~~I 27 (79)
T cd01670 2 LDKLAKKLGKDWKKLARKL-GLSDGEI 27 (79)
T ss_pred HHHHHHHHhhHHHHHHHHh-CCCHHHH
Confidence 4456778899999999998 4444444
No 159
>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.72 E-value=79 Score=27.97 Aligned_cols=37 Identities=32% Similarity=0.440 Sum_probs=30.4
Q ss_pred CCCHHHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHH
Q 045583 70 NFTEDEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKN 107 (319)
Q Consensus 70 ~WT~EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKn 107 (319)
.||+|-.+.|.+|..+ |-.=++||.+|.|=+.+.+--
T Consensus 2 nWtdERve~LkKLWse-GLSASQIAaQLGGVsRnAVIG 38 (169)
T COG5352 2 NWTDERVETLKKLWSE-GLSASQIAAQLGGVSRNAVIG 38 (169)
T ss_pred CchHHHHHHHHHHHHc-ccCHHHHHHHhcCcchhhhhe
Confidence 5999999999988776 667789999998888776644
No 160
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=20.71 E-value=1.6e+02 Score=24.66 Aligned_cols=28 Identities=25% Similarity=0.254 Sum_probs=22.0
Q ss_pred CCchhhhcccCCCCCHHHHHHHHHHHhhh
Q 045583 87 GSRWSIIASRLPGRTDNDVKNYWNTKLKK 115 (319)
Q Consensus 87 G~kWs~IA~~lpgRT~~qcKnRW~~~lkk 115 (319)
|-.-..||..| |-+...|+.|....+++
T Consensus 121 ~~s~~eIA~~l-gis~~tv~~~l~ra~~~ 148 (159)
T PRK12527 121 GLSHQQIAEHL-GISRSLVEKHIVNAMKH 148 (159)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 45668999999 99999999997655443
No 161
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=20.65 E-value=1.4e+02 Score=26.40 Aligned_cols=32 Identities=19% Similarity=0.077 Sum_probs=24.0
Q ss_pred CCchhhhcccCCCCCHHHHHHHHHHH---hhhHHhc
Q 045583 87 GSRWSIIASRLPGRTDNDVKNYWNTK---LKKKLLA 119 (319)
Q Consensus 87 G~kWs~IA~~lpgRT~~qcKnRW~~~---lkkkl~~ 119 (319)
|-.-..||..| |.+...||.|.... |++.+..
T Consensus 155 g~s~~EIA~~l-gis~~tVk~~l~RAr~~Lr~~l~~ 189 (201)
T PRK12545 155 DFEIDDICTEL-TLTANHCSVLLYRARTRLRTCLSE 189 (201)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHHHHHH
Confidence 56789999999 99999999987544 4444443
No 162
>PRK00118 putative DNA-binding protein; Validated
Probab=20.57 E-value=1.6e+02 Score=24.35 Aligned_cols=39 Identities=13% Similarity=0.072 Sum_probs=31.1
Q ss_pred HHHHHHHHHHhhhCCchhhhcccCCCCCHHHHHHHHHHHh
Q 045583 74 DEDHVICTLYSQIGSRWSIIASRLPGRTDNDVKNYWNTKL 113 (319)
Q Consensus 74 EED~~Ll~lv~~~G~kWs~IA~~lpgRT~~qcKnRW~~~l 113 (319)
+.+..++.+....|.....||+.+ |-|...|+.+-...+
T Consensus 20 ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~RAr 58 (104)
T PRK00118 20 EKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKRTE 58 (104)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 456667777777788999999999 999999988865543
No 163
>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=20.24 E-value=1.9e+02 Score=28.78 Aligned_cols=87 Identities=21% Similarity=0.373 Sum_probs=59.8
Q ss_pred cCCCCHHHHHHHHHHHHHh-CC-CCCcccccccccCcccccccccccccccCCCCCCCCCCHHHHHHHHHHHhh-h----
Q 045583 14 RGPWSPEEDATLKRYVETH-GT-GGNWIALPQKAGLKRCGKSCRLRWLNYLRPDIKHGNFTEDEDHVICTLYSQ-I---- 86 (319)
Q Consensus 14 kg~WT~EEDe~L~~lV~k~-G~-~~~W~~IA~~lg~~Rt~kQCr~Rw~n~L~p~lkrg~WT~EED~~Ll~lv~~-~---- 86 (319)
-..||.-|...|+++.+.. |. .-+-.+|++.+. +|+..+++. |.+.|+ ++.+.+++.+ +
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 4579999999999998765 42 123456677776 888887776 334442 3444455444 1
Q ss_pred -CCc------------hhhhcccCCCCCHHHHHHHHHHHhh
Q 045583 87 -GSR------------WSIIASRLPGRTDNDVKNYWNTKLK 114 (319)
Q Consensus 87 -G~k------------Ws~IA~~lpgRT~~qcKnRW~~~lk 114 (319)
|.+ |..+|+.+.|.-...+-.-|-.+|.
T Consensus 87 ~~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~ 127 (344)
T PF11035_consen 87 KGPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLT 127 (344)
T ss_pred ccccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHH
Confidence 221 9999999999999998888866653
Done!