Query 022144
Match_columns 302
No_of_seqs 254 out of 1312
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 08:22:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022144.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022144hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0048 Transcription factor, 100.0 2.7E-35 5.7E-40 270.6 10.2 111 7-117 4-115 (238)
2 PLN03212 Transcription repress 100.0 6E-33 1.3E-37 254.1 12.9 112 6-117 19-131 (249)
3 PLN03091 hypothetical protein; 100.0 3.6E-31 7.7E-36 258.1 12.8 110 7-116 9-119 (459)
4 KOG0049 Transcription factor, 99.8 7.3E-19 1.6E-23 177.5 6.3 99 6-104 354-453 (939)
5 KOG0049 Transcription factor, 99.7 1.4E-17 3.1E-22 168.3 9.1 112 10-121 303-418 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.7 1E-16 2.2E-21 117.0 5.1 60 15-75 1-60 (60)
7 COG5147 REB1 Myb superfamily p 99.6 1.7E-15 3.8E-20 152.1 7.3 108 7-114 15-122 (512)
8 KOG0050 mRNA splicing protein 99.5 8.6E-15 1.9E-19 145.3 4.3 108 10-118 5-112 (617)
9 PF00249 Myb_DNA-binding: Myb- 99.4 3.3E-14 7.2E-19 99.9 1.5 47 12-58 1-48 (48)
10 PF00249 Myb_DNA-binding: Myb- 99.4 3.5E-13 7.7E-18 94.6 5.9 46 64-109 1-48 (48)
11 PF13921 Myb_DNA-bind_6: Myb-l 99.4 7E-13 1.5E-17 96.7 5.0 55 67-121 1-55 (60)
12 KOG0051 RNA polymerase I termi 99.4 9.5E-13 2.1E-17 133.9 7.1 103 11-115 383-513 (607)
13 PLN03212 Transcription repress 99.3 8.1E-12 1.8E-16 115.3 6.5 76 42-124 10-87 (249)
14 smart00717 SANT SANT SWI3, AD 99.2 1.9E-11 4.2E-16 83.2 5.9 47 64-110 1-48 (49)
15 smart00717 SANT SANT SWI3, AD 99.1 3E-11 6.6E-16 82.2 3.7 48 12-59 1-48 (49)
16 PLN03091 hypothetical protein; 99.1 5E-11 1.1E-15 117.5 5.7 66 58-123 8-75 (459)
17 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 1.4E-10 3E-15 77.9 5.7 44 66-109 1-45 (45)
18 KOG0048 Transcription factor, 99.1 9.8E-11 2.1E-15 108.0 4.4 64 61-124 6-71 (238)
19 cd00167 SANT 'SWI3, ADA2, N-Co 99.0 2.3E-10 5E-15 76.8 3.3 45 14-58 1-45 (45)
20 KOG0051 RNA polymerase I termi 99.0 1.3E-09 2.8E-14 111.3 8.5 99 12-113 308-432 (607)
21 COG5147 REB1 Myb superfamily p 98.2 1.6E-07 3.4E-12 95.2 -1.5 101 8-110 287-397 (512)
22 TIGR01557 myb_SHAQKYF myb-like 98.0 1.4E-05 2.9E-10 58.8 6.0 48 63-110 2-55 (57)
23 KOG0457 Histone acetyltransfer 97.8 3.4E-05 7.3E-10 76.5 6.6 51 61-111 69-120 (438)
24 PF13325 MCRS_N: N-terminal re 97.8 8.2E-05 1.8E-09 67.5 7.5 98 14-113 1-130 (199)
25 KOG0457 Histone acetyltransfer 97.7 2E-05 4.3E-10 78.1 3.0 52 7-58 67-118 (438)
26 KOG0050 mRNA splicing protein 97.6 3.5E-05 7.6E-10 77.8 3.4 61 62-122 5-66 (617)
27 TIGR01557 myb_SHAQKYF myb-like 97.6 4.8E-05 1E-09 55.9 3.1 47 12-58 3-54 (57)
28 TIGR02894 DNA_bind_RsfA transc 97.4 0.00019 4.1E-09 63.0 4.3 53 63-116 3-62 (161)
29 COG5259 RSC8 RSC chromatin rem 97.2 0.0002 4.4E-09 71.7 2.8 46 11-57 278-323 (531)
30 COG5259 RSC8 RSC chromatin rem 97.1 0.0005 1.1E-08 68.9 4.5 45 63-107 278-322 (531)
31 KOG1279 Chromatin remodeling f 97.1 0.00066 1.4E-08 69.3 5.1 46 62-107 251-296 (506)
32 KOG1279 Chromatin remodeling f 97.0 0.00041 8.9E-09 70.7 3.2 49 8-57 249-297 (506)
33 PF13837 Myb_DNA-bind_4: Myb/S 97.0 0.00087 1.9E-08 51.8 3.9 49 64-112 1-67 (90)
34 PF08914 Myb_DNA-bind_2: Rap1 96.9 0.0017 3.7E-08 48.9 4.6 50 64-113 2-61 (65)
35 PRK13923 putative spore coat p 96.9 0.0011 2.3E-08 58.9 3.9 53 62-115 3-62 (170)
36 PLN03142 Probable chromatin-re 96.7 0.0036 7.9E-08 68.9 7.3 100 13-112 825-987 (1033)
37 COG5114 Histone acetyltransfer 96.6 0.0027 5.9E-08 61.3 4.5 47 64-110 63-110 (432)
38 PF08914 Myb_DNA-bind_2: Rap1 96.4 0.001 2.2E-08 50.1 0.7 51 12-62 2-61 (65)
39 PF13873 Myb_DNA-bind_5: Myb/S 96.2 0.015 3.3E-07 44.1 6.0 48 64-111 2-71 (78)
40 PF13837 Myb_DNA-bind_4: Myb/S 96.2 0.0023 5E-08 49.4 1.4 46 12-57 1-63 (90)
41 TIGR02894 DNA_bind_RsfA transc 95.9 0.0046 9.9E-08 54.4 2.1 49 11-60 3-57 (161)
42 COG5114 Histone acetyltransfer 95.4 0.0058 1.3E-07 59.1 1.0 47 13-59 64-110 (432)
43 PF13873 Myb_DNA-bind_5: Myb/S 95.3 0.0065 1.4E-07 46.2 0.8 47 12-58 2-69 (78)
44 PF09111 SLIDE: SLIDE; InterP 94.9 0.058 1.3E-06 45.2 5.5 52 61-112 46-113 (118)
45 PRK13923 putative spore coat p 94.4 0.015 3.3E-07 51.6 0.9 48 11-59 4-57 (170)
46 KOG2656 DNA methyltransferase 94.4 0.031 6.6E-07 55.3 2.9 84 32-115 73-187 (445)
47 PF12776 Myb_DNA-bind_3: Myb/S 93.7 0.19 4.1E-06 39.2 5.7 45 66-110 1-63 (96)
48 KOG4282 Transcription factor G 91.5 0.3 6.5E-06 47.3 5.1 49 64-112 54-116 (345)
49 KOG1194 Predicted DNA-binding 91.3 0.6 1.3E-05 47.3 6.9 50 63-112 186-235 (534)
50 PF08281 Sigma70_r4_2: Sigma-7 91.1 0.66 1.4E-05 32.4 5.3 42 69-111 12-53 (54)
51 COG5118 BDP1 Transcription ini 90.3 0.22 4.7E-06 49.4 2.8 44 13-57 366-409 (507)
52 COG5118 BDP1 Transcription ini 89.0 0.8 1.7E-05 45.6 5.6 48 64-111 365-412 (507)
53 PF11626 Rap1_C: TRF2-interact 87.4 0.82 1.8E-05 35.9 3.8 31 8-41 43-81 (87)
54 KOG4282 Transcription factor G 84.8 0.57 1.2E-05 45.3 2.1 46 13-58 55-113 (345)
55 PF09111 SLIDE: SLIDE; InterP 84.8 1.1 2.3E-05 37.7 3.4 34 9-42 46-82 (118)
56 KOG4167 Predicted DNA-binding 83.5 0.78 1.7E-05 49.0 2.5 42 13-55 620-661 (907)
57 PF12776 Myb_DNA-bind_3: Myb/S 82.1 1.1 2.4E-05 34.7 2.4 43 14-56 1-60 (96)
58 KOG4468 Polycomb-group transcr 79.7 2.7 5.8E-05 44.2 4.7 52 63-114 87-148 (782)
59 PF04545 Sigma70_r4: Sigma-70, 78.7 7.5 0.00016 26.7 5.5 41 70-111 7-47 (50)
60 KOG4329 DNA-binding protein [G 77.1 25 0.00053 35.3 10.3 42 65-106 278-320 (445)
61 smart00595 MADF subfamily of S 76.3 4.7 0.0001 30.9 4.3 23 86-109 30-52 (89)
62 KOG4167 Predicted DNA-binding 76.0 4.8 0.0001 43.3 5.4 43 65-107 620-662 (907)
63 PF11035 SnAPC_2_like: Small n 74.2 93 0.002 30.6 13.2 86 13-111 22-128 (344)
64 PF13404 HTH_AsnC-type: AsnC-t 73.5 12 0.00026 25.5 5.2 38 70-108 3-41 (42)
65 PRK11179 DNA-binding transcrip 72.3 8.7 0.00019 32.8 5.4 45 69-114 8-53 (153)
66 KOG3841 TEF-1 and related tran 72.3 10 0.00022 37.9 6.4 56 62-117 74-150 (455)
67 PF07750 GcrA: GcrA cell cycle 71.1 5.5 0.00012 35.0 3.9 41 66-107 2-42 (162)
68 TIGR02985 Sig70_bacteroi1 RNA 69.8 12 0.00026 30.7 5.5 38 73-111 119-156 (161)
69 PF04504 DUF573: Protein of un 69.6 10 0.00022 30.6 4.8 48 64-111 4-64 (98)
70 PRK11169 leucine-responsive tr 68.2 10 0.00022 32.8 5.0 45 69-114 13-58 (164)
71 KOG1194 Predicted DNA-binding 66.7 4.6 9.9E-05 41.2 2.7 44 11-55 186-229 (534)
72 PF11626 Rap1_C: TRF2-interact 65.2 4.4 9.5E-05 31.8 1.9 17 60-76 43-59 (87)
73 PF13325 MCRS_N: N-terminal re 64.8 12 0.00026 34.2 4.8 46 66-112 1-49 (199)
74 KOG3554 Histone deacetylase co 63.7 16 0.00034 37.7 5.8 79 36-124 267-353 (693)
75 PF01388 ARID: ARID/BRIGHT DNA 60.6 19 0.00041 27.8 4.7 37 74-110 40-89 (92)
76 KOG1878 Nuclear receptor coreg 59.1 5.5 0.00012 45.7 1.9 43 11-54 224-266 (1672)
77 TIGR02937 sigma70-ECF RNA poly 58.7 23 0.0005 28.0 5.1 37 74-111 117-153 (158)
78 cd06171 Sigma70_r4 Sigma70, re 58.6 35 0.00075 22.1 5.2 41 67-109 11-51 (55)
79 cd08319 Death_RAIDD Death doma 58.1 15 0.00032 28.9 3.7 29 72-101 2-30 (83)
80 KOG4468 Polycomb-group transcr 58.1 7.5 0.00016 41.0 2.5 47 11-58 87-143 (782)
81 PF13404 HTH_AsnC-type: AsnC-t 58.1 6.1 0.00013 27.0 1.3 38 18-56 3-40 (42)
82 KOG4329 DNA-binding protein [G 54.8 9 0.0002 38.2 2.4 41 13-54 278-319 (445)
83 PRK12529 RNA polymerase sigma 54.6 32 0.0007 29.6 5.6 39 76-115 136-174 (178)
84 PRK09652 RNA polymerase sigma 54.6 30 0.00064 29.0 5.3 31 80-111 141-171 (182)
85 smart00344 HTH_ASNC helix_turn 53.9 34 0.00074 26.9 5.3 46 69-115 2-48 (108)
86 PRK11179 DNA-binding transcrip 53.7 8.2 0.00018 33.0 1.7 44 17-61 8-51 (153)
87 PF11035 SnAPC_2_like: Small n 53.4 39 0.00084 33.2 6.3 48 64-111 21-72 (344)
88 smart00501 BRIGHT BRIGHT, ARID 52.6 34 0.00073 26.7 5.0 38 74-111 36-86 (93)
89 PF02954 HTH_8: Bacterial regu 52.3 38 0.00083 22.7 4.5 34 71-105 6-39 (42)
90 PRK04217 hypothetical protein; 51.6 40 0.00087 27.9 5.4 45 65-111 41-85 (110)
91 PRK11924 RNA polymerase sigma 50.9 35 0.00075 28.5 5.2 29 81-110 139-167 (179)
92 PRK09643 RNA polymerase sigma 50.4 37 0.00079 29.7 5.4 30 79-109 146-175 (192)
93 KOG2009 Transcription initiati 49.6 18 0.00038 38.1 3.6 50 62-111 407-456 (584)
94 PRK11169 leucine-responsive tr 49.6 8.1 0.00018 33.4 1.0 45 17-62 13-57 (164)
95 COG2963 Transposase and inacti 49.6 54 0.0012 26.3 5.9 48 64-112 5-53 (116)
96 PF10545 MADF_DNA_bdg: Alcohol 47.7 21 0.00046 26.3 3.0 25 86-110 29-54 (85)
97 PRK09641 RNA polymerase sigma 47.2 42 0.00091 28.6 5.1 29 82-111 151-179 (187)
98 PRK09047 RNA polymerase factor 46.8 49 0.0011 27.4 5.4 30 81-111 120-149 (161)
99 cd08803 Death_ank3 Death domai 46.6 33 0.00071 27.0 4.0 29 72-101 4-32 (84)
100 PF09420 Nop16: Ribosome bioge 46.5 49 0.0011 28.8 5.5 48 62-109 112-163 (164)
101 PRK12523 RNA polymerase sigma 45.4 53 0.0011 27.9 5.5 39 73-112 125-163 (172)
102 KOG0384 Chromodomain-helicase 45.3 30 0.00064 39.6 4.7 70 13-88 1134-1204(1373)
103 TIGR02954 Sig70_famx3 RNA poly 45.2 48 0.001 27.9 5.2 30 81-111 133-162 (169)
104 PF07638 Sigma70_ECF: ECF sigm 45.2 50 0.0011 28.9 5.4 38 71-109 139-176 (185)
105 TIGR02943 Sig70_famx1 RNA poly 45.2 51 0.0011 28.7 5.4 35 76-111 140-174 (188)
106 TIGR02939 RpoE_Sigma70 RNA pol 44.9 40 0.00086 28.8 4.7 29 82-111 153-181 (190)
107 PF09905 DUF2132: Uncharacteri 44.8 29 0.00064 26.2 3.2 23 20-45 12-34 (64)
108 PRK09645 RNA polymerase sigma 44.8 53 0.0012 27.7 5.4 31 80-111 131-161 (173)
109 cd08317 Death_ank Death domain 44.3 27 0.00058 26.9 3.1 28 72-100 4-31 (84)
110 KOG2656 DNA methyltransferase 44.0 5.7 0.00012 39.8 -0.9 45 12-57 130-180 (445)
111 PLN03162 golden-2 like transcr 43.7 1.7E+02 0.0038 29.5 9.2 46 64-109 237-287 (526)
112 PRK09637 RNA polymerase sigma 43.2 54 0.0012 28.4 5.3 30 81-111 120-149 (181)
113 PRK11923 algU RNA polymerase s 43.1 52 0.0011 28.4 5.2 29 82-111 153-181 (193)
114 PRK12515 RNA polymerase sigma 42.5 60 0.0013 28.0 5.5 30 81-111 145-174 (189)
115 PRK09648 RNA polymerase sigma 41.7 63 0.0014 27.8 5.5 30 81-111 153-182 (189)
116 TIGR02948 SigW_bacill RNA poly 41.6 53 0.0012 27.9 4.9 29 82-111 151-179 (187)
117 PRK12512 RNA polymerase sigma 41.6 62 0.0014 27.6 5.4 30 81-111 145-174 (184)
118 PRK09642 RNA polymerase sigma 41.2 66 0.0014 26.7 5.4 30 81-111 120-149 (160)
119 COG2197 CitB Response regulato 40.7 49 0.0011 29.7 4.8 45 65-112 147-191 (211)
120 cd08318 Death_NMPP84 Death dom 40.5 40 0.00086 26.3 3.6 25 76-101 11-35 (86)
121 PRK12530 RNA polymerase sigma 40.5 65 0.0014 28.0 5.4 29 81-110 148-176 (189)
122 KOG0385 Chromatin remodeling c 40.2 46 0.001 36.5 5.0 96 14-110 797-957 (971)
123 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 39.2 85 0.0018 22.5 4.8 35 70-105 7-41 (50)
124 PF09197 Rap1-DNA-bind: Rap1, 38.9 19 0.00042 29.7 1.6 17 14-30 1-17 (105)
125 smart00005 DEATH DEATH domain, 38.6 46 0.001 25.1 3.7 29 71-100 4-33 (88)
126 PRK12524 RNA polymerase sigma 38.2 74 0.0016 27.7 5.4 29 81-110 150-178 (196)
127 PRK12531 RNA polymerase sigma 38.2 76 0.0016 27.6 5.4 30 81-111 155-184 (194)
128 PF00196 GerE: Bacterial regul 37.1 57 0.0012 22.9 3.7 44 66-112 3-46 (58)
129 PRK12527 RNA polymerase sigma 36.9 89 0.0019 26.0 5.5 29 82-111 120-148 (159)
130 PRK06759 RNA polymerase factor 36.5 91 0.002 25.6 5.4 29 82-111 121-149 (154)
131 TIGR02999 Sig-70_X6 RNA polyme 36.4 87 0.0019 26.6 5.5 30 81-111 148-177 (183)
132 PF07750 GcrA: GcrA cell cycle 36.3 40 0.00088 29.6 3.4 38 14-53 2-39 (162)
133 PRK12516 RNA polymerase sigma 36.2 83 0.0018 27.4 5.4 37 73-110 122-158 (187)
134 PRK09649 RNA polymerase sigma 36.2 78 0.0017 27.4 5.2 31 81-112 144-174 (185)
135 PRK12528 RNA polymerase sigma 36.1 93 0.002 25.9 5.5 35 76-111 122-156 (161)
136 PRK12532 RNA polymerase sigma 35.5 80 0.0017 27.3 5.2 29 80-109 149-177 (195)
137 TIGR02952 Sig70_famx2 RNA poly 34.8 97 0.0021 25.7 5.4 29 82-111 137-165 (170)
138 PRK00118 putative DNA-binding 34.8 1.1E+02 0.0023 25.1 5.4 40 69-109 19-58 (104)
139 KOG2009 Transcription initiati 34.6 20 0.00044 37.7 1.4 48 8-56 405-452 (584)
140 PRK01905 DNA-binding protein F 34.5 1.1E+02 0.0023 23.3 5.1 37 69-106 36-72 (77)
141 cd08804 Death_ank2 Death domai 34.3 55 0.0012 25.5 3.5 31 72-103 4-34 (84)
142 PRK09651 RNA polymerase sigma 34.3 78 0.0017 26.9 4.8 29 82-111 134-162 (172)
143 PF04504 DUF573: Protein of un 34.1 55 0.0012 26.3 3.6 68 12-80 4-93 (98)
144 PRK12536 RNA polymerase sigma 33.9 98 0.0021 26.5 5.4 31 80-111 142-172 (181)
145 PRK12547 RNA polymerase sigma 33.8 1E+02 0.0022 25.9 5.5 31 80-111 125-155 (164)
146 cd08777 Death_RIP1 Death Domai 33.5 52 0.0011 25.8 3.3 29 74-103 4-32 (86)
147 PRK12514 RNA polymerase sigma 33.3 1E+02 0.0022 26.2 5.4 29 82-111 144-172 (179)
148 PRK12542 RNA polymerase sigma 32.8 1E+02 0.0022 26.4 5.4 30 81-111 136-165 (185)
149 PRK13919 putative RNA polymera 32.8 1.1E+02 0.0023 26.2 5.4 29 82-111 150-178 (186)
150 TIGR02950 SigM_subfam RNA poly 32.7 37 0.00081 27.9 2.5 28 83-111 121-148 (154)
151 PF09420 Nop16: Ribosome bioge 32.4 35 0.00076 29.7 2.4 31 10-41 112-142 (164)
152 TIGR02983 SigE-fam_strep RNA p 32.1 1E+02 0.0022 25.6 5.1 40 71-111 114-153 (162)
153 TIGR02984 Sig-70_plancto1 RNA 31.5 1.2E+02 0.0025 25.8 5.4 30 81-111 154-183 (189)
154 PF13936 HTH_38: Helix-turn-he 31.5 64 0.0014 21.9 3.1 38 65-104 3-40 (44)
155 PRK12520 RNA polymerase sigma 31.4 1.1E+02 0.0024 26.3 5.4 29 82-111 146-174 (191)
156 PRK12545 RNA polymerase sigma 31.3 1.1E+02 0.0024 26.9 5.4 27 82-109 154-180 (201)
157 cd08311 Death_p75NR Death doma 31.1 63 0.0014 25.0 3.3 33 69-103 2-34 (77)
158 TIGR02960 SigX5 RNA polymerase 30.6 92 0.002 29.2 5.0 29 82-111 157-185 (324)
159 PLN03142 Probable chromatin-re 30.6 93 0.002 35.2 5.7 42 66-107 826-868 (1033)
160 cd08779 Death_PIDD Death Domai 30.4 63 0.0014 25.2 3.2 21 73-93 3-23 (86)
161 PRK00430 fis global DNA-bindin 30.1 1.3E+02 0.0029 24.0 5.1 35 70-105 55-89 (95)
162 PRK12537 RNA polymerase sigma 29.9 1.2E+02 0.0026 25.9 5.3 30 81-111 147-176 (182)
163 cd00569 HTH_Hin_like Helix-tur 29.3 1.1E+02 0.0025 17.2 5.2 36 66-103 5-40 (42)
164 PRK12546 RNA polymerase sigma 29.2 1.1E+02 0.0025 26.7 5.1 31 79-110 125-155 (188)
165 PRK05602 RNA polymerase sigma 28.9 1.2E+02 0.0026 25.9 5.1 28 81-109 142-169 (186)
166 COG1522 Lrp Transcriptional re 28.8 1.4E+02 0.003 24.7 5.3 46 69-115 7-53 (154)
167 PF00046 Homeobox: Homeobox do 28.3 2E+02 0.0044 19.7 5.5 45 63-108 3-51 (57)
168 cd08805 Death_ank1 Death domai 28.2 77 0.0017 24.9 3.4 22 72-93 4-25 (84)
169 PRK10100 DNA-binding transcrip 28.1 1.3E+02 0.0027 27.3 5.3 44 66-112 155-198 (216)
170 PRK09647 RNA polymerase sigma 27.5 1.4E+02 0.0031 26.4 5.5 29 82-111 153-181 (203)
171 PRK11922 RNA polymerase sigma 26.8 77 0.0017 28.6 3.7 27 83-110 165-191 (231)
172 PRK09638 RNA polymerase sigma 26.6 67 0.0015 27.1 3.1 29 82-111 141-169 (176)
173 PRK06811 RNA polymerase factor 26.3 1.6E+02 0.0034 25.4 5.4 29 82-111 146-174 (189)
174 KOG0724 Zuotin and related mol 26.1 47 0.001 31.8 2.2 48 64-111 53-100 (335)
175 PRK09639 RNA polymerase sigma 25.9 1.6E+02 0.0036 24.3 5.3 29 82-111 126-154 (166)
176 PRK06986 fliA flagellar biosyn 25.8 1.4E+02 0.0031 26.8 5.2 37 74-111 191-227 (236)
177 cd08306 Death_FADD Fas-associa 25.7 98 0.0021 24.1 3.6 27 75-102 5-31 (86)
178 PRK13991 cell division topolog 25.6 90 0.0019 24.9 3.3 32 253-284 34-65 (87)
179 PRK09646 RNA polymerase sigma 25.3 1.7E+02 0.0036 25.4 5.4 29 82-111 157-185 (194)
180 PRK09636 RNA polymerase sigma 25.3 1.5E+02 0.0032 27.8 5.4 29 82-111 130-158 (293)
181 PRK12538 RNA polymerase sigma 25.2 1.3E+02 0.0028 27.4 4.9 29 82-111 186-214 (233)
182 smart00344 HTH_ASNC helix_turn 24.9 49 0.0011 25.9 1.8 43 18-61 3-45 (108)
183 PF13384 HTH_23: Homeodomain-l 24.6 1.1E+02 0.0024 20.5 3.4 30 73-104 8-37 (50)
184 PRK12519 RNA polymerase sigma 24.4 1.4E+02 0.003 25.7 4.7 29 82-111 156-184 (194)
185 KOG4834 Predicted DNA-binding 24.3 23 0.00049 33.4 -0.3 44 8-52 7-50 (280)
186 PRK12544 RNA polymerase sigma 24.2 1.8E+02 0.0038 25.9 5.5 29 82-111 163-191 (206)
187 PF09650 PHA_gran_rgn: Putativ 23.9 89 0.0019 24.6 3.1 21 255-275 65-85 (87)
188 PRK08241 RNA polymerase factor 23.8 1.3E+02 0.0028 28.5 4.8 30 82-112 168-197 (339)
189 PF10440 WIYLD: Ubiquitin-bind 23.7 52 0.0011 25.0 1.6 18 74-91 31-48 (65)
190 PRK09415 RNA polymerase factor 23.5 1.7E+02 0.0036 25.0 5.0 29 82-111 142-170 (179)
191 TIGR02957 SigX4 RNA polymerase 22.6 1.8E+02 0.0039 27.1 5.4 30 81-111 122-151 (281)
192 PRK10360 DNA-binding transcrip 22.6 2.2E+02 0.0047 23.5 5.5 45 65-112 136-180 (196)
193 PRK12526 RNA polymerase sigma 22.5 2E+02 0.0044 25.3 5.5 29 82-111 168-196 (206)
194 TIGR02980 SigBFG RNA polymeras 22.4 2E+02 0.0042 25.6 5.4 30 81-111 192-221 (227)
195 PRK12525 RNA polymerase sigma 22.4 2.2E+02 0.0048 23.9 5.5 30 82-112 133-162 (168)
196 PRK06930 positive control sigm 22.2 2.1E+02 0.0045 25.1 5.4 36 75-111 122-157 (170)
197 PRK09483 response regulator; P 22.0 1.4E+02 0.0031 25.1 4.3 45 65-112 147-191 (217)
198 TIGR02959 SigZ RNA polymerase 22.0 2.3E+02 0.0049 24.0 5.5 30 81-111 114-143 (170)
199 cd01670 Death Death Domain: a 21.6 1.1E+02 0.0023 22.5 3.0 19 75-93 2-20 (79)
200 PRK12511 RNA polymerase sigma 21.6 2.1E+02 0.0046 24.7 5.3 28 82-110 126-153 (182)
201 TIGR02989 Sig-70_gvs1 RNA poly 21.5 2.4E+02 0.0051 23.1 5.4 28 82-110 126-153 (159)
202 PRK15201 fimbriae regulatory p 21.5 2.4E+02 0.0051 25.9 5.6 44 66-112 133-176 (198)
203 PRK12541 RNA polymerase sigma 21.4 2.1E+02 0.0046 23.7 5.1 29 82-111 127-155 (161)
204 PRK12540 RNA polymerase sigma 21.4 2.1E+02 0.0047 24.7 5.3 28 81-109 125-152 (182)
205 PF09197 Rap1-DNA-bind: Rap1, 20.9 1.5E+02 0.0032 24.5 3.9 47 66-112 1-78 (105)
206 PRK08301 sporulation sigma fac 20.6 2.1E+02 0.0046 25.6 5.3 27 83-110 198-224 (234)
207 TIGR03001 Sig-70_gmx1 RNA poly 20.1 2.3E+02 0.0049 26.1 5.4 28 82-110 176-203 (244)
No 1
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=2.7e-35 Score=270.61 Aligned_cols=111 Identities=44% Similarity=0.833 Sum_probs=106.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHhhCC-CCCcccccccccccCCCCCCCCCCChHHHHHHHHHHHhcCCc
Q 022144 7 DVDRIKGPWSPEEDEALQRLVQNYGPRNWSLISKSIP-GRSGKSCRLRWCNQLSPQVEHRPFTPEEDETILRAHARFGNK 85 (302)
Q Consensus 7 ~~~~~Kg~WT~EED~~L~~lV~k~G~~nW~~IA~~lp-~Rt~kqCr~Rw~n~L~p~~kk~~WT~EED~~Ll~lv~~~Gnk 85 (302)
++.++||+||+|||++|+++|++||+++|..|++.++ +|++++||+||+|||+|+++++.||+|||++|+++|+.|||+
T Consensus 4 k~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNr 83 (238)
T KOG0048|consen 4 NPELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNR 83 (238)
T ss_pred CccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcH
Confidence 3446789999999999999999999999999999998 999999999999999999999999999999999999999999
Q ss_pred HHHHhhhcCCCCHHHHHHHHHHHhhhhccCCC
Q 022144 86 WATIARLLSGRTDNAIKNHWNSTLKRKCSSMS 117 (302)
Q Consensus 86 W~~IA~~l~gRT~~q~knRw~~~Lkrk~~~~~ 117 (302)
|+.||++|||||+++|||||+..+|+|+....
T Consensus 84 Ws~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 84 WSLIAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred HHHHHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 99999999999999999999999999987765
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=6e-33 Score=254.11 Aligned_cols=112 Identities=42% Similarity=0.778 Sum_probs=106.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHhhC-CCCCcccccccccccCCCCCCCCCCChHHHHHHHHHHHhcCC
Q 022144 6 KDVDRIKGPWSPEEDEALQRLVQNYGPRNWSLISKSI-PGRSGKSCRLRWCNQLSPQVEHRPFTPEEDETILRAHARFGN 84 (302)
Q Consensus 6 ~~~~~~Kg~WT~EED~~L~~lV~k~G~~nW~~IA~~l-p~Rt~kqCr~Rw~n~L~p~~kk~~WT~EED~~Ll~lv~~~Gn 84 (302)
.+..++|++||+|||++|+++|++||..+|..||+.+ ++|+++|||+||.++|+|.+++++||.|||++|++++.+||+
T Consensus 19 ~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~~Gn 98 (249)
T PLN03212 19 TKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLGN 98 (249)
T ss_pred ccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHhccc
Confidence 3567899999999999999999999999999999988 699999999999999999999999999999999999999999
Q ss_pred cHHHHhhhcCCCCHHHHHHHHHHHhhhhccCCC
Q 022144 85 KWATIARLLSGRTDNAIKNHWNSTLKRKCSSMS 117 (302)
Q Consensus 85 kW~~IA~~l~gRT~~q~knRw~~~Lkrk~~~~~ 117 (302)
+|..||++|+|||+++|||||+.++++++....
T Consensus 99 KWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~ 131 (249)
T PLN03212 99 RWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQG 131 (249)
T ss_pred cHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcC
Confidence 999999999999999999999999999876643
No 3
>PLN03091 hypothetical protein; Provisional
Probab=99.97 E-value=3.6e-31 Score=258.11 Aligned_cols=110 Identities=48% Similarity=0.843 Sum_probs=104.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHhhC-CCCCcccccccccccCCCCCCCCCCChHHHHHHHHHHHhcCCc
Q 022144 7 DVDRIKGPWSPEEDEALQRLVQNYGPRNWSLISKSI-PGRSGKSCRLRWCNQLSPQVEHRPFTPEEDETILRAHARFGNK 85 (302)
Q Consensus 7 ~~~~~Kg~WT~EED~~L~~lV~k~G~~nW~~IA~~l-p~Rt~kqCr~Rw~n~L~p~~kk~~WT~EED~~Ll~lv~~~Gnk 85 (302)
+..++||+||+|||++|+++|++||..+|..||+.+ ++|+++|||+||.++|+|.+++++||+|||++|++++++||++
T Consensus 9 KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k~~GnK 88 (459)
T PLN03091 9 KQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHAVLGNR 88 (459)
T ss_pred CCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHHHhCcc
Confidence 457889999999999999999999999999999988 5999999999999999999999999999999999999999999
Q ss_pred HHHHhhhcCCCCHHHHHHHHHHHhhhhccCC
Q 022144 86 WATIARLLSGRTDNAIKNHWNSTLKRKCSSM 116 (302)
Q Consensus 86 W~~IA~~l~gRT~~q~knRw~~~Lkrk~~~~ 116 (302)
|.+||++|+|||+++|||||+.+++++++..
T Consensus 89 WskIAk~LPGRTDnqIKNRWnslLKKklr~~ 119 (459)
T PLN03091 89 WSQIAAQLPGRTDNEIKNLWNSCLKKKLRQR 119 (459)
T ss_pred hHHHHHhcCCCCHHHHHHHHHHHHHHHHHHc
Confidence 9999999999999999999999999987643
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.75 E-value=7.3e-19 Score=177.48 Aligned_cols=99 Identities=31% Similarity=0.599 Sum_probs=93.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCcccccccccccCCCCCCCCCCChHHHHHHHHHHHhcC-C
Q 022144 6 KDVDRIKGPWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWCNQLSPQVEHRPFTPEEDETILRAHARFG-N 84 (302)
Q Consensus 6 ~~~~~~Kg~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~n~L~p~~kk~~WT~EED~~Ll~lv~~~G-n 84 (302)
-++.+++|+||++||.+|..+|++||.++|.+|-..+|||+..|||+||.|.|+...|++.||-.||+.|+.+|.+|| +
T Consensus 354 LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~~V~~YG~g 433 (939)
T KOG0049|consen 354 LDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLYAVKVYGKG 433 (939)
T ss_pred cCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHHhhccCceeecchHHHHHHHHHHccc
Confidence 368899999999999999999999999999999999999999999999999999999999999999999999999999 8
Q ss_pred cHHHHhhhcCCCCHHHHHHH
Q 022144 85 KWATIARLLSGRTDNAIKNH 104 (302)
Q Consensus 85 kW~~IA~~l~gRT~~q~knR 104 (302)
+|.+||.+|++||..|...|
T Consensus 434 ~WakcA~~Lp~~t~~q~~rr 453 (939)
T KOG0049|consen 434 NWAKCAMLLPKKTSRQLRRR 453 (939)
T ss_pred hHHHHHHHccccchhHHHHH
Confidence 99999999999999554433
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.71 E-value=1.4e-17 Score=168.26 Aligned_cols=112 Identities=26% Similarity=0.484 Sum_probs=103.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC---CCHHHHHhhCCCCCcccccccccccCCCCCCCCCCChHHHHHHHHHHHhcC-Cc
Q 022144 10 RIKGPWSPEEDEALQRLVQNYGP---RNWSLISKSIPGRSGKSCRLRWCNQLSPQVEHRPFTPEEDETILRAHARFG-NK 85 (302)
Q Consensus 10 ~~Kg~WT~EED~~L~~lV~k~G~---~nW~~IA~~lp~Rt~kqCr~Rw~n~L~p~~kk~~WT~EED~~Ll~lv~~~G-nk 85 (302)
+....||.|||.+|+++|..... .+|.+|-.+|+||+..|...||.+.|+|.+++|.||.+||.+|+.+|.+|| ..
T Consensus 303 L~ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kd 382 (939)
T KOG0049|consen 303 LSEKEWSEEEDTKLIALVKITSINSHIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKD 382 (939)
T ss_pred HHhhhcchhhhHHHHHHHHHhhccCccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccc
Confidence 34578999999999999998743 479999999999999999999999999999999999999999999999999 56
Q ss_pred HHHHhhhcCCCCHHHHHHHHHHHhhhhccCCCcccc
Q 022144 86 WATIARLLSGRTDNAIKNHWNSTLKRKCSSMSDESQ 121 (302)
Q Consensus 86 W~~IA~~l~gRT~~q~knRw~~~Lkrk~~~~~~~~~ 121 (302)
|.+|-..||||++.||+.||.+.|.+..+...|.-.
T Consensus 383 w~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~rW~l~ 418 (939)
T KOG0049|consen 383 WAKVRQAVPNRSDSQCRERYTNVLNRSAKVERWTLV 418 (939)
T ss_pred hhhHHHhcCCccHHHHHHHHHHHHHHhhccCceeec
Confidence 999999999999999999999999999888766543
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=99.66 E-value=1e-16 Score=117.02 Aligned_cols=60 Identities=43% Similarity=0.926 Sum_probs=54.9
Q ss_pred CCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCcccccccccccCCCCCCCCCCChHHHHHH
Q 022144 15 WSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWCNQLSPQVEHRPFTPEEDETI 75 (302)
Q Consensus 15 WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~n~L~p~~kk~~WT~EED~~L 75 (302)
||+|||++|+++|.+|| .+|..||+.|++|+..+|+.||.++|++.+++++||.+||++|
T Consensus 1 WT~eEd~~L~~~~~~~g-~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYG-NDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHT-S-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC-cCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 99999999999999999 5799999999779999999999999999999999999999987
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=99.59 E-value=1.7e-15 Score=152.09 Aligned_cols=108 Identities=33% Similarity=0.645 Sum_probs=103.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCcccccccccccCCCCCCCCCCChHHHHHHHHHHHhcCCcH
Q 022144 7 DVDRIKGPWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWCNQLSPQVEHRPFTPEEDETILRAHARFGNKW 86 (302)
Q Consensus 7 ~~~~~Kg~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~n~L~p~~kk~~WT~EED~~Ll~lv~~~GnkW 86 (302)
...++.|.|+..||+.|..+|+.||+.+|..||..+.-|++++|+.||.++++|.+++..|+.|||..|+.+..++|.+|
T Consensus 15 ~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~w 94 (512)
T COG5147 15 QTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQW 94 (512)
T ss_pred cceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCchh
Confidence 34688999999999999999999999999999999988999999999999999999999999999999999999999999
Q ss_pred HHHhhhcCCCCHHHHHHHHHHHhhhhcc
Q 022144 87 ATIARLLSGRTDNAIKNHWNSTLKRKCS 114 (302)
Q Consensus 87 ~~IA~~l~gRT~~q~knRw~~~Lkrk~~ 114 (302)
..||..+++||..+|.++|..++....+
T Consensus 95 stia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 95 STIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhccccCccchHHHHHHHHHHhhhhhc
Confidence 9999999999999999999999887765
No 8
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.51 E-value=8.6e-15 Score=145.33 Aligned_cols=108 Identities=30% Similarity=0.556 Sum_probs=102.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCcccccccccccCCCCCCCCCCChHHHHHHHHHHHhcCCcHHHH
Q 022144 10 RIKGPWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWCNQLSPQVEHRPFTPEEDETILRAHARFGNKWATI 89 (302)
Q Consensus 10 ~~Kg~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~n~L~p~~kk~~WT~EED~~Ll~lv~~~GnkW~~I 89 (302)
++-|-|+.-||+.|...|.+||...|++|++.+.-.+.+||+.||..+|+|.+++..|+.|||++|+.+...+-..|..|
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrtI 84 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRTI 84 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccchH
Confidence 46789999999999999999999899999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcCCCCHHHHHHHHHHHhhhhccCCCc
Q 022144 90 ARLLSGRTDNAIKNHWNSTLKRKCSSMSD 118 (302)
Q Consensus 90 A~~l~gRT~~q~knRw~~~Lkrk~~~~~~ 118 (302)
+..+ |||.+||-.||+++|-...+....
T Consensus 85 a~i~-gr~~~qc~eRy~~ll~~~~s~~~~ 112 (617)
T KOG0050|consen 85 ADIM-GRTSQQCLERYNNLLDVYVSYHYH 112 (617)
T ss_pred HHHh-hhhHHHHHHHHHHHHHHHHhhhcc
Confidence 9999 999999999999999887766543
No 9
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.43 E-value=3.3e-14 Score=99.89 Aligned_cols=47 Identities=51% Similarity=1.032 Sum_probs=42.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCHHHHHhhCC-CCCcccccccccccC
Q 022144 12 KGPWSPEEDEALQRLVQNYGPRNWSLISKSIP-GRSGKSCRLRWCNQL 58 (302)
Q Consensus 12 Kg~WT~EED~~L~~lV~k~G~~nW~~IA~~lp-~Rt~kqCr~Rw~n~L 58 (302)
|++||+|||++|+++|.+||.++|..||..|+ +||..||+.||.++|
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 68999999999999999999877999999999 999999999999875
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=99.42 E-value=3.5e-13 Score=94.65 Aligned_cols=46 Identities=35% Similarity=0.731 Sum_probs=41.8
Q ss_pred CCCCChHHHHHHHHHHHhcCCc-HHHHhhhcC-CCCHHHHHHHHHHHh
Q 022144 64 HRPFTPEEDETILRAHARFGNK-WATIARLLS-GRTDNAIKNHWNSTL 109 (302)
Q Consensus 64 k~~WT~EED~~Ll~lv~~~Gnk-W~~IA~~l~-gRT~~q~knRw~~~L 109 (302)
+++||+|||++|++++.+||.+ |..||..|+ +||..||++||+.++
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 5799999999999999999987 999999999 999999999999875
No 11
>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=99.37 E-value=7e-13 Score=96.67 Aligned_cols=55 Identities=35% Similarity=0.589 Sum_probs=46.1
Q ss_pred CChHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhhhccCCCcccc
Q 022144 67 FTPEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKRKCSSMSDESQ 121 (302)
Q Consensus 67 WT~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkrk~~~~~~~~~ 121 (302)
||+|||++|++++.+||++|..||++|+.||..+|++||+..|+.+++...+...
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~e 55 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKE 55 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHH
Confidence 9999999999999999999999999996699999999999988777766655443
No 12
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.36 E-value=9.5e-13 Score=133.94 Aligned_cols=103 Identities=26% Similarity=0.572 Sum_probs=93.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCcccccccccccCCCCC--CCCCCChHHHHHHHHHHH-------h
Q 022144 11 IKGPWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWCNQLSPQV--EHRPFTPEEDETILRAHA-------R 81 (302)
Q Consensus 11 ~Kg~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~n~L~p~~--kk~~WT~EED~~Ll~lv~-------~ 81 (302)
.||.||+||++.|..+|.++| .+|..|++.| ||.+..|++||.++...+. +++.||-||++.|+++|. +
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g-~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~q 460 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHG-NDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREALQ 460 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhc-ccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhhc
Confidence 799999999999999999999 5699999888 8999999999999999885 889999999999999995 3
Q ss_pred c-------------------CCcHHHHhhhcCCCCHHHHHHHHHHHhhhhccC
Q 022144 82 F-------------------GNKWATIARLLSGRTDNAIKNHWNSTLKRKCSS 115 (302)
Q Consensus 82 ~-------------------GnkW~~IA~~l~gRT~~q~knRw~~~Lkrk~~~ 115 (302)
| +-+|..|++.+..|+..+|+.+|+.++.+....
T Consensus 461 ~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n 513 (607)
T KOG0051|consen 461 PQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFN 513 (607)
T ss_pred ccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhh
Confidence 3 125999999999999999999999998876544
No 13
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.25 E-value=8.1e-12 Score=115.29 Aligned_cols=76 Identities=17% Similarity=0.352 Sum_probs=64.8
Q ss_pred CCCCCcccccccccccCCCCCCCCCCChHHHHHHHHHHHhcC-CcHHHHhhhc-CCCCHHHHHHHHHHHhhhhccCCCcc
Q 022144 42 IPGRSGKSCRLRWCNQLSPQVEHRPFTPEEDETILRAHARFG-NKWATIARLL-SGRTDNAIKNHWNSTLKRKCSSMSDE 119 (302)
Q Consensus 42 lp~Rt~kqCr~Rw~n~L~p~~kk~~WT~EED~~Ll~lv~~~G-nkW~~IA~~l-~gRT~~q~knRw~~~Lkrk~~~~~~~ 119 (302)
++.|+..-|. ++.+++++||+|||++|+++|++|| ++|..||+++ ++||..||+.||.++|+..+.+..+.
T Consensus 10 ~~~~~~pcc~-------K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT 82 (249)
T PLN03212 10 VSKKTTPCCT-------KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGIT 82 (249)
T ss_pred CCCCCCCCcc-------cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCC
Confidence 4555555553 3578999999999999999999999 6899999988 59999999999999999999998877
Q ss_pred ccccc
Q 022144 120 SQVDA 124 (302)
Q Consensus 120 ~~~~~ 124 (302)
.+++.
T Consensus 83 ~EED~ 87 (249)
T PLN03212 83 SDEED 87 (249)
T ss_pred hHHHH
Confidence 66554
No 14
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.23 E-value=1.9e-11 Score=83.23 Aligned_cols=47 Identities=38% Similarity=0.762 Sum_probs=44.3
Q ss_pred CCCCChHHHHHHHHHHHhcC-CcHHHHhhhcCCCCHHHHHHHHHHHhh
Q 022144 64 HRPFTPEEDETILRAHARFG-NKWATIARLLSGRTDNAIKNHWNSTLK 110 (302)
Q Consensus 64 k~~WT~EED~~Ll~lv~~~G-nkW~~IA~~l~gRT~~q~knRw~~~Lk 110 (302)
++.||++||.+|+.++.+|| .+|..||..|++||..+|++||+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 46899999999999999999 999999999999999999999998765
No 15
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.15 E-value=3e-11 Score=82.24 Aligned_cols=48 Identities=52% Similarity=1.052 Sum_probs=44.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCcccccccccccCC
Q 022144 12 KGPWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWCNQLS 59 (302)
Q Consensus 12 Kg~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~n~L~ 59 (302)
++.||++||++|..++.+||..+|..||..|++||..+|+.||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 478999999999999999997789999999999999999999988764
No 16
>PLN03091 hypothetical protein; Provisional
Probab=99.13 E-value=5e-11 Score=117.52 Aligned_cols=66 Identities=20% Similarity=0.444 Sum_probs=58.4
Q ss_pred CCCCCCCCCCChHHHHHHHHHHHhcC-CcHHHHhhhcC-CCCHHHHHHHHHHHhhhhccCCCcccccc
Q 022144 58 LSPQVEHRPFTPEEDETILRAHARFG-NKWATIARLLS-GRTDNAIKNHWNSTLKRKCSSMSDESQVD 123 (302)
Q Consensus 58 L~p~~kk~~WT~EED~~Ll~lv~~~G-nkW~~IA~~l~-gRT~~q~knRw~~~Lkrk~~~~~~~~~~~ 123 (302)
.+..+++++||+|||++|+++|++|| ++|..||+++. ||+++||+.||.++|+..+.+..+..++|
T Consensus 8 ~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED 75 (459)
T PLN03091 8 YKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEE 75 (459)
T ss_pred cCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHH
Confidence 34678999999999999999999999 68999999884 99999999999999999998877665544
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=99.12 E-value=1.4e-10 Score=77.86 Aligned_cols=44 Identities=43% Similarity=0.860 Sum_probs=41.7
Q ss_pred CCChHHHHHHHHHHHhcC-CcHHHHhhhcCCCCHHHHHHHHHHHh
Q 022144 66 PFTPEEDETILRAHARFG-NKWATIARLLSGRTDNAIKNHWNSTL 109 (302)
Q Consensus 66 ~WT~EED~~Ll~lv~~~G-nkW~~IA~~l~gRT~~q~knRw~~~L 109 (302)
+||.|||.+|+.++.+|| .+|..||+.+++||..+|++||+.++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 99999999999999999999998753
No 18
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.07 E-value=9.8e-11 Score=107.96 Aligned_cols=64 Identities=20% Similarity=0.369 Sum_probs=57.1
Q ss_pred CCCCCCCChHHHHHHHHHHHhcC-CcHHHHhhhcC-CCCHHHHHHHHHHHhhhhccCCCccccccc
Q 022144 61 QVEHRPFTPEEDETILRAHARFG-NKWATIARLLS-GRTDNAIKNHWNSTLKRKCSSMSDESQVDA 124 (302)
Q Consensus 61 ~~kk~~WT~EED~~Ll~lv~~~G-nkW~~IA~~l~-gRT~~q~knRw~~~Lkrk~~~~~~~~~~~~ 124 (302)
.+.+|+||+|||++|+++|++|| ++|..|++.++ +|+.++|+-||.++|+..+++.....+++.
T Consensus 6 ~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~ 71 (238)
T KOG0048|consen 6 ELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEED 71 (238)
T ss_pred cccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHH
Confidence 34579999999999999999999 67999999999 999999999999999999998776654443
No 19
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.01 E-value=2.3e-10 Score=76.79 Aligned_cols=45 Identities=53% Similarity=1.069 Sum_probs=42.1
Q ss_pred CCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCcccccccccccC
Q 022144 14 PWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWCNQL 58 (302)
Q Consensus 14 ~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~n~L 58 (302)
+||.+||++|++++.+||..+|..||..+++|+..+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999778999999999999999999997753
No 20
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.97 E-value=1.3e-09 Score=111.33 Aligned_cols=99 Identities=28% Similarity=0.467 Sum_probs=86.0
Q ss_pred CCCCCHHHHHHHHHHHHHh-----------------CC------CCHHHHHhhCCCCCcccccc---cccccCCCCCCCC
Q 022144 12 KGPWSPEEDEALQRLVQNY-----------------GP------RNWSLISKSIPGRSGKSCRL---RWCNQLSPQVEHR 65 (302)
Q Consensus 12 Kg~WT~EED~~L~~lV~k~-----------------G~------~nW~~IA~~lp~Rt~kqCr~---Rw~n~L~p~~kk~ 65 (302)
-+.|+.+||..|.+.|..| .. .-|+.|...||-|+.++++. |-++.|.+ ++|
T Consensus 308 ~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp~R~~~siy~~~rR~y~~FE~--~rg 385 (607)
T KOG0051|consen 308 LKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLPYRDRKSIYHHLRRAYTPFEN--KRG 385 (607)
T ss_pred hhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcCcccchhHHHHHHhcCCcccc--ccC
Confidence 3789999999999999988 11 01788899999999999887 55555554 999
Q ss_pred CCChHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhhhc
Q 022144 66 PFTPEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKRKC 113 (302)
Q Consensus 66 ~WT~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkrk~ 113 (302)
.||+||++.|..+|.++|+.|..|++.| ||.+.+|+.||+.+.+..-
T Consensus 386 ~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~ 432 (607)
T KOG0051|consen 386 KWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGS 432 (607)
T ss_pred CCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhcccc
Confidence 9999999999999999999999999999 9999999999999887653
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=98.22 E-value=1.6e-07 Score=95.16 Aligned_cols=101 Identities=24% Similarity=0.516 Sum_probs=86.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCcccccccccccCCC--CCCCCCCChHHHHHHHHHHHhc--C
Q 022144 8 VDRIKGPWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWCNQLSP--QVEHRPFTPEEDETILRAHARF--G 83 (302)
Q Consensus 8 ~~~~Kg~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~n~L~p--~~kk~~WT~EED~~Ll~lv~~~--G 83 (302)
+...+|.||.||+..|..++..+| ..|..|.+.+ +|-+..|++||.++... .+++++|+.||+.+|...+... +
T Consensus 287 ~f~~~~~wt~e~~~eL~~~~~~~~-~~w~~ig~~~-~rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e~~~~ 364 (512)
T COG5147 287 IFEQRGKWTKEEEQELAKLVVEHG-GSWTEIGKLL-GRMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNEMRLE 364 (512)
T ss_pred HHhhhccCcccccccccccccccc-chhhHhhhhh-ccCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHHHHHH
Confidence 345689999999999999999999 5699999876 89999999999999988 6888999999999999888632 1
Q ss_pred ------CcHHHHhhhcCCCCHHHHHHHHHHHhh
Q 022144 84 ------NKWATIARLLSGRTDNAIKNHWNSTLK 110 (302)
Q Consensus 84 ------nkW~~IA~~l~gRT~~q~knRw~~~Lk 110 (302)
..|..|+.++.+|....|+.++..+..
T Consensus 365 ~~~~~~~~~~li~~~~~~~~~~~~~~~~~~~~~ 397 (512)
T COG5147 365 AQQSSRILWLLIAQNIRNRLQHHCRDKYGVLIS 397 (512)
T ss_pred HhhhhhhhHHHHHHhhhccccCCCCCccccccc
Confidence 359999999999998888887765443
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=98.04 E-value=1.4e-05 Score=58.78 Aligned_cols=48 Identities=19% Similarity=0.369 Sum_probs=41.8
Q ss_pred CCCCCChHHHHHHHHHHHhcCC-cH---HHHhhhcC-CC-CHHHHHHHHHHHhh
Q 022144 63 EHRPFTPEEDETILRAHARFGN-KW---ATIARLLS-GR-TDNAIKNHWNSTLK 110 (302)
Q Consensus 63 kk~~WT~EED~~Ll~lv~~~Gn-kW---~~IA~~l~-gR-T~~q~knRw~~~Lk 110 (302)
.+-.||+||++++++++..||. +| ..|++.+. .| |..+|+.|++.+..
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 3568999999999999999995 99 99999875 35 99999999987754
No 23
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.83 E-value=3.4e-05 Score=76.48 Aligned_cols=51 Identities=22% Similarity=0.461 Sum_probs=45.8
Q ss_pred CCCCCCCChHHHHHHHHHHHhcC-CcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 61 QVEHRPFTPEEDETILRAHARFG-NKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 61 ~~kk~~WT~EED~~Ll~lv~~~G-nkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.+-...||.+|+.+|++++..|| ++|..||.++..||..+|+.||.+++-.
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv~ 120 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFVN 120 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHhc
Confidence 34557899999999999999999 9999999999999999999999876543
No 24
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.76 E-value=8.2e-05 Score=67.45 Aligned_cols=98 Identities=17% Similarity=0.319 Sum_probs=74.0
Q ss_pred CCCHHHHHHHHHHHHHhCCCCHHHHHhhC---CCCCcccccccccccCC----------------C-----CCCCCCCCh
Q 022144 14 PWSPEEDEALQRLVQNYGPRNWSLISKSI---PGRSGKSCRLRWCNQLS----------------P-----QVEHRPFTP 69 (302)
Q Consensus 14 ~WT~EED~~L~~lV~k~G~~nW~~IA~~l---p~Rt~kqCr~Rw~n~L~----------------p-----~~kk~~WT~ 69 (302)
+|++++|-+|+.+|.+-. +-..|+..+ ..-|.+.+.+||+..|- | ...+..||.
T Consensus 1 rW~~~DDl~Li~av~~~~--~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~~is~~a~~~m~~l~p~~~~~iq~kalfS~ 78 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTN--DLESVHLGVKFSCKFTLQEIEERWYALLYDPVISRIAVAAMRNLHPELIAAIQSKALFSK 78 (199)
T ss_pred CCCchhhHHHHHHHHHhc--CHHHHHccCCcCCcCcHHHHHHHHHHHHcChhhHHHHHHHHHhCCcchhhcccccCCCCH
Confidence 599999999999999866 688887765 33455667789998763 2 234568999
Q ss_pred HHHHHHHHHHHhcCC---cHHHHhh-----hcCCCCHHHHHHHHHHHhhhhc
Q 022144 70 EEDETILRAHARFGN---KWATIAR-----LLSGRTDNAIKNHWNSTLKRKC 113 (302)
Q Consensus 70 EED~~Ll~lv~~~Gn---kW~~IA~-----~l~gRT~~q~knRw~~~Lkrk~ 113 (302)
+|+++|......... .+.+|-. +-++||+.++.+||+.+.+..+
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~L 130 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHL 130 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhch
Confidence 999999998766653 4666633 3478999999999996655543
No 25
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.71 E-value=2e-05 Score=78.05 Aligned_cols=52 Identities=19% Similarity=0.502 Sum_probs=47.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCcccccccccccC
Q 022144 7 DVDRIKGPWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWCNQL 58 (302)
Q Consensus 7 ~~~~~Kg~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~n~L 58 (302)
...+...-||.+|+-+|+++++.||.+||..||.+|..|+...|+++|.+++
T Consensus 67 s~~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 67 SFPILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHH
Confidence 3456778899999999999999999999999999999999999999998865
No 26
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.63 E-value=3.5e-05 Score=77.80 Aligned_cols=61 Identities=25% Similarity=0.432 Sum_probs=54.2
Q ss_pred CCCCCCChHHHHHHHHHHHhcC-CcHHHHhhhcCCCCHHHHHHHHHHHhhhhccCCCccccc
Q 022144 62 VEHRPFTPEEDETILRAHARFG-NKWATIARLLSGRTDNAIKNHWNSTLKRKCSSMSDESQV 122 (302)
Q Consensus 62 ~kk~~WT~EED~~Ll~lv~~~G-nkW~~IA~~l~gRT~~q~knRw~~~Lkrk~~~~~~~~~~ 122 (302)
++-+-|+..||+.|..++.+|| |.|++|+.+++-.|..||++||+..+...++.-.++..+
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~ee 66 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREE 66 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhH
Confidence 4668999999999999999999 889999999999999999999999999888776555433
No 27
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.62 E-value=4.8e-05 Score=55.90 Aligned_cols=47 Identities=13% Similarity=0.249 Sum_probs=41.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCH---HHHHhhCC-CC-CcccccccccccC
Q 022144 12 KGPWSPEEDEALQRLVQNYGPRNW---SLISKSIP-GR-SGKSCRLRWCNQL 58 (302)
Q Consensus 12 Kg~WT~EED~~L~~lV~k~G~~nW---~~IA~~lp-~R-t~kqCr~Rw~n~L 58 (302)
+-.||+||.++++++|+.+|.++| ..|+..|. .| |..||+.+++.|.
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 557999999999999999997799 99999883 45 9999999988764
No 28
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=97.39 E-value=0.00019 Score=62.95 Aligned_cols=53 Identities=25% Similarity=0.441 Sum_probs=46.3
Q ss_pred CCCCCChHHHHHHHHHHHhc---C----CcHHHHhhhcCCCCHHHHHHHHHHHhhhhccCC
Q 022144 63 EHRPFTPEEDETILRAHARF---G----NKWATIARLLSGRTDNAIKNHWNSTLKRKCSSM 116 (302)
Q Consensus 63 kk~~WT~EED~~Ll~lv~~~---G----nkW~~IA~~l~gRT~~q~knRw~~~Lkrk~~~~ 116 (302)
+...||.|||.+|.+.|-+| | .-+..+++.| +||..+|.=|||.++|+++...
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~~ 62 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEEA 62 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHHH
Confidence 56789999999999999887 3 2388999999 9999999999999999987653
No 29
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.21 E-value=0.0002 Score=71.67 Aligned_cols=46 Identities=20% Similarity=0.474 Sum_probs=42.5
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCccccccccccc
Q 022144 11 IKGPWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWCNQ 57 (302)
Q Consensus 11 ~Kg~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~n~ 57 (302)
....||.+|..+|++.|+.|| .+|.+||.++.+|+..||..|+.+.
T Consensus 278 ~dk~WS~qE~~LLLEGIe~yg-DdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYG-DDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhh-hhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 556899999999999999999 5799999999999999999998764
No 30
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.11 E-value=0.0005 Score=68.92 Aligned_cols=45 Identities=18% Similarity=0.391 Sum_probs=42.0
Q ss_pred CCCCCChHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHH
Q 022144 63 EHRPFTPEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNS 107 (302)
Q Consensus 63 kk~~WT~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~ 107 (302)
....||.+|..+|++++..||..|.+||+++++||..||.-||.+
T Consensus 278 ~dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~ 322 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQ 322 (531)
T ss_pred ccccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHc
Confidence 445899999999999999999999999999999999999999964
No 31
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.08 E-value=0.00066 Score=69.29 Aligned_cols=46 Identities=15% Similarity=0.318 Sum_probs=42.8
Q ss_pred CCCCCCChHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHH
Q 022144 62 VEHRPFTPEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNS 107 (302)
Q Consensus 62 ~kk~~WT~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~ 107 (302)
..+..||++|.-+|++++..||-+|.+||.++.+||..+|..|+..
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~ 296 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLR 296 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHh
Confidence 4467899999999999999999999999999999999999999864
No 32
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.04 E-value=0.00041 Score=70.73 Aligned_cols=49 Identities=18% Similarity=0.514 Sum_probs=44.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCccccccccccc
Q 022144 8 VDRIKGPWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWCNQ 57 (302)
Q Consensus 8 ~~~~Kg~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~n~ 57 (302)
..-.++.||.+|+-+|++.|+.|| .+|.+|+.++.+||..||..++.+.
T Consensus 249 ~~~~~~~WT~qE~lLLLE~ie~y~-ddW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 249 GESARPNWTEQETLLLLEAIEMYG-DDWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred cccCCCCccHHHHHHHHHHHHHhc-ccHHHHHhccCCCCHHHHHHHHHhc
Confidence 456788999999999999999999 6799999999999999999988653
No 33
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.98 E-value=0.00087 Score=51.81 Aligned_cols=49 Identities=29% Similarity=0.541 Sum_probs=34.8
Q ss_pred CCCCChHHHHHHHHHHHh------cC--C------cHHHHhhhcC----CCCHHHHHHHHHHHhhhh
Q 022144 64 HRPFTPEEDETILRAHAR------FG--N------KWATIARLLS----GRTDNAIKNHWNSTLKRK 112 (302)
Q Consensus 64 k~~WT~EED~~Ll~lv~~------~G--n------kW~~IA~~l~----gRT~~q~knRw~~~Lkrk 112 (302)
+..||.+|...||++... ++ + -|..||..|. .||..||+++|.++.+.-
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 357999999999999877 21 1 3999999773 599999999999866554
No 34
>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=96.89 E-value=0.0017 Score=48.93 Aligned_cols=50 Identities=22% Similarity=0.374 Sum_probs=32.6
Q ss_pred CCCCChHHHHHHHHHHHhcC--------Cc-HHHHhhhcC-CCCHHHHHHHHHHHhhhhc
Q 022144 64 HRPFTPEEDETILRAHARFG--------NK-WATIARLLS-GRTDNAIKNHWNSTLKRKC 113 (302)
Q Consensus 64 k~~WT~EED~~Ll~lv~~~G--------nk-W~~IA~~l~-gRT~~q~knRw~~~Lkrk~ 113 (302)
+.+||.|||+.|++.|+++. |+ |.++++.-+ .+|-.+.++||...|+.+.
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 45899999999999997542 22 999998766 9999999999998887664
No 35
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.86 E-value=0.0011 Score=58.88 Aligned_cols=53 Identities=21% Similarity=0.355 Sum_probs=44.8
Q ss_pred CCCCCCChHHHHHHHHHHHhcCCc-------HHHHhhhcCCCCHHHHHHHHHHHhhhhccC
Q 022144 62 VEHRPFTPEEDETILRAHARFGNK-------WATIARLLSGRTDNAIKNHWNSTLKRKCSS 115 (302)
Q Consensus 62 ~kk~~WT~EED~~Ll~lv~~~Gnk-------W~~IA~~l~gRT~~q~knRw~~~Lkrk~~~ 115 (302)
.++..||.|||.+|-+.|.+|+.. ...++..| +||..+|..|||.++++++..
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Yee 62 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQE 62 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHHH
Confidence 456799999999999999888732 66667788 999999999999999988654
No 36
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=96.70 E-value=0.0036 Score=68.91 Aligned_cols=100 Identities=17% Similarity=0.369 Sum_probs=79.0
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCcccccc-------ccccc------C---------------------
Q 022144 13 GPWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRL-------RWCNQ------L--------------------- 58 (302)
Q Consensus 13 g~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~-------Rw~n~------L--------------------- 58 (302)
..|+.-|=..++.+..+||..+...||..|.++|...++. ||..+ +
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~~ 904 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAIG 904 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3599999999999999999889999999998888865542 22211 0
Q ss_pred ----------------CCCCCCCCCChHHHHHHHHHHHhcC-CcHHHHhhh------------cCCCCHHHHHHHHHHHh
Q 022144 59 ----------------SPQVEHRPFTPEEDETILRAHARFG-NKWATIARL------------LSGRTDNAIKNHWNSTL 109 (302)
Q Consensus 59 ----------------~p~~kk~~WT~EED~~Ll~lv~~~G-nkW~~IA~~------------l~gRT~~q~knRw~~~L 109 (302)
.+..++..||+|||+.|+-.+.+|| .+|.+|-.. |..||+..|..|.+.++
T Consensus 905 ~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~ 984 (1033)
T PLN03142 905 KKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLI 984 (1033)
T ss_pred HHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHH
Confidence 0233456799999999999999999 789999442 36899999999999888
Q ss_pred hhh
Q 022144 110 KRK 112 (302)
Q Consensus 110 krk 112 (302)
+-.
T Consensus 985 ~~~ 987 (1033)
T PLN03142 985 RLI 987 (1033)
T ss_pred HHH
Confidence 765
No 37
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.55 E-value=0.0027 Score=61.26 Aligned_cols=47 Identities=19% Similarity=0.473 Sum_probs=43.1
Q ss_pred CCCCChHHHHHHHHHHHhcC-CcHHHHhhhcCCCCHHHHHHHHHHHhh
Q 022144 64 HRPFTPEEDETILRAHARFG-NKWATIARLLSGRTDNAIKNHWNSTLK 110 (302)
Q Consensus 64 k~~WT~EED~~Ll~lv~~~G-nkW~~IA~~l~gRT~~q~knRw~~~Lk 110 (302)
-..|+.+|+-+|+++....| ++|..||.++..|+...||.||..+.-
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 35799999999999999999 999999999999999999999987654
No 38
>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=96.44 E-value=0.001 Score=50.11 Aligned_cols=51 Identities=25% Similarity=0.444 Sum_probs=32.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCC------CC--HHHHHhhCC-CCCcccccccccccCCCCC
Q 022144 12 KGPWSPEEDEALQRLVQNYGP------RN--WSLISKSIP-GRSGKSCRLRWCNQLSPQV 62 (302)
Q Consensus 12 Kg~WT~EED~~L~~lV~k~G~------~n--W~~IA~~lp-~Rt~kqCr~Rw~n~L~p~~ 62 (302)
|-+||.|||+.|+++|..+.. +| |.+++..-+ .+|-.+-++||.+.|.+..
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 467999999999999976521 12 999998776 8899999999999887543
No 39
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=96.20 E-value=0.015 Score=44.15 Aligned_cols=48 Identities=25% Similarity=0.486 Sum_probs=39.4
Q ss_pred CCCCChHHHHHHHHHHHhcC----C-------------cHHHHhhhc-----CCCCHHHHHHHHHHHhhh
Q 022144 64 HRPFTPEEDETILRAHARFG----N-------------KWATIARLL-----SGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 64 k~~WT~EED~~Ll~lv~~~G----n-------------kW~~IA~~l-----~gRT~~q~knRw~~~Lkr 111 (302)
...||.+|...|++++.+|- + -|..|+..| +.||..+|+.+|..+...
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 45799999999999998872 1 199999876 359999999999877543
No 40
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.16 E-value=0.0023 Score=49.41 Aligned_cols=46 Identities=28% Similarity=0.607 Sum_probs=32.0
Q ss_pred CCCCCHHHHHHHHHHHHH--h----C--C--C---CHHHHHhhC----CCCCccccccccccc
Q 022144 12 KGPWSPEEDEALQRLVQN--Y----G--P--R---NWSLISKSI----PGRSGKSCRLRWCNQ 57 (302)
Q Consensus 12 Kg~WT~EED~~L~~lV~k--~----G--~--~---nW~~IA~~l----p~Rt~kqCr~Rw~n~ 57 (302)
|-.||.+|...|+.++.. + + . . -|..||..| ..||+.||+.||.+.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L 63 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL 63 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 357999999999999987 2 1 1 1 399999887 579999999999874
No 41
>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=95.89 E-value=0.0046 Score=54.36 Aligned_cols=49 Identities=22% Similarity=0.537 Sum_probs=40.8
Q ss_pred CCCCCCHHHHHHHHHHHHHh---CC---CCHHHHHhhCCCCCcccccccccccCCC
Q 022144 11 IKGPWSPEEDEALQRLVQNY---GP---RNWSLISKSIPGRSGKSCRLRWCNQLSP 60 (302)
Q Consensus 11 ~Kg~WT~EED~~L~~lV~k~---G~---~nW~~IA~~lp~Rt~kqCr~Rw~n~L~p 60 (302)
....||.|||.+|.+.|-+| |. .-+.+|+..| +||..-|.-||..++..
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRk 57 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRK 57 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHH
Confidence 35679999999999999999 21 1388888887 89999999999988753
No 42
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.40 E-value=0.0058 Score=59.07 Aligned_cols=47 Identities=19% Similarity=0.390 Sum_probs=43.9
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCcccccccccccCC
Q 022144 13 GPWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWCNQLS 59 (302)
Q Consensus 13 g~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~n~L~ 59 (302)
--|+.+|+-+|++..+..|.+||..||.++..|+...|+.+|.+++.
T Consensus 64 e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 64 EGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 46999999999999999999999999999999999999999988764
No 43
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.31 E-value=0.0065 Score=46.16 Aligned_cols=47 Identities=32% Similarity=0.477 Sum_probs=38.5
Q ss_pred CCCCCHHHHHHHHHHHHHh-----CC-----------CCHHHHHhhC-----CCCCcccccccccccC
Q 022144 12 KGPWSPEEDEALQRLVQNY-----GP-----------RNWSLISKSI-----PGRSGKSCRLRWCNQL 58 (302)
Q Consensus 12 Kg~WT~EED~~L~~lV~k~-----G~-----------~nW~~IA~~l-----p~Rt~kqCr~Rw~n~L 58 (302)
+..||.+|.+.|+++|++| +. .-|..|+..| ..|+..+|+.+|.++.
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk 69 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLK 69 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 4679999999999999998 21 1299999877 4689999999998754
No 44
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=94.93 E-value=0.058 Score=45.23 Aligned_cols=52 Identities=21% Similarity=0.432 Sum_probs=41.6
Q ss_pred CCCCCCCChHHHHHHHHHHHhcCC----cHHHHhhh------------cCCCCHHHHHHHHHHHhhhh
Q 022144 61 QVEHRPFTPEEDETILRAHARFGN----KWATIARL------------LSGRTDNAIKNHWNSTLKRK 112 (302)
Q Consensus 61 ~~kk~~WT~EED~~Ll~lv~~~Gn----kW~~IA~~------------l~gRT~~q~knRw~~~Lkrk 112 (302)
..++..||+|||+-|+-.+.+||- .|..|-.. |..||+..|..|.+.+++-.
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i 113 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLI 113 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHH
Confidence 556789999999999999999995 79998653 36799999999999888654
No 45
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=94.41 E-value=0.015 Score=51.61 Aligned_cols=48 Identities=19% Similarity=0.479 Sum_probs=37.5
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCC------HHHHHhhCCCCCcccccccccccCC
Q 022144 11 IKGPWSPEEDEALQRLVQNYGPRN------WSLISKSIPGRSGKSCRLRWCNQLS 59 (302)
Q Consensus 11 ~Kg~WT~EED~~L~~lV~k~G~~n------W~~IA~~lp~Rt~kqCr~Rw~n~L~ 59 (302)
.+..||.|||.+|.+.|.+|+... ...++..| +|+...|..||..++.
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vr 57 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVR 57 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHH
Confidence 467899999999999999996433 45555555 8999999999965543
No 46
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=94.35 E-value=0.031 Score=55.35 Aligned_cols=84 Identities=17% Similarity=0.322 Sum_probs=66.5
Q ss_pred CCCHHHHHhhCCCCCcccccccccccCCC-------------------------CCCCCCCChHHHHHHHHHHHhcCCcH
Q 022144 32 PRNWSLISKSIPGRSGKSCRLRWCNQLSP-------------------------QVEHRPFTPEEDETILRAHARFGNKW 86 (302)
Q Consensus 32 ~~nW~~IA~~lp~Rt~kqCr~Rw~n~L~p-------------------------~~kk~~WT~EED~~Ll~lv~~~GnkW 86 (302)
.+.|..+.-..+.|...-...||...-++ .+.-..||.||-+.|.+++++|.-+|
T Consensus 73 ~~~W~w~pFtn~aRkD~~~l~HWvr~~d~~~dypfakfNk~vdipsYt~eEYe~~l~dn~WskeETD~LF~lck~fDLRf 152 (445)
T KOG2656|consen 73 VRPWKWVPFTNSARKDDATLHHWVRVGDTPKDYPFAKFNKHVDIPSYTDEEYEAHLNDNSWSKEETDYLFDLCKRFDLRF 152 (445)
T ss_pred CCCceeeccCCccccCCceEEeeeeccCCCCCCchhhhccccCccccchHHHHHhhccccccHHHHHHHHHHHHhcCeeE
Confidence 35688877667778888888888776322 12335699999999999999999999
Q ss_pred HHHhhh-----cCC-CCHHHHHHHHHHHhhhhccC
Q 022144 87 ATIARL-----LSG-RTDNAIKNHWNSTLKRKCSS 115 (302)
Q Consensus 87 ~~IA~~-----l~g-RT~~q~knRw~~~Lkrk~~~ 115 (302)
--|+.. ++. ||-..+|.||+.+.++.+..
T Consensus 153 ~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kA 187 (445)
T KOG2656|consen 153 FVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKA 187 (445)
T ss_pred EEEeeccchhhccccccHHHHHHHHHHHHHHHHHc
Confidence 999875 555 99999999999888776554
No 47
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=93.68 E-value=0.19 Score=39.15 Aligned_cols=45 Identities=31% Similarity=0.547 Sum_probs=34.3
Q ss_pred CCChHHHHHHHHHHHhc---CC----------cHHHHhhhcC-----CCCHHHHHHHHHHHhh
Q 022144 66 PFTPEEDETILRAHARF---GN----------KWATIARLLS-----GRTDNAIKNHWNSTLK 110 (302)
Q Consensus 66 ~WT~EED~~Ll~lv~~~---Gn----------kW~~IA~~l~-----gRT~~q~knRw~~~Lk 110 (302)
.||+++++.|++++.+. |+ .|..|+..|. ..|..+|++||..+.+
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~ 63 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKK 63 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHH
Confidence 59999999999998543 21 2999998773 2588999999975443
No 48
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=91.54 E-value=0.3 Score=47.27 Aligned_cols=49 Identities=20% Similarity=0.378 Sum_probs=39.4
Q ss_pred CCCCChHHHHHHHHHHHhc----------CCcHHHHhhhcC----CCCHHHHHHHHHHHhhhh
Q 022144 64 HRPFTPEEDETILRAHARF----------GNKWATIARLLS----GRTDNAIKNHWNSTLKRK 112 (302)
Q Consensus 64 k~~WT~EED~~Ll~lv~~~----------GnkW~~IA~~l~----gRT~~q~knRw~~~Lkrk 112 (302)
...|+.+|-..||++..+. +..|..||+.+. -||+.+|+++|.++.++.
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 4789999999999997542 345999999552 499999999999877653
No 49
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=91.25 E-value=0.6 Score=47.33 Aligned_cols=50 Identities=20% Similarity=0.206 Sum_probs=44.5
Q ss_pred CCCCCChHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhhh
Q 022144 63 EHRPFTPEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKRK 112 (302)
Q Consensus 63 kk~~WT~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkrk 112 (302)
-+..||.||--++-++...||.++.+|-..||+|+-..|...|+...+.+
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK~~ 235 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKKTR 235 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHHHh
Confidence 45689999999999999999999999999999999999999887665544
No 50
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=91.10 E-value=0.66 Score=32.43 Aligned_cols=42 Identities=26% Similarity=0.424 Sum_probs=32.7
Q ss_pred hHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 69 PEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 69 ~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
+++++.++.++...|-.|.+||..+ |.+...|+.+....+++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARKK 53 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHhh
Confidence 4678889999999999999999999 99999999998876654
No 51
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=90.25 E-value=0.22 Score=49.43 Aligned_cols=44 Identities=27% Similarity=0.507 Sum_probs=40.7
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCccccccccccc
Q 022144 13 GPWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWCNQ 57 (302)
Q Consensus 13 g~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~n~ 57 (302)
-+|+.+|-+++.+++...| -++..|+..+|+|..+|+..+|.+-
T Consensus 366 ~~Ws~~e~ekFYKALs~wG-tdF~LIs~lfP~R~RkqIKaKfi~E 409 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWG-TDFSLISSLFPNRERKQIKAKFIKE 409 (507)
T ss_pred CcccHHHHHHHHHHHHHhc-chHHHHHHhcCchhHHHHHHHHHHH
Confidence 4799999999999999999 5699999999999999999998763
No 52
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=89.02 E-value=0.8 Score=45.57 Aligned_cols=48 Identities=21% Similarity=0.322 Sum_probs=43.2
Q ss_pred CCCCChHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 64 HRPFTPEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 64 k~~WT~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
-.+||.+|-+++..+...+|..++.|+.+||.|...|||-+|.+--|+
T Consensus 365 ~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~ 412 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKV 412 (507)
T ss_pred CCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhh
Confidence 358999999999999999999999999999999999999999754333
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=87.44 E-value=0.82 Score=35.94 Aligned_cols=31 Identities=39% Similarity=0.762 Sum_probs=19.3
Q ss_pred CCCCCCCCCHHHHHHH--------HHHHHHhCCCCHHHHHhh
Q 022144 8 VDRIKGPWSPEEDEAL--------QRLVQNYGPRNWSLISKS 41 (302)
Q Consensus 8 ~~~~Kg~WT~EED~~L--------~~lV~k~G~~nW~~IA~~ 41 (302)
|.-..|-||+|+|+.| .+++++|| +..|...
T Consensus 43 P~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG---~~~i~~R 81 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLRSGDKDDIERLIKKHG---EERIERR 81 (87)
T ss_dssp -TT-TT---HHHHHHHTS--HHHHHHHHHHH----HHHHHHH
T ss_pred CCCCCCCcCHHHHHHHHcCCHHHHHHHHHHhC---HHHHHHH
Confidence 5567899999999999 56777888 6677653
No 54
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=84.80 E-value=0.57 Score=45.30 Aligned_cols=46 Identities=24% Similarity=0.370 Sum_probs=37.2
Q ss_pred CCCCHHHHHHHHHHHHHh---------CCCCHHHHHhhC----CCCCcccccccccccC
Q 022144 13 GPWSPEEDEALQRLVQNY---------GPRNWSLISKSI----PGRSGKSCRLRWCNQL 58 (302)
Q Consensus 13 g~WT~EED~~L~~lV~k~---------G~~nW~~IA~~l----p~Rt~kqCr~Rw~n~L 58 (302)
..|+.+|-..|+++.... ....|..||..+ ..|++.||+.+|.|..
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 689999999999998754 113499999855 5699999999998743
No 55
>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=84.80 E-value=1.1 Score=37.66 Aligned_cols=34 Identities=35% Similarity=0.556 Sum_probs=28.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC---CCHHHHHhhC
Q 022144 9 DRIKGPWSPEEDEALQRLVQNYGP---RNWSLISKSI 42 (302)
Q Consensus 9 ~~~Kg~WT~EED~~L~~lV~k~G~---~nW~~IA~~l 42 (302)
...+..||.+||.-|+-++.+||. ++|..|-..+
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 556788999999999999999998 7899998765
No 56
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=83.48 E-value=0.78 Score=48.95 Aligned_cols=42 Identities=14% Similarity=0.494 Sum_probs=38.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCccccccccc
Q 022144 13 GPWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWC 55 (302)
Q Consensus 13 g~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~ 55 (302)
..||+.|..++.+++-.|. +++.+|++.++++|.+||-+-|+
T Consensus 620 d~WTp~E~~lF~kA~y~~~-KDF~~v~km~~~KtVaqCVeyYY 661 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYS-KDFIFVQKMVKSKTVAQCVEYYY 661 (907)
T ss_pred ccccHHHHHHHHHHHHHhc-ccHHHHHHHhccccHHHHHHHHH
Confidence 4799999999999999999 68999999999999999976543
No 57
>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=82.09 E-value=1.1 Score=34.74 Aligned_cols=43 Identities=26% Similarity=0.560 Sum_probs=30.4
Q ss_pred CCCHHHHHHHHHHHHHh---CCC---------CHHHHHhhCCC-----CCcccccccccc
Q 022144 14 PWSPEEDEALQRLVQNY---GPR---------NWSLISKSIPG-----RSGKSCRLRWCN 56 (302)
Q Consensus 14 ~WT~EED~~L~~lV~k~---G~~---------nW~~IA~~lp~-----Rt~kqCr~Rw~n 56 (302)
.||+++++.|++++... |.. .|..|+..|.. .+..||+.||..
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~ 60 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKT 60 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHH
Confidence 59999999999998654 222 29999888733 345677777643
No 58
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=79.67 E-value=2.7 Score=44.18 Aligned_cols=52 Identities=13% Similarity=0.368 Sum_probs=42.3
Q ss_pred CCCCCChHHHHHHHHHHHhcCCcHHHHhh----------hcCCCCHHHHHHHHHHHhhhhcc
Q 022144 63 EHRPFTPEEDETILRAHARFGNKWATIAR----------LLSGRTDNAIKNHWNSTLKRKCS 114 (302)
Q Consensus 63 kk~~WT~EED~~Ll~lv~~~GnkW~~IA~----------~l~gRT~~q~knRw~~~Lkrk~~ 114 (302)
++..||..|..-+..+.+++|.++.+|-. .+.-+|..|++.+|+.++++-++
T Consensus 87 ~ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k 148 (782)
T KOG4468|consen 87 AKTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNK 148 (782)
T ss_pred cccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHh
Confidence 36789999999999999999999999832 22346889999999988776543
No 59
>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=78.72 E-value=7.5 Score=26.73 Aligned_cols=41 Identities=20% Similarity=0.297 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 70 EEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 70 EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
++++.++.+.--.|..+.+||+.+ |-+...|+.+....+++
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 556667777666678899999999 99999999988877665
No 60
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=77.10 E-value=25 Score=35.25 Aligned_cols=42 Identities=12% Similarity=0.197 Sum_probs=38.5
Q ss_pred CCCChHHHHHHHHHHHhcCCcHHHHhh-hcCCCCHHHHHHHHH
Q 022144 65 RPFTPEEDETILRAHARFGNKWATIAR-LLSGRTDNAIKNHWN 106 (302)
Q Consensus 65 ~~WT~EED~~Ll~lv~~~GnkW~~IA~-~l~gRT~~q~knRw~ 106 (302)
..|+++|.+.+-+..+.||+++..|.+ .+..|+--.|-..|+
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYY 320 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYY 320 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHH
Confidence 489999999999999999999999976 799999999988765
No 61
>smart00595 MADF subfamily of SANT domain.
Probab=76.32 E-value=4.7 Score=30.85 Aligned_cols=23 Identities=30% Similarity=0.608 Sum_probs=20.2
Q ss_pred HHHHhhhcCCCCHHHHHHHHHHHh
Q 022144 86 WATIARLLSGRTDNAIKNHWNSTL 109 (302)
Q Consensus 86 W~~IA~~l~gRT~~q~knRw~~~L 109 (302)
|..||..| |-|...|+.+|+++-
T Consensus 30 W~~Ia~~l-~~~~~~~~~kw~~LR 52 (89)
T smart00595 30 WEEIAEEL-GLSVEECKKRWKNLR 52 (89)
T ss_pred HHHHHHHH-CcCHHHHHHHHHHHH
Confidence 99999999 559999999998664
No 62
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=75.95 E-value=4.8 Score=43.27 Aligned_cols=43 Identities=12% Similarity=0.250 Sum_probs=40.1
Q ss_pred CCCChHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHH
Q 022144 65 RPFTPEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNS 107 (302)
Q Consensus 65 ~~WT~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~ 107 (302)
..||+.|-.++-+++..|..++..|++.++++|-.+|-..|+.
T Consensus 620 d~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYT 662 (907)
T ss_pred ccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHH
Confidence 5899999999999999999999999999999999999887653
No 63
>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=74.16 E-value=93 Score=30.64 Aligned_cols=86 Identities=27% Similarity=0.487 Sum_probs=63.5
Q ss_pred CCCCHHHHHHHHHHHHHh-CC--CCHHHHHhhCCCCCcccccccccccCCCCCCCCCCChHHHHHHHHHHHh-c-----C
Q 022144 13 GPWSPEEDEALQRLVQNY-GP--RNWSLISKSIPGRSGKSCRLRWCNQLSPQVEHRPFTPEEDETILRAHAR-F-----G 83 (302)
Q Consensus 13 g~WT~EED~~L~~lV~k~-G~--~nW~~IA~~lp~Rt~kqCr~Rw~n~L~p~~kk~~WT~EED~~Ll~lv~~-~-----G 83 (302)
..||.-|...|+++.+.. |. -+-.+|++.+++|+..++++ |.+.|+ ++.+.+++++ | |
T Consensus 22 ~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~-fl~~LK------------~rvareaiqkv~~~g~~~ 88 (344)
T PF11035_consen 22 AAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRD-FLQQLK------------GRVAREAIQKVHPGGLKG 88 (344)
T ss_pred ccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHH-HHHHHH------------HHHHHHHHHHhccccccc
Confidence 479999999999998865 31 24678999999999988865 333333 3445555554 2 2
Q ss_pred Cc------------HHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 84 NK------------WATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 84 nk------------W~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.+ |..+|+.+.|.-...|---|..+|.-
T Consensus 89 ~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~i 128 (344)
T PF11035_consen 89 PRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLTI 128 (344)
T ss_pred ccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHHH
Confidence 11 99999999999999998888877653
No 64
>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=73.48 E-value=12 Score=25.52 Aligned_cols=38 Identities=26% Similarity=0.399 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHhcC-CcHHHHhhhcCCCCHHHHHHHHHHH
Q 022144 70 EEDETILRAHARFG-NKWATIARLLSGRTDNAIKNHWNST 108 (302)
Q Consensus 70 EED~~Ll~lv~~~G-nkW~~IA~~l~gRT~~q~knRw~~~ 108 (302)
+=|..|+.+..+-| --|..||+.+ |=+...|..|++.+
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 45788899888888 5699999999 99999999999754
No 65
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=72.33 E-value=8.7 Score=32.80 Aligned_cols=45 Identities=18% Similarity=0.180 Sum_probs=38.7
Q ss_pred hHHHHHHHHHHHhcC-CcHHHHhhhcCCCCHHHHHHHHHHHhhhhcc
Q 022144 69 PEEDETILRAHARFG-NKWATIARLLSGRTDNAIKNHWNSTLKRKCS 114 (302)
Q Consensus 69 ~EED~~Ll~lv~~~G-nkW~~IA~~l~gRT~~q~knRw~~~Lkrk~~ 114 (302)
++-|..|+++.++-| -.|+.||+.+ |-+...|..|++.+...-+-
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 467889999988888 5799999999 99999999999988776544
No 66
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=72.26 E-value=10 Score=37.93 Aligned_cols=56 Identities=20% Similarity=0.317 Sum_probs=44.7
Q ss_pred CCCCCCChHHHHHHHHHHHhcC----------------CcHHHHhhhc-----CCCCHHHHHHHHHHHhhhhccCCC
Q 022144 62 VEHRPFTPEEDETILRAHARFG----------------NKWATIARLL-----SGRTDNAIKNHWNSTLKRKCSSMS 117 (302)
Q Consensus 62 ~kk~~WT~EED~~Ll~lv~~~G----------------nkW~~IA~~l-----~gRT~~q~knRw~~~Lkrk~~~~~ 117 (302)
..-|.|+++=|+.+.++.+.|- ++=..||+++ ..||.+||-.|-+.+-|++++...
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~reiq 150 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLREIQ 150 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHH
Confidence 4457999999999999998762 2357889876 348999999999888888876643
No 67
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=71.09 E-value=5.5 Score=35.05 Aligned_cols=41 Identities=27% Similarity=0.275 Sum_probs=35.9
Q ss_pred CCChHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHH
Q 022144 66 PFTPEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNS 107 (302)
Q Consensus 66 ~WT~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~ 107 (302)
.||+|+.++|.+|. .-|..=.+||+.|.|.|.|+|..+.+.
T Consensus 2 ~Wtde~~~~L~~lw-~~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 2 SWTDERVERLRKLW-AEGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred CCCHHHHHHHHHHH-HcCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 59999999999887 667888999999987999999887764
No 68
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=69.84 E-value=12 Score=30.73 Aligned_cols=38 Identities=24% Similarity=0.305 Sum_probs=28.7
Q ss_pred HHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 73 ETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 73 ~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
+.++.+.-..|-.+.+||..+ |.+...|++++...+++
T Consensus 119 r~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 119 RKIFILSRFEGKSYKEIAEEL-GISVKTVEYHISKALKE 156 (161)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 334444344577899999999 99999999999876554
No 69
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=69.59 E-value=10 Score=30.59 Aligned_cols=48 Identities=19% Similarity=0.355 Sum_probs=33.8
Q ss_pred CCCCChHHHHHHHHHHHhc----C----CcHHHHhhhcCC-----CCHHHHHHHHHHHhhh
Q 022144 64 HRPFTPEEDETILRAHARF----G----NKWATIARLLSG-----RTDNAIKNHWNSTLKR 111 (302)
Q Consensus 64 k~~WT~EED~~Ll~lv~~~----G----nkW~~IA~~l~g-----RT~~q~knRw~~~Lkr 111 (302)
...||+||+-.|++++..| | .+|..+-..+.+ =+.+|+.++-+.+-++
T Consensus 4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~K 64 (98)
T PF04504_consen 4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKK 64 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHH
Confidence 4579999999999998776 6 356665554433 2778888887655444
No 70
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=68.20 E-value=10 Score=32.76 Aligned_cols=45 Identities=11% Similarity=0.089 Sum_probs=39.0
Q ss_pred hHHHHHHHHHHHhcC-CcHHHHhhhcCCCCHHHHHHHHHHHhhhhcc
Q 022144 69 PEEDETILRAHARFG-NKWATIARLLSGRTDNAIKNHWNSTLKRKCS 114 (302)
Q Consensus 69 ~EED~~Ll~lv~~~G-nkW~~IA~~l~gRT~~q~knRw~~~Lkrk~~ 114 (302)
.+-|.+|+.+.++-| -.|.+||+.+ |=+...|..|++.+.+...-
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~GvI 58 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGFI 58 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 567888998888888 5799999999 99999999999988877654
No 71
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=66.72 E-value=4.6 Score=41.20 Aligned_cols=44 Identities=20% Similarity=0.406 Sum_probs=38.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCccccccccc
Q 022144 11 IKGPWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWC 55 (302)
Q Consensus 11 ~Kg~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~ 55 (302)
.+..||.||--+|.++...|| .++.+|-+.||.|+-.++..=|+
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~G-K~F~kIrq~LP~rsLaSlvqyYy 229 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFG-KDFHKIRQALPHRSLASLVQYYY 229 (534)
T ss_pred CcccchHHHHHHHHHHHHHhc-ccHHHHHHHccCccHHHHHHHHH
Confidence 456799999999999999999 67999999999999987765443
No 72
>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=65.19 E-value=4.4 Score=31.77 Aligned_cols=17 Identities=35% Similarity=0.548 Sum_probs=10.0
Q ss_pred CCCCCCCCChHHHHHHH
Q 022144 60 PQVEHRPFTPEEDETIL 76 (302)
Q Consensus 60 p~~kk~~WT~EED~~Ll 76 (302)
|.-..|-||+|+|+.|.
T Consensus 43 P~n~~GiWT~eDD~~L~ 59 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLR 59 (87)
T ss_dssp -TT-TT---HHHHHHHT
T ss_pred CCCCCCCcCHHHHHHHH
Confidence 55667899999999984
No 73
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=64.80 E-value=12 Score=34.23 Aligned_cols=46 Identities=22% Similarity=0.295 Sum_probs=36.1
Q ss_pred CCChHHHHHHHHHHHhcCCcHHHHhhh--cC-CCCHHHHHHHHHHHhhhh
Q 022144 66 PFTPEEDETILRAHARFGNKWATIARL--LS-GRTDNAIKNHWNSTLKRK 112 (302)
Q Consensus 66 ~WT~EED~~Ll~lv~~~GnkW~~IA~~--l~-gRT~~q~knRw~~~Lkrk 112 (302)
.|++++|-+|+.+| .+|+.-..|++- |. .-|-..|..||+.+|-..
T Consensus 1 rW~~~DDl~Li~av-~~~~~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~ 49 (199)
T PF13325_consen 1 RWKPEDDLLLINAV-EQTNDLESVHLGVKFSCKFTLQEIEERWYALLYDP 49 (199)
T ss_pred CCCchhhHHHHHHH-HHhcCHHHHHccCCcCCcCcHHHHHHHHHHHHcCh
Confidence 59999999999998 556777777663 32 358899999999988554
No 74
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=63.71 E-value=16 Score=37.73 Aligned_cols=79 Identities=15% Similarity=0.258 Sum_probs=54.7
Q ss_pred HHHHhhCCCCCcccccccccccCCCCCCCCCCChHHHHHHHHHHHhcCCcHHHHh-hhcCCCCHHHHHHHHH-------H
Q 022144 36 SLISKSIPGRSGKSCRLRWCNQLSPQVEHRPFTPEEDETILRAHARFGNKWATIA-RLLSGRTDNAIKNHWN-------S 107 (302)
Q Consensus 36 ~~IA~~lp~Rt~kqCr~Rw~n~L~p~~kk~~WT~EED~~Ll~lv~~~GnkW~~IA-~~l~gRT~~q~knRw~-------~ 107 (302)
+.|+..+|-=-+.-||+. -..|+.-|-.++-++..+||.++..|. .+||-++-..|-..|+ .
T Consensus 267 ~Ais~LVPlGGPvLCRDe----------mEEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYYmwKttdRY 336 (693)
T KOG3554|consen 267 KAISYLVPLGGPVLCRDE----------MEEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYYMWKTTDRY 336 (693)
T ss_pred HHHHHhhcCCCceeehhh----------hhhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHHHHhhhhHH
Confidence 345555554444555542 348999999999999999999999996 5889999999887764 2
Q ss_pred HhhhhccCCCccccccc
Q 022144 108 TLKRKCSSMSDESQVDA 124 (302)
Q Consensus 108 ~Lkrk~~~~~~~~~~~~ 124 (302)
+-+++++....+++...
T Consensus 337 vqqKrlKaaeadsKlkq 353 (693)
T KOG3554|consen 337 VQQKRLKAAEADSKLKQ 353 (693)
T ss_pred HHHHhhhhhhhhhhhhe
Confidence 34455555444444433
No 75
>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=60.63 E-value=19 Score=27.85 Aligned_cols=37 Identities=27% Similarity=0.495 Sum_probs=27.2
Q ss_pred HHHHHHHhcCC--------cHHHHhhhcCCC---C--HHHHHHHHHHHhh
Q 022144 74 TILRAHARFGN--------KWATIARLLSGR---T--DNAIKNHWNSTLK 110 (302)
Q Consensus 74 ~Ll~lv~~~Gn--------kW~~IA~~l~gR---T--~~q~knRw~~~Lk 110 (302)
.|..+|.++|+ +|..|++.|.-- + ..+++..|..+|.
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhH
Confidence 47778888873 599999988321 2 3689999988774
No 76
>KOG1878 consensus Nuclear receptor coregulator SMRT/SMRTER, contains Myb-like domains [Transcription]
Probab=59.12 E-value=5.5 Score=45.71 Aligned_cols=43 Identities=28% Similarity=0.461 Sum_probs=35.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCcccccccc
Q 022144 11 IKGPWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRW 54 (302)
Q Consensus 11 ~Kg~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw 54 (302)
+...|+++|-+.+..=...|- +|+..|+.+|..++..+|..-|
T Consensus 224 ~~n~Ws~~Ek~~fk~rf~~H~-knf~~~as~~erkSv~d~vlfy 266 (1672)
T KOG1878|consen 224 RMNEWSPEEKELFKSRFAQHV-KNFGLIASFFERKSVSDCVLFY 266 (1672)
T ss_pred HhhhccccccccccchhhhcC-cchhhhhhhhcccchhhceeee
Confidence 455799999888887777776 6799999999888888887655
No 77
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=58.74 E-value=23 Score=28.05 Aligned_cols=37 Identities=22% Similarity=0.292 Sum_probs=27.8
Q ss_pred HHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 74 TILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 74 ~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.++.++-..|..+..||+.+ |=+...|+++.+..+++
T Consensus 117 ~ii~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 117 EVLVLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred HHHhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 33344445678899999999 77999999988876554
No 78
>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=58.63 E-value=35 Score=22.14 Aligned_cols=41 Identities=15% Similarity=0.336 Sum_probs=29.7
Q ss_pred CChHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHh
Q 022144 67 FTPEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTL 109 (302)
Q Consensus 67 WT~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~L 109 (302)
+++ ++..++.++...|-.+..||..+ |=+...|+.+.....
T Consensus 11 l~~-~~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~~ 51 (55)
T cd06171 11 LPE-REREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRAL 51 (55)
T ss_pred CCH-HHHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 444 45566666666788899999998 788888877766543
No 79
>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=58.14 E-value=15 Score=28.88 Aligned_cols=29 Identities=24% Similarity=0.491 Sum_probs=23.0
Q ss_pred HHHHHHHHHhcCCcHHHHhhhcCCCCHHHH
Q 022144 72 DETILRAHARFGNKWATIARLLSGRTDNAI 101 (302)
Q Consensus 72 D~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~ 101 (302)
|+.|..+....|.+|..+|++| |=|..+|
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I 30 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDI 30 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 5668889999999999999998 5444443
No 80
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=58.09 E-value=7.5 Score=41.00 Aligned_cols=47 Identities=13% Similarity=0.375 Sum_probs=35.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCHHHHHhhC-C---------CCCcccccccccccC
Q 022144 11 IKGPWSPEEDEALQRLVQNYGPRNWSLISKSI-P---------GRSGKSCRLRWCNQL 58 (302)
Q Consensus 11 ~Kg~WT~EED~~L~~lV~k~G~~nW~~IA~~l-p---------~Rt~kqCr~Rw~n~L 58 (302)
.|..||.+|.+.+..+++++| +++..|-..+ . -++-.|+|.+|++.+
T Consensus 87 ~ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~ 143 (782)
T KOG4468|consen 87 AKTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLV 143 (782)
T ss_pred cccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHH
Confidence 367899999999999999999 7799984333 2 234456777776544
No 81
>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=58.06 E-value=6.1 Score=26.96 Aligned_cols=38 Identities=29% Similarity=0.446 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHhCCCCHHHHHhhCCCCCcccccccccc
Q 022144 18 EEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWCN 56 (302)
Q Consensus 18 EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~n 56 (302)
+=|.+|+.++.+.+...|..||+.+ |=+...|..|+.+
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l-glS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL-GLSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH-TS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH-CcCHHHHHHHHHH
Confidence 4588999999999988999999887 7788888888753
No 82
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=54.83 E-value=9 Score=38.22 Aligned_cols=41 Identities=24% Similarity=0.409 Sum_probs=35.3
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCHHHHH-hhCCCCCcccccccc
Q 022144 13 GPWSPEEDEALQRLVQNYGPRNWSLIS-KSIPGRSGKSCRLRW 54 (302)
Q Consensus 13 g~WT~EED~~L~~lV~k~G~~nW~~IA-~~lp~Rt~kqCr~Rw 54 (302)
.-|+.+|-..+.+.++.|| +++..|. ..++.|+...|.+-|
T Consensus 278 ~~wsEeEcr~FEegl~~yG-KDF~lIr~nkvrtRsvgElVeyY 319 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYG-KDFHLIRANKVRTRSVGELVEYY 319 (445)
T ss_pred ccCCHHHHHHHHHHHHHhc-ccHHHHHhcccccchHHHHHHHH
Confidence 3699999999999999999 7899995 567889988887654
No 83
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=54.62 E-value=32 Score=29.58 Aligned_cols=39 Identities=18% Similarity=0.006 Sum_probs=30.3
Q ss_pred HHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhhhccC
Q 022144 76 LRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKRKCSS 115 (302)
Q Consensus 76 l~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkrk~~~ 115 (302)
+.++...|-...+||..| |-+.+.|+.|...-+.+....
T Consensus 136 ~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 136 FLMATLDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred HHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHh
Confidence 334444578899999999 999999999998777665443
No 84
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=54.57 E-value=30 Score=28.99 Aligned_cols=31 Identities=13% Similarity=0.182 Sum_probs=24.4
Q ss_pred HhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 80 ARFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 80 ~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
...|-.+..||..| |-+...|+++....+++
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 34577899999999 89999999887654443
No 85
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=53.94 E-value=34 Score=26.87 Aligned_cols=46 Identities=17% Similarity=0.179 Sum_probs=38.6
Q ss_pred hHHHHHHHHHHHhcC-CcHHHHhhhcCCCCHHHHHHHHHHHhhhhccC
Q 022144 69 PEEDETILRAHARFG-NKWATIARLLSGRTDNAIKNHWNSTLKRKCSS 115 (302)
Q Consensus 69 ~EED~~Ll~lv~~~G-nkW~~IA~~l~gRT~~q~knRw~~~Lkrk~~~ 115 (302)
.+.|..|+.+..+.| -.+..|++.+ |-+...|..+.+.+.+..+-.
T Consensus 2 d~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 2 DEIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred CHHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 357888888888887 5799999999 999999999999888776443
No 86
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=53.66 E-value=8.2 Score=32.98 Aligned_cols=44 Identities=11% Similarity=0.124 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHhCCCCHHHHHhhCCCCCcccccccccccCCCC
Q 022144 17 PEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWCNQLSPQ 61 (302)
Q Consensus 17 ~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~n~L~p~ 61 (302)
.+-|.+|++++++.|...|.+||+.+ |-+...|+.|+.+....+
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~G 51 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAG 51 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCC
Confidence 36799999999999988999999988 889999999988765544
No 87
>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=53.41 E-value=39 Score=33.20 Aligned_cols=48 Identities=23% Similarity=0.374 Sum_probs=36.7
Q ss_pred CCCCChHHHHHHHHHHHhc-CC---cHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 64 HRPFTPEEDETILRAHARF-GN---KWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 64 k~~WT~EED~~Ll~lv~~~-Gn---kW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
-..||.-|.+.|+++.+.. |. +-..|++.++||+..+|++.-+.+..+
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~r 72 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGR 72 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHH
Confidence 4689999999888887644 54 356889999999999999966544433
No 88
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=52.60 E-value=34 Score=26.70 Aligned_cols=38 Identities=26% Similarity=0.447 Sum_probs=28.0
Q ss_pred HHHHHHHhcCC--------cHHHHhhhcCCC-----CHHHHHHHHHHHhhh
Q 022144 74 TILRAHARFGN--------KWATIARLLSGR-----TDNAIKNHWNSTLKR 111 (302)
Q Consensus 74 ~Ll~lv~~~Gn--------kW~~IA~~l~gR-----T~~q~knRw~~~Lkr 111 (302)
.|..+|.+.|+ +|..|++.|.-. ....++..|..+|..
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~ 86 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLP 86 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHH
Confidence 47777777773 699999988332 357889999887754
No 89
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=52.31 E-value=38 Score=22.67 Aligned_cols=34 Identities=29% Similarity=0.394 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHH
Q 022144 71 EDETILRAHARFGNKWATIARLLSGRTDNAIKNHW 105 (302)
Q Consensus 71 ED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw 105 (302)
|.+.|.++..++|++..+.|+.| |=+...+..+-
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~kl 39 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLL-GISRRTLYRKL 39 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHH
Confidence 67789999999999999999999 77776666554
No 90
>PRK04217 hypothetical protein; Provisional
Probab=51.62 E-value=40 Score=27.93 Aligned_cols=45 Identities=20% Similarity=0.097 Sum_probs=35.9
Q ss_pred CCCChHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 65 RPFTPEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 65 ~~WT~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
...|++| ..++.+....|-...+||+.+ |-+...|+++++...++
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 3456665 677788877888999999999 99999999999865443
No 91
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=50.94 E-value=35 Score=28.48 Aligned_cols=29 Identities=21% Similarity=0.285 Sum_probs=23.6
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHhh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTLK 110 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~Lk 110 (302)
..|-.+..||..| |-+...|++++....+
T Consensus 139 ~~~~~~~eIA~~l-gis~~tv~~~~~ra~~ 167 (179)
T PRK11924 139 VEGLSYREIAEIL-GVPVGTVKSRLRRARQ 167 (179)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 4567899999999 9999999998876443
No 92
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=50.42 E-value=37 Score=29.65 Aligned_cols=30 Identities=23% Similarity=0.263 Sum_probs=24.2
Q ss_pred HHhcCCcHHHHhhhcCCCCHHHHHHHHHHHh
Q 022144 79 HARFGNKWATIARLLSGRTDNAIKNHWNSTL 109 (302)
Q Consensus 79 v~~~GnkW~~IA~~l~gRT~~q~knRw~~~L 109 (302)
....|-...+||..+ |-+...|++|+...+
T Consensus 146 ~~~~g~s~~EIA~~l-g~s~~tV~~rl~rar 175 (192)
T PRK09643 146 VDMQGYSVADAARML-GVAEGTVKSRCARGR 175 (192)
T ss_pred HHHcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 334577899999999 999999999985443
No 93
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=49.64 E-value=18 Score=38.14 Aligned_cols=50 Identities=24% Similarity=0.385 Sum_probs=44.3
Q ss_pred CCCCCCChHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 62 VEHRPFTPEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 62 ~kk~~WT~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.....|+.+|-++...+...+|.+.+.|+..+++|+..+||.+|..--++
T Consensus 407 ~~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~eE~r 456 (584)
T KOG2009|consen 407 LETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKEEKR 456 (584)
T ss_pred cccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhhhhc
Confidence 44568999999999999999999999999999999999999999644433
No 94
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=49.57 E-value=8.1 Score=33.44 Aligned_cols=45 Identities=20% Similarity=0.131 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHhCCCCHHHHHhhCCCCCcccccccccccCCCCC
Q 022144 17 PEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWCNQLSPQV 62 (302)
Q Consensus 17 ~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~n~L~p~~ 62 (302)
.+-|.+|+.+.++.|...|.+||+.+ |-+...|+.|+.+..+.++
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 56799999999999988999999988 7899999999887765443
No 95
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=49.56 E-value=54 Score=26.31 Aligned_cols=48 Identities=17% Similarity=0.187 Sum_probs=39.3
Q ss_pred CCCCChHHHHHHHHHHHhcCCcHHHHhhhcCCC-CHHHHHHHHHHHhhhh
Q 022144 64 HRPFTPEEDETILRAHARFGNKWATIARLLSGR-TDNAIKNHWNSTLKRK 112 (302)
Q Consensus 64 k~~WT~EED~~Ll~lv~~~GnkW~~IA~~l~gR-T~~q~knRw~~~Lkrk 112 (302)
+..||.|+-..+++++..-|..=+.||+.+ |- ..++++.++..+....
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~~W~~~~~~~~ 53 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLYKWRIQLQKGG 53 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHHHHHHHHHHcc
Confidence 678999999999999999999889999999 75 7777777655444444
No 96
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=47.71 E-value=21 Score=26.33 Aligned_cols=25 Identities=28% Similarity=0.524 Sum_probs=20.2
Q ss_pred HHHHhhhcCC-CCHHHHHHHHHHHhh
Q 022144 86 WATIARLLSG-RTDNAIKNHWNSTLK 110 (302)
Q Consensus 86 W~~IA~~l~g-RT~~q~knRw~~~Lk 110 (302)
|..|+..|.. -+.+.|+.+|+++..
T Consensus 29 w~~Ia~~l~~~~~~~~~~~~w~~Lr~ 54 (85)
T PF10545_consen 29 WQEIARELGKEFSVDDCKKRWKNLRD 54 (85)
T ss_pred HHHHHHHHccchhHHHHHHHHHHHHH
Confidence 9999999953 578889999987543
No 97
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=47.18 E-value=42 Score=28.55 Aligned_cols=29 Identities=10% Similarity=0.053 Sum_probs=23.5
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|..+.+||..| |-+...|+++.....++
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 467799999999 99999999988755543
No 98
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=46.77 E-value=49 Score=27.36 Aligned_cols=30 Identities=17% Similarity=0.194 Sum_probs=24.2
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
..|-.-.+||..| |-+...|++|....+++
T Consensus 120 ~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 120 WEDMDVAETAAAM-GCSEGSVKTHCSRATHA 149 (161)
T ss_pred HhcCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466789999999 99999999998765544
No 99
>cd08803 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=46.56 E-value=33 Score=26.95 Aligned_cols=29 Identities=24% Similarity=0.390 Sum_probs=22.9
Q ss_pred HHHHHHHHHhcCCcHHHHhhhcCCCCHHHH
Q 022144 72 DETILRAHARFGNKWATIARLLSGRTDNAI 101 (302)
Q Consensus 72 D~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~ 101 (302)
|..|..+....|.+|..+|+.| |=+...|
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI 32 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEI 32 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHH
Confidence 5678888899999999999988 5444433
No 100
>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=46.48 E-value=49 Score=28.82 Aligned_cols=48 Identities=19% Similarity=0.227 Sum_probs=38.9
Q ss_pred CCCCCCChHHHHHHHHHHHhcCCcHHHHhhh--cC--CCCHHHHHHHHHHHh
Q 022144 62 VEHRPFTPEEDETILRAHARFGNKWATIARL--LS--GRTDNAIKNHWNSTL 109 (302)
Q Consensus 62 ~kk~~WT~EED~~Ll~lv~~~GnkW~~IA~~--l~--gRT~~q~knRw~~~L 109 (302)
......|+.|...|..|+++||.++...++- |+ -.|..+|+.+...+.
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~k 163 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKYK 163 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHhc
Confidence 3456789999999999999999999999873 32 389999998876543
No 101
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=45.42 E-value=53 Score=27.87 Aligned_cols=39 Identities=18% Similarity=0.142 Sum_probs=29.6
Q ss_pred HHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhhh
Q 022144 73 ETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKRK 112 (302)
Q Consensus 73 ~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkrk 112 (302)
+.++.+....|-...+||..+ |-+...|+.+...-+++.
T Consensus 125 r~v~~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 125 RAAFLYNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 334444445677899999999 999999999987766654
No 102
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=45.26 E-value=30 Score=39.59 Aligned_cols=70 Identities=14% Similarity=0.129 Sum_probs=45.6
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCcccccccccccCCCCCCCCCCChHHHHHHHHHHHhc-CCcHHH
Q 022144 13 GPWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWCNQLSPQVEHRPFTPEEDETILRAHARF-GNKWAT 88 (302)
Q Consensus 13 g~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~n~L~p~~kk~~WT~EED~~Ll~lv~~~-GnkW~~ 88 (302)
.-|..+||..|+-.|-+||.++|..|-. ++.-|... +..+...+-...|=...-..|+.+...+ +.+|.+
T Consensus 1134 ~~W~~e~Ds~LLiGI~khGygswe~Ir~-----Dp~L~l~d-Ki~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~ 1204 (1373)
T KOG0384|consen 1134 CDWGSEDDSMLLIGIFKHGYGSWEAIRL-----DPDLGLTD-KIFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPK 1204 (1373)
T ss_pred cCCCchhhhhHhhhhhhcccccHHHhcc-----Cccccchh-hhcccccCCchHHHHHHHHHHHHHHhhcccCCCch
Confidence 4699999999999999999999999853 22223221 1222222445566666777777776665 344443
No 103
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=45.17 E-value=48 Score=27.90 Aligned_cols=30 Identities=17% Similarity=0.298 Sum_probs=23.8
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
-.|.....||..| |-|...|++++...+++
T Consensus 133 ~~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~ 162 (169)
T TIGR02954 133 YHDLTIKEIAEVM-NKPEGTVKTYLHRALKK 162 (169)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466789999988 88999999998766554
No 104
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=45.16 E-value=50 Score=28.85 Aligned_cols=38 Identities=13% Similarity=0.179 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHh
Q 022144 71 EDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTL 109 (302)
Q Consensus 71 ED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~L 109 (302)
++..++++..-.|-.+.+||..+ |-+...|+.+|....
T Consensus 139 ~~~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR 176 (185)
T PF07638_consen 139 RQRRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 33444555555678899999999 999999999998654
No 105
>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=45.16 E-value=51 Score=28.70 Aligned_cols=35 Identities=9% Similarity=-0.031 Sum_probs=26.5
Q ss_pred HHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 76 LRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 76 l~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
+.+....|.....||..| |-+.+.|+.|....+++
T Consensus 140 ~~l~~~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 140 FMMREVLGFESDEICQEL-EISTSNCHVLLYRARLS 174 (188)
T ss_pred HHHHHHhCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 333344577899999999 99999999998765444
No 106
>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=44.90 E-value=40 Score=28.77 Aligned_cols=29 Identities=14% Similarity=0.208 Sum_probs=23.4
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|-...+||..+ |=|...|+++....+++
T Consensus 153 ~~~s~~EIA~~l-gis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 153 EGLSYEDIARIM-DCPVGTVRSRIFRAREA 181 (190)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 356799999999 88999999998765544
No 107
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=44.82 E-value=29 Score=26.20 Aligned_cols=23 Identities=30% Similarity=0.661 Sum_probs=18.9
Q ss_pred HHHHHHHHHHhCCCCHHHHHhhCCCC
Q 022144 20 DEALQRLVQNYGPRNWSLISKSIPGR 45 (302)
Q Consensus 20 D~~L~~lV~k~G~~nW~~IA~~lp~R 45 (302)
+.+|.++|+.|| |..++..+.-|
T Consensus 12 e~il~~Lv~~yG---W~~L~~~i~i~ 34 (64)
T PF09905_consen 12 ETILTELVEHYG---WEELGERININ 34 (64)
T ss_dssp HHHHHHHHHHT----HHHHHHHTTSS
T ss_pred HHHHHHHHHHhC---HHHHHhhcccc
Confidence 578999999999 99999988544
No 108
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=44.80 E-value=53 Score=27.68 Aligned_cols=31 Identities=26% Similarity=0.235 Sum_probs=24.3
Q ss_pred HhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 80 ARFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 80 ~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.-.|-.-.+||..| |.+...|+.|....+++
T Consensus 131 ~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 161 (173)
T PRK09645 131 YYRGWSTAQIAADL-GIPEGTVKSRLHYALRA 161 (173)
T ss_pred HHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 34567789999999 99999999998765543
No 109
>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=44.26 E-value=27 Score=26.93 Aligned_cols=28 Identities=25% Similarity=0.527 Sum_probs=21.9
Q ss_pred HHHHHHHHHhcCCcHHHHhhhcCCCCHHH
Q 022144 72 DETILRAHARFGNKWATIARLLSGRTDNA 100 (302)
Q Consensus 72 D~~Ll~lv~~~GnkW~~IA~~l~gRT~~q 100 (302)
|..|..+....|.+|.++|+.| |=+...
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~d 31 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETD 31 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHH
Confidence 4567788889999999999998 544433
No 110
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=44.02 E-value=5.7 Score=39.83 Aligned_cols=45 Identities=22% Similarity=0.413 Sum_probs=37.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCHHHHHhh-----CCC-CCccccccccccc
Q 022144 12 KGPWSPEEDEALQRLVQNYGPRNWSLISKS-----IPG-RSGKSCRLRWCNQ 57 (302)
Q Consensus 12 Kg~WT~EED~~L~~lV~k~G~~nW~~IA~~-----lp~-Rt~kqCr~Rw~n~ 57 (302)
-..||.+|-+.|.+++.+|.-+ |--|+.. ++. ||.....+||+..
T Consensus 130 dn~WskeETD~LF~lck~fDLR-f~VIaDRyd~qq~~~sRTvEdLKeRyY~v 180 (445)
T KOG2656|consen 130 DNSWSKEETDYLFDLCKRFDLR-FFVIADRYDNQQYKKSRTVEDLKERYYSV 180 (445)
T ss_pred cccccHHHHHHHHHHHHhcCee-EEEEeeccchhhccccccHHHHHHHHHHH
Confidence 3679999999999999999865 8888765 444 9999999998754
No 111
>PLN03162 golden-2 like transcription factor; Provisional
Probab=43.68 E-value=1.7e+02 Score=29.53 Aligned_cols=46 Identities=22% Similarity=0.265 Sum_probs=36.9
Q ss_pred CCCCChHHHHHHHHHHHhcCCc---HHHHhhh--cCCCCHHHHHHHHHHHh
Q 022144 64 HRPFTPEEDETILRAHARFGNK---WATIARL--LSGRTDNAIKNHWNSTL 109 (302)
Q Consensus 64 k~~WT~EED~~Ll~lv~~~Gnk---W~~IA~~--l~gRT~~q~knRw~~~L 109 (302)
|-.||+|=+++++++|.++|.. =+.|-+. ++|=|..+|+.|.+.+.
T Consensus 237 RLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYR 287 (526)
T PLN03162 237 KVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYR 287 (526)
T ss_pred cccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHH
Confidence 3589999999999999999932 4566654 47889999999987653
No 112
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=43.17 E-value=54 Score=28.39 Aligned_cols=30 Identities=20% Similarity=0.068 Sum_probs=24.1
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
..|-...+||..| |-+...|+++....+++
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 3577899999999 99999999998755443
No 113
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=43.05 E-value=52 Score=28.36 Aligned_cols=29 Identities=10% Similarity=0.121 Sum_probs=22.8
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|-....||..| |-+.+.|++++...+++
T Consensus 153 ~g~s~~eIA~~l-gis~~tv~~~l~Rar~~ 181 (193)
T PRK11923 153 DGLSYEDIASVM-QCPVGTVRSRIFRAREA 181 (193)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456789999999 88999999998755443
No 114
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=42.49 E-value=60 Score=27.97 Aligned_cols=30 Identities=10% Similarity=0.205 Sum_probs=24.2
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
..|-....||..| |-+...|++++...+++
T Consensus 145 ~~~~s~~eIA~~l-gis~~tV~~~l~Rar~~ 174 (189)
T PRK12515 145 YHEKSVEEVGEIV-GIPESTVKTRMFYARKK 174 (189)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3567799999999 88999999998765544
No 115
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=41.68 E-value=63 Score=27.78 Aligned_cols=30 Identities=23% Similarity=0.245 Sum_probs=23.9
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
..|....+||..| |-+...|+.+....+++
T Consensus 153 ~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 153 VVGLSAEETAEAV-GSTPGAVRVAQHRALAR 182 (189)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 4567899999999 98999999987765543
No 116
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=41.63 E-value=53 Score=27.89 Aligned_cols=29 Identities=10% Similarity=0.053 Sum_probs=23.0
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|....+||..| |-+...|+++....+++
T Consensus 151 ~g~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T TIGR02948 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 356789999998 88999999988765544
No 117
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=41.57 E-value=62 Score=27.63 Aligned_cols=30 Identities=17% Similarity=0.136 Sum_probs=24.1
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
..|....+||..| |-+...|+.++...+++
T Consensus 145 ~~g~s~~eIA~~l-~is~~tV~~~l~ra~~~ 174 (184)
T PRK12512 145 VEGASIKETAAKL-SMSEGAVRVALHRGLAA 174 (184)
T ss_pred HcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3467789999999 99999999988765544
No 118
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=41.21 E-value=66 Score=26.73 Aligned_cols=30 Identities=10% Similarity=-0.076 Sum_probs=23.8
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
..|-.-.+||..+ |-+...|++|....+++
T Consensus 120 ~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (160)
T PRK09642 120 LEEKSYQEIALQE-KIEVKTVEMKLYRARKW 149 (160)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 4567789999999 99999999997655443
No 119
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=40.65 E-value=49 Score=29.72 Aligned_cols=45 Identities=24% Similarity=0.300 Sum_probs=36.9
Q ss_pred CCCChHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhhh
Q 022144 65 RPFTPEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKRK 112 (302)
Q Consensus 65 ~~WT~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkrk 112 (302)
...|+.|-+.|.-+.+ |-.=++||..| +.+...||+|..++++|.
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 3688888887766553 54457999999 999999999999999875
No 120
>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=40.46 E-value=40 Score=26.29 Aligned_cols=25 Identities=28% Similarity=0.478 Sum_probs=19.1
Q ss_pred HHHHHhcCCcHHHHhhhcCCCCHHHH
Q 022144 76 LRAHARFGNKWATIARLLSGRTDNAI 101 (302)
Q Consensus 76 l~lv~~~GnkW~~IA~~l~gRT~~q~ 101 (302)
..+....|.+|.++|+.| |=+..+|
T Consensus 11 ~~ia~~iG~~Wk~Lar~L-Gls~~dI 35 (86)
T cd08318 11 TVFANKLGEDWKTLAPHL-EMKDKEI 35 (86)
T ss_pred HHHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 335678899999999999 6665555
No 121
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=40.46 E-value=65 Score=27.99 Aligned_cols=29 Identities=3% Similarity=-0.135 Sum_probs=23.6
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHhh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTLK 110 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~Lk 110 (302)
-.|-...+||..| |-+...|+.|....++
T Consensus 148 ~~g~s~~EIA~~l-gis~~tVk~~l~RAr~ 176 (189)
T PRK12530 148 YLELSSEQICQEC-DISTSNLHVLLYRARL 176 (189)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3467799999999 9999999999765443
No 122
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=40.16 E-value=46 Score=36.55 Aligned_cols=96 Identities=15% Similarity=0.316 Sum_probs=63.1
Q ss_pred CCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCcccc-------------------------------------------
Q 022144 14 PWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSC------------------------------------------- 50 (302)
Q Consensus 14 ~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqC------------------------------------------- 50 (302)
.||.-+=..++.+.++||..+=..|+..+.+ +...+
T Consensus 797 ~w~k~df~~fi~a~eKygr~di~~ia~~~e~-~~eev~~y~rvfwer~~el~d~ek~~~~ie~~e~~i~r~~~~~~~ld~ 875 (971)
T KOG0385|consen 797 NWTKRDFNQFIKANEKYGRDDIENIAAEVEG-TPEEVGEYARVFWERLEELSDIEKIIYQIERGEKRIQRGDSIKKALDD 875 (971)
T ss_pred chhhhhHHHHHHHhhccCcchhhhhHHhhcC-CHHHHHHHHHHHHHHHHHhhhhHHHHHHHhhhHhhhhHHHHHHHHHhh
Confidence 5888888888999999988777777776654 22110
Q ss_pred -ccccccc----C-CCCCCCCCCChHHHHHHHHHHHhcC----CcHHHHhhh------------cCCCCHHHHHHHHHHH
Q 022144 51 -RLRWCNQ----L-SPQVEHRPFTPEEDETILRAHARFG----NKWATIARL------------LSGRTDNAIKNHWNST 108 (302)
Q Consensus 51 -r~Rw~n~----L-~p~~kk~~WT~EED~~Ll~lv~~~G----nkW~~IA~~------------l~gRT~~q~knRw~~~ 108 (302)
..||++. | .+..+....|.+||.-|+....++| +.|..+-.. +..||...+..|++++
T Consensus 876 k~~~~k~p~~l~i~~~~nk~~~ys~~edrfL~~~l~K~g~~~~~~~e~lr~~~~~~~~frfdw~~~sRt~~el~Rr~ntl 955 (971)
T KOG0385|consen 876 KIARYKAPHQLRIQYGTNKGKNYSEEEDRFLECMLHKLGFDAENVYEELRQPIRNSPQFRFDWFIKSRTAMELQRRCNTL 955 (971)
T ss_pred hHhhhcCchheeeeeccccCCCCchhhHHHHHHHHHHhccCchhHHHHHHHHHhcCcccccceeeehhhHHHHHhcCCee
Confidence 1123321 1 1123667899999999999999998 346665332 2457777777777665
Q ss_pred hh
Q 022144 109 LK 110 (302)
Q Consensus 109 Lk 110 (302)
+.
T Consensus 956 i~ 957 (971)
T KOG0385|consen 956 IT 957 (971)
T ss_pred EE
Confidence 43
No 123
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=39.22 E-value=85 Score=22.49 Aligned_cols=35 Identities=17% Similarity=0.391 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHH
Q 022144 70 EEDETILRAHARFGNKWATIARLLSGRTDNAIKNHW 105 (302)
Q Consensus 70 EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw 105 (302)
++|+-.+.++.+.|-.-.+||+.+ ||+.+.|++.-
T Consensus 7 ~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl 41 (50)
T PF11427_consen 7 DAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRYL 41 (50)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHHH
T ss_pred HHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHHh
Confidence 455566778889999999999999 99998887743
No 124
>PF09197 Rap1-DNA-bind: Rap1, DNA-binding; InterPro: IPR015280 Members of this entry, which are predominantly found in the yeast protein Rap1, assume a secondary structure consisting of a three-helix bundle and an N-terminal arm. They contain an Arg-Asp-Arg-Lys sequence that interacts with an ACAregion in the 3, region of the DNA-binding site []. ; PDB: 1IGN_A 3UKG_A.
Probab=38.91 E-value=19 Score=29.73 Aligned_cols=17 Identities=18% Similarity=0.421 Sum_probs=13.0
Q ss_pred CCCHHHHHHHHHHHHHh
Q 022144 14 PWSPEEDEALQRLVQNY 30 (302)
Q Consensus 14 ~WT~EED~~L~~lV~k~ 30 (302)
++|++||-.|-..|.+|
T Consensus 1 kfTA~dDY~Lc~~i~~~ 17 (105)
T PF09197_consen 1 KFTADDDYALCKAIKKQ 17 (105)
T ss_dssp ---HHHHHHHHHHHHHH
T ss_pred CCChHHHHHHHHHHHHH
Confidence 58999999999999877
No 125
>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=38.58 E-value=46 Score=25.10 Aligned_cols=29 Identities=24% Similarity=0.509 Sum_probs=20.5
Q ss_pred HHHHHHHHHHh-cCCcHHHHhhhcCCCCHHH
Q 022144 71 EDETILRAHAR-FGNKWATIARLLSGRTDNA 100 (302)
Q Consensus 71 ED~~Ll~lv~~-~GnkW~~IA~~l~gRT~~q 100 (302)
-++.|..+... .|++|..+|+.| |=+...
T Consensus 4 ~~~~~~~l~~~~~g~~W~~la~~L-g~~~~~ 33 (88)
T smart00005 4 TREKLAKLLDHPLGLDWRELARKL-GLSEAD 33 (88)
T ss_pred HHHHHHHHHcCccchHHHHHHHHc-CCCHHH
Confidence 34566666667 899999999998 434333
No 126
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=38.21 E-value=74 Score=27.68 Aligned_cols=29 Identities=14% Similarity=0.006 Sum_probs=22.8
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHhh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTLK 110 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~Lk 110 (302)
..|-.+.+||+.| |=+...|+++....++
T Consensus 150 ~~g~s~~eIA~~l-gis~~tV~~~l~Ra~~ 178 (196)
T PRK12524 150 IEGLSNPEIAEVM-EIGVEAVESLTARGKR 178 (196)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 4567799999999 8888889888765443
No 127
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=38.20 E-value=76 Score=27.58 Aligned_cols=30 Identities=7% Similarity=0.065 Sum_probs=23.6
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
-.|-...+||..| |-+...|++|....+++
T Consensus 155 ~eg~s~~EIA~~l-gis~~tVk~rl~ra~~~ 184 (194)
T PRK12531 155 LEELPHQQVAEMF-DIPLGTVKSRLRLAVEK 184 (194)
T ss_pred HcCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 3467789999999 99999999987765544
No 128
>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=37.07 E-value=57 Score=22.94 Aligned_cols=44 Identities=25% Similarity=0.287 Sum_probs=32.1
Q ss_pred CCChHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhhh
Q 022144 66 PFTPEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKRK 112 (302)
Q Consensus 66 ~WT~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkrk 112 (302)
.+|+.|-+.|.-+. -|..=.+||..+ |.+...|+.|...+.++-
T Consensus 3 ~LT~~E~~vl~~l~--~G~~~~eIA~~l-~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLA--QGMSNKEIAEEL-GISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHH--TTS-HHHHHHHH-TSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHH--hcCCcchhHHhc-CcchhhHHHHHHHHHHHh
Confidence 45667766555443 466668999999 999999999998887764
No 129
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=36.90 E-value=89 Score=25.97 Aligned_cols=29 Identities=24% Similarity=0.323 Sum_probs=23.0
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|-.-.+||..| |-+...|++|....+++
T Consensus 120 ~~~s~~eIA~~l-gis~~tv~~~l~ra~~~ 148 (159)
T PRK12527 120 EGLSHQQIAEHL-GISRSLVEKHIVNAMKH 148 (159)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 456689999999 99999999997755443
No 130
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=36.53 E-value=91 Score=25.58 Aligned_cols=29 Identities=17% Similarity=0.184 Sum_probs=22.5
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|....+||..+ |-+...|+++-...+++
T Consensus 121 ~~~s~~EIA~~l-~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 121 VGKTMGEIALET-EMTYYQVRWIYRQALEK 149 (154)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456688899888 89999999887665544
No 131
>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=36.39 E-value=87 Score=26.57 Aligned_cols=30 Identities=23% Similarity=0.307 Sum_probs=24.0
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
..|-...+||..+ |-+...|++|....+++
T Consensus 148 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 177 (183)
T TIGR02999 148 FAGLTVEEIAELL-GVSVRTVERDWRFARAW 177 (183)
T ss_pred HcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3567799999999 99999999998765443
No 132
>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=36.35 E-value=40 Score=29.60 Aligned_cols=38 Identities=26% Similarity=0.395 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCccccccc
Q 022144 14 PWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLR 53 (302)
Q Consensus 14 ~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~R 53 (302)
.||+|+.++|.++... | -.-.+||..|.+.|-..+.-+
T Consensus 2 ~Wtde~~~~L~~lw~~-G-~SasqIA~~lg~vsRnAViGk 39 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-G-LSASQIARQLGGVSRNAVIGK 39 (162)
T ss_pred CCCHHHHHHHHHHHHc-C-CCHHHHHHHhCCcchhhhhhh
Confidence 4999999999999966 5 358999999975665555443
No 133
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=36.24 E-value=83 Score=27.41 Aligned_cols=37 Identities=16% Similarity=0.154 Sum_probs=27.2
Q ss_pred HHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhh
Q 022144 73 ETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLK 110 (302)
Q Consensus 73 ~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lk 110 (302)
+.++.+....|-...+||+.| |-+...|++|....++
T Consensus 122 r~i~~L~~~~g~s~~EIA~~L-gis~~tVk~~l~Rar~ 158 (187)
T PRK12516 122 REAIILVGASGFAYEEAAEIC-GCAVGTIKSRVNRARQ 158 (187)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 334444445678899999999 9999999998765443
No 134
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=36.23 E-value=78 Score=27.37 Aligned_cols=31 Identities=16% Similarity=0.165 Sum_probs=25.3
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHhhhh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTLKRK 112 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkrk 112 (302)
-.|-...+||..+ |-+...|++|....+++.
T Consensus 144 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~L 174 (185)
T PRK09649 144 LLGLSYADAAAVC-GCPVGTIRSRVARARDAL 174 (185)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3466789999999 999999999987666554
No 135
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=36.15 E-value=93 Score=25.92 Aligned_cols=35 Identities=23% Similarity=0.171 Sum_probs=26.8
Q ss_pred HHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 76 LRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 76 l~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
+.+..-.|-...+||..+ |-+...|++|....+++
T Consensus 122 ~~L~~~~g~s~~EIA~~l-~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 122 FLLAQVDGLGYGEIATEL-GISLATVKRYLNKAAMR 156 (161)
T ss_pred HHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 333344577899999999 99999999998776554
No 136
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=35.50 E-value=80 Score=27.33 Aligned_cols=29 Identities=10% Similarity=0.106 Sum_probs=23.0
Q ss_pred HhcCCcHHHHhhhcCCCCHHHHHHHHHHHh
Q 022144 80 ARFGNKWATIARLLSGRTDNAIKNHWNSTL 109 (302)
Q Consensus 80 ~~~GnkW~~IA~~l~gRT~~q~knRw~~~L 109 (302)
...|-.-.+||..| |-+...|++|....+
T Consensus 149 ~~~g~s~~EIA~~l-gis~~tVk~~l~Rar 177 (195)
T PRK12532 149 EILGFSSDEIQQMC-GISTSNYHTIMHRAR 177 (195)
T ss_pred HHhCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 34567789999999 999999999877543
No 137
>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=34.85 E-value=97 Score=25.75 Aligned_cols=29 Identities=31% Similarity=0.391 Sum_probs=22.5
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|-...+||+.| |-+...|+++....+++
T Consensus 137 ~g~s~~eIA~~l-~is~~tv~~~l~ra~~~ 165 (170)
T TIGR02952 137 QNLPIAEVARIL-GKTEGAVKILQFRAIKK 165 (170)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 366788999998 88999999887655443
No 138
>PRK00118 putative DNA-binding protein; Validated
Probab=34.85 E-value=1.1e+02 Score=25.13 Aligned_cols=40 Identities=13% Similarity=0.061 Sum_probs=32.6
Q ss_pred hHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHh
Q 022144 69 PEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTL 109 (302)
Q Consensus 69 ~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~L 109 (302)
++.++.++.+....|-...+||+.+ |-+...|+++.....
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~RAr 58 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKRTE 58 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 4566777788888899999999999 999999988866443
No 139
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=34.63 E-value=20 Score=37.71 Aligned_cols=48 Identities=23% Similarity=0.400 Sum_probs=42.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCcccccccccc
Q 022144 8 VDRIKGPWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWCN 56 (302)
Q Consensus 8 ~~~~Kg~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~n 56 (302)
.....++|+.+|-+++.......| .+.+.|+..+++|+.+|++.++..
T Consensus 405 k~~~~~~w~~se~e~fyka~~~~g-s~~slis~l~p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 405 KKLETDKWDASETELFYKALSERG-SDFSLISNLFPLRDRKQIKAKFKK 452 (584)
T ss_pred CccccCcccchhhHHhhhHHhhhc-ccccccccccccccHHHHHHHHhh
Confidence 355678999999999999999999 569999999999999999987653
No 140
>PRK01905 DNA-binding protein Fis; Provisional
Probab=34.48 E-value=1.1e+02 Score=23.26 Aligned_cols=37 Identities=16% Similarity=0.181 Sum_probs=28.8
Q ss_pred hHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHH
Q 022144 69 PEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWN 106 (302)
Q Consensus 69 ~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~ 106 (302)
.-|.+.|.+++..+|+++.+.|+.+ |=+...++.+.+
T Consensus 36 ~~E~~~i~~aL~~~~gn~s~aAr~L-GIsrstL~rklk 72 (77)
T PRK01905 36 CVEKPLLEVVMEQAGGNQSLAAEYL-GINRNTLRKKLQ 72 (77)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHH
Confidence 3467789999999999999999988 666666655443
No 141
>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=34.33 E-value=55 Score=25.51 Aligned_cols=31 Identities=26% Similarity=0.473 Sum_probs=23.5
Q ss_pred HHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHH
Q 022144 72 DETILRAHARFGNKWATIARLLSGRTDNAIKN 103 (302)
Q Consensus 72 D~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~kn 103 (302)
|..|-.+....|.+|..+|+.| |=+...|.+
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 4567777788999999999998 666555544
No 142
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=34.32 E-value=78 Score=26.92 Aligned_cols=29 Identities=21% Similarity=0.250 Sum_probs=24.2
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|-...+||+.+ |-+...|++|....+++
T Consensus 134 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 162 (172)
T PRK09651 134 DGLTYSEIAHKL-GVSVSSVKKYVAKATEH 162 (172)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 456799999999 99999999998766554
No 143
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=34.05 E-value=55 Score=26.30 Aligned_cols=68 Identities=13% Similarity=0.322 Sum_probs=39.8
Q ss_pred CCCCCHHHHHHHHHHHHHh----CC---CCHHHHHhhCCCC-----Cccc-------ccccccccCCCCCCCC---CCCh
Q 022144 12 KGPWSPEEDEALQRLVQNY----GP---RNWSLISKSIPGR-----SGKS-------CRLRWCNQLSPQVEHR---PFTP 69 (302)
Q Consensus 12 Kg~WT~EED~~L~~lV~k~----G~---~nW~~IA~~lp~R-----t~kq-------Cr~Rw~n~L~p~~kk~---~WT~ 69 (302)
...||+|++-.|++.+..| |. .+|..+...+.+. +..| .+.||.+.... .++| .++.
T Consensus 4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~~~k-~~~g~~~~~~~ 82 (98)
T PF04504_consen 4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNAVKK-SKNGKDPSFSK 82 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHhhh-cccCcCCCCCC
Confidence 4569999999999998877 52 2565554444221 2222 23455554443 2222 5777
Q ss_pred HHHHHHHHHHH
Q 022144 70 EEDETILRAHA 80 (302)
Q Consensus 70 EED~~Ll~lv~ 80 (302)
.-|+.+.+|-+
T Consensus 83 ~hd~~~f~Lsk 93 (98)
T PF04504_consen 83 PHDRRLFELSK 93 (98)
T ss_pred HhHHHHHHHHH
Confidence 77777777654
No 144
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=33.95 E-value=98 Score=26.49 Aligned_cols=31 Identities=29% Similarity=0.240 Sum_probs=24.7
Q ss_pred HhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 80 ARFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 80 ~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
...|-...+||+.| |.+...|+++....+++
T Consensus 142 ~~~g~s~~EIA~~l-~is~~tV~~~l~rar~~ 172 (181)
T PRK12536 142 KLEGLSVAETAQLT-GLSESAVKVGIHRGLKA 172 (181)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 34567899999999 99999999997665443
No 145
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=33.76 E-value=1e+02 Score=25.88 Aligned_cols=31 Identities=19% Similarity=0.227 Sum_probs=24.2
Q ss_pred HhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 80 ARFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 80 ~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
...|-...+||..+ |-+...|+++-...+++
T Consensus 125 ~~~g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 155 (164)
T PRK12547 125 GASGFSYEDAAAIC-GCAVGTIKSRVSRARNR 155 (164)
T ss_pred HHcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 34567789999999 88999999988765544
No 146
>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=33.50 E-value=52 Score=25.80 Aligned_cols=29 Identities=31% Similarity=0.526 Sum_probs=21.6
Q ss_pred HHHHHHHhcCCcHHHHhhhcCCCCHHHHHH
Q 022144 74 TILRAHARFGNKWATIARLLSGRTDNAIKN 103 (302)
Q Consensus 74 ~Ll~lv~~~GnkW~~IA~~l~gRT~~q~kn 103 (302)
.|-.+....|.+|..+|+.| |=+..+|..
T Consensus 4 ~l~~l~~~lG~~Wk~lar~L-G~s~~eI~~ 32 (86)
T cd08777 4 HLDLLRENLGKKWKRCARKL-GFTESEIEE 32 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHc-CCCHHHHHH
Confidence 34445577899999999999 766666644
No 147
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=33.28 E-value=1e+02 Score=26.19 Aligned_cols=29 Identities=14% Similarity=0.162 Sum_probs=22.9
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|-.-.+||..| |.+...|+++....+++
T Consensus 144 ~g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 172 (179)
T PRK12514 144 EGLSYKELAERH-DVPLNTMRTWLRRSLLK 172 (179)
T ss_pred cCCCHHHHHHHH-CCChHHHHHHHHHHHHH
Confidence 366788999999 99999999988755443
No 148
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=32.80 E-value=1e+02 Score=26.41 Aligned_cols=30 Identities=17% Similarity=0.444 Sum_probs=23.9
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
-+|-...+||..| |-+...|++|....+++
T Consensus 136 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 165 (185)
T PRK12542 136 FYNLTYQEISSVM-GITEANVRKQFERARKR 165 (185)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 4567789999999 99999999987654443
No 149
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=32.77 E-value=1.1e+02 Score=26.18 Aligned_cols=29 Identities=28% Similarity=0.310 Sum_probs=23.2
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|-.-.+||..+ |-+...|+++.+..+++
T Consensus 150 ~~~s~~eIA~~l-gis~~~V~~~l~ra~~~ 178 (186)
T PRK13919 150 QGYTHREAAQLL-GLPLGTLKTRARRALSR 178 (186)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 456688999999 99999999988765544
No 150
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=32.68 E-value=37 Score=27.86 Aligned_cols=28 Identities=21% Similarity=0.192 Sum_probs=23.2
Q ss_pred CCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 83 GNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 83 GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
|-.+.+||..| |=+...|++++....++
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 45699999999 99999999998766544
No 151
>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=32.45 E-value=35 Score=29.73 Aligned_cols=31 Identities=16% Similarity=0.314 Sum_probs=25.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCHHHHHhh
Q 022144 10 RIKGPWSPEEDEALQRLVQNYGPRNWSLISKS 41 (302)
Q Consensus 10 ~~Kg~WT~EED~~L~~lV~k~G~~nW~~IA~~ 41 (302)
.....=|..|.+-|..||++|| .|+...+.-
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhG-dDy~aMarD 142 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHG-DDYKAMARD 142 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHC-ccHHHHhcc
Confidence 4566788999999999999999 678888753
No 152
>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=32.08 E-value=1e+02 Score=25.56 Aligned_cols=40 Identities=18% Similarity=0.179 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 71 EDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 71 ED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
+++.++.+.--.|-.-.+||..| |-+...|+++....+++
T Consensus 114 ~~r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~ra~~~ 153 (162)
T TIGR02983 114 RQRAVVVLRYYEDLSEAQVAEAL-GISVGTVKSRLSRALAR 153 (162)
T ss_pred HHHHHhhhHHHhcCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 34444444445567789999998 99999999998766554
No 153
>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=31.50 E-value=1.2e+02 Score=25.76 Aligned_cols=30 Identities=27% Similarity=0.444 Sum_probs=23.6
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
-.|-...+||..+ |-+...|+.+....+++
T Consensus 154 ~~g~s~~eIA~~l-gis~~~v~~~l~Ra~~~ 183 (189)
T TIGR02984 154 LEGLSFAEVAERM-DRSEGAVSMLWVRGLAR 183 (189)
T ss_pred hcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 4567789999988 99999999988765544
No 154
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=31.48 E-value=64 Score=21.87 Aligned_cols=38 Identities=29% Similarity=0.425 Sum_probs=18.8
Q ss_pred CCCChHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHH
Q 022144 65 RPFTPEEDETILRAHARFGNKWATIARLLSGRTDNAIKNH 104 (302)
Q Consensus 65 ~~WT~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knR 104 (302)
..+|.+|=..|..+ .+-|..=.+||+.| ||+...|.+.
T Consensus 3 ~~Lt~~eR~~I~~l-~~~G~s~~~IA~~l-g~s~sTV~re 40 (44)
T PF13936_consen 3 KHLTPEERNQIEAL-LEQGMSIREIAKRL-GRSRSTVSRE 40 (44)
T ss_dssp ---------HHHHH-HCS---HHHHHHHT-T--HHHHHHH
T ss_pred cchhhhHHHHHHHH-HHcCCCHHHHHHHH-CcCcHHHHHH
Confidence 35666666666555 46788889999999 9999888763
No 155
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=31.39 E-value=1.1e+02 Score=26.29 Aligned_cols=29 Identities=14% Similarity=-0.078 Sum_probs=23.2
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|..-.+||..| |-+.+.|++|....+++
T Consensus 146 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 174 (191)
T PRK12520 146 LELETEEICQEL-QITATNAWVLLYRARMR 174 (191)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466788999999 99999999998765443
No 156
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=31.30 E-value=1.1e+02 Score=26.86 Aligned_cols=27 Identities=15% Similarity=-0.040 Sum_probs=21.9
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTL 109 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~L 109 (302)
.|-.-.+||..| |.+...|++|....+
T Consensus 154 eg~s~~EIA~~l-gis~~tVk~~l~RAr 180 (201)
T PRK12545 154 LDFEIDDICTEL-TLTANHCSVLLYRAR 180 (201)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 456789999999 999999999876443
No 157
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptor
Probab=31.06 E-value=63 Score=24.95 Aligned_cols=33 Identities=39% Similarity=0.638 Sum_probs=23.9
Q ss_pred hHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHH
Q 022144 69 PEEDETILRAHARFGNKWATIARLLSGRTDNAIKN 103 (302)
Q Consensus 69 ~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~kn 103 (302)
.||-++|+.. -..|.+|..+|+.| |=+...|.+
T Consensus 2 ~~~v~~ll~~-~nlG~dW~~LA~~L-G~~~~~I~~ 34 (77)
T cd08311 2 QEEVEKLLES-GRPGRDWRSLAGEL-GYEDEAIDT 34 (77)
T ss_pred hHHHHHHHhC-CCCccCHHHHHHHc-CCCHHHHHH
Confidence 5777777732 25688999999999 766666654
No 158
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=30.62 E-value=92 Score=29.24 Aligned_cols=29 Identities=21% Similarity=0.311 Sum_probs=23.7
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
+|-.-.+||..| |.+...|++|....+++
T Consensus 157 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 185 (324)
T TIGR02960 157 LGWRAAETAELL-GTSTASVNSALQRARAT 185 (324)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 467789999999 99999999998755443
No 159
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=30.61 E-value=93 Score=35.19 Aligned_cols=42 Identities=19% Similarity=0.417 Sum_probs=35.4
Q ss_pred CCChHHHHHHHHHHHhcC-CcHHHHhhhcCCCCHHHHHHHHHH
Q 022144 66 PFTPEEDETILRAHARFG-NKWATIARLLSGRTDNAIKNHWNS 107 (302)
Q Consensus 66 ~WT~EED~~Ll~lv~~~G-nkW~~IA~~l~gRT~~q~knRw~~ 107 (302)
.|+.-|=..++.+..+|| ++-..||..+.|+|...|+.....
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~~ 868 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAKV 868 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHHH
Confidence 577777788888888999 779999999999999999875443
No 160
>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=30.39 E-value=63 Score=25.25 Aligned_cols=21 Identities=29% Similarity=0.572 Sum_probs=18.7
Q ss_pred HHHHHHHHhcCCcHHHHhhhc
Q 022144 73 ETILRAHARFGNKWATIARLL 93 (302)
Q Consensus 73 ~~Ll~lv~~~GnkW~~IA~~l 93 (302)
..|..+..+.|.+|..++++|
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L 23 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL 23 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc
Confidence 457888899999999999988
No 161
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=30.08 E-value=1.3e+02 Score=23.97 Aligned_cols=35 Identities=11% Similarity=0.069 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHH
Q 022144 70 EEDETILRAHARFGNKWATIARLLSGRTDNAIKNHW 105 (302)
Q Consensus 70 EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw 105 (302)
-|...|.+++..+|+++.+.|+.| |=+...++.+-
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~L-GIsRsTL~rKL 89 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALML-GINRGTLRKKL 89 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 467789999999999999999998 66666665544
No 162
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=29.94 E-value=1.2e+02 Score=25.93 Aligned_cols=30 Identities=30% Similarity=0.277 Sum_probs=23.4
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
..|-.-..||..+ |-+...|++++...+++
T Consensus 147 ~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 176 (182)
T PRK12537 147 VDGCSHAEIAQRL-GAPLGTVKAWIKRSLKA 176 (182)
T ss_pred HcCCCHHHHHHHH-CCChhhHHHHHHHHHHH
Confidence 3456688889888 88999999988776654
No 163
>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=29.29 E-value=1.1e+02 Score=17.25 Aligned_cols=36 Identities=33% Similarity=0.378 Sum_probs=23.1
Q ss_pred CCChHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHH
Q 022144 66 PFTPEEDETILRAHARFGNKWATIARLLSGRTDNAIKN 103 (302)
Q Consensus 66 ~WT~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~kn 103 (302)
.++.++-..+++++ .-|..+..|++.+ |.+...+.+
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 35555444555443 4566789999888 777776655
No 164
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=29.17 E-value=1.1e+02 Score=26.66 Aligned_cols=31 Identities=16% Similarity=0.164 Sum_probs=24.2
Q ss_pred HHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhh
Q 022144 79 HARFGNKWATIARLLSGRTDNAIKNHWNSTLK 110 (302)
Q Consensus 79 v~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lk 110 (302)
....|-...+||..| |-+...|+++....++
T Consensus 125 ~~~~g~s~~EIA~~L-giS~~tVk~~l~Rar~ 155 (188)
T PRK12546 125 VGASGFSYEEAAEMC-GVAVGTVKSRANRARA 155 (188)
T ss_pred HHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 334577899999999 8999999998765443
No 165
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=28.87 E-value=1.2e+02 Score=25.93 Aligned_cols=28 Identities=11% Similarity=0.000 Sum_probs=21.2
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTL 109 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~L 109 (302)
-.|-...+||+.+ |-+...|+++....+
T Consensus 142 ~~g~s~~EIA~~l-gis~~tV~~~l~Rar 169 (186)
T PRK05602 142 YQGLSNIEAAAVM-DISVDALESLLARGR 169 (186)
T ss_pred hcCCCHHHHHHHh-CcCHHHHHHHHHHHH
Confidence 3466788888888 888888888876543
No 166
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=28.83 E-value=1.4e+02 Score=24.73 Aligned_cols=46 Identities=15% Similarity=0.099 Sum_probs=37.8
Q ss_pred hHHHHHHHHHHHhcC-CcHHHHhhhcCCCCHHHHHHHHHHHhhhhccC
Q 022144 69 PEEDETILRAHARFG-NKWATIARLLSGRTDNAIKNHWNSTLKRKCSS 115 (302)
Q Consensus 69 ~EED~~Ll~lv~~~G-nkW~~IA~~l~gRT~~q~knRw~~~Lkrk~~~ 115 (302)
.+-|..|+++.++-| .-+..||+.+ |-+...|.+|-+.+.+.-+-.
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~GiI~ 53 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGVIK 53 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCcee
Confidence 456788888888877 5699999999 999999999998887776443
No 167
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=28.26 E-value=2e+02 Score=19.72 Aligned_cols=45 Identities=20% Similarity=0.292 Sum_probs=35.3
Q ss_pred CCCCCChHHHHHHHHHHHhcC----CcHHHHhhhcCCCCHHHHHHHHHHH
Q 022144 63 EHRPFTPEEDETILRAHARFG----NKWATIARLLSGRTDNAIKNHWNST 108 (302)
Q Consensus 63 kk~~WT~EED~~Ll~lv~~~G----nkW~~IA~~l~gRT~~q~knRw~~~ 108 (302)
.+..||.++-..|.+...... ..-..||..+ |=+..+|+++|.+-
T Consensus 3 ~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l-~l~~~~V~~WF~nr 51 (57)
T PF00046_consen 3 KRTRFTKEQLKVLEEYFQENPYPSKEEREELAKEL-GLTERQVKNWFQNR 51 (57)
T ss_dssp SSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHH-TSSHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHhccccccccccccccc-cccccccccCHHHh
Confidence 456789998888888888743 2367888888 99999999977643
No 168
>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=28.16 E-value=77 Score=24.93 Aligned_cols=22 Identities=27% Similarity=0.513 Sum_probs=18.9
Q ss_pred HHHHHHHHHhcCCcHHHHhhhc
Q 022144 72 DETILRAHARFGNKWATIARLL 93 (302)
Q Consensus 72 D~~Ll~lv~~~GnkW~~IA~~l 93 (302)
|..|..+....|.+|.++|+.|
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L 25 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL 25 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc
Confidence 4567778889999999999987
No 169
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=28.10 E-value=1.3e+02 Score=27.27 Aligned_cols=44 Identities=27% Similarity=0.296 Sum_probs=34.8
Q ss_pred CCChHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhhh
Q 022144 66 PFTPEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKRK 112 (302)
Q Consensus 66 ~WT~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkrk 112 (302)
..|+-|-+.| +++.+ |....+||+.| +-+...+++|...++++-
T Consensus 155 ~Lt~rE~~Vl-~l~~~-G~s~~eIA~~L-~iS~~TVk~~~~~i~~Kl 198 (216)
T PRK10100 155 LLTHREKEIL-NKLRI-GASNNEIARSL-FISENTVKTHLYNLFKKI 198 (216)
T ss_pred CCCHHHHHHH-HHHHc-CCCHHHHHHHh-CCCHHHHHHHHHHHHHHh
Confidence 4787665554 45555 88899999999 899999999998887765
No 170
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=27.54 E-value=1.4e+02 Score=26.44 Aligned_cols=29 Identities=17% Similarity=0.234 Sum_probs=22.8
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|..-.+||..| |-+...|++++...+++
T Consensus 153 ~g~s~~EIA~~L-gis~~tV~~~l~RArk~ 181 (203)
T PRK09647 153 EGLSYEEIAATL-GVKLGTVRSRIHRGRQQ 181 (203)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466788889988 89999999988765444
No 171
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=26.82 E-value=77 Score=28.56 Aligned_cols=27 Identities=15% Similarity=0.214 Sum_probs=22.2
Q ss_pred CCcHHHHhhhcCCCCHHHHHHHHHHHhh
Q 022144 83 GNKWATIARLLSGRTDNAIKNHWNSTLK 110 (302)
Q Consensus 83 GnkW~~IA~~l~gRT~~q~knRw~~~Lk 110 (302)
|-...+||..| |-+...|++++...++
T Consensus 165 g~s~~EIAe~l-gis~~tVk~~l~Rar~ 191 (231)
T PRK11922 165 ELSVEETAQAL-GLPEETVKTRLHRARR 191 (231)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 56789999999 9999999999875543
No 172
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=26.60 E-value=67 Score=27.08 Aligned_cols=29 Identities=21% Similarity=0.515 Sum_probs=23.1
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
+|.....||..| |-+...|+.+....+++
T Consensus 141 ~g~s~~eIA~~l-~is~~~V~~~l~ra~~~ 169 (176)
T PRK09638 141 YGYTYEEIAKML-NIPEGTVKSRVHHGIKQ 169 (176)
T ss_pred cCCCHHHHHHHH-CCChhHHHHHHHHHHHH
Confidence 567799999999 88999998887655443
No 173
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=26.33 E-value=1.6e+02 Score=25.44 Aligned_cols=29 Identities=38% Similarity=0.497 Sum_probs=22.6
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|..-.+||+.+ |-+...|+++-...+++
T Consensus 146 ~g~s~~EIAe~l-gis~~~V~~~l~Ra~~~ 174 (189)
T PRK06811 146 LGEKIEEIAKKL-GLTRSAIDNRLSRGRKK 174 (189)
T ss_pred ccCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 356678899988 99999999987765544
No 174
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=26.11 E-value=47 Score=31.82 Aligned_cols=48 Identities=13% Similarity=0.024 Sum_probs=35.2
Q ss_pred CCCCChHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 64 HRPFTPEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 64 k~~WT~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
+..||+++...+.+++..|+.-|..|-+++.-++..+++.+|+..+-.
T Consensus 53 ~~~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~p~ 100 (335)
T KOG0724|consen 53 EPRRTPDSWDKFAEALPLEKRLEDKIEEYIGLVFDVNIRESGQKPFPK 100 (335)
T ss_pred ccccchhhhhHHHhcCccccccchhHHhhhhhHHHHhhhhccCCCccc
Confidence 345888888888777777777788888888777877777777655433
No 175
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=25.86 E-value=1.6e+02 Score=24.34 Aligned_cols=29 Identities=21% Similarity=0.347 Sum_probs=22.0
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|-.-..||..| |-+...|+++....+++
T Consensus 126 ~g~s~~eIA~~l-gis~~tV~~~i~ra~~~ 154 (166)
T PRK09639 126 SGYSYKEIAEAL-GIKESSVGTTLARAKKK 154 (166)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 566678889888 88999998887654443
No 176
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=25.77 E-value=1.4e+02 Score=26.85 Aligned_cols=37 Identities=16% Similarity=0.232 Sum_probs=26.7
Q ss_pred HHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 74 TILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 74 ~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.++.++...|-...+||+.+ |-+...|+++....+++
T Consensus 191 ~vl~l~~~~g~s~~EIA~~l-gis~~tV~~~~~ra~~~ 227 (236)
T PRK06986 191 LVLSLYYQEELNLKEIGAVL-GVSESRVSQIHSQAIKR 227 (236)
T ss_pred HHHHhHhccCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 33333334566799999999 99999999887765544
No 177
>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=25.67 E-value=98 Score=24.10 Aligned_cols=27 Identities=26% Similarity=0.496 Sum_probs=19.1
Q ss_pred HHHHHHhcCCcHHHHhhhcCCCCHHHHH
Q 022144 75 ILRAHARFGNKWATIARLLSGRTDNAIK 102 (302)
Q Consensus 75 Ll~lv~~~GnkW~~IA~~l~gRT~~q~k 102 (302)
+--+....|.+|..+++.| |=|..+|.
T Consensus 5 f~~i~~~lG~~Wk~laR~L-Glse~~Id 31 (86)
T cd08306 5 FDVICENVGRDWRKLARKL-GLSETKIE 31 (86)
T ss_pred HHHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 3444566799999999998 55555543
No 178
>PRK13991 cell division topological specificity factor MinE; Provisional
Probab=25.57 E-value=90 Score=24.88 Aligned_cols=32 Identities=13% Similarity=0.486 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHHHHHHHHHHHhcCCCCCccch
Q 022144 253 FSPEFLAVMQEMIRKEVRNYMSGVERNGLCLP 284 (302)
Q Consensus 253 ~~~~~~~~mqemi~~ev~~ym~~~~~~~~~~~ 284 (302)
.++++|..|++=|-+=|+.||..++.+.+..+
T Consensus 34 ~~p~~l~~lk~eil~VIsKYv~~Id~~~i~V~ 65 (87)
T PRK13991 34 LTPEMMEQMKADLAEVIKRYVPAIDAEAIEVT 65 (87)
T ss_pred CCHHHHHHHHHHHHHHHHHHhcccCccceEEE
Confidence 69999999999999999999997766655543
No 179
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=25.31 E-value=1.7e+02 Score=25.42 Aligned_cols=29 Identities=21% Similarity=0.208 Sum_probs=22.2
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|-...+||+.| |-+...|+++-...+++
T Consensus 157 ~~~s~~EIA~~L-gis~~tVk~~l~ra~~~ 185 (194)
T PRK09646 157 GGLTYREVAERL-AVPLGTVKTRMRDGLIR 185 (194)
T ss_pred cCCCHHHHHHHh-CCChHhHHHHHHHHHHH
Confidence 456689999999 88999998887655443
No 180
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=25.28 E-value=1.5e+02 Score=27.75 Aligned_cols=29 Identities=31% Similarity=0.424 Sum_probs=23.7
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
+|-.-.+||+.| |.+...|+++...-.++
T Consensus 130 ~g~s~~EIA~~l-g~s~~tVk~~l~RAr~~ 158 (293)
T PRK09636 130 FGVPFDEIASTL-GRSPAACRQLASRARKH 158 (293)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466789999999 99999999998755444
No 181
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=25.19 E-value=1.3e+02 Score=27.40 Aligned_cols=29 Identities=14% Similarity=0.084 Sum_probs=23.0
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|-.-.+||..| |-+...|++|....+++
T Consensus 186 eg~s~~EIA~~L-gis~~tVk~~l~RAr~k 214 (233)
T PRK12538 186 ENMSNGEIAEVM-DTTVAAVESLLKRGRQQ 214 (233)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 456789999999 99999999987755443
No 182
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=24.90 E-value=49 Score=25.93 Aligned_cols=43 Identities=16% Similarity=0.088 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHhCCCCHHHHHhhCCCCCcccccccccccCCCC
Q 022144 18 EEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRLRWCNQLSPQ 61 (302)
Q Consensus 18 EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~Rw~n~L~p~ 61 (302)
+.|..|+.++.+.+...++.|++.+ |-+...|+.|..+..+.+
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g 45 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEG 45 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCC
Confidence 5788999999999888899999988 778888888776655443
No 183
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.62 E-value=1.1e+02 Score=20.48 Aligned_cols=30 Identities=23% Similarity=0.307 Sum_probs=20.1
Q ss_pred HHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHH
Q 022144 73 ETILRAHARFGNKWATIARLLSGRTDNAIKNH 104 (302)
Q Consensus 73 ~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knR 104 (302)
..++.++.+ |.....||+.| |-+...|.+.
T Consensus 8 ~~ii~l~~~-G~s~~~ia~~l-gvs~~Tv~~w 37 (50)
T PF13384_consen 8 AQIIRLLRE-GWSIREIAKRL-GVSRSTVYRW 37 (50)
T ss_dssp --HHHHHHH-T--HHHHHHHH-TS-HHHHHHH
T ss_pred HHHHHHHHC-CCCHHHHHHHH-CcCHHHHHHH
Confidence 356666666 99999999999 8888877764
No 184
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=24.38 E-value=1.4e+02 Score=25.66 Aligned_cols=29 Identities=24% Similarity=0.201 Sum_probs=21.7
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|-.-.+||..| |-+...|+.+....+++
T Consensus 156 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 184 (194)
T PRK12519 156 EGLSQSEIAKRL-GIPLGTVKARARQGLLK 184 (194)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 456688888888 88999998887654443
No 185
>KOG4834 consensus Predicted DNA-binding protein, contains SANT domain [General function prediction only]
Probab=24.32 E-value=23 Score=33.37 Aligned_cols=44 Identities=9% Similarity=-0.201 Sum_probs=34.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHhhCCCCCcccccc
Q 022144 8 VDRIKGPWSPEEDEALQRLVQNYGPRNWSLISKSIPGRSGKSCRL 52 (302)
Q Consensus 8 ~~~~Kg~WT~EED~~L~~lV~k~G~~nW~~IA~~lp~Rt~kqCr~ 52 (302)
...-.|+|+.+|...|..-+.++|+ +-.+|+..+.+|+..|.+.
T Consensus 7 ~~~p~~~~~~~~i~~~~~s~~r~~~-~~~~~sls~~~~~~~q~~~ 50 (280)
T KOG4834|consen 7 GHVPPVASNTVTIGTSANSQVRIGP-STQIRSLSNVALRHHQPVP 50 (280)
T ss_pred CCCCCccccceeecccccceEEecC-cceeeeehhhhhhcccchh
Confidence 3456789999999999999999995 4777777777777776654
No 186
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=24.23 E-value=1.8e+02 Score=25.87 Aligned_cols=29 Identities=7% Similarity=-0.049 Sum_probs=23.0
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|-.-.+||..| |-|.+.+++|....+++
T Consensus 163 ~g~s~~EIAe~l-gis~~tV~~~l~RAr~~ 191 (206)
T PRK12544 163 IELETNEICHAV-DLSVSNLNVLLYRARLR 191 (206)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 466689999999 99999999997655433
No 187
>PF09650 PHA_gran_rgn: Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn); InterPro: IPR013433 Proteins in this entry are encoded by genes involved in either polyhydroxyalkanoic acid (PHA) biosynthesis or utilisation, including proteins at found at the surface of PHA granules. These proteins have so far been predominantly found in the Pseudomonadales, Xanthomonadales, and Vibrionales, all of which belong to the Gammaproteobacteria.
Probab=23.88 E-value=89 Score=24.57 Aligned_cols=21 Identities=14% Similarity=0.244 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhc
Q 022144 255 PEFLAVMQEMIRKEVRNYMSG 275 (302)
Q Consensus 255 ~~~~~~mqemi~~ev~~ym~~ 275 (302)
+-++..|..+|..||+.|+..
T Consensus 65 g~Ll~~f~~~Ie~~I~~~Ld~ 85 (87)
T PF09650_consen 65 GFLLSPFKGKIEQEIEKNLDK 85 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 568899999999999999864
No 188
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=23.84 E-value=1.3e+02 Score=28.54 Aligned_cols=30 Identities=20% Similarity=0.200 Sum_probs=24.2
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKRK 112 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkrk 112 (302)
+|-.-.+||..| |-+...|++|....+++.
T Consensus 168 ~g~s~~EIA~~l-gis~~tVk~~l~RAr~~L 197 (339)
T PRK08241 168 LGWSAAEVAELL-DTSVAAVNSALQRARATL 197 (339)
T ss_pred hCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 466789999999 999999999987655543
No 189
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=23.72 E-value=52 Score=24.95 Aligned_cols=18 Identities=11% Similarity=0.353 Sum_probs=15.0
Q ss_pred HHHHHHHhcCCcHHHHhh
Q 022144 74 TILRAHARFGNKWATIAR 91 (302)
Q Consensus 74 ~Ll~lv~~~GnkW~~IA~ 91 (302)
.|.+|.+.||++|.-|-.
T Consensus 31 vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 31 VLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHcCCchhhhc
Confidence 577888999999999864
No 190
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=23.53 E-value=1.7e+02 Score=25.02 Aligned_cols=29 Identities=17% Similarity=0.171 Sum_probs=21.8
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|..-..||..| |-+...|++|....+++
T Consensus 142 ~g~s~~EIA~~l-~is~~tv~~~l~Ra~~~ 170 (179)
T PRK09415 142 EELSIKEIAEVT-GVNENTVKTRLKKAKEL 170 (179)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355678888888 77889999888766544
No 191
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=22.57 E-value=1.8e+02 Score=27.12 Aligned_cols=30 Identities=13% Similarity=0.346 Sum_probs=24.1
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
-+|-.-.+||+.| |.+...|+++.....++
T Consensus 122 ~~g~s~~EIA~~l-g~s~~tVr~~l~RAr~~ 151 (281)
T TIGR02957 122 VFDYPYEEIASIV-GKSEANCRQLVSRARRH 151 (281)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3566789999999 89999999988755444
No 192
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=22.56 E-value=2.2e+02 Score=23.55 Aligned_cols=45 Identities=20% Similarity=0.282 Sum_probs=34.8
Q ss_pred CCCChHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhhh
Q 022144 65 RPFTPEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKRK 112 (302)
Q Consensus 65 ~~WT~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkrk 112 (302)
..+|+.|-+.|.-+.. |-....||+.+ +-+...++.|.+++.++.
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 4688888877665554 55788999999 789999999888776654
No 193
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=22.46 E-value=2e+02 Score=25.27 Aligned_cols=29 Identities=14% Similarity=0.092 Sum_probs=22.5
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|-.-.+||..+ |.+.+.|+++....+++
T Consensus 168 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 196 (206)
T PRK12526 168 QELSQEQLAQQL-NVPLGTVKSRLRLALAK 196 (206)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 356678999999 99999999987655443
No 194
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=22.41 E-value=2e+02 Score=25.64 Aligned_cols=30 Identities=20% Similarity=0.179 Sum_probs=23.3
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
..|..-.+||+.+ |-+...|+.+....+++
T Consensus 192 ~~~~s~~eIA~~l-gis~~~v~~~~~ra~~~ 221 (227)
T TIGR02980 192 FEDKTQSEIAERL-GISQMHVSRLLRRALKK 221 (227)
T ss_pred hcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3466789999999 88999998887665554
No 195
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=22.36 E-value=2.2e+02 Score=23.94 Aligned_cols=30 Identities=20% Similarity=0.156 Sum_probs=23.6
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKRK 112 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkrk 112 (302)
.|-...+||..| |-+...|+++....++..
T Consensus 133 eg~s~~EIA~~l-~is~~tV~~~l~ra~~~~ 162 (168)
T PRK12525 133 EGLTYVEIGERL-GVSLSRIHQYMVEAFKCC 162 (168)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 456789999999 889999999887665543
No 196
>PRK06930 positive control sigma-like factor; Validated
Probab=22.21 E-value=2.1e+02 Score=25.12 Aligned_cols=36 Identities=17% Similarity=0.330 Sum_probs=26.4
Q ss_pred HHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 75 ILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 75 Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
++.++...|.....||..| |-+...|+.+....+++
T Consensus 122 V~~L~~~eg~s~~EIA~~l-giS~~tVk~~l~Ra~~k 157 (170)
T PRK06930 122 VYLMHRGYGLSYSEIADYL-NIKKSTVQSMIERAEKK 157 (170)
T ss_pred HHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3334445677899999999 88999999887765544
No 197
>PRK09483 response regulator; Provisional
Probab=22.00 E-value=1.4e+02 Score=25.14 Aligned_cols=45 Identities=13% Similarity=0.162 Sum_probs=34.5
Q ss_pred CCCChHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhhh
Q 022144 65 RPFTPEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKRK 112 (302)
Q Consensus 65 ~~WT~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkrk 112 (302)
...|+-|-+.|.-++ .|..=.+||..| +-+...|++|-+++++|-
T Consensus 147 ~~Lt~rE~~vl~~~~--~G~~~~~Ia~~l-~is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 147 ASLSERELQIMLMIT--KGQKVNEISEQL-NLSPKTVNSYRYRMFSKL 191 (217)
T ss_pred cccCHHHHHHHHHHH--CCCCHHHHHHHh-CCCHHHHHHHHHHHHHHc
Confidence 358998888875443 555556999999 779999999888777765
No 198
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=21.97 E-value=2.3e+02 Score=24.03 Aligned_cols=30 Identities=23% Similarity=0.124 Sum_probs=22.2
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
..|-.=.+||..| |-+...++++....+++
T Consensus 114 ~~g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 143 (170)
T TIGR02959 114 LEGLSQQEIAEKL-GLSLSGAKSRVQRGRKK 143 (170)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3456678888888 88899998887654433
No 199
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=21.61 E-value=1.1e+02 Score=22.47 Aligned_cols=19 Identities=26% Similarity=0.656 Sum_probs=15.4
Q ss_pred HHHHHHhcCCcHHHHhhhc
Q 022144 75 ILRAHARFGNKWATIARLL 93 (302)
Q Consensus 75 Ll~lv~~~GnkW~~IA~~l 93 (302)
+..+....|++|..+|+.|
T Consensus 2 ~~~ia~~lg~~W~~la~~L 20 (79)
T cd01670 2 LDKLAKKLGKDWKKLARKL 20 (79)
T ss_pred HHHHHHHHhhHHHHHHHHh
Confidence 3456677899999999988
No 200
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=21.58 E-value=2.1e+02 Score=24.74 Aligned_cols=28 Identities=14% Similarity=0.135 Sum_probs=22.1
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLK 110 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lk 110 (302)
.|-...+||..| |-+...|+++....++
T Consensus 126 eg~s~~EIA~~l-gis~~tV~~~l~Rar~ 153 (182)
T PRK12511 126 EGLSYQEAAAVL-GIPIGTLMSRIGRARA 153 (182)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHH
Confidence 466789999999 8899999998765443
No 201
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=21.55 E-value=2.4e+02 Score=23.13 Aligned_cols=28 Identities=29% Similarity=0.272 Sum_probs=19.5
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLK 110 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lk 110 (302)
.|-.=.+||..+ |=+...|+.+.....+
T Consensus 126 ~g~~~~eIA~~l-~is~~tv~~~l~Rar~ 153 (159)
T TIGR02989 126 RGVSLTALAEQL-GRTVNAVYKALSRLRV 153 (159)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 355677788777 7788888887655443
No 202
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=21.52 E-value=2.4e+02 Score=25.86 Aligned_cols=44 Identities=18% Similarity=0.246 Sum_probs=35.7
Q ss_pred CCChHHHHHHHHHHHhcCCcHHHHhhhcCCCCHHHHHHHHHHHhhhh
Q 022144 66 PFTPEEDETILRAHARFGNKWATIARLLSGRTDNAIKNHWNSTLKRK 112 (302)
Q Consensus 66 ~WT~EED~~Ll~lv~~~GnkW~~IA~~l~gRT~~q~knRw~~~Lkrk 112 (302)
..|+-|-+.|.-+.+ |....+||..| +-+...|+++...++++-
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 478888776655443 88899999999 999999999988887765
No 203
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=21.41 E-value=2.1e+02 Score=23.72 Aligned_cols=29 Identities=21% Similarity=0.304 Sum_probs=22.1
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLKR 111 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lkr 111 (302)
.|-...+||..| |=+...|+.|.....++
T Consensus 127 ~~~s~~eIA~~l-gis~~tv~~~l~Rar~~ 155 (161)
T PRK12541 127 YGFSYKEIAEMT-GLSLAKVKIELHRGRKE 155 (161)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355678999988 88889999887655544
No 204
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=21.39 E-value=2.1e+02 Score=24.67 Aligned_cols=28 Identities=21% Similarity=0.214 Sum_probs=21.5
Q ss_pred hcCCcHHHHhhhcCCCCHHHHHHHHHHHh
Q 022144 81 RFGNKWATIARLLSGRTDNAIKNHWNSTL 109 (302)
Q Consensus 81 ~~GnkW~~IA~~l~gRT~~q~knRw~~~L 109 (302)
..|-...+||..| |-+...|+.+....+
T Consensus 125 ~~g~s~~EIA~~L-gis~~tV~~~l~RAr 152 (182)
T PRK12540 125 ASGFSYEDAAAIC-GCAVGTIKSRVNRAR 152 (182)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 3566789999999 888999988865443
No 205
>PF09197 Rap1-DNA-bind: Rap1, DNA-binding; InterPro: IPR015280 Members of this entry, which are predominantly found in the yeast protein Rap1, assume a secondary structure consisting of a three-helix bundle and an N-terminal arm. They contain an Arg-Asp-Arg-Lys sequence that interacts with an ACAregion in the 3, region of the DNA-binding site []. ; PDB: 1IGN_A 3UKG_A.
Probab=20.94 E-value=1.5e+02 Score=24.52 Aligned_cols=47 Identities=19% Similarity=0.362 Sum_probs=32.4
Q ss_pred CCChHHHHHHHHHHHhc------------CC-c------------------HHHHhhhcCCCCHHHHHHHHHHHhhhh
Q 022144 66 PFTPEEDETILRAHARF------------GN-K------------------WATIARLLSGRTDNAIKNHWNSTLKRK 112 (302)
Q Consensus 66 ~WT~EED~~Ll~lv~~~------------Gn-k------------------W~~IA~~l~gRT~~q~knRw~~~Lkrk 112 (302)
.||.+||-.|-..+.+| |. . ....++..|..|.++=++||++.+...
T Consensus 1 kfTA~dDY~Lc~~i~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~fF~~~~~~~p~HT~~sWRDR~RKfv~~~ 78 (105)
T PF09197_consen 1 KFTADDDYALCKAIKKQFYRDIYQKDPDTGSSLISDGDSKEFIPKRDMRSFFKDLARKNPRHTENSWRDRYRKFVSEY 78 (105)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHSB-TTSS-B----------------TTHHHHHHHHTTTS-HHHHHHHHHHTHHHH
T ss_pred CCChHHHHHHHHHHHHHHHHHHHhhCcccccccccCCCccccccchhhHHHHHHHHHcCCccchhHHHHHHHHHHHHc
Confidence 47999999998888653 11 1 556677889999999999998766554
No 206
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=20.57 E-value=2.1e+02 Score=25.60 Aligned_cols=27 Identities=19% Similarity=0.229 Sum_probs=21.9
Q ss_pred CCcHHHHhhhcCCCCHHHHHHHHHHHhh
Q 022144 83 GNKWATIARLLSGRTDNAIKNHWNSTLK 110 (302)
Q Consensus 83 GnkW~~IA~~l~gRT~~q~knRw~~~Lk 110 (302)
|-...+||..+ |-+...|+++-...++
T Consensus 198 g~s~~EIA~~l-gis~~tVk~~~~rA~~ 224 (234)
T PRK08301 198 EKTQKEVADML-GISQSYISRLEKRIIK 224 (234)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 67899999999 9999999888665443
No 207
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=20.11 E-value=2.3e+02 Score=26.14 Aligned_cols=28 Identities=7% Similarity=0.025 Sum_probs=22.4
Q ss_pred cCCcHHHHhhhcCCCCHHHHHHHHHHHhh
Q 022144 82 FGNKWATIARLLSGRTDNAIKNHWNSTLK 110 (302)
Q Consensus 82 ~GnkW~~IA~~l~gRT~~q~knRw~~~Lk 110 (302)
.|-...+||..+ |=+.+.|+.|....++
T Consensus 176 eg~S~~EIA~~L-gis~~TVk~rl~RAr~ 203 (244)
T TIGR03001 176 DGLSMDRIGAMY-QVHRSTVSRWVAQARE 203 (244)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 466799999999 8899999988765443
Done!