Query 025351
Match_columns 254
No_of_seqs 239 out of 1465
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 04:57:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025351.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025351hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0048 Transcription factor, 100.0 2.2E-34 4.8E-39 256.4 9.5 111 33-143 4-115 (238)
2 PLN03212 Transcription repress 100.0 3.5E-33 7.6E-38 246.6 9.0 113 31-143 18-131 (249)
3 PLN03091 hypothetical protein; 100.0 1.3E-31 2.8E-36 252.1 8.8 109 33-141 9-118 (459)
4 KOG0049 Transcription factor, 99.8 3.2E-20 6.9E-25 180.8 8.0 127 36-164 303-433 (939)
5 KOG0049 Transcription factor, 99.7 2E-18 4.3E-23 168.4 5.5 104 28-131 350-457 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.7 2.5E-17 5.4E-22 116.4 4.5 60 41-101 1-60 (60)
7 KOG0050 mRNA splicing protein 99.6 6.6E-17 1.4E-21 154.6 3.0 105 36-141 5-109 (617)
8 COG5147 REB1 Myb superfamily p 99.6 1.7E-16 3.6E-21 154.0 5.4 109 32-140 14-122 (512)
9 PF13921 Myb_DNA-bind_6: Myb-l 99.5 4.5E-14 9.7E-19 99.7 6.3 60 93-154 1-60 (60)
10 PLN03212 Transcription repress 99.5 4E-14 8.6E-19 125.8 7.4 86 68-162 10-97 (249)
11 PF00249 Myb_DNA-binding: Myb- 99.5 1.1E-14 2.3E-19 98.9 1.5 47 38-84 1-48 (48)
12 PF00249 Myb_DNA-binding: Myb- 99.4 1.2E-13 2.6E-18 93.8 4.8 46 90-135 1-48 (48)
13 PLN03091 hypothetical protein; 99.4 3.9E-13 8.4E-18 127.6 7.5 76 85-162 9-86 (459)
14 KOG0051 RNA polymerase I termi 99.4 7.6E-13 1.6E-17 130.0 8.3 104 37-142 383-514 (607)
15 KOG0051 RNA polymerase I termi 99.4 1.2E-12 2.7E-17 128.5 7.9 124 35-159 305-452 (607)
16 KOG0048 Transcription factor, 99.4 1.4E-12 3E-17 116.4 7.1 75 87-163 6-82 (238)
17 smart00717 SANT SANT SWI3, AD 99.3 7.9E-12 1.7E-16 82.7 5.4 47 90-136 1-48 (49)
18 smart00717 SANT SANT SWI3, AD 99.2 1.5E-11 3.3E-16 81.3 3.1 48 38-85 1-48 (49)
19 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 7.7E-11 1.7E-15 76.8 5.1 44 92-135 1-45 (45)
20 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 1E-10 2.2E-15 76.2 2.8 45 40-84 1-45 (45)
21 COG5147 REB1 Myb superfamily p 99.0 2.8E-10 6E-15 110.9 5.2 137 20-158 53-358 (512)
22 KOG0050 mRNA splicing protein 98.0 5.6E-06 1.2E-10 80.4 3.9 71 88-160 5-76 (617)
23 TIGR01557 myb_SHAQKYF myb-like 97.9 3.3E-05 7.3E-10 54.5 5.6 47 90-136 3-55 (57)
24 KOG0457 Histone acetyltransfer 97.9 1.4E-05 3E-10 76.3 4.5 58 27-84 58-118 (438)
25 KOG0457 Histone acetyltransfer 97.7 4.3E-05 9.4E-10 73.0 5.5 52 87-138 69-121 (438)
26 TIGR01557 myb_SHAQKYF myb-like 97.7 3E-05 6.4E-10 54.8 3.1 47 38-84 3-54 (57)
27 PF08914 Myb_DNA-bind_2: Rap1 97.5 0.0001 2.2E-09 53.4 3.9 51 90-140 2-62 (65)
28 TIGR02894 DNA_bind_RsfA transc 97.5 7.4E-05 1.6E-09 63.0 2.9 53 88-141 2-61 (161)
29 PF13325 MCRS_N: N-terminal re 97.3 0.00049 1.1E-08 60.2 6.3 96 40-137 1-128 (199)
30 COG5259 RSC8 RSC chromatin rem 97.3 0.00012 2.5E-09 70.7 2.3 46 37-83 278-323 (531)
31 KOG1279 Chromatin remodeling f 97.2 0.0002 4.2E-09 70.5 2.9 48 35-83 250-297 (506)
32 COG5259 RSC8 RSC chromatin rem 97.0 0.00051 1.1E-08 66.4 3.7 44 89-132 278-321 (531)
33 PF13837 Myb_DNA-bind_4: Myb/S 97.0 0.00035 7.5E-09 52.4 1.9 48 90-137 1-66 (90)
34 KOG1279 Chromatin remodeling f 97.0 0.00086 1.9E-08 66.1 4.8 44 89-132 252-295 (506)
35 PRK13923 putative spore coat p 96.7 0.0011 2.4E-08 56.6 2.4 52 88-140 3-61 (170)
36 PLN03142 Probable chromatin-re 96.5 0.0051 1.1E-07 65.5 6.7 102 39-140 825-989 (1033)
37 PF13837 Myb_DNA-bind_4: Myb/S 96.3 0.0017 3.8E-08 48.5 1.2 45 39-83 2-63 (90)
38 PF08914 Myb_DNA-bind_2: Rap1 96.2 0.0022 4.7E-08 46.5 1.5 51 38-88 2-61 (65)
39 TIGR02894 DNA_bind_RsfA transc 96.2 0.0018 4E-08 54.7 1.0 48 37-85 3-56 (161)
40 COG5114 Histone acetyltransfer 95.8 0.0082 1.8E-07 55.9 3.7 47 90-136 63-110 (432)
41 PF13873 Myb_DNA-bind_5: Myb/S 95.7 0.0074 1.6E-07 44.3 2.4 47 38-84 2-69 (78)
42 COG5114 Histone acetyltransfer 95.6 0.004 8.6E-08 57.9 0.6 47 39-85 64-110 (432)
43 PF13873 Myb_DNA-bind_5: Myb/S 95.5 0.018 3.9E-07 42.2 3.6 48 90-137 2-71 (78)
44 PRK13923 putative spore coat p 94.7 0.011 2.4E-07 50.5 0.7 48 37-85 4-57 (170)
45 PF09111 SLIDE: SLIDE; InterP 93.2 0.11 2.3E-06 42.0 3.7 52 87-138 46-113 (118)
46 KOG2656 DNA methyltransferase 92.9 0.12 2.5E-06 49.5 4.0 80 60-139 75-185 (445)
47 PF12776 Myb_DNA-bind_3: Myb/S 92.9 0.13 2.8E-06 38.7 3.6 47 92-139 1-65 (96)
48 COG5118 BDP1 Transcription ini 91.8 0.1 2.3E-06 49.7 2.2 43 39-82 366-408 (507)
49 KOG4282 Transcription factor G 91.3 0.24 5.2E-06 46.3 4.1 49 90-138 54-116 (345)
50 PF08281 Sigma70_r4_2: Sigma-7 90.6 0.48 1E-05 31.9 4.0 41 95-136 12-52 (54)
51 COG5118 BDP1 Transcription ini 90.3 0.38 8.2E-06 46.0 4.3 47 91-137 366-412 (507)
52 KOG1194 Predicted DNA-binding 89.9 0.45 9.8E-06 46.4 4.6 51 89-139 186-236 (534)
53 PF09111 SLIDE: SLIDE; InterP 88.0 0.27 5.9E-06 39.6 1.4 47 35-81 46-107 (118)
54 PF11626 Rap1_C: TRF2-interact 86.8 0.38 8.3E-06 36.4 1.6 30 34-66 43-80 (87)
55 KOG4167 Predicted DNA-binding 85.9 3.3 7.2E-05 42.8 8.0 44 91-134 620-663 (907)
56 KOG4167 Predicted DNA-binding 84.5 0.54 1.2E-05 48.3 1.8 44 38-82 619-662 (907)
57 KOG2656 DNA methyltransferase 84.2 1.9 4.1E-05 41.5 5.1 80 39-130 131-227 (445)
58 KOG4282 Transcription factor G 82.3 0.8 1.7E-05 42.8 1.9 47 38-84 54-113 (345)
59 PF12776 Myb_DNA-bind_3: Myb/S 79.8 1.4 2.9E-05 33.1 2.1 43 40-82 1-60 (96)
60 PF04504 DUF573: Protein of un 76.9 7 0.00015 30.3 5.4 43 90-132 4-59 (98)
61 PF04545 Sigma70_r4: Sigma-70, 76.7 4.7 0.0001 26.7 3.9 41 96-137 7-47 (50)
62 smart00595 MADF subfamily of S 76.6 2.8 6.1E-05 31.0 3.0 24 111-135 29-52 (89)
63 KOG4468 Polycomb-group transcr 74.0 3.5 7.6E-05 41.8 3.6 51 90-140 88-148 (782)
64 PF13404 HTH_AsnC-type: AsnC-t 72.8 7.1 0.00015 25.5 3.8 38 96-134 3-41 (42)
65 PF13325 MCRS_N: N-terminal re 71.1 7.2 0.00016 34.3 4.6 44 92-136 1-47 (199)
66 PRK11179 DNA-binding transcrip 69.6 7.3 0.00016 32.1 4.2 46 95-141 8-54 (153)
67 KOG3841 TEF-1 and related tran 65.3 26 0.00056 33.9 7.2 54 88-141 74-148 (455)
68 PF07750 GcrA: GcrA cell cycle 65.0 6.6 0.00014 33.3 3.0 41 92-133 2-42 (162)
69 TIGR02985 Sig70_bacteroi1 RNA 64.8 11 0.00024 29.9 4.2 37 100-137 120-156 (161)
70 KOG2009 Transcription initiati 63.6 9.6 0.00021 38.6 4.3 52 87-138 406-457 (584)
71 PF01388 ARID: ARID/BRIGHT DNA 62.7 13 0.00029 27.6 4.1 38 99-136 39-89 (92)
72 PRK11169 leucine-responsive tr 62.2 11 0.00024 31.4 3.9 46 95-141 13-59 (164)
73 KOG1194 Predicted DNA-binding 61.4 6.1 0.00013 38.8 2.4 48 34-82 183-230 (534)
74 PF11035 SnAPC_2_like: Small n 60.2 19 0.00042 33.8 5.3 47 90-137 21-71 (344)
75 KOG2009 Transcription initiati 57.7 12 0.00027 37.8 3.9 49 33-82 404-452 (584)
76 PF11626 Rap1_C: TRF2-interact 57.3 4.3 9.3E-05 30.6 0.5 19 86-104 43-61 (87)
77 smart00501 BRIGHT BRIGHT, ARID 56.5 19 0.0004 27.1 3.9 39 99-137 35-86 (93)
78 KOG4468 Polycomb-group transcr 56.4 9.1 0.0002 38.9 2.7 46 38-84 88-143 (782)
79 PF13404 HTH_AsnC-type: AsnC-t 53.1 8 0.00017 25.3 1.2 38 44-82 3-40 (42)
80 smart00344 HTH_ASNC helix_turn 52.0 27 0.00059 26.5 4.3 45 96-141 3-48 (108)
81 cd08319 Death_RAIDD Death doma 51.9 16 0.00035 27.5 2.9 29 98-127 2-30 (83)
82 TIGR02937 sigma70-ECF RNA poly 51.8 22 0.00048 27.3 3.8 34 103-137 120-153 (158)
83 PLN03142 Probable chromatin-re 50.1 9.6 0.00021 41.3 1.9 34 35-68 923-956 (1033)
84 cd06171 Sigma70_r4 Sigma70, re 49.3 36 0.00077 21.3 4.0 37 97-134 14-50 (55)
85 KOG0384 Chromodomain-helicase 49.0 15 0.00032 40.4 3.0 73 39-117 1134-1207(1373)
86 PF11035 SnAPC_2_like: Small n 48.7 85 0.0018 29.7 7.6 85 39-136 22-127 (344)
87 cd08803 Death_ank3 Death domai 48.5 24 0.00051 26.6 3.3 30 98-128 4-33 (84)
88 PRK09652 RNA polymerase sigma 46.7 30 0.00065 28.0 4.0 30 107-137 142-171 (182)
89 cd08311 Death_p75NR Death doma 46.4 20 0.00042 26.6 2.5 33 95-129 2-34 (77)
90 KOG4329 DNA-binding protein [G 45.7 16 0.00034 35.2 2.4 42 39-81 278-320 (445)
91 PRK11924 RNA polymerase sigma 45.4 31 0.00067 27.9 3.9 30 107-137 139-168 (179)
92 PF10545 MADF_DNA_bdg: Alcohol 44.1 17 0.00036 26.0 1.9 26 111-136 28-54 (85)
93 TIGR02957 SigX4 RNA polymerase 43.9 65 0.0014 29.1 6.1 52 107-159 122-174 (281)
94 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 43.7 33 0.00072 23.5 3.1 35 96-131 7-41 (50)
95 COG2963 Transposase and inacti 43.0 1.3E+02 0.0028 23.2 6.9 48 90-138 5-53 (116)
96 KOG4329 DNA-binding protein [G 42.8 41 0.00088 32.5 4.6 44 91-134 278-322 (445)
97 PRK09643 RNA polymerase sigma 42.4 38 0.00082 28.5 4.1 30 107-137 148-177 (192)
98 KOG1878 Nuclear receptor coreg 42.0 11 0.00023 42.0 0.7 44 37-81 224-267 (1672)
99 cd08317 Death_ank Death domain 41.7 24 0.00053 26.1 2.5 29 98-127 4-32 (84)
100 PRK09641 RNA polymerase sigma 41.6 37 0.00081 27.9 3.9 29 108-137 151-179 (187)
101 PRK04217 hypothetical protein; 41.2 46 0.00099 26.5 4.1 43 92-136 42-84 (110)
102 PRK09047 RNA polymerase factor 39.9 47 0.001 26.6 4.1 30 107-137 120-149 (161)
103 PRK12523 RNA polymerase sigma 39.9 47 0.001 27.2 4.2 32 106-138 132-163 (172)
104 PF02954 HTH_8: Bacterial regu 39.5 53 0.0011 21.0 3.5 34 97-131 6-39 (42)
105 PRK11179 DNA-binding transcrip 39.0 17 0.00036 29.9 1.3 43 44-87 9-51 (153)
106 TIGR02954 Sig70_famx3 RNA poly 38.4 46 0.001 27.1 3.9 29 108-137 134-162 (169)
107 PF09420 Nop16: Ribosome bioge 38.4 27 0.00059 29.3 2.5 45 36-81 112-160 (164)
108 PF09420 Nop16: Ribosome bioge 38.1 65 0.0014 27.0 4.8 47 89-135 113-163 (164)
109 PRK09637 RNA polymerase sigma 37.6 49 0.0011 27.6 4.0 30 107-137 120-149 (181)
110 PRK09645 RNA polymerase sigma 37.6 52 0.0011 26.8 4.1 29 108-137 133-161 (173)
111 PRK09648 RNA polymerase sigma 37.6 52 0.0011 27.3 4.2 30 107-137 153-182 (189)
112 PF09905 DUF2132: Uncharacteri 37.2 19 0.00041 26.0 1.2 23 46-71 12-34 (64)
113 TIGR02943 Sig70_famx1 RNA poly 37.1 53 0.0011 27.6 4.2 32 105-137 143-174 (188)
114 TIGR02939 RpoE_Sigma70 RNA pol 37.0 40 0.00087 27.8 3.4 29 108-137 153-181 (190)
115 PRK13858 type IV secretion sys 36.9 67 0.0014 27.0 4.5 82 25-119 15-96 (147)
116 PRK12512 RNA polymerase sigma 36.8 54 0.0012 27.1 4.1 29 108-137 146-174 (184)
117 PRK09642 RNA polymerase sigma 36.4 57 0.0012 26.2 4.1 30 107-137 120-149 (160)
118 TIGR02960 SigX5 RNA polymerase 35.9 79 0.0017 28.7 5.4 29 108-137 157-185 (324)
119 PF07638 Sigma70_ECF: ECF sigm 35.8 60 0.0013 27.4 4.3 34 101-135 143-176 (185)
120 cd08804 Death_ank2 Death domai 35.5 39 0.00085 25.3 2.7 31 98-129 4-34 (84)
121 TIGR02948 SigW_bacill RNA poly 35.2 50 0.0011 27.1 3.7 29 108-137 151-179 (187)
122 PRK12515 RNA polymerase sigma 35.0 61 0.0013 27.0 4.2 30 107-137 145-174 (189)
123 PRK12530 RNA polymerase sigma 34.9 59 0.0013 27.3 4.1 29 108-137 149-177 (189)
124 PRK11923 algU RNA polymerase s 34.8 54 0.0012 27.3 3.8 28 109-137 154-181 (193)
125 PRK12529 RNA polymerase sigma 34.3 65 0.0014 26.7 4.2 32 107-139 141-172 (178)
126 PRK12527 RNA polymerase sigma 33.7 70 0.0015 25.7 4.2 29 108-137 120-148 (159)
127 PRK12531 RNA polymerase sigma 33.6 66 0.0014 27.0 4.2 29 108-137 156-184 (194)
128 PRK09636 RNA polymerase sigma 33.5 1.1E+02 0.0025 27.5 6.0 31 108-139 130-160 (293)
129 smart00005 DEATH DEATH domain, 33.4 46 0.001 24.2 2.9 29 98-127 5-34 (88)
130 PF04844 Ovate: Transcriptiona 32.7 38 0.00082 24.0 2.1 15 223-237 4-18 (59)
131 TIGR02999 Sig-70_X6 RNA polyme 32.4 73 0.0016 26.1 4.2 29 108-137 149-177 (183)
132 PF13936 HTH_38: Helix-turn-he 31.7 49 0.0011 21.5 2.4 36 92-129 4-39 (44)
133 PRK12524 RNA polymerase sigma 31.7 71 0.0015 26.8 4.1 29 108-137 151-179 (196)
134 cd08805 Death_ank1 Death domai 31.1 51 0.0011 24.8 2.8 28 98-126 4-31 (84)
135 PF07750 GcrA: GcrA cell cycle 31.0 31 0.00066 29.2 1.7 40 40-81 2-41 (162)
136 cd08318 Death_NMPP84 Death dom 31.0 52 0.0011 24.6 2.8 23 104-127 13-35 (86)
137 PRK11169 leucine-responsive tr 30.8 20 0.00044 29.8 0.6 45 43-88 13-57 (164)
138 PRK08241 RNA polymerase factor 30.7 1.1E+02 0.0025 27.9 5.6 32 108-140 168-199 (339)
139 PRK12536 RNA polymerase sigma 30.5 79 0.0017 26.1 4.1 30 107-137 143-172 (181)
140 PRK06759 RNA polymerase factor 30.4 84 0.0018 24.9 4.2 29 108-137 121-149 (154)
141 TIGR02952 Sig70_famx2 RNA poly 30.1 82 0.0018 25.3 4.1 29 108-137 137-165 (170)
142 COG1522 Lrp Transcriptional re 29.9 79 0.0017 25.3 3.9 47 95-142 7-54 (154)
143 PF09197 Rap1-DNA-bind: Rap1, 29.6 94 0.002 24.6 4.1 47 92-138 1-78 (105)
144 PRK09651 RNA polymerase sigma 29.5 70 0.0015 26.3 3.6 29 108-137 134-162 (172)
145 PRK09649 RNA polymerase sigma 29.5 78 0.0017 26.4 3.9 30 108-138 145-174 (185)
146 PRK00118 putative DNA-binding 29.4 94 0.002 24.4 4.1 41 95-136 19-59 (104)
147 PRK12514 RNA polymerase sigma 29.1 84 0.0018 25.7 4.1 28 109-137 145-172 (179)
148 cd08777 Death_RIP1 Death Domai 29.1 51 0.0011 24.8 2.4 28 101-129 5-32 (86)
149 PRK12516 RNA polymerase sigma 29.0 85 0.0018 26.4 4.1 31 106-137 129-159 (187)
150 PRK12547 RNA polymerase sigma 28.8 93 0.002 25.2 4.2 30 107-137 126-155 (164)
151 PRK12528 RNA polymerase sigma 28.8 94 0.002 25.0 4.2 29 107-136 127-155 (161)
152 PRK12532 RNA polymerase sigma 28.7 80 0.0017 26.4 3.9 30 107-137 150-179 (195)
153 PRK12542 RNA polymerase sigma 28.5 88 0.0019 25.9 4.1 30 107-137 136-165 (185)
154 cd08312 Death_MyD88 Death doma 27.7 36 0.00078 25.1 1.4 22 106-128 13-34 (79)
155 PRK13919 putative RNA polymera 27.7 95 0.0021 25.6 4.1 29 108-137 150-178 (186)
156 PRK12545 RNA polymerase sigma 27.5 92 0.002 26.4 4.1 28 108-136 154-181 (201)
157 TIGR02950 SigM_subfam RNA poly 27.4 34 0.00074 27.2 1.3 28 109-137 121-148 (154)
158 TIGR02983 SigE-fam_strep RNA p 27.1 91 0.002 25.0 3.9 38 99-137 116-153 (162)
159 PF09650 PHA_gran_rgn: Putativ 26.8 75 0.0016 24.0 3.0 22 225-246 65-86 (87)
160 PF01527 HTH_Tnp_1: Transposas 26.4 1E+02 0.0022 21.5 3.6 46 89-136 3-48 (76)
161 PRK09635 sigI RNA polymerase s 26.3 1.7E+02 0.0036 26.8 5.8 50 108-158 133-183 (290)
162 PRK13987 cell division topolog 26.3 74 0.0016 24.5 2.9 23 222-244 31-53 (91)
163 cd08779 Death_PIDD Death Domai 25.3 68 0.0015 24.0 2.5 26 99-125 3-28 (86)
164 PRK06811 RNA polymerase factor 25.1 1E+02 0.0023 25.6 4.0 30 108-138 146-175 (189)
165 TIGR02984 Sig-70_plancto1 RNA 25.0 1.1E+02 0.0024 25.0 4.1 30 107-137 154-183 (189)
166 PF05678 VQ: VQ motif; InterP 25.0 50 0.0011 20.4 1.4 12 223-234 11-22 (31)
167 PRK12520 RNA polymerase sigma 24.8 1.1E+02 0.0025 25.4 4.1 29 108-137 146-174 (191)
168 PRK12537 RNA polymerase sigma 24.7 1.1E+02 0.0024 25.2 4.0 29 108-137 148-176 (182)
169 PF10440 WIYLD: Ubiquitin-bind 24.6 47 0.001 24.1 1.4 19 47-66 30-48 (65)
170 TIGR01568 A_thal_3678 uncharac 24.4 62 0.0013 23.5 2.0 15 223-237 10-24 (66)
171 PRK05602 RNA polymerase sigma 24.2 1.1E+02 0.0024 25.3 3.9 28 108-136 143-170 (186)
172 PRK12546 RNA polymerase sigma 24.2 1.1E+02 0.0023 25.9 3.8 31 106-137 126-156 (188)
173 PF09862 DUF2089: Protein of u 24.1 3.1E+02 0.0068 21.9 6.2 65 95-160 35-100 (113)
174 PRK11922 RNA polymerase sigma 24.0 62 0.0013 28.2 2.4 28 109-137 165-192 (231)
175 PF00046 Homeobox: Homeobox do 23.2 2E+02 0.0043 18.9 4.4 44 90-134 4-51 (57)
176 KOG3554 Histone deacetylase co 23.1 47 0.001 33.0 1.6 40 40-80 287-327 (693)
177 PRK09639 RNA polymerase sigma 23.0 1.3E+02 0.0028 24.1 4.0 29 108-137 126-154 (166)
178 PRK12519 RNA polymerase sigma 23.0 1E+02 0.0022 25.6 3.5 29 108-137 156-184 (194)
179 PRK01905 DNA-binding protein F 23.0 1.7E+02 0.0037 21.3 4.2 36 95-131 36-71 (77)
180 COG4628 Uncharacterized conser 22.4 71 0.0015 25.9 2.2 44 46-101 21-71 (136)
181 PRK09415 RNA polymerase factor 21.9 1.2E+02 0.0027 24.9 3.8 28 109-137 143-170 (179)
182 KOG0385 Chromatin remodeling c 21.7 1E+02 0.0023 32.7 3.8 98 40-138 797-959 (971)
183 PRK06986 fliA flagellar biosyn 21.5 1.3E+02 0.0028 26.2 3.9 36 101-137 192-227 (236)
184 cd00569 HTH_Hin_like Helix-tur 21.4 1.5E+02 0.0033 16.0 3.6 35 93-129 6-40 (42)
185 PRK09646 RNA polymerase sigma 21.2 1.5E+02 0.0032 24.8 4.1 28 109-137 158-185 (194)
186 PRK09647 RNA polymerase sigma 20.8 1.5E+02 0.0033 25.3 4.2 29 108-137 153-181 (203)
187 PRK00430 fis global DNA-bindin 20.5 2E+02 0.0043 22.0 4.4 35 96-131 55-89 (95)
188 TIGR00673 cynS cyanate hydrata 20.4 1E+02 0.0023 25.9 2.9 30 99-129 11-40 (150)
189 PF11198 DUF2857: Protein of u 20.3 3.7E+02 0.0081 22.9 6.4 63 95-159 73-136 (180)
190 PF05263 DUF722: Protein of un 20.3 1.1E+02 0.0023 25.1 2.9 33 96-129 84-118 (130)
191 TIGR02980 SigBFG RNA polymeras 20.2 1.5E+02 0.0033 25.4 4.1 33 104-137 189-221 (227)
No 1
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=2.2e-34 Score=256.40 Aligned_cols=111 Identities=47% Similarity=0.854 Sum_probs=106.1
Q ss_pred CCCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccc-cCChhhhhhhccccCCCCCCCCCCChHHHHHHHHHHHhcCCC
Q 025351 33 KPERIKGPWSAEEDRILTRLVERYGPRNWSLISRYIK-GRSGKSCRLRWCNQLSPSVAHRPFSPAEDDTILAAHARFGNR 111 (254)
Q Consensus 33 ~p~~~kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~-~Rs~~qcr~Rw~~~L~p~~~~~~WT~EED~~Ll~~v~~~G~~ 111 (254)
++.+.||+||+|||++|+++|++||.++|..|++.++ +|++++||.||.|||+|.++++.||+|||.+|+++|+.|||+
T Consensus 4 k~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNr 83 (238)
T KOG0048|consen 4 NPELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNR 83 (238)
T ss_pred CccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcH
Confidence 3445689999999999999999999999999999998 999999999999999999999999999999999999999999
Q ss_pred hhhhhhcCCCCCHHHHHHHHHHhhcccccCCC
Q 025351 112 WATIARLLPGRTDNAVKNHWNSTLKRRTREHP 143 (254)
Q Consensus 112 W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~~~~ 143 (254)
|+.||++|||||++.|||+|+..+|+++....
T Consensus 84 Ws~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 84 WSLIAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred HHHHHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 99999999999999999999999999987764
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=3.5e-33 Score=246.64 Aligned_cols=113 Identities=42% Similarity=0.781 Sum_probs=107.1
Q ss_pred cCCCCCCcCCCCHHHHHHHHHHHHHhCCCCcccccccc-ccCChhhhhhhccccCCCCCCCCCCChHHHHHHHHHHHhcC
Q 025351 31 THKPERIKGPWSAEEDRILTRLVERYGPRNWSLISRYI-KGRSGKSCRLRWCNQLSPSVAHRPFSPAEDDTILAAHARFG 109 (254)
Q Consensus 31 ~~~p~~~kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l-~~Rs~~qcr~Rw~~~L~p~~~~~~WT~EED~~Ll~~v~~~G 109 (254)
-.++.+++++||+|||++|+++|++||..+|..||+.+ ++|+++|||+||.++|+|.+++++||+|||++|++++..||
T Consensus 18 c~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~~G 97 (249)
T PLN03212 18 CTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLG 97 (249)
T ss_pred cccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHhcc
Confidence 34678889999999999999999999998999999998 69999999999999999999999999999999999999999
Q ss_pred CChhhhhhcCCCCCHHHHHHHHHHhhcccccCCC
Q 025351 110 NRWATIARLLPGRTDNAVKNHWNSTLKRRTREHP 143 (254)
Q Consensus 110 ~~W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~~~~ 143 (254)
++|+.||+.|+|||+++|||||+.+++++..+..
T Consensus 98 nKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~ 131 (249)
T PLN03212 98 NRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQG 131 (249)
T ss_pred ccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcC
Confidence 9999999999999999999999999998876554
No 3
>PLN03091 hypothetical protein; Provisional
Probab=99.97 E-value=1.3e-31 Score=252.13 Aligned_cols=109 Identities=49% Similarity=0.870 Sum_probs=103.8
Q ss_pred CCCCCcCCCCHHHHHHHHHHHHHhCCCCcccccccc-ccCChhhhhhhccccCCCCCCCCCCChHHHHHHHHHHHhcCCC
Q 025351 33 KPERIKGPWSAEEDRILTRLVERYGPRNWSLISRYI-KGRSGKSCRLRWCNQLSPSVAHRPFSPAEDDTILAAHARFGNR 111 (254)
Q Consensus 33 ~p~~~kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l-~~Rs~~qcr~Rw~~~L~p~~~~~~WT~EED~~Ll~~v~~~G~~ 111 (254)
+..++||+||+|||++|+++|.+||..+|..||+.+ ++|+++|||+||.++|+|.+++++||+|||++|++++++||++
T Consensus 9 KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k~~GnK 88 (459)
T PLN03091 9 KQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHAVLGNR 88 (459)
T ss_pred CCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHHHhCcc
Confidence 457889999999999999999999999999999988 5999999999999999999999999999999999999999999
Q ss_pred hhhhhhcCCCCCHHHHHHHHHHhhcccccC
Q 025351 112 WATIARLLPGRTDNAVKNHWNSTLKRRTRE 141 (254)
Q Consensus 112 W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~~ 141 (254)
|++||+.|+|||+++||+||+.+++++.+.
T Consensus 89 WskIAk~LPGRTDnqIKNRWnslLKKklr~ 118 (459)
T PLN03091 89 WSQIAAQLPGRTDNEIKNLWNSCLKKKLRQ 118 (459)
T ss_pred hHHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999987553
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.81 E-value=3.2e-20 Score=180.76 Aligned_cols=127 Identities=27% Similarity=0.505 Sum_probs=114.6
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCC---CCccccccccccCChhhhhhhccccCCCCCCCCCCChHHHHHHHHHHHhcCC-C
Q 025351 36 RIKGPWSAEEDRILTRLVERYGP---RNWSLISRYIKGRSGKSCRLRWCNQLSPSVAHRPFSPAEDDTILAAHARFGN-R 111 (254)
Q Consensus 36 ~~kg~WT~eED~~L~~lV~~~g~---~nW~~Ia~~l~~Rs~~qcr~Rw~~~L~p~~~~~~WT~EED~~Ll~~v~~~G~-~ 111 (254)
.....||+|||.+|+.||..... .+|.+|-.+||||+..|...||...|+|.+++++||++||.+|+.+|.+||. .
T Consensus 303 L~ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kd 382 (939)
T KOG0049|consen 303 LSEKEWSEEEDTKLIALVKITSINSHIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKD 382 (939)
T ss_pred HHhhhcchhhhHHHHHHHHHhhccCccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccc
Confidence 34577999999999999998754 4699999999999999999999999999999999999999999999999996 5
Q ss_pred hhhhhhcCCCCCHHHHHHHHHHhhcccccCCCCCCChhHHHHHHHHhhcCCCC
Q 025351 112 WATIARLLPGRTDNAVKNHWNSTLKRRTREHPVQMQPHQQQQLMDSVDNGGDN 164 (254)
Q Consensus 112 W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~~~~~~~~~~e~~~L~~~~~~~~~~ 164 (254)
|.+|-..||||++.|||.||.+.|.+..+...| .-.++.+|+.+|..+|..
T Consensus 383 w~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~rW--~l~edeqL~~~V~~YG~g 433 (939)
T KOG0049|consen 383 WAKVRQAVPNRSDSQCRERYTNVLNRSAKVERW--TLVEDEQLLYAVKVYGKG 433 (939)
T ss_pred hhhHHHhcCCccHHHHHHHHHHHHHHhhccCce--eecchHHHHHHHHHHccc
Confidence 999999999999999999999999999888774 445667888888887753
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.73 E-value=2e-18 Score=168.36 Aligned_cols=104 Identities=31% Similarity=0.570 Sum_probs=97.1
Q ss_pred ccccCCCCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhccccCCCCCCCCCCChHHHHHHHHHHHh
Q 025351 28 RRATHKPERIKGPWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCNQLSPSVAHRPFSPAEDDTILAAHAR 107 (254)
Q Consensus 28 r~~~~~p~~~kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~~L~p~~~~~~WT~EED~~Ll~~v~~ 107 (254)
....++|.+++|+||++||.+|+.+|.+||.++|-+|-..+|+|+..|||+||.|.|+...+.+.||-.||+.|+.+|..
T Consensus 350 ~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~~V~~ 429 (939)
T KOG0049|consen 350 FSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLYAVKV 429 (939)
T ss_pred heeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHHhhccCceeecchHHHHHHHHH
Confidence 35678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cC-CChhhhhhcCCCCCHHH---HHHHH
Q 025351 108 FG-NRWATIARLLPGRTDNA---VKNHW 131 (254)
Q Consensus 108 ~G-~~W~~IA~~l~gRT~~q---~k~Rw 131 (254)
|| .+|.+||..||.||..| ||.|+
T Consensus 430 YG~g~WakcA~~Lp~~t~~q~~rrR~R~ 457 (939)
T KOG0049|consen 430 YGKGNWAKCAMLLPKKTSRQLRRRRLRL 457 (939)
T ss_pred HccchHHHHHHHccccchhHHHHHHHHH
Confidence 99 58999999999999954 44444
No 6
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.68 E-value=2.5e-17 Score=116.43 Aligned_cols=60 Identities=38% Similarity=0.896 Sum_probs=55.0
Q ss_pred CCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhccccCCCCCCCCCCChHHHHHH
Q 025351 41 WSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCNQLSPSVAHRPFSPAEDDTI 101 (254)
Q Consensus 41 WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~~L~p~~~~~~WT~EED~~L 101 (254)
||+|||++|+.+|.+|| .+|..||+.|+.|++.+|+.||.+.|.|.+.+++||++||++|
T Consensus 1 WT~eEd~~L~~~~~~~g-~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYG-NDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHT-S-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC-cCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 99999999999999999 5799999999779999999999999999999999999999987
No 7
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.64 E-value=6.6e-17 Score=154.57 Aligned_cols=105 Identities=28% Similarity=0.569 Sum_probs=99.4
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhccccCCCCCCCCCCChHHHHHHHHHHHhcCCChhhh
Q 025351 36 RIKGPWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCNQLSPSVAHRPFSPAEDDTILAAHARFGNRWATI 115 (254)
Q Consensus 36 ~~kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~~L~p~~~~~~WT~EED~~Ll~~v~~~G~~W~~I 115 (254)
++.|.|+.-||+.|...|.+||...|.+|++.++-.+++||+.||..+|+|.+++..|+.|||+.||.+...+..+|..|
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrtI 84 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRTI 84 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccchH
Confidence 45689999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCCCCCHHHHHHHHHHhhcccccC
Q 025351 116 ARLLPGRTDNAVKNHWNSTLKRRTRE 141 (254)
Q Consensus 116 A~~l~gRT~~q~k~Rw~~~lk~~~~~ 141 (254)
+..| ||+.+||..||++++-.....
T Consensus 85 a~i~-gr~~~qc~eRy~~ll~~~~s~ 109 (617)
T KOG0050|consen 85 ADIM-GRTSQQCLERYNNLLDVYVSY 109 (617)
T ss_pred HHHh-hhhHHHHHHHHHHHHHHHHhh
Confidence 9999 999999999999988765443
No 8
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.63 E-value=1.7e-16 Score=153.96 Aligned_cols=109 Identities=29% Similarity=0.599 Sum_probs=104.6
Q ss_pred CCCCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhccccCCCCCCCCCCChHHHHHHHHHHHhcCCC
Q 025351 32 HKPERIKGPWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCNQLSPSVAHRPFSPAEDDTILAAHARFGNR 111 (254)
Q Consensus 32 ~~p~~~kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~~L~p~~~~~~WT~EED~~Ll~~v~~~G~~ 111 (254)
+.-+++.|.|+..||+.|..+|+.||++||..||..+.-++++||+.||.++++|.+++..|+.|||..|+.+..++|.+
T Consensus 14 ~~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~ 93 (512)
T COG5147 14 MQTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQ 93 (512)
T ss_pred ccceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCch
Confidence 55677889999999999999999999999999999998899999999999999999999999999999999999999999
Q ss_pred hhhhhhcCCCCCHHHHHHHHHHhhccccc
Q 025351 112 WATIARLLPGRTDNAVKNHWNSTLKRRTR 140 (254)
Q Consensus 112 W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~ 140 (254)
|+.||..++|||..+|.+||..++.....
T Consensus 94 wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 94 WSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 99999999999999999999999888766
No 9
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.50 E-value=4.5e-14 Score=99.70 Aligned_cols=60 Identities=28% Similarity=0.612 Sum_probs=50.4
Q ss_pred CChHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHHHHhhcccccCCCCCCChhHHHHH
Q 025351 93 FSPAEDDTILAAHARFGNRWATIARLLPGRTDNAVKNHWNSTLKRRTREHPVQMQPHQQQQL 154 (254)
Q Consensus 93 WT~EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~~~~~~~~~~e~~~L 154 (254)
||+|||++|++++..||++|..||..|+.||+.+|++||+..|++...+.+ |+.++++.|
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~--wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGP--WTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSS--SSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCC--cCHHHHhcC
Confidence 999999999999999999999999999559999999999998888776665 777776665
No 10
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.50 E-value=4e-14 Score=125.82 Aligned_cols=86 Identities=13% Similarity=0.341 Sum_probs=73.5
Q ss_pred cccCChhhhhhhccccCCCCCCCCCCChHHHHHHHHHHHhcC-CChhhhhhcC-CCCCHHHHHHHHHHhhcccccCCCCC
Q 025351 68 IKGRSGKSCRLRWCNQLSPSVAHRPFSPAEDDTILAAHARFG-NRWATIARLL-PGRTDNAVKNHWNSTLKRRTREHPVQ 145 (254)
Q Consensus 68 l~~Rs~~qcr~Rw~~~L~p~~~~~~WT~EED~~Ll~~v~~~G-~~W~~IA~~l-~gRT~~q~k~Rw~~~lk~~~~~~~~~ 145 (254)
+++|+..-|. ++.+++++||+|||++|+++|++|| ++|..||+.+ ++||+.||+.||.++|++.+++.+
T Consensus 10 ~~~~~~pcc~-------K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgp-- 80 (249)
T PLN03212 10 VSKKTTPCCT-------KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGG-- 80 (249)
T ss_pred CCCCCCCCcc-------cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCC--
Confidence 4566665443 2578899999999999999999999 5799999988 599999999999999999998876
Q ss_pred CChhHHHHHHHHhhcCC
Q 025351 146 MQPHQQQQLMDSVDNGG 162 (254)
Q Consensus 146 ~~~~e~~~L~~~~~~~~ 162 (254)
|+.+|+..|+..+...|
T Consensus 81 WT~EED~lLlel~~~~G 97 (249)
T PLN03212 81 ITSDEEDLILRLHRLLG 97 (249)
T ss_pred CChHHHHHHHHHHHhcc
Confidence 77778888888887765
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=99.47 E-value=1.1e-14 Score=98.91 Aligned_cols=47 Identities=45% Similarity=0.941 Sum_probs=42.7
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccccccc-cCChhhhhhhccccC
Q 025351 38 KGPWSAEEDRILTRLVERYGPRNWSLISRYIK-GRSGKSCRLRWCNQL 84 (254)
Q Consensus 38 kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~-~Rs~~qcr~Rw~~~L 84 (254)
|++||+|||++|+++|.+||..+|..||..|+ +||..||+.||.++|
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 68999999999999999999878999999999 999999999998865
No 12
>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=99.44 E-value=1.2e-13 Score=93.76 Aligned_cols=46 Identities=30% Similarity=0.743 Sum_probs=41.8
Q ss_pred CCCCChHHHHHHHHHHHhcCCC-hhhhhhcCC-CCCHHHHHHHHHHhh
Q 025351 90 HRPFSPAEDDTILAAHARFGNR-WATIARLLP-GRTDNAVKNHWNSTL 135 (254)
Q Consensus 90 ~~~WT~EED~~Ll~~v~~~G~~-W~~IA~~l~-gRT~~q~k~Rw~~~l 135 (254)
+++||+|||++|++++.+||.+ |..||..|+ |||..||++||++++
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 5799999999999999999988 999999999 999999999998764
No 13
>PLN03091 hypothetical protein; Provisional
Probab=99.41 E-value=3.9e-13 Score=127.61 Aligned_cols=76 Identities=14% Similarity=0.394 Sum_probs=68.5
Q ss_pred CCCCCCCCCChHHHHHHHHHHHhcCC-ChhhhhhcCC-CCCHHHHHHHHHHhhcccccCCCCCCChhHHHHHHHHhhcCC
Q 025351 85 SPSVAHRPFSPAEDDTILAAHARFGN-RWATIARLLP-GRTDNAVKNHWNSTLKRRTREHPVQMQPHQQQQLMDSVDNGG 162 (254)
Q Consensus 85 ~p~~~~~~WT~EED~~Ll~~v~~~G~-~W~~IA~~l~-gRT~~q~k~Rw~~~lk~~~~~~~~~~~~~e~~~L~~~~~~~~ 162 (254)
++.+++++||+|||++|+++|++||. +|..||+.+. ||++.|||.||.++|++.+++.+ |+.+|++.|++.+...|
T Consensus 9 KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgp--WT~EED~lLLeL~k~~G 86 (459)
T PLN03091 9 KQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGT--FSQQEENLIIELHAVLG 86 (459)
T ss_pred CCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCC--CCHHHHHHHHHHHHHhC
Confidence 46789999999999999999999995 7999999884 89999999999999999998875 88889999998887665
No 14
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.39 E-value=7.6e-13 Score=130.00 Aligned_cols=104 Identities=22% Similarity=0.480 Sum_probs=92.9
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhccccCCCCC--CCCCCChHHHHHHHHHHH-------h
Q 025351 37 IKGPWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCNQLSPSV--AHRPFSPAEDDTILAAHA-------R 107 (254)
Q Consensus 37 ~kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~~L~p~~--~~~~WT~EED~~Ll~~v~-------~ 107 (254)
.+|.||+||++.|..+|.++| .+|..|++.| +|.+..|++||.++..+.- +++.||.||.++|+++|. +
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g-~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~q 460 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHG-NDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREALQ 460 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhc-ccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhhc
Confidence 899999999999999999999 5799999999 6999999999999998874 889999999999999995 3
Q ss_pred cC-------------------CChhhhhhcCCCCCHHHHHHHHHHhhcccccCC
Q 025351 108 FG-------------------NRWATIARLLPGRTDNAVKNHWNSTLKRRTREH 142 (254)
Q Consensus 108 ~G-------------------~~W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~~~ 142 (254)
+. =+|..|+..+..|+..||+.+|+.++.+.....
T Consensus 461 ~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n~ 514 (607)
T KOG0051|consen 461 PQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFNK 514 (607)
T ss_pred ccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhhc
Confidence 31 159999998888999999999999988765444
No 15
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.36 E-value=1.2e-12 Score=128.53 Aligned_cols=124 Identities=20% Similarity=0.354 Sum_probs=107.4
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCC----C-------------------CccccccccccCChhhhhhhccccCCCCC-CC
Q 025351 35 ERIKGPWSAEEDRILTRLVERYGP----R-------------------NWSLISRYIKGRSGKSCRLRWCNQLSPSV-AH 90 (254)
Q Consensus 35 ~~~kg~WT~eED~~L~~lV~~~g~----~-------------------nW~~Ia~~l~~Rs~~qcr~Rw~~~L~p~~-~~ 90 (254)
..+-+.|+.+||.+|.+.|..|-. . -|+.|...||.|+.+.++.+-++...|.- .+
T Consensus 305 e~~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp~R~~~siy~~~rR~y~~FE~~r 384 (607)
T KOG0051|consen 305 EINLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLPYRDRKSIYHHLRRAYTPFENKR 384 (607)
T ss_pred hhhhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcCcccchhHHHHHHhcCCcccccc
Confidence 344588999999999999998711 1 17889999999999999885555444444 99
Q ss_pred CCCChHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHHHHhhcccccCCCCCCChhHHHHHHHHhh
Q 025351 91 RPFSPAEDDTILAAHARFGNRWATIARLLPGRTDNAVKNHWNSTLKRRTREHPVQMQPHQQQQLMDSVD 159 (254)
Q Consensus 91 ~~WT~EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~~~~~~~~~~e~~~L~~~~~ 159 (254)
|.||+||++.|..+|.++|+.|..|++.| ||.+.+|++||+++.+.........|+-++.+.|++.|+
T Consensus 385 g~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~ 452 (607)
T KOG0051|consen 385 GKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVN 452 (607)
T ss_pred CCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHH
Confidence 99999999999999999999999999999 999999999999999999867777799999999999996
No 16
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.35 E-value=1.4e-12 Score=116.38 Aligned_cols=75 Identities=15% Similarity=0.311 Sum_probs=66.2
Q ss_pred CCCCCCCChHHHHHHHHHHHhcCC-ChhhhhhcCC-CCCHHHHHHHHHHhhcccccCCCCCCChhHHHHHHHHhhcCCC
Q 025351 87 SVAHRPFSPAEDDTILAAHARFGN-RWATIARLLP-GRTDNAVKNHWNSTLKRRTREHPVQMQPHQQQQLMDSVDNGGD 163 (254)
Q Consensus 87 ~~~~~~WT~EED~~Ll~~v~~~G~-~W~~IA~~l~-gRT~~q~k~Rw~~~lk~~~~~~~~~~~~~e~~~L~~~~~~~~~ 163 (254)
.+.+|+||+|||++|+++|+.||. +|..|++.++ +|+..+||-||.++|++.+++.. |+++|+..++++....|+
T Consensus 6 ~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~--fT~eEe~~Ii~lH~~~GN 82 (238)
T KOG0048|consen 6 ELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGN--FSDEEEDLIIKLHALLGN 82 (238)
T ss_pred cccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCC--CCHHHHHHHHHHHHHHCc
Confidence 345799999999999999999995 6999999998 99999999999999999999776 777788888887776553
No 17
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.27 E-value=7.9e-12 Score=82.70 Aligned_cols=47 Identities=34% Similarity=0.775 Sum_probs=44.2
Q ss_pred CCCCChHHHHHHHHHHHhcC-CChhhhhhcCCCCCHHHHHHHHHHhhc
Q 025351 90 HRPFSPAEDDTILAAHARFG-NRWATIARLLPGRTDNAVKNHWNSTLK 136 (254)
Q Consensus 90 ~~~WT~EED~~Ll~~v~~~G-~~W~~IA~~l~gRT~~q~k~Rw~~~lk 136 (254)
+++||++||.+|+.+++.|| .+|..||..|++||+.+|++||+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 36899999999999999999 999999999999999999999988765
No 18
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.18 E-value=1.5e-11 Score=81.33 Aligned_cols=48 Identities=46% Similarity=1.001 Sum_probs=44.4
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhccccCC
Q 025351 38 KGPWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCNQLS 85 (254)
Q Consensus 38 kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~~L~ 85 (254)
+++||++||++|..++..||..+|..||..|++|++.+|+.||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 468999999999999999997789999999999999999999988654
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=99.14 E-value=7.7e-11 Score=76.79 Aligned_cols=44 Identities=39% Similarity=0.874 Sum_probs=41.6
Q ss_pred CCChHHHHHHHHHHHhcC-CChhhhhhcCCCCCHHHHHHHHHHhh
Q 025351 92 PFSPAEDDTILAAHARFG-NRWATIARLLPGRTDNAVKNHWNSTL 135 (254)
Q Consensus 92 ~WT~EED~~Ll~~v~~~G-~~W~~IA~~l~gRT~~q~k~Rw~~~l 135 (254)
+||++||..|+.++..|| .+|..||..|++||..+|++||++++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 89999999999999999999997653
No 20
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.05 E-value=1e-10 Score=76.22 Aligned_cols=45 Identities=47% Similarity=1.007 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhccccC
Q 025351 40 PWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCNQL 84 (254)
Q Consensus 40 ~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~~L 84 (254)
+||++||++|+.++..||..+|..||..|++|+..+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999778999999999999999999997653
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=99.01 E-value=2.8e-10 Score=110.95 Aligned_cols=137 Identities=25% Similarity=0.442 Sum_probs=112.1
Q ss_pred CCCCCCcCcc-ccCCCCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhccccC--------------
Q 025351 20 SLSGNNKTRR-ATHKPERIKGPWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCNQL-------------- 84 (254)
Q Consensus 20 s~s~~~k~r~-~~~~p~~~kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~~L-------------- 84 (254)
+...+++.|| ...+|.++++.|+.+||+.|+.+-..+|.. |..||..+++|+..+|..||.+.+
T Consensus 53 ~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~-wstia~~~d~rt~~~~~ery~~~~~~~~s~~~s~~~~~ 131 (512)
T COG5147 53 STGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQ-WSTIADYKDRRTAQQCVERYVNTLEDLSSTHDSKLQRR 131 (512)
T ss_pred cccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCch-hhhhccccCccchHHHHHHHHHHhhhhhccccccccch
Confidence 3455566666 678999999999999999999999999976 999999999999999999999554
Q ss_pred --------------------------------------------------------------------------------
Q 025351 85 -------------------------------------------------------------------------------- 84 (254)
Q Consensus 85 -------------------------------------------------------------------------------- 84 (254)
T Consensus 132 ~~f~k~d~f~~~~~~~~~~~~~~~~~~~~N~~~~~~~~~~rv~~~~vk~~~~~~~~~~~~~~~qem~~~~~~s~~~~~~~ 211 (512)
T COG5147 132 NEFDKIDPFNENSARRPDIYEDELLEREVNREASYRLRVPRVSKADVKPREKGEENNPDIEDLQEMKELKSASITRHLIL 211 (512)
T ss_pred hhccccCchhhhhhhhhhhhhcccchhhhhHHHHHHHHcccchHhhhhHHhhcccccccHHHHHHHhHHHHHHHHHHHhh
Confidence
Q ss_pred --------------------------------------------------------------------------CCCCCC
Q 025351 85 --------------------------------------------------------------------------SPSVAH 90 (254)
Q Consensus 85 --------------------------------------------------------------------------~p~~~~ 90 (254)
++.-.+
T Consensus 212 ~~~~~~~k~f~~~~~~~~e~~i~~~~~~~~~sr~q~~~~Iws~~~~~~~f~~n~~~~l~~R~~ksiy~~~rrky~~f~~~ 291 (512)
T COG5147 212 PSKSEINKAFKKGETLALEQEINEYKEKKGLSRKQFCERIWSTDRDEDKFWPNIYKKLPYRDKKSIYKHLRRKYNIFEQR 291 (512)
T ss_pred hhhhhhccccchhHHHHHHHHHHHHHHHhcccHHHHHhhccccccccccccchhhcccccccccchHHHHHHhhhHHhhh
Confidence 011122
Q ss_pred CCCChHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHHHHhhcccccCCCCCCChhHHHHHHHHh
Q 025351 91 RPFSPAEDDTILAAHARFGNRWATIARLLPGRTDNAVKNHWNSTLKRRTREHPVQMQPHQQQQLMDSV 158 (254)
Q Consensus 91 ~~WT~EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~~~~~~~~~~e~~~L~~~~ 158 (254)
+.||.+|+..|...+.++|..|..|.+.+ +|-++.|++||..+.+.....+...|..++...|...+
T Consensus 292 ~~wt~e~~~eL~~~~~~~~~~w~~ig~~~-~rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv 358 (512)
T COG5147 292 GKWTKEEEQELAKLVVEHGGSWTEIGKLL-GRMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVV 358 (512)
T ss_pred ccCccccccccccccccccchhhHhhhhh-ccCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHH
Confidence 57999999999999999999999999999 99999999999999999644444445555544444433
No 22
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.97 E-value=5.6e-06 Score=80.42 Aligned_cols=71 Identities=23% Similarity=0.449 Sum_probs=61.8
Q ss_pred CCCCCCChHHHHHHHHHHHhcC-CChhhhhhcCCCCCHHHHHHHHHHhhcccccCCCCCCChhHHHHHHHHhhc
Q 025351 88 VAHRPFSPAEDDTILAAHARFG-NRWATIARLLPGRTDNAVKNHWNSTLKRRTREHPVQMQPHQQQQLMDSVDN 160 (254)
Q Consensus 88 ~~~~~WT~EED~~Ll~~v~~~G-~~W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~~~~~~~~~~e~~~L~~~~~~ 160 (254)
++-+-|+.-||+.|-.++..|| |+|+.|+..++-.|+.||++||...+.+.+++.. |+-+++.+|+.++-.
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~te--ws~eederlLhlakl 76 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTE--WSREEDERLLHLAKL 76 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhh--hhhhHHHHHHHHHHh
Confidence 4567899999999999999999 5799999999999999999999999999998876 556667777776554
No 23
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.88 E-value=3.3e-05 Score=54.51 Aligned_cols=47 Identities=21% Similarity=0.345 Sum_probs=41.4
Q ss_pred CCCCChHHHHHHHHHHHhcCC-Ch---hhhhhcCC-CC-CHHHHHHHHHHhhc
Q 025351 90 HRPFSPAEDDTILAAHARFGN-RW---ATIARLLP-GR-TDNAVKNHWNSTLK 136 (254)
Q Consensus 90 ~~~WT~EED~~Ll~~v~~~G~-~W---~~IA~~l~-gR-T~~q~k~Rw~~~lk 136 (254)
+-.||+||...+++++..||. +| ..|+..|. .| |..||+.|++.+.-
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 458999999999999999996 99 99999885 35 99999999987654
No 24
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.87 E-value=1.4e-05 Score=76.30 Aligned_cols=58 Identities=21% Similarity=0.452 Sum_probs=49.6
Q ss_pred CccccCCC---CCCcCCCCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhccccC
Q 025351 27 TRRATHKP---ERIKGPWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCNQL 84 (254)
Q Consensus 27 ~r~~~~~p---~~~kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~~L 84 (254)
..++.+.+ .+-...||.+|+-+|+++++.||.+||..||.+|+.|+..+|+.+|.+.+
T Consensus 58 H~Yrim~~~s~~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 58 HPYRIMDTNSFPILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHF 118 (438)
T ss_pred CCceeecCCCCCCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHH
Confidence 34444444 34557799999999999999999999999999999999999999999854
No 25
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.74 E-value=4.3e-05 Score=73.01 Aligned_cols=52 Identities=19% Similarity=0.420 Sum_probs=46.1
Q ss_pred CCCCCCCChHHHHHHHHHHHhcC-CChhhhhhcCCCCCHHHHHHHHHHhhccc
Q 025351 87 SVAHRPFSPAEDDTILAAHARFG-NRWATIARLLPGRTDNAVKNHWNSTLKRR 138 (254)
Q Consensus 87 ~~~~~~WT~EED~~Ll~~v~~~G-~~W~~IA~~l~gRT~~q~k~Rw~~~lk~~ 138 (254)
.+-...||.+|+.+||+++..|| ++|..||.++..||..+|+.+|.+++-..
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv~s 121 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFVNS 121 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHhcC
Confidence 34456899999999999999999 89999999998899999999998776554
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=97.72 E-value=3e-05 Score=54.78 Aligned_cols=47 Identities=11% Similarity=0.237 Sum_probs=41.2
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCc---cccccccc-cC-ChhhhhhhccccC
Q 025351 38 KGPWSAEEDRILTRLVERYGPRNW---SLISRYIK-GR-SGKSCRLRWCNQL 84 (254)
Q Consensus 38 kg~WT~eED~~L~~lV~~~g~~nW---~~Ia~~l~-~R-s~~qcr~Rw~~~L 84 (254)
+-.||+||..+++.+|+.+|..+| ..|++.|. .+ |..||+.|++.+.
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 456999999999999999998799 99999884 56 9999999988764
No 27
>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=97.54 E-value=0.0001 Score=53.42 Aligned_cols=51 Identities=24% Similarity=0.486 Sum_probs=33.2
Q ss_pred CCCCChHHHHHHHHHHHhc--------CCC-hhhhhhcCC-CCCHHHHHHHHHHhhccccc
Q 025351 90 HRPFSPAEDDTILAAHARF--------GNR-WATIARLLP-GRTDNAVKNHWNSTLKRRTR 140 (254)
Q Consensus 90 ~~~WT~EED~~Ll~~v~~~--------G~~-W~~IA~~l~-gRT~~q~k~Rw~~~lk~~~~ 140 (254)
+.+||.+||+.|++.|+++ ||+ |.+++..-+ .+|-...|+||...|+.+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~~ 62 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRPR 62 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT-----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcccc
Confidence 4589999999999999764 222 999999877 89999999999988887653
No 28
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=97.49 E-value=7.4e-05 Score=62.97 Aligned_cols=53 Identities=23% Similarity=0.419 Sum_probs=45.9
Q ss_pred CCCCCCChHHHHHHHHHHHhc---CC----ChhhhhhcCCCCCHHHHHHHHHHhhcccccC
Q 025351 88 VAHRPFSPAEDDTILAAHARF---GN----RWATIARLLPGRTDNAVKNHWNSTLKRRTRE 141 (254)
Q Consensus 88 ~~~~~WT~EED~~Ll~~v~~~---G~----~W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~~ 141 (254)
.+...||.|||.+|.+.|.+| |. -+..++..| +||+.+|.-|||.++++++..
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~ 61 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEE 61 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHH
Confidence 356789999999999999887 43 388889999 999999999999999998753
No 29
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.34 E-value=0.00049 Score=60.19 Aligned_cols=96 Identities=19% Similarity=0.339 Sum_probs=71.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCCcccccccc---ccCChhhhhhhccccCC----------------CC-----CCCCCCCh
Q 025351 40 PWSAEEDRILTRLVERYGPRNWSLISRYI---KGRSGKSCRLRWCNQLS----------------PS-----VAHRPFSP 95 (254)
Q Consensus 40 ~WT~eED~~L~~lV~~~g~~nW~~Ia~~l---~~Rs~~qcr~Rw~~~L~----------------p~-----~~~~~WT~ 95 (254)
+|++++|-+|+.+|..-. +-..|+..+ ..-|...+..||+..|. |. ..+.+||.
T Consensus 1 rW~~~DDl~Li~av~~~~--~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~~is~~a~~~m~~l~p~~~~~iq~kalfS~ 78 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTN--DLESVHLGVKFSCKFTLQEIEERWYALLYDPVISRIAVAAMRNLHPELIAAIQSKALFSK 78 (199)
T ss_pred CCCchhhHHHHHHHHHhc--CHHHHHccCCcCCcCcHHHHHHHHHHHHcChhhHHHHHHHHHhCCcchhhcccccCCCCH
Confidence 599999999999999865 467777665 34577888899998762 22 24568999
Q ss_pred HHHHHHHHHHHhcCC---Chhhhhh-----cCCCCCHHHHHHHHHHhhcc
Q 025351 96 AEDDTILAAHARFGN---RWATIAR-----LLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 96 EED~~Ll~~v~~~G~---~W~~IA~-----~l~gRT~~q~k~Rw~~~lk~ 137 (254)
+|+++|......... .+.+|=. .-++||+.++.++|..+.+.
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy 128 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQY 128 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHh
Confidence 999999998766654 3666633 23689999999999744433
No 30
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.31 E-value=0.00012 Score=70.68 Aligned_cols=46 Identities=24% Similarity=0.533 Sum_probs=42.5
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhcccc
Q 025351 37 IKGPWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCNQ 83 (254)
Q Consensus 37 ~kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~~ 83 (254)
....||.+|..+|++.|+.|| .+|.+||.++.+|+..||..||.++
T Consensus 278 ~dk~WS~qE~~LLLEGIe~yg-DdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYG-DDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhh-hhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 556899999999999999999 4799999999999999999999864
No 31
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.23 E-value=0.0002 Score=70.53 Aligned_cols=48 Identities=23% Similarity=0.591 Sum_probs=43.5
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhcccc
Q 025351 35 ERIKGPWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCNQ 83 (254)
Q Consensus 35 ~~~kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~~ 83 (254)
...++.||.+|+-+|++.|+.|| .+|.+||.++.+||..||..|+.+.
T Consensus 250 ~~~~~~WT~qE~lLLLE~ie~y~-ddW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 250 ESARPNWTEQETLLLLEAIEMYG-DDWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred ccCCCCccHHHHHHHHHHHHHhc-ccHHHHHhccCCCCHHHHHHHHHhc
Confidence 34567899999999999999999 5799999999999999999999863
No 32
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.05 E-value=0.00051 Score=66.37 Aligned_cols=44 Identities=20% Similarity=0.357 Sum_probs=41.1
Q ss_pred CCCCCChHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHHH
Q 025351 89 AHRPFSPAEDDTILAAHARFGNRWATIARLLPGRTDNAVKNHWN 132 (254)
Q Consensus 89 ~~~~WT~EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~ 132 (254)
....||.+|..+|+++|..||..|.+||+++..||..||--||-
T Consensus 278 ~dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL 321 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFL 321 (531)
T ss_pred ccccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHH
Confidence 34489999999999999999999999999999999999999994
No 33
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.02 E-value=0.00035 Score=52.35 Aligned_cols=48 Identities=25% Similarity=0.504 Sum_probs=33.6
Q ss_pred CCCCChHHHHHHHHHHHh------cC--C------ChhhhhhcC----CCCCHHHHHHHHHHhhcc
Q 025351 90 HRPFSPAEDDTILAAHAR------FG--N------RWATIARLL----PGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 90 ~~~WT~EED~~Ll~~v~~------~G--~------~W~~IA~~l----~gRT~~q~k~Rw~~~lk~ 137 (254)
+..||.+|...||+++.+ ++ . -|..||..| ..||+.||+++|+++.+.
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 357999999999999877 22 1 399999976 359999999999775554
No 34
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.98 E-value=0.00086 Score=66.06 Aligned_cols=44 Identities=16% Similarity=0.313 Sum_probs=41.4
Q ss_pred CCCCCChHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHHH
Q 025351 89 AHRPFSPAEDDTILAAHARFGNRWATIARLLPGRTDNAVKNHWN 132 (254)
Q Consensus 89 ~~~~WT~EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~ 132 (254)
....||.+|..+||+++..||-+|.+||.++.+||..||-.||.
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL 295 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFL 295 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHH
Confidence 45689999999999999999999999999999999999999994
No 35
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.67 E-value=0.0011 Score=56.56 Aligned_cols=52 Identities=17% Similarity=0.329 Sum_probs=43.9
Q ss_pred CCCCCCChHHHHHHHHHHHhcCCC-------hhhhhhcCCCCCHHHHHHHHHHhhccccc
Q 025351 88 VAHRPFSPAEDDTILAAHARFGNR-------WATIARLLPGRTDNAVKNHWNSTLKRRTR 140 (254)
Q Consensus 88 ~~~~~WT~EED~~Ll~~v~~~G~~-------W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~ 140 (254)
.++..||.|||.+|.+.+..|+.. ...++..| +||..+|..|||.++++++.
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Ye 61 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQ 61 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHH
Confidence 456799999999999988888642 56667788 99999999999999998874
No 36
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=96.51 E-value=0.0051 Score=65.49 Aligned_cols=102 Identities=14% Similarity=0.334 Sum_probs=78.6
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhh-------cccc------C---------------------
Q 025351 39 GPWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLR-------WCNQ------L--------------------- 84 (254)
Q Consensus 39 g~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~R-------w~~~------L--------------------- 84 (254)
+.||.-+=..++.+..+||..+...||..|.+++...++.. |..+ +
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~~ 904 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAIG 904 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35888888888888899998889999999988887666531 1110 0
Q ss_pred ----------------CCCCCCCCCChHHHHHHHHHHHhcC-CChhhhhh------------cCCCCCHHHHHHHHHHhh
Q 025351 85 ----------------SPSVAHRPFSPAEDDTILAAHARFG-NRWATIAR------------LLPGRTDNAVKNHWNSTL 135 (254)
Q Consensus 85 ----------------~p~~~~~~WT~EED~~Ll~~v~~~G-~~W~~IA~------------~l~gRT~~q~k~Rw~~~l 135 (254)
.+..+...||.|||..||-++.+|| .+|..|-. .|..||+..|..|.+.++
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 1334455799999999999999999 57999833 236899999999998888
Q ss_pred ccccc
Q 025351 136 KRRTR 140 (254)
Q Consensus 136 k~~~~ 140 (254)
+-..+
T Consensus 985 ~~~~~ 989 (1033)
T PLN03142 985 RLIEK 989 (1033)
T ss_pred HHHHH
Confidence 77543
No 37
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.29 E-value=0.0017 Score=48.49 Aligned_cols=45 Identities=27% Similarity=0.613 Sum_probs=32.3
Q ss_pred CCCCHHHHHHHHHHHHH--h----C--CC-----Ccccccccc----ccCChhhhhhhcccc
Q 025351 39 GPWSAEEDRILTRLVER--Y----G--PR-----NWSLISRYI----KGRSGKSCRLRWCNQ 83 (254)
Q Consensus 39 g~WT~eED~~L~~lV~~--~----g--~~-----nW~~Ia~~l----~~Rs~~qcr~Rw~~~ 83 (254)
-.||.+|...|+.++.. + + .. -|..||..| ..||+.||+.||.+.
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L 63 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL 63 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 46999999999999988 2 1 11 299999988 369999999999874
No 38
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=96.24 E-value=0.0022 Score=46.48 Aligned_cols=51 Identities=22% Similarity=0.335 Sum_probs=32.4
Q ss_pred cCCCCHHHHHHHHHHHHHhCC------CC--ccccccccc-cCChhhhhhhccccCCCCC
Q 025351 38 KGPWSAEEDRILTRLVERYGP------RN--WSLISRYIK-GRSGKSCRLRWCNQLSPSV 88 (254)
Q Consensus 38 kg~WT~eED~~L~~lV~~~g~------~n--W~~Ia~~l~-~Rs~~qcr~Rw~~~L~p~~ 88 (254)
+.+||.+||++|+..|..+.. +| |..+++.-+ .+|..+-++||.+.|.+..
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 467999999999999976531 12 999998877 8889999999999887654
No 39
>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=96.19 E-value=0.0018 Score=54.66 Aligned_cols=48 Identities=27% Similarity=0.605 Sum_probs=40.0
Q ss_pred CcCCCCHHHHHHHHHHHHHh---CCC---CccccccccccCChhhhhhhccccCC
Q 025351 37 IKGPWSAEEDRILTRLVERY---GPR---NWSLISRYIKGRSGKSCRLRWCNQLS 85 (254)
Q Consensus 37 ~kg~WT~eED~~L~~lV~~~---g~~---nW~~Ia~~l~~Rs~~qcr~Rw~~~L~ 85 (254)
+...||.|||.+|...|-+| |.. -+..|+..| +||+..|.-||+.++.
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VR 56 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVR 56 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHH
Confidence 45679999999999999999 221 278888888 6999999999998874
No 40
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.85 E-value=0.0082 Score=55.87 Aligned_cols=47 Identities=17% Similarity=0.427 Sum_probs=42.8
Q ss_pred CCCCChHHHHHHHHHHHhcC-CChhhhhhcCCCCCHHHHHHHHHHhhc
Q 025351 90 HRPFSPAEDDTILAAHARFG-NRWATIARLLPGRTDNAVKNHWNSTLK 136 (254)
Q Consensus 90 ~~~WT~EED~~Ll~~v~~~G-~~W~~IA~~l~gRT~~q~k~Rw~~~lk 136 (254)
-..|+.+|+.+|+++...+| ++|..||.++..|+...||.||..+..
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 34799999999999999999 799999999978999999999977655
No 41
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.73 E-value=0.0074 Score=44.29 Aligned_cols=47 Identities=34% Similarity=0.465 Sum_probs=38.4
Q ss_pred cCCCCHHHHHHHHHHHHHh-----CCC-----------Ccccccccc-----ccCChhhhhhhccccC
Q 025351 38 KGPWSAEEDRILTRLVERY-----GPR-----------NWSLISRYI-----KGRSGKSCRLRWCNQL 84 (254)
Q Consensus 38 kg~WT~eED~~L~~lV~~~-----g~~-----------nW~~Ia~~l-----~~Rs~~qcr~Rw~~~L 84 (254)
+..||++|.+.|+.+|.+| +.. -|..|+..| +.|+..||+.+|.++.
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk 69 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLK 69 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 4579999999999999998 211 299999887 3699999999998753
No 42
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.60 E-value=0.004 Score=57.93 Aligned_cols=47 Identities=23% Similarity=0.521 Sum_probs=43.9
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhccccCC
Q 025351 39 GPWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCNQLS 85 (254)
Q Consensus 39 g~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~~L~ 85 (254)
-.|+..|+-+|++..+..|.+||..||.+++.|+...|+.+|.+.+.
T Consensus 64 e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 64 EGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 34999999999999999999999999999999999999999998664
No 43
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.46 E-value=0.018 Score=42.19 Aligned_cols=48 Identities=23% Similarity=0.488 Sum_probs=38.9
Q ss_pred CCCCChHHHHHHHHHHHhc-----CC------------ChhhhhhcC----C-CCCHHHHHHHHHHhhcc
Q 025351 90 HRPFSPAEDDTILAAHARF-----GN------------RWATIARLL----P-GRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 90 ~~~WT~EED~~Ll~~v~~~-----G~------------~W~~IA~~l----~-gRT~~q~k~Rw~~~lk~ 137 (254)
...||++|...|++++.+| |. -|..|+..| + .||..+|+.+|.++...
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~ 71 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSK 71 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Confidence 3579999999999999876 31 399999865 2 49999999999877654
No 44
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=94.70 E-value=0.011 Score=50.51 Aligned_cols=48 Identities=21% Similarity=0.504 Sum_probs=37.7
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCC------ccccccccccCChhhhhhhccccCC
Q 025351 37 IKGPWSAEEDRILTRLVERYGPRN------WSLISRYIKGRSGKSCRLRWCNQLS 85 (254)
Q Consensus 37 ~kg~WT~eED~~L~~lV~~~g~~n------W~~Ia~~l~~Rs~~qcr~Rw~~~L~ 85 (254)
+...||.|||.+|...|-.|+... ...++..| +|++.+|..||+.++.
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vr 57 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVR 57 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHH
Confidence 457899999999999999996543 44555555 6999999999966554
No 45
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=93.24 E-value=0.11 Score=41.99 Aligned_cols=52 Identities=21% Similarity=0.432 Sum_probs=40.8
Q ss_pred CCCCCCCChHHHHHHHHHHHhcCC----Chhhhhh------------cCCCCCHHHHHHHHHHhhccc
Q 025351 87 SVAHRPFSPAEDDTILAAHARFGN----RWATIAR------------LLPGRTDNAVKNHWNSTLKRR 138 (254)
Q Consensus 87 ~~~~~~WT~EED~~Ll~~v~~~G~----~W~~IA~------------~l~gRT~~q~k~Rw~~~lk~~ 138 (254)
...+..||++||.-||-++.+||- .|..|-. .|..||+..|..|-+.+++-.
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i 113 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLI 113 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHH
Confidence 566779999999999999999997 6988854 236899999999998877654
No 46
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=92.95 E-value=0.12 Score=49.48 Aligned_cols=80 Identities=19% Similarity=0.293 Sum_probs=59.1
Q ss_pred CccccccccccCChhhhhhhccccCCC-------------------------CCCCCCCChHHHHHHHHHHHhcCCChhh
Q 025351 60 NWSLISRYIKGRSGKSCRLRWCNQLSP-------------------------SVAHRPFSPAEDDTILAAHARFGNRWAT 114 (254)
Q Consensus 60 nW~~Ia~~l~~Rs~~qcr~Rw~~~L~p-------------------------~~~~~~WT~EED~~Ll~~v~~~G~~W~~ 114 (254)
+|..+.-..+-|...-...||....++ .++-..||.+|-+-|+++++.|.-+|.-
T Consensus 75 ~W~w~pFtn~aRkD~~~l~HWvr~~d~~~dypfakfNk~vdipsYt~eEYe~~l~dn~WskeETD~LF~lck~fDLRf~V 154 (445)
T KOG2656|consen 75 PWKWVPFTNSARKDDATLHHWVRVGDTPKDYPFAKFNKHVDIPSYTDEEYEAHLNDNSWSKEETDYLFDLCKRFDLRFFV 154 (445)
T ss_pred CceeeccCCccccCCceEEeeeeccCCCCCCchhhhccccCccccchHHHHHhhccccccHHHHHHHHHHHHhcCeeEEE
Confidence 466666666666665556666554221 1223469999999999999999999999
Q ss_pred hhhc-----CCC-CCHHHHHHHHHHhhcccc
Q 025351 115 IARL-----LPG-RTDNAVKNHWNSTLKRRT 139 (254)
Q Consensus 115 IA~~-----l~g-RT~~q~k~Rw~~~lk~~~ 139 (254)
||.. ++. ||-.++|+||..+.+.-.
T Consensus 155 IaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~ 185 (445)
T KOG2656|consen 155 IADRYDNQQYKKSRTVEDLKERYYSVCRKLL 185 (445)
T ss_pred EeeccchhhccccccHHHHHHHHHHHHHHHH
Confidence 9986 655 999999999987766543
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=92.89 E-value=0.13 Score=38.75 Aligned_cols=47 Identities=32% Similarity=0.577 Sum_probs=35.2
Q ss_pred CCChHHHHHHHHHHHhc---CC----------ChhhhhhcC---CC--CCHHHHHHHHHHhhcccc
Q 025351 92 PFSPAEDDTILAAHARF---GN----------RWATIARLL---PG--RTDNAVKNHWNSTLKRRT 139 (254)
Q Consensus 92 ~WT~EED~~Ll~~v~~~---G~----------~W~~IA~~l---~g--RT~~q~k~Rw~~~lk~~~ 139 (254)
.||++++..||+++.+. |+ .|..|+..| .| .|..||++|| ..||+.+
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~-~~lk~~y 65 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKW-KTLKKDY 65 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHH-HHHHHHH
Confidence 49999999999998653 21 299998876 23 5789999999 5555544
No 48
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=91.85 E-value=0.1 Score=49.70 Aligned_cols=43 Identities=23% Similarity=0.424 Sum_probs=40.2
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhccc
Q 025351 39 GPWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCN 82 (254)
Q Consensus 39 g~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~ 82 (254)
-+||.+|-+++.+++..+|+ +++.|+..+|+|..+|++.+|.+
T Consensus 366 ~~Ws~~e~ekFYKALs~wGt-dF~LIs~lfP~R~RkqIKaKfi~ 408 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGT-DFSLISSLFPNRERKQIKAKFIK 408 (507)
T ss_pred CcccHHHHHHHHHHHHHhcc-hHHHHHHhcCchhHHHHHHHHHH
Confidence 47999999999999999995 69999999999999999999865
No 49
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=91.33 E-value=0.24 Score=46.35 Aligned_cols=49 Identities=20% Similarity=0.328 Sum_probs=39.6
Q ss_pred CCCCChHHHHHHHHHHHhc----------CCChhhhhhcC----CCCCHHHHHHHHHHhhccc
Q 025351 90 HRPFSPAEDDTILAAHARF----------GNRWATIARLL----PGRTDNAVKNHWNSTLKRR 138 (254)
Q Consensus 90 ~~~WT~EED~~Ll~~v~~~----------G~~W~~IA~~l----~gRT~~q~k~Rw~~~lk~~ 138 (254)
...|+.+|-..||++..+. +.-|..||+.+ .-||+.+|+++|.++.++-
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Y 116 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKY 116 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHH
Confidence 4689999999999998643 23499999954 2499999999998887764
No 50
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=90.59 E-value=0.48 Score=31.93 Aligned_cols=41 Identities=27% Similarity=0.386 Sum_probs=31.8
Q ss_pred hHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHHHHhhc
Q 025351 95 PAEDDTILAAHARFGNRWATIARLLPGRTDNAVKNHWNSTLK 136 (254)
Q Consensus 95 ~EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk 136 (254)
++++..++.++...|-.|.+||..+ |.|...|+.+....++
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 5678889999999999999999999 9999999999876654
No 51
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=90.30 E-value=0.38 Score=46.00 Aligned_cols=47 Identities=21% Similarity=0.338 Sum_probs=43.3
Q ss_pred CCCChHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 91 RPFSPAEDDTILAAHARFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 91 ~~WT~EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.+||.+|-++..+|....|-.++.|+.+||.|...|||-+|.+--|+
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~ 412 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKV 412 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhh
Confidence 48999999999999999999999999999999999999999765554
No 52
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=89.94 E-value=0.45 Score=46.42 Aligned_cols=51 Identities=20% Similarity=0.212 Sum_probs=45.3
Q ss_pred CCCCCChHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHHHHhhcccc
Q 025351 89 AHRPFSPAEDDTILAAHARFGNRWATIARLLPGRTDNAVKNHWNSTLKRRT 139 (254)
Q Consensus 89 ~~~~WT~EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~~~ 139 (254)
.+..||.||-.++-+++..||.++.+|-..||.|+-..|...|...-|.+.
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK~~~ 236 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKKTRE 236 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHHHhh
Confidence 456899999999999999999999999999999999999998877666543
No 53
>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=88.02 E-value=0.27 Score=39.65 Aligned_cols=47 Identities=34% Similarity=0.506 Sum_probs=35.0
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCC---CCcccccccc------------ccCChhhhhhhcc
Q 025351 35 ERIKGPWSAEEDRILTRLVERYGP---RNWSLISRYI------------KGRSGKSCRLRWC 81 (254)
Q Consensus 35 ~~~kg~WT~eED~~L~~lV~~~g~---~nW~~Ia~~l------------~~Rs~~qcr~Rw~ 81 (254)
...+..||.+||.-|+-++.+||. ++|..|-..+ ..||+..+..|-.
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~ 107 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCN 107 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHH
Confidence 455678999999999999999998 7899998765 2467766666653
No 54
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=86.79 E-value=0.38 Score=36.38 Aligned_cols=30 Identities=37% Similarity=0.811 Sum_probs=17.9
Q ss_pred CCCCcCCCCHHHHHHH--------HHHHHHhCCCCcccccc
Q 025351 34 PERIKGPWSAEEDRIL--------TRLVERYGPRNWSLISR 66 (254)
Q Consensus 34 p~~~kg~WT~eED~~L--------~~lV~~~g~~nW~~Ia~ 66 (254)
|....|-||+|+|+.| .+|+++|| +..|+.
T Consensus 43 P~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG---~~~i~~ 80 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLRSGDKDDIERLIKKHG---EERIER 80 (87)
T ss_dssp -TT-TT---HHHHHHHTS--HHHHHHHHHHH----HHHHHH
T ss_pred CCCCCCCcCHHHHHHHHcCCHHHHHHHHHHhC---HHHHHH
Confidence 6667899999999999 56677787 455554
No 55
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=85.92 E-value=3.3 Score=42.81 Aligned_cols=44 Identities=9% Similarity=0.191 Sum_probs=40.5
Q ss_pred CCCChHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHHHHh
Q 025351 91 RPFSPAEDDTILAAHARFGNRWATIARLLPGRTDNAVKNHWNST 134 (254)
Q Consensus 91 ~~WT~EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~ 134 (254)
..||+.|-.+.-+|+..|.+++-.|++.++++|-.+|...|...
T Consensus 620 d~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtW 663 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTW 663 (907)
T ss_pred ccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHH
Confidence 47999999999999999999999999999999999998877543
No 56
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=84.50 E-value=0.54 Score=48.33 Aligned_cols=44 Identities=11% Similarity=0.483 Sum_probs=39.7
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhccc
Q 025351 38 KGPWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCN 82 (254)
Q Consensus 38 kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~ 82 (254)
...||+.|-.++.+++..|. +++.+|++.++++|.+||-+.|..
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~-KDF~~v~km~~~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYS-KDFIFVQKMVKSKTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhc-ccHHHHHHHhccccHHHHHHHHHH
Confidence 35799999999999999998 689999999999999999887753
No 57
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=84.17 E-value=1.9 Score=41.48 Aligned_cols=80 Identities=23% Similarity=0.361 Sum_probs=54.9
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCccccccc-----ccc-CChhhhhhhccccC----------CCC-CCCCCCChHHHHHH
Q 025351 39 GPWSAEEDRILTRLVERYGPRNWSLISRY-----IKG-RSGKSCRLRWCNQL----------SPS-VAHRPFSPAEDDTI 101 (254)
Q Consensus 39 g~WT~eED~~L~~lV~~~g~~nW~~Ia~~-----l~~-Rs~~qcr~Rw~~~L----------~p~-~~~~~WT~EED~~L 101 (254)
..||.+|.+.|..|+.+|..+ |--|+.. ++. ||....++||..+. ++. ++.-.+..|-|..=
T Consensus 131 n~WskeETD~LF~lck~fDLR-f~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~~s~sdllk~~~yd~e~Er~R 209 (445)
T KOG2656|consen 131 NSWSKEETDYLFDLCKRFDLR-FFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARAPSNSDLLKSLVYDAEHERER 209 (445)
T ss_pred ccccHHHHHHHHHHHHhcCee-EEEEeeccchhhccccccHHHHHHHHHHHHHHHHHccCCCchhhhhccccchHHHHHH
Confidence 569999999999999999976 9999977 555 99999999986532 111 22334444444332
Q ss_pred HHHHHhcCCChhhhhhcCCCCCHHHHHHH
Q 025351 102 LAAHARFGNRWATIARLLPGRTDNAVKNH 130 (254)
Q Consensus 102 l~~v~~~G~~W~~IA~~l~gRT~~q~k~R 130 (254)
.+ .+.+.+ .||+.|+..-
T Consensus 210 Kk----------~L~~L~-sRt~~qvaEE 227 (445)
T KOG2656|consen 210 KK----------YLERLL-SRTPEQVAEE 227 (445)
T ss_pred HH----------HHHHHH-hcCHHHHHHH
Confidence 11 233444 7888888654
No 58
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=82.28 E-value=0.8 Score=42.84 Aligned_cols=47 Identities=26% Similarity=0.383 Sum_probs=37.2
Q ss_pred cCCCCHHHHHHHHHHHHHh---------CCCCcccccccc----ccCChhhhhhhccccC
Q 025351 38 KGPWSAEEDRILTRLVERY---------GPRNWSLISRYI----KGRSGKSCRLRWCNQL 84 (254)
Q Consensus 38 kg~WT~eED~~L~~lV~~~---------g~~nW~~Ia~~l----~~Rs~~qcr~Rw~~~L 84 (254)
-..|+.+|-..|+.+.... ....|..||..+ ..|++.||+.+|.+..
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 3679999999999998853 112499999855 4599999999998743
No 59
>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=79.78 E-value=1.4 Score=33.08 Aligned_cols=43 Identities=26% Similarity=0.539 Sum_probs=31.5
Q ss_pred CCCHHHHHHHHHHHHHh---CCC---------Ccccccccccc-----CChhhhhhhccc
Q 025351 40 PWSAEEDRILTRLVERY---GPR---------NWSLISRYIKG-----RSGKSCRLRWCN 82 (254)
Q Consensus 40 ~WT~eED~~L~~lV~~~---g~~---------nW~~Ia~~l~~-----Rs~~qcr~Rw~~ 82 (254)
.||+++++.|++++... |.. .|..|+..|.. .+..||+.||..
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~ 60 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKT 60 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHH
Confidence 49999999999998754 222 28888888732 456788888754
No 60
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=76.87 E-value=7 Score=30.28 Aligned_cols=43 Identities=19% Similarity=0.261 Sum_probs=27.8
Q ss_pred CCCCChHHHHHHHHHHHhc----CC----Chhhhhhc----CCC-CCHHHHHHHHH
Q 025351 90 HRPFSPAEDDTILAAHARF----GN----RWATIARL----LPG-RTDNAVKNHWN 132 (254)
Q Consensus 90 ~~~WT~EED~~Ll~~v~~~----G~----~W~~IA~~----l~g-RT~~q~k~Rw~ 132 (254)
..-||++++..||+++..| |. .|..+-.. +.- =+.+|+.++-+
T Consensus 4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~Kir 59 (98)
T PF04504_consen 4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIR 59 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHH
Confidence 4579999999999999877 62 35444333 321 25666666553
No 61
>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=76.74 E-value=4.7 Score=26.66 Aligned_cols=41 Identities=20% Similarity=0.255 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 96 AEDDTILAAHARFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 96 EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
+++..++.++--.|..+.+||..| |-|...|+.+....+++
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 556667777666677899999999 99999999988777664
No 62
>smart00595 MADF subfamily of SANT domain.
Probab=76.58 E-value=2.8 Score=30.95 Aligned_cols=24 Identities=29% Similarity=0.590 Sum_probs=20.4
Q ss_pred ChhhhhhcCCCCCHHHHHHHHHHhh
Q 025351 111 RWATIARLLPGRTDNAVKNHWNSTL 135 (254)
Q Consensus 111 ~W~~IA~~l~gRT~~q~k~Rw~~~l 135 (254)
-|..||..| |-|..+|+.+|+++-
T Consensus 29 aW~~Ia~~l-~~~~~~~~~kw~~LR 52 (89)
T smart00595 29 AWEEIAEEL-GLSVEECKKRWKNLR 52 (89)
T ss_pred HHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 399999999 559999999996554
No 63
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=74.03 E-value=3.5 Score=41.75 Aligned_cols=51 Identities=12% Similarity=0.375 Sum_probs=42.0
Q ss_pred CCCCChHHHHHHHHHHHhcCCChhhhhh----------cCCCCCHHHHHHHHHHhhccccc
Q 025351 90 HRPFSPAEDDTILAAHARFGNRWATIAR----------LLPGRTDNAVKNHWNSTLKRRTR 140 (254)
Q Consensus 90 ~~~WT~EED~~Ll~~v~~~G~~W~~IA~----------~l~gRT~~q~k~Rw~~~lk~~~~ 140 (254)
+..||-+|+.-...+++++|+++.+|-. ...-+|-.|++.+|+.++.+-++
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k 148 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNK 148 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHh
Confidence 6789999999999999999999988822 23446888999999888877544
No 64
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=72.78 E-value=7.1 Score=25.51 Aligned_cols=38 Identities=24% Similarity=0.315 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHhcCC-ChhhhhhcCCCCCHHHHHHHHHHh
Q 025351 96 AEDDTILAAHARFGN-RWATIARLLPGRTDNAVKNHWNST 134 (254)
Q Consensus 96 EED~~Ll~~v~~~G~-~W~~IA~~l~gRT~~q~k~Rw~~~ 134 (254)
+=|..|+.+...-|. .|.+||+.+ |=|...|..|++.+
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l-glS~~~v~~Ri~rL 41 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL-GLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH-TS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH-CcCHHHHHHHHHHh
Confidence 347889999888885 699999999 99999999999653
No 65
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=71.10 E-value=7.2 Score=34.28 Aligned_cols=44 Identities=16% Similarity=0.241 Sum_probs=34.3
Q ss_pred CCChHHHHHHHHHHHhcCCChhhhhhc--CCC-CCHHHHHHHHHHhhc
Q 025351 92 PFSPAEDDTILAAHARFGNRWATIARL--LPG-RTDNAVKNHWNSTLK 136 (254)
Q Consensus 92 ~WT~EED~~Ll~~v~~~G~~W~~IA~~--l~g-RT~~q~k~Rw~~~lk 136 (254)
.|++.+|-+|+.+| +.|+.-..|+.. |.. -|-..|..||+.+|-
T Consensus 1 rW~~~DDl~Li~av-~~~~~L~~v~~gvkFS~~fT~~Ei~~RW~~lly 47 (199)
T PF13325_consen 1 RWKPEDDLLLINAV-EQTNDLESVHLGVKFSCKFTLQEIEERWYALLY 47 (199)
T ss_pred CCCchhhHHHHHHH-HHhcCHHHHHccCCcCCcCcHHHHHHHHHHHHc
Confidence 49999999999998 457777777664 333 588999999987653
No 66
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=69.57 E-value=7.3 Score=32.08 Aligned_cols=46 Identities=15% Similarity=0.149 Sum_probs=39.6
Q ss_pred hHHHHHHHHHHHhcCC-ChhhhhhcCCCCCHHHHHHHHHHhhcccccC
Q 025351 95 PAEDDTILAAHARFGN-RWATIARLLPGRTDNAVKNHWNSTLKRRTRE 141 (254)
Q Consensus 95 ~EED~~Ll~~v~~~G~-~W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~~ 141 (254)
.+-|..||.+..+-|. .|++||+.+ |-+...|+.|++.+.......
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGIIT 54 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 3568899999888884 699999999 999999999998888877654
No 67
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=65.31 E-value=26 Score=33.86 Aligned_cols=54 Identities=30% Similarity=0.356 Sum_probs=40.4
Q ss_pred CCCCCCChHHHHHHHHHHHhcCC----------------ChhhhhhcC-----CCCCHHHHHHHHHHhhcccccC
Q 025351 88 VAHRPFSPAEDDTILAAHARFGN----------------RWATIARLL-----PGRTDNAVKNHWNSTLKRRTRE 141 (254)
Q Consensus 88 ~~~~~WT~EED~~Ll~~v~~~G~----------------~W~~IA~~l-----~gRT~~q~k~Rw~~~lk~~~~~ 141 (254)
..-|-|+++=|+...+|.+.|.. +=..||+++ ..||..||..|-+-+.|++.++
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~re 148 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLRE 148 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHH
Confidence 45578999999999999988742 345677765 3489999999987666665544
No 68
>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=65.02 E-value=6.6 Score=33.26 Aligned_cols=41 Identities=22% Similarity=0.189 Sum_probs=35.2
Q ss_pred CCChHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHHHH
Q 025351 92 PFSPAEDDTILAAHARFGNRWATIARLLPGRTDNAVKNHWNS 133 (254)
Q Consensus 92 ~WT~EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~ 133 (254)
.||+|+.+.|.++. .-|..=++||..|.|.|.++|.-+-+.
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 59999999999988 448889999999977999999877654
No 69
>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=64.79 E-value=11 Score=29.92 Aligned_cols=37 Identities=27% Similarity=0.324 Sum_probs=27.8
Q ss_pred HHHHHHHhcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 100 TILAAHARFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 100 ~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.++.+....|..+.+||..+ |.+...|+.+....+++
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 33334334577899999999 99999999999775543
No 70
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=63.65 E-value=9.6 Score=38.56 Aligned_cols=52 Identities=19% Similarity=0.368 Sum_probs=45.6
Q ss_pred CCCCCCCChHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHHHHhhccc
Q 025351 87 SVAHRPFSPAEDDTILAAHARFGNRWATIARLLPGRTDNAVKNHWNSTLKRR 138 (254)
Q Consensus 87 ~~~~~~WT~EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~~ 138 (254)
.....+|+.+|-++...+..++|.+.+.|+..+++|...|||.+|..--++.
T Consensus 406 ~~~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~eE~r~ 457 (584)
T KOG2009|consen 406 KLETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKEEKRN 457 (584)
T ss_pred ccccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhhhhcc
Confidence 3445689999999999999999999999999999999999999996555443
No 71
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=62.67 E-value=13 Score=27.65 Aligned_cols=38 Identities=24% Similarity=0.400 Sum_probs=28.0
Q ss_pred HHHHHHHHhcCC--------ChhhhhhcCCC-C--C--HHHHHHHHHHhhc
Q 025351 99 DTILAAHARFGN--------RWATIARLLPG-R--T--DNAVKNHWNSTLK 136 (254)
Q Consensus 99 ~~Ll~~v~~~G~--------~W~~IA~~l~g-R--T--~~q~k~Rw~~~lk 136 (254)
-.|..+|..+|+ +|..||+.|.- . + ..+++..|..+|-
T Consensus 39 ~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 39 YKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhH
Confidence 357788888875 59999998832 1 1 3689999988774
No 72
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=62.16 E-value=11 Score=31.38 Aligned_cols=46 Identities=11% Similarity=0.097 Sum_probs=39.5
Q ss_pred hHHHHHHHHHHHhcCC-ChhhhhhcCCCCCHHHHHHHHHHhhcccccC
Q 025351 95 PAEDDTILAAHARFGN-RWATIARLLPGRTDNAVKNHWNSTLKRRTRE 141 (254)
Q Consensus 95 ~EED~~Ll~~v~~~G~-~W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~~ 141 (254)
.+-|.+||.+..+-|. .|++||+.+ |=+...|..|++.+.+....+
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCeE
Confidence 4568899998888774 699999999 999999999999998887654
No 73
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=61.40 E-value=6.1 Score=38.83 Aligned_cols=48 Identities=17% Similarity=0.316 Sum_probs=40.7
Q ss_pred CCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhccc
Q 025351 34 PERIKGPWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCN 82 (254)
Q Consensus 34 p~~~kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~ 82 (254)
-......||.||--+|.++...|| +++.+|-+.||.|+-.++...|..
T Consensus 183 r~~~~d~WT~Ed~vlFe~aF~~~G-K~F~kIrq~LP~rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 183 RTEFPDEWTAEDIVLFEQAFQFFG-KDFHKIRQALPHRSLASLVQYYYS 230 (534)
T ss_pred cCCCcccchHHHHHHHHHHHHHhc-ccHHHHHHHccCccHHHHHHHHHH
Confidence 344567799999999999999999 579999999999999888776653
No 74
>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=60.15 E-value=19 Score=33.85 Aligned_cols=47 Identities=26% Similarity=0.410 Sum_probs=36.2
Q ss_pred CCCCChHHHHHHHHHHHhc-CCC---hhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 90 HRPFSPAEDDTILAAHARF-GNR---WATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 90 ~~~WT~EED~~Ll~~v~~~-G~~---W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
-..||.-|...|+++.... |.. -..|++.++||+..+|++.- +.||.
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl-~~LK~ 71 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFL-QQLKG 71 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHH-HHHHH
Confidence 4589999999999888654 543 56788899999999998855 44443
No 75
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=57.68 E-value=12 Score=37.83 Aligned_cols=49 Identities=20% Similarity=0.379 Sum_probs=43.3
Q ss_pred CCCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhccc
Q 025351 33 KPERIKGPWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCN 82 (254)
Q Consensus 33 ~p~~~kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~ 82 (254)
-+....++||.+|-++........|. +.+.|+..+++|+.+|++.+|..
T Consensus 404 sk~~~~~~w~~se~e~fyka~~~~gs-~~slis~l~p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 404 SKKLETDKWDASETELFYKALSERGS-DFSLISNLFPLRDRKQIKAKFKK 452 (584)
T ss_pred cCccccCcccchhhHHhhhHHhhhcc-cccccccccccccHHHHHHHHhh
Confidence 34556789999999999999999995 69999999999999999998854
No 76
>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=57.34 E-value=4.3 Score=30.61 Aligned_cols=19 Identities=16% Similarity=0.438 Sum_probs=10.6
Q ss_pred CCCCCCCCChHHHHHHHHH
Q 025351 86 PSVAHRPFSPAEDDTILAA 104 (254)
Q Consensus 86 p~~~~~~WT~EED~~Ll~~ 104 (254)
|....|-||+|+|..|...
T Consensus 43 P~n~~GiWT~eDD~~L~~~ 61 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLRSG 61 (87)
T ss_dssp -TT-TT---HHHHHHHTS-
T ss_pred CCCCCCCcCHHHHHHHHcC
Confidence 6667889999999998443
No 77
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=56.46 E-value=19 Score=27.12 Aligned_cols=39 Identities=21% Similarity=0.336 Sum_probs=28.5
Q ss_pred HHHHHHHHhcCC--------ChhhhhhcCCCC-----CHHHHHHHHHHhhcc
Q 025351 99 DTILAAHARFGN--------RWATIARLLPGR-----TDNAVKNHWNSTLKR 137 (254)
Q Consensus 99 ~~Ll~~v~~~G~--------~W~~IA~~l~gR-----T~~q~k~Rw~~~lk~ 137 (254)
-.|..+|..+|+ .|..|+..|.-. ...+++..|.++|.+
T Consensus 35 ~~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~ 86 (93)
T smart00501 35 YRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLP 86 (93)
T ss_pred HHHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHH
Confidence 357777777775 699999988322 356889999887754
No 78
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=56.45 E-value=9.1 Score=38.91 Aligned_cols=46 Identities=11% Similarity=0.335 Sum_probs=35.9
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCcccccccc----------ccCChhhhhhhccccC
Q 025351 38 KGPWSAEEDRILTRLVERYGPRNWSLISRYI----------KGRSGKSCRLRWCNQL 84 (254)
Q Consensus 38 kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l----------~~Rs~~qcr~Rw~~~L 84 (254)
|..||..|.+.+..++..+| +|+..|-..+ .-++..|+|.+|.+.+
T Consensus 88 ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~ 143 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLV 143 (782)
T ss_pred ccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHH
Confidence 77899999999999999999 6798883222 2356678888876644
No 79
>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=53.11 E-value=8 Score=25.26 Aligned_cols=38 Identities=29% Similarity=0.426 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHhCCCCccccccccccCChhhhhhhccc
Q 025351 44 EEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCN 82 (254)
Q Consensus 44 eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~ 82 (254)
+=|..|+.+++..+...|..||+.+ |=+...|..|+.+
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l-glS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL-GLSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH-TS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH-CcCHHHHHHHHHH
Confidence 3478899999999988999999998 5888899888753
No 80
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=52.04 E-value=27 Score=26.46 Aligned_cols=45 Identities=18% Similarity=0.181 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHhcCC-ChhhhhhcCCCCCHHHHHHHHHHhhcccccC
Q 025351 96 AEDDTILAAHARFGN-RWATIARLLPGRTDNAVKNHWNSTLKRRTRE 141 (254)
Q Consensus 96 EED~~Ll~~v~~~G~-~W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~~ 141 (254)
+.|..|+.+..+.|. .+..||+.+ |-+...|+.+.+.+.+...-.
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 568889999988774 799999999 999999999999888876544
No 81
>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=51.93 E-value=16 Score=27.48 Aligned_cols=29 Identities=21% Similarity=0.444 Sum_probs=23.7
Q ss_pred HHHHHHHHHhcCCChhhhhhcCCCCCHHHH
Q 025351 98 DDTILAAHARFGNRWATIARLLPGRTDNAV 127 (254)
Q Consensus 98 D~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~ 127 (254)
|+.|..+....|..|..+|.+| |=|..+|
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I 30 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDI 30 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 4668888999999999999998 6666554
No 82
>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=51.78 E-value=22 Score=27.29 Aligned_cols=34 Identities=24% Similarity=0.269 Sum_probs=25.8
Q ss_pred HHHHhcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 103 AAHARFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 103 ~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.++...|..+.+||..+ |=+...|+++.+..+++
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 78999999988776544
No 83
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=50.15 E-value=9.6 Score=41.27 Aligned_cols=34 Identities=21% Similarity=0.387 Sum_probs=28.5
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCCcccccccc
Q 025351 35 ERIKGPWSAEEDRILTRLVERYGPRNWSLISRYI 68 (254)
Q Consensus 35 ~~~kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l 68 (254)
..++..||.|||.-|+-++.+||..+|.+|-..+
T Consensus 923 ~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i 956 (1033)
T PLN03142 923 QNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAF 956 (1033)
T ss_pred CCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHH
Confidence 3345569999999999999999999999996544
No 84
>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=49.33 E-value=36 Score=21.27 Aligned_cols=37 Identities=16% Similarity=0.324 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHHHHh
Q 025351 97 EDDTILAAHARFGNRWATIARLLPGRTDNAVKNHWNST 134 (254)
Q Consensus 97 ED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~ 134 (254)
++..++.++...|..+..||..+ |=+...|+.+.+..
T Consensus 14 ~~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~ 50 (55)
T cd06171 14 REREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRA 50 (55)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 45566666666778899999998 88888887766443
No 85
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=49.00 E-value=15 Score=40.38 Aligned_cols=73 Identities=16% Similarity=0.164 Sum_probs=44.8
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhccccCCCCCCCCCCChHHHHHHHHHHHhc-CCChhhhhh
Q 025351 39 GPWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCNQLSPSVAHRPFSPAEDDTILAAHARF-GNRWATIAR 117 (254)
Q Consensus 39 g~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~~L~p~~~~~~WT~EED~~Ll~~v~~~-G~~W~~IA~ 117 (254)
.-|..++|..|+-.|-+||.++|..|-.- .....-=...++..+-.+.|-...-..|+.++..+ +.+|....+
T Consensus 1134 ~~W~~e~Ds~LLiGI~khGygswe~Ir~D------p~L~l~dKi~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~~~~ 1207 (1373)
T KOG0384|consen 1134 CDWGSEDDSMLLIGIFKHGYGSWEAIRLD------PDLGLTDKIFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPKKLK 1207 (1373)
T ss_pred cCCCchhhhhHhhhhhhcccccHHHhccC------ccccchhhhcccccCCchHHHHHHHHHHHHHHhhcccCCCchhhh
Confidence 56999999999999999999999999421 11111101122222344455566666666666665 444554443
No 86
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=48.72 E-value=85 Score=29.71 Aligned_cols=85 Identities=25% Similarity=0.386 Sum_probs=59.6
Q ss_pred CCCCHHHHHHHHHHHHHhCCC---CccccccccccCChhhhhhhccccCCCCCCCCCCChHHHHHHHHHHHh-c-----C
Q 025351 39 GPWSAEEDRILTRLVERYGPR---NWSLISRYIKGRSGKSCRLRWCNQLSPSVAHRPFSPAEDDTILAAHAR-F-----G 109 (254)
Q Consensus 39 g~WT~eED~~L~~lV~~~g~~---nW~~Ia~~l~~Rs~~qcr~Rw~~~L~p~~~~~~WT~EED~~Ll~~v~~-~-----G 109 (254)
..||.-|...|+++.+..... +-.+|++.+++|+..++++- .++|+ +..+-+++.+ | |
T Consensus 22 ~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~f-l~~LK------------~rvareaiqkv~~~g~~~ 88 (344)
T PF11035_consen 22 AAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDF-LQQLK------------GRVAREAIQKVHPGGLKG 88 (344)
T ss_pred ccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHH-HHHHH------------HHHHHHHHHHhccccccc
Confidence 469999999999999876333 35578889999999888763 33332 2223333333 1 1
Q ss_pred C------------ChhhhhhcCCCCCHHHHHHHHHHhhc
Q 025351 110 N------------RWATIARLLPGRTDNAVKNHWNSTLK 136 (254)
Q Consensus 110 ~------------~W~~IA~~l~gRT~~q~k~Rw~~~lk 136 (254)
. -|..+|+.+.|.-...+-.-|.++|-
T Consensus 89 ~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~ 127 (344)
T PF11035_consen 89 PRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLT 127 (344)
T ss_pred ccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHH
Confidence 1 29999999999988888888876654
No 87
>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=48.53 E-value=24 Score=26.62 Aligned_cols=30 Identities=20% Similarity=0.378 Sum_probs=24.6
Q ss_pred HHHHHHHHHhcCCChhhhhhcCCCCCHHHHH
Q 025351 98 DDTILAAHARFGNRWATIARLLPGRTDNAVK 128 (254)
Q Consensus 98 D~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k 128 (254)
|..|.......|..|..+|+.| |=+...|.
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI~ 33 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEIN 33 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHHH
Confidence 5677888889999999999999 77776653
No 88
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=46.66 E-value=30 Score=28.04 Aligned_cols=30 Identities=17% Similarity=0.187 Sum_probs=24.1
Q ss_pred hcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 107 RFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 107 ~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
..|..+.+||..| |-+...|+.+....+++
T Consensus 142 ~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 171 (182)
T PRK09652 142 IEGLSYEEIAEIM-GCPIGTVRSRIFRAREA 171 (182)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3467899999999 99999999888655443
No 89
>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=46.45 E-value=20 Score=26.64 Aligned_cols=33 Identities=30% Similarity=0.552 Sum_probs=25.8
Q ss_pred hHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHH
Q 025351 95 PAEDDTILAAHARFGNRWATIARLLPGRTDNAVKN 129 (254)
Q Consensus 95 ~EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~ 129 (254)
.||.++||..- ..|.+|..+|..| |=+...|.+
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 57888888432 6788999999999 877777754
No 90
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=45.74 E-value=16 Score=35.15 Aligned_cols=42 Identities=29% Similarity=0.428 Sum_probs=36.4
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCccccc-cccccCChhhhhhhcc
Q 025351 39 GPWSAEEDRILTRLVERYGPRNWSLIS-RYIKGRSGKSCRLRWC 81 (254)
Q Consensus 39 g~WT~eED~~L~~lV~~~g~~nW~~Ia-~~l~~Rs~~qcr~Rw~ 81 (254)
-.|+.+|-..+...++.|| +++..|- ..+++|+...|-..|.
T Consensus 278 ~~wsEeEcr~FEegl~~yG-KDF~lIr~nkvrtRsvgElVeyYY 320 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYG-KDFHLIRANKVRTRSVGELVEYYY 320 (445)
T ss_pred ccCCHHHHHHHHHHHHHhc-ccHHHHHhcccccchHHHHHHHHH
Confidence 4699999999999999999 6799997 4679999999987664
No 91
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=45.42 E-value=31 Score=27.87 Aligned_cols=30 Identities=23% Similarity=0.252 Sum_probs=24.0
Q ss_pred hcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 107 RFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 107 ~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
..|..+.+||..| |-+...|+++.....++
T Consensus 139 ~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 168 (179)
T PRK11924 139 VEGLSYREIAEIL-GVPVGTVKSRLRRARQL 168 (179)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466899999999 99999999988665443
No 92
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=44.14 E-value=17 Score=25.96 Aligned_cols=26 Identities=27% Similarity=0.484 Sum_probs=20.6
Q ss_pred ChhhhhhcCCC-CCHHHHHHHHHHhhc
Q 025351 111 RWATIARLLPG-RTDNAVKNHWNSTLK 136 (254)
Q Consensus 111 ~W~~IA~~l~g-RT~~q~k~Rw~~~lk 136 (254)
-|..||..|.. -+..+|+.+|+++..
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~ 54 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRD 54 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHH
Confidence 49999999953 678899999976543
No 93
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=43.86 E-value=65 Score=29.05 Aligned_cols=52 Identities=13% Similarity=0.343 Sum_probs=33.7
Q ss_pred hcCCChhhhhhcCCCCCHHHHHHHHHHhhcccccCCC-CCCChhHHHHHHHHhh
Q 025351 107 RFGNRWATIARLLPGRTDNAVKNHWNSTLKRRTREHP-VQMQPHQQQQLMDSVD 159 (254)
Q Consensus 107 ~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~~~~-~~~~~~e~~~L~~~~~ 159 (254)
-+|-.-.+||..| |.|...|+.+.....++-....+ ....+++.+.+.+.+-
T Consensus 122 ~~g~s~~EIA~~l-g~s~~tVr~~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~f~ 174 (281)
T TIGR02957 122 VFDYPYEEIASIV-GKSEANCRQLVSRARRHLDARRPRFEVSREESRQLLERFV 174 (281)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHhhCCCCCCChHHHHHHHHHHH
Confidence 3566789999999 89999999998766554333222 2234445555555433
No 94
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=43.69 E-value=33 Score=23.49 Aligned_cols=35 Identities=14% Similarity=0.343 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHH
Q 025351 96 AEDDTILAAHARFGNRWATIARLLPGRTDNAVKNHW 131 (254)
Q Consensus 96 EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw 131 (254)
+.|+..+.++.+.|-.-.+||+.+ ||+.+.|++.-
T Consensus 7 ~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl 41 (50)
T PF11427_consen 7 DAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRYL 41 (50)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHHH
T ss_pred HHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHHh
Confidence 445666777889999999999999 99999887643
No 95
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=43.01 E-value=1.3e+02 Score=23.20 Aligned_cols=48 Identities=19% Similarity=0.171 Sum_probs=38.0
Q ss_pred CCCCChHHHHHHHHHHHhcCCChhhhhhcCCCC-CHHHHHHHHHHhhccc
Q 025351 90 HRPFSPAEDDTILAAHARFGNRWATIARLLPGR-TDNAVKNHWNSTLKRR 138 (254)
Q Consensus 90 ~~~WT~EED~~Ll~~v~~~G~~W~~IA~~l~gR-T~~q~k~Rw~~~lk~~ 138 (254)
+..||+|.-..+++.+.+-|..=+.||+.+ |- ..++++..++.+....
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~~W~~~~~~~~ 53 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLYKWRIQLQKGG 53 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHHHHHHHHHHcc
Confidence 568999999999999999999889999999 86 7777665444444433
No 96
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=42.76 E-value=41 Score=32.47 Aligned_cols=44 Identities=11% Similarity=0.097 Sum_probs=38.5
Q ss_pred CCCChHHHHHHHHHHHhcCCChhhhhh-cCCCCCHHHHHHHHHHh
Q 025351 91 RPFSPAEDDTILAAHARFGNRWATIAR-LLPGRTDNAVKNHWNST 134 (254)
Q Consensus 91 ~~WT~EED~~Ll~~v~~~G~~W~~IA~-~l~gRT~~q~k~Rw~~~ 134 (254)
..|+++|=...-+.++.||+++..|.. .++.|+--.|...|...
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlW 322 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLW 322 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHh
Confidence 479999999999999999999999966 78999999998877433
No 97
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=42.44 E-value=38 Score=28.53 Aligned_cols=30 Identities=30% Similarity=0.336 Sum_probs=24.0
Q ss_pred hcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 107 RFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 107 ~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
..|....+||..| |-+...|++|.....++
T Consensus 148 ~~g~s~~EIA~~l-g~s~~tV~~rl~rar~~ 177 (192)
T PRK09643 148 MQGYSVADAARML-GVAEGTVKSRCARGRAR 177 (192)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3467899999999 99999999999554443
No 98
>KOG1878 consensus Nuclear receptor coregulator SMRT/SMRTER, contains Myb-like domains [Transcription]
Probab=41.95 E-value=11 Score=41.99 Aligned_cols=44 Identities=23% Similarity=0.465 Sum_probs=34.5
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhcc
Q 025351 37 IKGPWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWC 81 (254)
Q Consensus 37 ~kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~ 81 (254)
....|+++|-+....=...|- +|...|+.++..++..+|..-|.
T Consensus 224 ~~n~Ws~~Ek~~fk~rf~~H~-knf~~~as~~erkSv~d~vlfyy 267 (1672)
T KOG1878|consen 224 RMNEWSPEEKELFKSRFAQHV-KNFGLIASFFERKSVSDCVLFYY 267 (1672)
T ss_pred HhhhccccccccccchhhhcC-cchhhhhhhhcccchhhceeeee
Confidence 345799999887777777775 67888999998888888877653
No 99
>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=41.69 E-value=24 Score=26.11 Aligned_cols=29 Identities=24% Similarity=0.523 Sum_probs=23.1
Q ss_pred HHHHHHHHHhcCCChhhhhhcCCCCCHHHH
Q 025351 98 DDTILAAHARFGNRWATIARLLPGRTDNAV 127 (254)
Q Consensus 98 D~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~ 127 (254)
|..|.......|..|.++|+.| |=+..+|
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 4567778888999999999999 6666554
No 100
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=41.65 E-value=37 Score=27.90 Aligned_cols=29 Identities=14% Similarity=0.053 Sum_probs=23.6
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.|..+.+||..+ |-|...++++.....++
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466899999999 99999999988655543
No 101
>PRK04217 hypothetical protein; Provisional
Probab=41.17 E-value=46 Score=26.46 Aligned_cols=43 Identities=16% Similarity=0.018 Sum_probs=34.2
Q ss_pred CCChHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHHHHhhc
Q 025351 92 PFSPAEDDTILAAHARFGNRWATIARLLPGRTDNAVKNHWNSTLK 136 (254)
Q Consensus 92 ~WT~EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk 136 (254)
.-|++| ..++.++...|-...+||+.+ |-+...|+.+++...+
T Consensus 42 ~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArk 84 (110)
T PRK04217 42 FMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARK 84 (110)
T ss_pred cCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 455555 677777777888999999999 9999999999965433
No 102
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=39.89 E-value=47 Score=26.57 Aligned_cols=30 Identities=20% Similarity=0.189 Sum_probs=24.5
Q ss_pred hcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 107 RFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 107 ~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
..|-.-.+||..| |-+...|+++....+++
T Consensus 120 ~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 120 WEDMDVAETAAAM-GCSEGSVKTHCSRATHA 149 (161)
T ss_pred HhcCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466899999999 99999999998765554
No 103
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=39.88 E-value=47 Score=27.22 Aligned_cols=32 Identities=25% Similarity=0.194 Sum_probs=26.1
Q ss_pred HhcCCChhhhhhcCCCCCHHHHHHHHHHhhccc
Q 025351 106 ARFGNRWATIARLLPGRTDNAVKNHWNSTLKRR 138 (254)
Q Consensus 106 ~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~~ 138 (254)
.-.|....+||..+ |-+...|+.+...-+++-
T Consensus 132 ~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 132 RLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 34577899999999 999999999987766653
No 104
>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=39.50 E-value=53 Score=21.02 Aligned_cols=34 Identities=29% Similarity=0.355 Sum_probs=26.5
Q ss_pred HHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHH
Q 025351 97 EDDTILAAHARFGNRWATIARLLPGRTDNAVKNHW 131 (254)
Q Consensus 97 ED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw 131 (254)
|-..|.++...++++....|+.| |=+...+..+-
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~kl 39 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLL-GISRRTLYRKL 39 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHH
Confidence 66788999999999999999998 77777776554
No 105
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=39.00 E-value=17 Score=29.92 Aligned_cols=43 Identities=12% Similarity=0.110 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHhCCCCccccccccccCChhhhhhhccccCCCC
Q 025351 44 EEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCNQLSPS 87 (254)
Q Consensus 44 eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~~L~p~ 87 (254)
+-|.+|+.+.++.|...|..||+.+ |-+...|+.|+.+.....
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~G 51 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAG 51 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCC
Confidence 5799999999999988999999999 699999999998765443
No 106
>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=38.41 E-value=46 Score=27.06 Aligned_cols=29 Identities=21% Similarity=0.329 Sum_probs=23.3
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.|....+||..+ |-|...|+++....+++
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 466789999999 88999999988766554
No 107
>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=38.37 E-value=27 Score=29.30 Aligned_cols=45 Identities=18% Similarity=0.207 Sum_probs=32.3
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCccccccccc----cCChhhhhhhcc
Q 025351 36 RIKGPWSAEEDRILTRLVERYGPRNWSLISRYIK----GRSGKSCRLRWC 81 (254)
Q Consensus 36 ~~kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~----~Rs~~qcr~Rw~ 81 (254)
.....-|..|..-|..||++|| .|+...+.... -.|+.||+.+..
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhG-dDy~aMarD~KLN~~Q~T~~qlrrki~ 160 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHG-DDYKAMARDRKLNYMQHTPGQLRRKIR 160 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHC-ccHHHHhccCCCCcccCCHHHHHHHHH
Confidence 4456689999999999999999 57888886542 245555555443
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=38.08 E-value=65 Score=27.00 Aligned_cols=47 Identities=17% Similarity=0.141 Sum_probs=38.5
Q ss_pred CCCCCChHHHHHHHHHHHhcCCChhhhhhcC----CCCCHHHHHHHHHHhh
Q 025351 89 AHRPFSPAEDDTILAAHARFGNRWATIARLL----PGRTDNAVKNHWNSTL 135 (254)
Q Consensus 89 ~~~~WT~EED~~Ll~~v~~~G~~W~~IA~~l----~gRT~~q~k~Rw~~~l 135 (254)
....-|+.|..-|..++.+||.++...+.-. --.|..||+.+...+.
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~k 163 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKYK 163 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHhc
Confidence 4457889999999999999999999998732 2489999999886653
No 109
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=37.63 E-value=49 Score=27.65 Aligned_cols=30 Identities=20% Similarity=0.075 Sum_probs=24.1
Q ss_pred hcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 107 RFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 107 ~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
..|....+||..| |-+...|+++....+++
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 4577899999999 99999999988655443
No 110
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=37.60 E-value=52 Score=26.80 Aligned_cols=29 Identities=31% Similarity=0.297 Sum_probs=23.6
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.|..-.+||..| |.+...|+.|....++.
T Consensus 133 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 161 (173)
T PRK09645 133 RGWSTAQIAADL-GIPEGTVKSRLHYALRA 161 (173)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 466789999999 99999999998766554
No 111
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=37.57 E-value=52 Score=27.33 Aligned_cols=30 Identities=27% Similarity=0.245 Sum_probs=24.1
Q ss_pred hcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 107 RFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 107 ~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
..|....+||..| |-+...|+.+....+++
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 3467899999999 99999999988765554
No 112
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=37.15 E-value=19 Score=25.97 Aligned_cols=23 Identities=43% Similarity=0.774 Sum_probs=18.8
Q ss_pred HHHHHHHHHHhCCCCccccccccccC
Q 025351 46 DRILTRLVERYGPRNWSLISRYIKGR 71 (254)
Q Consensus 46 D~~L~~lV~~~g~~nW~~Ia~~l~~R 71 (254)
+.+|.+||+.|| |..+++.+.-|
T Consensus 12 e~il~~Lv~~yG---W~~L~~~i~i~ 34 (64)
T PF09905_consen 12 ETILTELVEHYG---WEELGERININ 34 (64)
T ss_dssp HHHHHHHHHHT----HHHHHHHTTSS
T ss_pred HHHHHHHHHHhC---HHHHHhhcccc
Confidence 578999999999 99999988544
No 113
>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=37.14 E-value=53 Score=27.57 Aligned_cols=32 Identities=9% Similarity=-0.027 Sum_probs=25.5
Q ss_pred HHhcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 105 HARFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 105 v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
+.-.|....+||..| |-+...|+.|....+++
T Consensus 143 ~~~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 143 REVLGFESDEICQEL-EISTSNCHVLLYRARLS 174 (188)
T ss_pred HHHhCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 334567899999999 99999999998666554
No 114
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=36.96 E-value=40 Score=27.77 Aligned_cols=29 Identities=17% Similarity=0.208 Sum_probs=23.3
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.|....+||..+ |=|...|+++....+++
T Consensus 153 ~~~s~~EIA~~l-gis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 153 EGLSYEDIARIM-DCPVGTVRSRIFRAREA 181 (190)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 356789999999 88999999988665554
No 115
>PRK13858 type IV secretion system T-DNA border endonuclease VirD1; Provisional
Probab=36.86 E-value=67 Score=26.98 Aligned_cols=82 Identities=10% Similarity=0.020 Sum_probs=58.5
Q ss_pred CcCccccCCCCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhccccCCCCCCCCCCChHHHHHHHHH
Q 025351 25 NKTRRATHKPERIKGPWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCNQLSPSVAHRPFSPAEDDTILAA 104 (254)
Q Consensus 25 ~k~r~~~~~p~~~kg~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~~L~p~~~~~~WT~EED~~Ll~~ 104 (254)
.+.......+.+..-+.|++|-..|..-....|.. .++.-.. |-.+-. +.+.-..-|.|+-..|+..
T Consensus 15 ~~~~~~~~~~kvVsvRLTe~Ey~~L~~rA~~aGlS-~SEfIRq--------Ai~~~~----g~V~v~r~T~e~~~~lir~ 81 (147)
T PRK13858 15 RRESAKVEGFKVVSTRLRSAEYESFSAQARLLGLS-DSMAIRV--------AVRRIG----GFLEIDAETREKMEAILQS 81 (147)
T ss_pred cccCccccCCeEEEEecCHHHHHHHHHHHHHcCCC-HHHHHHH--------HHHhcC----CeEeecccCHHHHHHHHHH
Confidence 33444455778889999999999999999999953 3333221 111100 2333357788888889999
Q ss_pred HHhcCCChhhhhhcC
Q 025351 105 HARFGNRWATIARLL 119 (254)
Q Consensus 105 v~~~G~~W~~IA~~l 119 (254)
+...|++-.+||+++
T Consensus 82 l~gianNLNQLAr~a 96 (147)
T PRK13858 82 IGTLSSNIAALLSAY 96 (147)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999999987
No 116
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=36.81 E-value=54 Score=27.07 Aligned_cols=29 Identities=21% Similarity=0.163 Sum_probs=23.6
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.|....+||..| |-+...|+.+....+++
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 466789999999 99999999988765554
No 117
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=36.37 E-value=57 Score=26.21 Aligned_cols=30 Identities=13% Similarity=-0.076 Sum_probs=23.9
Q ss_pred hcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 107 RFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 107 ~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
..|..-.+||..+ |-+...|++|....+++
T Consensus 120 ~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (160)
T PRK09642 120 LEEKSYQEIALQE-KIEVKTVEMKLYRARKW 149 (160)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466789999999 99999999988655543
No 118
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=35.91 E-value=79 Score=28.67 Aligned_cols=29 Identities=28% Similarity=0.337 Sum_probs=23.7
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
+|..-.+||..| |.+...|++|....+++
T Consensus 157 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 185 (324)
T TIGR02960 157 LGWRAAETAELL-GTSTASVNSALQRARAT 185 (324)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466789999999 99999999998655543
No 119
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=35.76 E-value=60 Score=27.35 Aligned_cols=34 Identities=18% Similarity=0.181 Sum_probs=26.2
Q ss_pred HHHHHHhcCCChhhhhhcCCCCCHHHHHHHHHHhh
Q 025351 101 ILAAHARFGNRWATIARLLPGRTDNAVKNHWNSTL 135 (254)
Q Consensus 101 Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~l 135 (254)
++.+..-.|-.+.+||..+ |-+...++.+|...-
T Consensus 143 ~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR 176 (185)
T PF07638_consen 143 VVELRFFEGLSVEEIAERL-GISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 3333344577899999999 999999999996543
No 120
>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=35.45 E-value=39 Score=25.27 Aligned_cols=31 Identities=19% Similarity=0.473 Sum_probs=24.6
Q ss_pred HHHHHHHHHhcCCChhhhhhcCCCCCHHHHHH
Q 025351 98 DDTILAAHARFGNRWATIARLLPGRTDNAVKN 129 (254)
Q Consensus 98 D~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~ 129 (254)
|..|.......|.+|..+|+.| |=+...|..
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 4566777788999999999999 777777644
No 121
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=35.17 E-value=50 Score=27.09 Aligned_cols=29 Identities=14% Similarity=0.053 Sum_probs=22.8
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.|....+||..| |-+...|+++.....++
T Consensus 151 ~g~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T TIGR02948 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 356789999999 88999999988655443
No 122
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=34.99 E-value=61 Score=26.98 Aligned_cols=30 Identities=13% Similarity=0.205 Sum_probs=24.1
Q ss_pred hcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 107 RFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 107 ~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
..|-...+||..| |-|...|+++....+++
T Consensus 145 ~~~~s~~eIA~~l-gis~~tV~~~l~Rar~~ 174 (189)
T PRK12515 145 YHEKSVEEVGEIV-GIPESTVKTRMFYARKK 174 (189)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3466899999999 88999999998665543
No 123
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=34.86 E-value=59 Score=27.27 Aligned_cols=29 Identities=3% Similarity=-0.112 Sum_probs=24.0
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.|-...+||..| |-+...|+.|....+++
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 466899999999 99999999998665543
No 124
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=34.80 E-value=54 Score=27.29 Aligned_cols=28 Identities=14% Similarity=0.178 Sum_probs=22.6
Q ss_pred CCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 109 GNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 109 G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
|....+||..+ |-+...|+++....+++
T Consensus 154 g~s~~eIA~~l-gis~~tv~~~l~Rar~~ 181 (193)
T PRK11923 154 GLSYEDIASVM-QCPVGTVRSRIFRAREA 181 (193)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 56789999999 88999999998665544
No 125
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=34.31 E-value=65 Score=26.69 Aligned_cols=32 Identities=19% Similarity=0.023 Sum_probs=26.5
Q ss_pred hcCCChhhhhhcCCCCCHHHHHHHHHHhhcccc
Q 025351 107 RFGNRWATIARLLPGRTDNAVKNHWNSTLKRRT 139 (254)
Q Consensus 107 ~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~~~ 139 (254)
..|....+||..| |-+...|+.|....+..-.
T Consensus 141 ~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~ 172 (178)
T PRK12529 141 LDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCL 172 (178)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 3467899999999 9999999999987766544
No 126
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=33.71 E-value=70 Score=25.69 Aligned_cols=29 Identities=28% Similarity=0.323 Sum_probs=23.3
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.|..-.+||..| |-+...|+.|....++.
T Consensus 120 ~~~s~~eIA~~l-gis~~tv~~~l~ra~~~ 148 (159)
T PRK12527 120 EGLSHQQIAEHL-GISRSLVEKHIVNAMKH 148 (159)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 455789999999 99999999998765554
No 127
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=33.56 E-value=66 Score=27.00 Aligned_cols=29 Identities=10% Similarity=0.092 Sum_probs=23.3
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.|-...+||..| |-+...|+.|....+++
T Consensus 156 eg~s~~EIA~~l-gis~~tVk~rl~ra~~~ 184 (194)
T PRK12531 156 EELPHQQVAEMF-DIPLGTVKSRLRLAVEK 184 (194)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 466789999999 99999999988665554
No 128
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=33.45 E-value=1.1e+02 Score=27.53 Aligned_cols=31 Identities=29% Similarity=0.382 Sum_probs=25.1
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcccc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKRRT 139 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~~~ 139 (254)
+|..-.+||..| |.+...|+++.....++-.
T Consensus 130 ~g~s~~EIA~~l-g~s~~tVk~~l~RAr~~Lr 160 (293)
T PRK09636 130 FGVPFDEIASTL-GRSPAACRQLASRARKHVR 160 (293)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 466789999999 9999999999876655433
No 129
>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=33.41 E-value=46 Score=24.16 Aligned_cols=29 Identities=21% Similarity=0.491 Sum_probs=21.0
Q ss_pred HHHHHHHHHh-cCCChhhhhhcCCCCCHHHH
Q 025351 98 DDTILAAHAR-FGNRWATIARLLPGRTDNAV 127 (254)
Q Consensus 98 D~~Ll~~v~~-~G~~W~~IA~~l~gRT~~q~ 127 (254)
+..|..+... .|++|..+|+.| |=+..+|
T Consensus 5 ~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i 34 (88)
T smart00005 5 REKLAKLLDHPLGLDWRELARKL-GLSEADI 34 (88)
T ss_pred HHHHHHHHcCccchHHHHHHHHc-CCCHHHH
Confidence 4456666666 799999999999 5555554
No 130
>PF04844 Ovate: Transcriptional repressor, ovate; InterPro: IPR006458 This group of sequences contain an uncharacterised domain of about 70 residues found exclusively in plants, generally toward the C terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana (Mouse-ear cress). Other regions of these proteins tend to consist largely of low-complexity sequence. Function is not known.
Probab=32.69 E-value=38 Score=24.05 Aligned_cols=15 Identities=20% Similarity=0.255 Sum_probs=12.6
Q ss_pred CchHHHHHHHHHHHH
Q 025351 223 LPAGFWDAMRGVIAR 237 (254)
Q Consensus 223 ~~~~~~~~~~~~i~~ 237 (254)
+-.+|...|+|||..
T Consensus 4 P~~DFr~SM~EMI~~ 18 (59)
T PF04844_consen 4 PYEDFRESMVEMIEE 18 (59)
T ss_pred HHHHHHHHHHHHHHH
Confidence 357899999999974
No 131
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=32.36 E-value=73 Score=26.13 Aligned_cols=29 Identities=28% Similarity=0.354 Sum_probs=23.8
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.|....+||..+ |-+...|+.|....++.
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 177 (183)
T TIGR02999 149 AGLTVEEIAELL-GVSVRTVERDWRFARAW 177 (183)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 466799999999 99999999998765543
No 132
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=31.72 E-value=49 Score=21.48 Aligned_cols=36 Identities=31% Similarity=0.417 Sum_probs=18.3
Q ss_pred CCChHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHH
Q 025351 92 PFSPAEDDTILAAHARFGNRWATIARLLPGRTDNAVKN 129 (254)
Q Consensus 92 ~WT~EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~ 129 (254)
.+|.+|=..|..+ ..-|..-.+||+.| ||+...|.+
T Consensus 4 ~Lt~~eR~~I~~l-~~~G~s~~~IA~~l-g~s~sTV~r 39 (44)
T PF13936_consen 4 HLTPEERNQIEAL-LEQGMSIREIAKRL-GRSRSTVSR 39 (44)
T ss_dssp --------HHHHH-HCS---HHHHHHHT-T--HHHHHH
T ss_pred chhhhHHHHHHHH-HHcCCCHHHHHHHH-CcCcHHHHH
Confidence 4677776666655 46788899999999 999988854
No 133
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=31.71 E-value=71 Score=26.81 Aligned_cols=29 Identities=17% Similarity=0.027 Sum_probs=23.2
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.|-.+.+||..| |=+...|+++....+++
T Consensus 151 ~g~s~~eIA~~l-gis~~tV~~~l~Ra~~~ 179 (196)
T PRK12524 151 EGLSNPEIAEVM-EIGVEAVESLTARGKRA 179 (196)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 466899999999 98999998888655444
No 134
>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=31.13 E-value=51 Score=24.84 Aligned_cols=28 Identities=21% Similarity=0.354 Sum_probs=21.6
Q ss_pred HHHHHHHHHhcCCChhhhhhcCCCCCHHH
Q 025351 98 DDTILAAHARFGNRWATIARLLPGRTDNA 126 (254)
Q Consensus 98 D~~Ll~~v~~~G~~W~~IA~~l~gRT~~q 126 (254)
|..|.......|..|.++|+.| |=+..+
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L-~vs~~d 31 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL-QFSVED 31 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc-CCCHHH
Confidence 5567777888999999999988 544443
No 135
>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=30.99 E-value=31 Score=29.20 Aligned_cols=40 Identities=23% Similarity=0.179 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhcc
Q 025351 40 PWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWC 81 (254)
Q Consensus 40 ~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~ 81 (254)
.||.|+.++|.+|....- .-.+||..|.+.|...+.-+.+
T Consensus 2 ~Wtde~~~~L~~lw~~G~--SasqIA~~lg~vsRnAViGk~h 41 (162)
T PF07750_consen 2 SWTDERVERLRKLWAEGL--SASQIARQLGGVSRNAVIGKAH 41 (162)
T ss_pred CCCHHHHHHHHHHHHcCC--CHHHHHHHhCCcchhhhhhhhh
Confidence 499999999999997643 3789999998666665555443
No 136
>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=30.98 E-value=52 Score=24.60 Aligned_cols=23 Identities=26% Similarity=0.543 Sum_probs=19.3
Q ss_pred HHHhcCCChhhhhhcCCCCCHHHH
Q 025351 104 AHARFGNRWATIARLLPGRTDNAV 127 (254)
Q Consensus 104 ~v~~~G~~W~~IA~~l~gRT~~q~ 127 (254)
+....|..|..+|+.| |=+..+|
T Consensus 13 ia~~iG~~Wk~Lar~L-Gls~~dI 35 (86)
T cd08318 13 FANKLGEDWKTLAPHL-EMKDKEI 35 (86)
T ss_pred HHHHHhhhHHHHHHHc-CCCHHHH
Confidence 5567799999999999 8787777
No 137
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=30.77 E-value=20 Score=29.80 Aligned_cols=45 Identities=18% Similarity=0.151 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHhCCCCccccccccccCChhhhhhhccccCCCCC
Q 025351 43 AEEDRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCNQLSPSV 88 (254)
Q Consensus 43 ~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~~L~p~~ 88 (254)
.+-|.+|+.+.++.|...|..||+.+ |-+...|+.|+.+..+-.+
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 46789999999999988999999998 6899999999987665443
No 138
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=30.72 E-value=1.1e+02 Score=27.95 Aligned_cols=32 Identities=22% Similarity=0.197 Sum_probs=25.3
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhccccc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKRRTR 140 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~ 140 (254)
.|..-.+||..| |-+...|+.|....+++-..
T Consensus 168 ~g~s~~EIA~~l-gis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 168 LGWSAAEVAELL-DTSVAAVNSALQRARATLAE 199 (339)
T ss_pred hCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHhh
Confidence 456789999999 99999999998766655443
No 139
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=30.49 E-value=79 Score=26.13 Aligned_cols=30 Identities=33% Similarity=0.253 Sum_probs=24.5
Q ss_pred hcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 107 RFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 107 ~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
..|....+||..| |.+...|+++-...+++
T Consensus 143 ~~g~s~~EIA~~l-~is~~tV~~~l~rar~~ 172 (181)
T PRK12536 143 LEGLSVAETAQLT-GLSESAVKVGIHRGLKA 172 (181)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 4567899999999 99999999998665544
No 140
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=30.41 E-value=84 Score=24.88 Aligned_cols=29 Identities=21% Similarity=0.184 Sum_probs=22.7
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.|....+||..+ |-+...|+++-...+++
T Consensus 121 ~~~s~~EIA~~l-~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 121 VGKTMGEIALET-EMTYYQVRWIYRQALEK 149 (154)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355788999999 99999999887665554
No 141
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=30.11 E-value=82 Score=25.31 Aligned_cols=29 Identities=34% Similarity=0.391 Sum_probs=22.9
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.|....+||..| |-+...|+++....+++
T Consensus 137 ~g~s~~eIA~~l-~is~~tv~~~l~ra~~~ 165 (170)
T TIGR02952 137 QNLPIAEVARIL-GKTEGAVKILQFRAIKK 165 (170)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 366789999999 99999999888655543
No 142
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=29.87 E-value=79 Score=25.27 Aligned_cols=47 Identities=15% Similarity=0.049 Sum_probs=39.1
Q ss_pred hHHHHHHHHHHHhcCC-ChhhhhhcCCCCCHHHHHHHHHHhhcccccCC
Q 025351 95 PAEDDTILAAHARFGN-RWATIARLLPGRTDNAVKNHWNSTLKRRTREH 142 (254)
Q Consensus 95 ~EED~~Ll~~v~~~G~-~W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~~~ 142 (254)
.+-|..||++...-+. .+..||+.+ |-+...|.+|=+.+.+....++
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~GiI~~ 54 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGVIKG 54 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCceee
Confidence 3557888888887774 699999999 9999999999999888875544
No 143
>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=29.64 E-value=94 Score=24.61 Aligned_cols=47 Identities=19% Similarity=0.357 Sum_probs=32.3
Q ss_pred CCChHHHHHHHHHHHhc------------CC-C------------------hhhhhhcCCCCCHHHHHHHHHHhhccc
Q 025351 92 PFSPAEDDTILAAHARF------------GN-R------------------WATIARLLPGRTDNAVKNHWNSTLKRR 138 (254)
Q Consensus 92 ~WT~EED~~Ll~~v~~~------------G~-~------------------W~~IA~~l~gRT~~q~k~Rw~~~lk~~ 138 (254)
.||++||-.|...|..| |. . ....+...|..|..+=|+||+..+...
T Consensus 1 kfTA~dDY~Lc~~i~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~fF~~~~~~~p~HT~~sWRDR~RKfv~~~ 78 (105)
T PF09197_consen 1 KFTADDDYALCKAIKKQFYRDIYQKDPDTGSSLISDGDSKEFIPKRDMRSFFKDLARKNPRHTENSWRDRYRKFVSEY 78 (105)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHSB-TTSS-B----------------TTHHHHHHHHTTTS-HHHHHHHHHHTHHHH
T ss_pred CCChHHHHHHHHHHHHHHHHHHHhhCcccccccccCCCccccccchhhHHHHHHHHHcCCccchhHHHHHHHHHHHHc
Confidence 37999999999988654 11 0 445667789999999999998777653
No 144
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=29.54 E-value=70 Score=26.26 Aligned_cols=29 Identities=24% Similarity=0.250 Sum_probs=23.8
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.|....+||..+ |-+...|+++....++.
T Consensus 134 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 162 (172)
T PRK09651 134 DGLTYSEIAHKL-GVSVSSVKKYVAKATEH 162 (172)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 356799999999 99999999998766554
No 145
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=29.45 E-value=78 Score=26.42 Aligned_cols=30 Identities=13% Similarity=0.181 Sum_probs=24.3
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhccc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKRR 138 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~~ 138 (254)
.|-...+||..| |-+...|+.+....+++-
T Consensus 145 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~L 174 (185)
T PRK09649 145 LGLSYADAAAVC-GCPVGTIRSRVARARDAL 174 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 456789999999 999999999996665543
No 146
>PRK00118 putative DNA-binding protein; Validated
Probab=29.40 E-value=94 Score=24.43 Aligned_cols=41 Identities=15% Similarity=0.047 Sum_probs=32.8
Q ss_pred hHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHHHHhhc
Q 025351 95 PAEDDTILAAHARFGNRWATIARLLPGRTDNAVKNHWNSTLK 136 (254)
Q Consensus 95 ~EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk 136 (254)
++.+..++.+....|....+||..+ |-|...|+.+.....+
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 4566777778778889999999999 9999999888755443
No 147
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=29.15 E-value=84 Score=25.74 Aligned_cols=28 Identities=14% Similarity=0.200 Sum_probs=23.0
Q ss_pred CCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 109 GNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 109 G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
|..-.+||..| |.+...|+.+....+++
T Consensus 145 g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 172 (179)
T PRK12514 145 GLSYKELAERH-DVPLNTMRTWLRRSLLK 172 (179)
T ss_pred CCCHHHHHHHH-CCChHHHHHHHHHHHHH
Confidence 66789999999 99999999988665544
No 148
>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=29.05 E-value=51 Score=24.81 Aligned_cols=28 Identities=25% Similarity=0.544 Sum_probs=21.9
Q ss_pred HHHHHHhcCCChhhhhhcCCCCCHHHHHH
Q 025351 101 ILAAHARFGNRWATIARLLPGRTDNAVKN 129 (254)
Q Consensus 101 Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~ 129 (254)
|-.+....|.+|..+|+.| |=+..+|..
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 4445577899999999999 878777754
No 149
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=29.01 E-value=85 Score=26.38 Aligned_cols=31 Identities=19% Similarity=0.258 Sum_probs=24.4
Q ss_pred HhcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 106 ARFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 106 ~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
...|....+||..| |-+...|+.|-...+++
T Consensus 129 ~~~g~s~~EIA~~L-gis~~tVk~~l~Rar~~ 159 (187)
T PRK12516 129 GASGFAYEEAAEIC-GCAVGTIKSRVNRARQR 159 (187)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 33467899999999 99999999988655543
No 150
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=28.83 E-value=93 Score=25.24 Aligned_cols=30 Identities=17% Similarity=0.215 Sum_probs=23.8
Q ss_pred hcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 107 RFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 107 ~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
..|-...+||..+ |-+...|+++-...+++
T Consensus 126 ~~g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 155 (164)
T PRK12547 126 ASGFSYEDAAAIC-GCAVGTIKSRVSRARNR 155 (164)
T ss_pred HcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3466789999999 99999999988665554
No 151
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=28.82 E-value=94 Score=24.98 Aligned_cols=29 Identities=28% Similarity=0.185 Sum_probs=23.8
Q ss_pred hcCCChhhhhhcCCCCCHHHHHHHHHHhhc
Q 025351 107 RFGNRWATIARLLPGRTDNAVKNHWNSTLK 136 (254)
Q Consensus 107 ~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk 136 (254)
-.|....+||..+ |-+...|+.|....++
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 3467899999999 9999999998866554
No 152
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=28.65 E-value=80 Score=26.40 Aligned_cols=30 Identities=10% Similarity=0.105 Sum_probs=23.8
Q ss_pred hcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 107 RFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 107 ~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
..|..-.+||..| |-+...|+.|....++.
T Consensus 150 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 179 (195)
T PRK12532 150 ILGFSSDEIQQMC-GISTSNYHTIMHRARES 179 (195)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466789999999 99999999988665443
No 153
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=28.48 E-value=88 Score=25.89 Aligned_cols=30 Identities=20% Similarity=0.444 Sum_probs=24.2
Q ss_pred hcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 107 RFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 107 ~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
-.|-...+||..| |-+...|+++....+++
T Consensus 136 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 165 (185)
T PRK12542 136 FYNLTYQEISSVM-GITEANVRKQFERARKR 165 (185)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466889999999 99999999988655554
No 154
>cd08312 Death_MyD88 Death domain of Myeloid Differentation primary response protein MyD88. Death Domain (DD) of Myeloid Differentiation primary response protein 88 (MyD88). MyD88 is an adaptor protein involved in interleukin-1 receptor (IL-1R)- and Toll-like receptor (TLR)-induced activation of nuclear factor-kappaB (NF-kB) and mitogen activated protein kinase pathways that lead to the induction of proinflammatory cytokines. It is a key component in the signaling pathway of pathogen recognition in the innate immune system. MyD88 contains an N-terminal DD and a C-terminal Toll/IL-1 Receptor (TIR) homology domain that mediates interaction with TLRs and IL-1R. 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
Probab=27.68 E-value=36 Score=25.13 Aligned_cols=22 Identities=14% Similarity=0.330 Sum_probs=17.0
Q ss_pred HhcCCChhhhhhcCCCCCHHHHH
Q 025351 106 ARFGNRWATIARLLPGRTDNAVK 128 (254)
Q Consensus 106 ~~~G~~W~~IA~~l~gRT~~q~k 128 (254)
..+|++|..+|..| |-+...|+
T Consensus 13 ~~~g~DWr~LA~~L-g~~~~~I~ 34 (79)
T cd08312 13 RVVAADWTALAEEM-GFEYLEIR 34 (79)
T ss_pred CCcccCHHHHHHHc-CCCHHHHH
Confidence 34789999999999 66665554
No 155
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=27.67 E-value=95 Score=25.56 Aligned_cols=29 Identities=28% Similarity=0.295 Sum_probs=23.1
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.|..-.+||..+ |-+...|+.+.+..+++
T Consensus 150 ~~~s~~eIA~~l-gis~~~V~~~l~ra~~~ 178 (186)
T PRK13919 150 QGYTHREAAQLL-GLPLGTLKTRARRALSR 178 (186)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 355788999999 99999999988766554
No 156
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=27.55 E-value=92 Score=26.41 Aligned_cols=28 Identities=14% Similarity=-0.034 Sum_probs=22.8
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLK 136 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk 136 (254)
.|..-.+||..| |.+...|+.|....++
T Consensus 154 eg~s~~EIA~~l-gis~~tVk~~l~RAr~ 181 (201)
T PRK12545 154 LDFEIDDICTEL-TLTANHCSVLLYRART 181 (201)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 456789999999 9999999998865444
No 157
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=27.39 E-value=34 Score=27.16 Aligned_cols=28 Identities=25% Similarity=0.192 Sum_probs=22.9
Q ss_pred CCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 109 GNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 109 G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
|-.+.+||..| |=+...|+++.....++
T Consensus 121 g~s~~eIA~~l-gis~~tv~~~l~Ra~~~ 148 (154)
T TIGR02950 121 EFSYKEIAELL-NLSLAKVKSNLFRARKE 148 (154)
T ss_pred cCcHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 45799999999 99999999998765543
No 158
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=27.09 E-value=91 Score=24.96 Aligned_cols=38 Identities=21% Similarity=0.189 Sum_probs=27.5
Q ss_pred HHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 99 DTILAAHARFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 99 ~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
..++.+..-.|-.-.+||..| |-+...|+++....+++
T Consensus 116 r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~ra~~~ 153 (162)
T TIGR02983 116 RAVVVLRYYEDLSEAQVAEAL-GISVGTVKSRLSRALAR 153 (162)
T ss_pred HHHhhhHHHhcCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 334444444567788999999 99999999988766554
No 159
>PF09650 PHA_gran_rgn: Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn); InterPro: IPR013433 Proteins in this entry are encoded by genes involved in either polyhydroxyalkanoic acid (PHA) biosynthesis or utilisation, including proteins at found at the surface of PHA granules. These proteins have so far been predominantly found in the Pseudomonadales, Xanthomonadales, and Vibrionales, all of which belong to the Gammaproteobacteria.
Probab=26.77 E-value=75 Score=23.98 Aligned_cols=22 Identities=14% Similarity=0.311 Sum_probs=19.0
Q ss_pred hHHHHHHHHHHHHHHHHHHhhc
Q 025351 225 AGFWDAMRGVIAREVRDYMSST 246 (254)
Q Consensus 225 ~~~~~~~~~~i~~ev~~~~~~~ 246 (254)
+=+|..|.++|..||+.++...
T Consensus 65 g~Ll~~f~~~Ie~~I~~~Ld~~ 86 (87)
T PF09650_consen 65 GFLLSPFKGKIEQEIEKNLDKL 86 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHhh
Confidence 5678999999999999998765
No 160
>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=26.38 E-value=1e+02 Score=21.51 Aligned_cols=46 Identities=20% Similarity=0.338 Sum_probs=32.4
Q ss_pred CCCCCChHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHHHHhhc
Q 025351 89 AHRPFSPAEDDTILAAHARFGNRWATIARLLPGRTDNAVKNHWNSTLK 136 (254)
Q Consensus 89 ~~~~WT~EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk 136 (254)
.+..||+|+-..++..+..-|..-..||+.+ |=+..++.+ |...++
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~g~sv~~va~~~-gi~~~~l~~-W~~~~~ 48 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLESGESVSEVAREY-GISPSTLYN-WRKQYR 48 (76)
T ss_dssp SS----HHHHHHHHHHHHHHHCHHHHHHHHH-TS-HHHHHH-HHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHCCCceEeeeccc-ccccccccH-HHHHHh
Confidence 3468999999999999988888999999988 556666654 766655
No 161
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=26.35 E-value=1.7e+02 Score=26.75 Aligned_cols=50 Identities=14% Similarity=0.300 Sum_probs=32.6
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcccccCCC-CCCChhHHHHHHHHh
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKRRTREHP-VQMQPHQQQQLMDSV 158 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~~~~-~~~~~~e~~~L~~~~ 158 (254)
+|-.-.+||..| |.|...|+.+.....++-....+ ....+++.+.+.+.+
T Consensus 133 ~g~s~~EIA~~L-gis~~tVr~~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~f 183 (290)
T PRK09635 133 FGLPYQQIATTI-GSQASTCRQLAHRARRKINESRIAASVEPAQHRVVTRAF 183 (290)
T ss_pred hCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHhhCCCCCCChHHHHHHHHHH
Confidence 567889999999 99999999988655554333222 223444555555543
No 162
>PRK13987 cell division topological specificity factor MinE; Provisional
Probab=26.28 E-value=74 Score=24.49 Aligned_cols=23 Identities=9% Similarity=0.343 Sum_probs=21.2
Q ss_pred CCchHHHHHHHHHHHHHHHHHHh
Q 025351 222 SLPAGFWDAMRGVIAREVRDYMS 244 (254)
Q Consensus 222 ~~~~~~~~~~~~~i~~ev~~~~~ 244 (254)
..+++||..|++-|-.-|+.||.
T Consensus 31 ~~sp~~l~~lk~eIl~VI~kYv~ 53 (91)
T PRK13987 31 DISPDVLEMIKEDILKVISKYVE 53 (91)
T ss_pred CCCHHHHHHHHHHHHHHHHHhee
Confidence 46899999999999999999996
No 163
>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=25.33 E-value=68 Score=24.04 Aligned_cols=26 Identities=27% Similarity=0.516 Sum_probs=20.8
Q ss_pred HHHHHHHHhcCCChhhhhhcCCCCCHH
Q 025351 99 DTILAAHARFGNRWATIARLLPGRTDN 125 (254)
Q Consensus 99 ~~Ll~~v~~~G~~W~~IA~~l~gRT~~ 125 (254)
..|..+..+.|..|..+++.| |=+..
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L-Glse~ 28 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL-GLSYR 28 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc-CCCHH
Confidence 457888899999999999988 54444
No 164
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=25.09 E-value=1e+02 Score=25.63 Aligned_cols=30 Identities=30% Similarity=0.441 Sum_probs=23.4
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhccc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKRR 138 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~~ 138 (254)
.|..-.+||..| |-|...|+++-...+++-
T Consensus 146 ~g~s~~EIAe~l-gis~~~V~~~l~Ra~~~L 175 (189)
T PRK06811 146 LGEKIEEIAKKL-GLTRSAIDNRLSRGRKKL 175 (189)
T ss_pred ccCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 356778999999 999999999886665553
No 165
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=25.05 E-value=1.1e+02 Score=24.96 Aligned_cols=30 Identities=30% Similarity=0.444 Sum_probs=23.4
Q ss_pred hcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 107 RFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 107 ~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
-.|....+||..+ |-|...|+.+....+++
T Consensus 154 ~~g~s~~eIA~~l-gis~~~v~~~l~Ra~~~ 183 (189)
T TIGR02984 154 LEGLSFAEVAERM-DRSEGAVSMLWVRGLAR 183 (189)
T ss_pred hcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3466789999999 99999998888665544
No 166
>PF05678 VQ: VQ motif; InterPro: IPR008889 This short motif is found in a variety of plant proteins. These proteins vary greatly in length and are mostly composed of low complexity regions. They all conserve a short motif FXhVQChTG, where X is any amino acid and h is a hydrophobic amino acid. The function of this motif is uncertain, however one protein in this family has been found to bind the SigA sigma factor Q9LDH1 from SWISSPROT. It would seem plausible that this motif is needed for this activity and that this whole family might be involved in modulating plastid sigma factors.
Probab=24.99 E-value=50 Score=20.37 Aligned_cols=12 Identities=17% Similarity=0.360 Sum_probs=10.0
Q ss_pred CchHHHHHHHHH
Q 025351 223 LPAGFWDAMRGV 234 (254)
Q Consensus 223 ~~~~~~~~~~~~ 234 (254)
-..+|++|+|++
T Consensus 11 d~~~Fr~lVQ~L 22 (31)
T PF05678_consen 11 DPSNFRALVQRL 22 (31)
T ss_pred CHHHHHHHHHHh
Confidence 358999999986
No 167
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=24.77 E-value=1.1e+02 Score=25.35 Aligned_cols=29 Identities=14% Similarity=-0.076 Sum_probs=23.3
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.|..-.+||..| |-+...|++|....+++
T Consensus 146 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 174 (191)
T PRK12520 146 LELETEEICQEL-QITATNAWVLLYRARMR 174 (191)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466789999999 99999999998665544
No 168
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=24.66 E-value=1.1e+02 Score=25.23 Aligned_cols=29 Identities=34% Similarity=0.310 Sum_probs=23.3
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.|..-.+||..+ |-+...|+++....+++
T Consensus 148 ~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 176 (182)
T PRK12537 148 DGCSHAEIAQRL-GAPLGTVKAWIKRSLKA 176 (182)
T ss_pred cCCCHHHHHHHH-CCChhhHHHHHHHHHHH
Confidence 456788899999 89999999988766654
No 169
>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=24.60 E-value=47 Score=24.07 Aligned_cols=19 Identities=37% Similarity=0.791 Sum_probs=14.9
Q ss_pred HHHHHHHHHhCCCCcccccc
Q 025351 47 RILTRLVERYGPRNWSLISR 66 (254)
Q Consensus 47 ~~L~~lV~~~g~~nW~~Ia~ 66 (254)
.-|.+|++.|| +||..|-.
T Consensus 30 ~vl~~LL~lY~-~nW~lIEe 48 (65)
T PF10440_consen 30 PVLKNLLKLYD-GNWELIEE 48 (65)
T ss_pred HHHHHHHHHHc-CCchhhhc
Confidence 35788889998 56999864
No 170
>TIGR01568 A_thal_3678 uncharacterized plant-specific domain TIGR01568. This model describes an uncharacterized domain of about 70 residues found exclusively in plants, generally toward the C-terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana. Other regions of these proteins tend to consist largely of low-complexity sequence.
Probab=24.45 E-value=62 Score=23.53 Aligned_cols=15 Identities=20% Similarity=0.242 Sum_probs=12.8
Q ss_pred CchHHHHHHHHHHHH
Q 025351 223 LPAGFWDAMRGVIAR 237 (254)
Q Consensus 223 ~~~~~~~~~~~~i~~ 237 (254)
+-.+|...|+|||..
T Consensus 10 Py~DFr~SM~EMI~~ 24 (66)
T TIGR01568 10 PYEDFRRSMEEMIEE 24 (66)
T ss_pred hHHHHHHHHHHHHHH
Confidence 458999999999974
No 171
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=24.25 E-value=1.1e+02 Score=25.29 Aligned_cols=28 Identities=11% Similarity=0.038 Sum_probs=20.6
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLK 136 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk 136 (254)
.|....+||..+ |-+...|+.+....++
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 356788888888 8888888887755443
No 172
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=24.18 E-value=1.1e+02 Score=25.91 Aligned_cols=31 Identities=23% Similarity=0.236 Sum_probs=24.6
Q ss_pred HhcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 106 ARFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 106 ~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
...|....+||..| |-+...|+++....+++
T Consensus 126 ~~~g~s~~EIA~~L-giS~~tVk~~l~Rar~~ 156 (188)
T PRK12546 126 GASGFSYEEAAEMC-GVAVGTVKSRANRARAR 156 (188)
T ss_pred HhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 34577899999999 99999999988665544
No 173
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=24.15 E-value=3.1e+02 Score=21.91 Aligned_cols=65 Identities=11% Similarity=0.246 Sum_probs=43.2
Q ss_pred hHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHHHHhhccccc-CCCCCCChhHHHHHHHHhhc
Q 025351 95 PAEDDTILAAHARFGNRWATIARLLPGRTDNAVKNHWNSTLKRRTR-EHPVQMQPHQQQQLMDSVDN 160 (254)
Q Consensus 95 ~EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~-~~~~~~~~~e~~~L~~~~~~ 160 (254)
.+||...+...-...++-..+++.+ |=+-..+|+|...++.+-.. ..............++.+..
T Consensus 35 ~~E~~~Fi~~Fi~~rGnlKe~e~~l-giSYPTvR~rLd~ii~~lg~~~~~~~~~~~~~~~IL~~L~~ 100 (113)
T PF09862_consen 35 SPEQLEFIKLFIKNRGNLKEMEKEL-GISYPTVRNRLDKIIEKLGYEEDEEEEEEDERKEILDKLEK 100 (113)
T ss_pred CHHHHHHHHHHHHhcCCHHHHHHHH-CCCcHHHHHHHHHHHHHhCCCCCcccccchhHHHHHHHHHc
Confidence 3455555555556666888999999 98999999999999887655 22222333444555555553
No 174
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=23.97 E-value=62 Score=28.17 Aligned_cols=28 Identities=18% Similarity=0.181 Sum_probs=22.6
Q ss_pred CCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 109 GNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 109 G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
|....+||..| |-+...|++++...+++
T Consensus 165 g~s~~EIAe~l-gis~~tVk~~l~Rar~k 192 (231)
T PRK11922 165 ELSVEETAQAL-GLPEETVKTRLHRARRL 192 (231)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 55789999999 99999999998655543
No 175
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=23.17 E-value=2e+02 Score=18.93 Aligned_cols=44 Identities=18% Similarity=0.225 Sum_probs=34.7
Q ss_pred CCCCChHHHHHHHHHHHhcCC----ChhhhhhcCCCCCHHHHHHHHHHh
Q 025351 90 HRPFSPAEDDTILAAHARFGN----RWATIARLLPGRTDNAVKNHWNST 134 (254)
Q Consensus 90 ~~~WT~EED~~Ll~~v~~~G~----~W~~IA~~l~gRT~~q~k~Rw~~~ 134 (254)
+..||+++-..|...+..... .-..||..+ |=+..+|++.|.+-
T Consensus 4 r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l-~l~~~~V~~WF~nr 51 (57)
T PF00046_consen 4 RTRFTKEQLKVLEEYFQENPYPSKEEREELAKEL-GLTERQVKNWFQNR 51 (57)
T ss_dssp SSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHH-TSSHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhccccccccccccccc-cccccccccCHHHh
Confidence 457899999999888887442 367888888 99999999987543
No 176
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=23.05 E-value=47 Score=33.05 Aligned_cols=40 Identities=25% Similarity=0.449 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccc-cccCChhhhhhhc
Q 025351 40 PWSAEEDRILTRLVERYGPRNWSLISRY-IKGRSGKSCRLRW 80 (254)
Q Consensus 40 ~WT~eED~~L~~lV~~~g~~nW~~Ia~~-l~~Rs~~qcr~Rw 80 (254)
.|+.-|-.++.+++++|| ++++.|-.. +|-++-.++.+.|
T Consensus 287 EWSasEanLFEeALeKyG-KDFndIrqdfLPWKSl~sIveyY 327 (693)
T KOG3554|consen 287 EWSASEANLFEEALEKYG-KDFNDIRQDFLPWKSLTSIVEYY 327 (693)
T ss_pred hccchhhHHHHHHHHHhc-ccHHHHHHhhcchHHHHHHHHHH
Confidence 499999999999999999 679988754 4777766665443
No 177
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=23.02 E-value=1.3e+02 Score=24.11 Aligned_cols=29 Identities=24% Similarity=0.347 Sum_probs=22.8
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.|-.-..||..| |-+...|+++....+++
T Consensus 126 ~g~s~~eIA~~l-gis~~tV~~~i~ra~~~ 154 (166)
T PRK09639 126 SGYSYKEIAEAL-GIKESSVGTTLARAKKK 154 (166)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 566788899999 89999998888655543
No 178
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=23.01 E-value=1e+02 Score=25.60 Aligned_cols=29 Identities=28% Similarity=0.201 Sum_probs=21.7
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.|..-.+||..| |-+...|+.+....+++
T Consensus 156 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 184 (194)
T PRK12519 156 EGLSQSEIAKRL-GIPLGTVKARARQGLLK 184 (194)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 355678889888 88888898887655543
No 179
>PRK01905 DNA-binding protein Fis; Provisional
Probab=22.98 E-value=1.7e+02 Score=21.25 Aligned_cols=36 Identities=17% Similarity=0.202 Sum_probs=28.3
Q ss_pred hHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHH
Q 025351 95 PAEDDTILAAHARFGNRWATIARLLPGRTDNAVKNHW 131 (254)
Q Consensus 95 ~EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw 131 (254)
.-|...|.+++..+|.++.+.|+.+ |=+...++.+.
T Consensus 36 ~~E~~~i~~aL~~~~gn~s~aAr~L-GIsrstL~rkl 71 (77)
T PRK01905 36 CVEKPLLEVVMEQAGGNQSLAAEYL-GINRNTLRKKL 71 (77)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 3466788899999999999999988 66666665554
No 180
>COG4628 Uncharacterized conserved protein [Function unknown]
Probab=22.43 E-value=71 Score=25.86 Aligned_cols=44 Identities=27% Similarity=0.624 Sum_probs=29.6
Q ss_pred HHHHHHHHHHhCCCCccccccccccCChhhhhhhccccCCCC-------CCCCCCChHHHHHH
Q 025351 46 DRILTRLVERYGPRNWSLISRYIKGRSGKSCRLRWCNQLSPS-------VAHRPFSPAEDDTI 101 (254)
Q Consensus 46 D~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qcr~Rw~~~L~p~-------~~~~~WT~EED~~L 101 (254)
+.+|.++|..|| |.-++..|+ ..|.. -+|. +++.+|..|..+.|
T Consensus 21 E~llt~Lvd~YG---Wd~L~~ri~----inCF~-----ndPSi~SSlKfLrkT~WARekvEa~ 71 (136)
T COG4628 21 ETLLTELVDFYG---WDGLATRIR----INCFH-----NDPSIKSSLKFLRKTPWAREKVEAL 71 (136)
T ss_pred HHHHHHHHHHhC---hHHHHhhce----ecccc-----CCccHHHHHHHHhcCHhHHHHHHHH
Confidence 678999999999 999998763 22221 1222 45678888776544
No 181
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=21.85 E-value=1.2e+02 Score=24.90 Aligned_cols=28 Identities=21% Similarity=0.223 Sum_probs=21.6
Q ss_pred CCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 109 GNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 109 G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
|..-.+||..| |-+...|+.|....+++
T Consensus 143 g~s~~EIA~~l-~is~~tv~~~l~Ra~~~ 170 (179)
T PRK09415 143 ELSIKEIAEVT-GVNENTVKTRLKKAKEL 170 (179)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 55678888888 77888998888666544
No 182
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=21.71 E-value=1e+02 Score=32.73 Aligned_cols=98 Identities=14% Similarity=0.266 Sum_probs=63.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccccCChhhh-------------------------------------------
Q 025351 40 PWSAEEDRILTRLVERYGPRNWSLISRYIKGRSGKSC------------------------------------------- 76 (254)
Q Consensus 40 ~WT~eED~~L~~lV~~~g~~nW~~Ia~~l~~Rs~~qc------------------------------------------- 76 (254)
.||.-+=...+.+..+||..+-..||..+.+ +...+
T Consensus 797 ~w~k~df~~fi~a~eKygr~di~~ia~~~e~-~~eev~~y~rvfwer~~el~d~ek~~~~ie~~e~~i~r~~~~~~~ld~ 875 (971)
T KOG0385|consen 797 NWTKRDFNQFIKANEKYGRDDIENIAAEVEG-TPEEVGEYARVFWERLEELSDIEKIIYQIERGEKRIQRGDSIKKALDD 875 (971)
T ss_pred chhhhhHHHHHHHhhccCcchhhhhHHhhcC-CHHHHHHHHHHHHHHHHHhhhhHHHHHHHhhhHhhhhHHHHHHHHHhh
Confidence 5999999999999999998776777766644 22111
Q ss_pred -hhhcccc-----CCCCCCCCCCChHHHHHHHHHHHhcCC----Chhhhhh------------cCCCCCHHHHHHHHHHh
Q 025351 77 -RLRWCNQ-----LSPSVAHRPFSPAEDDTILAAHARFGN----RWATIAR------------LLPGRTDNAVKNHWNST 134 (254)
Q Consensus 77 -r~Rw~~~-----L~p~~~~~~WT~EED~~Ll~~v~~~G~----~W~~IA~------------~l~gRT~~q~k~Rw~~~ 134 (254)
..||++. ..+..+....|.+||.-|+-+..++|- .|..+-. ++..||...+..|++.+
T Consensus 876 k~~~~k~p~~l~i~~~~nk~~~ys~~edrfL~~~l~K~g~~~~~~~e~lr~~~~~~~~frfdw~~~sRt~~el~Rr~ntl 955 (971)
T KOG0385|consen 876 KIARYKAPHQLRIQYGTNKGKNYSEEEDRFLECMLHKLGFDAENVYEELRQPIRNSPQFRFDWFIKSRTAMELQRRCNTL 955 (971)
T ss_pred hHhhhcCchheeeeeccccCCCCchhhHHHHHHHHHHhccCchhHHHHHHHHHhcCcccccceeeehhhHHHHHhcCCee
Confidence 0122221 112235668999999999999999883 2555432 23457777777777666
Q ss_pred hccc
Q 025351 135 LKRR 138 (254)
Q Consensus 135 lk~~ 138 (254)
+.-.
T Consensus 956 i~~i 959 (971)
T KOG0385|consen 956 ITLI 959 (971)
T ss_pred EEee
Confidence 5443
No 183
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=21.47 E-value=1.3e+02 Score=26.18 Aligned_cols=36 Identities=19% Similarity=0.260 Sum_probs=26.6
Q ss_pred HHHHHHhcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 101 ILAAHARFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 101 Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
++.++...|....+||..+ |-+...|+.+....+++
T Consensus 192 vl~l~~~~g~s~~EIA~~l-gis~~tV~~~~~ra~~~ 227 (236)
T PRK06986 192 VLSLYYQEELNLKEIGAVL-GVSESRVSQIHSQAIKR 227 (236)
T ss_pred HHHhHhccCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3333334466799999999 99999999888766654
No 184
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=21.40 E-value=1.5e+02 Score=15.99 Aligned_cols=35 Identities=23% Similarity=0.280 Sum_probs=21.6
Q ss_pred CChHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHH
Q 025351 93 FSPAEDDTILAAHARFGNRWATIARLLPGRTDNAVKN 129 (254)
Q Consensus 93 WT~EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~ 129 (254)
++.++-..++..+ .-|..+..|++.+ |.+...+.+
T Consensus 6 ~~~~~~~~i~~~~-~~~~s~~~ia~~~-~is~~tv~~ 40 (42)
T cd00569 6 LTPEQIEEARRLL-AAGESVAEIARRL-GVSRSTLYR 40 (42)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHH-CCCHHHHHH
Confidence 4554444444443 4456788999888 777666644
No 185
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=21.17 E-value=1.5e+02 Score=24.82 Aligned_cols=28 Identities=25% Similarity=0.277 Sum_probs=21.6
Q ss_pred CCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 109 GNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 109 G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
|-...+||..| |-+...|+++-...+++
T Consensus 158 ~~s~~EIA~~L-gis~~tVk~~l~ra~~~ 185 (194)
T PRK09646 158 GLTYREVAERL-AVPLGTVKTRMRDGLIR 185 (194)
T ss_pred CCCHHHHHHHh-CCChHhHHHHHHHHHHH
Confidence 55789999999 88999998887655443
No 186
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=20.79 E-value=1.5e+02 Score=25.31 Aligned_cols=29 Identities=21% Similarity=0.234 Sum_probs=22.6
Q ss_pred cCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 108 FGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 108 ~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
.|..-.+||..| |-+...|+++.....++
T Consensus 153 ~g~s~~EIA~~L-gis~~tV~~~l~RArk~ 181 (203)
T PRK09647 153 EGLSYEEIAATL-GVKLGTVRSRIHRGRQQ 181 (203)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 356788899999 99999999888655443
No 187
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=20.51 E-value=2e+02 Score=21.99 Aligned_cols=35 Identities=11% Similarity=0.081 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHH
Q 025351 96 AEDDTILAAHARFGNRWATIARLLPGRTDNAVKNHW 131 (254)
Q Consensus 96 EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw 131 (254)
-|...|..++..++.++.+.|+.+ |=+...++.+-
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~L-GIsRsTL~rKL 89 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALML-GINRGTLRKKL 89 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 467788899999999999999999 76666665544
No 188
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=20.38 E-value=1e+02 Score=25.88 Aligned_cols=30 Identities=30% Similarity=0.377 Sum_probs=25.6
Q ss_pred HHHHHHHHhcCCChhhhhhcCCCCCHHHHHH
Q 025351 99 DTILAAHARFGNRWATIARLLPGRTDNAVKN 129 (254)
Q Consensus 99 ~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~ 129 (254)
+.|+++-++-|-.|.+||+.+ |++...+-.
T Consensus 11 ~~Ll~AK~~KGLTwe~IAe~i-G~sevwvaa 40 (150)
T TIGR00673 11 DALLESKKKKGLTFADIADGL-GLAEVFVAA 40 (150)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHH
Confidence 568888888999999999999 899886644
No 189
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=20.35 E-value=3.7e+02 Score=22.88 Aligned_cols=63 Identities=14% Similarity=0.298 Sum_probs=41.1
Q ss_pred hHHHHHHHHHHHhcCCChhhhhhcCCCCCHHHHHHHHHHhhcccccC-CCCCCChhHHHHHHHHhh
Q 025351 95 PAEDDTILAAHARFGNRWATIARLLPGRTDNAVKNHWNSTLKRRTRE-HPVQMQPHQQQQLMDSVD 159 (254)
Q Consensus 95 ~EED~~Ll~~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~~~~~-~~~~~~~~e~~~L~~~~~ 159 (254)
.+++..+++-.-.+|.....+.++| |-|..+|..| +.++.-.... .+...+++++..+-..-.
T Consensus 73 ~~~~~~~idr~L~lGAS~~mm~~~F-Gls~~ev~~r-R~llgi~~~~GR~~~~~ee~~~~iW~~W~ 136 (180)
T PF11198_consen 73 EQQEQQLIDRALRLGASIEMMQRLF-GLSSAEVAAR-RRLLGIPVRKGRPPALSEEEEAAIWRRWQ 136 (180)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHH-HHHhCCCCCCCCCCCcCHHHHHHHHHHHH
Confidence 3445667777778999999999999 9899998664 3555433333 333445555555555444
No 190
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=20.26 E-value=1.1e+02 Score=25.14 Aligned_cols=33 Identities=18% Similarity=0.322 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHhc--CCChhhhhhcCCCCCHHHHHH
Q 025351 96 AEDDTILAAHARF--GNRWATIARLLPGRTDNAVKN 129 (254)
Q Consensus 96 EED~~Ll~~v~~~--G~~W~~IA~~l~gRT~~q~k~ 129 (254)
+|+..++.+.-.- |..|-.||..+ +-+..+|+.
T Consensus 84 de~k~Ii~lry~~r~~~TW~~IA~~l-~i~erta~r 118 (130)
T PF05263_consen 84 DEEKRIIKLRYDRRSRRTWYQIAQKL-HISERTARR 118 (130)
T ss_pred HHHHHHHHHHHcccccchHHHHHHHh-CccHHHHHH
Confidence 3456666665443 36799999987 555555543
No 191
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=20.16 E-value=1.5e+02 Score=25.45 Aligned_cols=33 Identities=21% Similarity=0.133 Sum_probs=24.6
Q ss_pred HHHhcCCChhhhhhcCCCCCHHHHHHHHHHhhcc
Q 025351 104 AHARFGNRWATIARLLPGRTDNAVKNHWNSTLKR 137 (254)
Q Consensus 104 ~v~~~G~~W~~IA~~l~gRT~~q~k~Rw~~~lk~ 137 (254)
++...|..-.+||..+ |-+...|+.+....+++
T Consensus 189 l~y~~~~s~~eIA~~l-gis~~~v~~~~~ra~~~ 221 (227)
T TIGR02980 189 LRFFEDKTQSEIAERL-GISQMHVSRLLRRALKK 221 (227)
T ss_pred HHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3334466899999999 88999998887665554
Done!