Query 044161
Match_columns 229
No_of_seqs 187 out of 1383
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 12:00:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044161.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044161hhsearch_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 1.7E-35 3.6E-40 257.3 11.6 113 2-114 3-115 (238)
2 PLN03212 Transcription repress 100.0 4.5E-35 9.7E-40 251.7 13.3 114 3-116 20-133 (249)
3 PLN03091 hypothetical protein; 100.0 5.2E-33 1.1E-37 254.6 12.4 112 3-114 9-120 (459)
4 KOG0049 Transcription factor, 99.8 1.4E-18 3.1E-23 164.9 7.5 98 3-101 355-453 (939)
5 PF13921 Myb_DNA-bind_6: Myb-l 99.7 4E-18 8.6E-23 117.6 5.6 60 11-72 1-60 (60)
6 KOG0049 Transcription factor, 99.7 2E-17 4.3E-22 157.2 8.6 110 3-112 248-412 (939)
7 COG5147 REB1 Myb superfamily p 99.7 1.3E-16 2.7E-21 150.8 7.7 108 3-111 15-122 (512)
8 KOG0050 mRNA splicing protein 99.6 1.1E-16 2.4E-21 149.0 5.3 109 5-115 4-112 (617)
9 PF00249 Myb_DNA-binding: Myb- 99.5 3.8E-15 8.2E-20 98.6 3.1 48 8-55 1-48 (48)
10 KOG0051 RNA polymerase I termi 99.5 1.3E-14 2.9E-19 138.5 8.0 103 7-112 383-513 (607)
11 PF00249 Myb_DNA-binding: Myb- 99.4 4.4E-13 9.6E-18 88.6 5.5 46 61-106 1-48 (48)
12 PLN03212 Transcription repress 99.3 9.5E-13 2.1E-17 113.9 1.2 56 3-60 73-128 (249)
13 PF13921 Myb_DNA-bind_6: Myb-l 99.3 5.2E-12 1.1E-16 86.9 4.3 46 64-109 1-46 (60)
14 smart00717 SANT SANT SWI3, AD 99.3 5.6E-12 1.2E-16 81.6 4.0 48 8-56 1-48 (49)
15 smart00717 SANT SANT SWI3, AD 99.2 3.8E-11 8.3E-16 77.6 6.0 47 61-107 1-48 (49)
16 KOG0048 Transcription factor, 99.2 5E-12 1.1E-16 110.1 2.3 53 3-57 57-109 (238)
17 PLN03091 hypothetical protein; 99.2 4.9E-12 1.1E-16 117.0 2.0 54 3-58 62-115 (459)
18 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 4.1E-11 8.9E-16 76.3 3.6 45 10-55 1-45 (45)
19 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 3.1E-10 6.8E-15 72.2 6.0 43 63-105 1-44 (45)
20 KOG0051 RNA polymerase I termi 98.9 2.4E-09 5.2E-14 102.9 6.5 102 6-109 306-431 (607)
21 COG5147 REB1 Myb superfamily p 98.6 4.4E-09 9.5E-14 100.0 -1.1 98 7-107 290-397 (512)
22 TIGR01557 myb_SHAQKYF myb-like 98.1 2.7E-06 5.9E-11 58.3 3.7 49 7-55 2-54 (57)
23 KOG0457 Histone acetyltransfer 98.0 5.2E-06 1.1E-10 77.1 3.6 49 6-55 70-118 (438)
24 KOG0457 Histone acetyltransfer 97.5 0.00025 5.4E-09 66.1 6.2 49 58-106 69-118 (438)
25 KOG0050 mRNA splicing protein 97.4 0.00016 3.4E-09 68.7 4.4 56 59-114 5-61 (617)
26 TIGR01557 myb_SHAQKYF myb-like 97.4 0.00057 1.2E-08 46.8 5.8 46 61-106 3-54 (57)
27 COG5259 RSC8 RSC chromatin rem 97.2 0.00022 4.8E-09 67.0 3.1 46 7-54 278-323 (531)
28 PF13325 MCRS_N: N-terminal re 97.2 0.00099 2.1E-08 56.7 6.8 99 10-110 1-130 (199)
29 COG5259 RSC8 RSC chromatin rem 97.1 0.00059 1.3E-08 64.2 4.9 45 61-105 279-323 (531)
30 KOG1279 Chromatin remodeling f 97.1 0.00038 8.3E-09 66.7 3.2 47 6-54 251-297 (506)
31 PF08914 Myb_DNA-bind_2: Rap1 97.0 0.0013 2.8E-08 46.3 4.7 50 61-110 2-61 (65)
32 PF13837 Myb_DNA-bind_4: Myb/S 97.0 0.00071 1.5E-08 49.4 3.4 48 61-108 1-66 (90)
33 TIGR02894 DNA_bind_RsfA transc 97.0 0.0013 2.8E-08 54.0 5.1 53 60-113 3-62 (161)
34 KOG1279 Chromatin remodeling f 97.0 0.0012 2.6E-08 63.4 5.4 48 59-106 251-298 (506)
35 PF13837 Myb_DNA-bind_4: Myb/S 96.9 0.00061 1.3E-08 49.8 2.1 49 8-56 1-65 (90)
36 TIGR02894 DNA_bind_RsfA transc 96.8 0.00072 1.6E-08 55.5 2.4 50 6-57 2-57 (161)
37 PF08914 Myb_DNA-bind_2: Rap1 96.7 0.00094 2E-08 47.0 1.9 52 8-59 2-61 (65)
38 COG5114 Histone acetyltransfer 96.5 0.0015 3.3E-08 58.9 2.0 47 9-56 64-110 (432)
39 PF13873 Myb_DNA-bind_5: Myb/S 96.2 0.0026 5.6E-08 45.6 1.8 50 7-56 1-70 (78)
40 PRK13923 putative spore coat p 96.1 0.0096 2.1E-07 49.5 4.7 53 60-113 4-63 (170)
41 PLN03142 Probable chromatin-re 95.9 0.039 8.5E-07 57.4 9.1 99 10-109 826-987 (1033)
42 PF13873 Myb_DNA-bind_5: Myb/S 95.8 0.029 6.2E-07 40.1 5.5 49 61-109 2-72 (78)
43 PRK13923 putative spore coat p 95.6 0.0067 1.4E-07 50.4 1.7 50 5-56 2-57 (170)
44 COG5114 Histone acetyltransfer 94.7 0.039 8.5E-07 50.1 4.3 46 61-106 63-109 (432)
45 KOG2656 DNA methyltransferase 93.1 0.063 1.4E-06 49.8 2.4 86 30-116 75-191 (445)
46 KOG4282 Transcription factor G 92.2 0.27 5.9E-06 44.9 5.4 53 61-113 54-120 (345)
47 PF12776 Myb_DNA-bind_3: Myb/S 92.2 0.46 9.9E-06 34.8 5.7 46 63-108 1-64 (96)
48 PF09111 SLIDE: SLIDE; InterP 92.1 0.34 7.3E-06 38.0 5.0 51 58-108 46-112 (118)
49 PF11626 Rap1_C: TRF2-interact 91.3 0.31 6.7E-06 35.9 3.8 31 4-37 43-81 (87)
50 PF09111 SLIDE: SLIDE; InterP 91.1 0.33 7.2E-06 38.0 4.1 35 4-38 45-82 (118)
51 COG5118 BDP1 Transcription ini 90.3 0.5 1.1E-05 44.0 5.0 45 62-106 366-410 (507)
52 COG5118 BDP1 Transcription ini 90.2 0.34 7.3E-06 45.1 3.8 48 5-54 362-409 (507)
53 KOG4282 Transcription factor G 87.0 0.53 1.2E-05 43.0 3.0 48 9-56 55-114 (345)
54 PF12776 Myb_DNA-bind_3: Myb/S 86.1 0.98 2.1E-05 33.0 3.5 45 10-54 1-61 (96)
55 PF08281 Sigma70_r4_2: Sigma-7 85.4 2.8 6.1E-05 27.3 5.1 41 66-107 12-52 (54)
56 KOG4167 Predicted DNA-binding 84.7 0.67 1.5E-05 46.4 2.5 44 9-54 620-663 (907)
57 KOG1194 Predicted DNA-binding 82.6 7.5 0.00016 37.2 8.3 49 61-109 187-235 (534)
58 PF13404 HTH_AsnC-type: AsnC-t 75.5 2.9 6.2E-05 26.6 2.3 38 14-53 3-40 (42)
59 PF01388 ARID: ARID/BRIGHT DNA 71.2 2.2 4.7E-05 31.2 1.2 39 18-56 40-89 (92)
60 PF11035 SnAPC_2_like: Small n 70.7 6.7 0.00015 35.8 4.4 85 8-106 21-126 (344)
61 KOG4167 Predicted DNA-binding 69.0 39 0.00084 34.4 9.5 45 61-105 619-663 (907)
62 PF02954 HTH_8: Bacterial regu 68.2 6.2 0.00014 24.7 2.7 29 14-43 5-33 (42)
63 PF04545 Sigma70_r4: Sigma-70, 67.8 17 0.00036 23.3 4.8 41 67-108 7-47 (50)
64 PRK11169 leucine-responsive tr 67.3 4.6 0.0001 32.9 2.5 47 12-60 12-58 (164)
65 smart00501 BRIGHT BRIGHT, ARID 65.8 3.8 8.2E-05 30.1 1.5 40 18-57 36-86 (93)
66 PF07750 GcrA: GcrA cell cycle 65.8 8.3 0.00018 31.8 3.7 41 10-53 2-42 (162)
67 PRK11179 DNA-binding transcrip 64.9 5.9 0.00013 31.8 2.6 46 13-60 8-53 (153)
68 PLN03142 Probable chromatin-re 64.1 6.4 0.00014 41.5 3.3 35 5-39 923-957 (1033)
69 smart00595 MADF subfamily of S 62.9 9.1 0.0002 27.4 3.1 26 82-108 29-54 (89)
70 KOG1194 Predicted DNA-binding 61.4 8 0.00017 37.0 3.1 47 6-54 185-231 (534)
71 PF07750 GcrA: GcrA cell cycle 60.1 14 0.0003 30.4 4.0 41 63-104 2-42 (162)
72 KOG2656 DNA methyltransferase 57.7 3.4 7.3E-05 38.7 -0.0 49 6-55 128-181 (445)
73 PRK09413 IS2 repressor TnpA; R 57.6 37 0.00079 26.1 5.9 46 7-56 9-54 (121)
74 PF09905 DUF2132: Uncharacteri 56.4 17 0.00037 25.4 3.2 44 16-72 12-62 (64)
75 KOG2009 Transcription initiati 56.1 12 0.00027 36.8 3.5 46 59-104 407-452 (584)
76 smart00595 MADF subfamily of S 55.5 4.4 9.6E-05 29.1 0.3 23 30-54 29-51 (89)
77 PF09197 Rap1-DNA-bind: Rap1, 55.5 13 0.00028 28.6 2.8 46 10-56 1-76 (105)
78 PF04504 DUF573: Protein of un 55.0 24 0.00053 26.5 4.3 49 62-110 5-66 (98)
79 PF11035 SnAPC_2_like: Small n 54.1 71 0.0015 29.4 7.7 51 61-111 21-75 (344)
80 TIGR02985 Sig70_bacteroi1 RNA 53.7 34 0.00074 26.3 5.2 37 71-108 120-156 (161)
81 PF01388 ARID: ARID/BRIGHT DNA 52.3 42 0.00092 24.2 5.2 38 71-108 40-90 (92)
82 KOG0384 Chromodomain-helicase 52.2 18 0.0004 38.7 4.2 73 9-88 1134-1207(1373)
83 KOG4468 Polycomb-group transcr 51.8 25 0.00054 35.0 4.7 48 61-108 88-145 (782)
84 PF11626 Rap1_C: TRF2-interact 50.3 8.8 0.00019 28.1 1.2 17 57-73 43-59 (87)
85 KOG2009 Transcription initiati 49.5 9.5 0.00021 37.6 1.6 49 3-53 404-452 (584)
86 PRK11179 DNA-binding transcrip 48.9 45 0.00097 26.6 5.3 43 67-110 9-52 (153)
87 KOG4329 DNA-binding protein [G 48.1 38 0.00083 31.7 5.1 44 62-105 278-322 (445)
88 smart00501 BRIGHT BRIGHT, ARID 47.7 50 0.0011 24.0 5.0 39 71-109 36-87 (93)
89 PF08281 Sigma70_r4_2: Sigma-7 46.6 13 0.00027 24.1 1.4 38 13-53 12-49 (54)
90 PF10545 MADF_DNA_bdg: Alcohol 46.1 35 0.00075 23.6 3.8 27 82-108 28-55 (85)
91 PF09420 Nop16: Ribosome bioge 45.1 28 0.00061 28.4 3.6 48 6-54 112-162 (164)
92 COG4628 Uncharacterized conser 44.6 29 0.00063 27.2 3.3 44 16-72 21-71 (136)
93 PF04504 DUF573: Protein of un 41.4 93 0.002 23.3 5.6 71 7-78 3-94 (98)
94 cd08803 Death_ank3 Death domai 40.3 54 0.0012 23.9 4.1 28 69-97 4-31 (84)
95 COG1168 MalY Bifunctional PLP- 39.8 28 0.0006 32.7 3.0 27 2-28 165-192 (388)
96 KOG4468 Polycomb-group transcr 39.8 17 0.00038 36.0 1.7 49 7-56 87-144 (782)
97 cd08319 Death_RAIDD Death doma 39.5 31 0.00067 25.2 2.7 28 16-44 2-29 (83)
98 cd08319 Death_RAIDD Death doma 38.2 55 0.0012 23.9 3.8 27 69-96 2-28 (83)
99 PRK11169 leucine-responsive tr 38.1 65 0.0014 26.0 4.7 44 66-110 13-57 (164)
100 TIGR01565 homeo_ZF_HD homeobox 38.0 71 0.0015 21.8 4.1 40 5-44 2-48 (58)
101 PF13325 MCRS_N: N-terminal re 37.9 75 0.0016 27.2 5.1 51 63-114 1-55 (199)
102 PRK01905 DNA-binding protein F 37.3 39 0.00084 24.0 2.9 31 13-44 36-66 (77)
103 TIGR02937 sigma70-ECF RNA poly 36.5 1E+02 0.0022 22.9 5.3 34 74-108 120-153 (158)
104 smart00344 HTH_ASNC helix_turn 36.3 38 0.00083 24.9 2.8 45 14-60 3-47 (108)
105 KOG4329 DNA-binding protein [G 36.2 33 0.00071 32.2 2.8 43 10-54 279-322 (445)
106 PRK00430 fis global DNA-bindin 35.9 41 0.00088 25.1 2.9 30 14-44 55-84 (95)
107 smart00351 PAX Paired Box doma 35.3 1.6E+02 0.0035 22.8 6.3 73 6-80 13-92 (125)
108 PF09420 Nop16: Ribosome bioge 35.1 1E+02 0.0022 25.1 5.4 45 61-105 114-162 (164)
109 cd08317 Death_ank Death domain 34.3 53 0.0012 23.6 3.2 29 69-98 4-32 (84)
110 PRK09652 RNA polymerase sigma 34.2 93 0.002 24.4 5.0 33 75-108 139-171 (182)
111 COG1522 Lrp Transcriptional re 33.6 35 0.00076 26.7 2.4 45 14-60 8-52 (154)
112 cd08803 Death_ank3 Death domai 32.6 48 0.001 24.2 2.7 25 16-41 4-28 (84)
113 PF07638 Sigma70_ECF: ECF sigm 32.3 1.3E+02 0.0028 24.6 5.7 37 69-106 140-176 (185)
114 PRK04217 hypothetical protein; 31.1 1.9E+02 0.0041 22.3 5.9 45 63-109 42-86 (110)
115 PRK11924 RNA polymerase sigma 30.6 1.1E+02 0.0024 23.9 4.9 30 78-108 139-168 (179)
116 PRK09641 RNA polymerase sigma 29.2 1.2E+02 0.0026 24.1 4.9 28 79-107 151-178 (187)
117 PRK12529 RNA polymerase sigma 29.0 1.7E+02 0.0037 23.5 5.8 33 77-110 140-172 (178)
118 PRK09643 RNA polymerase sigma 28.9 1.6E+02 0.0035 24.0 5.7 31 77-108 147-177 (192)
119 cd08804 Death_ank2 Death domai 28.8 89 0.0019 22.6 3.6 31 69-100 4-34 (84)
120 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 28.7 1.5E+02 0.0033 19.6 4.4 34 67-101 7-40 (50)
121 PRK12523 RNA polymerase sigma 28.4 1.4E+02 0.0031 23.6 5.2 34 75-109 130-163 (172)
122 PRK12532 RNA polymerase sigma 28.1 2.2E+02 0.0048 23.0 6.4 29 78-107 150-178 (195)
123 PRK09047 RNA polymerase factor 27.7 1.6E+02 0.0034 22.8 5.3 29 79-108 121-149 (161)
124 cd08311 Death_p75NR Death doma 27.5 81 0.0018 22.6 3.1 33 66-100 2-34 (77)
125 PRK12531 RNA polymerase sigma 27.4 2E+02 0.0043 23.4 6.0 30 79-109 156-185 (194)
126 cd08318 Death_NMPP84 Death dom 27.2 1E+02 0.0022 22.3 3.7 24 74-98 12-35 (86)
127 PRK12524 RNA polymerase sigma 26.0 1.6E+02 0.0034 24.1 5.1 31 77-108 149-179 (196)
128 PRK12530 RNA polymerase sigma 25.9 2.4E+02 0.0053 22.8 6.3 29 79-108 149-177 (189)
129 TIGR02948 SigW_bacill RNA poly 25.6 1.4E+02 0.003 23.8 4.7 28 80-108 152-179 (187)
130 PRK09642 RNA polymerase sigma 25.3 1.8E+02 0.0039 22.6 5.2 29 79-108 121-149 (160)
131 cd08779 Death_PIDD Death Domai 25.3 53 0.0011 23.9 1.9 34 70-103 3-38 (86)
132 TIGR02943 Sig70_famx1 RNA poly 25.2 1.8E+02 0.0038 23.7 5.3 31 77-108 144-174 (188)
133 PF01527 HTH_Tnp_1: Transposas 24.9 86 0.0019 21.3 2.9 46 7-56 3-48 (76)
134 PF01710 HTH_Tnp_IS630: Transp 24.8 1.5E+02 0.0034 22.6 4.6 56 13-71 56-111 (119)
135 TIGR02939 RpoE_Sigma70 RNA pol 24.8 1.6E+02 0.0035 23.5 4.9 28 80-108 154-181 (190)
136 cd08805 Death_ank1 Death domai 24.7 75 0.0016 23.2 2.6 35 69-103 4-40 (84)
137 PRK09648 RNA polymerase sigma 24.6 2.3E+02 0.0049 22.8 5.8 30 78-108 153-182 (189)
138 PRK09637 RNA polymerase sigma 24.6 1.7E+02 0.0037 23.7 5.0 30 78-108 120-149 (181)
139 TIGR02954 Sig70_famx3 RNA poly 23.9 1.8E+02 0.0039 22.9 4.9 29 79-108 134-162 (169)
140 PF10440 WIYLD: Ubiquitin-bind 23.8 62 0.0013 22.7 1.9 18 17-35 30-47 (65)
141 PRK06759 RNA polymerase factor 23.7 2E+02 0.0044 22.0 5.2 28 79-107 121-148 (154)
142 COG2197 CitB Response regulato 23.5 1.3E+02 0.0029 25.2 4.3 45 62-109 147-191 (211)
143 COG3795 Uncharacterized protei 23.2 58 0.0013 25.7 1.8 60 9-72 15-79 (123)
144 PRK09645 RNA polymerase sigma 23.1 2E+02 0.0044 22.6 5.1 29 79-108 133-161 (173)
145 PRK12536 RNA polymerase sigma 22.9 2.5E+02 0.0055 22.4 5.8 31 77-108 142-172 (181)
146 cd08777 Death_RIP1 Death Domai 22.9 1.2E+02 0.0025 22.2 3.3 28 72-100 5-32 (86)
147 smart00005 DEATH DEATH domain, 22.7 1.2E+02 0.0027 21.2 3.5 24 69-92 5-29 (88)
148 PRK12512 RNA polymerase sigma 22.7 2.6E+02 0.0056 22.3 5.8 29 79-108 146-174 (184)
149 KOG3841 TEF-1 and related tran 22.5 5.2E+02 0.011 24.5 8.1 54 59-112 74-148 (455)
150 TIGR02952 Sig70_famx2 RNA poly 22.0 2.2E+02 0.0047 22.2 5.1 27 80-107 138-164 (170)
151 PRK12528 RNA polymerase sigma 21.8 2.4E+02 0.0051 22.0 5.2 29 78-107 127-155 (161)
152 PRK12515 RNA polymerase sigma 21.7 2.2E+02 0.0048 22.9 5.2 29 79-108 146-174 (189)
153 smart00344 HTH_ASNC helix_turn 21.5 2.6E+02 0.0056 20.3 5.1 42 67-109 3-45 (108)
154 PF01466 Skp1: Skp1 family, di 21.5 92 0.002 22.0 2.5 36 31-74 36-71 (78)
155 cd06171 Sigma70_r4 Sigma70, re 21.5 1.9E+02 0.0042 17.1 4.9 39 64-104 11-49 (55)
156 PRK00118 putative DNA-binding 21.1 2.7E+02 0.0058 21.2 5.1 41 66-107 19-59 (104)
157 PRK05602 RNA polymerase sigma 20.8 2.7E+02 0.0058 22.3 5.5 28 79-107 143-170 (186)
158 PRK11923 algU RNA polymerase s 20.8 2.6E+02 0.0056 22.5 5.4 28 80-108 154-181 (193)
159 TIGR02999 Sig-70_X6 RNA polyme 20.6 2.5E+02 0.0054 22.3 5.2 28 79-107 149-176 (183)
160 PRK12547 RNA polymerase sigma 20.2 2.6E+02 0.0057 21.9 5.2 29 79-108 127-155 (164)
No 1
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=1.7e-35 Score=257.31 Aligned_cols=113 Identities=49% Similarity=0.885 Sum_probs=107.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccccCCCCCCCCCHHHHHHHHHHHHHhCC
Q 044161 2 QEEKLSKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLCPNIKHGYISTEEEQIIIQLHKKWGN 81 (229)
Q Consensus 2 ~~~~~kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~~~~~~WT~eEd~~L~~~v~~~G~ 81 (229)
.++.+.||+||+|||++|+.+|.+||.++|..||+.+|++|++++||.||+|||+|.+++|.||+|||.+|++++..+|+
T Consensus 3 kk~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GN 82 (238)
T KOG0048|consen 3 RNPELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGN 82 (238)
T ss_pred CCccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCc
Confidence 34556789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHhhCCCCCHHHHHHHHHHhhhHHHHHHh
Q 044161 82 KWSRIARNLPGRTDNEIKNYWRTRIRKKIQAQE 114 (229)
Q Consensus 82 ~W~~Ia~~l~gRt~~qiknrw~~~l~~~~~~~~ 114 (229)
+|+.||++|||||++.|||+|++.+++++....
T Consensus 83 rWs~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 83 RWSLIAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred HHHHHHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 999999999999999999999999999887765
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=4.5e-35 Score=251.66 Aligned_cols=114 Identities=53% Similarity=1.018 Sum_probs=108.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccccCCCCCCCCCHHHHHHHHHHHHHhCCC
Q 044161 3 EEKLSKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLCPNIKHGYISTEEEQIIIQLHKKWGNK 82 (229)
Q Consensus 3 ~~~~kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~~~~~~WT~eEd~~L~~~v~~~G~~ 82 (229)
++++++++||+|||++|+++|++||..+|..||+.++++|+++|||+||.++|+|.+++++||+|||++|++++.+||++
T Consensus 20 K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~~GnK 99 (249)
T PLN03212 20 KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLGNR 99 (249)
T ss_pred cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHhcccc
Confidence 57899999999999999999999999999999999966999999999999999999999999999999999999999999
Q ss_pred HHHHHhhCCCCCHHHHHHHHHHhhhHHHHHHhhh
Q 044161 83 WSRIARNLPGRTDNEIKNYWRTRIRKKIQAQEQE 116 (229)
Q Consensus 83 W~~Ia~~l~gRt~~qiknrw~~~l~~~~~~~~~~ 116 (229)
|+.||++|||||+++|||||+.++++.+.+....
T Consensus 100 Ws~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~ 133 (249)
T PLN03212 100 WSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGID 133 (249)
T ss_pred HHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCC
Confidence 9999999999999999999999999987765533
No 3
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=5.2e-33 Score=254.58 Aligned_cols=112 Identities=51% Similarity=0.985 Sum_probs=107.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccccCCCCCCCCCHHHHHHHHHHHHHhCCC
Q 044161 3 EEKLSKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLCPNIKHGYISTEEEQIIIQLHKKWGNK 82 (229)
Q Consensus 3 ~~~~kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~~~~~~WT~eEd~~L~~~v~~~G~~ 82 (229)
+++++||+||+|||++|+++|.+||.++|..||+.++++|+++|||+||.++|+|.+++++||+|||++|++++++||++
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 57899999999999999999999999999999999977999999999999999999999999999999999999999999
Q ss_pred HHHHHhhCCCCCHHHHHHHHHHhhhHHHHHHh
Q 044161 83 WSRIARNLPGRTDNEIKNYWRTRIRKKIQAQE 114 (229)
Q Consensus 83 W~~Ia~~l~gRt~~qiknrw~~~l~~~~~~~~ 114 (229)
|+.||++|||||+++|||||+.+++++++...
T Consensus 89 WskIAk~LPGRTDnqIKNRWnslLKKklr~~~ 120 (459)
T PLN03091 89 WSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRG 120 (459)
T ss_pred hHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcC
Confidence 99999999999999999999999999877543
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.75 E-value=1.4e-18 Score=164.92 Aligned_cols=98 Identities=27% Similarity=0.530 Sum_probs=93.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccccCCCCCCCCCHHHHHHHHHHHHHhC-C
Q 044161 3 EEKLSKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLCPNIKHGYISTEEEQIIIQLHKKWG-N 81 (229)
Q Consensus 3 ~~~~kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~~~~~~WT~eEd~~L~~~v~~~G-~ 81 (229)
.|.+++|+||++||.+|..+|.+||...|.+|-..+| ||+..|||+||++.|....+.+.||-.||+.|+.+|++|| .
T Consensus 355 dPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vP-nRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~~V~~YG~g 433 (939)
T KOG0049|consen 355 DPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVP-NRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLYAVKVYGKG 433 (939)
T ss_pred CccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcC-CccHHHHHHHHHHHHHHhhccCceeecchHHHHHHHHHHccc
Confidence 6899999999999999999999999999999999999 9999999999999999999999999999999999999999 6
Q ss_pred CHHHHHhhCCCCCHHHHHHH
Q 044161 82 KWSRIARNLPGRTDNEIKNY 101 (229)
Q Consensus 82 ~W~~Ia~~l~gRt~~qiknr 101 (229)
+|.+||.+||+||..|...|
T Consensus 434 ~WakcA~~Lp~~t~~q~~rr 453 (939)
T KOG0049|consen 434 NWAKCAMLLPKKTSRQLRRR 453 (939)
T ss_pred hHHHHHHHccccchhHHHHH
Confidence 89999999999999665433
No 5
>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=99.73 E-value=4e-18 Score=117.61 Aligned_cols=60 Identities=43% Similarity=0.806 Sum_probs=55.3
Q ss_pred CCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccccCCCCCCCCCHHHHHHH
Q 044161 11 WHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLCPNIKHGYISTEEEQII 72 (229)
Q Consensus 11 WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~~~~~~WT~eEd~~L 72 (229)
||+|||++|+++|..|| ++|..||+.|| .|++.+|+.||.++|.|.+++++||++||++|
T Consensus 1 WT~eEd~~L~~~~~~~g-~~W~~Ia~~l~-~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYG-NDWKKIAEHLG-NRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHT-S-HHHHHHHST-TS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC-cCHHHHHHHHC-cCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 99999999999999999 78999999997 89999999999999999999999999999987
No 6
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.71 E-value=2e-17 Score=157.22 Aligned_cols=110 Identities=23% Similarity=0.476 Sum_probs=99.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCccccccccccc----------------------------
Q 044161 3 EEKLSKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNY---------------------------- 54 (229)
Q Consensus 3 ~~~~kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~---------------------------- 54 (229)
.|+++|-.|+.||||+|+.+...+|..+|.+||..||.+|+..||..||++.
T Consensus 248 ~P~~nk~~WS~EE~E~L~AiA~A~~~~~W~~IA~~Lgt~RS~yQC~~kF~t~~~~L~ekeWsEEed~kL~alV~~~~~nS 327 (939)
T KOG0049|consen 248 NPKWNKEHWSNEEVEKLKALAEAPKFVSWPMIALNLGTNRSSYQCMEKFKTEVSQLSEKEWSEEEDTKLIALVKITSINS 327 (939)
T ss_pred CCccchhccChHHHHHHHHHHhccccccHHHHHHHhCCCcchHHHHHHHHHHHHHHHhhhcchhhhHHHHHHHHHhhccC
Confidence 5889999999999999999999999999999999999779999996665554
Q ss_pred --------------------------ccCCCCCCCCCHHHHHHHHHHHHHhCC-CHHHHHhhCCCCCHHHHHHHHHHhhh
Q 044161 55 --------------------------LCPNIKHGYISTEEEQIIIQLHKKWGN-KWSRIARNLPGRTDNEIKNYWRTRIR 107 (229)
Q Consensus 55 --------------------------L~p~~~~~~WT~eEd~~L~~~v~~~G~-~W~~Ia~~l~gRt~~qiknrw~~~l~ 107 (229)
|+|.+++|+||.+||.+|+.+|.+||. .|.+|-..+|||++.||+.||.+.|.
T Consensus 328 hI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~ 407 (939)
T KOG0049|consen 328 HIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLN 407 (939)
T ss_pred ccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHH
Confidence 789999999999999999999999995 59999999999999999999999886
Q ss_pred HHHHH
Q 044161 108 KKIQA 112 (229)
Q Consensus 108 ~~~~~ 112 (229)
...++
T Consensus 408 ~s~K~ 412 (939)
T KOG0049|consen 408 RSAKV 412 (939)
T ss_pred Hhhcc
Confidence 65443
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=99.66 E-value=1.3e-16 Score=150.78 Aligned_cols=108 Identities=30% Similarity=0.487 Sum_probs=102.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccccCCCCCCCCCHHHHHHHHHHHHHhCCC
Q 044161 3 EEKLSKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLCPNIKHGYISTEEEQIIIQLHKKWGNK 82 (229)
Q Consensus 3 ~~~~kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~~~~~~WT~eEd~~L~~~v~~~G~~ 82 (229)
..+++.|.|+..||+.|..+|++||+++|+.||..+. -|+++||+.||+++++|.++++.|+.+||..|+.+..++|++
T Consensus 15 ~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~-~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~ 93 (512)
T COG5147 15 QTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLI-SSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQ 93 (512)
T ss_pred cceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhc-ccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCch
Confidence 3467899999999999999999999999999999998 799999999999999999999999999999999999999999
Q ss_pred HHHHHhhCCCCCHHHHHHHHHHhhhHHHH
Q 044161 83 WSRIARNLPGRTDNEIKNYWRTRIRKKIQ 111 (229)
Q Consensus 83 W~~Ia~~l~gRt~~qiknrw~~~l~~~~~ 111 (229)
|+.||..+++||..+|.+||..++....+
T Consensus 94 wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 94 WSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 99999999999999999999998877655
No 8
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.65 E-value=1.1e-16 Score=148.99 Aligned_cols=109 Identities=27% Similarity=0.532 Sum_probs=103.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccccCCCCCCCCCHHHHHHHHHHHHHhCCCHH
Q 044161 5 KLSKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLCPNIKHGYISTEEEQIIIQLHKKWGNKWS 84 (229)
Q Consensus 5 ~~kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~~~~~~WT~eEd~~L~~~v~~~G~~W~ 84 (229)
-++.|-|+--||+.|..+|.+||.+.|+.||+.++ -.+++||+.||..+|+|.+++..|+.|||.+|+.+.+.+.+.|.
T Consensus 4 ~~kggvwrntEdeilkaav~kyg~nqws~i~sll~-~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwr 82 (617)
T KOG0050|consen 4 EIKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLN-RKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWR 82 (617)
T ss_pred EEecceecccHHHHHHHHHHHcchHHHHHHHHHHh-hcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccc
Confidence 46889999999999999999999999999999998 89999999999999999999999999999999999999999999
Q ss_pred HHHhhCCCCCHHHHHHHHHHhhhHHHHHHhh
Q 044161 85 RIARNLPGRTDNEIKNYWRTRIRKKIQAQEQ 115 (229)
Q Consensus 85 ~Ia~~l~gRt~~qiknrw~~~l~~~~~~~~~ 115 (229)
.||..+ ||+++||..||..++-...+....
T Consensus 83 tIa~i~-gr~~~qc~eRy~~ll~~~~s~~~~ 112 (617)
T KOG0050|consen 83 TIADIM-GRTSQQCLERYNNLLDVYVSYHYH 112 (617)
T ss_pred hHHHHh-hhhHHHHHHHHHHHHHHHHhhhcc
Confidence 999999 899999999999999877766554
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=99.54 E-value=3.8e-15 Score=98.56 Aligned_cols=48 Identities=44% Similarity=0.778 Sum_probs=43.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccc
Q 044161 8 KGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYL 55 (229)
Q Consensus 8 kg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L 55 (229)
|++||+|||++|+++|.+||.++|..||..||.+||+.||+.||.++|
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 689999999999999999997779999999988999999999999875
No 10
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.54 E-value=1.3e-14 Score=138.48 Aligned_cols=103 Identities=26% Similarity=0.444 Sum_probs=92.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccccCC--CCCCCCCHHHHHHHHHHHH-------
Q 044161 7 SKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLCPN--IKHGYISTEEEQIIIQLHK------- 77 (229)
Q Consensus 7 kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~--~~~~~WT~eEd~~L~~~v~------- 77 (229)
++|+||+||++.|..+|..+| +.|..|++.|+ |.+..|++||+++.... .+++.||.||+++|+++|.
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g-~~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~ 459 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHG-NDWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREAL 459 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhc-ccHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhh
Confidence 899999999999999999999 99999999996 99999999999999887 4899999999999999995
Q ss_pred Hh-------------------CCCHHHHHhhCCCCCHHHHHHHHHHhhhHHHHH
Q 044161 78 KW-------------------GNKWSRIARNLPGRTDNEIKNYWRTRIRKKIQA 112 (229)
Q Consensus 78 ~~-------------------G~~W~~Ia~~l~gRt~~qiknrw~~~l~~~~~~ 112 (229)
++ +-+|+.|++.+..|+..||+.+|..++......
T Consensus 460 q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n 513 (607)
T KOG0051|consen 460 QPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFN 513 (607)
T ss_pred cccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhh
Confidence 23 124999999999999999999999988665443
No 11
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.40 E-value=4.4e-13 Score=88.59 Aligned_cols=46 Identities=28% Similarity=0.695 Sum_probs=41.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCC-HHHHHhhCC-CCCHHHHHHHHHHhh
Q 044161 61 HGYISTEEEQIIIQLHKKWGNK-WSRIARNLP-GRTDNEIKNYWRTRI 106 (229)
Q Consensus 61 ~~~WT~eEd~~L~~~v~~~G~~-W~~Ia~~l~-gRt~~qiknrw~~~l 106 (229)
+++||+||+.+|++++.+||.. |..||..+| +||..||++||..++
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 5799999999999999999998 999999999 999999999999864
No 12
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.27 E-value=9.5e-13 Score=113.89 Aligned_cols=56 Identities=21% Similarity=0.433 Sum_probs=52.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccccCCCC
Q 044161 3 EEKLSKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLCPNIK 60 (229)
Q Consensus 3 ~~~~kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~~~ 60 (229)
+|.+++++||+|||++|++++..|| ++|..||+.|+ |||+.+|+.||+.+|++.+.
T Consensus 73 ~P~I~kgpWT~EED~lLlel~~~~G-nKWs~IAk~Lp-GRTDnqIKNRWns~LrK~l~ 128 (249)
T PLN03212 73 RPSVKRGGITSDEEDLILRLHRLLG-NRWSLIAGRIP-GRTDNEIKNYWNTHLRKKLL 128 (249)
T ss_pred chhcccCCCChHHHHHHHHHHHhcc-ccHHHHHhhcC-CCCHHHHHHHHHHHHhHHHH
Confidence 6899999999999999999999999 88999999998 99999999999998876433
No 13
>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=99.26 E-value=5.2e-12 Score=86.91 Aligned_cols=46 Identities=39% Similarity=0.836 Sum_probs=40.0
Q ss_pred CCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHhhhHH
Q 044161 64 ISTEEEQIIIQLHKKWGNKWSRIARNLPGRTDNEIKNYWRTRIRKK 109 (229)
Q Consensus 64 WT~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~~ 109 (229)
||+|||++|+++|.+||++|..||+.|+.||..+|++||...|++.
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~ 46 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPK 46 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTT
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCccc
Confidence 9999999999999999999999999997799999999999966543
No 14
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.25 E-value=5.6e-12 Score=81.58 Aligned_cols=48 Identities=46% Similarity=0.878 Sum_probs=45.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCccccccccccccc
Q 044161 8 KGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLC 56 (229)
Q Consensus 8 kg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~ 56 (229)
++.||++||++|+.++..||..+|..||..|+ +|++.+|+.||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~-~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELP-GRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcC-CCCHHHHHHHHHHHcC
Confidence 47899999999999999999888999999999 9999999999998764
No 15
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.21 E-value=3.8e-11 Score=77.61 Aligned_cols=47 Identities=38% Similarity=0.883 Sum_probs=44.3
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCHHHHHhhCCCCCHHHHHHHHHHhhh
Q 044161 61 HGYISTEEEQIIIQLHKKWG-NKWSRIARNLPGRTDNEIKNYWRTRIR 107 (229)
Q Consensus 61 ~~~WT~eEd~~L~~~v~~~G-~~W~~Ia~~l~gRt~~qiknrw~~~l~ 107 (229)
+++||++|+.+|+.++..+| .+|..||..|++||..+|++||..+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 36899999999999999999 999999999999999999999998764
No 16
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.20 E-value=5e-12 Score=110.09 Aligned_cols=53 Identities=26% Similarity=0.556 Sum_probs=50.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccccC
Q 044161 3 EEKLSKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLCP 57 (229)
Q Consensus 3 ~~~~kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p 57 (229)
||+++||.||+|||++|++|+..+| ++|+.||+.|| |||++.++.+|+..|+.
T Consensus 57 rP~ikrg~fT~eEe~~Ii~lH~~~G-NrWs~IA~~LP-GRTDNeIKN~Wnt~lkk 109 (238)
T KOG0048|consen 57 RPDLKRGNFSDEEEDLIIKLHALLG-NRWSLIAGRLP-GRTDNEVKNHWNTHLKK 109 (238)
T ss_pred CCCccCCCCCHHHHHHHHHHHHHHC-cHHHHHHhhCC-CcCHHHHHHHHHHHHHH
Confidence 7999999999999999999999999 99999999999 99999999999888743
No 17
>PLN03091 hypothetical protein; Provisional
Probab=99.20 E-value=4.9e-12 Score=116.98 Aligned_cols=54 Identities=22% Similarity=0.498 Sum_probs=50.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccccCC
Q 044161 3 EEKLSKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLCPN 58 (229)
Q Consensus 3 ~~~~kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~ 58 (229)
+|.++||+||+|||++|++++.+|| ++|..||+.|+ ||++.+|+.||+..|++.
T Consensus 62 dP~IkKgpWT~EED~lLLeL~k~~G-nKWskIAk~LP-GRTDnqIKNRWnslLKKk 115 (459)
T PLN03091 62 RPDLKRGTFSQQEENLIIELHAVLG-NRWSQIAAQLP-GRTDNEIKNLWNSCLKKK 115 (459)
T ss_pred CCcccCCCCCHHHHHHHHHHHHHhC-cchHHHHHhcC-CCCHHHHHHHHHHHHHHH
Confidence 6889999999999999999999999 78999999998 999999999999887653
No 18
>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=99.14 E-value=4.1e-11 Score=76.34 Aligned_cols=45 Identities=49% Similarity=0.908 Sum_probs=42.2
Q ss_pred CCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccc
Q 044161 10 PWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYL 55 (229)
Q Consensus 10 ~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L 55 (229)
+||++||+.|+.++..||..+|..||..|+ +|++.+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~-~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELP-GRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcC-CCCHHHHHHHHHHhC
Confidence 599999999999999999888999999998 899999999998753
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=99.08 E-value=3.1e-10 Score=72.18 Aligned_cols=43 Identities=37% Similarity=0.844 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHHHHhC-CCHHHHHhhCCCCCHHHHHHHHHHh
Q 044161 63 YISTEEEQIIIQLHKKWG-NKWSRIARNLPGRTDNEIKNYWRTR 105 (229)
Q Consensus 63 ~WT~eEd~~L~~~v~~~G-~~W~~Ia~~l~gRt~~qiknrw~~~ 105 (229)
+||++|+..|+.++..+| .+|..||..+++||..+|++||..+
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 599999999999999999 9999999999999999999999875
No 20
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.89 E-value=2.4e-09 Score=102.87 Aligned_cols=102 Identities=25% Similarity=0.377 Sum_probs=85.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC-----------------------CChhHHHHhhCCCCCcccccccccccccCCC-CC
Q 044161 6 LSKGPWHEEEDELLVTFVTLFGE-----------------------RRWDYIAKASGLKRSGKSCGLRWLNYLCPNI-KH 61 (229)
Q Consensus 6 ~kkg~WT~eEDe~L~~lv~~~g~-----------------------~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~~-~~ 61 (229)
++-++|+++||+.|...|..|-. +-|..|...|| -|+...+..+-++.-.|-- .+
T Consensus 306 ~~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp-~R~~~siy~~~rR~y~~FE~~r 384 (607)
T KOG0051|consen 306 INLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLP-YRDRKSIYHHLRRAYTPFENKR 384 (607)
T ss_pred hhhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcC-cccchhHHHHHHhcCCcccccc
Confidence 44589999999999999998810 12788999999 5999999884444434433 89
Q ss_pred CCCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHhhhHH
Q 044161 62 GYISTEEEQIIIQLHKKWGNKWSRIARNLPGRTDNEIKNYWRTRIRKK 109 (229)
Q Consensus 62 ~~WT~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~~ 109 (229)
|.||+||++.|..+|.++|+.|..|++.+ ||.+..|+.||+.+.+..
T Consensus 385 g~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g 431 (607)
T KOG0051|consen 385 GKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCG 431 (607)
T ss_pred CCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccc
Confidence 99999999999999999999999999999 799999999999988655
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=98.62 E-value=4.4e-09 Score=100.01 Aligned_cols=98 Identities=28% Similarity=0.518 Sum_probs=87.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccccC--CCCCCCCCHHHHHHHHHHHHHhC----
Q 044161 7 SKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLCP--NIKHGYISTEEEQIIIQLHKKWG---- 80 (229)
Q Consensus 7 kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p--~~~~~~WT~eEd~~L~~~v~~~G---- 80 (229)
.+|+||+||++.|..++.++| ..|..|.+.++ |-+..|++||++|... .+++++|+.||+.+|...+.+.-
T Consensus 290 ~~~~wt~e~~~eL~~~~~~~~-~~w~~ig~~~~--rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e~~~~~~ 366 (512)
T COG5147 290 QRGKWTKEEEQELAKLVVEHG-GSWTEIGKLLG--RMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNEMRLEAQ 366 (512)
T ss_pred hhccCcccccccccccccccc-chhhHhhhhhc--cCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHHHHHHHh
Confidence 579999999999999999999 88999999885 9999999999999988 78899999999999998887542
Q ss_pred ----CCHHHHHhhCCCCCHHHHHHHHHHhhh
Q 044161 81 ----NKWSRIARNLPGRTDNEIKNYWRTRIR 107 (229)
Q Consensus 81 ----~~W~~Ia~~l~gRt~~qiknrw~~~l~ 107 (229)
-.|..|+.++++|...+|+..+..+..
T Consensus 367 ~~~~~~~~li~~~~~~~~~~~~~~~~~~~~~ 397 (512)
T COG5147 367 QSSRILWLLIAQNIRNRLQHHCRDKYGVLIS 397 (512)
T ss_pred hhhhhhHHHHHHhhhccccCCCCCccccccc
Confidence 359999999999999999988877654
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=98.13 E-value=2.7e-06 Score=58.34 Aligned_cols=49 Identities=14% Similarity=0.289 Sum_probs=43.5
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCh---hHHHHhhCCCC-Ccccccccccccc
Q 044161 7 SKGPWHEEEDELLVTFVTLFGERRW---DYIAKASGLKR-SGKSCGLRWLNYL 55 (229)
Q Consensus 7 kkg~WT~eEDe~L~~lv~~~g~~~W---~~IA~~l~~~R-t~~qcr~Rw~~~L 55 (229)
++-.||+||..+++.+|+.+|.++| ..|++.|...| |..||+.|...|.
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 4567999999999999999997799 99999987556 9999999988774
No 23
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.98 E-value=5.2e-06 Score=77.08 Aligned_cols=49 Identities=22% Similarity=0.532 Sum_probs=45.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccc
Q 044161 6 LSKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYL 55 (229)
Q Consensus 6 ~kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L 55 (229)
+-...||.+|+-+|+++++.||.+||..||.++| .|+..+|++||.+++
T Consensus 70 i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIG-tKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETYGFGNWQDIADHIG-TKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHc-ccchHHHHHHHHHHH
Confidence 4456899999999999999999999999999999 999999999998875
No 24
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.46 E-value=0.00025 Score=66.11 Aligned_cols=49 Identities=20% Similarity=0.434 Sum_probs=44.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhC-CCHHHHHhhCCCCCHHHHHHHHHHhh
Q 044161 58 NIKHGYISTEEEQIIIQLHKKWG-NKWSRIARNLPGRTDNEIKNYWRTRI 106 (229)
Q Consensus 58 ~~~~~~WT~eEd~~L~~~v~~~G-~~W~~Ia~~l~gRt~~qiknrw~~~l 106 (229)
.+-...||.+|+.+|++++..|| .+|..||.+++.|+..+|+.+|.++.
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHH
Confidence 34556899999999999999999 89999999999999999999998765
No 25
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.41 E-value=0.00016 Score=68.66 Aligned_cols=56 Identities=32% Similarity=0.550 Sum_probs=51.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHhC-CCHHHHHhhCCCCCHHHHHHHHHHhhhHHHHHHh
Q 044161 59 IKHGYISTEEEQIIIQLHKKWG-NKWSRIARNLPGRTDNEIKNYWRTRIRKKIQAQE 114 (229)
Q Consensus 59 ~~~~~WT~eEd~~L~~~v~~~G-~~W~~Ia~~l~gRt~~qiknrw~~~l~~~~~~~~ 114 (229)
++.|-|+.-||+.|.-+|.+|| +.|++|++.++..|..||++||...+.+.+++..
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~te 61 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTE 61 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhh
Confidence 4578999999999999999999 5799999999999999999999999999887754
No 26
>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=97.38 E-value=0.00057 Score=46.83 Aligned_cols=46 Identities=15% Similarity=0.240 Sum_probs=40.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-CH---HHHHhhCC-CC-CHHHHHHHHHHhh
Q 044161 61 HGYISTEEEQIIIQLHKKWGN-KW---SRIARNLP-GR-TDNEIKNYWRTRI 106 (229)
Q Consensus 61 ~~~WT~eEd~~L~~~v~~~G~-~W---~~Ia~~l~-gR-t~~qiknrw~~~l 106 (229)
+-.||+||..+.++++..+|. .| ..|+..+. .| |..||+.+...+.
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 457999999999999999997 99 99999884 45 9999999987654
No 27
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.23 E-value=0.00022 Score=66.99 Aligned_cols=46 Identities=26% Similarity=0.630 Sum_probs=42.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCccccccccccc
Q 044161 7 SKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNY 54 (229)
Q Consensus 7 kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~ 54 (229)
....||.+|..+|++.|+.|| .+|.+||.++| +|+..||..|+.+.
T Consensus 278 ~dk~WS~qE~~LLLEGIe~yg-DdW~kVA~HVg-tKt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYG-DDWDKVARHVG-TKTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhh-hhHHHHHHHhC-CCCHHHHHHHHHcC
Confidence 556899999999999999999 88999999999 99999999998765
No 28
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.23 E-value=0.00099 Score=56.68 Aligned_cols=99 Identities=21% Similarity=0.335 Sum_probs=71.8
Q ss_pred CCCHHHHHHHHHHHHHhCCCChhHHHHhhC--CCCCcccccccccccccC-CC--------------------CCCCCCH
Q 044161 10 PWHEEEDELLVTFVTLFGERRWDYIAKASG--LKRSGKSCGLRWLNYLCP-NI--------------------KHGYIST 66 (229)
Q Consensus 10 ~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~--~~Rt~~qcr~Rw~~~L~p-~~--------------------~~~~WT~ 66 (229)
+|++++|-.|+.+|.. + ++-..|+..+. ..-|...+.+||+..|.. .+ .+.+||.
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 RWKPEDDLLLINAVEQ-T-NDLESVHLGVKFSCKFTLQEIEERWYALLYDPVISRIAVAAMRNLHPELIAAIQSKALFSK 78 (199)
T ss_pred CCCchhhHHHHHHHHH-h-cCHHHHHccCCcCCcCcHHHHHHHHHHHHcChhhHHHHHHHHHhCCcchhhcccccCCCCH
Confidence 6999999999999987 4 56788876542 235667778999998742 22 2358999
Q ss_pred HHHHHHHHHHHHhCC---CHHHH-----HhhCCCCCHHHHHHHHHHhhhHHH
Q 044161 67 EEEQIIIQLHKKWGN---KWSRI-----ARNLPGRTDNEIKNYWRTRIRKKI 110 (229)
Q Consensus 67 eEd~~L~~~v~~~G~---~W~~I-----a~~l~gRt~~qiknrw~~~l~~~~ 110 (229)
+|+++|......... .+.+| +-+.++||+.++.++|..+.+-.+
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 999999987655443 35555 223478999999999996554443
No 29
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.14 E-value=0.00059 Score=64.20 Aligned_cols=45 Identities=16% Similarity=0.318 Sum_probs=42.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHh
Q 044161 61 HGYISTEEEQIIIQLHKKWGNKWSRIARNLPGRTDNEIKNYWRTR 105 (229)
Q Consensus 61 ~~~WT~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~qiknrw~~~ 105 (229)
...||.+|..+|++.++.||..|.+||.+++.||..||.-||-++
T Consensus 279 dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred cccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 348999999999999999999999999999999999999999775
No 30
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.08 E-value=0.00038 Score=66.72 Aligned_cols=47 Identities=28% Similarity=0.678 Sum_probs=43.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCccccccccccc
Q 044161 6 LSKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNY 54 (229)
Q Consensus 6 ~kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~ 54 (229)
--++.||.+|.-+|+++|+.|| .+|.+||.+++ +||..||..|+.+.
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~-ddW~kVa~hVg-~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYG-DDWNKVADHVG-TKSQEQCILKFLRL 297 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhc-ccHHHHHhccC-CCCHHHHHHHHHhc
Confidence 3567899999999999999999 88999999999 99999999987664
No 31
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=97.04 E-value=0.0013 Score=46.31 Aligned_cols=50 Identities=16% Similarity=0.341 Sum_probs=32.9
Q ss_pred CCCCCHHHHHHHHHHHHHhC--------CC-HHHHHhhCC-CCCHHHHHHHHHHhhhHHH
Q 044161 61 HGYISTEEEQIIIQLHKKWG--------NK-WSRIARNLP-GRTDNEIKNYWRTRIRKKI 110 (229)
Q Consensus 61 ~~~WT~eEd~~L~~~v~~~G--------~~-W~~Ia~~l~-gRt~~qiknrw~~~l~~~~ 110 (229)
+.++|.+||+.|+..|.++. ++ |.+++...+ .+|-...++||...|+...
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 46899999999999997652 22 999999988 8999999999998887654
No 32
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.01 E-value=0.00071 Score=49.43 Aligned_cols=48 Identities=29% Similarity=0.576 Sum_probs=34.1
Q ss_pred CCCCCHHHHHHHHHHHHH------hC--C------CHHHHHhhC----CCCCHHHHHHHHHHhhhH
Q 044161 61 HGYISTEEEQIIIQLHKK------WG--N------KWSRIARNL----PGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 61 ~~~WT~eEd~~L~~~v~~------~G--~------~W~~Ia~~l----~gRt~~qiknrw~~~l~~ 108 (229)
+..||.+|...||+++.+ ++ . -|..||..| ..||+.||+++|.++.+.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~ 66 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKK 66 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Confidence 358999999999999877 21 1 399999997 359999999999996544
No 33
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=96.99 E-value=0.0013 Score=53.95 Aligned_cols=53 Identities=17% Similarity=0.321 Sum_probs=45.4
Q ss_pred CCCCCCHHHHHHHHHHHHHhC----C---CHHHHHhhCCCCCHHHHHHHHHHhhhHHHHHH
Q 044161 60 KHGYISTEEEQIIIQLHKKWG----N---KWSRIARNLPGRTDNEIKNYWRTRIRKKIQAQ 113 (229)
Q Consensus 60 ~~~~WT~eEd~~L~~~v~~~G----~---~W~~Ia~~l~gRt~~qiknrw~~~l~~~~~~~ 113 (229)
....||.|||.+|.+.|-.|- + ...+++..| +||+.+|-=||++.+|+++...
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 467899999999999998873 2 378888888 7999999999999999987754
No 34
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.97 E-value=0.0012 Score=63.40 Aligned_cols=48 Identities=8% Similarity=0.263 Sum_probs=44.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHhh
Q 044161 59 IKHGYISTEEEQIIIQLHKKWGNKWSRIARNLPGRTDNEIKNYWRTRI 106 (229)
Q Consensus 59 ~~~~~WT~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~qiknrw~~~l 106 (229)
..+..||.+|..+|++++..||..|.+||.++.+||..||-.||..+-
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~LP 298 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRLP 298 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhcC
Confidence 345789999999999999999999999999999999999999997753
No 35
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.88 E-value=0.00061 Score=49.78 Aligned_cols=49 Identities=27% Similarity=0.605 Sum_probs=34.1
Q ss_pred CCCCCHHHHHHHHHHHHH--h----CC--C-----ChhHHHHhh---CCCCCccccccccccccc
Q 044161 8 KGPWHEEEDELLVTFVTL--F----GE--R-----RWDYIAKAS---GLKRSGKSCGLRWLNYLC 56 (229)
Q Consensus 8 kg~WT~eEDe~L~~lv~~--~----g~--~-----~W~~IA~~l---~~~Rt~~qcr~Rw~~~L~ 56 (229)
+-+||.+|...|+.++.. + +. . -|..||..| |..||+.||+.+|.+...
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~ 65 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKK 65 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence 357999999999999887 2 11 1 499999887 557999999999988643
No 36
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=96.83 E-value=0.00072 Score=55.46 Aligned_cols=50 Identities=28% Similarity=0.567 Sum_probs=42.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC------CChhHHHHhhCCCCCcccccccccccccC
Q 044161 6 LSKGPWHEEEDELLVTFVTLFGE------RRWDYIAKASGLKRSGKSCGLRWLNYLCP 57 (229)
Q Consensus 6 ~kkg~WT~eEDe~L~~lv~~~g~------~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p 57 (229)
.++..||.|||.+|.+.|-+|-. .....++..|+ ||+..|.-||+.++.+
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~--RTsAACGFRWNs~VRk 57 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN--RTAAACGFRWNAYVRK 57 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc--ccHHHhcchHHHHHHH
Confidence 46778999999999999999921 15889999985 9999999999999874
No 37
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=96.70 E-value=0.00094 Score=46.99 Aligned_cols=52 Identities=21% Similarity=0.328 Sum_probs=33.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCC------C--ChhHHHHhhCCCCCcccccccccccccCCC
Q 044161 8 KGPWHEEEDELLVTFVTLFGE------R--RWDYIAKASGLKRSGKSCGLRWLNYLCPNI 59 (229)
Q Consensus 8 kg~WT~eEDe~L~~lv~~~g~------~--~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~~ 59 (229)
+.+||.|||+.|+..|..+.. + =|..+++.-+..+|-.+-|+||...|.+..
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 468999999999999976521 1 299999988768888899999999987653
No 38
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.46 E-value=0.0015 Score=58.93 Aligned_cols=47 Identities=23% Similarity=0.455 Sum_probs=44.4
Q ss_pred CCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCccccccccccccc
Q 044161 9 GPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLC 56 (229)
Q Consensus 9 g~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~ 56 (229)
-.|+..|+-+|++..+..|-+||..||..+| .|+...|+.||..++.
T Consensus 64 e~WgadEEllli~~~~TlGlGNW~dIadyiG-sr~kee~k~HylK~y~ 110 (432)
T COG5114 64 EGWGADEELLLIECLDTLGLGNWEDIADYIG-SRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCcCchHHHHHHHHHHhcCCCcHHHHHHHHh-hhhhHHHHHHHHHHHh
Confidence 4699999999999999999999999999999 9999999999988865
No 39
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=96.23 E-value=0.0026 Score=45.55 Aligned_cols=50 Identities=34% Similarity=0.473 Sum_probs=40.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC----------------CChhHHHHhh----CCCCCccccccccccccc
Q 044161 7 SKGPWHEEEDELLVTFVTLFGE----------------RRWDYIAKAS----GLKRSGKSCGLRWLNYLC 56 (229)
Q Consensus 7 kkg~WT~eEDe~L~~lv~~~g~----------------~~W~~IA~~l----~~~Rt~~qcr~Rw~~~L~ 56 (229)
++.+||++|.+.|+.+|.+|.. ..|..|+..| |..|+..||+.+|.++..
T Consensus 1 R~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~ 70 (78)
T PF13873_consen 1 RKPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKS 70 (78)
T ss_pred CCCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHH
Confidence 4678999999999999999821 1499999887 226999999999988653
No 40
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.09 E-value=0.0096 Score=49.48 Aligned_cols=53 Identities=17% Similarity=0.323 Sum_probs=42.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCC-------HHHHHhhCCCCCHHHHHHHHHHhhhHHHHHH
Q 044161 60 KHGYISTEEEQIIIQLHKKWGNK-------WSRIARNLPGRTDNEIKNYWRTRIRKKIQAQ 113 (229)
Q Consensus 60 ~~~~WT~eEd~~L~~~v~~~G~~-------W~~Ia~~l~gRt~~qiknrw~~~l~~~~~~~ 113 (229)
.++.||.|+|.+|.+.|-.++.. -..++..| +||+.+|.-||++.+++++...
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Yee~ 63 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQEQ 63 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHHHH
Confidence 46789999999998888887632 45556667 7999999999999999876543
No 41
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=95.89 E-value=0.039 Score=57.44 Aligned_cols=99 Identities=16% Similarity=0.298 Sum_probs=78.1
Q ss_pred CCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccc-------ccccc----------------------------
Q 044161 10 PWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGL-------RWLNY---------------------------- 54 (229)
Q Consensus 10 ~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~-------Rw~~~---------------------------- 54 (229)
.||.-+=..++.+..+||..+-..||..|. ++|..+++. ||...
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~-~k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~~ 904 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEME-GKTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAIG 904 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhc-CCCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 588888889999999999999999999998 899988863 22211
Q ss_pred --------------c-cCCCCCCCCCHHHHHHHHHHHHHhC-CCHHHHHhh------------CCCCCHHHHHHHHHHhh
Q 044161 55 --------------L-CPNIKHGYISTEEEQIIIQLHKKWG-NKWSRIARN------------LPGRTDNEIKNYWRTRI 106 (229)
Q Consensus 55 --------------L-~p~~~~~~WT~eEd~~L~~~v~~~G-~~W~~Ia~~------------l~gRt~~qiknrw~~~l 106 (229)
+ .+.-++..+|+|||..|+-.+.+|| .+|.+|-.. +..||+..|..|..+++
T Consensus 905 ~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~ 984 (1033)
T PLN03142 905 KKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLI 984 (1033)
T ss_pred HHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHH
Confidence 0 1223345699999999999999999 679998433 24699999999999988
Q ss_pred hHH
Q 044161 107 RKK 109 (229)
Q Consensus 107 ~~~ 109 (229)
+-.
T Consensus 985 ~~~ 987 (1033)
T PLN03142 985 RLI 987 (1033)
T ss_pred HHH
Confidence 654
No 42
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.75 E-value=0.029 Score=40.05 Aligned_cols=49 Identities=31% Similarity=0.531 Sum_probs=39.9
Q ss_pred CCCCCHHHHHHHHHHHHHhC----C-------------CHHHHHhhC-----CCCCHHHHHHHHHHhhhHH
Q 044161 61 HGYISTEEEQIIIQLHKKWG----N-------------KWSRIARNL-----PGRTDNEIKNYWRTRIRKK 109 (229)
Q Consensus 61 ~~~WT~eEd~~L~~~v~~~G----~-------------~W~~Ia~~l-----~gRt~~qiknrw~~~l~~~ 109 (229)
...||.+|...|++++.++. + .|..|+..| +.||..+++.+|..+....
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~ 72 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKA 72 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHH
Confidence 35799999999999998862 1 299999887 2499999999999876543
No 43
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.55 E-value=0.0067 Score=50.41 Aligned_cols=50 Identities=26% Similarity=0.537 Sum_probs=40.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCC------ChhHHHHhhCCCCCccccccccccccc
Q 044161 5 KLSKGPWHEEEDELLVTFVTLFGER------RWDYIAKASGLKRSGKSCGLRWLNYLC 56 (229)
Q Consensus 5 ~~kkg~WT~eEDe~L~~lv~~~g~~------~W~~IA~~l~~~Rt~~qcr~Rw~~~L~ 56 (229)
+.++..||.|||.+|.+.|-+|+.. -...++..|. |+..+|..||..+++
T Consensus 2 k~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~--rt~aac~fRwNs~vr 57 (170)
T PRK13923 2 KTRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALK--RTAAACGFRWNSVVR 57 (170)
T ss_pred cchhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHh--hhHHHHHhHHHHHHH
Confidence 3578899999999999999998643 3666777775 999999999977665
No 44
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=94.75 E-value=0.039 Score=50.06 Aligned_cols=46 Identities=24% Similarity=0.399 Sum_probs=42.2
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCHHHHHhhCCCCCHHHHHHHHHHhh
Q 044161 61 HGYISTEEEQIIIQLHKKWG-NKWSRIARNLPGRTDNEIKNYWRTRI 106 (229)
Q Consensus 61 ~~~WT~eEd~~L~~~v~~~G-~~W~~Ia~~l~gRt~~qiknrw~~~l 106 (229)
...|+..|+.+|++...-.| .+|..||..++.|+...||.+|..+.
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y 109 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMY 109 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHH
Confidence 34799999999999999999 78999999999999999999998764
No 45
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=93.10 E-value=0.063 Score=49.82 Aligned_cols=86 Identities=19% Similarity=0.330 Sum_probs=66.5
Q ss_pred ChhHHHHhhCCCCCcccccccccccccCC-------------------------CCCCCCCHHHHHHHHHHHHHhCCCHH
Q 044161 30 RWDYIAKASGLKRSGKSCGLRWLNYLCPN-------------------------IKHGYISTEEEQIIIQLHKKWGNKWS 84 (229)
Q Consensus 30 ~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~-------------------------~~~~~WT~eEd~~L~~~v~~~G~~W~ 84 (229)
+|.-+.-..+ -|.+.-...||.....+. ++...||.+|-+-|+++++.|.-+|-
T Consensus 75 ~W~w~pFtn~-aRkD~~~l~HWvr~~d~~~dypfakfNk~vdipsYt~eEYe~~l~dn~WskeETD~LF~lck~fDLRf~ 153 (445)
T KOG2656|consen 75 PWKWVPFTNS-ARKDDATLHHWVRVGDTPKDYPFAKFNKHVDIPSYTDEEYEAHLNDNSWSKEETDYLFDLCKRFDLRFF 153 (445)
T ss_pred CceeeccCCc-cccCCceEEeeeeccCCCCCCchhhhccccCccccchHHHHHhhccccccHHHHHHHHHHHHhcCeeEE
Confidence 5776665555 677777777887763221 22346999999999999999999999
Q ss_pred HHHhh-----CCC-CCHHHHHHHHHHhhhHHHHHHhhh
Q 044161 85 RIARN-----LPG-RTDNEIKNYWRTRIRKKIQAQEQE 116 (229)
Q Consensus 85 ~Ia~~-----l~g-Rt~~qiknrw~~~l~~~~~~~~~~ 116 (229)
.||.. ++. ||-..+|+||..+.++-++.....
T Consensus 154 VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~~s 191 (445)
T KOG2656|consen 154 VIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARAPS 191 (445)
T ss_pred EEeeccchhhccccccHHHHHHHHHHHHHHHHHccCCC
Confidence 99988 555 999999999999888876665443
No 46
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=92.23 E-value=0.27 Score=44.86 Aligned_cols=53 Identities=21% Similarity=0.303 Sum_probs=41.5
Q ss_pred CCCCCHHHHHHHHHHHHHh----------CCCHHHHHhhC----CCCCHHHHHHHHHHhhhHHHHHH
Q 044161 61 HGYISTEEEQIIIQLHKKW----------GNKWSRIARNL----PGRTDNEIKNYWRTRIRKKIQAQ 113 (229)
Q Consensus 61 ~~~WT~eEd~~L~~~v~~~----------G~~W~~Ia~~l----~gRt~~qiknrw~~~l~~~~~~~ 113 (229)
...|+.+|-..||++..+. +.-|..||+.+ .-||+.+|+++|.++.++-.+..
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k 120 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEK 120 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 4789999999999998764 24499999965 23999999999999766544433
No 47
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=92.18 E-value=0.46 Score=34.80 Aligned_cols=46 Identities=28% Similarity=0.564 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHHh---CC----------CHHHHHhhC---CC--CCHHHHHHHHHHhhhH
Q 044161 63 YISTEEEQIIIQLHKKW---GN----------KWSRIARNL---PG--RTDNEIKNYWRTRIRK 108 (229)
Q Consensus 63 ~WT~eEd~~L~~~v~~~---G~----------~W~~Ia~~l---~g--Rt~~qiknrw~~~l~~ 108 (229)
.||++.+..|++++.+. |+ .|..|+..| +| .+..||++||..+.+.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~ 64 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKD 64 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHH
Confidence 59999999999887653 22 299998887 22 5788999999876544
No 48
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=92.11 E-value=0.34 Score=38.01 Aligned_cols=51 Identities=27% Similarity=0.487 Sum_probs=39.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC----CHHHHHhh------------CCCCCHHHHHHHHHHhhhH
Q 044161 58 NIKHGYISTEEEQIIIQLHKKWGN----KWSRIARN------------LPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 58 ~~~~~~WT~eEd~~L~~~v~~~G~----~W~~Ia~~------------l~gRt~~qiknrw~~~l~~ 108 (229)
.-++..+|++||.-|+-.+.++|- .|..|-.. +..||+..|..|-.++++-
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~ 112 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKL 112 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHH
Confidence 455779999999999999999997 79888554 2459999999999988754
No 49
>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=91.26 E-value=0.31 Score=35.91 Aligned_cols=31 Identities=26% Similarity=0.474 Sum_probs=19.3
Q ss_pred CCCCCCCCCHHHHHHH--------HHHHHHhCCCChhHHHHh
Q 044161 4 EKLSKGPWHEEEDELL--------VTFVTLFGERRWDYIAKA 37 (229)
Q Consensus 4 ~~~kkg~WT~eEDe~L--------~~lv~~~g~~~W~~IA~~ 37 (229)
|....|-||+|+|+.| .+|+++|| +..|+..
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 3345889999999999 55788888 7777654
No 50
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=91.15 E-value=0.33 Score=38.02 Aligned_cols=35 Identities=26% Similarity=0.483 Sum_probs=29.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCC---CChhHHHHhh
Q 044161 4 EKLSKGPWHEEEDELLVTFVTLFGE---RRWDYIAKAS 38 (229)
Q Consensus 4 ~~~kkg~WT~eEDe~L~~lv~~~g~---~~W~~IA~~l 38 (229)
|+.++..||++||.-|+-++.+||. +.|..|-..+
T Consensus 45 ~~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~I 82 (118)
T PF09111_consen 45 PNNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEI 82 (118)
T ss_dssp STSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHH
T ss_pred CCCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHH
Confidence 3667888999999999999999998 8999998776
No 51
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=90.35 E-value=0.5 Score=43.97 Aligned_cols=45 Identities=22% Similarity=0.302 Sum_probs=41.9
Q ss_pred CCCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHhh
Q 044161 62 GYISTEEEQIIIQLHKKWGNKWSRIARNLPGRTDNEIKNYWRTRI 106 (229)
Q Consensus 62 ~~WT~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~qiknrw~~~l 106 (229)
.+||.+|-.+...+...+|...+.||..||.|...|||.+|.+--
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Ee 410 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEE 410 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHh
Confidence 479999999999999999999999999999999999999997643
No 52
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=90.18 E-value=0.34 Score=45.06 Aligned_cols=48 Identities=17% Similarity=0.304 Sum_probs=42.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCccccccccccc
Q 044161 5 KLSKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNY 54 (229)
Q Consensus 5 ~~kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~ 54 (229)
+...-+||.+|-+++.+++...| -+++.||..+| +|..+|++.+|.+-
T Consensus 362 ~~~~~~Ws~~e~ekFYKALs~wG-tdF~LIs~lfP-~R~RkqIKaKfi~E 409 (507)
T COG5118 362 KKGALRWSKKEIEKFYKALSIWG-TDFSLISSLFP-NRERKQIKAKFIKE 409 (507)
T ss_pred CCCCCcccHHHHHHHHHHHHHhc-chHHHHHHhcC-chhHHHHHHHHHHH
Confidence 33455899999999999999999 78999999999 99999999988765
No 53
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=87.04 E-value=0.53 Score=42.95 Aligned_cols=48 Identities=27% Similarity=0.416 Sum_probs=38.2
Q ss_pred CCCCHHHHHHHHHHHHHh----CC-----CChhHHHHhh---CCCCCccccccccccccc
Q 044161 9 GPWHEEEDELLVTFVTLF----GE-----RRWDYIAKAS---GLKRSGKSCGLRWLNYLC 56 (229)
Q Consensus 9 g~WT~eEDe~L~~lv~~~----g~-----~~W~~IA~~l---~~~Rt~~qcr~Rw~~~L~ 56 (229)
..|+.+|-..|+.+..+. .. .-|..||+.+ |..|++.||+.+|.+..+
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k 114 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKK 114 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 679999999999987654 11 3499999854 446999999999988654
No 54
>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=86.14 E-value=0.98 Score=33.01 Aligned_cols=45 Identities=24% Similarity=0.514 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHHHh---CCC---------ChhHHHHhhC----CCCCccccccccccc
Q 044161 10 PWHEEEDELLVTFVTLF---GER---------RWDYIAKASG----LKRSGKSCGLRWLNY 54 (229)
Q Consensus 10 ~WT~eEDe~L~~lv~~~---g~~---------~W~~IA~~l~----~~Rt~~qcr~Rw~~~ 54 (229)
+||+++++.|+.++... |.. .|..|+..|. ...+..||+.||...
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~l 61 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTL 61 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHH
Confidence 69999999999987655 211 3888988773 245667788877554
No 55
>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=85.39 E-value=2.8 Score=27.29 Aligned_cols=41 Identities=24% Similarity=0.327 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHhhh
Q 044161 66 TEEEQIIIQLHKKWGNKWSRIARNLPGRTDNEIKNYWRTRIR 107 (229)
Q Consensus 66 ~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~ 107 (229)
++++..++.++...|-.+.+||..+ |.|...|+.+....++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARK 52 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHh
Confidence 4677888889999999999999999 7999999998876554
No 56
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=84.72 E-value=0.67 Score=46.39 Aligned_cols=44 Identities=11% Similarity=0.335 Sum_probs=41.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCccccccccccc
Q 044161 9 GPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNY 54 (229)
Q Consensus 9 g~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~ 54 (229)
.+||+.|-.++.+++-.|. .++-.|+++++ ++|..||-+.|++.
T Consensus 620 d~WTp~E~~lF~kA~y~~~-KDF~~v~km~~-~KtVaqCVeyYYtW 663 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYS-KDFIFVQKMVK-SKTVAQCVEYYYTW 663 (907)
T ss_pred ccccHHHHHHHHHHHHHhc-ccHHHHHHHhc-cccHHHHHHHHHHH
Confidence 5799999999999999999 89999999998 99999999988765
No 57
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=82.60 E-value=7.5 Score=37.19 Aligned_cols=49 Identities=16% Similarity=0.335 Sum_probs=43.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHhhhHH
Q 044161 61 HGYISTEEEQIIIQLHKKWGNKWSRIARNLPGRTDNEIKNYWRTRIRKK 109 (229)
Q Consensus 61 ~~~WT~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~~ 109 (229)
...||.||--++-++...||....+|-+.||.|+-..|...|....+..
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK~~ 235 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKKTR 235 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHHHh
Confidence 4689999999999999999999999999999999999998887755443
No 58
>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=75.46 E-value=2.9 Score=26.56 Aligned_cols=38 Identities=21% Similarity=0.237 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccc
Q 044161 14 EEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLN 53 (229)
Q Consensus 14 eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~ 53 (229)
+=|.+|+.+++.-|...+..||+.+| =+...|..|+..
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lg--lS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELG--LSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHT--S-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHC--cCHHHHHHHHHH
Confidence 34788999999999889999999997 678888888754
No 59
>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=71.20 E-value=2.2 Score=31.18 Aligned_cols=39 Identities=23% Similarity=0.382 Sum_probs=26.9
Q ss_pred HHHHHHHHhCC-------CChhHHHHhhCCCCC----ccccccccccccc
Q 044161 18 LLVTFVTLFGE-------RRWDYIAKASGLKRS----GKSCGLRWLNYLC 56 (229)
Q Consensus 18 ~L~~lv~~~g~-------~~W~~IA~~l~~~Rt----~~qcr~Rw~~~L~ 56 (229)
.|..+|.++|. +.|..||..|+...+ ..+++..|.++|-
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 56777887762 269999999975432 3557777777764
No 60
>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=70.71 E-value=6.7 Score=35.80 Aligned_cols=85 Identities=16% Similarity=0.277 Sum_probs=62.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCC---ChhHHHHhhCCCCCcccccccccccccCCCCCCCCCHHHHHHHHHHHHH-h----
Q 044161 8 KGPWHEEEDELLVTFVTLFGER---RWDYIAKASGLKRSGKSCGLRWLNYLCPNIKHGYISTEEEQIIIQLHKK-W---- 79 (229)
Q Consensus 8 kg~WT~eEDe~L~~lv~~~g~~---~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~~~~~~WT~eEd~~L~~~v~~-~---- 79 (229)
...||.-|...|+.+.+..... +-..|++.++ +|+..++++ |.+.|+- ..+.+++++ +
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~-~Rs~aEI~~-fl~~LK~------------rvareaiqkv~~~g~ 86 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELP-GRSEAEIRD-FLQQLKG------------RVAREAIQKVHPGGL 86 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhcc-CcCHHHHHH-HHHHHHH------------HHHHHHHHHhccccc
Confidence 3469999999999998876423 4678999998 999999986 3444442 233444444 1
Q ss_pred -CCC------------HHHHHhhCCCCCHHHHHHHHHHhh
Q 044161 80 -GNK------------WSRIARNLPGRTDNEIKNYWRTRI 106 (229)
Q Consensus 80 -G~~------------W~~Ia~~l~gRt~~qiknrw~~~l 106 (229)
|.+ |..+|+.+.|.-...+-.-|.++|
T Consensus 87 ~~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l 126 (344)
T PF11035_consen 87 KGPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVL 126 (344)
T ss_pred ccccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHH
Confidence 221 999999999999988888887765
No 61
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=68.99 E-value=39 Score=34.42 Aligned_cols=45 Identities=9% Similarity=0.150 Sum_probs=41.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHh
Q 044161 61 HGYISTEEEQIIIQLHKKWGNKWSRIARNLPGRTDNEIKNYWRTR 105 (229)
Q Consensus 61 ~~~WT~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~qiknrw~~~ 105 (229)
...||+.|-.+.-+++..|......|++.++++|-.||-..|...
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtW 663 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTW 663 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHH
Confidence 458999999999999999999999999999999999998887654
No 62
>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=68.22 E-value=6.2 Score=24.72 Aligned_cols=29 Identities=21% Similarity=0.229 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHhCCCChhHHHHhhCCCCC
Q 044161 14 EEDELLVTFVTLFGERRWDYIAKASGLKRS 43 (229)
Q Consensus 14 eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt 43 (229)
=|.+.|.+++.+++ ++....|+.||..|+
T Consensus 5 ~E~~~i~~aL~~~~-gn~~~aA~~Lgisr~ 33 (42)
T PF02954_consen 5 FEKQLIRQALERCG-GNVSKAARLLGISRR 33 (42)
T ss_dssp HHHHHHHHHHHHTT-T-HHHHHHHHTS-HH
T ss_pred HHHHHHHHHHHHhC-CCHHHHHHHHCCCHH
Confidence 37788999999999 889999999986654
No 63
>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=67.80 E-value=17 Score=23.26 Aligned_cols=41 Identities=22% Similarity=0.343 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 67 EEEQIIIQLHKKWGNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 67 eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
+++..++.++-..|-.+.+||..+ |-|...|+.+....+++
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 455666666666778899999999 68888998888776654
No 64
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=67.34 E-value=4.6 Score=32.87 Aligned_cols=47 Identities=15% Similarity=0.015 Sum_probs=39.9
Q ss_pred CHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccccCCCC
Q 044161 12 HEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLCPNIK 60 (229)
Q Consensus 12 T~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~~~ 60 (229)
-.+-|.+|+.+.++-|.-.|+.||+.++ -+...|+.|+.+.....+-
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~lg--lS~~tv~~Ri~rL~~~GvI 58 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRVG--LSPTPCLERVRRLERQGFI 58 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCe
Confidence 4567899999999999889999999997 7888999999888766544
No 65
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=65.83 E-value=3.8 Score=30.14 Aligned_cols=40 Identities=28% Similarity=0.484 Sum_probs=27.9
Q ss_pred HHHHHHHHhCC-------CChhHHHHhhCCCC----CcccccccccccccC
Q 044161 18 LLVTFVTLFGE-------RRWDYIAKASGLKR----SGKSCGLRWLNYLCP 57 (229)
Q Consensus 18 ~L~~lv~~~g~-------~~W~~IA~~l~~~R----t~~qcr~Rw~~~L~p 57 (229)
+|..+|.+.|. +.|..||..|+..- ...+.+..|.++|.|
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 57777888763 36999999998432 245567777777654
No 66
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=65.79 E-value=8.3 Score=31.76 Aligned_cols=41 Identities=22% Similarity=0.166 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccc
Q 044161 10 PWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLN 53 (229)
Q Consensus 10 ~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~ 53 (229)
.||.|+.++|.+|... | .-=++||+.|| +.|.+.+.-+-+.
T Consensus 2 ~Wtde~~~~L~~lw~~-G-~SasqIA~~lg-~vsRnAViGk~hR 42 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-G-LSASQIARQLG-GVSRNAVIGKAHR 42 (162)
T ss_pred CCCHHHHHHHHHHHHc-C-CCHHHHHHHhC-Ccchhhhhhhhhc
Confidence 4999999999999976 6 55899999998 6666666554443
No 67
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=64.91 E-value=5.9 Score=31.82 Aligned_cols=46 Identities=15% Similarity=0.062 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccccCCCC
Q 044161 13 EEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLCPNIK 60 (229)
Q Consensus 13 ~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~~~ 60 (229)
.+-|.+|+.+.++-|.-.|+.||+.++ -+...|+.|+.+.....+-
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lg--lS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFG--VSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCe
Confidence 357899999999999889999999996 8899999999888765544
No 68
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=64.13 E-value=6.4 Score=41.46 Aligned_cols=35 Identities=23% Similarity=0.377 Sum_probs=30.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhC
Q 044161 5 KLSKGPWHEEEDELLVTFVTLFGERRWDYIAKASG 39 (229)
Q Consensus 5 ~~kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~ 39 (229)
..++..||.|||..|+-.+.+||.++|..|-..+.
T Consensus 923 ~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~ 957 (1033)
T PLN03142 923 QNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFR 957 (1033)
T ss_pred CCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHH
Confidence 34555699999999999999999999999987763
No 69
>smart00595 MADF subfamily of SANT domain.
Probab=62.93 E-value=9.1 Score=27.42 Aligned_cols=26 Identities=27% Similarity=0.507 Sum_probs=21.8
Q ss_pred CHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 82 KWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 82 ~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
-|.+||..|.. |..+|+.+|+++...
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~LR~~ 54 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKNLRDR 54 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHHHHHH
Confidence 39999999955 999999999986533
No 70
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=61.40 E-value=8 Score=36.99 Aligned_cols=47 Identities=21% Similarity=0.279 Sum_probs=41.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCccccccccccc
Q 044161 6 LSKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNY 54 (229)
Q Consensus 6 ~kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~ 54 (229)
-.+..||.||--++.++...|| .+..+|-+.|| .|+-.++...|...
T Consensus 185 ~~~d~WT~Ed~vlFe~aF~~~G-K~F~kIrq~LP-~rsLaSlvqyYy~~ 231 (534)
T KOG1194|consen 185 EFPDEWTAEDIVLFEQAFQFFG-KDFHKIRQALP-HRSLASLVQYYYSW 231 (534)
T ss_pred CCcccchHHHHHHHHHHHHHhc-ccHHHHHHHcc-CccHHHHHHHHHHH
Confidence 3456799999999999999999 88999999999 99999998877655
No 71
>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=60.15 E-value=14 Score=30.45 Aligned_cols=41 Identities=24% Similarity=0.191 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHH
Q 044161 63 YISTEEEQIIIQLHKKWGNKWSRIARNLPGRTDNEIKNYWRT 104 (229)
Q Consensus 63 ~WT~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~qiknrw~~ 104 (229)
.||+|+.+.|.++. .-|..=++||..|++.|.|.|.-+-+.
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 59999999998888 447778999999988999998777654
No 72
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=57.66 E-value=3.4 Score=38.70 Aligned_cols=49 Identities=22% Similarity=0.345 Sum_probs=41.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCChhHHHHh-----hCCCCCcccccccccccc
Q 044161 6 LSKGPWHEEEDELLVTFVTLFGERRWDYIAKA-----SGLKRSGKSCGLRWLNYL 55 (229)
Q Consensus 6 ~kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~-----l~~~Rt~~qcr~Rw~~~L 55 (229)
+.-..||++|-+.|..|+.+|. -.|--||.. .+..||....++||+...
T Consensus 128 l~dn~WskeETD~LF~lck~fD-LRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~ 181 (445)
T KOG2656|consen 128 LNDNSWSKEETDYLFDLCKRFD-LRFFVIADRYDNQQYKKSRTVEDLKERYYSVC 181 (445)
T ss_pred hccccccHHHHHHHHHHHHhcC-eeEEEEeeccchhhccccccHHHHHHHHHHHH
Confidence 3446799999999999999999 779999877 674599999999997653
No 73
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=57.59 E-value=37 Score=26.15 Aligned_cols=46 Identities=13% Similarity=0.164 Sum_probs=34.4
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCccccccccccccc
Q 044161 7 SKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLC 56 (229)
Q Consensus 7 kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~ 56 (229)
++.+||.|+-..++..+...| ..-..||+.++. +..++ .+|.+.+.
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g-~sv~evA~e~gI--s~~tl-~~W~r~y~ 54 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPG-MTVSLVARQHGV--AASQL-FLWRKQYQ 54 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCC-CCHHHHHHHHCc--CHHHH-HHHHHHHh
Confidence 457899999988888887777 678899999984 44444 46777653
No 74
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=56.35 E-value=17 Score=25.40 Aligned_cols=44 Identities=16% Similarity=0.406 Sum_probs=29.3
Q ss_pred HHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccccCC-------CCCCCCCHHHHHHH
Q 044161 16 DELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLCPN-------IKHGYISTEEEQII 72 (229)
Q Consensus 16 De~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~-------~~~~~WT~eEd~~L 72 (229)
+.+|.+||+.|| |...++.+. ..|.. -+|. +.+.+|..+.-+.|
T Consensus 12 e~il~~Lv~~yG---W~~L~~~i~-----i~CF~-----~~PsikSSLkFLRkTpWAR~KVE~l 62 (64)
T PF09905_consen 12 ETILTELVEHYG---WEELGERIN-----INCFK-----NNPSIKSSLKFLRKTPWAREKVENL 62 (64)
T ss_dssp HHHHHHHHHHT----HHHHHHHTT-----SSSTT-----SS--HHHHHHHHHHSHHHHHHHHHH
T ss_pred HHHHHHHHHHhC---HHHHHhhcc-----cccCC-----CCCchHHHHHHHhcCHhHHHHHHHh
Confidence 568999999999 999999887 33432 2343 33678877765544
No 75
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=56.11 E-value=12 Score=36.81 Aligned_cols=46 Identities=17% Similarity=0.327 Sum_probs=42.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHH
Q 044161 59 IKHGYISTEEEQIIIQLHKKWGNKWSRIARNLPGRTDNEIKNYWRT 104 (229)
Q Consensus 59 ~~~~~WT~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~qiknrw~~ 104 (229)
...++|+.+|-.+...+..+.|..-+.|+..+|+|...|||.+|..
T Consensus 407 ~~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 407 LETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKK 452 (584)
T ss_pred cccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhh
Confidence 3456899999999999999999999999999999999999999975
No 76
>smart00595 MADF subfamily of SANT domain.
Probab=55.53 E-value=4.4 Score=29.10 Aligned_cols=23 Identities=39% Similarity=0.764 Sum_probs=20.4
Q ss_pred ChhHHHHhhCCCCCccccccccccc
Q 044161 30 RWDYIAKASGLKRSGKSCGLRWLNY 54 (229)
Q Consensus 30 ~W~~IA~~l~~~Rt~~qcr~Rw~~~ 54 (229)
.|..||..|+ -++.+|+.+|.+.
T Consensus 29 aW~~Ia~~l~--~~~~~~~~kw~~L 51 (89)
T smart00595 29 AWEEIAEELG--LSVEECKKRWKNL 51 (89)
T ss_pred HHHHHHHHHC--cCHHHHHHHHHHH
Confidence 4999999998 4999999999876
No 77
>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=55.48 E-value=13 Score=28.63 Aligned_cols=46 Identities=13% Similarity=0.263 Sum_probs=29.6
Q ss_pred CCCHHHHHHHHHHHHHh------------CC------------------CChhHHHHhhCCCCCccccccccccccc
Q 044161 10 PWHEEEDELLVTFVTLF------------GE------------------RRWDYIAKASGLKRSGKSCGLRWLNYLC 56 (229)
Q Consensus 10 ~WT~eEDe~L~~lv~~~------------g~------------------~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~ 56 (229)
+||++||..|-..|.+| |. .-....+...| ..|..+=|+||++++.
T Consensus 1 kfTA~dDY~Lc~~i~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~fF~~~~~~~p-~HT~~sWRDR~RKfv~ 76 (105)
T PF09197_consen 1 KFTADDDYALCKAIKKQFYRDIYQKDPDTGSSLISDGDSKEFIPKRDMRSFFKDLARKNP-RHTENSWRDRYRKFVS 76 (105)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHSB-TTSS-B----------------TTHHHHHHHHTT-TS-HHHHHHHHHHTHH
T ss_pred CCChHHHHHHHHHHHHHHHHHHHhhCcccccccccCCCccccccchhhHHHHHHHHHcCC-ccchhHHHHHHHHHHH
Confidence 68999999999999877 11 11455566666 7777777777777654
No 78
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=55.02 E-value=24 Score=26.46 Aligned_cols=49 Identities=20% Similarity=0.192 Sum_probs=33.6
Q ss_pred CCCCHHHHHHHHHHHHHh----C----CCHHHH----HhhC-CCCCHHHHHHHHHHhhhHHH
Q 044161 62 GYISTEEEQIIIQLHKKW----G----NKWSRI----ARNL-PGRTDNEIKNYWRTRIRKKI 110 (229)
Q Consensus 62 ~~WT~eEd~~L~~~v~~~----G----~~W~~I----a~~l-~gRt~~qiknrw~~~l~~~~ 110 (229)
.-||+++|-.|++.+..| | ..+... ...+ ..=+..|+.++.+.+.++-.
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~ 66 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYR 66 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHH
Confidence 469999999999998776 5 235443 3333 22477899888887655543
No 79
>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=54.13 E-value=71 Score=29.35 Aligned_cols=51 Identities=22% Similarity=0.437 Sum_probs=38.3
Q ss_pred CCCCCHHHHHHHHHHHHHh-CCC---HHHHHhhCCCCCHHHHHHHHHHhhhHHHH
Q 044161 61 HGYISTEEEQIIIQLHKKW-GNK---WSRIARNLPGRTDNEIKNYWRTRIRKKIQ 111 (229)
Q Consensus 61 ~~~WT~eEd~~L~~~v~~~-G~~---W~~Ia~~l~gRt~~qiknrw~~~l~~~~~ 111 (229)
-..||.-|...|+.+.+.. |.. -.+|++.++||+..+|++--..+..+.++
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rvar 75 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRVAR 75 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHHHH
Confidence 4579998888888776654 533 57899999999999999977665544433
No 80
>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=53.72 E-value=34 Score=26.34 Aligned_cols=37 Identities=19% Similarity=0.291 Sum_probs=27.2
Q ss_pred HHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 71 IIIQLHKKWGNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 71 ~L~~~v~~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
.++.+.-..|-...+||..+ |.+...|+.+....+++
T Consensus 120 ~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 120 KIFILSRFEGKSYKEIAEEL-GISVKTVEYHISKALKE 156 (161)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 33344334577899999998 78999999998875543
No 81
>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=52.29 E-value=42 Score=24.17 Aligned_cols=38 Identities=21% Similarity=0.378 Sum_probs=26.6
Q ss_pred HHHHHHHHhC--------CCHHHHHhhCCC---CC--HHHHHHHHHHhhhH
Q 044161 71 IIIQLHKKWG--------NKWSRIARNLPG---RT--DNEIKNYWRTRIRK 108 (229)
Q Consensus 71 ~L~~~v~~~G--------~~W~~Ia~~l~g---Rt--~~qiknrw~~~l~~ 108 (229)
.|..+|...| ..|..||..|.- -+ ..+++..|..+|-+
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 4666777766 459999999833 12 36789988887654
No 82
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=52.20 E-value=18 Score=38.66 Aligned_cols=73 Identities=14% Similarity=0.186 Sum_probs=47.0
Q ss_pred CCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccccCCCCCCCCCHHHHHHHHHHHHHh-CCCHHHHH
Q 044161 9 GPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLCPNIKHGYISTEEEQIIIQLHKKW-GNKWSRIA 87 (229)
Q Consensus 9 g~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~~~~~~WT~eEd~~L~~~v~~~-G~~W~~Ia 87 (229)
--|..++|..|+-.|-+||.++|..|-.- +.-|.. =...+...+-.+.+=..+-..|+.+.... +.+|....
T Consensus 1134 ~~W~~e~Ds~LLiGI~khGygswe~Ir~D------p~L~l~-dKi~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~~~ 1206 (1373)
T KOG0384|consen 1134 CDWGSEDDSMLLIGIFKHGYGSWEAIRLD------PDLGLT-DKIFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPKKL 1206 (1373)
T ss_pred cCCCchhhhhHhhhhhhcccccHHHhccC------ccccch-hhhcccccCCchHHHHHHHHHHHHHHhhcccCCCchhh
Confidence 35999999999999999999999999321 111111 11222223445666677777777777666 45555544
Q ss_pred h
Q 044161 88 R 88 (229)
Q Consensus 88 ~ 88 (229)
+
T Consensus 1207 ~ 1207 (1373)
T KOG0384|consen 1207 K 1207 (1373)
T ss_pred h
Confidence 3
No 83
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=51.81 E-value=25 Score=34.97 Aligned_cols=48 Identities=13% Similarity=0.421 Sum_probs=37.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHH----------hhCCCCCHHHHHHHHHHhhhH
Q 044161 61 HGYISTEEEQIIIQLHKKWGNKWSRIA----------RNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 61 ~~~WT~eEd~~L~~~v~~~G~~W~~Ia----------~~l~gRt~~qiknrw~~~l~~ 108 (229)
+..||..|+.-...+.+++|.....|- ....-+|..|++.+|..++++
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~ 145 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRR 145 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHH
Confidence 568999999999999999999998882 222336777888888776654
No 84
>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=50.27 E-value=8.8 Score=28.06 Aligned_cols=17 Identities=18% Similarity=0.468 Sum_probs=10.0
Q ss_pred CCCCCCCCCHHHHHHHH
Q 044161 57 PNIKHGYISTEEEQIII 73 (229)
Q Consensus 57 p~~~~~~WT~eEd~~L~ 73 (229)
|.-..|-||+++|..|.
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 55667899999999983
No 85
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=49.51 E-value=9.5 Score=37.58 Aligned_cols=49 Identities=20% Similarity=0.328 Sum_probs=43.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccc
Q 044161 3 EEKLSKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLN 53 (229)
Q Consensus 3 ~~~~kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~ 53 (229)
++....++||.+|-++........| .+.+.||..++ +|...|++..+..
T Consensus 404 sk~~~~~~w~~se~e~fyka~~~~g-s~~slis~l~p-~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 404 SKKLETDKWDASETELFYKALSERG-SDFSLISNLFP-LRDRKQIKAKFKK 452 (584)
T ss_pred cCccccCcccchhhHHhhhHHhhhc-ccccccccccc-cccHHHHHHHHhh
Confidence 4566788999999999999999999 78999999998 9999999987754
No 86
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=48.93 E-value=45 Score=26.61 Aligned_cols=43 Identities=12% Similarity=0.160 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHhC-CCHHHHHhhCCCCCHHHHHHHHHHhhhHHH
Q 044161 67 EEEQIIIQLHKKWG-NKWSRIARNLPGRTDNEIKNYWRTRIRKKI 110 (229)
Q Consensus 67 eEd~~L~~~v~~~G-~~W~~Ia~~l~gRt~~qiknrw~~~l~~~~ 110 (229)
+-|..|+.+.++-| ..|++||+.+ |-|...|..|++.+....+
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 46777888777777 5699999999 7999999999988765543
No 87
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=48.06 E-value=38 Score=31.74 Aligned_cols=44 Identities=20% Similarity=0.225 Sum_probs=39.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCCHHHH-HhhCCCCCHHHHHHHHHHh
Q 044161 62 GYISTEEEQIIIQLHKKWGNKWSRI-ARNLPGRTDNEIKNYWRTR 105 (229)
Q Consensus 62 ~~WT~eEd~~L~~~v~~~G~~W~~I-a~~l~gRt~~qiknrw~~~ 105 (229)
..|+++|-...-+..+.||.....| +..++.|+--.|...|..-
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlW 322 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLW 322 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHh
Confidence 4799999999999999999999999 5568999999999888654
No 88
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=47.74 E-value=50 Score=24.04 Aligned_cols=39 Identities=21% Similarity=0.371 Sum_probs=27.4
Q ss_pred HHHHHHHHhC--------CCHHHHHhhCCCC-----CHHHHHHHHHHhhhHH
Q 044161 71 IIIQLHKKWG--------NKWSRIARNLPGR-----TDNEIKNYWRTRIRKK 109 (229)
Q Consensus 71 ~L~~~v~~~G--------~~W~~Ia~~l~gR-----t~~qiknrw~~~l~~~ 109 (229)
.|..+|...| +.|..||..|.-. ...+++..|...|.+-
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~y 87 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLPF 87 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHHH
Confidence 3566666665 4699999998432 3567888888877653
No 89
>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=46.58 E-value=13 Score=24.06 Aligned_cols=38 Identities=18% Similarity=0.156 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccc
Q 044161 13 EEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLN 53 (229)
Q Consensus 13 ~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~ 53 (229)
++++..++.++--.| -.+..||..++ .+...++.+.+.
T Consensus 12 ~~~~r~i~~l~~~~g-~s~~eIa~~l~--~s~~~v~~~l~r 49 (54)
T PF08281_consen 12 PERQREIFLLRYFQG-MSYAEIAEILG--ISESTVKRRLRR 49 (54)
T ss_dssp -HHHHHHHHHHHTS----HHHHHHHCT--S-HHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHC-cCHHHHHHHHC--cCHHHHHHHHHH
Confidence 456666777766667 77999999986 888888876654
No 90
>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=46.12 E-value=35 Score=23.58 Aligned_cols=27 Identities=26% Similarity=0.548 Sum_probs=21.5
Q ss_pred CHHHHHhhCCC-CCHHHHHHHHHHhhhH
Q 044161 82 KWSRIARNLPG-RTDNEIKNYWRTRIRK 108 (229)
Q Consensus 82 ~W~~Ia~~l~g-Rt~~qiknrw~~~l~~ 108 (229)
.|..||..++. -+...|+.+|.++...
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~ 55 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRDR 55 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHHH
Confidence 39999999963 6788999999986533
No 91
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=45.10 E-value=28 Score=28.43 Aligned_cols=48 Identities=15% Similarity=0.182 Sum_probs=35.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCC---CCCccccccccccc
Q 044161 6 LSKGPWHEEEDELLVTFVTLFGERRWDYIAKASGL---KRSGKSCGLRWLNY 54 (229)
Q Consensus 6 ~kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~---~Rt~~qcr~Rw~~~ 54 (229)
.+...=|+.|-+-|..||++|| .++..+|.-..+ ..|..||+.+...|
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhG-dDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHG-DDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHC-ccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 4556789999999999999999 789888865431 35666776655443
No 92
>COG4628 Uncharacterized conserved protein [Function unknown]
Probab=44.57 E-value=29 Score=27.19 Aligned_cols=44 Identities=23% Similarity=0.477 Sum_probs=31.0
Q ss_pred HHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccccCC-------CCCCCCCHHHHHHH
Q 044161 16 DELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLCPN-------IKHGYISTEEEQII 72 (229)
Q Consensus 16 De~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~-------~~~~~WT~eEd~~L 72 (229)
+.+|.+||..|| |..+|..++ ..|..- +|. +++.+|..|.-+.|
T Consensus 21 E~llt~Lvd~YG---Wd~L~~ri~-----inCF~n-----dPSi~SSlKfLrkT~WARekvEa~ 71 (136)
T COG4628 21 ETLLTELVDFYG---WDGLATRIR-----INCFHN-----DPSIKSSLKFLRKTPWAREKVEAL 71 (136)
T ss_pred HHHHHHHHHHhC---hHHHHhhce-----eccccC-----CccHHHHHHHHhcCHhHHHHHHHH
Confidence 567889999999 999998776 455431 332 44678887766554
No 93
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=41.41 E-value=93 Score=23.28 Aligned_cols=71 Identities=18% Similarity=0.266 Sum_probs=40.2
Q ss_pred CCCCCCHHHHHHHHHHHHHh----CCC---ChhHHHHhhC----CCCCcccc-------cccccccccCCCCCC---CCC
Q 044161 7 SKGPWHEEEDELLVTFVTLF----GER---RWDYIAKASG----LKRSGKSC-------GLRWLNYLCPNIKHG---YIS 65 (229)
Q Consensus 7 kkg~WT~eEDe~L~~lv~~~----g~~---~W~~IA~~l~----~~Rt~~qc-------r~Rw~~~L~p~~~~~---~WT 65 (229)
-...||+|++-.|++.+..| |.. ++..+-..+. ..=+..|+ +.||.+.... .+.| .++
T Consensus 3 ~qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~~~k-~~~g~~~~~~ 81 (98)
T PF04504_consen 3 FQRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNAVKK-SKNGKDPSFS 81 (98)
T ss_pred CcCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHhhh-cccCcCCCCC
Confidence 45679999999999998887 422 4444433332 11122222 3455555443 2222 566
Q ss_pred HHHHHHHHHHHHH
Q 044161 66 TEEEQIIIQLHKK 78 (229)
Q Consensus 66 ~eEd~~L~~~v~~ 78 (229)
..-|..+.++.+.
T Consensus 82 ~~hd~~~f~Lsk~ 94 (98)
T PF04504_consen 82 KPHDRRLFELSKK 94 (98)
T ss_pred CHhHHHHHHHHHH
Confidence 6777777766554
No 94
>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=40.28 E-value=54 Score=23.93 Aligned_cols=28 Identities=21% Similarity=0.427 Sum_probs=22.4
Q ss_pred HHHHHHHHHHhCCCHHHHHhhCCCCCHHH
Q 044161 69 EQIIIQLHKKWGNKWSRIARNLPGRTDNE 97 (229)
Q Consensus 69 d~~L~~~v~~~G~~W~~Ia~~l~gRt~~q 97 (229)
|..|..+....|..|.++|..| |=+...
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~d 31 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDE 31 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHH
Confidence 5678888899999999999999 344433
No 95
>COG1168 MalY Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]
Probab=39.83 E-value=28 Score=32.70 Aligned_cols=27 Identities=19% Similarity=0.302 Sum_probs=23.6
Q ss_pred CCCCCCCCC-CCHHHHHHHHHHHHHhCC
Q 044161 2 QEEKLSKGP-WHEEEDELLVTFVTLFGE 28 (229)
Q Consensus 2 ~~~~~kkg~-WT~eEDe~L~~lv~~~g~ 28 (229)
+.|+..-|+ ||+||=.+|.+++.+||.
T Consensus 165 CnPHNP~Grvwt~eeL~~i~elc~kh~v 192 (388)
T COG1168 165 CNPHNPTGRVWTKEELRKIAELCLRHGV 192 (388)
T ss_pred eCCCCCCCccccHHHHHHHHHHHHHcCC
Confidence 567777776 999999999999999973
No 96
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=39.80 E-value=17 Score=35.98 Aligned_cols=49 Identities=12% Similarity=0.292 Sum_probs=36.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCC---------CCCccccccccccccc
Q 044161 7 SKGPWHEEEDELLVTFVTLFGERRWDYIAKASGL---------KRSGKSCGLRWLNYLC 56 (229)
Q Consensus 7 kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~---------~Rt~~qcr~Rw~~~L~ 56 (229)
+|..||..|.+-+..++..+| .++..|-..+-. -+|-.|+|.+|++.+.
T Consensus 87 ~ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~ 144 (782)
T KOG4468|consen 87 AKTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVR 144 (782)
T ss_pred cccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHH
Confidence 366899999999999999999 889888322210 3456677887776643
No 97
>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=39.50 E-value=31 Score=25.19 Aligned_cols=28 Identities=21% Similarity=0.459 Sum_probs=23.0
Q ss_pred HHHHHHHHHHhCCCChhHHHHhhCCCCCc
Q 044161 16 DELLVTFVTLFGERRWDYIAKASGLKRSG 44 (229)
Q Consensus 16 De~L~~lv~~~g~~~W~~IA~~l~~~Rt~ 44 (229)
|+.|..+....| ..|..+|..||..-+.
T Consensus 2 ~~~L~~la~~LG-~~W~~Lar~Lgls~~~ 29 (83)
T cd08319 2 DRELNQLAQRLG-PEWEQVLLDLGLSQTD 29 (83)
T ss_pred HHHHHHHHHHHh-hhHHHHHHHcCCCHHH
Confidence 577889999999 8899999999854333
No 98
>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=38.22 E-value=55 Score=23.88 Aligned_cols=27 Identities=22% Similarity=0.580 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhCCCHHHHHhhCCCCCHH
Q 044161 69 EQIIIQLHKKWGNKWSRIARNLPGRTDN 96 (229)
Q Consensus 69 d~~L~~~v~~~G~~W~~Ia~~l~gRt~~ 96 (229)
|+-|..+....|..|..+|.+| |=|..
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~ 28 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQT 28 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHH
Confidence 4568888999999999999999 34443
No 99
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=38.11 E-value=65 Score=26.02 Aligned_cols=44 Identities=14% Similarity=0.108 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHhC-CCHHHHHhhCCCCCHHHHHHHHHHhhhHHH
Q 044161 66 TEEEQIIIQLHKKWG-NKWSRIARNLPGRTDNEIKNYWRTRIRKKI 110 (229)
Q Consensus 66 ~eEd~~L~~~v~~~G-~~W~~Ia~~l~gRt~~qiknrw~~~l~~~~ 110 (229)
.+-|.+|+.+.++-| -.|++||+.+ |-+...|..|++.+.+..+
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 456777777777766 5699999999 7999999999998876654
No 100
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=38.02 E-value=71 Score=21.76 Aligned_cols=40 Identities=18% Similarity=0.258 Sum_probs=29.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC----C---ChhHHHHhhCCCCCc
Q 044161 5 KLSKGPWHEEEDELLVTFVTLFGE----R---RWDYIAKASGLKRSG 44 (229)
Q Consensus 5 ~~kkg~WT~eEDe~L~~lv~~~g~----~---~W~~IA~~l~~~Rt~ 44 (229)
+..+..||++.-+.|....++.|- - .=..+|..+|+.+..
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~v 48 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKV 48 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHH
Confidence 456789999999999999999882 0 126677777754433
No 101
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=37.86 E-value=75 Score=27.17 Aligned_cols=51 Identities=16% Similarity=0.204 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHHhCCCHHHHHhhC---CCCCHHHHHHHHHHhh-hHHHHHHh
Q 044161 63 YISTEEEQIIIQLHKKWGNKWSRIARNL---PGRTDNEIKNYWRTRI-RKKIQAQE 114 (229)
Q Consensus 63 ~WT~eEd~~L~~~v~~~G~~W~~Ia~~l---~gRt~~qiknrw~~~l-~~~~~~~~ 114 (229)
.|++++|-+|+.+|.. |+.=..|+.-+ -.-|-..|..||..++ .+.+++..
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~~is~~a 55 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALLYDPVISRIA 55 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHHcChhhHHHH
Confidence 4999999999999865 44455554443 2467889999999987 44444433
No 102
>PRK01905 DNA-binding protein Fis; Provisional
Probab=37.30 E-value=39 Score=24.00 Aligned_cols=31 Identities=23% Similarity=0.210 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHhCCCChhHHHHhhCCCCCc
Q 044161 13 EEEDELLVTFVTLFGERRWDYIAKASGLKRSG 44 (229)
Q Consensus 13 ~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~ 44 (229)
.-|.+.++.++..+| ++....|+.+|.+|+.
T Consensus 36 ~~E~~~i~~aL~~~~-gn~s~aAr~LGIsrst 66 (77)
T PRK01905 36 CVEKPLLEVVMEQAG-GNQSLAAEYLGINRNT 66 (77)
T ss_pred HHHHHHHHHHHHHcC-CCHHHHHHHHCCCHHH
Confidence 346778889999999 8899999999866553
No 103
>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=36.48 E-value=1e+02 Score=22.94 Aligned_cols=34 Identities=24% Similarity=0.232 Sum_probs=24.0
Q ss_pred HHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 74 QLHKKWGNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 74 ~~v~~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
.++...|..+.+||+.+ |-+...|+++....+++
T Consensus 120 ~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 120 VLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred hhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 33334577899999999 45888888887765443
No 104
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=36.29 E-value=38 Score=24.91 Aligned_cols=45 Identities=16% Similarity=-0.006 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccccCCCC
Q 044161 14 EEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLCPNIK 60 (229)
Q Consensus 14 eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~~~ 60 (229)
+.|.+|+.++...+.-.++.||+.++ -+...|+.|........+-
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~--~s~~tv~~~l~~L~~~g~i 47 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVG--LSPSTVHNRVKRLEEEGVI 47 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCe
Confidence 56888899999988789999999996 7888898888777665443
No 105
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=36.20 E-value=33 Score=32.17 Aligned_cols=43 Identities=21% Similarity=0.274 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHHhCCCChhHHHH-hhCCCCCccccccccccc
Q 044161 10 PWHEEEDELLVTFVTLFGERRWDYIAK-ASGLKRSGKSCGLRWLNY 54 (229)
Q Consensus 10 ~WT~eEDe~L~~lv~~~g~~~W~~IA~-~l~~~Rt~~qcr~Rw~~~ 54 (229)
-|+.+|-..+-+.++.|| .++..|-+ +++ .|+...|-..|+-.
T Consensus 279 ~wsEeEcr~FEegl~~yG-KDF~lIr~nkvr-tRsvgElVeyYYlW 322 (445)
T KOG4329|consen 279 GWSEEECRNFEEGLELYG-KDFHLIRANKVR-TRSVGELVEYYYLW 322 (445)
T ss_pred cCCHHHHHHHHHHHHHhc-ccHHHHHhcccc-cchHHHHHHHHHHh
Confidence 599999999999999999 88888854 576 99999999887554
No 106
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=35.90 E-value=41 Score=25.13 Aligned_cols=30 Identities=20% Similarity=0.109 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHhCCCChhHHHHhhCCCCCc
Q 044161 14 EEDELLVTFVTLFGERRWDYIAKASGLKRSG 44 (229)
Q Consensus 14 eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~ 44 (229)
-|...|..++..++ ++....|+.+|.+|+.
T Consensus 55 ~Er~~i~~aL~~~~-gn~s~AAr~LGIsRsT 84 (95)
T PRK00430 55 VEAPLLDMVMQYTR-GNQTRAALMLGINRGT 84 (95)
T ss_pred HHHHHHHHHHHHcC-CCHHHHHHHhCCCHHH
Confidence 46778888999998 8899999999866653
No 107
>smart00351 PAX Paired Box domain.
Probab=35.28 E-value=1.6e+02 Score=22.75 Aligned_cols=73 Identities=14% Similarity=0.103 Sum_probs=46.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCC-Cccccccccccc--ccCCCC----CCCCCHHHHHHHHHHHHH
Q 044161 6 LSKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKR-SGKSCGLRWLNY--LCPNIK----HGYISTEEEQIIIQLHKK 78 (229)
Q Consensus 6 ~kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~R-t~~qcr~Rw~~~--L~p~~~----~~~WT~eEd~~L~~~v~~ 78 (229)
.+..+++.++-++++.++. -| ..-..||+.++..| |...+..||... +.|.-. ...-+.+.+..|++++.+
T Consensus 13 ~~~~~~s~~~R~riv~~~~-~G-~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~ 90 (125)
T smart00351 13 VNGRPLPDEERQRIVELAQ-NG-VRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQE 90 (125)
T ss_pred cCCCCCCHHHHHHHHHHHH-cC-CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHH
Confidence 3456799999999998886 35 56899999998553 344456666542 344211 122455666666666665
Q ss_pred hC
Q 044161 79 WG 80 (229)
Q Consensus 79 ~G 80 (229)
.+
T Consensus 91 ~p 92 (125)
T smart00351 91 NP 92 (125)
T ss_pred CC
Confidence 54
No 108
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=35.07 E-value=1e+02 Score=25.14 Aligned_cols=45 Identities=22% Similarity=0.298 Sum_probs=38.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHhhCC-C---CCHHHHHHHHHHh
Q 044161 61 HGYISTEEEQIIIQLHKKWGNKWSRIARNLP-G---RTDNEIKNYWRTR 105 (229)
Q Consensus 61 ~~~WT~eEd~~L~~~v~~~G~~W~~Ia~~l~-g---Rt~~qiknrw~~~ 105 (229)
...-|+.|..-|..++..||..+...|.... + .|..||+.+....
T Consensus 114 ~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 114 PRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 4567899999999999999999999988764 3 8999998887654
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=34.33 E-value=53 Score=23.55 Aligned_cols=29 Identities=24% Similarity=0.653 Sum_probs=22.1
Q ss_pred HHHHHHHHHHhCCCHHHHHhhCCCCCHHHH
Q 044161 69 EQIIIQLHKKWGNKWSRIARNLPGRTDNEI 98 (229)
Q Consensus 69 d~~L~~~v~~~G~~W~~Ia~~l~gRt~~qi 98 (229)
|..|..+....|..|.++|..| |=+..+|
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI 32 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDI 32 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHH
Confidence 4567788889999999999999 3444433
No 110
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=34.22 E-value=93 Score=24.44 Aligned_cols=33 Identities=15% Similarity=0.126 Sum_probs=24.2
Q ss_pred HHHHhCCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 75 LHKKWGNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 75 ~v~~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
+....|-...+||..+ |.+...|+.+....+++
T Consensus 139 l~~~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 171 (182)
T PRK09652 139 LREIEGLSYEEIAEIM-GCPIGTVRSRIFRAREA 171 (182)
T ss_pred HHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3334577899999999 68888998887754433
No 111
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=33.65 E-value=35 Score=26.69 Aligned_cols=45 Identities=11% Similarity=-0.023 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccccCCCC
Q 044161 14 EEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLCPNIK 60 (229)
Q Consensus 14 eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~~~ 60 (229)
+-|.+|+++.++-+...+..||+.++ -+...|+.|-.+.....+-
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~lg--lS~~~v~~Ri~~L~~~GiI 52 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERVG--LSPSTVLRRIKRLEEEGVI 52 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCCce
Confidence 55888999999999889999999996 7888898887776555433
No 112
>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=32.59 E-value=48 Score=24.18 Aligned_cols=25 Identities=16% Similarity=0.353 Sum_probs=20.9
Q ss_pred HHHHHHHHHHhCCCChhHHHHhhCCC
Q 044161 16 DELLVTFVTLFGERRWDYIAKASGLK 41 (229)
Q Consensus 16 De~L~~lv~~~g~~~W~~IA~~l~~~ 41 (229)
|.+|..+....| .+|..+|..|+..
T Consensus 4 d~~l~~ia~~LG-~dW~~LA~eLg~s 28 (84)
T cd08803 4 DIRMAIVADHLG-LSWTELARELNFS 28 (84)
T ss_pred HHHHHHHHHHhh-ccHHHHHHHcCCC
Confidence 567788888889 8999999999843
No 113
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=32.29 E-value=1.3e+02 Score=24.58 Aligned_cols=37 Identities=19% Similarity=0.262 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHhh
Q 044161 69 EQIIIQLHKKWGNKWSRIARNLPGRTDNEIKNYWRTRI 106 (229)
Q Consensus 69 d~~L~~~v~~~G~~W~~Ia~~l~gRt~~qiknrw~~~l 106 (229)
...++++....|-.+.+||..+ |-+...|+.+|..+.
T Consensus 140 ~~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR 176 (185)
T PF07638_consen 140 QRRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 3444455555688899999999 799999999998754
No 114
>PRK04217 hypothetical protein; Provisional
Probab=31.10 E-value=1.9e+02 Score=22.27 Aligned_cols=45 Identities=13% Similarity=0.161 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHhhhHH
Q 044161 63 YISTEEEQIIIQLHKKWGNKWSRIARNLPGRTDNEIKNYWRTRIRKK 109 (229)
Q Consensus 63 ~WT~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~~ 109 (229)
.-|.++ ..++.+....|-.-.+||+.+ |-+...|+.++....++.
T Consensus 42 ~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 42 FMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKKV 86 (110)
T ss_pred cCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 455555 577777877888999999999 799999999988754443
No 115
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=30.57 E-value=1.1e+02 Score=23.89 Aligned_cols=30 Identities=23% Similarity=0.199 Sum_probs=22.6
Q ss_pred HhCCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 78 KWGNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 78 ~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
..|-...+||..+ |-|...|+++....+++
T Consensus 139 ~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 168 (179)
T PRK11924 139 VEGLSYREIAEIL-GVPVGTVKSRLRRARQL 168 (179)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3467799999999 68888888887764433
No 116
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=29.17 E-value=1.2e+02 Score=24.14 Aligned_cols=28 Identities=11% Similarity=-0.052 Sum_probs=21.7
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHhhh
Q 044161 79 WGNKWSRIARNLPGRTDNEIKNYWRTRIR 107 (229)
Q Consensus 79 ~G~~W~~Ia~~l~gRt~~qiknrw~~~l~ 107 (229)
.|....+||..+ |-|...|+++.....+
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar~ 178 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGRE 178 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 466789999999 6888888888765443
No 117
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=28.98 E-value=1.7e+02 Score=23.49 Aligned_cols=33 Identities=21% Similarity=0.133 Sum_probs=26.1
Q ss_pred HHhCCCHHHHHhhCCCCCHHHHHHHHHHhhhHHH
Q 044161 77 KKWGNKWSRIARNLPGRTDNEIKNYWRTRIRKKI 110 (229)
Q Consensus 77 ~~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~~~ 110 (229)
...|-...+||..+ |-+...|+.|....+.+-.
T Consensus 140 ~~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~ 172 (178)
T PRK12529 140 TLDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCL 172 (178)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 34467799999999 7899999999887666543
No 118
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=28.94 E-value=1.6e+02 Score=23.97 Aligned_cols=31 Identities=19% Similarity=0.201 Sum_probs=23.8
Q ss_pred HHhCCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 77 KKWGNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 77 ~~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
...|-...+||..+ |-+...|++|....+++
T Consensus 147 ~~~g~s~~EIA~~l-g~s~~tV~~rl~rar~~ 177 (192)
T PRK09643 147 DMQGYSVADAARML-GVAEGTVKSRCARGRAR 177 (192)
T ss_pred HHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 34567799999999 68889999998664433
No 119
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=28.76 E-value=89 Score=22.63 Aligned_cols=31 Identities=26% Similarity=0.542 Sum_probs=23.6
Q ss_pred HHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHH
Q 044161 69 EQIIIQLHKKWGNKWSRIARNLPGRTDNEIKN 100 (229)
Q Consensus 69 d~~L~~~v~~~G~~W~~Ia~~l~gRt~~qikn 100 (229)
|..|.......|..|.++|+.| |=+...|.+
T Consensus 4 ~~~l~~ia~~LG~dWk~LAr~L-g~se~dI~~ 34 (84)
T cd08804 4 EERLAVIADHLGFSWTELAREL-DFTEEQIHQ 34 (84)
T ss_pred hhHHHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 4567778888999999999999 455555543
No 120
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=28.73 E-value=1.5e+02 Score=19.57 Aligned_cols=34 Identities=29% Similarity=0.538 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHH
Q 044161 67 EEEQIIIQLHKKWGNKWSRIARNLPGRTDNEIKNY 101 (229)
Q Consensus 67 eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~qiknr 101 (229)
+.|+-.+.+..+.|-.=.+||+.+ ||+.+.|++.
T Consensus 7 ~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~y 40 (50)
T PF11427_consen 7 DAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRY 40 (50)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHH
T ss_pred HHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHH
Confidence 456667788899999999999999 7888777664
No 121
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=28.36 E-value=1.4e+02 Score=23.61 Aligned_cols=34 Identities=21% Similarity=0.339 Sum_probs=25.7
Q ss_pred HHHHhCCCHHHHHhhCCCCCHHHHHHHHHHhhhHH
Q 044161 75 LHKKWGNKWSRIARNLPGRTDNEIKNYWRTRIRKK 109 (229)
Q Consensus 75 ~v~~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~~ 109 (229)
+....|-...+||..+ |-+...|+.+....+++-
T Consensus 130 L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 130 YNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred HHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3334567799999999 789999999887765554
No 122
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=28.06 E-value=2.2e+02 Score=23.03 Aligned_cols=29 Identities=10% Similarity=0.048 Sum_probs=22.2
Q ss_pred HhCCCHHHHHhhCCCCCHHHHHHHHHHhhh
Q 044161 78 KWGNKWSRIARNLPGRTDNEIKNYWRTRIR 107 (229)
Q Consensus 78 ~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~ 107 (229)
..|-.-.+||..+ |-+...|+.+....++
T Consensus 150 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~ 178 (195)
T PRK12532 150 ILGFSSDEIQQMC-GISTSNYHTIMHRARE 178 (195)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3466689999999 7888899888776443
No 123
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=27.66 E-value=1.6e+02 Score=22.80 Aligned_cols=29 Identities=10% Similarity=0.095 Sum_probs=23.1
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 79 WGNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 79 ~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
.|-.-.+||..| |-+...|+.+....+++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 121 EDMDVAETAAAM-GCSEGSVKTHCSRATHA 149 (161)
T ss_pred hcCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466789999999 68999999988765544
No 124
>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=27.47 E-value=81 Score=22.61 Aligned_cols=33 Identities=27% Similarity=0.526 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHH
Q 044161 66 TEEEQIIIQLHKKWGNKWSRIARNLPGRTDNEIKN 100 (229)
Q Consensus 66 ~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~qikn 100 (229)
.||-++|+..- ..|..|..+|..| |=+...|.+
T Consensus 2 ~~~v~~ll~~~-nlG~dW~~LA~~L-G~~~~~I~~ 34 (77)
T cd08311 2 QEEVEKLLESG-RPGRDWRSLAGEL-GYEDEAIDT 34 (77)
T ss_pred hHHHHHHHhCC-CCccCHHHHHHHc-CCCHHHHHH
Confidence 56777777322 5688999999999 455555544
No 125
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=27.42 E-value=2e+02 Score=23.38 Aligned_cols=30 Identities=13% Similarity=0.048 Sum_probs=22.7
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHhhhHH
Q 044161 79 WGNKWSRIARNLPGRTDNEIKNYWRTRIRKK 109 (229)
Q Consensus 79 ~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~~ 109 (229)
.|-...+||..+ |-+...|+.|....+++-
T Consensus 156 eg~s~~EIA~~l-gis~~tVk~rl~ra~~~L 185 (194)
T PRK12531 156 EELPHQQVAEMF-DIPLGTVKSRLRLAVEKL 185 (194)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHHH
Confidence 466688999988 788889988877655443
No 126
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=27.23 E-value=1e+02 Score=22.35 Aligned_cols=24 Identities=33% Similarity=0.630 Sum_probs=18.6
Q ss_pred HHHHHhCCCHHHHHhhCCCCCHHHH
Q 044161 74 QLHKKWGNKWSRIARNLPGRTDNEI 98 (229)
Q Consensus 74 ~~v~~~G~~W~~Ia~~l~gRt~~qi 98 (229)
.+....|..|.++|+.| |=+..+|
T Consensus 12 ~ia~~iG~~Wk~Lar~L-Gls~~dI 35 (86)
T cd08318 12 VFANKLGEDWKTLAPHL-EMKDKEI 35 (86)
T ss_pred HHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 36678899999999999 4555555
No 127
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=26.05 E-value=1.6e+02 Score=24.05 Aligned_cols=31 Identities=13% Similarity=-0.015 Sum_probs=23.1
Q ss_pred HHhCCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 77 KKWGNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 77 ~~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
...|-...+||..+ |-+...|+.+....+++
T Consensus 149 ~~~g~s~~eIA~~l-gis~~tV~~~l~Ra~~~ 179 (196)
T PRK12524 149 HIEGLSNPEIAEVM-EIGVEAVESLTARGKRA 179 (196)
T ss_pred HHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 33466799999999 67888888887765443
No 128
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=25.90 E-value=2.4e+02 Score=22.83 Aligned_cols=29 Identities=3% Similarity=-0.053 Sum_probs=23.3
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 79 WGNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 79 ~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
.|-...+||..+ |-|...|+.|....+++
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~RAr~~ 177 (189)
T PRK12530 149 LELSSEQICQEC-DISTSNLHVLLYRARLQ 177 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466799999999 79999999987765433
No 129
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=25.60 E-value=1.4e+02 Score=23.76 Aligned_cols=28 Identities=11% Similarity=-0.006 Sum_probs=20.8
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 80 GNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 80 G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
|..-.+||..+ |.+...|+++....+++
T Consensus 152 g~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T TIGR02948 152 DLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 56688889888 67888888887654433
No 130
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=25.31 E-value=1.8e+02 Score=22.61 Aligned_cols=29 Identities=7% Similarity=-0.108 Sum_probs=22.5
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 79 WGNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 79 ~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
.|-.-.+||..+ |-+...|+++....+++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (160)
T PRK09642 121 EEKSYQEIALQE-KIEVKTVEMKLYRARKW 149 (160)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466689999999 78899999987765433
No 131
>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=25.27 E-value=53 Score=23.92 Aligned_cols=34 Identities=24% Similarity=0.322 Sum_probs=24.1
Q ss_pred HHHHHHHHHhCCCHHHHHhhCCC--CCHHHHHHHHH
Q 044161 70 QIIIQLHKKWGNKWSRIARNLPG--RTDNEIKNYWR 103 (229)
Q Consensus 70 ~~L~~~v~~~G~~W~~Ia~~l~g--Rt~~qiknrw~ 103 (229)
.-|..+....|..|..+|..|+= ..-..|+.+|.
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~LGlse~~Id~Ie~~~~ 38 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHLGLSYRELQRIKYNNR 38 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHcCCCHHHHHHHHHHCc
Confidence 35778889999999999999942 22234566653
No 132
>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=25.22 E-value=1.8e+02 Score=23.72 Aligned_cols=31 Identities=10% Similarity=0.020 Sum_probs=23.6
Q ss_pred HHhCCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 77 KKWGNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 77 ~~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
...|-.-.+||..| |-|...|+.|....+++
T Consensus 144 ~~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 144 EVLGFESDEICQEL-EISTSNCHVLLYRARLS 174 (188)
T ss_pred HHhCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 33467789999999 78899998887765443
No 133
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=24.88 E-value=86 Score=21.33 Aligned_cols=46 Identities=15% Similarity=0.105 Sum_probs=32.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCChhHHHHhhCCCCCccccccccccccc
Q 044161 7 SKGPWHEEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLC 56 (229)
Q Consensus 7 kkg~WT~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~ 56 (229)
++..||+|+-..++..+..-| .....||..+|. ..+...+|...+.
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~g-~sv~~va~~~gi---~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLESG-ESVSEVAREYGI---SPSTLYNWRKQYR 48 (76)
T ss_dssp SS----HHHHHHHHHHHHHHH-CHHHHHHHHHTS----HHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHCC-CceEeeeccccc---ccccccHHHHHHh
Confidence 457899999999999997767 779999999983 3445556877664
No 134
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=24.82 E-value=1.5e+02 Score=22.55 Aligned_cols=56 Identities=18% Similarity=0.127 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHHHhCCCChhHHHHhhCCCCCcccccccccccccCCCCCCCCCHHHHHH
Q 044161 13 EEEDELLVTFVTLFGERRWDYIAKASGLKRSGKSCGLRWLNYLCPNIKHGYISTEEEQI 71 (229)
Q Consensus 13 ~eEDe~L~~lv~~~g~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~~~~~~WT~eEd~~ 71 (229)
+=+.+.|..+|+.++...-.+||+.++. ..+...+....|.-..++..+..+++..
T Consensus 56 Kid~~~L~~~v~~~pd~tl~Ela~~l~V---s~~ti~~~Lkrlg~t~KK~~~~~~~~~~ 111 (119)
T PF01710_consen 56 KIDRDELKALVEENPDATLRELAERLGV---SPSTIWRALKRLGITRKKKTLHSEKDRE 111 (119)
T ss_pred cccHHHHHHHHHHCCCcCHHHHHHHcCC---CHHHHHHHHHHcCchhccCcccchhHHH
Confidence 3356779999999998888899999973 4444456666666677788876655544
No 135
>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=24.81 E-value=1.6e+02 Score=23.50 Aligned_cols=28 Identities=14% Similarity=0.132 Sum_probs=21.3
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 80 GNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 80 G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
|-...+||..+ |-|...|+++....+++
T Consensus 154 ~~s~~EIA~~l-gis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 154 GLSYEDIARIM-DCPVGTVRSRIFRAREA 181 (190)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 55689999999 67788898888765433
No 136
>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=24.75 E-value=75 Score=23.24 Aligned_cols=35 Identities=23% Similarity=0.325 Sum_probs=24.6
Q ss_pred HHHHHHHHHHhCCCHHHHHhhCC--CCCHHHHHHHHH
Q 044161 69 EQIIIQLHKKWGNKWSRIARNLP--GRTDNEIKNYWR 103 (229)
Q Consensus 69 d~~L~~~v~~~G~~W~~Ia~~l~--gRt~~qiknrw~ 103 (229)
|..|.......|..|.++|+.|. ..--..|+..+.
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L~vs~~dI~~I~~e~p 40 (84)
T cd08805 4 EMKMAVIREHLGLSWAELARELQFSVEDINRIRVENP 40 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHcCCCHHHHHHHHHhCC
Confidence 55677888999999999999983 233334555544
No 137
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=24.60 E-value=2.3e+02 Score=22.81 Aligned_cols=30 Identities=13% Similarity=0.137 Sum_probs=22.6
Q ss_pred HhCCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 78 KWGNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 78 ~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
..|....+||..+ |-+...|+.+....+++
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 3467789999999 67888888887665443
No 138
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=24.59 E-value=1.7e+02 Score=23.68 Aligned_cols=30 Identities=23% Similarity=0.077 Sum_probs=23.2
Q ss_pred HhCCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 78 KWGNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 78 ~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
..|-...+||..| |-+...|+.+....+++
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 3466789999999 68888999988765443
No 139
>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=23.85 E-value=1.8e+02 Score=22.91 Aligned_cols=29 Identities=17% Similarity=0.359 Sum_probs=21.2
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 79 WGNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 79 ~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
.|-...+||..+ |-|...|+++....+++
T Consensus 134 ~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~ 162 (169)
T TIGR02954 134 HDLTIKEIAEVM-NKPEGTVKTYLHRALKK 162 (169)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456688888888 56888888887765443
No 140
>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=23.79 E-value=62 Score=22.72 Aligned_cols=18 Identities=22% Similarity=0.693 Sum_probs=14.4
Q ss_pred HHHHHHHHHhCCCChhHHH
Q 044161 17 ELLVTFVTLFGERRWDYIA 35 (229)
Q Consensus 17 e~L~~lv~~~g~~~W~~IA 35 (229)
..|.+|+..|| +||.-|-
T Consensus 30 ~vl~~LL~lY~-~nW~lIE 47 (65)
T PF10440_consen 30 PVLKNLLKLYD-GNWELIE 47 (65)
T ss_pred HHHHHHHHHHc-CCchhhh
Confidence 35778899999 6799885
No 141
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=23.67 E-value=2e+02 Score=22.03 Aligned_cols=28 Identities=18% Similarity=0.227 Sum_probs=20.3
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHhhh
Q 044161 79 WGNKWSRIARNLPGRTDNEIKNYWRTRIR 107 (229)
Q Consensus 79 ~G~~W~~Ia~~l~gRt~~qiknrw~~~l~ 107 (229)
.|-.-.+||..+ |-+...|+.+-...++
T Consensus 121 ~~~s~~EIA~~l-~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 121 VGKTMGEIALET-EMTYYQVRWIYRQALE 148 (154)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 355678888888 6888888887665443
No 142
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=23.46 E-value=1.3e+02 Score=25.23 Aligned_cols=45 Identities=20% Similarity=0.233 Sum_probs=35.9
Q ss_pred CCCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHhhhHH
Q 044161 62 GYISTEEEQIIIQLHKKWGNKWSRIARNLPGRTDNEIKNYWRTRIRKK 109 (229)
Q Consensus 62 ~~WT~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~~ 109 (229)
...|+.|-+.|.-+. -|..-.+||..| +.+...||++-.++++|-
T Consensus 147 ~~LT~RE~eVL~lla--~G~snkeIA~~L-~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 147 ELLTPRELEVLRLLA--EGLSNKEIAEEL-NLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCCCHHHHHHHHHHH--CCCCHHHHHHHH-CCCHhHHHHHHHHHHHHc
Confidence 368888888765554 355668999999 799999999999988774
No 143
>COG3795 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.15 E-value=58 Score=25.74 Aligned_cols=60 Identities=17% Similarity=0.194 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHHHHHHHhC-----CCChhHHHHhhCCCCCcccccccccccccCCCCCCCCCHHHHHHH
Q 044161 9 GPWHEEEDELLVTFVTLFG-----ERRWDYIAKASGLKRSGKSCGLRWLNYLCPNIKHGYISTEEEQII 72 (229)
Q Consensus 9 g~WT~eEDe~L~~lv~~~g-----~~~W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~~~~~~WT~eEd~~L 72 (229)
--|++++|+.|.....+|. .+.|-..+...| .+++..++.+ --+..+..||+.+..|+++
T Consensus 15 ~a~~~e~daalm~~~~~y~e~L~~aG~l~~~~~L~p-t~~a~tlr~~---~G~~~viDGPFaEtKEql~ 79 (123)
T COG3795 15 AAWSVEEDAALMAALGKYNERLAKAGVLGPGARLHP-TTAATTLRFR---GGKRTVIDGPFAETKEQLA 79 (123)
T ss_pred hcCCcCccHHHHHHHHHHHHHHHHcCCccccccccC-CccceEEEec---CCcceecCCCchhHHHHhC
Confidence 3599999999999988873 134666666666 6676666533 2344567799998888764
No 144
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=23.06 E-value=2e+02 Score=22.62 Aligned_cols=29 Identities=24% Similarity=0.344 Sum_probs=22.0
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 79 WGNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 79 ~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
.|-.-.+||..| |.+...|+.+....+++
T Consensus 133 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 161 (173)
T PRK09645 133 RGWSTAQIAADL-GIPEGTVKSRLHYALRA 161 (173)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 456678999998 68888898887765433
No 145
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=22.95 E-value=2.5e+02 Score=22.43 Aligned_cols=31 Identities=16% Similarity=0.117 Sum_probs=24.1
Q ss_pred HHhCCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 77 KKWGNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 77 ~~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
...|-...+||..| |.+...|+++....+++
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 34467789999999 79999999988765444
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=22.85 E-value=1.2e+02 Score=22.15 Aligned_cols=28 Identities=43% Similarity=0.749 Sum_probs=20.9
Q ss_pred HHHHHHHhCCCHHHHHhhCCCCCHHHHHH
Q 044161 72 IIQLHKKWGNKWSRIARNLPGRTDNEIKN 100 (229)
Q Consensus 72 L~~~v~~~G~~W~~Ia~~l~gRt~~qikn 100 (229)
|-.+....|..|..+|+.| |=+..+|..
T Consensus 5 l~~l~~~lG~~Wk~lar~L-G~s~~eI~~ 32 (86)
T cd08777 5 LDLLRENLGKKWKRCARKL-GFTESEIEE 32 (86)
T ss_pred HHHHHHHHHHHHHHHHHHc-CCCHHHHHH
Confidence 4455677899999999999 566666544
No 147
>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=22.73 E-value=1.2e+02 Score=21.20 Aligned_cols=24 Identities=25% Similarity=0.462 Sum_probs=18.6
Q ss_pred HHHHHHHHHH-hCCCHHHHHhhCCC
Q 044161 69 EQIIIQLHKK-WGNKWSRIARNLPG 92 (229)
Q Consensus 69 d~~L~~~v~~-~G~~W~~Ia~~l~g 92 (229)
...|..++.. .|..|..+|+.|+-
T Consensus 5 ~~~~~~l~~~~~g~~W~~la~~Lg~ 29 (88)
T smart00005 5 REKLAKLLDHPLGLDWRELARKLGL 29 (88)
T ss_pred HHHHHHHHcCccchHHHHHHHHcCC
Confidence 4556666666 89999999999953
No 148
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=22.71 E-value=2.6e+02 Score=22.30 Aligned_cols=29 Identities=10% Similarity=0.140 Sum_probs=22.0
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 79 WGNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 79 ~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
.|....+||..| |-+...|+.+....+++
T Consensus 146 ~g~s~~eIA~~l-~is~~tV~~~l~ra~~~ 174 (184)
T PRK12512 146 EGASIKETAAKL-SMSEGAVRVALHRGLAA 174 (184)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 466688999988 68888888887765544
No 149
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=22.45 E-value=5.2e+02 Score=24.53 Aligned_cols=54 Identities=20% Similarity=0.214 Sum_probs=39.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC----------------CHHHHHhhC-----CCCCHHHHHHHHHHhhhHHHHH
Q 044161 59 IKHGYISTEEEQIIIQLHKKWGN----------------KWSRIARNL-----PGRTDNEIKNYWRTRIRKKIQA 112 (229)
Q Consensus 59 ~~~~~WT~eEd~~L~~~v~~~G~----------------~W~~Ia~~l-----~gRt~~qiknrw~~~l~~~~~~ 112 (229)
.-.|.|+++=|+...++...|.. +-..||+.+ ..||..||-.|-.-+.|++.+.
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~re 148 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLRE 148 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHH
Confidence 34578999999999999888732 256778775 2388889988877666665544
No 150
>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=21.97 E-value=2.2e+02 Score=22.18 Aligned_cols=27 Identities=26% Similarity=0.326 Sum_probs=19.9
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHhhh
Q 044161 80 GNKWSRIARNLPGRTDNEIKNYWRTRIR 107 (229)
Q Consensus 80 G~~W~~Ia~~l~gRt~~qiknrw~~~l~ 107 (229)
|-.-.+||+.| |-+...|+.+....++
T Consensus 138 g~s~~eIA~~l-~is~~tv~~~l~ra~~ 164 (170)
T TIGR02952 138 NLPIAEVARIL-GKTEGAVKILQFRAIK 164 (170)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 56678888888 6778888887765443
No 151
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=21.77 E-value=2.4e+02 Score=21.98 Aligned_cols=29 Identities=24% Similarity=0.276 Sum_probs=22.2
Q ss_pred HhCCCHHHHHhhCCCCCHHHHHHHHHHhhh
Q 044161 78 KWGNKWSRIARNLPGRTDNEIKNYWRTRIR 107 (229)
Q Consensus 78 ~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~ 107 (229)
..|-.-.+||..+ |-+...|+.|....++
T Consensus 127 ~~g~s~~EIA~~l-~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 127 VDGLGYGEIATEL-GISLATVKRYLNKAAM 155 (161)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3467789999998 6888888888766543
No 152
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=21.74 E-value=2.2e+02 Score=22.89 Aligned_cols=29 Identities=10% Similarity=0.116 Sum_probs=22.6
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 79 WGNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 79 ~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
.|-...+||..| |-|...|+++....+++
T Consensus 146 ~~~s~~eIA~~l-gis~~tV~~~l~Rar~~ 174 (189)
T PRK12515 146 HEKSVEEVGEIV-GIPESTVKTRMFYARKK 174 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 466789999999 67999999988765433
No 153
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=21.52 E-value=2.6e+02 Score=20.32 Aligned_cols=42 Identities=14% Similarity=0.181 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHhC-CCHHHHHhhCCCCCHHHHHHHHHHhhhHH
Q 044161 67 EEEQIIIQLHKKWG-NKWSRIARNLPGRTDNEIKNYWRTRIRKK 109 (229)
Q Consensus 67 eEd~~L~~~v~~~G-~~W~~Ia~~l~gRt~~qiknrw~~~l~~~ 109 (229)
+.|..|+.+..+.| ..+++||+.+ |-+...|..+...+....
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 45777887777766 4799999999 789999999998876654
No 154
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=21.50 E-value=92 Score=22.02 Aligned_cols=36 Identities=25% Similarity=0.252 Sum_probs=25.3
Q ss_pred hhHHHHhhCCCCCcccccccccccccCCCCCCCCCHHHHHHHHH
Q 044161 31 WDYIAKASGLKRSGKSCGLRWLNYLCPNIKHGYISTEEEQIIIQ 74 (229)
Q Consensus 31 W~~IA~~l~~~Rt~~qcr~Rw~~~L~p~~~~~~WT~eEd~~L~~ 74 (229)
-..||..+. |+|+.++|..+. + ....|+||+..|.+
T Consensus 36 ~~~iA~~i~-gks~eeir~~fg------i-~~d~t~eee~~i~~ 71 (78)
T PF01466_consen 36 CKYIANMIK-GKSPEEIRKYFG------I-ENDLTPEEEEEIRK 71 (78)
T ss_dssp HHHHHHHHT-TS-HHHHHHHHT----------TSSHHHHHHHHH
T ss_pred HHHHHHHhc-CCCHHHHHHHcC------C-CCCCCHHHHHHHHH
Confidence 578899997 999999998651 2 24689888877543
No 155
>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=21.49 E-value=1.9e+02 Score=17.15 Aligned_cols=39 Identities=21% Similarity=0.295 Sum_probs=24.7
Q ss_pred CCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHH
Q 044161 64 ISTEEEQIIIQLHKKWGNKWSRIARNLPGRTDNEIKNYWRT 104 (229)
Q Consensus 64 WT~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~qiknrw~~ 104 (229)
.+++ +..++.++...|-....||..+ |-+...|+.+...
T Consensus 11 l~~~-~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~ 49 (55)
T cd06171 11 LPER-EREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHR 49 (55)
T ss_pred CCHH-HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHH
Confidence 3343 4445555556778899999998 4666666555443
No 156
>PRK00118 putative DNA-binding protein; Validated
Probab=21.13 E-value=2.7e+02 Score=21.21 Aligned_cols=41 Identities=12% Similarity=0.123 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHhhh
Q 044161 66 TEEEQIIIQLHKKWGNKWSRIARNLPGRTDNEIKNYWRTRIR 107 (229)
Q Consensus 66 ~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~qiknrw~~~l~ 107 (229)
++.+..++.+....|-.-.+||..+ |-|...|+.+.....+
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~RArk 59 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKRTEK 59 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 4556667778788899999999999 7888888887765443
No 157
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=20.84 E-value=2.7e+02 Score=22.30 Aligned_cols=28 Identities=11% Similarity=0.012 Sum_probs=19.8
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHhhh
Q 044161 79 WGNKWSRIARNLPGRTDNEIKNYWRTRIR 107 (229)
Q Consensus 79 ~G~~W~~Ia~~l~gRt~~qiknrw~~~l~ 107 (229)
.|-.-.+||..+ |-+...|+.+....++
T Consensus 143 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~ 170 (186)
T PRK05602 143 QGLSNIEAAAVM-DISVDALESLLARGRR 170 (186)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHH
Confidence 456678888888 6777788887765443
No 158
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=20.77 E-value=2.6e+02 Score=22.48 Aligned_cols=28 Identities=11% Similarity=0.068 Sum_probs=20.8
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 80 GNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 80 G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
|-...+||..+ |-|...|+.+....+++
T Consensus 154 g~s~~eIA~~l-gis~~tv~~~l~Rar~~ 181 (193)
T PRK11923 154 GLSYEDIASVM-QCPVGTVRSRIFRAREA 181 (193)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 55678899988 67788888887765433
No 159
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=20.55 E-value=2.5e+02 Score=22.29 Aligned_cols=28 Identities=25% Similarity=0.290 Sum_probs=21.7
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHhhh
Q 044161 79 WGNKWSRIARNLPGRTDNEIKNYWRTRIR 107 (229)
Q Consensus 79 ~G~~W~~Ia~~l~gRt~~qiknrw~~~l~ 107 (229)
.|-...+||..+ |-+...|+.+....++
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~ 176 (183)
T TIGR02999 149 AGLTVEEIAELL-GVSVRTVERDWRFARA 176 (183)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 356689999999 6888899988876443
No 160
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=20.24 E-value=2.6e+02 Score=21.92 Aligned_cols=29 Identities=17% Similarity=0.079 Sum_probs=22.0
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHhhhH
Q 044161 79 WGNKWSRIARNLPGRTDNEIKNYWRTRIRK 108 (229)
Q Consensus 79 ~G~~W~~Ia~~l~gRt~~qiknrw~~~l~~ 108 (229)
.|-.-.+||..+ |-+...|+++....+++
T Consensus 127 ~g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 155 (164)
T PRK12547 127 SGFSYEDAAAIC-GCAVGTIKSRVSRARNR 155 (164)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 466689999999 68888888887765443
Done!