Query 020106
Match_columns 331
No_of_seqs 200 out of 1396
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 07:03:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020106.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020106hhsearch_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 9.1E-35 2E-39 270.4 12.0 110 18-127 5-115 (238)
2 PLN03212 Transcription repress 100.0 1.7E-32 3.8E-37 255.4 14.5 111 16-126 19-130 (249)
3 PLN03091 hypothetical protein; 100.0 8.4E-31 1.8E-35 259.7 16.9 109 18-126 10-119 (459)
4 KOG0049 Transcription factor, 99.8 2.9E-19 6.2E-24 183.4 8.5 114 13-126 351-465 (939)
5 PF13921 Myb_DNA-bind_6: Myb-l 99.7 1.7E-16 3.8E-21 117.4 6.1 60 25-85 1-60 (60)
6 KOG0049 Transcription factor, 99.6 3.9E-16 8.4E-21 160.7 8.4 105 20-124 303-411 (939)
7 COG5147 REB1 Myb superfamily p 99.6 4.3E-15 9.3E-20 151.6 7.9 109 16-124 14-122 (512)
8 KOG0050 mRNA splicing protein 99.5 4.9E-15 1.1E-19 149.6 4.9 106 20-126 5-110 (617)
9 KOG0051 RNA polymerase I termi 99.5 1E-13 2.3E-18 143.1 8.0 104 21-126 383-514 (607)
10 PF00249 Myb_DNA-binding: Myb- 99.4 6.1E-14 1.3E-18 100.2 3.2 47 22-68 1-48 (48)
11 PF00249 Myb_DNA-binding: Myb- 99.3 1E-12 2.2E-17 93.8 4.8 46 74-119 1-48 (48)
12 smart00717 SANT SANT SWI3, AD 99.2 2.6E-11 5.7E-16 83.5 5.2 47 74-120 1-48 (49)
13 smart00717 SANT SANT SWI3, AD 99.2 3.4E-11 7.3E-16 83.0 4.5 48 22-69 1-48 (49)
14 PF13921 Myb_DNA-bind_6: Myb-l 99.2 1.8E-11 3.9E-16 90.5 2.9 44 77-120 1-44 (60)
15 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 2.1E-10 4.6E-15 77.9 5.3 43 76-118 1-44 (45)
16 cd00167 SANT 'SWI3, ADA2, N-Co 99.0 3.3E-10 7.1E-15 77.0 4.2 45 24-68 1-45 (45)
17 KOG0051 RNA polymerase I termi 99.0 5.5E-10 1.2E-14 115.9 7.1 115 19-134 305-443 (607)
18 PLN03212 Transcription repress 99.0 1.5E-10 3.3E-15 108.9 1.9 57 14-71 70-126 (249)
19 PLN03091 hypothetical protein; 98.9 3E-10 6.5E-15 114.1 2.7 56 14-70 59-114 (459)
20 KOG0048 Transcription factor, 98.7 1.7E-08 3.7E-13 94.4 4.1 55 13-68 53-107 (238)
21 COG5147 REB1 Myb superfamily p 98.3 9.9E-08 2.2E-12 98.2 -0.8 101 17-119 286-396 (512)
22 KOG0457 Histone acetyltransfer 97.8 2E-05 4.3E-10 79.5 4.7 51 19-69 69-119 (438)
23 TIGR01557 myb_SHAQKYF myb-like 97.7 4.7E-05 1E-09 57.1 4.2 48 21-68 2-54 (57)
24 TIGR01557 myb_SHAQKYF myb-like 97.5 0.00018 3.8E-09 54.0 5.4 46 74-119 3-54 (57)
25 KOG0457 Histone acetyltransfer 97.5 0.00015 3.2E-09 73.3 5.8 48 72-119 70-118 (438)
26 PF13325 MCRS_N: N-terminal re 97.2 0.0011 2.4E-08 61.3 7.8 98 24-123 1-130 (199)
27 KOG0050 mRNA splicing protein 97.2 0.0003 6.5E-09 72.5 4.0 54 72-125 5-59 (617)
28 TIGR02894 DNA_bind_RsfA transc 97.2 0.00051 1.1E-08 61.4 4.8 53 73-126 3-62 (161)
29 COG5259 RSC8 RSC chromatin rem 97.0 0.00051 1.1E-08 70.1 3.5 46 21-67 278-323 (531)
30 PF13837 Myb_DNA-bind_4: Myb/S 97.0 0.00071 1.5E-08 53.1 3.4 52 74-125 1-70 (90)
31 KOG1279 Chromatin remodeling f 96.9 0.00065 1.4E-08 70.5 3.7 48 19-67 250-297 (506)
32 PF08914 Myb_DNA-bind_2: Rap1 96.9 0.0014 3.1E-08 50.3 4.1 50 74-123 2-61 (65)
33 PLN03142 Probable chromatin-re 96.8 0.0071 1.5E-07 67.7 10.2 109 24-132 826-997 (1033)
34 COG5259 RSC8 RSC chromatin rem 96.7 0.0018 3.9E-08 66.2 4.3 44 75-118 280-323 (531)
35 PRK13923 putative spore coat p 96.5 0.0031 6.6E-08 57.1 4.5 53 73-126 4-63 (170)
36 KOG1279 Chromatin remodeling f 96.5 0.0033 7.1E-08 65.4 5.1 46 73-118 252-297 (506)
37 PF08914 Myb_DNA-bind_2: Rap1 96.4 0.003 6.4E-08 48.6 3.0 50 22-71 2-60 (65)
38 PF13837 Myb_DNA-bind_4: Myb/S 96.3 0.0023 5E-08 50.1 2.2 47 22-68 1-64 (90)
39 TIGR02894 DNA_bind_RsfA transc 96.1 0.0047 1E-07 55.3 3.1 48 21-69 3-56 (161)
40 PF13873 Myb_DNA-bind_5: Myb/S 96.0 0.011 2.3E-07 45.7 4.3 47 22-68 2-69 (78)
41 PF13873 Myb_DNA-bind_5: Myb/S 96.0 0.02 4.3E-07 44.2 5.8 52 74-125 2-75 (78)
42 COG5114 Histone acetyltransfer 95.5 0.014 2.9E-07 57.7 4.0 46 74-119 63-109 (432)
43 COG5114 Histone acetyltransfer 95.4 0.0095 2.1E-07 58.8 2.6 48 22-69 63-110 (432)
44 PRK13923 putative spore coat p 94.7 0.018 4E-07 52.1 2.0 49 20-69 3-57 (170)
45 KOG4282 Transcription factor G 94.4 0.055 1.2E-06 53.1 4.8 56 74-129 54-123 (345)
46 PF09111 SLIDE: SLIDE; InterP 93.9 0.11 2.4E-06 44.4 5.2 54 71-124 46-115 (118)
47 KOG2656 DNA methyltransferase 92.8 0.12 2.7E-06 52.2 4.2 83 45-127 76-189 (445)
48 PF12776 Myb_DNA-bind_3: Myb/S 91.9 0.27 5.9E-06 38.8 4.5 46 76-121 1-64 (96)
49 COG5118 BDP1 Transcription ini 91.2 0.31 6.7E-06 49.4 4.9 46 75-120 366-411 (507)
50 COG5118 BDP1 Transcription ini 89.4 0.34 7.5E-06 49.0 3.5 61 23-84 366-434 (507)
51 PF08281 Sigma70_r4_2: Sigma-7 88.3 1.1 2.4E-05 31.8 4.7 41 79-120 12-52 (54)
52 KOG1194 Predicted DNA-binding 88.3 2.4 5.3E-05 44.0 8.7 50 74-123 187-236 (534)
53 PF09111 SLIDE: SLIDE; InterP 87.8 0.55 1.2E-05 40.1 3.3 48 19-66 46-108 (118)
54 PF11626 Rap1_C: TRF2-interact 87.7 0.83 1.8E-05 36.6 4.1 32 18-52 43-82 (87)
55 KOG4282 Transcription factor G 85.3 1.7 3.6E-05 42.7 5.6 47 22-68 54-113 (345)
56 PF12776 Myb_DNA-bind_3: Myb/S 84.7 1.4 3E-05 34.7 3.9 44 24-67 1-61 (96)
57 PF04545 Sigma70_r4: Sigma-70, 77.1 6.7 0.00014 27.5 4.9 42 80-122 7-48 (50)
58 KOG4167 Predicted DNA-binding 75.9 2.6 5.6E-05 46.1 3.5 41 23-64 620-660 (907)
59 PF13404 HTH_AsnC-type: AsnC-t 75.2 3.5 7.5E-05 28.9 2.9 38 28-66 3-40 (42)
60 KOG2656 DNA methyltransferase 73.6 2.4 5.1E-05 43.3 2.4 87 20-118 128-231 (445)
61 TIGR02985 Sig70_bacteroi1 RNA 69.4 12 0.00026 31.1 5.5 37 85-122 121-157 (161)
62 KOG4468 Polycomb-group transcr 69.3 9 0.0002 41.2 5.6 49 20-69 86-144 (782)
63 smart00595 MADF subfamily of S 69.0 7.1 0.00015 30.3 3.8 29 96-125 30-58 (89)
64 PF11035 SnAPC_2_like: Small n 68.8 19 0.00041 36.0 7.3 53 74-126 21-77 (344)
65 PF11035 SnAPC_2_like: Small n 68.6 28 0.0006 34.9 8.4 86 22-120 21-127 (344)
66 PF13404 HTH_AsnC-type: AsnC-t 66.8 14 0.0003 25.8 4.4 38 80-118 3-41 (42)
67 PRK11179 DNA-binding transcrip 66.0 6.5 0.00014 34.2 3.3 44 28-72 9-52 (153)
68 PRK11179 DNA-binding transcrip 64.3 12 0.00026 32.5 4.6 44 79-123 8-52 (153)
69 PF07750 GcrA: GcrA cell cycle 63.3 7.8 0.00017 34.7 3.3 41 76-117 2-42 (162)
70 PF11626 Rap1_C: TRF2-interact 62.3 3.2 7E-05 33.2 0.6 18 70-87 43-60 (87)
71 KOG4167 Predicted DNA-binding 60.3 15 0.00033 40.4 5.3 45 74-118 619-663 (907)
72 TIGR02937 sigma70-ECF RNA poly 60.2 21 0.00045 28.7 5.1 37 85-122 118-154 (158)
73 PF10545 MADF_DNA_bdg: Alcohol 60.2 12 0.00026 28.1 3.5 33 95-127 28-61 (85)
74 PRK11169 leucine-responsive tr 60.1 7.3 0.00016 34.3 2.5 45 27-72 13-57 (164)
75 KOG1194 Predicted DNA-binding 58.8 9.3 0.0002 39.9 3.3 46 20-66 185-230 (534)
76 KOG4468 Polycomb-group transcr 58.1 18 0.00039 39.0 5.3 48 74-121 88-145 (782)
77 PRK11169 leucine-responsive tr 57.4 17 0.00037 32.0 4.4 44 79-123 13-57 (164)
78 PF13325 MCRS_N: N-terminal re 54.3 24 0.00053 32.9 5.0 44 76-120 1-47 (199)
79 PLN03142 Probable chromatin-re 54.1 14 0.00031 42.1 4.1 34 19-52 923-956 (1033)
80 PRK11924 RNA polymerase sigma 53.2 36 0.00079 28.8 5.7 31 92-123 140-170 (179)
81 PF04504 DUF573: Protein of un 53.2 30 0.00065 28.4 4.9 51 75-125 5-68 (98)
82 PRK09652 RNA polymerase sigma 53.1 35 0.00076 29.0 5.6 32 91-123 142-173 (182)
83 KOG4329 DNA-binding protein [G 52.5 24 0.00052 36.1 4.9 46 74-119 277-323 (445)
84 PF07638 Sigma70_ECF: ECF sigm 51.5 34 0.00075 30.4 5.4 40 81-121 139-178 (185)
85 cd06171 Sigma70_r4 Sigma70, re 51.2 40 0.00087 22.2 4.6 38 81-119 14-51 (55)
86 KOG2009 Transcription initiati 49.2 18 0.00038 38.8 3.6 44 74-117 409-452 (584)
87 PRK09643 RNA polymerase sigma 49.0 46 0.00099 29.5 5.8 34 91-125 148-181 (192)
88 PF09905 DUF2132: Uncharacteri 48.7 24 0.00051 27.4 3.3 44 30-85 12-62 (64)
89 PF04504 DUF573: Protein of un 48.5 58 0.0013 26.7 5.9 69 22-91 4-94 (98)
90 PF01388 ARID: ARID/BRIGHT DNA 48.1 33 0.00071 27.0 4.3 37 84-120 40-89 (92)
91 cd08319 Death_RAIDD Death doma 47.9 25 0.00054 28.2 3.5 29 82-111 2-30 (83)
92 PRK09047 RNA polymerase factor 46.0 65 0.0014 27.0 6.1 32 92-124 121-152 (161)
93 PRK09641 RNA polymerase sigma 45.8 49 0.0011 28.5 5.4 31 92-123 151-181 (187)
94 PRK04217 hypothetical protein; 45.4 69 0.0015 27.1 6.0 47 75-123 41-87 (110)
95 KOG0385 Chromatin remodeling c 45.1 29 0.00062 38.8 4.5 104 16-120 787-957 (971)
96 cd08803 Death_ank3 Death domai 44.9 31 0.00067 27.7 3.7 31 82-113 4-34 (84)
97 cd08311 Death_p75NR Death doma 43.5 21 0.00047 28.2 2.5 35 78-114 1-35 (77)
98 PF07750 GcrA: GcrA cell cycle 43.3 30 0.00066 31.0 3.7 41 24-66 2-42 (162)
99 TIGR02939 RpoE_Sigma70 RNA pol 43.3 45 0.00097 28.9 4.8 31 92-123 153-183 (190)
100 TIGR02954 Sig70_famx3 RNA poly 43.2 55 0.0012 28.0 5.3 31 92-123 134-164 (169)
101 PRK09637 RNA polymerase sigma 42.1 67 0.0014 28.3 5.7 32 92-124 121-152 (181)
102 smart00501 BRIGHT BRIGHT, ARID 41.6 49 0.0011 26.3 4.4 39 83-121 35-86 (93)
103 PRK11923 algU RNA polymerase s 41.5 68 0.0015 28.1 5.7 33 92-125 153-185 (193)
104 PRK12515 RNA polymerase sigma 41.4 75 0.0016 27.8 6.0 31 92-123 146-176 (189)
105 PRK09648 RNA polymerase sigma 40.8 67 0.0015 28.1 5.5 31 92-123 154-184 (189)
106 TIGR02948 SigW_bacill RNA poly 40.7 60 0.0013 28.0 5.2 31 92-123 151-181 (187)
107 smart00344 HTH_ASNC helix_turn 40.0 59 0.0013 25.9 4.7 43 80-123 3-46 (108)
108 PRK09642 RNA polymerase sigma 39.7 76 0.0016 26.8 5.5 30 92-122 121-150 (160)
109 PRK12529 RNA polymerase sigma 39.6 72 0.0016 27.8 5.5 33 91-124 141-173 (178)
110 PRK12512 RNA polymerase sigma 39.1 74 0.0016 27.6 5.5 31 92-123 146-176 (184)
111 PRK05602 RNA polymerase sigma 38.5 82 0.0018 27.4 5.7 33 92-125 143-175 (186)
112 PRK12523 RNA polymerase sigma 38.4 80 0.0017 27.2 5.6 35 88-123 130-164 (172)
113 PRK12530 RNA polymerase sigma 38.2 81 0.0018 27.8 5.7 31 92-123 149-179 (189)
114 TIGR02943 Sig70_famx1 RNA poly 38.1 76 0.0017 28.0 5.5 32 91-123 145-176 (188)
115 smart00344 HTH_ASNC helix_turn 37.8 40 0.00086 26.9 3.3 44 28-72 3-46 (108)
116 PRK09645 RNA polymerase sigma 37.7 81 0.0018 27.0 5.5 31 92-123 133-163 (173)
117 PRK12524 RNA polymerase sigma 37.6 90 0.002 27.6 5.9 33 92-125 151-183 (196)
118 cd08317 Death_ank Death domain 37.6 38 0.00082 26.6 3.1 30 82-112 4-33 (84)
119 PF09420 Nop16: Ribosome bioge 37.1 64 0.0014 28.6 4.8 46 73-118 113-162 (164)
120 smart00595 MADF subfamily of S 36.5 16 0.00035 28.3 0.8 22 45-67 30-51 (89)
121 PRK06759 RNA polymerase factor 36.2 79 0.0017 26.4 5.1 29 92-121 121-149 (154)
122 cd08804 Death_ank2 Death domai 35.9 48 0.001 26.4 3.4 31 82-113 4-34 (84)
123 PRK12531 RNA polymerase sigma 35.6 90 0.002 27.5 5.6 31 92-123 156-186 (194)
124 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 35.6 70 0.0015 23.5 4.0 34 81-115 8-41 (50)
125 KOG0384 Chromodomain-helicase 34.6 56 0.0012 38.2 4.8 72 21-99 1132-1205(1373)
126 PF08281 Sigma70_r4_2: Sigma-7 34.2 35 0.00076 24.0 2.2 38 27-66 12-49 (54)
127 PRK00118 putative DNA-binding 33.9 1.2E+02 0.0027 25.3 5.7 44 79-123 19-62 (104)
128 PRK12527 RNA polymerase sigma 33.4 1.3E+02 0.0028 25.4 6.0 32 92-124 120-151 (159)
129 cd08318 Death_NMPP84 Death dom 32.9 59 0.0013 25.9 3.5 32 77-112 5-36 (86)
130 TIGR02952 Sig70_famx2 RNA poly 32.8 1.1E+02 0.0023 25.9 5.4 30 92-122 137-166 (170)
131 PRK09413 IS2 repressor TnpA; R 32.5 2E+02 0.0044 23.9 6.9 47 20-69 8-54 (121)
132 PRK12536 RNA polymerase sigma 32.4 1.1E+02 0.0024 26.6 5.5 31 92-123 144-174 (181)
133 smart00005 DEATH DEATH domain, 32.2 54 0.0012 25.2 3.2 30 81-111 4-34 (88)
134 TIGR02999 Sig-70_X6 RNA polyme 32.1 1.1E+02 0.0025 26.2 5.6 30 92-122 149-178 (183)
135 PF09197 Rap1-DNA-bind: Rap1, 32.1 52 0.0011 27.8 3.2 46 24-69 1-76 (105)
136 PRK09649 RNA polymerase sigma 32.1 96 0.0021 27.3 5.1 31 92-123 145-175 (185)
137 PF00196 GerE: Bacterial regul 32.0 50 0.0011 23.8 2.7 44 76-122 3-46 (58)
138 COG2197 CitB Response regulato 31.8 64 0.0014 29.5 4.1 45 75-122 147-191 (211)
139 PRK12516 RNA polymerase sigma 31.6 1.3E+02 0.0029 26.6 6.0 33 91-124 130-162 (187)
140 COG1522 Lrp Transcriptional re 30.9 46 0.00099 28.1 2.8 44 28-72 8-51 (154)
141 PRK12532 RNA polymerase sigma 30.7 1.1E+02 0.0024 26.8 5.3 31 92-123 151-181 (195)
142 PRK12514 RNA polymerase sigma 30.5 1.2E+02 0.0026 26.1 5.4 29 93-122 145-173 (179)
143 PRK13919 putative RNA polymera 30.4 1.2E+02 0.0027 26.2 5.5 30 93-123 151-180 (186)
144 PRK06811 RNA polymerase factor 30.3 1.3E+02 0.0028 26.4 5.7 33 93-126 147-179 (189)
145 TIGR02983 SigE-fam_strep RNA p 29.9 1.3E+02 0.0028 25.4 5.4 40 83-123 116-155 (162)
146 PF02954 HTH_8: Bacterial regu 29.5 91 0.002 21.3 3.6 34 81-115 6-39 (42)
147 PF13936 HTH_38: Helix-turn-he 29.4 48 0.001 23.0 2.2 37 75-113 3-39 (44)
148 PRK12542 RNA polymerase sigma 29.3 1.3E+02 0.0028 26.2 5.5 30 92-122 137-166 (185)
149 PRK12520 RNA polymerase sigma 29.2 1.6E+02 0.0034 25.8 6.0 33 92-125 146-178 (191)
150 TIGR02950 SigM_subfam RNA poly 29.2 45 0.00098 27.8 2.4 29 93-122 121-149 (154)
151 PRK09639 RNA polymerase sigma 29.2 1.5E+02 0.0033 24.9 5.8 31 92-123 126-156 (166)
152 COG4628 Uncharacterized conser 29.1 68 0.0015 27.8 3.4 45 30-86 21-72 (136)
153 PRK09651 RNA polymerase sigma 28.6 89 0.0019 27.0 4.2 31 92-123 134-164 (172)
154 TIGR02984 Sig-70_plancto1 RNA 28.2 1.3E+02 0.0029 25.8 5.3 31 92-123 155-185 (189)
155 PRK12547 RNA polymerase sigma 28.2 1.5E+02 0.0033 25.3 5.6 31 92-123 127-157 (164)
156 cd08805 Death_ank1 Death domai 28.0 70 0.0015 25.7 3.2 26 82-108 4-29 (84)
157 KOG2009 Transcription initiati 27.7 33 0.00071 36.9 1.5 47 19-66 406-452 (584)
158 COG5201 SKP1 SCF ubiquitin lig 27.6 1.4E+02 0.0031 26.5 5.2 55 26-87 88-150 (158)
159 PRK12528 RNA polymerase sigma 27.6 1.3E+02 0.0028 25.5 5.0 30 91-121 127-156 (161)
160 TIGR02960 SigX5 RNA polymerase 27.1 1.2E+02 0.0026 28.9 5.2 31 92-123 157-187 (324)
161 cd08777 Death_RIP1 Death Domai 27.1 75 0.0016 25.5 3.2 30 84-114 4-33 (86)
162 PF08870 DUF1832: Domain of un 26.9 2.4E+02 0.0052 23.9 6.4 90 26-125 5-99 (113)
163 PRK09647 RNA polymerase sigma 26.8 1.7E+02 0.0036 26.5 5.8 33 92-125 153-185 (203)
164 COG1522 Lrp Transcriptional re 26.7 1.3E+02 0.0028 25.4 4.8 44 79-123 7-51 (154)
165 PRK11922 RNA polymerase sigma 26.3 92 0.002 28.5 4.1 32 93-125 165-196 (231)
166 KOG4329 DNA-binding protein [G 25.4 61 0.0013 33.2 2.9 40 24-64 279-319 (445)
167 PRK09646 RNA polymerase sigma 25.3 1.7E+02 0.0036 25.8 5.5 30 92-122 157-186 (194)
168 PRK12545 RNA polymerase sigma 25.2 1.6E+02 0.0036 26.2 5.5 30 92-122 154-183 (201)
169 PRK12537 RNA polymerase sigma 24.7 1.7E+02 0.0036 25.5 5.3 30 92-122 148-177 (182)
170 PRK12546 RNA polymerase sigma 24.6 2.2E+02 0.0048 25.3 6.1 32 91-123 127-158 (188)
171 TIGR02959 SigZ RNA polymerase 24.4 2.1E+02 0.0046 24.7 5.8 34 92-126 115-148 (170)
172 PF09420 Nop16: Ribosome bioge 23.7 1E+02 0.0022 27.4 3.7 45 20-65 112-160 (164)
173 cd08779 Death_PIDD Death Domai 23.2 1E+02 0.0022 24.6 3.3 32 83-115 3-37 (86)
174 PRK09638 RNA polymerase sigma 23.1 84 0.0018 26.9 3.0 30 92-122 141-170 (176)
175 PRK10100 DNA-binding transcrip 22.8 1.5E+02 0.0033 27.2 4.9 44 76-122 155-198 (216)
176 PRK06986 fliA flagellar biosyn 22.3 1.8E+02 0.0039 26.7 5.2 31 92-123 199-229 (236)
177 PRK12538 RNA polymerase sigma 21.9 1.4E+02 0.0031 27.6 4.5 31 92-123 186-216 (233)
178 TIGR02980 SigBFG RNA polymeras 21.7 2E+02 0.0044 26.0 5.4 31 92-123 193-223 (227)
179 PRK12544 RNA polymerase sigma 21.4 2.2E+02 0.0048 25.7 5.6 32 92-124 163-194 (206)
180 PF01466 Skp1: Skp1 family, di 21.4 1E+02 0.0022 23.9 2.9 36 45-87 36-71 (78)
181 KOG3554 Histone deacetylase co 21.3 1.5E+02 0.0032 31.6 4.8 60 47-116 268-328 (693)
182 PRK12511 RNA polymerase sigma 21.0 2.6E+02 0.0056 24.6 5.8 33 92-125 126-158 (182)
183 PRK08301 sporulation sigma fac 20.9 1.9E+02 0.0042 26.3 5.1 31 93-124 198-228 (234)
184 PRK12519 RNA polymerase sigma 20.9 1.8E+02 0.004 25.3 4.8 31 92-123 156-186 (194)
185 KOG3841 TEF-1 and related tran 20.9 6.3E+02 0.014 26.3 8.9 72 20-127 74-150 (455)
186 PRK12541 RNA polymerase sigma 20.8 2E+02 0.0043 24.3 4.9 29 93-122 128-156 (161)
187 PRK09636 RNA polymerase sigma 20.5 2.1E+02 0.0045 27.2 5.4 31 92-123 130-160 (293)
188 TIGR02989 Sig-70_gvs1 RNA poly 20.4 2.1E+02 0.0046 23.8 4.9 27 93-120 127-153 (159)
189 COG2963 Transposase and inacti 20.3 2.6E+02 0.0057 22.7 5.3 41 74-116 5-46 (116)
190 COG1168 MalY Bifunctional PLP- 20.1 1E+02 0.0023 31.6 3.4 25 18-42 167-192 (388)
No 1
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=9.1e-35 Score=270.45 Aligned_cols=110 Identities=37% Similarity=0.742 Sum_probs=105.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhc-CCCccccchhhhcccCCCCCCCCCCHHHHHHHHHHHHHhCChh
Q 020106 18 STCPRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQ-GRSGKSCRLRWFNQLDPRINRRPFTEDEEERLLAAHRIHGNKW 96 (331)
Q Consensus 18 p~~kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~lp-gRt~kQCr~Rw~n~L~p~i~kg~WT~EED~~Llelv~~~G~kW 96 (331)
+.+.||+||+|||++|+++|++||.++|..||+.++ +|++++||+||.|||+|+++++.||+|||++|++||..+|++|
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrW 84 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRW 84 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHH
Confidence 345589999999999999999999999999999998 9999999999999999999999999999999999999999999
Q ss_pred HHHhhcCCCCCHHHHHHHHHHHHHHHHHhhh
Q 020106 97 ALIARLFPGRTDNAVKNHWHVIMARKQREQS 127 (331)
Q Consensus 97 s~IAk~LpgRT~nq~KnRW~~ilkrk~~~~~ 127 (331)
++||++|||||+|+|||+|++.+|||..+..
T Consensus 85 s~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 85 SLIAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred HHHHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 9999999999999999999999999987765
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=1.7e-32 Score=255.36 Aligned_cols=111 Identities=42% Similarity=0.792 Sum_probs=105.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHh-cCCCccccchhhhcccCCCCCCCCCCHHHHHHHHHHHHHhCC
Q 020106 16 STSTCPRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKL-QGRSGKSCRLRWFNQLDPRINRRPFTEDEEERLLAAHRIHGN 94 (331)
Q Consensus 16 ~~p~~kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~l-pgRt~kQCr~Rw~n~L~p~i~kg~WT~EED~~Llelv~~~G~ 94 (331)
.++.++|++||+|||++|+++|++||..+|..||+.| ++|+++|||+||.++|+|.+++++||+|||++|++++..||+
T Consensus 19 ~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~~Gn 98 (249)
T PLN03212 19 TKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLGN 98 (249)
T ss_pred ccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHhccc
Confidence 4567889999999999999999999998999999998 699999999999999999999999999999999999999999
Q ss_pred hhHHHhhcCCCCCHHHHHHHHHHHHHHHHHhh
Q 020106 95 KWALIARLFPGRTDNAVKNHWHVIMARKQREQ 126 (331)
Q Consensus 95 kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~~~ 126 (331)
+|+.||++|||||+++|||||+.+++++..+.
T Consensus 99 KWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~ 130 (249)
T PLN03212 99 RWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQ 130 (249)
T ss_pred cHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhc
Confidence 99999999999999999999999998887654
No 3
>PLN03091 hypothetical protein; Provisional
Probab=99.97 E-value=8.4e-31 Score=259.75 Aligned_cols=109 Identities=41% Similarity=0.864 Sum_probs=104.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHh-cCCCccccchhhhcccCCCCCCCCCCHHHHHHHHHHHHHhCChh
Q 020106 18 STCPRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKL-QGRSGKSCRLRWFNQLDPRINRRPFTEDEEERLLAAHRIHGNKW 96 (331)
Q Consensus 18 p~~kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~l-pgRt~kQCr~Rw~n~L~p~i~kg~WT~EED~~Llelv~~~G~kW 96 (331)
..++||+||+|||++|+++|++||..+|..||+.+ ++|+++|||+||.++|+|.+++++||+|||++|+++|++||++|
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k~~GnKW 89 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHAVLGNRW 89 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHHHhCcch
Confidence 47889999999999999999999999999999988 48999999999999999999999999999999999999999999
Q ss_pred HHHhhcCCCCCHHHHHHHHHHHHHHHHHhh
Q 020106 97 ALIARLFPGRTDNAVKNHWHVIMARKQREQ 126 (331)
Q Consensus 97 s~IAk~LpgRT~nq~KnRW~~ilkrk~~~~ 126 (331)
++||++|||||+++|||||+.++||+.+..
T Consensus 90 skIAk~LPGRTDnqIKNRWnslLKKklr~~ 119 (459)
T PLN03091 90 SQIAAQLPGRTDNEIKNLWNSCLKKKLRQR 119 (459)
T ss_pred HHHHHhcCCCCHHHHHHHHHHHHHHHHHHc
Confidence 999999999999999999999999987654
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.78 E-value=2.9e-19 Score=183.44 Aligned_cols=114 Identities=29% Similarity=0.516 Sum_probs=102.4
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcccCCCCCCCCCCHHHHHHHHHHHHHh
Q 020106 13 TKSSTSTCPRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQLDPRINRRPFTEDEEERLLAAHRIH 92 (331)
Q Consensus 13 ~ks~~p~~kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L~p~i~kg~WT~EED~~Llelv~~~ 92 (331)
+.++.|++++|+||++||.+|+.+|++||.++|.+|.+.+|+|+..|||+||.|.|+...+++.||-.||+.||.+|.+|
T Consensus 351 ~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~~V~~Y 430 (939)
T KOG0049|consen 351 SHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLYAVKVY 430 (939)
T ss_pred eeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHHhhccCceeecchHHHHHHHHHH
Confidence 57889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred C-ChhHHHhhcCCCCCHHHHHHHHHHHHHHHHHhh
Q 020106 93 G-NKWALIARLFPGRTDNAVKNHWHVIMARKQREQ 126 (331)
Q Consensus 93 G-~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~~~ 126 (331)
| ++|++||.+||+||..|...|=...+.-+++-.
T Consensus 431 G~g~WakcA~~Lp~~t~~q~~rrR~R~~~~k~rl~ 465 (939)
T KOG0049|consen 431 GKGNWAKCAMLLPKKTSRQLRRRRLRLIAAKLRLA 465 (939)
T ss_pred ccchHHHHHHHccccchhHHHHHHHHHHHHHHHHh
Confidence 9 789999999999999665554444444444333
No 5
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.65 E-value=1.7e-16 Score=117.42 Aligned_cols=60 Identities=50% Similarity=1.005 Sum_probs=54.9
Q ss_pred CCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcccCCCCCCCCCCHHHHHHH
Q 020106 25 WRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQLDPRINRRPFTEDEEERL 85 (331)
Q Consensus 25 WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L~p~i~kg~WT~EED~~L 85 (331)
||+|||++|+.+|.+||. +|..||++|+.|+..||+.||.++|+|.+++++||+|||++|
T Consensus 1 WT~eEd~~L~~~~~~~g~-~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN-DWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS--HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc-CHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 999999999999999995 799999999669999999999999999999999999999987
No 6
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.63 E-value=3.9e-16 Score=160.66 Aligned_cols=105 Identities=25% Similarity=0.526 Sum_probs=97.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCC---CHHHHHHHhcCCCccccchhhhcccCCCCCCCCCCHHHHHHHHHHHHHhCCh-
Q 020106 20 CPRGHWRPAEDEKLRQLVEQYGAQ---NWNSIAEKLQGRSGKSCRLRWFNQLDPRINRRPFTEDEEERLLAAHRIHGNK- 95 (331)
Q Consensus 20 ~kKG~WT~EED~~L~~lV~kyG~~---nW~~IA~~lpgRt~kQCr~Rw~n~L~p~i~kg~WT~EED~~Llelv~~~G~k- 95 (331)
+....||.|||.+|+++|+....+ +|.+|-..||||+..|..-||...|+|.+++|+||.+||.+|+.+|.+||.+
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 445789999999999999987543 6999999999999999999999999999999999999999999999999965
Q ss_pred hHHHhhcCCCCCHHHHHHHHHHHHHHHHH
Q 020106 96 WALIARLFPGRTDNAVKNHWHVIMARKQR 124 (331)
Q Consensus 96 Ws~IAk~LpgRT~nq~KnRW~~ilkrk~~ 124 (331)
|.+|-..+|||++.|||.||...|.+..+
T Consensus 383 w~k~R~~vPnRSdsQcR~RY~nvL~~s~K 411 (939)
T KOG0049|consen 383 WAKVRQAVPNRSDSQCRERYTNVLNRSAK 411 (939)
T ss_pred hhhHHHhcCCccHHHHHHHHHHHHHHhhc
Confidence 99999999999999999999998876653
No 7
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.56 E-value=4.3e-15 Score=151.65 Aligned_cols=109 Identities=28% Similarity=0.584 Sum_probs=102.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcccCCCCCCCCCCHHHHHHHHHHHHHhCCh
Q 020106 16 STSTCPRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQLDPRINRRPFTEDEEERLLAAHRIHGNK 95 (331)
Q Consensus 16 ~~p~~kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L~p~i~kg~WT~EED~~Llelv~~~G~k 95 (331)
..-.++.|.|+..||+.|..+|+.||+.+|..||..+.-|+++||+.||.++++|.+++..|+.|||+.|+.+..++|.+
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 34456789999999999999999999999999999998899999999999999999999999999999999999999999
Q ss_pred hHHHhhcCCCCCHHHHHHHHHHHHHHHHH
Q 020106 96 WALIARLFPGRTDNAVKNHWHVIMARKQR 124 (331)
Q Consensus 96 Ws~IAk~LpgRT~nq~KnRW~~ilkrk~~ 124 (331)
|+.||..+++|+..+|.+||...+.....
T Consensus 94 wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 94 WSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 99999999999999999999988876554
No 8
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.53 E-value=4.9e-15 Score=149.59 Aligned_cols=106 Identities=30% Similarity=0.648 Sum_probs=100.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcccCCCCCCCCCCHHHHHHHHHHHHHhCChhHHH
Q 020106 20 CPRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQLDPRINRRPFTEDEEERLLAAHRIHGNKWALI 99 (331)
Q Consensus 20 ~kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L~p~i~kg~WT~EED~~Llelv~~~G~kWs~I 99 (331)
++.|.|+.-||+.|..+|.+||...|.+|++.++..+.+||+.||..+|+|.+++..|+.|||++|+.+...+...|..|
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 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCCCCCHHHHHHHHHHHHHHHHHhh
Q 020106 100 ARLFPGRTDNAVKNHWHVIMARKQREQ 126 (331)
Q Consensus 100 Ak~LpgRT~nq~KnRW~~ilkrk~~~~ 126 (331)
|..| ||+.+||-.||+.++-......
T Consensus 85 a~i~-gr~~~qc~eRy~~ll~~~~s~~ 110 (617)
T KOG0050|consen 85 ADIM-GRTSQQCLERYNNLLDVYVSYH 110 (617)
T ss_pred HHHh-hhhHHHHHHHHHHHHHHHHhhh
Confidence 9999 9999999999999987665443
No 9
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.46 E-value=1e-13 Score=143.10 Aligned_cols=104 Identities=29% Similarity=0.612 Sum_probs=93.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcccCCCC--CCCCCCHHHHHHHHHHHH-------H
Q 020106 21 PRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQLDPRI--NRRPFTEDEEERLLAAHR-------I 91 (331)
Q Consensus 21 kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L~p~i--~kg~WT~EED~~Llelv~-------~ 91 (331)
.+|.||+||++.|..+|.++|. +|.+|++.| ||.+..|++||+++....- ++++||.||+++|+++|. +
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 KRGKWTPEEEEELKKLVVEHGN-DWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREALQ 460 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcc-cHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhhc
Confidence 8999999999999999999996 699999998 8999999999999999874 899999999999999995 3
Q ss_pred h-------------------CChhHHHhhcCCCCCHHHHHHHHHHHHHHHHHhh
Q 020106 92 H-------------------GNKWALIARLFPGRTDNAVKNHWHVIMARKQREQ 126 (331)
Q Consensus 92 ~-------------------G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~~~ 126 (331)
+ +..|+.|++.+..|+.-|||.+|..++.+.....
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 3 2359999999999999999999999998765443
No 10
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.44 E-value=6.1e-14 Score=100.15 Aligned_cols=47 Identities=49% Similarity=0.972 Sum_probs=42.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhc-CCCccccchhhhccc
Q 020106 22 RGHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQ-GRSGKSCRLRWFNQL 68 (331)
Q Consensus 22 KG~WT~EED~~L~~lV~kyG~~nW~~IA~~lp-gRt~kQCr~Rw~n~L 68 (331)
|++||+|||++|+++|.+||..+|..||..|+ +||..||+.||.++|
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 68999999999999999999877999999999 999999999999875
No 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=99.35 E-value=1e-12 Score=93.85 Aligned_cols=46 Identities=37% Similarity=0.767 Sum_probs=41.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCCh-hHHHhhcCC-CCCHHHHHHHHHHHH
Q 020106 74 RRPFTEDEEERLLAAHRIHGNK-WALIARLFP-GRTDNAVKNHWHVIM 119 (331)
Q Consensus 74 kg~WT~EED~~Llelv~~~G~k-Ws~IAk~Lp-gRT~nq~KnRW~~il 119 (331)
+++||+|||++|++++.+||.+ |..||..|| +||..||++||+.++
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 999999999998763
No 12
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.20 E-value=2.6e-11 Score=83.55 Aligned_cols=47 Identities=32% Similarity=0.704 Sum_probs=44.2
Q ss_pred CCCCCHHHHHHHHHHHHHhC-ChhHHHhhcCCCCCHHHHHHHHHHHHH
Q 020106 74 RRPFTEDEEERLLAAHRIHG-NKWALIARLFPGRTDNAVKNHWHVIMA 120 (331)
Q Consensus 74 kg~WT~EED~~Llelv~~~G-~kWs~IAk~LpgRT~nq~KnRW~~ilk 120 (331)
+++||+|||.+|+.++.+|| .+|..||..|++||+.+|++||..+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 46899999999999999999 999999999999999999999998764
No 13
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.17 E-value=3.4e-11 Score=82.99 Aligned_cols=48 Identities=48% Similarity=0.994 Sum_probs=44.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcccC
Q 020106 22 RGHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQLD 69 (331)
Q Consensus 22 KG~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L~ 69 (331)
+++||++||++|+.++.+||..+|..||..|++|+..+|+.||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 478999999999999999996689999999999999999999998764
No 14
>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=99.15 E-value=1.8e-11 Score=90.54 Aligned_cols=44 Identities=32% Similarity=0.576 Sum_probs=38.3
Q ss_pred CCHHHHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHHHHH
Q 020106 77 FTEDEEERLLAAHRIHGNKWALIARLFPGRTDNAVKNHWHVIMA 120 (331)
Q Consensus 77 WT~EED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~ilk 120 (331)
||+|||++|+++|.+||.+|.+||+.|+.||+.+|++||...++
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~ 44 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLR 44 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTS
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCc
Confidence 99999999999999999999999999966999999999998553
No 15
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.08 E-value=2.1e-10 Score=77.94 Aligned_cols=43 Identities=42% Similarity=0.829 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHHHHhC-ChhHHHhhcCCCCCHHHHHHHHHHH
Q 020106 76 PFTEDEEERLLAAHRIHG-NKWALIARLFPGRTDNAVKNHWHVI 118 (331)
Q Consensus 76 ~WT~EED~~Llelv~~~G-~kWs~IAk~LpgRT~nq~KnRW~~i 118 (331)
+||+||+.+|+.++.++| .+|..||+.|++||..+|++||..+
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 599999999999999999 9999999999999999999999875
No 16
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.01 E-value=3.3e-10 Score=77.02 Aligned_cols=45 Identities=49% Similarity=0.939 Sum_probs=42.0
Q ss_pred CCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhccc
Q 020106 24 HWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQL 68 (331)
Q Consensus 24 ~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L 68 (331)
+||++||++|+.++.+||..+|..||..|++|+..+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999768999999999999999999998753
No 17
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.00 E-value=5.5e-10 Score=115.89 Aligned_cols=115 Identities=23% Similarity=0.335 Sum_probs=94.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCC---------------C--------HHHHHHHhcCCCccccchhhhcccCCCC-CC
Q 020106 19 TCPRGHWRPAEDEKLRQLVEQYGAQ---------------N--------WNSIAEKLQGRSGKSCRLRWFNQLDPRI-NR 74 (331)
Q Consensus 19 ~~kKG~WT~EED~~L~~lV~kyG~~---------------n--------W~~IA~~lpgRt~kQCr~Rw~n~L~p~i-~k 74 (331)
..+-+.|+++||+.|...|..|-.. + |+.|.+.||-|+...++.+-++..+|.- .+
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 4556899999999999999877110 1 7888888999999999884444444433 89
Q ss_pred CCCCHHHHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHHHHHHHHHhhhhhcCCCC
Q 020106 75 RPFTEDEEERLLAAHRIHGNKWALIARLFPGRTDNAVKNHWHVIMARKQREQSKLCGKRS 134 (331)
Q Consensus 75 g~WT~EED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~~~~~~~~~~s 134 (331)
|.||+||++.|..+|.++|+.|..|++.| ||.+.+|+.||+.+++.........+..+.
T Consensus 385 g~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eE 443 (607)
T KOG0051|consen 385 GKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEE 443 (607)
T ss_pred CCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHH
Confidence 99999999999999999999999999999 999999999999998876544445554443
No 18
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.98 E-value=1.5e-10 Score=108.85 Aligned_cols=57 Identities=21% Similarity=0.443 Sum_probs=52.2
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcccCCC
Q 020106 14 KSSTSTCPRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQLDPR 71 (331)
Q Consensus 14 ks~~p~~kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L~p~ 71 (331)
..+.|.+++++||+|||++|++++..||. .|..||+.|||||..+|+.||..+|+..
T Consensus 70 N~L~P~I~kgpWT~EED~lLlel~~~~Gn-KWs~IAk~LpGRTDnqIKNRWns~LrK~ 126 (249)
T PLN03212 70 NYLRPSVKRGGITSDEEDLILRLHRLLGN-RWSLIAGRIPGRTDNEIKNYWNTHLRKK 126 (249)
T ss_pred HhhchhcccCCCChHHHHHHHHHHHhccc-cHHHHHhhcCCCCHHHHHHHHHHHHhHH
Confidence 35678999999999999999999999996 5999999999999999999999887744
No 19
>PLN03091 hypothetical protein; Provisional
Probab=98.95 E-value=3e-10 Score=114.06 Aligned_cols=56 Identities=23% Similarity=0.442 Sum_probs=51.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcccCC
Q 020106 14 KSSTSTCPRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQLDP 70 (331)
Q Consensus 14 ks~~p~~kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L~p 70 (331)
..+.|.++||+||+|||++|++++.+||. +|.+||+.|+||+..+|+.||+.+|+.
T Consensus 59 NyLdP~IkKgpWT~EED~lLLeL~k~~Gn-KWskIAk~LPGRTDnqIKNRWnslLKK 114 (459)
T PLN03091 59 NYLRPDLKRGTFSQQEENLIIELHAVLGN-RWSQIAAQLPGRTDNEIKNLWNSCLKK 114 (459)
T ss_pred hccCCcccCCCCCHHHHHHHHHHHHHhCc-chHHHHHhcCCCCHHHHHHHHHHHHHH
Confidence 35789999999999999999999999997 599999999999999999999987754
No 20
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.66 E-value=1.7e-08 Score=94.38 Aligned_cols=55 Identities=25% Similarity=0.520 Sum_probs=50.6
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhccc
Q 020106 13 TKSSTSTCPRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQL 68 (331)
Q Consensus 13 ~ks~~p~~kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L 68 (331)
...+.|.++||.||+|||++|+++...+|.+ |.+||++|||||...++.+|+.+|
T Consensus 53 ~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNr-Ws~IA~~LPGRTDNeIKN~Wnt~l 107 (238)
T KOG0048|consen 53 TNYLRPDLKRGNFSDEEEDLIIKLHALLGNR-WSLIAGRLPGRTDNEVKNHWNTHL 107 (238)
T ss_pred hcccCCCccCCCCCHHHHHHHHHHHHHHCcH-HHHHHhhCCCcCHHHHHHHHHHHH
Confidence 3568899999999999999999999999975 999999999999999999986665
No 21
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=98.30 E-value=9.9e-08 Score=98.19 Aligned_cols=101 Identities=28% Similarity=0.525 Sum_probs=87.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcccCC--CCCCCCCCHHHHHHHHHHHHHhC-
Q 020106 17 TSTCPRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQLDP--RINRRPFTEDEEERLLAAHRIHG- 93 (331)
Q Consensus 17 ~p~~kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L~p--~i~kg~WT~EED~~Llelv~~~G- 93 (331)
.+...+|.||+||++.|..++..+|. .|..|.+.+ +|-+..||+||+++... .+++++|+.||+.+|...+..+-
T Consensus 286 ~~f~~~~~wt~e~~~eL~~~~~~~~~-~w~~ig~~~-~rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e~~~ 363 (512)
T COG5147 286 NIFEQRGKWTKEEEQELAKLVVEHGG-SWTEIGKLL-GRMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNEMRL 363 (512)
T ss_pred hHHhhhccCccccccccccccccccc-hhhHhhhhh-ccCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHHHHH
Confidence 34556899999999999999999996 599999987 89999999999999998 67888999999999998876432
Q ss_pred -------ChhHHHhhcCCCCCHHHHHHHHHHHH
Q 020106 94 -------NKWALIARLFPGRTDNAVKNHWHVIM 119 (331)
Q Consensus 94 -------~kWs~IAk~LpgRT~nq~KnRW~~il 119 (331)
..|..|++.+++|...+|+.++.++.
T Consensus 364 ~~~~~~~~~~~li~~~~~~~~~~~~~~~~~~~~ 396 (512)
T COG5147 364 EAQQSSRILWLLIAQNIRNRLQHHCRDKYGVLI 396 (512)
T ss_pred HHhhhhhhhHHHHHHhhhccccCCCCCcccccc
Confidence 45999999999999988888776543
No 22
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.81 E-value=2e-05 Score=79.51 Aligned_cols=51 Identities=22% Similarity=0.527 Sum_probs=47.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcccC
Q 020106 19 TCPRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQLD 69 (331)
Q Consensus 19 ~~kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L~ 69 (331)
++-...||.+|+-+|+++++.||.+||..||.+|..|+...|+++|.+++-
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHh
Confidence 455678999999999999999999999999999999999999999999763
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=97.71 E-value=4.7e-05 Score=57.08 Aligned_cols=48 Identities=19% Similarity=0.365 Sum_probs=42.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCH---HHHHHHhc-CC-Cccccchhhhccc
Q 020106 21 PRGHWRPAEDEKLRQLVEQYGAQNW---NSIAEKLQ-GR-SGKSCRLRWFNQL 68 (331)
Q Consensus 21 kKG~WT~EED~~L~~lV~kyG~~nW---~~IA~~lp-gR-t~kQCr~Rw~n~L 68 (331)
++-.||+||.++++++++.+|.++| +.|++.|. .| |..||+.|+..|.
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 4568999999999999999998899 99999884 45 9999999987764
No 24
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.55 E-value=0.00018 Score=53.98 Aligned_cols=46 Identities=30% Similarity=0.409 Sum_probs=40.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-hh---HHHhhcCCC-C-CHHHHHHHHHHHH
Q 020106 74 RRPFTEDEEERLLAAHRIHGN-KW---ALIARLFPG-R-TDNAVKNHWHVIM 119 (331)
Q Consensus 74 kg~WT~EED~~Llelv~~~G~-kW---s~IAk~Lpg-R-T~nq~KnRW~~il 119 (331)
+-.||+||..++++++..+|. +| ..|++.|.. | |..||+.|...+.
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 568999999999999999996 99 999998853 5 9999999987654
No 25
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.50 E-value=0.00015 Score=73.29 Aligned_cols=48 Identities=31% Similarity=0.400 Sum_probs=43.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHhC-ChhHHHhhcCCCCCHHHHHHHHHHHH
Q 020106 72 INRRPFTEDEEERLLAAHRIHG-NKWALIARLFPGRTDNAVKNHWHVIM 119 (331)
Q Consensus 72 i~kg~WT~EED~~Llelv~~~G-~kWs~IAk~LpgRT~nq~KnRW~~il 119 (331)
+-...||.+||.+|++++..|| ++|..||.+++.|+..+||.||..++
T Consensus 70 i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHH
Confidence 4456899999999999999999 89999999999999999999998654
No 26
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.24 E-value=0.0011 Score=61.34 Aligned_cols=98 Identities=22% Similarity=0.427 Sum_probs=73.7
Q ss_pred CCCHHHHHHHHHHHHHhCCCCHHHHHHHh---cCCCccccchhhhcccC-CCC--------------------CCCCCCH
Q 020106 24 HWRPAEDEKLRQLVEQYGAQNWNSIAEKL---QGRSGKSCRLRWFNQLD-PRI--------------------NRRPFTE 79 (331)
Q Consensus 24 ~WT~EED~~L~~lV~kyG~~nW~~IA~~l---pgRt~kQCr~Rw~n~L~-p~i--------------------~kg~WT~ 79 (331)
+|++++|-.|+.+|..-. +-..|+.-+ ..-|-.-+.+||..+|. |.+ .+.+||.
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 699999999999999876 477787765 34566777889998773 221 4568999
Q ss_pred HHHHHHHHHHHHhCC---hhHHHhh-----cCCCCCHHHHHHHHHHHHHHHH
Q 020106 80 DEEERLLAAHRIHGN---KWALIAR-----LFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 80 EED~~Llelv~~~G~---kWs~IAk-----~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
+|+++|......... .+.+|-. +-++||+.++.++|..+.+...
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~L 130 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHL 130 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhch
Confidence 999999997665543 3666643 4578999999999996654443
No 27
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.20 E-value=0.0003 Score=72.54 Aligned_cols=54 Identities=28% Similarity=0.432 Sum_probs=48.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHhC-ChhHHHhhcCCCCCHHHHHHHHHHHHHHHHHh
Q 020106 72 INRRPFTEDEEERLLAAHRIHG-NKWALIARLFPGRTDNAVKNHWHVIMARKQRE 125 (331)
Q Consensus 72 i~kg~WT~EED~~Llelv~~~G-~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~~ 125 (331)
++.+.|+.-||+.|..+|.+|| ++|++|+..|+-+|+.||++||...+....+.
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~ 59 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKK 59 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhh
Confidence 5678999999999999999999 67999999999999999999999888655444
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=97.18 E-value=0.00051 Score=61.43 Aligned_cols=53 Identities=19% Similarity=0.309 Sum_probs=45.6
Q ss_pred CCCCCCHHHHHHHHHHHHHhC---C----hhHHHhhcCCCCCHHHHHHHHHHHHHHHHHhh
Q 020106 73 NRRPFTEDEEERLLAAHRIHG---N----KWALIARLFPGRTDNAVKNHWHVIMARKQREQ 126 (331)
Q Consensus 73 ~kg~WT~EED~~Llelv~~~G---~----kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~~~ 126 (331)
....||.|||.+|.+.|..|= . -...+++.| +||+.+|.=|||..+|++....
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~~ 62 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEEA 62 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHHH
Confidence 457899999999999998873 2 288999999 9999999999999999876554
No 29
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.01 E-value=0.00051 Score=70.14 Aligned_cols=46 Identities=22% Similarity=0.531 Sum_probs=42.4
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcc
Q 020106 21 PRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQ 67 (331)
Q Consensus 21 kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~ 67 (331)
....||.+|..+|++.|+.||. +|.+||.++..|+..||..|+.++
T Consensus 278 ~dk~WS~qE~~LLLEGIe~ygD-dW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYGD-DWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhhh-hHHHHHHHhCCCCHHHHHHHHHcC
Confidence 4568999999999999999997 699999999999999999999773
No 30
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.98 E-value=0.00071 Score=53.06 Aligned_cols=52 Identities=25% Similarity=0.495 Sum_probs=36.7
Q ss_pred CCCCCHHHHHHHHHHHHH------hCC--------hhHHHhhcCC----CCCHHHHHHHHHHHHHHHHHh
Q 020106 74 RRPFTEDEEERLLAAHRI------HGN--------KWALIARLFP----GRTDNAVKNHWHVIMARKQRE 125 (331)
Q Consensus 74 kg~WT~EED~~Llelv~~------~G~--------kWs~IAk~Lp----gRT~nq~KnRW~~ilkrk~~~ 125 (331)
+..||.+|...||+++.. ++. -|..||..|. .||+.||+++|+.+.++-...
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~~ 70 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKKI 70 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHCS
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHH
Confidence 357999999999999877 211 3999998763 599999999999977665533
No 31
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.94 E-value=0.00065 Score=70.45 Aligned_cols=48 Identities=27% Similarity=0.646 Sum_probs=43.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcc
Q 020106 19 TCPRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQ 67 (331)
Q Consensus 19 ~~kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~ 67 (331)
..-++.||.+|..+|+++|+.||. +|.+||.++.+|+..||..|+.+.
T Consensus 250 ~~~~~~WT~qE~lLLLE~ie~y~d-dW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 250 ESARPNWTEQETLLLLEAIEMYGD-DWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred ccCCCCccHHHHHHHHHHHHHhcc-cHHHHHhccCCCCHHHHHHHHHhc
Confidence 445788999999999999999997 699999999999999999999764
No 32
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=96.86 E-value=0.0014 Score=50.33 Aligned_cols=50 Identities=24% Similarity=0.446 Sum_probs=32.6
Q ss_pred CCCCCHHHHHHHHHHHHHhC--------Ch-hHHHhhcCC-CCCHHHHHHHHHHHHHHHH
Q 020106 74 RRPFTEDEEERLLAAHRIHG--------NK-WALIARLFP-GRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 74 kg~WT~EED~~Llelv~~~G--------~k-Ws~IAk~Lp-gRT~nq~KnRW~~ilkrk~ 123 (331)
+.+||.|||.+|++.|..+. ++ |.++++.-| .+|-.+.|+||...|+.+.
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 46899999999999997642 22 999999877 8999999999987776554
No 33
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=96.76 E-value=0.0071 Score=67.73 Aligned_cols=109 Identities=15% Similarity=0.332 Sum_probs=84.7
Q ss_pred CCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccch-------hhhc------cc----------------------
Q 020106 24 HWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRL-------RWFN------QL---------------------- 68 (331)
Q Consensus 24 ~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~-------Rw~n------~L---------------------- 68 (331)
.|+..+=..++.+.++||..+...||..|.+++...++. ||.. ++
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~~~ 905 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAIGK 905 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 599999999999999999999999999998888766642 2211 11
Q ss_pred ---------------CCCCCCCCCCHHHHHHHHHHHHHhC-ChhHHHhh------------cCCCCCHHHHHHHHHHHHH
Q 020106 69 ---------------DPRINRRPFTEDEEERLLAAHRIHG-NKWALIAR------------LFPGRTDNAVKNHWHVIMA 120 (331)
Q Consensus 69 ---------------~p~i~kg~WT~EED~~Llelv~~~G-~kWs~IAk------------~LpgRT~nq~KnRW~~ilk 120 (331)
.+..++..||+|||..|+-++.+|| .+|.+|-. ++..||+..|..|-+.+++
T Consensus 906 k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~ 985 (1033)
T PLN03142 906 KLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIR 985 (1033)
T ss_pred HHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHH
Confidence 1223445699999999999999999 67999843 3468999999999999999
Q ss_pred HHHHhhhhhcCC
Q 020106 121 RKQREQSKLCGK 132 (331)
Q Consensus 121 rk~~~~~~~~~~ 132 (331)
-..++......+
T Consensus 986 ~~~~e~~~~~~~ 997 (1033)
T PLN03142 986 LIEKENQEYDER 997 (1033)
T ss_pred HHHHHHhhhhhh
Confidence 887765544433
No 34
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.66 E-value=0.0018 Score=66.24 Aligned_cols=44 Identities=20% Similarity=0.366 Sum_probs=41.4
Q ss_pred CCCCHHHHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHHH
Q 020106 75 RPFTEDEEERLLAAHRIHGNKWALIARLFPGRTDNAVKNHWHVI 118 (331)
Q Consensus 75 g~WT~EED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~i 118 (331)
..||.+|..+|++.+..||..|.+||+++++||..||--||-++
T Consensus 280 k~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred ccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 48999999999999999999999999999999999999998653
No 35
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.54 E-value=0.0031 Score=57.08 Aligned_cols=53 Identities=17% Similarity=0.314 Sum_probs=44.6
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCh-------hHHHhhcCCCCCHHHHHHHHHHHHHHHHHhh
Q 020106 73 NRRPFTEDEEERLLAAHRIHGNK-------WALIARLFPGRTDNAVKNHWHVIMARKQREQ 126 (331)
Q Consensus 73 ~kg~WT~EED~~Llelv~~~G~k-------Ws~IAk~LpgRT~nq~KnRW~~ilkrk~~~~ 126 (331)
....||.|||.+|.+.|..|+.. ...++..| +||..+|.-|||.+++++....
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Yee~ 63 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQEQ 63 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHHHH
Confidence 46789999999999999888732 67777888 9999999999999998776543
No 36
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.51 E-value=0.0033 Score=65.39 Aligned_cols=46 Identities=22% Similarity=0.336 Sum_probs=42.4
Q ss_pred CCCCCCHHHHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHHH
Q 020106 73 NRRPFTEDEEERLLAAHRIHGNKWALIARLFPGRTDNAVKNHWHVI 118 (331)
Q Consensus 73 ~kg~WT~EED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~i 118 (331)
.+..||++|..+|++++..||-+|.+||.++++||..+|--|+..+
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhc
Confidence 3568999999999999999999999999999999999999988643
No 37
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=96.38 E-value=0.003 Score=48.63 Aligned_cols=50 Identities=26% Similarity=0.429 Sum_probs=33.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCC------CC--HHHHHHHhc-CCCccccchhhhcccCCC
Q 020106 22 RGHWRPAEDEKLRQLVEQYGA------QN--WNSIAEKLQ-GRSGKSCRLRWFNQLDPR 71 (331)
Q Consensus 22 KG~WT~EED~~L~~lV~kyG~------~n--W~~IA~~lp-gRt~kQCr~Rw~n~L~p~ 71 (331)
|-++|.|||+.|++.|..+.. +| |.++++.-+ .+|-.+-|+||.+.|.+.
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~ 60 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGR 60 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT---
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcc
Confidence 457999999999999976521 12 999999887 899999999999998764
No 38
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.33 E-value=0.0023 Score=50.13 Aligned_cols=47 Identities=32% Similarity=0.634 Sum_probs=33.2
Q ss_pred CCCCCHHHHHHHHHHHHH--h----C---CC----CHHHHHHHh----cCCCccccchhhhccc
Q 020106 22 RGHWRPAEDEKLRQLVEQ--Y----G---AQ----NWNSIAEKL----QGRSGKSCRLRWFNQL 68 (331)
Q Consensus 22 KG~WT~EED~~L~~lV~k--y----G---~~----nW~~IA~~l----pgRt~kQCr~Rw~n~L 68 (331)
|..||.+|...|+.++.. + + .. -|..||..| ..|++.||+.||.++.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~ 64 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLK 64 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 457999999999999987 2 1 11 299999998 3599999999998854
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=96.08 E-value=0.0047 Score=55.34 Aligned_cols=48 Identities=21% Similarity=0.434 Sum_probs=41.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC---C---CHHHHHHHhcCCCccccchhhhcccC
Q 020106 21 PRGHWRPAEDEKLRQLVEQYGA---Q---NWNSIAEKLQGRSGKSCRLRWFNQLD 69 (331)
Q Consensus 21 kKG~WT~EED~~L~~lV~kyG~---~---nW~~IA~~lpgRt~kQCr~Rw~n~L~ 69 (331)
+.-.||.|||.+|.+.|-+|-. . .+.+++..+ +||...|.-||+.+++
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 4568999999999999999822 1 388899988 8999999999999886
No 40
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.97 E-value=0.011 Score=45.67 Aligned_cols=47 Identities=34% Similarity=0.493 Sum_probs=39.2
Q ss_pred CCCCCHHHHHHHHHHHHHh-----CCC-----------CHHHHHHHh-----cCCCccccchhhhccc
Q 020106 22 RGHWRPAEDEKLRQLVEQY-----GAQ-----------NWNSIAEKL-----QGRSGKSCRLRWFNQL 68 (331)
Q Consensus 22 KG~WT~EED~~L~~lV~ky-----G~~-----------nW~~IA~~l-----pgRt~kQCr~Rw~n~L 68 (331)
+..||++|...|+++|++| +.. -|..|+..| +.|+..||+.+|.++.
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 5689999999999999988 211 299999988 3599999999998864
No 41
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.97 E-value=0.02 Score=44.17 Aligned_cols=52 Identities=25% Similarity=0.491 Sum_probs=41.7
Q ss_pred CCCCCHHHHHHHHHHHHHhC----C-------------hhHHHhhcC-----CCCCHHHHHHHHHHHHHHHHHh
Q 020106 74 RRPFTEDEEERLLAAHRIHG----N-------------KWALIARLF-----PGRTDNAVKNHWHVIMARKQRE 125 (331)
Q Consensus 74 kg~WT~EED~~Llelv~~~G----~-------------kWs~IAk~L-----pgRT~nq~KnRW~~ilkrk~~~ 125 (331)
...||.+|.+.|++++.+|. + -|..|+..| +.||..+||.+|..+....+++
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk~ 75 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKKK 75 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 35799999999999998863 1 299999854 2499999999999987765543
No 42
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.53 E-value=0.014 Score=57.71 Aligned_cols=46 Identities=24% Similarity=0.420 Sum_probs=42.1
Q ss_pred CCCCCHHHHHHHHHHHHHhC-ChhHHHhhcCCCCCHHHHHHHHHHHH
Q 020106 74 RRPFTEDEEERLLAAHRIHG-NKWALIARLFPGRTDNAVKNHWHVIM 119 (331)
Q Consensus 74 kg~WT~EED~~Llelv~~~G-~kWs~IAk~LpgRT~nq~KnRW~~il 119 (331)
-..|+.+|+.+|++++...| ++|..||.+++.|+..+||.||-.+.
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y 109 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMY 109 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHH
Confidence 35799999999999999999 88999999998899999999997654
No 43
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.44 E-value=0.0095 Score=58.78 Aligned_cols=48 Identities=21% Similarity=0.479 Sum_probs=45.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcccC
Q 020106 22 RGHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQLD 69 (331)
Q Consensus 22 KG~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L~ 69 (331)
--.|+..|+-+|++..+..|.+||..||.++..|+...|+++|.+++.
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 456999999999999999999999999999999999999999999875
No 44
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=94.65 E-value=0.018 Score=52.11 Aligned_cols=49 Identities=18% Similarity=0.472 Sum_probs=39.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCC------HHHHHHHhcCCCccccchhhhcccC
Q 020106 20 CPRGHWRPAEDEKLRQLVEQYGAQN------WNSIAEKLQGRSGKSCRLRWFNQLD 69 (331)
Q Consensus 20 ~kKG~WT~EED~~L~~lV~kyG~~n------W~~IA~~lpgRt~kQCr~Rw~n~L~ 69 (331)
.+...||.|||.+|.+.|-.|+... ...++..| +|+..+|..||+.+++
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vr 57 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVR 57 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHH
Confidence 3567899999999999999886432 55566666 7999999999977765
No 45
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=94.41 E-value=0.055 Score=53.08 Aligned_cols=56 Identities=20% Similarity=0.326 Sum_probs=45.1
Q ss_pred CCCCCHHHHHHHHHHHHHh----------CChhHHHhhcCC----CCCHHHHHHHHHHHHHHHHHhhhhh
Q 020106 74 RRPFTEDEEERLLAAHRIH----------GNKWALIARLFP----GRTDNAVKNHWHVIMARKQREQSKL 129 (331)
Q Consensus 74 kg~WT~EED~~Llelv~~~----------G~kWs~IAk~Lp----gRT~nq~KnRW~~ilkrk~~~~~~~ 129 (331)
...|+.+|-..||++..++ +.-|..||+.+. -||+.+||++|.++.++.++.+...
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k~~~ 123 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEKAKK 123 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 4789999999999998653 234999998442 3999999999999998887776543
No 46
>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=93.94 E-value=0.11 Score=44.37 Aligned_cols=54 Identities=19% Similarity=0.413 Sum_probs=43.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC----hhHHHhh------------cCCCCCHHHHHHHHHHHHHHHHH
Q 020106 71 RINRRPFTEDEEERLLAAHRIHGN----KWALIAR------------LFPGRTDNAVKNHWHVIMARKQR 124 (331)
Q Consensus 71 ~i~kg~WT~EED~~Llelv~~~G~----kWs~IAk------------~LpgRT~nq~KnRW~~ilkrk~~ 124 (331)
..++..||+|||.-|+-++.+||- .|..|-. .+..||+.+|..|-+.+++-..+
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i~K 115 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLIEK 115 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHHHC
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHHHH
Confidence 566789999999999999999996 7988865 34679999999999999886543
No 47
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=92.78 E-value=0.12 Score=52.18 Aligned_cols=83 Identities=14% Similarity=0.308 Sum_probs=61.6
Q ss_pred HHHHHHHhcCCCccccchhhhcccCCC-------------------------CCCCCCCHHHHHHHHHHHHHhCChhHHH
Q 020106 45 WNSIAEKLQGRSGKSCRLRWFNQLDPR-------------------------INRRPFTEDEEERLLAAHRIHGNKWALI 99 (331)
Q Consensus 45 W~~IA~~lpgRt~kQCr~Rw~n~L~p~-------------------------i~kg~WT~EED~~Llelv~~~G~kWs~I 99 (331)
|.-+.-..+.|...-.-.||.+..++. ++...||.||-+-|.++++.|.-+|-.|
T Consensus 76 W~w~pFtn~aRkD~~~l~HWvr~~d~~~dypfakfNk~vdipsYt~eEYe~~l~dn~WskeETD~LF~lck~fDLRf~VI 155 (445)
T KOG2656|consen 76 WKWVPFTNSARKDDATLHHWVRVGDTPKDYPFAKFNKHVDIPSYTDEEYEAHLNDNSWSKEETDYLFDLCKRFDLRFFVI 155 (445)
T ss_pred ceeeccCCccccCCceEEeeeeccCCCCCCchhhhccccCccccchHHHHHhhccccccHHHHHHHHHHHHhcCeeEEEE
Confidence 555544445566666666776653221 1235699999999999999999999999
Q ss_pred hhc-----CCC-CCHHHHHHHHHHHHHHHHHhhh
Q 020106 100 ARL-----FPG-RTDNAVKNHWHVIMARKQREQS 127 (331)
Q Consensus 100 Ak~-----Lpg-RT~nq~KnRW~~ilkrk~~~~~ 127 (331)
|.. ++. ||-.++|.||..+.++-.+...
T Consensus 156 aDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~ 189 (445)
T KOG2656|consen 156 ADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARA 189 (445)
T ss_pred eeccchhhccccccHHHHHHHHHHHHHHHHHccC
Confidence 976 666 9999999999988776665443
No 48
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=91.95 E-value=0.27 Score=38.82 Aligned_cols=46 Identities=30% Similarity=0.494 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHHh---CC----------hhHHHhhcCC---C--CCHHHHHHHHHHHHHH
Q 020106 76 PFTEDEEERLLAAHRIH---GN----------KWALIARLFP---G--RTDNAVKNHWHVIMAR 121 (331)
Q Consensus 76 ~WT~EED~~Llelv~~~---G~----------kWs~IAk~Lp---g--RT~nq~KnRW~~ilkr 121 (331)
.||+++++.|++++.+. |+ .|..|+..|. | .+..||++||..+.+.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~ 64 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKD 64 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHH
Confidence 49999999999987543 21 2999988652 2 5889999999876543
No 49
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=91.19 E-value=0.31 Score=49.37 Aligned_cols=46 Identities=26% Similarity=0.453 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHHHHH
Q 020106 75 RPFTEDEEERLLAAHRIHGNKWALIARLFPGRTDNAVKNHWHVIMA 120 (331)
Q Consensus 75 g~WT~EED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~ilk 120 (331)
.+|+.+|-++...+...+|..++.|+..+|.|...|||.+|..--|
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek 411 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEK 411 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhh
Confidence 4899999999999999999999999999999999999999975443
No 50
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=89.37 E-value=0.34 Score=49.03 Aligned_cols=61 Identities=20% Similarity=0.460 Sum_probs=48.7
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhccc--CCC------CCCCCCCHHHHHH
Q 020106 23 GHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQL--DPR------INRRPFTEDEEER 84 (331)
Q Consensus 23 G~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L--~p~------i~kg~WT~EED~~ 84 (331)
-+|+.+|-.++..+....|+ ++..|+..+|.|..+|+..+|.+-- +|. ..+.|+..+|--.
T Consensus 366 ~~Ws~~e~ekFYKALs~wGt-dF~LIs~lfP~R~RkqIKaKfi~Eek~nP~rIn~aL~~kkp~d~~eY~k 434 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGT-DFSLISSLFPNRERKQIKAKFIKEEKVNPERINEALNEKKPFDQVEYNK 434 (507)
T ss_pred CcccHHHHHHHHHHHHHhcc-hHHHHHHhcCchhHHHHHHHHHHHhhhCHHHHHHHHhccCCCCHHHHhh
Confidence 47999999999999999997 6999999999999999999997743 221 1245666666543
No 51
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=88.32 E-value=1.1 Score=31.80 Aligned_cols=41 Identities=17% Similarity=0.332 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHHHHH
Q 020106 79 EDEEERLLAAHRIHGNKWALIARLFPGRTDNAVKNHWHVIMA 120 (331)
Q Consensus 79 ~EED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~ilk 120 (331)
++++..++.++...|-.|.+||+.+ |.+...|+.+....++
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 4678889999999999999999999 9999999998876554
No 52
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=88.26 E-value=2.4 Score=43.96 Aligned_cols=50 Identities=12% Similarity=0.204 Sum_probs=44.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 74 RRPFTEDEEERLLAAHRIHGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 74 kg~WT~EED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
...||.||-.++-++...||..+.+|-+.||.|+-..+..+|....|.+.
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK~~~ 236 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKKTRE 236 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHHHhh
Confidence 46899999999999999999999999999999999999998877765443
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=87.85 E-value=0.55 Score=40.13 Aligned_cols=48 Identities=21% Similarity=0.389 Sum_probs=36.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC---CCHHHHHHHh------------cCCCccccchhhhc
Q 020106 19 TCPRGHWRPAEDEKLRQLVEQYGA---QNWNSIAEKL------------QGRSGKSCRLRWFN 66 (331)
Q Consensus 19 ~~kKG~WT~EED~~L~~lV~kyG~---~nW~~IA~~l------------pgRt~kQCr~Rw~n 66 (331)
..++..||.+||.-|+-++.+||. +.|..|...+ ..||+..+..|-..
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~t 108 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNT 108 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHH
Confidence 566788999999999999999999 7899998865 24666666665543
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=87.68 E-value=0.83 Score=36.57 Aligned_cols=32 Identities=28% Similarity=0.547 Sum_probs=19.5
Q ss_pred CCCCCCCCCHHHHHHH--------HHHHHHhCCCCHHHHHHHh
Q 020106 18 STCPRGHWRPAEDEKL--------RQLVEQYGAQNWNSIAEKL 52 (331)
Q Consensus 18 p~~kKG~WT~EED~~L--------~~lV~kyG~~nW~~IA~~l 52 (331)
|.-..|-||+|+|+.| .+++++|| +..|+...
T Consensus 43 P~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG---~~~i~~R~ 82 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLRSGDKDDIERLIKKHG---EERIERRK 82 (87)
T ss_dssp -TT-TT---HHHHHHHTS--HHHHHHHHHHH----HHHHHHHH
T ss_pred CCCCCCCcCHHHHHHHHcCCHHHHHHHHHHhC---HHHHHHHH
Confidence 5567899999999999 56667777 66676543
No 55
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=85.26 E-value=1.7 Score=42.74 Aligned_cols=47 Identities=23% Similarity=0.409 Sum_probs=37.1
Q ss_pred CCCCCHHHHHHHHHHHHHh---------CCCCHHHHHHHh----cCCCccccchhhhccc
Q 020106 22 RGHWRPAEDEKLRQLVEQY---------GAQNWNSIAEKL----QGRSGKSCRLRWFNQL 68 (331)
Q Consensus 22 KG~WT~EED~~L~~lV~ky---------G~~nW~~IA~~l----pgRt~kQCr~Rw~n~L 68 (331)
-..|+.+|-..|+.+.... ....|..||+.+ .-|++.||+.+|.++.
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 3689999999999988633 112399999976 2499999999998854
No 56
>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=84.70 E-value=1.4 Score=34.75 Aligned_cols=44 Identities=27% Similarity=0.570 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHHHh---CCC---------CHHHHHHHhcC-----CCccccchhhhcc
Q 020106 24 HWRPAEDEKLRQLVEQY---GAQ---------NWNSIAEKLQG-----RSGKSCRLRWFNQ 67 (331)
Q Consensus 24 ~WT~EED~~L~~lV~ky---G~~---------nW~~IA~~lpg-----Rt~kQCr~Rw~n~ 67 (331)
.||+++++.|++++... |.. .|..|++.|.. .+..||+.||..+
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~l 61 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTL 61 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHH
Confidence 59999999999988654 222 29999998832 4567888887553
No 57
>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=77.07 E-value=6.7 Score=27.54 Aligned_cols=42 Identities=14% Similarity=0.201 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHHHHHHH
Q 020106 80 DEEERLLAAHRIHGNKWALIARLFPGRTDNAVKNHWHVIMARK 122 (331)
Q Consensus 80 EED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk 122 (331)
+++..++.++-..|..+.+||+.| |-+...|+.+....+++-
T Consensus 7 ~~er~vi~~~y~~~~t~~eIa~~l-g~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 7 PREREVIRLRYFEGLTLEEIAERL-GISRSTVRRILKRALKKL 48 (50)
T ss_dssp HHHHHHHHHHHTST-SHHHHHHHH-TSCHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHH-CCcHHHHHHHHHHHHHHh
Confidence 566677777766677899999999 999999999988877654
No 58
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=75.86 E-value=2.6 Score=46.07 Aligned_cols=41 Identities=12% Similarity=0.417 Sum_probs=37.9
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhh
Q 020106 23 GHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRW 64 (331)
Q Consensus 23 G~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw 64 (331)
-.||+.|-.++.+++-.|. +++-.|++++++++.+||-+-|
T Consensus 620 d~WTp~E~~lF~kA~y~~~-KDF~~v~km~~~KtVaqCVeyY 660 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYS-KDFIFVQKMVKSKTVAQCVEYY 660 (907)
T ss_pred ccccHHHHHHHHHHHHHhc-ccHHHHHHHhccccHHHHHHHH
Confidence 4799999999999999998 5899999999999999998766
No 59
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=75.18 E-value=3.5 Score=28.86 Aligned_cols=38 Identities=29% Similarity=0.442 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhc
Q 020106 28 AEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFN 66 (331)
Q Consensus 28 EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n 66 (331)
+=|.+|+.+.+.-+...|.+||+.+ |=+...|+.|+.+
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 8999999999865
No 60
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=73.56 E-value=2.4 Score=43.28 Aligned_cols=87 Identities=16% Similarity=0.332 Sum_probs=58.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHH-----hcC-CCccccchhhhcccC----------CC-CCCCCCCHHHH
Q 020106 20 CPRGHWRPAEDEKLRQLVEQYGAQNWNSIAEK-----LQG-RSGKSCRLRWFNQLD----------PR-INRRPFTEDEE 82 (331)
Q Consensus 20 ~kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~-----lpg-Rt~kQCr~Rw~n~L~----------p~-i~kg~WT~EED 82 (331)
++-..||++|-+-|.++++.|.- .|-.||.. ++. ||....++||..+.. ++ ++.-.+..|-|
T Consensus 128 l~dn~WskeETD~LF~lck~fDL-Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~~s~sdllk~~~yd~e~E 206 (445)
T KOG2656|consen 128 LNDNSWSKEETDYLFDLCKRFDL-RFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARAPSNSDLLKSLVYDAEHE 206 (445)
T ss_pred hccccccHHHHHHHHHHHHhcCe-eEEEEeeccchhhccccccHHHHHHHHHHHHHHHHHccCCCchhhhhccccchHHH
Confidence 34467999999999999999997 49999977 454 999999999976542 11 23334444444
Q ss_pred HHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHHH
Q 020106 83 ERLLAAHRIHGNKWALIARLFPGRTDNAVKNHWHVI 118 (331)
Q Consensus 83 ~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~i 118 (331)
..=.+ .+...+ .||+.||+.-=.-+
T Consensus 207 r~RKk----------~L~~L~-sRt~~qvaEEe~Ll 231 (445)
T KOG2656|consen 207 RERKK----------YLERLL-SRTPEQVAEEEALL 231 (445)
T ss_pred HHHHH----------HHHHHH-hcCHHHHHHHHHHH
Confidence 33222 233344 78888887653333
No 61
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=69.42 E-value=12 Score=31.10 Aligned_cols=37 Identities=19% Similarity=0.296 Sum_probs=28.0
Q ss_pred HHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHHHHHHH
Q 020106 85 LLAAHRIHGNKWALIARLFPGRTDNAVKNHWHVIMARK 122 (331)
Q Consensus 85 Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk 122 (331)
++.+.-..|..+.+||+.| |.+...|++++....++-
T Consensus 121 il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~L 157 (161)
T TIGR02985 121 IFILSRFEGKSYKEIAEEL-GISVKTVEYHISKALKEL 157 (161)
T ss_pred HHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3333334567899999999 999999999998765543
No 62
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=69.30 E-value=9 Score=41.22 Aligned_cols=49 Identities=12% Similarity=0.388 Sum_probs=37.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHh-c---------CCCccccchhhhcccC
Q 020106 20 CPRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKL-Q---------GRSGKSCRLRWFNQLD 69 (331)
Q Consensus 20 ~kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~l-p---------gRt~kQCr~Rw~n~L~ 69 (331)
..|..||-.|..-+..++.++| +++.+|-..+ . -++..|+|.+|.+.+.
T Consensus 86 ~~ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~ 144 (782)
T KOG4468|consen 86 WAKTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVR 144 (782)
T ss_pred ccccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHH
Confidence 3477899999999999999999 5899884433 2 2455788888877654
No 63
>smart00595 MADF subfamily of SANT domain.
Probab=68.98 E-value=7.1 Score=30.33 Aligned_cols=29 Identities=31% Similarity=0.595 Sum_probs=23.7
Q ss_pred hHHHhhcCCCCCHHHHHHHHHHHHHHHHHh
Q 020106 96 WALIARLFPGRTDNAVKNHWHVIMARKQRE 125 (331)
Q Consensus 96 Ws~IAk~LpgRT~nq~KnRW~~ilkrk~~~ 125 (331)
|.+||..| |-+..+|+.+|+.+..+-.++
T Consensus 30 W~~Ia~~l-~~~~~~~~~kw~~LR~~y~~e 58 (89)
T smart00595 30 WEEIAEEL-GLSVEECKKRWKNLRDRYRRE 58 (89)
T ss_pred HHHHHHHH-CcCHHHHHHHHHHHHHHHHHH
Confidence 99999999 559999999999886544433
No 64
>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=68.76 E-value=19 Score=36.04 Aligned_cols=53 Identities=23% Similarity=0.430 Sum_probs=41.6
Q ss_pred CCCCCHHHHHHHHHHHHHh-CCh---hHHHhhcCCCCCHHHHHHHHHHHHHHHHHhh
Q 020106 74 RRPFTEDEEERLLAAHRIH-GNK---WALIARLFPGRTDNAVKNHWHVIMARKQREQ 126 (331)
Q Consensus 74 kg~WT~EED~~Llelv~~~-G~k---Ws~IAk~LpgRT~nq~KnRW~~ilkrk~~~~ 126 (331)
-..||.-|...|+++.+-. |.. -++|++.++||+..+|++.-+.+..|..++.
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rvarea 77 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRVAREA 77 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHHHHHH
Confidence 4689999999999887654 433 5789999999999999998777666655553
No 65
>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=68.56 E-value=28 Score=34.90 Aligned_cols=86 Identities=23% Similarity=0.395 Sum_probs=63.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCC---CHHHHHHHhcCCCccccchhhhcccCCCCCCCCCCHHHHHHHHHHHHH-h-----
Q 020106 22 RGHWRPAEDEKLRQLVEQYGAQ---NWNSIAEKLQGRSGKSCRLRWFNQLDPRINRRPFTEDEEERLLAAHRI-H----- 92 (331)
Q Consensus 22 KG~WT~EED~~L~~lV~kyG~~---nW~~IA~~lpgRt~kQCr~Rw~n~L~p~i~kg~WT~EED~~Llelv~~-~----- 92 (331)
...||..|...|+.+.+..... +-.+|++.+++|+..++++ |.+.|+ +..+.+++++ |
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~-fl~~LK------------~rvareaiqkv~~~g~~ 87 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRD-FLQQLK------------GRVAREAIQKVHPGGLK 87 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHH-HHHHHH------------HHHHHHHHHHhcccccc
Confidence 4579999999999998766322 4678999999999988876 434444 3345555554 2
Q ss_pred CC------------hhHHHhhcCCCCCHHHHHHHHHHHHH
Q 020106 93 GN------------KWALIARLFPGRTDNAVKNHWHVIMA 120 (331)
Q Consensus 93 G~------------kWs~IAk~LpgRT~nq~KnRW~~ilk 120 (331)
|. -|..+|+.+-|.-...+-.-|.++|-
T Consensus 88 ~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~ 127 (344)
T PF11035_consen 88 GPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLT 127 (344)
T ss_pred cccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHH
Confidence 21 19999999999999999888887764
No 66
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=66.77 E-value=14 Score=25.79 Aligned_cols=38 Identities=16% Similarity=0.354 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHhCC-hhHHHhhcCCCCCHHHHHHHHHHH
Q 020106 80 DEEERLLAAHRIHGN-KWALIARLFPGRTDNAVKNHWHVI 118 (331)
Q Consensus 80 EED~~Llelv~~~G~-kWs~IAk~LpgRT~nq~KnRW~~i 118 (331)
+=|.+|+++...-|. -|.+||+.+ |=|...|..|++.+
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 457788888877774 499999999 99999999998764
No 67
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=66.04 E-value=6.5 Score=34.18 Aligned_cols=44 Identities=14% Similarity=0.169 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcccCCCC
Q 020106 28 AEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQLDPRI 72 (331)
Q Consensus 28 EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L~p~i 72 (331)
+-|.+|+.+.++.|...|.+||+.+ |-+...|+.|+.++....+
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 5789999999999988999999998 8999999999998776543
No 68
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=64.31 E-value=12 Score=32.46 Aligned_cols=44 Identities=14% Similarity=0.211 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHHhC-ChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 79 EDEEERLLAAHRIHG-NKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 79 ~EED~~Llelv~~~G-~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.+-|.+|+++.++-| ..|++||+.+ |-+...|+.|++.+.....
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 357888888887777 4599999999 9999999999988766443
No 69
>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=63.34 E-value=7.8 Score=34.73 Aligned_cols=41 Identities=32% Similarity=0.342 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHH
Q 020106 76 PFTEDEEERLLAAHRIHGNKWALIARLFPGRTDNAVKNHWHV 117 (331)
Q Consensus 76 ~WT~EED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~ 117 (331)
.||+|+.++|.+|. .-|..=++||+.|+|.|.|+|--+-+.
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 567778999999988999998776543
No 70
>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=62.33 E-value=3.2 Score=33.17 Aligned_cols=18 Identities=22% Similarity=0.304 Sum_probs=10.6
Q ss_pred CCCCCCCCCHHHHHHHHH
Q 020106 70 PRINRRPFTEDEEERLLA 87 (331)
Q Consensus 70 p~i~kg~WT~EED~~Lle 87 (331)
|....|-||+|+|+.|..
T Consensus 43 P~n~~GiWT~eDD~~L~~ 60 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLRS 60 (87)
T ss_dssp -TT-TT---HHHHHHHTS
T ss_pred CCCCCCCcCHHHHHHHHc
Confidence 566789999999999843
No 71
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=60.32 E-value=15 Score=40.43 Aligned_cols=45 Identities=9% Similarity=0.089 Sum_probs=40.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHHH
Q 020106 74 RRPFTEDEEERLLAAHRIHGNKWALIARLFPGRTDNAVKNHWHVI 118 (331)
Q Consensus 74 kg~WT~EED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~i 118 (331)
...||+.|-.+.-+++..|.+.+-.|++.++++|-.+|-.+|...
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtW 663 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTW 663 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHH
Confidence 357999999999999999999999999999999999998775544
No 72
>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=60.22 E-value=21 Score=28.71 Aligned_cols=37 Identities=19% Similarity=0.270 Sum_probs=27.8
Q ss_pred HHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHHHHHHH
Q 020106 85 LLAAHRIHGNKWALIARLFPGRTDNAVKNHWHVIMARK 122 (331)
Q Consensus 85 Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk 122 (331)
++.++...|..+.+||+.+ |-+...|+++....+++-
T Consensus 118 ii~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~kl 154 (158)
T TIGR02937 118 VLVLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKKL 154 (158)
T ss_pred HHhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3344444677899999999 779999999988765543
No 73
>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=60.22 E-value=12 Score=28.11 Aligned_cols=33 Identities=27% Similarity=0.452 Sum_probs=25.3
Q ss_pred hhHHHhhcCCC-CCHHHHHHHHHHHHHHHHHhhh
Q 020106 95 KWALIARLFPG-RTDNAVKNHWHVIMARKQREQS 127 (331)
Q Consensus 95 kWs~IAk~Lpg-RT~nq~KnRW~~ilkrk~~~~~ 127 (331)
-|..||..|+. -+..+|+.+|+.+..+-.++..
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y~~~~~ 61 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRDRYRRELK 61 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHHHHHHHHH
Confidence 39999999954 5788999999998765544443
No 74
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=60.13 E-value=7.3 Score=34.30 Aligned_cols=45 Identities=13% Similarity=0.135 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcccCCCC
Q 020106 27 PAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQLDPRI 72 (331)
Q Consensus 27 ~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L~p~i 72 (331)
.+-|.+|+.+.++.|...|.+||+.+ |-+...|+.|++++.+..+
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 56789999999999988999999998 8999999999998876554
No 75
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=58.76 E-value=9.3 Score=39.85 Aligned_cols=46 Identities=17% Similarity=0.278 Sum_probs=39.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhc
Q 020106 20 CPRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFN 66 (331)
Q Consensus 20 ~kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n 66 (331)
.-.-.||.||--++.++...||. ++.+|-+.||.|+..++..-|..
T Consensus 185 ~~~d~WT~Ed~vlFe~aF~~~GK-~F~kIrq~LP~rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 185 EFPDEWTAEDIVLFEQAFQFFGK-DFHKIRQALPHRSLASLVQYYYS 230 (534)
T ss_pred CCcccchHHHHHHHHHHHHHhcc-cHHHHHHHccCccHHHHHHHHHH
Confidence 34567999999999999999995 79999999999999888765543
No 76
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=58.14 E-value=18 Score=39.04 Aligned_cols=48 Identities=21% Similarity=0.398 Sum_probs=37.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCChhHHHhh----------cCCCCCHHHHHHHHHHHHHH
Q 020106 74 RRPFTEDEEERLLAAHRIHGNKWALIAR----------LFPGRTDNAVKNHWHVIMAR 121 (331)
Q Consensus 74 kg~WT~EED~~Llelv~~~G~kWs~IAk----------~LpgRT~nq~KnRW~~ilkr 121 (331)
+..||-.|++-...+++++|.++..|-. ...-+|..|++.+|...+++
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~ 145 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRR 145 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHH
Confidence 5689999999999999999999988822 23336777888887665543
No 77
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=57.43 E-value=17 Score=31.97 Aligned_cols=44 Identities=7% Similarity=0.071 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHhC-ChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 79 EDEEERLLAAHRIHG-NKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 79 ~EED~~Llelv~~~G-~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.+-|.+|+.+.++-| -.|++||+.+ |-+...|..|++.+.+...
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 466888888887777 4599999999 9999999999998876554
No 78
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=54.33 E-value=24 Score=32.93 Aligned_cols=44 Identities=14% Similarity=0.249 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHHHhCChhHHHhhc--CCC-CCHHHHHHHHHHHHH
Q 020106 76 PFTEDEEERLLAAHRIHGNKWALIARL--FPG-RTDNAVKNHWHVIMA 120 (331)
Q Consensus 76 ~WT~EED~~Llelv~~~G~kWs~IAk~--Lpg-RT~nq~KnRW~~ilk 120 (331)
.|++++|-+|+.+|. .++.-..|+.- |.. -|-.+|..||..++-
T Consensus 1 rW~~~DDl~Li~av~-~~~~L~~v~~gvkFS~~fT~~Ei~~RW~~lly 47 (199)
T PF13325_consen 1 RWKPEDDLLLINAVE-QTNDLESVHLGVKFSCKFTLQEIEERWYALLY 47 (199)
T ss_pred CCCchhhHHHHHHHH-HhcCHHHHHccCCcCCcCcHHHHHHHHHHHHc
Confidence 599999999999994 45555666553 433 588999999999873
No 79
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=54.07 E-value=14 Score=42.11 Aligned_cols=34 Identities=15% Similarity=0.300 Sum_probs=29.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHh
Q 020106 19 TCPRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKL 52 (331)
Q Consensus 19 ~~kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~l 52 (331)
..++..||.|||..|+-++.+||.++|.+|...+
T Consensus 923 ~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i 956 (1033)
T PLN03142 923 QNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAF 956 (1033)
T ss_pred CCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHH
Confidence 3445669999999999999999999999998776
No 80
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=53.22 E-value=36 Score=28.77 Aligned_cols=31 Identities=19% Similarity=0.214 Sum_probs=25.4
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|..+.+||+.| |-+...|++++...+++-+
T Consensus 140 ~~~~~~eIA~~l-gis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 140 EGLSYREIAEIL-GVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 466799999999 9999999999887665544
No 81
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=53.20 E-value=30 Score=28.43 Aligned_cols=51 Identities=12% Similarity=0.119 Sum_probs=33.7
Q ss_pred CCCCHHHHHHHHHHHHHh----C----ChhHHHhh----cCCC-CCHHHHHHHHHHHHHHHHHh
Q 020106 75 RPFTEDEEERLLAAHRIH----G----NKWALIAR----LFPG-RTDNAVKNHWHVIMARKQRE 125 (331)
Q Consensus 75 g~WT~EED~~Llelv~~~----G----~kWs~IAk----~Lpg-RT~nq~KnRW~~ilkrk~~~ 125 (331)
.-||+|+|..|++++..| | ..|..... .|.- =+.+|+.++-+.+-+|-...
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~ 68 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNA 68 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHH
Confidence 469999999999998776 5 23544433 3322 37788888877665554433
No 82
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=53.13 E-value=35 Score=28.96 Aligned_cols=32 Identities=19% Similarity=0.234 Sum_probs=25.7
Q ss_pred HhCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 91 IHGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 91 ~~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
..|..+..||+.| |.+...|+++....+++-.
T Consensus 142 ~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~Lr 173 (182)
T PRK09652 142 IEGLSYEEIAEIM-GCPIGTVRSRIFRAREALR 173 (182)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 4567899999999 8999999998876555444
No 83
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=52.46 E-value=24 Score=36.08 Aligned_cols=46 Identities=13% Similarity=0.176 Sum_probs=40.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCChhHHHhh-cCCCCCHHHHHHHHHHHH
Q 020106 74 RRPFTEDEEERLLAAHRIHGNKWALIAR-LFPGRTDNAVKNHWHVIM 119 (331)
Q Consensus 74 kg~WT~EED~~Llelv~~~G~kWs~IAk-~LpgRT~nq~KnRW~~il 119 (331)
-..|+++|....-+..+.||+.+..|.+ .++.|+--.|-.+|....
T Consensus 277 l~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWK 323 (445)
T KOG4329|consen 277 LSGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWK 323 (445)
T ss_pred cccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhh
Confidence 3579999999999999999999999965 699999999988776543
No 84
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=51.53 E-value=34 Score=30.41 Aligned_cols=40 Identities=18% Similarity=0.217 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHHHHHH
Q 020106 81 EEERLLAAHRIHGNKWALIARLFPGRTDNAVKNHWHVIMAR 121 (331)
Q Consensus 81 ED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~ilkr 121 (331)
+...++++..-.|-.+.+||+.| |-+...|+.+|..+...
T Consensus 139 ~~~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR~~ 178 (185)
T PF07638_consen 139 RQRRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRARAW 178 (185)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 33444445445678899999999 99999999999877543
No 85
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=51.19 E-value=40 Score=22.22 Aligned_cols=38 Identities=18% Similarity=0.322 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHHHH
Q 020106 81 EEERLLAAHRIHGNKWALIARLFPGRTDNAVKNHWHVIM 119 (331)
Q Consensus 81 ED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~il 119 (331)
++..++.++...|..+..||+.+ |-+...|+.+.....
T Consensus 14 ~~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~~ 51 (55)
T cd06171 14 REREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRAL 51 (55)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 34556666656778899999998 788888877765543
No 86
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=49.24 E-value=18 Score=38.83 Aligned_cols=44 Identities=25% Similarity=0.441 Sum_probs=41.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHH
Q 020106 74 RRPFTEDEEERLLAAHRIHGNKWALIARLFPGRTDNAVKNHWHV 117 (331)
Q Consensus 74 kg~WT~EED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~ 117 (331)
...|+.+|-++...+....|.+.+.|+..+|+|...+||.+|..
T Consensus 409 ~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 409 TDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKK 452 (584)
T ss_pred cCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhh
Confidence 46899999999999999999999999999999999999998864
No 87
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=49.05 E-value=46 Score=29.51 Aligned_cols=34 Identities=26% Similarity=0.250 Sum_probs=26.4
Q ss_pred HhCChhHHHhhcCCCCCHHHHHHHHHHHHHHHHHh
Q 020106 91 IHGNKWALIARLFPGRTDNAVKNHWHVIMARKQRE 125 (331)
Q Consensus 91 ~~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~~ 125 (331)
..|....+||..| |-+...|++|+....++-+..
T Consensus 148 ~~g~s~~EIA~~l-g~s~~tV~~rl~rar~~Lr~~ 181 (192)
T PRK09643 148 MQGYSVADAARML-GVAEGTVKSRCARGRARLAEL 181 (192)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHHH
Confidence 3566799999999 999999999997665544433
No 88
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=48.66 E-value=24 Score=27.37 Aligned_cols=44 Identities=27% Similarity=0.663 Sum_probs=30.1
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcccCCC-------CCCCCCCHHHHHHH
Q 020106 30 DEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQLDPR-------INRRPFTEDEEERL 85 (331)
Q Consensus 30 D~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L~p~-------i~kg~WT~EED~~L 85 (331)
+.+|.++|+.|| |...++.+.-||= .-+|. +.+.||-.+..+.|
T Consensus 12 e~il~~Lv~~yG---W~~L~~~i~i~CF---------~~~PsikSSLkFLRkTpWAR~KVE~l 62 (64)
T PF09905_consen 12 ETILTELVEHYG---WEELGERININCF---------KNNPSIKSSLKFLRKTPWAREKVENL 62 (64)
T ss_dssp HHHHHHHHHHT----HHHHHHHTTSSST---------TSS--HHHHHHHHHHSHHHHHHHHHH
T ss_pred HHHHHHHHHHhC---HHHHHhhcccccC---------CCCCchHHHHHHHhcCHhHHHHHHHh
Confidence 578899999999 9999999865543 12333 24678887776665
No 89
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=48.48 E-value=58 Score=26.74 Aligned_cols=69 Identities=14% Similarity=0.331 Sum_probs=42.5
Q ss_pred CCCCCHHHHHHHHHHHHHh----CC---CCHHHHHHHhcCC-----Ccccc-------chhhhcccCCCCCCC---CCCH
Q 020106 22 RGHWRPAEDEKLRQLVEQY----GA---QNWNSIAEKLQGR-----SGKSC-------RLRWFNQLDPRINRR---PFTE 79 (331)
Q Consensus 22 KG~WT~EED~~L~~lV~ky----G~---~nW~~IA~~lpgR-----t~kQC-------r~Rw~n~L~p~i~kg---~WT~ 79 (331)
...||+|++-.|++.+..| |. .+|..+...+.+. +..|+ +.||.+.... .+.| .++.
T Consensus 4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~~~k-~~~g~~~~~~~ 82 (98)
T PF04504_consen 4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNAVKK-SKNGKDPSFSK 82 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHhhh-cccCcCCCCCC
Confidence 4569999999999988777 52 2577766666332 22233 3455554443 2222 5777
Q ss_pred HHHHHHHHHHHH
Q 020106 80 DEEERLLAAHRI 91 (331)
Q Consensus 80 EED~~Llelv~~ 91 (331)
.-|..+.+|.++
T Consensus 83 ~hd~~~f~Lsk~ 94 (98)
T PF04504_consen 83 PHDRRLFELSKK 94 (98)
T ss_pred HhHHHHHHHHHH
Confidence 777777777643
No 90
>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=48.13 E-value=33 Score=26.97 Aligned_cols=37 Identities=22% Similarity=0.384 Sum_probs=26.6
Q ss_pred HHHHHHHHhC--------ChhHHHhhcCCCCC-----HHHHHHHHHHHHH
Q 020106 84 RLLAAHRIHG--------NKWALIARLFPGRT-----DNAVKNHWHVIMA 120 (331)
Q Consensus 84 ~Llelv~~~G--------~kWs~IAk~LpgRT-----~nq~KnRW~~ilk 120 (331)
.|..+|...| .+|..||+.|.--. ..++|..|..+|.
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhH
Confidence 4788888887 35999999883322 3678888887654
No 91
>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=47.90 E-value=25 Score=28.20 Aligned_cols=29 Identities=14% Similarity=0.310 Sum_probs=23.9
Q ss_pred HHHHHHHHHHhCChhHHHhhcCCCCCHHHH
Q 020106 82 EERLLAAHRIHGNKWALIARLFPGRTDNAV 111 (331)
Q Consensus 82 D~~Llelv~~~G~kWs~IAk~LpgRT~nq~ 111 (331)
|+.|..+....|..|..+|.+| |=|..+|
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 4668889999999999999999 6666544
No 92
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=45.95 E-value=65 Score=27.04 Aligned_cols=32 Identities=19% Similarity=0.158 Sum_probs=25.6
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQR 124 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~ 124 (331)
.|-.-.+||..| |-+...|+++....+++-+.
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 121 EDMDVAETAAAM-GCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred hcCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 456689999999 89999999998876655443
No 93
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=45.82 E-value=49 Score=28.53 Aligned_cols=31 Identities=13% Similarity=0.030 Sum_probs=24.6
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|..+.+||..| |-+...|+++.....++-+
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar~~Lr 181 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREALR 181 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 456789999999 9999999998876655443
No 94
>PRK04217 hypothetical protein; Provisional
Probab=45.42 E-value=69 Score=27.09 Aligned_cols=47 Identities=13% Similarity=-0.008 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 75 RPFTEDEEERLLAAHRIHGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 75 g~WT~EED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
..-|++| ..++.+....|-...+||+.| |-+...|+.+++...++-+
T Consensus 41 ~~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkkLr 87 (110)
T PRK04217 41 IFMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKKVA 87 (110)
T ss_pred ccCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 3455555 677788877888999999999 9999999999987665544
No 95
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=45.09 E-value=29 Score=38.79 Aligned_cols=104 Identities=15% Similarity=0.306 Sum_probs=67.7
Q ss_pred CCCCCCCC--CCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCcccc---------------------------------
Q 020106 16 STSTCPRG--HWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSC--------------------------------- 60 (331)
Q Consensus 16 ~~p~~kKG--~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQC--------------------------------- 60 (331)
..+-+..| .||+.+=...+.+.++||..+-..||+.+.+ |...+
T Consensus 787 k~~ll~~gft~w~k~df~~fi~a~eKygr~di~~ia~~~e~-~~eev~~y~rvfwer~~el~d~ek~~~~ie~~e~~i~r 865 (971)
T KOG0385|consen 787 KEELLSQGFTNWTKRDFNQFIKANEKYGRDDIENIAAEVEG-TPEEVGEYARVFWERLEELSDIEKIIYQIERGEKRIQR 865 (971)
T ss_pred hhhhhhccccchhhhhHHHHHHHhhccCcchhhhhHHhhcC-CHHHHHHHHHHHHHHHHHhhhhHHHHHHHhhhHhhhhH
Confidence 34445555 5999999999999999998887777766644 22111
Q ss_pred -----------chhhhc-----ccCCCCCCCCCCHHHHHHHHHHHHHhC----ChhHHHhh------------cCCCCCH
Q 020106 61 -----------RLRWFN-----QLDPRINRRPFTEDEEERLLAAHRIHG----NKWALIAR------------LFPGRTD 108 (331)
Q Consensus 61 -----------r~Rw~n-----~L~p~i~kg~WT~EED~~Llelv~~~G----~kWs~IAk------------~LpgRT~ 108 (331)
..||++ +-.+..+....|.+||..|+.++.++| +.|..+-. ++..||.
T Consensus 866 ~~~~~~~ld~k~~~~k~p~~l~i~~~~nk~~~ys~~edrfL~~~l~K~g~~~~~~~e~lr~~~~~~~~frfdw~~~sRt~ 945 (971)
T KOG0385|consen 866 GDSIKKALDDKIARYKAPHQLRIQYGTNKGKNYSEEEDRFLECMLHKLGFDAENVYEELRQPIRNSPQFRFDWFIKSRTA 945 (971)
T ss_pred HHHHHHHHhhhHhhhcCchheeeeeccccCCCCchhhHHHHHHHHHHhccCchhHHHHHHHHHhcCcccccceeeehhhH
Confidence 112222 001223567899999999999999998 33655533 2345777
Q ss_pred HHHHHHHHHHHH
Q 020106 109 NAVKNHWHVIMA 120 (331)
Q Consensus 109 nq~KnRW~~ilk 120 (331)
..+..|+++++.
T Consensus 946 ~el~Rr~ntli~ 957 (971)
T KOG0385|consen 946 MELQRRCNTLIT 957 (971)
T ss_pred HHHHhcCCeeEE
Confidence 777777776653
No 96
>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=44.93 E-value=31 Score=27.67 Aligned_cols=31 Identities=16% Similarity=0.301 Sum_probs=25.3
Q ss_pred HHHHHHHHHHhCChhHHHhhcCCCCCHHHHHH
Q 020106 82 EERLLAAHRIHGNKWALIARLFPGRTDNAVKN 113 (331)
Q Consensus 82 D~~Llelv~~~G~kWs~IAk~LpgRT~nq~Kn 113 (331)
|..|..+....|..|.++|+.| |=+..+|.+
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI~~ 34 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEINQ 34 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHHHH
Confidence 5678888899999999999999 766665543
No 97
>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=43.47 E-value=21 Score=28.16 Aligned_cols=35 Identities=29% Similarity=0.531 Sum_probs=27.2
Q ss_pred CHHHHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHH
Q 020106 78 TEDEEERLLAAHRIHGNKWALIARLFPGRTDNAVKNH 114 (331)
Q Consensus 78 T~EED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnR 114 (331)
..||.++|+..- ..|.+|..+|..| |=+...|++-
T Consensus 1 ~~~~v~~ll~~~-nlG~dW~~LA~~L-G~~~~~I~~i 35 (77)
T cd08311 1 KQEEVEKLLESG-RPGRDWRSLAGEL-GYEDEAIDTF 35 (77)
T ss_pred ChHHHHHHHhCC-CCccCHHHHHHHc-CCCHHHHHHH
Confidence 368888888432 5788999999999 8888887763
No 98
>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=43.34 E-value=30 Score=30.98 Aligned_cols=41 Identities=27% Similarity=0.371 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhc
Q 020106 24 HWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFN 66 (331)
Q Consensus 24 ~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n 66 (331)
.||.|+.++|.+|... |. .=.+||+.|.+.+...+.-+.++
T Consensus 2 ~Wtde~~~~L~~lw~~-G~-SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GL-SASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred CCCHHHHHHHHHHHHc-CC-CHHHHHHHhCCcchhhhhhhhhc
Confidence 4999999999999965 53 48999999976777777665544
No 99
>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=43.27 E-value=45 Score=28.87 Aligned_cols=31 Identities=16% Similarity=0.154 Sum_probs=24.6
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|....+||..| |-+.+.|+++.....++-+
T Consensus 153 ~~~s~~EIA~~l-gis~~tv~~~l~rar~~Lr 183 (190)
T TIGR02939 153 EGLSYEDIARIM-DCPVGTVRSRIFRAREAIA 183 (190)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 356689999999 8899999999877665544
No 100
>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=43.18 E-value=55 Score=27.99 Aligned_cols=31 Identities=19% Similarity=0.294 Sum_probs=24.3
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|....+||..| |-|...|++++...+++-.
T Consensus 134 ~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~Lr 164 (169)
T TIGR02954 134 HDLTIKEIAEVM-NKPEGTVKTYLHRALKKLK 164 (169)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 456688999999 7899999999887665543
No 101
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=42.14 E-value=67 Score=28.29 Aligned_cols=32 Identities=16% Similarity=0.065 Sum_probs=25.5
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQR 124 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~ 124 (331)
.|-...+||..| |-+...|+++.....++-+.
T Consensus 121 ~g~~~~EIA~~l-gis~~tV~~~l~Rar~~Lr~ 152 (181)
T PRK09637 121 EGLSQKEIAEKL-GLSLSGAKSRVQRGRVKLKE 152 (181)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHH
Confidence 466799999999 99999999998766555443
No 102
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=41.62 E-value=49 Score=26.26 Aligned_cols=39 Identities=23% Similarity=0.362 Sum_probs=28.3
Q ss_pred HHHHHHHHHhCC--------hhHHHhhcCCCC-----CHHHHHHHHHHHHHH
Q 020106 83 ERLLAAHRIHGN--------KWALIARLFPGR-----TDNAVKNHWHVIMAR 121 (331)
Q Consensus 83 ~~Llelv~~~G~--------kWs~IAk~LpgR-----T~nq~KnRW~~ilkr 121 (331)
-.|..+|.+.|+ +|..||+.|.-. ...++|..|..+|..
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 357778888773 599999987443 356788888877653
No 103
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=41.50 E-value=68 Score=28.08 Aligned_cols=33 Identities=12% Similarity=0.112 Sum_probs=25.3
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHHHh
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQRE 125 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~~ 125 (331)
.|-...+||..| |-+...|++++....++-+..
T Consensus 153 ~g~s~~eIA~~l-gis~~tv~~~l~Rar~~Lr~~ 185 (193)
T PRK11923 153 DGLSYEDIASVM-QCPVGTVRSRIFRAREAIDKA 185 (193)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHH
Confidence 345689999999 889999999988766655443
No 104
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=41.39 E-value=75 Score=27.80 Aligned_cols=31 Identities=13% Similarity=0.207 Sum_probs=24.8
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|-...+||..| |-+...|++++....++-.
T Consensus 146 ~~~s~~eIA~~l-gis~~tV~~~l~Rar~~Lr 176 (189)
T PRK12515 146 HEKSVEEVGEIV-GIPESTVKTRMFYARKKLA 176 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 456689999999 8899999999887655443
No 105
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=40.84 E-value=67 Score=28.06 Aligned_cols=31 Identities=29% Similarity=0.220 Sum_probs=24.9
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|....+||..| |-+...|+.+....+++-+
T Consensus 154 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~Lr 184 (189)
T PRK09648 154 VGLSAEETAEAV-GSTPGAVRVAQHRALARLR 184 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 466799999999 8899999999876665543
No 106
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=40.65 E-value=60 Score=27.99 Aligned_cols=31 Identities=13% Similarity=0.030 Sum_probs=23.7
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|....+||+.| |-+.+.|+++.....++-.
T Consensus 151 ~g~s~~eIA~~l-gis~~~v~~~l~Rar~~Lr 181 (187)
T TIGR02948 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREALR 181 (187)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 355689999999 8899999998876555433
No 107
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=40.00 E-value=59 Score=25.92 Aligned_cols=43 Identities=14% Similarity=0.179 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHhC-ChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 80 DEEERLLAAHRIHG-NKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 80 EED~~Llelv~~~G-~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
+.|..|+++....| ..+.+||+.+ |-+...|..+.+.+.++..
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~ 46 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGV 46 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 56788888888776 4699999999 9999999999998877543
No 108
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=39.71 E-value=76 Score=26.80 Aligned_cols=30 Identities=10% Similarity=-0.145 Sum_probs=24.0
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARK 122 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk 122 (331)
.|-.-.+||+.| |-+...|++|.....++-
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~L 150 (160)
T PRK09642 121 EEKSYQEIALQE-KIEVKTVEMKLYRARKWI 150 (160)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 456689999999 999999999987655543
No 109
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=39.56 E-value=72 Score=27.81 Aligned_cols=33 Identities=21% Similarity=0.089 Sum_probs=27.1
Q ss_pred HhCChhHHHhhcCCCCCHHHHHHHHHHHHHHHHH
Q 020106 91 IHGNKWALIARLFPGRTDNAVKNHWHVIMARKQR 124 (331)
Q Consensus 91 ~~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~ 124 (331)
..|....+||..| |-+.+.||.|....+++-..
T Consensus 141 ~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 141 LDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 3567799999999 99999999998877766543
No 110
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=39.09 E-value=74 Score=27.59 Aligned_cols=31 Identities=19% Similarity=0.140 Sum_probs=24.9
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|....+||..| |-+...|+.+....+++-.
T Consensus 146 ~g~s~~eIA~~l-~is~~tV~~~l~ra~~~Lr 176 (184)
T PRK12512 146 EGASIKETAAKL-SMSEGAVRVALHRGLAALA 176 (184)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 456689999999 9999999999887665544
No 111
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=38.45 E-value=82 Score=27.43 Aligned_cols=33 Identities=9% Similarity=-0.052 Sum_probs=24.7
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHHHh
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQRE 125 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~~ 125 (331)
.|....+||+.| |-+.+.|+++....+++-.+.
T Consensus 143 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr~~ 175 (186)
T PRK05602 143 QGLSNIEAAAVM-DISVDALESLLARGRRALRAQ 175 (186)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHHHHHH
Confidence 456688999998 889999999887666554433
No 112
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=38.42 E-value=80 Score=27.19 Aligned_cols=35 Identities=20% Similarity=0.149 Sum_probs=27.2
Q ss_pred HHHHhCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 88 AHRIHGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 88 lv~~~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
+....|-...+||+.| |.+...|+.+...-+++-.
T Consensus 130 L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~~ 164 (172)
T PRK12523 130 YNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQCY 164 (172)
T ss_pred HHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 3334566799999999 9999999999877666544
No 113
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=38.18 E-value=81 Score=27.83 Aligned_cols=31 Identities=6% Similarity=-0.174 Sum_probs=24.9
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|-...+||..| |-+...||.|.....++-+
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~RAr~~Lr 179 (189)
T PRK12530 149 LELSSEQICQEC-DISTSNLHVLLYRARLQLQ 179 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 466799999999 9999999999876655433
No 114
>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=38.08 E-value=76 Score=28.04 Aligned_cols=32 Identities=6% Similarity=-0.094 Sum_probs=25.5
Q ss_pred HhCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 91 IHGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 91 ~~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
..|....+||..| |-+.+.|+.|....+++-+
T Consensus 145 ~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~Lr 176 (188)
T TIGR02943 145 VLGFESDEICQEL-EISTSNCHVLLYRARLSLR 176 (188)
T ss_pred HhCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 3466789999999 9999999999877665544
No 115
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=37.79 E-value=40 Score=26.93 Aligned_cols=44 Identities=16% Similarity=0.154 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcccCCCC
Q 020106 28 AEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQLDPRI 72 (331)
Q Consensus 28 EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L~p~i 72 (331)
+.|.+|+.+..+.+...+..||+.+ |-+...|+.|..++....+
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~ 46 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGV 46 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 5688899999998888899999998 8899999998887766443
No 116
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=37.69 E-value=81 Score=26.99 Aligned_cols=31 Identities=26% Similarity=0.274 Sum_probs=24.6
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|-.-.+||+.| |.+...|+.|....+++-+
T Consensus 133 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~Lr 163 (173)
T PRK09645 133 RGWSTAQIAADL-GIPEGTVKSRLHYALRALR 163 (173)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 455679999999 9999999999877665544
No 117
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=37.60 E-value=90 Score=27.58 Aligned_cols=33 Identities=15% Similarity=-0.110 Sum_probs=26.0
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHHHh
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQRE 125 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~~ 125 (331)
.|-.+.+||+.| |-+...|+++....+++-+..
T Consensus 151 ~g~s~~eIA~~l-gis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 151 EGLSNPEIAEVM-EIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHHH
Confidence 456799999999 999999999887766555443
No 118
>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=37.57 E-value=38 Score=26.62 Aligned_cols=30 Identities=23% Similarity=0.556 Sum_probs=23.7
Q ss_pred HHHHHHHHHHhCChhHHHhhcCCCCCHHHHH
Q 020106 82 EERLLAAHRIHGNKWALIARLFPGRTDNAVK 112 (331)
Q Consensus 82 D~~Llelv~~~G~kWs~IAk~LpgRT~nq~K 112 (331)
|..|..+....|..|.++|+.| |=+..+|.
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI~ 33 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDID 33 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHHH
Confidence 4567788889999999999999 66665543
No 119
>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=37.14 E-value=64 Score=28.64 Aligned_cols=46 Identities=20% Similarity=0.221 Sum_probs=37.5
Q ss_pred CCCCCCHHHHHHHHHHHHHhCChhHHHhhcCC-C---CCHHHHHHHHHHH
Q 020106 73 NRRPFTEDEEERLLAAHRIHGNKWALIARLFP-G---RTDNAVKNHWHVI 118 (331)
Q Consensus 73 ~kg~WT~EED~~Llelv~~~G~kWs~IAk~Lp-g---RT~nq~KnRW~~i 118 (331)
....-+..|..-|..|+.+||.++..+|.-.. + .|..||+.+.+.+
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 34567899999999999999999999997432 3 8999999887654
No 120
>smart00595 MADF subfamily of SANT domain.
Probab=36.55 E-value=16 Score=28.30 Aligned_cols=22 Identities=45% Similarity=0.871 Sum_probs=19.0
Q ss_pred HHHHHHHhcCCCccccchhhhcc
Q 020106 45 WNSIAEKLQGRSGKSCRLRWFNQ 67 (331)
Q Consensus 45 W~~IA~~lpgRt~kQCr~Rw~n~ 67 (331)
|..||..|. -+...|+.+|.++
T Consensus 30 W~~Ia~~l~-~~~~~~~~kw~~L 51 (89)
T smart00595 30 WEEIAEELG-LSVEECKKRWKNL 51 (89)
T ss_pred HHHHHHHHC-cCHHHHHHHHHHH
Confidence 999999994 5999999999764
No 121
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=36.19 E-value=79 Score=26.35 Aligned_cols=29 Identities=17% Similarity=0.062 Sum_probs=22.0
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMAR 121 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkr 121 (331)
.|....+||+.| |-+...|+++-...+++
T Consensus 121 ~~~s~~EIA~~l-~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 121 VGKTMGEIALET-EMTYYQVRWIYRQALEK 149 (154)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 345578899988 88999998887665554
No 122
>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=35.88 E-value=48 Score=26.39 Aligned_cols=31 Identities=29% Similarity=0.439 Sum_probs=25.6
Q ss_pred HHHHHHHHHHhCChhHHHhhcCCCCCHHHHHH
Q 020106 82 EERLLAAHRIHGNKWALIARLFPGRTDNAVKN 113 (331)
Q Consensus 82 D~~Llelv~~~G~kWs~IAk~LpgRT~nq~Kn 113 (331)
|..|..+....|.+|.++|+.| |=+..+|.+
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 4567778889999999999999 777777755
No 123
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=35.62 E-value=90 Score=27.54 Aligned_cols=31 Identities=13% Similarity=0.180 Sum_probs=24.1
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|-...+||..| |-+...|+.|....+++-+
T Consensus 156 eg~s~~EIA~~l-gis~~tVk~rl~ra~~~Lr 186 (194)
T PRK12531 156 EELPHQQVAEMF-DIPLGTVKSRLRLAVEKLR 186 (194)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHHHH
Confidence 356689999999 9999999999776655443
No 124
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=35.56 E-value=70 Score=23.50 Aligned_cols=34 Identities=18% Similarity=0.265 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHH
Q 020106 81 EEERLLAAHRIHGNKWALIARLFPGRTDNAVKNHW 115 (331)
Q Consensus 81 ED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW 115 (331)
+|+..+.+..+.|-.-.+||+.+ ||+.+.|+++-
T Consensus 8 ~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl 41 (50)
T PF11427_consen 8 AEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRYL 41 (50)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHHH
T ss_pred HHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHHh
Confidence 44555666668999999999999 99999888764
No 125
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=34.58 E-value=56 Score=38.18 Aligned_cols=72 Identities=18% Similarity=0.187 Sum_probs=44.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHh-cCCCccccchhhhcccCCCCCCCCCCHHHHHHHHHHHHHh-CChhHH
Q 020106 21 PRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKL-QGRSGKSCRLRWFNQLDPRINRRPFTEDEEERLLAAHRIH-GNKWAL 98 (331)
Q Consensus 21 kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~l-pgRt~kQCr~Rw~n~L~p~i~kg~WT~EED~~Llelv~~~-G~kWs~ 98 (331)
.---|..+||..|+-.|-+||.++|..|---= .+-+.+ ..+.-.+..+.|=...-..|+.+...+ +.+|..
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir~Dp~L~l~dK-------i~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~ 1204 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIRLDPDLGLTDK-------IFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPK 1204 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhccCccccchhh-------hcccccCCchHHHHHHHHHHHHHHhhcccCCCch
Confidence 34569999999999999999999999985320 011111 111111344555566666677766665 344444
Q ss_pred H
Q 020106 99 I 99 (331)
Q Consensus 99 I 99 (331)
.
T Consensus 1205 ~ 1205 (1373)
T KOG0384|consen 1205 K 1205 (1373)
T ss_pred h
Confidence 3
No 126
>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=34.19 E-value=35 Score=23.96 Aligned_cols=38 Identities=26% Similarity=0.309 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhc
Q 020106 27 PAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFN 66 (331)
Q Consensus 27 ~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n 66 (331)
++++..++.+..-.|. .|.+||+.+ |.+...++.+..+
T Consensus 12 ~~~~r~i~~l~~~~g~-s~~eIa~~l-~~s~~~v~~~l~r 49 (54)
T PF08281_consen 12 PERQREIFLLRYFQGM-SYAEIAEIL-GISESTVKRRLRR 49 (54)
T ss_dssp -HHHHHHHHHHHTS----HHHHHHHC-TS-HHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCc-CHHHHHHHH-CcCHHHHHHHHHH
Confidence 4667777777777775 699999998 7888888776654
No 127
>PRK00118 putative DNA-binding protein; Validated
Probab=33.90 E-value=1.2e+02 Score=25.34 Aligned_cols=44 Identities=11% Similarity=0.096 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 79 EDEEERLLAAHRIHGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 79 ~EED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
++.+..++.+....|...++||+.+ |-+.+.|+.+-....++-+
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~RArkkLr 62 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKRTEKLLE 62 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 4566777788888899999999999 9999999988776554443
No 128
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=33.40 E-value=1.3e+02 Score=25.42 Aligned_cols=32 Identities=22% Similarity=0.203 Sum_probs=24.7
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQR 124 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~ 124 (331)
.|..-.+||..| |-+...|+.|....+++-..
T Consensus 120 ~~~s~~eIA~~l-gis~~tv~~~l~ra~~~Lr~ 151 (159)
T PRK12527 120 EGLSHQQIAEHL-GISRSLVEKHIVNAMKHCRV 151 (159)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHH
Confidence 345578999999 99999999998766655443
No 129
>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=32.95 E-value=59 Score=25.86 Aligned_cols=32 Identities=16% Similarity=0.319 Sum_probs=23.1
Q ss_pred CCHHHHHHHHHHHHHhCChhHHHhhcCCCCCHHHHH
Q 020106 77 FTEDEEERLLAAHRIHGNKWALIARLFPGRTDNAVK 112 (331)
Q Consensus 77 WT~EED~~Llelv~~~G~kWs~IAk~LpgRT~nq~K 112 (331)
-|+++-. .+....|..|.++|+.| |-+..+|.
T Consensus 5 ~t~~~l~---~ia~~iG~~Wk~Lar~L-Gls~~dI~ 36 (86)
T cd08318 5 VTGEQIT---VFANKLGEDWKTLAPHL-EMKDKEIR 36 (86)
T ss_pred CCHHHHH---HHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 3444433 35578899999999999 77777663
No 130
>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=32.84 E-value=1.1e+02 Score=25.92 Aligned_cols=30 Identities=27% Similarity=0.303 Sum_probs=22.9
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARK 122 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk 122 (331)
.|-...+||+.| |-+...|+++-....++-
T Consensus 137 ~g~s~~eIA~~l-~is~~tv~~~l~ra~~~L 166 (170)
T TIGR02952 137 QNLPIAEVARIL-GKTEGAVKILQFRAIKKL 166 (170)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 355678999999 889999999876655543
No 131
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=32.52 E-value=2e+02 Score=23.91 Aligned_cols=47 Identities=19% Similarity=0.151 Sum_probs=33.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcccC
Q 020106 20 CPRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQLD 69 (331)
Q Consensus 20 ~kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L~ 69 (331)
.++..||.|+-..++..+...|. .-..||+.+ |= ..+-..+|.+.+.
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g~-sv~evA~e~-gI-s~~tl~~W~r~y~ 54 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPGM-TVSLVARQH-GV-AASQLFLWRKQYQ 54 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCCC-CHHHHHHHH-Cc-CHHHHHHHHHHHh
Confidence 44678999999888888777774 578899887 33 3344456777653
No 132
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=32.41 E-value=1.1e+02 Score=26.63 Aligned_cols=31 Identities=29% Similarity=0.199 Sum_probs=25.1
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|....+||+.| |.+...|+++-...+++-+
T Consensus 144 ~g~s~~EIA~~l-~is~~tV~~~l~rar~~Lr 174 (181)
T PRK12536 144 EGLSVAETAQLT-GLSESAVKVGIHRGLKALA 174 (181)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 456789999999 9999999999876655443
No 133
>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=32.24 E-value=54 Score=25.18 Aligned_cols=30 Identities=23% Similarity=0.416 Sum_probs=21.8
Q ss_pred HHHHHHHHHHH-hCChhHHHhhcCCCCCHHHH
Q 020106 81 EEERLLAAHRI-HGNKWALIARLFPGRTDNAV 111 (331)
Q Consensus 81 ED~~Llelv~~-~G~kWs~IAk~LpgRT~nq~ 111 (331)
-.+.|..++.. .|.+|..+|+.| |-+..+|
T Consensus 4 ~~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i 34 (88)
T smart00005 4 TREKLAKLLDHPLGLDWRELARKL-GLSEADI 34 (88)
T ss_pred HHHHHHHHHcCccchHHHHHHHHc-CCCHHHH
Confidence 34566666666 899999999999 4455554
No 134
>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=32.12 E-value=1.1e+02 Score=26.23 Aligned_cols=30 Identities=27% Similarity=0.344 Sum_probs=24.0
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARK 122 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk 122 (331)
.|-...+||..| |-+...|+.|.....++-
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~L 178 (183)
T TIGR02999 149 AGLTVEEIAELL-GVSVRTVERDWRFARAWL 178 (183)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 456689999999 999999999987665543
No 135
>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=32.12 E-value=52 Score=27.82 Aligned_cols=46 Identities=15% Similarity=0.193 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHHHHHhC--------C----CC------------------HHHHHHHhcCCCccccchhhhcccC
Q 020106 24 HWRPAEDEKLRQLVEQYG--------A----QN------------------WNSIAEKLQGRSGKSCRLRWFNQLD 69 (331)
Q Consensus 24 ~WT~EED~~L~~lV~kyG--------~----~n------------------W~~IA~~lpgRt~kQCr~Rw~n~L~ 69 (331)
++|++||-.|-..|.+|- . .. ....+...|..|..+=|+||++.+.
T Consensus 1 kfTA~dDY~Lc~~i~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~fF~~~~~~~p~HT~~sWRDR~RKfv~ 76 (105)
T PF09197_consen 1 KFTADDDYALCKAIKKQFYRDIYQKDPDTGSSLISDGDSKEFIPKRDMRSFFKDLARKNPRHTENSWRDRYRKFVS 76 (105)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHSB-TTSS-B----------------TTHHHHHHHHTTTS-HHHHHHHHHHTHH
T ss_pred CCChHHHHHHHHHHHHHHHHHHHhhCcccccccccCCCccccccchhhHHHHHHHHHcCCccchhHHHHHHHHHHH
Confidence 589999999999997761 0 00 4455555677777777777777654
No 136
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=32.11 E-value=96 Score=27.27 Aligned_cols=31 Identities=13% Similarity=0.042 Sum_probs=24.7
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|-...+||..| |-+...|+.|....+++-+
T Consensus 145 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr 175 (185)
T PRK09649 145 LGLSYADAAAVC-GCPVGTIRSRVARARDALL 175 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 455689999999 9999999999876655443
No 137
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=31.99 E-value=50 Score=23.76 Aligned_cols=44 Identities=32% Similarity=0.327 Sum_probs=31.5
Q ss_pred CCCHHHHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHHHHHHH
Q 020106 76 PFTEDEEERLLAAHRIHGNKWALIARLFPGRTDNAVKNHWHVIMARK 122 (331)
Q Consensus 76 ~WT~EED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk 122 (331)
..|+.|-+.|.-+. -|..=.+||..+ |.+...|+.+...+++|-
T Consensus 3 ~LT~~E~~vl~~l~--~G~~~~eIA~~l-~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLA--QGMSNKEIAEEL-GISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHH--TTS-HHHHHHHH-TSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHH--hcCCcchhHHhc-CcchhhHHHHHHHHHHHh
Confidence 35666666554443 455667999999 999999999998887764
No 138
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=31.83 E-value=64 Score=29.52 Aligned_cols=45 Identities=24% Similarity=0.186 Sum_probs=36.2
Q ss_pred CCCCHHHHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHHHHHHH
Q 020106 75 RPFTEDEEERLLAAHRIHGNKWALIARLFPGRTDNAVKNHWHVIMARK 122 (331)
Q Consensus 75 g~WT~EED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk 122 (331)
...|+.|-+.|.-+.+ |..=.+||..| +.+..-||+|...+++|-
T Consensus 147 ~~LT~RE~eVL~lla~--G~snkeIA~~L-~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 147 ELLTPRELEVLRLLAE--GLSNKEIAEEL-NLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCCCHHHHHHHHHHHC--CCCHHHHHHHH-CCCHhHHHHHHHHHHHHc
Confidence 3688888887766553 44456999999 999999999999998764
No 139
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=31.57 E-value=1.3e+02 Score=26.59 Aligned_cols=33 Identities=18% Similarity=0.183 Sum_probs=25.8
Q ss_pred HhCChhHHHhhcCCCCCHHHHHHHHHHHHHHHHH
Q 020106 91 IHGNKWALIARLFPGRTDNAVKNHWHVIMARKQR 124 (331)
Q Consensus 91 ~~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~ 124 (331)
..|-...+||+.| |-+...||.|-...+++-..
T Consensus 130 ~~g~s~~EIA~~L-gis~~tVk~~l~Rar~~Lr~ 162 (187)
T PRK12516 130 ASGFAYEEAAEIC-GCAVGTIKSRVNRARQRLQE 162 (187)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 3566789999999 99999999997766654443
No 140
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=30.91 E-value=46 Score=28.10 Aligned_cols=44 Identities=16% Similarity=0.182 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcccCCCC
Q 020106 28 AEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQLDPRI 72 (331)
Q Consensus 28 EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L~p~i 72 (331)
+-|.+|+++.++.+...+.+||+.+ |-+...|+.|-+++.+-.+
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~Gi 51 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGV 51 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCc
Confidence 5588899999999988999999998 7999999998888765443
No 141
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=30.71 E-value=1.1e+02 Score=26.85 Aligned_cols=31 Identities=13% Similarity=0.071 Sum_probs=24.2
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|..-.+||..| |-+...|+.|....+++-+
T Consensus 151 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr 181 (195)
T PRK12532 151 LGFSSDEIQQMC-GISTSNYHTIMHRARESLR 181 (195)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 456689999999 9999999999876554433
No 142
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=30.54 E-value=1.2e+02 Score=26.12 Aligned_cols=29 Identities=10% Similarity=0.103 Sum_probs=23.2
Q ss_pred CChhHHHhhcCCCCCHHHHHHHHHHHHHHH
Q 020106 93 GNKWALIARLFPGRTDNAVKNHWHVIMARK 122 (331)
Q Consensus 93 G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk 122 (331)
|..-.+||+.| |.+...|+++....+++-
T Consensus 145 g~s~~eIA~~l-gis~~tV~~~l~Rar~~L 173 (179)
T PRK12514 145 GLSYKELAERH-DVPLNTMRTWLRRSLLKL 173 (179)
T ss_pred CCCHHHHHHHH-CCChHHHHHHHHHHHHHH
Confidence 55678999999 999999999887665543
No 143
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=30.37 E-value=1.2e+02 Score=26.16 Aligned_cols=30 Identities=20% Similarity=0.224 Sum_probs=23.7
Q ss_pred CChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 93 GNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 93 G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
|..-.+||..| |-+...|+.+.+..+++-+
T Consensus 151 ~~s~~eIA~~l-gis~~~V~~~l~ra~~~Lr 180 (186)
T PRK13919 151 GYTHREAAQLL-GLPLGTLKTRARRALSRLK 180 (186)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 45578999999 9999999999877665543
No 144
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=30.30 E-value=1.3e+02 Score=26.39 Aligned_cols=33 Identities=27% Similarity=0.324 Sum_probs=24.2
Q ss_pred CChhHHHhhcCCCCCHHHHHHHHHHHHHHHHHhh
Q 020106 93 GNKWALIARLFPGRTDNAVKNHWHVIMARKQREQ 126 (331)
Q Consensus 93 G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~~~ 126 (331)
|..-.+||+.| |.+...|+++-....++-+..+
T Consensus 147 g~s~~EIAe~l-gis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 147 GEKIEEIAKKL-GLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred cCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHcc
Confidence 44568899999 8999999998776665544433
No 145
>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=29.89 E-value=1.3e+02 Score=25.38 Aligned_cols=40 Identities=18% Similarity=0.158 Sum_probs=28.2
Q ss_pred HHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 83 ERLLAAHRIHGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 83 ~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
..++.+....|-.-.+||..| |-+...|+++....+++-+
T Consensus 116 r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~ra~~~Lr 155 (162)
T TIGR02983 116 RAVVVLRYYEDLSEAQVAEAL-GISVGTVKSRLSRALARLR 155 (162)
T ss_pred HHHhhhHHHhcCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 333444444566678999999 8899999999887666544
No 146
>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=29.48 E-value=91 Score=21.29 Aligned_cols=34 Identities=21% Similarity=0.243 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHH
Q 020106 81 EEERLLAAHRIHGNKWALIARLFPGRTDNAVKNHW 115 (331)
Q Consensus 81 ED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW 115 (331)
|-..|.++...++++.++.|+.| |=+...+..+-
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 66788889999999999999998 76666665543
No 147
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=29.44 E-value=48 Score=23.03 Aligned_cols=37 Identities=24% Similarity=0.348 Sum_probs=18.3
Q ss_pred CCCCHHHHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHH
Q 020106 75 RPFTEDEEERLLAAHRIHGNKWALIARLFPGRTDNAVKN 113 (331)
Q Consensus 75 g~WT~EED~~Llelv~~~G~kWs~IAk~LpgRT~nq~Kn 113 (331)
..+|.+|-..|..++ .-|..=.+||+.| ||+...|.+
T Consensus 3 ~~Lt~~eR~~I~~l~-~~G~s~~~IA~~l-g~s~sTV~r 39 (44)
T PF13936_consen 3 KHLTPEERNQIEALL-EQGMSIREIAKRL-GRSRSTVSR 39 (44)
T ss_dssp ---------HHHHHH-CS---HHHHHHHT-T--HHHHHH
T ss_pred cchhhhHHHHHHHHH-HcCCCHHHHHHHH-CcCcHHHHH
Confidence 356777777766664 5677789999999 999988765
No 148
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=29.27 E-value=1.3e+02 Score=26.18 Aligned_cols=30 Identities=17% Similarity=0.265 Sum_probs=24.1
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARK 122 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk 122 (331)
.|-...+||..| |-+...|++|.....++-
T Consensus 137 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~L 166 (185)
T PRK12542 137 YNLTYQEISSVM-GITEANVRKQFERARKRV 166 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 456689999999 999999999887655544
No 149
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=29.21 E-value=1.6e+02 Score=25.82 Aligned_cols=33 Identities=9% Similarity=-0.206 Sum_probs=25.3
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHHHh
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQRE 125 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~~ 125 (331)
.|..-.+||..| |-+.+.|++|....+++-+..
T Consensus 146 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr~~ 178 (191)
T PRK12520 146 LELETEEICQEL-QITATNAWVLLYRARMRLREC 178 (191)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHH
Confidence 355578999999 999999999987766654433
No 150
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=29.21 E-value=45 Score=27.78 Aligned_cols=29 Identities=17% Similarity=0.074 Sum_probs=23.4
Q ss_pred CChhHHHhhcCCCCCHHHHHHHHHHHHHHH
Q 020106 93 GNKWALIARLFPGRTDNAVKNHWHVIMARK 122 (331)
Q Consensus 93 G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk 122 (331)
|-.+.+||..| |-+...|++++....++-
T Consensus 121 g~s~~eIA~~l-gis~~tv~~~l~Ra~~~L 149 (154)
T TIGR02950 121 EFSYKEIAELL-NLSLAKVKSNLFRARKEL 149 (154)
T ss_pred cCcHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 45689999999 999999999987665543
No 151
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=29.20 E-value=1.5e+02 Score=24.92 Aligned_cols=31 Identities=16% Similarity=0.216 Sum_probs=23.6
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|-.-.+||+.| |-+...|+++....+++-+
T Consensus 126 ~g~s~~eIA~~l-gis~~tV~~~i~ra~~~Lr 156 (166)
T PRK09639 126 SGYSYKEIAEAL-GIKESSVGTTLARAKKKFR 156 (166)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 455568899999 8999999998876655544
No 152
>COG4628 Uncharacterized conserved protein [Function unknown]
Probab=29.12 E-value=68 Score=27.81 Aligned_cols=45 Identities=29% Similarity=0.725 Sum_probs=30.4
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcccCCC-------CCCCCCCHHHHHHHH
Q 020106 30 DEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQLDPR-------INRRPFTEDEEERLL 86 (331)
Q Consensus 30 D~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L~p~-------i~kg~WT~EED~~Ll 86 (331)
+.+|.++|+.|| |..++..|+ ..|.. -+|. +.+.+|..|..+.|.
T Consensus 21 E~llt~Lvd~YG---Wd~L~~ri~----inCF~-----ndPSi~SSlKfLrkT~WARekvEa~Y 72 (136)
T COG4628 21 ETLLTELVDFYG---WDGLATRIR----INCFH-----NDPSIKSSLKFLRKTPWAREKVEALY 72 (136)
T ss_pred HHHHHHHHHHhC---hHHHHhhce----ecccc-----CCccHHHHHHHHhcCHhHHHHHHHHH
Confidence 577889999999 999998874 22311 1222 357888887766543
No 153
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=28.60 E-value=89 Score=27.02 Aligned_cols=31 Identities=19% Similarity=0.147 Sum_probs=24.7
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|....+||+.| |-+.+.|+++....+++-+
T Consensus 134 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 134 DGLTYSEIAHKL-GVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 355689999999 9999999999877665443
No 154
>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=28.25 E-value=1.3e+02 Score=25.77 Aligned_cols=31 Identities=29% Similarity=0.418 Sum_probs=24.1
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|....+||..| |-+...|+.+....+++-+
T Consensus 155 ~g~s~~eIA~~l-gis~~~v~~~l~Ra~~~Lr 185 (189)
T TIGR02984 155 EGLSFAEVAERM-DRSEGAVSMLWVRGLARLR 185 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 456688999999 8999999998876665443
No 155
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=28.18 E-value=1.5e+02 Score=25.30 Aligned_cols=31 Identities=19% Similarity=0.164 Sum_probs=24.3
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|-...+||..| |-+...|+++-....++-+
T Consensus 127 ~g~s~~eIA~~l-gis~~tV~~~l~Rar~~Lr 157 (164)
T PRK12547 127 SGFSYEDAAAIC-GCAVGTIKSRVSRARNRLQ 157 (164)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 456689999999 8899999998876655543
No 156
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=27.98 E-value=70 Score=25.72 Aligned_cols=26 Identities=23% Similarity=0.298 Sum_probs=21.0
Q ss_pred HHHHHHHHHHhCChhHHHhhcCCCCCH
Q 020106 82 EERLLAAHRIHGNKWALIARLFPGRTD 108 (331)
Q Consensus 82 D~~Llelv~~~G~kWs~IAk~LpgRT~ 108 (331)
|..|.......|..|.++|+.| |=+.
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L-~vs~ 29 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL-QFSV 29 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc-CCCH
Confidence 5567788899999999999987 5444
No 157
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=27.73 E-value=33 Score=36.90 Aligned_cols=47 Identities=15% Similarity=0.333 Sum_probs=42.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhc
Q 020106 19 TCPRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFN 66 (331)
Q Consensus 19 ~~kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n 66 (331)
....++|+.+|-.+...+....|. +.+.|+..+|.|..+|++.++..
T Consensus 406 ~~~~~~w~~se~e~fyka~~~~gs-~~slis~l~p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 406 KLETDKWDASETELFYKALSERGS-DFSLISNLFPLRDRKQIKAKFKK 452 (584)
T ss_pred ccccCcccchhhHHhhhHHhhhcc-cccccccccccccHHHHHHHHhh
Confidence 445689999999999999999997 69999999999999999998854
No 158
>COG5201 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]
Probab=27.58 E-value=1.4e+02 Score=26.51 Aligned_cols=55 Identities=24% Similarity=0.320 Sum_probs=37.9
Q ss_pred CHHHHHHHHHHHHHhCCC--------CHHHHHHHhcCCCccccchhhhcccCCCCCCCCCCHHHHHHHHH
Q 020106 26 RPAEDEKLRQLVEQYGAQ--------NWNSIAEKLQGRSGKSCRLRWFNQLDPRINRRPFTEDEEERLLA 87 (331)
Q Consensus 26 T~EED~~L~~lV~kyG~~--------nW~~IA~~lpgRt~kQCr~Rw~n~L~p~i~kg~WT~EED~~Lle 87 (331)
-.-+.+.|++.+..-..- -.+.||+++.||+...+|+-+ + --..||+||++.+.+
T Consensus 88 m~vDqemL~eI~laaNYL~ikpLLd~gCKivaemirgkSpeeir~tf-n------i~ndfTpEEe~~irk 150 (158)
T COG5201 88 MEVDQEMLLEICLAANYLEIKPLLDLGCKIVAEMIRGKSPEEIRETF-N------IENDFTPEEERRIRK 150 (158)
T ss_pred HHhhHHHHHHHHHhhccccchHHHHHHHHHHHHHHccCCHHHHHHHh-C------CCCCCCHHHHHHHHH
Confidence 344556666666433211 178899999999999888765 2 235799999998754
No 159
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=27.57 E-value=1.3e+02 Score=25.47 Aligned_cols=30 Identities=23% Similarity=0.237 Sum_probs=23.6
Q ss_pred HhCChhHHHhhcCCCCCHHHHHHHHHHHHHH
Q 020106 91 IHGNKWALIARLFPGRTDNAVKNHWHVIMAR 121 (331)
Q Consensus 91 ~~G~kWs~IAk~LpgRT~nq~KnRW~~ilkr 121 (331)
-.|-...+||..| |-+.+.|+.|....+++
T Consensus 127 ~~g~s~~EIA~~l-~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 127 VDGLGYGEIATEL-GISLATVKRYLNKAAMR 156 (161)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3566789999999 88999999987766543
No 160
>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=27.13 E-value=1.2e+02 Score=28.92 Aligned_cols=31 Identities=23% Similarity=0.196 Sum_probs=24.6
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|..-.+||+.| |.+...||+|....+++-+
T Consensus 157 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr 187 (324)
T TIGR02960 157 LGWRAAETAELL-GTSTASVNSALQRARATLD 187 (324)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 456689999999 9999999999876655443
No 161
>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=27.11 E-value=75 Score=25.45 Aligned_cols=30 Identities=27% Similarity=0.391 Sum_probs=23.6
Q ss_pred HHHHHHHHhCChhHHHhhcCCCCCHHHHHHH
Q 020106 84 RLLAAHRIHGNKWALIARLFPGRTDNAVKNH 114 (331)
Q Consensus 84 ~Llelv~~~G~kWs~IAk~LpgRT~nq~KnR 114 (331)
.|-.+....|.+|..+|+.| |=+..+|..-
T Consensus 4 ~l~~l~~~lG~~Wk~lar~L-G~s~~eI~~i 33 (86)
T cd08777 4 HLDLLRENLGKKWKRCARKL-GFTESEIEEI 33 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHc-CCCHHHHHHH
Confidence 34455578899999999999 8888877663
No 162
>PF08870 DUF1832: Domain of unknown function (DUF1832); InterPro: IPR014969 This entry describes the DndE protein encoded by an operon associated with a sulphur-containing modification to DNA []. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndE is a putative carboxylase homologous to NCAIR synthetases.
Probab=26.86 E-value=2.4e+02 Score=23.85 Aligned_cols=90 Identities=17% Similarity=0.185 Sum_probs=57.6
Q ss_pred CHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhh-cccC----CCCCCCCCCHHHHHHHHHHHHHhCChhHHHh
Q 020106 26 RPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWF-NQLD----PRINRRPFTEDEEERLLAAHRIHGNKWALIA 100 (331)
Q Consensus 26 T~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~-n~L~----p~i~kg~WT~EED~~Llelv~~~G~kWs~IA 100 (331)
|++-+++|.++-.+.|...|+.+|+..-.|+-..=. .+. .-+. -.+++..|+-|-+..++.+++++-
T Consensus 5 S~~~~~~L~~Lk~~tgi~~~Nil~R~A~~~SL~~~~-~~~~~~~~~d~g~e~~~~t~~Ge~~~~~~~ll~q~~------- 76 (113)
T PF08870_consen 5 SKKAKEQLKKLKRRTGITPWNILCRIAFCRSLEEPS-IPSDEDIKDDSGLELNWKTFTGEYDDIYEALLKQRY------- 76 (113)
T ss_pred CHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHccCC-CCCCCccCCCCCeEEeeeeecCchHHHHHHHHHHHh-------
Confidence 677889999999999999999998864222221110 010 0111 124566788777777666554432
Q ss_pred hcCCCCCHHHHHHHHHHHHHHHHHh
Q 020106 101 RLFPGRTDNAVKNHWHVIMARKQRE 125 (331)
Q Consensus 101 k~LpgRT~nq~KnRW~~ilkrk~~~ 125 (331)
-++.++..+...|+.++.|-...
T Consensus 77 --g~~~d~~~l~~~~~~Hl~rGi~~ 99 (113)
T PF08870_consen 77 --GPELDDEELPKYFKLHLDRGIEY 99 (113)
T ss_pred --CCCCCHHHHHHHHHHHHHHhHHH
Confidence 23458888999999998876543
No 163
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=26.82 E-value=1.7e+02 Score=26.46 Aligned_cols=33 Identities=18% Similarity=0.177 Sum_probs=25.2
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHHHh
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQRE 125 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~~ 125 (331)
.|..-.+||+.| |-+...|+++....+++-+..
T Consensus 153 ~g~s~~EIA~~L-gis~~tV~~~l~RArk~Lr~~ 185 (203)
T PRK09647 153 EGLSYEEIAATL-GVKLGTVRSRIHRGRQQLRAA 185 (203)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHH
Confidence 345678999999 999999999988776554433
No 164
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=26.70 E-value=1.3e+02 Score=25.35 Aligned_cols=44 Identities=16% Similarity=0.126 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHhC-ChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 79 EDEEERLLAAHRIHG-NKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 79 ~EED~~Llelv~~~G-~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.+-|.+|+++.+.-+ ..++.||+.+ |-+...|.+|-+.+.+...
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~Gi 51 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGV 51 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCc
Confidence 356777888777766 4599999999 8999999999888766543
No 165
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=26.29 E-value=92 Score=28.54 Aligned_cols=32 Identities=16% Similarity=0.100 Sum_probs=25.4
Q ss_pred CChhHHHhhcCCCCCHHHHHHHHHHHHHHHHHh
Q 020106 93 GNKWALIARLFPGRTDNAVKNHWHVIMARKQRE 125 (331)
Q Consensus 93 G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~~ 125 (331)
|....+||+.| |.+...|++++...+++-+..
T Consensus 165 g~s~~EIAe~l-gis~~tVk~~l~Rar~kLr~~ 196 (231)
T PRK11922 165 ELSVEETAQAL-GLPEETVKTRLHRARRLLRES 196 (231)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHHH
Confidence 45689999999 999999999988766555443
No 166
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=25.44 E-value=61 Score=33.23 Aligned_cols=40 Identities=23% Similarity=0.380 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHHhCCCCHHHHHH-HhcCCCccccchhh
Q 020106 24 HWRPAEDEKLRQLVEQYGAQNWNSIAE-KLQGRSGKSCRLRW 64 (331)
Q Consensus 24 ~WT~EED~~L~~lV~kyG~~nW~~IA~-~lpgRt~kQCr~Rw 64 (331)
.|+.+|-..+.+.++.|| +++..|.. +|+.|+..-|-+-|
T Consensus 279 ~wsEeEcr~FEegl~~yG-KDF~lIr~nkvrtRsvgElVeyY 319 (445)
T KOG4329|consen 279 GWSEEECRNFEEGLELYG-KDFHLIRANKVRTRSVGELVEYY 319 (445)
T ss_pred cCCHHHHHHHHHHHHHhc-ccHHHHHhcccccchHHHHHHHH
Confidence 599999999999999999 58999965 56788887776655
No 167
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=25.29 E-value=1.7e+02 Score=25.81 Aligned_cols=30 Identities=17% Similarity=0.100 Sum_probs=22.7
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARK 122 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk 122 (331)
.|-...+||+.| |-+...||++-...+++-
T Consensus 157 ~~~s~~EIA~~L-gis~~tVk~~l~ra~~~L 186 (194)
T PRK09646 157 GGLTYREVAERL-AVPLGTVKTRMRDGLIRL 186 (194)
T ss_pred cCCCHHHHHHHh-CCChHhHHHHHHHHHHHH
Confidence 345689999999 889999998876555443
No 168
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=25.24 E-value=1.6e+02 Score=26.18 Aligned_cols=30 Identities=13% Similarity=-0.137 Sum_probs=23.3
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARK 122 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk 122 (331)
.|..-.+||..| |.+...||.|.....++-
T Consensus 154 eg~s~~EIA~~l-gis~~tVk~~l~RAr~~L 183 (201)
T PRK12545 154 LDFEIDDICTEL-TLTANHCSVLLYRARTRL 183 (201)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 345689999999 999999999977555433
No 169
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=24.66 E-value=1.7e+02 Score=25.50 Aligned_cols=30 Identities=23% Similarity=0.170 Sum_probs=23.3
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARK 122 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk 122 (331)
.|-.-.+||+.| |-+...|+++....+++-
T Consensus 148 ~~~s~~eIA~~l-gis~~tV~~~l~ra~~~L 177 (182)
T PRK12537 148 DGCSHAEIAQRL-GAPLGTVKAWIKRSLKAL 177 (182)
T ss_pred cCCCHHHHHHHH-CCChhhHHHHHHHHHHHH
Confidence 345578899998 889999999887766543
No 170
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=24.63 E-value=2.2e+02 Score=25.28 Aligned_cols=32 Identities=22% Similarity=0.181 Sum_probs=25.1
Q ss_pred HhCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 91 IHGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 91 ~~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
..|-...+||..| |-+...|+++....+++-+
T Consensus 127 ~~g~s~~EIA~~L-giS~~tVk~~l~Rar~~Lr 158 (188)
T PRK12546 127 ASGFSYEEAAEMC-GVAVGTVKSRANRARARLA 158 (188)
T ss_pred hcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 3566789999999 8999999998876655443
No 171
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=24.39 E-value=2.1e+02 Score=24.66 Aligned_cols=34 Identities=15% Similarity=0.015 Sum_probs=25.2
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHHHhh
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQREQ 126 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~~~ 126 (331)
.|-.=.+||..| |-+...|+++....+++-....
T Consensus 115 ~g~s~~eIA~~l-gis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 115 EGLSQQEIAEKL-GLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHH
Confidence 445578999999 8999999998877665544433
No 172
>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=23.67 E-value=1e+02 Score=27.38 Aligned_cols=45 Identities=16% Similarity=0.172 Sum_probs=31.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhc----CCCccccchhhh
Q 020106 20 CPRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQ----GRSGKSCRLRWF 65 (331)
Q Consensus 20 ~kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~lp----gRt~kQCr~Rw~ 65 (331)
.+...-+..|..-|..||++||. |+...|.-.. ..|..||+.+..
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhGd-Dy~aMarD~KLN~~Q~T~~qlrrki~ 160 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHGD-DYKAMARDRKLNYMQHTPGQLRRKIR 160 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHCc-cHHHHhccCCCCcccCCHHHHHHHHH
Confidence 55677899999999999999996 6777665431 245555554443
No 173
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=23.16 E-value=1e+02 Score=24.58 Aligned_cols=32 Identities=22% Similarity=0.286 Sum_probs=24.0
Q ss_pred HHHHHHHHHhCChhHHHhhcCCCCCHH---HHHHHH
Q 020106 83 ERLLAAHRIHGNKWALIARLFPGRTDN---AVKNHW 115 (331)
Q Consensus 83 ~~Llelv~~~G~kWs~IAk~LpgRT~n---q~KnRW 115 (331)
..|..+..+.|..|..+|.+| |=+.. .|+.+|
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L-Glse~~Id~Ie~~~ 37 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL-GLSYRELQRIKYNN 37 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc-CCCHHHHHHHHHHC
Confidence 457888999999999999998 54443 445555
No 174
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=23.05 E-value=84 Score=26.90 Aligned_cols=30 Identities=20% Similarity=0.297 Sum_probs=23.2
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARK 122 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk 122 (331)
+|.....||+.| |-+...|+.+....+++-
T Consensus 141 ~g~s~~eIA~~l-~is~~~V~~~l~ra~~~l 170 (176)
T PRK09638 141 YGYTYEEIAKML-NIPEGTVKSRVHHGIKQL 170 (176)
T ss_pred cCCCHHHHHHHH-CCChhHHHHHHHHHHHHH
Confidence 456789999999 889999988876655443
No 175
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=22.82 E-value=1.5e+02 Score=27.18 Aligned_cols=44 Identities=32% Similarity=0.325 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHHhCChhHHHhhcCCCCCHHHHHHHHHHHHHHH
Q 020106 76 PFTEDEEERLLAAHRIHGNKWALIARLFPGRTDNAVKNHWHVIMARK 122 (331)
Q Consensus 76 ~WT~EED~~Llelv~~~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk 122 (331)
..|+-|-+.| +++.+ |....+||+.| +-+...||++...+++|-
T Consensus 155 ~Lt~rE~~Vl-~l~~~-G~s~~eIA~~L-~iS~~TVk~~~~~i~~Kl 198 (216)
T PRK10100 155 LLTHREKEIL-NKLRI-GASNNEIARSL-FISENTVKTHLYNLFKKI 198 (216)
T ss_pred CCCHHHHHHH-HHHHc-CCCHHHHHHHh-CCCHHHHHHHHHHHHHHh
Confidence 4777555554 44444 88899999999 899999999998887654
No 176
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=22.26 E-value=1.8e+02 Score=26.67 Aligned_cols=31 Identities=13% Similarity=0.166 Sum_probs=24.7
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|-...+||+.| |-+...|+.+....+++-+
T Consensus 199 ~g~s~~EIA~~l-gis~~tV~~~~~ra~~~Lr 229 (236)
T PRK06986 199 EELNLKEIGAVL-GVSESRVSQIHSQAIKRLR 229 (236)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 455689999999 9999999998877666544
No 177
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=21.91 E-value=1.4e+02 Score=27.63 Aligned_cols=31 Identities=16% Similarity=0.009 Sum_probs=24.0
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|..-.+||+.| |-+...|+++....+++-+
T Consensus 186 eg~s~~EIA~~L-gis~~tVk~~l~RAr~kLr 216 (233)
T PRK12538 186 ENMSNGEIAEVM-DTTVAAVESLLKRGRQQLR 216 (233)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 345679999999 9999999998876655443
No 178
>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=21.71 E-value=2e+02 Score=25.98 Aligned_cols=31 Identities=13% Similarity=0.117 Sum_probs=24.0
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|..-.+||+.| |-+...|+.+.+..+++-+
T Consensus 193 ~~~s~~eIA~~l-gis~~~v~~~~~ra~~~Lr 223 (227)
T TIGR02980 193 EDKTQSEIAERL-GISQMHVSRLLRRALKKLR 223 (227)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 456688999999 8899999888777666543
No 179
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=21.43 E-value=2.2e+02 Score=25.69 Aligned_cols=32 Identities=6% Similarity=-0.162 Sum_probs=24.6
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQR 124 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~ 124 (331)
.|..-.+||..| |-+.+.|+.|....+++-+.
T Consensus 163 ~g~s~~EIAe~l-gis~~tV~~~l~RAr~~Lr~ 194 (206)
T PRK12544 163 IELETNEICHAV-DLSVSNLNVLLYRARLRLRE 194 (206)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHH
Confidence 345579999999 99999999998766654443
No 180
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=21.40 E-value=1e+02 Score=23.92 Aligned_cols=36 Identities=28% Similarity=0.407 Sum_probs=25.8
Q ss_pred HHHHHHHhcCCCccccchhhhcccCCCCCCCCCCHHHHHHHHH
Q 020106 45 WNSIAEKLQGRSGKSCRLRWFNQLDPRINRRPFTEDEEERLLA 87 (331)
Q Consensus 45 W~~IA~~lpgRt~kQCr~Rw~n~L~p~i~kg~WT~EED~~Lle 87 (331)
...||..+.|++..++|..+ ++ ...+|+||++.|.+
T Consensus 36 ~~~iA~~i~gks~eeir~~f------gi-~~d~t~eee~~i~~ 71 (78)
T PF01466_consen 36 CKYIANMIKGKSPEEIRKYF------GI-ENDLTPEEEEEIRK 71 (78)
T ss_dssp HHHHHHHHTTS-HHHHHHHH------T----TSSHHHHHHHHH
T ss_pred HHHHHHHhcCCCHHHHHHHc------CC-CCCCCHHHHHHHHH
Confidence 67789999999999998866 12 34699998887543
No 181
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=21.35 E-value=1.5e+02 Score=31.55 Aligned_cols=60 Identities=13% Similarity=0.166 Sum_probs=44.7
Q ss_pred HHHHHhcCCCccccchhhhcccCCCCCCCCCCHHHHHHHHHHHHHhCChhHHHh-hcCCCCCHHHHHHHHH
Q 020106 47 SIAEKLQGRSGKSCRLRWFNQLDPRINRRPFTEDEEERLLAAHRIHGNKWALIA-RLFPGRTDNAVKNHWH 116 (331)
Q Consensus 47 ~IA~~lpgRt~kQCr~Rw~n~L~p~i~kg~WT~EED~~Llelv~~~G~kWs~IA-k~LpgRT~nq~KnRW~ 116 (331)
.|.-.+|-=-+.-||+.. ..|+.-|-.+.-++..+||..+..|- .+||=++-..|-.+|.
T Consensus 268 Ais~LVPlGGPvLCRDem----------EEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYY 328 (693)
T KOG3554|consen 268 AISYLVPLGGPVLCRDEM----------EEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYY 328 (693)
T ss_pred HHHHhhcCCCceeehhhh----------hhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHH
Confidence 344444544445555533 57999999999999999999999996 5789888888876653
No 182
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=20.96 E-value=2.6e+02 Score=24.64 Aligned_cols=33 Identities=12% Similarity=0.027 Sum_probs=25.1
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHHHh
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQRE 125 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~~ 125 (331)
.|..-.+||..| |-+...|+++....+++-+..
T Consensus 126 eg~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr~~ 158 (182)
T PRK12511 126 EGLSYQEAAAVL-GIPIGTLMSRIGRARAALRAF 158 (182)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHHHHHH
Confidence 355679999999 999999999987666654433
No 183
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=20.95 E-value=1.9e+02 Score=26.28 Aligned_cols=31 Identities=13% Similarity=0.199 Sum_probs=24.5
Q ss_pred CChhHHHhhcCCCCCHHHHHHHHHHHHHHHHH
Q 020106 93 GNKWALIARLFPGRTDNAVKNHWHVIMARKQR 124 (331)
Q Consensus 93 G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~~ 124 (331)
|....+||..| |-+...|+++-...+++-+.
T Consensus 198 g~s~~EIA~~l-gis~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 198 EKTQKEVADML-GISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 56789999999 99999999987766655443
No 184
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=20.88 E-value=1.8e+02 Score=25.34 Aligned_cols=31 Identities=19% Similarity=0.126 Sum_probs=22.6
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|-.-.+||..| |-+...|+.+....+++-.
T Consensus 156 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 156 EGLSQSEIAKRL-GIPLGTVKARARQGLLKLR 186 (194)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 345568899988 8899999988766555443
No 185
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=20.87 E-value=6.3e+02 Score=26.28 Aligned_cols=72 Identities=28% Similarity=0.371 Sum_probs=47.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhcCCCccccchhhhcccCCCCCCCCCCHHHHHHHHHHHHHhCChhHHH
Q 020106 20 CPRGHWRPAEDEKLRQLVEQYGAQNWNSIAEKLQGRSGKSCRLRWFNQLDPRINRRPFTEDEEERLLAAHRIHGNKWALI 99 (331)
Q Consensus 20 ~kKG~WT~EED~~L~~lV~kyG~~nW~~IA~~lpgRt~kQCr~Rw~n~L~p~i~kg~WT~EED~~Llelv~~~G~kWs~I 99 (331)
.--|.|+++=|+-..++...|.+ .||...-+++.-+ -||. =..|
T Consensus 74 daegvWSpdIEqsFqEALaiypp----------cGrrKIilsdegk-------------------------myGR-NELI 117 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPP----------CGRRKIILSDEGK-------------------------MYGR-NELI 117 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCC----------CCceeEEEccCcc-------------------------ccch-HHHH
Confidence 34588999999999999999876 3666544333211 1121 1233
Q ss_pred hhcC-----CCCCHHHHHHHHHHHHHHHHHhhh
Q 020106 100 ARLF-----PGRTDNAVKNHWHVIMARKQREQS 127 (331)
Q Consensus 100 Ak~L-----pgRT~nq~KnRW~~ilkrk~~~~~ 127 (331)
|+++ ..||..||-.|-..+-||+.++..
T Consensus 118 arYIKlrtgktRTrKQVSSHIQVlarrk~reiq 150 (455)
T KOG3841|consen 118 ARYIKLRTGKTRTRKQVSSHIQVLARRKLREIQ 150 (455)
T ss_pred HHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHH
Confidence 3322 259999999999998888887744
No 186
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=20.82 E-value=2e+02 Score=24.26 Aligned_cols=29 Identities=24% Similarity=0.169 Sum_probs=21.7
Q ss_pred CChhHHHhhcCCCCCHHHHHHHHHHHHHHH
Q 020106 93 GNKWALIARLFPGRTDNAVKNHWHVIMARK 122 (331)
Q Consensus 93 G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk 122 (331)
|-...+||..| |=+...|+.+-....++-
T Consensus 128 ~~s~~eIA~~l-gis~~tv~~~l~Rar~~L 156 (161)
T PRK12541 128 GFSYKEIAEMT-GLSLAKVKIELHRGRKET 156 (161)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 44578999999 888888988876655443
No 187
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=20.47 E-value=2.1e+02 Score=27.22 Aligned_cols=31 Identities=19% Similarity=0.201 Sum_probs=24.2
Q ss_pred hCChhHHHhhcCCCCCHHHHHHHHHHHHHHHH
Q 020106 92 HGNKWALIARLFPGRTDNAVKNHWHVIMARKQ 123 (331)
Q Consensus 92 ~G~kWs~IAk~LpgRT~nq~KnRW~~ilkrk~ 123 (331)
.|-.-.+||+.| |.+...||++.....++-+
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 455679999999 9999999999876554433
No 188
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=20.36 E-value=2.1e+02 Score=23.81 Aligned_cols=27 Identities=30% Similarity=0.321 Sum_probs=18.8
Q ss_pred CChhHHHhhcCCCCCHHHHHHHHHHHHH
Q 020106 93 GNKWALIARLFPGRTDNAVKNHWHVIMA 120 (331)
Q Consensus 93 G~kWs~IAk~LpgRT~nq~KnRW~~ilk 120 (331)
|..=.+||+.| |=+...|+.+.....+
T Consensus 127 g~~~~eIA~~l-~is~~tv~~~l~Rar~ 153 (159)
T TIGR02989 127 GVSLTALAEQL-GRTVNAVYKALSRLRV 153 (159)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 45567888887 7788888877654433
No 189
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.33 E-value=2.6e+02 Score=22.69 Aligned_cols=41 Identities=20% Similarity=0.360 Sum_probs=34.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCChhHHHhhcCCCC-CHHHHHHHHH
Q 020106 74 RRPFTEDEEERLLAAHRIHGNKWALIARLFPGR-TDNAVKNHWH 116 (331)
Q Consensus 74 kg~WT~EED~~Llelv~~~G~kWs~IAk~LpgR-T~nq~KnRW~ 116 (331)
+..||+|+-..+++++..-|..=+.||+.+ |- .++++.. |.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~~-W~ 46 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLYK-WR 46 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHHH-HH
Confidence 578999999999999999998889999999 64 6665554 54
No 190
>COG1168 MalY Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]
Probab=20.09 E-value=1e+02 Score=31.60 Aligned_cols=25 Identities=28% Similarity=0.542 Sum_probs=20.9
Q ss_pred CCCCCCC-CCHHHHHHHHHHHHHhCC
Q 020106 18 STCPRGH-WRPAEDEKLRQLVEQYGA 42 (331)
Q Consensus 18 p~~kKG~-WT~EED~~L~~lV~kyG~ 42 (331)
|+-+-|+ ||+||-.+|.+++++||.
T Consensus 167 PHNP~Grvwt~eeL~~i~elc~kh~v 192 (388)
T COG1168 167 PHNPTGRVWTKEELRKIAELCLRHGV 192 (388)
T ss_pred CCCCCCccccHHHHHHHHHHHHHcCC
Confidence 4555554 999999999999999975
Done!